diff options
Diffstat (limited to 'tools/src/h5repack')
| -rw-r--r-- | tools/src/h5repack/Makefile.am | 10 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack.c | 895 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack.h | 34 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack_copy.c | 247 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack_filters.c | 10 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack_main.c | 97 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack_opttable.c | 10 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack_parse.c | 10 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack_refs.c | 56 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack_verify.c | 29 |
10 files changed, 733 insertions, 665 deletions
diff --git a/tools/src/h5repack/Makefile.am b/tools/src/h5repack/Makefile.am index 31d368d..c71e65b 100644 --- a/tools/src/h5repack/Makefile.am +++ b/tools/src/h5repack/Makefile.am @@ -5,12 +5,10 @@ # # This file is part of HDF5. The full HDF5 copyright notice, including # terms governing use, modification, and redistribution, is contained in -# the files COPYING and Copyright.html. COPYING can be found at the root -# of the source code distribution tree; Copyright.html can be found at the -# root level of an installed copy of the electronic HDF5 document set and -# is linked from the top-level documents page. It can also be found at -# http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have -# access to either file, you may request a copy from help@hdfgroup.org. +# the COPYING file, which can be found at the root of the source code +# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. +# If you do not have access to either file, you may request a copy from +# help@hdfgroup.org. ## ## Makefile.am ## Run automake to generate a Makefile.in from this file. diff --git a/tools/src/h5repack/h5repack.c b/tools/src/h5repack/h5repack.c index c09dee6..bc8527b 100644 --- a/tools/src/h5repack/h5repack.c +++ b/tools/src/h5repack/h5repack.c @@ -5,12 +5,10 @@ * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * - * the files COPYING and Copyright.html. COPYING can be found at the root * - * of the source code distribution tree; Copyright.html can be found at the * - * root level of an installed copy of the electronic HDF5 document set and * - * is linked from the top-level documents page. It can also be found at * - * http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have * - * access to either file, you may request a copy from help@hdfgroup.org. * + * the COPYING file, which can be found at the root of the source code * + * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * If you do not have access to either file, you may request a copy from * + * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #include <stdlib.h> @@ -53,19 +51,19 @@ static int have_request(pack_opt_t *options); *------------------------------------------------------------------------- */ int h5repack(const char* infile, const char* outfile, pack_opt_t *options) { - /* check input */ - if (check_options(options) < 0) - return -1; + /* check input */ + if (check_options(options) < 0) + return -1; - /* check for objects in input that are in the file */ - if (check_objects(infile, options) < 0) - return -1; + /* check for objects in input that are in the file */ + if (check_objects(infile, options) < 0) + return -1; - /* copy the objects */ - if (copy_objects(infile, outfile, options) < 0) - return -1; + /* copy the objects */ + if (copy_objects(infile, outfile, options) < 0) + return -1; - return 0; + return 0; } /*------------------------------------------------------------------------- @@ -107,7 +105,7 @@ h5repack_init(pack_opt_t *options, int verbose, hbool_t latest) */ int h5repack_end(pack_opt_t *options) { - return options_table_free(options->op_tbl); + return options_table_free(options->op_tbl); } /*------------------------------------------------------------------------- @@ -123,10 +121,10 @@ int h5repack_end(pack_opt_t *options) { int h5repack_addfilter(const char* str, pack_opt_t *options) { - obj_list_t *obj_list = NULL; /* one object list for the -f and -l option entry */ - filter_info_t filter; /* filter info for the current -f option entry */ - unsigned n_objs; /* number of objects in the current -f or -l option entry */ - int is_glb; /* is the filter global */ + obj_list_t *obj_list = NULL; /* one object list for the -f and -l option entry */ + filter_info_t filter; /* filter info for the current -f option entry */ + unsigned n_objs; /* number of objects in the current -f or -l option entry */ + int is_glb; /* is the filter global */ /* parse the -f option */ if (NULL == (obj_list = parse_filter(str, &n_objs, &filter, options, &is_glb))) @@ -165,10 +163,10 @@ int h5repack_addlayout(const char* str, pack_opt_t *options) { obj_list_t *obj_list = NULL; /*one object list for the -t and -c option entry */ - unsigned n_objs; /*number of objects in the current -t or -c option entry */ - pack_info_t pack; /*info about layout to extract from parse */ - int j; - int ret_value = -1; + unsigned n_objs; /*number of objects in the current -t or -c option entry */ + pack_info_t pack; /*info about layout to extract from parse */ + int j; + int ret_value = -1; init_packobject(&pack); @@ -234,87 +232,84 @@ h5repack_addlayout(const char* str, pack_opt_t *options) *------------------------------------------------------------------------- */ hid_t copy_named_datatype(hid_t type_in, hid_t fidout, - named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options) { - named_dt_t *dt = *named_dt_head_p; /* Stack pointer */ - named_dt_t *dt_ret = NULL; /* Datatype to return */ - H5O_info_t oinfo; /* Object info of input dtype */ - hid_t ret_value = -1; /* The identifier of the named dtype in the out file */ - - if (H5Oget_info(type_in, &oinfo) < 0) - goto done; - - if (*named_dt_head_p) { - /* Stack already exists, search for the datatype */ - while (dt && dt->addr_in != oinfo.addr) - dt = dt->next; - - dt_ret = dt; - } - else { - /* Create the stack */ - size_t i; - - for (i = 0; i < travt->nobjs; i++) { - if (travt->objs[i].type == H5TRAV_TYPE_NAMED_DATATYPE) { - /* Push onto the stack */ - if (NULL == (dt = (named_dt_t *) HDmalloc(sizeof(named_dt_t)))) { - goto done; - } - dt->next = *named_dt_head_p; - *named_dt_head_p = dt; - - /* Update the address and id */ - dt->addr_in = travt->objs[i].objno; - dt->id_out = -1; - - /* Check if this type is the one requested */ - if (oinfo.addr == dt->addr_in) { - HDassert(!dt_ret); - dt_ret = dt; - } /* end if */ - } /* end if */ - } /* end for */ - } /* end else */ - - /* Handle the case that the requested datatype was not found. This is - * possible if the datatype was committed anonymously in the input file. */ - if (!dt_ret) { - /* Push the new datatype onto the stack */ - if (NULL == (dt_ret = (named_dt_t *) HDmalloc(sizeof(named_dt_t)))) { - goto done; - } - dt_ret->next = *named_dt_head_p; - *named_dt_head_p = dt_ret; - - /* Update the address and id */ - dt_ret->addr_in = oinfo.addr; - dt_ret->id_out = -1; - } /* end if */ - - /* If the requested datatype does not yet exist in the output file, copy it - * anonymously */ - if (dt_ret->id_out < 0) { - if (options->use_native == 1) - dt_ret->id_out = h5tools_get_native_type(type_in); - else - dt_ret->id_out = H5Tcopy(type_in); - if (dt_ret->id_out < 0) - goto done; - if (H5Tcommit_anon(fidout, dt_ret->id_out, H5P_DEFAULT, H5P_DEFAULT) < 0) - goto done; - } /* end if */ - - /* Set return value */ - ret_value = dt_ret->id_out; - - /* Increment the ref count on id_out, because the calling function will try - * to close it */ - if(H5Iinc_ref(ret_value) < 0) { - ret_value = -1; - } + named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options) { + named_dt_t *dt = *named_dt_head_p; /* Stack pointer */ + named_dt_t *dt_ret = NULL; /* Datatype to return */ + H5O_info_t oinfo; /* Object info of input dtype */ + hid_t ret_value = -1; /* The identifier of the named dtype in the out file */ + + if (H5Oget_info(type_in, &oinfo) < 0) + goto done; + + if (*named_dt_head_p) { + /* Stack already exists, search for the datatype */ + while (dt && dt->addr_in != oinfo.addr) + dt = dt->next; + + dt_ret = dt; + } + else { + /* Create the stack */ + size_t i; + + for (i = 0; i < travt->nobjs; i++) { + if (travt->objs[i].type == H5TRAV_TYPE_NAMED_DATATYPE) { + /* Push onto the stack */ + if (NULL == (dt = (named_dt_t *)HDmalloc(sizeof(named_dt_t)))) + goto done; + dt->next = *named_dt_head_p; + *named_dt_head_p = dt; + + /* Update the address and id */ + dt->addr_in = travt->objs[i].objno; + dt->id_out = -1; + + /* Check if this type is the one requested */ + if (oinfo.addr == dt->addr_in) { + HDassert(!dt_ret); + dt_ret = dt; + } /* end if */ + } /* end if */ + } /* end for */ + } /* end else */ + + /* Handle the case that the requested datatype was not found. This is + * possible if the datatype was committed anonymously in the input file. */ + if (!dt_ret) { + /* Push the new datatype onto the stack */ + if (NULL == (dt_ret = (named_dt_t *)HDmalloc(sizeof(named_dt_t)))) + goto done; + dt_ret->next = *named_dt_head_p; + *named_dt_head_p = dt_ret; + + /* Update the address and id */ + dt_ret->addr_in = oinfo.addr; + dt_ret->id_out = -1; + } /* end if */ + + /* If the requested datatype does not yet exist in the output file, copy it + * anonymously */ + if (dt_ret->id_out < 0) { + if (options->use_native == 1) + dt_ret->id_out = H5Tget_native_type(type_in, H5T_DIR_DEFAULT); + else + dt_ret->id_out = H5Tcopy(type_in); + if (dt_ret->id_out < 0) + goto done; + if (H5Tcommit_anon(fidout, dt_ret->id_out, H5P_DEFAULT, H5P_DEFAULT) < 0) + goto done; + } /* end if */ + + /* Set return value */ + ret_value = dt_ret->id_out; + + /* Increment the ref count on id_out, because the calling function will try + * to close it */ + if(H5Iinc_ref(ret_value) < 0) + ret_value = -1; done: - return (ret_value); + return (ret_value); } /* end copy_named_datatype */ /*------------------------------------------------------------------------- @@ -329,22 +324,22 @@ done: *------------------------------------------------------------------------- */ int named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err) { - named_dt_t *dt = *named_dt_head_p; - int ret_value = -1; + named_dt_t *dt = *named_dt_head_p; + int ret_value = -1; - while (dt) { - /* Pop the datatype off the stack and free it */ - if (H5Tclose(dt->id_out) < 0 && !ignore_err) - goto done; - dt = dt->next; - HDfree(*named_dt_head_p); - *named_dt_head_p = dt; - } /* end while */ + while (dt) { + /* Pop the datatype off the stack and free it */ + if (H5Tclose(dt->id_out) < 0 && !ignore_err) + goto done; + dt = dt->next; + HDfree(*named_dt_head_p); + *named_dt_head_p = dt; + } /* end while */ - ret_value = 0; + ret_value = 0; done: - return (ret_value); + return (ret_value); } /* end named_datatype_free */ /*------------------------------------------------------------------------- @@ -365,25 +360,25 @@ done: */ int copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p, - trav_table_t *travt, pack_opt_t *options) + trav_table_t *travt, pack_opt_t *options) { - int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ - hid_t attr_id = -1; /* attr ID */ - hid_t attr_out = -1; /* attr ID */ - hid_t space_id = -1; /* space ID */ - hid_t ftype_id = -1; /* file type ID */ - hid_t wtype_id = -1; /* read/write type ID */ - size_t msize; /* size of type */ - void *buf = NULL; /* data buffer */ - hsize_t nelmts; /* number of elements in dataset */ - int rank; /* rank of dataset */ - htri_t is_named; /* Whether the datatype is named */ - hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */ - char name[255]; - H5O_info_t oinfo; /* object info */ - int j; - unsigned u; - hbool_t is_ref = 0; + int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ + hid_t attr_id = -1; /* attr ID */ + hid_t attr_out = -1; /* attr ID */ + hid_t space_id = -1; /* space ID */ + hid_t ftype_id = -1; /* file type ID */ + hid_t wtype_id = -1; /* read/write type ID */ + size_t msize; /* size of type */ + void *buf = NULL; /* data buffer */ + hsize_t nelmts; /* number of elements in dataset */ + int rank; /* rank of dataset */ + htri_t is_named; /* Whether the datatype is named */ + hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */ + char name[255]; + H5O_info_t oinfo; /* object info */ + int j; + unsigned u; + hbool_t is_ref = 0; H5T_class_t type_class = -1; if (H5Oget_info(loc_in, &oinfo) < 0) @@ -427,7 +422,7 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p, } /* end if */ else { if (options->use_native == 1) - wtype_id = h5tools_get_native_type(ftype_id); + wtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT); else wtype_id = H5Tcopy(ftype_id); } /* end else */ @@ -468,7 +463,7 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p, int nmembers = H5Tget_nmembers(wtype_id); for (j = 0; j < nmembers; j++) { - hid_t mtid = H5Tget_member_type(wtype_id, (unsigned) j); + hid_t mtid = H5Tget_member_type(wtype_id, (unsigned)j); H5T_class_t mtclass = H5Tget_class(mtid); H5Tclose(mtid); @@ -479,16 +474,13 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p, } /* for (j=0; i<nmembers; j++) */ } /* if (type_class == H5T_COMPOUND) */ - if (is_ref) { - ; /* handled by copy_refs_attr() */ - } - else { + if (!is_ref) { /*------------------------------------------------------------------------- * read to memory *------------------------------------------------------------------------- */ - buf = (void *) HDmalloc((size_t)(nelmts * msize)); + buf = (void *)HDmalloc((size_t)(nelmts * msize)); if (buf == NULL) { error_msg("h5repack", "cannot read into memory\n"); HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed"); @@ -570,193 +562,188 @@ done: * Programmer: pvn@ncsa.uiuc.edu * * Date: September, 22, 2003 - * - * Modification: - * Peter Cao, July 9, 2007 - * Add "-L, --latest" and other options to pack a file with the latest file format - * *------------------------------------------------------------------------- */ static int check_options(pack_opt_t *options) { - unsigned int i; - int k, j, has_cp = 0, has_ck = 0; - char slayout[30]; - - /*------------------------------------------------------------------------- - * objects to layout - *------------------------------------------------------------------------- - */ - if (options->verbose && have_request(options) /* only print if requested */) { - printf("Objects to modify layout are...\n"); - if (options->all_layout == 1) { - switch (options->layout_g) { - case H5D_COMPACT: - strcpy(slayout, "compact"); - break; - case H5D_CONTIGUOUS: - strcpy(slayout, "contiguous"); - break; - case H5D_CHUNKED: - strcpy(slayout, "chunked"); - break; - case H5D_VIRTUAL: - strcpy(slayout, "virtual"); - break; - case H5D_LAYOUT_ERROR: - case H5D_NLAYOUTS: - error_msg("invalid layout\n"); - return -1; - default: - strcpy(slayout, "invalid layout\n"); - return -1; - } - printf(" Apply %s layout to all\n", slayout); - if (H5D_CHUNKED == options->layout_g) { - printf("with dimension ["); - for (j = 0; j < options->chunk_g.rank; j++) - printf("%d ", (int) options->chunk_g.chunk_lengths[j]); - printf("]\n"); - } - } - }/* verbose */ - - for (i = 0; i < options->op_tbl->nelems; i++) { - char* name = options->op_tbl->objs[i].path; - - if (options->op_tbl->objs[i].chunk.rank > 0) { - if (options->verbose) { - printf(" <%s> with chunk size ", name); - for (k = 0; k < options->op_tbl->objs[i].chunk.rank; k++) - printf("%d ", - (int) options->op_tbl->objs[i].chunk.chunk_lengths[k]); - printf("\n"); - } - has_ck = 1; - } - else if (options->op_tbl->objs[i].chunk.rank == -2) { - if (options->verbose) - printf(" <%s> %s\n", name, "NONE (contigous)"); - has_ck = 1; - } - } - - if (options->all_layout == 1 && has_ck) { - error_msg( - "invalid chunking input: 'all' option\ + unsigned int i; + int k, j, has_cp = 0, has_ck = 0; + char slayout[30]; + + /*------------------------------------------------------------------------- + * objects to layout + *------------------------------------------------------------------------- + */ + if (options->verbose && have_request(options) /* only print if requested */) { + printf("Objects to modify layout are...\n"); + if (options->all_layout == 1) { + switch (options->layout_g) { + case H5D_COMPACT: + strcpy(slayout, "compact"); + break; + case H5D_CONTIGUOUS: + strcpy(slayout, "contiguous"); + break; + case H5D_CHUNKED: + strcpy(slayout, "chunked"); + break; + case H5D_VIRTUAL: + strcpy(slayout, "virtual"); + break; + case H5D_LAYOUT_ERROR: + case H5D_NLAYOUTS: + error_msg("invalid layout\n"); + return -1; + default: + strcpy(slayout, "invalid layout\n"); + return -1; + } + printf(" Apply %s layout to all\n", slayout); + if (H5D_CHUNKED == options->layout_g) { + printf("with dimension ["); + for (j = 0; j < options->chunk_g.rank; j++) + printf("%d ", (int) options->chunk_g.chunk_lengths[j]); + printf("]\n"); + } + } + }/* verbose */ + + for (i = 0; i < options->op_tbl->nelems; i++) { + char* name = options->op_tbl->objs[i].path; + + if (options->op_tbl->objs[i].chunk.rank > 0) { + if (options->verbose) { + printf(" <%s> with chunk size ", name); + for (k = 0; k < options->op_tbl->objs[i].chunk.rank; k++) + printf("%d ", + (int) options->op_tbl->objs[i].chunk.chunk_lengths[k]); + printf("\n"); + } + has_ck = 1; + } + else if (options->op_tbl->objs[i].chunk.rank == -2) { + if (options->verbose) + printf(" <%s> %s\n", name, "NONE (contigous)"); + has_ck = 1; + } + } + + if (options->all_layout == 1 && has_ck) { + error_msg( + "invalid chunking input: 'all' option\ is present with other objects\n"); - return -1; - } - - /*------------------------------------------------------------------------- - * objects to filter - *------------------------------------------------------------------------- - */ - - if (options->verbose && have_request(options) /* only print if requested */) { - printf("Objects to apply filter are...\n"); - if (options->all_filter == 1) { - for (k = 0; k < options->n_filter_g; k++) { - H5Z_filter_t filtn = options->filter_g[k].filtn; - switch (filtn) { - case H5Z_FILTER_NONE: - printf(" Uncompress all\n"); - break; - case H5Z_FILTER_SHUFFLE: - case H5Z_FILTER_FLETCHER32: - printf(" All with %s\n", get_sfilter(filtn)); - break; - case H5Z_FILTER_SZIP: - case H5Z_FILTER_DEFLATE: - printf(" All with %s, parameter %d\n", get_sfilter(filtn), - options->filter_g[k].cd_values[0]); - break; - default: - printf(" User Defined %d\n", filtn); - break; - } /* k */ - }; - } - } /* verbose */ - - for (i = 0; i < options->op_tbl->nelems; i++) { - pack_info_t pack = options->op_tbl->objs[i]; - char* name = pack.path; - - for (j = 0; j < pack.nfilters; j++) { - if (options->verbose) { - printf(" <%s> with %s filter\n", name, - get_sfilter(pack.filter[j].filtn)); - } - - has_cp = 1; - - } /* j */ - } /* i */ - - if (options->all_filter == 1 && has_cp) { - error_msg( - "invalid compression input: 'all' option\ + return -1; + } + + /*------------------------------------------------------------------------- + * objects to filter + *------------------------------------------------------------------------- + */ + + if (options->verbose && have_request(options) /* only print if requested */) { + printf("Objects to apply filter are...\n"); + if (options->all_filter == 1) { + for (k = 0; k < options->n_filter_g; k++) { + H5Z_filter_t filtn = options->filter_g[k].filtn; + switch (filtn) { + case H5Z_FILTER_NONE: + printf(" Uncompress all\n"); + break; + case H5Z_FILTER_SHUFFLE: + case H5Z_FILTER_FLETCHER32: + printf(" All with %s\n", get_sfilter(filtn)); + break; + case H5Z_FILTER_SZIP: + case H5Z_FILTER_DEFLATE: + printf(" All with %s, parameter %d\n", get_sfilter(filtn), + options->filter_g[k].cd_values[0]); + break; + default: + printf(" User Defined %d\n", filtn); + break; + } /* k */ + }; + } + } /* verbose */ + + for (i = 0; i < options->op_tbl->nelems; i++) { + pack_info_t pack = options->op_tbl->objs[i]; + char* name = pack.path; + + for (j = 0; j < pack.nfilters; j++) { + if (options->verbose) { + printf(" <%s> with %s filter\n", name, + get_sfilter(pack.filter[j].filtn)); + } + + has_cp = 1; + + } /* j */ + } /* i */ + + if (options->all_filter == 1 && has_cp) { + error_msg( + "invalid compression input: 'all' option\ is present with other objects\n"); - return -1; - } - - /*------------------------------------------------------------------------- - * check options for the latest format - *------------------------------------------------------------------------- - */ - - if (options->grp_compact < 0) { - error_msg( - "invalid maximum number of links to store as header messages\n"); - return -1; - } - if (options->grp_indexed < 0) { - error_msg( - "invalid minimum number of links to store in the indexed format\n"); - return -1; - } - if (options->grp_indexed > options->grp_compact) { - error_msg( - "minimum indexed size is greater than the maximum compact size\n"); - return -1; - } - for (i = 0; i < 8; i++) { - if (options->msg_size[i] < 0) { - error_msg("invalid shared message size\n"); - return -1; - } - } - - /*-------------------------------------------------------------------------------- - * verify new user userblock options; file name must be present - *--------------------------------------------------------------------------------- - */ - if (options->ublock_filename != NULL && options->ublock_size == 0) { - if (options->verbose) { - printf( - "Warning: user block size missing for file %s. Assigning a default size of 1024...\n", - options->ublock_filename); - options->ublock_size = 1024; - } - } - - if (options->ublock_filename == NULL && options->ublock_size != 0) { - error_msg("file name missing for user block\n", - options->ublock_filename); - return -1; - } - - /*-------------------------------------------------------------------------------- - * verify alignment options; threshold is zero default but alignment not - *--------------------------------------------------------------------------------- - */ - - if (options->alignment == 0 && options->threshold != 0) { - error_msg("alignment for H5Pset_alignment missing\n"); - return -1; - } - - return 0; + return -1; + } + + /*------------------------------------------------------------------------- + * check options for the latest format + *------------------------------------------------------------------------- + */ + + if (options->grp_compact < 0) { + error_msg( + "invalid maximum number of links to store as header messages\n"); + return -1; + } + if (options->grp_indexed < 0) { + error_msg( + "invalid minimum number of links to store in the indexed format\n"); + return -1; + } + if (options->grp_indexed > options->grp_compact) { + error_msg( + "minimum indexed size is greater than the maximum compact size\n"); + return -1; + } + for (i = 0; i < 8; i++) { + if (options->msg_size[i] < 0) { + error_msg("invalid shared message size\n"); + return -1; + } + } + + /*-------------------------------------------------------------------------------- + * verify new user userblock options; file name must be present + *--------------------------------------------------------------------------------- + */ + if (options->ublock_filename != NULL && options->ublock_size == 0) { + if (options->verbose) { + printf( + "Warning: user block size missing for file %s. Assigning a default size of 1024...\n", + options->ublock_filename); + options->ublock_size = 1024; + } + } + + if (options->ublock_filename == NULL && options->ublock_size != 0) { + error_msg("file name missing for user block\n", + options->ublock_filename); + return -1; + } + + /*-------------------------------------------------------------------------------- + * verify alignment options; threshold is zero default but alignment not + *--------------------------------------------------------------------------------- + */ + + if (options->alignment == 0 && options->threshold != 0) { + error_msg("alignment for H5Pset_alignment missing\n"); + return -1; + } + + return 0; } /*------------------------------------------------------------------------- @@ -774,119 +761,121 @@ static int check_options(pack_opt_t *options) { *------------------------------------------------------------------------- */ static int check_objects(const char* fname, pack_opt_t *options) { - hid_t fid; - unsigned int i; - trav_table_t *travt = NULL; - - /* nothing to do */ - if (options->op_tbl->nelems == 0) - return 0; - - /*------------------------------------------------------------------------- - * open the file - *------------------------------------------------------------------------- - */ - if ((fid = h5tools_fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, 0)) - < 0) { - printf("<%s>: %s\n", fname, H5FOPENERROR); - return -1; - } - - /*------------------------------------------------------------------------- - * get the list of objects in the file - *------------------------------------------------------------------------- - */ - - /* init table */ - trav_table_init(&travt); - - /* get the list of objects in the file */ - if (h5trav_gettable(fid, travt) < 0) - goto out; - - /*------------------------------------------------------------------------- - * compare with user supplied list - *------------------------------------------------------------------------- - */ - - if (options->verbose) - printf("Opening file <%s>. Searching for objects to modify...\n", - fname); - - for (i = 0; i < options->op_tbl->nelems; i++) { - char* name = options->op_tbl->objs[i].path; - if (options->verbose) - printf(" <%s>", name); - - /* the input object names are present in the file and are valid */ - if (h5trav_getindext(name, travt) < 0) { - error_msg("%s Could not find <%s> in file <%s>. Exiting...\n", - (options->verbose ? "\n" : ""), name, fname); - goto out; - } - if (options->verbose) - printf("...Found\n"); - - /* check for extra filter conditions */ - switch (options->op_tbl->objs[i].filter->filtn) { - /* chunk size must be smaller than pixels per block */ - case H5Z_FILTER_SZIP: - { - int j; - hsize_t csize = 1; - unsigned ppb = options->op_tbl->objs[i].filter->cd_values[0]; - hsize_t dims[H5S_MAX_RANK]; - int rank; - hid_t did; - hid_t sid; - - if (options->op_tbl->objs[i].chunk.rank > 0) { - rank = options->op_tbl->objs[i].chunk.rank; - for (j = 0; j < rank; j++) - csize *= options->op_tbl->objs[i].chunk.chunk_lengths[j]; - } - else { - if ((did = H5Dopen2(fid, name, H5P_DEFAULT)) < 0) - goto out; - if ((sid = H5Dget_space(did)) < 0) - goto out; - if ((rank = H5Sget_simple_extent_ndims(sid)) < 0) - goto out; - HDmemset(dims, 0, sizeof dims); - if (H5Sget_simple_extent_dims(sid, dims, NULL) < 0) - goto out; - for (j = 0; j < rank; j++) - csize *= dims[j]; - if (H5Sclose(sid) < 0) - goto out; - if (H5Dclose(did) < 0) - goto out; - } - - if (csize < ppb) { - printf( - " <warning: SZIP settins, chunk size is smaller than pixels per block>\n"); - goto out; - } - } - break; - default: - break; - } - } /* i */ - - /*------------------------------------------------------------------------- - * close - *------------------------------------------------------------------------- - */ - H5Fclose(fid); - trav_table_free(travt); - return 0; + hid_t fid; + unsigned int i; + trav_table_t *travt = NULL; + + /* nothing to do */ + if (options->op_tbl->nelems == 0) + return 0; + + /*------------------------------------------------------------------------- + * open the file + *------------------------------------------------------------------------- + */ + if ((fid = h5tools_fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, 0)) + < 0) { + printf("<%s>: %s\n", fname, H5FOPENERROR); + return -1; + } + + /*------------------------------------------------------------------------- + * get the list of objects in the file + *------------------------------------------------------------------------- + */ + + /* Initialize indexing options */ + h5trav_set_index(sort_by, sort_order); + /* init table */ + trav_table_init(&travt); + + /* get the list of objects in the file */ + if (h5trav_gettable(fid, travt) < 0) + goto out; + + /*------------------------------------------------------------------------- + * compare with user supplied list + *------------------------------------------------------------------------- + */ + + if (options->verbose) + printf("Opening file <%s>. Searching for objects to modify...\n", + fname); + + for (i = 0; i < options->op_tbl->nelems; i++) { + char* name = options->op_tbl->objs[i].path; + if (options->verbose) + printf(" <%s>", name); + + /* the input object names are present in the file and are valid */ + if (h5trav_getindext(name, travt) < 0) { + error_msg("%s Could not find <%s> in file <%s>. Exiting...\n", + (options->verbose ? "\n" : ""), name, fname); + goto out; + } + if (options->verbose) + printf("...Found\n"); + + /* check for extra filter conditions */ + switch (options->op_tbl->objs[i].filter->filtn) { + /* chunk size must be smaller than pixels per block */ + case H5Z_FILTER_SZIP: + { + int j; + hsize_t csize = 1; + unsigned ppb = options->op_tbl->objs[i].filter->cd_values[0]; + hsize_t dims[H5S_MAX_RANK]; + int rank; + hid_t did; + hid_t sid; + + if (options->op_tbl->objs[i].chunk.rank > 0) { + rank = options->op_tbl->objs[i].chunk.rank; + for (j = 0; j < rank; j++) + csize *= options->op_tbl->objs[i].chunk.chunk_lengths[j]; + } + else { + if ((did = H5Dopen2(fid, name, H5P_DEFAULT)) < 0) + goto out; + if ((sid = H5Dget_space(did)) < 0) + goto out; + if ((rank = H5Sget_simple_extent_ndims(sid)) < 0) + goto out; + HDmemset(dims, 0, sizeof dims); + if (H5Sget_simple_extent_dims(sid, dims, NULL) < 0) + goto out; + for (j = 0; j < rank; j++) + csize *= dims[j]; + if (H5Sclose(sid) < 0) + goto out; + if (H5Dclose(did) < 0) + goto out; + } + + if (csize < ppb) { + printf( + " <warning: SZIP settins, chunk size is smaller than pixels per block>\n"); + goto out; + } + } + break; + default: + break; + } + } /* i */ + + /*------------------------------------------------------------------------- + * close + *------------------------------------------------------------------------- + */ + H5Fclose(fid); + trav_table_free(travt); + return 0; out: - H5Fclose(fid); - trav_table_free(travt); - return -1; + H5Fclose(fid); + trav_table_free(travt); + return -1; } /*------------------------------------------------------------------------- @@ -902,10 +891,10 @@ out: */ static int have_request(pack_opt_t *options) { - if (options->all_filter || options->all_layout || options->op_tbl->nelems) - return 1; + if (options->all_filter || options->all_layout || options->op_tbl->nelems) + return 1; - return 0; + return 0; } @@ -920,21 +909,21 @@ static int have_request(pack_opt_t *options) { */ static const char* get_sfilter(H5Z_filter_t filtn) { - if (filtn == H5Z_FILTER_NONE) - return "NONE"; - else if (filtn == H5Z_FILTER_DEFLATE) - return "GZIP"; - else if (filtn == H5Z_FILTER_SZIP) - return "SZIP"; - else if (filtn == H5Z_FILTER_SHUFFLE) - return "SHUFFLE"; - else if (filtn == H5Z_FILTER_FLETCHER32) - return "FLETCHER32"; - else if (filtn == H5Z_FILTER_NBIT) - return "NBIT"; - else if (filtn == H5Z_FILTER_SCALEOFFSET) - return "SOFF"; - else - return "UD"; + if (filtn == H5Z_FILTER_NONE) + return "NONE"; + else if (filtn == H5Z_FILTER_DEFLATE) + return "GZIP"; + else if (filtn == H5Z_FILTER_SZIP) + return "SZIP"; + else if (filtn == H5Z_FILTER_SHUFFLE) + return "SHUFFLE"; + else if (filtn == H5Z_FILTER_FLETCHER32) + return "FLETCHER32"; + else if (filtn == H5Z_FILTER_NBIT) + return "NBIT"; + else if (filtn == H5Z_FILTER_SCALEOFFSET) + return "SOFF"; + else + return "UD"; } diff --git a/tools/src/h5repack/h5repack.h b/tools/src/h5repack/h5repack.h index 5ad0b80..e5ae03f 100644 --- a/tools/src/h5repack/h5repack.h +++ b/tools/src/h5repack/h5repack.h @@ -5,12 +5,10 @@ * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * - * the files COPYING and Copyright.html. COPYING can be found at the root * - * of the source code distribution tree; Copyright.html can be found at the * - * root level of an installed copy of the electronic HDF5 document set and * - * is linked from the top-level documents page. It can also be found at * - * http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have * - * access to either file, you may request a copy from help@hdfgroup.org. * + * the COPYING file, which can be found at the root of the source code * + * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * If you do not have access to either file, you may request a copy from * + * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -31,10 +29,10 @@ #define MAX_COMPACT_DSIZE 64512 /* max data size for compact layout. -1k for header size */ /* File space default information */ -#define FS_PAGESIZE_DEF 4096 -#define FS_STRATEGY_DEF H5F_FSPACE_STRATEGY_FSM_AGGR -#define FS_PERSIST_DEF FALSE -#define FS_THRESHOLD_DEF 1 +#define FS_PAGESIZE_DEF 4096 +#define FS_STRATEGY_DEF H5F_FSPACE_STRATEGY_FSM_AGGR +#define FS_PERSIST_DEF FALSE +#define FS_THRESHOLD_DEF 1 /*------------------------------------------------------------------------- @@ -122,10 +120,10 @@ typedef struct { hsize_t meta_block_size; /* metadata aggregation block size (for H5Pset_meta_block_size) */ hsize_t threshold; /* alignment threshold for H5Pset_alignment */ hsize_t alignment; /* alignment for H5Pset_alignment */ - H5F_fspace_strategy_t fs_strategy; /* File space handling strategy */ - int fs_persist; /* Free space section threshold */ - long fs_threshold; /* Free space section threshold */ - long long fs_pagesize; /* File space page size */ + H5F_fspace_strategy_t fs_strategy; /* File space handling strategy */ + int fs_persist; /* Free space section threshold */ + long fs_threshold; /* Free space section threshold */ + long long fs_pagesize; /* File space page size */ } pack_opt_t; @@ -152,10 +150,10 @@ 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); -/* 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 - * bugfix1726. - * Made shared functions as copy_attr() was needed in h5repack_refs.c. +/* 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 + * bugfix1726. + * Made shared functions as copy_attr() was needed in h5repack_refs.c. * However copy_attr() may be obsoleted when H5Acopy is available and put back * others to static in h5repack_copy.c. */ diff --git a/tools/src/h5repack/h5repack_copy.c b/tools/src/h5repack/h5repack_copy.c index 45d52bf..946f5ad 100644 --- a/tools/src/h5repack/h5repack_copy.c +++ b/tools/src/h5repack/h5repack_copy.c @@ -5,12 +5,10 @@ * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * - * the files COPYING and Copyright.html. COPYING can be found at the root * - * of the source code distribution tree; Copyright.html can be found at the * - * root level of an installed copy of the electronic HDF5 document set and * - * is linked from the top-level documents page. It can also be found at * - * http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have * - * access to either file, you may request a copy from help@hdfgroup.org. * + * the COPYING file, which can be found at the root of the source code * + * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * If you do not have access to either file, you may request a copy from * + * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #include "h5repack.h" @@ -33,7 +31,7 @@ */ /* size of buffer/# of bytes to xfer at a time when copying userblock */ -#define USERBLOCK_XFER_SIZE 512 +#define USERBLOCK_XFER_SIZE 512 /* check H5Dread()/H5Dwrite() error, e.g. memory allocation error inside the library. */ #define CHECK_H5DRW_ERROR(_fun, _fail, _did, _mtid, _msid, _fsid, _pid, _buf) { \ @@ -54,12 +52,12 @@ *------------------------------------------------------------------------- */ static int Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[], - size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p); + size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p); static void print_dataset_info(hid_t dcpl_id, char *objname, double per, int pr); static int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, - pack_opt_t *options); + pack_opt_t *options); static int copy_user_block(const char *infile, const char *outfile, - hsize_t size); + hsize_t size); #if defined (H5REPACK_DEBUG_USER_BLOCK) static void print_user_block(const char *filename, hid_t fid); #endif @@ -67,18 +65,19 @@ static herr_t walk_error_callback(unsigned n, const H5E_error2_t *err_desc, void /* get the major number from the error stack. */ static herr_t walk_error_callback(H5_ATTR_UNUSED unsigned n, const H5E_error2_t *err_desc, void *udata) { - if (err_desc) - *((hid_t *) udata) = err_desc->maj_num; + if (err_desc) + *((hid_t *) udata) = err_desc->maj_num; - return 0; + return 0; } /*------------------------------------------------------------------------- * Function: copy_objects * - * Purpose: duplicate all HDF5 objects in the file + * Purpose: duplicate all HDF5 objects in the file * - * Return: 0, ok, -1 no + * Return: 0, ok, + * -1 no * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * @@ -89,21 +88,22 @@ static herr_t walk_error_callback(H5_ATTR_UNUSED unsigned n, const H5E_error2_t int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options) { - int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ + int ret_value = 0; /* no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ hid_t fidin; hid_t fidout = -1; trav_table_t *travt = NULL; - hsize_t ub_size = 0; /* size of user block */ - hid_t fcpl = H5P_DEFAULT; /* file creation property list ID */ - hid_t fapl = H5P_DEFAULT; /* file access property list ID */ - H5F_fspace_strategy_t set_strategy; /* Strategy to be set in outupt file */ - hbool_t set_persist; /* Persist free-space status to be set in output file */ - hsize_t set_threshold; /* Free-space section threshold to be set in output file */ - hsize_t set_pagesize; /* File space page size to be set in output file */ - H5F_fspace_strategy_t in_strategy; /* Strategy from input file */ - hbool_t in_persist; /* Persist free-space status from input file */ - hsize_t in_threshold; /* Free-space section threshold from input file */ - hsize_t in_pagesize; /* File space page size from input file */ + hsize_t ub_size = 0; /* size of user block */ + hid_t fcpl = H5P_DEFAULT; /* file creation property list ID */ + hid_t fapl = H5P_DEFAULT; /* file access property list ID */ + H5F_fspace_strategy_t set_strategy; /* Strategy to be set in outupt file */ + hbool_t set_persist; /* Persist free-space status to be set in output file */ + hsize_t set_threshold; /* Free-space section threshold to be set in output file */ + hsize_t set_pagesize; /* File space page size to be set in output file */ + H5F_fspace_strategy_t in_strategy; /* Strategy from input file */ + hbool_t in_persist; /* Persist free-space status from input file */ + hsize_t in_threshold; /* Free-space section threshold from input file */ + hsize_t in_pagesize; /* File space page size from input file */ + unsigned crt_order_flags; /* group creation order flag */ /*------------------------------------------------------------------------- * open input file @@ -117,6 +117,8 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options) /* get user block size and file space strategy/persist/threshold */ { hid_t fcpl_in; /* file creation property list ID for input file */ + hid_t grp_in = -1; /* group ID */ + hid_t gcpl_in = -1; /* group creation property list */ if ((fcpl_in = H5Fget_create_plist(fidin)) < 0) { error_msg("failed to retrieve file creation property list\n"); @@ -128,17 +130,28 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); } - /* If the -S option is not set, get "strategy" from the input file */ - if(H5Pget_file_space_strategy(fcpl_in, &in_strategy, &in_persist, &in_threshold) < 0) { - error_msg("failed to retrieve file space strategy\n"); + /* If the -S option is not set, get "strategy" from the input file */ + if(H5Pget_file_space_strategy(fcpl_in, &in_strategy, &in_persist, &in_threshold) < 0) { + error_msg("failed to retrieve file space strategy\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + + /* If the -G option is not set, get "pagesize" from the input file */ + if(H5Pget_file_space_page_size(fcpl_in, &in_pagesize) < 0) { + error_msg("failed to retrieve file space threshold\n"); HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); } + /* open root group */ + if ((grp_in = H5Gopen2(fidin, "/", H5P_DEFAULT)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed"); - /* If the -G option is not set, get "pagesize" from the input file */ - if(H5Pget_file_space_page_size(fcpl_in, &in_pagesize) < 0) { - error_msg("failed to retrieve file space threshold\n"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); - } + /* get root group creation property list */ + if ((gcpl_in = H5Gget_create_plist(grp_in)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gget_create_plist failed"); + + /* query and set the group creation properties */ + if (H5Pget_link_creation_order(gcpl_in, &crt_order_flags) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_link_creation_order failed"); if (H5Pclose(fcpl_in) < 0) { error_msg("failed to close property list\n"); @@ -297,9 +310,9 @@ print_user_block(fnamein, fidin); } /*------------------------------------------------------------------------- - * Set file space information - *------------------------------------------------------------------------- - */ + * Set file space information + *------------------------------------------------------------------------- + */ /* either use the FCPL already created or create a new one */ if (fcpl == H5P_DEFAULT) { @@ -310,6 +323,9 @@ print_user_block(fnamein, fidin); } } + if(H5Pset_link_creation_order(fcpl, crt_order_flags ) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_link_creation_order failed"); + /* Set file space info to those from input file */ set_strategy = in_strategy; set_persist = in_persist; @@ -325,7 +341,7 @@ print_user_block(fnamein, fidin); set_persist = FS_PERSIST_DEF; else if(options->fs_persist != 0) /* Set "persist" as specified by user */ set_persist = (hbool_t)options->fs_persist; - + if(options->fs_threshold == -1) /* A "0" threshold is specified by user */ set_threshold = (hsize_t)0; else if(options->fs_threshold != 0) /* Set threshold as specified by user */ @@ -333,7 +349,7 @@ print_user_block(fnamein, fidin); /* Set file space information as specified */ if(H5Pset_file_space_strategy(fcpl, set_strategy, set_persist, set_threshold) < 0) { - error_msg("failed to set file space strategy\n"); + error_msg("failed to set file space strategy\n"); HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); } @@ -345,7 +361,7 @@ print_user_block(fnamein, fidin); if(set_pagesize != FS_PAGESIZE_DEF) /* Set non-default file space page size as specified */ if(H5Pset_file_space_page_size(fcpl, set_pagesize) < 0) { error_msg("failed to set file space page size\n"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); } /*------------------------------------------------------------------------- @@ -376,6 +392,8 @@ print_user_block(fnamein, fidin); *------------------------------------------------------------------------- */ + /* Initialize indexing options */ + h5trav_set_index(sort_by, sort_order); /* init table */ trav_table_init(&travt); @@ -492,10 +510,10 @@ done: int Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[], size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p) { - int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ - int k; + int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ + int k; H5D_layout_t dset_layout; - int rank_chunk; + int rank_chunk; hsize_t dims_chunk[H5S_MAX_RANK]; hsize_t size_chunk = 1; hsize_t nchunk_fit; /* number of chunks that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */ @@ -707,36 +725,36 @@ done: */ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, - pack_opt_t *options) /* repack options */ + pack_opt_t *options) /* repack options */ { int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ - hid_t grp_in = -1; /* group ID */ - hid_t grp_out = -1; /* group ID */ - hid_t dset_in = -1; /* read dataset ID */ + hid_t grp_in = -1; /* group ID */ + hid_t grp_out = -1; /* group ID */ + hid_t dset_in = -1; /* read dataset ID */ hid_t dset_out = -1; /* write dataset ID */ - hid_t gcpl_in = -1; /* group creation property list */ + hid_t gcpl_in = -1; /* group creation property list */ hid_t gcpl_out = -1; /* group creation property list */ - hid_t type_in = -1; /* named type ID */ + hid_t type_in = -1; /* named type ID */ hid_t type_out = -1; /* named type ID */ - hid_t dcpl_in = -1; /* dataset creation property list ID */ + hid_t dcpl_in = -1; /* dataset creation property list ID */ hid_t dcpl_out = -1; /* dataset creation property list ID */ hid_t f_space_id = -1; /* file space ID */ hid_t ftype_id = -1; /* file type ID */ hid_t wtype_id = -1; /* read/write type ID */ named_dt_t *named_dt_head = NULL; /* Pointer to the stack of named datatypes copied */ - size_t msize; /* size of type */ - hsize_t nelmts; /* number of elements in dataset */ + size_t msize; /* size of type */ + hsize_t nelmts; /* number of elements in dataset */ H5D_space_status_t space_status; /* determines whether space has been allocated for the dataset */ - int rank; /* rank of dataset */ + int rank; /* rank of dataset */ hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */ - hsize_t dsize_in; /* input dataset size before filter */ - hsize_t dsize_out; /* output dataset size after filter */ - int apply_s; /* flag for apply filter to small dataset sizes */ - int apply_f; /* flag for apply filter to return error on H5Dcreate */ - void *buf = NULL; /* buffer for raw data */ + hsize_t dsize_in; /* input dataset size before filter */ + hsize_t dsize_out; /* output dataset size after filter */ + int apply_s; /* flag for apply filter to small dataset sizes */ + int apply_f; /* flag for apply filter to return error on H5Dcreate */ + void *buf = NULL; /* buffer for raw data */ void *hslab_buf = NULL; /* hyperslab buffer for raw data */ - int has_filter; /* current object has a filter */ - int req_filter; /* there was a request for a filter */ + int has_filter; /* current object has a filter */ + int req_filter; /* there was a request for a filter */ int req_obj_layout = 0; /* request layout to current object */ unsigned crt_order_flags; /* group creation order flag */ unsigned i; @@ -917,7 +935,7 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, /* wtype_id will have already been set if using a named dtype */ if (!is_named) { if (options->use_native == 1) - wtype_id = h5tools_get_native_type(ftype_id); + wtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT); else wtype_id = H5Tcopy(ftype_id); } /* end if */ @@ -1351,20 +1369,19 @@ done: * *------------------------------------------------------------------------- */ -static void print_dataset_info(hid_t dcpl_id, char *objname, double ratio, - int pr) +static void print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr) { - char strfilter[255]; + char strfilter[255]; #if defined (PRINT_DEBUG ) - char temp[255]; + char temp[255]; #endif - int nfilters; /* number of filters */ - unsigned filt_flags; /* filter flags */ - H5Z_filter_t filtn; /* filter identification number */ - unsigned cd_values[20]; /* filter client data values */ - size_t cd_nelmts; /* filter client number of values */ - char f_objname[256]; /* filter objname */ - int i; + int nfilters; /* number of filters */ + unsigned filt_flags; /* filter flags */ + H5Z_filter_t filtn; /* filter identification number */ + unsigned cd_values[20]; /* filter client data values */ + size_t cd_nelmts; /* filter client number of values */ + char f_objname[256]; /* filter objname */ + int i; HDstrcpy(strfilter, "\0"); @@ -1463,19 +1480,18 @@ static void print_dataset_info(hid_t dcpl_id, char *objname, double ratio, * *------------------------------------------------------------------------- */ -static int copy_user_block(const char *infile, const char *outfile, - hsize_t size) +static int copy_user_block(const char *infile, const char *outfile, hsize_t size) { - int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ + int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ int infid = -1, outfid = -1; /* File descriptors */ /* User block must be any power of 2 equal to 512 or greater (512, 1024, 2048, etc.) */ HDassert(size > 0); /* Open files */ - if ((infid = HDopen(infile, O_RDONLY, 0)) < 0) + if ((infid = HDopen(infile, O_RDONLY)) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDopen failed"); - if ((outfid = HDopen(outfile, O_WRONLY, 0644)) < 0) + if ((outfid = HDopen(outfile, O_WRONLY)) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDopen failed"); /* Copy the userblock from the input file to the output file */ @@ -1543,67 +1559,68 @@ done: static void print_user_block(const char *filename, hid_t fid) { - int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ - int fh; /* file handle */ - hsize_t ub_size; /* user block size */ - hsize_t size; /* size read */ - hid_t fcpl; /* file creation property list ID for HDF5 file */ - int i; - - /* get user block size */ - if(( fcpl = H5Fget_create_plist(fid)) < 0) { - error_msg("failed to retrieve file creation property list\n"); + int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ + int fh; /* file handle */ + hsize_t ub_size; /* user block size */ + hsize_t size; /* size read */ + hid_t fcpl; /* file creation property list ID for HDF5 file */ + int i; + + /* get user block size */ + if(( fcpl = H5Fget_create_plist(fid)) < 0) { + error_msg("failed to retrieve file creation property list\n"); HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Fget_create_plist failed"); } - if(H5Pget_userblock(fcpl, &ub_size) < 0) { - error_msg("failed to retrieve userblock size\n"); + if(H5Pget_userblock(fcpl, &ub_size) < 0) { + error_msg("failed to retrieve userblock size\n"); HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pget_userblock failed"); } - if(H5Pclose(fcpl) < 0) { - error_msg("failed to close property list\n"); + if(H5Pclose(fcpl) < 0) { + error_msg("failed to close property list\n"); HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed"); } - /* open file */ - if((fh = HDopen(filename, O_RDONLY, 0)) < 0) { + /* open file */ + if((fh = HDopen(filename, O_RDONLY)) < 0) { + error_msg("failed to open file\n"); HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "HDopen failed"); } - size = ub_size; + size = ub_size; - /* read file */ - while(size > 0) { - ssize_t nread; /* # of bytes read */ - char rbuf[USERBLOCK_XFER_SIZE]; /* buffer for reading */ + /* read file */ + while(size > 0) { + ssize_t nread; /* # of bytes read */ + char rbuf[USERBLOCK_XFER_SIZE]; /* buffer for reading */ - /* read buffer */ - if(size > USERBLOCK_XFER_SIZE) - nread = HDread(fh, rbuf, (size_t)USERBLOCK_XFER_SIZE); - else - nread = HDread(fh, rbuf, (size_t)size); + /* read buffer */ + if(size > USERBLOCK_XFER_SIZE) + nread = HDread(fh, rbuf, (size_t)USERBLOCK_XFER_SIZE); + else + nread = HDread(fh, rbuf, (size_t)size); - for(i = 0; i < nread; i++) { + for(i = 0; i < nread; i++) { - printf("%c ", rbuf[i]); + printf("%c ", rbuf[i]); - } - printf("\n"); + } + printf("\n"); - if(nread < 0) { + if(nread < 0) { HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "nread < 0"); } - /* update size of userblock left to transfer */ - size -= nread; - } + /* update size of userblock left to transfer */ + size -= nread; + } done: - if(fh > 0) - HDclose(fh); + if(fh > 0) + HDclose(fh); - return; + return; } #endif diff --git a/tools/src/h5repack/h5repack_filters.c b/tools/src/h5repack/h5repack_filters.c index e21b829..804727b 100644 --- a/tools/src/h5repack/h5repack_filters.c +++ b/tools/src/h5repack/h5repack_filters.c @@ -5,12 +5,10 @@ * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * - * the files COPYING and Copyright.html. COPYING can be found at the root * - * of the source code distribution tree; Copyright.html can be found at the * - * root level of an installed copy of the electronic HDF5 document set and * - * is linked from the top-level documents page. It can also be found at * - * http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have * - * access to either file, you may request a copy from help@hdfgroup.org. * + * the COPYING file, which can be found at the root of the source code * + * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * If you do not have access to either file, you may request a copy from * + * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #include "h5repack.h" diff --git a/tools/src/h5repack/h5repack_main.c b/tools/src/h5repack/h5repack_main.c index 07c2b7d..31b1e14 100644 --- a/tools/src/h5repack/h5repack_main.c +++ b/tools/src/h5repack/h5repack_main.c @@ -5,12 +5,10 @@ * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * - * the files COPYING and Copyright.html. COPYING can be found at the root * - * of the source code distribution tree; Copyright.html can be found at the * - * root level of an installed copy of the electronic HDF5 document set and * - * is linked from the top-level documents page. It can also be found at * - * http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have * - * access to either file, you may request a copy from help@hdfgroup.org. * + * the COPYING file, which can be found at the root of the source code * + * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * If you do not have access to either file, you may request a copy from * + * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #include "h5tools.h" @@ -33,7 +31,7 @@ const char *outfile = NULL; * Command-line options: The user can specify short or long-named * parameters. */ -static const char *s_opts = "hVvf:l:m:e:nLc:d:s:u:b:M:t:a:i:o:S:P:T:G:E"; +static const char *s_opts = "hVvf:l:m:e:nLc:d:s:u:b:M:t:a:i:o:S:P:T:G:q:z:E"; static struct long_options l_opts[] = { { "help", no_arg, 'h' }, { "version", no_arg, 'V' }, @@ -58,6 +56,8 @@ static struct long_options l_opts[] = { { "fs_persist", require_arg, 'P' }, { "fs_threshold", require_arg, 'T' }, { "fs_pagesize", require_arg, 'G' }, + { "sort_by", require_arg, 'q' }, + { "sort_order", require_arg, 'z' }, { "enable-error-stack", no_arg, 'E' }, { NULL, 0, '\0' } }; @@ -92,6 +92,8 @@ static void usage(const char *prog) { PRINTVALSTREAM(rawoutstream, " -M A, --metadata_block_size=A Metadata block size for H5Pset_meta_block_size\n"); PRINTVALSTREAM(rawoutstream, " -t T, --threshold=T Threshold value for H5Pset_alignment\n"); PRINTVALSTREAM(rawoutstream, " -a A, --alignment=A Alignment value for H5Pset_alignment\n"); + PRINTVALSTREAM(rawoutstream, " -q Q, --sort_by=Q Sort groups and attributes by index Q\n"); + PRINTVALSTREAM(rawoutstream, " -z Z, --sort_order=Z Sort groups and attributes by order Z\n"); PRINTVALSTREAM(rawoutstream, " -f FILT, --filter=FILT Filter type\n"); PRINTVALSTREAM(rawoutstream, " -l LAYT, --layout=LAYT Layout type\n"); PRINTVALSTREAM(rawoutstream, " -S FS_STRATEGY, --fs_strategy=FS_STRATEGY File space management strategy for H5Pset_file_space_strategy\n"); @@ -105,6 +107,8 @@ static void usage(const char *prog) { PRINTVALSTREAM(rawoutstream, " U - is a filename.\n"); PRINTVALSTREAM(rawoutstream, " T - is an integer\n"); PRINTVALSTREAM(rawoutstream, " A - is an integer greater than zero\n"); + PRINTVALSTREAM(rawoutstream, " Q - is the sort index type for the input file. It can be \"name\" or \"creation_order\" (default)\n"); + PRINTVALSTREAM(rawoutstream, " Z - is the sort order type for the input file. It can be \"descending\" or \"ascending\" (default)\n"); PRINTVALSTREAM(rawoutstream, " B - is the user block size, any value that is 512 or greater and is\n"); PRINTVALSTREAM(rawoutstream, " a power of 2 (1024 default)\n"); PRINTVALSTREAM(rawoutstream, " F - is the shared object header message type, any of <dspace|dtype|fill|\n"); @@ -372,6 +376,52 @@ done: } /*------------------------------------------------------------------------- + * 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")==0) /* H5_INDEX_NAME */ + idx_type = H5_INDEX_NAME; + else if (HDstrcmp(form,"creation_order")==0) /* H5_INDEX_CRT_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")==0) /* H5_ITER_INC */ + iter_order = H5_ITER_INC; + else if (HDstrcmp(form,"descending")==0) /* H5_ITER_DEC */ + iter_order = H5_ITER_DEC; + + return iter_order; +} + +/*------------------------------------------------------------------------- * Function: parse_command_line * * Purpose: parse command line input @@ -555,14 +605,14 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options) break; case 'P': - options->fs_persist = HDatoi( opt_arg ); + 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 ); + options->fs_threshold = HDatol(opt_arg); if(options->fs_threshold == 0) /* To distinguish the "specified" zero value */ options->fs_threshold = -1; @@ -572,12 +622,30 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options) options->fs_pagesize = HDstrtoll(opt_arg, NULL, 0); if(options->fs_pagesize == 0) /* To distinguish the "specified" zero value */ - options->fs_pagesize = -1; + options->fs_pagesize = -1; break; - case 'E': - enable_error_stack = TRUE; - break; + case 'q': + if((sort_by = set_sort_by(opt_arg)) < 0) { + 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((sort_order = set_sort_order(opt_arg)) < 0) { + error_msg(" failed to set sort order form <%s>\n", opt_arg); + h5tools_setstatus(EXIT_FAILURE); + ret_value = -1; + goto done; + } + break; + + case 'E': + enable_error_stack = TRUE; + break; default: break; @@ -646,6 +714,9 @@ int main(int argc, const char **argv) /* initialize options */ h5repack_init(&options, 0, FALSE); + /* Initialize default indexing options */ + sort_by = H5_INDEX_CRT_ORDER; + if (parse_command_line(argc, argv, &options) < 0) goto done; diff --git a/tools/src/h5repack/h5repack_opttable.c b/tools/src/h5repack/h5repack_opttable.c index 8c98b76..93e34b3 100644 --- a/tools/src/h5repack/h5repack_opttable.c +++ b/tools/src/h5repack/h5repack_opttable.c @@ -5,12 +5,10 @@ * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * - * the files COPYING and Copyright.html. COPYING can be found at the root * - * of the source code distribution tree; Copyright.html can be found at the * - * root level of an installed copy of the electronic HDF5 document set and * - * is linked from the top-level documents page. It can also be found at * - * http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have * - * access to either file, you may request a copy from help@hdfgroup.org. * + * the COPYING file, which can be found at the root of the source code * + * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * If you do not have access to either file, you may request a copy from * + * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #include "h5repack.h" diff --git a/tools/src/h5repack/h5repack_parse.c b/tools/src/h5repack/h5repack_parse.c index 6759169..a9a890d 100644 --- a/tools/src/h5repack/h5repack_parse.c +++ b/tools/src/h5repack/h5repack_parse.c @@ -5,12 +5,10 @@ * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * - * the files COPYING and Copyright.html. COPYING can be found at the root * - * of the source code distribution tree; Copyright.html can be found at the * - * root level of an installed copy of the electronic HDF5 document set and * - * is linked from the top-level documents page. It can also be found at * - * http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have * - * access to either file, you may request a copy from help@hdfgroup.org. * + * the COPYING file, which can be found at the root of the source code * + * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * If you do not have access to either file, you may request a copy from * + * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #include "h5repack.h" diff --git a/tools/src/h5repack/h5repack_refs.c b/tools/src/h5repack/h5repack_refs.c index f0f32c3..408142c 100644 --- a/tools/src/h5repack/h5repack_refs.c +++ b/tools/src/h5repack/h5repack_refs.c @@ -5,12 +5,10 @@ * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * - * the files COPYING and Copyright.html. COPYING can be found at the root * - * of the source code distribution tree; Copyright.html can be found at the * - * root level of an installed copy of the electronic HDF5 document set and * - * is linked from the top-level documents page. It can also be found at * - * http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have * - * access to either file, you may request a copy from help@hdfgroup.org. * + * the COPYING file, which can be found at the root of the source code * + * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * If you do not have access to either file, you may request a copy from * + * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #include "h5repack.h" @@ -27,7 +25,7 @@ static const char* MapIdToName(hid_t refobj_id,trav_table_t *travt); static int copy_refs_attr(hid_t loc_in, hid_t loc_out, pack_opt_t *options, trav_table_t *travt, hid_t fidout); static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in, - hid_t fid_out, void *ref_out, trav_table_t *travt); + hid_t fid_out, void *ref_out, trav_table_t *travt); /*------------------------------------------------------------------------- * Function: do_copy_refobjs @@ -128,8 +126,8 @@ int do_copy_refobjs(hid_t fidin, for(k = 0; k < rank; k++) nelmts *= dims[k]; - if((mtype_id = h5tools_get_native_type(ftype_id)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5tools_get_native_type failed"); + if((mtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_native_type failed"); if((msize = H5Tget_size(mtype_id)) == 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed"); @@ -427,13 +425,13 @@ done: * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Modifier: xcao@hdfgroup.org, 9/12/2011 - * Update values of references(object and region) for the following types: + * Update values of references(object and region) for the following types: * 1) References, * 2) ARRAY of reference, * 3) VLEN of references. * 4) COMPOUND of references. * This function does not handle references in other complicated structures, - * such as references in nested compound datatypes. + * such as references in nested compound datatypes. * * Date: October, 28, 2003 * @@ -474,7 +472,7 @@ static int copy_refs_attr(hid_t loc_in, HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Oget_info failed"); for(u = 0; u < (unsigned)oinfo.num_attrs; u++) { - is_ref = is_ref_vlen = is_ref_array = is_ref_comp = 0; + is_ref = is_ref_vlen = is_ref_array = is_ref_comp = 0; /* open attribute */ if((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)u, H5P_DEFAULT, H5P_DEFAULT)) < 0) @@ -486,8 +484,8 @@ static int copy_refs_attr(hid_t loc_in, type_class = H5Tget_class(ftype_id); - if((mtype_id = h5tools_get_native_type(ftype_id)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5tools_get_native_type failed"); + if((mtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_native_type failed"); if((msize = H5Tget_size(mtype_id)) == 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed"); @@ -530,9 +528,9 @@ static int copy_refs_attr(hid_t loc_in, } H5Tclose(mtid); } - - /* if compound don't contain reference type member, free the above - * mallocs. Otherwise there can be memory leaks by the 'continue' + + /* if compound don't contain reference type member, free the above + * mallocs. Otherwise there can be memory leaks by the 'continue' * statement below. */ if (!ref_comp_field_n) { if (ref_comp_index) { @@ -541,7 +539,7 @@ static int copy_refs_attr(hid_t loc_in, } if (ref_comp_size) { - HDfree(ref_comp_size); + HDfree(ref_comp_size); ref_comp_size = NULL; } } @@ -590,7 +588,7 @@ static int copy_refs_attr(hid_t loc_in, array_rank = (unsigned)H5Tget_array_ndims(mtype_id); H5Tget_array_dims2(mtype_id, array_dims); for(j = 0; j <array_rank; j++) - array_size *= array_dims[j]; + array_size *= array_dims[j]; nelmts *= array_size; } @@ -650,7 +648,7 @@ static int copy_refs_attr(hid_t loc_in, } } /* H5T_STD_REF_DSETREG */ else if (is_ref_vlen) { - /* handle VLEN of references */ + /* handle VLEN of references */ buf = (hvl_t *)HDmalloc((unsigned)(nelmts * sizeof(hvl_t))); refbuf = buf; /* reuse the read buffer for write */ @@ -690,7 +688,7 @@ static int copy_refs_attr(hid_t loc_in, } } /* else if (is_ref_vlen) */ else if (is_ref_comp) { - /* handle ref fields in a compound */ + /* handle ref fields in a compound */ buf = HDmalloc((unsigned)(nelmts * msize)); refbuf = buf; /* reuse the read buffer for write */ @@ -730,7 +728,7 @@ static int copy_refs_attr(hid_t loc_in, HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Awrite failed"); if (is_ref_vlen && buf) - H5Dvlen_reclaim (mtype_id, space_id, H5P_DEFAULT, buf); + H5Dvlen_reclaim (mtype_id, space_id, H5P_DEFAULT, buf); } /* if (nelmts) */ if (refbuf == buf) @@ -782,10 +780,10 @@ done: HDfree(buf); if (ref_comp_index) - HDfree(ref_comp_index); + HDfree(ref_comp_index); if (ref_comp_size) - HDfree(ref_comp_size); + HDfree(ref_comp_size); H5E_BEGIN_TRY { H5Tclose(ftype_id); @@ -799,9 +797,9 @@ done: } /*------------------------------------------------------------------------- - * Function: MapIdToName + * Function: MapIdToName * - * Purpose: map a ID from a reference to a dataset name + * Purpose: map a ID from a reference to a dataset name * *------------------------------------------------------------------------- */ @@ -834,16 +832,16 @@ out: } /*------------------------------------------------------------------------- - * Function: Update_Ref_value + * Function: Update_Ref_value * - * Purpose: Update a reference value + * Purpose: Update a reference value * * Programmer: xcao@hdfgroup.org 9/12/2011 * *------------------------------------------------------------------------- */ static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in, - hid_t fid_out, void *ref_out, trav_table_t *travt) + hid_t fid_out, void *ref_out, trav_table_t *travt) { int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ const char* ref_obj_name; diff --git a/tools/src/h5repack/h5repack_verify.c b/tools/src/h5repack/h5repack_verify.c index 1022d7a..1a0dab7 100644 --- a/tools/src/h5repack/h5repack_verify.c +++ b/tools/src/h5repack/h5repack_verify.c @@ -5,12 +5,10 @@ * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * - * the files COPYING and Copyright.html. COPYING can be found at the root * - * of the source code distribution tree; Copyright.html can be found at the * - * root level of an installed copy of the electronic HDF5 document set and * - * is linked from the top-level documents page. It can also be found at * - * http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have * - * access to either file, you may request a copy from help@hdfgroup.org. * + * the COPYING file, which can be found at the root of the source code * + * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * If you do not have access to either file, you may request a copy from * + * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #include "h5repack.h" @@ -57,11 +55,11 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options trav_table_t *travt = NULL; int ok = 1; hid_t fcpl_in = -1; /* file creation property for input file */ - hid_t fcpl_out = -1; /* file creation property for output file */ - H5F_fspace_strategy_t in_strategy, out_strategy; /* file space handling strategy for in/output file */ - hbool_t in_persist, out_persist; /* free-space persist status for in/output file */ - hsize_t in_threshold, out_threshold; /* free-space section threshold for in/output file */ - hsize_t in_pagesize, out_pagesize; /* file space page size for input/output file */ + hid_t fcpl_out = -1; /* file creation property for output file */ + H5F_fspace_strategy_t in_strategy, out_strategy; /* file space handling strategy for in/output file */ + hbool_t in_persist, out_persist; /* free-space persist status for in/output file */ + hsize_t in_threshold, out_threshold; /* free-space section threshold for in/output file */ + hsize_t in_pagesize, out_pagesize; /* file space page size for input/output file */ /* open the output file */ if((fidout = H5Fopen(out_fname, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0 ) @@ -124,6 +122,8 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options if(options->all_filter == 1 || options->all_layout == 1) { + /* Initialize indexing options */ + h5trav_set_index(sort_by, sort_order); /* init table */ trav_table_init(&travt); @@ -249,7 +249,7 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options * the same as the input file's strategy. */ if(options->fs_strategy) { - if(out_strategy != (options->fs_strategy == (-1) ? 0 : options->fs_strategy)) { + if(out_strategy != (options->fs_strategy == (H5F_fspace_strategy_t)-1 ? 0 : options->fs_strategy)) { error_msg("file space strategy not set as unexpected\n"); HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "file space strategy not set as unexpected"); } @@ -457,6 +457,9 @@ int h5repack_cmp_pl(const char *fname1, * get file table list of objects *------------------------------------------------------------------------- */ + /* Initialize indexing options */ + h5trav_set_index(sort_by, sort_order); + /* init table */ trav_table_init(&trav); if(h5trav_gettable(fid1, trav) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5trav_gettable failed"); @@ -645,7 +648,7 @@ int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter) { case H5Z_FILTER_NONE: - break; + break; case H5Z_FILTER_SHUFFLE: /* 1 private client value is returned by DCPL */ |