/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 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. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #include "h5tools.h" #include "h5tools_utils.h" #include "h5repack.h" /* Name of tool */ #define PROGRAMNAME "h5repack" 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 = 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 = "a:b:c:d:e:f:hi:j:k:l:m:no:q:s:t:u:v*z:E*G:LM:P:S:T:VXW"; static struct 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'}, {NULL, 0, '\0'}}; /*------------------------------------------------------------------------- * Function: usage * * Purpose: print usage * * Return: void * *------------------------------------------------------------------------- */ 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 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, " --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, " -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"); 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, " -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, " -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, " -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, " -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\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, " 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\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 . 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\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, " 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\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\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\n"); PRINTVALSTREAM(rawoutstream, " virtual file driver.\n"); PRINTVALSTREAM(rawoutstream, " NONE:\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, " 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\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\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, " :=\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " 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, " can be:\n"); PRINTVALSTREAM(rawoutstream, " GZIP, to apply the HDF5 GZIP filter (GZIP compression)\n"); PRINTVALSTREAM(rawoutstream, " SZIP, to apply the HDF5 SZIP filter (SZIP compression)\n"); PRINTVALSTREAM(rawoutstream, " SHUF, to apply the HDF5 shuffle filter\n"); PRINTVALSTREAM(rawoutstream, " FLET, to apply the HDF5 checksum filter\n"); PRINTVALSTREAM(rawoutstream, " NBIT, to apply the HDF5 NBIT filter (NBIT compression)\n"); PRINTVALSTREAM(rawoutstream, " SOFF, to apply the HDF5 Scale/Offset filter\n"); PRINTVALSTREAM(rawoutstream, " UD, to apply a user defined filter\n"); PRINTVALSTREAM(rawoutstream, " NONE, to remove all filters\n"); PRINTVALSTREAM(rawoutstream, " is optional filter parameter information\n"); PRINTVALSTREAM(rawoutstream, " GZIP= from 1-9\n"); PRINTVALSTREAM(rawoutstream, " SZIP= 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 is an integer and scale_type\n"); PRINTVALSTREAM(rawoutstream, " is either IN or DS\n"); PRINTVALSTREAM(rawoutstream, " UD=\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, " :=\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " 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, " can be:\n"); PRINTVALSTREAM(rawoutstream, " CHUNK, to apply chunking layout\n"); PRINTVALSTREAM(rawoutstream, " COMPA, to apply compact layout\n"); PRINTVALSTREAM(rawoutstream, " CONTI, to apply contiguous layout\n"); PRINTVALSTREAM(rawoutstream, " is optional layout information\n"); PRINTVALSTREAM(rawoutstream, " CHUNK=DIM[xDIM...xDIM], the chunk size of each dimension\n"); PRINTVALSTREAM(rawoutstream, " COMPA (no parameter)\n"); PRINTVALSTREAM(rawoutstream, " CONTI (no parameter)\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, "Examples of use:\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, "1) h5repack -v -f GZIP=1 file1 file2\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " GZIP compression with level 1 to all objects\n"); 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, "\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, " 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, " 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"); PRINTVALSTREAM(rawoutstream, " Add both filters SHUF and GZIP in this order to all datasets\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, "6) h5repack -f UD=307,0,1,9 file1 file2\n"); 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"); } /*------------------------------------------------------------------------- * Function: leave * * Purpose: Shutdown MPI & HDF5 and call exit() * * Return: Does not return *------------------------------------------------------------------------- */ static void leave(int ret) { h5tools_close(); HDexit(ret); } /*------------------------------------------------------------------------- * Function: read_info * * Purpose: read comp and chunk options from a file * * Return: void, exit on error *------------------------------------------------------------------------- */ 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]; FILE *fp = NULL; char c; int i; int ret_value = EXIT_SUCCESS; if (NULL == (fp = HDfopen(filename, "r"))) { error_msg("cannot open options file %s\n", filename); h5tools_setstatus(EXIT_FAILURE); ret_value = EXIT_FAILURE; goto done; } /* cycle until end of file reached */ while (1) { if (EOF == HDfscanf(fp, "%9s", stype)) break; /* 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; } /* 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; } 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++] = 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 chunk option\n"); h5tools_setstatus(EXIT_FAILURE); ret_value = EXIT_FAILURE; goto done; } } else { 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) HDfclose(fp); return ret_value; } /*------------------------------------------------------------------------- * 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 *------------------------------------------------------------------------- */ static H5_index_t set_sort_by(const char *form) { H5_index_t idx_type = H5_INDEX_UNKNOWN; if (!HDstrcmp(form, "name")) idx_type = H5_INDEX_NAME; else if (!HDstrcmp(form, "creation_order")) idx_type = H5_INDEX_CRT_ORDER; return idx_type; } /*------------------------------------------------------------------------- * 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 *------------------------------------------------------------------------- */ static H5_iter_order_t set_sort_order(const char *form) { H5_iter_order_t iter_order = H5_ITER_UNKNOWN; if (!HDstrcmp(form, "ascending")) iter_order = H5_ITER_INC; else if (!HDstrcmp(form, "descending")) iter_order = H5_ITER_DEC; return iter_order; } /*------------------------------------------------------------------------- * Function: parse_command_line * * Purpose: parse command line input *------------------------------------------------------------------------- */ static int parse_command_line(int argc, const char *const *argv, pack_opt_t *options) { h5tools_vol_info_t in_vol_info; h5tools_vol_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; /* Initialize fapl info structs */ HDmemset(&in_vol_info, 0, sizeof(h5tools_vol_info_t)); HDmemset(&out_vol_info, 0, sizeof(h5tools_vol_info_t)); /* parse command line options */ while (EOF != (opt = get_option(argc, argv, s_opts, l_opts))) { switch ((char)opt) { /* -i for backward compatibility */ case 'i': infile = opt_arg; has_i++; break; /* -o for backward compatibility */ case 'o': outfile = opt_arg; has_o++; break; case 'h': usage(h5tools_getprogname()); h5tools_setstatus(EXIT_SUCCESS); ret_value = 1; goto done; case 'V': print_version(h5tools_getprogname()); h5tools_setstatus(EXIT_SUCCESS); ret_value = 1; goto done; case 'v': if (opt_arg != NULL) { if (2 == HDatoi(opt_arg)) options->verbose = 2; } else options->verbose = 1; break; case 'f': /* parse the -f filter option */ if (h5repack_addfilter(opt_arg, options) < 0) { error_msg("in parsing filter\n"); h5tools_setstatus(EXIT_FAILURE); ret_value = -1; goto done; } break; case 'l': /* parse the -l layout option */ if (h5repack_addlayout(opt_arg, options) < 0) { error_msg("in parsing layout\n"); h5tools_setstatus(EXIT_FAILURE); ret_value = -1; goto done; } 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); h5tools_setstatus(EXIT_FAILURE); ret_value = -1; goto done; } break; case 'e': 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': options->use_native = 1; break; case 'L': options->latest = TRUE; break; case 'j': 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; break; case 'k': 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; break; case 'X': options->merge = TRUE; break; case 'W': options->prune = TRUE; break; case 'c': options->grp_compact = HDatoi(opt_arg); if (options->grp_compact > 0) options->latest = TRUE; /* must use latest format */ break; case 'd': options->grp_indexed = HDatoi(opt_arg); 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)) 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; break; case 'b': options->ublock_size = (hsize_t)HDatol(opt_arg); break; case 'M': options->meta_block_size = (hsize_t)HDatol(opt_arg); break; case 't': options->threshold = (hsize_t)HDatol(opt_arg); break; case 'a': options->alignment = HDstrtoull(opt_arg, NULL, 0); if (options->alignment < 1) { error_msg("invalid alignment size\n", opt_arg); 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; } break; case 'P': options->fs_persist = HDatoi(opt_arg); 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) /* 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) /* To distinguish the "specified" zero value */ options->fs_pagesize = -1; break; case 'q': 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; } break; case 'z': 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; } break; case 'E': if (opt_arg != NULL) enable_error_stack = HDatoi(opt_arg); 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(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_string = opt_arg; break; case '4': out_vol_info.type = VOL_BY_VALUE; out_vol_info.u.value = (H5VL_class_value_t)HDatoi(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_string = opt_arg; break; default: break; } /* end switch */ } /* end while there are more options to parse */ /* 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; } /* Setup FAPL for input and output file accesses */ if (custom_in_fapl) { if ((tmp_fapl = h5tools_get_fapl(options->fin_fapl, &in_vol_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_fapl) { if ((tmp_fapl = h5tools_get_fapl(options->fout_fapl, &out_vol_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; } /*------------------------------------------------------------------------- * Function: main * * Purpose: h5repack main program * * Return: Success: EXIT_SUCCESS(0) * * Failure: EXIT_FAILURE(1) *------------------------------------------------------------------------- */ int main(int argc, char **argv) { pack_opt_t options; /*the global options */ int parse_ret; HDmemset(&options, 0, sizeof(pack_opt_t)); /* Initialize h5tools lib */ h5tools_init(); 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; 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; } 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 */ 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()); }