diff options
| -rw-r--r-- | tools/h5repack/h5repack.c | 546 | ||||
| -rw-r--r-- | tools/h5repack/h5repack_copy.c | 2513 | ||||
| -rw-r--r-- | tools/h5repack/h5repack_filters.c | 14 | ||||
| -rw-r--r-- | tools/h5repack/h5repack_main.c | 402 | ||||
| -rw-r--r-- | tools/h5repack/h5repack_plugin.sh.in | 2 | ||||
| -rw-r--r-- | tools/h5repack/h5repack_refs.c | 256 | ||||
| -rw-r--r-- | tools/h5repack/h5repack_verify.c | 247 | ||||
| -rw-r--r-- | tools/h5repack/h5repacktst.c | 200 | ||||
| -rw-r--r-- | tools/h5repack/testfiles/h5repack_filters.h5-gzip_verbose_filters.tst | 13 |
9 files changed, 2064 insertions, 2129 deletions
diff --git a/tools/h5repack/h5repack.c b/tools/h5repack/h5repack.c index 8a9090a..3f99374 100644 --- a/tools/h5repack/h5repack.c +++ b/tools/h5repack/h5repack.c @@ -118,35 +118,36 @@ 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 */ - int 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))) - return -1; - - /* if it applies to all objects */ - if (is_glb) { - int n; - - n = options->n_filter_g++; /* increase # of global filters */ - - if (options->n_filter_g > H5_REPACK_MAX_NFILTERS) { - error_msg("maximum number of filters exceeded for <%s>\n", str); - HDfree(obj_list); - return -1; - } - - options->filter_g[n] = filter; - } - else - options_add_filter(obj_list, n_objs, filter, options->op_tbl); - - HDfree(obj_list); - return 0; +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 */ + + /* parse the -f option */ + if (NULL == (obj_list = parse_filter(str, &n_objs, &filter, options, &is_glb))) + return -1; + + /* if it applies to all objects */ + if (is_glb) { + int n; + + n = options->n_filter_g++; /* increase # of global filters */ + if (options->n_filter_g > H5_REPACK_MAX_NFILTERS) { + error_msg("maximum number of filters exceeded for <%s>\n", str); + HDfree(obj_list); + return -1; + } + + options->filter_g[n] = filter; + } + else + options_add_filter(obj_list, n_objs, filter, options->op_tbl); + + HDfree(obj_list); + return 0; } /*------------------------------------------------------------------------- @@ -158,59 +159,53 @@ int h5repack_addfilter(const char* str, pack_opt_t *options) { * *------------------------------------------------------------------------- */ - -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 */ - int 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); - - if (options->all_layout == 1) { - error_msg( - "invalid layout input: 'all' option \ - is present with other objects <%s>\n", - str); - return ret_value; - } - - /* parse the layout option */ - obj_list = parse_layout(str, &n_objs, &pack, options); - if (obj_list) { - - /* set layout option */ - options->layout_g = pack.layout; - - /* no individual dataset specified */ - if (options->all_layout == 1) { - if (pack.layout == H5D_CHUNKED) { - /* -2 means the NONE option, remove chunking - and set the global layout to contiguous */ - if (pack.chunk.rank == -2) { - options->layout_g = H5D_CONTIGUOUS; - } - /* otherwise set the global chunking type */ - else { - options->chunk_g.rank = pack.chunk.rank; - for (j = 0; j < pack.chunk.rank; j++) - options->chunk_g.chunk_lengths[j] = - pack.chunk.chunk_lengths[j]; - } - } - } - - /* individual dataset specified */ - if (options->all_layout == 0) - ret_value = options_add_layout(obj_list, n_objs, &pack, options->op_tbl); - - HDfree(obj_list); - ret_value = 0; - } - - return ret_value; +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; + + init_packobject(&pack); + + if (options->all_layout == 1) { + error_msg( "invalid layout input: 'all' option is present with other objects <%s>\n", str); + return ret_value; + } + + /* parse the layout option */ + obj_list = parse_layout(str, &n_objs, &pack, options); + if (obj_list) { + /* set layout option */ + options->layout_g = pack.layout; + + /* no individual dataset specified */ + if (options->all_layout == 1) { + if (pack.layout == H5D_CHUNKED) { + /* -2 means the NONE option, remove chunking + and set the global layout to contiguous */ + if (pack.chunk.rank == -2) + options->layout_g = H5D_CONTIGUOUS; + /* otherwise set the global chunking type */ + else { + options->chunk_g.rank = pack.chunk.rank; + for (j = 0; j < pack.chunk.rank; j++) + options->chunk_g.chunk_lengths[j] = pack.chunk.chunk_lengths[j]; + } + } + } + + /* individual dataset specified */ + if (options->all_layout == 0) + ret_value = options_add_layout(obj_list, n_objs, &pack, options->op_tbl); + + HDfree(obj_list); + ret_value = 0; + } + + return ret_value; } /* Note: The below copy_named_datatype(), named_datatype_free(), copy_attr() @@ -366,200 +361,201 @@ 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) { - 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) - goto error; - - /*------------------------------------------------------------------------- - * copy all attributes - *------------------------------------------------------------------------- - */ - for (u = 0; u < (unsigned) oinfo.num_attrs; u++) { - /* open attribute */ - if ((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, - H5_ITER_INC, (hsize_t) u, H5P_DEFAULT, H5P_DEFAULT)) < 0) - goto error; - - /* get name */ - if (H5Aget_name(attr_id, (size_t) 255, name) < 0) - goto error; - - /* get the file datatype */ - if ((ftype_id = H5Aget_type(attr_id)) < 0) - goto error; - - /* Check if the datatype is committed */ - if ((is_named = H5Tcommitted(ftype_id)) < 0) - goto error; - if (is_named && travt) { - hid_t fidout; - - /* Create out file id */ - if ((fidout = H5Iget_file_id(loc_out)) < 0) - goto error; - - /* Copy named dt */ - if ((wtype_id = copy_named_datatype(ftype_id, fidout, - named_dt_head_p, travt, options)) < 0) { - H5Fclose(fidout); - goto error; - } /* end if */ - - if (H5Fclose(fidout) < 0) - goto error; - } /* end if */ - else { - if (options->use_native == 1) - wtype_id = h5tools_get_native_type(ftype_id); - else - wtype_id = H5Tcopy(ftype_id); - } /* end else */ - - /* get the dataspace handle */ - if ((space_id = H5Aget_space(attr_id)) < 0) - goto error; - - /* get dimensions */ - if ((rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0) - goto error; - - nelmts = 1; - for (j = 0; j < rank; j++) - nelmts *= dims[j]; - - if ((msize = H5Tget_size(wtype_id)) == 0) - goto error; - - /*------------------------------------------------------------------------- - * object references are a special case. We cannot just copy the buffers, - * but instead we recreate the reference. - * This is done on a second sweep of the file that just copies the referenced - * objects at copy_refs_attr() - *------------------------------------------------------------------------- - */ - type_class = H5Tget_class(wtype_id); - is_ref = (type_class == H5T_REFERENCE); - if (type_class == H5T_VLEN || type_class == H5T_ARRAY) { - hid_t base_type = -1; - base_type = H5Tget_super(ftype_id); - is_ref = (is_ref || (H5Tget_class(base_type) == H5T_REFERENCE)); - H5Tclose(base_type); - } +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) +{ + 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) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Oget_info failed"); + + /*------------------------------------------------------------------------- + * copy all attributes + *------------------------------------------------------------------------- + */ + for (u = 0; u < (unsigned) oinfo.num_attrs; u++) { + /* open attribute */ + if ((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t) u, H5P_DEFAULT, H5P_DEFAULT)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aopen_by_idx failed"); + + /* get name */ + if (H5Aget_name(attr_id, (size_t) 255, name) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + + /* get the file datatype */ + if ((ftype_id = H5Aget_type(attr_id)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aget_type failed"); + + /* Check if the datatype is committed */ + if ((is_named = H5Tcommitted(ftype_id)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tcommitted failed"); + if (is_named && travt) { + hid_t fidout; + + /* Create out file id */ + if ((fidout = H5Iget_file_id(loc_out)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Iget_file_id failed"); + + /* Copy named dt */ + if ((wtype_id = copy_named_datatype(ftype_id, fidout, named_dt_head_p, travt, options)) < 0) { + H5Fclose(fidout); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_named_datatype failed"); + } /* end if */ + + if (H5Fclose(fidout) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fclose failed"); + } /* end if */ + else { + if (options->use_native == 1) + wtype_id = h5tools_get_native_type(ftype_id); + else + wtype_id = H5Tcopy(ftype_id); + } /* end else */ + + /* get the dataspace handle */ + if ((space_id = H5Aget_space(attr_id)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aget_space failed"); + + /* get dimensions */ + if ((rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed"); + + nelmts = 1; + for (j = 0; j < rank; j++) + nelmts *= dims[j]; + + if ((msize = H5Tget_size(wtype_id)) == 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed"); + + /*------------------------------------------------------------------------- + * object references are a special case. We cannot just copy the buffers, + * but instead we recreate the reference. + * This is done on a second sweep of the file that just copies the referenced + * objects at copy_refs_attr() + *------------------------------------------------------------------------- + */ + type_class = H5Tget_class(wtype_id); + is_ref = (type_class == H5T_REFERENCE); + if (type_class == H5T_VLEN || type_class == H5T_ARRAY) { + hid_t base_type = -1; + + base_type = H5Tget_super(ftype_id); + is_ref = (is_ref || (H5Tget_class(base_type) == H5T_REFERENCE)); + H5Tclose(base_type); + } + + if (type_class == H5T_COMPOUND) { + int nmembers = H5Tget_nmembers(wtype_id); + + for (j = 0; j < nmembers; j++) { + hid_t mtid = H5Tget_member_type(wtype_id, (unsigned) j); + H5T_class_t mtclass = H5Tget_class(mtid); + H5Tclose(mtid); + + if (mtclass == H5T_REFERENCE) { + is_ref = 1; + break; + } + } /* for (j=0; i<nmembers; j++) */ + } /* if (type_class == H5T_COMPOUND) */ + + if (is_ref) { + ; /* handled by copy_refs_attr() */ + } + else { + /*------------------------------------------------------------------------- + * read to memory + *------------------------------------------------------------------------- + */ + + 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"); + } /* end if */ + if (H5Aread(attr_id, wtype_id, buf) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread failed"); + + /*------------------------------------------------------------------------- + * copy + *------------------------------------------------------------------------- + */ + + if ((attr_out = H5Acreate2(loc_out, name, wtype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Acreate2 failed"); + if (H5Awrite(attr_out, wtype_id, buf) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Awrite failed"); + + /*close*/ + if (H5Aclose(attr_out) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aclose failed"); + + /* Check if we have VL data and string in the attribute's datatype that must + * be reclaimed */ + if (TRUE == h5tools_detect_vlen(wtype_id)) + H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf); + HDfree(buf); + buf = NULL; + } /*H5T_REFERENCE*/ + + if (options->verbose) + printf(FORMAT_OBJ_ATTR, "attr", name); + + /*------------------------------------------------------------------------- + * close + *------------------------------------------------------------------------- + */ + + if (H5Tclose(ftype_id) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); + if (H5Tclose(wtype_id) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); + if (H5Sclose(space_id) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed"); + if (H5Aclose(attr_id) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aclose failed"); + } /* u */ + + return 0; - if (type_class == H5T_COMPOUND) { - int nmembers = H5Tget_nmembers(wtype_id); - for (j = 0; j < nmembers; j++) { - hid_t mtid = H5Tget_member_type(wtype_id, (unsigned) j); - H5T_class_t mtclass = H5Tget_class(mtid); - H5Tclose(mtid); - - if (mtclass == H5T_REFERENCE) { - is_ref = 1; - break; - } - } /* for (j=0; i<nmembers; j++) */ - } /* if (type_class == H5T_COMPOUND) */ - - if (is_ref) { - ; /* handled by copy_refs_attr() */ - } - else { - /*------------------------------------------------------------------------- - * read to memory - *------------------------------------------------------------------------- - */ - - buf = (void *) HDmalloc((size_t)(nelmts * msize)); - if (buf == NULL) { - error_msg("h5repack", "cannot read into memory\n"); - goto error; - } /* end if */ - if (H5Aread(attr_id, wtype_id, buf) < 0) - goto error; - - /*------------------------------------------------------------------------- - * copy - *------------------------------------------------------------------------- - */ - - if ((attr_out = H5Acreate2(loc_out, name, wtype_id, space_id, - H5P_DEFAULT, H5P_DEFAULT)) < 0) - goto error; - if (H5Awrite(attr_out, wtype_id, buf) < 0) - goto error; - - /*close*/ - if (H5Aclose(attr_out) < 0) - goto error; - - /* Check if we have VL data and string in the attribute's datatype that must - * be reclaimed */ - if (TRUE == h5tools_detect_vlen(wtype_id)) - H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf); - HDfree(buf); - buf = NULL; - } /*H5T_REFERENCE*/ - - if (options->verbose) - printf(FORMAT_OBJ_ATTR, "attr", name); - - /*------------------------------------------------------------------------- - * close - *------------------------------------------------------------------------- - */ - - if (H5Tclose(ftype_id) < 0) - goto error; - if (H5Tclose(wtype_id) < 0) - goto error; - if (H5Sclose(space_id) < 0) - goto error; - if (H5Aclose(attr_id) < 0) - goto error; - } /* u */ - - return 0; - -error: - H5E_BEGIN_TRY - { - if (buf) { - /* Check if we have VL data and string in the attribute's datatype that must - * be reclaimed */ - if (TRUE == h5tools_detect_vlen(wtype_id)) - H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf); - - /* Free buf */ - HDfree(buf); - } /* end if */ - - H5Tclose(ftype_id); - H5Tclose(wtype_id); - H5Sclose(space_id); - H5Aclose(attr_id); - H5Aclose(attr_out); - } H5E_END_TRY; - - return -1; +done: + H5E_BEGIN_TRY { + if (buf) { + /* Check if we have VL data and string in the attribute's datatype that must + * be reclaimed */ + if (TRUE == h5tools_detect_vlen(wtype_id)) + H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf); + + /* Free buf */ + HDfree(buf); + } /* end if */ + + H5Tclose(ftype_id); + H5Tclose(wtype_id); + H5Sclose(space_id); + H5Aclose(attr_id); + H5Aclose(attr_out); + } H5E_END_TRY; + + return ret_value; } /* end copy_attr() */ /*------------------------------------------------------------------------- diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c index 1963750..547f61a 100644 --- a/tools/h5repack/h5repack_copy.c +++ b/tools/h5repack/h5repack_copy.c @@ -36,7 +36,7 @@ #define USERBLOCK_XFER_SIZE 512 /* check H5Dread()/H5Dwrite() error, e.g. memory allocation error inside the library. */ -#define CHECK_H5DRW_ERROR(_fun, _did, _mtid, _msid, _fsid, _pid, _buf) { \ +#define CHECK_H5DRW_ERROR(_fun, _fail, _did, _mtid, _msid, _fsid, _pid, _buf) { \ H5E_BEGIN_TRY { \ if(_fun(_did, _mtid, _msid, _fsid, _pid, _buf) < 0) { \ hid_t _err_num = 0; \ @@ -44,7 +44,7 @@ H5Ewalk2(H5E_DEFAULT, H5E_WALK_DOWNWARD, walk_error_callback, &_err_num); \ H5Eget_msg(_err_num, NULL, _msg, (size_t)80); \ error_msg("%s %s -- %s\n", #_fun, "failed", _msg); \ - goto error; \ + HGOTO_DONE(_fail) \ } \ } H5E_END_TRY; \ } @@ -68,7 +68,7 @@ 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) - *((int *) udata) = err_desc->maj_num; + *((hid_t *) udata) = err_desc->maj_num; return 0; } @@ -97,306 +97,331 @@ 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) { - 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 */ - - /*------------------------------------------------------------------------- - * open input file - *------------------------------------------------------------------------- - */ - if ((fidin = h5tools_fopen(fnamein, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, - (size_t) 0)) < 0) { - error_msg("<%s>: %s\n", fnamein, H5FOPENERROR); - goto out; - } - - /* get user block size and file space strategy/threshold */ - { - hid_t fcpl_in; /* file creation property list ID for input file */ - - if ((fcpl_in = H5Fget_create_plist(fidin)) < 0) { - error_msg("failed to retrieve file creation property list\n"); - goto out; - } - - if (H5Pget_userblock(fcpl_in, &ub_size) < 0) { - error_msg("failed to retrieve userblock size\n"); - goto out; - } - - if (H5Pclose(fcpl_in) < 0) { - error_msg("failed to close property list\n"); - goto out; - } - } - - /* Check if we need to create a non-default file creation property list */ - if (options->latest || ub_size > 0) { - /* Create file creation property list */ - if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) { - error_msg("fail to create a file creation property list\n"); - goto out; - } - - if (ub_size > 0) { - if (H5Pset_userblock(fcpl, ub_size) < 0) { - error_msg("failed to set non-default userblock size\n"); - goto out; - } - } - - if (options->latest) { - unsigned i = 0, nindex = 0, mesg_type_flags[5], min_mesg_sizes[5]; - - /* Adjust group creation parameters for root group */ - /* (So that it is created in "dense storage" form) */ - if (H5Pset_link_phase_change(fcpl, (unsigned) options->grp_compact, - (unsigned) options->grp_indexed) < 0) { - error_msg( - "fail to adjust group creation parameters for root group\n"); - goto out; - } - - for (i = 0; i < 5; i++) { - if (options->msg_size[i] > 0) { - switch (i) { - case 0: - mesg_type_flags[nindex] = H5O_SHMESG_SDSPACE_FLAG; - break; - - case 1: - mesg_type_flags[nindex] = H5O_SHMESG_DTYPE_FLAG; - break; - - case 2: - mesg_type_flags[nindex] = H5O_SHMESG_FILL_FLAG; - break; - - case 3: - mesg_type_flags[nindex] = H5O_SHMESG_PLINE_FLAG; - break; - - case 4: - mesg_type_flags[nindex] = H5O_SHMESG_ATTR_FLAG; - break; - default: - break; - } /* end switch */ - min_mesg_sizes[nindex] = (unsigned) options->msg_size[i]; - - nindex++; - } /* end if */ - } /* end for */ - - if (nindex > 0) { - if (H5Pset_shared_mesg_nindexes(fcpl, nindex) < 0) { - error_msg( - "fail to set the number of shared object header message indexes\n"); - goto out; - } - - /* msg_size[0]=dataspace, 1=datatype, 2=file value, 3=filter pipleline, 4=attribute */ - for (i = 0; i < (nindex - 1); i++) { - if (H5Pset_shared_mesg_index(fcpl, i, mesg_type_flags[i], - min_mesg_sizes[i]) < 0) { - error_msg( - "fail to configure the specified shared object header message index\n"); - goto out; - } /* end if */ - } /* end for */ - } /* if (nindex>0) */ - - /* Create file access property list */ - if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) { - error_msg("Could not create file access property list\n"); - goto out; - } /* end if */ - - if (H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) { - error_msg( - "Could not set property for using latest version of the format\n"); - goto out; - } /* end if */ - } /* end if */ - } /* end if */ +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) */ + 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 */ + + /*------------------------------------------------------------------------- + * open input file + *------------------------------------------------------------------------- + */ + if ((fidin = h5tools_fopen(fnamein, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, (size_t) 0)) < 0) { + error_msg("<%s>: %s\n", fnamein, H5FOPENERROR); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + + /* get user block size and file space strategy/threshold */ + { + hid_t fcpl_in; /* file creation property list ID for input file */ + + if ((fcpl_in = H5Fget_create_plist(fidin)) < 0) { + error_msg("failed to retrieve file creation property list\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + + if (H5Pget_userblock(fcpl_in, &ub_size) < 0) { + error_msg("failed to retrieve userblock size\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + + if (!options->fs_strategy) { + if (H5Pget_file_space(fcpl_in, &options->fs_strategy, NULL) < 0) { + error_msg("failed to retrieve file space strategy\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + } + + if (!options->fs_threshold) { + if (H5Pget_file_space(fcpl_in, NULL, &options->fs_threshold) < 0) { + error_msg("failed to retrieve file space threshold\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + } + + if (H5Pclose(fcpl_in) < 0) { + error_msg("failed to close property list\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + } + + /* Check if we need to create a non-default file creation property list */ + if (options->latest || ub_size > 0) { + /* Create file creation property list */ + if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) { + error_msg("fail to create a file creation property list\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + + if (ub_size > 0) { + if (H5Pset_userblock(fcpl, ub_size) < 0) { + error_msg("failed to set non-default userblock size\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + } + + if (options->latest) { + unsigned i = 0, nindex = 0, mesg_type_flags[5], min_mesg_sizes[5]; + + /* Adjust group creation parameters for root group */ + /* (So that it is created in "dense storage" form) */ + if (H5Pset_link_phase_change(fcpl, (unsigned) options->grp_compact, + (unsigned) options->grp_indexed) < 0) { + error_msg("fail to adjust group creation parameters for root group\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + + for (i = 0; i < 5; i++) { + if (options->msg_size[i] > 0) { + switch (i) { + case 0: + mesg_type_flags[nindex] = H5O_SHMESG_SDSPACE_FLAG; + break; + + case 1: + mesg_type_flags[nindex] = H5O_SHMESG_DTYPE_FLAG; + break; + + case 2: + mesg_type_flags[nindex] = H5O_SHMESG_FILL_FLAG; + break; + + case 3: + mesg_type_flags[nindex] = H5O_SHMESG_PLINE_FLAG; + break; + + case 4: + mesg_type_flags[nindex] = H5O_SHMESG_ATTR_FLAG; + break; + + default: + break; + } /* end switch */ + min_mesg_sizes[nindex] = (unsigned) options->msg_size[i]; + + nindex++; + } /* end if */ + } /* end for */ + + if (nindex > 0) { + if (H5Pset_shared_mesg_nindexes(fcpl, nindex) < 0) { + error_msg("fail to set the number of shared object header message indexes\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + + /* msg_size[0]=dataspace, 1=datatype, 2=file value, 3=filter pipleline, 4=attribute */ + for (i = 0; i < (nindex - 1); i++) { + if (H5Pset_shared_mesg_index(fcpl, i, mesg_type_flags[i], min_mesg_sizes[i]) < 0) { + error_msg("fail to configure the specified shared object header message index\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } /* end if */ + } /* end for */ + } /* if (nindex>0) */ + + /* Create file access property list */ + if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) { + error_msg("Could not create file access property list\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } /* end if */ + + if (H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) { + error_msg("Could not set property for using latest version of the format\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } /* end if */ + } /* end if */ + } /* end if */ #if defined (H5REPACK_DEBUG_USER_BLOCK) - print_user_block(fnamein, fidin); +print_user_block(fnamein, fidin); #endif - /*------------------------------------------------------------------------- - * set the new user userblock options in the FCPL (before H5Fcreate ) - *------------------------------------------------------------------------- - */ - if (options->ublock_size > 0) { - /* either use the FCPL already created or create a new one */ - if (fcpl == H5P_DEFAULT) { - /* create a file creation property list */ - if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) { - error_msg("fail to create a file creation property list\n"); - goto out; - } - } - - /* set user block size */ - if (H5Pset_userblock(fcpl, options->ublock_size) < 0) { - error_msg("failed to set userblock size\n"); - goto out; - } - } - - /*------------------------------------------------------------------------- - * set alignment options - *------------------------------------------------------------------------- - */ - if (options->alignment > 0) { - /* either use the FAPL already created or create a new one */ - if (fapl == H5P_DEFAULT) { - /* create a file access property list */ - if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) { - error_msg("Could not create file access property list\n"); - goto out; - } - } - - if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0) { - error_msg("failed to set alignment\n"); - goto out; - } - } - - /*------------------------------------------------------------------------- - * set metadata block size option - *------------------------------------------------------------------------- - */ - if (options->meta_block_size > 0) { - /* either use the FAPL already created or create a new one */ - if (fapl == H5P_DEFAULT) { - /* create a file access property list */ - if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) { - error_msg("Could not create file access property list\n"); - goto out; - } - } - - if (H5Pset_meta_block_size(fapl, options->meta_block_size) < 0) { - error_msg("failed to set metadata block size\n"); - goto out; - } - } - - - /*------------------------------------------------------------------------- - * create the output file - *------------------------------------------------------------------------- - */ - if (options->verbose) - printf("Making file <%s>...\n", fnameout); - - if ((fidout = H5Fcreate(fnameout, H5F_ACC_TRUNC, fcpl, fapl)) < 0) { - error_msg("<%s>: Could not create file\n", fnameout); - goto out; - } - - /*------------------------------------------------------------------------- - * write a new user block if requested - *------------------------------------------------------------------------- - */ - if (options->ublock_size > 0) { - if (copy_user_block(options->ublock_filename, fnameout, - options->ublock_size) < 0) { - error_msg("Could not copy user block. Exiting...\n"); - goto out; - - } - } - - /*------------------------------------------------------------------------- - * get list of objects - *------------------------------------------------------------------------- - */ - - /* init table */ - trav_table_init(&travt); - - /* get the list of objects in the file */ - if (h5trav_gettable(fidin, travt) < 0) - goto out; - - /*------------------------------------------------------------------------- - * do the copy - *------------------------------------------------------------------------- - */ - if (do_copy_objects(fidin, fidout, travt, options) < 0) { - error_msg("<%s>: Could not copy data to: %s\n", fnamein, fnameout); - goto out; - } /* end if */ - - /*------------------------------------------------------------------------- - * do the copy of referenced objects - * and create hard links - *------------------------------------------------------------------------- - */ - if (do_copy_refobjs(fidin, fidout, travt, options) < 0) { - printf("h5repack: <%s>: Could not copy data to: %s\n", fnamein, - fnameout); - goto out; - } - - /*------------------------------------------------------------------------- - * close - *------------------------------------------------------------------------- - */ - - if (fapl > 0) - H5Pclose(fapl); - - if (fcpl > 0) - H5Pclose(fcpl); - - H5Fclose(fidin); - H5Fclose(fidout); - - /* free table */ - trav_table_free(travt); - travt = NULL; - - /*------------------------------------------------------------------------- - * write only the input file user block if there is no user block file input - *------------------------------------------------------------------------- - */ - - if (ub_size > 0 && options->ublock_size == 0) { - if (copy_user_block(fnamein, fnameout, ub_size) < 0) { - error_msg("Could not copy user block. Exiting...\n"); - goto out; - - } - } - - return 0; + /*------------------------------------------------------------------------- + * set the new user userblock options in the FCPL (before H5Fcreate ) + *------------------------------------------------------------------------- + */ + if (options->ublock_size > 0) { + /* either use the FCPL already created or create a new one */ + if (fcpl == H5P_DEFAULT) { + /* create a file creation property list */ + if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) { + error_msg("fail to create a file creation property list\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + } + + /* set user block size */ + if (H5Pset_userblock(fcpl, options->ublock_size) < 0) { + error_msg("failed to set userblock size\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + } + + /*------------------------------------------------------------------------- + * set alignment options + *------------------------------------------------------------------------- + */ + if (options->alignment > 0) { + /* either use the FAPL already created or create a new one */ + if (fapl == H5P_DEFAULT) { + /* create a file access property list */ + if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) { + error_msg("Could not create file access property list\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + } + + if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0) { + error_msg("failed to set alignment\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + } + + /*------------------------------------------------------------------------- + * set metadata block size option + *------------------------------------------------------------------------- + */ + if (options->meta_block_size > 0) { + /* either use the FAPL already created or create a new one */ + if (fapl == H5P_DEFAULT) { + /* create a file access property list */ + if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) { + error_msg("Could not create file access property list\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + } + + if (H5Pset_meta_block_size(fapl, options->meta_block_size) < 0) { + error_msg("failed to set metadata block size\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + } + + /*------------------------------------------------------------------------- + * set free-space strategy options + *------------------------------------------------------------------------- + */ + + /* either use the FCPL already created or create a new one */ + if (fcpl == H5P_DEFAULT) { + /* create a file creation property list */ + if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) { + error_msg("fail to create a file creation property list\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + } + + /* set file space strategy and free space threshold */ + if (H5Pset_file_space(fcpl, options->fs_strategy, options->fs_threshold) < 0) { + error_msg("failed to set file space strategy & threshold \n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + + /*------------------------------------------------------------------------- + * create the output file + *------------------------------------------------------------------------- + */ + if (options->verbose) + printf("Making file <%s>...\n", fnameout); + + if ((fidout = H5Fcreate(fnameout, H5F_ACC_TRUNC, fcpl, fapl)) < 0) { + error_msg("<%s>: Could not create file\n", fnameout); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + + /*------------------------------------------------------------------------- + * write a new user block if requested + *------------------------------------------------------------------------- + */ + if (options->ublock_size > 0) { + if (copy_user_block(options->ublock_filename, fnameout, options->ublock_size) < 0) { + error_msg("Could not copy user block. Exiting...\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + } + + /*------------------------------------------------------------------------- + * get list of objects + *------------------------------------------------------------------------- + */ + + /* init table */ + trav_table_init(&travt); + + /* get the list of objects in the file */ + if (h5trav_gettable(fidin, travt) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + + /*------------------------------------------------------------------------- + * do the copy + *------------------------------------------------------------------------- + */ + if (do_copy_objects(fidin, fidout, travt, options) < 0) { + error_msg("<%s>: Could not copy data to: %s\n", fnamein, fnameout); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } /* end if */ + + /*------------------------------------------------------------------------- + * do the copy of referenced objects + * and create hard links + *------------------------------------------------------------------------- + */ + if (do_copy_refobjs(fidin, fidout, travt, options) < 0) { + printf("h5repack: <%s>: Could not copy data to: %s\n", fnamein, fnameout); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + + /*------------------------------------------------------------------------- + * close + *------------------------------------------------------------------------- + */ + + if (fapl > 0) + H5Pclose(fapl); + + if (fcpl > 0) + H5Pclose(fcpl); + + H5Fclose(fidin); + H5Fclose(fidout); + + /* free table */ + trav_table_free(travt); + travt = NULL; + + /*------------------------------------------------------------------------- + * write only the input file user block if there is no user block file input + *------------------------------------------------------------------------- + */ + + if (ub_size > 0 && options->ublock_size == 0) { + if (copy_user_block(fnamein, fnameout, ub_size) < 0) { + error_msg("Could not copy user block. Exiting...\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + } + + return 0; + + /*------------------------------------------------------------------------- + * out + *------------------------------------------------------------------------- + */ - /*------------------------------------------------------------------------- - * out - *------------------------------------------------------------------------- - */ - -out: - H5E_BEGIN_TRY - { - H5Pclose(fapl); - H5Pclose(fcpl); - H5Fclose(fidin); - H5Fclose(fidout); - }H5E_END_TRY; - if (travt) - trav_table_free(travt); - - return -1; +done: + H5E_BEGIN_TRY { + H5Pclose(fapl); + H5Pclose(fcpl); + H5Fclose(fidin); + H5Fclose(fidout); + } H5E_END_TRY; + if (travt) + trav_table_free(travt); + + return ret_value; } /*------------------------------------------------------------------------- @@ -437,132 +462,126 @@ out: *-----------------------------------------*/ 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 status = 0; - int k; - H5D_layout_t dset_layout; - int rank_chunk; - hsize_t dims_chunk[H5S_MAX_RANK]; - hsize_t size_chunk = 1; - hsize_t nchunk_fit; /* number of chunks that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */ - hsize_t ndatum_fit; /* number of dataum that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */ - hsize_t chunk_dims_map[H5S_MAX_RANK]; /* mapped chunk dimentions */ - hsize_t hs_dims_map[H5S_MAX_RANK]; /* mapped hyperslab dimentions */ - hsize_t hslab_nbytes; /* size of hyperslab in byte */ - - /* init to set as size of a data element */ - hslab_nbytes = size_datum; - - /* get layout of dataset */ - dset_layout = H5Pget_layout(dcpl_id); - - /* if dataset is chunked */ - if (dset_layout == H5D_CHUNKED) { - /* get chunk dims */ - rank_chunk = H5Pget_chunk(dcpl_id, rank_dset, dims_chunk); - if (rank_chunk < 0) { - status = -1; - goto out; - } - - for (k = rank_dset; k > 0; --k) - size_chunk *= dims_chunk[k - 1]; - - /* figure out how many chunks can fit in the hyperslab buffer */ - nchunk_fit = (H5TOOLS_BUFSIZE / size_datum) / size_chunk; - - /* 1. if a chunk fit in hyperslab buffer */ - if (nchunk_fit >= 1) { - /* Calulate a hyperslab that contains as many chunks that can fit - * in hyperslab buffer. Hyperslab will be increased starting from - * the last dimention of the dataset (see h5dump's dims output). - * The calculation boundary is dataset dims. - * In the loop, used mapping from a datum to a chunk to figure out - * chunk based hyperslab. - */ - for (k = rank_dset; k > 0; --k) { - /* map dataset dimentions with a chunk dims */ - chunk_dims_map[k - 1] = dims_dset[k - 1] / dims_chunk[k - 1]; - - /* if reminder exist, increse by 1 to cover partial edge chunks */ - if (dims_dset[k - 1] % dims_chunk[k - 1] > 0) - chunk_dims_map[k - 1]++; - - /* get mapped hyperslab dims */ - hs_dims_map[k - 1] = MIN (nchunk_fit, chunk_dims_map[k-1]); - - /* prepare next round */ - nchunk_fit = nchunk_fit / chunk_dims_map[k - 1]; - /* if a chunk is bigger than the rest of buffer */ - if (nchunk_fit == 0) - nchunk_fit = 1; - - /* get hyperslab dimentions as unmapping to actual size */ - dims_hslab[k - 1] = - MIN( (hs_dims_map[k-1] * dims_chunk[k-1]), dims_dset[k-1]); - - /* calculate total size for the hyperslab */ - hslab_nbytes *= dims_hslab[k - 1]; - } - } - /* 2. if a chunk is bigger than hyperslab buffer */ - else { - /* Calulate a hyperslab that contains as many data elements that - * can fit in hyperslab buffer. Hyperslab will be increased - * starting from the last dimention of the chunk (see h5dump's dims - * output). - * The calculation boundary is a chunk dims. - */ - for (k = rank_dset; k > 0; --k) { - ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes; - - /* if a datum is bigger than rest of buffer */ - if (ndatum_fit == 0) - ndatum_fit = 1; - /* get hyperslab dimentions within a chunk boundary */ - dims_hslab[k - 1] = MIN (dims_chunk[k-1], ndatum_fit); - - /* calculate total size for the hyperslab */ - hslab_nbytes *= dims_hslab[k - 1]; - - if (hslab_nbytes <= 0) { - status = -1; - goto out; - } - } - } - } - /* 3. if dataset is not chunked */ - else { - /* Calulate a hyperslab that contains as many data elements that can - * fit in hyperslab buffer. Hyperslab will be increased starting from - * the last dimention of the dataset (see h5dump's dims output). - * The calculation boundary is dataset dims. - */ - for (k = rank_dset; k > 0; --k) { - ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes; - - /* if a datum is bigger than rest of buffer */ - if (ndatum_fit == 0) - ndatum_fit = 1; - /* get hyperslab dimentions within dataset boundary */ - dims_hslab[k - 1] = MIN(dims_dset[k - 1], ndatum_fit); - - /* calculate total size for the hyperslab */ - hslab_nbytes *= dims_hslab[k - 1]; - - if (hslab_nbytes <= 0) { - status = -1; - goto out; - } - } - } - - /* pass out the hyperslab size*/ - *hslab_nbytes_p = hslab_nbytes; + 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; + H5D_layout_t dset_layout; + int rank_chunk; + hsize_t dims_chunk[H5S_MAX_RANK]; + hsize_t size_chunk = 1; + hsize_t nchunk_fit; /* number of chunks that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */ + hsize_t ndatum_fit; /* number of dataum that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */ + hsize_t chunk_dims_map[H5S_MAX_RANK]; /* mapped chunk dimentions */ + hsize_t hs_dims_map[H5S_MAX_RANK]; /* mapped hyperslab dimentions */ + hsize_t hslab_nbytes; /* size of hyperslab in byte */ + + /* init to set as size of a data element */ + hslab_nbytes = size_datum; + + /* get layout of dataset */ + dset_layout = H5Pget_layout(dcpl_id); + + /* if dataset is chunked */ + if (dset_layout == H5D_CHUNKED) { + /* get chunk dims */ + rank_chunk = H5Pget_chunk(dcpl_id, rank_dset, dims_chunk); + if (rank_chunk < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + + for (k = rank_dset; k > 0; --k) + size_chunk *= dims_chunk[k - 1]; + + /* figure out how many chunks can fit in the hyperslab buffer */ + nchunk_fit = (H5TOOLS_BUFSIZE / size_datum) / size_chunk; + + /* 1. if a chunk fit in hyperslab buffer */ + if (nchunk_fit >= 1) { + /* Calulate a hyperslab that contains as many chunks that can fit + * in hyperslab buffer. Hyperslab will be increased starting from + * the last dimention of the dataset (see h5dump's dims output). + * The calculation boundary is dataset dims. + * In the loop, used mapping from a datum to a chunk to figure out + * chunk based hyperslab. + */ + for (k = rank_dset; k > 0; --k) { + /* map dataset dimentions with a chunk dims */ + chunk_dims_map[k - 1] = dims_dset[k - 1] / dims_chunk[k - 1]; + + /* if reminder exist, increse by 1 to cover partial edge chunks */ + if (dims_dset[k - 1] % dims_chunk[k - 1] > 0) + chunk_dims_map[k - 1]++; + + /* get mapped hyperslab dims */ + hs_dims_map[k - 1] = MIN (nchunk_fit, chunk_dims_map[k-1]); + + /* prepare next round */ + nchunk_fit = nchunk_fit / chunk_dims_map[k - 1]; + /* if a chunk is bigger than the rest of buffer */ + if (nchunk_fit == 0) + nchunk_fit = 1; + + /* get hyperslab dimentions as unmapping to actual size */ + dims_hslab[k - 1] = MIN( (hs_dims_map[k-1] * dims_chunk[k-1]), dims_dset[k-1]); + + /* calculate total size for the hyperslab */ + hslab_nbytes *= dims_hslab[k - 1]; + } + } + /* 2. if a chunk is bigger than hyperslab buffer */ + else { + /* Calulate a hyperslab that contains as many data elements that + * can fit in hyperslab buffer. Hyperslab will be increased + * starting from the last dimention of the chunk (see h5dump's dims + * output). + * The calculation boundary is a chunk dims. + */ + for (k = rank_dset; k > 0; --k) { + ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes; + + /* if a datum is bigger than rest of buffer */ + if (ndatum_fit == 0) + ndatum_fit = 1; + /* get hyperslab dimentions within a chunk boundary */ + dims_hslab[k - 1] = MIN (dims_chunk[k-1], ndatum_fit); + + /* calculate total size for the hyperslab */ + hslab_nbytes *= dims_hslab[k - 1]; + + if (hslab_nbytes <= 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + } + } + /* 3. if dataset is not chunked */ + else { + /* Calulate a hyperslab that contains as many data elements that can + * fit in hyperslab buffer. Hyperslab will be increased starting from + * the last dimention of the dataset (see h5dump's dims output). + * The calculation boundary is dataset dims. + */ + for (k = rank_dset; k > 0; --k) { + ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes; + + /* if a datum is bigger than rest of buffer */ + if (ndatum_fit == 0) + ndatum_fit = 1; + /* get hyperslab dimentions within dataset boundary */ + dims_hslab[k - 1] = MIN(dims_dset[k - 1], ndatum_fit); + + /* calculate total size for the hyperslab */ + hslab_nbytes *= dims_hslab[k - 1]; + + if (hslab_nbytes <= 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + } + + /* pass out the hyperslab size*/ + *hslab_nbytes_p = hslab_nbytes; -out: - return status; +done: + return ret_value; } /*------------------------------------------------------------------------- @@ -662,716 +681,639 @@ out: int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *options) /* repack options */ { - hid_t grp_in = -1; /* group ID */ - hid_t grp_out = -1; /* group ID */ - hid_t dset_in = -1; /* read dataset ID */ - hid_t dset_out = -1; /* write dataset ID */ - hid_t gcpl_in = -1; /* group creation property list */ - hid_t gcpl_out = -1; /* group creation property list */ - hid_t type_in = -1; /* named type ID */ - hid_t type_out = -1; /* named type ID */ - hid_t dcpl_in = -1; /* dataset creation property list ID */ - hid_t dcpl_out = -1; /* dataset creation property list ID */ - hid_t f_space_id = -1; /* file space ID */ - hid_t ftype_id = -1; /* file type ID */ - hid_t wtype_id = -1; /* read/write type ID */ - named_dt_t *named_dt_head = NULL; /* Pointer to the stack of named datatypes copied */ - size_t msize; /* size of type */ - hsize_t nelmts; /* number of elements in dataset */ - H5D_space_status_t space_status; /* determines whether space has been allocated for the dataset */ - int rank; /* rank of dataset */ - hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */ - hsize_t dsize_in; /* input dataset size before filter */ - hsize_t dsize_out; /* output dataset size after filter */ - int apply_s; /* flag for apply filter to small dataset sizes */ - int apply_f; /* flag for apply filter to return error on H5Dcreate */ - void *buf = NULL; /* buffer for raw data */ - void *hslab_buf = NULL; /* hyperslab buffer for raw data */ - int has_filter; /* current object has a filter */ - int req_filter; /* there was a request for a filter */ - int req_obj_layout = 0; /* request layout to current object */ - unsigned crt_order_flags; /* group creation order flag */ - unsigned i; - unsigned u; - int is_ref = 0; - htri_t is_named; - hbool_t limit_maxdims; - hsize_t size_dset; - - /*------------------------------------------------------------------------- - * copy the suppplied object list - *------------------------------------------------------------------------- - */ - - if (options->verbose) { - printf("-----------------------------------------\n"); - printf(" Type Filter (Compression) Name\n"); - printf("-----------------------------------------\n"); - } - - for (i = 0; i < travt->nobjs; i++) { - /* init variables per obj */ - buf = NULL; - limit_maxdims = FALSE; - - switch (travt->objs[i].type) { - - case H5TRAV_TYPE_UNKNOWN: - HDassert(0); - break; - /*------------------------------------------------------------------------- - * H5TRAV_TYPE_GROUP - *------------------------------------------------------------------------- - */ - case H5TRAV_TYPE_GROUP: - - if (options->verbose) { - printf(FORMAT_OBJ, "group", travt->objs[i].name); - } - - /* open input group */ - if ((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) - < 0) - goto error; - - /* get input group creation property list */ - if ((gcpl_in = H5Gget_create_plist(grp_in)) < 0) - goto error; - - /* query and set the group creation properties */ - if (H5Pget_link_creation_order(gcpl_in, &crt_order_flags) < 0) - goto error; - - /* set up group creation property list */ - if ((gcpl_out = H5Pcreate(H5P_GROUP_CREATE)) < 0) - goto error; - - if (H5Pset_link_creation_order(gcpl_out, crt_order_flags) < 0) - goto error; - - /*------------------------------------------------------------------------- - * the root is a special case, we get an ID for the root group - * and copy its attributes using that ID - *------------------------------------------------------------------------- - */ - if (HDstrcmp(travt->objs[i].name, "/") == 0) { - if ((grp_out = H5Gopen2(fidout, "/", H5P_DEFAULT)) < 0) - goto error; - } - else { - - if (options->grp_compact > 0 || options->grp_indexed > 0) { - if (H5Pset_link_phase_change(gcpl_out, - (unsigned) options->grp_compact, - (unsigned) options->grp_indexed) < 0) - goto error; - } - - if ((grp_out = H5Gcreate2(fidout, travt->objs[i].name, - H5P_DEFAULT, gcpl_out, H5P_DEFAULT)) < 0) - goto error; - - } - - /*------------------------------------------------------------------------- - * copy attrs - *------------------------------------------------------------------------- - */ - if (copy_attr(grp_in, grp_out, &named_dt_head, travt, options) < 0) - goto error; - - if (H5Pclose(gcpl_out) < 0) - goto error; - if (H5Pclose(gcpl_in) < 0) - goto error; - if (H5Gclose(grp_out) < 0) - goto error; - if (H5Gclose(grp_in) < 0) - goto error; - - break; - - /*------------------------------------------------------------------------- - * H5TRAV_TYPE_DATASET - *------------------------------------------------------------------------- - */ - case H5TRAV_TYPE_DATASET: - - has_filter = 0; - req_filter = 0; - - /* check if global filters were requested */ - if (options->n_filter_g) - req_filter = 1; - - /* check if filters were requested for individual objects */ - for (u = 0; u < options->op_tbl->nelems; u++) { - - if (HDstrcmp(travt->objs[i].name, options->op_tbl->objs[u].path) == 0) { - if (options->op_tbl->objs[u].filter->filtn > 0) { - req_filter = 1; - } - } - } - - /* check if layout change requested individual object */ - if (options->layout_g != H5D_LAYOUT_ERROR) { - pack_info_t *pckinfo; - /* any dataset is specified */ - if (options->op_tbl->nelems > 0) { - /* check if object exist */ - pckinfo = options_get_object(travt->objs[i].name, - options->op_tbl); - if (pckinfo) { - req_obj_layout = 1; - } - } - } - - /* early detection of references */ - if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) - < 0) - goto error; - if ((ftype_id = H5Dget_type(dset_in)) < 0) - goto error; - if (H5T_REFERENCE == H5Tget_class(ftype_id)) - is_ref = 1; - - /* Check if the datatype is committed */ - if ((is_named = H5Tcommitted(ftype_id)) < 0) - goto error; - if (is_named) - if ((wtype_id = copy_named_datatype(ftype_id, fidout, - &named_dt_head, travt, options)) < 0) - goto error; - - if (H5Tclose(ftype_id) < 0) - goto error; - if (H5Dclose(dset_in) < 0) - goto error; - - /*------------------------------------------------------------------------- - * check if we should use H5Ocopy or not - * if there is a request for filters/layout, we read/write the object - * otherwise we do a copy using H5Ocopy - *------------------------------------------------------------------------- - */ - if (options->op_tbl->nelems || options->all_filter == 1 - || options->all_layout == 1 || is_ref || is_named) { - - int j; - - if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) - goto error; - if ((f_space_id = H5Dget_space(dset_in)) < 0) - goto error; - if ((ftype_id = H5Dget_type(dset_in)) < 0) - goto error; - if ((dcpl_in = H5Dget_create_plist(dset_in)) < 0) - goto error; - if ((dcpl_out = H5Pcopy(dcpl_in)) < 0) - goto error; - if ((rank = H5Sget_simple_extent_ndims(f_space_id)) < 0) - goto error; - HDmemset(dims, 0, sizeof dims); - if (H5Sget_simple_extent_dims(f_space_id, dims, NULL) < 0) - goto error; - - if (H5Dget_space_status(dset_in, &space_status) < 0) - goto error; - - nelmts = 1; - for (j = 0; j < rank; j++) - nelmts *= dims[j]; - - /* wtype_id will have already been set if using a named dtype */ - if (!is_named) { - if (options->use_native == 1) - wtype_id = h5tools_get_native_type(ftype_id); - else - wtype_id = H5Tcopy(ftype_id); - } /* end if */ - - if ((msize = H5Tget_size(wtype_id)) == 0) - goto error; - - /* size of current dset */ - size_dset = nelmts * msize; - - /*------------------------------------------------------------------------- - * check if the dataset creation property list has filters that - * are not registered in the current configuration - * 1) the external filters GZIP and SZIP might not be available - * 2) the internal filters might be turned off - *------------------------------------------------------------------------- - */ - if (h5tools_canreadf((travt->objs[i].name), dcpl_in) == 1) { - apply_s = 1; - apply_f = 1; - - /*------------------------------------------------------------------------- - * references are a special case - * we cannot just copy the buffers, but instead we recreate the reference - * in a second traversal of the output file - *------------------------------------------------------------------------- - */ - if (H5T_REFERENCE != H5Tget_class(wtype_id)) { - /* get the storage size of the input dataset */ - dsize_in = H5Dget_storage_size(dset_in); - - /* check for small size datasets (less than 1k) except - * changing to COMPACT. For the reference, COMPACT is limited - * by size 64K by library. - */ - if (options->layout_g != H5D_COMPACT) { - if (size_dset < options->min_comp) - apply_s = 0; - } - - /* apply the filter */ - if (apply_s) { - if (apply_filters(travt->objs[i].name, rank, dims, - msize, dcpl_out, options, &has_filter) < 0) - goto error; - } - - /* only if layout change requested for entire file or - * individual obj */ - if (options->all_layout > 0 || req_obj_layout == 1) - /*------------------------------------------------- - * Unset the unlimited max dims if convert to other - * than chunk layouts, because unlimited max dims - * only can be applied to chunk layout. - * Also perform only for targeted dataset - * Also check for size limit to convert to compact - *-------------------------------------------------*/ - if (options->layout_g != H5D_CHUNKED) { - /* any dataset is specified */ - if (options->op_tbl->nelems > 0) { - /* if current obj match specified obj */ - if (options_get_object(travt->objs[i].name, - options->op_tbl)) - limit_maxdims = TRUE; - } - else { /* no dataset is specified */ - limit_maxdims = TRUE; - } - - /* if convert to COMPACT */ - if (options->layout_g == H5D_COMPACT) { - /* should be smaller than 64K */ - if (size_dset > MAX_COMPACT_DSIZE) - limit_maxdims = FALSE; - } - - /* unset unlimited max dims */ - if (limit_maxdims) - H5Sset_extent_simple(f_space_id, rank, dims, - NULL); - } - - /*------------------------------------------------------------------------- - * create the output dataset; - * disable error checking in case the dataset cannot be created with the - * modified dcpl; in that case use the original instead - *------------------------------------------------------------------------- - */ - H5E_BEGIN_TRY - { - dset_out = H5Dcreate2(fidout, - travt->objs[i].name, wtype_id, - f_space_id, H5P_DEFAULT, dcpl_out, - H5P_DEFAULT); - }H5E_END_TRY; - - if (dset_out == FAIL) { - if (options->verbose) - printf( - " warning: could not create dataset <%s>. Applying original settings\n", - travt->objs[i].name); - - if ((dset_out = H5Dcreate2(fidout, - travt->objs[i].name, wtype_id, f_space_id, - H5P_DEFAULT, dcpl_in, H5P_DEFAULT)) < 0) - goto error; - apply_f = 0; - } - - /*------------------------------------------------------------------------- - * read/write - *------------------------------------------------------------------------- - */ - if (nelmts > 0 && space_status != H5D_SPACE_STATUS_NOT_ALLOCATED) { - size_t need = (size_t)(nelmts * msize); /* bytes needed */ - - /* have to read the whole dataset if there is only one element in the dataset */ - if (need < H5TOOLS_MALLOCSIZE) - buf = HDmalloc(need); - - if (buf != NULL) { - /* read/write: use the macro to check error, e.g. memory allocation error inside the library. */ - CHECK_H5DRW_ERROR(H5Dread, dset_in, wtype_id, - H5S_ALL, H5S_ALL, H5P_DEFAULT, buf); - CHECK_H5DRW_ERROR(H5Dwrite, dset_out, wtype_id, - H5S_ALL, H5S_ALL, H5P_DEFAULT, buf); - - /* Check if we have VL data in the dataset's - * datatype that must be reclaimed */ - if (TRUE == H5Tdetect_class(wtype_id, H5T_VLEN)) - if (H5Dvlen_reclaim(wtype_id, f_space_id, - H5P_DEFAULT, buf) < 0) - goto error; - } - else { /* possibly not enough memory, read/write by hyperslabs */ - size_t p_type_nbytes = msize; /*size of memory type */ - hsize_t p_nelmts = nelmts; /*total elements */ - hsize_t elmtno; /*counter */ - int carry; /*counter carry value */ - unsigned int vl_data = 0; /*contains VL datatypes */ - - /* hyperslab info */ - hsize_t hslab_dims[H5S_MAX_RANK]; /*hyperslab dims */ - hsize_t hslab_nbytes; /*bytes per hyperslab */ - hsize_t hslab_nelmts; /*elements per hyperslab*/ - hid_t hslab_space; /*hyperslab data space */ - - /* hyperslab selection info */ - hsize_t hs_sel_offset[H5S_MAX_RANK];/* selection offset */ - hsize_t hs_sel_count[H5S_MAX_RANK]; /* selection count */ - hsize_t hs_select_nelmts; /* selected elements */ - hsize_t zero[8]; /*vector of zeros */ - int k; - H5D_layout_t dset_layout; - hid_t dcpl_tmp = -1; /* dataset creation property list ID */ - - /* check if we have VL data in the dataset's datatype */ - if (H5Tdetect_class(wtype_id, H5T_VLEN) == TRUE) - vl_data = TRUE; - - /* check first if writing dataset is chunked, - * if so use its chunk layout for better performance. */ - dset_layout = H5Pget_layout(dcpl_out); - if (dset_layout == H5D_CHUNKED) - dcpl_tmp = dcpl_out; /* writing dataset */ - else { /* if reading dataset is chunked */ - dset_layout = H5Pget_layout(dcpl_in); - if (dset_layout == H5D_CHUNKED) - dcpl_tmp = dcpl_in; /* reading dataset */ - } - - /* get hyperslab dims and size in byte */ - if (Get_hyperslab(dcpl_tmp, rank, dims, - p_type_nbytes, hslab_dims, - &hslab_nbytes) < 0) - goto error; - - hslab_buf = HDmalloc((size_t)hslab_nbytes); - - hslab_nelmts = hslab_nbytes / p_type_nbytes; - hslab_space = H5Screate_simple(1, &hslab_nelmts, - NULL); - - /* the hyperslab selection loop */ - HDmemset(hs_sel_offset, 0, - sizeof hs_sel_offset); - HDmemset(zero, 0, sizeof zero); - - for (elmtno = 0; elmtno < p_nelmts; elmtno += - hs_select_nelmts) { - if (rank > 0) { - /* calculate the hyperslab selections. The selection would be same as the hyperslab except for remaining edge portion of the dataset which is smaller then the hyperslab. - */ - for (k = 0, hs_select_nelmts = 1; - k < rank; k++) { - /* MIN() is used to get the remaining edge portion if exist. - * "dims[k] - hs_sel_offset[k]" is remaining edge portion that is smaller then the hyperslab.*/ - hs_sel_count[k] = - MIN(dims[k] - hs_sel_offset[k], hslab_dims[k]); - hs_select_nelmts *= hs_sel_count[k]; - } - - if (H5Sselect_hyperslab(f_space_id, - H5S_SELECT_SET, hs_sel_offset, - NULL, hs_sel_count, NULL) < 0) - goto error; - if (H5Sselect_hyperslab(hslab_space, - H5S_SELECT_SET, zero, NULL, - &hs_select_nelmts, NULL) < 0) - goto error; - } - else { - H5Sselect_all(f_space_id); - H5Sselect_all(hslab_space); - hs_select_nelmts = 1; - } /* rank */ - - /* read/write: use the macro to check error, e.g. memory allocation error inside the library. */ - CHECK_H5DRW_ERROR(H5Dread, dset_in, - wtype_id, hslab_space, f_space_id, - H5P_DEFAULT, hslab_buf); - CHECK_H5DRW_ERROR(H5Dwrite, dset_out, - wtype_id, hslab_space, f_space_id, - H5P_DEFAULT, hslab_buf); - - /* reclaim any VL memory, if necessary */ - if (vl_data) - H5Dvlen_reclaim(wtype_id, hslab_space, - H5P_DEFAULT, hslab_buf); - - /* calculate the next hyperslab offset */ - for (k = rank, carry = 1; k > 0 && carry; - --k) { - hs_sel_offset[k - 1] += hs_sel_count[k - - 1]; - /* if reached the end of a dim */ - if (hs_sel_offset[k - 1] == dims[k - 1]) - hs_sel_offset[k - 1] = 0; - else - carry = 0; - } /* k */ - } /* elmtno */ - - H5Sclose(hslab_space); - /* free */ - if (hslab_buf != NULL) { - HDfree(hslab_buf); - hslab_buf = NULL; - } - } /* hyperslab read */ - } /* if (nelmts>0 && space_status==H5D_SPACE_STATUS_NOT_ALLOCATED) */ - - /*------------------------------------------------------------------------- - * amount of compression used - *------------------------------------------------------------------------- - */ - if (options->verbose) { - double ratio = 0; - - /* only print the compression ration if there was a filter request */ - if (apply_s && apply_f && req_filter) { - /* get the storage size of the output dataset */ - dsize_out = H5Dget_storage_size(dset_out); - - /* compression ratio = uncompressed size / compressed size */ - if (dsize_out != 0) - ratio = (double) dsize_in - / (double) dsize_out; - - print_dataset_info(dcpl_out, - travt->objs[i].name, ratio, 1); - } - else - print_dataset_info(dcpl_in, travt->objs[i].name, - ratio, 0); - - /* print a message that the filter was not applied - (in case there was a filter) - */ - if (has_filter && apply_s == 0) - printf( - " <warning: filter not applied to %s. dataset smaller than %d bytes>\n", - travt->objs[i].name, - (int) options->min_comp); - - if (has_filter && apply_f == 0) - printf( - " <warning: could not apply the filter to %s>\n", - travt->objs[i].name); - - } /* verbose */ - - /*------------------------------------------------------------------------- - * copy attrs - *------------------------------------------------------------------------- - */ - if (copy_attr(dset_in, dset_out, &named_dt_head, travt, - options) < 0) - goto error; - /*close */ - if (H5Dclose(dset_out) < 0) - goto error; - - }/*!H5T_REFERENCE*/ - }/*h5tools_canreadf*/ - - /*------------------------------------------------------------------------- - * close - *------------------------------------------------------------------------- - */ - if (H5Tclose(ftype_id) < 0) - goto error; - if (H5Tclose(wtype_id) < 0) - goto error; - if (H5Pclose(dcpl_in) < 0) - goto error; - if (H5Pclose(dcpl_out) < 0) - goto error; - if (H5Sclose(f_space_id) < 0) - goto error; - if (H5Dclose(dset_in) < 0) - goto error; - - } - /*------------------------------------------------------------------------- - * we do not have request for filter/chunking use H5Ocopy instead - *------------------------------------------------------------------------- - */ - else { - hid_t pid; - - /* create property to pass copy options */ - if ((pid = H5Pcreate(H5P_OBJECT_COPY)) < 0) - goto error; - - /* set options for object copy */ - if (H5Pset_copy_object(pid, H5O_COPY_WITHOUT_ATTR_FLAG) < 0) - goto error; - - /*------------------------------------------------------------------------- - * do the copy - *------------------------------------------------------------------------- - */ - - if (H5Ocopy(fidin, /* Source file or group identifier */ - travt->objs[i].name, /* Name of the source object to be copied */ - fidout, /* Destination file or group identifier */ - travt->objs[i].name, /* Name of the destination object */ - pid, /* Properties which apply to the copy */ - H5P_DEFAULT) < 0) /* Properties which apply to the new hard link */ - goto error; - - /* close property */ - if (H5Pclose(pid) < 0) - goto error; - - /*------------------------------------------------------------------------- - * copy attrs manually - *------------------------------------------------------------------------- - */ - if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) - < 0) - goto error; - if ((dset_out = H5Dopen2(fidout, travt->objs[i].name, - H5P_DEFAULT)) < 0) - goto error; - if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options) - < 0) - goto error; - if (H5Dclose(dset_in) < 0) - goto error; - if (H5Dclose(dset_out) < 0) - goto error; - - if (options->verbose) - printf(FORMAT_OBJ, "dset", travt->objs[i].name); - - } /* end do we have request for filter/chunking */ - - break; - - /*------------------------------------------------------------------------- - * H5TRAV_TYPE_NAMED_DATATYPE - *------------------------------------------------------------------------- - */ - case H5TRAV_TYPE_NAMED_DATATYPE: - - if (options->verbose) - printf(FORMAT_OBJ, "type", travt->objs[i].name); - - if ((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) - < 0) - goto error; - - /* Copy the datatype anonymously */ - if ((type_out = copy_named_datatype(type_in, fidout, &named_dt_head, - travt, options)) < 0) - goto error; - - /* Link in to group structure */ - if (H5Lcreate_hard(type_out, ".", fidout, travt->objs[i].name, - H5P_DEFAULT, H5P_DEFAULT) < 0) - goto error; - - /*------------------------------------------------------------------------- - * copy attrs - *------------------------------------------------------------------------- - */ - if (copy_attr(type_in, type_out, &named_dt_head, travt, options) - < 0) - goto error; - - if (H5Tclose(type_in) < 0) - goto error; - if (H5Tclose(type_out) < 0) - goto error; - - break; - - /*------------------------------------------------------------------------- - * H5TRAV_TYPE_LINK - * H5TRAV_TYPE_UDLINK - * - * Only handles external links; H5Lcopy will fail for other UD link types - * since we don't have creation or copy callbacks for them. - *------------------------------------------------------------------------- - */ - - case H5TRAV_TYPE_LINK: - case H5TRAV_TYPE_UDLINK: { - - if (options->verbose) - printf(FORMAT_OBJ, "link", travt->objs[i].name); - - if (H5Lcopy(fidin, travt->objs[i].name, fidout, travt->objs[i].name, - H5P_DEFAULT, H5P_DEFAULT) < 0) - goto error; - - if (options->verbose) - printf(FORMAT_OBJ, "link", travt->objs[i].name); - - } - break; - - default: - goto error; - } /* switch */ - - /* free */ - if (buf != NULL) { - HDfree(buf); - buf = NULL; - } - - } /* i */ - - /* Finalize (link) the stack of named datatypes (if any) */ - named_datatype_free(&named_dt_head, 0); + 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 dset_out = -1; /* write dataset ID */ + hid_t gcpl_in = -1; /* group creation property list */ + hid_t gcpl_out = -1; /* group creation property list */ + hid_t type_in = -1; /* named type ID */ + hid_t type_out = -1; /* named type ID */ + hid_t dcpl_in = -1; /* dataset creation property list ID */ + hid_t dcpl_out = -1; /* dataset creation property list ID */ + hid_t f_space_id = -1; /* file space ID */ + hid_t ftype_id = -1; /* file type ID */ + hid_t wtype_id = -1; /* read/write type ID */ + named_dt_t *named_dt_head = NULL; /* Pointer to the stack of named datatypes copied */ + size_t msize; /* size of type */ + hsize_t nelmts; /* number of elements in dataset */ + H5D_space_status_t space_status; /* determines whether space has been allocated for the dataset */ + int rank; /* rank of dataset */ + hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */ + hsize_t dsize_in; /* input dataset size before filter */ + hsize_t dsize_out; /* output dataset size after filter */ + int apply_s; /* flag for apply filter to small dataset sizes */ + int apply_f; /* flag for apply filter to return error on H5Dcreate */ + void *buf = NULL; /* buffer for raw data */ + void *hslab_buf = NULL; /* hyperslab buffer for raw data */ + int has_filter; /* current object has a filter */ + int req_filter; /* there was a request for a filter */ + int req_obj_layout = 0; /* request layout to current object */ + unsigned crt_order_flags; /* group creation order flag */ + unsigned i; + unsigned u; + int is_ref = 0; + htri_t is_named; + hbool_t limit_maxdims; + hsize_t size_dset; + + /*------------------------------------------------------------------------- + * copy the suppplied object list + *------------------------------------------------------------------------- + */ + + if (options->verbose) { + printf("-----------------------------------------\n"); + printf(" Type Filter (Compression) Name\n"); + printf("-----------------------------------------\n"); + } + + for (i = 0; i < travt->nobjs; i++) { + /* init variables per obj */ + buf = NULL; + limit_maxdims = FALSE; + + switch (travt->objs[i].type) { + case H5TRAV_TYPE_UNKNOWN: + HDassert(0); + break; + + /*------------------------------------------------------------------------- + * H5TRAV_TYPE_GROUP + *------------------------------------------------------------------------- + */ + case H5TRAV_TYPE_GROUP: + if (options->verbose) + printf(FORMAT_OBJ, "group", travt->objs[i].name); + + /* open input group */ + if ((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed"); + + /* get input group creation property list */ + if ((gcpl_in = H5Gget_create_plist(grp_in)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gget_create_plist failed"); + + /* 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"); + + /* set up group creation property list */ + if ((gcpl_out = H5Pcreate(H5P_GROUP_CREATE)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed"); + + if (H5Pset_link_creation_order(gcpl_out, crt_order_flags) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_link_creation_order failed"); + + /*------------------------------------------------------------------------- + * the root is a special case, we get an ID for the root group + * and copy its attributes using that ID + *------------------------------------------------------------------------- + */ + if (HDstrcmp(travt->objs[i].name, "/") == 0) { + if ((grp_out = H5Gopen2(fidout, "/", H5P_DEFAULT)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed"); + } + else { + if (options->grp_compact > 0 || options->grp_indexed > 0) + if (H5Pset_link_phase_change(gcpl_out, (unsigned) options->grp_compact, (unsigned) options->grp_indexed) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_link_phase_change failed"); + + if ((grp_out = H5Gcreate2(fidout, travt->objs[i].name, H5P_DEFAULT, gcpl_out, H5P_DEFAULT)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gcreate2 failed"); + } + + /*------------------------------------------------------------------------- + * copy attrs + *------------------------------------------------------------------------- + */ + if (copy_attr(grp_in, grp_out, &named_dt_head, travt, options) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed"); + + if (H5Pclose(gcpl_out) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + if (H5Pclose(gcpl_in) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + if (H5Gclose(grp_out) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed"); + if (H5Gclose(grp_in) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed"); + + break; + + /*------------------------------------------------------------------------- + * H5TRAV_TYPE_DATASET + *------------------------------------------------------------------------- + */ + case H5TRAV_TYPE_DATASET: + has_filter = 0; + req_filter = 0; + + /* check if global filters were requested */ + if (options->n_filter_g) + req_filter = 1; + + /* check if filters were requested for individual objects */ + for (u = 0; u < options->op_tbl->nelems; u++) + if (HDstrcmp(travt->objs[i].name, options->op_tbl->objs[u].path) == 0) + if (options->op_tbl->objs[u].filter->filtn > 0) + req_filter = 1; + + /* check if layout change requested individual object */ + if (options->layout_g != H5D_LAYOUT_ERROR) { + pack_info_t *pckinfo; + + /* any dataset is specified */ + if (options->op_tbl->nelems > 0) { + /* check if object exist */ + pckinfo = options_get_object(travt->objs[i].name, options->op_tbl); + if (pckinfo) + req_obj_layout = 1; + } + } + + /* early detection of references */ + if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed"); + if ((ftype_id = H5Dget_type(dset_in)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_type failed"); + if (H5T_REFERENCE == H5Tget_class(ftype_id)) + is_ref = 1; + + /* Check if the datatype is committed */ + if ((is_named = H5Tcommitted(ftype_id)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tcommitted failed"); + if (is_named) + if ((wtype_id = copy_named_datatype(ftype_id, fidout, &named_dt_head, travt, options)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_named_datatype failed"); + + if (H5Tclose(ftype_id) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); + if (H5Dclose(dset_in) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); + + /*------------------------------------------------------------------------- + * check if we should use H5Ocopy or not + * if there is a request for filters/layout, we read/write the object + * otherwise we do a copy using H5Ocopy + *------------------------------------------------------------------------- + */ + if (options->op_tbl->nelems || options->all_filter == 1 + || options->all_layout == 1 || is_ref || is_named) { + + int j; + + if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed"); + if ((f_space_id = H5Dget_space(dset_in)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed"); + if ((ftype_id = H5Dget_type(dset_in)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_type failed"); + if ((dcpl_in = H5Dget_create_plist(dset_in)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed"); + if ((dcpl_out = H5Pcopy(dcpl_in)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcopy failed"); + if ((rank = H5Sget_simple_extent_ndims(f_space_id)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed"); + HDmemset(dims, 0, sizeof dims); + if (H5Sget_simple_extent_dims(f_space_id, dims, NULL) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed"); + if (H5Dget_space_status(dset_in, &space_status) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space_status failed"); + + nelmts = 1; + for (j = 0; j < rank; j++) + nelmts *= dims[j]; + + /* wtype_id will have already been set if using a named dtype */ + if (!is_named) { + if (options->use_native == 1) + wtype_id = h5tools_get_native_type(ftype_id); + else + wtype_id = H5Tcopy(ftype_id); + } /* end if */ + + if ((msize = H5Tget_size(wtype_id)) == 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed"); + + /* size of current dset */ + size_dset = nelmts * msize; + + /*------------------------------------------------------------------------- + * check if the dataset creation property list has filters that + * are not registered in the current configuration + * 1) the external filters GZIP and SZIP might not be available + * 2) the internal filters might be turned off + *------------------------------------------------------------------------- + */ + if (h5tools_canreadf((travt->objs[i].name), dcpl_in) == 1) { + apply_s = 1; + apply_f = 1; + + /*------------------------------------------------------------------------- + * references are a special case + * we cannot just copy the buffers, but instead we recreate the reference + * in a second traversal of the output file + *------------------------------------------------------------------------- + */ + if (H5T_REFERENCE != H5Tget_class(wtype_id)) { + /* get the storage size of the input dataset */ + dsize_in = H5Dget_storage_size(dset_in); + + /* check for small size datasets (less than 1k) except + * changing to COMPACT. For the reference, COMPACT is limited + * by size 64K by library. + */ + if (options->layout_g != H5D_COMPACT) + if (size_dset < options->min_comp) + apply_s = 0; + + /* apply the filter */ + if (apply_s) + if (apply_filters(travt->objs[i].name, rank, dims, msize, dcpl_out, options, &has_filter) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "apply_filters failed"); + + /* only if layout change requested for entire file or + * individual obj */ + if (options->all_layout > 0 || req_obj_layout == 1) + /*------------------------------------------------- + * Unset the unlimited max dims if convert to other + * than chunk layouts, because unlimited max dims + * only can be applied to chunk layout. + * Also perform only for targeted dataset + * Also check for size limit to convert to compact + *-------------------------------------------------*/ + if (options->layout_g != H5D_CHUNKED) { + /* any dataset is specified */ + if (options->op_tbl->nelems > 0) { + /* if current obj match specified obj */ + if (options_get_object(travt->objs[i].name, options->op_tbl)) + limit_maxdims = TRUE; + } + else /* no dataset is specified */ + limit_maxdims = TRUE; + + /* if convert to COMPACT */ + if (options->layout_g == H5D_COMPACT) + /* should be smaller than 64K */ + if (size_dset > MAX_COMPACT_DSIZE) + limit_maxdims = FALSE; + + /* unset unlimited max dims */ + if (limit_maxdims) + H5Sset_extent_simple(f_space_id, rank, dims, NULL); + } + + /*------------------------------------------------------------------------- + * create the output dataset; + * disable error checking in case the dataset cannot be created with the + * modified dcpl; in that case use the original instead + *------------------------------------------------------------------------- + */ + dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_out, H5P_DEFAULT); + if (dset_out == FAIL) { + H5Epush2(H5tools_ERR_STACK_g, __FILE__, FUNC, __LINE__, H5tools_ERR_CLS_g, H5E_tools_g, H5E_tools_min_id_g, "H5Dcreate2 failed"); + if (options->verbose) + printf(" warning: could not create dataset <%s>. Applying original settings\n", travt->objs[i].name); + + if ((dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_in, H5P_DEFAULT)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dcreate2 failed"); + apply_f = 0; + } + + /*------------------------------------------------------------------------- + * read/write + *------------------------------------------------------------------------- + */ + if (nelmts > 0 && space_status != H5D_SPACE_STATUS_NOT_ALLOCATED) { + size_t need = (size_t)(nelmts * msize); /* bytes needed */ + + /* have to read the whole dataset if there is only one element in the dataset */ + if (need < H5TOOLS_MALLOCSIZE) + buf = HDmalloc(need); + + if (buf != NULL) { + /* read/write: use the macro to check error, e.g. memory allocation error inside the library. */ + CHECK_H5DRW_ERROR(H5Dread, FAIL, dset_in, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf); + CHECK_H5DRW_ERROR(H5Dwrite, FAIL, dset_out, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf); + + /* Check if we have VL data in the dataset's + * datatype that must be reclaimed */ + if (TRUE == H5Tdetect_class(wtype_id, H5T_VLEN)) + if (H5Dvlen_reclaim(wtype_id, f_space_id, H5P_DEFAULT, buf) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dvlen_reclaim failed"); + } + else { /* possibly not enough memory, read/write by hyperslabs */ + size_t p_type_nbytes = msize; /*size of memory type */ + hsize_t p_nelmts = nelmts; /*total elements */ + hsize_t elmtno; /*counter */ + int carry; /*counter carry value */ + unsigned int vl_data = 0; /*contains VL datatypes */ + + /* hyperslab info */ + hsize_t hslab_dims[H5S_MAX_RANK]; /*hyperslab dims */ + hsize_t hslab_nbytes; /*bytes per hyperslab */ + hsize_t hslab_nelmts; /*elements per hyperslab*/ + hid_t hslab_space; /*hyperslab data space */ + + /* hyperslab selection info */ + hsize_t hs_sel_offset[H5S_MAX_RANK];/* selection offset */ + hsize_t hs_sel_count[H5S_MAX_RANK]; /* selection count */ + hsize_t hs_select_nelmts; /* selected elements */ + hsize_t zero[8]; /*vector of zeros */ + int k; + H5D_layout_t dset_layout; + hid_t dcpl_tmp = -1; /* dataset creation property list ID */ + + /* check if we have VL data in the dataset's datatype */ + if (H5Tdetect_class(wtype_id, H5T_VLEN) == TRUE) + vl_data = TRUE; + + /* check first if writing dataset is chunked, + * if so use its chunk layout for better performance. */ + dset_layout = H5Pget_layout(dcpl_out); + if (dset_layout == H5D_CHUNKED) + dcpl_tmp = dcpl_out; /* writing dataset */ + else { /* if reading dataset is chunked */ + dset_layout = H5Pget_layout(dcpl_in); + if (dset_layout == H5D_CHUNKED) + dcpl_tmp = dcpl_in; /* reading dataset */ + } + + /* get hyperslab dims and size in byte */ + if (Get_hyperslab(dcpl_tmp, rank, dims, p_type_nbytes, hslab_dims, &hslab_nbytes) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Get_hyperslab failed"); + + hslab_buf = HDmalloc((size_t)hslab_nbytes); + + hslab_nelmts = hslab_nbytes / p_type_nbytes; + hslab_space = H5Screate_simple(1, &hslab_nelmts, NULL); + + /* the hyperslab selection loop */ + HDmemset(hs_sel_offset, 0, sizeof hs_sel_offset); + HDmemset(zero, 0, sizeof zero); + + for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_select_nelmts) { + if (rank > 0) { + /* calculate the hyperslab selections. + * The selection would be same as the hyperslab + * except for remaining edge portion of the dataset + * which is smaller then the hyperslab. + */ + for (k = 0, hs_select_nelmts = 1; k < rank; k++) { + /* MIN() is used to get the remaining edge portion if exist. + * "dims[k] - hs_sel_offset[k]" is remaining edge portion that is smaller then the hyperslab.*/ + hs_sel_count[k] = MIN(dims[k] - hs_sel_offset[k], hslab_dims[k]); + hs_select_nelmts *= hs_sel_count[k]; + } + + if (H5Sselect_hyperslab(f_space_id, H5S_SELECT_SET, hs_sel_offset, NULL, hs_sel_count, NULL) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sselect_hyperslab failed"); + if (H5Sselect_hyperslab(hslab_space, H5S_SELECT_SET, zero, NULL, &hs_select_nelmts, NULL) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sselect_hyperslab failed"); + } + else { + H5Sselect_all(f_space_id); + H5Sselect_all(hslab_space); + hs_select_nelmts = 1; + } /* rank */ + + /* read/write: use the macro to check error, e.g. memory allocation error inside the library. */ + CHECK_H5DRW_ERROR(H5Dread, FAIL, dset_in, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf); + CHECK_H5DRW_ERROR(H5Dwrite, FAIL, dset_out, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf); + + /* reclaim any VL memory, if necessary */ + if (vl_data) + H5Dvlen_reclaim(wtype_id, hslab_space, H5P_DEFAULT, hslab_buf); + + /* calculate the next hyperslab offset */ + for (k = rank, carry = 1; k > 0 && carry; --k) { + hs_sel_offset[k - 1] += hs_sel_count[k - 1]; + /* if reached the end of a dim */ + if (hs_sel_offset[k - 1] == dims[k - 1]) + hs_sel_offset[k - 1] = 0; + else + carry = 0; + } /* k */ + } /* elmtno */ + + H5Sclose(hslab_space); + /* free */ + if (hslab_buf != NULL) { + HDfree(hslab_buf); + hslab_buf = NULL; + } + } /* hyperslab read */ + } /* if (nelmts>0 && space_status==H5D_SPACE_STATUS_NOT_ALLOCATED) */ + + /*------------------------------------------------------------------------- + * amount of compression used + *------------------------------------------------------------------------- + */ + if (options->verbose) { + double ratio = 0; + + /* only print the compression ration if there was a filter request */ + if (apply_s && apply_f && req_filter) { + /* get the storage size of the output dataset */ + dsize_out = H5Dget_storage_size(dset_out); + + /* compression ratio = uncompressed size / compressed size */ + if (dsize_out != 0) + ratio = (double) dsize_in / (double) dsize_out; + print_dataset_info(dcpl_out, travt->objs[i].name, ratio, 1); + } + else + print_dataset_info(dcpl_in, travt->objs[i].name, ratio, 0); + + /* print a message that the filter was not applied + (in case there was a filter) + */ + if (has_filter && apply_s == 0) + printf(" <warning: filter not applied to %s. dataset smaller than %d bytes>\n", travt->objs[i].name, (int) options->min_comp); + + if (has_filter && apply_f == 0) + printf(" <warning: could not apply the filter to %s>\n", travt->objs[i].name); + } /* verbose */ + + /*------------------------------------------------------------------------- + * copy attrs + *------------------------------------------------------------------------- + */ + if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed"); + + /*close */ + if (H5Dclose(dset_out) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); + }/*!H5T_REFERENCE*/ + }/*h5tools_canreadf*/ + + /*------------------------------------------------------------------------- + * close + *------------------------------------------------------------------------- + */ + if (H5Tclose(ftype_id) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); + if (H5Tclose(wtype_id) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); + if (H5Pclose(dcpl_in) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + if (H5Pclose(dcpl_out) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + if (H5Sclose(f_space_id) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed"); + if (H5Dclose(dset_in) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); + } + /*------------------------------------------------------------------------- + * we do not have request for filter/chunking use H5Ocopy instead + *------------------------------------------------------------------------- + */ + else { + hid_t pid; + + /* create property to pass copy options */ + if ((pid = H5Pcreate(H5P_OBJECT_COPY)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed"); + + /* set options for object copy */ + if (H5Pset_copy_object(pid, H5O_COPY_WITHOUT_ATTR_FLAG) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_copy_object failed"); + + /*------------------------------------------------------------------------- + * do the copy + *------------------------------------------------------------------------- + */ + + if (H5Ocopy(fidin, /* Source file or group identifier */ + travt->objs[i].name, /* Name of the source object to be copied */ + fidout, /* Destination file or group identifier */ + travt->objs[i].name, /* Name of the destination object */ + pid, /* Properties which apply to the copy */ + H5P_DEFAULT) < 0) /* Properties which apply to the new hard link */ + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Ocopy failed"); + + /* close property */ + if (H5Pclose(pid) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + + /*------------------------------------------------------------------------- + * copy attrs manually + *------------------------------------------------------------------------- + */ + if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed"); + if ((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed"); + if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed"); + if (H5Dclose(dset_in) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); + if (H5Dclose(dset_out) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); + + if (options->verbose) + printf(FORMAT_OBJ, "dset", travt->objs[i].name); + + } /* end do we have request for filter/chunking */ + break; + + /*------------------------------------------------------------------------- + * H5TRAV_TYPE_NAMED_DATATYPE + *------------------------------------------------------------------------- + */ + case H5TRAV_TYPE_NAMED_DATATYPE: + if (options->verbose) + printf(FORMAT_OBJ, "type", travt->objs[i].name); + + if ((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Topen2 failed"); + + /* Copy the datatype anonymously */ + if ((type_out = copy_named_datatype(type_in, fidout, &named_dt_head, travt, options)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_named_datatype failed"); + + /* Link in to group structure */ + if (H5Lcreate_hard(type_out, ".", fidout, travt->objs[i].name, H5P_DEFAULT, H5P_DEFAULT) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Lcreate_hard failed"); + + /*------------------------------------------------------------------------- + * copy attrs + *------------------------------------------------------------------------- + */ + if (copy_attr(type_in, type_out, &named_dt_head, travt, options) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed"); + + if (H5Tclose(type_in) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); + if (H5Tclose(type_out) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); + + break; + + /*------------------------------------------------------------------------- + * H5TRAV_TYPE_LINK + * H5TRAV_TYPE_UDLINK + * + * Only handles external links; H5Lcopy will fail for other UD link types + * since we don't have creation or copy callbacks for them. + *------------------------------------------------------------------------- + */ + case H5TRAV_TYPE_LINK: + case H5TRAV_TYPE_UDLINK: + if (options->verbose) + printf(FORMAT_OBJ, "link", travt->objs[i].name); + + if (H5Lcopy(fidin, travt->objs[i].name, fidout, travt->objs[i].name, H5P_DEFAULT, H5P_DEFAULT) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Lcopy failed"); + + if (options->verbose) + printf(FORMAT_OBJ, "link", travt->objs[i].name); + break; + + default: + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Object type not found"); + } /* switch */ + + /* free */ + if (buf != NULL) { + HDfree(buf); + buf = NULL; + } + } /* i */ + + /* Finalize (link) the stack of named datatypes (if any) */ + named_datatype_free(&named_dt_head, 0); + + return ret_value; - return 0; - -error: - H5E_BEGIN_TRY - { - H5Gclose(grp_in); - H5Gclose(grp_out); - H5Pclose(dcpl_in); - H5Pclose(gcpl_in); - H5Pclose(gcpl_out); - H5Sclose(f_space_id); - H5Dclose(dset_in); - H5Dclose(dset_out); - H5Tclose(ftype_id); - H5Tclose(wtype_id); - H5Tclose(type_in); - H5Tclose(type_out); - named_datatype_free(&named_dt_head, 1); - }H5E_END_TRY; - /* free */ - if (buf != NULL) - HDfree(buf); - if (hslab_buf != NULL) - HDfree(hslab_buf); - return -1; +done: + H5E_BEGIN_TRY + { + H5Gclose(grp_in); + H5Gclose(grp_out); + H5Pclose(dcpl_in); + H5Pclose(gcpl_in); + H5Pclose(gcpl_out); + H5Sclose(f_space_id); + H5Dclose(dset_in); + H5Dclose(dset_out); + H5Tclose(ftype_id); + H5Tclose(wtype_id); + H5Tclose(type_in); + H5Tclose(type_out); + named_datatype_free(&named_dt_head, 1); + }H5E_END_TRY; + + /* free */ + if (buf != NULL) + HDfree(buf); + if (hslab_buf != NULL) + HDfree(hslab_buf); + + return ret_value; } /*------------------------------------------------------------------------- @@ -1382,101 +1324,102 @@ error: *------------------------------------------------------------------------- */ static void print_dataset_info(hid_t dcpl_id, char *objname, double ratio, - int pr) { - char strfilter[255]; + int pr) +{ + 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; - - HDstrcpy(strfilter, "\0"); + 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; - /* get information about input filters */ - if ((nfilters = H5Pget_nfilters(dcpl_id)) < 0) - return; + HDstrcpy(strfilter, "\0"); - for (i = 0; i < nfilters; i++) { - cd_nelmts = NELMTS(cd_values); + /* get information about input filters */ + if ((nfilters = H5Pget_nfilters(dcpl_id)) < 0) + return; - filtn = H5Pget_filter2(dcpl_id, (unsigned) i, &filt_flags, &cd_nelmts, - cd_values, sizeof(f_objname), f_objname, NULL); + for (i = 0; i < nfilters; i++) { + cd_nelmts = NELMTS(cd_values); - switch (filtn) { + filtn = H5Pget_filter2(dcpl_id, (unsigned) i, &filt_flags, &cd_nelmts, + cd_values, sizeof(f_objname), f_objname, NULL); - case H5Z_FILTER_NONE: - HDstrcat(strfilter, "NONE "); - break; + switch (filtn) { + case H5Z_FILTER_NONE: + HDstrcat(strfilter, "NONE "); + break; - case H5Z_FILTER_DEFLATE: - HDstrcat(strfilter, "GZIP "); + case H5Z_FILTER_DEFLATE: + HDstrcat(strfilter, "GZIP "); #if defined (PRINT_DEBUG) - { - unsigned level=cd_values[0]; - sprintf(temp,"(%d)",level); - HDstrcat(strfilter,temp); - } + { + unsigned level = cd_values[0]; + + sprintf(temp,"(%d)", level); + HDstrcat(strfilter, temp); + } #endif - break; + break; - case H5Z_FILTER_SZIP: - HDstrcat(strfilter, "SZIP "); + case H5Z_FILTER_SZIP: + HDstrcat(strfilter, "SZIP "); #if defined (PRINT_DEBUG) - { - unsigned options_mask=cd_values[0]; /* from dcpl, not filt*/ - unsigned ppb=cd_values[1]; - sprintf(temp,"(%d,",ppb); - HDstrcat(strfilter,temp); - if (options_mask & H5_SZIP_EC_OPTION_MASK) - HDstrcpy(temp,"EC) "); - else if (options_mask & H5_SZIP_NN_OPTION_MASK) - HDstrcpy(temp,"NN) "); - } - HDstrcat(strfilter,temp); - + { + unsigned options_mask = cd_values[0]; /* from dcpl, not filt*/ + unsigned ppb = cd_values[1]; + + sprintf(temp,"(%d,", ppb); + HDstrcat(strfilter, temp); + if (options_mask & H5_SZIP_EC_OPTION_MASK) + HDstrcpy(temp, "EC) "); + else if (options_mask & H5_SZIP_NN_OPTION_MASK) + HDstrcpy(temp, "NN) "); + } + HDstrcat(strfilter, temp); #endif - - break; - - case H5Z_FILTER_SHUFFLE: - HDstrcat(strfilter, "SHUF "); - break; - - case H5Z_FILTER_FLETCHER32: - HDstrcat(strfilter, "FLET "); - break; - - case H5Z_FILTER_NBIT: - HDstrcat(strfilter, "NBIT "); - break; - - case H5Z_FILTER_SCALEOFFSET: - HDstrcat(strfilter, "SCALEOFFSET "); - break; - - default: - HDstrcat(strfilter, "UD "); - break; - } /* switch */ - }/*i*/ - - if (!pr) - printf(FORMAT_OBJ, "dset", objname); - else { - char str[255], temp[28]; - HDstrcpy(str, "dset "); - HDstrcat(str, strfilter); - sprintf(temp, " (%.3f:1)", ratio); - HDstrcat(str, temp); - printf(FORMAT_OBJ, str, objname); - } + break; + + case H5Z_FILTER_SHUFFLE: + HDstrcat(strfilter, "SHUF "); + break; + + case H5Z_FILTER_FLETCHER32: + HDstrcat(strfilter, "FLET "); + break; + + case H5Z_FILTER_NBIT: + HDstrcat(strfilter, "NBIT "); + break; + + case H5Z_FILTER_SCALEOFFSET: + HDstrcat(strfilter, "SCALEOFFSET "); + break; + + default: + HDstrcat(strfilter, "UD "); + break; + } /* switch */ + }/*i*/ + + if (!pr) + printf(FORMAT_OBJ, "dset", objname); + else { + char str[255], temp[28]; + + HDstrcpy(str, "dset "); + HDstrcat(str, strfilter); + sprintf(temp, " (%.3f:1)", ratio); + HDstrcat(str, temp); + printf(FORMAT_OBJ, str, objname); + } } /*------------------------------------------------------------------------- @@ -1493,73 +1436,66 @@ 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) { - int infid = -1, outfid = -1; /* File descriptors */ - int status = 0; /* Return value */ - - /* 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) { - status = -1; - goto done; - } - if ((outfid = HDopen(outfile, O_WRONLY, 0644)) < 0) { - status = -1; - goto done; - } - - /* Copy the userblock from the input file to the output file */ - while (size > 0) { - ssize_t nread, nbytes; /* # of bytes transfered, etc. */ - char rbuf[USERBLOCK_XFER_SIZE]; /* Buffer for reading */ - const char *wbuf; /* Pointer into buffer, for writing */ - - /* Read buffer from source file */ - if (size > USERBLOCK_XFER_SIZE) - nread = HDread(infid, rbuf, (size_t)USERBLOCK_XFER_SIZE); - else - nread = HDread(infid, rbuf, (size_t)size); - if (nread < 0) { - status = -1; - goto done; - } /* end if */ - - /* Write buffer to destination file */ - /* (compensating for interrupted writes & checking for errors, etc.) */ - nbytes = nread; - wbuf = rbuf; - while (nbytes > 0) { - ssize_t nwritten; /* # of bytes written */ - - do { - nwritten = HDwrite(outfid, wbuf, (size_t)nbytes); - } while (-1 == nwritten && EINTR == errno); - if (-1 == nwritten) { /* error */ - status = -1; - goto done; - } /* end if */ - HDassert(nwritten > 0); - HDassert(nwritten <= nbytes); - - /* Update # of bytes left & offset in buffer */ - nbytes -= nwritten; - wbuf += nwritten; - HDassert(nbytes == 0 || wbuf < (rbuf + USERBLOCK_XFER_SIZE)); - } /* end while */ - - /* Update size of userblock left to transfer */ - size = size - (hsize_t) nread; - } /* end while */ + hsize_t size) +{ + 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) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDopen failed"); + if ((outfid = HDopen(outfile, O_WRONLY, 0644)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDopen failed"); + + /* Copy the userblock from the input file to the output file */ + while (size > 0) { + ssize_t nread, nbytes; /* # of bytes transfered, etc. */ + char rbuf[USERBLOCK_XFER_SIZE]; /* Buffer for reading */ + const char *wbuf; /* Pointer into buffer, for writing */ + + /* Read buffer from source file */ + if (size > USERBLOCK_XFER_SIZE) + nread = HDread(infid, rbuf, (size_t)USERBLOCK_XFER_SIZE); + else + nread = HDread(infid, rbuf, (size_t)size); + if (nread < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDread failed"); + + /* Write buffer to destination file */ + /* (compensating for interrupted writes & checking for errors, etc.) */ + nbytes = nread; + wbuf = rbuf; + while (nbytes > 0) { + ssize_t nwritten; /* # of bytes written */ + + do { + nwritten = HDwrite(outfid, wbuf, (size_t)nbytes); + } while (-1 == nwritten && EINTR == errno); + if (-1 == nwritten) /* error */ + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDwrite failed"); + HDassert(nwritten > 0); + HDassert(nwritten <= nbytes); + + /* Update # of bytes left & offset in buffer */ + nbytes -= nwritten; + wbuf += nwritten; + HDassert(nbytes == 0 || wbuf < (rbuf + USERBLOCK_XFER_SIZE)); + } /* end while */ + + /* Update size of userblock left to transfer */ + size = size - (hsize_t) nread; + } /* end while */ done: - if (infid > 0) - HDclose(infid); - if (outfid > 0) - HDclose(outfid); + if (infid > 0) + HDclose(infid); + if (outfid > 0) + HDclose(outfid); - return status; + return ret_value; } /*------------------------------------------------------------------------- @@ -1579,7 +1515,8 @@ done: static void print_user_block(const char *filename, hid_t fid) { - int fh; /* file handle */ + 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 */ @@ -1588,23 +1525,23 @@ void print_user_block(const char *filename, hid_t fid) /* get user block size */ if(( fcpl = H5Fget_create_plist(fid)) < 0) { error_msg("failed to retrieve file creation property list\n"); - goto done; - } + 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"); - goto done; - } + 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"); - goto done; - } + HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed"); + } /* open file */ if((fh = HDopen(filename, O_RDONLY, 0)) < 0) { - goto done; - } + HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "HDopen failed"); + } size = ub_size; @@ -1627,8 +1564,8 @@ void print_user_block(const char *filename, hid_t fid) printf("\n"); if(nread < 0) { - goto done; - } + HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "nread < 0"); + } /* update size of userblock left to transfer */ size -= nread; diff --git a/tools/h5repack/h5repack_filters.c b/tools/h5repack/h5repack_filters.c index 56e08ef..e873a53 100644 --- a/tools/h5repack/h5repack_filters.c +++ b/tools/h5repack/h5repack_filters.c @@ -34,8 +34,8 @@ * *------------------------------------------------------------------------- */ -static -int aux_find_obj(const char* name, /* object name from traverse list */ +static int +aux_find_obj(const char* name, /* object name from traverse list */ pack_opt_t *options, /* repack options */ pack_info_t *obj /*OUT*/) /* info about object to filter */ { @@ -48,7 +48,7 @@ int aux_find_obj(const char* name, /* object name from traverse list */ if (HDstrcmp(options->op_tbl->objs[i].path,name)==0) { *obj = options->op_tbl->objs[i]; - return i; + return (int)i; } pdest = HDstrstr(name,options->op_tbl->objs[i].path); @@ -58,7 +58,7 @@ int aux_find_obj(const char* name, /* object name from traverse list */ if( pdest != NULL && result==1 ) { *obj = options->op_tbl->objs[i]; - return i; + return (int)i; } }/*i*/ @@ -76,8 +76,8 @@ int aux_find_obj(const char* name, /* object name from traverse list */ * *------------------------------------------------------------------------- */ -static -int aux_assign_obj(const char* name, /* object name from traverse list */ +static int +aux_assign_obj(const char* name, /* object name from traverse list */ pack_opt_t *options, /* repack options */ pack_info_t *obj /*OUT*/) /* info about object to filter */ { @@ -433,7 +433,7 @@ int apply_filters(const char* name, /* object name from traverse list */ int scale_factor; scale_type = (H5Z_SO_scale_type_t)obj.filter[i].cd_values[0]; - scale_factor = obj.filter[i].cd_values[1]; + scale_factor = (int)obj.filter[i].cd_values[1]; if(H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths)<0) return -1; diff --git a/tools/h5repack/h5repack_main.c b/tools/h5repack/h5repack_main.c index f3fd469..7998ae8 100644 --- a/tools/h5repack/h5repack_main.c +++ b/tools/h5repack/h5repack_main.c @@ -33,28 +33,29 @@ 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:"; +static const char *s_opts = "hVvf:l:m:e:nLc:d:s:u:b:M:t:a:i:o:E"; static struct long_options l_opts[] = { - { "help", no_arg, 'h' }, - { "version", no_arg, 'V' }, - { "verbose", no_arg, 'v' }, - { "filter", require_arg, 'f' }, - { "layout", require_arg, 'l' }, - { "minimum", require_arg, 'm' }, - { "file", require_arg, 'e' }, - { "native", no_arg, 'n' }, - { "latest", no_arg, 'L' }, - { "compact", require_arg, 'c' }, - { "indexed", require_arg, 'd' }, - { "ssize", require_arg, 's' }, - { "ublock", require_arg, 'u' }, - { "block", require_arg, 'b' }, - { "metadata_block_size", require_arg, 'M' }, - { "threshold", require_arg, 't' }, - { "alignment", require_arg, 'a' }, - { "infile", require_arg, 'i' }, /* -i for backward compability */ - { "outfile", require_arg, 'o' }, /* -o for backward compability */ - { NULL, 0, '\0' } + { "help", no_arg, 'h' }, + { "version", no_arg, 'V' }, + { "verbose", no_arg, 'v' }, + { "filter", require_arg, 'f' }, + { "layout", require_arg, 'l' }, + { "minimum", require_arg, 'm' }, + { "file", require_arg, 'e' }, + { "native", no_arg, 'n' }, + { "latest", no_arg, 'L' }, + { "compact", require_arg, 'c' }, + { "indexed", require_arg, 'd' }, + { "ssize", require_arg, 's' }, + { "ublock", require_arg, 'u' }, + { "block", require_arg, 'b' }, + { "metadata_block_size", require_arg, 'M' }, + { "threshold", require_arg, 't' }, + { "alignment", require_arg, 'a' }, + { "infile", require_arg, 'i' }, /* -i for backward compability */ + { "outfile", require_arg, 'o' }, /* -o for backward compability */ + { "enable-error-stack", no_arg, 'E' }, + { NULL, 0, '\0' } }; /*------------------------------------------------------------------------- @@ -67,113 +68,117 @@ static struct long_options l_opts[] = { *------------------------------------------------------------------------- */ static void usage(const char *prog) { - printf("usage: %s [OPTIONS] file1 file2\n", prog); - printf(" file1 Input HDF5 File\n"); - printf(" file2 Output HDF5 File\n"); - printf(" OPTIONS\n"); - printf(" -h, --help Print a usage message and exit\n"); - printf(" -v, --verbose Verbose mode, print object information\n"); - printf(" -V, --version Print version number and exit\n"); - printf(" -n, --native Use a native HDF5 type when repacking\n"); - printf(" -L, --latest Use latest version of file format\n"); - printf(" -c L1, --compact=L1 Maximum number of links in header messages\n"); - printf(" -d L2, --indexed=L2 Minimum number of links in the indexed format\n"); - printf(" -s S[:F], --ssize=S[:F] Shared object header message minimum size\n"); - printf(" -m M, --minimum=M Do not apply the filter to datasets smaller than M\n"); - printf(" -e E, --file=E Name of file E with the -f and -l options\n"); - printf(" -u U, --ublock=U Name of file U with user block data to be added\n"); - printf(" -b B, --block=B Size of user block to be added\n"); - printf(" -M A, --metadata_block_size=A Metadata block size for H5Pset_meta_block_size\n"); - printf(" -t T, --threshold=T Threshold value for H5Pset_alignment\n"); - printf(" -a A, --alignment=A Alignment value for H5Pset_alignment\n"); - printf(" -f FILT, --filter=FILT Filter type\n"); - printf(" -l LAYT, --layout=LAYT Layout type\n"); - printf("\n"); - printf(" M - is an integer greater than 1, size of dataset in bytes (default is 0) \n"); - printf(" E - is a filename.\n"); - printf(" S - is an integer\n"); - printf(" U - is a filename.\n"); - printf(" T - is an integer\n"); - printf(" A - is an integer greater than zero\n"); - printf(" B - is the user block size, any value that is 512 or greater and is\n"); - printf(" a power of 2 (1024 default)\n"); - printf(" F - is the shared object header message type, any of <dspace|dtype|fill|\n"); - printf(" pline|attr>. If F is not specified, S applies to all messages\n"); - printf("\n"); - printf(" FILT - is a string with the format:\n"); - printf("\n"); - printf(" <list of objects>:<name of filter>=<filter parameters>\n"); - printf("\n"); - printf(" <list of objects> is a comma separated list of object names, meaning apply\n"); - printf(" compression only to those objects. If no names are specified, the filter\n"); - printf(" is applied to all objects\n"); - printf(" <name of filter> can be:\n"); - printf(" GZIP, to apply the HDF5 GZIP filter (GZIP compression)\n"); - printf(" SZIP, to apply the HDF5 SZIP filter (SZIP compression)\n"); - printf(" SHUF, to apply the HDF5 shuffle filter\n"); - printf(" FLET, to apply the HDF5 checksum filter\n"); - printf(" NBIT, to apply the HDF5 NBIT filter (NBIT compression)\n"); - printf(" SOFF, to apply the HDF5 Scale/Offset filter\n"); - printf(" UD, to apply a user defined filter\n"); - printf(" NONE, to remove all filters\n"); - printf(" <filter parameters> is optional filter parameter information\n"); - printf(" GZIP=<deflation level> from 1-9\n"); - printf(" SZIP=<pixels per block,coding> pixels per block is a even number in\n"); - printf(" 2-32 and coding method is either EC or NN\n"); - printf(" SHUF (no parameter)\n"); - printf(" FLET (no parameter)\n"); - printf(" NBIT (no parameter)\n"); - printf(" SOFF=<scale_factor,scale_type> scale_factor is an integer and scale_type\n"); - printf(" is either IN or DS\n"); - printf(" UD=<filter_number,cd_value_count,value_1[,value_2,...,value_N]>\n"); - printf(" required values for filter_number,cd_value_count,value_1\n"); - printf(" optional values for value_2 to value_N\n"); - printf(" NONE (no parameter)\n"); - printf("\n"); - printf(" LAYT - is a string with the format:\n"); - printf("\n"); - printf(" <list of objects>:<layout type>=<layout parameters>\n"); - printf("\n"); - printf(" <list of objects> is a comma separated list of object names, meaning that\n"); - printf(" layout information is supplied for those objects. If no names are\n"); - printf(" specified, the layout type is applied to all objects\n"); - printf(" <layout type> can be:\n"); - printf(" CHUNK, to apply chunking layout\n"); - printf(" COMPA, to apply compact layout\n"); - printf(" CONTI, to apply contiguous layout\n"); - printf(" <layout parameters> is optional layout information\n"); - printf(" CHUNK=DIM[xDIM...xDIM], the chunk size of each dimension\n"); - printf(" COMPA (no parameter)\n"); - printf(" CONTI (no parameter)\n"); - printf("\n"); - printf("Examples of use:\n"); - printf("\n"); - printf("1) h5repack -v -f GZIP=1 file1 file2\n"); - printf("\n"); - printf(" GZIP compression with level 1 to all objects\n"); - printf("\n"); - printf("2) h5repack -v -f dset1:SZIP=8,NN file1 file2\n"); - printf("\n"); - printf(" SZIP compression with 8 pixels per block and NN coding method to object dset1\n"); - printf("\n"); - printf("3) h5repack -v -l dset1,dset2:CHUNK=20x10 -f dset3,dset4,dset5:NONE file1 file2\n"); - printf("\n"); - printf(" Chunked layout, with a layout size of 20x10, to objects dset1 and dset2\n"); - printf(" and remove filters to objects dset3, dset4, dset5\n"); - printf("\n"); - printf("4) h5repack -L -c 10 -s 20:dtype file1 file2 \n"); - printf("\n"); - printf(" Using latest file format with maximum compact group size of 10 and\n"); - printf(" and minimum shared datatype size of 20\n"); - printf("\n"); - printf("5) h5repack -f SHUF -f GZIP=1 file1 file2 \n"); - printf("\n"); - printf(" Add both filters SHUF and GZIP in this order to all datasets\n"); - printf("\n"); - printf("6) h5repack -f UD=307,1,9 file1 file2 \n"); - printf("\n"); - printf(" Add bzip2 filter to all datasets\n"); - printf("\n"); + 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, " OPTIONS\n"); + PRINTVALSTREAM(rawoutstream, " -h, --help Print a usage message and exit\n"); + PRINTVALSTREAM(rawoutstream, " -v, --verbose Verbose mode, print object information\n"); + PRINTVALSTREAM(rawoutstream, " -V, --version Print version number and exit\n"); + PRINTVALSTREAM(rawoutstream, " -n, --native Use a native HDF5 type when repacking\n"); + PRINTVALSTREAM(rawoutstream, " -L, --latest Use latest version of file format\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, " -f FILT, --filter=FILT Filter type\n"); + PRINTVALSTREAM(rawoutstream, " -l LAYT, --layout=LAYT Layout type\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, " B - is the user block size, any value that is 512 or greater and is\n"); + PRINTVALSTREAM(rawoutstream, " a power of 2 (1024 default)\n"); + PRINTVALSTREAM(rawoutstream, " F - is the shared object header message type, any of <dspace|dtype|fill|\n"); + PRINTVALSTREAM(rawoutstream, " pline|attr>. If F is not specified, S applies to all messages\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, " --enable-error-stack Prints messages from the HDF5 error stack as they\n"); + PRINTVALSTREAM(rawoutstream, " occur.\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, " FILT - is a string with the format:\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, " <list of objects>:<name of filter>=<filter parameters>\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, " <list of objects> is a comma separated list of object names, meaning apply\n"); + PRINTVALSTREAM(rawoutstream, " compression only to those objects. If no names are specified, the filter\n"); + PRINTVALSTREAM(rawoutstream, " is applied to all objects\n"); + PRINTVALSTREAM(rawoutstream, " <name of filter> can be:\n"); + PRINTVALSTREAM(rawoutstream, " GZIP, to apply the HDF5 GZIP filter (GZIP compression)\n"); + 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, " <filter parameters> is optional filter parameter information\n"); + PRINTVALSTREAM(rawoutstream, " GZIP=<deflation level> from 1-9\n"); + PRINTVALSTREAM(rawoutstream, " SZIP=<pixels per block,coding> pixels per block is a even number in\n"); + PRINTVALSTREAM(rawoutstream, " 2-32 and coding method is either EC or NN\n"); + PRINTVALSTREAM(rawoutstream, " SHUF (no parameter)\n"); + PRINTVALSTREAM(rawoutstream, " FLET (no parameter)\n"); + PRINTVALSTREAM(rawoutstream, " NBIT (no parameter)\n"); + PRINTVALSTREAM(rawoutstream, " SOFF=<scale_factor,scale_type> scale_factor is an integer and scale_type\n"); + PRINTVALSTREAM(rawoutstream, " is either IN or DS\n"); + PRINTVALSTREAM(rawoutstream, " UD=<filter_number,cd_value_count,value_1[,value_2,...,value_N]>\n"); + PRINTVALSTREAM(rawoutstream, " required values for filter_number,cd_value_count,value_1\n"); + PRINTVALSTREAM(rawoutstream, " optional values for value_2 to value_N\n"); + PRINTVALSTREAM(rawoutstream, " NONE (no parameter)\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, " LAYT - is a string with the format:\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, " <list of objects>:<layout type>=<layout parameters>\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, " <list of objects> is a comma separated list of object names, meaning that\n"); + PRINTVALSTREAM(rawoutstream, " layout information is supplied for those objects. If no names are\n"); + PRINTVALSTREAM(rawoutstream, " specified, the layout type is applied to all objects\n"); + PRINTVALSTREAM(rawoutstream, " <layout type> can be:\n"); + PRINTVALSTREAM(rawoutstream, " CHUNK, to apply chunking layout\n"); + PRINTVALSTREAM(rawoutstream, " COMPA, to apply compact layout\n"); + PRINTVALSTREAM(rawoutstream, " CONTI, to apply contiguous layout\n"); + PRINTVALSTREAM(rawoutstream, " <layout parameters> 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, " and 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=307,1,9 file1 file2 \n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, " Add bzip2 filter to all datasets\n"); + PRINTVALSTREAM(rawoutstream, "\n"); } /*------------------------------------------------------------------------- @@ -242,14 +247,24 @@ int read_info(const char *filename, pack_opt_t *options) { i = 0; c = '0'; while (c != ' ') { - fscanf(fp, "%c", &c); + if(fscanf(fp, "%c", &c) < 0 && HDferror(fp)) { + error_msg("fscanf error\n"); + h5tools_setstatus(EXIT_FAILURE); + ret_value = EXIT_FAILURE; + goto done; + } /* end if */ if (HDfeof(fp)) break; } c = '0'; /* go until end */ while (c != ' ') { - fscanf(fp, "%c", &c); + if(fscanf(fp, "%c", &c) < 0 && HDferror(fp)) { + error_msg("fscanf error\n"); + h5tools_setstatus(EXIT_FAILURE); + ret_value = EXIT_FAILURE; + goto done; + } /* end if */ comp_info[i] = c; i++; if (HDfeof(fp)) @@ -276,14 +291,24 @@ int read_info(const char *filename, pack_opt_t *options) { i = 0; c = '0'; while (c != ' ') { - fscanf(fp, "%c", &c); + if(fscanf(fp, "%c", &c) < 0 && HDferror(fp)) { + error_msg("fscanf error\n"); + h5tools_setstatus(EXIT_FAILURE); + ret_value = EXIT_FAILURE; + goto done; + } /* end if */ if (HDfeof(fp)) break; } c = '0'; /* go until end */ while (c != ' ') { - fscanf(fp, "%c", &c); + if(fscanf(fp, "%c", &c) < 0 && HDferror(fp)) { + error_msg("fscanf error\n"); + h5tools_setstatus(EXIT_FAILURE); + ret_value = EXIT_FAILURE; + goto done; + } /* end if */ comp_info[i] = c; i++; if (HDfeof(fp)) @@ -343,7 +368,7 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options) { has_i_o = 1; break; - /* -o for backward compability */ + /* -o for backward compability */ case 'o': outfile = opt_arg; has_i_o = 1; @@ -386,7 +411,7 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options) { break; case 'm': - options->min_comp = HDatoi( opt_arg ); + 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); @@ -473,7 +498,7 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options) { break; case 'a': - options->alignment = HDatol( opt_arg ); + options->alignment = HDstrtoull(opt_arg , NULL, 0); if (options->alignment < 1) { error_msg("invalid alignment size\n", opt_arg); h5tools_setstatus(EXIT_FAILURE); @@ -482,13 +507,17 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options) { } break; - default: - break; - } /* switch */ + case 'E': + enable_error_stack = TRUE; + break; + + default: + break; + } /* switch */ - } /* while */ + } /* while */ - if (has_i_o == 0) { + if (has_i_o == 0) { /* check for file names to be processed */ if (argc <= opt_ind || argv[opt_ind + 1] == NULL) { error_msg("missing file names\n"); @@ -520,50 +549,67 @@ done: *------------------------------------------------------------------------- */ int main(int argc, const char **argv) { + H5E_auto2_t func; + H5E_auto2_t tools_func; + void *edata; + void *tools_edata; pack_opt_t options; /*the global options */ h5tools_setprogname(PROGRAMNAME); h5tools_setstatus(EXIT_SUCCESS); - /* Initialize h5tools lib */ - h5tools_init(); - - /* update hyperslab buffer size from H5TOOLS_BUFSIZE env if exist */ - if (h5tools_getenv_update_hyperslab_bufsize() < 0) { - h5tools_setstatus(EXIT_FAILURE); - goto done; - } - - /* initialize options */ - h5repack_init(&options, 0); - - if (parse_command_line(argc, argv, &options) < 0) - goto done; - - /* get file names if they were not yet got */ - if (has_i_o == 0) { - - if (argv[opt_ind] != NULL && argv[opt_ind + 1] != NULL) { - infile = argv[opt_ind]; - outfile = argv[opt_ind + 1]; - - if ( HDstrcmp( infile, outfile ) == 0) { - error_msg("file names cannot be the same\n"); - usage(h5tools_getprogname()); - h5tools_setstatus(EXIT_FAILURE); - goto done; - } - } - else { - error_msg("file names missing\n"); - usage(h5tools_getprogname()); - h5tools_setstatus(EXIT_FAILURE); - goto done; - } - } - - /* pack it */ + /* Disable error reporting */ + H5Eget_auto2(H5E_DEFAULT, &func, &edata); + H5Eset_auto2(H5E_DEFAULT, NULL, NULL); + + /* Initialize h5tools lib */ + h5tools_init(); + + /* Disable tools error reporting */ + H5Eget_auto2(H5tools_ERR_STACK_g, &tools_func, &tools_edata); + H5Eset_auto2(H5tools_ERR_STACK_g, NULL, NULL); + + /* update hyperslab buffer size from H5TOOLS_BUFSIZE env if exist */ + if (h5tools_getenv_update_hyperslab_bufsize() < 0) { + h5tools_setstatus(EXIT_FAILURE); + goto done; + } + + /* initialize options */ + h5repack_init(&options, 0); + + if (parse_command_line(argc, argv, &options) < 0) + goto done; + + /* get file names if they were not yet got */ + if (has_i_o == 0) { + + if (argv[opt_ind] != NULL && argv[opt_ind + 1] != NULL) { + infile = argv[opt_ind]; + outfile = argv[opt_ind + 1]; + + if ( HDstrcmp( infile, outfile ) == 0) { + error_msg("file names cannot be the same\n"); + usage(h5tools_getprogname()); + h5tools_setstatus(EXIT_FAILURE); + goto done; + } + } + else { + error_msg("file names missing\n"); + usage(h5tools_getprogname()); + h5tools_setstatus(EXIT_FAILURE); + goto done; + } + } + + if (enable_error_stack) { + H5Eset_auto2(H5E_DEFAULT, func, edata); + H5Eset_auto2(H5tools_ERR_STACK_g, tools_func, tools_edata); + } + + /* pack it */ h5tools_setstatus(h5repack(infile, outfile, &options)); done: diff --git a/tools/h5repack/h5repack_plugin.sh.in b/tools/h5repack/h5repack_plugin.sh.in index 7502397..a064db6 100644 --- a/tools/h5repack/h5repack_plugin.sh.in +++ b/tools/h5repack/h5repack_plugin.sh.in @@ -127,7 +127,7 @@ CLEAN_TESTFILES_AND_TESTDIR() # skip rm if srcdir is same as destdir # this occurs when build/test performed in source dir and # make cp fail - SDIR=`$DIRNAME $tstfile` + SDIR=$SRC_H5REPACK_TESTFILES INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'` INODE_DDIR=`$LS -i -d $TESTDIR | $AWK -F' ' '{print $1}'` if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then diff --git a/tools/h5repack/h5repack_refs.c b/tools/h5repack/h5repack_refs.c index 2b39249..f0f32c3 100644 --- a/tools/h5repack/h5repack_refs.c +++ b/tools/h5repack/h5repack_refs.c @@ -1,4 +1,3 @@ - /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * @@ -50,6 +49,7 @@ int do_copy_refobjs(hid_t fidin, trav_table_t *travt, pack_opt_t *options) /* repack options */ { + int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ hid_t grp_in = (-1); /* read group ID */ hid_t grp_out = (-1); /* write group ID */ hid_t dset_in = (-1); /* read dataset ID */ @@ -85,18 +85,18 @@ int do_copy_refobjs(hid_t fidin, *------------------------------------------------------------------------- */ if((grp_out = H5Gopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed"); if((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed"); if(copy_refs_attr(grp_in, grp_out, options, travt, fidout) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_refs_attr failed"); if(H5Gclose(grp_out) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed"); if(H5Gclose(grp_in) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed"); /*------------------------------------------------------------------------- * check for hard links @@ -113,26 +113,26 @@ int do_copy_refobjs(hid_t fidin, */ case H5TRAV_TYPE_DATASET: if((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed"); if((space_id = H5Dget_space(dset_in)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed"); if((ftype_id = H5Dget_type(dset_in)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_type failed"); if((dcpl_id = H5Dget_create_plist(dset_in)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed"); if((rank = H5Sget_simple_extent_ndims(space_id)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed"); if(H5Sget_simple_extent_dims(space_id, dims, NULL) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed"); nelmts = 1; for(k = 0; k < rank; k++) nelmts *= dims[k]; if((mtype_id = h5tools_get_native_type(ftype_id)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5tools_get_native_type failed"); if((msize = H5Tget_size(mtype_id)) == 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed"); /*------------------------------------------------------------------------- * check if the dataset creation property list has filters that @@ -168,19 +168,19 @@ int do_copy_refobjs(hid_t fidin, buf = (hobj_ref_t *)HDmalloc((unsigned)(nelmts * msize)); if(buf==NULL) { printf("cannot read into memory\n" ); - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed"); } /* end if */ if(H5Dread(dset_in, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed"); refbuf = (hobj_ref_t*) HDcalloc((unsigned)nelmts, msize); if(refbuf == NULL){ printf("cannot allocate memory\n" ); - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDcalloc failed"); } /* end if */ for(u = 0; u < nelmts; u++) { H5E_BEGIN_TRY { - if((refobj_id = H5Rdereference(dset_in, H5R_OBJECT, &buf[u])) < 0) + if((refobj_id = H5Rdereference2(dset_in, H5P_DEFAULT, H5R_OBJECT, &buf[u])) < 0) continue; } H5E_END_TRY; @@ -190,7 +190,7 @@ int do_copy_refobjs(hid_t fidin, if((refname = MapIdToName(refobj_id, travt)) != NULL) { /* create the reference, -1 parameter for objects */ if(H5Rcreate(&refbuf[u], fidout, refname, H5R_OBJECT, (hid_t)-1) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rcreate failed"); if(options->verbose) { printf(FORMAT_OBJ,"dset",travt->objs[i].name ); @@ -208,10 +208,10 @@ int do_copy_refobjs(hid_t fidin, *------------------------------------------------------------------------- */ if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, mtype_id, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dcreate2 failed"); if(nelmts) if(H5Dwrite(dset_out, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, refbuf) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dwrite failed"); if(buf) HDfree(buf); @@ -222,7 +222,7 @@ int do_copy_refobjs(hid_t fidin, * copy attrs *----------------------------------------------------*/ if(copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed"); } /*H5T_STD_REF_OBJ*/ /*------------------------------------------------------------------------- @@ -245,10 +245,10 @@ int do_copy_refobjs(hid_t fidin, buf = (hdset_reg_ref_t *)HDmalloc((unsigned)(nelmts * msize)); if(buf == NULL) { printf("cannot read into memory\n"); - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed"); } /* end if */ if(H5Dread(dset_in, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed"); /*------------------------------------------------------------------------- * create output @@ -257,12 +257,12 @@ int do_copy_refobjs(hid_t fidin, refbuf = (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), (size_t)nelmts); /*init to zero */ if(refbuf == NULL) { printf("cannot allocate memory\n"); - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDcalloc failed"); } /* end if */ for(u = 0; u < nelmts; u++) { H5E_BEGIN_TRY { - if((refobj_id = H5Rdereference(dset_in, H5R_DATASET_REGION, &buf[u])) < 0) + if((refobj_id = H5Rdereference2(dset_in, H5P_DEFAULT, H5R_DATASET_REGION, &buf[u])) < 0) continue; } H5E_END_TRY; @@ -273,18 +273,15 @@ int do_copy_refobjs(hid_t fidin, hid_t region_id; /* region id of the referenced dataset */ if((region_id = H5Rget_region(dset_in, H5R_DATASET_REGION, &buf[u])) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rget_region failed"); /* create the reference, we need the space_id */ if(H5Rcreate(&refbuf[u], fidout, refname, H5R_DATASET_REGION, region_id) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rcreate failed"); if(H5Sclose(region_id) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed"); if(options->verbose) { - - - printf(FORMAT_OBJ,"dset",travt->objs[i].name ); printf("object <%s> region reference created to <%s>\n", travt->objs[i].name, @@ -300,10 +297,10 @@ int do_copy_refobjs(hid_t fidin, *------------------------------------------------------------------------- */ if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, mtype_id, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dcreate2 failed"); if(nelmts) if(H5Dwrite(dset_out, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, refbuf) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dwrite failed"); if(buf) HDfree(buf); @@ -314,7 +311,7 @@ int do_copy_refobjs(hid_t fidin, * copy attrs *----------------------------------------------------*/ if(copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed"); } /* H5T_STD_REF_DSETREG */ /*------------------------------------------------------------------------- * not references, open previously created object in 1st traversal @@ -322,7 +319,7 @@ int do_copy_refobjs(hid_t fidin, */ else { if((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed"); } /* end else */ HDassert(dset_out != FAIL); @@ -332,7 +329,7 @@ int do_copy_refobjs(hid_t fidin, *------------------------------------------------------------------------- */ if(copy_refs_attr(dset_in, dset_out, options, travt, fidout) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_refs_attr failed"); /*------------------------------------------------------------------------- * check for hard links @@ -343,7 +340,7 @@ int do_copy_refobjs(hid_t fidin, H5Lcreate_hard(fidout, travt->objs[i].name, H5L_SAME_LOC, travt->objs[i].links[j].new_name, H5P_DEFAULT, H5P_DEFAULT); if(H5Dclose(dset_out) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); } /*can_read*/ /*------------------------------------------------------------------------- @@ -351,15 +348,15 @@ int do_copy_refobjs(hid_t fidin, *------------------------------------------------------------------------- */ if(H5Tclose(ftype_id) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); if(H5Tclose(mtype_id) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); if(H5Pclose(dcpl_id) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); if(H5Sclose(space_id) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed"); if(H5Dclose(dset_in) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); break; /*------------------------------------------------------------------------- @@ -368,9 +365,9 @@ int do_copy_refobjs(hid_t fidin, */ case H5TRAV_TYPE_NAMED_DATATYPE: if((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Topen2 failed"); if(H5Tclose(type_in) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); break; /*------------------------------------------------------------------------- @@ -383,7 +380,7 @@ int do_copy_refobjs(hid_t fidin, case H5TRAV_TYPE_UNKNOWN: case H5TRAV_TYPE_UDLINK: - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5TRAV invalid type"); default: break; @@ -396,9 +393,9 @@ int do_copy_refobjs(hid_t fidin, */ named_datatype_free(&named_dt_head, 0); - return 0; + return ret_value; -error: +done: H5E_BEGIN_TRY { H5Gclose(grp_in); H5Gclose(grp_out); @@ -412,7 +409,7 @@ error: named_datatype_free(&named_dt_head, 0); } H5E_END_TRY; - return -1; + return ret_value; } @@ -450,6 +447,7 @@ static int copy_refs_attr(hid_t loc_in, hid_t fidout /* for saving references */ ) { + int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ hid_t attr_id = -1; /* attr ID */ hid_t attr_out = -1; /* attr ID */ hid_t space_id = -1; /* space ID */ @@ -467,32 +465,32 @@ static int copy_refs_attr(hid_t loc_in, void *refbuf = NULL; void *buf = NULL; const char* refname = NULL; - int *ref_comp_index = NULL; + unsigned *ref_comp_index = NULL; size_t *ref_comp_size = NULL; int ref_comp_field_n = 0; if(H5Oget_info(loc_in, &oinfo) < 0) - goto error; + 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; /* 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) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aopen_by_idx failed"); /* get the file datatype */ if((ftype_id = H5Aget_type(attr_id)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aget_type failed"); type_class = H5Tget_class(ftype_id); if((mtype_id = h5tools_get_native_type(ftype_id)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5tools_get_native_type failed"); if((msize = H5Tget_size(mtype_id)) == 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed"); is_ref = (type_class == H5T_REFERENCE); @@ -516,10 +514,10 @@ static int copy_refs_attr(hid_t loc_in, int nmembers = H5Tget_nmembers(ftype_id) ; if (nmembers < 1) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_nmembers failed"); - ref_comp_index = (int *)HDmalloc(nmembers*sizeof (int)); - ref_comp_size = (size_t *)HDmalloc(nmembers*sizeof(ref_comp_size)); + ref_comp_index = (unsigned *)HDmalloc((size_t)nmembers*sizeof(unsigned)); + ref_comp_size = (size_t *)HDmalloc((size_t)nmembers*sizeof(ref_comp_size)); ref_comp_field_n = 0; for (i=0; i<(unsigned)nmembers; i++) { @@ -560,15 +558,15 @@ static int copy_refs_attr(hid_t loc_in, /* get name */ if(H5Aget_name(attr_id, 255, name) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aget_name failed"); /* get the dataspace handle */ if((space_id = H5Aget_space(attr_id)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aget_space failed"); /* get dimensions */ if((rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed"); /*------------------------------------------------------------------------- @@ -580,8 +578,8 @@ static int copy_refs_attr(hid_t loc_in, nelmts *= dims[j]; if (is_ref_array) { - unsigned array_rank = 0; - hsize_t array_size = 1; + unsigned array_rank = 0; + hsize_t array_size = 1; hsize_t array_dims[H5S_MAX_RANK]; hid_t base_type; @@ -589,7 +587,7 @@ static int copy_refs_attr(hid_t loc_in, msize = H5Tget_size(base_type); H5Tclose(base_type); - array_rank = H5Tget_array_ndims(mtype_id); + 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]; @@ -597,7 +595,7 @@ static int copy_refs_attr(hid_t loc_in, } if((attr_out = H5Acreate2(loc_out, name, ftype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Acreate2 failed"); if (nelmts>0) { /* handle object references */ @@ -605,15 +603,15 @@ static int copy_refs_attr(hid_t loc_in, buf = (hobj_ref_t *)HDmalloc((unsigned)(nelmts * msize)); if(buf == NULL) { printf("cannot read into memory\n"); - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed"); } /* end if */ if(H5Aread(attr_id, mtype_id, buf) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread failed"); refbuf = (hobj_ref_t *)HDcalloc((unsigned)nelmts, msize); if(refbuf == NULL) { printf("cannot allocate memory\n"); - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDcalloc failed"); } /* end if */ for(i = 0; i < (unsigned)nelmts; i++) { @@ -629,10 +627,10 @@ static int copy_refs_attr(hid_t loc_in, if(buf == NULL) { printf( "cannot read into memory\n" ); - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed"); } /* end if */ if(H5Aread(attr_id, mtype_id, buf) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread failed"); /*------------------------------------------------------------------------- * create output @@ -641,7 +639,7 @@ static int copy_refs_attr(hid_t loc_in, refbuf = (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), (size_t)nelmts); /*init to zero */ if(refbuf == NULL) { printf( "cannot allocate memory\n" ); - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDcalloc failed"); } /* end if */ for(i = 0; i < (unsigned)nelmts; i++) { @@ -659,11 +657,11 @@ static int copy_refs_attr(hid_t loc_in, if(buf == NULL) { printf( "cannot read into memory\n" ); - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed"); } /* end if */ if(H5Aread(attr_id, mtype_id, buf) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread failed"); if (H5R_OBJ_REF_BUF_SIZE==msize) { hobj_ref_t ref_out; @@ -700,41 +698,43 @@ static int copy_refs_attr(hid_t loc_in, if(buf == NULL) { printf( "cannot read into memory\n" ); - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed"); } /* end if */ if(H5Aread(attr_id, mtype_id, buf) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread failed"); for (i=0; i<(unsigned)nelmts; i++) { - for (j=0; j<(unsigned)ref_comp_field_n; j++) { - if (ref_comp_size[j] == H5R_OBJ_REF_BUF_SIZE) { - int idx = i*msize+H5Tget_member_offset( mtype_id, (unsigned)ref_comp_index[j]); - hobj_ref_t ref_out; - if (update_ref_value(attr_id, H5R_OBJECT, (hobj_ref_t *)(((char *)buf)+idx), fidout, &ref_out, travt)<0) - continue; - HDmemcpy(((char *)buf)+idx, &ref_out, ref_comp_size[j]); - } /* if */ - else if (ref_comp_size[j] == H5R_DSET_REG_REF_BUF_SIZE) { - int idx = i*msize+H5Tget_member_offset( mtype_id, (unsigned)ref_comp_index[j]); - hdset_reg_ref_t ref_out; - if (update_ref_value(attr_id, H5R_DATASET_REGION, (hdset_reg_ref_t *)(((char *)buf)+idx), fidout, &ref_out, travt)<0) - continue; - HDmemcpy(((char *)buf)+idx, &ref_out, ref_comp_size[j]); - } /* else if */ - } /* j */ + for (j=0; j<(unsigned)ref_comp_field_n; j++) { + if (ref_comp_size[j] == H5R_OBJ_REF_BUF_SIZE) { + size_t idx = (i * msize) + H5Tget_member_offset(mtype_id, ref_comp_index[j]); + hobj_ref_t ref_out; + + if (update_ref_value(attr_id, H5R_OBJECT, (hobj_ref_t *)(((char *)buf)+idx), fidout, &ref_out, travt)<0) + continue; + HDmemcpy(((char *)buf)+idx, &ref_out, ref_comp_size[j]); + } /* if */ + else if (ref_comp_size[j] == H5R_DSET_REG_REF_BUF_SIZE) { + size_t idx = i * msize + H5Tget_member_offset(mtype_id, ref_comp_index[j]); + hdset_reg_ref_t ref_out; + + if (update_ref_value(attr_id, H5R_DATASET_REGION, (hdset_reg_ref_t *)(((char *)buf)+idx), fidout, &ref_out, travt)<0) + continue; + HDmemcpy(((char *)buf)+idx, &ref_out, ref_comp_size[j]); + } /* else if */ + } /* j */ } /* i */ } /* else if (is_ref_comp) */ if(H5Awrite(attr_out, mtype_id, refbuf) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Awrite failed"); if (is_ref_vlen && buf) H5Dvlen_reclaim (mtype_id, space_id, H5P_DEFAULT, buf); } /* if (nelmts) */ if (refbuf == buf) - refbuf = NULL; /* set it to NULL to avoid double free since buf and refbuf are the same. */ + refbuf = NULL; /* set it to NULL to avoid double free since buf and refbuf are the same. */ if(buf) { HDfree(buf); @@ -747,39 +747,39 @@ static int copy_refs_attr(hid_t loc_in, } if (ref_comp_index) { - HDfree(ref_comp_index); - ref_comp_index = NULL; + HDfree(ref_comp_index); + ref_comp_index = NULL; } if (ref_comp_size) { - HDfree(ref_comp_size); - ref_comp_size = NULL; + HDfree(ref_comp_size); + ref_comp_size = NULL; } if(H5Aclose(attr_out) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aclose failed"); /*------------------------------------------------------------------------- * close *------------------------------------------------------------------------- */ if(H5Tclose(ftype_id) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); if(H5Tclose(mtype_id) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); if(H5Sclose(space_id) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed"); if(H5Aclose(attr_id) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aclose failed"); } /* for(u = 0; u < (unsigned)oinfo.num_attrs; u++) */ - return 0; + return ret_value; -error: - if(refbuf) - HDfree(refbuf); - if(buf) - HDfree(buf); +done: + if(refbuf) + HDfree(refbuf); + if(buf) + HDfree(buf); if (ref_comp_index) HDfree(ref_comp_index); @@ -795,7 +795,7 @@ error: H5Aclose(attr_out); } H5E_END_TRY; - return -1; + return ret_value; } /*------------------------------------------------------------------------- @@ -845,30 +845,26 @@ out: 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) { - herr_t ret = -1; - const char* ref_obj_name; - hid_t space_id=-1, ref_obj_id=-1; - - ref_obj_id = H5Rdereference(obj_id, ref_type, ref_in); - if (ref_obj_id<0) - goto done; - - ref_obj_name = MapIdToName(ref_obj_id, travt); - if (ref_obj_name == NULL) - goto done; + int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ + const char* ref_obj_name; + hid_t space_id=-1, ref_obj_id=-1; - if (ref_type == H5R_DATASET_REGION) { - space_id = H5Rget_region(obj_id, H5R_DATASET_REGION, ref_in); - if (space_id < 0) - goto done; - } + ref_obj_id = H5Rdereference2(obj_id, H5P_DEFAULT, ref_type, ref_in); + if (ref_obj_id < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rdereference2 failed"); - ret = H5Rcreate(ref_out, fid_out, ref_obj_name, ref_type, space_id); + ref_obj_name = MapIdToName(ref_obj_id, travt); + if (ref_obj_name == NULL) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "MapIdToName failed"); - if (ret < 0) - goto done; + if (ref_type == H5R_DATASET_REGION) { + space_id = H5Rget_region(obj_id, H5R_DATASET_REGION, ref_in); + if (space_id < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rget_region failed"); + } - ret = 0; + if(H5Rcreate(ref_out, fid_out, ref_obj_name, ref_type, space_id) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rcreate failed"); done: H5E_BEGIN_TRY { @@ -876,6 +872,6 @@ done: H5Oclose(ref_obj_id); } H5E_END_TRY; - return ret; + return ret_value; } diff --git a/tools/h5repack/h5repack_verify.c b/tools/h5repack/h5repack_verify.c index cec9c86..f393dd1 100644 --- a/tools/h5repack/h5repack_verify.c +++ b/tools/h5repack/h5repack_verify.c @@ -51,11 +51,12 @@ static int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *fil int h5repack_verify(const char *out_fname, pack_opt_t *options) { - hid_t fidout; /* file ID for output file*/ - hid_t did; /* dataset ID */ - hid_t pid; /* dataset creation property list ID */ - hid_t sid; /* space ID */ - hid_t tid; /* type ID */ + int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ + hid_t fidout = -1; /* file ID for output file*/ + hid_t did = -1; /* dataset ID */ + hid_t pid = -1; /* dataset creation property list ID */ + hid_t sid = -1; /* space ID */ + hid_t tid = -1; /* type ID */ unsigned int i; trav_table_t *travt = NULL; int ok = 1; @@ -74,20 +75,20 @@ h5repack_verify(const char *out_fname, pack_opt_t *options) *------------------------------------------------------------------------- */ if((did = H5Dopen2(fidout, name, H5P_DEFAULT)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed"); if((sid = H5Dget_space(did)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed"); if((pid = H5Dget_create_plist(did)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed"); if((tid = H5Dget_type(did)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_type failed"); /*------------------------------------------------------------------------- * filter check *------------------------------------------------------------------------- */ if(verify_filters(pid, tid, obj->nfilters, obj->filter) <= 0) - ok = 0; + ok = 0; /*------------------------------------------------------------------------- @@ -102,13 +103,13 @@ h5repack_verify(const char *out_fname, pack_opt_t *options) *------------------------------------------------------------------------- */ if(H5Pclose(pid) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); if (H5Sclose(sid) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed"); if (H5Dclose(did) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); if (H5Tclose(tid) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); } @@ -126,7 +127,7 @@ h5repack_verify(const char *out_fname, pack_opt_t *options) /* get the list of objects in the file */ if(h5trav_gettable(fidout, travt) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5trav_gettable failed"); for(i = 0; i < travt->nobjs; i++) { @@ -140,13 +141,13 @@ h5repack_verify(const char *out_fname, pack_opt_t *options) *------------------------------------------------------------------------- */ if((did = H5Dopen2(fidout, name, H5P_DEFAULT)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed"); if((sid = H5Dget_space(did)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed"); if((pid = H5Dget_create_plist(did)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed"); if((tid = H5Dget_type(did)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_type failed"); /*------------------------------------------------------------------------- * filter check @@ -154,7 +155,6 @@ h5repack_verify(const char *out_fname, pack_opt_t *options) */ if(options->all_filter == 1) { - if(verify_filters(pid, tid, options->n_filter_g, options->filter_g) <= 0) ok = 0; } @@ -166,6 +166,7 @@ h5repack_verify(const char *out_fname, pack_opt_t *options) if(options->all_layout == 1) { pack_info_t pack; + init_packobject(&pack); pack.layout = options->layout_g; pack.chunk = options->chunk_g; @@ -179,13 +180,13 @@ h5repack_verify(const char *out_fname, pack_opt_t *options) *------------------------------------------------------------------------- */ if (H5Pclose(pid) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); if (H5Sclose(sid) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed"); if (H5Dclose(did) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); if (H5Tclose(tid) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); } /* if */ } /* i */ @@ -200,20 +201,24 @@ h5repack_verify(const char *out_fname, pack_opt_t *options) */ if (H5Fclose(fidout) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fclose failed"); return ok; -error: +done: H5E_BEGIN_TRY { + H5Pclose(fcpl_in); + H5Pclose(fcpl_out); H5Pclose(pid); H5Sclose(sid); H5Dclose(did); + H5Fclose(fidin); H5Fclose(fidout); if (travt) trav_table_free(travt); } H5E_END_TRY; - return -1; + + return ret_value; } /* h5repack_verify() */ @@ -291,6 +296,7 @@ int verify_layout(hid_t pid, int h5repack_cmp_pl(const char *fname1, const char *fname2) { + int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ hid_t fid1=-1; /* file ID */ hid_t fid2=-1; /* file ID */ hid_t dset1=-1; /* dataset ID */ @@ -315,12 +321,12 @@ int h5repack_cmp_pl(const char *fname1, { /* Open the files */ - if ((fid1=H5Fopen(fname1,H5F_ACC_RDONLY,H5P_DEFAULT)) < 0 ) + if ((fid1 = H5Fopen(fname1,H5F_ACC_RDONLY,H5P_DEFAULT)) < 0 ) { error_msg("<%s>: %s\n", fname1, H5FOPENERROR ); return -1; } - if ((fid2=H5Fopen(fname2,H5F_ACC_RDONLY,H5P_DEFAULT)) < 0 ) + if ((fid2 = H5Fopen(fname2,H5F_ACC_RDONLY,H5P_DEFAULT)) < 0 ) { error_msg("<%s>: %s\n", fname2, H5FOPENERROR ); H5Fclose(fid1); @@ -335,7 +341,7 @@ int h5repack_cmp_pl(const char *fname1, */ trav_table_init(&trav); if(h5trav_gettable(fid1, trav) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5trav_gettable failed"); /*------------------------------------------------------------------------- * traverse the suppplied object list @@ -348,31 +354,30 @@ int h5repack_cmp_pl(const char *fname1, { if ((gid = H5Gopen2(fid1, trav->objs[i].name, H5P_DEFAULT)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed"); if ((gcplid = H5Gget_create_plist(gid)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gget_create_plist failed"); if (H5Pget_link_creation_order(gcplid, &crt_order_flag1) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_link_creation_order failed"); if (H5Pclose(gcplid) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); if (H5Gclose(gid) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed"); if ((gid = H5Gopen2(fid2, trav->objs[i].name, H5P_DEFAULT)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed"); if ((gcplid = H5Gget_create_plist(gid)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gget_create_plist failed"); if (H5Pget_link_creation_order(gcplid, &crt_order_flag2) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_link_creation_order failed"); if (H5Pclose(gcplid) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); if (H5Gclose(gid) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed"); - if ( crt_order_flag1 != crt_order_flag2 ) - { + if (crt_order_flag1 != crt_order_flag2) { error_msg("property lists for <%s> are different\n",trav->objs[i].name); - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "property lists failed"); } } @@ -382,25 +387,24 @@ int h5repack_cmp_pl(const char *fname1, else if(trav->objs[i].type == H5TRAV_TYPE_DATASET) { if((dset1 = H5Dopen2(fid1, trav->objs[i].name, H5P_DEFAULT)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed"); if((dset2 = H5Dopen2(fid2, trav->objs[i].name, H5P_DEFAULT)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed"); if((dcpl1 = H5Dget_create_plist(dset1)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed"); if((dcpl2 = H5Dget_create_plist(dset2)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed"); /*------------------------------------------------------------------------- * compare the property lists *------------------------------------------------------------------------- */ if((ret = H5Pequal(dcpl1, dcpl2)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pequal failed"); - if(ret == 0) - { + if(ret == 0) { error_msg("property lists for <%s> are different\n",trav->objs[i].name); - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "property lists failed"); } /*------------------------------------------------------------------------- @@ -408,13 +412,13 @@ int h5repack_cmp_pl(const char *fname1, *------------------------------------------------------------------------- */ if(H5Pclose(dcpl1) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); if(H5Pclose(dcpl2) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); if(H5Dclose(dset1) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); if(H5Dclose(dset2) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); } /*if*/ } /*i*/ @@ -432,14 +436,14 @@ int h5repack_cmp_pl(const char *fname1, H5Fclose(fid1); H5Fclose(fid2); - return ret; - /*------------------------------------------------------------------------- - * error - *------------------------------------------------------------------------- - */ + return ret; -error: +/*------------------------------------------------------------------------- +* error +*------------------------------------------------------------------------- +*/ +done: H5E_BEGIN_TRY { H5Pclose(dcpl1); @@ -452,8 +456,8 @@ error: H5Gclose(gid); trav_table_free(trav); } H5E_END_TRY; - return -1; + return ret_value; } @@ -522,100 +526,71 @@ int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter) switch (filtn) { - case H5Z_FILTER_NONE: + case H5Z_FILTER_NONE: break; - case H5Z_FILTER_SHUFFLE: - - /* 1 private client value is returned by DCPL */ - if ( cd_nelmts != H5Z_SHUFFLE_TOTAL_NPARMS && filter[i].cd_nelmts != H5Z_SHUFFLE_USER_NPARMS ) - return 0; - - /* get dataset's type size */ - if((size = H5Tget_size(tid)) <= 0) - return -1; - - /* the private client value holds the dataset's type size */ - if ( size != cd_values[0] ) - return 0; - - - break; - - case H5Z_FILTER_SZIP: - - /* 4 private client values are returned by DCPL */ - if ( cd_nelmts != H5Z_SZIP_TOTAL_NPARMS && filter[i].cd_nelmts != H5Z_SZIP_USER_NPARMS ) - return 0; - - /* "User" parameter for pixels-per-block (index 1) */ - if ( cd_values[H5Z_SZIP_PARM_PPB] != filter[i].cd_values[H5Z_SZIP_PARM_PPB] ) - return 0; - - - break; - - case H5Z_FILTER_NBIT: - - /* only client data values number of values checked */ - if ( H5Z_NBIT_USER_NPARMS != filter[i].cd_nelmts) - return 0; - - - - break; + case H5Z_FILTER_SHUFFLE: + /* 1 private client value is returned by DCPL */ + if ( cd_nelmts != H5Z_SHUFFLE_TOTAL_NPARMS && filter[i].cd_nelmts != H5Z_SHUFFLE_USER_NPARMS ) + return 0; - case H5Z_FILTER_SCALEOFFSET: + /* get dataset's type size */ + if((size = H5Tget_size(tid)) <= 0) + return -1; - /* only client data values checked */ - for( j = 0; j < H5Z_SCALEOFFSET_USER_NPARMS; j++) - { - if (cd_values[j] != filter[i].cd_values[j]) - { + /* the private client value holds the dataset's type size */ + if ( size != cd_values[0] ) return 0; - } - - } + break; - break; + case H5Z_FILTER_SZIP: + /* 4 private client values are returned by DCPL */ + if ( cd_nelmts != H5Z_SZIP_TOTAL_NPARMS && filter[i].cd_nelmts != H5Z_SZIP_USER_NPARMS ) + return 0; - /* for these filters values must match, no local values set in DCPL */ - case H5Z_FILTER_FLETCHER32: - case H5Z_FILTER_DEFLATE: + /* "User" parameter for pixels-per-block (index 1) */ + if ( cd_values[H5Z_SZIP_PARM_PPB] != filter[i].cd_values[H5Z_SZIP_PARM_PPB] ) + return 0; - if ( cd_nelmts != filter[i].cd_nelmts) - return 0; + break; - for( j = 0; j < cd_nelmts; j++) - { - if (cd_values[j] != filter[i].cd_values[j]) - { + case H5Z_FILTER_NBIT: + /* only client data values number of values checked */ + if ( H5Z_NBIT_USER_NPARMS != filter[i].cd_nelmts) return 0; - } + break; - } + case H5Z_FILTER_SCALEOFFSET: + /* only client data values checked */ + for( j = 0; j < H5Z_SCALEOFFSET_USER_NPARMS; j++) + if (cd_values[j] != filter[i].cd_values[j]) + return 0; + break; + /* for these filters values must match, no local values set in DCPL */ + case H5Z_FILTER_FLETCHER32: + case H5Z_FILTER_DEFLATE: + if ( cd_nelmts != filter[i].cd_nelmts) + return 0; - break; + for( j = 0; j < cd_nelmts; j++) + if (cd_values[j] != filter[i].cd_values[j]) + return 0; - default: - if ( cd_nelmts != filter[i].cd_nelmts) - return 0; + break; - for( j = 0; j < cd_nelmts; j++) - { - if (cd_values[j] != filter[i].cd_values[j]) - { - return 0; - } + default: + if ( cd_nelmts != filter[i].cd_nelmts) + return 0; - } - break; + for( j = 0; j < cd_nelmts; j++) + if (cd_values[j] != filter[i].cd_values[j]) + return 0; + break; } /* switch */ - } return 1; diff --git a/tools/h5repack/h5repacktst.c b/tools/h5repack/h5repacktst.c index f49e587..d0b182c 100644 --- a/tools/h5repack/h5repacktst.c +++ b/tools/h5repack/h5repacktst.c @@ -1536,15 +1536,15 @@ int main (void) { hid_t fapl; - /* setup */ - h5_reset(); fapl = h5_fileaccess(); - h5_cleanup(H5REPACK_FILENAMES, fapl); + h5_clean_files(H5REPACK_FILENAMES, fapl); } puts("All h5repack tests passed."); + h5tools_close(); + return 0; error: @@ -3361,7 +3361,7 @@ make_userblock(void) /* Initialize userblock data */ for(u = 0; u < USERBLOCK_SIZE; u++) - ub[u] = 'a' + (char)(u % 26); + ub[u] = (char)('a' + (char)(u % 26)); /* Re-open HDF5 file, as "plain" file */ if((fd = HDopen(FNAME16, O_WRONLY, 0644)) < 0) @@ -3474,7 +3474,7 @@ make_userblock_file(void) /* initialize userblock data */ for(u = 0; u < USERBLOCK_SIZE; u++) - ub[u] = 'a' + (char)(u % 26); + ub[u] = (char)('a' + (char)(u % 26)); /* open file */ if((fd = HDopen(FNAME_UB,O_WRONLY|O_CREAT|O_TRUNC, 0644 )) < 0) @@ -3531,7 +3531,8 @@ int write_dset_in(hid_t loc_id, hid_t sid=-1; hid_t tid=-1; hid_t pid=-1; - int val, i, j, k, n; + unsigned i, j; + int val, k, n; float f; /* create 1D attributes with dimension [2], 2 elements */ @@ -3586,13 +3587,10 @@ int write_dset_in(hid_t loc_id, */ - if (make_diffs) - { - for (i=0; i<2; i++) - for (j=0; j<2; j++) - { - buf1[i][j]='z'; - } + if(make_diffs) { + for(i = 0; i < 2; i++) + for(j = 0; j < 2; j++) + buf1[i][j] = 'z'; } @@ -3615,10 +3613,9 @@ int write_dset_in(hid_t loc_id, *------------------------------------------------------------------------- */ - if (make_diffs) - { - for (i=0; i<2; i++) - buf2[i]=buf2[1]=0; + if(make_diffs) { + for(i = 0; i < 2; i++) + buf2[i] = buf2[1] = 0; } if ((tid = H5Tcopy(H5T_STD_B8LE)) < 0) @@ -3633,11 +3630,10 @@ int write_dset_in(hid_t loc_id, *------------------------------------------------------------------------- */ - if (make_diffs) - { - for (i=0; i<2; i++) - { - buf3[i].a=0; buf3[i].b=0; + if(make_diffs) { + for(i = 0; i < 2; i++) { + buf3[i].a = 0; + buf3[i].b = 0; } } @@ -3656,12 +3652,9 @@ int write_dset_in(hid_t loc_id, */ - if (make_diffs) - { - for (i=0; i<2; i++) - { - buf45[i]=GREEN; - } + if(make_diffs) { + for(i = 0; i < 2; i++) + buf45[i] = GREEN; } if ((tid = H5Tcreate (H5T_COMPOUND, sizeof(s_t))) < 0) @@ -3753,13 +3746,10 @@ int write_dset_in(hid_t loc_id, *------------------------------------------------------------------------- */ - if (make_diffs) - { - for (i=0; i<2; i++) - for (j=0; j<3; j++) - { - buf6[i][j]=0; - } + if(make_diffs) { + for(i = 0; i < 2; i++) + for(j = 0; j < 3; j++) + buf6[i][j] = 0; } if ((tid = H5Tarray_create2(H5T_NATIVE_INT, 1, dimarray)) < 0) @@ -3820,12 +3810,10 @@ int write_dset_in(hid_t loc_id, *------------------------------------------------------------------------- */ - if (make_diffs) - { - for (i=0; i<2; i++) - { - buf7[i]=0; - buf8[i]=0; + if(make_diffs) { + for(i = 0; i < 2; i++) { + buf7[i] = 0; + buf8[i] = 0; } } @@ -3948,16 +3936,13 @@ int write_dset_in(hid_t loc_id, /* Allocate and initialize VL dataset to write */ n = 0; - for(i = 0; i < 3; i++) - { - for(j = 0; j < 2; j++) - { - int l; + for(i = 0; i < 3; i++) { + for(j = 0; j < 2; j++) { + unsigned l; buf52[i][j].p = HDmalloc((i + 1) * sizeof(int)); buf52[i][j].len = (size_t)(i + 1); - for(l = 0; l < i + 1; l++) - { + for(l = 0; l < i + 1; l++) { if(make_diffs) ((int *)buf52[i][j].p)[l] = 0; else @@ -4068,11 +4053,13 @@ int write_dset_in(hid_t loc_id, n=1; - for (i = 0; i < 4; i++) { - for (j = 0; j < 3; j++) { - for (k = 0; k < 2; k++) { - if (make_diffs) buf23[i][j][k]=0; - else buf23[i][j][k]=n++; + for(i = 0; i < 4; i++) { + for(j = 0; j < 3; j++) { + for(k = 0; k < 2; k++) { + if(make_diffs) + buf23[i][j][k] = 0; + else + buf23[i][j][k] = (char)(n++); } } } @@ -4104,16 +4091,16 @@ int write_dset_in(hid_t loc_id, */ n=1; - for (i = 0; i < 4; i++) { - for (j = 0; j < 3; j++) { - for (k = 0; k < 2; k++) { - if (make_diffs) { - buf33[i][j][k].a=0; - buf33[i][j][k].b=0; + for(i = 0; i < 4; i++) { + for(j = 0; j < 3; j++) { + for(k = 0; k < 2; k++) { + if(make_diffs) { + buf33[i][j][k].a = 0; + buf33[i][j][k].b = 0; } else { - buf33[i][j][k].a=n++; - buf33[i][j][k].b=n++; + buf33[i][j][k].a = (char)(n++); + buf33[i][j][k].b = n++; } } } @@ -4167,18 +4154,14 @@ int write_dset_in(hid_t loc_id, /* Allocate and initialize VL dataset to write */ n = 0; - for(i = 0; i < 4; i++) - { - for(j = 0; j < 3; j++) - { - for(k = 0; k < 2; k++) - { - int l; + for(i = 0; i < 4; i++) { + for(j = 0; j < 3; j++) { + for(k = 0; k < 2; k++) { + unsigned l; buf53[i][j][k].p = HDmalloc((i + 1) * sizeof(int)); buf53[i][j][k].len = (size_t)(i + 1); - for(l = 0; l < i + 1; l++) - { + for(l = 0; l < i + 1; l++) { if(make_diffs) ((int *)buf53[i][j][k].p)[l] = 0; else @@ -4214,10 +4197,8 @@ int write_dset_in(hid_t loc_id, n = 1; - for(i = 0; i < 24; i++) - { - for(j = 0; j < (int)dimarray[0]; j++) - { + for(i = 0; i < 24; i++) { + for(j = 0; j < dimarray[0]; j++) { if(make_diffs) buf63[i][j] = 0; else @@ -4256,13 +4237,10 @@ int write_dset_in(hid_t loc_id, if (write_dset(loc_id,3,dims3,"float3D",H5T_NATIVE_FLOAT,buf83) < 0) goto out; - return 0; - out: - H5E_BEGIN_TRY - { + H5E_BEGIN_TRY { H5Pclose(pid); H5Sclose(sid); H5Dclose(did); @@ -4411,7 +4389,8 @@ int write_attr_in(hid_t loc_id, hid_t aid = -1; hid_t sid = -1; hid_t tid = -1; - int val, i, j, k, n; + int val, j, k, n; + unsigned i; float f; /* create 1D attributes with dimension [2], 2 elements */ @@ -4961,16 +4940,17 @@ int write_attr_in(hid_t loc_id, /* Allocate and initialize VL dataset to write */ n=0; - for (i = 0; i < 3; i++) - { - for (j = 0; j < 2; j++) - { - int l; + for(i = 0; i < 3; i++) { + for(j = 0; j < 2; j++) { + unsigned l; + buf52[i][j].p = HDmalloc((i + 1) * sizeof(int)); buf52[i][j].len = (size_t)(i + 1); - for (l = 0; l < i + 1; l++) - if (make_diffs)((int *)buf52[i][j].p)[l] = 0; - else ((int *)buf52[i][j].p)[l] = n++; + for(l = 0; l < i + 1; l++) + if(make_diffs) + ((int *)buf52[i][j].p)[l] = 0; + else + ((int *)buf52[i][j].p)[l] = n++; } } @@ -5179,14 +5159,13 @@ int write_attr_in(hid_t loc_id, */ n=1; - for (i = 0; i < 4; i++) - { - for (j = 0; j < 3; j++) - { - for (k = 0; k < 2; k++) - { - if (make_diffs) buf23[i][j][k]=0; - else buf23[i][j][k]=n++; + for(i = 0; i < 4; i++) { + for(j = 0; j < 3; j++) { + for(k = 0; k < 2; k++) { + if(make_diffs) + buf23[i][j][k] = 0; + else + buf23[i][j][k] = (char)(n++); } } } @@ -5248,21 +5227,16 @@ int write_attr_in(hid_t loc_id, */ n=1; - for (i = 0; i < 4; i++) - { - for (j = 0; j < 3; j++) - { - for (k = 0; k < 2; k++) - { - if (make_diffs) - { - buf33[i][j][k].a=0; - buf33[i][j][k].b=0; + for(i = 0; i < 4; i++) { + for(j = 0; j < 3; j++) { + for(k = 0; k < 2; k++) { + if(make_diffs) { + buf33[i][j][k].a = 0; + buf33[i][j][k].b = 0; } - else - { - buf33[i][j][k].a=n++; - buf33[i][j][k].b=n++; + else { + buf33[i][j][k].a = (char)(n++); + buf33[i][j][k].b = n++; } } } @@ -5431,14 +5405,13 @@ int write_attr_in(hid_t loc_id, { for (k = 0; k < 2; k++) { - int l; + unsigned l; + buf53[i][j][k].p = HDmalloc((i + 1) * sizeof(int)); buf53[i][j][k].len = (size_t)i + 1; for (l = 0; l < i + 1; l++) if (make_diffs) - { ((int *)buf53[i][j][k].p)[l] = 0; - } else ((int *)buf53[i][j][k].p)[l] = n++; } @@ -5562,8 +5535,7 @@ int write_attr_in(hid_t loc_id, return 0; out: - H5E_BEGIN_TRY - { + H5E_BEGIN_TRY { H5Aclose(aid); H5Sclose(sid); H5Tclose(tid); diff --git a/tools/h5repack/testfiles/h5repack_filters.h5-gzip_verbose_filters.tst b/tools/h5repack/testfiles/h5repack_filters.h5-gzip_verbose_filters.tst new file mode 100644 index 0000000..36e65b9 --- /dev/null +++ b/tools/h5repack/testfiles/h5repack_filters.h5-gzip_verbose_filters.tst @@ -0,0 +1,13 @@ +Objects to modify layout are... +Objects to apply filter are... + </dset_deflate> with GZIP filter + </dset_deflate>...Found +----------------------------------------- + Type Filter (Compression) Name +----------------------------------------- + group / + dset /dset_all + dset GZIP (0.995:1) /dset_deflate + dset /dset_fletcher32 + dset /dset_nbit + dset /dset_shuffle |