diff options
Diffstat (limited to 'tools/src')
65 files changed, 22014 insertions, 12780 deletions
diff --git a/tools/src/CMakeLists.txt b/tools/src/CMakeLists.txt index 757c9cd..e291f61 100644 --- a/tools/src/CMakeLists.txt +++ b/tools/src/CMakeLists.txt @@ -1,4 +1,4 @@ -cmake_minimum_required (VERSION 3.10) +cmake_minimum_required (VERSION 3.12) project (HDF5_TOOLS_SRC C) #-- Add the h5diff and test executables @@ -13,7 +13,7 @@ add_subdirectory (misc) #-- Add the h5import and test executables add_subdirectory (h5import) -#-- h5Repack executables +#-- h5repack executables add_subdirectory (h5repack) #-- Add the h5dump and test executables @@ -30,3 +30,6 @@ add_subdirectory (h5dump) #-- Add the h5format_convert and test executables add_subdirectory (h5format_convert) + +#-- h5perf executables +add_subdirectory (h5perf) diff --git a/tools/src/Makefile.am b/tools/src/Makefile.am index beceee5..5af7d06 100644 --- a/tools/src/Makefile.am +++ b/tools/src/Makefile.am @@ -6,7 +6,7 @@ # This file is part of HDF5. The full HDF5 copyright notice, including # terms governing use, modification, and redistribution, is contained in # the COPYING file, which can be found at the root of the source code -# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. +# distribution tree, or in https://www.hdfgroup.org/licenses. # If you do not have access to either file, you may request a copy from # help@hdfgroup.org. ## @@ -23,6 +23,6 @@ CONFIG=ordered # All subdirectories SUBDIRS=h5diff h5ls h5dump misc h5import h5repack h5jam h5copy \ - h5format_convert h5stat + h5format_convert h5stat h5perf include $(top_srcdir)/config/conclude.am diff --git a/tools/src/h5copy/CMakeLists.txt b/tools/src/h5copy/CMakeLists.txt index 85233ef..2f924a2 100644 --- a/tools/src/h5copy/CMakeLists.txt +++ b/tools/src/h5copy/CMakeLists.txt @@ -1,4 +1,4 @@ -cmake_minimum_required (VERSION 3.10) +cmake_minimum_required (VERSION 3.12) project (HDF5_TOOLS_SRC_H5COPY C) # -------------------------------------------------------------------- @@ -6,7 +6,8 @@ project (HDF5_TOOLS_SRC_H5COPY C) # -------------------------------------------------------------------- if (NOT ONLY_SHARED_LIBS) add_executable (h5copy ${HDF5_TOOLS_SRC_H5COPY_SOURCE_DIR}/h5copy.c) - target_include_directories (h5copy PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5copy PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_compile_options(h5copy PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5copy STATIC) target_link_libraries (h5copy PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) set_target_properties (h5copy PROPERTIES FOLDER tools) @@ -17,7 +18,8 @@ endif () if (BUILD_SHARED_LIBS) add_executable (h5copy-shared ${HDF5_TOOLS_SRC_H5COPY_SOURCE_DIR}/h5copy.c) - target_include_directories (h5copy-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5copy-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_compile_options(h5copy-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5copy-shared SHARED) target_link_libraries (h5copy-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET}) set_target_properties (h5copy-shared PROPERTIES FOLDER tools) @@ -26,6 +28,17 @@ if (BUILD_SHARED_LIBS) set (H5_DEP_EXECUTABLES ${H5_DEP_EXECUTABLES} h5copy-shared) endif () +#----------------------------------------------------------------------------- +# Add Target to clang-format +#----------------------------------------------------------------------------- +if (HDF5_ENABLE_FORMATTERS) + if (NOT ONLY_SHARED_LIBS) + clang_format (HDF5_H5COPY_SRC_FORMAT h5copy) + else () + clang_format (HDF5_H5COPY_SRC_FORMAT h5copy-shared) + endif () +endif () + ############################################################################## ############################################################################## ### I N S T A L L A T I O N ### diff --git a/tools/src/h5copy/Makefile.am b/tools/src/h5copy/Makefile.am index d67fafc..328c6f3 100644 --- a/tools/src/h5copy/Makefile.am +++ b/tools/src/h5copy/Makefile.am @@ -6,7 +6,7 @@ # This file is part of HDF5. The full HDF5 copyright notice, including # terms governing use, modification, and redistribution, is contained in # the COPYING file, which can be found at the root of the source code -# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. +# distribution tree, or in https://www.hdfgroup.org/licenses. # If you do not have access to either file, you may request a copy from # help@hdfgroup.org. ## diff --git a/tools/src/h5copy/h5copy.c b/tools/src/h5copy/h5copy.c index 9490cd9..eacd05b 100644 --- a/tools/src/h5copy/h5copy.c +++ b/tools/src/h5copy/h5copy.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -19,25 +19,23 @@ #define PROGRAMNAME "h5copy" /* command-line options: short and long-named parameters */ -static const char *s_opts = "d:f:hi:o:ps:vVE"; -static struct long_options l_opts[] = { - { "destination", require_arg, 'd' }, - { "flag", require_arg, 'f' }, - { "help", no_arg, 'h' }, - { "input", require_arg, 'i' }, - { "output", require_arg, 'o' }, - { "parents", no_arg, 'p' }, - { "source", require_arg, 's' }, - { "verbose", no_arg, 'v' }, - { "version", no_arg, 'V' }, - { "enable-error-stack", no_arg, 'E' }, - { NULL, 0, '\0' } -}; -char *fname_src = NULL; -char *fname_dst = NULL; -char *oname_src = NULL; -char *oname_dst = NULL; -char *str_flag = NULL; +static const char * s_opts = "d:f:hi:o:ps:vVE*"; +static struct h5_long_options l_opts[] = {{"destination", require_arg, 'd'}, + {"flag", require_arg, 'f'}, + {"help", no_arg, 'h'}, + {"input", require_arg, 'i'}, + {"output", require_arg, 'o'}, + {"parents", no_arg, 'p'}, + {"source", require_arg, 's'}, + {"verbose", no_arg, 'v'}, + {"version", no_arg, 'V'}, + {"enable-error-stack", optional_arg, 'E'}, + {NULL, 0, '\0'}}; +char * fname_src = NULL; +char * fname_dst = NULL; +char * oname_src = NULL; +char * oname_dst = NULL; +char * str_flag = NULL; /*------------------------------------------------------------------------- * Function: leave @@ -71,7 +69,6 @@ leave(int ret) HDexit(ret); } - /*------------------------------------------------------------------------- * Function: usage * @@ -86,7 +83,7 @@ leave(int ret) *------------------------------------------------------------------------- */ static void -usage (void) +usage(void) { FLUSHSTREAM(rawoutstream); PRINTVALSTREAM(rawoutstream, "\n"); @@ -96,31 +93,45 @@ usage (void) PRINTVALSTREAM(rawoutstream, " -o, --output output file name\n"); PRINTVALSTREAM(rawoutstream, " -s, --source source object name\n"); PRINTVALSTREAM(rawoutstream, " -d, --destination destination object name\n"); + PRINTVALSTREAM(rawoutstream, " ERROR\n"); + PRINTVALSTREAM(rawoutstream, + " --enable-error-stack Prints messages from the HDF5 error stack as they occur.\n"); + PRINTVALSTREAM(rawoutstream, + " Optional value 2 also prints file open errors.\n"); PRINTVALSTREAM(rawoutstream, " OPTIONS\n"); PRINTVALSTREAM(rawoutstream, " -h, --help Print a usage message and exit\n"); - PRINTVALSTREAM(rawoutstream, " -p, --parents No error if existing, make parent groups as needed\n"); + PRINTVALSTREAM(rawoutstream, + " -p, --parents No error if existing, make parent groups as needed\n"); PRINTVALSTREAM(rawoutstream, " -v, --verbose Print information about OBJECTS and OPTIONS\n"); PRINTVALSTREAM(rawoutstream, " -V, --version Print version number and exit\n"); - PRINTVALSTREAM(rawoutstream, " --enable-error-stack\n"); - PRINTVALSTREAM(rawoutstream, " Prints messages from the HDF5 error stack as they occur.\n"); PRINTVALSTREAM(rawoutstream, " -f, --flag Flag type\n\n"); PRINTVALSTREAM(rawoutstream, " Flag type is one of the following strings:\n\n"); PRINTVALSTREAM(rawoutstream, " shallow Copy only immediate members for groups\n\n"); PRINTVALSTREAM(rawoutstream, " soft Expand soft links into new objects\n\n"); PRINTVALSTREAM(rawoutstream, " ext Expand external links into new objects\n\n"); - PRINTVALSTREAM(rawoutstream, " ref Copy references and any referenced objects, i.e., objects\n"); + PRINTVALSTREAM(rawoutstream, + " ref Copy references and any referenced objects, i.e., objects\n"); PRINTVALSTREAM(rawoutstream, " that the references point to.\n"); - PRINTVALSTREAM(rawoutstream, " Referenced objects are copied in addition to the objects\n"); - PRINTVALSTREAM(rawoutstream, " specified on the command line and reference datasets are\n"); - PRINTVALSTREAM(rawoutstream, " populated with correct reference values. Copies of referenced\n"); - PRINTVALSTREAM(rawoutstream, " datasets outside the copy range specified on the command line\n"); - PRINTVALSTREAM(rawoutstream, " will normally have a different name from the original.\n"); - PRINTVALSTREAM(rawoutstream, " (Default:Without this option, reference value(s) in any\n"); - PRINTVALSTREAM(rawoutstream, " reference datasets are set to NULL and referenced objects are\n"); - PRINTVALSTREAM(rawoutstream, " not copied unless they are otherwise within the copy range\n"); + PRINTVALSTREAM(rawoutstream, + " Referenced objects are copied in addition to the objects\n"); + PRINTVALSTREAM(rawoutstream, + " specified on the command line and reference datasets are\n"); + PRINTVALSTREAM(rawoutstream, + " populated with correct reference values. Copies of referenced\n"); + PRINTVALSTREAM(rawoutstream, + " datasets outside the copy range specified on the command line\n"); + PRINTVALSTREAM(rawoutstream, + " will normally have a different name from the original.\n"); + PRINTVALSTREAM(rawoutstream, + " (Default:Without this option, reference value(s) in any\n"); + PRINTVALSTREAM(rawoutstream, + " reference datasets are set to NULL and referenced objects are\n"); + PRINTVALSTREAM(rawoutstream, + " not copied unless they are otherwise within the copy range\n"); PRINTVALSTREAM(rawoutstream, " specified on the command line.)\n\n"); PRINTVALSTREAM(rawoutstream, " noattr Copy object without copying attributes\n\n"); - PRINTVALSTREAM(rawoutstream, " allflags Switches all flags from the default to the non-default setting\n\n"); + PRINTVALSTREAM(rawoutstream, + " allflags Switches all flags from the default to the non-default setting\n\n"); PRINTVALSTREAM(rawoutstream, " These flag types correspond to the following API symbols\n\n"); PRINTVALSTREAM(rawoutstream, " H5O_COPY_SHALLOW_HIERARCHY_FLAG\n"); PRINTVALSTREAM(rawoutstream, " H5O_COPY_EXPAND_SOFT_LINK_FLAG\n"); @@ -130,8 +141,6 @@ usage (void) PRINTVALSTREAM(rawoutstream, " H5O_COPY_ALL\n"); } - - /*------------------------------------------------------------------------- * Function: parse_flag * @@ -156,30 +165,30 @@ usage (void) *------------------------------------------------------------------------- */ - -static int parse_flag(const char* s_flag, unsigned *flag) +static int +parse_flag(const char *s_flag, unsigned *flag) { - unsigned fla=0; + unsigned fla = 0; if (HDstrcmp(s_flag, "shallow") == 0) { fla = H5O_COPY_SHALLOW_HIERARCHY_FLAG; } - else if (HDstrcmp(s_flag, "soft") == 0) { + else if (HDstrcmp(s_flag, "soft") == 0) { fla = H5O_COPY_EXPAND_SOFT_LINK_FLAG; } - else if (HDstrcmp(s_flag, "ext") == 0) { + else if (HDstrcmp(s_flag, "ext") == 0) { fla = H5O_COPY_EXPAND_EXT_LINK_FLAG; } - else if (HDstrcmp(s_flag, "ref") == 0) { + else if (HDstrcmp(s_flag, "ref") == 0) { fla = H5O_COPY_EXPAND_REFERENCE_FLAG; } - else if (HDstrcmp(s_flag, "noattr") == 0) { + else if (HDstrcmp(s_flag, "noattr") == 0) { fla = H5O_COPY_WITHOUT_ATTR_FLAG; } - else if (HDstrcmp(s_flag, "allflags") == 0) { + else if (HDstrcmp(s_flag, "allflags") == 0) { fla = H5O_COPY_ALL; } - else if (HDstrcmp(s_flag, "nullmsg") == 0) { + else if (HDstrcmp(s_flag, "nullmsg") == 0) { fla = H5O_COPY_PRESERVE_NULL_FLAG; } else { @@ -205,270 +214,255 @@ static int parse_flag(const char* s_flag, unsigned *flag) */ int -main (int argc, const char *argv[]) +main(int argc, char *argv[]) { - int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ - H5E_auto2_t func; - H5E_auto2_t tools_func; - void *edata; - void *tools_edata; - hid_t fid_src = -1; - hid_t fid_dst = -1; - unsigned flag = 0; - unsigned verbose = 0; - unsigned parents = 0; - hid_t ocpl_id = (-1); /* Object copy property list */ - hid_t lcpl_id = (-1); /* Link creation property list */ - int opt; - int li_ret; + hid_t fid_src = H5I_INVALID_HID; + hid_t fid_dst = H5I_INVALID_HID; + unsigned flag = 0; + unsigned verbose = 0; + unsigned parents = 0; + hid_t ocpl_id = H5I_INVALID_HID; /* Object copy property list */ + hid_t lcpl_id = H5I_INVALID_HID; /* Link creation property list */ + int opt; + int li_ret; h5tool_link_info_t linkinfo; + int ret_value = 0; h5tools_setprogname(PROGRAMNAME); h5tools_setstatus(EXIT_SUCCESS); - /* Disable error reporting */ - H5Eget_auto2(H5E_DEFAULT, &func, &edata); - H5Eset_auto2(H5E_DEFAULT, NULL, NULL); - /* Initialize h5tools lib */ h5tools_init(); - /* Disable tools error reporting */ - H5Eget_auto2(H5tools_ERR_STACK_g, &tools_func, &tools_edata); - H5Eset_auto2(H5tools_ERR_STACK_g, NULL, NULL); - /* init linkinfo struct */ HDmemset(&linkinfo, 0, sizeof(h5tool_link_info_t)); /* Check for no command line parameters */ - if(argc == 1) { + if (argc == 1) { usage(); leave(EXIT_FAILURE); } /* end if */ /* parse command line options */ - while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) { + while ((opt = H5_get_option(argc, (const char *const *)argv, s_opts, l_opts)) != EOF) { switch ((char)opt) { - case 'd': - oname_dst = HDstrdup(opt_arg); - break; + case 'd': + oname_dst = HDstrdup(H5_optarg); + break; + + case 'f': + /* validate flag */ + if (parse_flag(H5_optarg, &flag) < 0) { + usage(); + leave(EXIT_FAILURE); + } + str_flag = HDstrdup(H5_optarg); + break; - case 'f': - /* validate flag */ - if (parse_flag(opt_arg, &flag) < 0) { + case 'h': + usage(); + leave(EXIT_SUCCESS); + break; + + case 'i': + fname_src = HDstrdup(H5_optarg); + break; + + case 'o': + fname_dst = HDstrdup(H5_optarg); + break; + + case 'p': + parents = 1; + break; + + case 's': + oname_src = HDstrdup(H5_optarg); + break; + + case 'V': + print_version(h5tools_getprogname()); + leave(EXIT_SUCCESS); + break; + + case 'v': + verbose = 1; + break; + + case 'E': + if (H5_optarg != NULL) + enable_error_stack = HDatoi(H5_optarg); + else + enable_error_stack = 1; + break; + + default: usage(); leave(EXIT_FAILURE); - } - str_flag = HDstrdup(opt_arg); - break; - - case 'h': - usage(); - leave(EXIT_SUCCESS); - break; - - case 'i': - fname_src = HDstrdup(opt_arg); - break; - - case 'o': - fname_dst = HDstrdup(opt_arg); - break; - - case 'p': - parents = 1; - break; - - case 's': - oname_src = HDstrdup(opt_arg); - break; - - case 'V': - print_version(h5tools_getprogname()); - leave(EXIT_SUCCESS); - break; - - case 'v': - verbose = 1; - break; - - case 'E': - enable_error_stack = 1; - break; - - default: - usage(); - leave(EXIT_FAILURE); } } /* end of while */ -/*------------------------------------------------------------------------- - * check for missing file/object names - *-------------------------------------------------------------------------*/ + /*------------------------------------------------------------------------- + * check for missing file/object names + *-------------------------------------------------------------------------*/ - if (fname_src==NULL) { + if (fname_src == NULL) { error_msg("Input file name missing\n"); usage(); leave(EXIT_FAILURE); } - if (fname_dst==NULL) { + if (fname_dst == NULL) { error_msg("Output file name missing\n"); usage(); leave(EXIT_FAILURE); } - if (oname_src==NULL) { + if (oname_src == NULL) { error_msg("Source object name missing\n"); usage(); leave(EXIT_FAILURE); } - if (oname_dst==NULL) { + if (oname_dst == NULL) { error_msg("Destination object name missing\n"); usage(); leave(EXIT_FAILURE); } - if (enable_error_stack > 0) { - H5Eset_auto2(H5E_DEFAULT, func, edata); - H5Eset_auto2(H5tools_ERR_STACK_g, tools_func, tools_edata); - } + /* enable error reporting if command line option */ + h5tools_error_report(); - /*------------------------------------------------------------------------- - * open output file - *-------------------------------------------------------------------------*/ + /*------------------------------------------------------------------------- + * open output file + *-------------------------------------------------------------------------*/ /* Attempt to open an existing HDF5 file first. Need to open the dst file before the src file just in case that the dst and src are the same file */ - fid_dst = h5tools_fopen(fname_dst, H5F_ACC_RDWR, H5P_DEFAULT, NULL, NULL, 0); + fid_dst = h5tools_fopen(fname_dst, H5F_ACC_RDWR, H5P_DEFAULT, FALSE, NULL, 0); - /*------------------------------------------------------------------------- - * open input file - *-------------------------------------------------------------------------*/ + /*------------------------------------------------------------------------- + * open input file + *-------------------------------------------------------------------------*/ - fid_src = h5tools_fopen(fname_src, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, 0); + fid_src = h5tools_fopen(fname_src, H5F_ACC_RDONLY, H5P_DEFAULT, FALSE, NULL, 0); - /*------------------------------------------------------------------------- - * test for error in opening input file - *-------------------------------------------------------------------------*/ - if (fid_src==-1) { + /*------------------------------------------------------------------------- + * test for error in opening input file + *-------------------------------------------------------------------------*/ + if (fid_src == -1) { error_msg("Could not open input file <%s>...Exiting\n", fname_src); leave(EXIT_FAILURE); } - - /*------------------------------------------------------------------------- - * create an output file when failed to open it - *-------------------------------------------------------------------------*/ + /*------------------------------------------------------------------------- + * create an output file when failed to open it + *-------------------------------------------------------------------------*/ /* If we couldn't open an existing file, try creating file */ /* (use "EXCL" instead of "TRUNC", so we don't blow away existing non-HDF5 file) */ - if(fid_dst < 0) + if (fid_dst < 0) fid_dst = H5Fcreate(fname_dst, H5F_ACC_EXCL, H5P_DEFAULT, H5P_DEFAULT); - /*------------------------------------------------------------------------- - * test for error in opening output file - *-------------------------------------------------------------------------*/ - if (fid_dst==-1) { + /*------------------------------------------------------------------------- + * test for error in opening output file + *-------------------------------------------------------------------------*/ + if (fid_dst == -1) { error_msg("Could not open output file <%s>...Exiting\n", fname_dst); leave(EXIT_FAILURE); } - /*------------------------------------------------------------------------- - * print some info - *-------------------------------------------------------------------------*/ + /*------------------------------------------------------------------------- + * print some info + *-------------------------------------------------------------------------*/ if (verbose) { - HDprintf("Copying file <%s> and object <%s> to file <%s> and object <%s>\n", - fname_src, oname_src, fname_dst, oname_dst); + HDprintf("Copying file <%s> and object <%s> to file <%s> and object <%s>\n", fname_src, oname_src, + fname_dst, oname_dst); if (flag) { HDprintf("Using %s flag\n", str_flag); } } - - /*------------------------------------------------------------------------- - * create property lists for copy - *-------------------------------------------------------------------------*/ + /*------------------------------------------------------------------------- + * create property lists for copy + *-------------------------------------------------------------------------*/ /* create property to pass copy options */ - if ( (ocpl_id = H5Pcreate(H5P_OBJECT_COPY)) < 0) - HGOTO_ERROR(EXIT_FAILURE, H5E_tools_min_id_g, "H5Pcreate failed"); + if ((ocpl_id = H5Pcreate(H5P_OBJECT_COPY)) < 0) + H5TOOLS_GOTO_ERROR(EXIT_FAILURE, "H5Pcreate failed"); /* set options for object copy */ if (flag) { - if ( H5Pset_copy_object(ocpl_id, flag) < 0) - HGOTO_ERROR(EXIT_FAILURE, H5E_tools_min_id_g, "H5Pset_copy_object failed"); + if (H5Pset_copy_object(ocpl_id, flag) < 0) + H5TOOLS_GOTO_ERROR(EXIT_FAILURE, "H5Pset_copy_object failed"); } /* Create link creation property list */ - if((lcpl_id = H5Pcreate(H5P_LINK_CREATE)) < 0) { + if ((lcpl_id = H5Pcreate(H5P_LINK_CREATE)) < 0) { error_msg("Could not create link creation property list\n"); - HGOTO_ERROR(EXIT_FAILURE, H5E_tools_min_id_g, "H5Pcreate failed"); + H5TOOLS_GOTO_ERROR(EXIT_FAILURE, "H5Pcreate failed"); } /* end if */ /* Check for creating intermediate groups */ - if(parents) { + if (parents) { /* Set the intermediate group creation property */ - if(H5Pset_create_intermediate_group(lcpl_id, 1) < 0) { + if (H5Pset_create_intermediate_group(lcpl_id, 1) < 0) { error_msg("Could not set property for creating parent groups\n"); - HGOTO_ERROR(EXIT_FAILURE, H5E_tools_min_id_g, "H5Pset_create_intermediate_group failed"); + H5TOOLS_GOTO_ERROR(EXIT_FAILURE, "H5Pset_create_intermediate_group failed"); } /* end if */ /* Display some output if requested */ - if(verbose) + if (verbose) HDprintf("%s: Creating parent groups\n", h5tools_getprogname()); } /* end if */ else { /* error, if parent groups doesn't already exist in destination file */ - size_t i, len; + size_t i, len; len = HDstrlen(oname_dst); /* check if all the parents groups exist. skip root group */ for (i = 1; i < len; i++) { - if ('/'==oname_dst[i]) { - char *str_ptr; + if ('/' == oname_dst[i]) { + char *str_ptr; str_ptr = (char *)HDcalloc(i + 1, sizeof(char)); HDstrncpy(str_ptr, oname_dst, i); - str_ptr[i]='\0'; + str_ptr[i] = '\0'; if (H5Lexists(fid_dst, str_ptr, H5P_DEFAULT) <= 0) { error_msg("group <%s> doesn't exist. Use -p to create parent groups.\n", str_ptr); HDfree(str_ptr); - HGOTO_ERROR(EXIT_FAILURE, H5E_tools_min_id_g, "H5Lexists failed"); + H5TOOLS_GOTO_ERROR(EXIT_FAILURE, "H5Lexists failed"); } HDfree(str_ptr); } } } - /*------------------------------------------------------------------------- - * do the copy - *-------------------------------------------------------------------------*/ + /*------------------------------------------------------------------------- + * do the copy + *-------------------------------------------------------------------------*/ - if(verbose) + if (verbose) linkinfo.opt.msg_mode = 1; li_ret = H5tools_get_symlink_info(fid_src, oname_src, &linkinfo, 1); if (li_ret == 0) { /* dangling link */ - if(H5Lcopy(fid_src, oname_src, - fid_dst, oname_dst, - H5P_DEFAULT, H5P_DEFAULT) < 0) - HGOTO_ERROR(EXIT_FAILURE, H5E_tools_min_id_g, "H5Lcopy failed"); + if (H5Lcopy(fid_src, oname_src, fid_dst, oname_dst, H5P_DEFAULT, H5P_DEFAULT) < 0) + H5TOOLS_GOTO_ERROR(EXIT_FAILURE, "H5Lcopy failed"); } else { /* valid link */ - if (H5Ocopy(fid_src, /* Source file or group identifier */ - oname_src, /* Name of the source object to be copied */ - fid_dst, /* Destination file or group identifier */ - oname_dst, /* Name of the destination object */ - ocpl_id, /* Object copy property list */ - lcpl_id)<0) /* Link creation property list */ - HGOTO_ERROR(EXIT_FAILURE, H5E_tools_min_id_g, "H5Ocopy failed"); + if (H5Ocopy(fid_src, /* Source file or group identifier */ + oname_src, /* Name of the source object to be copied */ + fid_dst, /* Destination file or group identifier */ + oname_dst, /* Name of the destination object */ + ocpl_id, /* Object copy property list */ + lcpl_id) < 0) /* Link creation property list */ + H5TOOLS_GOTO_ERROR(EXIT_FAILURE, "H5Ocopy failed"); } /* free link info path */ @@ -476,16 +470,16 @@ main (int argc, const char *argv[]) HDfree(linkinfo.trg_path); /* close propertis */ - if(H5Pclose(ocpl_id)<0) - HGOTO_ERROR(EXIT_FAILURE, H5E_tools_min_id_g, "H5Pclose failed"); - if(H5Pclose(lcpl_id)<0) - HGOTO_ERROR(EXIT_FAILURE, H5E_tools_min_id_g, "H5Pclose failed"); + if (H5Pclose(ocpl_id) < 0) + H5TOOLS_GOTO_ERROR(EXIT_FAILURE, "H5Pclose failed"); + if (H5Pclose(lcpl_id) < 0) + H5TOOLS_GOTO_ERROR(EXIT_FAILURE, "H5Pclose failed"); /* close files */ - if (H5Fclose(fid_src)<0) - HGOTO_ERROR(EXIT_FAILURE, H5E_tools_min_id_g, "H5Fclose failed"); - if (H5Fclose(fid_dst)<0) - HGOTO_ERROR(EXIT_FAILURE, H5E_tools_min_id_g, "H5Fclose failed"); + if (H5Fclose(fid_src) < 0) + H5TOOLS_GOTO_ERROR(EXIT_FAILURE, "H5Fclose failed"); + if (H5Fclose(fid_dst) < 0) + H5TOOLS_GOTO_ERROR(EXIT_FAILURE, "H5Fclose failed"); leave(EXIT_SUCCESS); @@ -496,13 +490,14 @@ done: if (linkinfo.trg_path) HDfree(linkinfo.trg_path); - H5E_BEGIN_TRY { + H5E_BEGIN_TRY + { H5Pclose(ocpl_id); H5Pclose(lcpl_id); H5Fclose(fid_src); H5Fclose(fid_dst); - } H5E_END_TRY; + } + H5E_END_TRY; leave(ret_value); } - diff --git a/tools/src/h5diff/CMakeLists.txt b/tools/src/h5diff/CMakeLists.txt index 96ed6ad..e54b2da 100644 --- a/tools/src/h5diff/CMakeLists.txt +++ b/tools/src/h5diff/CMakeLists.txt @@ -1,4 +1,4 @@ -cmake_minimum_required (VERSION 3.10) +cmake_minimum_required (VERSION 3.12) project (HDF5_TOOLS_SRC_H5DIFF C) # -------------------------------------------------------------------- @@ -8,8 +8,11 @@ if (NOT ONLY_SHARED_LIBS) add_executable (h5diff ${HDF5_TOOLS_SRC_H5DIFF_SOURCE_DIR}/h5diff_common.c ${HDF5_TOOLS_SRC_H5DIFF_SOURCE_DIR}/h5diff_main.c + ${HDF5_TOOLS_SRC_H5DIFF_SOURCE_DIR}/h5diff_common.h ) - target_include_directories (h5diff PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5diff PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_compile_options(h5diff PRIVATE "${HDF5_CMAKE_C_FLAGS}") + #target_compile_definitions (h5diff PRIVATE H5_TOOLS_DEBUG) TARGET_C_PROPERTIES (h5diff STATIC) target_link_libraries (h5diff PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) set_target_properties (h5diff PROPERTIES FOLDER tools) @@ -21,8 +24,11 @@ if (BUILD_SHARED_LIBS) add_executable (h5diff-shared ${HDF5_TOOLS_SRC_H5DIFF_SOURCE_DIR}/h5diff_common.c ${HDF5_TOOLS_SRC_H5DIFF_SOURCE_DIR}/h5diff_main.c + ${HDF5_TOOLS_SRC_H5DIFF_SOURCE_DIR}/h5diff_common.h ) - target_include_directories (h5diff-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5diff-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_compile_options(h5diff-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}") + #target_compile_definitions (h5diff-shared PRIVATE H5_TOOLS_DEBUG) TARGET_C_PROPERTIES (h5diff-shared SHARED) target_link_libraries (h5diff-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET}) set_target_properties (h5diff-shared PROPERTIES FOLDER tools) @@ -31,13 +37,25 @@ if (BUILD_SHARED_LIBS) set (H5_DEP_EXECUTABLES ${H5_DEP_EXECUTABLES} h5diff-shared) endif () +#----------------------------------------------------------------------------- +# Add Target to clang-format +#----------------------------------------------------------------------------- +if (HDF5_ENABLE_FORMATTERS) + if (NOT ONLY_SHARED_LIBS) + clang_format (HDF5_H5DIFF_SRC_FORMAT h5diff) + else () + clang_format (HDF5_H5DIFF_SRC_FORMAT h5diff-shared) + endif () +endif () + if (H5_HAVE_PARALLEL) if (NOT ONLY_SHARED_LIBS) add_executable (ph5diff ${HDF5_TOOLS_SRC_H5DIFF_SOURCE_DIR}/h5diff_common.c ${HDF5_TOOLS_SRC_H5DIFF_SOURCE_DIR}/ph5diff_main.c ) - target_include_directories (ph5diff PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (ph5diff PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_compile_options(ph5diff PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (ph5diff STATIC) target_link_libraries (ph5diff PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET} "$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_LIBRARIES}>") set_target_properties (ph5diff PROPERTIES FOLDER tools) @@ -49,7 +67,8 @@ if (H5_HAVE_PARALLEL) ${HDF5_TOOLS_SRC_H5DIFF_SOURCE_DIR}/h5diff_common.c ${HDF5_TOOLS_SRC_H5DIFF_SOURCE_DIR}/ph5diff_main.c ) - target_include_directories (ph5diff-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (ph5diff-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_compile_options(ph5diff-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (ph5diff-shared SHARED) target_link_libraries (ph5diff-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET} "$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_LIBRARIES}>") set_target_properties (ph5diff-shared PROPERTIES FOLDER tools) diff --git a/tools/src/h5diff/Makefile.am b/tools/src/h5diff/Makefile.am index 3957e59..451ad20 100644 --- a/tools/src/h5diff/Makefile.am +++ b/tools/src/h5diff/Makefile.am @@ -6,7 +6,7 @@ # This file is part of HDF5. The full HDF5 copyright notice, including # terms governing use, modification, and redistribution, is contained in # the COPYING file, which can be found at the root of the source code -# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. +# distribution tree, or in https://www.hdfgroup.org/licenses. # If you do not have access to either file, you may request a copy from # help@hdfgroup.org. ## diff --git a/tools/src/h5diff/h5diff_common.c b/tools/src/h5diff/h5diff_common.c index 362e3f2..2619a9d 100644 --- a/tools/src/h5diff/h5diff_common.c +++ b/tools/src/h5diff/h5diff_common.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -17,42 +17,53 @@ #include "h5tools.h" #include "h5tools_utils.h" -static int check_n_input(const char*); -static int check_p_input(const char*); -static int check_d_input(const char*); +static int check_n_input(const char *); +static int check_p_input(const char *); +static int check_d_input(const char *); /* * Command-line options: The user can specify short or long-named * parameters. */ -static const char *s_opts = "hVrv:qn:d:p:NcelxE:S"; -static struct long_options l_opts[] = { - { "help", no_arg, 'h' }, - { "version", no_arg, 'V' }, - { "report", no_arg, 'r' }, - { "verbose", optional_arg, 'v' }, - { "quiet", no_arg, 'q' }, - { "count", require_arg, 'n' }, - { "delta", require_arg, 'd' }, - { "relative", require_arg, 'p' }, - { "nan", no_arg, 'N' }, - { "compare", no_arg, 'c' }, - { "use-system-epsilon", no_arg, 'e' }, - { "follow-symlinks", no_arg, 'l' }, - { "no-dangling-links", no_arg, 'x' }, - { "exclude-path", require_arg, 'E' }, - { "enable-error-stack", no_arg, 'S' }, - { NULL, 0, '\0' } -}; +static const char * s_opts = "hVrv*qn:d:p:NcelxE:A:S*"; +static struct h5_long_options l_opts[] = {{"help", no_arg, 'h'}, + {"version", no_arg, 'V'}, + {"report", no_arg, 'r'}, + {"verbose", optional_arg, 'v'}, + {"quiet", no_arg, 'q'}, + {"count", require_arg, 'n'}, + {"delta", require_arg, 'd'}, + {"relative", require_arg, 'p'}, + {"nan", no_arg, 'N'}, + {"compare", no_arg, 'c'}, + {"use-system-epsilon", no_arg, 'e'}, + {"follow-symlinks", no_arg, 'l'}, + {"no-dangling-links", no_arg, 'x'}, + {"exclude-path", require_arg, 'E'}, + {"exclude-attribute", require_arg, 'A'}, + {"enable-error-stack", optional_arg, 'S'}, + {"vol-value-1", require_arg, '1'}, + {"vol-name-1", require_arg, '2'}, + {"vol-info-1", require_arg, '3'}, + {"vol-value-2", require_arg, '4'}, + {"vol-name-2", require_arg, '5'}, + {"vol-info-2", require_arg, '6'}, + {"vfd-value-1", require_arg, '7'}, + {"vfd-name-1", require_arg, '8'}, + {"vfd-info-1", require_arg, '9'}, + {"vfd-value-2", require_arg, '0'}, + {"vfd-name-2", require_arg, 'Y'}, + {"vfd-info-2", require_arg, 'Z'}, + {NULL, 0, '\0'}}; /*------------------------------------------------------------------------- * Function: check_options * * Purpose: parse command line input - * *------------------------------------------------------------------------- */ -static void check_options(diff_opt_t* opts) +static void +check_options(diff_opt_t *opts) { /*-------------------------------------------------------------- * check for mutually exclusive options @@ -61,37 +72,151 @@ static void check_options(diff_opt_t* opts) /* check between -d , -p, --use-system-epsilon. * These options are mutually exclusive. */ - if ((opts->d + opts->p + opts->use_system_epsilon) > 1) { + if ((opts->delta_bool + opts->percent_bool + opts->use_system_epsilon) > 1) { HDprintf("%s error: -d, -p and --use-system-epsilon options are mutually-exclusive;\n", PROGRAMNAME); HDprintf("use no more than one.\n"); - HDprintf("Try '-h' or '--help' option for more information or see the %s entry in the 'HDF5 Reference Manual'.\n", PROGRAMNAME); + HDprintf("Try '-h' or '--help' option for more information or see the %s entry in the 'HDF5 " + "Reference Manual'.\n", + PROGRAMNAME); h5diff_exit(EXIT_FAILURE); } } +/*------------------------------------------------------------------------- + * Function: parse_hsize_list + * + * Purpose: Parse a list of comma or space separated integers and return + * them in a list. The string being passed into this function + * should be at the start of the list you want to parse. You are + * responsible for freeing the array returned from here. + * + * Lists in the so-called "terse" syntax are separated by + * semicolons (;). The lists themselves can be separated by + * either commas (,) or white spaces. + * + * Return: <none> + *------------------------------------------------------------------------- + */ +static void +parse_hsize_list(const char *h_list, subset_d *d) +{ + hsize_t * p_list; + const char * ptr; + unsigned int size_count = 0; + unsigned int i = 0; + unsigned int last_digit = 0; + + if (!h_list || !*h_list || *h_list == ';') + return; + + H5TOOLS_START_DEBUG(" - h_list:%s", h_list); + /* count how many integers do we have */ + for (ptr = h_list; ptr && *ptr && *ptr != ';' && *ptr != ']'; ptr++) + if (HDisdigit(*ptr)) { + if (!last_digit) + /* the last read character wasn't a digit */ + size_count++; + + last_digit = 1; + } + else + last_digit = 0; + + if (size_count == 0) { + /* there aren't any integers to read */ + H5TOOLS_ENDDEBUG("No integers to read"); + return; + } + H5TOOLS_DEBUG("Number integers to read=%ld", size_count); + + /* allocate an array for the integers in the list */ + if ((p_list = (hsize_t *)HDcalloc(size_count, sizeof(hsize_t))) == NULL) + H5TOOLS_INFO("Unable to allocate space for subset data"); + + for (ptr = h_list; i < size_count && ptr && *ptr && *ptr != ';' && *ptr != ']'; ptr++) + if (HDisdigit(*ptr)) { + /* we should have an integer now */ + p_list[i++] = (hsize_t)HDstrtoull(ptr, NULL, 0); + + while (HDisdigit(*ptr)) + /* scroll to end of integer */ + ptr++; + } + d->data = p_list; + d->len = size_count; + H5TOOLS_ENDDEBUG(" "); +} + +/*------------------------------------------------------------------------- + * Function: parse_subset_params + * + * Purpose: Parse the so-called "terse" syntax for specifying subsetting parameters. + * + * Return: Success: struct subset_t object + * Failure: NULL + *------------------------------------------------------------------------- + */ +static struct subset_t * +parse_subset_params(const char *dset) +{ + struct subset_t *s = NULL; + char * brace; + + H5TOOLS_START_DEBUG(" - dset:%s", dset); + if ((brace = HDstrrchr(dset, '[')) != NULL) { + *brace++ = '\0'; + + s = (struct subset_t *)HDcalloc(1, sizeof(struct subset_t)); + parse_hsize_list(brace, &s->start); + + while (*brace && *brace != ';') + brace++; + + if (*brace) + brace++; + + parse_hsize_list(brace, &s->stride); + + while (*brace && *brace != ';') + brace++; + + if (*brace) + brace++; + + parse_hsize_list(brace, &s->count); + + while (*brace && *brace != ';') + brace++; + + if (*brace) + brace++; + + parse_hsize_list(brace, &s->block); + } + H5TOOLS_ENDDEBUG(" "); + + return s; +} /*------------------------------------------------------------------------- * Function: parse_command_line * * Purpose: parse command line input - * *------------------------------------------------------------------------- */ -void parse_command_line(int argc, - const char* argv[], - const char** fname1, - const char** fname2, - const char** objname1, - const char** objname2, - diff_opt_t* opts) +void +parse_command_line(int argc, const char *const *argv, const char **fname1, const char **fname2, + const char **objname1, const char **objname2, diff_opt_t *opts) { - int i; - int opt; + int i; + int opt; struct exclude_path_list *exclude_head, *exclude_prev, *exclude_node; + struct exclude_path_list *exclude_attr_head, *exclude_attr_prev, *exclude_attr_node; + H5TOOLS_START_DEBUG(" "); /* process the command-line */ - memset(opts, 0, sizeof (diff_opt_t)); + HDmemset(opts, 0, sizeof(diff_opt_t)); /* assume equal contents initially */ opts->contents = 1; @@ -100,164 +225,254 @@ void parse_command_line(int argc, opts->do_nans = 1; /* not Listing objects that are not comparable */ - opts->m_list_not_cmp = 0; + opts->mode_list_not_cmp = 0; /* initially no not-comparable. */ /**this is bad in mixing option with results**/ - opts->not_cmp=0; + opts->not_cmp = 0; /* init for exclude-path option */ exclude_head = NULL; + /* init for exclude-attribute option */ + exclude_attr_head = NULL; + /* parse command line options */ - while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) { + while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) { switch ((char)opt) { - default: - usage(); - h5diff_exit(EXIT_FAILURE); - break; - - case 'h': - usage(); - h5diff_exit(EXIT_SUCCESS); - break; - - case 'V': - print_version(h5tools_getprogname()); - h5diff_exit(EXIT_SUCCESS); - break; - - case 'v': - opts->m_verbose = 1; - /* This for loop is for handling style like - * -v, -v1, --verbose, --verbose=1. - */ - for (i = 1; i < argc; i++) { - /* - * short opt - */ - if (!strcmp (argv[i], "-v")) { /* no arg */ - opt_ind--; - opts->m_verbose_level = 0; - break; - } - else if (!strncmp (argv[i], "-v", (size_t)2)) { - opts->m_verbose_level = atoi(&argv[i][2]); - break; - } + default: + usage(); + h5diff_exit(EXIT_FAILURE); + break; - /* - * long opt - */ - if (!strcmp (argv[i], "--verbose")) { /* no arg */ - opts->m_verbose_level = 0; - break; + case 'h': + usage(); + h5diff_exit(EXIT_SUCCESS); + break; + + case 'V': + print_version(h5tools_getprogname()); + h5diff_exit(EXIT_SUCCESS); + break; + + case 'v': + opts->mode_verbose = 1; + for (i = 1; i < argc; i++) { + /* + * special check for short opt + */ + if (!strcmp(argv[i], "-v")) { + if (H5_optarg != NULL) + H5_optind--; + opts->mode_verbose_level = 0; + break; + } + else if (!strncmp(argv[i], "-v", (size_t)2)) { + if (H5_optarg != NULL) + H5_optind--; + opts->mode_verbose_level = atoi(&argv[i][2]); + break; + } + else { + if (H5_optarg != NULL) + opts->mode_verbose_level = HDatoi(H5_optarg); + else + opts->mode_verbose_level = 0; + } } - else if ( !strncmp (argv[i], "--verbose", (size_t)9) && argv[i][9]=='=') { - opts->m_verbose_level = atoi(&argv[i][10]); - break; + break; + + case 'q': + /* use quiet mode; suppress the message "0 differences found" */ + opts->mode_quiet = 1; + break; + + case 'r': + opts->mode_report = 1; + break; + + case 'l': + opts->follow_links = TRUE; + break; + + case 'x': + opts->no_dangle_links = 1; + break; + + case 'S': + if (H5_optarg != NULL) + enable_error_stack = HDatoi(H5_optarg); + else + enable_error_stack = 1; + break; + + case 'E': + opts->exclude_path = 1; + + /* create linked list of excluding objects */ + if ((exclude_node = (struct exclude_path_list *)HDmalloc(sizeof(struct exclude_path_list))) == + NULL) { + HDprintf("Error: lack of memory!\n"); + h5diff_exit(EXIT_FAILURE); } - } - break; - case 'q': - /* use quiet mode; supress the message "0 differences found" */ - opts->m_quiet = 1; - break; + /* init */ + exclude_node->obj_path = H5_optarg; + exclude_node->obj_type = H5TRAV_TYPE_UNKNOWN; + exclude_prev = exclude_head; - case 'r': - opts->m_report = 1; - break; + if (NULL == exclude_head) { + exclude_head = exclude_node; + exclude_head->next = NULL; + } + else { + while (NULL != exclude_prev->next) + exclude_prev = exclude_prev->next; - case 'l': - opts->follow_links = TRUE; - break; + exclude_node->next = NULL; + exclude_prev->next = exclude_node; + } + break; - case 'x': - opts->no_dangle_links = 1; - break; + case 'A': + opts->exclude_attr_path = 1; - case 'S': - enable_error_stack = 1; - break; + /* create linked list of excluding objects */ + if ((exclude_attr_node = + (struct exclude_path_list *)HDmalloc(sizeof(struct exclude_path_list))) == NULL) { + HDprintf("Error: lack of memory!\n"); + h5diff_exit(EXIT_FAILURE); + } - case 'E': - opts->exclude_path = 1; + /* init */ + exclude_attr_node->obj_path = H5_optarg; + exclude_attr_node->obj_type = H5TRAV_TYPE_UNKNOWN; + exclude_attr_prev = exclude_attr_head; - /* create linked list of excluding objects */ - if( (exclude_node = (struct exclude_path_list*) HDmalloc(sizeof(struct exclude_path_list))) == NULL) { - HDprintf("Error: lack of memory!\n"); - h5diff_exit(EXIT_FAILURE); - } - - /* init */ - exclude_node->obj_path = (char*)opt_arg; - exclude_node->obj_type = H5TRAV_TYPE_UNKNOWN; - exclude_prev = exclude_head; - - if (NULL == exclude_head) { - exclude_head = exclude_node; - exclude_head->next = NULL; - } - else { - while(NULL != exclude_prev->next) - exclude_prev=exclude_prev->next; - - exclude_node->next = NULL; - exclude_prev->next = exclude_node; - } - break; - - case 'd': - opts->d=1; - - if (check_d_input(opt_arg) == - 1) { - HDprintf("<-d %s> is not a valid option\n", opt_arg); - usage(); - h5diff_exit(EXIT_FAILURE); - } - opts->delta = atof(opt_arg); - - /* -d 0 is the same as default */ - if (H5_DBL_ABS_EQUAL(opts->delta, (double)0.0F)) - opts->d=0; - break; - - case 'p': - opts->p=1; - if (check_p_input(opt_arg) == -1) { - HDprintf("<-p %s> is not a valid option\n", opt_arg); - usage(); - h5diff_exit(EXIT_FAILURE); - } - opts->percent = atof(opt_arg); - - /* -p 0 is the same as default */ - if (H5_DBL_ABS_EQUAL(opts->percent, (double)0.0F)) - opts->p = 0; - break; - - case 'n': - opts->n=1; - if ( check_n_input(opt_arg) == -1) { - HDprintf("<-n %s> is not a valid option\n", opt_arg); - usage(); - h5diff_exit(EXIT_FAILURE); - } - opts->count = HDstrtoull(opt_arg, NULL, 0); - break; + if (NULL == exclude_attr_head) { + exclude_attr_head = exclude_attr_node; + exclude_attr_head->next = NULL; + } + else { + while (NULL != exclude_attr_prev->next) + exclude_attr_prev = exclude_attr_prev->next; - case 'N': - opts->do_nans = 0; - break; + exclude_attr_node->next = NULL; + exclude_attr_prev->next = exclude_attr_node; + } + break; - case 'c': - opts->m_list_not_cmp = 1; - break; + case 'd': + opts->delta_bool = 1; - case 'e': - opts->use_system_epsilon = 1; - break; + if (check_d_input(H5_optarg) == -1) { + HDprintf("<-d %s> is not a valid option\n", H5_optarg); + usage(); + h5diff_exit(EXIT_FAILURE); + } + opts->delta = HDatof(H5_optarg); + /* do not check against default, the DBL_EPSILON is being replaced by user */ + break; + + case 'p': + opts->percent_bool = 1; + if (check_p_input(H5_optarg) == -1) { + HDprintf("<-p %s> is not a valid option\n", H5_optarg); + usage(); + h5diff_exit(EXIT_FAILURE); + } + opts->percent = HDatof(H5_optarg); + + /* -p 0 is the same as default */ + if (H5_DBL_ABS_EQUAL(opts->percent, 0.0)) + opts->percent_bool = 0; + break; + + case 'n': + opts->count_bool = 1; + if (check_n_input(H5_optarg) == -1) { + HDprintf("<-n %s> is not a valid option\n", H5_optarg); + usage(); + h5diff_exit(EXIT_FAILURE); + } + opts->count = HDstrtoull(H5_optarg, NULL, 0); + break; + + case 'N': + opts->do_nans = 0; + break; + + case 'c': + opts->mode_list_not_cmp = 1; + break; + + case 'e': + opts->use_system_epsilon = 1; + break; + + case '1': + opts->vol_info[0].type = VOL_BY_VALUE; + opts->vol_info[0].u.value = (H5VL_class_value_t)HDatoi(H5_optarg); + opts->custom_vol[0] = TRUE; + break; + + case '2': + opts->vol_info[0].type = VOL_BY_NAME; + opts->vol_info[0].u.name = H5_optarg; + opts->custom_vol[0] = TRUE; + break; + + case '3': + opts->vol_info[0].info_string = H5_optarg; + break; + + case '4': + opts->vol_info[1].type = VOL_BY_VALUE; + opts->vol_info[1].u.value = (H5VL_class_value_t)HDatoi(H5_optarg); + opts->custom_vol[1] = TRUE; + break; + + case '5': + opts->vol_info[1].type = VOL_BY_NAME; + opts->vol_info[1].u.name = H5_optarg; + opts->custom_vol[1] = TRUE; + break; + + case '6': + opts->vol_info[1].info_string = H5_optarg; + break; + + case '7': + opts->vfd_info[0].type = VFD_BY_VALUE; + opts->vfd_info[0].u.value = (H5FD_class_value_t)HDatoi(H5_optarg); + opts->custom_vfd[0] = TRUE; + break; + + case '8': + opts->vfd_info[0].type = VFD_BY_NAME; + opts->vfd_info[0].u.name = H5_optarg; + opts->custom_vol[0] = TRUE; + break; + + case '9': + opts->vfd_info[0].info = (const void *)H5_optarg; + break; + + case '0': + opts->vfd_info[1].type = VFD_BY_VALUE; + opts->vfd_info[1].u.value = (H5FD_class_value_t)HDatoi(H5_optarg); + opts->custom_vfd[1] = TRUE; + break; + + case 'Y': + opts->vfd_info[1].type = VFD_BY_NAME; + opts->vfd_info[1].u.name = H5_optarg; + opts->custom_vfd[1] = TRUE; + break; + + case 'Z': + opts->vfd_info[1].info = (const void *)H5_optarg; + break; } } @@ -268,64 +483,79 @@ void parse_command_line(int argc, if (opts->exclude_path) opts->exclude = exclude_head; + /* if exclude-attribute option is used, keep the exclude attr list */ + if (opts->exclude_attr_path) + opts->exclude_attr = exclude_attr_head; + /* check for file names to be processed */ - if (argc <= opt_ind || argv[ opt_ind + 1 ] == NULL) { + if (argc <= H5_optind || argv[H5_optind + 1] == NULL) { error_msg("missing file names\n"); usage(); h5diff_exit(EXIT_FAILURE); } - *fname1 = argv[ opt_ind ]; - *fname2 = argv[ opt_ind + 1 ]; - *objname1 = argv[ opt_ind + 2 ]; + *fname1 = argv[H5_optind]; + *fname2 = argv[H5_optind + 1]; + *objname1 = argv[H5_optind + 2]; + H5TOOLS_DEBUG("file1 = %s", *fname1); + H5TOOLS_DEBUG("file2 = %s", *fname2); if (*objname1 == NULL) { *objname2 = NULL; + H5TOOLS_ENDDEBUG("No obj names"); return; } + H5TOOLS_DEBUG("objname1 = %s", *objname1); - if (argv[ opt_ind + 3 ] != NULL) { - *objname2 = argv[ opt_ind + 3 ]; + if (argv[H5_optind + 3] != NULL) { + *objname2 = argv[H5_optind + 3]; } else { *objname2 = *objname1; } + H5TOOLS_DEBUG("objname2 = %s", *objname2); + + /* + * TRILABS_227 is complete except for an issue with printing indices + * the following calls will enable subsetting + */ + opts->sset[0] = parse_subset_params(*objname1); + opts->sset[1] = parse_subset_params(*objname2); + H5TOOLS_ENDDEBUG(" "); } - /*------------------------------------------------------------------------- * Function: print_info * * Purpose: print several information messages after h5diff call - * *------------------------------------------------------------------------- */ +void +print_info(diff_opt_t *opts) +{ + if (opts->mode_quiet || opts->err_stat) + return; - void print_info(diff_opt_t* opts) - { - if (opts->m_quiet || opts->err_stat) - return; - - if (opts->cmn_objs == 0) { - HDprintf("No common objects found. Files are not comparable.\n"); - if (!opts->m_verbose) - HDprintf("Use -v for a list of objects.\n"); - } - - if (opts->not_cmp == 1) { - if (opts->m_list_not_cmp == 0) { - HDprintf("--------------------------------\n"); - HDprintf("Some objects are not comparable\n"); - HDprintf("--------------------------------\n"); - if (opts->m_verbose) - HDprintf("Use -c for a list of objects without details of differences.\n"); - else - HDprintf("Use -c for a list of objects.\n"); - } - } - } + if (opts->cmn_objs == 0) { + HDprintf("No common objects found. Files are not comparable.\n"); + if (!opts->mode_verbose) + HDprintf("Use -v for a list of objects.\n"); + } + + if (opts->not_cmp == 1) { + if (opts->mode_list_not_cmp == 0) { + HDprintf("--------------------------------\n"); + HDprintf("Some objects are not comparable\n"); + HDprintf("--------------------------------\n"); + if (opts->mode_verbose) + HDprintf("Use -c for a list of objects without details of differences.\n"); + else + HDprintf("Use -c for a list of objects.\n"); + } + } +} /*------------------------------------------------------------------------- * Function: check_n_input @@ -333,22 +563,13 @@ void parse_command_line(int argc, * Purpose: check for valid input * * Return: 1 for ok, -1 for fail - * - * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu - * - * Date: May 9, 2003 - * - * Comments: - * - * Modifications: - * *------------------------------------------------------------------------- */ H5_ATTR_PURE static int -check_n_input( const char *str ) +check_n_input(const char *str) { unsigned i; - char c; + char c; for (i = 0; i < HDstrlen(str); i++) { c = str[i]; @@ -356,9 +577,8 @@ check_n_input( const char *str ) if (c < 49 || c > 57) /* ascii values between 1 and 9 */ return -1; } - else - if (c < 48 || c > 57) /* 0 also */ - return -1; + else if (c < 48 || c > 57) /* 0 also */ + return -1; } return 1; } @@ -369,28 +589,21 @@ check_n_input( const char *str ) * Purpose: check for a valid p option input * * Return: 1 for ok, -1 for fail - * - * Date: May 9, 2003 - * - * Comments: - * - * Modifications: - * *------------------------------------------------------------------------- */ static int -check_p_input( const char *str ) +check_p_input(const char *str) { double x; /* - the atof return value on a hexadecimal input is different - on some systems; we do a character check for this - */ + * the atof return value on a hexadecimal input is different + * on some systems; we do a character check for this + */ if (HDstrlen(str) > 2 && str[0] == '0' && str[1] == 'x') return -1; - x = atof(str); + x = HDatof(str); if (x < 0) return -1; @@ -403,28 +616,21 @@ check_p_input( const char *str ) * Purpose: check for a valid d option input * * Return: 1 for ok, -1 for fail - * - * Date: November 11, 2007 - * - * Comments: - * - * Modifications: - * *------------------------------------------------------------------------- */ static int -check_d_input( const char *str ) +check_d_input(const char *str) { double x; /* - the atof return value on a hexadecimal input is different - on some systems; we do a character check for this - */ + * the atof return value on a hexadecimal input is different + * on some systems; we do a character check for this + */ if (HDstrlen(str) > 2 && str[0] == '0' && str[1] == 'x') return -1; - x = atof(str); + x = HDatof(str); if (x < 0) return -1; @@ -437,159 +643,278 @@ check_d_input( const char *str ) * Purpose: print a usage message * * Return: void - * *------------------------------------------------------------------------- */ -void usage(void) +void +usage(void) { - PRINTVALSTREAM(rawoutstream, "usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]\n"); - PRINTVALSTREAM(rawoutstream, " file1 File name of the first HDF5 file\n"); - PRINTVALSTREAM(rawoutstream, " file2 File name of the second HDF5 file\n"); - PRINTVALSTREAM(rawoutstream, " [obj1] Name of an HDF5 object, in absolute path\n"); - PRINTVALSTREAM(rawoutstream, " [obj2] Name of an HDF5 object, in absolute path\n"); - PRINTVALSTREAM(rawoutstream, "\n"); - PRINTVALSTREAM(rawoutstream, " OPTIONS\n"); - PRINTVALSTREAM(rawoutstream, " -h, --help\n"); - PRINTVALSTREAM(rawoutstream, " Print a usage message and exit.\n"); - PRINTVALSTREAM(rawoutstream, " -V, --version\n"); - PRINTVALSTREAM(rawoutstream, " Print version number and exit.\n"); - PRINTVALSTREAM(rawoutstream, " -r, --report\n"); - PRINTVALSTREAM(rawoutstream, " Report mode. Print differences.\n"); - PRINTVALSTREAM(rawoutstream, " -v --verbose\n"); - PRINTVALSTREAM(rawoutstream, " Verbose mode. Print differences information and list of objects.\n"); - PRINTVALSTREAM(rawoutstream, " -vN --verbose=N\n"); - PRINTVALSTREAM(rawoutstream, " Verbose mode with level. Print differences and list of objects.\n"); - PRINTVALSTREAM(rawoutstream, " Level of detail depends on value of N:\n"); - PRINTVALSTREAM(rawoutstream, " 0 : Identical to '-v' or '--verbose'.\n"); - PRINTVALSTREAM(rawoutstream, " 1 : All level 0 information plus one-line attribute\n"); - PRINTVALSTREAM(rawoutstream, " status summary.\n"); - PRINTVALSTREAM(rawoutstream, " 2 : All level 1 information plus extended attribute\n"); - PRINTVALSTREAM(rawoutstream, " status report.\n"); - PRINTVALSTREAM(rawoutstream, " -q, --quiet\n"); - PRINTVALSTREAM(rawoutstream, " Quiet mode. Do not produce output.\n"); - PRINTVALSTREAM(rawoutstream, " --enable-error-stack\n"); - PRINTVALSTREAM(rawoutstream, " Prints messages from the HDF5 error stack as they occur.\n"); - PRINTVALSTREAM(rawoutstream, " --follow-symlinks\n"); - PRINTVALSTREAM(rawoutstream, " Follow symbolic links (soft links and external links and compare the)\n"); - PRINTVALSTREAM(rawoutstream, " links' target objects.\n"); - PRINTVALSTREAM(rawoutstream, " If symbolic link(s) with the same name exist in the files being\n"); - PRINTVALSTREAM(rawoutstream, " compared, then determine whether the target of each link is an existing\n"); - PRINTVALSTREAM(rawoutstream, " object (dataset, group, or named datatype) or the link is a dangling\n"); - PRINTVALSTREAM(rawoutstream, " link (a soft or external link pointing to a target object that does\n"); - PRINTVALSTREAM(rawoutstream, " not yet exist).\n"); - PRINTVALSTREAM(rawoutstream, " - If both symbolic links are dangling links, they are treated as being\n"); - PRINTVALSTREAM(rawoutstream, " the same; by default, h5diff returns an exit code of 0.\n"); - PRINTVALSTREAM(rawoutstream, " If, however, --no-dangling-links is used with --follow-symlinks,\n"); - PRINTVALSTREAM(rawoutstream, " this situation is treated as an error and h5diff returns an\n"); - PRINTVALSTREAM(rawoutstream, " exit code of 2.\n"); - PRINTVALSTREAM(rawoutstream, " - If only one of the two links is a dangling link,they are treated as\n"); - PRINTVALSTREAM(rawoutstream, " being different and h5diff returns an exit code of 1.\n"); - PRINTVALSTREAM(rawoutstream, " If, however, --no-dangling-links is used with --follow-symlinks,\n"); - PRINTVALSTREAM(rawoutstream, " this situation is treated as an error and h5diff returns an\n"); - PRINTVALSTREAM(rawoutstream, " exit code of 2.\n"); - PRINTVALSTREAM(rawoutstream, " - If both symbolic links point to existing objects, h5diff compares the\n"); - PRINTVALSTREAM(rawoutstream, " two objects.\n"); - PRINTVALSTREAM(rawoutstream, " If any symbolic link specified in the call to h5diff does not exist,\n"); - PRINTVALSTREAM(rawoutstream, " h5diff treats it as an error and returns an exit code of 2.\n"); - PRINTVALSTREAM(rawoutstream, " --no-dangling-links\n"); - PRINTVALSTREAM(rawoutstream, " Must be used with --follow-symlinks option; otherwise, h5diff shows\n"); - PRINTVALSTREAM(rawoutstream, " error message and returns an exit code of 2.\n"); - PRINTVALSTREAM(rawoutstream, " Check for any symbolic links (soft links or external links) that do not\n"); - PRINTVALSTREAM(rawoutstream, " resolve to an existing object (dataset, group, or named datatype).\n"); - PRINTVALSTREAM(rawoutstream, " If any dangling link is found, this situation is treated as an error\n"); - PRINTVALSTREAM(rawoutstream, " and h5diff returns an exit code of 2.\n"); - PRINTVALSTREAM(rawoutstream, " -c, --compare\n"); - PRINTVALSTREAM(rawoutstream, " List objects that are not comparable\n"); - PRINTVALSTREAM(rawoutstream, " -N, --nan\n"); - PRINTVALSTREAM(rawoutstream, " Avoid NaNs detection\n"); - PRINTVALSTREAM(rawoutstream, " -n C, --count=C\n"); - PRINTVALSTREAM(rawoutstream, " Print differences up to C. C must be a positive integer.\n"); - PRINTVALSTREAM(rawoutstream, " -d D, --delta=D\n"); - PRINTVALSTREAM(rawoutstream, " Print difference if (|a-b| > D). D must be a positive number. Where a\n"); - PRINTVALSTREAM(rawoutstream, " is the data point value in file1 and b is the data point value in file2.\n"); - PRINTVALSTREAM(rawoutstream, " Can not use with '-p' or '--use-system-epsilon'.\n"); - PRINTVALSTREAM(rawoutstream, " -p R, --relative=R\n"); - PRINTVALSTREAM(rawoutstream, " Print difference if (|(a-b)/b| > R). R must be a positive number. Where a\n"); - PRINTVALSTREAM(rawoutstream, " is the data point value in file1 and b is the data point value in file2.\n"); - PRINTVALSTREAM(rawoutstream, " Can not use with '-d' or '--use-system-epsilon'.\n"); - PRINTVALSTREAM(rawoutstream, " --use-system-epsilon\n"); - PRINTVALSTREAM(rawoutstream, " Print difference if (|a-b| > EPSILON), EPSILON is system defined value. Where a\n"); - PRINTVALSTREAM(rawoutstream, " is the data point value in file1 and b is the data point value in file2.\n"); - PRINTVALSTREAM(rawoutstream, " If the system epsilon is not defined,one of the following predefined\n"); - PRINTVALSTREAM(rawoutstream, " values will be used:\n"); - PRINTVALSTREAM(rawoutstream, " FLT_EPSILON = 1.19209E-07 for floating-point type\n"); - PRINTVALSTREAM(rawoutstream, " DBL_EPSILON = 2.22045E-16 for double precision type\n"); - PRINTVALSTREAM(rawoutstream, " Can not use with '-p' or '-d'.\n"); - PRINTVALSTREAM(rawoutstream, " --exclude-path \"path\"\n"); - PRINTVALSTREAM(rawoutstream, " Exclude the specified path to an object when comparing files or groups.\n"); - PRINTVALSTREAM(rawoutstream, " If a group is excluded, all member objects will also be excluded.\n"); - PRINTVALSTREAM(rawoutstream, " The specified path is excluded wherever it occurs.\n"); - PRINTVALSTREAM(rawoutstream, " This flexibility enables the same option to exclude either objects that\n"); - PRINTVALSTREAM(rawoutstream, " exist only in one file or common objects that are known to differ.\n"); - PRINTVALSTREAM(rawoutstream, "\n"); - PRINTVALSTREAM(rawoutstream, " When comparing files, \"path\" is the absolute path to the excluded;\n"); - PRINTVALSTREAM(rawoutstream, " object; when comparing groups, \"path\" is similar to the relative\n"); - PRINTVALSTREAM(rawoutstream, " path from the group to the excluded object. This \"path\" can be\n"); - PRINTVALSTREAM(rawoutstream, " taken from the first section of the output of the --verbose option.\n"); - PRINTVALSTREAM(rawoutstream, " For example, if you are comparing the group /groupA in two files and\n"); - PRINTVALSTREAM(rawoutstream, " you want to exclude /groupA/groupB/groupC in both files, the exclude\n"); - PRINTVALSTREAM(rawoutstream, " option would read as follows:\n"); - PRINTVALSTREAM(rawoutstream, " --exclude-path \"/groupB/groupC\"\n"); - PRINTVALSTREAM(rawoutstream, "\n"); - PRINTVALSTREAM(rawoutstream, " If there are multiple paths to an object, only the specified path(s)\n"); - PRINTVALSTREAM(rawoutstream, " will be excluded; the comparison will include any path not explicitly\n"); - PRINTVALSTREAM(rawoutstream, " excluded.\n"); - PRINTVALSTREAM(rawoutstream, " This option can be used repeatedly to exclude multiple paths.\n"); - PRINTVALSTREAM(rawoutstream, "\n"); - - PRINTVALSTREAM(rawoutstream, " Modes of output:\n"); - PRINTVALSTREAM(rawoutstream, " Default mode: print the number of differences found and where they occured\n"); - PRINTVALSTREAM(rawoutstream, " -r Report mode: print the above plus the differences\n"); - PRINTVALSTREAM(rawoutstream, " -v Verbose mode: print the above plus a list of objects and warnings\n"); - PRINTVALSTREAM(rawoutstream, " -q Quiet mode: do not print output\n"); - - PRINTVALSTREAM(rawoutstream, "\n"); - - PRINTVALSTREAM(rawoutstream, " File comparison:\n"); - PRINTVALSTREAM(rawoutstream, " If no objects [obj1[ obj2]] are specified, the h5diff comparison proceeds as\n"); - PRINTVALSTREAM(rawoutstream, " a comparison of the two files' root groups. That is, h5diff first compares\n"); - PRINTVALSTREAM(rawoutstream, " the names of root group members, generates a report of root group objects\n"); - PRINTVALSTREAM(rawoutstream, " that appear in only one file or in both files, and recursively compares\n"); - PRINTVALSTREAM(rawoutstream, " common objects.\n"); - PRINTVALSTREAM(rawoutstream, "\n"); - - PRINTVALSTREAM(rawoutstream, " Object comparison:\n"); - PRINTVALSTREAM(rawoutstream, " 1) Groups\n"); - PRINTVALSTREAM(rawoutstream, " First compares the names of member objects (relative path, from the\n"); - PRINTVALSTREAM(rawoutstream, " specified group) and generates a report of objects that appear in only\n"); - PRINTVALSTREAM(rawoutstream, " one group or in both groups. Common objects are then compared recursively.\n"); - PRINTVALSTREAM(rawoutstream, " 2) Datasets\n"); - PRINTVALSTREAM(rawoutstream, " Array rank and dimensions, datatypes, and data values are compared.\n"); - PRINTVALSTREAM(rawoutstream, " 3) Datatypes\n"); - PRINTVALSTREAM(rawoutstream, " The comparison is based on the return value of H5Tequal.\n"); - PRINTVALSTREAM(rawoutstream, " 4) Symbolic links\n"); - PRINTVALSTREAM(rawoutstream, " The paths to the target objects are compared.\n"); - PRINTVALSTREAM(rawoutstream, " (The option --follow-symlinks overrides the default behavior when\n"); - PRINTVALSTREAM(rawoutstream, " symbolic links are compared.).\n"); - PRINTVALSTREAM(rawoutstream, "\n"); - - PRINTVALSTREAM(rawoutstream, " Exit code:\n"); - PRINTVALSTREAM(rawoutstream, " 0 if no differences, 1 if differences found, 2 if error\n"); - PRINTVALSTREAM(rawoutstream, "\n"); - PRINTVALSTREAM(rawoutstream, " Examples of use:\n"); - PRINTVALSTREAM(rawoutstream, " 1) h5diff file1 file2 /g1/dset1 /g1/dset2\n"); - PRINTVALSTREAM(rawoutstream, " Compares object '/g1/dset1' in file1 with '/g1/dset2' in file2\n"); - PRINTVALSTREAM(rawoutstream, "\n"); - PRINTVALSTREAM(rawoutstream, " 2) h5diff file1 file2 /g1/dset1\n"); - PRINTVALSTREAM(rawoutstream, " Compares object '/g1/dset1' in both files\n"); - PRINTVALSTREAM(rawoutstream, "\n"); - PRINTVALSTREAM(rawoutstream, " 3) h5diff file1 file2\n"); - PRINTVALSTREAM(rawoutstream, " Compares all objects in both files\n"); - PRINTVALSTREAM(rawoutstream, "\n"); - PRINTVALSTREAM(rawoutstream, " Notes:\n"); - PRINTVALSTREAM(rawoutstream, " file1 and file2 can be the same file.\n"); - PRINTVALSTREAM(rawoutstream, " Use h5diff file1 file1 /g1/dset1 /g1/dset2 to compare\n"); - PRINTVALSTREAM(rawoutstream, " '/g1/dset1' and '/g1/dset2' in the same file\n"); - PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, "usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]\n"); + PRINTVALSTREAM(rawoutstream, " file1 File name of the first HDF5 file\n"); + PRINTVALSTREAM(rawoutstream, " file2 File name of the second HDF5 file\n"); + PRINTVALSTREAM(rawoutstream, " [obj1] Name of an HDF5 object, in absolute path\n"); + PRINTVALSTREAM(rawoutstream, " [obj2] Name of an HDF5 object, in absolute path\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, " ERROR\n"); + PRINTVALSTREAM(rawoutstream, + " --enable-error-stack Prints messages from the HDF5 error stack as they occur.\n"); + PRINTVALSTREAM(rawoutstream, " Optional value 2 also prints file open errors.\n"); + PRINTVALSTREAM(rawoutstream, " OPTIONS\n"); + PRINTVALSTREAM(rawoutstream, " -h, --help\n"); + PRINTVALSTREAM(rawoutstream, " Print a usage message and exit.\n"); + PRINTVALSTREAM(rawoutstream, " -V, --version\n"); + PRINTVALSTREAM(rawoutstream, " Print version number and exit.\n"); + PRINTVALSTREAM(rawoutstream, " -r, --report\n"); + PRINTVALSTREAM(rawoutstream, " Report mode. Print differences.\n"); + PRINTVALSTREAM(rawoutstream, " -v --verbose\n"); + PRINTVALSTREAM(rawoutstream, + " Verbose mode. Print differences information and list of objects.\n"); + PRINTVALSTREAM(rawoutstream, " -vN --verbose=N\n"); + PRINTVALSTREAM(rawoutstream, + " Verbose mode with level. Print differences and list of objects.\n"); + PRINTVALSTREAM(rawoutstream, " Level of detail depends on value of N:\n"); + PRINTVALSTREAM(rawoutstream, " 0 : Identical to '-v' or '--verbose'.\n"); + PRINTVALSTREAM(rawoutstream, + " 1 : All level 0 information plus one-line attribute status summary.\n"); + PRINTVALSTREAM(rawoutstream, + " 2 : All level 1 information plus extended attribute status report.\n"); + PRINTVALSTREAM(rawoutstream, " 3 : All level 2 information plus file names.\n"); + PRINTVALSTREAM(rawoutstream, " -q, --quiet\n"); + PRINTVALSTREAM(rawoutstream, " Quiet mode. Do not produce output.\n"); + PRINTVALSTREAM(rawoutstream, + " --vol-value-1 Value (ID) of the VOL connector to use for opening the\n"); + PRINTVALSTREAM(rawoutstream, " first HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, + " --vol-name-1 Name of the VOL connector to use for opening the first\n"); + PRINTVALSTREAM(rawoutstream, " HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, + " --vol-info-1 VOL-specific info to pass to the VOL connector used for\n"); + PRINTVALSTREAM(rawoutstream, " opening the first HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, + " --vol-value-2 Value (ID) of the VOL connector to use for opening the\n"); + PRINTVALSTREAM(rawoutstream, " second HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, + " --vol-name-2 Name of the VOL connector to use for opening the second\n"); + PRINTVALSTREAM(rawoutstream, " HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, + " --vol-info-2 VOL-specific info to pass to the VOL connector used for\n"); + PRINTVALSTREAM(rawoutstream, " opening the second HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, + " --vfd-value-1 Value (ID) of the VFL driver to use for opening the\n"); + PRINTVALSTREAM(rawoutstream, " first HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, + " --vfd-name-1 Name of the VFL driver to use for opening the first\n"); + PRINTVALSTREAM(rawoutstream, " HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, + " --vfd-info-1 VFD-specific info to pass to the VFL driver used for\n"); + PRINTVALSTREAM(rawoutstream, " opening the first HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, + " --vfd-value-2 Value (ID) of the VFL driver to use for opening the\n"); + PRINTVALSTREAM(rawoutstream, " second HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, + " --vfd-name-2 Name of the VFL driver to use for opening the second\n"); + PRINTVALSTREAM(rawoutstream, " HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, + " --vfd-info-2 VFD-specific info to pass to the VFL driver used for\n"); + PRINTVALSTREAM(rawoutstream, " opening the second HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, " --follow-symlinks\n"); + PRINTVALSTREAM(rawoutstream, + " Follow symbolic links (soft links and external links and compare the)\n"); + PRINTVALSTREAM(rawoutstream, " links' target objects.\n"); + PRINTVALSTREAM(rawoutstream, + " If symbolic link(s) with the same name exist in the files being\n"); + PRINTVALSTREAM(rawoutstream, + " compared, then determine whether the target of each link is an existing\n"); + PRINTVALSTREAM(rawoutstream, + " object (dataset, group, or named datatype) or the link is a dangling\n"); + PRINTVALSTREAM(rawoutstream, + " link (a soft or external link pointing to a target object that does\n"); + PRINTVALSTREAM(rawoutstream, " not yet exist).\n"); + PRINTVALSTREAM(rawoutstream, + " - If both symbolic links are dangling links, they are treated as being\n"); + PRINTVALSTREAM(rawoutstream, " the same; by default, h5diff returns an exit code of 0.\n"); + PRINTVALSTREAM(rawoutstream, + " If, however, --no-dangling-links is used with --follow-symlinks,\n"); + PRINTVALSTREAM(rawoutstream, " this situation is treated as an error and h5diff returns an\n"); + PRINTVALSTREAM(rawoutstream, " exit code of 2.\n"); + PRINTVALSTREAM(rawoutstream, + " - If only one of the two links is a dangling link,they are treated as\n"); + PRINTVALSTREAM(rawoutstream, " being different and h5diff returns an exit code of 1.\n"); + PRINTVALSTREAM(rawoutstream, + " If, however, --no-dangling-links is used with --follow-symlinks,\n"); + PRINTVALSTREAM(rawoutstream, " this situation is treated as an error and h5diff returns an\n"); + PRINTVALSTREAM(rawoutstream, " exit code of 2.\n"); + PRINTVALSTREAM(rawoutstream, + " - If both symbolic links point to existing objects, h5diff compares the\n"); + PRINTVALSTREAM(rawoutstream, " two objects.\n"); + PRINTVALSTREAM(rawoutstream, + " If any symbolic link specified in the call to h5diff does not exist,\n"); + PRINTVALSTREAM(rawoutstream, " h5diff treats it as an error and returns an exit code of 2.\n"); + PRINTVALSTREAM(rawoutstream, " --no-dangling-links\n"); + PRINTVALSTREAM(rawoutstream, + " Must be used with --follow-symlinks option; otherwise, h5diff shows\n"); + PRINTVALSTREAM(rawoutstream, " error message and returns an exit code of 2.\n"); + PRINTVALSTREAM(rawoutstream, + " Check for any symbolic links (soft links or external links) that do not\n"); + PRINTVALSTREAM(rawoutstream, + " resolve to an existing object (dataset, group, or named datatype).\n"); + PRINTVALSTREAM(rawoutstream, + " If any dangling link is found, this situation is treated as an error\n"); + PRINTVALSTREAM(rawoutstream, " and h5diff returns an exit code of 2.\n"); + PRINTVALSTREAM(rawoutstream, " -c, --compare\n"); + PRINTVALSTREAM(rawoutstream, " List objects that are not comparable\n"); + PRINTVALSTREAM(rawoutstream, " -N, --nan\n"); + PRINTVALSTREAM(rawoutstream, " Avoid NaNs detection\n"); + PRINTVALSTREAM(rawoutstream, " -n C, --count=C\n"); + PRINTVALSTREAM(rawoutstream, " Print differences up to C. C must be a positive integer.\n"); + PRINTVALSTREAM(rawoutstream, " -d D, --delta=D\n"); + PRINTVALSTREAM(rawoutstream, + " Print difference if (|a-b| > D). D must be a positive number. Where a\n"); + PRINTVALSTREAM(rawoutstream, + " is the data point value in file1 and b is the data point value in file2.\n"); + PRINTVALSTREAM(rawoutstream, " Can not use with '-p' or '--use-system-epsilon'.\n"); + PRINTVALSTREAM(rawoutstream, " -p R, --relative=R\n"); + PRINTVALSTREAM(rawoutstream, + " Print difference if (|(a-b)/b| > R). R must be a positive number. Where a\n"); + PRINTVALSTREAM(rawoutstream, + " is the data point value in file1 and b is the data point value in file2.\n"); + PRINTVALSTREAM(rawoutstream, " Can not use with '-d' or '--use-system-epsilon'.\n"); + PRINTVALSTREAM(rawoutstream, " --use-system-epsilon\n"); + PRINTVALSTREAM( + rawoutstream, + " Print difference if (|a-b| > EPSILON), EPSILON is system defined value. Where a\n"); + PRINTVALSTREAM(rawoutstream, + " is the data point value in file1 and b is the data point value in file2.\n"); + PRINTVALSTREAM(rawoutstream, + " If the system epsilon is not defined,one of the following predefined\n"); + PRINTVALSTREAM(rawoutstream, " values will be used:\n"); + PRINTVALSTREAM(rawoutstream, " FLT_EPSILON = 1.19209E-07 for floating-point type\n"); + PRINTVALSTREAM(rawoutstream, " DBL_EPSILON = 2.22045E-16 for double precision type\n"); + PRINTVALSTREAM(rawoutstream, " Can not use with '-p' or '-d'.\n"); + PRINTVALSTREAM(rawoutstream, " --exclude-path \"path\"\n"); + PRINTVALSTREAM(rawoutstream, + " Exclude the specified path to an object when comparing files or groups.\n"); + PRINTVALSTREAM(rawoutstream, + " If a group is excluded, all member objects will also be excluded.\n"); + PRINTVALSTREAM(rawoutstream, " The specified path is excluded wherever it occurs.\n"); + PRINTVALSTREAM(rawoutstream, + " This flexibility enables the same option to exclude either objects that\n"); + PRINTVALSTREAM(rawoutstream, + " exist only in one file or common objects that are known to differ.\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, + " When comparing files, \"path\" is the absolute path to the excluded;\n"); + PRINTVALSTREAM(rawoutstream, + " object; when comparing groups, \"path\" is similar to the relative\n"); + PRINTVALSTREAM(rawoutstream, + " path from the group to the excluded object. This \"path\" can be\n"); + PRINTVALSTREAM(rawoutstream, + " taken from the first section of the output of the --verbose option.\n"); + PRINTVALSTREAM(rawoutstream, + " For example, if you are comparing the group /groupA in two files and\n"); + PRINTVALSTREAM(rawoutstream, + " you want to exclude /groupA/groupB/groupC in both files, the exclude\n"); + PRINTVALSTREAM(rawoutstream, " option would read as follows:\n"); + PRINTVALSTREAM(rawoutstream, " --exclude-path \"/groupB/groupC\"\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, + " If there are multiple paths to an object, only the specified path(s)\n"); + PRINTVALSTREAM(rawoutstream, + " will be excluded; the comparison will include any path not explicitly\n"); + PRINTVALSTREAM(rawoutstream, " excluded.\n"); + PRINTVALSTREAM(rawoutstream, " This option can be used repeatedly to exclude multiple paths.\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, " --exclude-attribute \"path/to/object/with/attribute\"\n"); + PRINTVALSTREAM( + rawoutstream, + " Exclude attributes on the specified path to an object when comparing files or groups.\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, + " If there are multiple paths to an object, only the specified path(s)\n"); + PRINTVALSTREAM(rawoutstream, + " will be excluded; the comparison will include any path not explicitly\n"); + PRINTVALSTREAM(rawoutstream, " excluded.\n"); + PRINTVALSTREAM(rawoutstream, " This option can be used repeatedly to exclude multiple paths.\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, " Modes of output:\n"); + PRINTVALSTREAM(rawoutstream, + " Default mode: print the number of differences found and where they occurred\n"); + PRINTVALSTREAM(rawoutstream, " -r Report mode: print the above plus the differences\n"); + PRINTVALSTREAM(rawoutstream, " -v Verbose mode: print the above plus a list of objects and warnings\n"); + PRINTVALSTREAM(rawoutstream, " -q Quiet mode: do not print output\n"); + + PRINTVALSTREAM(rawoutstream, "\n"); + + PRINTVALSTREAM(rawoutstream, " File comparison:\n"); + PRINTVALSTREAM(rawoutstream, + " If no objects [obj1[ obj2]] are specified, the h5diff comparison proceeds as\n"); + PRINTVALSTREAM(rawoutstream, + " a comparison of the two files' root groups. That is, h5diff first compares\n"); + PRINTVALSTREAM(rawoutstream, + " the names of root group members, generates a report of root group objects\n"); + PRINTVALSTREAM(rawoutstream, + " that appear in only one file or in both files, and recursively compares\n"); + PRINTVALSTREAM(rawoutstream, " common objects.\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + + PRINTVALSTREAM(rawoutstream, " Object comparison:\n"); + PRINTVALSTREAM(rawoutstream, " 1) Groups\n"); + PRINTVALSTREAM(rawoutstream, + " First compares the names of member objects (relative path, from the\n"); + PRINTVALSTREAM(rawoutstream, + " specified group) and generates a report of objects that appear in only\n"); + PRINTVALSTREAM(rawoutstream, + " one group or in both groups. Common objects are then compared recursively.\n"); + PRINTVALSTREAM(rawoutstream, " 2) Datasets\n"); + PRINTVALSTREAM(rawoutstream, + " Array rank and dimensions, datatypes, and data values are compared.\n"); + PRINTVALSTREAM(rawoutstream, " 3) Datatypes\n"); + PRINTVALSTREAM(rawoutstream, " The comparison is based on the return value of H5Tequal.\n"); + PRINTVALSTREAM(rawoutstream, " 4) Symbolic links\n"); + PRINTVALSTREAM(rawoutstream, " The paths to the target objects are compared.\n"); + PRINTVALSTREAM(rawoutstream, " (The option --follow-symlinks overrides the default behavior when\n"); + PRINTVALSTREAM(rawoutstream, " symbolic links are compared.).\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + /* + * TRILABS_227 is complete except for an issue with printing indices + * the following will be needed for subsetting + */ + PRINTVALSTREAM(rawoutstream, " Subsetting options:\n"); + PRINTVALSTREAM(rawoutstream, + " Subsetting is available by using the fcompact form of subsetting, as follows:\n"); + PRINTVALSTREAM(rawoutstream, " obj1 /foo/mydataset[START;STRIDE;COUNT;BLOCK]\n"); + PRINTVALSTREAM(rawoutstream, + " It is not required to use all parameters, but until the last parameter value used,\n"); + PRINTVALSTREAM( + rawoutstream, + " all of the semicolons (;) are required, even when a parameter value is not specified. Example:\n"); + PRINTVALSTREAM(rawoutstream, " obj1 /foo/mydataset[START;;COUNT;BLOCK]\n"); + PRINTVALSTREAM(rawoutstream, " obj1 /foo/mydataset[START]\n"); + PRINTVALSTREAM(rawoutstream, + " The STRIDE, COUNT, and BLOCK parameters are optional and will default to 1 in\n"); + PRINTVALSTREAM(rawoutstream, + " each dimension. START is optional and will default to 0 in each dimension.\n"); + PRINTVALSTREAM( + rawoutstream, + " Each of START, STRIDE, COUNT, and BLOCK must be a comma-separated list of integers with\n"); + PRINTVALSTREAM(rawoutstream, " one integer for each dimension of the dataset.\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, " Exit code:\n"); + PRINTVALSTREAM(rawoutstream, " 0 if no differences, 1 if differences found, 2 if error\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, " Examples of use:\n"); + PRINTVALSTREAM(rawoutstream, " 1) h5diff file1 file2 /g1/dset1 /g1/dset2\n"); + PRINTVALSTREAM(rawoutstream, " Compares object '/g1/dset1' in file1 with '/g1/dset2' in file2\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, " 2) h5diff file1 file2 /g1/dset1\n"); + PRINTVALSTREAM(rawoutstream, " Compares object '/g1/dset1' in both files\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, " 3) h5diff file1 file2\n"); + PRINTVALSTREAM(rawoutstream, " Compares all objects in both files\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, " Notes:\n"); + PRINTVALSTREAM(rawoutstream, " file1 and file2 can be the same file.\n"); + PRINTVALSTREAM(rawoutstream, " Use h5diff file1 file1 /g1/dset1 /g1/dset2 to compare\n"); + PRINTVALSTREAM(rawoutstream, " '/g1/dset1' and '/g1/dset2' in the same file\n"); + PRINTVALSTREAM(rawoutstream, "\n"); } diff --git a/tools/src/h5diff/h5diff_common.h b/tools/src/h5diff/h5diff_common.h index dc0676c..35e5dfb 100644 --- a/tools/src/h5diff/h5diff_common.h +++ b/tools/src/h5diff/h5diff_common.h @@ -6,13 +6,13 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -#ifndef H5DIFFCOMMON_H__ -#define H5DIFFCOMMON_H__ +#ifndef H5DIFFCOMMON_H +#define H5DIFFCOMMON_H #include "h5tools.h" /* Name of tool */ @@ -23,12 +23,13 @@ extern "C" { #endif void usage(void); -void parse_command_line(int argc, const char* argv[], const char** fname1, const char** fname2, const char** objname1, const char** objname2, diff_opt_t* opts); +void parse_command_line(int argc, const char *const *argv, const char **fname1, const char **fname2, + const char **objname1, const char **objname2, diff_opt_t *opts); void h5diff_exit(int status); -void print_info(diff_opt_t* opts); +void print_info(diff_opt_t *opts); #ifdef __cplusplus } #endif -#endif /* H5DIFFCOMMON_H__ */ +#endif /* H5DIFFCOMMON_H */ diff --git a/tools/src/h5diff/h5diff_main.c b/tools/src/h5diff/h5diff_main.c index c5a0cbf..2a43b56 100644 --- a/tools/src/h5diff/h5diff_main.c +++ b/tools/src/h5diff/h5diff_main.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -17,7 +17,6 @@ #include "h5tools.h" #include "h5tools_utils.h" - /*------------------------------------------------------------------------- * Function: main * @@ -26,7 +25,7 @@ * Return: An exit status of 0 means no differences were found, 1 means some * differences were found. * - * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu + * Programmer: Pedro Vicente * * Date: May 9, 2003 * @@ -34,7 +33,7 @@ * * Modifications: July 2004 * Introduced the four modes: - * Normal mode: print the number of differences found and where they occured + * Normal mode: print the number of differences found and where they occurred * Report mode: print the above plus the differences * Verbose mode: print the above plus a list of objects and warnings * Quiet mode: do not print output @@ -65,60 +64,47 @@ *------------------------------------------------------------------------- */ - -int main(int argc, const char *argv[]) +int +main(int argc, char *argv[]) { - int ret; - H5E_auto2_t func; - H5E_auto2_t tools_func; - void *edata; - void *tools_edata; - const char *fname1 = NULL; - const char *fname2 = NULL; - const char *objname1 = NULL; - const char *objname2 = NULL; - hsize_t nfound=0; - diff_opt_t opts; + int ret; + int i; + const char *fname1 = NULL; + const char *fname2 = NULL; + const char *objname1 = NULL; + const char *objname2 = NULL; + hsize_t nfound = 0; + diff_opt_t opts; h5tools_setprogname(PROGRAMNAME); h5tools_setstatus(EXIT_SUCCESS); - /* Disable error reporting */ - H5Eget_auto2(H5E_DEFAULT, &func, &edata); - H5Eset_auto2(H5E_DEFAULT, NULL, NULL); - /* Initialize h5tools lib */ h5tools_init(); - /* Disable tools error reporting */ - H5Eget_auto2(H5tools_ERR_STACK_g, &tools_func, &tools_edata); - H5Eset_auto2(H5tools_ERR_STACK_g, NULL, NULL); - /*------------------------------------------------------------------------- - * process the command-line - *------------------------------------------------------------------------- - */ - parse_command_line(argc, argv, &fname1, &fname2, &objname1, &objname2, &opts); - - if (enable_error_stack > 0) { - H5Eset_auto2(H5E_DEFAULT, func, edata); - H5Eset_auto2(H5tools_ERR_STACK_g, tools_func, tools_edata); - } + * process the command-line + *------------------------------------------------------------------------- + */ + parse_command_line(argc, (const char *const *)argv, &fname1, &fname2, &objname1, &objname2, &opts); + + /* enable error reporting if command line option */ + h5tools_error_report(); /*------------------------------------------------------------------------- - * do the diff - *------------------------------------------------------------------------- - */ + * do the diff + *------------------------------------------------------------------------- + */ nfound = h5diff(fname1, fname2, objname1, objname2, &opts); print_info(&opts); - /*------------------------------------------------------------------------- - * exit code - * 1 if differences, 0 if no differences, 2 if error - *------------------------------------------------------------------------- - */ + /*------------------------------------------------------------------------- + * exit code + * 1 if differences, 0 if no differences, 2 if error + *------------------------------------------------------------------------- + */ ret = (nfound == 0 ? 0 : 1); @@ -130,6 +116,23 @@ int main(int argc, const char *argv[]) if (opts.err_stat) ret = 2; + /* free any buffers */ + for (i = 0; i < 2; i++) { + if (opts.sset[i]) { + if (opts.sset[i]->start.data) + HDfree(opts.sset[i]->start.data); + if (opts.sset[i]->stride.data) + HDfree(opts.sset[i]->stride.data); + if (opts.sset[i]->count.data) + HDfree(opts.sset[i]->count.data); + if (opts.sset[i]->block.data) + HDfree(opts.sset[i]->block.data); + + HDfree(opts.sset[i]); + opts.sset[i] = NULL; + } + } + h5diff_exit(ret); } @@ -156,4 +159,3 @@ h5diff_exit(int status) HDexit(status); } - diff --git a/tools/src/h5diff/ph5diff_main.c b/tools/src/h5diff/ph5diff_main.c index 380ab3b..8e5c3e8 100644 --- a/tools/src/h5diff/ph5diff_main.c +++ b/tools/src/h5diff/ph5diff_main.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -21,7 +21,7 @@ /* Name of tool */ #define PROGRAMNAME "h5diff" -static void ph5diff_worker(int ); +static void ph5diff_worker(int); /*------------------------------------------------------------------------- * Function: main @@ -31,7 +31,7 @@ static void ph5diff_worker(int ); * Return: An exit status of 0 means no differences were found, 1 means some * differences were found. * - * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu + * Programmer: Pedro Vicente * * Date: May 9, 2003 * @@ -43,14 +43,15 @@ static void ph5diff_worker(int ); *------------------------------------------------------------------------- */ -int main(int argc, const char *argv[]) +int +main(int argc, char *argv[]) { - int nID = 0; - const char *fname1 = NULL; - const char *fname2 = NULL; - const char *objname1 = NULL; - const char *objname2 = NULL; - diff_opt_t opts; + int nID = 0; + const char *fname1 = NULL; + const char *fname2 = NULL; + const char *objname1 = NULL; + const char *objname2 = NULL; + diff_opt_t opts; h5tools_setprogname(PROGRAMNAME); h5tools_setstatus(EXIT_SUCCESS); @@ -59,20 +60,19 @@ int main(int argc, const char *argv[]) h5tools_init(); outBuffOffset = 0; - g_Parallel = 1; + g_Parallel = 1; - MPI_Init(&argc, (char***) &argv); + MPI_Init(&argc, (char ***)&argv); MPI_Comm_rank(MPI_COMM_WORLD, &nID); MPI_Comm_size(MPI_COMM_WORLD, &g_nTasks); - if(g_nTasks == 1) - { + if (g_nTasks == 1) { HDprintf("Only 1 task available...doing serial diff\n"); g_Parallel = 0; - parse_command_line(argc, argv, &fname1, &fname2, &objname1, &objname2, &opts); + parse_command_line(argc, (const char *const *)argv, &fname1, &fname2, &objname1, &objname2, &opts); h5diff(fname1, fname2, objname1, objname2, &opts); @@ -82,9 +82,9 @@ int main(int argc, const char *argv[]) else { /* Have the manager process the command-line */ - if(nID == 0) - { - parse_command_line(argc, argv, &fname1, &fname2, &objname1, &objname2, &opts); + if (nID == 0) { + parse_command_line(argc, (const char *const *)argv, &fname1, &fname2, &objname1, &objname2, + &opts); h5diff(fname1, fname2, objname1, objname2, &opts); @@ -126,33 +126,30 @@ int main(int argc, const char *argv[]) static void ph5diff_worker(int nID) { - hid_t file1_id = -1, file2_id = -1; + hid_t file1_id = H5I_INVALID_HID; + hid_t file2_id = H5I_INVALID_HID; - while(1) - { + while (1) { MPI_Status Status; MPI_Probe(0, MPI_ANY_TAG, MPI_COMM_WORLD, &Status); /* Check for filenames */ - if(Status.MPI_TAG == MPI_TAG_PARALLEL) - { - char filenames[2][MAX_FILENAME]; + if (Status.MPI_TAG == MPI_TAG_PARALLEL) { + char filenames[2][MAX_FILENAME]; /* Retrieve filenames */ - MPI_Recv(filenames, MAX_FILENAME*2, MPI_CHAR, 0, MPI_ANY_TAG, MPI_COMM_WORLD, &Status); + MPI_Recv(filenames, MAX_FILENAME * 2, MPI_CHAR, 0, MPI_ANY_TAG, MPI_COMM_WORLD, &Status); /* disable error reporting */ H5E_BEGIN_TRY { /* Open the files */ - if ((file1_id = H5Fopen (filenames[0], H5F_ACC_RDONLY, H5P_DEFAULT)) < 0) - { + if ((file1_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, H5P_DEFAULT)) < 0) { HDprintf("h5diff Task [%d]: <%s>: unable to open file\n", nID, filenames[0]); MPI_Abort(MPI_COMM_WORLD, 0); } - if ((file2_id = H5Fopen (filenames[1], H5F_ACC_RDONLY, H5P_DEFAULT)) < 0) - { + if ((file2_id = H5Fopen(filenames[1], H5F_ACC_RDONLY, H5P_DEFAULT)) < 0) { HDprintf("h5diff Task [%d]: <%s>: unable to open file\n", nID, filenames[1]); MPI_Abort(MPI_COMM_WORLD, 0); } @@ -161,15 +158,13 @@ ph5diff_worker(int nID) H5E_END_TRY; } /* Check for work */ - else if(Status.MPI_TAG == MPI_TAG_ARGS) - { + else if (Status.MPI_TAG == MPI_TAG_ARGS) { struct diff_mpi_args args; - struct diffs_found diffs; - int i; + struct diffs_found diffs; + unsigned i; /* Make certain we've received the filenames and opened the files already */ - if(file1_id < 0 || file2_id < 0) - { + if (file1_id < 0 || file2_id < 0) { HDprintf("ph5diff_worker: ERROR: work received before/without filenames\n"); break; } @@ -178,44 +173,43 @@ ph5diff_worker(int nID) MPI_Recv(&args, sizeof(args), MPI_BYTE, 0, MPI_TAG_ARGS, MPI_COMM_WORLD, &Status); /* Do the diff */ - diffs.nfound = diff(file1_id, args.name1, file2_id, args.name2, &(args.opts), &(args.argdata)); + diffs.nfound = diff(file1_id, args.name1, file2_id, args.name2, &(args.opts), &(args.argdata)); diffs.not_cmp = args.opts.not_cmp; /* If print buffer has something in it, request print token.*/ - if(outBuffOffset>0) - { + if (outBuffOffset > 0) { MPI_Send(NULL, 0, MPI_BYTE, 0, MPI_TAG_TOK_REQUEST, MPI_COMM_WORLD); /* Wait for print token. */ MPI_Recv(NULL, 0, MPI_BYTE, 0, MPI_TAG_PRINT_TOK, MPI_COMM_WORLD, &Status); /* When get token, send all of our output to the manager task and then return the token */ - for(i=0; i<outBuffOffset; i+=PRINT_DATA_MAX_SIZE) - MPI_Send(outBuff+i, PRINT_DATA_MAX_SIZE, MPI_BYTE, 0, MPI_TAG_PRINT_DATA, MPI_COMM_WORLD); + for (i = 0; i < outBuffOffset; i += PRINT_DATA_MAX_SIZE) + MPI_Send(outBuff + i, PRINT_DATA_MAX_SIZE, MPI_BYTE, 0, MPI_TAG_PRINT_DATA, + MPI_COMM_WORLD); /* An overflow file exists, so we send it's output to the manager too and then delete it */ - if(overflow_file) - { + if (overflow_file) { char out_data[PRINT_DATA_MAX_SIZE]; - int tmp; + int tmp; HDmemset(out_data, 0, PRINT_DATA_MAX_SIZE); - i=0; + i = 0; rewind(overflow_file); - while((tmp = getc(overflow_file)) >= 0) - { + while ((tmp = getc(overflow_file)) >= 0) { *(out_data + i++) = (char)tmp; - if(i==PRINT_DATA_MAX_SIZE) - { - MPI_Send(out_data, PRINT_DATA_MAX_SIZE, MPI_BYTE, 0, MPI_TAG_PRINT_DATA, MPI_COMM_WORLD); - i=0; + if (i == PRINT_DATA_MAX_SIZE) { + MPI_Send(out_data, PRINT_DATA_MAX_SIZE, MPI_BYTE, 0, MPI_TAG_PRINT_DATA, + MPI_COMM_WORLD); + i = 0; HDmemset(out_data, 0, PRINT_DATA_MAX_SIZE); } } - if(i>0) - MPI_Send(out_data, PRINT_DATA_MAX_SIZE, MPI_BYTE, 0, MPI_TAG_PRINT_DATA, MPI_COMM_WORLD); + if (i > 0) + MPI_Send(out_data, PRINT_DATA_MAX_SIZE, MPI_BYTE, 0, MPI_TAG_PRINT_DATA, + MPI_COMM_WORLD); fclose(overflow_file); overflow_file = NULL; @@ -231,17 +225,14 @@ ph5diff_worker(int nID) MPI_Send(&diffs, sizeof(diffs), MPI_BYTE, 0, MPI_TAG_DONE, MPI_COMM_WORLD); } /* Check for leaving */ - else if(Status.MPI_TAG == MPI_TAG_END) - { + else if (Status.MPI_TAG == MPI_TAG_END) { MPI_Recv(NULL, 0, MPI_BYTE, 0, MPI_TAG_END, MPI_COMM_WORLD, &Status); break; } - else - { + else { HDprintf("ph5diff_worker: ERROR: invalid tag (%d) received\n", Status.MPI_TAG); break; } - } return; @@ -261,18 +252,17 @@ ph5diff_worker(int nID) * *------------------------------------------------------------------------- */ -void print_manager_output(void) +void +print_manager_output(void) { /* If there was something we buffered, let's print it now */ - if( (outBuffOffset>0) && g_Parallel) - { + if ((outBuffOffset > 0) && g_Parallel) { HDprintf("%s", outBuff); - if(overflow_file) - { - int tmp; + if (overflow_file) { + int tmp; rewind(overflow_file); - while((tmp = HDgetc(overflow_file)) >= 0) + while ((tmp = HDgetc(overflow_file)) >= 0) HDputchar(tmp); fclose(overflow_file); overflow_file = NULL; @@ -282,8 +272,7 @@ void print_manager_output(void) HDmemset(outBuff, 0, OUTBUFF_SIZE); outBuffOffset = 0; } - else if( (outBuffOffset>0) && !g_Parallel) - { + else if ((outBuffOffset > 0) && !g_Parallel) { HDfprintf(stderr, "h5diff error: outBuffOffset>0, but we're not in parallel!\n"); } } @@ -304,16 +293,18 @@ void print_manager_output(void) * *------------------------------------------------------------------------- */ -void h5diff_exit(int status) +void +h5diff_exit(int status) { /* if in parallel mode, dismiss workers, close down MPI, then exit */ - if(g_Parallel) { - if(g_nTasks > 1) { + if (g_Parallel) { + if (g_nTasks > 1) { phdiff_dismiss_workers(); MPI_Barrier(MPI_COMM_WORLD); } MPI_Finalize(); - status = EXIT_SUCCESS; /* Reset exit status, since some mpiexec commands generate output on failure status */ + status = EXIT_SUCCESS; /* Reset exit status, since some mpiexec commands generate output on failure + status */ } h5tools_close(); @@ -323,4 +314,3 @@ void h5diff_exit(int status) */ HDexit(0); } - diff --git a/tools/src/h5dump/CMakeLists.txt b/tools/src/h5dump/CMakeLists.txt index 383b04e..8a12434 100644 --- a/tools/src/h5dump/CMakeLists.txt +++ b/tools/src/h5dump/CMakeLists.txt @@ -1,4 +1,4 @@ -cmake_minimum_required (VERSION 3.10) +cmake_minimum_required (VERSION 3.12) project (HDF5_TOOLS_SRC_H5DUMP C) # -------------------------------------------------------------------- @@ -9,8 +9,14 @@ if (NOT ONLY_SHARED_LIBS) ${HDF5_TOOLS_SRC_H5DUMP_SOURCE_DIR}/h5dump.c ${HDF5_TOOLS_SRC_H5DUMP_SOURCE_DIR}/h5dump_ddl.c ${HDF5_TOOLS_SRC_H5DUMP_SOURCE_DIR}/h5dump_xml.c + ${HDF5_TOOLS_SRC_H5DUMP_SOURCE_DIR}/h5dump.h + ${HDF5_TOOLS_SRC_H5DUMP_SOURCE_DIR}/h5dump_defines.h + ${HDF5_TOOLS_SRC_H5DUMP_SOURCE_DIR}/h5dump_extern.h + ${HDF5_TOOLS_SRC_H5DUMP_SOURCE_DIR}/h5dump_ddl.h + ${HDF5_TOOLS_SRC_H5DUMP_SOURCE_DIR}/h5dump_xml.h ) - target_include_directories (h5dump PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5dump PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_compile_options(h5dump PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5dump STATIC) target_link_libraries (h5dump PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) set_target_properties (h5dump PROPERTIES FOLDER tools) @@ -24,8 +30,14 @@ if (BUILD_SHARED_LIBS) ${HDF5_TOOLS_SRC_H5DUMP_SOURCE_DIR}/h5dump.c ${HDF5_TOOLS_SRC_H5DUMP_SOURCE_DIR}/h5dump_ddl.c ${HDF5_TOOLS_SRC_H5DUMP_SOURCE_DIR}/h5dump_xml.c + ${HDF5_TOOLS_SRC_H5DUMP_SOURCE_DIR}/h5dump.h + ${HDF5_TOOLS_SRC_H5DUMP_SOURCE_DIR}/h5dump_defines.h + ${HDF5_TOOLS_SRC_H5DUMP_SOURCE_DIR}/h5dump_extern.h + ${HDF5_TOOLS_SRC_H5DUMP_SOURCE_DIR}/h5dump_ddl.h + ${HDF5_TOOLS_SRC_H5DUMP_SOURCE_DIR}/h5dump_xml.h ) - target_include_directories (h5dump-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5dump-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_compile_options(h5dump-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5dump-shared SHARED) target_link_libraries (h5dump-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET}) set_target_properties (h5dump-shared PROPERTIES FOLDER tools) @@ -34,6 +46,17 @@ if (BUILD_SHARED_LIBS) set (H5_DEP_EXECUTABLES ${H5_DEP_EXECUTABLES} h5dump-shared) endif () +#----------------------------------------------------------------------------- +# Add Target to clang-format +#----------------------------------------------------------------------------- +if (HDF5_ENABLE_FORMATTERS) + if (NOT ONLY_SHARED_LIBS) + clang_format (HDF5_H5DUMP_SRC_FORMAT h5dump) + else () + clang_format (HDF5_H5DUMP_SRC_FORMAT h5dump-shared) + endif () +endif () + ############################################################################## ############################################################################## ### I N S T A L L A T I O N ### diff --git a/tools/src/h5dump/Makefile.am b/tools/src/h5dump/Makefile.am index 86109d5..faf9ec6 100644 --- a/tools/src/h5dump/Makefile.am +++ b/tools/src/h5dump/Makefile.am @@ -6,7 +6,7 @@ # This file is part of HDF5. The full HDF5 copyright notice, including # terms governing use, modification, and redistribution, is contained in # the COPYING file, which can be found at the root of the source code -# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. +# distribution tree, or in https://www.hdfgroup.org/licenses. # If you do not have access to either file, you may request a copy from # help@hdfgroup.org. ## diff --git a/tools/src/h5dump/h5dump.c b/tools/src/h5dump/h5dump.c index b1e736a..d82ea94 100644 --- a/tools/src/h5dump/h5dump.c +++ b/tools/src/h5dump/h5dump.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -18,66 +18,59 @@ /* Name of tool */ #define PROGRAMNAME "h5dump" -static const char *driver = NULL; /* The driver to open the file with. */ -const char *outfname=NULL; -static int doxml = 0; -static int useschema = 1; -static const char *xml_dtd_uri = NULL; +const char * outfname_g = NULL; +static hbool_t doxml_g = FALSE; +static hbool_t useschema_g = TRUE; +static const char *xml_dtd_uri_g = NULL; + +static hbool_t use_custom_vol_g = FALSE; +static hbool_t use_custom_vfd_g = FALSE; +static h5tools_vol_info_t vol_info_g; +static h5tools_vfd_info_t vfd_info_g; #ifdef H5_HAVE_ROS3_VFD -static H5FD_ros3_fapl_t ros3_fa = { - 1, /* version */ - false, /* authenticate */ - "", /* aws region */ - "", /* access key id */ - "", /* secret access key */ +/* Default "anonymous" S3 configuration */ +static H5FD_ros3_fapl_t ros3_fa_g = { + 1, /* Structure Version */ + FALSE, /* Authenticate? */ + "", /* AWS Region */ + "", /* Access Key ID */ + "", /* Secret Access Key */ }; #endif /* H5_HAVE_ROS3_VFD */ #ifdef H5_HAVE_LIBHDFS -static H5FD_hdfs_fapl_t hdfs_fa = { - 1, /* fapl version */ - "localhost", /* namenode name */ - 0, /* namenode port */ - "", /* kerberos ticket cache */ - "", /* user name */ - 2048, /* stream buffer size */ +/* "Default" HDFS configuration */ +static H5FD_hdfs_fapl_t hdfs_fa_g = { + 1, /* Structure Version */ + "localhost", /* Namenode Name */ + 0, /* Namenode Port */ + "", /* Kerberos ticket cache */ + "", /* User name */ + 2048, /* Stream buffer size */ }; #endif /* H5_HAVE_LIBHDFS */ /* module-scoped variables for XML option */ -#define DEFAULT_XSD "http://www.hdfgroup.org/HDF5/XML/schema/HDF5-File.xsd" -#define DEFAULT_DTD "http://www.hdfgroup.org/HDF5/XML/DTD/HDF5-File.dtd" +#define DEFAULT_XSD "http://www.hdfgroup.org/HDF5/XML/schema/HDF5-File.xsd" +#define DEFAULT_DTD "http://www.hdfgroup.org/HDF5/XML/DTD/HDF5-File.dtd" /* Standard DDL output */ static const dump_functions ddl_function_table = { - dump_group, - dump_named_datatype, - dump_dataset, - dump_dataspace, - dump_datatype, - dump_attr_cb, - dump_data -}; + dump_group, dump_named_datatype, dump_dataset, dump_dataspace, dump_datatype, dump_attr_cb, dump_data}; /* XML output */ static const dump_functions xml_function_table = { - xml_dump_group, - xml_dump_named_datatype, - xml_dump_dataset, - xml_dump_dataspace, - xml_dump_datatype, - xml_dump_attr, - xml_dump_data -}; + xml_dump_group, xml_dump_named_datatype, xml_dump_dataset, xml_dump_dataspace, + xml_dump_datatype, xml_dump_attr, xml_dump_data}; /* internal functions */ -static void init_prefix(char **prfx, size_t prfx_len); +static void init_prefix(char **prfx, size_t prfx_len); /* a structure for handling the order command-line parameters come in */ struct handler_t { void (*func)(hid_t, const char *, void *, int, const char *); - char *obj; + char * obj; struct subset_t *subset_info; }; @@ -88,132 +81,57 @@ struct handler_t { */ /* The following initialization makes use of C language concatenating */ /* "xxx" "yyy" into "xxxyyy". */ -static const char *s_opts = "hn*peyBHirVa:c:d:f:g:k:l:t:w:xD:uX:o*b*F:s:S:A*q:z:m:RE*CM:O*N:vG:"; -static struct long_options l_opts[] = { - { "help", no_arg, 'h' }, - { "hel", no_arg, 'h' }, - { "contents", optional_arg, 'n' }, - { "properties", no_arg, 'p' }, - { "superblock", no_arg, 'B' }, - { "boot-block", no_arg, 'B' }, - { "boot-bloc", no_arg, 'B' }, - { "boot-blo", no_arg, 'B' }, - { "boot-bl", no_arg, 'B' }, - { "boot-b", no_arg, 'B' }, - { "boot", no_arg, 'B' }, - { "boo", no_arg, 'B' }, - { "bo", no_arg, 'B' }, - { "header", no_arg, 'H' }, - { "heade", no_arg, 'H' }, - { "head", no_arg, 'H' }, - { "hea", no_arg, 'H' }, - { "object-ids", no_arg, 'i' }, - { "object-id", no_arg, 'i' }, - { "object-i", no_arg, 'i' }, - { "object", no_arg, 'i' }, - { "objec", no_arg, 'i' }, - { "obje", no_arg, 'i' }, - { "obj", no_arg, 'i' }, - { "ob", no_arg, 'i' }, - { "version", no_arg, 'V' }, - { "versio", no_arg, 'V' }, - { "versi", no_arg, 'V' }, - { "vers", no_arg, 'V' }, - { "ver", no_arg, 'V' }, - { "ve", no_arg, 'V' }, - { "attribute", require_arg, 'a' }, - { "attribut", require_arg, 'a' }, - { "attribu", require_arg, 'a' }, - { "attrib", require_arg, 'a' }, - { "attri", require_arg, 'a' }, - { "attr", require_arg, 'a' }, - { "att", require_arg, 'a' }, - { "at", require_arg, 'a' }, - { "block", require_arg, 'k' }, - { "bloc", require_arg, 'k' }, - { "blo", require_arg, 'k' }, - { "bl", require_arg, 'k' }, - { "count", require_arg, 'c' }, - { "coun", require_arg, 'c' }, - { "cou", require_arg, 'c' }, - { "co", require_arg, 'c' }, - { "dataset", require_arg, 'd' }, - { "datase", require_arg, 'd' }, - { "datas", require_arg, 'd' }, - { "datatype", require_arg, 't' }, - { "datatyp", require_arg, 't' }, - { "dataty", require_arg, 't' }, - { "datat", require_arg, 't' }, - { "filedriver", require_arg, 'f' }, - { "filedrive", require_arg, 'f' }, - { "filedriv", require_arg, 'f' }, - { "filedri", require_arg, 'f' }, - { "filedr", require_arg, 'f' }, - { "filed", require_arg, 'f' }, - { "file", require_arg, 'f' }, - { "fil", require_arg, 'f' }, - { "fi", require_arg, 'f' }, - { "group", require_arg, 'g' }, - { "grou", require_arg, 'g' }, - { "gro", require_arg, 'g' }, - { "gr", require_arg, 'g' }, - { "output", optional_arg, 'o' }, - { "outpu", optional_arg, 'o' }, - { "outp", optional_arg, 'o' }, - { "out", optional_arg, 'o' }, - { "ou", optional_arg, 'o' }, - { "soft-link", require_arg, 'l' }, - { "soft-lin", require_arg, 'l' }, - { "soft-li", require_arg, 'l' }, - { "soft-l", require_arg, 'l' }, - { "soft", require_arg, 'l' }, - { "sof", require_arg, 'l' }, - { "start", require_arg, 's' }, - { "star", require_arg, 's' }, - { "sta", require_arg, 's' }, - { "stride", require_arg, 'S' }, - { "strid", require_arg, 'S' }, - { "string", no_arg, 'r' }, - { "strin", no_arg, 'r' }, - { "use-dtd", no_arg, 'u' }, - { "use-dt", no_arg, 'u' }, - { "use-d", no_arg, 'u' }, - { "use-", no_arg, 'u' }, - { "use", no_arg, 'u' }, - { "us", no_arg, 'u' }, - { "u", no_arg, 'u' }, - { "width", require_arg, 'w' }, - { "widt", require_arg, 'w' }, - { "wid", require_arg, 'w' }, - { "wi", require_arg, 'w' }, - { "xml-dtd", require_arg, 'D' }, - { "xml-dt", require_arg, 'D' }, - { "xml-d", require_arg, 'D' }, - { "xml-ns", require_arg, 'X' }, - { "xml-n", require_arg, 'X' }, - { "xml", no_arg, 'x' }, - { "xm", no_arg, 'x' }, - { "onlyattr", optional_arg, 'A' }, - { "escape", no_arg, 'e' }, - { "noindex", no_arg, 'y' }, - { "binary", optional_arg, 'b' }, - { "form", require_arg, 'F' }, - { "sort_by", require_arg, 'q' }, - { "sort_order", require_arg, 'z' }, - { "format", require_arg, 'm' }, - { "region", no_arg, 'R' }, - { "enable-error-stack", optional_arg, 'E' }, - { "packed-bits", require_arg, 'M' }, - { "no-compact-subset", no_arg, 'C' }, - { "ddl", optional_arg, 'O' }, - { "any_path", require_arg, 'N' }, - { "vds-view-first-missing", no_arg, 'v' }, - { "vds-gap-size", require_arg, 'G' }, - { "s3-cred", require_arg, '$' }, - { "hdfs-attrs", require_arg, '#' }, - { NULL, 0, '\0' } -}; - +static const char * s_opts = "a:b*c:d:ef:g:hik:l:m:n*o*pq:rs:t:uvw:xyz:A*BCD:E*F:G:HM:N:O*RS:VX:"; +static struct h5_long_options l_opts[] = {{"attribute", require_arg, 'a'}, + {"binary", optional_arg, 'b'}, + {"count", require_arg, 'c'}, + {"dataset", require_arg, 'd'}, + {"escape", no_arg, 'e'}, + {"filedriver", require_arg, 'f'}, + {"group", require_arg, 'g'}, + {"help", no_arg, 'h'}, + {"object-ids", no_arg, 'i'}, + {"block", require_arg, 'k'}, + {"soft-link", require_arg, 'l'}, + {"format", require_arg, 'm'}, + {"contents", optional_arg, 'n'}, + {"output", optional_arg, 'o'}, + {"properties", no_arg, 'p'}, + {"sort_by", require_arg, 'q'}, + {"string", no_arg, 'r'}, + {"start", require_arg, 's'}, + {"datatype", require_arg, 't'}, + {"use-dtd", no_arg, 'u'}, + {"vds-view-first-missing", no_arg, 'v'}, + {"width", require_arg, 'w'}, + {"xml", no_arg, 'x'}, + {"noindex", no_arg, 'y'}, + {"sort_order", require_arg, 'z'}, + {"onlyattr", optional_arg, 'A'}, + {"superblock", no_arg, 'B'}, + {"boot-block", no_arg, 'B'}, + {"no-compact-subset", no_arg, 'C'}, + {"xml-dtd", require_arg, 'D'}, + {"enable-error-stack", optional_arg, 'E'}, + {"form", require_arg, 'F'}, + {"vds-gap-size", require_arg, 'G'}, + {"header", no_arg, 'H'}, + {"packed-bits", require_arg, 'M'}, + {"any_path", require_arg, 'N'}, + {"ddl", optional_arg, 'O'}, + {"region", no_arg, 'R'}, + {"stride", require_arg, 'S'}, + {"version", no_arg, 'V'}, + {"xml-ns", require_arg, 'X'}, + {"s3-cred", require_arg, '$'}, + {"hdfs-attrs", require_arg, '#'}, + {"vol-value", require_arg, '1'}, + {"vol-name", require_arg, '2'}, + {"vol-info", require_arg, '3'}, + {"vfd-value", require_arg, '4'}, + {"vfd-name", require_arg, '5'}, + {"vfd-info", require_arg, '6'}, + {NULL, 0, '\0'}}; /*------------------------------------------------------------------------- * Function: leave @@ -221,12 +139,6 @@ static struct long_options l_opts[] = { * Purpose: Shutdown MPI & HDF5 and call exit() * * Return: Does not return - * - * Programmer: Quincey Koziol - * Saturday, 31. January 2004 - * - * Modifications: - * *------------------------------------------------------------------------- */ static void @@ -237,7 +149,6 @@ leave(int ret) HDexit(ret); } - /*------------------------------------------------------------------------- * Function: usage * @@ -254,6 +165,12 @@ usage(const char *prog) PRINTVALSTREAM(rawoutstream, " OPTIONS\n"); PRINTVALSTREAM(rawoutstream, " -h, --help Print a usage message and exit\n"); PRINTVALSTREAM(rawoutstream, " -V, --version Print version number and exit\n"); + PRINTVALSTREAM(rawoutstream, "--------------- Error Options ---------------\n"); + PRINTVALSTREAM(rawoutstream, + " --enable-error-stack Prints messages from the HDF5 error stack as they occur.\n"); + PRINTVALSTREAM(rawoutstream, + " Optional value 2 also prints file open errors.\n"); + PRINTVALSTREAM(rawoutstream, " Default setting disables any error reporting.\n"); PRINTVALSTREAM(rawoutstream, "--------------- File Options ---------------\n"); PRINTVALSTREAM(rawoutstream, " -n, --contents Print a list of the file contents and exit\n"); PRINTVALSTREAM(rawoutstream, " Optional value 1 also prints attributes.\n"); @@ -263,40 +180,76 @@ usage(const char *prog) PRINTVALSTREAM(rawoutstream, " -o F, --output=F Output raw data into file F\n"); PRINTVALSTREAM(rawoutstream, " -b B, --binary=B Binary file output, of form B\n"); PRINTVALSTREAM(rawoutstream, " -O F, --ddl=F Output ddl text into file F\n"); - PRINTVALSTREAM(rawoutstream, " Use blank(empty) filename F to suppress ddl display\n"); - PRINTVALSTREAM(rawoutstream, " --s3-cred=<cred> Supply S3 authentication information to \"ros3\" vfd.\n"); - PRINTVALSTREAM(rawoutstream, " <cred> :: \"(<aws-region>,<access-id>,<access-key>)\"\n"); - PRINTVALSTREAM(rawoutstream, " If absent or <cred> -> \"(,,)\", no authentication.\n"); - PRINTVALSTREAM(rawoutstream, " Has no effect is filedriver is not `ros3'.\n"); - PRINTVALSTREAM(rawoutstream, " --hdfs-attrs=<attrs> Supply configuration information for HDFS file access.\n"); + PRINTVALSTREAM(rawoutstream, + " Use blank(empty) filename F to suppress ddl display\n"); + PRINTVALSTREAM(rawoutstream, + " --s3-cred=<cred> Supply S3 authentication information to \"ros3\" vfd.\n"); + PRINTVALSTREAM(rawoutstream, + " <cred> :: \"(<aws-region>,<access-id>,<access-key>)\"\n"); + PRINTVALSTREAM(rawoutstream, + " If absent or <cred> -> \"(,,)\", no authentication.\n"); + PRINTVALSTREAM(rawoutstream, " Has no effect if filedriver is not \"ros3\".\n"); + PRINTVALSTREAM(rawoutstream, + " --hdfs-attrs=<attrs> Supply configuration information for HDFS file access.\n"); PRINTVALSTREAM(rawoutstream, " For use with \"--filedriver=hdfs\"\n"); PRINTVALSTREAM(rawoutstream, " <attrs> :: (<namenode name>,<namenode port>,\n"); PRINTVALSTREAM(rawoutstream, " <kerberos cache path>,<username>,\n"); PRINTVALSTREAM(rawoutstream, " <buffer size>)\n"); - PRINTVALSTREAM(rawoutstream, " Any absent attribute will use a default value.\n"); + PRINTVALSTREAM(rawoutstream, + " Any absent attribute will use a default value.\n"); + PRINTVALSTREAM(rawoutstream, + " --vol-value Value (ID) of the VOL connector to use for opening the\n"); + PRINTVALSTREAM(rawoutstream, " HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, + " --vol-name Name of the VOL connector to use for opening the\n"); + PRINTVALSTREAM(rawoutstream, " HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, + " --vol-info VOL-specific info to pass to the VOL connector used for\n"); + PRINTVALSTREAM(rawoutstream, " opening the HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, + " --vfd-value Value (ID) of the VFL driver to use for opening the\n"); + PRINTVALSTREAM(rawoutstream, " HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, " --vfd-name Name of the VFL driver to use for opening the\n"); + PRINTVALSTREAM(rawoutstream, " HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, + " --vfd-info VFD-specific info to pass to the VFL driver used for\n"); + PRINTVALSTREAM(rawoutstream, " opening the HDF5 file specified\n"); PRINTVALSTREAM(rawoutstream, "--------------- Object Options ---------------\n"); PRINTVALSTREAM(rawoutstream, " -a P, --attribute=P Print the specified attribute\n"); - PRINTVALSTREAM(rawoutstream, " If an attribute name contains a slash (/), escape the\n"); + PRINTVALSTREAM(rawoutstream, + " If an attribute name contains a slash (/), escape the\n"); PRINTVALSTREAM(rawoutstream, " slash with a preceding backslash (\\).\n"); PRINTVALSTREAM(rawoutstream, " (See example section below.)\n"); PRINTVALSTREAM(rawoutstream, " -d P, --dataset=P Print the specified dataset\n"); PRINTVALSTREAM(rawoutstream, " -g P, --group=P Print the specified group and all members\n"); PRINTVALSTREAM(rawoutstream, " -l P, --soft-link=P Print the value(s) of the specified soft link\n"); PRINTVALSTREAM(rawoutstream, " -t P, --datatype=P Print the specified named datatype\n"); - PRINTVALSTREAM(rawoutstream, " -N P, --any_path=P Print any attribute, dataset, group, datatype, or link that matches P\n"); - PRINTVALSTREAM(rawoutstream, " P can be the absolute path or just a relative path.\n"); + PRINTVALSTREAM( + rawoutstream, + " -N P, --any_path=P Print any attribute, dataset, group, datatype, or link that matches P\n"); + PRINTVALSTREAM(rawoutstream, + " P can be the absolute path or just a relative path.\n"); PRINTVALSTREAM(rawoutstream, " -A, --onlyattr Print the header and value of attributes\n"); - PRINTVALSTREAM(rawoutstream, " Optional value 0 suppresses printing attributes.\n"); - PRINTVALSTREAM(rawoutstream, " --vds-view-first-missing Set the VDS bounds to first missing mapped elements.\n"); - PRINTVALSTREAM(rawoutstream, " --vds-gap-size=N Set the missing file gap size, N=non-negative integers\n"); + PRINTVALSTREAM(rawoutstream, + " Optional value 0 suppresses printing attributes.\n"); + PRINTVALSTREAM(rawoutstream, + " --vds-view-first-missing Set the VDS bounds to first missing mapped elements.\n"); + PRINTVALSTREAM(rawoutstream, + " --vds-gap-size=N Set the missing file gap size, N=non-negative integers\n"); PRINTVALSTREAM(rawoutstream, "--------------- Object Property Options ---------------\n"); PRINTVALSTREAM(rawoutstream, " -i, --object-ids Print the object ids\n"); - PRINTVALSTREAM(rawoutstream, " -p, --properties Print dataset filters, storage layout and fill value\n"); - PRINTVALSTREAM(rawoutstream, " -M L, --packedbits=L Print packed bits as unsigned integers, using mask\n"); - PRINTVALSTREAM(rawoutstream, " format L for an integer dataset specified with\n"); - PRINTVALSTREAM(rawoutstream, " option -d. L is a list of offset,length values,\n"); - PRINTVALSTREAM(rawoutstream, " separated by commas. Offset is the beginning bit in\n"); - PRINTVALSTREAM(rawoutstream, " the data value and length is the number of bits of\n"); + PRINTVALSTREAM(rawoutstream, + " -p, --properties Print dataset filters, storage layout and fill value\n"); + PRINTVALSTREAM(rawoutstream, + " -M L, --packedbits=L Print packed bits as unsigned integers, using mask\n"); + PRINTVALSTREAM(rawoutstream, + " format L for an integer dataset specified with\n"); + PRINTVALSTREAM(rawoutstream, + " option -d. L is a list of offset,length values,\n"); + PRINTVALSTREAM(rawoutstream, + " separated by commas. Offset is the beginning bit in\n"); + PRINTVALSTREAM(rawoutstream, + " the data value and length is the number of bits of\n"); PRINTVALSTREAM(rawoutstream, " the mask.\n"); PRINTVALSTREAM(rawoutstream, " -R, --region Print dataset pointed by region references\n"); PRINTVALSTREAM(rawoutstream, "--------------- Formatting Options ---------------\n"); @@ -306,12 +259,13 @@ usage(const char *prog) PRINTVALSTREAM(rawoutstream, " -m T, --format=T Set the floating point output format\n"); PRINTVALSTREAM(rawoutstream, " -q Q, --sort_by=Q Sort groups and attributes by index Q\n"); PRINTVALSTREAM(rawoutstream, " -z Z, --sort_order=Z Sort groups and attributes by order Z\n"); - PRINTVALSTREAM(rawoutstream, " --enable-error-stack Prints messages from the HDF5 error stack as they occur.\n"); - PRINTVALSTREAM(rawoutstream, " Optional value 2 also prints file open errors.\n"); - PRINTVALSTREAM(rawoutstream, " --no-compact-subset Disable compact form of subsetting and allow the use\n"); + PRINTVALSTREAM(rawoutstream, + " --no-compact-subset Disable compact form of subsetting and allow the use\n"); PRINTVALSTREAM(rawoutstream, " of \"[\" in dataset names.\n"); - PRINTVALSTREAM(rawoutstream, " -w N, --width=N Set the number of columns of output. A value of 0 (zero)\n"); - PRINTVALSTREAM(rawoutstream, " sets the number of columns to the maximum (65535).\n"); + PRINTVALSTREAM(rawoutstream, + " -w N, --width=N Set the number of columns of output. A value of 0 (zero)\n"); + PRINTVALSTREAM(rawoutstream, + " sets the number of columns to the maximum (65535).\n"); PRINTVALSTREAM(rawoutstream, " Default width is 80 columns.\n"); PRINTVALSTREAM(rawoutstream, "--------------- XML Options ---------------\n"); PRINTVALSTREAM(rawoutstream, " -x, --xml Output in XML using Schema\n"); @@ -319,31 +273,44 @@ usage(const char *prog) PRINTVALSTREAM(rawoutstream, " -D U, --xml-dtd=U Use the DTD or schema at U\n"); PRINTVALSTREAM(rawoutstream, " -X S, --xml-ns=S (XML Schema) Use qualified names n the XML\n"); PRINTVALSTREAM(rawoutstream, " \":\": no namespace, default: \"hdf5:\"\n"); - PRINTVALSTREAM(rawoutstream, " E.g., to dump a file called `-f', use h5dump -- -f\n"); + PRINTVALSTREAM(rawoutstream, + " E.g., to dump a file called \"-f\", use h5dump -- -f\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, "--------------- Subsetting Options ---------------\n"); PRINTVALSTREAM(rawoutstream, " Subsetting is available by using the following options with a dataset\n"); PRINTVALSTREAM(rawoutstream, " option. Subsetting is done by selecting a hyperslab from the data.\n"); PRINTVALSTREAM(rawoutstream, " Thus, the options mirror those for performing a hyperslab selection.\n"); - PRINTVALSTREAM(rawoutstream, " One of the START, COUNT, STRIDE, or BLOCK parameters are mandatory if you do subsetting.\n"); - PRINTVALSTREAM(rawoutstream, " The STRIDE, COUNT, and BLOCK parameters are optional and will default to 1 in\n"); - PRINTVALSTREAM(rawoutstream, " each dimension. START is optional and will default to 0 in each dimension.\n"); + PRINTVALSTREAM( + rawoutstream, + " One of the START, COUNT, STRIDE, or BLOCK parameters are mandatory if you do subsetting.\n"); + PRINTVALSTREAM(rawoutstream, + " The STRIDE, COUNT, and BLOCK parameters are optional and will default to 1 in\n"); + PRINTVALSTREAM(rawoutstream, + " each dimension. START is optional and will default to 0 in each dimension.\n"); PRINTVALSTREAM(rawoutstream, "\n"); - PRINTVALSTREAM(rawoutstream, " -s START, --start=START Offset of start of subsetting selection\n"); + PRINTVALSTREAM(rawoutstream, + " -s START, --start=START Offset of start of subsetting selection\n"); PRINTVALSTREAM(rawoutstream, " -S STRIDE, --stride=STRIDE Hyperslab stride\n"); - PRINTVALSTREAM(rawoutstream, " -c COUNT, --count=COUNT Number of blocks to include in selection\n"); + PRINTVALSTREAM(rawoutstream, + " -c COUNT, --count=COUNT Number of blocks to include in selection\n"); PRINTVALSTREAM(rawoutstream, " -k BLOCK, --block=BLOCK Size of block in hyperslab\n"); - PRINTVALSTREAM(rawoutstream, " START, COUNT, STRIDE, and BLOCK - is a list of integers the number of which are equal to the\n"); + PRINTVALSTREAM( + rawoutstream, + " START, COUNT, STRIDE, and BLOCK - is a list of integers the number of which are equal to the\n"); PRINTVALSTREAM(rawoutstream, " number of dimensions in the dataspace being queried\n"); - PRINTVALSTREAM(rawoutstream, " (Alternate compact form of subsetting is described in the Reference Manual)\n"); + PRINTVALSTREAM(rawoutstream, + " (Alternate compact form of subsetting is described in the Reference Manual)\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, "--------------- Option Argument Conventions ---------------\n"); PRINTVALSTREAM(rawoutstream, " D - is the file driver to use in opening the file. Acceptable values\n"); - PRINTVALSTREAM(rawoutstream, " are \"sec2\", \"family\", \"split\", \"multi\", \"direct\", and \"stream\". Without\n"); + PRINTVALSTREAM( + rawoutstream, + " are \"sec2\", \"family\", \"split\", \"multi\", \"direct\", and \"stream\". Without\n"); PRINTVALSTREAM(rawoutstream, " the file driver flag, the file will be opened with each driver in\n"); PRINTVALSTREAM(rawoutstream, " turn and in the order specified above until one driver succeeds\n"); PRINTVALSTREAM(rawoutstream, " in opening the file.\n"); - PRINTVALSTREAM(rawoutstream, " See examples below for family, split, and multi driver special file name usage.\n"); + PRINTVALSTREAM(rawoutstream, + " See examples below for family, split, and multi driver special file name usage.\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " F - is a filename.\n"); PRINTVALSTREAM(rawoutstream, " P - is the full path from the root group to the object.\n"); @@ -351,12 +318,17 @@ usage(const char *prog) PRINTVALSTREAM(rawoutstream, " T - is a string containing the floating point format, e.g '%%.3f'\n"); PRINTVALSTREAM(rawoutstream, " U - is a URI reference (as defined in [IETF RFC 2396],\n"); PRINTVALSTREAM(rawoutstream, " updated by [IETF RFC 2732])\n"); - PRINTVALSTREAM(rawoutstream, " B - is the form of binary output: NATIVE for a memory type, FILE for the\n"); - PRINTVALSTREAM(rawoutstream, " file type, LE or BE for pre-existing little or big endian types.\n"); + PRINTVALSTREAM(rawoutstream, + " B - is the form of binary output: NATIVE for a memory type, FILE for the\n"); + PRINTVALSTREAM(rawoutstream, + " file type, LE or BE for pre-existing little or big endian types.\n"); PRINTVALSTREAM(rawoutstream, " Must be used with -o (output file) and it is recommended that\n"); - PRINTVALSTREAM(rawoutstream, " -d (dataset) is used. B is an optional argument, defaults to NATIVE\n"); - PRINTVALSTREAM(rawoutstream, " Q - is the sort index type. It can be \"creation_order\" or \"name\" (default)\n"); - PRINTVALSTREAM(rawoutstream, " Z - is the sort order type. It can be \"descending\" or \"ascending\" (default)\n"); + PRINTVALSTREAM(rawoutstream, + " -d (dataset) is used. B is an optional argument, defaults to NATIVE\n"); + PRINTVALSTREAM(rawoutstream, + " Q - is the sort index type. It can be \"creation_order\" or \"name\" (default)\n"); + PRINTVALSTREAM(rawoutstream, + " Z - is the sort order type. It can be \"descending\" or \"ascending\" (default)\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, "--------------- Examples ---------------\n"); PRINTVALSTREAM(rawoutstream, "\n"); @@ -370,14 +342,16 @@ usage(const char *prog) PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " 2) Selecting a subset from dataset /foo in file quux.h5\n"); PRINTVALSTREAM(rawoutstream, "\n"); - PRINTVALSTREAM(rawoutstream, " h5dump -d /foo -s \"0,1\" -S \"1,1\" -c \"2,3\" -k \"2,2\" quux.h5\n"); + PRINTVALSTREAM(rawoutstream, + " h5dump -d /foo -s \"0,1\" -S \"1,1\" -c \"2,3\" -k \"2,2\" quux.h5\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " 3) Saving dataset 'dset' in file quux.h5 to binary file 'out.bin'\n"); PRINTVALSTREAM(rawoutstream, " using a little-endian type\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " h5dump -d /dset -b LE -o out.bin quux.h5\n"); PRINTVALSTREAM(rawoutstream, "\n"); - PRINTVALSTREAM(rawoutstream, " 4) Display two packed bits (bits 0-1 and bits 4-6) in the dataset /dset\n"); + PRINTVALSTREAM(rawoutstream, + " 4) Display two packed bits (bits 0-1 and bits 4-6) in the dataset /dset\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " h5dump -d /dset -M 0,1,4,3 quux.h5\n"); PRINTVALSTREAM(rawoutstream, "\n"); @@ -389,57 +363,54 @@ usage(const char *prog) PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " h5dump -d /foo -f split splitfile\n"); PRINTVALSTREAM(rawoutstream, "\n"); - PRINTVALSTREAM(rawoutstream, " 7) Dataset foo in multi files mf-s.h5, mf-b.h5, mf-r.h5, mf-g.h5, mf-l.h5 and mf-o.h5\n"); + PRINTVALSTREAM( + rawoutstream, + " 7) Dataset foo in multi files mf-s.h5, mf-b.h5, mf-r.h5, mf-g.h5, mf-l.h5 and mf-o.h5\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " h5dump -d /foo -f multi mf\n"); PRINTVALSTREAM(rawoutstream, "\n"); - PRINTVALSTREAM(rawoutstream, " 8) Dataset foo in family files fam00000.h5 fam00001.h5 and fam00002.h5\n"); + PRINTVALSTREAM(rawoutstream, + " 8) Dataset foo in family files fam00000.h5 fam00001.h5 and fam00002.h5\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " h5dump -d /foo -f family fam%%05d.h5\n"); PRINTVALSTREAM(rawoutstream, "\n"); } - /*------------------------------------------------------------------------- - * Function: table_list_add - * - * Purpose: Add a new set of tables - * - * Return: index of added table on success, -1 on failure + * Function: table_list_add * - * Programmer: Neil Fortner, nfortne2@hdfgroup.org - * Adapted from trav_addr_add in h5trav.c by Quincey Koziol - * - * Date: October 13, 2008 + * Purpose: Add a new set of tables * + * Return: index of added table on success, -1 on failure *------------------------------------------------------------------------- */ ssize_t table_list_add(hid_t oid, unsigned long file_no) { - size_t idx; /* Index of table to use */ + size_t idx; /* Index of table to use */ find_objs_t info; /* Allocate space if necessary */ - if(table_list.nused == table_list.nalloc) { - h5dump_table_items_t *tmp_ptr; + if (table_list.nused == table_list.nalloc) { + h5dump_table_items_t *tmp_ptr; table_list.nalloc = MAX(1, table_list.nalloc * 2); - if(NULL == (tmp_ptr = (h5dump_table_items_t *)HDrealloc(table_list.tables, table_list.nalloc * sizeof(table_list.tables[0])))) + if (NULL == (tmp_ptr = (h5dump_table_items_t *)HDrealloc( + table_list.tables, table_list.nalloc * sizeof(table_list.tables[0])))) return -1; table_list.tables = tmp_ptr; } /* end if */ /* Append it */ - idx = table_list.nused++; + idx = table_list.nused++; table_list.tables[idx].fileno = file_no; - table_list.tables[idx].oid = oid; - if(H5Iinc_ref(oid) < 0) { + table_list.tables[idx].oid = oid; + if (H5Iinc_ref(oid) < 0) { table_list.nused--; return -1; } - if(init_objs(oid, &info, &table_list.tables[idx].group_table, - &table_list.tables[idx].dset_table, &table_list.tables[idx].type_table) < 0) { + if (init_objs(oid, &info, &table_list.tables[idx].group_table, &table_list.tables[idx].dset_table, + &table_list.tables[idx].type_table) < 0) { H5Idec_ref(oid); table_list.nused--; return -1; @@ -449,71 +420,55 @@ table_list_add(hid_t oid, unsigned long file_no) dump_tables(&info); #endif /* H5DUMP_DEBUG */ - return((ssize_t) idx); + return ((ssize_t)idx); } /* end table_list_add() */ - /*------------------------------------------------------------------------- - * Function: table_list_visited + * Function: table_list_visited * - * Purpose: Check if a table already exists for the specified fileno - * - * Return: The index of the matching table, or -1 if no matches found - * - * Programmer: Neil Fortner, nfortne2@hdfgroup.org - * Adapted from trav_addr_visited in h5trav.c by Quincey Koziol - * - * Date: October 13, 2008 + * Purpose: Check if a table already exists for the specified fileno * + * Return: The index of the matching table, or -1 if no matches found *------------------------------------------------------------------------- */ H5_ATTR_PURE ssize_t table_list_visited(unsigned long file_no) { - size_t u; /* Local index variable */ + size_t u; /* Local index variable */ /* Look for table */ - for(u = 0; u < table_list.nused; u++) + for (u = 0; u < table_list.nused; u++) /* Check for fileno value already in array */ - if(table_list.tables[u].fileno == file_no) - return((ssize_t) u); + if (table_list.tables[u].fileno == file_no) + return ((ssize_t)u); /* Didn't find table */ - return(-1); + return (-1); } /* end table_list_visited() */ - /*------------------------------------------------------------------------- - * Function: table_list_free + * Function: table_list_free * - * Purpose: Frees the table list - * - * Return: void - * - * Programmer: Neil Fortner, nfortne2@hdfgroup.org - * - * Date: October 13, 2008 + * Purpose: Frees the table list * + * Return: void *------------------------------------------------------------------------- */ static void table_list_free(void) { - size_t u; /* Local index variable */ + size_t u; /* Local index variable */ /* Iterate over tables */ - for(u = 0; u < table_list.nused; u++) { + for (u = 0; u < table_list.nused; u++) { /* Release object id */ - if(H5Idec_ref(table_list.tables[u].oid) < 0) + if (H5Idec_ref(table_list.tables[u].oid) < 0) h5tools_setstatus(EXIT_FAILURE); /* Free each table */ free_table(table_list.tables[u].group_table); - HDfree(table_list.tables[u].group_table); free_table(table_list.tables[u].dset_table); - HDfree(table_list.tables[u].dset_table); free_table(table_list.tables[u].type_table); - HDfree(table_list.tables[u].type_table); } /* Free the table list */ @@ -525,16 +480,10 @@ table_list_free(void) /*------------------------------------------------------------------------- * Function: set_binary_form * - * Purpose: set the binary form of output by translating from a string input - * parameter to a integer return value - * - * Return: integer form of binary output or -1 if none found - * - * Programmer: Pedro Vicente Nunes - * June 28, 2006 - * - * Modifications: + * Purpose: set the binary form of output by translating from a string input + * parameter to a integer return value * + * Return: integer form of binary output or -1 if none found *------------------------------------------------------------------------- */ static int @@ -542,15 +491,15 @@ set_binary_form(const char *form) { int bform = -1; - if (HDstrcmp(form,"NATIVE") == 0 || HDstrcmp(form,"MEMORY") == 0) { + if (HDstrcmp(form, "NATIVE") == 0 || HDstrcmp(form, "MEMORY") == 0) { /* native form */ bform = 0; } - else if (HDstrcmp(form,"FILE") == 0) /* file type form */ + else if (HDstrcmp(form, "FILE") == 0) /* file type form */ bform = 1; - else if (HDstrcmp(form,"LE") == 0) /* convert to little endian */ + else if (HDstrcmp(form, "LE") == 0) /* convert to little endian */ bform = 2; - else if (HDstrcmp(form,"BE") == 0) /* convert to big endian */ + else if (HDstrcmp(form, "BE") == 0) /* convert to big endian */ bform = 3; return bform; @@ -559,17 +508,11 @@ set_binary_form(const char *form) /*------------------------------------------------------------------------- * Function: set_sort_by * - * Purpose: set the "by" form of sorting by translating from a string input - * parameter to a H5_index_t return value - * current sort values are [creation_order | name] - * - * Return: H5_index_t form of sort or H5_INDEX_UNKNOWN if none found - * - * Programmer: Pedro Vicente Nunes - * October 1, 2007 - * - * Modifications: + * Purpose: set the "by" form of sorting by translating from a string input + * parameter to a H5_index_t return value + * current sort values are [creation_order | name] * + * Return: H5_index_t form of sort or H5_INDEX_UNKNOWN if none found *------------------------------------------------------------------------- */ static H5_index_t @@ -577,9 +520,9 @@ set_sort_by(const char *form) { H5_index_t idx_type = H5_INDEX_UNKNOWN; - if (HDstrcmp(form,"name")==0) /* H5_INDEX_NAME */ + if (HDstrcmp(form, "name") == 0) /* H5_INDEX_NAME */ idx_type = H5_INDEX_NAME; - else if (HDstrcmp(form,"creation_order")==0) /* H5_INDEX_CRT_ORDER */ + else if (HDstrcmp(form, "creation_order") == 0) /* H5_INDEX_CRT_ORDER */ idx_type = H5_INDEX_CRT_ORDER; return idx_type; @@ -588,17 +531,11 @@ set_sort_by(const char *form) /*------------------------------------------------------------------------- * Function: set_sort_order * - * Purpose: set the order of sorting by translating from a string input - * parameter to a H5_iter_order_t return value - * current order values are [ascending | descending ] - * - * Return: H5_iter_order_t form of order or H5_ITER_UNKNOWN if none found - * - * Programmer: Pedro Vicente Nunes - * October 1, 2007 - * - * Modifications: + * Purpose: set the order of sorting by translating from a string input + * parameter to a H5_iter_order_t return value + * current order values are [ascending | descending ] * + * Return: H5_iter_order_t form of order or H5_ITER_UNKNOWN if none found *------------------------------------------------------------------------- */ static H5_iter_order_t @@ -606,9 +543,9 @@ set_sort_order(const char *form) { H5_iter_order_t iter_order = H5_ITER_UNKNOWN; - if (HDstrcmp(form,"ascending")==0) /* H5_ITER_INC */ + if (HDstrcmp(form, "ascending") == 0) /* H5_ITER_INC */ iter_order = H5_ITER_INC; - else if (HDstrcmp(form,"descending")==0) /* H5_ITER_DEC */ + else if (HDstrcmp(form, "descending") == 0) /* H5_ITER_DEC */ iter_order = H5_ITER_DEC; return iter_order; @@ -627,20 +564,16 @@ set_sort_order(const char *form) * either commas (,) or white spaces. * * Return: <none> - * - * Programmer: Bill Wendling - * Tuesday, 6. February 2001 - * *------------------------------------------------------------------------- */ static void parse_hsize_list(const char *h_list, subset_d *d) { - hsize_t *p_list; - const char *ptr; - unsigned int size_count = 0; - unsigned int i = 0; - unsigned int last_digit = 0; + hsize_t * p_list; + const char * ptr; + unsigned int size_count = 0; + unsigned int i = 0; + unsigned int last_digit = 0; if (!h_list || !*h_list || *h_list == ';') return; @@ -665,7 +598,7 @@ parse_hsize_list(const char *h_list, subset_d *d) p_list = (hsize_t *)HDcalloc(size_count, sizeof(hsize_t)); for (ptr = h_list; i < size_count && ptr && *ptr && *ptr != ';' && *ptr != ']'; ptr++) - if(HDisdigit(*ptr)) { + if (HDisdigit(*ptr)) { /* we should have an integer now */ p_list[i++] = (hsize_t)HDstrtoull(ptr, NULL, 0); @@ -674,32 +607,25 @@ parse_hsize_list(const char *h_list, subset_d *d) ptr++; } d->data = p_list; - d->len = size_count; + d->len = size_count; } /*------------------------------------------------------------------------- * Function: parse_subset_params * - * Purpose: Parse the so-called "terse" syntax for specifying subsetting - * parameters. + * Purpose: Parse the so-called "terse" syntax for specifying subsetting parameters. * * Return: Success: struct subset_t object * Failure: NULL - * - * Programmer: Bill Wendling - * Tuesday, 6. February 2001 - * - * Modifications: - * *------------------------------------------------------------------------- */ static struct subset_t * -parse_subset_params(char *dset) +parse_subset_params(const char *dset) { struct subset_t *s = NULL; - char *brace; + char * brace; - if (!disable_compact_subset && ((brace = HDstrrchr(dset, '[')) != NULL)) { + if (!dump_opts.disable_compact_subset && ((brace = HDstrrchr(dset, '[')) != NULL)) { *brace++ = '\0'; s = (struct subset_t *)HDcalloc(1, sizeof(struct subset_t)); @@ -708,21 +634,24 @@ parse_subset_params(char *dset) while (*brace && *brace != ';') brace++; - if (*brace) brace++; + if (*brace) + brace++; parse_hsize_list(brace, &s->stride); while (*brace && *brace != ';') brace++; - if (*brace) brace++; + if (*brace) + brace++; parse_hsize_list(brace, &s->count); while (*brace && *brace != ';') brace++; - if (*brace) brace++; + if (*brace) + brace++; parse_hsize_list(brace, &s->block); } @@ -738,9 +667,7 @@ parse_subset_params(char *dset) * should be at the start of the list you want to parse. * * Return: Success: SUCCEED - * * Failure: FAIL - * *------------------------------------------------------------------------- */ static int @@ -751,11 +678,11 @@ parse_mask_list(const char *h_list) int slength_value; unsigned length_value; unsigned long long temp_mask; - const char *ptr = NULL; + const char * ptr = NULL; /* sanity check */ - if(h_list) { - HDmemset(packed_mask,0,sizeof(packed_mask)); + if (h_list) { + HDmemset(packed_mask, 0, sizeof(packed_mask)); packed_bits_num = 0; /* scan in pair of offset,length separated by commas. */ @@ -767,10 +694,10 @@ parse_mask_list(const char *h_list) return FAIL; } soffset_value = HDatoi(ptr); - offset_value = (unsigned)soffset_value; + offset_value = (unsigned)soffset_value; if (soffset_value < 0 || offset_value >= PACKED_BITS_SIZE_MAX) { - error_msg("Packed Bit offset value(%d) must be between 0 and %u\n", - soffset_value, (unsigned)(PACKED_BITS_SIZE_MAX - 1)); + error_msg("Packed Bit offset value(%d) must be between 0 and %u\n", soffset_value, + (unsigned)(PACKED_BITS_SIZE_MAX - 1)); return FAIL; } @@ -796,7 +723,7 @@ parse_mask_list(const char *h_list) length_value = (unsigned)slength_value; if ((offset_value + length_value) > PACKED_BITS_SIZE_MAX) { error_msg("Packed Bit offset+length value(%u) too large. Max is %u\n", - offset_value+length_value, (unsigned)PACKED_BITS_SIZE_MAX); + offset_value + length_value, (unsigned)PACKED_BITS_SIZE_MAX); return FAIL; } @@ -816,8 +743,8 @@ parse_mask_list(const char *h_list) /* After packed_mask is calculated, packed_length is not needed but */ /* keep it for debug purpose. */ temp_mask = ~0ULL; - if(length_value < (int)(8 *sizeof(unsigned long long))) { - temp_mask = temp_mask << length_value; + if (length_value < (int)(8 * sizeof(unsigned long long))) { + temp_mask = temp_mask << length_value; packed_mask[packed_bits_num] = ~temp_mask; } else @@ -833,7 +760,7 @@ parse_mask_list(const char *h_list) } } } - if(packed_bits_num > PACKED_BITS_MAX) { + if (packed_bits_num > PACKED_BITS_MAX) { error_msg("Maximum number of packed bits exceeded\n"); return FAIL; } @@ -844,13 +771,12 @@ parse_mask_list(const char *h_list) } return SUCCEED; } - else { + else { error_msg("Bad mask list argument\n"); return FAIL; } } - /*------------------------------------------------------------------------- * Function: free_handler * @@ -859,12 +785,6 @@ parse_mask_list(const char *h_list) * to free * * Return: Nothing - * - * Programmer: Bill Wendling - * Tuesday, 20. February 2001 - * - * Modifications: - * *------------------------------------------------------------------------- */ static void @@ -872,25 +792,25 @@ free_handler(struct handler_t *hand, int len) { int i; - if(hand) { + if (hand) { for (i = 0; i < len; i++) { - if(hand[i].obj) { + if (hand[i].obj) { HDfree(hand[i].obj); - hand[i].obj=NULL; + hand[i].obj = NULL; } if (hand[i].subset_info) { - if(hand[i].subset_info->start.data) + if (hand[i].subset_info->start.data) HDfree(hand[i].subset_info->start.data); - if(hand[i].subset_info->stride.data) + if (hand[i].subset_info->stride.data) HDfree(hand[i].subset_info->stride.data); - if(hand[i].subset_info->count.data) + if (hand[i].subset_info->count.data) HDfree(hand[i].subset_info->count.data); - if(hand[i].subset_info->block.data) + if (hand[i].subset_info->block.data) HDfree(hand[i].subset_info->block.data); HDfree(hand[i].subset_info); - hand[i].subset_info=NULL; + hand[i].subset_info = NULL; } } @@ -898,7 +818,6 @@ free_handler(struct handler_t *hand, int len) } } - /*------------------------------------------------------------------------- * Function: parse_command_line * @@ -907,544 +826,484 @@ free_handler(struct handler_t *hand, int len) * Return: Success: A pointer to an array of handler_t structures. * These contain all the information needed to dump * the necessary object. - * * Failure: Exits program with EXIT_FAILURE value. - * - * Programmer: Bill Wendling - * Tuesday, 20. February 2001 - * - * Modifications: - * pvn June, 1, 2006. Add a switch for binary output - * *------------------------------------------------------------------------- */ static struct handler_t * -parse_command_line(int argc, const char *argv[]) +parse_command_line(int argc, const char *const *argv) { - struct handler_t *hand = NULL; - struct handler_t *last_dset = NULL; - int i; - int opt; - int last_was_dset = FALSE; + struct handler_t *hand = NULL; + struct handler_t *last_dset = NULL; + int i; + int opt; + int last_was_dset = FALSE; - /* no arguments */ + /* no arguments */ if (argc == 1) { usage(h5tools_getprogname()); goto error; } /* this will be plenty big enough to hold the info */ - if((hand = (struct handler_t *)HDcalloc((size_t)argc, sizeof(struct handler_t)))==NULL) { + if ((hand = (struct handler_t *)HDcalloc((size_t)argc, sizeof(struct handler_t))) == NULL) { goto error; } /* parse command line options */ - while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) { + while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) { parse_start: switch ((char)opt) { - case 'R': - display_region = TRUE; - region_output = TRUE; - break; - case 'B': - display_bb = TRUE; - last_was_dset = FALSE; - break; - case 'n': - display_fi = TRUE; - last_was_dset = FALSE; - if (opt_arg != NULL) - h5trav_set_verbose(HDatoi(opt_arg)); - break; - case 'p': - display_dcpl = TRUE; - break; - case 'y': - display_ai = FALSE; - break; - case 'e': - display_escape = TRUE; - break; - case 'H': - display_data = FALSE; - display_attr_data = FALSE; - last_was_dset = FALSE; - break; - case 'A': - if (opt_arg != NULL) { - if(0 == HDatoi(opt_arg)) - include_attrs = FALSE; - } - else { - display_data = FALSE; - display_attr_data = TRUE; - last_was_dset = FALSE; - } - break; - case 'i': - display_oid = TRUE; - last_was_dset = FALSE; - break; - case 'r': - display_char = TRUE; - break; - case 'V': - print_version(h5tools_getprogname()); - free_handler(hand, argc); - hand = NULL; - h5tools_setstatus(EXIT_SUCCESS); - goto done; - break; - case 'w': - { - int sh5tools_nCols = HDatoi(opt_arg); + case 'R': + dump_opts.display_region = TRUE; + region_output = TRUE; + break; + case 'B': + dump_opts.display_bb = TRUE; + last_was_dset = FALSE; + break; + case 'n': + dump_opts.display_fi = TRUE; + last_was_dset = FALSE; + if (H5_optarg != NULL) + h5trav_set_verbose(HDatoi(H5_optarg)); + break; + case 'p': + dump_opts.display_dcpl = TRUE; + break; + case 'y': + dump_opts.display_ai = FALSE; + break; + case 'e': + dump_opts.display_escape = TRUE; + break; + case 'H': + dump_opts.display_data = FALSE; + dump_opts.display_attr_data = FALSE; + last_was_dset = FALSE; + break; + case 'A': + if (H5_optarg != NULL) { + if (0 == HDatoi(H5_optarg)) + dump_opts.include_attrs = FALSE; + } + else { + dump_opts.display_data = FALSE; + dump_opts.display_attr_data = TRUE; + last_was_dset = FALSE; + } + break; + case 'i': + dump_opts.display_oid = TRUE; + last_was_dset = FALSE; + break; + case 'r': + dump_opts.display_char = TRUE; + break; + case 'V': + print_version(h5tools_getprogname()); + free_handler(hand, argc); + hand = NULL; + h5tools_setstatus(EXIT_SUCCESS); + goto done; + break; + case 'w': { + int sh5tools_nCols = HDatoi(H5_optarg); if (sh5tools_nCols <= 0) h5tools_nCols = 65535; else h5tools_nCols = (unsigned)sh5tools_nCols; last_was_dset = FALSE; - } - break; - case 'N': - display_all = 0; - - for (i = 0; i < argc; i++) - if (!hand[i].func) { - hand[i].func = handle_paths; - hand[i].obj = HDstrdup(opt_arg); - break; - } - - last_was_dset = FALSE; - break; - case 'a': - display_all = 0; + } break; + case 'N': + dump_opts.display_all = 0; + + for (i = 0; i < argc; i++) + if (!hand[i].func) { + hand[i].func = handle_paths; + hand[i].obj = HDstrdup(H5_optarg); + break; + } - for (i = 0; i < argc; i++) - if (!hand[i].func) { - hand[i].func = handle_attributes; - hand[i].obj = HDstrdup(opt_arg); - break; - } + last_was_dset = FALSE; + break; + case 'a': + dump_opts.display_all = 0; + + for (i = 0; i < argc; i++) + if (!hand[i].func) { + hand[i].func = handle_attributes; + hand[i].obj = HDstrdup(H5_optarg); + break; + } - last_was_dset = FALSE; - break; - case 'd': - display_all = 0; - - for (i = 0; i < argc; i++) - if (!hand[i].func) { - hand[i].func = handle_datasets; - hand[i].obj = HDstrdup(opt_arg); - hand[i].subset_info = parse_subset_params(hand[i].obj); - last_dset = &hand[i]; - break; - } + last_was_dset = FALSE; + break; + case 'd': + dump_opts.display_all = 0; + + for (i = 0; i < argc; i++) + if (!hand[i].func) { + hand[i].func = handle_datasets; + hand[i].obj = HDstrdup(H5_optarg); + hand[i].subset_info = parse_subset_params(hand[i].obj); + last_dset = &hand[i]; + break; + } - last_was_dset = TRUE; - break; - case 'f': - driver = opt_arg; - break; - case 'g': - display_all = 0; - - for (i = 0; i < argc; i++) - if (!hand[i].func) { - hand[i].func = handle_groups; - hand[i].obj = HDstrdup(opt_arg); - break; - } + last_was_dset = TRUE; + break; + case 'f': + vfd_info_g.type = VFD_BY_NAME; + vfd_info_g.u.name = H5_optarg; + vfd_info_g.info = NULL; + use_custom_vfd_g = TRUE; + break; + case 'g': + dump_opts.display_all = 0; + + for (i = 0; i < argc; i++) + if (!hand[i].func) { + hand[i].func = handle_groups; + hand[i].obj = HDstrdup(H5_optarg); + break; + } - last_was_dset = FALSE; - break; - case 'l': - display_all = 0; + last_was_dset = FALSE; + break; + case 'l': + dump_opts.display_all = 0; + + for (i = 0; i < argc; i++) + if (!hand[i].func) { + hand[i].func = handle_links; + hand[i].obj = HDstrdup(H5_optarg); + break; + } - for (i = 0; i < argc; i++) - if (!hand[i].func) { - hand[i].func = handle_links; - hand[i].obj = HDstrdup(opt_arg); - break; - } + last_was_dset = FALSE; + break; + case 't': + dump_opts.display_all = 0; + + for (i = 0; i < argc; i++) + if (!hand[i].func) { + hand[i].func = handle_datatypes; + hand[i].obj = HDstrdup(H5_optarg); + break; + } - last_was_dset = FALSE; - break; - case 't': - display_all = 0; + last_was_dset = FALSE; + break; - for (i = 0; i < argc; i++) - if (!hand[i].func) { - hand[i].func = handle_datatypes; - hand[i].obj = HDstrdup(opt_arg); - break; + case 'O': + if (h5tools_set_output_file(H5_optarg, 0) < 0) { + usage(h5tools_getprogname()); + goto error; } + break; - last_was_dset = FALSE; - break; + case 'o': + if (bin_output) { + if (h5tools_set_data_output_file(H5_optarg, 1) < 0) { + usage(h5tools_getprogname()); + goto error; + } + } + else { + if (dump_opts.display_attr_data && !dump_opts.display_data) { + if (h5tools_set_attr_output_file(H5_optarg, 0) < 0) { + usage(h5tools_getprogname()); + goto error; + } + } + if (dump_opts.display_data || dump_opts.display_all) { + if (h5tools_set_data_output_file(H5_optarg, 0) < 0) { + usage(h5tools_getprogname()); + goto error; + } + } + } - case 'O': - if (h5tools_set_output_file(opt_arg, 0) < 0) { - usage(h5tools_getprogname()); - goto error; - } - break; + dump_opts.usingdasho = TRUE; + last_was_dset = FALSE; + outfname_g = H5_optarg; + break; - case 'o': - if (bin_output) { - if (h5tools_set_data_output_file(opt_arg, 1) < 0) { - usage(h5tools_getprogname()); - goto error; - } - } - else { - if(display_attr_data && !display_data) { - if (h5tools_set_attr_output_file(opt_arg, 0) < 0) { + case 'b': + if (H5_optarg != NULL) { + if ((bin_form = set_binary_form(H5_optarg)) < 0) { + /* failed to set binary form */ usage(h5tools_getprogname()); goto error; } } - if(display_data || display_all) { - if (h5tools_set_data_output_file(opt_arg, 0) < 0) { + bin_output = TRUE; + if (outfname_g != NULL) { + if (h5tools_set_data_output_file(outfname_g, 1) < 0) { + /* failed to set output file */ usage(h5tools_getprogname()); goto error; } + + last_was_dset = FALSE; } - } + break; - usingdasho = TRUE; - last_was_dset = FALSE; - outfname = opt_arg; - break; + case 'q': + if ((sort_by = set_sort_by(H5_optarg)) < 0) { + /* failed to set "sort by" form */ + usage(h5tools_getprogname()); + goto error; + } + break; - case 'b': - if (opt_arg != NULL) { - if ((bin_form = set_binary_form(opt_arg)) < 0) { - /* failed to set binary form */ + case 'z': + if ((sort_order = set_sort_order(H5_optarg)) < 0) { + /* failed to set "sort order" form */ usage(h5tools_getprogname()); goto error; } - } - bin_output = TRUE; - if (outfname!=NULL) { - if (h5tools_set_data_output_file(outfname, 1) < 0) { - /* failed to set output file */ + break; + + case 'M': + if (!last_was_dset) { + error_msg("option \"-%c\" can only be used after --dataset option\n", opt); + goto error; + } + if (parse_mask_list(H5_optarg) != SUCCEED) { + usage(h5tools_getprogname()); + goto error; + } + dump_opts.display_packed_bits = TRUE; + break; + case 'v': + dump_opts.display_vds_first = TRUE; + break; + case 'G': + dump_opts.vds_gap_size = HDatoi(H5_optarg); + if (dump_opts.vds_gap_size < 0) { usage(h5tools_getprogname()); goto error; } + break; - last_was_dset = FALSE; - } - break; + /** begin XML parameters **/ + case 'x': + /* select XML output */ + doxml_g = TRUE; + useschema_g = TRUE; + h5tools_dump_header_format = NULL; + dump_function_table = &xml_function_table; + h5tools_nCols = 0; + break; + case 'u': + doxml_g = TRUE; + useschema_g = FALSE; + xmlnsprefix = ""; + h5tools_dump_header_format = NULL; + dump_function_table = &xml_function_table; + h5tools_nCols = 0; + break; + case 'D': + /* specify alternative XML DTD or schema */ + /* To Do: check format of this value? */ + xml_dtd_uri_g = H5_optarg; + h5tools_nCols = 0; + break; - case 'q': - if ((sort_by = set_sort_by(opt_arg)) < 0) { - /* failed to set "sort by" form */ - usage(h5tools_getprogname()); - goto error; - } - break; + case 'm': + /* specify alternative floating point printing format */ + fp_format = H5_optarg; + h5tools_nCols = 0; + break; - case 'z': - if ((sort_order = set_sort_order(opt_arg)) < 0) { - /* failed to set "sort order" form */ - usage(h5tools_getprogname()); - goto error; - } - break; + case 'X': + /* specify XML namespace (default="hdf5:"), or none */ + /* To Do: check format of this value? */ + if (!useschema_g) { + usage(h5tools_getprogname()); + goto error; + } + if (HDstrcmp(H5_optarg, ":") == 0) + xmlnsprefix = ""; + else + xmlnsprefix = H5_optarg; + h5tools_nCols = 0; + break; + /** end XML parameters **/ - case 'M': - if (!last_was_dset) { - error_msg("option `-%c' can only be used after --dataset option\n", opt); - goto error; - } - if (parse_mask_list(opt_arg) != SUCCEED){ - usage(h5tools_getprogname()); - goto error; - } - display_packed_bits = TRUE; - break; - case 'v': - display_vds_first = TRUE; - break; - case 'G': - vds_gap_size = HDatoi(opt_arg); - if (vds_gap_size < 0) { - usage(h5tools_getprogname()); - goto error; - } - break; - - /** begin XML parameters **/ - case 'x': - /* select XML output */ - doxml = TRUE; - useschema = TRUE; - h5tools_dump_header_format = NULL; - dump_function_table = &xml_function_table; - h5tools_nCols = 0; - break; - case 'u': - doxml = TRUE; - useschema = FALSE; - xmlnsprefix = ""; - h5tools_dump_header_format = NULL; - dump_function_table = &xml_function_table; - h5tools_nCols = 0; - break; - case 'D': - /* specify alternative XML DTD or schema */ - /* To Do: check format of this value? */ - xml_dtd_uri = opt_arg; - h5tools_nCols = 0; - break; - - case 'm': - /* specify alternative floating point printing format */ - fp_format = opt_arg; - h5tools_nCols = 0; - break; - - case 'X': - /* specify XML namespace (default="hdf5:"), or none */ - /* To Do: check format of this value? */ - if (!useschema) { - usage(h5tools_getprogname()); - goto error; - } - if (HDstrcmp(opt_arg,":") == 0) - xmlnsprefix = ""; - else - xmlnsprefix = opt_arg; - h5tools_nCols = 0; - break; - /** end XML parameters **/ - - /** begin subsetting parameters **/ - case 's': - case 'S': - case 'c': - case 'k': { - struct subset_t *s; - - if (!last_was_dset) { - error_msg("option `-%c' can only be used after --dataset option\n", opt); - goto error; - } + /** begin subsetting parameters **/ + case 's': + case 'S': + case 'c': + case 'k': { + struct subset_t *s; + + if (!last_was_dset) { + error_msg("option \"-%c\" can only be used after --dataset option\n", opt); + goto error; + } + + if (last_dset->subset_info) { + /* + * This overrides the "terse" syntax if they actually mixed + * the two. + */ + s = last_dset->subset_info; + } + else { + last_dset->subset_info = s = (struct subset_t *)HDcalloc(1, sizeof(struct subset_t)); + } - if (last_dset->subset_info) { /* - * This overrides the "terse" syntax if they actually mixed - * the two. + * slightly convoluted, but...we are only interested in options + * for subsetting: "--start", "--stride", "--count", and "--block" + * which can come in any order. If we run out of parameters (EOF) + * or run into one which isn't a subsetting parameter (NOT s, S, + * c, or K), then we exit the do-while look, set the subset_info + * to the structure we've been filling. If we've reached the end + * of the options, we exit the parsing (goto parse_end) otherwise, + * since we've "read" the next option, we need to parse it. So we + * jump to the beginning of the switch statement (goto parse_start). */ - s = last_dset->subset_info; - } - else { - last_dset->subset_info = s = (struct subset_t *)HDcalloc(1, sizeof(struct subset_t)); - } - - /* - * slightly convoluted, but...we are only interested in options - * for subsetting: "--start", "--stride", "--count", and "--block" - * which can come in any order. If we run out of parameters (EOF) - * or run into one which isn't a subsetting parameter (NOT s, S, - * c, or K), then we exit the do-while look, set the subset_info - * to the structure we've been filling. If we've reached the end - * of the options, we exit the parsing (goto parse_end) otherwise, - * since we've "read" the next option, we need to parse it. So we - * jump to the beginning of the switch statement (goto parse_start). - */ - do { - switch ((char)opt) { - case 's': - if (s->start.data) { - HDfree(s->start.data); - s->start.data = NULL; - } - parse_hsize_list(opt_arg, &s->start); - break; - case 'S': - if (s->stride.data) { - HDfree(s->stride.data); - s->stride.data = NULL; - } - parse_hsize_list(opt_arg, &s->stride); - break; - case 'c': - if (s->count.data) { - HDfree(s->count.data); - s->count.data = NULL; + do { + switch ((char)opt) { + case 's': + if (s->start.data) { + HDfree(s->start.data); + s->start.data = NULL; + } + parse_hsize_list(H5_optarg, &s->start); + break; + case 'S': + if (s->stride.data) { + HDfree(s->stride.data); + s->stride.data = NULL; + } + parse_hsize_list(H5_optarg, &s->stride); + break; + case 'c': + if (s->count.data) { + HDfree(s->count.data); + s->count.data = NULL; + } + parse_hsize_list(H5_optarg, &s->count); + break; + case 'k': + if (s->block.data) { + HDfree(s->block.data); + s->block.data = NULL; + } + parse_hsize_list(H5_optarg, &s->block); + break; + default: + goto end_collect; } - parse_hsize_list(opt_arg, &s->count); - break; - case 'k': - if (s->block.data) { - HDfree(s->block.data); - s->block.data = NULL; - } - parse_hsize_list(opt_arg, &s->block); - break; - default: - goto end_collect; - } - } while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF); + } while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF); end_collect: - last_was_dset = FALSE; + last_was_dset = FALSE; - if (opt != EOF) - goto parse_start; - else - goto parse_end; - } - /** end subsetting parameters **/ + if (opt != EOF) + goto parse_start; + else + goto parse_end; + } + /** end subsetting parameters **/ - case 'E': - if (opt_arg != NULL) - enable_error_stack = HDatoi(opt_arg); - else - enable_error_stack = 1; - break; - case 'C': - disable_compact_subset = TRUE; - break; - case 'h': - usage(h5tools_getprogname()); - free_handler(hand, argc); - hand = NULL; - h5tools_setstatus(EXIT_SUCCESS); - goto done; + case 'E': + if (H5_optarg != NULL) + enable_error_stack = HDatoi(H5_optarg); + else + enable_error_stack = 1; + break; + case 'C': + dump_opts.disable_compact_subset = TRUE; + break; + case 'h': + usage(h5tools_getprogname()); + free_handler(hand, argc); + hand = NULL; + h5tools_setstatus(EXIT_SUCCESS); + goto done; - case '$': -#ifndef H5_HAVE_ROS3_VFD - error_msg("Read-Only S3 VFD not enabled.\n"); - h5tools_setstatus(EXIT_FAILURE); - goto done; -#else - /* s3 credential */ - { - char **s3_cred = NULL; - char *s3_cred_string = NULL; - const char *ccred[3]; - unsigned nelems = 0; - if ( FAIL == - parse_tuple(opt_arg, ',', - &s3_cred_string, &nelems, &s3_cred)) - { - error_msg("unable to parse malformed s3 credentials\n"); - usage(h5tools_getprogname()); - free_handler(hand, argc); - hand= NULL; - h5tools_setstatus(EXIT_FAILURE); - goto done; - } - if (nelems != 3) { - error_msg("s3 credentials expects 3 elements\n"); + case '$': +#ifdef H5_HAVE_ROS3_VFD + if (h5tools_parse_ros3_fapl_tuple(H5_optarg, ',', &ros3_fa_g) < 0) { + error_msg("failed to parse S3 VFD credential info\n"); usage(h5tools_getprogname()); free_handler(hand, argc); - hand= NULL; + hand = NULL; h5tools_setstatus(EXIT_FAILURE); goto done; } - ccred[0] = (const char *)s3_cred[0]; - ccred[1] = (const char *)s3_cred[1]; - ccred[2] = (const char *)s3_cred[2]; - if (0 == h5tools_populate_ros3_fapl(&ros3_fa, ccred)) { - error_msg("Invalid S3 credentials\n"); +#else + error_msg("Read-Only S3 VFD not enabled.\n"); + h5tools_setstatus(EXIT_FAILURE); + goto done; +#endif + break; + + case '#': +#ifdef H5_HAVE_LIBHDFS + if (h5tools_parse_hdfs_fapl_tuple(H5_optarg, ',', &hdfs_fa_g) < 0) { + error_msg("failed to parse HDFS VFD configuration info\n"); usage(h5tools_getprogname()); free_handler(hand, argc); - hand= NULL; + hand = NULL; h5tools_setstatus(EXIT_FAILURE); goto done; } - HDfree(s3_cred); - HDfree(s3_cred_string); - } /* s3 credential block */ - break; -#endif /* H5_HAVE_ROS3_VFD */ - - case '#': -#ifndef H5_HAVE_LIBHDFS - error_msg("HDFS VFD is not enabled.\n"); - goto error; #else - { - /* read hdfs properties tuple and store values in `hdfs_fa` - */ - unsigned nelems = 0; - char *props_src = NULL; - char **props = NULL; - unsigned long k = 0; - if (FAIL == parse_tuple( - (const char *)opt_arg, - ',', - &props_src, - &nelems, - &props)) - { - error_msg("unable to parse hdfs properties tuple\n"); - goto error; - } - /* sanity-check tuple count - */ - if (nelems != 5) { - h5tools_setstatus(EXIT_FAILURE); - goto error; - } - /* Populate fapl configuration structure with given - * properties. - * WARNING: No error-checking is done on length of input - * strings... Silent overflow is possible, albeit - * unlikely. - */ - if (strncmp(props[0], "", 1)) { - HDstrncpy(hdfs_fa.namenode_name, - (const char *)props[0], - HDstrlen(props[0])); - } - if (strncmp(props[1], "", 1)) { - k = strtoul((const char *)props[1], NULL, 0); - if (errno == ERANGE) { - h5tools_setstatus(EXIT_FAILURE); - goto error; - } - hdfs_fa.namenode_port = (int32_t)k; - } - if (strncmp(props[2], "", 1)) { - HDstrncpy(hdfs_fa.kerberos_ticket_cache, - (const char *)props[2], - HDstrlen(props[2])); - } - if (strncmp(props[3], "", 1)) { - HDstrncpy(hdfs_fa.user_name, - (const char *)props[3], - HDstrlen(props[3])); - } - if (strncmp(props[4], "", 1)) { - k = strtoul((const char *)props[4], NULL, 0); - if (errno == ERANGE) { - h5tools_setstatus(EXIT_FAILURE); - goto error; - } - hdfs_fa.stream_buffer_size = (int32_t)k; - } - HDfree(props); - HDfree(props_src); - } -#endif /* H5_HAVE_LIBHDFS */ - break; + error_msg("HDFS VFD not enabled.\n"); + h5tools_setstatus(EXIT_FAILURE); + goto done; +#endif + break; - case '?': - default: - usage(h5tools_getprogname()); - goto error; + case '1': + vol_info_g.type = VOL_BY_VALUE; + vol_info_g.u.value = (H5VL_class_value_t)HDatoi(H5_optarg); + use_custom_vol_g = TRUE; + break; + + case '2': + vol_info_g.type = VOL_BY_NAME; + vol_info_g.u.name = H5_optarg; + use_custom_vol_g = TRUE; + break; + + case '3': + vol_info_g.info_string = H5_optarg; + break; + + case '4': + vfd_info_g.type = VFD_BY_VALUE; + vfd_info_g.u.value = (H5FD_class_value_t)HDatoi(H5_optarg); + use_custom_vfd_g = TRUE; + break; + + case '5': + vfd_info_g.type = VFD_BY_NAME; + vfd_info_g.u.name = H5_optarg; + use_custom_vfd_g = TRUE; + break; + + case '6': + vfd_info_g.info = (const void *)H5_optarg; + break; + + case '?': + default: + usage(h5tools_getprogname()); + goto error; } } parse_end: /* check for file name to be processed */ - if (argc <= opt_ind) { + if (argc <= H5_optind) { error_msg("missing file name\n"); usage(h5tools_getprogname()); goto error; @@ -1462,7 +1321,6 @@ error: return hand; } - /*------------------------------------------------------------------------- * Function: main * @@ -1470,180 +1328,99 @@ error: * * Return: Success: 0 * Failure: 1 - * - * Programmer: Ruey-Hsia Li - * - * Modifications: - * Albert Cheng - * 30. September 2000 - * Add the -o option--output file for datasets raw data - * - * REMcG - * November 2000 - * Changes to support XML. - * - * Bill Wendling - * Wednesday, 10. January 2001 - * Modified the way command line parameters are interpreted. They go - * through one function call now (get_option). - * - * Bill Wendling - * Tuesday, 20. February 2001 - * Moved command line parsing to separate function. Made various - * "display_*" flags global. - * - * REMcG - * August 2003 - * Major upgrade to XML support. - * - * Pedro Vicente - * September 2007 - * list objects in requested order (creation order or alphabetically) - * *------------------------------------------------------------------------- */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { - hid_t fid = -1; - hid_t gid = -1; - hid_t fapl_id = H5P_DEFAULT; - H5E_auto2_t func; - H5E_auto2_t tools_func; - H5O_info_t oi; - struct handler_t *hand = NULL; - int i; - unsigned u; - void *edata; - void *tools_edata; - char *fname = NULL; + hid_t fid = H5I_INVALID_HID; + hid_t gid = H5I_INVALID_HID; + hid_t fapl_id = H5P_DEFAULT; + H5O_info2_t oi; + struct handler_t *hand = NULL; + int i; + unsigned u; + char * fname = NULL; h5tools_setprogname(PROGRAMNAME); h5tools_setstatus(EXIT_SUCCESS); h5tools_dump_header_format = &h5tools_standardformat; - dump_function_table = &ddl_function_table; - dump_indent = 0; - - /* Disable error reporting */ - H5Eget_auto2(H5E_DEFAULT, &func, &edata); - H5Eset_auto2(H5E_DEFAULT, NULL, NULL); + dump_function_table = &ddl_function_table; + dump_indent = 0; /* Initialize h5tools lib */ h5tools_init(); - /* Disable tools error reporting */ - H5Eget_auto2(H5tools_ERR_STACK_g, &tools_func, &tools_edata); - H5Eset_auto2(H5tools_ERR_STACK_g, NULL, NULL); - - if((hand = parse_command_line(argc, argv))==NULL) { + if ((hand = parse_command_line(argc, (const char *const *)argv)) == NULL) { goto done; } - if (bin_output && outfname == NULL) { + if (bin_output && outfname_g == NULL) { error_msg("binary output requires a file name, use -o <filename>\n"); h5tools_setstatus(EXIT_FAILURE); goto done; } - if (enable_error_stack > 0) { - H5Eset_auto2(H5E_DEFAULT, func, edata); - H5Eset_auto2(H5tools_ERR_STACK_g, tools_func, tools_edata); - } - /* Check for conflicting options */ - if (doxml) { - if (!display_all) { - error_msg("option \"%s\" not available for XML\n", - "to display selected objects"); + if (doxml_g) { + if (!dump_opts.display_all) { + error_msg("option \"%s\" not available for XML\n", "to display selected objects"); h5tools_setstatus(EXIT_FAILURE); goto done; } - else if (display_bb) { + else if (dump_opts.display_bb) { error_msg("option \"%s\" not available for XML\n", "--boot-block"); h5tools_setstatus(EXIT_FAILURE); goto done; } - else if (display_oid == 1) { + else if (dump_opts.display_oid == 1) { error_msg("option \"%s\" not available for XML\n", "--object-ids"); h5tools_setstatus(EXIT_FAILURE); goto done; } - else if (display_char == TRUE) { + else if (dump_opts.display_char == TRUE) { error_msg("option \"%s\" not available for XML\n", "--string"); h5tools_setstatus(EXIT_FAILURE); goto done; } - else if (usingdasho) { + else if (dump_opts.usingdasho) { error_msg("option \"%s\" not available for XML\n", "--output"); h5tools_setstatus(EXIT_FAILURE); goto done; } } else { - if (xml_dtd_uri) { - warn_msg("option \"%s\" only applies with XML: %s\n", "--xml-dtd", xml_dtd_uri); + if (xml_dtd_uri_g) { + warn_msg("option \"%s\" only applies with XML: %s\n", "--xml-dtd", xml_dtd_uri_g); } } - if (argc <= opt_ind) { + if (argc <= H5_optind) { error_msg("missing file name\n"); usage(h5tools_getprogname()); h5tools_setstatus(EXIT_FAILURE); goto done; } + + /* enable error reporting if command line option */ + h5tools_error_report(); + /* Initialize indexing options */ h5trav_set_index(sort_by, sort_order); - if (driver != NULL) { - void *conf_fa = NULL; - - if (!strcmp(driver, "ros3")) { -#ifndef H5_HAVE_ROS3_VFD - error_msg("Read-Only S3 VFD not enabled.\n"); + if (use_custom_vol_g || use_custom_vfd_g) { + if ((fapl_id = h5tools_get_fapl(H5P_DEFAULT, use_custom_vol_g ? &vol_info_g : NULL, + use_custom_vfd_g ? &vfd_info_g : NULL)) < 0) { + error_msg("unable to create FAPL for file access\n"); h5tools_setstatus(EXIT_FAILURE); goto done; -#else - conf_fa = (void *)&ros3_fa; -#endif /* H5_HAVE_ROS3_VFD */ - } else if (!HDstrcmp(driver, "hdfs")) { -#ifndef H5_HAVE_LIBHDFS - error_msg("HDFS VFD is not enabled.\n"); - h5tools_setstatus(EXIT_FAILURE); - goto done; -#else - conf_fa = (void *)&hdfs_fa; -#endif /* H5_HAVE_LIBHDFS */ } + } - if (conf_fa != NULL) { - fapl_id = H5Pcreate(H5P_FILE_ACCESS); - if (fapl_id < 0) { - error_msg("unable to create fapl entry\n"); - h5tools_setstatus(EXIT_FAILURE); - goto done; - } - if (0 == h5tools_set_configured_fapl( - fapl_id, - driver, /* guaranteed "ros3" or "hdfs" */ - conf_fa)) /* appropriate to driver */ - { - error_msg("unable to set fapl\n"); - h5tools_setstatus(EXIT_FAILURE); - goto done; - } - } - } /* driver defined */ - - while(opt_ind < argc) { - fname = HDstrdup(argv[opt_ind++]); + while (H5_optind < argc) { + fname = HDstrdup(argv[H5_optind++]); - if (fapl_id != H5P_DEFAULT) { - fid = H5Fopen(fname, H5F_ACC_RDONLY, fapl_id); - } - else { - fid = h5tools_fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT, - driver, NULL, 0); - } + fid = h5tools_fopen(fname, H5F_ACC_RDONLY, fapl_id, (fapl_id != H5P_DEFAULT), NULL, 0); if (fid < 0) { error_msg("unable to open file \"%s\"\n", fname); @@ -1657,24 +1434,25 @@ main(int argc, const char *argv[]) /* Prepare to find objects that might be targets of a reference */ fill_ref_path_table(fid); - if(doxml) { + if (doxml_g) { /* initialize XML */ /* reset prefix! */ HDstrcpy(prefix, ""); /* make sure the URI is initialized to something */ - if (xml_dtd_uri == NULL) { - if (useschema) { - xml_dtd_uri = DEFAULT_XSD; + if (xml_dtd_uri_g == NULL) { + if (useschema_g) { + xml_dtd_uri_g = DEFAULT_XSD; } else { - xml_dtd_uri = DEFAULT_DTD; - xmlnsprefix = ""; + xml_dtd_uri_g = DEFAULT_DTD; + xmlnsprefix = ""; } } else { - if (useschema && HDstrcmp(xmlnsprefix,"")) { - error_msg("Cannot set Schema URL for a qualified namespace--use -X or -U option with -D \n"); + if (useschema_g && HDstrcmp(xmlnsprefix, "") != 0) { + error_msg( + "Cannot set Schema URL for a qualified namespace--use -X or -U option with -D \n"); h5tools_setstatus(EXIT_FAILURE); goto done; } @@ -1682,23 +1460,23 @@ main(int argc, const char *argv[]) } /* Get object info for root group */ - if(H5Oget_info_by_name2(fid, "/", &oi, H5O_INFO_BASIC, H5P_DEFAULT) < 0) { + if (H5Oget_info_by_name3(fid, "/", &oi, H5O_INFO_BASIC, H5P_DEFAULT) < 0) { error_msg("internal error (file %s:line %d)\n", __FILE__, __LINE__); h5tools_setstatus(EXIT_FAILURE); goto done; } /* Initialize object tables */ - if(table_list_add(fid, oi.fileno) < 0) { + if (table_list_add(fid, oi.fileno) < 0) { error_msg("internal error (file %s:line %d)\n", __FILE__, __LINE__); h5tools_setstatus(EXIT_FAILURE); goto done; } group_table = table_list.tables[0].group_table; - dset_table = table_list.tables[0].dset_table; - type_table = table_list.tables[0].type_table; + dset_table = table_list.tables[0].dset_table; + type_table = table_list.tables[0].type_table; - /* does there exist unamed committed datatype */ + /* does there exist unnamed committed datatype */ for (u = 0; u < type_table->nobjs; u++) if (!type_table->objs[u].recorded) { unamedtype = 1; @@ -1706,90 +1484,96 @@ main(int argc, const char *argv[]) } /* end if */ /* start to dump - display file header information */ - if (!doxml) { - begin_obj(h5tools_dump_header_format->filebegin, fname, h5tools_dump_header_format->fileblockbegin); + if (!doxml_g) { + begin_obj(h5tools_dump_header_format->filebegin, fname, + h5tools_dump_header_format->fileblockbegin); } else { PRINTVALSTREAM(rawoutstream, "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"); /* alternative first element, depending on schema or DTD. */ - if (useschema) { - if (HDstrcmp(xmlnsprefix,"") == 0) { - PRINTSTREAM(rawoutstream, "<HDF5-File xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:noNamespaceSchemaLocation=\"%s\">\n", - xml_dtd_uri); + if (useschema_g) { + if (HDstrcmp(xmlnsprefix, "") == 0) { + PRINTSTREAM(rawoutstream, + "<HDF5-File xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" " + "xsi:noNamespaceSchemaLocation=\"%s\">\n", + xml_dtd_uri_g); } else { /* TO DO: make -url option work in this case (may need new option) */ char *ns; char *indx; - ns = HDstrdup(xmlnsprefix); - indx = HDstrrchr(ns,(int)':'); - if (indx) *indx = '\0'; - - PRINTSTREAM(rawoutstream, "<%sHDF5-File xmlns:%s=\"http://hdfgroup.org/HDF5/XML/schema/HDF5-File.xsd\" " - "xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" " - "xsi:schemaLocation=\"http://hdfgroup.org/HDF5/XML/schema/HDF5-File " - "http://www.hdfgroup.org/HDF5/XML/schema/HDF5-File.xsd\">\n",xmlnsprefix,ns); + ns = HDstrdup(xmlnsprefix); + indx = HDstrrchr(ns, (int)':'); + if (indx) + *indx = '\0'; + + PRINTSTREAM(rawoutstream, + "<%sHDF5-File xmlns:%s=\"http://hdfgroup.org/HDF5/XML/schema/HDF5-File.xsd\" " + "xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" " + "xsi:schemaLocation=\"http://hdfgroup.org/HDF5/XML/schema/HDF5-File " + "http://www.hdfgroup.org/HDF5/XML/schema/HDF5-File.xsd\">\n", + xmlnsprefix, ns); HDfree(ns); } } else { - PRINTSTREAM(rawoutstream, "<!DOCTYPE HDF5-File PUBLIC \"HDF5-File.dtd\" \"%s\">\n", xml_dtd_uri); + PRINTSTREAM(rawoutstream, "<!DOCTYPE HDF5-File PUBLIC \"HDF5-File.dtd\" \"%s\">\n", + xml_dtd_uri_g); PRINTVALSTREAM(rawoutstream, "<HDF5-File>\n"); } } - if (!doxml) { - if (display_fi) { + if (!doxml_g) { + if (dump_opts.display_fi) { PRINTVALSTREAM(rawoutstream, "\n"); dump_fcontents(fid); - end_obj(h5tools_dump_header_format->fileend,h5tools_dump_header_format->fileblockend); + end_obj(h5tools_dump_header_format->fileend, h5tools_dump_header_format->fileblockend); PRINTVALSTREAM(rawoutstream, "\n"); goto done; } - if (display_bb) + if (dump_opts.display_bb) dump_fcpl(fid); } - if(display_all) { - if((gid = H5Gopen2(fid, "/", H5P_DEFAULT)) < 0) { + if (dump_opts.display_all) { + if ((gid = H5Gopen2(fid, "/", H5P_DEFAULT)) < 0) { error_msg("unable to open root group\n"); h5tools_setstatus(EXIT_FAILURE); } else { - if (!doxml) + if (!doxml_g) dump_indent += COL; - dump_function_table->dump_group_function(gid, "/" ); - if (!doxml) + dump_function_table->dump_group_function(gid, "/"); + if (!doxml_g) dump_indent -= COL; PRINTVALSTREAM(rawoutstream, "\n"); } - if(H5Gclose(gid) < 0) { + if (H5Gclose(gid) < 0) { error_msg("unable to close root group\n"); h5tools_setstatus(EXIT_FAILURE); } - } else { /* Note: this option is not supported for XML */ - if(doxml) { + if (doxml_g) { error_msg("internal error (file %s:line %d)\n", __FILE__, __LINE__); h5tools_setstatus(EXIT_FAILURE); goto done; } /* end if */ - for(i = 0; i < argc; i++) { - if(hand[i].func) { + for (i = 0; i < argc; i++) { + if (hand[i].func) { hand[i].func(fid, hand[i].obj, hand[i].subset_info, 1, NULL); } } PRINTVALSTREAM(rawoutstream, "\n"); } - if (!doxml) { + if (!doxml_g) { end_obj(h5tools_dump_header_format->fileend, h5tools_dump_header_format->fileblockend); PRINTVALSTREAM(rawoutstream, "\n"); } @@ -1799,21 +1583,21 @@ main(int argc, const char *argv[]) /* Free tables for objects */ table_list_free(); - if(fid >=0) + if (fid >= 0) if (H5Fclose(fid) < 0) h5tools_setstatus(EXIT_FAILURE); - if(prefix) { + if (prefix) { HDfree(prefix); prefix = NULL; } - if(fname) { + if (fname) { HDfree(fname); fname = NULL; } } /* end while */ - if(hand) + if (hand) free_handler(hand, argc); /* To Do: clean up XML table */ @@ -1829,30 +1613,27 @@ done: h5tools_setstatus(EXIT_FAILURE); } - if(fid >=0) + if (fid >= 0) if (H5Fclose(fid) < 0) h5tools_setstatus(EXIT_FAILURE); - if(prefix) { + if (prefix) { HDfree(prefix); prefix = NULL; } - if(fname) { + if (fname) { HDfree(fname); fname = NULL; } - if(hand) + if (hand) free_handler(hand, argc); /* To Do: clean up XML table */ - H5Eset_auto2(H5E_DEFAULT, func, edata); - leave(h5tools_getstatus()); } /* main */ - /*------------------------------------------------------------------------- * Function: init_prefix * @@ -1867,13 +1648,12 @@ done: static void init_prefix(char **prfx, size_t prfx_len) { - if(prfx_len > 0) + if (prfx_len > 0) *prfx = (char *)HDcalloc(prfx_len, 1); else error_msg("unable to allocate prefix buffer\n"); } - /*------------------------------------------------------------------------- * Function: add_prefix * @@ -1889,12 +1669,11 @@ add_prefix(char **prfx, size_t *prfx_len, const char *name) size_t new_len = HDstrlen(*prfx) + HDstrlen(name) + 2; /* Check if we need more space */ - if(*prfx_len <= new_len) { + if (*prfx_len <= new_len) { *prfx_len = new_len + 1; - *prfx = (char *)HDrealloc(*prfx, *prfx_len); + *prfx = (char *)HDrealloc(*prfx, *prfx_len); } /* Append object name to prefix */ HDstrcat(HDstrcat(*prfx, "/"), name); } /* end add_prefix */ - diff --git a/tools/src/h5dump/h5dump.h b/tools/src/h5dump/h5dump.h index 801f60d..a53d1ba 100644 --- a/tools/src/h5dump/h5dump.h +++ b/tools/src/h5dump/h5dump.h @@ -6,12 +6,12 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -#ifndef H5DUMP_H__ -#define H5DUMP_H__ +#ifndef H5DUMP_H +#define H5DUMP_H #include "hdf5.h" #include "H5private.h" @@ -26,62 +26,67 @@ **/ /* the table of dump functions */ typedef struct dump_functions_t { - void (*dump_group_function) (hid_t, const char *); - void (*dump_named_datatype_function) (hid_t, const char *); - void (*dump_dataset_function) (hid_t, const char *, struct subset_t *); - void (*dump_dataspace_function) (hid_t); - void (*dump_datatype_function) (hid_t); - herr_t (*dump_attribute_function) (hid_t, const char *, const H5A_info_t *, void *); - void (*dump_data_function) (hid_t, int, struct subset_t *, int); + void (*dump_group_function)(hid_t, const char *); + void (*dump_named_datatype_function)(hid_t, const char *); + void (*dump_dataset_function)(hid_t, const char *, struct subset_t *); + void (*dump_dataspace_function)(hid_t); + void (*dump_datatype_function)(hid_t); + herr_t (*dump_attribute_function)(hid_t, const char *, const H5A_info_t *, void *); + void (*dump_data_function)(hid_t, int, struct subset_t *, int); } dump_functions; /* List of table structures. There is one table structure for each file */ typedef struct h5dump_table_items_t { - unsigned long fileno; /* File number that these tables refer to */ - hid_t oid; /* ID of an object in this file, held open so fileno is consistent */ - table_t *group_table; /* Table of groups */ - table_t *dset_table; /* Table of datasets */ - table_t *type_table; /* Table of datatypes */ + unsigned long fileno; /* File number that these tables refer to */ + hid_t oid; /* ID of an object in this file, held open so fileno is consistent */ + table_t * group_table; /* Table of groups */ + table_t * dset_table; /* Table of datasets */ + table_t * type_table; /* Table of datatypes */ } h5dump_table_items_t; + typedef struct h5dump_table_list_t { - size_t nalloc; - size_t nused; - h5dump_table_items_t *tables; + size_t nalloc; + size_t nused; + h5dump_table_items_t *tables; } h5dump_table_list_t; -h5dump_table_list_t table_list = {0, 0, NULL}; -table_t *group_table = NULL, *dset_table = NULL, *type_table = NULL; -unsigned dump_indent = 0; /*how far in to indent the line */ +h5dump_table_list_t table_list = {0, 0, NULL}; +table_t * group_table = NULL, *dset_table = NULL, *type_table = NULL; -int unamedtype = 0; /* shared datatype with no name */ -hbool_t hit_elink = FALSE; /* whether we have traversed an external link */ -size_t prefix_len = 1024; -char *prefix = NULL; -const char *fp_format = NULL; +unsigned dump_indent = 0; /* how far in to indent the line */ +int unamedtype = 0; /* shared datatype with no name */ +hbool_t hit_elink = FALSE; /* whether we have traversed an external link */ +size_t prefix_len = 1024; +char * prefix = NULL; +const char *fp_format = NULL; /* things to display or which are set via command line parameters */ -int display_all = TRUE; -int display_oid = FALSE; -int display_data = TRUE; -int display_attr_data = TRUE; -int display_char = FALSE; /*print 1-byte numbers as ASCII */ -int usingdasho = FALSE; -int display_bb = FALSE; /*superblock */ -int display_dcpl = FALSE; /*dcpl */ -int display_fi = FALSE; /*file index */ -int display_ai = TRUE; /*array index */ -int display_escape = FALSE; /*escape non printable characters */ -int display_region = FALSE; /*print region reference data */ -int disable_compact_subset= FALSE; /* disable compact form of subset notation */ -int display_packed_bits = FALSE; /*print 1-8 byte numbers as packed bits*/ -int include_attrs = TRUE; /* Display attributes */ -int display_vds_first = FALSE; /* vds display to all by default*/ -int vds_gap_size = 0; /* vds skip missing files default is none */ +typedef struct { + int display_all; + int display_oid; + int display_data; + int display_attr_data; + int display_char; /* print 1-byte numbers as ASCII */ + int usingdasho; + int display_bb; /* superblock */ + int display_dcpl; /* dcpl */ + int display_fi; /* file index */ + int display_ai; /* array index */ + int display_escape; /* escape non printable characters */ + int display_region; /* print region reference data */ + int disable_compact_subset; /* disable compact form of subset notation */ + int display_packed_bits; /* print 1-8 byte numbers as packed bits */ + int include_attrs; /* Display attributes */ + int display_vds_first; /* vds display to all by default */ + int vds_gap_size; /* vds skip missing files default is none */ +} dump_opt_t; +dump_opt_t dump_opts = {TRUE, FALSE, TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, + TRUE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE, 0}; -#define PACKED_BITS_MAX 8 /* Maximum number of packed-bits to display */ -#define PACKED_BITS_SIZE_MAX (8*sizeof(long long)) /* Maximum bits size of integer types of packed-bits */ +#define PACKED_BITS_MAX 8 /* Maximum number of packed-bits to display */ +#define PACKED_BITS_SIZE_MAX (8 * sizeof(long long)) /* Maximum bits size of integer types of packed-bits */ /* mask list for packed bits */ -unsigned long long packed_mask[PACKED_BITS_MAX]; /* packed bits are restricted to 8*sizeof(llong) bytes */ +unsigned long long packed_mask[PACKED_BITS_MAX]; /* packed bits are restricted to 8*sizeof(llong) bytes */ /* packed bits display parameters */ unsigned packed_offset[PACKED_BITS_MAX]; @@ -94,16 +99,17 @@ unsigned packed_length[PACKED_BITS_MAX]; const dump_functions *dump_function_table; #ifdef __cplusplus -"C" { +"C" +{ #endif -void add_prefix(char **prfx, size_t *prfx_len, const char *name); -hid_t h5_fileaccess(void); -ssize_t table_list_add(hid_t oid, unsigned long file_no); -ssize_t table_list_visited(unsigned long file_no); + void add_prefix(char **prfx, size_t *prfx_len, const char *name); + hid_t h5_fileaccess(void); + ssize_t table_list_add(hid_t oid, unsigned long file_no); + ssize_t table_list_visited(unsigned long file_no); #ifdef __cplusplus } #endif -#endif /* !H5DUMP_H__ */ +#endif /* H5DUMP_H */ diff --git a/tools/src/h5dump/h5dump_ddl.c b/tools/src/h5dump/h5dump_ddl.c index d7c7b1a..b0bce0c 100644 --- a/tools/src/h5dump/h5dump_ddl.c +++ b/tools/src/h5dump/h5dump_ddl.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -21,18 +21,18 @@ #include "h5dump_ddl.h" typedef struct { - hid_t fid; /* File ID being traversed */ - const char *op_name; /* Object name wanted */ + hid_t fid; /* File ID being traversed */ + const char *op_name; /* Object name wanted */ } trav_handle_udata_t; typedef struct { - const char *path; /* Path of object being searched */ - const char *op_name; /* Object name wanted */ + const char *path; /* Path of object being searched */ + const char *op_name; /* Object name wanted */ } trav_attr_udata_t; /* callback function used by H5Literate() */ -static herr_t dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void *op_data); -static int dump_extlink(hid_t group, const char *linkname, const char *objname); +static herr_t dump_all_cb(hid_t group, const char *name, const H5L_info2_t *linfo, void *op_data); +static int dump_extlink(hid_t group, const char *linkname, const char *objname); /*------------------------------------------------------------------------- * Function: dump_datatype @@ -41,22 +41,17 @@ static int dump_extlink(hid_t group, const char *linkname, const char *objn * atomic datatype or committed/transient datatype. * * Return: void - * - * Programmer: Ruey-Hsia Li - * - * Modifications: - * *------------------------------------------------------------------------- */ void dump_datatype(hid_t type) { - h5tools_context_t ctx; /* print context */ - h5tool_format_t *outputformat = &h5tools_dataformat; + h5tools_context_t ctx; /* print context */ + h5tool_format_t * outputformat = &h5tools_dataformat; HDmemset(&ctx, 0, sizeof(ctx)); ctx.indent_level = dump_indent / COL; - ctx.cur_column = dump_indent; + ctx.cur_column = dump_indent; h5dump_type_table = type_table; h5tools_dump_datatype(rawoutstream, outputformat, &ctx, type); @@ -70,84 +65,74 @@ dump_datatype(hid_t type) * array, or others. * * Return: void - * - * Programmer: Ruey-Hsia Li - * - * Modifications: - * *------------------------------------------------------------------------- */ void dump_dataspace(hid_t space) { - h5tools_context_t ctx; /* print context */ - h5tool_format_t *outputformat = &h5tools_dataformat; + h5tools_context_t ctx; /* print context */ + h5tool_format_t * outputformat = &h5tools_dataformat; HDmemset(&ctx, 0, sizeof(ctx)); ctx.indent_level = dump_indent / COL; - ctx.cur_column = dump_indent; + ctx.cur_column = dump_indent; h5tools_dump_dataspace(rawoutstream, outputformat, &ctx, space); } - /*------------------------------------------------------------------------- * Function: dump_attr_cb * * Purpose: attribute function callback called by H5Aiterate2, displays the attribute * * Return: Success: SUCCEED - * * Failure: FAIL - * - * Programmer: Ruey-Hsia Li - * - * Modifications: Pedro Vicente, October 4, 2007 - * Added H5A_info_t parameter to conform with H5Aiterate2 - * *------------------------------------------------------------------------- */ herr_t -dump_attr_cb(hid_t oid, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED *info, void H5_ATTR_UNUSED *_op_data) +dump_attr_cb(hid_t oid, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED *info, + void H5_ATTR_UNUSED *_op_data) { - h5tools_context_t ctx; /* print context */ - h5tool_format_t *outputformat = &h5tools_dataformat; + h5tools_context_t ctx; /* print context */ + h5tool_format_t * outputformat = &h5tools_dataformat; h5tool_format_t string_dataformat; - hid_t attr_id; - herr_t ret = SUCCEED; + hid_t attr_id; + herr_t ret = SUCCEED; HDmemset(&ctx, 0, sizeof(ctx)); - ctx.indent_level = dump_indent / COL; - ctx.cur_column = dump_indent; + ctx.indent_level = dump_indent / COL; + ctx.cur_column = dump_indent; + ctx.display_index = dump_opts.display_ai; + ctx.display_char = dump_opts.display_char; - attr_id = H5Aopen(oid, attr_name, H5P_DEFAULT); - oid_output = display_oid; - data_output = display_data; - attr_data_output = display_attr_data; + attr_id = H5Aopen(oid, attr_name, H5P_DEFAULT); + oid_output = dump_opts.display_oid; + data_output = dump_opts.display_data; + attr_data_output = dump_opts.display_attr_data; string_dataformat = *outputformat; if (fp_format) { string_dataformat.fmt_double = fp_format; - string_dataformat.fmt_float = fp_format; + string_dataformat.fmt_float = fp_format; } if (h5tools_nCols == 0) { - string_dataformat.line_ncols = 65535; + string_dataformat.line_ncols = 65535; string_dataformat.line_per_line = 1; } else string_dataformat.line_ncols = h5tools_nCols; - string_dataformat.do_escape = display_escape; - outputformat = &string_dataformat; + string_dataformat.do_escape = dump_opts.display_escape; + outputformat = &string_dataformat; h5dump_type_table = type_table; - h5tools_dump_attribute(rawoutstream, outputformat, &ctx, attr_name, attr_id, display_ai, display_char); + h5tools_dump_attribute(rawoutstream, outputformat, &ctx, attr_name, attr_id); h5dump_type_table = NULL; - if(attr_id < 0) { + if (attr_id < 0) { h5tools_setstatus(EXIT_FAILURE); ret = FAIL; } @@ -155,7 +140,6 @@ dump_attr_cb(hid_t oid, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED * return ret; } - /*------------------------------------------------------------------------- * Function: dump_all_cb * @@ -163,60 +147,49 @@ dump_attr_cb(hid_t oid, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED * * displays everything in the specified object * * Return: Success: SUCCEED - * * Failure: FAIL - * - * Programmer: Ruey-Hsia Li - * - * Modifications: - * RMcG, November 2000 - * Added XML support. Also, optionally checks the op_data argument - * - * PVN, May 2008 - * Dump external links - * *------------------------------------------------------------------------- */ static herr_t -dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void H5_ATTR_UNUSED *op_data) +dump_all_cb(hid_t group, const char *name, const H5L_info2_t *linfo, void H5_ATTR_UNUSED *op_data) { - hid_t obj; - hid_t dapl_id = H5P_DEFAULT; /* dataset access property list ID */ - herr_t ret = SUCCEED; - char *obj_path = NULL; /* Full path of object */ - h5tools_str_t buffer; /* string into which to render */ - h5tools_context_t ctx; /* print context */ - h5tool_format_t *outputformat = &h5tools_dataformat; + hid_t obj; + hid_t dapl_id = H5P_DEFAULT; /* dataset access property list ID */ + herr_t ret = SUCCEED; + char * obj_path = NULL; /* Full path of object */ + h5tools_str_t buffer; /* string into which to render */ + h5tools_context_t ctx; /* print context */ + h5tool_format_t * outputformat = &h5tools_dataformat; h5tool_format_t string_dataformat; - hsize_t curr_pos = 0; /* total data element position */ + hsize_t curr_pos = 0; /* total data element position */ /* setup */ HDmemset(&buffer, 0, sizeof(h5tools_str_t)); HDmemset(&ctx, 0, sizeof(ctx)); ctx.indent_level = dump_indent / COL; - ctx.cur_column = dump_indent; + ctx.cur_column = dump_indent; string_dataformat = *outputformat; if (fp_format) { string_dataformat.fmt_double = fp_format; - string_dataformat.fmt_float = fp_format; + string_dataformat.fmt_float = fp_format; } if (h5tools_nCols == 0) { - string_dataformat.line_ncols = 65535; + string_dataformat.line_ncols = 65535; string_dataformat.line_per_line = 1; } else string_dataformat.line_ncols = h5tools_nCols; - string_dataformat.do_escape = display_escape; - outputformat = &string_dataformat; + string_dataformat.do_escape = dump_opts.display_escape; + outputformat = &string_dataformat; /* Build the object's path name */ obj_path = (char *)HDmalloc(HDstrlen(prefix) + HDstrlen(name) + 2); - if(!obj_path) { + if (!obj_path) { ret = FAIL; goto done; } @@ -225,355 +198,369 @@ dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void H5_ATTR HDstrcat(obj_path, "/"); HDstrcat(obj_path, name); - if(linfo->type == H5L_TYPE_HARD) { - H5O_info_t oinfo; + if (linfo->type == H5L_TYPE_HARD) { + H5O_info2_t oinfo; /* Stat the object */ - if(H5Oget_info_by_name2(group, name, &oinfo, H5O_INFO_BASIC, H5P_DEFAULT) < 0) { + if (H5Oget_info_by_name3(group, name, &oinfo, H5O_INFO_BASIC, H5P_DEFAULT) < 0) { error_msg("unable to get object information for \"%s\"\n", name); h5tools_setstatus(EXIT_FAILURE); ret = FAIL; goto done; } /* end if */ - switch(oinfo.type) { - case H5O_TYPE_GROUP: - if((obj = H5Gopen2(group, name, H5P_DEFAULT)) < 0) { - error_msg("unable to dump group \"%s\"\n", name); - h5tools_setstatus(EXIT_FAILURE); - ret = FAIL; - } - else { - char *old_prefix; /* Pointer to previous prefix */ + switch (oinfo.type) { + case H5O_TYPE_GROUP: + if ((obj = H5Gopen2(group, name, H5P_DEFAULT)) < 0) { + error_msg("unable to dump group \"%s\"\n", name); + h5tools_setstatus(EXIT_FAILURE); + ret = FAIL; + } + else { + char *old_prefix; /* Pointer to previous prefix */ - /* Keep copy of prefix before iterating into group */ - old_prefix = HDstrdup(prefix); - if (old_prefix) { - /* Append group name to prefix */ - add_prefix(&prefix, &prefix_len, name); + /* Keep copy of prefix before iterating into group */ + old_prefix = HDstrdup(prefix); + if (old_prefix) { + /* Append group name to prefix */ + add_prefix(&prefix, &prefix_len, name); - /* Iterate into group */ - dump_function_table->dump_group_function(obj, name); + /* Iterate into group */ + dump_function_table->dump_group_function(obj, name); - /* Restore old prefix name */ - HDstrcpy(prefix, old_prefix); - HDfree(old_prefix); - } - else - error_msg("warning: null prefix\n"); + /* Restore old prefix name */ + HDstrcpy(prefix, old_prefix); + HDfree(old_prefix); + } + else + error_msg("warning: null prefix\n"); - /* Close group */ - H5Gclose(obj); - } - break; + /* Close group */ + H5Gclose(obj); + } + break; - case H5O_TYPE_DATASET: - if(display_data) { - if ((dapl_id = H5Pcreate(H5P_DATASET_ACCESS)) < 0) { - error_msg("error in creating default access property list ID\n"); + case H5O_TYPE_DATASET: + if (dump_opts.display_data) { + if ((dapl_id = H5Pcreate(H5P_DATASET_ACCESS)) < 0) { + error_msg("error in creating default access property list ID\n"); + } + if (dump_opts.display_vds_first) { + if (H5Pset_virtual_view(dapl_id, H5D_VDS_FIRST_MISSING) < 0) + error_msg("error in setting access property list ID, virtual_view\n"); + } + if (dump_opts.vds_gap_size > 0) { + if (H5Pset_virtual_printf_gap(dapl_id, (hsize_t)dump_opts.vds_gap_size) < 0) + error_msg("error in setting access property list ID, virtual_printf_gap\n"); + } } - if (display_vds_first) { - if(H5Pset_virtual_view(dapl_id, H5D_VDS_FIRST_MISSING) < 0) - error_msg("error in setting access property list ID, virtual_view\n"); + if ((obj = H5Dopen2(group, name, dapl_id)) >= 0) { + if (oinfo.rc > 1 || hit_elink) { + obj_t *found_obj; /* Found object */ + + found_obj = search_obj(dset_table, &oinfo.token); + + if (found_obj == NULL) { + ctx.indent_level++; + + ctx.need_prefix = TRUE; + + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "%s \"%s\" %s", + h5tools_dump_header_format->datasetbegin, name, + h5tools_dump_header_format->datasetblockbegin); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + + error_msg("internal error (file %s:line %d)\n", __FILE__, __LINE__); + + ctx.need_prefix = TRUE; + + /* Render the element */ + h5tools_str_reset(&buffer); + if (HDstrlen(h5tools_dump_header_format->datasetblockend)) { + h5tools_str_append(&buffer, "%s", + h5tools_dump_header_format->datasetblockend); + if (HDstrlen(h5tools_dump_header_format->datasetend)) + h5tools_str_append(&buffer, " "); + } + if (HDstrlen(h5tools_dump_header_format->datasetend)) + h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->datasetend); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + + ctx.indent_level--; + + h5tools_setstatus(EXIT_FAILURE); + ret = FAIL; + if (dapl_id != H5P_DEFAULT) + H5Pclose(dapl_id); + H5Dclose(obj); + goto done; + } + else if (found_obj->displayed) { + ctx.need_prefix = TRUE; + + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "%s \"%s\" %s", + h5tools_dump_header_format->datasetbegin, name, + h5tools_dump_header_format->datasetblockbegin); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + + ctx.indent_level++; + + ctx.need_prefix = TRUE; + + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "%s \"%s\"", HARDLINK, found_obj->objname); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + + ctx.indent_level--; + + ctx.need_prefix = TRUE; + + /* Render the element */ + h5tools_str_reset(&buffer); + if (HDstrlen(h5tools_dump_header_format->datasetblockend)) { + h5tools_str_append(&buffer, "%s", + h5tools_dump_header_format->datasetblockend); + if (HDstrlen(h5tools_dump_header_format->datasetend)) + h5tools_str_append(&buffer, " "); + } + if (HDstrlen(h5tools_dump_header_format->datasetend)) + h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->datasetend); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + + if (dapl_id != H5P_DEFAULT) + H5Pclose(dapl_id); + H5Dclose(obj); + goto done; + } + else { + found_obj->displayed = TRUE; + } + } /* end if */ + + dump_function_table->dump_dataset_function(obj, name, NULL); + if (dapl_id != H5P_DEFAULT) + H5Pclose(dapl_id); + H5Dclose(obj); } - if (vds_gap_size > 0) { - if(H5Pset_virtual_printf_gap(dapl_id, (hsize_t)vds_gap_size) < 0) - error_msg("error in setting access property list ID, virtual_printf_gap\n"); + else { + if (dapl_id != H5P_DEFAULT) + H5Pclose(dapl_id); + error_msg("unable to dump dataset \"%s\"\n", name); + h5tools_setstatus(EXIT_FAILURE); + ret = FAIL; } - } - if((obj = H5Dopen2(group, name, dapl_id)) >= 0) { - if(oinfo.rc > 1 || hit_elink) { - obj_t *found_obj; /* Found object */ - - found_obj = search_obj(dset_table, oinfo.addr); - - if(found_obj == NULL) { - ctx.indent_level++; - - ctx.need_prefix = TRUE; + break; - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "%s \"%s\" %s", - h5tools_dump_header_format->datasetbegin, name, - h5tools_dump_header_format->datasetblockbegin); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + case H5O_TYPE_NAMED_DATATYPE: + if ((obj = H5Topen2(group, name, H5P_DEFAULT)) < 0) { + error_msg("unable to dump datatype \"%s\"\n", name); + h5tools_setstatus(EXIT_FAILURE); + ret = FAIL; + } + else { + dump_function_table->dump_named_datatype_function(obj, name); + H5Tclose(obj); + } + break; - error_msg("internal error (file %s:line %d)\n", __FILE__, __LINE__); + case H5O_TYPE_MAP: + case H5O_TYPE_UNKNOWN: + case H5O_TYPE_NTYPES: + default: + error_msg("unknown object \"%s\"\n", name); + h5tools_setstatus(EXIT_FAILURE); + ret = FAIL; + } + } /* end if */ + else { + char *targbuf; - ctx.need_prefix = TRUE; + switch (linfo->type) { + case H5L_TYPE_SOFT: + if ((targbuf = (char *)HDmalloc(linfo->u.val_size)) == NULL) { + error_msg("unable to allocate buffer\n"); + h5tools_setstatus(EXIT_FAILURE); + ret = FAIL; + } + else { + ctx.need_prefix = TRUE; - /* Render the element */ - h5tools_str_reset(&buffer); - if(HDstrlen(h5tools_dump_header_format->datasetblockend)) { - h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->datasetblockend); - if(HDstrlen(h5tools_dump_header_format->datasetend)) - h5tools_str_append(&buffer, " "); - } - if(HDstrlen(h5tools_dump_header_format->datasetend)) - h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->datasetend); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "%s \"%s\" %s", h5tools_dump_header_format->softlinkbegin, + name, h5tools_dump_header_format->softlinkblockbegin); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - ctx.indent_level--; + ctx.indent_level++; + if (H5Lget_val(group, name, targbuf, linfo->u.val_size, H5P_DEFAULT) < 0) { + error_msg("unable to get link value\n"); h5tools_setstatus(EXIT_FAILURE); ret = FAIL; - if (dapl_id != H5P_DEFAULT) - H5Pclose(dapl_id); - H5Dclose(obj); - goto done; } - else if(found_obj->displayed) { - ctx.need_prefix = TRUE; - - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "%s \"%s\" %s", - h5tools_dump_header_format->datasetbegin, name, - h5tools_dump_header_format->datasetblockbegin); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - - ctx.indent_level++; - - ctx.need_prefix = TRUE; - - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "%s \"%s\"", HARDLINK, found_obj->objname); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - - ctx.indent_level--; - + else { + /* print the value of a soft link */ + /* Standard DDL: no modification */ ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - if(HDstrlen(h5tools_dump_header_format->datasetblockend)) { - h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->datasetblockend); - if(HDstrlen(h5tools_dump_header_format->datasetend)) - h5tools_str_append(&buffer, " "); - } - if(HDstrlen(h5tools_dump_header_format->datasetend)) - h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->datasetend); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - - if (dapl_id != H5P_DEFAULT) - H5Pclose(dapl_id); - H5Dclose(obj); - goto done; + h5tools_str_append(&buffer, "LINKTARGET \"%s\"", targbuf); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); } - else { - found_obj->displayed = TRUE; - } - } /* end if */ - - dump_function_table->dump_dataset_function(obj, name, NULL); - if (dapl_id != H5P_DEFAULT) - H5Pclose(dapl_id); - H5Dclose(obj); - } - else { - if (dapl_id != H5P_DEFAULT) - H5Pclose(dapl_id); - error_msg("unable to dump dataset \"%s\"\n", name); - h5tools_setstatus(EXIT_FAILURE); - ret = FAIL; - } - break; - - case H5O_TYPE_NAMED_DATATYPE: - if((obj = H5Topen2(group, name, H5P_DEFAULT)) < 0) { - error_msg("unable to dump datatype \"%s\"\n", name); - h5tools_setstatus(EXIT_FAILURE); - ret = FAIL; - } - else { - dump_function_table->dump_named_datatype_function(obj, name); - H5Tclose(obj); - } - break; - case H5O_TYPE_MAP: - case H5O_TYPE_UNKNOWN: - case H5O_TYPE_NTYPES: - default: - error_msg("unknown object \"%s\"\n", name); - h5tools_setstatus(EXIT_FAILURE); - ret = FAIL; - } - } /* end if */ - else { - char *targbuf; + ctx.indent_level--; - switch(linfo->type) { - case H5L_TYPE_SOFT: - if((targbuf = (char *)HDmalloc(linfo->u.val_size)) == NULL) { - error_msg("unable to allocate buffer\n"); - h5tools_setstatus(EXIT_FAILURE); - ret = FAIL; - } - else { - ctx.need_prefix = TRUE; + ctx.need_prefix = TRUE; - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "%s \"%s\" %s", - h5tools_dump_header_format->softlinkbegin, name, - h5tools_dump_header_format->softlinkblockbegin); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + /* Render the element */ + h5tools_str_reset(&buffer); + if (HDstrlen(h5tools_dump_header_format->softlinkblockend)) { + h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->softlinkblockend); + if (HDstrlen(h5tools_dump_header_format->softlinkend)) + h5tools_str_append(&buffer, " "); + } + if (HDstrlen(h5tools_dump_header_format->softlinkend)) + h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->softlinkend); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - ctx.indent_level++; + HDfree(targbuf); + } + break; - if(H5Lget_val(group, name, targbuf, linfo->u.val_size, H5P_DEFAULT) < 0) { - error_msg("unable to get link value\n"); + case H5L_TYPE_EXTERNAL: + if ((targbuf = (char *)HDmalloc(linfo->u.val_size)) == NULL) { + error_msg("unable to allocate buffer\n"); h5tools_setstatus(EXIT_FAILURE); ret = FAIL; } else { - /* print the value of a soft link */ - /* Standard DDL: no modification */ ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "LINKTARGET \"%s\"", targbuf); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - } + h5tools_str_append(&buffer, "%s \"%s\" %s", h5tools_dump_header_format->extlinkbegin, + name, h5tools_dump_header_format->extlinkblockbegin); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - ctx.indent_level--; + if (H5Lget_val(group, name, targbuf, linfo->u.val_size, H5P_DEFAULT) < 0) { + indentation(dump_indent); + error_msg("unable to get external link value\n"); + h5tools_setstatus(EXIT_FAILURE); + ret = FAIL; + } /* end if */ + else { + const char *filename; + const char *targname; + + if (H5Lunpack_elink_val(targbuf, linfo->u.val_size, NULL, &filename, &targname) < 0) { + indentation(dump_indent); + error_msg("unable to unpack external link value\n"); + h5tools_setstatus(EXIT_FAILURE); + ret = FAIL; + } /* end if */ + else { + ctx.indent_level++; + + ctx.need_prefix = TRUE; + + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "TARGETFILE \"%s\"", filename); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + + ctx.need_prefix = TRUE; + + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "TARGETPATH \"%s\"", targname); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + + /* dump the external link */ + dump_extlink(group, name, targname); + ctx.indent_level--; + } /* end else */ + } /* end else */ + ctx.need_prefix = TRUE; - ctx.need_prefix = TRUE; + /* Render the element */ + h5tools_str_reset(&buffer); + if (HDstrlen(h5tools_dump_header_format->extlinkblockend)) { + h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->extlinkblockend); + if (HDstrlen(h5tools_dump_header_format->extlinkend)) + h5tools_str_append(&buffer, " "); + } + if (HDstrlen(h5tools_dump_header_format->extlinkend)) + h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->extlinkend); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - /* Render the element */ - h5tools_str_reset(&buffer); - if(HDstrlen(h5tools_dump_header_format->softlinkblockend)) { - h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->softlinkblockend); - if(HDstrlen(h5tools_dump_header_format->softlinkend)) - h5tools_str_append(&buffer, " "); + HDfree(targbuf); } - if(HDstrlen(h5tools_dump_header_format->softlinkend)) - h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->softlinkend); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - - HDfree(targbuf); - } - break; + break; - case H5L_TYPE_EXTERNAL: - if((targbuf = (char *)HDmalloc(linfo->u.val_size)) == NULL) { - error_msg("unable to allocate buffer\n"); - h5tools_setstatus(EXIT_FAILURE); - ret = FAIL; - } - else { + case H5L_TYPE_ERROR: + case H5L_TYPE_MAX: + case H5L_TYPE_HARD: + default: ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "%s \"%s\" %s", - h5tools_dump_header_format->extlinkbegin, name, - h5tools_dump_header_format->extlinkblockbegin); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - - if(H5Lget_val(group, name, targbuf, linfo->u.val_size, H5P_DEFAULT) < 0) { - indentation(dump_indent); - error_msg("unable to get external link value\n"); - h5tools_setstatus(EXIT_FAILURE); - ret = FAIL; - } /* end if */ - else { - const char *filename; - const char *targname; - - if(H5Lunpack_elink_val(targbuf, linfo->u.val_size, NULL, &filename, &targname) < 0) { - indentation(dump_indent); - error_msg("unable to unpack external link value\n"); - h5tools_setstatus(EXIT_FAILURE); - ret = FAIL; - } /* end if */ - else { - ctx.indent_level++; + h5tools_str_append(&buffer, "%s \"%s\" %s", h5tools_dump_header_format->udlinkbegin, name, + h5tools_dump_header_format->udlinkblockbegin); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - ctx.need_prefix = TRUE; + ctx.indent_level++; - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "TARGETFILE \"%s\"", filename); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + ctx.need_prefix = TRUE; + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "LINKCLASS %d", linfo->type); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - ctx.need_prefix = TRUE; + ctx.indent_level--; - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "TARGETPATH \"%s\"", targname); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - - /* dump the external link */ - dump_extlink(group, name, targname); - ctx.indent_level--; - } /* end else */ - } /* end else */ ctx.need_prefix = TRUE; - /* Render the element */ h5tools_str_reset(&buffer); - if(HDstrlen(h5tools_dump_header_format->extlinkblockend)) { - h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->extlinkblockend); - if(HDstrlen(h5tools_dump_header_format->extlinkend)) + if (HDstrlen(h5tools_dump_header_format->udlinkblockend)) { + h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->udlinkblockend); + if (HDstrlen(h5tools_dump_header_format->udlinkend)) h5tools_str_append(&buffer, " "); } - if(HDstrlen(h5tools_dump_header_format->extlinkend)) - h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->extlinkend); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - - HDfree(targbuf); - } - break; - - case H5L_TYPE_ERROR: - case H5L_TYPE_MAX: - case H5L_TYPE_HARD: - default: - ctx.need_prefix = TRUE; - - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "%s \"%s\" %s", - h5tools_dump_header_format->udlinkbegin, name, - h5tools_dump_header_format->udlinkblockbegin); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - - ctx.indent_level++; - - ctx.need_prefix = TRUE; - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "LINKCLASS %d", linfo->type); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - - ctx.indent_level--; - - ctx.need_prefix = TRUE; - /* Render the element */ - h5tools_str_reset(&buffer); - if(HDstrlen(h5tools_dump_header_format->udlinkblockend)) { - h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->udlinkblockend); - if(HDstrlen(h5tools_dump_header_format->udlinkend)) - h5tools_str_append(&buffer, " "); - } - if(HDstrlen(h5tools_dump_header_format->udlinkend)) - h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->udlinkend); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + if (HDstrlen(h5tools_dump_header_format->udlinkend)) + h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->udlinkend); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - break; + break; } /* end switch */ - } /* end else */ + } /* end else */ done: h5tools_str_close(&buffer); - if(obj_path) + if (obj_path) HDfree(obj_path); return ret; } @@ -584,7 +571,6 @@ done: * Purpose: Iterate and display attributes within the specified group * * Return: void - * *------------------------------------------------------------------------- */ void @@ -592,19 +578,19 @@ attr_iteration(hid_t gid, unsigned attr_crt_order_flags) { /* attribute iteration: if there is a request to do H5_INDEX_CRT_ORDER and tracking order is set in the group for attributes, then, sort by creation order, otherwise by name */ - if(include_attrs) { - if((sort_by == H5_INDEX_CRT_ORDER) && (attr_crt_order_flags & H5P_CRT_ORDER_TRACKED)) { - if(H5Aiterate2(gid, sort_by, sort_order, NULL, dump_attr_cb, NULL) < 0) { + if (dump_opts.include_attrs) { + if ((sort_by == H5_INDEX_CRT_ORDER) && (attr_crt_order_flags & H5P_CRT_ORDER_TRACKED)) { + if (H5Aiterate2(gid, sort_by, sort_order, NULL, dump_attr_cb, NULL) < 0) { error_msg("error getting attribute information\n"); h5tools_setstatus(EXIT_FAILURE); } /* end if */ - } /* end if */ + } /* end if */ else { - if(H5Aiterate2(gid, H5_INDEX_NAME, sort_order, NULL, dump_attr_cb, NULL) < 0) { + if (H5Aiterate2(gid, H5_INDEX_NAME, sort_order, NULL, dump_attr_cb, NULL) < 0) { error_msg("error getting attribute information\n"); h5tools_setstatus(EXIT_FAILURE); } /* end if */ - } /* end else */ + } /* end else */ } } @@ -614,7 +600,6 @@ attr_iteration(hid_t gid, unsigned attr_crt_order_flags) * Purpose: Iterate and display links within the specified group * * Return: void - * *------------------------------------------------------------------------- */ void @@ -623,10 +608,10 @@ link_iteration(hid_t gid, unsigned crt_order_flags) /* if there is a request to do H5_INDEX_CRT_ORDER and tracking order is set in the group, then, sort by creation order, otherwise by name */ - if((sort_by == H5_INDEX_CRT_ORDER) && (crt_order_flags & H5P_CRT_ORDER_TRACKED)) - H5Literate(gid, sort_by, sort_order, NULL, dump_all_cb, NULL); + if ((sort_by == H5_INDEX_CRT_ORDER) && (crt_order_flags & H5P_CRT_ORDER_TRACKED)) + H5Literate2(gid, sort_by, sort_order, NULL, dump_all_cb, NULL); else - H5Literate(gid, H5_INDEX_NAME, sort_order, NULL, dump_all_cb, NULL); + H5Literate2(gid, H5_INDEX_NAME, sort_order, NULL, dump_all_cb, NULL); } /*------------------------------------------------------------------------- @@ -635,27 +620,18 @@ link_iteration(hid_t gid, unsigned crt_order_flags) * Purpose: Dump named datatype * * Return: void - * - * Programmer: Ruey-Hsia Li - * - * Modifications: - * Pedro Vicente, March 27, 2006 - * added display of attributes - * Pedro Vicente, October 4, 2007, added parameters to H5Aiterate2() to allow for - * other iteration orders - * *------------------------------------------------------------------------- */ void dump_named_datatype(hid_t tid, const char *name) { - H5O_info_t oinfo; + H5O_info2_t oinfo; unsigned attr_crt_order_flags; - hid_t tcpl_id = -1; /* datatype creation property list ID */ - hsize_t curr_pos = 0; /* total data element position */ - h5tools_str_t buffer; /* string into which to render */ - h5tools_context_t ctx; /* print context */ - h5tool_format_t *outputformat = &h5tools_dataformat; + hid_t tcpl_id = H5I_INVALID_HID; /* datatype creation property list ID */ + hsize_t curr_pos = 0; /* total data element position */ + h5tools_str_t buffer; /* string into which to render */ + h5tools_context_t ctx; /* print context */ + h5tool_format_t * outputformat = &h5tools_dataformat; h5tool_format_t string_dataformat; /* setup */ @@ -663,24 +639,24 @@ dump_named_datatype(hid_t tid, const char *name) HDmemset(&ctx, 0, sizeof(ctx)); ctx.indent_level = dump_indent / COL; - ctx.cur_column = dump_indent; + ctx.cur_column = dump_indent; string_dataformat = *outputformat; if (fp_format) { string_dataformat.fmt_double = fp_format; - string_dataformat.fmt_float = fp_format; + string_dataformat.fmt_float = fp_format; } if (h5tools_nCols == 0) { - string_dataformat.line_ncols = 65535; + string_dataformat.line_ncols = 65535; string_dataformat.line_per_line = 1; } else string_dataformat.line_ncols = h5tools_nCols; - string_dataformat.do_escape = display_escape; - outputformat = &string_dataformat; + string_dataformat.do_escape = dump_opts.display_escape; + outputformat = &string_dataformat; if ((tcpl_id = H5Tget_create_plist(tid)) < 0) { error_msg("error in getting creation property list ID\n"); @@ -693,7 +669,7 @@ dump_named_datatype(hid_t tid, const char *name) h5tools_setstatus(EXIT_FAILURE); } - if(H5Pclose(tcpl_id) < 0) { + if (H5Pclose(tcpl_id) < 0) { error_msg("error in closing creation property list ID\n"); h5tools_setstatus(EXIT_FAILURE); } @@ -702,20 +678,20 @@ dump_named_datatype(hid_t tid, const char *name) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "%s \"%s\" %s", - h5tools_dump_header_format->datatypebegin, name, - h5tools_dump_header_format->datatypeblockbegin); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "%s \"%s\" %s", h5tools_dump_header_format->datatypebegin, name, + h5tools_dump_header_format->datatypeblockbegin); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - H5Oget_info2(tid, &oinfo, H5O_INFO_BASIC); + H5Oget_info3(tid, &oinfo, H5O_INFO_BASIC); /* Must check for uniqueness of all objects if we've traversed an elink, * otherwise only check if the reference count > 1. */ - if(oinfo.rc > 1 || hit_elink) { - obj_t *found_obj; /* Found object */ + if (oinfo.rc > 1 || hit_elink) { + obj_t *found_obj; /* Found object */ - found_obj = search_obj(type_table, oinfo.addr); + found_obj = search_obj(type_table, &oinfo.token); if (found_obj == NULL) { error_msg("internal error (file %s:line %d)\n", __FILE__, __LINE__); @@ -726,7 +702,8 @@ dump_named_datatype(hid_t tid, const char *name) /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "%s \"%s\"", HARDLINK, found_obj->objname); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); goto done; } else @@ -737,11 +714,12 @@ dump_named_datatype(hid_t tid, const char *name) h5tools_str_reset(&buffer); h5tools_print_datatype(rawoutstream, &buffer, outputformat, &ctx, tid, FALSE); - if(H5Tget_class(tid) != H5T_COMPOUND) { + if (H5Tget_class(tid) != H5T_COMPOUND) { h5tools_str_append(&buffer, ";"); } - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); /* print attributes */ dump_indent += COL; @@ -753,14 +731,15 @@ dump_named_datatype(hid_t tid, const char *name) done: /* Render the element */ h5tools_str_reset(&buffer); - if(HDstrlen(h5tools_dump_header_format->datatypeblockend)) { + if (HDstrlen(h5tools_dump_header_format->datatypeblockend)) { h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->datatypeblockend); - if(HDstrlen(h5tools_dump_header_format->datatypeend)) + if (HDstrlen(h5tools_dump_header_format->datatypeend)) h5tools_str_append(&buffer, " "); } - if(HDstrlen(h5tools_dump_header_format->datatypeend)) + if (HDstrlen(h5tools_dump_header_format->datatypeend)) h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->datatypeend); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); h5tools_str_close(&buffer); } @@ -771,33 +750,23 @@ done: * Purpose: Dump everything within the specified group * * Return: void - * - * Programmer: Ruey-Hsia Li - * - * Modifications: - * - * Call to dump_all_cb -- add parameter to select everything. - * - * Pedro Vicente, October 1, 2007 - * handle several iteration orders for attributes and groups - * *------------------------------------------------------------------------- */ void dump_group(hid_t gid, const char *name) { - H5O_info_t oinfo; - hid_t dset; - hid_t type; - hid_t gcpl_id; - unsigned crt_order_flags; - unsigned attr_crt_order_flags; - char type_name[1024]; - h5tools_str_t buffer; /* string into which to render */ - h5tools_context_t ctx; /* print context */ - h5tool_format_t *outputformat = &h5tools_dataformat; + H5O_info2_t oinfo; + hid_t dset; + hid_t type; + hid_t gcpl_id; + unsigned crt_order_flags; + unsigned attr_crt_order_flags; + char type_name[1024]; + h5tools_str_t buffer; /* string into which to render */ + h5tools_context_t ctx; /* print context */ + h5tool_format_t * outputformat = &h5tools_dataformat; h5tool_format_t string_dataformat; - hsize_t curr_pos = 0; /* total data element position */ + hsize_t curr_pos = 0; /* total data element position */ if ((gcpl_id = H5Gget_create_plist(gid)) < 0) { error_msg("error in getting group creation property list ID\n"); @@ -811,12 +780,12 @@ dump_group(hid_t gid, const char *name) } /* query the group creation properties */ - if(H5Pget_link_creation_order(gcpl_id, &crt_order_flags) < 0) { + if (H5Pget_link_creation_order(gcpl_id, &crt_order_flags) < 0) { error_msg("error in getting group creation properties\n"); h5tools_setstatus(EXIT_FAILURE); } - if(H5Pclose(gcpl_id) < 0) { + if (H5Pclose(gcpl_id) < 0) { error_msg("error in closing group creation property list ID\n"); h5tools_setstatus(EXIT_FAILURE); } @@ -826,66 +795,72 @@ dump_group(hid_t gid, const char *name) HDmemset(&ctx, 0, sizeof(ctx)); ctx.indent_level = dump_indent / COL; - ctx.cur_column = dump_indent; + ctx.cur_column = dump_indent; string_dataformat = *outputformat; if (fp_format) { string_dataformat.fmt_double = fp_format; - string_dataformat.fmt_float = fp_format; + string_dataformat.fmt_float = fp_format; } if (h5tools_nCols == 0) { - string_dataformat.line_ncols = 65535; + string_dataformat.line_ncols = 65535; string_dataformat.line_per_line = 1; } else string_dataformat.line_ncols = h5tools_nCols; - string_dataformat.do_escape = display_escape; - outputformat = &string_dataformat; + string_dataformat.do_escape = dump_opts.display_escape; + outputformat = &string_dataformat; ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "%s \"%s\" %s", - h5tools_dump_header_format->groupbegin, name, - h5tools_dump_header_format->groupblockbegin); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "%s \"%s\" %s", h5tools_dump_header_format->groupbegin, name, + h5tools_dump_header_format->groupblockbegin); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level++; dump_indent += COL; - if(!HDstrcmp(name, "/") && unamedtype) { - unsigned u; /* Local index variable */ + if (!HDstrcmp(name, "/") && unamedtype) { + unsigned u; /* Local index variable */ + + /* dump unnamed type in root group */ + for (u = 0; u < type_table->nobjs; u++) + if (!type_table->objs[u].recorded) { + char *obj_tok_str = NULL; - /* dump unamed type in root group */ - for(u = 0; u < type_table->nobjs; u++) - if(!type_table->objs[u].recorded) { dset = H5Dopen2(gid, type_table->objs[u].objname, H5P_DEFAULT); type = H5Dget_type(dset); - HDsprintf(type_name, "#"H5_PRINTF_HADDR_FMT, type_table->objs[u].objno); + + H5Otoken_to_str(dset, &type_table->objs[u].obj_token, &obj_tok_str); + HDsnprintf(type_name, sizeof(type_name), "#%s", obj_tok_str); + H5free_memory(obj_tok_str); + dump_function_table->dump_named_datatype_function(type, type_name); H5Tclose(type); H5Dclose(dset); } } /* end if */ - if(display_oid) + if (dump_opts.display_oid) h5tools_dump_oid(rawoutstream, outputformat, &ctx, gid); h5tools_dump_comment(rawoutstream, outputformat, &ctx, gid); - H5Oget_info2(gid, &oinfo, H5O_INFO_BASIC); + H5Oget_info3(gid, &oinfo, H5O_INFO_BASIC); /* Must check for uniqueness of all objects if we've traversed an elink, * otherwise only check if the reference count > 1. */ - if(oinfo.rc > 1 || hit_elink) { - obj_t *found_obj; /* Found object */ + if (oinfo.rc > 1 || hit_elink) { + obj_t *found_obj; /* Found object */ - found_obj = search_obj(group_table, oinfo.addr); + found_obj = search_obj(group_table, &oinfo.token); if (found_obj == NULL) { error_msg("internal error (file %s:line %d)\n", __FILE__, __LINE__); @@ -897,7 +872,8 @@ dump_group(hid_t gid, const char *name) /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "%s \"%s\"", HARDLINK, found_obj->objname); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); } else { found_obj->displayed = TRUE; @@ -917,14 +893,15 @@ dump_group(hid_t gid, const char *name) /* Render the element */ h5tools_str_reset(&buffer); - if(HDstrlen(h5tools_dump_header_format->groupblockend)) { + if (HDstrlen(h5tools_dump_header_format->groupblockend)) { h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->groupblockend); - if(HDstrlen(h5tools_dump_header_format->groupend)) + if (HDstrlen(h5tools_dump_header_format->groupend)) h5tools_str_append(&buffer, " "); } - if(HDstrlen(h5tools_dump_header_format->groupend)) + if (HDstrlen(h5tools_dump_header_format->groupend)) h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->groupend); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); h5tools_str_close(&buffer); } @@ -935,48 +912,40 @@ dump_group(hid_t gid, const char *name) * Purpose: Dump the specified data set * * Return: void - * - * Programmer: Ruey-Hsia Li - * - * Modifications: - * Pedro Vicente, 2004, added dataset creation property list display - * Pedro Vicente, October 4, 2007, added parameters to H5Aiterate2() to allow for - * other iteration orders - * *------------------------------------------------------------------------- */ void dump_dataset(hid_t did, const char *name, struct subset_t *sset) { - h5tools_context_t ctx; /* print context */ - h5tool_format_t *outputformat = &h5tools_dataformat; + h5tools_context_t ctx; /* print context */ + h5tool_format_t * outputformat = &h5tools_dataformat; h5tool_format_t string_dataformat; - hid_t type, space; - unsigned attr_crt_order_flags; - hid_t dcpl_id; /* dataset creation property list ID */ - h5tools_str_t buffer; /* string into which to render */ - hsize_t curr_pos = 0; /* total data element position */ + hid_t type, space; + unsigned attr_crt_order_flags; + hid_t dcpl_id; /* dataset creation property list ID */ + h5tools_str_t buffer; /* string into which to render */ + hsize_t curr_pos = 0; /* total data element position */ HDmemset(&ctx, 0, sizeof(ctx)); ctx.indent_level = dump_indent / COL; - ctx.cur_column = dump_indent; + ctx.cur_column = dump_indent; string_dataformat = *outputformat; if (fp_format) { string_dataformat.fmt_double = fp_format; - string_dataformat.fmt_float = fp_format; + string_dataformat.fmt_float = fp_format; } if (h5tools_nCols == 0) { - string_dataformat.line_ncols = 65535; + string_dataformat.line_ncols = 65535; string_dataformat.line_per_line = 1; } else string_dataformat.line_ncols = h5tools_nCols; - string_dataformat.do_escape = display_escape; - outputformat = &string_dataformat; + string_dataformat.do_escape = dump_opts.display_escape; + outputformat = &string_dataformat; if ((dcpl_id = H5Dget_create_plist(did)) < 0) { error_msg("error in getting creation property list ID\n"); @@ -995,19 +964,19 @@ dump_dataset(hid_t did, const char *name, struct subset_t *sset) ctx.need_prefix = TRUE; h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); - /* Render the element */ + /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "%s \"%s\" %s", - h5tools_dump_header_format->datasetbegin, name, - h5tools_dump_header_format->datasetblockbegin); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "%s \"%s\" %s", h5tools_dump_header_format->datasetbegin, name, + h5tools_dump_header_format->datasetblockbegin); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); h5tools_dump_comment(rawoutstream, outputformat, &ctx, did); dump_indent += COL; ctx.indent_level++; - type = H5Dget_type(did); + type = H5Dget_type(did); h5dump_type_table = type_table; h5tools_dump_datatype(rawoutstream, outputformat, &ctx, type); h5dump_type_table = NULL; @@ -1016,71 +985,74 @@ dump_dataset(hid_t did, const char *name, struct subset_t *sset) h5tools_dump_dataspace(rawoutstream, outputformat, &ctx, space); H5Sclose(space); - if(display_oid) { + if (dump_opts.display_oid) { h5tools_dump_oid(rawoutstream, outputformat, &ctx, did); } - if(display_dcpl) { + if (dump_opts.display_dcpl) { h5dump_type_table = type_table; h5tools_dump_dcpl(rawoutstream, outputformat, &ctx, dcpl_id, type, did); h5dump_type_table = NULL; } H5Pclose(dcpl_id); - if(display_data) { - unsigned data_loop = 1; - unsigned u; + ctx.sset = sset; + ctx.display_index = dump_opts.display_ai; + ctx.display_char = dump_opts.display_char; + if (dump_opts.display_data) { + unsigned data_loop = 1; + unsigned u; - if(display_packed_bits) + if (dump_opts.display_packed_bits) data_loop = packed_bits_num; - for(u = 0; u < data_loop; u++) { - if(display_packed_bits) { + for (u = 0; u < data_loop; u++) { + if (dump_opts.display_packed_bits) { ctx.need_prefix = TRUE; h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); /* Render the element */ h5tools_str_reset(&buffer); - packed_data_mask = packed_mask[u]; + packed_data_mask = packed_mask[u]; packed_data_offset = packed_offset[u]; packed_data_length = packed_length[u]; h5tools_print_packed_bits(&buffer, type); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); } - switch(H5Tget_class(type)) { - case H5T_TIME: - ctx.indent_level++; - - ctx.need_prefix = TRUE; - h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "DATA{ not yet implemented.}"); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + switch (H5Tget_class(type)) { + case H5T_TIME: + ctx.indent_level++; - ctx.indent_level--; - break; + ctx.need_prefix = TRUE; + h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "DATA{ not yet implemented.}"); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - case H5T_INTEGER: - case H5T_FLOAT: - case H5T_STRING: - case H5T_BITFIELD: - case H5T_OPAQUE: - case H5T_COMPOUND: - case H5T_REFERENCE: - case H5T_ENUM: - case H5T_VLEN: - case H5T_ARRAY: - { - h5tools_dump_data(rawoutstream, outputformat, &ctx, did, TRUE, sset, display_ai, display_char); - } - break; + ctx.indent_level--; + break; - case H5T_NO_CLASS: - case H5T_NCLASSES: - default: - error_msg("invalid H5TCLASS type\n"); - break; + case H5T_INTEGER: + case H5T_FLOAT: + case H5T_STRING: + case H5T_BITFIELD: + case H5T_OPAQUE: + case H5T_COMPOUND: + case H5T_REFERENCE: + case H5T_ENUM: + case H5T_VLEN: + case H5T_ARRAY: { + h5tools_dump_data(rawoutstream, outputformat, &ctx, did, TRUE); + } break; + + case H5T_NO_CLASS: + case H5T_NCLASSES: + default: + error_msg("invalid H5TCLASS type\n"); + break; } /* end switch */ - } /* for(u=0; u<data_loop; u++) */ + } /* for(u=0; u<data_loop; u++) */ } H5Tclose(type); @@ -1095,14 +1067,15 @@ dump_dataset(hid_t did, const char *name, struct subset_t *sset) /* Render the element */ h5tools_str_reset(&buffer); - if(HDstrlen(h5tools_dump_header_format->datasetblockend)) { + if (HDstrlen(h5tools_dump_header_format->datasetblockend)) { h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->datasetblockend); - if(HDstrlen(h5tools_dump_header_format->datasetend)) + if (HDstrlen(h5tools_dump_header_format->datasetend)) h5tools_str_append(&buffer, " "); } - if(HDstrlen(h5tools_dump_header_format->datasetend)) + if (HDstrlen(h5tools_dump_header_format->datasetend)) h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->datasetend); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); h5tools_str_close(&buffer); } @@ -1113,20 +1086,13 @@ dump_dataset(hid_t did, const char *name, struct subset_t *sset) * Purpose: Dump attribute or dataset data * * Return: void - * - * Programmer: Ruey-Hsia Li - * - * Modifications: pvn, print the matrix indices - * Albert Cheng, 2004/11/18 - * Add --string printing for attributes too. - * *------------------------------------------------------------------------- */ void dump_data(hid_t obj_id, int obj_data, struct subset_t *sset, int display_index) { - h5tools_context_t ctx; /* print context */ - h5tool_format_t *outputformat = &h5tools_dataformat; + h5tools_context_t ctx; /* print context */ + h5tool_format_t * outputformat = &h5tools_dataformat; h5tool_format_t string_dataformat; int print_dataset = FALSE; @@ -1134,160 +1100,174 @@ dump_data(hid_t obj_id, int obj_data, struct subset_t *sset, int display_index) if (fp_format) { string_dataformat.fmt_double = fp_format; - string_dataformat.fmt_float = fp_format; + string_dataformat.fmt_float = fp_format; } if (h5tools_nCols == 0) { - string_dataformat.line_ncols = 65535; + string_dataformat.line_ncols = 65535; string_dataformat.line_per_line = 1; } else string_dataformat.line_ncols = h5tools_nCols; - string_dataformat.do_escape = display_escape; - outputformat = &string_dataformat; + string_dataformat.do_escape = dump_opts.display_escape; + outputformat = &string_dataformat; HDmemset(&ctx, 0, sizeof(ctx)); - ctx.indent_level = dump_indent / COL; - ctx.cur_column = dump_indent; + ctx.indent_level = dump_indent / COL; + ctx.cur_column = dump_indent; + ctx.sset = sset; + ctx.display_index = display_index; + ctx.display_char = dump_opts.display_char; - if(obj_data == DATASET_DATA) + if (obj_data == DATASET_DATA) print_dataset = TRUE; - h5tools_dump_data(rawoutstream, outputformat, &ctx, obj_id, print_dataset, sset, display_index, display_char); + h5tools_dump_data(rawoutstream, outputformat, &ctx, obj_id, print_dataset); } - /*------------------------------------------------------------------------- * Function: dump_fcpl * * Purpose: prints file creation property list information * * Return: void - * - * Programmer: pvn - * - * Modifications: - * *------------------------------------------------------------------------- */ void dump_fcpl(hid_t fid) { - hid_t fcpl; /* file creation property list ID */ - hsize_t userblock; /* userblock size retrieved from FCPL */ - size_t off_size; /* size of offsets in the file */ - size_t len_size; /* size of lengths in the file */ - H5F_fspace_strategy_t fs_strategy; /* file space strategy */ - hbool_t fs_persist; /* Persisting free-space or not */ - hsize_t fs_threshold; /* free-space section threshold */ - hsize_t fsp_size; /* file space page size */ - H5F_info2_t finfo; /* file information */ + hid_t fcpl; /* file creation property list ID */ + hsize_t userblock; /* userblock size retrieved from FCPL */ + size_t off_size; /* size of offsets in the file */ + size_t len_size; /* size of lengths in the file */ + H5F_fspace_strategy_t fs_strategy; /* file space strategy */ + hbool_t fs_persist; /* Persisting free-space or not */ + hsize_t fs_threshold; /* free-space section threshold */ + hsize_t fsp_size; /* file space page size */ + H5F_info2_t finfo; /* file information */ #ifdef SHOW_FILE_DRIVER - hid_t fapl; /* file access property list ID */ - hid_t fdriver; /* file driver */ - char dname[32]; /* buffer to store driver name */ + hid_t fapl; /* file access property list ID */ + hid_t fdriver; /* file driver */ + char dname[32]; /* buffer to store driver name */ #endif unsigned sym_lk; /* symbol table B-tree leaf 'K' value */ unsigned sym_ik; /* symbol table B-tree internal 'K' value */ unsigned istore_ik; /* indexed storage B-tree internal 'K' value */ - fcpl=H5Fget_create_plist(fid); + uint64_t supported = 0; + + /* Dumping the information here only makes sense for the native + * VOL connector. The only VOL call here is H5Fget_info(), so we'll + * use that as a proxy for "native-ness". If that isn't supported, we'll + * just return. + */ + H5VLquery_optional(fid, H5VL_SUBCLS_FILE, H5VL_NATIVE_FILE_GET_INFO, &supported); + + if (!(supported & H5VL_OPT_QUERY_SUPPORTED)) + return; + + fcpl = H5Fget_create_plist(fid); H5Fget_info2(fid, &finfo); - H5Pget_userblock(fcpl,&userblock); - H5Pget_sizes(fcpl,&off_size,&len_size); - H5Pget_sym_k(fcpl,&sym_ik,&sym_lk); - H5Pget_istore_k(fcpl,&istore_ik); + H5Pget_userblock(fcpl, &userblock); + H5Pget_sizes(fcpl, &off_size, &len_size); + H5Pget_sym_k(fcpl, &sym_ik, &sym_lk); + H5Pget_istore_k(fcpl, &istore_ik); H5Pget_file_space_strategy(fcpl, &fs_strategy, &fs_persist, &fs_threshold); H5Pget_file_space_page_size(fcpl, &fsp_size); H5Pclose(fcpl); #ifdef SHOW_FILE_DRIVER - fapl=h5_fileaccess(); - fdriver=H5Pget_driver(fapl); + fapl = h5_fileaccess(); + fdriver = H5Pget_driver(fapl); H5Pclose(fapl); #endif - /*------------------------------------------------------------------------- - * SUPER_BLOCK - *------------------------------------------------------------------------- - */ - PRINTSTREAM(rawoutstream, "\n%s %s\n",SUPER_BLOCK, BEGIN); + /*------------------------------------------------------------------------- + * SUPER_BLOCK + *------------------------------------------------------------------------- + */ + PRINTSTREAM(rawoutstream, "\n%s %s\n", SUPER_BLOCK, BEGIN); indentation(dump_indent + COL); - PRINTSTREAM(rawoutstream, "%s %u\n","SUPERBLOCK_VERSION", finfo.super.version); + PRINTSTREAM(rawoutstream, "%s %u\n", "SUPERBLOCK_VERSION", finfo.super.version); indentation(dump_indent + COL); - PRINTSTREAM(rawoutstream, "%s %u\n","FREELIST_VERSION", finfo.free.version); + PRINTSTREAM(rawoutstream, "%s %u\n", "FREELIST_VERSION", finfo.free.version); indentation(dump_indent + COL); - PRINTSTREAM(rawoutstream, "%s %u\n","SYMBOLTABLE_VERSION", 0); /* Retain this for backward compatibility, for now (QAK) */ + PRINTSTREAM(rawoutstream, "%s %u\n", "SYMBOLTABLE_VERSION", + 0); /* Retain this for backward compatibility, for now (QAK) */ indentation(dump_indent + COL); - PRINTSTREAM(rawoutstream, "%s %u\n","OBJECTHEADER_VERSION", finfo.sohm.version); + PRINTSTREAM(rawoutstream, "%s %u\n", "OBJECTHEADER_VERSION", finfo.sohm.version); indentation(dump_indent + COL); - PRINTSTREAM(rawoutstream,"%s %zu\n","OFFSET_SIZE", off_size); + PRINTSTREAM(rawoutstream, "%s %zu\n", "OFFSET_SIZE", off_size); indentation(dump_indent + COL); - PRINTSTREAM(rawoutstream,"%s %zu\n","LENGTH_SIZE", len_size); + PRINTSTREAM(rawoutstream, "%s %zu\n", "LENGTH_SIZE", len_size); indentation(dump_indent + COL); - PRINTSTREAM(rawoutstream, "%s %u\n","BTREE_RANK", sym_ik); + PRINTSTREAM(rawoutstream, "%s %u\n", "BTREE_RANK", sym_ik); indentation(dump_indent + COL); - PRINTSTREAM(rawoutstream, "%s %d\n","BTREE_LEAF", sym_lk); + PRINTSTREAM(rawoutstream, "%s %d\n", "BTREE_LEAF", sym_lk); #ifdef SHOW_FILE_DRIVER - if(H5FD_CORE==fdriver) - HDstrcpy(dname,"H5FD_CORE"); + if (H5FD_CORE == fdriver) + HDstrcpy(dname, "H5FD_CORE"); #ifdef H5_HAVE_DIRECT - else if(H5FD_DIRECT==fdriver) - HDstrcpy(dname,"H5FD_DIRECT"); + else if (H5FD_DIRECT == fdriver) + HDstrcpy(dname, "H5FD_DIRECT"); #endif - else if(H5FD_FAMILY==fdriver) - HDstrcpy(dname,"H5FD_FAMILY"); - else if(H5FD_LOG==fdriver) - HDstrcpy(dname,"H5FD_LOG"); - else if(H5FD_MPIO==fdriver) - HDstrcpy(dname,"H5FD_MPIO"); - else if(H5FD_MULTI==fdriver) - HDstrcpy(dname,"H5FD_MULTI"); - else if(H5FD_SEC2==fdriver) - HDstrcpy(dname,"H5FD_SEC2"); - else if(H5FD_STDIO==fdriver) - HDstrcpy(dname,"H5FD_STDIO"); + else if (H5FD_FAMILY == fdriver) + HDstrcpy(dname, "H5FD_FAMILY"); + else if (H5FD_LOG == fdriver) + HDstrcpy(dname, "H5FD_LOG"); + else if (H5FD_MPIO == fdriver) + HDstrcpy(dname, "H5FD_MPIO"); + else if (H5FD_MULTI == fdriver) + HDstrcpy(dname, "H5FD_MULTI"); + else if (H5FD_SEC2 == fdriver) + HDstrcpy(dname, "H5FD_SEC2"); + else if (H5FD_STDIO == fdriver) + HDstrcpy(dname, "H5FD_STDIO"); else - HDstrcpy(dname,"Unknown driver"); + HDstrcpy(dname, "Unknown driver"); - /* Take out this because the driver used can be different from the - * standard output. */ - /*indentation(dump_indent + COL); - PRINTSTREAM(rawoutstream, "%s %s\n","FILE_DRIVER", dname);*/ + /* Take out this because the driver used can be different from the + * standard output. */ + /*indentation(dump_indent + COL); + PRINTSTREAM(rawoutstream, "%s %s\n","FILE_DRIVER", dname);*/ #endif indentation(dump_indent + COL); - PRINTSTREAM(rawoutstream, "%s %u\n","ISTORE_K", istore_ik); + PRINTSTREAM(rawoutstream, "%s %u\n", "ISTORE_K", istore_ik); indentation(dump_indent + COL); - if(fs_strategy == H5F_FSPACE_STRATEGY_FSM_AGGR) { + if (fs_strategy == H5F_FSPACE_STRATEGY_FSM_AGGR) { PRINTSTREAM(rawoutstream, "%s %s\n", "FILE_SPACE_STRATEGY", "H5F_FSPACE_STRATEGY_FSM_AGGR"); - } else if(fs_strategy == H5F_FSPACE_STRATEGY_PAGE) { + } + else if (fs_strategy == H5F_FSPACE_STRATEGY_PAGE) { PRINTSTREAM(rawoutstream, "%s %s\n", "FILE_SPACE_STRATEGY", "H5F_FSPACE_STRATEGY_PAGE"); - } else if(fs_strategy == H5F_FSPACE_STRATEGY_AGGR) { + } + else if (fs_strategy == H5F_FSPACE_STRATEGY_AGGR) { PRINTSTREAM(rawoutstream, "%s %s\n", "FILE_SPACE_STRATEGY", "H5F_FSPACE_STRATEGY_AGGR"); - } else if(fs_strategy == H5F_FSPACE_STRATEGY_NONE) { + } + else if (fs_strategy == H5F_FSPACE_STRATEGY_NONE) { PRINTSTREAM(rawoutstream, "%s %s\n", "FILE_SPACE_STRATEGY", "H5F_FSPACE_STRATEGY_NONE"); - } else + } + else PRINTSTREAM(rawoutstream, "%s %s\n", "FILE_SPACE_STRATEGY", "Unknown strategy"); indentation(dump_indent + COL); - PRINTSTREAM(rawoutstream, "%s %s\n","FREE_SPACE_PERSIST", fs_persist ? "TRUE" : "FALSE"); + PRINTSTREAM(rawoutstream, "%s %s\n", "FREE_SPACE_PERSIST", fs_persist ? "TRUE" : "FALSE"); indentation(dump_indent + COL); - PRINTSTREAM(rawoutstream, "%s %Hu\n","FREE_SPACE_SECTION_THRESHOLD", fs_threshold); + PRINTSTREAM(rawoutstream, "%s %" PRIuHSIZE "\n", "FREE_SPACE_SECTION_THRESHOLD", fs_threshold); indentation(dump_indent + COL); - PRINTSTREAM(rawoutstream, "%s %Hu\n","FILE_SPACE_PAGE_SIZE", fsp_size); + PRINTSTREAM(rawoutstream, "%s %" PRIuHSIZE "\n", "FILE_SPACE_PAGE_SIZE", fsp_size); /*------------------------------------------------------------------------- - * USER_BLOCK - *------------------------------------------------------------------------- - */ + * USER_BLOCK + *------------------------------------------------------------------------- + */ indentation(dump_indent + COL); - PRINTSTREAM(rawoutstream, "USER_BLOCK %s\n",BEGIN); + PRINTSTREAM(rawoutstream, "USER_BLOCK %s\n", BEGIN); indentation(dump_indent + COL + COL); - PRINTSTREAM(rawoutstream,"%s %Hu\n","USERBLOCK_SIZE", userblock); + PRINTSTREAM(rawoutstream, "%s %" PRIuHSIZE "\n", "USERBLOCK_SIZE", userblock); indentation(dump_indent + COL); - PRINTSTREAM(rawoutstream, "%s\n",END); + PRINTSTREAM(rawoutstream, "%s\n", END); - PRINTSTREAM(rawoutstream, "%s",END); + PRINTSTREAM(rawoutstream, "%s", END); } /*------------------------------------------------------------------------- @@ -1296,80 +1276,88 @@ dump_fcpl(hid_t fid) * Purpose: prints all objects * * Return: void - * - * Programmer: pvn - * - * Modifications: - * *------------------------------------------------------------------------- */ void dump_fcontents(hid_t fid) { - PRINTSTREAM(rawoutstream, "%s %s\n",FILE_CONTENTS, BEGIN); + PRINTSTREAM(rawoutstream, "%s %s\n", FILE_CONTENTS, BEGIN); - /* special case of unamed types in root group */ + /* special case of unnamed types in root group */ if (unamedtype) { unsigned u; for (u = 0; u < type_table->nobjs; u++) { - if (!type_table->objs[u].recorded) - PRINTSTREAM(rawoutstream, " %-10s /#"H5_PRINTF_HADDR_FMT"\n", "datatype", type_table->objs[u].objno); + if (!type_table->objs[u].recorded) { + char *obj_tok_str = NULL; + + H5Otoken_to_str(fid, &type_table->objs[u].obj_token, &obj_tok_str); + PRINTSTREAM(rawoutstream, " %-10s /#%s\n", "datatype", obj_tok_str); + H5free_memory(obj_tok_str); + } } } /* print objects in the files */ h5trav_print(fid); - PRINTSTREAM(rawoutstream, " %s\n",END); + PRINTSTREAM(rawoutstream, " %s\n", END); } static herr_t attr_search(hid_t oid, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED *ainfo, void *_op_data) { - herr_t ret = SUCCEED; - int j; - char *obj_op_name; - char *obj_name; - trav_attr_udata_t *attr_data = (trav_attr_udata_t*)_op_data; - const char *buf = attr_data->path; - const char *op_name = attr_data->op_name; + herr_t ret = SUCCEED; + int j; + char * obj_op_name; + char * obj_name; + trav_attr_udata_t *attr_data = (trav_attr_udata_t *)_op_data; + const char * buf = attr_data->path; + const char * op_name = attr_data->op_name; j = (int)HDstrlen(op_name) - 1; /* find the last / */ - while(j >= 0) { - if(op_name[j] == '/' && (j == 0 || (j > 0 && op_name[j - 1] != '\\'))) + while (j >= 0) { + if (op_name[j] == '/' && (j == 0 || (op_name[j - 1] != '\\'))) break; j--; } obj_op_name = h5tools_str_replace(op_name + j + 1, "\\/", "/"); - if(obj_op_name == NULL) { + if (obj_op_name == NULL) { h5tools_setstatus(EXIT_FAILURE); ret = FAIL; } else { - if(HDstrcmp(attr_name, obj_op_name)==0) { + if (HDstrcmp(attr_name, obj_op_name) == 0) { size_t u, v, w; /* object name */ - u = HDstrlen(buf); - v = HDstrlen(op_name); - w = u + 1 + v + 1 + 2; + u = HDstrlen(buf); + v = HDstrlen(op_name); + w = u + 1 + v + 1 + 2; obj_name = (char *)HDmalloc(w); - if(obj_name == NULL) { + if (obj_name == NULL) { h5tools_setstatus(EXIT_FAILURE); ret = FAIL; } else { + size_t buffer_space = w - 1; + HDmemset(obj_name, '\0', w); - if(op_name[0] != '/') { - HDstrncat(obj_name, buf, u + 1); - if(buf[u - 1] != '/') - HDstrncat(obj_name, "/", (size_t)2); + if (op_name[0] != '/') { + HDstrncat(obj_name, buf, buffer_space); + buffer_space -= MIN(buffer_space, u); + + if (buf[u - 1] != '/') { + HDstrncat(obj_name, "/", buffer_space); + buffer_space -= MIN(buffer_space, 2); + } } - HDstrncat(obj_name, op_name, v + 1); + + HDstrncat(obj_name, op_name, buffer_space); + buffer_space -= MIN(buffer_space, v); handle_attributes(oid, obj_name, NULL, 0, NULL); HDfree(obj_name); @@ -1381,18 +1369,20 @@ attr_search(hid_t oid, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED *a } /* end attr_search() */ static herr_t -obj_search(const char *path, const H5O_info_t *oi, const char H5_ATTR_UNUSED *already_visited, void *_op_data) +obj_search(const char *path, const H5O_info2_t *oi, const char H5_ATTR_UNUSED *already_visited, + void *_op_data) { - trav_handle_udata_t *handle_data = (trav_handle_udata_t*)_op_data; - const char *op_name = handle_data->op_name; - trav_attr_udata_t attr_data; + trav_handle_udata_t *handle_data = (trav_handle_udata_t *)_op_data; + const char * op_name = handle_data->op_name; + trav_attr_udata_t attr_data; - attr_data.path = path; + attr_data.path = path; attr_data.op_name = op_name; - H5Aiterate_by_name(handle_data->fid, path, H5_INDEX_NAME, H5_ITER_INC, NULL, attr_search, (void*)&attr_data, H5P_DEFAULT); + H5Aiterate_by_name(handle_data->fid, path, H5_INDEX_NAME, H5_ITER_INC, NULL, attr_search, + (void *)&attr_data, H5P_DEFAULT); - if(HDstrcmp(path, op_name) == 0) { - switch(oi->type) { + if (HDstrcmp(path, op_name) == 0) { + switch (oi->type) { case H5O_TYPE_GROUP: handle_groups(handle_data->fid, path, NULL, 0, NULL); break; @@ -1418,47 +1408,47 @@ obj_search(const char *path, const H5O_info_t *oi, const char H5_ATTR_UNUSED *al } /* end obj_search() */ static herr_t -lnk_search(const char *path, const H5L_info_t *li, void *_op_data) +lnk_search(const char *path, const H5L_info2_t *li, void *_op_data) { - size_t search_len; - size_t k; - char *search_name; - trav_handle_udata_t *handle_data = (trav_handle_udata_t*)_op_data; - const char *op_name = handle_data->op_name; + size_t search_len; + size_t k; + char * search_name; + trav_handle_udata_t *handle_data = (trav_handle_udata_t *)_op_data; + const char * op_name = handle_data->op_name; search_len = HDstrlen(op_name); - if(search_len > 0 && op_name[0] != '/') + if (search_len > 0 && op_name[0] != '/') k = 2; else k = 1; search_name = (char *)HDmalloc(search_len + k); - if(search_name == NULL) { + if (search_name == NULL) { error_msg("creating temporary link\n"); h5tools_setstatus(EXIT_FAILURE); } else { if (k == 2) { HDstrcpy(search_name, "/"); - HDstrncat(search_name, op_name, search_len + 1); + HDstrcat(search_name, op_name); } else - HDstrncpy(search_name, op_name, search_len + 1); + HDstrcpy(search_name, op_name); search_name[search_len + k - 1] = '\0'; - if(HDstrcmp(path, search_name) == 0) { - switch(li->type) { - case H5L_TYPE_SOFT: - case H5L_TYPE_EXTERNAL: - handle_links(handle_data->fid, op_name, NULL, 0, NULL); - break; + if (HDstrcmp(path, search_name) == 0) { + switch (li->type) { + case H5L_TYPE_SOFT: + case H5L_TYPE_EXTERNAL: + handle_links(handle_data->fid, op_name, NULL, 0, NULL); + break; - case H5L_TYPE_HARD: - case H5L_TYPE_MAX: - case H5L_TYPE_ERROR: - default: - error_msg("unknown link type value\n"); - h5tools_setstatus(EXIT_FAILURE); - break; + case H5L_TYPE_HARD: + case H5L_TYPE_MAX: + case H5L_TYPE_ERROR: + default: + error_msg("unknown link type value\n"); + h5tools_setstatus(EXIT_FAILURE); + break; } /* end switch() */ } HDfree(search_name); @@ -1472,23 +1462,23 @@ lnk_search(const char *path, const H5L_info_t *li, void *_op_data) * Purpose: Handle objects from the command. * * Return: void - * *------------------------------------------------------------------------- */ void -handle_paths(hid_t fid, const char *path_name, void H5_ATTR_UNUSED * data, int H5_ATTR_UNUSED pe, const char H5_ATTR_UNUSED *display_name) +handle_paths(hid_t fid, const char *path_name, void H5_ATTR_UNUSED *data, int H5_ATTR_UNUSED pe, + const char H5_ATTR_UNUSED *display_name) { - hid_t gid = -1; + hid_t gid = H5I_INVALID_HID; - if((gid = H5Gopen2(fid, "/", H5P_DEFAULT)) < 0) { + if ((gid = H5Gopen2(fid, "/", H5P_DEFAULT)) < 0) { error_msg("unable to open root group\n"); h5tools_setstatus(EXIT_FAILURE); } else { - hid_t gcpl_id; - unsigned crt_order_flags; - unsigned attr_crt_order_flags; - trav_handle_udata_t handle_udata; /* User data for traversal */ + hid_t gcpl_id; + unsigned crt_order_flags; + unsigned attr_crt_order_flags; + trav_handle_udata_t handle_udata; /* User data for traversal */ if ((gcpl_id = H5Gget_create_plist(gid)) < 0) { error_msg("error in getting group creation property list ID\n"); @@ -1502,19 +1492,19 @@ handle_paths(hid_t fid, const char *path_name, void H5_ATTR_UNUSED * data, int H } /* query the group creation properties */ - if(H5Pget_link_creation_order(gcpl_id, &crt_order_flags) < 0) { + if (H5Pget_link_creation_order(gcpl_id, &crt_order_flags) < 0) { error_msg("error in getting group creation properties\n"); h5tools_setstatus(EXIT_FAILURE); } - if(H5Pclose(gcpl_id) < 0) { + if (H5Pclose(gcpl_id) < 0) { error_msg("error in closing group creation property list ID\n"); h5tools_setstatus(EXIT_FAILURE); } - handle_udata.fid = fid; + handle_udata.fid = fid; handle_udata.op_name = path_name; - if(h5trav_visit(fid, "/", TRUE, TRUE, obj_search, lnk_search, &handle_udata, H5O_INFO_BASIC) < 0) { + if (h5trav_visit(fid, "/", TRUE, TRUE, obj_search, lnk_search, &handle_udata, H5O_INFO_BASIC) < 0) { error_msg("error traversing information\n"); h5tools_setstatus(EXIT_FAILURE); } @@ -1527,45 +1517,37 @@ handle_paths(hid_t fid, const char *path_name, void H5_ATTR_UNUSED * data, int H * Purpose: Handle the attributes from the command. * * Return: void - * - * Programmer: Bill Wendling - * Tuesday, 9. January 2001 - * - * Modifications: - * - * PVN, May 2008 - * add an extra parameter PE, to allow printing/not printing of error messages - * *------------------------------------------------------------------------- */ void -handle_attributes(hid_t fid, const char *attr, void H5_ATTR_UNUSED * data, int H5_ATTR_UNUSED pe, const char H5_ATTR_UNUSED *display_name) +handle_attributes(hid_t fid, const char *attr, void H5_ATTR_UNUSED *data, int H5_ATTR_UNUSED pe, + const char H5_ATTR_UNUSED *display_name) { - hid_t oid = -1; - hid_t attr_id = -1; - char *obj_name = NULL; - char *attr_name = NULL; - int j; - h5tools_str_t buffer; /* string into which to render */ - h5tools_context_t ctx; /* print context */ - h5tool_format_t *outputformat = &h5tools_dataformat; + hid_t oid = H5I_INVALID_HID; + hid_t attr_id = H5I_INVALID_HID; + char * obj_name = NULL; + char * attr_name = NULL; + int j; + h5tools_str_t buffer; /* string into which to render */ + h5tools_context_t ctx; /* print context */ + h5tool_format_t * outputformat = &h5tools_dataformat; h5tool_format_t string_dataformat; - hsize_t curr_pos = 0; /* total data element position */ + hsize_t curr_pos = 0; /* total data element position */ - j = (int)HDstrlen(attr) - 1; + j = (int)HDstrlen(attr) - 1; obj_name = (char *)HDmalloc((size_t)j + 2); - if(obj_name == NULL) + if (obj_name == NULL) goto error; /* find the last / */ - while(j >= 0) { - if (attr[j] == '/' && (j==0 || (j>0 && attr[j-1]!='\\'))) + while (j >= 0) { + if (attr[j] == '/' && (j == 0 || (attr[j - 1] != '\\'))) break; j--; } /* object name */ - if(j == -1) + if (j == -1) HDstrcpy(obj_name, "/"); else { HDstrncpy(obj_name, attr, (size_t)j + 1); @@ -1574,30 +1556,32 @@ handle_attributes(hid_t fid, const char *attr, void H5_ATTR_UNUSED * data, int H dump_indent += COL; HDmemset(&ctx, 0, sizeof(ctx)); - ctx.indent_level = dump_indent / COL; - ctx.cur_column = dump_indent; + ctx.indent_level = dump_indent / COL; + ctx.cur_column = dump_indent; + ctx.display_index = dump_opts.display_ai; + ctx.display_char = dump_opts.display_char; string_dataformat = *outputformat; if (fp_format) { string_dataformat.fmt_double = fp_format; - string_dataformat.fmt_float = fp_format; + string_dataformat.fmt_float = fp_format; } if (h5tools_nCols == 0) { - string_dataformat.line_ncols = 65535; + string_dataformat.line_ncols = 65535; string_dataformat.line_per_line = 1; } else string_dataformat.line_ncols = h5tools_nCols; - string_dataformat.do_escape = display_escape; - outputformat = &string_dataformat; + string_dataformat.do_escape = dump_opts.display_escape; + outputformat = &string_dataformat; attr_name = h5tools_str_replace(attr + j + 1, "\\/", "/"); /* handle error case: cannot open the object with the attribute */ - if((oid = H5Oopen(fid, obj_name, H5P_DEFAULT)) < 0) { + if ((oid = H5Oopen(fid, obj_name, H5P_DEFAULT)) < 0) { /* setup */ HDmemset(&buffer, 0, sizeof(h5tools_str_t)); @@ -1605,45 +1589,46 @@ handle_attributes(hid_t fid, const char *attr, void H5_ATTR_UNUSED * data, int H /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "%s \"%s\" %s", - h5tools_dump_header_format->attributebegin, attr, - h5tools_dump_header_format->attributeblockbegin); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "%s \"%s\" %s", h5tools_dump_header_format->attributebegin, attr, + h5tools_dump_header_format->attributeblockbegin); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); error_msg("unable to open object \"%s\"\n", obj_name); ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - if(HDstrlen(h5tools_dump_header_format->attributeblockend)) { + if (HDstrlen(h5tools_dump_header_format->attributeblockend)) { h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->attributeblockend); - if(HDstrlen(h5tools_dump_header_format->attributeend)) + if (HDstrlen(h5tools_dump_header_format->attributeend)) h5tools_str_append(&buffer, " "); } - if(HDstrlen(h5tools_dump_header_format->attributeend)) + if (HDstrlen(h5tools_dump_header_format->attributeend)) h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->attributeend); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); h5tools_str_close(&buffer); goto error; } /* end if */ - attr_id = H5Aopen(oid, attr_name, H5P_DEFAULT); - oid_output = display_oid; - data_output = display_data; - attr_data_output = display_attr_data; + attr_id = H5Aopen(oid, attr_name, H5P_DEFAULT); + oid_output = dump_opts.display_oid; + data_output = dump_opts.display_data; + attr_data_output = dump_opts.display_attr_data; h5dump_type_table = type_table; - h5tools_dump_attribute(rawoutstream, outputformat, &ctx, attr_name, attr_id, display_ai, display_char); + h5tools_dump_attribute(rawoutstream, outputformat, &ctx, attr_name, attr_id); h5dump_type_table = NULL; - if(attr_id < 0) { + if (attr_id < 0) { goto error; } /* Close object */ - if(H5Oclose(oid) < 0) { + if (H5Oclose(oid) < 0) { goto error; } /* end if */ @@ -1654,16 +1639,18 @@ handle_attributes(hid_t fid, const char *attr, void H5_ATTR_UNUSED * data, int H error: h5tools_setstatus(EXIT_FAILURE); - if(obj_name) + if (obj_name) HDfree(obj_name); if (attr_name) HDfree(attr_name); - H5E_BEGIN_TRY { + H5E_BEGIN_TRY + { H5Oclose(oid); H5Aclose(attr_id); - } H5E_END_TRY; + } + H5E_END_TRY; dump_indent -= COL; } @@ -1673,89 +1660,76 @@ error: * Purpose: Handle the datasets from the command. * * Return: void - * - * Programmer: Bill Wendling - * Tuesday, 9. January 2001 - * - * Modifications: - * Pedro Vicente, Tuesday, January 15, 2008 - * check for block overlap\ - * - * Pedro Vicente, May 8, 2008 - * added a flag PE that prints/not prints error messages - * added for cases of external links not found, to avoid printing of - * objects not found, since external links are dumped on a trial error basis - * *------------------------------------------------------------------------- */ void handle_datasets(hid_t fid, const char *dset, void *data, int pe, const char *display_name) { - H5O_info_t oinfo; + H5O_info2_t oinfo; hid_t dsetid; - hid_t dapl_id = H5P_DEFAULT; /* dataset access property list ID */ - struct subset_t *sset = (struct subset_t *)data; - const char *real_name = display_name ? display_name : dset; + hid_t dapl_id = H5P_DEFAULT; /* dataset access property list ID */ + struct subset_t *sset = (struct subset_t *)data; + const char * real_name = display_name ? display_name : dset; - if(display_data) { + if (dump_opts.display_data) { if ((dapl_id = H5Pcreate(H5P_DATASET_ACCESS)) < 0) { error_msg("error in creating default access property list ID\n"); } - if (display_vds_first) { - if(H5Pset_virtual_view(dapl_id, H5D_VDS_FIRST_MISSING) < 0) + if (dump_opts.display_vds_first) { + if (H5Pset_virtual_view(dapl_id, H5D_VDS_FIRST_MISSING) < 0) error_msg("error in setting access property list ID, virtual_view\n"); } - if (vds_gap_size > 0) { - if(H5Pset_virtual_printf_gap(dapl_id, (hsize_t)vds_gap_size) < 0) + if (dump_opts.vds_gap_size > 0) { + if (H5Pset_virtual_printf_gap(dapl_id, (hsize_t)dump_opts.vds_gap_size) < 0) error_msg("error in setting access property list ID, virtual_printf_gap\n"); } } - if((dsetid = H5Dopen2(fid, dset, dapl_id)) < 0) { + if ((dsetid = H5Dopen2(fid, dset, dapl_id)) < 0) { if (pe) handle_links(fid, dset, data, pe, display_name); return; } /* end if */ - if(sset) { + if (sset) { unsigned int i; unsigned int ndims; - hid_t sid = H5Dget_space(dsetid); - int ndims_res = H5Sget_simple_extent_ndims(sid); + hid_t sid = H5Dget_space(dsetid); + int ndims_res = H5Sget_simple_extent_ndims(sid); H5Sclose(sid); - if(ndims_res < 0) { + if (ndims_res < 0) { error_msg("H5Sget_simple_extent_ndims failed\n"); h5tools_setstatus(EXIT_FAILURE); return; } ndims = (unsigned)ndims_res; - if(!sset->start.data || !sset->stride.data || !sset->count.data || !sset->block.data) { + if (!sset->start.data || !sset->stride.data || !sset->count.data || !sset->block.data) { /* they didn't specify a ``stride'' or ``block''. default to 1 in all * dimensions */ - if(!sset->start.data) { + if (!sset->start.data) { /* default to (0, 0, ...) for the start coord */ sset->start.data = (hsize_t *)HDcalloc((size_t)ndims, sizeof(hsize_t)); - sset->start.len = ndims; + sset->start.len = ndims; } - if(!sset->stride.data) { + if (!sset->stride.data) { sset->stride.data = (hsize_t *)HDcalloc((size_t)ndims, sizeof(hsize_t)); - sset->stride.len = ndims; + sset->stride.len = ndims; for (i = 0; i < ndims; i++) sset->stride.data[i] = 1; } - if(!sset->count.data) { + if (!sset->count.data) { sset->count.data = (hsize_t *)HDcalloc((size_t)ndims, sizeof(hsize_t)); - sset->count.len = ndims; + sset->count.len = ndims; for (i = 0; i < ndims; i++) sset->count.data[i] = 1; } - if(!sset->block.data) { + if (!sset->block.data) { sset->block.data = (hsize_t *)HDcalloc((size_t)ndims, sizeof(hsize_t)); - sset->block.len = ndims; + sset->block.len = ndims; for (i = 0; i < ndims; i++) sset->block.data[i] = 1; } @@ -1765,22 +1739,22 @@ handle_datasets(hid_t fid, const char *dset, void *data, int pe, const char *dis * check for dimension overflow *------------------------------------------------------------------------- */ - if(sset->start.len > ndims) { + if (sset->start.len > ndims) { error_msg("number of start dims (%u) exceed dataset dims (%u)\n", sset->start.len, ndims); h5tools_setstatus(EXIT_FAILURE); return; } - if(sset->stride.len > ndims) { + if (sset->stride.len > ndims) { error_msg("number of stride dims (%u) exceed dataset dims (%u)\n", sset->stride.len, ndims); h5tools_setstatus(EXIT_FAILURE); return; } - if(sset->count.len > ndims) { + if (sset->count.len > ndims) { error_msg("number of count dims (%u) exceed dataset dims (%u)\n", sset->count.len, ndims); h5tools_setstatus(EXIT_FAILURE); return; } - if(sset->block.len > ndims) { + if (sset->block.len > ndims) { error_msg("number of block dims (%u) exceed dataset dims (%u)\n", sset->block.len, ndims); h5tools_setstatus(EXIT_FAILURE); return; @@ -1790,29 +1764,29 @@ handle_datasets(hid_t fid, const char *dset, void *data, int pe, const char *dis * check for block overlap *------------------------------------------------------------------------- */ - for(i = 0; i < ndims; i++) { - if(sset->count.data[i] > 1) { - if(sset->stride.data[i] < sset->block.data[i]) { + for (i = 0; i < ndims; i++) { + if (sset->count.data[i] > 1) { + if (sset->stride.data[i] < sset->block.data[i]) { error_msg("wrong subset selection; blocks overlap\n"); h5tools_setstatus(EXIT_FAILURE); return; } /* end if */ - } /* end if */ - } /* end for */ - } /* end if */ - + } /* end if */ + } /* end for */ + } /* end if */ - H5Oget_info2(dsetid, &oinfo, H5O_INFO_BASIC); - if(oinfo.rc > 1 || hit_elink) { - obj_t *found_obj; /* Found object */ + H5Oget_info3(dsetid, &oinfo, H5O_INFO_BASIC); + if (oinfo.rc > 1 || hit_elink) { + obj_t *found_obj; /* Found object */ - found_obj = search_obj(dset_table, oinfo.addr); + found_obj = search_obj(dset_table, &oinfo.token); - if(found_obj) { + if (found_obj) { if (found_obj->displayed) { PRINTVALSTREAM(rawoutstream, "\n"); indentation(dump_indent); - begin_obj(h5tools_dump_header_format->datasetbegin, real_name, h5tools_dump_header_format->datasetblockbegin); + begin_obj(h5tools_dump_header_format->datasetbegin, real_name, + h5tools_dump_header_format->datasetblockbegin); PRINTVALSTREAM(rawoutstream, "\n"); indentation(dump_indent + COL); PRINTSTREAM(rawoutstream, "%s \"%s\"\n", HARDLINK, found_obj->objname); @@ -1836,7 +1810,7 @@ handle_datasets(hid_t fid, const char *dset, void *data, int pe, const char *dis } if (dapl_id != H5P_DEFAULT) H5Pclose(dapl_id); - if(H5Dclose(dsetid) < 0) + if (H5Dclose(dsetid) < 0) h5tools_setstatus(EXIT_FAILURE); } @@ -1846,30 +1820,19 @@ handle_datasets(hid_t fid, const char *dset, void *data, int pe, const char *dis * Purpose: Handle the groups from the command. * * Return: void - * - * Programmer: Bill Wendling - * Tuesday, 9. January 2001 - * - * Modifications: Pedro Vicente, September 26, 2007 - * handle creation order - * - * Pedro Vicente, May 8, 2008 - * added a flag PE that prints/not prints error messages - * added for cases of external links not found, to avoid printing of - * objects not found, since external links are dumped on a trial error basis - * *------------------------------------------------------------------------- */ void handle_groups(hid_t fid, const char *group, void H5_ATTR_UNUSED *data, int pe, const char *display_name) { hid_t gid; - const char *real_name = display_name ? display_name : group; + const char *real_name = display_name ? display_name : group; - if((gid = H5Gopen2(fid, group, H5P_DEFAULT)) < 0) { + if ((gid = H5Gopen2(fid, group, H5P_DEFAULT)) < 0) { if (pe) { PRINTVALSTREAM(rawoutstream, "\n"); - begin_obj(h5tools_dump_header_format->groupbegin, real_name, h5tools_dump_header_format->groupblockbegin); + begin_obj(h5tools_dump_header_format->groupbegin, real_name, + h5tools_dump_header_format->groupblockbegin); PRINTVALSTREAM(rawoutstream, "\n"); indentation(COL); error_msg("unable to open group \"%s\"\n", real_name); @@ -1880,9 +1843,9 @@ handle_groups(hid_t fid, const char *group, void H5_ATTR_UNUSED *data, int pe, c else { size_t new_len = HDstrlen(group) + 1; - if(prefix_len <= new_len) { + if (prefix_len <= new_len) { prefix_len = new_len; - prefix = (char *)HDrealloc(prefix, prefix_len); + prefix = (char *)HDrealloc(prefix, prefix_len); } /* end if */ HDstrcpy(prefix, group); @@ -1891,7 +1854,7 @@ handle_groups(hid_t fid, const char *group, void H5_ATTR_UNUSED *data, int pe, c dump_group(gid, real_name); dump_indent -= COL; - if(H5Gclose(gid) < 0) + if (H5Gclose(gid) < 0) h5tools_setstatus(EXIT_FAILURE); } /* end else */ } /* end handle_groups() */ @@ -1902,24 +1865,19 @@ handle_groups(hid_t fid, const char *group, void H5_ATTR_UNUSED *data, int pe, c * Purpose: Handle soft or UD links from the command. * * Return: void - * - * Programmer: Bill Wendling - * Tuesday, 9. January 2001 - * - * Modifications: - * *------------------------------------------------------------------------- */ void -handle_links(hid_t fid, const char *links, void H5_ATTR_UNUSED * data, int H5_ATTR_UNUSED pe, const char H5_ATTR_UNUSED *display_name) +handle_links(hid_t fid, const char *links, void H5_ATTR_UNUSED *data, int H5_ATTR_UNUSED pe, + const char H5_ATTR_UNUSED *display_name) { - H5L_info_t linfo; + H5L_info2_t linfo; - if(H5Lget_info(fid, links, &linfo, H5P_DEFAULT) < 0) { + if (H5Lget_info2(fid, links, &linfo, H5P_DEFAULT) < 0) { error_msg("unable to get link info from \"%s\"\n", links); h5tools_setstatus(EXIT_FAILURE); } - else if(linfo.type == H5L_TYPE_HARD) { + else if (linfo.type == H5L_TYPE_HARD) { error_msg("\"%s\" is a hard link\n", links); h5tools_setstatus(EXIT_FAILURE); } @@ -1927,56 +1885,60 @@ handle_links(hid_t fid, const char *links, void H5_ATTR_UNUSED * data, int H5_AT char *buf = (char *)HDmalloc(linfo.u.val_size); PRINTVALSTREAM(rawoutstream, "\n"); - switch(linfo.type) { - case H5L_TYPE_SOFT: /* Soft link */ - begin_obj(h5tools_dump_header_format->softlinkbegin, links, h5tools_dump_header_format->softlinkblockbegin); - PRINTVALSTREAM(rawoutstream, "\n"); - indentation(COL); - if(H5Lget_val(fid, links, buf, linfo.u.val_size, H5P_DEFAULT) >= 0) { - PRINTSTREAM(rawoutstream, "LINKTARGET \"%s\"\n", buf); - } - else { - error_msg("h5dump error: unable to get link value for \"%s\"\n", links); - h5tools_setstatus(EXIT_FAILURE); - } - end_obj(h5tools_dump_header_format->softlinkend, h5tools_dump_header_format->softlinkblockend); - break; + switch (linfo.type) { + case H5L_TYPE_SOFT: /* Soft link */ + begin_obj(h5tools_dump_header_format->softlinkbegin, links, + h5tools_dump_header_format->softlinkblockbegin); + PRINTVALSTREAM(rawoutstream, "\n"); + indentation(COL); + if (H5Lget_val(fid, links, buf, linfo.u.val_size, H5P_DEFAULT) >= 0) { + PRINTSTREAM(rawoutstream, "LINKTARGET \"%s\"\n", buf); + } + else { + error_msg("h5dump error: unable to get link value for \"%s\"\n", links); + h5tools_setstatus(EXIT_FAILURE); + } + end_obj(h5tools_dump_header_format->softlinkend, + h5tools_dump_header_format->softlinkblockend); + break; - case H5L_TYPE_EXTERNAL: - begin_obj(h5tools_dump_header_format->extlinkbegin, links, h5tools_dump_header_format->extlinkblockbegin); - PRINTVALSTREAM(rawoutstream, "\n"); - if(H5Lget_val(fid, links, buf, linfo.u.val_size, H5P_DEFAULT) >= 0) { - const char *elink_file; - const char *elink_path; - - if(H5Lunpack_elink_val(buf, linfo.u.val_size, NULL, &elink_file, &elink_path)>=0) { - indentation(COL); - PRINTSTREAM(rawoutstream, "TARGETFILE \"%s\"\n", elink_file); - indentation(COL); - PRINTSTREAM(rawoutstream, "TARGETPATH \"%s\"\n", elink_path); + case H5L_TYPE_EXTERNAL: + begin_obj(h5tools_dump_header_format->extlinkbegin, links, + h5tools_dump_header_format->extlinkblockbegin); + PRINTVALSTREAM(rawoutstream, "\n"); + if (H5Lget_val(fid, links, buf, linfo.u.val_size, H5P_DEFAULT) >= 0) { + const char *elink_file; + const char *elink_path; + + if (H5Lunpack_elink_val(buf, linfo.u.val_size, NULL, &elink_file, &elink_path) >= 0) { + indentation(COL); + PRINTSTREAM(rawoutstream, "TARGETFILE \"%s\"\n", elink_file); + indentation(COL); + PRINTSTREAM(rawoutstream, "TARGETPATH \"%s\"\n", elink_path); + } + else { + error_msg("h5dump error: unable to unpack external link value for \"%s\"\n", links); + h5tools_setstatus(EXIT_FAILURE); + } } else { - error_msg("h5dump error: unable to unpack external link value for \"%s\"\n", links); + error_msg("h5dump error: unable to get external link value for \"%s\"\n", links); h5tools_setstatus(EXIT_FAILURE); } - } - else { - error_msg("h5dump error: unable to get external link value for \"%s\"\n", links); - h5tools_setstatus(EXIT_FAILURE); - } - end_obj(h5tools_dump_header_format->extlinkend, h5tools_dump_header_format->extlinkblockend); - break; + end_obj(h5tools_dump_header_format->extlinkend, h5tools_dump_header_format->extlinkblockend); + break; - case H5L_TYPE_ERROR: - case H5L_TYPE_MAX: - case H5L_TYPE_HARD: - default: - begin_obj(h5tools_dump_header_format->udlinkbegin, links, h5tools_dump_header_format->udlinkblockbegin); - PRINTVALSTREAM(rawoutstream, "\n"); - indentation(COL); - PRINTSTREAM(rawoutstream, "LINKCLASS %d\n", linfo.type); - end_obj(h5tools_dump_header_format->udlinkend, h5tools_dump_header_format->udlinkblockend); - break; + case H5L_TYPE_ERROR: + case H5L_TYPE_MAX: + case H5L_TYPE_HARD: + default: + begin_obj(h5tools_dump_header_format->udlinkbegin, links, + h5tools_dump_header_format->udlinkblockbegin); + PRINTVALSTREAM(rawoutstream, "\n"); + indentation(COL); + PRINTSTREAM(rawoutstream, "LINKCLASS %d\n", linfo.type); + end_obj(h5tools_dump_header_format->udlinkend, h5tools_dump_header_format->udlinkblockend); + break; } /* end switch */ HDfree(buf); } /* end else */ @@ -1988,58 +1950,53 @@ handle_links(hid_t fid, const char *links, void H5_ATTR_UNUSED * data, int H5_AT * Purpose: Handle the datatypes from the command. * * Return: void - * - * Programmer: Bill Wendling - * Tuesday, 9. January 2001 - * - * Modifications: - * - * Pedro Vicente, May 8, 2008 - * added a flag PE that prints/not prints error messages - * added for cases of external links not found, to avoid printing of - * objects not found, since external links are dumped on a trial error basis - * *------------------------------------------------------------------------- */ void -handle_datatypes(hid_t fid, const char *type, void H5_ATTR_UNUSED * data, int pe, const char *display_name) +handle_datatypes(hid_t fid, const char *type, void H5_ATTR_UNUSED *data, int pe, const char *display_name) { hid_t type_id; - const char *real_name = display_name ? display_name : type; + const char *real_name = display_name ? display_name : type; - if((type_id = H5Topen2(fid, type, H5P_DEFAULT)) < 0) { - /* check if type is unamed datatype */ + if ((type_id = H5Topen2(fid, type, H5P_DEFAULT)) < 0) { + /* check if type is unnamed datatype */ unsigned idx = 0; - while(idx < type_table->nobjs ) { + while (idx < type_table->nobjs) { char name[128]; - if(!type_table->objs[idx].recorded) { - /* unamed datatype */ - HDsprintf(name, "/#"H5_PRINTF_HADDR_FMT, type_table->objs[idx].objno); + if (!type_table->objs[idx].recorded) { + char *obj_tok_str = NULL; - if(!HDstrcmp(name, real_name)) + /* unnamed datatype */ + H5Otoken_to_str(fid, &type_table->objs[idx].obj_token, &obj_tok_str); + HDsnprintf(name, sizeof(name), "/#%s", obj_tok_str); + H5free_memory(obj_tok_str); + + if (!HDstrcmp(name, real_name)) break; } /* end if */ idx++; } /* end while */ - if(idx == type_table->nobjs) { + if (idx == type_table->nobjs) { if (pe) { /* unknown type */ PRINTVALSTREAM(rawoutstream, "\n"); - begin_obj(h5tools_dump_header_format->datatypebegin, real_name, h5tools_dump_header_format->datatypeblockbegin); + begin_obj(h5tools_dump_header_format->datatypebegin, real_name, + h5tools_dump_header_format->datatypeblockbegin); PRINTVALSTREAM(rawoutstream, "\n"); indentation(COL); error_msg("unable to open datatype \"%s\"\n", real_name); - end_obj(h5tools_dump_header_format->datatypeend, h5tools_dump_header_format->datatypeblockend); + end_obj(h5tools_dump_header_format->datatypeend, + h5tools_dump_header_format->datatypeblockend); h5tools_setstatus(EXIT_FAILURE); } } else { hid_t dsetid = H5Dopen2(fid, type_table->objs[idx].objname, H5P_DEFAULT); - type_id = H5Dget_type(dsetid); + type_id = H5Dget_type(dsetid); dump_indent += COL; dump_named_datatype(type_id, real_name); @@ -2054,28 +2011,18 @@ handle_datatypes(hid_t fid, const char *type, void H5_ATTR_UNUSED * data, int pe dump_named_datatype(type_id, real_name); dump_indent -= COL; - if(H5Tclose(type_id) < 0) + if (H5Tclose(type_id) < 0) h5tools_setstatus(EXIT_FAILURE); } } - /*------------------------------------------------------------------------- * Function: dump_extlink * - * made by: PVN - * * Purpose: Dump an external link - * Since external links are soft links, they are dumped on a trial error - * basis, attempting to dump as a dataset, as a group and as a named datatype - * Error messages are supressed - * - * Modifications: - * Neil Fortner - * 13 October 2008 - * Function basically rewritten. No longer directly opens the target file, - * now initializes a new set of tables for the external file. No longer - * dumps on a trial and error basis, but errors are still suppressed. + * Function does not directly open the target file, + * it initializes a new set of tables for the external file. + * Errors are suppressed. * *------------------------------------------------------------------------- */ @@ -2083,10 +2030,10 @@ static int dump_extlink(hid_t group, const char *linkname, const char *objname) { hid_t oid; - H5O_info_t oi; - table_t *old_group_table = group_table; - table_t *old_dset_table = dset_table; - table_t *old_type_table = type_table; + H5O_info2_t oi; + table_t * old_group_table = group_table; + table_t * old_dset_table = dset_table; + table_t * old_type_table = type_table; hbool_t old_hit_elink; ssize_t idx; @@ -2095,7 +2042,7 @@ dump_extlink(hid_t group, const char *linkname, const char *objname) goto fail; /* Get object info */ - if (H5Oget_info2(oid, &oi, H5O_INFO_BASIC) < 0) { + if (H5Oget_info3(oid, &oi, H5O_INFO_BASIC) < 0) { H5Oclose(oid); goto fail; } @@ -2113,12 +2060,12 @@ dump_extlink(hid_t group, const char *linkname, const char *objname) if (idx) { /* Update table pointers */ group_table = table_list.tables[idx].group_table; - dset_table = table_list.tables[idx].dset_table; - type_table = table_list.tables[idx].type_table; + dset_table = table_list.tables[idx].dset_table; + type_table = table_list.tables[idx].type_table; /* We will now traverse the external link, set this global to indicate this */ old_hit_elink = hit_elink; - hit_elink = TRUE; + hit_elink = TRUE; /* add some indentation to distinguish that these objects are external */ dump_indent += COL; @@ -2148,8 +2095,8 @@ dump_extlink(hid_t group, const char *linkname, const char *objname) /* Reset table pointers */ group_table = old_group_table; - dset_table = old_dset_table; - type_table = old_type_table; + dset_table = old_dset_table; + type_table = old_type_table; /* Reset hit_elink */ hit_elink = old_hit_elink; @@ -2163,4 +2110,3 @@ dump_extlink(hid_t group, const char *linkname, const char *objname) fail: return FAIL; } - diff --git a/tools/src/h5dump/h5dump_ddl.h b/tools/src/h5dump/h5dump_ddl.h index ae01086..8487270 100644 --- a/tools/src/h5dump/h5dump_ddl.h +++ b/tools/src/h5dump/h5dump_ddl.h @@ -6,13 +6,13 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -#ifndef H5DUMP_DDL_H__ -#define H5DUMP_DDL_H__ +#ifndef H5DUMP_DDL_H +#define H5DUMP_DDL_H #ifdef __cplusplus extern "C" { @@ -20,17 +20,17 @@ extern "C" { /* The dump functions of the dump_function_table */ /* standard format: no change */ -void dump_group(hid_t, const char *); -void dump_named_datatype(hid_t, const char *); -void dump_dataset(hid_t, const char *, struct subset_t *); -void dump_dataspace(hid_t space); -void dump_datatype(hid_t type); -void dump_data(hid_t, int, struct subset_t *, int); -void dump_fcpl(hid_t fid); -void dump_fcontents(hid_t fid); +void dump_group(hid_t, const char *); +void dump_named_datatype(hid_t, const char *); +void dump_dataset(hid_t, const char *, struct subset_t *); +void dump_dataspace(hid_t space); +void dump_datatype(hid_t type); +void dump_data(hid_t, int, struct subset_t *, int); +void dump_fcpl(hid_t fid); +void dump_fcontents(hid_t fid); /* callback function used by H5Aiterate2() */ -herr_t dump_attr_cb(hid_t loc_id, const char *attr_name, const H5A_info_t *info, void *_op_data); +herr_t dump_attr_cb(hid_t loc_id, const char *attr_name, const H5A_info_t *info, void *_op_data); /* other iteration functions */ void link_iteration(hid_t gid, unsigned crt_order_flags); @@ -38,13 +38,16 @@ void attr_iteration(hid_t gid, unsigned attr_crt_order_flags); void handle_paths(hid_t fid, const char *path_name, void *data, int pe, const char *display_name); void handle_datasets(hid_t fid, const char *dset, void *data, int pe, const char *display_name); -void handle_attributes(hid_t fid, const char *attr, void H5_ATTR_UNUSED * data, int H5_ATTR_UNUSED pe, const char H5_ATTR_UNUSED *display_name); +void handle_attributes(hid_t fid, const char *attr, void H5_ATTR_UNUSED *data, int H5_ATTR_UNUSED pe, + const char H5_ATTR_UNUSED *display_name); void handle_groups(hid_t fid, const char *group, void H5_ATTR_UNUSED *data, int pe, const char *display_name); -void handle_links(hid_t fid, const char *links, void H5_ATTR_UNUSED * data, int H5_ATTR_UNUSED pe, const char H5_ATTR_UNUSED *display_name); -void handle_datatypes(hid_t fid, const char *type, void H5_ATTR_UNUSED * data, int pe, const char *display_name); +void handle_links(hid_t fid, const char *links, void H5_ATTR_UNUSED *data, int H5_ATTR_UNUSED pe, + const char H5_ATTR_UNUSED *display_name); +void handle_datatypes(hid_t fid, const char *type, void H5_ATTR_UNUSED *data, int pe, + const char *display_name); #ifdef __cplusplus } #endif -#endif /* !H5DUMP_DDL_H__ */ +#endif /* H5DUMP_DDL_H */ diff --git a/tools/src/h5dump/h5dump_defines.h b/tools/src/h5dump/h5dump_defines.h index 7a9d4c0..21a31dd 100644 --- a/tools/src/h5dump/h5dump_defines.h +++ b/tools/src/h5dump/h5dump_defines.h @@ -6,49 +6,48 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -#ifndef H5DUMP_DEFINES_H__ -#define H5DUMP_DEFINES_H__ +#ifndef H5DUMP_DEFINES_H +#define H5DUMP_DEFINES_H -#define H5DUMP_MAX_RANK H5S_MAX_RANK +#define H5DUMP_MAX_RANK H5S_MAX_RANK -#define ATTRIBUTE_DATA 0 -#define DATASET_DATA 1 -#define ENUM_DATA 2 -#define COL 3 +#define ATTRIBUTE_DATA 0 +#define DATASET_DATA 1 +#define ENUM_DATA 2 +#define COL 3 /* Macros for displaying objects */ -#define begin_obj(obj,name,begin) \ - do { \ - if ((name)) { \ - PRINTSTREAM(rawoutstream, "%s \"%s\" %s", (obj), (name), (begin)); \ - } \ - else { \ - PRINTSTREAM(rawoutstream, "%s %s", (obj), (begin)); \ - } \ - } while(0); - -#define end_obj(obj,end) \ - do { \ - if(HDstrlen(end)) { \ - PRINTSTREAM(rawoutstream, "%s", end); \ - if(HDstrlen(obj)) \ - PRINTVALSTREAM(rawoutstream, " "); \ - } \ - if(HDstrlen(obj)) \ - PRINTSTREAM(rawoutstream, "%s", obj); \ - } while(0); +#define begin_obj(obj, name, begin) \ + do { \ + if ((name)) { \ + PRINTSTREAM(rawoutstream, "%s \"%s\" %s", (obj), (name), (begin)); \ + } \ + else { \ + PRINTSTREAM(rawoutstream, "%s %s", (obj), (begin)); \ + } \ + } while (0); +#define end_obj(obj, end) \ + do { \ + if (HDstrlen(end)) { \ + PRINTSTREAM(rawoutstream, "%s", end); \ + if (HDstrlen(obj)) \ + PRINTVALSTREAM(rawoutstream, " "); \ + } \ + if (HDstrlen(obj)) \ + PRINTSTREAM(rawoutstream, "%s", obj); \ + } while (0); /* 3 private values: can't be set, but can be read. Note: these are defined in H5Zprivate, they are duplicated here. */ -#define H5_SZIP_LSB_OPTION_MASK 8 -#define H5_SZIP_MSB_OPTION_MASK 16 -#define H5_SZIP_RAW_OPTION_MASK 128 +#define H5_SZIP_LSB_OPTION_MASK 8 +#define H5_SZIP_MSB_OPTION_MASK 16 +#define H5_SZIP_RAW_OPTION_MASK 128 -#endif /* !H5DUMP_DEFINES_H__ */ +#endif /* H5DUMP_DEFINES_H */ diff --git a/tools/src/h5dump/h5dump_extern.h b/tools/src/h5dump/h5dump_extern.h index 00d3bd2..308f602 100644 --- a/tools/src/h5dump/h5dump_extern.h +++ b/tools/src/h5dump/h5dump_extern.h @@ -6,12 +6,12 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -#ifndef H5DUMP_EXTERN_H__ -#define H5DUMP_EXTERN_H__ +#ifndef H5DUMP_EXTERN_H +#define H5DUMP_EXTERN_H #include "hdf5.h" #include "H5private.h" @@ -26,61 +26,65 @@ **/ /* the table of dump functions */ typedef struct dump_functions_t { - void (*dump_group_function) (hid_t, const char *); - void (*dump_named_datatype_function) (hid_t, const char *); - void (*dump_dataset_function) (hid_t, const char *, struct subset_t *); - void (*dump_dataspace_function) (hid_t); - void (*dump_datatype_function) (hid_t); - herr_t (*dump_attribute_function) (hid_t, const char *, const H5A_info_t *, void *); - void (*dump_data_function) (hid_t, int, struct subset_t *, int); + void (*dump_group_function)(hid_t, const char *); + void (*dump_named_datatype_function)(hid_t, const char *); + void (*dump_dataset_function)(hid_t, const char *, struct subset_t *); + void (*dump_dataspace_function)(hid_t); + void (*dump_datatype_function)(hid_t); + herr_t (*dump_attribute_function)(hid_t, const char *, const H5A_info_t *, void *); + void (*dump_data_function)(hid_t, int, struct subset_t *, int); } dump_functions; /* List of table structures. There is one table structure for each file */ typedef struct h5dump_table_list_t { - size_t nalloc; - size_t nused; + size_t nalloc; + size_t nused; struct { - unsigned long fileno; /* File number that these tables refer to */ - hid_t oid; /* ID of an object in this file, held open so fileno is consistent */ - table_t *group_table; /* Table of groups */ - table_t *dset_table; /* Table of datasets */ - table_t *type_table; /* Table of datatypes */ - } *tables; + unsigned long fileno; /* File number that these tables refer to */ + hid_t oid; /* ID of an object in this file, held open so fileno is consistent */ + table_t * group_table; /* Table of groups */ + table_t * dset_table; /* Table of datasets */ + table_t * type_table; /* Table of datatypes */ + } * tables; } h5dump_table_list_t; -extern h5dump_table_list_t table_list; -extern table_t *group_table, *dset_table, *type_table; -extern unsigned dump_indent; /*how far in to indent the line */ +extern h5dump_table_list_t table_list; +extern table_t * group_table, *dset_table, *type_table; -extern int unamedtype; /* shared datatype with no name */ -extern hbool_t hit_elink; /* whether we have traversed an external link */ -extern size_t prefix_len; -extern char *prefix; -extern const char *fp_format; +extern unsigned dump_indent; /* how far in to indent the line */ +extern int unamedtype; /* shared datatype with no name */ +extern hbool_t hit_elink; /* whether we have traversed an external link */ +extern size_t prefix_len; +extern char * prefix; +extern const char *fp_format; /* things to display or which are set via command line parameters */ -extern int display_all; -extern int display_oid; -extern int display_data; -extern int display_attr_data; -extern int display_char; /*print 1-byte numbers as ASCII */ -extern int usingdasho; -extern int display_bb; /*superblock */ -extern int display_dcpl; /*dcpl */ -extern int display_fi; /*file index */ -extern int display_ai; /*array index */ -extern int display_escape; /*escape non printable characters */ -extern int display_region; /*print region reference data */ -extern int disable_compact_subset; /* disable compact form of subset notation */ -extern int display_packed_bits; /*print 1-8 byte numbers as packed bits*/ -extern int include_attrs; /* Display attributes */ -extern int display_vds_first; /* vds display to first missing */ -extern int vds_gap_size; /* vds skip missing files */ +typedef struct { + int display_all; + int display_oid; + int display_data; + int display_attr_data; + int display_char; /* print 1-byte numbers as ASCII */ + int usingdasho; + int display_bb; /* superblock */ + int display_dcpl; /* dcpl */ + int display_fi; /* file index */ + int display_ai; /* array index */ + int display_escape; /* escape non printable characters */ + int display_region; /* print region reference data */ + int disable_compact_subset; /* disable compact form of subset notation */ + int display_packed_bits; /* print 1-8 byte numbers as packed bits */ + int include_attrs; /* Display attributes */ + int display_vds_first; /* vds display to all by default */ + int vds_gap_size; /* vds skip missing files default is none */ +} dump_opt_t; +extern dump_opt_t dump_opts; -#define PACKED_BITS_MAX 8 /* Maximum number of packed-bits to display */ -#define PACKED_BITS_SIZE_MAX 8*sizeof(long long) /* Maximum bits size of integer types of packed-bits */ +#define PACKED_BITS_MAX 8 /* Maximum number of packed-bits to display */ +#define PACKED_BITS_SIZE_MAX 8 * sizeof(long long) /* Maximum bits size of integer types of packed-bits */ /* mask list for packed bits */ -extern unsigned long long packed_mask[PACKED_BITS_MAX]; /* packed bits are restricted to 8*sizeof(llong) bytes */ +extern unsigned long long + packed_mask[PACKED_BITS_MAX]; /* packed bits are restricted to 8*sizeof(llong) bytes */ /* packed bits display parameters */ extern unsigned packed_offset[PACKED_BITS_MAX]; @@ -96,13 +100,13 @@ extern const dump_functions *dump_function_table; extern "C" { #endif -void add_prefix(char **prfx, size_t *prfx_len, const char *name); -hid_t h5_fileaccess(void); -ssize_t table_list_add(hid_t oid, unsigned long file_no); -ssize_t table_list_visited(unsigned long file_no); +void add_prefix(char **prfx, size_t *prfx_len, const char *name); +hid_t h5_fileaccess(void); +ssize_t table_list_add(hid_t oid, unsigned long file_no); +ssize_t table_list_visited(unsigned long file_no); #ifdef __cplusplus } #endif -#endif /* !H5DUMP_EXTERN_H__ */ +#endif /* H5DUMP_EXTERN_H */ diff --git a/tools/src/h5dump/h5dump_xml.c b/tools/src/h5dump/h5dump_xml.c index c4fd948..827daf3 100644 --- a/tools/src/h5dump/h5dump_xml.c +++ b/tools/src/h5dump/h5dump_xml.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -20,10 +20,10 @@ #include "h5dump_extern.h" #include "h5dump_xml.h" -const char *xmlnsprefix="hdf5:"; +const char *xmlnsprefix = "hdf5:"; /* - * Alternative formating for data dumped to XML + * Alternative formatting for data dumped to XML * In general, the numbers are the same, but separators * except spaces are not used. * @@ -34,53 +34,54 @@ const char *xmlnsprefix="hdf5:"; * * This table only affects XML output. */ -static h5tool_format_t xml_dataformat = { - 0, /*raw */ - - "", /*fmt_raw */ - "%d", /*fmt_int */ - "%u", /*fmt_uint */ - "%hhd", /*fmt_schar */ - "%u", /*fmt_uchar */ - "%d", /*fmt_short */ - "%u", /*fmt_ushort */ - "%ld", /*fmt_long */ - "%lu", /*fmt_ulong */ - NULL, /*fmt_llong */ - NULL, /*fmt_ullong */ - "%g", /*fmt_double */ - "%g", /*fmt_float */ - - 0, /*ascii */ - 0, /*str_locale */ - 0, /*str_repeat */ - - "", /*arr_pre */ - "", /*arr_sep */ - "", /*arr_suf */ - 1, /*arr_linebreak */ - - "", /*cmpd_name */ - "", /*cmpd_sep */ - "", /*cmpd_pre */ - "", /*cmpd_suf */ - "", /*cmpd_end */ - NULL, /*cmpd_listv */ - - " ", /*vlen_sep */ - " ", /*vlen_pre */ - "", /*vlen_suf */ - "", /*vlen_end */ - - "%s", /*elmt_fmt */ - "", /*elmt_suf1 */ - " ", /*elmt_suf2 */ - - "", /*idx_n_fmt */ - "", /*idx_sep */ - "", /*idx_fmt */ - - 80, /*line_ncols *//*standard default columns */ +static h5tool_format_t xml_dataformat = { + 0, /*raw */ + + "", /*fmt_raw */ + "%d", /*fmt_int */ + "%u", /*fmt_uint */ + "%hhd", /*fmt_schar */ + "%u", /*fmt_uchar */ + "%d", /*fmt_short */ + "%u", /*fmt_ushort */ + "%ld", /*fmt_long */ + "%lu", /*fmt_ulong */ + NULL, /*fmt_llong */ + NULL, /*fmt_ullong */ + "%g", /*fmt_double */ + "%g", /*fmt_float */ + + 0, /*ascii */ + 0, /*str_locale */ + 0, /*str_repeat */ + + "", /*arr_pre */ + "", /*arr_sep */ + "", /*arr_suf */ + 1, /*arr_linebreak */ + + "", /*cmpd_name */ + "", /*cmpd_sep */ + "", /*cmpd_pre */ + "", /*cmpd_suf */ + "", /*cmpd_end */ + NULL, /*cmpd_listv */ + + " ", /*vlen_sep */ + " ", /*vlen_pre */ + "", /*vlen_suf */ + "", /*vlen_end */ + + "%s", /*elmt_fmt */ + "", /*elmt_suf1 */ + " ", /*elmt_suf2 */ + + "", /*idx_n_fmt */ + "", /*idx_sep */ + "", /*idx_fmt */ + + 80, + /*line_ncols */ /*standard default columns */ 0, /*line_per_line */ "", /*line_pre */ "%s", /*line_1st */ @@ -90,31 +91,30 @@ static h5tool_format_t xml_dataformat = { 1, /*line_multi_new */ " ", /*line_indent */ - 1, /*skip_first */ + 1, /*skip_first */ 1, /*obj_hidefileno */ - " "H5_PRINTF_HADDR_FMT, /*obj_format */ - - 1, /*dset_hidefileno */ - "DATASET %s ", /*dset_format */ - "%s", /*dset_blockformat_pre */ - "%s", /*dset_ptformat_pre */ - "%s", /*dset_ptformat */ - 0, /*array indices */ - 0 /*escape non printable characters */ + " %" PRIuHADDR, /*obj_format */ + + 1, /*dset_hidefileno */ + "DATASET %s ", /*dset_format */ + "%s", /*dset_blockformat_pre */ + "%s", /*dset_ptformat_pre */ + "%s", /*dset_ptformat */ + 0, /*array indices */ + 0 /*escape non printable characters */ }; - /* internal functions */ -static int xml_name_to_XID(const char *, char *, int , int ); +static int xml_name_to_XID(hid_t, const char *, char *, int, int); /* internal functions used by XML option */ -static void xml_print_datatype(hid_t, unsigned); -static void xml_print_enum(hid_t); -static int xml_print_refs(hid_t, int); -static int xml_print_strs(hid_t, int); -static char *xml_escape_the_string(const char *, int); -static char *xml_escape_the_name(const char *); +static void xml_print_datatype(hid_t, unsigned); +static void xml_print_enum(hid_t); +static int xml_print_refs(hid_t, int); +static int xml_print_strs(hid_t, int); +static char *xml_escape_the_string(const char *, int); +static char *xml_escape_the_name(const char *); /*------------------------------------------------------------------------- * Function: xml_dump_all_cb @@ -130,44 +130,44 @@ static char *xml_escape_the_name(const char *); *------------------------------------------------------------------------- */ static herr_t -xml_dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void H5_ATTR_UNUSED *op_data) +xml_dump_all_cb(hid_t group, const char *name, const H5L_info2_t *linfo, void H5_ATTR_UNUSED *op_data) { hid_t obj; - herr_t ret = SUCCEED; - char *obj_path = NULL; /* Full path of object */ - h5tools_str_t buffer; /* string into which to render */ - h5tools_context_t ctx; /* print context */ - h5tool_format_t *outputformat = &xml_dataformat; + herr_t ret = SUCCEED; + char * obj_path = NULL; /* Full path of object */ + h5tools_str_t buffer; /* string into which to render */ + h5tools_context_t ctx; /* print context */ + h5tool_format_t * outputformat = &xml_dataformat; h5tool_format_t string_dataformat; - hsize_t curr_pos = 0; /* total data element position */ + hsize_t curr_pos = 0; /* total data element position */ /* setup */ HDmemset(&buffer, 0, sizeof(h5tools_str_t)); HDmemset(&ctx, 0, sizeof(ctx)); ctx.indent_level = dump_indent / COL; - ctx.cur_column = dump_indent; + ctx.cur_column = dump_indent; string_dataformat = *outputformat; if (fp_format) { string_dataformat.fmt_double = fp_format; - string_dataformat.fmt_float = fp_format; + string_dataformat.fmt_float = fp_format; } - if (h5tools_nCols==0) { - string_dataformat.line_ncols = 65535; + if (h5tools_nCols == 0) { + string_dataformat.line_ncols = 65535; string_dataformat.line_per_line = 1; } else string_dataformat.line_ncols = h5tools_nCols; - string_dataformat.do_escape = display_escape; - outputformat = &string_dataformat; + string_dataformat.do_escape = dump_opts.display_escape; + outputformat = &string_dataformat; /* Build the object's path name */ obj_path = (char *)HDmalloc(HDstrlen(prefix) + HDstrlen(name) + 2); - if(!obj_path) { + if (!obj_path) { ret = FAIL; goto done; } @@ -176,393 +176,400 @@ xml_dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void H5_ HDstrcat(obj_path, "/"); HDstrcat(obj_path, name); - if(linfo->type == H5L_TYPE_HARD) { - H5O_info_t oinfo; + if (linfo->type == H5L_TYPE_HARD) { + H5O_info2_t oinfo; /* Stat the object */ - if(H5Oget_info_by_name2(group, name, &oinfo, H5O_INFO_BASIC, H5P_DEFAULT) < 0) { + if (H5Oget_info_by_name3(group, name, &oinfo, H5O_INFO_BASIC, H5P_DEFAULT) < 0) { error_msg("unable to get object information for \"%s\"\n", name); h5tools_setstatus(EXIT_FAILURE); ret = FAIL; goto done; } /* end if */ - switch(oinfo.type) { - case H5O_TYPE_GROUP: - if((obj = H5Gopen2(group, name, H5P_DEFAULT)) < 0) { - error_msg("unable to dump group \"%s\"\n", name); - h5tools_setstatus(EXIT_FAILURE); - ret = FAIL; - } - else { - char *old_prefix; /* Pointer to previous prefix */ - - /* Keep copy of prefix before iterating into group */ - if((old_prefix = HDstrdup(prefix)) == NULL) { - error_msg("unable to allocate buffer\n"); + switch (oinfo.type) { + case H5O_TYPE_GROUP: + if ((obj = H5Gopen2(group, name, H5P_DEFAULT)) < 0) { + error_msg("unable to dump group \"%s\"\n", name); h5tools_setstatus(EXIT_FAILURE); ret = FAIL; } else { - /* Append group name to prefix */ - add_prefix(&prefix, &prefix_len, name); - - /* Iterate into group */ - dump_function_table->dump_group_function(obj, name); - - /* Restore old prefix name */ - HDstrcpy(prefix, old_prefix); - HDfree(old_prefix); - } - - /* Close group */ - H5Gclose(obj); - } - break; - - case H5O_TYPE_DATASET: - if((obj = H5Dopen2(group, name, H5P_DEFAULT)) >= 0) { - if(oinfo.rc > 1 || hit_elink) { - obj_t *found_obj; /* Found object */ - - found_obj = search_obj(dset_table, oinfo.addr); - - if(found_obj == NULL) { - ctx.indent_level++; - - ctx.need_prefix = TRUE; - - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "%s \"%s\" %s", - h5tools_dump_header_format->datasetbegin, name, - h5tools_dump_header_format->datasetblockbegin); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - - error_msg("internal error (file %s:line %d)\n", __FILE__, __LINE__); - - ctx.need_prefix = TRUE; - - /* Render the element */ - h5tools_str_reset(&buffer); - if(HDstrlen(h5tools_dump_header_format->datasetblockend)) { - h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->datasetblockend); - if(HDstrlen(h5tools_dump_header_format->datasetend)) - h5tools_str_append(&buffer, " "); - } - if(HDstrlen(h5tools_dump_header_format->datasetend)) - h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->datasetend); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - - ctx.indent_level--; + char *old_prefix; /* Pointer to previous prefix */ + /* Keep copy of prefix before iterating into group */ + if ((old_prefix = HDstrdup(prefix)) == NULL) { + error_msg("unable to allocate buffer\n"); h5tools_setstatus(EXIT_FAILURE); ret = FAIL; - H5Dclose(obj); - goto done; } - else if(found_obj->displayed) { - /* the XML version */ - char *t_obj_path = xml_escape_the_name(obj_path); - char *t_prefix = xml_escape_the_name(HDstrcmp(prefix,"") ? prefix : "/"); - char *t_name = xml_escape_the_name(name); - char *t_objname = xml_escape_the_name(found_obj->objname); - char dsetxid[100]; - char parentxid[100]; - char pointerxid[100]; - - /* Create OBJ-XIDs for the parent and object */ - xml_name_to_XID(obj_path, dsetxid, (int)sizeof(dsetxid), 1); - xml_name_to_XID(prefix, parentxid, (int)sizeof(parentxid), 1); - - ctx.need_prefix = TRUE; - - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sDataset Name=\"%s\" OBJ-XID=\"%s-%d\" " - "H5Path=\"%s\" Parents=\"%s\" " - "H5ParentPaths=\"%s\">", - xmlnsprefix, - t_name, /* Dataset Name */ - dsetxid, get_next_xid(), /* OBJ-XID */ - t_obj_path, /* H5Path */ - parentxid, /* Parents */ - t_prefix); /* H5ParentPaths */ - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - - xml_name_to_XID(found_obj->objname, pointerxid, (int)sizeof(pointerxid), 1); - - ctx.indent_level++; - - ctx.need_prefix = TRUE; - - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sDatasetPtr OBJ-XID=\"%s\" H5Path=\"%s\"/>", - xmlnsprefix, - pointerxid,t_objname); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + else { + /* Append group name to prefix */ + add_prefix(&prefix, &prefix_len, name); - ctx.indent_level--; + /* Iterate into group */ + dump_function_table->dump_group_function(obj, name); - ctx.need_prefix = TRUE; + /* Restore old prefix name */ + HDstrcpy(prefix, old_prefix); + HDfree(old_prefix); + } - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "</%sDataset>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + /* Close group */ + H5Gclose(obj); + } + break; - HDfree(t_name); - HDfree(t_obj_path); - HDfree(t_prefix); - HDfree(t_objname); + case H5O_TYPE_DATASET: + if ((obj = H5Dopen2(group, name, H5P_DEFAULT)) >= 0) { + if (oinfo.rc > 1 || hit_elink) { + obj_t *found_obj; /* Found object */ + + found_obj = search_obj(dset_table, &oinfo.token); + + if (found_obj == NULL) { + ctx.indent_level++; + + ctx.need_prefix = TRUE; + + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "%s \"%s\" %s", + h5tools_dump_header_format->datasetbegin, name, + h5tools_dump_header_format->datasetblockbegin); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + + error_msg("internal error (file %s:line %d)\n", __FILE__, __LINE__); + + ctx.need_prefix = TRUE; + + /* Render the element */ + h5tools_str_reset(&buffer); + if (HDstrlen(h5tools_dump_header_format->datasetblockend)) { + h5tools_str_append(&buffer, "%s", + h5tools_dump_header_format->datasetblockend); + if (HDstrlen(h5tools_dump_header_format->datasetend)) + h5tools_str_append(&buffer, " "); + } + if (HDstrlen(h5tools_dump_header_format->datasetend)) + h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->datasetend); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + + ctx.indent_level--; + + h5tools_setstatus(EXIT_FAILURE); + ret = FAIL; + H5Dclose(obj); + goto done; + } + else if (found_obj->displayed) { + /* the XML version */ + char *t_obj_path = xml_escape_the_name(obj_path); + char *t_prefix = xml_escape_the_name(HDstrcmp(prefix, "") ? prefix : "/"); + char *t_name = xml_escape_the_name(name); + char *t_objname = xml_escape_the_name(found_obj->objname); + char dsetxid[100]; + char parentxid[100]; + char pointerxid[100]; + + /* Create OBJ-XIDs for the parent and object */ + xml_name_to_XID(obj, obj_path, dsetxid, (int)sizeof(dsetxid), 1); + xml_name_to_XID(obj, prefix, parentxid, (int)sizeof(parentxid), 1); + + ctx.need_prefix = TRUE; + + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, + "<%sDataset Name=\"%s\" OBJ-XID=\"%s-%d\" " + "H5Path=\"%s\" Parents=\"%s\" " + "H5ParentPaths=\"%s\">", + xmlnsprefix, t_name, /* Dataset Name */ + dsetxid, get_next_xid(), /* OBJ-XID */ + t_obj_path, /* H5Path */ + parentxid, /* Parents */ + t_prefix); /* H5ParentPaths */ + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + + xml_name_to_XID(obj, found_obj->objname, pointerxid, (int)sizeof(pointerxid), 1); + + ctx.indent_level++; + + ctx.need_prefix = TRUE; + + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<%sDatasetPtr OBJ-XID=\"%s\" H5Path=\"%s\"/>", + xmlnsprefix, pointerxid, t_objname); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + + ctx.indent_level--; + + ctx.need_prefix = TRUE; + + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "</%sDataset>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + + HDfree(t_name); + HDfree(t_obj_path); + HDfree(t_prefix); + HDfree(t_objname); + + H5Dclose(obj); + goto done; + } + else + found_obj->displayed = TRUE; + } /* end if */ - H5Dclose(obj); - goto done; - } - else - found_obj->displayed = TRUE; - } /* end if */ + dump_function_table->dump_dataset_function(obj, name, NULL); + H5Dclose(obj); + } + else { + error_msg("unable to dump dataset \"%s\"\n", name); + h5tools_setstatus(EXIT_FAILURE); + ret = FAIL; + } + break; - dump_function_table->dump_dataset_function(obj, name, NULL); - H5Dclose(obj); - } - else { - error_msg("unable to dump dataset \"%s\"\n", name); - h5tools_setstatus(EXIT_FAILURE); - ret = FAIL; - } - break; + case H5O_TYPE_NAMED_DATATYPE: + if ((obj = H5Topen2(group, name, H5P_DEFAULT)) < 0) { + error_msg("unable to dump datatype \"%s\"\n", name); + h5tools_setstatus(EXIT_FAILURE); + ret = FAIL; + } + else { + dump_function_table->dump_named_datatype_function(obj, name); + H5Tclose(obj); + } + break; - case H5O_TYPE_NAMED_DATATYPE: - if((obj = H5Topen2(group, name, H5P_DEFAULT)) < 0) { - error_msg("unable to dump datatype \"%s\"\n", name); + case H5O_TYPE_MAP: + case H5O_TYPE_UNKNOWN: + case H5O_TYPE_NTYPES: + default: + error_msg("unknown object \"%s\"\n", name); h5tools_setstatus(EXIT_FAILURE); ret = FAIL; - } - else { - dump_function_table->dump_named_datatype_function(obj, name); - H5Tclose(obj); - } - break; - - case H5O_TYPE_MAP: - case H5O_TYPE_UNKNOWN: - case H5O_TYPE_NTYPES: - default: - error_msg("unknown object \"%s\"\n", name); - h5tools_setstatus(EXIT_FAILURE); - ret = FAIL; } } /* end if */ else { - char *targbuf; + char *targbuf; - switch(linfo->type) { - case H5L_TYPE_SOFT: - if((targbuf = (char *)HDmalloc(linfo->u.val_size)) == NULL) { - error_msg("unable to allocate buffer\n"); - h5tools_setstatus(EXIT_FAILURE); - ret = FAIL; - } - else { - if(H5Lget_val(group, name, targbuf, linfo->u.val_size, H5P_DEFAULT) < 0) { - error_msg("unable to get link value\n"); + switch (linfo->type) { + case H5L_TYPE_SOFT: + if ((targbuf = (char *)HDmalloc(linfo->u.val_size)) == NULL) { + error_msg("unable to allocate buffer\n"); h5tools_setstatus(EXIT_FAILURE); ret = FAIL; } else { - /* print the value of a soft link */ - /* XML */ - char linkxid[100]; - char parentxid[100]; - char targetxid[100]; - char *t_prefix = xml_escape_the_name(HDstrcmp(prefix,"") ? prefix : "/"); - char *t_name = xml_escape_the_name(name); - char *t_targbuf = xml_escape_the_name(targbuf); - char *t_obj_path = xml_escape_the_name(obj_path); - char *t_link_path; - int res; - - t_link_path = (char *)HDmalloc(HDstrlen(prefix) + linfo->u.val_size + 1); - if(targbuf[0] == '/') - HDstrcpy(t_link_path, targbuf); - else { - HDstrcpy(t_link_path, prefix); - HDstrcat(HDstrcat(t_link_path, "/"), targbuf); - } /* end else */ - - /* Create OBJ-XIDs for the parent and object */ - xml_name_to_XID(t_obj_path, linkxid, (int)sizeof(linkxid), 1); - xml_name_to_XID(prefix, parentxid, (int)sizeof(parentxid), 1); - - /* Try to create an OBJ-XID for the object pointed to */ - res = xml_name_to_XID(t_link_path, targetxid, (int)sizeof(targetxid), 0); - if (res == 0) { - /* target obj found */ - ctx.need_prefix = TRUE; - - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sSoftLink LinkName=\"%s\" " - "OBJ-XID=\"%s\" " - "H5SourcePath=\"%s\" " - "TargetPath=\"%s\" TargetObj=\"%s\" " - "Parents=\"%s\" H5ParentPaths=\"%s\" />", - xmlnsprefix, - t_name, /* LinkName */ - linkxid, /* OBJ-XID */ - t_obj_path, /* H5SourcePath */ - t_targbuf, /* TargetPath */ - targetxid, /* TargetObj */ - parentxid, /* Parents */ - t_prefix); /* H5ParentPaths */ - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + if (H5Lget_val(group, name, targbuf, linfo->u.val_size, H5P_DEFAULT) < 0) { + error_msg("unable to get link value\n"); + h5tools_setstatus(EXIT_FAILURE); + ret = FAIL; } else { - /* dangling link -- omit from xml attributes */ - ctx.need_prefix = TRUE; + /* print the value of a soft link */ + /* XML */ + char linkxid[100]; + char parentxid[100]; + char targetxid[100]; + char *t_prefix = xml_escape_the_name(HDstrcmp(prefix, "") ? prefix : "/"); + char *t_name = xml_escape_the_name(name); + char *t_targbuf = xml_escape_the_name(targbuf); + char *t_obj_path = xml_escape_the_name(obj_path); + char *t_link_path; + int res; - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sSoftLink LinkName=\"%s\" " - "OBJ-XID=\"%s\" " - "H5SourcePath=\"%s\" " - "TargetPath=\"%s\" " - "Parents=\"%s\" H5ParentPaths=\"%s\" />", - xmlnsprefix, - t_name, /* LinkName */ - linkxid, /* OBJ-XID */ - t_obj_path, /* H5SourcePath */ - t_targbuf, /* TargetPath */ - parentxid, /* Parents */ - t_prefix); /* H5ParentPaths */ - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + t_link_path = (char *)HDmalloc(HDstrlen(prefix) + linfo->u.val_size + 1); + if (targbuf[0] == '/') + HDstrcpy(t_link_path, targbuf); + else { + HDstrcpy(t_link_path, prefix); + HDstrcat(HDstrcat(t_link_path, "/"), targbuf); + } /* end else */ + + /* Create OBJ-XIDs for the parent and object */ + xml_name_to_XID(group, t_obj_path, linkxid, (int)sizeof(linkxid), 1); + xml_name_to_XID(group, prefix, parentxid, (int)sizeof(parentxid), 1); + + /* Try to create an OBJ-XID for the object pointed to */ + res = xml_name_to_XID(group, t_link_path, targetxid, (int)sizeof(targetxid), 0); + if (res == 0) { + /* target obj found */ + ctx.need_prefix = TRUE; + + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, + "<%sSoftLink LinkName=\"%s\" " + "OBJ-XID=\"%s\" " + "H5SourcePath=\"%s\" " + "TargetPath=\"%s\" TargetObj=\"%s\" " + "Parents=\"%s\" H5ParentPaths=\"%s\" />", + xmlnsprefix, t_name, /* LinkName */ + linkxid, /* OBJ-XID */ + t_obj_path, /* H5SourcePath */ + t_targbuf, /* TargetPath */ + targetxid, /* TargetObj */ + parentxid, /* Parents */ + t_prefix); /* H5ParentPaths */ + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + } + else { + /* dangling link -- omit from xml attributes */ + ctx.need_prefix = TRUE; + + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, + "<%sSoftLink LinkName=\"%s\" " + "OBJ-XID=\"%s\" " + "H5SourcePath=\"%s\" " + "TargetPath=\"%s\" " + "Parents=\"%s\" H5ParentPaths=\"%s\" />", + xmlnsprefix, t_name, /* LinkName */ + linkxid, /* OBJ-XID */ + t_obj_path, /* H5SourcePath */ + t_targbuf, /* TargetPath */ + parentxid, /* Parents */ + t_prefix); /* H5ParentPaths */ + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + } + + HDfree(t_prefix); + HDfree(t_name); + HDfree(t_targbuf); + HDfree(t_obj_path); + HDfree(t_link_path); } - HDfree(t_prefix); - HDfree(t_name); - HDfree(t_targbuf); - HDfree(t_obj_path); - HDfree(t_link_path); + HDfree(targbuf); } + break; - HDfree(targbuf); - } - break; - - case H5L_TYPE_EXTERNAL: - if((targbuf = (char *)HDmalloc(linfo->u.val_size)) == NULL) { - error_msg("unable to allocate buffer\n"); - h5tools_setstatus(EXIT_FAILURE); - ret = FAIL; - } - else { - if(H5Lget_val(group, name, targbuf, linfo->u.val_size, H5P_DEFAULT) < 0) { - error_msg("unable to get external link value\n"); + case H5L_TYPE_EXTERNAL: + if ((targbuf = (char *)HDmalloc(linfo->u.val_size)) == NULL) { + error_msg("unable to allocate buffer\n"); h5tools_setstatus(EXIT_FAILURE); ret = FAIL; - } /* end if */ + } else { - const char *filename; - const char *targname; - - if(H5Lunpack_elink_val(targbuf, linfo->u.val_size, NULL, &filename, &targname) < 0) { - error_msg("unable to unpack external link value\n"); + if (H5Lget_val(group, name, targbuf, linfo->u.val_size, H5P_DEFAULT) < 0) { + error_msg("unable to get external link value\n"); h5tools_setstatus(EXIT_FAILURE); ret = FAIL; } /* end if */ else { - char linkxid[100]; - char parentxid[100]; - char *t_name = xml_escape_the_name(name); - char *t_prefix = xml_escape_the_name(HDstrcmp(prefix,"") ? prefix : "/"); - char *t_obj_path = xml_escape_the_name(obj_path); - char *t_filename = xml_escape_the_name(filename); - char *t_targname = xml_escape_the_name(targname); - - /* Create OBJ-XIDs for the parent and object */ - xml_name_to_XID(t_obj_path, linkxid, (int)sizeof(linkxid), 1); - xml_name_to_XID(prefix, parentxid, (int)sizeof(parentxid), 1); - - ctx.need_prefix = TRUE; - - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sExternalLink LinkName=\"%s\" " - "OBJ-XID=\"%s\" " - "H5SourcePath=\"%s\" " - "TargetFilename=\"%s\" " - "TargetPath=\"%s\" " - "Parents=\"%s\" H5ParentPaths=\"%s\" />", - xmlnsprefix, - t_name, /* LinkName */ - linkxid, /* OBJ-XID */ - t_obj_path, /* H5SourcePath */ - filename, /* TargetFilename */ - targname, /* TargetPath*/ - parentxid, /* Parents */ - t_prefix); /* H5ParentPaths */ - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - - HDfree(t_prefix); - HDfree(t_name); - HDfree(t_filename); - HDfree(t_targname); - HDfree(t_obj_path); - } /* end else */ - } /* end else */ - HDfree(targbuf); - } - break; + const char *filename; + const char *targname; + + if (H5Lunpack_elink_val(targbuf, linfo->u.val_size, NULL, &filename, &targname) < 0) { + error_msg("unable to unpack external link value\n"); + h5tools_setstatus(EXIT_FAILURE); + ret = FAIL; + } /* end if */ + else { + char linkxid[100]; + char parentxid[100]; + char *t_name = xml_escape_the_name(name); + char *t_prefix = xml_escape_the_name(HDstrcmp(prefix, "") ? prefix : "/"); + char *t_obj_path = xml_escape_the_name(obj_path); + char *t_filename = xml_escape_the_name(filename); + char *t_targname = xml_escape_the_name(targname); + + /* Create OBJ-XIDs for the parent and object */ + xml_name_to_XID(group, t_obj_path, linkxid, (int)sizeof(linkxid), 1); + xml_name_to_XID(group, prefix, parentxid, (int)sizeof(parentxid), 1); + + ctx.need_prefix = TRUE; + + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, + "<%sExternalLink LinkName=\"%s\" " + "OBJ-XID=\"%s\" " + "H5SourcePath=\"%s\" " + "TargetFilename=\"%s\" " + "TargetPath=\"%s\" " + "Parents=\"%s\" H5ParentPaths=\"%s\" />", + xmlnsprefix, t_name, /* LinkName */ + linkxid, /* OBJ-XID */ + t_obj_path, /* H5SourcePath */ + filename, /* TargetFilename */ + targname, /* TargetPath*/ + parentxid, /* Parents */ + t_prefix); /* H5ParentPaths */ + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + + HDfree(t_prefix); + HDfree(t_name); + HDfree(t_filename); + HDfree(t_targname); + HDfree(t_obj_path); + } /* end else */ + } /* end else */ + HDfree(targbuf); + } + break; - case H5L_TYPE_ERROR: - case H5L_TYPE_MAX: - case H5L_TYPE_HARD: - default: - { - char linkxid[100]; - char parentxid[100]; - char *t_name = xml_escape_the_name(name); - char *t_prefix = xml_escape_the_name(HDstrcmp(prefix,"") ? prefix : "/"); + case H5L_TYPE_ERROR: + case H5L_TYPE_MAX: + case H5L_TYPE_HARD: + default: { + char linkxid[100]; + char parentxid[100]; + char *t_name = xml_escape_the_name(name); + char *t_prefix = xml_escape_the_name(HDstrcmp(prefix, "") ? prefix : "/"); char *t_obj_path = xml_escape_the_name(obj_path); /* Create OBJ-XIDs for the parent and object */ - xml_name_to_XID(t_obj_path, linkxid, (int)sizeof(linkxid), 1); - xml_name_to_XID(prefix, parentxid, (int)sizeof(parentxid), 1); + xml_name_to_XID(group, t_obj_path, linkxid, (int)sizeof(linkxid), 1); + xml_name_to_XID(group, prefix, parentxid, (int)sizeof(parentxid), 1); ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sUserDefined LinkName=\"%s\" " - "OBJ-XID=\"%s\" " - "H5SourcePath=\"%s\" " - "LinkClass=\"%d\" " - "Parents=\"%s\" H5ParentPaths=\"%s\" />", - xmlnsprefix, - t_name, /* LinkName */ - linkxid, /* OBJ-XID */ - t_obj_path, /* H5SourcePath */ - linfo->type, /* LinkClass */ - parentxid, /* Parents */ - t_prefix); /* H5ParentPaths */ - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, + "<%sUserDefined LinkName=\"%s\" " + "OBJ-XID=\"%s\" " + "H5SourcePath=\"%s\" " + "LinkClass=\"%d\" " + "Parents=\"%s\" H5ParentPaths=\"%s\" />", + xmlnsprefix, t_name, /* LinkName */ + linkxid, /* OBJ-XID */ + t_obj_path, /* H5SourcePath */ + linfo->type, /* LinkClass */ + parentxid, /* Parents */ + t_prefix); /* H5ParentPaths */ + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); HDfree(t_prefix); HDfree(t_name); HDfree(t_obj_path); - } - break; + } break; } /* end switch */ - } /* end else */ + } /* end else */ done: h5tools_str_close(&buffer); - if(obj_path) + if (obj_path) HDfree(obj_path); return ret; } @@ -575,20 +582,29 @@ done: * 1 - generate a fake entry and return fake id. */ int -xml_name_to_XID(const char *str , char *outstr, int outlen, int gen) +xml_name_to_XID(hid_t loc_id, const char *str, char *outstr, int outlen, int gen) { - haddr_t objno; /* Object ID for object at path */ + H5O_token_t obj_token; + char * obj_tok_str = NULL; + int lookup_ret; + + if (outlen < 22) + return 1; - if (outlen < 22) return 1; + H5_CHECK_OVERFLOW(outlen, int, size_t); - objno = ref_path_table_lookup(str); - if (objno == HADDR_UNDEF) { + lookup_ret = ref_path_table_lookup(str, &obj_token); + if (lookup_ret < 0) { if (HDstrlen(str) == 0) { - objno = ref_path_table_lookup("/"); - if (objno == HADDR_UNDEF) { + lookup_ret = ref_path_table_lookup("/", &obj_token); + if (lookup_ret < 0) { if (gen) { - objno = ref_path_table_gen_fake(str); - HDsprintf(outstr, "xid_"H5_PRINTF_HADDR_FMT, objno); + ref_path_table_gen_fake(str, &obj_token); + + H5Otoken_to_str(loc_id, &obj_token, &obj_tok_str); + HDsnprintf(outstr, (size_t)outlen, "xid_%s", obj_tok_str); + H5free_memory(obj_tok_str); + return 0; } else { @@ -598,8 +614,12 @@ xml_name_to_XID(const char *str , char *outstr, int outlen, int gen) } else { if (gen) { - objno = ref_path_table_gen_fake(str); - HDsprintf(outstr, "xid_"H5_PRINTF_HADDR_FMT, objno); + ref_path_table_gen_fake(str, &obj_token); + + H5Otoken_to_str(loc_id, &obj_token, &obj_tok_str); + HDsnprintf(outstr, (size_t)outlen, "xid_%s", obj_tok_str); + H5free_memory(obj_tok_str); + return 0; } else { @@ -608,16 +628,18 @@ xml_name_to_XID(const char *str , char *outstr, int outlen, int gen) } } - HDsprintf(outstr, "xid_"H5_PRINTF_HADDR_FMT, objno); + H5Otoken_to_str(loc_id, &obj_token, &obj_tok_str); + HDsnprintf(outstr, (size_t)outlen, "xid_%s", obj_tok_str); + H5free_memory(obj_tok_str); - return(0); + return 0; } -static const char *quote = """; -static const char *amp = "&"; -static const char *lt = "<"; -static const char *gt = ">"; -static const char *apos = "'"; +static const char *quote = """; +static const char *amp = "&"; +static const char *lt = "<"; +static const char *gt = ">"; +static const char *apos = "'"; /*------------------------------------------------------------------------- * Function: xml_escape_the_name @@ -630,22 +652,22 @@ static const char *apos = "'"; * Programmer: REMcG *------------------------------------------------------------------------- */ -static char * +static char * xml_escape_the_name(const char *str) { size_t extra; size_t len; size_t i; const char *cp; - char *ncp; - char *rcp; + char * ncp; + char * rcp; size_t ncp_len; if (!str) return NULL; - cp = str; - len = HDstrlen(str); + cp = str; + len = HDstrlen(str); extra = 0; for (i = 0; i < len; i++) { @@ -666,12 +688,12 @@ xml_escape_the_name(const char *str) if (extra == 0) return HDstrdup(str); - cp = str; + cp = str; ncp_len = len + extra + 1; rcp = ncp = (char *)HDmalloc(ncp_len); if (!ncp) - return NULL; /* ?? */ + return NULL; /* ?? */ for (i = 0; i < len; i++) { size_t esc_len; @@ -697,7 +719,7 @@ xml_escape_the_name(const char *str) esc_len = HDstrlen(amp); } else { - *ncp = *cp; + *ncp = *cp; esc_len = 1; } ncp += esc_len; @@ -720,15 +742,15 @@ xml_escape_the_name(const char *str) * Programmer: REMcG *------------------------------------------------------------------------- */ -static char * +static char * xml_escape_the_string(const char *str, int slen) { size_t extra; size_t len; size_t i; - const char *cp; - char *ncp; - char *rcp; + const char *cp = NULL; + char * ncp = NULL; + char * rcp = NULL; size_t ncp_len; if (!str) @@ -759,9 +781,9 @@ xml_escape_the_string(const char *str, int slen) cp++; } - cp = str; + cp = str; ncp_len = len + extra + 1; - rcp = ncp = (char *) HDcalloc(ncp_len, sizeof(char)); + rcp = ncp = (char *)HDcalloc(ncp_len, sizeof(char)); if (ncp == NULL) return NULL; /* ?? */ @@ -771,32 +793,34 @@ xml_escape_the_string(const char *str, int slen) if (*cp == '\\') { *ncp++ = '\\'; - *ncp = *cp; + ncp_len--; + *ncp = *cp; esc_len = 1; } else if (*cp == '\"') { *ncp++ = '\\'; - *ncp = *cp; + ncp_len--; + *ncp = *cp; esc_len = 1; } else if (*cp == '\'') { + HDstrncpy(ncp, apos, ncp_len); esc_len = HDstrlen(apos); - HDstrncpy(ncp, apos, esc_len); } else if (*cp == '<') { + HDstrncpy(ncp, lt, ncp_len); esc_len = HDstrlen(lt); - HDstrncpy(ncp, lt, esc_len); } else if (*cp == '>') { + HDstrncpy(ncp, gt, ncp_len); esc_len = HDstrlen(gt); - HDstrncpy(ncp, gt, esc_len); } else if (*cp == '&') { + HDstrncpy(ncp, amp, ncp_len); esc_len = HDstrlen(amp); - HDstrncpy(ncp, amp, esc_len); } else { - *ncp = *cp; + *ncp = *cp; esc_len = 1; } ncp += esc_len; @@ -827,71 +851,71 @@ xml_escape_the_string(const char *str, int slen) static void xml_print_datatype(hid_t type, unsigned in_group) { - char *mname; - hid_t mtype; - unsigned nmembers; - unsigned ndims; - unsigned i; - size_t size; - hsize_t dims[H5DUMP_MAX_RANK]; - H5T_str_t str_pad; - H5T_cset_t cset; - hid_t super; - H5T_order_t ord; - H5T_sign_t sgn; - size_t sz; - size_t spos; - size_t epos; - size_t esize; - size_t mpos; - size_t msize; - int nmembs; - htri_t is_vlstr = FALSE; - h5tools_str_t buffer; /* string into which to render */ - h5tools_context_t ctx; /* print context */ - h5tool_format_t *outputformat = &xml_dataformat; - h5tool_format_t string_dataformat; - hsize_t curr_pos = 0; /* total data element position */ + char * mname; + hid_t mtype; + unsigned nmembers; + unsigned ndims; + unsigned i; + size_t size; + hsize_t dims[H5DUMP_MAX_RANK]; + H5T_str_t str_pad; + H5T_cset_t cset; + hid_t super; + H5T_order_t ord; + H5T_sign_t sgn; + size_t sz; + size_t spos; + size_t epos; + size_t esize; + size_t mpos; + size_t msize; + int nmembs; + htri_t is_vlstr = FALSE; + h5tools_str_t buffer; /* string into which to render */ + h5tools_context_t ctx; /* print context */ + h5tool_format_t * outputformat = &xml_dataformat; + h5tool_format_t string_dataformat; + hsize_t curr_pos = 0; /* total data element position */ /* setup */ HDmemset(&buffer, 0, sizeof(h5tools_str_t)); HDmemset(&ctx, 0, sizeof(ctx)); ctx.indent_level = dump_indent / COL; - ctx.cur_column = dump_indent; + ctx.cur_column = dump_indent; string_dataformat = *outputformat; if (fp_format) { string_dataformat.fmt_double = fp_format; - string_dataformat.fmt_float = fp_format; + string_dataformat.fmt_float = fp_format; } - if (h5tools_nCols==0) { - string_dataformat.line_ncols = 65535; + if (h5tools_nCols == 0) { + string_dataformat.line_ncols = 65535; string_dataformat.line_per_line = 1; } else string_dataformat.line_ncols = h5tools_nCols; - string_dataformat.do_escape = display_escape; - outputformat = &string_dataformat; + string_dataformat.do_escape = dump_opts.display_escape; + outputformat = &string_dataformat; - if(!in_group && H5Tcommitted(type) > 0) { - H5O_info_t oinfo; - obj_t *found_obj; /* Found object */ + if (!in_group && H5Tcommitted(type) > 0) { + H5O_info2_t oinfo; + obj_t * found_obj; /* Found object */ /* detect a shared datatype, output only once */ - H5Oget_info2(type, &oinfo, H5O_INFO_BASIC); - found_obj = search_obj(type_table, oinfo.addr); + H5Oget_info3(type, &oinfo, H5O_INFO_BASIC); + found_obj = search_obj(type_table, &oinfo.token); - if(found_obj) { + if (found_obj) { /* This should be defined somewhere else */ /* These 2 cases are handled the same right now, but probably will have something different eventually */ - char * dtxid = (char *)HDmalloc((size_t)100); + char *dtxid = (char *)HDmalloc((size_t)100); - xml_name_to_XID(found_obj->objname, dtxid, 100, 1); + xml_name_to_XID(type, found_obj->objname, dtxid, 100, 1); if (!found_obj->recorded) { /* 'anonymous' NDT. Use it's object num. as it's name. */ @@ -900,9 +924,9 @@ xml_print_datatype(hid_t type, unsigned in_group) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sNamedDataTypePtr OBJ-XID=\"/%s\"/>", - xmlnsprefix, dtxid); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "<%sNamedDataTypePtr OBJ-XID=\"/%s\"/>", xmlnsprefix, dtxid); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); } else { /* point to the NDT by name */ @@ -912,9 +936,10 @@ xml_print_datatype(hid_t type, unsigned in_group) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sNamedDataTypePtr OBJ-XID=\"%s\" H5Path=\"%s\"/>", - xmlnsprefix, dtxid, t_objname); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "<%sNamedDataTypePtr OBJ-XID=\"%s\" H5Path=\"%s\"/>", xmlnsprefix, + dtxid, t_objname); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); HDfree(t_objname); } HDfree(dtxid); @@ -925,7 +950,8 @@ xml_print_datatype(hid_t type, unsigned in_group) /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "<!-- h5dump error: unknown committed type. -->"); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); h5tools_setstatus(EXIT_FAILURE); } } @@ -936,8 +962,9 @@ xml_print_datatype(hid_t type, unsigned in_group) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sAtomicType>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "<%sAtomicType>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level++; /* <hdf5:IntegerType ByteOrder="bo" Sign="torf" Size="bytes"/> */ @@ -948,7 +975,7 @@ xml_print_datatype(hid_t type, unsigned in_group) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sIntegerType ByteOrder=\"",xmlnsprefix); + h5tools_str_append(&buffer, "<%sIntegerType ByteOrder=\"", xmlnsprefix); switch (ord) { case H5T_ORDER_LE: h5tools_str_append(&buffer, "LE"); @@ -985,15 +1012,17 @@ xml_print_datatype(hid_t type, unsigned in_group) sz = H5Tget_size(type); h5tools_str_append(&buffer, "%lu", (unsigned long)sz); h5tools_str_append(&buffer, "\" />"); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "</%sAtomicType>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "</%sAtomicType>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); break; case H5T_FLOAT: @@ -1007,15 +1036,16 @@ xml_print_datatype(hid_t type, unsigned in_group) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sAtomicType>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "<%sAtomicType>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level++; ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sFloatType ByteOrder=\"",xmlnsprefix); + h5tools_str_append(&buffer, "<%sFloatType ByteOrder=\"", xmlnsprefix); switch (ord) { case H5T_ORDER_LE: @@ -1039,17 +1069,21 @@ xml_print_datatype(hid_t type, unsigned in_group) h5tools_str_append(&buffer, "%lu", (unsigned long)sz); H5Tget_fields(type, &spos, &epos, &esize, &mpos, &msize); h5tools_str_append(&buffer, "\" SignBitLocation=\"%lu\" ", (unsigned long)spos); - h5tools_str_append(&buffer, "ExponentBits=\"%lu\" ExponentLocation=\"%lu\" ", (unsigned long)esize, (unsigned long)epos); - h5tools_str_append(&buffer, "MantissaBits=\"%lu\" MantissaLocation=\"%lu\" />", (unsigned long)msize, (unsigned long)mpos); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "ExponentBits=\"%lu\" ExponentLocation=\"%lu\" ", + (unsigned long)esize, (unsigned long)epos); + h5tools_str_append(&buffer, "MantissaBits=\"%lu\" MantissaLocation=\"%lu\" />", + (unsigned long)msize, (unsigned long)mpos); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "</%sAtomicType>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "</%sAtomicType>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); break; case H5T_TIME: @@ -1057,16 +1091,18 @@ xml_print_datatype(hid_t type, unsigned in_group) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sAtomicType>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "<%sAtomicType>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level++; ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sTimeType />",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "<%sTimeType />", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); h5tools_str_append(&buffer, "<!-- H5T_TIME: not yet implemented -->"); ctx.indent_level--; @@ -1074,23 +1110,25 @@ xml_print_datatype(hid_t type, unsigned in_group) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "</%sAtomicType>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "</%sAtomicType>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); break; case H5T_STRING: /* <hdf5:StringType Cset="cs" StrSize="chars" StrPad="pad" /> */ - size = H5Tget_size(type); - str_pad = H5Tget_strpad(type); - cset = H5Tget_cset(type); + size = H5Tget_size(type); + str_pad = H5Tget_strpad(type); + cset = H5Tget_cset(type); is_vlstr = H5Tis_variable_str(type); ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sAtomicType>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "<%sAtomicType>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level++; @@ -1098,17 +1136,17 @@ xml_print_datatype(hid_t type, unsigned in_group) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sStringType Cset=\"",xmlnsprefix); + h5tools_str_append(&buffer, "<%sStringType Cset=\"", xmlnsprefix); if (cset == H5T_CSET_ASCII) h5tools_str_append(&buffer, "H5T_CSET_ASCII\" "); else h5tools_str_append(&buffer, "unknown_cset\" "); - if(is_vlstr) + if (is_vlstr) h5tools_str_append(&buffer, "StrSize=\"H5T_VARIABLE\" StrPad=\""); else - h5tools_str_append(&buffer, "StrSize=\"%d\" StrPad=\"", (int) size); + h5tools_str_append(&buffer, "StrSize=\"%d\" StrPad=\"", (int)size); if (str_pad == H5T_STR_NULLTERM) h5tools_str_append(&buffer, "H5T_STR_NULLTERM\"/>"); @@ -1118,15 +1156,17 @@ xml_print_datatype(hid_t type, unsigned in_group) h5tools_str_append(&buffer, "H5T_STR_SPACEPAD\"/>"); else h5tools_str_append(&buffer, "H5T_STR_ERROR\"/>"); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "</%sAtomicType>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "</%sAtomicType>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); break; case H5T_BITFIELD: @@ -1137,15 +1177,16 @@ xml_print_datatype(hid_t type, unsigned in_group) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sAtomicType>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "<%sAtomicType>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level++; ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sBitfieldType ByteOrder=\"",xmlnsprefix); + h5tools_str_append(&buffer, "<%sBitfieldType ByteOrder=\"", xmlnsprefix); switch (ord) { case H5T_ORDER_LE: @@ -1164,15 +1205,17 @@ xml_print_datatype(hid_t type, unsigned in_group) size = H5Tget_size(type); h5tools_str_append(&buffer, "\" Size=\"%lu\"/>", (unsigned long)size); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "</%sAtomicType>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "</%sAtomicType>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); break; case H5T_OPAQUE: @@ -1182,8 +1225,9 @@ xml_print_datatype(hid_t type, unsigned in_group) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sAtomicType>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "<%sAtomicType>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level++; mname = H5Tget_tag(type); @@ -1191,19 +1235,21 @@ xml_print_datatype(hid_t type, unsigned in_group) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sOpaqueType Tag=\"%s\" ",xmlnsprefix, mname); + h5tools_str_append(&buffer, "<%sOpaqueType Tag=\"%s\" ", xmlnsprefix, mname); H5free_memory(mname); size = H5Tget_size(type); h5tools_str_append(&buffer, "Size=\"%lu\"/>", (unsigned long)size); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "</%sAtomicType>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "</%sAtomicType>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); break; case H5T_COMPOUND: @@ -1216,8 +1262,9 @@ xml_print_datatype(hid_t type, unsigned in_group) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sCompoundType>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "<%sCompoundType>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); /* List each member Field of the type */ /* <hdf5:Field FieldName="name" > */ @@ -1227,16 +1274,17 @@ xml_print_datatype(hid_t type, unsigned in_group) for (i = 0; i < nmembers; i++) { char *t_fname; - mname = H5Tget_member_name(type, i); - mtype = H5Tget_member_type(type, i); + mname = H5Tget_member_name(type, i); + mtype = H5Tget_member_type(type, i); t_fname = xml_escape_the_name(mname); ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sField FieldName=\"%s\">",xmlnsprefix, t_fname); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "<%sField FieldName=\"%s\">", xmlnsprefix, t_fname); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); H5free_memory(mname); HDfree(t_fname); @@ -1247,11 +1295,12 @@ xml_print_datatype(hid_t type, unsigned in_group) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sDataType>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "<%sDataType>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level++; dump_indent += COL; - xml_print_datatype(mtype,0); + xml_print_datatype(mtype, 0); dump_indent -= COL; ctx.indent_level--; @@ -1259,8 +1308,9 @@ xml_print_datatype(hid_t type, unsigned in_group) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "</%sDataType>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "</%sDataType>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); dump_indent -= COL; ctx.indent_level--; @@ -1268,8 +1318,9 @@ xml_print_datatype(hid_t type, unsigned in_group) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "</%sField>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "</%sField>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); } dump_indent -= COL; ctx.indent_level--; @@ -1278,8 +1329,9 @@ xml_print_datatype(hid_t type, unsigned in_group) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "</%sCompoundType>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "</%sCompoundType>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); break; case H5T_REFERENCE: @@ -1287,8 +1339,9 @@ xml_print_datatype(hid_t type, unsigned in_group) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sAtomicType>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "<%sAtomicType>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level++; /* Only Object references supported at this time */ @@ -1296,32 +1349,36 @@ xml_print_datatype(hid_t type, unsigned in_group) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sReferenceType>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "<%sReferenceType>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level++; ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sObjectReferenceType />",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "<%sObjectReferenceType />", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "</%sReferenceType>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "</%sReferenceType>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "</%sAtomicType>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "</%sAtomicType>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); break; case H5T_ENUM: @@ -1332,8 +1389,9 @@ xml_print_datatype(hid_t type, unsigned in_group) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sAtomicType>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "<%sAtomicType>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); dump_indent += COL; ctx.indent_level++; @@ -1341,16 +1399,18 @@ xml_print_datatype(hid_t type, unsigned in_group) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sEnumType Nelems=\"%d\">",xmlnsprefix, nmembs); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "<%sEnumType Nelems=\"%d\">", xmlnsprefix, nmembs); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); xml_print_enum(type); ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "</%sEnumType>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "</%sEnumType>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); dump_indent -= COL; ctx.indent_level--; @@ -1358,8 +1418,9 @@ xml_print_datatype(hid_t type, unsigned in_group) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "</%sAtomicType>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "</%sAtomicType>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); break; case H5T_VLEN: @@ -1367,8 +1428,9 @@ xml_print_datatype(hid_t type, unsigned in_group) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sVLType>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "<%sVLType>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); super = H5Tget_super(type); dump_indent += COL; ctx.indent_level++; @@ -1377,11 +1439,12 @@ xml_print_datatype(hid_t type, unsigned in_group) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sDataType>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "<%sDataType>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); dump_indent += COL; ctx.indent_level++; - xml_print_datatype(super,0); + xml_print_datatype(super, 0); dump_indent -= COL; ctx.indent_level--; @@ -1389,8 +1452,9 @@ xml_print_datatype(hid_t type, unsigned in_group) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "</%sDataType>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "</%sDataType>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); dump_indent -= COL; ctx.indent_level--; @@ -1398,8 +1462,9 @@ xml_print_datatype(hid_t type, unsigned in_group) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "</%sVLType>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "</%sVLType>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); H5Tclose(super); break; @@ -1413,10 +1478,11 @@ xml_print_datatype(hid_t type, unsigned in_group) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sArrayType Ndims=\"",xmlnsprefix); + h5tools_str_append(&buffer, "<%sArrayType Ndims=\"", xmlnsprefix); ndims = (unsigned)H5Tget_array_ndims(type); h5tools_str_append(&buffer, "%u\">", ndims); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); /* Get array information */ H5Tget_array_dims2(type, dims); @@ -1428,8 +1494,10 @@ xml_print_datatype(hid_t type, unsigned in_group) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sArrayDimension DimSize=\"%u\"/>", xmlnsprefix, (int) dims[i]); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "<%sArrayDimension DimSize=\"%u\"/>", xmlnsprefix, + (int)dims[i]); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); } ctx.indent_level--; @@ -1440,11 +1508,12 @@ xml_print_datatype(hid_t type, unsigned in_group) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sDataType>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "<%sDataType>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); dump_indent += COL; ctx.indent_level++; - xml_print_datatype(super,0); + xml_print_datatype(super, 0); dump_indent -= COL; ctx.indent_level--; @@ -1452,8 +1521,9 @@ xml_print_datatype(hid_t type, unsigned in_group) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "</%sDataType>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "</%sDataType>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); dump_indent -= COL; ctx.indent_level--; @@ -1461,8 +1531,9 @@ xml_print_datatype(hid_t type, unsigned in_group) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "</%sArrayType>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "</%sArrayType>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); /* Close array base type */ H5Tclose(super); break; @@ -1475,7 +1546,8 @@ xml_print_datatype(hid_t type, unsigned in_group) /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "<!-- unknown datatype -->"); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); h5tools_setstatus(EXIT_FAILURE); break; } @@ -1497,53 +1569,53 @@ xml_print_datatype(hid_t type, unsigned in_group) void xml_dump_datatype(hid_t type) { - h5tools_str_t buffer; /* string into which to render */ - h5tools_context_t ctx; /* print context */ - h5tool_format_t *outputformat = &xml_dataformat; + h5tools_str_t buffer; /* string into which to render */ + h5tools_context_t ctx; /* print context */ + h5tool_format_t * outputformat = &xml_dataformat; h5tool_format_t string_dataformat; - hsize_t curr_pos = 0; /* total data element position */ + hsize_t curr_pos = 0; /* total data element position */ /* setup */ HDmemset(&buffer, 0, sizeof(h5tools_str_t)); HDmemset(&ctx, 0, sizeof(ctx)); ctx.indent_level = dump_indent / COL; - ctx.cur_column = dump_indent; + ctx.cur_column = dump_indent; string_dataformat = *outputformat; if (fp_format) { string_dataformat.fmt_double = fp_format; - string_dataformat.fmt_float = fp_format; + string_dataformat.fmt_float = fp_format; } if (h5tools_nCols == 0) { - string_dataformat.line_ncols = 65535; + string_dataformat.line_ncols = 65535; string_dataformat.line_per_line = 1; } else string_dataformat.line_ncols = h5tools_nCols; - string_dataformat.do_escape = display_escape; - outputformat = &string_dataformat; + string_dataformat.do_escape = dump_opts.display_escape; + outputformat = &string_dataformat; ctx.indent_level++; dump_indent += COL; - if(H5Tcommitted(type) > 0) { - H5O_info_t oinfo; - obj_t *found_obj; /* Found object */ + if (H5Tcommitted(type) > 0) { + H5O_info2_t oinfo; + obj_t * found_obj; /* Found object */ /* Datatype is a shared or named datatype */ - H5Oget_info2(type, &oinfo, H5O_INFO_BASIC); - found_obj = search_obj(type_table, oinfo.addr); + H5Oget_info3(type, &oinfo, H5O_INFO_BASIC); + found_obj = search_obj(type_table, &oinfo.token); - if(found_obj) { + if (found_obj) { /* Shared datatype, must be entered as an object */ /* These 2 cases are the same now, but may change */ char *dtxid = (char *)HDmalloc((size_t)100); - xml_name_to_XID(found_obj->objname, dtxid, 100, 1); + xml_name_to_XID(type, found_obj->objname, dtxid, 100, 1); if (!found_obj->recorded) { /* anonymous stored datatype: following the dumper's current @@ -1555,9 +1627,9 @@ xml_dump_datatype(hid_t type) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sNamedDataTypePtr OBJ-XID=\"%s\"/>", - xmlnsprefix, dtxid); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "<%sNamedDataTypePtr OBJ-XID=\"%s\"/>", xmlnsprefix, dtxid); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); } else { /* pointer to a named datatype already in XML */ @@ -1568,8 +1640,9 @@ xml_dump_datatype(hid_t type) /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "<%sNamedDataTypePtr OBJ-XID=\"%s\" H5Path=\"%s\" />", - xmlnsprefix, dtxid, t_objname); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + xmlnsprefix, dtxid, t_objname); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); HDfree(t_objname); } HDfree(dtxid); @@ -1580,7 +1653,8 @@ xml_dump_datatype(hid_t type) /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "<!-- h5dump error: unknown committed type. -->"); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); } } else { @@ -1589,7 +1663,8 @@ xml_dump_datatype(hid_t type) /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "<%sDataType>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level++; dump_indent += COL; xml_print_datatype(type, 0); @@ -1601,7 +1676,8 @@ xml_dump_datatype(hid_t type) /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "</%sDataType>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); } ctx.indent_level--; dump_indent -= COL; @@ -1625,38 +1701,38 @@ xml_dump_dataspace(hid_t space) hsize_t size[H5DUMP_MAX_RANK]; hsize_t maxsize[H5DUMP_MAX_RANK]; int i; - h5tools_str_t buffer; /* string into which to render */ - h5tools_context_t ctx; /* print context */ - h5tool_format_t *outputformat = &xml_dataformat; + h5tools_str_t buffer; /* string into which to render */ + h5tools_context_t ctx; /* print context */ + h5tool_format_t * outputformat = &xml_dataformat; h5tool_format_t string_dataformat; - hsize_t curr_pos = 0; /* total data element position */ + hsize_t curr_pos = 0; /* total data element position */ - int ndims = H5Sget_simple_extent_dims(space, size, maxsize); - H5S_class_t space_type = H5Sget_simple_extent_type(space); + int ndims = H5Sget_simple_extent_dims(space, size, maxsize); + H5S_class_t space_type = H5Sget_simple_extent_type(space); /* setup */ HDmemset(&buffer, 0, sizeof(h5tools_str_t)); HDmemset(&ctx, 0, sizeof(ctx)); ctx.indent_level = dump_indent / COL; - ctx.cur_column = dump_indent; + ctx.cur_column = dump_indent; string_dataformat = *outputformat; if (fp_format) { string_dataformat.fmt_double = fp_format; - string_dataformat.fmt_float = fp_format; + string_dataformat.fmt_float = fp_format; } if (h5tools_nCols == 0) { - string_dataformat.line_ncols = 65535; + string_dataformat.line_ncols = 65535; string_dataformat.line_per_line = 1; } else string_dataformat.line_ncols = h5tools_nCols; - string_dataformat.do_escape = display_escape; - outputformat = &string_dataformat; + string_dataformat.do_escape = dump_opts.display_escape; + outputformat = &string_dataformat; ctx.indent_level++; @@ -1665,96 +1741,108 @@ xml_dump_dataspace(hid_t space) /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "<%sDataspace>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level++; switch (space_type) { - case H5S_SCALAR: - /* scalar dataspace (just a tag, no XML attrs. defined */ + case H5S_SCALAR: + /* scalar dataspace (just a tag, no XML attrs. defined */ - ctx.need_prefix = TRUE; + ctx.need_prefix = TRUE; - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sScalarDataspace />",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - break; + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<%sScalarDataspace />", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + break; - case H5S_SIMPLE: - /* simple dataspace */ - /* <hdf5:SimpleDataspace Ndims="nd"> */ + case H5S_SIMPLE: + /* simple dataspace */ + /* <hdf5:SimpleDataspace Ndims="nd"> */ - ctx.need_prefix = TRUE; + ctx.need_prefix = TRUE; - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sSimpleDataspace Ndims=\"%d\">",xmlnsprefix, ndims); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<%sSimpleDataspace Ndims=\"%d\">", xmlnsprefix, ndims); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - /* print the <hdf5:Dimension> elements */ - ctx.indent_level++; - for (i = 0; i < ndims; i++) { - if (maxsize[i] == H5S_UNLIMITED) { - ctx.need_prefix = TRUE; + /* print the <hdf5:Dimension> elements */ + ctx.indent_level++; + for (i = 0; i < ndims; i++) { + if (maxsize[i] == H5S_UNLIMITED) { + ctx.need_prefix = TRUE; - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sDimension DimSize=\"%" H5_PRINTF_LL_WIDTH "u\" MaxDimSize=\"UNLIMITED\"/>", - xmlnsprefix,size[i]); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - } - else if (maxsize[i] == (hsize_t) 0) { - ctx.need_prefix = TRUE; + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, + "<%sDimension DimSize=\"%" PRIuHSIZE "\" MaxDimSize=\"UNLIMITED\"/>", + xmlnsprefix, size[i]); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + } + else if (maxsize[i] == (hsize_t)0) { + ctx.need_prefix = TRUE; - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sDimension DimSize=\"%" H5_PRINTF_LL_WIDTH "u\" MaxDimSize=\"%" H5_PRINTF_LL_WIDTH "u\"/>", - xmlnsprefix,size[i], size[i]); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - } - else { - ctx.need_prefix = TRUE; + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append( + &buffer, "<%sDimension DimSize=\"%" PRIuHSIZE "\" MaxDimSize=\"%" PRIuHSIZE "\"/>", + xmlnsprefix, size[i], size[i]); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + } + else { + ctx.need_prefix = TRUE; - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sDimension DimSize=\"%" H5_PRINTF_LL_WIDTH "u\" MaxDimSize=\"%" H5_PRINTF_LL_WIDTH "u\"/>", + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append( + &buffer, "<%sDimension DimSize=\"%" PRIuHSIZE "\" MaxDimSize=\"%" PRIuHSIZE "\"/>", xmlnsprefix, size[i], maxsize[i]); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + } } - } - ctx.indent_level--; + ctx.indent_level--; - ctx.need_prefix = TRUE; + ctx.need_prefix = TRUE; - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "</%sSimpleDataspace>", xmlnsprefix ); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - break; + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "</%sSimpleDataspace>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + break; #ifdef TMP - /* Commented out: wait until the schema is updated first */ - case H5S_NULL: - /* null dataspace (just a tag, no XML attrs. defined */ + /* Commented out: wait until the schema is updated first */ + case H5S_NULL: + /* null dataspace (just a tag, no XML attrs. defined */ - ctx.need_prefix = TRUE; - h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sNullDataspace />",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - break; + ctx.need_prefix = TRUE; + h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<%sNullDataspace />", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + break; #endif /* TMP */ - case H5S_NULL: - case H5S_NO_CLASS: - default: - ctx.need_prefix = TRUE; + case H5S_NULL: + case H5S_NO_CLASS: + default: + ctx.need_prefix = TRUE; - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<!-- unknown dataspace -->"); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<!-- unknown dataspace -->"); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); } ctx.indent_level--; @@ -1764,7 +1852,8 @@ xml_dump_dataspace(hid_t space) /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "</%sDataspace>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; h5tools_str_close(&buffer); @@ -1778,31 +1867,24 @@ xml_dump_dataspace(hid_t space) * the h5tools library. * * Return: void - * - * Programmer: REMcG *------------------------------------------------------------------------- */ void -xml_dump_data(hid_t obj_id, int obj_data, struct subset_t H5_ATTR_UNUSED * sset, int H5_ATTR_UNUSED pindex) +xml_dump_data(hid_t obj_id, int obj_data, struct subset_t H5_ATTR_UNUSED *sset, int H5_ATTR_UNUSED pindex) { - hid_t space = -1; - hid_t type = -1; - hid_t p_type = -1; - hsize_t size[64]; - hsize_t nelmts = 1; - int ndims; - int i; - int status = -1; - void *buf = NULL; - hsize_t curr_pos = 0; /* total data element position */ - h5tools_str_t buffer; /* string into which to render */ - h5tools_context_t ctx; /* print context */ - h5tool_format_t *outputformat = &xml_dataformat; - h5tool_format_t string_dataformat; + hid_t space = H5I_INVALID_HID; + hid_t type = H5I_INVALID_HID; + hid_t p_type = H5I_INVALID_HID; + int status = -1; + hsize_t curr_pos = 0; /* total data element position */ + h5tools_str_t buffer; /* string into which to render */ + h5tools_context_t ctx; /* print context */ + h5tool_format_t * outputformat = &xml_dataformat; + h5tool_format_t string_dataformat; HDmemset(&ctx, 0, sizeof(ctx)); ctx.indent_level = dump_indent / COL; - ctx.cur_column = dump_indent; + ctx.cur_column = dump_indent; /* Print all the values. */ /* setup */ @@ -1812,29 +1894,30 @@ xml_dump_data(hid_t obj_id, int obj_data, struct subset_t H5_ATTR_UNUSED * sset, if (fp_format) { string_dataformat.fmt_double = fp_format; - string_dataformat.fmt_float = fp_format; + string_dataformat.fmt_float = fp_format; } if (h5tools_nCols == 0) { - string_dataformat.line_ncols = 65535; + string_dataformat.line_ncols = 65535; string_dataformat.line_per_line = 1; } else string_dataformat.line_ncols = h5tools_nCols; - string_dataformat.cmpd_sep = " "; - string_dataformat.cmpd_pre = ""; - string_dataformat.cmpd_suf = ""; - string_dataformat.cmpd_end = ""; + string_dataformat.cmpd_sep = " "; + string_dataformat.cmpd_pre = ""; + string_dataformat.cmpd_suf = ""; + string_dataformat.cmpd_end = ""; string_dataformat.arr_linebreak = 0; - string_dataformat.arr_pre = ""; - outputformat = &string_dataformat; + string_dataformat.arr_pre = ""; + outputformat = &string_dataformat; ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "<%sData>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level++; @@ -1843,7 +1926,8 @@ xml_dump_data(hid_t obj_id, int obj_data, struct subset_t H5_ATTR_UNUSED * sset, /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "<%sDataFromFile>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; @@ -1859,10 +1943,10 @@ xml_dump_data(hid_t obj_id, int obj_data, struct subset_t H5_ATTR_UNUSED * sset, else { h5tools_context_t datactx; HDmemset(&datactx, 0, sizeof(datactx)); - datactx.need_prefix = TRUE; + datactx.need_prefix = TRUE; datactx.indent_level = ctx.indent_level; - datactx.cur_column = ctx.cur_column; - status = h5tools_dump_dset(rawoutstream, outputformat, &datactx, obj_id, NULL); + datactx.cur_column = ctx.cur_column; + status = h5tools_dump_dset(rawoutstream, outputformat, &datactx, obj_id); } } else { @@ -1881,48 +1965,18 @@ xml_dump_data(hid_t obj_id, int obj_data, struct subset_t H5_ATTR_UNUSED * sset, else if (H5Tget_class(type) == H5T_STRING) { status = xml_print_strs(obj_id, ATTRIBUTE_DATA); } - else { /* all other data */ - /* VL data special information */ - unsigned int vl_data = 0; /* contains VL datatypes */ - - p_type = H5Tget_native_type(type, H5T_DIR_DEFAULT); - - /* Check if we have VL data in the dataset's datatype */ - if (h5tools_detect_vlen(p_type) == TRUE) - vl_data = TRUE; - - H5Tclose(type); - + else { /* all other data */ space = H5Aget_space(obj_id); - if(space == H5S_NULL || space == H5S_NO_CLASS) { + if (space == H5S_NULL || space == H5S_NO_CLASS) { status = SUCCEED; } else { - ndims = H5Sget_simple_extent_dims(space, size, NULL); - - for (i = 0; i < ndims; i++) - nelmts *= size[i]; - - if((buf = HDmalloc((size_t)(nelmts * MAX(H5Tget_size(type), H5Tget_size(p_type))))) == NULL) { - error_msg("unable to allocate buffer\n"); - h5tools_setstatus(EXIT_FAILURE); - status = FAIL; - } - else { - if (H5Aread(obj_id, p_type, buf) >= 0) { - h5tools_context_t datactx; - HDmemset(&datactx, 0, sizeof(datactx)); - datactx.need_prefix = TRUE; - datactx.indent_level = ctx.indent_level; - datactx.cur_column = ctx.cur_column; - status = h5tools_dump_mem(rawoutstream, outputformat, &datactx, obj_id, p_type, space, buf); - } - /* Reclaim any VL memory, if necessary */ - if (vl_data) - H5Dvlen_reclaim(p_type, space, H5P_DEFAULT, buf); - - HDfree(buf); - } + h5tools_context_t datactx; + HDmemset(&datactx, 0, sizeof(datactx)); + datactx.need_prefix = TRUE; + datactx.indent_level = ctx.indent_level; + datactx.cur_column = ctx.cur_column; + status = h5tools_dump_mem(rawoutstream, outputformat, &datactx, obj_id); } H5Tclose(p_type); H5Sclose(space); @@ -1938,7 +1992,8 @@ xml_dump_data(hid_t obj_id, int obj_data, struct subset_t H5_ATTR_UNUSED * sset, /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "Unable to print data."); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; @@ -1953,8 +2008,9 @@ xml_dump_data(hid_t obj_id, int obj_data, struct subset_t H5_ATTR_UNUSED * sset, /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "</%sDataFromFile>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "</%sDataFromFile>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; @@ -1963,7 +2019,8 @@ xml_dump_data(hid_t obj_id, int obj_data, struct subset_t H5_ATTR_UNUSED * sset, /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "</%sData>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); h5tools_str_close(&buffer); } @@ -1980,16 +2037,16 @@ xml_dump_data(hid_t obj_id, int obj_data, struct subset_t H5_ATTR_UNUSED * sset, */ herr_t xml_dump_attr(hid_t attr, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED *info, - void H5_ATTR_UNUSED * op_data) + void H5_ATTR_UNUSED *op_data) { - hid_t attr_id = -1; - hid_t type = -1; - hid_t space = -1; + hid_t attr_id = H5I_INVALID_HID; + hid_t type = H5I_INVALID_HID; + hid_t space = H5I_INVALID_HID; H5S_class_t space_type; - hsize_t curr_pos = 0; /* total data element position */ - h5tools_str_t buffer; /* string into which to render */ - h5tools_context_t ctx; /* print context */ - h5tool_format_t *outputformat = &xml_dataformat; + hsize_t curr_pos = 0; /* total data element position */ + h5tools_str_t buffer; /* string into which to render */ + h5tools_context_t ctx; /* print context */ + h5tool_format_t * outputformat = &xml_dataformat; h5tool_format_t string_dataformat; char *t_aname = xml_escape_the_name(attr_name); @@ -1999,36 +2056,37 @@ xml_dump_attr(hid_t attr, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED HDmemset(&ctx, 0, sizeof(ctx)); ctx.indent_level = dump_indent / COL; - ctx.cur_column = dump_indent; + ctx.cur_column = dump_indent; string_dataformat = *outputformat; if (fp_format) { string_dataformat.fmt_double = fp_format; - string_dataformat.fmt_float = fp_format; + string_dataformat.fmt_float = fp_format; } if (h5tools_nCols == 0) { - string_dataformat.line_ncols = 65535; + string_dataformat.line_ncols = 65535; string_dataformat.line_per_line = 1; } else string_dataformat.line_ncols = h5tools_nCols; - string_dataformat.do_escape = display_escape; - outputformat = &string_dataformat; + string_dataformat.do_escape = dump_opts.display_escape; + outputformat = &string_dataformat; ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "<%sAttribute Name=\"%s\">", xmlnsprefix, t_aname); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); HDfree(t_aname); if ((attr_id = H5Aopen(attr, attr_name, H5P_DEFAULT)) >= 0) { - type = H5Aget_type(attr_id); - space = H5Aget_space(attr_id); + type = H5Aget_type(attr_id); + space = H5Aget_space(attr_id); space_type = H5Sget_simple_extent_type(space); dump_function_table->dump_dataspace_function(space); @@ -2037,160 +2095,177 @@ xml_dump_attr(hid_t attr, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED ctx.indent_level++; dump_indent += COL; - if (display_attr_data && space_type != H5S_NULL) { + if (dump_opts.display_attr_data && space_type != H5S_NULL) { switch (H5Tget_class(type)) { - case H5T_INTEGER: - case H5T_FLOAT: - case H5T_STRING: - case H5T_BITFIELD: - case H5T_OPAQUE: - case H5T_ENUM: - case H5T_ARRAY: - dump_function_table->dump_data_function(attr_id, ATTRIBUTE_DATA, NULL, 0); - break; + case H5T_INTEGER: + case H5T_FLOAT: + case H5T_STRING: + case H5T_BITFIELD: + case H5T_OPAQUE: + case H5T_ENUM: + case H5T_ARRAY: + dump_function_table->dump_data_function(attr_id, ATTRIBUTE_DATA, NULL, 0); + break; + + case H5T_TIME: + ctx.indent_level++; + dump_indent += COL; - case H5T_TIME: - ctx.indent_level++; - dump_indent += COL; + ctx.need_prefix = TRUE; - ctx.need_prefix = TRUE; + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<%sData>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sData>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + ctx.need_prefix = TRUE; - ctx.need_prefix = TRUE; + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<!-- Time data not yet implemented. -->"); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<!-- Time data not yet implemented. -->"); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + ctx.need_prefix = TRUE; - ctx.need_prefix = TRUE; + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<%sNoData/>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sNoData/>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + ctx.need_prefix = TRUE; - ctx.need_prefix = TRUE; + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<hdf5:Data>"); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<hdf5:Data>"); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + ctx.need_prefix = TRUE; - ctx.need_prefix = TRUE; + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "</%sData>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "</%sData>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + ctx.indent_level--; + dump_indent -= COL; + break; - ctx.indent_level--; - dump_indent -= COL; - break; + case H5T_COMPOUND: + ctx.need_prefix = TRUE; - case H5T_COMPOUND: - ctx.need_prefix = TRUE; + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<!-- Note: format of compound data not specified -->"); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + dump_function_table->dump_data_function(attr_id, ATTRIBUTE_DATA, NULL, 0); + break; - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<!-- Note: format of compound data not specified -->"); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - dump_function_table->dump_data_function(attr_id, ATTRIBUTE_DATA, NULL, 0); - break; + case H5T_REFERENCE: + ctx.need_prefix = TRUE; - case H5T_REFERENCE: - ctx.need_prefix = TRUE; + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<%sData>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + if (!H5Tequal(type, H5T_STD_REF_OBJ)) { + ctx.need_prefix = TRUE; + + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<!-- Note: Region references not supported -->"); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + + ctx.need_prefix = TRUE; + + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<%sNoData />", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + } + else { + ctx.need_prefix = TRUE; + + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<%sDataFromFile>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + + xml_print_refs(attr_id, ATTRIBUTE_DATA); + + ctx.need_prefix = TRUE; + + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "</%sDataFromFile>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + } - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sData>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - if (!H5Tequal(type, H5T_STD_REF_OBJ)) { ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<!-- Note: Region references not supported -->"); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "</%sData>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + break; + case H5T_VLEN: ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sNoData />", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - } - else { + h5tools_str_append(&buffer, "<!-- Note: format of VL data not specified -->"); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + + dump_function_table->dump_data_function(attr_id, ATTRIBUTE_DATA, NULL, 0); + break; + case H5T_NO_CLASS: + case H5T_NCLASSES: + default: ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sDataFromFile>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - - xml_print_refs(attr_id, ATTRIBUTE_DATA); + h5tools_str_append(&buffer, "<%sData>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "</%sDataFromFile>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - } - - ctx.need_prefix = TRUE; - - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "</%sData>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - break; - - case H5T_VLEN: - ctx.need_prefix = TRUE; - - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<!-- Note: format of VL data not specified -->"); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - - dump_function_table->dump_data_function(attr_id, ATTRIBUTE_DATA, NULL, 0); - break; - case H5T_NO_CLASS: - case H5T_NCLASSES: - default: - ctx.need_prefix = TRUE; - - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sData>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - - ctx.need_prefix = TRUE; + h5tools_str_append(&buffer, "<!-- Unknown datatype: %d -->", H5Tget_class(type)); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<!-- Unknown datatype: %d -->", H5Tget_class(type)); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - - ctx.need_prefix = TRUE; + ctx.need_prefix = TRUE; - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sNoData/>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<%sNoData/>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - ctx.need_prefix = TRUE; + ctx.need_prefix = TRUE; - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "</%sData>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - break; + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "</%sData>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + break; } } else { @@ -2201,7 +2276,8 @@ xml_dump_attr(hid_t attr, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "<%sData>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level++; @@ -2210,7 +2286,8 @@ xml_dump_attr(hid_t attr, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "<%sNoData/>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; @@ -2219,7 +2296,8 @@ xml_dump_attr(hid_t attr, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "</%sData>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); } ctx.indent_level--; dump_indent -= COL; @@ -2233,7 +2311,8 @@ xml_dump_attr(hid_t attr, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "</%sAttribute>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); h5tools_str_close(&buffer); return SUCCEED; @@ -2247,7 +2326,8 @@ xml_dump_attr(hid_t attr, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "<!-- h5dump error: unable to open attribute. -->"); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; @@ -2256,7 +2336,8 @@ xml_dump_attr(hid_t attr, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "</%sAttribute>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); h5tools_str_close(&buffer); @@ -2278,19 +2359,26 @@ xml_dump_attr(hid_t attr, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED void xml_dump_named_datatype(hid_t type, const char *name) { - hsize_t curr_pos = 0; /* total data element position */ - h5tools_str_t buffer; /* string into which to render */ - h5tools_context_t ctx; /* print context */ - h5tool_format_t *outputformat = &xml_dataformat; + hsize_t curr_pos = 0; /* total data element position */ + h5tools_str_t buffer; /* string into which to render */ + h5tools_context_t ctx; /* print context */ + h5tool_format_t * outputformat = &xml_dataformat; h5tool_format_t string_dataformat; - char *tmp; - char *dtxid; - char *parentxid; - char *t_tmp; - char *t_prefix; - char *t_name; + char * tmp = NULL; + char * dtxid = NULL; + char * parentxid = NULL; + char * t_tmp = NULL; + char * t_prefix = NULL; + char * t_name = NULL; tmp = (char *)HDmalloc(HDstrlen(prefix) + HDstrlen(name) + 2); + if (tmp == NULL) { + indentation(dump_indent); + error_msg("internal error (file %s:line %d)\n", __FILE__, __LINE__); + h5tools_setstatus(EXIT_FAILURE); + goto done; + } + HDstrcpy(tmp, prefix); HDstrcat(tmp, "/"); HDstrcat(tmp, name); @@ -2300,34 +2388,34 @@ xml_dump_named_datatype(hid_t type, const char *name) HDmemset(&ctx, 0, sizeof(ctx)); ctx.indent_level = dump_indent / COL; - ctx.cur_column = dump_indent; + ctx.cur_column = dump_indent; string_dataformat = *outputformat; if (fp_format) { string_dataformat.fmt_double = fp_format; - string_dataformat.fmt_float = fp_format; + string_dataformat.fmt_float = fp_format; } if (h5tools_nCols == 0) { - string_dataformat.line_ncols = 65535; + string_dataformat.line_ncols = 65535; string_dataformat.line_per_line = 1; } else string_dataformat.line_ncols = h5tools_nCols; - string_dataformat.do_escape = display_escape; - outputformat = &string_dataformat; + string_dataformat.do_escape = dump_opts.display_escape; + outputformat = &string_dataformat; - dtxid = (char *)HDmalloc((size_t)100); + dtxid = (char *)HDmalloc((size_t)100); parentxid = (char *)HDmalloc((size_t)100); - t_tmp = xml_escape_the_name(tmp); - t_prefix = xml_escape_the_name(prefix); - t_name = xml_escape_the_name(name); + t_tmp = xml_escape_the_name(tmp); + t_prefix = xml_escape_the_name(prefix); + t_name = xml_escape_the_name(name); - xml_name_to_XID(tmp, dtxid, 100, 1); - xml_name_to_XID(prefix, parentxid, 100, 1); - if(HDstrncmp(name, "#", (size_t)1) == 0) { + xml_name_to_XID(type, tmp, dtxid, 100, 1); + xml_name_to_XID(type, prefix, parentxid, 100, 1); + if (HDstrncmp(name, "#", (size_t)1) == 0) { /* Special: this is an 'anonymous' NDT, deleted but still in use. We follow the dumper's undocumented practice, and @@ -2341,34 +2429,35 @@ xml_dump_named_datatype(hid_t type, const char *name) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sNamedDataType Name=\"%s\" OBJ-XID=\"%s\" " - "Parents=\"%s\" H5ParentPaths=\"%s\">", - xmlnsprefix, - name, dtxid, - parentxid, HDstrcmp(prefix,"") ? t_prefix : "/"); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, + "<%sNamedDataType Name=\"%s\" OBJ-XID=\"%s\" " + "Parents=\"%s\" H5ParentPaths=\"%s\">", + xmlnsprefix, name, dtxid, parentxid, HDstrcmp(prefix, "") ? t_prefix : "/"); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); } else { - H5O_info_t oinfo; /* Object info */ + H5O_info2_t oinfo; /* Object info */ ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sNamedDataType Name=\"%s\" OBJ-XID=\"%s\" " - "H5Path=\"%s\" Parents=\"%s\" H5ParentPaths=\"%s\">", - xmlnsprefix, - t_name, dtxid, - t_tmp, parentxid, (HDstrcmp(prefix, "") ? t_prefix : "/")); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, + "<%sNamedDataType Name=\"%s\" OBJ-XID=\"%s\" " + "H5Path=\"%s\" Parents=\"%s\" H5ParentPaths=\"%s\">", + xmlnsprefix, t_name, dtxid, t_tmp, parentxid, + (HDstrcmp(prefix, "") ? t_prefix : "/")); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); /* Check uniqueness of named datatype */ - H5Oget_info2(type, &oinfo, H5O_INFO_BASIC); - if(oinfo.rc > 1) { - obj_t *found_obj; /* Found object */ + H5Oget_info3(type, &oinfo, H5O_INFO_BASIC); + if (oinfo.rc > 1) { + obj_t *found_obj; /* Found object */ /* Group with more than one link to it... */ - found_obj = search_obj(type_table, oinfo.addr); + found_obj = search_obj(type_table, &oinfo.token); if (found_obj == NULL) { indentation(dump_indent); @@ -2376,23 +2465,25 @@ xml_dump_named_datatype(hid_t type, const char *name) h5tools_setstatus(EXIT_FAILURE); goto done; } - else if(found_obj->displayed) { + else if (found_obj->displayed) { /* We have already printed this named datatype, print it as a * NamedDatatypePtr */ - char pointerxid[100]; + char pointerxid[100]; char *t_objname = xml_escape_the_name(found_obj->objname); ctx.indent_level++; - xml_name_to_XID(found_obj->objname, pointerxid, (int)sizeof(pointerxid), 1); + xml_name_to_XID(type, found_obj->objname, pointerxid, (int)sizeof(pointerxid), 1); ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sNamedDatatypePtr OBJ-XID=\"%s\" H5Path=\"%s\"/>", xmlnsprefix, pointerxid, t_objname); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "<%sNamedDatatypePtr OBJ-XID=\"%s\" H5Path=\"%s\"/>", xmlnsprefix, + pointerxid, t_objname); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; @@ -2401,7 +2492,8 @@ xml_dump_named_datatype(hid_t type, const char *name) /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "</%sNamedDataType>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); HDfree(t_objname); goto done; } @@ -2417,12 +2509,13 @@ xml_dump_named_datatype(hid_t type, const char *name) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sDataType>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "<%sDataType>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level++; dump_indent += COL; - xml_print_datatype(type,1); + xml_print_datatype(type, 1); ctx.indent_level--; dump_indent -= COL; @@ -2430,8 +2523,9 @@ xml_dump_named_datatype(hid_t type, const char *name) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "</%sDataType>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "</%sDataType>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; dump_indent -= COL; @@ -2440,8 +2534,9 @@ xml_dump_named_datatype(hid_t type, const char *name) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "</%sNamedDataType>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "</%sNamedDataType>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); done: @@ -2468,23 +2563,23 @@ done: void xml_dump_group(hid_t gid, const char *name) { - H5O_info_t oinfo; - hid_t gcpl_id; - hid_t dset, type; - unsigned crt_order_flags; - unsigned attr_crt_order_flags; - int isRoot = 0; - char type_name[1024]; - char *t_objname = NULL; - char *par_name = NULL; - char *cp = NULL; - char *tmp = NULL; - char *par = NULL; - h5tools_str_t buffer; /* string into which to render */ - h5tools_context_t ctx; /* print context */ - h5tool_format_t *outputformat = &xml_dataformat; - h5tool_format_t string_dataformat; - hsize_t curr_pos = 0; /* total data element position */ + H5O_info2_t oinfo; + hid_t gcpl_id; + hid_t dset, type; + unsigned crt_order_flags; + unsigned attr_crt_order_flags; + int isRoot = 0; + char type_name[1024]; + char * t_objname = NULL; + char * par_name = NULL; + char * cp = NULL; + char * tmp = NULL; + char * par = NULL; + h5tools_str_t buffer; /* string into which to render */ + h5tools_context_t ctx; /* print context */ + h5tool_format_t * outputformat = &xml_dataformat; + h5tool_format_t string_dataformat; + hsize_t curr_pos = 0; /* total data element position */ if ((gcpl_id = H5Gget_create_plist(gid)) < 0) { error_msg("error in getting group creation property list ID\n"); @@ -2498,12 +2593,12 @@ xml_dump_group(hid_t gid, const char *name) } /* query the group creation properties */ - if(H5Pget_link_creation_order(gcpl_id, &crt_order_flags) < 0) { + if (H5Pget_link_creation_order(gcpl_id, &crt_order_flags) < 0) { error_msg("error in getting group creation properties\n"); h5tools_setstatus(EXIT_FAILURE); } - if(H5Pclose(gcpl_id) < 0) { + if (H5Pclose(gcpl_id) < 0) { error_msg("error in closing group creation property list ID\n"); h5tools_setstatus(EXIT_FAILURE); } @@ -2513,49 +2608,56 @@ xml_dump_group(hid_t gid, const char *name) HDmemset(&ctx, 0, sizeof(ctx)); ctx.indent_level = dump_indent / COL; - ctx.cur_column = dump_indent; + ctx.cur_column = dump_indent; string_dataformat = *outputformat; if (fp_format) { string_dataformat.fmt_double = fp_format; - string_dataformat.fmt_float = fp_format; + string_dataformat.fmt_float = fp_format; } if (h5tools_nCols == 0) { - string_dataformat.line_ncols = 65535; + string_dataformat.line_ncols = 65535; string_dataformat.line_per_line = 1; } else string_dataformat.line_ncols = h5tools_nCols; - string_dataformat.do_escape = display_escape; - outputformat = &string_dataformat; + string_dataformat.do_escape = dump_opts.display_escape; + outputformat = &string_dataformat; - if(HDstrcmp(name, "/") == 0) { + if (HDstrcmp(name, "/") == 0) { isRoot = 1; - tmp = HDstrdup("/"); + tmp = HDstrdup("/"); } else { tmp = (char *)HDmalloc(HDstrlen(prefix) + HDstrlen(name) + 2); + if (tmp == NULL) { + indentation(dump_indent); + error_msg("internal error (file %s:line %d)\n", __FILE__, __LINE__); + h5tools_setstatus(EXIT_FAILURE); + return; + } + HDstrcpy(tmp, prefix); par = HDstrdup(tmp); - cp = HDstrrchr(par, '/'); - if(cp) { - if((cp == par) && HDstrlen(par) > 1) + cp = HDstrrchr(par, '/'); + if (cp) { + if ((cp == par) && HDstrlen(par) > 1) *(cp + 1) = '\0'; else *cp = '\0'; } } - H5Oget_info2(gid, &oinfo, H5O_INFO_BASIC); + H5Oget_info3(gid, &oinfo, H5O_INFO_BASIC); - if(oinfo.rc > 1) { - obj_t *found_obj; /* Found object */ + if (oinfo.rc > 1) { + obj_t *found_obj; /* Found object */ /* Group with more than one link to it... */ - found_obj = search_obj(group_table, oinfo.addr); + found_obj = search_obj(group_table, &oinfo.token); if (found_obj == NULL) { indentation(dump_indent); @@ -2563,60 +2665,64 @@ xml_dump_group(hid_t gid, const char *name) h5tools_setstatus(EXIT_FAILURE); } else { - char *t_name = xml_escape_the_name(name); - char *grpxid = (char *)HDmalloc((size_t)100); + char *t_name = xml_escape_the_name(name); + char *grpxid = (char *)HDmalloc((size_t)100); char *parentxid = (char *)HDmalloc((size_t)100); - if(found_obj->displayed) { + if (found_obj->displayed) { char *ptrstr = (char *)HDmalloc((size_t)100); /* already seen: enter a groupptr */ - if(isRoot) { + if (isRoot) { /* probably can't happen! */ - xml_name_to_XID("/", grpxid, 100, 1); + xml_name_to_XID(gid, "/", grpxid, 100, 1); ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sRootGroup OBJ-XID=\"%s\" H5Path=\"%s\">", - xmlnsprefix, grpxid, "/"); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "<%sRootGroup OBJ-XID=\"%s\" H5Path=\"%s\">", xmlnsprefix, + grpxid, "/"); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); } else { t_objname = xml_escape_the_name(found_obj->objname); - par_name = xml_escape_the_name(par); - xml_name_to_XID(tmp, grpxid, 100, 1); - xml_name_to_XID(par, parentxid, 100, 1); + par_name = xml_escape_the_name(par); + xml_name_to_XID(gid, tmp, grpxid, 100, 1); + xml_name_to_XID(gid, par, parentxid, 100, 1); ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sGroup Name=\"%s\" OBJ-XID=\"%s-%d\" H5Path=\"%s\" " - "Parents=\"%s\" H5ParentPaths=\"%s\">", - xmlnsprefix,t_name, grpxid, get_next_xid(), - t_objname, parentxid, par_name); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, + "<%sGroup Name=\"%s\" OBJ-XID=\"%s-%d\" H5Path=\"%s\" " + "Parents=\"%s\" H5ParentPaths=\"%s\">", + xmlnsprefix, t_name, grpxid, get_next_xid(), t_objname, parentxid, + par_name); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); HDfree(t_objname); HDfree(par_name); ctx.indent_level++; - t_objname = xml_escape_the_name(found_obj->objname);/* point to the NDT by name */ - par_name = xml_escape_the_name(par); - xml_name_to_XID(found_obj->objname, ptrstr, 100, 1); - xml_name_to_XID(par, parentxid, 100, 1); + t_objname = xml_escape_the_name(found_obj->objname); /* point to the NDT by name */ + par_name = xml_escape_the_name(par); + xml_name_to_XID(gid, found_obj->objname, ptrstr, 100, 1); + xml_name_to_XID(gid, par, parentxid, 100, 1); ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sGroupPtr OBJ-XID=\"%s\" H5Path=\"%s\" " - "Parents=\"%s\" H5ParentPaths=\"%s\" />", - xmlnsprefix, - ptrstr, t_objname, parentxid, par_name); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, + "<%sGroupPtr OBJ-XID=\"%s\" H5Path=\"%s\" " + "Parents=\"%s\" H5ParentPaths=\"%s\" />", + xmlnsprefix, ptrstr, t_objname, parentxid, par_name); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; @@ -2628,32 +2734,35 @@ xml_dump_group(hid_t gid, const char *name) else { /* first time this group has been seen -- describe it */ - if(isRoot) { - xml_name_to_XID("/", grpxid, 100, 1); + if (isRoot) { + xml_name_to_XID(gid, "/", grpxid, 100, 1); ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sRootGroup OBJ-XID=\"%s\" H5Path=\"%s\">", - xmlnsprefix, grpxid, "/"); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "<%sRootGroup OBJ-XID=\"%s\" H5Path=\"%s\">", xmlnsprefix, + grpxid, "/"); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); } else { char *t_tmp = xml_escape_the_name(tmp); par_name = xml_escape_the_name(par); - xml_name_to_XID(tmp, grpxid, 100, 1); - xml_name_to_XID(par, parentxid, 100, 1); + xml_name_to_XID(gid, tmp, grpxid, 100, 1); + xml_name_to_XID(gid, par, parentxid, 100, 1); ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sGroup Name=\"%s\" OBJ-XID=\"%s\" H5Path=\"%s\" " - "Parents=\"%s\" H5ParentPaths=\"%s\" >", - xmlnsprefix,t_name, grpxid, t_tmp, parentxid, par_name); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, + "<%sGroup Name=\"%s\" OBJ-XID=\"%s\" H5Path=\"%s\" " + "Parents=\"%s\" H5ParentPaths=\"%s\" >", + xmlnsprefix, t_name, grpxid, t_tmp, parentxid, par_name); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); HDfree(t_tmp); HDfree(par_name); @@ -2665,28 +2774,36 @@ xml_dump_group(hid_t gid, const char *name) ctx.indent_level++; dump_indent += COL; - if((sort_by == H5_INDEX_CRT_ORDER) && (attr_crt_order_flags & H5P_CRT_ORDER_TRACKED)) { - if(H5Aiterate2(gid, sort_by, sort_order, NULL, dump_function_table->dump_attribute_function, NULL) < 0) { + if ((sort_by == H5_INDEX_CRT_ORDER) && (attr_crt_order_flags & H5P_CRT_ORDER_TRACKED)) { + if (H5Aiterate2(gid, sort_by, sort_order, NULL, + dump_function_table->dump_attribute_function, NULL) < 0) { error_msg("error getting attribute information\n"); h5tools_setstatus(EXIT_FAILURE); } /* end if */ - } /* end if */ + } /* end if */ else { - if(H5Aiterate2(gid, H5_INDEX_NAME, sort_order, NULL, dump_function_table->dump_attribute_function, NULL) < 0) { + if (H5Aiterate2(gid, H5_INDEX_NAME, sort_order, NULL, + dump_function_table->dump_attribute_function, NULL) < 0) { error_msg("error getting attribute information\n"); h5tools_setstatus(EXIT_FAILURE); } /* end if */ - } /* end else */ + } /* end else */ - if(isRoot && unamedtype) { + if (isRoot && unamedtype) { unsigned u; - /* Very special case: dump unamed type in root group */ - for(u = 0; u < type_table->nobjs; u++) { - if(!type_table->objs[u].recorded) { + /* Very special case: dump unnamed type in root group */ + for (u = 0; u < type_table->nobjs; u++) { + if (!type_table->objs[u].recorded) { + char *obj_tok_str = NULL; + dset = H5Dopen2(gid, type_table->objs[u].objname, H5P_DEFAULT); type = H5Dget_type(dset); - HDsprintf(type_name, "#"H5_PRINTF_HADDR_FMT, type_table->objs[u].objno); + + H5Otoken_to_str(dset, &type_table->objs[u].obj_token, &obj_tok_str); + HDsnprintf(type_name, sizeof(type_name), "#%s", obj_tok_str); + H5free_memory(obj_tok_str); + dump_function_table->dump_named_datatype_function(type, type_name); H5Tclose(type); H5Dclose(dset); @@ -2696,10 +2813,10 @@ xml_dump_group(hid_t gid, const char *name) /* iterate through all the links */ - if((sort_by == H5_INDEX_CRT_ORDER) && (crt_order_flags & H5P_CRT_ORDER_TRACKED)) - H5Literate(gid, sort_by, sort_order, NULL, xml_dump_all_cb, NULL); + if ((sort_by == H5_INDEX_CRT_ORDER) && (crt_order_flags & H5P_CRT_ORDER_TRACKED)) + H5Literate2(gid, sort_by, sort_order, NULL, xml_dump_all_cb, NULL); else - H5Literate(gid, H5_INDEX_NAME, sort_order, NULL, xml_dump_all_cb, NULL); + H5Literate2(gid, H5_INDEX_NAME, sort_order, NULL, xml_dump_all_cb, NULL); dump_indent -= COL; ctx.indent_level--; @@ -2711,8 +2828,8 @@ xml_dump_group(hid_t gid, const char *name) } else { /* only link -- must be first time! */ - char *t_name = xml_escape_the_name(name); - char *grpxid = (char *)HDmalloc((size_t)100); + char *t_name = xml_escape_the_name(name); + char *grpxid = (char *)HDmalloc((size_t)100); char *parentxid = (char *)HDmalloc((size_t)100); ctx.need_prefix = TRUE; @@ -2720,23 +2837,26 @@ xml_dump_group(hid_t gid, const char *name) /* Render the element */ h5tools_str_reset(&buffer); - if(isRoot) { - xml_name_to_XID("/", grpxid, 100, 1); - h5tools_str_append(&buffer, "<%sRootGroup OBJ-XID=\"%s\" H5Path=\"%s\">", xmlnsprefix, grpxid, "/"); + if (isRoot) { + xml_name_to_XID(gid, "/", grpxid, 100, 1); + h5tools_str_append(&buffer, "<%sRootGroup OBJ-XID=\"%s\" H5Path=\"%s\">", xmlnsprefix, grpxid, + "/"); } else { char *t_tmp = xml_escape_the_name(tmp); par_name = xml_escape_the_name(par); - xml_name_to_XID(tmp, grpxid, 100, 1); - xml_name_to_XID(par, parentxid, 100, 1); - h5tools_str_append(&buffer, "<%sGroup Name=\"%s\" OBJ-XID=\"%s\" H5Path=\"%s\" " - "Parents=\"%s\" H5ParentPaths=\"%s\" >", - xmlnsprefix, t_name, grpxid, t_tmp, parentxid, par_name); + xml_name_to_XID(gid, tmp, grpxid, 100, 1); + xml_name_to_XID(gid, par, parentxid, 100, 1); + h5tools_str_append(&buffer, + "<%sGroup Name=\"%s\" OBJ-XID=\"%s\" H5Path=\"%s\" " + "Parents=\"%s\" H5ParentPaths=\"%s\" >", + xmlnsprefix, t_name, grpxid, t_tmp, parentxid, par_name); HDfree(t_tmp); HDfree(par_name); } - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); HDfree(t_name); HDfree(grpxid); @@ -2747,28 +2867,36 @@ xml_dump_group(hid_t gid, const char *name) ctx.indent_level++; dump_indent += COL; - if((sort_by == H5_INDEX_CRT_ORDER) && (attr_crt_order_flags & H5P_CRT_ORDER_TRACKED)) { - if(H5Aiterate2(gid, sort_by, sort_order, NULL, dump_function_table->dump_attribute_function, NULL) < 0) { + if ((sort_by == H5_INDEX_CRT_ORDER) && (attr_crt_order_flags & H5P_CRT_ORDER_TRACKED)) { + if (H5Aiterate2(gid, sort_by, sort_order, NULL, dump_function_table->dump_attribute_function, + NULL) < 0) { error_msg("error getting attribute information\n"); h5tools_setstatus(EXIT_FAILURE); } /* end if */ - } /* end if */ + } /* end if */ else { - if(H5Aiterate2(gid, H5_INDEX_NAME, sort_order, NULL, dump_function_table->dump_attribute_function, NULL) < 0) { + if (H5Aiterate2(gid, H5_INDEX_NAME, sort_order, NULL, + dump_function_table->dump_attribute_function, NULL) < 0) { error_msg("error getting attribute information\n"); h5tools_setstatus(EXIT_FAILURE); } /* end if */ - } /* end else */ + } /* end else */ - if(isRoot && unamedtype) { + if (isRoot && unamedtype) { unsigned u; - /* Very special case: dump unamed type in root group */ - for(u = 0; u < type_table->nobjs; u++) { - if(!type_table->objs[u].recorded) { + /* Very special case: dump unnamed type in root group */ + for (u = 0; u < type_table->nobjs; u++) { + if (!type_table->objs[u].recorded) { + char *obj_tok_str = NULL; + dset = H5Dopen2(gid, type_table->objs[u].objname, H5P_DEFAULT); type = H5Dget_type(dset); - HDsprintf(type_name, "#"H5_PRINTF_HADDR_FMT, type_table->objs[u].objno); + + H5Otoken_to_str(dset, &type_table->objs[u].obj_token, &obj_tok_str); + HDsnprintf(type_name, sizeof(type_name), "#%s", obj_tok_str); + H5free_memory(obj_tok_str); + dump_function_table->dump_named_datatype_function(type, type_name); H5Tclose(type); H5Dclose(dset); @@ -2778,10 +2906,10 @@ xml_dump_group(hid_t gid, const char *name) /* iterate through all the links */ - if((sort_by == H5_INDEX_CRT_ORDER) && (crt_order_flags & H5P_CRT_ORDER_TRACKED)) - H5Literate(gid, sort_by, sort_order, NULL, xml_dump_all_cb, NULL); + if ((sort_by == H5_INDEX_CRT_ORDER) && (crt_order_flags & H5P_CRT_ORDER_TRACKED)) + H5Literate2(gid, sort_by, sort_order, NULL, xml_dump_all_cb, NULL); else - H5Literate(gid, H5_INDEX_NAME, sort_order, NULL, xml_dump_all_cb, NULL); + H5Literate2(gid, H5_INDEX_NAME, sort_order, NULL, xml_dump_all_cb, NULL); dump_indent -= COL; ctx.indent_level--; @@ -2791,24 +2919,25 @@ xml_dump_group(hid_t gid, const char *name) /* Render the element */ h5tools_str_reset(&buffer); - if(isRoot) + if (isRoot) h5tools_str_append(&buffer, "</%sRootGroup>", xmlnsprefix); else h5tools_str_append(&buffer, "</%sGroup>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); h5tools_str_close(&buffer); - if(par) + if (par) HDfree(par); - if(tmp) + if (tmp) HDfree(tmp); } /*------------------------------------------------------------------------- * Function: xml_print_refs * - * Purpose: Print a path to the objects referenced by HDF5 Referneces. + * Purpose: Print a path to the objects referenced by HDF5 References. * * Return: void * @@ -2819,18 +2948,17 @@ static int xml_print_refs(hid_t did, int source) { herr_t e; - hid_t type = -1; - hid_t space = -1; - hssize_t ssiz = -1; + hid_t type = H5I_INVALID_HID; + hid_t space = H5I_INVALID_HID; + hssize_t ssiz = -1; hsize_t i; - size_t tsiz; - hobj_ref_t *refbuf = NULL; - char *buf = NULL; - h5tools_str_t buffer; /* string into which to render */ - h5tools_context_t ctx; /* print context */ - h5tool_format_t *outputformat = &xml_dataformat; + H5R_ref_t * refbuf = NULL; + char * buf = NULL; + h5tools_str_t buffer; /* string into which to render */ + h5tools_context_t ctx; /* print context */ + h5tool_format_t * outputformat = &xml_dataformat; h5tool_format_t string_dataformat; - hsize_t curr_pos = 0; /* total data element position */ + hsize_t curr_pos = 0; /* total data element position */ if (source == DATASET_DATA) { type = H5Dget_type(did); @@ -2855,13 +2983,11 @@ xml_print_refs(hid_t did, int source) space = H5Dget_space(did); if ((ssiz = H5Sget_simple_extent_npoints(space)) < 0) goto error; - if ((tsiz = H5Tget_size(type)) == 0) - goto error; - buf = (char *) HDcalloc((size_t)ssiz, tsiz); + buf = (char *)HDcalloc((size_t)ssiz, sizeof(H5R_ref_t)); if (buf == NULL) goto error; - e = H5Dread(did, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf); + e = H5Dread(did, H5T_STD_REF, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf); /* need to check result here */ if (e < 0) goto error; @@ -2870,43 +2996,41 @@ xml_print_refs(hid_t did, int source) space = H5Aget_space(did); if ((ssiz = H5Sget_simple_extent_npoints(space)) < 0) goto error; - if ((tsiz = H5Tget_size(type)) == 0) - goto error; - buf = (char *) HDcalloc((size_t)ssiz, tsiz); + buf = (char *)HDcalloc((size_t)ssiz, sizeof(H5R_ref_t)); if (buf == NULL) goto error; - e = H5Aread(did, H5T_STD_REF_OBJ, buf); + e = H5Aread(did, H5T_STD_REF, buf); /* need to check the result here */ if (e < 0) goto error; } - refbuf = (hobj_ref_t *)((void *)buf); + refbuf = (H5R_ref_t *)((void *)buf); /* setup */ HDmemset(&buffer, 0, sizeof(h5tools_str_t)); HDmemset(&ctx, 0, sizeof(ctx)); ctx.indent_level = dump_indent / COL; - ctx.cur_column = dump_indent; + ctx.cur_column = dump_indent; string_dataformat = *outputformat; if (fp_format) { string_dataformat.fmt_double = fp_format; - string_dataformat.fmt_float = fp_format; + string_dataformat.fmt_float = fp_format; } if (h5tools_nCols == 0) { - string_dataformat.line_ncols = 65535; + string_dataformat.line_ncols = 65535; string_dataformat.line_per_line = 1; } else string_dataformat.line_ncols = h5tools_nCols; - string_dataformat.do_escape = display_escape; - outputformat = &string_dataformat; + string_dataformat.do_escape = dump_opts.display_escape; + outputformat = &string_dataformat; for (i = 0; i < (hsize_t)ssiz; i++) { const char *path = lookup_ref_path(*refbuf); @@ -2918,7 +3042,8 @@ xml_print_refs(hid_t did, int source) /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "\"%s\"", "NULL"); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); } else { char *t_path = xml_escape_the_string(path, -1); @@ -2928,11 +3053,14 @@ xml_print_refs(hid_t did, int source) /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "\"%s\"", t_path); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); HDfree(t_path); } ctx.indent_level--; + H5Rdestroy(refbuf); + refbuf++; } @@ -2944,13 +3072,15 @@ xml_print_refs(hid_t did, int source) return SUCCEED; error: - if(buf) + if (buf) HDfree(buf); - H5E_BEGIN_TRY { + H5E_BEGIN_TRY + { H5Tclose(type); H5Sclose(space); - } H5E_END_TRY; + } + H5E_END_TRY; return FAIL; } @@ -2968,21 +3098,21 @@ static int xml_print_strs(hid_t did, int source) { herr_t e; - hid_t type = -1; - hid_t space = -1; - hssize_t ssiz = -1; + hid_t type = H5I_INVALID_HID; + hid_t space = H5I_INVALID_HID; + hssize_t ssiz = -1; htri_t is_vlstr = FALSE; - size_t tsiz = 0; + size_t tsiz = 0; hsize_t i; - size_t str_size = 0; - char *bp = NULL; - char *onestring = NULL; - void *buf = NULL; - h5tools_str_t buffer; /* string into which to render */ - h5tools_context_t ctx; /* print context */ - h5tool_format_t *outputformat = &xml_dataformat; + size_t str_size = 0; + char * bp = NULL; + char * onestring = NULL; + void * buf = NULL; + h5tools_str_t buffer; /* string into which to render */ + h5tools_context_t ctx; /* print context */ + h5tool_format_t * outputformat = &xml_dataformat; h5tool_format_t string_dataformat; - hsize_t curr_pos = 0; /* total data element position */ + hsize_t curr_pos = 0; /* total data element position */ if (source == DATASET_DATA) type = H5Dget_type(did); @@ -2999,9 +3129,9 @@ xml_print_strs(hid_t did, int source) if (source == DATASET_DATA) { space = H5Dget_space(did); - if((ssiz = H5Sget_simple_extent_npoints(space)) < 0) + if ((ssiz = H5Sget_simple_extent_npoints(space)) < 0) goto error; - if((tsiz = H5Tget_size(type)) == 0) + if ((tsiz = H5Tget_size(type)) == 0) goto error; buf = HDmalloc((size_t)ssiz * tsiz); @@ -3014,9 +3144,9 @@ xml_print_strs(hid_t did, int source) } else if (source == ATTRIBUTE_DATA) { space = H5Aget_space(did); - if((ssiz = H5Sget_simple_extent_npoints(space)) < 0) + if ((ssiz = H5Sget_simple_extent_npoints(space)) < 0) goto error; - if((tsiz = H5Tget_size(type)) == 0) + if ((tsiz = H5Tget_size(type)) == 0) goto error; buf = HDmalloc((size_t)ssiz * tsiz); @@ -3028,33 +3158,36 @@ xml_print_strs(hid_t did, int source) goto error; } - bp = (char*) buf; - if (!is_vlstr) - onestring = (char *) HDcalloc(tsiz, sizeof(char)); + bp = (char *)buf; + if (!is_vlstr) { + onestring = (char *)HDcalloc(tsiz, sizeof(char)); + if (onestring == NULL) + goto error; + } /* setup */ HDmemset(&buffer, 0, sizeof(h5tools_str_t)); HDmemset(&ctx, 0, sizeof(ctx)); ctx.indent_level = dump_indent / COL; - ctx.cur_column = dump_indent; + ctx.cur_column = dump_indent; string_dataformat = *outputformat; if (fp_format) { string_dataformat.fmt_double = fp_format; - string_dataformat.fmt_float = fp_format; + string_dataformat.fmt_float = fp_format; } if (h5tools_nCols == 0) { - string_dataformat.line_ncols = 65535; + string_dataformat.line_ncols = 65535; string_dataformat.line_per_line = 1; } else string_dataformat.line_ncols = h5tools_nCols; - string_dataformat.do_escape = display_escape; - outputformat = &string_dataformat; + string_dataformat.do_escape = dump_opts.display_escape; + outputformat = &string_dataformat; for (i = 0; i < (hsize_t)ssiz; i++) { if (is_vlstr) { @@ -3073,7 +3206,8 @@ xml_print_strs(hid_t did, int source) /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "NULL"); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); } else { char *t_onestring = xml_escape_the_string(onestring, (int)str_size); @@ -3084,7 +3218,8 @@ xml_print_strs(hid_t did, int source) /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "\"%s\"", t_onestring); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); HDfree(t_onestring); } } @@ -3099,7 +3234,7 @@ xml_print_strs(hid_t did, int source) HDfree(onestring); if (buf) { if (is_vlstr) - H5Dvlen_reclaim(type, space, H5P_DEFAULT, buf); + H5Treclaim(type, space, H5P_DEFAULT, buf); HDfree(buf); } H5Tclose(type); @@ -3107,13 +3242,15 @@ xml_print_strs(hid_t did, int source) return SUCCEED; error: - if(buf) + if (buf) HDfree(buf); - H5E_BEGIN_TRY { + H5E_BEGIN_TRY + { H5Tclose(type); H5Sclose(space); - } H5E_END_TRY; + } + H5E_END_TRY; return FAIL; } @@ -3138,41 +3275,42 @@ check_filters(hid_t dcpl) size_t cd_nelmts = 20; unsigned int cd_values[20]; unsigned int flags; - h5tools_str_t buffer; /* string into which to render */ - h5tools_context_t ctx; /* print context */ - h5tool_format_t *outputformat = &xml_dataformat; + h5tools_str_t buffer; /* string into which to render */ + h5tools_context_t ctx; /* print context */ + h5tool_format_t * outputformat = &xml_dataformat; h5tool_format_t string_dataformat; - hsize_t curr_pos = 0; /* total data element position */ + hsize_t curr_pos = 0; /* total data element position */ /* setup */ HDmemset(&buffer, 0, sizeof(h5tools_str_t)); HDmemset(&ctx, 0, sizeof(ctx)); ctx.indent_level = dump_indent / COL; - ctx.cur_column = dump_indent; + ctx.cur_column = dump_indent; string_dataformat = *outputformat; if (fp_format) { string_dataformat.fmt_double = fp_format; - string_dataformat.fmt_float = fp_format; + string_dataformat.fmt_float = fp_format; } if (h5tools_nCols == 0) { - string_dataformat.line_ncols = 65535; + string_dataformat.line_ncols = 65535; string_dataformat.line_per_line = 1; } else string_dataformat.line_ncols = h5tools_nCols; - string_dataformat.do_escape = display_escape; - outputformat = &string_dataformat; + string_dataformat.do_escape = dump_opts.display_escape; + outputformat = &string_dataformat; nfilt = H5Pget_nfilters(dcpl); if (nfilt <= 0) return; for (i = 0; i < nfilt; i++) { - filter = H5Pget_filter2(dcpl, (unsigned) i, &flags, (size_t *) &cd_nelmts, cd_values, (size_t)120, namebuf, NULL); + filter = H5Pget_filter2(dcpl, (unsigned)i, &flags, (size_t *)&cd_nelmts, cd_values, (size_t)120, + namebuf, NULL); if (filter == H5Z_FILTER_DEFLATE) { ctx.indent_level++; ctx.need_prefix = TRUE; @@ -3188,7 +3326,8 @@ check_filters(hid_t dcpl) h5tools_str_append(&buffer, "%d", cd_values[0]); } h5tools_str_append(&buffer, "\"/>"); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; } else if (filter == H5Z_FILTER_FLETCHER32) { @@ -3198,7 +3337,8 @@ check_filters(hid_t dcpl) /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "<%sFletcher32 />", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; } else if (filter == H5Z_FILTER_SHUFFLE) { @@ -3208,7 +3348,8 @@ check_filters(hid_t dcpl) /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "<%sShuffle />", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; } else if (filter == H5Z_FILTER_SZIP) { @@ -3255,7 +3396,8 @@ check_filters(hid_t dcpl) h5tools_str_append(&buffer, "Header=\"Raw\""); } h5tools_str_append(&buffer, "/>"); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; } else { @@ -3272,37 +3414,37 @@ xml_dump_fill_value(hid_t dcpl, hid_t type) size_t sz; size_t i; hsize_t space; - void *buf; - char *name; - h5tools_str_t buffer; /* string into which to render */ - h5tools_context_t ctx; /* print context */ - h5tool_format_t *outputformat = &xml_dataformat; + void * buf; + char * name; + h5tools_str_t buffer; /* string into which to render */ + h5tools_context_t ctx; /* print context */ + h5tool_format_t * outputformat = &xml_dataformat; h5tool_format_t string_dataformat; - hsize_t curr_pos = 0; /* total data element position */ + hsize_t curr_pos = 0; /* total data element position */ /* setup */ HDmemset(&buffer, 0, sizeof(h5tools_str_t)); HDmemset(&ctx, 0, sizeof(ctx)); ctx.indent_level = dump_indent / COL; - ctx.cur_column = dump_indent; + ctx.cur_column = dump_indent; string_dataformat = *outputformat; if (fp_format) { string_dataformat.fmt_double = fp_format; - string_dataformat.fmt_float = fp_format; + string_dataformat.fmt_float = fp_format; } if (h5tools_nCols == 0) { - string_dataformat.line_ncols = 65535; + string_dataformat.line_ncols = 65535; string_dataformat.line_per_line = 1; } else string_dataformat.line_ncols = h5tools_nCols; - string_dataformat.do_escape = display_escape; - outputformat = &string_dataformat; + string_dataformat.do_escape = dump_opts.display_escape; + outputformat = &string_dataformat; ctx.indent_level++; dump_indent += COL; @@ -3312,31 +3454,34 @@ xml_dump_fill_value(hid_t dcpl, hid_t type) /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "<%sData>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level++; dump_indent += COL; space = H5Tget_size(type); - buf = HDmalloc((size_t) space); + buf = HDmalloc((size_t)space); H5Pget_fill_value(dcpl, type, buf); if (H5Tget_class(type) == H5T_REFERENCE) { - const char * path = lookup_ref_path(*(hobj_ref_t *) buf); + const char *path = lookup_ref_path(*(H5R_ref_t *)buf); ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "<%sDataFromFile>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); if (!path) { ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "\"%s\"", "NULL"); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); } else { char *t_path = xml_escape_the_string(path, -1); @@ -3346,7 +3491,8 @@ xml_dump_fill_value(hid_t dcpl, hid_t type) /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "\"%s\"", t_path); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); HDfree(t_path); } @@ -3355,7 +3501,10 @@ xml_dump_fill_value(hid_t dcpl, hid_t type) /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "</%sDataFromFile>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + + H5Rdestroy((H5R_ref_t *)buf); } else if (H5Tget_class(type) == H5T_STRING) { /* ????? */ @@ -3364,197 +3513,224 @@ xml_dump_fill_value(hid_t dcpl, hid_t type) /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "<!-- String fill values not yet implemented. -->"); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "<%sNoData />", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); } else { /* all other data */ switch (H5Tget_class(type)) { - case H5T_INTEGER: - ctx.need_prefix = TRUE; + case H5T_INTEGER: + ctx.need_prefix = TRUE; - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sDataFromFile>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<%sDataFromFile>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - ctx.need_prefix = TRUE; - h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); + ctx.need_prefix = TRUE; + h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "\"%d\"", *(int *) buf); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "\"%d\"", *(int *)buf); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - ctx.need_prefix = TRUE; + ctx.need_prefix = TRUE; - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "</%sDataFromFile>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - break; - case H5T_FLOAT: - ctx.need_prefix = TRUE; + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "</%sDataFromFile>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + break; + case H5T_FLOAT: + ctx.need_prefix = TRUE; - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sDataFromFile>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<%sDataFromFile>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - ctx.need_prefix = TRUE; - h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); + ctx.need_prefix = TRUE; + h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "\"%f\"", (double)*(float *)buf); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "\"%f\"", (double)*(float *)buf); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - ctx.need_prefix = TRUE; + ctx.need_prefix = TRUE; - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "</%sDataFromFile>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - break; - case H5T_BITFIELD: - case H5T_OPAQUE: - ctx.need_prefix = TRUE; + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "</%sDataFromFile>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + break; + case H5T_BITFIELD: + case H5T_OPAQUE: + ctx.need_prefix = TRUE; - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sDataFromFile>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - sz = H5Tget_size(type); + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<%sDataFromFile>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + sz = H5Tget_size(type); - ctx.need_prefix = TRUE; - h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); + ctx.need_prefix = TRUE; + h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "\""); - for (i = 0; i < sz; i++) { - h5tools_str_append(&buffer, "%x ", *(unsigned int *) buf + (i * sizeof(unsigned int))); - } - h5tools_str_append(&buffer, "\""); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "\""); + for (i = 0; i < sz; i++) { + unsigned long val = *(unsigned int *)buf + (i * sizeof(unsigned int)); - ctx.need_prefix = TRUE; + H5_CHECK_OVERFLOW(val, unsigned long, unsigned); + h5tools_str_append(&buffer, "%x ", (unsigned)val); + } + h5tools_str_append(&buffer, "\""); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "</%sDataFromFile>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - break; - case H5T_ENUM: - ctx.need_prefix = TRUE; + ctx.need_prefix = TRUE; - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sDataFromFile>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - name = H5Tget_member_name(type, *(unsigned *) buf); + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "</%sDataFromFile>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + break; + case H5T_ENUM: + ctx.need_prefix = TRUE; - ctx.need_prefix = TRUE; - h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<%sDataFromFile>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + name = H5Tget_member_name(type, *(unsigned *)buf); - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "\"%s\"", name); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - if(name) - H5free_memory(name); - ctx.need_prefix = TRUE; + ctx.need_prefix = TRUE; + h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "</%sDataFromFile>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - break; - case H5T_ARRAY: - ctx.need_prefix = TRUE; + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "\"%s\"", name); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + if (name) + H5free_memory(name); + ctx.need_prefix = TRUE; - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<!-- Array fill values not yet implemented. -->"); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "</%sDataFromFile>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + break; + case H5T_ARRAY: + ctx.need_prefix = TRUE; - ctx.need_prefix = TRUE; + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<!-- Array fill values not yet implemented. -->"); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sNoData />", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - break; - case H5T_TIME: - ctx.need_prefix = TRUE; + ctx.need_prefix = TRUE; - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<!-- Time fill not yet implemented. -->"); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<%sNoData />", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + break; + case H5T_TIME: + ctx.need_prefix = TRUE; - ctx.need_prefix = TRUE; + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<!-- Time fill not yet implemented. -->"); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sNoData />", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - break; - case H5T_COMPOUND: - ctx.need_prefix = TRUE; + ctx.need_prefix = TRUE; - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<!-- Compound fill not yet implemented. -->"); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<%sNoData />", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + break; + case H5T_COMPOUND: + ctx.need_prefix = TRUE; - ctx.need_prefix = TRUE; + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<!-- Compound fill not yet implemented. -->"); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sNoData />", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - break; - case H5T_VLEN: - ctx.need_prefix = TRUE; + ctx.need_prefix = TRUE; - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<!-- VL fill not yet implemented. -->"); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<%sNoData />", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + break; + case H5T_VLEN: + ctx.need_prefix = TRUE; - ctx.need_prefix = TRUE; + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<!-- VL fill not yet implemented. -->"); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sNoData />", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - break; - case H5T_NO_CLASS: - case H5T_NCLASSES: - case H5T_STRING: - case H5T_REFERENCE: - default: - ctx.need_prefix = TRUE; + ctx.need_prefix = TRUE; - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<!-- Unknown fill datatype: %d -->", H5Tget_class(type)); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<%sNoData />", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + break; + case H5T_NO_CLASS: + case H5T_NCLASSES: + case H5T_STRING: + case H5T_REFERENCE: + default: + ctx.need_prefix = TRUE; - ctx.need_prefix = TRUE; + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<!-- Unknown fill datatype: %d -->", H5Tget_class(type)); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sNoData/>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - break; + ctx.need_prefix = TRUE; + + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<%sNoData/>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + break; } } HDfree(buf); @@ -3566,7 +3742,8 @@ xml_dump_fill_value(hid_t dcpl, hid_t type) /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "</%sData>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; dump_indent -= COL; @@ -3579,39 +3756,45 @@ xml_dump_fill_value(hid_t dcpl, hid_t type) * Purpose: Dump a description of an HDF5 dataset in XML. * * Return: void - * - * Programmer: REMcG *------------------------------------------------------------------------- */ void -xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED * sset) +xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED *sset) { - hid_t type; - hid_t space; - hid_t dcpl; - H5D_fill_value_t fvstatus; - int maxdims; - hsize_t *chsize; - int ndims; - int i; - H5D_alloc_time_t at; - H5D_fill_time_t ft; - hsize_t tempi; - char *tmp; - char *t_name; - char *t_tmp; - char *t_prefix; - unsigned attr_crt_order_flags; - h5tools_str_t buffer; /* string into which to render */ - h5tools_context_t ctx; /* print context */ - h5tool_format_t *outputformat = &xml_dataformat; - h5tool_format_t string_dataformat; - hsize_t curr_pos = 0; /* total data element position */ - - char *rstr = (char*) HDmalloc((size_t)100); - char *pstr = (char*) HDmalloc((size_t)100); - - tmp = (char*) HDmalloc(HDstrlen(prefix) + HDstrlen(name) + 2); + hid_t type; + hid_t space; + hid_t dcpl; + H5D_fill_value_t fvstatus; + int maxdims; + hsize_t * chsize; + int ndims; + int i; + H5D_alloc_time_t at; + H5D_fill_time_t ft; + hsize_t tempi; + char * tmp; + char * t_name; + char * t_tmp; + char * t_prefix; + unsigned attr_crt_order_flags; + h5tools_str_t buffer; /* string into which to render */ + h5tools_context_t ctx; /* print context */ + h5tool_format_t * outputformat = &xml_dataformat; + h5tool_format_t string_dataformat; + hsize_t curr_pos = 0; /* total data element position */ + + char *rstr = (char *)HDmalloc((size_t)100); + char *pstr = (char *)HDmalloc((size_t)100); + + tmp = (char *)HDmalloc(HDstrlen(prefix) + HDstrlen(name) + 2); + if (tmp == NULL) { + error_msg("buffer allocation failed\n"); + h5tools_setstatus(EXIT_FAILURE); + HDfree(rstr); + HDfree(pstr); + return; + } + HDstrcpy(tmp, prefix); HDstrcat(tmp, "/"); HDstrcat(tmp, name); @@ -3621,40 +3804,41 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED * s HDmemset(&ctx, 0, sizeof(ctx)); ctx.indent_level = dump_indent / COL; - ctx.cur_column = dump_indent; + ctx.cur_column = dump_indent; - t_name = xml_escape_the_name(name); - t_tmp = xml_escape_the_name(tmp); + t_name = xml_escape_the_name(name); + t_tmp = xml_escape_the_name(tmp); t_prefix = xml_escape_the_name(prefix); string_dataformat = *outputformat; if (fp_format) { string_dataformat.fmt_double = fp_format; - string_dataformat.fmt_float = fp_format; + string_dataformat.fmt_float = fp_format; } if (h5tools_nCols == 0) { - string_dataformat.line_ncols = 65535; + string_dataformat.line_ncols = 65535; string_dataformat.line_per_line = 1; } else string_dataformat.line_ncols = h5tools_nCols; - string_dataformat.do_escape = display_escape; - outputformat = &string_dataformat; + string_dataformat.do_escape = dump_opts.display_escape; + outputformat = &string_dataformat; - xml_name_to_XID(tmp, rstr, 100, 1); - xml_name_to_XID(prefix, pstr, 100, 1); + xml_name_to_XID(did, tmp, rstr, 100, 1); + xml_name_to_XID(did, prefix, pstr, 100, 1); ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sDataset Name=\"%s\" OBJ-XID=\"%s\" H5Path= \"%s\" Parents=\"%s\" H5ParentPaths=\"%s\">", - xmlnsprefix, t_name, rstr, t_tmp, pstr, - strcmp(prefix, "") ? t_prefix : "/"); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append( + &buffer, "<%sDataset Name=\"%s\" OBJ-XID=\"%s\" H5Path= \"%s\" Parents=\"%s\" H5ParentPaths=\"%s\">", + xmlnsprefix, t_name, rstr, t_tmp, pstr, strcmp(prefix, "") ? t_prefix : "/"); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); HDfree(t_name); HDfree(t_tmp); @@ -3663,8 +3847,8 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED * s HDfree(pstr); HDfree(tmp); - dcpl = H5Dget_create_plist(did); - type = H5Dget_type(did); + dcpl = H5Dget_create_plist(did); + type = H5Dget_type(did); space = H5Dget_space(did); /* query the creation properties for attributes */ @@ -3672,7 +3856,7 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED * s /* Print information about storage layout */ if (H5D_CHUNKED == H5Pget_layout(dcpl)) { - if((maxdims = H5Sget_simple_extent_ndims(space)) < 0) { + if ((maxdims = H5Sget_simple_extent_ndims(space)) < 0) { error_msg("unable to get maxdims\n"); h5tools_setstatus(EXIT_FAILURE); } @@ -3686,7 +3870,8 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED * s /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "<%sStorageLayout>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level++; dump_indent += COL; @@ -3697,7 +3882,8 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED * s h5tools_str_append(&buffer, "<%sChunkedLayout ", xmlnsprefix); ndims = H5Pget_chunk(dcpl, maxdims, chsize); h5tools_str_append(&buffer, "Ndims=\"%d\">", ndims); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level++; dump_indent += COL; @@ -3708,8 +3894,10 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED * s /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sChunkDimension DimSize=\"%" H5_PRINTF_LL_WIDTH "u\" />", xmlnsprefix, chsize[i]); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "<%sChunkDimension DimSize=\"%" PRIuHSIZE "\" />", xmlnsprefix, + chsize[i]); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); } ctx.need_prefix = TRUE; @@ -3717,7 +3905,8 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED * s /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "<%sRequiredFilter>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level++; dump_indent += COL; @@ -3730,7 +3919,8 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED * s /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "</%sRequiredFilter>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; dump_indent -= COL; @@ -3740,7 +3930,8 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED * s /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "</%sChunkedLayout>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; dump_indent -= COL; @@ -3749,7 +3940,8 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED * s /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "</%sStorageLayout>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; dump_indent -= COL; HDfree(chsize); @@ -3763,7 +3955,8 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED * s /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "<%sStorageLayout>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level++; ctx.need_prefix = TRUE; @@ -3771,7 +3964,8 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED * s /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "<%sContiguousLayout/>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; ctx.need_prefix = TRUE; @@ -3779,7 +3973,8 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED * s /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "</%sStorageLayout>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; } else if (H5D_COMPACT == H5Pget_layout(dcpl)) { @@ -3790,7 +3985,8 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED * s /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "<%sStorageLayout>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level++; ctx.need_prefix = TRUE; @@ -3798,7 +3994,8 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED * s /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "<%sCompactLayout/>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; ctx.need_prefix = TRUE; @@ -3806,7 +4003,8 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED * s /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "</%sStorageLayout>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; } /* and check for external.... ?? */ @@ -3859,7 +4057,8 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED * s } /* end switch */ h5tools_str_append(&buffer, "\""); h5tools_str_append(&buffer, ">"); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level++; dump_indent += COL; @@ -3869,10 +4068,12 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED * s /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "<%sFillValue>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); H5Pfill_value_defined(dcpl, &fvstatus); - if (fvstatus == H5D_FILL_VALUE_UNDEFINED || (fvstatus == H5D_FILL_VALUE_DEFAULT && ft == H5D_FILL_TIME_IFSET)) { + if (fvstatus == H5D_FILL_VALUE_UNDEFINED || + (fvstatus == H5D_FILL_VALUE_DEFAULT && ft == H5D_FILL_TIME_IFSET)) { ctx.indent_level++; ctx.need_prefix = TRUE; @@ -3880,7 +4081,8 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED * s /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "<%sNoFill/>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; } else { @@ -3892,7 +4094,8 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED * s /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "</%sFillValue>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; dump_indent -= COL; @@ -3902,7 +4105,8 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED * s /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "</%sFillValueInfo>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; dump_indent -= COL; @@ -3914,184 +4118,202 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED * s dump_indent += COL; if ((sort_by == H5_INDEX_CRT_ORDER) && (attr_crt_order_flags & H5P_CRT_ORDER_TRACKED)) { - if (H5Aiterate2(did, sort_by, sort_order, NULL, dump_function_table->dump_attribute_function, NULL) < 0) { + if (H5Aiterate2(did, sort_by, sort_order, NULL, dump_function_table->dump_attribute_function, NULL) < + 0) { error_msg("error getting attribute information\n"); h5tools_setstatus(EXIT_FAILURE); } /* end if */ - } /* end if */ + } /* end if */ else { - if (H5Aiterate2(did, H5_INDEX_NAME, sort_order, NULL, dump_function_table->dump_attribute_function, NULL) < 0) { + if (H5Aiterate2(did, H5_INDEX_NAME, sort_order, NULL, dump_function_table->dump_attribute_function, + NULL) < 0) { error_msg("error getting attribute information\n"); h5tools_setstatus(EXIT_FAILURE); } /* end if */ - } /* end else */ + } /* end else */ ctx.indent_level--; dump_indent -= COL; tempi = H5Dget_storage_size(did); - if (display_data && (tempi > 0)) { + if (dump_opts.display_data && (tempi > 0)) { switch (H5Tget_class(type)) { - case H5T_INTEGER: - case H5T_FLOAT: - case H5T_STRING: - case H5T_BITFIELD: - case H5T_OPAQUE: - case H5T_ENUM: - case H5T_ARRAY: - ctx.indent_level++; - dump_indent += COL; - dump_function_table->dump_data_function(did, DATASET_DATA, NULL, 0); - ctx.indent_level--; - dump_indent -= COL; - break; - - case H5T_TIME: - ctx.indent_level++; + case H5T_INTEGER: + case H5T_FLOAT: + case H5T_STRING: + case H5T_BITFIELD: + case H5T_OPAQUE: + case H5T_ENUM: + case H5T_ARRAY: + ctx.indent_level++; + dump_indent += COL; + dump_function_table->dump_data_function(did, DATASET_DATA, NULL, 0); + ctx.indent_level--; + dump_indent -= COL; + break; - ctx.need_prefix = TRUE; + case H5T_TIME: + ctx.indent_level++; - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sData>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + ctx.need_prefix = TRUE; - ctx.need_prefix = TRUE; + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<%sData>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<!-- Time data not yet implemented. -->"); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + ctx.need_prefix = TRUE; - ctx.need_prefix = TRUE; + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<!-- Time data not yet implemented. -->"); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sNoData />", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + ctx.need_prefix = TRUE; - ctx.need_prefix = TRUE; + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<%sNoData />", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sData>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + ctx.need_prefix = TRUE; - ctx.indent_level--; - break; + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<%sData>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - case H5T_COMPOUND: - ctx.need_prefix = TRUE; + ctx.indent_level--; + break; - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<!-- Note: format of compound data not specified -->"); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + case H5T_COMPOUND: + ctx.need_prefix = TRUE; - ctx.indent_level++; - dump_indent += COL; - dump_function_table->dump_data_function(did, DATASET_DATA, NULL, 0); - ctx.indent_level--; - dump_indent -= COL; - break; + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<!-- Note: format of compound data not specified -->"); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - case H5T_REFERENCE: - ctx.need_prefix = TRUE; + ctx.indent_level++; + dump_indent += COL; + dump_function_table->dump_data_function(did, DATASET_DATA, NULL, 0); + ctx.indent_level--; + dump_indent -= COL; + break; - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sData>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - if (!H5Tequal(type, H5T_STD_REF_OBJ)) { + case H5T_REFERENCE: ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<!-- Note: Region references not supported -->"); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "<%sData>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + if (!H5Tequal(type, H5T_STD_REF_OBJ)) { + ctx.need_prefix = TRUE; + + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<!-- Note: Region references not supported -->"); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + + ctx.need_prefix = TRUE; + + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<%sNoData />", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + } + else { + ctx.need_prefix = TRUE; + + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<%sDataFromFile>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + + xml_print_refs(did, DATASET_DATA); + + ctx.need_prefix = TRUE; + + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "</%sDataFromFile>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + } ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sNoData />", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - } - else { + h5tools_str_append(&buffer, "</%sData>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + break; + + case H5T_VLEN: + ctx.indent_level--; + dump_indent -= COL; ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sDataFromFile>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - - xml_print_refs(did, DATASET_DATA); + h5tools_str_append(&buffer, "<!-- Note: format of VL data not specified -->"); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + ctx.indent_level++; + dump_indent += COL; + ctx.indent_level++; + dump_indent += COL; + dump_function_table->dump_data_function(did, DATASET_DATA, NULL, 0); + ctx.indent_level--; + dump_indent -= COL; + break; + case H5T_NO_CLASS: + case H5T_NCLASSES: + default: ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "</%sDataFromFile>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - } - - ctx.need_prefix = TRUE; - - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "</%sData>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - break; - - case H5T_VLEN: - ctx.indent_level--; - dump_indent -= COL; - ctx.need_prefix = TRUE; - - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<!-- Note: format of VL data not specified -->"); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - ctx.indent_level++; - dump_indent += COL; - - ctx.indent_level++; - dump_indent += COL; - dump_function_table->dump_data_function(did, DATASET_DATA, NULL, 0); - ctx.indent_level--; - dump_indent -= COL; - break; - case H5T_NO_CLASS: - case H5T_NCLASSES: - default: - ctx.need_prefix = TRUE; - - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sData>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "<%sData>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - ctx.need_prefix = TRUE; + ctx.need_prefix = TRUE; - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<!-- Unknown datatype: %d -->", H5Tget_class(type)); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<!-- Unknown datatype: %d -->", H5Tget_class(type)); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - ctx.need_prefix = TRUE; + ctx.need_prefix = TRUE; - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sNoData/>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "<%sNoData/>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - ctx.need_prefix = TRUE; + ctx.need_prefix = TRUE; - /* Render the element */ - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "</%sData>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - break; + /* Render the element */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "</%sData>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + break; } } else { @@ -4103,7 +4325,8 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED * s /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "<%sData>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level++; ctx.need_prefix = TRUE; @@ -4111,7 +4334,8 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED * s /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "<%sNoData/>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; ctx.need_prefix = TRUE; @@ -4119,7 +4343,8 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED * s /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "</%sData>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; } @@ -4132,7 +4357,8 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED * s /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "</%sDataset>", xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); h5tools_str_close(&buffer); } @@ -4151,62 +4377,64 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED * s static void xml_print_enum(hid_t type) { - char **name = NULL; /*member names */ - unsigned char *value = NULL; /*value array */ - unsigned nmembs; /*number of members */ - hid_t super; /*enum base integer type */ - hid_t native = -1; /*native integer datatype */ - size_t dst_size; /*destination value type size */ - unsigned i; /*miscellaneous counters */ - size_t j; - h5tools_str_t buffer; /* string into which to render */ - h5tools_context_t ctx; /* print context */ - h5tool_format_t *outputformat = &xml_dataformat; - h5tool_format_t string_dataformat; - hsize_t curr_pos = 0; /* total data element position */ + char ** name = NULL; /*member names */ + unsigned char * value = NULL; /*value array */ + unsigned nmembs; /*number of members */ + hid_t super; /*enum base integer type */ + hid_t native = H5I_INVALID_HID; /*native integer datatype */ + size_t dst_size; /*destination value type size */ + unsigned i; /*miscellaneous counters */ + size_t j; + h5tools_str_t buffer; /* string into which to render */ + h5tools_context_t ctx; /* print context */ + h5tool_format_t * outputformat = &xml_dataformat; + h5tool_format_t string_dataformat; + hsize_t curr_pos = 0; /* total data element position */ /* setup */ HDmemset(&buffer, 0, sizeof(h5tools_str_t)); HDmemset(&ctx, 0, sizeof(ctx)); ctx.indent_level = dump_indent / COL; - ctx.cur_column = dump_indent; + ctx.cur_column = dump_indent; string_dataformat = *outputformat; if (fp_format) { string_dataformat.fmt_double = fp_format; - string_dataformat.fmt_float = fp_format; + string_dataformat.fmt_float = fp_format; } if (h5tools_nCols == 0) { - string_dataformat.line_ncols = 65535; + string_dataformat.line_ncols = 65535; string_dataformat.line_per_line = 1; } else string_dataformat.line_ncols = h5tools_nCols; - string_dataformat.do_escape = display_escape; - outputformat = &string_dataformat; + string_dataformat.do_escape = dump_opts.display_escape; + outputformat = &string_dataformat; nmembs = (unsigned)H5Tget_nmembers(type); - super = H5Tget_super(type); + super = H5Tget_super(type); ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sDataType>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "<%sDataType>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - xml_print_datatype(super,0); + xml_print_datatype(super, 0); ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "</%sDataType>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "</%sDataType>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); /* * Determine what datatype to use for the native values. To simplify @@ -4230,7 +4458,7 @@ xml_print_enum(hid_t type) } /* Get the names and raw values of all members */ - name = (char **)HDcalloc((size_t)nmembs, sizeof(char *)); + name = (char **)HDcalloc((size_t)nmembs, sizeof(char *)); value = (unsigned char *)HDcalloc((size_t)nmembs, MAX(H5Tget_size(type), dst_size)); for (i = 0; i < nmembs; i++) { @@ -4255,8 +4483,9 @@ xml_print_enum(hid_t type) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sEnumElement>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "<%sEnumElement>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level++; ctx.need_prefix = TRUE; h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); @@ -4264,7 +4493,8 @@ xml_print_enum(hid_t type) /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "%s", t_name); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); HDfree(t_name); ctx.indent_level--; @@ -4272,15 +4502,17 @@ xml_print_enum(hid_t type) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "</%sEnumElement>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "</%sEnumElement>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sEnumValue>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "<%sEnumValue>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level++; ctx.need_prefix = TRUE; h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); @@ -4294,22 +4526,28 @@ xml_print_enum(hid_t type) h5tools_str_append(&buffer, "%02x", value[i * dst_size + j]); } else if (H5T_SGN_NONE == H5Tget_sign(native)) { - h5tools_str_append(&buffer,"%" H5_PRINTF_LL_WIDTH "u", *((unsigned long long *) - ((void *) (value + i * dst_size)))); + unsigned long long copy; + + HDmemcpy(©, value + i * dst_size, sizeof(copy)); + h5tools_str_append(&buffer, "%llu", copy); } else { - h5tools_str_append(&buffer,"%" H5_PRINTF_LL_WIDTH "d", - *((long long *) ((void *) (value + i * dst_size)))); + long long copy; + + HDmemcpy(©, value + i * dst_size, sizeof(copy)); + h5tools_str_append(&buffer, "%lld", copy); } - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "</%sEnumValue>",xmlnsprefix); - h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_str_append(&buffer, "</%sEnumValue>", xmlnsprefix); + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, + (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); } ctx.indent_level--; dump_indent -= COL; @@ -4324,4 +4562,3 @@ xml_print_enum(hid_t type) HDfree(value); H5Tclose(super); } - diff --git a/tools/src/h5dump/h5dump_xml.h b/tools/src/h5dump/h5dump_xml.h index 3c59917..d69f6d5 100644 --- a/tools/src/h5dump/h5dump_xml.h +++ b/tools/src/h5dump/h5dump_xml.h @@ -6,14 +6,14 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -#ifndef H5DUMP_XML_H__ -#define H5DUMP_XML_H__ +#ifndef H5DUMP_XML_H +#define H5DUMP_XML_H -extern const char *xmlnsprefix; +extern const char *xmlnsprefix; #ifdef __cplusplus extern "C" { @@ -22,16 +22,16 @@ extern "C" { /* The dump functions of the dump_function_table */ /* XML format: same interface, alternative output */ -void xml_dump_group(hid_t, const char *); -void xml_dump_named_datatype(hid_t, const char *); -void xml_dump_dataset(hid_t, const char *, struct subset_t *); -void xml_dump_dataspace(hid_t space); -void xml_dump_datatype(hid_t type); -herr_t xml_dump_attr(hid_t, const char *, const H5A_info_t *, void *); -void xml_dump_data(hid_t, int, struct subset_t *, int); +void xml_dump_group(hid_t, const char *); +void xml_dump_named_datatype(hid_t, const char *); +void xml_dump_dataset(hid_t, const char *, struct subset_t *); +void xml_dump_dataspace(hid_t space); +void xml_dump_datatype(hid_t type); +herr_t xml_dump_attr(hid_t, const char *, const H5A_info_t *, void *); +void xml_dump_data(hid_t, int, struct subset_t *, int); #ifdef __cplusplus } #endif -#endif /* !H5DUMP_XML_H__ */ +#endif /* H5DUMP_XML_H */ diff --git a/tools/src/h5format_convert/CMakeLists.txt b/tools/src/h5format_convert/CMakeLists.txt index 540be8c..d0ddb32 100644 --- a/tools/src/h5format_convert/CMakeLists.txt +++ b/tools/src/h5format_convert/CMakeLists.txt @@ -1,4 +1,4 @@ -cmake_minimum_required (VERSION 3.10) +cmake_minimum_required (VERSION 3.12) project (HDF5_TOOLS_SRC_H5FC C) # -------------------------------------------------------------------- @@ -6,7 +6,8 @@ project (HDF5_TOOLS_SRC_H5FC C) # -------------------------------------------------------------------- if (NOT ONLY_SHARED_LIBS) add_executable (h5format_convert ${HDF5_TOOLS_SRC_H5FC_SOURCE_DIR}/h5format_convert.c) - target_include_directories (h5format_convert PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5format_convert PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_compile_options(h5format_convert PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5format_convert STATIC) target_link_libraries (h5format_convert PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) set_target_properties (h5format_convert PROPERTIES FOLDER tools) @@ -16,7 +17,8 @@ if (NOT ONLY_SHARED_LIBS) endif () if (BUILD_SHARED_LIBS) add_executable (h5format_convert-shared ${HDF5_TOOLS_SRC_H5FC_SOURCE_DIR}/h5format_convert.c) - target_include_directories (h5format_convert-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5format_convert-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_compile_options(h5format_convert-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5format_convert-shared SHARED) target_link_libraries (h5format_convert-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET}) set_target_properties (h5format_convert-shared PROPERTIES FOLDER tools) @@ -25,6 +27,17 @@ if (BUILD_SHARED_LIBS) set (H5_DEP_EXECUTABLES ${H5_DEP_EXECUTABLES} h5format_convert-shared) endif () +#----------------------------------------------------------------------------- +# Add Target to clang-format +#----------------------------------------------------------------------------- +if (HDF5_ENABLE_FORMATTERS) + if (NOT ONLY_SHARED_LIBS) + clang_format (HDF5_H5FORMAT_SRC_FORMAT h5format_convert) + else () + clang_format (HDF5_H5FORMAT_SRC_FORMAT h5format_convert-shared) + endif () +endif () + ############################################################################## ############################################################################## ### I N S T A L L A T I O N ### diff --git a/tools/src/h5format_convert/Makefile.am b/tools/src/h5format_convert/Makefile.am index 2b36949..2c968a3 100644 --- a/tools/src/h5format_convert/Makefile.am +++ b/tools/src/h5format_convert/Makefile.am @@ -6,7 +6,7 @@ # This file is part of HDF5. The full HDF5 copyright notice, including # terms governing use, modification, and redistribution, is contained in # the COPYING file, which can be found at the root of the source code -# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. +# distribution tree, or in https://www.hdfgroup.org/licenses. # If you do not have access to either file, you may request a copy from # help@hdfgroup.org. ## diff --git a/tools/src/h5format_convert/h5format_convert.c b/tools/src/h5format_convert/h5format_convert.c index 257a047..50d0f5d 100644 --- a/tools/src/h5format_convert/h5format_convert.c +++ b/tools/src/h5format_convert/h5format_convert.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -15,10 +15,9 @@ * Programmer: Vailin Choi; Feb 2015 */ - /* * We include the private header file so we can get to the uniform - * programming environment it declares. + * programming environment it declares. * HDF5 API functions (except for H5G_basename()) */ #include "H5private.h" @@ -29,41 +28,22 @@ /* Name of tool */ #define PROGRAMNAME "h5format_convert" -static char *fname_g = NULL; -static char *dname_g = NULL; -static int dset_g = FALSE; -static int noop_g = FALSE; -static int verbose_g = 0; +static char *fname_g = NULL; +static char *dname_g = NULL; +static int dset_g = FALSE; +static int noop_g = FALSE; +static int verbose_g = 0; /* * Command-line options: The user can specify short or long-named * parameters. */ -static const char *s_opts = "hVvd:n"; -static struct long_options l_opts[] = { - { "help", no_arg, 'h' }, - { "hel", no_arg, 'h'}, - { "he", no_arg, 'h'}, - { "version", no_arg, 'V' }, - { "version", no_arg, 'V' }, - { "versio", no_arg, 'V' }, - { "versi", no_arg, 'V' }, - { "vers", no_arg, 'V' }, - { "verbose", no_arg, 'v' }, - { "verbos", no_arg, 'v' }, - { "verbo", no_arg, 'v' }, - { "verb", no_arg, 'v' }, - { "dname", require_arg, 'd' }, - { "dnam", require_arg, 'd' }, - { "dna", require_arg, 'd' }, - { "dn", require_arg, 'd' }, - { "noop", no_arg, 'n' }, - { "noo", no_arg, 'n' }, - { "no", no_arg, 'n' }, - { NULL, 0, '\0' } -}; - - +static const char * s_opts = "hVvd:n"; +static struct h5_long_options l_opts[] = {{"help", no_arg, 'h'}, {"version", no_arg, 'V'}, + {"verbose", no_arg, 'v'}, {"dname", require_arg, 'd'}, + {"noop", no_arg, 'n'}, {"enable-error-stack", no_arg, 'E'}, + {NULL, 0, '\0'}}; + /*------------------------------------------------------------------------- * Function: usage * @@ -73,7 +53,8 @@ static struct long_options l_opts[] = { * *------------------------------------------------------------------------- */ -static void usage(const char *prog) +static void +usage(const char *prog) { HDfprintf(stdout, "usage: %s [OPTIONS] file_name\n", prog); HDfprintf(stdout, " OPTIONS\n"); @@ -108,79 +89,83 @@ static void usage(const char *prog) * Purpose: parse command line input * * Return: Success: 0 - * Failure: 1 + * Failure: 1 * *------------------------------------------------------------------------- */ static int -parse_command_line(int argc, const char **argv) +parse_command_line(int argc, const char *const *argv) { int opt; - /* no arguments */ + /* no arguments */ if (argc == 1) { usage(h5tools_getprogname()); - h5tools_setstatus(EXIT_FAILURE); + h5tools_setstatus(EXIT_FAILURE); goto error; } /* parse command line options */ - while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) { - switch((char) opt) { - case 'h': - usage(h5tools_getprogname()); - h5tools_setstatus(EXIT_SUCCESS); - goto error; - - case 'V': - print_version(h5tools_getprogname()); - h5tools_setstatus(EXIT_SUCCESS); - goto error; - - case 'v': - verbose_g = TRUE; - break; - - case 'd': /* -d dname */ - if(opt_arg != NULL && *opt_arg) - dname_g = HDstrdup(opt_arg); - if(dname_g == NULL) { - h5tools_setstatus(EXIT_FAILURE); - error_msg("No dataset name\n", opt_arg); - usage(h5tools_getprogname()); - goto error; - } - dset_g = TRUE; - break; - - case 'n': /* -n */ - noop_g = TRUE; - break; - - default: - h5tools_setstatus(EXIT_FAILURE); - usage(h5tools_getprogname()); - goto error; - break; - } /* switch */ - } /* while */ - - if (argc <= opt_ind) { + while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) { + switch ((char)opt) { + case 'h': + usage(h5tools_getprogname()); + h5tools_setstatus(EXIT_SUCCESS); + goto error; + + case 'V': + print_version(h5tools_getprogname()); + h5tools_setstatus(EXIT_SUCCESS); + goto error; + + case 'v': + verbose_g = TRUE; + break; + + case 'd': /* -d dname */ + if (H5_optarg != NULL && *H5_optarg) + dname_g = HDstrdup(H5_optarg); + if (dname_g == NULL) { + h5tools_setstatus(EXIT_FAILURE); + error_msg("No dataset name `%s`\n", H5_optarg); + usage(h5tools_getprogname()); + goto error; + } + dset_g = TRUE; + break; + + case 'n': /* -n */ + noop_g = TRUE; + break; + + case 'E': + enable_error_stack = 1; + break; + + default: + h5tools_setstatus(EXIT_FAILURE); + usage(h5tools_getprogname()); + goto error; + break; + } /* switch */ + } /* while */ + + if (argc <= H5_optind) { error_msg("missing file name\n"); usage(h5tools_getprogname()); - h5tools_setstatus(EXIT_FAILURE); + h5tools_setstatus(EXIT_FAILURE); goto error; } - fname_g = HDstrdup(argv[opt_ind]); + fname_g = HDstrdup(argv[H5_optind]); - return(0); + return 0; error: - return(-1); ; + return -1; + ; } /* parse_command_line() */ - /*------------------------------------------------------------------------- * Function: leave * @@ -202,151 +187,155 @@ leave(int ret) * Function: convert() * * Purpose: To downgrade a dataset's indexing type or layout version: - * For chunked: - * Downgrade the chunk indexing type to version 1 B-tree - * If type is already version 1 B-tree, no further action - * For compact/contiguous: - * Downgrade the layout version from 4 to 3 - * If version is already <= 3, no further action - * For virtual: - * No further action + * For chunked: + * Downgrade the chunk indexing type to version 1 B-tree + * If type is already version 1 B-tree, no further action + * For compact/contiguous: + * Downgrade the layout version from 4 to 3 + * If version is already <= 3, no further action + * For virtual: + * No further action * * Return: Success: 0 - * Failure: 1 + * Failure: 1 * *------------------------------------------------------------------------- */ static int convert(hid_t fid, const char *dname) { - hid_t dcpl = -1; - hid_t did = -1; - H5D_layout_t layout_type; + hid_t dcpl = H5I_INVALID_HID; + hid_t did = H5I_INVALID_HID; + H5D_layout_t layout_type; H5D_chunk_index_t idx_type; /* Open the dataset */ - if((did = H5Dopen2(fid, dname, H5P_DEFAULT)) < 0) { + if ((did = H5Dopen2(fid, dname, H5P_DEFAULT)) < 0) { error_msg("unable to open dataset \"%s\"\n", dname); h5tools_setstatus(EXIT_FAILURE); goto error; } - else if(verbose_g) + else if (verbose_g) HDfprintf(stdout, "Open the dataset\n"); /* Get the dataset's creation property list */ - if((dcpl = H5Dget_create_plist(did)) < 0) { + if ((dcpl = H5Dget_create_plist(did)) < 0) { error_msg("unable to get the dataset creation property list\n"); h5tools_setstatus(EXIT_FAILURE); goto error; } /* Get the dataset's layout */ - if((layout_type = H5Pget_layout(dcpl)) < 0) { + if ((layout_type = H5Pget_layout(dcpl)) < 0) { error_msg("unable to get the dataset layout type\n"); h5tools_setstatus(EXIT_FAILURE); goto error; } - else if(verbose_g) + else if (verbose_g) HDfprintf(stdout, "Retrieve the dataset's layout\n"); - switch(layout_type) { - case H5D_CHUNKED: - if(verbose_g) - HDfprintf(stdout, "Dataset is a chunked dataset\n"); + switch (layout_type) { + case H5D_CHUNKED: + if (verbose_g) + HDfprintf(stdout, "Dataset is a chunked dataset\n"); + + /* Get the dataset's chunk indexing type */ + if (H5Dget_chunk_index_type(did, &idx_type) < 0) { + error_msg("unable to get the chunk indexing type for \"%s\"\n", dname); + h5tools_setstatus(EXIT_FAILURE); + goto error; + } + else if (verbose_g) + HDfprintf(stdout, "Retrieve the dataset's chunk indexing type\n"); + + if (idx_type == H5D_CHUNK_IDX_BTREE) { + if (verbose_g) + HDfprintf( + stdout, + "Dataset's chunk indexing type is already version 1 B-tree: no further action\n"); + h5tools_setstatus(EXIT_SUCCESS); + goto done; + } + else if (verbose_g) + HDfprintf(stdout, "Dataset's chunk indexing type is not version 1 B-tree\n"); + + break; + + case H5D_CONTIGUOUS: + if (verbose_g) + HDfprintf(stdout, "Dataset is a contiguous dataset: downgrade layout version as needed\n"); + break; + + case H5D_COMPACT: + if (verbose_g) + HDfprintf(stdout, "Dataset is a compact dataset: downgrade layout version as needed\n"); + break; + + case H5D_VIRTUAL: + if (verbose_g) + HDfprintf(stdout, "No further action for virtual dataset\n"); + goto done; - /* Get the dataset's chunk indexing type */ - if(H5Dget_chunk_index_type(did, &idx_type) < 0) { - error_msg("unable to get the chunk indexing type for \"%s\"\n", dname); + case H5D_NLAYOUTS: + case H5D_LAYOUT_ERROR: + default: + error_msg("unknown layout type for \"%s\"\n", dname); h5tools_setstatus(EXIT_FAILURE); goto error; - } - else if(verbose_g) - HDfprintf(stdout, "Retrieve the dataset's chunk indexing type\n"); - - if(idx_type == H5D_CHUNK_IDX_BTREE) { - if(verbose_g) - HDfprintf(stdout, "Dataset's chunk indexing type is already version 1 B-tree: no further action\n"); - h5tools_setstatus(EXIT_SUCCESS); - goto done; - } - else if (verbose_g) - HDfprintf(stdout, "Dataset's chunk indexing type is not version 1 B-tree\n"); - - break; - - case H5D_CONTIGUOUS: - if(verbose_g) - HDfprintf(stdout, "Dataset is a contiguous dataset: downgrade layout version as needed\n"); - break; - - case H5D_COMPACT: - if(verbose_g) - HDfprintf(stdout, "Dataset is a compact dataset: downgrade layout version as needed\n"); - break; - - case H5D_VIRTUAL: - if(verbose_g) - HDfprintf(stdout, "No further action for virtual dataset\n"); - goto done; - - case H5D_NLAYOUTS: - case H5D_LAYOUT_ERROR: - default: - error_msg("unknown layout type for \"%s\"\n", dname); - h5tools_setstatus(EXIT_FAILURE); - goto error; } /* end switch */ /* No further action if it is a noop */ - if(noop_g) { - if(verbose_g) + if (noop_g) { + if (verbose_g) HDfprintf(stdout, "Not converting the dataset\n"); h5tools_setstatus(EXIT_SUCCESS); goto done; } - if(verbose_g) - HDfprintf(stdout, "Converting the dataset...\n"); + if (verbose_g) + HDfprintf(stdout, "Converting the dataset...\n"); /* Downgrade the dataset */ - if(H5Dformat_convert(did) < 0) { + if (H5Dformat_convert(did) < 0) { error_msg("unable to downgrade dataset \"%s\"\n", dname); h5tools_setstatus(EXIT_FAILURE); goto error; } - else if(verbose_g) + else if (verbose_g) HDfprintf(stdout, "Done\n"); done: /* Close the dataset */ - if(H5Dclose(did) < 0) { + if (H5Dclose(did) < 0) { error_msg("unable to close dataset \"%s\"\n", dname); h5tools_setstatus(EXIT_FAILURE); goto error; } - else if(verbose_g) + else if (verbose_g) HDfprintf(stdout, "Close the dataset\n"); - + /* Close the dataset creation property list */ - if(H5Pclose(dcpl) < 0) { + if (H5Pclose(dcpl) < 0) { error_msg("unable to close dataset creation property list\n"); h5tools_setstatus(EXIT_FAILURE); goto error; } - else if(verbose_g) + else if (verbose_g) HDprintf("Close the dataset creation property list\n"); return 0; error: - if(verbose_g) + if (verbose_g) HDfprintf(stdout, "Error encountered\n"); - H5E_BEGIN_TRY { + H5E_BEGIN_TRY + { H5Pclose(dcpl); H5Dclose(did); - } H5E_END_TRY; + } + H5E_END_TRY; return -1; } /* convert() */ @@ -362,19 +351,19 @@ error: *------------------------------------------------------------------------- */ static int -convert_dsets_cb(const char *path, const H5O_info_t *oi, const char *already_visited, void *_fid) +convert_dsets_cb(const char *path, const H5O_info2_t *oi, const char *already_visited, void *_fid) { hid_t fid = *(hid_t *)_fid; /* If the object has already been seen then just return */ - if(NULL == already_visited) { - if(oi->type == H5O_TYPE_DATASET) { - if(verbose_g) + if (NULL == already_visited) { + if (oi->type == H5O_TYPE_DATASET) { + if (verbose_g) HDfprintf(stdout, "Going to process dataset:%s...\n", path); - if(convert(fid, path) < 0) - goto error; + if (convert(fid, path) < 0) + goto error; } /* end if */ - } /* end if */ + } /* end if */ return 0; @@ -382,66 +371,64 @@ error: return -1; } /* end convert_dsets_cb() */ - /*------------------------------------------------------------------------- * Function: main * * Purpose: To convert the chunk indexing type of a dataset in a file to - * version 1 B-tree. + * version 1 B-tree. * * Return: Success: 0 - * Failure: 1 + * Failure: 1 * *------------------------------------------------------------------------- */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { - H5E_auto2_t func; - void *edata; - hid_t fid = -1; + hid_t fid = H5I_INVALID_HID; h5tools_setprogname(PROGRAMNAME); h5tools_setstatus(EXIT_SUCCESS); - /* Disable error reporting */ - H5Eget_auto2(H5E_DEFAULT, &func, &edata); - H5Eset_auto2(H5E_DEFAULT, NULL, NULL); - /* Initialize h5tools lib */ h5tools_init(); /* Parse command line options */ - if(parse_command_line(argc, argv) < 0) - goto done; - else if(verbose_g) - HDfprintf(stdout, "Process command line options\n"); + if (parse_command_line(argc, (const char *const *)argv) < 0) + goto done; + else if (verbose_g) + HDfprintf(stdout, "Process command line options\n"); - if(noop_g && verbose_g) - HDfprintf(stdout, "It is noop...\n"); + if (noop_g && verbose_g) + HDfprintf(stdout, "It is noop...\n"); + + /* enable error reporting if command line option */ + h5tools_error_report(); /* Open the HDF5 file */ - if((fid = h5tools_fopen(fname_g, H5F_ACC_RDWR, H5P_DEFAULT, NULL, NULL, 0)) < 0) { - error_msg("unable to open file \"%s\"\n", fname_g); - h5tools_setstatus(EXIT_FAILURE); - goto done; - } else if(verbose_g) - HDfprintf(stdout, "Open the file %s\n", fname_g); - - if(dset_g) { /* Convert a specified dataset in the file */ - if(verbose_g) - HDfprintf(stdout, "Going to process dataset: %s...\n", dname_g); - if(convert(fid, dname_g) < 0) - goto done; - } else { /* Convert all datasets in the file */ - if(verbose_g) - HDfprintf(stdout, "Processing all datasets in the file...\n"); - if(h5trav_visit(fid, "/", TRUE, TRUE, convert_dsets_cb, NULL, &fid, H5O_INFO_BASIC) < 0) - goto done; + if ((fid = h5tools_fopen(fname_g, H5F_ACC_RDWR, H5P_DEFAULT, FALSE, NULL, 0)) < 0) { + error_msg("unable to open file \"%s\"\n", fname_g); + h5tools_setstatus(EXIT_FAILURE); + goto done; + } + else if (verbose_g) + HDfprintf(stdout, "Open the file %s\n", fname_g); + + if (dset_g) { /* Convert a specified dataset in the file */ + if (verbose_g) + HDfprintf(stdout, "Going to process dataset: %s...\n", dname_g); + if (convert(fid, dname_g) < 0) + goto done; + } + else { /* Convert all datasets in the file */ + if (verbose_g) + HDfprintf(stdout, "Processing all datasets in the file...\n"); + if (h5trav_visit(fid, "/", TRUE, TRUE, convert_dsets_cb, NULL, &fid, H5O_INFO_BASIC) < 0) + goto done; } /* end else */ - if(verbose_g) { - if(noop_g) { + if (verbose_g) { + if (noop_g) { HDfprintf(stdout, "Not processing the file's superblock...\n"); h5tools_setstatus(EXIT_SUCCESS); goto done; @@ -450,7 +437,7 @@ main(int argc, const char *argv[]) } /* end if */ /* Process superblock */ - if(H5Fformat_convert(fid) < 0) { + if (H5Fformat_convert(fid) < 0) { error_msg("unable to convert file's superblock\"%s\"\n", fname_g); h5tools_setstatus(EXIT_FAILURE); goto done; @@ -458,21 +445,21 @@ main(int argc, const char *argv[]) done: /* Close the file */ - if(fid >= 0) { - if(H5Fclose(fid) < 0) { - error_msg("unable to close file \"%s\"\n", fname_g); - h5tools_setstatus(EXIT_FAILURE); - } else if(verbose_g) - HDfprintf(stdout, "Close the file\n"); - } /* end if */ - - if(fname_g) - HDfree(fname_g); - if(dname_g) - HDfree(dname_g); - - H5Eset_auto2(H5E_DEFAULT, func, edata); + if (fid >= 0) { + if (H5Fclose(fid) < 0) { + error_msg("unable to close file \"%s\"\n", fname_g); + h5tools_setstatus(EXIT_FAILURE); + } + else if (verbose_g) { + HDfprintf(stdout, "Close the file\n"); + } + } /* end if */ + + if (fname_g) + HDfree(fname_g); + if (dname_g) + HDfree(dname_g); + leave(h5tools_getstatus()); } /* end main() */ - diff --git a/tools/src/h5import/CMakeLists.txt b/tools/src/h5import/CMakeLists.txt index dd7921d..a7f238e 100644 --- a/tools/src/h5import/CMakeLists.txt +++ b/tools/src/h5import/CMakeLists.txt @@ -1,12 +1,12 @@ -cmake_minimum_required (VERSION 3.10) +cmake_minimum_required (VERSION 3.12) project (HDF5_TOOLS_SRC_H5IMPORT C) # -------------------------------------------------------------------- # Add the h5import executables # -------------------------------------------------------------------- if (NOT ONLY_SHARED_LIBS) - add_executable (h5import ${HDF5_TOOLS_SRC_H5IMPORT_SOURCE_DIR}/h5import.c) - target_include_directories (h5import PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + add_executable (h5import ${HDF5_TOOLS_SRC_H5IMPORT_SOURCE_DIR}/h5import.c ${HDF5_TOOLS_SRC_H5IMPORT_SOURCE_DIR}/h5import.h) + target_include_directories (h5import PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") TARGET_C_PROPERTIES (h5import STATIC) target_link_libraries (h5import PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) #set_target_properties (h5import PROPERTIES COMPILE_DEFINITIONS H5DEBUGIMPORT) @@ -17,8 +17,8 @@ if (NOT ONLY_SHARED_LIBS) endif () if (BUILD_SHARED_LIBS) - add_executable (h5import-shared ${HDF5_TOOLS_SRC_H5IMPORT_SOURCE_DIR}/h5import.c) - target_include_directories (h5import-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + add_executable (h5import-shared ${HDF5_TOOLS_SRC_H5IMPORT_SOURCE_DIR}/h5import.c ${HDF5_TOOLS_SRC_H5IMPORT_SOURCE_DIR}/h5import.h) + target_include_directories (h5import-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") TARGET_C_PROPERTIES (h5import-shared SHARED) target_link_libraries (h5import-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET}) #set_target_properties (h5import-shared PROPERTIES COMPILE_DEFINITIONS H5DEBUGIMPORT) @@ -28,6 +28,17 @@ if (BUILD_SHARED_LIBS) set (H5_DEP_EXECUTABLES ${H5_DEP_EXECUTABLES} h5import-shared) endif () +#----------------------------------------------------------------------------- +# Add Target to clang-format +#----------------------------------------------------------------------------- +if (HDF5_ENABLE_FORMATTERS) + if (NOT ONLY_SHARED_LIBS) + clang_format (HDF5_H5IMPORT_SRC_FORMAT h5import) + else () + clang_format (HDF5_H5IMPORT_SRC_FORMAT h5import-shared) + endif () +endif () + ############################################################################## ############################################################################## ### I N S T A L L A T I O N ### diff --git a/tools/src/h5import/Makefile.am b/tools/src/h5import/Makefile.am index 4623eb5..14a8670 100644 --- a/tools/src/h5import/Makefile.am +++ b/tools/src/h5import/Makefile.am @@ -6,7 +6,7 @@ # This file is part of HDF5. The full HDF5 copyright notice, including # terms governing use, modification, and redistribution, is contained in # the COPYING file, which can be found at the root of the source code -# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. +# distribution tree, or in https://www.hdfgroup.org/licenses. # If you do not have access to either file, you may request a copy from # help@hdfgroup.org. ## diff --git a/tools/src/h5import/h5import.c b/tools/src/h5import/h5import.c index 1eef5ab..317db81 100644 --- a/tools/src/h5import/h5import.c +++ b/tools/src/h5import/h5import.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -27,68 +27,69 @@ #endif /* Local function declarations */ -static int gtoken(char *s); -static int process(struct Options *opt); -static int processConfigurationFile(char *infile, struct Input *in); -static int mapKeywordToIndex(char *key); -static int parsePathInfo(struct path_info *path, char *strm); -static int parseDimensions(struct Input *in, char *strm); -static int getInputSize(struct Input *in, int ival); -static int getInputClass(struct Input *in, char * strm); -static int getInputClassType(struct Input *in, char * strm); -static int getInputByteOrder(struct Input *in, FILE *strm); -static int InputClassStrToInt(char *temp); -static int getRank(struct Input *in, FILE *strm); -static int getDimensionSizes(struct Input *in, FILE *strm); -static int getOutputSize(struct Input *in, FILE *strm); -static int getOutputClass(struct Input *in, FILE *strm); -static int OutputClassStrToInt(char *temp); -static int getOutputArchitecture(struct Input *in, FILE *strm); -static int OutputArchStrToInt(const char *temp); -static int getOutputByteOrder(struct Input *in, FILE *strm); -static int OutputByteOrderStrToInt(const char *temp); -static int getChunkedDimensionSizes(struct Input *in, FILE *strm); -static int getCompressionType(struct Input *in, FILE *strm); -static int CompressionTypeStrToInt(char *temp); -static int getCompressionParameter(struct Input *in, FILE *strm); -static int getExternalFilename(struct Input *in, FILE *strm); -static int getMaximumDimensionSizes(struct Input *in, FILE *strm); -static int processDataFile(char *infile, struct Input *in, hid_t file_id); -static int readIntegerData(FILE *strm, struct Input *in); -static int readFloatData(FILE *strm, struct Input *in); -static int allocateIntegerStorage(struct Input *in); -static int allocateFloatStorage(struct Input *in); -static int readUIntegerData(FILE *strm, struct Input *in); -static int allocateUIntegerStorage(struct Input *in); -static int validateConfigurationParameters(struct Input *in); -static int processStrData(FILE *strm, struct Input *in, hid_t file_id); -static int processStrHDFData(FILE *strm, struct Input *in, hid_t file_id); -uint16_t swap_uint16(uint16_t val); -int16_t swap_int16(int16_t val); -uint32_t swap_uint32(uint32_t val); -int32_t swap_int32(int32_t val); -int64_t swap_int64(int64_t val); -uint64_t swap_uint64(uint64_t val); - -int main(int argc, char *argv[]) +static int gtoken(char *s); +static int process(struct Options *opt); +static int processConfigurationFile(char *infile, struct Input *in); +static int mapKeywordToIndex(char *key); +static int parsePathInfo(struct path_info *path, char *strm); +static int parseDimensions(struct Input *in, char *strm); +static int getInputSize(struct Input *in, int ival); +static int getInputClass(struct Input *in, char *strm); +static int getInputClassType(struct Input *in, char *strm); +static int getInputByteOrder(struct Input *in, FILE *strm); +static int InputClassStrToInt(char *temp); +static int getRank(struct Input *in, FILE *strm); +static int getDimensionSizes(struct Input *in, FILE *strm); +static int getOutputSize(struct Input *in, FILE *strm); +static int getOutputClass(struct Input *in, FILE *strm); +static int OutputClassStrToInt(char *temp); +static int getOutputArchitecture(struct Input *in, FILE *strm); +static int OutputArchStrToInt(const char *temp); +static int getOutputByteOrder(struct Input *in, FILE *strm); +static int OutputByteOrderStrToInt(const char *temp); +static int getChunkedDimensionSizes(struct Input *in, FILE *strm); +static int getCompressionType(struct Input *in, FILE *strm); +static int CompressionTypeStrToInt(char *temp); +static int getCompressionParameter(struct Input *in, FILE *strm); +static int getExternalFilename(struct Input *in, FILE *strm); +static int getMaximumDimensionSizes(struct Input *in, FILE *strm); +static int processDataFile(char *infile, struct Input *in, hid_t file_id); +static int readIntegerData(FILE *strm, struct Input *in); +static int readFloatData(FILE *strm, struct Input *in); +static int allocateIntegerStorage(struct Input *in); +static int allocateFloatStorage(struct Input *in); +static int readUIntegerData(FILE *strm, struct Input *in); +static int allocateUIntegerStorage(struct Input *in); +static int validateConfigurationParameters(struct Input *in); +static int processStrData(FILE *strm, struct Input *in, hid_t file_id); +static int processStrHDFData(FILE *strm, struct Input *in, hid_t file_id); +uint16_t swap_uint16(uint16_t val); +int16_t swap_int16(int16_t val); +uint32_t swap_uint32(uint32_t val); +int32_t swap_int32(int32_t val); +int64_t swap_int64(int64_t val); +uint64_t swap_uint64(uint64_t val); + +int +main(int argc, char *argv[]) { - struct Options opt; + struct Options *opt; int outfile_named = FALSE; int token; int i; int state = 0; - struct Input *in = NULL; - - const char *err1 = "Invalid number of arguments: %d.\n"; - const char *err2 = "Error in state table.\n"; - const char *err3 = "No output file given.\n"; - const char *err4 = "Program aborted.\n"; - const char *err5 = "Invalid path %s.\n"; - const char *err6 = "Invalid dimensions - %s.\n"; - const char *err7 = "Invalid type of data - %s.\n"; - const char *err8 = "Invalid size of data - %s.\n"; - const char *err9 = "Cannot specify more than 30 input files in one call to h5import.\n"; - const char *err10 = "Length of output file name limited to 255 chars.\n"; + struct Input * in = NULL; + + const char *err1 = "Invalid number of arguments: %d.\n"; + const char *err2 = "Error in state table.\n"; + const char *err3 = "No output file given.\n"; + const char *err4 = "Program aborted.\n"; + const char *err5 = "Invalid path %s.\n"; + const char *err6 = "Invalid dimensions - %s.\n"; + const char *err7 = "Invalid type of data - %s.\n"; + const char *err8 = "Invalid size of data - %s.\n"; + const char *err9 = "Cannot specify more than 30 input files in one call to h5import.\n"; + const char *err10 = "Length of output file name limited to 255 chars.\n"; h5tools_setprogname(PROGRAMNAME); h5tools_setstatus(EXIT_SUCCESS); @@ -96,11 +97,11 @@ int main(int argc, char *argv[]) /* Initialize h5tools lib */ h5tools_init(); - (void) HDsetvbuf(stderr, (char *) NULL, _IOLBF, 0); - (void) HDsetvbuf(stdout, (char *) NULL, _IOLBF, 0); + (void)HDsetvbuf(stderr, (char *)NULL, _IOLBF, 0); + (void)HDsetvbuf(stdout, (char *)NULL, _IOLBF, 0); - /* Initialize the file structure to 0 */ - HDmemset(&opt, 0, sizeof(struct Options)); + if ((opt = (struct Options *)HDcalloc(1, sizeof(struct Options))) == NULL) + goto err; if (argv[1] && (HDstrcmp("-V", argv[1]) == 0)) { print_version(PROGRAMNAME); @@ -111,7 +112,7 @@ int main(int argc, char *argv[]) * validate the number of command line arguments */ if (argc < 2) { - (void) HDfprintf(stderr, err1, argc); + (void)HDfprintf(stderr, err1, argc); usage(argv[0]); goto err; } @@ -129,114 +130,114 @@ int main(int argc, char *argv[]) switch (state) { - case 1: /* counting input files */ - if (opt.fcount < 29) { - (void) HDstrcpy(opt.infiles[opt.fcount].datafile, argv[i]); - in = &(opt.infiles[opt.fcount].in); - opt.infiles[opt.fcount].config = 0; - setDefaultValues(in, opt.fcount); - opt.fcount++; - } - else { - (void) HDfprintf(stderr, err9, argv[i]); - goto err; - } + case 1: /* counting input files */ + if (opt->fcount < 29) { + (void)HDstrcpy(opt->infiles[opt->fcount].datafile, argv[i]); + in = &(opt->infiles[opt->fcount].in); + opt->infiles[opt->fcount].config = 0; + setDefaultValues(in, opt->fcount); + opt->fcount++; + } + else { + (void)HDfprintf(stderr, err9, argv[i]); + goto err; + } - break; + break; - case 2: /* -c found; look for configfile */ - break; + case 2: /* -c found; look for configfile */ + break; - case 3: /* get configfile name */ - (void) HDstrcpy(opt.infiles[opt.fcount-1].configfile, argv[i]); - opt.infiles[opt.fcount - 1].config = 1; - break; + case 3: /* get configfile name */ + (void)HDstrcpy(opt->infiles[opt->fcount - 1].configfile, argv[i]); + opt->infiles[opt->fcount - 1].config = 1; + break; - case 4: /* -o found; look for outfile */ - break; + case 4: /* -o found; look for outfile */ + break; - case 5: /* get outfile found */ - if (HDstrlen(argv[i]) > MAX_PATH_NAME_LENGTH) { - (void) HDfprintf(stderr, err10, argv[i]); - goto err; - } - (void) HDstrcpy(opt.outfile, argv[i]); - outfile_named = TRUE; - break; + case 5: /* get outfile found */ + if (HDstrlen(argv[i]) > MAX_PATH_NAME_LENGTH) { + (void)HDfprintf(stderr, err10, argv[i]); + goto err; + } + (void)HDstrcpy(opt->outfile, argv[i]); + outfile_named = TRUE; + break; - case 6: /* -h found; help, then exit */ - help(argv[0]); - HDexit(EXIT_SUCCESS); - break; + case 6: /* -h found; help, then exit */ + help(argv[0]); + HDexit(EXIT_SUCCESS); + break; - case 7: /* -d found; look for dimensions */ - break; + case 7: /* -d found; look for dimensions */ + break; - case 8: /* read dimensions */ - if (parseDimensions(in, argv[i]) == -1) { - (void) HDfprintf(stderr, err6, argv[i]); - goto err; - } - break; + case 8: /* read dimensions */ + if (parseDimensions(in, argv[i]) == -1) { + (void)HDfprintf(stderr, err6, argv[i]); + goto err; + } + break; - case 9: /* -p found; look for path name */ - break; + case 9: /* -p found; look for path name */ + break; - case 10: /* read path name */ - if (parsePathInfo(&in->path, argv[i]) == -1) { - (void) HDfprintf(stderr, err5, argv[i]); - goto err; - } - break; + case 10: /* read path name */ + if (parsePathInfo(&in->path, argv[i]) == -1) { + (void)HDfprintf(stderr, err5, argv[i]); + goto err; + } + break; - case 11: /* -t found; look for data type */ - break; + case 11: /* -t found; look for data type */ + break; - case 12: /* read data type */ - if (getInputClass(in, argv[i]) == -1) { - (void) HDfprintf(stderr, err7, argv[i]); - goto err; - } + case 12: /* read data type */ + if (getInputClass(in, argv[i]) == -1) { + (void)HDfprintf(stderr, err7, argv[i]); + goto err; + } - if (in->inputClass == 0 || in->inputClass == 4) - in->outputClass = 0; - if (in->inputClass == 1 || in->inputClass == 2 || in->inputClass == 3) - in->outputClass = 1; - if (in->inputClass == 6 || in->inputClass == 7) - in->outputClass = 2; - break; + if (in->inputClass == 0 || in->inputClass == 4) + in->outputClass = 0; + if (in->inputClass == 1 || in->inputClass == 2 || in->inputClass == 3) + in->outputClass = 1; + if (in->inputClass == 6 || in->inputClass == 7) + in->outputClass = 2; + break; - case 13: /* -s found; look for data size */ - break; + case 13: /* -s found; look for data size */ + break; - case 14: /* read data size */ - if (getInputSize(in, (int) HDstrtol(argv[i], NULL, BASE_10)) == -1) { - (void) HDfprintf(stderr, err8, argv[i]); - goto err; - } - /*set default value for output-size */ - in->outputSize = in->inputSize; - break; + case 14: /* read data size */ + if (getInputSize(in, (int)HDstrtol(argv[i], NULL, BASE_10)) == -1) { + (void)HDfprintf(stderr, err8, argv[i]); + goto err; + } + /*set default value for output-size */ + in->outputSize = in->inputSize; + break; - case ERR: /* command syntax error */ - default: - (void) HDfprintf(stderr, "%s", err2); - usage(argv[0]); - goto err; + case ERR: /* command syntax error */ + default: + (void)HDfprintf(stderr, "%s", err2); + usage(argv[0]); + goto err; } } if (FALSE == outfile_named) { - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err3); usage(argv[0]); goto err; } - if (process(&opt) == -1) + if (process(opt) == -1) goto err; - for (i = 0; i < opt.fcount; i++) { - in = &(opt.infiles[i].in); + for (i = 0; i < opt->fcount; i++) { + in = &(opt->infiles[i].in); if (in->sizeOfDimension) HDfree(in->sizeOfDimension); if (in->sizeOfChunk) @@ -248,12 +249,13 @@ int main(int argc, char *argv[]) if (in->data) HDfree(in->data); } + HDfree(opt); - return (EXIT_SUCCESS); + return EXIT_SUCCESS; err: - (void) HDfprintf(stderr, "%s", err4); - for (i = 0; i < opt.fcount; i++) { - in = &(opt.infiles[i].in); + (void)HDfprintf(stderr, "%s", err4); + for (i = 0; i < opt->fcount; i++) { + in = &(opt->infiles[i].in); if (in->sizeOfDimension) HDfree(in->sizeOfDimension); if (in->sizeOfChunk) @@ -265,13 +267,16 @@ err: if (in->data) HDfree(in->data); } - return (EXIT_FAILURE); + HDfree(opt); + + return EXIT_FAILURE; } -static int gtoken(char *s) +static int +gtoken(char *s) { - size_t len; - int token = ERR; + size_t len; + int token = ERR; const char *err1 = "Illegal argument: %s.\n"; @@ -281,47 +286,47 @@ static int gtoken(char *s) if (s[0] == '-') { /* option name (or negative number) */ len = HDstrlen(&s[1]); switch (s[1]) { - case 'o': - if (!HDstrncmp("outfile", &s[1], len)) - token = OPT_o; - break; + case 'o': + if (!HDstrncmp("outfile", &s[1], len)) + token = OPT_o; + break; - case 'c': - if (!HDstrncmp("config", &s[1], len)) - token = OPT_c; - break; + case 'c': + if (!HDstrncmp("config", &s[1], len)) + token = OPT_c; + break; - case 'h': - if (!HDstrncmp("help", &s[1], len)) - token = OPT_h; - break; + case 'h': + if (!HDstrncmp("help", &s[1], len)) + token = OPT_h; + break; - case 'd': - if (!HDstrncmp("dims", &s[1], len)) - token = OPT_d; - break; + case 'd': + if (!HDstrncmp("dims", &s[1], len)) + token = OPT_d; + break; - case 'p': - if (!HDstrncmp("path", &s[1], len)) - token = OPT_p; - break; + case 'p': + if (!HDstrncmp("path", &s[1], len)) + token = OPT_p; + break; - case 't': - if (!HDstrncmp("type", &s[1], len)) - token = OPT_t; - break; + case 't': + if (!HDstrncmp("type", &s[1], len)) + token = OPT_t; + break; - case 's': - if (!HDstrncmp("size", &s[1], len)) - token = OPT_s; - break; - default: - token = ERR; /* not a supported option tag */ - break; + case 's': + if (!HDstrncmp("size", &s[1], len)) + token = OPT_s; + break; + default: + token = ERR; /* not a supported option tag */ + break; } if (token == ERR) - (void) HDfprintf(stderr, err1, s); + (void)HDfprintf(stderr, err1, s); } else { /* filename */ token = FILNAME; @@ -344,19 +349,20 @@ static int gtoken(char *s) *------------------------------------------------------------------------- */ -static int processDataFile(char *infile, struct Input *in, hid_t file_id) +static int +processDataFile(char *infile, struct Input *in, hid_t file_id) { - FILE *strm = NULL; - const char *err1 = "Unable to open the input file %s for reading.\n"; - const char *err2 = "Error in allocating integer data storage.\n"; - const char *err3 = "Error in allocating floating-point data storage.\n"; - const char *err4 = "Error in reading integer data.\n"; - const char *err5 = "Error in reading floating-point data.\n"; - const char *err6 = "Error in allocating unsigned integer data storage.\n"; - const char *err7 = "Error in reading unsigned integer data.\n"; - const char *err10 = "Unrecognized input class type.\n"; - const char *err11 = "Error in reading string data.\n"; - int retval = -1; + FILE * strm = NULL; + const char *err1 = "Unable to open the input file %s for reading.\n"; + const char *err2 = "Error in allocating integer data storage.\n"; + const char *err3 = "Error in allocating floating-point data storage.\n"; + const char *err4 = "Error in reading integer data.\n"; + const char *err5 = "Error in reading floating-point data.\n"; + const char *err6 = "Error in allocating unsigned integer data storage.\n"; + const char *err7 = "Error in reading unsigned integer data.\n"; + const char *err10 = "Unrecognized input class type.\n"; + const char *err11 = "Error in reading string data.\n"; + int retval = -1; /*------------------------------------------------------------------------- * special case for opening binary classes in H5_HAVE_WIN32_API @@ -365,10 +371,10 @@ static int processDataFile(char *infile, struct Input *in, hid_t file_id) * "UIN" denotes an unsigned integer binary file, *------------------------------------------------------------------------- */ - if (in->inputClass == 4 /* "IN" */|| in->inputClass == 3 /* "FP" */|| in->inputClass == 7 /* "UIN" */) { + if (in->inputClass == 4 /* "IN" */ || in->inputClass == 3 /* "FP" */ || in->inputClass == 7 /* "UIN" */) { if ((strm = HDfopen(infile, READ_OPEN_FLAGS)) == NULL) { - (void) HDfprintf(stderr, err1, infile); + (void)HDfprintf(stderr, err1, infile); goto error; } } @@ -378,94 +384,92 @@ static int processDataFile(char *infile, struct Input *in, hid_t file_id) */ else { if ((strm = HDfopen(infile, "r")) == NULL) { - (void) HDfprintf(stderr, err1, infile); + (void)HDfprintf(stderr, err1, infile); goto error; } } switch (in->inputClass) { - case 0: /* TEXTIN */ - case 4: /* IN */ - if (allocateIntegerStorage(in) == -1) { - (void) HDfprintf(stderr, err2, infile); - goto error; - } + case 0: /* TEXTIN */ + case 4: /* IN */ + if (allocateIntegerStorage(in) == -1) { + (void)HDfprintf(stderr, err2, infile); + goto error; + } - if (readIntegerData(strm, in) == -1) { - (void) HDfprintf(stderr, err4, infile); - goto error; - } - break; + if (readIntegerData(strm, in) == -1) { + (void)HDfprintf(stderr, err4, infile); + goto error; + } + break; - case 1: /* TEXTFP */ - case 2: /* TEXTFPE */ - case 3: /* FP */ - if (allocateFloatStorage(in) == -1) { - (void) HDfprintf(stderr, err3, infile); - goto error; + case 1: /* TEXTFP */ + case 2: /* TEXTFPE */ + case 3: /* FP */ + if (allocateFloatStorage(in) == -1) { + (void)HDfprintf(stderr, err3, infile); + goto error; + } - } + if (readFloatData(strm, in) == -1) { + (void)HDfprintf(stderr, err5, infile); + goto error; + } + break; - if (readFloatData(strm, in) == -1) { - (void) HDfprintf(stderr, err5, infile); - goto error; - } - break; + case 5: /* STR */ + if (in->h5dumpInput) { + if (processStrHDFData(strm, in, file_id) == -1) { + (void)HDfprintf(stderr, err11, infile); + goto error; + } + } + else { + if (processStrData(strm, in, file_id) == -1) { + (void)HDfprintf(stderr, err11, infile); + goto error; + } + } + + break; - case 5: /* STR */ - if (in->h5dumpInput) { - if (processStrHDFData(strm, in, file_id) == -1) { - (void) HDfprintf(stderr, err11, infile); + case 6: /* TEXTUIN */ + case 7: /* UIN */ + if (allocateUIntegerStorage(in) == -1) { + (void)HDfprintf(stderr, err6, infile); goto error; } - } - else { - if (processStrData(strm, in, file_id) == -1) { - (void) HDfprintf(stderr, err11, infile); + if (readUIntegerData(strm, in) == -1) { + (void)HDfprintf(stderr, err7, infile); goto error; } - } - - break; + break; - case 6: /* TEXTUIN */ - case 7: /* UIN */ - if (allocateUIntegerStorage(in) == -1) { - (void) HDfprintf(stderr, err6, infile); - goto error; - } - if (readUIntegerData(strm, in) == -1) { - (void) HDfprintf(stderr, err7, infile); + default: + (void)HDfprintf(stderr, "%s", err10); goto error; - } - break; - - default: - (void) HDfprintf(stderr, "%s", err10); - goto error; } /* Set success return value */ retval = 0; error: - if(strm) + if (strm) HDfclose(strm); - return(retval); + return (retval); } -static int readIntegerData(FILE *strm, struct Input *in) +static int +readIntegerData(FILE *strm, struct Input *in) { - H5DT_INT8 *in08; + H5DT_INT8 * in08; H5DT_INT16 *in16; H5DT_INT16 temp16; H5DT_INT32 *in32; H5DT_INT32 temp32; -#ifdef H5_SIZEOF_LONG_LONG H5DT_INT64 *in64; H5DT_INT64 temp64; char buffer[256]; -#endif hsize_t len = 1; hsize_t i; int j; @@ -478,335 +482,331 @@ static int readIntegerData(FILE *strm, struct Input *in) len *= in->sizeOfDimension[j]; switch (in->inputSize) { - case 8: - switch (in->inputClass) { - case 0: /* TEXTIN */ - in08 = (H5DT_INT8 *) in->data; - for (i = 0; i < len; i++, in08++) { - if (fscanf(strm, "%hd", &temp16) != 1) { - (void) HDfprintf(stderr, "%s", err1); - return (-1); - } - (*in08) = (H5DT_INT8) temp16; - } - break; + case 8: + switch (in->inputClass) { + case 0: /* TEXTIN */ + in08 = (H5DT_INT8 *)in->data; + for (i = 0; i < len; i++, in08++) { + if (HDfscanf(strm, "%hd", &temp16) != 1) { + (void)HDfprintf(stderr, "%s", err1); + return (-1); + } + (*in08) = (H5DT_INT8)temp16; + } + break; - case 4: /* IN */ - in08 = (H5DT_INT8 *) in->data; - for (i = 0; i < len; i++, in08++) { - if (HDfread((char *) in08, sizeof(H5DT_INT8), 1, strm) != 1) { - (void) HDfprintf(stderr, "%s", err1); - return (-1); - } + case 4: /* IN */ + in08 = (H5DT_INT8 *)in->data; + for (i = 0; i < len; i++, in08++) { + if (HDfread((char *)in08, sizeof(H5DT_INT8), 1, strm) != 1) { + (void)HDfprintf(stderr, "%s", err1); + return (-1); + } #ifdef H5DEBUGIMPORT - HDprintf("readIntegerData %d (0x%.8X)\n", *in08, *in08); + HDprintf("readIntegerData %d (0x%.8X)\n", *in08, *in08); #endif - } - break; - - default: - (void) HDfprintf(stderr, "%s", err2); - return (-1); - } - break; + } + break; - case 16: - in16 = (H5DT_INT16 *) in->data; - switch (in->inputClass) { - case 0: /* TEXTIN */ - for (i = 0; i < len; i++, in16++) { - if (fscanf(strm, "%hd", in16) != 1) { - (void) HDfprintf(stderr, "%s", err1); + default: + (void)HDfprintf(stderr, "%s", err2); return (-1); - } } - in16 = (H5DT_INT16 *) in->data; break; - case 4: /* IN */ - for (i = 0; i < len; i++, in16++) { - if (HDfread((char *)&temp16, sizeof(H5DT_INT16), 1, strm) != 1) { - (void) HDfprintf(stderr, "%s", err1); - return (-1); - } -/* - if (in-> h5dumpInput && (in->inputByteOrder != in->outputByteOrder)) - *in16 = swap_int16(temp16); - else -*/ - *in16 = temp16; + case 16: + in16 = (H5DT_INT16 *)in->data; + switch (in->inputClass) { + case 0: /* TEXTIN */ + for (i = 0; i < len; i++, in16++) { + if (HDfscanf(strm, "%hd", in16) != 1) { + (void)HDfprintf(stderr, "%s", err1); + return (-1); + } + } + in16 = (H5DT_INT16 *)in->data; + break; + + case 4: /* IN */ + for (i = 0; i < len; i++, in16++) { + if (HDfread((char *)&temp16, sizeof(H5DT_INT16), 1, strm) != 1) { + (void)HDfprintf(stderr, "%s", err1); + return (-1); + } + /* + if (in-> h5dumpInput && (in->inputByteOrder != in->outputByteOrder)) + *in16 = swap_int16(temp16); + else + */ + *in16 = temp16; #ifdef H5DEBUGIMPORT - HDprintf("readIntegerData %d (0x%.8X)\n", *in16, temp16); + HDprintf("readIntegerData %d (0x%.8X)\n", *in16, temp16); #endif - } - break; - - default: - (void) HDfprintf(stderr, "%s", err2); - return (-1); - } - break; + } + break; - case 32: - in32 = (H5DT_INT32 *) in->data; - switch (in->inputClass) { - case 0: /* TEXTIN */ - for (i = 0; i < len; i++, in32++) { - if (fscanf(strm, "%d", in32) != 1) { - (void) HDfprintf(stderr, "%s", err1); + default: + (void)HDfprintf(stderr, "%s", err2); return (-1); - } } break; - case 4: /* IN */ - for (i = 0; i < len; i++, in32++) { - if (HDfread((char *)&temp32, sizeof(H5DT_INT32), 1, strm) != 1) { - (void) HDfprintf(stderr, "%s", err1); - return (-1); - } -/* - if (in-> h5dumpInput && (in->inputByteOrder != in->outputByteOrder)) - *in32 = swap_int32(temp32); - else -*/ - *in32 = temp32; + case 32: + in32 = (H5DT_INT32 *)in->data; + switch (in->inputClass) { + case 0: /* TEXTIN */ + for (i = 0; i < len; i++, in32++) { + if (HDfscanf(strm, "%d", in32) != 1) { + (void)HDfprintf(stderr, "%s", err1); + return (-1); + } + } + break; + + case 4: /* IN */ + for (i = 0; i < len; i++, in32++) { + if (HDfread((char *)&temp32, sizeof(H5DT_INT32), 1, strm) != 1) { + (void)HDfprintf(stderr, "%s", err1); + return (-1); + } + /* + if (in-> h5dumpInput && (in->inputByteOrder != in->outputByteOrder)) + *in32 = swap_int32(temp32); + else + */ + *in32 = temp32; #ifdef H5DEBUGIMPORT - HDprintf("readIntegerData %d (0x%.8X = 0x%.8X)\n", *in32, *in32, temp32); + HDprintf("readIntegerData %d (0x%.8X = 0x%.8X)\n", *in32, *in32, temp32); #endif - } - break; - - default: - (void) HDfprintf(stderr, "%s", err2); - return (-1); - } - break; + } + break; -#ifdef H5_SIZEOF_LONG_LONG - case 64: - in64 = (H5DT_INT64 *) in->data; - switch (in->inputClass) { - case 0: /* TEXTIN */ - for (i = 0; i < len; i++, in64++) { - if (fscanf(strm, "%s", buffer) < 1) { - (void) HDfprintf(stderr, "%s", err1); + default: + (void)HDfprintf(stderr, "%s", err2); return (-1); - } - *in64 = (H5DT_INT64) HDstrtoll(buffer, NULL, 10); } break; - case 4: /* IN */ - for (i = 0; i < len; i++, in64++) { - if (HDfread((char *)&temp64, sizeof(H5DT_INT64), 1, strm) != 1) { - (void) HDfprintf(stderr, "%s", err1); - return (-1); - } -/* - if (in-> h5dumpInput && (in->inputByteOrder != in->outputByteOrder)) - *in64 = swap_int64(temp64); - else -*/ - *in64 = temp64; + case 64: + in64 = (H5DT_INT64 *)in->data; + switch (in->inputClass) { + case 0: /* TEXTIN */ + for (i = 0; i < len; i++, in64++) { + if (HDfscanf(strm, "%s", buffer) < 1) { + (void)HDfprintf(stderr, "%s", err1); + return (-1); + } + *in64 = (H5DT_INT64)HDstrtoll(buffer, NULL, 10); + } + break; + + case 4: /* IN */ + for (i = 0; i < len; i++, in64++) { + if (HDfread((char *)&temp64, sizeof(H5DT_INT64), 1, strm) != 1) { + (void)HDfprintf(stderr, "%s", err1); + return (-1); + } + /* + if (in-> h5dumpInput && (in->inputByteOrder != in->outputByteOrder)) + *in64 = swap_int64(temp64); + else + */ + *in64 = temp64; #ifdef H5DEBUGIMPORT - HDprintf("readIntegerData %d (0x%.8X)\n", *in64, temp64); + HDprintf("readIntegerData %d (0x%.8X)\n", *in64, temp64); #endif + } + break; + + default: + (void)HDfprintf(stderr, "%s", err2); + return (-1); } break; default: - (void) HDfprintf(stderr, "%s", err2); - return (-1); - } - break; -#endif /* ifdef H5_SIZEOF_LONG_LONG */ - - default: - (void) HDfprintf(stderr, "%s", err3); - break; + (void)HDfprintf(stderr, "%s", err3); + break; } return (0); } -static int readUIntegerData(FILE *strm, struct Input *in) +static int +readUIntegerData(FILE *strm, struct Input *in) { - H5DT_UINT8 *in08; + H5DT_UINT8 * in08; H5DT_UINT16 *in16; H5DT_UINT16 temp16; H5DT_UINT32 *in32; H5DT_UINT32 temp32; -#ifdef H5_SIZEOF_LONG_LONG H5DT_UINT64 *in64; H5DT_UINT64 temp64; - char buffer[256]; -#endif - hsize_t len = 1; - hsize_t i; - int j; - const char *err1 = "Unable to get unsigned integer value from file.\n"; - const char *err2 = "Unrecognized input class type.\n"; - const char *err3 = "Invalid input size.\n"; + char buffer[256]; + hsize_t len = 1; + hsize_t i; + int j; + const char * err1 = "Unable to get unsigned integer value from file.\n"; + const char * err2 = "Unrecognized input class type.\n"; + const char * err3 = "Invalid input size.\n"; for (j = 0; j < in->rank; j++) len *= in->sizeOfDimension[j]; switch (in->inputSize) { - case 8: - switch (in->inputClass) { - case 6: /* TEXTUIN */ - in08 = (H5DT_UINT8 *) in->data; - for (i = 0; i < len; i++, in08++) { - if (fscanf(strm, "%hu", &temp16) != 1) { - (void) HDfprintf(stderr, "%s", err1); - return (-1); - } - (*in08) = (H5DT_UINT8) temp16; - } - break; - - case 7: /* UIN */ - in08 = (H5DT_UINT8 *) in->data; - for (i = 0; i < len; i++, in08++) { - if (HDfread((char *) in08, sizeof(H5DT_UINT8), 1, strm) != 1) { - (void) HDfprintf(stderr, "%s", err1); - return (-1); - } - } - break; + case 8: + switch (in->inputClass) { + case 6: /* TEXTUIN */ + in08 = (H5DT_UINT8 *)in->data; + for (i = 0; i < len; i++, in08++) { + if (HDfscanf(strm, "%hu", &temp16) != 1) { + (void)HDfprintf(stderr, "%s", err1); + return (-1); + } + (*in08) = (H5DT_UINT8)temp16; + } + break; - default: - (void) HDfprintf(stderr, "%s", err2); - return (-1); - } - break; + case 7: /* UIN */ + in08 = (H5DT_UINT8 *)in->data; + for (i = 0; i < len; i++, in08++) { + if (HDfread((char *)in08, sizeof(H5DT_UINT8), 1, strm) != 1) { + (void)HDfprintf(stderr, "%s", err1); + return (-1); + } + } + break; - case 16: - in16 = (H5DT_UINT16 *) in->data; - switch (in->inputClass) { - case 6: /* TEXTUIN */ - for (i = 0; i < len; i++, in16++) { - if (fscanf(strm, "%hu", in16) != 1) { - (void) HDfprintf(stderr, "%s", err1); + default: + (void)HDfprintf(stderr, "%s", err2); return (-1); - } } break; - case 7: /* UIN */ - for (i = 0; i < len; i++, in16++) { - if (HDfread((char *)&temp16, sizeof(H5DT_UINT16), 1, strm) != 1) { - (void) HDfprintf(stderr, "%s", err1); - return (-1); - } -/* - if (in-> h5dumpInput && (in->inputByteOrder != in->outputByteOrder)) - *in16 = swap_uint16(temp16); - else -*/ - *in16 = temp16; + case 16: + in16 = (H5DT_UINT16 *)in->data; + switch (in->inputClass) { + case 6: /* TEXTUIN */ + for (i = 0; i < len; i++, in16++) { + if (HDfscanf(strm, "%hu", in16) != 1) { + (void)HDfprintf(stderr, "%s", err1); + return (-1); + } + } + break; + + case 7: /* UIN */ + for (i = 0; i < len; i++, in16++) { + if (HDfread((char *)&temp16, sizeof(H5DT_UINT16), 1, strm) != 1) { + (void)HDfprintf(stderr, "%s", err1); + return (-1); + } + /* + if (in-> h5dumpInput && (in->inputByteOrder != in->outputByteOrder)) + *in16 = swap_uint16(temp16); + else + */ + *in16 = temp16; #ifdef H5DEBUGIMPORT - HDprintf("readUIntegerData %d (0x%.4X = 0x%.4X)\n", *in16, *in16, temp16); + HDprintf("readUIntegerData %d (0x%.4X = 0x%.4X)\n", *in16, *in16, temp16); #endif - } - break; - - default: - (void) HDfprintf(stderr, "%s", err2); - return (-1); - } - break; + } + break; - case 32: - in32 = (H5DT_UINT32 *) in->data; - switch (in->inputClass) { - case 6: /* TEXTUIN */ - for (i = 0; i < len; i++, in32++) { - if (fscanf(strm, "%u", in32) != 1) { - (void) HDfprintf(stderr, "%s", err1); + default: + (void)HDfprintf(stderr, "%s", err2); return (-1); - } } break; - case 7: /* UIN */ - for (i = 0; i < len; i++, in32++) { - if (HDfread((char *)&temp32, sizeof(H5DT_UINT32), 1, strm) != 1) { - (void) HDfprintf(stderr, "%s", err1); - return (-1); - } -/* - if (in-> h5dumpInput && (in->inputByteOrder != in->outputByteOrder)) - *in32 = swap_uint32(temp32); - else -*/ - *in32 = temp32; + case 32: + in32 = (H5DT_UINT32 *)in->data; + switch (in->inputClass) { + case 6: /* TEXTUIN */ + for (i = 0; i < len; i++, in32++) { + if (HDfscanf(strm, "%u", in32) != 1) { + (void)HDfprintf(stderr, "%s", err1); + return (-1); + } + } + break; + + case 7: /* UIN */ + for (i = 0; i < len; i++, in32++) { + if (HDfread((char *)&temp32, sizeof(H5DT_UINT32), 1, strm) != 1) { + (void)HDfprintf(stderr, "%s", err1); + return (-1); + } + /* + if (in-> h5dumpInput && (in->inputByteOrder != in->outputByteOrder)) + *in32 = swap_uint32(temp32); + else + */ + *in32 = temp32; #ifdef H5DEBUGIMPORT - HDprintf("readUIntegerData %d (0x%.8X = 0x%.8X)\n", *in32, *in32, temp32); + HDprintf("readUIntegerData %d (0x%.8X = 0x%.8X)\n", *in32, *in32, temp32); #endif - } - break; - - default: - (void) HDfprintf(stderr, "%s", err2); - return (-1); - } - break; + } + break; -#ifdef H5_SIZEOF_LONG_LONG - case 64: - in64 = (H5DT_UINT64 *) in->data; - switch (in->inputClass) { - case 6: /* TEXTUIN */ - for (i = 0; i < len; i++, in64++) { - if (fscanf(strm, "%s", buffer) < 1) { - (void) HDfprintf(stderr, "%s", err1); + default: + (void)HDfprintf(stderr, "%s", err2); return (-1); - } - *in64 = (H5DT_UINT64) HDstrtoll(buffer, NULL, 10); } break; - case 7: /* UIN */ - for (i = 0; i < len; i++, in64++) { - if (HDfread((char *)&temp64, sizeof(H5DT_UINT64), 1, strm) != 1) { - (void) HDfprintf(stderr, "%s", err1); - return (-1); - } -/* - if (in-> h5dumpInput && (in->inputByteOrder != in->outputByteOrder)) - *in64 = swap_uint64(temp64); - else -*/ - *in64 = temp64; + case 64: + in64 = (H5DT_UINT64 *)in->data; + switch (in->inputClass) { + case 6: /* TEXTUIN */ + for (i = 0; i < len; i++, in64++) { + if (HDfscanf(strm, "%s", buffer) < 1) { + (void)HDfprintf(stderr, "%s", err1); + return (-1); + } + *in64 = (H5DT_UINT64)HDstrtoll(buffer, NULL, 10); + } + break; + + case 7: /* UIN */ + for (i = 0; i < len; i++, in64++) { + if (HDfread((char *)&temp64, sizeof(H5DT_UINT64), 1, strm) != 1) { + (void)HDfprintf(stderr, "%s", err1); + return (-1); + } + /* + if (in-> h5dumpInput && (in->inputByteOrder != in->outputByteOrder)) + *in64 = swap_uint64(temp64); + else + */ + *in64 = temp64; #ifdef H5DEBUGIMPORT - HDprintf("readUIntegerData %ld (0x%.8X = 0x%.8X)\n", *in64, *in64, temp64); + HDprintf("readUIntegerData %ld (0x%.8X = 0x%.8X)\n", *in64, *in64, temp64); #endif + } + break; + + default: + (void)HDfprintf(stderr, "%s", err2); + return (-1); } break; default: - (void) HDfprintf(stderr, "%s", err2); - return (-1); - } - break; -#endif /* ifdef H5_SIZEOF_LONG_LONG */ - - default: - (void) HDfprintf(stderr, "%s", err3); - break; + (void)HDfprintf(stderr, "%s", err3); + break; } return (0); } -static int readFloatData(FILE *strm, struct Input *in) +static int +readFloatData(FILE *strm, struct Input *in) { H5DT_FLOAT32 *fp32; - uint32_t *bfp32; - uint32_t temp32; + uint32_t * bfp32; + uint32_t temp32; H5DT_FLOAT64 *fp64; - uint64_t *bfp64; - uint64_t temp64; + uint64_t * bfp64; + uint64_t temp64; hsize_t len = 1; hsize_t i; @@ -819,113 +819,113 @@ static int readFloatData(FILE *strm, struct Input *in) len *= in->sizeOfDimension[j]; switch (in->inputSize) { - case 32: - fp32 = (H5DT_FLOAT32 *) in->data; - switch (in->inputClass) { - case 1: /* TEXTFP */ - for (i = 0; i < len; i++, fp32++) { - if (fscanf(strm, "%f", fp32) != 1) { - (void) HDfprintf(stderr, "%s", err1); - return (-1); - } - } + case 32: + fp32 = (H5DT_FLOAT32 *)in->data; + switch (in->inputClass) { + case 1: /* TEXTFP */ + for (i = 0; i < len; i++, fp32++) { + if (HDfscanf(strm, "%f", fp32) != 1) { + (void)HDfprintf(stderr, "%s", err1); + return (-1); + } + } - fp32 = (H5DT_FLOAT32 *) in->data; - break; + fp32 = (H5DT_FLOAT32 *)in->data; + break; - /* same as TEXTFP */ - case 2: /*TEXTFPE */ + /* same as TEXTFP */ + case 2: /*TEXTFPE */ - for (i = 0; i < len; i++, fp32++) { - if (fscanf(strm, "%f", fp32) != 1) { - (void) HDfprintf(stderr, "%s", err1); - return (-1); - } - } + for (i = 0; i < len; i++, fp32++) { + if (HDfscanf(strm, "%f", fp32) != 1) { + (void)HDfprintf(stderr, "%s", err1); + return (-1); + } + } - fp32 = (H5DT_FLOAT32 *) in->data; - break; + fp32 = (H5DT_FLOAT32 *)in->data; + break; - case 3: /* FP */ - bfp32 = (uint32_t *) in->data; - for (i = 0; i < len; i++, bfp32++) { - if (HDfread((char *)&temp32, sizeof(uint32_t), 1, strm) != 1) { - (void) HDfprintf(stderr, "%s", err1); - return (-1); - } -/* - if (in-> h5dumpInput && (in->inputByteOrder != in->outputByteOrder)) - *bfp32 = swap_uint32(temp32); - else -*/ - *bfp32 = temp32; + case 3: /* FP */ + bfp32 = (uint32_t *)in->data; + for (i = 0; i < len; i++, bfp32++) { + if (HDfread((char *)&temp32, sizeof(uint32_t), 1, strm) != 1) { + (void)HDfprintf(stderr, "%s", err1); + return (-1); + } + /* + if (in-> h5dumpInput && (in->inputByteOrder != in->outputByteOrder)) + *bfp32 = swap_uint32(temp32); + else + */ + *bfp32 = temp32; #ifdef H5DEBUGIMPORT - HDprintf("readFloatData %ld (0x%.8X = 0x%.8X)\n", *bfp32, *bfp32, temp32); + HDprintf("readFloatData %ld (0x%.8X = 0x%.8X)\n", *bfp32, *bfp32, temp32); #endif - } - break; - - default: - (void) HDfprintf(stderr, "%s", err2); - return (-1); - } - break; + } + break; - case 64: - fp64 = (H5DT_FLOAT64 *) in->data; - switch (in->inputClass) { - case 1: /* TEXTFP */ - for (i = 0; i < len; i++, fp64++) { - if (fscanf(strm, "%lf", fp64) != 1) { - (void) HDfprintf(stderr, "%s", err1); + default: + (void)HDfprintf(stderr, "%s", err2); return (-1); - } } - - fp64 = (H5DT_FLOAT64 *) in->data; break; - /* same as TEXTFP */ - case 2: /*TEXTFPE */ + case 64: + fp64 = (H5DT_FLOAT64 *)in->data; + switch (in->inputClass) { + case 1: /* TEXTFP */ + for (i = 0; i < len; i++, fp64++) { + if (HDfscanf(strm, "%lf", fp64) != 1) { + (void)HDfprintf(stderr, "%s", err1); + return (-1); + } + } - for (i = 0; i < len; i++, fp64++) { - if (fscanf(strm, "%lf", fp64) != 1) { - (void) HDfprintf(stderr, "%s", err1); - return (-1); - } - } + fp64 = (H5DT_FLOAT64 *)in->data; + break; - fp64 = (H5DT_FLOAT64 *) in->data; - break; + /* same as TEXTFP */ + case 2: /*TEXTFPE */ - case 3: /* FP */ - bfp64 = (uint64_t *) in->data; - for (i = 0; i < len; i++, bfp64++) { - if (HDfread((char *)&temp64, sizeof(uint64_t), 1, strm) != 1) { - (void) HDfprintf(stderr, "%s", err1); - return (-1); - } -/* - if (in-> h5dumpInput && (in->inputByteOrder != in->outputByteOrder)) - *bfp64 = swap_uint64(temp64); - else -*/ - *bfp64 = temp64; + for (i = 0; i < len; i++, fp64++) { + if (HDfscanf(strm, "%lf", fp64) != 1) { + (void)HDfprintf(stderr, "%s", err1); + return (-1); + } + } + + fp64 = (H5DT_FLOAT64 *)in->data; + break; + + case 3: /* FP */ + bfp64 = (uint64_t *)in->data; + for (i = 0; i < len; i++, bfp64++) { + if (HDfread((char *)&temp64, sizeof(uint64_t), 1, strm) != 1) { + (void)HDfprintf(stderr, "%s", err1); + return (-1); + } + /* + if (in-> h5dumpInput && (in->inputByteOrder != in->outputByteOrder)) + *bfp64 = swap_uint64(temp64); + else + */ + *bfp64 = temp64; #ifdef H5DEBUGIMPORT - HDprintf("readFloatData %ld (0x%.16lX)\n", *bfp64, temp64); + HDprintf("readFloatData %ld (0x%.16lX)\n", *bfp64, temp64); #endif + } + break; + + default: + (void)HDfprintf(stderr, "%s", err2); + return (-1); } break; default: - (void) HDfprintf(stderr, "%s", err2); - return (-1); - } - break; - - default: - (void) HDfprintf(stderr, "%s", err3); - break; + (void)HDfprintf(stderr, "%s", err3); + break; } return (0); } @@ -938,13 +938,14 @@ static int readFloatData(FILE *strm, struct Input *in) * * Return: 0, ok, -1 no * - * Programmer: Pedro Vicente, pvn@hdfgroup.org + * Programmer: Pedro Vicente * * Date: July, 26, 2007 * *------------------------------------------------------------------------- */ -static int processStrData(FILE *strm, struct Input *in, hid_t file_id) +static int +processStrData(FILE *strm, struct Input *in, hid_t file_id) { hid_t group_id; hid_t dset_id; @@ -965,8 +966,8 @@ static int processStrData(FILE *strm, struct Input *in, hid_t file_id) *------------------------------------------------------------------------- */ - while(EOF != (c = HDfgetc(strm))) - if (c == 10) /* eol */ + while (EOF != (c = HDfgetc(strm))) + if (c == 10) /* eol */ nlines++; if (!nlines) @@ -994,13 +995,14 @@ static int processStrData(FILE *strm, struct Input *in, hid_t file_id) { /* create parent groups */ if (in->path.count > 1) { - j = 0; + j = 0; handle = file_id; while (j < in->path.count - 1) { if ((group_id = H5Gopen2(handle, in->path.group[j], H5P_DEFAULT)) < 0) { group_id = H5Gcreate2(handle, in->path.group[j++], H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); for (; j < in->path.count - 1; j++) - group_id = H5Gcreate2(group_id, in->path.group[j], H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + group_id = + H5Gcreate2(group_id, in->path.group[j], H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); handle = group_id; break; } @@ -1010,7 +1012,7 @@ static int processStrData(FILE *strm, struct Input *in, hid_t file_id) } else { handle = file_id; - j = 0; + j = 0; } /*enable error reporting */ @@ -1023,21 +1025,22 @@ static int processStrData(FILE *strm, struct Input *in, hid_t file_id) if ((mspace_id = H5Screate(H5S_SCALAR)) < 0) goto out; - if ((dset_id = H5Dcreate2(handle, in->path.group[j], type_id, space_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0) + if ((dset_id = H5Dcreate2(handle, in->path.group[j], type_id, space_id, H5P_DEFAULT, H5P_DEFAULT, + H5P_DEFAULT)) < 0) goto out; line = 0; - while(EOF != (c = HDfgetc(strm))) { + while (EOF != (c = HDfgetc(strm))) { str[i] = (char)c; i++; if (c == 10) { /* eol */ - char *str2 = str; - hid_t fspace_id; + char * str2 = str; + hid_t fspace_id; hsize_t start[1]; - hsize_t count[1] = { 1 }; + hsize_t count[1] = {1}; str[i - 1] = '\0'; /* terminate string */ @@ -1055,9 +1058,8 @@ static int processStrData(FILE *strm, struct Input *in, hid_t file_id) if (H5Sclose(fspace_id) < 0) goto out; - i = 0; + i = 0; str[0] = '\0'; - } } @@ -1084,20 +1086,21 @@ out: * *------------------------------------------------------------------------- */ -static int processStrHDFData(FILE *strm, struct Input *in, hid_t file_id) +static int +processStrHDFData(FILE *strm, struct Input *in, hid_t file_id) { - hid_t group_id = -1; - hid_t dset_id = -1; - hid_t space_id = -1; - hid_t mspace_id = -1; - hid_t type_id = -1; - hid_t handle = -1; - char *str1 = NULL; - char *str2 = NULL; - char *str3 = NULL; - char str[1024] = ""; + hid_t group_id = H5I_INVALID_HID; + hid_t dset_id = H5I_INVALID_HID; + hid_t space_id = H5I_INVALID_HID; + hid_t mspace_id = H5I_INVALID_HID; + hid_t type_id = H5I_INVALID_HID; + hid_t handle = H5I_INVALID_HID; + char * str1 = NULL; + char * str2 = NULL; + char * str3 = NULL; + char str[1024] = ""; int j; - hsize_t line; + hsize_t line; /*------------------------------------------------------------------------- * read file and generate an HDF5 dataset @@ -1118,13 +1121,14 @@ static int processStrHDFData(FILE *strm, struct Input *in, hid_t file_id) { /* create parent groups */ if (in->path.count > 1) { - j = 0; + j = 0; handle = file_id; while (j < in->path.count - 1) { if ((group_id = H5Gopen2(handle, in->path.group[j], H5P_DEFAULT)) < 0) { group_id = H5Gcreate2(handle, in->path.group[j++], H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); for (; j < in->path.count - 1; j++) - group_id = H5Gcreate2(group_id, in->path.group[j], H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + group_id = + H5Gcreate2(group_id, in->path.group[j], H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); handle = group_id; break; } @@ -1134,7 +1138,7 @@ static int processStrHDFData(FILE *strm, struct Input *in, hid_t file_id) } else { handle = file_id; - j = 0; + j = 0; } /*enable error reporting */ @@ -1150,67 +1154,69 @@ static int processStrHDFData(FILE *strm, struct Input *in, hid_t file_id) if ((mspace_id = H5Screate(H5S_SCALAR)) < 0) goto out; - if ((dset_id = H5Dcreate2(handle, in->path.group[j], type_id, space_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0) + if ((dset_id = H5Dcreate2(handle, in->path.group[j], type_id, space_id, H5P_DEFAULT, H5P_DEFAULT, + H5P_DEFAULT)) < 0) goto out; #ifdef H5DEBUGIMPORT HDprintf("processStrHDFData DATATYPE STRING ready to process strings\n"); #endif line = 0; - j = 0; + j = 0; - while (HDfgets(str,sizeof(str),strm)) { + while (HDfgets(str, sizeof(str), strm)) { str1 = str; str2 = NULL; str3 = NULL; #ifdef H5DEBUGIMPORT - HDprintf("processStrHDFData DATATYPE STRING[%llu]={%s}\n", (unsigned long long)line, str1); + HDprintf("processStrHDFData DATATYPE STRING[%llu]={%s}\n", (unsigned long long)line, str1); #endif - /* process string to remove the first and last quote char */ - str2 = strchr(str1, '"'); - if (str2 != NULL) { + /* process string to remove the first and last quote char */ + str2 = strchr(str1, '"'); + if (str2 != NULL) { #ifdef H5DEBUGIMPORT - HDprintf("processStrHDFData DATATYPE STRING len:%d for {%s}\n", HDstrlen(str2), str2); + HDprintf("processStrHDFData DATATYPE STRING len:%d for {%s}\n", HDstrlen(str2), str2); #endif - str2++; + str2++; #ifdef H5DEBUGIMPORT - HDprintf("processStrHDFData DATATYPE STRING len:%d for {%s}\n", HDstrlen(str2), str2); + HDprintf("processStrHDFData DATATYPE STRING len:%d for {%s}\n", HDstrlen(str2), str2); #endif - str3 = strrchr(str2, '"'); - if (str3 != NULL) { + str3 = strrchr(str2, '"'); + if (str3 != NULL) { #ifdef H5DEBUGIMPORT - HDprintf("processStrHDFData DATATYPE STRING len:%d for {%s}\n", HDstrlen(str3), str3); + HDprintf("processStrHDFData DATATYPE STRING len:%d for {%s}\n", HDstrlen(str3), str3); #endif - *str3 = '\0'; + *str3 = '\0'; #ifdef H5DEBUGIMPORT - HDprintf("processStrHDFData DATATYPE STRING len:%d for {%s}\n", HDstrlen(str2), str2); + HDprintf("processStrHDFData DATATYPE STRING len:%d for {%s}\n", HDstrlen(str2), str2); #endif - if(HDstrlen(str2) > 0) { - hid_t fspace_id; - hsize_t start[1]; - hsize_t count[1] = { 1 }; + if (HDstrlen(str2) > 0) { + hid_t fspace_id; + hsize_t start[1]; + hsize_t count[1] = {1}; #ifdef H5DEBUGIMPORT - HDprintf("processStrHDFData DATATYPE STRING[%llu] store %s\n", (unsigned long long)line, str2); + HDprintf("processStrHDFData DATATYPE STRING[%llu] store %s\n", (unsigned long long)line, + str2); #endif - if ((fspace_id = H5Dget_space(dset_id)) < 0) - goto out; + if ((fspace_id = H5Dget_space(dset_id)) < 0) + goto out; - start[0] = line++; + start[0] = line++; - if (H5Sselect_hyperslab(fspace_id, H5S_SELECT_SET, start, NULL, count, NULL) < 0) - goto out; + if (H5Sselect_hyperslab(fspace_id, H5S_SELECT_SET, start, NULL, count, NULL) < 0) + goto out; - if (H5Dwrite(dset_id, type_id, mspace_id, fspace_id, H5P_DEFAULT, &str2) < 0) - goto out; + if (H5Dwrite(dset_id, type_id, mspace_id, fspace_id, H5P_DEFAULT, &str2) < 0) + goto out; - if (H5Sclose(fspace_id) < 0) - goto out; - } + if (H5Sclose(fspace_id) < 0) + goto out; } } + } str[0] = '\0'; j++; } @@ -1230,21 +1236,22 @@ out: #ifdef H5DEBUGIMPORT HDprintf("processStrHDFData DATATYPE STRING error exit\n"); #endif -/* disable error reporting */ -H5E_BEGIN_TRY -{ - /* close */ - H5Dclose(dset_id); - H5Sclose(space_id); - H5Sclose(mspace_id); - H5Tclose(type_id); -} -H5E_END_TRY; + /* disable error reporting */ + H5E_BEGIN_TRY + { + /* close */ + H5Dclose(dset_id); + H5Sclose(space_id); + H5Sclose(mspace_id); + H5Tclose(type_id); + } + H5E_END_TRY; return (-1); } -static int allocateIntegerStorage(struct Input *in) +static int +allocateIntegerStorage(struct Input *in) { hsize_t len = 1; int j; @@ -1255,44 +1262,45 @@ static int allocateIntegerStorage(struct Input *in) len *= in->sizeOfDimension[j]; switch (in->inputSize) { - case 8: - if ((in->data = (VOIDP) HDmalloc((size_t) len * sizeof(H5DT_INT8))) == NULL) { - (void) HDfprintf(stderr, "%s", err1); - return (-1); - } - break; + case 8: + if ((in->data = (VOIDP)HDmalloc((size_t)len * sizeof(H5DT_INT8))) == NULL) { + (void)HDfprintf(stderr, "%s", err1); + return (-1); + } + break; - case 16: - if ((in->data = (VOIDP) HDmalloc((size_t) len * sizeof(H5DT_INT16))) == NULL) { - (void) HDfprintf(stderr, "%s", err1); - return (-1); - } - break; + case 16: + if ((in->data = (VOIDP)HDmalloc((size_t)len * sizeof(H5DT_INT16))) == NULL) { + (void)HDfprintf(stderr, "%s", err1); + return (-1); + } + break; - case 32: - if ((in->data = (VOIDP) HDmalloc((size_t) len * sizeof(H5DT_INT32))) == NULL) { - (void) HDfprintf(stderr, "%s", err1); - return (-1); - } - break; + case 32: + if ((in->data = (VOIDP)HDmalloc((size_t)len * sizeof(H5DT_INT32))) == NULL) { + (void)HDfprintf(stderr, "%s", err1); + return (-1); + } + break; - case 64: - if ((in->data = (VOIDP) HDmalloc((size_t) len * sizeof(H5DT_INT64))) == NULL) { - (void) HDfprintf(stderr, "%s", err1); - return (-1); - } - break; + case 64: + if ((in->data = (VOIDP)HDmalloc((size_t)len * sizeof(H5DT_INT64))) == NULL) { + (void)HDfprintf(stderr, "%s", err1); + return (-1); + } + break; - default: - (void) HDfprintf(stderr, "%s", err2); - break; + default: + (void)HDfprintf(stderr, "%s", err2); + break; } return (0); } -static int allocateUIntegerStorage(struct Input *in) +static int +allocateUIntegerStorage(struct Input *in) { - hsize_t len = 1; + hsize_t len = 1; const char *err1 = "Unable to allocate dynamic memory.\n"; const char *err2 = "Invalid storage size for unsigned integer input data.\n"; int j; @@ -1301,42 +1309,43 @@ static int allocateUIntegerStorage(struct Input *in) len *= in->sizeOfDimension[j]; switch (in->inputSize) { - case 8: - if ((in->data = (VOIDP) HDmalloc((size_t) len * sizeof(H5DT_UINT8))) == NULL) { - (void) HDfprintf(stderr, "%s", err1); - return (-1); - } - break; + case 8: + if ((in->data = (VOIDP)HDmalloc((size_t)len * sizeof(H5DT_UINT8))) == NULL) { + (void)HDfprintf(stderr, "%s", err1); + return (-1); + } + break; - case 16: - if ((in->data = (VOIDP) HDmalloc((size_t) len * sizeof(H5DT_UINT16))) == NULL) { - (void) HDfprintf(stderr, "%s", err1); - return (-1); - } - break; + case 16: + if ((in->data = (VOIDP)HDmalloc((size_t)len * sizeof(H5DT_UINT16))) == NULL) { + (void)HDfprintf(stderr, "%s", err1); + return (-1); + } + break; - case 32: - if ((in->data = (VOIDP) HDmalloc((size_t) len * sizeof(H5DT_UINT32))) == NULL) { - (void) HDfprintf(stderr, "%s", err1); - return (-1); - } - break; + case 32: + if ((in->data = (VOIDP)HDmalloc((size_t)len * sizeof(H5DT_UINT32))) == NULL) { + (void)HDfprintf(stderr, "%s", err1); + return (-1); + } + break; - case 64: - if ((in->data = (VOIDP) HDmalloc((size_t) len * sizeof(H5DT_UINT64))) == NULL) { - (void) HDfprintf(stderr, "%s", err1); - return (-1); - } - break; + case 64: + if ((in->data = (VOIDP)HDmalloc((size_t)len * sizeof(H5DT_UINT64))) == NULL) { + (void)HDfprintf(stderr, "%s", err1); + return (-1); + } + break; - default: - (void) HDfprintf(stderr, "%s", err2); - break; + default: + (void)HDfprintf(stderr, "%s", err2); + break; } return (0); } -static int allocateFloatStorage(struct Input *in) +static int +allocateFloatStorage(struct Input *in) { hsize_t len = 1; int j; @@ -1347,54 +1356,55 @@ static int allocateFloatStorage(struct Input *in) len *= in->sizeOfDimension[j]; switch (in->inputSize) { - case 32: - if ((in->data = (VOIDP) HDmalloc((size_t) len * sizeof(H5DT_FLOAT32))) == NULL) { - (void) HDfprintf(stderr, "%s", err1); - return (-1); - } - break; + case 32: + if ((in->data = (VOIDP)HDmalloc((size_t)len * sizeof(H5DT_FLOAT32))) == NULL) { + (void)HDfprintf(stderr, "%s", err1); + return (-1); + } + break; - case 64: - if ((in->data = (VOIDP) HDmalloc((size_t) len * sizeof(H5DT_FLOAT64))) == NULL) { - (void) HDfprintf(stderr, "%s", err1); - return (-1); - } - break; + case 64: + if ((in->data = (VOIDP)HDmalloc((size_t)len * sizeof(H5DT_FLOAT64))) == NULL) { + (void)HDfprintf(stderr, "%s", err1); + return (-1); + } + break; - default: - (void) HDfprintf(stderr, "%s", err2); - break; + default: + (void)HDfprintf(stderr, "%s", err2); + break; } return (0); } -static int processConfigurationFile(char *infile, struct Input *in) +static int +processConfigurationFile(char *infile, struct Input *in) { - FILE *strm = NULL; - char key[MAX_PATH_NAME_LENGTH]; - int kindex; - char temp[MAX_PATH_NAME_LENGTH]; - int ival; - int scanret; - int retval = -1; - - const char *err1 = "Unable to open the configuration file: %s for reading.\n"; - const char *err2 = "Unknown keyword: %s in configuration file: %s\n"; - const char *err3a = "PATH keyword appears twice in %s.\n"; - const char *err3b = "Error in parsing the path information from %s.\n"; - const char *err4a = "INPUT-CLASS keyword appears twice in %s.\n"; - const char *err4b = "Error in retrieving the input class from %s.\n"; - const char *err5a = "INPUT-SIZE keyword appears twice in %s.\n"; - const char *err5b = "Error in retrieving the input size from %s.\n"; - const char *err6a = "RANK keyword appears twice in %s.\n"; - const char *err6b = "Error in retrieving the rank from %s.\n"; - const char *err7a = "DIMENSION-SIZES keyword appears twice in %s.\n"; - const char *err7b = "DIMENSION-SIZES cannot appear before RANK is provided.\n"; - const char *err7c = "Error in retrieving the dimension sizes from %s.\n"; - const char *err8a = "OUTPUT-CLASS keyword appears twice in %s.\n"; - const char *err8b = "Error in retrieving the output class from %s.\n"; - const char *err9a = "OUTPUT-SIZE keyword appears twice in %s.\n"; - const char *err9b = "Error in retrieving the output size from %s.\n"; + FILE *strm = NULL; + char key[MAX_PATH_NAME_LENGTH]; + int kindex; + char temp[MAX_PATH_NAME_LENGTH]; + int ival; + int scanret; + int retval = -1; + + const char *err1 = "Unable to open the configuration file: %s for reading.\n"; + const char *err2 = "Unknown keyword: %s in configuration file: %s\n"; + const char *err3a = "PATH keyword appears twice in %s.\n"; + const char *err3b = "Error in parsing the path information from %s.\n"; + const char *err4a = "INPUT-CLASS keyword appears twice in %s.\n"; + const char *err4b = "Error in retrieving the input class from %s.\n"; + const char *err5a = "INPUT-SIZE keyword appears twice in %s.\n"; + const char *err5b = "Error in retrieving the input size from %s.\n"; + const char *err6a = "RANK keyword appears twice in %s.\n"; + const char *err6b = "Error in retrieving the rank from %s.\n"; + const char *err7a = "DIMENSION-SIZES keyword appears twice in %s.\n"; + const char *err7b = "DIMENSION-SIZES cannot appear before RANK is provided.\n"; + const char *err7c = "Error in retrieving the dimension sizes from %s.\n"; + const char *err8a = "OUTPUT-CLASS keyword appears twice in %s.\n"; + const char *err8b = "Error in retrieving the output class from %s.\n"; + const char *err9a = "OUTPUT-SIZE keyword appears twice in %s.\n"; + const char *err9b = "Error in retrieving the output size from %s.\n"; const char *err10a = "OUTPUT-ARCHITECTURE keyword appears twice in %s.\n"; const char *err10b = "Error in retrieving the output architecture from %s.\n"; const char *err11a = "OUTPUT-BYTE-ORDER keyword appears twice in %s.\n"; @@ -1414,10 +1424,10 @@ static int processConfigurationFile(char *infile, struct Input *in) const char *err16a = "MAXIMUM-DIMENSIONS keyword appears twice in %s.\n"; const char *err16b = "MAXIMUM-DIMENSIONS cannot appear before DIMENSION-SIZES are provided.\n"; const char *err16c = "Error in retrieving the maximum dimension sizes from %s.\n"; - const char *err17 = "Configuration parameters are invalid in %s.\n"; - const char *err18 = "Unable to get string value.\n"; - const char *err19 = "Unable to get integer value.\n"; - const char *err20 = "Unable to get subset values.\n"; + const char *err17 = "Configuration parameters are invalid in %s.\n"; + const char *err18 = "Unable to get string value.\n"; + const char *err19 = "Unable to get integer value.\n"; + const char *err20 = "Unable to get subset values.\n"; /* create vector to map which keywords have been found check vector after each keyword to check for violation @@ -1426,17 +1436,17 @@ static int processConfigurationFile(char *infile, struct Input *in) */ /* Initialize machine endian */ - volatile uint32_t ibyte=0x01234567; + volatile uint32_t ibyte = 0x01234567; /* 0 for big endian, 1 for little endian. */ - if ((*((uint8_t*)(&ibyte))) == 0x67) { + if ((*((volatile uint8_t *)(&ibyte))) == 0x67) { if ((kindex = OutputByteOrderStrToInt("LE")) == -1) { - (void) HDfprintf(stderr, "%s", err11e); + (void)HDfprintf(stderr, "%s", err11e); return (-1); } } else { if ((kindex = OutputByteOrderStrToInt("BE")) == -1) { - (void) HDfprintf(stderr, "%s", err11e); + (void)HDfprintf(stderr, "%s", err11e); return (-1); } } @@ -1447,64 +1457,64 @@ static int processConfigurationFile(char *infile, struct Input *in) in->inputArchitecture = 0; /* default to NATIVE */ if ((strm = HDfopen(infile, "r")) == NULL) { - (void) HDfprintf(stderr, err1, infile); + (void)HDfprintf(stderr, err1, infile); goto error; } - scanret = fscanf(strm, "%254s", key); - if((scanret == 1) && !HDstrcmp("HDF5", key)) { + scanret = HDfscanf(strm, "%254s", key); + if ((scanret == 1) && !HDstrcmp("HDF5", key)) { #ifdef H5DEBUGIMPORT int pndx; HDprintf("\nh5dump file\n"); #endif in->h5dumpInput = 1; - scanret = fscanf(strm, "%254s", temp); /* filename */ - scanret = fscanf(strm, "%254s", temp); /* start bracket */ - scanret = fscanf(strm, "%254s", key); /* DATASET */ + scanret = HDfscanf(strm, "%254s", temp); /* filename */ + scanret = HDfscanf(strm, "%254s", temp); /* start bracket */ + scanret = HDfscanf(strm, "%254s", key); /* DATASET */ while (scanret == 1) { - if(!HDstrcmp("DATASET", key)) { /* PATH */ + if (!HDstrcmp("DATASET", key)) { /* PATH */ #ifdef H5DEBUGIMPORT HDprintf("h5dump DATASET key\n"); #endif if (in->configOptionVector[PATH] == 1) { - (void) HDfprintf(stderr, err3a, infile); + (void)HDfprintf(stderr, err3a, infile); goto error; } - if (fscanf(strm, "%254s", temp) != 1) { - (void) HDfprintf(stderr, "%s", err18); + if (HDfscanf(strm, "%254s", temp) != 1) { + (void)HDfprintf(stderr, "%s", err18); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump DATASET %s found\n", temp); #endif if (parsePathInfo(&in->path, temp) == -1) { - (void) HDfprintf(stderr, err3b, infile); + (void)HDfprintf(stderr, err3b, infile); goto error; } in->configOptionVector[PATH] = 1; - scanret = fscanf(strm, "%254s", temp); /* start bracket */ + scanret = HDfscanf(strm, "%254s", temp); /* start bracket */ #ifdef H5DEBUGIMPORT HDprintf("h5dump DATASET %s found\n", temp); #endif - } /* if(!HDstrcmp("DATASET", key)) PATH */ - else if(!HDstrcmp("DATATYPE", key)) { /* INPUT-CLASS */ + } /* if(!HDstrcmp("DATASET", key)) PATH */ + else if (!HDstrcmp("DATATYPE", key)) { /* INPUT-CLASS */ #ifdef H5DEBUGIMPORT HDprintf("h5dump DATATYPE key\n"); #endif if (in->configOptionVector[INPUT_CLASS] == 1) { - (void) HDfprintf(stderr, err4a, infile); + (void)HDfprintf(stderr, err4a, infile); goto error; } - if (fscanf(strm, "%254s", temp) != 1) { - (void) HDfprintf(stderr, "%s", err18); + if (HDfscanf(strm, "%254s", temp) != 1) { + (void)HDfprintf(stderr, "%s", err18); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump DATATYPE %s found\n", temp); #endif if ((kindex = getInputClassType(in, temp)) == -1) { - (void) HDfprintf(stderr, err4b, infile); + (void)HDfprintf(stderr, err4b, infile); goto error; } #ifdef H5DEBUGIMPORT @@ -1517,8 +1527,7 @@ static int processConfigurationFile(char *infile, struct Input *in) if (in->configOptionVector[OUTPUT_CLASS] == 0) { if (in->inputClass == 0 || in->inputClass == 4) in->outputClass = 0; - if (in->inputClass == 1 || in->inputClass == 2 - || in->inputClass == 3) + if (in->inputClass == 1 || in->inputClass == 2 || in->inputClass == 3) in->outputClass = 1; if (in->inputClass == 6 || in->inputClass == 7) in->outputClass = 2; @@ -1527,37 +1536,37 @@ static int processConfigurationFile(char *infile, struct Input *in) HDprintf("h5dump DATATYPE type %d outputClass\n", in->outputClass); #endif - if(in->inputClass == 5) { /* STRING */ + if (in->inputClass == 5) { /* STRING */ int get_next_prop = 1; - in->outputClass = -1; + in->outputClass = -1; #ifdef H5DEBUGIMPORT HDprintf("h5dump DATATYPE STRING found\n"); #endif - if (fscanf(strm, "%254s", temp) != 1) { /* start bracket */ - (void) HDfprintf(stderr, "%s", err18); + if (HDfscanf(strm, "%254s", temp) != 1) { /* start bracket */ + (void)HDfprintf(stderr, "%s", err18); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump DATATYPE STRING %s found\n", temp); #endif - if (fscanf(strm, "%254s", temp) != 1) { /* string properties */ - (void) HDfprintf(stderr, "%s", err18); + if (HDfscanf(strm, "%254s", temp) != 1) { /* string properties */ + (void)HDfprintf(stderr, "%s", err18); goto error; } while (get_next_prop) { - if(!HDstrcmp("STRSIZE", temp)) { /* STRSIZE */ - if (fscanf(strm, "%254s", temp) != 1) { - (void) HDfprintf(stderr, "%s", err19); + if (!HDstrcmp("STRSIZE", temp)) { /* STRSIZE */ + if (HDfscanf(strm, "%254s", temp) != 1) { + (void)HDfprintf(stderr, "%s", err19); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump DATATYPE STRING STRSIZE %s found\n", temp); #endif - if (HDstrcmp("H5T_VARIABLE;", temp)) { + if (HDstrcmp("H5T_VARIABLE;", temp) != 0) { char *more = temp; - ival = (int)HDstrtol(more, &more, 10); + ival = (int)HDstrtol(more, &more, 10); if (getInputSize(in, ival) == -1) { - (void) HDfprintf(stderr, err5b, infile); + (void)HDfprintf(stderr, err5b, infile); goto error; } #ifdef H5DEBUGIMPORT @@ -1565,119 +1574,119 @@ static int processConfigurationFile(char *infile, struct Input *in) #endif } } - else if(!HDstrcmp("STRPAD", temp)) { /* STRPAD */ - if (fscanf(strm, "%254s", temp) != 1) { /* STRPAD type */ - (void) HDfprintf(stderr, "%s", err18); + else if (!HDstrcmp("STRPAD", temp)) { /* STRPAD */ + if (HDfscanf(strm, "%254s", temp) != 1) { /* STRPAD type */ + (void)HDfprintf(stderr, "%s", err18); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump DATATYPE STRING STRPAD %s found\n", temp); #endif } - else if(!HDstrcmp("CSET", key)) { /* CSET */ - if (fscanf(strm, "%254s", temp) != 1) { /* CSET type */ - (void) HDfprintf(stderr, "%s", err18); + else if (!HDstrcmp("CSET", key)) { /* CSET */ + if (HDfscanf(strm, "%254s", temp) != 1) { /* CSET type */ + (void)HDfprintf(stderr, "%s", err18); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump DATATYPE STRING CSET %s found\n", temp); #endif - } - else if(!HDstrcmp("CTYPE", temp)) { /* CTYPE */ - if (fscanf(strm, "%254s", temp) != 1) { /* CTYPE type */ - (void) HDfprintf(stderr, "%s", err18); + else if (!HDstrcmp("CTYPE", temp)) { /* CTYPE */ + if (HDfscanf(strm, "%254s", temp) != 1) { /* CTYPE type */ + (void)HDfprintf(stderr, "%s", err18); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump DATATYPE STRING CTYPE %s found\n", temp); #endif } /* if(!HDstrcmp("CSET", key)) */ - if (fscanf(strm, "%254s", temp) != 1) { - (void) HDfprintf(stderr, "%s", err18); + if (HDfscanf(strm, "%254s", temp) != 1) { + (void)HDfprintf(stderr, "%s", err18); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump DATATYPE STRING %s found\n", temp); #endif - if(!HDstrcmp("}", temp)) { /* end bracket */ + if (!HDstrcmp("}", temp)) { /* end bracket */ get_next_prop = 0; } - } /* while (get_next_prop) */ - } /* if(kindex == 5) STRING */ - } /* else if(!HDstrcmp("DATATYPE", key)) INPUT-CLASS */ - else if(!HDstrcmp("DATASPACE", key)) { /* RANK and DIMENSIONS */ - hsize_t temp_dims[MAX_NUM_DIMENSION]; + } /* while (get_next_prop) */ + } /* if(kindex == 5) STRING */ + } /* else if(!HDstrcmp("DATATYPE", key)) INPUT-CLASS */ + else if (!HDstrcmp("DATASPACE", key)) { /* RANK and DIMENSIONS */ + hsize_t temp_dims[MAX_NUM_DIMENSION]; #ifdef H5DEBUGIMPORT HDprintf("h5dump DATASPACE key\n"); #endif - if (fscanf(strm, "%254s", temp) != 1) { - (void) HDfprintf(stderr, "%s", err18); + if (HDfscanf(strm, "%254s", temp) != 1) { + (void)HDfprintf(stderr, "%s", err18); goto error; } - if(!HDstrcmp("SCALAR", temp)) { /* SCALAR */ + if (!HDstrcmp("SCALAR", temp)) { /* SCALAR */ in->rank = 0; - } /* if(!HDstrcmp("SCALAR", key)) */ - else if(!HDstrcmp("NULL", temp)) { /* NULL */ - (void) HDfprintf(stderr, err6b, infile); + } /* if(!HDstrcmp("SCALAR", key)) */ + else if (!HDstrcmp("NULL", temp)) { /* NULL */ + (void)HDfprintf(stderr, err6b, infile); goto error; - } /* else if(!HDstrcmp("NULL", key)) */ - else if(!HDstrcmp("SIMPLE", temp)) { /* SIMPLE */ + } /* else if(!HDstrcmp("NULL", key)) */ + else if (!HDstrcmp("SIMPLE", temp)) { /* SIMPLE */ int icount = 0; #ifdef H5DEBUGIMPORT HDprintf("h5dump DATASPACE SIMPLE found\n"); #endif - if (fscanf(strm, "%254s", temp) != 1) { /* start bracket */ - (void) HDfprintf(stderr, err6b, infile); + if (HDfscanf(strm, "%254s", temp) != 1) { /* start bracket */ + (void)HDfprintf(stderr, err6b, infile); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump DATASPACE SIMPLE %s found\n", temp); #endif - if (fscanf(strm, "%254s", temp) != 1) { /* start paren */ - (void) HDfprintf(stderr, err6b, infile); + if (HDfscanf(strm, "%254s", temp) != 1) { /* start paren */ + (void)HDfprintf(stderr, err6b, infile); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump DATASPACE SIMPLE %s found\n", temp); #endif - if(!HDstrcmp("(", temp)) { /* start paren */ + if (!HDstrcmp("(", temp)) { /* start paren */ int get_next_dim = 1; - int i = 0; + int i = 0; - if (fscanf(strm, "%254s", temp) != 1) { /* Dimension with optional comma */ - (void) HDfprintf(stderr, err16c, infile); + if (HDfscanf(strm, "%254s", temp) != 1) { /* Dimension with optional comma */ + (void)HDfprintf(stderr, err16c, infile); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump DATASPACE SIMPLE %s found\n", temp); #endif while (get_next_dim) { - char *more = temp; + char *more = temp; temp_dims[icount] = HDstrtoull(more, &more, 10); - if (fscanf(strm, "%254s", temp) != 1) { /* Dimension or end paren */ - (void) HDfprintf(stderr, err6b, infile); + if (HDfscanf(strm, "%254s", temp) != 1) { /* Dimension or end paren */ + (void)HDfprintf(stderr, err6b, infile); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump DATASPACE SIMPLE %s found\n", temp); #endif - if(!HDstrcmp(")", temp)) { /* end paren */ - in->rank = ++icount; + if (!HDstrcmp(")", temp)) { /* end paren */ + in->rank = ++icount; in->configOptionVector[RANK] = 1; - get_next_dim = 0; + get_next_dim = 0; } else { /* Dimension */ icount++; if (icount > MAX_NUM_DIMENSION) { - (void) HDfprintf(stderr, "Invalid value for rank.\n"); + (void)HDfprintf(stderr, "Invalid value for rank.\n"); goto error; } } } /* while (get_next_dim) */ - if ((in->sizeOfDimension = (hsize_t *) HDmalloc ((size_t) in->rank * sizeof(hsize_t))) == NULL) { + if ((in->sizeOfDimension = (hsize_t *)HDmalloc((size_t)in->rank * sizeof(hsize_t))) == + NULL) { goto error; } #ifdef H5DEBUGIMPORT @@ -1696,36 +1705,37 @@ static int processConfigurationFile(char *infile, struct Input *in) in->configOptionVector[DIM] = 1; } /* if(!HDstrcmp("(", key)) start paren */ else { - (void) HDfprintf(stderr, err5b, infile); + (void)HDfprintf(stderr, err5b, infile); goto error; } - if (fscanf(strm, "%254s", temp) != 1) { - (void) HDfprintf(stderr, "%s", err18); + if (HDfscanf(strm, "%254s", temp) != 1) { + (void)HDfprintf(stderr, "%s", err18); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump DATASPACE SIMPLE %s found\n", temp); #endif - if(!HDstrcmp("/", temp)) { /* / max dims */ - if ((in->maxsizeOfDimension = (hsize_t *) HDmalloc ((size_t) in->rank * sizeof(hsize_t))) == NULL) { + if (!HDstrcmp("/", temp)) { /* / max dims */ + if ((in->maxsizeOfDimension = + (hsize_t *)HDmalloc((size_t)in->rank * sizeof(hsize_t))) == NULL) { goto error; } - if (fscanf(strm, "%254s", temp) != 1) { /* start paren */ - (void) HDfprintf(stderr, err6b, infile); + if (HDfscanf(strm, "%254s", temp) != 1) { /* start paren */ + (void)HDfprintf(stderr, err6b, infile); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump DATASPACE SIMPLE %s found\n", temp); #endif - if(!HDstrcmp("(", temp)) { /* start paren */ + if (!HDstrcmp("(", temp)) { /* start paren */ int get_next_dim = 1; - int i = 0; + int i = 0; #ifdef H5DEBUGIMPORT HDprintf("h5dump DATASPACE SIMPLE process max dim values\n"); #endif - if (fscanf(strm, "%254s", temp) != 1) { /* max dim with optional comma */ - (void) HDfprintf(stderr, err16c, infile); + if (HDfscanf(strm, "%254s", temp) != 1) { /* max dim with optional comma */ + (void)HDfprintf(stderr, err16c, infile); goto error; } #ifdef H5DEBUGIMPORT @@ -1735,28 +1745,29 @@ static int processConfigurationFile(char *infile, struct Input *in) #ifdef H5DEBUGIMPORT HDprintf("h5dump DATASPACE SIMPLE get max dim value\n"); #endif - if(!HDstrcmp("H5S_UNLIMITED", temp) || !HDstrcmp("H5S_UNLIMITED,", temp)) { /* unlimited */ - in->maxsizeOfDimension[i] = H5S_UNLIMITED; + if (!HDstrcmp("H5S_UNLIMITED", temp) || + !HDstrcmp("H5S_UNLIMITED,", temp)) { /* unlimited */ + in->maxsizeOfDimension[i] = H5S_UNLIMITED; in->configOptionVector[EXTEND] = 1; } else { - char *more = temp; + char *more = temp; in->maxsizeOfDimension[i] = HDstrtoull(more, &more, 10); } - if (fscanf(strm, "%254s", temp) != 1) { /* max dim or end paren */ - (void) HDfprintf(stderr, err16c, infile); + if (HDfscanf(strm, "%254s", temp) != 1) { /* max dim or end paren */ + (void)HDfprintf(stderr, err16c, infile); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump DATASPACE SIMPLE %s found\n", temp); #endif - if(!HDstrcmp(")", temp)) { /* end paren */ + if (!HDstrcmp(")", temp)) { /* end paren */ get_next_dim = 0; } else { /* comma */ i++; if (i >= MAX_NUM_DIMENSION) { - (void) HDfprintf(stderr, "Invalid value for rank.\n"); + (void)HDfprintf(stderr, "Invalid value for rank.\n"); goto error; } } @@ -1771,79 +1782,79 @@ static int processConfigurationFile(char *infile, struct Input *in) #endif } /* if(!HDstrcmp("(", key)) start paren */ else { - (void) HDfprintf(stderr, err16c, infile); + (void)HDfprintf(stderr, err16c, infile); goto error; } - scanret = fscanf(strm, "%254s", temp); /* end bracket */ + scanret = HDfscanf(strm, "%254s", temp); /* end bracket */ #ifdef H5DEBUGIMPORT HDprintf("h5dump DATASPACE SIMPLE %s found\n", temp); #endif } /* if(!HDstrcmp("/", key)) max dims separator */ - } /* else if(!HDstrcmp("SIMPLE", key)) */ + } /* else if(!HDstrcmp("SIMPLE", key)) */ else { - (void) HDfprintf(stderr, err5b, infile); + (void)HDfprintf(stderr, err5b, infile); goto error; } } /* else if(!HDstrcmp("DATASPACE", key)) RANK and DIMENSIONS */ - else if(!HDstrcmp("STORAGE_LAYOUT", key)) { /* CHUNKED-DIMENSION-SIZES */ + else if (!HDstrcmp("STORAGE_LAYOUT", key)) { /* CHUNKED-DIMENSION-SIZES */ #ifdef H5DEBUGIMPORT HDprintf("h5dump STORAGE_LAYOUT key\n"); #endif - if (fscanf(strm, "%254s", temp) != 1) { /* start bracket */ - (void) HDfprintf(stderr, err6b, infile); + if (HDfscanf(strm, "%254s", temp) != 1) { /* start bracket */ + (void)HDfprintf(stderr, err6b, infile); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump STORAGE_LAYOUT %s found\n", temp); #endif - if (fscanf(strm, "%254s", temp) != 1) { /* CHUNKED */ - (void) HDfprintf(stderr, err6b, infile); + if (HDfscanf(strm, "%254s", temp) != 1) { /* CHUNKED */ + (void)HDfprintf(stderr, err6b, infile); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump STORAGE_LAYOUT %s found\n", temp); #endif - if(!HDstrcmp("CHUNKED", temp)) { /* CHUNKED */ - if ((in->sizeOfChunk = (hsize_t *) HDmalloc ((size_t) in->rank * sizeof(hsize_t))) == NULL) { - (void) HDfprintf(stderr, "Unable to allocate dynamic memory.\n"); + if (!HDstrcmp("CHUNKED", temp)) { /* CHUNKED */ + if ((in->sizeOfChunk = (hsize_t *)HDmalloc((size_t)in->rank * sizeof(hsize_t))) == NULL) { + (void)HDfprintf(stderr, "Unable to allocate dynamic memory.\n"); goto error; } - if (fscanf(strm, "%254s", temp) != 1) { /* start paren */ - (void) HDfprintf(stderr, err6b, infile); + if (HDfscanf(strm, "%254s", temp) != 1) { /* start paren */ + (void)HDfprintf(stderr, err6b, infile); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump STORAGE_LAYOUT CHUNKED %s found\n", temp); #endif - if(!HDstrcmp("(", temp)) { /* start paren */ + if (!HDstrcmp("(", temp)) { /* start paren */ int get_next_dim = 1; - int icount = 0; + int icount = 0; - if (fscanf(strm, "%254s", temp) != 1) { /* Dimension with optional comma */ - (void) HDfprintf(stderr, err16c, infile); + if (HDfscanf(strm, "%254s", temp) != 1) { /* Dimension with optional comma */ + (void)HDfprintf(stderr, err16c, infile); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump STORAGE_LAYOUT CHUNKED %s found\n", temp); #endif while (get_next_dim) { - char *more = temp; + char *more = temp; in->sizeOfChunk[icount] = HDstrtoull(more, &more, 10); - if (fscanf(strm, "%254s", temp) != 1) { /* Dimension or end paren */ - (void) HDfprintf(stderr, err6b, infile); + if (HDfscanf(strm, "%254s", temp) != 1) { /* Dimension or end paren */ + (void)HDfprintf(stderr, err6b, infile); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump STORAGE_LAYOUT CHUNKED %s found\n", temp); #endif - if(!HDstrcmp(")", temp)) { /* end paren */ + if (!HDstrcmp(")", temp)) { /* end paren */ in->configOptionVector[RANK] = 1; - get_next_dim = 0; + get_next_dim = 0; } else { /* Dimension */ icount++; if (icount > MAX_NUM_DIMENSION) { - (void) HDfprintf(stderr, "Invalid value for rank.\n"); + (void)HDfprintf(stderr, "Invalid value for rank.\n"); goto error; } } @@ -1858,28 +1869,28 @@ static int processConfigurationFile(char *infile, struct Input *in) in->configOptionVector[DIM] = 1; } /* if(!HDstrcmp("(", key)) start paren */ else { - (void) HDfprintf(stderr, err5b, infile); + (void)HDfprintf(stderr, err5b, infile); goto error; } - if (fscanf(strm, "%254s", temp) != 1) { /* SIZE */ - (void) HDfprintf(stderr, err6b, infile); + if (HDfscanf(strm, "%254s", temp) != 1) { /* SIZE */ + (void)HDfprintf(stderr, err6b, infile); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump STORAGE_LAYOUT CHUNKED %s found\n", temp); #endif - if(!HDstrcmp("SIZE", temp)) { /* SIZE */ - if (fscanf(strm, "%d", (&ival)) != 1) { - (void) HDfprintf(stderr, "%s", err19); + if (!HDstrcmp("SIZE", temp)) { /* SIZE */ + if (HDfscanf(strm, "%d", (&ival)) != 1) { + (void)HDfprintf(stderr, "%s", err19); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump STORAGE_LAYOUT CHUNKED SIZE %d found\n", ival); #endif } - while (HDstrcmp("}", temp)) { - if (fscanf(strm, "%254s", temp) != 1) { /* end bracket */ - (void) HDfprintf(stderr, "%s", err18); + while (HDstrcmp("}", temp) != 0) { + if (HDfscanf(strm, "%254s", temp) != 1) { /* end bracket */ + (void)HDfprintf(stderr, "%s", err18); goto error; } #ifdef H5DEBUGIMPORT @@ -1888,148 +1899,148 @@ static int processConfigurationFile(char *infile, struct Input *in) } in->configOptionVector[CHUNK] = 1; } /* if(!HDstrcmp("CHUNKED", key)) CHUNKED */ - } /* else if(!HDstrcmp("STORAGE_LAYOUT", key)) CHUNKED-DIMENSION-SIZES */ - else if(!HDstrcmp("FILTERS", key)) { /* FILTERS */ + } /* else if(!HDstrcmp("STORAGE_LAYOUT", key)) CHUNKED-DIMENSION-SIZES */ + else if (!HDstrcmp("FILTERS", key)) { /* FILTERS */ #ifdef H5DEBUGIMPORT HDprintf("h5dump FILTERS key\n"); #endif - if (fscanf(strm, "%254s", temp) != 1) { /* start bracket */ - (void) HDfprintf(stderr, err6b, infile); + if (HDfscanf(strm, "%254s", temp) != 1) { /* start bracket */ + (void)HDfprintf(stderr, err6b, infile); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump FILTERS %s found\n", temp); #endif - if (fscanf(strm, "%254s", temp) != 1) { - (void) HDfprintf(stderr, err6b, infile); + if (HDfscanf(strm, "%254s", temp) != 1) { + (void)HDfprintf(stderr, err6b, infile); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump FILTERS %s found\n", temp); #endif - if(!HDstrcmp("COMPRESSION", temp)) { /* COMPRESSION */ + if (!HDstrcmp("COMPRESSION", temp)) { /* COMPRESSION */ #ifdef H5DEBUGIMPORT HDprintf("h5dump FILTERS COMPRESSION found\n"); #endif - if (fscanf(strm, "%254s", temp) != 1) { /* DEFLATE */ - (void) HDfprintf(stderr, "%s", err18); + if (HDfscanf(strm, "%254s", temp) != 1) { /* DEFLATE */ + (void)HDfprintf(stderr, "%s", err18); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump FILTERS COMPRESSION %s found\n", temp); #endif - if (fscanf(strm, "%254s", temp) != 1) { /* bgin bracket */ - (void) HDfprintf(stderr, "%s", err18); + if (HDfscanf(strm, "%254s", temp) != 1) { /* bgin bracket */ + (void)HDfprintf(stderr, "%s", err18); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump FILTERS COMPRESSION %s found\n", temp); #endif - if (fscanf(strm, "%254s", temp) != 1) { /* LEVEL */ - (void) HDfprintf(stderr, "%s", err18); + if (HDfscanf(strm, "%254s", temp) != 1) { /* LEVEL */ + (void)HDfprintf(stderr, "%s", err18); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump FILTERS COMPRESSION %s found\n", temp); #endif - if (fscanf(strm, "%d", (&ival)) != 1) { - (void) HDfprintf(stderr, "%s", err19); + if (HDfscanf(strm, "%d", (&ival)) != 1) { + (void)HDfprintf(stderr, "%s", err19); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump FILTERS COMPRESSION LEVEL %d found\n", ival); #endif in->compressionParam = ival; - if (fscanf(strm, "%254s", temp) != 1) { /* end bracket */ - (void) HDfprintf(stderr, "%s", err18); + if (HDfscanf(strm, "%254s", temp) != 1) { /* end bracket */ + (void)HDfprintf(stderr, "%s", err18); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump FILTERS COMPRESSION %s found\n", temp); #endif - in->compressionType = 0; /* ONLY GZIP supported */ + in->compressionType = 0; /* ONLY GZIP supported */ in->configOptionVector[COMPRESS] = 1; } - else if(!HDstrcmp("CONTIGUOUS", temp)) { /* CONTIGUOUS */ + else if (!HDstrcmp("CONTIGUOUS", temp)) { /* CONTIGUOUS */ #ifdef H5DEBUGIMPORT - HDprintf("h5dump FILTERS CONTIGUOUS found\n"); + HDprintf("h5dump FILTERS CONTIGUOUS found\n"); #endif in->configOptionVector[COMPRESS] = 0; } - else if(!HDstrcmp("NONE", temp)) { /* NONE */ + else if (!HDstrcmp("NONE", temp)) { /* NONE */ #ifdef H5DEBUGIMPORT - HDprintf("h5dump FILTERS NONE found\n"); + HDprintf("h5dump FILTERS NONE found\n"); #endif in->configOptionVector[COMPRESS] = 0; } - if (fscanf(strm, "%254s", temp) != 1) { /* end bracket */ - (void) HDfprintf(stderr, "%s", err18); + if (HDfscanf(strm, "%254s", temp) != 1) { /* end bracket */ + (void)HDfprintf(stderr, "%s", err18); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump FILTERS %s found\n", temp); #endif } - else if(!HDstrcmp("SUBSET", key)) { /* reduce dimensions */ - hsize_t temp_dims[MAX_NUM_DIMENSION]; - int get_next_prop = 1; + else if (!HDstrcmp("SUBSET", key)) { /* reduce dimensions */ + hsize_t temp_dims[MAX_NUM_DIMENSION]; + int get_next_prop = 1; #ifdef H5DEBUGIMPORT HDprintf("h5dump SUBSET key\n"); #endif - if (fscanf(strm, "%254s", temp) != 1) { /* start bracket */ - (void) HDfprintf(stderr, err20, infile); + if (HDfscanf(strm, "%254s", temp) != 1) { /* start bracket */ + (void)HDfprintf(stderr, err20, infile); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump SUBSET %s found\n", temp); #endif - if (fscanf(strm, "%254s", temp) != 1) { /* SUBSET keyword */ - (void) HDfprintf(stderr, "%s", err18); + if (HDfscanf(strm, "%254s", temp) != 1) { /* SUBSET keyword */ + (void)HDfprintf(stderr, "%s", err18); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump SUBSET %s found\n", temp); #endif while (get_next_prop) { - if(!HDstrcmp("COUNT", temp)) { /* COUNT */ + if (!HDstrcmp("COUNT", temp)) { /* COUNT */ int icount = 0; - if (fscanf(strm, "%254s", temp) != 1) { /* start paren */ - (void) HDfprintf(stderr, err6b, infile); + if (HDfscanf(strm, "%254s", temp) != 1) { /* start paren */ + (void)HDfprintf(stderr, err6b, infile); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump SUBSET %s found\n", temp); #endif - if(!HDstrcmp("(", temp)) { /* start paren */ + if (!HDstrcmp("(", temp)) { /* start paren */ int get_next_dim = 1; - int i = 0; + int i = 0; - if (fscanf(strm, "%254s", temp) != 1) { /* Dimension with optional comma */ - (void) HDfprintf(stderr, err16c, infile); + if (HDfscanf(strm, "%254s", temp) != 1) { /* Dimension with optional comma */ + (void)HDfprintf(stderr, err16c, infile); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump SUBSET COUNT [%s] found\n", temp); #endif while (get_next_dim) { - char *more = temp; + char *more = temp; temp_dims[icount] = HDstrtoull(more, &more, 10); - if (fscanf(strm, "%254s", temp) != 1) { /* Dimension or end paren */ - (void) HDfprintf(stderr, err6b, infile); + if (HDfscanf(strm, "%254s", temp) != 1) { /* Dimension or end paren */ + (void)HDfprintf(stderr, err6b, infile); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump SUBSET COUNT %s found\n", temp); #endif - if(!HDstrcmp(");", temp)) { /* end paren */ - in->rank = ++icount; + if (!HDstrcmp(");", temp)) { /* end paren */ + in->rank = ++icount; in->configOptionVector[RANK] = 1; - get_next_dim = 0; + get_next_dim = 0; } else { /* Dimension */ icount++; if (icount >= MAX_NUM_DIMENSION) { - (void) HDfprintf(stderr, "Invalid value for rank.\n"); + (void)HDfprintf(stderr, "Invalid value for rank.\n"); goto error; } } @@ -2045,47 +2056,47 @@ static int processConfigurationFile(char *infile, struct Input *in) HDprintf("\n"); #endif in->configOptionVector[DIM] = 1; - } /* if(!HDstrcmp("(", key)) start paren */ - } /* if(!HDstrcmp("COUNT", temp)) COUNT */ - if(!HDstrcmp("BLOCK", temp)) { /* BLOCK */ + } /* if(!HDstrcmp("(", key)) start paren */ + } /* if(!HDstrcmp("COUNT", temp)) COUNT */ + if (!HDstrcmp("BLOCK", temp)) { /* BLOCK */ int icount = 0; - if (fscanf(strm, "%254s", temp) != 1) { /* start paren */ - (void) HDfprintf(stderr, err6b, infile); + if (HDfscanf(strm, "%254s", temp) != 1) { /* start paren */ + (void)HDfprintf(stderr, err6b, infile); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump SUBSET %s found\n", temp); #endif - if(!HDstrcmp("(", temp)) { /* start paren */ + if (!HDstrcmp("(", temp)) { /* start paren */ int get_next_dim = 1; - int i = 0; + int i = 0; - if (fscanf(strm, "%254s", temp) != 1) { /* Dimension with optional comma */ - (void) HDfprintf(stderr, err16c, infile); + if (HDfscanf(strm, "%254s", temp) != 1) { /* Dimension with optional comma */ + (void)HDfprintf(stderr, err16c, infile); goto error; } #ifdef H5DEBUGIMPORT - HDprintf("h5dump SUBSET BLOCK [%s] found\n", temp); + HDprintf("h5dump SUBSET BLOCK [%s] found\n", temp); #endif while (get_next_dim) { - char *more = temp; + char *more = temp; temp_dims[icount] = HDstrtoull(more, &more, 10); - if (fscanf(strm, "%254s", temp) != 1) { /* Dimension or end paren */ - (void) HDfprintf(stderr, err6b, infile); + if (HDfscanf(strm, "%254s", temp) != 1) { /* Dimension or end paren */ + (void)HDfprintf(stderr, err6b, infile); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump SUBSET BLOCK %s found\n", temp); #endif - if(!HDstrcmp(");", temp)) { /* end paren */ - in->rank = ++icount; + if (!HDstrcmp(");", temp)) { /* end paren */ + in->rank = ++icount; in->configOptionVector[RANK] = 1; - get_next_dim = 0; + get_next_dim = 0; } else { /* Dimension */ icount++; if (icount > MAX_NUM_DIMENSION) { - (void) HDfprintf(stderr, "Invalid value for rank.\n"); + (void)HDfprintf(stderr, "Invalid value for rank.\n"); goto error; } } @@ -2102,27 +2113,27 @@ static int processConfigurationFile(char *infile, struct Input *in) #endif in->configOptionVector[DIM] = 1; } /* if(!HDstrcmp("(", key)) start paren */ - } /* if(!HDstrcmp("BLOCK", temp)) BLOCK */ - if (fscanf(strm, "%254s", temp) != 1) { - (void) HDfprintf(stderr, "%s", err18); + } /* if(!HDstrcmp("BLOCK", temp)) BLOCK */ + if (HDfscanf(strm, "%254s", temp) != 1) { + (void)HDfprintf(stderr, "%s", err18); goto error; } #ifdef H5DEBUGIMPORT HDprintf("h5dump SUBSET %s found\n", temp); #endif - if(!HDstrcmp("}", temp)) { /* end bracket */ + if (!HDstrcmp("}", temp)) { /* end bracket */ get_next_prop = 0; } - } /* while (get_next_prop) */ - } /* else if(!HDstrcmp("SUBSET", key)) */ - else if(!HDstrcmp("DATA", key)) { /* FINSHED */ + } /* while (get_next_prop) */ + } /* else if(!HDstrcmp("SUBSET", key)) */ + else if (!HDstrcmp("DATA", key)) { /* FINISHED */ #ifdef H5DEBUGIMPORT HDprintf("h5dump DATA key\n"); #endif scanret = 0; break; } - scanret = fscanf(strm, "%254s", key); + scanret = HDfscanf(strm, "%254s", key); } #ifdef H5DEBUGIMPORT HDprintf("h5dump path"); @@ -2154,258 +2165,257 @@ static int processConfigurationFile(char *infile, struct Input *in) #endif while (scanret == 1) { if ((kindex = mapKeywordToIndex(key)) == -1) { - (void) HDfprintf(stderr, err2, key, infile); + (void)HDfprintf(stderr, err2, key, infile); goto error; } switch (kindex) { - case 0: /* PATH */ - if (in->configOptionVector[PATH] == 1) { - (void) HDfprintf(stderr, err3a, infile); - goto error; - } - if (fscanf(strm, "%254s", temp) != 1) { - (void) HDfprintf(stderr, "%s", err18); - goto error; - } - if (parsePathInfo(&in->path, temp) == -1) { - (void) HDfprintf(stderr, err3b, infile); - goto error; - } - in->configOptionVector[PATH] = 1; - break; + case 0: /* PATH */ + if (in->configOptionVector[PATH] == 1) { + (void)HDfprintf(stderr, err3a, infile); + goto error; + } + if (HDfscanf(strm, "%254s", temp) != 1) { + (void)HDfprintf(stderr, "%s", err18); + goto error; + } + if (parsePathInfo(&in->path, temp) == -1) { + (void)HDfprintf(stderr, err3b, infile); + goto error; + } + in->configOptionVector[PATH] = 1; + break; - case 1: /* INPUT-CLASS */ - if (in->configOptionVector[INPUT_CLASS] == 1) { - (void) HDfprintf(stderr, err4a, infile); - goto error; - } + case 1: /* INPUT-CLASS */ + if (in->configOptionVector[INPUT_CLASS] == 1) { + (void)HDfprintf(stderr, err4a, infile); + goto error; + } - if (fscanf(strm, "%254s", temp) != 1) { - (void) HDfprintf(stderr, "%s", err18); - goto error; - } - if (getInputClass(in, temp) == -1) { - (void) HDfprintf(stderr, err4b, infile); - goto error; - } + if (HDfscanf(strm, "%254s", temp) != 1) { + (void)HDfprintf(stderr, "%s", err18); + goto error; + } + if (getInputClass(in, temp) == -1) { + (void)HDfprintf(stderr, err4b, infile); + goto error; + } - in->configOptionVector[INPUT_CLASS] = 1; + in->configOptionVector[INPUT_CLASS] = 1; - /*set default value for output-class */ - if (in->configOptionVector[OUTPUT_CLASS] == 0) { - if (in->inputClass == 0 || in->inputClass == 4) - in->outputClass = 0; - if (in->inputClass == 1 || in->inputClass == 2 - || in->inputClass == 3) - in->outputClass = 1; - if (in->inputClass == 6 || in->inputClass == 7) - in->outputClass = 2; - } - break; + /*set default value for output-class */ + if (in->configOptionVector[OUTPUT_CLASS] == 0) { + if (in->inputClass == 0 || in->inputClass == 4) + in->outputClass = 0; + if (in->inputClass == 1 || in->inputClass == 2 || in->inputClass == 3) + in->outputClass = 1; + if (in->inputClass == 6 || in->inputClass == 7) + in->outputClass = 2; + } + break; - case 2: /* INPUT-SIZE */ - if (in->configOptionVector[INPUT_SIZE] == 1) { - (void) HDfprintf(stderr, err5a, infile); - goto error; - } - if (fscanf(strm, "%254d", (&ival)) != 1) { - (void) HDfprintf(stderr, "%s", err19); - goto error; - } - if (getInputSize(in, ival) == -1) { - (void) HDfprintf(stderr, err5b, infile); - goto error; - } - in->configOptionVector[INPUT_SIZE] = 1; + case 2: /* INPUT-SIZE */ + if (in->configOptionVector[INPUT_SIZE] == 1) { + (void)HDfprintf(stderr, err5a, infile); + goto error; + } + if (HDfscanf(strm, "%254d", (&ival)) != 1) { + (void)HDfprintf(stderr, "%s", err19); + goto error; + } + if (getInputSize(in, ival) == -1) { + (void)HDfprintf(stderr, err5b, infile); + goto error; + } + in->configOptionVector[INPUT_SIZE] = 1; - /*set default value for output-size */ - if (in->configOptionVector[OUTPUT_SIZE] == 0) - in->outputSize = in->inputSize; - break; + /*set default value for output-size */ + if (in->configOptionVector[OUTPUT_SIZE] == 0) + in->outputSize = in->inputSize; + break; - case 3: /* RANK */ - if (in->configOptionVector[RANK] == 1) { - (void) HDfprintf(stderr, err6a, infile); - goto error; - } + case 3: /* RANK */ + if (in->configOptionVector[RANK] == 1) { + (void)HDfprintf(stderr, err6a, infile); + goto error; + } - if (getRank(in, strm) == -1) { - (void) HDfprintf(stderr, err6b, infile); - goto error; - } - in->configOptionVector[RANK] = 1; - break; + if (getRank(in, strm) == -1) { + (void)HDfprintf(stderr, err6b, infile); + goto error; + } + in->configOptionVector[RANK] = 1; + break; - case 4: /* DIMENSION-SIZES */ - if (in->configOptionVector[DIM] == 1) { - (void) HDfprintf(stderr, err7a, infile); - goto error; - } + case 4: /* DIMENSION-SIZES */ + if (in->configOptionVector[DIM] == 1) { + (void)HDfprintf(stderr, err7a, infile); + goto error; + } - if (in->configOptionVector[RANK] == 0) { - (void) HDfprintf(stderr, err7b, infile); - goto error; - } - if (getDimensionSizes(in, strm) == -1) { - (void) HDfprintf(stderr, err7c, infile); - goto error; - } - in->configOptionVector[DIM] = 1; - break; + if (in->configOptionVector[RANK] == 0) { + (void)HDfprintf(stderr, err7b, infile); + goto error; + } + if (getDimensionSizes(in, strm) == -1) { + (void)HDfprintf(stderr, err7c, infile); + goto error; + } + in->configOptionVector[DIM] = 1; + break; - case 5: /* OUTPUT-CLASS */ - if (in->configOptionVector[OUTPUT_CLASS] == 1) { - (void) HDfprintf(stderr, err8a, infile); - goto error; - } + case 5: /* OUTPUT-CLASS */ + if (in->configOptionVector[OUTPUT_CLASS] == 1) { + (void)HDfprintf(stderr, err8a, infile); + goto error; + } - if (getOutputClass(in, strm) == -1) { - (void) HDfprintf(stderr, err8b, infile); - goto error; - } - in->configOptionVector[OUTPUT_CLASS] = 1; - break; + if (getOutputClass(in, strm) == -1) { + (void)HDfprintf(stderr, err8b, infile); + goto error; + } + in->configOptionVector[OUTPUT_CLASS] = 1; + break; - case 6: /* OUTPUT-SIZE */ - if (in->configOptionVector[OUTPUT_SIZE] == 1) { - (void) HDfprintf(stderr, err9a, infile); - goto error; - } + case 6: /* OUTPUT-SIZE */ + if (in->configOptionVector[OUTPUT_SIZE] == 1) { + (void)HDfprintf(stderr, err9a, infile); + goto error; + } - if (getOutputSize(in, strm) == -1) { - (void) HDfprintf(stderr, err9b, infile); - goto error; - } - in->configOptionVector[OUTPUT_SIZE] = 1; - break; + if (getOutputSize(in, strm) == -1) { + (void)HDfprintf(stderr, err9b, infile); + goto error; + } + in->configOptionVector[OUTPUT_SIZE] = 1; + break; - case 7: /* OUTPUT-ARCHITECTURE */ - if (in->configOptionVector[OUTPUT_ARCH] == 1) { - (void) HDfprintf(stderr, err10a, infile); - goto error; - } + case 7: /* OUTPUT-ARCHITECTURE */ + if (in->configOptionVector[OUTPUT_ARCH] == 1) { + (void)HDfprintf(stderr, err10a, infile); + goto error; + } - if (getOutputArchitecture(in, strm) == -1) { - (void) HDfprintf(stderr, err10b, infile); - goto error; - } - in->configOptionVector[OUTPUT_ARCH] = 1; - break; + if (getOutputArchitecture(in, strm) == -1) { + (void)HDfprintf(stderr, err10b, infile); + goto error; + } + in->configOptionVector[OUTPUT_ARCH] = 1; + break; - case 8: /* OUTPUT-BYTE-ORDER */ - if (in->configOptionVector[OUTPUT_B_ORDER] == 1) { - (void) HDfprintf(stderr, err11a, infile); - goto error; - } + case 8: /* OUTPUT-BYTE-ORDER */ + if (in->configOptionVector[OUTPUT_B_ORDER] == 1) { + (void)HDfprintf(stderr, err11a, infile); + goto error; + } - if (getOutputByteOrder(in, strm) == -1) { - (void) HDfprintf(stderr, err11b, infile); - goto error; - } - in->configOptionVector[OUTPUT_B_ORDER] = 1; - break; + if (getOutputByteOrder(in, strm) == -1) { + (void)HDfprintf(stderr, err11b, infile); + goto error; + } + in->configOptionVector[OUTPUT_B_ORDER] = 1; + break; - case 9: /* CHUNKED-DIMENSION-SIZES */ - if (in->configOptionVector[CHUNK] == 1) { - (void) HDfprintf(stderr, err12a, infile); - goto error; - } - /* cant appear before dimension sizes have been provided */ - if (in->configOptionVector[DIM] == 0) { - (void) HDfprintf(stderr, err12b, infile); - goto error; - } + case 9: /* CHUNKED-DIMENSION-SIZES */ + if (in->configOptionVector[CHUNK] == 1) { + (void)HDfprintf(stderr, err12a, infile); + goto error; + } + /* can't appear before dimension sizes have been provided */ + if (in->configOptionVector[DIM] == 0) { + (void)HDfprintf(stderr, err12b, infile); + goto error; + } - if (getChunkedDimensionSizes(in, strm) == -1) { - (void) HDfprintf(stderr, err12c, infile); - goto error; - } - in->configOptionVector[CHUNK] = 1; - break; + if (getChunkedDimensionSizes(in, strm) == -1) { + (void)HDfprintf(stderr, err12c, infile); + goto error; + } + in->configOptionVector[CHUNK] = 1; + break; - case 10: /* COMPRESSION-TYPE */ - if (in->configOptionVector[COMPRESS] == 1) { - (void) HDfprintf(stderr, err13a, infile); - goto error; - } + case 10: /* COMPRESSION-TYPE */ + if (in->configOptionVector[COMPRESS] == 1) { + (void)HDfprintf(stderr, err13a, infile); + goto error; + } - if (getCompressionType(in, strm) == -1) { - (void) HDfprintf(stderr, err13b, infile); - goto error; - } - in->configOptionVector[COMPRESS] = 1; + if (getCompressionType(in, strm) == -1) { + (void)HDfprintf(stderr, err13b, infile); + goto error; + } + in->configOptionVector[COMPRESS] = 1; - if (in->configOptionVector[COMPRESS_PARAM] == 0) { - if (in->compressionType == 0) - in->compressionParam = 6; /* default value if compressionType is GZIP */ - } - break; + if (in->configOptionVector[COMPRESS_PARAM] == 0) { + if (in->compressionType == 0) + in->compressionParam = 6; /* default value if compressionType is GZIP */ + } + break; - case 11: /* COMPRESSION-PARAM */ - if (in->configOptionVector[COMPRESS_PARAM] == 1) { - (void) HDfprintf(stderr, err14a, infile); - goto error; - } + case 11: /* COMPRESSION-PARAM */ + if (in->configOptionVector[COMPRESS_PARAM] == 1) { + (void)HDfprintf(stderr, err14a, infile); + goto error; + } - if (getCompressionParameter(in, strm) == -1) { - (void) HDfprintf(stderr, err14b, infile); - goto error; - } + if (getCompressionParameter(in, strm) == -1) { + (void)HDfprintf(stderr, err14b, infile); + goto error; + } - in->configOptionVector[COMPRESS_PARAM] = 1; + in->configOptionVector[COMPRESS_PARAM] = 1; - if (in->configOptionVector[COMPRESS] == 0) - in->compressionType = 0; + if (in->configOptionVector[COMPRESS] == 0) + in->compressionType = 0; - break; + break; - case 12: /* EXTERNAL-STORAGE */ - if (in->configOptionVector[EXTERNALSTORE] == 1) { - (void) HDfprintf(stderr, err15a, infile); - goto error; - } + case 12: /* EXTERNAL-STORAGE */ + if (in->configOptionVector[EXTERNALSTORE] == 1) { + (void)HDfprintf(stderr, err15a, infile); + goto error; + } - if (getExternalFilename(in, strm) == -1) { - (void) HDfprintf(stderr, err15b, infile); - goto error; - } - in->configOptionVector[EXTERNALSTORE] = 1; - break; + if (getExternalFilename(in, strm) == -1) { + (void)HDfprintf(stderr, err15b, infile); + goto error; + } + in->configOptionVector[EXTERNALSTORE] = 1; + break; - case 13: /* MAXIMUM-DIMENSIONS */ - if (in->configOptionVector[EXTEND] == 1) { - (void) HDfprintf(stderr, err16a, infile); - goto error; - } - /* cant appear before dimension sizes have been provided */ - if (in->configOptionVector[DIM] == 0) { - (void) HDfprintf(stderr, err16b, infile); - goto error; - } - if (getMaximumDimensionSizes(in, strm) == -1) { - (void) HDfprintf(stderr, err16c, infile); - goto error; - } - in->configOptionVector[EXTEND] = 1; - break; + case 13: /* MAXIMUM-DIMENSIONS */ + if (in->configOptionVector[EXTEND] == 1) { + (void)HDfprintf(stderr, err16a, infile); + goto error; + } + /* can't appear before dimension sizes have been provided */ + if (in->configOptionVector[DIM] == 0) { + (void)HDfprintf(stderr, err16b, infile); + goto error; + } + if (getMaximumDimensionSizes(in, strm) == -1) { + (void)HDfprintf(stderr, err16c, infile); + goto error; + } + in->configOptionVector[EXTEND] = 1; + break; - case 14: /* INPUT-BYTE-ORDER */ - if (in->configOptionVector[INPUT_B_ORDER] == 1) { - (void) HDfprintf(stderr, err11c, infile); - goto error; - } + case 14: /* INPUT-BYTE-ORDER */ + if (in->configOptionVector[INPUT_B_ORDER] == 1) { + (void)HDfprintf(stderr, err11c, infile); + goto error; + } - if (getInputByteOrder(in, strm) == -1) { - (void) HDfprintf(stderr, err11d, infile); - goto error; - } - in->configOptionVector[INPUT_B_ORDER] = 1; - break; + if (getInputByteOrder(in, strm) == -1) { + (void)HDfprintf(stderr, err11d, infile); + goto error; + } + in->configOptionVector[INPUT_B_ORDER] = 1; + break; - default: - break; + default: + break; } - scanret = fscanf(strm, "%254s", key); + scanret = HDfscanf(strm, "%254s", key); } /* @@ -2414,7 +2424,7 @@ static int processConfigurationFile(char *infile, struct Input *in) */ if (validateConfigurationParameters(in) == -1) { - (void) HDfprintf(stderr, err17, infile); + (void)HDfprintf(stderr, err17, infile); goto error; } } @@ -2423,76 +2433,72 @@ static int processConfigurationFile(char *infile, struct Input *in) retval = 0; error: - if(strm) + if (strm) HDfclose(strm); - return(retval); + return (retval); } -static int validateConfigurationParameters(struct Input *in) +static int +validateConfigurationParameters(struct Input *in) { const char *err1 = "One or more of the required fields (RANK, DIMENSION-SIZES) missing.\n"; - const char *err2 = "Cannot specify chunking or compression or extendible data sets with the external file option.\n"; - const char *err3 = "Cannot specify the compression or the extendible data sets without the chunking option.\n"; + const char *err2 = + "Cannot specify chunking or compression or extendible data sets with the external file option.\n"; + const char *err3 = + "Cannot specify the compression or the extendible data sets without the chunking option.\n"; const char *err4a = "OUTPUT-ARCHITECTURE cannot be STD if OUTPUT-CLASS is floating point (FP).\n"; const char *err4b = "OUTPUT-ARCHITECTURE cannot be IEEE if OUTPUT-CLASS is integer (IN).\n"; - const char *err5 = "For OUTPUT-CLASS FP, valid values for OUTPUT-SIZE are (32, 64) .\n"; -#ifndef H5_SIZEOF_LONG_LONG - const char *err6 = "No support for reading 64-bit integer (INPUT-CLASS: IN, TEXTIN, UIN, TEXTUIN files\n"; -#endif + const char *err5 = "For OUTPUT-CLASS FP, valid values for OUTPUT-SIZE are (32, 64) .\n"; /* for class STR other parameters are ignored */ if (in->inputClass == 5) /* STR */ return (0); if ((in->configOptionVector[DIM] != 1) || (in->configOptionVector[RANK] != 1)) { - (void) HDfprintf(stderr, "%s", err1); + (void)HDfprintf(stderr, "%s", err1); return (-1); } if (in->configOptionVector[EXTERNALSTORE] == 1) { - if ((in->configOptionVector[COMPRESS] == 1) || (in->configOptionVector[CHUNK] == 1) || (in->configOptionVector[EXTEND] == 1)) { - (void) HDfprintf(stderr, "%s", err2); + if ((in->configOptionVector[COMPRESS] == 1) || (in->configOptionVector[CHUNK] == 1) || + (in->configOptionVector[EXTEND] == 1)) { + (void)HDfprintf(stderr, "%s", err2); return (-1); } } if ((in->configOptionVector[COMPRESS] == 1) || (in->configOptionVector[EXTEND] == 1)) { if (in->configOptionVector[CHUNK] != 1) { - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err3); return (-1); } } - /* Arch cant be STD if O/p class is FP */ + /* Arch can't be STD if O/p class is FP */ if (in->outputArchitecture == 1) if (in->outputClass == 1) { - (void) HDfprintf(stderr, "%s", err4a); + (void)HDfprintf(stderr, "%s", err4a); return (-1); } - /* Arch cant be IEEE if O/p class is IN */ + /* Arch can't be IEEE if O/p class is IN */ if (in->outputArchitecture == 2) if (in->outputClass == 0) { - (void) HDfprintf(stderr, "%s", err4b); + (void)HDfprintf(stderr, "%s", err4b); return (-1); } if (in->outputClass == 1) if (in->outputSize != 32 && in->outputSize != 64) { - (void) HDfprintf(stderr, "%s", err5); + (void)HDfprintf(stderr, "%s", err5); return (-1); } -#ifndef H5_SIZEOF_LONG_LONG - if (in->inputSize == 64 && (in->inputClass == 0 || in->inputClass == 4 || in->inputClass == 6 || in->inputClass == 7) ) { - (void) HDfprintf(stderr, "%s", err6); - return -1; - } -#endif return (0); } -static int mapKeywordToIndex(char *key) +static int +mapKeywordToIndex(char *key) { int i; @@ -2502,66 +2508,67 @@ static int mapKeywordToIndex(char *key) return -1; } -static int parsePathInfo(struct path_info *path, char *temp) +static int +parsePathInfo(struct path_info *path, char *temp) { const char delimiter[] = "/\""; - char *token; - int i = 0; + char * token; + int i = 0; const char *err1 = "Path string larger than MAX_PATH_NAME_LENGTH.\n"; - token = HDstrtok (temp, delimiter); + token = HDstrtok(temp, delimiter); if (HDstrlen(token) >= MAX_PATH_NAME_LENGTH) { - (void) HDfprintf(stderr, err1); + (void)HDfprintf(stderr, "%s", err1); return (-1); } - HDstrcpy(path->group[i++],token); + HDstrcpy(path->group[i++], token); while (1) { - token = HDstrtok (NULL, delimiter); + token = HDstrtok(NULL, delimiter); if (token == NULL) break; if (HDstrlen(token) >= MAX_PATH_NAME_LENGTH) { - (void) HDfprintf(stderr, err1); + (void)HDfprintf(stderr, "%s", err1); return (-1); } - HDstrcpy(path->group[i++],token); + HDstrcpy(path->group[i++], token); } path->count = i; return (0); } -static int parseDimensions(struct Input *in, char *strm) +static int +parseDimensions(struct Input *in, char *strm) { const char delimiter[] = ","; char temp[255]; - char *token; - int i = 0; + char * token; + int i = 0; const char *err1 = "Unable to allocate dynamic memory.\n"; HDstrncpy(temp, strm, sizeof(temp)); temp[sizeof(temp) - 1] = '\0'; - HDstrtok (temp, delimiter); + HDstrtok(temp, delimiter); while (1) { - token = HDstrtok (NULL, delimiter); + token = HDstrtok(NULL, delimiter); if (token == NULL) break; i++; } in->rank = i + 1; - if ((in->sizeOfDimension = (hsize_t *) HDmalloc ((size_t) in->rank * sizeof(hsize_t))) == NULL) { - (void) HDfprintf(stderr, "%s", err1); + if ((in->sizeOfDimension = (hsize_t *)HDmalloc((size_t)in->rank * sizeof(hsize_t))) == NULL) { + (void)HDfprintf(stderr, "%s", err1); return (-1); } i = 0; HDstrncpy(temp, strm, sizeof(temp)); - temp[sizeof(temp) - 1] = '\0'; - in->sizeOfDimension[i++] - = HDstrtoull(HDstrtok (temp, delimiter), NULL, BASE_10); + temp[sizeof(temp) - 1] = '\0'; + in->sizeOfDimension[i++] = HDstrtoull(HDstrtok(temp, delimiter), NULL, BASE_10); while (1) { - token = HDstrtok (NULL, delimiter); + token = HDstrtok(NULL, delimiter); if (token == NULL) break; in->sizeOfDimension[i++] = HDstrtoull(token, NULL, BASE_10); @@ -2569,20 +2576,21 @@ static int parseDimensions(struct Input *in, char *strm) return (0); } -static int getOutputClass(struct Input *in, FILE *strm) +static int +getOutputClass(struct Input *in, FILE *strm) { char temp[255]; int kindex; const char *err1 = "Unable to get 'string' value.\n"; const char *err2 = "Invalid value for output class.\n"; - if (fscanf(strm, "%254s", temp) != 1) { - (void) HDfprintf(stderr, "%s", err1); + if (HDfscanf(strm, "%254s", temp) != 1) { + (void)HDfprintf(stderr, "%s", err1); return (-1); } if ((kindex = OutputClassStrToInt(temp)) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } @@ -2590,10 +2598,11 @@ static int getOutputClass(struct Input *in, FILE *strm) return (0); } -static int OutputClassStrToInt(char *temp) +static int +OutputClassStrToInt(char *temp) { - int i; - char classKeywordTable[3][15] = { "IN", "FP", "UIN" }; + int i; + char classKeywordTable[3][15] = {"IN", "FP", "UIN"}; for (i = 0; i < 3; i++) if (!HDstrcmp(classKeywordTable[i], temp)) return i; @@ -2601,16 +2610,17 @@ static int OutputClassStrToInt(char *temp) return -1; } /* same as getInputSize. But defined separately for extensibility */ -static int getOutputSize(struct Input *in, FILE *strm) +static int +getOutputSize(struct Input *in, FILE *strm) { int ival; int i; - int outputSizeValidValues[4] = { 8, 16, 32, 64 }; - const char *err1 = "Unable to get integer value.\n"; - const char *err2 = "Invalid value for output size.\n"; + int outputSizeValidValues[4] = {8, 16, 32, 64}; + const char *err1 = "Unable to get integer value.\n"; + const char *err2 = "Invalid value for output size.\n"; - if (fscanf(strm, "%d", (&ival)) != 1) { - (void) HDfprintf(stderr, "%s", err1); + if (HDfscanf(strm, "%d", (&ival)) != 1) { + (void)HDfprintf(stderr, "%s", err1); return (-1); } @@ -2619,17 +2629,18 @@ static int getOutputSize(struct Input *in, FILE *strm) in->outputSize = ival; return (0); } - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } -static int getInputClass(struct Input *in, char * temp) +static int +getInputClass(struct Input *in, char *temp) { int kindex; const char *err1 = "Invalid value for input class.\n"; if ((kindex = InputClassStrToInt(temp)) == -1) { - (void) HDfprintf(stderr, "%s", err1); + (void)HDfprintf(stderr, "%s", err1); return (-1); } @@ -2637,355 +2648,356 @@ static int getInputClass(struct Input *in, char * temp) return (0); } -static int getInputClassType(struct Input *in, char * buffer) +static int +getInputClassType(struct Input *in, char *buffer) { int kindex = -1; - const char *err1 = "Invalid value for input class.\n"; - const char *err2 = "Invalid value for output architecture.\n"; - const char *err3 = "Invalid value for input byte-order.\n"; + const char *err1 = "Invalid value for input class.\n"; + const char *err2 = "Invalid value for output architecture.\n"; + const char *err3 = "Invalid value for input byte-order.\n"; if (!HDstrcmp(buffer, "H5T_STD_I8BE")) { - in->inputSize = 8; + in->inputSize = 8; in->configOptionVector[INPUT_SIZE] = 1; if ((kindex = OutputArchStrToInt("STD")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; if ((kindex = OutputByteOrderStrToInt("BE")) == -1) { - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err3); return (-1); } in->outputByteOrder = kindex; - #ifdef H5DEBUGIMPORT +#ifdef H5DEBUGIMPORT HDprintf("h5dump inputByteOrder %d\n", in->inputByteOrder); - #endif +#endif kindex = 4; } else if (!HDstrcmp(buffer, "H5T_STD_I8LE")) { - in->inputSize = 8; + in->inputSize = 8; in->configOptionVector[INPUT_SIZE] = 1; if ((kindex = OutputArchStrToInt("STD")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; if ((kindex = OutputByteOrderStrToInt("LE")) == -1) { - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err3); return (-1); } in->outputByteOrder = kindex; - #ifdef H5DEBUGIMPORT +#ifdef H5DEBUGIMPORT HDprintf("h5dump inputByteOrder %d\n", in->inputByteOrder); - #endif +#endif kindex = 4; } else if (!HDstrcmp(buffer, "H5T_STD_I16BE")) { - in->inputSize = 16; + in->inputSize = 16; in->configOptionVector[INPUT_SIZE] = 1; if ((kindex = OutputArchStrToInt("STD")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; if ((kindex = OutputByteOrderStrToInt("BE")) == -1) { - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err3); return (-1); } in->outputByteOrder = kindex; - #ifdef H5DEBUGIMPORT +#ifdef H5DEBUGIMPORT HDprintf("h5dump inputByteOrder %d\n", in->inputByteOrder); - #endif +#endif kindex = 4; } else if (!HDstrcmp(buffer, "H5T_STD_I16LE")) { - in->inputSize = 16; + in->inputSize = 16; in->configOptionVector[INPUT_SIZE] = 1; if ((kindex = OutputArchStrToInt("STD")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; if ((kindex = OutputByteOrderStrToInt("LE")) == -1) { - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err3); return (-1); } in->outputByteOrder = kindex; - #ifdef H5DEBUGIMPORT +#ifdef H5DEBUGIMPORT HDprintf("h5dump inputByteOrder %d\n", in->inputByteOrder); - #endif +#endif kindex = 4; } else if (!HDstrcmp(buffer, "H5T_STD_I32BE")) { - in->inputSize = 32; + in->inputSize = 32; in->configOptionVector[INPUT_SIZE] = 1; if ((kindex = OutputArchStrToInt("STD")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; if ((kindex = OutputByteOrderStrToInt("BE")) == -1) { - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err3); return (-1); } in->outputByteOrder = kindex; - #ifdef H5DEBUGIMPORT +#ifdef H5DEBUGIMPORT HDprintf("h5dump inputByteOrder %d\n", in->inputByteOrder); - #endif +#endif kindex = 4; } else if (!HDstrcmp(buffer, "H5T_STD_I32LE")) { - in->inputSize = 32; + in->inputSize = 32; in->configOptionVector[INPUT_SIZE] = 1; if ((kindex = OutputArchStrToInt("STD")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; if ((kindex = OutputByteOrderStrToInt("LE")) == -1) { - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err3); return (-1); } in->outputByteOrder = kindex; - #ifdef H5DEBUGIMPORT +#ifdef H5DEBUGIMPORT HDprintf("h5dump inputByteOrder %d\n", in->inputByteOrder); - #endif +#endif kindex = 4; } else if (!HDstrcmp(buffer, "H5T_STD_I64BE")) { - in->inputSize = 64; + in->inputSize = 64; in->configOptionVector[INPUT_SIZE] = 1; if ((kindex = OutputArchStrToInt("STD")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; if ((kindex = OutputByteOrderStrToInt("BE")) == -1) { - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err3); return (-1); } in->outputByteOrder = kindex; - #ifdef H5DEBUGIMPORT +#ifdef H5DEBUGIMPORT HDprintf("h5dump inputByteOrder %d\n", in->inputByteOrder); - #endif +#endif kindex = 4; } else if (!HDstrcmp(buffer, "H5T_STD_I64LE")) { - in->inputSize = 64; + in->inputSize = 64; in->configOptionVector[INPUT_SIZE] = 1; if ((kindex = OutputArchStrToInt("STD")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; if ((kindex = OutputByteOrderStrToInt("LE")) == -1) { - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err3); return (-1); } in->outputByteOrder = kindex; - #ifdef H5DEBUGIMPORT +#ifdef H5DEBUGIMPORT HDprintf("h5dump inputByteOrder %d\n", in->inputByteOrder); - #endif +#endif kindex = 4; } else if (!HDstrcmp(buffer, "H5T_STD_U8BE")) { - in->inputSize = 8; + in->inputSize = 8; in->configOptionVector[INPUT_SIZE] = 1; if ((kindex = OutputArchStrToInt("STD")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; if ((kindex = OutputByteOrderStrToInt("BE")) == -1) { - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err3); return (-1); } in->outputByteOrder = kindex; - #ifdef H5DEBUGIMPORT +#ifdef H5DEBUGIMPORT HDprintf("h5dump inputByteOrder %d\n", in->inputByteOrder); - #endif +#endif kindex = 7; } else if (!HDstrcmp(buffer, "H5T_STD_U8LE")) { - in->inputSize = 8; + in->inputSize = 8; in->configOptionVector[INPUT_SIZE] = 1; if ((kindex = OutputArchStrToInt("STD")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; if ((kindex = OutputByteOrderStrToInt("LE")) == -1) { - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err3); return (-1); } in->outputByteOrder = kindex; - #ifdef H5DEBUGIMPORT +#ifdef H5DEBUGIMPORT HDprintf("h5dump inputByteOrder %d\n", in->inputByteOrder); - #endif +#endif kindex = 7; } else if (!HDstrcmp(buffer, "H5T_STD_U16BE")) { - in->inputSize = 16; + in->inputSize = 16; in->configOptionVector[INPUT_SIZE] = 1; if ((kindex = OutputArchStrToInt("STD")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; if ((kindex = OutputByteOrderStrToInt("BE")) == -1) { - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err3); return (-1); } in->outputByteOrder = kindex; - #ifdef H5DEBUGIMPORT +#ifdef H5DEBUGIMPORT HDprintf("h5dump inputByteOrder %d\n", in->inputByteOrder); - #endif +#endif kindex = 7; } else if (!HDstrcmp(buffer, "H5T_STD_U16LE")) { - in->inputSize = 16; + in->inputSize = 16; in->configOptionVector[INPUT_SIZE] = 1; if ((kindex = OutputArchStrToInt("STD")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; if ((kindex = OutputByteOrderStrToInt("LE")) == -1) { - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err3); return (-1); } in->outputByteOrder = kindex; - #ifdef H5DEBUGIMPORT +#ifdef H5DEBUGIMPORT HDprintf("h5dump inputByteOrder %d\n", in->inputByteOrder); - #endif +#endif kindex = 7; } else if (!HDstrcmp(buffer, "H5T_STD_U32BE")) { - in->inputSize = 32; + in->inputSize = 32; in->configOptionVector[INPUT_SIZE] = 1; if ((kindex = OutputArchStrToInt("STD")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; if ((kindex = OutputByteOrderStrToInt("BE")) == -1) { - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err3); return (-1); } in->outputByteOrder = kindex; - #ifdef H5DEBUGIMPORT +#ifdef H5DEBUGIMPORT HDprintf("h5dump inputByteOrder %d\n", in->inputByteOrder); - #endif +#endif kindex = 7; } else if (!HDstrcmp(buffer, "H5T_STD_U32LE")) { - in->inputSize = 32; + in->inputSize = 32; in->configOptionVector[INPUT_SIZE] = 1; if ((kindex = OutputArchStrToInt("STD")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; if ((kindex = OutputByteOrderStrToInt("LE")) == -1) { - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err3); return (-1); } in->outputByteOrder = kindex; - #ifdef H5DEBUGIMPORT +#ifdef H5DEBUGIMPORT HDprintf("h5dump inputByteOrder %d\n", in->inputByteOrder); - #endif +#endif kindex = 7; } else if (!HDstrcmp(buffer, "H5T_STD_U64BE")) { - in->inputSize = 64; + in->inputSize = 64; in->configOptionVector[INPUT_SIZE] = 1; if ((kindex = OutputArchStrToInt("STD")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; if ((kindex = OutputByteOrderStrToInt("BE")) == -1) { - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err3); return (-1); } in->outputByteOrder = kindex; - #ifdef H5DEBUGIMPORT +#ifdef H5DEBUGIMPORT HDprintf("h5dump inputByteOrder %d\n", in->inputByteOrder); - #endif +#endif kindex = 7; } else if (!HDstrcmp(buffer, "H5T_STD_U64LE")) { - in->inputSize = 64; + in->inputSize = 64; in->configOptionVector[INPUT_SIZE] = 1; if ((kindex = OutputArchStrToInt("STD")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; if ((kindex = OutputByteOrderStrToInt("LE")) == -1) { - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err3); return (-1); } in->outputByteOrder = kindex; - #ifdef H5DEBUGIMPORT +#ifdef H5DEBUGIMPORT HDprintf("h5dump inputByteOrder %d\n", in->inputByteOrder); - #endif +#endif kindex = 7; } else if (!HDstrcmp(buffer, "H5T_NATIVE_SCHAR")) { - in->inputSize = 8; + in->inputSize = 8; in->configOptionVector[INPUT_SIZE] = 1; if ((kindex = OutputArchStrToInt("NATIVE")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; @@ -2993,11 +3005,11 @@ static int getInputClassType(struct Input *in, char * buffer) kindex = 4; } else if (!HDstrcmp(buffer, "H5T_NATIVE_UCHAR")) { - in->inputSize = 8; + in->inputSize = 8; in->configOptionVector[INPUT_SIZE] = 1; if ((kindex = OutputArchStrToInt("NATIVE")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; @@ -3005,11 +3017,11 @@ static int getInputClassType(struct Input *in, char * buffer) kindex = 7; } else if (!HDstrcmp(buffer, "H5T_NATIVE_SHORT")) { - in->inputSize = 16; + in->inputSize = 16; in->configOptionVector[INPUT_SIZE] = 1; if ((kindex = OutputArchStrToInt("NATIVE")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; @@ -3017,11 +3029,11 @@ static int getInputClassType(struct Input *in, char * buffer) kindex = 4; } else if (!HDstrcmp(buffer, "H5T_NATIVE_USHORT")) { - in->inputSize = 16; + in->inputSize = 16; in->configOptionVector[INPUT_SIZE] = 1; if ((kindex = OutputArchStrToInt("NATIVE")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; @@ -3029,11 +3041,11 @@ static int getInputClassType(struct Input *in, char * buffer) kindex = 7; } else if (!HDstrcmp(buffer, "H5T_NATIVE_INT")) { - in->inputSize = 32; + in->inputSize = 32; in->configOptionVector[INPUT_SIZE] = 1; if ((kindex = OutputArchStrToInt("NATIVE")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; @@ -3041,11 +3053,11 @@ static int getInputClassType(struct Input *in, char * buffer) kindex = 4; } else if (!HDstrcmp(buffer, "H5T_NATIVE_UINT")) { - in->inputSize = 32; + in->inputSize = 32; in->configOptionVector[INPUT_SIZE] = 1; if ((kindex = OutputArchStrToInt("NATIVE")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; @@ -3053,11 +3065,11 @@ static int getInputClassType(struct Input *in, char * buffer) kindex = 7; } else if (!HDstrcmp(buffer, "H5T_NATIVE_LONG")) { - in->inputSize = 32; + in->inputSize = 32; in->configOptionVector[INPUT_SIZE] = 1; if ((kindex = OutputArchStrToInt("NATIVE")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; @@ -3065,11 +3077,11 @@ static int getInputClassType(struct Input *in, char * buffer) kindex = 4; } else if (!HDstrcmp(buffer, "H5T_NATIVE_ULONG")) { - in->inputSize = 32; + in->inputSize = 32; in->configOptionVector[INPUT_SIZE] = 1; if ((kindex = OutputArchStrToInt("NATIVE")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; @@ -3077,11 +3089,11 @@ static int getInputClassType(struct Input *in, char * buffer) kindex = 7; } else if (!HDstrcmp(buffer, "H5T_NATIVE_LLONG")) { - in->inputSize = 64; + in->inputSize = 64; in->configOptionVector[INPUT_SIZE] = 1; if ((kindex = OutputArchStrToInt("NATIVE")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; @@ -3089,11 +3101,11 @@ static int getInputClassType(struct Input *in, char * buffer) kindex = 4; } else if (!HDstrcmp(buffer, "H5T_NATIVE_ULLONG")) { - in->inputSize = 64; + in->inputSize = 64; in->configOptionVector[INPUT_SIZE] = 1; if ((kindex = OutputArchStrToInt("NATIVE")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; @@ -3101,107 +3113,107 @@ static int getInputClassType(struct Input *in, char * buffer) kindex = 7; } else if (!HDstrcmp(buffer, "H5T_IEEE_F32BE")) { - in->inputSize = 32; + in->inputSize = 32; in->configOptionVector[INPUT_SIZE] = 1; if ((kindex = OutputArchStrToInt("IEEE")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; if ((kindex = OutputByteOrderStrToInt("BE")) == -1) { - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err3); return (-1); } in->outputByteOrder = kindex; - #ifdef H5DEBUGIMPORT +#ifdef H5DEBUGIMPORT HDprintf("h5dump inputByteOrder %d\n", in->inputByteOrder); - #endif +#endif kindex = 3; } else if (!HDstrcmp(buffer, "H5T_IEEE_F32LE")) { - in->inputSize = 32; + in->inputSize = 32; in->configOptionVector[INPUT_SIZE] = 1; if ((kindex = OutputArchStrToInt("IEEE")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; if ((kindex = OutputByteOrderStrToInt("LE")) == -1) { - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err3); return (-1); } in->outputByteOrder = kindex; - #ifdef H5DEBUGIMPORT +#ifdef H5DEBUGIMPORT HDprintf("h5dump inputByteOrder %d\n", in->inputByteOrder); - #endif +#endif kindex = 3; } else if (!HDstrcmp(buffer, "H5T_IEEE_F64BE")) { - in->inputSize = 64; + in->inputSize = 64; in->configOptionVector[INPUT_SIZE] = 1; if ((kindex = OutputArchStrToInt("IEEE")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; if ((kindex = OutputByteOrderStrToInt("BE")) == -1) { - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err3); return (-1); } in->outputByteOrder = kindex; - #ifdef H5DEBUGIMPORT +#ifdef H5DEBUGIMPORT HDprintf("h5dump inputByteOrder %d\n", in->inputByteOrder); - #endif +#endif kindex = 3; } else if (!HDstrcmp(buffer, "H5T_IEEE_F64LE")) { - in->inputSize = 64; + in->inputSize = 64; in->configOptionVector[INPUT_SIZE] = 1; if ((kindex = OutputArchStrToInt("IEEE")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; if ((kindex = OutputByteOrderStrToInt("LE")) == -1) { - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err3); return (-1); } in->outputByteOrder = kindex; - #ifdef H5DEBUGIMPORT +#ifdef H5DEBUGIMPORT HDprintf("h5dump inputByteOrder %d\n", in->inputByteOrder); - #endif +#endif kindex = 3; } else if (!HDstrcmp(buffer, "H5T_VAX_F32")) { - in->inputSize = 32; + in->inputSize = 32; in->configOptionVector[INPUT_SIZE] = 1; kindex = 3; } else if (!HDstrcmp(buffer, "H5T_VAX_F64")) { - in->inputSize = 64; + in->inputSize = 64; in->configOptionVector[INPUT_SIZE] = 1; kindex = 3; } else if (!HDstrcmp(buffer, "H5T_NATIVE_FLOAT")) { - in->inputSize = 32; + in->inputSize = 32; in->configOptionVector[INPUT_SIZE] = 1; if ((kindex = OutputArchStrToInt("NATIVE")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; @@ -3209,217 +3221,215 @@ static int getInputClassType(struct Input *in, char * buffer) kindex = 3; } else if (!HDstrcmp(buffer, "H5T_NATIVE_DOUBLE")) { - in->inputSize = 64; + in->inputSize = 64; in->configOptionVector[INPUT_SIZE] = 1; if ((kindex = OutputArchStrToInt("NATIVE")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; kindex = 3; } -#if H5_SIZEOF_LONG_DOUBLE !=0 else if (!HDstrcmp(buffer, "H5T_NATIVE_LDOUBLE")) { - in->inputSize = H5_SIZEOF_LONG_DOUBLE; + in->inputSize = H5_SIZEOF_LONG_DOUBLE; in->configOptionVector[INPUT_SIZE] = 1; if ((kindex = OutputArchStrToInt("NATIVE")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; kindex = 3; } -#endif - else if(!HDstrcmp(buffer, "H5T_TIME: not yet implemented")) { + else if (!HDstrcmp(buffer, "H5T_TIME: not yet implemented")) { kindex = -1; } - else if(!HDstrcmp(buffer, "H5T_STRING")) { + else if (!HDstrcmp(buffer, "H5T_STRING")) { kindex = 5; } /* case H5T_BITFIELD: */ else if (!HDstrcmp(buffer, "H5T_STD_B8BE")) { if ((kindex = OutputArchStrToInt("STD")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; if ((kindex = OutputByteOrderStrToInt("BE")) == -1) { - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err3); return (-1); } in->outputByteOrder = kindex; - #ifdef H5DEBUGIMPORT +#ifdef H5DEBUGIMPORT HDprintf("h5dump inputByteOrder %d\n", in->inputByteOrder); - #endif +#endif kindex = -1; } else if (!HDstrcmp(buffer, "H5T_STD_B8LE")) { if ((kindex = OutputArchStrToInt("STD")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; if ((kindex = OutputByteOrderStrToInt("LE")) == -1) { - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err3); return (-1); } in->outputByteOrder = kindex; - #ifdef H5DEBUGIMPORT +#ifdef H5DEBUGIMPORT HDprintf("h5dump inputByteOrder %d\n", in->inputByteOrder); - #endif +#endif kindex = -1; } else if (!HDstrcmp(buffer, "H5T_STD_B16BE")) { if ((kindex = OutputArchStrToInt("STD")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; if ((kindex = OutputByteOrderStrToInt("BE")) == -1) { - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err3); return (-1); } in->outputByteOrder = kindex; - #ifdef H5DEBUGIMPORT +#ifdef H5DEBUGIMPORT HDprintf("h5dump inputByteOrder %d\n", in->inputByteOrder); - #endif +#endif kindex = -1; } else if (!HDstrcmp(buffer, "H5T_STD_B16LE")) { if ((kindex = OutputArchStrToInt("STD")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; if ((kindex = OutputByteOrderStrToInt("LE")) == -1) { - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err3); return (-1); } in->outputByteOrder = kindex; - #ifdef H5DEBUGIMPORT +#ifdef H5DEBUGIMPORT HDprintf("h5dump inputByteOrder %d\n", in->inputByteOrder); - #endif +#endif kindex = -1; } else if (!HDstrcmp(buffer, "H5T_STD_B32BE")) { if ((kindex = OutputArchStrToInt("STD")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; if ((kindex = OutputByteOrderStrToInt("BE")) == -1) { - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err3); return (-1); } in->outputByteOrder = kindex; - #ifdef H5DEBUGIMPORT +#ifdef H5DEBUGIMPORT HDprintf("h5dump inputByteOrder %d\n", in->inputByteOrder); - #endif +#endif kindex = -1; } else if (!HDstrcmp(buffer, "H5T_STD_B32LE")) { if ((kindex = OutputArchStrToInt("STD")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; if ((kindex = OutputByteOrderStrToInt("LE")) == -1) { - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err3); return (-1); } in->outputByteOrder = kindex; - #ifdef H5DEBUGIMPORT +#ifdef H5DEBUGIMPORT HDprintf("h5dump inputByteOrder %d\n", in->inputByteOrder); - #endif +#endif kindex = -1; } else if (!HDstrcmp(buffer, "H5T_STD_B64BE")) { if ((kindex = OutputArchStrToInt("STD")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; if ((kindex = OutputByteOrderStrToInt("BE")) == -1) { - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err3); return (-1); } in->outputByteOrder = kindex; - #ifdef H5DEBUGIMPORT +#ifdef H5DEBUGIMPORT HDprintf("h5dump inputByteOrder %d\n", in->inputByteOrder); - #endif +#endif kindex = -1; } else if (!HDstrcmp(buffer, "H5T_STD_B64LE")) { if ((kindex = OutputArchStrToInt("STD")) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->outputArchitecture = kindex; if ((kindex = OutputByteOrderStrToInt("LE")) == -1) { - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err3); return (-1); } in->outputByteOrder = kindex; - #ifdef H5DEBUGIMPORT +#ifdef H5DEBUGIMPORT HDprintf("h5dump inputByteOrder %d\n", in->inputByteOrder); - #endif +#endif kindex = -1; } /* case H5T_OPAQUE: */ - else if(!HDstrcmp(buffer, "H5T_OPAQUE")) { + else if (!HDstrcmp(buffer, "H5T_OPAQUE")) { kindex = -1; } /* case H5T_COMPOUND: */ - else if(!HDstrcmp(buffer, "H5T_COMPOUND")) { + else if (!HDstrcmp(buffer, "H5T_COMPOUND")) { kindex = -1; } /* case H5T_REFERENCE: */ - else if(!HDstrcmp(buffer, "H5T_REFERENCE")) { + else if (!HDstrcmp(buffer, "H5T_REFERENCE")) { kindex = -1; } /* case H5T_ENUM: */ - else if(!HDstrcmp(buffer, "H5T_ENUM")) { + else if (!HDstrcmp(buffer, "H5T_ENUM")) { kindex = -1; } /* case H5T_VLEN: */ - else if(!HDstrcmp(buffer, "H5T_VLEN")) { + else if (!HDstrcmp(buffer, "H5T_VLEN")) { kindex = -1; } /* case H5T_ARRAY: */ - else if(!HDstrcmp(buffer, "H5T_ARRAY")) { + else if (!HDstrcmp(buffer, "H5T_ARRAY")) { kindex = -1; } if (kindex == -1) { - (void) HDfprintf(stderr, "%s", err1); + (void)HDfprintf(stderr, "%s", err1); return (-1); } @@ -3436,10 +3446,11 @@ static int getInputClassType(struct Input *in, char * buffer) return (0); } -static int InputClassStrToInt(char *temp) +static int +InputClassStrToInt(char *temp) { - int i; - char classKeywordTable[8][15] = { "TEXTIN", "TEXTFP", "TEXTFPE", "FP", "IN", "STR", "TEXTUIN", "UIN" }; + int i; + char classKeywordTable[8][15] = {"TEXTIN", "TEXTFP", "TEXTFPE", "FP", "IN", "STR", "TEXTUIN", "UIN"}; for (i = 0; i < 8; i++) if (!HDstrcmp(classKeywordTable[i], temp)) return i; @@ -3447,35 +3458,37 @@ static int InputClassStrToInt(char *temp) } /* same as getOutputSize. But defined separately for extensibility */ -static int getInputSize(struct Input *in, int ival) +static int +getInputSize(struct Input *in, int ival) { int i; - int inputSizeValidValues[4] = { 8, 16, 32, 64 }; - const char *err1 = "Invalid value for input size.\n"; + int inputSizeValidValues[4] = {8, 16, 32, 64}; + const char *err1 = "Invalid value for input size.\n"; for (i = 0; i < 4; i++) if (inputSizeValidValues[i] == ival) { in->inputSize = ival; return (0); } - (void) HDfprintf(stderr, "%s", err1); + (void)HDfprintf(stderr, "%s", err1); return (-1); } -static int getInputByteOrder(struct Input *in, FILE *strm) +static int +getInputByteOrder(struct Input *in, FILE *strm) { char temp[255]; int kindex; const char *err1 = "Unable to get 'string' value.\n"; const char *err2 = "Invalid value for input byte-order.\n"; - if (fscanf(strm, "%254s", temp) != 1) { - (void) HDfprintf(stderr, "%s", err1); + if (HDfscanf(strm, "%254s", temp) != 1) { + (void)HDfprintf(stderr, "%s", err1); return (-1); } if ((kindex = OutputByteOrderStrToInt(temp)) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } @@ -3483,15 +3496,16 @@ static int getInputByteOrder(struct Input *in, FILE *strm) return (0); } -static int getRank(struct Input *in, FILE *strm) +static int +getRank(struct Input *in, FILE *strm) { - int ival; + int ival; const char *err1 = "Unable to get integer value.\n"; const char *err2 = "Invalid value for rank.\n"; - if (fscanf(strm, "%d", (&ival)) != 1) { - (void) HDfprintf(stderr, "%s", err1); + if (HDfscanf(strm, "%d", (&ival)) != 1) { + (void)HDfprintf(stderr, "%s", err1); return (-1); } if (ival >= MIN_NUM_DIMENSION && ival <= MAX_NUM_DIMENSION) { @@ -3499,79 +3513,86 @@ static int getRank(struct Input *in, FILE *strm) return (0); } - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } /* same as getChunkedDimensionSizes. But defined separately for extensibility */ -static int getDimensionSizes(struct Input *in, FILE *strm) +static int +getDimensionSizes(struct Input *in, FILE *strm) { unsigned long long ullval; - int i = 0; + int i = 0; const char *err1 = "Unable to allocate dynamic memory.\n"; - const char *err2 = "No. of dimensions for which dimension sizes provided is not equal to provided rank.\n"; + const char *err2 = + "No. of dimensions for which dimension sizes provided is not equal to provided rank.\n"; - if ((in->sizeOfDimension = (hsize_t *) HDmalloc ((size_t) in->rank * sizeof(hsize_t))) == NULL) { - (void) HDfprintf(stderr, "%s", err1); + if ((in->sizeOfDimension = (hsize_t *)HDmalloc((size_t)in->rank * sizeof(hsize_t))) == NULL) { + (void)HDfprintf(stderr, "%s", err1); return (-1); } - while (fscanf(strm, "%llu", (&ullval)) == 1) + while (HDfscanf(strm, "%llu", (&ullval)) == 1) in->sizeOfDimension[i++] = ullval; if (in->rank != i) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } return (0); } /* same as getDimensionSizes. But defined separately for extensibility */ -static int getChunkedDimensionSizes(struct Input *in, FILE *strm) +static int +getChunkedDimensionSizes(struct Input *in, FILE *strm) { unsigned long long ullval; - int i = 0; + int i = 0; const char *err1 = "Unable to allocate dynamic memory.\n"; - const char *err2 = "No. of dimensions for which chunked dimension sizes provided is not equal to provided rank.\n"; + const char *err2 = + "No. of dimensions for which chunked dimension sizes provided is not equal to provided rank.\n"; const char *err3 = "The CHUNKED-DIMENSION-SIZES cannot exceed the sizes of DIMENSION-SIZES\n"; - if ((in->sizeOfChunk = (hsize_t *) HDmalloc ((size_t) in->rank * sizeof(hsize_t))) == NULL) { - (void) HDfprintf(stderr, "%s", err1); + if ((in->sizeOfChunk = (hsize_t *)HDmalloc((size_t)in->rank * sizeof(hsize_t))) == NULL) { + (void)HDfprintf(stderr, "%s", err1); return (-1); } - while (fscanf(strm, "%llu", (&ullval)) == 1) + while (HDfscanf(strm, "%llu", (&ullval)) == 1) in->sizeOfChunk[i++] = ullval; if (in->rank != i) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } for (i = 0; i < in->rank; i++) if (in->sizeOfChunk[i] > in->sizeOfDimension[i]) { - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err3); return (-1); } return (0); } -static int getMaximumDimensionSizes(struct Input *in, FILE *strm) +static int +getMaximumDimensionSizes(struct Input *in, FILE *strm) { long long llval; - int i = 0; + int i = 0; const char *err1 = "Unable to allocate dynamic memory.\n"; - const char *err2 = "No. of dimensions for which maximum dimension sizes provided is not equal to provided rank.\n"; - const char *err3 = "The MAXIMUM-DIMENSIONS cannot be less than the sizes of DIMENSION-SIZES. Exception: can be -1 to indicate unlimited size\n"; + const char *err2 = + "No. of dimensions for which maximum dimension sizes provided is not equal to provided rank.\n"; + const char *err3 = "The MAXIMUM-DIMENSIONS cannot be less than the sizes of DIMENSION-SIZES. Exception: " + "can be -1 to indicate unlimited size\n"; - if ((in->maxsizeOfDimension = (hsize_t *) HDmalloc ((size_t) in->rank * sizeof(hsize_t))) == NULL) { - (void) HDfprintf(stderr, "%s", err1); + if ((in->maxsizeOfDimension = (hsize_t *)HDmalloc((size_t)in->rank * sizeof(hsize_t))) == NULL) { + (void)HDfprintf(stderr, "%s", err1); return (-1); } - while (fscanf(strm, "%lld", (&llval)) == 1) { + while (HDfscanf(strm, "%lld", (&llval)) == 1) { if (llval == -1) in->maxsizeOfDimension[i++] = H5S_UNLIMITED; else @@ -3579,34 +3600,35 @@ static int getMaximumDimensionSizes(struct Input *in, FILE *strm) } if (in->rank != i) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } for (i = 0; i < in->rank; i++) { if (in->maxsizeOfDimension[i] != H5S_UNLIMITED) if (in->maxsizeOfDimension[i] < in->sizeOfDimension[i]) { - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err3); return (-1); } } return (0); } -static int getOutputArchitecture(struct Input *in, FILE *strm) +static int +getOutputArchitecture(struct Input *in, FILE *strm) { char temp[255]; int kindex; const char *err1 = "Unable to get 'string' value.\n"; const char *err2 = "Invalid value for output architecture.\n"; - if (fscanf(strm, "%254s", temp) != 1) { - (void) HDfprintf(stderr, "%s", err1); + if (HDfscanf(strm, "%254s", temp) != 1) { + (void)HDfprintf(stderr, "%s", err1); return (-1); } if ((kindex = OutputArchStrToInt(temp)) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } @@ -3614,31 +3636,32 @@ static int getOutputArchitecture(struct Input *in, FILE *strm) return (0); } -static int OutputArchStrToInt(const char *temp) +static int +OutputArchStrToInt(const char *temp) { - int i; - char outputArchKeywordTable[8][15] = { "NATIVE", "STD", "IEEE", "INTEL", - "CRAY", "MIPS", "ALPHA", "UNIX" }; + int i; + char outputArchKeywordTable[8][15] = {"NATIVE", "STD", "IEEE", "INTEL", "CRAY", "MIPS", "ALPHA", "UNIX"}; for (i = 0; i < 8; i++) if (!HDstrcmp(outputArchKeywordTable[i], temp)) return i; return -1; } -static int getOutputByteOrder(struct Input *in, FILE *strm) +static int +getOutputByteOrder(struct Input *in, FILE *strm) { char temp[255]; int kindex; const char *err1 = "Unable to get 'string' value.\n"; const char *err2 = "Invalid value for output byte-order.\n"; - if (fscanf(strm, "%254s", temp) != 1) { - (void) HDfprintf(stderr, "%s", err1); + if (HDfscanf(strm, "%254s", temp) != 1) { + (void)HDfprintf(stderr, "%s", err1); return (-1); } if ((kindex = OutputByteOrderStrToInt(temp)) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } @@ -3646,52 +3669,55 @@ static int getOutputByteOrder(struct Input *in, FILE *strm) return (0); } -static int OutputByteOrderStrToInt(const char *temp) +static int +OutputByteOrderStrToInt(const char *temp) { - int i; - char outputByteOrderKeywordTable[2][15] = { "BE", "LE" }; + int i; + char outputByteOrderKeywordTable[2][15] = {"BE", "LE"}; for (i = 0; i < 2; i++) if (!HDstrcmp(outputByteOrderKeywordTable[i], temp)) return i; return -1; } -static int getCompressionType(struct Input *in, FILE *strm) +static int +getCompressionType(struct Input *in, FILE *strm) { char temp[255]; int kindex; const char *err1 = "Unable to get 'string' value.\n"; const char *err2 = "Invalid value for compression.\n"; - if (fscanf(strm, "%254s", temp) != 1) { - (void) HDfprintf(stderr, "%s", err1); + if (HDfscanf(strm, "%254s", temp) != 1) { + (void)HDfprintf(stderr, "%s", err1); return (-1); } if ((kindex = CompressionTypeStrToInt(temp)) == -1) { - (void) HDfprintf(stderr, "%s", err2); + (void)HDfprintf(stderr, "%s", err2); return (-1); } in->compressionType = kindex; return (0); - } -static int CompressionTypeStrToInt(char *temp) +static int +CompressionTypeStrToInt(char *temp) { /* currently supports only GZIP */ /* can be extended by adding fields to the table */ - int i; - char CompressionTypeKeywordTable[1][15] = { "GZIP" }; + int i; + char CompressionTypeKeywordTable[1][15] = {"GZIP"}; for (i = 0; i < 1; i++) if (!HDstrcmp(CompressionTypeKeywordTable[i], temp)) return i; return -1; } -static int getCompressionParameter(struct Input *in, FILE *strm) +static int +getCompressionParameter(struct Input *in, FILE *strm) { /* currently supports only GZIP */ /* can be extended by adding more values to COMPRESSION-TYPE and */ @@ -3699,887 +3725,896 @@ static int getCompressionParameter(struct Input *in, FILE *strm) int ival; const char *err1 = "Unable to get integer value.\n"; - const char *err2 = "Invalid value for compression paramter.\n"; + const char *err2 = "Invalid value for compression parameter.\n"; const char *err3 = "Unsupported Compression Type.\n"; switch (in->compressionType) { - case 0: /* GZIP */ - if (fscanf(strm, "%d", (&ival)) != 1) { - (void) HDfprintf(stderr, "%s", err1); - return (-1); - } + case 0: /* GZIP */ + if (HDfscanf(strm, "%d", (&ival)) != 1) { + (void)HDfprintf(stderr, "%s", err1); + return (-1); + } - if (ival < 0 || ival > 9) { - (void) HDfprintf(stderr, "%s", err2); - return (-1); - } - in->compressionParam = ival; - return (0); + if (ival < 0 || ival > 9) { + (void)HDfprintf(stderr, "%s", err2); + return (-1); + } + in->compressionParam = ival; + return (0); - default: - (void) HDfprintf(stderr, "%s", err3); - return (-1); + default: + (void)HDfprintf(stderr, "%s", err3); + return (-1); } } -static int getExternalFilename(struct Input *in, FILE *strm) +static int +getExternalFilename(struct Input *in, FILE *strm) { + size_t temp_len; char temp[255]; const char *err1 = "Unable to get 'string' value.\n"; - if (fscanf(strm, "%254s", temp) != 1) { - (void) HDfprintf(stderr, "%s", err1); + if (HDfscanf(strm, "%254s", temp) != 1) { + (void)HDfprintf(stderr, "%s", err1); return (-1); } - in->externFilename = (char *) HDmalloc ((size_t) (HDstrlen(temp)) * sizeof(char)); - (void) HDstrcpy(in->externFilename, temp); + temp_len = HDstrlen(temp); + in->externFilename = (char *)HDmalloc((temp_len + 1) * sizeof(char)); + (void)HDstrcpy(in->externFilename, temp); + in->externFilename[temp_len] = '\0'; return (0); } -void setDefaultValues(struct Input *in, int count) +void +setDefaultValues(struct Input *in, int count) { - int i; - char temp[255]; - char num[255]; - - in->h5dumpInput = 0; - in->inputClass = 3; /* FP */ - in->inputSize = 32; - in->outputClass = 1; /* FP */ - in->outputSize = 32; + int i; + char temp[255]; + char num[255]; + + in->h5dumpInput = 0; + in->inputClass = 3; /* FP */ + in->inputSize = 32; + in->outputClass = 1; /* FP */ + in->outputSize = 32; in->inputByteOrder = -1; /* use default */ - in->rank = 0; - in->path.count = 1; + in->rank = 0; + in->path.count = 1; HDstrcpy(temp, "dataset"); - HDsprintf(num, "%d", count); + HDsnprintf(num, sizeof(num), "%d", count); HDstrcat(temp, num); HDstrcpy(in->path.group[0], temp); - in->outputArchitecture = 0; /* NATIVE */ - in->outputByteOrder = -1; /* use default */ - in->compressionType = 0; /* GZIP */ + in->outputArchitecture = 0; /* NATIVE */ + in->outputByteOrder = -1; /* use default */ + in->compressionType = 0; /* GZIP */ for (i = 0; i < NUM_KEYS; i++) in->configOptionVector[i] = 0; } -hid_t createOutputDataType(struct Input *in) +hid_t +createOutputDataType(struct Input *in) { hid_t new_type = (-1); - const char *err1 = "Invalid value for output class.\n"; - const char *err2 = "Invalid value for output size.\n"; - const char *err3 = "Invalid value for output byte order.\n"; - const char *err4 = "Invalid value for output architecture.\n"; - const char *err5 = "STD not supported for float.\n"; - const char *err6 = "IEEE not supported for INT.\n"; + const char *err1 = "Invalid value for output class.\n"; + const char *err2 = "Invalid value for output size.\n"; + const char *err3 = "Invalid value for output byte order.\n"; + const char *err4 = "Invalid value for output architecture.\n"; + const char *err5 = "STD not supported for float.\n"; + const char *err6 = "IEEE not supported for INT.\n"; switch (in->outputClass) { - case 0: - switch (in->outputArchitecture) { - case 0: /* NATIVE */ - switch (in->outputSize) { - case 8: - new_type = H5Tcopy(H5T_NATIVE_CHAR); - break; - - case 16: - new_type = H5Tcopy(H5T_NATIVE_SHORT); - break; + case 0: + switch (in->outputArchitecture) { + case 0: /* NATIVE */ + switch (in->outputSize) { + case 8: + new_type = H5Tcopy(H5T_NATIVE_CHAR); + break; - case 32: - new_type = H5Tcopy(H5T_NATIVE_INT); - break; + case 16: + new_type = H5Tcopy(H5T_NATIVE_SHORT); + break; - case 64: - new_type = H5Tcopy(H5T_NATIVE_LLONG); - break; + case 32: + new_type = H5Tcopy(H5T_NATIVE_INT); + break; - default: - (void) HDfprintf(stderr, "%s", err2); - return (-1); - } - switch (in->outputByteOrder) { - case -1: /* default */ - break; - case 0: - H5Tset_order(new_type, H5T_ORDER_BE); - break; + case 64: + new_type = H5Tcopy(H5T_NATIVE_LLONG); + break; - case 1: - H5Tset_order(new_type, H5T_ORDER_LE); - break; + default: + (void)HDfprintf(stderr, "%s", err2); + return (-1); + } + switch (in->outputByteOrder) { + case -1: /* default */ + break; + case 0: + H5Tset_order(new_type, H5T_ORDER_BE); + break; - default: - (void) HDfprintf(stderr, "%s", err3); - return (-1); - } - break; + case 1: + H5Tset_order(new_type, H5T_ORDER_LE); + break; - case 1: /* STD */ - switch (in->outputSize) { - case 8: - switch (in->outputByteOrder) { - case -1: - case 0: - new_type = H5Tcopy(H5T_STD_I8BE); + default: + (void)HDfprintf(stderr, "%s", err3); + return (-1); + } break; - case 1: - new_type = H5Tcopy(H5T_STD_I8LE); - break; + case 1: /* STD */ + switch (in->outputSize) { + case 8: + switch (in->outputByteOrder) { + case -1: + case 0: + new_type = H5Tcopy(H5T_STD_I8BE); + break; + + case 1: + new_type = H5Tcopy(H5T_STD_I8LE); + break; + + default: + (void)HDfprintf(stderr, "%s", err3); + return (-1); + } + break; - default: - (void) HDfprintf(stderr, "%s", err3); - return (-1); - } - break; + case 16: + switch (in->outputByteOrder) { + case -1: + case 0: + new_type = H5Tcopy(H5T_STD_I16BE); + break; - case 16: - switch (in->outputByteOrder) { - case -1: - case 0: - new_type = H5Tcopy(H5T_STD_I16BE); - break; + case 1: + new_type = H5Tcopy(H5T_STD_I16LE); + break; - case 1: - new_type = H5Tcopy(H5T_STD_I16LE); - break; + default: + (void)HDfprintf(stderr, "%s", err3); + return (-1); + } + break; - default: - (void) HDfprintf(stderr, "%s", err3); - return (-1); - } - break; + case 32: + switch (in->outputByteOrder) { + case -1: + case 0: + new_type = H5Tcopy(H5T_STD_I32BE); + break; - case 32: - switch (in->outputByteOrder) { - case -1: - case 0: - new_type = H5Tcopy(H5T_STD_I32BE); - break; + case 1: + new_type = H5Tcopy(H5T_STD_I32LE); + break; - case 1: - new_type = H5Tcopy(H5T_STD_I32LE); - break; + default: + (void)HDfprintf(stderr, "%s", err3); + return (-1); + } + break; - default: - (void) HDfprintf(stderr, "%s", err3); - return (-1); - } - break; + case 64: + switch (in->outputByteOrder) { + case -1: + case 0: + new_type = H5Tcopy(H5T_STD_I64BE); + break; - case 64: - switch (in->outputByteOrder) { - case -1: - case 0: - new_type = H5Tcopy(H5T_STD_I64BE); - break; + case 1: + new_type = H5Tcopy(H5T_STD_I64LE); + break; - case 1: - new_type = H5Tcopy(H5T_STD_I64LE); + default: + (void)HDfprintf(stderr, "%s", err3); + return (-1); + } + break; + + default: + (void)HDfprintf(stderr, "%s", err2); + return (-1); + } break; default: - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err4); return (-1); - } - break; - - default: - (void) HDfprintf(stderr, "%s", err2); - return (-1); } break; - default: - (void) HDfprintf(stderr, "%s", err4); - return (-1); - } - break; - - case 1: - switch (in->outputArchitecture) { - case 0: - switch (in->outputSize) { - case 32: - new_type = H5Tcopy(H5T_NATIVE_FLOAT); - break; - - case 64: - new_type = H5Tcopy(H5T_NATIVE_DOUBLE); - break; - - default: - (void) HDfprintf(stderr, "%s", err2); - return (-1); - } - switch (in->outputByteOrder) { - case -1: /* DEFAULT */ - break; - case 0: - H5Tset_order(new_type, H5T_ORDER_BE); - break; + case 1: + switch (in->outputArchitecture) { + case 0: + switch (in->outputSize) { + case 32: + new_type = H5Tcopy(H5T_NATIVE_FLOAT); + break; - case 1: - H5Tset_order(new_type, H5T_ORDER_LE); - break; + case 64: + new_type = H5Tcopy(H5T_NATIVE_DOUBLE); + break; - default: - (void) HDfprintf(stderr, "%s", err3); - return (-1); - } - break; + default: + (void)HDfprintf(stderr, "%s", err2); + return (-1); + } + switch (in->outputByteOrder) { + case -1: /* DEFAULT */ + break; + case 0: + H5Tset_order(new_type, H5T_ORDER_BE); + break; - case 1: - (void) HDfprintf(stderr, "%s", err5); - return (-1); + case 1: + H5Tset_order(new_type, H5T_ORDER_LE); + break; - case 2: - switch (in->outputSize) { - case 32: - switch (in->outputByteOrder) { - case -1: - case 0: - new_type = H5Tcopy(H5T_IEEE_F32BE); + default: + (void)HDfprintf(stderr, "%s", err3); + return (-1); + } break; case 1: - new_type = H5Tcopy(H5T_IEEE_F32LE); - break; - - default: - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err5); return (-1); - } - break; - case 64: - switch (in->outputByteOrder) { - case -1: - case 0: - new_type = H5Tcopy(H5T_IEEE_F64BE); - break; + case 2: + switch (in->outputSize) { + case 32: + switch (in->outputByteOrder) { + case -1: + case 0: + new_type = H5Tcopy(H5T_IEEE_F32BE); + break; + + case 1: + new_type = H5Tcopy(H5T_IEEE_F32LE); + break; + + default: + (void)HDfprintf(stderr, "%s", err3); + return (-1); + } + break; - case 1: - new_type = H5Tcopy(H5T_IEEE_F64LE); + case 64: + switch (in->outputByteOrder) { + case -1: + case 0: + new_type = H5Tcopy(H5T_IEEE_F64BE); + break; + + case 1: + new_type = H5Tcopy(H5T_IEEE_F64LE); + break; + + default: + (void)HDfprintf(stderr, "%s", err3); + return (-1); + } + break; + + default: + (void)HDfprintf(stderr, "%s", err2); + return (-1); + } break; default: - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err4); return (-1); - } - break; - - default: - (void) HDfprintf(stderr, "%s", err2); - return (-1); } break; - default: - (void) HDfprintf(stderr, "%s", err4); - return (-1); - } - break; - - case 2: - switch (in->outputArchitecture) { - case 0: - switch (in->outputSize) { - case 8: - new_type = H5Tcopy(H5T_NATIVE_UCHAR); - break; - - case 16: - new_type = H5Tcopy(H5T_NATIVE_USHORT); - break; + case 2: + switch (in->outputArchitecture) { + case 0: + switch (in->outputSize) { + case 8: + new_type = H5Tcopy(H5T_NATIVE_UCHAR); + break; - case 32: - new_type = H5Tcopy(H5T_NATIVE_UINT); - break; + case 16: + new_type = H5Tcopy(H5T_NATIVE_USHORT); + break; - case 64: - new_type = H5Tcopy(H5T_NATIVE_ULLONG); - break; + case 32: + new_type = H5Tcopy(H5T_NATIVE_UINT); + break; - default: - (void) HDfprintf(stderr, "%s", err2); - return (-1); - } - switch (in->outputByteOrder) { - case -1: /* Default */ - break; - case 0: - H5Tset_order(new_type, H5T_ORDER_BE); - break; + case 64: + new_type = H5Tcopy(H5T_NATIVE_ULLONG); + break; - case 1: - H5Tset_order(new_type, H5T_ORDER_LE); - break; + default: + (void)HDfprintf(stderr, "%s", err2); + return (-1); + } + switch (in->outputByteOrder) { + case -1: /* Default */ + break; + case 0: + H5Tset_order(new_type, H5T_ORDER_BE); + break; - default: - (void) HDfprintf(stderr, "%s", err3); - return (-1); - } - break; + case 1: + H5Tset_order(new_type, H5T_ORDER_LE); + break; - case 1: - switch (in->outputSize) { - case 8: - switch (in->outputByteOrder) { - case -1: - case 0: - new_type = H5Tcopy(H5T_STD_U8BE); + default: + (void)HDfprintf(stderr, "%s", err3); + return (-1); + } break; case 1: - new_type = H5Tcopy(H5T_STD_U8LE); - break; + switch (in->outputSize) { + case 8: + switch (in->outputByteOrder) { + case -1: + case 0: + new_type = H5Tcopy(H5T_STD_U8BE); + break; + + case 1: + new_type = H5Tcopy(H5T_STD_U8LE); + break; + + default: + (void)HDfprintf(stderr, "%s", err3); + return (-1); + } + break; - default: - (void) HDfprintf(stderr, "%s", err3); - return (-1); - } - break; + case 16: + switch (in->outputByteOrder) { + case -1: + case 0: + new_type = H5Tcopy(H5T_STD_U16BE); + break; - case 16: - switch (in->outputByteOrder) { - case -1: - case 0: - new_type = H5Tcopy(H5T_STD_U16BE); - break; + case 1: + new_type = H5Tcopy(H5T_STD_U16LE); + break; - case 1: - new_type = H5Tcopy(H5T_STD_U16LE); - break; + default: + (void)HDfprintf(stderr, "%s", err3); + return (-1); + } + break; - default: - (void) HDfprintf(stderr, "%s", err3); - return (-1); - } - break; + case 32: + switch (in->outputByteOrder) { + case -1: + case 0: + new_type = H5Tcopy(H5T_STD_U32BE); + break; - case 32: - switch (in->outputByteOrder) { - case -1: - case 0: - new_type = H5Tcopy(H5T_STD_U32BE); - break; + case 1: + new_type = H5Tcopy(H5T_STD_U32LE); + break; - case 1: - new_type = H5Tcopy(H5T_STD_U32LE); - break; + default: + (void)HDfprintf(stderr, "%s", err3); + return (-1); + } + break; - default: - (void) HDfprintf(stderr, "%s", err3); - return (-1); - } - break; + case 64: + switch (in->outputByteOrder) { + case -1: + case 0: + new_type = H5Tcopy(H5T_STD_U64BE); + break; - case 64: - switch (in->outputByteOrder) { - case -1: - case 0: - new_type = H5Tcopy(H5T_STD_U64BE); - break; + case 1: + new_type = H5Tcopy(H5T_STD_U64LE); + break; - case 1: - new_type = H5Tcopy(H5T_STD_U64LE); + default: + (void)HDfprintf(stderr, "%s", err3); + return (-1); + } + break; + + default: + (void)HDfprintf(stderr, "%s", err2); + return (-1); + } break; - default: - (void) HDfprintf(stderr, "%s", err3); + case 2: + (void)HDfprintf(stderr, "%s", err6); return (-1); - } - break; - default: - (void) HDfprintf(stderr, "%s", err2); - return (-1); + default: + (void)HDfprintf(stderr, "%s", err4); + return (-1); } break; - case 2: - (void) HDfprintf(stderr, "%s", err6); - return (-1); - default: - (void) HDfprintf(stderr, "%s", err4); + (void)HDfprintf(stderr, "%s", err1); return (-1); - } - break; - - default: - (void) HDfprintf(stderr, "%s", err1); - return (-1); } return new_type; } -hid_t createInputDataType(struct Input *in) +hid_t +createInputDataType(struct Input *in) { hid_t new_type = (-1); - const char *err1 = "Invalid value for input class.\n"; - const char *err2 = "Invalid value for input size.\n"; - const char *err3 = "Invalid value for input byte order.\n"; - const char *err4 = "Invalid value for output architecture.\n"; - const char *err5 = "STD not supported for float.\n"; - const char *err6 = "IEEE not supported for INT.\n"; + const char *err1 = "Invalid value for input class.\n"; + const char *err2 = "Invalid value for input size.\n"; + const char *err3 = "Invalid value for input byte order.\n"; + const char *err4 = "Invalid value for output architecture.\n"; + const char *err5 = "STD not supported for float.\n"; + const char *err6 = "IEEE not supported for INT.\n"; if (in->h5dumpInput) { switch (in->inputClass) { - case 4: - switch (in->inputArchitecture) { - case 0: /*NATIVE*/ - switch (in->inputSize) { - case 8: - new_type = H5Tcopy(H5T_NATIVE_CHAR); - break; - - case 16: - new_type = H5Tcopy(H5T_NATIVE_SHORT); - break; - - case 32: - new_type = H5Tcopy(H5T_NATIVE_INT); - break; - - case 64: - new_type = H5Tcopy(H5T_NATIVE_LLONG); - break; + case 4: + switch (in->inputArchitecture) { + case 0: /*NATIVE*/ + switch (in->inputSize) { + case 8: + new_type = H5Tcopy(H5T_NATIVE_CHAR); + break; + + case 16: + new_type = H5Tcopy(H5T_NATIVE_SHORT); + break; + + case 32: + new_type = H5Tcopy(H5T_NATIVE_INT); + break; + + case 64: + new_type = H5Tcopy(H5T_NATIVE_LLONG); + break; + + default: + (void)HDfprintf(stderr, "%s", err2); + return (-1); + } + switch (in->inputByteOrder) { + case -1: /* default */ + break; + case 0: + H5Tset_order(new_type, H5T_ORDER_BE); + break; + + case 1: + H5Tset_order(new_type, H5T_ORDER_LE); + break; + + default: + (void)HDfprintf(stderr, "%s", err3); + return (-1); + } + break; - default: - (void) HDfprintf(stderr, "%s", err2); - return (-1); - } - switch (in->inputByteOrder) { - case -1: /* default */ - break; - case 0: - H5Tset_order(new_type, H5T_ORDER_BE); - break; + case 1: /*STD*/ + switch (in->inputSize) { + case 8: + switch (in->inputByteOrder) { + case -1: + case 0: + new_type = H5Tcopy(H5T_STD_I8BE); + break; + + case 1: + new_type = H5Tcopy(H5T_STD_I8LE); + break; + + default: + (void)HDfprintf(stderr, "%s", err3); + return (-1); + } + break; + + case 16: + switch (in->inputByteOrder) { + case -1: + case 0: + new_type = H5Tcopy(H5T_STD_I16BE); + break; + + case 1: + new_type = H5Tcopy(H5T_STD_I16LE); + break; + + default: + (void)HDfprintf(stderr, "%s", err3); + return (-1); + } + break; + + case 32: + switch (in->inputByteOrder) { + case -1: + case 0: + new_type = H5Tcopy(H5T_STD_I32BE); + break; + + case 1: + new_type = H5Tcopy(H5T_STD_I32LE); + break; + + default: + (void)HDfprintf(stderr, "%s", err3); + return (-1); + } + break; + + case 64: + switch (in->inputByteOrder) { + case -1: + case 0: + new_type = H5Tcopy(H5T_STD_I64BE); + break; + + case 1: + new_type = H5Tcopy(H5T_STD_I64LE); + break; + + default: + (void)HDfprintf(stderr, "%s", err3); + return (-1); + } + break; - case 1: - H5Tset_order(new_type, H5T_ORDER_LE); - break; + default: + (void)HDfprintf(stderr, "%s", err2); + return (-1); + } + break; - default: - (void) HDfprintf(stderr, "%s", err3); - return (-1); + default: + (void)HDfprintf(stderr, "%s", err4); + return (-1); } break; - case 1: /*STD*/ - switch (in->inputSize) { - case 8: - switch (in->inputByteOrder) { - case -1: + case 3: + switch (in->inputArchitecture) { case 0: - new_type = H5Tcopy(H5T_STD_I8BE); + switch (in->inputSize) { + case 32: + new_type = H5Tcopy(H5T_NATIVE_FLOAT); + break; + + case 64: + new_type = H5Tcopy(H5T_NATIVE_DOUBLE); + break; + + default: + (void)HDfprintf(stderr, "%s", err2); + return (-1); + } + switch (in->inputByteOrder) { + case -1: /* DEFAULT */ + break; + case 0: + H5Tset_order(new_type, H5T_ORDER_BE); + break; + + case 1: + H5Tset_order(new_type, H5T_ORDER_LE); + break; + + default: + (void)HDfprintf(stderr, "%s", err3); + return (-1); + } break; case 1: - new_type = H5Tcopy(H5T_STD_I8LE); - break; - - default: - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err5); return (-1); - } - break; - case 16: - switch (in->inputByteOrder) { - case -1: - case 0: - new_type = H5Tcopy(H5T_STD_I16BE); - break; + case 2: + switch (in->inputSize) { + case 32: + switch (in->inputByteOrder) { + case -1: + case 0: + new_type = H5Tcopy(H5T_IEEE_F32BE); + break; + + case 1: + new_type = H5Tcopy(H5T_IEEE_F32LE); + break; + + default: + (void)HDfprintf(stderr, "%s", err3); + return (-1); + } + break; + + case 64: + switch (in->inputByteOrder) { + case -1: + case 0: + new_type = H5Tcopy(H5T_IEEE_F64BE); + break; + + case 1: + new_type = H5Tcopy(H5T_IEEE_F64LE); + break; + + default: + (void)HDfprintf(stderr, "%s", err3); + return (-1); + } + break; - case 1: - new_type = H5Tcopy(H5T_STD_I16LE); + default: + (void)HDfprintf(stderr, "%s", err2); + return (-1); + } break; default: - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err4); return (-1); - } - break; + } + break; - case 32: - switch (in->inputByteOrder) { - case -1: + case 7: + switch (in->inputArchitecture) { case 0: - new_type = H5Tcopy(H5T_STD_I32BE); + switch (in->inputSize) { + case 8: + new_type = H5Tcopy(H5T_NATIVE_UCHAR); + break; + + case 16: + new_type = H5Tcopy(H5T_NATIVE_USHORT); + break; + + case 32: + new_type = H5Tcopy(H5T_NATIVE_UINT); + break; + + case 64: + new_type = H5Tcopy(H5T_NATIVE_ULLONG); + break; + + default: + (void)HDfprintf(stderr, "%s", err2); + return (-1); + } + switch (in->inputByteOrder) { + case -1: /* Default */ + break; + case 0: + H5Tset_order(new_type, H5T_ORDER_BE); + break; + + case 1: + H5Tset_order(new_type, H5T_ORDER_LE); + break; + + default: + (void)HDfprintf(stderr, "%s", err3); + return (-1); + } break; case 1: - new_type = H5Tcopy(H5T_STD_I32LE); - break; - - default: - (void) HDfprintf(stderr, "%s", err3); - return (-1); - } - break; + switch (in->inputSize) { + case 8: + switch (in->inputByteOrder) { + case -1: + case 0: + new_type = H5Tcopy(H5T_STD_U8BE); + break; + + case 1: + new_type = H5Tcopy(H5T_STD_U8LE); + break; + + default: + (void)HDfprintf(stderr, "%s", err3); + return (-1); + } + break; + + case 16: + switch (in->inputByteOrder) { + case -1: + case 0: + new_type = H5Tcopy(H5T_STD_U16BE); + break; + + case 1: + new_type = H5Tcopy(H5T_STD_U16LE); + break; + + default: + (void)HDfprintf(stderr, "%s", err3); + return (-1); + } + break; + + case 32: + switch (in->inputByteOrder) { + case -1: + case 0: + new_type = H5Tcopy(H5T_STD_U32BE); + break; + + case 1: + new_type = H5Tcopy(H5T_STD_U32LE); + break; + + default: + (void)HDfprintf(stderr, "%s", err3); + return (-1); + } + break; + + case 64: + switch (in->inputByteOrder) { + case -1: + case 0: + new_type = H5Tcopy(H5T_STD_U64BE); + break; + + case 1: + new_type = H5Tcopy(H5T_STD_U64LE); + break; + + default: + (void)HDfprintf(stderr, "%s", err3); + return (-1); + } + break; - case 64: - switch (in->inputByteOrder) { - case -1: - case 0: - new_type = H5Tcopy(H5T_STD_I64BE); + default: + (void)HDfprintf(stderr, "%s", err2); + return (-1); + } break; - case 1: - new_type = H5Tcopy(H5T_STD_I64LE); - break; + case 2: + (void)HDfprintf(stderr, "%s", err6); + return (-1); default: - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err4); return (-1); - } - break; - - default: - (void) HDfprintf(stderr, "%s", err2); - return (-1); } break; default: - (void) HDfprintf(stderr, "%s", err4); + (void)HDfprintf(stderr, "%s", err1); return (-1); - } - break; - - case 3: - switch (in->inputArchitecture) { + } + } + else { + switch (in->inputClass) { case 0: + case 4: switch (in->inputSize) { - case 32: - new_type = H5Tcopy(H5T_NATIVE_FLOAT); - break; - - case 64: - new_type = H5Tcopy(H5T_NATIVE_DOUBLE); - break; - - default: - (void) HDfprintf(stderr, "%s", err2); - return (-1); - } - switch (in->inputByteOrder) { - case -1: /* DEFAULT */ - break; - case 0: - H5Tset_order(new_type, H5T_ORDER_BE); - break; - - case 1: - H5Tset_order(new_type, H5T_ORDER_LE); - break; - - default: - (void) HDfprintf(stderr, "%s", err3); - return (-1); - } - break; - - case 1: - (void) HDfprintf(stderr, "%s", err5); - return (-1); - - case 2: - switch (in->inputSize) { - case 32: - switch (in->inputByteOrder) { - case -1: - case 0: - new_type = H5Tcopy(H5T_IEEE_F32BE); + case 8: + new_type = H5Tcopy(H5T_NATIVE_CHAR); break; - case 1: - new_type = H5Tcopy(H5T_IEEE_F32LE); + case 16: + new_type = H5Tcopy(H5T_NATIVE_SHORT); break; - default: - (void) HDfprintf(stderr, "%s", err3); - return (-1); - } - break; - - case 64: - switch (in->inputByteOrder) { - case -1: - case 0: - new_type = H5Tcopy(H5T_IEEE_F64BE); + case 32: + new_type = H5Tcopy(H5T_NATIVE_INT); break; - case 1: - new_type = H5Tcopy(H5T_IEEE_F64LE); + case 64: + new_type = H5Tcopy(H5T_NATIVE_LLONG); break; default: - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err2); return (-1); - } - break; - - default: - (void) HDfprintf(stderr, "%s", err2); - return (-1); - } - break; - - default: - (void) HDfprintf(stderr, "%s", err4); - return (-1); - } - break; - - case 7: - switch (in->inputArchitecture) { - case 0: - switch (in->inputSize) { - case 8: - new_type = H5Tcopy(H5T_NATIVE_UCHAR); - break; - - case 16: - new_type = H5Tcopy(H5T_NATIVE_USHORT); - break; - - case 32: - new_type = H5Tcopy(H5T_NATIVE_UINT); - break; - - case 64: - new_type = H5Tcopy(H5T_NATIVE_ULLONG); - break; - - default: - (void) HDfprintf(stderr, "%s", err2); - return (-1); - } - switch (in->inputByteOrder) { - case -1: /* Default */ - break; - case 0: - H5Tset_order(new_type, H5T_ORDER_BE); - break; - - case 1: - H5Tset_order(new_type, H5T_ORDER_LE); - break; - - default: - (void) HDfprintf(stderr, "%s", err3); - return (-1); } break; case 1: + case 2: + case 3: switch (in->inputSize) { - case 8: - switch (in->inputByteOrder) { - case -1: - case 0: - new_type = H5Tcopy(H5T_STD_U8BE); + case 32: + new_type = H5Tcopy(H5T_NATIVE_FLOAT); break; - case 1: - new_type = H5Tcopy(H5T_STD_U8LE); + case 64: + new_type = H5Tcopy(H5T_NATIVE_DOUBLE); break; default: - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err2); return (-1); - } - break; + } + break; - case 16: - switch (in->inputByteOrder) { - case -1: - case 0: - new_type = H5Tcopy(H5T_STD_U16BE); - break; + case 5: + (void)HDfprintf(stderr, "%s", err1); + return (-1); + break; - case 1: - new_type = H5Tcopy(H5T_STD_U16LE); + case 6: + case 7: + switch (in->inputSize) { + case 8: + new_type = H5Tcopy(H5T_NATIVE_UCHAR); break; - default: - (void) HDfprintf(stderr, "%s", err3); - return (-1); - } - break; - - case 32: - switch (in->inputByteOrder) { - case -1: - case 0: - new_type = H5Tcopy(H5T_STD_U32BE); + case 16: + new_type = H5Tcopy(H5T_NATIVE_USHORT); break; - case 1: - new_type = H5Tcopy(H5T_STD_U32LE); + case 32: + new_type = H5Tcopy(H5T_NATIVE_UINT); break; - default: - (void) HDfprintf(stderr, "%s", err3); - return (-1); - } - break; - - case 64: - switch (in->inputByteOrder) { - case -1: - case 0: - new_type = H5Tcopy(H5T_STD_U64BE); - break; - - case 1: - new_type = H5Tcopy(H5T_STD_U64LE); + case 64: + new_type = H5Tcopy(H5T_NATIVE_ULLONG); break; default: - (void) HDfprintf(stderr, "%s", err3); + (void)HDfprintf(stderr, "%s", err2); return (-1); - } - break; - - default: - (void) HDfprintf(stderr, "%s", err2); - return (-1); } break; - case 2: - (void) HDfprintf(stderr, "%s", err6); - return (-1); - default: - (void) HDfprintf(stderr, "%s", err4); + (void)HDfprintf(stderr, "%s", err1); return (-1); - } - break; - - default: - (void) HDfprintf(stderr, "%s", err1); - return (-1); - } - } - else { - switch (in->inputClass) { - case 0: - case 4: - switch (in->inputSize) { - case 8: - new_type = H5Tcopy(H5T_NATIVE_CHAR); - break; - - case 16: - new_type = H5Tcopy(H5T_NATIVE_SHORT); - break; - - case 32: - new_type = H5Tcopy(H5T_NATIVE_INT); - break; - - case 64: - new_type = H5Tcopy(H5T_NATIVE_LLONG); - break; - - default: - (void) HDfprintf(stderr, "%s", err2); - return (-1); - } - break; - - case 1: - case 2: - case 3: - switch (in->inputSize) { - case 32: - new_type = H5Tcopy(H5T_NATIVE_FLOAT); - break; - - case 64: - new_type = H5Tcopy(H5T_NATIVE_DOUBLE); - break; - - default: - (void) HDfprintf(stderr, "%s", err2); - return (-1); - } - break; - - case 5: - (void) HDfprintf(stderr, "%s", err1); - return (-1); - break; - - case 6: - case 7: - switch (in->inputSize) { - case 8: - new_type = H5Tcopy(H5T_NATIVE_UCHAR); - break; - - case 16: - new_type = H5Tcopy(H5T_NATIVE_USHORT); - break; - - case 32: - new_type = H5Tcopy(H5T_NATIVE_UINT); - break; - - case 64: - new_type = H5Tcopy(H5T_NATIVE_ULLONG); - break; - - default: - (void) HDfprintf(stderr, "%s", err2); - return (-1); - } - break; - - default: - (void) HDfprintf(stderr, "%s", err1); - return (-1); } } return new_type; } -static int process(struct Options *opt) +static int +process(struct Options *opt) { - struct Input *in; - FILE *extfile; - hid_t file_id; - hid_t group_id; - hid_t handle; - hid_t dataset; - hid_t dataspace = (-1); - hid_t intype; - hid_t outtype; - hid_t proplist; - hsize_t numOfElements = 1; - int j; - int k; + struct Input *in; + FILE * extfile; + hid_t file_id; + hid_t group_id; + hid_t handle; + hid_t dataset; + hid_t dataspace = (-1); + hid_t intype; + hid_t outtype; + hid_t proplist; + hsize_t numOfElements = 1; + int j; + int k; const char *err1 = "Error creating HDF output file: %s.\n"; const char *err2 = "Error in processing the configuration file: %s.\n"; const char *err3 = "Error in reading the input file: %s.\n"; const char *err4 = "Error in creating or opening external file.\n"; - const char *err5 = "Error in creating the output data set. Dataset with the same name may exist at the specified path\n"; + const char *err5 = + "Error in creating the output data set. Dataset with the same name may exist at the specified path\n"; const char *err6 = "Error in writing the output data set.\n"; H5E_BEGIN_TRY { if ((file_id = H5Fopen(opt->outfile, H5F_ACC_RDWR, H5P_DEFAULT)) < 0) { if ((file_id = H5Fcreate(opt->outfile, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) == FAIL) { - (void) HDfprintf(stderr, err1, opt->outfile); + (void)HDfprintf(stderr, err1, opt->outfile); return (-1); } } @@ -4590,13 +4625,13 @@ static int process(struct Options *opt) in = &(opt->infiles[k].in); if (opt->infiles[k].config == 1) { if (processConfigurationFile(opt->infiles[k].configfile, in) == -1) { - (void) HDfprintf(stderr, err2, opt->infiles[k].configfile); + (void)HDfprintf(stderr, err2, opt->infiles[k].configfile); return (-1); } } if (processDataFile(opt->infiles[k].datafile, in, file_id) == -1) { - (void) HDfprintf(stderr, err3, opt->infiles[k].datafile); + (void)HDfprintf(stderr, err3, opt->infiles[k].datafile); return (-1); } @@ -4609,13 +4644,15 @@ static int process(struct Options *opt) { /* create parent groups */ if (in->path.count > 1) { - j = 0; + j = 0; handle = file_id; while (j < in->path.count - 1) { if ((group_id = H5Gopen2(handle, in->path.group[j], H5P_DEFAULT)) < 0) { - group_id = H5Gcreate2(handle, in->path.group[j++], H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + group_id = H5Gcreate2(handle, in->path.group[j++], H5P_DEFAULT, H5P_DEFAULT, + H5P_DEFAULT); for (; j < in->path.count - 1; j++) - group_id = H5Gcreate2(group_id, in->path.group[j], H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + group_id = H5Gcreate2(group_id, in->path.group[j], H5P_DEFAULT, H5P_DEFAULT, + H5P_DEFAULT); handle = group_id; break; } @@ -4625,7 +4662,7 @@ static int process(struct Options *opt) } else { handle = file_id; - j = 0; + j = 0; } /*enable error reporting */ @@ -4633,7 +4670,7 @@ static int process(struct Options *opt) H5E_END_TRY; /*create data type */ - intype = createInputDataType(in); + intype = createInputDataType(in); outtype = createOutputDataType(in); #ifdef H5DEBUGIMPORT HDprintf("process intype %ld outtype %ld\n", intype, outtype); @@ -4648,20 +4685,21 @@ static int process(struct Options *opt) } if (in->configOptionVector[COMPRESS] == 1) { - H5Pset_deflate(proplist, (unsigned) in->compressionParam); + H5Pset_deflate(proplist, (unsigned)in->compressionParam); } if (in->configOptionVector[EXTERNALSTORE] == 1) { - /* creating the external file if it doesnt exist */ + /* creating the external file if it doesn't exist */ if ((extfile = HDfopen(in->externFilename, "ab")) == NULL) { - (void) HDfprintf(stderr, "%s", err4); + (void)HDfprintf(stderr, "%s", err4); H5Pclose(proplist); H5Sclose(dataspace); H5Fclose(file_id); return (-1); } HDfclose(extfile); - H5Pset_external(proplist, in->externFilename, (off_t)0, numOfElements * (hsize_t)in->inputSize / 8); + H5Pset_external(proplist, in->externFilename, (off_t)0, + numOfElements * (hsize_t)in->inputSize / 8); } /* create dataspace */ @@ -4674,8 +4712,9 @@ static int process(struct Options *opt) H5E_BEGIN_TRY { /* create data set */ - if ((dataset = H5Dcreate2(handle, in->path.group[j], outtype, dataspace, H5P_DEFAULT, proplist, H5P_DEFAULT)) < 0) { - (void) HDfprintf(stderr, "%s", err5); + if ((dataset = H5Dcreate2(handle, in->path.group[j], outtype, dataspace, H5P_DEFAULT, + proplist, H5P_DEFAULT)) < 0) { + (void)HDfprintf(stderr, "%s", err5); H5Pclose(proplist); H5Sclose(dataspace); H5Fclose(file_id); @@ -4687,8 +4726,8 @@ static int process(struct Options *opt) H5E_END_TRY; /* write dataset */ - if (H5Dwrite(dataset, intype, H5S_ALL, H5S_ALL, H5P_DEFAULT, (VOIDP) in->data) < 0) { - (void) HDfprintf(stderr, "%s", err6); + if (H5Dwrite(dataset, intype, H5S_ALL, H5S_ALL, H5P_DEFAULT, (VOIDP)in->data) < 0) { + (void)HDfprintf(stderr, "%s", err6); H5Dclose(dataset); H5Pclose(proplist); H5Sclose(dataspace); @@ -4707,36 +4746,44 @@ static int process(struct Options *opt) return (0); } -uint16_t swap_uint16( uint16_t val) +uint16_t +swap_uint16(uint16_t val) { - return (val << 8) | (val >> 8); + return (uint16_t)((val << 8) | (val >> 8)); } -int16_t swap_int16(int16_t val) +int16_t +swap_int16(int16_t val) { - return (val << 8) | ((val >> 8) & 0xFF); + return (int16_t)((val << 8) | ((val >> 8) & 0xFF)); } -uint32_t swap_uint32(uint32_t val) +uint32_t +swap_uint32(uint32_t val) { val = ((val << 8) & 0xFF00FF00) | ((val >> 8) & 0xFF00FF); return (val << 16) | (val >> 16); } -int32_t swap_int32(int32_t val) +int32_t +swap_int32(int32_t val) { - val = ((val << 8) & 0xFF00FF00) | ((val >> 8) & 0xFF00FF); + val = (int32_t)(((uint32_t)(val << 8) & 0xFF00FF00) | ((val >> 8) & 0xFF00FF)); return (val << 16) | ((val >> 16) & 0xFFFF); } -int64_t swap_int64(int64_t val) +int64_t +swap_int64(int64_t val) { - val = ((val << 8) & 0xFF00FF00FF00FF00ULL) | ((val >> 8) & 0x00FF00FF00FF00FFULL); - val = ((val << 16) & 0xFFFF0000FFFF0000ULL) | ((val >> 16) & 0x0000FFFF0000FFFFULL); - return (val << 32) | ((val >> 32) & 0xFFFFFFFFULL); + val = (int64_t)(((uint64_t)(val << 8) & 0xFF00FF00FF00FF00ULL) | + ((uint64_t)(val >> 8) & 0x00FF00FF00FF00FFULL)); + val = (int64_t)(((uint64_t)(val << 16) & 0xFFFF0000FFFF0000ULL) | + ((uint64_t)(val >> 16) & 0x0000FFFF0000FFFFULL)); + return (int64_t)((uint64_t)(val << 32) | ((uint64_t)(val >> 32) & 0xFFFFFFFFULL)); } -uint64_t swap_uint64(uint64_t val) +uint64_t +swap_uint64(uint64_t val) { val = ((val << 8) & 0xFF00FF00FF00FF00ULL) | ((val >> 8) & 0x00FF00FF00FF00FFULL); val = ((val << 16) & 0xFFFF0000FFFF0000ULL) | ((val >> 16) & 0x0000FFFF0000FFFFULL); @@ -4751,414 +4798,295 @@ uint64_t swap_uint64(uint64_t val) * Print a helpful summary of command usage and features. */ -void help(char *name) +void +help(char *name) { - (void) HDfprintf(stdout, "Name:\n\n"); - (void) HDfprintf(stdout, "\t%s\n\n", name); - (void) HDfprintf(stdout, "\t TOOL NAME:\n"); - (void) HDfprintf(stdout, "\t %s\n", name); - (void) HDfprintf(stdout, "\t SYNTAX:\n"); - (void) HDfprintf(stdout, "\t %s -h[elp], OR\n", name); - (void) HDfprintf(stdout, - "\t %s <infile> -c[onfig] <configfile> [<infile> -c[config] <configfile>...]", name); - (void) HDfprintf(stdout, "\t\t\t\t -o[utfile] <outfile>\n\n"); - (void) HDfprintf(stdout, "\t PURPOSE:\n"); - (void) HDfprintf(stdout, - "\t To convert data stored in one or more ASCII or binary files\n"); - (void) HDfprintf(stdout, - "\t into one or more datasets (in accordance with the \n"); - (void) HDfprintf(stdout, - "\t user-specified type and storage properties) in an existing \n"); - (void) HDfprintf(stdout, "\t or new HDF5 file.\n\n"); - (void) HDfprintf(stdout, "\t DESCRIPTION:\n"); - (void) HDfprintf(stdout, - "\t The primary objective of the utility is to convert floating\n"); - (void) HDfprintf(stdout, - "\t point or integer data stored in ASCII text or binary form \n"); - (void) HDfprintf(stdout, - "\t into a data-set according to the type and storage properties\n"); - (void) HDfprintf(stdout, - "\t specified by the user. The utility can also accept ASCII\n"); - (void) HDfprintf(stdout, - "\t text files and store the contents in a compact form as an\n"); - (void) HDfprintf(stdout, "\t array of one-dimensional strings.\n\n"); - (void) HDfprintf(stdout, - "\t The input data to be written as a data-set can be provided\n"); - (void) HDfprintf(stdout, "\t to the utility in one of the following forms:\n"); - (void) HDfprintf(stdout, - "\t 1. ASCII text file with numeric data (floating point or \n"); - (void) HDfprintf(stdout, "\t integer data). \n"); - (void) HDfprintf(stdout, - "\t 2. Binary file with native floating point data (32-bit or \n"); - (void) HDfprintf(stdout, "\t 64-bit) \n"); - (void) HDfprintf(stdout, - "\t 3. Binary file with native integer (signed or unsigned)\n"); - (void) HDfprintf(stdout, "\t data (8-bit or 16-bit or 32-bit or 64-bit). \n"); - (void) HDfprintf(stdout, - "\t 4. ASCII text file containing strings (text data).\n"); - (void) HDfprintf(stdout, "\t \n"); - (void) HDfprintf(stdout, - "\t Every input file is associated with a configuration file \n"); - (void) HDfprintf(stdout, - "\t also provided as an input to the utility. (See Section \n"); - (void) HDfprintf(stdout, - "\t \"CONFIGURATION FILE\" to know how it is to be organized).\n"); - (void) HDfprintf(stdout, - "\t The class, size and dimensions of the input data is \n"); - (void) HDfprintf(stdout, - "\t specified in this configuration file. A point to note is\n"); - (void) HDfprintf(stdout, - "\t that the floating point data in the ASCII text file may be\n"); - (void) HDfprintf(stdout, - "\t organized in the fixed floating form (for example 323.56)\n"); - (void) HDfprintf(stdout, - "\t or in a scientific notation (for example 3.23E+02). A \n"); - (void) HDfprintf(stdout, - "\t different input-class specification is to be used for both\n"); - (void) HDfprintf(stdout, "\t forms.\n\n"); - (void) HDfprintf(stdout, - "\t The utility extracts the input data from the input file \n"); - (void) HDfprintf(stdout, - "\t according to the specified parameters and saves it into \n"); - (void) HDfprintf(stdout, "\t an H5 dataset. \n\n"); - (void) HDfprintf(stdout, - "\t The user can specify output type and storage properties in \n"); - (void) HDfprintf(stdout, - "\t the configuration file. The user is required to specify the \n"); - (void) HDfprintf(stdout, - "\t path of the dataset. If the groups in the path leading to \n"); - (void) HDfprintf(stdout, - "\t the data-set do not exist, the groups will be created by the\n"); - (void) HDfprintf(stdout, - "\t utility. If no group is specified, the dataset will be\n"); - (void) HDfprintf(stdout, "\t created under the root group.\n\n"); - (void) HDfprintf(stdout, - "\t In addition to the name, the user is also required to \n"); - (void) HDfprintf(stdout, - "\t provide the class and size of output data to be written to \n"); - (void) HDfprintf(stdout, - "\t the dataset and may optionally specify the output-architecture,\n"); - (void) HDfprintf(stdout, - "\t and the output-byte-order. If output-architecture is not \n"); - (void) HDfprintf(stdout, - "\t specified the default is NATIVE. Output-byte-orders are fixed\n"); - (void) HDfprintf(stdout, - "\t for some architectures and may be specified only if output-\n"); - (void) HDfprintf(stdout, "\t architecture is IEEE, UNIX or STD.\n\n"); - (void) HDfprintf(stdout, - "\t Also, layout and other storage properties such as \n"); - (void) HDfprintf(stdout, - "\t compression, external storage and extendible data-sets may be\n"); - (void) HDfprintf(stdout, - "\t optionally specified. The layout and storage properties \n"); - (void) HDfprintf(stdout, - "\t denote how raw data is to be organized on the disk. If these \n"); - (void) HDfprintf(stdout, - "\t options are not specified the default is Contiguous layout \n"); - (void) HDfprintf(stdout, "\t and storage.\n\n"); - (void) HDfprintf(stdout, - "\t The dataset can be organized in any of the following ways:\n"); - (void) HDfprintf(stdout, "\t 1. Contiguous.\n"); - (void) HDfprintf(stdout, "\t 2. Chunked.\n"); - (void) HDfprintf(stdout, - "\t 3. External Storage File (has to be contiguous)\n"); - (void) HDfprintf(stdout, - "\t 4. Extendible data sets (has to be chunked)\n"); - (void) HDfprintf(stdout, "\t 5. Compressed. (has to be chunked)\n"); - (void) HDfprintf(stdout, - "\t 6. Compressed & Extendible (has to be chunked)\n\n"); - (void) HDfprintf(stdout, - "\t If the user wants to store raw data in a non-HDF file then \n"); - (void) HDfprintf(stdout, - "\t the external storage file option is to be used and the name \n"); - (void) HDfprintf(stdout, "\t of the file is to be specified. \n\n"); - (void) HDfprintf(stdout, - "\t If the user wants the dimensions of the data-set to be\n"); - (void) HDfprintf(stdout, - "\t unlimited, the extendible data set option can be chosen. \n\n"); - (void) HDfprintf(stdout, - "\t The user may also specify the type of compression and the \n"); - (void) HDfprintf(stdout, - "\t level to which the data set must be compresses by setting \n"); - (void) HDfprintf(stdout, "\t the compressed option.\n\n"); - (void) HDfprintf(stdout, "\t SYNOPSIS:\n"); - (void) HDfprintf(stdout, "\t h5import -h[elp], OR\n"); - (void) HDfprintf( stdout, - "\t h5import <infile> -c[onfig] <configfile> \ + (void)HDfprintf(stdout, "Name:\n\n"); + (void)HDfprintf(stdout, "\t%s\n\n", name); + (void)HDfprintf(stdout, "\t TOOL NAME:\n"); + (void)HDfprintf(stdout, "\t %s\n", name); + (void)HDfprintf(stdout, "\t SYNTAX:\n"); + (void)HDfprintf(stdout, "\t %s -h[elp], OR\n", name); + (void)HDfprintf(stdout, "\t %s <infile> -c[onfig] <configfile> [<infile> -c[config] <configfile>...]", + name); + (void)HDfprintf(stdout, "\t\t\t\t -o[utfile] <outfile>\n\n"); + (void)HDfprintf(stdout, "\t PURPOSE:\n"); + (void)HDfprintf(stdout, "\t To convert data stored in one or more ASCII or binary files\n"); + (void)HDfprintf(stdout, "\t into one or more datasets (in accordance with the \n"); + (void)HDfprintf(stdout, "\t user-specified type and storage properties) in an existing \n"); + (void)HDfprintf(stdout, "\t or new HDF5 file.\n\n"); + (void)HDfprintf(stdout, "\t DESCRIPTION:\n"); + (void)HDfprintf(stdout, "\t The primary objective of the utility is to convert floating\n"); + (void)HDfprintf(stdout, "\t point or integer data stored in ASCII text or binary form \n"); + (void)HDfprintf(stdout, "\t into a data-set according to the type and storage properties\n"); + (void)HDfprintf(stdout, "\t specified by the user. The utility can also accept ASCII\n"); + (void)HDfprintf(stdout, "\t text files and store the contents in a compact form as an\n"); + (void)HDfprintf(stdout, "\t array of one-dimensional strings.\n\n"); + (void)HDfprintf(stdout, "\t The input data to be written as a data-set can be provided\n"); + (void)HDfprintf(stdout, "\t to the utility in one of the following forms:\n"); + (void)HDfprintf(stdout, "\t 1. ASCII text file with numeric data (floating point or \n"); + (void)HDfprintf(stdout, "\t integer data). \n"); + (void)HDfprintf(stdout, "\t 2. Binary file with native floating point data (32-bit or \n"); + (void)HDfprintf(stdout, "\t 64-bit) \n"); + (void)HDfprintf(stdout, "\t 3. Binary file with native integer (signed or unsigned)\n"); + (void)HDfprintf(stdout, "\t data (8-bit or 16-bit or 32-bit or 64-bit). \n"); + (void)HDfprintf(stdout, "\t 4. ASCII text file containing strings (text data).\n"); + (void)HDfprintf(stdout, "\t \n"); + (void)HDfprintf(stdout, "\t Every input file is associated with a configuration file \n"); + (void)HDfprintf(stdout, "\t also provided as an input to the utility. (See Section \n"); + (void)HDfprintf(stdout, "\t \"CONFIGURATION FILE\" to know how it is to be organized).\n"); + (void)HDfprintf(stdout, "\t The class, size and dimensions of the input data is \n"); + (void)HDfprintf(stdout, "\t specified in this configuration file. A point to note is\n"); + (void)HDfprintf(stdout, "\t that the floating point data in the ASCII text file may be\n"); + (void)HDfprintf(stdout, "\t organized in the fixed floating form (for example 323.56)\n"); + (void)HDfprintf(stdout, "\t or in a scientific notation (for example 3.23E+02). A \n"); + (void)HDfprintf(stdout, "\t different input-class specification is to be used for both\n"); + (void)HDfprintf(stdout, "\t forms.\n\n"); + (void)HDfprintf(stdout, "\t The utility extracts the input data from the input file \n"); + (void)HDfprintf(stdout, "\t according to the specified parameters and saves it into \n"); + (void)HDfprintf(stdout, "\t an H5 dataset. \n\n"); + (void)HDfprintf(stdout, "\t The user can specify output type and storage properties in \n"); + (void)HDfprintf(stdout, "\t the configuration file. The user is required to specify the \n"); + (void)HDfprintf(stdout, "\t path of the dataset. If the groups in the path leading to \n"); + (void)HDfprintf(stdout, "\t the data-set do not exist, the groups will be created by the\n"); + (void)HDfprintf(stdout, "\t utility. If no group is specified, the dataset will be\n"); + (void)HDfprintf(stdout, "\t created under the root group.\n\n"); + (void)HDfprintf(stdout, "\t In addition to the name, the user is also required to \n"); + (void)HDfprintf(stdout, "\t provide the class and size of output data to be written to \n"); + (void)HDfprintf(stdout, "\t the dataset and may optionally specify the output-architecture,\n"); + (void)HDfprintf(stdout, "\t and the output-byte-order. If output-architecture is not \n"); + (void)HDfprintf(stdout, "\t specified the default is NATIVE. Output-byte-orders are fixed\n"); + (void)HDfprintf(stdout, "\t for some architectures and may be specified only if output-\n"); + (void)HDfprintf(stdout, "\t architecture is IEEE, UNIX or STD.\n\n"); + (void)HDfprintf(stdout, "\t Also, layout and other storage properties such as \n"); + (void)HDfprintf(stdout, "\t compression, external storage and extendible data-sets may be\n"); + (void)HDfprintf(stdout, "\t optionally specified. The layout and storage properties \n"); + (void)HDfprintf(stdout, "\t denote how raw data is to be organized on the disk. If these \n"); + (void)HDfprintf(stdout, "\t options are not specified the default is Contiguous layout \n"); + (void)HDfprintf(stdout, "\t and storage.\n\n"); + (void)HDfprintf(stdout, "\t The dataset can be organized in any of the following ways:\n"); + (void)HDfprintf(stdout, "\t 1. Contiguous.\n"); + (void)HDfprintf(stdout, "\t 2. Chunked.\n"); + (void)HDfprintf(stdout, "\t 3. External Storage File (has to be contiguous)\n"); + (void)HDfprintf(stdout, "\t 4. Extendible data sets (has to be chunked)\n"); + (void)HDfprintf(stdout, "\t 5. Compressed. (has to be chunked)\n"); + (void)HDfprintf(stdout, "\t 6. Compressed & Extendible (has to be chunked)\n\n"); + (void)HDfprintf(stdout, "\t If the user wants to store raw data in a non-HDF file then \n"); + (void)HDfprintf(stdout, "\t the external storage file option is to be used and the name \n"); + (void)HDfprintf(stdout, "\t of the file is to be specified. \n\n"); + (void)HDfprintf(stdout, "\t If the user wants the dimensions of the data-set to be\n"); + (void)HDfprintf(stdout, "\t unlimited, the extendible data set option can be chosen. \n\n"); + (void)HDfprintf(stdout, "\t The user may also specify the type of compression and the \n"); + (void)HDfprintf(stdout, "\t level to which the data set must be compresses by setting \n"); + (void)HDfprintf(stdout, "\t the compressed option.\n\n"); + (void)HDfprintf(stdout, "\t SYNOPSIS:\n"); + (void)HDfprintf(stdout, "\t h5import -h[elp], OR\n"); + (void)HDfprintf(stdout, "\t h5import <infile> -c[onfig] <configfile> \ [<infile> -c[config] <confile2>...] -o[utfile] <outfile>\n\n"); - (void) HDfprintf(stdout, "\t -h[elp]:\n"); - (void) HDfprintf(stdout, - "\t Prints this summary of usage, and exits.\n\n"); - (void) HDfprintf(stdout, "\t <infile(s)>:\n"); - (void) HDfprintf(stdout, - "\t Name of the Input file(s), containing a \n"); - (void) HDfprintf(stdout, - "\t single n-dimensional floating point or integer array \n"); - (void) HDfprintf(stdout, - "\t in either ASCII text, native floating point(32-bit \n"); - (void) HDfprintf(stdout, - "\t or 64-bit) or native integer(8-bit or 16-bit or \n"); - (void) HDfprintf(stdout, - "\t 32-bit or 64-bit). Data to be specified in the order\n"); - (void) HDfprintf(stdout, "\t of fastest changing dimensions first.\n\n"); - (void) HDfprintf(stdout, "\t -c[config] <configfile>:\n"); - (void) HDfprintf(stdout, - "\t Every input file should be associated with a \n"); - (void) HDfprintf(stdout, - "\t configuration file and this is done by the -c option.\n"); - (void) HDfprintf(stdout, - "\t <configfile> is the name of the configuration file.\n"); - (void) HDfprintf(stdout, "\t (See Section \"CONFIGURATION FILE\")\n\n"); - (void) HDfprintf(stdout, "\t -o[utfile] <outfile>:\n"); - (void) HDfprintf(stdout, - "\t Name of the HDF5 output file. Data from one or more \n"); - (void) HDfprintf(stdout, - "\t input files are stored as one or more data sets in \n"); - (void) HDfprintf(stdout, - "\t <outfile>. The output file may be an existing file or \n"); - (void) HDfprintf(stdout, - "\t it maybe new in which case it will be created.\n\n\n"); - (void) HDfprintf(stdout, "\t CONFIGURATION FILE:\n"); - (void) HDfprintf(stdout, - "\t The configuration file is an ASCII text file and must be \n"); - (void) HDfprintf(stdout, - "\t the ddl formatted file (without data values) produced by h5dump \n"); - (void) HDfprintf(stdout, - "\t when used with the options '-o outfilename -b' of a single dataset (-d) \n"); - (void) HDfprintf(stdout, - "\t OR organized as \"CONFIG-KEYWORD VALUE\" pairs, one pair on each \n"); - (void) HDfprintf(stdout, "\t line.\n\n"); - (void) HDfprintf(stdout, - "\t The configuration file may have the following keywords each \n"); - (void) HDfprintf(stdout, "\t followed by an acceptable value.\n\n"); - (void) HDfprintf(stdout, "\t Required KEYWORDS:\n"); - (void) HDfprintf(stdout, "\t PATH\n"); - (void) HDfprintf(stdout, "\t INPUT-CLASS\n"); - (void) HDfprintf(stdout, "\t INPUT-SIZE\n"); - (void) HDfprintf(stdout, "\t INPUT-BYTE-ORDER\n"); - (void) HDfprintf(stdout, "\t RANK\n"); - (void) HDfprintf(stdout, "\t DIMENSION-SIZES\n"); - (void) HDfprintf(stdout, "\t OUTPUT-CLASS\n"); - (void) HDfprintf(stdout, "\t OUTPUT-SIZE\n\n"); - (void) HDfprintf(stdout, "\t Optional KEYWORDS:\n"); - (void) HDfprintf(stdout, "\t OUTPUT-ARCHITECTURE\n"); - (void) HDfprintf(stdout, "\t OUTPUT-BYTE-ORDER\n"); - (void) HDfprintf(stdout, "\t CHUNKED-DIMENSION-SIZES\n"); - (void) HDfprintf(stdout, "\t COMPRESSION-TYPE\n"); - (void) HDfprintf(stdout, "\t COMPRESSION-PARAM\n"); - (void) HDfprintf(stdout, "\t EXTERNAL-STORAGE\n"); - (void) HDfprintf(stdout, "\t MAXIMUM-DIMENSIONS\n\n\n"); - (void) HDfprintf(stdout, "\t Values for keywords:\n"); - (void) HDfprintf(stdout, "\t PATH:\n"); - (void) HDfprintf(stdout, "\t Strings separated by spaces to represent\n"); - (void) HDfprintf(stdout, "\t the path of the data-set. If the groups in\n"); - (void) HDfprintf(stdout, - "\t the path do not exist, they will be created. \n"); - (void) HDfprintf(stdout, "\t For example,\n"); - (void) HDfprintf(stdout, "\t PATH grp1/grp2/dataset1\n"); - (void) HDfprintf(stdout, "\t PATH: keyword\n"); - (void) HDfprintf(stdout, "\t grp1: group under the root. If\n"); - (void) HDfprintf(stdout, "\t non-existent will be created.\n"); - (void) HDfprintf(stdout, "\t grp2: group under grp1. If \n"); - (void) HDfprintf(stdout, "\t non-existent will be created \n"); - (void) HDfprintf(stdout, "\t under grp1.\n"); - (void) HDfprintf(stdout, "\t dataset1: the name of the data-set \n"); - (void) HDfprintf(stdout, "\t to be created.\n\n"); - (void) HDfprintf(stdout, "\t INPUT-CLASS:\n"); - (void) HDfprintf(stdout, "\t String denoting the type of input data.\n"); - (void) HDfprintf(stdout, "\t (\"TEXTIN\", \"TEXTFP\", \"FP\", \"IN\", \n"); - (void) HDfprintf(stdout, "\t \"STR\", \"TEXTUIN\", \"UIN\"). \n"); - (void) HDfprintf(stdout, - "\t INPUT-CLASS \"TEXTIN\" denotes an ASCII text \n"); - (void) HDfprintf(stdout, - "\t file with signed integer data in ASCII form,\n"); - (void) HDfprintf(stdout, - "\t INPUT-CLASS \"TEXTUIN\" denotes an ASCII text \n"); - (void) HDfprintf(stdout, - "\t file with unsigned integer data in ASCII form,\n"); - (void) HDfprintf(stdout, - "\t \"TEXTFP\" denotes an ASCII text file containing\n"); - (void) HDfprintf(stdout, "\t floating point data in the fixed notation\n"); - (void) HDfprintf(stdout, "\t (325.34),\n"); - (void) HDfprintf(stdout, - "\t \"FP\" denotes a floating point binary file,\n"); - (void) HDfprintf(stdout, - "\t \"IN\" denotes a signed integer binary file,\n"); - (void) HDfprintf(stdout, - "\t \"UIN\" denotes an unsigned integer binary file,\n"); - (void) HDfprintf(stdout, "\t & \"STR\" denotes an ASCII text file the \n"); - (void) HDfprintf(stdout, - "\t contents of which should be stored as an 1-D \n"); - (void) HDfprintf(stdout, "\t array of strings.\n"); - (void) HDfprintf(stdout, "\t If INPUT-CLASS is \"STR\", then RANK, \n"); - (void) HDfprintf(stdout, - "\t DIMENSION-SIZES, OUTPUT-CLASS, OUTPUT-SIZE, \n"); - (void) HDfprintf(stdout, "\t OUTPUT-ARCHITECTURE and OUTPUT-BYTE-ORDER \n"); - (void) HDfprintf(stdout, "\t will be ignored.\n\n\n"); - (void) HDfprintf(stdout, "\t INPUT-SIZE:\n"); - (void) HDfprintf(stdout, - "\t Integer denoting the size of the input data \n"); - (void) HDfprintf(stdout, "\t (8, 16, 32, 64). \n\n"); - (void) HDfprintf(stdout, "\t For floating point,\n"); - (void) HDfprintf(stdout, "\t INPUT-SIZE can be 32 or 64.\n"); - (void) HDfprintf(stdout, "\t For integers (signed and unsigned)\n"); - (void) HDfprintf(stdout, "\t INPUT-SIZE can be 8, 16, 32 or 64.\n\n"); - (void) HDfprintf(stdout, "\t RANK:\n"); - (void) HDfprintf(stdout, - "\t Integer denoting the number of dimensions.\n\n"); - (void) HDfprintf(stdout, "\t DIMENSION-SIZES:\n"); - (void) HDfprintf(stdout, - "\t Integers separated by spaces to denote the \n"); - (void) HDfprintf(stdout, "\t dimension sizes for the no. of dimensions \n"); - (void) HDfprintf(stdout, "\t determined by rank.\n\n"); - (void) HDfprintf(stdout, "\t OUTPUT-CLASS:\n"); - (void) HDfprintf(stdout, - "\t String dentoting data type of the dataset to \n"); - (void) HDfprintf(stdout, "\t be written (\"IN\",\"FP\", \"UIN\")\n\n"); - (void) HDfprintf(stdout, "\t OUTPUT-SIZE:\n"); - (void) HDfprintf(stdout, - "\t Integer denoting the size of the data in the \n"); - (void) HDfprintf(stdout, "\t output dataset to be written.\n"); - (void) HDfprintf(stdout, - "\t If OUTPUT-CLASS is \"FP\", OUTPUT-SIZE can be \n"); - (void) HDfprintf(stdout, "\t 32 or 64.\n"); - (void) HDfprintf(stdout, - "\t If OUTPUT-CLASS is \"IN\" or \"UIN\", OUTPUT-SIZE\n"); - (void) HDfprintf(stdout, "\t can be 8, 16, 32 or 64.\n\n"); - (void) HDfprintf(stdout, "\t OUTPUT-ARCHITECTURE:\n"); - (void) HDfprintf(stdout, "\t STRING denoting the type of output \n"); - (void) HDfprintf(stdout, - "\t architecture. Can accept the following values\n"); - (void) HDfprintf(stdout, "\t STD\n"); - (void) HDfprintf(stdout, "\t IEEE\n"); - (void) HDfprintf(stdout, "\t INTEL\n"); - (void) HDfprintf(stdout, "\t CRAY\n"); - (void) HDfprintf(stdout, "\t MIPS\n"); - (void) HDfprintf(stdout, "\t ALPHA\n"); - (void) HDfprintf(stdout, "\t NATIVE (default)\n"); - (void) HDfprintf(stdout, "\t UNIX\n\n"); - (void) HDfprintf(stdout, "\t OUTPUT-BYTE-ORDER:\n"); - (void) HDfprintf(stdout, - "\t String denoting the output-byte-order. Ignored\n"); - (void) HDfprintf(stdout, - "\t if the OUTPUT-ARCHITECTURE is not specified or\n"); - (void) HDfprintf(stdout, "\t if it is IEEE, UNIX or STD. Can accept the \n"); - (void) HDfprintf(stdout, "\t following values.\n"); - (void) HDfprintf(stdout, "\t BE (default)\n"); - (void) HDfprintf(stdout, "\t LE\n\n"); - (void) HDfprintf(stdout, "\t CHUNKED-DIMENSION-SIZES:\n"); - (void) HDfprintf(stdout, "\t Integers separated by spaces to denote the \n"); - (void) HDfprintf(stdout, - "\t dimension sizes of the chunk for the no. of \n"); - (void) HDfprintf(stdout, - "\t dimensions determined by rank. Required field\n"); - (void) HDfprintf(stdout, - "\t to denote that the dataset will be stored with\n"); - (void) HDfprintf(stdout, - "\t chunked storage. If this field is absent the\n"); - (void) HDfprintf(stdout, - "\t dataset will be stored with contiguous storage.\n\n"); - (void) HDfprintf(stdout, "\t COMPRESSION-TYPE:\n"); - (void) HDfprintf(stdout, - "\t String denoting the type of compression to be\n"); - (void) HDfprintf(stdout, "\t used with the chunked storage. Requires the\n"); - (void) HDfprintf(stdout, - "\t CHUNKED-DIMENSION-SIZES to be specified. The only \n"); - (void) HDfprintf(stdout, - "\t currently supported compression method is GZIP. \n"); - (void) HDfprintf(stdout, "\t Will accept the following value\n"); - (void) HDfprintf(stdout, "\t GZIP\n\n"); - (void) HDfprintf(stdout, "\t COMPRESSION-PARAM:\n"); - (void) HDfprintf(stdout, - "\t Integer used to denote compression level and \n"); - (void) HDfprintf(stdout, "\t this option is to be always specified when \n"); - (void) HDfprintf(stdout, - "\t the COMPRESSION-TYPE option is specified. The\n"); - (void) HDfprintf(stdout, "\t values are applicable only to GZIP \n"); - (void) HDfprintf(stdout, "\t compression.\n"); - (void) HDfprintf(stdout, "\t Value 1-9: The level of Compression. \n"); - (void) HDfprintf(stdout, "\t 1 will result in the fastest \n"); - (void) HDfprintf(stdout, "\t compression while 9 will result in \n"); - (void) HDfprintf(stdout, "\t the best compression ratio. The default\n"); - (void) HDfprintf(stdout, "\t level of compression is 6.\n\n"); - (void) HDfprintf(stdout, "\t EXTERNAL-STORAGE:\n"); - (void) HDfprintf(stdout, - "\t String to denote the name of the non-HDF5 file \n"); - (void) HDfprintf(stdout, - "\t to store data to. Cannot be used if CHUNKED-\n"); - (void) HDfprintf(stdout, - "\t DIMENSIONS or COMPRESSION-TYPE or EXTENDIBLE-\n"); - (void) HDfprintf(stdout, "\t DATASET is specified.\n"); - (void) HDfprintf(stdout, "\t Value <external-filename>: the name of the \n"); - (void) HDfprintf(stdout, "\t external file as a string to be used.\n\n"); - (void) HDfprintf(stdout, "\t MAXIMUM-DIMENSIONS:\n"); - (void) HDfprintf(stdout, "\t Integers separated by spaces to denote the \n"); - (void) HDfprintf(stdout, "\t maximum dimension sizes of all the \n"); - (void) HDfprintf(stdout, "\t dimensions determined by rank. Requires the\n"); - (void) HDfprintf(stdout, - "\t CHUNKED-DIMENSION-SIZES to be specified. A value of \n"); - (void) HDfprintf(stdout, "\t -1 for any dimension implies UNLIMITED \n"); - (void) HDfprintf(stdout, - "\t DIMENSION size for that particular dimension.\n\n"); - (void) HDfprintf(stdout, "\t EXAMPLES:\n"); - (void) HDfprintf(stdout, "\t 1. Configuration File may look like:\n\n"); - (void) HDfprintf(stdout, "\t PATH work h5 pkamat First-set\n"); - (void) HDfprintf(stdout, "\t INPUT-CLASS TEXTFP\n"); - (void) HDfprintf(stdout, "\t RANK 3\n"); - (void) HDfprintf(stdout, "\t DIMENSION-SIZES 5 2 4\n"); - (void) HDfprintf(stdout, "\t OUTPUT-CLASS FP\n"); - (void) HDfprintf(stdout, "\t OUTPUT-SIZE 64\n"); - (void) HDfprintf(stdout, "\t OUTPUT-ARCHITECTURE IEEE\n"); - (void) HDfprintf(stdout, "\t OUTPUT-BYTE-ORDER LE\n"); - (void) HDfprintf(stdout, "\t CHUNKED-DIMENSION-SIZES 2 2 2 \n\n"); - (void) HDfprintf(stdout, - "\t The above configuration will accept a floating point array \n"); - (void) HDfprintf(stdout, - "\t (5 x 2 x 4) in an ASCII file with the rank and dimension sizes \n"); - (void) HDfprintf(stdout, - "\t specified and will save it in a chunked data-set (of pattern \n"); - (void) HDfprintf(stdout, - "\t 2 X 2 X 2) of 64-bit floating point in the little-endian order \n"); - (void) HDfprintf(stdout, - "\t and IEEE architecture. The dataset will be stored at\n"); - (void) HDfprintf(stdout, "\t \"/work/h5/pkamat/First-set\"\n\n"); - (void) HDfprintf(stdout, "\t 2. Another configuration could be:\n\n"); - (void) HDfprintf(stdout, "\t PATH Second-set\n"); - (void) HDfprintf(stdout, "\t INPUT-CLASS IN \n"); - (void) HDfprintf(stdout, "\t RANK 5\n"); - (void) HDfprintf(stdout, "\t DIMENSION-SIZES 6 3 5 2 4\n"); - (void) HDfprintf(stdout, "\t OUTPUT-CLASS IN\n"); - (void) HDfprintf(stdout, "\t OUTPUT-SIZE 32\n"); - (void) HDfprintf(stdout, "\t CHUNKED-DIMENSION-SIZES 2 2 2 2 2\n"); - (void) HDfprintf(stdout, "\t EXTENDIBLE-DATASET 1 3 \n"); - (void) HDfprintf(stdout, "\t COMPRESSION-TYPE GZIP\n"); - (void) HDfprintf(stdout, "\t COMPRESSION-PARAM 7\n\n\n"); - (void) HDfprintf(stdout, - "\t The above configuration will accept an integer array \n"); - (void) HDfprintf(stdout, - "\t (6 X 3 X 5 x 2 x 4) in a binary file with the rank and \n"); - (void) HDfprintf(stdout, - "\t dimension sizes specified and will save it in a chunked data-set\n"); - (void) HDfprintf(stdout, - "\t (of pattern 2 X 2 X 2 X 2 X 2) of 32-bit floating point in \n"); - (void) HDfprintf(stdout, - "\t native format (as output-architecture is not specified). The \n"); - (void) HDfprintf(stdout, - "\t first and the third dimension will be defined as unlimited. The \n"); - (void) HDfprintf(stdout, - "\t data-set will be compressed using GZIP and a compression level \n"); - (void) HDfprintf(stdout, "\t of 7.\n"); - (void) HDfprintf(stdout, - "\t The dataset will be stored at \"/Second-set\"\n\n"); - return; + (void)HDfprintf(stdout, "\t -h[elp]:\n"); + (void)HDfprintf(stdout, "\t Prints this summary of usage, and exits.\n\n"); + (void)HDfprintf(stdout, "\t <infile(s)>:\n"); + (void)HDfprintf(stdout, "\t Name of the Input file(s), containing a \n"); + (void)HDfprintf(stdout, "\t single n-dimensional floating point or integer array \n"); + (void)HDfprintf(stdout, "\t in either ASCII text, native floating point(32-bit \n"); + (void)HDfprintf(stdout, "\t or 64-bit) or native integer(8-bit or 16-bit or \n"); + (void)HDfprintf(stdout, "\t 32-bit or 64-bit). Data to be specified in the order\n"); + (void)HDfprintf(stdout, "\t of fastest changing dimensions first.\n\n"); + (void)HDfprintf(stdout, "\t -c[config] <configfile>:\n"); + (void)HDfprintf(stdout, "\t Every input file should be associated with a \n"); + (void)HDfprintf(stdout, "\t configuration file and this is done by the -c option.\n"); + (void)HDfprintf(stdout, "\t <configfile> is the name of the configuration file.\n"); + (void)HDfprintf(stdout, "\t (See Section \"CONFIGURATION FILE\")\n\n"); + (void)HDfprintf(stdout, "\t -o[utfile] <outfile>:\n"); + (void)HDfprintf(stdout, "\t Name of the HDF5 output file. Data from one or more \n"); + (void)HDfprintf(stdout, "\t input files are stored as one or more data sets in \n"); + (void)HDfprintf(stdout, "\t <outfile>. The output file may be an existing file or \n"); + (void)HDfprintf(stdout, "\t it maybe new in which case it will be created.\n\n\n"); + (void)HDfprintf(stdout, "\t CONFIGURATION FILE:\n"); + (void)HDfprintf(stdout, "\t The configuration file is an ASCII text file and must be \n"); + (void)HDfprintf(stdout, "\t the ddl formatted file (without data values) produced by h5dump \n"); + (void)HDfprintf(stdout, "\t when used with the options '-o outfilename -b' of a single dataset (-d) \n"); + (void)HDfprintf(stdout, "\t OR organized as \"CONFIG-KEYWORD VALUE\" pairs, one pair on each \n"); + (void)HDfprintf(stdout, "\t line.\n\n"); + (void)HDfprintf(stdout, "\t The configuration file may have the following keywords each \n"); + (void)HDfprintf(stdout, "\t followed by an acceptable value.\n\n"); + (void)HDfprintf(stdout, "\t Required KEYWORDS:\n"); + (void)HDfprintf(stdout, "\t PATH\n"); + (void)HDfprintf(stdout, "\t INPUT-CLASS\n"); + (void)HDfprintf(stdout, "\t INPUT-SIZE\n"); + (void)HDfprintf(stdout, "\t INPUT-BYTE-ORDER\n"); + (void)HDfprintf(stdout, "\t RANK\n"); + (void)HDfprintf(stdout, "\t DIMENSION-SIZES\n"); + (void)HDfprintf(stdout, "\t OUTPUT-CLASS\n"); + (void)HDfprintf(stdout, "\t OUTPUT-SIZE\n\n"); + (void)HDfprintf(stdout, "\t Optional KEYWORDS:\n"); + (void)HDfprintf(stdout, "\t OUTPUT-ARCHITECTURE\n"); + (void)HDfprintf(stdout, "\t OUTPUT-BYTE-ORDER\n"); + (void)HDfprintf(stdout, "\t CHUNKED-DIMENSION-SIZES\n"); + (void)HDfprintf(stdout, "\t COMPRESSION-TYPE\n"); + (void)HDfprintf(stdout, "\t COMPRESSION-PARAM\n"); + (void)HDfprintf(stdout, "\t EXTERNAL-STORAGE\n"); + (void)HDfprintf(stdout, "\t MAXIMUM-DIMENSIONS\n\n\n"); + (void)HDfprintf(stdout, "\t Values for keywords:\n"); + (void)HDfprintf(stdout, "\t PATH:\n"); + (void)HDfprintf(stdout, "\t Strings separated by spaces to represent\n"); + (void)HDfprintf(stdout, "\t the path of the data-set. If the groups in\n"); + (void)HDfprintf(stdout, "\t the path do not exist, they will be created. \n"); + (void)HDfprintf(stdout, "\t For example,\n"); + (void)HDfprintf(stdout, "\t PATH grp1/grp2/dataset1\n"); + (void)HDfprintf(stdout, "\t PATH: keyword\n"); + (void)HDfprintf(stdout, "\t grp1: group under the root. If\n"); + (void)HDfprintf(stdout, "\t non-existent will be created.\n"); + (void)HDfprintf(stdout, "\t grp2: group under grp1. If \n"); + (void)HDfprintf(stdout, "\t non-existent will be created \n"); + (void)HDfprintf(stdout, "\t under grp1.\n"); + (void)HDfprintf(stdout, "\t dataset1: the name of the data-set \n"); + (void)HDfprintf(stdout, "\t to be created.\n\n"); + (void)HDfprintf(stdout, "\t INPUT-CLASS:\n"); + (void)HDfprintf(stdout, "\t String denoting the type of input data.\n"); + (void)HDfprintf(stdout, "\t (\"TEXTIN\", \"TEXTFP\", \"FP\", \"IN\", \n"); + (void)HDfprintf(stdout, "\t \"STR\", \"TEXTUIN\", \"UIN\"). \n"); + (void)HDfprintf(stdout, "\t INPUT-CLASS \"TEXTIN\" denotes an ASCII text \n"); + (void)HDfprintf(stdout, "\t file with signed integer data in ASCII form,\n"); + (void)HDfprintf(stdout, "\t INPUT-CLASS \"TEXTUIN\" denotes an ASCII text \n"); + (void)HDfprintf(stdout, "\t file with unsigned integer data in ASCII form,\n"); + (void)HDfprintf(stdout, "\t \"TEXTFP\" denotes an ASCII text file containing\n"); + (void)HDfprintf(stdout, "\t floating point data in the fixed notation\n"); + (void)HDfprintf(stdout, "\t (325.34),\n"); + (void)HDfprintf(stdout, "\t \"FP\" denotes a floating point binary file,\n"); + (void)HDfprintf(stdout, "\t \"IN\" denotes a signed integer binary file,\n"); + (void)HDfprintf(stdout, "\t \"UIN\" denotes an unsigned integer binary file,\n"); + (void)HDfprintf(stdout, "\t & \"STR\" denotes an ASCII text file the \n"); + (void)HDfprintf(stdout, "\t contents of which should be stored as an 1-D \n"); + (void)HDfprintf(stdout, "\t array of strings.\n"); + (void)HDfprintf(stdout, "\t If INPUT-CLASS is \"STR\", then RANK, \n"); + (void)HDfprintf(stdout, "\t DIMENSION-SIZES, OUTPUT-CLASS, OUTPUT-SIZE, \n"); + (void)HDfprintf(stdout, "\t OUTPUT-ARCHITECTURE and OUTPUT-BYTE-ORDER \n"); + (void)HDfprintf(stdout, "\t will be ignored.\n\n\n"); + (void)HDfprintf(stdout, "\t INPUT-SIZE:\n"); + (void)HDfprintf(stdout, "\t Integer denoting the size of the input data \n"); + (void)HDfprintf(stdout, "\t (8, 16, 32, 64). \n\n"); + (void)HDfprintf(stdout, "\t For floating point,\n"); + (void)HDfprintf(stdout, "\t INPUT-SIZE can be 32 or 64.\n"); + (void)HDfprintf(stdout, "\t For integers (signed and unsigned)\n"); + (void)HDfprintf(stdout, "\t INPUT-SIZE can be 8, 16, 32 or 64.\n\n"); + (void)HDfprintf(stdout, "\t RANK:\n"); + (void)HDfprintf(stdout, "\t Integer denoting the number of dimensions.\n\n"); + (void)HDfprintf(stdout, "\t DIMENSION-SIZES:\n"); + (void)HDfprintf(stdout, "\t Integers separated by spaces to denote the \n"); + (void)HDfprintf(stdout, "\t dimension sizes for the no. of dimensions \n"); + (void)HDfprintf(stdout, "\t determined by rank.\n\n"); + (void)HDfprintf(stdout, "\t OUTPUT-CLASS:\n"); + (void)HDfprintf(stdout, "\t String dentoting data type of the dataset to \n"); + (void)HDfprintf(stdout, "\t be written (\"IN\",\"FP\", \"UIN\")\n\n"); + (void)HDfprintf(stdout, "\t OUTPUT-SIZE:\n"); + (void)HDfprintf(stdout, "\t Integer denoting the size of the data in the \n"); + (void)HDfprintf(stdout, "\t output dataset to be written.\n"); + (void)HDfprintf(stdout, "\t If OUTPUT-CLASS is \"FP\", OUTPUT-SIZE can be \n"); + (void)HDfprintf(stdout, "\t 32 or 64.\n"); + (void)HDfprintf(stdout, "\t If OUTPUT-CLASS is \"IN\" or \"UIN\", OUTPUT-SIZE\n"); + (void)HDfprintf(stdout, "\t can be 8, 16, 32 or 64.\n\n"); + (void)HDfprintf(stdout, "\t OUTPUT-ARCHITECTURE:\n"); + (void)HDfprintf(stdout, "\t STRING denoting the type of output \n"); + (void)HDfprintf(stdout, "\t architecture. Can accept the following values\n"); + (void)HDfprintf(stdout, "\t STD\n"); + (void)HDfprintf(stdout, "\t IEEE\n"); + (void)HDfprintf(stdout, "\t INTEL\n"); + (void)HDfprintf(stdout, "\t CRAY\n"); + (void)HDfprintf(stdout, "\t MIPS\n"); + (void)HDfprintf(stdout, "\t ALPHA\n"); + (void)HDfprintf(stdout, "\t NATIVE (default)\n"); + (void)HDfprintf(stdout, "\t UNIX\n\n"); + (void)HDfprintf(stdout, "\t OUTPUT-BYTE-ORDER:\n"); + (void)HDfprintf(stdout, "\t String denoting the output-byte-order. Ignored\n"); + (void)HDfprintf(stdout, "\t if the OUTPUT-ARCHITECTURE is not specified or\n"); + (void)HDfprintf(stdout, "\t if it is IEEE, UNIX or STD. Can accept the \n"); + (void)HDfprintf(stdout, "\t following values.\n"); + (void)HDfprintf(stdout, "\t BE (default)\n"); + (void)HDfprintf(stdout, "\t LE\n\n"); + (void)HDfprintf(stdout, "\t CHUNKED-DIMENSION-SIZES:\n"); + (void)HDfprintf(stdout, "\t Integers separated by spaces to denote the \n"); + (void)HDfprintf(stdout, "\t dimension sizes of the chunk for the no. of \n"); + (void)HDfprintf(stdout, "\t dimensions determined by rank. Required field\n"); + (void)HDfprintf(stdout, "\t to denote that the dataset will be stored with\n"); + (void)HDfprintf(stdout, "\t chunked storage. If this field is absent the\n"); + (void)HDfprintf(stdout, "\t dataset will be stored with contiguous storage.\n\n"); + (void)HDfprintf(stdout, "\t COMPRESSION-TYPE:\n"); + (void)HDfprintf(stdout, "\t String denoting the type of compression to be\n"); + (void)HDfprintf(stdout, "\t used with the chunked storage. Requires the\n"); + (void)HDfprintf(stdout, "\t CHUNKED-DIMENSION-SIZES to be specified. The only \n"); + (void)HDfprintf(stdout, "\t currently supported compression method is GZIP. \n"); + (void)HDfprintf(stdout, "\t Will accept the following value\n"); + (void)HDfprintf(stdout, "\t GZIP\n\n"); + (void)HDfprintf(stdout, "\t COMPRESSION-PARAM:\n"); + (void)HDfprintf(stdout, "\t Integer used to denote compression level and \n"); + (void)HDfprintf(stdout, "\t this option is to be always specified when \n"); + (void)HDfprintf(stdout, "\t the COMPRESSION-TYPE option is specified. The\n"); + (void)HDfprintf(stdout, "\t values are applicable only to GZIP \n"); + (void)HDfprintf(stdout, "\t compression.\n"); + (void)HDfprintf(stdout, "\t Value 1-9: The level of Compression. \n"); + (void)HDfprintf(stdout, "\t 1 will result in the fastest \n"); + (void)HDfprintf(stdout, "\t compression while 9 will result in \n"); + (void)HDfprintf(stdout, "\t the best compression ratio. The default\n"); + (void)HDfprintf(stdout, "\t level of compression is 6.\n\n"); + (void)HDfprintf(stdout, "\t EXTERNAL-STORAGE:\n"); + (void)HDfprintf(stdout, "\t String to denote the name of the non-HDF5 file \n"); + (void)HDfprintf(stdout, "\t to store data to. Cannot be used if CHUNKED-\n"); + (void)HDfprintf(stdout, "\t DIMENSIONS or COMPRESSION-TYPE or EXTENDIBLE-\n"); + (void)HDfprintf(stdout, "\t DATASET is specified.\n"); + (void)HDfprintf(stdout, "\t Value <external-filename>: the name of the \n"); + (void)HDfprintf(stdout, "\t external file as a string to be used.\n\n"); + (void)HDfprintf(stdout, "\t MAXIMUM-DIMENSIONS:\n"); + (void)HDfprintf(stdout, "\t Integers separated by spaces to denote the \n"); + (void)HDfprintf(stdout, "\t maximum dimension sizes of all the \n"); + (void)HDfprintf(stdout, "\t dimensions determined by rank. Requires the\n"); + (void)HDfprintf(stdout, "\t CHUNKED-DIMENSION-SIZES to be specified. A value of \n"); + (void)HDfprintf(stdout, "\t -1 for any dimension implies UNLIMITED \n"); + (void)HDfprintf(stdout, "\t DIMENSION size for that particular dimension.\n\n"); + (void)HDfprintf(stdout, "\t EXAMPLES:\n"); + (void)HDfprintf(stdout, "\t 1. Configuration File may look like:\n\n"); + (void)HDfprintf(stdout, "\t PATH work h5 pkamat First-set\n"); + (void)HDfprintf(stdout, "\t INPUT-CLASS TEXTFP\n"); + (void)HDfprintf(stdout, "\t RANK 3\n"); + (void)HDfprintf(stdout, "\t DIMENSION-SIZES 5 2 4\n"); + (void)HDfprintf(stdout, "\t OUTPUT-CLASS FP\n"); + (void)HDfprintf(stdout, "\t OUTPUT-SIZE 64\n"); + (void)HDfprintf(stdout, "\t OUTPUT-ARCHITECTURE IEEE\n"); + (void)HDfprintf(stdout, "\t OUTPUT-BYTE-ORDER LE\n"); + (void)HDfprintf(stdout, "\t CHUNKED-DIMENSION-SIZES 2 2 2 \n\n"); + (void)HDfprintf(stdout, "\t The above configuration will accept a floating point array \n"); + (void)HDfprintf(stdout, "\t (5 x 2 x 4) in an ASCII file with the rank and dimension sizes \n"); + (void)HDfprintf(stdout, "\t specified and will save it in a chunked data-set (of pattern \n"); + (void)HDfprintf(stdout, "\t 2 X 2 X 2) of 64-bit floating point in the little-endian order \n"); + (void)HDfprintf(stdout, "\t and IEEE architecture. The dataset will be stored at\n"); + (void)HDfprintf(stdout, "\t \"/work/h5/pkamat/First-set\"\n\n"); + (void)HDfprintf(stdout, "\t 2. Another configuration could be:\n\n"); + (void)HDfprintf(stdout, "\t PATH Second-set\n"); + (void)HDfprintf(stdout, "\t INPUT-CLASS IN \n"); + (void)HDfprintf(stdout, "\t RANK 5\n"); + (void)HDfprintf(stdout, "\t DIMENSION-SIZES 6 3 5 2 4\n"); + (void)HDfprintf(stdout, "\t OUTPUT-CLASS IN\n"); + (void)HDfprintf(stdout, "\t OUTPUT-SIZE 32\n"); + (void)HDfprintf(stdout, "\t CHUNKED-DIMENSION-SIZES 2 2 2 2 2\n"); + (void)HDfprintf(stdout, "\t EXTENDIBLE-DATASET 1 3 \n"); + (void)HDfprintf(stdout, "\t COMPRESSION-TYPE GZIP\n"); + (void)HDfprintf(stdout, "\t COMPRESSION-PARAM 7\n\n\n"); + (void)HDfprintf(stdout, "\t The above configuration will accept an integer array \n"); + (void)HDfprintf(stdout, "\t (6 X 3 X 5 x 2 x 4) in a binary file with the rank and \n"); + (void)HDfprintf(stdout, "\t dimension sizes specified and will save it in a chunked data-set\n"); + (void)HDfprintf(stdout, "\t (of pattern 2 X 2 X 2 X 2 X 2) of 32-bit floating point in \n"); + (void)HDfprintf(stdout, "\t native format (as output-architecture is not specified). The \n"); + (void)HDfprintf(stdout, "\t first and the third dimension will be defined as unlimited. The \n"); + (void)HDfprintf(stdout, "\t data-set will be compressed using GZIP and a compression level \n"); + (void)HDfprintf(stdout, "\t of 7.\n"); + (void)HDfprintf(stdout, "\t The dataset will be stored at \"/Second-set\"\n\n"); } -void usage(char *name) +void +usage(char *name) { - (void) HDfprintf(stdout, "\nUsage:\t%s -h[elp], OR\n", name); - (void) HDfprintf(stdout, - "\t%s <infile> -c[onfig] <configfile> \ - [<infile> -c[config] <configfile>...] -o[utfile] <outfile> \n\n", name); - return; + (void)HDfprintf(stdout, "\nUsage:\t%s -h[elp], OR\n", name); + (void)HDfprintf(stdout, "\t%s <infile> -c[onfig] <configfile> \ + [<infile> -c[config] <configfile>...] -o[utfile] <outfile> \n\n", + name); } - diff --git a/tools/src/h5import/h5import.h b/tools/src/h5import/h5import.h index 00c41f6..efd40e1 100644 --- a/tools/src/h5import/h5import.h +++ b/tools/src/h5import/h5import.h @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -17,124 +17,117 @@ * */ -#ifndef H5IMPORT_H__ -#define H5IMPORT_H__ +#ifndef H5IMPORT_H +#define H5IMPORT_H /* * state table tokens */ #define FILNAME 0 /* filename */ -#define OPT_o 1 +#define OPT_o 1 /* output filename */ -#define OPT_c 2 /* configuration filename */ -#define OPT_h 3 /* request for explanation */ -#define OPT_d 4 /* dimensions */ -#define OPT_p 5 /* pathname */ -#define OPT_t 6 /* data type */ -#define OPT_s 7 /* data size */ -#define ERR 20 /* invalid token */ - -#define MAX_GROUPS_IN_PATH 20 +#define OPT_c 2 /* configuration filename */ +#define OPT_h 3 /* request for explanation */ +#define OPT_d 4 /* dimensions */ +#define OPT_p 5 /* pathname */ +#define OPT_t 6 /* data type */ +#define OPT_s 7 /* data size */ +#define ERR 20 /* invalid token */ + +#define MAX_GROUPS_IN_PATH 20 #define MAX_PATH_NAME_LENGTH 255 -#define NUM_KEYS 15 -#define MIN_NUM_DIMENSION 1 -#define MAX_NUM_DIMENSION 32 -#define BASE_10 10 - -#define PATH 0 -#define INPUT_CLASS 1 -#define INPUT_SIZE 2 -#define RANK 3 -#define DIM 4 -#define OUTPUT_CLASS 5 -#define OUTPUT_SIZE 6 -#define OUTPUT_ARCH 7 -#define OUTPUT_B_ORDER 8 -#define CHUNK 9 -#define COMPRESS 10 -#define COMPRESS_PARAM 11 -#define EXTERNALSTORE 12 -#define EXTEND 13 -#define INPUT_B_ORDER 14 +#define NUM_KEYS 15 +#define MIN_NUM_DIMENSION 1 +#define MAX_NUM_DIMENSION 32 +#define BASE_10 10 + +#define PATH 0 +#define INPUT_CLASS 1 +#define INPUT_SIZE 2 +#define RANK 3 +#define DIM 4 +#define OUTPUT_CLASS 5 +#define OUTPUT_SIZE 6 +#define OUTPUT_ARCH 7 +#define OUTPUT_B_ORDER 8 +#define CHUNK 9 +#define COMPRESS 10 +#define COMPRESS_PARAM 11 +#define EXTERNALSTORE 12 +#define EXTEND 13 +#define INPUT_B_ORDER 14 /* data types */ -#define H5DT_INT8 signed char -#define H5DT_INT16 short -#define H5DT_INT32 int -#define H5DT_FLOAT32 float -#define H5DT_FLOAT64 double -#define VOIDP void* -#define H5DT_UINT8 unsigned char -#define H5DT_UINT16 unsigned short -#define H5DT_UINT32 unsigned int -#define H5DT_INT64 long long -#define H5DT_UINT64 unsigned H5DT_INT64 - -struct path_info -{ +#define H5DT_INT8 signed char +#define H5DT_INT16 short +#define H5DT_INT32 int +#define H5DT_FLOAT32 float +#define H5DT_FLOAT64 double +#define VOIDP void * +#define H5DT_UINT8 unsigned char +#define H5DT_UINT16 unsigned short +#define H5DT_UINT32 unsigned int +#define H5DT_INT64 long long +#define H5DT_UINT64 unsigned H5DT_INT64 + +struct path_info { char group[MAX_GROUPS_IN_PATH][MAX_PATH_NAME_LENGTH]; - int count; + int count; }; -struct Input -{ - int h5dumpInput; +struct Input { + int h5dumpInput; struct path_info path; - int inputClass; - int inputSize; - int inputArchitecture; - int inputByteOrder; - int rank; - hsize_t* sizeOfDimension; - int outputClass; - int outputSize; - int outputArchitecture; - int outputByteOrder; - hsize_t* sizeOfChunk; - hsize_t* maxsizeOfDimension; - int compressionType; - int compressionParam; - char *externFilename; - VOIDP data; - int configOptionVector[NUM_KEYS]; + int inputClass; + int inputSize; + int inputArchitecture; + int inputByteOrder; + int rank; + hsize_t * sizeOfDimension; + int outputClass; + int outputSize; + int outputArchitecture; + int outputByteOrder; + hsize_t * sizeOfChunk; + hsize_t * maxsizeOfDimension; + int compressionType; + int compressionParam; + char * externFilename; + VOIDP data; + int configOptionVector[NUM_KEYS]; }; -struct infilesformat -{ - char datafile[MAX_PATH_NAME_LENGTH]; - char configfile[MAX_PATH_NAME_LENGTH]; +struct infilesformat { + char datafile[MAX_PATH_NAME_LENGTH]; + char configfile[MAX_PATH_NAME_LENGTH]; struct Input in; - int config; /* Configfile present? No - 0. Yes - 1 */ + int config; /* Configfile present? No - 0. Yes - 1 */ }; -struct Options -{ - struct infilesformat infiles[30]; /* structure to hold the list of input file names. Limited to 30*/ - char outfile[256]; /* output file name */ - int fcount; /* number of input files */ +struct Options { + struct infilesformat infiles[30]; /* structure to hold the list of input file names. Limited to 30*/ + char outfile[256]; /* output file name */ + int fcount; /* number of input files */ }; -char keytable[NUM_KEYS][30] = { - "PATH", - "INPUT-CLASS", - "INPUT-SIZE", - "RANK", - "DIMENSION-SIZES", - "OUTPUT-CLASS", - "OUTPUT-SIZE", - "OUTPUT-ARCHITECTURE", - "OUTPUT-BYTE-ORDER", - "CHUNKED-DIMENSION-SIZES", - "COMPRESSION-TYPE", - "COMPRESSION-PARAM", - "EXTERNAL-STORAGE", - "MAXIMUM-DIMENSIONS", - "INPUT-BYTE-ORDER" -}; - -static int state_table[15][8] = -{ +char keytable[NUM_KEYS][30] = {"PATH", + "INPUT-CLASS", + "INPUT-SIZE", + "RANK", + "DIMENSION-SIZES", + "OUTPUT-CLASS", + "OUTPUT-SIZE", + "OUTPUT-ARCHITECTURE", + "OUTPUT-BYTE-ORDER", + "CHUNKED-DIMENSION-SIZES", + "COMPRESSION-TYPE", + "COMPRESSION-PARAM", + "EXTERNAL-STORAGE", + "MAXIMUM-DIMENSIONS", + "INPUT-BYTE-ORDER"}; + +static int state_table[15][8] = { /* token ordering: FILNAME OPT_o OPT_c OPT_h OPT_d OPT_p OPT_t OPT_s */ /* state 0: start */ @@ -189,12 +182,11 @@ static int state_table[15][8] = * Function declarations for h5import * */ -void usage(char *); -void setDefaultValues(struct Input *in, int count); -void help(char *); - -hid_t createOutputDataType(struct Input *in); -hid_t createInputDataType(struct Input *in); +void usage(char *); +void setDefaultValues(struct Input *in, int count); +void help(char *); -#endif /* H5IMPORT_H__ */ +hid_t createOutputDataType(struct Input *in); +hid_t createInputDataType(struct Input *in); +#endif /* H5IMPORT_H */ diff --git a/tools/src/h5jam/CMakeLists.txt b/tools/src/h5jam/CMakeLists.txt index f430417..0a31215 100644 --- a/tools/src/h5jam/CMakeLists.txt +++ b/tools/src/h5jam/CMakeLists.txt @@ -1,4 +1,4 @@ -cmake_minimum_required (VERSION 3.10) +cmake_minimum_required (VERSION 3.12) project (HDF5_TOOLS_SRC_H5JAM C) # -------------------------------------------------------------------- @@ -6,14 +6,14 @@ project (HDF5_TOOLS_SRC_H5JAM C) # -------------------------------------------------------------------- if (NOT ONLY_SHARED_LIBS) add_executable (h5jam ${HDF5_TOOLS_SRC_H5JAM_SOURCE_DIR}/h5jam.c) - target_include_directories (h5jam PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5jam PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") TARGET_C_PROPERTIES (h5jam STATIC) target_link_libraries (h5jam PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) set_target_properties (h5jam PROPERTIES FOLDER tools) set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5jam") add_executable (h5unjam ${HDF5_TOOLS_SRC_H5JAM_SOURCE_DIR}/h5unjam.c) - target_include_directories (h5unjam PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5unjam PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") TARGET_C_PROPERTIES (h5unjam STATIC) target_link_libraries (h5unjam PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) set_target_properties (h5unjam PROPERTIES FOLDER tools) @@ -27,14 +27,14 @@ endif () if (BUILD_SHARED_LIBS) add_executable (h5jam-shared ${HDF5_TOOLS_SRC_H5JAM_SOURCE_DIR}/h5jam.c) - target_include_directories (h5jam-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5jam-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") TARGET_C_PROPERTIES (h5jam-shared SHARED) target_link_libraries (h5jam-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET}) set_target_properties (h5jam-shared PROPERTIES FOLDER tools) set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5jam-shared") add_executable (h5unjam-shared ${HDF5_TOOLS_SRC_H5JAM_SOURCE_DIR}/h5unjam.c) - target_include_directories (h5unjam-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5unjam-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") TARGET_C_PROPERTIES (h5unjam-shared SHARED) target_link_libraries (h5unjam-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET}) set_target_properties (h5unjam-shared PROPERTIES FOLDER tools) @@ -46,6 +46,19 @@ if (BUILD_SHARED_LIBS) ) endif () +#----------------------------------------------------------------------------- +# Add Target to clang-format +#----------------------------------------------------------------------------- +if (HDF5_ENABLE_FORMATTERS) + if (NOT ONLY_SHARED_LIBS) + clang_format (HDF5_H5JAM_SRC_FORMAT h5jam) + clang_format (HDF5_H5UNJAM_SRC_FORMAT h5unjam) + else () + clang_format (HDF5_H5JAM_SRC_FORMAT h5jam-shared) + clang_format (HDF5_H5UNJAM_SRC_FORMAT h5unjam-shared) + endif () +endif () + ############################################################################## ############################################################################## ### I N S T A L L A T I O N ### diff --git a/tools/src/h5jam/Makefile.am b/tools/src/h5jam/Makefile.am index 4c44b08..2dd496d 100644 --- a/tools/src/h5jam/Makefile.am +++ b/tools/src/h5jam/Makefile.am @@ -6,7 +6,7 @@ # This file is part of HDF5. The full HDF5 copyright notice, including # terms governing use, modification, and redistribution, is contained in # the COPYING file, which can be found at the root of the source code -# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. +# distribution tree, or in https://www.hdfgroup.org/licenses. # If you do not have access to either file, you may request a copy from # help@hdfgroup.org. ## diff --git a/tools/src/h5jam/h5jam.c b/tools/src/h5jam/h5jam.c index 8222e06..45978bb 100644 --- a/tools/src/h5jam/h5jam.c +++ b/tools/src/h5jam/h5jam.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -19,36 +19,25 @@ /* Name of tool */ #define PROGRAMNAME "h5jam" -herr_t write_pad(int ofile, hsize_t old_where, hsize_t *new_where); -hsize_t compute_user_block_size (hsize_t); -hsize_t copy_some_to_file (int, int, hsize_t, hsize_t, ssize_t); -void parse_command_line (int, const char *[]); +herr_t write_pad(int ofile, hsize_t old_where, hsize_t *new_where); +hsize_t compute_user_block_size(hsize_t); +hsize_t copy_some_to_file(int, int, hsize_t, hsize_t, ssize_t); +void parse_command_line(int, const char *const *); -int do_clobber = FALSE; +int do_clobber = FALSE; char *output_file = NULL; -char *input_file = NULL; -char *ub_file = NULL; +char *input_file = NULL; +char *ub_file = NULL; /* * Command-line options: The user can specify short or long-named * parameters. The long-named ones can be partially spelled. When * adding more, make sure that they don't clash with each other. */ -static const char *s_opts = "hi:u:o:c:V"; /* add more later ? */ -static struct long_options l_opts[] = { - {"help", no_arg, 'h'}, - {"hel", no_arg, 'h'}, - {"i", require_arg, 'i'}, /* input file */ - {"u", require_arg, 'u'}, /* user block file */ - {"o", require_arg, 'o'}, /* output file */ - {"clobber", no_arg, 'c'}, /* clobber existing UB */ - {"clobbe", no_arg, 'c'}, - {"clobb", no_arg, 'c'}, - {"clob", no_arg, 'c'}, - {"clo", no_arg, 'c'}, - {"cl", no_arg, 'c'}, - {NULL, 0, '\0'} -}; +static const char * s_opts = "hi:u:o:c:V"; +static struct h5_long_options l_opts[] = {{"help", no_arg, 'h'}, {"i", require_arg, 'i'}, + {"u", require_arg, 'u'}, {"o", require_arg, 'o'}, + {"clobber", no_arg, 'c'}, {NULL, 0, '\0'}}; /*------------------------------------------------------------------------- * Function: usage @@ -59,56 +48,35 @@ static struct long_options l_opts[] = { *------------------------------------------------------------------------- */ static void -usage (const char *prog) +usage(const char *prog) { - HDfflush (stdout); - HDfprintf (stdout, - "usage: %s -i <in_file.h5> -u <in_user_file> [-o <out_file.h5>] [--clobber]\n", prog); - HDfprintf (stdout, "\n"); - HDfprintf (stdout, - "Adds user block to front of an HDF5 file and creates a new concatenated file.\n"); - HDfprintf (stdout, "\n"); - HDfprintf (stdout, - "OPTIONS\n"); - HDfprintf (stdout, - " -i in_file.h5 Specifies the input HDF5 file.\n"); - HDfprintf (stdout, - " -u in_user_file Specifies the file to be inserted into the user block.\n"); - HDfprintf (stdout, - " Can be any file format except an HDF5 format.\n"); - HDfprintf (stdout, - " -o out_file.h5 Specifies the output HDF5 file.\n"); - HDfprintf (stdout, - " If not specified, the user block will be concatenated in\n"); - HDfprintf (stdout, - " place to the input HDF5 file.\n"); - HDfprintf (stdout, - " --clobber Wipes out any existing user block before concatenating\n"); - HDfprintf (stdout, - " the given user block.\n"); - HDfprintf (stdout, - " The size of the new user block will be the larger of;\n"); - HDfprintf (stdout, - " - the size of existing user block in the input HDF5 file\n"); - HDfprintf (stdout, - " - the size of user block required by new input user file\n"); - HDfprintf (stdout, - " (size = 512 x 2N, N is positive integer.)\n"); - HDfprintf (stdout, "\n"); - HDfprintf (stdout, - " -h Prints a usage message and exits.\n"); - HDfprintf (stdout, - " -V Prints the HDF5 library version and exits.\n"); - HDfprintf (stdout, "\n"); - HDfprintf (stdout, - "Exit Status:\n"); - HDfprintf (stdout, - " 0 Succeeded.\n"); - HDfprintf (stdout, - " >0 An error occurred.\n"); + HDfflush(stdout); + HDfprintf(stdout, "usage: %s -i <in_file.h5> -u <in_user_file> [-o <out_file.h5>] [--clobber]\n", prog); + HDfprintf(stdout, "\n"); + HDfprintf(stdout, "Adds user block to front of an HDF5 file and creates a new concatenated file.\n"); + HDfprintf(stdout, "\n"); + HDfprintf(stdout, "OPTIONS\n"); + HDfprintf(stdout, " -i in_file.h5 Specifies the input HDF5 file.\n"); + HDfprintf(stdout, " -u in_user_file Specifies the file to be inserted into the user block.\n"); + HDfprintf(stdout, " Can be any file format except an HDF5 format.\n"); + HDfprintf(stdout, " -o out_file.h5 Specifies the output HDF5 file.\n"); + HDfprintf(stdout, " If not specified, the user block will be concatenated in\n"); + HDfprintf(stdout, " place to the input HDF5 file.\n"); + HDfprintf(stdout, " --clobber Wipes out any existing user block before concatenating\n"); + HDfprintf(stdout, " the given user block.\n"); + HDfprintf(stdout, " The size of the new user block will be the larger of;\n"); + HDfprintf(stdout, " - the size of existing user block in the input HDF5 file\n"); + HDfprintf(stdout, " - the size of user block required by new input user file\n"); + HDfprintf(stdout, " (size = 512 x 2N, N is positive integer.)\n"); + HDfprintf(stdout, "\n"); + HDfprintf(stdout, " -h Prints a usage message and exits.\n"); + HDfprintf(stdout, " -V Prints the HDF5 library version and exits.\n"); + HDfprintf(stdout, "\n"); + HDfprintf(stdout, "Exit Status:\n"); + HDfprintf(stdout, " 0 Succeeded.\n"); + HDfprintf(stdout, " >0 An error occurred.\n"); } - /*------------------------------------------------------------------------- * Function: leave * @@ -120,13 +88,6 @@ usage (const char *prog) static void leave(int ret) { - if (ub_file) - HDfree (ub_file); - if (input_file) - HDfree (input_file); - if (output_file) - HDfree (output_file); - h5tools_close(); HDexit(ret); @@ -143,40 +104,38 @@ leave(int ret) */ void -parse_command_line (int argc, const char *argv[]) +parse_command_line(int argc, const char *const *argv) { - int opt = FALSE; - - /* parse command line options */ - while ((opt = get_option (argc, argv, s_opts, l_opts)) != EOF) - { - switch ((char) opt) - { - case 'o': - output_file = HDstrdup (opt_arg); - break; - case 'i': - input_file = HDstrdup (opt_arg); - break; - case 'u': - ub_file = HDstrdup (opt_arg); - break; - case 'c': - do_clobber = TRUE; - break; - case 'h': - usage (h5tools_getprogname()); - leave (EXIT_SUCCESS); - break; - case 'V': - print_version (h5tools_getprogname()); - leave (EXIT_SUCCESS); - break; - case '?': - default: - usage (h5tools_getprogname()); - leave (EXIT_FAILURE); - } + int opt = FALSE; + + /* parse command line options */ + while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) { + switch ((char)opt) { + case 'o': + output_file = HDstrdup(H5_optarg); + break; + case 'i': + input_file = HDstrdup(H5_optarg); + break; + case 'u': + ub_file = HDstrdup(H5_optarg); + break; + case 'c': + do_clobber = TRUE; + break; + case 'h': + usage(h5tools_getprogname()); + leave(EXIT_SUCCESS); + break; + case 'V': + print_version(h5tools_getprogname()); + leave(EXIT_SUCCESS); + break; + case '?': + default: + usage(h5tools_getprogname()); + leave(EXIT_FAILURE); + } } } @@ -190,44 +149,42 @@ parse_command_line (int argc, const char *argv[]) *------------------------------------------------------------------------- */ int -main (int argc, const char *argv[]) +main(int argc, char *argv[]) { - int ufid = -1; - int h5fid = -1; - int ofid = -1; - void *edata; - H5E_auto2_t func; - hid_t ifile = -1; - hid_t plist = -1; - herr_t status; - htri_t testval; - hsize_t usize; - hsize_t h5fsize; - hsize_t startub; - hsize_t where; - hsize_t newubsize; - off_t fsize; - h5_stat_t sbuf; - h5_stat_t sbuf2; - int res; + int ufid = -1; + int h5fid = -1; + int ofid = -1; + hid_t ifile = H5I_INVALID_HID; + hid_t plist = H5I_INVALID_HID; + herr_t status; + htri_t testval; + hsize_t usize; + hsize_t h5fsize; + hsize_t startub; + hsize_t where; + hsize_t newubsize; + off_t fsize; + h5_stat_t sbuf; + h5_stat_t sbuf2; + int res; h5tools_setprogname(PROGRAMNAME); h5tools_setstatus(EXIT_SUCCESS); - /* Disable error reporting */ - H5Eget_auto2(H5E_DEFAULT, &func, &edata); - H5Eset_auto2(H5E_DEFAULT, NULL, NULL); - /* Initialize h5tools lib */ h5tools_init(); - parse_command_line(argc, argv); + parse_command_line(argc, (const char *const *)argv); + + /* enable error reporting if command line option */ + h5tools_error_report(); if (ub_file == NULL) { /* no user block */ error_msg("missing argument for -u <user_file>.\n"); help_ref_msg(stderr); - leave (EXIT_FAILURE); + h5tools_setstatus(EXIT_FAILURE); + goto done; } testval = H5Fis_accessible(ub_file, H5P_DEFAULT); @@ -235,13 +192,15 @@ main (int argc, const char *argv[]) if (testval > 0) { error_msg("-u <user_file> cannot be HDF5 file, but it appears to be an HDF5 file.\n"); help_ref_msg(stderr); - leave (EXIT_FAILURE); + h5tools_setstatus(EXIT_FAILURE); + goto done; } if (input_file == NULL) { error_msg("missing argument for -i <HDF5 file>.\n"); help_ref_msg(stderr); - leave (EXIT_FAILURE); + h5tools_setstatus(EXIT_FAILURE); + goto done; } testval = H5Fis_accessible(input_file, H5P_DEFAULT); @@ -249,62 +208,65 @@ main (int argc, const char *argv[]) if (testval <= 0) { error_msg("Input HDF5 file \"%s\" is not HDF5 format.\n", input_file); help_ref_msg(stderr); - leave (EXIT_FAILURE); + h5tools_setstatus(EXIT_FAILURE); + goto done; } ifile = H5Fopen(input_file, H5F_ACC_RDONLY, H5P_DEFAULT); if (ifile < 0) { error_msg("Can't open input HDF5 file \"%s\"\n", input_file); - leave (EXIT_FAILURE); + h5tools_setstatus(EXIT_FAILURE); + goto done; } plist = H5Fget_create_plist(ifile); if (plist < 0) { error_msg("Can't get file creation plist for file \"%s\"\n", input_file); - H5Fclose(ifile); - leave (EXIT_FAILURE); + h5tools_setstatus(EXIT_FAILURE); + goto done; } status = H5Pget_userblock(plist, &usize); if (status < 0) { error_msg("Can't get user block for file \"%s\"\n", input_file); - H5Pclose(plist); - H5Fclose(ifile); - leave (EXIT_FAILURE); + h5tools_setstatus(EXIT_FAILURE); + goto done; } H5Pclose(plist); + plist = H5I_INVALID_HID; H5Fclose(ifile); + ifile = H5I_INVALID_HID; ufid = HDopen(ub_file, O_RDONLY); - if(ufid < 0) { + if (ufid < 0) { error_msg("unable to open user block file \"%s\"\n", ub_file); - leave (EXIT_FAILURE); + h5tools_setstatus(EXIT_FAILURE); + goto done; } res = HDfstat(ufid, &sbuf); - if(res < 0) { + if (res < 0) { error_msg("Can't stat file \"%s\"\n", ub_file); - HDclose (ufid); - leave (EXIT_FAILURE); + h5tools_setstatus(EXIT_FAILURE); + goto done; } fsize = (off_t)sbuf.st_size; h5fid = HDopen(input_file, O_RDONLY); - if(h5fid < 0) { + if (h5fid < 0) { error_msg("unable to open HDF5 file for read \"%s\"\n", input_file); - HDclose (ufid); - leave (EXIT_FAILURE); + h5tools_setstatus(EXIT_FAILURE); + goto done; } res = HDfstat(h5fid, &sbuf2); - if(res < 0) { + if (res < 0) { error_msg("Can't stat file \"%s\"\n", input_file); - HDclose (h5fid); - HDclose (ufid); - leave (EXIT_FAILURE); + h5tools_setstatus(EXIT_FAILURE); + goto done; } h5fsize = (hsize_t)sbuf2.st_size; @@ -314,9 +276,8 @@ main (int argc, const char *argv[]) if (ofid < 0) { error_msg("unable to open output file \"%s\"\n", output_file); - HDclose (h5fid); - HDclose (ufid); - leave (EXIT_FAILURE); + h5tools_setstatus(EXIT_FAILURE); + goto done; } } else { @@ -324,13 +285,12 @@ main (int argc, const char *argv[]) if (ofid < 0) { error_msg("unable to create output file \"%s\"\n", output_file); - HDclose (h5fid); - HDclose (ufid); - leave (EXIT_FAILURE); + h5tools_setstatus(EXIT_FAILURE); + goto done; } } - newubsize = compute_user_block_size((hsize_t) fsize); + newubsize = compute_user_block_size((hsize_t)fsize); startub = usize; @@ -340,52 +300,56 @@ main (int argc, const char *argv[]) if (usize > newubsize) { newubsize = usize; } - startub = 0; /*blast the old */ + startub = 0; /*blast the old */ } else { /* add new ub to current ublock, pad to new offset */ newubsize += usize; - newubsize = compute_user_block_size((hsize_t) newubsize); + newubsize = compute_user_block_size((hsize_t)newubsize); } } /* copy the HDF5 from starting at usize to starting at newubsize: * makes room at 'from' for new ub */ /* if no current ub, usize is 0 */ - copy_some_to_file(h5fid, ofid, usize, newubsize, (ssize_t) (h5fsize - usize)); + copy_some_to_file(h5fid, ofid, usize, newubsize, (ssize_t)(h5fsize - usize)); /* copy the old ub to the beginning of the new file */ if (!do_clobber) { - where = copy_some_to_file(h5fid, ofid, (hsize_t) 0, (hsize_t) 0, (ssize_t) usize); + where = copy_some_to_file(h5fid, ofid, (hsize_t)0, (hsize_t)0, (ssize_t)usize); } /* copy the new ub to the end of the ub */ - where = copy_some_to_file(ufid, ofid, (hsize_t) 0, startub, (ssize_t) - 1); + where = copy_some_to_file(ufid, ofid, (hsize_t)0, startub, (ssize_t)-1); /* pad the ub */ - if(write_pad(ofid, where, &where) < 0) { + if (write_pad(ofid, where, &where) < 0) { error_msg("Can't pad file \"%s\"\n", output_file); - HDclose (h5fid); - HDclose (ufid); - HDclose (ofid); - leave (EXIT_FAILURE); + h5tools_setstatus(EXIT_FAILURE); + goto done; } /* end if */ - if(ub_file) +done: + if (ub_file) HDfree(ub_file); - if(input_file) + if (input_file) HDfree(input_file); - if(output_file) + if (output_file) HDfree(output_file); - if(ufid >= 0) + if (plist >= 0) + H5Pclose(plist); + if (ifile >= 0) + H5Fclose(ifile); + + if (ufid >= 0) HDclose(ufid); - if(h5fid >= 0) + if (h5fid >= 0) HDclose(h5fid); - if(ofid >= 0) + if (ofid >= 0) HDclose(ofid); - return h5tools_getstatus(); + leave(h5tools_getstatus()); } /*------------------------------------------------------------------------- @@ -394,7 +358,7 @@ main (int argc, const char *argv[]) * Purpose: Copy part of the input file to output. * infid: fd of file to read * outfid: fd of file to write - * startin: offset of where to read from infid + * starting: offset of where to read from infid * startout: offset of where to write to outfid * limit: bytes to read/write * @@ -409,29 +373,28 @@ main (int argc, const char *argv[]) *------------------------------------------------------------------------- */ hsize_t -copy_some_to_file(int infid, int outfid, hsize_t startin, hsize_t startout, - ssize_t limit) +copy_some_to_file(int infid, int outfid, hsize_t starting, hsize_t startout, ssize_t limit) { - char buf[1024]; + char buf[1024]; h5_stat_t sbuf; - int res; - ssize_t tot = 0; - ssize_t howmuch = 0; - ssize_t nchars = -1; - ssize_t to; - ssize_t from; - ssize_t toend; - ssize_t fromend; - - if(startin > startout) { + int res; + ssize_t tot = 0; + ssize_t howmuch = 0; + ssize_t nchars = -1; + ssize_t to; + ssize_t from; + ssize_t toend; + ssize_t fromend; + + if (starting > startout) { /* this case is prohibited */ - error_msg("copy_some_to_file: panic: startin > startout?\n"); - exit (EXIT_FAILURE); + error_msg("copy_some_to_file: panic: starting > startout?\n"); + exit(EXIT_FAILURE); } /* end if */ - if(limit < 0) { + if (limit < 0) { res = HDfstat(infid, &sbuf); - if(res < 0) { + if (res < 0) { error_msg("Can't stat file \n"); HDexit(EXIT_FAILURE); } /* end if */ @@ -442,27 +405,27 @@ copy_some_to_file(int infid, int outfid, hsize_t startin, hsize_t startout, howmuch = limit; } /* end if */ - if(0 == howmuch) + if (0 == howmuch) return 0; - toend = (ssize_t) startout + howmuch; - fromend = (ssize_t) startin + howmuch; + toend = (ssize_t)startout + howmuch; + fromend = (ssize_t)starting + howmuch; if (howmuch > 512) { - to = toend - 512; + to = toend - 512; from = fromend - 512; } else { - to = toend - howmuch; + to = toend - howmuch; from = fromend - howmuch; } /* end if */ while (howmuch > 0) { - HDlseek(outfid, (off_t) to, SEEK_SET); - HDlseek(infid, (off_t) from, SEEK_SET); + HDlseek(outfid, (off_t)to, SEEK_SET); + HDlseek(infid, (off_t)from, SEEK_SET); if (howmuch > 512) { - nchars = HDread(infid, buf, (unsigned) 512); + nchars = HDread(infid, buf, (unsigned)512); } else { nchars = HDread(infid, buf, (unsigned)howmuch); @@ -473,14 +436,14 @@ copy_some_to_file(int infid, int outfid, hsize_t startin, hsize_t startout, HDexit(EXIT_FAILURE); } /* end if */ - if(HDwrite (outfid, buf, (unsigned) nchars) < 0) { + if (HDwrite(outfid, buf, (unsigned)nchars) < 0) { error_msg("Write error \n"); HDexit(EXIT_FAILURE); } tot += nchars; howmuch -= nchars; - if(howmuch > 512) { + if (howmuch > 512) { to -= nchars; from -= nchars; } @@ -488,12 +451,11 @@ copy_some_to_file(int infid, int outfid, hsize_t startin, hsize_t startout, to -= howmuch; from -= howmuch; } /* end if */ - } /* end while */ + } /* end while */ return (hsize_t)tot + (hsize_t)startout; } /* end copy_some_to_file() */ - /*------------------------------------------------------------------------- * Function: compute_user_block_size * @@ -510,10 +472,10 @@ compute_user_block_size(hsize_t ublock_size) { hsize_t where = 512; - if(0 == ublock_size) + if (0 == ublock_size) return 0; - while(where < ublock_size) + while (where < ublock_size) where *= 2; return where; @@ -530,10 +492,10 @@ herr_t write_pad(int ofile, hsize_t old_where, hsize_t *new_where) { unsigned int i; - char buf[1]; - hsize_t psize; + char buf[1]; + hsize_t psize; - if(new_where == NULL) + if (new_where == NULL) return FAIL; buf[0] = '\0'; @@ -543,8 +505,8 @@ write_pad(int ofile, hsize_t old_where, hsize_t *new_where) psize = compute_user_block_size(old_where); psize -= old_where; - for(i = 0; i < psize; i++) - if(HDwrite(ofile, buf, 1) < 0) + for (i = 0; i < psize; i++) + if (HDwrite(ofile, buf, 1) < 0) return FAIL; /* Set the new size of the file. */ @@ -552,4 +514,3 @@ write_pad(int ofile, hsize_t old_where, hsize_t *new_where) return SUCCEED; } /* end write_pad() */ - diff --git a/tools/src/h5jam/h5unjam.c b/tools/src/h5jam/h5unjam.c index aa893f9..8ff354e 100644 --- a/tools/src/h5jam/h5unjam.c +++ b/tools/src/h5jam/h5unjam.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -21,34 +21,24 @@ #define COPY_BUF_SIZE 1024 -hsize_t write_pad( int , hsize_t ); -hsize_t compute_pad( hsize_t ); -herr_t copy_to_file( FILE *, FILE * , ssize_t, ssize_t ); +hsize_t write_pad(int, hsize_t); +hsize_t compute_pad(hsize_t); +herr_t copy_to_file(FILE *, FILE *, ssize_t, ssize_t); -int do_delete = FALSE; +int do_delete = FALSE; char *output_file = NULL; -char *input_file = NULL; -char *ub_file = NULL; +char *input_file = NULL; +char *ub_file = NULL; /* * Command-line options: The user can specify short or long-named * parameters. The long-named ones can be partially spelled. When * adding more, make sure that they don't clash with each other. */ -static const char *s_opts = "hu:i:o:d:V"; -static struct long_options l_opts[] = { - { "help", no_arg, 'h' }, - { "hel", no_arg, 'h' }, - {"i", require_arg, 'i'}, /* input file */ - {"u", require_arg, 'u'}, /* user block file */ - {"o", require_arg, 'o'}, /* output file */ - {"delete", no_arg, 'd'}, /* delete ub */ - {"delet", no_arg, 'd'}, - {"dele", no_arg, 'd'}, - {"del", no_arg, 'd'}, - {"de", no_arg, 'd'}, - { NULL, 0, '\0' } -}; +static const char * s_opts = "hu:i:o:d:V"; +static struct h5_long_options l_opts[] = {{"help", no_arg, 'h'}, {"i", require_arg, 'i'}, + {"u", require_arg, 'u'}, {"o", require_arg, 'o'}, + {"delete", no_arg, 'd'}, {NULL, 0, '\0'}}; /*------------------------------------------------------------------------- * Function: usage @@ -62,55 +52,34 @@ static void usage(const char *prog) { HDfflush(stdout); - HDfprintf(stdout, - "usage: %s -i <in_file.h5> [-o <out_file.h5> ] [-u <out_user_file> | --delete]\n", prog); + HDfprintf(stdout, "usage: %s -i <in_file.h5> [-o <out_file.h5> ] [-u <out_user_file> | --delete]\n", + prog); HDfprintf(stdout, "\n"); - HDfprintf(stdout, - "Splits user file and HDF5 file into two files: user block data and HDF5 data.\n"); + HDfprintf(stdout, "Splits user file and HDF5 file into two files: user block data and HDF5 data.\n"); HDfprintf(stdout, "\n"); - HDfprintf(stdout, - "OPTIONS\n"); - HDfprintf(stdout, - " -i in_file.h5 Specifies the HDF5 as input. If the input HDF5 file\n"); - HDfprintf(stdout, - " contains no user block, exit with an error message.\n"); - HDfprintf(stdout, - " -o out_file.h5 Specifies output HDF5 file without a user block.\n"); - HDfprintf(stdout, - " If not specified, the user block will be removed from the\n"); - HDfprintf(stdout, - " input HDF5 file.\n"); - HDfprintf(stdout, - " -u out_user_file\n"); - HDfprintf(stdout, - " Specifies the output file containing the data from the\n"); - HDfprintf(stdout, - " user block.\n"); - HDfprintf(stdout, - " Cannot be used with --delete option.\n"); - HDfprintf(stdout, - " --delete Remove the user block from the input HDF5 file. The content\n"); - HDfprintf(stdout, - " of the user block is discarded.\n"); - HDfprintf(stdout, - " Cannot be used with the -u option.\n"); + HDfprintf(stdout, "OPTIONS\n"); + HDfprintf(stdout, " -i in_file.h5 Specifies the HDF5 as input. If the input HDF5 file\n"); + HDfprintf(stdout, " contains no user block, exit with an error message.\n"); + HDfprintf(stdout, " -o out_file.h5 Specifies output HDF5 file without a user block.\n"); + HDfprintf(stdout, " If not specified, the user block will be removed from the\n"); + HDfprintf(stdout, " input HDF5 file.\n"); + HDfprintf(stdout, " -u out_user_file\n"); + HDfprintf(stdout, " Specifies the output file containing the data from the\n"); + HDfprintf(stdout, " user block.\n"); + HDfprintf(stdout, " Cannot be used with --delete option.\n"); + HDfprintf(stdout, " --delete Remove the user block from the input HDF5 file. The content\n"); + HDfprintf(stdout, " of the user block is discarded.\n"); + HDfprintf(stdout, " Cannot be used with the -u option.\n"); HDfprintf(stdout, "\n"); - HDfprintf(stdout, - " -h Prints a usage message and exits.\n"); - HDfprintf(stdout, - " -V Prints the HDF5 library version and exits.\n"); + HDfprintf(stdout, " -h Prints a usage message and exits.\n"); + HDfprintf(stdout, " -V Prints the HDF5 library version and exits.\n"); HDfprintf(stdout, "\n"); - HDfprintf(stdout, - " If neither --delete nor -u is specified, the user block from the input file\n"); - HDfprintf(stdout, - " will be displayed to stdout.\n"); + HDfprintf(stdout, " If neither --delete nor -u is specified, the user block from the input file\n"); + HDfprintf(stdout, " will be displayed to stdout.\n"); HDfprintf(stdout, "\n"); - HDfprintf(stdout, - "Exit Status:\n"); - HDfprintf(stdout, - " 0 Succeeded.\n"); - HDfprintf(stdout, - " >0 An error occurred.\n"); + HDfprintf(stdout, "Exit Status:\n"); + HDfprintf(stdout, " 0 Succeeded.\n"); + HDfprintf(stdout, " >0 An error occurred.\n"); } /*------------------------------------------------------------------------- @@ -123,27 +92,28 @@ usage(const char *prog) *------------------------------------------------------------------------- */ static int -parse_command_line(int argc, const char *argv[]) +parse_command_line(int argc, const char *const *argv) { int opt = FALSE; - /* parse command line options */ - while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) { - switch((char)opt) { + /* parse command line options */ + while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) { + switch ((char)opt) { case 'o': - output_file = HDstrdup(opt_arg); + output_file = HDstrdup(H5_optarg); if (output_file) h5tools_set_data_output_file(output_file, 1); break; case 'i': - input_file = HDstrdup(opt_arg); + input_file = HDstrdup(H5_optarg); if (input_file) h5tools_set_input_file(input_file, 1); - break;; + break; + ; case 'u': - ub_file = HDstrdup(opt_arg); + ub_file = HDstrdup(H5_optarg); if (ub_file) h5tools_set_output_file(ub_file, 1); else @@ -160,7 +130,7 @@ parse_command_line(int argc, const char *argv[]) goto done; case 'V': - print_version (h5tools_getprogname()); + print_version(h5tools_getprogname()); h5tools_setstatus(EXIT_SUCCESS); goto done; @@ -175,16 +145,23 @@ parse_command_line(int argc, const char *argv[]) return EXIT_SUCCESS; done: - if(input_file) + if (input_file) HDfree(input_file); - if(output_file) + if (output_file) HDfree(output_file); - if(ub_file) + if (ub_file) HDfree(ub_file); return EXIT_FAILURE; } +static void +leave(int ret) +{ + h5tools_close(); + HDexit(ret); +} + /*------------------------------------------------------------------------- * Function: main * @@ -195,32 +172,29 @@ done: *------------------------------------------------------------------------- */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { - void *edata; - H5E_auto2_t func; - hid_t ifile = -1; - hid_t plist = -1; - off_t fsize; - hsize_t usize; - htri_t testval; - herr_t status; - int res; - h5_stat_t sbuf; + hid_t ifile = H5I_INVALID_HID; + hid_t plist = H5I_INVALID_HID; + off_t fsize; + hsize_t usize; + htri_t testval; + herr_t status; + int res; + h5_stat_t sbuf; h5tools_setprogname(PROGRAMNAME); h5tools_setstatus(EXIT_SUCCESS); - /* Disable error reporting */ - H5Eget_auto2(H5E_DEFAULT, &func, &edata); - H5Eset_auto2(H5E_DEFAULT, NULL, NULL); - /* Initialize h5tools lib */ h5tools_init(); - if(EXIT_FAILURE == parse_command_line(argc, argv)) + if (EXIT_FAILURE == parse_command_line(argc, (const char *const *)argv)) goto done; + /* enable error reporting if command line option */ + h5tools_error_report(); + if (input_file == NULL) { /* no user block */ error_msg("missing argument for HDF5 file input.\n"); @@ -233,12 +207,12 @@ main(int argc, const char *argv[]) if (testval <= 0) { error_msg("Input HDF5 file \"%s\" is not HDF\n", input_file); - help_ref_msg (stderr); + help_ref_msg(stderr); h5tools_setstatus(EXIT_FAILURE); goto done; } - ifile = H5Fopen(input_file, H5F_ACC_RDONLY , H5P_DEFAULT); + ifile = H5Fopen(input_file, H5F_ACC_RDONLY, H5P_DEFAULT); if (ifile < 0) { error_msg("Can't open input HDF5 file \"%s\"\n", input_file); @@ -253,7 +227,7 @@ main(int argc, const char *argv[]) goto done; } - status = H5Pget_userblock(plist, & usize); + status = H5Pget_userblock(plist, &usize); if (status < 0) { error_msg("Can't get user block for file \"%s\"\n", input_file); h5tools_setstatus(EXIT_FAILURE); @@ -264,14 +238,14 @@ main(int argc, const char *argv[]) H5Fclose(ifile); if (usize == 0) { - /* no user block to remove: message? */ + /* no user block to remove: message? */ error_msg("\"%s\" has no user block: no change to file\n", input_file); h5tools_setstatus(EXIT_SUCCESS); goto done; } res = HDfstat(HDfileno(rawinstream), &sbuf); - if(res < 0) { + if (res < 0) { error_msg("Can't stat file \"%s\"\n", input_file); h5tools_setstatus(EXIT_FAILURE); goto done; @@ -286,14 +260,14 @@ main(int argc, const char *argv[]) } if (output_file == NULL) { - error_msg("unable to open output HDF5 file \"%s\"\n", input_file); - h5tools_setstatus(EXIT_FAILURE); - goto done; + error_msg("unable to open output HDF5 file \"%s\"\n", input_file); + h5tools_setstatus(EXIT_FAILURE); + goto done; } /* copy from 0 to 'usize - 1' into ufid */ if (!do_delete) { - if(copy_to_file(rawinstream, rawoutstream, 0, (ssize_t) usize) < 0) { + if (copy_to_file(rawinstream, rawoutstream, 0, (ssize_t)usize) < 0) { error_msg("unable to copy user block to output file \"%s\"\n", ub_file); h5tools_setstatus(EXIT_FAILURE); goto done; @@ -302,26 +276,24 @@ main(int argc, const char *argv[]) /* copy from usize to end of file into h5fid, * starting at end of user block if present */ - if(copy_to_file(rawinstream, rawdatastream, (ssize_t) usize, (ssize_t)(fsize - (ssize_t)usize)) < 0) { + if (copy_to_file(rawinstream, rawdatastream, (ssize_t)usize, (ssize_t)(fsize - (ssize_t)usize)) < 0) { error_msg("unable to copy hdf5 data to output file \"%s\"\n", output_file); h5tools_setstatus(EXIT_FAILURE); goto done; } done: - if(input_file) + if (input_file) HDfree(input_file); - if(output_file) + if (output_file) HDfree(output_file); - if(ub_file) { + if (ub_file) { HDfree(ub_file); } - h5tools_close(); - - return h5tools_getstatus(); + leave(h5tools_getstatus()); } /*------------------------------------------------------------------------- @@ -332,17 +304,17 @@ done: *------------------------------------------------------------------------- */ herr_t -copy_to_file( FILE *infid, FILE *ofid, ssize_t _where, ssize_t show_much ) +copy_to_file(FILE *infid, FILE *ofid, ssize_t _where, ssize_t show_much) { static char buf[COPY_BUF_SIZE]; - size_t how_much; - off_t where = (off_t)_where; - off_t to; - off_t from; - herr_t ret_value = 0; + size_t how_much; + off_t where = (off_t)_where; + off_t to; + off_t from; + herr_t ret_value = 0; /* nothing to copy */ - if(show_much <= 0) + if (show_much <= 0) goto done; how_much = (size_t)show_much; @@ -350,27 +322,27 @@ copy_to_file( FILE *infid, FILE *ofid, ssize_t _where, ssize_t show_much ) HDfseek(infid, 0L, 0); from = where; - to = 0; - while(how_much > 0) { - size_t bytes_in = 0; /* # of bytes to read */ - size_t bytes_read = 0; /* # of bytes actually read */ - size_t bytes_wrote = 0; /* # of bytes written */ + to = 0; + while (how_much > 0) { + size_t bytes_in = 0; /* # of bytes to read */ + size_t bytes_read = 0; /* # of bytes actually read */ + size_t bytes_wrote = 0; /* # of bytes written */ if (how_much > COPY_BUF_SIZE) bytes_in = COPY_BUF_SIZE; else bytes_in = how_much; - /* Seek to correct position in input file */ + /* Seek to correct position in input file */ HDfseek(infid, from, SEEK_SET); /* Read data to buffer */ bytes_read = HDfread(buf, (size_t)1, bytes_in, infid); - if(0 == bytes_read && HDferror(infid)) { + if (0 == bytes_read && HDferror(infid)) { ret_value = -1; goto done; } /* end if */ - if(0 == bytes_read && HDfeof(infid)) { + if (0 == bytes_read && HDfeof(infid)) { goto done; } /* end if */ @@ -382,15 +354,14 @@ copy_to_file( FILE *infid, FILE *ofid, ssize_t _where, ssize_t show_much ) from += (off_t)bytes_read; to += (off_t)bytes_read; - /* Write nchars bytes to output file */ + /* Write nchars bytes to output file */ bytes_wrote = HDfwrite(buf, (size_t)1, bytes_read, ofid); - if(bytes_wrote != bytes_read || (0 == bytes_wrote && HDferror(ofid))) { /* error */ + if (bytes_wrote != bytes_read || (0 == bytes_wrote && HDferror(ofid))) { /* error */ ret_value = -1; goto done; } /* end if */ - } /* end while */ + } /* end while */ done: return ret_value; -} /* end copy_to_file */ - +} /* end copy_to_file */ diff --git a/tools/src/h5ls/CMakeLists.txt b/tools/src/h5ls/CMakeLists.txt index f2470fb..80b9b0c 100644 --- a/tools/src/h5ls/CMakeLists.txt +++ b/tools/src/h5ls/CMakeLists.txt @@ -1,4 +1,4 @@ -cmake_minimum_required (VERSION 3.10) +cmake_minimum_required (VERSION 3.12) project (HDF5_TOOLS_SRC_H5LS C) #----------------------------------------------------------------------------- @@ -6,7 +6,9 @@ project (HDF5_TOOLS_SRC_H5LS C) #----------------------------------------------------------------------------- if (NOT ONLY_SHARED_LIBS) add_executable (h5ls ${HDF5_TOOLS_SRC_H5LS_SOURCE_DIR}/h5ls.c) - target_include_directories (h5ls PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5ls PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_compile_options(h5ls PRIVATE "${HDF5_CMAKE_C_FLAGS}") + #target_compile_definitions(h5ls PRIVATE H5_TOOLS_DEBUG) TARGET_C_PROPERTIES (h5ls STATIC) target_link_libraries (h5ls PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) set_target_properties (h5ls PROPERTIES FOLDER tools) @@ -17,7 +19,9 @@ endif () if (BUILD_SHARED_LIBS) add_executable (h5ls-shared ${HDF5_TOOLS_SRC_H5LS_SOURCE_DIR}/h5ls.c) - target_include_directories (h5ls-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5ls-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_compile_options(h5ls-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}") + #target_compile_definitions(h5ls-shared PRIVATE H5_TOOLS_DEBUG) TARGET_C_PROPERTIES (h5ls-shared SHARED) target_link_libraries (h5ls-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET}) set_target_properties (h5ls-shared PROPERTIES FOLDER tools) @@ -26,6 +30,17 @@ if (BUILD_SHARED_LIBS) set (H5_DEP_EXECUTABLES ${H5_DEP_EXECUTABLES} h5ls-shared) endif () +#----------------------------------------------------------------------------- +# Add Target to clang-format +#----------------------------------------------------------------------------- +if (HDF5_ENABLE_FORMATTERS) + if (NOT ONLY_SHARED_LIBS) + clang_format (HDF5_H5LS_SRC_FORMAT h5ls) + else () + clang_format (HDF5_H5LS_SRC_FORMAT h5ls-shared) + endif () +endif () + ############################################################################## ############################################################################## ### I N S T A L L A T I O N ### diff --git a/tools/src/h5ls/Makefile.am b/tools/src/h5ls/Makefile.am index 07279c1..9a4466d 100644 --- a/tools/src/h5ls/Makefile.am +++ b/tools/src/h5ls/Makefile.am @@ -6,7 +6,7 @@ # This file is part of HDF5. The full HDF5 copyright notice, including # terms governing use, modification, and redistribution, is contained in # the COPYING file, which can be found at the root of the source code -# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. +# distribution tree, or in https://www.hdfgroup.org/licenses. # If you do not have access to either file, you may request a copy from # help@hdfgroup.org. ## diff --git a/tools/src/h5ls/h5ls.c b/tools/src/h5ls/h5ls.c index 20a68e8..c30c08f 100644 --- a/tools/src/h5ls/h5ls.c +++ b/tools/src/h5ls/h5ls.c @@ -6,17 +6,16 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ /* - * Programmer: Robb Matzke <matzke@llnl.gov> + * Programmer: Robb Matzke * Monday, March 23, 1998 */ - /* * We include the private header file so we can get to the uniform * programming environment it declares. Other than that, h5ls only calls @@ -31,112 +30,112 @@ /* Name of tool */ #define PROGRAMNAME "h5ls" -#define NAME_BUF_SIZE 2048 +#define NAME_BUF_SIZE 2048 /* - * Alternative formating for data dumped by H5LS + * Alternative formatting for data dumped by H5LS * * This table only affects H5LS output. */ -static h5tool_format_t ls_dataformat = { - 0, /*raw */ - - "", /*fmt_raw */ - "%d", /*fmt_int */ - "%u", /*fmt_uint */ - "%hhd", /*fmt_schar */ - "%u", /*fmt_uchar */ - "%d", /*fmt_short */ - "%u", /*fmt_ushort */ - "%ld", /*fmt_long */ - "%lu", /*fmt_ulong */ - NULL, /*fmt_llong */ - NULL, /*fmt_ullong */ - "%g", /*fmt_double */ - "%g", /*fmt_float */ - - 0, /*ascii */ - 0, /*str_locale */ - 0, /*str_repeat */ - - "[", /*arr_pre */ - ",", /*arr_sep */ - "]", /*arr_suf */ - 1, /*arr_linebreak */ - - "", /*cmpd_name */ - ",", /*cmpd_sep */ - "{", /*cmpd_pre */ - "}", /*cmpd_suf */ - "", /*cmpd_end */ - NULL, /* cmpd_listv */ - - ",", /*vlen_sep */ - "(", /*vlen_pre */ - ")", /*vlen_suf */ - "", /*vlen_end */ - - "%s", /*elmt_fmt */ - ",", /*elmt_suf1 */ - " ", /*elmt_suf2 */ - - HSIZE_T_FORMAT, /*idx_n_fmt */ - ",", /*idx_sep */ - "(%s)", /*idx_fmt */ - - 65535, /*line_ncols *//*standard default columns */ - 0, /*line_per_line */ - "", /*line_pre */ - "%s", /*line_1st */ - "%s", /*line_cont */ - "", /*line_suf */ - "", /*line_sep */ - 1, /*line_multi_new */ - "", /*line_indent */ - - 0, /*skip_first */ - - 0, /*obj_hidefileno */ - "-%lu:"H5_PRINTF_HADDR_FMT, /*obj_format */ - - 0, /*dset_hidefileno */ - "DSET-%s ", /*dset_format */ - "%sBlk%lu: ", /*dset_blockformat_pre */ - "%sPt%lu: ", /*dset_ptformat_pre */ - "%s", /*dset_ptformat */ - 1, /*array indices */ - 1 /*escape non printable characters */ +static h5tool_format_t ls_dataformat = { + 0, /*raw */ + + "", /*fmt_raw */ + "%d", /*fmt_int */ + "%u", /*fmt_uint */ + "%hhd", /*fmt_schar */ + "%u", /*fmt_uchar */ + "%d", /*fmt_short */ + "%u", /*fmt_ushort */ + "%ld", /*fmt_long */ + "%lu", /*fmt_ulong */ + NULL, /*fmt_llong */ + NULL, /*fmt_ullong */ + "%g", /*fmt_double */ + "%g", /*fmt_float */ + + 0, /*ascii */ + 0, /*str_locale */ + 0, /*str_repeat */ + + "[", /*arr_pre */ + ",", /*arr_sep */ + "]", /*arr_suf */ + 1, /*arr_linebreak */ + + "", /*cmpd_name */ + ",", /*cmpd_sep */ + "{", /*cmpd_pre */ + "}", /*cmpd_suf */ + "", /*cmpd_end */ + NULL, /* cmpd_listv */ + + ",", /*vlen_sep */ + "(", /*vlen_pre */ + ")", /*vlen_suf */ + "", /*vlen_end */ + + "%s", /*elmt_fmt */ + ",", /*elmt_suf1 */ + " ", /*elmt_suf2 */ + + "%" PRIuHSIZE, /*idx_n_fmt */ + ",", /*idx_sep */ + "(%s)", /*idx_fmt */ + + 65535, + /*line_ncols */ /*standard default columns */ + 0, /*line_per_line */ + "", /*line_pre */ + "%s", /*line_1st */ + "%s", /*line_cont */ + "", /*line_suf */ + "", /*line_sep */ + 1, /*line_multi_new */ + " ", /*line_indent */ + + 0, /*skip_first */ + + 0, /*obj_hidefileno */ + "-%lu:%" PRIuHADDR, /*obj_format */ + + 0, /*dset_hidefileno */ + "DSET-%s ", /*dset_format */ + "%sBlk%lu: ", /*dset_blockformat_pre */ + "%sPt%lu: ", /*dset_ptformat_pre */ + "%s", /*dset_ptformat */ + 1, /*array indices */ + 1 /*escape non printable characters */ }; /* Struct to pass through to visitors */ typedef struct { - const char *fname; /* Filename */ - hid_t fid; /* File ID */ - hid_t gid; /* Group ID */ - hbool_t symlink_target; /* Whether this is the target of an symbolic link */ - symlink_trav_t *symlink_list; /* List of visited symbolic links */ - size_t base_len; /* Length of base path name, if not root */ - size_t name_start; /* # of leading characters to strip off path names on output */ -}iter_t; + const char * fname; /* Filename */ + hid_t fid; /* File ID */ + hid_t gid; /* Group ID */ + hbool_t symlink_target; /* Whether this is the target of an symbolic link */ + symlink_trav_t *symlink_list; /* List of visited symbolic links */ + size_t base_len; /* Length of base path name, if not root */ + size_t name_start; /* # of leading characters to strip off path names on output */ +} iter_t; /* Command-line switches */ -static int verbose_g = 0; /* lots of extra output */ -static int width_g = 80; /* output width in characters */ -static hbool_t address_g = FALSE; /* print raw data addresses */ -static hbool_t data_g = FALSE; /* display dataset values? */ -static hbool_t label_g = FALSE; /* label compound values? */ -static hbool_t string_g = FALSE; /* print 1-byte numbers as ASCII? */ -static hbool_t fullname_g = FALSE; /* print full path names */ -static hbool_t recursive_g = FALSE; /* recursive descent listing */ -static hbool_t follow_symlink_g = FALSE; /* follow symbolic links */ -static hbool_t no_dangling_link_g = FALSE; /* treat dangling link is error */ -static hbool_t follow_elink_g = FALSE; /* follow external links */ -static hbool_t grp_literal_g = FALSE; /* list group, not contents */ -static hbool_t hexdump_g = FALSE; /* show data as raw hexadecimal */ -static hbool_t show_errors_g = FALSE; /* print HDF5 error messages */ -static hbool_t simple_output_g = FALSE; /* make output more machine-readable */ -static hbool_t show_file_name_g = FALSE; /* show file name for full names */ -static hbool_t no_line_wrap_g = FALSE; /* show data content without line wrap */ -static hbool_t display_root_g = FALSE; /* show root group in output? */ +static int verbose_g = 0; /* lots of extra output */ +static int width_g = 80; /* output width in characters */ +static hbool_t address_g = FALSE; /* print raw data addresses */ +static hbool_t data_g = FALSE; /* display dataset values? */ +static hbool_t label_g = FALSE; /* label compound values? */ +static hbool_t string_g = FALSE; /* print 1-byte numbers as ASCII? */ +static hbool_t fullname_g = FALSE; /* print full path names */ +static hbool_t recursive_g = FALSE; /* recursive descent listing */ +static hbool_t follow_symlink_g = FALSE; /* follow symbolic links */ +static hbool_t no_dangling_link_g = FALSE; /* treat dangling link is error */ +static hbool_t follow_elink_g = FALSE; /* follow external links */ +static hbool_t grp_literal_g = FALSE; /* list group, not contents */ +static hbool_t hexdump_g = FALSE; /* show data as raw hexadecimal */ +static hbool_t simple_output_g = FALSE; /* make output more machine-readable */ +static hbool_t show_file_name_g = FALSE; /* show file name for full names */ +static hbool_t no_line_wrap_g = FALSE; /* show data content without line wrap */ +static hbool_t display_root_g = FALSE; /* show root group in output? */ /* Information about how to display each type of object */ static struct dispatch_t { @@ -147,17 +146,17 @@ static struct dispatch_t { herr_t (*list2)(hid_t obj, const char *name); } dispatch_g[H5O_TYPE_NTYPES]; -#define DISPATCH(TYPE, NAME, LIST1, LIST2) { \ - dispatch_g[TYPE].name = (NAME); \ - dispatch_g[TYPE].list1 = (LIST1); \ - dispatch_g[TYPE].list2 = (LIST2); \ -} +#define DISPATCH(TYPE, NAME, LIST1, LIST2) \ + { \ + dispatch_g[TYPE].name = (NAME); \ + dispatch_g[TYPE].list1 = (LIST1); \ + dispatch_g[TYPE].list2 = (LIST2); \ + } -static void print_type(h5tools_str_t *buffer, hid_t type, int ind); +static void print_type(h5tools_str_t *buffer, hid_t type, int ind); static hbool_t print_int_type(h5tools_str_t *buffer, hid_t type, int ind); static hbool_t print_float_type(h5tools_str_t *buffer, hid_t type, int ind); -static herr_t visit_obj(hid_t file, const char *oname, iter_t *iter); - +static herr_t visit_obj(hid_t file, const char *oname, iter_t *iter); /*------------------------------------------------------------------------- * Function: usage @@ -168,36 +167,46 @@ static herr_t visit_obj(hid_t file, const char *oname, iter_t *iter); *------------------------------------------------------------------------- */ static void -usage (void) +usage(void) { FLUSHSTREAM(rawoutstream); PRINTVALSTREAM(rawoutstream, "usage: h5ls [OPTIONS] file[/OBJECT] [file[/[OBJECT]...]\n"); PRINTVALSTREAM(rawoutstream, " OPTIONS\n"); PRINTVALSTREAM(rawoutstream, " -h, -?, --help Print a usage message and exit\n"); - PRINTVALSTREAM(rawoutstream, " -a, --address Print raw data address. If dataset is contiguous, address\n"); - PRINTVALSTREAM(rawoutstream, " is offset in file of beginning of raw data. If chunked,\n"); - PRINTVALSTREAM(rawoutstream, " returned list of addresses indicates offset of each chunk.\n"); + PRINTVALSTREAM(rawoutstream, + " -a, --address Print raw data address. If dataset is contiguous, address\n"); + PRINTVALSTREAM(rawoutstream, + " is offset in file of beginning of raw data. If chunked,\n"); + PRINTVALSTREAM(rawoutstream, + " returned list of addresses indicates offset of each chunk.\n"); PRINTVALSTREAM(rawoutstream, " Must be used with -v, --verbose option.\n"); PRINTVALSTREAM(rawoutstream, " Provides no information for non-dataset objects.\n"); PRINTVALSTREAM(rawoutstream, " -d, --data Print the values of datasets\n"); PRINTVALSTREAM(rawoutstream, " --enable-error-stack\n"); - PRINTVALSTREAM(rawoutstream, " Prints messages from the HDF5 error stack as they occur.\n"); + PRINTVALSTREAM(rawoutstream, + " Prints messages from the HDF5 error stack as they occur.\n"); PRINTVALSTREAM(rawoutstream, " --follow-symlinks\n"); - PRINTVALSTREAM(rawoutstream, " Follow symbolic links (soft links and external links)\n"); + PRINTVALSTREAM(rawoutstream, + " Follow symbolic links (soft links and external links)\n"); PRINTVALSTREAM(rawoutstream, " to display target object information.\n"); PRINTVALSTREAM(rawoutstream, " Without this option, h5ls identifies a symbolic link\n"); PRINTVALSTREAM(rawoutstream, " as a soft link or external link and prints the value\n"); - PRINTVALSTREAM(rawoutstream, " assigned to the symbolic link; it does not provide any\n"); + PRINTVALSTREAM(rawoutstream, + " assigned to the symbolic link; it does not provide any\n"); PRINTVALSTREAM(rawoutstream, " information regarding the target object or determine\n"); PRINTVALSTREAM(rawoutstream, " whether the link is a dangling link.\n"); PRINTVALSTREAM(rawoutstream, " --no-dangling-links\n"); PRINTVALSTREAM(rawoutstream, " Must be used with --follow-symlinks option;\n"); - PRINTVALSTREAM(rawoutstream, " otherwise, h5ls shows error message and returns an exit\n"); - PRINTVALSTREAM(rawoutstream, " code of 1. \n"); - PRINTVALSTREAM(rawoutstream, " Check for any symbolic links (soft links or external links)\n"); - PRINTVALSTREAM(rawoutstream, " that do not resolve to an existing object (dataset, group,\n"); + PRINTVALSTREAM(rawoutstream, + " otherwise, h5ls shows error message and returns an exit\n"); + PRINTVALSTREAM(rawoutstream, " code of 1.\n"); + PRINTVALSTREAM(rawoutstream, + " Check for any symbolic links (soft links or external links)\n"); + PRINTVALSTREAM(rawoutstream, + " that do not resolve to an existing object (dataset, group,\n"); PRINTVALSTREAM(rawoutstream, " or named datatype).\n"); - PRINTVALSTREAM(rawoutstream, " If any dangling link is found, this situation is treated\n"); + PRINTVALSTREAM(rawoutstream, + " If any dangling link is found, this situation is treated\n"); PRINTVALSTREAM(rawoutstream, " as an error and h5ls returns an exit code of 1.\n"); PRINTVALSTREAM(rawoutstream, " -f, --full Print full path names instead of base names\n"); PRINTVALSTREAM(rawoutstream, " -g, --group Show information about a group, not its contents\n"); @@ -210,15 +219,33 @@ usage (void) PRINTVALSTREAM(rawoutstream, " -V, --version Print version number and exit\n"); PRINTVALSTREAM(rawoutstream, " --vfd=DRIVER Use the specified virtual file driver\n"); PRINTVALSTREAM(rawoutstream, " -x, --hexdump Show raw data in hexadecimal format\n"); - PRINTVALSTREAM(rawoutstream, " --s3-cred=C Supply S3 authentication information to \"ros3\" vfd.\n"); - PRINTVALSTREAM(rawoutstream, " Accepts tuple of \"(<aws-region>,<access-id>,<access-key>)\".\n"); - PRINTVALSTREAM(rawoutstream, " If absent or C->\"(,,)\", defaults to no-authentication.\n"); + PRINTVALSTREAM(rawoutstream, + " --s3-cred=C Supply S3 authentication information to \"ros3\" vfd.\n"); + PRINTVALSTREAM(rawoutstream, + " Accepts tuple of \"(<aws-region>,<access-id>,<access-key>)\".\n"); + PRINTVALSTREAM(rawoutstream, + " If absent or C->\"(,,)\", defaults to no-authentication.\n"); PRINTVALSTREAM(rawoutstream, " Has no effect if vfd flag not set to \"ros3\".\n"); PRINTVALSTREAM(rawoutstream, " --hdfs-attrs=A Supply configuration information to Hadoop VFD.\n"); PRINTVALSTREAM(rawoutstream, " Accepts tuple of (<namenode name>,<namenode port>,\n"); PRINTVALSTREAM(rawoutstream, " ...<kerberos cache path>,<username>,<buffer size>)\n"); - PRINTVALSTREAM(rawoutstream, " If absent or A == '(,,,,)', all default values are used.\n"); + PRINTVALSTREAM(rawoutstream, + " If absent or A == '(,,,,)', all default values are used.\n"); PRINTVALSTREAM(rawoutstream, " Has no effect if vfd flag is not 'hdfs'.\n"); + PRINTVALSTREAM(rawoutstream, + " --vol-value Value (ID) of the VOL connector to use for opening the\n"); + PRINTVALSTREAM(rawoutstream, " HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, " --vol-name Name of the VOL connector to use for opening the\n"); + PRINTVALSTREAM(rawoutstream, " HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, + " --vol-info VOL-specific info to pass to the VOL connector used for\n"); + PRINTVALSTREAM(rawoutstream, " opening the HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, " --vfd-value Value (ID) of the VFL driver to use for opening the\n"); + PRINTVALSTREAM(rawoutstream, " HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, " --vfd-name Name of the VFL driver to use for opening the\n"); + PRINTVALSTREAM(rawoutstream, " HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, " --vfd-info VFD-specific info to pass to the VFL driver used for\n"); + PRINTVALSTREAM(rawoutstream, " opening the HDF5 file specified\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " file/OBJECT\n"); PRINTVALSTREAM(rawoutstream, " Each object consists of an HDF5 file name optionally followed by a\n"); @@ -228,11 +255,9 @@ usage (void) PRINTVALSTREAM(rawoutstream, " \"%%05d\" to open a file family.\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " Deprecated Options\n"); - PRINTVALSTREAM(rawoutstream, " The following options have been deprecated in HDF5. While they remain\n"); - PRINTVALSTREAM(rawoutstream, " available, they have been superseded as indicated and may be removed\n"); - PRINTVALSTREAM(rawoutstream, " from HDF5 in the future. Use the indicated replacement option in all\n"); - PRINTVALSTREAM(rawoutstream, " new work; where possible, existing scripts, et cetera, should also be\n"); - PRINTVALSTREAM(rawoutstream, " updated to use the replacement option.\n"); + PRINTVALSTREAM(rawoutstream, + " The following options have been removed in HDF5 1.12. Use the indicated\n"); + PRINTVALSTREAM(rawoutstream, " replacement option in all work.\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " -E or --external Follow external links.\n"); PRINTVALSTREAM(rawoutstream, " Replaced by --follow-symlinks.\n"); @@ -240,20 +265,19 @@ usage (void) PRINTVALSTREAM(rawoutstream, " Replaced by --enable-error-stack.\n"); } - /*------------------------------------------------------------------------- - * Function: print_string + * Function: print_string * - * Purpose: Print a string value by escaping unusual characters. If - * STREAM is null then we only count how large the output would be. + * Purpose: Print a string value by escaping unusual characters. If + * STREAM is null then we only count how large the output would be. * - * Return: Number of characters printed. + * Return: Number of characters printed. *------------------------------------------------------------------------- */ static int print_string(h5tools_str_t *buffer, const char *s, hbool_t escape_spaces) { - int nprint=0; + int nprint = 0; for (/*void*/; s && *s; s++) { switch (*s) { @@ -288,7 +312,8 @@ print_string(h5tools_str_t *buffer, const char *s, hbool_t escape_spaces) nprint += 2; break; case '\t': - if (buffer) h5tools_str_append(buffer, "\\t"); + if (buffer) + h5tools_str_append(buffer, "\\t"); nprint += 2; break; case ' ': @@ -311,7 +336,7 @@ print_string(h5tools_str_t *buffer, const char *s, hbool_t escape_spaces) } else { if (buffer) - h5tools_str_append(buffer, "\\%03o", *((const unsigned char*)s)); + h5tools_str_append(buffer, "\\%03o", *((const unsigned char *)s)); nprint += 4; } break; @@ -320,23 +345,21 @@ print_string(h5tools_str_t *buffer, const char *s, hbool_t escape_spaces) return nprint; } - /*------------------------------------------------------------------------- - * Function: print_obj_name + * Function: print_obj_name * - * Purpose: Print an object name and another string. + * Purpose: Print an object name and another string. * - * Return: Success: TRUE - * Failure: FALSE, nothing printed + * Return: Success: TRUE + * Failure: FALSE, nothing printed *------------------------------------------------------------------------- */ static int -print_obj_name(h5tools_str_t *buffer, const iter_t *iter, const char *oname, - const char *s) +print_obj_name(h5tools_str_t *buffer, const iter_t *iter, const char *oname, const char *s) { - static char fullname[NAME_BUF_SIZE]; /* Buffer for file and/or object name */ - const char *name = fullname; /* Pointer to buffer for printing */ - int n; + static char fullname[NAME_BUF_SIZE]; /* Buffer for file and/or object name */ + const char *name = fullname; /* Pointer to buffer for printing */ + int n; if (show_file_name_g) HDsnprintf(fullname, sizeof(fullname), "%s/%s", iter->fname, oname + iter->name_start); @@ -347,7 +370,7 @@ print_obj_name(h5tools_str_t *buffer, const iter_t *iter, const char *oname, if (fullname_g) n = print_string(buffer, name, TRUE); else { - const char *last_sep; /* The location of the last group separator */ + const char *last_sep; /* The location of the last group separator */ /* Find the last component of the path name */ if (NULL == (last_sep = HDstrrchr(name, '/'))) @@ -362,14 +385,13 @@ print_obj_name(h5tools_str_t *buffer, const iter_t *iter, const char *oname, return TRUE; } - /*------------------------------------------------------------------------- - * Function: print_native_type + * Function: print_native_type * - * Purpose: Prints the name of a native C data type. + * Purpose: Prints the name of a native C data type. * - * Return: Success: TRUE - * Failure: FALSE, nothing printed. + * Return: Success: TRUE + * Failure: FALSE, nothing printed. *------------------------------------------------------------------------- */ static hbool_t @@ -412,11 +434,6 @@ print_native_type(h5tools_str_t *buffer, hid_t type, int ind) else if (H5Tequal(type, H5T_NATIVE_DOUBLE) == TRUE) { h5tools_str_append(buffer, "native double"); } -#if H5_SIZEOF_LONG_DOUBLE !=0 - else if (H5Tequal(type, H5T_NATIVE_LDOUBLE) == TRUE) { - h5tools_str_append(buffer, "native long double"); - } -#endif else if (H5Tequal(type, H5T_NATIVE_INT8) == TRUE) { h5tools_str_append(buffer, "native int8_t"); } @@ -516,20 +533,20 @@ print_native_type(h5tools_str_t *buffer, hid_t type, int ind) else { return print_int_type(buffer, type, ind); } - } else { + } + else { return print_int_type(buffer, type, ind); } return TRUE; } - /*------------------------------------------------------------------------- - * Function: print_ieee_type + * Function: print_ieee_type * - * Purpose: Print the name of an IEEE floating-point data type. + * Purpose: Print the name of an IEEE floating-point data type. * - * Return: Success: TRUE - * Failure: FALSE, nothing printed + * Return: Success: TRUE + * Failure: FALSE, nothing printed *------------------------------------------------------------------------- */ static hbool_t @@ -553,36 +570,35 @@ print_ieee_type(h5tools_str_t *buffer, hid_t type, int ind) return TRUE; } - /*------------------------------------------------------------------------- - * Function: print_precision + * Function: print_precision * - * Purpose: Prints information on the next line about precision and - * padding if the precision is less than the total data type - * size. + * Purpose: Prints information on the next line about precision and + * padding if the precision is less than the total data type + * size. * - * Return: void + * Return: void *------------------------------------------------------------------------- */ static void print_precision(h5tools_str_t *buffer, hid_t type, int ind) { - size_t prec; /* precision */ - H5T_pad_t plsb, pmsb; /* lsb and msb padding */ - const char *plsb_s=NULL; /* lsb padding string */ - const char *pmsb_s=NULL; /* msb padding string */ - size_t nbits; /* number of bits */ + size_t prec; /* precision */ + H5T_pad_t plsb, pmsb; /* lsb and msb padding */ + const char *plsb_s = NULL; /* lsb padding string */ + const char *pmsb_s = NULL; /* msb padding string */ + size_t nbits; /* number of bits */ /* If the precision is less than the total size then show the precision * and offset on the following line. Also display the padding * information. */ if (8 * H5Tget_size(type) != (prec = H5Tget_precision(type))) { - h5tools_str_append(buffer, "\n%*s(%lu bit%s of precision beginning at bit %lu)", - ind, "", (unsigned long)prec, 1 == prec ? "" : "s", (unsigned long)H5Tget_offset(type)); + h5tools_str_append(buffer, "\n%*s(%lu bit%s of precision beginning at bit %lu)", ind, "", + (unsigned long)prec, 1 == prec ? "" : "s", (unsigned long)H5Tget_offset(type)); H5Tget_pad(type, &plsb, &pmsb); if (H5Tget_offset(type) > 0) { - switch(plsb) { + switch (plsb) { case H5T_PAD_ZERO: plsb_s = "zero"; break; @@ -601,7 +617,7 @@ print_precision(h5tools_str_t *buffer, hid_t type, int ind) } } if ((unsigned)H5Tget_offset(type) + prec < 8 * H5Tget_size(type)) { - switch(pmsb) { + switch (pmsb) { case H5T_PAD_ZERO: pmsb_s = "zero"; break; @@ -623,39 +639,40 @@ print_precision(h5tools_str_t *buffer, hid_t type, int ind) h5tools_str_append(buffer, "\n%*s(", ind, ""); if (plsb_s) { nbits = (unsigned)H5Tget_offset(type); - h5tools_str_append(buffer, "%lu %s bit%s at bit 0", (unsigned long)nbits, plsb_s, 1 == nbits ? "" : "s"); + h5tools_str_append(buffer, "%lu %s bit%s at bit 0", (unsigned long)nbits, plsb_s, + 1 == nbits ? "" : "s"); } if (plsb_s && pmsb_s) h5tools_str_append(buffer, ", "); if (pmsb_s) { nbits = (8 * H5Tget_size(type)) - ((unsigned)H5Tget_offset(type) + prec); - h5tools_str_append(buffer, "%lu %s bit%s at bit %lu", (unsigned long)nbits, pmsb_s, 1 == nbits ? "" : "s", (unsigned long)(8 * H5Tget_size(type) - nbits)); + h5tools_str_append(buffer, "%lu %s bit%s at bit %lu", (unsigned long)nbits, pmsb_s, + 1 == nbits ? "" : "s", (unsigned long)(8 * H5Tget_size(type) - nbits)); } h5tools_str_append(buffer, ")"); } } } - /*------------------------------------------------------------------------- - * Function: print_int_type + * Function: print_int_type * - * Purpose: Print the name of an integer data type. Common information - * like number of bits, byte order, and sign scheme appear on - * the first line. Additional information might appear in - * parentheses on the following lines. + * Purpose: Print the name of an integer data type. Common information + * like number of bits, byte order, and sign scheme appear on + * the first line. Additional information might appear in + * parentheses on the following lines. * - * Return: Success: TRUE - * Failure: FALSE, nothing printed + * Return: Success: TRUE + * Failure: FALSE, nothing printed *------------------------------------------------------------------------- */ static hbool_t print_int_type(h5tools_str_t *buffer, hid_t type, int ind) { - H5T_order_t order; /* byte order value */ - const char *order_s = NULL; /* byte order string */ - H5T_sign_t sign; /* sign scheme value */ - const char *sign_s = NULL; /* sign scheme string */ + H5T_order_t order; /* byte order value */ + const char *order_s = NULL; /* byte order string */ + H5T_sign_t sign; /* sign scheme value */ + const char *sign_s = NULL; /* sign scheme string */ if (H5T_INTEGER != H5Tget_class(type)) return FALSE; @@ -698,34 +715,34 @@ print_int_type(h5tools_str_t *buffer, hid_t type, int ind) /* Print size, order, and sign on first line, precision and padding * information on the subsequent lines */ - h5tools_str_append(buffer, "%lu-bit%s%s integer", (unsigned long)(8*H5Tget_size(type)), order_s, sign_s); + h5tools_str_append(buffer, "%lu-bit%s%s integer", (unsigned long)(8 * H5Tget_size(type)), order_s, + sign_s); print_precision(buffer, type, ind); return TRUE; } - /*------------------------------------------------------------------------- - * Function: print_float_type + * Function: print_float_type * - * Purpose: Print info about a floating point data type. + * Purpose: Print info about a floating point data type. * - * Return: Success: TRUE - * Failure: FALSE, nothing printed + * Return: Success: TRUE + * Failure: FALSE, nothing printed *------------------------------------------------------------------------- */ static hbool_t print_float_type(h5tools_str_t *buffer, hid_t type, int ind) { H5T_order_t order; /* byte order value */ - const char *order_s=NULL; /* byte order string */ + const char *order_s = NULL; /* byte order string */ size_t spos; /* sign bit position */ size_t esize, epos; /* exponent size and position */ size_t msize, mpos; /* significand size and position */ size_t ebias; /* exponent bias */ H5T_norm_t norm; /* significand normalization */ - const char *norm_s=NULL; /* normalization string */ + const char *norm_s = NULL; /* normalization string */ H5T_pad_t pad; /* internal padding value */ - const char *pad_s=NULL; /* internal padding string */ + const char *pad_s = NULL; /* internal padding string */ if (H5T_FLOAT != H5Tget_class(type)) return FALSE; @@ -752,13 +769,13 @@ print_float_type(h5tools_str_t *buffer, hid_t type, int ind) /* Print size and byte order on first line, precision and padding on * subsequent lines. */ - h5tools_str_append(buffer, "%lu-bit%s floating-point", (unsigned long)(8*H5Tget_size(type)), order_s); + h5tools_str_append(buffer, "%lu-bit%s floating-point", (unsigned long)(8 * H5Tget_size(type)), order_s); print_precision(buffer, type, ind); /* Print sizes, locations, and other information about each field */ - H5Tget_fields (type, &spos, &epos, &esize, &mpos, &msize); + H5Tget_fields(type, &spos, &epos, &esize, &mpos, &msize); ebias = H5Tget_ebias(type); - norm = H5Tget_norm(type); + norm = H5Tget_norm(type); switch (norm) { case H5T_NORM_IMPLIED: norm_s = ", msb implied"; @@ -772,14 +789,14 @@ print_float_type(h5tools_str_t *buffer, hid_t type, int ind) case H5T_NORM_ERROR: norm_s = ", unknown normalization"; break; - default: - ; - break; + default:; + break; } - h5tools_str_append(buffer, "\n%*s(significant for %lu bit%s at bit %lu%s)", ind, "", - (unsigned long)msize, 1==msize?"":"s", (unsigned long)mpos, norm_s); - h5tools_str_append(buffer, "\n%*s(exponent for %lu bit%s at bit %lu, bias is 0x%lx)", - ind, "", (unsigned long)esize, 1==esize?"":"s", (unsigned long)epos, (unsigned long)ebias); + h5tools_str_append(buffer, "\n%*s(significant for %lu bit%s at bit %lu%s)", ind, "", (unsigned long)msize, + 1 == msize ? "" : "s", (unsigned long)mpos, norm_s); + h5tools_str_append(buffer, "\n%*s(exponent for %lu bit%s at bit %lu, bias is 0x%lx)", ind, "", + (unsigned long)esize, 1 == esize ? "" : "s", (unsigned long)epos, + (unsigned long)ebias); h5tools_str_append(buffer, "\n%*s(sign bit at %lu)", ind, "", (unsigned long)spos); /* Display internal padding */ @@ -799,75 +816,73 @@ print_float_type(h5tools_str_t *buffer, hid_t type, int ind) case H5T_NPAD: pad_s = "unknown"; break; - default: - ; - break; + default:; + break; } h5tools_str_append(buffer, "\n%*s(internal padding bits are %s)", ind, "", pad_s); } return TRUE; } - /*------------------------------------------------------------------------- - * Function: print_cmpd_type + * Function: print_cmpd_type * - * Purpose: Print info about a compound data type. + * Purpose: Print info about a compound data type. * - * Return: Success: TRUE - * Failure: FALSE, nothing printed + * Return: Success: TRUE + * Failure: FALSE, nothing printed *------------------------------------------------------------------------- */ static hbool_t print_cmpd_type(h5tools_str_t *buffer, hid_t type, int ind) { - char *name=NULL; /* member name */ - size_t size; /* total size of type in bytes */ - hid_t subtype; /* member data type */ - int nmembs; /* number of members */ - int n; /* miscellaneous counters */ - unsigned i; /* miscellaneous counters */ - - if(H5T_COMPOUND != H5Tget_class(type)) + char * name = NULL; /* member name */ + size_t size; /* total size of type in bytes */ + hid_t subtype; /* member data type */ + int nmembs; /* number of members */ + int n; /* miscellaneous counters */ + unsigned i; /* miscellaneous counters */ + + if (H5T_COMPOUND != H5Tget_class(type)) return FALSE; - if((nmembs = H5Tget_nmembers(type)) < 0) + if ((nmembs = H5Tget_nmembers(type)) < 0) return FALSE; h5tools_str_append(buffer, "struct {"); for (i = 0; i < (unsigned)nmembs; i++) { /* Name and offset */ name = H5Tget_member_name(type, i); - h5tools_str_append(buffer, "\n%*s\"", ind+4, ""); + h5tools_str_append(buffer, "\n%*s\"", ind + 4, ""); n = print_string(buffer, name, FALSE); - h5tools_str_append(buffer, "\"%*s +%-4lu ", MAX(0, 16-n), "", (unsigned long)H5Tget_member_offset(type, i)); + h5tools_str_append(buffer, "\"%*s +%-4lu ", MAX(0, 16 - n), "", + (unsigned long)H5Tget_member_offset(type, i)); H5free_memory(name); /* Member's type */ subtype = H5Tget_member_type(type, i); - print_type(buffer, subtype, ind+4); + print_type(buffer, subtype, ind + 4); H5Tclose(subtype); } size = H5Tget_size(type); - h5tools_str_append(buffer, "\n%*s} %lu byte%s", ind, "", (unsigned long)size, 1==size?"":"s"); + h5tools_str_append(buffer, "\n%*s} %lu byte%s", ind, "", (unsigned long)size, 1 == size ? "" : "s"); return TRUE; } - /*------------------------------------------------------------------------- - * Function: print_enum_type + * Function: print_enum_type * - * Purpose: Print info about an enumeration data type. + * Purpose: Print info about an enumeration data type. * - * Return: Success: TRUE - * Failure: FALSE, nothing printed + * Return: Success: TRUE + * Failure: FALSE, nothing printed *------------------------------------------------------------------------- */ static hbool_t print_enum_type(h5tools_str_t *buffer, hid_t type, int ind) { - int nmembs; /* number of members */ - hid_t super; /* enum base integer type */ + int nmembs; /* number of members */ + hid_t super; /* enum base integer type */ if (H5T_ENUM != H5Tget_class(type)) return FALSE; @@ -880,11 +895,11 @@ print_enum_type(h5tools_str_t *buffer, hid_t type, int ind) h5tools_str_append(buffer, " {"); if (nmembs > 0) { - char **name; /* member names */ - unsigned char *value; /* value array */ - hid_t native = -1; /* native integer data type */ - size_t dst_size; /* destination value type size */ - unsigned i; /* miscellaneous counters */ + char ** name; /* member names */ + unsigned char *value; /* value array */ + hid_t native = H5I_INVALID_HID; /* native integer data type */ + size_t dst_size; /* destination value type size */ + unsigned i; /* miscellaneous counters */ /* Determine what data type to use for the native values. To simplify * things we entertain three possibilities: @@ -902,7 +917,7 @@ print_enum_type(h5tools_str_t *buffer, hid_t type, int ind) dst_size = H5Tget_size(type); /* Get the names and raw values of all members */ - name = (char **)HDcalloc((size_t)nmembs, sizeof(char *)); + name = (char **)HDcalloc((size_t)nmembs, sizeof(char *)); value = (unsigned char *)HDcalloc((size_t)nmembs, MAX(H5Tget_size(type), dst_size)); for (i = 0; i < (unsigned)nmembs; i++) { name[i] = H5Tget_member_name(type, i); @@ -917,6 +932,7 @@ print_enum_type(h5tools_str_t *buffer, hid_t type, int ind) H5free_memory(name[i]); HDfree(name); HDfree(value); + H5Tclose(super); return FALSE; } @@ -926,10 +942,9 @@ print_enum_type(h5tools_str_t *buffer, hid_t type, int ind) /* Print members */ for (i = 0; i < (unsigned)nmembs; i++) { - unsigned char *copy; /* a pointer to value array */ - int nchars; /* number of output characters */ + int nchars; /* number of output characters */ - h5tools_str_append(buffer, "\n%*s", ind+4, ""); + h5tools_str_append(buffer, "\n%*s", ind + 4, ""); nchars = print_string(buffer, name[i], TRUE); h5tools_str_append(buffer, "%*s = ", MAX(0, 16 - nchars), ""); @@ -938,30 +953,30 @@ print_enum_type(h5tools_str_t *buffer, hid_t type, int ind) h5tools_str_append(buffer, "0x"); for (j = 0; j < dst_size; j++) - h5tools_str_append(buffer, "%02x", value[i*dst_size+j]); + h5tools_str_append(buffer, "%02x", value[i * dst_size + j]); } else if (H5T_SGN_NONE == H5Tget_sign(native)) { - /*On SGI Altix(cobalt), wrong values were printed out with "value+i*dst_size" - *strangely, unless use another pointer "copy".*/ - copy = value + i * dst_size; - h5tools_str_append(buffer, HSIZE_T_FORMAT, *((unsigned long long*)((void*)copy))); + unsigned long long copy; + + HDmemcpy(©, value + i * dst_size, sizeof(copy)); + h5tools_str_append(buffer, "%llu", copy); } else { - /*On SGI Altix(cobalt), wrong values were printed out with "value+i*dst_size" - *strangely, unless use another pointer "copy".*/ - copy = value + i * dst_size; - h5tools_str_append(buffer, "%"H5_PRINTF_LL_WIDTH"d", *((long long*)((void*)copy))); + long long copy; + + HDmemcpy(©, value + i * dst_size, sizeof(copy)); + h5tools_str_append(buffer, "%lld", copy); } } /* Release resources */ - for(i = 0; i < (unsigned)nmembs; i++) + for (i = 0; i < (unsigned)nmembs; i++) H5free_memory(name[i]); HDfree(name); HDfree(value); } else - h5tools_str_append(buffer, "\n%*s <empty>", ind+4, ""); + h5tools_str_append(buffer, "\n%*s <empty>", ind + 4, ""); h5tools_str_append(buffer, "\n%*s}", ind, ""); @@ -970,23 +985,22 @@ print_enum_type(h5tools_str_t *buffer, hid_t type, int ind) return TRUE; } - /*------------------------------------------------------------------------- - * Function: print_string_type + * Function: print_string_type * - * Purpose: Print information about a string data type. + * Purpose: Print information about a string data type. * - * Return: Success: TRUE - * Failure: FALSE, nothing printed + * Return: Success: TRUE + * Failure: FALSE, nothing printed *------------------------------------------------------------------------- */ static hbool_t print_string_type(h5tools_str_t *buffer, hid_t type, int H5_ATTR_UNUSED ind) { - H5T_str_t pad; - const char *pad_s=NULL; + H5T_str_t pad; + const char *pad_s = NULL; H5T_cset_t cset; - const char *cset_s=NULL; + const char *cset_s = NULL; if (H5T_STRING != H5Tget_class(type)) return FALSE; @@ -1019,9 +1033,8 @@ print_string_type(h5tools_str_t *buffer, hid_t type, int H5_ATTR_UNUSED ind) case H5T_STR_ERROR: pad_s = "unknown-format"; break; - default: - ; - break; + default:; + break; } /* Character set */ @@ -1050,9 +1063,8 @@ print_string_type(h5tools_str_t *buffer, hid_t type, int H5_ATTR_UNUSED ind) case H5T_CSET_ERROR: cset_s = "unknown-character-set"; break; - default: - ; - break; + default:; + break; } if (H5Tis_variable_str(type)) { @@ -1065,14 +1077,13 @@ print_string_type(h5tools_str_t *buffer, hid_t type, int H5_ATTR_UNUSED ind) return TRUE; } - /*------------------------------------------------------------------------- - * Function: print_reference_type + * Function: print_reference_type * - * Purpose: Prints information about a reference data type. + * Purpose: Prints information about a reference data type. * - * Return: Success: TRUE - * Failure: FALSE, nothing printed + * Return: Success: TRUE + * Failure: FALSE, nothing printed *------------------------------------------------------------------------- */ static hbool_t @@ -1081,7 +1092,10 @@ print_reference_type(h5tools_str_t *buffer, hid_t type, int H5_ATTR_UNUSED ind) if (H5T_REFERENCE != H5Tget_class(type)) return FALSE; - if (H5Tequal(type, H5T_STD_REF_OBJ) == TRUE) { + if (H5Tequal(type, H5T_STD_REF) == TRUE) { + h5tools_str_append(buffer, "standard reference"); + } + else if (H5Tequal(type, H5T_STD_REF_OBJ) == TRUE) { h5tools_str_append(buffer, "object reference"); } else if (H5Tequal(type, H5T_STD_REF_DSETREG) == TRUE) { @@ -1094,20 +1108,19 @@ print_reference_type(h5tools_str_t *buffer, hid_t type, int H5_ATTR_UNUSED ind) return TRUE; } - /*------------------------------------------------------------------------- - * Function: print_opaque_type + * Function: print_opaque_type * - * Purpose: Prints information about an opaque data type. + * Purpose: Prints information about an opaque data type. * - * Return: Success: TRUE - * Failure: FALSE, nothing printed + * Return: Success: TRUE + * Failure: FALSE, nothing printed *------------------------------------------------------------------------- */ static hbool_t print_opaque_type(h5tools_str_t *buffer, hid_t type, int ind) { - char *tag; + char * tag; size_t size; if (H5T_OPAQUE != H5Tget_class(type)) @@ -1124,7 +1137,6 @@ print_opaque_type(h5tools_str_t *buffer, hid_t type, int ind) return TRUE; } - /*------------------------------------------------------------------------- * Function: print_vlen_type * @@ -1137,7 +1149,7 @@ print_opaque_type(h5tools_str_t *buffer, hid_t type, int ind) static hbool_t print_vlen_type(h5tools_str_t *buffer, hid_t type, int ind) { - hid_t super; + hid_t super; if (H5T_VLEN != H5Tget_class(type)) return FALSE; @@ -1149,7 +1161,6 @@ print_vlen_type(h5tools_str_t *buffer, hid_t type, int ind) return TRUE; } - /*--------------------------------------------------------------------------- * Purpose: Print information about an array type * @@ -1160,9 +1171,9 @@ print_vlen_type(h5tools_str_t *buffer, hid_t type, int ind) static hbool_t print_array_type(h5tools_str_t *buffer, hid_t type, int ind) { - hid_t super; - int ndims, i; - hsize_t *dims=NULL; + hid_t super; + int ndims, i; + hsize_t *dims = NULL; if (H5T_ARRAY != H5Tget_class(type)) return FALSE; @@ -1173,42 +1184,40 @@ print_array_type(h5tools_str_t *buffer, hid_t type, int ind) /* Print dimensions */ for (i = 0; i < ndims; i++) - h5tools_str_append(buffer, "%s" HSIZE_T_FORMAT , i?",":"[", dims[i]); + h5tools_str_append(buffer, "%s%" PRIuHSIZE, i ? "," : "[", dims[i]); h5tools_str_append(buffer, "]"); HDfree(dims); } else - h5tools_str_append(buffer, " [SCALAR]\n", rawoutstream); - + h5tools_str_append(buffer, " [SCALAR]\n"); /* Print parent type */ h5tools_str_append(buffer, " "); super = H5Tget_super(type); - print_type(buffer, super, ind+4); + print_type(buffer, super, ind + 4); H5Tclose(super); return TRUE; } - /*------------------------------------------------------------------------- - * Function: print_bitfield_type + * Function: print_bitfield_type * - * Purpose: Print information about a bitfield type. + * Purpose: Print information about a bitfield type. * - * Return: Success: TRUE - * Failure: FALSE, nothing printed + * Return: Success: TRUE + * Failure: FALSE, nothing printed *------------------------------------------------------------------------- */ static hbool_t print_bitfield_type(h5tools_str_t *buffer, hid_t type, int ind) { H5T_order_t order; /* byte order value */ - const char *order_s=NULL; /* byte order string */ + const char *order_s = NULL; /* byte order string */ if (H5T_BITFIELD != H5Tget_class(type)) return FALSE; - if (H5Tget_size(type)>1) { + if (H5Tget_size(type) > 1) { order = H5Tget_order(type); if (H5T_ORDER_LE == order) { order_s = " little-endian"; @@ -1227,98 +1236,107 @@ print_bitfield_type(h5tools_str_t *buffer, hid_t type, int ind) order_s = ""; } - h5tools_str_append(buffer, "%lu-bit%s bitfield", (unsigned long)(8*H5Tget_size(type)), order_s); + h5tools_str_append(buffer, "%lu-bit%s bitfield", (unsigned long)(8 * H5Tget_size(type)), order_s); print_precision(buffer, type, ind); return TRUE; } - /*------------------------------------------------------------------------- - * Function: print_type + * Function: print_type * - * Purpose: Prints a data type definition. The definition is printed - * without any leading space or trailing line-feed (although - * there might be line-feeds inside the type definition). The - * first line is assumed to have IND characters before it on - * the same line (printed by the caller). - * Prints the OID of shared data types. + * Purpose: Prints a data type definition. The definition is printed + * without any leading space or trailing line-feed (although + * there might be line-feeds inside the type definition). The + * first line is assumed to have IND characters before it on + * the same line (printed by the caller). + * Prints the OID of shared data types. * - * Return: void + * Return: void *------------------------------------------------------------------------- */ static void print_type(h5tools_str_t *buffer, hid_t type, int ind) { - H5T_class_t data_class = H5Tget_class(type); + H5T_class_t data_class = H5Tget_class(type); /* Bad data type */ if (type < 0) { - h5tools_str_append(buffer,"<ERROR>"); + h5tools_str_append(buffer, "<ERROR>"); return; } /* Shared? If so then print the type's OID */ if (H5Tcommitted(type)) { - H5O_info_t oi; + H5O_info2_t oi; - if (H5Oget_info2(type, &oi, H5O_INFO_BASIC) >= 0) - h5tools_str_append(buffer,"shared-%lu:"H5_PRINTF_HADDR_FMT" ", oi.fileno, oi.addr); + if (H5Oget_info3(type, &oi, H5O_INFO_BASIC) >= 0) { + char *type_string = NULL; + + H5Otoken_to_str(type, &oi.token, &type_string); + + h5tools_str_append(buffer, "shared-%lu:%s", oi.fileno, type_string); + + H5free_memory(type_string); + } /* end if */ else - h5tools_str_append(buffer,"shared "); + h5tools_str_append(buffer, "shared "); } /* end if */ /* Print the type */ - if (print_native_type(buffer, type, ind) || - print_ieee_type(buffer, type, ind) || - print_cmpd_type(buffer, type, ind) || - print_enum_type(buffer, type, ind) || - print_string_type(buffer, type, ind) || - print_reference_type(buffer, type, ind) || - print_vlen_type(buffer, type, ind) || - print_array_type(buffer, type, ind) || - print_opaque_type(buffer, type, ind) || - print_bitfield_type(buffer, type, ind)) + if (print_native_type(buffer, type, ind) || print_ieee_type(buffer, type, ind) || + print_cmpd_type(buffer, type, ind) || print_enum_type(buffer, type, ind) || + print_string_type(buffer, type, ind) || print_reference_type(buffer, type, ind) || + print_vlen_type(buffer, type, ind) || print_array_type(buffer, type, ind) || + print_opaque_type(buffer, type, ind) || print_bitfield_type(buffer, type, ind)) return; /* Unknown type */ - h5tools_str_append(buffer,"%lu-byte class-%u unknown", (unsigned long)H5Tget_size(type), (unsigned)data_class); + h5tools_str_append(buffer, "%lu-byte class-%u unknown", (unsigned long)H5Tget_size(type), + (unsigned)data_class); } - /*------------------------------------------------------------------------- - * Function: dump_dataset_values + * Function: dump_dataset_values * - * Purpose: Prints all values of a dataset. + * Purpose: Prints all values of a dataset. * - * Return: void + * Return: void *------------------------------------------------------------------------- */ static void dump_dataset_values(hid_t dset) { - char string_prefix[64]; - static char fmt_double[16]; - static char fmt_float[16]; - hsize_t curr_pos = 0; /* total data element position */ - h5tools_str_t buffer; /* string into which to render */ - h5tools_context_t ctx; /* print context */ - h5tool_format_t outputformat; - h5tool_format_t *info = &ls_dataformat; - - hid_t f_type = H5Dget_type(dset); - size_t size = H5Tget_size(f_type); + hid_t f_type = H5I_INVALID_HID; + hid_t space = H5I_INVALID_HID; + hsize_t total_size[H5S_MAX_RANK]; + int ndims; + char string_prefix[64]; + static char fmt_double[16]; + static char fmt_float[16]; + hsize_t curr_pos = 0; /* total data element position */ + h5tools_str_t buffer; /* string into which to render */ + h5tools_context_t ctx; /* print context */ + h5tool_format_t outputformat; + h5tool_format_t * info = &ls_dataformat; + H5R_ref_t * ref_buf = NULL; + + H5TOOLS_START_DEBUG(" "); + + f_type = H5Dget_type(dset); + space = H5Dget_space(dset); HDmemset(&ctx, 0, sizeof(ctx)); HDmemset(&buffer, 0, sizeof(h5tools_str_t)); - outputformat = *info; - outputformat.line_1st = NULL; + outputformat = *info; + outputformat.line_1st = NULL; + outputformat.idx_fmt = ""; if (simple_output_g) { - outputformat.idx_fmt = ""; - outputformat.line_per_line = 1; + outputformat.idx_fmt = ""; + outputformat.line_per_line = 1; outputformat.line_multi_new = 0; - outputformat.line_pre = " "; - outputformat.line_cont = " "; + outputformat.line_pre = " "; + outputformat.line_cont = " "; outputformat.arr_pre = ""; outputformat.arr_suf = ""; @@ -1333,9 +1351,8 @@ dump_dataset_values(hid_t dset) if (label_g) outputformat.cmpd_name = "%s="; - outputformat.elmt_suf1 = " "; + outputformat.elmt_suf1 = " "; outputformat.str_locale = ESCAPE_HTML; - } else { if (no_line_wrap_g) { @@ -1344,9 +1361,10 @@ dump_dataset_values(hid_t dset) else { outputformat.line_ncols = (unsigned)width_g; } - if (label_g) outputformat.cmpd_name = "%s="; - outputformat.line_pre = " %s "; - outputformat.line_cont = " %s "; + if (label_g) + outputformat.cmpd_name = "%s="; + outputformat.line_pre = " %s "; + outputformat.line_cont = " %s "; outputformat.str_repeat = 8; outputformat.arr_pre = NULL; @@ -1374,10 +1392,10 @@ dump_dataset_values(hid_t dset) * command line switch was given. */ outputformat.raw = TRUE; } - else if (string_g && 1 == size && H5T_INTEGER == H5Tget_class(f_type)) { + else if (string_g && H5Tget_size(f_type) == 1 && (H5Tget_class(f_type) == H5T_INTEGER)) { /* Print 1-byte integer data as an ASCI character string instead of * integers if the `-s' or `--string' command-line option was given. */ - outputformat.ascii = TRUE; + outputformat.ascii = TRUE; outputformat.elmt_suf1 = ""; outputformat.elmt_suf2 = ""; HDsnprintf(string_prefix, sizeof(string_prefix), "%s\"", outputformat.line_pre); @@ -1386,232 +1404,377 @@ dump_dataset_values(hid_t dset) } info = &outputformat; - ctx.indent_level = 2; - ctx.cur_column = (size_t)curr_pos; + ctx.indent_level = 1; + ctx.cur_column = (size_t)curr_pos; /* Print all the values. */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, " Data:\n"); - h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); + + h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, + (hsize_t)0); + ctx.need_prefix = TRUE; - ctx.cur_column = (size_t)curr_pos; - if (h5tools_dump_dset(rawoutstream, info, &ctx, dset, NULL) < 0) { - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, " Unable to print data."); - h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); - } + ctx.cur_column = (size_t)curr_pos; + if (H5Tget_class(f_type) == H5T_REFERENCE) { + H5TOOLS_DEBUG("reference class type"); + if (!H5Tequal(f_type, H5T_STD_REF) && !H5Tequal(f_type, H5T_STD_REF_DSETREG) && + !H5Tequal(f_type, H5T_STD_REF_OBJ)) { + H5TOOLS_GOTO_DONE_NO_RET(); + } + + ndims = (int)H5Sget_simple_extent_npoints(space); + H5TOOLS_DEBUG("ndims=%d - ctx.ndims=%d", ndims, ctx.ndims); + + /* Assume entire data space to be printed */ + H5Sget_simple_extent_dims(space, total_size, NULL); + init_acc_pos(ctx.ndims, total_size, ctx.acc, ctx.pos, ctx.p_min_idx); + + ctx.need_prefix = TRUE; + + if (NULL != + (ref_buf = (H5R_ref_t *)HDcalloc(MAX(sizeof(unsigned), sizeof(H5R_ref_t)), (size_t)ndims))) { + H5TOOLS_DEBUG("H5Dread reference read"); + if (H5Dread(dset, H5T_STD_REF, H5S_ALL, H5S_ALL, H5P_DEFAULT, ref_buf) < 0) { + HDfree(ref_buf); + H5TOOLS_INFO("H5Dread reference failed"); + H5TOOLS_GOTO_DONE_NO_RET(); + } + h5tools_dump_reference(rawoutstream, info, &ctx, dset, ref_buf, ndims); + PRINTVALSTREAM(rawoutstream, "\n"); + HDfree(ref_buf); + } + } + else { + if (h5tools_dump_dset(rawoutstream, info, &ctx, dset) < 0) { + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, " Unable to print data."); + h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, + (hsize_t)0, (hsize_t)0); + } + } +done: + H5Sclose(space); H5Tclose(f_type); h5tools_str_close(&buffer); PRINTVALSTREAM(rawoutstream, "\n"); + + H5TOOLS_ENDDEBUG(" "); } +/*------------------------------------------------------------------------- + * Function: dump_attribute_values + * + * Purpose: Prints all values of a attribute. + * + * Return: void + *------------------------------------------------------------------------- + */ +static void +dump_attribute_values(hid_t attr) +{ + hid_t f_type = H5I_INVALID_HID; + hid_t space = H5I_INVALID_HID; + hsize_t total_size[H5S_MAX_RANK]; + int ndims; + char string_prefix[64]; + static char fmt_double[16]; + static char fmt_float[16]; + hsize_t curr_pos = 0; /* total data element position */ + h5tools_str_t buffer; /* string into which to render */ + h5tools_context_t ctx; /* print context */ + h5tool_format_t outputformat; + h5tool_format_t * info = &ls_dataformat; + H5R_ref_t * ref_buf = NULL; + + H5TOOLS_START_DEBUG(" "); + + f_type = H5Aget_type(attr); + space = H5Aget_space(attr); + + HDmemset(&ctx, 0, sizeof(ctx)); + HDmemset(&buffer, 0, sizeof(h5tools_str_t)); + + outputformat = *info; + outputformat.line_1st = NULL; + outputformat.idx_fmt = ""; + if (simple_output_g) { + outputformat.idx_fmt = ""; + outputformat.line_per_line = 1; + outputformat.line_multi_new = 0; + outputformat.line_pre = " "; + outputformat.line_cont = " "; + + outputformat.arr_pre = ""; + outputformat.arr_suf = ""; + outputformat.arr_sep = " "; + + if (!label_g) { + outputformat.cmpd_pre = ""; + outputformat.cmpd_suf = ""; + } + outputformat.cmpd_sep = " "; + + if (label_g) + outputformat.cmpd_name = "%s="; + + outputformat.elmt_suf1 = " "; + outputformat.str_locale = ESCAPE_HTML; + } + else { + if (no_line_wrap_g) { + outputformat.line_per_line = 1; + } + else { + outputformat.line_ncols = (unsigned)width_g; + } + if (label_g) + outputformat.cmpd_name = "%s="; + outputformat.line_pre = " %s "; + outputformat.line_cont = " %s "; + outputformat.str_repeat = 8; + + outputformat.arr_pre = NULL; + outputformat.arr_suf = NULL; + outputformat.arr_sep = NULL; + + outputformat.cmpd_pre = NULL; + outputformat.cmpd_suf = NULL; + outputformat.cmpd_sep = NULL; + + outputformat.vlen_sep = NULL; + outputformat.vlen_pre = NULL; + outputformat.vlen_suf = NULL; + outputformat.vlen_end = NULL; + } + outputformat.arr_linebreak = 0; + /* Floating point types should display full precision */ + HDsnprintf(fmt_float, sizeof(fmt_float), "%%1.%dg", FLT_DIG); + outputformat.fmt_float = fmt_float; + HDsnprintf(fmt_double, sizeof(fmt_double), "%%1.%dg", DBL_DIG); + outputformat.fmt_double = fmt_double; + + if (hexdump_g) { + /* Print all data in hexadecimal format if the `-x' or `--hexdump' + * command line switch was given. */ + outputformat.raw = TRUE; + } + else if (string_g && H5Tget_size(f_type) == 1 && (H5Tget_class(f_type) == H5T_INTEGER)) { + /* Print 1-byte integer data as an ASCI character string instead of + * integers if the `-s' or `--string' command-line option was given. */ + outputformat.ascii = TRUE; + outputformat.elmt_suf1 = ""; + outputformat.elmt_suf2 = ""; + HDsnprintf(string_prefix, sizeof(string_prefix), "%s\"", outputformat.line_pre); + outputformat.line_pre = string_prefix; + outputformat.line_suf = "\""; + } + info = &outputformat; + + ctx.indent_level = 2; + ctx.cur_column = (size_t)curr_pos; + + /* Print all the values. */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, " Data:\n"); + + h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, + (hsize_t)0); + + ctx.need_prefix = TRUE; + ctx.cur_column = (size_t)curr_pos; + if (H5Tget_class(f_type) == H5T_REFERENCE) { + H5TOOLS_DEBUG("reference class type"); + if (!H5Tequal(f_type, H5T_STD_REF) && !H5Tequal(f_type, H5T_STD_REF_DSETREG) && + !H5Tequal(f_type, H5T_STD_REF_OBJ)) { + H5TOOLS_GOTO_DONE_NO_RET(); + } + + ndims = (int)H5Sget_simple_extent_npoints(space); + H5TOOLS_DEBUG("ndims=%d - ctx.ndims=%d", ndims, ctx.ndims); + + /* Assume entire data space to be printed */ + H5Sget_simple_extent_dims(space, total_size, NULL); + init_acc_pos(ctx.ndims, total_size, ctx.acc, ctx.pos, ctx.p_min_idx); + + ctx.need_prefix = TRUE; + + if (NULL != + (ref_buf = (H5R_ref_t *)HDcalloc(MAX(sizeof(unsigned), sizeof(H5R_ref_t)), (size_t)ndims))) { + H5TOOLS_DEBUG("H5Aread reference read"); + if (H5Aread(attr, H5T_STD_REF, ref_buf) < 0) { + HDfree(ref_buf); + H5TOOLS_INFO("H5Aread reference failed"); + H5TOOLS_GOTO_DONE_NO_RET(); + } + ctx.indent_level++; + h5tools_dump_reference(rawoutstream, info, &ctx, attr, ref_buf, ndims); + + PRINTVALSTREAM(rawoutstream, "\n"); + ctx.indent_level--; + HDfree(ref_buf); + } + } + else { + H5TOOLS_DEBUG("Attribute data read"); + ctx.indent_level++; + if (h5tools_dump_mem(rawoutstream, info, &ctx, attr) < 0) { + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, " Unable to print data."); + h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, + (hsize_t)0, (hsize_t)0); + } + ctx.indent_level--; + H5TOOLS_DEBUG("Attribute data read complete"); + } +done: + H5Sclose(space); + H5Tclose(f_type); + + h5tools_str_close(&buffer); + + PRINTVALSTREAM(rawoutstream, "\n"); + + H5TOOLS_ENDDEBUG(" "); +} /*------------------------------------------------------------------------- - * Function: list_attr + * Function: list_attr * - * Purpose: Prints information about attributes. + * Purpose: Prints information about attributes. * - * Return: Success: 0 - * Failure: -1 + * Return: Success: 0 + * Failure: -1 *------------------------------------------------------------------------- */ static herr_t list_attr(hid_t obj, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED *ainfo, - void H5_ATTR_UNUSED *op_data) + void H5_ATTR_UNUSED *op_data) { - hid_t attr = -1; - hid_t space = -1; - hid_t type = -1; - hid_t p_type = -1; - hsize_t size[H5S_MAX_RANK]; - hsize_t nelmts = 1; - hsize_t temp_need; - size_t need; - int ndims; - int i; - void *buf; - H5S_class_t space_type; - hsize_t curr_pos = 0; /* total data element position */ - h5tools_str_t buffer; /* string into which to render */ - h5tools_context_t ctx; /* print context */ - h5tool_format_t *info = &ls_dataformat; - h5tool_format_t outputformat; + hid_t attr = H5I_INVALID_HID; + hid_t space = H5I_INVALID_HID; + hid_t type = H5I_INVALID_HID; + hsize_t size[H5S_MAX_RANK]; + hsize_t nelmts = 1; + int ndims; + int i; + H5S_class_t space_type; + hsize_t curr_pos = 0; /* total data element position */ + h5tools_str_t buffer; /* string into which to render */ + h5tools_context_t ctx; /* print context */ + h5tool_format_t * info = &ls_dataformat; + + H5TOOLS_START_DEBUG(" "); HDmemset(&ctx, 0, sizeof(ctx)); HDmemset(&buffer, 0, sizeof(h5tools_str_t)); + ctx.indent_level = 2; + ctx.cur_column = (size_t)curr_pos; + h5tools_str_reset(&buffer); h5tools_str_append(&buffer, " Attribute: "); print_string(&buffer, attr_name, TRUE); - if ((attr = H5Aopen(obj, attr_name, H5P_DEFAULT))) { + H5TOOLS_DEBUG("Attribute name:%s", attr_name); + if ((attr = H5Aopen(obj, attr_name, H5P_DEFAULT)) >= 0) { space = H5Aget_space(attr); - type = H5Aget_type(attr); + type = H5Aget_type(attr); /* Data space */ - ndims = H5Sget_simple_extent_dims(space, size, NULL); + ndims = H5Sget_simple_extent_dims(space, size, NULL); space_type = H5Sget_simple_extent_type(space); - switch(space_type) { + H5TOOLS_DEBUG("Attribute ndims:%d", ndims); + switch (space_type) { case H5S_SCALAR: /* scalar dataspace */ h5tools_str_append(&buffer, " scalar\n"); - h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, + (hsize_t)0, (hsize_t)0); break; case H5S_SIMPLE: /* simple dataspace */ h5tools_str_append(&buffer, " {"); for (i = 0; i < ndims; i++) { - h5tools_str_append(&buffer, "%s" HSIZE_T_FORMAT, i?", ":"", size[i]); + h5tools_str_append(&buffer, "%s%" PRIuHSIZE, i ? ", " : "", size[i]); nelmts *= size[i]; } h5tools_str_append(&buffer, "}\n"); - h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, + (hsize_t)0, (hsize_t)0); break; case H5S_NULL: /* null dataspace */ h5tools_str_append(&buffer, " null\n"); - h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, + (hsize_t)0, (hsize_t)0); break; case H5S_NO_CLASS: default: /* Unknown dataspace type */ h5tools_str_append(&buffer, " unknown\n"); - h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, + (hsize_t)0, (hsize_t)0); break; } /* end switch */ /* Data type */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, " Type: "); + h5tools_str_append(&buffer, " %-10s ", "Type:"); print_type(&buffer, type, 15); h5tools_str_append(&buffer, "\n"); - h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); - - /* Data */ - outputformat = *info; - - if (nelmts < 5) { - outputformat.idx_fmt = ""; - outputformat.line_1st = " Data: "; - outputformat.line_pre = " "; - outputformat.line_cont = " "; - outputformat.str_repeat = 8; - - } - else { - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, " Data:\n"); - h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); - outputformat.line_1st = NULL; - outputformat.line_pre = " %s "; - outputformat.line_cont = " %s "; - outputformat.str_repeat = 8; - } - - outputformat.line_ncols = (unsigned)width_g; - if (label_g) - outputformat.cmpd_name = "%s="; - if (string_g && 1 == H5Tget_size(type) && H5T_INTEGER == H5Tget_class(type)) { - outputformat.ascii = TRUE; - outputformat.elmt_suf1 = ""; - outputformat.elmt_suf2 = ""; - outputformat.line_pre = " %s \""; - outputformat.line_suf = "\""; - } /* end if */ - - - outputformat.arr_pre = NULL; - outputformat.arr_suf = NULL; - outputformat.arr_sep = NULL; - - outputformat.cmpd_pre = NULL; - outputformat.cmpd_suf = NULL; - outputformat.cmpd_sep = NULL; - - outputformat.vlen_sep = NULL; - outputformat.vlen_pre = NULL; - outputformat.vlen_suf = NULL; - outputformat.vlen_end = NULL; - - info = &outputformat; - - if (space_type != H5S_NULL && space_type != H5S_NO_CLASS) { - if (hexdump_g) - p_type = H5Tcopy(type); - else - p_type = H5Tget_native_type(type, H5T_DIR_DEFAULT); - - if (p_type >= 0) { - /* VL data special information */ - unsigned int vl_data = 0; /* contains VL datatypes */ - - /* Check if we have VL data in the dataset's datatype */ - if (h5tools_detect_vlen(p_type) == TRUE) - vl_data = TRUE; - - temp_need = nelmts * MAX(H5Tget_size(type), H5Tget_size(p_type)); - need = (size_t)temp_need; - if((buf = HDmalloc(need)) != NULL) { - if(H5Aread(attr, p_type, buf) >= 0) { - ctx.need_prefix = TRUE; - ctx.indent_level = 2; - ctx.cur_column = (size_t)curr_pos; - h5tools_dump_mem(rawoutstream, info, &ctx, attr, p_type, space, buf); - } - - /* Reclaim any VL memory, if necessary */ - if (vl_data) - H5Dvlen_reclaim(p_type, space, H5P_DEFAULT, buf); - - HDfree(buf); - } - H5Tclose(p_type); - } /* end if */ - } + h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, + (hsize_t)0, (hsize_t)0); H5Sclose(space); H5Tclose(type); + + h5tools_str_close(&buffer); + + if (data_g) + dump_attribute_values(attr); H5Aclose(attr); } - h5tools_str_close(&buffer); - - PRINTVALSTREAM(rawoutstream, "\n"); + else { + H5TOOLS_DEBUG("Attribute open failed"); + h5tools_str_close(&buffer); + } + H5TOOLS_ENDDEBUG(" "); return 0; } - /*------------------------------------------------------------------------- - * Function: dataset_list1 + * Function: dataset_list1 * - * Purpose: List information about a dataset which should appear on the - * same line as the dataset name. This information will precede - * information which is applicable to all objects which will be - * printed by the caller. + * Purpose: List information about a dataset which should appear on the + * same line as the dataset name. This information will precede + * information which is applicable to all objects which will be + * printed by the caller. * - * Return: Success: 0 - * Failure: -1 + * Return: Success: 0 + * Failure: -1 *------------------------------------------------------------------------- */ static herr_t dataset_list1(hid_t dset) { - hsize_t cur_size[H5S_MAX_RANK]; /* current dataset dimensions */ - hsize_t max_size[H5S_MAX_RANK]; /* maximum dataset dimensions */ - hid_t space; /* data space */ - int ndims; /* dimensionality */ - H5S_class_t space_type; /* type of dataspace */ - int i; - hsize_t curr_pos = 0; /* total data element position */ - h5tools_str_t buffer; /* string into which to render */ - h5tools_context_t ctx; /* print context */ - h5tool_format_t *info = &ls_dataformat; + hsize_t cur_size[H5S_MAX_RANK]; /* current dataset dimensions */ + hsize_t max_size[H5S_MAX_RANK]; /* maximum dataset dimensions */ + hid_t space; /* data space */ + int ndims; /* dimensionality */ + H5S_class_t space_type; /* type of dataspace */ + int i; + hsize_t curr_pos = 0; /* total data element position */ + h5tools_str_t buffer; /* string into which to render */ + h5tools_context_t ctx; /* print context */ + h5tool_format_t * info = &ls_dataformat; HDmemset(&ctx, 0, sizeof(ctx)); HDmemset(&buffer, 0, sizeof(h5tools_str_t)); @@ -1620,17 +1783,17 @@ dataset_list1(hid_t dset) /* Information that goes on the same row as the name. The name has * already been printed. */ - space = H5Dget_space(dset); + space = H5Dget_space(dset); space_type = H5Sget_simple_extent_type(space); - ndims = H5Sget_simple_extent_dims(space, cur_size, max_size); + ndims = H5Sget_simple_extent_dims(space, cur_size, max_size); h5tools_str_append(&buffer, " {"); for (i = 0; i < ndims; i++) { - h5tools_str_append(&buffer, "%s"HSIZE_T_FORMAT, i?", ":"", cur_size[i]); - if (max_size[i]==H5S_UNLIMITED) { + h5tools_str_append(&buffer, "%s%" PRIuHSIZE, i ? ", " : "", cur_size[i]); + if (max_size[i] == H5S_UNLIMITED) { h5tools_str_append(&buffer, "/%s", "Inf"); } else if (max_size[i] != cur_size[i] || verbose_g > 0) { - h5tools_str_append(&buffer, "/"HSIZE_T_FORMAT, max_size[i]); + h5tools_str_append(&buffer, "/%" PRIuHSIZE, max_size[i]); } } if (space_type == H5S_SCALAR) @@ -1638,52 +1801,52 @@ dataset_list1(hid_t dset) else if (space_type == H5S_NULL) h5tools_str_append(&buffer, "NULL"); h5tools_str_append(&buffer, "}"); - h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); - H5Sclose (space); + h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, + (hsize_t)0); + H5Sclose(space); h5tools_str_close(&buffer); return 0; } - /*------------------------------------------------------------------------- - * Function: dataset_list2 + * Function: dataset_list2 * - * Purpose: List information about a dataset which should appear after - * information which is general to all objects. + * Purpose: List information about a dataset which should appear after + * information which is general to all objects. * - * Return: Success: 0 - * Failure: -1 + * Return: Success: 0 + * Failure: -1 *------------------------------------------------------------------------- */ static herr_t dataset_list2(hid_t dset, const char H5_ATTR_UNUSED *name) { - hid_t dcpl; /* dataset creation property list */ - hid_t type; /* data type of dataset */ - hid_t space; /* data space of dataset */ - int nf; /* number of filters */ - unsigned filt_flags; /* filter flags */ - H5Z_filter_t filt_id; /* filter identification number */ - unsigned cd_values[20]; /* filter client data values */ - size_t cd_nelmts; /* filter client number of values */ - size_t cd_num; /* filter client data counter */ - char f_name[256]; /* filter/file name */ - char s[64]; /* temporary string buffer */ - off_t f_offset; /* offset in external file */ - hsize_t f_size; /* bytes used in external file */ - hsize_t total, used; /* total size or offset */ - int ndims; /* dimensionality */ - int n, max_len; /* max extern file name length */ - double utilization; /* percent utilization of storage */ - H5T_class_t tclass; /* datatype class identifier */ - int i; - H5D_layout_t stl; - hsize_t curr_pos = 0; /* total data element position */ - h5tools_str_t buffer; /* string into which to render */ - h5tools_context_t ctx; /* print context */ - h5tool_format_t *info = &ls_dataformat; + hid_t dcpl; /* dataset creation property list */ + hid_t type; /* data type of dataset */ + hid_t space; /* data space of dataset */ + int nf; /* number of filters */ + unsigned filt_flags; /* filter flags */ + H5Z_filter_t filt_id; /* filter identification number */ + unsigned cd_values[20]; /* filter client data values */ + size_t cd_nelmts; /* filter client number of values */ + size_t cd_num; /* filter client data counter */ + char f_name[256]; /* filter/file name */ + char s[64]; /* temporary string buffer */ + off_t f_offset; /* offset in external file */ + hsize_t f_size; /* bytes used in external file */ + hsize_t total, used; /* total size or offset */ + int ndims; /* dimensionality */ + int n, max_len; /* max extern file name length */ + double utilization; /* percent utilization of storage */ + H5T_class_t tclass; /* datatype class identifier */ + int i; + H5D_layout_t stl; + hsize_t curr_pos = 0; /* total data element position */ + h5tools_str_t buffer; /* string into which to render */ + h5tools_context_t ctx; /* print context */ + h5tool_format_t * info = &ls_dataformat; HDmemset(&ctx, 0, sizeof(ctx)); HDmemset(&buffer, 0, sizeof(h5tools_str_t)); @@ -1691,26 +1854,24 @@ dataset_list2(hid_t dset, const char H5_ATTR_UNUSED *name) h5tools_str_reset(&buffer); if (verbose_g > 0) { - dcpl = H5Dget_create_plist(dset); + dcpl = H5Dget_create_plist(dset); space = H5Dget_space(dset); - type = H5Dget_type(dset); + type = H5Dget_type(dset); stl = H5Pget_layout(dcpl); switch (stl) { - case H5D_CHUNKED: - { - hsize_t chsize[64]; /* chunk size in elements */ - - ndims = H5Pget_chunk(dcpl, (int)NELMTS(chsize), chsize/*out*/); - h5tools_str_append(&buffer, " %-10s {", "Chunks:"); - total = H5Tget_size(type); - for (i = 0; i < ndims; i++) { - h5tools_str_append(&buffer, "%s"HSIZE_T_FORMAT, i?", ":"", chsize[i]); - total *= chsize[i]; - } - h5tools_str_append(&buffer, "} "HSIZE_T_FORMAT" bytes\n", total); + case H5D_CHUNKED: { + hsize_t chsize[64]; /* chunk size in elements */ + + ndims = H5Pget_chunk(dcpl, (int)NELMTS(chsize), chsize /*out*/); + h5tools_str_append(&buffer, " %-10s {", "Chunks:"); + total = H5Tget_size(type); + for (i = 0; i < ndims; i++) { + h5tools_str_append(&buffer, "%s%" PRIuHSIZE, i ? ", " : "", chsize[i]); + total *= chsize[i]; } - break; + h5tools_str_append(&buffer, "} %" PRIuHSIZE " bytes\n", total); + } break; case H5D_COMPACT: break; case H5D_CONTIGUOUS: @@ -1719,64 +1880,70 @@ dataset_list2(hid_t dset, const char H5_ATTR_UNUSED *name) for (i = 0, max_len = 0; i < nf; i++) { if (H5Pget_external(dcpl, (unsigned)i, sizeof(f_name), f_name, NULL, NULL) < 0) continue; - n = print_string(NULL, f_name, TRUE); + n = print_string(NULL, f_name, TRUE); max_len = MAX(max_len, n); } /* end for */ - h5tools_str_append(&buffer, " %-10s %d external file%s\n", "Extern:", nf, 1==nf?"":"s"); - h5tools_str_append(&buffer, " %4s %10s %10s %10s %s\n", "ID", "DSet-Addr", "File-Addr", "Bytes", "File"); - h5tools_str_append(&buffer, " %4s %10s %10s %10s ", "----", "----------", "----------", "----------"); + h5tools_str_append(&buffer, " %-10s %d external file%s\n", "Extern:", nf, + 1 == nf ? "" : "s"); + h5tools_str_append(&buffer, " %4s %10s %10s %10s %s\n", "ID", "DSet-Addr", + "File-Addr", "Bytes", "File"); + h5tools_str_append(&buffer, " %4s %10s %10s %10s ", "----", "----------", + "----------", "----------"); for (i = 0; i < max_len; i++) h5tools_str_append(&buffer, "-"); h5tools_str_append(&buffer, "\n"); - for (i = 0, total=0; i < nf; i++) { - if (H5Pget_external(dcpl, (unsigned)i, sizeof(f_name), f_name, &f_offset, &f_size)<0) { - h5tools_str_append(&buffer, " #%03d %10"H5_PRINTF_LL_WIDTH"u %10s %10s ***ERROR*** %s\n", - i, total, "", "", i+1<nf?"Following addresses are incorrect":""); + for (i = 0, total = 0; i < nf; i++) { + if (H5Pget_external(dcpl, (unsigned)i, sizeof(f_name), f_name, &f_offset, &f_size) < + 0) { + h5tools_str_append( + &buffer, " #%03d %10" PRIuHSIZE " %10s %10s ***ERROR*** %s\n", i, + total, "", "", i + 1 < nf ? "Following addresses are incorrect" : ""); } else if (H5S_UNLIMITED == f_size) { - h5tools_str_append(&buffer, " #%03d %10"H5_PRINTF_LL_WIDTH"u %10"H5_PRINTF_LL_WIDTH"u %10s ", - i, total, (hsize_t)f_offset, "INF"); + h5tools_str_append(&buffer, + " #%03d %10" PRIuHSIZE " %10" PRIuHSIZE " %10s ", i, + total, (hsize_t)f_offset, "INF"); print_string(&buffer, f_name, TRUE); } else { - h5tools_str_append(&buffer, " #%03d %10"H5_PRINTF_LL_WIDTH"u %10"H5_PRINTF_LL_WIDTH"u %10"H5_PRINTF_LL_WIDTH"u ", - i, total, (hsize_t)f_offset, f_size); + h5tools_str_append( + &buffer, " #%03d %10" PRIuHSIZE " %10" PRIuHSIZE " %10" PRIuHSIZE " ", + i, total, (hsize_t)f_offset, f_size); print_string(&buffer, f_name, TRUE); } h5tools_str_append(&buffer, "\n"); total += f_size; } - h5tools_str_append(&buffer, " %4s %10s %10s %10s ", "----", "----------", "----------", "----------"); + h5tools_str_append(&buffer, " %4s %10s %10s %10s ", "----", "----------", + "----------", "----------"); for (i = 0; i < max_len; i++) h5tools_str_append(&buffer, "-"); h5tools_str_append(&buffer, "\n"); } /* end if */ break; - case H5D_VIRTUAL: - { - char dset_name[256]; /* Dataset name */ - size_t vmaps; + case H5D_VIRTUAL: { + char dset_name[256]; /* Dataset name */ + size_t vmaps; - H5Pget_virtual_count(dcpl, &vmaps); + H5Pget_virtual_count(dcpl, &vmaps); - if (vmaps) { - size_t next; + if (vmaps) { + size_t next; - h5tools_str_append(&buffer, " %-10s {%ld} Source {\n", "Maps:", vmaps); - for (next = 0; next < (unsigned) vmaps; next++) { - H5Pget_virtual_filename(dcpl, next, f_name, sizeof(f_name)); - H5Pget_virtual_dsetname(dcpl, next, dset_name, sizeof(dset_name)); - h5tools_str_append(&buffer, " %-10s ", " "); - print_string(&buffer, f_name, TRUE); - h5tools_str_append(&buffer, " "); - print_string(&buffer, dset_name, TRUE); - h5tools_str_append(&buffer, "\n"); - } - h5tools_str_append(&buffer, " %-10s}\n", " "); + h5tools_str_append(&buffer, " %-10s {%ld} Source {\n", "Maps:", vmaps); + for (next = 0; next < (unsigned)vmaps; next++) { + H5Pget_virtual_filename(dcpl, next, f_name, sizeof(f_name)); + H5Pget_virtual_dsetname(dcpl, next, dset_name, sizeof(dset_name)); + h5tools_str_append(&buffer, " %-10s ", " "); + print_string(&buffer, f_name, TRUE); + h5tools_str_append(&buffer, " "); + print_string(&buffer, dset_name, TRUE); + h5tools_str_append(&buffer, "\n"); } + h5tools_str_append(&buffer, " %-10s}\n", " "); } - break; + } break; case H5D_LAYOUT_ERROR: case H5D_NLAYOUTS: @@ -1785,38 +1952,42 @@ dataset_list2(hid_t dset, const char H5_ATTR_UNUSED *name) break; } /* Print total raw storage size */ - total = (hsize_t)H5Sget_simple_extent_npoints(space) * H5Tget_size(type); - used = H5Dget_storage_size(dset); + total = (hsize_t)H5Sget_simple_extent_npoints(space) * H5Tget_size(type); + used = H5Dget_storage_size(dset); tclass = H5Tget_class(type); h5tools_str_append(&buffer, " %-10s ", "Storage:"); switch (tclass) { - case H5T_VLEN: - h5tools_str_append(&buffer, "information not available"); - break; - - case H5T_REFERENCE: - if (H5Tequal(type, H5T_STD_REF_DSETREG)) { + case H5T_VLEN: h5tools_str_append(&buffer, "information not available"); - } - break; + break; - case H5T_NO_CLASS: - case H5T_INTEGER: - case H5T_FLOAT: - case H5T_TIME: - case H5T_STRING: - case H5T_BITFIELD: - case H5T_OPAQUE: - case H5T_COMPOUND: - case H5T_ENUM: - case H5T_ARRAY: - case H5T_NCLASSES: - default: - h5tools_str_append(&buffer, HSIZE_T_FORMAT" logical byte%s, "HSIZE_T_FORMAT" allocated byte%s", total, 1==total?"":"s", used, 1==used?"":"s"); - if (used>0) { - utilization = ((double)total * (double)100.0f) / (double)used; - h5tools_str_append(&buffer, ", %1.2f%% utilization", utilization); - } + case H5T_REFERENCE: + if (H5Tequal(dset, H5T_STD_REF)) { + h5tools_str_append(&buffer, "reference information not available"); + } + else if (H5Tequal(dset, H5T_STD_REF_DSETREG)) { + h5tools_str_append(&buffer, "information not available"); + } + break; + + case H5T_NO_CLASS: + case H5T_INTEGER: + case H5T_FLOAT: + case H5T_TIME: + case H5T_STRING: + case H5T_BITFIELD: + case H5T_OPAQUE: + case H5T_COMPOUND: + case H5T_ENUM: + case H5T_ARRAY: + case H5T_NCLASSES: + default: + h5tools_str_append(&buffer, "%" PRIuHSIZE " logical byte%s, %" PRIuHSIZE " allocated byte%s", + total, 1 == total ? "" : "s", used, 1 == used ? "" : "s"); + if (used > 0) { + utilization = ((double)total * 100.0) / (double)used; + h5tools_str_append(&buffer, ", %1.2f%% utilization", utilization); + } } h5tools_str_append(&buffer, "\n"); @@ -1825,21 +1996,27 @@ dataset_list2(hid_t dset, const char H5_ATTR_UNUSED *name) if ((nf = H5Pget_nfilters(dcpl)) > 0) { for (i = 0; i < nf; i++) { cd_nelmts = NELMTS(cd_values); - filt_id = H5Pget_filter2(dcpl, (unsigned)i, &filt_flags, &cd_nelmts, cd_values, sizeof(f_name), f_name, NULL); + filt_id = H5Pget_filter2(dcpl, (unsigned)i, &filt_flags, &cd_nelmts, cd_values, + sizeof(f_name), f_name, NULL); f_name[sizeof(f_name) - 1] = '\0'; HDsnprintf(s, sizeof(s), "Filter-%d:", i); - h5tools_str_append(&buffer, " %-10s %s-%u %s {", s, (f_name[0] ? f_name : "method"), (unsigned)filt_id, ((filt_flags & H5Z_FLAG_OPTIONAL) ? "OPT" : "")); + h5tools_str_append(&buffer, " %-10s %s-%u %s {", s, (f_name[0] ? f_name : "method"), + (unsigned)filt_id, ((filt_flags & H5Z_FLAG_OPTIONAL) ? "OPT" : "")); for (cd_num = 0; cd_num < cd_nelmts; cd_num++) h5tools_str_append(&buffer, "%s%u", (cd_num ? ", " : ""), cd_values[cd_num]); h5tools_str_append(&buffer, "}\n"); } /* end for */ - } /* end if */ + } /* end if */ + h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, + (hsize_t)0, (hsize_t)0); /* Print data type */ + h5tools_str_reset(&buffer); h5tools_str_append(&buffer, " %-10s ", "Type:"); print_type(&buffer, type, 15); h5tools_str_append(&buffer, "\n"); - h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, + (hsize_t)0, (hsize_t)0); /* Print address information */ if (address_g) @@ -1859,25 +2036,24 @@ dataset_list2(hid_t dset, const char H5_ATTR_UNUSED *name) return 0; } /* end dataset_list2() */ - /*------------------------------------------------------------------------- - * Function: datatype_list2 + * Function: datatype_list2 * - * Purpose: List information about a datatype which should appear after - * information which is general to all objects. + * Purpose: List information about a datatype which should appear after + * information which is general to all objects. * - * Return: Success: 0 - * Failure: -1 + * Return: Success: 0 + * Failure: -1 *------------------------------------------------------------------------- */ static herr_t datatype_list2(hid_t type, const char H5_ATTR_UNUSED *name) { if (verbose_g > 0) { - hsize_t curr_pos = 0; /* total data element position */ - h5tools_str_t buffer; /* string into which to render */ - h5tools_context_t ctx; /* print context */ - h5tool_format_t *info = &ls_dataformat; + hsize_t curr_pos = 0; /* total data element position */ + h5tools_str_t buffer; /* string into which to render */ + h5tools_context_t ctx; /* print context */ + h5tool_format_t * info = &ls_dataformat; HDmemset(&ctx, 0, sizeof(ctx)); HDmemset(&buffer, 0, sizeof(h5tools_str_t)); @@ -1887,38 +2063,41 @@ datatype_list2(hid_t type, const char H5_ATTR_UNUSED *name) h5tools_str_append(&buffer, " %-10s ", "Type:"); print_type(&buffer, type, 15); h5tools_str_append(&buffer, "\n"); - h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, + (hsize_t)0, (hsize_t)0); h5tools_str_close(&buffer); } return 0; } - /*------------------------------------------------------------------------- - * Function: list_obj + * Function: list_obj * - * Purpose: Prints information about an object + * Purpose: Prints information about an object * - * Return: Success: 0 - * Failure: -1 + * Return: Success: 0 + * Failure: -1 *------------------------------------------------------------------------- */ static herr_t -list_obj(const char *name, const H5O_info_t *oinfo, const char *first_seen, void *_iter) +list_obj(const char *name, const H5O_info2_t *oinfo, const char *first_seen, void *_iter) { - H5O_type_t obj_type = oinfo->type; /* Type of the object */ - iter_t *iter = (iter_t*)_iter; - hsize_t curr_pos = 0; /* total data element position */ - h5tools_str_t buffer; /* string into which to render */ - h5tools_context_t ctx; /* print context */ - h5tool_format_t *info = &ls_dataformat; + H5O_type_t obj_type = oinfo->type; /* Type of the object */ + iter_t * iter = (iter_t *)_iter; + hsize_t curr_pos = 0; /* total data element position */ + h5tools_str_t buffer; /* string into which to render */ + h5tools_context_t ctx; /* print context */ + h5tool_format_t * info = &ls_dataformat; + + H5TOOLS_START_DEBUG(" "); HDmemset(&ctx, 0, sizeof(ctx)); HDmemset(&buffer, 0, sizeof(h5tools_str_t)); h5tools_str_reset(&buffer); + H5TOOLS_DEBUG("Object name:%s", name); /* Print the link's name, either full name or base name */ if (!iter->symlink_target) print_obj_name(&buffer, iter, name, ""); @@ -1932,7 +2111,8 @@ list_obj(const char *name, const H5O_info_t *oinfo, const char *first_seen, void h5tools_str_append(&buffer, "{"); if (obj_type >= 0 && dispatch_g[obj_type].name) h5tools_str_append(&buffer, "%s", dispatch_g[obj_type].name); - h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, + (hsize_t)0); /* Check if we've seen this object before */ if (first_seen) { @@ -1942,53 +2122,66 @@ list_obj(const char *name, const H5O_info_t *oinfo, const char *first_seen, void if (!iter->symlink_target) { h5tools_str_append(&buffer, "\n"); } - h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, + (hsize_t)0, (hsize_t)0); } /* end if */ else { - hid_t obj = (-1); /* ID of object opened */ + hid_t obj_id = H5I_INVALID_HID; /* ID of object opened */ /* Open the object. Not all objects can be opened. If this is the case * then return right away. */ - if (obj_type >= 0 && (obj = H5Oopen(iter->fid, name, H5P_DEFAULT)) < 0) { + H5TOOLS_DEBUG("Open object name=%s", name); + if (obj_type >= 0 && (obj_id = H5Oopen(iter->fid, name, H5P_DEFAULT)) < 0) { h5tools_str_reset(&buffer); h5tools_str_append(&buffer, " *ERROR*\n"); - h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, + (hsize_t)0, (hsize_t)0); goto done; } /* end if */ /* List the first line of information for the object. */ + H5TOOLS_DEBUG("Object type:%d", obj_type); if (obj_type >= 0 && dispatch_g[obj_type].list1) - (dispatch_g[obj_type].list1)(obj); + (dispatch_g[obj_type].list1)(obj_id); if (!iter->symlink_target || (verbose_g > 0)) { h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "\n"); - h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, + (hsize_t)0, (hsize_t)0); } /* Show detailed information about the object, beginning with information * which is common to all objects. */ if (verbose_g > 0) { - size_t buf_size = 0; - char* comment = NULL; - ssize_t cmt_bufsize = -1; + size_t buf_size = 0; + char * comment = NULL; + char * obj_tok_str = NULL; + ssize_t cmt_bufsize = -1; + uint64_t supported = 0; /* Display attributes */ + H5TOOLS_DEBUG("Display attributes"); if (obj_type >= 0) - H5Aiterate2(obj, H5_INDEX_NAME, H5_ITER_INC, NULL, list_attr, NULL); + H5Aiterate2(obj_id, H5_INDEX_NAME, H5_ITER_INC, NULL, list_attr, NULL); /* Object location & reference count */ + H5Otoken_to_str(obj_id, &oinfo->token, &obj_tok_str); + h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, " %-10s %lu:"H5_PRINTF_HADDR_FMT"\n", "Location:", oinfo->fileno, oinfo->addr); + h5tools_str_append(&buffer, " %-10s %lu:%s\n", "Location:", oinfo->fileno, obj_tok_str); h5tools_str_append(&buffer, " %-10s %u\n", "Links:", (unsigned)oinfo->rc); - h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, + (hsize_t)0, (hsize_t)0); + + H5free_memory(obj_tok_str); /* Modification time */ if (oinfo->mtime > 0) { - char buf[256]; + char buf[256]; struct tm *tm; - if(simple_output_g) + if (simple_output_g) tm = HDgmtime(&(oinfo->mtime)); else tm = HDlocaltime(&(oinfo->mtime)); @@ -1996,55 +2189,66 @@ list_obj(const char *name, const H5O_info_t *oinfo, const char *first_seen, void HDstrftime(buf, sizeof(buf), "%Y-%m-%d %H:%M:%S %Z", tm); h5tools_str_reset(&buffer); h5tools_str_append(&buffer, " %-10s %s\n", "Modified:", buf); - h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, + (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); } /* end if */ - } /* end if */ - - /* Object comment */ - cmt_bufsize = H5Oget_comment(obj, comment, buf_size); - - /* if the actual length of the comment is longer than cmt_bufsize, then call - * H5Oget_comment again with the correct value. - * If the call to H5Oget_comment returned an error, skip this block */ - if (cmt_bufsize > 0) { - comment = (char *)HDmalloc((size_t)cmt_bufsize + 1); /* new_size including null terminator */ - if (comment) { - cmt_bufsize = H5Oget_comment(obj, comment, (size_t)cmt_bufsize); - if (cmt_bufsize > 0) { - comment[cmt_bufsize] = 0; - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, " %-10s \"", "Comment:"); - print_string(&buffer, comment, FALSE); - h5tools_str_append(&buffer, "\"\n"); - h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); - } /* end if */ - HDfree(comment); + } /* end if */ + + /* Only emit comments if the VOL connector supports that */ + H5VLquery_optional(obj_id, H5VL_SUBCLS_OBJECT, H5VL_NATIVE_OBJECT_GET_COMMENT, &supported); + + if (supported & H5VL_OPT_QUERY_SUPPORTED) { + + /* Object comment */ + cmt_bufsize = H5Oget_comment(obj_id, comment, buf_size); + + /* if the actual length of the comment is longer than cmt_bufsize, then call + * H5Oget_comment again with the correct value. + */ + if (cmt_bufsize > 0) { + comment = + (char *)HDmalloc((size_t)cmt_bufsize + 1); /* new_size including null terminator */ + if (comment) { + cmt_bufsize = H5Oget_comment(obj_id, comment, (size_t)cmt_bufsize); + if (cmt_bufsize > 0) { + comment[cmt_bufsize] = 0; + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, " %-10s \"", "Comment:"); + print_string(&buffer, comment, FALSE); + h5tools_str_append(&buffer, "\"\n"); + h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, + (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); + } /* end if */ + HDfree(comment); + } } } } /* end if */ /* Detailed list for object */ if (obj_type >= 0 && dispatch_g[obj_type].list2) - (dispatch_g[obj_type].list2)(obj, name); + (dispatch_g[obj_type].list2)(obj_id, name); /* Close the object. */ if (obj_type >= 0) - H5Oclose(obj); + H5Oclose(obj_id); } /* end else */ done: if (iter->symlink_target) { h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "}\n"); - h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, + (hsize_t)0, (hsize_t)0); iter->symlink_target = FALSE; } h5tools_str_close(&buffer); + H5TOOLS_ENDDEBUG(" "); + return 0; } /* end list_obj() */ - /*------------------------------------------------------------------------- * Function: list_lnk * @@ -2055,16 +2259,16 @@ done: *------------------------------------------------------------------------- */ static herr_t -list_lnk(const char *name, const H5L_info_t *linfo, void *_iter) +list_lnk(const char *name, const H5L_info2_t *linfo, void *_iter) { - char *buf=NULL; - iter_t *iter = (iter_t*)_iter; - int ret; - hsize_t curr_pos = 0; /* total data element position */ + char * buf = NULL; + iter_t * iter = (iter_t *)_iter; + int ret; + hsize_t curr_pos = 0; /* total data element position */ h5tool_link_info_t lnk_info; - h5tools_str_t buffer; /* string into which to render */ - h5tools_context_t ctx; /* print context */ - h5tool_format_t *info = &ls_dataformat; + h5tools_str_t buffer; /* string into which to render */ + h5tools_context_t ctx; /* print context */ + h5tool_format_t * info = &ls_dataformat; HDmemset(&ctx, 0, sizeof(ctx)); HDmemset(&buffer, 0, sizeof(h5tools_str_t)); @@ -2076,17 +2280,17 @@ list_lnk(const char *name, const H5L_info_t *linfo, void *_iter) /* if verbose, make H5tools_get_symlink_info() display more */ if (verbose_g) - lnk_info.opt.msg_mode=1; + lnk_info.opt.msg_mode = 1; /* Print the link's name, either full name or base name */ print_obj_name(&buffer, iter, name, ""); - switch(linfo->type) { + switch (linfo->type) { case H5L_TYPE_SOFT: ret = H5tools_get_symlink_info(iter->fid, name, &lnk_info, follow_symlink_g); /* lnk_info.trg_path is malloced in H5tools_get_symlink_info() * so it will be freed via buf later */ - buf = (char*)lnk_info.trg_path; + buf = (char *)lnk_info.trg_path; /* error */ if (ret < 0) goto done; @@ -2095,9 +2299,10 @@ list_lnk(const char *name, const H5L_info_t *linfo, void *_iter) iter->symlink_list->dangle_link = TRUE; h5tools_str_append(&buffer, "Soft Link {"); - h5tools_str_append(&buffer, buf); + h5tools_str_append(&buffer, "%s", buf); h5tools_str_append(&buffer, "}"); - h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, + (hsize_t)0, (hsize_t)0); if (follow_symlink_g) { hbool_t orig_grp_literal = grp_literal_g; h5tools_str_reset(&buffer); @@ -2106,10 +2311,12 @@ list_lnk(const char *name, const H5L_info_t *linfo, void *_iter) /* Check if we have already seen this softlink */ if (symlink_is_visited(iter->symlink_list, linfo->type, NULL, buf)) { h5tools_str_append(&buffer, "{Already Visited}\n"); - h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, + (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); goto done; } - h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, + (hsize_t)0, (hsize_t)0); /* Add this link to the list of seen softlinks */ if (symlink_visit_add(iter->symlink_list, linfo->type, NULL, buf) < 0) @@ -2134,21 +2341,21 @@ list_lnk(const char *name, const H5L_info_t *linfo, void *_iter) else { h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "\n"); - h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, + (hsize_t)0, (hsize_t)0); } break; - case H5L_TYPE_EXTERNAL: - { + case H5L_TYPE_EXTERNAL: { const char *filename; const char *path; - hbool_t follow_link = follow_symlink_g || follow_elink_g; + hbool_t follow_link = follow_symlink_g || follow_elink_g; ret = H5tools_get_symlink_info(iter->fid, name, &lnk_info, follow_link); /* lnk_info.trg_path is malloced in H5tools_get_symlink_info() * so it will be freed via buf later */ - buf = (char*)lnk_info.trg_path; + buf = (char *)lnk_info.trg_path; /* error */ if (ret < 0) goto done; @@ -2160,13 +2367,14 @@ list_lnk(const char *name, const H5L_info_t *linfo, void *_iter) goto done; h5tools_str_append(&buffer, "External Link {"); - h5tools_str_append(&buffer, filename); + h5tools_str_append(&buffer, "%s", filename); h5tools_str_append(&buffer, "/"); - if(*path != '/') + if (*path != '/') h5tools_str_append(&buffer, "/"); - h5tools_str_append(&buffer, path); + h5tools_str_append(&buffer, "%s", path); h5tools_str_append(&buffer, "}"); - h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, + (hsize_t)0, (hsize_t)0); /* Recurse through the external link */ /* keep the follow_elink_g for backward compatibility with -E */ @@ -2178,10 +2386,12 @@ list_lnk(const char *name, const H5L_info_t *linfo, void *_iter) /* Check if we have already seen this elink */ if (symlink_is_visited(iter->symlink_list, linfo->type, filename, path)) { h5tools_str_append(&buffer, "{Already Visited}\n"); - h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, + (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); goto done; } - h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, + (hsize_t)0, (hsize_t)0); /* Add this link to the list of seen elinks */ if (symlink_visit_add(iter->symlink_list, linfo->type, filename, path) < 0) { @@ -2207,15 +2417,15 @@ list_lnk(const char *name, const H5L_info_t *linfo, void *_iter) } else PRINTVALSTREAM(rawoutstream, "\n"); - } - break; + } break; case H5L_TYPE_ERROR: case H5L_TYPE_HARD: case H5L_TYPE_MAX: default: h5tools_str_append(&buffer, "UD Link {cannot follow UD links}\n"); - h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, + (hsize_t)0, (hsize_t)0); break; } /* end switch */ @@ -2227,26 +2437,24 @@ done: return 0; } /* end list_lnk() */ - /*------------------------------------------------------------------------- - * Function: visit_obj + * Function: visit_obj * - * Purpose: Begins iteration on an object + * Purpose: Begins iteration on an object * - * Return: - * Success: 0 - * Failure: -1 + * Return: Success: 0 + * Failure: -1 *------------------------------------------------------------------------- */ static herr_t visit_obj(hid_t file, const char *oname, iter_t *iter) { - int retval = 0; - H5O_info_t oi; /* Information for object */ - hsize_t curr_pos = 0; /* total data element position */ - h5tools_str_t buffer; /* string into which to render */ - h5tools_context_t ctx; /* print context */ - h5tool_format_t *info = &ls_dataformat; + int retval = 0; + H5O_info2_t oi; /* Information for object */ + hsize_t curr_pos = 0; /* total data element position */ + h5tools_str_t buffer; /* string into which to render */ + h5tools_context_t ctx; /* print context */ + h5tool_format_t * info = &ls_dataformat; HDmemset(&ctx, 0, sizeof(ctx)); HDmemset(&buffer, 0, sizeof(h5tools_str_t)); @@ -2254,14 +2462,15 @@ visit_obj(hid_t file, const char *oname, iter_t *iter) h5tools_str_reset(&buffer); /* Retrieve info for object to list */ - if (H5Oget_info_by_name2(file, oname, &oi, H5O_INFO_BASIC|H5O_INFO_TIME, H5P_DEFAULT) < 0) { + if (H5Oget_info_by_name3(file, oname, &oi, H5O_INFO_BASIC | H5O_INFO_TIME, H5P_DEFAULT) < 0) { if (iter->symlink_target) { h5tools_str_append(&buffer, "{**NOT FOUND**}\n"); iter->symlink_target = FALSE; } else print_obj_name(&buffer, iter, oname, "**NOT FOUND**"); - h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, + (hsize_t)0, (hsize_t)0); retval = -1; goto done; } /* end if */ @@ -2271,18 +2480,20 @@ visit_obj(hid_t file, const char *oname, iter_t *iter) /* Get ID for group */ if (!iter->symlink_target && (iter->gid = H5Gopen2(file, oname, H5P_DEFAULT)) < 0) { h5tools_str_append(&buffer, "%s: unable to open '%s' as group\n", iter->fname, oname); - h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); - goto done; /* Previously "continue", when this code was in main(). - * We don't "continue" here in order to close the file - * and free the file name properly. */ - } /* end if */ + h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, + (hsize_t)0, (hsize_t)0); + goto done; /* Previously "continue", when this code was in main(). + * We don't "continue" here in order to close the file + * and free the file name properly. */ + } /* end if */ /* Delay specifying the name start point so the original object name is * displayed if it is a link or non-group object */ iter->name_start = iter->base_len; /* Specified name is a group. List the complete contents of the group. */ - h5trav_visit(file, oname, (hbool_t) (display_root_g || iter->symlink_target), recursive_g, list_obj, list_lnk, iter, H5O_INFO_BASIC|H5O_INFO_TIME); + h5trav_visit(file, oname, (hbool_t)(display_root_g || iter->symlink_target), recursive_g, list_obj, + list_lnk, iter, H5O_INFO_BASIC | H5O_INFO_TIME); /* Close group */ if (!iter->symlink_target) @@ -2302,23 +2513,22 @@ done: return retval; } - /*------------------------------------------------------------------------- - * Function: get_width + * Function: get_width * - * Purpose: Figure out how wide the screen is. This is highly - * unportable, but the user can always override the width we - * detect by giving a command-line option. These code snippets - * were borrowed from the GNU less(1). + * Purpose: Figure out how wide the screen is. This is highly + * unportable, but the user can always override the width we + * detect by giving a command-line option. These code snippets + * were borrowed from the GNU less(1). * - * Return: Success: Number of columns. - * Failure: Some default number of columms. + * Return: Success: Number of columns. + * Failure: Some default number of columns. *------------------------------------------------------------------------- */ static int get_width(void) { - int width = 80; /*the default */ + int width = 80; /*the default */ char *s; /* Try to get it from the COLUMNS environment variable first since it's @@ -2358,14 +2568,14 @@ get_width(void) { /* Unix with ioctl(TIOCGWINSZ) */ struct winsize w; - if (ioctl(2, (int)TIOCGWINSZ, &w)>=0 && w.ws_col>0) + if (ioctl(2, (int)TIOCGWINSZ, &w) >= 0 && w.ws_col > 0) width = w.ws_col; } #elif defined(H5_HAVE_TIOCGETD) && defined(H5_HAVE_IOCTL) { /* Unix with ioctl(TIOCGETD) */ struct uwdata w; - if (ioctl(2, WIOCGETD, &w)>=0 && w.uw_width>0) + if (ioctl(2, WIOCGETD, &w) >= 0 && w.uw_width > 0) width = w.uw_width / w.uw_hs; } #endif @@ -2377,13 +2587,12 @@ get_width(void) } /*------------------------------------------------------------------------- - * Function: is_valid_args + * Function: is_valid_args * - * Purpose: check if command line arguments are valid + * Purpose: check if command line arguments are valid * - * Return: - * Success: TRUE (1) - * Failure: FALSE (0) + * Return: Success: TRUE (1) + * Failure: FALSE (0) *-------------------------------------------------------------------------*/ static hbool_t is_valid_args(void) @@ -2397,7 +2606,8 @@ is_valid_args(void) } if (no_dangling_link_g && !follow_symlink_g) { - HDfprintf(rawerrorstream, "Error: --no-dangling-links must be used along with --follow-symlinks option!\n\n"); + HDfprintf(rawerrorstream, + "Error: --no-dangling-links must be used along with --follow-symlinks option!\n\n"); ret = FALSE; goto out; } @@ -2406,13 +2616,12 @@ out: return ret; } - /*------------------------------------------------------------------------- - * Function: leave + * Function: leave * - * Purpose: Close HDF5 and MPI and call exit() + * Purpose: Close HDF5 and MPI and call exit() * - * Return: Does not return + * Return: Does not return *------------------------------------------------------------------------- */ static void @@ -2423,50 +2632,52 @@ leave(int ret) HDexit(ret); } - /*------------------------------------------------------------------------- - * Function: main + * Function: main * - * Purpose: Opens a file and lists the specified group + * Purpose: Opens a file and lists the specified group * - * Return: Success: 0 - * Failure: 1 + * Return: Success: 0 + * Failure: 1 *------------------------------------------------------------------------- */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { - hid_t file = -1; - char *fname = NULL, *oname = NULL, *x; - const char *s = NULL; - char *rest; - int argno; - static char root_name[] = "/"; - char drivername[50]; - const char *preferred_driver = NULL; - int err_exit = 0; - hid_t fapl_id = H5P_DEFAULT; + hid_t file_id = H5I_INVALID_HID; + char * fname = NULL, *oname = NULL, *x = NULL; + const char * s = NULL; + char * rest; + int argno; + static char root_name[] = "/"; + char drivername[50]; + int err_exit = 0; + hid_t fapl_id = H5P_DEFAULT; + hbool_t custom_vol_fapl = FALSE; + hbool_t custom_vfd_fapl = FALSE; + h5tools_vol_info_t vol_info; + h5tools_vfd_info_t vfd_info; #ifdef H5_HAVE_ROS3_VFD - /* default "anonymous" s3 configuration */ + /* Default "anonymous" S3 configuration */ H5FD_ros3_fapl_t ros3_fa = { - 1, /* fapl version */ - false, /* authenticate */ - "", /* aws region */ - "", /* access key id */ - "", /* secret access key */ + 1, /* Structure Version */ + FALSE, /* Authenticate? */ + "", /* AWS Region */ + "", /* Access Key ID */ + "", /* Secret Access Key */ }; -#endif /* H5_HVAE_ROS3_VFD */ +#endif /* H5_HAVE_ROS3_VFD */ #ifdef H5_HAVE_LIBHDFS - /* "default" HDFS configuration */ + /* "Default" HDFS configuration */ H5FD_hdfs_fapl_t hdfs_fa = { - 1, /* fapl version */ - "localhost", /* namenode name */ - 0, /* namenode port */ - "", /* kerberos ticket cache */ - "", /* user name */ - 2048, /* stream buffer size */ + 1, /* Structure Version */ + "localhost", /* Namenode Name */ + 0, /* Namenode Port */ + "", /* Kerberos ticket cache */ + "", /* User name */ + 2048, /* Stream buffer size */ }; #endif /* H5_HAVE_LIBHDFS */ @@ -2476,6 +2687,10 @@ main(int argc, const char *argv[]) /* Initialize h5tools lib */ h5tools_init(); + /* Initialize fapl info structs */ + HDmemset(&vol_info, 0, sizeof(h5tools_vol_info_t)); + HDmemset(&vfd_info, 0, sizeof(h5tools_vfd_info_t)); + /* Build object display table */ DISPATCH(H5O_TYPE_GROUP, "Group", NULL, NULL); DISPATCH(H5O_TYPE_DATASET, "Dataset", dataset_list1, dataset_list2); @@ -2498,15 +2713,15 @@ main(int argc, const char *argv[]) else if (!HDstrcmp(argv[argno], "--address")) { address_g = TRUE; } - else if(!HDstrcmp(argv[argno], "--data")) { + else if (!HDstrcmp(argv[argno], "--data")) { data_g = TRUE; } else if (!HDstrcmp(argv[argno], "--enable-error-stack")) { - show_errors_g = TRUE; - /* deprecated --errors */ + enable_error_stack = 1; } else if (!HDstrcmp(argv[argno], "--errors")) { - show_errors_g = TRUE; + /* deprecated --errors */ + enable_error_stack = 1; } else if (!HDstrcmp(argv[argno], "--follow-symlinks")) { follow_symlink_g = TRUE; @@ -2528,7 +2743,7 @@ main(int argc, const char *argv[]) } else if (!HDstrcmp(argv[argno], "--recursive")) { recursive_g = TRUE; - fullname_g = TRUE; + fullname_g = TRUE; } else if (!HDstrcmp(argv[argno], "--simple")) { simple_output_g = TRUE; @@ -2536,11 +2751,40 @@ main(int argc, const char *argv[]) else if (!HDstrcmp(argv[argno], "--string")) { string_g = TRUE; } + else if (!HDstrncmp(argv[argno], "--vol-value=", (size_t)12)) { + vol_info.type = VOL_BY_VALUE; + vol_info.u.value = (H5VL_class_value_t)HDatoi(argv[argno] + 12); + custom_vol_fapl = TRUE; + } + else if (!HDstrncmp(argv[argno], "--vol-name=", (size_t)11)) { + vol_info.type = VOL_BY_NAME; + vol_info.u.name = argv[argno] + 11; + custom_vol_fapl = TRUE; + } + else if (!HDstrncmp(argv[argno], "--vol-info=", (size_t)11)) { + vol_info.info_string = argv[argno] + 11; + } else if (!HDstrncmp(argv[argno], "--vfd=", (size_t)6)) { - preferred_driver = argv[argno]+6; + vfd_info.type = VFD_BY_NAME; + vfd_info.u.name = argv[argno] + 6; + vfd_info.info = NULL; + custom_vfd_fapl = TRUE; + } + else if (!HDstrncmp(argv[argno], "--vfd-value=", (size_t)12)) { + vfd_info.type = VFD_BY_VALUE; + vfd_info.u.value = (H5FD_class_value_t)HDatoi(argv[argno] + 12); + custom_vfd_fapl = TRUE; + } + else if (!HDstrncmp(argv[argno], "--vfd-name=", (size_t)11)) { + vfd_info.type = VFD_BY_NAME; + vfd_info.u.name = argv[argno] + 11; + custom_vfd_fapl = TRUE; + } + else if (!HDstrncmp(argv[argno], "--vfd-info=", (size_t)11)) { + vfd_info.info = (const void *)(argv[argno] + 11); } else if (!HDstrncmp(argv[argno], "--width=", (size_t)8)) { - width_g = (int)HDstrtol(argv[argno]+8, &rest, 0); + width_g = (int)HDstrtol(argv[argno] + 8, &rest, 0); if (0 == width_g) no_line_wrap_g = TRUE; @@ -2586,27 +2830,18 @@ main(int argc, const char *argv[]) } width_g = (int)HDstrtol(s, &rest, 0); - if(0 == width_g) { + if (0 == width_g) { no_line_wrap_g = TRUE; } - else if(width_g < 0 || *rest) { + else if (width_g < 0 || *rest) { usage(); leave(EXIT_FAILURE); } + } + else if (!HDstrncmp(argv[argno], "--s3-cred=", (size_t)10)) { +#ifdef H5_HAVE_ROS3_VFD + char const *start = NULL; - } else if (!HDstrncmp(argv[argno], "--s3-cred=", (size_t)10)) { -#ifndef H5_HAVE_ROS3_VFD - HDfprintf(rawerrorstream, "Error: Read-Only S3 VFD is not enabled\n\n"); - usage(); - leave(EXIT_FAILURE); -#else - unsigned nelems = 0; - char *start = NULL; - char *s3cred_src = NULL; - char **s3cred = NULL; - char const *ccred[3]; - /* try to parse s3 credentials tuple - */ start = strchr(argv[argno], '='); if (start == NULL) { HDfprintf(rawerrorstream, @@ -2616,130 +2851,43 @@ main(int argc, const char *argv[]) leave(EXIT_FAILURE); } start++; - if (FAIL == parse_tuple((const char *)start, ',', &s3cred_src, &nelems, &s3cred)) { - HDfprintf(rawerrorstream, "Error: Unable to parse S3 credentials\n\n"); - usage(); - leave(EXIT_FAILURE); - } - /* sanity-check tuple count - */ - if (nelems != 3) { - HDfprintf(rawerrorstream, "Error: Invalid S3 credentials\n\n"); - usage(); - leave(EXIT_FAILURE); - } - ccred[0] = (const char *)s3cred[0]; - ccred[1] = (const char *)s3cred[1]; - ccred[2] = (const char *)s3cred[2]; - if (0 == h5tools_populate_ros3_fapl(&ros3_fa, ccred)) { - HDfprintf(rawerrorstream, "Error: Invalid S3 credentials\n\n"); + + if (h5tools_parse_ros3_fapl_tuple(start, ',', &ros3_fa) < 0) { + HDfprintf(rawerrorstream, "Error: failed to parse S3 VFD credential info\n\n"); usage(); leave(EXIT_FAILURE); } - HDfree(s3cred); - HDfree(s3cred_src); -#endif /* H5_HAVE_ROS3_VFD */ - +#else + HDfprintf(rawerrorstream, "Error: Read-Only S3 VFD is not enabled\n\n"); + usage(); + leave(EXIT_FAILURE); +#endif } else if (!HDstrncmp(argv[argno], "--hdfs-attrs=", (size_t)13)) { -#ifndef H5_HAVE_LIBHDFS - PRINTVALSTREAM(rawoutstream, "The HDFS VFD is not enabled.\n"); - leave(EXIT_FAILURE); -#else - /* Parse received configuration data and set fapl config struct */ - - hbool_t _debug = FALSE; - unsigned nelems = 0; - char const *start = NULL; - char *props_src = NULL; - char **props = NULL; - unsigned long k = 0; - - /* try to parse tuple - */ - if (_debug) { - HDfprintf(stderr, "configuring hdfs...\n"); - } - start = argv[argno]+13; /* should never segfault: worst case of */ - if (*start != '(') { /* null-termintor after '='. */ - - if (_debug) { - HDfprintf(stderr, " no tuple.\n"); - } - usage(); - leave(EXIT_FAILURE); - } - if (FAIL == parse_tuple((const char *)start, ',', &props_src, &nelems, &props)) { - HDfprintf(stderr, " unable to parse tuple.\n"); +#ifdef H5_HAVE_LIBHDFS + char const *start = NULL; + + start = argv[argno] + 13; /* should never segfault: worst case of */ + if (*start != '(') { /* null-termintor after '='. */ usage(); leave(EXIT_FAILURE); } - /* sanity-check tuple count - */ - if (nelems != 5) { - HDfprintf(stderr, " expected 5-ple, got `%d`\n", nelems); + if (h5tools_parse_hdfs_fapl_tuple(start, ',', &hdfs_fa) < 0) { + HDfprintf(rawerrorstream, "Error: failed to parse HDFS VFD configuration info\n\n"); usage(); leave(EXIT_FAILURE); } - if (_debug) { - HDfprintf(stderr, " got hdfs-attrs tuple: `(%s,%s,%s,%s,%s)`\n", - props[0], props[1], props[2], props[3], props[4]); - } - - /* Populate fapl configuration structure with given properties. - * WARNING: No error-checking is done on length of input strings... - * Silent overflow is possible, albeit unlikely. - */ - if (HDstrncmp(props[0], "", 1)) { - if (_debug) { - HDfprintf(stderr, " setting namenode name: %s\n", props[0]); - } - HDstrncpy(hdfs_fa.namenode_name, (const char *)props[0], HDstrlen(props[0])); - } - if (HDstrncmp(props[1], "", 1)) { - k = strtoul((const char *)props[1], NULL, 0); - if (errno == ERANGE) { - HDfprintf(stderr, " supposed port number wasn't.\n"); - leave(EXIT_FAILURE); - } - if (_debug) { - HDfprintf(stderr, " setting namenode port: %lu\n", k); - } - hdfs_fa.namenode_port = (int32_t)k; - } - if (HDstrncmp(props[2], "", 1)) { - if (_debug) { - HDfprintf(stderr, " setting kerb cache path: %s\n", props[2]); - } - HDstrncpy(hdfs_fa.kerberos_ticket_cache, (const char *)props[2], HDstrlen(props[2])); - } - if (HDstrncmp(props[3], "", 1)) { - if (_debug) { - HDfprintf(stderr, " setting username: %s\n", props[3]); - } - HDstrncpy(hdfs_fa.user_name, (const char *)props[3], HDstrlen(props[3])); - } - if (HDstrncmp(props[4], "", 1)) { - k = HDstrtoul((const char *)props[4], NULL, 0); - if (errno == ERANGE) { - HDfprintf(stderr, " supposed buffersize number wasn't.\n"); - leave(EXIT_FAILURE); - } - if (_debug) { - HDfprintf(stderr, " setting stream buffer size: %lu\n", k); - } - hdfs_fa.stream_buffer_size = (int32_t)k; - } - HDfree(props); - HDfree(props_src); -#endif /* H5_HAVE_LIBHDFS */ - +#else + HDfprintf(rawerrorstream, "Error: The HDFS VFD is not enabled\n\n"); + usage(); + leave(EXIT_FAILURE); +#endif } - else if('-'!=argv[argno][1]) { + else if ('-' != argv[argno][1]) { /* Single-letter switches */ - for(s = argv[argno] + 1; *s; s++) { - switch(*s) { + for (s = argv[argno] + 1; *s; s++) { + switch (*s) { case '?': case 'h': /* --help */ usage(); @@ -2756,7 +2904,7 @@ main(int argc, const char *argv[]) /* deprecated -e */ case 'e': /* --errors */ - show_errors_g = TRUE; + enable_error_stack = 1; break; case 'E': /* --external */ @@ -2777,7 +2925,7 @@ main(int argc, const char *argv[]) case 'r': /* --recursive */ recursive_g = TRUE; - fullname_g = TRUE; + fullname_g = TRUE; break; case 'S': /* --simple */ @@ -2805,7 +2953,7 @@ main(int argc, const char *argv[]) usage(); leave(EXIT_FAILURE); } /* end switch */ - } /* end for */ + } /* end for */ } else { HDfprintf(stderr, "Unknown argument: %s\n", argv[argno]); @@ -2814,6 +2962,9 @@ main(int argc, const char *argv[]) } } /* end for */ + /* enable error reporting if command line option */ + h5tools_error_report(); + /* If no arguments remain then print a usage message (instead of doing * absolutely nothing ;-) */ if (argno >= argc) { @@ -2827,47 +2978,14 @@ main(int argc, const char *argv[]) leave(EXIT_FAILURE); } - if (preferred_driver) { - void *conf_fa = NULL; - - if (!HDstrcmp(preferred_driver, "ros3")) { -#ifndef H5_HAVE_ROS3_VFD - HDfprintf(rawerrorstream, "Error: Read-Only S3 VFD not enabled.\n\n"); - usage(); + /* Setup a custom fapl for file accesses */ + if (custom_vol_fapl || custom_vfd_fapl) { + if ((fapl_id = h5tools_get_fapl(H5P_DEFAULT, custom_vol_fapl ? &vol_info : NULL, + custom_vfd_fapl ? &vfd_info : NULL)) < 0) { + error_msg("failed to setup file access property list (fapl) for file\n"); leave(EXIT_FAILURE); -#else - conf_fa = (void *)&ros3_fa; -#endif /* H5_HAVE_ROS3_VFD */ - } - else if (!HDstrcmp(preferred_driver, "hdfs")) { -#ifndef H5_HAVE_LIBHDFS - PRINTVALSTREAM(rawoutstream, "The HDFS VFD is not enabled.\n"); - leave(EXIT_FAILURE); -#else - conf_fa = (void *)&hdfs_fa; -#endif /* H5_HAVE_LIBHDFS */ - } - - if (conf_fa != NULL) { - HDassert(fapl_id == H5P_DEFAULT); - fapl_id = H5Pcreate(H5P_FILE_ACCESS); - if (fapl_id < 0) { - HDfprintf(rawerrorstream, "Error: Unable to create fapl entry\n\n"); - leave(EXIT_FAILURE); - } - if (0 == h5tools_set_configured_fapl(fapl_id, preferred_driver, conf_fa)) { - HDfprintf(rawerrorstream, "Error: Unable to set fapl\n\n"); - usage(); - leave(EXIT_FAILURE); - } - } - } /* preferred_driver defined */ - - /* Turn off HDF5's automatic error printing unless you're debugging h5ls */ - if(!show_errors_g) - H5Eset_auto2(H5E_DEFAULT, NULL, NULL); - + } /* Each remaining argument is an hdf5 file followed by an optional slash * and object name. @@ -2881,33 +2999,29 @@ main(int argc, const char *argv[]) * chops off the last component. If we reach the beginning of the name * then there must have been something wrong with the file (perhaps it * doesn't exist). */ - show_file_name_g = (argc-argno > 1); /*show file names if more than one*/ - while(argno < argc) { - H5L_info_t li; - iter_t iter; + show_file_name_g = (argc - argno > 1); /*show file names if more than one*/ + while (argno < argc) { + H5L_info2_t li; + iter_t iter; symlink_trav_t symlink_list; - size_t u; + size_t u; - fname = HDstrdup(argv[argno++]); - oname = NULL; - file = -1; + fname = HDstrdup(argv[argno++]); + oname = NULL; + file_id = H5I_INVALID_HID; while (fname && *fname) { - if (fapl_id != H5P_DEFAULT) { - file = H5Fopen(fname, H5F_ACC_RDONLY, fapl_id); - } - else { - file = h5tools_fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT, preferred_driver, drivername, sizeof drivername); - } + file_id = h5tools_fopen(fname, H5F_ACC_RDONLY, fapl_id, (fapl_id != H5P_DEFAULT), drivername, + sizeof drivername); - if (file >= 0) { + if (file_id >= 0) { if (verbose_g) PRINTSTREAM(rawoutstream, "Opened \"%s\" with %s driver.\n", fname, drivername); break; /*success*/ - } /* end if */ + } /* end if */ /* Shorten the file name; lengthen the object name */ - x = oname; + x = oname; oname = HDstrrchr(fname, '/'); if (x) *x = '/'; @@ -2916,8 +3030,8 @@ main(int argc, const char *argv[]) *oname = '\0'; } /* end while */ - if (file < 0) { - HDfprintf(rawerrorstream, "%s: unable to open file\n", argv[argno-1]); + if (file_id < 0) { + HDfprintf(rawerrorstream, "%s: unable to open file\n", argv[argno - 1]); HDfree(fname); err_exit = 1; continue; @@ -2925,9 +3039,9 @@ main(int argc, const char *argv[]) if (oname) { /* Always use absolute paths to avoid confusion, keep track of where * to begin path name output */ - *oname = '/'; + *oname = '/'; iter.base_len = HDstrlen(oname); - iter.base_len -= oname[iter.base_len-1] == '/'; + iter.base_len -= oname[iter.base_len - 1] == '/'; x = oname; if (NULL == (oname = HDstrdup(oname))) { HDfprintf(rawerrorstream, "memory allocation failed\n"); @@ -2942,57 +3056,59 @@ main(int argc, const char *argv[]) oname = root_name; if (recursive_g) display_root_g = TRUE; - iter.base_len = 0; + iter.base_len = 0; iter.name_start = 0; /* Use x to remember if we have allocated space in oname */ x = NULL; } /* end if */ /* Remember the file information for later */ - iter.fname = fname; - iter.fid = file; - iter.gid = -1; - iter.symlink_target = FALSE; - iter.symlink_list = &symlink_list; + iter.fname = fname; + iter.fid = file_id; + iter.gid = H5I_INVALID_HID; + iter.symlink_target = FALSE; + iter.symlink_list = &symlink_list; iter.symlink_list->dangle_link = FALSE; /* Initialize list of visited symbolic links */ symlink_list.nused = symlink_list.nalloc = 0; - symlink_list.objs = NULL; + symlink_list.objs = NULL; /* Check for root group as object name */ - if (HDstrcmp(oname, root_name)) { + if (HDstrcmp(oname, root_name) != 0) { /* Check the type of link given */ - if (H5Lget_info(file, oname, &li, H5P_DEFAULT) < 0) { - hsize_t curr_pos = 0; /* total data element position */ - h5tools_str_t buffer; /* string into which to render */ - h5tools_context_t ctx; /* print context */ - h5tool_format_t *info = &ls_dataformat; + if (H5Lget_info2(file_id, oname, &li, H5P_DEFAULT) < 0) { + hsize_t curr_pos = 0; /* total data element position */ + h5tools_str_t buffer; /* string into which to render */ + h5tools_context_t ctx; /* print context */ + h5tool_format_t * info = &ls_dataformat; HDmemset(&ctx, 0, sizeof(ctx)); HDmemset(&buffer, 0, sizeof(h5tools_str_t)); h5tools_str_reset(&buffer); print_obj_name(&buffer, &iter, oname, "**NOT FOUND**"); - h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, + (hsize_t)0, (hsize_t)0); leave(EXIT_FAILURE); } /* end if */ - } /* end if */ + } /* end if */ else li.type = H5L_TYPE_HARD; /* Open the object and display it's information */ if (li.type == H5L_TYPE_HARD) { - if (visit_obj(file, oname, &iter) < 0) + if (visit_obj(file_id, oname, &iter) < 0) { leave(EXIT_FAILURE); + } } /* end if(li.type == H5L_TYPE_HARD) */ else { /* Specified name is not for object -- list that link */ - /* Use file ID for root group ID */ - iter.gid = file; + /* Use file_id ID for root group ID */ + iter.gid = file_id; list_lnk(oname, &li, &iter); } - H5Fclose(file); + H5Fclose(file_id); HDfree(fname); if (x) HDfree(oname); @@ -3022,4 +3138,3 @@ main(int argc, const char *argv[]) else leave(EXIT_SUCCESS); } /* end main() */ - diff --git a/tools/src/h5perf/CMakeLists.txt b/tools/src/h5perf/CMakeLists.txt new file mode 100644 index 0000000..36b0b2f --- /dev/null +++ b/tools/src/h5perf/CMakeLists.txt @@ -0,0 +1,103 @@ +cmake_minimum_required (VERSION 3.12) +project (HDF5_TOOLS_SRC_H5PERF C) + +# -------------------------------------------------------------------- +# Add the executables +# -------------------------------------------------------------------- +#-- Adding test for h5perf_serial +set (h5perf_serial_SOURCES + ${HDF5_TOOLS_SRC_H5PERF_SOURCE_DIR}/sio_perf.c + ${HDF5_TOOLS_SRC_H5PERF_SOURCE_DIR}/sio_engine.c +) +add_executable (h5perf_serial ${h5perf_serial_SOURCES}) +target_include_directories (h5perf_serial PRIVATE "${HDF5_TEST_SRC_DIR};${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") +if (NOT ONLY_SHARED_LIBS) + TARGET_C_PROPERTIES (h5perf_serial STATIC) + target_link_libraries (h5perf_serial PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) +else () + TARGET_C_PROPERTIES (h5perf_serial SHARED) + target_link_libraries (h5perf_serial PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET}) +endif () +set_target_properties (h5perf_serial PROPERTIES FOLDER perform) +set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5perf_serial") + +set (H5_DEP_EXECUTABLES h5perf_serial) + +#----------------------------------------------------------------------------- +# Add Target to clang-format +#----------------------------------------------------------------------------- +if (HDF5_ENABLE_FORMATTERS) + clang_format (HDF5_TOOLS_SRC_H5PERF_h5perf_serial_FORMAT h5perf_serial) +endif () + +if (H5_HAVE_PARALLEL) + if (UNIX) + #-- Adding test for perf - only on unix systems + set (perf_SOURCES + ${HDF5_TOOLS_SRC_H5PERF_SOURCE_DIR}/perf.c + ) + add_executable (perf ${perf_SOURCES}) + target_include_directories (perf PRIVATE "${HDF5_TEST_SRC_DIR};${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + if (NOT ONLY_SHARED_LIBS) + TARGET_C_PROPERTIES (perf STATIC) + target_link_libraries (perf PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET} "$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_LIBRARIES}>") + else () + TARGET_C_PROPERTIES (perf SHARED) + target_link_libraries (perf PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET} "$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_LIBRARIES}>") + endif () + set_target_properties (perf PROPERTIES FOLDER perform) + set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};perf") + + set (H5_DEP_EXECUTABLES perf) + + #----------------------------------------------------------------------------- + # Add Target to clang-format + #----------------------------------------------------------------------------- + if (HDF5_ENABLE_FORMATTERS) + clang_format (HDF5_TOOLS_SRC_H5PERF_perf_FORMAT perf) + endif () + endif () + + #-- Adding test for h5perf + set (h5perf_SOURCES + ${HDF5_TOOLS_SRC_H5PERF_SOURCE_DIR}/pio_perf.c + ${HDF5_TOOLS_SRC_H5PERF_SOURCE_DIR}/pio_engine.c + ) + add_executable (h5perf ${h5perf_SOURCES}) + target_include_directories (h5perf PRIVATE "${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + if (NOT ONLY_SHARED_LIBS) + TARGET_C_PROPERTIES (h5perf STATIC) + target_link_libraries (h5perf PRIVATE ${LINK_LIBS} ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET} "$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_LIBRARIES}>") + else () + TARGET_C_PROPERTIES (h5perf SHARED) + target_link_libraries (h5perf PRIVATE ${LINK_LIBS} ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET} "$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_LIBRARIES}>") + endif () + set_target_properties (h5perf PROPERTIES FOLDER perform) + set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5perf") + + set (H5_DEP_EXECUTABLES h5perf) + + #----------------------------------------------------------------------------- + # Add Target to clang-format + #----------------------------------------------------------------------------- + if (HDF5_ENABLE_FORMATTERS) + clang_format (HDF5_TOOLS_SRC_H5PERF_h5perf_FORMAT h5perf) + endif () +endif () + +#----------------------------------------------------------------------------- +# Rules for Installation of tools using make Install target +#----------------------------------------------------------------------------- +if (HDF5_EXPORTED_TARGETS) + foreach (exec ${H5_DEP_EXECUTABLES}) + INSTALL_PROGRAM_PDB (${exec} ${HDF5_INSTALL_BIN_DIR} toolsapplications) + endforeach () + + install ( + TARGETS + ${H5_DEP_EXECUTABLES} + EXPORT + ${HDF5_EXPORTED_TARGETS} + RUNTIME DESTINATION ${HDF5_INSTALL_BIN_DIR} COMPONENT toolsapplications + ) +endif () diff --git a/tools/src/h5perf/Makefile.am b/tools/src/h5perf/Makefile.am new file mode 100644 index 0000000..e8a9fdd --- /dev/null +++ b/tools/src/h5perf/Makefile.am @@ -0,0 +1,63 @@ +# +# Copyright by The HDF Group. +# Copyright by the Board of Trustees of the University of Illinois. +# All rights reserved. +# +# This file is part of HDF5. The full HDF5 copyright notice, including +# terms governing use, modification, and redistribution, is contained in +# the COPYING file, which can be found at the root of the source code +# distribution tree, or in https://www.hdfgroup.org/licenses. +# If you do not have access to either file, you may request a copy from +# help@hdfgroup.org. +## +## Makefile.am +## Run automake to generate a Makefile.in from this file. +## +# +# HDF5 Library Performance Makefile(.in) +# + +include $(top_srcdir)/config/commence.am + +AM_CPPFLAGS+=-I$(top_srcdir)/src -I$(top_srcdir)/test -I$(top_srcdir)/tools/lib + +# bin_PROGRAMS will be installed. +if BUILD_PARALLEL_CONDITIONAL + bin_PROGRAMS=h5perf_serial perf h5perf +else + bin_PROGRAMS=h5perf_serial +endif + +# Add h5perf and h5perf_serial specific linker flags here +h5perf_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS) +h5perf_serial_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS) + +# Some programs are not built or run by default, but can be built by hand or by +# specifying --enable-build-all at configure time. +# Also, some of these programs should only be built in parallel. +# Currently there is no such program. +if BUILD_PARALLEL_CONDITIONAL + PARA_BUILD_ALL= +endif +if BUILD_ALL_CONDITIONAL + BUILD_ALL_PROGS=$(PARA_BUILD_ALL) +endif + +# Define programs that will be run in 'make check' +# List them in the order they should be run. +# Parallel test programs. +if BUILD_PARALLEL_CONDITIONAL + TEST_PROG_PARA=h5perf perf +endif + +h5perf_SOURCES=pio_perf.c pio_engine.c +h5perf_serial_SOURCES=sio_perf.c sio_engine.c + +# All of the programs depend on the main hdf5 library, and some of them +# depend on test or tools library. +LDADD=$(LIBHDF5) +h5perf_LDADD=$(LIBH5TOOLS) $(LIBHDF5) +h5perf_serial_LDADD=$(LIBH5TOOLS) $(LIBHDF5) +perf_LDADD=$(LIBHDF5) + +include $(top_srcdir)/config/conclude.am diff --git a/tools/src/h5perf/perf.c b/tools/src/h5perf/perf.c new file mode 100644 index 0000000..84be7e8 --- /dev/null +++ b/tools/src/h5perf/perf.c @@ -0,0 +1,796 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * Copyright by The HDF Group. * + * Copyright by the Board of Trustees of the University of Illinois. * + * All rights reserved. * + * * + * This file is part of HDF5. The full HDF5 copyright notice, including * + * terms governing use, modification, and redistribution, is contained in * + * the COPYING file, which can be found at the root of the source code * + * distribution tree, or in https://www.hdfgroup.org/licenses. * + * If you do not have access to either file, you may request a copy from * + * help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + +/* + * Author: Albert Cheng of NCSA, May 1, 2001. + * This is derived from code given to me by Robert Ross. + * + * NOTE: This code assumes that all command line arguments make it out to all + * the processes that make up the parallel job, which isn't always the case. + * So if it doesn't work on some platform, that might be why. + */ + +#include "hdf5.h" +#include "H5private.h" + +#ifdef H5_HAVE_PARALLEL + +#include <errno.h> +#include <fcntl.h> +#include <stdio.h> +#include <stdlib.h> +#include <string.h> +#include <time.h> + +#ifdef H5_HAVE_SYS_STAT_H +#include <sys/stat.h> +#endif + +#ifdef H5_HAVE_SYS_TIME_H +#include <sys/time.h> +#endif + +#ifdef H5_HAVE_SYS_TYPES_H +#include <sys/types.h> +#endif + +#ifdef H5_HAVE_UNISTD_H +#include <unistd.h> +#endif + +#include <mpi.h> +#ifndef MPI_FILE_NULL /*MPIO may be defined in mpi.h already */ +#include <mpio.h> +#endif + +/* Macro definitions */ +/* Verify: + * if val is false (0), print mesg and if fatal is true (non-zero), die. + */ +#define H5FATAL 1 +#define VRFY(val, mesg, fatal) \ + do { \ + if (!val) { \ + printf("Proc %d: ", mynod); \ + printf("*** Assertion failed (%s) at line %4d in %s\n", mesg, (int)__LINE__, __FILE__); \ + if (fatal) { \ + fflush(stdout); \ + goto die_jar_jar_die; \ + } \ + } \ + } while (0) +#define RANK 1 +#define MAX_PATH 1024 + +hsize_t dims[RANK]; /* dataset dim sizes */ +hsize_t block[RANK], stride[RANK], count[RANK]; +hsize_t start[RANK]; +hid_t fid; /* HDF5 file ID */ +hid_t acc_tpl; /* File access templates */ +hid_t sid; /* Dataspace ID */ +hid_t file_dataspace; /* File dataspace ID */ +hid_t mem_dataspace; /* memory dataspace ID */ +hid_t dataset; /* Dataset ID */ +hsize_t opt_alignment = 1; +hsize_t opt_threshold = 1; +int opt_split_vfd = 0; +char * meta_ext, *raw_ext; /* holds the meta and raw file extension if */ + /* opt_split_vfd is set */ + +/* DEFAULT VALUES FOR OPTIONS */ +int64_t opt_block = 1048576 * 16; +int opt_iter = 1; +int opt_stripe = -1; +int opt_correct = 0; +int amode = O_RDWR | O_CREAT; +char opt_file[256] = "perftest.out"; +char opt_pvfstab[256] = "notset"; +int opt_pvfstab_set = 0; + +const char *FILENAME[] = {opt_file, NULL}; + +/* function prototypes */ +static int parse_args(int argc, char **argv); + +#ifndef H5_HAVE_UNISTD_H +/* globals needed for getopt */ +extern char *optarg; +#endif + +#ifndef HDF5_PARAPREFIX +#define HDF5_PARAPREFIX "" +#endif +char * paraprefix = NULL; /* for command line option para-prefix */ +MPI_Info h5_io_info_g = MPI_INFO_NULL; /* MPI INFO object for IO */ + +static char *h5_fixname_real(const char *base_name, hid_t fapl, const char *_suffix, char *fullname, + size_t size, hbool_t nest_printf, hbool_t subst_for_superblock); + +int +main(int argc, char **argv) +{ + char * buf = NULL, *tmp = NULL, *buf2 = NULL, *tmp2 = NULL, *check = NULL; + int i, j, mynod = 0, nprocs = 1, my_correct = 1, correct, myerrno; + double stim, etim; + double write_tim = 0; + double read_tim = 0; + double read_bw, write_bw; + double max_read_tim, max_write_tim; + double min_read_tim, min_write_tim; + double ave_read_tim, ave_write_tim; + int64_t iter_jump = 0; + char filename[MAX_PATH]; + herr_t ret; /* Generic return value */ + + /* startup MPI and determine the rank of this process */ + MPI_Init(&argc, &argv); + MPI_Comm_size(MPI_COMM_WORLD, &nprocs); + MPI_Comm_rank(MPI_COMM_WORLD, &mynod); + + /* parse the command line arguments */ + parse_args(argc, argv); + + if (mynod == 0) + printf("# Using hdf5-io calls.\n"); + +#ifdef H5_HAVE_UNISTD_H + /* Kind of a weird hack- if the location of the pvfstab file was + * specified on the command line, then spit out this location into + * the appropriate environment variable. + */ + if (opt_pvfstab_set) { + if ((setenv("PVFSTAB_FILE", opt_pvfstab, 1)) < 0) { + perror("setenv"); + goto die_jar_jar_die; + } + } +#endif + + /* this is how much of the file data is covered on each iteration of + * the test. used to help determine the seek offset on each + * iteration */ + iter_jump = nprocs * opt_block; + + /* setup a buffer of data to write */ + if (!(tmp = (char *)malloc((size_t)opt_block + 256))) { + perror("malloc"); + goto die_jar_jar_die; + } + buf = tmp + 128 - (((long)tmp) % 128); /* align buffer */ + + if (opt_correct) { + /* do the same buffer setup for verifiable data */ + if (!(tmp2 = (char *)malloc((size_t)opt_block + 256))) { + perror("malloc2"); + goto die_jar_jar_die; + } + buf2 = tmp + 128 - (((long)tmp) % 128); + } + + /* setup file access template with parallel IO access. */ + if (opt_split_vfd) { + hid_t mpio_pl; + + mpio_pl = H5Pcreate(H5P_FILE_ACCESS); + VRFY((acc_tpl >= 0), "", H5FATAL); + ret = H5Pset_fapl_mpio(mpio_pl, MPI_COMM_WORLD, MPI_INFO_NULL); + VRFY((ret >= 0), "", H5FATAL); + + /* set optional allocation alignment */ + if (opt_alignment * opt_threshold != 1) { + ret = H5Pset_alignment(acc_tpl, opt_threshold, opt_alignment); + VRFY((ret >= 0), "H5Pset_alignment succeeded", !H5FATAL); + } + + /* setup file access template */ + acc_tpl = H5Pcreate(H5P_FILE_ACCESS); + VRFY((acc_tpl >= 0), "", H5FATAL); + ret = H5Pset_fapl_split(acc_tpl, meta_ext, mpio_pl, raw_ext, mpio_pl); + VRFY((ret >= 0), "H5Pset_fapl_split succeeded", H5FATAL); + ret = H5Pclose(mpio_pl); + VRFY((ret >= 0), "H5Pclose mpio_pl succeeded", H5FATAL); + } + else { + /* setup file access template */ + acc_tpl = H5Pcreate(H5P_FILE_ACCESS); + VRFY((acc_tpl >= 0), "", H5FATAL); + ret = H5Pset_fapl_mpio(acc_tpl, MPI_COMM_WORLD, MPI_INFO_NULL); + VRFY((ret >= 0), "", H5FATAL); + + /* set optional allocation alignment */ + if (opt_alignment * opt_threshold != 1) { + ret = H5Pset_alignment(acc_tpl, opt_threshold, opt_alignment); + VRFY((ret >= 0), "H5Pset_alignment succeeded", !H5FATAL); + } + } + + h5_fixname_real(FILENAME[0], acc_tpl, NULL, filename, sizeof filename, FALSE, FALSE); + + /* create the parallel file */ + fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl); + VRFY((fid >= 0), "H5Fcreate succeeded", H5FATAL); + + /* define a contiquous dataset of opt_iter*nprocs*opt_block chars */ + dims[0] = (hsize_t)opt_iter * (hsize_t)nprocs * (hsize_t)opt_block; + sid = H5Screate_simple(RANK, dims, NULL); + VRFY((sid >= 0), "H5Screate_simple succeeded", H5FATAL); + dataset = H5Dcreate2(fid, "Dataset1", H5T_NATIVE_CHAR, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + VRFY((dataset >= 0), "H5Dcreate2 succeeded", H5FATAL); + + /* create the memory dataspace and the file dataspace */ + dims[0] = (hsize_t)opt_block; + mem_dataspace = H5Screate_simple(RANK, dims, NULL); + VRFY((mem_dataspace >= 0), "", H5FATAL); + file_dataspace = H5Dget_space(dataset); + VRFY((file_dataspace >= 0), "H5Dget_space succeeded", H5FATAL); + + /* now each process writes a block of opt_block chars in round robbin + * fashion until the whole dataset is covered. + */ + for (j = 0; j < opt_iter; j++) { + /* setup a file dataspace selection */ + start[0] = (hsize_t)((j * iter_jump) + (mynod * opt_block)); + stride[0] = block[0] = (hsize_t)opt_block; + count[0] = 1; + ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); + VRFY((ret >= 0), "H5Sset_hyperslab succeeded", H5FATAL); + + if (opt_correct) /* fill in buffer for iteration */ { + for (i = mynod + j, check = buf; i < opt_block; i++, check++) + *check = (char)i; + } + + /* discover the starting time of the operation */ + MPI_Barrier(MPI_COMM_WORLD); + stim = MPI_Wtime(); + + /* write data */ + ret = H5Dwrite(dataset, H5T_NATIVE_CHAR, mem_dataspace, file_dataspace, H5P_DEFAULT, buf); + VRFY((ret >= 0), "H5Dwrite dataset1 succeeded", !H5FATAL); + + /* discover the ending time of the operation */ + etim = MPI_Wtime(); + + write_tim += (etim - stim); + + /* we are done with this "write" iteration */ + } + + /* close dataset and file */ + ret = H5Dclose(dataset); + VRFY((ret >= 0), "H5Dclose succeeded", H5FATAL); + ret = H5Fclose(fid); + VRFY((ret >= 0), "H5Fclose succeeded", H5FATAL); + + /* wait for everyone to synchronize at this point */ + MPI_Barrier(MPI_COMM_WORLD); + + /* reopen the file for reading */ + fid = H5Fopen(filename, H5F_ACC_RDONLY, acc_tpl); + VRFY((fid >= 0), "", H5FATAL); + + /* open the dataset */ + dataset = H5Dopen2(fid, "Dataset1", H5P_DEFAULT); + VRFY((dataset >= 0), "H5Dopen succeeded", H5FATAL); + + /* we can re-use the same mem_dataspace and file_dataspace + * the H5Dwrite used since the dimension size is the same. + */ + + /* we are going to repeat the read the same pattern the write used */ + for (j = 0; j < opt_iter; j++) { + /* setup a file dataspace selection */ + start[0] = (hsize_t)((j * iter_jump) + (mynod * opt_block)); + stride[0] = block[0] = (hsize_t)opt_block; + count[0] = 1; + ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); + VRFY((ret >= 0), "H5Sset_hyperslab succeeded", H5FATAL); + /* seek to the appropriate spot give the current iteration and + * rank within the MPI processes */ + + /* discover the start time */ + MPI_Barrier(MPI_COMM_WORLD); + stim = MPI_Wtime(); + + /* read in the file data */ + if (!opt_correct) { + ret = H5Dread(dataset, H5T_NATIVE_CHAR, mem_dataspace, file_dataspace, H5P_DEFAULT, buf); + } + else { + ret = H5Dread(dataset, H5T_NATIVE_CHAR, mem_dataspace, file_dataspace, H5P_DEFAULT, buf2); + } + myerrno = errno; + + /* discover the end time */ + etim = MPI_Wtime(); + read_tim += (etim - stim); + VRFY((ret >= 0), "H5Dwrite dataset1 succeeded", !H5FATAL); + + if (ret < 0) + HDfprintf(stderr, "node %d, read error, loc = %" PRId64 ": %s\n", mynod, mynod * opt_block, + strerror(myerrno)); + + /* if the user wanted to check correctness, compare the write + * buffer to the read buffer */ + if (opt_correct && memcmp(buf, buf2, (size_t)opt_block)) { + HDfprintf(stderr, "node %d, correctness test failed\n", mynod); + my_correct = 0; + MPI_Allreduce(&my_correct, &correct, 1, MPI_INT, MPI_MIN, MPI_COMM_WORLD); + } + + /* we are done with this read iteration */ + } + + /* close dataset and file */ + ret = H5Dclose(dataset); + VRFY((ret >= 0), "H5Dclose succeeded", H5FATAL); + ret = H5Fclose(fid); + VRFY((ret >= 0), "H5Fclose succeeded", H5FATAL); + ret = H5Pclose(acc_tpl); + VRFY((ret >= 0), "H5Pclose succeeded", H5FATAL); + + /* compute the read and write times */ + MPI_Allreduce(&read_tim, &max_read_tim, 1, MPI_DOUBLE, MPI_MAX, MPI_COMM_WORLD); + MPI_Allreduce(&read_tim, &min_read_tim, 1, MPI_DOUBLE, MPI_MIN, MPI_COMM_WORLD); + MPI_Allreduce(&read_tim, &ave_read_tim, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); + + /* calculate the average from the sum */ + ave_read_tim = ave_read_tim / nprocs; + + MPI_Allreduce(&write_tim, &max_write_tim, 1, MPI_DOUBLE, MPI_MAX, MPI_COMM_WORLD); + MPI_Allreduce(&write_tim, &min_write_tim, 1, MPI_DOUBLE, MPI_MIN, MPI_COMM_WORLD); + MPI_Allreduce(&write_tim, &ave_write_tim, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); + + /* calculate the average from the sum */ + ave_write_tim = ave_write_tim / nprocs; + + /* print out the results on one node */ + if (mynod == 0) { + read_bw = (double)((int64_t)(opt_block * nprocs * opt_iter)) / (max_read_tim * 1000000.0); + write_bw = (double)((int64_t)(opt_block * nprocs * opt_iter)) / (max_write_tim * 1000000.0); + + printf("nr_procs = %d, nr_iter = %d, blk_sz = %ld\n", nprocs, opt_iter, (long)opt_block); + + printf("# total_size = %ld\n", (long)(opt_block * nprocs * opt_iter)); + + printf("# Write: min_time = %f, max_time = %f, mean_time = %f\n", min_write_tim, max_write_tim, + ave_write_tim); + printf("# Read: min_time = %f, max_time = %f, mean_time = %f\n", min_read_tim, max_read_tim, + ave_read_tim); + + printf("Write bandwidth = %f Mbytes/sec\n", write_bw); + printf("Read bandwidth = %f Mbytes/sec\n", read_bw); + + if (opt_correct) { + printf("Correctness test %s.\n", correct ? "passed" : "failed"); + } + } + +die_jar_jar_die: + +#ifdef H5_HAVE_UNISTD + /* Clear the environment variable if it was set earlier */ + if (opt_pvfstab_set) { + unsetenv("PVFSTAB_FILE"); + } +#endif + + free(tmp); + if (opt_correct) + free(tmp2); + + MPI_Finalize(); + + return (0); +} + +static int +parse_args(int argc, char **argv) +{ + int c; + + while ((c = getopt(argc, argv, "s:b:i:f:p:a:2:c")) != EOF) { + switch (c) { + case 's': /* stripe */ + opt_stripe = atoi(optarg); + break; + case 'b': /* block size */ + opt_block = atoi(optarg); + break; + case 'i': /* iterations */ + opt_iter = atoi(optarg); + break; + case 'f': /* filename */ + strncpy(opt_file, optarg, 255); + FILENAME[0] = opt_file; + break; + case 'p': /* pvfstab file */ + strncpy(opt_pvfstab, optarg, 255); + opt_pvfstab_set = 1; + break; + case 'a': /* aligned allocation. + * syntax: -a<alignment>/<threshold> + * e.g., -a4096/512 allocate at 4096 bytes + * boundary if request size >= 512. + */ + { + char *p; + + opt_alignment = (hsize_t)HDatoi(optarg); + if (NULL != (p = (char *)HDstrchr(optarg, '/'))) + opt_threshold = (hsize_t)HDatoi(p + 1); + } + HDfprintf(stdout, "alignment/threshold=%" PRIuHSIZE "/%" PRIuHSIZE "\n", opt_alignment, + opt_threshold); + break; + case '2': /* use 2-files, i.e., split file driver */ + opt_split_vfd = 1; + /* get meta and raw file extension. */ + /* syntax is <raw_ext>,<meta_ext> */ + meta_ext = raw_ext = optarg; + while (*raw_ext != '\0') { + if (*raw_ext == ',') { + *raw_ext = '\0'; + raw_ext++; + break; + } + raw_ext++; + } + printf("split-file-vfd used: %s,%s\n", meta_ext, raw_ext); + break; + case 'c': /* correctness */ + opt_correct = 1; + break; + case '?': /* unknown */ + default: + break; + } + } + + return (0); +} +/*------------------------------------------------------------------------- + * Function: getenv_all + * + * Purpose: Used to get the environment that the root MPI task has. + * name specifies which environment variable to look for + * val is the string to which the value of that environment + * variable will be copied. + * + * NOTE: The pointer returned by this function is only + * valid until the next call to getenv_all and the data + * stored there must be copied somewhere else before any + * further calls to getenv_all take place. + * + * Return: pointer to a string containing the value of the environment variable + * NULL if the varialbe doesn't exist in task 'root's environment. + * + * Programmer: Leon Arber + * 4/4/05 + * + * Modifications: + * Use original getenv if MPI is not initialized. This happens + * one uses the PHDF5 library to build a serial nature code. + * Albert 2006/04/07 + * + *------------------------------------------------------------------------- + */ +char * +getenv_all(MPI_Comm comm, int root, const char *name) +{ + int mpi_size, mpi_rank, mpi_initialized, mpi_finalized; + int len; + static char *env = NULL; + + HDassert(name); + + MPI_Initialized(&mpi_initialized); + MPI_Finalized(&mpi_finalized); + + if (mpi_initialized && !mpi_finalized) { + MPI_Comm_rank(comm, &mpi_rank); + MPI_Comm_size(comm, &mpi_size); + HDassert(root < mpi_size); + + /* The root task does the getenv call + * and sends the result to the other tasks */ + if (mpi_rank == root) { + env = HDgetenv(name); + if (env) { + len = (int)HDstrlen(env); + MPI_Bcast(&len, 1, MPI_INT, root, comm); + MPI_Bcast(env, len, MPI_CHAR, root, comm); + } + else { + /* len -1 indicates that the variable was not in the environment */ + len = -1; + MPI_Bcast(&len, 1, MPI_INT, root, comm); + } + } + else { + MPI_Bcast(&len, 1, MPI_INT, root, comm); + if (len >= 0) { + if (env == NULL) + env = (char *)HDmalloc((size_t)len + 1); + else if (HDstrlen(env) < (size_t)len) + env = (char *)HDrealloc(env, (size_t)len + 1); + + MPI_Bcast(env, len, MPI_CHAR, root, comm); + env[len] = '\0'; + } + else { + if (env) + HDfree(env); + env = NULL; + } + } +#ifndef NDEBUG + MPI_Barrier(comm); +#endif + } + else { + /* use original getenv */ + if (env) + HDfree(env); + env = HDgetenv(name); + } /* end if */ + + return env; +} + +/*------------------------------------------------------------------------- + * Function: h5_fixname_real + * + * Purpose: Create a file name from a file base name like `test' and + * return it through the FULLNAME (at most SIZE characters + * counting the null terminator). The full name is created by + * prepending the contents of HDF5_PREFIX (separated from the + * base name by a slash) and appending a file extension based on + * the driver supplied, resulting in something like + * `ufs:/u/matzke/test.h5'. + * + * Return: Success: The FULLNAME pointer. + * + * Failure: NULL if BASENAME or FULLNAME is the null + * pointer or if FULLNAME isn't large enough for + * the result. + * + * Programmer: Robb Matzke + * Thursday, November 19, 1998 + * + *------------------------------------------------------------------------- + */ +static char * +h5_fixname_real(const char *base_name, hid_t fapl, const char *_suffix, char *fullname, size_t size, + hbool_t nest_printf, hbool_t subst_for_superblock) +{ + const char *prefix = NULL; + const char *env = NULL; /* HDF5_DRIVER environment variable */ + char * ptr, last = '\0'; + const char *suffix = _suffix; + size_t i, j; + hid_t driver = -1; + int isppdriver = 0; /* if the driver is MPI parallel */ + + if (!base_name || !fullname || size < 1) + return NULL; + + HDmemset(fullname, 0, size); + + /* figure out the suffix */ + if (H5P_DEFAULT != fapl) { + if ((driver = H5Pget_driver(fapl)) < 0) + return NULL; + + if (suffix) { + if (H5FD_FAMILY == driver) { + if (subst_for_superblock) + suffix = "00000.h5"; + else + suffix = nest_printf ? "%%05d.h5" : "%05d.h5"; + } + else if (H5FD_MULTI == driver) { + + /* Get the environment variable, if it exists, in case + * we are using the split driver since both of those + * use the multi VFD under the hood. + */ + env = HDgetenv(HDF5_DRIVER); +#ifdef HDF5_DRIVER + /* Use the environment variable, then the compile-time constant */ + if (!env) + env = HDF5_DRIVER; +#endif + if (env && !HDstrcmp(env, "split")) { + /* split VFD */ + if (subst_for_superblock) + suffix = "-m.h5"; + else + suffix = NULL; + } + else { + /* multi VFD */ + if (subst_for_superblock) + suffix = "-s.h5"; + else + suffix = NULL; + } + } + } + } + + /* Must first check fapl is not H5P_DEFAULT (-1) because H5FD_XXX + * could be of value -1 if it is not defined. + */ + isppdriver = H5P_DEFAULT != fapl && (H5FD_MPIO == driver); + + /* Check what prefix to use for test files. Process HDF5_PARAPREFIX and + * HDF5_PREFIX. + * Use different ones depending on parallel or serial driver used. + * (The #ifdef is needed to prevent compile failure in case MPI is not + * configured.) + */ + if (isppdriver) { + /* + * For parallel: + * First use command line option, then the environment + * variable, then try the constant + */ + static int explained = 0; + + prefix = (paraprefix ? paraprefix : getenv_all(MPI_COMM_WORLD, 0, "HDF5_PARAPREFIX")); + + if (!prefix && !explained) { + /* print hint by process 0 once. */ + int mpi_rank; + + MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); + + if (mpi_rank == 0) + HDprintf("*** Hint ***\n" + "You can use environment variable HDF5_PARAPREFIX to " + "run parallel test files in a\n" + "different directory or to add file type prefix. e.g.,\n" + " HDF5_PARAPREFIX=pfs:/PFS/user/me\n" + " export HDF5_PARAPREFIX\n" + "*** End of Hint ***\n"); + + explained = TRUE; +#ifdef HDF5_PARAPREFIX + prefix = HDF5_PARAPREFIX; +#endif /* HDF5_PARAPREFIX */ + } + } + else { + /* + * For serial: + * First use the environment variable, then try the constant + */ + prefix = HDgetenv("HDF5_PREFIX"); + +#ifdef HDF5_PREFIX + if (!prefix) + prefix = HDF5_PREFIX; +#endif /* HDF5_PREFIX */ + } + + /* Prepend the prefix value to the base name */ + if (prefix && *prefix) { + if (isppdriver) { + /* This is a parallel system */ + char *subdir; + + if (!HDstrcmp(prefix, HDF5_PARAPREFIX)) { + /* + * If the prefix specifies the HDF5_PARAPREFIX directory, then + * default to using the "/tmp/$USER" or "/tmp/$LOGIN" + * directory instead. + */ + char *user, *login; + + user = HDgetenv("USER"); + login = HDgetenv("LOGIN"); + subdir = (user ? user : login); + + if (subdir) { + for (i = 0; i < size && prefix[i]; i++) + fullname[i] = prefix[i]; + + fullname[i++] = '/'; + + for (j = 0; i < size && subdir[j]; ++i, ++j) + fullname[i] = subdir[j]; + } + } + + if (!fullname[0]) { + /* We didn't append the prefix yet */ + HDstrncpy(fullname, prefix, size); + fullname[size - 1] = '\0'; + } + + if (HDstrlen(fullname) + HDstrlen(base_name) + 1 < size) { + /* + * Append the base_name with a slash first. Multiple + * slashes are handled below. + */ + h5_stat_t buf; + + if (HDstat(fullname, &buf) < 0) + /* The directory doesn't exist just yet */ + if (HDmkdir(fullname, (mode_t)0755) < 0 && errno != EEXIST) + /* + * We couldn't make the "/tmp/${USER,LOGIN}" + * subdirectory. Default to PREFIX's original + * prefix value. + */ + HDstrcpy(fullname, prefix); + + HDstrcat(fullname, "/"); + HDstrcat(fullname, base_name); + } + else { + /* Buffer is too small */ + return NULL; + } + } + else { + if (HDsnprintf(fullname, size, "%s/%s", prefix, base_name) == (int)size) + /* Buffer is too small */ + return NULL; + } + } + else if (HDstrlen(base_name) >= size) { + /* Buffer is too small */ + return NULL; + } + else { + HDstrcpy(fullname, base_name); + } + + /* Append a suffix */ + if (suffix) { + if (HDstrlen(fullname) + HDstrlen(suffix) >= size) + return NULL; + + HDstrcat(fullname, suffix); + } + + /* Remove any double slashes in the filename */ + for (ptr = fullname, i = j = 0; ptr && i < size; i++, ptr++) { + if (*ptr != '/' || last != '/') + fullname[j++] = *ptr; + + last = *ptr; + } + + return fullname; +} + +/* + * Local variables: + * c-indent-level: 3 + * c-basic-offset: 3 + * tab-width: 3 + * End: + */ + +#else /* H5_HAVE_PARALLEL */ +/* dummy program since H5_HAVE_PARALLEL is not configured in */ +int +main(int H5_ATTR_UNUSED argc, char H5_ATTR_UNUSED **argv) +{ + printf("No parallel performance because parallel is not configured in\n"); + return (0); +} +#endif /* H5_HAVE_PARALLEL */ diff --git a/tools/src/h5perf/pio_engine.c b/tools/src/h5perf/pio_engine.c new file mode 100644 index 0000000..1baaca2 --- /dev/null +++ b/tools/src/h5perf/pio_engine.c @@ -0,0 +1,2745 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * Copyright by The HDF Group. * + * All rights reserved. * + * * + * This file is part of HDF5. The full HDF5 copyright notice, including * + * terms governing use, modification, and redistribution, is contained in * + * the COPYING file, which can be found at the root of the source code * + * distribution tree, or in https://www.hdfgroup.org/licenses. * + * If you do not have access to either file, you may request a copy from * + * help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + +/* + * Author: Albert Cheng of NCSA, Oct 24, 2001. + */ + +#include "hdf5.h" + +#include <errno.h> +#include <fcntl.h> +#include <stdio.h> +#include <stdlib.h> + +#ifdef H5_HAVE_UNISTD_H +#include <sys/types.h> +#include <unistd.h> +#endif + +#ifdef H5_HAVE_SYS_STAT_H +#include <sys/stat.h> +#endif + +#ifdef H5_HAVE_PARALLEL + +#include <mpi.h> + +#ifndef MPI_FILE_NULL /*MPIO may be defined in mpi.h already */ +#include <mpio.h> +#endif /* !MPI_FILE_NULL */ + +#include "pio_perf.h" + +/* Macro definitions */ + +#if H5_VERS_MAJOR == 1 && H5_VERS_MINOR == 6 +#define H5DCREATE(fd, name, type, space, dcpl) H5Dcreate(fd, name, type, space, dcpl) +#define H5DOPEN(fd, name) H5Dopen(fd, name) +#else +#define H5DCREATE(fd, name, type, space, dcpl) \ + H5Dcreate2(fd, name, type, space, H5P_DEFAULT, dcpl, H5P_DEFAULT) +#define H5DOPEN(fd, name) H5Dopen2(fd, name, H5P_DEFAULT) +#endif + +/* sizes of various items. these sizes won't change during program execution */ +/* The following three must have the same type */ +#define ELMT_H5_TYPE H5T_NATIVE_UCHAR + +#define GOTOERROR(errcode) \ + { \ + ret_code = errcode; \ + goto done; \ + } +#define ERRMSG(mesg) \ + { \ + HDfprintf(stderr, "Proc %d: ", pio_mpi_rank_g); \ + HDfprintf(stderr, "*** Assertion failed (%s) at line %4d in %s\n", mesg, (int)__LINE__, __FILE__); \ + } + +/* verify: if val is false (0), print mesg. */ +#define VRFY(val, mesg) \ + do { \ + if (!val) { \ + ERRMSG(mesg); \ + GOTOERROR(FAIL); \ + } \ + } while (0) + +/* POSIX I/O macros */ +#ifdef H5_HAVE_WIN32_API +/* Can't link against the library, so this test will use the older, non-Unicode + * _open() call on Windows. + */ +#define HDopen(S, F, ...) _open(S, F | _O_BINARY, __VA_ARGS__) +#endif /* H5_HAVE_WIN32_API */ +#define POSIXCREATE(fn) HDopen(fn, O_CREAT | O_TRUNC | O_RDWR, 0600) +#define POSIXOPEN(fn, F) HDopen(fn, F, 0600) +#define POSIXCLOSE(F) HDclose(F) +#define POSIXSEEK(F, L) HDlseek(F, L, SEEK_SET) +#define POSIXWRITE(F, B, S) HDwrite(F, B, S) +#define POSIXREAD(F, B, S) HDread(F, B, S) + +enum { PIO_CREATE = 1, PIO_WRITE = 2, PIO_READ = 4 }; + +/* Global variables */ +static int clean_file_g = -1; /*whether to cleanup temporary test */ +/*files. -1 is not defined; */ +/*0 is no cleanup; 1 is do cleanup */ + +/* + * In a parallel machine, the filesystem suitable for compiling is + * unlikely a parallel file system that is suitable for parallel I/O. + * There is no standard pathname for the parallel file system. /tmp + * is about the best guess. + */ +#ifndef HDF5_PARAPREFIX +#define HDF5_PARAPREFIX "" +#endif /* !HDF5_PARAPREFIX */ + +#ifndef MIN +#define MIN(a, b) ((a) < (b) ? (a) : (b)) +#endif /* !MIN */ + +/* the different types of file descriptors we can expect */ +typedef union _file_descr { + int posixfd; /* POSIX file handle*/ + MPI_File mpifd; /* MPI file */ + hid_t h5fd; /* HDF5 file */ +} file_descr; + +/* local functions */ +static char * pio_create_filename(iotype iot, const char *base_name, char *fullname, size_t size); +static herr_t do_write(results *res, file_descr *fd, parameters *parms, long ndsets, off_t nelmts, + size_t buf_size, void *buffer); +static herr_t do_read(results *res, file_descr *fd, parameters *parms, long ndsets, off_t nelmts, + size_t buf_size, void *buffer /*out*/); +static herr_t do_fopen(parameters *param, char *fname, file_descr *fd /*out*/, int flags); +static herr_t do_fclose(iotype iot, file_descr *fd); +static void do_cleanupfile(iotype iot, char *fname); +static off_t sqrto(off_t); + +/* + * Function: do_pio + * Purpose: PIO Engine where Parallel IO are executed. + * Return: results + * Programmer: Albert Cheng, Bill Wendling 2001/12/12 + * Modifications: + * Added 2D testing (Christian Chilan, 10. August 2005) + */ +results +do_pio(parameters param) +{ + /* return codes */ + herr_t ret_code = 0; /*return code */ + results res; + + file_descr fd; + iotype iot; + + char fname[FILENAME_MAX]; + long nf; + long ndsets; + off_t nbytes; /*number of bytes per dataset */ + off_t snbytes; /*general dataset size */ + /*for 1D, it is the actual dataset size */ + /*for 2D, it is the size of a side of the dataset square */ + char * buffer = NULL; /*data buffer pointer */ + size_t buf_size; /*general buffer size in bytes */ + /*for 1D, it is the actual buffer size */ + /*for 2D, it is the length of the buffer rectangle */ + size_t blk_size; /*data block size in bytes */ + size_t bsize; /*actual buffer size */ + + /* HDF5 variables */ + herr_t hrc; /*HDF5 return code */ + + /* Sanity check parameters */ + + /* IO type */ + iot = param.io_type; + + switch (iot) { + case MPIO: + fd.mpifd = MPI_FILE_NULL; + res.timers = io_time_new(MPI_CLOCK); + break; + case POSIXIO: + fd.posixfd = -1; + res.timers = io_time_new(MPI_CLOCK); + break; + case PHDF5: + fd.h5fd = -1; + res.timers = io_time_new(MPI_CLOCK); + break; + default: + /* unknown request */ + HDfprintf(stderr, "Unknown IO type request (%d)\n", iot); + GOTOERROR(FAIL); + } + + ndsets = param.num_dsets; /* number of datasets per file */ + nbytes = param.num_bytes; /* number of bytes per dataset */ + buf_size = param.buf_size; + blk_size = param.blk_size; + + if (!param.dim2d) { + snbytes = nbytes; /* General dataset size */ + bsize = buf_size; /* Actual buffer size */ + } + else { + snbytes = sqrto(nbytes); /* General dataset size */ + bsize = buf_size * blk_size; /* Actual buffer size */ + } + + if (param.num_files < 0) { + HDfprintf(stderr, "number of files must be >= 0 (%ld)\n", param.num_files); + GOTOERROR(FAIL); + } + + if (ndsets < 0) { + HDfprintf(stderr, "number of datasets per file must be >= 0 (%ld)\n", ndsets); + GOTOERROR(FAIL); + } + + if (param.num_procs <= 0) { + HDfprintf(stderr, "maximum number of process to use must be > 0 (%d)\n", param.num_procs); + GOTOERROR(FAIL); + } + + /* Validate transfer buffer size & block size*/ + if (blk_size <= 0) { + HDfprintf(stderr, "Transfer block size (%zu) must be > 0\n", blk_size); + GOTOERROR(FAIL); + } + if (buf_size <= 0) { + HDfprintf(stderr, "Transfer buffer size (%zu) must be > 0\n", buf_size); + GOTOERROR(FAIL); + } + if ((buf_size % blk_size) != 0) { + HDfprintf(stderr, + "Transfer buffer size (%zu) must be a multiple of the " + "interleaved I/O block size (%zu)\n", + buf_size, blk_size); + GOTOERROR(FAIL); + } + if ((snbytes % pio_mpi_nprocs_g) != 0) { + HDfprintf(stderr, + "Dataset size (%" H5_PRINTF_LL_WIDTH "d) must be a multiple of the " + "number of processes (%d)\n", + (long long)snbytes, pio_mpi_nprocs_g); + GOTOERROR(FAIL); + } + + if (!param.dim2d) { + if (((size_t)(snbytes / pio_mpi_nprocs_g) % buf_size) != 0) { + HDfprintf(stderr, + "Dataset size/process (%" H5_PRINTF_LL_WIDTH "d) must be a multiple of the " + "transfer buffer size (%zu)\n", + (long long)(snbytes / pio_mpi_nprocs_g), buf_size); + GOTOERROR(FAIL); + } + } + else { + if (((size_t)snbytes % buf_size) != 0) { + HDfprintf(stderr, + "Dataset side size (%" H5_PRINTF_LL_WIDTH "d) must be a multiple of the " + "transfer buffer size (%zu)\n", + (long long)snbytes, buf_size); + GOTOERROR(FAIL); + } + } + + /* Allocate transfer buffer */ + if ((buffer = malloc(bsize)) == NULL) { + HDfprintf(stderr, "malloc for transfer buffer size (%zu) failed\n", bsize); + GOTOERROR(FAIL); + } + + if (pio_debug_level >= 4) { + int myrank; + + MPI_Comm_rank(pio_comm_g, &myrank); + + /* output all of the times for all iterations */ + if (myrank == 0) + HDfprintf(output, "Timer details:\n"); + } + + for (nf = 1; nf <= param.num_files; nf++) { + /* + * Write performance measurement + */ + /* Open file for write */ + char base_name[256]; + + HDsnprintf(base_name, sizeof(base_name), "#pio_tmp_%lu", nf); + pio_create_filename(iot, base_name, fname, sizeof(fname)); + if (pio_debug_level > 0) + HDfprintf(output, "rank %d: data filename=%s\n", pio_mpi_rank_g, fname); + + /* Need barrier to make sure everyone starts at the same time */ + MPI_Barrier(pio_comm_g); + + io_time_set(res.timers, HDF5_GROSS_WRITE_FIXED_DIMS, TSTART); + hrc = do_fopen(¶m, fname, &fd, PIO_CREATE | PIO_WRITE); + + VRFY((hrc == SUCCESS), "do_fopen failed"); + + io_time_set(res.timers, HDF5_FINE_WRITE_FIXED_DIMS, TSTART); + hrc = do_write(&res, &fd, ¶m, ndsets, nbytes, buf_size, buffer); + io_time_set(res.timers, HDF5_FINE_WRITE_FIXED_DIMS, TSTOP); + + VRFY((hrc == SUCCESS), "do_write failed"); + + /* Close file for write */ + hrc = do_fclose(iot, &fd); + + io_time_set(res.timers, HDF5_GROSS_WRITE_FIXED_DIMS, TSTOP); + VRFY((hrc == SUCCESS), "do_fclose failed"); + + if (!param.h5_write_only) { + /* + * Read performance measurement + */ + /* Need barrier to make sure everyone is done writing and has + * closed the file. Also to make sure everyone starts reading + * at the same time. + */ + MPI_Barrier(pio_comm_g); + + /* Open file for read */ + io_time_set(res.timers, HDF5_GROSS_READ_FIXED_DIMS, TSTART); + hrc = do_fopen(¶m, fname, &fd, PIO_READ); + + VRFY((hrc == SUCCESS), "do_fopen failed"); + + io_time_set(res.timers, HDF5_FINE_READ_FIXED_DIMS, TSTART); + hrc = do_read(&res, &fd, ¶m, ndsets, nbytes, buf_size, buffer); + io_time_set(res.timers, HDF5_FINE_READ_FIXED_DIMS, TSTOP); + VRFY((hrc == SUCCESS), "do_read failed"); + + /* Close file for read */ + hrc = do_fclose(iot, &fd); + + io_time_set(res.timers, HDF5_GROSS_READ_FIXED_DIMS, TSTOP); + VRFY((hrc == SUCCESS), "do_fclose failed"); + } + + /* Need barrier to make sure everyone is done with the file */ + /* before it may be removed by do_cleanupfile */ + MPI_Barrier(pio_comm_g); + do_cleanupfile(iot, fname); + } + +done: + /* clean up */ + /* release HDF5 objects */ + + /* close any opened files */ + /* no remove(fname) because that should have happened normally. */ + switch (iot) { + case POSIXIO: + if (fd.posixfd != -1) + hrc = do_fclose(iot, &fd); + break; + case MPIO: + if (fd.mpifd != MPI_FILE_NULL) + hrc = do_fclose(iot, &fd); + break; + case PHDF5: + if (fd.h5fd != -1) + hrc = do_fclose(iot, &fd); + break; + default: + break; + } + + /* release generic resources */ + if (buffer) + HDfree(buffer); + res.ret_code = ret_code; + return res; +} + +/* + * Function: pio_create_filename + * Purpose: Create a new filename to write to. Determine the correct + * suffix to append to the filename by the type of I/O we're + * doing. Also, place in the /tmp/{$USER,$LOGIN} directory if + * USER or LOGIN are specified in the environment. + * Return: Pointer to filename or NULL + * Programmer: Bill Wendling, 21. November 2001 + * Modifications: + */ +static char * +pio_create_filename(iotype iot, const char *base_name, char *fullname, size_t size) +{ + const char *prefix, *suffix = ""; + char * ptr, last = '\0'; + size_t i, j; + + if (!base_name || !fullname || size < 1) + return NULL; + + HDmemset(fullname, 0, size); + + switch (iot) { + case POSIXIO: + suffix = ".posix"; + break; + case MPIO: + suffix = ".mpio"; + break; + case PHDF5: + suffix = ".h5"; + break; + default: + break; + } + + /* First use the environment variable and then try the constant */ + prefix = HDgetenv("HDF5_PARAPREFIX"); + +#ifdef HDF5_PARAPREFIX + if (!prefix) + prefix = HDF5_PARAPREFIX; +#endif /* HDF5_PARAPREFIX */ + + /* Prepend the prefix value to the base name */ + if (prefix && *prefix) { + /* If the prefix specifies the HDF5_PARAPREFIX directory, then + * default to using the "/tmp/$USER" or "/tmp/$LOGIN" + * directory instead. */ + char *user, *login, *subdir; + + user = HDgetenv("USER"); + login = HDgetenv("LOGIN"); + subdir = (user ? user : login); + + if (subdir) { + for (i = 0; i < size - 1 && prefix[i]; i++) + fullname[i] = prefix[i]; + + fullname[i++] = '/'; + + for (j = 0; i < size && subdir[j]; i++, j++) + fullname[i] = subdir[j]; + } + else { + /* We didn't append the prefix yet */ + HDstrncpy(fullname, prefix, size); + fullname[size - 1] = '\0'; + } + + if ((HDstrlen(fullname) + HDstrlen(base_name) + 1) < size) { + /* Append the base_name with a slash first. Multiple slashes are + * handled below. */ + h5_stat_t buf; + + if (HDstat(fullname, &buf) < 0) + /* The directory doesn't exist just yet */ + if (HDmkdir(fullname, (mode_t)0755) < 0 && errno != EEXIST) { + /* We couldn't make the "/tmp/${USER,LOGIN}" subdirectory. + * Default to PREFIX's original prefix value. */ + HDstrcpy(fullname, prefix); + } + + HDstrcat(fullname, "/"); + HDstrcat(fullname, base_name); + } + else { + /* Buffer is too small */ + return NULL; + } + } + else if (HDstrlen(base_name) >= size) { + /* Buffer is too small */ + return NULL; + } + else { + HDstrcpy(fullname, base_name); + } + + /* Append a suffix */ + if (suffix) { + if (HDstrlen(fullname) + HDstrlen(suffix) >= size) + return NULL; + + HDstrcat(fullname, suffix); + } + + /* Remove any double slashes in the filename */ + for (ptr = fullname, i = j = 0; ptr && i < size; i++, ptr++) { + if (*ptr != '/' || last != '/') + fullname[j++] = *ptr; + + last = *ptr; + } + + return fullname; +} + +/* + * Function: do_write + * Purpose: Write the required amount of data to the file. + * Return: SUCCESS or FAIL + * Programmer: Albert Cheng, Bill Wendling, 2001/12/13 + * Modifications: + * Added 2D testing (Christian Chilan, 10. August 2005) + */ +static herr_t +do_write(results *res, file_descr *fd, parameters *parms, long ndsets, off_t nbytes, size_t buf_size, + void *buffer) +{ + int ret_code = SUCCESS; + int rc; /*routine return code */ + long ndset; + size_t blk_size; /* The block size to subdivide the xfer buffer into */ + off_t nbytes_xfer; /* Total number of bytes transferred so far */ + size_t nbytes_xfer_advance; /* Number of bytes transferred in a single I/O operation */ + size_t nbytes_toxfer; /* Number of bytes to transfer a particular time */ + char dname[64]; + off_t dset_offset = 0; /*dataset offset in a file */ + off_t bytes_begin[2]; /*first elmt this process transfer */ + off_t bytes_count; /*number of elmts this process transfer */ + off_t snbytes = 0; /*size of a side of the dataset square */ + unsigned char *buf_p; /* Current buffer pointer */ + + /* POSIX variables */ + off_t file_offset; /* File offset of the next transfer */ + off_t file_offset_advance; /* File offset advance after each I/O operation */ + off_t posix_file_offset; /* Base file offset of the next transfer */ + + /* MPI variables */ + MPI_Offset mpi_file_offset; /* Base file offset of the next transfer*/ + MPI_Offset mpi_offset; /* Offset in MPI file */ + MPI_Offset mpi_offset_advance; /* Offset advance after each I/O operation */ + MPI_Datatype mpi_file_type; /* MPI derived type for 1D file */ + MPI_Datatype mpi_blk_type; /* MPI derived type for 1D buffer */ + MPI_Datatype mpi_cont_type; /* MPI derived type for 2D contiguous file */ + MPI_Datatype mpi_partial_buffer_cont; /* MPI derived type for partial 2D contiguous buffer */ + MPI_Datatype mpi_inter_type; /* MPI derived type for 2D interleaved file */ + MPI_Datatype mpi_partial_buffer_inter; /* MPI derived type for partial 2D interleaved buffer */ + MPI_Datatype mpi_full_buffer; /* MPI derived type for 2D full buffer */ + MPI_Datatype mpi_full_chunk; /* MPI derived type for 2D full chunk */ + MPI_Datatype mpi_chunk_inter_type; /* MPI derived type for 2D chunk interleaved file */ + MPI_Datatype mpi_collective_type; /* Generic MPI derived type for 2D collective access */ + MPI_Status mpi_status; + int mrc; /* MPI return code */ + + /* HDF5 variables */ + herr_t hrc; /*HDF5 return code */ + hsize_t h5dims[2]; /*dataset dim sizes */ + hid_t h5dset_space_id = H5I_INVALID_HID; /*dataset space ID */ + hid_t h5mem_space_id = H5I_INVALID_HID; /*memory dataspace ID */ + hid_t h5ds_id = H5I_INVALID_HID; /*dataset handle */ + hsize_t h5block[2]; /*dataspace selection */ + hsize_t h5stride[2]; + hsize_t h5count[2]; + hsize_t h5start[2]; + hssize_t h5offset[2]; /* Selection offset within dataspace */ + hid_t h5dcpl = H5I_INVALID_HID; /* Dataset creation property list */ + hid_t h5dxpl = H5I_INVALID_HID; /* Dataset transfer property list */ + + /* Get the parameters from the parameter block */ + blk_size = parms->blk_size; + + /* There are two kinds of transfer patterns, contiguous and interleaved. + * Let 0,1,2,...,n be data accessed by process 0,1,2,...,n + * where n is rank of the last process. + * In contiguous pattern, data are accessed as + * 000...111...222...nnn... + * In interleaved pattern, data are accessed as + * 012...n012...n... + * These are all in the scope of one dataset. + */ + + /* 1D dataspace */ + if (!parms->dim2d) { + /* Contiguous Pattern: */ + if (!parms->interleaved) { + bytes_begin[0] = (off_t)(((double)nbytes * pio_mpi_rank_g) / pio_mpi_nprocs_g); + } /* end if */ + /* Interleaved Pattern: */ + else { + bytes_begin[0] = (off_t)(blk_size * (size_t)pio_mpi_rank_g); + } /* end else */ + + /* Prepare buffer for verifying data */ + if (parms->verify) + memset(buffer, pio_mpi_rank_g + 1, buf_size); + } /* end if */ + /* 2D dataspace */ + else { + /* nbytes is always the number of bytes per dataset (1D or 2D). If the + dataspace is 2D, snbytes is the size of a side of the dataset square. + */ + snbytes = sqrto(nbytes); + + /* Contiguous Pattern: */ + if (!parms->interleaved) { + bytes_begin[0] = (off_t)((double)snbytes * pio_mpi_rank_g / pio_mpi_nprocs_g); + bytes_begin[1] = 0; + } /* end if */ + /* Interleaved Pattern: */ + else { + bytes_begin[0] = 0; + + if (!parms->h5_use_chunks || parms->io_type == PHDF5) + bytes_begin[1] = (off_t)(blk_size * (size_t)pio_mpi_rank_g); + else + bytes_begin[1] = (off_t)(blk_size * blk_size * (size_t)pio_mpi_rank_g); + } /* end else */ + + /* Prepare buffer for verifying data */ + if (parms->verify) + HDmemset(buffer, pio_mpi_rank_g + 1, buf_size * blk_size); + } /* end else */ + + /* Calculate the total number of bytes (bytes_count) to be + * transferred by this process. It may be different for different + * transfer pattern due to rounding to integral values. + */ + /* + * Calculate the beginning bytes of this process and the next. + * bytes_count is the difference between these two beginnings. + * This way, it eliminates any rounding errors. + * (This is tricky, don't mess with the formula, rounding errors + * can easily get introduced) */ + bytes_count = (off_t)(((double)nbytes * (pio_mpi_rank_g + 1)) / pio_mpi_nprocs_g) - + (off_t)(((double)nbytes * pio_mpi_rank_g) / pio_mpi_nprocs_g); + + /* debug */ + if (pio_debug_level >= 4) { + HDprint_rank(output); + if (!parms->dim2d) { + HDfprintf(output, + "Debug(do_write): " + "buf_size=%zu, bytes_begin=%" H5_PRINTF_LL_WIDTH "d, bytes_count=%" H5_PRINTF_LL_WIDTH + "d\n", + buf_size, (long long)bytes_begin[0], (long long)bytes_count); + } + else { + HDfprintf(output, + "Debug(do_write): " + "linear buf_size=%zu, bytes_begin=(%" H5_PRINTF_LL_WIDTH "d,%" H5_PRINTF_LL_WIDTH + "d), bytes_count=%" H5_PRINTF_LL_WIDTH "d\n", + buf_size * blk_size, (long long)bytes_begin[0], (long long)bytes_begin[1], + (long long)bytes_count); + } + } + + /* I/O Access specific setup */ + switch (parms->io_type) { + case POSIXIO: + /* No extra setup */ + break; + + case MPIO: /* MPI-I/O setup */ + /* 1D dataspace */ + if (!parms->dim2d) { + /* Build block's derived type */ + mrc = MPI_Type_contiguous((int)blk_size, MPI_BYTE, &mpi_blk_type); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_CREATE"); + + /* Build file's derived type */ + mrc = MPI_Type_vector((int)(buf_size / blk_size), (int)1, (int)pio_mpi_nprocs_g, mpi_blk_type, + &mpi_file_type); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_CREATE"); + + /* Commit file type */ + mrc = MPI_Type_commit(&mpi_file_type); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_COMMIT"); + + /* Commit buffer type */ + mrc = MPI_Type_commit(&mpi_blk_type); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_COMMIT"); + } /* end if */ + /* 2D dataspace */ + else { + /* Build partial buffer derived type for contiguous access */ + + mrc = MPI_Type_contiguous((int)buf_size, MPI_BYTE, &mpi_partial_buffer_cont); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_CREATE"); + + /* Commit partial buffer derived type */ + mrc = MPI_Type_commit(&mpi_partial_buffer_cont); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_COMMIT"); + + /* Build contiguous file's derived type */ + mrc = MPI_Type_vector((int)blk_size, (int)1, (int)((size_t)snbytes / buf_size), + mpi_partial_buffer_cont, &mpi_cont_type); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_CREATE"); + + /* Commit contiguous file type */ + mrc = MPI_Type_commit(&mpi_cont_type); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_COMMIT"); + + /* Build partial buffer derived type for interleaved access */ + mrc = MPI_Type_contiguous((int)blk_size, MPI_BYTE, &mpi_partial_buffer_inter); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_CREATE"); + + /* Commit partial buffer derived type */ + mrc = MPI_Type_commit(&mpi_partial_buffer_inter); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_COMMIT"); + + /* Build interleaved file's derived type */ + mrc = MPI_Type_vector((int)buf_size, (int)1, (int)((size_t)snbytes / blk_size), + mpi_partial_buffer_inter, &mpi_inter_type); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_CREATE"); + + /* Commit interleaved file type */ + mrc = MPI_Type_commit(&mpi_inter_type); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_COMMIT"); + + /* Build full buffer derived type */ + mrc = MPI_Type_contiguous((int)(blk_size * buf_size), MPI_BYTE, &mpi_full_buffer); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_CREATE"); + + /* Commit full buffer derived type */ + mrc = MPI_Type_commit(&mpi_full_buffer); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_COMMIT"); + + /* Build full chunk derived type */ + mrc = MPI_Type_contiguous((int)(blk_size * blk_size), MPI_BYTE, &mpi_full_chunk); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_CREATE"); + + /* Commit full chunk derived type */ + mrc = MPI_Type_commit(&mpi_full_chunk); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_COMMIT"); + + /* Build chunk interleaved file's derived type */ + mrc = MPI_Type_vector((int)(buf_size / blk_size), (int)1, (int)((size_t)snbytes / blk_size), + mpi_full_chunk, &mpi_chunk_inter_type); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_CREATE"); + + /* Commit chunk interleaved file type */ + mrc = MPI_Type_commit(&mpi_chunk_inter_type); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_COMMIT"); + + } /* end else */ + break; + + case PHDF5: /* HDF5 setup */ + /* 1D dataspace */ + if (!parms->dim2d) { + if (nbytes > 0) { + /* define a contiguous dataset of nbytes native bytes */ + h5dims[0] = (hsize_t)nbytes; + h5dset_space_id = H5Screate_simple(1, h5dims, NULL); + VRFY((h5dset_space_id >= 0), "H5Screate_simple"); + + /* Set up the file dset space id to select the pattern to access */ + if (!parms->interleaved) { + /* Contiguous pattern */ + h5start[0] = (hsize_t)bytes_begin[0]; + h5stride[0] = h5block[0] = blk_size; + h5count[0] = buf_size / blk_size; + } /* end if */ + else { + /* Interleaved access pattern */ + /* Skip offset over blocks of other processes */ + h5start[0] = (hsize_t)bytes_begin[0]; + h5stride[0] = blk_size * (size_t)pio_mpi_nprocs_g; + h5block[0] = blk_size; + h5count[0] = buf_size / blk_size; + } /* end else */ + hrc = H5Sselect_hyperslab(h5dset_space_id, H5S_SELECT_SET, h5start, h5stride, h5count, + h5block); + VRFY((hrc >= 0), "H5Sselect_hyperslab"); + } /* end if */ + else { + h5dset_space_id = H5Screate(H5S_SCALAR); + VRFY((h5dset_space_id >= 0), "H5Screate"); + } /* end else */ + + /* Create the memory dataspace that corresponds to the xfer buffer */ + if (buf_size > 0) { + h5dims[0] = buf_size; + h5mem_space_id = H5Screate_simple(1, h5dims, NULL); + VRFY((h5mem_space_id >= 0), "H5Screate_simple"); + } /* end if */ + else { + h5mem_space_id = H5Screate(H5S_SCALAR); + VRFY((h5mem_space_id >= 0), "H5Screate"); + } /* end else */ + } /* end if */ + /* 2D dataspace */ + else { + if (nbytes > 0) { + /* define a contiguous dataset of nbytes native bytes */ + h5dims[0] = (hsize_t)snbytes; + h5dims[1] = (hsize_t)snbytes; + h5dset_space_id = H5Screate_simple(2, h5dims, NULL); + VRFY((h5dset_space_id >= 0), "H5Screate_simple"); + + /* Set up the file dset space id to select the pattern to access */ + if (!parms->interleaved) { + /* Contiguous pattern */ + h5start[0] = (hsize_t)bytes_begin[0]; + h5start[1] = (hsize_t)bytes_begin[1]; + h5stride[0] = 1; + h5stride[1] = h5block[0] = h5block[1] = blk_size; + h5count[0] = 1; + h5count[1] = buf_size / blk_size; + } /* end if */ + else { + /* Interleaved access pattern */ + /* Skip offset over blocks of other processes */ + h5start[0] = (hsize_t)bytes_begin[0]; + h5start[1] = (hsize_t)bytes_begin[1]; + h5stride[0] = blk_size; + h5stride[1] = blk_size * (size_t)pio_mpi_nprocs_g; + h5block[0] = h5block[1] = blk_size; + h5count[0] = buf_size / blk_size; + h5count[1] = 1; + } /* end else */ + hrc = H5Sselect_hyperslab(h5dset_space_id, H5S_SELECT_SET, h5start, h5stride, h5count, + h5block); + VRFY((hrc >= 0), "H5Sselect_hyperslab"); + } /* end if */ + else { + h5dset_space_id = H5Screate(H5S_SCALAR); + VRFY((h5dset_space_id >= 0), "H5Screate"); + } /* end else */ + + /* Create the memory dataspace that corresponds to the xfer buffer */ + if (buf_size > 0) { + if (!parms->interleaved) { + h5dims[0] = blk_size; + h5dims[1] = buf_size; + } + else { + h5dims[0] = buf_size; + h5dims[1] = blk_size; + } + h5mem_space_id = H5Screate_simple(2, h5dims, NULL); + VRFY((h5mem_space_id >= 0), "H5Screate_simple"); + } /* end if */ + else { + h5mem_space_id = H5Screate(H5S_SCALAR); + VRFY((h5mem_space_id >= 0), "H5Screate"); + } /* end else */ + } /* end else */ + + /* Create the dataset transfer property list */ + h5dxpl = H5Pcreate(H5P_DATASET_XFER); + if (h5dxpl < 0) { + HDfprintf(stderr, "HDF5 Property List Create failed\n"); + GOTOERROR(FAIL); + } + + /* Change to collective I/O, if asked */ + if (parms->collective) { + hrc = H5Pset_dxpl_mpio(h5dxpl, H5FD_MPIO_COLLECTIVE); + if (hrc < 0) { + HDfprintf(stderr, "HDF5 Property List Set failed\n"); + GOTOERROR(FAIL); + } /* end if */ + } /* end if */ + break; + + default: + break; + } /* end switch */ + + for (ndset = 1; ndset <= ndsets; ++ndset) { + + /* Calculate dataset offset within a file */ + + /* create dataset */ + switch (parms->io_type) { + case POSIXIO: + case MPIO: + /* both posix and mpi io just need dataset offset in file*/ + dset_offset = (ndset - 1) * nbytes; + break; + + case PHDF5: + h5dcpl = H5Pcreate(H5P_DATASET_CREATE); + if (h5dcpl < 0) { + HDfprintf(stderr, "HDF5 Property List Create failed\n"); + GOTOERROR(FAIL); + } + /* 1D dataspace */ + if (!parms->dim2d) { + /* Make the dataset chunked if asked */ + if (parms->h5_use_chunks) { + /* Set the chunk size to be the same as the buffer size */ + h5dims[0] = blk_size; + hrc = H5Pset_chunk(h5dcpl, 1, h5dims); + if (hrc < 0) { + HDfprintf(stderr, "HDF5 Property List Set failed\n"); + GOTOERROR(FAIL); + } /* end if */ + } /* end if */ + } /* end if */ + else { + /* 2D dataspace */ + if (parms->h5_use_chunks) { + /* Set the chunk size to be the same as the block size */ + h5dims[0] = blk_size; + h5dims[1] = blk_size; + hrc = H5Pset_chunk(h5dcpl, 2, h5dims); + if (hrc < 0) { + HDfprintf(stderr, "HDF5 Property List Set failed\n"); + GOTOERROR(FAIL); + } /* end if */ + } /* end if */ + } /* end else */ + + HDsnprintf(dname, sizeof(dname), "Dataset_%ld", ndset); + h5ds_id = H5DCREATE(fd->h5fd, dname, ELMT_H5_TYPE, h5dset_space_id, h5dcpl); + + if (h5ds_id < 0) { + HDfprintf(stderr, "HDF5 Dataset Create failed\n"); + GOTOERROR(FAIL); + } + + hrc = H5Pclose(h5dcpl); + /* verifying the close of the dcpl */ + if (hrc < 0) { + HDfprintf(stderr, "HDF5 Property List Close failed\n"); + GOTOERROR(FAIL); + } + break; + + default: + break; + } + + /* The task is to transfer bytes_count bytes, starting at + * bytes_begin position, using transfer buffer of buf_size bytes. + * If interleaved, select buf_size at a time, in round robin + * fashion, according to number of process. Otherwise, select + * all bytes_count in contiguous. + */ + nbytes_xfer = 0; + + /* 1D dataspace */ + if (!parms->dim2d) { + /* Set base file offset for all I/O patterns and POSIX access */ + posix_file_offset = dset_offset + bytes_begin[0]; + + /* Set base file offset for all I/O patterns and MPI access */ + mpi_file_offset = (MPI_Offset)(dset_offset + bytes_begin[0]); + } /* end if */ + else { + /* Set base file offset for all I/O patterns and POSIX access */ + posix_file_offset = dset_offset + bytes_begin[0] * snbytes + bytes_begin[1]; + + /* Set base file offset for all I/O patterns and MPI access */ + mpi_file_offset = (MPI_Offset)(dset_offset + bytes_begin[0] * snbytes + bytes_begin[1]); + } /* end else */ + + /* Start "raw data" write timer */ + io_time_set(res->timers, HDF5_RAW_WRITE_FIXED_DIMS, TSTART); + + while (nbytes_xfer < bytes_count) { + /* Write */ + /* Calculate offset of write within a dataset/file */ + switch (parms->io_type) { + case POSIXIO: + /* 1D dataspace */ + if (!parms->dim2d) { + /* Contiguous pattern */ + if (!parms->interleaved) { + /* Compute file offset */ + file_offset = posix_file_offset + (off_t)nbytes_xfer; + + /* only care if seek returns error */ + rc = POSIXSEEK(fd->posixfd, file_offset) < 0 ? -1 : 0; + VRFY((rc == 0), "POSIXSEEK"); + + /* check if all bytes are written */ + rc = ((ssize_t)buf_size == POSIXWRITE(fd->posixfd, buffer, buf_size)); + VRFY((rc != 0), "POSIXWRITE"); + + /* Advance global offset in dataset */ + nbytes_xfer += (ssize_t)buf_size; + } /* end if */ + /* Interleaved access pattern */ + else { + /* Set the base of user's buffer */ + buf_p = (unsigned char *)buffer; + + /* Set the number of bytes to transfer this time */ + nbytes_toxfer = buf_size; + + /* Loop over the buffers to write */ + while (nbytes_toxfer > 0) { + /* Skip offset over blocks of other processes */ + file_offset = posix_file_offset + (off_t)(nbytes_xfer * pio_mpi_nprocs_g); + + /* only care if seek returns error */ + rc = POSIXSEEK(fd->posixfd, file_offset) < 0 ? -1 : 0; + VRFY((rc == 0), "POSIXSEEK"); + + /* check if all bytes are written */ + rc = ((ssize_t)blk_size == POSIXWRITE(fd->posixfd, buf_p, blk_size)); + VRFY((rc != 0), "POSIXWRITE"); + + /* Advance location in buffer */ + buf_p += blk_size; + + /* Advance global offset in dataset */ + nbytes_xfer += (ssize_t)blk_size; + + /* Decrement number of bytes left this time */ + nbytes_toxfer -= blk_size; + } /* end while */ + } /* end else */ + } /* end if */ + /* 2D dataspace */ + else { + /* Contiguous storage */ + if (!parms->h5_use_chunks) { + /* Contiguous access pattern */ + if (!parms->interleaved) { + /* Compute file offset */ + file_offset = posix_file_offset + + (off_t)((((size_t)nbytes_xfer / blk_size) / (size_t)snbytes) * + (blk_size * (size_t)snbytes) + + (((size_t)nbytes_xfer / blk_size) % (size_t)snbytes)); + + /* Number of bytes to be transferred per I/O operation */ + nbytes_xfer_advance = buf_size; + + /* Global offset advance after each I/O operation */ + file_offset_advance = (off_t)snbytes; + } /* end if */ + /* Interleaved access pattern */ + else { + /* Compute file offset */ + file_offset = + posix_file_offset + + (off_t)(((((size_t)nbytes_xfer / buf_size) * (size_t)pio_mpi_nprocs_g) / + (size_t)snbytes) * + (buf_size * (size_t)snbytes) + + (((size_t)nbytes_xfer / buf_size) * (size_t)pio_mpi_nprocs_g) % + (size_t)snbytes); + + /* Number of bytes to be transferred per I/O operation */ + nbytes_xfer_advance = blk_size; + + /* Global offset advance after each I/O operation */ + file_offset_advance = (off_t)snbytes; + } /* end else */ + } /* end if */ + /* Chunked storage */ + else { + /*Contiguous access pattern */ + if (!parms->interleaved) { + /* Compute file offset */ + file_offset = posix_file_offset + (off_t)nbytes_xfer; + + /* Number of bytes to be transferred per I/O operation */ + nbytes_xfer_advance = blk_size * buf_size; + + /* Global offset advance after each I/O operation */ + file_offset_advance = 0; + } /* end if */ + /*Interleaved access pattern */ + else { + /* Compute file offset */ + /* Before simplification */ + /* file_offset=posix_file_offset+(off_t)((nbytes_xfer/(buf_size/blk_size) + *pio_mpi_nprocs_g)/(snbytes/blk_size*(blk_size*blk_size))*(buf_size/blk_size + *snbytes/blk_size*(blk_size*blk_size))+((nbytes_xfer/(buf_size/blk_size)) + *pio_mpi_nprocs_g)%(snbytes/blk_size*(blk_size*blk_size))); */ + + file_offset = posix_file_offset + + (off_t)((((size_t)nbytes_xfer / (buf_size / blk_size) * + (size_t)pio_mpi_nprocs_g) / + ((size_t)snbytes * blk_size)) * + (buf_size * (size_t)snbytes) + + (((size_t)nbytes_xfer / (buf_size / blk_size)) * + (size_t)pio_mpi_nprocs_g) % + ((size_t)snbytes * blk_size)); + + /* Number of bytes to be transferred per I/O operation */ + nbytes_xfer_advance = blk_size * blk_size; + + /* Global offset advance after each I/O operation */ + /* file_offset_advance = (off_t)(snbytes/blk_size*(blk_size*blk_size)); */ + file_offset_advance = (off_t)snbytes * (off_t)blk_size; + } /* end else */ + } /* end else */ + + /* Common code for file access */ + + /* Set the base of user's buffer */ + buf_p = (unsigned char *)buffer; + + /* Set the number of bytes to transfer this time */ + nbytes_toxfer = buf_size * blk_size; + + /* Loop over portions of the buffer to write */ + while (nbytes_toxfer > 0) { + /* only care if seek returns error */ + rc = POSIXSEEK(fd->posixfd, file_offset) < 0 ? -1 : 0; + VRFY((rc == 0), "POSIXSEEK"); + + /* check if all bytes are written */ + rc = ((ssize_t)nbytes_xfer_advance == + POSIXWRITE(fd->posixfd, buf_p, nbytes_xfer_advance)); + VRFY((rc != 0), "POSIXWRITE"); + + /* Advance location in buffer */ + buf_p += nbytes_xfer_advance; + + /* Advance global offset in dataset */ + nbytes_xfer += (ssize_t)nbytes_xfer_advance; + + /* Decrement number of bytes left this time */ + nbytes_toxfer -= nbytes_xfer_advance; + + /* Partially advance file offset */ + file_offset += file_offset_advance; + } /* end while */ + + } /* end else */ + + break; + + case MPIO: + /* 1D dataspace */ + if (!parms->dim2d) { + /* Independent file access */ + if (!parms->collective) { + /* Contiguous pattern */ + if (!parms->interleaved) { + /* Compute offset in file */ + mpi_offset = mpi_file_offset + nbytes_xfer; + + /* Perform independent write */ + mrc = + MPI_File_write_at(fd->mpifd, mpi_offset, buffer, + (int)(buf_size / blk_size), mpi_blk_type, &mpi_status); + VRFY((mrc == MPI_SUCCESS), "MPIO_WRITE"); + + /* Advance global offset in dataset */ + nbytes_xfer += (ssize_t)buf_size; + } /* end if */ + /* Interleaved access pattern */ + else { + /* Set the base of user's buffer */ + buf_p = (unsigned char *)buffer; + + /* Set the number of bytes to transfer this time */ + nbytes_toxfer = buf_size; + + /* Loop over the buffers to write */ + while (nbytes_toxfer > 0) { + /* Skip offset over blocks of other processes */ + mpi_offset = mpi_file_offset + (nbytes_xfer * pio_mpi_nprocs_g); + + /* Perform independent write */ + mrc = MPI_File_write_at(fd->mpifd, mpi_offset, buf_p, (int)1, + mpi_blk_type, &mpi_status); + VRFY((mrc == MPI_SUCCESS), "MPIO_WRITE"); + + /* Advance location in buffer */ + buf_p += blk_size; + + /* Advance global offset in dataset */ + nbytes_xfer += (ssize_t)blk_size; + + /* Decrement number of bytes left this time */ + nbytes_toxfer -= blk_size; + } /* end while */ + } /* end else */ + } /* end if */ + /* Collective file access */ + else { + /* Contiguous access pattern */ + if (!parms->interleaved) { + /* Compute offset in file */ + mpi_offset = mpi_file_offset + nbytes_xfer; + + /* Perform independent write */ + mrc = MPI_File_write_at_all(fd->mpifd, mpi_offset, buffer, + (int)(buf_size / blk_size), mpi_blk_type, + &mpi_status); + VRFY((mrc == MPI_SUCCESS), "MPIO_WRITE"); + + /* Advance global offset in dataset */ + nbytes_xfer += (ssize_t)buf_size; + } /* end if */ + /* Interleaved access pattern */ + else { + /* Compute offset in file */ + mpi_offset = mpi_file_offset + (nbytes_xfer * pio_mpi_nprocs_g); + + /* Set the file view */ + mrc = MPI_File_set_view(fd->mpifd, mpi_offset, mpi_blk_type, mpi_file_type, + "native", h5_io_info_g); + VRFY((mrc == MPI_SUCCESS), "MPIO_VIEW"); + + /* Perform write */ + mrc = MPI_File_write_at_all(fd->mpifd, 0, buffer, (int)(buf_size / blk_size), + mpi_blk_type, &mpi_status); + VRFY((mrc == MPI_SUCCESS), "MPIO_WRITE"); + + /* Advance global offset in dataset */ + nbytes_xfer += (ssize_t)buf_size; + } /* end else */ + } /* end else */ + } /* end if */ + /* 2D dataspace */ + else { + /* Contiguous storage */ + if (!parms->h5_use_chunks) { + /* Contiguous access pattern */ + if (!parms->interleaved) { + /* Compute offset in file */ + mpi_offset = + mpi_file_offset + + (MPI_Offset)((((size_t)nbytes_xfer / blk_size) / (size_t)snbytes) * + (blk_size * (size_t)snbytes)) + + (MPI_Offset)(((size_t)nbytes_xfer / blk_size) % (size_t)snbytes); + + /* Number of bytes to be transferred per I/O operation */ + nbytes_xfer_advance = buf_size; + + /* Global offset advance after each I/O operation */ + mpi_offset_advance = snbytes; + + /* MPI type to be used for collective access */ + mpi_collective_type = mpi_cont_type; + } /* end if */ + /* Interleaved access pattern */ + else { + /* Compute offset in file */ + mpi_offset = + mpi_file_offset + + (MPI_Offset)( + ((((size_t)nbytes_xfer / buf_size) * (size_t)pio_mpi_nprocs_g) / + (size_t)snbytes) * + (buf_size * (size_t)snbytes)) + + (MPI_Offset)( + (((size_t)nbytes_xfer / buf_size) * (size_t)pio_mpi_nprocs_g) % + (size_t)snbytes); + + /* Number of bytes to be transferred per I/O operation */ + nbytes_xfer_advance = blk_size; + + /* Global offset advance after each I/O operation */ + mpi_offset_advance = snbytes; + + /* MPI type to be used for collective access */ + mpi_collective_type = mpi_inter_type; + } /* end else */ + } /* end if */ + /* Chunked storage */ + else { + /*Contiguous access pattern */ + if (!parms->interleaved) { + /* Compute offset in file */ + mpi_offset = mpi_file_offset + nbytes_xfer; + + /* Number of bytes to be transferred per I/O operation */ + nbytes_xfer_advance = blk_size * buf_size; + + /* Global offset advance after each I/O operation */ + mpi_offset_advance = 0; + + /* MPI type to be used for collective access */ + mpi_collective_type = mpi_full_buffer; + } /* end if */ + /*Interleaved access pattern */ + else { + /* Compute offset in file */ + /* Before simplification */ + /* mpi_offset=mpi_file_offset+(nbytes_xfer/(buf_size/blk_size) + *pio_mpi_nprocs_g)/(snbytes/blk_size*(blk_size*blk_size))* + (buf_size/blk_size*snbytes/blk_size*(blk_size*blk_size))+ + ((nbytes_xfer/(buf_size/blk_size))*pio_mpi_nprocs_g)%(snbytes + /blk_size*(blk_size*blk_size)); */ + mpi_offset = mpi_file_offset + + (MPI_Offset)((((size_t)nbytes_xfer / (buf_size / blk_size) * + (size_t)pio_mpi_nprocs_g) / + ((size_t)snbytes * blk_size)) * + (buf_size * (size_t)snbytes)) + + (MPI_Offset)((((size_t)nbytes_xfer / (buf_size / blk_size)) * + (size_t)pio_mpi_nprocs_g) % + ((size_t)snbytes * blk_size)); + + /* Number of bytes to be transferred per I/O operation */ + nbytes_xfer_advance = blk_size * blk_size; + + /* Global offset advance after each I/O operation */ + /* mpi_offset_advance = (MPI_Offset)(snbytes/blk_size*(blk_size*blk_size)); */ + mpi_offset_advance = (MPI_Offset)((size_t)snbytes * blk_size); + + /* MPI type to be used for collective access */ + mpi_collective_type = mpi_chunk_inter_type; + } /* end else */ + } /* end else */ + + /* Common code for independent file access */ + if (!parms->collective) { + /* Set the base of user's buffer */ + buf_p = (unsigned char *)buffer; + + /* Set the number of bytes to transfer this time */ + nbytes_toxfer = buf_size * blk_size; + + /* Loop over portions of the buffer to write */ + while (nbytes_toxfer > 0) { + /* Perform independent write */ + mrc = MPI_File_write_at(fd->mpifd, mpi_offset, buf_p, + (int)nbytes_xfer_advance, MPI_BYTE, &mpi_status); + VRFY((mrc == MPI_SUCCESS), "MPIO_WRITE"); + + /* Advance location in buffer */ + buf_p += nbytes_xfer_advance; + + /* Advance global offset in dataset */ + nbytes_xfer += (ssize_t)nbytes_xfer_advance; + + /* Decrement number of bytes left this time */ + nbytes_toxfer -= nbytes_xfer_advance; + + /* Partially advance global offset in dataset */ + mpi_offset += mpi_offset_advance; + } /* end while */ + } /* end if */ + + /* Common code for collective file access */ + else { + /* Set the file view */ + mrc = MPI_File_set_view(fd->mpifd, mpi_offset, MPI_BYTE, mpi_collective_type, + "native", h5_io_info_g); + VRFY((mrc == MPI_SUCCESS), "MPIO_VIEW"); + + /* Perform write */ + MPI_File_write_at_all(fd->mpifd, 0, buffer, (int)(buf_size * blk_size), MPI_BYTE, + &mpi_status); + VRFY((mrc == MPI_SUCCESS), "MPIO_WRITE"); + + /* Advance global offset in dataset */ + nbytes_xfer += (off_t)buf_size * (off_t)blk_size; + } /* end else */ + + } /* end else */ + + break; + + case PHDF5: + /* 1D dataspace */ + if (!parms->dim2d) { + /* Set up the file dset space id to move the selection to process */ + if (!parms->interleaved) { + /* Contiguous pattern */ + h5offset[0] = nbytes_xfer; + } /* end if */ + else { + /* Interleaved access pattern */ + /* Skip offset over blocks of other processes */ + h5offset[0] = (nbytes_xfer * pio_mpi_nprocs_g); + } /* end else */ + hrc = H5Soffset_simple(h5dset_space_id, h5offset); + VRFY((hrc >= 0), "H5Soffset_simple"); + + /* Write the buffer out */ + hrc = + H5Dwrite(h5ds_id, ELMT_H5_TYPE, h5mem_space_id, h5dset_space_id, h5dxpl, buffer); + VRFY((hrc >= 0), "H5Dwrite"); + + /* Increment number of bytes transferred */ + nbytes_xfer += (ssize_t)buf_size; + } /* end if */ + /* 2D dataspace */ + else { + /* Set up the file dset space id to move the selection to process */ + if (!parms->interleaved) { + /* Contiguous pattern */ + h5offset[0] = + (hssize_t)(((size_t)nbytes_xfer / ((size_t)snbytes * blk_size)) * blk_size); + h5offset[1] = + (hssize_t)(((size_t)nbytes_xfer % ((size_t)snbytes * blk_size)) / blk_size); + + } /* end if */ + else { + /* Interleaved access pattern */ + /* Skip offset over blocks of other processes */ + h5offset[0] = (hssize_t)((((size_t)nbytes_xfer * (size_t)pio_mpi_nprocs_g) / + ((size_t)snbytes * buf_size)) * + buf_size); + h5offset[1] = (hssize_t)((((size_t)nbytes_xfer * (size_t)pio_mpi_nprocs_g) % + ((size_t)snbytes * buf_size)) / + buf_size); + + } /* end else */ + hrc = H5Soffset_simple(h5dset_space_id, h5offset); + VRFY((hrc >= 0), "H5Soffset_simple"); + + /* Write the buffer out */ + hrc = + H5Dwrite(h5ds_id, ELMT_H5_TYPE, h5mem_space_id, h5dset_space_id, h5dxpl, buffer); + VRFY((hrc >= 0), "H5Dwrite"); + + /* Increment number of bytes transferred */ + nbytes_xfer += (off_t)buf_size * (off_t)blk_size; + + } /* end else */ + + break; + + default: + break; + } /* switch (parms->io_type) */ + } /* end while */ + + /* Stop "raw data" write timer */ + io_time_set(res->timers, HDF5_RAW_WRITE_FIXED_DIMS, TSTOP); + + /* Calculate write time */ + + /* Close dataset. Only HDF5 needs to do an explicit close. */ + if (parms->io_type == PHDF5) { + hrc = H5Dclose(h5ds_id); + + if (hrc < 0) { + HDfprintf(stderr, "HDF5 Dataset Close failed\n"); + GOTOERROR(FAIL); + } + + h5ds_id = H5I_INVALID_HID; + } /* end if */ + } /* end for */ + +done: + /* release MPI-I/O objects */ + if (parms->io_type == MPIO) { + /* 1D dataspace */ + if (!parms->dim2d) { + /* Free file type */ + mrc = MPI_Type_free(&mpi_file_type); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_FREE"); + + /* Free buffer type */ + mrc = MPI_Type_free(&mpi_blk_type); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_FREE"); + } /* end if */ + /* 2D dataspace */ + else { + /* Free partial buffer type for contiguous access */ + mrc = MPI_Type_free(&mpi_partial_buffer_cont); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_FREE"); + + /* Free contiguous file type */ + mrc = MPI_Type_free(&mpi_cont_type); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_FREE"); + + /* Free partial buffer type for interleaved access */ + mrc = MPI_Type_free(&mpi_partial_buffer_inter); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_FREE"); + + /* Free interleaved file type */ + mrc = MPI_Type_free(&mpi_inter_type); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_FREE"); + + /* Free full buffer type */ + mrc = MPI_Type_free(&mpi_full_buffer); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_FREE"); + + /* Free full chunk type */ + mrc = MPI_Type_free(&mpi_full_chunk); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_FREE"); + + /* Free chunk interleaved file type */ + mrc = MPI_Type_free(&mpi_chunk_inter_type); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_FREE"); + } /* end else */ + } /* end if */ + + /* release HDF5 objects */ + if (h5dset_space_id != -1) { + hrc = H5Sclose(h5dset_space_id); + if (hrc < 0) { + HDfprintf(stderr, "HDF5 Dataset Space Close failed\n"); + ret_code = FAIL; + } + else { + h5dset_space_id = H5I_INVALID_HID; + } + } + + if (h5mem_space_id != -1) { + hrc = H5Sclose(h5mem_space_id); + if (hrc < 0) { + HDfprintf(stderr, "HDF5 Memory Space Close failed\n"); + ret_code = FAIL; + } + else { + h5mem_space_id = H5I_INVALID_HID; + } + } + + if (h5dxpl != -1) { + hrc = H5Pclose(h5dxpl); + if (hrc < 0) { + HDfprintf(stderr, "HDF5 Dataset Transfer Property List Close failed\n"); + ret_code = FAIL; + } + else { + h5dxpl = H5I_INVALID_HID; + } + } + + return ret_code; +} + +static off_t +sqrto(off_t x) +{ + double root_x = sqrt((double)x); + return (off_t)root_x; +} + +/* + * Function: do_read + * Purpose: read the required amount of data from the file. + * Return: SUCCESS or FAIL + * Programmer: Albert Cheng 2001/12/13 + * Modifications: + * Added 2D testing (Christian Chilan, 10. August 2005) + */ +static herr_t +do_read(results *res, file_descr *fd, parameters *parms, long ndsets, off_t nbytes, size_t buf_size, + void *buffer /*out*/) +{ + int ret_code = SUCCESS; + int rc; /*routine return code */ + long ndset; + size_t blk_size; /* The block size to subdivide the xfer buffer into */ + size_t bsize; /* Size of the actual buffer */ + off_t nbytes_xfer; /* Total number of bytes transferred so far */ + size_t nbytes_xfer_advance; /* Number of bytes transferred in a single I/O operation */ + size_t nbytes_toxfer; /* Number of bytes to transfer a particular time */ + char dname[64]; + off_t dset_offset = 0; /*dataset offset in a file */ + off_t bytes_begin[2]; /*first elmt this process transfer */ + off_t bytes_count; /*number of elmts this process transfer */ + off_t snbytes = 0; /*size of a side of the dataset square */ + unsigned char *buf_p; /* Current buffer pointer */ + + /* POSIX variables */ + off_t file_offset; /* File offset of the next transfer */ + off_t file_offset_advance; /* File offset advance after each I/O operation */ + off_t posix_file_offset; /* Base file offset of the next transfer */ + + /* MPI variables */ + MPI_Offset mpi_file_offset; /* Base file offset of the next transfer*/ + MPI_Offset mpi_offset; /* Offset in MPI file */ + MPI_Offset mpi_offset_advance; /* Offset advance after each I/O operation */ + MPI_Datatype mpi_file_type; /* MPI derived type for 1D file */ + MPI_Datatype mpi_blk_type; /* MPI derived type for 1D buffer */ + MPI_Datatype mpi_cont_type; /* MPI derived type for 2D contiguous file */ + MPI_Datatype mpi_partial_buffer_cont; /* MPI derived type for partial 2D contiguous buffer */ + MPI_Datatype mpi_inter_type; /* MPI derived type for 2D interleaved file */ + MPI_Datatype mpi_partial_buffer_inter; /* MPI derived type for partial 2D interleaved buffer */ + MPI_Datatype mpi_full_buffer; /* MPI derived type for 2D full buffer */ + MPI_Datatype mpi_full_chunk; /* MPI derived type for 2D full chunk */ + MPI_Datatype mpi_chunk_inter_type; /* MPI derived type for 2D chunk interleaved file */ + MPI_Datatype mpi_collective_type; /* Generic MPI derived type for 2D collective access */ + MPI_Status mpi_status; + int mrc; /* MPI return code */ + + /* HDF5 variables */ + herr_t hrc; /*HDF5 return code */ + hsize_t h5dims[2]; /*dataset dim sizes */ + hid_t h5dset_space_id = H5I_INVALID_HID; /*dataset space ID */ + hid_t h5mem_space_id = H5I_INVALID_HID; /*memory dataspace ID */ + hid_t h5ds_id = H5I_INVALID_HID; /*dataset handle */ + hsize_t h5block[2]; /*dataspace selection */ + hsize_t h5stride[2]; + hsize_t h5count[2]; + hsize_t h5start[2]; + hssize_t h5offset[2]; /* Selection offset within dataspace */ + hid_t h5dxpl = H5I_INVALID_HID; /* Dataset transfer property list */ + + /* Get the parameters from the parameter block */ + blk_size = parms->blk_size; + + /* There are two kinds of transfer patterns, contiguous and interleaved. + * Let 0,1,2,...,n be data accessed by process 0,1,2,...,n + * where n is rank of the last process. + * In contiguous pattern, data are accessed as + * 000...111...222...nnn... + * In interleaved pattern, data are accessed as + * 012...n012...n... + * These are all in the scope of one dataset. + */ + + /* 1D dataspace */ + if (!parms->dim2d) { + bsize = buf_size; + /* Contiguous Pattern: */ + if (!parms->interleaved) { + bytes_begin[0] = (off_t)(((double)nbytes * pio_mpi_rank_g) / pio_mpi_nprocs_g); + } /* end if */ + /* Interleaved Pattern: */ + else { + bytes_begin[0] = (off_t)blk_size * (off_t)pio_mpi_rank_g; + } /* end else */ + } /* end if */ + /* 2D dataspace */ + else { + /* nbytes is always the number of bytes per dataset (1D or 2D). If the + dataspace is 2D, snbytes is the size of a side of the 'dataset square'. + */ + snbytes = sqrto(nbytes); + + bsize = buf_size * blk_size; + + /* Contiguous Pattern: */ + if (!parms->interleaved) { + bytes_begin[0] = (off_t)((double)snbytes * pio_mpi_rank_g / pio_mpi_nprocs_g); + bytes_begin[1] = 0; + } /* end if */ + /* Interleaved Pattern: */ + else { + bytes_begin[0] = 0; + + if (!parms->h5_use_chunks || parms->io_type == PHDF5) + bytes_begin[1] = (off_t)blk_size * (off_t)pio_mpi_rank_g; + else + bytes_begin[1] = (off_t)blk_size * (off_t)blk_size * (off_t)pio_mpi_rank_g; + } /* end else */ + } /* end else */ + + /* Calculate the total number of bytes (bytes_count) to be + * transferred by this process. It may be different for different + * transfer pattern due to rounding to integral values. + */ + /* + * Calculate the beginning bytes of this process and the next. + * bytes_count is the difference between these two beginnings. + * This way, it eliminates any rounding errors. + * (This is tricky, don't mess with the formula, rounding errors + * can easily get introduced) */ + bytes_count = (off_t)(((double)nbytes * (pio_mpi_rank_g + 1)) / pio_mpi_nprocs_g) - + (off_t)(((double)nbytes * pio_mpi_rank_g) / pio_mpi_nprocs_g); + + /* debug */ + if (pio_debug_level >= 4) { + HDprint_rank(output); + if (!parms->dim2d) { + HDfprintf(output, + "Debug(do_write): " + "buf_size=%zu, bytes_begin=%" H5_PRINTF_LL_WIDTH "d, bytes_count=%" H5_PRINTF_LL_WIDTH + "d\n", + buf_size, (long long)bytes_begin[0], (long long)bytes_count); + } + else { + HDfprintf(output, + "Debug(do_write): " + "linear buf_size=%zu, bytes_begin=(%" H5_PRINTF_LL_WIDTH "d,%" H5_PRINTF_LL_WIDTH + "d), bytes_count=%" H5_PRINTF_LL_WIDTH "d\n", + buf_size * blk_size, (long long)bytes_begin[0], (long long)bytes_begin[1], + (long long)bytes_count); + } + } + + /* I/O Access specific setup */ + switch (parms->io_type) { + case POSIXIO: + /* No extra setup */ + break; + + case MPIO: /* MPI-I/O setup */ + /* 1D dataspace */ + if (!parms->dim2d) { + /* Build block's derived type */ + mrc = MPI_Type_contiguous((int)blk_size, MPI_BYTE, &mpi_blk_type); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_CREATE"); + + /* Build file's derived type */ + mrc = MPI_Type_vector((int)(buf_size / blk_size), (int)1, (int)pio_mpi_nprocs_g, mpi_blk_type, + &mpi_file_type); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_CREATE"); + + /* Commit file type */ + mrc = MPI_Type_commit(&mpi_file_type); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_COMMIT"); + + /* Commit buffer type */ + mrc = MPI_Type_commit(&mpi_blk_type); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_COMMIT"); + } /* end if */ + /* 2D dataspace */ + else { + /* Build partial buffer derived type for contiguous access */ + mrc = MPI_Type_contiguous((int)buf_size, MPI_BYTE, &mpi_partial_buffer_cont); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_CREATE"); + + /* Commit partial buffer derived type */ + mrc = MPI_Type_commit(&mpi_partial_buffer_cont); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_COMMIT"); + + /* Build contiguous file's derived type */ + mrc = MPI_Type_vector((int)blk_size, (int)1, (int)((size_t)snbytes / buf_size), + mpi_partial_buffer_cont, &mpi_cont_type); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_CREATE"); + + /* Commit contiguous file type */ + mrc = MPI_Type_commit(&mpi_cont_type); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_COMMIT"); + + /* Build partial buffer derived type for interleaved access */ + mrc = MPI_Type_contiguous((int)blk_size, MPI_BYTE, &mpi_partial_buffer_inter); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_CREATE"); + + /* Commit partial buffer derived type */ + mrc = MPI_Type_commit(&mpi_partial_buffer_inter); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_COMMIT"); + + /* Build interleaved file's derived type */ + mrc = MPI_Type_vector((int)buf_size, (int)1, (int)((size_t)snbytes / blk_size), + mpi_partial_buffer_inter, &mpi_inter_type); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_CREATE"); + + /* Commit interleaved file type */ + mrc = MPI_Type_commit(&mpi_inter_type); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_COMMIT"); + + /* Build full buffer derived type */ + mrc = MPI_Type_contiguous((int)(blk_size * buf_size), MPI_BYTE, &mpi_full_buffer); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_CREATE"); + + /* Commit full buffer derived type */ + mrc = MPI_Type_commit(&mpi_full_buffer); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_COMMIT"); + + /* Build full chunk derived type */ + mrc = MPI_Type_contiguous((int)(blk_size * blk_size), MPI_BYTE, &mpi_full_chunk); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_CREATE"); + + /* Commit full chunk derived type */ + mrc = MPI_Type_commit(&mpi_full_chunk); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_COMMIT"); + + /* Build chunk interleaved file's derived type */ + mrc = MPI_Type_vector((int)(buf_size / blk_size), (int)1, (int)((size_t)snbytes / blk_size), + mpi_full_chunk, &mpi_chunk_inter_type); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_CREATE"); + + /* Commit chunk interleaved file type */ + mrc = MPI_Type_commit(&mpi_chunk_inter_type); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_COMMIT"); + } /* end else */ + break; + + case PHDF5: /* HDF5 setup */ + /* 1D dataspace */ + if (!parms->dim2d) { + if (nbytes > 0) { + /* define a contiguous dataset of nbytes native bytes */ + h5dims[0] = (hsize_t)nbytes; + h5dset_space_id = H5Screate_simple(1, h5dims, NULL); + VRFY((h5dset_space_id >= 0), "H5Screate_simple"); + + /* Set up the file dset space id to select the pattern to access */ + if (!parms->interleaved) { + /* Contiguous pattern */ + h5start[0] = (hsize_t)bytes_begin[0]; + h5stride[0] = h5block[0] = blk_size; + h5count[0] = buf_size / blk_size; + } /* end if */ + else { + /* Interleaved access pattern */ + /* Skip offset over blocks of other processes */ + h5start[0] = (hsize_t)bytes_begin[0]; + h5stride[0] = blk_size * (size_t)pio_mpi_nprocs_g; + h5block[0] = blk_size; + h5count[0] = buf_size / blk_size; + } /* end else */ + hrc = H5Sselect_hyperslab(h5dset_space_id, H5S_SELECT_SET, h5start, h5stride, h5count, + h5block); + VRFY((hrc >= 0), "H5Sselect_hyperslab"); + } /* end if */ + else { + h5dset_space_id = H5Screate(H5S_SCALAR); + VRFY((h5dset_space_id >= 0), "H5Screate"); + } /* end else */ + + /* Create the memory dataspace that corresponds to the xfer buffer */ + if (buf_size > 0) { + h5dims[0] = buf_size; + h5mem_space_id = H5Screate_simple(1, h5dims, NULL); + VRFY((h5mem_space_id >= 0), "H5Screate_simple"); + } /* end if */ + else { + h5mem_space_id = H5Screate(H5S_SCALAR); + VRFY((h5mem_space_id >= 0), "H5Screate"); + } /* end else */ + } /* end if */ + /* 2D dataspace */ + else { + if (nbytes > 0) { + /* define a contiguous dataset of nbytes native bytes */ + h5dims[0] = (hsize_t)snbytes; + h5dims[1] = (hsize_t)snbytes; + h5dset_space_id = H5Screate_simple(2, h5dims, NULL); + VRFY((h5dset_space_id >= 0), "H5Screate_simple"); + + /* Set up the file dset space id to select the pattern to access */ + if (!parms->interleaved) { + /* Contiguous pattern */ + h5start[0] = (hsize_t)bytes_begin[0]; + h5start[1] = (hsize_t)bytes_begin[1]; + h5stride[0] = 1; + h5stride[1] = h5block[0] = h5block[1] = blk_size; + h5count[0] = 1; + h5count[1] = buf_size / blk_size; + } /* end if */ + else { + /* Interleaved access pattern */ + /* Skip offset over blocks of other processes */ + h5start[0] = (hsize_t)bytes_begin[0]; + h5start[1] = (hsize_t)bytes_begin[1]; + h5stride[0] = blk_size; + h5stride[1] = blk_size * (size_t)pio_mpi_nprocs_g; + h5block[0] = h5block[1] = blk_size; + h5count[0] = buf_size / blk_size; + h5count[1] = 1; + } /* end else */ + hrc = H5Sselect_hyperslab(h5dset_space_id, H5S_SELECT_SET, h5start, h5stride, h5count, + h5block); + VRFY((hrc >= 0), "H5Sselect_hyperslab"); + } /* end if */ + else { + h5dset_space_id = H5Screate(H5S_SCALAR); + VRFY((h5dset_space_id >= 0), "H5Screate"); + } /* end else */ + + /* Create the memory dataspace that corresponds to the xfer buffer */ + if (buf_size > 0) { + if (!parms->interleaved) { + h5dims[0] = blk_size; + h5dims[1] = buf_size; + } + else { + h5dims[0] = buf_size; + h5dims[1] = blk_size; + } + h5mem_space_id = H5Screate_simple(2, h5dims, NULL); + VRFY((h5mem_space_id >= 0), "H5Screate_simple"); + } /* end if */ + else { + h5mem_space_id = H5Screate(H5S_SCALAR); + VRFY((h5mem_space_id >= 0), "H5Screate"); + } /* end else */ + } /* end else */ + + /* Create the dataset transfer property list */ + h5dxpl = H5Pcreate(H5P_DATASET_XFER); + if (h5dxpl < 0) { + HDfprintf(stderr, "HDF5 Property List Create failed\n"); + GOTOERROR(FAIL); + } + + /* Change to collective I/O, if asked */ + if (parms->collective) { + hrc = H5Pset_dxpl_mpio(h5dxpl, H5FD_MPIO_COLLECTIVE); + if (hrc < 0) { + HDfprintf(stderr, "HDF5 Property List Set failed\n"); + GOTOERROR(FAIL); + } /* end if */ + } /* end if */ + break; + + default: + break; + } /* end switch */ + + for (ndset = 1; ndset <= ndsets; ++ndset) { + + /* Calculate dataset offset within a file */ + + /* create dataset */ + switch (parms->io_type) { + case POSIXIO: + case MPIO: + /* both posix and mpi io just need dataset offset in file*/ + dset_offset = (ndset - 1) * nbytes; + break; + + case PHDF5: + HDsnprintf(dname, sizeof(dname), "Dataset_%ld", ndset); + h5ds_id = H5DOPEN(fd->h5fd, dname); + if (h5ds_id < 0) { + HDfprintf(stderr, "HDF5 Dataset open failed\n"); + GOTOERROR(FAIL); + } + break; + + default: + break; + } + + /* The task is to transfer bytes_count bytes, starting at + * bytes_begin position, using transfer buffer of buf_size bytes. + * If interleaved, select buf_size at a time, in round robin + * fashion, according to number of process. Otherwise, select + * all bytes_count in contiguous. + */ + nbytes_xfer = 0; + + /* 1D dataspace */ + if (!parms->dim2d) { + /* Set base file offset for all I/O patterns and POSIX access */ + posix_file_offset = dset_offset + bytes_begin[0]; + + /* Set base file offset for all I/O patterns and MPI access */ + mpi_file_offset = (MPI_Offset)(dset_offset + bytes_begin[0]); + } /* end if */ + else { + /* Set base file offset for all I/O patterns and POSIX access */ + posix_file_offset = dset_offset + bytes_begin[0] * snbytes + bytes_begin[1]; + + /* Set base file offset for all I/O patterns and MPI access */ + mpi_file_offset = (MPI_Offset)(dset_offset + bytes_begin[0] * snbytes + bytes_begin[1]); + } /* end else */ + + /* Start "raw data" read timer */ + io_time_set(res->timers, HDF5_RAW_READ_FIXED_DIMS, TSTART); + + while (nbytes_xfer < bytes_count) { + /* Read */ + /* Calculate offset of read within a dataset/file */ + switch (parms->io_type) { + case POSIXIO: + /* 1D dataspace */ + if (!parms->dim2d) { + /* Contiguous pattern */ + if (!parms->interleaved) { + /* Compute file offset */ + file_offset = posix_file_offset + (off_t)nbytes_xfer; + + /* only care if seek returns error */ + rc = POSIXSEEK(fd->posixfd, file_offset) < 0 ? -1 : 0; + VRFY((rc == 0), "POSIXSEEK"); + + /* check if all bytes are read */ + rc = ((ssize_t)buf_size == POSIXREAD(fd->posixfd, buffer, buf_size)); + VRFY((rc != 0), "POSIXREAD"); + + /* Advance global offset in dataset */ + nbytes_xfer += (off_t)buf_size; + } /* end if */ + /* Interleaved access pattern */ + else { + /* Set the base of user's buffer */ + buf_p = (unsigned char *)buffer; + + /* Set the number of bytes to transfer this time */ + nbytes_toxfer = buf_size; + + /* Loop over the buffers to read */ + while (nbytes_toxfer > 0) { + /* Skip offset over blocks of other processes */ + file_offset = posix_file_offset + (off_t)(nbytes_xfer * pio_mpi_nprocs_g); + + /* only care if seek returns error */ + rc = POSIXSEEK(fd->posixfd, file_offset) < 0 ? -1 : 0; + VRFY((rc == 0), "POSIXSEEK"); + + /* check if all bytes are read */ + rc = ((ssize_t)blk_size == POSIXREAD(fd->posixfd, buf_p, blk_size)); + VRFY((rc != 0), "POSIXREAD"); + + /* Advance location in buffer */ + buf_p += blk_size; + + /* Advance global offset in dataset */ + nbytes_xfer += (off_t)blk_size; + + /* Decrement number of bytes left this time */ + nbytes_toxfer -= blk_size; + } /* end while */ + } /* end else */ + } /* end if */ + /* 2D dataspace */ + else { + /* Contiguous storage */ + if (!parms->h5_use_chunks) { + /* Contiguous access pattern */ + if (!parms->interleaved) { + /* Compute file offset */ + file_offset = posix_file_offset + + (off_t)((((size_t)nbytes_xfer / blk_size) / (size_t)snbytes) * + (blk_size * (size_t)snbytes) + + (((size_t)nbytes_xfer / blk_size) % (size_t)snbytes)); + + /* Number of bytes to be transferred per I/O operation */ + nbytes_xfer_advance = buf_size; + + /* Global offset advance after each I/O operation */ + file_offset_advance = (off_t)snbytes; + } /* end if */ + /* Interleaved access pattern */ + else { + /* Compute file offset */ + file_offset = + posix_file_offset + + (off_t)(((((size_t)nbytes_xfer / buf_size) * (size_t)pio_mpi_nprocs_g) / + (size_t)snbytes) * + (buf_size * (size_t)snbytes) + + (((size_t)nbytes_xfer / buf_size) * (size_t)pio_mpi_nprocs_g) % + (size_t)snbytes); + + /* Number of bytes to be transferred per I/O operation */ + nbytes_xfer_advance = blk_size; + + /* Global offset advance after each I/O operation */ + file_offset_advance = (off_t)snbytes; + } /* end else */ + } /* end if */ + /* Chunked storage */ + else { + /*Contiguous access pattern */ + if (!parms->interleaved) { + /* Compute file offset */ + file_offset = posix_file_offset + (off_t)nbytes_xfer; + + /* Number of bytes to be transferred per I/O operation */ + nbytes_xfer_advance = blk_size * buf_size; + + /* Global offset advance after each I/O operation */ + file_offset_advance = 0; + } /* end if */ + /*Interleaved access pattern */ + else { + /* Compute file offset */ + /* Before simplification */ + /* file_offset=posix_file_offset+(off_t)((nbytes_xfer/(buf_size/blk_size) + *pio_mpi_nprocs_g)/(snbytes/blk_size*(blk_size*blk_size))*(buf_size/blk_size + *snbytes/blk_size*(blk_size*blk_size))+((nbytes_xfer/(buf_size/blk_size)) + *pio_mpi_nprocs_g)%(snbytes/blk_size*(blk_size*blk_size))); */ + + file_offset = posix_file_offset + + (off_t)((((size_t)nbytes_xfer / (buf_size / blk_size) * + (size_t)pio_mpi_nprocs_g) / + ((size_t)snbytes * blk_size)) * + (buf_size * (size_t)snbytes) + + (((size_t)nbytes_xfer / (buf_size / blk_size)) * + (size_t)pio_mpi_nprocs_g) % + ((size_t)snbytes * blk_size)); + + /* Number of bytes to be transferred per I/O operation */ + nbytes_xfer_advance = blk_size * blk_size; + + /* Global offset advance after each I/O operation */ + /* file_offset_advance = (off_t)(snbytes/blk_size*(blk_size*blk_size)); */ + file_offset_advance = (off_t)((size_t)snbytes * blk_size); + } /* end else */ + } /* end else */ + + /* Common code for file access */ + + /* Set the base of user's buffer */ + buf_p = (unsigned char *)buffer; + + /* Set the number of bytes to transfer this time */ + nbytes_toxfer = buf_size * blk_size; + + /* Loop over portions of the buffer to read */ + while (nbytes_toxfer > 0) { + /* only care if seek returns error */ + rc = POSIXSEEK(fd->posixfd, file_offset) < 0 ? -1 : 0; + VRFY((rc == 0), "POSIXSEEK"); + + /* check if all bytes are read */ + rc = ((ssize_t)nbytes_xfer_advance == + POSIXREAD(fd->posixfd, buf_p, nbytes_xfer_advance)); + VRFY((rc != 0), "POSIXREAD"); + + /* Advance location in buffer */ + buf_p += nbytes_xfer_advance; + + /* Advance global offset in dataset */ + nbytes_xfer += (off_t)nbytes_xfer_advance; + + /* Decrement number of bytes left this time */ + nbytes_toxfer -= nbytes_xfer_advance; + + /* Partially advance file offset */ + file_offset += file_offset_advance; + } /* end while */ + + } /* end else */ + break; + + case MPIO: + /* 1D dataspace */ + if (!parms->dim2d) { + /* Independent file access */ + if (!parms->collective) { + /* Contiguous pattern */ + if (!parms->interleaved) { + /* Compute offset in file */ + mpi_offset = mpi_file_offset + nbytes_xfer; + + /* Perform independent read */ + mrc = MPI_File_read_at(fd->mpifd, mpi_offset, buffer, + (int)(buf_size / blk_size), mpi_blk_type, &mpi_status); + VRFY((mrc == MPI_SUCCESS), "MPIO_READ"); + + /* Advance global offset in dataset */ + nbytes_xfer += (off_t)buf_size; + } /* end if */ + /* Interleaved access pattern */ + else { + /* Set the base of user's buffer */ + buf_p = (unsigned char *)buffer; + + /* Set the number of bytes to transfer this time */ + nbytes_toxfer = buf_size; + + /* Loop over the buffers to read */ + while (nbytes_toxfer > 0) { + /* Skip offset over blocks of other processes */ + mpi_offset = mpi_file_offset + (nbytes_xfer * pio_mpi_nprocs_g); + + /* Perform independent read */ + mrc = MPI_File_read_at(fd->mpifd, mpi_offset, buf_p, (int)1, mpi_blk_type, + &mpi_status); + VRFY((mrc == MPI_SUCCESS), "MPIO_READ"); + + /* Advance location in buffer */ + buf_p += blk_size; + + /* Advance global offset in dataset */ + nbytes_xfer += (off_t)blk_size; + + /* Decrement number of bytes left this time */ + nbytes_toxfer -= blk_size; + } /* end while */ + } /* end else */ + } /* end if */ + /* Collective file access */ + else { + /* Contiguous access pattern */ + if (!parms->interleaved) { + /* Compute offset in file */ + mpi_offset = mpi_file_offset + nbytes_xfer; + + /* Perform collective read */ + mrc = MPI_File_read_at_all(fd->mpifd, mpi_offset, buffer, + (int)(buf_size / blk_size), mpi_blk_type, + &mpi_status); + VRFY((mrc == MPI_SUCCESS), "MPIO_READ"); + + /* Advance global offset in dataset */ + nbytes_xfer += (off_t)buf_size; + } /* end if */ + /* Interleaved access pattern */ + else { + /* Compute offset in file */ + mpi_offset = mpi_file_offset + (nbytes_xfer * pio_mpi_nprocs_g); + + /* Set the file view */ + mrc = MPI_File_set_view(fd->mpifd, mpi_offset, mpi_blk_type, mpi_file_type, + "native", h5_io_info_g); + VRFY((mrc == MPI_SUCCESS), "MPIO_VIEW"); + + /* Perform collective read */ + mrc = MPI_File_read_at_all(fd->mpifd, 0, buffer, (int)(buf_size / blk_size), + mpi_blk_type, &mpi_status); + VRFY((mrc == MPI_SUCCESS), "MPIO_READ"); + + /* Advance global offset in dataset */ + nbytes_xfer += (off_t)buf_size; + } /* end else */ + } /* end else */ + } /* end if */ + /* 2D dataspace */ + else { + /* Contiguous storage */ + if (!parms->h5_use_chunks) { + /* Contiguous access pattern */ + if (!parms->interleaved) { + /* Compute offset in file */ + mpi_offset = + mpi_file_offset + + (MPI_Offset)((((size_t)nbytes_xfer / blk_size) / (size_t)snbytes) * + (blk_size * (size_t)snbytes)) + + (MPI_Offset)(((size_t)nbytes_xfer / blk_size) % (size_t)snbytes); + + /* Number of bytes to be transferred per I/O operation */ + nbytes_xfer_advance = buf_size; + + /* Global offset advance after each I/O operation */ + mpi_offset_advance = snbytes; + + /* MPI type to be used for collective access */ + mpi_collective_type = mpi_cont_type; + } /* end if */ + /* Interleaved access pattern */ + else { + /* Compute offset in file */ + mpi_offset = + mpi_file_offset + + (MPI_Offset)( + ((((size_t)nbytes_xfer / buf_size) * (size_t)pio_mpi_nprocs_g) / + (size_t)snbytes) * + (buf_size * (size_t)snbytes)) + + (MPI_Offset)( + (((size_t)nbytes_xfer / buf_size) * (size_t)pio_mpi_nprocs_g) % + (size_t)snbytes); + + /* Number of bytes to be transferred per I/O operation */ + nbytes_xfer_advance = blk_size; + + /* Global offset advance after each I/O operation */ + mpi_offset_advance = snbytes; + + /* MPI type to be used for collective access */ + mpi_collective_type = mpi_inter_type; + } /* end else */ + } /* end if */ + /* Chunked storage */ + else { + /*Contiguous access pattern */ + if (!parms->interleaved) { + /* Compute offset in file */ + mpi_offset = mpi_file_offset + nbytes_xfer; + + /* Number of bytes to be transferred per I/O operation */ + nbytes_xfer_advance = blk_size * buf_size; + + /* Global offset advance after each I/O operation */ + mpi_offset_advance = 0; + + /* MPI type to be used for collective access */ + mpi_collective_type = mpi_full_buffer; + } /* end if */ + /*Interleaved access pattern */ + else { + /* Compute offset in file */ + /* Before simplification */ + /* mpi_offset=mpi_file_offset+(nbytes_xfer/(buf_size/blk_size) + *pio_mpi_nprocs_g)/(snbytes/blk_size*(blk_size*blk_size))* + (buf_size/blk_size*snbytes/blk_size*(blk_size*blk_size))+ + ((nbytes_xfer/(buf_size/blk_size))*pio_mpi_nprocs_g)%(snbytes + /blk_size*(blk_size*blk_size)); */ + mpi_offset = mpi_file_offset + + (MPI_Offset)((((size_t)nbytes_xfer / (buf_size / blk_size) * + (size_t)pio_mpi_nprocs_g) / + ((size_t)snbytes * blk_size)) * + (buf_size * (size_t)snbytes)) + + (MPI_Offset)((((size_t)nbytes_xfer / (buf_size / blk_size)) * + (size_t)pio_mpi_nprocs_g) % + ((size_t)snbytes * blk_size)); + + /* Number of bytes to be transferred per I/O operation */ + nbytes_xfer_advance = blk_size * blk_size; + + /* Global offset advance after each I/O operation */ + /* mpi_offset_advance = (MPI_Offset)(snbytes/blk_size*(blk_size*blk_size)); */ + mpi_offset_advance = (MPI_Offset)((size_t)snbytes * blk_size); + + /* MPI type to be used for collective access */ + mpi_collective_type = mpi_chunk_inter_type; + } /* end else */ + } /* end else */ + + /* Common code for independent file access */ + if (!parms->collective) { + /* Set the base of user's buffer */ + buf_p = (unsigned char *)buffer; + + /* Set the number of bytes to transfer this time */ + nbytes_toxfer = buf_size * blk_size; + + /* Loop over portions of the buffer to read */ + while (nbytes_toxfer > 0) { + /* Perform independent read */ + mrc = MPI_File_read_at(fd->mpifd, mpi_offset, buf_p, (int)nbytes_xfer_advance, + MPI_BYTE, &mpi_status); + VRFY((mrc == MPI_SUCCESS), "MPIO_READ"); + + /* Advance location in buffer */ + buf_p += nbytes_xfer_advance; + + /* Advance global offset in dataset */ + nbytes_xfer += (off_t)nbytes_xfer_advance; + + /* Decrement number of bytes left this time */ + nbytes_toxfer -= nbytes_xfer_advance; + + /* Partially advance global offset in dataset */ + mpi_offset += mpi_offset_advance; + } /* end while */ + } /* end if */ + + /* Common code for collective file access */ + else { + /* Set the file view */ + mrc = MPI_File_set_view(fd->mpifd, mpi_offset, MPI_BYTE, mpi_collective_type, + "native", h5_io_info_g); + VRFY((mrc == MPI_SUCCESS), "MPIO_VIEW"); + + /* Perform read */ + MPI_File_read_at_all(fd->mpifd, 0, buffer, (int)(buf_size * blk_size), MPI_BYTE, + &mpi_status); + VRFY((mrc == MPI_SUCCESS), "MPIO_READ"); + + /* Advance global offset in dataset */ + nbytes_xfer += (off_t)buf_size * (off_t)blk_size; + } /* end else */ + + } /* end else */ + break; + + case PHDF5: + /* 1D dataspace */ + if (!parms->dim2d) { + /* Set up the file dset space id to move the selection to process */ + if (!parms->interleaved) { + /* Contiguous pattern */ + h5offset[0] = nbytes_xfer; + } /* end if */ + else { + /* Interleaved access pattern */ + /* Skip offset over blocks of other processes */ + h5offset[0] = (nbytes_xfer * pio_mpi_nprocs_g); + } /* end else */ + hrc = H5Soffset_simple(h5dset_space_id, h5offset); + VRFY((hrc >= 0), "H5Soffset_simple"); + + /* Read the buffer in */ + hrc = H5Dread(h5ds_id, ELMT_H5_TYPE, h5mem_space_id, h5dset_space_id, h5dxpl, buffer); + VRFY((hrc >= 0), "H5Dread"); + + /* Increment number of bytes transferred */ + nbytes_xfer += (off_t)buf_size; + } /* end if */ + /* 2D dataspace */ + else { + /* Set up the file dset space id to move the selection to process */ + if (!parms->interleaved) { + /* Contiguous pattern */ + h5offset[0] = + (hssize_t)(((size_t)nbytes_xfer / ((size_t)snbytes * blk_size)) * blk_size); + h5offset[1] = + (hssize_t)(((size_t)nbytes_xfer % ((size_t)snbytes * blk_size)) / blk_size); + } /* end if */ + else { + /* Interleaved access pattern */ + /* Skip offset over blocks of other processes */ + h5offset[0] = (hssize_t)((((size_t)nbytes_xfer * (size_t)pio_mpi_nprocs_g) / + ((size_t)snbytes * buf_size)) * + buf_size); + h5offset[1] = (hssize_t)((((size_t)nbytes_xfer * (size_t)pio_mpi_nprocs_g) % + ((size_t)snbytes * buf_size)) / + buf_size); + + } /* end else */ + hrc = H5Soffset_simple(h5dset_space_id, h5offset); + VRFY((hrc >= 0), "H5Soffset_simple"); + + /* Write the buffer out */ + hrc = H5Dread(h5ds_id, ELMT_H5_TYPE, h5mem_space_id, h5dset_space_id, h5dxpl, buffer); + VRFY((hrc >= 0), "H5Dread"); + + /* Increment number of bytes transferred */ + nbytes_xfer += (off_t)buf_size * (off_t)blk_size; + + } /* end else */ + break; + + default: + break; + } /* switch (parms->io_type) */ + + /* Verify raw data, if asked */ + if (parms->verify) { + /* Verify data read */ + unsigned char *ucharptr = (unsigned char *)buffer; + size_t i; + int nerror = 0; + + for (i = 0; i < bsize; ++i) { + if (*ucharptr++ != pio_mpi_rank_g + 1) { + if (++nerror < 20) { + /* report at most 20 errors */ + HDprint_rank(output); + HDfprintf(output, + "read data error, expected (%d), " + "got (%d)\n", + pio_mpi_rank_g + 1, (int)*(ucharptr - 1)); + } /* end if */ + } /* end if */ + } /* end for */ + if (nerror >= 20) { + HDprint_rank(output); + HDfprintf(output, "..."); + HDfprintf(output, "total read data errors=%d\n", nerror); + } /* end if */ + } /* if (parms->verify) */ + + } /* end while */ + + /* Stop "raw data" read timer */ + io_time_set(res->timers, HDF5_RAW_READ_FIXED_DIMS, TSTOP); + + /* Calculate read time */ + + /* Close dataset. Only HDF5 needs to do an explicit close. */ + if (parms->io_type == PHDF5) { + hrc = H5Dclose(h5ds_id); + + if (hrc < 0) { + HDfprintf(stderr, "HDF5 Dataset Close failed\n"); + GOTOERROR(FAIL); + } + + h5ds_id = H5I_INVALID_HID; + } /* end if */ + } /* end for */ + +done: + /* release MPI-I/O objects */ + if (parms->io_type == MPIO) { + /* 1D dataspace */ + if (!parms->dim2d) { + /* Free file type */ + mrc = MPI_Type_free(&mpi_file_type); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_FREE"); + + /* Free buffer type */ + mrc = MPI_Type_free(&mpi_blk_type); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_FREE"); + } /* end if */ + /* 2D dataspace */ + else { + /* Free partial buffer type for contiguous access */ + mrc = MPI_Type_free(&mpi_partial_buffer_cont); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_FREE"); + + /* Free contiguous file type */ + mrc = MPI_Type_free(&mpi_cont_type); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_FREE"); + + /* Free partial buffer type for interleaved access */ + mrc = MPI_Type_free(&mpi_partial_buffer_inter); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_FREE"); + + /* Free interleaved file type */ + mrc = MPI_Type_free(&mpi_inter_type); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_FREE"); + + /* Free full buffer type */ + mrc = MPI_Type_free(&mpi_full_buffer); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_FREE"); + + /* Free full chunk type */ + mrc = MPI_Type_free(&mpi_full_chunk); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_FREE"); + + /* Free chunk interleaved file type */ + mrc = MPI_Type_free(&mpi_chunk_inter_type); + VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_FREE"); + } /* end else */ + } /* end if */ + + /* release HDF5 objects */ + if (h5dset_space_id != -1) { + hrc = H5Sclose(h5dset_space_id); + if (hrc < 0) { + HDfprintf(stderr, "HDF5 Dataset Space Close failed\n"); + ret_code = FAIL; + } + else { + h5dset_space_id = H5I_INVALID_HID; + } + } + + if (h5mem_space_id != -1) { + hrc = H5Sclose(h5mem_space_id); + if (hrc < 0) { + HDfprintf(stderr, "HDF5 Memory Space Close failed\n"); + ret_code = FAIL; + } + else { + h5mem_space_id = H5I_INVALID_HID; + } + } + + if (h5dxpl != -1) { + hrc = H5Pclose(h5dxpl); + if (hrc < 0) { + HDfprintf(stderr, "HDF5 Dataset Transfer Property List Close failed\n"); + ret_code = FAIL; + } + else { + h5dxpl = H5I_INVALID_HID; + } + } + + return ret_code; +} + +/* + * Function: do_fopen + * Purpose: Open the specified file. + * Return: SUCCESS or FAIL + * Programmer: Albert Cheng, Bill Wendling, 2001/12/13 + * Modifications: + */ +static herr_t +do_fopen(parameters *param, char *fname, file_descr *fd /*out*/, int flags) +{ + int ret_code = SUCCESS, mrc; + hid_t acc_tpl = H5I_INVALID_HID; /* file access templates */ + + switch (param->io_type) { + case POSIXIO: + if (flags & (PIO_CREATE | PIO_WRITE)) + fd->posixfd = POSIXCREATE(fname); + else + fd->posixfd = POSIXOPEN(fname, O_RDONLY); + + if (fd->posixfd < 0) { + HDfprintf(stderr, "POSIX File Open failed(%s)\n", fname); + GOTOERROR(FAIL); + } + + /* The perils of POSIX I/O in a parallel environment. The problem is: + * + * - Process n opens a file with truncation and then starts + * writing to the file. + * - Process m also opens the file with truncation, but after + * process n has already started to write to the file. Thus, + * all of the stuff process n wrote is now lost. + */ + MPI_Barrier(pio_comm_g); + + break; + + case MPIO: + if (flags & (PIO_CREATE | PIO_WRITE)) { + MPI_File_delete(fname, h5_io_info_g); + mrc = MPI_File_open(pio_comm_g, fname, MPI_MODE_CREATE | MPI_MODE_RDWR, h5_io_info_g, + &fd->mpifd); + + if (mrc != MPI_SUCCESS) { + HDfprintf(stderr, "MPI File Open failed(%s)\n", fname); + GOTOERROR(FAIL); + } + + /*since MPI_File_open with MPI_MODE_CREATE does not truncate */ + /*filesize , set size to 0 explicitedly. */ + mrc = MPI_File_set_size(fd->mpifd, (MPI_Offset)0); + if (mrc != MPI_SUCCESS) { + HDfprintf(stderr, "MPI_File_set_size failed\n"); + GOTOERROR(FAIL); + } + } + else { + mrc = MPI_File_open(pio_comm_g, fname, MPI_MODE_RDONLY, h5_io_info_g, &fd->mpifd); + if (mrc != MPI_SUCCESS) { + HDfprintf(stderr, "MPI File Open failed(%s)\n", fname); + GOTOERROR(FAIL); + } + } + + break; + + case PHDF5: + if ((acc_tpl = H5Pcreate(H5P_FILE_ACCESS)) < 0) { + HDfprintf(stderr, "HDF5 Property List Create failed\n"); + GOTOERROR(FAIL); + } + + /* Set the file driver to the MPI-IO driver */ + if (H5Pset_fapl_mpio(acc_tpl, pio_comm_g, h5_io_info_g) < 0) { + HDfprintf(stderr, "HDF5 Property List Set failed\n"); + GOTOERROR(FAIL); + } + + /* Set the alignment of objects in HDF5 file */ + if (H5Pset_alignment(acc_tpl, param->h5_thresh, param->h5_align) < 0) { + HDfprintf(stderr, "HDF5 Property List Set failed\n"); + GOTOERROR(FAIL); + } + + /* create the parallel file */ + if (flags & (PIO_CREATE | PIO_WRITE)) + fd->h5fd = H5Fcreate(fname, H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl); + else + fd->h5fd = H5Fopen(fname, H5F_ACC_RDONLY, acc_tpl); + if (fd->h5fd < 0) { + HDfprintf(stderr, "HDF5 File Create failed(%s)\n", fname); + GOTOERROR(FAIL); + } + + /* verifying the close of the acc_tpl */ + if (H5Pclose(acc_tpl) < 0) { + HDfprintf(stderr, "HDF5 Property List Close failed\n"); + GOTOERROR(FAIL); + } + + break; + + default: + break; + } + +done: + return ret_code; +} + +/* + * Function: do_fclose + * Purpose: Close the specified file descriptor. + * Return: SUCCESS or FAIL + * Programmer: Albert Cheng, Bill Wendling, 2001/12/13 + * Modifications: + */ +static herr_t +do_fclose(iotype iot, file_descr *fd /*out*/) +{ + herr_t ret_code = SUCCESS, hrc; + int mrc = 0, rc = 0; + + switch (iot) { + case POSIXIO: + rc = POSIXCLOSE(fd->posixfd); + + if (rc != 0) { + HDfprintf(stderr, "POSIX File Close failed\n"); + GOTOERROR(FAIL); + } + + fd->posixfd = -1; + break; + + case MPIO: + mrc = MPI_File_close(&fd->mpifd); + + if (mrc != MPI_SUCCESS) { + HDfprintf(stderr, "MPI File close failed\n"); + GOTOERROR(FAIL); + } + + fd->mpifd = MPI_FILE_NULL; + break; + + case PHDF5: + hrc = H5Fclose(fd->h5fd); + + if (hrc < 0) { + HDfprintf(stderr, "HDF5 File Close failed\n"); + GOTOERROR(FAIL); + } + + fd->h5fd = -1; + break; + + default: + break; + } + +done: + return ret_code; +} + +/* + * Function: do_fclose + * Purpose: Cleanup temporary file unless HDF5_NOCLEANUP is set. + * Only Proc 0 of the PIO communicator will do the cleanup. + * Other processes just return. + * Return: void + * Programmer: Albert Cheng 2001/12/12 + * Modifications: + */ +static void +do_cleanupfile(iotype iot, char *fname) +{ + if (pio_mpi_rank_g != 0) + return; + + if (clean_file_g == -1) + clean_file_g = (getenv(HDF5_NOCLEANUP) == NULL) ? 1 : 0; + + if (clean_file_g) { + switch (iot) { + case POSIXIO: + HDremove(fname); + break; + case MPIO: + case PHDF5: + MPI_File_delete(fname, h5_io_info_g); + break; + default: + break; + } + } +} + +#ifdef TIME_MPI +/* instrument the MPI_File_wrirte_xxx and read_xxx calls to measure + * pure time spent in MPI_File code. + */ +int +MPI_File_read_at(MPI_File fh, MPI_Offset offset, void *buf, int count, MPI_Datatype datatype, + MPI_Status *status) +{ + int err; + io_time_set(timer_g, HDF5_MPI_READ, TSTART); + err = PMPI_File_read_at(fh, offset, buf, count, datatype, status); + io_time_set(timer_g, HDF5_MPI_READ, TSTOP); + return err; +} + +int +MPI_File_read_at_all(MPI_File fh, MPI_Offset offset, void *buf, int count, MPI_Datatype datatype, + MPI_Status *status) +{ + int err; + io_time_set(timer_g, HDF5_MPI_READ, TSTART); + err = PMPI_File_read_at_all(fh, offset, buf, count, datatype, status); + io_time_set(timer_g, HDF5_MPI_READ, TSTOP); + return err; +} + +int +MPI_File_write_at(MPI_File fh, MPI_Offset offset, void *buf, int count, MPI_Datatype datatype, + MPI_Status *status) +{ + int err; + io_time_set(timer_g, HDF5_MPI_WRITE, TSTART); + err = PMPI_File_write_at(fh, offset, buf, count, datatype, status); + io_time_set(timer_g, HDF5_MPI_WRITE, TSTOP); + return err; +} + +int +MPI_File_write_at_all(MPI_File fh, MPI_Offset offset, void *buf, int count, MPI_Datatype datatype, + MPI_Status *status) +{ + int err; + io_time_set(timer_g, HDF5_MPI_WRITE, TSTART); + err = PMPI_File_write_at_all(fh, offset, buf, count, datatype, status); + io_time_set(timer_g, HDF5_MPI_WRITE, TSTOP); + return err; +} + +#endif /* TIME_MPI */ +#endif /* H5_HAVE_PARALLEL */ diff --git a/tools/src/h5perf/pio_perf.c b/tools/src/h5perf/pio_perf.c new file mode 100644 index 0000000..003c4f2 --- /dev/null +++ b/tools/src/h5perf/pio_perf.c @@ -0,0 +1,1717 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * Copyright by The HDF Group. * + * All rights reserved. * + * * + * This file is part of HDF5. The full HDF5 copyright notice, including * + * terms governing use, modification, and redistribution, is contained in * + * the COPYING file, which can be found at the root of the source code * + * distribution tree, or in https://www.hdfgroup.org/licenses. * + * If you do not have access to either file, you may request a copy from * + * help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + +/* + * Parallel HDF5 Performance Testing Code + * -------------------------------------- + * + * Portable code to test performance on the different platforms we support. + * This is what the report should look like: + * + * nprocs = Max#Procs + * IO API = POSIXIO + * # Files = 1, # of dsets = 1000, Elements per dset = 37000 + * Write Results = x MB/s + * Read Results = x MB/s + * # Files = 1, # of dsets = 3000, Elements per dset = 37000 + * Write Results = x MB/s + * Read Results = x MB/s + * + * . . . + * + * IO API = MPIO + * # Files = 1, # of dsets = 1000, Elements per dset = 37000 + * Write Results = x MB/s + * Read Results = x MB/s + * # Files = 1, # of dsets = 3000, Elements per dset = 37000 + * Write Results = x MB/s + * Read Results = x MB/s + * + * . . . + * + * IO API = PHDF5 + * # Files = 1, # of dsets = 1000, Elements per dset = 37000 + * Write Results = x MB/s + * Read Results = x MB/s + * # Files = 1, # of dsets = 3000, Elements per dset = 37000 + * Write Results = x MB/s + * Read Results = x MB/s + * + * . . . + * + * nprocs = Max#Procs / 2 + * + * . . . + * + */ + +/* system header files */ +#include <stdarg.h> +#include <stdio.h> +#include <stdlib.h> + +#include "hdf5.h" + +#ifdef H5_HAVE_PARALLEL + +/* library header files */ +#include <mpi.h> + +/* our header files */ +#include "pio_perf.h" + +/* useful macros */ +#define TAB_SPACE 4 + +#define ONE_KB 1024 +#define ONE_MB (ONE_KB * ONE_KB) +#define ONE_GB (ONE_MB * ONE_KB) + +#define PIO_POSIX 0x1 +#define PIO_MPI 0x2 +#define PIO_HDF5 0x4 + +#ifdef STANDALONE +#define DBL_EPSILON 2.2204460492503131e-16 +#define H5_DBL_ABS_EQUAL(X, Y) (fabs((X) - (Y)) < DBL_EPSILON) +#endif + +/* report 0.0 in case t is zero too */ +#define MB_PER_SEC(bytes, t) (H5_DBL_ABS_EQUAL((t), 0.0) ? 0.0 : ((((double)bytes) / ONE_MB) / (t))) + +#ifndef TRUE +#define TRUE 1 +#endif /* TRUE */ +#ifndef FALSE +#define FALSE (!TRUE) +#endif /* FALSE */ + +/* global variables */ +FILE * output; /* output file */ +int comm_world_rank_g; /* my rank in MPI_COMM_RANK */ +int comm_world_nprocs_g; /* num. of processes of MPI_COMM_WORLD */ +MPI_Comm pio_comm_g; /* Communicator to run the PIO */ +int pio_mpi_rank_g; /* MPI rank of pio_comm_g */ +int pio_mpi_nprocs_g; /* Number of processes of pio_comm_g */ +int pio_debug_level = 0; /* The debug level: + * 0 - Off + * 1 - Minimal + * 2 - Some more + * 3 - Maximal + * 4 - Maximal & then some + */ + +/* local variables */ +static const char *progname = "h5perf"; + +#ifndef HDF5_PARAPREFIX +#define HDF5_PARAPREFIX "" +#endif +char * paraprefix = NULL; /* for command line option para-prefix */ +MPI_Info h5_io_info_g = MPI_INFO_NULL; /* MPI INFO object for IO */ + +/* + * Command-line options: The user can specify short or long-named + * parameters. The long-named ones can be partially spelled. When + * adding more, make sure that they don't clash with each other. + */ +#if 1 +static const char *s_opts = "a:A:B:cCd:D:e:F:ghi:Imno:p:P:stT:wx:X:"; +#else +static const char *s_opts = "a:A:bB:cCd:D:e:F:ghi:Imno:p:P:stT:wx:X:"; +#endif /* 1 */ +static struct h5_long_options l_opts[] = {{"align", require_arg, 'a'}, + {"api", require_arg, 'A'}, +#if 0 + /* a sighting of the elusive binary option */ + { "binary", no_arg, 'b' }, +#endif /* 0 */ + {"block-size", require_arg, 'B'}, + {"chunk", no_arg, 'c'}, + {"collective", no_arg, 'C'}, + {"debug", require_arg, 'D'}, + {"geometry", no_arg, 'g'}, + {"help", no_arg, 'h'}, + {"interleaved", require_arg, 'I'}, + {"max-num-processes", require_arg, 'P'}, + {"min-num-processes", require_arg, 'p'}, + {"max-xfer-size", require_arg, 'X'}, + {"min-xfer-size", require_arg, 'x'}, + {"num-bytes", require_arg, 'e'}, + {"num-dsets", require_arg, 'd'}, + {"num-files", require_arg, 'F'}, + {"num-iterations", require_arg, 'i'}, + {"output", require_arg, 'o'}, + {"threshold", require_arg, 'T'}, + {"write-only", require_arg, 'w'}, + {NULL, 0, '\0'}}; + +struct options { + long io_types; /* bitmask of which I/O types to test */ + const char *output_file; /* file to print report to */ + long num_dsets; /* number of datasets */ + long num_files; /* number of files */ + off_t num_bpp; /* number of bytes per proc per dset */ + int num_iters; /* number of iterations */ + int max_num_procs; /* maximum number of processes to use */ + int min_num_procs; /* minimum number of processes to use */ + size_t max_xfer_size; /* maximum transfer buffer size */ + size_t min_xfer_size; /* minimum transfer buffer size */ + size_t blk_size; /* Block size */ + unsigned interleaved; /* Interleaved vs. contiguous blocks */ + unsigned collective; /* Collective vs. independent I/O */ + unsigned dim2d; /* 1D vs. 2D geometry */ + int print_times; /* print times as well as throughputs */ + int print_raw; /* print raw data throughput info */ + off_t h5_alignment; /* alignment in HDF5 file */ + off_t h5_threshold; /* threshold for alignment in HDF5 file */ + int h5_use_chunks; /* Make HDF5 dataset chunked */ + int h5_write_only; /* Perform the write tests only */ + int verify; /* Verify data correctness */ +}; + +typedef struct _minmax { + double min; + double max; + double sum; + int num; +} minmax; + +/* local functions */ +static off_t parse_size_directive(const char *size); +static struct options *parse_command_line(int argc, const char *const *argv); +static void run_test_loop(struct options *options); +static int run_test(iotype iot, parameters parms, struct options *opts); +static void output_all_info(minmax *mm, int count, int indent_level); +static void get_minmax(minmax *mm, double val); +static minmax accumulate_minmax_stuff(minmax *mm, int count); +static int create_comm_world(int num_procs, int *doing_pio); +static int destroy_comm_world(void); +static void output_results(const struct options *options, const char *name, minmax *table, int table_size, + off_t data_size); +static void output_times(const struct options *options, const char *name, minmax *table, int table_size); +static void output_report(const char *fmt, ...); +static void print_indent(int indent); +static void usage(const char *prog); +static void report_parameters(struct options *opts); +static off_t squareo(off_t); + +/* + * Function: main + * Purpose: Start things up. Initialize MPI and then call the test looping + * function. + * Return: EXIT_SUCCESS or EXIT_FAILURE + * Programmer: Bill Wendling, 30. October 2001 + * Modifications: + */ +int +main(int argc, char *argv[]) +{ + int ret; + int exit_value = EXIT_SUCCESS; + struct options *opts = NULL; + +#ifndef STANDALONE + /* Initialize h5tools lib */ + h5tools_init(); +#endif + + output = stdout; + + /* initialize MPI and get the maximum num of processors we started with */ + MPI_Init(&argc, &argv); + ret = MPI_Comm_size(MPI_COMM_WORLD, &comm_world_nprocs_g); + + if (ret != MPI_SUCCESS) { + HDfprintf(stderr, "%s: MPI_Comm_size call failed\n", progname); + + if (ret == MPI_ERR_COMM) + HDfprintf(stderr, "invalid MPI communicator\n"); + else + HDfprintf(stderr, "invalid argument\n"); + + exit_value = EXIT_FAILURE; + goto finish; + } + + ret = MPI_Comm_rank(MPI_COMM_WORLD, &comm_world_rank_g); + + if (ret != MPI_SUCCESS) { + HDfprintf(stderr, "%s: MPI_Comm_rank call failed\n", progname); + + if (ret == MPI_ERR_COMM) + HDfprintf(stderr, "invalid MPI communicator\n"); + else + HDfprintf(stderr, "invalid argument\n"); + + exit_value = EXIT_FAILURE; + goto finish; + } + + pio_comm_g = MPI_COMM_WORLD; + + h5_set_info_object(); + opts = parse_command_line(argc, (const char *const *)argv); + + if (!opts) { + exit_value = EXIT_FAILURE; + goto finish; + } + + if (opts->output_file) { + if ((output = HDfopen(opts->output_file, "w")) == NULL) { + HDfprintf(stderr, "%s: cannot open output file\n", progname); + perror(opts->output_file); + goto finish; + } + } + + if ((pio_debug_level == 0 && comm_world_rank_g == 0) || pio_debug_level > 0) + report_parameters(opts); + + run_test_loop(opts); + +finish: + MPI_Finalize(); + free(opts); + return exit_value; +} + +off_t +squareo(off_t x) +{ + return x * x; +} + +/* + * Function: run_test_loop + * Purpose: Run the I/O tests. Write the results to OUTPUT. + * + * - The slowest changing part of the test is the number of + * processors to use. For each loop iteration, we divide that + * number by 2 and rerun the test. + * + * - The second slowest is what type of IO API to perform. We have + * three choices: POSIXIO, MPI-IO, and PHDF5. + * + * - Then we change the size of the buffer. This information is + * inferred from the number of datasets to create and the number + * of integers to put into each dataset. The backend code figures + * this out. + * + * Return: Nothing + * Programmer: Bill Wendling, 30. October 2001 + * Modifications: + * Added 2D testing (Christian Chilan, 10. August 2005) + */ +static void +run_test_loop(struct options *opts) +{ + parameters parms; + int num_procs; + int doing_pio; /* if this process is doing PIO */ + + parms.num_files = opts->num_files; + parms.num_dsets = opts->num_dsets; + parms.num_iters = opts->num_iters; + parms.blk_size = opts->blk_size; + parms.interleaved = opts->interleaved; + parms.collective = opts->collective; + parms.dim2d = opts->dim2d; + parms.h5_align = (hsize_t)opts->h5_alignment; + parms.h5_thresh = (hsize_t)opts->h5_threshold; + parms.h5_use_chunks = opts->h5_use_chunks; + parms.h5_write_only = opts->h5_write_only; + parms.verify = opts->verify; + + /* start with max_num_procs and decrement it by half for each loop. */ + /* if performance needs restart, fewer processes may be needed. */ + for (num_procs = opts->max_num_procs; num_procs >= opts->min_num_procs; num_procs >>= 1) { + size_t buf_size; + + parms.num_procs = num_procs; + + if (create_comm_world(parms.num_procs, &doing_pio) != SUCCESS) { + /* do something harsh */ + } + + /* only processes doing PIO will run the tests */ + if (doing_pio) { + output_report("Number of processors = %ld\n", parms.num_procs); + + /* multiply the xfer buffer size by 2 for each loop iteration */ + for (buf_size = opts->min_xfer_size; buf_size <= opts->max_xfer_size; buf_size <<= 1) { + parms.buf_size = buf_size; + + if (parms.dim2d) { + parms.num_bytes = squareo(opts->num_bpp * parms.num_procs); + if (parms.interleaved) + output_report("Transfer Buffer Size: %ldx%ld bytes, File size: %.2f MB\n", buf_size, + opts->blk_size, + ((double)parms.num_dsets * (double)parms.num_bytes) / ONE_MB); + else + output_report("Transfer Buffer Size: %ldx%ld bytes, File size: %.2f MB\n", + opts->blk_size, buf_size, + ((double)parms.num_dsets * (double)parms.num_bytes) / ONE_MB); + + print_indent(1); + output_report(" # of files: %ld, # of datasets: %ld, dataset size: %.2fx%.2f KB\n", + parms.num_files, parms.num_dsets, + (double)(opts->num_bpp * parms.num_procs) / ONE_KB, + (double)(opts->num_bpp * parms.num_procs) / ONE_KB); + } + else { + parms.num_bytes = (off_t)opts->num_bpp * parms.num_procs; + output_report("Transfer Buffer Size: %ld bytes, File size: %.2f MB\n", buf_size, + ((double)parms.num_dsets * (double)parms.num_bytes) / ONE_MB); + + print_indent(1); + output_report(" # of files: %ld, # of datasets: %ld, dataset size: %.2f MB\n", + parms.num_files, parms.num_dsets, + (double)(opts->num_bpp * parms.num_procs) / ONE_MB); + } + + if (opts->io_types & PIO_POSIX) + run_test(POSIXIO, parms, opts); + + if (opts->io_types & PIO_MPI) + run_test(MPIO, parms, opts); + + if (opts->io_types & PIO_HDF5) + run_test(PHDF5, parms, opts); + + /* Run the tests once if buf_size==0, but then break out */ + if (buf_size == 0) + break; + } + + if (destroy_comm_world() != SUCCESS) { + /* do something harsh */ + } + } + } +} + +/* + * Function: run_test + * Purpose: Inner loop call to actually run the I/O test. + * Return: Nothing + * Programmer: Bill Wendling, 18. December 2001 + * Modifications: + */ +static int +run_test(iotype iot, parameters parms, struct options *opts) +{ + results res; + int i, ret_value = SUCCESS; + int comm_size; + off_t raw_size; + minmax *write_mpi_mm_table = NULL; + minmax *write_mm_table = NULL; + minmax *write_gross_mm_table = NULL; + minmax *write_raw_mm_table = NULL; + minmax *read_mpi_mm_table = NULL; + minmax *read_mm_table = NULL; + minmax *read_gross_mm_table = NULL; + minmax *read_raw_mm_table = NULL; + minmax *read_open_mm_table = NULL; + minmax *read_close_mm_table = NULL; + minmax *write_open_mm_table = NULL; + minmax *write_close_mm_table = NULL; + minmax write_mpi_mm = {0.0, 0.0, 0.0, 0}; + minmax write_mm = {0.0, 0.0, 0.0, 0}; + minmax write_gross_mm = {0.0, 0.0, 0.0, 0}; + minmax write_raw_mm = {0.0, 0.0, 0.0, 0}; + minmax read_mpi_mm = {0.0, 0.0, 0.0, 0}; + minmax read_mm = {0.0, 0.0, 0.0, 0}; + minmax read_gross_mm = {0.0, 0.0, 0.0, 0}; + minmax read_raw_mm = {0.0, 0.0, 0.0, 0}; + minmax read_open_mm = {0.0, 0.0, 0.0, 0}; + minmax read_close_mm = {0.0, 0.0, 0.0, 0}; + minmax write_open_mm = {0.0, 0.0, 0.0, 0}; + minmax write_close_mm = {0.0, 0.0, 0.0, 0}; + + raw_size = parms.num_files * (off_t)parms.num_dsets * (off_t)parms.num_bytes; + parms.io_type = iot; + print_indent(2); + output_report("IO API = "); + + switch (iot) { + case POSIXIO: + output_report("POSIX\n"); + break; + case MPIO: + output_report("MPIO\n"); + break; + case PHDF5: + output_report("PHDF5 (w/MPI-IO driver)\n"); + break; + default: + break; + } + + MPI_Comm_size(pio_comm_g, &comm_size); + + /* allocate space for tables minmax and that it is sufficient */ + /* to initialize all elements to zeros by calloc. */ + write_mpi_mm_table = calloc((size_t)parms.num_iters, sizeof(minmax)); + write_mm_table = calloc((size_t)parms.num_iters, sizeof(minmax)); + write_gross_mm_table = calloc((size_t)parms.num_iters, sizeof(minmax)); + write_raw_mm_table = calloc((size_t)parms.num_iters, sizeof(minmax)); + write_open_mm_table = calloc((size_t)parms.num_iters, sizeof(minmax)); + write_close_mm_table = calloc((size_t)parms.num_iters, sizeof(minmax)); + if (!parms.h5_write_only) { + read_mpi_mm_table = calloc((size_t)parms.num_iters, sizeof(minmax)); + read_mm_table = calloc((size_t)parms.num_iters, sizeof(minmax)); + read_gross_mm_table = calloc((size_t)parms.num_iters, sizeof(minmax)); + read_raw_mm_table = calloc((size_t)parms.num_iters, sizeof(minmax)); + read_open_mm_table = calloc((size_t)parms.num_iters, sizeof(minmax)); + read_close_mm_table = calloc((size_t)parms.num_iters, sizeof(minmax)); + } + + /* Do IO iteration times, collecting statistics each time */ + for (i = 0; i < parms.num_iters; ++i) { + double t; + + MPI_Barrier(pio_comm_g); + res = do_pio(parms); + + /* gather all of the "mpi write" times */ + t = io_time_get(res.timers, HDF5_MPI_WRITE); + get_minmax(&write_mpi_mm, t); + + write_mpi_mm_table[i] = write_mpi_mm; + + /* gather all of the "write" times */ + t = io_time_get(res.timers, HDF5_FINE_WRITE_FIXED_DIMS); + get_minmax(&write_mm, t); + + write_mm_table[i] = write_mm; + + /* gather all of the "write" times from open to close */ + t = io_time_get(res.timers, HDF5_GROSS_WRITE_FIXED_DIMS); + get_minmax(&write_gross_mm, t); + + write_gross_mm_table[i] = write_gross_mm; + + /* gather all of the raw "write" times */ + t = io_time_get(res.timers, HDF5_RAW_WRITE_FIXED_DIMS); + get_minmax(&write_raw_mm, t); + + write_raw_mm_table[i] = write_raw_mm; + + /* gather all of the file open times (time from open to first write) */ + t = io_time_get(res.timers, HDF5_FILE_WRITE_OPEN); + get_minmax(&write_open_mm, t); + + write_open_mm_table[i] = write_open_mm; + + /* gather all of the file close times (time from last write to close) */ + t = io_time_get(res.timers, HDF5_FILE_WRITE_CLOSE); + get_minmax(&write_close_mm, t); + + write_close_mm_table[i] = write_close_mm; + + if (!parms.h5_write_only) { + /* gather all of the "mpi read" times */ + t = io_time_get(res.timers, HDF5_MPI_READ); + get_minmax(&read_mpi_mm, t); + + read_mpi_mm_table[i] = read_mpi_mm; + + /* gather all of the "read" times */ + t = io_time_get(res.timers, HDF5_FINE_READ_FIXED_DIMS); + get_minmax(&read_mm, t); + + read_mm_table[i] = read_mm; + + /* gather all of the "read" times from open to close */ + t = io_time_get(res.timers, HDF5_GROSS_READ_FIXED_DIMS); + get_minmax(&read_gross_mm, t); + + read_gross_mm_table[i] = read_gross_mm; + + /* gather all of the raw "read" times */ + t = io_time_get(res.timers, HDF5_RAW_READ_FIXED_DIMS); + get_minmax(&read_raw_mm, t); + + read_raw_mm_table[i] = read_raw_mm; + + /* gather all of the file open times (time from open to first read) */ + t = io_time_get(res.timers, HDF5_FILE_READ_OPEN); + get_minmax(&read_open_mm, t); + + read_open_mm_table[i] = read_open_mm; + + /* gather all of the file close times (time from last read to close) */ + t = io_time_get(res.timers, HDF5_FILE_READ_CLOSE); + get_minmax(&read_close_mm, t); + + read_close_mm_table[i] = read_close_mm; + } + + io_time_destroy(res.timers); + } + + /* + * Show various statistics + */ + /* Write statistics */ + /* Print the raw data throughput if desired */ + if (opts->print_raw) { + /* accumulate and output the max, min, and average "raw write" times */ + if (pio_debug_level >= 3) { + /* output all of the times for all iterations */ + print_indent(3); + output_report("Raw Data Write details:\n"); + output_all_info(write_raw_mm_table, parms.num_iters, 4); + } + + output_results(opts, "Raw Data Write", write_raw_mm_table, parms.num_iters, raw_size); + } /* end if */ + + /* show mpi write statistics */ + if (pio_debug_level >= 3) { + /* output all of the times for all iterations */ + print_indent(3); + output_report("MPI Write details:\n"); + output_all_info(write_mpi_mm_table, parms.num_iters, 4); + } + + /* We don't currently output the MPI write results */ + + /* accumulate and output the max, min, and average "write" times */ + if (pio_debug_level >= 3) { + /* output all of the times for all iterations */ + print_indent(3); + output_report("Write details:\n"); + output_all_info(write_mm_table, parms.num_iters, 4); + } + + output_results(opts, "Write", write_mm_table, parms.num_iters, raw_size); + + /* accumulate and output the max, min, and average "gross write" times */ + if (pio_debug_level >= 3) { + /* output all of the times for all iterations */ + print_indent(3); + output_report("Write Open-Close details:\n"); + output_all_info(write_gross_mm_table, parms.num_iters, 4); + } + + output_results(opts, "Write Open-Close", write_gross_mm_table, parms.num_iters, raw_size); + + if (opts->print_times) { + output_times(opts, "Write File Open", write_open_mm_table, parms.num_iters); + output_times(opts, "Write File Close", write_close_mm_table, parms.num_iters); + } + + /* Print out time from open to first write */ + if (pio_debug_level >= 3) { + /* output all of the times for all iterations */ + print_indent(3); + output_report("Write file open details:\n"); + output_all_info(write_open_mm_table, parms.num_iters, 4); + } + + /* Print out time from last write to close */ + if (pio_debug_level >= 3) { + /* output all of the times for all iterations */ + print_indent(3); + output_report("Write file close details:\n"); + output_all_info(write_close_mm_table, parms.num_iters, 4); + } + + if (!parms.h5_write_only) { + /* Read statistics */ + /* Print the raw data throughput if desired */ + if (opts->print_raw) { + /* accumulate and output the max, min, and average "raw read" times */ + if (pio_debug_level >= 3) { + /* output all of the times for all iterations */ + print_indent(3); + output_report("Raw Data Read details:\n"); + output_all_info(read_raw_mm_table, parms.num_iters, 4); + } + + output_results(opts, "Raw Data Read", read_raw_mm_table, parms.num_iters, raw_size); + } /* end if */ + + /* show mpi read statistics */ + if (pio_debug_level >= 3) { + /* output all of the times for all iterations */ + print_indent(3); + output_report("MPI Read details:\n"); + output_all_info(read_mpi_mm_table, parms.num_iters, 4); + } + + /* We don't currently output the MPI read results */ + + /* accumulate and output the max, min, and average "read" times */ + if (pio_debug_level >= 3) { + /* output all of the times for all iterations */ + print_indent(3); + output_report("Read details:\n"); + output_all_info(read_mm_table, parms.num_iters, 4); + } + + output_results(opts, "Read", read_mm_table, parms.num_iters, raw_size); + + /* accumulate and output the max, min, and average "gross read" times */ + if (pio_debug_level >= 3) { + /* output all of the times for all iterations */ + print_indent(3); + output_report("Read Open-Close details:\n"); + output_all_info(read_gross_mm_table, parms.num_iters, 4); + } + + output_results(opts, "Read Open-Close", read_gross_mm_table, parms.num_iters, raw_size); + + if (opts->print_times) { + output_times(opts, "Read File Open", read_open_mm_table, parms.num_iters); + output_times(opts, "Read File Close", read_close_mm_table, parms.num_iters); + } + + /* Print out time from open to first read */ + if (pio_debug_level >= 3) { + /* output all of the times for all iterations */ + print_indent(3); + output_report("Read file open details:\n"); + output_all_info(read_open_mm_table, parms.num_iters, 4); + } + + /* Print out time from last read to close */ + if (pio_debug_level >= 3) { + /* output all of the times for all iterations */ + print_indent(3); + output_report("Read file close details:\n"); + output_all_info(read_close_mm_table, parms.num_iters, 4); + } + } + + /* clean up our mess */ + free(write_mpi_mm_table); + free(write_mm_table); + free(write_gross_mm_table); + free(write_raw_mm_table); + free(write_open_mm_table); + free(write_close_mm_table); + + if (!parms.h5_write_only) { + free(read_mpi_mm_table); + free(read_mm_table); + free(read_gross_mm_table); + free(read_raw_mm_table); + free(read_open_mm_table); + free(read_close_mm_table); + } + + return ret_value; +} + +/* + * Function: output_all_info + * Purpose: + * Return: Nothing + * Programmer: Bill Wendling, 29. January 2002 + * Modifications: + */ +static void +output_all_info(minmax *mm, int count, int indent_level) +{ + int i; + + for (i = 0; i < count; ++i) { + print_indent(indent_level); + output_report("Iteration %d:\n", i + 1); + print_indent(indent_level + 1); + output_report("Minimum Time: %.2fs\n", mm[i].min); + print_indent(indent_level + 1); + output_report("Maximum Time: %.2fs\n", mm[i].max); + } +} + +/* + * Function: h5_set_info_object + * Purpose: Process environment variables setting to set up MPI Info + * object. + * Return: 0 if all is fine; otherwise non-zero. + * Programmer: Albert Cheng, 2002/05/21. + * Modifications: + * Bill Wendling, 2002/05/31 + * Modified so that the HDF5_MPI_INFO environment variable can + * be a semicolon separated list of "key=value" pairings. Most + * of the code is to remove any whitespaces which might be + * surrounding the "key=value" pairs. + */ +int +h5_set_info_object(void) +{ + char *envp; /* environment pointer */ + int ret_value = 0; + + /* handle any MPI INFO hints via $HDF5_MPI_INFO */ + if ((envp = HDgetenv("HDF5_MPI_INFO")) != NULL) { + char *next, *valp; + + valp = envp = next = HDstrdup(envp); + + if (!valp) + return 0; + + /* create an INFO object if not created yet */ + if (h5_io_info_g == MPI_INFO_NULL) + MPI_Info_create(&h5_io_info_g); + + do { + size_t len; + char * key_val, *endp, *namep; + + if (*valp == ';') + valp++; + + /* copy key/value pair into temporary buffer */ + len = strcspn(valp, ";"); + next = &valp[len]; + key_val = (char *)HDcalloc(1, len + 1); + + /* increment the next pointer past the terminating semicolon */ + if (*next == ';') + ++next; + + namep = HDstrncpy(key_val, valp, len); + + /* pass up any beginning whitespaces */ + while (*namep && (*namep == ' ' || *namep == '\t')) + namep++; + + if (!*namep) + continue; /* was all white space, so move to next k/v pair */ + + /* eat up any ending white spaces */ + endp = &namep[HDstrlen(namep) - 1]; + + while (endp && (*endp == ' ' || *endp == '\t')) + *endp-- = '\0'; + + /* find the '=' */ + valp = HDstrchr(namep, '='); + + if (valp != NULL) { /* it's a valid key/value pairing */ + char *tmp_val = valp + 1; + + /* change '=' to \0, move valp down one */ + *valp-- = '\0'; + + /* eat up ending whitespace on the "key" part */ + while (*valp == ' ' || *valp == '\t') + *valp-- = '\0'; + + valp = tmp_val; + + /* eat up beginning whitespace on the "value" part */ + while (*valp == ' ' || *valp == '\t') + *valp++ = '\0'; + + /* actually set the darned thing */ + if (MPI_SUCCESS != MPI_Info_set(h5_io_info_g, namep, valp)) { + HDprintf("MPI_Info_set failed\n"); + ret_value = -1; + } + } + + valp = next; + HDfree(key_val); + } while (next && *next); + + HDfree(envp); + } + + return ret_value; +} + +/* + * Function: h5_dump_info_object + * Purpose: Display content of an MPI Info object + * Return: void + * Programmer: Albert Cheng 2002/05/21 + * Modifications: + */ +void +h5_dump_info_object(MPI_Info info) +{ + char key[MPI_MAX_INFO_KEY + 1]; + char value[MPI_MAX_INFO_VAL + 1]; + int flag; + int i, nkeys; + + HDprintf("Dumping MPI Info Object (up to %d bytes per item):\n", MPI_MAX_INFO_VAL); + if (info == MPI_INFO_NULL) { + HDprintf("object is MPI_INFO_NULL\n"); + } + else { + MPI_Info_get_nkeys(info, &nkeys); + HDprintf("object has %d items\n", nkeys); + for (i = 0; i < nkeys; i++) { + MPI_Info_get_nthkey(info, i, key); + MPI_Info_get(info, key, MPI_MAX_INFO_VAL, value, &flag); + HDprintf("%s=%s\n", key, value); + } + } +} + +/* + * Function: get_minmax + * Purpose: Gather all the min, max and total of val. + * Return: Nothing + * Programmer: Bill Wendling, 21. December 2001 + * Modifications: + * Use MPI_Allreduce to do it. -akc, 2002/01/11 + */ +static void +get_minmax(minmax *mm, double val) +{ + int myrank; + + MPI_Comm_rank(pio_comm_g, &myrank); + MPI_Comm_size(pio_comm_g, &mm->num); + + MPI_Allreduce(&val, &mm->max, 1, MPI_DOUBLE, MPI_MAX, pio_comm_g); + MPI_Allreduce(&val, &mm->min, 1, MPI_DOUBLE, MPI_MIN, pio_comm_g); + MPI_Allreduce(&val, &mm->sum, 1, MPI_DOUBLE, MPI_SUM, pio_comm_g); +} + +/* + * Function: accumulate_minmax_stuff + * Purpose: Accumulate the minimum, maximum, and average of the times + * across all processes. + * Return: TOTAL_MM - the total of all of these. + * Programmer: Bill Wendling, 21. December 2001 + * Modifications: + * Changed to use seconds instead of MB/s - QAK, 5/9/02 + */ +static minmax +accumulate_minmax_stuff(minmax *mm, int count) +{ + int i; + minmax total_mm; + + total_mm.sum = 0.0; + total_mm.max = -DBL_MAX; + total_mm.min = DBL_MAX; + total_mm.num = count; + + for (i = 0; i < count; ++i) { + double m = mm[i].max; + + total_mm.sum += m; + + if (m < total_mm.min) + total_mm.min = m; + + if (m > total_mm.max) + total_mm.max = m; + } + + return total_mm; +} + +/* + * Function: create_comm_world + * Purpose: Create an MPI Comm world and store it in pio_comm_g, which + * is a global variable. + * Return: SUCCESS on success. + * FAIL otherwise. + * Programmer: Bill Wendling, 19. December 2001 + * Modifications: + */ +static int +create_comm_world(int num_procs, int *doing_pio) +{ + /* MPI variables */ + int mrc; /* return values */ + int color; /* for communicator creation */ + int myrank, nprocs; + + pio_comm_g = MPI_COMM_NULL; + + /* + * Create a sub communicator for this PIO run. Easier to use the first N + * processes. + */ + MPI_Comm_size(MPI_COMM_WORLD, &nprocs); + + if (num_procs > nprocs) { + HDfprintf(stderr, "number of process(%d) must be <= number of processes in MPI_COMM_WORLD(%d)\n", + num_procs, nprocs); + goto error_done; + } + + MPI_Comm_rank(MPI_COMM_WORLD, &myrank); + color = (myrank < num_procs); + mrc = MPI_Comm_split(MPI_COMM_WORLD, color, myrank, &pio_comm_g); + + if (mrc != MPI_SUCCESS) { + HDfprintf(stderr, "MPI_Comm_split failed\n"); + goto error_done; + } + + if (!color) { + /* not involved in this run */ + mrc = destroy_comm_world(); + goto done; + } + + /* determine the MPI rank in the PIO communicator */ + MPI_Comm_size(pio_comm_g, &pio_mpi_nprocs_g); + MPI_Comm_rank(pio_comm_g, &pio_mpi_rank_g); + +done: + *doing_pio = color; + return SUCCESS; + +error_done: + destroy_comm_world(); + return FAIL; +} + +/* + * Function: destroy_comm_world + * Purpose: Destroy the created MPI Comm world which is stored in the + * pio_comm_g global variable. + * Return: SUCCESS on success. + * FAIL otherwise. + * Programmer: Bill Wendling, 19. December 2001 + * Modifications: + */ +static int +destroy_comm_world(void) +{ + int mrc = SUCCESS; /* return code */ + + /* release MPI resources */ + if (pio_comm_g != MPI_COMM_NULL) + mrc = (MPI_Comm_free(&pio_comm_g) == MPI_SUCCESS ? SUCCESS : FAIL); + + return mrc; +} + +/* + * Function: output_results + * Purpose: Print information about the time & bandwidth for a given + * minmax & # of iterations. + * Return: Nothing + * Programmer: Quincey Koziol, 9. May 2002 + * Modifications: + */ +static void +output_results(const struct options *opts, const char *name, minmax *table, int table_size, off_t data_size) +{ + minmax total_mm; + + total_mm = accumulate_minmax_stuff(table, table_size); + + print_indent(3); + output_report("%s (%d iteration(s)):\n", name, table_size); + + /* Note: The maximum throughput uses the minimum amount of time & vice versa */ + + print_indent(4); + output_report("Maximum Throughput: %6.2f MB/s", MB_PER_SEC(data_size, total_mm.min)); + if (opts->print_times) + output_report(" (%7.3f s)\n", total_mm.min); + else + output_report("\n"); + + print_indent(4); + output_report("Average Throughput: %6.2f MB/s", MB_PER_SEC(data_size, total_mm.sum / total_mm.num)); + if (opts->print_times) + output_report(" (%7.3f s)\n", (total_mm.sum / total_mm.num)); + else + output_report("\n"); + + print_indent(4); + output_report("Minimum Throughput: %6.2f MB/s", MB_PER_SEC(data_size, total_mm.max)); + if (opts->print_times) + output_report(" (%7.3f s)\n", total_mm.max); + else + output_report("\n"); +} + +static void +output_times(const struct options *opts, const char *name, minmax *table, int table_size) +{ + minmax total_mm; + + total_mm = accumulate_minmax_stuff(table, table_size); + + print_indent(3); + output_report("%s (%d iteration(s)):\n", name, table_size); + + /* Note: The maximum throughput uses the minimum amount of time & vice versa */ + + print_indent(4); + output_report("Minimum Accumulated Time using %d file(s): %7.5f s\n", opts->num_files, (total_mm.min)); + + print_indent(4); + output_report("Average Accumulated Time using %d file(s): %7.5f s\n", opts->num_files, + (total_mm.sum / total_mm.num)); + + print_indent(4); + output_report("Maximum Accumulated Time using %d file(s): %7.5f s\n", opts->num_files, (total_mm.max)); +} + +/* + * Function: output_report + * Purpose: Print a line of the report. Only do so if I'm the 0 process. + * Return: Nothing + * Programmer: Bill Wendling, 19. December 2001 + * Modifications: + */ +static void +output_report(const char *fmt, ...) +{ + int myrank; + + MPI_Comm_rank(pio_comm_g, &myrank); + + if (myrank == 0) { + va_list ap; + + HDva_start(ap, fmt); + HDvfprintf(output, fmt, ap); + HDva_end(ap); + } +} + +/* + * Function: print_indent + * Purpose: Print spaces to indent a new line of text for pretty printing + * things. + * Return: Nothing + * Programmer: Bill Wendling, 29. October 2001 + */ +static void +print_indent(int indent) +{ + int myrank; + + MPI_Comm_rank(pio_comm_g, &myrank); + + if (myrank == 0) { + indent *= TAB_SPACE; + + for (; indent > 0; --indent) + HDfputc(' ', output); + } +} + +static void +recover_size_and_print(long long val, const char *end) +{ + if (val >= ONE_KB && (val % ONE_KB) == 0) { + if (val >= ONE_MB && (val % ONE_MB) == 0) { + if (val >= ONE_GB && (val % ONE_GB) == 0) + HDfprintf(output, + "%" H5_PRINTF_LL_WIDTH "d" + "GB%s", + val / ONE_GB, end); + else + HDfprintf(output, + "%" H5_PRINTF_LL_WIDTH "d" + "MB%s", + val / ONE_MB, end); + } + else { + HDfprintf(output, + "%" H5_PRINTF_LL_WIDTH "d" + "KB%s", + val / ONE_KB, end); + } + } + else { + HDfprintf(output, + "%" H5_PRINTF_LL_WIDTH "d" + "%s", + val, end); + } +} + +static void +print_io_api(long io_types) +{ + if (io_types & PIO_POSIX) + HDfprintf(output, "posix "); + if (io_types & PIO_MPI) + HDfprintf(output, "mpiio "); + if (io_types & PIO_HDF5) + HDfprintf(output, "phdf5 "); + HDfprintf(output, "\n"); +} + +static void +report_parameters(struct options *opts) +{ + int rank = comm_world_rank_g; + + print_version("HDF5 Library"); /* print library version */ + HDfprintf(output, "rank %d: ==== Parameters ====\n", rank); + + HDfprintf(output, "rank %d: IO API=", rank); + print_io_api(opts->io_types); + + HDfprintf(output, "rank %d: Number of files=%ld\n", rank, opts->num_files); + HDfprintf(output, "rank %d: Number of datasets=%ld\n", rank, opts->num_dsets); + HDfprintf(output, "rank %d: Number of iterations=%d\n", rank, opts->num_iters); + HDfprintf(output, "rank %d: Number of processes=%d:%d\n", rank, opts->min_num_procs, opts->max_num_procs); + + if (opts->dim2d) { + HDfprintf(output, "rank %d: Number of bytes per process per dataset=", rank); + recover_size_and_print((long long)(opts->num_bpp * opts->num_bpp * opts->min_num_procs), ":"); + recover_size_and_print((long long)(opts->num_bpp * opts->num_bpp * opts->max_num_procs), "\n"); + + HDfprintf(output, "rank %d: Size of dataset(s)=", rank); + recover_size_and_print((long long)(opts->num_bpp * opts->min_num_procs), "x"); + recover_size_and_print((long long)(opts->num_bpp * opts->min_num_procs), ":"); + recover_size_and_print((long long)(opts->num_bpp * opts->max_num_procs), "x"); + recover_size_and_print((long long)(opts->num_bpp * opts->max_num_procs), "\n"); + + HDfprintf(output, "rank %d: File size=", rank); + recover_size_and_print((long long)(squareo(opts->num_bpp * opts->min_num_procs) * opts->num_dsets), + ":"); + recover_size_and_print((long long)(squareo(opts->num_bpp * opts->max_num_procs) * opts->num_dsets), + "\n"); + + HDfprintf(output, "rank %d: Transfer buffer size=", rank); + if (opts->interleaved) { + recover_size_and_print((long long)opts->min_xfer_size, "x"); + recover_size_and_print((long long)opts->blk_size, ":"); + recover_size_and_print((long long)opts->max_xfer_size, "x"); + recover_size_and_print((long long)opts->blk_size, "\n"); + } + else { + recover_size_and_print((long long)opts->blk_size, "x"); + recover_size_and_print((long long)opts->min_xfer_size, ":"); + recover_size_and_print((long long)opts->blk_size, "x"); + recover_size_and_print((long long)opts->max_xfer_size, "\n"); + } + HDfprintf(output, "rank %d: Block size=", rank); + recover_size_and_print((long long)opts->blk_size, "x"); + recover_size_and_print((long long)opts->blk_size, "\n"); + } + else { + HDfprintf(output, "rank %d: Number of bytes per process per dataset=", rank); + recover_size_and_print((long long)opts->num_bpp, "\n"); + + HDfprintf(output, "rank %d: Size of dataset(s)=", rank); + recover_size_and_print((long long)(opts->num_bpp * opts->min_num_procs), ":"); + recover_size_and_print((long long)(opts->num_bpp * opts->max_num_procs), "\n"); + + HDfprintf(output, "rank %d: File size=", rank); + recover_size_and_print((long long)(opts->num_bpp * opts->min_num_procs * opts->num_dsets), ":"); + recover_size_and_print((long long)(opts->num_bpp * opts->max_num_procs * opts->num_dsets), "\n"); + + HDfprintf(output, "rank %d: Transfer buffer size=", rank); + recover_size_and_print((long long)opts->min_xfer_size, ":"); + recover_size_and_print((long long)opts->max_xfer_size, "\n"); + HDfprintf(output, "rank %d: Block size=", rank); + recover_size_and_print((long long)opts->blk_size, "\n"); + } + + HDfprintf(output, "rank %d: Block Pattern in Dataset=", rank); + if (opts->interleaved) + HDfprintf(output, "Interleaved\n"); + else + HDfprintf(output, "Contiguous\n"); + + HDfprintf(output, "rank %d: I/O Method for MPI and HDF5=", rank); + if (opts->collective) + HDfprintf(output, "Collective\n"); + else + HDfprintf(output, "Independent\n"); + + HDfprintf(output, "rank %d: Geometry=", rank); + if (opts->dim2d) + HDfprintf(output, "2D\n"); + else + HDfprintf(output, "1D\n"); + + HDfprintf(output, "rank %d: VFL used for HDF5 I/O=%s\n", rank, "MPI-IO driver"); + + HDfprintf(output, "rank %d: Data storage method in HDF5=", rank); + if (opts->h5_use_chunks) + HDfprintf(output, "Chunked\n"); + else + HDfprintf(output, "Contiguous\n"); + + { + char *prefix = HDgetenv("HDF5_PARAPREFIX"); + + HDfprintf(output, "rank %d: Env HDF5_PARAPREFIX=%s\n", rank, (prefix ? prefix : "not set")); + } + + HDfprintf(output, "rank %d: ", rank); + h5_dump_info_object(h5_io_info_g); + + HDfprintf(output, "rank %d: ==== End of Parameters ====\n", rank); + HDfprintf(output, "\n"); +} + +/* + * Function: parse_command_line + * Purpose: Parse the command line options and return a STRUCT OPTIONS + * structure which will need to be freed by the calling function. + * Return: Pointer to an OPTIONS structure + * Programmer: Bill Wendling, 31. October 2001 + * Modifications: + * Added 2D testing (Christian Chilan, 10. August 2005) + */ +static struct options * +parse_command_line(int argc, const char *const *argv) +{ + int opt; + struct options *cl_opts; + + cl_opts = (struct options *)malloc(sizeof(struct options)); + + cl_opts->output_file = NULL; + cl_opts->io_types = 0; /* will set default after parsing options */ + cl_opts->num_dsets = 1; + cl_opts->num_files = 1; + cl_opts->num_bpp = 0; + cl_opts->num_iters = 1; + cl_opts->max_num_procs = comm_world_nprocs_g; + cl_opts->min_num_procs = 1; + cl_opts->max_xfer_size = 0; + cl_opts->min_xfer_size = 0; + cl_opts->blk_size = 0; + cl_opts->interleaved = 0; /* Default to contiguous blocks in dataset */ + cl_opts->collective = 0; /* Default to independent I/O access */ + cl_opts->dim2d = 0; /* Default to 1D */ + cl_opts->print_times = FALSE; /* Printing times is off by default */ + cl_opts->print_raw = FALSE; /* Printing raw data throughput is off by default */ + cl_opts->h5_alignment = 1; /* No alignment for HDF5 objects by default */ + cl_opts->h5_threshold = 1; /* No threshold for aligning HDF5 objects by default */ + cl_opts->h5_use_chunks = FALSE; /* Don't chunk the HDF5 dataset by default */ + cl_opts->h5_write_only = FALSE; /* Do both read and write by default */ + cl_opts->verify = FALSE; /* No Verify data correctness by default */ + + while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) { + switch ((char)opt) { + case 'a': + cl_opts->h5_alignment = parse_size_directive(H5_optarg); + break; + case 'A': { + const char *end = H5_optarg; + + while (end && *end != '\0') { + char buf[10]; + int i; + + HDmemset(buf, '\0', sizeof(buf)); + + for (i = 0; *end != '\0' && *end != ','; ++end) + if (isalnum(*end) && i < 10) + buf[i++] = *end; + + if (!HDstrcasecmp(buf, "phdf5")) { + cl_opts->io_types |= PIO_HDF5; + } + else if (!HDstrcasecmp(buf, "mpiio")) { + cl_opts->io_types |= PIO_MPI; + } + else if (!HDstrcasecmp(buf, "posix")) { + cl_opts->io_types |= PIO_POSIX; + } + else { + HDfprintf(stderr, "pio_perf: invalid --api option %s\n", buf); + HDexit(EXIT_FAILURE); + } + + if (*end == '\0') + break; + + end++; + } + } + + break; +#if 0 + case 'b': + /* the future "binary" option */ + break; +#endif /* 0 */ + case 'B': + cl_opts->blk_size = (size_t)parse_size_directive(H5_optarg); + break; + case 'c': + /* Turn on chunked HDF5 dataset creation */ + cl_opts->h5_use_chunks = TRUE; + break; + case 'C': + cl_opts->collective = 1; + break; + case 'd': + cl_opts->num_dsets = atoi(H5_optarg); + break; + case 'D': { + const char *end = H5_optarg; + + while (end && *end != '\0') { + char buf[10]; + int i; + + HDmemset(buf, '\0', sizeof(buf)); + + for (i = 0; *end != '\0' && *end != ','; ++end) + if (HDisalnum(*end) && i < 10) + buf[i++] = *end; + + if (HDstrlen(buf) > 1 || HDisdigit(buf[0])) { + size_t j; + + for (j = 0; j < 10 && buf[j] != '\0'; ++j) + if (!isdigit(buf[j])) { + HDfprintf(stderr, "pio_perf: invalid --debug option %s\n", buf); + HDexit(EXIT_FAILURE); + } + + pio_debug_level = atoi(buf); + + if (pio_debug_level > 4) + pio_debug_level = 4; + else if (pio_debug_level < 0) + pio_debug_level = 0; + } + else { + switch (*buf) { + case 'r': + /* Turn on raw data throughput info */ + cl_opts->print_raw = TRUE; + break; + case 't': + /* Turn on time printing */ + cl_opts->print_times = TRUE; + break; + case 'v': + /* Turn on verify data correctness*/ + cl_opts->verify = TRUE; + break; + default: + HDfprintf(stderr, "pio_perf: invalid --debug option %s\n", buf); + HDexit(EXIT_FAILURE); + } + } + + if (*end == '\0') + break; + + end++; + } + } + + break; + case 'e': + cl_opts->num_bpp = parse_size_directive(H5_optarg); + break; + case 'F': + cl_opts->num_files = HDatoi(H5_optarg); + break; + case 'g': + cl_opts->dim2d = 1; + break; + case 'i': + cl_opts->num_iters = HDatoi(H5_optarg); + break; + case 'I': + cl_opts->interleaved = 1; + break; + case 'o': + cl_opts->output_file = H5_optarg; + break; + case 'p': + cl_opts->min_num_procs = HDatoi(H5_optarg); + break; + case 'P': + cl_opts->max_num_procs = HDatoi(H5_optarg); + break; + case 'T': + cl_opts->h5_threshold = parse_size_directive(H5_optarg); + break; + case 'w': + cl_opts->h5_write_only = TRUE; + break; + case 'x': + cl_opts->min_xfer_size = (size_t)parse_size_directive(H5_optarg); + break; + case 'X': + cl_opts->max_xfer_size = (size_t)parse_size_directive(H5_optarg); + break; + case 'h': + case '?': + default: + usage(progname); + HDfree(cl_opts); + return NULL; + } + } + + if (cl_opts->num_bpp == 0) { + if (cl_opts->dim2d == 0) + cl_opts->num_bpp = 256 * ONE_KB; + else + cl_opts->num_bpp = 8 * ONE_KB; + } + + if (cl_opts->max_xfer_size == 0) + cl_opts->max_xfer_size = (size_t)cl_opts->num_bpp; + + if (cl_opts->min_xfer_size == 0) + cl_opts->min_xfer_size = (size_t)(cl_opts->num_bpp) / 2; + + if (cl_opts->blk_size == 0) + cl_opts->blk_size = (size_t)(cl_opts->num_bpp) / 2; + + /* set default if none specified yet */ + if (!cl_opts->io_types) + cl_opts->io_types = PIO_HDF5 | PIO_MPI | PIO_POSIX; /* run all API */ + + /* verify parameters sanity. Adjust if needed. */ + /* cap xfer_size with bytes per process */ + if (!cl_opts->dim2d) { + if (cl_opts->min_xfer_size > (size_t)cl_opts->num_bpp) + cl_opts->min_xfer_size = (size_t)cl_opts->num_bpp; + if (cl_opts->max_xfer_size > (size_t)cl_opts->num_bpp) + cl_opts->max_xfer_size = (size_t)cl_opts->num_bpp; + } + if (cl_opts->min_xfer_size > cl_opts->max_xfer_size) + cl_opts->min_xfer_size = cl_opts->max_xfer_size; + if (cl_opts->blk_size > (size_t)cl_opts->num_bpp) + cl_opts->blk_size = (size_t)cl_opts->num_bpp; + /* check range of number of processes */ + if (cl_opts->min_num_procs <= 0) + cl_opts->min_num_procs = 1; + if (cl_opts->max_num_procs <= 0) + cl_opts->max_num_procs = 1; + if (cl_opts->min_num_procs > cl_opts->max_num_procs) + cl_opts->min_num_procs = cl_opts->max_num_procs; + /* check iteration */ + if (cl_opts->num_iters <= 0) + cl_opts->num_iters = 1; + + return cl_opts; +} + +/* + * Function: parse_size_directive + * Purpose: Parse the size directive passed on the commandline. The size + * directive is an integer followed by a size indicator: + * + * K, k - Kilobyte + * M, m - Megabyte + * G, g - Gigabyte + * + * Return: The size as a off_t because this is related to file size. + * If an unknown size indicator is used, then the program will + * exit with EXIT_FAILURE as the return value. + * Programmer: Bill Wendling, 18. December 2001 + * Modifications: + */ +static off_t +parse_size_directive(const char *size) +{ + off_t s; + char *endptr; + + s = HDstrtol(size, &endptr, 10); + + if (endptr && *endptr) { + while (*endptr != '\0' && (*endptr == ' ' || *endptr == '\t')) + ++endptr; + + switch (*endptr) { + case 'K': + case 'k': + s *= ONE_KB; + break; + case 'M': + case 'm': + s *= ONE_MB; + break; + case 'G': + case 'g': + s *= ONE_GB; + break; + default: + HDfprintf(stderr, "Illegal size specifier '%c'\n", *endptr); + HDexit(EXIT_FAILURE); + } + } + + return s; +} + +/* + * Function: usage + * Purpose: Print a usage message and then exit. + * Return: Nothing + * Programmer: Bill Wendling, 31. October 2001 + * Modifications: + * Added 2D testing (Christian Chilan, 10. August 2005) + */ +static void +usage(const char *prog) +{ + int myrank; + + MPI_Comm_rank(pio_comm_g, &myrank); + + if (myrank == 0) { + print_version(prog); + HDprintf("usage: %s [OPTIONS]\n", prog); + HDprintf(" OPTIONS\n"); + HDprintf(" -h, --help Print a usage message and exit\n"); + HDprintf(" -a S, --align=S Alignment of objects in HDF5 file [default: 1]\n"); + HDprintf(" -A AL, --api=AL Which APIs to test [default: all of them]\n"); +#if 0 + HDprintf(" -b, --binary The elusive binary option\n"); +#endif /* 0 */ + HDprintf(" -B S, --block-size=S Block size within transfer buffer\n"); + HDprintf(" (see below for description)\n"); + HDprintf(" [default: half the number of bytes per process\n"); + HDprintf(" per dataset]\n"); + HDprintf(" -c, --chunk Create HDF5 datasets using chunked storage\n"); + HDprintf(" [default: contiguous storage]\n"); + HDprintf(" -C, --collective Use collective I/O for MPI and HDF5 APIs\n"); + HDprintf(" [default: independent I/O)\n"); + HDprintf(" -d N, --num-dsets=N Number of datasets per file [default: 1]\n"); + HDprintf(" -D DL, --debug=DL Indicate the debugging level\n"); + HDprintf(" [default: no debugging]\n"); + HDprintf(" -e S, --num-bytes=S Number of bytes per process per dataset\n"); + HDprintf(" (see below for description)\n"); + HDprintf(" [default: 256K for 1D, 8K for 2D]\n"); + HDprintf(" -F N, --num-files=N Number of files [default: 1]\n"); + HDprintf(" -g, --geometry Use 2D geometry [default: 1D geometry]\n"); + HDprintf(" -i N, --num-iterations=N Number of iterations to perform [default: 1]\n"); + HDprintf(" -I, --interleaved Interleaved access pattern\n"); + HDprintf(" (see below for example)\n"); + HDprintf(" [default: Contiguous access pattern]\n"); + HDprintf(" -o F, --output=F Output raw data into file F [default: none]\n"); + HDprintf(" -p N, --min-num-processes=N Minimum number of processes to use [default: 1]\n"); + HDprintf(" -P N, --max-num-processes=N Maximum number of processes to use\n"); + HDprintf(" [default: all MPI_COMM_WORLD processes ]\n"); + HDprintf(" -T S, --threshold=S Threshold for alignment of objects in HDF5 file\n"); + HDprintf(" [default: 1]\n"); + HDprintf(" -w, --write-only Perform write tests not the read tests\n"); + HDprintf(" -x S, --min-xfer-size=S Minimum transfer buffer size\n"); + HDprintf(" (see below for description)\n"); + HDprintf(" [default: half the number of bytes per process\n"); + HDprintf(" per dataset]\n"); + HDprintf(" -X S, --max-xfer-size=S Maximum transfer buffer size\n"); + HDprintf(" [default: the number of bytes per process per\n"); + HDprintf(" dataset]\n"); + HDprintf("\n"); + HDprintf(" F - is a filename.\n"); + HDprintf(" N - is an integer >=0.\n"); + HDprintf(" S - is a size specifier, an integer >=0 followed by a size indicator:\n"); + HDprintf(" K - Kilobyte (%d)\n", ONE_KB); + HDprintf(" M - Megabyte (%d)\n", ONE_MB); + HDprintf(" G - Gigabyte (%d)\n", ONE_GB); + HDprintf("\n"); + HDprintf(" Example: '37M' is 37 megabytes or %d bytes\n", 37 * ONE_MB); + HDprintf("\n"); + HDprintf(" AL - is an API list. Valid values are:\n"); + HDprintf(" phdf5 - Parallel HDF5\n"); + HDprintf(" mpiio - MPI-I/O\n"); + HDprintf(" posix - POSIX\n"); + HDprintf("\n"); + HDprintf(" Example: --api=mpiio,phdf5\n"); + HDprintf("\n"); + HDprintf(" Dataset size:\n"); + HDprintf(" Depending on the selected geometry, each test dataset is either a linear\n"); + HDprintf(" array of size bytes-per-process * num-processes, or a square array of size\n"); + HDprintf(" (bytes-per-process * num-processes) x (bytes-per-process * num-processes).\n"); + HDprintf("\n"); + HDprintf(" Block size vs. Transfer buffer size:\n"); + HDprintf(" buffer-size controls the size of the memory buffer, which is broken into\n"); + HDprintf(" blocks and written to the file. Depending on the selected geometry, each\n"); + HDprintf(" block can be a linear array of size block-size or a square array of size\n"); + HDprintf(" block-size x block-size. The arrangement in which blocks are written is\n"); + HDprintf(" determined by the access pattern.\n"); + HDprintf("\n"); + HDprintf(" In 1D geometry, the transfer buffer is a linear array of size buffer-size.\n"); + HDprintf(" In 2D geometry, it is a rectangular array of size block-size x buffer-size\n"); + HDprintf(" or buffer-size x block-size if interleaved pattern is selected.\n"); + HDprintf("\n"); + HDprintf(" Interleaved and Contiguous patterns in 1D geometry:\n"); + HDprintf(" When contiguous access pattern is chosen, the dataset is evenly divided\n"); + HDprintf(" into num-processes regions and each process writes data to its own region.\n"); + HDprintf(" When interleaved blocks are written to a dataset, space for the first\n"); + HDprintf(" block of the first process is allocated in the dataset, then space is\n"); + HDprintf(" allocated for the first block of the second process, etc. until space is\n"); + HDprintf(" allocated for the first block of each process, then space is allocated for\n"); + HDprintf(" the second block of the first process, the second block of the second\n"); + HDprintf(" process, etc.\n"); + HDprintf("\n"); + HDprintf(" For example, with a 3 process run, 512KB bytes-per-process, 256KB transfer\n"); + HDprintf(" buffer size, and 64KB block size, each process must issue 2 transfer\n"); + HDprintf(" requests to complete access to the dataset.\n"); + HDprintf(" Contiguous blocks of the first transfer request are written like so:\n"); + HDprintf(" 1111----2222----3333----\n"); + HDprintf(" Interleaved blocks of the first transfer request are written like so:\n"); + HDprintf(" 123123123123------------\n"); + HDprintf(" The actual number of I/O operations involved in a transfer request\n"); + HDprintf(" depends on the access pattern and communication mode.\n"); + HDprintf(" When using independent I/O with interleaved pattern, each process\n"); + HDprintf(" performs 4 small non-contiguous I/O operations per transfer request.\n"); + HDprintf(" If collective I/O is turned on, the combined content of the buffers of\n"); + HDprintf(" the 3 processes will be written using one collective I/O operation\n"); + HDprintf(" per transfer request.\n"); + HDprintf("\n"); + HDprintf(" For information about access patterns in 2D geometry, please refer to the\n"); + HDprintf(" HDF5 Reference Manual.\n"); + HDprintf("\n"); + HDprintf(" DL - is a list of debugging flags. Valid values are:\n"); + HDprintf(" 1 - Minimal\n"); + HDprintf(" 2 - Not quite everything\n"); + HDprintf(" 3 - Everything\n"); + HDprintf(" 4 - The kitchen sink\n"); + HDprintf(" r - Raw data I/O throughput information\n"); + HDprintf(" t - Times as well as throughputs\n"); + HDprintf(" v - Verify data correctness\n"); + HDprintf("\n"); + HDprintf(" Example: --debug=2,r,t\n"); + HDprintf("\n"); + HDprintf(" Environment variables:\n"); + HDprintf(" HDF5_NOCLEANUP Do not remove data files if set [default remove]\n"); + HDprintf(" HDF5_MPI_INFO MPI INFO object key=value separated by ;\n"); + HDprintf(" HDF5_PARAPREFIX Paralllel data files prefix\n"); + fflush(stdout); + } /* end if */ +} /* end usage() */ + +#else /* H5_HAVE_PARALLEL */ + +/* + * Function: main + * Purpose: Dummy main() function for if HDF5 was configured without + * parallel stuff. + * Return: EXIT_SUCCESS + * Programmer: Bill Wendling, 14. November 2001 + */ +int +main(void) +{ + HDprintf("No parallel IO performance because parallel is not configured\n"); + return EXIT_SUCCESS; +} /* end main */ + +#endif /* !H5_HAVE_PARALLEL */ diff --git a/tools/src/h5perf/pio_perf.h b/tools/src/h5perf/pio_perf.h new file mode 100644 index 0000000..8924c20 --- /dev/null +++ b/tools/src/h5perf/pio_perf.h @@ -0,0 +1,109 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * Copyright by The HDF Group. * + * All rights reserved. * + * * + * This file is part of HDF5. The full HDF5 copyright notice, including * + * terms governing use, modification, and redistribution, is contained in * + * the COPYING file, which can be found at the root of the source code * + * distribution tree, or in https://www.hdfgroup.org/licenses. * + * If you do not have access to either file, you may request a copy from * + * help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + +#ifndef PIO_PERF_H +#define PIO_PERF_H + +#ifndef STANDALONE +#include "io_timer.h" +#include "H5private.h" +#include "h5tools.h" +#include "h5tools_utils.h" +#else +#include "io_timer.h" +#include "pio_standalone.h" +#endif + +#ifdef H5_HAVE_PARALLEL +extern MPI_Info h5_io_info_g; /* MPI INFO object for IO */ +#endif + +#ifdef H5_HAVE_PARALLEL +int h5_set_info_object(void); +void h5_dump_info_object(MPI_Info info); +#endif + +/* setup the dataset no fill option if this is v1.5 or more */ +#if H5_VERS_MAJOR > 1 || H5_VERS_MINOR > 4 +#define H5_HAVE_NOFILL 1 +#endif + +typedef enum iotype_ { + POSIXIO, + MPIO, + PHDF5 + /*NUM_TYPES*/ +} iotype; + +typedef struct parameters_ { + iotype io_type; /* The type of IO test to perform */ + int num_procs; /* Maximum number of processes to use */ + long num_files; /* Number of files to create */ + long num_dsets; /* Number of datasets to create */ + off_t num_bytes; /* Number of bytes in each dset */ + int num_iters; /* Number of times to loop doing the IO */ + size_t buf_size; /* Buffer size */ + size_t blk_size; /* Block size */ + unsigned interleaved; /* Interleaved vs. contiguous blocks */ + unsigned collective; /* Collective vs. independent I/O */ + unsigned dim2d; /* 1D vs. 2D */ + hsize_t h5_align; /* HDF5 object alignment */ + hsize_t h5_thresh; /* HDF5 object alignment threshold */ + int h5_use_chunks; /* Make HDF5 dataset chunked */ + int h5_write_only; /* Perform the write tests only */ + int verify; /* Verify data correctness */ +} parameters; + +typedef struct results_ { + herr_t ret_code; + io_time_t *timers; +} results; + +#ifndef SUCCESS +#define SUCCESS 0 +#endif /* !SUCCESS */ + +#ifndef FAIL +#define FAIL -1 +#endif /* !FAIL */ + +extern FILE * output; /* output file */ +extern io_time_t *timer_g; /* timer: global for stub functions */ +extern int comm_world_rank_g; /* my rank in MPI_COMM_RANK */ +extern int comm_world_nprocs_g; /* num. of processes of MPI_COMM_WORLD */ +extern MPI_Comm pio_comm_g; /* Communicator to run the PIO */ +extern int pio_mpi_rank_g; /* MPI rank of pio_comm_g */ +extern int pio_mpi_nprocs_g; /* number of processes of pio_comm_g */ +extern int pio_debug_level; /* The debug level: + * 0 - Off + * 1 - Minimal + * 2 - Some more + * 3 - Maximal + * 4 - Even More Debugging (timer stuff) + */ + +#define HDprint_rank(f) /* print rank in MPI_COMM_WORLD */ HDfprintf(f, "%d: ", comm_world_rank_g); +#define HDprint_size(f) /* print size of MPI_COMM_WORLD */ HDfprintf(f, "%d", comm_world_nprocs_g); +#define HDprint_rank_size(f) /* print rank/size of MPI_COMM_WORLD */ \ + HDfprintf(f, "%d/%d: ", comm_world_rank_g, comm_world_nprocs_g); + +#ifdef __cplusplus +extern "C" { +#endif /* __cplusplus */ + +extern results do_pio(parameters param); + +#ifdef __cplusplus +} +#endif /* __cplusplus */ + +#endif /* PIO_PERF_H */ diff --git a/tools/src/h5perf/sio_engine.c b/tools/src/h5perf/sio_engine.c new file mode 100644 index 0000000..bdd2c08 --- /dev/null +++ b/tools/src/h5perf/sio_engine.c @@ -0,0 +1,1328 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * Copyright by The HDF Group. * + * All rights reserved. * + * * + * This file is part of HDF5. The full HDF5 copyright notice, including * + * terms governing use, modification, and redistribution, is contained in * + * the COPYING file, which can be found at the root of the source code * + * distribution tree, or in https://www.hdfgroup.org/licenses. * + * If you do not have access to either file, you may request a copy from * + * help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + +/* + * Author: Christian Chilan, April 2008 + */ + +#include "hdf5.h" + +#include <errno.h> +#include <fcntl.h> +#include <stdio.h> +#include <stdlib.h> + +#ifdef H5_HAVE_UNISTD_H +#include <sys/types.h> +#include <unistd.h> +#endif + +#ifdef H5_HAVE_SYS_STAT_H +#include <sys/stat.h> +#endif + +#include "sio_perf.h" + +/* Macro definitions */ + +/* sizes of various items. these sizes won't change during program execution */ +#define ELMT_H5_TYPE H5T_NATIVE_UCHAR + +#define GOTOERROR(errcode) \ + { \ + ret_code = errcode; \ + goto done; \ + } +#define ERRMSG(mesg) \ + { \ + HDfprintf(stderr, "*** Assertion failed (%s) at line %4d in %s\n", mesg, (int)__LINE__, __FILE__); \ + } + +/* verify: if val is false (0), print mesg. */ +#define VRFY(val, mesg) \ + do { \ + if (!(val)) { \ + ERRMSG(mesg); \ + GOTOERROR(FAIL); \ + } \ + } while (0) + +/* POSIX I/O macros */ +#ifdef H5_HAVE_WIN32_API +/* Can't link against the library, so this test will use the older, non-Unicode + * _open() call on Windows. + */ +#define HDopen(S, F, ...) _open(S, F | _O_BINARY, __VA_ARGS__) +#endif /* H5_HAVE_WIN32_API */ +#define POSIXCREATE(fn) HDopen(fn, O_CREAT | O_TRUNC | O_RDWR, 0600) +#define POSIXOPEN(fn, F) HDopen(fn, F, 0600) +#define POSIXCLOSE(F) HDclose(F) +#define POSIXSEEK(F, L) HDlseek(F, L, SEEK_SET) +#define POSIXWRITE(F, B, S) HDwrite(F, B, S) +#define POSIXREAD(F, B, S) HDread(F, B, S) + +enum { SIO_CREATE = 1, SIO_WRITE = 2, SIO_READ = 4 }; + +/* Global variables */ +static int clean_file_g = -1; /*whether to cleanup temporary test */ +/*files. -1 is not defined; */ +/*0 is no cleanup; 1 is do cleanup */ + +/* the different types of file descriptors we can expect */ +typedef union { + int posixfd; /* POSIX file handle*/ + hid_t h5fd; /* HDF5 file */ +} file_descr; + +/* local functions */ +static char * sio_create_filename(iotype iot, const char *base_name, char *fullname, size_t size, + parameters *param); +static herr_t do_write(results *res, file_descr *fd, parameters *parms, void *buffer); +static herr_t do_read(results *res, file_descr *fd, parameters *parms, void *buffer); +static herr_t dset_write(int local_dim, file_descr *fd, parameters *parms, void *buffer); +static herr_t posix_buffer_write(int local_dim, file_descr *fd, parameters *parms, void *buffer); +static herr_t dset_read(int localrank, file_descr *fd, parameters *parms, void *buffer, const char *buffer2); +static herr_t posix_buffer_read(int local_dim, file_descr *fd, parameters *parms, void *buffer); +static herr_t do_fopen(parameters *param, char *fname, file_descr *fd /*out*/, int flags); +hid_t set_vfd(parameters *param); +static herr_t do_fclose(iotype iot, file_descr *fd); +static void do_cleanupfile(iotype iot, char *fname); + +/* global variables */ +static HDoff_t offset[MAX_DIMS]; /* dataset size in bytes */ +static size_t buf_offset[MAX_DIMS]; /* dataset size in bytes */ +static int order[MAX_DIMS]; /* dimension access order */ +static size_t linear_buf_size; /* linear buffer size */ +static int cont_dim; /* lowest dimension for contiguous POSIX + access */ +static size_t cont_size; /* size of contiguous POSIX access */ +static hid_t fapl; /* file access list */ +static unsigned char *buf_p; /* buffer pointer */ +static const char * multi_letters = "msbrglo"; /* string for multi driver */ + +/* HDF5 global variables */ +static hsize_t h5count[MAX_DIMS]; /*selection count */ +static hssize_t h5offset[MAX_DIMS]; /* Selection offset within dataspace */ +static hid_t h5dset_space_id = H5I_INVALID_HID; /*dataset space ID */ +static hid_t h5mem_space_id = H5I_INVALID_HID; /*memory dataspace ID */ +static hid_t h5ds_id = H5I_INVALID_HID; /*dataset handle */ +static hid_t h5dcpl = H5I_INVALID_HID; /* Dataset creation property list */ +static hid_t h5dxpl = H5I_INVALID_HID; /* Dataset transfer property list */ + +/* + * Function: do_sio + * Purpose: SIO Engine where IO are executed. + * Return: results + * Programmer: Christian Chilan, April, 2008 + * Modifications: + */ +void +do_sio(parameters param, results *res) +{ + char * buffer = NULL; /*data buffer pointer */ + size_t buf_size[MAX_DIMS]; /* general buffer size in bytes */ + file_descr fd; /* file handles */ + iotype iot; /* API type */ + char base_name[256]; /* test file base name */ + /* return codes */ + herr_t ret_code = 0; /*return code */ + + char fname[FILENAME_MAX]; /* test file name */ + int i; + /* HDF5 variables */ + herr_t hrc; /*HDF5 return code */ + + /* Sanity check parameters */ + + /* IO type */ + iot = param.io_type; + + switch (iot) { + case POSIXIO: + fd.posixfd = -1; + res->timers = io_time_new(SYS_CLOCK); + break; + case HDF5: + fd.h5fd = -1; + res->timers = io_time_new(SYS_CLOCK); + break; + default: + /* unknown request */ + HDfprintf(stderr, "Unknown IO type request (%d)\n", (int)iot); + GOTOERROR(FAIL); + } + + linear_buf_size = 1; + + for (i = 0; i < param.rank; i++) { + buf_size[i] = param.buf_size[i]; + order[i] = param.order[i]; + linear_buf_size *= buf_size[i]; + buf_offset[i] = 0; + offset[i] = 0; + + /* Validate transfer buffer size */ + if (param.buf_size[i] <= 0) { + HDfprintf(stderr, "Transfer buffer size[%d] (%zu) must be > 0\n", i, buf_size[i]); + GOTOERROR(FAIL); + } + + if ((param.dset_size[i] % param.buf_size[i]) != 0) { + HDfprintf(stderr, + "Dataset size[%d] (%" H5_PRINTF_LL_WIDTH "d) must be a multiple of the " + "transfer buffer size[%d] (%zu)\n", + param.rank, (long long)param.dset_size[i], param.rank, param.buf_size[i]); + GOTOERROR(FAIL); + } + } + + /* Allocate transfer buffer */ + if ((buffer = (char *)malloc(linear_buf_size)) == NULL) { + HDfprintf(stderr, "malloc for transfer buffer size (%zu) failed\n", linear_buf_size); + GOTOERROR(FAIL); + } + + if (sio_debug_level >= 4) + + /* output all of the times for all iterations */ + HDfprintf(output, "Timer details:\n"); + + /* + * Write performance measurement + */ + /* Open file for write */ + + HDstrcpy(base_name, "#sio_tmp"); + sio_create_filename(iot, base_name, fname, sizeof(fname), ¶m); + + if (sio_debug_level > 0) + HDfprintf(output, "data filename=%s\n", fname); + + io_time_set(res->timers, HDF5_GROSS_WRITE_FIXED_DIMS, TSTART); + hrc = do_fopen(¶m, fname, &fd, SIO_CREATE | SIO_WRITE); + VRFY((hrc == SUCCESS), "do_fopen failed"); + + io_time_set(res->timers, HDF5_FINE_WRITE_FIXED_DIMS, TSTART); + hrc = do_write(res, &fd, ¶m, buffer); + io_time_set(res->timers, HDF5_FINE_WRITE_FIXED_DIMS, TSTOP); + VRFY((hrc == SUCCESS), "do_write failed"); + + /* Close file for write */ + hrc = do_fclose(iot, &fd); + io_time_set(res->timers, HDF5_GROSS_WRITE_FIXED_DIMS, TSTOP); + VRFY((hrc == SUCCESS), "do_fclose failed"); + + if (!param.h5_write_only) { + /* + * Read performance measurement + */ + + /* Open file for read */ + io_time_set(res->timers, HDF5_GROSS_READ_FIXED_DIMS, TSTART); + hrc = do_fopen(¶m, fname, &fd, SIO_READ); + VRFY((hrc == SUCCESS), "do_fopen failed"); + + io_time_set(res->timers, HDF5_FINE_READ_FIXED_DIMS, TSTART); + hrc = do_read(res, &fd, ¶m, buffer); + io_time_set(res->timers, HDF5_FINE_READ_FIXED_DIMS, TSTOP); + VRFY((hrc == SUCCESS), "do_read failed"); + + /* Close file for read */ + hrc = do_fclose(iot, &fd); + + io_time_set(res->timers, HDF5_GROSS_READ_FIXED_DIMS, TSTOP); + VRFY((hrc == SUCCESS), "do_fclose failed"); + } + + do_cleanupfile(iot, fname); + +done: + /* clean up */ + /* release HDF5 objects */ + + /* close any opened files */ + /* no remove(fname) because that should have happened normally. */ + switch (iot) { + case POSIXIO: + if (fd.posixfd != -1) + hrc = do_fclose(iot, &fd); + break; + case HDF5: + if (fd.h5fd != -1) + hrc = do_fclose(iot, &fd); + break; + default: + /* unknown request */ + HDassert(0 && "Unknown IO type"); + break; + } + + /* release generic resources */ + if (buffer) + free(buffer); + + res->ret_code = ret_code; +} + +/* + * Function: sio_create_filename + * Purpose: Create a new filename to write to. Determine the correct + * suffix to append to the filename by the type of I/O we're + * doing. Also, place in the /tmp/{$USER,$LOGIN} directory if + * USER or LOGIN are specified in the environment. + * Return: Pointer to filename or NULL + * Programmer: Bill Wendling, 21. November 2001 + * Modifications: Support for file drivers. Christian Chilan, April, 2008 + */ +static char * +sio_create_filename(iotype iot, const char *base_name, char *fullname, size_t size, parameters *param) +{ + const char *prefix, *suffix = ""; + char * ptr, last = '\0'; + size_t i, j; + vfdtype vfd; + vfd = param->vfd; + + if (!base_name || !fullname || size < 1) + return NULL; + + memset(fullname, 0, size); + + switch (iot) { + case POSIXIO: + suffix = ".posix"; + break; + case HDF5: + suffix = ".h5"; + if (vfd == family) + suffix = "%05d.h5"; + else if (vfd == multi) + suffix = NULL; + break; + default: + /* unknown request */ + HDfprintf(stderr, "Unknown IO type request (%d)\n", (int)iot); + HDassert(0 && "Unknown IO type"); + break; + } + + /* First use the environment variable and then try the constant */ + prefix = HDgetenv("HDF5_PREFIX"); + +#ifdef HDF5_PREFIX + if (!prefix) + prefix = HDF5_PREFIX; +#endif /* HDF5_PREFIX */ + + /* Prepend the prefix value to the base name */ + if (prefix && *prefix) { + /* If the prefix specifies the HDF5_PREFIX directory, then + * default to using the "/tmp/$USER" or "/tmp/$LOGIN" + * directory instead. */ + char *user, *login, *subdir; + + user = HDgetenv("USER"); + login = HDgetenv("LOGIN"); + subdir = (user ? user : login); + + if (subdir) { + for (i = 0; i < size - 1 && prefix[i]; i++) + fullname[i] = prefix[i]; + + fullname[i++] = '/'; + + for (j = 0; i < size && subdir[j]; i++, j++) + fullname[i] = subdir[j]; + } + else { + /* We didn't append the prefix yet */ + HDstrncpy(fullname, prefix, size); + fullname[size - 1] = '\0'; + } + + if ((HDstrlen(fullname) + HDstrlen(base_name) + 1) < size) { + /* Append the base_name with a slash first. Multiple slashes are + * handled below. */ + h5_stat_t buf; + + if (HDstat(fullname, &buf) < 0) + /* The directory doesn't exist just yet */ + if (HDmkdir(fullname, 0755) < 0 && errno != EEXIST) { + /* We couldn't make the "/tmp/${USER,LOGIN}" subdirectory. + * Default to PREFIX's original prefix value. */ + HDstrcpy(fullname, prefix); + } + + HDstrcat(fullname, "/"); + HDstrcat(fullname, base_name); + } + else { + /* Buffer is too small */ + return NULL; + } + } + else if (strlen(base_name) >= size) { + /* Buffer is too small */ + return NULL; + } + else { + HDstrcpy(fullname, base_name); + } + + /* Append a suffix */ + if (suffix) { + if (HDstrlen(fullname) + HDstrlen(suffix) >= size) + return NULL; + + HDstrcat(fullname, suffix); + } + + /* Remove any double slashes in the filename */ + for (ptr = fullname, i = j = 0; ptr && (i < size); i++, ptr++) { + if (*ptr != '/' || last != '/') + fullname[j++] = *ptr; + + last = *ptr; + } + + return fullname; +} + +/* + * Function: do_write + * Purpose: Write the required amount of data to the file. + * Return: SUCCESS or FAIL + * Programmer: Christian Chilan, April, 2008 + * Modifications: + */ +static herr_t +do_write(results *res, file_descr *fd, parameters *parms, void *buffer) +{ + int ret_code = SUCCESS; + char dname[64]; + int i; + size_t u; + /* HDF5 variables */ + herr_t hrc; /*HDF5 return code */ + hsize_t h5dims[MAX_DIMS]; /*dataset dim sizes */ + hsize_t h5chunk[MAX_DIMS]; /*dataset dim sizes */ + hsize_t h5block[MAX_DIMS]; /*dataspace selection */ + hsize_t h5stride[MAX_DIMS]; /*selection stride */ + hsize_t h5start[MAX_DIMS]; /*selection start */ + hsize_t h5maxdims[MAX_DIMS]; + int rank; /*rank of dataset */ + + /* Prepare buffer for verifying data */ + /* if (parms->verify) + memset(buffer,1,linear_buf_size); */ + + buf_p = (unsigned char *)buffer; + + for (u = 0; u < linear_buf_size; u++) + buf_p[u] = u % 128; + + rank = parms->rank; + + for (i = 0; i < rank; i++) + h5offset[i] = offset[i] = 0; + + /* I/O Access specific setup */ + switch (parms->io_type) { + case POSIXIO: + + /* determine lowest dimension for contiguous POSIX access */ + cont_dim = rank; + + for (i = rank - 1; i >= 0; i--) { + if (parms->buf_size[i] == parms->dset_size[i]) + cont_dim = i; + else + break; + } + + /* determine size of the contiguous POSIX access */ + cont_size = (!cont_dim) ? 1 : parms->buf_size[cont_dim - 1]; + for (i = cont_dim; i < rank; i++) + cont_size *= parms->buf_size[i]; + + break; + + case HDF5: /* HDF5 setup */ + + for (i = 0; i < rank; i++) { + h5dims[i] = parms->dset_size[i]; + h5start[i] = 0; + h5stride[i] = 1; + h5block[i] = 1; + h5count[i] = parms->buf_size[i]; + h5chunk[i] = parms->chk_size[i]; + h5maxdims[i] = H5S_UNLIMITED; + } + + if (parms->h5_use_chunks && parms->h5_extendable) { + h5dset_space_id = H5Screate_simple(rank, h5count, h5maxdims); + VRFY((h5dset_space_id >= 0), "H5Screate_simple"); + } + else { + h5dset_space_id = H5Screate_simple(rank, h5dims, NULL); + VRFY((h5dset_space_id >= 0), "H5Screate_simple"); + } + + hrc = H5Sselect_hyperslab(h5dset_space_id, H5S_SELECT_SET, h5start, h5stride, h5count, h5block); + VRFY((hrc >= 0), "H5Sselect_hyperslab"); + + /* Create the memory dataspace that corresponds to the xfer buffer */ + h5mem_space_id = H5Screate_simple(rank, h5count, NULL); + VRFY((h5mem_space_id >= 0), "H5Screate_simple"); + + /* Create the dataset transfer property list */ + h5dxpl = H5Pcreate(H5P_DATASET_XFER); + if (h5dxpl < 0) { + HDfprintf(stderr, "HDF5 Property List Create failed\n"); + GOTOERROR(FAIL); + } + + break; + + default: + HDfprintf(stderr, "Unknown IO type request (%d)\n", (int)parms->io_type); + GOTOERROR(FAIL); + break; + } /* end switch */ + + /* create dataset */ + switch (parms->io_type) { + case POSIXIO: + break; + + case HDF5: + h5dcpl = H5Pcreate(H5P_DATASET_CREATE); + + if (h5dcpl < 0) { + HDfprintf(stderr, "HDF5 Property List Create failed\n"); + GOTOERROR(FAIL); + } + + if (parms->h5_use_chunks) { + /* Set the chunk size to be the same as the buffer size */ + hrc = H5Pset_chunk(h5dcpl, rank, h5chunk); + if (hrc < 0) { + HDfprintf(stderr, "HDF5 Property List Set failed\n"); + GOTOERROR(FAIL); + } /* end if */ + } /* end if */ + + HDsprintf(dname, "Dataset_%ld", (unsigned long)parms->num_bytes); + h5ds_id = + H5Dcreate2(fd->h5fd, dname, ELMT_H5_TYPE, h5dset_space_id, H5P_DEFAULT, h5dcpl, H5P_DEFAULT); + + if (h5ds_id < 0) { + HDfprintf(stderr, "HDF5 Dataset Create failed\n"); + GOTOERROR(FAIL); + } + + hrc = H5Pclose(h5dcpl); + /* verifying the close of the dcpl */ + if (hrc < 0) { + HDfprintf(stderr, "HDF5 Property List Close failed\n"); + GOTOERROR(FAIL); + } + break; + + default: + /* unknown request */ + HDfprintf(stderr, "Unknown IO type request (%d)\n", (int)parms->io_type); + GOTOERROR(FAIL); + break; + } + + /* Start "raw data" write timer */ + io_time_set(res->timers, HDF5_RAW_WRITE_FIXED_DIMS, TSTART); + + /* Perform write */ + hrc = dset_write(rank - 1, fd, parms, buffer); + + if (hrc < 0) { + HDfprintf(stderr, "Error in dataset write\n"); + GOTOERROR(FAIL); + } + + /* Stop "raw data" write timer */ + io_time_set(res->timers, HDF5_RAW_WRITE_FIXED_DIMS, TSTOP); + + /* Calculate write time */ + + /* Close dataset. Only HDF5 needs to do an explicit close. */ + if (parms->io_type == HDF5) { + hrc = H5Dclose(h5ds_id); + + if (hrc < 0) { + HDfprintf(stderr, "HDF5 Dataset Close failed\n"); + GOTOERROR(FAIL); + } + + h5ds_id = H5I_INVALID_HID; + } /* end if */ + +done: + + /* release HDF5 objects */ + if (h5dset_space_id != -1) { + hrc = H5Sclose(h5dset_space_id); + if (hrc < 0) { + HDfprintf(stderr, "HDF5 Dataset Space Close failed\n"); + ret_code = FAIL; + } + else { + h5dset_space_id = H5I_INVALID_HID; + } + } + + if (h5mem_space_id != -1) { + hrc = H5Sclose(h5mem_space_id); + if (hrc < 0) { + HDfprintf(stderr, "HDF5 Memory Space Close failed\n"); + ret_code = FAIL; + } + else { + h5mem_space_id = H5I_INVALID_HID; + } + } + + if (h5dxpl != -1) { + hrc = H5Pclose(h5dxpl); + if (hrc < 0) { + HDfprintf(stderr, "HDF5 Dataset Transfer Property List Close failed\n"); + ret_code = FAIL; + } + else { + h5dxpl = H5I_INVALID_HID; + } + } + + return ret_code; +} + +/* + * Function: dset_write + * Purpose: Write buffer into the dataset. + * Return: SUCCESS or FAIL + * Programmer: Christian Chilan, April, 2008 + * Modifications: + */ +static herr_t +dset_write(int local_dim, file_descr *fd, parameters *parms, void *buffer) +{ + int cur_dim = order[local_dim] - 1; + int ret_code = SUCCESS; + int k; + hsize_t dims[MAX_DIMS], maxdims[MAX_DIMS]; + hsize_t i; + int j; + herr_t hrc; + + /* iterates according to the dimensions in order array */ + for (i = 0; i < parms->dset_size[cur_dim]; i += parms->buf_size[cur_dim]) { + + h5offset[cur_dim] = (hssize_t)i; + offset[cur_dim] = (HDoff_t)i; + + if (local_dim > 0) { + + dset_write(local_dim - 1, fd, parms, buffer); + } + else { + + switch (parms->io_type) { + + case POSIXIO: + /* initialize POSIX offset in the buffer */ + for (j = 0; j < parms->rank; j++) + buf_offset[j] = 0; + buf_p = (unsigned char *)buffer; + /* write POSIX buffer */ + posix_buffer_write(0, fd, parms, buffer); + break; + + case HDF5: + /* if dimensions are extendable, extend them as needed during access */ + if (parms->h5_use_chunks && parms->h5_extendable) { + + hrc = H5Sget_simple_extent_dims(h5dset_space_id, dims, maxdims); + VRFY((hrc >= 0), "H5Sget_simple_extent_dims"); + + for (k = 0; k < parms->rank; k++) { + + HDassert(h5offset[k] >= 0); + if (dims[k] <= (hsize_t)h5offset[k]) { + dims[k] = dims[k] + h5count[k]; + hrc = H5Sset_extent_simple(h5dset_space_id, parms->rank, dims, maxdims); + VRFY((hrc >= 0), "H5Sset_extent_simple"); + hrc = H5Dset_extent(h5ds_id, dims); + VRFY((hrc >= 0), "H5Dextend"); + } + } + } + /* applies offset */ + hrc = H5Soffset_simple(h5dset_space_id, h5offset); + VRFY((hrc >= 0), "H5Soffset_simple"); + + /* Write the buffer out */ + hrc = H5Sget_simple_extent_dims(h5dset_space_id, dims, maxdims); + hrc = H5Dwrite(h5ds_id, ELMT_H5_TYPE, h5mem_space_id, h5dset_space_id, h5dxpl, buffer); + VRFY((hrc >= 0), "H5Dwrite"); + + break; + + default: + /* unknown request */ + HDfprintf(stderr, "Unknown IO type request (%d)\n", (int)parms->io_type); + HDassert(0 && "Unknown IO type"); + break; + } /* switch (parms->io_type) */ + } + } +done: + return ret_code; +} + +/* + * Function: posix_buffer_write + * Purpose: Write buffer into the POSIX file considering contiguity. + * Return: SUCCESS or FAIL + * Programmer: Christian Chilan, April, 2008 + * Modifications: + */ + +static herr_t +posix_buffer_write(int local_dim, file_descr *fd, parameters *parms, void *buffer) +{ + int ret_code = SUCCESS; + + /* if dimension is not contiguous, call recursively */ + if (local_dim < parms->rank - 1 && local_dim != cont_dim) { + size_t u; + + for (u = 0; u < parms->buf_size[local_dim]; u++) { + buf_offset[local_dim] = u; + posix_buffer_write(local_dim + 1, fd, parms, buffer); + + /* if next dimension is cont_dim, it will fill out the buffer + traversing the entire dimension local_dim without the need + of performing iteration */ + if (local_dim + 1 == cont_dim) + break; + } + /* otherwise, perform contiguous POSIX access */ + } + else { + HDoff_t d_offset; + HDoff_t linear_dset_offset = 0; + int i, j, rc; + + buf_offset[local_dim] = 0; + + /* determine offset in the buffer */ + for (i = 0; i < parms->rank; i++) { + d_offset = 1; + + for (j = i + 1; j < parms->rank; j++) + d_offset *= (HDoff_t)parms->dset_size[j]; + + linear_dset_offset += (offset[i] + (HDoff_t)buf_offset[i]) * d_offset; + } + + /* only care if seek returns error */ + rc = POSIXSEEK(fd->posixfd, linear_dset_offset) < 0 ? -1 : 0; + VRFY((rc == 0), "POSIXSEEK"); + /* check if all bytes are written */ + rc = ((ssize_t)cont_size == POSIXWRITE(fd->posixfd, buf_p, cont_size)); + VRFY((rc != 0), "POSIXWRITE"); + + /* Advance location in buffer */ + buf_p += cont_size; + } + +done: + return ret_code; +} + +/* + * Function: do_read + * Purpose: Read the required amount of data to the file. + * Return: SUCCESS or FAIL + * Programmer: Christian Chilan, April, 2008 + * Modifications: + */ +static herr_t +do_read(results *res, file_descr *fd, parameters *parms, void *buffer) +{ + char * buffer2 = NULL; /* Buffer for data verification */ + int ret_code = SUCCESS; + char dname[64]; + int i; + size_t u; + /* HDF5 variables */ + herr_t hrc; /*HDF5 return code */ + hsize_t h5dims[MAX_DIMS]; /*dataset dim sizes */ + hsize_t h5block[MAX_DIMS]; /*dataspace selection */ + hsize_t h5stride[MAX_DIMS]; /*selection stride */ + hsize_t h5start[MAX_DIMS]; /*selection start */ + int rank; + + /* Allocate data verification buffer */ + if (NULL == (buffer2 = (char *)malloc(linear_buf_size))) { + HDfprintf(stderr, "malloc for data verification buffer size (%zu) failed\n", linear_buf_size); + GOTOERROR(FAIL); + } /* end if */ + + /* Prepare buffer for verifying data */ + for (u = 0; u < linear_buf_size; u++) + buffer2[u] = (char)(u % 128); + + rank = parms->rank; + for (i = 0; i < rank; i++) + h5offset[i] = offset[i] = 0; + + /* I/O Access specific setup */ + switch (parms->io_type) { + case POSIXIO: + cont_dim = rank; + + for (i = rank - 1; i >= 0; i--) { + if (parms->buf_size[i] == parms->dset_size[i]) + cont_dim = i; + else + break; + } + cont_size = (!cont_dim) ? 1 : parms->buf_size[cont_dim - 1]; + for (i = cont_dim; i < rank; i++) + cont_size *= parms->buf_size[i]; + + break; + + case HDF5: /* HDF5 setup */ + for (i = 0; i < rank; i++) { + h5dims[i] = parms->dset_size[i]; + h5start[i] = 0; + h5stride[i] = 1; + h5block[i] = 1; + h5count[i] = parms->buf_size[i]; + } + + h5dset_space_id = H5Screate_simple(rank, h5dims, NULL); + VRFY((h5dset_space_id >= 0), "H5Screate_simple"); + + hrc = H5Sselect_hyperslab(h5dset_space_id, H5S_SELECT_SET, h5start, h5stride, h5count, h5block); + VRFY((hrc >= 0), "H5Sselect_hyperslab"); + + /* Create the memory dataspace that corresponds to the xfer buffer */ + h5mem_space_id = H5Screate_simple(rank, h5count, NULL); + VRFY((h5mem_space_id >= 0), "H5Screate_simple"); + + /* Create the dataset transfer property list */ + h5dxpl = H5Pcreate(H5P_DATASET_XFER); + if (h5dxpl < 0) { + HDfprintf(stderr, "HDF5 Property List Create failed\n"); + GOTOERROR(FAIL); + } + break; + + default: + /* unknown request */ + HDfprintf(stderr, "Unknown IO type request (%d)\n", (int)parms->io_type); + GOTOERROR(FAIL); + break; + } /* end switch */ + + /* create dataset */ + switch (parms->io_type) { + case POSIXIO: + break; + + case HDF5: + HDsprintf(dname, "Dataset_%ld", (long)parms->num_bytes); + h5ds_id = H5Dopen2(fd->h5fd, dname, H5P_DEFAULT); + if (h5ds_id < 0) { + HDfprintf(stderr, "HDF5 Dataset open failed\n"); + GOTOERROR(FAIL); + } + break; + + default: + /* unknown request */ + HDfprintf(stderr, "Unknown IO type request (%d)\n", (int)parms->io_type); + GOTOERROR(FAIL); + break; + } /* end switch */ + + /* Start "raw data" read timer */ + io_time_set(res->timers, HDF5_RAW_READ_FIXED_DIMS, TSTART); + hrc = dset_read(rank - 1, fd, parms, buffer, buffer2); + + if (hrc < 0) { + HDfprintf(stderr, "Error in dataset read\n"); + GOTOERROR(FAIL); + } + + /* Stop "raw data" read timer */ + io_time_set(res->timers, HDF5_RAW_READ_FIXED_DIMS, TSTOP); + + /* Calculate read time */ + + /* Close dataset. Only HDF5 needs to do an explicit close. */ + if (parms->io_type == HDF5) { + hrc = H5Dclose(h5ds_id); + + if (hrc < 0) { + HDfprintf(stderr, "HDF5 Dataset Close failed\n"); + GOTOERROR(FAIL); + } + + h5ds_id = H5I_INVALID_HID; + } /* end if */ + +done: + + /* release HDF5 objects */ + if (h5dset_space_id != -1) { + hrc = H5Sclose(h5dset_space_id); + if (hrc < 0) { + HDfprintf(stderr, "HDF5 Dataset Space Close failed\n"); + ret_code = FAIL; + } + else { + h5dset_space_id = H5I_INVALID_HID; + } + } + + if (h5mem_space_id != -1) { + hrc = H5Sclose(h5mem_space_id); + if (hrc < 0) { + HDfprintf(stderr, "HDF5 Memory Space Close failed\n"); + ret_code = FAIL; + } + else { + h5mem_space_id = H5I_INVALID_HID; + } + } + + if (h5dxpl != -1) { + hrc = H5Pclose(h5dxpl); + if (hrc < 0) { + HDfprintf(stderr, "HDF5 Dataset Transfer Property List Close failed\n"); + ret_code = FAIL; + } + else { + h5dxpl = H5I_INVALID_HID; + } + } + + /* release generic resources */ + if (buffer2) + free(buffer2); + + return ret_code; +} + +/* + * Function: dset_read + * Purpose: Read buffer into the dataset. + * Return: SUCCESS or FAIL + * Programmer: Christian Chilan, April, 2008 + * Modifications: + */ + +static herr_t +dset_read(int local_dim, file_descr *fd, parameters *parms, void *buffer, const char *buffer2) +{ + int cur_dim = order[local_dim] - 1; + hsize_t i; + int j; + herr_t hrc; + int ret_code = SUCCESS; + + /* iterate on the current dimension */ + for (i = 0; i < parms->dset_size[cur_dim]; i += parms->buf_size[cur_dim]) { + + h5offset[cur_dim] = (hssize_t)i; + offset[cur_dim] = (HDoff_t)i; + + /* if traverse in order array is incomplete, recurse */ + if (local_dim > 0) { + + ret_code = dset_read(local_dim - 1, fd, parms, buffer, buffer2); + + /* otherwise, write buffer into dataset */ + } + else { + + switch (parms->io_type) { + + case POSIXIO: + for (j = 0; j < parms->rank; j++) { + buf_offset[j] = 0; + } + buf_p = (unsigned char *)buffer; + posix_buffer_read(0, fd, parms, buffer); + break; + + case HDF5: + hrc = H5Soffset_simple(h5dset_space_id, h5offset); + VRFY((hrc >= 0), "H5Soffset_simple"); + /* Read the buffer out */ + hrc = H5Dread(h5ds_id, ELMT_H5_TYPE, h5mem_space_id, h5dset_space_id, h5dxpl, buffer); + VRFY((hrc >= 0), "H5Dread"); + break; + + default: + /* unknown request */ + HDfprintf(stderr, "Unknown IO type request (%d)\n", (int)parms->io_type); + HDassert(0 && "Unknown IO type"); + break; + } /* switch (parms->io_type) */ + } + } +done: + return ret_code; +} + +/* + * Function: posix_buffer_read + * Purpose: Read buffer into the POSIX file considering contiguity. + * Return: SUCCESS or FAIL + * Programmer: Christian Chilan, April, 2008 + * Modifications: + */ + +static herr_t +posix_buffer_read(int local_dim, file_descr *fd, parameters *parms, void *buffer) +{ + int ret_code = SUCCESS; + + /* if local dimension is not contiguous, recurse */ + if (local_dim < parms->rank - 1 && local_dim != cont_dim) { + size_t u; + + for (u = 0; u < parms->buf_size[local_dim]; u++) { + buf_offset[local_dim] = u; + ret_code = posix_buffer_read(local_dim + 1, fd, parms, buffer); + if (local_dim + 1 == cont_dim) + break; + } + /* otherwise, perform contiguous POSIX access */ + } + else { + HDoff_t d_offset; + HDoff_t linear_dset_offset = 0; + int i, j, rc; + + buf_offset[local_dim] = 0; + /* determine offset in buffer */ + for (i = 0; i < parms->rank; i++) { + d_offset = 1; + + for (j = i + 1; j < parms->rank; j++) + d_offset *= (HDoff_t)parms->dset_size[j]; + + linear_dset_offset += (offset[i] + (HDoff_t)buf_offset[i]) * d_offset; + } + + /* only care if seek returns error */ + rc = POSIXSEEK(fd->posixfd, linear_dset_offset) < 0 ? -1 : 0; + VRFY((rc == 0), "POSIXSEEK"); + /* check if all bytes are read */ + rc = ((ssize_t)cont_size == POSIXREAD(fd->posixfd, buf_p, cont_size)); + VRFY((rc != 0), "POSIXREAD"); + + /* Advance location in buffer */ + buf_p += cont_size; + } +done: + return ret_code; +} + +/* + * Function: do_fopen + * Purpose: Open the specified file. + * Return: SUCCESS or FAIL + * Programmer: Albert Cheng, Bill Wendling, 2001/12/13 + * Modifications: Support for file drivers, Christian Chilan, April, 2008 + */ +static herr_t +do_fopen(parameters *param, char *fname, file_descr *fd /*out*/, int flags) +{ + int ret_code = SUCCESS; + hid_t fcpl; + + switch (param->io_type) { + case POSIXIO: + if (flags & (SIO_CREATE | SIO_WRITE)) + fd->posixfd = POSIXCREATE(fname); + else + fd->posixfd = POSIXOPEN(fname, O_RDONLY); + + if (fd->posixfd < 0) { + HDfprintf(stderr, "POSIX File Open failed(%s)\n", fname); + GOTOERROR(FAIL); + } + + break; + + case HDF5: + + fapl = set_vfd(param); + + if (fapl < 0) { + HDfprintf(stderr, "HDF5 Property List Create failed\n"); + GOTOERROR(FAIL); + } + + fcpl = H5Pcreate(H5P_FILE_CREATE); + if (param->page_size) { + H5Pset_file_space_strategy(fcpl, H5F_FSPACE_STRATEGY_PAGE, 0, (hsize_t)1); + H5Pset_file_space_page_size(fcpl, param->page_size); + if (param->page_buffer_size) + H5Pset_page_buffer_size(fapl, param->page_buffer_size, 0, 0); + } + + /* create the parallel file */ + if (flags & (SIO_CREATE | SIO_WRITE)) { + fd->h5fd = H5Fcreate(fname, H5F_ACC_TRUNC, fcpl, fapl); + } + else { + fd->h5fd = H5Fopen(fname, H5F_ACC_RDONLY, fapl); + } + + if (fd->h5fd < 0) { + HDfprintf(stderr, "HDF5 File Create failed(%s)\n", fname); + GOTOERROR(FAIL); + } + break; + + default: + /* unknown request */ + HDfprintf(stderr, "Unknown IO type request (%d)\n", (int)param->io_type); + GOTOERROR(FAIL); + break; + } + +done: + return ret_code; +} + +/* + * Function: set_vfd + * Purpose: Sets file driver. + * Return: SUCCESS or FAIL + * Programmer: Christian Chilan, April, 2008 + * Modifications: + */ + +hid_t +set_vfd(parameters *param) +{ + hid_t my_fapl = H5I_INVALID_HID; + vfdtype vfd; + + vfd = param->vfd; + + if ((my_fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) + return -1; + + if (vfd == sec2) { + /* Unix read() and write() system calls */ + if (H5Pset_fapl_sec2(my_fapl) < 0) + return -1; + } + else if (vfd == stdio) { + /* Standard C fread() and fwrite() system calls */ + if (H5Pset_fapl_stdio(my_fapl) < 0) + return -1; + } + else if (vfd == core) { + /* In-core temporary file with 1MB increment */ + if (H5Pset_fapl_core(my_fapl, (size_t)1024 * 1024, TRUE) < 0) + return -1; + } + else if (vfd == split) { + /* Split meta data and raw data each using default driver */ + if (H5Pset_fapl_split(my_fapl, "-m.h5", H5P_DEFAULT, "-r.h5", H5P_DEFAULT) < 0) + return -1; + } + else if (vfd == multi) { + /* Multi-file driver, general case of the split driver */ + H5FD_mem_t memb_map[H5FD_MEM_NTYPES]; + hid_t memb_fapl[H5FD_MEM_NTYPES]; + const char *memb_name[H5FD_MEM_NTYPES]; + char sv[H5FD_MEM_NTYPES][1024]; + haddr_t memb_addr[H5FD_MEM_NTYPES]; + H5FD_mem_t mt; + + HDmemset(memb_map, 0, sizeof memb_map); + HDmemset(memb_fapl, 0, sizeof memb_fapl); + HDmemset(memb_name, 0, sizeof memb_name); + HDmemset(memb_addr, 0, sizeof memb_addr); + + HDassert(HDstrlen(multi_letters) == H5FD_MEM_NTYPES); + for (mt = H5FD_MEM_DEFAULT; mt < H5FD_MEM_NTYPES; mt++) { + memb_fapl[mt] = H5P_DEFAULT; + HDsprintf(sv[mt], "%%s-%c.h5", multi_letters[mt]); + memb_name[mt] = sv[mt]; + memb_addr[mt] = (haddr_t)MAX(mt - 1, 0) * (HADDR_MAX / 10); + } + + if (H5Pset_fapl_multi(my_fapl, memb_map, memb_fapl, memb_name, memb_addr, FALSE) < 0) { + return -1; + } + } + else if (vfd == family) { + hsize_t fam_size = 1 * 1024 * 1024; /*100 MB*/ + + /* Family of files, each 1MB and using the default driver */ + /* if ((val=HDstrtok(NULL, " \t\n\r"))) + fam_size = (hsize_t)(HDstrtod(val, NULL) * 1024*1024); */ + if (H5Pset_fapl_family(my_fapl, fam_size, H5P_DEFAULT) < 0) + return -1; + } + else if (vfd == direct) { +#ifdef H5_HAVE_DIRECT + /* Linux direct read() and write() system calls. Set memory boundary, file block size, + * and copy buffer size to the default values. */ + if (H5Pset_fapl_direct(my_fapl, 1024, 4096, 8 * 4096) < 0) + return -1; +#endif + } + else { + /* Unknown driver */ + return -1; + } + + return my_fapl; +} + +/* + * Function: do_fclose + * Purpose: Close the specified file descriptor. + * Return: SUCCESS or FAIL + * Programmer: Albert Cheng, Bill Wendling, 2001/12/13 + * Modifications: + */ +static herr_t +do_fclose(iotype iot, file_descr *fd /*out*/) +{ + herr_t ret_code = SUCCESS, hrc; + int rc = 0; + + switch (iot) { + case POSIXIO: + rc = POSIXCLOSE(fd->posixfd); + + if (rc != 0) { + HDfprintf(stderr, "POSIX File Close failed\n"); + GOTOERROR(FAIL); + } + + fd->posixfd = -1; + break; + + case HDF5: + hrc = H5Fclose(fd->h5fd); + + if (hrc < 0) { + HDfprintf(stderr, "HDF5 File Close failed\n"); + GOTOERROR(FAIL); + } + + fd->h5fd = -1; + break; + + default: + /* unknown request */ + HDfprintf(stderr, "Unknown IO type request (%d)\n", (int)iot); + GOTOERROR(FAIL); + break; + } + +done: + return ret_code; +} + +/* + * Function: do_cleanupfile + * Purpose: Cleanup temporary file unless HDF5_NOCLEANUP is set. + * Return: void + * Programmer: Albert Cheng 2001/12/12 + * Modifications: Support for file drivers. Christian Chilan, April, 2008 + */ +static void +do_cleanupfile(iotype iot, char *filename) +{ + char temp[4096 + sizeof("-?.h5")]; + int j; + hid_t driver; + + if (clean_file_g == -1) + clean_file_g = (HDgetenv(HDF5_NOCLEANUP) == NULL) ? 1 : 0; + + if (clean_file_g) { + + switch (iot) { + case POSIXIO: + HDremove(filename); + break; + + case HDF5: + driver = H5Pget_driver(fapl); + + if (driver == H5FD_FAMILY) { + for (j = 0; /*void*/; j++) { + HDsnprintf(temp, sizeof temp, filename, j); + + if (HDaccess(temp, F_OK) < 0) + break; + + HDremove(temp); + } + } + else if (driver == H5FD_CORE) { + hbool_t backing; /* Whether the core file has backing store */ + + H5Pget_fapl_core(fapl, NULL, &backing); + + /* If the file was stored to disk with bacing store, remove it */ + if (backing) + HDremove(filename); + } + else if (driver == H5FD_MULTI) { + H5FD_mem_t mt; + assert(HDstrlen(multi_letters) == H5FD_MEM_NTYPES); + + for (mt = H5FD_MEM_DEFAULT; mt < H5FD_MEM_NTYPES; mt++) { + HDsnprintf(temp, sizeof temp, "%s-%c.h5", filename, multi_letters[mt]); + HDremove(temp); /*don't care if it fails*/ + } + } + else { + HDremove(filename); + } + H5Pclose(fapl); + break; + + default: + /* unknown request */ + HDfprintf(stderr, "Unknown IO type request (%d)\n", (int)iot); + HDassert(0 && "Unknown IO type"); + break; + } + } +} diff --git a/tools/src/h5perf/sio_perf.c b/tools/src/h5perf/sio_perf.c new file mode 100644 index 0000000..dc2e15e --- /dev/null +++ b/tools/src/h5perf/sio_perf.c @@ -0,0 +1,1300 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * Copyright by The HDF Group. * + * All rights reserved. * + * * + * This file is part of HDF5. The full HDF5 copyright notice, including * + * terms governing use, modification, and redistribution, is contained in * + * the COPYING file, which can be found at the root of the source code * + * distribution tree, or in https://www.hdfgroup.org/licenses. * + * If you do not have access to either file, you may request a copy from * + * help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + +/* + * Serial HDF5 Performance Testing Code + * -------------------------------------- + * + * Portable code to test performance on the different platforms we support. + * This is what the report should look like: + * + * nprocs = Max#Procs + * IO API = POSIXIO + * # Files = 1, # of dsets = 1000, Elements per dset = 37000 + * Write Results = x MB/s + * Read Results = x MB/s + * # Files = 1, # of dsets = 3000, Elements per dset = 37000 + * Write Results = x MB/s + * Read Results = x MB/s + * + * . . . + * + * + * IO API = HDF5 + * # Files = 1, # of dsets = 1000, Elements per dset = 37000 + * Write Results = x MB/s + * Read Results = x MB/s + * # Files = 1, # of dsets = 3000, Elements per dset = 37000 + * Write Results = x MB/s + * Read Results = x MB/s + * + * . . . + * + * + * . . . + * + */ + +/* system header files */ +#include <stdarg.h> +#include <stdio.h> +#include <stdlib.h> + +#include "hdf5.h" + +/* our header files */ +#include "sio_perf.h" + +/* useful macros */ +#define TAB_SPACE 4 + +#define ONE_KB 1024 +#define ONE_MB (ONE_KB * ONE_KB) +#define ONE_GB (ONE_MB * ONE_KB) + +#define SIO_POSIX 0x1 +#define SIO_HDF5 0x4 + +/* report 0.0 in case t is zero too */ +#define MB_PER_SEC(bytes, t) (H5_DBL_ABS_EQUAL(t, 0.0) ? 0.0 : ((((double)(bytes)) / (double)ONE_MB) / (t))) + +#ifndef TRUE +#define TRUE 1 +#endif /* TRUE */ +#ifndef FALSE +#define FALSE (!TRUE) +#endif /* FALSE */ + +/* global variables */ +FILE *output; /* output file */ +int sio_debug_level = 0; /* The debug level: + * 0 - Off + * 1 - Minimal + * 2 - Some more + * 3 - Maximal + * 4 - Maximal & then some + */ + +/* local variables */ +static const char *progname = "h5perf_serial"; + +/* + * Command-line options: The user can specify short or long-named + * parameters. The long-named ones can be partially spelled. When + * adding more, make sure that they don't clash with each other. + */ + +/* + * It seems that only the options that accept additional information + * such as dataset size (-e) require the colon next to it. + */ +static const char * s_opts = "a:A:B:c:Cd:D:e:F:ghi:Imno:p:P:r:stT:v:wx:X:"; +static struct h5_long_options l_opts[] = {{"align", require_arg, 'a'}, + {"api", require_arg, 'A'}, +#if 0 + /* a sighting of the elusive binary option */ + { "binary", no_arg, 'b' }, +#endif /* 0 */ + {"block-size", require_arg, 'B'}, + {"chunk", no_arg, 'c'}, + {"collective", no_arg, 'C'}, + {"debug", require_arg, 'D'}, + {"file-driver", require_arg, 'v'}, + {"geometry", no_arg, 'g'}, + {"help", no_arg, 'h'}, + {"interleaved", require_arg, 'I'}, + {"max-num-processes", require_arg, 'P'}, + {"min-num-processes", require_arg, 'p'}, + {"max-xfer-size", require_arg, 'X'}, + {"min-xfer-size", require_arg, 'x'}, + {"num-bytes", require_arg, 'e'}, + {"num-dsets", require_arg, 'd'}, + {"num-files", require_arg, 'F'}, + {"num-iterations", require_arg, 'i'}, + {"order", require_arg, 'r'}, + {"output", require_arg, 'o'}, + {"extendable", no_arg, 't'}, + {"threshold", require_arg, 'T'}, + {"write-only", require_arg, 'w'}, + {NULL, 0, '\0'}}; + +struct options { + long io_types; /* bitmask of which I/O types to test */ + const char *output_file; /* file to print report to */ + long num_dsets; /* number of datasets */ + long num_files; /* number of files */ + off_t num_bpp; /* number of bytes per proc per dset */ + int num_iters; /* number of iterations */ + hsize_t dset_size[MAX_DIMS]; /* Dataset size */ + size_t buf_size[MAX_DIMS]; /* Buffer size */ + size_t chk_size[MAX_DIMS]; /* Chunk size */ + int order[MAX_DIMS]; /* Dimension access order */ + int dset_rank; /* Rank */ + int buf_rank; /* Rank */ + int order_rank; /* Rank */ + int chk_rank; /* Rank */ + int print_times; /* print times as well as throughputs */ + int print_raw; /* print raw data throughput info */ + hsize_t h5_alignment; /* alignment in HDF5 file */ + hsize_t h5_threshold; /* threshold for alignment in HDF5 file */ + int h5_use_chunks; /* Make HDF5 dataset chunked */ + int h5_write_only; /* Perform the write tests only */ + int h5_extendable; /* Perform the write tests only */ + int verify; /* Verify data correctness */ + vfdtype vfd; /* File driver */ + size_t page_buffer_size; + size_t page_size; +}; + +typedef struct { + double min; + double max; + double sum; + int num; +} minmax; + +/* local functions */ +static hsize_t parse_size_directive(const char *size); +static struct options *parse_command_line(int argc, const char *const *argv); +static void run_test_loop(struct options *options); +static int run_test(iotype iot, parameters parms, struct options *opts); +static void output_all_info(minmax *mm, int count, int indent_level); +static void get_minmax(minmax *mm, double val); +static void accumulate_minmax_stuff(const minmax *mm, int count, minmax *total_mm); +static void output_results(const struct options *options, const char *name, minmax *table, int table_size, + off_t data_size); +static void output_report(const char *fmt, ...); +static void print_indent(int indent); +static void usage(const char *prog); +static void report_parameters(struct options *opts); + +/* + * Function: main + * Purpose: Start things up. + * Return: EXIT_SUCCESS or EXIT_FAILURE + * Programmer: Bill Wendling, 30. October 2001 + * Modifications: + */ +int +main(int argc, char *argv[]) +{ + int exit_value = EXIT_SUCCESS; + struct options *opts = NULL; + +#ifndef STANDALONE + /* Initialize h5tools lib */ + h5tools_init(); +#endif + + output = stdout; + + opts = parse_command_line(argc, (const char *const *)argv); + + if (!opts) { + exit_value = EXIT_FAILURE; + goto finish; + } + + if (opts->output_file) { + if ((output = HDfopen(opts->output_file, "w")) == NULL) { + HDfprintf(stderr, "%s: cannot open output file\n", progname); + HDperror(opts->output_file); + goto finish; + } + } + + report_parameters(opts); + + run_test_loop(opts); + +finish: + HDfree(opts); + return exit_value; +} + +/* + * Function: run_test_loop + * Purpose: Run the I/O tests. Write the results to OUTPUT. + * + * - The slowest changing part of the test is the number of + * processors to use. For each loop iteration, we divide that + * number by 2 and rerun the test. + * + * - The second slowest is what type of IO API to perform. We have + * three choices: POSIXIO, and HDF5. + * + * - Then we change the size of the buffer. This information is + * inferred from the number of datasets to create and the number + * of integers to put into each dataset. The backend code figures + * this out. + * + * Return: Nothing + * Programmer: Bill Wendling, 30. October 2001 + * Modifications: + * Added multidimensional testing (Christian Chilan, April, 2008) + */ +static void +run_test_loop(struct options *opts) +{ + parameters parms; + int i; + size_t buf_bytes; + + /* load options into parameter structure */ + parms.num_files = opts->num_files; + parms.num_dsets = opts->num_dsets; + parms.num_iters = opts->num_iters; + parms.rank = opts->dset_rank; + parms.h5_align = opts->h5_alignment; + parms.h5_thresh = opts->h5_threshold; + parms.h5_use_chunks = opts->h5_use_chunks; + parms.h5_extendable = opts->h5_extendable; + parms.h5_write_only = opts->h5_write_only; + parms.verify = opts->verify; + parms.vfd = opts->vfd; + parms.page_buffer_size = opts->page_buffer_size; + parms.page_size = opts->page_size; + + /* load multidimensional options */ + parms.num_bytes = 1; + buf_bytes = 1; + for (i = 0; i < parms.rank; i++) { + parms.buf_size[i] = opts->buf_size[i]; + parms.dset_size[i] = opts->dset_size[i]; + parms.chk_size[i] = opts->chk_size[i]; + parms.order[i] = opts->order[i]; + parms.num_bytes *= opts->dset_size[i]; + buf_bytes *= opts->buf_size[i]; + } + + /* print size information */ + output_report("Transfer Buffer Size (bytes): %zu\n", buf_bytes); + output_report("File Size(MB): %.2f\n", ((double)parms.num_bytes) / ONE_MB); + + print_indent(0); + if (opts->io_types & SIO_POSIX) + run_test(POSIXIO, parms, opts); + + print_indent(0); + if (opts->io_types & SIO_HDF5) + run_test(HDF5, parms, opts); +} + +/* + * Function: run_test + * Purpose: Inner loop call to actually run the I/O test. + * Return: Nothing + * Programmer: Bill Wendling, 18. December 2001 + * Modifications: + */ +static int +run_test(iotype iot, parameters parms, struct options *opts) +{ + results res; + int i, ret_value = SUCCESS; + off_t raw_size; + minmax *write_sys_mm_table = NULL; + minmax *write_mm_table = NULL; + minmax *write_gross_mm_table = NULL; + minmax *write_raw_mm_table = NULL; + minmax *read_sys_mm_table = NULL; + minmax *read_mm_table = NULL; + minmax *read_gross_mm_table = NULL; + minmax *read_raw_mm_table = NULL; + minmax write_sys_mm = {0.0, 0.0, 0.0, 0}; + minmax write_mm = {0.0, 0.0, 0.0, 0}; + minmax write_gross_mm = {0.0, 0.0, 0.0, 0}; + minmax write_raw_mm = {0.0, 0.0, 0.0, 0}; + minmax read_sys_mm = {0.0, 0.0, 0.0, 0}; + minmax read_mm = {0.0, 0.0, 0.0, 0}; + minmax read_gross_mm = {0.0, 0.0, 0.0, 0}; + minmax read_raw_mm = {0.0, 0.0, 0.0, 0}; + + raw_size = (off_t)parms.num_bytes; + parms.io_type = iot; + print_indent(2); + output_report("IO API = "); + + switch (iot) { + case POSIXIO: + output_report("POSIX\n"); + break; + case HDF5: + output_report("HDF5\n"); + break; + default: + /* unknown request */ + HDfprintf(stderr, "Unknown IO type request (%d)\n", (int)iot); + HDassert(0 && "Unknown IO tpe"); + break; + } + + /* allocate space for tables minmax and that it is sufficient */ + /* to initialize all elements to zeros by calloc. */ + write_sys_mm_table = (minmax *)calloc((size_t)parms.num_iters, sizeof(minmax)); + write_mm_table = (minmax *)calloc((size_t)parms.num_iters, sizeof(minmax)); + write_gross_mm_table = (minmax *)calloc((size_t)parms.num_iters, sizeof(minmax)); + write_raw_mm_table = (minmax *)calloc((size_t)parms.num_iters, sizeof(minmax)); + + if (!parms.h5_write_only) { + read_sys_mm_table = (minmax *)calloc((size_t)parms.num_iters, sizeof(minmax)); + read_mm_table = (minmax *)calloc((size_t)parms.num_iters, sizeof(minmax)); + read_gross_mm_table = (minmax *)calloc((size_t)parms.num_iters, sizeof(minmax)); + read_raw_mm_table = (minmax *)calloc((size_t)parms.num_iters, sizeof(minmax)); + } + + /* Do IO iteration times, collecting statistics each time */ + for (i = 0; i < parms.num_iters; ++i) { + double t; + + do_sio(parms, &res); + + /* gather all of the "sys write" times */ + t = io_time_get(res.timers, HDF5_MPI_WRITE); + get_minmax(&write_sys_mm, t); + + write_sys_mm_table[i] = write_sys_mm; + + /* gather all of the "write" times */ + t = io_time_get(res.timers, HDF5_FINE_WRITE_FIXED_DIMS); + get_minmax(&write_mm, t); + + write_mm_table[i] = write_mm; + + /* gather all of the "write" times from open to close */ + t = io_time_get(res.timers, HDF5_GROSS_WRITE_FIXED_DIMS); + get_minmax(&write_gross_mm, t); + + write_gross_mm_table[i] = write_gross_mm; + + /* gather all of the raw "write" times */ + t = io_time_get(res.timers, HDF5_RAW_WRITE_FIXED_DIMS); + get_minmax(&write_raw_mm, t); + + write_raw_mm_table[i] = write_raw_mm; + + if (!parms.h5_write_only) { + /* gather all of the "mpi read" times */ + t = io_time_get(res.timers, HDF5_MPI_READ); + get_minmax(&read_sys_mm, t); + + read_sys_mm_table[i] = read_sys_mm; + + /* gather all of the "read" times */ + t = io_time_get(res.timers, HDF5_FINE_READ_FIXED_DIMS); + get_minmax(&read_mm, t); + + read_mm_table[i] = read_mm; + + /* gather all of the "read" times from open to close */ + t = io_time_get(res.timers, HDF5_GROSS_READ_FIXED_DIMS); + get_minmax(&read_gross_mm, t); + + read_gross_mm_table[i] = read_gross_mm; + + /* gather all of the raw "read" times */ + t = io_time_get(res.timers, HDF5_RAW_READ_FIXED_DIMS); + get_minmax(&read_raw_mm, t); + + read_raw_mm_table[i] = read_gross_mm; + } + io_time_destroy(res.timers); + } + + /* + * Show various statistics + */ + /* Write statistics */ + /* Print the raw data throughput if desired */ + if (opts->print_raw) { + /* accumulate and output the max, min, and average "raw write" times */ + if (sio_debug_level >= 3) { + /* output all of the times for all iterations */ + print_indent(3); + output_report("Raw Data Write details:\n"); + output_all_info(write_raw_mm_table, parms.num_iters, 4); + } + + output_results(opts, "Raw Data Write", write_raw_mm_table, parms.num_iters, raw_size); + } /* end if */ + + /* show sys write statistics */ +#if 0 + if (sio_debug_level >= 3) { + /* output all of the times for all iterations */ + print_indent(3); + output_report("MPI Write details:\n"); + output_all_info(write_sys_mm_table, parms.num_iters, 4); + } +#endif + /* We don't currently output the MPI write results */ + + /* accumulate and output the max, min, and average "write" times */ + if (sio_debug_level >= 3) { + /* output all of the times for all iterations */ + print_indent(3); + output_report("Write details:\n"); + output_all_info(write_mm_table, parms.num_iters, 4); + } + + output_results(opts, "Write", write_mm_table, parms.num_iters, raw_size); + + /* accumulate and output the max, min, and average "gross write" times */ + if (sio_debug_level >= 3) { + /* output all of the times for all iterations */ + print_indent(3); + output_report("Write Open-Close details:\n"); + output_all_info(write_gross_mm_table, parms.num_iters, 4); + } + + output_results(opts, "Write Open-Close", write_gross_mm_table, parms.num_iters, raw_size); + + if (!parms.h5_write_only) { + /* Read statistics */ + /* Print the raw data throughput if desired */ + if (opts->print_raw) { + /* accumulate and output the max, min, and average "raw read" times */ + if (sio_debug_level >= 3) { + /* output all of the times for all iterations */ + print_indent(3); + output_report("Raw Data Read details:\n"); + output_all_info(read_raw_mm_table, parms.num_iters, 4); + } + + output_results(opts, "Raw Data Read", read_raw_mm_table, parms.num_iters, raw_size); + } /* end if */ + + /* show mpi read statistics */ +#if 0 + if (sio_debug_level >= 3) { + /* output all of the times for all iterations */ + print_indent(3); + output_report("MPI Read details:\n"); + output_all_info(read_sys_mm_table, parms.num_iters, 4); + } +#endif + /* We don't currently output the MPI read results */ + + /* accumulate and output the max, min, and average "read" times */ + if (sio_debug_level >= 3) { + /* output all of the times for all iterations */ + print_indent(3); + output_report("Read details:\n"); + output_all_info(read_mm_table, parms.num_iters, 4); + } + + output_results(opts, "Read", read_mm_table, parms.num_iters, raw_size); + + /* accumulate and output the max, min, and average "gross read" times */ + if (sio_debug_level >= 3) { + /* output all of the times for all iterations */ + print_indent(3); + output_report("Read Open-Close details:\n"); + output_all_info(read_gross_mm_table, parms.num_iters, 4); + } + + output_results(opts, "Read Open-Close", read_gross_mm_table, parms.num_iters, raw_size); + } + + /* clean up our mess */ + HDfree(write_sys_mm_table); + HDfree(write_mm_table); + HDfree(write_gross_mm_table); + HDfree(write_raw_mm_table); + + if (!parms.h5_write_only) { + HDfree(read_sys_mm_table); + HDfree(read_mm_table); + HDfree(read_gross_mm_table); + HDfree(read_raw_mm_table); + } + + return ret_value; +} + +/* + * Function: output_all_info + * Purpose: + * Return: Nothing + * Programmer: Bill Wendling, 29. January 2002 + * Modifications: + */ +static void +output_all_info(minmax *mm, int count, int indent_level) +{ + int i; + + for (i = 0; i < count; ++i) { + print_indent(indent_level); + output_report("Iteration %d:\n", i + 1); + print_indent(indent_level + 1); + output_report("Minimum Time: %.2fs\n", mm[i].min); + print_indent(indent_level + 1); + output_report("Maximum Time: %.2fs\n", mm[i].max); + } +} + +/* + * Function: get_minmax + * Purpose: Gather all the min, max and total of val. + * Return: Nothing + * Programmer: Bill Wendling, 21. December 2001 + * Modifications: + * Use MPI_Allreduce to do it. -akc, 2002/01/11 + */ + +static void +get_minmax(minmax *mm, double val) +{ + mm->max = val; + mm->min = val; + mm->sum = val; +} + +/* + * Function: accumulate_minmax_stuff + * Purpose: Accumulate the minimum, maximum, and average of the times + * across all processes. + * Return: TOTAL_MM - the total of all of these. + * Programmer: Bill Wendling, 21. December 2001 + * Modifications: + * Changed to use seconds instead of MB/s - QAK, 5/9/02 + */ +static void +accumulate_minmax_stuff(const minmax *mm, int count, minmax *total_mm) +{ + int i; + + total_mm->sum = 0.0; + total_mm->max = -DBL_MAX; + total_mm->min = DBL_MAX; + total_mm->num = count; + + for (i = 0; i < count; ++i) { + double m = mm[i].max; + + total_mm->sum += m; + + if (m < total_mm->min) + total_mm->min = m; + + if (m > total_mm->max) + total_mm->max = m; + } +} + +/* + * Function: output_results + * Purpose: Print information about the time & bandwidth for a given + * minmax & # of iterations. + * Return: Nothing + * Programmer: Quincey Koziol, 9. May 2002 + * Modifications: + */ +static void +output_results(const struct options *opts, const char *name, minmax *table, int table_size, off_t data_size) +{ + minmax total_mm; + + accumulate_minmax_stuff(table, table_size, &total_mm); + + print_indent(3); + output_report("%s (%d iteration(s)):\n", name, table_size); + + /* Note: The maximum throughput uses the minimum amount of time & vice versa */ + + print_indent(4); + output_report("Maximum Throughput: %6.2f MB/s", MB_PER_SEC(data_size, total_mm.min)); + if (opts->print_times) + output_report(" (%7.3f s)\n", total_mm.min); + else + output_report("\n"); + + print_indent(4); + output_report("Average Throughput: %6.2f MB/s", MB_PER_SEC(data_size, total_mm.sum / total_mm.num)); + if (opts->print_times) + output_report(" (%7.3f s)\n", (total_mm.sum / total_mm.num)); + else + output_report("\n"); + + print_indent(4); + output_report("Minimum Throughput: %6.2f MB/s", MB_PER_SEC(data_size, total_mm.max)); + if (opts->print_times) + output_report(" (%7.3f s)\n", total_mm.max); + else + output_report("\n"); +} + +/* + * Function: output_report + * Purpose: Print a line of the report. Only do so if I'm the 0 process. + * Return: Nothing + * Programmer: Bill Wendling, 19. December 2001 + * Modifications: + */ +static void +output_report(const char *fmt, ...) +{ + va_list ap; + + HDva_start(ap, fmt); + HDvfprintf(output, fmt, ap); + HDva_end(ap); +} + +/* + * Function: print_indent + * Purpose: Print spaces to indent a new line of text for pretty printing + * things. + * Return: Nothing + * Programmer: Bill Wendling, 29. October 2001 + */ +static void +print_indent(int indent) +{ + indent *= TAB_SPACE; + + for (; indent > 0; --indent) + HDfputc(' ', output); +} + +static void +recover_size_and_print(long long val, const char *end) +{ + if (val >= ONE_KB && (val % ONE_KB) == 0) { + if (val >= ONE_MB && (val % ONE_MB) == 0) { + if (val >= ONE_GB && (val % ONE_GB) == 0) + HDfprintf(output, + "%" H5_PRINTF_LL_WIDTH "d" + "GB%s", + val / ONE_GB, end); + else + HDfprintf(output, + "%" H5_PRINTF_LL_WIDTH "d" + "MB%s", + val / ONE_MB, end); + } + else { + HDfprintf(output, + "%" H5_PRINTF_LL_WIDTH "d" + "KB%s", + val / ONE_KB, end); + } + } + else { + HDfprintf(output, + "%" H5_PRINTF_LL_WIDTH "d" + "%s", + val, end); + } +} + +static void +print_io_api(long io_types) +{ + if (io_types & SIO_POSIX) + HDfprintf(output, "posix "); + if (io_types & SIO_HDF5) + HDfprintf(output, "hdf5 "); + HDfprintf(output, "\n"); +} + +static void +report_parameters(struct options *opts) +{ + int i, rank; + rank = opts->dset_rank; + + print_version("HDF5 Library"); /* print library version */ + HDfprintf(output, "==== Parameters ====\n"); + + HDfprintf(output, "IO API="); + print_io_api(opts->io_types); + + HDfprintf(output, "Number of iterations=%d\n", opts->num_iters); + + HDfprintf(output, "Dataset size="); + + for (i = 0; i < rank; i++) + recover_size_and_print((long long)opts->dset_size[i], " "); + HDfprintf(output, "\n"); + + HDfprintf(output, "Transfer buffer size="); + for (i = 0; i < rank; i++) + recover_size_and_print((long long)opts->buf_size[i], " "); + HDfprintf(output, "\n"); + + if (opts->page_size) { + HDfprintf(output, "Page Aggregation Enabled. Page size = %zu\n", opts->page_size); + if (opts->page_buffer_size) + HDfprintf(output, "Page Buffering Enabled. Page Buffer size = %zu\n", opts->page_buffer_size); + else + HDfprintf(output, "Page Buffering Disabled\n"); + } + else + HDfprintf(output, "Page Aggregation Disabled\n"); + + HDfprintf(output, "Dimension access order="); + for (i = 0; i < rank; i++) + recover_size_and_print((long long)opts->order[i], " "); + HDfprintf(output, "\n"); + + if (opts->io_types & SIO_HDF5) { + + HDfprintf(output, "HDF5 data storage method="); + + if (opts->h5_use_chunks) { + + HDfprintf(output, "Chunked\n"); + HDfprintf(output, "HDF5 chunk size="); + for (i = 0; i < rank; i++) + recover_size_and_print((long long)opts->chk_size[i], " "); + HDfprintf(output, "\n"); + + HDfprintf(output, "HDF5 dataset dimensions="); + if (opts->h5_extendable) { + HDfprintf(output, "Extendable\n"); + } + else { + HDfprintf(output, "Fixed\n"); + } + } + else { + HDfprintf(output, "Contiguous\n"); + } + + HDfprintf(output, "HDF5 file driver="); + if (opts->vfd == sec2) { + HDfprintf(output, "sec2\n"); + } + else if (opts->vfd == stdio) { + HDfprintf(output, "stdio\n"); + } + else if (opts->vfd == core) { + HDfprintf(output, "core\n"); + } + else if (opts->vfd == split) { + HDfprintf(output, "split\n"); + } + else if (opts->vfd == multi) { + HDfprintf(output, "multi\n"); + } + else if (opts->vfd == family) { + HDfprintf(output, "family\n"); + } + else if (opts->vfd == direct) { + HDfprintf(output, "direct\n"); + } + } + + { + char *prefix = HDgetenv("HDF5_PREFIX"); + + HDfprintf(output, "Env HDF5_PREFIX=%s\n", (prefix ? prefix : "not set")); + } + + HDfprintf(output, "==== End of Parameters ====\n"); + HDfprintf(output, "\n"); +} + +/* + * Function: parse_command_line + * Purpose: Parse the command line options and return a STRUCT OPTIONS + * structure which will need to be freed by the calling function. + * Return: Pointer to an OPTIONS structure + * Programmer: Bill Wendling, 31. October 2001 + * Modifications: + * Added multidimensional testing (Christian Chilan, April, 2008) + */ +static struct options * +parse_command_line(int argc, const char *const *argv) +{ + int opt; + struct options *cl_opts; + int i, default_rank, actual_rank, ranks[4]; + + cl_opts = (struct options *)HDmalloc(sizeof(struct options)); + + cl_opts->page_buffer_size = 0; + cl_opts->page_size = 0; + + cl_opts->output_file = NULL; + cl_opts->io_types = 0; /* will set default after parsing options */ + cl_opts->num_iters = 1; + + default_rank = 2; + + cl_opts->dset_rank = 0; + cl_opts->buf_rank = 0; + cl_opts->chk_rank = 0; + cl_opts->order_rank = 0; + + for (i = 0; i < MAX_DIMS; i++) { + cl_opts->buf_size[i] = (size_t)((i + 1) * 10); + cl_opts->dset_size[i] = (hsize_t)((i + 1) * 100); + cl_opts->chk_size[i] = (size_t)((i + 1) * 10); + cl_opts->order[i] = i + 1; + } + + cl_opts->vfd = sec2; + + cl_opts->print_times = FALSE; /* Printing times is off by default */ + cl_opts->print_raw = FALSE; /* Printing raw data throughput is off by default */ + cl_opts->h5_alignment = 1; /* No alignment for HDF5 objects by default */ + cl_opts->h5_threshold = 1; /* No threshold for aligning HDF5 objects by default */ + cl_opts->h5_use_chunks = FALSE; /* Don't chunk the HDF5 dataset by default */ + cl_opts->h5_write_only = FALSE; /* Do both read and write by default */ + cl_opts->h5_extendable = FALSE; /* Use extendable dataset */ + cl_opts->verify = FALSE; /* No Verify data correctness by default */ + + while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) { + switch ((char)opt) { + case 'a': + cl_opts->h5_alignment = parse_size_directive(H5_optarg); + break; + case 'G': + cl_opts->page_size = parse_size_directive(H5_optarg); + break; + case 'b': + cl_opts->page_buffer_size = parse_size_directive(H5_optarg); + break; + case 'A': { + const char *end = H5_optarg; + while (end && *end != '\0') { + char buf[10]; + + HDmemset(buf, '\0', sizeof(buf)); + + for (i = 0; *end != '\0' && *end != ','; ++end) + if (HDisalnum(*end) && i < 10) + buf[i++] = *end; + + if (!HDstrcasecmp(buf, "hdf5")) { + cl_opts->io_types |= SIO_HDF5; + } + else if (!HDstrcasecmp(buf, "posix")) { + cl_opts->io_types |= SIO_POSIX; + } + else { + HDfprintf(stderr, "sio_perf: invalid --api option %s\n", buf); + HDexit(EXIT_FAILURE); + } + + if (*end == '\0') + break; + + end++; + } + } + + break; +#if 0 + case 'b': + /* the future "binary" option */ + break; +#endif /* 0 */ + case 'c': + /* Turn on chunked HDF5 dataset creation */ + cl_opts->h5_use_chunks = 1; + { + const char *end = H5_optarg; + int j = 0; + + while (end && *end != '\0') { + char buf[10]; + + HDmemset(buf, '\0', sizeof(buf)); + + for (i = 0; *end != '\0' && *end != ','; ++end) + if (HDisalnum(*end) && i < 10) + buf[i++] = *end; + + cl_opts->chk_size[j] = parse_size_directive(buf); + + j++; + + if (*end == '\0') + break; + + end++; + } + cl_opts->chk_rank = j; + } + + break; + + case 'D': { + const char *end = H5_optarg; + + while (end && *end != '\0') { + char buf[10]; + + HDmemset(buf, '\0', sizeof(buf)); + + for (i = 0; *end != '\0' && *end != ','; ++end) + if (HDisalnum(*end) && i < 10) + buf[i++] = *end; + + if (HDstrlen(buf) > 1 || HDisdigit(buf[0])) { + size_t j; + + for (j = 0; j < 10 && buf[j] != '\0'; ++j) + if (!HDisdigit(buf[j])) { + HDfprintf(stderr, "sio_perf: invalid --debug option %s\n", buf); + HDexit(EXIT_FAILURE); + } + + sio_debug_level = atoi(buf); + + if (sio_debug_level > 4) + sio_debug_level = 4; + else if (sio_debug_level < 0) + sio_debug_level = 0; + } + else { + switch (*buf) { + case 'r': + /* Turn on raw data throughput info */ + cl_opts->print_raw = TRUE; + break; + case 't': + /* Turn on time printing */ + cl_opts->print_times = TRUE; + break; + case 'v': + /* Turn on verify data correctness*/ + cl_opts->verify = TRUE; + break; + default: + HDfprintf(stderr, "sio_perf: invalid --debug option %s\n", buf); + HDexit(EXIT_FAILURE); + } + } + + if (*end == '\0') + break; + + end++; + } + } + + break; + case 'e': { + const char *end = H5_optarg; + int j = 0; + + while (end && *end != '\0') { + char buf[10]; + + HDmemset(buf, '\0', sizeof(buf)); + + for (i = 0; *end != '\0' && *end != ','; ++end) + if (HDisalnum(*end) && i < 10) + buf[i++] = *end; + + cl_opts->dset_size[j] = parse_size_directive(buf); + + j++; + + if (*end == '\0') + break; + + end++; + } + cl_opts->dset_rank = j; + } + + break; + + case 'i': + cl_opts->num_iters = HDatoi(H5_optarg); + break; + case 'o': + cl_opts->output_file = H5_optarg; + break; + case 'T': + cl_opts->h5_threshold = parse_size_directive(H5_optarg); + break; + case 'v': + if (!HDstrcasecmp(H5_optarg, "sec2")) { + cl_opts->vfd = sec2; + } + else if (!HDstrcasecmp(H5_optarg, "stdio")) { + cl_opts->vfd = stdio; + } + else if (!HDstrcasecmp(H5_optarg, "core")) { + cl_opts->vfd = core; + } + else if (!HDstrcasecmp(H5_optarg, "split")) { + cl_opts->vfd = split; + } + else if (!HDstrcasecmp(H5_optarg, "multi")) { + cl_opts->vfd = multi; + } + else if (!HDstrcasecmp(H5_optarg, "family")) { + cl_opts->vfd = family; + } + else if (!HDstrcasecmp(H5_optarg, "direct")) { + cl_opts->vfd = direct; + } + else { + HDfprintf(stderr, "sio_perf: invalid --api option %s\n", H5_optarg); + HDexit(EXIT_FAILURE); + } + break; + case 'w': + cl_opts->h5_write_only = TRUE; + break; + case 't': + cl_opts->h5_extendable = TRUE; + break; + case 'x': { + const char *end = H5_optarg; + int j = 0; + + while (end && *end != '\0') { + char buf[10]; + + HDmemset(buf, '\0', sizeof(buf)); + + for (i = 0; *end != '\0' && *end != ','; ++end) + if (HDisalnum(*end) && i < 10) + buf[i++] = *end; + + cl_opts->buf_size[j] = parse_size_directive(buf); + + j++; + + if (*end == '\0') + break; + + end++; + } + cl_opts->buf_rank = j; + } + + break; + + case 'r': { + const char *end = H5_optarg; + int j = 0; + + while (end && *end != '\0') { + char buf[10]; + + HDmemset(buf, '\0', sizeof(buf)); + + for (i = 0; *end != '\0' && *end != ','; ++end) + if (HDisalnum(*end) && i < 10) + buf[i++] = *end; + + cl_opts->order[j] = (int)parse_size_directive(buf); + + j++; + + if (*end == '\0') + break; + + end++; + } + + cl_opts->order_rank = j; + } + + break; + + case 'h': + case '?': + default: + usage(progname); + HDfree(cl_opts); + return NULL; + } + } + + /* perform rank consistency analysis */ + actual_rank = 0; + + ranks[0] = cl_opts->dset_rank; + ranks[1] = cl_opts->buf_rank; + ranks[2] = cl_opts->order_rank; + ranks[3] = cl_opts->chk_rank; + + for (i = 0; i < 4; i++) { + if (ranks[i] > 0) { + if (!actual_rank) { + actual_rank = ranks[i]; + } + else { + if (actual_rank != ranks[i]) + exit(EXIT_FAILURE); + } + } + } + + if (!actual_rank) + actual_rank = default_rank; + + cl_opts->dset_rank = actual_rank; + cl_opts->buf_rank = actual_rank; + cl_opts->order_rank = actual_rank; + cl_opts->chk_rank = actual_rank; + + for (i = 0; i < actual_rank; i++) { + if (cl_opts->order[i] > actual_rank) { + exit(EXIT_FAILURE); + } + } + + /* set default if none specified yet */ + if (!cl_opts->io_types) + cl_opts->io_types = SIO_HDF5 | SIO_POSIX; /* run all API */ + + /* verify parameters sanity. Adjust if needed. */ + /* cap xfer_size with bytes per process */ + if (cl_opts->num_iters <= 0) + cl_opts->num_iters = 1; + + return cl_opts; +} + +/* + * Function: parse_size_directive + * Purpose: Parse the size directive passed on the commandline. The size + * directive is an integer followed by a size indicator: + * + * K, k - Kilobyte + * M, m - Megabyte + * G, g - Gigabyte + * + * Return: The size as a off_t because this is related to file size. + * If an unknown size indicator is used, then the program will + * exit with EXIT_FAILURE as the return value. + * Programmer: Bill Wendling, 18. December 2001 + * Modifications: + */ + +static hsize_t +parse_size_directive(const char *size) +{ + hsize_t s; + char * endptr; + + s = HDstrtoull(size, &endptr, 10); + + if (endptr && *endptr) { + while (*endptr != '\0' && (*endptr == ' ' || *endptr == '\t')) + ++endptr; + + switch (*endptr) { + case 'K': + case 'k': + s *= ONE_KB; + break; + + case 'M': + case 'm': + s *= ONE_MB; + break; + + case 'G': + case 'g': + s *= ONE_GB; + break; + + default: + HDfprintf(stderr, "Illegal size specifier '%c'\n", *endptr); + HDexit(EXIT_FAILURE); + } + } + + return s; +} + +/* + * Function: usage + * Purpose: Print a usage message and then exit. + * Return: Nothing + * Programmer: Bill Wendling, 31. October 2001 + * Modifications: + */ +static void +usage(const char *prog) +{ + print_version(prog); + HDprintf("usage: %s [OPTIONS]\n", prog); + HDprintf(" OPTIONS\n"); + HDprintf(" -h Print an usage message and exit\n"); + HDprintf(" -A AL Which APIs to test\n"); + HDprintf(" [default: all of them]\n"); + HDprintf(" -c SL Selects chunked storage and defines chunks dimensions\n"); + HDprintf(" and sizes\n"); + HDprintf(" [default: Off]\n"); + HDprintf(" -e SL Dimensions and sizes of dataset\n"); + HDprintf(" [default: 100,200]\n"); + HDprintf(" -i N Number of iterations to perform\n"); + HDprintf(" [default: 1]\n"); + HDprintf(" -r NL Dimension access order (see below for description)\n"); + HDprintf(" [default: 1,2]\n"); + HDprintf(" -t Selects extendable dimensions for HDF5 dataset\n"); + HDprintf(" [default: Off]\n"); + HDprintf(" -v VFD Selects file driver for HDF5 access\n"); + HDprintf(" [default: sec2]\n"); + HDprintf(" -w Perform write tests, not the read tests\n"); + HDprintf(" [default: Off]\n"); + HDprintf(" -x SL Dimensions and sizes of the transfer buffer\n"); + HDprintf(" [default: 10,20]\n"); + HDprintf("\n"); + HDprintf(" N - is an integer > 0.\n"); + HDprintf("\n"); + HDprintf(" S - is a size specifier, an integer > 0 followed by a size indicator:\n"); + HDprintf(" K - Kilobyte (%d)\n", ONE_KB); + HDprintf(" M - Megabyte (%d)\n", ONE_MB); + HDprintf(" G - Gigabyte (%d)\n", ONE_GB); + HDprintf("\n"); + HDprintf(" Example: '37M' is 37 megabytes or %d bytes\n", 37 * ONE_MB); + HDprintf("\n"); + HDprintf(" AL - is an API list. Valid values are:\n"); + HDprintf(" hdf5 - HDF5\n"); + HDprintf(" posix - POSIX\n"); + HDprintf("\n"); + HDprintf(" Example: -A posix,hdf5\n"); + HDprintf("\n"); + HDprintf(" NL - is list of integers (N) separated by commas.\n"); + HDprintf("\n"); + HDprintf(" Example: 1,2,3\n"); + HDprintf("\n"); + HDprintf(" SL - is list of size specifiers (S) separated by commas.\n"); + HDprintf("\n"); + HDprintf(" Example: 2K,2K,3K\n"); + HDprintf("\n"); + HDprintf(" The example defines an object (dataset, transfer buffer) with three\n"); + HDprintf(" dimensions. Be aware that as the number of dimensions increases, the\n"); + HDprintf(" the total size of the object increases exponentially.\n"); + HDprintf("\n"); + HDprintf(" VFD - is an HDF5 file driver specifier. Valid values are:\n"); + HDprintf(" sec2, stdio, core, split, multi, family, direct\n"); + HDprintf("\n"); + HDprintf(" Dimension access order:\n"); + HDprintf(" Data access starts at the cardinal origin of the dataset using the\n"); + HDprintf(" transfer buffer. The next access occurs on a dataset region next to\n"); + HDprintf(" the previous one. For a multidimensional dataset, there are several\n"); + HDprintf(" directions as to where to proceed. This can be specified in the dimension\n"); + HDprintf(" access order. For example, -r 1,2 states that the tool should traverse\n"); + HDprintf(" dimension 1 first, and then dimension 2.\n"); + HDprintf("\n"); + HDprintf(" Environment variables:\n"); + HDprintf(" HDF5_NOCLEANUP Do not remove data files if set [default remove]\n"); + HDprintf(" HDF5_PREFIX Data file prefix\n"); + HDprintf("\n"); + HDfflush(stdout); +} /* end usage() */ diff --git a/tools/src/h5perf/sio_perf.h b/tools/src/h5perf/sio_perf.h new file mode 100644 index 0000000..d998377 --- /dev/null +++ b/tools/src/h5perf/sio_perf.h @@ -0,0 +1,104 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * Copyright by The HDF Group. * + * All rights reserved. * + * * + * This file is part of HDF5. The full HDF5 copyright notice, including * + * terms governing use, modification, and redistribution, is contained in * + * the COPYING file, which can be found at the root of the source code * + * distribution tree, or in https://www.hdfgroup.org/licenses. * + * If you do not have access to either file, you may request a copy from * + * help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + +#ifndef SIO_PERF_H +#define SIO_PERF_H + +#ifndef STANDALONE +#include "io_timer.h" +#include "H5private.h" +#include "h5tools.h" +#include "h5tools_utils.h" +#else +#include "io_timer.h" +#include "sio_standalone.h" +#endif + +/* setup the dataset no fill option if this is v1.5 or more */ +#if H5_VERS_MAJOR > 1 || H5_VERS_MINOR > 4 +#define H5_HAVE_NOFILL 1 +#endif + +#define MAX_DIMS 32 + +typedef enum iotype_ { + POSIXIO, + HDF5 + /*NUM_TYPES*/ +} iotype; + +typedef enum vfdtype_ { + sec2, + stdio, + core, + split, + multi, + family, + direct + /*NUM_TYPES*/ +} vfdtype; + +typedef struct parameters_ { + iotype io_type; /* The type of IO test to perform */ + vfdtype vfd; + long num_files; /* Number of files to create */ + long num_dsets; /* Number of datasets to create */ + hsize_t num_bytes; /* Number of bytes in each dset */ + int num_iters; /* Number of times to loop doing the IO */ + int rank; /* Rank of dataset */ + hsize_t dset_size[MAX_DIMS]; /* Dataset size */ + size_t buf_size[MAX_DIMS]; /* Buffer size */ + size_t chk_size[MAX_DIMS]; /* Chunk size */ + int order[MAX_DIMS]; /* Buffer size */ + hsize_t h5_align; /* HDF5 object alignment */ + hsize_t h5_thresh; /* HDF5 object alignment threshold */ + int h5_use_chunks; /* Make HDF5 dataset chunked */ + int h5_extendable; /* Make HDF5 dataset chunked */ + int h5_write_only; /* Perform the write tests only */ + int verify; /* Verify data correctness */ + size_t page_size; + size_t page_buffer_size; +} parameters; + +typedef struct results_ { + herr_t ret_code; + io_time_t *timers; +} results; + +#ifndef SUCCESS +#define SUCCESS 0 +#endif /* !SUCCESS */ + +#ifndef FAIL +#define FAIL -1 +#endif /* !FAIL */ + +extern FILE * output; /* output file */ +extern io_time_t *timer_g; /* timer: global for stub functions */ +extern int sio_debug_level; /* The debug level: + * 0 - Off + * 1 - Minimal + * 2 - Some more + * 3 - Maximal + * 4 - Even More Debugging (timer stuff) + */ +#ifdef __cplusplus +extern "C" { +#endif /* __cplusplus */ + +extern void do_sio(parameters param, results *res); + +#ifdef __cplusplus +} +#endif /* __cplusplus */ + +#endif /* SIO_PERF_H */ diff --git a/tools/src/h5repack/CMakeLists.txt b/tools/src/h5repack/CMakeLists.txt index 4a1430e..b8b4709 100644 --- a/tools/src/h5repack/CMakeLists.txt +++ b/tools/src/h5repack/CMakeLists.txt @@ -1,4 +1,4 @@ -cmake_minimum_required (VERSION 3.10) +cmake_minimum_required (VERSION 3.12) project (HDF5_TOOLS_SRC_H5REPACK C) # -------------------------------------------------------------------- @@ -12,11 +12,13 @@ set (REPACK_COMMON_SOURCES ${HDF5_TOOLS_SRC_H5REPACK_SOURCE_DIR}/h5repack_refs.c ${HDF5_TOOLS_SRC_H5REPACK_SOURCE_DIR}/h5repack_verify.c ${HDF5_TOOLS_SRC_H5REPACK_SOURCE_DIR}/h5repack.c + ${HDF5_TOOLS_SRC_H5REPACK_SOURCE_DIR}/h5repack.h ) if (NOT ONLY_SHARED_LIBS) add_executable (h5repack ${REPACK_COMMON_SOURCES} ${HDF5_TOOLS_SRC_H5REPACK_SOURCE_DIR}/h5repack_main.c) - target_include_directories (h5repack PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5repack PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_compile_options(h5repack PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5repack STATIC) target_link_libraries (h5repack PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) set_target_properties (h5repack PROPERTIES FOLDER tools) @@ -27,7 +29,8 @@ endif () if (BUILD_SHARED_LIBS) add_executable (h5repack-shared ${REPACK_COMMON_SOURCES} ${HDF5_TOOLS_SRC_H5REPACK_SOURCE_DIR}/h5repack_main.c) - target_include_directories (h5repack-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5repack-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_compile_options(h5repack-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5repack-shared SHARED) target_link_libraries (h5repack-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET}) set_target_properties (h5repack-shared PROPERTIES FOLDER tools) @@ -36,6 +39,17 @@ if (BUILD_SHARED_LIBS) set (H5_DEP_EXECUTABLES ${H5_DEP_EXECUTABLES} h5repack-shared) endif () +#----------------------------------------------------------------------------- +# Add Target to clang-format +#----------------------------------------------------------------------------- +if (HDF5_ENABLE_FORMATTERS) + if (NOT ONLY_SHARED_LIBS) + clang_format (HDF5_H5REPACK_SRC_FORMAT h5repack) + else () + clang_format (HDF5_H5REPACK_SRC_FORMAT h5repack-shared) + endif () +endif () + ############################################################################## ############################################################################## ### I N S T A L L A T I O N ### diff --git a/tools/src/h5repack/Makefile.am b/tools/src/h5repack/Makefile.am index 925b8a7..245329d 100644 --- a/tools/src/h5repack/Makefile.am +++ b/tools/src/h5repack/Makefile.am @@ -6,7 +6,7 @@ # This file is part of HDF5. The full HDF5 copyright notice, including # terms governing use, modification, and redistribution, is contained in # the COPYING file, which can be found at the root of the source code -# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. +# distribution tree, or in https://www.hdfgroup.org/licenses. # If you do not have access to either file, you may request a copy from # help@hdfgroup.org. ## diff --git a/tools/src/h5repack/h5repack.c b/tools/src/h5repack/h5repack.c index c18df6c..d0aad79 100644 --- a/tools/src/h5repack/h5repack.c +++ b/tools/src/h5repack/h5repack.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -22,10 +22,10 @@ *------------------------------------------------------------------------- */ -static int check_options(pack_opt_t *options); -static int check_objects(const char* fname, pack_opt_t *options); -static const char* get_sfilter(H5Z_filter_t filtn); -static int have_request(pack_opt_t *options); +static int check_options(pack_opt_t *options); +static int check_objects(const char *fname, pack_opt_t *options); +static const char *get_sfilter(H5Z_filter_t filtn); +static int have_request(pack_opt_t *options); /*------------------------------------------------------------------------- * Function: h5repack @@ -41,7 +41,9 @@ static int have_request(pack_opt_t *options); * Return: 0, ok, -1, fail *------------------------------------------------------------------------- */ -int h5repack(const char* infile, const char* outfile, pack_opt_t *options) { +int +h5repack(const char *infile, const char *outfile, pack_opt_t *options) +{ /* check input */ if (check_options(options) < 0) return -1; @@ -55,7 +57,7 @@ int h5repack(const char* infile, const char* outfile, pack_opt_t *options) { return -1; return 0; -} +} /* end h5repack() */ /*------------------------------------------------------------------------- * Function: h5repack_init @@ -71,22 +73,24 @@ h5repack_init(pack_opt_t *options, int verbose, hbool_t latest) int k, n; HDmemset(options, 0, sizeof(pack_opt_t)); - options->min_comp = 0; - options->verbose = verbose; - options->latest = latest; - options->layout_g = H5D_LAYOUT_ERROR; - options->low_bound = H5F_LIBVER_EARLIEST; + options->min_comp = 0; + options->verbose = verbose; + options->latest = latest; + options->layout_g = H5D_LAYOUT_ERROR; + options->low_bound = H5F_LIBVER_EARLIEST; options->high_bound = H5F_LIBVER_LATEST; + options->fin_fapl = H5P_DEFAULT; + options->fout_fapl = H5P_DEFAULT; for (n = 0; n < H5_REPACK_MAX_NFILTERS; n++) { - options->filter_g[n].filtn = -1; + options->filter_g[n].filtn = -1; options->filter_g[n].cd_nelmts = 0; for (k = 0; k < CD_VALUES; k++) options->filter_g[n].cd_values[k] = 0; } return (options_table_init(&(options->op_tbl))); -} +} /* end h5repack_init() */ /*------------------------------------------------------------------------- * Function: h5repack_end @@ -95,9 +99,11 @@ h5repack_init(pack_opt_t *options, int verbose, hbool_t latest) *------------------------------------------------------------------------- */ -int h5repack_end(pack_opt_t *options) { +int +h5repack_end(pack_opt_t *options) +{ return options_table_free(options->op_tbl); -} +} /* end h5repack_end() */ /*------------------------------------------------------------------------- * Function: h5repack_addfilter @@ -111,7 +117,7 @@ int h5repack_end(pack_opt_t *options) { int h5repack_addfilter(const char *str, pack_opt_t *options) { - obj_list_t *obj_list = NULL; /* one object list for the -f and -l option entry */ + obj_list_t * obj_list = NULL; /* one object list for the -f and -l option entry */ filter_info_t filter; /* filter info for the current -f option entry */ unsigned n_objs; /* number of objects in the current -f or -l option entry */ int is_glb; /* is the filter global */ @@ -138,7 +144,7 @@ h5repack_addfilter(const char *str, pack_opt_t *options) HDfree(obj_list); return 0; -} +} /* end h5repack_addfilter() */ /*------------------------------------------------------------------------- * Function: h5repack_addlayout @@ -160,7 +166,7 @@ h5repack_addlayout(const char *str, pack_opt_t *options) init_packobject(&pack); if (options->all_layout == 1) { - error_msg( "invalid layout input: 'all' option is present with other objects <%s>\n", str); + error_msg("invalid layout input: 'all' option is present with other objects <%s>\n", str); return ret_value; } @@ -175,7 +181,7 @@ h5repack_addlayout(const char *str, pack_opt_t *options) if (pack.layout == H5D_CHUNKED) { /* -2 means the NONE option, remove chunking and set the global layout to contiguous */ - if (pack.chunk.rank == -2) + if (pack.chunk.rank == -2) /* TODO: fix 'magic number' */ options->layout_g = H5D_CONTIGUOUS; /* otherwise set the global chunking type */ else { @@ -192,10 +198,10 @@ h5repack_addlayout(const char *str, pack_opt_t *options) HDfree(obj_list); ret_value = 0; - } + } /* end if obj_list exists */ return ret_value; -} +} /* end h5repack_addlayout() */ /* Note: The below copy_named_datatype(), named_datatype_free(), copy_attr() * were located in h5repack_copy.c as static prior to bugfix1726. @@ -215,20 +221,30 @@ h5repack_addlayout(const char *str, pack_opt_t *options) * to free the stack. *------------------------------------------------------------------------- */ -hid_t copy_named_datatype(hid_t type_in, hid_t fidout, - named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options) { - named_dt_t *dt = *named_dt_head_p; /* Stack pointer */ - named_dt_t *dt_ret = NULL; /* Datatype to return */ - H5O_info_t oinfo; /* Object info of input dtype */ - hid_t ret_value = -1; /* The identifier of the named dtype in the out file */ - if (H5Oget_info2(type_in, &oinfo, H5O_INFO_BASIC) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Oget_info failed"); +hid_t +copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, trav_table_t *travt, + pack_opt_t *options) +{ + named_dt_t *dt = NULL; /* Stack pointer */ + named_dt_t *dt_ret = NULL; /* Datatype to return */ + H5O_info2_t oinfo; /* Object info of input dtype */ + int token_cmp; + hid_t ret_value = H5I_INVALID_HID; + + if (H5Oget_info3(type_in, &oinfo, H5O_INFO_BASIC) < 0) + H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "H5Oget_info failed"); if (*named_dt_head_p) { - /* Stack already exists, search for the datatype */ - while (dt && dt->addr_in != oinfo.addr) - dt = dt->next; + /* Search the stack for the datatype. */ + for (dt = *named_dt_head_p; dt != NULL; dt = dt->next) { + if (H5Otoken_cmp(type_in, &dt->obj_token, &oinfo.token, &token_cmp) < 0) + H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "failed to compare object tokens"); + + if (token_cmp == 0) + break; // found it! + } + dt_ret = dt; } else { @@ -239,59 +255,64 @@ hid_t copy_named_datatype(hid_t type_in, hid_t fidout, if (travt->objs[i].type == H5TRAV_TYPE_NAMED_DATATYPE) { /* Push onto the stack */ if (NULL == (dt = (named_dt_t *)HDmalloc(sizeof(named_dt_t)))) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "buffer allocation failed failed"); - dt->next = *named_dt_head_p; + H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "buffer allocation failed failed"); + dt->next = *named_dt_head_p; *named_dt_head_p = dt; - /* Update the address and id */ - dt->addr_in = travt->objs[i].objno; - dt->id_out = -1; + /* Update the token/address and id */ + HDmemcpy(&dt->obj_token, &travt->objs[i].obj_token, sizeof(H5O_token_t)); + dt->id_out = H5I_INVALID_HID; /* Check if this type is the one requested */ - if (oinfo.addr == dt->addr_in) { + if (H5Otoken_cmp(type_in, &oinfo.token, &dt->obj_token, &token_cmp) < 0) + H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "failed to compare object tokens"); + if (!token_cmp) dt_ret = dt; - } /* end if */ - } /* end if */ - } /* end for */ - } /* end else */ + } /* end if named datatype */ + } /* end for each object in traversal table */ + } /* end else (create the stack) */ /* Handle the case that the requested datatype was not found. This is - * possible if the datatype was committed anonymously in the input file. */ + * possible if the datatype was committed anonymously in the input file. + */ if (!dt_ret) { /* Push the new datatype onto the stack */ if (NULL == (dt_ret = (named_dt_t *)HDmalloc(sizeof(named_dt_t)))) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "buffer allocation failed failed"); - dt_ret->next = *named_dt_head_p; + H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "buffer allocation failed failed"); + dt_ret->next = *named_dt_head_p; *named_dt_head_p = dt_ret; - /* Update the address and id */ - dt_ret->addr_in = oinfo.addr; - dt_ret->id_out = -1; - } /* end if */ + /* Update the token/address and id */ + HDmemcpy(&dt_ret->obj_token, &oinfo.token, sizeof(H5O_token_t)); + dt_ret->id_out = H5I_INVALID_HID; + } /* end if requested datatype not found */ /* If the requested datatype does not yet exist in the output file, copy it - * anonymously */ + * anonymously + */ if (dt_ret->id_out < 0) { if (options->use_native == 1) dt_ret->id_out = H5Tget_native_type(type_in, H5T_DIR_DEFAULT); else dt_ret->id_out = H5Tcopy(type_in); if (dt_ret->id_out < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_native_type-H5Tcopy failed"); + H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "H5Tget_native_type-H5Tcopy failed"); if (H5Tcommit_anon(fidout, dt_ret->id_out, H5P_DEFAULT, H5P_DEFAULT) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tcommit_anon failed"); - } /* end if */ + H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "H5Tcommit_anon failed"); + } /* end if named datatype not yet in output file */ /* Set return value */ ret_value = dt_ret->id_out; - /* Increment the ref count on id_out, because the calling function will try to close it */ - if(H5Iinc_ref(ret_value) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Iinc_ref failed"); + /* Increment the ref count on id_out, because the calling function will try + * to close it. (TODO: fix scope envy) + */ + if (H5Iinc_ref(ret_value) < 0) + H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "H5Iinc_ref failed"); done: return ret_value; -} /* end copy_named_datatype */ +} /* end copy_named_datatype() */ /*------------------------------------------------------------------------- * Function: named_datatype_free @@ -299,24 +320,26 @@ done: * Purpose: Frees the stack of named datatypes. *------------------------------------------------------------------------- */ -int named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err) { - named_dt_t *dt = *named_dt_head_p; +int +named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err) +{ + named_dt_t *dt = *named_dt_head_p; int ret_value = -1; while (dt) { /* Pop the datatype off the stack and free it */ if (H5Tclose(dt->id_out) < 0 && !ignore_err) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); dt = dt->next; HDfree(*named_dt_head_p); *named_dt_head_p = dt; - } /* end while */ + } ret_value = 0; done: return (ret_value); -} /* end named_datatype_free */ +} /* end named_datatype_free() */ /*------------------------------------------------------------------------- * Function: copy_attr @@ -330,283 +353,317 @@ done: *------------------------------------------------------------------------- */ int -copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p, - trav_table_t *travt, pack_opt_t *options) +copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options) { - int ret_value = 0; - hid_t attr_id = -1; /* attr ID */ - hid_t attr_out = -1; /* attr ID */ - hid_t space_id = -1; /* space ID */ - hid_t ftype_id = -1; /* file type ID */ - hid_t wtype_id = -1; /* read/write type ID */ - size_t msize; /* size of type */ - void *buf = NULL; /* data buffer */ - hsize_t nelmts; /* number of elements in dataset */ - int rank; /* rank of dataset */ - htri_t is_named; /* Whether the datatype is named */ - hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */ - char name[255]; - H5O_info_t oinfo; /* object info */ - int j; - unsigned u; - hbool_t is_ref = 0; - H5T_class_t type_class = -1; - - if (H5Oget_info2(loc_in, &oinfo, H5O_INFO_NUM_ATTRS) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Oget_info failed"); + hid_t attr_id = H5I_INVALID_HID; /* attr ID */ + hid_t attr_out = H5I_INVALID_HID; /* attr ID */ + hid_t space_id = H5I_INVALID_HID; /* space ID */ + hid_t ftype_id = H5I_INVALID_HID; /* file type ID */ + hid_t wtype_id = H5I_INVALID_HID; /* read/write type ID */ + size_t msize; /* size of type */ + void * buf = NULL; /* data buffer */ + hsize_t nelmts; /* number of elements in dataset */ + int rank; /* rank of dataset */ + htri_t is_named; /* Whether the datatype is named */ + hsize_t dims[H5S_MAX_RANK]; /* dimensions of dataset */ + H5_timer_t timer; /* Timer for read/write operations */ + H5_timevals_t times; /* Elapsed time for each operation */ + static double read_time = 0; + static double write_time = 0; + char name[255]; + H5O_info2_t oinfo; /* object info */ + int j; + unsigned u; + hbool_t is_ref = 0; + H5T_class_t type_class = -1; + int ret_value = 0; + + if (H5Oget_info3(loc_in, &oinfo, H5O_INFO_NUM_ATTRS) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Oget_info failed"); /*------------------------------------------------------------------------- * copy all attributes *------------------------------------------------------------------------- */ - for (u = 0; u < (unsigned) oinfo.num_attrs; u++) { + for (u = 0; u < (unsigned)oinfo.num_attrs; u++) { /* open attribute */ - if ((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t) u, H5P_DEFAULT, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aopen_by_idx failed"); + if ((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)u, H5P_DEFAULT, + H5P_DEFAULT)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Aopen_by_idx failed"); - /* get name */ - if (H5Aget_name(attr_id, (size_t) 255, name) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + if (H5Aget_name(attr_id, (size_t)255, name) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); /* get the file datatype */ if ((ftype_id = H5Aget_type(attr_id)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aget_type failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Aget_type failed"); /* Check if the datatype is committed */ if ((is_named = H5Tcommitted(ftype_id)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tcommitted failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Tcommitted failed"); if (is_named && travt) { - hid_t fidout = -1; + hid_t fidout = H5I_INVALID_HID; /* Create out file id */ if ((fidout = H5Iget_file_id(loc_out)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Iget_file_id failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Iget_file_id failed"); /* Copy named dt */ if ((wtype_id = copy_named_datatype(ftype_id, fidout, named_dt_head_p, travt, options)) < 0) { H5Fclose(fidout); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_named_datatype failed"); - } /* end if */ + H5TOOLS_GOTO_ERROR((-1), "copy_named_datatype failed"); + } if (H5Fclose(fidout) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fclose failed"); - } /* end if */ + H5TOOLS_GOTO_ERROR((-1), "H5Fclose failed"); + } /* end if datatype is committed and we have a traversal table */ else { if (options->use_native == 1) wtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT); else wtype_id = H5Tcopy(ftype_id); - } /* end else */ + } /* end else: uncommitted datatype and/or no traversal table */ /* get the dataspace handle */ if ((space_id = H5Aget_space(attr_id)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aget_space failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Aget_space failed"); /* get dimensions */ if ((rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Sget_simple_extent_dims failed"); nelmts = 1; for (j = 0; j < rank; j++) nelmts *= dims[j]; if ((msize = H5Tget_size(wtype_id)) == 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed"); - - /*------------------------------------------------------------------------- - * object references are a special case. We cannot just copy the buffers, - * but instead we recreate the reference. - * This is done on a second sweep of the file that just copies the referenced - * objects at copy_refs_attr() - *------------------------------------------------------------------------- + H5TOOLS_GOTO_ERROR((-1), "H5Tget_size failed"); + + /*--------------------------------------------------------------------- + * object references are a special case. We cannot just copy the + * buffers, but instead we recreate the reference. + * This is done on a second sweep of the file that just copies the + * referenced objects at copy_refs_attr(). + *--------------------------------------------------------------------- */ type_class = H5Tget_class(wtype_id); - is_ref = (type_class == H5T_REFERENCE); + is_ref = (type_class == H5T_REFERENCE); if (type_class == H5T_VLEN || type_class == H5T_ARRAY) { - hid_t base_type = -1; + hid_t base_type = H5I_INVALID_HID; base_type = H5Tget_super(ftype_id); - is_ref = (is_ref || (H5Tget_class(base_type) == H5T_REFERENCE)); + is_ref = (is_ref || (H5Tget_class(base_type) == H5T_REFERENCE)); if (H5Tclose(base_type) < 0) - H5TOOLS_INFO(H5E_tools_min_id_g, "H5Tclose base_type failed"); - } + H5TOOLS_ERROR((-1), "H5Tclose base_type failed"); + } /* end if type_class is variable length or array */ if (type_class == H5T_COMPOUND) { int nmembers = H5Tget_nmembers(wtype_id); for (j = 0; j < nmembers; j++) { - hid_t mtid = H5Tget_member_type(wtype_id, (unsigned)j); + hid_t mtid = H5Tget_member_type(wtype_id, (unsigned)j); H5T_class_t mtclass = H5Tget_class(mtid); if (H5Tclose(mtid) < 0) - H5TOOLS_INFO(H5E_tools_min_id_g, "H5Tclose mtid failed"); + H5TOOLS_ERROR((-1), "H5Tclose mtid failed"); if (mtclass == H5T_REFERENCE) { is_ref = 1; break; } - } /* for (j=0; i<nmembers; j++) */ - } /* if (type_class == H5T_COMPOUND) */ + } /* end for each member */ + } /* end if type_class is H5T_COMPOUND */ + + read_time = 0; + write_time = 0; if (!is_ref) { - /*------------------------------------------------------------------------- + /*----------------------------------------------------------------- * read to memory - *------------------------------------------------------------------------- + *----------------------------------------------------------------- */ buf = (void *)HDmalloc((size_t)(nelmts * msize)); if (buf == NULL) { - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed"); + H5TOOLS_GOTO_ERROR((-1), "HDmalloc failed"); } /* end if */ + if (options->verbose == 2) { + H5_timer_init(&timer); + H5_timer_start(&timer); + } if (H5Aread(attr_id, wtype_id, buf) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Aread failed"); + if (options->verbose == 2) { + H5_timer_stop(&timer); + H5_timer_get_times(timer, ×); + read_time += times.elapsed; + } - /*------------------------------------------------------------------------- + /*----------------------------------------------------------------- * copy - *------------------------------------------------------------------------- + *----------------------------------------------------------------- */ if ((attr_out = H5Acreate2(loc_out, name, wtype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Acreate2 failed on ,%s>", name); + H5TOOLS_GOTO_ERROR((-1), "H5Acreate2 failed on ,%s>", name); + + if (options->verbose == 2) { + H5_timer_init(&timer); + H5_timer_start(&timer); + } if (H5Awrite(attr_out, wtype_id, buf) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Awrite failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Awrite failed"); + if (options->verbose == 2) { + H5_timer_stop(&timer); + H5_timer_get_times(timer, ×); + write_time += times.elapsed; + } /*close*/ if (H5Aclose(attr_out) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aclose failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Aclose failed"); /* Check if we have VL data and string in the attribute's datatype that must * be reclaimed */ if (TRUE == h5tools_detect_vlen(wtype_id)) - H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf); + H5Treclaim(wtype_id, space_id, H5P_DEFAULT, buf); + HDfree(buf); buf = NULL; } /*H5T_REFERENCE*/ - if (options->verbose) + if (options->verbose == 2) + HDprintf(FORMAT_OBJ_ATTR_TIME, "attr", read_time, write_time, name); + else HDprintf(FORMAT_OBJ_ATTR, "attr", name); - /*------------------------------------------------------------------------- + /*--------------------------------------------------------------------- * close - *------------------------------------------------------------------------- + *--------------------------------------------------------------------- */ if (H5Sclose(space_id) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed"); - space_id = -1; + H5TOOLS_GOTO_ERROR((-1), "H5Sclose failed"); + space_id = H5I_INVALID_HID; if (H5Tclose(wtype_id) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); - wtype_id = -1; + H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); + wtype_id = H5I_INVALID_HID; if (H5Tclose(ftype_id) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); - ftype_id = -1; + H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); + ftype_id = H5I_INVALID_HID; if (H5Aclose(attr_id) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aclose failed"); - attr_id = -1; - } /* for u */ + H5TOOLS_GOTO_ERROR((-1), "H5Aclose failed"); + attr_id = H5I_INVALID_HID; + } /* for u (each attribute) */ done: - H5E_BEGIN_TRY { + H5E_BEGIN_TRY + { if (buf) { - /* Check if we have VL data and string in the attribute's datatype that must - * be reclaimed */ + /* Check if we have VL data and string in the attribute's + * datatype that must be reclaimed + */ if (TRUE == h5tools_detect_vlen(wtype_id)) - H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf); + H5Treclaim(wtype_id, space_id, H5P_DEFAULT, buf); /* Free buf */ HDfree(buf); - } /* end if */ + } H5Aclose(attr_out); H5Sclose(space_id); H5Tclose(wtype_id); H5Tclose(ftype_id); H5Aclose(attr_id); - } H5E_END_TRY; + } + H5E_END_TRY; return ret_value; } /* end copy_attr() */ -/*------------------------------------------------------------------------- +/*----------------------------------------------------------------------------- * Function: check_options * * Purpose: print options, checks for invalid options * * Return: void, return -1 on error - *------------------------------------------------------------------------- + *----------------------------------------------------------------------------- */ -static int check_options(pack_opt_t *options) { - int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ +static int +check_options(pack_opt_t *options) +{ unsigned int i; int k, j, has_cp = 0, has_ck = 0; char slayout[30]; + int ret_value = 0; /*------------------------------------------------------------------------- - * objects to layout - *------------------------------------------------------------------------- - */ - if (options->verbose && have_request(options) /* only print if requested */) { + * Objects to layout + *------------------------------------------------------------------------- + */ + if (options->verbose > 0 && have_request(options)) { if (options->all_layout == 1) { HDprintf("All objects to modify layout are...\n"); switch (options->layout_g) { - case H5D_COMPACT: - strcpy(slayout, "compact"); - break; - case H5D_CONTIGUOUS: - strcpy(slayout, "contiguous"); - break; - case H5D_CHUNKED: - strcpy(slayout, "chunked"); - break; - case H5D_VIRTUAL: - strcpy(slayout, "virtual"); - break; - case H5D_LAYOUT_ERROR: - case H5D_NLAYOUTS: - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid layout"); - default: - strcpy(slayout, "invalid layout\n"); - HGOTO_DONE(FAIL); + case H5D_COMPACT: + strcpy(slayout, "compact"); + break; + case H5D_CONTIGUOUS: + strcpy(slayout, "contiguous"); + break; + case H5D_CHUNKED: + strcpy(slayout, "chunked"); + break; + case H5D_VIRTUAL: + strcpy(slayout, "virtual"); + break; + case H5D_LAYOUT_ERROR: + case H5D_NLAYOUTS: + H5TOOLS_GOTO_ERROR((-1), "invalid layout"); + break; + default: + strcpy(slayout, "invalid layout\n"); + H5TOOLS_GOTO_DONE((-1)); } HDprintf(" Apply %s layout to all", slayout); if (H5D_CHUNKED == options->layout_g) { HDprintf("with dimension [ "); for (j = 0; j < options->chunk_g.rank; j++) - HDprintf("%d ", (int) options->chunk_g.chunk_lengths[j]); + HDprintf("%d ", (int)options->chunk_g.chunk_lengths[j]); HDprintf("]"); } HDprintf("\n"); } else HDprintf("No all objects to modify layout\n"); - }/* verbose */ + } /* end if verbose */ for (i = 0; i < options->op_tbl->nelems; i++) { - char* name = options->op_tbl->objs[i].path; + char *name = options->op_tbl->objs[i].path; if (options->op_tbl->objs[i].chunk.rank > 0) { - if (options->verbose) { + if (options->verbose > 0) { HDprintf(" <%s> with chunk size ", name); for (k = 0; k < options->op_tbl->objs[i].chunk.rank; k++) - HDprintf("%d ", (int) options->op_tbl->objs[i].chunk.chunk_lengths[k]); + HDprintf("%d ", (int)options->op_tbl->objs[i].chunk.chunk_lengths[k]); HDprintf("\n"); } has_ck = 1; } - else if (options->op_tbl->objs[i].chunk.rank == -2) { - if (options->verbose) + else if (options->op_tbl->objs[i].chunk.rank == -2) { /* TODO: replace 'magic number' */ + if (options->verbose > 0) HDprintf(" <%s> %s\n", name, "NONE (contiguous)"); has_ck = 1; } - } + } /* end for each object in options */ if (options->all_layout == 1 && has_ck) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid chunking input: 'all' option is present with other objects"); + H5TOOLS_GOTO_ERROR((-1), "invalid chunking input: 'all' option is present with other objects"); /*------------------------------------------------------------------------- - * objects to filter - *------------------------------------------------------------------------- - */ + * Objects to filter + *------------------------------------------------------------------------- + */ - if (options->verbose && have_request(options) /* only print if requested */) { + if (options->verbose > 0 && have_request(options)) { if (options->all_filter == 1) { HDprintf("All objects to apply filter are...\n"); for (k = 0; k < options->n_filter_g; k++) { @@ -616,116 +673,124 @@ static int check_options(pack_opt_t *options) { continue; } switch (filtn) { - case H5Z_FILTER_NONE: - HDprintf(" Uncompress all\n"); - break; - case H5Z_FILTER_SHUFFLE: - case H5Z_FILTER_FLETCHER32: - HDprintf(" All with %s\n", get_sfilter(filtn)); - break; - case H5Z_FILTER_SZIP: - case H5Z_FILTER_DEFLATE: - HDprintf(" All with %s, parameter %d\n", get_sfilter(filtn), options->filter_g[k].cd_values[0]); - break; - default: - HDprintf(" User Defined %d\n", filtn); - break; - } /* k */ - }; - } + case H5Z_FILTER_NONE: + HDprintf(" Uncompress all\n"); + break; + case H5Z_FILTER_SHUFFLE: + case H5Z_FILTER_FLETCHER32: + HDprintf(" All with %s\n", get_sfilter(filtn)); + break; + case H5Z_FILTER_SZIP: + case H5Z_FILTER_DEFLATE: + HDprintf(" All with %s, parameter %d\n", get_sfilter(filtn), + options->filter_g[k].cd_values[0]); + break; + default: + HDprintf(" User Defined %d\n", filtn); + break; + } /* end switch */ + } /* end for each filter */ + } /* end if options->all_filter == 1 (TODO: meaning) */ else HDprintf("No all objects to apply filter\n"); - } /* verbose */ + } /* end if verbose */ for (i = 0; i < options->op_tbl->nelems; i++) { pack_info_t pack = options->op_tbl->objs[i]; - char* name = pack.path; + char * name = pack.path; for (j = 0; j < pack.nfilters; j++) { - if (options->verbose) { - if(pack.filter[j].filtn >= 0) { - if(pack.filter[j].filtn > H5Z_FILTER_SCALEOFFSET) - HDprintf(" <%s> with %s filter %d\n", name, get_sfilter(pack.filter[j].filtn), pack.filter[j].filtn); - else + if (options->verbose > 0) { + if (pack.filter[j].filtn >= 0) { + if (pack.filter[j].filtn > H5Z_FILTER_SCALEOFFSET) { + HDprintf(" <%s> with %s filter %d\n", name, get_sfilter(pack.filter[j].filtn), + pack.filter[j].filtn); + } + else { HDprintf(" <%s> with %s filter\n", name, get_sfilter(pack.filter[j].filtn)); + } } } has_cp = 1; - } /* j */ - } /* i */ + } /* end for each filter */ + } /* end for each object in options table */ if (options->all_filter == 1 && has_cp) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid compression input: 'all' option is present with other objects"); + H5TOOLS_GOTO_ERROR((-1), "invalid compression input: 'all' option is present with other objects"); /*------------------------------------------------------------------------- - * check options for the latest format - *------------------------------------------------------------------------- - */ + * Check options for the latest format + *------------------------------------------------------------------------- + */ if (options->grp_compact < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid maximum number of links to store as header messages"); + H5TOOLS_GOTO_ERROR((-1), "invalid maximum number of links to store as header messages"); if (options->grp_indexed < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid minimum number of links to store in the indexed format"); + H5TOOLS_GOTO_ERROR((-1), "invalid minimum number of links to store in the indexed format"); if (options->grp_indexed > options->grp_compact) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "minimum indexed size is greater than the maximum compact size"); + H5TOOLS_GOTO_ERROR((-1), "minimum indexed size is greater than the maximum compact size"); for (i = 0; i < 8; i++) if (options->msg_size[i] < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid shared message size"); + H5TOOLS_GOTO_ERROR((-1), "invalid shared message size"); - /*-------------------------------------------------------------------------------- - * verify new user userblock options; file name must be present - *--------------------------------------------------------------------------------- - */ + /*------------------------------------------------------------------------ + * Verify new user userblock options; file name must be present + *------------------------------------------------------------------------ + */ if (options->ublock_filename != NULL && options->ublock_size == 0) { - if (options->verbose) { - HDprintf("Warning: user block size missing for file %s. Assigning a default size of 1024...\n", options->ublock_filename); + if (options->verbose > 0) { + HDprintf("Warning: user block size missing for file %s. Assigning a default size of 1024...\n", + options->ublock_filename); options->ublock_size = 1024; } } if (options->ublock_filename == NULL && options->ublock_size != 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "file name missing for user block", options->ublock_filename); + H5TOOLS_GOTO_ERROR((-1), "file name missing for user block"); - /*-------------------------------------------------------------------------------- - * verify alignment options; threshold is zero default but alignment not - *--------------------------------------------------------------------------------- - */ + /*------------------------------------------------------------------------ + * Verify alignment options; threshold is zero default but alignment not + *------------------------------------------------------------------------ + */ if (options->alignment == 0 && options->threshold != 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "alignment for H5Pset_alignment missing"); + H5TOOLS_GOTO_ERROR((-1), "alignment for H5Pset_alignment missing"); done: return ret_value; -} +} /* end check_options() */ /*------------------------------------------------------------------------- * Function: check_objects * - * Purpose: locate all HDF5 objects in the file and compare with user - * supplied list + * Purpose: Locate all HDF5 objects in the file and compare with user-supplied + * list. * * Return: 0, ok, -1 no *------------------------------------------------------------------------- */ -static int check_objects(const char* fname, pack_opt_t *options) { - int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ - hid_t fid = -1; - hid_t did = -1; - hid_t sid = -1; +static int +check_objects(const char *fname, pack_opt_t *options) +{ + hid_t fid = H5I_INVALID_HID; + hid_t did = H5I_INVALID_HID; + hid_t sid = H5I_INVALID_HID; unsigned int i; - int ifil; - trav_table_t *travt = NULL; + int ifil; + trav_table_t *travt = NULL; + int ret_value = 0; /* nothing to do */ if (options->op_tbl->nelems == 0) - HGOTO_DONE(0); + H5TOOLS_GOTO_DONE(0); /*------------------------------------------------------------------------- * open the file *------------------------------------------------------------------------- */ - if ((fid = h5tools_fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, 0)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5tools_fopen failed <%s>: %s", fname, H5FOPENERROR); + if ((fid = h5tools_fopen(fname, H5F_ACC_RDONLY, options->fin_fapl, (options->fin_fapl != H5P_DEFAULT), + NULL, 0)) < 0) + H5TOOLS_GOTO_ERROR((-1), "h5tools_fopen failed <%s>: %s", fname, H5FOPENERROR); /*------------------------------------------------------------------------- * get the list of objects in the file @@ -735,91 +800,94 @@ static int check_objects(const char* fname, pack_opt_t *options) { /* Initialize indexing options */ h5trav_set_index(sort_by, sort_order); /* init table */ - trav_table_init(&travt); + trav_table_init(fid, &travt); /* get the list of objects in the file */ if (h5trav_gettable(fid, travt) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5trav_gettable failed"); + H5TOOLS_GOTO_ERROR((-1), "h5trav_gettable failed"); /*------------------------------------------------------------------------- * compare with user supplied list *------------------------------------------------------------------------- */ - if (options->verbose) + if (options->verbose > 0) HDprintf("Opening file. Searching %zu objects to modify ...\n", travt->nobjs); for (i = 0; i < options->op_tbl->nelems; i++) { - char* name = options->op_tbl->objs[i].path; - if (options->verbose) + pack_info_t obj = options->op_tbl->objs[i]; + char * name = obj.path; + + if (options->verbose > 0) HDprintf(" <%s>", name); /* the input object names are present in the file and are valid */ if (h5trav_getindext(name, travt) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "%s Could not find <%s> in file <%s>. Exiting...\n", - (options->verbose ? "\n" : ""), name, fname); - if (options->verbose) + H5TOOLS_GOTO_ERROR((-1), "%s Could not find <%s> in file <%s>. Exiting...\n", + (options->verbose > 0 ? "\n" : ""), name, fname); + if (options->verbose > 0) HDprintf("...Found\n"); - for (ifil = 0; ifil < options->op_tbl->objs[i].nfilters; ifil++) { - if (options->op_tbl->objs[i].filter[ifil].filtn < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid filter"); + for (ifil = 0; ifil < obj.nfilters; ifil++) { + if (obj.filter[ifil].filtn < 0) + H5TOOLS_GOTO_ERROR((-1), "invalid filter"); /* check for extra filter conditions */ - switch (options->op_tbl->objs[i].filter[ifil].filtn) { - /* chunk size must be smaller than pixels per block */ - case H5Z_FILTER_SZIP: - { - int j; - hsize_t csize = 1; - unsigned ppb = options->op_tbl->objs[i].filter[ifil].cd_values[0]; - hsize_t dims[H5S_MAX_RANK]; - int rank; - - if (options->op_tbl->objs[i].chunk.rank > 0) { - rank = options->op_tbl->objs[i].chunk.rank; + switch (obj.filter[ifil].filtn) { + /* chunk size must be smaller than pixels per block */ + case H5Z_FILTER_SZIP: { + int j; + hsize_t csize = 1; + unsigned ppb = obj.filter[ifil].cd_values[0]; + hsize_t dims[H5S_MAX_RANK]; + int rank; + + if (obj.chunk.rank > 0) { + rank = obj.chunk.rank; for (j = 0; j < rank; j++) - csize *= options->op_tbl->objs[i].chunk.chunk_lengths[j]; + csize *= obj.chunk.chunk_lengths[j]; } else { if ((did = H5Dopen2(fid, name, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Dopen2 failed"); if ((sid = H5Dget_space(did)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Dget_space failed"); if ((rank = H5Sget_simple_extent_ndims(sid)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Sget_simple_extent_ndims failed"); HDmemset(dims, 0, sizeof dims); if (H5Sget_simple_extent_dims(sid, dims, NULL) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Sget_simple_extent_dims failed"); for (j = 0; j < rank; j++) csize *= dims[j]; if (H5Sclose(sid) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Sclose failed"); if (H5Dclose(did) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Dclose failed"); } if (csize < ppb) { HDprintf(" <warning: SZIP settings, chunk size is smaller than pixels per block>\n"); - HGOTO_DONE(0); + H5TOOLS_GOTO_DONE(0); } - } - break; - default: + } /* end case SZIP */ break; - } - } /* for ifil */ - } /* for i */ + default: + break; + } /* end switch */ + } /* for ifil (each user-defined filter) */ + } /* for i (each object in options traversal table) */ done: - H5E_BEGIN_TRY { + H5E_BEGIN_TRY + { H5Sclose(sid); H5Dclose(did); H5Fclose(fid); - } H5E_END_TRY; + } + H5E_END_TRY; if (travt) trav_table_free(travt); return ret_value; -} +} /* end check_objects() */ /*------------------------------------------------------------------------- * Function: have_request @@ -829,14 +897,15 @@ done: * Return: 1 yes, 0 no *------------------------------------------------------------------------- */ -static int have_request(pack_opt_t *options) { +static int +have_request(pack_opt_t *options) +{ if (options->all_filter || options->all_layout || options->op_tbl->nelems) return 1; return 0; - -} +} /* end have_request() */ /*------------------------------------------------------------------------- * Function: get_sfilter @@ -846,8 +915,9 @@ static int have_request(pack_opt_t *options) { * Return: name of filter, exit on error *------------------------------------------------------------------------- */ - -static const char* get_sfilter(H5Z_filter_t filtn) { +static const char * +get_sfilter(H5Z_filter_t filtn) +{ if (filtn < 0) return NULL; else if (filtn == H5Z_FILTER_NONE) @@ -866,5 +936,4 @@ static const char* get_sfilter(H5Z_filter_t filtn) { return "SOFF"; else return "UD"; -} - +} /* end get_sfilter() */ diff --git a/tools/src/h5repack/h5repack.h b/tools/src/h5repack/h5repack.h index a0e0387..65e5d40 100644 --- a/tools/src/h5repack/h5repack.h +++ b/tools/src/h5repack/h5repack.h @@ -6,34 +6,38 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -#ifndef H5REPACK_H__ -#define H5REPACK_H__ +#ifndef H5REPACK_H +#define H5REPACK_H #include "H5private.h" #include "hdf5.h" #include "h5trav.h" -#define H5FOPENERROR "unable to open file" -#define PFORMAT "%-7s %-7s %-7s\n" /* chunk info, compression info, name*/ -#define PFORMAT1 "%-7s %-7s %-7s" /* chunk info, compression info, name*/ -#define MAX_NC_NAME 256 /* max length of a name */ -#define MAX_VAR_DIMS 32 /* max per variable dimensions */ -#define FORMAT_OBJ " %-27s %s\n" /* obj type, name */ -#define FORMAT_OBJ_ATTR " %-27s %s\n" /* obj type, name */ -#define MAX_COMPACT_DSIZE 64512 /* max data size for compact layout. -1k for header size */ +#define H5FOPENERROR "unable to open file" +#define PFORMAT "%-7s %-7s %-7s\n" /* chunk info, compression info, name*/ +#define PFORMAT1 "%-7s %-7s %-7s" /* chunk info, compression info, name*/ +#define MAX_NC_NAME 256 /* max length of a name */ +#define MAX_VAR_DIMS 32 /* max per variable dimensions */ +#define FORMAT_OBJ " %-27s %s\n" /* obj type, name */ +#define FORMAT_OBJ_ATTR " %-27s %s\n" /* obj type, name */ +#define MAX_COMPACT_DSIZE 64512 /* max data size for compact layout. -1k for header size */ + +/* timing formats */ +#define FORMAT_OBJ_TIME " %-27s %e/%e %s\n" /* obj type, name */ +#define FORMAT_OBJ_ATTR_TIME " %-27s %e/%e %s\n" /* obj type, name */ +#define FORMAT_OBJ_NOTIME " %-27s %s\n" /* obj type, name */ +#define FORMAT_OBJ_ATTR_NOTIME " %-27s %s\n" /* obj type, name */ /* File space default information */ -#define FS_PAGESIZE_DEF 4096 -#define FS_STRATEGY_DEF H5F_FSPACE_STRATEGY_FSM_AGGR -#define FS_PERSIST_DEF FALSE -#define FS_THRESHOLD_DEF 1 - +#define FS_PAGESIZE_DEF 4096 +#define FS_STRATEGY_DEF H5F_FSPACE_STRATEGY_FSM_AGGR +#define FS_PERSIST_DEF FALSE +#define FS_THRESHOLD_DEF 1 /*------------------------------------------------------------------------- * data structures for command line options @@ -42,7 +46,7 @@ /* a list of names */ typedef struct { - char obj[MAX_NC_NAME]; + char obj[MAX_NC_NAME]; } obj_list_t; /* @@ -60,16 +64,16 @@ typedef struct { #define CD_VALUES 20 typedef struct { - H5Z_filter_t filtn; /* filter identification number */ - unsigned filt_flag; /* filter definition flag */ - unsigned cd_values[CD_VALUES]; /* filter client data values */ - size_t cd_nelmts; /* filter client number of values */ + H5Z_filter_t filtn; /* filter identification number */ + unsigned filt_flag; /* filter definition flag */ + unsigned cd_values[CD_VALUES]; /* filter client data values */ + size_t cd_nelmts; /* filter client number of values */ } filter_info_t; /* chunk lengths along each dimension and rank */ typedef struct { - hsize_t chunk_lengths[MAX_VAR_DIMS]; - int rank; + hsize_t chunk_lengths[MAX_VAR_DIMS]; + int rank; } chunk_info_t; /* we currently define a maximum value for the filters array, @@ -78,22 +82,21 @@ typedef struct { /* information for one object, contains PATH, CHUNK info and FILTER info */ typedef struct { - char path[MAX_NC_NAME]; /* name of object */ - filter_info_t filter[H5_REPACK_MAX_NFILTERS]; /* filter array */ - int nfilters; /* current number of filters */ - H5D_layout_t layout; /* layout information */ - chunk_info_t chunk; /* chunk information */ - hid_t refobj_id; /* object ID, references */ + char path[MAX_NC_NAME]; /* name of object */ + filter_info_t filter[H5_REPACK_MAX_NFILTERS]; /* filter array */ + int nfilters; /* current number of filters */ + H5D_layout_t layout; /* layout information */ + chunk_info_t chunk; /* chunk information */ + hid_t refobj_id; /* object ID, references */ } pack_info_t; /* store a table of all objects */ typedef struct { - unsigned int size; - unsigned int nelems; - pack_info_t *objs; + unsigned int size; + unsigned int nelems; + pack_info_t *objs; } pack_opttbl_t; - /*------------------------------------------------------------------------- * command line options *------------------------------------------------------------------------- @@ -101,39 +104,42 @@ typedef struct { /* all the above, ready to go to the hrepack call */ typedef struct { - pack_opttbl_t *op_tbl; /*table with all -c and -f options */ - int all_layout; /*apply the layout to all objects */ - int all_filter; /*apply the filter to all objects */ - filter_info_t filter_g[H5_REPACK_MAX_NFILTERS]; /*global filter array for the ALL case */ - int n_filter_g; /*number of global filters */ - chunk_info_t chunk_g; /*global chunk INFO for the ALL case */ - H5D_layout_t layout_g; /*global layout information for the ALL case */ - int verbose; /*verbose mode */ - hsize_t min_comp; /*minimum size to compress, in bytes */ - int use_native; /*use a native type in write */ - hbool_t latest; /*pack file with the latest file format */ - H5F_libver_t low_bound; /* The file's low bound as in H5Fset_libver_bounds() */ - H5F_libver_t high_bound; /* The file's high bound as in H5Fset_libver_bounds() */ - int grp_compact; /* Set the maximum number of links to store as header messages in the group */ - int grp_indexed; /* Set the minimum number of links to store in the indexed format */ - int msg_size[8]; /* Minimum size of shared messages: dataspace, - datatype, fill value, filter pipleline, attribute */ - const char *ublock_filename; /* user block file name */ - hsize_t ublock_size; /* user block size */ - hsize_t meta_block_size; /* metadata aggregation block size (for H5Pset_meta_block_size) */ - hsize_t threshold; /* alignment threshold for H5Pset_alignment */ - hsize_t alignment; /* alignment for H5Pset_alignment */ - H5F_fspace_strategy_t fs_strategy; /* File space handling strategy */ - int fs_persist; /* Free space section threshold */ - long fs_threshold; /* Free space section threshold */ - long long fs_pagesize; /* File space page size */ + pack_opttbl_t *op_tbl; /* table with all -c and -f options */ + int all_layout; /* apply the layout to all objects */ + int all_filter; /* apply the filter to all objects */ + filter_info_t filter_g[H5_REPACK_MAX_NFILTERS]; /*global filter array for the ALL case */ + int n_filter_g; /* number of global filters */ + chunk_info_t chunk_g; /* global chunk INFO for the ALL case */ + H5D_layout_t layout_g; /* global layout information for the ALL case */ + int verbose; /* verbose mode */ + hbool_t merge; /* Merge external file. */ + hbool_t prune; /* Don't follow external file. */ + hsize_t min_comp; /* minimum size to compress, in bytes */ + int use_native; /* use a native type in write */ + hbool_t latest; /* pack file with the latest file format */ + H5F_libver_t low_bound; /* The file's low bound as in H5Fset_libver_bounds() */ + H5F_libver_t high_bound; /* The file's high bound as in H5Fset_libver_bounds() */ + hid_t fin_fapl; /* FAPL to use for opening the input file */ + hid_t fout_fapl; /* FAPL to use for opening/creating the output file */ + int grp_compact; /* Set the maximum number of links to store as header messages in the group */ + int grp_indexed; /* Set the minimum number of links to store in the indexed format */ + int msg_size[8]; /* Minimum size of shared messages: dataspace, + datatype, fill value, filter pipeline, attribute */ + const char * ublock_filename; /* user block file name */ + hsize_t ublock_size; /* user block size */ + hsize_t meta_block_size; /* metadata aggregation block size (for H5Pset_meta_block_size) */ + hsize_t threshold; /* alignment threshold for H5Pset_alignment */ + hsize_t alignment; /* alignment for H5Pset_alignment */ + H5F_fspace_strategy_t fs_strategy; /* File space handling strategy */ + int fs_persist; /* Free space section threshold */ + long fs_threshold; /* Free space section threshold */ + long long fs_pagesize; /* File space page size */ } pack_opt_t; - typedef struct named_dt_t { - haddr_t addr_in; /* Address of the named dtype in the in file */ - hid_t id_out; /* Open identifier for the dtype in the out file */ - struct named_dt_t *next; /* Next dtype */ + H5O_token_t obj_token; /* Object token for the named dtype in the in file */ + hid_t id_out; /* Open identifier for the dtype in the out file */ + struct named_dt_t *next; /* Next dtype */ } named_dt_t; /*------------------------------------------------------------------------- @@ -145,13 +151,13 @@ typedef struct named_dt_t { extern "C" { #endif -int h5repack(const char* infile, const char* outfile, pack_opt_t *options); -int h5repack_addfilter(const char* str, pack_opt_t *options); -int h5repack_addlayout(const char* str, pack_opt_t *options); +int h5repack(const char *infile, const char *outfile, pack_opt_t *options); +int h5repack_addfilter(const char *str, pack_opt_t *options); +int h5repack_addlayout(const char *str, pack_opt_t *options); int h5repack_init(pack_opt_t *options, int verbose, hbool_t latest); int h5repack_end(pack_opt_t *options); int h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options); -int h5repack_cmp_pl(const char *fname1, const char *fname2); +int h5repack_cmp_pl(const char *fname1, hid_t fname1_fapl, const char *fname2, hid_t fname2_fapl); /* Note: The below copy_named_datatype(), named_datatype_free(), copy_attr() * and struct named_dt_t were located in h5repack_copy.c as static prior to @@ -160,36 +166,29 @@ int h5repack_cmp_pl(const char *fname1, const char *fname2); * However copy_attr() may be obsoleted when H5Acopy is available and put back * others to static in h5repack_copy.c. */ -hid_t copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options); -int named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err); -int copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p, - trav_table_t *travt, pack_opt_t *options); +hid_t copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, trav_table_t *travt, + pack_opt_t *options); +int named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err); +int copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p, trav_table_t *travt, + pack_opt_t *options); #ifdef __cplusplus } #endif - - /*------------------------------------------------------------------------- * private functions *------------------------------------------------------------------------- */ - /*------------------------------------------------------------------------- * copy module *------------------------------------------------------------------------- */ -int copy_objects (const char* fnamein, - const char* fnameout, - pack_opt_t *options); +int copy_objects(const char *fnamein, const char *fnameout, pack_opt_t *options); -int do_copy_refobjs(hid_t fidin, - hid_t fidout, - trav_table_t *travt, - pack_opt_t *options); +int do_copy_refobjs(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *options); /*------------------------------------------------------------------------- * filters and verify module @@ -197,56 +196,38 @@ int do_copy_refobjs(hid_t fidin, */ void init_packobject(pack_info_t *obj); - /*------------------------------------------------------------------------- * filters and copy module *------------------------------------------------------------------------- */ -int apply_filters(const char* name, /* object name from traverse list */ - int rank, /* rank of dataset */ - hsize_t *dims, /* dimensions of dataset */ - size_t msize, /* size of type */ - hid_t dcpl_id, /* dataset creation property list */ - pack_opt_t *options, /* repack options */ - int *has_filter); /* (OUT) object NAME has a filter */ - +int apply_filters(const char * name, /* object name from traverse list */ + int rank, /* rank of dataset */ + const hsize_t *dims, /* dimensions of dataset */ + size_t msize, /* size of type */ + hid_t dcpl_id, /* dataset creation property list */ + pack_opt_t * options, /* repack options */ + int * has_filter); /* (OUT) object NAME has a filter */ /*------------------------------------------------------------------------- * options table *------------------------------------------------------------------------- */ -int options_table_init(pack_opttbl_t **tbl); -int options_table_free(pack_opttbl_t *table); -int options_add_layout(obj_list_t *obj_list, - unsigned n_objs, - pack_info_t *pack, - pack_opttbl_t *table); -int options_add_filter(obj_list_t *obj_list, - unsigned n_objs, - filter_info_t filt, - pack_opttbl_t *table); -pack_info_t* options_get_object(const char *path, - pack_opttbl_t *table); +int options_table_init(pack_opttbl_t **tbl); +int options_table_free(pack_opttbl_t *table); +int options_add_layout(obj_list_t *obj_list, unsigned n_objs, pack_info_t *pack, pack_opttbl_t *table); +int options_add_filter(obj_list_t *obj_list, unsigned n_objs, filter_info_t filt, pack_opttbl_t *table); +pack_info_t *options_get_object(const char *path, pack_opttbl_t *table); /*------------------------------------------------------------------------- * parse functions *------------------------------------------------------------------------- */ -obj_list_t* parse_filter(const char *str, - unsigned *n_objs, - filter_info_t *filt, - pack_opt_t *options, +obj_list_t *parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t *options, int *is_glb); -obj_list_t* parse_layout(const char *str, - unsigned *n_objs, - pack_info_t *pack, /* info about object */ +obj_list_t *parse_layout(const char *str, unsigned *n_objs, pack_info_t *pack, /* info about object */ pack_opt_t *options); - - - -#endif /* H5REPACK_H__ */ - +#endif /* H5REPACK_H */ diff --git a/tools/src/h5repack/h5repack_copy.c b/tools/src/h5repack/h5repack_copy.c index 13adb7c..c38a431 100644 --- a/tools/src/h5repack/h5repack_copy.c +++ b/tools/src/h5repack/h5repack_copy.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -31,24 +31,22 @@ */ /* size of buffer/# of bytes to xfer at a time when copying userblock */ -#define USERBLOCK_XFER_SIZE 512 +#define USERBLOCK_XFER_SIZE 512 /*------------------------------------------------------------------------- * local functions *------------------------------------------------------------------------- */ -static int Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[], - size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p); -static void print_dataset_info(hid_t dcpl_id, char *objname, double per, int pr); -static int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, - pack_opt_t *options); -static int copy_user_block(const char *infile, const char *outfile, - hsize_t size); -#if defined (H5REPACK_DEBUG_USER_BLOCK) +static int get_hyperslab(hid_t dcpl_id, int rank_dset, const hsize_t dims_dset[], size_t size_datum, + hsize_t dims_hslab[], hsize_t *hslab_nbytes_p); +static void print_dataset_info(hid_t dcpl_id, char *objname, double per, int pr, pack_opt_t *options, + double read_time, double write_time); +static int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *options); +static int copy_user_block(const char *infile, const char *outfile, hsize_t size); +#if defined(H5REPACK_DEBUG_USER_BLOCK) static void print_user_block(const char *filename, hid_t fid); #endif - /*------------------------------------------------------------------------- * Function: copy_objects * @@ -58,96 +56,100 @@ static void print_user_block(const char *filename, hid_t fid); * -1 no *------------------------------------------------------------------------- */ - -int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options) +int +copy_objects(const char *fnamein, const char *fnameout, pack_opt_t *options) { - int ret_value = 0; - hid_t fidin = -1; - hid_t fidout = -1; - hid_t fcpl_in = -1; /* file creation property list ID for input file */ - hid_t grp_in = -1; /* group ID */ - hid_t gcpl_in = -1; /* group creation property list */ - hid_t fcpl = H5P_DEFAULT; /* file creation property list ID */ - hid_t fapl = H5P_DEFAULT; /* file access property list ID */ - trav_table_t *travt = NULL; - hsize_t ub_size = 0; /* size of user block */ - H5F_fspace_strategy_t set_strategy; /* Strategy to be set in outupt file */ - hbool_t set_persist; /* Persist free-space status to be set in output file */ - hsize_t set_threshold; /* Free-space section threshold to be set in output file */ - hsize_t set_pagesize; /* File space page size to be set in output file */ - H5F_fspace_strategy_t in_strategy; /* Strategy from input file */ - hbool_t in_persist; /* Persist free-space status from input file */ - hsize_t in_threshold; /* Free-space section threshold from input file */ - hsize_t in_pagesize; /* File space page size from input file */ - unsigned crt_order_flags; /* group creation order flag */ + hid_t fidin = H5I_INVALID_HID; + hid_t fidout = H5I_INVALID_HID; + hid_t fcpl_in = H5I_INVALID_HID; /* file creation property list ID for input file */ + hid_t grp_in = H5I_INVALID_HID; /* group ID */ + hid_t gcpl_in = H5I_INVALID_HID; /* group creation property list */ + hid_t fcpl = H5P_DEFAULT; /* file creation property list ID */ + trav_table_t * travt = NULL; + hsize_t ub_size = 0; /* size of user block */ + H5F_fspace_strategy_t set_strategy; /* Strategy to be set in output file */ + hbool_t set_persist; /* Persist free-space status to be set in output file */ + hsize_t set_threshold; /* Free-space section threshold to be set in output file */ + hsize_t set_pagesize; /* File space page size to be set in output file */ + H5F_fspace_strategy_t in_strategy; /* Strategy from input file */ + hbool_t in_persist; /* Persist free-space status from input file */ + hsize_t in_threshold; /* Free-space section threshold from input file */ + hsize_t in_pagesize; /* File space page size from input file */ + unsigned crt_order_flags; /* group creation order flag */ + int ret_value = 0; /*------------------------------------------------------------------------- * open input file *------------------------------------------------------------------------- */ - if ((fidin = h5tools_fopen(fnamein, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, (size_t) 0)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5tools_fopen failed <%s>: %s", fnamein, H5FOPENERROR); + if ((fidin = h5tools_fopen(fnamein, H5F_ACC_RDONLY, options->fin_fapl, (options->fin_fapl != H5P_DEFAULT), + NULL, (size_t)0)) < 0) + H5TOOLS_GOTO_ERROR((-1), "h5tools_fopen failed <%s>: %s", fnamein, H5FOPENERROR); /* get user block size and file space strategy/persist/threshold */ { if ((fcpl_in = H5Fget_create_plist(fidin)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fget_create_plist failed to retrieve file creation property list"); + H5TOOLS_GOTO_ERROR((-1), "H5Fget_create_plist failed to retrieve file creation property list"); if (H5Pget_userblock(fcpl_in, &ub_size) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_userblock failed to retrieve userblock size"); + H5TOOLS_GOTO_ERROR((-1), "H5Pget_userblock failed to retrieve userblock size"); /* If the -S option is not set, get "strategy" from the input file */ - if(H5Pget_file_space_strategy(fcpl_in, &in_strategy, &in_persist, &in_threshold) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_file_space_strategy failed to retrieve file space strategy"); + if (H5Pget_file_space_strategy(fcpl_in, &in_strategy, &in_persist, &in_threshold) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pget_file_space_strategy failed to retrieve file space strategy"); /* If the -G option is not set, get "pagesize" from the input file */ - if(H5Pget_file_space_page_size(fcpl_in, &in_pagesize) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_file_space_page_size failed to retrieve file space threshold"); + if (H5Pget_file_space_page_size(fcpl_in, &in_pagesize) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pget_file_space_page_size failed to retrieve file space threshold"); /* open root group */ if ((grp_in = H5Gopen2(fidin, "/", H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Gopen2 failed"); /* get root group creation property list */ if ((gcpl_in = H5Gget_create_plist(grp_in)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gget_create_plist failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Gget_create_plist failed"); /* query and set the group creation properties */ if (H5Pget_link_creation_order(gcpl_in, &crt_order_flags) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_link_creation_order failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Pget_link_creation_order failed"); if (H5Pclose(fcpl_in) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed to close property list"); + H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed to close property list"); } - if(options->latest) + if (options->latest) options->low_bound = options->high_bound = H5F_LIBVER_LATEST; + /* Create file access property list */ - if((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed to create file access property list"); + if (options->fout_fapl == H5P_DEFAULT) + if ((options->fout_fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pcreate failed to create file access property list"); /* It can be default, latest or other settings by users */ - if(H5Pset_libver_bounds(fapl, options->low_bound, options->high_bound) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_libver_bounds failed to set format version bounds"); + if (H5Pset_libver_bounds(options->fout_fapl, options->low_bound, options->high_bound) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pset_libver_bounds failed to set format version bounds"); /* Check if we need to create a non-default file creation property list */ if (options->low_bound >= H5F_LIBVER_V18 || ub_size > 0) { /* Create file creation property list */ if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed to create a file creation property list"); + H5TOOLS_GOTO_ERROR((-1), "H5Pcreate failed to create a file creation property list"); if (ub_size > 0) if (H5Pset_userblock(fcpl, ub_size) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_userblock failed to set non-default userblock size"); + H5TOOLS_GOTO_ERROR((-1), "H5Pset_userblock failed to set non-default userblock size"); if (options->low_bound >= H5F_LIBVER_V18) { unsigned i = 0, nindex = 0, mesg_type_flags[5], min_mesg_sizes[5]; /* Adjust group creation parameters for root group */ /* (So that it is created in "dense storage" form) */ - if (H5Pset_link_phase_change(fcpl, (unsigned) options->grp_compact, - (unsigned) options->grp_indexed) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_link_phase_change failed to adjust group creation parameters for root group"); + if (H5Pset_link_phase_change(fcpl, (unsigned)options->grp_compact, + (unsigned)options->grp_indexed) < 0) + H5TOOLS_GOTO_ERROR( + (-1), + "H5Pset_link_phase_change failed to adjust group creation parameters for root group"); for (i = 0; i < 5; i++) { if (options->msg_size[i] > 0) { @@ -175,26 +177,28 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options) default: break; } /* end switch */ - min_mesg_sizes[nindex] = (unsigned) options->msg_size[i]; + min_mesg_sizes[nindex] = (unsigned)options->msg_size[i]; nindex++; } /* end if */ - } /* end for */ + } /* end for */ if (nindex > 0) { if (H5Pset_shared_mesg_nindexes(fcpl, nindex) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_shared_mesg_nindexes failed to set the number of shared object header message indexes"); + H5TOOLS_GOTO_ERROR((-1), "H5Pset_shared_mesg_nindexes failed to set the number of shared " + "object header message indexes"); - /* msg_size[0]=dataspace, 1=datatype, 2=file value, 3=filter pipleline, 4=attribute */ + /* msg_size[0]=dataspace, 1=datatype, 2=file value, 3=filter pipeline, 4=attribute */ for (i = 0; i < (nindex - 1); i++) if (H5Pset_shared_mesg_index(fcpl, i, mesg_type_flags[i], min_mesg_sizes[i]) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_shared_mesg_index failed to configure the specified shared object header message index"); + H5TOOLS_GOTO_ERROR((-1), "H5Pset_shared_mesg_index failed to configure the specified " + "shared object header message index"); } /* if (nindex>0) */ } /* end if */ - } /* end if */ -#if defined (H5REPACK_DEBUG_USER_BLOCK) -print_user_block(fnamein, fidin); + } /* end if */ +#if defined(H5REPACK_DEBUG_USER_BLOCK) + print_user_block(fnamein, fidin); #endif /*------------------------------------------------------------------------- @@ -206,11 +210,11 @@ print_user_block(fnamein, fidin); if (fcpl == H5P_DEFAULT) /* create a file creation property list */ if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed to create a file creation property list"); + H5TOOLS_GOTO_ERROR((-1), "H5Pcreate failed to create a file creation property list"); /* set user block size */ if (H5Pset_userblock(fcpl, options->ublock_size) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_userblock failed to set userblock size"); + H5TOOLS_GOTO_ERROR((-1), "H5Pset_userblock failed to set userblock size"); } /*------------------------------------------------------------------------- @@ -219,13 +223,13 @@ print_user_block(fnamein, fidin); */ if (options->alignment > 0) { /* either use the FAPL already created or create a new one */ - if (fapl == H5P_DEFAULT) + if (options->fout_fapl == H5P_DEFAULT) /* create a file access property list */ - if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed to create file access property list"); + if ((options->fout_fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pcreate failed to create file access property list"); - if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_alignment failed to set alignment"); + if (H5Pset_alignment(options->fout_fapl, options->threshold, options->alignment) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pset_alignment failed to set alignment"); } /*------------------------------------------------------------------------- @@ -234,13 +238,13 @@ print_user_block(fnamein, fidin); */ if (options->meta_block_size > 0) { /* either use the FAPL already created or create a new one */ - if (fapl == H5P_DEFAULT) + if (options->fout_fapl == H5P_DEFAULT) /* create a file access property list */ - if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed to create file access property list"); + if ((options->fout_fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pcreate failed to create file access property list"); - if (H5Pset_meta_block_size(fapl, options->meta_block_size) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_meta_block_size failed to set metadata block size"); + if (H5Pset_meta_block_size(options->fout_fapl, options->meta_block_size) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pset_meta_block_size failed to set metadata block size"); } /*------------------------------------------------------------------------- @@ -252,62 +256,54 @@ print_user_block(fnamein, fidin); if (fcpl == H5P_DEFAULT) /* create a file creation property list */ if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed to create a file creation property list"); + H5TOOLS_GOTO_ERROR((-1), "H5Pcreate failed to create a file creation property list"); - if(H5Pset_link_creation_order(fcpl, crt_order_flags ) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_link_creation_order failed"); + if (H5Pset_link_creation_order(fcpl, crt_order_flags) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pset_link_creation_order failed"); /* Set file space info to those from input file */ - set_strategy = in_strategy; - set_persist = in_persist; + set_strategy = in_strategy; + set_persist = in_persist; set_threshold = in_threshold; - set_pagesize = in_pagesize; + set_pagesize = in_pagesize; - if(options->fs_strategy == (H5F_fspace_strategy_t)-1) /* A default strategy is specified by user */ + if (options->fs_strategy == (H5F_fspace_strategy_t)-1) /* A default strategy is specified by user */ set_strategy = FS_STRATEGY_DEF; - else if(options->fs_strategy != (H5F_fspace_strategy_t)0) /* Set strategy as specified by user */ + else if (options->fs_strategy != (H5F_fspace_strategy_t)0) /* Set strategy as specified by user */ set_strategy = options->fs_strategy; - if(options->fs_persist == -1) /* A default "persist" is specified by user */ + if (options->fs_persist == -1) /* A default "persist" is specified by user */ set_persist = FS_PERSIST_DEF; - else if(options->fs_persist != 0) /* Set "persist" as specified by user */ + else if (options->fs_persist != 0) /* Set "persist" as specified by user */ set_persist = (hbool_t)options->fs_persist; - if(options->fs_threshold == -1) /* A "0" threshold is specified by user */ + if (options->fs_threshold == -1) /* A "0" threshold is specified by user */ set_threshold = (hsize_t)0; - else if(options->fs_threshold != 0) /* Set threshold as specified by user */ + else if (options->fs_threshold != 0) /* Set threshold as specified by user */ set_threshold = (hsize_t)options->fs_threshold; /* Set file space information as specified */ - if(H5Pset_file_space_strategy(fcpl, set_strategy, set_persist, set_threshold) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_file_space_strategy failed to set file space strategy"); + if (H5Pset_file_space_strategy(fcpl, set_strategy, set_persist, set_threshold) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pset_file_space_strategy failed to set file space strategy"); - if(options->fs_pagesize == -1) /* A "0" file space page size is specified by user */ + if (options->fs_pagesize == -1) /* A "0" file space page size is specified by user */ set_pagesize = (hsize_t)0; - else if(options->fs_pagesize != 0) /* Set file space page size as specified by user */ + else if (options->fs_pagesize != 0) /* Set file space page size as specified by user */ set_pagesize = (hsize_t)options->fs_pagesize; - if(set_pagesize != FS_PAGESIZE_DEF) /* Set non-default file space page size as specified */ - if(H5Pset_file_space_page_size(fcpl, set_pagesize) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_file_space_page_size failed to set file space page size"); + if (set_pagesize != FS_PAGESIZE_DEF) /* Set non-default file space page size as specified */ + if (H5Pset_file_space_page_size(fcpl, set_pagesize) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pset_file_space_page_size failed to set file space page size"); /*------------------------------------------------------------------------- * create the output file *------------------------------------------------------------------------- */ - if (options->verbose) + if (options->verbose > 0) HDprintf("Making new file ...\n"); - if ((fidout = H5Fcreate(fnameout, H5F_ACC_TRUNC, fcpl, fapl)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fcreate could not create file <%s>:", fnameout); - - /*------------------------------------------------------------------------- - * write a new user block if requested - *------------------------------------------------------------------------- - */ - if (options->ublock_size > 0) - if (copy_user_block(options->ublock_filename, fnameout, options->ublock_size) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Could not copy user block. Exiting..."); + if ((fidout = H5Fcreate(fnameout, H5F_ACC_TRUNC, fcpl, options->fout_fapl)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Fcreate could not create file <%s>:", fnameout); /*------------------------------------------------------------------------- * get list of objects @@ -317,71 +313,107 @@ print_user_block(fnamein, fidin); /* Initialize indexing options */ h5trav_set_index(sort_by, sort_order); /* init table */ - trav_table_init(&travt); + trav_table_init(fidin, &travt); if (travt) { /* get the list of objects in the file */ if (h5trav_gettable(fidin, travt) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5trav_gettable failed"); + H5TOOLS_GOTO_ERROR((-1), "h5trav_gettable failed"); /*------------------------------------------------------------------------- - * do the copy - *------------------------------------------------------------------------- - */ + * do the copy + *------------------------------------------------------------------------- + */ if (do_copy_objects(fidin, fidout, travt, options) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "do_copy_objects from <%s> could not copy data to <%s>", fnamein, fnameout); + H5TOOLS_GOTO_ERROR((-1), "do_copy_objects from <%s> could not copy data to <%s>", fnamein, + fnameout); /*------------------------------------------------------------------------- - * do the copy of referenced objects - * and create hard links - *------------------------------------------------------------------------- - */ + * do the copy of referenced objects + * and create hard links + *------------------------------------------------------------------------- + */ if (do_copy_refobjs(fidin, fidout, travt, options) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "do_copy_refobjs from <%s> could not copy data to <%s>", fnamein, fnameout); + H5TOOLS_GOTO_ERROR((-1), "do_copy_refobjs from <%s> could not copy data to <%s>", fnamein, + fnameout); } /*------------------------------------------------------------------------- - * write only the input file user block if there is no user block file input + * Close the file and everything in it so the lock is removed *------------------------------------------------------------------------- */ + if (H5Pclose(fcpl) < 0) + H5TOOLS_GOTO_ERROR((-1), "could not close fcpl"); + if (H5Pclose(options->fout_fapl) < 0) + H5TOOLS_GOTO_ERROR((-1), "could not close fcpl"); + options->fout_fapl = H5P_DEFAULT; + if (H5Pclose(gcpl_in) < 0) + H5TOOLS_GOTO_ERROR((-1), "could not close fcpl"); + if (H5Gclose(grp_in) < 0) + H5TOOLS_GOTO_ERROR((-1), "could not close fcpl"); + if (H5Fclose(fidout) < 0) + H5TOOLS_GOTO_ERROR((-1), "could not close fcpl"); + if (H5Fclose(fidin) < 0) + H5TOOLS_GOTO_ERROR((-1), "could not close fcpl"); - if (ub_size > 0 && options->ublock_size == 0) + /*------------------------------------------------------------------------- + * NOTE: The userblock MUST be written out AFTER the file is closed or + * the file locking will cause failures on Windows, where file locks + * are mandatory, not advisory. + *------------------------------------------------------------------------- + */ + + /*------------------------------------------------------------------------- + * Write a new user block if requested, using the input file user block if + * there is no separate user block file input + *------------------------------------------------------------------------- + */ + + if (options->ublock_size > 0) { + if (copy_user_block(options->ublock_filename, fnameout, options->ublock_size) < 0) + H5TOOLS_GOTO_ERROR((-1), "Could not copy user block. Exiting..."); + } + else if (ub_size > 0 && options->ublock_size == 0) { if (copy_user_block(fnamein, fnameout, ub_size) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Could not copy user block. Exiting..."); + H5TOOLS_GOTO_ERROR((-1), "Could not copy user block. Exiting..."); + } done: - H5E_BEGIN_TRY { - H5Pclose(fcpl_in); - H5Pclose(gcpl_in); - H5Pclose(fapl); - H5Pclose(fcpl); - H5Gclose(grp_in); - H5Fclose(fidin); - H5Fclose(fidout); - H5Fclose(fidin); - H5Fclose(fidout); - } H5E_END_TRY; + if (-1 == ret_value) { + H5E_BEGIN_TRY + { + H5Pclose(fcpl); + H5Pclose(options->fout_fapl); + options->fout_fapl = H5P_DEFAULT; + H5Pclose(gcpl_in); + H5Gclose(grp_in); + H5Pclose(fcpl_in); + H5Fclose(fidout); + H5Fclose(fidin); + } + H5E_END_TRY; + } if (travt) trav_table_free(travt); return ret_value; -} +} /* end copy_objects() */ /*------------------------------------------------------------------------- - * Function: Get_hyperslab + * Function: get_hyperslab * - * Purpose: Calulate a hyperslab from a dataset for higher performance. - * The size of hyperslab is limitted by H5TOOLS_BUFSIZE. - * Return the hyperslab dimentions and size in byte. + * Purpose: Calculate a hyperslab from a dataset for higher performance. + * The size of hyperslab is limited by H5TOOLS_BUFSIZE. + * Return the hyperslab dimensions and size in byte. * * Return: 0 - SUCCEED, -1 FAILED * * Parameters: * dcpl_id : [IN] dataset creation property. * rank_dset : [IN] dataset rank - * dims_dset[] : [IN] dataset dimentions + * dims_dset[] : [IN] dataset dimensions * size_datum : [IN] size of a data element in byte - * dims_hslab[] : [OUT] calculated hyperslab dimentions + * dims_hslab[] : [OUT] calculated hyperslab dimensions * * hslab_nbytes_p : [OUT] total byte of the hyperslab * * Update: @@ -396,24 +428,24 @@ done: * 3. If not chunked, each data element would be a unit of collection and * the boundary would be dataset's dims. * - * The calulation starts from the last dimention (h5dump dims output). + * The calculation starts from the last dimension (h5dump dims output). *-----------------------------------------*/ int -Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[], - size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p) +get_hyperslab(hid_t dcpl_id, int rank_dset, const hsize_t dims_dset[], size_t size_datum, + hsize_t dims_hslab[], hsize_t *hslab_nbytes_p) { - int ret_value = 0; - int k; + int k; H5D_layout_t dset_layout; - int rank_chunk; - hsize_t dims_chunk[H5S_MAX_RANK]; - hsize_t size_chunk = 1; - hsize_t nchunk_fit; /* number of chunks that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */ - hsize_t ndatum_fit; /* number of dataum that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */ - hsize_t chunk_dims_map[H5S_MAX_RANK]; /* mapped chunk dimentions */ - hsize_t hs_dims_map[H5S_MAX_RANK]; /* mapped hyperslab dimentions */ - hsize_t hslab_nbytes; /* size of hyperslab in byte */ + int rank_chunk; + hsize_t dims_chunk[H5S_MAX_RANK]; + hsize_t size_chunk = 1; + hsize_t nchunk_fit; /* number of chunks that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */ + hsize_t ndatum_fit; /* number of dataum that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */ + hsize_t chunk_dims_map[H5S_MAX_RANK]; /* mapped chunk dimensions */ + hsize_t hs_dims_map[H5S_MAX_RANK]; /* mapped hyperslab dimensions */ + hsize_t hslab_nbytes; /* size of hyperslab in byte */ + int ret_value = 0; /* init to set as size of a data element */ hslab_nbytes = size_datum; @@ -426,7 +458,7 @@ Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[], /* get chunk dims */ rank_chunk = H5Pget_chunk(dcpl_id, rank_dset, dims_chunk); if (rank_chunk < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_chunk failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Pget_chunk failed"); for (k = rank_dset; k > 0; --k) size_chunk *= dims_chunk[k - 1]; @@ -436,23 +468,23 @@ Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[], /* 1. if a chunk fit in hyperslab buffer */ if (nchunk_fit >= 1) { - /* Calulate a hyperslab that contains as many chunks that can fit + /* Calculate a hyperslab that contains as many chunks that can fit * in hyperslab buffer. Hyperslab will be increased starting from - * the last dimention of the dataset (see h5dump's dims output). + * the last dimension of the dataset (see h5dump's dims output). * The calculation boundary is dataset dims. * In the loop, used mapping from a datum to a chunk to figure out * chunk based hyperslab. */ for (k = rank_dset; k > 0; --k) { - /* map dataset dimentions with a chunk dims */ + /* map dataset dimensions with a chunk dims */ chunk_dims_map[k - 1] = dims_dset[k - 1] / dims_chunk[k - 1]; - /* if reminder exist, increse by 1 to cover partial edge chunks */ + /* if reminder exist, increase by 1 to cover partial edge chunks */ if (dims_dset[k - 1] % dims_chunk[k - 1] > 0) chunk_dims_map[k - 1]++; /* get mapped hyperslab dims */ - hs_dims_map[k - 1] = MIN (nchunk_fit, chunk_dims_map[k-1]); + hs_dims_map[k - 1] = MIN(nchunk_fit, chunk_dims_map[k - 1]); /* prepare next round */ nchunk_fit = nchunk_fit / chunk_dims_map[k - 1]; @@ -460,8 +492,8 @@ Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[], if (nchunk_fit == 0) nchunk_fit = 1; - /* get hyperslab dimentions as unmapping to actual size */ - dims_hslab[k - 1] = MIN( (hs_dims_map[k-1] * dims_chunk[k-1]), dims_dset[k-1]); + /* get hyperslab dimensions as unmapping to actual size */ + dims_hslab[k - 1] = MIN((hs_dims_map[k - 1] * dims_chunk[k - 1]), dims_dset[k - 1]); /* calculate total size for the hyperslab */ hslab_nbytes *= dims_hslab[k - 1]; @@ -469,9 +501,9 @@ Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[], } /* 2. if a chunk is bigger than hyperslab buffer */ else { - /* Calulate a hyperslab that contains as many data elements that + /* Calculate a hyperslab that contains as many data elements that * can fit in hyperslab buffer. Hyperslab will be increased - * starting from the last dimention of the chunk (see h5dump's dims + * starting from the last dimension of the chunk (see h5dump's dims * output). * The calculation boundary is a chunk dims. */ @@ -481,22 +513,22 @@ Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[], /* if a datum is bigger than rest of buffer */ if (ndatum_fit == 0) ndatum_fit = 1; - /* get hyperslab dimentions within a chunk boundary */ - dims_hslab[k - 1] = MIN (dims_chunk[k-1], ndatum_fit); + /* get hyperslab dimensions within a chunk boundary */ + dims_hslab[k - 1] = MIN(dims_chunk[k - 1], ndatum_fit); /* calculate total size for the hyperslab */ hslab_nbytes *= dims_hslab[k - 1]; if (hslab_nbytes <= 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "calculate total size for the hyperslab failed"); + H5TOOLS_GOTO_ERROR((-1), "calculate total size for the hyperslab failed"); } } } /* 3. if dataset is not chunked */ else { - /* Calulate a hyperslab that contains as many data elements that can + /* Calculate a hyperslab that contains as many data elements that can * fit in hyperslab buffer. Hyperslab will be increased starting from - * the last dimention of the dataset (see h5dump's dims output). + * the last dimension of the dataset (see h5dump's dims output). * The calculation boundary is dataset dims. */ for (k = rank_dset; k > 0; --k) { @@ -505,14 +537,14 @@ Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[], /* if a datum is bigger than rest of buffer */ if (ndatum_fit == 0) ndatum_fit = 1; - /* get hyperslab dimentions within dataset boundary */ + /* get hyperslab dimensions within dataset boundary */ dims_hslab[k - 1] = MIN(dims_dset[k - 1], ndatum_fit); /* calculate total size for the hyperslab */ hslab_nbytes *= dims_hslab[k - 1]; if (hslab_nbytes <= 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "calculate total size for the hyperslab failed"); + H5TOOLS_GOTO_ERROR((-1), "calculate total size for the hyperslab failed"); } } @@ -521,7 +553,7 @@ Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[], done: return ret_value; -} +} /* end get_hyperslab() */ /*------------------------------------------------------------------------- * Function: do_copy_objects @@ -569,7 +601,7 @@ done: * in (2) is that, when using the strip mine size, it assures that the "remaining" part * of the dataset that does not fill an entire strip mine is processed. * - * 1. figure out a hyperslab (dimentions) and size (refer to Get_hyperslab()). + * 1. figure out a hyperslab (dimensions) and size (refer to get_hyperslab()). * 2. Calculate the hyperslab selections as the selection is moving forward. * Selection would be same as the hyperslab except for the remaining edge portion * of the dataset. The code take care of the remaining portion if exist. @@ -577,53 +609,69 @@ done: *------------------------------------------------------------------------- */ -int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, - pack_opt_t *options) /* repack options */ +int +do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *options) /* repack options */ { - int ret_value = 0; - hid_t grp_in = -1; /* group ID */ - hid_t grp_out = -1; /* group ID */ - hid_t dset_in = -1; /* read dataset ID */ - hid_t dset_out = -1; /* write dataset ID */ - hid_t gcpl_in = -1; /* group creation property list */ - hid_t gcpl_out = -1; /* group creation property list */ - hid_t type_in = -1; /* named type ID */ - hid_t type_out = -1; /* named type ID */ - hid_t dcpl_in = -1; /* dataset creation property list ID */ - hid_t dcpl_out = -1; /* dataset creation property list ID */ - hid_t f_space_id = -1; /* file space ID */ - hid_t ftype_id = -1; /* file type ID */ - hid_t wtype_id = -1; /* read/write type ID */ - named_dt_t *named_dt_head = NULL; /* Pointer to the stack of named datatypes copied */ - size_t msize; /* size of type */ - hsize_t nelmts; /* number of elements in dataset */ - H5D_space_status_t space_status; /* determines whether space has been allocated for the dataset */ - int rank; /* rank of dataset */ - hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */ - hsize_t dsize_in; /* input dataset size before filter */ - hsize_t dsize_out; /* output dataset size after filter */ - int apply_s; /* flag for apply filter to small dataset sizes */ - int apply_f; /* flag for apply filter to return error on H5Dcreate */ - void *buf = NULL; /* buffer for raw data */ - void *hslab_buf = NULL; /* hyperslab buffer for raw data */ - int has_filter; /* current object has a filter */ - int req_filter; /* there was a request for a filter */ - int req_obj_layout = 0; /* request layout to current object */ - unsigned crt_order_flags; /* group creation order flag */ - unsigned i; - unsigned u; - int ifil; - int is_ref = 0; - htri_t is_named; - hbool_t limit_maxdims; - hsize_t size_dset; + hid_t grp_in = H5I_INVALID_HID; /* group ID */ + hid_t grp_out = H5I_INVALID_HID; /* group ID */ + hid_t dset_in = H5I_INVALID_HID; /* read dataset ID */ + hid_t dset_out = H5I_INVALID_HID; /* write dataset ID */ + hid_t gcpl_in = H5I_INVALID_HID; /* group creation property list */ + hid_t gcpl_out = H5I_INVALID_HID; /* group creation property list */ + hid_t type_in = H5I_INVALID_HID; /* named type ID */ + hid_t type_out = H5I_INVALID_HID; /* named type ID */ + hid_t dcpl_in = H5I_INVALID_HID; /* dataset creation property list ID */ + hid_t dcpl_out = H5I_INVALID_HID; /* dataset creation property list ID */ + hid_t f_space_id = H5I_INVALID_HID; /* file space ID */ + hid_t ftype_id = H5I_INVALID_HID; /* file type ID */ + hid_t wtype_id = H5I_INVALID_HID; /* read/write type ID */ + hid_t ocpl_id = H5I_INVALID_HID; /* property to pass copy options */ + hid_t lcpl_id = H5I_INVALID_HID; /* link creation property list */ + hid_t dxpl_id = H5I_INVALID_HID; /* dataset transfer property list */ + named_dt_t * named_dt_head = NULL; /* Pointer to the stack of named datatypes copied */ + size_t msize; /* size of type */ + hsize_t nelmts; /* number of elements in dataset */ + H5D_space_status_t space_status; /* determines whether space has been allocated for the dataset */ + int rank; /* rank of dataset */ + hsize_t dims[H5S_MAX_RANK]; /* dimensions of dataset */ + hsize_t dsize_in; /* input dataset size before filter */ + hsize_t dsize_out; /* output dataset size after filter */ + int apply_s; /* flag for apply filter to small dataset sizes */ + int apply_f; /* flag for apply filter to return error on H5Dcreate */ + void * buf = NULL; /* buffer for raw data */ + void * hslab_buf = NULL; /* hyperslab buffer for raw data */ + int has_filter; /* current object has a filter */ + int req_filter; /* there was a request for a filter */ + int req_obj_layout = 0; /* request layout to current object */ + unsigned crt_order_flags; /* group creation order flag */ + H5_timer_t timer; /* Timer for read/write operations */ + H5_timevals_t times; /* Elapsed time for each operation */ + static double read_time = 0; + static double write_time = 0; + h5tool_link_info_t linkinfo; + unsigned i; + unsigned u; + int ifil; + int is_ref = 0; + htri_t is_named; + hbool_t limit_maxdims; + hsize_t size_dset; + int ret_value = 0; + + /* init linkinfo struct */ + HDmemset(&linkinfo, 0, sizeof(h5tool_link_info_t)); /*------------------------------------------------------------------------- * copy the supplied object list *------------------------------------------------------------------------- */ - if (options->verbose) { + if (options->verbose == 2) { + HDprintf("-----------------------------------------------------------------\n"); + HDprintf(" Type Filter (Compression) Timing read/write Name\n"); + HDprintf("-----------------------------------------------------------------\n"); + } + else { HDprintf("-----------------------------------------\n"); HDprintf(" Type Filter (Compression) Name\n"); HDprintf("-----------------------------------------\n"); @@ -632,565 +680,758 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, if (travt->objs) { for (i = 0; i < travt->nobjs; i++) { /* init variables per obj */ - buf = NULL; + buf = NULL; limit_maxdims = FALSE; switch (travt->objs[i].type) { - case H5TRAV_TYPE_UNKNOWN: - break; + case H5TRAV_TYPE_UNKNOWN: + break; - /*------------------------------------------------------------------------- - * H5TRAV_TYPE_GROUP - *------------------------------------------------------------------------- - */ - case H5TRAV_TYPE_GROUP: - if (options->verbose) - HDprintf(FORMAT_OBJ, "group", travt->objs[i].name); + /*------------------------------------------------------------------------- + * H5TRAV_TYPE_GROUP + *------------------------------------------------------------------------- + */ + case H5TRAV_TYPE_GROUP: + if (options->verbose == 2) + HDprintf(FORMAT_OBJ_NOTIME, "group", travt->objs[i].name); + else + HDprintf(FORMAT_OBJ, "group", travt->objs[i].name); - /* open input group */ - if ((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed"); + /* open input group */ + if ((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Gopen2 failed"); - /* get input group creation property list */ - if ((gcpl_in = H5Gget_create_plist(grp_in)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gget_create_plist failed"); + /* get input group creation property list */ + if ((gcpl_in = H5Gget_create_plist(grp_in)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Gget_create_plist failed"); - /* query and set the group creation properties */ - if (H5Pget_link_creation_order(gcpl_in, &crt_order_flags) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_link_creation_order failed"); + /* query and set the group creation properties */ + if (H5Pget_link_creation_order(gcpl_in, &crt_order_flags) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pget_link_creation_order failed"); - /* set up group creation property list */ - if ((gcpl_out = H5Pcreate(H5P_GROUP_CREATE)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed"); + /* set up group creation property list */ + if ((gcpl_out = H5Pcreate(H5P_GROUP_CREATE)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pcreate failed"); - if (H5Pset_link_creation_order(gcpl_out, crt_order_flags) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_link_creation_order failed"); + if (H5Pset_link_creation_order(gcpl_out, crt_order_flags) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pset_link_creation_order failed"); - /*------------------------------------------------------------------------- - * the root is a special case, we get an ID for the root group - * and copy its attributes using that ID - *------------------------------------------------------------------------- - */ - if (HDstrcmp(travt->objs[i].name, "/") == 0) { - if ((grp_out = H5Gopen2(fidout, "/", H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed"); - } - else { - if (options->grp_compact > 0 || options->grp_indexed > 0) - if (H5Pset_link_phase_change(gcpl_out, (unsigned) options->grp_compact, (unsigned) options->grp_indexed) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_link_phase_change failed"); + /*------------------------------------------------------------------------- + * the root is a special case, we get an ID for the root group + * and copy its attributes using that ID + *------------------------------------------------------------------------- + */ + if (HDstrcmp(travt->objs[i].name, "/") == 0) { + if ((grp_out = H5Gopen2(fidout, "/", H5P_DEFAULT)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Gopen2 failed"); + } + else { + if (options->grp_compact > 0 || options->grp_indexed > 0) + if (H5Pset_link_phase_change(gcpl_out, (unsigned)options->grp_compact, + (unsigned)options->grp_indexed) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pset_link_phase_change failed"); + + if ((grp_out = H5Gcreate2(fidout, travt->objs[i].name, H5P_DEFAULT, gcpl_out, + H5P_DEFAULT)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Gcreate2 failed"); + } - if ((grp_out = H5Gcreate2(fidout, travt->objs[i].name, H5P_DEFAULT, gcpl_out, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gcreate2 failed"); - } + /*------------------------------------------------------------------------- + * copy attrs + *------------------------------------------------------------------------- + */ + if (copy_attr(grp_in, grp_out, &named_dt_head, travt, options) < 0) + H5TOOLS_GOTO_ERROR((-1), "copy_attr failed"); - /*------------------------------------------------------------------------- - * copy attrs - *------------------------------------------------------------------------- - */ - if (copy_attr(grp_in, grp_out, &named_dt_head, travt, options) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed"); - - if (H5Pclose(gcpl_out) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); - if (H5Pclose(gcpl_in) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); - if (H5Gclose(grp_out) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed"); - if (H5Gclose(grp_in) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed"); + if (H5Pclose(gcpl_out) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); + if (H5Pclose(gcpl_in) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); + if (H5Gclose(grp_out) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Gclose failed"); + if (H5Gclose(grp_in) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Gclose failed"); - break; + break; /*------------------------------------------------------------------------- * H5TRAV_TYPE_DATASET *------------------------------------------------------------------------- */ - case H5TRAV_TYPE_DATASET: - has_filter = 0; - req_filter = 0; - - /* check if global filters were requested */ - if (options->n_filter_g) - req_filter = 1; - - /* check if filters were requested for individual objects */ - if (options->op_tbl->objs) { - for (u = 0; u < options->op_tbl->nelems; u++) { - if (HDstrcmp(travt->objs[i].name, options->op_tbl->objs[u].path) == 0) - for (ifil = 0; ifil < options->op_tbl->objs[ifil].nfilters; ifil++) { - if (options->op_tbl->objs[u].filter[ifil].filtn > 0) - req_filter = 1; - } + case H5TRAV_TYPE_DATASET: { + hbool_t use_h5ocopy; + + read_time = 0.0; + write_time = 0.0; + + has_filter = 0; + req_filter = 0; + + /* check if global filters were requested */ + if (options->n_filter_g) + req_filter = 1; + + /* check if filters were requested for individual objects */ + if (options->op_tbl->objs) { + for (u = 0; u < options->op_tbl->nelems; u++) { + if (HDstrcmp(travt->objs[i].name, options->op_tbl->objs[u].path) == 0) + for (ifil = 0; ifil < options->op_tbl->objs[ifil].nfilters; ifil++) { + if (options->op_tbl->objs[u].filter[ifil].filtn > 0) + req_filter = 1; + } + } } - } - /* check if layout change requested individual object */ - if (options->layout_g != H5D_LAYOUT_ERROR) { - pack_info_t *pckinfo; - - /* any dataset is specified */ - if (options->op_tbl->nelems > 0) { - /* check if object exist */ - pckinfo = options_get_object(travt->objs[i].name, options->op_tbl); - if (pckinfo) - req_obj_layout = 1; + /* check if layout change requested individual object */ + if (options->layout_g != H5D_LAYOUT_ERROR) { + pack_info_t *pckinfo; + + /* any dataset is specified */ + if (options->op_tbl->nelems > 0) { + /* check if object exist */ + pckinfo = options_get_object(travt->objs[i].name, options->op_tbl); + if (pckinfo) + req_obj_layout = 1; + } } - } - - /* early detection of references */ - if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed"); - if ((ftype_id = H5Dget_type(dset_in)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_type failed"); - if (H5T_REFERENCE == H5Tget_class(ftype_id)) - is_ref = 1; - - /* Check if the datatype is committed */ - if ((is_named = H5Tcommitted(ftype_id)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tcommitted failed"); - if (is_named) - if ((wtype_id = copy_named_datatype(ftype_id, fidout, &named_dt_head, travt, options)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_named_datatype failed"); - - if (H5Tclose(ftype_id) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); - if (H5Dclose(dset_in) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); - - /*------------------------------------------------------------------------- - * check if we should use H5Ocopy or not - * if there is a request for filters/layout, we read/write the object - * otherwise we do a copy using H5Ocopy - *------------------------------------------------------------------------- - */ - if (options->op_tbl->nelems || options->all_filter == 1 - || options->all_layout == 1 || is_ref || is_named) { - - int j; + /* early detection of references */ if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed"); - if ((f_space_id = H5Dget_space(dset_in)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Dopen2 failed"); if ((ftype_id = H5Dget_type(dset_in)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_type failed"); - if ((dcpl_in = H5Dget_create_plist(dset_in)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed"); - if ((dcpl_out = H5Pcopy(dcpl_in)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcopy failed"); - if ((rank = H5Sget_simple_extent_ndims(f_space_id)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed"); - HDmemset(dims, 0, sizeof dims); - if (H5Sget_simple_extent_dims(f_space_id, dims, NULL) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed"); - if (H5Dget_space_status(dset_in, &space_status) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space_status failed"); - - nelmts = 1; - for (j = 0; j < rank; j++) - nelmts *= dims[j]; - - /* wtype_id will have already been set if using a named dtype */ - if (!is_named) { - if (options->use_native == 1) - wtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT); - else - wtype_id = H5Tcopy(ftype_id); - } /* end if */ - - if ((msize = H5Tget_size(wtype_id)) == 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Dget_type failed"); + if (H5T_REFERENCE == H5Tget_class(ftype_id)) + is_ref = 1; + + /* Check if the datatype is committed */ + if ((is_named = H5Tcommitted(ftype_id)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Tcommitted failed"); + if (is_named) + if ((wtype_id = + copy_named_datatype(ftype_id, fidout, &named_dt_head, travt, options)) < 0) + H5TOOLS_GOTO_ERROR((-1), "copy_named_datatype failed"); - /* size of current dset */ - size_dset = nelmts * msize; + if (H5Tclose(ftype_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); + if (H5Dclose(dset_in) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dclose failed"); /*------------------------------------------------------------------------- - * check if the dataset creation property list has filters that - * are not registered in the current configuration - * 1) the external filters GZIP and SZIP might not be available - * 2) the internal filters might be turned off + * check if we should use H5Ocopy or not + * if there is a request for filters/layout, we read/write the object + * otherwise we do a copy using H5Ocopy *------------------------------------------------------------------------- */ - if (h5tools_canreadf((travt->objs[i].name), dcpl_in) == 1) { - apply_s = 1; - apply_f = 1; + use_h5ocopy = !(options->op_tbl->nelems || options->all_filter == 1 || + options->all_layout == 1 || is_ref || is_named); + + /* + * Check if we are using different source and destination VOL connectors. + * In this case, we currently have to avoid usage of H5Ocopy since it + * doesn't support this. + */ + if (use_h5ocopy && + (options->fin_fapl != H5P_DEFAULT || options->fout_fapl != H5P_DEFAULT)) { + hid_t in_vol_id; + hid_t out_vol_id; + hid_t default_vol_id; + + if (H5Pget_vol_id(H5P_FILE_ACCESS_DEFAULT, &default_vol_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pget_vol_id failed"); + + if (options->fin_fapl == H5P_DEFAULT) + in_vol_id = default_vol_id; + else if (H5Pget_vol_id(options->fin_fapl, &in_vol_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pget_vol_id failed"); + if (options->fout_fapl == H5P_DEFAULT) + out_vol_id = default_vol_id; + else if (H5Pget_vol_id(options->fout_fapl, &out_vol_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pget_vol_id failed"); + + if (in_vol_id != out_vol_id) + use_h5ocopy = FALSE; + + if (in_vol_id != default_vol_id) + if (H5VLclose(in_vol_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5VLclose failed"); + if (out_vol_id != default_vol_id) + if (H5VLclose(out_vol_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5VLclose failed"); + if (H5VLclose(default_vol_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5VLclose failed"); + } + + if (!use_h5ocopy) { + int j; + + if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dopen2 failed"); + if ((f_space_id = H5Dget_space(dset_in)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dget_space failed"); + if ((ftype_id = H5Dget_type(dset_in)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dget_type failed"); + if ((dcpl_in = H5Dget_create_plist(dset_in)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dget_create_plist failed"); + if ((rank = H5Sget_simple_extent_ndims(f_space_id)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Sget_simple_extent_ndims failed"); + HDmemset(dims, 0, sizeof dims); + if (H5Sget_simple_extent_dims(f_space_id, dims, NULL) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Sget_simple_extent_dims failed"); + if (H5Dget_space_status(dset_in, &space_status) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dget_space_status failed"); + + /* If the input dataset has external storage, it must be contiguous. + * Accordingly, there would be no filter or chunk properties to preserve, + * so create a new DCPL. + * Otherwise, copy dcpl_in. + */ + if (H5Pget_external_count(dcpl_in)) { + if ((dcpl_out = H5Pcreate(H5P_DATASET_CREATE)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pcreate failed"); + } + else if ((dcpl_out = H5Pcopy(dcpl_in)) < 0) { + H5TOOLS_GOTO_ERROR((-1), "H5Pcopy failed"); + } + + nelmts = 1; + for (j = 0; j < rank; j++) + nelmts *= dims[j]; + + /* wtype_id will have already been set if using a named dtype */ + if (!is_named) { + if (options->use_native == 1) + wtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT); + else + wtype_id = H5Tcopy(ftype_id); + } + + if ((msize = H5Tget_size(wtype_id)) == 0) + H5TOOLS_GOTO_ERROR((-1), "H5Tget_size failed"); + + /* size of current dset */ + size_dset = nelmts * msize; /*------------------------------------------------------------------------- - * references are a special case - * we cannot just copy the buffers, but instead we recreate the reference - * in a second traversal of the output file + * check if the dataset creation property list has filters that + * are not registered in the current configuration + * 1) the external filters GZIP and SZIP might not be available + * 2) the internal filters might be turned off *------------------------------------------------------------------------- */ - if (H5T_REFERENCE != H5Tget_class(wtype_id)) { - /* get the storage size of the input dataset */ - dsize_in = H5Dget_storage_size(dset_in); - - /* check for small size datasets (less than 1k) except - * changing to COMPACT. For the reference, COMPACT is limited - * by size 64K by library. - */ - if (options->layout_g != H5D_COMPACT) - if (size_dset < options->min_comp) - apply_s = 0; - - /* apply the filter */ - if (apply_s) - if (apply_filters(travt->objs[i].name, rank, dims, msize, dcpl_out, options, &has_filter) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "apply_filters failed"); - - /* only if layout change requested for entire file or - * individual obj */ - if (options->all_layout > 0 || req_obj_layout == 1) - /*------------------------------------------------- - * Unset the unlimited max dims if convert to other - * than chunk layouts, because unlimited max dims - * only can be applied to chunk layout. - * Also perform only for targeted dataset - * Also check for size limit to convert to compact - *-------------------------------------------------*/ - if (options->layout_g != H5D_CHUNKED) { - /* any dataset is specified */ - if (options->op_tbl->nelems > 0) { - /* if current obj match specified obj */ - if (options_get_object(travt->objs[i].name, options->op_tbl)) - limit_maxdims = TRUE; - } - else /* no dataset is specified */ - limit_maxdims = TRUE; - - /* if convert to COMPACT */ - if (options->layout_g == H5D_COMPACT) - /* should be smaller than 64K */ - if (size_dset > MAX_COMPACT_DSIZE) - limit_maxdims = FALSE; - - /* unset unlimited max dims */ - if (limit_maxdims) - H5Sset_extent_simple(f_space_id, rank, dims, NULL); - } + if (h5tools_canreadf((travt->objs[i].name), dcpl_in) == 1) { + apply_s = 1; + apply_f = 1; /*------------------------------------------------------------------------- - * create the output dataset; - * disable error checking in case the dataset cannot be created with the - * modified dcpl; in that case use the original instead + * references are a special case + * we cannot just copy the buffers, but instead we recreate the reference + * in a second traversal of the output file *------------------------------------------------------------------------- */ - dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_out, H5P_DEFAULT); - if (dset_out == FAIL) { - H5Epush2(H5tools_ERR_STACK_g, __FILE__, FUNC, __LINE__, H5tools_ERR_CLS_g, H5E_tools_g, H5E_tools_min_id_g, "H5Dcreate2 failed"); - if (options->verbose) - HDprintf(" warning: could not create dataset <%s>. Applying original settings\n", travt->objs[i].name); - - if ((dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_in, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dcreate2 failed"); - apply_f = 0; - } + if (H5T_REFERENCE != H5Tget_class(wtype_id)) { + /* get the storage size of the input dataset */ + dsize_in = H5Dget_storage_size(dset_in); - /*------------------------------------------------------------------------- - * read/write - *------------------------------------------------------------------------- - */ - if (nelmts > 0 && space_status != H5D_SPACE_STATUS_NOT_ALLOCATED) { - size_t need = (size_t)(nelmts * msize); /* bytes needed */ - - /* have to read the whole dataset if there is only one element in the dataset */ - if (need < H5TOOLS_MALLOCSIZE) - buf = HDmalloc(need); - - if (buf != NULL) { - if(H5Dread(dset_in, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed"); - if(H5Dwrite(dset_out, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dwrite failed"); - - /* Check if we have VL data in the dataset's - * datatype that must be reclaimed */ - if (TRUE == H5Tdetect_class(wtype_id, H5T_VLEN)) - if (H5Dvlen_reclaim(wtype_id, f_space_id, H5P_DEFAULT, buf) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dvlen_reclaim failed"); - /* free */ - if (buf != NULL) { - HDfree(buf); - buf = NULL; - } - } - else { /* possibly not enough memory, read/write by hyperslabs */ - size_t p_type_nbytes = msize; /*size of memory type */ - hsize_t p_nelmts = nelmts; /*total elements */ - hsize_t elmtno; /*counter */ - int carry; /*counter carry value */ - unsigned int vl_data = 0; /*contains VL datatypes */ - - /* hyperslab info */ - hsize_t hslab_dims[H5S_MAX_RANK]; /*hyperslab dims */ - hsize_t hslab_nbytes; /*bytes per hyperslab */ - hsize_t hslab_nelmts; /*elements per hyperslab*/ - hid_t hslab_space; /*hyperslab data space */ - - /* hyperslab selection info */ - hsize_t hs_sel_offset[H5S_MAX_RANK];/* selection offset */ - hsize_t hs_sel_count[H5S_MAX_RANK]; /* selection count */ - hsize_t hs_select_nelmts; /* selected elements */ - hsize_t zero[8]; /*vector of zeros */ - int k; - H5D_layout_t dset_layout; - hid_t dcpl_tmp = -1; /* dataset creation property list ID */ - - /* check if we have VL data in the dataset's datatype */ - if (H5Tdetect_class(wtype_id, H5T_VLEN) == TRUE) - vl_data = TRUE; - - /* check first if writing dataset is chunked, - * if so use its chunk layout for better performance. */ - dset_layout = H5Pget_layout(dcpl_out); - if (dset_layout == H5D_CHUNKED) - dcpl_tmp = dcpl_out; /* writing dataset */ - else { /* if reading dataset is chunked */ - dset_layout = H5Pget_layout(dcpl_in); - if (dset_layout == H5D_CHUNKED) - dcpl_tmp = dcpl_in; /* reading dataset */ + /* check for small size datasets (less than 1k) except + * changing to COMPACT. For the reference, COMPACT is limited + * by size 64K by library. + */ + if (options->layout_g != H5D_COMPACT) + if (size_dset < options->min_comp) + apply_s = 0; + + /* apply the filter */ + if (apply_s) + if (apply_filters(travt->objs[i].name, rank, dims, msize, dcpl_out, + options, &has_filter) < 0) + H5TOOLS_GOTO_ERROR((-1), "apply_filters failed"); + + /* only if layout change requested for entire file or + * individual obj */ + if (options->all_layout > 0 || req_obj_layout == 1) { + /*------------------------------------------------- + * Unset the unlimited max dims if convert to other + * than chunk layouts, because unlimited max dims + * only can be applied to chunk layout. + * Also perform only for targeted dataset + * Also check for size limit to convert to compact + *-------------------------------------------------*/ + if (options->layout_g != H5D_CHUNKED) { + /* any dataset is specified */ + if (options->op_tbl->nelems > 0) { + /* if current obj match specified obj */ + if (options_get_object(travt->objs[i].name, options->op_tbl)) + limit_maxdims = TRUE; + } + else /* no dataset is specified */ + limit_maxdims = TRUE; + + /* if convert to COMPACT */ + if (options->layout_g == H5D_COMPACT) + if (size_dset > MAX_COMPACT_DSIZE) + limit_maxdims = FALSE; + + /* unset unlimited max dims */ + if (limit_maxdims) + H5Sset_extent_simple(f_space_id, rank, dims, NULL); + } /* end if not chunked */ + } /* end if layout change requested for entire file or individual object */ + + /*------------------------------------------------------------------------- + * create the output dataset; + * disable error checking in case the dataset cannot be created with the + * modified dcpl; in that case use the original instead + *------------------------------------------------------------------------- + */ + dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, + H5P_DEFAULT, dcpl_out, H5P_DEFAULT); + if (dset_out == H5I_INVALID_HID) { + H5TOOLS_INFO("H5Dcreate2 failed"); + if (options->verbose > 0) + HDprintf(" warning: could not create dataset <%s>. Applying original " + "settings\n", + travt->objs[i].name); + + if ((dset_out = + H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, + H5P_DEFAULT, dcpl_in, H5P_DEFAULT)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dcreate2 failed"); + apply_f = 0; + } /* end if retry dataset create */ + + /*------------------------------------------------------------------------- + * read/write + *------------------------------------------------------------------------- + */ + if (nelmts > 0 && space_status != H5D_SPACE_STATUS_NOT_ALLOCATED) { + size_t need = (size_t)(nelmts * msize); /* bytes needed */ + + /* have to read the whole dataset if there is only one element in the + * dataset */ + if (need < H5TOOLS_MALLOCSIZE) + buf = HDmalloc(need); + + /* Set up collective write if using filters in parallel */ + { +#ifdef H5_HAVE_PARALLEL + hbool_t parallel = (H5FD_MPIO == H5Pget_driver(options->fout_fapl)); + + if (parallel && apply_s && apply_f) { + if ((dxpl_id = H5Pcreate(H5P_DATASET_XFER)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pcreate failed"); + if (H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_COLLECTIVE) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pset_dxpl_mpio failed"); + } + else +#endif + dxpl_id = H5P_DEFAULT; } - /* get hyperslab dims and size in byte */ - if (Get_hyperslab(dcpl_tmp, rank, dims, p_type_nbytes, hslab_dims, &hslab_nbytes) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Get_hyperslab failed"); - - hslab_buf = HDmalloc((size_t)hslab_nbytes); - - hslab_nelmts = hslab_nbytes / p_type_nbytes; - hslab_space = H5Screate_simple(1, &hslab_nelmts, NULL); - - /* the hyperslab selection loop */ - HDmemset(hs_sel_offset, 0, sizeof hs_sel_offset); - HDmemset(zero, 0, sizeof zero); - - for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_select_nelmts) { - if (rank > 0) { - /* calculate the hyperslab selections. - * The selection would be same as the hyperslab - * except for remaining edge portion of the dataset - * which is smaller then the hyperslab. - */ - for (k = 0, hs_select_nelmts = 1; k < rank; k++) { - /* MIN() is used to get the remaining edge portion if exist. - * "dims[k] - hs_sel_offset[k]" is remaining edge portion that is smaller then the hyperslab.*/ - hs_sel_count[k] = MIN(dims[k] - hs_sel_offset[k], hslab_dims[k]); - hs_select_nelmts *= hs_sel_count[k]; - } + if (buf != NULL) { + if (options->verbose == 2) { + H5_timer_init(&timer); + H5_timer_start(&timer); + } + if (H5Dread(dset_in, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < + 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dread failed"); + if (options->verbose == 2) { + H5_timer_stop(&timer); + H5_timer_get_times(timer, ×); + read_time += times.elapsed; + H5_timer_init(&timer); + H5_timer_start(&timer); + } + if (H5Dwrite(dset_out, wtype_id, H5S_ALL, H5S_ALL, dxpl_id, buf) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dwrite failed"); + if (options->verbose == 2) { + H5_timer_stop(&timer); + H5_timer_get_times(timer, ×); + write_time += times.elapsed; + } + + /* Check if we have VL data in the dataset's + * datatype that must be reclaimed */ + if (TRUE == H5Tdetect_class(wtype_id, H5T_VLEN)) + if (H5Treclaim(wtype_id, f_space_id, H5P_DEFAULT, buf) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Treclaim failed"); - if (H5Sselect_hyperslab(f_space_id, H5S_SELECT_SET, hs_sel_offset, NULL, hs_sel_count, NULL) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sselect_hyperslab failed"); - if (H5Sselect_hyperslab(hslab_space, H5S_SELECT_SET, zero, NULL, &hs_select_nelmts, NULL) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sselect_hyperslab failed"); + if (buf != NULL) { /* TODO: is buf potentially released by + H5Dvlen_reclaim()? */ + HDfree(buf); + buf = NULL; } - else { - H5Sselect_all(f_space_id); - H5Sselect_all(hslab_space); - hs_select_nelmts = 1; - } /* rank */ - - if(H5Dread(dset_in, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed"); - if(H5Dwrite(dset_out, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dwrite failed"); - - /* reclaim any VL memory, if necessary */ - if (vl_data) - H5Dvlen_reclaim(wtype_id, hslab_space, H5P_DEFAULT, hslab_buf); - - /* calculate the next hyperslab offset */ - for (k = rank, carry = 1; k > 0 && carry; --k) { - hs_sel_offset[k - 1] += hs_sel_count[k - 1]; - /* if reached the end of a dim */ - if (hs_sel_offset[k - 1] == dims[k - 1]) - hs_sel_offset[k - 1] = 0; - else - carry = 0; - } /* k */ - } /* elmtno */ - - H5Sclose(hslab_space); - /* free */ - if (hslab_buf != NULL) { - HDfree(hslab_buf); - hslab_buf = NULL; } - } /* hyperslab read */ - } /* if (nelmts>0 && space_status==H5D_SPACE_STATUS_NOT_ALLOCATED) */ + else { /* possibly not enough memory, read/write by hyperslabs */ + size_t p_type_nbytes = msize; /*size of memory type */ + hsize_t p_nelmts = nelmts; /*total elements */ + hsize_t elmtno; /*counter */ + int carry; /*counter carry value */ + unsigned int vl_data = 0; /*contains VL datatypes */ + + /* hyperslab info */ + hsize_t hslab_dims[H5S_MAX_RANK]; /*hyperslab dims */ + hsize_t hslab_nbytes; /*bytes per hyperslab */ + hsize_t hslab_nelmts; /*elements per hyperslab*/ + hid_t hslab_space; /*hyperslab data space */ + + /* hyperslab selection info */ + hsize_t hs_sel_offset[H5S_MAX_RANK]; /* selection offset */ + hsize_t hs_sel_count[H5S_MAX_RANK]; /* selection count */ + hsize_t hs_select_nelmts; /* selected elements */ + hsize_t zero[8]; /*vector of zeros */ + int k; + H5D_layout_t dset_layout; + hid_t dcpl_tmp = + H5I_INVALID_HID; /* dataset creation property list ID */ + + /* check if we have VL data in the dataset's datatype */ + if (H5Tdetect_class(wtype_id, H5T_VLEN) == TRUE) + vl_data = TRUE; + + /* check first if writing dataset is chunked, + * if so use its chunk layout for better performance. */ + dset_layout = H5Pget_layout(dcpl_out); + if (dset_layout == H5D_CHUNKED) + dcpl_tmp = dcpl_out; /* writing dataset */ + else { + dset_layout = H5Pget_layout(dcpl_in); + if (dset_layout == H5D_CHUNKED) + dcpl_tmp = dcpl_in; /* reading dataset */ + } - /*------------------------------------------------------------------------- - * amount of compression used - *------------------------------------------------------------------------- - */ - if (options->verbose) { - double ratio = 0; - - /* only print the compression ration if there was a filter request */ - if (apply_s && apply_f && req_filter) { - /* get the storage size of the output dataset */ - dsize_out = H5Dget_storage_size(dset_out); - - /* compression ratio = uncompressed size / compressed size */ - if (dsize_out != 0) - ratio = (double) dsize_in / (double) dsize_out; - print_dataset_info(dcpl_out, travt->objs[i].name, ratio, 1); - } - else - print_dataset_info(dcpl_in, travt->objs[i].name, ratio, 0); + /* get hyperslab dims and size in byte */ + if (get_hyperslab(dcpl_tmp, rank, dims, p_type_nbytes, hslab_dims, + &hslab_nbytes) < 0) + H5TOOLS_GOTO_ERROR((-1), "get_hyperslab failed"); + + hslab_buf = HDmalloc((size_t)hslab_nbytes); + if (hslab_buf == NULL) + H5TOOLS_GOTO_ERROR((-1), "can't allocate space for hyperslab"); + + hslab_nelmts = hslab_nbytes / p_type_nbytes; + hslab_space = H5Screate_simple(1, &hslab_nelmts, NULL); + + /* the hyperslab selection loop */ + HDmemset(hs_sel_offset, 0, sizeof hs_sel_offset); + HDmemset(zero, 0, sizeof zero); + + for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_select_nelmts) { + if (rank > 0) { + /* calculate the hyperslab selections. + * The selection would be same as the hyperslab + * except for remaining edge portion of the dataset + * which is smaller then the hyperslab. + */ + for (k = 0, hs_select_nelmts = 1; k < rank; k++) { + /* MIN() is used to get the remaining edge portion if + * exist. "dims[k] - hs_sel_offset[k]" is remaining edge + * portion that is smaller then the hyperslab.*/ + hs_sel_count[k] = + MIN(dims[k] - hs_sel_offset[k], hslab_dims[k]); + hs_select_nelmts *= hs_sel_count[k]; + } + + if (H5Sselect_hyperslab(f_space_id, H5S_SELECT_SET, + hs_sel_offset, NULL, hs_sel_count, + NULL) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Sselect_hyperslab failed"); + if (H5Sselect_hyperslab(hslab_space, H5S_SELECT_SET, zero, + NULL, &hs_select_nelmts, NULL) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Sselect_hyperslab failed"); + } /* end if rank > 0 */ + else { + H5Sselect_all(f_space_id); + H5Sselect_all(hslab_space); + hs_select_nelmts = 1; + } /* end (else) rank == 0 */ + + if (options->verbose == 2) { + H5_timer_init(&timer); + H5_timer_start(&timer); + } + if (H5Dread(dset_in, wtype_id, hslab_space, f_space_id, + H5P_DEFAULT, hslab_buf) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dread failed"); + if (options->verbose == 2) { + H5_timer_stop(&timer); + H5_timer_get_times(timer, ×); + read_time += times.elapsed; + H5_timer_init(&timer); + H5_timer_start(&timer); + } + if (H5Dwrite(dset_out, wtype_id, hslab_space, f_space_id, dxpl_id, + hslab_buf) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dwrite failed"); + if (options->verbose == 2) { + H5_timer_stop(&timer); + H5_timer_get_times(timer, ×); + write_time += times.elapsed; + } - /* print a message that the filter was not applied - (in case there was a filter) - */ - if (has_filter && apply_s == 0) - HDprintf(" <warning: filter not applied to %s. dataset smaller than %d bytes>\n", travt->objs[i].name, (int) options->min_comp); + /* reclaim any VL memory, if necessary */ + if (vl_data) + H5Treclaim(wtype_id, hslab_space, H5P_DEFAULT, hslab_buf); + + /* calculate the next hyperslab offset */ + for (k = rank, carry = 1; k > 0 && carry; --k) { + hs_sel_offset[k - 1] += hs_sel_count[k - 1]; + /* if reached the end of a dim */ + if (hs_sel_offset[k - 1] == dims[k - 1]) + hs_sel_offset[k - 1] = 0; + else + carry = 0; + } + } /* end for (hyperslab selection loop) */ - if (has_filter && apply_f == 0) - HDprintf(" <warning: could not apply the filter to %s>\n", travt->objs[i].name); - } /* verbose */ + H5Sclose(hslab_space); + if (hslab_buf != NULL) { + HDfree(hslab_buf); + hslab_buf = NULL; + } + } /* end if reading/writing by hyperslab */ + } /* end if (nelmts > 0 && space_status != H5D_SPACE_STATUS_NOT_ALLOCATED) */ - /*------------------------------------------------------------------------- - * copy attrs - *------------------------------------------------------------------------- - */ - if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed"); + /*------------------------------------------------------------------------- + * print amount of compression used + *------------------------------------------------------------------------- + */ + if (options->verbose > 0) { + double ratio = 0; + + /* only print the compression ration if there was a filter request */ + if (apply_s && apply_f && req_filter) { + /* get the storage size of the output dataset */ + dsize_out = H5Dget_storage_size(dset_out); + + /* compression ratio = uncompressed size / compressed size */ + if (dsize_out != 0) + ratio = (double)dsize_in / (double)dsize_out; + print_dataset_info(dcpl_out, travt->objs[i].name, ratio, 1, options, + read_time, write_time); + } + else + print_dataset_info(dcpl_in, travt->objs[i].name, ratio, 0, options, + read_time, write_time); + + /* print a message that the filter was not applied + * (in case there was a filter) + */ + if (has_filter && apply_s == 0) + HDprintf(" <warning: filter not applied to %s. dataset smaller than " + "%d bytes>\n", + travt->objs[i].name, (int)options->min_comp); + + if (has_filter && apply_f == 0) + HDprintf(" <warning: could not apply the filter to %s>\n", + travt->objs[i].name); + } /* end if verbose (print compression) */ + + /*------------------------------------------------------------------------- + * copy attrs + *------------------------------------------------------------------------- + */ + if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0) + H5TOOLS_GOTO_ERROR((-1), "copy_attr failed"); - /*close */ - if (H5Dclose(dset_out) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); - }/*!H5T_REFERENCE*/ - }/*h5tools_canreadf*/ + if (H5Dclose(dset_out) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dclose failed"); + } /* end if not a reference */ + } /* end if h5tools_canreadf (filter availability check) */ + /*------------------------------------------------------------------------- + * Close + *------------------------------------------------------------------------- + */ + if (H5Tclose(ftype_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); + if (H5Tclose(wtype_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); + if (H5Pclose(dcpl_in) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); + if (H5Pclose(dcpl_out) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); + if (H5Sclose(f_space_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Sclose failed"); + if (H5Dclose(dset_in) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dclose failed"); + } /*------------------------------------------------------------------------- - * close + * We do not have request for filter/chunking; use H5Ocopy instead *------------------------------------------------------------------------- */ - if (H5Tclose(ftype_id) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); - if (H5Tclose(wtype_id) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); - if (H5Pclose(dcpl_in) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); - if (H5Pclose(dcpl_out) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); - if (H5Sclose(f_space_id) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed"); - if (H5Dclose(dset_in) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); - } + else { + /* create property to pass copy options */ + if ((ocpl_id = H5Pcreate(H5P_OBJECT_COPY)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pcreate failed"); + + /* set options for object copy */ + if (H5Pset_copy_object(ocpl_id, H5O_COPY_WITHOUT_ATTR_FLAG) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pset_copy_object failed"); + + if (options->verbose == 2) { + H5_timer_init(&timer); + H5_timer_start(&timer); + } + if (H5Ocopy(fidin, /* Source file or group identifier */ + travt->objs[i].name, /* Name of the source object to be copied */ + fidout, /* Destination file or group identifier */ + travt->objs[i].name, /* Name of the destination object */ + ocpl_id, /* Properties which apply to the copy */ + H5P_DEFAULT) < 0) /* Properties which apply to the new hard link */ + H5TOOLS_GOTO_ERROR((-1), "H5Ocopy failed"); + if (options->verbose == 2) { + H5_timer_stop(&timer); + H5_timer_get_times(timer, ×); + write_time += times.elapsed; + } + + if (H5Pclose(ocpl_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); + ocpl_id = H5I_INVALID_HID; + + /*------------------------------------------------------------------------- + * Copy attrs manually + *------------------------------------------------------------------------- + */ + if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dopen2 failed"); + if ((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dopen2 failed"); + if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0) + H5TOOLS_GOTO_ERROR((-1), "copy_attr failed"); + if (H5Dclose(dset_in) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dclose failed"); + if (H5Dclose(dset_out) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dclose failed"); + + if (options->verbose == 2) + HDprintf(FORMAT_OBJ_TIME, "dset", 0.0, write_time, travt->objs[i].name); + else + HDprintf(FORMAT_OBJ, "dset", travt->objs[i].name); + + } /* end whether we have request for filter/chunking */ + + break; + } /* H5TRAV_TYPE_DATASET */ + /*------------------------------------------------------------------------- - * we do not have request for filter/chunking use H5Ocopy instead + * H5TRAV_TYPE_NAMED_DATATYPE *------------------------------------------------------------------------- */ - else { - hid_t pid = -1; + case H5TRAV_TYPE_NAMED_DATATYPE: + if (options->verbose == 2) + HDprintf(FORMAT_OBJ_NOTIME, "type", travt->objs[i].name); + else + HDprintf(FORMAT_OBJ, "type", travt->objs[i].name); - /* create property to pass copy options */ - if ((pid = H5Pcreate(H5P_OBJECT_COPY)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed"); + if ((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Topen2 failed"); - /* set options for object copy */ - if (H5Pset_copy_object(pid, H5O_COPY_WITHOUT_ATTR_FLAG) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_copy_object failed"); + /* Copy the datatype anonymously */ + if ((type_out = copy_named_datatype(type_in, fidout, &named_dt_head, travt, options)) < 0) + H5TOOLS_GOTO_ERROR((-1), "copy_named_datatype failed"); - /*------------------------------------------------------------------------- - * do the copy - *------------------------------------------------------------------------- - */ - - if (H5Ocopy(fidin, /* Source file or group identifier */ - travt->objs[i].name, /* Name of the source object to be copied */ - fidout, /* Destination file or group identifier */ - travt->objs[i].name, /* Name of the destination object */ - pid, /* Properties which apply to the copy */ - H5P_DEFAULT) < 0) /* Properties which apply to the new hard link */ - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Ocopy failed"); - - /* close property */ - if (H5Pclose(pid) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + /* Link in to group structure */ + if (H5Lcreate_hard(type_out, ".", fidout, travt->objs[i].name, H5P_DEFAULT, H5P_DEFAULT) < + 0) + H5TOOLS_GOTO_ERROR((-1), "H5Lcreate_hard failed"); /*------------------------------------------------------------------------- - * copy attrs manually + * copy attrs *------------------------------------------------------------------------- */ - if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed"); - if ((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed"); - if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed"); - if (H5Dclose(dset_in) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); - if (H5Dclose(dset_out) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); - - if (options->verbose) - HDprintf(FORMAT_OBJ, "dset", travt->objs[i].name); - - } /* end do we have request for filter/chunking */ - break; - - /*------------------------------------------------------------------------- - * H5TRAV_TYPE_NAMED_DATATYPE - *------------------------------------------------------------------------- - */ - case H5TRAV_TYPE_NAMED_DATATYPE: - if (options->verbose) - HDprintf(FORMAT_OBJ, "type", travt->objs[i].name); + if (copy_attr(type_in, type_out, &named_dt_head, travt, options) < 0) + H5TOOLS_GOTO_ERROR((-1), "copy_attr failed"); - if ((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Topen2 failed"); + if (H5Tclose(type_in) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); + if (H5Tclose(type_out) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); + type_out = H5I_INVALID_HID; /* named datatypes stack, named_dt_head, manages allocation */ - /* Copy the datatype anonymously */ - if ((type_out = copy_named_datatype(type_in, fidout, &named_dt_head, travt, options)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_named_datatype failed"); - - /* Link in to group structure */ - if (H5Lcreate_hard(type_out, ".", fidout, travt->objs[i].name, H5P_DEFAULT, H5P_DEFAULT) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Lcreate_hard failed"); + break; /*------------------------------------------------------------------------- - * copy attrs + * H5TRAV_TYPE_LINK + * H5TRAV_TYPE_UDLINK + * + * Only handles external links; H5Lcopy will fail for other UD link types + * since we don't have creation or copy callbacks for them. *------------------------------------------------------------------------- */ - if (copy_attr(type_in, type_out, &named_dt_head, travt, options) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed"); - - if (H5Tclose(type_in) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); - if (H5Tclose(type_out) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); - type_out = -1; /* named datatypes stack, named_dt_head, manages allocation */ - - break; - - /*------------------------------------------------------------------------- - * H5TRAV_TYPE_LINK - * H5TRAV_TYPE_UDLINK - * - * Only handles external links; H5Lcopy will fail for other UD link types - * since we don't have creation or copy callbacks for them. - *------------------------------------------------------------------------- - */ - case H5TRAV_TYPE_LINK: - case H5TRAV_TYPE_UDLINK: - if (options->verbose) - HDprintf(FORMAT_OBJ, "link", travt->objs[i].name); - - if (H5Lcopy(fidin, travt->objs[i].name, fidout, travt->objs[i].name, H5P_DEFAULT, H5P_DEFAULT) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Lcopy failed"); + case H5TRAV_TYPE_LINK: + case H5TRAV_TYPE_UDLINK: + if (options->verbose == 2) + HDprintf(FORMAT_OBJ_NOTIME, "link", travt->objs[i].name); + else + HDprintf(FORMAT_OBJ, "link", travt->objs[i].name); + + /* Check -X option. */ + if (options->merge) { + if (H5tools_get_symlink_info(fidin, travt->objs[i].name, &linkinfo, 1) == 0) { + /* dangling link */ + if (options->prune) { + HDprintf("Pruned %s.\n", travt->objs[i].name); + } + else { + if (H5Lcopy(fidin, travt->objs[i].name, fidout, travt->objs[i].name, + H5P_DEFAULT, H5P_DEFAULT) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Lcopy failed"); + } + } + else { + /* valid link */ + /* create property to pass copy options */ + if ((ocpl_id = H5Pcreate(H5P_OBJECT_COPY)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pcreate create property failed"); + + /* set options for object copy */ + if (H5Pset_copy_object(ocpl_id, H5O_COPY_EXPAND_EXT_LINK_FLAG) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pset_copy_object failed"); + + /* Create link creation property list */ + if ((lcpl_id = H5Pcreate(H5P_LINK_CREATE)) < 0) { + H5TOOLS_GOTO_ERROR((-1), "H5Pcreate link creation property failed"); + } - if (options->verbose) - HDprintf(FORMAT_OBJ, "link", travt->objs[i].name); - break; + /* Set flag for intermediate group creation */ + if (H5Pset_create_intermediate_group(lcpl_id, TRUE) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pset_create_intermediate_group failed"); + + if (H5Ocopy(fidin, travt->objs[i].name, fidout, travt->objs[i].name, ocpl_id, + lcpl_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Ocopy failed"); + + if (H5Pclose(lcpl_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); + + if (H5Pclose(ocpl_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); + } + + /* free link info path */ + if (linkinfo.trg_path) + HDfree(linkinfo.trg_path); + linkinfo.trg_path = NULL; + } /* options->merge */ + else { + if (options->prune) { + HDprintf("Pruned %s.\n", travt->objs[i].name); + } + else { + if (H5Lcopy(fidin, travt->objs[i].name, fidout, travt->objs[i].name, H5P_DEFAULT, + H5P_DEFAULT) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Lcopy failed"); + } + } + break; - default: - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Object type not found"); + default: + H5TOOLS_GOTO_ERROR((-1), "Object type not found"); } /* switch */ - } /* end for */ - } /* end if */ + } /* end for each object to traverse */ + } /* end if there are objects */ done: @@ -1198,20 +1439,30 @@ done: * because of reference counting */ if (0 == ret_value && named_dt_head != NULL) { if (named_datatype_free(&named_dt_head, 0) < 0) - H5TOOLS_INFO(H5E_tools_min_id_g, "named_datatype_free failed"); + H5TOOLS_ERROR((-1), "named_datatype_free failed"); } - else - H5E_BEGIN_TRY { + else { + H5E_BEGIN_TRY + { named_datatype_free(&named_dt_head, 1); - } H5E_END_TRY; + } + H5E_END_TRY; + } + + /* free link info path */ + if (linkinfo.trg_path) + HDfree(linkinfo.trg_path); H5E_BEGIN_TRY { H5Gclose(grp_in); H5Gclose(grp_out); + H5Pclose(lcpl_id); + H5Pclose(ocpl_id); H5Pclose(dcpl_in); H5Pclose(gcpl_in); H5Pclose(gcpl_out); + H5Pclose(dxpl_id); H5Sclose(f_space_id); H5Dclose(dset_in); H5Dclose(dset_out); @@ -1219,7 +1470,8 @@ done: H5Tclose(wtype_id); H5Tclose(type_in); H5Tclose(type_out); - } H5E_END_TRY; + } + H5E_END_TRY; /* free */ if (buf != NULL) @@ -1228,7 +1480,7 @@ done: HDfree(hslab_buf); return ret_value; -} +} /* end do_copy_objects() */ /*------------------------------------------------------------------------- * Function: print_dataset_info @@ -1237,19 +1489,20 @@ done: *------------------------------------------------------------------------- */ static void -print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr) +print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr, pack_opt_t *options, double read_time, + double write_time) { - char strfilter[255]; -#if defined (PRINT_DEBUG ) - char temp[255]; + char strfilter[255]; +#if defined(PRINT_DEBUG) + char temp[255]; #endif - int nfilters; /* number of filters */ - unsigned filt_flags; /* filter flags */ - H5Z_filter_t filtn; /* filter identification number */ - unsigned cd_values[20]; /* filter client data values */ - size_t cd_nelmts; /* filter client number of values */ - char f_objname[256]; /* filter objname */ - int i; + int nfilters; /* number of filters */ + unsigned filt_flags; /* filter flags */ + H5Z_filter_t filtn; /* filter identification number */ + unsigned cd_values[20]; /* filter client data values */ + size_t cd_nelmts; /* filter client number of values */ + char f_objname[256]; /* filter objname */ + int i; HDstrcpy(strfilter, "\0"); @@ -1260,8 +1513,8 @@ print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr) for (i = 0; i < nfilters; i++) { cd_nelmts = NELMTS(cd_values); - if ((filtn = H5Pget_filter2(dcpl_id, (unsigned) i, &filt_flags, &cd_nelmts, - cd_values, sizeof(f_objname), f_objname, NULL)) < 0) { + if ((filtn = H5Pget_filter2(dcpl_id, (unsigned)i, &filt_flags, &cd_nelmts, cd_values, + sizeof(f_objname), f_objname, NULL)) < 0) { HDstrcat(strfilter, "ERROR "); continue; } @@ -1274,11 +1527,11 @@ print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr) case H5Z_FILTER_DEFLATE: HDstrcat(strfilter, "GZIP "); -#if defined (PRINT_DEBUG) +#if defined(PRINT_DEBUG) { unsigned level = cd_values[0]; - HDsprintf(temp,"(%d)", level); + HDsprintf(temp, "(%d)", level); HDstrcat(strfilter, temp); } #endif @@ -1287,12 +1540,12 @@ print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr) case H5Z_FILTER_SZIP: HDstrcat(strfilter, "SZIP "); -#if defined (PRINT_DEBUG) +#if defined(PRINT_DEBUG) { unsigned options_mask = cd_values[0]; /* from dcpl, not filt*/ - unsigned ppb = cd_values[1]; + unsigned ppb = cd_values[1]; - HDsprintf(temp,"(%d,", ppb); + HDsprintf(temp, "(%d,", ppb); HDstrcat(strfilter, temp); if (options_mask & H5_SZIP_EC_OPTION_MASK) HDstrcpy(temp, "EC) "); @@ -1322,11 +1575,14 @@ print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr) default: HDstrcat(strfilter, "UD "); break; - } /* switch */ - }/*i*/ + } /* end switch */ + } /* end for each filter */ if (!pr) - HDprintf(FORMAT_OBJ, "dset", objname); + if (options->verbose == 2) + HDprintf(FORMAT_OBJ_TIME, "dset", read_time, write_time, objname); + else + HDprintf(FORMAT_OBJ, "dset", objname); else { char str[512], temp[512]; @@ -1334,9 +1590,12 @@ print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr) HDstrcat(str, strfilter); HDsprintf(temp, " (%.3f:1)", ratio); HDstrcat(str, temp); - HDprintf(FORMAT_OBJ, str, objname); + if (options->verbose == 2) + HDprintf(FORMAT_OBJ_TIME, str, read_time, write_time, objname); + else + HDprintf(FORMAT_OBJ, str, objname); } -} +} /* end print_dataset_info() */ /*------------------------------------------------------------------------- * Function: copy_user_block @@ -1349,22 +1608,22 @@ print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr) static int copy_user_block(const char *infile, const char *outfile, hsize_t size) { - int ret_value = 0; int infid = -1, outfid = -1; /* File descriptors */ + int ret_value = 0; /* User block must be any power of 2 equal to 512 or greater (512, 1024, 2048, etc.) */ /* Open files */ if ((infid = HDopen(infile, O_RDONLY)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDopen failed input file <%s>", infile); + H5TOOLS_GOTO_ERROR((-1), "HDopen failed input file <%s>", infile); if ((outfid = HDopen(outfile, O_WRONLY)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDopen failed output file <%s>", outfile); + H5TOOLS_GOTO_ERROR((-1), "HDopen failed output file <%s>", outfile); /* Copy the userblock from the input file to the output file */ while (size > 0) { - ssize_t nread, nbytes; /* # of bytes transfered, etc. */ - char rbuf[USERBLOCK_XFER_SIZE]; /* Buffer for reading */ - const char *wbuf; /* Pointer into buffer, for writing */ + ssize_t nread, nbytes; /* # of bytes transferred, etc. */ + char rbuf[USERBLOCK_XFER_SIZE]; /* Buffer for reading */ + const char *wbuf; /* Pointer into buffer, for writing */ /* Read buffer from source file */ if (size > USERBLOCK_XFER_SIZE) @@ -1372,20 +1631,20 @@ copy_user_block(const char *infile, const char *outfile, hsize_t size) else nread = HDread(infid, rbuf, (size_t)size); if (nread < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDread failed to read userblock"); + H5TOOLS_GOTO_ERROR((-1), "HDread failed to read userblock"); /* Write buffer to destination file */ /* (compensating for interrupted writes & checking for errors, etc.) */ nbytes = nread; - wbuf = rbuf; + wbuf = rbuf; while (nbytes > 0) { ssize_t nwritten; /* # of bytes written */ do { nwritten = HDwrite(outfid, wbuf, (size_t)nbytes); } while (-1 == nwritten && EINTR == errno); - if (-1 == nwritten) /* error */ - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDwrite failed"); + if (-1 == nwritten) /* error */ + H5TOOLS_GOTO_ERROR((-1), "HDwrite failed"); HDassert(nwritten > 0); HDassert(nwritten <= nbytes); @@ -1396,7 +1655,7 @@ copy_user_block(const char *infile, const char *outfile, hsize_t size) } /* end while */ /* Update size of userblock left to transfer */ - size = size - (hsize_t) nread; + size = size - (hsize_t)nread; } /* end while */ done: @@ -1406,7 +1665,7 @@ done: HDclose(outfid); return ret_value; -} +} /* end copy_user_block() */ /*------------------------------------------------------------------------- * Function: print_user_block @@ -1416,42 +1675,41 @@ done: * Return: 0, ok, -1 no *------------------------------------------------------------------------- */ -#if defined (H5REPACK_DEBUG_USER_BLOCK) -static -void +#if defined(H5REPACK_DEBUG_USER_BLOCK) +static void print_user_block(const char *filename, hid_t fid) { - int ret_value = 0; - int fh = -1; /* file handle */ - hsize_t ub_size; /* user block size */ - hsize_t size; /* size read */ - hid_t fcpl = -1; /* file creation property list ID for HDF5 file */ + int fh = -1; /* file handle */ + hsize_t ub_size; /* user block size */ + hsize_t size; /* size read */ + hid_t fcpl = H5I_INVALID_HID; /* file creation property list ID for HDF5 file */ int i; + int ret_value = 0; /* get user block size */ if ((fcpl = H5Fget_create_plist(fid)) < 0) { - HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Fget_create_plist failed to retrieve file creation property list"); + H5TOOLS_GOTO_ERROR((-1), "H5Fget_create_plist failed to retrieve file creation property list"); } if (H5Pget_userblock(fcpl, &ub_size) < 0) { - HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pget_userblock failed to retrieve userblock size"); + H5TOOLS_GOTO_ERROR((-1), "H5Pget_userblock failed to retrieve userblock size"); } if (H5Pclose(fcpl) < 0) { - HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed to close property list"); + H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed to close property list"); } /* open file */ if ((fh = HDopen(filename, O_RDONLY)) < 0) { - HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "HDopen failed to open file <%s>", filename); + H5TOOLS_GOTO_ERROR((-1), "HDopen failed to open file <%s>", filename); } size = ub_size; /* read file */ while (size > 0) { - ssize_t nread; /* # of bytes read */ - char rbuf[USERBLOCK_XFER_SIZE]; /* buffer for reading */ + ssize_t nread; /* # of bytes read */ + char rbuf[USERBLOCK_XFER_SIZE]; /* buffer for reading */ /* read buffer */ if (size > USERBLOCK_XFER_SIZE) @@ -1462,12 +1720,11 @@ print_user_block(const char *filename, hid_t fid) for (i = 0; i < nread; i++) { HDprintf("%c ", rbuf[i]); - } HDprintf("\n"); if (nread < 0) { - HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "nread < 0"); + H5TOOLS_GOTO_ERROR((-1), "nread < 0"); } /* update size of userblock left to transfer */ @@ -1479,6 +1736,5 @@ done: HDclose(fh); return; -} +} /* end print_user_block() */ #endif - diff --git a/tools/src/h5repack/h5repack_filters.c b/tools/src/h5repack/h5repack_filters.c index 7e32def..76bac5e 100644 --- a/tools/src/h5repack/h5repack_filters.c +++ b/tools/src/h5repack/h5repack_filters.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -17,12 +17,12 @@ /* number of members in an array */ #ifndef NELMTS -# define NELMTS(X) (sizeof(X)/sizeof(X[0])) +#define NELMTS(X) (sizeof(X) / sizeof(X[0])) #endif /* minimum of two values */ #undef MIN -#define MIN(a,b) (((a)<(b)) ? (a) : (b)) +#define MIN(a, b) (((a) < (b)) ? (a) : (b)) /*------------------------------------------------------------------------- * Function: aux_copy_obj @@ -32,39 +32,41 @@ * Return: 0 success, -1 failure *------------------------------------------------------------------------- */ -static int aux_copy_obj(hid_t dcpl_id, /* dataset creation property list */ - const char* name, /* object name from traverse list */ - pack_info_t *objout /*OUT*/) /* info about object to filter */ +static int +aux_copy_obj(hid_t dcpl_id, /* dataset creation property list */ + const char * name, /* object name from traverse list */ + pack_info_t *objout /*OUT*/) /* info about object to filter */ { - int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ int nfilters; /* number of filters in DCPL */ char f_objname[256]; /* filter objname */ H5D_layout_t layout; - int rank; /* rank of dataset */ - hsize_t chsize[64]; /* chunk size in elements */ - int i; - unsigned u; + int rank; /* rank of dataset */ + hsize_t chsize[64]; /* chunk size in elements */ + int i; + unsigned u; + int ret_value = 0; /* get information about input filters */ if ((nfilters = H5Pget_nfilters(dcpl_id)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_nfilters failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Pget_nfilters failed"); /* copy filter_info_t structure */ for (i = 0; i < nfilters; i++) { - if ((objout->filter[i].filtn = H5Pget_filter2(dcpl_id, (unsigned) i, &objout->filter[i].filt_flag, &objout->filter[i].cd_nelmts, - objout->filter[i].cd_values, sizeof(f_objname), f_objname, NULL)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_filter2 failed"); + if ((objout->filter[i].filtn = H5Pget_filter2( + dcpl_id, (unsigned)i, &objout->filter[i].filt_flag, &objout->filter[i].cd_nelmts, + objout->filter[i].cd_values, sizeof(f_objname), f_objname, NULL)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pget_filter2 failed"); } objout->nfilters = nfilters; HDstrcpy(objout->path, name); if ((layout = H5Pget_layout(dcpl_id)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_layout failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Pget_layout failed"); objout->layout = layout; if (layout == H5D_CHUNKED) { - if ((rank = H5Pget_chunk(dcpl_id, NELMTS(chsize), chsize/*out*/)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_chunk failed"); + if ((rank = H5Pget_chunk(dcpl_id, NELMTS(chsize), chsize /*out*/)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pget_chunk failed"); objout->chunk.rank = rank; for (u = 0; u < (unsigned)rank; u++) objout->chunk.chunk_lengths[u] = chsize[u]; @@ -81,30 +83,33 @@ done: * in the repack options list *------------------------------------------------------------------------- */ -static int aux_find_obj(const char* name, /* object name from traverse list */ - pack_opt_t *options, /* repack options */ - pack_info_t *obj /*OUT*/) /* info about object to filter */ +static int +aux_find_obj(const char * name, /* object name from traverse list */ + pack_opt_t * options, /* repack options */ + pack_info_t *obj /*OUT*/) /* info about object to filter */ { - char *pdest = NULL; - const char *pname = NULL; + char * pdest = NULL; + const char * pname = NULL; unsigned int i; for (i = 0; i < options->op_tbl->nelems; i++) { if (HDstrcmp(options->op_tbl->objs[i].path, name) == 0) { *obj = options->op_tbl->objs[i]; - return (int) i; + return (int)i; } pdest = options->op_tbl->objs[i].path; - if (pdest[0] == '/') pdest++; + if (pdest[0] == '/') + pdest++; pname = name; - if (pname[0] == '/') pname++; + if (pname[0] == '/') + pname++; if (HDstrcmp(pdest, pname) == 0) { *obj = options->op_tbl->objs[i]; - return (int) i; + return (int)i; } - }/*i*/ + } /*i*/ return -1; } @@ -118,9 +123,10 @@ static int aux_find_obj(const char* name, /* object name from traverse list */ * Return: 0 not found, 1 found *------------------------------------------------------------------------- */ -static int aux_assign_obj(const char* name, /* object name from traverse list */ - pack_opt_t *options, /* repack options */ - pack_info_t *obj /*OUT*/) /* info about object to filter */ +static int +aux_assign_obj(const char * name, /* object name from traverse list */ + pack_opt_t * options, /* repack options */ + pack_info_t *obj /*OUT*/) /* info about object to filter */ { int idx, i; pack_info_t tmp; @@ -136,44 +142,44 @@ static int aux_assign_obj(const char* name, /* object name from traverse list */ /* assign the global layout info to the OBJ info */ tmp.layout = options->layout_g; switch (options->layout_g) { - case H5D_CHUNKED: - tmp.chunk.rank = options->chunk_g.rank; - for (i = 0; i < tmp.chunk.rank; i++) - tmp.chunk.chunk_lengths[i] = options->chunk_g.chunk_lengths[i]; - break; - case H5D_LAYOUT_ERROR: - case H5D_COMPACT: - case H5D_CONTIGUOUS: - case H5D_VIRTUAL: - case H5D_NLAYOUTS: - break; - default: - break; - }/*switch*/ + case H5D_CHUNKED: + tmp.chunk.rank = options->chunk_g.rank; + for (i = 0; i < tmp.chunk.rank; i++) + tmp.chunk.chunk_lengths[i] = options->chunk_g.chunk_lengths[i]; + break; + case H5D_LAYOUT_ERROR: + case H5D_COMPACT: + case H5D_CONTIGUOUS: + case H5D_VIRTUAL: + case H5D_NLAYOUTS: + break; + default: + break; + } /*switch*/ } else { tmp.layout = options->op_tbl->objs[idx].layout; switch (tmp.layout) { - case H5D_CHUNKED: - tmp.chunk.rank = options->op_tbl->objs[idx].chunk.rank; - for (i = 0; i < tmp.chunk.rank; i++) - tmp.chunk.chunk_lengths[i] = options->op_tbl->objs[idx].chunk.chunk_lengths[i]; - break; - case H5D_LAYOUT_ERROR: - case H5D_COMPACT: - case H5D_CONTIGUOUS: - case H5D_VIRTUAL: - case H5D_NLAYOUTS: - break; - default: - break; - }/*switch*/ + case H5D_CHUNKED: + tmp.chunk.rank = options->op_tbl->objs[idx].chunk.rank; + for (i = 0; i < tmp.chunk.rank; i++) + tmp.chunk.chunk_lengths[i] = options->op_tbl->objs[idx].chunk.chunk_lengths[i]; + break; + case H5D_LAYOUT_ERROR: + case H5D_COMPACT: + case H5D_CONTIGUOUS: + case H5D_VIRTUAL: + case H5D_NLAYOUTS: + break; + default: + break; + } /*switch*/ } /* applying to all objects */ if (options->all_filter) { /* assign the global filter */ - tmp.nfilters = 1; + tmp.nfilters = 1; tmp.filter[0] = options->filter_g[0]; } /* if all */ else { @@ -197,21 +203,20 @@ static int aux_assign_obj(const char* name, /* object name from traverse list */ /* assign the global layout info to the OBJ info */ tmp.layout = options->layout_g; switch (options->layout_g) { - case H5D_CHUNKED: - tmp.chunk.rank = options->chunk_g.rank; - for (i = 0; i < tmp.chunk.rank; i++) - tmp.chunk.chunk_lengths[i] = - options->chunk_g.chunk_lengths[i]; - break; - case H5D_LAYOUT_ERROR: - case H5D_COMPACT: - case H5D_CONTIGUOUS: - case H5D_VIRTUAL: - case H5D_NLAYOUTS: - break; - default: - break; - }/*switch*/ + case H5D_CHUNKED: + tmp.chunk.rank = options->chunk_g.rank; + for (i = 0; i < tmp.chunk.rank; i++) + tmp.chunk.chunk_lengths[i] = options->chunk_g.chunk_lengths[i]; + break; + case H5D_LAYOUT_ERROR: + case H5D_COMPACT: + case H5D_CONTIGUOUS: + case H5D_VIRTUAL: + case H5D_NLAYOUTS: + break; + default: + break; + } /*switch*/ } } @@ -226,33 +231,34 @@ static int aux_assign_obj(const char* name, /* object name from traverse list */ * do extra checking in the case of SZIP; delete all filters in the case * of H5Z_FILTER_NONE present in the PACK_INFO_T filter array * - * Return: 0 success, -1 an error occured + * Return: 0 success, -1 an error occurred *------------------------------------------------------------------------- */ -int apply_filters(const char* name, /* object name from traverse list */ - int rank, /* rank of dataset */ - hsize_t *dims, /* dimensions of dataset */ - size_t msize, /* size of type */ - hid_t dcpl_id, /* dataset creation property list */ - pack_opt_t *options, /* repack options */ - int *has_filter) /* (OUT) object NAME has a filter */ +int +apply_filters(const char * name, /* object name from traverse list */ + int rank, /* rank of dataset */ + const hsize_t *dims, /* dimensions of dataset */ + size_t msize, /* size of type */ + hid_t dcpl_id, /* dataset creation property list */ + pack_opt_t * options, /* repack options */ + int * has_filter) /* (OUT) object NAME has a filter */ { - int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ - int nfilters; /* number of filters in DCPL */ - hsize_t chsize[64]; /* chunk size in elements */ + int nfilters; /* number of filters in DCPL */ + hsize_t chsize[64]; /* chunk size in elements */ H5D_layout_t layout; - int i; - pack_info_t obj; - pack_info_t filtobj; + int i; + pack_info_t obj; + pack_info_t filtobj; + int ret_value = 0; *has_filter = 0; if (rank == 0) /* scalar dataset, do not apply */ - HGOTO_DONE(0); + H5TOOLS_GOTO_DONE(0); /*------------------------------------------------------------------------- - * initialize the assigment object + * initialize the assignment object *------------------------------------------------------------------------- */ init_packobject(&obj); @@ -263,12 +269,11 @@ int apply_filters(const char* name, /* object name from traverse list */ *------------------------------------------------------------------------- */ if (aux_assign_obj(name, options, &obj) == 0) - HGOTO_DONE(0); + H5TOOLS_GOTO_DONE(0); /* get information about input filters */ if ((nfilters = H5Pget_nfilters(dcpl_id)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_nfilters failed"); - + H5TOOLS_GOTO_ERROR((-1), "H5Pget_nfilters failed"); /*------------------------------------------------------------------------- * check if we have filters in the pipeline @@ -279,12 +284,12 @@ int apply_filters(const char* name, /* object name from traverse list */ if (nfilters && obj.nfilters) { *has_filter = 1; if (H5Premove_filter(dcpl_id, H5Z_FILTER_ALL) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Premove_filter failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Premove_filter failed"); } - else if(nfilters) { + else if (nfilters) { *has_filter = 1; if (aux_copy_obj(dcpl_id, name, &filtobj) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "aux_copy_obj failed"); + H5TOOLS_GOTO_ERROR((-1), "aux_copy_obj failed"); } /*------------------------------------------------------------------------- @@ -294,12 +299,12 @@ int apply_filters(const char* name, /* object name from traverse list */ */ if (obj.layout == -1) { if ((layout = H5Pget_layout(dcpl_id)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_layout failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Pget_layout failed"); if (layout == H5D_CHUNKED) { - if ((rank = H5Pget_chunk(dcpl_id, NELMTS(chsize), chsize/*out*/)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_chunk failed"); - obj.layout = H5D_CHUNKED; + if ((rank = H5Pget_chunk(dcpl_id, NELMTS(chsize), chsize /*out*/)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pget_chunk failed"); + obj.layout = H5D_CHUNKED; obj.chunk.rank = rank; for (i = 0; i < rank; i++) obj.chunk.chunk_lengths[i] = chsize[i]; @@ -327,7 +332,7 @@ int apply_filters(const char* name, /* object name from traverse list */ if (obj.layout == -1) { /* stripmine info */ hsize_t sm_size[H5S_MAX_RANK]; /*stripmine size */ - hsize_t sm_nbytes; /*bytes per stripmine */ + hsize_t sm_nbytes; /*bytes per stripmine */ obj.chunk.rank = rank; @@ -339,8 +344,8 @@ int apply_filters(const char* name, /* object name from traverse list */ sm_nbytes = msize; for (i = rank; i > 0; --i) { hsize_t size = 0; - if(sm_nbytes == 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "number of bytes per stripmine must be > 0"); + if (sm_nbytes == 0) + H5TOOLS_GOTO_ERROR((-1), "number of bytes per stripmine must be > 0"); size = H5TOOLS_BUFSIZE / sm_nbytes; if (size == 0) /* datum size > H5TOOLS_BUFSIZE */ size = 1; @@ -355,126 +360,117 @@ int apply_filters(const char* name, /* object name from traverse list */ for (i = 0; i < obj.nfilters; i++) { if (obj.filter[i].filtn < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid filter"); + H5TOOLS_GOTO_ERROR((-1), "invalid filter"); switch (obj.filter[i].filtn) { - /*------------------------------------------------------------------------- - * H5Z_FILTER_NONE 0 , uncompress if compressed - *------------------------------------------------------------------------- - */ - case H5Z_FILTER_NONE: - break; - - /*------------------------------------------------------------------------- - * H5Z_FILTER_DEFLATE 1 , deflation like gzip - *------------------------------------------------------------------------- - */ - case H5Z_FILTER_DEFLATE: - { + /*------------------------------------------------------------------------- + * H5Z_FILTER_NONE 0 , uncompress if compressed + *------------------------------------------------------------------------- + */ + case H5Z_FILTER_NONE: + break; + + /*------------------------------------------------------------------------- + * H5Z_FILTER_DEFLATE 1 , deflation like gzip + *------------------------------------------------------------------------- + */ + case H5Z_FILTER_DEFLATE: { unsigned aggression; /* the deflate level */ aggression = obj.filter[i].cd_values[0]; /* set up for deflated data */ if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_chunk failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Pset_chunk failed"); if (H5Pset_deflate(dcpl_id, aggression) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_deflate failed"); - } - break; - - /*------------------------------------------------------------------------- - * H5Z_FILTER_SZIP 4 , szip compression - *------------------------------------------------------------------------- - */ - case H5Z_FILTER_SZIP: - { + H5TOOLS_GOTO_ERROR((-1), "H5Pset_deflate failed"); + } break; + + /*------------------------------------------------------------------------- + * H5Z_FILTER_SZIP 4 , szip compression + *------------------------------------------------------------------------- + */ + case H5Z_FILTER_SZIP: { unsigned options_mask; unsigned pixels_per_block; - options_mask = obj.filter[i].cd_values[0]; + options_mask = obj.filter[i].cd_values[0]; pixels_per_block = obj.filter[i].cd_values[1]; /* set up for szip data */ if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_chunk failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Pset_chunk failed"); if (H5Pset_szip(dcpl_id, options_mask, pixels_per_block) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_szip failed"); - } - break; - - /*------------------------------------------------------------------------- - * H5Z_FILTER_SHUFFLE 2 , shuffle the data - *------------------------------------------------------------------------- - */ - case H5Z_FILTER_SHUFFLE: - if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_chunk failed"); - if (H5Pset_shuffle(dcpl_id) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_shuffle failed"); - break; - - /*------------------------------------------------------------------------- - * H5Z_FILTER_FLETCHER32 3 , fletcher32 checksum of EDC - *------------------------------------------------------------------------- - */ - case H5Z_FILTER_FLETCHER32: - if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_chunk failed"); - if (H5Pset_fletcher32(dcpl_id) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_fletcher32 failed"); - break; - /*----------- ------------------------------------------------------------- - * H5Z_FILTER_NBIT , NBIT compression - *------------------------------------------------------------------------- - */ - case H5Z_FILTER_NBIT: - if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_chunk failed"); - if (H5Pset_nbit(dcpl_id) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_nbit failed"); - break; - /*----------- ------------------------------------------------------------- - * H5Z_FILTER_SCALEOFFSET , scale+offset compression - *------------------------------------------------------------------------- - */ - case H5Z_FILTER_SCALEOFFSET: - { + H5TOOLS_GOTO_ERROR((-1), "H5Pset_szip failed"); + } break; + + /*------------------------------------------------------------------------- + * H5Z_FILTER_SHUFFLE 2 , shuffle the data + *------------------------------------------------------------------------- + */ + case H5Z_FILTER_SHUFFLE: + if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pset_chunk failed"); + if (H5Pset_shuffle(dcpl_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pset_shuffle failed"); + break; + + /*------------------------------------------------------------------------- + * H5Z_FILTER_FLETCHER32 3 , fletcher32 checksum of EDC + *------------------------------------------------------------------------- + */ + case H5Z_FILTER_FLETCHER32: + if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pset_chunk failed"); + if (H5Pset_fletcher32(dcpl_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pset_fletcher32 failed"); + break; + /*----------- ------------------------------------------------------------- + * H5Z_FILTER_NBIT , NBIT compression + *------------------------------------------------------------------------- + */ + case H5Z_FILTER_NBIT: + if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pset_chunk failed"); + if (H5Pset_nbit(dcpl_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pset_nbit failed"); + break; + /*----------- ------------------------------------------------------------- + * H5Z_FILTER_SCALEOFFSET , scale+offset compression + *------------------------------------------------------------------------- + */ + case H5Z_FILTER_SCALEOFFSET: { H5Z_SO_scale_type_t scale_type; - int scale_factor; + int scale_factor; - scale_type = (H5Z_SO_scale_type_t) obj.filter[i].cd_values[0]; - scale_factor = (int) obj.filter[i].cd_values[1]; + scale_type = (H5Z_SO_scale_type_t)obj.filter[i].cd_values[0]; + scale_factor = (int)obj.filter[i].cd_values[1]; if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_chunk failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Pset_chunk failed"); if (H5Pset_scaleoffset(dcpl_id, scale_type, scale_factor) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_scaleoffset failed"); - } - break; - default: - { + H5TOOLS_GOTO_ERROR((-1), "H5Pset_scaleoffset failed"); + } break; + default: { if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_chunk failed"); - if (H5Pset_filter(dcpl_id, obj.filter[i].filtn, - obj.filter[i].filt_flag, obj.filter[i].cd_nelmts, - obj.filter[i].cd_values) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_filter failed"); - } - break; + H5TOOLS_GOTO_ERROR((-1), "H5Pset_chunk failed"); + if (H5Pset_filter(dcpl_id, obj.filter[i].filtn, obj.filter[i].filt_flag, + obj.filter[i].cd_nelmts, obj.filter[i].cd_values) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pset_filter failed"); + } break; } /* switch */ - }/*i*/ + } /*i*/ } /*obj.nfilters*/ if (filtobj.nfilters) { for (i = 0; i < filtobj.nfilters; i++) { if (filtobj.filter[i].filtn < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid filter"); + H5TOOLS_GOTO_ERROR((-1), "invalid filter"); if (H5Zfilter_avail(filtobj.filter[i].filtn) <= 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "%d filter unavailable", filtobj.filter[i].filtn); + H5TOOLS_GOTO_ERROR((-1), "%d filter unavailable", filtobj.filter[i].filtn); } /* for */ - } /* nfilters */ + } /* nfilters */ /*------------------------------------------------------------------------- * layout @@ -484,24 +480,23 @@ int apply_filters(const char* name, /* object name from traverse list */ if (obj.layout >= 0) { /* a layout was defined */ if (H5Pset_layout(dcpl_id, obj.layout) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_layout failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Pset_layout failed"); if (H5D_CHUNKED == obj.layout) { if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_chunk failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Pset_chunk failed"); } else if (H5D_COMPACT == obj.layout) { if (H5Pset_alloc_time(dcpl_id, H5D_ALLOC_TIME_EARLY) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_alloc_time failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Pset_alloc_time failed"); } /* remove filters for the H5D_CONTIGUOUS case */ else if (H5D_CONTIGUOUS == obj.layout) { if (H5Premove_filter(dcpl_id, H5Z_FILTER_ALL) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Premove_filter failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Premove_filter failed"); } } done: return ret_value; } - diff --git a/tools/src/h5repack/h5repack_main.c b/tools/src/h5repack/h5repack_main.c index b961765..a805b3d 100644 --- a/tools/src/h5repack/h5repack_main.c +++ b/tools/src/h5repack/h5repack_main.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -18,51 +18,63 @@ /* Name of tool */ #define PROGRAMNAME "h5repack" -static int parse_command_line(int argc, const char **argv, pack_opt_t* options); +static int parse_command_line(int argc, const char *const *argv, pack_opt_t *options); static void leave(int ret) H5_ATTR_NORETURN; - /* module-scoped variables */ -static int has_i_o = 0; -const char *infile = NULL; +static int has_i = 0; +static int has_o = 0; +const char *infile = NULL; const char *outfile = NULL; /* * Command-line options: The user can specify short or long-named * parameters. */ -static const char *s_opts = "hVvf:l:m:e:nLj:k:c:d:s:u:b:M:t:a:i:o:S:P:T:G:q:z:E"; -static struct long_options l_opts[] = { - { "help", no_arg, 'h' }, - { "version", no_arg, 'V' }, - { "verbose", no_arg, 'v' }, - { "filter", require_arg, 'f' }, - { "layout", require_arg, 'l' }, - { "minimum", require_arg, 'm' }, - { "file", require_arg, 'e' }, - { "native", no_arg, 'n' }, - { "latest", no_arg, 'L' }, - { "low", require_arg, 'j' }, - { "high", require_arg, 'k' }, - { "compact", require_arg, 'c' }, - { "indexed", require_arg, 'd' }, - { "ssize", require_arg, 's' }, - { "ublock", require_arg, 'u' }, - { "block", require_arg, 'b' }, - { "metadata_block_size", require_arg, 'M' }, - { "threshold", require_arg, 't' }, - { "alignment", require_arg, 'a' }, - { "infile", require_arg, 'i' }, /* -i for backward compability */ - { "outfile", require_arg, 'o' }, /* -o for backward compability */ - { "fs_strategy", require_arg, 'S' }, - { "fs_persist", require_arg, 'P' }, - { "fs_threshold", require_arg, 'T' }, - { "fs_pagesize", require_arg, 'G' }, - { "sort_by", require_arg, 'q' }, - { "sort_order", require_arg, 'z' }, - { "enable-error-stack", no_arg, 'E' }, - { NULL, 0, '\0' } -}; +static const char *s_opts = "a:b:c:d:e:f:hi:j:k:l:m:no:q:s:t:u:v*z:E*G:LM:P:S:T:VXWY:Z:1:2:3:4:5:6:7:8:9:0:"; +static struct h5_long_options l_opts[] = {{"alignment", require_arg, 'a'}, + {"block", require_arg, 'b'}, + {"compact", require_arg, 'c'}, + {"indexed", require_arg, 'd'}, + {"file", require_arg, 'e'}, + {"filter", require_arg, 'f'}, + {"help", no_arg, 'h'}, + {"infile", require_arg, 'i'}, /* for backward compatibility */ + {"low", require_arg, 'j'}, + {"high", require_arg, 'k'}, + {"layout", require_arg, 'l'}, + {"minimum", require_arg, 'm'}, + {"native", no_arg, 'n'}, + {"outfile", require_arg, 'o'}, /* for backward compatibility */ + {"sort_by", require_arg, 'q'}, + {"ssize", require_arg, 's'}, + {"threshold", require_arg, 't'}, + {"ublock", require_arg, 'u'}, + {"verbose", optional_arg, 'v'}, + {"sort_order", require_arg, 'z'}, + {"enable-error-stack", optional_arg, 'E'}, + {"fs_pagesize", require_arg, 'G'}, + {"latest", no_arg, 'L'}, + {"metadata_block_size", require_arg, 'M'}, + {"fs_persist", require_arg, 'P'}, + {"fs_strategy", require_arg, 'S'}, + {"fs_threshold", require_arg, 'T'}, + {"version", no_arg, 'V'}, + {"merge", no_arg, 'X'}, + {"prune", no_arg, 'W'}, + {"src-vol-value", require_arg, '1'}, + {"src-vol-name", require_arg, '2'}, + {"src-vol-info", require_arg, '3'}, + {"dst-vol-value", require_arg, '4'}, + {"dst-vol-name", require_arg, '5'}, + {"dst-vol-info", require_arg, '6'}, + {"src-vfd-value", require_arg, '7'}, + {"src-vfd-name", require_arg, '8'}, + {"src-vfd-info", require_arg, '9'}, + {"dst-vfd-value", require_arg, '0'}, + {"dst-vfd-name", require_arg, 'Y'}, + {"dst-vfd-info", require_arg, 'Z'}, + {NULL, 0, '\0'}}; /*------------------------------------------------------------------------- * Function: usage @@ -73,91 +85,184 @@ static struct long_options l_opts[] = { * *------------------------------------------------------------------------- */ -static void usage(const char *prog) { +static void +usage(const char *prog) +{ FLUSHSTREAM(rawoutstream); PRINTSTREAM(rawoutstream, "usage: %s [OPTIONS] file1 file2\n", prog); PRINTVALSTREAM(rawoutstream, " file1 Input HDF5 File\n"); PRINTVALSTREAM(rawoutstream, " file2 Output HDF5 File\n"); + PRINTVALSTREAM(rawoutstream, " ERROR\n"); + PRINTVALSTREAM(rawoutstream, + " --enable-error-stack Prints messages from the HDF5 error stack as they occur.\n"); + PRINTVALSTREAM(rawoutstream, + " Optional value 2 also prints file open errors.\n"); PRINTVALSTREAM(rawoutstream, " OPTIONS\n"); PRINTVALSTREAM(rawoutstream, " -h, --help Print a usage message and exit\n"); - PRINTVALSTREAM(rawoutstream, " -v, --verbose Verbose mode, print object information\n"); + PRINTVALSTREAM(rawoutstream, " -v N, --verbose=N Verbose mode, print object information.\n"); + PRINTVALSTREAM(rawoutstream, " N - is an integer greater than 1, 2 displays read/write timing\n"); PRINTVALSTREAM(rawoutstream, " -V, --version Print version number and exit\n"); PRINTVALSTREAM(rawoutstream, " -n, --native Use a native HDF5 type when repacking\n"); - PRINTVALSTREAM(rawoutstream, " --enable-error-stack Prints messages from the HDF5 error stack as they occur\n"); + PRINTVALSTREAM(rawoutstream, + " --src-vol-value Value (ID) of the VOL connector to use for opening the\n"); + PRINTVALSTREAM(rawoutstream, " input HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, + " --src-vol-name Name of the VOL connector to use for opening the input\n"); + PRINTVALSTREAM(rawoutstream, " HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, + " --src-vol-info VOL-specific info to pass to the VOL connector used for\n"); + PRINTVALSTREAM(rawoutstream, " opening the input HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, + " --dst-vol-value Value (ID) of the VOL connector to use for opening the\n"); + PRINTVALSTREAM(rawoutstream, " output HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, + " --dst-vol-name Name of the VOL connector to use for opening the output\n"); + PRINTVALSTREAM(rawoutstream, " HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, + " --dst-vol-info VOL-specific info to pass to the VOL connector used for\n"); + PRINTVALSTREAM(rawoutstream, " opening the output HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, + " --src-vfd-value Value (ID) of the VFL driver to use for opening the\n"); + PRINTVALSTREAM(rawoutstream, " input HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, + " --src-vfd-name Name of the VFL driver to use for opening the input\n"); + PRINTVALSTREAM(rawoutstream, " HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, + " --src-vfd-info VFD-specific info to pass to the VFL driver used for\n"); + PRINTVALSTREAM(rawoutstream, " opening the input HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, + " --dst-vfd-value Value (ID) of the VFL driver to use for opening the\n"); + PRINTVALSTREAM(rawoutstream, " output HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, + " --dst-vfd-name Name of the VFL driver to use for opening the output\n"); + PRINTVALSTREAM(rawoutstream, " HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, + " --dst-vfd-info VFD-specific info to pass to the VFL driver used for\n"); + PRINTVALSTREAM(rawoutstream, " opening the output HDF5 file specified\n"); PRINTVALSTREAM(rawoutstream, " -L, --latest Use latest version of file format\n"); - PRINTVALSTREAM(rawoutstream, " This option will take precedence over the -j and -k options\n"); - PRINTVALSTREAM(rawoutstream, " --low=BOUND The low bound for library release versions to use when creating\n"); - PRINTVALSTREAM(rawoutstream, " objects in the file (default is H5F_LIBVER_EARLIEST)\n"); - PRINTVALSTREAM(rawoutstream, " --high=BOUND The high bound for library release versions to use when creating\n"); - PRINTVALSTREAM(rawoutstream, " objects in the file (default is H5F_LIBVER_LATEST)\n"); + PRINTVALSTREAM(rawoutstream, + " This option will take precedence over the options\n"); + PRINTVALSTREAM(rawoutstream, " --low and --high\n"); + PRINTVALSTREAM(rawoutstream, + " --low=BOUND The low bound for library release versions to use\n"); + PRINTVALSTREAM(rawoutstream, " when creating objects in the file\n"); + PRINTVALSTREAM(rawoutstream, " (default is H5F_LIBVER_EARLIEST)\n"); + PRINTVALSTREAM(rawoutstream, + " --high=BOUND The high bound for library release versions to use\n"); + PRINTVALSTREAM(rawoutstream, " when creating objects in the file\n"); + PRINTVALSTREAM(rawoutstream, " (default is H5F_LIBVER_LATEST)\n"); + PRINTVALSTREAM(rawoutstream, + " --merge Follow external soft link recursively and merge data\n"); + PRINTVALSTREAM(rawoutstream, + " --prune Do not follow external soft links and remove link\n"); + PRINTVALSTREAM(rawoutstream, + " --merge --prune Follow external link, merge data and remove dangling link\n"); PRINTVALSTREAM(rawoutstream, " -c L1, --compact=L1 Maximum number of links in header messages\n"); - PRINTVALSTREAM(rawoutstream, " -d L2, --indexed=L2 Minimum number of links in the indexed format\n"); + PRINTVALSTREAM(rawoutstream, + " -d L2, --indexed=L2 Minimum number of links in the indexed format\n"); PRINTVALSTREAM(rawoutstream, " -s S[:F], --ssize=S[:F] Shared object header message minimum size\n"); - PRINTVALSTREAM(rawoutstream, " -m M, --minimum=M Do not apply the filter to datasets smaller than M\n"); + PRINTVALSTREAM(rawoutstream, + " -m M, --minimum=M Do not apply the filter to datasets smaller than M\n"); PRINTVALSTREAM(rawoutstream, " -e E, --file=E Name of file E with the -f and -l options\n"); - PRINTVALSTREAM(rawoutstream, " -u U, --ublock=U Name of file U with user block data to be added\n"); + PRINTVALSTREAM(rawoutstream, + " -u U, --ublock=U Name of file U with user block data to be added\n"); PRINTVALSTREAM(rawoutstream, " -b B, --block=B Size of user block to be added\n"); - PRINTVALSTREAM(rawoutstream, " -M A, --metadata_block_size=A Metadata block size for H5Pset_meta_block_size\n"); + PRINTVALSTREAM(rawoutstream, + " -M A, --metadata_block_size=A Metadata block size for H5Pset_meta_block_size\n"); PRINTVALSTREAM(rawoutstream, " -t T, --threshold=T Threshold value for H5Pset_alignment\n"); PRINTVALSTREAM(rawoutstream, " -a A, --alignment=A Alignment value for H5Pset_alignment\n"); PRINTVALSTREAM(rawoutstream, " -q Q, --sort_by=Q Sort groups and attributes by index Q\n"); PRINTVALSTREAM(rawoutstream, " -z Z, --sort_order=Z Sort groups and attributes by order Z\n"); PRINTVALSTREAM(rawoutstream, " -f FILT, --filter=FILT Filter type\n"); PRINTVALSTREAM(rawoutstream, " -l LAYT, --layout=LAYT Layout type\n"); - PRINTVALSTREAM(rawoutstream, " -S FS_STRATEGY, --fs_strategy=FS_STRATEGY File space management strategy for H5Pset_file_space_strategy\n"); - PRINTVALSTREAM(rawoutstream, " -P FS_PERSIST, --fs_persist=FS_PERSIST Persisting or not persisting free-space for H5Pset_file_space_strategy\n"); - PRINTVALSTREAM(rawoutstream, " -T FS_THRESHOLD, --fs_threshold=FS_THRESHOLD Free-space section threshold for H5Pset_file_space_strategy\n"); - PRINTVALSTREAM(rawoutstream, " -G FS_PAGESIZE, --fs_pagesize=FS_PAGESIZE File space page size for H5Pset_file_space_page_size\n"); + PRINTVALSTREAM(rawoutstream, + " -S FS_STRATEGY, --fs_strategy=FS_STRATEGY File space management strategy for\n"); + PRINTVALSTREAM(rawoutstream, " H5Pset_file_space_strategy\n"); + PRINTVALSTREAM(rawoutstream, + " -P FS_PERSIST, --fs_persist=FS_PERSIST Persisting or not persisting free-\n"); + PRINTVALSTREAM(rawoutstream, " space for H5Pset_file_space_strategy\n"); + PRINTVALSTREAM(rawoutstream, + " -T FS_THRESHOLD, --fs_threshold=FS_THRESHOLD Free-space section threshold\n"); + PRINTVALSTREAM(rawoutstream, " for H5Pset_file_space_strategy\n"); + PRINTVALSTREAM(rawoutstream, " -G FS_PAGESIZE, --fs_pagesize=FS_PAGESIZE File space page size for\n"); + PRINTVALSTREAM(rawoutstream, " H5Pset_file_space_page_size\n"); PRINTVALSTREAM(rawoutstream, "\n"); - PRINTVALSTREAM(rawoutstream, " M - is an integer greater than 1, size of dataset in bytes (default is 0)\n"); + PRINTVALSTREAM(rawoutstream, + " M - is an integer greater than 1, size of dataset in bytes (default is 0)\n"); PRINTVALSTREAM(rawoutstream, " E - is a filename.\n"); PRINTVALSTREAM(rawoutstream, " S - is an integer\n"); PRINTVALSTREAM(rawoutstream, " U - is a filename.\n"); PRINTVALSTREAM(rawoutstream, " T - is an integer\n"); PRINTVALSTREAM(rawoutstream, " A - is an integer greater than zero\n"); - PRINTVALSTREAM(rawoutstream, " Q - is the sort index type for the input file. It can be \"name\" or \"creation_order\" (default)\n"); - PRINTVALSTREAM(rawoutstream, " Z - is the sort order type for the input file. It can be \"descending\" or \"ascending\" (default)\n"); + PRINTVALSTREAM(rawoutstream, + " Q - is the sort index type for the input file. It can be \"name\" or\n"); + PRINTVALSTREAM(rawoutstream, " \"creation_order\" (default)\n"); + PRINTVALSTREAM(rawoutstream, + " Z - is the sort order type for the input file. It can be \"descending\" or\n"); + PRINTVALSTREAM(rawoutstream, " \"ascending\" (default)\n"); PRINTVALSTREAM(rawoutstream, " B - is the user block size, any value that is 512 or greater and is\n"); PRINTVALSTREAM(rawoutstream, " a power of 2 (1024 default)\n"); - PRINTVALSTREAM(rawoutstream, " F - is the shared object header message type, any of <dspace|dtype|fill|\n"); + PRINTVALSTREAM(rawoutstream, + " F - is the shared object header message type, any of <dspace|dtype|fill|\n"); PRINTVALSTREAM(rawoutstream, " pline|attr>. If F is not specified, S applies to all messages\n"); PRINTVALSTREAM(rawoutstream, "\n"); - PRINTVALSTREAM(rawoutstream, " BOUND is an integer indicating the library release versions to use when creating\n"); - PRINTVALSTREAM(rawoutstream, " objects in the file (see H5Pset_libver_bounds()):\n"); + PRINTVALSTREAM(rawoutstream, + " BOUND is an integer indicating the library release versions to use when\n"); + PRINTVALSTREAM(rawoutstream, " creating objects in the file (see H5Pset_libver_bounds()):\n"); PRINTVALSTREAM(rawoutstream, " 0: This is H5F_LIBVER_EARLIEST in H5F_libver_t struct\n"); PRINTVALSTREAM(rawoutstream, " 1: This is H5F_LIBVER_V18 in H5F_libver_t struct\n"); PRINTVALSTREAM(rawoutstream, " 2: This is H5F_LIBVER_V110 in H5F_libver_t struct\n"); PRINTVALSTREAM(rawoutstream, " 3: This is H5F_LIBVER_V112 in H5F_libver_t struct\n"); - PRINTVALSTREAM(rawoutstream, " (H5F_LIBVER_LATEST is aliased to H5F_LIBVER_V112 for this release\n"); + PRINTVALSTREAM(rawoutstream, " 4: This is H5F_LIBVER_V114 in H5F_libver_t struct\n"); + PRINTVALSTREAM(rawoutstream, + " (H5F_LIBVER_LATEST is aliased to H5F_LIBVER_V114 for this release\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " FS_STRATEGY is a string indicating the file space strategy used:\n"); PRINTVALSTREAM(rawoutstream, " FSM_AGGR:\n"); - PRINTVALSTREAM(rawoutstream, " The mechanisms used in managing file space are free-space managers, aggregators and virtual file driver.\n"); + PRINTVALSTREAM(rawoutstream, + " The mechanisms used in managing file space are free-space\n"); + PRINTVALSTREAM(rawoutstream, " managers, aggregators and virtual file driver.\n"); PRINTVALSTREAM(rawoutstream, " PAGE:\n"); - PRINTVALSTREAM(rawoutstream, " The mechanisms used in managing file space are free-space managers with embedded paged aggregation and virtual file driver.\n"); + PRINTVALSTREAM(rawoutstream, + " The mechanisms used in managing file space are free-space\n"); + PRINTVALSTREAM(rawoutstream, + " managers with embedded paged aggregation and virtual file driver.\n"); PRINTVALSTREAM(rawoutstream, " AGGR:\n"); - PRINTVALSTREAM(rawoutstream, " The mechanisms used in managing file space are aggregators and virtual file driver.\n"); + PRINTVALSTREAM(rawoutstream, + " The mechanisms used in managing file space are aggregators and\n"); + PRINTVALSTREAM(rawoutstream, " virtual file driver.\n"); PRINTVALSTREAM(rawoutstream, " NONE:\n"); - PRINTVALSTREAM(rawoutstream, " The mechanisms used in managing file space are virtual file driver.\n"); - PRINTVALSTREAM(rawoutstream, " The default strategy when not set is FSM_AGGR without persisting free-space.\n"); + PRINTVALSTREAM(rawoutstream, + " The mechanisms used in managing file space are virtual file\n"); + PRINTVALSTREAM(rawoutstream, " driver.\n"); + PRINTVALSTREAM(rawoutstream, + " The default strategy when not set is FSM_AGGR without persisting free-\n"); + PRINTVALSTREAM(rawoutstream, " space.\n"); PRINTVALSTREAM(rawoutstream, "\n"); - PRINTVALSTREAM(rawoutstream, " FS_PERSIST is 1 to persisting free-space or 0 to not persisting free-space.\n"); + PRINTVALSTREAM(rawoutstream, + " FS_PERSIST is 1 to persisting free-space or 0 to not persisting free-space.\n"); PRINTVALSTREAM(rawoutstream, " The default when not set is not persisting free-space.\n"); PRINTVALSTREAM(rawoutstream, " The value is ignored for AGGR and NONE strategies.\n"); PRINTVALSTREAM(rawoutstream, "\n"); - PRINTVALSTREAM(rawoutstream, " FS_THRESHOLD is the minimum size (in bytes) of free-space sections to be tracked by the library.\n"); + PRINTVALSTREAM(rawoutstream, + " FS_THRESHOLD is the minimum size (in bytes) of free-space sections to be\n"); + PRINTVALSTREAM(rawoutstream, " tracked by the library.\n"); PRINTVALSTREAM(rawoutstream, " The default when not set is 1.\n"); PRINTVALSTREAM(rawoutstream, " The value is ignored for AGGR and NONE strategies.\n"); PRINTVALSTREAM(rawoutstream, "\n"); - PRINTVALSTREAM(rawoutstream, " FS_PAGESIZE is the size (in bytes) >=512 that is used by the library when the file space strategy PAGE is used.\n"); + PRINTVALSTREAM(rawoutstream, + " FS_PAGESIZE is the size (in bytes) >=512 that is used by the library when\n"); + PRINTVALSTREAM(rawoutstream, " the file space strategy PAGE is used.\n"); PRINTVALSTREAM(rawoutstream, " The default when not set is 4096.\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " FILT - is a string with the format:\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " <list of objects>:<name of filter>=<filter parameters>\n"); PRINTVALSTREAM(rawoutstream, "\n"); - PRINTVALSTREAM(rawoutstream, " <list of objects> is a comma separated list of object names, meaning apply\n"); - PRINTVALSTREAM(rawoutstream, " compression only to those objects. If no names are specified, the filter\n"); + PRINTVALSTREAM(rawoutstream, + " <list of objects> is a comma separated list of object names, meaning apply\n"); + PRINTVALSTREAM(rawoutstream, + " compression only to those objects. If no names are specified, the filter\n"); PRINTVALSTREAM(rawoutstream, " is applied to all objects\n"); PRINTVALSTREAM(rawoutstream, " <name of filter> can be:\n"); PRINTVALSTREAM(rawoutstream, " GZIP, to apply the HDF5 GZIP filter (GZIP compression)\n"); @@ -170,24 +275,31 @@ static void usage(const char *prog) { PRINTVALSTREAM(rawoutstream, " NONE, to remove all filters\n"); PRINTVALSTREAM(rawoutstream, " <filter parameters> is optional filter parameter information\n"); PRINTVALSTREAM(rawoutstream, " GZIP=<deflation level> from 1-9\n"); - PRINTVALSTREAM(rawoutstream, " SZIP=<pixels per block,coding> pixels per block is a even number in\n"); + PRINTVALSTREAM(rawoutstream, + " SZIP=<pixels per block,coding> pixels per block is a even number in\n"); PRINTVALSTREAM(rawoutstream, " 2-32 and coding method is either EC or NN\n"); PRINTVALSTREAM(rawoutstream, " SHUF (no parameter)\n"); PRINTVALSTREAM(rawoutstream, " FLET (no parameter)\n"); PRINTVALSTREAM(rawoutstream, " NBIT (no parameter)\n"); - PRINTVALSTREAM(rawoutstream, " SOFF=<scale_factor,scale_type> scale_factor is an integer and scale_type\n"); + PRINTVALSTREAM(rawoutstream, + " SOFF=<scale_factor,scale_type> scale_factor is an integer and scale_type\n"); PRINTVALSTREAM(rawoutstream, " is either IN or DS\n"); - PRINTVALSTREAM(rawoutstream, " UD=<filter_number,filter_flag,cd_value_count,value_1[,value_2,...,value_N]>\n"); - PRINTVALSTREAM(rawoutstream, " required values for filter_number,filter_flag,cd_value_count,value_1\n"); - PRINTVALSTREAM(rawoutstream, " optional values for value_2 to value_N\n"); + PRINTVALSTREAM(rawoutstream, + " UD=<filter_number,filter_flag,cd_value_count,value1[,value2,...,valueN]>\n"); + PRINTVALSTREAM(rawoutstream, + " Required values: filter_number, filter_flag, cd_value_count, value1\n"); + PRINTVALSTREAM(rawoutstream, " Optional values: value2 to valueN\n"); + PRINTVALSTREAM(rawoutstream, " filter_flag: 1 is OPTIONAL or 0 is MANDATORY\n"); PRINTVALSTREAM(rawoutstream, " NONE (no parameter)\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " LAYT - is a string with the format:\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " <list of objects>:<layout type>=<layout parameters>\n"); PRINTVALSTREAM(rawoutstream, "\n"); - PRINTVALSTREAM(rawoutstream, " <list of objects> is a comma separated list of object names, meaning that\n"); - PRINTVALSTREAM(rawoutstream, " layout information is supplied for those objects. If no names are\n"); + PRINTVALSTREAM(rawoutstream, + " <list of objects> is a comma separated list of object names, meaning that\n"); + PRINTVALSTREAM(rawoutstream, + " layout information is supplied for those objects. If no names are\n"); PRINTVALSTREAM(rawoutstream, " specified, the layout type is applied to all objects\n"); PRINTVALSTREAM(rawoutstream, " <layout type> can be:\n"); PRINTVALSTREAM(rawoutstream, " CHUNK, to apply chunking layout\n"); @@ -206,22 +318,20 @@ static void usage(const char *prog) { PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, "2) h5repack -v -f dset1:SZIP=8,NN file1 file2\n"); PRINTVALSTREAM(rawoutstream, "\n"); - PRINTVALSTREAM(rawoutstream, " SZIP compression with 8 pixels per block and NN coding method to object dset1\n"); + PRINTVALSTREAM(rawoutstream, + " SZIP compression with 8 pixels per block and NN coding method to object dset1\n"); PRINTVALSTREAM(rawoutstream, "\n"); - PRINTVALSTREAM(rawoutstream, "3) h5repack -v -l dset1,dset2:CHUNK=20x10 -f dset3,dset4,dset5:NONE file1 file2\n"); + PRINTVALSTREAM(rawoutstream, + "3) h5repack -v -l dset1,dset2:CHUNK=20x10 -f dset3,dset4,dset5:NONE file1 file2\n"); PRINTVALSTREAM(rawoutstream, "\n"); - PRINTVALSTREAM(rawoutstream, " Chunked layout, with a layout size of 20x10, to objects dset1 and dset2\n"); + PRINTVALSTREAM(rawoutstream, + " Chunked layout, with a layout size of 20x10, to objects dset1 and dset2\n"); PRINTVALSTREAM(rawoutstream, " and remove filters to objects dset3, dset4, dset5\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, "4) h5repack -L -c 10 -s 20:dtype file1 file2\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " Using latest file format with maximum compact group size of 10 and\n"); - PRINTVALSTREAM(rawoutstream, " and minimum shared datatype size of 20\n"); - PRINTVALSTREAM(rawoutstream, "\n"); - PRINTVALSTREAM(rawoutstream, "5) h5repack --low=0 --high=1 file1 file2\n"); - PRINTVALSTREAM(rawoutstream, "\n"); - PRINTVALSTREAM(rawoutstream, " Set low=H5F_LIBVER_EARLIEST and high=H5F_LIBVER_V18 via H5Pset_libver_bounds() when\n"); - PRINTVALSTREAM(rawoutstream, " creating the repacked file: file2\n"); + PRINTVALSTREAM(rawoutstream, " minimum shared datatype size of 20\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, "5) h5repack -f SHUF -f GZIP=1 file1 file2\n"); PRINTVALSTREAM(rawoutstream, "\n"); @@ -231,6 +341,11 @@ static void usage(const char *prog) { PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " Add bzip2 filter to all datasets\n"); PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, "7) h5repack --low=0 --high=1 file1 file2\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, " Set low=H5F_LIBVER_EARLIEST and high=H5F_LIBVER_V18 via\n"); + PRINTVALSTREAM(rawoutstream, " H5Pset_libver_bounds() when creating the repacked file, file2\n"); + PRINTVALSTREAM(rawoutstream, "\n"); } /*------------------------------------------------------------------------- @@ -241,7 +356,8 @@ static void usage(const char *prog) { * Return: Does not return *------------------------------------------------------------------------- */ -static void leave(int ret) +static void +leave(int ret) { h5tools_close(); HDexit(ret); @@ -255,17 +371,17 @@ static void leave(int ret) * Return: void, exit on error *------------------------------------------------------------------------- */ -static -int read_info(const char *filename, pack_opt_t *options) +static int +read_info(const char *filename, pack_opt_t *options) { - char stype[10] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; - char comp_info[1024]; + char stype[10] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; + char comp_info[1024]; FILE *fp = NULL; - char c; - int i, rc = 1; - int ret_value = EXIT_SUCCESS; + char c; + int i; + int ret_value = EXIT_SUCCESS; - if ((fp = HDfopen(filename, "r")) == (FILE *) NULL) { + if (NULL == (fp = HDfopen(filename, "r"))) { error_msg("cannot open options file %s\n", filename); h5tools_setstatus(EXIT_FAILURE); ret_value = EXIT_FAILURE; @@ -274,108 +390,64 @@ int read_info(const char *filename, pack_opt_t *options) /* cycle until end of file reached */ while (1) { - rc = fscanf(fp, "%s", stype); - if (rc == -1) + if (EOF == HDfscanf(fp, "%9s", stype)) break; - /*------------------------------------------------------------------------- - * filter - *------------------------------------------------------------------------- - */ - if (HDstrcmp(stype,"-f") == 0) { - /* find begining of info */ - i = 0; - c = '0'; - while (c != ' ') { - if(fscanf(fp, "%c", &c) < 0 && HDferror(fp)) { - error_msg("fscanf error\n"); - h5tools_setstatus(EXIT_FAILURE); - ret_value = EXIT_FAILURE; - goto done; - } /* end if */ - if (HDfeof(fp)) - break; - } - c = '0'; - /* go until end */ - while (c != ' ') { - if(fscanf(fp, "%c", &c) < 0 && HDferror(fp)) { - error_msg("fscanf error\n"); - h5tools_setstatus(EXIT_FAILURE); - ret_value = EXIT_FAILURE; - goto done; - } /* end if */ - comp_info[i] = c; - i++; - if (HDfeof(fp)) - break; - if (c == 10 /*eol*/) - break; - } - comp_info[i - 1] = '\0'; /*cut the last " */ + /* Info indicator must be for layout or filter */ + if (HDstrcmp(stype, "-l") != 0 && HDstrcmp(stype, "-f") != 0) { + error_msg("bad file format for %s", filename); + h5tools_setstatus(EXIT_FAILURE); + ret_value = EXIT_FAILURE; + goto done; + } - if (h5repack_addfilter(comp_info, options) == -1) { - error_msg("could not add compression option\n"); + /* find beginning of info */ + i = 0; + c = '0'; + while (c != ' ') { + if (HDfscanf(fp, "%c", &c) < 0 && HDferror(fp)) { + error_msg("fscanf error\n"); h5tools_setstatus(EXIT_FAILURE); ret_value = EXIT_FAILURE; goto done; } + if (HDfeof(fp)) + break; } - /*------------------------------------------------------------------------- - * layout - *------------------------------------------------------------------------- - */ - else if (HDstrcmp(stype,"-l") == 0) { - - /* find begining of info */ - i = 0; - c = '0'; - while (c != ' ') { - if(fscanf(fp, "%c", &c) < 0 && HDferror(fp)) { - error_msg("fscanf error\n"); - h5tools_setstatus(EXIT_FAILURE); - ret_value = EXIT_FAILURE; - goto done; - } /* end if */ - if (HDfeof(fp)) - break; - } - c = '0'; - /* go until end */ - while (c != ' ') { - if(fscanf(fp, "%c", &c) < 0 && HDferror(fp)) { - error_msg("fscanf error\n"); - h5tools_setstatus(EXIT_FAILURE); - ret_value = EXIT_FAILURE; - goto done; - } /* end if */ - comp_info[i] = c; - i++; - if (HDfeof(fp)) - break; - if (c == 10 /*eol*/) - break; + c = '0'; + /* go until end */ + while (c != ' ') { + if (HDfscanf(fp, "%c", &c) < 0 && HDferror(fp)) { + error_msg("fscanf error\n"); + h5tools_setstatus(EXIT_FAILURE); + ret_value = EXIT_FAILURE; + goto done; } - comp_info[i - 1] = '\0'; /*cut the last " */ + comp_info[i++] = c; + if (HDfeof(fp)) + break; + if (c == 10 /*eol*/) + break; + } + comp_info[i - 1] = '\0'; /*cut the last " */ + if (!HDstrcmp(stype, "-l")) { if (h5repack_addlayout(comp_info, options) == -1) { - error_msg("could not add chunck option\n"); + error_msg("could not add chunk option\n"); h5tools_setstatus(EXIT_FAILURE); ret_value = EXIT_FAILURE; goto done; } } - /*------------------------------------------------------------------------- - * not valid - *------------------------------------------------------------------------- - */ else { - error_msg("bad file format for %s", filename); - h5tools_setstatus(EXIT_FAILURE); - ret_value = EXIT_FAILURE; - goto done; + if (h5repack_addfilter(comp_info, options) == -1) { + error_msg("could not add compression option\n"); + h5tools_setstatus(EXIT_FAILURE); + ret_value = EXIT_FAILURE; + goto done; + } } - } + } /* end while info-read cycling */ done: if (fp) @@ -399,9 +471,9 @@ set_sort_by(const char *form) { H5_index_t idx_type = H5_INDEX_UNKNOWN; - if (HDstrcmp(form,"name")==0) /* H5_INDEX_NAME */ + if (!HDstrcmp(form, "name")) idx_type = H5_INDEX_NAME; - else if (HDstrcmp(form,"creation_order")==0) /* H5_INDEX_CRT_ORDER */ + else if (!HDstrcmp(form, "creation_order")) idx_type = H5_INDEX_CRT_ORDER; return idx_type; @@ -422,9 +494,9 @@ set_sort_order(const char *form) { H5_iter_order_t iter_order = H5_ITER_UNKNOWN; - if (HDstrcmp(form,"ascending")==0) /* H5_ITER_INC */ + if (!HDstrcmp(form, "ascending")) iter_order = H5_ITER_INC; - else if (HDstrcmp(form,"descending")==0) /* H5_ITER_DEC */ + else if (!HDstrcmp(form, "descending")) iter_order = H5_ITER_DEC; return iter_order; @@ -436,47 +508,67 @@ set_sort_order(const char *form) * Purpose: parse command line input *------------------------------------------------------------------------- */ -static -int parse_command_line(int argc, const char **argv, pack_opt_t* options) +static int +parse_command_line(int argc, const char *const *argv, pack_opt_t *options) { - int opt; - int ret_value = 0; + h5tools_vol_info_t in_vol_info; + h5tools_vol_info_t out_vol_info; + h5tools_vfd_info_t in_vfd_info; + h5tools_vfd_info_t out_vfd_info; + hbool_t custom_in_vol = FALSE; + hbool_t custom_in_vfd = FALSE; + hbool_t custom_out_vol = FALSE; + hbool_t custom_out_vfd = FALSE; + hid_t tmp_fapl = H5I_INVALID_HID; + int bound, opt; + int ret_value = 0; + + /* Initialize fapl info structs */ + HDmemset(&in_vol_info, 0, sizeof(h5tools_vol_info_t)); + HDmemset(&out_vol_info, 0, sizeof(h5tools_vol_info_t)); + HDmemset(&in_vfd_info, 0, sizeof(h5tools_vfd_info_t)); + HDmemset(&out_vfd_info, 0, sizeof(h5tools_vfd_info_t)); /* parse command line options */ - while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) { - switch ((char) opt) { + while (EOF != (opt = H5_get_option(argc, argv, s_opts, l_opts))) { + switch ((char)opt) { /* -i for backward compatibility */ case 'i': - infile = opt_arg; - has_i_o = 1; + infile = H5_optarg; + has_i++; break; /* -o for backward compatibility */ case 'o': - outfile = opt_arg; - has_i_o = 1; + outfile = H5_optarg; + has_o++; break; case 'h': usage(h5tools_getprogname()); h5tools_setstatus(EXIT_SUCCESS); - ret_value = -1; + ret_value = 1; goto done; case 'V': print_version(h5tools_getprogname()); h5tools_setstatus(EXIT_SUCCESS); - ret_value = -1; + ret_value = 1; goto done; case 'v': - options->verbose = 1; + if (H5_optarg != NULL) { + if (2 == HDatoi(H5_optarg)) + options->verbose = 2; + } + else + options->verbose = 1; break; case 'f': /* parse the -f filter option */ - if (h5repack_addfilter(opt_arg, options) < 0) { + if (h5repack_addfilter(H5_optarg, options) < 0) { error_msg("in parsing filter\n"); h5tools_setstatus(EXIT_FAILURE); ret_value = -1; @@ -486,7 +578,7 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options) case 'l': /* parse the -l layout option */ - if (h5repack_addlayout(opt_arg, options) < 0) { + if (h5repack_addlayout(H5_optarg, options) < 0) { error_msg("in parsing layout\n"); h5tools_setstatus(EXIT_FAILURE); ret_value = -1; @@ -495,9 +587,9 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options) break; case 'm': - options->min_comp = HDstrtoull(opt_arg , NULL, 0); - if ((int) options->min_comp <= 0) { - error_msg("invalid minimum compress size <%s>\n", opt_arg); + options->min_comp = HDstrtoull(H5_optarg, NULL, 0); + if ((int)options->min_comp <= 0) { + error_msg("invalid minimum compress size <%s>\n", H5_optarg); h5tools_setstatus(EXIT_FAILURE); ret_value = -1; goto done; @@ -505,9 +597,12 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options) break; case 'e': - ret_value = read_info(opt_arg, options); - if (ret_value < 0) + if ((ret_value = read_info(H5_optarg, options)) < 0) { + error_msg("failed to read from repack options file <%s>\n", H5_optarg); + h5tools_setstatus(EXIT_FAILURE); + ret_value = -1; goto done; + } break; case 'n': @@ -519,139 +614,149 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options) break; case 'j': - options->low_bound = (H5F_libver_t)HDatoi(opt_arg); - if(options->low_bound < H5F_LIBVER_EARLIEST || options->low_bound > H5F_LIBVER_LATEST) { + bound = HDatoi(H5_optarg); + if (bound < H5F_LIBVER_EARLIEST || bound > H5F_LIBVER_LATEST) { error_msg("in parsing low bound\n"); + h5tools_setstatus(EXIT_FAILURE); + ret_value = -1; goto done; } + options->low_bound = bound; break; case 'k': - options->high_bound = (H5F_libver_t)HDatoi(opt_arg); - if(options->high_bound < H5F_LIBVER_EARLIEST || options->high_bound > H5F_LIBVER_LATEST) { + bound = HDatoi(H5_optarg); + if (bound < H5F_LIBVER_EARLIEST || bound > H5F_LIBVER_LATEST) { error_msg("in parsing high bound\n"); + h5tools_setstatus(EXIT_FAILURE); + ret_value = -1; goto done; } + options->high_bound = bound; + break; + + case 'X': + options->merge = TRUE; + break; + + case 'W': + options->prune = TRUE; break; case 'c': - options->grp_compact = HDatoi( opt_arg ); + options->grp_compact = HDatoi(H5_optarg); if (options->grp_compact > 0) options->latest = TRUE; /* must use latest format */ break; case 'd': - options->grp_indexed = HDatoi( opt_arg ); + options->grp_indexed = HDatoi(H5_optarg); if (options->grp_indexed > 0) options->latest = TRUE; /* must use latest format */ break; - case 's': - { - int idx = 0; - int ssize = 0; - char *msgPtr = HDstrchr( opt_arg, ':'); - options->latest = TRUE; /* must use latest format */ - if (msgPtr == NULL) { - ssize = HDatoi( opt_arg ); - for (idx = 0; idx < 5; idx++) - options->msg_size[idx] = ssize; - } - else { - char msgType[10]; - - HDstrcpy(msgType, msgPtr + 1); - msgPtr[0] = '\0'; - ssize = HDatoi( opt_arg ); - if (HDstrncmp(msgType, "dspace",6) == 0) - options->msg_size[0] = ssize; - else if (HDstrncmp(msgType, "dtype", 5) == 0) - options->msg_size[1] = ssize; - else if (HDstrncmp(msgType, "fill", 4) == 0) - options->msg_size[2] = ssize; - else if (HDstrncmp(msgType, "pline", 5) == 0) - options->msg_size[3] = ssize; - else if (HDstrncmp(msgType, "attr", 4) == 0) - options->msg_size[4] = ssize; - } + case 's': { + int idx = 0; + int ssize = 0; + char *msgPtr = HDstrchr(H5_optarg, ':'); + options->latest = TRUE; /* must use latest format */ + if (msgPtr == NULL) { + ssize = HDatoi(H5_optarg); + for (idx = 0; idx < 5; idx++) + options->msg_size[idx] = ssize; } - break; + else { + char msgType[10]; + + HDstrcpy(msgType, msgPtr + 1); + msgPtr[0] = '\0'; + ssize = HDatoi(H5_optarg); + if (!HDstrncmp(msgType, "dspace", 6)) + options->msg_size[0] = ssize; + else if (!HDstrncmp(msgType, "dtype", 5)) + options->msg_size[1] = ssize; + else if (!HDstrncmp(msgType, "fill", 4)) + options->msg_size[2] = ssize; + else if (!HDstrncmp(msgType, "pline", 5)) + options->msg_size[3] = ssize; + else if (!HDstrncmp(msgType, "attr", 4)) + options->msg_size[4] = ssize; + } + } break; case 'u': - options->ublock_filename = opt_arg; + options->ublock_filename = H5_optarg; break; case 'b': - options->ublock_size = (hsize_t) HDatol( opt_arg ); + options->ublock_size = (hsize_t)HDatol(H5_optarg); break; case 'M': - options->meta_block_size = (hsize_t) HDatol( opt_arg ); + options->meta_block_size = (hsize_t)HDatol(H5_optarg); break; case 't': - options->threshold = (hsize_t) HDatol( opt_arg ); + options->threshold = (hsize_t)HDatol(H5_optarg); break; case 'a': - options->alignment = HDstrtoull(opt_arg , NULL, 0); + options->alignment = HDstrtoull(H5_optarg, NULL, 0); if (options->alignment < 1) { - error_msg("invalid alignment size\n", opt_arg); + error_msg("invalid alignment size `%s`\n", H5_optarg); h5tools_setstatus(EXIT_FAILURE); ret_value = -1; goto done; } break; - case 'S': - { - char strategy[MAX_NC_NAME]; - - HDstrcpy(strategy, opt_arg); - if(!HDstrcmp(strategy, "FSM_AGGR")) - options->fs_strategy = H5F_FSPACE_STRATEGY_FSM_AGGR; - else if(!HDstrcmp(strategy, "PAGE")) - options->fs_strategy = H5F_FSPACE_STRATEGY_PAGE; - else if(!HDstrcmp(strategy, "AGGR")) - options->fs_strategy = H5F_FSPACE_STRATEGY_AGGR; - else if(!HDstrcmp(strategy, "NONE")) - options->fs_strategy = H5F_FSPACE_STRATEGY_NONE; - else { - error_msg("invalid file space management strategy\n", opt_arg); - h5tools_setstatus(EXIT_FAILURE); - ret_value = -1; - goto done; - } - if(options->fs_strategy == (H5F_fspace_strategy_t)0) - /* To distinguish the "specified" zero value */ - options->fs_strategy = (H5F_fspace_strategy_t)-1; + case 'S': { + char strategy[MAX_NC_NAME]; + + HDstrcpy(strategy, H5_optarg); + if (!HDstrcmp(strategy, "FSM_AGGR")) + options->fs_strategy = H5F_FSPACE_STRATEGY_FSM_AGGR; + else if (!HDstrcmp(strategy, "PAGE")) + options->fs_strategy = H5F_FSPACE_STRATEGY_PAGE; + else if (!HDstrcmp(strategy, "AGGR")) + options->fs_strategy = H5F_FSPACE_STRATEGY_AGGR; + else if (!HDstrcmp(strategy, "NONE")) + options->fs_strategy = H5F_FSPACE_STRATEGY_NONE; + else { + error_msg("invalid file space management strategy `%s`\n", H5_optarg); + h5tools_setstatus(EXIT_FAILURE); + ret_value = -1; + goto done; } - break; + if (options->fs_strategy == (H5F_fspace_strategy_t)0) + /* To distinguish the "specified" zero value */ + options->fs_strategy = (H5F_fspace_strategy_t)-1; + } break; case 'P': - options->fs_persist = HDatoi(opt_arg); - if(options->fs_persist == 0) + options->fs_persist = HDatoi(H5_optarg); + if (options->fs_persist == 0) /* To distinguish the "specified" zero value */ options->fs_persist = -1; break; case 'T': - options->fs_threshold = HDatol(opt_arg); - if(options->fs_threshold == 0) + options->fs_threshold = HDatol(H5_optarg); + if (options->fs_threshold == 0) /* To distinguish the "specified" zero value */ options->fs_threshold = -1; break; case 'G': - options->fs_pagesize = HDstrtoll(opt_arg, NULL, 0); - if(options->fs_pagesize == 0) + options->fs_pagesize = HDstrtoll(H5_optarg, NULL, 0); + if (options->fs_pagesize == 0) /* To distinguish the "specified" zero value */ - options->fs_pagesize = -1; + options->fs_pagesize = -1; break; case 'q': - if((sort_by = set_sort_by(opt_arg)) < 0) { - error_msg(" failed to set sort by form <%s>\n", opt_arg); + if (H5_INDEX_UNKNOWN == (sort_by = set_sort_by(H5_optarg))) { + error_msg("failed to set sort by form <%s>\n", H5_optarg); h5tools_setstatus(EXIT_FAILURE); ret_value = -1; goto done; @@ -659,8 +764,8 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options) break; case 'z': - if((sort_order = set_sort_order(opt_arg)) < 0) { - error_msg(" failed to set sort order form <%s>\n", opt_arg); + if (H5_ITER_UNKNOWN == (sort_order = set_sort_order(H5_optarg))) { + error_msg("failed to set sort order form <%s>\n", H5_optarg); h5tools_setstatus(EXIT_FAILURE); ret_value = -1; goto done; @@ -668,23 +773,150 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options) break; case 'E': - enable_error_stack = 1; + if (H5_optarg != NULL) + enable_error_stack = HDatoi(H5_optarg); + else + enable_error_stack = 1; + break; + + case '1': + in_vol_info.type = VOL_BY_VALUE; + in_vol_info.u.value = (H5VL_class_value_t)HDatoi(H5_optarg); + custom_in_vol = TRUE; + break; + + case '2': + in_vol_info.type = VOL_BY_NAME; + in_vol_info.u.name = H5_optarg; + custom_in_vol = TRUE; + break; + + case '3': + in_vol_info.info_string = H5_optarg; + break; + + case '4': + out_vol_info.type = VOL_BY_VALUE; + out_vol_info.u.value = (H5VL_class_value_t)HDatoi(H5_optarg); + custom_out_vol = TRUE; + break; + + case '5': + out_vol_info.type = VOL_BY_NAME; + out_vol_info.u.name = H5_optarg; + custom_out_vol = TRUE; + break; + + case '6': + out_vol_info.info_string = H5_optarg; + break; + + case '7': + in_vfd_info.type = VFD_BY_VALUE; + in_vfd_info.u.value = (H5FD_class_value_t)HDatoi(H5_optarg); + custom_in_vfd = TRUE; + break; + + case '8': + in_vfd_info.type = VFD_BY_NAME; + in_vfd_info.u.name = H5_optarg; + custom_in_vfd = TRUE; + break; + + case '9': + in_vfd_info.info = (const void *)H5_optarg; + break; + + case '0': + out_vfd_info.type = VFD_BY_VALUE; + out_vfd_info.u.value = (H5FD_class_value_t)HDatoi(H5_optarg); + custom_out_vfd = TRUE; + break; + + case 'Y': + out_vfd_info.type = VFD_BY_NAME; + out_vfd_info.u.name = H5_optarg; + custom_out_vfd = TRUE; + break; + + case 'Z': + out_vfd_info.info = (const void *)H5_optarg; break; default: break; - } /* switch */ - } /* while */ + } /* end switch */ + } /* end while there are more options to parse */ - if (has_i_o == 0) { - /* check for file names to be processed */ - if (argc <= opt_ind || argv[opt_ind + 1] == NULL) { - error_msg("missing file names\n"); + /* If neither -i nor -o given, get in and out files positionally */ + if (0 == (has_i + has_o)) { + if (argv[H5_optind] != NULL && argv[H5_optind + 1] != NULL) { + infile = argv[H5_optind]; + outfile = argv[H5_optind + 1]; + + if (!HDstrcmp(infile, outfile)) { + error_msg("file names cannot be the same\n"); + usage(h5tools_getprogname()); + h5tools_setstatus(EXIT_FAILURE); + ret_value = -1; + } + } + else { + error_msg("file names missing\n"); usage(h5tools_getprogname()); h5tools_setstatus(EXIT_FAILURE); ret_value = -1; } } + else if (has_i != 1 || has_o != 1) { + error_msg("filenames must be either both -i -o or both positional\n"); + usage(h5tools_getprogname()); + h5tools_setstatus(EXIT_FAILURE); + ret_value = -1; + } + + /* Setup FAPL for input and output file accesses */ + if (custom_in_vol || custom_in_vfd) { + if ((tmp_fapl = h5tools_get_fapl(options->fin_fapl, custom_in_vol ? &in_vol_info : NULL, + custom_in_vfd ? &in_vfd_info : NULL)) < 0) { + error_msg("failed to setup FAPL for input file\n"); + h5tools_setstatus(EXIT_FAILURE); + ret_value = -1; + goto done; + } + + /* Close old FAPL */ + if (options->fin_fapl != H5P_DEFAULT) + if (H5Pclose(options->fin_fapl) < 0) { + error_msg("failed to close FAPL\n"); + h5tools_setstatus(EXIT_FAILURE); + ret_value = -1; + goto done; + } + + options->fin_fapl = tmp_fapl; + } + + if (custom_out_vol || custom_out_vfd) { + if ((tmp_fapl = h5tools_get_fapl(options->fout_fapl, custom_out_vol ? &out_vol_info : NULL, + custom_out_vfd ? &out_vfd_info : NULL)) < 0) { + error_msg("failed to setup FAPL for output file\n"); + h5tools_setstatus(EXIT_FAILURE); + ret_value = -1; + goto done; + } + + /* Close old FAPL */ + if (options->fout_fapl != H5P_DEFAULT) + if (H5Pclose(options->fout_fapl) < 0) { + error_msg("failed to close FAPL\n"); + h5tools_setstatus(EXIT_FAILURE); + ret_value = -1; + goto done; + } + + options->fout_fapl = tmp_fapl; + } done: return ret_value; @@ -700,81 +932,69 @@ done: * Failure: EXIT_FAILURE(1) *------------------------------------------------------------------------- */ -int main(int argc, const char **argv) +int +main(int argc, char **argv) { pack_opt_t options; /*the global options */ - H5E_auto2_t func; - H5E_auto2_t tools_func; - void *edata; - void *tools_edata; + int parse_ret; HDmemset(&options, 0, sizeof(pack_opt_t)); - h5tools_setprogname(PROGRAMNAME); - h5tools_setstatus(EXIT_SUCCESS); - - /* Disable error reporting */ - H5Eget_auto2(H5E_DEFAULT, &func, &edata); - H5Eset_auto2(H5E_DEFAULT, NULL, NULL); - /* Initialize h5tools lib */ h5tools_init(); - /* Disable tools error reporting */ - H5Eget_auto2(H5tools_ERR_STACK_g, &tools_func, &tools_edata); - H5Eset_auto2(H5tools_ERR_STACK_g, NULL, NULL); + h5tools_setprogname(PROGRAMNAME); + h5tools_setstatus(EXIT_SUCCESS); /* update hyperslab buffer size from H5TOOLS_BUFSIZE env if exist */ if (h5tools_getenv_update_hyperslab_bufsize() < 0) { + HDprintf("Error occurred while retrieving H5TOOLS_BUFSIZE value\n"); h5tools_setstatus(EXIT_FAILURE); goto done; } /* initialize options */ if (h5repack_init(&options, 0, FALSE) < 0) { + HDprintf("Error occurred while initializing repack options\n"); h5tools_setstatus(EXIT_FAILURE); goto done; } + /* Initialize default indexing options */ sort_by = H5_INDEX_CRT_ORDER; - if (parse_command_line(argc, argv, &options) < 0) + parse_ret = parse_command_line(argc, (const char *const *)argv, &options); + if (parse_ret < 0) { + HDprintf("Error occurred while parsing command-line options\n"); + h5tools_setstatus(EXIT_FAILURE); goto done; - - /* get file names if they were not yet got */ - if (has_i_o == 0) { - - if (argv[opt_ind] != NULL && argv[opt_ind + 1] != NULL) { - infile = argv[opt_ind]; - outfile = argv[opt_ind + 1]; - - if ( HDstrcmp( infile, outfile ) == 0) { - error_msg("file names cannot be the same\n"); - usage(h5tools_getprogname()); - h5tools_setstatus(EXIT_FAILURE); - goto done; - } - } - else { - error_msg("file names missing\n"); - usage(h5tools_getprogname()); - h5tools_setstatus(EXIT_FAILURE); - goto done; - } } - - if (enable_error_stack > 0) { - H5Eset_auto2(H5E_DEFAULT, func, edata); - H5Eset_auto2(H5tools_ERR_STACK_g, tools_func, tools_edata); + else if (parse_ret > 0) { + /* Short-circuit success */ + h5tools_setstatus(EXIT_SUCCESS); + goto done; } + /* enable error reporting if command line option */ + h5tools_error_report(); + /* pack it */ - h5tools_setstatus(h5repack(infile, outfile, &options)); + if (h5repack(infile, outfile, &options) < 0) { + HDprintf("Error occurred while repacking\n"); + h5tools_setstatus(EXIT_FAILURE); + goto done; + } + + h5tools_setstatus(EXIT_SUCCESS); done: + if (options.fin_fapl >= 0 && options.fin_fapl != H5P_DEFAULT) + H5Pclose(options.fin_fapl); + if (options.fout_fapl >= 0 && options.fout_fapl != H5P_DEFAULT) + H5Pclose(options.fout_fapl); + /* free tables */ h5repack_end(&options); leave(h5tools_getstatus()); } - diff --git a/tools/src/h5repack/h5repack_opttable.c b/tools/src/h5repack/h5repack_opttable.c index 7ab8c6e..167506f 100644 --- a/tools/src/h5repack/h5repack_opttable.c +++ b/tools/src/h5repack/h5repack_opttable.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -21,23 +21,25 @@ * Purpose: initialize a pack_info_t structure * * Return: void - *------------------------------------------------------------------------- + *------------------------------------------------------------------------- */ -void init_packobject(pack_info_t *obj) { +void +init_packobject(pack_info_t *obj) +{ int j, k; HDstrcpy(obj->path, "\0"); for (j = 0; j < H5_REPACK_MAX_NFILTERS; j++) { - obj->filter[j].filtn = -1; + obj->filter[j].filtn = -1; obj->filter[j].cd_nelmts = CD_VALUES; for (k = 0; k < CD_VALUES; k++) obj->filter[j].cd_values[k] = 0; } obj->chunk.rank = -1; - obj->refobj_id = -1; - obj->layout = H5D_LAYOUT_ERROR; - obj->nfilters = 0; + obj->refobj_id = -1; + obj->layout = H5D_LAYOUT_ERROR; + obj->nfilters = 0; } /*------------------------------------------------------------------------- @@ -49,11 +51,13 @@ void init_packobject(pack_info_t *obj) { *------------------------------------------------------------------------- */ -static void aux_tblinsert_filter(pack_opttbl_t *table, unsigned int I, filter_info_t filt) { +static void +aux_tblinsert_filter(pack_opttbl_t *table, unsigned int I, filter_info_t filt) +{ if (table->objs[I].nfilters < H5_REPACK_MAX_NFILTERS) table->objs[I].filter[table->objs[I].nfilters++] = filt; else - H5TOOLS_INFO(H5E_tools_min_id_g, "cannot insert the filter in this object. Maximum capacity exceeded"); + H5TOOLS_INFO("cannot insert the filter in this object. Maximum capacity exceeded"); } /*------------------------------------------------------------------------- @@ -64,7 +68,9 @@ static void aux_tblinsert_filter(pack_opttbl_t *table, unsigned int I, filter_in * Return: void *------------------------------------------------------------------------- */ -static void aux_tblinsert_layout(pack_opttbl_t *table, unsigned int I, pack_info_t *pack) { +static void +aux_tblinsert_layout(pack_opttbl_t *table, unsigned int I, pack_info_t *pack) +{ int k; table->objs[I].layout = pack->layout; @@ -72,15 +78,14 @@ static void aux_tblinsert_layout(pack_opttbl_t *table, unsigned int I, pack_info /* -2 means the NONE option, remove chunking and set the layout to contiguous */ if (pack->chunk.rank == -2) { - table->objs[I].layout = H5D_CONTIGUOUS; + table->objs[I].layout = H5D_CONTIGUOUS; table->objs[I].chunk.rank = -2; } /* otherwise set the chunking type */ else { table->objs[I].chunk.rank = pack->chunk.rank; for (k = 0; k < pack->chunk.rank; k++) - table->objs[I].chunk.chunk_lengths[k] = - pack->chunk.chunk_lengths[k]; + table->objs[I].chunk.chunk_lengths[k] = pack->chunk.chunk_lengths[k]; } } } @@ -97,54 +102,56 @@ static int aux_inctable(pack_opttbl_t *table, unsigned n_objs) { unsigned u; + int ret_value = 0; table->size += n_objs; - table->objs = (pack_info_t*) HDrealloc(table->objs, table->size * sizeof(pack_info_t)); + table->objs = (pack_info_t *)HDrealloc(table->objs, table->size * sizeof(pack_info_t)); if (table->objs == NULL) { - H5TOOLS_INFO(H5E_tools_min_id_g, "not enough memory for options table"); - return -1; + H5TOOLS_INFO("not enough memory for options table"); + ret_value = -1; + } + else { + for (u = table->nelems; u < table->size; u++) + init_packobject(&table->objs[u]); } - for (u = table->nelems; u < table->size; u++) - init_packobject(&table->objs[u]); - - return 0; + return ret_value; } - /*------------------------------------------------------------------------- * Function: options_table_init * * Purpose: init options table * * Return: 0, ok, -1, fail - *------------------------------------------------------------------------- + *------------------------------------------------------------------------- */ -int options_table_init(pack_opttbl_t **tbl) { - unsigned int i; +int +options_table_init(pack_opttbl_t **tbl) +{ + unsigned int i; pack_opttbl_t *table; + int ret_value = 0; - if (NULL == (table = (pack_opttbl_t *) HDmalloc(sizeof(pack_opttbl_t)))) { - H5TOOLS_INFO(H5E_tools_min_id_g, "not enough memory for options table"); - return -1; + if (NULL == (table = (pack_opttbl_t *)HDmalloc(sizeof(pack_opttbl_t)))) { + H5TOOLS_GOTO_ERROR((-1), "not enough memory for options table"); } - table->size = 30; + table->size = 30; table->nelems = 0; - if (NULL == (table->objs = (pack_info_t*) HDmalloc(table->size * sizeof(pack_info_t)))) { - H5TOOLS_INFO(H5E_tools_min_id_g, "not enough memory for options table"); + if (NULL == (table->objs = (pack_info_t *)HDmalloc(table->size * sizeof(pack_info_t)))) { HDfree(table); - return -1; + H5TOOLS_GOTO_ERROR((-1), "not enough memory for options table"); } for (i = 0; i < table->size; i++) init_packobject(&table->objs[i]); *tbl = table; - return 0; +done: + return ret_value; } - /*------------------------------------------------------------------------- * Function: options_table_free * @@ -154,7 +161,9 @@ int options_table_init(pack_opttbl_t **tbl) { *------------------------------------------------------------------------- */ -int options_table_free(pack_opttbl_t *table) { +int +options_table_free(pack_opttbl_t *table) +{ HDfree(table->objs); HDfree(table); return 0; @@ -166,14 +175,15 @@ int options_table_free(pack_opttbl_t *table) { * Purpose: add a layout option to the option list * * Return: 0, ok, -1, fail - *------------------------------------------------------------------------- + *------------------------------------------------------------------------- */ int -options_add_layout(obj_list_t *obj_list, unsigned n_objs, pack_info_t *pack, pack_opttbl_t *table) +options_add_layout(obj_list_t *obj_list, unsigned n_objs, pack_info_t *pack, pack_opttbl_t *table) { unsigned i, j, I; - unsigned added = 0; - hbool_t found = FALSE; + unsigned added = 0; + hbool_t found = FALSE; + int ret_value = 0; /* increase the size of the collection by N_OBJS if necessary */ if (table->nelems + n_objs >= table->size) @@ -187,10 +197,10 @@ options_add_layout(obj_list_t *obj_list, unsigned n_objs, pack_info_t *pack, pa /* linear table search */ for (i = 0; i < table->nelems; i++) { /*already on the table */ - if (HDstrcmp(obj_list[j].obj,table->objs[i].path) == 0) { + if (HDstrcmp(obj_list[j].obj, table->objs[i].path) == 0) { /* already chunk info inserted for this one; exit */ if (table->objs[i].chunk.rank > 0) { - H5TOOLS_INFO(H5E_tools_min_id_g, "chunk information already inserted for <%s>\n", obj_list[j].obj); + H5TOOLS_INFO("chunk information already inserted for <%s>\n", obj_list[j].obj); HDexit(EXIT_FAILURE); } /* insert the layout info */ @@ -200,7 +210,7 @@ options_add_layout(obj_list_t *obj_list, unsigned n_objs, pack_info_t *pack, pa break; } } /* if */ - } /* i */ + } /* i */ if (!found) { /* keep the grow in a temp var */ @@ -214,14 +224,13 @@ options_add_layout(obj_list_t *obj_list, unsigned n_objs, pack_info_t *pack, pa -f dset1:GZIP=1 -l dset1,dset2:CHUNK=20x20 dset1 is already inserted, but dset2 must also be */ - else - if(found && HDstrcmp(obj_list[j].obj,table->objs[i].path) != 0) { - /* keep the grow in a temp var */ - I = table->nelems + added; - added++; - HDstrcpy(table->objs[I].path, obj_list[j].obj); - aux_tblinsert_layout(table, I, pack); - } + else if (found && HDstrcmp(obj_list[j].obj, table->objs[i].path) != 0) { + /* keep the grow in a temp var */ + I = table->nelems + added; + added++; + HDstrcpy(table->objs[I].path, obj_list[j].obj); + aux_tblinsert_layout(table, I, pack); + } } /* j */ } /* first time insertion */ @@ -237,7 +246,7 @@ options_add_layout(obj_list_t *obj_list, unsigned n_objs, pack_info_t *pack, pa table->nelems += added; - return 0; + return ret_value; } /*------------------------------------------------------------------------- @@ -252,8 +261,8 @@ int options_add_filter(obj_list_t *obj_list, unsigned n_objs, filter_info_t filt, pack_opttbl_t *table) { unsigned int i, j, I; - unsigned added = 0; - hbool_t found = FALSE; + unsigned added = 0; + hbool_t found = FALSE; /* increase the size of the collection by N_OBJS if necessary */ if (table->nelems + n_objs >= table->size) @@ -273,7 +282,7 @@ options_add_filter(obj_list_t *obj_list, unsigned n_objs, filter_info_t filt, pa found = TRUE; break; } /* if */ - } /* i */ + } /* i */ if (!found) { /* keep the grow in a temp var */ @@ -287,14 +296,13 @@ options_add_filter(obj_list_t *obj_list, unsigned n_objs, filter_info_t filt, pa -l dset1:CHUNK=20x20 -f dset1,dset2:GZIP=1 dset1 is already inserted, but dset2 must also be */ - else - if(found && HDstrcmp(obj_list[j].obj,table->objs[i].path) != 0) { - /* keep the grow in a temp var */ - I = table->nelems + added; - added++; - HDstrcpy(table->objs[I].path, obj_list[j].obj); - aux_tblinsert_filter(table, I, filt); - } + else if (found && HDstrcmp(obj_list[j].obj, table->objs[i].path) != 0) { + /* keep the grow in a temp var */ + I = table->nelems + added; + added++; + HDstrcpy(table->objs[I].path, obj_list[j].obj); + aux_tblinsert_filter(table, I, filt); + } } /* j */ } @@ -323,13 +331,15 @@ options_add_filter(obj_list_t *obj_list, unsigned n_objs, filter_info_t filt, pa *------------------------------------------------------------------------- */ -pack_info_t* options_get_object(const char *path, pack_opttbl_t *table) { +pack_info_t * +options_get_object(const char *path, pack_opttbl_t *table) +{ unsigned int i; - char tbl_path[MAX_NC_NAME + 1]; /* +1 for start with "/" case */ + char tbl_path[MAX_NC_NAME + 1]; /* +1 for start with "/" case */ for (i = 0; i < table->nelems; i++) { /* make full path (start with "/") to compare correctly */ - if (HDstrncmp(table->objs[i].path, "/", 1)) { + if (HDstrncmp(table->objs[i].path, "/", 1) != 0) { HDstrcpy(tbl_path, "/"); HDstrcat(tbl_path, table->objs[i].path); } diff --git a/tools/src/h5repack/h5repack_parse.c b/tools/src/h5repack/h5repack_parse.c index 03fcf0e..1c06cae 100644 --- a/tools/src/h5repack/h5repack_parse.c +++ b/tools/src/h5repack/h5repack_parse.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -37,8 +37,9 @@ * "A,B:NONE" *------------------------------------------------------------------------- */ -obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, - pack_opt_t *options, int *is_glb) { +obj_list_t * +parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t *options, int *is_glb) +{ size_t i, m, u; char c; size_t len = HDstrlen(str); @@ -48,7 +49,7 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, char scomp[16] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; char stype[16] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; char smask[16] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; - obj_list_t* obj_list = NULL; + obj_list_t *obj_list = NULL; unsigned pixels_per_block; /* initialize compression info */ @@ -59,7 +60,7 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, for (i = 0, n = 0; i < len; i++) { c = str[i]; if (c == ':') { - end_obj = (int) i; + end_obj = (int)i; break; } if (c == ',') @@ -71,13 +72,13 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, if (end_obj == -1) { /* apply to all objects */ options->all_filter = 1; - *is_glb = 1; - *n_objs = 1; + *is_glb = 1; + *n_objs = 1; } else *n_objs = n; - obj_list = (obj_list_t *) HDmalloc(n * sizeof(obj_list_t)); + obj_list = (obj_list_t *)HDmalloc(n * sizeof(obj_list_t)); if (obj_list == NULL) { error_msg("could not allocate object list\n"); return NULL; @@ -85,10 +86,10 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, /* get object list */ if (end_obj > 0) - for (j = 0, k = 0, n = 0; j < (unsigned) end_obj; j++, k++) { - c = str[j]; + for (j = 0, k = 0, n = 0; j < (unsigned)end_obj; j++, k++) { + c = str[j]; sobj[k] = c; - if (c == ',' || j == (unsigned) (end_obj - 1)) { + if (c == ',' || j == (unsigned)(end_obj - 1)) { if (c == ',') sobj[k] = '\0'; else @@ -101,7 +102,7 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, } } /* nothing after : */ - if (end_obj + 1 == (int) len) { + if (end_obj + 1 == (int)len) { if (obj_list) HDfree(obj_list); error_msg("input Error: Invalid compression type in <%s>\n", str); @@ -111,25 +112,25 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, /* get filter additional parameters */ m = 0; for (i = (size_t)(end_obj + 1), k = 0, j = 0; i < len; i++, k++) { - c = str[i]; + c = str[i]; scomp[k] = c; if (c == '=' || i == len - 1) { - if (c == '=') { /*one more parameter */ + if (c == '=') { /*one more parameter */ scomp[k] = '\0'; /*cut space */ /*------------------------------------------------------------------------- - * H5Z_FILTER_SZIP - * szip has the format SZIP=<pixels per block,coding> - * pixels per block is a even number in 2-32 and coding method is 'EC' or 'NN' - * example SZIP=8,NN - *------------------------------------------------------------------------- - */ + * H5Z_FILTER_SZIP + * szip has the format SZIP=<pixels per block,coding> + * pixels per block is a even number in 2-32 and coding method is 'EC' or 'NN' + * example SZIP=8,NN + *------------------------------------------------------------------------- + */ if (HDstrcmp(scomp, "SZIP") == 0) { l = -1; /* mask index check */ for (m = 0, u = i + 1; u < len; u++, m++) { if (str[u] == ',') { stype[m] = '\0'; /* end digit of szip */ - l = 0; /* start EC or NN search */ - u++; /* skip ',' */ + l = 0; /* start EC or NN search */ + u++; /* skip ',' */ } c = str[u]; if (!HDisdigit(c) && l == -1) { @@ -145,10 +146,10 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, l++; if (l == 2) { smask[l] = '\0'; - i = len - 1; /* end */ - if (HDstrcmp(smask,"NN") == 0) + i = len - 1; /* end */ + if (HDstrcmp(smask, "NN") == 0) filt->cd_values[j++] = H5_SZIP_NN_OPTION_MASK; - else if (HDstrcmp(smask,"EC") == 0) + else if (HDstrcmp(smask, "EC") == 0) filt->cd_values[j++] = H5_SZIP_EC_OPTION_MASK; else { error_msg("szip mask must be 'NN' or 'EC' \n"); @@ -157,29 +158,29 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, } } } /* u */ - } /*if */ + } /*if */ /*------------------------------------------------------------------------- - * H5Z_FILTER_SCALEOFFSET - * scaleoffset has the format SOFF=<scale_factor,scale_type> - * scale_type can be - * integer datatype, H5Z_SO_INT (IN) - * float datatype using D-scaling method, H5Z_SO_FLOAT_DSCALE (DS) - * float datatype using E-scaling method, H5Z_SO_FLOAT_ESCALE (ES) , not yet implemented - * for integer datatypes, scale_factor denotes Minimum Bits - * for float datatypes, scale_factor denotes decimal scale factor - * examples - * SOFF=31,IN - * SOFF=3,DF - *------------------------------------------------------------------------- - */ + * H5Z_FILTER_SCALEOFFSET + * scaleoffset has the format SOFF=<scale_factor,scale_type> + * scale_type can be + * integer datatype, H5Z_SO_INT (IN) + * float datatype using D-scaling method, H5Z_SO_FLOAT_DSCALE (DS) + * float datatype using E-scaling method, H5Z_SO_FLOAT_ESCALE (ES) , not yet implemented + * for integer datatypes, scale_factor denotes Minimum Bits + * for float datatypes, scale_factor denotes decimal scale factor + * examples + * SOFF=31,IN + * SOFF=3,DF + *------------------------------------------------------------------------- + */ else if (HDstrcmp(scomp, "SOFF") == 0) { l = -1; /* mask index check */ for (m = 0, u = i + 1; u < len; u++, m++) { if (str[u] == ',') { stype[m] = '\0'; /* end digit */ - l = 0; /* start 'IN' , 'DS', or 'ES' search */ - u++; /* skip ',' */ + l = 0; /* start 'IN' , 'DS', or 'ES' search */ + u++; /* skip ',' */ } c = str[u]; if (!HDisdigit(c) && l == -1) { @@ -195,8 +196,8 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, l++; if (l == 2) { smask[l] = '\0'; - i = len - 1; /* end */ - if (HDstrcmp(smask,"IN") == 0) + i = len - 1; /* end */ + if (HDstrcmp(smask, "IN") == 0) filt->cd_values[j++] = H5Z_SO_INT; else if (HDstrcmp(smask, "DS") == H5Z_SO_FLOAT_DSCALE) filt->cd_values[j++] = H5Z_SO_FLOAT_DSCALE; @@ -207,15 +208,15 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, } } } /* u */ - } /*if */ + } /*if */ /*------------------------------------------------------------------------- - * User Defined - * has the format UD=<filter_number,filter_flag,cd_value_count,value_1[,value_2,...,value_N]> - * BZIP2 example - * UD=307,0,1,9 - *------------------------------------------------------------------------- - */ + * User Defined + * has the format + *UD=<filter_number,filter_flag,cd_value_count,value_1[,value_2,...,value_N]> BZIP2 example + * UD=307,0,1,9 + *------------------------------------------------------------------------- + */ else if (HDstrcmp(scomp, "UD") == 0) { l = -1; /* filter number index check */ f = -1; /* filter flag index check */ @@ -225,15 +226,15 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, stype[q] = '\0'; /* end digit */ if (l == -1) { filt->filtn = HDatoi(stype); - l = 0; + l = 0; } else if (f == -1) { - filt->filt_flag = HDstrtoul(stype, NULL, 0); - f = 0; + filt->filt_flag = (unsigned)HDstrtoul(stype, NULL, 0); + f = 0; } else if (p == -1) { filt->cd_nelmts = HDstrtoull(stype, NULL, 0); - p = 0; + p = 0; } else { filt->cd_values[j++] = (unsigned)HDstrtoul(stype, NULL, 0); @@ -260,9 +261,9 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, } /*if */ /*------------------------------------------------------------------------- - * all other filters - *------------------------------------------------------------------------- - */ + * all other filters + *------------------------------------------------------------------------- + */ else { /* here we could have 1 or 2 digits */ for (m = 0, u = i + 1; u < len; u++, m++) { @@ -279,36 +280,36 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, stype[m] = '\0'; } /*if */ - filt->cd_values[j++] = (unsigned) HDstrtoul(stype, NULL, 0); - if(filt->cd_nelmts == 0) + filt->cd_values[j++] = (unsigned)HDstrtoul(stype, NULL, 0); + if (filt->cd_nelmts == 0) j = 0; i += m; /* jump */ } else if (i == len - 1) { /*no more parameters */ scomp[k + 1] = '\0'; - no_param = 1; + no_param = 1; } /*------------------------------------------------------------------------- - * translate from string to filter symbol - *------------------------------------------------------------------------- - */ + * translate from string to filter symbol + *------------------------------------------------------------------------- + */ /*------------------------------------------------------------------------- - * H5Z_FILTER_NONE - *------------------------------------------------------------------------- - */ + * H5Z_FILTER_NONE + *------------------------------------------------------------------------- + */ if (HDstrcmp(scomp, "NONE") == 0) { - filt->filtn = H5Z_FILTER_NONE; + filt->filtn = H5Z_FILTER_NONE; filt->cd_nelmts = 0; } /*------------------------------------------------------------------------- - * H5Z_FILTER_DEFLATE - *------------------------------------------------------------------------- - */ + * H5Z_FILTER_DEFLATE + *------------------------------------------------------------------------- + */ else if (HDstrcmp(scomp, "GZIP") == 0) { - filt->filtn = H5Z_FILTER_DEFLATE; + filt->filtn = H5Z_FILTER_DEFLATE; filt->cd_nelmts = 1; if (no_param) { /*no more parameters, GZIP must have parameter */ if (obj_list) @@ -319,11 +320,11 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, } /*------------------------------------------------------------------------- - * H5Z_FILTER_SZIP - *------------------------------------------------------------------------- - */ + * H5Z_FILTER_SZIP + *------------------------------------------------------------------------- + */ else if (HDstrcmp(scomp, "SZIP") == 0) { - filt->filtn = H5Z_FILTER_SZIP; + filt->filtn = H5Z_FILTER_SZIP; filt->cd_nelmts = 2; if (no_param) { /*no more parameters, SZIP must have parameter */ if (obj_list) @@ -334,11 +335,11 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, } /*------------------------------------------------------------------------- - * H5Z_FILTER_SHUFFLE - *------------------------------------------------------------------------- - */ + * H5Z_FILTER_SHUFFLE + *------------------------------------------------------------------------- + */ else if (HDstrcmp(scomp, "SHUF") == 0) { - filt->filtn = H5Z_FILTER_SHUFFLE; + filt->filtn = H5Z_FILTER_SHUFFLE; filt->cd_nelmts = 0; if (m > 0) { /*shuffle does not have parameter */ if (obj_list) @@ -348,11 +349,11 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, } } /*------------------------------------------------------------------------- - * H5Z_FILTER_FLETCHER32 - *------------------------------------------------------------------------- - */ + * H5Z_FILTER_FLETCHER32 + *------------------------------------------------------------------------- + */ else if (HDstrcmp(scomp, "FLET") == 0) { - filt->filtn = H5Z_FILTER_FLETCHER32; + filt->filtn = H5Z_FILTER_FLETCHER32; filt->cd_nelmts = 0; if (m > 0) { /*shuffle does not have parameter */ if (obj_list) @@ -362,11 +363,11 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, } } /*------------------------------------------------------------------------- - * H5Z_FILTER_NBIT - *------------------------------------------------------------------------- - */ + * H5Z_FILTER_NBIT + *------------------------------------------------------------------------- + */ else if (HDstrcmp(scomp, "NBIT") == 0) { - filt->filtn = H5Z_FILTER_NBIT; + filt->filtn = H5Z_FILTER_NBIT; filt->cd_nelmts = 0; if (m > 0) { /*nbit does not have parameter */ if (obj_list) @@ -376,11 +377,11 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, } } /*------------------------------------------------------------------------- - * H5Z_FILTER_SCALEOFFSET - *------------------------------------------------------------------------- - */ + * H5Z_FILTER_SCALEOFFSET + *------------------------------------------------------------------------- + */ else if (HDstrcmp(scomp, "SOFF") == 0) { - filt->filtn = H5Z_FILTER_SCALEOFFSET; + filt->filtn = H5Z_FILTER_SCALEOFFSET; filt->cd_nelmts = 2; if (no_param) { /*no more parameters, SOFF must have parameter */ if (obj_list) @@ -390,9 +391,9 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, } } /*------------------------------------------------------------------------- - * User Defined Filter - *------------------------------------------------------------------------- - */ + * User Defined Filter + *------------------------------------------------------------------------- + */ else if (HDstrcmp(scomp, "UD") == 0) { /* parameters does not match count */ if (filt->cd_nelmts != j) { @@ -413,56 +414,55 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, } /*i*/ /*------------------------------------------------------------------------- - * check valid parameters - *------------------------------------------------------------------------- - */ + * check valid parameters + *------------------------------------------------------------------------- + */ switch (filt->filtn) { - /*------------------------------------------------------------------------- - * H5Z_FILTER_DEFLATE - *------------------------------------------------------------------------- - */ - case H5Z_FILTER_DEFLATE: - if (filt->cd_values[0] > 9) { - if (obj_list) - HDfree(obj_list); - error_msg("invalid compression parameter in <%s>\n", str); - HDexit(EXIT_FAILURE); - } - break; /*------------------------------------------------------------------------- - * H5Z_FILTER_SZIP - *------------------------------------------------------------------------- - */ - case H5Z_FILTER_SZIP: - pixels_per_block = filt->cd_values[0]; - if ((pixels_per_block % 2) == 1) { - if (obj_list) - HDfree(obj_list); - error_msg("pixels_per_block is not even in <%s>\n", str); - HDexit(EXIT_FAILURE); - } - if (pixels_per_block > H5_SZIP_MAX_PIXELS_PER_BLOCK) { - if (obj_list) - HDfree(obj_list); - error_msg("pixels_per_block is too large in <%s>\n", str); - HDexit(EXIT_FAILURE); - } - if ((HDstrcmp(smask,"NN") != 0) && (HDstrcmp(smask,"EC") != 0)) { - if (obj_list) - HDfree(obj_list); - error_msg("szip mask must be 'NN' or 'EC' \n"); - HDexit(EXIT_FAILURE); - } - break; - default: - break; + * H5Z_FILTER_DEFLATE + *------------------------------------------------------------------------- + */ + case H5Z_FILTER_DEFLATE: + if (filt->cd_values[0] > 9) { + if (obj_list) + HDfree(obj_list); + error_msg("invalid compression parameter in <%s>\n", str); + HDexit(EXIT_FAILURE); + } + break; + /*------------------------------------------------------------------------- + * H5Z_FILTER_SZIP + *------------------------------------------------------------------------- + */ + case H5Z_FILTER_SZIP: + pixels_per_block = filt->cd_values[0]; + if ((pixels_per_block % 2) == 1) { + if (obj_list) + HDfree(obj_list); + error_msg("pixels_per_block is not even in <%s>\n", str); + HDexit(EXIT_FAILURE); + } + if (pixels_per_block > H5_SZIP_MAX_PIXELS_PER_BLOCK) { + if (obj_list) + HDfree(obj_list); + error_msg("pixels_per_block is too large in <%s>\n", str); + HDexit(EXIT_FAILURE); + } + if ((HDstrcmp(smask, "NN") != 0) && (HDstrcmp(smask, "EC") != 0)) { + if (obj_list) + HDfree(obj_list); + error_msg("szip mask must be 'NN' or 'EC' \n"); + HDexit(EXIT_FAILURE); + } + break; + default: + break; }; return obj_list; } - /*------------------------------------------------------------------------- * Function: parse_layout * @@ -478,15 +478,17 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, * Example: * "AA,B,CDE:CHUNK=10X10" * - * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu + * Programmer: Pedro Vicente * * Date: December 30, 2003 * *------------------------------------------------------------------------- */ -obj_list_t* parse_layout(const char *str, unsigned *n_objs, pack_info_t *pack, /* info about layout needed */ -pack_opt_t *options) { - obj_list_t* obj_list = NULL; +obj_list_t * +parse_layout(const char *str, unsigned *n_objs, pack_info_t *pack, /* info about layout needed */ + pack_opt_t *options) +{ + obj_list_t *obj_list = NULL; unsigned i, j, n; char c; size_t len = HDstrlen(str); @@ -503,7 +505,7 @@ pack_opt_t *options) { for (i = 0, n = 0; i < len; i++) { c = str[i]; if (c == ':') - end_obj = (int) i; + end_obj = (int)i; if (c == ',') n++; } @@ -513,7 +515,7 @@ pack_opt_t *options) { } n++; - obj_list = (obj_list_t*) HDmalloc(n * sizeof(obj_list_t)); + obj_list = (obj_list_t *)HDmalloc(n * sizeof(obj_list_t)); if (obj_list == NULL) { error_msg("could not allocate object list\n"); return NULL; @@ -522,10 +524,10 @@ pack_opt_t *options) { /* get object list */ if (end_obj > 0) - for (j = 0, k = 0, n = 0; j < (unsigned) end_obj; j++, k++) { - c = str[j]; + for (j = 0, k = 0, n = 0; j < (unsigned)end_obj; j++, k++) { + c = str[j]; sobj[k] = c; - if (c == ',' || j == (unsigned) (end_obj - 1)) { + if (c == ',' || j == (unsigned)(end_obj - 1)) { if (c == ',') sobj[k] = '\0'; else @@ -538,7 +540,7 @@ pack_opt_t *options) { } /* nothing after : */ - if (end_obj + 1 == (int) len) { + if (end_obj + 1 == (int)len) { if (obj_list) HDfree(obj_list); error_msg("in parse layout, no characters after : in <%s>\n", str); @@ -546,7 +548,7 @@ pack_opt_t *options) { } /* get layout info */ - for (j = (unsigned) (end_obj + 1), n = 0; n <= 5; j++, n++) { + for (j = (unsigned)(end_obj + 1), n = 0; n <= 5; j++, n++) { if (n == 5) { slayout[n] = '\0'; /*cut string */ if (HDstrcmp(slayout, "COMPA") == 0) @@ -561,16 +563,16 @@ pack_opt_t *options) { } } else { - c = str[j]; + c = str[j]; slayout[n] = c; } } /* j */ if (pack->layout == H5D_CHUNKED) { /*------------------------------------------------------------------------- - * get chunk info - *------------------------------------------------------------------------- - */ + * get chunk info + *------------------------------------------------------------------------- + */ k = 0; if (j > len) { if (obj_list) @@ -580,7 +582,7 @@ pack_opt_t *options) { } for (i = j, c_index = 0; i < len; i++) { - c = str[i]; + c = str[i]; sdim[k] = c; k++; /*increment sdim index */ @@ -593,8 +595,8 @@ pack_opt_t *options) { if (c == 'x' || i == len - 1) { if (c == 'x') { - sdim[k - 1] = '\0'; - k = 0; + sdim[k - 1] = '\0'; + k = 0; pack->chunk.chunk_lengths[c_index] = HDstrtoull(sdim, NULL, 0); if (pack->chunk.chunk_lengths[c_index] == 0) { if (obj_list) @@ -606,8 +608,8 @@ pack_opt_t *options) { } else if (i == len - 1) { /*no more parameters */ sdim[k] = '\0'; - k = 0; - if (HDstrcmp(sdim,"NONE") == 0) { + k = 0; + if (HDstrcmp(sdim, "NONE") == 0) { pack->chunk.rank = -2; } else { @@ -621,9 +623,9 @@ pack_opt_t *options) { pack->chunk.rank = c_index + 1; } } /*if */ - } /*if c=='x' || i==len-1 */ - } /*i*/ - } /*H5D_CHUNKED*/ + } /*if c=='x' || i==len-1 */ + } /*i*/ + } /*H5D_CHUNKED*/ return obj_list; } diff --git a/tools/src/h5repack/h5repack_refs.c b/tools/src/h5repack/h5repack_refs.c index 7e8951f..3259b89 100644 --- a/tools/src/h5repack/h5repack_refs.c +++ b/tools/src/h5repack/h5repack_refs.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -15,17 +15,15 @@ #include "h5diff.h" #include "h5tools.h" - /*------------------------------------------------------------------------- * local functions *------------------------------------------------------------------------- */ -static const char* MapIdToName(hid_t refobj_id,trav_table_t *travt); -static int copy_refs_attr(hid_t loc_in, hid_t loc_out, - trav_table_t *travt, hid_t fidout); -static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in, - hid_t fid_out, void *ref_out, trav_table_t *travt); +static const char *MapIdToName(hid_t refobj_id, trav_table_t *travt); +static int copy_refs_attr(hid_t loc_in, hid_t loc_out, trav_table_t *travt, hid_t fidout); +static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in, hid_t fid_out, void *ref_out, + trav_table_t *travt); /*------------------------------------------------------------------------- * Function: do_copy_refobjs @@ -37,35 +35,33 @@ static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in, *------------------------------------------------------------------------- */ -int do_copy_refobjs(hid_t fidin, - hid_t fidout, - trav_table_t *travt, - pack_opt_t *options) /* repack options */ +int +do_copy_refobjs(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *options) /* repack options */ { - int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ - hid_t grp_in = -1; /* read group ID */ - hid_t grp_out = -1; /* write group ID */ - hid_t dset_in = -1; /* read dataset ID */ - hid_t dset_out = -1; /* write dataset ID */ - hid_t type_in = -1; /* named type ID */ - hid_t dcpl_id = -1; /* dataset creation property list ID */ - hid_t space_id = -1; /* space ID */ - hid_t ftype_id = -1; /* file data type ID */ - hid_t mtype_id = -1; /* memory data type ID */ - size_t msize; /* memory size of memory type */ - hsize_t nelmts; /* number of elements in dataset */ - int rank; /* rank of dataset */ - hsize_t dims[H5S_MAX_RANK]; /* dimensions of dataset */ + hid_t grp_in = H5I_INVALID_HID; /* read group ID */ + hid_t grp_out = H5I_INVALID_HID; /* write group ID */ + hid_t dset_in = H5I_INVALID_HID; /* read dataset ID */ + hid_t dset_out = H5I_INVALID_HID; /* write dataset ID */ + hid_t type_in = H5I_INVALID_HID; /* named type ID */ + hid_t dcpl_id = H5I_INVALID_HID; /* dataset creation property list ID */ + hid_t space_id = H5I_INVALID_HID; /* space ID */ + hid_t ftype_id = H5I_INVALID_HID; /* file data type ID */ + hid_t mtype_id = H5I_INVALID_HID; /* memory data type ID */ + size_t msize; /* memory size of memory type */ + hsize_t nelmts; /* number of elements in dataset */ + int rank; /* rank of dataset */ + hsize_t dims[H5S_MAX_RANK]; /* dimensions of dataset */ unsigned int i, j; - int k; - named_dt_t *named_dt_head = NULL; /* Pointer to the stack of named datatypes copied */ + int k; + named_dt_t * named_dt_head = NULL; /* Pointer to the stack of named datatypes copied */ + int ret_value = 0; /*------------------------------------------------------------------------- - * browse - *------------------------------------------------------------------------- - */ - for(i = 0; i < travt->nobjs; i++) { - switch(travt->objs[i].type) { + * browse + *------------------------------------------------------------------------- + */ + for (i = 0; i < travt->nobjs; i++) { + switch (travt->objs[i].type) { /*------------------------------------------------------------------------- * H5TRAV_TYPE_GROUP *------------------------------------------------------------------------- @@ -75,27 +71,28 @@ int do_copy_refobjs(hid_t fidin, * copy referenced objects in attributes *------------------------------------------------------------------------- */ - if((grp_out = H5Gopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed"); + if ((grp_out = H5Gopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Gopen2 failed"); - if((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed"); + if ((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Gopen2 failed"); - if(copy_refs_attr(grp_in, grp_out, travt, fidout) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_refs_attr failed"); + if (copy_refs_attr(grp_in, grp_out, travt, fidout) < 0) + H5TOOLS_GOTO_ERROR((-1), "copy_refs_attr failed"); - if(H5Gclose(grp_out) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed"); - if(H5Gclose(grp_in) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed"); + if (H5Gclose(grp_out) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Gclose failed"); + if (H5Gclose(grp_in) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Gclose failed"); /*------------------------------------------------------------------------- * check for hard links *------------------------------------------------------------------------- */ - if(travt->objs[i].nlinks) - for(j = 0; j < travt->objs[i].nlinks; j++) - H5Lcreate_hard(fidout, travt->objs[i].name, H5L_SAME_LOC, travt->objs[i].links[j].new_name, H5P_DEFAULT, H5P_DEFAULT); + if (travt->objs[i].nlinks) + for (j = 0; j < travt->objs[i].nlinks; j++) + H5Lcreate_hard(fidout, travt->objs[i].name, H5L_SAME_LOC, + travt->objs[i].links[j].new_name, H5P_DEFAULT, H5P_DEFAULT); break; /*------------------------------------------------------------------------- @@ -103,27 +100,27 @@ int do_copy_refobjs(hid_t fidin, *------------------------------------------------------------------------- */ case H5TRAV_TYPE_DATASET: - if((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed"); - if((space_id = H5Dget_space(dset_in)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed"); - if((ftype_id = H5Dget_type(dset_in)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_type failed"); - if((dcpl_id = H5Dget_create_plist(dset_in)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed"); - if((rank = H5Sget_simple_extent_ndims(space_id)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed"); - if(H5Sget_simple_extent_dims(space_id, dims, NULL) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed"); + if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dopen2 failed"); + if ((space_id = H5Dget_space(dset_in)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dget_space failed"); + if ((ftype_id = H5Dget_type(dset_in)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dget_type failed"); + if ((dcpl_id = H5Dget_create_plist(dset_in)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dget_create_plist failed"); + if ((rank = H5Sget_simple_extent_ndims(space_id)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Sget_simple_extent_ndims failed"); + if (H5Sget_simple_extent_dims(space_id, dims, NULL) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Sget_simple_extent_dims failed"); nelmts = 1; - for(k = 0; k < rank; k++) + for (k = 0; k < rank; k++) nelmts *= dims[k]; - if((mtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_native_type failed"); + if ((mtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Tget_native_type failed"); - if((msize = H5Tget_size(mtype_id)) == 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed"); + if ((msize = H5Tget_size(mtype_id)) == 0) + H5TOOLS_GOTO_ERROR((-1), "H5Tget_size failed"); /*------------------------------------------------------------------------- * check if the dataset creation property list has filters that @@ -132,7 +129,7 @@ int do_copy_refobjs(hid_t fidin, * 2) the internal filters might be turned off *------------------------------------------------------------------------- */ - if(h5tools_canreadf(NULL, dcpl_id) == 1) { + if (h5tools_canreadf(NULL, dcpl_id) == 1) { /*------------------------------------------------------------------------- * test for a valid output dataset *------------------------------------------------------------------------- @@ -144,207 +141,220 @@ int do_copy_refobjs(hid_t fidin, * we cannot just copy the buffers, but instead we recreate the reference *------------------------------------------------------------------------- */ - if(H5Tequal(mtype_id, H5T_STD_REF_OBJ)) { - hid_t refobj_id = -1; - hobj_ref_t *refbuf = NULL; /* buffer for object references */ - hobj_ref_t *buf = NULL; - const char* refname; - unsigned u; + if (H5Tequal(mtype_id, H5T_STD_REF_OBJ)) { + hid_t refobj_id = H5I_INVALID_HID; + hobj_ref_t *refbuf = NULL; /* buffer for object references */ + hobj_ref_t *buf = NULL; + const char *refname; + unsigned u; /*------------------------------------------------------------------------- * read to memory *------------------------------------------------------------------------- */ - if(nelmts) { + if (nelmts) { buf = (hobj_ref_t *)HDmalloc((unsigned)(nelmts * msize)); - if(buf==NULL) { - HDprintf("cannot read into memory\n" ); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed"); + if (buf == NULL) { + HDprintf("cannot read into memory\n"); + H5TOOLS_GOTO_ERROR((-1), "HDmalloc failed"); } /* end if */ - if(H5Dread(dset_in, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed"); + if (H5Dread(dset_in, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dread failed"); - refbuf = (hobj_ref_t*) HDcalloc((unsigned)nelmts, msize); - if(refbuf == NULL){ - HDprintf("cannot allocate memory\n" ); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDcalloc failed"); + refbuf = (hobj_ref_t *)HDcalloc((unsigned)nelmts, msize); + if (refbuf == NULL) { + HDprintf("cannot allocate memory\n"); + H5TOOLS_GOTO_ERROR((-1), "HDcalloc failed"); } /* end if */ - for(u = 0; u < nelmts; u++) { - H5E_BEGIN_TRY { - if((refobj_id = H5Rdereference2(dset_in, H5P_DEFAULT, H5R_OBJECT, &buf[u])) < 0) + for (u = 0; u < nelmts; u++) { + H5E_BEGIN_TRY + { + if ((refobj_id = + H5Rdereference2(dset_in, H5P_DEFAULT, H5R_OBJECT, &buf[u])) < 0) continue; - } H5E_END_TRY; + } + H5E_END_TRY; /* get the name. a valid name could only occur * in the second traversal of the file */ - if((refname = MapIdToName(refobj_id, travt)) != NULL) { + if ((refname = MapIdToName(refobj_id, travt)) != NULL) { /* create the reference, -1 parameter for objects */ - if(H5Rcreate(&refbuf[u], fidout, refname, H5R_OBJECT, (hid_t)-1) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rcreate failed"); - if(options->verbose) { - HDprintf(FORMAT_OBJ,"dset",travt->objs[i].name ); + if (H5Rcreate(&refbuf[u], fidout, refname, H5R_OBJECT, (hid_t)-1) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Rcreate failed"); + if (options->verbose > 0) { + if (options->verbose == 2) + HDprintf(FORMAT_OBJ_NOTIME, "dset", travt->objs[i].name); + else + HDprintf(FORMAT_OBJ, "dset", travt->objs[i].name); HDprintf("object <%s> object reference created to <%s>\n", - travt->objs[i].name, - refname); + travt->objs[i].name, refname); } } /*refname*/ if (H5Oclose(refobj_id) < 0) - H5TOOLS_INFO(H5E_tools_min_id_g, "H5Oclose refob failed"); + H5TOOLS_ERROR((-1), "H5Oclose refob failed"); } /* u */ - } /*nelmts*/ + } /*nelmts*/ /*------------------------------------------------------------------------- * create/write dataset/close *------------------------------------------------------------------------- */ - if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, mtype_id, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dcreate2 failed"); - if(nelmts) - if(H5Dwrite(dset_out, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, refbuf) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dwrite failed"); - - if(buf) + if ((dset_out = H5Dcreate2(fidout, travt->objs[i].name, mtype_id, space_id, + H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dcreate2 failed"); + if (nelmts) + if (H5Dwrite(dset_out, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, refbuf) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dwrite failed"); + + if (buf) HDfree(buf); - if(refbuf) + if (refbuf) HDfree(refbuf); - /*------------------------------------------------------ - * copy attrs - *----------------------------------------------------*/ - if(copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed"); + /*------------------------------------------------------ + * copy attrs + *----------------------------------------------------*/ + if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0) + H5TOOLS_GOTO_ERROR((-1), "copy_attr failed"); } /*H5T_STD_REF_OBJ*/ /*------------------------------------------------------------------------- * dataset region references *------------------------------------------------------------------------- */ - else if(H5Tequal(mtype_id, H5T_STD_REF_DSETREG)) { - hid_t refobj_id = -1; - hdset_reg_ref_t *refbuf = NULL; /* input buffer for region references */ - hdset_reg_ref_t *buf = NULL; /* output buffer */ - const char* refname; + else if (H5Tequal(mtype_id, H5T_STD_REF_DSETREG)) { + hid_t refobj_id = H5I_INVALID_HID; + hdset_reg_ref_t *refbuf = NULL; /* input buffer for region references */ + hdset_reg_ref_t *buf = NULL; /* output buffer */ + const char * refname; unsigned u; /*------------------------------------------------------------------------- * read input to memory *------------------------------------------------------------------------- */ - if(nelmts) { + if (nelmts) { buf = (hdset_reg_ref_t *)HDmalloc((unsigned)(nelmts * msize)); - if(buf == NULL) { + if (buf == NULL) { HDprintf("cannot read into memory\n"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed"); + H5TOOLS_GOTO_ERROR((-1), "HDmalloc failed"); } /* end if */ - if(H5Dread(dset_in, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed"); + if (H5Dread(dset_in, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dread failed"); /*------------------------------------------------------------------------- * create output *------------------------------------------------------------------------- */ - refbuf = (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), (size_t)nelmts); /*init to zero */ - if(refbuf == NULL) { + refbuf = (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), + (size_t)nelmts); /*init to zero */ + if (refbuf == NULL) { HDprintf("cannot allocate memory\n"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDcalloc failed"); + H5TOOLS_GOTO_ERROR((-1), "HDcalloc failed"); } /* end if */ - for(u = 0; u < nelmts; u++) { - H5E_BEGIN_TRY { - if((refobj_id = H5Rdereference2(dset_in, H5P_DEFAULT, H5R_DATASET_REGION, &buf[u])) < 0) + for (u = 0; u < nelmts; u++) { + H5E_BEGIN_TRY + { + if ((refobj_id = H5Rdereference2(dset_in, H5P_DEFAULT, H5R_DATASET_REGION, + &buf[u])) < 0) continue; - } H5E_END_TRY; + } + H5E_END_TRY; /* get the name. a valid name could only occur * in the second traversal of the file */ - if((refname = MapIdToName(refobj_id, travt)) != NULL) { - hid_t region_id = -1; /* region id of the referenced dataset */ + if ((refname = MapIdToName(refobj_id, travt)) != NULL) { + hid_t region_id = + H5I_INVALID_HID; /* region id of the referenced dataset */ - if((region_id = H5Rget_region(dset_in, H5R_DATASET_REGION, &buf[u])) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rget_region failed"); + if ((region_id = H5Rget_region(dset_in, H5R_DATASET_REGION, &buf[u])) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Rget_region failed"); /* create the reference, we need the space_id */ - if(H5Rcreate(&refbuf[u], fidout, refname, H5R_DATASET_REGION, region_id) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rcreate failed"); - if(H5Sclose(region_id) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed"); - if(options->verbose) { - HDprintf(FORMAT_OBJ,"dset",travt->objs[i].name ); + if (H5Rcreate(&refbuf[u], fidout, refname, H5R_DATASET_REGION, + region_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Rcreate failed"); + if (H5Sclose(region_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Sclose failed"); + if (options->verbose > 0) { + HDprintf(FORMAT_OBJ, "dset", travt->objs[i].name); HDprintf("object <%s> region reference created to <%s>\n", - travt->objs[i].name, - refname); + travt->objs[i].name, refname); } } /*refname*/ if (H5Oclose(refobj_id) < 0) - H5TOOLS_INFO(H5E_tools_min_id_g, "H5Oclose refobj_id failed"); + H5TOOLS_ERROR((-1), "H5Oclose refobj_id failed"); } /* u */ - } /*nelmts*/ + } /*nelmts*/ /*------------------------------------------------------------------------- * create/write dataset/close *------------------------------------------------------------------------- */ - if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, mtype_id, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dcreate2 failed"); - if(nelmts) - if(H5Dwrite(dset_out, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, refbuf) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dwrite failed"); - - if(buf) + if ((dset_out = H5Dcreate2(fidout, travt->objs[i].name, mtype_id, space_id, + H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dcreate2 failed"); + if (nelmts) + if (H5Dwrite(dset_out, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, refbuf) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dwrite failed"); + + if (buf) HDfree(buf); - if(refbuf) + if (refbuf) HDfree(refbuf); - /*----------------------------------------------------- - * copy attrs - *----------------------------------------------------*/ - if(copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed"); + /*----------------------------------------------------- + * copy attrs + *----------------------------------------------------*/ + if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0) + H5TOOLS_GOTO_ERROR((-1), "copy_attr failed"); } /* H5T_STD_REF_DSETREG */ /*------------------------------------------------------------------------- * not references, open previously created object in 1st traversal *------------------------------------------------------------------------- */ else { - if((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed"); + if ((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dopen2 failed"); } /* end else */ /*------------------------------------------------------------------------- * copy referenced objects in attributes *------------------------------------------------------------------------- */ - if(copy_refs_attr(dset_in, dset_out, travt, fidout) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_refs_attr failed"); + if (copy_refs_attr(dset_in, dset_out, travt, fidout) < 0) + H5TOOLS_GOTO_ERROR((-1), "copy_refs_attr failed"); /*------------------------------------------------------------------------- * check for hard links *------------------------------------------------------------------------- */ - if(travt->objs[i].nlinks) - for(j = 0; j < travt->objs[i].nlinks; j++) - H5Lcreate_hard(fidout, travt->objs[i].name, H5L_SAME_LOC, travt->objs[i].links[j].new_name, H5P_DEFAULT, H5P_DEFAULT); + if (travt->objs[i].nlinks) + for (j = 0; j < travt->objs[i].nlinks; j++) + H5Lcreate_hard(fidout, travt->objs[i].name, H5L_SAME_LOC, + travt->objs[i].links[j].new_name, H5P_DEFAULT, H5P_DEFAULT); - if(H5Dclose(dset_out) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); + if (H5Dclose(dset_out) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dclose failed"); } /*can_read*/ /*------------------------------------------------------------------------- * close *------------------------------------------------------------------------- */ - if(H5Tclose(ftype_id) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); - if(H5Tclose(mtype_id) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); - if(H5Pclose(dcpl_id) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); - if(H5Sclose(space_id) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed"); - if(H5Dclose(dset_in) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); + if (H5Tclose(ftype_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); + if (H5Tclose(mtype_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); + if (H5Pclose(dcpl_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); + if (H5Sclose(space_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Sclose failed"); + if (H5Dclose(dset_in) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dclose failed"); break; /*------------------------------------------------------------------------- @@ -352,10 +362,10 @@ int do_copy_refobjs(hid_t fidin, *------------------------------------------------------------------------- */ case H5TRAV_TYPE_NAMED_DATATYPE: - if((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Topen2 failed"); - if(H5Tclose(type_in) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); + if ((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Topen2 failed"); + if (H5Tclose(type_in) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); break; /*------------------------------------------------------------------------- @@ -368,24 +378,26 @@ int do_copy_refobjs(hid_t fidin, case H5TRAV_TYPE_UNKNOWN: case H5TRAV_TYPE_UDLINK: - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5TRAV invalid type"); + H5TOOLS_GOTO_ERROR((-1), "H5TRAV invalid type"); + break; default: break; } /* end switch */ - } /* end for */ + } /* end for */ /* Finalize (link) the stack of named datatypes (if any) * This function is paired with copy_named_datatype() which is called * in copy_attr(), so need to free. */ if (named_datatype_free(&named_dt_head, 0) < 0) - H5TOOLS_INFO(H5E_tools_min_id_g, "named_datatype_free failed"); + H5TOOLS_ERROR((-1), "named_datatype_free failed"); return ret_value; done: - H5E_BEGIN_TRY { + H5E_BEGIN_TRY + { H5Gclose(grp_in); H5Gclose(grp_out); H5Pclose(dcpl_id); @@ -396,12 +408,12 @@ done: H5Tclose(mtype_id); H5Tclose(type_in); named_datatype_free(&named_dt_head, 1); - } H5E_END_TRY; + } + H5E_END_TRY; return ret_value; } - /*------------------------------------------------------------------------- * Function: copy_refs_attr * @@ -424,96 +436,91 @@ done: *------------------------------------------------------------------------- */ -static int copy_refs_attr(hid_t loc_in, - hid_t loc_out, - trav_table_t *travt, - hid_t fidout) /* for saving references */ +static int +copy_refs_attr(hid_t loc_in, hid_t loc_out, trav_table_t *travt, hid_t fidout) /* for saving references */ { - int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ - hid_t attr_id = -1; /* attr ID */ - hid_t attr_out = -1; /* attr ID */ - hid_t space_id = -1; /* space ID */ - hid_t ftype_id = -1; /* file data type ID */ - hid_t mtype_id = -1; /* memory data type ID */ - size_t msize; /* memory size of type */ - hsize_t nelmts; /* number of elements in dataset */ - hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */ + hid_t attr_id = H5I_INVALID_HID; /* attr ID */ + hid_t attr_out = H5I_INVALID_HID; /* attr ID */ + hid_t space_id = H5I_INVALID_HID; /* space ID */ + hid_t ftype_id = H5I_INVALID_HID; /* file data type ID */ + hid_t mtype_id = H5I_INVALID_HID; /* memory data type ID */ + size_t msize; /* memory size of type */ + hsize_t nelmts; /* number of elements in dataset */ + hsize_t dims[H5S_MAX_RANK]; /* dimensions of dataset */ char name[255]; - H5O_info_t oinfo; /* Object info */ + H5O_info2_t oinfo; /* Object info */ unsigned u, i, j; int rank; H5T_class_t type_class = -1; - hbool_t is_ref = 0, - is_ref_vlen = 0, - is_ref_array = 0, - is_ref_comp = 0; - void *refbuf = NULL; - void *buf = NULL; - unsigned *ref_comp_index = NULL; - size_t *ref_comp_size = NULL; + hbool_t is_ref = 0, is_ref_vlen = 0, is_ref_array = 0, is_ref_comp = 0; + void * refbuf = NULL; + void * buf = NULL; + unsigned * ref_comp_index = NULL; + size_t * ref_comp_size = NULL; int ref_comp_field_n = 0; + int ret_value = 0; + if (H5Oget_info3(loc_in, &oinfo, H5O_INFO_NUM_ATTRS) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Oget_info failed"); - if(H5Oget_info2(loc_in, &oinfo, H5O_INFO_NUM_ATTRS) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Oget_info failed"); - - for(u = 0; u < (unsigned)oinfo.num_attrs; u++) { + for (u = 0; u < (unsigned)oinfo.num_attrs; u++) { is_ref = is_ref_vlen = is_ref_array = is_ref_comp = 0; /* open attribute */ - if((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)u, H5P_DEFAULT, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aopen_by_idx failed"); + if ((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)u, H5P_DEFAULT, + H5P_DEFAULT)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Aopen_by_idx failed"); /* get the file datatype */ - if((ftype_id = H5Aget_type(attr_id)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aget_type failed"); + if ((ftype_id = H5Aget_type(attr_id)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Aget_type failed"); type_class = H5Tget_class(ftype_id); - if((mtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_native_type failed"); + if ((mtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Tget_native_type failed"); - if((msize = H5Tget_size(mtype_id)) == 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed"); + if ((msize = H5Tget_size(mtype_id)) == 0) + H5TOOLS_GOTO_ERROR((-1), "H5Tget_size failed"); is_ref = (type_class == H5T_REFERENCE); - if(type_class == H5T_VLEN ) { + if (type_class == H5T_VLEN) { hid_t base_type = H5Tget_super(ftype_id); is_ref_vlen = (H5Tget_class(base_type) == H5T_REFERENCE); - msize = H5Tget_size(base_type); + msize = H5Tget_size(base_type); if (H5Tclose(base_type) < 0) - H5TOOLS_INFO(H5E_tools_min_id_g, "H5Tclose base_type failed"); + H5TOOLS_ERROR((-1), "H5Tclose base_type failed"); } - else if(type_class == H5T_ARRAY ) { + else if (type_class == H5T_ARRAY) { hid_t base_type = H5Tget_super(ftype_id); is_ref_array = (H5Tget_class(base_type) == H5T_REFERENCE); - msize = H5Tget_size(base_type); + msize = H5Tget_size(base_type); if (H5Tclose(base_type) < 0) - H5TOOLS_INFO(H5E_tools_min_id_g, "H5Tclose base_type failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Tclose base_type failed"); } - else if(type_class == H5T_COMPOUND) { - int nmembers = H5Tget_nmembers(ftype_id) ; + else if (type_class == H5T_COMPOUND) { + int nmembers = H5Tget_nmembers(ftype_id); if (nmembers < 1) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_nmembers failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Tget_nmembers failed"); - ref_comp_index = (unsigned *)HDmalloc((size_t)nmembers*sizeof(unsigned)); - ref_comp_size = (size_t *)HDmalloc((size_t)nmembers*sizeof(ref_comp_size)); + ref_comp_index = (unsigned *)HDmalloc((size_t)nmembers * sizeof(unsigned)); + ref_comp_size = (size_t *)HDmalloc((size_t)nmembers * sizeof(ref_comp_size)); ref_comp_field_n = 0; - for (i=0; i<(unsigned)nmembers; i++) { + for (i = 0; i < (unsigned)nmembers; i++) { hid_t mtid = H5Tget_member_type(ftype_id, i); if ((H5Tget_class(mtid) == H5T_REFERENCE)) { ref_comp_index[ref_comp_field_n] = i; - ref_comp_size[ref_comp_field_n] = H5Tget_size(mtid); + ref_comp_size[ref_comp_field_n] = H5Tget_size(mtid); ref_comp_field_n++; } if (H5Tclose(mtid) < 0) - H5TOOLS_INFO(H5E_tools_min_id_g, "H5Tclose mtid failed"); + H5TOOLS_ERROR((-1), "H5Tclose mtid failed"); } /* if compound don't contain reference type member, free the above @@ -530,200 +537,214 @@ static int copy_refs_attr(hid_t loc_in, ref_comp_size = NULL; } } + /* This line below needs to be moved in this loop instead of inserting outside. Otherwise, + ref_comp_field_n may be >0 for the next attribute, which may not be + the reference type and will be accidentally treated as the reference type. + It will then cause the H5Acreate2 failed since that attribute is already created. + KY 2020-02-07 + */ + is_ref_comp = (ref_comp_field_n > 0); } - is_ref_comp = (ref_comp_field_n > 0); - if (!(is_ref || is_ref_vlen || is_ref_array || is_ref_comp)) { if (H5Tclose(mtype_id) < 0) - H5TOOLS_INFO(H5E_tools_min_id_g, "H5Tclose mtype_id failed"); + H5TOOLS_ERROR((-1), "H5Tclose mtype_id failed"); if (H5Tclose(ftype_id) < 0) - H5TOOLS_INFO(H5E_tools_min_id_g, "H5Tclose ftype_id failed"); + H5TOOLS_ERROR((-1), "H5Tclose ftype_id failed"); if (H5Aclose(attr_id) < 0) - H5TOOLS_INFO(H5E_tools_min_id_g, "H5Aclose attr_id failed"); + H5TOOLS_ERROR((-1), "H5Aclose attr_id failed"); continue; } /* get name */ - if(H5Aget_name(attr_id, 255, name) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aget_name failed"); + if (H5Aget_name(attr_id, 255, name) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Aget_name failed"); /* get the dataspace handle */ - if((space_id = H5Aget_space(attr_id)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aget_space failed"); + if ((space_id = H5Aget_space(attr_id)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Aget_space failed"); /* get dimensions */ - if((rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed"); - + if ((rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Sget_simple_extent_dims failed"); /*------------------------------------------------------------------------- - * elements - *------------------------------------------------------------------------- - */ + * elements + *------------------------------------------------------------------------- + */ nelmts = 1; - for(j = 0; j < (unsigned)rank; j++) + for (j = 0; j < (unsigned)rank; j++) nelmts *= dims[j]; if (is_ref_array) { - unsigned array_rank = 0; - hsize_t array_size = 1; - hsize_t array_dims[H5S_MAX_RANK]; - hid_t base_type = H5Tget_super(ftype_id); + unsigned array_rank = 0; + hsize_t array_size = 1; + hsize_t array_dims[H5S_MAX_RANK]; + hid_t base_type = H5Tget_super(ftype_id); msize = H5Tget_size(base_type); if (H5Tclose(base_type) < 0) - H5TOOLS_INFO(H5E_tools_min_id_g, "H5Tclose base_type failed"); + H5TOOLS_ERROR((-1), "H5Tclose base_type failed"); array_rank = (unsigned)H5Tget_array_ndims(mtype_id); H5Tget_array_dims2(mtype_id, array_dims); - for(j = 0; j <array_rank; j++) + for (j = 0; j < array_rank; j++) array_size *= array_dims[j]; nelmts *= array_size; } - if((attr_out = H5Acreate2(loc_out, name, ftype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Acreate2 failed"); + if ((attr_out = H5Acreate2(loc_out, name, ftype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Acreate2 failed"); - if (nelmts>0) { + if (nelmts > 0) { /* handle object references */ - if((is_ref || is_ref_array) && (H5R_OBJ_REF_BUF_SIZE==msize)) { + if ((is_ref || is_ref_array) && (H5R_OBJ_REF_BUF_SIZE == msize)) { buf = (hobj_ref_t *)HDmalloc((unsigned)(nelmts * msize)); - if(buf == NULL) { + if (buf == NULL) { HDprintf("cannot read into memory\n"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed"); + H5TOOLS_GOTO_ERROR((-1), "HDmalloc failed"); } /* end if */ - if(H5Aread(attr_id, mtype_id, buf) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread failed"); + if (H5Aread(attr_id, mtype_id, buf) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Aread failed"); refbuf = (hobj_ref_t *)HDcalloc((unsigned)nelmts, msize); - if(refbuf == NULL) { + if (refbuf == NULL) { HDprintf("cannot allocate memory\n"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDcalloc failed"); + H5TOOLS_GOTO_ERROR((-1), "HDcalloc failed"); } /* end if */ - for(i = 0; i < (unsigned)nelmts; i++) - if(update_ref_value(attr_id, H5R_OBJECT, &((hobj_ref_t *)buf)[i], fidout, &((hobj_ref_t *)refbuf)[i], travt) < 0) + for (i = 0; i < (unsigned)nelmts; i++) + if (update_ref_value(attr_id, H5R_OBJECT, &((hobj_ref_t *)buf)[i], fidout, + &((hobj_ref_t *)refbuf)[i], travt) < 0) continue; } /* H5T_STD_REF_OBJ */ /* handle region references */ - else if((is_ref || is_ref_array) && (H5R_DSET_REG_REF_BUF_SIZE == msize)) { + else if ((is_ref || is_ref_array) && (H5R_DSET_REG_REF_BUF_SIZE == msize)) { buf = (hdset_reg_ref_t *)HDmalloc((unsigned)(nelmts * msize)); - if(buf == NULL) { - HDprintf( "cannot read into memory\n" ); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed"); + if (buf == NULL) { + HDprintf("cannot read into memory\n"); + H5TOOLS_GOTO_ERROR((-1), "HDmalloc failed"); } /* end if */ - if(H5Aread(attr_id, mtype_id, buf) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread failed"); + if (H5Aread(attr_id, mtype_id, buf) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Aread failed"); /*------------------------------------------------------------------------- * create output *------------------------------------------------------------------------- */ - refbuf = (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), (size_t)nelmts); /*init to zero */ - if(refbuf == NULL) { - HDprintf( "cannot allocate memory\n" ); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDcalloc failed"); + refbuf = + (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), (size_t)nelmts); /*init to zero */ + if (refbuf == NULL) { + HDprintf("cannot allocate memory\n"); + H5TOOLS_GOTO_ERROR((-1), "HDcalloc failed"); } /* end if */ - for(i = 0; i < (unsigned)nelmts; i++) - if(update_ref_value(attr_id, H5R_DATASET_REGION, &((hdset_reg_ref_t *)buf)[i], fidout, &((hdset_reg_ref_t *)refbuf)[i], travt) < 0) + for (i = 0; i < (unsigned)nelmts; i++) + if (update_ref_value(attr_id, H5R_DATASET_REGION, &((hdset_reg_ref_t *)buf)[i], fidout, + &((hdset_reg_ref_t *)refbuf)[i], travt) < 0) continue; } /* H5T_STD_REF_DSETREG */ else if (is_ref_vlen) { /* handle VLEN of references */ - buf = (hvl_t *)HDmalloc((unsigned)(nelmts * sizeof(hvl_t))); + buf = (hvl_t *)HDmalloc((unsigned)(nelmts * sizeof(hvl_t))); refbuf = buf; /* reuse the read buffer for write */ - if(buf == NULL) { - HDprintf( "cannot read into memory\n" ); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed"); + if (buf == NULL) { + HDprintf("cannot read into memory\n"); + H5TOOLS_GOTO_ERROR((-1), "HDmalloc failed"); } /* end if */ - if(H5Aread(attr_id, mtype_id, buf) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread failed"); + if (H5Aread(attr_id, mtype_id, buf) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Aread failed"); - if (H5R_OBJ_REF_BUF_SIZE==msize) { + if (H5R_OBJ_REF_BUF_SIZE == msize) { hobj_ref_t ref_out; - for (i=0; i<(unsigned)nelmts; i++) { + for (i = 0; i < (unsigned)nelmts; i++) { hobj_ref_t *ptr = (hobj_ref_t *)((hvl_t *)buf)[i].p; - for (j=0; j<((hvl_t *)buf)[i].len; j++ ) { - if (update_ref_value(attr_id, H5R_OBJECT, &(ptr[j]), fidout, &ref_out, travt)<0) + for (j = 0; j < ((hvl_t *)buf)[i].len; j++) { + if (update_ref_value(attr_id, H5R_OBJECT, &(ptr[j]), fidout, &ref_out, travt) < 0) continue; HDmemcpy(&(ptr[j]), &ref_out, msize); } - } /* for (i=0; i<nelems; i++) */ + } /* for (i=0; i<nelems; i++) */ } else if (H5R_DSET_REG_REF_BUF_SIZE == msize) { hdset_reg_ref_t ref_out; - for (i=0; i<(unsigned)nelmts; i++) { + for (i = 0; i < (unsigned)nelmts; i++) { hdset_reg_ref_t *ptr = (hdset_reg_ref_t *)((hvl_t *)buf)[i].p; - for (j=0; j<((hvl_t *)buf)[i].len; j++ ) { - if (update_ref_value(attr_id, H5R_DATASET_REGION, &(ptr[j]), fidout, &ref_out, travt)<0) + for (j = 0; j < ((hvl_t *)buf)[i].len; j++) { + if (update_ref_value(attr_id, H5R_DATASET_REGION, &(ptr[j]), fidout, &ref_out, + travt) < 0) continue; HDmemcpy(&(ptr[j]), &ref_out, msize); } - } /* for (i=0; i<nelems; i++) */ + } /* for (i=0; i<nelems; i++) */ } } /* else if (is_ref_vlen) */ else if (is_ref_comp) { /* handle ref fields in a compound */ - buf = HDmalloc((unsigned)(nelmts * msize)); + buf = HDmalloc((unsigned)(nelmts * msize)); refbuf = buf; /* reuse the read buffer for write */ - if(buf == NULL) { - HDprintf( "cannot read into memory\n" ); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed"); + if (buf == NULL) { + HDprintf("cannot read into memory\n"); + H5TOOLS_GOTO_ERROR((-1), "HDmalloc failed"); } /* end if */ - if(H5Aread(attr_id, mtype_id, buf) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread failed"); + if (H5Aread(attr_id, mtype_id, buf) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Aread failed"); - for (i=0; i<(unsigned)nelmts; i++) { - for (j=0; j<(unsigned)ref_comp_field_n; j++) { + for (i = 0; i < (unsigned)nelmts; i++) { + for (j = 0; j < (unsigned)ref_comp_field_n; j++) { if (ref_comp_size[j] == H5R_OBJ_REF_BUF_SIZE) { - size_t idx = (i * msize) + H5Tget_member_offset(mtype_id, ref_comp_index[j]); + size_t idx = (i * msize) + H5Tget_member_offset(mtype_id, ref_comp_index[j]); hobj_ref_t ref_out; - if (update_ref_value(attr_id, H5R_OBJECT, (hobj_ref_t *)((void *)(((char *)buf)+idx)), fidout, &ref_out, travt) < 0) /* Extra (void *) cast to quiet "cast to create alignment" warning - 2019/07/05, QAK */ + if (update_ref_value(attr_id, H5R_OBJECT, + (hobj_ref_t *)((void *)(((char *)buf) + idx)), fidout, + &ref_out, + travt) < 0) /* Extra (void *) cast to quiet "cast to create + alignment" warning - 2019/07/05, QAK */ continue; - HDmemcpy(((char *)buf)+idx, &ref_out, ref_comp_size[j]); + HDmemcpy(((char *)buf) + idx, &ref_out, ref_comp_size[j]); } /* if */ else if (ref_comp_size[j] == H5R_DSET_REG_REF_BUF_SIZE) { size_t idx = i * msize + H5Tget_member_offset(mtype_id, ref_comp_index[j]); hdset_reg_ref_t ref_out; - if (update_ref_value(attr_id, H5R_DATASET_REGION, (hdset_reg_ref_t *)(((char *)buf)+idx), fidout, &ref_out, travt)<0) + if (update_ref_value(attr_id, H5R_DATASET_REGION, + (hdset_reg_ref_t *)(((char *)buf) + idx), fidout, &ref_out, + travt) < 0) continue; - HDmemcpy(((char *)buf)+idx, &ref_out, ref_comp_size[j]); + HDmemcpy(((char *)buf) + idx, &ref_out, ref_comp_size[j]); } /* else if */ - } /* j */ - } /* i */ - } /* else if (is_ref_comp) */ + } /* j */ + } /* i */ + } /* else if (is_ref_comp) */ - if(H5Awrite(attr_out, mtype_id, refbuf) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Awrite failed"); + if (H5Awrite(attr_out, mtype_id, refbuf) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Awrite failed"); if (is_ref_vlen && buf) - H5Dvlen_reclaim (mtype_id, space_id, H5P_DEFAULT, buf); + H5Treclaim(mtype_id, space_id, H5P_DEFAULT, buf); } /* if (nelmts) */ if (refbuf == buf) refbuf = NULL; /* set it to NULL to avoid double free since buf and refbuf are the same. */ - if(buf) { + if (buf) { HDfree(buf); buf = NULL; } - if(refbuf) { + if (refbuf) { HDfree(refbuf); refbuf = NULL; } @@ -738,27 +759,27 @@ static int copy_refs_attr(hid_t loc_in, ref_comp_size = NULL; } - if(H5Aclose(attr_out) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aclose failed"); + if (H5Aclose(attr_out) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Aclose failed"); /*------------------------------------------------------------------------- - * close - *------------------------------------------------------------------------- - */ - if(H5Tclose(ftype_id) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); - if(H5Tclose(mtype_id) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); - if(H5Sclose(space_id) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed"); - if(H5Aclose(attr_id) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aclose failed"); + * close + *------------------------------------------------------------------------- + */ + if (H5Tclose(ftype_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); + if (H5Tclose(mtype_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); + if (H5Sclose(space_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Sclose failed"); + if (H5Aclose(attr_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Aclose failed"); } /* for(u = 0; u < (unsigned)oinfo.num_attrs; u++) */ done: - if(refbuf) + if (refbuf) HDfree(refbuf); - if(buf) + if (buf) HDfree(buf); if (ref_comp_index) @@ -767,13 +788,15 @@ done: if (ref_comp_size) HDfree(ref_comp_size); - H5E_BEGIN_TRY { + H5E_BEGIN_TRY + { H5Tclose(ftype_id); H5Tclose(mtype_id); H5Sclose(space_id); H5Aclose(attr_id); H5Aclose(attr_out); - } H5E_END_TRY; + } + H5E_END_TRY; return ret_value; } @@ -785,29 +808,32 @@ done: * *------------------------------------------------------------------------- */ -static const char* +static const char * MapIdToName(hid_t refobj_id, trav_table_t *travt) { unsigned int u; - const char *ret = NULL; + const char * ret = NULL; /* linear search */ - for(u = 0; u < travt->nobjs; u++) { - if(travt->objs[u].type == (h5trav_type_t)H5O_TYPE_DATASET || - travt->objs[u].type == (h5trav_type_t)H5O_TYPE_GROUP || - travt->objs[u].type == (h5trav_type_t)H5O_TYPE_NAMED_DATATYPE) { - H5O_info_t ref_oinfo; /* Stat for the refobj id */ + for (u = 0; u < travt->nobjs; u++) { + if (travt->objs[u].type == (h5trav_type_t)H5O_TYPE_DATASET || + travt->objs[u].type == (h5trav_type_t)H5O_TYPE_GROUP || + travt->objs[u].type == (h5trav_type_t)H5O_TYPE_NAMED_DATATYPE) { + H5O_info2_t ref_oinfo; /* Stat for the refobj id */ + int token_cmp; /* obtain information to identify the referenced object uniquely */ - if(H5Oget_info2(refobj_id, &ref_oinfo, H5O_INFO_BASIC) < 0) + if (H5Oget_info3(refobj_id, &ref_oinfo, H5O_INFO_BASIC) < 0) goto out; - if(ref_oinfo.addr == travt->objs[u].objno) { + if (H5Otoken_cmp(refobj_id, &ref_oinfo.token, &travt->objs[u].obj_token, &token_cmp) < 0) + goto out; + if (!token_cmp) { ret = travt->objs[u].name; goto out; - } /* end if */ - } /* end if */ - } /* u */ + } + } /* end if */ + } /* u */ out: return ret; @@ -819,37 +845,39 @@ out: * Purpose: Update a reference value *------------------------------------------------------------------------- */ -static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in, - hid_t fid_out, void *ref_out, trav_table_t *travt) +static herr_t +update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in, hid_t fid_out, void *ref_out, + trav_table_t *travt) { - int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ const char *ref_obj_name; - hid_t space_id = -1; - hid_t ref_obj_id = -1; + hid_t space_id = H5I_INVALID_HID; + hid_t ref_obj_id = H5I_INVALID_HID; + herr_t ret_value = SUCCEED; ref_obj_id = H5Rdereference2(obj_id, H5P_DEFAULT, ref_type, ref_in); if (ref_obj_id < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rdereference2 failed"); + H5TOOLS_GOTO_ERROR(FAIL, "H5Rdereference2 failed"); ref_obj_name = MapIdToName(ref_obj_id, travt); if (ref_obj_name == NULL) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "MapIdToName failed"); + H5TOOLS_GOTO_ERROR(FAIL, "MapIdToName failed"); if (ref_type == H5R_DATASET_REGION) { space_id = H5Rget_region(obj_id, H5R_DATASET_REGION, ref_in); if (space_id < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rget_region failed"); + H5TOOLS_GOTO_ERROR(FAIL, "H5Rget_region failed"); } - if(H5Rcreate(ref_out, fid_out, ref_obj_name, ref_type, space_id) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rcreate failed"); + if (H5Rcreate(ref_out, fid_out, ref_obj_name, ref_type, space_id) < 0) + H5TOOLS_GOTO_ERROR(FAIL, "H5Rcreate failed"); done: - H5E_BEGIN_TRY { - H5Sclose(space_id); - H5Oclose(ref_obj_id); - } H5E_END_TRY; + H5E_BEGIN_TRY + { + H5Sclose(space_id); + H5Oclose(ref_obj_id); + } + H5E_END_TRY; return ret_value; } - diff --git a/tools/src/h5repack/h5repack_verify.c b/tools/src/h5repack/h5repack_verify.c index dbe8e1a..71ee72e 100644 --- a/tools/src/h5repack/h5repack_verify.c +++ b/tools/src/h5repack/h5repack_verify.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -17,13 +17,12 @@ /* number of members in an array */ #ifndef NELMTS -# define NELMTS(X) (sizeof(X)/sizeof(X[0])) +#define NELMTS(X) (sizeof(X) / sizeof(X[0])) #endif static int verify_layout(hid_t pid, pack_info_t *obj); static int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter); - /*------------------------------------------------------------------------- * Function: h5repack_verify * @@ -39,193 +38,195 @@ static int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *fil int h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options) { - int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ - hid_t fidin = -1; /* file ID for input file*/ - hid_t fidout = -1; /* file ID for output file*/ - hid_t did = -1; /* dataset ID */ - hid_t pid = -1; /* dataset creation property list ID */ - hid_t sid = -1; /* space ID */ - hid_t tid = -1; /* type ID */ - int ok = 1; /* step results */ - unsigned int i; - trav_table_t *travt = NULL; - hid_t fcpl_in = -1; /* file creation property for input file */ - hid_t fcpl_out = -1; /* file creation property for output file */ - H5F_fspace_strategy_t in_strategy, out_strategy; /* file space handling strategy for in/output file */ - hbool_t in_persist, out_persist; /* free-space persist status for in/output file */ - hsize_t in_threshold, out_threshold; /* free-space section threshold for in/output file */ - hsize_t in_pagesize, out_pagesize; /* file space page size for input/output file */ + hid_t fidin = H5I_INVALID_HID; /* file ID for input file*/ + hid_t fidout = H5I_INVALID_HID; /* file ID for output file*/ + hid_t did = H5I_INVALID_HID; /* dataset ID */ + hid_t pid = H5I_INVALID_HID; /* dataset creation property list ID */ + hid_t sid = H5I_INVALID_HID; /* space ID */ + hid_t tid = H5I_INVALID_HID; /* type ID */ + int ok = 1; /* step results */ + unsigned int i; + trav_table_t * travt = NULL; + hid_t fcpl_in = H5I_INVALID_HID; /* file creation property for input file */ + hid_t fcpl_out = H5I_INVALID_HID; /* file creation property for output file */ + H5F_fspace_strategy_t in_strategy, out_strategy; /* file space handling strategy for in/output file */ + hbool_t in_persist, out_persist; /* free-space persist status for in/output file */ + hsize_t in_threshold, out_threshold; /* free-space section threshold for in/output file */ + hsize_t in_pagesize, out_pagesize; /* file space page size for input/output file */ + int ret_value = 0; /* open the output file */ - if((fidout = H5Fopen(out_fname, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0 ) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fopen failed on <%s>", out_fname); - - for(i = 0; i < options->op_tbl->nelems; i++) { - char *name = options->op_tbl->objs[i].path; - pack_info_t *obj = &options->op_tbl->objs[i]; - - /*------------------------------------------------------------------------- - * open - *------------------------------------------------------------------------- - */ - if((did = H5Dopen2(fidout, name, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed on <%s>", name); - if((sid = H5Dget_space(did)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed"); - if((pid = H5Dget_create_plist(did)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed"); - if((tid = H5Dget_type(did)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_type failed"); - - /*------------------------------------------------------------------------- - * filter check - *------------------------------------------------------------------------- - */ - if(verify_filters(pid, tid, obj->nfilters, obj->filter) <= 0) + if ((fidout = H5Fopen(out_fname, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Fopen failed on <%s>", out_fname); + + for (i = 0; i < options->op_tbl->nelems; i++) { + char * name = options->op_tbl->objs[i].path; + pack_info_t *obj = &options->op_tbl->objs[i]; + + /*------------------------------------------------------------------------- + * open + *------------------------------------------------------------------------- + */ + if ((did = H5Dopen2(fidout, name, H5P_DEFAULT)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dopen2 failed on <%s>", name); + if ((sid = H5Dget_space(did)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dget_space failed"); + if ((pid = H5Dget_create_plist(did)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dget_create_plist failed"); + if ((tid = H5Dget_type(did)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dget_type failed"); + + /*------------------------------------------------------------------------- + * filter check + *------------------------------------------------------------------------- + */ + if (verify_filters(pid, tid, obj->nfilters, obj->filter) <= 0) ok = 0; - /*------------------------------------------------------------------------- - * layout check - *------------------------------------------------------------------------- - */ - if((obj->layout != -1) && (verify_layout(pid, obj) == 0)) + /*------------------------------------------------------------------------- + * layout check + *------------------------------------------------------------------------- + */ + if ((obj->layout != -1) && (verify_layout(pid, obj) == 0)) ok = 0; - /*------------------------------------------------------------------------- - * close - *------------------------------------------------------------------------- - */ - if(H5Pclose(pid) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + /*------------------------------------------------------------------------- + * close + *------------------------------------------------------------------------- + */ + if (H5Pclose(pid) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); if (H5Sclose(sid) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Sclose failed"); if (H5Dclose(did) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Dclose failed"); if (H5Tclose(tid) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); } - /*------------------------------------------------------------------------- - * check for the "all" objects option - *------------------------------------------------------------------------- - */ + /*------------------------------------------------------------------------- + * check for the "all" objects option + *------------------------------------------------------------------------- + */ - if(options->all_filter == 1 || options->all_layout == 1) { + if (options->all_filter == 1 || options->all_layout == 1) { /* Initialize indexing options */ h5trav_set_index(sort_by, sort_order); /* init table */ - trav_table_init(&travt); + trav_table_init(fidout, &travt); /* get the list of objects in the file */ - if(h5trav_gettable(fidout, travt) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5trav_gettable failed"); + if (h5trav_gettable(fidout, travt) < 0) + H5TOOLS_GOTO_ERROR((-1), "h5trav_gettable failed"); - for(i = 0; i < travt->nobjs; i++) { + for (i = 0; i < travt->nobjs; i++) { char *name = travt->objs[i].name; - if(travt->objs[i].type == H5TRAV_TYPE_DATASET) { - /*------------------------------------------------------------------------- - * open - *------------------------------------------------------------------------- - */ - if((did = H5Dopen2(fidout, name, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed on <%s>", name); - if((sid = H5Dget_space(did)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed"); - if((pid = H5Dget_create_plist(did)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed"); - if((tid = H5Dget_type(did)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_type failed"); - - /*------------------------------------------------------------------------- - * filter check - *------------------------------------------------------------------------- - */ - if(options->all_filter == 1) { - if(verify_filters(pid, tid, options->n_filter_g, options->filter_g) <= 0) + if (travt->objs[i].type == H5TRAV_TYPE_DATASET) { + /*------------------------------------------------------------------------- + * open + *------------------------------------------------------------------------- + */ + if ((did = H5Dopen2(fidout, name, H5P_DEFAULT)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dopen2 failed on <%s>", name); + if ((sid = H5Dget_space(did)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dget_space failed"); + if ((pid = H5Dget_create_plist(did)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dget_create_plist failed"); + if ((tid = H5Dget_type(did)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dget_type failed"); + + /*------------------------------------------------------------------------- + * filter check + *------------------------------------------------------------------------- + */ + if (options->all_filter == 1) { + if (verify_filters(pid, tid, options->n_filter_g, options->filter_g) <= 0) ok = 0; } - /*------------------------------------------------------------------------- - * layout check - *------------------------------------------------------------------------- - */ - if(options->all_layout == 1) { + /*------------------------------------------------------------------------- + * layout check + *------------------------------------------------------------------------- + */ + if (options->all_layout == 1) { pack_info_t pack; init_packobject(&pack); pack.layout = options->layout_g; - pack.chunk = options->chunk_g; - if(verify_layout(pid, &pack) == 0) + pack.chunk = options->chunk_g; + if (verify_layout(pid, &pack) == 0) ok = 0; } - /*------------------------------------------------------------------------- - * close - *------------------------------------------------------------------------- - */ + /*------------------------------------------------------------------------- + * close + *------------------------------------------------------------------------- + */ if (H5Pclose(pid) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); if (H5Sclose(sid) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Sclose failed"); if (H5Dclose(did) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Dclose failed"); if (H5Tclose(tid) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); } /* if */ - } /* i */ + } /* i */ /* free table */ trav_table_free(travt); travt = NULL; } - /*------------------------------------------------------------------------- - * Verify that file space info are set as expected - *------------------------------------------------------------------------- - */ + /*------------------------------------------------------------------------- + * Verify that file space info are set as expected + *------------------------------------------------------------------------- + */ /* open the input file */ - if((fidin = H5Fopen(in_fname, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fopen failed on file <%s>", in_fname); + if ((fidin = H5Fopen(in_fname, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Fopen failed on file <%s>", in_fname); /* Get file creation property list for input file */ - if((fcpl_in = H5Fget_create_plist(fidin)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fget_create_plist failed to retrieve file creation property list"); + if ((fcpl_in = H5Fget_create_plist(fidin)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Fget_create_plist failed to retrieve file creation property list"); /* Get file space info for input file */ - if(H5Pget_file_space_strategy(fcpl_in, &in_strategy, &in_persist, &in_threshold) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_file_space_strategy failed to retrieve file space strategy & threshold"); + if (H5Pget_file_space_strategy(fcpl_in, &in_strategy, &in_persist, &in_threshold) < 0) + H5TOOLS_GOTO_ERROR((-1), + "H5Pget_file_space_strategy failed to retrieve file space strategy & threshold"); /* Get file space page size for input file */ - if(H5Pget_file_space_page_size(fcpl_in, &in_pagesize) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_file_space_page_size failed to retrieve file space page size"); + if (H5Pget_file_space_page_size(fcpl_in, &in_pagesize) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pget_file_space_page_size failed to retrieve file space page size"); /* Output file is already opened */ /* Get file creation property list for output file */ - if((fcpl_out = H5Fget_create_plist(fidout)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fget_create_plist failed to retrieve file creation property list"); + if ((fcpl_out = H5Fget_create_plist(fidout)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Fget_create_plist failed to retrieve file creation property list"); /* Get file space info for output file */ - if(H5Pget_file_space_strategy(fcpl_out, &out_strategy, &out_persist, &out_threshold) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_file_space_strategy failed to retrieve file space strategy & threshold"); + if (H5Pget_file_space_strategy(fcpl_out, &out_strategy, &out_persist, &out_threshold) < 0) + H5TOOLS_GOTO_ERROR((-1), + "H5Pget_file_space_strategy failed to retrieve file space strategy & threshold"); /* Get file space page size for output file */ - if(H5Pget_file_space_page_size(fcpl_out, &out_pagesize) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_file_space_page_size failed to retrieve file space page size"); + if (H5Pget_file_space_page_size(fcpl_out, &out_pagesize) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pget_file_space_page_size failed to retrieve file space page size"); /* * If -S option is set, the file space handling strategy should be set as specified. * If -S option is not set, the file space handling strategy should be * the same as the input file's strategy. */ - if(options->fs_strategy) { - if(out_strategy != (options->fs_strategy == (H5F_fspace_strategy_t)-1 ? 0 : options->fs_strategy)) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "file space strategy not set as unexpected"); + if (options->fs_strategy) { + if (out_strategy != (options->fs_strategy == (H5F_fspace_strategy_t)-1 ? 0 : options->fs_strategy)) + H5TOOLS_GOTO_ERROR((-1), "file space strategy not set as unexpected"); } else { - if(out_strategy != in_strategy) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "file space strategy not set as unexpected"); + if (out_strategy != in_strategy) + H5TOOLS_GOTO_ERROR((-1), "file space strategy not set as unexpected"); } /* @@ -233,13 +234,13 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options * If the -P option is not set, the free-space persist status should be * the same as the input file's free-space persist status */ - if(options->fs_persist) { - if(out_persist != (hbool_t)(options->fs_persist == (-1) ? FALSE : options->fs_persist)) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "free-space persist status not set as unexpected"); + if (options->fs_persist) { + if (out_persist != (hbool_t)(options->fs_persist == (-1) ? FALSE : options->fs_persist)) + H5TOOLS_GOTO_ERROR((-1), "free-space persist status not set as unexpected"); } else { - if(out_persist != in_persist) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "free-space persist status not set as unexpected"); + if (out_persist != in_persist) + H5TOOLS_GOTO_ERROR((-1), "free-space persist status not set as unexpected"); } /* @@ -247,13 +248,13 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options * If the -T option is not set, the threshold should be the same as the * input file's threshold size. */ - if(options->fs_threshold) { - if(out_threshold != (hsize_t)(options->fs_threshold == (-1) ? 0 : options->fs_threshold)) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "threshold not set as unexpected"); + if (options->fs_threshold) { + if (out_threshold != (hsize_t)(options->fs_threshold == (-1) ? 0 : options->fs_threshold)) + H5TOOLS_GOTO_ERROR((-1), "threshold not set as unexpected"); } else { - if(out_threshold != in_threshold) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "threshold not set as unexpected"); + if (out_threshold != in_threshold) + H5TOOLS_GOTO_ERROR((-1), "threshold not set as unexpected"); } /* @@ -261,20 +262,20 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options * If the -G option is not set, the file space page size should be * the same as the input file's file space page size. */ - if(options->fs_pagesize) { - if(out_pagesize != (hsize_t)(options->fs_pagesize == (-1) ? 0 : options->fs_pagesize)) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "file space page size not set as unexpected"); + if (options->fs_pagesize) { + if (out_pagesize != (hsize_t)(options->fs_pagesize == (-1) ? 0 : options->fs_pagesize)) + H5TOOLS_GOTO_ERROR((-1), "file space page size not set as unexpected"); } else { /* "-G" is not set */ - if(out_pagesize != in_pagesize) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "file space page size not set as unexpected"); - + if (out_pagesize != in_pagesize) + H5TOOLS_GOTO_ERROR((-1), "file space page size not set as unexpected"); } ret_value = ok; done: - H5E_BEGIN_TRY { + H5E_BEGIN_TRY + { H5Pclose(fcpl_in); H5Pclose(fcpl_out); H5Pclose(pid); @@ -285,7 +286,8 @@ done: H5Fclose(fidout); if (travt) trav_table_free(travt); - } H5E_END_TRY; + } + H5E_END_TRY; return ret_value; } /* h5repack_verify() */ @@ -305,13 +307,14 @@ done: *------------------------------------------------------------------------- */ -int verify_layout(hid_t pid, pack_info_t *obj) +int +verify_layout(hid_t pid, pack_info_t *obj) { - hsize_t chsize[64]; /* chunk size in elements */ - H5D_layout_t layout; /* layout */ - int nfilters; /* number of filters */ - int rank; /* rank */ - int i; /* index */ + hsize_t chsize[64]; /* chunk size in elements */ + H5D_layout_t layout; /* layout */ + int nfilters; /* number of filters */ + int rank; /* rank */ + int i; /* index */ /* check if we have filters in the input object */ if ((nfilters = H5Pget_nfilters(pid)) < 0) @@ -328,8 +331,8 @@ int verify_layout(hid_t pid, pack_info_t *obj) if (obj->layout != layout) return 0; - if (layout==H5D_CHUNKED) { - if ((rank = H5Pget_chunk(pid, NELMTS(chsize), chsize/*out*/)) < 0) + if (layout == H5D_CHUNKED) { + if ((rank = H5Pget_chunk(pid, NELMTS(chsize), chsize /*out*/)) < 0) return -1; if (obj->chunk.rank != rank) return 0; @@ -353,108 +356,111 @@ int verify_layout(hid_t pid, pack_info_t *obj) *------------------------------------------------------------------------- */ -int h5repack_cmp_pl(const char *fname1, const char *fname2) +int +h5repack_cmp_pl(const char *fname1, hid_t fname1_fapl, const char *fname2, hid_t fname2_fapl) { - int ret_value = 1; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ - hid_t fid1 =-1; /* file ID */ - hid_t fid2 =-1; /* file ID */ - hid_t dset1 =-1; /* dataset ID */ - hid_t dset2 =-1; /* dataset ID */ - hid_t gid =-1; /* group ID */ - hid_t dcpl1 =-1; /* dataset creation property list ID */ - hid_t dcpl2 =-1; /* dataset creation property list ID */ - hid_t gcplid =-1; /* group creation property list */ - unsigned crt_order_flag1; /* group creation order flag */ - unsigned crt_order_flag2; /* group creation order flag */ - trav_table_t *trav = NULL; + hid_t fid1 = H5I_INVALID_HID; /* file ID */ + hid_t fid2 = H5I_INVALID_HID; /* file ID */ + hid_t dset1 = H5I_INVALID_HID; /* dataset ID */ + hid_t dset2 = H5I_INVALID_HID; /* dataset ID */ + hid_t gid = H5I_INVALID_HID; /* group ID */ + hid_t dcpl1 = H5I_INVALID_HID; /* dataset creation property list ID */ + hid_t dcpl2 = H5I_INVALID_HID; /* dataset creation property list ID */ + hid_t gcplid = H5I_INVALID_HID; /* group creation property list */ + unsigned crt_order_flag1; /* group creation order flag */ + unsigned crt_order_flag2; /* group creation order flag */ + trav_table_t *trav = NULL; unsigned int i; + int ret_value = 1; - /*------------------------------------------------------------------------- - * open the files - *------------------------------------------------------------------------- - */ + /*------------------------------------------------------------------------- + * open the files + *------------------------------------------------------------------------- + */ /* Open the files */ - if ((fid1 = H5Fopen(fname1, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5tools_fopen failed <%s>: %s", fname1, H5FOPENERROR); - if ((fid2 = H5Fopen(fname2, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5tools_fopen failed <%s>: %s", fname2, H5FOPENERROR); - - /*------------------------------------------------------------------------- - * get file table list of objects - *------------------------------------------------------------------------- - */ + if ((fid1 = h5tools_fopen(fname1, H5F_ACC_RDONLY, fname1_fapl, (fname1_fapl != H5P_DEFAULT), NULL, 0)) < + 0) + H5TOOLS_GOTO_ERROR((-1), "h5tools_fopen failed <%s>: %s", fname1, H5FOPENERROR); + if ((fid2 = h5tools_fopen(fname2, H5F_ACC_RDONLY, fname2_fapl, (fname2_fapl != H5P_DEFAULT), NULL, 0)) < + 0) + H5TOOLS_GOTO_ERROR((-1), "h5tools_fopen failed <%s>: %s", fname2, H5FOPENERROR); + + /*------------------------------------------------------------------------- + * get file table list of objects + *------------------------------------------------------------------------- + */ /* Initialize indexing options */ h5trav_set_index(sort_by, sort_order); /* init table */ - trav_table_init(&trav); - if(h5trav_gettable(fid1, trav) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5trav_gettable failed"); - - /*------------------------------------------------------------------------- - * traverse the suppplied object list - *------------------------------------------------------------------------- - */ - for(i = 0; i < trav->nobjs; i++) { - if(trav->objs[i].type == H5TRAV_TYPE_GROUP) { + trav_table_init(fid1, &trav); + if (h5trav_gettable(fid1, trav) < 0) + H5TOOLS_GOTO_ERROR((-1), "h5trav_gettable failed"); + + /*------------------------------------------------------------------------- + * traverse the supplied object list + *------------------------------------------------------------------------- + */ + for (i = 0; i < trav->nobjs; i++) { + if (trav->objs[i].type == H5TRAV_TYPE_GROUP) { if ((gid = H5Gopen2(fid1, trav->objs[i].name, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed on first <%s>", trav->objs[i].name); + H5TOOLS_GOTO_ERROR((-1), "H5Gopen2 failed on first <%s>", trav->objs[i].name); if ((gcplid = H5Gget_create_plist(gid)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gget_create_plist failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Gget_create_plist failed"); if (H5Pget_link_creation_order(gcplid, &crt_order_flag1) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_link_creation_order failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Pget_link_creation_order failed"); if (H5Pclose(gcplid) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); if (H5Gclose(gid) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Gclose failed"); if ((gid = H5Gopen2(fid2, trav->objs[i].name, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed on second <%s>", trav->objs[i].name); + H5TOOLS_GOTO_ERROR((-1), "H5Gopen2 failed on second <%s>", trav->objs[i].name); if ((gcplid = H5Gget_create_plist(gid)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gget_create_plist failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Gget_create_plist failed"); if (H5Pget_link_creation_order(gcplid, &crt_order_flag2) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_link_creation_order failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Pget_link_creation_order failed"); if (H5Pclose(gcplid) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); if (H5Gclose(gid) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed"); + H5TOOLS_GOTO_ERROR((-1), "H5Gclose failed"); if (crt_order_flag1 != crt_order_flag2) - HGOTO_ERROR(0, H5E_tools_min_id_g, "property lists failed for <%s> are different", trav->objs[i].name); + H5TOOLS_GOTO_ERROR(0, "property lists failed for <%s> are different", trav->objs[i].name); } - else if(trav->objs[i].type == H5TRAV_TYPE_DATASET) { - if((dset1 = H5Dopen2(fid1, trav->objs[i].name, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed on first <%s>", trav->objs[i].name); - if((dset2 = H5Dopen2(fid2, trav->objs[i].name, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed on second <%s>", trav->objs[i].name); - if((dcpl1 = H5Dget_create_plist(dset1)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed"); - if((dcpl2 = H5Dget_create_plist(dset2)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed"); - - /*------------------------------------------------------------------------- - * compare the property lists - *------------------------------------------------------------------------- - */ - if((ret_value = H5Pequal(dcpl1, dcpl2)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pequal failed"); - - if(ret_value == 0) - HGOTO_ERROR(0, H5E_tools_min_id_g, "property lists failed for <%s> are different", trav->objs[i].name); - - /*------------------------------------------------------------------------- - * close - *------------------------------------------------------------------------- - */ - if(H5Pclose(dcpl1) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); - if(H5Pclose(dcpl2) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); - if(H5Dclose(dset1) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); - if(H5Dclose(dset2) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); + else if (trav->objs[i].type == H5TRAV_TYPE_DATASET) { + if ((dset1 = H5Dopen2(fid1, trav->objs[i].name, H5P_DEFAULT)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dopen2 failed on first <%s>", trav->objs[i].name); + if ((dset2 = H5Dopen2(fid2, trav->objs[i].name, H5P_DEFAULT)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dopen2 failed on second <%s>", trav->objs[i].name); + if ((dcpl1 = H5Dget_create_plist(dset1)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dget_create_plist failed"); + if ((dcpl2 = H5Dget_create_plist(dset2)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dget_create_plist failed"); + + /*------------------------------------------------------------------------- + * compare the property lists + *------------------------------------------------------------------------- + */ + if ((ret_value = H5Pequal(dcpl1, dcpl2)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pequal failed"); + + if (ret_value == 0) + H5TOOLS_GOTO_ERROR(0, "property lists failed for <%s> are different", trav->objs[i].name); + + /*------------------------------------------------------------------------- + * close + *------------------------------------------------------------------------- + */ + if (H5Pclose(dcpl1) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); + if (H5Pclose(dcpl2) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); + if (H5Dclose(dset1) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dclose failed"); + if (H5Dclose(dset2) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dclose failed"); } /*if*/ - } /*for*/ + } /*for*/ done: H5E_BEGIN_TRY @@ -467,14 +473,14 @@ done: H5Fclose(fid2); H5Pclose(gcplid); H5Gclose(gid); - if(trav) + if (trav) trav_table_free(trav); - } H5E_END_TRY; + } + H5E_END_TRY; return ret_value; } - /*------------------------------------------------------------------------- * Function: verify_filters * @@ -489,27 +495,25 @@ done: *------------------------------------------------------------------------- */ -static -int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter) +static int +verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter) { - int nfilters_dcpl; /* number of filters in DCPL*/ - unsigned filt_flags; /* filter flags */ - H5Z_filter_t filtn; /* filter identification number */ - unsigned cd_values[20]; /* filter client data values */ - size_t cd_nelmts; /* filter client number of values */ - char f_name[256]; /* filter name */ - size_t size; /* type size */ - int i; /* index */ - unsigned j; /* index */ + int nfilters_dcpl; /* number of filters in DCPL*/ + unsigned filt_flags; /* filter flags */ + H5Z_filter_t filtn; /* filter identification number */ + unsigned cd_values[20]; /* filter client data values */ + size_t cd_nelmts; /* filter client number of values */ + char f_name[256]; /* filter name */ + size_t size; /* type size */ + int i; /* index */ + unsigned j; /* index */ /* get information about filters */ - if((nfilters_dcpl = H5Pget_nfilters(pid)) < 0) + if ((nfilters_dcpl = H5Pget_nfilters(pid)) < 0) return -1; /* if we do not have filters and the requested filter is NONE, return 1 */ - if(!nfilters_dcpl && - nfilters == 1 && - filter[0].filtn == H5Z_FILTER_NONE) + if (!nfilters_dcpl && nfilters == 1 && filter[0].filtn == H5Z_FILTER_NONE) return 1; /* else the numbers of filters must match */ @@ -523,8 +527,8 @@ int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter) for (i = 0; i < nfilters_dcpl; i++) { cd_nelmts = NELMTS(cd_values); - filtn = H5Pget_filter2(pid, (unsigned)i, &filt_flags, &cd_nelmts, - cd_values, sizeof(f_name), f_name, NULL); + filtn = H5Pget_filter2(pid, (unsigned)i, &filt_flags, &cd_nelmts, cd_values, sizeof(f_name), f_name, + NULL); /* filter ID */ if (filtn < 0) @@ -535,7 +539,7 @@ int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter) /* compare client data values. some filters do return local values */ switch (filtn) { case H5Z_FILTER_NONE: - break; + break; case H5Z_FILTER_SHUFFLE: /* 1 private client value is returned by DCPL */ @@ -543,7 +547,7 @@ int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter) return 0; /* get dataset's type size */ - if((size = H5Tget_size(tid)) <= 0) + if ((size = H5Tget_size(tid)) <= 0) return -1; /* the private client value holds the dataset's type size */ diff --git a/tools/src/h5stat/CMakeLists.txt b/tools/src/h5stat/CMakeLists.txt index 55c675f..88c0d3d 100644 --- a/tools/src/h5stat/CMakeLists.txt +++ b/tools/src/h5stat/CMakeLists.txt @@ -1,4 +1,4 @@ -cmake_minimum_required (VERSION 3.10) +cmake_minimum_required (VERSION 3.12) project (HDF5_TOOLS_SRC_H5STAT C) # -------------------------------------------------------------------- @@ -6,7 +6,8 @@ project (HDF5_TOOLS_SRC_H5STAT C) # -------------------------------------------------------------------- if (NOT ONLY_SHARED_LIBS) add_executable (h5stat ${HDF5_TOOLS_SRC_H5STAT_SOURCE_DIR}/h5stat.c) - target_include_directories (h5stat PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5stat PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_compile_options(h5stat PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5stat STATIC) target_link_libraries (h5stat PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) set_target_properties (h5stat PROPERTIES FOLDER tools) @@ -17,7 +18,8 @@ endif () if (BUILD_SHARED_LIBS) add_executable (h5stat-shared ${HDF5_TOOLS_SRC_H5STAT_SOURCE_DIR}/h5stat.c) - target_include_directories (h5stat-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5stat-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_compile_options(h5stat-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5stat-shared SHARED) target_link_libraries (h5stat-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET}) set_target_properties (h5stat-shared PROPERTIES FOLDER tools) @@ -26,6 +28,17 @@ if (BUILD_SHARED_LIBS) set (H5_DEP_EXECUTABLES ${H5_DEP_EXECUTABLES} h5stat-shared) endif () +#----------------------------------------------------------------------------- +# Add Target to clang-format +#----------------------------------------------------------------------------- +if (HDF5_ENABLE_FORMATTERS) + if (NOT ONLY_SHARED_LIBS) + clang_format (HDF5_H5STAT_SRC_FORMAT h5stat) + else () + clang_format (HDF5_H5STAT_SRC_FORMAT h5stat-shared) + endif () +endif () + ############################################################################## ############################################################################## ### I N S T A L L A T I O N ### diff --git a/tools/src/h5stat/Makefile.am b/tools/src/h5stat/Makefile.am index c228b48..9231633 100644 --- a/tools/src/h5stat/Makefile.am +++ b/tools/src/h5stat/Makefile.am @@ -6,7 +6,7 @@ # This file is part of HDF5. The full HDF5 copyright notice, including # terms governing use, modification, and redistribution, is contained in # the COPYING file, which can be found at the root of the source code -# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. +# distribution tree, or in https://www.hdfgroup.org/licenses. # If you do not have access to either file, you may request a copy from # help@hdfgroup.org. ## diff --git a/tools/src/h5stat/h5stat.c b/tools/src/h5stat/h5stat.c index 9528d2c..e42af10 100644 --- a/tools/src/h5stat/h5stat.c +++ b/tools/src/h5stat/h5stat.c @@ -6,12 +6,12 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -#include "H5private.h" /* Generic Functions */ +#include "H5private.h" /* Generic Functions */ #include "h5tools.h" #include "h5tools_utils.h" #include "h5tools_ref.h" @@ -24,148 +24,144 @@ /* Parameters to control statistics gathered */ /* Default threshold for small groups/datasets/attributes */ -#define DEF_SIZE_SMALL_GROUPS 10 -#define DEF_SIZE_SMALL_DSETS 10 -#define DEF_SIZE_SMALL_ATTRS 10 +#define DEF_SIZE_SMALL_GROUPS 10 +#define DEF_SIZE_SMALL_DSETS 10 +#define DEF_SIZE_SMALL_ATTRS 10 -#define SIZE_SMALL_SECTS 10 +#define SIZE_SMALL_SECTS 10 -#define H5_NFILTERS_IMPL 8 /* Number of currently implemented filters + one to - accommodate for user-define filters + one - to accomodate datasets whithout any filters */ +#define H5_NFILTERS_IMPL \ + 8 /* Number of currently implemented filters + one to \ + accommodate for user-define filters + one \ + to accommodate datasets without any filters */ /* File space management strategies: see H5Fpublic.h for declarations */ -const char *FS_STRATEGY_NAME[] = { - "H5F_FSPACE_STRATEGY_FSM_AGGR", - "H5F_FSPACE_STRATEGY_PAGE", - "H5F_FSPACE_STRATEGY_AGGR", - "H5F_FSPACE_STRATEGY_NONE", - "unknown", - NULL -}; +const char *FS_STRATEGY_NAME[] = {"H5F_FSPACE_STRATEGY_FSM_AGGR", + "H5F_FSPACE_STRATEGY_PAGE", + "H5F_FSPACE_STRATEGY_AGGR", + "H5F_FSPACE_STRATEGY_NONE", + "unknown", + NULL}; /* Datatype statistics for datasets */ typedef struct dtype_info_t { - hid_t tid; /* ID of datatype */ - unsigned long count; /* Number of types found */ - unsigned long named; /* Number of types that are named */ + hid_t tid; /* ID of datatype */ + unsigned long count; /* Number of types found */ + unsigned long named; /* Number of types that are named */ } dtype_info_t; typedef struct ohdr_info_t { - hsize_t total_size; /* Total size of object headers */ - hsize_t free_size; /* Total free space in object headers */ + hsize_t total_size; /* Total size of object headers */ + hsize_t free_size; /* Total free space in object headers */ } ohdr_info_t; /* Info to pass to the iteration functions */ typedef struct iter_t { - hid_t fid; /* File ID */ - hsize_t filesize; /* Size of the file */ - unsigned long uniq_groups; /* Number of unique groups */ - unsigned long uniq_dsets; /* Number of unique datasets */ - unsigned long uniq_dtypes; /* Number of unique named datatypes */ - unsigned long uniq_links; /* Number of unique links */ - unsigned long uniq_others; /* Number of other unique objects */ - - unsigned long max_links; /* Maximum # of links to an object */ - hsize_t max_fanout; /* Maximum fanout from a group */ - unsigned long *num_small_groups; /* Size of small groups tracked */ - unsigned group_nbins; /* Number of bins for group counts */ - unsigned long *group_bins; /* Pointer to array of bins for group counts */ - ohdr_info_t group_ohdr_info; /* Object header information for groups */ - - hsize_t max_attrs; /* Maximum attributes from a group */ - unsigned long *num_small_attrs; /* Size of small attributes tracked */ - unsigned attr_nbins; /* Number of bins for attribute counts */ - unsigned long *attr_bins; /* Pointer to array of bins for attribute counts */ - - unsigned max_dset_rank; /* Maximum rank of dataset */ - unsigned long dset_rank_count[H5S_MAX_RANK]; /* Number of datasets of each rank */ - hsize_t max_dset_dims; /* Maximum dimension size of dataset */ - unsigned long *small_dset_dims; /* Size of dimensions of small datasets tracked */ - unsigned long dset_layouts[H5D_NLAYOUTS]; /* Type of storage for each dataset */ - unsigned long dset_comptype[H5_NFILTERS_IMPL]; /* Number of currently implemented filters */ - unsigned long dset_ntypes; /* Number of diff. dataset datatypes found */ - dtype_info_t *dset_type_info; /* Pointer to dataset datatype information found */ - unsigned dset_dim_nbins; /* Number of bins for dataset dimensions */ - unsigned long *dset_dim_bins; /* Pointer to array of bins for dataset dimensions */ - ohdr_info_t dset_ohdr_info; /* Object header information for datasets */ - hsize_t dset_storage_size; /* Size of raw data for datasets */ - hsize_t dset_external_storage_size; /* Size of raw data for datasets with external storage */ - ohdr_info_t dtype_ohdr_info; /* Object header information for datatypes */ - hsize_t groups_btree_storage_size; /* btree size for group */ - hsize_t groups_heap_storage_size; /* heap size for group */ - hsize_t attrs_btree_storage_size; /* btree size for attributes (1.8) */ - hsize_t attrs_heap_storage_size; /* fractal heap size for attributes (1.8) */ - hsize_t SM_hdr_storage_size; /* header size for SOHM table (1.8) */ - hsize_t SM_index_storage_size; /* index (btree & list) size for SOHM table (1.8) */ - hsize_t SM_heap_storage_size; /* fractal heap size for SOHM table (1.8) */ - hsize_t super_size; /* superblock size */ - hsize_t super_ext_size; /* superblock extension size */ - hsize_t ublk_size; /* user block size (if exists) */ - H5F_fspace_strategy_t fs_strategy; /* File space management strategy */ - hbool_t fs_persist; /* Free-space persist or not */ - hsize_t fs_threshold; /* Free-space section threshold */ - hsize_t fsp_size; /* File space page size */ - hsize_t free_space; /* Amount of freespace in the file */ - hsize_t free_hdr; /* Size of free space manager metadata in the file */ - unsigned long num_small_sects[SIZE_SMALL_SECTS]; /* Size of small free-space sections */ - unsigned sect_nbins; /* Number of bins for free-space section sizes */ - unsigned long *sect_bins; /* Pointer to array of bins for free-space section sizes */ - hsize_t datasets_index_storage_size;/* meta size for chunked dataset's indexing type */ - hsize_t datasets_heap_storage_size; /* heap size for dataset with external storage */ - unsigned long nexternal; /* Number of external files for a dataset */ - int local; /* Flag to indicate iteration over the object*/ + hid_t fid; /* File ID */ + hsize_t filesize; /* Size of the file */ + unsigned long uniq_groups; /* Number of unique groups */ + unsigned long uniq_dsets; /* Number of unique datasets */ + unsigned long uniq_dtypes; /* Number of unique named datatypes */ + unsigned long uniq_links; /* Number of unique links */ + unsigned long uniq_others; /* Number of other unique objects */ + + unsigned long max_links; /* Maximum # of links to an object */ + hsize_t max_fanout; /* Maximum fanout from a group */ + unsigned long *num_small_groups; /* Size of small groups tracked */ + unsigned group_nbins; /* Number of bins for group counts */ + unsigned long *group_bins; /* Pointer to array of bins for group counts */ + ohdr_info_t group_ohdr_info; /* Object header information for groups */ + + hsize_t max_attrs; /* Maximum attributes from a group */ + unsigned long *num_small_attrs; /* Size of small attributes tracked */ + unsigned attr_nbins; /* Number of bins for attribute counts */ + unsigned long *attr_bins; /* Pointer to array of bins for attribute counts */ + + unsigned max_dset_rank; /* Maximum rank of dataset */ + unsigned long dset_rank_count[H5S_MAX_RANK]; /* Number of datasets of each rank */ + hsize_t max_dset_dims; /* Maximum dimension size of dataset */ + unsigned long *small_dset_dims; /* Size of dimensions of small datasets tracked */ + unsigned long dset_layouts[H5D_NLAYOUTS]; /* Type of storage for each dataset */ + unsigned long dset_comptype[H5_NFILTERS_IMPL]; /* Number of currently implemented filters */ + unsigned long dset_ntypes; /* Number of diff. dataset datatypes found */ + dtype_info_t * dset_type_info; /* Pointer to dataset datatype information found */ + unsigned dset_dim_nbins; /* Number of bins for dataset dimensions */ + unsigned long *dset_dim_bins; /* Pointer to array of bins for dataset dimensions */ + ohdr_info_t dset_ohdr_info; /* Object header information for datasets */ + hsize_t dset_storage_size; /* Size of raw data for datasets */ + hsize_t dset_external_storage_size; /* Size of raw data for datasets with external storage */ + ohdr_info_t dtype_ohdr_info; /* Object header information for datatypes */ + hsize_t groups_btree_storage_size; /* btree size for group */ + hsize_t groups_heap_storage_size; /* heap size for group */ + hsize_t attrs_btree_storage_size; /* btree size for attributes (1.8) */ + hsize_t attrs_heap_storage_size; /* fractal heap size for attributes (1.8) */ + hsize_t SM_hdr_storage_size; /* header size for SOHM table (1.8) */ + hsize_t SM_index_storage_size; /* index (btree & list) size for SOHM table (1.8) */ + hsize_t SM_heap_storage_size; /* fractal heap size for SOHM table (1.8) */ + hsize_t super_size; /* superblock size */ + hsize_t super_ext_size; /* superblock extension size */ + hsize_t ublk_size; /* user block size (if exists) */ + H5F_fspace_strategy_t fs_strategy; /* File space management strategy */ + hbool_t fs_persist; /* Free-space persist or not */ + hsize_t fs_threshold; /* Free-space section threshold */ + hsize_t fsp_size; /* File space page size */ + hsize_t free_space; /* Amount of freespace in the file */ + hsize_t free_hdr; /* Size of free space manager metadata in the file */ + unsigned long num_small_sects[SIZE_SMALL_SECTS]; /* Size of small free-space sections */ + unsigned sect_nbins; /* Number of bins for free-space section sizes */ + unsigned long * sect_bins; /* Pointer to array of bins for free-space section sizes */ + hsize_t datasets_index_storage_size; /* meta size for chunked dataset's indexing type */ + hsize_t datasets_heap_storage_size; /* heap size for dataset with external storage */ + unsigned long nexternal; /* Number of external files for a dataset */ + int local; /* Flag to indicate iteration over the object*/ } iter_t; - -static const char *drivername = ""; +static const char *drivername = NULL; #ifdef H5_HAVE_ROS3_VFD -/* default "anonymous" s3 configuration - */ +/* Default "anonymous" S3 configuration */ static H5FD_ros3_fapl_t ros3_fa = { - 1, /* fapl version */ - false, /* authenticate */ - "", /* aws region */ - "", /* access key id */ - "", /* secret access key */ + 1, /* Structure Version */ + FALSE, /* Authenticate? */ + "", /* AWS Region */ + "", /* Access Key ID */ + "", /* Secret Access Key */ }; #endif /* H5_HAVE_ROS3_VFD */ #ifdef H5_HAVE_LIBHDFS -/* default HDFS access configuration - */ +/* "Default" HDFS configuration */ static H5FD_hdfs_fapl_t hdfs_fa = { - 1, /* fapl version */ - "localhost", /* namenode name */ - 0, /* namenode port */ - "", /* kerberos ticket cache */ - "", /* user name */ - 2048, /* stream buffer size */ + 1, /* Structure Version */ + "localhost", /* Namenode Name */ + 0, /* Namenode Port */ + "", /* Kerberos ticket cache */ + "", /* User name */ + 2048, /* Stream buffer size */ }; #endif /* H5_HAVE_LIBHDFS */ -static int display_all = TRUE; +static int display_all = TRUE; /* Enable the printing of selected statistics */ -static int display_file = FALSE; /* display file information */ -static int display_group = FALSE; /* display groups information */ -static int display_dset = FALSE; /* display datasets information */ -static int display_dset_dtype_meta = FALSE; /* display datasets' datatype information */ -static int display_attr = FALSE; /* display attributes information */ -static int display_free_sections = FALSE; /* display free space information */ -static int display_summary = FALSE; /* display summary of file space information */ +static int display_file = FALSE; /* display file information */ +static int display_group = FALSE; /* display groups information */ +static int display_dset = FALSE; /* display datasets information */ +static int display_dset_dtype_meta = FALSE; /* display datasets' datatype information */ +static int display_attr = FALSE; /* display attributes information */ +static int display_free_sections = FALSE; /* display free space information */ +static int display_summary = FALSE; /* display summary of file space information */ -static int display_file_metadata = FALSE; /* display file space info for file's metadata */ -static int display_group_metadata = FALSE; /* display file space info for groups' metadata */ -static int display_dset_metadata = FALSE; /* display file space info for datasets' metadata */ +static int display_file_metadata = FALSE; /* display file space info for file's metadata */ +static int display_group_metadata = FALSE; /* display file space info for groups' metadata */ +static int display_dset_metadata = FALSE; /* display file space info for datasets' metadata */ -static int display_object = FALSE; /* not implemented yet */ +static int display_object = FALSE; /* not implemented yet */ /* Initialize threshold for small groups/datasets/attributes */ -static int sgroups_threshold = DEF_SIZE_SMALL_GROUPS; -static int sdsets_threshold = DEF_SIZE_SMALL_DSETS; -static int sattrs_threshold = DEF_SIZE_SMALL_ATTRS; +static int sgroups_threshold = DEF_SIZE_SMALL_GROUPS; +static int sdsets_threshold = DEF_SIZE_SMALL_DSETS; +static int sattrs_threshold = DEF_SIZE_SMALL_ATTRS; /* a structure for handling the order command-line parameters come in */ struct handler_t { @@ -173,120 +169,33 @@ struct handler_t { char **obj; }; -static const char *s_opts ="Aa:Ddm:EFfhGgl:sSTO:Vw:"; +static const char *s_opts = "Aa:Ddm:E*FfhGgl:sSTO:Vw:H:"; /* e.g. "filemetadata" has to precede "file"; "groupmetadata" has to precede "group" etc. */ -static struct long_options l_opts[] = { - {"help", no_arg, 'h'}, - {"hel", no_arg, 'h'}, - {"he", no_arg, 'h'}, - {"filemetadata", no_arg, 'F'}, - {"filemetadat", no_arg, 'F'}, - {"filemetada", no_arg, 'F'}, - {"filemetad", no_arg, 'F'}, - {"filemeta", no_arg, 'F'}, - {"filemet", no_arg, 'F'}, - {"fileme", no_arg, 'F'}, - {"filem", no_arg, 'F'}, - {"file", no_arg, 'f'}, - {"fil", no_arg, 'f'}, - {"fi", no_arg, 'f'}, - {"groupmetadata", no_arg, 'G'}, - {"groupmetadat", no_arg, 'G'}, - {"groupmetada", no_arg, 'G'}, - {"groupmetad", no_arg, 'G'}, - {"groupmeta", no_arg, 'G'}, - {"groupmet", no_arg, 'G'}, - {"groupme", no_arg, 'G'}, - {"groupm", no_arg, 'G'}, - {"group", no_arg, 'g'}, - {"grou", no_arg, 'g'}, - {"gro", no_arg, 'g'}, - {"gr", no_arg, 'g'}, - { "links", require_arg, 'l' }, - { "link", require_arg, 'l' }, - { "lin", require_arg, 'l' }, - { "li", require_arg, 'l' }, - {"dsetmetadata", no_arg, 'D'}, - {"dsetmetadat", no_arg, 'D'}, - {"dsetmetada", no_arg, 'D'}, - {"dsetmetad", no_arg, 'D'}, - {"dsetmeta", no_arg, 'D'}, - {"dsetmet", no_arg, 'D'}, - {"dsetme", no_arg, 'D'}, - {"dsetm", no_arg, 'D'}, - {"dset", no_arg, 'd'}, - {"dse", no_arg, 'd'}, - {"ds", no_arg, 'd'}, - {"dims", require_arg, 'm'}, - {"dim", require_arg, 'm'}, - {"di", require_arg, 'm'}, - {"dtypemetadata", no_arg, 'T'}, - {"dtypemetadat", no_arg, 'T'}, - {"dtypemetada", no_arg, 'T'}, - {"dtypemetad", no_arg, 'T'}, - {"dtypemeta", no_arg, 'T'}, - {"dtypemet", no_arg, 'T'}, - {"dtypeme", no_arg, 'T'}, - {"dtypem", no_arg, 'T'}, - {"dtype", no_arg, 'T'}, - {"dtyp", no_arg, 'T'}, - {"dty", no_arg, 'T'}, - {"dt", no_arg, 'T'}, - { "object", require_arg, 'O' }, - { "objec", require_arg, 'O' }, - { "obje", require_arg, 'O' }, - { "obj", require_arg, 'O' }, - { "ob", require_arg, 'O' }, - { "version", no_arg, 'V' }, - { "versio", no_arg, 'V' }, - { "versi", no_arg, 'V' }, - { "vers", no_arg, 'V' }, - { "ver", no_arg, 'V' }, - { "ve", no_arg, 'V' }, - { "attribute", no_arg, 'A' }, - { "attribut", no_arg, 'A' }, - { "attribu", no_arg, 'A' }, - { "attrib", no_arg, 'A' }, - { "attri", no_arg, 'A' }, - { "attr", no_arg, 'A' }, - { "att", no_arg, 'A' }, - { "at", no_arg, 'A' }, - { "enable-error-stack", no_arg, 'E' }, - { "numattrs", require_arg, 'a' }, - { "numattr", require_arg, 'a' }, - { "numatt", require_arg, 'a' }, - { "numat", require_arg, 'a' }, - { "numa", require_arg, 'a' }, - { "num", require_arg, 'a' }, - { "nu", require_arg, 'a' }, - { "freespace", no_arg, 's' }, - { "freespac", no_arg, 's' }, - { "freespa", no_arg, 's' }, - { "freesp", no_arg, 's' }, - { "frees", no_arg, 's' }, - { "free", no_arg, 's' }, - { "fre", no_arg, 's' }, - { "fr", no_arg, 's' }, - { "summary", no_arg, 'S' }, - { "summar", no_arg, 'S' }, - { "summa", no_arg, 'S' }, - { "summ", no_arg, 'S' }, - { "sum", no_arg, 'S' }, - { "su", no_arg, 'S' }, - { "s3-cred", require_arg, 'w' }, - { "hdfs-attrs", require_arg, 'H' }, - { NULL, 0, '\0' } -}; +static struct h5_long_options l_opts[] = {{"help", no_arg, 'h'}, + {"filemetadata", no_arg, 'F'}, + {"groupmetadata", no_arg, 'G'}, + {"links", require_arg, 'l'}, + {"dsetmetadata", no_arg, 'D'}, + {"dims", require_arg, 'm'}, + {"dtypemetadata", no_arg, 'T'}, + {"object", require_arg, 'O'}, + {"version", no_arg, 'V'}, + {"attribute", no_arg, 'A'}, + {"enable-error-stack", optional_arg, 'E'}, + {"numattrs", require_arg, 'a'}, + {"freespace", no_arg, 's'}, + {"summary", no_arg, 'S'}, + {"s3-cred", require_arg, 'w'}, + {"hdfs-attrs", require_arg, 'H'}, + {NULL, 0, '\0'}}; static void leave(int ret) { - h5tools_close(); - HDexit(ret); + h5tools_close(); + HDexit(ret); } - - /*------------------------------------------------------------------------- * Function: usage * @@ -296,47 +205,51 @@ leave(int ret) * *------------------------------------------------------------------------- */ -static void usage(const char *prog) +static void +usage(const char *prog) { - HDfflush(stdout); - HDfprintf(stdout, "Usage: %s [OPTIONS] file\n", prog); - HDfprintf(stdout, "\n"); - HDfprintf(stdout, " OPTIONS\n"); - HDfprintf(stdout, " -h, --help Print a usage message and exit\n"); - HDfprintf(stdout, " -V, --version Print version number and exit\n"); - HDfprintf(stdout, " -f, --file Print file information\n"); - HDfprintf(stdout, " -F, --filemetadata Print file space information for file's metadata\n"); - HDfprintf(stdout, " -g, --group Print group information\n"); - HDfprintf(stdout, " -l N, --links=N Set the threshold for the # of links when printing\n"); - HDfprintf(stdout, " information for small groups. N is an integer greater\n"); - HDfprintf(stdout, " than 0. The default threshold is 10.\n"); - HDfprintf(stdout, " -G, --groupmetadata Print file space information for groups' metadata\n"); - HDfprintf(stdout, " -d, --dset Print dataset information\n"); - HDfprintf(stdout, " -m N, --dims=N Set the threshold for the dimension sizes when printing\n"); - HDfprintf(stdout, " information for small datasets. N is an integer greater\n"); - HDfprintf(stdout, " than 0. The default threshold is 10.\n"); - HDfprintf(stdout, " -D, --dsetmetadata Print file space information for datasets' metadata\n"); - HDfprintf(stdout, " -T, --dtypemetadata Print datasets' datatype information\n"); - HDfprintf(stdout, " -A, --attribute Print attribute information\n"); - HDfprintf(stdout, " -a N, --numattrs=N Set the threshold for the # of attributes when printing\n"); - HDfprintf(stdout, " information for small # of attributes. N is an integer greater\n"); - HDfprintf(stdout, " than 0. The default threshold is 10.\n"); - HDfprintf(stdout, " -s, --freespace Print free space information\n"); - HDfprintf(stdout, " -S, --summary Print summary of file space information\n"); - HDfprintf(stdout, " --enable-error-stack Prints messages from the HDF5 error stack as they occur\n"); - HDfprintf(stdout, " --s3-cred=<cred> Access file on S3, using provided credential\n"); - HDfprintf(stdout, " <cred> :: (region,id,key)\n"); - HDfprintf(stdout, " If <cred> == \"(,,)\", no authentication is used.\n"); - HDfprintf(stdout, " --hdfs-attrs=<attrs> Access a file on HDFS with given configuration\n"); - HDfprintf(stdout, " attributes.\n"); - HDfprintf(stdout, " <attrs> :: (<namenode name>,<namenode port>,\n"); - HDfprintf(stdout, " <kerberos cache path>,<username>,\n"); - HDfprintf(stdout, " <buffer size>)\n"); - HDfprintf(stdout, " If an attribute is empty, a default value will be\n"); - HDfprintf(stdout, " used.\n"); + HDfflush(stdout); + HDfprintf(stdout, "Usage: %s [OPTIONS] file\n", prog); + HDfprintf(stdout, "\n"); + HDfprintf(stdout, " ERROR\n"); + HDfprintf(stdout, " --enable-error-stack Prints messages from the HDF5 error stack as they occur\n"); + HDfprintf(stdout, " Optional value 2 also prints file open errors\n"); + HDfprintf(stdout, " OPTIONS\n"); + HDfprintf(stdout, " -h, --help Print a usage message and exit\n"); + HDfprintf(stdout, " -V, --version Print version number and exit\n"); + HDfprintf(stdout, " -f, --file Print file information\n"); + HDfprintf(stdout, " -F, --filemetadata Print file space information for file's metadata\n"); + HDfprintf(stdout, " -g, --group Print group information\n"); + HDfprintf(stdout, " -l N, --links=N Set the threshold for the # of links when printing\n"); + HDfprintf(stdout, " information for small groups. N is an integer greater\n"); + HDfprintf(stdout, " than 0. The default threshold is 10.\n"); + HDfprintf(stdout, " -G, --groupmetadata Print file space information for groups' metadata\n"); + HDfprintf(stdout, " -d, --dset Print dataset information\n"); + HDfprintf(stdout, " -m N, --dims=N Set the threshold for the dimension sizes when printing\n"); + HDfprintf(stdout, + " information for small datasets. N is an integer greater\n"); + HDfprintf(stdout, " than 0. The default threshold is 10.\n"); + HDfprintf(stdout, " -D, --dsetmetadata Print file space information for datasets' metadata\n"); + HDfprintf(stdout, " -T, --dtypemetadata Print datasets' datatype information\n"); + HDfprintf(stdout, " -A, --attribute Print attribute information\n"); + HDfprintf(stdout, " -a N, --numattrs=N Set the threshold for the # of attributes when printing\n"); + HDfprintf(stdout, + " information for small # of attributes. N is an integer greater\n"); + HDfprintf(stdout, " than 0. The default threshold is 10.\n"); + HDfprintf(stdout, " -s, --freespace Print free space information\n"); + HDfprintf(stdout, " -S, --summary Print summary of file space information\n"); + HDfprintf(stdout, " --s3-cred=<cred> Access file on S3, using provided credential\n"); + HDfprintf(stdout, " <cred> :: (region,id,key)\n"); + HDfprintf(stdout, " If <cred> == \"(,,)\", no authentication is used.\n"); + HDfprintf(stdout, " --hdfs-attrs=<attrs> Access a file on HDFS with given configuration\n"); + HDfprintf(stdout, " attributes.\n"); + HDfprintf(stdout, " <attrs> :: (<namenode name>,<namenode port>,\n"); + HDfprintf(stdout, " <kerberos cache path>,<username>,\n"); + HDfprintf(stdout, " <buffer size>)\n"); + HDfprintf(stdout, " If an attribute is empty, a default value will be\n"); + HDfprintf(stdout, " used.\n"); } - /*------------------------------------------------------------------------- * Function: ceil_log10 * @@ -353,9 +266,9 @@ H5_ATTR_CONST static unsigned ceil_log10(unsigned long x) { unsigned long pow10 = 1; - unsigned ret = 0; + unsigned ret = 0; - while(x >= pow10) { + while (x >= pow10) { pow10 *= 10; ret++; } /* end while */ @@ -363,7 +276,6 @@ ceil_log10(unsigned long x) return ret; } /* ceil_log10() */ - /*------------------------------------------------------------------------- * Function: attribute_stats * @@ -379,41 +291,40 @@ ceil_log10(unsigned long x) *------------------------------------------------------------------------- */ static herr_t -attribute_stats(iter_t *iter, const H5O_info_t *oi) +attribute_stats(iter_t *iter, const H5O_info2_t *oi, const H5O_native_info_t *native_oi) { - unsigned bin; /* "bin" the number of objects falls in */ + unsigned bin; /* "bin" the number of objects falls in */ /* Update dataset & attribute metadata info */ - iter->attrs_btree_storage_size += oi->meta_size.attr.index_size; - iter->attrs_heap_storage_size += oi->meta_size.attr.heap_size; + iter->attrs_btree_storage_size += native_oi->meta_size.attr.index_size; + iter->attrs_heap_storage_size += native_oi->meta_size.attr.heap_size; /* Update small # of attribute count & limits */ - if(oi->num_attrs <= (hsize_t)sattrs_threshold) + if (oi->num_attrs <= (hsize_t)sattrs_threshold) (iter->num_small_attrs[(size_t)oi->num_attrs])++; - if(oi->num_attrs > iter->max_attrs) + if (oi->num_attrs > iter->max_attrs) iter->max_attrs = oi->num_attrs; /* Add attribute count to proper bin */ bin = ceil_log10((unsigned long)oi->num_attrs); - if((bin + 1) > iter->attr_nbins) { + if ((bin + 1) > iter->attr_nbins) { iter->attr_bins = (unsigned long *)HDrealloc(iter->attr_bins, (bin + 1) * sizeof(unsigned long)); HDassert(iter->attr_bins); - /* Initialize counts for intermediate bins */ - while(iter->attr_nbins < bin) + /* Initialize counts for intermediate bins */ + while (iter->attr_nbins < bin) iter->attr_bins[iter->attr_nbins++] = 0; iter->attr_nbins++; /* Initialize count for new bin */ iter->attr_bins[bin] = 1; - } /* end if */ - else - (iter->attr_bins[bin])++; + } /* end if */ + else + (iter->attr_bins[bin])++; - return 0; + return 0; } /* end attribute_stats() */ - /*------------------------------------------------------------------------- * Function: group_stats * @@ -440,40 +351,41 @@ attribute_stats(iter_t *iter, const H5O_info_t *oi) *------------------------------------------------------------------------- */ static herr_t -group_stats(iter_t *iter, const char *name, const H5O_info_t *oi) +group_stats(iter_t *iter, const char *name, const H5O_info2_t *oi, const H5O_native_info_t *native_oi) { - H5G_info_t ginfo; /* Group information */ - unsigned bin; /* "bin" the number of objects falls in */ - herr_t ret_value = SUCCEED; /* Return value */ + H5G_info_t ginfo; /* Group information */ + unsigned bin; /* "bin" the number of objects falls in */ + herr_t ret_value = SUCCEED; /* Gather statistics about this type of object */ iter->uniq_groups++; /* Get object header information */ - iter->group_ohdr_info.total_size += oi->hdr.space.total; - iter->group_ohdr_info.free_size += oi->hdr.space.free; + iter->group_ohdr_info.total_size += native_oi->hdr.space.total; + iter->group_ohdr_info.free_size += native_oi->hdr.space.free; /* Get group information */ - if((ret_value = H5Gget_info_by_name(iter->fid, name, &ginfo, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gget_info_by_name() failed"); + if ((ret_value = H5Gget_info_by_name(iter->fid, name, &ginfo, H5P_DEFAULT)) < 0) + H5TOOLS_GOTO_ERROR(FAIL, "H5Gget_info_by_name() failed"); /* Update link stats */ /* Collect statistics for small groups */ - if(ginfo.nlinks < (hsize_t)sgroups_threshold) + if (ginfo.nlinks < (hsize_t)sgroups_threshold) (iter->num_small_groups[(size_t)ginfo.nlinks])++; /* Determine maximum link count */ - if(ginfo.nlinks > iter->max_fanout) + if (ginfo.nlinks > iter->max_fanout) iter->max_fanout = ginfo.nlinks; /* Add group count to proper bin */ bin = ceil_log10((unsigned long)ginfo.nlinks); - if((bin + 1) > iter->group_nbins) { + if ((bin + 1) > iter->group_nbins) { /* Allocate more storage for info about dataset's datatype */ - if((iter->group_bins = (unsigned long *)HDrealloc(iter->group_bins, (bin + 1) * sizeof(unsigned long))) == NULL) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Drealloc() failed"); + if ((iter->group_bins = + (unsigned long *)HDrealloc(iter->group_bins, (bin + 1) * sizeof(unsigned long))) == NULL) + H5TOOLS_GOTO_ERROR(FAIL, "H5Drealloc() failed"); /* Initialize counts for intermediate bins */ - while(iter->group_nbins < bin) + while (iter->group_nbins < bin) iter->group_bins[iter->group_nbins++] = 0; iter->group_nbins++; @@ -484,18 +396,17 @@ group_stats(iter_t *iter, const char *name, const H5O_info_t *oi) (iter->group_bins[bin])++; /* Update group metadata info */ - iter->groups_btree_storage_size += oi->meta_size.obj.index_size; - iter->groups_heap_storage_size += oi->meta_size.obj.heap_size; + iter->groups_btree_storage_size += native_oi->meta_size.obj.index_size; + iter->groups_heap_storage_size += native_oi->meta_size.obj.heap_size; /* Update attribute metadata info */ - if((ret_value = attribute_stats(iter, oi)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "attribute_stats failed"); + if ((ret_value = attribute_stats(iter, oi, native_oi)) < 0) + H5TOOLS_GOTO_ERROR(FAIL, "attribute_stats failed"); done: return ret_value; } /* end group_stats() */ - /*------------------------------------------------------------------------- * Function: dataset_stats * @@ -510,68 +421,68 @@ done: *------------------------------------------------------------------------- */ static herr_t -dataset_stats(iter_t *iter, const char *name, const H5O_info_t *oi) +dataset_stats(iter_t *iter, const char *name, const H5O_info2_t *oi, const H5O_native_info_t *native_oi) { - unsigned bin; /* "bin" the number of objects falls in */ - hid_t did; /* Dataset ID */ - hid_t sid; /* Dataspace ID */ - hid_t tid; /* Datatype ID */ - hid_t dcpl; /* Dataset creation property list ID */ - hsize_t dims[H5S_MAX_RANK]; /* Dimensions of dataset */ - H5D_layout_t lout; /* Layout of dataset */ - unsigned type_found; /* Whether the dataset's datatype was */ - /* already found */ - int ndims; /* Number of dimensions of dataset */ - hsize_t storage; /* Size of dataset storage */ - unsigned u; /* Local index variable */ - int num_ext; /* Number of external files for a dataset */ - int nfltr; /* Number of filters for a dataset */ - H5Z_filter_t fltr; /* Filter identifier */ - herr_t ret_value = SUCCEED; /* Return value */ + unsigned bin; /* "bin" the number of objects falls in */ + hid_t did; /* Dataset ID */ + hid_t sid; /* Dataspace ID */ + hid_t tid; /* Datatype ID */ + hid_t dcpl; /* Dataset creation property list ID */ + hsize_t dims[H5S_MAX_RANK]; /* Dimensions of dataset */ + H5D_layout_t lout; /* Layout of dataset */ + unsigned type_found; /* Whether the dataset's datatype was */ + /* already found */ + int ndims; /* Number of dimensions of dataset */ + hsize_t storage; /* Size of dataset storage */ + unsigned u; /* Local index variable */ + int num_ext; /* Number of external files for a dataset */ + int nfltr; /* Number of filters for a dataset */ + H5Z_filter_t fltr; /* Filter identifier */ + herr_t ret_value = SUCCEED; /* Gather statistics about this type of object */ iter->uniq_dsets++; /* Get object header information */ - iter->dset_ohdr_info.total_size += oi->hdr.space.total; - iter->dset_ohdr_info.free_size += oi->hdr.space.free; + iter->dset_ohdr_info.total_size += native_oi->hdr.space.total; + iter->dset_ohdr_info.free_size += native_oi->hdr.space.free; - if((did = H5Dopen2(iter->fid, name, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen() failed"); + if ((did = H5Dopen2(iter->fid, name, H5P_DEFAULT)) < 0) + H5TOOLS_GOTO_ERROR(FAIL, "H5Dopen() failed"); /* Update dataset metadata info */ - iter->datasets_index_storage_size += oi->meta_size.obj.index_size; - iter->datasets_heap_storage_size += oi->meta_size.obj.heap_size; + iter->datasets_index_storage_size += native_oi->meta_size.obj.index_size; + iter->datasets_heap_storage_size += native_oi->meta_size.obj.heap_size; /* Update attribute metadata info */ - if((ret_value = attribute_stats(iter, oi)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "attribute_stats() failed"); + if ((ret_value = attribute_stats(iter, oi, native_oi)) < 0) + H5TOOLS_GOTO_ERROR(FAIL, "attribute_stats() failed"); /* Get storage info */ /* Failure 0 indistinguishable from no-data-stored 0 */ storage = H5Dget_storage_size(did); /* Gather layout statistics */ - if((dcpl = H5Dget_create_plist(did)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist() failed"); + if ((dcpl = H5Dget_create_plist(did)) < 0) + H5TOOLS_GOTO_ERROR(FAIL, "H5Dget_create_plist() failed"); - if((lout = H5Pget_layout(dcpl)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_layout() failed"); + if ((lout = H5Pget_layout(dcpl)) < 0) + H5TOOLS_GOTO_ERROR(FAIL, "H5Pget_layout() failed"); /* Object header's total size for H5D_COMPACT layout includes raw data size */ /* "storage" also includes H5D_COMPACT raw data size */ - if(lout == H5D_COMPACT) + if (lout == H5D_COMPACT) iter->dset_ohdr_info.total_size -= storage; /* Track the layout type for dataset */ (iter->dset_layouts[lout])++; /* Get the number of external files for the dataset */ - if((num_ext = H5Pget_external_count(dcpl)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_external_count() failed"); + if ((num_ext = H5Pget_external_count(dcpl)) < 0) + H5TOOLS_GOTO_ERROR(FAIL, "H5Pget_external_count() failed"); /* Accumulate raw data size accordingly */ - if(num_ext) { + if (num_ext) { iter->nexternal += (unsigned long)num_ext; iter->dset_external_storage_size += (unsigned long)storage; } @@ -579,37 +490,38 @@ dataset_stats(iter_t *iter, const char *name, const H5O_info_t *oi) iter->dset_storage_size += storage; /* Gather dataspace statistics */ - if((sid = H5Dget_space(did)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_space() failed"); + if ((sid = H5Dget_space(did)) < 0) + H5TOOLS_GOTO_ERROR(FAIL, "H5Sget_space() failed"); - if((ndims = H5Sget_simple_extent_dims(sid, dims, NULL)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims() failed"); + if ((ndims = H5Sget_simple_extent_dims(sid, dims, NULL)) < 0) + H5TOOLS_GOTO_ERROR(FAIL, "H5Sget_simple_extent_dims() failed"); /* Check for larger rank of dataset */ - if((unsigned)ndims > iter->max_dset_rank) + if ((unsigned)ndims > iter->max_dset_rank) iter->max_dset_rank = (unsigned)ndims; /* Track the number of datasets with each rank */ (iter->dset_rank_count[ndims])++; /* Only gather dim size statistics on 1-D datasets */ - if(ndims == 1) { + if (ndims == 1) { /* Determine maximum dimension size */ - if(dims[0] > iter->max_dset_dims) + if (dims[0] > iter->max_dset_dims) iter->max_dset_dims = dims[0]; /* Collect statistics for small datasets */ - if(dims[0] < (hsize_t)sdsets_threshold) + if (dims[0] < (hsize_t)sdsets_threshold) (iter->small_dset_dims[(size_t)dims[0]])++; /* Add dim count to proper bin */ bin = ceil_log10((unsigned long)dims[0]); - if((bin + 1) > iter->dset_dim_nbins) { + if ((bin + 1) > iter->dset_dim_nbins) { /* Allocate more storage for info about dataset's datatype */ - if((iter->dset_dim_bins = (unsigned long *)HDrealloc(iter->dset_dim_bins, (bin + 1) * sizeof(unsigned long))) == NULL) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Drealloc() failed"); + if ((iter->dset_dim_bins = (unsigned long *)HDrealloc(iter->dset_dim_bins, + (bin + 1) * sizeof(unsigned long))) == NULL) + H5TOOLS_GOTO_ERROR(FAIL, "H5Drealloc() failed"); /* Initialize counts for intermediate bins */ - while(iter->dset_dim_nbins < bin) + while (iter->dset_dim_nbins < bin) iter->dset_dim_bins[iter->dset_dim_nbins++] = 0; iter->dset_dim_nbins++; @@ -620,22 +532,22 @@ dataset_stats(iter_t *iter, const char *name, const H5O_info_t *oi) (iter->dset_dim_bins[bin])++; } /* end if */ - if(H5Sclose(sid) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose() failed"); + if (H5Sclose(sid) < 0) + H5TOOLS_GOTO_ERROR(FAIL, "H5Sclose() failed"); /* Gather datatype statistics */ - if((tid = H5Dget_type(did)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_type() failed"); + if ((tid = H5Dget_type(did)) < 0) + H5TOOLS_GOTO_ERROR(FAIL, "H5Dget_type() failed"); type_found = FALSE; - for(u = 0; u < iter->dset_ntypes; u++) - if(H5Tequal(iter->dset_type_info[u].tid, tid) > 0) { + for (u = 0; u < iter->dset_ntypes; u++) + if (H5Tequal(iter->dset_type_info[u].tid, tid) > 0) { type_found = TRUE; break; } /* end for */ - if(type_found) - (iter->dset_type_info[u].count)++; + if (type_found) + (iter->dset_type_info[u].count)++; else { unsigned curr_ntype = (unsigned)iter->dset_ntypes; @@ -643,12 +555,13 @@ dataset_stats(iter_t *iter, const char *name, const H5O_info_t *oi) iter->dset_ntypes++; /* Allocate more storage for info about dataset's datatype */ - if((iter->dset_type_info = (dtype_info_t *)HDrealloc(iter->dset_type_info, iter->dset_ntypes * sizeof(dtype_info_t))) == NULL) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Drealloc() failed"); + if ((iter->dset_type_info = (dtype_info_t *)HDrealloc( + iter->dset_type_info, iter->dset_ntypes * sizeof(dtype_info_t))) == NULL) + H5TOOLS_GOTO_ERROR(FAIL, "H5Drealloc() failed"); /* Initialize information about datatype */ - if((iter->dset_type_info[curr_ntype].tid = H5Tcopy(tid)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tcopy() failed"); + if ((iter->dset_type_info[curr_ntype].tid = H5Tcopy(tid)) < 0) + H5TOOLS_GOTO_ERROR(FAIL, "H5Tcopy() failed"); iter->dset_type_info[curr_ntype].count = 1; iter->dset_type_info[curr_ntype].named = 0; @@ -657,37 +570,36 @@ dataset_stats(iter_t *iter, const char *name, const H5O_info_t *oi) } /* end else */ /* Check if the datatype is a named datatype */ - if(H5Tcommitted(tid) > 0) + if (H5Tcommitted(tid) > 0) (iter->dset_type_info[u].named)++; - if(H5Tclose(tid) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose() failed"); + if (H5Tclose(tid) < 0) + H5TOOLS_GOTO_ERROR(FAIL, "H5Tclose() failed"); /* Track different filters */ - if((nfltr = H5Pget_nfilters(dcpl)) >= 0) { - if(nfltr == 0) - iter->dset_comptype[0]++; - for(u = 0; u < (unsigned)nfltr; u++) { + if ((nfltr = H5Pget_nfilters(dcpl)) >= 0) { + if (nfltr == 0) + iter->dset_comptype[0]++; + for (u = 0; u < (unsigned)nfltr; u++) { fltr = H5Pget_filter2(dcpl, u, 0, 0, 0, 0, 0, NULL); - if(fltr >= 0) { - if(fltr < (H5_NFILTERS_IMPL - 1)) + if (fltr >= 0) { + if (fltr < (H5_NFILTERS_IMPL - 1)) iter->dset_comptype[fltr]++; else iter->dset_comptype[H5_NFILTERS_IMPL - 1]++; /*other filters*/ - } /* end if */ - } /* end for */ - } /* endif nfltr */ + } /* end if */ + } /* end for */ + } /* endif nfltr */ - if(H5Pclose(dcpl) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose() failed"); + if (H5Pclose(dcpl) < 0) + H5TOOLS_GOTO_ERROR(FAIL, "H5Pclose() failed"); - if(H5Dclose(did) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose() failed"); + if (H5Dclose(did) < 0) + H5TOOLS_GOTO_ERROR(FAIL, "H5Dclose() failed"); done: - return ret_value; -} /* end dataset_stats() */ - + return ret_value; +} /* end dataset_stats() */ /*------------------------------------------------------------------------- * Function: datatype_stats @@ -702,7 +614,7 @@ done: *------------------------------------------------------------------------- */ static herr_t -datatype_stats(iter_t *iter, const H5O_info_t *oi) +datatype_stats(iter_t *iter, const H5O_info2_t *oi, const H5O_native_info_t *native_oi) { herr_t ret_value = SUCCEED; @@ -710,16 +622,15 @@ datatype_stats(iter_t *iter, const H5O_info_t *oi) iter->uniq_dtypes++; /* Get object header information */ - iter->dtype_ohdr_info.total_size += oi->hdr.space.total; - iter->dtype_ohdr_info.free_size += oi->hdr.space.free; + iter->dtype_ohdr_info.total_size += native_oi->hdr.space.total; + iter->dtype_ohdr_info.free_size += native_oi->hdr.space.free; /* Update attribute metadata info */ - if((ret_value = attribute_stats(iter, oi)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "attribute_stats() failed"); + if ((ret_value = attribute_stats(iter, oi, native_oi)) < 0) + H5TOOLS_GOTO_ERROR(FAIL, "attribute_stats() failed"); done: - return ret_value; -} /* end datatype_stats() */ - + return ret_value; +} /* end datatype_stats() */ /*------------------------------------------------------------------------- * Function: obj_stats @@ -735,32 +646,36 @@ done: *------------------------------------------------------------------------- */ static herr_t -obj_stats(const char *path, const H5O_info_t *oi, const char *already_visited, - void *_iter) +obj_stats(const char *path, const H5O_info2_t *oi, const char *already_visited, void *_iter) { - iter_t *iter = (iter_t *)_iter; - herr_t ret_value = SUCCEED; + H5O_native_info_t native_info; + iter_t * iter = (iter_t *)_iter; + herr_t ret_value = SUCCEED; /* If the object has already been seen then just return */ - if(NULL == already_visited) { + if (NULL == already_visited) { + /* Retrieve the native info for the object */ + if (H5Oget_native_info_by_name(iter->fid, path, &native_info, H5O_NATIVE_INFO_ALL, H5P_DEFAULT) < 0) + H5TOOLS_GOTO_ERROR(FAIL, "H5Oget_native_info_by_name failed"); + /* Gather some general statistics about the object */ - if(oi->rc > iter->max_links) + if (oi->rc > iter->max_links) iter->max_links = oi->rc; - switch(oi->type) { + switch (oi->type) { case H5O_TYPE_GROUP: - if(group_stats(iter, path, oi) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "group_stats failed"); + if (group_stats(iter, path, oi, &native_info) < 0) + H5TOOLS_GOTO_ERROR(FAIL, "group_stats failed"); break; case H5O_TYPE_DATASET: - if(dataset_stats(iter, path, oi) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "dataset_stats failed"); + if (dataset_stats(iter, path, oi, &native_info) < 0) + H5TOOLS_GOTO_ERROR(FAIL, "dataset_stats failed"); break; case H5O_TYPE_NAMED_DATATYPE: - if(datatype_stats(iter, oi) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "datatype_stats failed"); + if (datatype_stats(iter, oi, &native_info) < 0) + H5TOOLS_GOTO_ERROR(FAIL, "datatype_stats failed"); break; case H5O_TYPE_MAP: @@ -771,13 +686,12 @@ obj_stats(const char *path, const H5O_info_t *oi, const char *already_visited, iter->uniq_others++; break; } /* end switch */ - } /* end if */ + } /* end if */ done: return ret_value; } /* end obj_stats() */ - /*------------------------------------------------------------------------- * Function: lnk_stats * @@ -792,11 +706,11 @@ done: *------------------------------------------------------------------------- */ static herr_t -lnk_stats(const char H5_ATTR_UNUSED *path, const H5L_info_t *li, void *_iter) +lnk_stats(const char H5_ATTR_UNUSED *path, const H5L_info2_t *li, void *_iter) { iter_t *iter = (iter_t *)_iter; - switch(li->type) { + switch (li->type) { case H5L_TYPE_SOFT: case H5L_TYPE_EXTERNAL: /* Gather statistics about links and UD links */ @@ -830,35 +744,35 @@ lnk_stats(const char H5_ATTR_UNUSED *path, const H5L_info_t *li, void *_iter) static herr_t freespace_stats(hid_t fid, iter_t *iter) { - H5F_sect_info_t *sect_info = NULL; /* Free space sections */ - ssize_t nsects; /* Number of free space sections */ - size_t u; /* Local index variable */ + H5F_sect_info_t *sect_info = NULL; /* Free space sections */ + ssize_t nsects; /* Number of free space sections */ + size_t u; /* Local index variable */ /* Query section information */ - if((nsects = H5Fget_free_sections(fid, H5FD_MEM_DEFAULT, 0, NULL)) < 0) - return(FAIL); - else if(nsects) { - if(NULL == (sect_info = (H5F_sect_info_t *)HDcalloc((size_t)nsects, sizeof(H5F_sect_info_t)))) - return(FAIL); + if ((nsects = H5Fget_free_sections(fid, H5FD_MEM_DEFAULT, 0, NULL)) < 0) + return (FAIL); + else if (nsects) { + if (NULL == (sect_info = (H5F_sect_info_t *)HDcalloc((size_t)nsects, sizeof(H5F_sect_info_t)))) + return (FAIL); nsects = H5Fget_free_sections(fid, H5FD_MEM_DEFAULT, (size_t)nsects, sect_info); HDassert(nsects); } /* end else-if */ - for(u = 0; u < (size_t)nsects; u++) { - unsigned bin; /* "bin" the number of objects falls in */ + for (u = 0; u < (size_t)nsects; u++) { + unsigned bin; /* "bin" the number of objects falls in */ - if(sect_info[u].size < SIZE_SMALL_SECTS) + if (sect_info[u].size < SIZE_SMALL_SECTS) (iter->num_small_sects[(size_t)sect_info[u].size])++; /* Add section size to proper bin */ bin = ceil_log10((unsigned long)sect_info[u].size); - if(bin >= iter->sect_nbins) { + if (bin >= iter->sect_nbins) { /* Allocate more storage for section info */ iter->sect_bins = (unsigned long *)HDrealloc(iter->sect_bins, (bin + 1) * sizeof(unsigned long)); HDassert(iter->sect_bins); /* Initialize counts for intermediate bins */ - while(iter->sect_nbins < bin) + while (iter->sect_nbins < bin) iter->sect_bins[iter->sect_nbins++] = 0; iter->sect_nbins++; @@ -869,13 +783,12 @@ freespace_stats(hid_t fid, iter_t *iter) (iter->sect_bins[bin])++; } /* end for */ - if(sect_info) + if (sect_info) HDfree(sect_info); return 0; } /* end freespace_stats() */ - /*------------------------------------------------------------------------- * Function: hand_free * @@ -890,11 +803,11 @@ freespace_stats(hid_t fid, iter_t *iter) static void hand_free(struct handler_t *hand) { - if(hand) { + if (hand) { unsigned u; - for(u = 0; u < hand->obj_count; u++) - if(hand->obj[u]) { + for (u = 0; u < hand->obj_count; u++) + if (hand->obj[u]) { HDfree(hand->obj[u]); hand->obj[u] = NULL; } /* end if */ @@ -904,7 +817,6 @@ hand_free(struct handler_t *hand) } /* end if */ } /* end hand_free() */ - /*------------------------------------------------------------------------- * Function: parse_command_line * @@ -920,15 +832,15 @@ hand_free(struct handler_t *hand) *------------------------------------------------------------------------- */ static int -parse_command_line(int argc, const char *argv[], struct handler_t **hand_ret) +parse_command_line(int argc, const char *const *argv, struct handler_t **hand_ret) { - int opt; - unsigned u; - struct handler_t *hand = NULL; + int opt; + unsigned u; + struct handler_t *hand = NULL; /* parse command line options */ - while((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) { - switch((char)opt) { + while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) { + switch ((char)opt) { case 'h': usage(h5tools_getprogname()); h5tools_setstatus(EXIT_SUCCESS); @@ -942,33 +854,36 @@ parse_command_line(int argc, const char *argv[], struct handler_t **hand_ret) break; case 'E': - enable_error_stack = 1; + if (H5_optarg != NULL) + enable_error_stack = HDatoi(H5_optarg); + else + enable_error_stack = 1; break; case 'F': - display_all = FALSE; + display_all = FALSE; display_file_metadata = TRUE; break; case 'f': - display_all = FALSE; + display_all = FALSE; display_file = TRUE; break; case 'G': - display_all = FALSE; + display_all = FALSE; display_group_metadata = TRUE; break; case 'g': - display_all = FALSE; + display_all = FALSE; display_group = TRUE; break; case 'l': - if(opt_arg) { - sgroups_threshold = HDatoi(opt_arg); - if(sgroups_threshold < 1) { + if (H5_optarg) { + sgroups_threshold = HDatoi(H5_optarg); + if (sgroups_threshold < 1) { error_msg("Invalid threshold for small groups\n"); goto error; } @@ -979,19 +894,19 @@ parse_command_line(int argc, const char *argv[], struct handler_t **hand_ret) break; case 'D': - display_all = FALSE; + display_all = FALSE; display_dset_metadata = TRUE; break; case 'd': - display_all = FALSE; + display_all = FALSE; display_dset = TRUE; break; case 'm': - if(opt_arg) { - sdsets_threshold = HDatoi(opt_arg); - if(sdsets_threshold < 1) { + if (H5_optarg) { + sdsets_threshold = HDatoi(H5_optarg); + if (sdsets_threshold < 1) { error_msg("Invalid threshold for small datasets\n"); goto error; } @@ -1002,19 +917,19 @@ parse_command_line(int argc, const char *argv[], struct handler_t **hand_ret) break; case 'T': - display_all = FALSE; + display_all = FALSE; display_dset_dtype_meta = TRUE; break; case 'A': - display_all = FALSE; + display_all = FALSE; display_attr = TRUE; break; case 'a': - if(opt_arg) { - sattrs_threshold = HDatoi(opt_arg); - if(sattrs_threshold < 1) { + if (H5_optarg) { + sattrs_threshold = HDatoi(H5_optarg); + if (sattrs_threshold < 1) { error_msg("Invalid threshold for small # of attributes\n"); goto error; } @@ -1025,147 +940,76 @@ parse_command_line(int argc, const char *argv[], struct handler_t **hand_ret) break; case 's': - display_all = FALSE; + display_all = FALSE; display_free_sections = TRUE; break; case 'S': - display_all = FALSE; + display_all = FALSE; display_summary = TRUE; break; case 'O': - display_all = FALSE; + display_all = FALSE; display_object = TRUE; /* Allocate space to hold the command line info */ - if(NULL == (hand = (struct handler_t *)HDcalloc((size_t)1, sizeof(struct handler_t)))) { + if (NULL == (hand = (struct handler_t *)HDcalloc((size_t)1, sizeof(struct handler_t)))) { error_msg("unable to allocate memory for object struct\n"); goto error; } /* end if */ /* Allocate space to hold the object strings */ hand->obj_count = (size_t)argc; - if(NULL == (hand->obj = (char **)HDcalloc((size_t)argc, sizeof(char *)))) { + if (NULL == (hand->obj = (char **)HDcalloc((size_t)argc, sizeof(char *)))) { error_msg("unable to allocate memory for object array\n"); goto error; } /* end if */ /* Store object names */ - for(u = 0; u < hand->obj_count; u++) - if(NULL == (hand->obj[u] = HDstrdup(opt_arg))) { + for (u = 0; u < hand->obj_count; u++) + if (NULL == (hand->obj[u] = HDstrdup(H5_optarg))) { error_msg("unable to allocate memory for object name\n"); goto error; } /* end if */ break; case 'w': -#ifndef H5_HAVE_ROS3_VFD +#ifdef H5_HAVE_ROS3_VFD + if (h5tools_parse_ros3_fapl_tuple(H5_optarg, ',', &ros3_fa) < 0) { + error_msg("failed to parse S3 VFD credential info\n"); + goto error; + } + + drivername = drivernames[ROS3_VFD_IDX]; +#else error_msg("Read-Only S3 VFD not enabled.\n"); goto error; -#else - { - char *cred_str = NULL; - unsigned nelems = 0; - char **cred = NULL; - char const *ccred[3]; - - if (FAIL == parse_tuple((const char *)opt_arg, ',', &cred_str, &nelems, &cred)) { - error_msg("Unable to parse s3 credential\n"); - goto error; - } - if (nelems != 3) { - error_msg("s3 credential must have three elements\n"); - goto error; - } - ccred[0] = (const char *)cred[0]; - ccred[1] = (const char *)cred[1]; - ccred[2] = (const char *)cred[2]; - if (0 == h5tools_populate_ros3_fapl(&ros3_fa, ccred)) { - error_msg("Unable to set ros3 fapl config\n"); - goto error; - } - HDfree(cred); - HDfree(cred_str); - } /* parse s3-cred block */ - drivername = "ros3"; +#endif break; -#endif /* H5_HAVE_ROS3_VFD */ case 'H': -#ifndef H5_HAVE_LIBHDFS - error_msg("HDFS VFD is not enabled.\n"); - goto error; -#else - { - unsigned nelems = 0; - char *props_src = NULL; - char **props = NULL; - unsigned long k = 0; - if (FAIL == parse_tuple((const char *)opt_arg, - ',', &props_src, &nelems, &props)) { - error_msg("unable to parse hdfs properties tuple\n"); - goto error; - } - /* sanity-check tuple count - */ - if (nelems != 5) { - char str[64] = ""; - HDsprintf(str, - "expected 5 elements in hdfs properties tuple " - "but found %u\n", - nelems); - HDfree(props); - HDfree(props_src); - error_msg(str); - goto error; - } - /* Populate fapl configuration structure with given - * properties. - * TODO/WARNING: No error-checking is done on length of - * input strings... Silent overflow is possible, - * albeit unlikely. - */ - if (HDstrncmp(props[0], "", 1)) { - HDstrncpy(hdfs_fa.namenode_name,(const char *)props[0], HDstrlen(props[0])); - } - if (HDstrncmp(props[1], "", 1)) { - k = strtoul((const char *)props[1], NULL, 0); - if (errno == ERANGE) { - error_msg("supposed port number wasn't.\n"); - goto error; - } - hdfs_fa.namenode_port = (int32_t)k; - } - if (HDstrncmp(props[2], "", 1)) { - HDstrncpy(hdfs_fa.kerberos_ticket_cache, (const char *)props[2], HDstrlen(props[2])); - } - if (HDstrncmp(props[3], "", 1)) { - HDstrncpy(hdfs_fa.user_name, (const char *)props[3], HDstrlen(props[3])); - } - if (strncmp(props[4], "", 1)) { - k = HDstrtoul((const char *)props[4], NULL, 0); - if (errno == ERANGE) { - error_msg("supposed buffersize number wasn't.\n"); - goto error; - } - hdfs_fa.stream_buffer_size = (int32_t)k; - } - HDfree(props); - HDfree(props_src); - drivername = "hdfs"; +#ifdef H5_HAVE_LIBHDFS + if (h5tools_parse_hdfs_fapl_tuple(H5_optarg, ',', &hdfs_fa) < 0) { + error_msg("failed to parse HDFS VFD configuration info\n"); + goto error; } + + drivername = drivernames[HDFS_VFD_IDX]; +#else + error_msg("HDFS VFD not enabled.\n"); + goto error; +#endif break; -#endif /* H5_HAVE_LIBHDFS */ default: usage(h5tools_getprogname()); goto error; } /* end switch */ - } /* end while */ + } /* end while */ /* check for file name to be processed */ - if(argc <= opt_ind) { + if (argc <= H5_optind) { error_msg("missing file name\n"); usage(h5tools_getprogname()); goto error; @@ -1184,7 +1028,6 @@ error: return -1; } - /*------------------------------------------------------------------------- * Function: iter_free * @@ -1201,55 +1044,54 @@ iter_free(iter_t *iter) { /* Clear array of bins for group counts */ - if(iter->group_bins) { + if (iter->group_bins) { HDfree(iter->group_bins); iter->group_bins = NULL; } /* end if */ /* Clear array for tracking small groups */ - if(iter->num_small_groups) { + if (iter->num_small_groups) { HDfree(iter->num_small_groups); iter->num_small_groups = NULL; } /* end if */ /* Clear array of bins for attribute counts */ - if(iter->attr_bins) { + if (iter->attr_bins) { HDfree(iter->attr_bins); iter->attr_bins = NULL; } /* end if */ /* Clear array for tracking small attributes */ - if(iter->num_small_attrs) { + if (iter->num_small_attrs) { HDfree(iter->num_small_attrs); - iter->num_small_attrs= NULL; + iter->num_small_attrs = NULL; } /* end if */ /* Clear dataset datatype information found */ - if(iter->dset_type_info) { + if (iter->dset_type_info) { HDfree(iter->dset_type_info); iter->dset_type_info = NULL; } /* end if */ /* Clear array of bins for dataset dimensions */ - if(iter->dset_dim_bins) { + if (iter->dset_dim_bins) { HDfree(iter->dset_dim_bins); iter->dset_dim_bins = NULL; } /* end if */ /* Clear array of tracking 1-D small datasets */ - if(iter->small_dset_dims) { + if (iter->small_dset_dims) { HDfree(iter->small_dset_dims); iter->small_dset_dims = NULL; } /* end if */ /* Clear array of bins for free-space section sizes */ - if(iter->sect_bins) { + if (iter->sect_bins) { HDfree(iter->sect_bins); iter->sect_bins = NULL; } /* end if */ } /* end iter_free() */ - /*------------------------------------------------------------------------- * Function: print_file_info * @@ -1276,12 +1118,11 @@ print_file_info(const iter_t *iter) HDprintf("\t# of unique links: %lu\n", iter->uniq_links); HDprintf("\t# of unique other: %lu\n", iter->uniq_others); HDprintf("\tMax. # of links to object: %lu\n", iter->max_links); - HDfprintf(stdout, "\tMax. # of objects in group: %Hu\n", iter->max_fanout); + HDfprintf(stdout, "\tMax. # of objects in group: %" PRIuHSIZE "\n", iter->max_fanout); return 0; } /* print_file_info() */ - /*------------------------------------------------------------------------- * Function: print_file_metadata * @@ -1300,45 +1141,44 @@ static herr_t print_file_metadata(const iter_t *iter) { HDfprintf(stdout, "File space information for file metadata (in bytes):\n"); - HDfprintf(stdout, "\tSuperblock: %Hu\n", iter->super_size); - HDfprintf(stdout, "\tSuperblock extension: %Hu\n", iter->super_ext_size); - HDfprintf(stdout, "\tUser block: %Hu\n", iter->ublk_size); + HDfprintf(stdout, "\tSuperblock: %" PRIuHSIZE "\n", iter->super_size); + HDfprintf(stdout, "\tSuperblock extension: %" PRIuHSIZE "\n", iter->super_ext_size); + HDfprintf(stdout, "\tUser block: %" PRIuHSIZE "\n", iter->ublk_size); HDfprintf(stdout, "\tObject headers: (total/unused)\n"); - HDfprintf(stdout, "\t\tGroups: %Hu/%Hu\n", iter->group_ohdr_info.total_size, - iter->group_ohdr_info.free_size); - HDfprintf(stdout, "\t\tDatasets(exclude compact data): %Hu/%Hu\n", - iter->dset_ohdr_info.total_size, iter->dset_ohdr_info.free_size); - HDfprintf(stdout, "\t\tDatatypes: %Hu/%Hu\n", iter->dtype_ohdr_info.total_size, - iter->dtype_ohdr_info.free_size); + HDfprintf(stdout, "\t\tGroups: %" PRIuHSIZE "/%" PRIuHSIZE "\n", iter->group_ohdr_info.total_size, + iter->group_ohdr_info.free_size); + HDfprintf(stdout, "\t\tDatasets(exclude compact data): %" PRIuHSIZE "/%" PRIuHSIZE "\n", + iter->dset_ohdr_info.total_size, iter->dset_ohdr_info.free_size); + HDfprintf(stdout, "\t\tDatatypes: %" PRIuHSIZE "/%" PRIuHSIZE "\n", iter->dtype_ohdr_info.total_size, + iter->dtype_ohdr_info.free_size); HDfprintf(stdout, "\tGroups:\n"); - HDfprintf(stdout, "\t\tB-tree/List: %Hu\n", iter->groups_btree_storage_size); - HDfprintf(stdout, "\t\tHeap: %Hu\n", iter->groups_heap_storage_size); + HDfprintf(stdout, "\t\tB-tree/List: %" PRIuHSIZE "\n", iter->groups_btree_storage_size); + HDfprintf(stdout, "\t\tHeap: %" PRIuHSIZE "\n", iter->groups_heap_storage_size); HDfprintf(stdout, "\tAttributes:\n"); - HDfprintf(stdout, "\t\tB-tree/List: %Hu\n", iter->attrs_btree_storage_size); - HDfprintf(stdout, "\t\tHeap: %Hu\n", iter->attrs_heap_storage_size); + HDfprintf(stdout, "\t\tB-tree/List: %" PRIuHSIZE "\n", iter->attrs_btree_storage_size); + HDfprintf(stdout, "\t\tHeap: %" PRIuHSIZE "\n", iter->attrs_heap_storage_size); HDfprintf(stdout, "\tChunked datasets:\n"); - HDfprintf(stdout, "\t\tIndex: %Hu\n", iter->datasets_index_storage_size); + HDfprintf(stdout, "\t\tIndex: %" PRIuHSIZE "\n", iter->datasets_index_storage_size); HDfprintf(stdout, "\tDatasets:\n"); - HDfprintf(stdout, "\t\tHeap: %Hu\n", iter->datasets_heap_storage_size); + HDfprintf(stdout, "\t\tHeap: %" PRIuHSIZE "\n", iter->datasets_heap_storage_size); HDfprintf(stdout, "\tShared Messages:\n"); - HDfprintf(stdout, "\t\tHeader: %Hu\n", iter->SM_hdr_storage_size); - HDfprintf(stdout, "\t\tB-tree/List: %Hu\n", iter->SM_index_storage_size); - HDfprintf(stdout, "\t\tHeap: %Hu\n", iter->SM_heap_storage_size); + HDfprintf(stdout, "\t\tHeader: %" PRIuHSIZE "\n", iter->SM_hdr_storage_size); + HDfprintf(stdout, "\t\tB-tree/List: %" PRIuHSIZE "\n", iter->SM_index_storage_size); + HDfprintf(stdout, "\t\tHeap: %" PRIuHSIZE "\n", iter->SM_heap_storage_size); HDfprintf(stdout, "\tFree-space managers:\n"); - HDfprintf(stdout, "\t\tHeader: %Hu\n", iter->free_hdr); - HDfprintf(stdout, "\t\tAmount of free space: %Hu\n", iter->free_space); + HDfprintf(stdout, "\t\tHeader: %" PRIuHSIZE "\n", iter->free_hdr); + HDfprintf(stdout, "\t\tAmount of free space: %" PRIuHSIZE "\n", iter->free_space); return 0; } /* print_file_metadata() */ - /*------------------------------------------------------------------------- * Function: print_group_info * @@ -1361,32 +1201,32 @@ print_file_metadata(const iter_t *iter) static herr_t print_group_info(const iter_t *iter) { - unsigned long power; /* Temporary "power" for bins */ - unsigned long total; /* Total count for various statistics */ - unsigned u; /* Local index variable */ + unsigned long power; /* Temporary "power" for bins */ + unsigned long total; /* Total count for various statistics */ + unsigned u; /* Local index variable */ - HDprintf("Small groups (with 0 to %u links):\n", sgroups_threshold-1); + HDprintf("Small groups (with 0 to %u links):\n", sgroups_threshold - 1); total = 0; - for(u = 0; u < (unsigned)sgroups_threshold; u++) { - if(iter->num_small_groups[u] > 0) { + for (u = 0; u < (unsigned)sgroups_threshold; u++) { + if (iter->num_small_groups[u] > 0) { HDprintf("\t# of groups with %u link(s): %lu\n", u, iter->num_small_groups[u]); total += iter->num_small_groups[u]; } /* end if */ - } /* end for */ + } /* end for */ HDprintf("\tTotal # of small groups: %lu\n", total); HDprintf("Group bins:\n"); total = 0; - if((iter->group_nbins > 0) && (iter->group_bins[0] > 0)) { - HDprintf("\t# of groups with 0 link: %lu\n", iter->group_bins[0]); - total = iter->group_bins[0]; + if ((iter->group_nbins > 0) && (iter->group_bins[0] > 0)) { + HDprintf("\t# of groups with 0 link: %lu\n", iter->group_bins[0]); + total = iter->group_bins[0]; } /* end if */ power = 1; - for(u = 1; u < iter->group_nbins; u++) { - if(iter->group_bins[u] > 0) { - HDprintf("\t# of groups with %lu - %lu links: %lu\n", power, (power * 10) - 1, - iter->group_bins[u]); - total += iter->group_bins[u]; + for (u = 1; u < iter->group_nbins; u++) { + if (iter->group_bins[u] > 0) { + HDprintf("\t# of groups with %lu - %lu links: %lu\n", power, (power * 10) - 1, + iter->group_bins[u]); + total += iter->group_bins[u]; } /* end if */ power *= 10; } /* end for */ @@ -1395,7 +1235,6 @@ print_group_info(const iter_t *iter) return 0; } /* print_group_info() */ - /*------------------------------------------------------------------------- * Function: print_group_metadata * @@ -1413,16 +1252,15 @@ print_group_metadata(const iter_t *iter) { HDprintf("File space information for groups' metadata (in bytes):\n"); - HDfprintf(stdout, "\tObject headers (total/unused): %Hu/%Hu\n", - iter->group_ohdr_info.total_size, iter->group_ohdr_info.free_size); + HDfprintf(stdout, "\tObject headers (total/unused): %" PRIuHSIZE "/%" PRIuHSIZE "\n", + iter->group_ohdr_info.total_size, iter->group_ohdr_info.free_size); - HDfprintf(stdout, "\tB-tree/List: %Hu\n", iter->groups_btree_storage_size); - HDfprintf(stdout, "\tHeap: %Hu\n", iter->groups_heap_storage_size); + HDfprintf(stdout, "\tB-tree/List: %" PRIuHSIZE "\n", iter->groups_btree_storage_size); + HDfprintf(stdout, "\tHeap: %" PRIuHSIZE "\n", iter->groups_heap_storage_size); return 0; } /* print_group_metadata() */ - /*------------------------------------------------------------------------- * Function: print_dataset_info * @@ -1439,44 +1277,43 @@ print_group_metadata(const iter_t *iter) static herr_t print_dataset_info(const iter_t *iter) { - unsigned long power; /* Temporary "power" for bins */ - unsigned long total; /* Total count for various statistics */ - unsigned u; /* Local index variable */ + unsigned long power; /* Temporary "power" for bins */ + unsigned long total; /* Total count for various statistics */ + unsigned u; /* Local index variable */ - if(iter->uniq_dsets > 0) { + if (iter->uniq_dsets > 0) { HDprintf("Dataset dimension information:\n"); HDprintf("\tMax. rank of datasets: %u\n", iter->max_dset_rank); HDprintf("\tDataset ranks:\n"); - for(u = 0; u < H5S_MAX_RANK; u++) - if(iter->dset_rank_count[u] > 0) + for (u = 0; u < H5S_MAX_RANK; u++) + if (iter->dset_rank_count[u] > 0) HDprintf("\t\t# of dataset with rank %u: %lu\n", u, iter->dset_rank_count[u]); HDprintf("1-D Dataset information:\n"); - HDfprintf(stdout, "\tMax. dimension size of 1-D datasets: %Hu\n", iter->max_dset_dims); + HDfprintf(stdout, "\tMax. dimension size of 1-D datasets: %" PRIuHSIZE "\n", iter->max_dset_dims); HDprintf("\tSmall 1-D datasets (with dimension sizes 0 to %u):\n", sdsets_threshold - 1); total = 0; - for(u = 0; u < (unsigned)sdsets_threshold; u++) { - if(iter->small_dset_dims[u] > 0) { - HDprintf("\t\t# of datasets with dimension sizes %u: %lu\n", u, - iter->small_dset_dims[u]); + for (u = 0; u < (unsigned)sdsets_threshold; u++) { + if (iter->small_dset_dims[u] > 0) { + HDprintf("\t\t# of datasets with dimension sizes %u: %lu\n", u, iter->small_dset_dims[u]); total += iter->small_dset_dims[u]; } /* end if */ - } /* end for */ + } /* end for */ HDprintf("\t\tTotal # of small datasets: %lu\n", total); /* Protect against no datasets in file */ - if(iter->dset_dim_nbins > 0) { + if (iter->dset_dim_nbins > 0) { HDprintf("\t1-D Dataset dimension bins:\n"); total = 0; - if(iter->dset_dim_bins[0] > 0) { + if (iter->dset_dim_bins[0] > 0) { HDprintf("\t\t# of datasets with dimension size 0: %lu\n", iter->dset_dim_bins[0]); total = iter->dset_dim_bins[0]; } /* end if */ power = 1; - for(u = 1; u < iter->dset_dim_nbins; u++) { - if(iter->dset_dim_bins[u] > 0) { - HDprintf("\t\t# of datasets with dimension size %lu - %lu: %lu\n", power, (power * 10) - 1, - iter->dset_dim_bins[u]); + for (u = 1; u < iter->dset_dim_nbins; u++) { + if (iter->dset_dim_bins[u] > 0) { + HDprintf("\t\t# of datasets with dimension size %lu - %lu: %lu\n", power, + (power * 10) - 1, iter->dset_dim_bins[u]); total += iter->dset_dim_bins[u]; } /* end if */ power *= 10; @@ -1485,31 +1322,34 @@ print_dataset_info(const iter_t *iter) } /* end if */ HDprintf("Dataset storage information:\n"); - HDfprintf(stdout, "\tTotal raw data size: %Hu\n", iter->dset_storage_size); - HDfprintf(stdout, "\tTotal external raw data size: %Hu\n", iter->dset_external_storage_size); + HDfprintf(stdout, "\tTotal raw data size: %" PRIuHSIZE "\n", iter->dset_storage_size); + HDfprintf(stdout, "\tTotal external raw data size: %" PRIuHSIZE "\n", + iter->dset_external_storage_size); HDprintf("Dataset layout information:\n"); - for(u = 0; u < H5D_NLAYOUTS; u++) - HDprintf("\tDataset layout counts[%s]: %lu\n", (u == H5D_COMPACT ? "COMPACT" : - (u == H5D_CONTIGUOUS ? "CONTIG" : (u == H5D_CHUNKED ? "CHUNKED" : "VIRTUAL"))), iter->dset_layouts[u]); + for (u = 0; u < H5D_NLAYOUTS; u++) + HDprintf("\tDataset layout counts[%s]: %lu\n", + (u == H5D_COMPACT + ? "COMPACT" + : (u == H5D_CONTIGUOUS ? "CONTIG" : (u == H5D_CHUNKED ? "CHUNKED" : "VIRTUAL"))), + iter->dset_layouts[u]); HDprintf("\tNumber of external files : %lu\n", iter->nexternal); HDprintf("Dataset filters information:\n"); HDprintf("\tNumber of datasets with:\n"); - HDprintf("\t\tNO filter: %lu\n", iter->dset_comptype[H5Z_FILTER_ERROR+1]); + HDprintf("\t\tNO filter: %lu\n", iter->dset_comptype[H5Z_FILTER_ERROR + 1]); HDprintf("\t\tGZIP filter: %lu\n", iter->dset_comptype[H5Z_FILTER_DEFLATE]); HDprintf("\t\tSHUFFLE filter: %lu\n", iter->dset_comptype[H5Z_FILTER_SHUFFLE]); HDprintf("\t\tFLETCHER32 filter: %lu\n", iter->dset_comptype[H5Z_FILTER_FLETCHER32]); HDprintf("\t\tSZIP filter: %lu\n", iter->dset_comptype[H5Z_FILTER_SZIP]); HDprintf("\t\tNBIT filter: %lu\n", iter->dset_comptype[H5Z_FILTER_NBIT]); HDprintf("\t\tSCALEOFFSET filter: %lu\n", iter->dset_comptype[H5Z_FILTER_SCALEOFFSET]); - HDprintf("\t\tUSER-DEFINED filter: %lu\n", iter->dset_comptype[H5_NFILTERS_IMPL-1]); + HDprintf("\t\tUSER-DEFINED filter: %lu\n", iter->dset_comptype[H5_NFILTERS_IMPL - 1]); } /* end if */ return 0; } /* print_dataset_info() */ - /*------------------------------------------------------------------------- * Function: print_dataset_metadata * @@ -1528,17 +1368,15 @@ print_dset_metadata(const iter_t *iter) { HDprintf("File space information for datasets' metadata (in bytes):\n"); - HDfprintf(stdout, "\tObject headers (total/unused): %Hu/%Hu\n", - iter->dset_ohdr_info.total_size, iter->dset_ohdr_info.free_size); + HDfprintf(stdout, "\tObject headers (total/unused): %" PRIuHSIZE "/%" PRIuHSIZE "\n", + iter->dset_ohdr_info.total_size, iter->dset_ohdr_info.free_size); - HDfprintf(stdout, "\tIndex for Chunked datasets: %Hu\n", - iter->datasets_index_storage_size); - HDfprintf(stdout, "\tHeap: %Hu\n", iter->datasets_heap_storage_size); + HDfprintf(stdout, "\tIndex for Chunked datasets: %" PRIuHSIZE "\n", iter->datasets_index_storage_size); + HDfprintf(stdout, "\tHeap: %" PRIuHSIZE "\n", iter->datasets_heap_storage_size); return 0; } /* print_dset_metadata() */ - /*------------------------------------------------------------------------- * Function: print_dset_dtype_meta * @@ -1555,21 +1393,21 @@ print_dset_metadata(const iter_t *iter) static herr_t print_dset_dtype_meta(const iter_t *iter) { - unsigned long total; /* Total count for various statistics */ - size_t dtype_size; /* Size of encoded datatype */ - unsigned u; /* Local index variable */ + unsigned long total; /* Total count for various statistics */ + size_t dtype_size; /* Size of encoded datatype */ + unsigned u; /* Local index variable */ - if(iter->dset_ntypes) { + if (iter->dset_ntypes) { HDprintf("Dataset datatype information:\n"); HDprintf("\t# of unique datatypes used by datasets: %lu\n", iter->dset_ntypes); total = 0; - for(u = 0; u < iter->dset_ntypes; u++) { + for (u = 0; u < iter->dset_ntypes; u++) { H5Tencode(iter->dset_type_info[u].tid, NULL, &dtype_size); HDprintf("\tDataset datatype #%u:\n", u); - HDprintf("\t\tCount (total/named) = (%lu/%lu)\n", - iter->dset_type_info[u].count, iter->dset_type_info[u].named); + HDprintf("\t\tCount (total/named) = (%lu/%lu)\n", iter->dset_type_info[u].count, + iter->dset_type_info[u].named); HDprintf("\t\tSize (desc./elmt) = (%lu/%lu)\n", (unsigned long)dtype_size, - (unsigned long)H5Tget_size(iter->dset_type_info[u].tid)); + (unsigned long)H5Tget_size(iter->dset_type_info[u].tid)); H5Tclose(iter->dset_type_info[u].tid); total += iter->dset_type_info[u].count; } /* end for */ @@ -1579,7 +1417,6 @@ print_dset_dtype_meta(const iter_t *iter) return 0; } /* print_dset_dtype_meta() */ - /*------------------------------------------------------------------------- * Function: print_attr_info * @@ -1597,28 +1434,28 @@ print_dset_dtype_meta(const iter_t *iter) static herr_t print_attr_info(const iter_t *iter) { - unsigned long power; /* Temporary "power" for bins */ - unsigned long total; /* Total count for various statistics */ - unsigned u; /* Local index variable */ + unsigned long power; /* Temporary "power" for bins */ + unsigned long total; /* Total count for various statistics */ + unsigned u; /* Local index variable */ HDprintf("Small # of attributes (objects with 1 to %u attributes):\n", sattrs_threshold); total = 0; - for(u = 1; u <= (unsigned)sattrs_threshold; u++) { - if(iter->num_small_attrs[u] > 0) { + for (u = 1; u <= (unsigned)sattrs_threshold; u++) { + if (iter->num_small_attrs[u] > 0) { HDprintf("\t# of objects with %u attributes: %lu\n", u, iter->num_small_attrs[u]); total += iter->num_small_attrs[u]; } /* end if */ - } /* end for */ + } /* end for */ HDprintf("\tTotal # of objects with small # of attributes: %lu\n", total); HDprintf("Attribute bins:\n"); total = 0; power = 1; - for(u = 1; u < iter->attr_nbins; u++) { - if(iter->attr_bins[u] > 0) { - HDprintf("\t# of objects with %lu - %lu attributes: %lu\n", power, (power * 10) - 1, - iter->attr_bins[u]); - total += iter->attr_bins[u]; + for (u = 1; u < iter->attr_nbins; u++) { + if (iter->attr_bins[u] > 0) { + HDprintf("\t# of objects with %lu - %lu attributes: %lu\n", power, (power * 10) - 1, + iter->attr_bins[u]); + total += iter->attr_bins[u]; } /* end if */ power *= 10; } /* end for */ @@ -1628,7 +1465,6 @@ print_attr_info(const iter_t *iter) return 0; } /* print_attr_info() */ - /*------------------------------------------------------------------------- * Function: print_freespace_info * @@ -1645,31 +1481,30 @@ print_attr_info(const iter_t *iter) static herr_t print_freespace_info(const iter_t *iter) { - unsigned long power; /* Temporary "power" for bins */ - unsigned long total; /* Total count for various statistics */ - unsigned u; /* Local index variable */ + unsigned long power; /* Temporary "power" for bins */ + unsigned long total; /* Total count for various statistics */ + unsigned u; /* Local index variable */ HDfprintf(stdout, "Free-space persist: %s\n", iter->fs_persist ? "TRUE" : "FALSE"); - HDfprintf(stdout, "Free-space section threshold: %Hu bytes\n", iter->fs_threshold); + HDfprintf(stdout, "Free-space section threshold: %" PRIuHSIZE " bytes\n", iter->fs_threshold); HDprintf("Small size free-space sections (< %u bytes):\n", (unsigned)SIZE_SMALL_SECTS); total = 0; - for(u = 0; u < SIZE_SMALL_SECTS; u++) { - if(iter->num_small_sects[u] > 0) { + for (u = 0; u < SIZE_SMALL_SECTS; u++) { + if (iter->num_small_sects[u] > 0) { HDprintf("\t# of sections of size %u: %lu\n", u, iter->num_small_sects[u]); total += iter->num_small_sects[u]; } /* end if */ - } /* end for */ + } /* end for */ HDprintf("\tTotal # of small size sections: %lu\n", total); HDprintf("Free-space section bins:\n"); total = 0; power = 1; - for(u = 1; u < iter->sect_nbins; u++) { - if(iter->sect_bins[u] > 0) { - HDprintf("\t# of sections of size %lu - %lu: %lu\n", power, (power * 10) - 1, - iter->sect_bins[u]); - total += iter->sect_bins[u]; + for (u = 1; u < iter->sect_nbins; u++) { + if (iter->sect_bins[u] > 0) { + HDprintf("\t# of sections of size %lu - %lu: %lu\n", power, (power * 10) - 1, iter->sect_bins[u]); + total += iter->sect_bins[u]; } /* end if */ power *= 10; } /* end for */ @@ -1678,7 +1513,6 @@ print_freespace_info(const iter_t *iter) return 0; } /* print_freespace_info() */ - /*------------------------------------------------------------------------- * Function: print_storage_summary * @@ -1696,53 +1530,45 @@ static herr_t print_storage_summary(const iter_t *iter) { hsize_t total_meta = 0; - hsize_t unaccount = 0; - double percent = 0.0f; + hsize_t unaccount = 0; + double percent = 0.0; HDfprintf(stdout, "File space management strategy: %s\n", FS_STRATEGY_NAME[iter->fs_strategy]); - HDfprintf(stdout, "File space page size: %Hu bytes\n", iter->fsp_size); + HDfprintf(stdout, "File space page size: %" PRIuHSIZE " bytes\n", iter->fsp_size); HDprintf("Summary of file space information:\n"); total_meta = - iter->super_size + iter->super_ext_size + iter->ublk_size + - iter->group_ohdr_info.total_size + - iter->dset_ohdr_info.total_size + - iter->dtype_ohdr_info.total_size + - iter->groups_btree_storage_size + - iter->groups_heap_storage_size + - iter->attrs_btree_storage_size + - iter->attrs_heap_storage_size + - iter->datasets_index_storage_size + - iter->datasets_heap_storage_size + - iter->SM_hdr_storage_size + - iter->SM_index_storage_size + - iter->SM_heap_storage_size + - iter->free_hdr; - - HDfprintf(stdout, " File metadata: %Hu bytes\n", total_meta); - HDfprintf(stdout, " Raw data: %Hu bytes\n", iter->dset_storage_size); - - percent = ((double)iter->free_space / (double)iter->filesize) * (double)100.0f; - HDfprintf(stdout, " Amount/Percent of tracked free space: %Hu bytes/%3.1f%\n", - iter->free_space, percent); - - if(iter->filesize < (total_meta + iter->dset_storage_size + iter->free_space)) { + iter->super_size + iter->super_ext_size + iter->ublk_size + iter->group_ohdr_info.total_size + + iter->dset_ohdr_info.total_size + iter->dtype_ohdr_info.total_size + iter->groups_btree_storage_size + + iter->groups_heap_storage_size + iter->attrs_btree_storage_size + iter->attrs_heap_storage_size + + iter->datasets_index_storage_size + iter->datasets_heap_storage_size + iter->SM_hdr_storage_size + + iter->SM_index_storage_size + iter->SM_heap_storage_size + iter->free_hdr; + + HDfprintf(stdout, " File metadata: %" PRIuHSIZE " bytes\n", total_meta); + HDfprintf(stdout, " Raw data: %" PRIuHSIZE " bytes\n", iter->dset_storage_size); + + percent = ((double)iter->free_space / (double)iter->filesize) * 100.0; + HDfprintf(stdout, " Amount/Percent of tracked free space: %" PRIuHSIZE " bytes/%3.1f%%\n", + iter->free_space, percent); + + if (iter->filesize < (total_meta + iter->dset_storage_size + iter->free_space)) { unaccount = (total_meta + iter->dset_storage_size + iter->free_space) - iter->filesize; - HDfprintf(stdout, " ??? File has %Hu more bytes accounted for than its size! ???\n", unaccount); + HDfprintf(stdout, " ??? File has %" PRIuHSIZE " more bytes accounted for than its size! ???\n", + unaccount); } else { unaccount = iter->filesize - (total_meta + iter->dset_storage_size + iter->free_space); - HDfprintf(stdout, " Unaccounted space: %Hu bytes\n", unaccount); + HDfprintf(stdout, " Unaccounted space: %" PRIuHSIZE " bytes\n", unaccount); } - HDfprintf(stdout, "Total space: %Hu bytes\n", total_meta + iter->dset_storage_size + iter->free_space + unaccount); + HDfprintf(stdout, "Total space: %" PRIuHSIZE " bytes\n", + total_meta + iter->dset_storage_size + iter->free_space + unaccount); - if(iter->nexternal) - HDfprintf(stdout, "External raw data: %Hu bytes\n", iter->dset_external_storage_size); + if (iter->nexternal) + HDfprintf(stdout, "External raw data: %" PRIuHSIZE " bytes\n", iter->dset_external_storage_size); return 0; } /* print_storage_summary() */ - /*------------------------------------------------------------------------- * Function: print_file_statistics * @@ -1760,36 +1586,45 @@ print_storage_summary(const iter_t *iter) static void print_file_statistics(const iter_t *iter) { - if(display_all) { - display_file = TRUE; - display_group = TRUE; - display_dset = TRUE; + if (display_all) { + display_file = TRUE; + display_group = TRUE; + display_dset = TRUE; display_dset_dtype_meta = TRUE; - display_attr = TRUE; - display_free_sections = TRUE; - display_summary = TRUE; + display_attr = TRUE; + display_free_sections = TRUE; + display_summary = TRUE; - display_file_metadata = TRUE; + display_file_metadata = TRUE; display_group_metadata = TRUE; - display_dset_metadata = TRUE; + display_dset_metadata = TRUE; } - if(display_file) print_file_info(iter); - if(display_file_metadata) print_file_metadata(iter); - - if(display_group) print_group_info(iter); - if(!display_all && display_group_metadata) print_group_metadata(iter); - - if(display_dset) print_dataset_info(iter); - if(display_dset_dtype_meta) print_dset_dtype_meta(iter); - if(!display_all && display_dset_metadata) print_dset_metadata(iter); - - if(display_attr) print_attr_info(iter); - if(display_free_sections) print_freespace_info(iter); - if(display_summary) print_storage_summary(iter); + if (display_file) + print_file_info(iter); + if (display_file_metadata) + print_file_metadata(iter); + + if (display_group) + print_group_info(iter); + if (!display_all && display_group_metadata) + print_group_metadata(iter); + + if (display_dset) + print_dataset_info(iter); + if (display_dset_dtype_meta) + print_dset_dtype_meta(iter); + if (!display_all && display_dset_metadata) + print_dset_metadata(iter); + + if (display_attr) + print_attr_info(iter); + if (display_free_sections) + print_freespace_info(iter); + if (display_summary) + print_storage_summary(iter); } /* print_file_statistics() */ - /*------------------------------------------------------------------------- * Function: print_object_statistics * @@ -1812,7 +1647,6 @@ print_object_statistics(const char *name) HDprintf("Object name %s\n", name); } /* print_object_statistics() */ - /*------------------------------------------------------------------------- * Function: print_statistics * @@ -1832,13 +1666,12 @@ print_object_statistics(const char *name) static void print_statistics(const char *name, const iter_t *iter) { - if(display_object) + if (display_object) print_object_statistics(name); else print_file_statistics(iter); } /* print_statistics() */ - /*------------------------------------------------------------------------- * Function: main * @@ -1849,89 +1682,53 @@ print_statistics(const char *name, const iter_t *iter) *------------------------------------------------------------------------- */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { - iter_t iter; - const char *fname = NULL; - hid_t fid = -1; - H5E_auto2_t func; - H5E_auto2_t tools_func; - void *edata; - void *tools_edata; - struct handler_t *hand = NULL; - hid_t fapl_id = H5P_DEFAULT; + iter_t iter; + const char * fname = NULL; + hid_t fid = H5I_INVALID_HID; + struct handler_t *hand = NULL; + hid_t fapl_id = H5P_DEFAULT; h5tools_setprogname(PROGRAMNAME); h5tools_setstatus(EXIT_SUCCESS); - /* Disable error reporting */ - H5Eget_auto2(H5E_DEFAULT, &func, &edata); - H5Eset_auto2(H5E_DEFAULT, NULL, NULL); - /* Initialize h5tools lib */ h5tools_init(); - /* Disable tools error reporting */ - H5Eget_auto2(H5tools_ERR_STACK_g, &tools_func, &tools_edata); - H5Eset_auto2(H5tools_ERR_STACK_g, NULL, NULL); - HDmemset(&iter, 0, sizeof(iter)); - if(parse_command_line(argc, argv, &hand) < 0) + if (parse_command_line(argc, (const char *const *)argv, &hand) < 0) goto done; - /* if drivername is not null, probably need to set the fapl */ - if (HDstrcmp(drivername, "")) { - void *conf_fa = NULL; + /* enable error reporting if command line option */ + h5tools_error_report(); - if (!HDstrcmp(drivername, "ros3")) { -#ifndef H5_HAVE_ROS3_VFD - error_msg("Read-Only S3 VFD not enabled.\n\n"); - goto done; -#else - conf_fa = (void *)&ros3_fa; -#endif /* H5_HAVE_ROS3_VFD */ + if (drivername) { + h5tools_vfd_info_t vfd_info; - } - else if (!HDstrcmp(drivername, "hdfs")) { -#ifndef H5_HAVE_LIBHDFS - error_msg("HDFS VFD not enabled.\n\n"); - goto done; -#else - conf_fa = (void *)&hdfs_fa; -#endif /* H5_HAVE_LIBHDFS */ - } + vfd_info.type = VFD_BY_NAME; + vfd_info.info = NULL; + vfd_info.u.name = drivername; - if (conf_fa != NULL) { - HDassert(fapl_id == H5P_DEFAULT); - fapl_id = H5Pcreate(H5P_FILE_ACCESS); - if (fapl_id < 0) { - error_msg("Unable to create fapl entry\n"); - goto done; - } - if (1 > h5tools_set_configured_fapl(fapl_id, drivername, conf_fa)) { - error_msg("Unable to set fapl\n"); - goto done; - } + if ((fapl_id = h5tools_get_fapl(H5P_DEFAULT, NULL, &vfd_info)) < 0) { + error_msg("Unable to create FAPL for file access\n"); + goto done; } - } /* drivername set */ - - fname = argv[opt_ind]; - - if(enable_error_stack > 0) { - H5Eset_auto2(H5E_DEFAULT, func, edata); - H5Eset_auto2(H5tools_ERR_STACK_g, tools_func, tools_edata); } + fname = argv[H5_optind]; + /* Check for filename given */ - if(fname) { - hid_t fcpl; - H5F_info2_t finfo; + if (fname) { + hid_t fcpl; + H5F_info2_t finfo; HDprintf("Filename: %s\n", fname); - fid = H5Fopen(fname, H5F_ACC_RDONLY, fapl_id); - if(fid < 0) { + fid = h5tools_fopen(fname, H5F_ACC_RDONLY, fapl_id, (fapl_id != H5P_DEFAULT), NULL, 0); + + if (fid < 0) { error_msg("unable to open file \"%s\"\n", fname); h5tools_setstatus(EXIT_FAILURE); goto done; @@ -1940,72 +1737,74 @@ main(int argc, const char *argv[]) /* Initialize iter structure */ iter.fid = fid; - if(H5Fget_filesize(fid, &iter.filesize) < 0) + if (H5Fget_filesize(fid, &iter.filesize) < 0) warn_msg("Unable to retrieve file size\n"); HDassert(iter.filesize != 0); - /* Get storge info for file-level structures */ - if(H5Fget_info2(fid, &finfo) < 0) + /* Get storage info for file-level structures */ + if (H5Fget_info2(fid, &finfo) < 0) warn_msg("Unable to retrieve file info\n"); else { - iter.super_size = finfo.super.super_size; - iter.super_ext_size = finfo.super.super_ext_size; - iter.SM_hdr_storage_size = finfo.sohm.hdr_size; + iter.super_size = finfo.super.super_size; + iter.super_ext_size = finfo.super.super_ext_size; + iter.SM_hdr_storage_size = finfo.sohm.hdr_size; iter.SM_index_storage_size = finfo.sohm.msgs_info.index_size; - iter.SM_heap_storage_size = finfo.sohm.msgs_info.heap_size; - iter.free_space = finfo.free.tot_space; - iter.free_hdr = finfo.free.meta_size; + iter.SM_heap_storage_size = finfo.sohm.msgs_info.heap_size; + iter.free_space = finfo.free.tot_space; + iter.free_hdr = finfo.free.meta_size; } /* end else */ iter.num_small_groups = (unsigned long *)HDcalloc((size_t)sgroups_threshold, sizeof(unsigned long)); - iter.num_small_attrs = (unsigned long *)HDcalloc((size_t)(sattrs_threshold+1), sizeof(unsigned long)); + iter.num_small_attrs = + (unsigned long *)HDcalloc((size_t)(sattrs_threshold + 1), sizeof(unsigned long)); iter.small_dset_dims = (unsigned long *)HDcalloc((size_t)sdsets_threshold, sizeof(unsigned long)); - if(iter.num_small_groups == NULL || iter.num_small_attrs == NULL || iter.small_dset_dims == NULL) { + if (iter.num_small_groups == NULL || iter.num_small_attrs == NULL || iter.small_dset_dims == NULL) { error_msg("Unable to allocate memory for tracking small groups/datasets/attributes\n"); h5tools_setstatus(EXIT_FAILURE); goto done; } - if((fcpl = H5Fget_create_plist(fid)) < 0) + if ((fcpl = H5Fget_create_plist(fid)) < 0) warn_msg("Unable to retrieve file creation property\n"); - if(H5Pget_userblock(fcpl, &iter.ublk_size) < 0) + if (H5Pget_userblock(fcpl, &iter.ublk_size) < 0) warn_msg("Unable to retrieve userblock size\n"); - if(H5Pget_file_space_strategy(fcpl, &iter.fs_strategy, &iter.fs_persist, &iter.fs_threshold) < 0) + if (H5Pget_file_space_strategy(fcpl, &iter.fs_strategy, &iter.fs_persist, &iter.fs_threshold) < 0) warn_msg("Unable to retrieve file space information\n"); HDassert(iter.fs_strategy >= 0 && iter.fs_strategy < H5F_FSPACE_STRATEGY_NTYPES); - if(H5Pget_file_space_page_size(fcpl, &iter.fsp_size) < 0) + if (H5Pget_file_space_page_size(fcpl, &iter.fsp_size) < 0) warn_msg("Unable to retrieve file space page size\n"); /* get information for free-space sections */ - if(freespace_stats(fid, &iter) < 0) + if (freespace_stats(fid, &iter) < 0) warn_msg("Unable to retrieve freespace info\n"); /* Walk the objects or all file */ - if(display_object) { + if (display_object) { unsigned u; - for(u = 0; u < hand->obj_count; u++) { - if(h5trav_visit(fid, hand->obj[u], TRUE, TRUE, obj_stats, lnk_stats, &iter, H5O_INFO_ALL) < 0) { + for (u = 0; u < hand->obj_count; u++) { + if (h5trav_visit(fid, hand->obj[u], TRUE, TRUE, obj_stats, lnk_stats, &iter, H5O_INFO_ALL) < + 0) { error_msg("unable to traverse object \"%s\"\n", hand->obj[u]); h5tools_setstatus(EXIT_FAILURE); } else print_statistics(hand->obj[u], &iter); } /* end for */ - } /* end if */ + } /* end if */ else { - if(h5trav_visit(fid, "/", TRUE, TRUE, obj_stats, lnk_stats, &iter, H5O_INFO_ALL) < 0) { + if (h5trav_visit(fid, "/", TRUE, TRUE, obj_stats, lnk_stats, &iter, H5O_INFO_ALL) < 0) { error_msg("unable to traverse objects/links in file \"%s\"\n", fname); h5tools_setstatus(EXIT_FAILURE); } else print_statistics("/", &iter); } /* end else */ - } /* end if */ + } /* end if */ done: hand_free(hand); @@ -2014,19 +1813,16 @@ done: iter_free(&iter); if (fapl_id != H5P_DEFAULT) { - if (0 < H5Pclose(fapl_id)) { + if (H5Pclose(fapl_id) < 0) { error_msg("unable to close fapl entry\n"); h5tools_setstatus(EXIT_FAILURE); } } - if(fid >= 0 && H5Fclose(fid) < 0) { + if (fid >= 0 && H5Fclose(fid) < 0) { error_msg("unable to close file \"%s\"\n", fname); h5tools_setstatus(EXIT_FAILURE); } /* end if */ - H5Eset_auto2(H5E_DEFAULT, func, edata); - leave(h5tools_getstatus()); } /* end main() */ - diff --git a/tools/src/misc/CMakeLists.txt b/tools/src/misc/CMakeLists.txt index 6b41d7f..8811f97 100644 --- a/tools/src/misc/CMakeLists.txt +++ b/tools/src/misc/CMakeLists.txt @@ -1,4 +1,4 @@ -cmake_minimum_required (VERSION 3.10) +cmake_minimum_required (VERSION 3.12) project (HDF5_TOOLS_SRC_MISC C) # -------------------------------------------------------------------- @@ -7,77 +7,122 @@ project (HDF5_TOOLS_SRC_MISC C) #-- Misc Executables if (NOT ONLY_SHARED_LIBS) add_executable (h5debug ${HDF5_TOOLS_SRC_MISC_SOURCE_DIR}/h5debug.c) - target_include_directories (h5debug PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5debug PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_compile_options(h5debug PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5debug STATIC) target_link_libraries (h5debug PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) set_target_properties (h5debug PROPERTIES FOLDER tools) set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5debug") add_executable (h5repart ${HDF5_TOOLS_SRC_MISC_SOURCE_DIR}/h5repart.c) - target_include_directories (h5repart PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5repart PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_compile_options(h5repart PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5repart STATIC) target_link_libraries (h5repart PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) set_target_properties (h5repart PROPERTIES FOLDER tools) set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5repart") add_executable (h5mkgrp ${HDF5_TOOLS_SRC_MISC_SOURCE_DIR}/h5mkgrp.c) - target_include_directories (h5mkgrp PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5mkgrp PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_compile_options(h5mkgrp PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5mkgrp STATIC) target_link_libraries (h5mkgrp PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) set_target_properties (h5mkgrp PROPERTIES FOLDER tools) set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5mkgrp") add_executable (h5clear ${HDF5_TOOLS_SRC_MISC_SOURCE_DIR}/h5clear.c) - target_include_directories (h5clear PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5clear PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_compile_options(h5clear PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5clear STATIC) target_link_libraries (h5clear PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) set_target_properties (h5clear PROPERTIES FOLDER tools) set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5clear") + add_executable (h5delete ${HDF5_TOOLS_SRC_MISC_SOURCE_DIR}/h5delete.c) + target_include_directories (h5delete PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_compile_options(h5delete PRIVATE "${HDF5_CMAKE_C_FLAGS}") + TARGET_C_PROPERTIES (h5delete STATIC) + target_link_libraries (h5delete PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) + set_target_properties (h5delete PROPERTIES FOLDER tools) + set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5delete") + set (H5_DEP_EXECUTABLES h5debug h5repart h5mkgrp - h5clear + h5clear + h5delete ) endif () if (BUILD_SHARED_LIBS) add_executable (h5debug-shared ${HDF5_TOOLS_SRC_MISC_SOURCE_DIR}/h5debug.c) - target_include_directories (h5debug-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5debug-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") TARGET_C_PROPERTIES (h5debug-shared SHARED) + target_compile_options(h5debug-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}") target_link_libraries (h5debug-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET}) set_target_properties (h5debug-shared PROPERTIES FOLDER tools) set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5debug-shared") add_executable (h5repart-shared ${HDF5_TOOLS_SRC_MISC_SOURCE_DIR}/h5repart.c) - target_include_directories (h5repart-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5repart-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_compile_options(h5repart-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5repart-shared SHARED) target_link_libraries (h5repart-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET}) set_target_properties (h5repart-shared PROPERTIES FOLDER tools) set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5repart-shared") add_executable (h5mkgrp-shared ${HDF5_TOOLS_SRC_MISC_SOURCE_DIR}/h5mkgrp.c) - target_include_directories (h5mkgrp-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5mkgrp-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_compile_options(h5mkgrp-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5mkgrp-shared SHARED) target_link_libraries (h5mkgrp-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET}) set_target_properties (h5mkgrp-shared PROPERTIES FOLDER tools) set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5mkgrp-shared") add_executable (h5clear-shared ${HDF5_TOOLS_SRC_MISC_SOURCE_DIR}/h5clear.c) - target_include_directories (h5clear-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5clear-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_compile_options(h5clear-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5clear-shared SHARED) target_link_libraries (h5clear-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET}) set_target_properties (h5clear-shared PROPERTIES FOLDER tools) set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5clear-shared") + add_executable (h5delete-shared ${HDF5_TOOLS_SRC_MISC_SOURCE_DIR}/h5delete.c) + target_include_directories (h5delete-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_compile_options(h5delete-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}") + TARGET_C_PROPERTIES (h5delete-shared SHARED) + target_link_libraries (h5delete-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET}) + set_target_properties (h5delete-shared PROPERTIES FOLDER tools) + set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5delete-shared") + set (H5_DEP_EXECUTABLES ${H5_DEP_EXECUTABLES} h5debug-shared h5repart-shared h5mkgrp-shared h5clear-shared + h5delete-shared ) endif () +#----------------------------------------------------------------------------- +# Add Target to clang-format +#----------------------------------------------------------------------------- +if (HDF5_ENABLE_FORMATTERS) + if (NOT ONLY_SHARED_LIBS) + clang_format (HDF5_H5DEBUG_SRC_FORMAT h5debug) + clang_format (HDF5_H5REPART_SRC_FORMAT h5repart) + clang_format (HDF5_H5MKGRP_SRC_FORMAT h5mkgrp) + clang_format (HDF5_H5CLEAR_SRC_FORMAT h5clear) + clang_format (HDF5_H5DELETE_SRC_FORMAT h5delete) + else () + clang_format (HDF5_H5DEBUG_SRC_FORMAT h5debug-shared) + clang_format (HDF5_H5REPART_SRC_FORMAT h5repart-shared) + clang_format (HDF5_H5MKGRP_SRC_FORMAT h5mkgrp-shared) + clang_format (HDF5_H5CLEAR_SRC_FORMAT h5clear-shared) + clang_format (HDF5_H5DELETE_SRC_FORMAT h5delete-shared) + endif () +endif () + ############################################################################## ############################################################################## ### I N S T A L L A T I O N ### diff --git a/tools/src/misc/Makefile.am b/tools/src/misc/Makefile.am index f1d2aaf..cad13c1 100644 --- a/tools/src/misc/Makefile.am +++ b/tools/src/misc/Makefile.am @@ -6,7 +6,7 @@ # This file is part of HDF5. The full HDF5 copyright notice, including # terms governing use, modification, and redistribution, is contained in # the COPYING file, which can be found at the root of the source code -# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. +# distribution tree, or in https://www.hdfgroup.org/licenses. # If you do not have access to either file, you may request a copy from # help@hdfgroup.org. ## @@ -22,13 +22,14 @@ include $(top_srcdir)/config/commence.am AM_CPPFLAGS+=-I$(top_srcdir)/src -I$(top_srcdir)/tools/lib # These are our main targets, the tools -bin_PROGRAMS=h5debug h5repart h5mkgrp h5clear +bin_PROGRAMS=h5debug h5repart h5mkgrp h5clear h5delete # Add h5debug, h5repart, and h5mkgrp specific linker flags here h5debug_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS) h5repart_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS) h5mkgrp_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS) h5clear_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS) +h5delete_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS) # All programs rely on hdf5 library and h5tools library LDADD=$(LIBH5TOOLS) $(LIBHDF5) diff --git a/tools/src/misc/h5clear.c b/tools/src/misc/h5clear.c index ae57031..15c170d 100644 --- a/tools/src/misc/h5clear.c +++ b/tools/src/misc/h5clear.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -24,64 +24,31 @@ #include "h5tools_utils.h" /* Name of tool */ -#define PROGRAMNAME "h5clear" +#define PROGRAMNAME "h5clear" /* Make these private properties (defined in H5Fprivate.h) available to h5clear. */ -#define H5F_ACS_CLEAR_STATUS_FLAGS_NAME "clear_status_flags" -#define H5F_ACS_NULL_FSM_ADDR_NAME "null_fsm_addr" -#define H5F_ACS_SKIP_EOF_CHECK_NAME "skip_eof_check" +#define H5F_ACS_CLEAR_STATUS_FLAGS_NAME "clear_status_flags" +#define H5F_ACS_NULL_FSM_ADDR_NAME "null_fsm_addr" +#define H5F_ACS_SKIP_EOF_CHECK_NAME "skip_eof_check" /* Default increment is 1 megabytes for the --increment option */ -#define DEFAULT_INCREMENT 1024*1024 +#define DEFAULT_INCREMENT (1024 * 1024) -static char *fname_g = NULL; +static char * fname_g = NULL; static hbool_t clear_status_flags = FALSE; static hbool_t remove_cache_image = FALSE; -static hbool_t print_filesize = FALSE; -static hbool_t increment_eoa_eof = FALSE; -static hsize_t increment = DEFAULT_INCREMENT; +static hbool_t print_filesize = FALSE; +static hbool_t increment_eoa_eof = FALSE; +static hsize_t increment = DEFAULT_INCREMENT; /* * Command-line options: only publicize long options */ -static const char *s_opts = "hVsmzi*"; -static struct long_options l_opts[] = { - { "help", no_arg, 'h' }, - { "hel", no_arg, 'h'}, - { "he", no_arg, 'h'}, - { "version", no_arg, 'V' }, - { "version", no_arg, 'V' }, - { "versio", no_arg, 'V' }, - { "versi", no_arg, 'V' }, - { "vers", no_arg, 'V' }, - { "status", no_arg, 's' }, - { "statu", no_arg, 's' }, - { "stat", no_arg, 's' }, - { "sta", no_arg, 's' }, - { "st", no_arg, 's' }, - { "image", no_arg, 'm' }, - { "imag", no_arg, 'm' }, - { "ima", no_arg, 'm' }, - { "im", no_arg, 'm' }, - { "filesize", no_arg, 'z' }, - { "filesiz", no_arg, 'z' }, - { "filesi", no_arg, 'z' }, - { "files", no_arg, 'z' }, - { "file", no_arg, 'z' }, - { "fil", no_arg, 'z' }, - { "fi", no_arg, 'z' }, - { "increment", optional_arg, 'i' }, - { "incremen", optional_arg, 'i' }, - { "increme", optional_arg, 'i' }, - { "increm", optional_arg, 'i' }, - { "incre", optional_arg, 'i' }, - { "incr", optional_arg, 'i' }, - { "inc", optional_arg, 'i' }, - { "in", optional_arg, 'i' }, - { NULL, 0, '\0' } -}; - - +static const char * s_opts = "hVsmzi*"; +static struct h5_long_options l_opts[] = { + {"help", no_arg, 'h'}, {"version", no_arg, 'V'}, {"status", no_arg, 's'}, + {"image", no_arg, 'm'}, {"filesize", no_arg, 'z'}, {"increment", optional_arg, 'i'}, + {NULL, 0, '\0'}}; /*------------------------------------------------------------------------- * Function: usage @@ -92,7 +59,8 @@ static struct long_options l_opts[] = { * *------------------------------------------------------------------------- */ -static void usage(const char *prog) +static void +usage(const char *prog) { HDfprintf(stdout, "usage: %s [OPTIONS] file_name\n", prog); HDfprintf(stdout, " OPTIONS\n"); @@ -101,8 +69,18 @@ static void usage(const char *prog) HDfprintf(stdout, " -s, --status Clear the status_flags field in the file's superblock\n"); HDfprintf(stdout, " -m, --image Remove the metadata cache image from the file\n"); HDfprintf(stdout, " --filesize Print the file's EOA and EOF\n"); - HDfprintf(stdout, " --increment=C Set the file's EOA to the maximum of (EOA, EOF) + C for the file <file_name>\n"); - HDfprintf(stdout, " C is >= 0; C is optional and will default to 1M when not set"); + HDfprintf(stdout, + " --increment=C Set the file's EOA to the maximum of (EOA, EOF) + C for\n"); + HDfprintf(stdout, " the file <file_name>.\n"); + HDfprintf(stdout, + " C is >= 0; C is optional and will default to 1M when not set.\n"); + HDfprintf( + stdout, + " This option helps to repair a crashed file where the stored EOA\n"); + HDfprintf(stdout, " in the superblock is different from the actual EOF.\n"); + HDfprintf(stdout, + " The file’s EOA and EOF will be the same after applying\n"); + HDfprintf(stdout, " this option to the file.\n"); HDfprintf(stdout, "\n"); HDfprintf(stdout, "Examples of use:\n"); HDfprintf(stdout, "\n"); @@ -119,7 +97,6 @@ static void usage(const char *prog) HDfprintf(stdout, " Set the EOA to the maximum of (EOA, EOF) + 512 for the file <file_name>.\n"); } /* usage() */ - /*------------------------------------------------------------------------- * Function: parse_command_line * @@ -132,11 +109,11 @@ static void usage(const char *prog) *------------------------------------------------------------------------- */ static int -parse_command_line(int argc, const char **argv) +parse_command_line(int argc, const char *const *argv) { int opt; - /* no arguments */ + /* no arguments */ if (argc == 1) { usage(h5tools_getprogname()); h5tools_setstatus(EXIT_FAILURE); @@ -144,8 +121,8 @@ parse_command_line(int argc, const char **argv) } /* parse command line options */ - while((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) { - switch((char)opt) { + while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) { + switch ((char)opt) { case 'h': usage(h5tools_getprogname()); h5tools_setstatus(EXIT_SUCCESS); @@ -170,12 +147,12 @@ parse_command_line(int argc, const char **argv) case 'i': increment_eoa_eof = TRUE; - if(opt_arg != NULL) { - if (HDatoi(opt_arg) < 0) { + if (H5_optarg != NULL) { + if (HDatoi(H5_optarg) < 0) { usage(h5tools_getprogname()); goto done; } - increment = HDatoi(opt_arg); + increment = (hsize_t)HDatoi(H5_optarg); } break; @@ -184,20 +161,20 @@ parse_command_line(int argc, const char **argv) h5tools_setstatus(EXIT_FAILURE); goto error; } /* end switch */ - } /* end while */ + } /* end while */ /* check for file name to be processed */ - if(argc <= opt_ind) { + if (argc <= H5_optind) { error_msg("missing file name\n"); usage(h5tools_getprogname()); h5tools_setstatus(EXIT_FAILURE); goto error; } /* end if */ - fname_g = HDstrdup(argv[opt_ind]); + fname_g = HDstrdup(argv[H5_optind]); done: - return(0); + return (0); error: return -1; @@ -219,8 +196,6 @@ leave(int ret) HDexit(ret); } /* leave() */ - - /*------------------------------------------------------------------------- * Function: main * @@ -249,42 +224,40 @@ leave(int ret) *------------------------------------------------------------------------- */ int -main (int argc, const char *argv[]) +main(int argc, char *argv[]) { - char *fname = NULL; /* File name */ - hid_t fapl = -1; /* File access property list */ - hid_t fid = -1; /* File ID */ - haddr_t image_addr; - hsize_t image_len; - unsigned flags = H5F_ACC_RDWR; /* file access flags */ + char * fname = NULL; /* File name */ + hid_t fapl = H5I_INVALID_HID; /* File access property list */ + hid_t fid = H5I_INVALID_HID; /* File ID */ + haddr_t image_addr; + hsize_t image_len; + unsigned flags = H5F_ACC_RDWR; /* file access flags */ h5tools_setprogname(PROGRAMNAME); h5tools_setstatus(EXIT_SUCCESS); - /* Disable the HDF5 library's error reporting */ - H5Eset_auto2(H5E_DEFAULT, NULL, NULL); - /* initialize h5tools lib */ h5tools_init(); /* Parse command line options */ - if(parse_command_line(argc, argv) < 0) + if (parse_command_line(argc, (const char *const *)argv) < 0) goto done; - if(fname_g == NULL) + if (fname_g == NULL) goto done; + /* enable error reporting if command line option */ + h5tools_error_report(); + /* Print usage/exit if not using at least one of the options */ - if(!clear_status_flags && !remove_cache_image && - !increment_eoa_eof && !print_filesize) { + if (!clear_status_flags && !remove_cache_image && !increment_eoa_eof && !print_filesize) { usage(h5tools_getprogname()); h5tools_setstatus(EXIT_FAILURE); goto done; } /* Cannot combine the --filesize option with other options */ - if(print_filesize && - (clear_status_flags || remove_cache_image || increment_eoa_eof)) { + if (print_filesize && (clear_status_flags || remove_cache_image || increment_eoa_eof)) { error_msg("Cannot combine --filesize with other options\n"); h5tools_setstatus(EXIT_FAILURE); goto done; @@ -294,17 +267,17 @@ main (int argc, const char *argv[]) fname = HDstrdup(fname_g); /* Get a copy of the file access property list */ - if((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) { + if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) { error_msg("H5Pcreate\n"); h5tools_setstatus(EXIT_FAILURE); goto done; - } + } /* -s option */ - if(clear_status_flags) { + if (clear_status_flags) { /* Set to clear the status_flags in the file's superblock */ /* Activate this private property */ - if(H5Pset(fapl, H5F_ACS_CLEAR_STATUS_FLAGS_NAME, &clear_status_flags) < 0) { + if (H5Pset(fapl, H5F_ACS_CLEAR_STATUS_FLAGS_NAME, &clear_status_flags) < 0) { error_msg("H5Pset\n"); h5tools_setstatus(EXIT_FAILURE); goto done; @@ -312,15 +285,15 @@ main (int argc, const char *argv[]) } /* --increment option */ - if(increment_eoa_eof) { + if (increment_eoa_eof) { /* Activate this private property */ - if(H5Pset(fapl, H5F_ACS_SKIP_EOF_CHECK_NAME, &increment_eoa_eof) < 0) { + if (H5Pset(fapl, H5F_ACS_SKIP_EOF_CHECK_NAME, &increment_eoa_eof) < 0) { error_msg("H5Pset\n"); h5tools_setstatus(EXIT_FAILURE); goto done; } /* Activate this private property */ - if(H5Pset(fapl, H5F_ACS_NULL_FSM_ADDR_NAME, &increment_eoa_eof) < 0) { + if (H5Pset(fapl, H5F_ACS_NULL_FSM_ADDR_NAME, &increment_eoa_eof) < 0) { error_msg("H5Pset\n"); h5tools_setstatus(EXIT_FAILURE); goto done; @@ -328,9 +301,9 @@ main (int argc, const char *argv[]) } /* --filesize option; open the file read-only */ - if(print_filesize) { + if (print_filesize) { /* Activate this private property */ - if(H5Pset(fapl, H5F_ACS_SKIP_EOF_CHECK_NAME, &print_filesize) < 0) { + if (H5Pset(fapl, H5F_ACS_SKIP_EOF_CHECK_NAME, &print_filesize) < 0) { error_msg("H5Pset\n"); h5tools_setstatus(EXIT_FAILURE); goto done; @@ -339,30 +312,30 @@ main (int argc, const char *argv[]) } /* Open the file */ - if((fid = h5tools_fopen(fname, flags, fapl, NULL, NULL, (size_t)0)) < 0) { + if ((fid = h5tools_fopen(fname, flags, fapl, FALSE, NULL, (size_t)0)) < 0) { error_msg("h5tools_fopen\n"); h5tools_setstatus(EXIT_FAILURE); goto done; } /* --filesize option */ - if(print_filesize) { - h5_stat_t st; /* Stat info call */ - haddr_t eoa; /* The EOA value */ + if (print_filesize) { + h5_stat_t st; /* Stat info call */ + haddr_t eoa; /* The EOA value */ /* Get the file's EOA and EOF */ - if(H5Fget_eoa(fid, &eoa) < 0 || HDstat(fname, &st) < 0) { + if (H5Fget_eoa(fid, &eoa) < 0 || HDstat(fname, &st) < 0) { error_msg("H5Fget_eoa or HDstat\n"); h5tools_setstatus(EXIT_FAILURE); goto done; } - HDfprintf(stdout, "EOA is %a; EOF is %a \n", eoa, st.st_size); + HDfprintf(stdout, "EOA is %" PRIuHADDR "; EOF is %" PRIuHADDR " \n", eoa, (haddr_t)st.st_size); } /* --increment option */ - if(increment_eoa_eof) { + if (increment_eoa_eof) { /* Set the file's EOA to the maximum of (EOA, EOF) + increment */ - if(H5Fincrement_filesize(fid, increment) < 0) { + if (H5Fincrement_filesize(fid, increment) < 0) { error_msg("H5Fset_eoa\n"); h5tools_setstatus(EXIT_FAILURE); goto done; @@ -370,30 +343,30 @@ main (int argc, const char *argv[]) } /* -m option */ - if(remove_cache_image) { - if(H5Fget_mdc_image_info(fid, &image_addr, &image_len) < 0) { + if (remove_cache_image) { + if (H5Fget_mdc_image_info(fid, &image_addr, &image_len) < 0) { error_msg("H5Fget_mdc_image_info\n"); h5tools_setstatus(EXIT_FAILURE); goto done; } - if(image_addr == HADDR_UNDEF && image_len == 0) + if (image_addr == HADDR_UNDEF && image_len == 0) warn_msg("No cache image in the file\n"); } - h5tools_setstatus(EXIT_SUCCESS); done: - if(fname) + if (fname) HDfree(fname); - if(fname_g) + if (fname_g) HDfree(fname_g); - H5E_BEGIN_TRY { + H5E_BEGIN_TRY + { H5Pclose(fapl); H5Fclose(fid); - } H5E_END_TRY + } + H5E_END_TRY leave(h5tools_getstatus()); } /* main() */ - diff --git a/tools/src/misc/h5debug.c b/tools/src/misc/h5debug.c index 96d6b9f..e03c72d 100644 --- a/tools/src/misc/h5debug.c +++ b/tools/src/misc/h5debug.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -15,48 +15,47 @@ * * Created: debug.c * Jul 18 1997 - * Robb Matzke <matzke@llnl.gov> + * Robb Matzke * * Purpose: Debugs an existing HDF5 file at a low level. * *------------------------------------------------------------------------- */ -#define H5A_FRIEND /*suppress error about including H5Apkg */ -#define H5B2_FRIEND /*suppress error about including H5B2pkg */ -#define H5B2_TESTING /*suppress warning about H5B2 testing funcs*/ -#define H5D_FRIEND /*suppress error about including H5Dpkg */ -#define H5EA_FRIEND /*suppress error about including H5EApkg */ -#define H5EA_TESTING /*suppress warning about H5EA testing funcs*/ -#define H5FA_FRIEND /*suppress error about including H5FApkg */ -#define H5FA_TESTING /*suppress warning about H5FA testing funcs*/ -#define H5F_FRIEND /*suppress error about including H5Fpkg */ -#define H5G_FRIEND /*suppress error about including H5Gpkg */ -#define H5HF_FRIEND /*suppress error about including H5HFpkg */ -#define H5O_FRIEND /*suppress error about including H5Opkg */ -#define H5SM_FRIEND /*suppress error about including H5SMpkg */ - -#include "H5private.h" /* Generic Functions */ -#include "H5Apkg.h" /* Attributes */ -#include "H5B2pkg.h" /* v2 B-trees */ +#define H5A_FRIEND /*suppress error about including H5Apkg */ +#define H5B2_FRIEND /*suppress error about including H5B2pkg */ +#define H5B2_TESTING /*suppress warning about H5B2 testing funcs*/ +#define H5D_FRIEND /*suppress error about including H5Dpkg */ +#define H5EA_FRIEND /*suppress error about including H5EApkg */ +#define H5EA_TESTING /*suppress warning about H5EA testing funcs*/ +#define H5FA_FRIEND /*suppress error about including H5FApkg */ +#define H5FA_TESTING /*suppress warning about H5FA testing funcs*/ +#define H5F_FRIEND /*suppress error about including H5Fpkg */ +#define H5G_FRIEND /*suppress error about including H5Gpkg */ +#define H5HF_FRIEND /*suppress error about including H5HFpkg */ +#define H5O_FRIEND /*suppress error about including H5Opkg */ +#define H5SM_FRIEND /*suppress error about including H5SMpkg */ + +#include "H5private.h" /* Generic Functions */ +#include "H5Apkg.h" /* Attributes */ +#include "H5B2pkg.h" /* v2 B-trees */ #include "H5CXprivate.h" /* API Contexts */ -#include "H5Dpkg.h" /* Datasets */ -#include "H5Eprivate.h" /* Error handling */ -#include "H5EApkg.h" /* Extensible Arrays */ -#include "H5FApkg.h" /* Fixed Arrays */ -#include "H5Fpkg.h" /* File access */ +#include "H5Dpkg.h" /* Datasets */ +#include "H5Eprivate.h" /* Error handling */ +#include "H5EApkg.h" /* Extensible Arrays */ +#include "H5FApkg.h" /* Fixed Arrays */ +#include "H5Fpkg.h" /* File access */ #include "H5FSprivate.h" /* Free space manager */ -#include "H5Gpkg.h" /* Groups */ -#include "H5HFpkg.h" /* Fractal heaps */ +#include "H5Gpkg.h" /* Groups */ +#include "H5HFpkg.h" /* Fractal heaps */ #include "H5HGprivate.h" /* Global Heaps */ -#include "H5Iprivate.h" /* IDs */ -#include "H5Opkg.h" /* Object headers */ -#include "H5SMpkg.h" /* Implicitly shared messages */ +#include "H5Iprivate.h" /* IDs */ +#include "H5Opkg.h" /* Object headers */ +#include "H5SMpkg.h" /* Implicitly shared messages */ /* File drivers */ #include "H5FDfamily.h" -#define VCOL 50 - +#define VCOL 50 /*------------------------------------------------------------------------- * Function: get_H5B2_class @@ -68,7 +67,6 @@ * Return: Non-NULL on success/NULL on failure * * Programmer: Quincey Koziol - * koziol@hdfgroup.org * Sep 11 2008 * *------------------------------------------------------------------------- @@ -76,72 +74,70 @@ static const H5B2_class_t * get_H5B2_class(const uint8_t *sig) { - H5B2_subid_t subtype = (H5B2_subid_t)sig[H5_SIZEOF_MAGIC + 1]; - const H5B2_class_t *cls; - - switch(subtype) { - case H5B2_TEST_ID: - cls = H5B2_TEST; - break; - - case H5B2_FHEAP_HUGE_INDIR_ID: - cls = H5HF_HUGE_BT2_INDIR; - break; - - case H5B2_FHEAP_HUGE_FILT_INDIR_ID: - cls = H5HF_HUGE_BT2_FILT_INDIR; - break; - - case H5B2_FHEAP_HUGE_DIR_ID: - cls = H5HF_HUGE_BT2_DIR; - break; - - case H5B2_FHEAP_HUGE_FILT_DIR_ID: - cls = H5HF_HUGE_BT2_FILT_DIR; - break; - - case H5B2_GRP_DENSE_NAME_ID: - cls = H5G_BT2_NAME; - break; - - case H5B2_GRP_DENSE_CORDER_ID: - cls = H5G_BT2_CORDER; - break; - - case H5B2_SOHM_INDEX_ID: - cls = H5SM_INDEX; - break; - - case H5B2_ATTR_DENSE_NAME_ID: - cls = H5A_BT2_NAME; - break; - - case H5B2_ATTR_DENSE_CORDER_ID: - cls = H5A_BT2_CORDER; - break; - - case H5B2_CDSET_ID: - cls = H5D_BT2; - break; - - case H5B2_CDSET_FILT_ID: - cls = H5D_BT2_FILT; - break; - - case H5B2_TEST2_ID: - cls = H5B2_TEST2; - break; - - case H5B2_NUM_BTREE_ID: - default: - HDfprintf(stderr, "Unknown v2 B-tree subtype %u\n", (unsigned)(subtype)); - HDexit(4); + H5B2_subid_t subtype = (H5B2_subid_t)sig[H5_SIZEOF_MAGIC + 1]; + const H5B2_class_t *cls = NULL; + + switch (subtype) { + case H5B2_TEST_ID: + cls = H5B2_TEST; + break; + + case H5B2_FHEAP_HUGE_INDIR_ID: + cls = H5HF_HUGE_BT2_INDIR; + break; + + case H5B2_FHEAP_HUGE_FILT_INDIR_ID: + cls = H5HF_HUGE_BT2_FILT_INDIR; + break; + + case H5B2_FHEAP_HUGE_DIR_ID: + cls = H5HF_HUGE_BT2_DIR; + break; + + case H5B2_FHEAP_HUGE_FILT_DIR_ID: + cls = H5HF_HUGE_BT2_FILT_DIR; + break; + + case H5B2_GRP_DENSE_NAME_ID: + cls = H5G_BT2_NAME; + break; + + case H5B2_GRP_DENSE_CORDER_ID: + cls = H5G_BT2_CORDER; + break; + + case H5B2_SOHM_INDEX_ID: + cls = H5SM_INDEX; + break; + + case H5B2_ATTR_DENSE_NAME_ID: + cls = H5A_BT2_NAME; + break; + + case H5B2_ATTR_DENSE_CORDER_ID: + cls = H5A_BT2_CORDER; + break; + + case H5B2_CDSET_ID: + cls = H5D_BT2; + break; + + case H5B2_CDSET_FILT_ID: + cls = H5D_BT2_FILT; + break; + + case H5B2_TEST2_ID: + cls = H5B2_TEST2; + break; + + case H5B2_NUM_BTREE_ID: + default: + HDfprintf(stderr, "Unknown v2 B-tree subtype %u\n", (unsigned)(subtype)); } /* end switch */ - return(cls); + return (cls); } /* end get_H5B2_class() */ - /*------------------------------------------------------------------------- * Function: get_H5EA_class * @@ -152,7 +148,6 @@ get_H5B2_class(const uint8_t *sig) * Return: Non-NULL on success/NULL on failure * * Programmer: Quincey Koziol - * koziol@hdfgroup.org * Sep 11 2008 * *------------------------------------------------------------------------- @@ -160,32 +155,30 @@ get_H5B2_class(const uint8_t *sig) static const H5EA_class_t * get_H5EA_class(const uint8_t *sig) { - H5EA_cls_id_t clsid = (H5EA_cls_id_t)sig[H5_SIZEOF_MAGIC + 1]; - const H5EA_class_t *cls; - - switch(clsid) { - case H5EA_CLS_TEST_ID: - cls = H5EA_CLS_TEST; - break; - - case H5EA_CLS_CHUNK_ID: - cls = H5EA_CLS_CHUNK; - break; - - case H5EA_CLS_FILT_CHUNK_ID: - cls = H5EA_CLS_FILT_CHUNK; - break; - - case H5EA_NUM_CLS_ID: - default: - HDfprintf(stderr, "Unknown extensible array class %u\n", (unsigned)(clsid)); - HDexit(4); + H5EA_cls_id_t clsid = (H5EA_cls_id_t)sig[H5_SIZEOF_MAGIC + 1]; + const H5EA_class_t *cls = NULL; + + switch (clsid) { + case H5EA_CLS_TEST_ID: + cls = H5EA_CLS_TEST; + break; + + case H5EA_CLS_CHUNK_ID: + cls = H5EA_CLS_CHUNK; + break; + + case H5EA_CLS_FILT_CHUNK_ID: + cls = H5EA_CLS_FILT_CHUNK; + break; + + case H5EA_NUM_CLS_ID: + default: + HDfprintf(stderr, "Unknown extensible array class %u\n", (unsigned)(clsid)); } /* end switch */ - return(cls); + return (cls); } /* end get_H5EA_class() */ - /*------------------------------------------------------------------------- * Function: get_H5FA_class * @@ -196,7 +189,6 @@ get_H5EA_class(const uint8_t *sig) * Return: Non-NULL on success/NULL on failure * * Programmer: Quincey Koziol - * koziol@hdfgroup.org * Sep 11 2008 * *------------------------------------------------------------------------- @@ -204,32 +196,30 @@ get_H5EA_class(const uint8_t *sig) static const H5FA_class_t * get_H5FA_class(const uint8_t *sig) { - H5FA_cls_id_t clsid = (H5FA_cls_id_t)sig[H5_SIZEOF_MAGIC + 1]; - const H5FA_class_t *cls; - - switch(clsid) { - case H5FA_CLS_TEST_ID: - cls = H5FA_CLS_TEST; - break; - - case H5FA_CLS_CHUNK_ID: - cls = H5FA_CLS_CHUNK; - break; - - case H5FA_CLS_FILT_CHUNK_ID: - cls = H5FA_CLS_FILT_CHUNK; - break; - - case H5FA_NUM_CLS_ID: - default: - HDfprintf(stderr, "Unknown fixed array class %u\n", (unsigned)(clsid)); - HDexit(4); + H5FA_cls_id_t clsid = (H5FA_cls_id_t)sig[H5_SIZEOF_MAGIC + 1]; + const H5FA_class_t *cls = NULL; + + switch (clsid) { + case H5FA_CLS_TEST_ID: + cls = H5FA_CLS_TEST; + break; + + case H5FA_CLS_CHUNK_ID: + cls = H5FA_CLS_CHUNK; + break; + + case H5FA_CLS_FILT_CHUNK_ID: + cls = H5FA_CLS_FILT_CHUNK; + break; + + case H5FA_NUM_CLS_ID: + default: + HDfprintf(stderr, "Unknown fixed array class %u\n", (unsigned)(clsid)); } /* end switch */ - return(cls); + return (cls); } /* end get_H5FA_class() */ - /*------------------------------------------------------------------------- * Function: main * @@ -240,7 +230,6 @@ get_H5FA_class(const uint8_t *sig) * Failure: exit (non-zero) * * Programmer: Robb Matzke - * matzke@llnl.gov * Jul 18 1997 * *------------------------------------------------------------------------- @@ -248,25 +237,32 @@ get_H5FA_class(const uint8_t *sig) int main(int argc, char *argv[]) { - hid_t fid, fapl; - H5F_t *f; - haddr_t addr = 0, extra = 0, extra2 = 0, extra3 = 0, extra4 = 0; - uint8_t sig[H5F_SIGNATURE_LEN]; - size_t u; - H5E_auto2_t func; - void *edata; - hbool_t api_ctx_pushed = FALSE; /* Whether API context pushed */ - herr_t status = SUCCEED; - - if(argc == 1) { - HDfprintf(stderr, "Usage: %s filename [signature-addr [extra]]\n", argv[0]); - HDexit(1); + hid_t fid = H5I_INVALID_HID; + hid_t fapl = H5I_INVALID_HID; + H5VL_object_t *vol_obj; + H5F_t * f; + haddr_t addr = 0; + int extra_count = 0; /* Number of extra arguments */ + haddr_t extra[10]; + uint8_t sig[H5F_SIGNATURE_LEN]; + size_t u; + H5E_auto2_t func = NULL; + void * edata = NULL; + hbool_t api_ctx_pushed = FALSE; /* Whether API context pushed */ + herr_t status = SUCCEED; + int exit_value = 0; + + if (argc == 1) { + HDfprintf(stderr, "Usage: %s filename [signature-addr [extra]*]\n", argv[0]); + exit_value = 1; + goto done; } /* end if */ /* Initialize the library */ - if(H5open() < 0) { + if (H5open() < 0) { HDfprintf(stderr, "cannot initialize the library\n"); - HDexit(1); + exit_value = 1; + goto done; } /* end if */ /* Disable error reporting */ @@ -274,450 +270,523 @@ main(int argc, char *argv[]) H5Eset_auto2(H5E_DEFAULT, NULL, NULL); /* - * Open the file and get the file descriptor. - */ - if((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) { + * Open the file and get the file descriptor. + */ + if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) { HDfprintf(stderr, "cannot create file access property list\n"); - HDexit(1); + exit_value = 1; + goto done; } /* end if */ - if(HDstrchr(argv[1], '%')) - if(H5Pset_fapl_family (fapl, (hsize_t)0, H5P_DEFAULT) < 0) { + if (HDstrchr(argv[1], '%')) + if (H5Pset_fapl_family(fapl, (hsize_t)0, H5P_DEFAULT) < 0) { HDfprintf(stderr, "cannot set file access property list\n"); - HDexit(1); + exit_value = 1; + goto done; } - if((fid = H5Fopen(argv[1], H5F_ACC_RDONLY, fapl)) < 0) { + if ((fid = H5Fopen(argv[1], H5F_ACC_RDONLY, fapl)) < 0) { HDfprintf(stderr, "cannot open file\n"); - HDexit(1); + exit_value = 1; + goto done; } /* end if */ /* Push API context */ - if(H5CX_push() < 0) { + if (H5CX_push() < 0) { HDfprintf(stderr, "cannot set API context\n"); - HDexit(1); + exit_value = 1; + goto done; } api_ctx_pushed = TRUE; - if(NULL == (f = (H5F_t *)H5I_object(fid))) { + if (NULL == (vol_obj = (H5VL_object_t *)H5VL_vol_object(fid))) { + HDfprintf(stderr, "cannot obtain vol_obj pointer\n"); + exit_value = 2; + goto done; + } /* end if */ + + if (NULL == (f = (H5F_t *)H5VL_object_data(vol_obj))) { HDfprintf(stderr, "cannot obtain H5F_t pointer\n"); - HDexit(2); + exit_value = 2; + goto done; } /* end if */ /* Ignore metadata tags while using h5debug */ - if(H5AC_ignore_tags(f) < 0) { + if (H5AC_ignore_tags(f) < 0) { HDfprintf(stderr, "cannot ignore metadata tags\n"); - HDexit(1); + exit_value = 1; + goto done; } /* - * Parse command arguments. - */ - if(argc > 2) + * Parse command arguments. + */ + + /* Primary data structure to dump */ + if (argc > 2) addr = (haddr_t)HDstrtoll(argv[2], NULL, 0); - if(argc > 3) - extra = (haddr_t)HDstrtoll(argv[3], NULL, 0); - if(argc > 4) - extra2 = (haddr_t)HDstrtoll(argv[4], NULL, 0); - if(argc > 5) - extra3 = (haddr_t)HDstrtoll(argv[5], NULL, 0); - if(argc > 6) - extra4 = (haddr_t)HDstrtoll(argv[6], NULL, 0); + + /* Extra arguments for primary data structure */ + HDmemset(extra, 0, sizeof(extra)); + if (argc > 3) { + /* Number of extra arguments */ + extra_count = argc - 3; + + /* Range check against 'extra' array size */ + if (extra_count > (int)(sizeof(extra) / sizeof(haddr_t))) { + HDfprintf(stderr, "\nWARNING: Only using first %d extra parameters\n\n", + (int)(sizeof(extra) / sizeof(haddr_t))); + extra_count = (int)(sizeof(extra) / sizeof(haddr_t)); + } /* end if */ + + for (u = 0; u < (size_t)extra_count; u++) + extra[u] = (haddr_t)HDstrtoll(argv[u + 3], NULL, 0); + } /* end if */ /* - * Read the signature at the specified file position. - */ - HDfprintf(stdout, "Reading signature at address %a (rel)\n", addr); - if(H5F_block_read(f, H5FD_MEM_SUPER, addr, sizeof(sig), sig) < 0) { + * Read the signature at the specified file position. + */ + HDfprintf(stdout, "Reading signature at address %" PRIuHADDR " (rel)\n", addr); + if (H5F_block_read(f, H5FD_MEM_SUPER, addr, sizeof(sig), sig) < 0) { HDfprintf(stderr, "cannot read signature\n"); - HDexit(3); + exit_value = 3; + goto done; } - if(!HDmemcmp(sig, H5F_SIGNATURE, (size_t)H5F_SIGNATURE_LEN)) { + if (!HDmemcmp(sig, H5F_SIGNATURE, (size_t)H5F_SIGNATURE_LEN)) { /* - * Debug the file's super block. - */ + * Debug the file's super block. + */ status = H5F_debug(f, stdout, 0, VCOL); - - } else if(!HDmemcmp(sig, H5HL_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { + } + else if (!HDmemcmp(sig, H5HL_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* - * Debug a local heap. - */ + * Debug a local heap. + */ status = H5HL_debug(f, addr, stdout, 0, VCOL); - } - else if(!HDmemcmp (sig, H5HG_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { + else if (!HDmemcmp(sig, H5HG_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* - * Debug a global heap collection. - */ + * Debug a global heap collection. + */ status = H5HG_debug(f, addr, stdout, 0, VCOL); - } - else if(!HDmemcmp(sig, H5G_NODE_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { + else if (!HDmemcmp(sig, H5G_NODE_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* - * Debug a symbol table node. - */ + * Debug a symbol table node. + */ /* Check for extra parameters */ - if(extra == 0) { - HDfprintf(stderr, "\nWarning: Providing the group's local heap address will give more information\n"); + if (extra_count == 0 || extra[0] == 0) { + HDfprintf(stderr, + "\nWarning: Providing the group's local heap address will give more information\n"); HDfprintf(stderr, "Symbol table node usage:\n"); HDfprintf(stderr, "\th5debug <filename> <Symbol table node address> <address of local heap>\n\n"); } /* end if */ - status = H5G_node_debug(f, addr, stdout, 0, VCOL, extra); - + status = H5G_node_debug(f, addr, stdout, 0, VCOL, extra[0]); } - else if(!HDmemcmp(sig, H5B_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { + else if (!HDmemcmp(sig, H5B_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* - * Debug a B-tree. B-trees are debugged through the B-tree - * subclass. The subclass identifier is the byte immediately - * after the B-tree signature. - */ + * Debug a B-tree. B-trees are debugged through the B-tree + * subclass. The subclass identifier is the byte immediately + * after the B-tree signature. + */ H5B_subid_t subtype = (H5B_subid_t)sig[H5_SIZEOF_MAGIC]; unsigned ndims; uint32_t dim[H5O_LAYOUT_NDIMS]; - switch(subtype) { - case H5B_SNODE_ID: - /* Check for extra parameters */ - if(extra == 0) { - HDfprintf(stderr, "\nWarning: Providing the group's local heap address will give more information\n"); - HDfprintf(stderr, "B-tree symbol table node usage:\n"); - HDfprintf(stderr, "\th5debug <filename> <B-tree node address> <address of local heap>\n\n"); - HDexit(4); - } /* end if */ - - status = H5G_node_debug(f, addr, stdout, 0, VCOL, extra); - break; + switch (subtype) { + case H5B_SNODE_ID: + /* Check for extra parameters */ + if (extra_count == 0 || extra[0] == 0) { + HDfprintf( + stderr, + "\nWarning: Providing the group's local heap address will give more information\n"); + HDfprintf(stderr, "B-tree symbol table node usage:\n"); + HDfprintf(stderr, + "\th5debug <filename> <B-tree node address> <address of local heap>\n\n"); + exit_value = 4; + goto done; + } /* end if */ - case H5B_CHUNK_ID: - /* Check for extra parameters */ - if(extra == 0) { - HDfprintf(stderr, "ERROR: Need number of dimensions of chunk in order to dump chunk B-tree node\n"); - HDfprintf(stderr, "B-tree chunked storage node usage:\n"); - HDfprintf(stderr, "\th5debug <filename> <B-tree node address> <# of dimensions> <slowest chunk dim>...<fastest chunk dim>\n"); - HDexit(4); - } /* end if */ - - /* Build array of chunk dimensions */ - ndims = (unsigned)extra; - dim[0] = (uint32_t)extra2; - if(ndims > 1) - dim[1] = (uint32_t)extra3; - if(ndims > 2) - dim[2] = (uint32_t)extra4; - - /* Check for dimension error */ - if(ndims > 3) { - HDfprintf(stderr, "ERROR: Only 3 dimensions support currently (fix h5debug)\n"); - HDfprintf(stderr, "B-tree chunked storage node usage:\n"); - HDfprintf(stderr, "\th5debug <filename> <B-tree node address> <# of dimensions> <slowest chunk dim>...<fastest chunk dim>\n"); - HDexit(4); - } /* end for */ - for(u = 0; u < ndims; u++) - if(0 == dim[u]) { - HDfprintf(stderr, "ERROR: Chunk dimensions should be >0\n"); + status = H5G_node_debug(f, addr, stdout, 0, VCOL, extra[0]); + break; + + case H5B_CHUNK_ID: + /* Check for extra parameters */ + if (extra_count == 0 || extra[0] == 0) { + HDfprintf( + stderr, + "ERROR: Need number of dimensions of chunk in order to dump chunk B-tree node\n"); HDfprintf(stderr, "B-tree chunked storage node usage:\n"); - HDfprintf(stderr, "\th5debug <filename> <B-tree node address> <# of dimensions> <slowest chunk dim>...<fastest chunk dim>\n"); - HDexit(4); + HDfprintf(stderr, "\th5debug <filename> <B-tree node address> <# of dimensions> <slowest " + "chunk dim>...<fastest chunk dim>\n"); + exit_value = 4; + goto done; } /* end if */ - /* Set the last dimension (the element size) to zero */ - dim[ndims] = 0; - - status = H5D_btree_debug(f, addr, stdout, 0, VCOL, ndims, dim); - break; + /* Set # of dimensions */ + ndims = (unsigned)extra[0]; - case H5B_NUM_BTREE_ID: - default: - HDfprintf(stderr, "Unknown v1 B-tree subtype %u\n", (unsigned)(subtype)); - HDexit(4); + /* Check for dimension error */ + if (ndims > 9) { + HDfprintf(stderr, "ERROR: Only 9 dimensions support currently (fix h5debug)\n"); + HDfprintf(stderr, "B-tree chunked storage node usage:\n"); + HDfprintf(stderr, "\th5debug <filename> <B-tree node address> <# of dimensions> <slowest " + "chunk dim>...<fastest chunk dim>\n"); + exit_value = 4; + goto done; + } /* end for */ + + /* Build array of chunk dimensions */ + for (u = 0; u < ndims; u++) + dim[u] = (uint32_t)extra[u + 1]; + + /* Check for dimension error */ + for (u = 0; u < ndims; u++) + if (0 == dim[u]) { + HDfprintf(stderr, "ERROR: Chunk dimensions should be >0\n"); + HDfprintf(stderr, "B-tree chunked storage node usage:\n"); + HDfprintf(stderr, "\th5debug <filename> <B-tree node address> <# of dimensions> " + "<slowest chunk dim>...<fastest chunk dim>\n"); + exit_value = 4; + goto done; + } /* end if */ + + /* Set the last dimension (the element size) to zero */ + dim[ndims] = 0; + + status = H5D_btree_debug(f, addr, stdout, 0, VCOL, ndims, dim); + break; + + case H5B_NUM_BTREE_ID: + default: + HDfprintf(stderr, "Unknown v1 B-tree subtype %u\n", (unsigned)(subtype)); + exit_value = 4; + goto done; } - } - else if(!HDmemcmp(sig, H5B2_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { + else if (!HDmemcmp(sig, H5B2_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* - * Debug a v2 B-tree header. - */ + * Debug a v2 B-tree header. + */ const H5B2_class_t *cls = get_H5B2_class(sig); HDassert(cls); - if((cls == H5D_BT2 || cls == H5D_BT2_FILT) && extra == 0) { - HDfprintf(stderr, "ERROR: Need v2 B-tree header address and object header address containing the layout message in order to dump header\n"); + if ((cls == H5D_BT2 || cls == H5D_BT2_FILT) && (extra_count == 0 || extra[0] == 0)) { + HDfprintf(stderr, "ERROR: Need v2 B-tree header address and object header address containing the " + "layout message in order to dump header\n"); HDfprintf(stderr, "v2 B-tree hdr usage:\n"); HDfprintf(stderr, "\th5debug <filename> <v2 B-tree header address> <object header address>\n"); - HDexit(4); + exit_value = 4; + goto done; } /* end if */ - status = H5B2__hdr_debug(f, addr, stdout, 0, VCOL, cls, (haddr_t)extra); - + status = H5B2__hdr_debug(f, addr, stdout, 0, VCOL, cls, (haddr_t)extra[0]); } - else if(!HDmemcmp(sig, H5B2_INT_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { + else if (!HDmemcmp(sig, H5B2_INT_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* - * Debug a v2 B-tree internal node. - */ + * Debug a v2 B-tree internal node. + */ const H5B2_class_t *cls = get_H5B2_class(sig); HDassert(cls); /* Check for enough valid parameters */ - if((cls == H5D_BT2 || cls == H5D_BT2_FILT) && (extra == 0 || extra2 == 0 || extra3 == 0 || extra4 == 0)) { - HDfprintf(stderr, "ERROR: Need v2 B-tree header address, the node's number of records, depth, and object header address containing the layout message in order to dump internal node\n"); - HDfprintf(stderr, "NOTE: Leaf nodes are depth 0, the internal nodes above them are depth 1, etc.\n"); + if ((cls == H5D_BT2 || cls == H5D_BT2_FILT) && + (extra_count == 0 || extra[0] == 0 || extra[1] == 0 || extra[2] == 0 || extra[3] == 0)) { + HDfprintf(stderr, + "ERROR: Need v2 B-tree header address, the node's number of records, depth, and object " + "header address containing the layout message in order to dump internal node\n"); + HDfprintf(stderr, + "NOTE: Leaf nodes are depth 0, the internal nodes above them are depth 1, etc.\n"); HDfprintf(stderr, "v2 B-tree internal node usage:\n"); - HDfprintf(stderr, "\th5debug <filename> <internal node address> <v2 B-tree header address> <number of records> <depth> <object header address>\n"); - HDexit(4); - + HDfprintf(stderr, "\th5debug <filename> <internal node address> <v2 B-tree header address> " + "<number of records> <depth> <object header address>\n"); + exit_value = 4; + goto done; } - else if(extra == 0 || extra2 == 0 || extra3 == 0) { - HDfprintf(stderr, "ERROR: Need v2 B-tree header address and the node's number of records and depth in order to dump internal node\n"); - HDfprintf(stderr, "NOTE: Leaf nodes are depth 0, the internal nodes above them are depth 1, etc.\n"); + else if (extra_count == 0 || extra[0] == 0 || extra[1] == 0 || extra[2] == 0) { + HDfprintf(stderr, "ERROR: Need v2 B-tree header address and the node's number of records and " + "depth in order to dump internal node\n"); + HDfprintf(stderr, + "NOTE: Leaf nodes are depth 0, the internal nodes above them are depth 1, etc.\n"); HDfprintf(stderr, "v2 B-tree internal node usage:\n"); - HDfprintf(stderr, "\th5debug <filename> <internal node address> <v2 B-tree header address> <number of records> <depth>\n"); - HDexit(4); + HDfprintf(stderr, "\th5debug <filename> <internal node address> <v2 B-tree header address> " + "<number of records> <depth>\n"); + exit_value = 4; + goto done; } /* end if */ - status = H5B2__int_debug(f, addr, stdout, 0, VCOL, cls, extra, (unsigned)extra2, (unsigned)extra3, (haddr_t)extra4); - + status = H5B2__int_debug(f, addr, stdout, 0, VCOL, cls, extra[0], (unsigned)extra[1], + (unsigned)extra[2], (haddr_t)extra[3]); } - else if(!HDmemcmp(sig, H5B2_LEAF_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { + else if (!HDmemcmp(sig, H5B2_LEAF_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* - * Debug a v2 B-tree leaf node. - */ + * Debug a v2 B-tree leaf node. + */ const H5B2_class_t *cls = get_H5B2_class(sig); HDassert(cls); /* Check for enough valid parameters */ - if((cls == H5D_BT2 || cls == H5D_BT2_FILT) && (extra == 0 || extra2 == 0 || extra3 == 0 )) { + if ((cls == H5D_BT2 || cls == H5D_BT2_FILT) && + (extra_count == 0 || extra[0] == 0 || extra[1] == 0 || extra[2] == 0)) { - HDfprintf(stderr, "ERROR: Need v2 B-tree header address, number of records, and object header address containing the layout message in order to dump leaf node\n"); + HDfprintf(stderr, "ERROR: Need v2 B-tree header address, number of records, and object header " + "address containing the layout message in order to dump leaf node\n"); HDfprintf(stderr, "v2 B-tree leaf node usage:\n"); - HDfprintf(stderr, "\th5debug <filename> <leaf node address> <v2 B-tree header address> <number of records> <object header address>\n"); - HDexit(4); - + HDfprintf(stderr, "\th5debug <filename> <leaf node address> <v2 B-tree header address> <number " + "of records> <object header address>\n"); + exit_value = 4; + goto done; } - else if(extra == 0 || extra2 == 0) { - HDfprintf(stderr, "ERROR: Need v2 B-tree header address and number of records in order to dump leaf node\n"); + else if (extra_count == 0 || extra[0] == 0 || extra[1] == 0) { + HDfprintf( + stderr, + "ERROR: Need v2 B-tree header address and number of records in order to dump leaf node\n"); HDfprintf(stderr, "v2 B-tree leaf node usage:\n"); - HDfprintf(stderr, "\th5debug <filename> <leaf node address> <v2 B-tree header address> <number of records>\n"); - HDexit(4); + HDfprintf( + stderr, + "\th5debug <filename> <leaf node address> <v2 B-tree header address> <number of records>\n"); + exit_value = 4; + goto done; } /* end if */ - status = H5B2__leaf_debug(f, addr, stdout, 0, VCOL, cls, extra, (unsigned)extra2, (haddr_t)extra3); - + status = + H5B2__leaf_debug(f, addr, stdout, 0, VCOL, cls, extra[0], (unsigned)extra[1], (haddr_t)extra[2]); } - else if(!HDmemcmp(sig, H5HF_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { + else if (!HDmemcmp(sig, H5HF_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* - * Debug a fractal heap header. - */ + * Debug a fractal heap header. + */ status = H5HF_hdr_debug(f, addr, stdout, 0, VCOL); - } - else if(!HDmemcmp(sig, H5HF_DBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { + else if (!HDmemcmp(sig, H5HF_DBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* - * Debug a fractal heap direct block. - */ + * Debug a fractal heap direct block. + */ /* Check for enough valid parameters */ - if(extra == 0 || extra2 == 0) { - HDfprintf(stderr, "ERROR: Need fractal heap header address and size of direct block in order to dump direct block\n"); + if (extra_count == 0 || extra[0] == 0 || extra[1] == 0) { + HDfprintf(stderr, "ERROR: Need fractal heap header address and size of direct block in order to " + "dump direct block\n"); HDfprintf(stderr, "Fractal heap direct block usage:\n"); - HDfprintf(stderr, "\th5debug <filename> <direct block address> <heap header address> <size of direct block>\n"); - HDexit(4); + HDfprintf( + stderr, + "\th5debug <filename> <direct block address> <heap header address> <size of direct block>\n"); + exit_value = 4; + goto done; } /* end if */ - status = H5HF_dblock_debug(f, addr, stdout, 0, VCOL, extra, (size_t)extra2); - + status = H5HF_dblock_debug(f, addr, stdout, 0, VCOL, extra[0], (size_t)extra[1]); } - else if(!HDmemcmp(sig, H5HF_IBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { + else if (!HDmemcmp(sig, H5HF_IBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* - * Debug a fractal heap indirect block. - */ + * Debug a fractal heap indirect block. + */ /* Check for enough valid parameters */ - if(extra == 0 || extra2 == 0) { - HDfprintf(stderr, "ERROR: Need fractal heap header address and number of rows in order to dump indirect block\n"); + if (extra_count == 0 || extra[0] == 0 || extra[1] == 0) { + HDfprintf(stderr, "ERROR: Need fractal heap header address and number of rows in order to dump " + "indirect block\n"); HDfprintf(stderr, "Fractal heap indirect block usage:\n"); - HDfprintf(stderr, "\th5debug <filename> <indirect block address> <heap header address> <number of rows>\n"); - HDexit(4); + HDfprintf( + stderr, + "\th5debug <filename> <indirect block address> <heap header address> <number of rows>\n"); + exit_value = 4; + goto done; } /* end if */ - status = H5HF_iblock_debug(f, addr, stdout, 0, VCOL, extra, (unsigned)extra2); - + status = H5HF_iblock_debug(f, addr, stdout, 0, VCOL, extra[0], (unsigned)extra[1]); } - else if(!HDmemcmp(sig, H5FS_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { + else if (!HDmemcmp(sig, H5FS_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* - * Debug a free space header. - */ + * Debug a free space header. + */ status = H5FS_debug(f, addr, stdout, 0, VCOL); - } - else if(!HDmemcmp(sig, H5FS_SINFO_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { + else if (!HDmemcmp(sig, H5FS_SINFO_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* - * Debug free space serialized sections. - */ + * Debug free space serialized sections. + */ /* Check for enough valid parameters */ - if(extra == 0 || extra2 == 0) { - HDfprintf(stderr, "ERROR: Need free space header address and client address in order to dump serialized sections\n"); + if (extra_count == 0 || extra[0] == 0 || extra[1] == 0) { + HDfprintf(stderr, "ERROR: Need free space header address and client address in order to dump " + "serialized sections\n"); HDfprintf(stderr, "Free space serialized sections usage:\n"); - HDfprintf(stderr, "\th5debug <filename> <serialized sections address> <free space header address> <client address>\n"); - HDexit(4); + HDfprintf(stderr, "\th5debug <filename> <serialized sections address> <free space header " + "address> <client address>\n"); + exit_value = 4; + goto done; } /* end if */ - status = H5FS_sects_debug(f, addr, stdout, 0, VCOL, extra, extra2); - + status = H5FS_sects_debug(f, addr, stdout, 0, VCOL, extra[0], extra[1]); } - else if(!HDmemcmp(sig, H5SM_TABLE_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { + else if (!HDmemcmp(sig, H5SM_TABLE_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* - * Debug shared message master table. - */ - - status = H5SM_table_debug(f, addr, stdout, 0, VCOL, (unsigned) UFAIL, (unsigned) UFAIL); + * Debug shared message master table. + */ + status = H5SM_table_debug(f, addr, stdout, 0, VCOL, UINT_MAX, UINT_MAX); } - else if(!HDmemcmp(sig, H5SM_LIST_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { + else if (!HDmemcmp(sig, H5SM_LIST_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* - * Debug shared message list index. - */ + * Debug shared message list index. + */ /* Check for enough valid parameters */ - if(extra == 0) { + if (extra_count == 0 || extra[0] == 0) { HDfprintf(stderr, "ERROR: Need shared message header address in order to shared message list\n"); HDfprintf(stderr, "Shared message list usage:\n"); - HDfprintf(stderr, "\th5debug <filename> <shared message list address> <shared message header address>\n"); - HDexit(4); + HDfprintf(stderr, + "\th5debug <filename> <shared message list address> <shared message header address>\n"); + exit_value = 4; + goto done; } /* end if */ - status = H5SM_list_debug(f, addr, stdout, 0, VCOL, (haddr_t)extra); - + status = H5SM_list_debug(f, addr, stdout, 0, VCOL, (haddr_t)extra[0]); } - else if(!HDmemcmp(sig, H5EA_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { + else if (!HDmemcmp(sig, H5EA_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* - * Debug an extensible aray header. - */ + * Debug an extensible array header. + */ const H5EA_class_t *cls = get_H5EA_class(sig); HDassert(cls); /* Check for enough valid parameters */ - if(extra == 0) { - HDfprintf(stderr, "ERROR: Need object header address containing the layout message in order to dump header\n"); + if (extra_count == 0 || extra[0] == 0) { + HDfprintf( + stderr, + "ERROR: Need object header address containing the layout message in order to dump header\n"); HDfprintf(stderr, "Extensible array header block usage:\n"); - HDfprintf(stderr, "\th5debug <filename> <Extensible Array header address> <object header address>\n"); - HDexit(4); + HDfprintf(stderr, + "\th5debug <filename> <Extensible Array header address> <object header address>\n"); + exit_value = 4; + goto done; } /* end if */ - status = H5EA__hdr_debug(f, addr, stdout, 0, VCOL, cls, extra); - + status = H5EA__hdr_debug(f, addr, stdout, 0, VCOL, cls, extra[0]); } - else if(!HDmemcmp(sig, H5EA_IBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { + else if (!HDmemcmp(sig, H5EA_IBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* - * Debug an extensible aray index block. - */ + * Debug an extensible array index block. + */ const H5EA_class_t *cls = get_H5EA_class(sig); HDassert(cls); /* Check for enough valid parameters */ - if(extra == 0 || extra2 == 0) { - HDfprintf(stderr, "ERROR: Need extensible array header address and object header address containing the layout message in order to dump index block\n"); + if (extra_count == 0 || extra[0] == 0 || extra[1] == 0) { + HDfprintf(stderr, "ERROR: Need extensible array header address and object header address " + "containing the layout message in order to dump index block\n"); HDfprintf(stderr, "Extensible array index block usage:\n"); - HDfprintf(stderr, "\th5debug <filename> <index block address> <array header address> <object header address\n"); - HDexit(4); + HDfprintf( + stderr, + "\th5debug <filename> <index block address> <array header address> <object header address\n"); + exit_value = 4; + goto done; } /* end if */ - status = H5EA__iblock_debug(f, addr, stdout, 0, VCOL, cls, extra, extra2); - + status = H5EA__iblock_debug(f, addr, stdout, 0, VCOL, cls, extra[0], extra[1]); } - else if(!HDmemcmp(sig, H5EA_SBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { + else if (!HDmemcmp(sig, H5EA_SBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* - * Debug an extensible aray super block. - */ + * Debug an extensible array super block. + */ const H5EA_class_t *cls = get_H5EA_class(sig); HDassert(cls); /* Check for enough valid parameters */ - if(extra == 0 || extra2 == 0 || extra3 == 0) { - HDfprintf(stderr, "ERROR: Need extensible array header address, super block index and object header address containing the layout message in order to dump super block\n"); + if (extra_count == 0 || extra[0] == 0 || extra[1] == 0 || extra[2] == 0) { + HDfprintf(stderr, "ERROR: Need extensible array header address, super block index and object " + "header address containing the layout message in order to dump super block\n"); HDfprintf(stderr, "Extensible array super block usage:\n"); - HDfprintf(stderr, "\th5debug <filename> <super block address> <array header address> <super block index> <object header address>\n"); - HDexit(4); + HDfprintf(stderr, "\th5debug <filename> <super block address> <array header address> <super " + "block index> <object header address>\n"); + exit_value = 4; + goto done; } /* end if */ - status = H5EA__sblock_debug(f, addr, stdout, 0, VCOL, cls, extra, (unsigned)extra2, extra3); - + status = H5EA__sblock_debug(f, addr, stdout, 0, VCOL, cls, extra[0], (unsigned)extra[1], extra[2]); } - else if(!HDmemcmp(sig, H5EA_DBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { + else if (!HDmemcmp(sig, H5EA_DBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* - * Debug an extensible aray data block. - */ + * Debug an extensible array data block. + */ const H5EA_class_t *cls = get_H5EA_class(sig); HDassert(cls); /* Check for enough valid parameters */ - if(extra == 0 || extra2 == 0 || extra3 == 0) { - HDfprintf(stderr, "ERROR: Need extensible array header address, # of elements in data block and object header address containing the layout message in order to dump data block\n"); + if (extra_count == 0 || extra[0] == 0 || extra[1] == 0 || extra[2] == 0) { + HDfprintf(stderr, + "ERROR: Need extensible array header address, # of elements in data block and object " + "header address containing the layout message in order to dump data block\n"); HDfprintf(stderr, "Extensible array data block usage:\n"); - HDfprintf(stderr, "\th5debug <filename> <data block address> <array header address> <# of elements in data block> <object header address\n"); - HDexit(4); + HDfprintf(stderr, "\th5debug <filename> <data block address> <array header address> <# of " + "elements in data block> <object header address\n"); + exit_value = 4; + goto done; } /* end if */ - status = H5EA__dblock_debug(f, addr, stdout, 0, VCOL, cls, extra, (size_t)extra2, extra3); - + status = H5EA__dblock_debug(f, addr, stdout, 0, VCOL, cls, extra[0], (size_t)extra[1], extra[2]); } - else if(!HDmemcmp(sig, H5FA_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { + else if (!HDmemcmp(sig, H5FA_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* - * Debug a fixed array header. - */ + * Debug a fixed array header. + */ const H5FA_class_t *cls = get_H5FA_class(sig); HDassert(cls); /* Check for enough valid parameters */ - if(extra == 0) { - HDfprintf(stderr, "ERROR: Need object header address containing the layout message in order to dump header\n"); + if (extra_count == 0 || extra[0] == 0) { + HDfprintf( + stderr, + "ERROR: Need object header address containing the layout message in order to dump header\n"); HDfprintf(stderr, "Fixed array header block usage:\n"); HDfprintf(stderr, "\th5debug <filename> <Fixed Array header address> <object header address>\n"); - HDexit(4); + exit_value = 4; + goto done; } /* end if */ - status = H5FA__hdr_debug(f, addr, stdout, 0, VCOL, cls, extra); - + status = H5FA__hdr_debug(f, addr, stdout, 0, VCOL, cls, extra[0]); } - else if(!HDmemcmp(sig, H5FA_DBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { + else if (!HDmemcmp(sig, H5FA_DBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* - * Debug a fixed array data block. - */ + * Debug a fixed array data block. + */ const H5FA_class_t *cls = get_H5FA_class(sig); HDassert(cls); /* Check for enough valid parameters */ - if(extra == 0 || extra2 == 0) { - HDfprintf(stderr, "ERROR: Need fixed array header address and object header address containing the layout message in order to dump data block\n"); + if (extra_count == 0 || extra[0] == 0 || extra[1] == 0) { + HDfprintf(stderr, "ERROR: Need fixed array header address and object header address containing " + "the layout message in order to dump data block\n"); HDfprintf(stderr, "fixed array data block usage:\n"); - HDfprintf(stderr, "\th5debug <filename> <data block address> <array header address> <object header address>\n"); - HDexit(4); + HDfprintf( + stderr, + "\th5debug <filename> <data block address> <array header address> <object header address>\n"); + exit_value = 4; + goto done; } /* end if */ - status = H5FA__dblock_debug(f, addr, stdout, 0, VCOL, cls, extra, extra2); - + status = H5FA__dblock_debug(f, addr, stdout, 0, VCOL, cls, extra[0], extra[1]); } - else if(!HDmemcmp(sig, H5O_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { + else if (!HDmemcmp(sig, H5O_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* - * Debug v2 object header (which have signatures). - */ + * Debug v2 object header (which have signatures). + */ status = H5O_debug(f, addr, stdout, 0, VCOL); - } - else if(sig[0] == H5O_VERSION_1) { + else if (sig[0] == H5O_VERSION_1) { /* - * This could be a v1 object header. Since they don't have a signature - * it's a somewhat "ify" detection. - */ + * This could be a v1 object header. Since they don't have a signature + * it's a somewhat "ify" detection. + */ status = H5O_debug(f, addr, stdout, 0, VCOL); - } else { /* - * Got some other unrecognized signature. - */ + * Got some other unrecognized signature. + */ HDprintf("%-*s ", VCOL, "Signature:"); for (u = 0; u < sizeof(sig); u++) { if (sig[u] > ' ' && sig[u] <= '~' && '\\' != sig[u]) @@ -732,24 +801,29 @@ main(int argc, char *argv[]) HDputchar('\n'); HDfprintf(stderr, "unknown signature\n"); - HDexit(4); + exit_value = 4; + goto done; } /* end else */ /* Check for an error when dumping information */ - if(status < 0) { + if (status < 0) { HDfprintf(stderr, "An error occurred!\n"); H5Eprint2(H5E_DEFAULT, stderr); - HDexit(5); + exit_value = 5; + goto done; } /* end if */ - H5Pclose(fapl); - H5Fclose(fid); +done: + if (fapl > 0) + H5Pclose(fapl); + if (fid > 0) + H5Fclose(fid); /* Pop API context */ - if(api_ctx_pushed) H5CX_pop(); + if (api_ctx_pushed) + H5CX_pop(FALSE); H5Eset_auto2(H5E_DEFAULT, func, edata); - return 0; + return exit_value; } /* main() */ - diff --git a/tools/src/misc/h5delete.c b/tools/src/misc/h5delete.c new file mode 100644 index 0000000..20e81a1 --- /dev/null +++ b/tools/src/misc/h5delete.c @@ -0,0 +1,66 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * Copyright by The HDF Group. * + * All rights reserved. * + * * + * This file is part of HDF5. The full HDF5 copyright notice, including * + * terms governing use, modification, and redistribution, is contained in * + * the COPYING file, which can be found at the root of the source code * + * distribution tree, or in https://www.hdfgroup.org/licenses. * + * If you do not have access to either file, you may request a copy from * + * help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + +/* h5delete tool + * + * Deletes storage via H5Fdelete() using the VOL connector specified in the + * environment variable. + */ + +#include "H5private.h" +#include "H5Eprivate.h" +#include "H5Pprivate.h" + +static void usage(void); + +static void +usage(void) +{ + HDfprintf(stderr, "Usage: h5delete [-f] <filename>\n"); +} + +int +main(int argc, char *argv[]) +{ + hbool_t quiet = FALSE; + const char *name = NULL; + int ret = 0; + + switch (argc) { + case 3: + if (HDstrcmp(argv[1], "-f") != 0) { + usage(); + return EXIT_FAILURE; + } + quiet = TRUE; + name = argv[2]; + break; + case 2: + name = argv[1]; + break; + default: + usage(); + return EXIT_FAILURE; + } + + H5E_BEGIN_TRY + { + /* Only uses the environment variable at this time */ + ret = (int)H5Fdelete(name, H5P_DEFAULT); + } + H5E_END_TRY; + + if (ret < 0 && !quiet) + HDfprintf(stderr, "Unable to delete storage at: %s\n", name); + + return ret < 0 ? EXIT_FAILURE : EXIT_SUCCESS; +} diff --git a/tools/src/misc/h5mkgrp.c b/tools/src/misc/h5mkgrp.c index feb60d4..1b8b23d 100644 --- a/tools/src/misc/h5mkgrp.c +++ b/tools/src/misc/h5mkgrp.c @@ -6,12 +6,11 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - #include "H5private.h" #include "h5tools.h" #include "h5tools_utils.h" @@ -23,28 +22,26 @@ int d_status = EXIT_SUCCESS; /* command-line options: short and long-named parameters */ -static const char *s_opts = "hlpvV"; -static struct long_options l_opts[] = { - { "help", no_arg, 'h' }, - { "latest", no_arg, 'l' }, - { "parents", no_arg, 'p' }, - { "verbose", no_arg, 'v' }, - { "version", no_arg, 'V' }, - { NULL, 0, '\0' } -}; +static const char * s_opts = "hlpvV"; +static struct h5_long_options l_opts[] = { + {"help", no_arg, 'h'}, {"latest", no_arg, 'l'}, {"parents", no_arg, 'p'}, + {"verbose", no_arg, 'v'}, {"version", no_arg, 'V'}, {"vol-value", require_arg, '1'}, + {"vol-name", require_arg, '2'}, {"vol-info", require_arg, '3'}, {"vfd-value", require_arg, '4'}, + {"vfd-name", require_arg, '5'}, {"vfd-info", require_arg, '6'}, {NULL, 0, '\0'}}; /* Command line parameter settings */ -typedef struct { - char *fname; /* File name to operate on */ - hbool_t latest; /* Whether file should use latest format versions */ - hbool_t verbose; /* Whether output should be verbose */ - hbool_t parents; /* Whether to create intermediate groups */ - size_t ngroups; /* Number of groups to create */ - char **groups; /* Pointer to array of group names */ -} param_t; -param_t params; /* Command line parameter settings */ - - +typedef struct mkgrp_opt_t { + char * fname; /* File name to operate on */ + hbool_t latest; /* Whether file should use latest format versions */ + hbool_t verbose; /* Whether output should be verbose */ + hbool_t parents; /* Whether to create intermediate groups */ + size_t ngroups; /* Number of groups to create */ + char ** groups; /* Pointer to array of group names */ + hid_t fapl_id; /* fapl to use when opening the file */ +} mkgrp_opt_t; + +mkgrp_opt_t params_g; /* Command line parameter settings */ + /*------------------------------------------------------------------------- * Function: leave * @@ -61,18 +58,21 @@ leave(int ret) { size_t curr_group; - if (params.fname) - HDfree (params.fname); - if (params.ngroups) { - for(curr_group = 0; curr_group < params.ngroups; curr_group++) - HDfree (params.groups[curr_group]); - HDfree (params.groups); + if (params_g.fname) + HDfree(params_g.fname); + if (params_g.ngroups) { + for (curr_group = 0; curr_group < params_g.ngroups; curr_group++) + HDfree(params_g.groups[curr_group]); + HDfree(params_g.groups); } + if (H5I_INVALID_HID != params_g.fapl_id && H5P_DEFAULT != params_g.fapl_id) + if (H5Pclose(params_g.fapl_id) < 0) + error_msg("Could not close file access property list\n"); + h5tools_close(); HDexit(ret); } /* end leave() */ - /*------------------------------------------------------------------------- * Function: usage * @@ -85,65 +85,94 @@ leave(int ret) *------------------------------------------------------------------------- */ static void -usage(void) +usage(const char *prog) { - HDfprintf(stdout, "\ -usage: h5mkgrp [OPTIONS] FILE GROUP...\n\ - OPTIONS\n\ - -h, --help Print a usage message and exit\n\ - -l, --latest Use latest version of file format to create groups\n\ - -p, --parents No error if existing, make parent groups as needed\n\ - -v, --verbose Print information about OBJECTS and OPTIONS\n\ - -V, --version Print version number and exit\n"); + FLUSHSTREAM(rawoutstream); + PRINTSTREAM(rawoutstream, "usage: %s [OPTIONS] FILE GROUP...\n", prog); + PRINTVALSTREAM(rawoutstream, " OPTIONS\n"); + PRINTVALSTREAM(rawoutstream, " -h, --help Print a usage message and exit\n"); + PRINTVALSTREAM(rawoutstream, + " -l, --latest Use latest version of file format to create groups\n"); + PRINTVALSTREAM(rawoutstream, + " -p, --parents No error if existing, make parent groups as needed\n"); + PRINTVALSTREAM(rawoutstream, " -v, --verbose Print information about OBJECTS and OPTIONS\n"); + PRINTVALSTREAM(rawoutstream, " -V, --version Print version number and exit\n"); + PRINTVALSTREAM(rawoutstream, + " --vol-value Value (ID) of the VOL connector to use for opening the\n"); + PRINTVALSTREAM(rawoutstream, " HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, + " --vol-name Name of the VOL connector to use for opening the\n"); + PRINTVALSTREAM(rawoutstream, " HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, + " --vol-info VOL-specific info to pass to the VOL connector used for\n"); + PRINTVALSTREAM(rawoutstream, " opening the HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, + " --vfd-value Value (ID) of the VFL driver to use for opening the\n"); + PRINTVALSTREAM(rawoutstream, " HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, " --vfd-name Name of the VFL driver to use for opening the\n"); + PRINTVALSTREAM(rawoutstream, " HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, + " --vfd-info VFD-specific info to pass to the VFL driver used for\n"); + PRINTVALSTREAM(rawoutstream, " opening the HDF5 file specified\n"); + PRINTVALSTREAM(rawoutstream, "\n"); } /* end usage() */ - /*------------------------------------------------------------------------- - * Function: parse_command_line + * Function: parse_command_line * - * Purpose: Parses command line and sets up global variable to control output + * Purpose: Parses command line and sets up global variable to control + * output * - * Return: Success: 0 - * Failure: -1 + * Return: Success: 0 + * Failure: -1 * * Programmer: Quincey Koziol, 2/13/2007 * *------------------------------------------------------------------------- */ static int -parse_command_line(int argc, const char *argv[], param_t *parms) +parse_command_line(int argc, const char *const *argv, mkgrp_opt_t *options) { - int opt; /* Option from command line */ - size_t curr_group; /* Current group name to copy */ + int opt; /* Option from command line */ + size_t curr_group; /* Current group name to copy */ + hbool_t custom_vol = FALSE; + hbool_t custom_vfd = FALSE; + h5tools_vol_info_t vol_info; + h5tools_vfd_info_t vfd_info; + hid_t tmp_fapl_id = H5I_INVALID_HID; /* Check for empty command line */ - if(argc == 1) { - usage(); + if (argc == 1) { + usage(h5tools_getprogname()); leave(EXIT_SUCCESS); - } /* end if */ + } + + /* Initialize fapl info structs */ + HDmemset(&vol_info, 0, sizeof(h5tools_vol_info_t)); + HDmemset(&vfd_info, 0, sizeof(h5tools_vfd_info_t)); /* Parse command line options */ - while((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) { - switch((char)opt) { + while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) { + switch ((char)opt) { /* Display 'help' */ case 'h': - usage(); + usage(h5tools_getprogname()); leave(EXIT_SUCCESS); break; /* Create objects with the latest version of the format */ case 'l': - parms->latest = TRUE; + options->latest = TRUE; break; /* Create parent groups */ case 'p': - parms->parents = TRUE; + options->parents = TRUE; break; /* Verbose output */ case 'v': - parms->verbose = TRUE; + options->verbose = TRUE; break; /* Display version */ @@ -152,56 +181,96 @@ parse_command_line(int argc, const char *argv[], param_t *parms) leave(EXIT_SUCCESS); break; + case '1': + vol_info.type = VOL_BY_VALUE; + vol_info.u.value = (H5VL_class_value_t)HDatoi(H5_optarg); + custom_vol = TRUE; + break; + + case '2': + vol_info.type = VOL_BY_NAME; + vol_info.u.name = H5_optarg; + custom_vol = TRUE; + break; + + case '3': + vol_info.info_string = H5_optarg; + break; + + case '4': + vfd_info.type = VFD_BY_VALUE; + vfd_info.u.value = (H5FD_class_value_t)HDatoi(H5_optarg); + custom_vfd = TRUE; + break; + + case '5': + vfd_info.type = VFD_BY_NAME; + vfd_info.u.name = H5_optarg; + custom_vfd = TRUE; + break; + + case '6': + vfd_info.info = (const void *)H5_optarg; + break; + /* Bad command line argument */ default: - usage(); + usage(h5tools_getprogname()); leave(EXIT_FAILURE); } /* end switch */ - } /* end while */ + } /* end while */ /* Check for file name to be processed */ - if(argc <= opt_ind) { + if (argc <= H5_optind) { error_msg("missing file name\n"); - usage(); + usage(h5tools_getprogname()); leave(EXIT_FAILURE); - } /* end if */ + } /* Retrieve file name */ - parms->fname = HDstrdup(argv[opt_ind]); - opt_ind++; + options->fname = HDstrdup(argv[H5_optind]); + H5_optind++; /* Check for group(s) to be created */ - if(argc <= opt_ind) { + if (argc <= H5_optind) { error_msg("missing group name(s)\n"); - usage(); + usage(h5tools_getprogname()); leave(EXIT_FAILURE); - } /* end if */ + } /* Allocate space for the group name pointers */ - parms->ngroups = (size_t)(argc - opt_ind); - parms->groups = (char **)HDmalloc(parms->ngroups * sizeof(char *)); + options->ngroups = (size_t)(argc - H5_optind); + options->groups = (char **)HDmalloc(options->ngroups * sizeof(char *)); /* Retrieve the group names */ curr_group = 0; - while(opt_ind < argc) { - parms->groups[curr_group] = HDstrdup(argv[opt_ind]); + while (H5_optind < argc) { + options->groups[curr_group] = HDstrdup(argv[H5_optind]); curr_group++; - opt_ind++; - } /* end while */ - -#ifdef QAK -HDfprintf(stderr, "parms->parents = %t\n", parms->parents); -HDfprintf(stderr, "parms->verbose = %t\n", parms->verbose); -HDfprintf(stderr, "parms->fname = '%s'\n", parms->fname); -HDfprintf(stderr, "parms->ngroups = %Zu\n", parms->ngroups); -for(curr_group = 0; curr_group < parms->ngroups; curr_group++) - HDfprintf(stderr, "parms->group[%Zu] = '%s'\n", curr_group, parms->groups[curr_group]); -#endif /* QAK */ - - return(0); + H5_optind++; + } + + /* Setup a custom fapl for file accesses */ + if (custom_vol || custom_vfd) { + if ((tmp_fapl_id = h5tools_get_fapl(options->fapl_id, custom_vol ? &vol_info : NULL, + custom_vfd ? &vfd_info : NULL)) < 0) { + error_msg("failed to setup file access property list (fapl) for file\n"); + leave(EXIT_FAILURE); + } + + /* Close the old fapl */ + if (options->fapl_id != H5P_DEFAULT) + if (H5Pclose(options->fapl_id) < 0) { + error_msg("failed to close file access property list (fapl)\n"); + leave(EXIT_FAILURE); + } + + options->fapl_id = tmp_fapl_id; + } + + return 0; } /* parse_command_line() */ - /*------------------------------------------------------------------------- * Function: main * @@ -212,120 +281,115 @@ for(curr_group = 0; curr_group < parms->ngroups; curr_group++) *------------------------------------------------------------------------- */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { - hid_t fid; /* HDF5 file ID */ - hid_t fapl_id; /* File access property list ID */ - hid_t lcpl_id; /* Link creation property list ID */ - size_t curr_group; /* Current group to create */ + hid_t fid = H5I_INVALID_HID; /* HDF5 file ID */ + hid_t lcpl_id = H5I_INVALID_HID; /* Link creation property list ID */ + size_t curr_group; /* Current group to create */ h5tools_setprogname(PROGRAMNAME); h5tools_setstatus(EXIT_SUCCESS); - /* Disable the HDF5 library's error reporting */ - H5Eset_auto2(H5E_DEFAULT, NULL, NULL); - /* Initialize h5tools lib */ h5tools_init(); - /* Parse command line */ - HDmemset(¶ms, 0, sizeof(params)); - if(parse_command_line(argc, argv, ¶ms) < 0) { - error_msg("unable to parse command line arguments\n"); - leave(EXIT_FAILURE); - } /* end if */ + /* Initialize the parameters */ + HDmemset(¶ms_g, 0, sizeof(params_g)); /* Create file access property list */ - if((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) { + if ((params_g.fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) { error_msg("Could not create file access property list\n"); leave(EXIT_FAILURE); - } /* end if */ + } + + /* Parse command line */ + if (parse_command_line(argc, (const char *const *)argv, ¶ms_g) < 0) { + error_msg("unable to parse command line arguments\n"); + leave(EXIT_FAILURE); + } + + /* enable error reporting if command line option */ + h5tools_error_report(); /* Check for creating groups with new format version */ - if(params.latest) { + if (params_g.latest) { /* Set the "use the latest version of the format" bounds */ - if(H5Pset_libver_bounds(fapl_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) { + if (H5Pset_libver_bounds(params_g.fapl_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) { error_msg("Could not set property for using latest version of the format\n"); leave(EXIT_FAILURE); - } /* end if */ + } /* Display some output if requested */ - if(params.verbose) + if (params_g.verbose) HDprintf("%s: Creating groups with latest version of the format\n", h5tools_getprogname()); - } /* end if */ + } /* Attempt to open an existing HDF5 file first */ - fid = h5tools_fopen(params.fname, H5F_ACC_RDWR, fapl_id, NULL, NULL, 0); + fid = h5tools_fopen(params_g.fname, H5F_ACC_RDWR, params_g.fapl_id, (params_g.fapl_id != H5P_DEFAULT), + NULL, 0); /* If we couldn't open an existing file, try creating file */ /* (use "EXCL" instead of "TRUNC", so we don't blow away existing non-HDF5 file) */ - if(fid < 0) - fid = H5Fcreate(params.fname, H5F_ACC_EXCL, H5P_DEFAULT, fapl_id); + if (fid < 0) + fid = H5Fcreate(params_g.fname, H5F_ACC_EXCL, H5P_DEFAULT, params_g.fapl_id); /* Test for error in opening file */ - if(fid < 0) { - error_msg("Could not open output file '%s'\n", params.fname); + if (fid < 0) { + error_msg("Could not open output file '%s'\n", params_g.fname); leave(EXIT_FAILURE); - } /* end if */ + } /* Create link creation property list */ - if((lcpl_id = H5Pcreate(H5P_LINK_CREATE)) < 0) { + if ((lcpl_id = H5Pcreate(H5P_LINK_CREATE)) < 0) { error_msg("Could not create link creation property list\n"); leave(EXIT_FAILURE); - } /* end if */ + } /* Check for creating intermediate groups */ - if(params.parents) { + if (params_g.parents) { /* Set the intermediate group creation property */ - if(H5Pset_create_intermediate_group(lcpl_id, TRUE) < 0) { + if (H5Pset_create_intermediate_group(lcpl_id, TRUE) < 0) { error_msg("Could not set property for creating parent groups\n"); leave(EXIT_FAILURE); - } /* end if */ + } /* Display some output if requested */ - if(params.verbose) + if (params_g.verbose) HDprintf("%s: Creating parent groups\n", h5tools_getprogname()); - } /* end if */ + } /* Loop over creating requested groups */ - for(curr_group = 0; curr_group < params.ngroups; curr_group++) { - hid_t gid; /* Group ID */ + for (curr_group = 0; curr_group < params_g.ngroups; curr_group++) { + hid_t gid; /* Group ID */ /* Attempt to create a group */ - if((gid = H5Gcreate2(fid, params.groups[curr_group], lcpl_id, H5P_DEFAULT, H5P_DEFAULT)) < 0) { - error_msg("Could not create group '%s'\n", params.groups[curr_group]); + if ((gid = H5Gcreate2(fid, params_g.groups[curr_group], lcpl_id, H5P_DEFAULT, H5P_DEFAULT)) < 0) { + error_msg("Could not create group '%s'\n", params_g.groups[curr_group]); leave(EXIT_FAILURE); - } /* end if */ + } /* Close the group */ - if(H5Gclose(gid) < 0) { - error_msg("Could not close group '%s'??\n", params.groups[curr_group]); + if (H5Gclose(gid) < 0) { + error_msg("Could not close group '%s'??\n", params_g.groups[curr_group]); leave(EXIT_FAILURE); - } /* end if */ + } /* Display some output if requested */ - if(params.verbose) - HDprintf("%s: created group '%s'\n", h5tools_getprogname(), params.groups[curr_group]); + if (params_g.verbose) + HDprintf("%s: created group '%s'\n", h5tools_getprogname(), params_g.groups[curr_group]); } /* end for */ /* Close link creation property list */ - if(H5Pclose(lcpl_id) < 0) { + if (H5Pclose(lcpl_id) < 0) { error_msg("Could not close link creation property list\n"); leave(EXIT_FAILURE); - } /* end if */ + } /* Close file */ - if(H5Fclose(fid) < 0) { - error_msg("Could not close output file '%s'??\n", params.fname); - leave(EXIT_FAILURE); - } /* end if */ - - /* Close file access property list */ - if(H5Pclose(fapl_id) < 0) { - error_msg("Could not close file access property list\n"); + if (H5Fclose(fid) < 0) { + error_msg("Could not close output file '%s'??\n", params_g.fname); leave(EXIT_FAILURE); - } /* end if */ + } leave(EXIT_SUCCESS); } /* end main() */ - diff --git a/tools/src/misc/h5repart.c b/tools/src/misc/h5repart.c index d516fa0..f4cef6a 100644 --- a/tools/src/misc/h5repart.c +++ b/tools/src/misc/h5repart.c @@ -6,13 +6,13 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ /* - * Programmer: Robb Matzke <matzke@llnl.gov> + * Programmer: Robb Matzke * Wednesday, May 13, 1998 * * Purpose: Repartitions a file family. This program can be used to @@ -26,16 +26,15 @@ #include "hdf5.h" #include "H5private.h" -#define NAMELEN 4096 -#define GB *1024*1024*1024 +#define NAMELEN 4096 +#define GB *1024 * 1024 * 1024 /* Make these 2 private properties(defined in H5Fprivate.h) available to h5repart. * The first one updates the member file size in the superblock. The second one * change file driver from family to a single file driver. */ -#define H5F_ACS_FAMILY_NEWSIZE_NAME "family_newsize" -#define H5F_ACS_FAMILY_TO_SINGLE_NAME "family_to_single" - +#define H5F_ACS_FAMILY_NEWSIZE_NAME "family_newsize" +#define H5F_ACS_FAMILY_TO_SINGLE_NAME "family_to_single" /*------------------------------------------------------------------------- * Function: usage @@ -52,26 +51,26 @@ *------------------------------------------------------------------------- */ static void -usage (const char *progname) +usage(const char *progname) { HDfprintf(stderr, "usage: %s [-v] [-V] [-[b|m] N[g|m|k]] [-family_to_sec2|-family_to_single] SRC DST\n", - progname); + progname); HDfprintf(stderr, " -v Produce verbose output\n"); HDfprintf(stderr, " -V Print a version number and exit\n"); HDfprintf(stderr, " -b N The I/O block size, defaults to 1kB\n"); HDfprintf(stderr, " -m N The destination member size or 1GB\n"); HDfprintf(stderr, " -family_to_sec2 Deprecated version of -family_to_single (below)\n"); - HDfprintf(stderr, " -family_to_single Change file driver from family to the default single-file VFD (windows or sec2)\n"); + HDfprintf(stderr, " -family_to_single Change file driver from family to the default single-file VFD " + "(windows or sec2)\n"); HDfprintf(stderr, " SRC The name of the source file\n"); HDfprintf(stderr, " DST The name of the destination files\n"); - HDfprintf(stderr, "Sizes may be suffixed with `g' for GB, `m' for MB or " - "`k' for kB.\n"); + HDfprintf(stderr, "Sizes may be suffixed with 'g' for GB, 'm' for MB or " + "'k' for kB.\n"); HDfprintf(stderr, "File family names include an integer printf " - "format such as `%%d'\n"); - HDexit (EXIT_FAILURE); + "format such as '%%d'\n"); + HDexit(EXIT_FAILURE); } - /*------------------------------------------------------------------------- * Function: get_size * @@ -95,48 +94,47 @@ usage (const char *progname) *------------------------------------------------------------------------- */ static off_t -get_size (const char *progname, int *argno, int argc, char *argv[]) +get_size(const char *progname, int *argno, int argc, char *argv[]) { - off_t retval=-1; - char *suffix; + off_t retval = -1; + char *suffix = NULL; - if (isdigit ((int)(argv[*argno][2]))) { - retval = HDstrtol(argv[*argno]+2, &suffix, 10); + if (isdigit((int)(argv[*argno][2]))) { + retval = HDstrtol(argv[*argno] + 2, &suffix, 10); (*argno)++; } - else if (argv[*argno][2] || *argno+1>=argc) { - usage (progname); + else if (argv[*argno][2] || *argno + 1 >= argc) { + usage(progname); } else { - retval = HDstrtol(argv[*argno+1], &suffix, 0); - if (suffix == argv[*argno+1]) - usage (progname); + retval = HDstrtol(argv[*argno + 1], &suffix, 0); + if (suffix == argv[*argno + 1]) + usage(progname); *argno += 2; } if (suffix && suffix[0] && !suffix[1]) { switch (*suffix) { - case 'G': - case 'g': - retval *= 1024 * 1024 * 1024; - break; - case 'M': - case 'm': - retval *= 1024 * 1024; - break; - case 'k': - retval *= 1024; - break; - default: - usage(progname); + case 'G': + case 'g': + retval *= 1024 * 1024 * 1024; + break; + case 'M': + case 'm': + retval *= 1024 * 1024; + break; + case 'k': + retval *= 1024; + break; + default: + usage(progname); } } else if (suffix && suffix[0]) { - usage (progname); + usage(progname); } return retval; } - /*------------------------------------------------------------------------- * Function: main * @@ -154,47 +152,47 @@ get_size (const char *progname, int *argno, int argc, char *argv[]) *------------------------------------------------------------------------- */ int -main (int argc, char *argv[]) +main(int argc, char *argv[]) { - const char *prog_name; /*program name */ - size_t blk_size=1024; /*size of each I/O block */ - char *buf=NULL; /*I/O block buffer */ - size_t n, i; /*counters */ - ssize_t nio; /*I/O return value */ - int argno=1; /*program argument number */ - int src, dst=-1; /*source & destination files */ - int need_seek=FALSE; /*destination needs to seek? */ - int need_write; /*data needs to be written? */ - h5_stat_t sb; /*temporary file stat buffer */ - - int verbose=FALSE; /*display file names? */ - - const char *src_gen_name; /*general source name */ - char *src_name=NULL; /*source member name */ - - int src_is_family; /*is source name a family name? */ - int src_membno=0; /*source member number */ - - const char *dst_gen_name; /*general destination name */ - char *dst_name=NULL; /*destination member name */ - int dst_is_family; /*is dst name a family name? */ - int dst_membno=0; /*destination member number */ - - off_t left_overs=0; /*amount of zeros left over */ - off_t src_offset=0; /*offset in source member */ - off_t dst_offset=0; /*offset in destination member */ - off_t src_size; /*source logical member size */ - off_t src_act_size; /*source actual member size */ - off_t dst_size=1 GB; /*destination logical memb size */ - hid_t fapl; /*file access property list */ - hid_t file; - hsize_t hdsize; /*destination logical memb size */ - hbool_t family_to_single = FALSE; /*change family to single file driver? */ + const char *prog_name; /*program name */ + size_t blk_size = 1024; /*size of each I/O block */ + char * buf = NULL; /*I/O block buffer */ + size_t n, i; /*counters */ + ssize_t nio; /*I/O return value */ + int argno = 1; /*program argument number */ + int src, dst = -1; /*source & destination files */ + int need_seek = FALSE; /*destination needs to seek? */ + int need_write; /*data needs to be written? */ + h5_stat_t sb; /*temporary file stat buffer */ + + int verbose = FALSE; /*display file names? */ + + const char *src_gen_name; /*general source name */ + char * src_name = NULL; /*source member name */ + + int src_is_family; /*is source name a family name? */ + int src_membno = 0; /*source member number */ + + const char *dst_gen_name; /*general destination name */ + char * dst_name = NULL; /*destination member name */ + int dst_is_family; /*is dst name a family name? */ + int dst_membno = 0; /*destination member number */ + + off_t left_overs = 0; /*amount of zeros left over */ + off_t src_offset = 0; /*offset in source member */ + off_t dst_offset = 0; /*offset in destination member */ + off_t src_size; /*source logical member size */ + off_t src_act_size; /*source actual member size */ + off_t dst_size = 1 GB; /*destination logical memb size */ + hid_t fapl; /*file access property list */ + hid_t file; + hsize_t hdsize; /*destination logical memb size */ + hbool_t family_to_single = FALSE; /*change family to single file driver? */ /* * Get the program name from argv[0]. Use only the last component. */ - if ((prog_name = HDstrrchr (argv[0], '/'))) + if ((prog_name = HDstrrchr(argv[0], '/'))) prog_name++; else prog_name = argv[0]; @@ -206,28 +204,35 @@ main (int argc, char *argv[]) if (!HDstrcmp(argv[argno], "-v")) { verbose = TRUE; argno++; - } else if (!HDstrcmp(argv[argno], "-V")) { - HDprintf("This is %s version %u.%u release %u\n", prog_name, H5_VERS_MAJOR, H5_VERS_MINOR, H5_VERS_RELEASE); + } + else if (!HDstrcmp(argv[argno], "-V")) { + HDprintf("This is %s version %u.%u release %u\n", prog_name, H5_VERS_MAJOR, H5_VERS_MINOR, + H5_VERS_RELEASE); HDexit(EXIT_SUCCESS); - } else if (!HDstrcmp(argv[argno], "-family_to_sec2")) { + } + else if (!HDstrcmp(argv[argno], "-family_to_sec2")) { family_to_single = TRUE; argno++; - } else if (!HDstrcmp(argv[argno], "-family_to_single")) { + } + else if (!HDstrcmp(argv[argno], "-family_to_single")) { family_to_single = TRUE; argno++; - } else if ('b' == argv[argno][1]) { - blk_size = (size_t) get_size(prog_name, &argno, argc, argv); - } else if ('m' == argv[argno][1]) { + } + else if ('b' == argv[argno][1]) { + blk_size = (size_t)get_size(prog_name, &argno, argc, argv); + } + else if ('m' == argv[argno][1]) { dst_size = get_size(prog_name, &argno, argc, argv); - } else { + } + else { usage(prog_name); } /* end if */ - } /* end while */ + } /* end while */ /* allocate names */ - if(NULL == (src_name = (char *)HDcalloc((size_t)NAMELEN, sizeof(char)))) + if (NULL == (src_name = (char *)HDcalloc((size_t)NAMELEN, sizeof(char)))) HDexit(EXIT_FAILURE); - if(NULL == (dst_name = (char *)HDcalloc((size_t)NAMELEN, sizeof(char)))) + if (NULL == (dst_name = (char *)HDcalloc((size_t)NAMELEN, sizeof(char)))) HDexit(EXIT_FAILURE); /* @@ -238,7 +243,7 @@ main (int argc, char *argv[]) usage(prog_name); src_gen_name = argv[argno++]; HDsprintf(src_name, src_gen_name, src_membno); - src_is_family = strcmp (src_name, src_gen_name); + src_is_family = strcmp(src_name, src_gen_name); if ((src = HDopen(src_name, O_RDONLY)) < 0) { HDperror(src_name); @@ -256,13 +261,13 @@ main (int argc, char *argv[]) /* * Get the name for the destination file and open the first member. */ - if (argno>=argc) - usage (prog_name); + if (argno >= argc) + usage(prog_name); dst_gen_name = argv[argno++]; HDsprintf(dst_name, dst_gen_name, dst_membno); dst_is_family = HDstrcmp(dst_name, dst_gen_name); - if ((dst = HDopen(dst_name, O_RDWR|O_CREAT|O_TRUNC, H5_POSIX_CREATE_MODE_RW)) < 0) { + if ((dst = HDopen(dst_name, O_RDWR | O_CREAT | O_TRUNC, H5_POSIX_CREATE_MODE_RW)) < 0) { HDperror(dst_name); HDexit(EXIT_FAILURE); } @@ -271,32 +276,32 @@ main (int argc, char *argv[]) /* No more arguments */ if (argno < argc) - usage (prog_name); + usage(prog_name); /* Now the real work, split the file */ buf = (char *)HDmalloc(blk_size); - while (src_offset<src_size) { + while (src_offset < src_size) { - /* Read a block. The amount to read is the minimum of: - * 1. The I/O block size - * 2. What's left to write in the destination member - * 3. Left over zeros or what's left in the source member. - */ + /* Read a block. The amount to read is the minimum of: + * 1. The I/O block size + * 2. What's left to write in the destination member + * 3. Left over zeros or what's left in the source member. + */ n = blk_size; if (dst_is_family) - n = (size_t)MIN((off_t)n, dst_size-dst_offset); + n = (size_t)MIN((off_t)n, dst_size - dst_offset); if (left_overs) { - n = (size_t)MIN((off_t)n, left_overs); - left_overs = left_overs - (off_t) n; + n = (size_t)MIN((off_t)n, left_overs); + left_overs = left_overs - (off_t)n; need_write = FALSE; } else if (src_offset < src_act_size) { - n = (size_t)MIN((off_t)n, src_act_size-src_offset); + n = (size_t)MIN((off_t)n, src_act_size - src_offset); if ((nio = HDread(src, buf, n)) < 0) { HDperror("read"); HDexit(EXIT_FAILURE); } - else if ((size_t) nio != n) { + else if ((size_t)nio != n) { HDfprintf(stderr, "%s: short read\n", src_name); HDexit(EXIT_FAILURE); } @@ -307,18 +312,18 @@ main (int argc, char *argv[]) need_write = (i < n); } else { - n = 0; + n = 0; left_overs = src_size - src_act_size; need_write = FALSE; } - /* - * If the block contains non-zero data then write it to the - * destination, otherwise just remember that we'll have to do a seek - * later in the destination when we finally get non-zero data. - */ + /* + * If the block contains non-zero data then write it to the + * destination, otherwise just remember that we'll have to do a seek + * later in the destination when we finally get non-zero data. + */ if (need_write) { - if (need_seek && HDlseek (dst, dst_offset, SEEK_SET) < 0) { + if (need_seek && HDlseek(dst, dst_offset, SEEK_SET) < 0) { HDperror("HDlseek"); HDexit(EXIT_FAILURE); } @@ -326,7 +331,7 @@ main (int argc, char *argv[]) HDperror("write"); HDexit(EXIT_FAILURE); } - else if ((size_t) nio != n) { + else if ((size_t)nio != n) { HDfprintf(stderr, "%s: short write\n", dst_name); HDexit(EXIT_FAILURE); } @@ -336,64 +341,64 @@ main (int argc, char *argv[]) need_seek = TRUE; } - /* - * Update the source offset and open the next source family member if - * necessary. The source stream ends at the first member which - * cannot be opened because it doesn't exist. At the end of the - * source stream, update the destination offset and break out of the - * loop. The destination offset must be updated so we can fix - * trailing holes. - */ - src_offset = src_offset + (off_t) n; + /* + * Update the source offset and open the next source family member if + * necessary. The source stream ends at the first member which + * cannot be opened because it doesn't exist. At the end of the + * source stream, update the destination offset and break out of the + * loop. The destination offset must be updated so we can fix + * trailing holes. + */ + src_offset = src_offset + (off_t)n; if (src_offset == src_act_size) { HDclose(src); if (!src_is_family) { - dst_offset = dst_offset + (off_t) n; + dst_offset = dst_offset + (off_t)n; break; } HDsprintf(src_name, src_gen_name, ++src_membno); if ((src = HDopen(src_name, O_RDONLY)) < 0 && ENOENT == errno) { - dst_offset = dst_offset + (off_t) n; + dst_offset = dst_offset + (off_t)n; break; } else if (src < 0) { HDperror(src_name); HDexit(EXIT_FAILURE); } - if (HDfstat (src, &sb) < 0) { + if (HDfstat(src, &sb) < 0) { HDperror("fstat"); HDexit(EXIT_FAILURE); } src_act_size = sb.st_size; if (src_act_size > src_size) { - HDfprintf(stderr, "%s: member truncated to %lu bytes\n", src_name, (unsigned long) src_size); + HDfprintf(stderr, "%s: member truncated to %lu bytes\n", src_name, (unsigned long)src_size); } src_offset = 0; if (verbose) HDfprintf(stderr, "< %s\n", src_name); } - /* - * Update the destination offset, opening a new member if one will be - * needed. The first member is extended to the logical member size - * but other members might be smaller if they end with a hole. - */ - dst_offset = dst_offset + (off_t) n; + /* + * Update the destination offset, opening a new member if one will be + * needed. The first member is extended to the logical member size + * but other members might be smaller if they end with a hole. + */ + dst_offset = dst_offset + (off_t)n; if (dst_is_family && dst_offset == dst_size) { if (0 == dst_membno) { - if (HDlseek (dst, dst_size-1, SEEK_SET) < 0) { + if (HDlseek(dst, dst_size - 1, SEEK_SET) < 0) { HDperror("HDHDlseek"); HDexit(EXIT_FAILURE); } - if (HDread (dst, buf, 1) < 0) { + if (HDread(dst, buf, 1) < 0) { HDperror("read"); HDexit(EXIT_FAILURE); } - if (HDlseek (dst, dst_size-1, SEEK_SET) < 0) { + if (HDlseek(dst, dst_size - 1, SEEK_SET) < 0) { HDperror("HDlseek"); HDexit(EXIT_FAILURE); } - if (HDwrite (dst, buf, 1) < 0) { + if (HDwrite(dst, buf, 1) < 0) { HDperror("write"); HDexit(EXIT_FAILURE); } @@ -405,7 +410,7 @@ main (int argc, char *argv[]) HDexit(EXIT_FAILURE); } dst_offset = 0; - need_seek = FALSE; + need_seek = FALSE; if (verbose) HDfprintf(stderr, "> %s\n", dst_name); } @@ -417,56 +422,56 @@ main (int argc, char *argv[]) * family has been truncated. */ if (need_seek) { - if (HDlseek (dst, dst_offset-1, SEEK_SET)<0) { - HDperror ("HDlseek"); - HDexit (EXIT_FAILURE); + if (HDlseek(dst, dst_offset - 1, SEEK_SET) < 0) { + HDperror("HDlseek"); + HDexit(EXIT_FAILURE); } - if (HDread (dst, buf, 1)<0) { - HDperror ("read"); - HDexit (EXIT_FAILURE); + if (HDread(dst, buf, 1) < 0) { + HDperror("read"); + HDexit(EXIT_FAILURE); } - if (HDlseek (dst, dst_offset-1, SEEK_SET)<0) { - HDperror ("HDlseek"); - HDexit (EXIT_FAILURE); + if (HDlseek(dst, dst_offset - 1, SEEK_SET) < 0) { + HDperror("HDlseek"); + HDexit(EXIT_FAILURE); } - if (HDwrite (dst, buf, 1)<0) { - HDperror ("write"); - HDexit (EXIT_FAILURE); + if (HDwrite(dst, buf, 1) < 0) { + HDperror("write"); + HDexit(EXIT_FAILURE); } } - HDclose (dst); + HDclose(dst); /* Modify family driver information saved in superblock through private property. * These private properties are for this tool only. */ - if ((fapl=H5Pcreate(H5P_FILE_ACCESS)) < 0) { - HDperror ("H5Pcreate"); - HDexit (EXIT_FAILURE); + if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) { + HDperror("H5Pcreate"); + HDexit(EXIT_FAILURE); } - if(family_to_single) { + if (family_to_single) { /* The user wants to change file driver from family to a single-file VFD. * Open the file with the sec2, windows, etc. driver. This property signals * the library to ignore the family driver information saved in the superblock. */ - if(H5Pset(fapl, H5F_ACS_FAMILY_TO_SINGLE_NAME, &family_to_single) < 0) { - HDperror ("H5Pset"); - HDexit (EXIT_FAILURE); + if (H5Pset(fapl, H5F_ACS_FAMILY_TO_SINGLE_NAME, &family_to_single) < 0) { + HDperror("H5Pset"); + HDexit(EXIT_FAILURE); } } else { /* Modify family size saved in superblock through private property. It signals * library to save the new member size(specified in command line) in superblock. * This private property is for this tool only. */ - if(H5Pset_fapl_family(fapl, H5F_FAMILY_DEFAULT, H5P_DEFAULT) < 0) { - HDperror ("H5Pset_fapl_family"); - HDexit (EXIT_FAILURE); + if (H5Pset_fapl_family(fapl, H5F_FAMILY_DEFAULT, H5P_DEFAULT) < 0) { + HDperror("H5Pset_fapl_family"); + HDexit(EXIT_FAILURE); } /* Set the property of the new member size as hsize_t */ hdsize = (hsize_t)dst_size; - if(H5Pset(fapl, H5F_ACS_FAMILY_NEWSIZE_NAME, &hdsize) < 0) { - HDperror ("H5Pset"); - HDexit (EXIT_FAILURE); + if (H5Pset(fapl, H5F_ACS_FAMILY_NEWSIZE_NAME, &hdsize) < 0) { + HDperror("H5Pset"); + HDexit(EXIT_FAILURE); } } @@ -478,18 +483,20 @@ main (int argc, char *argv[]) * file and the new file can only be a single file, reopen the new file should fail. * There's nothing to do in this case. */ - H5E_BEGIN_TRY { + H5E_BEGIN_TRY + { file = H5Fopen(dst_gen_name, H5F_ACC_RDWR, fapl); - } H5E_END_TRY; + } + H5E_END_TRY; - if(file >= 0) { - if(H5Fclose(file) < 0) { + if (file >= 0) { + if (H5Fclose(file) < 0) { HDperror("H5Fclose"); HDexit(EXIT_FAILURE); } /* end if */ - } /* end if */ + } /* end if */ - if(H5Pclose(fapl) < 0) { + if (H5Pclose(fapl) < 0) { HDperror("H5Pclose"); HDexit(EXIT_FAILURE); } /* end if */ |