diff options
Diffstat (limited to 'tools/src')
| -rw-r--r-- | tools/src/h5dump/h5dump.c | 4 | ||||
| -rw-r--r-- | tools/src/h5dump/h5dump_ddl.c | 67 | ||||
| -rw-r--r-- | tools/src/h5dump/h5dump_xml.c | 171 | ||||
| -rw-r--r-- | tools/src/h5format_convert/h5format_convert.c | 2 | ||||
| -rw-r--r-- | tools/src/h5import/h5import.c | 41 | ||||
| -rw-r--r-- | tools/src/h5ls/h5ls.c | 32 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack.c | 36 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack.h | 2 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack_copy.c | 2 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack_refs.c | 15 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack_verify.c | 6 | ||||
| -rw-r--r-- | tools/src/h5stat/h5stat.c | 53 |
12 files changed, 251 insertions, 180 deletions
diff --git a/tools/src/h5dump/h5dump.c b/tools/src/h5dump/h5dump.c index 731fcd7..d97fdc0 100644 --- a/tools/src/h5dump/h5dump.c +++ b/tools/src/h5dump/h5dump.c @@ -1398,7 +1398,7 @@ main(int argc, const char *argv[]) hid_t fapl_id = H5P_DEFAULT; H5E_auto2_t func; H5E_auto2_t tools_func; - H5O_info_t oi; + H5O_info2_t oi; struct handler_t *hand = NULL; int i; unsigned u; @@ -1567,7 +1567,7 @@ main(int argc, const char *argv[]) } /* Get object info for root group */ - if(H5Oget_info_by_name2(fid, "/", &oi, H5O_INFO_BASIC, H5P_DEFAULT) < 0) { + if(H5Oget_info_by_name3(fid, "/", &oi, H5O_INFO_BASIC, H5P_DEFAULT) < 0) { error_msg("internal error (file %s:line %d)\n", __FILE__, __LINE__); h5tools_setstatus(EXIT_FAILURE); goto done; diff --git a/tools/src/h5dump/h5dump_ddl.c b/tools/src/h5dump/h5dump_ddl.c index 2eb11fd..a410fda 100644 --- a/tools/src/h5dump/h5dump_ddl.c +++ b/tools/src/h5dump/h5dump_ddl.c @@ -31,7 +31,7 @@ typedef struct { } trav_attr_udata_t; /* callback function used by H5Literate() */ -static herr_t dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void *op_data); +static herr_t dump_all_cb(hid_t group, const char *name, const H5L_info2_t *linfo, void *op_data); static int dump_extlink(hid_t group, const char *linkname, const char *objname); /*------------------------------------------------------------------------- @@ -152,7 +152,7 @@ dump_attr_cb(hid_t oid, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED * *------------------------------------------------------------------------- */ static herr_t -dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void H5_ATTR_UNUSED *op_data) +dump_all_cb(hid_t group, const char *name, const H5L_info2_t *linfo, void H5_ATTR_UNUSED *op_data) { hid_t obj; hid_t dapl_id = H5P_DEFAULT; /* dataset access property list ID */ @@ -200,10 +200,10 @@ dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void H5_ATTR HDstrcat(obj_path, name); if(linfo->type == H5L_TYPE_HARD) { - H5O_info_t oinfo; + H5O_info2_t oinfo; /* Stat the object */ - if(H5Oget_info_by_name2(group, name, &oinfo, H5O_INFO_BASIC, H5P_DEFAULT) < 0) { + if(H5Oget_info_by_name3(group, name, &oinfo, H5O_INFO_BASIC, H5P_DEFAULT) < 0) { error_msg("unable to get object information for \"%s\"\n", name); h5tools_setstatus(EXIT_FAILURE); ret = FAIL; @@ -259,7 +259,7 @@ dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void H5_ATTR if(oinfo.rc > 1 || hit_elink) { obj_t *found_obj; /* Found object */ - found_obj = search_obj(dset_table, oinfo.addr); + found_obj = search_obj(dset_table, &oinfo.token); if(found_obj == NULL) { ctx.indent_level++; @@ -596,9 +596,9 @@ link_iteration(hid_t gid, unsigned crt_order_flags) /* if there is a request to do H5_INDEX_CRT_ORDER and tracking order is set in the group, then, sort by creation order, otherwise by name */ if((sort_by == H5_INDEX_CRT_ORDER) && (crt_order_flags & H5P_CRT_ORDER_TRACKED)) - H5Literate(gid, sort_by, sort_order, NULL, dump_all_cb, NULL); + H5Literate2(gid, sort_by, sort_order, NULL, dump_all_cb, NULL); else - H5Literate(gid, H5_INDEX_NAME, sort_order, NULL, dump_all_cb, NULL); + H5Literate2(gid, H5_INDEX_NAME, sort_order, NULL, dump_all_cb, NULL); } /*------------------------------------------------------------------------- @@ -612,7 +612,7 @@ link_iteration(hid_t gid, unsigned crt_order_flags) void dump_named_datatype(hid_t tid, const char *name) { - H5O_info_t oinfo; + H5O_info2_t oinfo; unsigned attr_crt_order_flags; hid_t tcpl_id = H5I_INVALID_HID; /* datatype creation property list ID */ hsize_t curr_pos = 0; /* total data element position */ @@ -670,7 +670,7 @@ dump_named_datatype(hid_t tid, const char *name) h5tools_dump_header_format->datatypeblockbegin); h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - H5Oget_info2(tid, &oinfo, H5O_INFO_BASIC); + H5Oget_info3(tid, &oinfo, H5O_INFO_BASIC); /* Must check for uniqueness of all objects if we've traversed an elink, * otherwise only check if the reference count > 1. @@ -678,7 +678,7 @@ dump_named_datatype(hid_t tid, const char *name) if(oinfo.rc > 1 || hit_elink) { obj_t *found_obj; /* Found object */ - found_obj = search_obj(type_table, oinfo.addr); + found_obj = search_obj(type_table, &oinfo.token); if (found_obj == NULL) { error_msg("internal error (file %s:line %d)\n", __FILE__, __LINE__); @@ -739,7 +739,7 @@ done: void dump_group(hid_t gid, const char *name) { - H5O_info_t oinfo; + H5O_info2_t oinfo; hid_t dset; hid_t type; hid_t gcpl_id; @@ -816,9 +816,15 @@ dump_group(hid_t gid, const char *name) /* dump unamed type in root group */ for(u = 0; u < type_table->nobjs; u++) if(!type_table->objs[u].recorded) { + char *obj_addr_str = NULL; + dset = H5Dopen2(gid, type_table->objs[u].objname, H5P_DEFAULT); type = H5Dget_type(dset); - HDsprintf(type_name, "#"H5_PRINTF_HADDR_FMT, type_table->objs[u].objno); + + H5Otoken_to_str(dset, &type_table->objs[u].obj_token, &obj_addr_str); + HDsprintf(type_name, "#%s", obj_addr_str); + H5free_memory(obj_addr_str); + dump_function_table->dump_named_datatype_function(type, type_name); H5Tclose(type); H5Dclose(dset); @@ -830,7 +836,7 @@ dump_group(hid_t gid, const char *name) h5tools_dump_comment(rawoutstream, outputformat, &ctx, gid); - H5Oget_info2(gid, &oinfo, H5O_INFO_BASIC); + H5Oget_info3(gid, &oinfo, H5O_INFO_BASIC); /* Must check for uniqueness of all objects if we've traversed an elink, * otherwise only check if the reference count > 1. @@ -838,7 +844,7 @@ dump_group(hid_t gid, const char *name) if(oinfo.rc > 1 || hit_elink) { obj_t *found_obj; /* Found object */ - found_obj = search_obj(group_table, oinfo.addr); + found_obj = search_obj(group_table, &oinfo.token); if (found_obj == NULL) { error_msg("internal error (file %s:line %d)\n", __FILE__, __LINE__); @@ -1251,8 +1257,13 @@ dump_fcontents(hid_t fid) unsigned u; for (u = 0; u < type_table->nobjs; u++) { - if (!type_table->objs[u].recorded) - PRINTSTREAM(rawoutstream, " %-10s /#"H5_PRINTF_HADDR_FMT"\n", "datatype", type_table->objs[u].objno); + if (!type_table->objs[u].recorded) { + char *obj_addr_str = NULL; + + H5Otoken_to_str(fid, &type_table->objs[u].obj_token, &obj_addr_str); + PRINTSTREAM(rawoutstream, " %-10s /#%s\n", "datatype", obj_addr_str); + H5free_memory(obj_addr_str); + } } } @@ -1319,7 +1330,7 @@ attr_search(hid_t oid, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED *a } /* end attr_search() */ static herr_t -obj_search(const char *path, const H5O_info_t *oi, const char H5_ATTR_UNUSED *already_visited, void *_op_data) +obj_search(const char *path, const H5O_info2_t *oi, const char H5_ATTR_UNUSED *already_visited, void *_op_data) { trav_handle_udata_t *handle_data = (trav_handle_udata_t*)_op_data; const char *op_name = handle_data->op_name; @@ -1356,7 +1367,7 @@ obj_search(const char *path, const H5O_info_t *oi, const char H5_ATTR_UNUSED *al } /* end obj_search() */ static herr_t -lnk_search(const char *path, const H5L_info_t *li, void *_op_data) +lnk_search(const char *path, const H5L_info2_t *li, void *_op_data) { size_t search_len; size_t k; @@ -1608,7 +1619,7 @@ error: void handle_datasets(hid_t fid, const char *dset, void *data, int pe, const char *display_name) { - H5O_info_t oinfo; + H5O_info2_t oinfo; hid_t dsetid; hid_t dapl_id = H5P_DEFAULT; /* dataset access property list ID */ struct subset_t *sset = (struct subset_t *)data; @@ -1719,11 +1730,11 @@ handle_datasets(hid_t fid, const char *dset, void *data, int pe, const char *dis } /* end if */ - H5Oget_info2(dsetid, &oinfo, H5O_INFO_BASIC); + H5Oget_info3(dsetid, &oinfo, H5O_INFO_BASIC); if(oinfo.rc > 1 || hit_elink) { obj_t *found_obj; /* Found object */ - found_obj = search_obj(dset_table, oinfo.addr); + found_obj = search_obj(dset_table, &oinfo.token); if(found_obj) { if (found_obj->displayed) { @@ -1812,9 +1823,9 @@ handle_groups(hid_t fid, const char *group, void H5_ATTR_UNUSED *data, int pe, c void handle_links(hid_t fid, const char *links, void H5_ATTR_UNUSED * data, int H5_ATTR_UNUSED pe, const char H5_ATTR_UNUSED *display_name) { - H5L_info_t linfo; + H5L_info2_t linfo; - if(H5Lget_info(fid, links, &linfo, H5P_DEFAULT) < 0) { + if(H5Lget_info2(fid, links, &linfo, H5P_DEFAULT) < 0) { error_msg("unable to get link info from \"%s\"\n", links); h5tools_setstatus(EXIT_FAILURE); } @@ -1903,8 +1914,12 @@ handle_datatypes(hid_t fid, const char *type, void H5_ATTR_UNUSED * data, int pe char name[128]; if(!type_table->objs[idx].recorded) { + char *obj_addr_string = NULL; + /* unamed datatype */ - HDsprintf(name, "/#"H5_PRINTF_HADDR_FMT, type_table->objs[idx].objno); + H5Otoken_to_str(fid, &type_table->objs[idx].obj_token, &obj_addr_string); + HDsprintf(name, "/#%s", obj_addr_string); + H5free_memory(obj_addr_string); if(!HDstrcmp(name, real_name)) break; @@ -1962,7 +1977,7 @@ static int dump_extlink(hid_t group, const char *linkname, const char *objname) { hid_t oid; - H5O_info_t oi; + H5O_info2_t oi; table_t *old_group_table = group_table; table_t *old_dset_table = dset_table; table_t *old_type_table = type_table; @@ -1974,7 +1989,7 @@ dump_extlink(hid_t group, const char *linkname, const char *objname) goto fail; /* Get object info */ - if (H5Oget_info2(oid, &oi, H5O_INFO_BASIC) < 0) { + if (H5Oget_info3(oid, &oi, H5O_INFO_BASIC) < 0) { H5Oclose(oid); goto fail; } diff --git a/tools/src/h5dump/h5dump_xml.c b/tools/src/h5dump/h5dump_xml.c index 9340e44..d9f1f67 100644 --- a/tools/src/h5dump/h5dump_xml.c +++ b/tools/src/h5dump/h5dump_xml.c @@ -106,7 +106,7 @@ static h5tool_format_t xml_dataformat = { /* internal functions */ -static int xml_name_to_XID(const char *, char *, int , int ); +static int xml_name_to_XID(hid_t, const char *, char *, int, int); /* internal functions used by XML option */ static void xml_print_datatype(hid_t, unsigned); @@ -130,7 +130,7 @@ static char *xml_escape_the_name(const char *); *------------------------------------------------------------------------- */ static herr_t -xml_dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void H5_ATTR_UNUSED *op_data) +xml_dump_all_cb(hid_t group, const char *name, const H5L_info2_t *linfo, void H5_ATTR_UNUSED *op_data) { hid_t obj; herr_t ret = SUCCEED; @@ -177,10 +177,10 @@ xml_dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void H5_ HDstrcat(obj_path, name); if(linfo->type == H5L_TYPE_HARD) { - H5O_info_t oinfo; + H5O_info2_t oinfo; /* Stat the object */ - if(H5Oget_info_by_name2(group, name, &oinfo, H5O_INFO_BASIC, H5P_DEFAULT) < 0) { + if(H5Oget_info_by_name3(group, name, &oinfo, H5O_INFO_BASIC, H5P_DEFAULT) < 0) { error_msg("unable to get object information for \"%s\"\n", name); h5tools_setstatus(EXIT_FAILURE); ret = FAIL; @@ -225,7 +225,7 @@ xml_dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void H5_ if(oinfo.rc > 1 || hit_elink) { obj_t *found_obj; /* Found object */ - found_obj = search_obj(dset_table, oinfo.addr); + found_obj = search_obj(dset_table, &oinfo.token); if(found_obj == NULL) { ctx.indent_level++; @@ -272,8 +272,8 @@ xml_dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void H5_ char pointerxid[100]; /* Create OBJ-XIDs for the parent and object */ - xml_name_to_XID(obj_path, dsetxid, (int)sizeof(dsetxid), 1); - xml_name_to_XID(prefix, parentxid, (int)sizeof(parentxid), 1); + xml_name_to_XID(obj, obj_path, dsetxid, (int)sizeof(dsetxid), 1); + xml_name_to_XID(obj, prefix, parentxid, (int)sizeof(parentxid), 1); ctx.need_prefix = TRUE; @@ -290,7 +290,7 @@ xml_dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void H5_ t_prefix); /* H5ParentPaths */ h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - xml_name_to_XID(found_obj->objname, pointerxid, (int)sizeof(pointerxid), 1); + xml_name_to_XID(obj, found_obj->objname, pointerxid, (int)sizeof(pointerxid), 1); ctx.indent_level++; @@ -393,11 +393,11 @@ xml_dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void H5_ } /* end else */ /* Create OBJ-XIDs for the parent and object */ - xml_name_to_XID(t_obj_path, linkxid, (int)sizeof(linkxid), 1); - xml_name_to_XID(prefix, parentxid, (int)sizeof(parentxid), 1); + xml_name_to_XID(group, t_obj_path, linkxid, (int)sizeof(linkxid), 1); + xml_name_to_XID(group, prefix, parentxid, (int)sizeof(parentxid), 1); /* Try to create an OBJ-XID for the object pointed to */ - res = xml_name_to_XID(t_link_path, targetxid, (int)sizeof(targetxid), 0); + res = xml_name_to_XID(group, t_link_path, targetxid, (int)sizeof(targetxid), 0); if (res == 0) { /* target obj found */ ctx.need_prefix = TRUE; @@ -482,8 +482,8 @@ xml_dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void H5_ char *t_targname = xml_escape_the_name(targname); /* Create OBJ-XIDs for the parent and object */ - xml_name_to_XID(t_obj_path, linkxid, (int)sizeof(linkxid), 1); - xml_name_to_XID(prefix, parentxid, (int)sizeof(parentxid), 1); + xml_name_to_XID(group, t_obj_path, linkxid, (int)sizeof(linkxid), 1); + xml_name_to_XID(group, prefix, parentxid, (int)sizeof(parentxid), 1); ctx.need_prefix = TRUE; @@ -528,8 +528,8 @@ xml_dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void H5_ char *t_obj_path = xml_escape_the_name(obj_path); /* Create OBJ-XIDs for the parent and object */ - xml_name_to_XID(t_obj_path, linkxid, (int)sizeof(linkxid), 1); - xml_name_to_XID(prefix, parentxid, (int)sizeof(parentxid), 1); + xml_name_to_XID(group, t_obj_path, linkxid, (int)sizeof(linkxid), 1); + xml_name_to_XID(group, prefix, parentxid, (int)sizeof(parentxid), 1); ctx.need_prefix = TRUE; @@ -575,20 +575,26 @@ done: * 1 - generate a fake entry and return fake id. */ int -xml_name_to_XID(const char *str , char *outstr, int outlen, int gen) +xml_name_to_XID(hid_t loc_id, const char *str, char *outstr, int outlen, int gen) { - haddr_t objno; /* Object ID for object at path */ + H5O_token_t obj_token; + char *obj_addr_str = NULL; + int lookup_ret; if (outlen < 22) return 1; - objno = ref_path_table_lookup(str); - if (objno == HADDR_UNDEF) { + lookup_ret = ref_path_table_lookup(str, &obj_token); + if (lookup_ret < 0) { if (HDstrlen(str) == 0) { - objno = ref_path_table_lookup("/"); - if (objno == HADDR_UNDEF) { + lookup_ret = ref_path_table_lookup("/", &obj_token); + if (lookup_ret < 0) { if (gen) { - objno = ref_path_table_gen_fake(str); - HDsprintf(outstr, "xid_"H5_PRINTF_HADDR_FMT, objno); + ref_path_table_gen_fake(str, &obj_token); + + H5Otoken_to_str(loc_id, &obj_token, &obj_addr_str); + HDsprintf(outstr, "xid_%s", obj_addr_str); + H5free_memory(obj_addr_str); + return 0; } else { @@ -598,8 +604,12 @@ xml_name_to_XID(const char *str , char *outstr, int outlen, int gen) } else { if (gen) { - objno = ref_path_table_gen_fake(str); - HDsprintf(outstr, "xid_"H5_PRINTF_HADDR_FMT, objno); + ref_path_table_gen_fake(str, &obj_token); + + H5Otoken_to_str(loc_id, &obj_token, &obj_addr_str); + HDsprintf(outstr, "xid_%s", obj_addr_str); + H5free_memory(obj_addr_str); + return 0; } else { @@ -608,7 +618,9 @@ xml_name_to_XID(const char *str , char *outstr, int outlen, int gen) } } - HDsprintf(outstr, "xid_"H5_PRINTF_HADDR_FMT, objno); + H5Otoken_to_str(loc_id, &obj_token, &obj_addr_str); + HDsprintf(outstr, "xid_%s", obj_addr_str); + H5free_memory(obj_addr_str); return 0; } @@ -878,12 +890,12 @@ xml_print_datatype(hid_t type, unsigned in_group) outputformat = &string_dataformat; if(!in_group && H5Tcommitted(type) > 0) { - H5O_info_t oinfo; + H5O_info2_t oinfo; obj_t *found_obj; /* Found object */ /* detect a shared datatype, output only once */ - H5Oget_info2(type, &oinfo, H5O_INFO_BASIC); - found_obj = search_obj(type_table, oinfo.addr); + H5Oget_info3(type, &oinfo, H5O_INFO_BASIC); + found_obj = search_obj(type_table, &oinfo.token); if(found_obj) { /* This should be defined somewhere else */ @@ -891,7 +903,7 @@ xml_print_datatype(hid_t type, unsigned in_group) probably will have something different eventually */ char * dtxid = (char *)HDmalloc((size_t)100); - xml_name_to_XID(found_obj->objname, dtxid, 100, 1); + xml_name_to_XID(type, found_obj->objname, dtxid, 100, 1); if (!found_obj->recorded) { /* 'anonymous' NDT. Use it's object num. as it's name. */ @@ -1531,19 +1543,19 @@ xml_dump_datatype(hid_t type) dump_indent += COL; if(H5Tcommitted(type) > 0) { - H5O_info_t oinfo; + H5O_info2_t oinfo; obj_t *found_obj; /* Found object */ /* Datatype is a shared or named datatype */ - H5Oget_info2(type, &oinfo, H5O_INFO_BASIC); - found_obj = search_obj(type_table, oinfo.addr); + H5Oget_info3(type, &oinfo, H5O_INFO_BASIC); + found_obj = search_obj(type_table, &oinfo.token); if(found_obj) { /* Shared datatype, must be entered as an object */ /* These 2 cases are the same now, but may change */ char *dtxid = (char *)HDmalloc((size_t)100); - xml_name_to_XID(found_obj->objname, dtxid, 100, 1); + xml_name_to_XID(type, found_obj->objname, dtxid, 100, 1); if (!found_obj->recorded) { /* anonymous stored datatype: following the dumper's current @@ -2288,8 +2300,8 @@ xml_dump_named_datatype(hid_t type, const char *name) t_prefix = xml_escape_the_name(prefix); t_name = xml_escape_the_name(name); - xml_name_to_XID(tmp, dtxid, 100, 1); - xml_name_to_XID(prefix, parentxid, 100, 1); + xml_name_to_XID(type, tmp, dtxid, 100, 1); + xml_name_to_XID(type, prefix, parentxid, 100, 1); if(HDstrncmp(name, "#", (size_t)1) == 0) { /* Special: this is an 'anonymous' NDT, deleted but still in use. @@ -2312,7 +2324,7 @@ xml_dump_named_datatype(hid_t type, const char *name) h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); } else { - H5O_info_t oinfo; /* Object info */ + H5O_info2_t oinfo; /* Object info */ ctx.need_prefix = TRUE; @@ -2326,12 +2338,12 @@ xml_dump_named_datatype(hid_t type, const char *name) h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); /* Check uniqueness of named datatype */ - H5Oget_info2(type, &oinfo, H5O_INFO_BASIC); + H5Oget_info3(type, &oinfo, H5O_INFO_BASIC); if(oinfo.rc > 1) { obj_t *found_obj; /* Found object */ /* Group with more than one link to it... */ - found_obj = search_obj(type_table, oinfo.addr); + found_obj = search_obj(type_table, &oinfo.token); if (found_obj == NULL) { indentation(dump_indent); @@ -2348,7 +2360,7 @@ xml_dump_named_datatype(hid_t type, const char *name) ctx.indent_level++; - xml_name_to_XID(found_obj->objname, pointerxid, (int)sizeof(pointerxid), 1); + xml_name_to_XID(type, found_obj->objname, pointerxid, (int)sizeof(pointerxid), 1); ctx.need_prefix = TRUE; @@ -2431,7 +2443,7 @@ done: void xml_dump_group(hid_t gid, const char *name) { - H5O_info_t oinfo; + H5O_info2_t oinfo; hid_t gcpl_id; hid_t dset, type; unsigned crt_order_flags; @@ -2512,13 +2524,13 @@ xml_dump_group(hid_t gid, const char *name) } } - H5Oget_info2(gid, &oinfo, H5O_INFO_BASIC); + H5Oget_info3(gid, &oinfo, H5O_INFO_BASIC); if(oinfo.rc > 1) { obj_t *found_obj; /* Found object */ /* Group with more than one link to it... */ - found_obj = search_obj(group_table, oinfo.addr); + found_obj = search_obj(group_table, &oinfo.token); if (found_obj == NULL) { indentation(dump_indent); @@ -2536,7 +2548,7 @@ xml_dump_group(hid_t gid, const char *name) /* already seen: enter a groupptr */ if(isRoot) { /* probably can't happen! */ - xml_name_to_XID("/", grpxid, 100, 1); + xml_name_to_XID(gid, "/", grpxid, 100, 1); ctx.need_prefix = TRUE; @@ -2549,8 +2561,8 @@ xml_dump_group(hid_t gid, const char *name) else { t_objname = xml_escape_the_name(found_obj->objname); par_name = xml_escape_the_name(par); - xml_name_to_XID(tmp, grpxid, 100, 1); - xml_name_to_XID(par, parentxid, 100, 1); + xml_name_to_XID(gid, tmp, grpxid, 100, 1); + xml_name_to_XID(gid, par, parentxid, 100, 1); ctx.need_prefix = TRUE; @@ -2568,8 +2580,8 @@ xml_dump_group(hid_t gid, const char *name) t_objname = xml_escape_the_name(found_obj->objname);/* point to the NDT by name */ par_name = xml_escape_the_name(par); - xml_name_to_XID(found_obj->objname, ptrstr, 100, 1); - xml_name_to_XID(par, parentxid, 100, 1); + xml_name_to_XID(gid, found_obj->objname, ptrstr, 100, 1); + xml_name_to_XID(gid, par, parentxid, 100, 1); ctx.need_prefix = TRUE; @@ -2592,7 +2604,7 @@ xml_dump_group(hid_t gid, const char *name) /* first time this group has been seen -- describe it */ if(isRoot) { - xml_name_to_XID("/", grpxid, 100, 1); + xml_name_to_XID(gid, "/", grpxid, 100, 1); ctx.need_prefix = TRUE; @@ -2606,8 +2618,8 @@ xml_dump_group(hid_t gid, const char *name) char *t_tmp = xml_escape_the_name(tmp); par_name = xml_escape_the_name(par); - xml_name_to_XID(tmp, grpxid, 100, 1); - xml_name_to_XID(par, parentxid, 100, 1); + xml_name_to_XID(gid, tmp, grpxid, 100, 1); + xml_name_to_XID(gid, par, parentxid, 100, 1); ctx.need_prefix = TRUE; @@ -2647,9 +2659,15 @@ xml_dump_group(hid_t gid, const char *name) /* Very special case: dump unamed type in root group */ for(u = 0; u < type_table->nobjs; u++) { if(!type_table->objs[u].recorded) { + char *obj_addr_str = NULL; + dset = H5Dopen2(gid, type_table->objs[u].objname, H5P_DEFAULT); type = H5Dget_type(dset); - HDsprintf(type_name, "#"H5_PRINTF_HADDR_FMT, type_table->objs[u].objno); + + H5Otoken_to_str(dset, &type_table->objs[u].obj_token, &obj_addr_str); + HDsprintf(type_name, "#%s", obj_addr_str); + H5free_memory(obj_addr_str); + dump_function_table->dump_named_datatype_function(type, type_name); H5Tclose(type); H5Dclose(dset); @@ -2660,9 +2678,9 @@ xml_dump_group(hid_t gid, const char *name) /* iterate through all the links */ if((sort_by == H5_INDEX_CRT_ORDER) && (crt_order_flags & H5P_CRT_ORDER_TRACKED)) - H5Literate(gid, sort_by, sort_order, NULL, xml_dump_all_cb, NULL); + H5Literate2(gid, sort_by, sort_order, NULL, xml_dump_all_cb, NULL); else - H5Literate(gid, H5_INDEX_NAME, sort_order, NULL, xml_dump_all_cb, NULL); + H5Literate2(gid, H5_INDEX_NAME, sort_order, NULL, xml_dump_all_cb, NULL); dump_indent -= COL; ctx.indent_level--; @@ -2684,15 +2702,15 @@ xml_dump_group(hid_t gid, const char *name) h5tools_str_reset(&buffer); if(isRoot) { - xml_name_to_XID("/", grpxid, 100, 1); + xml_name_to_XID(gid, "/", grpxid, 100, 1); h5tools_str_append(&buffer, "<%sRootGroup OBJ-XID=\"%s\" H5Path=\"%s\">", xmlnsprefix, grpxid, "/"); } else { char *t_tmp = xml_escape_the_name(tmp); par_name = xml_escape_the_name(par); - xml_name_to_XID(tmp, grpxid, 100, 1); - xml_name_to_XID(par, parentxid, 100, 1); + xml_name_to_XID(gid, tmp, grpxid, 100, 1); + xml_name_to_XID(gid, par, parentxid, 100, 1); h5tools_str_append(&buffer, "<%sGroup Name=\"%s\" OBJ-XID=\"%s\" H5Path=\"%s\" " "Parents=\"%s\" H5ParentPaths=\"%s\" >", xmlnsprefix, t_name, grpxid, t_tmp, parentxid, par_name); @@ -2729,9 +2747,15 @@ xml_dump_group(hid_t gid, const char *name) /* Very special case: dump unamed type in root group */ for(u = 0; u < type_table->nobjs; u++) { if(!type_table->objs[u].recorded) { + char *obj_addr_str = NULL; + dset = H5Dopen2(gid, type_table->objs[u].objname, H5P_DEFAULT); type = H5Dget_type(dset); - HDsprintf(type_name, "#"H5_PRINTF_HADDR_FMT, type_table->objs[u].objno); + + H5Otoken_to_str(dset, &type_table->objs[u].obj_token, &obj_addr_str); + HDsprintf(type_name, "#%s", obj_addr_str); + H5free_memory(obj_addr_str); + dump_function_table->dump_named_datatype_function(type, type_name); H5Tclose(type); H5Dclose(dset); @@ -2742,9 +2766,9 @@ xml_dump_group(hid_t gid, const char *name) /* iterate through all the links */ if((sort_by == H5_INDEX_CRT_ORDER) && (crt_order_flags & H5P_CRT_ORDER_TRACKED)) - H5Literate(gid, sort_by, sort_order, NULL, xml_dump_all_cb, NULL); + H5Literate2(gid, sort_by, sort_order, NULL, xml_dump_all_cb, NULL); else - H5Literate(gid, H5_INDEX_NAME, sort_order, NULL, xml_dump_all_cb, NULL); + H5Literate2(gid, H5_INDEX_NAME, sort_order, NULL, xml_dump_all_cb, NULL); dump_indent -= COL; ctx.indent_level--; @@ -2786,8 +2810,7 @@ xml_print_refs(hid_t did, int source) hid_t space = H5I_INVALID_HID; hssize_t ssiz = -1; hsize_t i; - size_t tsiz; - hobj_ref_t *refbuf = NULL; + H5R_ref_t *refbuf = NULL; char *buf = NULL; h5tools_str_t buffer; /* string into which to render */ h5tools_context_t ctx; /* print context */ @@ -2818,13 +2841,11 @@ xml_print_refs(hid_t did, int source) space = H5Dget_space(did); if ((ssiz = H5Sget_simple_extent_npoints(space)) < 0) goto error; - if ((tsiz = H5Tget_size(type)) == 0) - goto error; - buf = (char *) HDcalloc((size_t)ssiz, tsiz); + buf = (char *) HDcalloc((size_t)ssiz, sizeof(H5R_ref_t)); if (buf == NULL) goto error; - e = H5Dread(did, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf); + e = H5Dread(did, H5T_STD_REF, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf); /* need to check result here */ if (e < 0) goto error; @@ -2833,19 +2854,17 @@ xml_print_refs(hid_t did, int source) space = H5Aget_space(did); if ((ssiz = H5Sget_simple_extent_npoints(space)) < 0) goto error; - if ((tsiz = H5Tget_size(type)) == 0) - goto error; - buf = (char *) HDcalloc((size_t)ssiz, tsiz); + buf = (char *) HDcalloc((size_t)ssiz, sizeof(H5R_ref_t)); if (buf == NULL) goto error; - e = H5Aread(did, H5T_STD_REF_OBJ, buf); + e = H5Aread(did, H5T_STD_REF, buf); /* need to check the result here */ if (e < 0) goto error; } - refbuf = (hobj_ref_t *)((void *)buf); + refbuf = (H5R_ref_t *)((void *)buf); /* setup */ HDmemset(&buffer, 0, sizeof(h5tools_str_t)); @@ -2896,6 +2915,8 @@ xml_print_refs(hid_t did, int source) } ctx.indent_level--; + H5Rdestroy(refbuf); + refbuf++; } @@ -3285,7 +3306,7 @@ xml_dump_fill_value(hid_t dcpl, hid_t type) H5Pget_fill_value(dcpl, type, buf); if (H5Tget_class(type) == H5T_REFERENCE) { - const char * path = lookup_ref_path(*(hobj_ref_t *) buf); + const char * path = lookup_ref_path(*(H5R_ref_t *) buf); ctx.need_prefix = TRUE; @@ -3319,6 +3340,8 @@ xml_dump_fill_value(hid_t dcpl, hid_t type) h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "</%sDataFromFile>", xmlnsprefix); h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); + + H5Rdestroy((H5R_ref_t *) buf); } else if (H5Tget_class(type) == H5T_STRING) { /* ????? */ @@ -3605,8 +3628,8 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED *ss string_dataformat.do_escape = display_escape; outputformat = &string_dataformat; - xml_name_to_XID(tmp, rstr, 100, 1); - xml_name_to_XID(prefix, pstr, 100, 1); + xml_name_to_XID(did, tmp, rstr, 100, 1); + xml_name_to_XID(did, prefix, pstr, 100, 1); ctx.need_prefix = TRUE; diff --git a/tools/src/h5format_convert/h5format_convert.c b/tools/src/h5format_convert/h5format_convert.c index f5234f4..bb606ac 100644 --- a/tools/src/h5format_convert/h5format_convert.c +++ b/tools/src/h5format_convert/h5format_convert.c @@ -362,7 +362,7 @@ error: *------------------------------------------------------------------------- */ static int -convert_dsets_cb(const char *path, const H5O_info_t *oi, const char *already_visited, void *_fid) +convert_dsets_cb(const char *path, const H5O_info2_t *oi, const char *already_visited, void *_fid) { hid_t fid = *(hid_t *)_fid; diff --git a/tools/src/h5import/h5import.c b/tools/src/h5import/h5import.c index 81f9a32..0c0e0fb 100644 --- a/tools/src/h5import/h5import.c +++ b/tools/src/h5import/h5import.c @@ -72,7 +72,7 @@ uint64_t swap_uint64(uint64_t val); int main(int argc, char *argv[]) { - struct Options opt; + struct Options *opt; int outfile_named = FALSE; int token; int i; @@ -99,8 +99,8 @@ int main(int argc, char *argv[]) (void) HDsetvbuf(stderr, (char *) NULL, _IOLBF, 0); (void) HDsetvbuf(stdout, (char *) NULL, _IOLBF, 0); - /* Initialize the file structure to 0 */ - HDmemset(&opt, 0, sizeof(struct Options)); + if((opt = (struct Options *)HDcalloc(1, sizeof(struct Options))) == NULL) + goto err; if (argv[1] && (HDstrcmp("-V", argv[1]) == 0)) { print_version(PROGRAMNAME); @@ -130,12 +130,12 @@ int main(int argc, char *argv[]) switch (state) { case 1: /* counting input files */ - if (opt.fcount < 29) { - (void) HDstrcpy(opt.infiles[opt.fcount].datafile, argv[i]); - in = &(opt.infiles[opt.fcount].in); - opt.infiles[opt.fcount].config = 0; - setDefaultValues(in, opt.fcount); - opt.fcount++; + if (opt->fcount < 29) { + (void) HDstrcpy(opt->infiles[opt->fcount].datafile, argv[i]); + in = &(opt->infiles[opt->fcount].in); + opt->infiles[opt->fcount].config = 0; + setDefaultValues(in, opt->fcount); + opt->fcount++; } else { (void) HDfprintf(stderr, err9, argv[i]); @@ -148,8 +148,8 @@ int main(int argc, char *argv[]) break; case 3: /* get configfile name */ - (void) HDstrcpy(opt.infiles[opt.fcount-1].configfile, argv[i]); - opt.infiles[opt.fcount - 1].config = 1; + (void) HDstrcpy(opt->infiles[opt->fcount-1].configfile, argv[i]); + opt->infiles[opt->fcount - 1].config = 1; break; case 4: /* -o found; look for outfile */ @@ -160,7 +160,7 @@ int main(int argc, char *argv[]) (void) HDfprintf(stderr, err10, argv[i]); goto err; } - (void) HDstrcpy(opt.outfile, argv[i]); + (void) HDstrcpy(opt->outfile, argv[i]); outfile_named = TRUE; break; @@ -232,11 +232,11 @@ int main(int argc, char *argv[]) goto err; } - if (process(&opt) == -1) + if (process(opt) == -1) goto err; - for (i = 0; i < opt.fcount; i++) { - in = &(opt.infiles[i].in); + for (i = 0; i < opt->fcount; i++) { + in = &(opt->infiles[i].in); if (in->sizeOfDimension) HDfree(in->sizeOfDimension); if (in->sizeOfChunk) @@ -248,12 +248,13 @@ int main(int argc, char *argv[]) if (in->data) HDfree(in->data); } + HDfree(opt); - return (EXIT_SUCCESS); + return EXIT_SUCCESS; err: (void) HDfprintf(stderr, "%s", err4); - for (i = 0; i < opt.fcount; i++) { - in = &(opt.infiles[i].in); + for (i = 0; i < opt->fcount; i++) { + in = &(opt->infiles[i].in); if (in->sizeOfDimension) HDfree(in->sizeOfDimension); if (in->sizeOfChunk) @@ -265,7 +266,9 @@ err: if (in->data) HDfree(in->data); } - return (EXIT_FAILURE); + HDfree(opt); + + return EXIT_FAILURE; } static int gtoken(char *s) diff --git a/tools/src/h5ls/h5ls.c b/tools/src/h5ls/h5ls.c index a926e0c..8f8272c 100644 --- a/tools/src/h5ls/h5ls.c +++ b/tools/src/h5ls/h5ls.c @@ -1260,10 +1260,17 @@ print_type(h5tools_str_t *buffer, hid_t type, int ind) /* Shared? If so then print the type's OID */ if (H5Tcommitted(type)) { - H5O_info_t oi; + H5O_info2_t oi; - if (H5Oget_info2(type, &oi, H5O_INFO_BASIC) >= 0) - h5tools_str_append(buffer,"shared-%lu:"H5_PRINTF_HADDR_FMT" ", oi.fileno, oi.addr); + if (H5Oget_info3(type, &oi, H5O_INFO_BASIC) >= 0) { + char *type_string = NULL; + + H5Otoken_to_str(type, &oi.token, &type_string); + + h5tools_str_append(buffer,"shared-%lu:%s", oi.fileno, type_string); + + H5free_memory(type_string); + } /* end if */ else h5tools_str_append(buffer,"shared "); } /* end if */ @@ -2284,7 +2291,7 @@ datatype_list2(hid_t type, const char H5_ATTR_UNUSED *name) *------------------------------------------------------------------------- */ static herr_t -list_obj(const char *name, const H5O_info_t *oinfo, const char *first_seen, void *_iter) +list_obj(const char *name, const H5O_info2_t *oinfo, const char *first_seen, void *_iter) { H5O_type_t obj_type = oinfo->type; /* Type of the object */ iter_t *iter = (iter_t*)_iter; @@ -2355,6 +2362,7 @@ list_obj(const char *name, const H5O_info_t *oinfo, const char *first_seen, void if (verbose_g > 0) { size_t buf_size = 0; char* comment = NULL; + char* obj_addr_str = NULL; ssize_t cmt_bufsize = -1; /* Display attributes */ @@ -2363,11 +2371,15 @@ list_obj(const char *name, const H5O_info_t *oinfo, const char *first_seen, void H5Aiterate2(obj, H5_INDEX_NAME, H5_ITER_INC, NULL, list_attr, NULL); /* Object location & reference count */ + H5Otoken_to_str(obj, &oinfo->token, &obj_addr_str); + h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, " %-10s %lu:"H5_PRINTF_HADDR_FMT"\n", "Location:", oinfo->fileno, oinfo->addr); + h5tools_str_append(&buffer, " %-10s %lu:%s\n", "Location:", oinfo->fileno, obj_addr_str); h5tools_str_append(&buffer, " %-10s %u\n", "Links:", (unsigned)oinfo->rc); h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); + H5free_memory(obj_addr_str); + /* Modification time */ if (oinfo->mtime > 0) { char buf[256]; @@ -2442,7 +2454,7 @@ done: *------------------------------------------------------------------------- */ static herr_t -list_lnk(const char *name, const H5L_info_t *linfo, void *_iter) +list_lnk(const char *name, const H5L_info2_t *linfo, void *_iter) { char *buf = NULL; iter_t *iter = (iter_t*)_iter; @@ -2628,7 +2640,7 @@ static herr_t visit_obj(hid_t file, const char *oname, iter_t *iter) { int retval = 0; - H5O_info_t oi; /* Information for object */ + H5O_info2_t oi; /* Information for object */ hsize_t curr_pos = 0; /* total data element position */ h5tools_str_t buffer; /* string into which to render */ h5tools_context_t ctx; /* print context */ @@ -2640,7 +2652,7 @@ visit_obj(hid_t file, const char *oname, iter_t *iter) h5tools_str_reset(&buffer); /* Retrieve info for object to list */ - if (H5Oget_info_by_name2(file, oname, &oi, H5O_INFO_BASIC|H5O_INFO_TIME, H5P_DEFAULT) < 0) { + if (H5Oget_info_by_name3(file, oname, &oi, H5O_INFO_BASIC|H5O_INFO_TIME, H5P_DEFAULT) < 0) { if (iter->symlink_target) { h5tools_str_append(&buffer, "{**NOT FOUND**}\n"); iter->symlink_target = FALSE; @@ -3279,7 +3291,7 @@ main(int argc, const char *argv[]) * doesn't exist). */ show_file_name_g = (argc-argno > 1); /*show file names if more than one*/ while(argno < argc) { - H5L_info_t li; + H5L_info2_t li; iter_t iter; symlink_trav_t symlink_list; size_t u; @@ -3360,7 +3372,7 @@ main(int argc, const char *argv[]) /* Check for root group as object name */ if (HDstrcmp(oname, root_name)) { /* Check the type of link given */ - if (H5Lget_info(file_id, oname, &li, H5P_DEFAULT) < 0) { + if (H5Lget_info2(file_id, oname, &li, H5P_DEFAULT) < 0) { hsize_t curr_pos = 0; /* total data element position */ h5tools_str_t buffer; /* string into which to render */ h5tools_context_t ctx; /* print context */ diff --git a/tools/src/h5repack/h5repack.c b/tools/src/h5repack/h5repack.c index b138896..8eeaa0e 100644 --- a/tools/src/h5repack/h5repack.c +++ b/tools/src/h5repack/h5repack.c @@ -222,18 +222,27 @@ h5repack_addlayout(const char *str, pack_opt_t *options) hid_t copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options) { - named_dt_t *dt = *named_dt_head_p; /* Stack pointer */ - named_dt_t *dt_ret = NULL; /* Datatype to return */ - H5O_info_t oinfo; /* Object info of input dtype */ - hid_t ret_value = H5I_INVALID_HID; + named_dt_t *dt = *named_dt_head_p; /* Stack pointer */ + named_dt_t *dt_ret = NULL; /* Datatype to return */ + H5O_info2_t oinfo; /* Object info of input dtype */ + int token_cmp; + hid_t ret_value = H5I_INVALID_HID; - if (H5Oget_info2(type_in, &oinfo, H5O_INFO_BASIC) < 0) + if (H5Oget_info3(type_in, &oinfo, H5O_INFO_BASIC) < 0) H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "H5Oget_info failed"); if (*named_dt_head_p) { + if (H5Otoken_cmp(type_in, &dt->obj_token, &oinfo.token, &token_cmp) < 0) + H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "failed to compare object tokens"); + /* Stack already exists, search for the datatype */ - while (dt && dt->addr_in != oinfo.addr) + while (dt && token_cmp) { dt = dt->next; + + if (H5Otoken_cmp(type_in, &dt->obj_token, &oinfo.token, &token_cmp) < 0) + H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "failed to compare object tokens"); + } + dt_ret = dt; } else { @@ -249,13 +258,14 @@ copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, t *named_dt_head_p = dt; /* Update the address and id */ - dt->addr_in = travt->objs[i].objno; + HDmemcpy(&dt->obj_token, &travt->objs[i].obj_token, sizeof(H5O_token_t)); dt->id_out = H5I_INVALID_HID; /* Check if this type is the one requested */ - if (oinfo.addr == dt->addr_in) { + if (H5Otoken_cmp(type_in, &oinfo.token, &dt->obj_token, &token_cmp) < 0) + H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "failed to compare object tokens"); + if (!token_cmp) dt_ret = dt; - } } /* end if named datatype */ } /* end for each object in traversal table */ } /* end else (create the stack) */ @@ -271,7 +281,7 @@ copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, t *named_dt_head_p = dt_ret; /* Update the address and id */ - dt_ret->addr_in = oinfo.addr; + HDmemcpy(&dt_ret->obj_token, &oinfo.token, sizeof(H5O_token_t)); dt_ret->id_out = H5I_INVALID_HID; } /* end if requested datatype not found */ @@ -355,14 +365,14 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p, trav_table_ 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 */ + H5O_info2_t oinfo; /* object info */ int j; unsigned u; hbool_t is_ref = 0; H5T_class_t type_class = -1; int ret_value = 0; - if (H5Oget_info2(loc_in, &oinfo, H5O_INFO_NUM_ATTRS) < 0) + if (H5Oget_info3(loc_in, &oinfo, H5O_INFO_NUM_ATTRS) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Oget_info failed"); /*------------------------------------------------------------------------- @@ -752,7 +762,7 @@ check_objects(const char* fname, pack_opt_t *options) /* Initialize indexing options */ h5trav_set_index(sort_by, sort_order); /* init table */ - trav_table_init(&travt); + trav_table_init(fid, &travt); /* get the list of objects in the file */ if (h5trav_gettable(fid, travt) < 0) diff --git a/tools/src/h5repack/h5repack.h b/tools/src/h5repack/h5repack.h index a0e0387..52ecb0e 100644 --- a/tools/src/h5repack/h5repack.h +++ b/tools/src/h5repack/h5repack.h @@ -131,7 +131,7 @@ typedef struct { typedef struct named_dt_t { - haddr_t addr_in; /* Address of the named dtype in the in file */ + H5O_token_t obj_token; /* Object token for the named dtype in the in file */ hid_t id_out; /* Open identifier for the dtype in the out file */ struct named_dt_t *next; /* Next dtype */ } named_dt_t; diff --git a/tools/src/h5repack/h5repack_copy.c b/tools/src/h5repack/h5repack_copy.c index 7336125..1044244 100644 --- a/tools/src/h5repack/h5repack_copy.c +++ b/tools/src/h5repack/h5repack_copy.c @@ -316,7 +316,7 @@ print_user_block(fnamein, fidin); /* Initialize indexing options */ h5trav_set_index(sort_by, sort_order); /* init table */ - trav_table_init(&travt); + trav_table_init(fidin, &travt); if (travt) { /* get the list of objects in the file */ diff --git a/tools/src/h5repack/h5repack_refs.c b/tools/src/h5repack/h5repack_refs.c index 70204c8..e6a747d 100644 --- a/tools/src/h5repack/h5repack_refs.c +++ b/tools/src/h5repack/h5repack_refs.c @@ -439,7 +439,7 @@ static int copy_refs_attr(hid_t loc_in, hsize_t nelmts; /* number of elements in dataset */ hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */ char name[255]; - H5O_info_t oinfo; /* Object info */ + H5O_info2_t oinfo; /* Object info */ unsigned u, i, j; int rank; H5T_class_t type_class = -1; @@ -454,7 +454,7 @@ static int copy_refs_attr(hid_t loc_in, int ref_comp_field_n = 0; int ret_value = 0; - if(H5Oget_info2(loc_in, &oinfo, H5O_INFO_NUM_ATTRS) < 0) + if(H5Oget_info3(loc_in, &oinfo, H5O_INFO_NUM_ATTRS) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Oget_info failed"); for(u = 0; u < (unsigned)oinfo.num_attrs; u++) { @@ -796,16 +796,19 @@ MapIdToName(hid_t refobj_id, trav_table_t *travt) if(travt->objs[u].type == (h5trav_type_t)H5O_TYPE_DATASET || travt->objs[u].type == (h5trav_type_t)H5O_TYPE_GROUP || travt->objs[u].type == (h5trav_type_t)H5O_TYPE_NAMED_DATATYPE) { - H5O_info_t ref_oinfo; /* Stat for the refobj id */ + H5O_info2_t ref_oinfo; /* Stat for the refobj id */ + int token_cmp; /* obtain information to identify the referenced object uniquely */ - if(H5Oget_info2(refobj_id, &ref_oinfo, H5O_INFO_BASIC) < 0) + if(H5Oget_info3(refobj_id, &ref_oinfo, H5O_INFO_BASIC) < 0) goto out; - if(ref_oinfo.addr == travt->objs[u].objno) { + if(H5Otoken_cmp(refobj_id, &ref_oinfo.token, &travt->objs[u].obj_token, &token_cmp) < 0) + goto out; + if(!token_cmp) { ret = travt->objs[u].name; goto out; - } /* end if */ + } } /* end if */ } /* u */ diff --git a/tools/src/h5repack/h5repack_verify.c b/tools/src/h5repack/h5repack_verify.c index 84cbf60..683988c 100644 --- a/tools/src/h5repack/h5repack_verify.c +++ b/tools/src/h5repack/h5repack_verify.c @@ -95,7 +95,7 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options * close *------------------------------------------------------------------------- */ - if(H5Pclose(pid) < 0) + if (H5Pclose(pid) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); if (H5Sclose(sid) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Sclose failed"); @@ -114,7 +114,7 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options /* Initialize indexing options */ h5trav_set_index(sort_by, sort_order); /* init table */ - trav_table_init(&travt); + trav_table_init(fidout, &travt); /* get the list of objects in the file */ if(h5trav_gettable(fidout, travt) < 0) @@ -386,7 +386,7 @@ int h5repack_cmp_pl(const char *fname1, const char *fname2) /* Initialize indexing options */ h5trav_set_index(sort_by, sort_order); /* init table */ - trav_table_init(&trav); + trav_table_init(fid1, &trav); if(h5trav_gettable(fid1, trav) < 0) H5TOOLS_GOTO_ERROR((-1), "h5trav_gettable failed"); diff --git a/tools/src/h5stat/h5stat.c b/tools/src/h5stat/h5stat.c index f160671..adc905a 100644 --- a/tools/src/h5stat/h5stat.c +++ b/tools/src/h5stat/h5stat.c @@ -379,13 +379,13 @@ ceil_log10(unsigned long x) *------------------------------------------------------------------------- */ static herr_t -attribute_stats(iter_t *iter, const H5O_info_t *oi) +attribute_stats(iter_t *iter, const H5O_info2_t *oi, const H5O_native_info_t *native_oi) { unsigned bin; /* "bin" the number of objects falls in */ /* Update dataset & attribute metadata info */ - iter->attrs_btree_storage_size += oi->meta_size.attr.index_size; - iter->attrs_heap_storage_size += oi->meta_size.attr.heap_size; + iter->attrs_btree_storage_size += native_oi->meta_size.attr.index_size; + iter->attrs_heap_storage_size += native_oi->meta_size.attr.heap_size; /* Update small # of attribute count & limits */ if(oi->num_attrs <= (hsize_t)sattrs_threshold) @@ -440,7 +440,7 @@ attribute_stats(iter_t *iter, const H5O_info_t *oi) *------------------------------------------------------------------------- */ static herr_t -group_stats(iter_t *iter, const char *name, const H5O_info_t *oi) +group_stats(iter_t *iter, const char *name, const H5O_info2_t *oi, const H5O_native_info_t *native_oi) { H5G_info_t ginfo; /* Group information */ unsigned bin; /* "bin" the number of objects falls in */ @@ -450,8 +450,8 @@ group_stats(iter_t *iter, const char *name, const H5O_info_t *oi) iter->uniq_groups++; /* Get object header information */ - iter->group_ohdr_info.total_size += oi->hdr.space.total; - iter->group_ohdr_info.free_size += oi->hdr.space.free; + iter->group_ohdr_info.total_size += native_oi->hdr.space.total; + iter->group_ohdr_info.free_size += native_oi->hdr.space.free; /* Get group information */ if((ret_value = H5Gget_info_by_name(iter->fid, name, &ginfo, H5P_DEFAULT)) < 0) @@ -484,11 +484,11 @@ group_stats(iter_t *iter, const char *name, const H5O_info_t *oi) (iter->group_bins[bin])++; /* Update group metadata info */ - iter->groups_btree_storage_size += oi->meta_size.obj.index_size; - iter->groups_heap_storage_size += oi->meta_size.obj.heap_size; + iter->groups_btree_storage_size += native_oi->meta_size.obj.index_size; + iter->groups_heap_storage_size += native_oi->meta_size.obj.heap_size; /* Update attribute metadata info */ - if((ret_value = attribute_stats(iter, oi)) < 0) + if((ret_value = attribute_stats(iter, oi, native_oi)) < 0) H5TOOLS_GOTO_ERROR(FAIL, "attribute_stats failed"); done: @@ -510,7 +510,7 @@ done: *------------------------------------------------------------------------- */ static herr_t -dataset_stats(iter_t *iter, const char *name, const H5O_info_t *oi) +dataset_stats(iter_t *iter, const char *name, const H5O_info2_t *oi, const H5O_native_info_t *native_oi) { unsigned bin; /* "bin" the number of objects falls in */ hid_t did; /* Dataset ID */ @@ -533,18 +533,18 @@ dataset_stats(iter_t *iter, const char *name, const H5O_info_t *oi) iter->uniq_dsets++; /* Get object header information */ - iter->dset_ohdr_info.total_size += oi->hdr.space.total; - iter->dset_ohdr_info.free_size += oi->hdr.space.free; + iter->dset_ohdr_info.total_size += native_oi->hdr.space.total; + iter->dset_ohdr_info.free_size += native_oi->hdr.space.free; if((did = H5Dopen2(iter->fid, name, H5P_DEFAULT)) < 0) H5TOOLS_GOTO_ERROR(FAIL, "H5Dopen() failed"); /* Update dataset metadata info */ - iter->datasets_index_storage_size += oi->meta_size.obj.index_size; - iter->datasets_heap_storage_size += oi->meta_size.obj.heap_size; + iter->datasets_index_storage_size += native_oi->meta_size.obj.index_size; + iter->datasets_heap_storage_size += native_oi->meta_size.obj.heap_size; /* Update attribute metadata info */ - if((ret_value = attribute_stats(iter, oi)) < 0) + if((ret_value = attribute_stats(iter, oi, native_oi)) < 0) H5TOOLS_GOTO_ERROR(FAIL, "attribute_stats() failed"); /* Get storage info */ @@ -702,7 +702,7 @@ done: *------------------------------------------------------------------------- */ static herr_t -datatype_stats(iter_t *iter, const H5O_info_t *oi) +datatype_stats(iter_t *iter, const H5O_info2_t *oi, const H5O_native_info_t *native_oi) { herr_t ret_value = SUCCEED; @@ -710,11 +710,11 @@ datatype_stats(iter_t *iter, const H5O_info_t *oi) iter->uniq_dtypes++; /* Get object header information */ - iter->dtype_ohdr_info.total_size += oi->hdr.space.total; - iter->dtype_ohdr_info.free_size += oi->hdr.space.free; + iter->dtype_ohdr_info.total_size += native_oi->hdr.space.total; + iter->dtype_ohdr_info.free_size += native_oi->hdr.space.free; /* Update attribute metadata info */ - if((ret_value = attribute_stats(iter, oi)) < 0) + if((ret_value = attribute_stats(iter, oi, native_oi)) < 0) H5TOOLS_GOTO_ERROR(FAIL, "attribute_stats() failed"); done: return ret_value; @@ -735,31 +735,36 @@ done: *------------------------------------------------------------------------- */ static herr_t -obj_stats(const char *path, const H5O_info_t *oi, const char *already_visited, +obj_stats(const char *path, const H5O_info2_t *oi, const char *already_visited, void *_iter) { + H5O_native_info_t native_info; iter_t *iter = (iter_t *)_iter; herr_t ret_value = SUCCEED; /* If the object has already been seen then just return */ if(NULL == already_visited) { + /* Retrieve the native info for the object */ + if(H5Oget_native_info_by_name(iter->fid, path, &native_info, H5O_NATIVE_INFO_ALL, H5P_DEFAULT) < 0) + H5TOOLS_GOTO_ERROR(FAIL, "H5Oget_native_info_by_name failed"); + /* Gather some general statistics about the object */ if(oi->rc > iter->max_links) iter->max_links = oi->rc; switch(oi->type) { case H5O_TYPE_GROUP: - if(group_stats(iter, path, oi) < 0) + if(group_stats(iter, path, oi, &native_info) < 0) H5TOOLS_GOTO_ERROR(FAIL, "group_stats failed"); break; case H5O_TYPE_DATASET: - if(dataset_stats(iter, path, oi) < 0) + if(dataset_stats(iter, path, oi, &native_info) < 0) H5TOOLS_GOTO_ERROR(FAIL, "dataset_stats failed"); break; case H5O_TYPE_NAMED_DATATYPE: - if(datatype_stats(iter, oi) < 0) + if(datatype_stats(iter, oi, &native_info) < 0) H5TOOLS_GOTO_ERROR(FAIL, "datatype_stats failed"); break; @@ -792,7 +797,7 @@ done: *------------------------------------------------------------------------- */ static herr_t -lnk_stats(const char H5_ATTR_UNUSED *path, const H5L_info_t *li, void *_iter) +lnk_stats(const char H5_ATTR_UNUSED *path, const H5L_info2_t *li, void *_iter) { iter_t *iter = (iter_t *)_iter; |