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-rw-r--r--tools/src/h5copy/CMakeLists.txt2
-rw-r--r--tools/src/h5copy/h5copy.c4
-rw-r--r--tools/src/h5diff/CMakeLists.txt4
-rw-r--r--tools/src/h5dump/CMakeLists.txt2
-rw-r--r--tools/src/h5dump/h5dump.c198
-rw-r--r--tools/src/h5dump/h5dump_ddl.c40
-rw-r--r--tools/src/h5dump/h5dump_xml.c36
-rw-r--r--tools/src/h5format_convert/CMakeLists.txt2
-rw-r--r--tools/src/h5format_convert/h5format_convert.c97
-rw-r--r--tools/src/h5ls/CMakeLists.txt2
-rw-r--r--tools/src/h5ls/h5ls.c337
-rw-r--r--tools/src/h5repack/CMakeLists.txt2
-rw-r--r--tools/src/h5repack/h5repack.c9
-rw-r--r--tools/src/h5repack/h5repack.h4
-rw-r--r--tools/src/h5repack/h5repack_copy.c82
-rw-r--r--tools/src/h5repack/h5repack_main.c210
-rw-r--r--tools/src/h5repack/h5repack_verify.c22
-rw-r--r--tools/src/h5stat/CMakeLists.txt2
-rw-r--r--tools/src/h5stat/h5stat.c194
-rw-r--r--tools/src/misc/CMakeLists.txt8
-rw-r--r--tools/src/misc/h5clear.c4
-rw-r--r--tools/src/misc/h5mkgrp.c2
22 files changed, 624 insertions, 639 deletions
diff --git a/tools/src/h5copy/CMakeLists.txt b/tools/src/h5copy/CMakeLists.txt
index 29888f2..8f230a0 100644
--- a/tools/src/h5copy/CMakeLists.txt
+++ b/tools/src/h5copy/CMakeLists.txt
@@ -7,6 +7,7 @@ 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_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)
@@ -18,6 +19,7 @@ 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_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)
diff --git a/tools/src/h5copy/h5copy.c b/tools/src/h5copy/h5copy.c
index e1370e2..8805d08 100644
--- a/tools/src/h5copy/h5copy.c
+++ b/tools/src/h5copy/h5copy.c
@@ -342,13 +342,13 @@ main (int argc, const char *argv[])
/* 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
*-------------------------------------------------------------------------*/
- 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
diff --git a/tools/src/h5diff/CMakeLists.txt b/tools/src/h5diff/CMakeLists.txt
index 93e99cf..4087ab4 100644
--- a/tools/src/h5diff/CMakeLists.txt
+++ b/tools/src/h5diff/CMakeLists.txt
@@ -10,6 +10,7 @@ if (NOT ONLY_SHARED_LIBS)
${HDF5_TOOLS_SRC_H5DIFF_SOURCE_DIR}/h5diff_main.c
)
target_include_directories (h5diff PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_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})
@@ -24,6 +25,7 @@ if (BUILD_SHARED_LIBS)
${HDF5_TOOLS_SRC_H5DIFF_SOURCE_DIR}/h5diff_main.c
)
target_include_directories (h5diff-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+ target_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})
@@ -40,6 +42,7 @@ if (H5_HAVE_PARALLEL)
${HDF5_TOOLS_SRC_H5DIFF_SOURCE_DIR}/ph5diff_main.c
)
target_include_directories (ph5diff PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+ target_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)
@@ -52,6 +55,7 @@ if (H5_HAVE_PARALLEL)
${HDF5_TOOLS_SRC_H5DIFF_SOURCE_DIR}/ph5diff_main.c
)
target_include_directories (ph5diff-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+ target_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/h5dump/CMakeLists.txt b/tools/src/h5dump/CMakeLists.txt
index dbf92cf..0b6c968 100644
--- a/tools/src/h5dump/CMakeLists.txt
+++ b/tools/src/h5dump/CMakeLists.txt
@@ -11,6 +11,7 @@ if (NOT ONLY_SHARED_LIBS)
${HDF5_TOOLS_SRC_H5DUMP_SOURCE_DIR}/h5dump_xml.c
)
target_include_directories (h5dump PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_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)
@@ -26,6 +27,7 @@ if (BUILD_SHARED_LIBS)
${HDF5_TOOLS_SRC_H5DUMP_SOURCE_DIR}/h5dump_xml.c
)
target_include_directories (h5dump-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+ target_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} ${HDF5_LIBSH_TARGET})
set_target_properties (h5dump-shared PROPERTIES FOLDER tools)
diff --git a/tools/src/h5dump/h5dump.c b/tools/src/h5dump/h5dump.c
index d97fdc0..e49141d 100644
--- a/tools/src/h5dump/h5dump.c
+++ b/tools/src/h5dump/h5dump.c
@@ -25,23 +25,25 @@ static int useschema = 1;
static const char *xml_dtd_uri = NULL;
#ifdef H5_HAVE_ROS3_VFD
+/* Default "anonymous" S3 configuration */
static H5FD_ros3_fapl_t ros3_fa = {
- 1, /* version */
- false, /* authenticate */
- "", /* aws region */
- "", /* access key id */
- "", /* secret access key */
+ 1, /* Structure Version */
+ false, /* Authenticate? */
+ "", /* AWS Region */
+ "", /* Access Key ID */
+ "", /* Secret Access Key */
};
#endif /* H5_HAVE_ROS3_VFD */
#ifdef H5_HAVE_LIBHDFS
+/* "Default" HDFS configuration */
static H5FD_hdfs_fapl_t hdfs_fa = {
- 1, /* fapl version */
- "localhost", /* namenode name */
- 0, /* namenode port */
- "", /* kerberos ticket cache */
- "", /* user name */
- 2048, /* stream buffer size */
+ 1, /* Structure Version */
+ "localhost", /* Namenode Name */
+ 0, /* Namenode Port */
+ "", /* Kerberos ticket cache */
+ "", /* User name */
+ 2048, /* Stream buffer size */
};
#endif /* H5_HAVE_LIBHDFS */
@@ -1251,106 +1253,37 @@ end_collect:
goto done;
case '$':
-#ifndef H5_HAVE_ROS3_VFD
+#ifdef H5_HAVE_ROS3_VFD
+ if (h5tools_parse_ros3_fapl_tuple(opt_arg, ',', &ros3_fa) < 0) {
+ error_msg("failed to parse S3 VFD credential info\n");
+ usage(h5tools_getprogname());
+ free_handler(hand, argc);
+ hand = NULL;
+ h5tools_setstatus(EXIT_FAILURE);
+ goto done;
+ }
+#else
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");
- usage(h5tools_getprogname());
- free_handler(hand, argc);
- 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");
- usage(h5tools_getprogname());
- free_handler(hand, argc);
- hand = NULL;
- h5tools_setstatus(EXIT_FAILURE);
- goto done;
- }
- HDfree(s3_cred);
- HDfree(s3_cred_string);
- } /* s3 credential block */
+#endif
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);
+#ifdef H5_HAVE_LIBHDFS
+ if (h5tools_parse_hdfs_fapl_tuple(opt_arg, ',', &hdfs_fa) < 0) {
+ error_msg("failed to parse HDFS VFD configuration info\n");
+ usage(h5tools_getprogname());
+ free_handler(hand, argc);
+ hand = NULL;
+ h5tools_setstatus(EXIT_FAILURE);
+ goto done;
}
-#endif /* H5_HAVE_LIBHDFS */
+#else
+ error_msg("HDFS VFD not enabled.\n");
+ h5tools_setstatus(EXIT_FAILURE);
+ goto done;
+#endif
break;
case '?':
@@ -1482,53 +1415,44 @@ main(int argc, const char *argv[])
h5trav_set_index(sort_by, sort_order);
if (driver != NULL) {
- void *conf_fa = NULL;
+ h5tools_fapl_info_t fapl_info;
+
+ /* Currently, only retrieval of VFDs is supported. */
+ fapl_info.type = VFD_BY_NAME;
+ fapl_info.info = NULL;
+ fapl_info.u.name = driver;
- if (!strcmp(driver, "ros3")) {
-#ifndef H5_HAVE_ROS3_VFD
+ if (!HDstrcmp(driver, drivernames[ROS3_VFD_IDX])) {
+#ifdef H5_HAVE_ROS3_VFD
+ fapl_info.info = (void *)&ros3_fa;
+#else
error_msg("Read-Only S3 VFD not enabled.\n");
h5tools_setstatus(EXIT_FAILURE);
goto done;
-#else
- conf_fa = (void *)&ros3_fa;
-#endif /* H5_HAVE_ROS3_VFD */
+#endif
}
- else if (!HDstrcmp(driver, "hdfs")) {
-#ifndef H5_HAVE_LIBHDFS
- error_msg("HDFS VFD is not enabled.\n");
+ else if (!HDstrcmp(driver, drivernames[HDFS_VFD_IDX])) {
+#ifdef H5_HAVE_LIBHDFS
+ fapl_info.info = (void *)&hdfs_fa;
+#else
+ error_msg("The HDFS VFD is not enabled.\n");
h5tools_setstatus(EXIT_FAILURE);
goto done;
-#else
- conf_fa = (void *)&hdfs_fa;
-#endif /* H5_HAVE_LIBHDFS */
+#endif
}
- 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;
- }
- /* driver guaranteed "ros3" or "hdfs" */
- /* conf_fa appropriate to driver */
- if (0 == h5tools_set_configured_fapl(fapl_id, driver, conf_fa)) {
- error_msg("unable to set fapl\n");
- h5tools_setstatus(EXIT_FAILURE);
- goto done;
- }
+ if ((fapl_id = h5tools_get_fapl(H5P_DEFAULT, &fapl_info)) < 0) {
+ error_msg("unable to create FAPL for file access\n");
+ h5tools_setstatus(EXIT_FAILURE);
+ goto done;
}
} /* driver defined */
while(opt_ind < argc) {
fname = HDstrdup(argv[opt_ind++]);
- 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) ? FALSE : TRUE, NULL, 0);
if (fid < 0) {
error_msg("unable to open file \"%s\"\n", fname);
@@ -1704,6 +1628,7 @@ main(int argc, const char *argv[])
/* To Do: clean up XML table */
H5Eset_auto2(H5E_DEFAULT, func, edata);
+ H5Eset_auto2(H5tools_ERR_STACK_g, tools_func, tools_edata);
leave(h5tools_getstatus());
@@ -1735,6 +1660,7 @@ done:
/* To Do: clean up XML table */
H5Eset_auto2(H5E_DEFAULT, func, edata);
+ H5Eset_auto2(H5tools_ERR_STACK_g, tools_func, tools_edata);
leave(h5tools_getstatus());
} /* main */
diff --git a/tools/src/h5dump/h5dump_ddl.c b/tools/src/h5dump/h5dump_ddl.c
index a410fda..e97ab7e 100644
--- a/tools/src/h5dump/h5dump_ddl.c
+++ b/tools/src/h5dump/h5dump_ddl.c
@@ -816,14 +816,14 @@ dump_group(hid_t gid, const char *name)
/* dump unamed type in root group */
for(u = 0; u < type_table->nobjs; u++)
if(!type_table->objs[u].recorded) {
- char *obj_addr_str = NULL;
+ char *obj_tok_str = NULL;
dset = H5Dopen2(gid, type_table->objs[u].objname, H5P_DEFAULT);
type = H5Dget_type(dset);
- H5Otoken_to_str(dset, &type_table->objs[u].obj_token, &obj_addr_str);
- HDsprintf(type_name, "#%s", obj_addr_str);
- H5free_memory(obj_addr_str);
+ H5Otoken_to_str(dset, &type_table->objs[u].obj_token, &obj_tok_str);
+ HDsprintf(type_name, "#%s", obj_tok_str);
+ H5free_memory(obj_tok_str);
dump_function_table->dump_named_datatype_function(type, type_name);
H5Tclose(type);
@@ -1136,6 +1136,22 @@ dump_fcpl(hid_t fid)
unsigned sym_ik; /* symbol table B-tree internal 'K' value */
unsigned istore_ik; /* indexed storage B-tree internal 'K' value */
+ void *obj = NULL;
+ hid_t connector_id = H5I_INVALID_HID;
+ hbool_t supported = FALSE;
+
+ /* 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.
+ */
+ obj = H5VLobject(fid);
+ connector_id = H5VLget_connector_id(fid);
+ H5VLintrospect_opt_query(obj, connector_id, H5VL_SUBCLS_FILE, H5VL_NATIVE_FILE_GET_INFO, &supported);
+ H5VLclose(connector_id);
+ if (!supported)
+ return;
+
fcpl=H5Fget_create_plist(fid);
H5Fget_info2(fid, &finfo);
H5Pget_userblock(fcpl,&userblock);
@@ -1258,11 +1274,11 @@ dump_fcontents(hid_t fid)
for (u = 0; u < type_table->nobjs; u++) {
if (!type_table->objs[u].recorded) {
- char *obj_addr_str = NULL;
+ char *obj_tok_str = NULL;
- H5Otoken_to_str(fid, &type_table->objs[u].obj_token, &obj_addr_str);
- PRINTSTREAM(rawoutstream, " %-10s /#%s\n", "datatype", obj_addr_str);
- H5free_memory(obj_addr_str);
+ 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);
}
}
}
@@ -1914,12 +1930,12 @@ handle_datatypes(hid_t fid, const char *type, void H5_ATTR_UNUSED * data, int pe
char name[128];
if(!type_table->objs[idx].recorded) {
- char *obj_addr_string = NULL;
+ char *obj_tok_str = NULL;
/* unamed datatype */
- H5Otoken_to_str(fid, &type_table->objs[idx].obj_token, &obj_addr_string);
- HDsprintf(name, "/#%s", obj_addr_string);
- H5free_memory(obj_addr_string);
+ H5Otoken_to_str(fid, &type_table->objs[idx].obj_token, &obj_tok_str);
+ HDsprintf(name, "/#%s", obj_tok_str);
+ H5free_memory(obj_tok_str);
if(!HDstrcmp(name, real_name))
break;
diff --git a/tools/src/h5dump/h5dump_xml.c b/tools/src/h5dump/h5dump_xml.c
index d9f1f67..4f58b73 100644
--- a/tools/src/h5dump/h5dump_xml.c
+++ b/tools/src/h5dump/h5dump_xml.c
@@ -578,7 +578,7 @@ int
xml_name_to_XID(hid_t loc_id, const char *str, char *outstr, int outlen, int gen)
{
H5O_token_t obj_token;
- char *obj_addr_str = NULL;
+ char *obj_tok_str = NULL;
int lookup_ret;
if (outlen < 22) return 1;
@@ -591,9 +591,9 @@ xml_name_to_XID(hid_t loc_id, const char *str, char *outstr, int outlen, int gen
if (gen) {
ref_path_table_gen_fake(str, &obj_token);
- H5Otoken_to_str(loc_id, &obj_token, &obj_addr_str);
- HDsprintf(outstr, "xid_%s", obj_addr_str);
- H5free_memory(obj_addr_str);
+ H5Otoken_to_str(loc_id, &obj_token, &obj_tok_str);
+ HDsprintf(outstr, "xid_%s", obj_tok_str);
+ H5free_memory(obj_tok_str);
return 0;
}
@@ -606,9 +606,9 @@ xml_name_to_XID(hid_t loc_id, const char *str, char *outstr, int outlen, int gen
if (gen) {
ref_path_table_gen_fake(str, &obj_token);
- H5Otoken_to_str(loc_id, &obj_token, &obj_addr_str);
- HDsprintf(outstr, "xid_%s", obj_addr_str);
- H5free_memory(obj_addr_str);
+ H5Otoken_to_str(loc_id, &obj_token, &obj_tok_str);
+ HDsprintf(outstr, "xid_%s", obj_tok_str);
+ H5free_memory(obj_tok_str);
return 0;
}
@@ -618,9 +618,9 @@ xml_name_to_XID(hid_t loc_id, const char *str, char *outstr, int outlen, int gen
}
}
- H5Otoken_to_str(loc_id, &obj_token, &obj_addr_str);
- HDsprintf(outstr, "xid_%s", obj_addr_str);
- H5free_memory(obj_addr_str);
+ H5Otoken_to_str(loc_id, &obj_token, &obj_tok_str);
+ HDsprintf(outstr, "xid_%s", obj_tok_str);
+ H5free_memory(obj_tok_str);
return 0;
}
@@ -2659,14 +2659,14 @@ xml_dump_group(hid_t gid, const char *name)
/* Very special case: dump unamed type in root group */
for(u = 0; u < type_table->nobjs; u++) {
if(!type_table->objs[u].recorded) {
- char *obj_addr_str = NULL;
+ char *obj_tok_str = NULL;
dset = H5Dopen2(gid, type_table->objs[u].objname, H5P_DEFAULT);
type = H5Dget_type(dset);
- H5Otoken_to_str(dset, &type_table->objs[u].obj_token, &obj_addr_str);
- HDsprintf(type_name, "#%s", obj_addr_str);
- H5free_memory(obj_addr_str);
+ H5Otoken_to_str(dset, &type_table->objs[u].obj_token, &obj_tok_str);
+ HDsprintf(type_name, "#%s", obj_tok_str);
+ H5free_memory(obj_tok_str);
dump_function_table->dump_named_datatype_function(type, type_name);
H5Tclose(type);
@@ -2747,14 +2747,14 @@ xml_dump_group(hid_t gid, const char *name)
/* Very special case: dump unamed type in root group */
for(u = 0; u < type_table->nobjs; u++) {
if(!type_table->objs[u].recorded) {
- char *obj_addr_str = NULL;
+ char *obj_tok_str = NULL;
dset = H5Dopen2(gid, type_table->objs[u].objname, H5P_DEFAULT);
type = H5Dget_type(dset);
- H5Otoken_to_str(dset, &type_table->objs[u].obj_token, &obj_addr_str);
- HDsprintf(type_name, "#%s", obj_addr_str);
- H5free_memory(obj_addr_str);
+ H5Otoken_to_str(dset, &type_table->objs[u].obj_token, &obj_tok_str);
+ HDsprintf(type_name, "#%s", obj_tok_str);
+ H5free_memory(obj_tok_str);
dump_function_table->dump_named_datatype_function(type, type_name);
H5Tclose(type);
diff --git a/tools/src/h5format_convert/CMakeLists.txt b/tools/src/h5format_convert/CMakeLists.txt
index 70c07ee..863ecbe 100644
--- a/tools/src/h5format_convert/CMakeLists.txt
+++ b/tools/src/h5format_convert/CMakeLists.txt
@@ -7,6 +7,7 @@ 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_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)
@@ -17,6 +18,7 @@ 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_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)
diff --git a/tools/src/h5format_convert/h5format_convert.c b/tools/src/h5format_convert/h5format_convert.c
index bb606ac..ae72ea9 100644
--- a/tools/src/h5format_convert/h5format_convert.c
+++ b/tools/src/h5format_convert/h5format_convert.c
@@ -42,13 +42,13 @@ static int verbose_g = 0;
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'},
+ { "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' },
+ { "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' },
@@ -60,6 +60,7 @@ static struct long_options l_opts[] = {
{ "noop", no_arg, 'n' },
{ "noo", no_arg, 'n' },
{ "no", no_arg, 'n' },
+ { "enable-error-stack", no_arg, 'E' },
{ NULL, 0, '\0' }
};
@@ -120,55 +121,59 @@ parse_command_line(int argc, const char **argv)
/* 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 */
+ 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;
+
+ case 'E':
+ enable_error_stack = 1;
+ break;
+
+ default:
+ h5tools_setstatus(EXIT_FAILURE);
+ usage(h5tools_getprogname());
+ goto error;
+ break;
+ } /* switch */
} /* while */
if (argc <= opt_ind) {
error_msg("missing file name\n");
usage(h5tools_getprogname());
- h5tools_setstatus(EXIT_FAILURE);
+ h5tools_setstatus(EXIT_FAILURE);
goto error;
}
@@ -421,7 +426,7 @@ main(int argc, const char *argv[])
HDfprintf(stdout, "It is noop...\n");
/* Open the HDF5 file */
- if((fid = h5tools_fopen(fname_g, H5F_ACC_RDWR, H5P_DEFAULT, NULL, NULL, 0)) < 0) {
+ 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;
diff --git a/tools/src/h5ls/CMakeLists.txt b/tools/src/h5ls/CMakeLists.txt
index 7be33b5..c1ce006 100644
--- a/tools/src/h5ls/CMakeLists.txt
+++ b/tools/src/h5ls/CMakeLists.txt
@@ -7,6 +7,7 @@ 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_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})
@@ -19,6 +20,7 @@ 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_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})
diff --git a/tools/src/h5ls/h5ls.c b/tools/src/h5ls/h5ls.c
index f3f9ede..f82827c 100644
--- a/tools/src/h5ls/h5ls.c
+++ b/tools/src/h5ls/h5ls.c
@@ -1333,10 +1333,10 @@ dump_reference(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx
switch (ref_type) {
case H5R_OBJECT1:
H5TOOLS_DEBUG("ref_type is H5R_OBJECT1");
- if (H5Rget_obj_type3((const H5R_ref_t *)&ref_buf[i], H5P_DEFAULT, &obj_type) >= 0) {
+ if (H5Rget_obj_type3(&ref_buf[i], H5P_DEFAULT, &obj_type) >= 0) {
switch (obj_type) {
case H5O_TYPE_DATASET:
- if((new_obj_id = H5Ropen_object((const H5R_ref_t *)&ref_buf[i], H5P_DEFAULT, H5P_DEFAULT)) >= 0) {
+ if((new_obj_id = H5Ropen_object(&ref_buf[i], H5P_DEFAULT, H5P_DEFAULT)) >= 0) {
datactx.indent_level++;
h5tools_dump_dset(stream, info, &datactx, new_obj_id);
datactx.indent_level--;
@@ -1363,7 +1363,7 @@ dump_reference(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx
break;
case H5R_DATASET_REGION1:
H5TOOLS_DEBUG("ref_type is H5R_DATASET_REGION1");
- if((new_obj_id = H5Ropen_object((const H5R_ref_t *)&ref_buf[i], H5P_DEFAULT, H5P_DEFAULT)) >= 0) {
+ if((new_obj_id = H5Ropen_object(&ref_buf[i], H5P_DEFAULT, H5P_DEFAULT)) >= 0) {
datactx.indent_level++;
h5tools_dump_dset(stream, info, &datactx, new_obj_id);
datactx.indent_level--;
@@ -1377,13 +1377,13 @@ dump_reference(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx
break;
case H5R_OBJECT2:
H5TOOLS_DEBUG("ref_type is H5R_OBJECT2");
- if (H5Rget_obj_type3((const H5R_ref_t *)&ref_buf[i], H5P_DEFAULT, &obj_type) >= 0) {
+ if (H5Rget_obj_type3(&ref_buf[i], H5P_DEFAULT, &obj_type) >= 0) {
switch (obj_type) {
case H5O_TYPE_GROUP:
break;
case H5O_TYPE_DATASET:
- if((new_obj_id = H5Ropen_object((const H5R_ref_t *)&ref_buf[i], H5P_DEFAULT, H5P_DEFAULT)) >= 0) {
+ if((new_obj_id = H5Ropen_object(&ref_buf[i], H5P_DEFAULT, H5P_DEFAULT)) >= 0) {
datactx.indent_level++;
h5tools_dump_dset(stream, info, &datactx, new_obj_id);
datactx.indent_level--;
@@ -1416,10 +1416,10 @@ dump_reference(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx
ncols = info->line_ncols;
/* if (new_obj_id < 0) - could mean that no reference was written do not throw failure */
- if((new_obj_id = H5Ropen_object((const H5R_ref_t *)&ref_buf[i], H5P_DEFAULT, H5P_DEFAULT)) < 0)
+ if((new_obj_id = H5Ropen_object(&ref_buf[i], H5P_DEFAULT, H5P_DEFAULT)) < 0)
H5TOOLS_INFO("H5Ropen_object H5R_DATASET_REGION2 failed");
else {
- if((new_obj_sid = H5Ropen_region((const H5R_ref_t *)&ref_buf[i], H5P_DEFAULT, H5P_DEFAULT)) >= 0) {
+ if((new_obj_sid = H5Ropen_region(&ref_buf[i], H5P_DEFAULT, H5P_DEFAULT)) >= 0) {
if (h5tools_is_zero(&ref_buf[i], H5Tget_size(H5T_STD_REF))) {
H5TOOLS_DEBUG("NULL H5R_DATASET_REGION2");
@@ -1471,7 +1471,7 @@ dump_reference(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx
break;
case H5R_ATTR:
H5TOOLS_DEBUG("ref_type is H5R_ATTR");
- if((new_obj_id = H5Ropen_attr((const H5R_ref_t *)&ref_buf[i], H5P_DEFAULT, H5P_DEFAULT)) >= 0) {
+ if((new_obj_id = H5Ropen_attr(&ref_buf[i], H5P_DEFAULT, H5P_DEFAULT)) >= 0) {
h5tools_dump_region_attribute(new_obj_id, stream, info, &datactx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0);
if(H5Aclose(new_obj_id) < 0)
H5TOOLS_INFO("H5Aclose H5R_ATTR failed");
@@ -2334,13 +2334,13 @@ list_obj(const char *name, const H5O_info2_t *oinfo, const char *first_seen, voi
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 = H5I_INVALID_HID; /* 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.
*/
H5TOOLS_DEBUG("Open object name=%s", name);
- if (obj_type >= 0 && (obj = H5Oopen(iter->fid, name, H5P_DEFAULT)) < 0) {
+ 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);
@@ -2350,7 +2350,7 @@ list_obj(const char *name, const H5O_info2_t *oinfo, const char *first_seen, voi
/* 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");
@@ -2362,23 +2362,26 @@ list_obj(const char *name, const H5O_info2_t *oinfo, const char *first_seen, voi
if (verbose_g > 0) {
size_t buf_size = 0;
char* comment = NULL;
- char* obj_addr_str = NULL;
+ char* obj_tok_str = NULL;
ssize_t cmt_bufsize = -1;
+ void *obj = NULL;
+ hid_t connector_id = H5I_INVALID_HID;
+ hbool_t supported = FALSE;
/* 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, &oinfo->token, &obj_addr_str);
+ H5Otoken_to_str(obj_id, &oinfo->token, &obj_tok_str);
h5tools_str_reset(&buffer);
- h5tools_str_append(&buffer, " %-10s %lu:%s\n", "Location:", oinfo->fileno, obj_addr_str);
+ 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);
- H5free_memory(obj_addr_str);
+ H5free_memory(obj_tok_str);
/* Modification time */
if (oinfo->mtime > 0) {
@@ -2397,36 +2400,45 @@ list_obj(const char *name, const H5O_info2_t *oinfo, const char *first_seen, voi
} /* 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);
+ /* Only emit comments if the VOL connector supports that */
+ obj = H5VLobject(obj_id);
+ connector_id = H5VLget_connector_id(obj_id);
+ H5VLintrospect_opt_query(obj, connector_id, H5VL_SUBCLS_OBJECT, H5VL_NATIVE_OBJECT_GET_COMMENT, &supported);
+ H5VLclose(connector_id);
+
+ if (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:
@@ -2833,41 +2845,41 @@ leave(int ret)
int
main(int argc, const char *argv[])
{
- hid_t file_id = H5I_INVALID_HID;
- 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;
- H5E_auto2_t func;
- H5E_auto2_t tools_func;
- void *edata;
- void *tools_edata;
+ hid_t file_id = H5I_INVALID_HID;
+ 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;
+ H5E_auto2_t func;
+ H5E_auto2_t tools_func;
+ void *edata;
+ void *tools_edata;
#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 */
@@ -3005,18 +3017,9 @@ main(int argc, const char *argv[])
}
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
- */
+#ifdef H5_HAVE_ROS3_VFD
+ char const *start = NULL;
+
start = strchr(argv[argno], '=');
if (start == NULL) {
HDfprintf(rawerrorstream, "Error: Unable to parse null credentials tuple\n"
@@ -3025,124 +3028,38 @@ 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");
- }
+#ifdef H5_HAVE_LIBHDFS
+ char const *start = NULL;
+
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");
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]) {
/* Single-letter switches */
@@ -3236,41 +3153,35 @@ main(int argc, const char *argv[])
}
if (preferred_driver) {
- void *conf_fa = NULL;
+ h5tools_fapl_info_t fapl_info;
- if (!HDstrcmp(preferred_driver, "ros3")) {
-#ifndef H5_HAVE_ROS3_VFD
- HDfprintf(rawerrorstream, "Error: Read-Only S3 VFD not enabled.\n\n");
- usage();
- leave(EXIT_FAILURE);
-#else
- conf_fa = (void *)&ros3_fa;
-#endif /* H5_HAVE_ROS3_VFD */
+ /* Currently, only retrieval of VFDs is supported. */
+ fapl_info.type = VFD_BY_NAME;
+ fapl_info.info = NULL;
+ fapl_info.u.name = preferred_driver;
- }
- else if (!HDstrcmp(preferred_driver, "hdfs")) {
-#ifndef H5_HAVE_LIBHDFS
- PRINTVALSTREAM(rawoutstream, "The HDFS VFD is not enabled.\n");
+ if (!HDstrcmp(preferred_driver, drivernames[ROS3_VFD_IDX])) {
+#ifdef H5_HAVE_ROS3_VFD
+ fapl_info.info = (void *)&ros3_fa;
+#else
+ HDfprintf(rawerrorstream, "Error: Read-Only S3 VFD is not enabled\n\n");
leave(EXIT_FAILURE);
+#endif
+ }
+ else if (!HDstrcmp(preferred_driver, drivernames[HDFS_VFD_IDX])) {
+#ifdef H5_HAVE_LIBHDFS
+ fapl_info.info = (void *)&hdfs_fa;
#else
- conf_fa = (void *)&hdfs_fa;
-#endif /* H5_HAVE_LIBHDFS */
+ HDfprintf(rawerrorstream, "Error: The HDFS VFD is not enabled\n\n");
+ leave(EXIT_FAILURE);
+#endif
}
- 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);
- }
+ if ((fapl_id = h5tools_get_fapl(H5P_DEFAULT, &fapl_info)) < 0) {
+ HDfprintf(rawerrorstream, "Error: Unable to create FAPL for file access\n\n");
+ leave(EXIT_FAILURE);
}
- } /* preferred_driver defined */
+ }
if (enable_error_stack > 0) {
H5Eset_auto2(H5E_DEFAULT, func, edata);
@@ -3301,12 +3212,8 @@ main(int argc, const char *argv[])
file_id = H5I_INVALID_HID;
while (fname && *fname) {
- if (fapl_id != H5P_DEFAULT) {
- file_id = H5Fopen(fname, H5F_ACC_RDONLY, fapl_id);
- }
- else {
- file_id = 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) ? FALSE : TRUE, drivername, sizeof drivername);
if (file_id >= 0) {
if (verbose_g)
diff --git a/tools/src/h5repack/CMakeLists.txt b/tools/src/h5repack/CMakeLists.txt
index 967e8d7..a4aa1ef 100644
--- a/tools/src/h5repack/CMakeLists.txt
+++ b/tools/src/h5repack/CMakeLists.txt
@@ -17,6 +17,7 @@ set (REPACK_COMMON_SOURCES
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_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)
@@ -28,6 +29,7 @@ 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_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)
diff --git a/tools/src/h5repack/h5repack.c b/tools/src/h5repack/h5repack.c
index 8eeaa0e..b2cb02b 100644
--- a/tools/src/h5repack/h5repack.c
+++ b/tools/src/h5repack/h5repack.c
@@ -79,6 +79,8 @@ h5repack_init(pack_opt_t *options, int verbose, hbool_t 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;
@@ -257,7 +259,7 @@ copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, t
dt->next = *named_dt_head_p;
*named_dt_head_p = dt;
- /* Update the address and id */
+ /* 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;
@@ -280,7 +282,7 @@ copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, t
dt_ret->next = *named_dt_head_p;
*named_dt_head_p = dt_ret;
- /* Update the address and id */
+ /* 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 */
@@ -751,7 +753,8 @@ check_objects(const char* fname, pack_opt_t *options)
* open the file
*-------------------------------------------------------------------------
*/
- if ((fid = h5tools_fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, 0)) < 0)
+ if ((fid = h5tools_fopen(fname, H5F_ACC_RDONLY, options->fin_fapl,
+ (options->fin_fapl == H5P_DEFAULT) ? FALSE : TRUE, NULL, 0)) < 0)
H5TOOLS_GOTO_ERROR((-1), "h5tools_fopen failed <%s>: %s", fname, H5FOPENERROR);
/*-------------------------------------------------------------------------
diff --git a/tools/src/h5repack/h5repack.h b/tools/src/h5repack/h5repack.h
index 52ecb0e..caa1166 100644
--- a/tools/src/h5repack/h5repack.h
+++ b/tools/src/h5repack/h5repack.h
@@ -114,6 +114,8 @@ typedef struct {
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,
@@ -151,7 +153,7 @@ 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
diff --git a/tools/src/h5repack/h5repack_copy.c b/tools/src/h5repack/h5repack_copy.c
index 1044244..ae93b30 100644
--- a/tools/src/h5repack/h5repack_copy.c
+++ b/tools/src/h5repack/h5repack_copy.c
@@ -67,7 +67,6 @@ copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
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 */
- 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 */
@@ -85,7 +84,8 @@ copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
* open input file
*-------------------------------------------------------------------------
*/
- if ((fidin = h5tools_fopen(fnamein, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, (size_t) 0)) < 0)
+ if ((fidin = h5tools_fopen(fnamein, H5F_ACC_RDONLY, options->fin_fapl,
+ (options->fin_fapl == H5P_DEFAULT) ? FALSE : TRUE, 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 */
@@ -122,12 +122,14 @@ copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
if(options->latest)
options->low_bound = options->high_bound = H5F_LIBVER_LATEST;
+
/* Create file access property list */
- if((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
- H5TOOLS_GOTO_ERROR((-1), "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)
+ 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 */
@@ -218,12 +220,12 @@ 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)
+ 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)
+ if (H5Pset_alignment(options->fout_fapl, options->threshold, options->alignment) < 0)
H5TOOLS_GOTO_ERROR((-1), "H5Pset_alignment failed to set alignment");
}
@@ -233,12 +235,12 @@ 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)
+ 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)
+ 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");
}
@@ -297,7 +299,7 @@ print_user_block(fnamein, fidin);
if (options->verbose)
HDprintf("Making new file ...\n");
- if ((fidout = H5Fcreate(fnameout, H5F_ACC_TRUNC, fcpl, fapl)) < 0)
+ if ((fidout = H5Fcreate(fnameout, H5F_ACC_TRUNC, fcpl, options->fout_fapl)) < 0)
H5TOOLS_GOTO_ERROR((-1), "H5Fcreate could not create file <%s>:", fnameout);
/*-------------------------------------------------------------------------
@@ -352,7 +354,6 @@ done:
H5E_BEGIN_TRY {
H5Pclose(fcpl_in);
H5Pclose(gcpl_in);
- H5Pclose(fapl);
H5Pclose(fcpl);
H5Gclose(grp_in);
H5Fclose(fidin);
@@ -702,11 +703,14 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
break;
- /*-------------------------------------------------------------------------
- * H5TRAV_TYPE_DATASET
- *-------------------------------------------------------------------------
- */
+ /*-------------------------------------------------------------------------
+ * H5TRAV_TYPE_DATASET
+ *-------------------------------------------------------------------------
+ */
case H5TRAV_TYPE_DATASET:
+ {
+ hbool_t use_h5ocopy;
+
has_filter = 0;
req_filter = 0;
@@ -764,9 +768,47 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
* otherwise we do a copy using H5Ocopy
*-------------------------------------------------------------------------
*/
- if (options->op_tbl->nelems || options->all_filter == 1
- || options->all_layout == 1 || is_ref || is_named) {
+ 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)
@@ -1135,7 +1177,9 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
HDprintf(FORMAT_OBJ, "dset", travt->objs[i].name);
} /* end whether we have request for filter/chunking */
+
break;
+ } /* H5TRAV_TYPE_DATASET */
/*-------------------------------------------------------------------------
* H5TRAV_TYPE_NAMED_DATATYPE
diff --git a/tools/src/h5repack/h5repack_main.c b/tools/src/h5repack/h5repack_main.c
index 16899a3..1761fb4 100644
--- a/tools/src/h5repack/h5repack_main.c
+++ b/tools/src/h5repack/h5repack_main.c
@@ -62,6 +62,12 @@ static struct long_options l_opts[] = {
{ "sort_by", require_arg, 'q' },
{ "sort_order", require_arg, 'z' },
{ "enable-error-stack", no_arg, 'E' },
+ { "src-vol-id", require_arg, '1' },
+ { "src-vol-name", require_arg, '2' },
+ { "src-vol-info", require_arg, '3' },
+ { "dst-vol-id", require_arg, '4' },
+ { "dst-vol-name", require_arg, '5' },
+ { "dst-vol-info", require_arg, '6' },
{ NULL, 0, '\0' }
};
@@ -86,6 +92,18 @@ static void usage(const char *prog) {
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\n");
PRINTVALSTREAM(rawoutstream, " occur\n");
+ PRINTVALSTREAM(rawoutstream, " --src-vol-id ID of the VOL connector to use for opening the input\n");
+ PRINTVALSTREAM(rawoutstream, " 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-id ID of the VOL connector to use for opening the output\n");
+ PRINTVALSTREAM(rawoutstream, " 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, " -L, --latest Use latest version of file format\n");
PRINTVALSTREAM(rawoutstream, " This option will take precedence over the options\n");
PRINTVALSTREAM(rawoutstream, " --low and --high\n");
@@ -293,6 +311,8 @@ int read_info(const char *filename, pack_opt_t *options)
/* cycle until end of file reached */
while (1) {
+ if (EOF == fscanf(fp, "%9s", stype))
+ break;
/* Info indicator must be for layout or filter */
if (HDstrcmp(stype,"-l") && HDstrcmp(stype, "-f")) {
@@ -334,7 +354,7 @@ int read_info(const char *filename, pack_opt_t *options)
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;
@@ -412,9 +432,17 @@ set_sort_order(const char *form)
static
int parse_command_line(int argc, const char **argv, pack_opt_t* options)
{
+ h5tools_fapl_info_t in_vol_info;
+ h5tools_fapl_info_t out_vol_info;
+ hbool_t custom_in_fapl = FALSE;
+ hbool_t custom_out_fapl = FALSE;
+ hid_t tmp_fapl = H5I_INVALID_HID;
int bound, opt;
int ret_value = 0;
+ HDmemset(&in_vol_info, 0, sizeof(h5tools_fapl_info_t));
+ HDmemset(&out_vol_info, 0, sizeof(h5tools_fapl_info_t));
+
/* parse command line options */
while (EOF != (opt = get_option(argc, argv, s_opts, l_opts))) {
switch ((char) opt) {
@@ -434,13 +462,13 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options)
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':
@@ -478,9 +506,12 @@ 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(opt_arg, options)) < 0) {
+ error_msg("failed to read from repack options file <%s>\n", opt_arg);
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = -1;
goto done;
+ }
break;
case 'n':
@@ -495,6 +526,8 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options)
bound = HDatoi(opt_arg);
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;
@@ -504,6 +537,8 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options)
bound = HDatoi(opt_arg);
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;
@@ -625,8 +660,8 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options)
break;
case 'q':
- if (H5_INDEX_UNKNOWN == set_sort_by(opt_arg)) {
- error_msg(" failed to set sort by form <%s>\n", opt_arg);
+ if (H5_INDEX_UNKNOWN == (sort_by = set_sort_by(opt_arg))) {
+ error_msg("failed to set sort by form <%s>\n", opt_arg);
h5tools_setstatus(EXIT_FAILURE);
ret_value = -1;
goto done;
@@ -634,8 +669,8 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options)
break;
case 'z':
- if (set_sort_order(opt_arg) == H5_ITER_UNKNOWN) {
- error_msg(" failed to set sort order form <%s>\n", opt_arg);
+ if (H5_ITER_UNKNOWN == (sort_order = set_sort_order(opt_arg))) {
+ error_msg("failed to set sort order form <%s>\n", opt_arg);
h5tools_setstatus(EXIT_FAILURE);
ret_value = -1;
goto done;
@@ -646,6 +681,38 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options)
enable_error_stack = 1;
break;
+ case '1':
+ in_vol_info.type = VOL_BY_ID;
+ in_vol_info.u.id = HDatol(opt_arg);
+ custom_in_fapl = TRUE;
+ break;
+
+ case '2':
+ in_vol_info.type = VOL_BY_NAME;
+ in_vol_info.u.name = opt_arg;
+ custom_in_fapl = TRUE;
+ break;
+
+ case '3':
+ in_vol_info.info = opt_arg;
+ break;
+
+ case '4':
+ out_vol_info.type = VOL_BY_ID;
+ out_vol_info.u.id = HDatol(opt_arg);
+ custom_out_fapl = TRUE;
+ break;
+
+ case '5':
+ out_vol_info.type = VOL_BY_NAME;
+ out_vol_info.u.name = opt_arg;
+ custom_out_fapl = TRUE;
+ break;
+
+ case '6':
+ out_vol_info.info = opt_arg;
+ break;
+
default:
break;
} /* end switch */
@@ -653,30 +720,71 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options)
/* If neither -i nor -o given, get in and out files positionally */
if (0 == (has_i + has_o)) {
- if (argv[opt_ind] != NULL && argv[opt_ind + 1] != NULL) {
- infile = argv[opt_ind];
- outfile = argv[opt_ind + 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;
- }
+ if (argv[opt_ind] != NULL && argv[opt_ind + 1] != NULL) {
+ infile = argv[opt_ind];
+ outfile = argv[opt_ind + 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_fapl) {
+ if ((tmp_fapl = h5tools_get_fapl(options->fin_fapl, &in_vol_info)) < 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_fapl) {
+ if ((tmp_fapl = h5tools_get_fapl(options->fout_fapl, &out_vol_info)) < 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;
@@ -694,14 +802,18 @@ done:
*/
int main(int argc, const char **argv)
{
- pack_opt_t options; /*the global options */
+ 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));
+ /* Initialize h5tools lib */
+ h5tools_init();
+
h5tools_setprogname(PROGRAMNAME);
h5tools_setstatus(EXIT_SUCCESS);
@@ -709,29 +821,38 @@ int main(int argc, const char **argv)
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);
/* 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, argv, &options);
+ if (parse_ret < 0) {
+ HDprintf("Error occurred while parsing command-line options\n");
+ h5tools_setstatus(EXIT_FAILURE);
goto done;
+ }
+ else if (parse_ret > 0) {
+ /* Short-circuit success */
+ h5tools_setstatus(EXIT_SUCCESS);
+ goto done;
+ }
if (enable_error_stack > 0) {
H5Eset_auto2(H5E_DEFAULT, func, edata);
@@ -739,9 +860,20 @@ int main(int argc, const char **argv)
}
/* 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);
diff --git a/tools/src/h5repack/h5repack_verify.c b/tools/src/h5repack/h5repack_verify.c
index 683988c..7bb5dfd 100644
--- a/tools/src/h5repack/h5repack_verify.c
+++ b/tools/src/h5repack/h5repack_verify.c
@@ -353,16 +353,16 @@ 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)
{
- 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 */
+ 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;
@@ -374,9 +374,9 @@ int h5repack_cmp_pl(const char *fname1, const char *fname2)
*-------------------------------------------------------------------------
*/
/* Open the files */
- if ((fid1 = H5Fopen(fname1, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0)
+ if ((fid1 = h5tools_fopen(fname1, H5F_ACC_RDONLY, fname1_fapl, TRUE, NULL, 0)) < 0)
H5TOOLS_GOTO_ERROR((-1), "h5tools_fopen failed <%s>: %s", fname1, H5FOPENERROR);
- if ((fid2 = H5Fopen(fname2, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0)
+ if ((fid2 = h5tools_fopen(fname2, H5F_ACC_RDONLY, fname2_fapl, TRUE, NULL, 0)) < 0)
H5TOOLS_GOTO_ERROR((-1), "h5tools_fopen failed <%s>: %s", fname2, H5FOPENERROR);
/*-------------------------------------------------------------------------
diff --git a/tools/src/h5stat/CMakeLists.txt b/tools/src/h5stat/CMakeLists.txt
index f6cc542..f0722fd 100644
--- a/tools/src/h5stat/CMakeLists.txt
+++ b/tools/src/h5stat/CMakeLists.txt
@@ -7,6 +7,7 @@ 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_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)
@@ -18,6 +19,7 @@ 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_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)
diff --git a/tools/src/h5stat/h5stat.c b/tools/src/h5stat/h5stat.c
index adc905a..fdf49cd 100644
--- a/tools/src/h5stat/h5stat.c
+++ b/tools/src/h5stat/h5stat.c
@@ -118,30 +118,28 @@ typedef struct iter_t {
} 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 */
@@ -1065,103 +1063,32 @@ parse_command_line(int argc, const char *argv[], struct handler_t **hand_ret)
break;
case 'w':
-#ifndef H5_HAVE_ROS3_VFD
+#ifdef H5_HAVE_ROS3_VFD
+ if (h5tools_parse_ros3_fapl_tuple(opt_arg, ',', &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(opt_arg, ',', &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());
@@ -1885,41 +1812,36 @@ main(int argc, const char *argv[])
if(parse_command_line(argc, argv, &hand) < 0)
goto done;
- /* if drivername is not null, probably need to set the fapl */
- if (HDstrcmp(drivername, "")) {
- void *conf_fa = NULL;
+ if (drivername) {
+ h5tools_fapl_info_t fapl_info;
- 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 */
+ /* Currently, only retrieval of VFDs is supported. */
+ fapl_info.type = VFD_BY_NAME;
+ fapl_info.info = NULL;
+ fapl_info.u.name = drivername;
- }
- else if (!HDstrcmp(drivername, "hdfs")) {
-#ifndef H5_HAVE_LIBHDFS
- error_msg("HDFS VFD not enabled.\n\n");
+ if (!HDstrcmp(drivername, drivernames[ROS3_VFD_IDX])) {
+#ifdef H5_HAVE_ROS3_VFD
+ fapl_info.info = (void *)&ros3_fa;
+#else
+ error_msg("Read-Only S3 VFD not enabled.\n");
goto done;
+#endif
+ }
+ else if (!HDstrcmp(drivername, drivernames[HDFS_VFD_IDX])) {
+#ifdef H5_HAVE_LIBHDFS
+ fapl_info.info = (void *)&hdfs_fa;
#else
- conf_fa = (void *)&hdfs_fa;
-#endif /* H5_HAVE_LIBHDFS */
+ error_msg("HDFS VFD not enabled.\n");
+ goto done;
+#endif
}
- 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, &fapl_info)) < 0) {
+ error_msg("Unable to create FAPL for file access\n");
+ goto done;
}
- } /* drivername set */
+ }
fname = argv[opt_ind];
@@ -1935,7 +1857,9 @@ main(int argc, const char *argv[])
HDprintf("Filename: %s\n", fname);
- fid = H5Fopen(fname, H5F_ACC_RDONLY, fapl_id);
+ fid = h5tools_fopen(fname, H5F_ACC_RDONLY, fapl_id,
+ (fapl_id == H5P_DEFAULT) ? FALSE : TRUE, NULL, 0);
+
if(fid < 0) {
error_msg("unable to open file \"%s\"\n", fname);
h5tools_setstatus(EXIT_FAILURE);
diff --git a/tools/src/misc/CMakeLists.txt b/tools/src/misc/CMakeLists.txt
index 16e4555..1e9cacc 100644
--- a/tools/src/misc/CMakeLists.txt
+++ b/tools/src/misc/CMakeLists.txt
@@ -8,6 +8,7 @@ project (HDF5_TOOLS_SRC_MISC C)
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_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)
@@ -15,6 +16,7 @@ if (NOT ONLY_SHARED_LIBS)
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_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)
@@ -22,6 +24,7 @@ if (NOT ONLY_SHARED_LIBS)
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_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)
@@ -29,6 +32,7 @@ if (NOT ONLY_SHARED_LIBS)
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_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)
@@ -45,12 +49,14 @@ 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_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_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)
@@ -58,6 +64,7 @@ if (BUILD_SHARED_LIBS)
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_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)
@@ -65,6 +72,7 @@ if (BUILD_SHARED_LIBS)
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_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)
diff --git a/tools/src/misc/h5clear.c b/tools/src/misc/h5clear.c
index 38fa6a2..2c85e75 100644
--- a/tools/src/misc/h5clear.c
+++ b/tools/src/misc/h5clear.c
@@ -267,6 +267,8 @@ main (int argc, const char *argv[])
/* initialize h5tools lib */
h5tools_init();
+ H5Eset_auto2(H5tools_ERR_STACK_g, NULL, NULL);
+
/* Parse command line options */
if(parse_command_line(argc, argv) < 0)
goto done;
@@ -339,7 +341,7 @@ 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;
diff --git a/tools/src/misc/h5mkgrp.c b/tools/src/misc/h5mkgrp.c
index feb60d4..a2cb68b 100644
--- a/tools/src/misc/h5mkgrp.c
+++ b/tools/src/misc/h5mkgrp.c
@@ -255,7 +255,7 @@ main(int argc, const char *argv[])
} /* 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.fname, H5F_ACC_RDWR, fapl_id, FALSE, 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) */
generated by cgit v0.12 at 2024-11-04 17:46:28 (GMT)