mirror of
https://github.com/HDFGroup/hdf5.git
synced 2024-11-27 02:10:55 +08:00
e54d15a26c
HDFFV-7770 - h5diff segmentation fault on JPSS files
Description:
Fixed segfault over non-comparable attribute with different dimention or
rank, along with '-c' option to display details.
Tested:
jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows, Cmake
535 lines
17 KiB
C
535 lines
17 KiB
C
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
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* Copyright by The HDF Group. *
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* Copyright by the Board of Trustees of the University of Illinois. *
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* All rights reserved. *
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* *
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* This file is part of HDF5. The full HDF5 copyright notice, including *
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* terms governing use, modification, and redistribution, is contained in *
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* the files COPYING and Copyright.html. COPYING can be found at the root *
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* of the source code distribution tree; Copyright.html can be found at the *
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* root level of an installed copy of the electronic HDF5 document set and *
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* is linked from the top-level documents page. It can also be found at *
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* http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
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* access to either file, you may request a copy from help@hdfgroup.org. *
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* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
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#include "H5private.h"
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#include "h5tools.h"
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#include "h5tools_utils.h"
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#include "h5diff.h"
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#define ATTR_NAME_MAX 255
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typedef struct table_attr_t {
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char *name;
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unsigned exist[2];
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} match_attr_t;
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typedef struct table_attrs_t {
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size_t size;
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size_t nattrs;
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size_t nattrs_only1;
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size_t nattrs_only2;
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match_attr_t *attrs;
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} table_attrs_t;
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/*-------------------------------------------------------------------------
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* Function: table_attrs_init
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*
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* Purpose: Initialize the table
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*
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* Parameter:
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* - tbl [OUT]
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*
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* Programmer: Jonathan Kim
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*
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* Date: March 15, 2011
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*------------------------------------------------------------------------*/
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static void table_attrs_init(table_attrs_t **tbl)
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{
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table_attrs_t* table_attrs = (table_attrs_t*) HDmalloc(sizeof(table_attrs_t));
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table_attrs->size = 0;
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table_attrs->nattrs = 0;
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table_attrs->nattrs_only1 = 0;
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table_attrs->nattrs_only2 = 0;
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table_attrs->attrs = NULL;
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*tbl = table_attrs;
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}
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/*-------------------------------------------------------------------------
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* Function: table_attrs_free
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*
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* Purpose: free given table
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*
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* Parameter:
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* - table [IN]
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*
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* Programmer: Jonathan Kim
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*
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* Date: March 15, 2011
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*------------------------------------------------------------------------*/
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static void table_attrs_free( table_attrs_t *table )
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{
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unsigned int i;
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if (table)
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{
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if(table->attrs)
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{
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for(i = 0; i < table->nattrs; i++)
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{
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if(table->attrs[i].name)
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HDfree(table->attrs[i].name );
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} /* end for */
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HDfree(table->attrs);
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table->attrs = NULL;
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} /* end if */
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HDfree(table);
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table = NULL;
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}
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}
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/*-------------------------------------------------------------------------
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* Function: table_attr_mark_exist
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*
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* Purpose: mark given attribute name to table as sign of exsit
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*
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* Parameter:
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* - exist [IN]
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* - name [IN] : attribute name
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* - table [OUT]
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*
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* Programmer: Jonathan Kim
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*
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* Date: March 15, 2011
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*------------------------------------------------------------------------*/
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static void table_attr_mark_exist(unsigned *exist, char *name, table_attrs_t *table)
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{
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unsigned int new;
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if(table->nattrs == table->size) {
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table->size = MAX(1, table->size * 2);
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table->attrs = (match_attr_t *)HDrealloc(table->attrs, table->size * sizeof(match_attr_t));
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} /* end if */
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new = table->nattrs++;
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table->attrs[new].exist[0] = exist[0];
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table->attrs[new].exist[1] = exist[1];
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table->attrs[new].name = (char *)HDstrdup(name);
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}
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/*-------------------------------------------------------------------------
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* Function: build_match_list_attrs
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*
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* Purpose: get list of matching attribute name from obj1 and obj2
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*
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* Note:
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* Find common attribute; the algorithm for search is referred from
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* build_match_list() in h5diff.c .
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*
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* Parameter:
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* table_out [OUT] : return the list
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*
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* Programmer: Jonathan Kim
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*
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* Date: March 15, 2011
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*------------------------------------------------------------------------*/
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static herr_t build_match_list_attrs(hid_t loc1_id, hid_t loc2_id, table_attrs_t ** table_out, diff_opt_t *options)
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{
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H5O_info_t oinfo1, oinfo2; /* Object info */
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hid_t attr1_id=-1; /* attr ID */
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hid_t attr2_id=-1; /* attr ID */
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size_t curr1 = 0;
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size_t curr2 = 0;
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unsigned infile[2];
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char name1[ATTR_NAME_MAX];
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char name2[ATTR_NAME_MAX];
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int cmp;
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unsigned i;
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table_attrs_t *table_lp = NULL;
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if(H5Oget_info(loc1_id, &oinfo1) < 0)
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goto error;
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if(H5Oget_info(loc2_id, &oinfo2) < 0)
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goto error;
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table_attrs_init( &table_lp );
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/*--------------------------------------------------
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* build the list
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*/
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while(curr1 < oinfo1.num_attrs && curr2 < oinfo2.num_attrs)
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{
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/*------------------
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* open attribute1 */
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if((attr1_id = H5Aopen_by_idx(loc1_id, ".", H5_INDEX_NAME, H5_ITER_INC, (hsize_t)curr1, H5P_DEFAULT, H5P_DEFAULT)) < 0)
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goto error;
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/* get name */
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if(H5Aget_name(attr1_id, ATTR_NAME_MAX, name1) < 0)
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goto error;
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/*------------------
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* open attribute2 */
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if((attr2_id = H5Aopen_by_idx(loc2_id, ".", H5_INDEX_NAME, H5_ITER_INC, (hsize_t)curr2, H5P_DEFAULT, H5P_DEFAULT)) < 0)
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goto error;
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/* get name */
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if(H5Aget_name(attr2_id, ATTR_NAME_MAX, name2) < 0)
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goto error;
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/* criteria is string compare */
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cmp = HDstrcmp(name1, name2);
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if(cmp == 0)
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{
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infile[0] = 1;
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infile[1] = 1;
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table_attr_mark_exist(infile, name1, table_lp);
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curr1++;
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curr2++;
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}
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else if(cmp < 0)
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{
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infile[0] = 1;
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infile[1] = 0;
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table_attr_mark_exist(infile, name1, table_lp);
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table_lp->nattrs_only1++;
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curr1++;
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}
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else
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{
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infile[0] = 0;
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infile[1] = 1;
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table_attr_mark_exist(infile, name2, table_lp);
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table_lp->nattrs_only2++;
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curr2++;
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}
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} /* end while */
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/* list1 did not end */
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infile[0] = 1;
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infile[1] = 0;
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while(curr1 < oinfo1.num_attrs)
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{
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/*------------------
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* open attribute1 */
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if((attr1_id = H5Aopen_by_idx(loc1_id, ".", H5_INDEX_NAME, H5_ITER_INC, (hsize_t)curr1, H5P_DEFAULT, H5P_DEFAULT)) < 0)
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goto error;
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/* get name */
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if(H5Aget_name(attr1_id, ATTR_NAME_MAX, name1) < 0)
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goto error;
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table_attr_mark_exist(infile, name1, table_lp);
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table_lp->nattrs_only1++;
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curr1++;
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}
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/* list2 did not end */
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infile[0] = 0;
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infile[1] = 1;
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while(curr2 < oinfo2.num_attrs)
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{
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/*------------------
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* open attribute2 */
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if((attr2_id = H5Aopen_by_idx(loc2_id, ".", H5_INDEX_NAME, H5_ITER_INC, (hsize_t)curr2, H5P_DEFAULT, H5P_DEFAULT)) < 0)
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goto error;
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/* get name */
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if(H5Aget_name(attr2_id, ATTR_NAME_MAX, name2) < 0)
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goto error;
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table_attr_mark_exist(infile, name2, table_lp);
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table_lp->nattrs_only2++;
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curr2++;
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}
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/*------------------------------------------------------
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* print the list
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*/
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if(options->m_verbose_level == 2)
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{
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/* if '-v2' is detected */
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parallel_print(" obj1 obj2\n");
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parallel_print(" --------------------------------------\n");
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for(i = 0; i < (unsigned int) table_lp->nattrs; i++)
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{
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char c1, c2;
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c1 = (table_lp->attrs[i].exist[0]) ? 'x' : ' ';
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c2 = (table_lp->attrs[i].exist[1]) ? 'x' : ' ';
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parallel_print("%5c %6c %-15s\n", c1, c2, table_lp->attrs[i].name);
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} /* end for */
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}
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if(options->m_verbose_level >= 1)
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{
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parallel_print("Attributes status: %d common, %d only in obj1, %d only in obj2\n", table_lp->nattrs - table_lp->nattrs_only1 - table_lp->nattrs_only2, table_lp->nattrs_only1, table_lp->nattrs_only2 );
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}
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*table_out = table_lp;
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return 0;
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error:
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return -1;
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}
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/*-------------------------------------------------------------------------
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* Function: diff_attr
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*
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* Purpose: compare attributes located in LOC1_ID and LOC2_ID, which are
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* obtained either from
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* loc_id = H5Gopen2(fid, name, H5P_DEFAULT);
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* loc_id = H5Dopen2(fid, name);
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* loc_id = H5Topen2(fid, name, H5P_DEFAULT);
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*
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* Return: number of differences found
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*
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* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
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*
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* Date: November, 03, 2003
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*
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* Modifications:
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* March, 02, 2007: return the number of differences found
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*
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*-------------------------------------------------------------------------
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*/
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hsize_t diff_attr(hid_t loc1_id,
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hid_t loc2_id,
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const char *path1,
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const char *path2,
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diff_opt_t *options)
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{
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hid_t attr1_id=-1; /* attr ID */
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hid_t attr2_id=-1; /* attr ID */
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hid_t space1_id=-1; /* space ID */
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hid_t space2_id=-1; /* space ID */
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hid_t ftype1_id=-1; /* file data type ID */
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hid_t ftype2_id=-1; /* file data type ID */
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hid_t mtype1_id=-1; /* memory data type ID */
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hid_t mtype2_id=-1; /* memory data type ID */
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size_t msize1; /* memory size of memory type */
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size_t msize2; /* memory size of memory type */
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void *buf1=NULL; /* data buffer */
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void *buf2=NULL; /* data buffer */
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hsize_t nelmts1; /* number of elements in dataset */
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int rank1; /* rank of dataset */
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int rank2; /* rank of dataset */
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hsize_t dims1[H5S_MAX_RANK];/* dimensions of dataset */
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hsize_t dims2[H5S_MAX_RANK];/* dimensions of dataset */
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char *name1;
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char *name2;
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char np1[512];
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char np2[512];
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unsigned u; /* Local index variable */
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hsize_t nfound = 0;
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hsize_t nfound_total = 0;
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int j;
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table_attrs_t * match_list_attrs = NULL;
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if( build_match_list_attrs(loc1_id, loc2_id, &match_list_attrs, options) < 0)
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goto error;
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for(u = 0; u < (unsigned)match_list_attrs->nattrs; u++)
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{
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if( (match_list_attrs->attrs[u].exist[0]) && (match_list_attrs->attrs[u].exist[1]) )
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{
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name1 = name2 = match_list_attrs->attrs[u].name;
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/*--------------
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* attribute 1 */
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if((attr1_id = H5Aopen(loc1_id, name1, H5P_DEFAULT)) < 0)
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goto error;
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/*--------------
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* attribute 2 */
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if((attr2_id = H5Aopen(loc2_id, name2, H5P_DEFAULT)) < 0)
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goto error;
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/* get the datatypes */
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if((ftype1_id = H5Aget_type(attr1_id)) < 0)
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goto error;
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if((ftype2_id = H5Aget_type(attr2_id)) < 0)
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goto error;
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if((mtype1_id = h5tools_get_native_type(ftype1_id))<0)
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goto error;
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if((mtype2_id = h5tools_get_native_type(ftype2_id))<0)
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goto error;
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if((msize1 = H5Tget_size(mtype1_id))==0)
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goto error;
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if((msize2 = H5Tget_size(mtype2_id))==0)
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goto error;
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/* get the dataspace */
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if((space1_id = H5Aget_space(attr1_id)) < 0)
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goto error;
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if((space2_id = H5Aget_space(attr2_id)) < 0)
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goto error;
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/* get dimensions */
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if((rank1 = H5Sget_simple_extent_dims(space1_id, dims1, NULL)) < 0)
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goto error;
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if((rank2 = H5Sget_simple_extent_dims(space2_id, dims2, NULL)) < 0)
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goto error;
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/*----------------------------------------------------------------------
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* check for comparable TYPE and SPACE
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*----------------------------------------------------------------------
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*/
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/* pass dims1 and dims2 for maxdims as well since attribute's maxdims
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* are always same */
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if( diff_can_type(ftype1_id, ftype2_id, rank1, rank2, dims1, dims2,
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dims1, dims2, name1, name2, options, 0) != 1 )
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{
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if(H5Tclose(ftype1_id) < 0)
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goto error;
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if(H5Tclose(ftype2_id) < 0)
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goto error;
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if(H5Sclose(space1_id) < 0)
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goto error;
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if(H5Sclose(space2_id) < 0)
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goto error;
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if(H5Aclose(attr1_id) < 0)
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goto error;
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if(H5Aclose(attr2_id) < 0)
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goto error;
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if(H5Tclose(mtype1_id) < 0)
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goto error;
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if(H5Tclose(mtype2_id) < 0)
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goto error;
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continue;
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}
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/*---------------------------------------------------------------------
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* read
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*----------------------------------------------------------------------
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*/
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nelmts1 = 1;
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for(j = 0; j < rank1; j++)
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nelmts1 *= dims1[j];
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buf1 = (void *)HDmalloc((unsigned)(nelmts1 * msize1));
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buf2 = (void *)HDmalloc((unsigned)(nelmts1 * msize2));
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if(buf1 == NULL || buf2 == NULL) {
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parallel_print( "cannot read into memory\n" );
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goto error;
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}
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if(H5Aread(attr1_id,mtype1_id,buf1) < 0)
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goto error;
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if(H5Aread(attr2_id,mtype2_id,buf2) < 0)
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goto error;
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/* format output string */
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sprintf(np1,"%s of <%s>",name1,path1);
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sprintf(np2,"%s of <%s>",name2,path2);
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/*---------------------------------------------------------------------
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* array compare
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*----------------------------------------------------------------------
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*/
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/* always print name */
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/* verbose (-v) and report (-r) mode */
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if(options->m_verbose || options->m_report) {
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do_print_attrname("attribute", np1, np2);
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nfound = diff_array(buf1, buf2, nelmts1, (hsize_t)0, rank1, dims1,
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options, np1, np2, mtype1_id, attr1_id, attr2_id);
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print_found(nfound);
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}
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/* quiet mode (-q), just count differences */
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else if(options->m_quiet) {
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nfound = diff_array(buf1, buf2, nelmts1, (hsize_t)0, rank1, dims1,
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options, np1, np2, mtype1_id, attr1_id, attr2_id);
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}
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/* the rest (-c, none, ...) */
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else {
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nfound = diff_array(buf1, buf2, nelmts1, (hsize_t)0, rank1, dims1,
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options, np1, np2, mtype1_id, attr1_id, attr2_id);
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/* print info if compatible and difference found */
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if(nfound) {
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do_print_attrname("attribute", np1, np2);
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print_found(nfound);
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} /* end if */
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} /* end else */
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/*----------------------------------------------------------------------
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* close
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*----------------------------------------------------------------------
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*/
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/* Free buf1 and buf2, check both VLEN-data VLEN-string to reclaim any
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* VLEN memory first */
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if(TRUE == h5tools_detect_vlen(mtype1_id))
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H5Dvlen_reclaim(mtype1_id, space1_id, H5P_DEFAULT, buf1);
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HDfree(buf1);
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buf1 = NULL;
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if(TRUE == h5tools_detect_vlen(mtype2_id))
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H5Dvlen_reclaim(mtype2_id, space2_id, H5P_DEFAULT, buf2);
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HDfree(buf2);
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buf2 = NULL;
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if(H5Tclose(ftype1_id) < 0)
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goto error;
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if(H5Tclose(ftype2_id) < 0)
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goto error;
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if(H5Sclose(space1_id) < 0)
|
|
goto error;
|
|
if(H5Sclose(space2_id) < 0)
|
|
goto error;
|
|
if(H5Aclose(attr1_id) < 0)
|
|
goto error;
|
|
if(H5Aclose(attr2_id) < 0)
|
|
goto error;
|
|
if(H5Tclose(mtype1_id) < 0)
|
|
goto error;
|
|
if(H5Tclose(mtype2_id) < 0)
|
|
goto error;
|
|
|
|
nfound_total += nfound;
|
|
}
|
|
} /* u */
|
|
|
|
table_attrs_free(match_list_attrs);
|
|
|
|
return nfound_total;
|
|
|
|
error:
|
|
H5E_BEGIN_TRY {
|
|
if(buf1) {
|
|
if(TRUE == h5tools_detect_vlen(mtype1_id))
|
|
H5Dvlen_reclaim(mtype1_id, space1_id, H5P_DEFAULT, buf1);
|
|
HDfree(buf1);
|
|
} /* end if */
|
|
if(buf2) {
|
|
if(TRUE == h5tools_detect_vlen(mtype2_id))
|
|
H5Dvlen_reclaim(mtype2_id, space2_id, H5P_DEFAULT, buf2);
|
|
HDfree(buf2);
|
|
} /* end if */
|
|
|
|
table_attrs_free(match_list_attrs);
|
|
|
|
H5Tclose(ftype1_id);
|
|
H5Tclose(ftype2_id);
|
|
H5Tclose(mtype1_id);
|
|
H5Tclose(mtype2_id);
|
|
H5Sclose(space1_id);
|
|
H5Sclose(space2_id);
|
|
H5Aclose(attr1_id);
|
|
H5Aclose(attr2_id);
|
|
} H5E_END_TRY;
|
|
|
|
options->err_stat = 1;
|
|
return nfound_total;
|
|
}
|
|
|