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* [svn-r20183] Add HDF5_USING_MEMCHECKER guards around script mode ADD_TEST. ↵Allen Byrne2011-03-047-198/+225
| | | | | | | | This will replace the list of ignore tests in CTestCustom.cmake file. Bring back from trunk Tested: local linux
* [svn-r20182] BZ2048: Add -E --enable-error-stack option to h5dump.Allen Byrne2011-03-0413-8/+126
| | | | | | Brought from trunk after one week of tests. Tested: local linux
* [svn-r20173] Add h5mkgrp utility to package listAllen Byrne2011-03-011-1/+1
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* [svn-r20160] Correct test properties for test orderAllen Byrne2011-02-251-3/+7
| | | | Tested: local linux
* [svn-r20158] Comment out reference to BZ2048 testsAllen Byrne2011-02-251-3/+3
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* [svn-r20157] Bring CMake changes to branch up to r20156 from trunkAllen Byrne2011-02-259-35/+43
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* [svn-r20133] Purpose:Jonathan Kim2011-02-2110-46/+3169
| | | | | | | | | | | | | | | | Fixing Bug 2092 - h5dump does not display index for a dataset Description: Merged from HDF5 trunk r20108 and r20132. h5dump skip displaying array indices every certain number when the array type dataset is relatively big. The certain number varies according to the size of each array. This checkin fix the skipping array indices problem. This fix also correct indentation of the dataset data output. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), Cmake - jam
* [svn-r20130] Add test dependencies to order testsAllen Byrne2011-02-216-1/+68
| | | | Tested: local linux
* [svn-r20128] Add fortran mod folder to INCLUDE_DIRS for gfortran 4.2.x.Allen Byrne2011-02-213-0/+40
| | | | | | Add test dependicies to correct the order of tests - cmake 2.8.4 bug - but also will improve cmake parallel testing. Tested: local linux, jam
* [svn-r20120] Description:Quincey Koziol2011-02-172-101/+102
| | | | | | | | | | | | | | | | | | | | | | Bring r20119 from trunk to 1.8 branch: Clean up MPI resource leaks in parallel tests, along with a bunch of compiler warnings. Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (amani) w/Intel compilers, w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, w/threadsafe, in production mode Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode Mac OS X/32 10.6.6 (amazon) in debug mode Mac OS X/32 10.6.6 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r20104] Purpose:Jonathan Kim2011-02-147-82/+61
| | | | | | | | | | | | | Change to use HDxxx macros. Description: Merged from hdf5 trunk r20103. Originally this started for fixing incorrect pointer usage. But that got fixed through coverity merge. So this is mainly changing to use HDxxx macros and clean up some related code. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE)
* [svn-r20071] Description:Quincey Koziol2011-02-091-1/+1
| | | | | | | | | Bring r20070 from trunk to 1.8 branch: Switch order of system includes, to correct error on FreeBSD machines. Tested on: FreeBSD/32 6.3 (duty) w/debug
* [svn-r20066] Description:Quincey Koziol2011-02-087-53/+40
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring r20065 from trunk to 1.8 branch: Bring changes from Coverity branch to trunk: r19975: Fixed potential mem leak at H5O_attr_open_by_name r19980: Fix coverity issue 792. Free tmp_env_prefix in H5Lexternal.c line 365 if it is not NULL but its contents are 0 when it goes out of scope. r20039: Eliminate warnings about nested extern and implicit declarations of parallel_print and address Coverity defects 712-781 by #including h5tools_utils.h in h5diff_array.c, h5diff_attr.c, h5diff_dset.c and h5diff_util.c. r20046: Purpose: Address TOCTOU warnings in h5jam and h5unjam Description: Coverity is afraid that the state of the input file could change between the call to stat() and the call to open(). This is called a time-of- check time-of-use (TOCTOU) vulnerability. Modified stat calls to fstat which uses an open file pointer so it (hopefully) won't complain any more. r20047: Addressed coverity issues 135-137, 462-464. Local pointers that needed to be freed in case of error were moved out of a switch statement in src/H5Tnative.c, set to NULL, and checked before freeing. Tested on: Mac OS X/32 10.6.6 (amazon) w/debug & production (h5committested on Coverity branch)
* [svn-r20062] Description:Quincey Koziol2011-02-082-173/+135
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring r20061 from trunk to 1.8 branch: Bring changes from Coverity branch to trunk: r19930: Fix memory leaks involving VL attributes in h5repack and h5diff. The buffers in copy_attr and diff_attr were not checked for the presence of a vlen before being freed, and vlen storage was never reclaimed. Added checks and calls to H5D_vlen_reclaim(). r19933: Purpose: Fix memory leak in H5L_move_cb() Description: H5L_move_cb copied the source link using H5O_msg_copy() but freed it manually using H5MM_xfree(). Since H5O_link_copy allocates the link using H5FL_MALLOC, this causes the link to be allocated from the free list but is never put back on the free list when it is freed. This prevents the link free list from shutting down properly. Modified H5L_move_cb() and H5L_move_dest_cb() to free the link properly using H5O_msg_free(). r19973: Fix resource leaks by freeing string created by HD5f2string r19974: Issue #345: Inialize buf variable to null Tested on: Mac OS X/32 10.6.6 (amazon) w/debug & production (h5committested on Coverity branch)
* [svn-r20056] Correct comment handling and remove cut/paste oversightsAllen Byrne2011-02-072-27/+25
| | | | Tested: local linux
* [svn-r20053] Description:Quincey Koziol2011-02-062-174/+134
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring r20052 from trunk to 1.8 branch: Clean up Coverity warnings, and fix some style issues: r19735: Fix for memory leak in test/mf found by valgrind. r19736: Fix memory leak in h5repack. The buffer in copy_objects, when copying the entire dataset at once, was not checked for the presence of a vlen, and vlen storage was never reclaimed. Added check and call to H5D_vlen_reclaim(). r19772: Change H5assert() to if (H5T_VLEN != src->shared->type || H5T_VLEN != dst->shared->type) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a H5T_VLEN datatype") r19774: removed unused priv. r19775: removed unused variables r19778: Fix memory leak comparing for variable length data types. r19834: Fixed memory leaks found by valgrind. Memory errors remain for another day. Tested on: Mac OS X/32 10.6.6 (amazon) w/debug & production (h5committested on branch)
* [svn-r20045] Fix bz2127 by dynamically allocating storgae for comments. Allen Byrne2011-02-048-10/+61
| | | | | | Bring 20044 from trunk Tested: local linux
* [svn-r20017] Purpose: fix compiler error on BP (AIX) from recent change for ↵Jonathan Kim2011-01-271-0/+1
| | | | h5repack svn r20007.
* [svn-r20007] Purpose:Jonathan Kim2011-01-263-2/+14
| | | | | | | | Clean up tool code. Remove "h5test.h" from tool code. Currently only in h5repack. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), linew (solaris-BE), tejeda (mac32-LE)
* [svn-r19992] Purpose:Jonathan Kim2011-01-253-0/+25
| | | | | | | | h5dump: add dangling external link test case as part of Chicago project. Merged from hdf5 trunk r19971. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), linew (solaris-BE)
* [svn-r19916] Add hh modifier to signed char printf format string. Added ↵Allen Byrne2011-01-056-18/+584
| | | | | | | h5dump test to verify that signed/unsigned datasets print correctly. Solves problem on heiwa with Signed char of 8 bits Tested: local linux, heiwa
* [svn-r19912] Add instruction to get native type before checking the type ↵Allen Byrne2011-01-051-11/+12
| | | | | | against H5T_NATIVE_xxxx Tested: heiwa where it had failed
* [svn-r19908] Change how LINK_FLAGS for fortran are appended on WindowsAllen Byrne2011-01-051-1/+0
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* [svn-r19906] Windows: Correct how fortran links in CRT library. Also correct ↵Allen Byrne2011-01-049-24/+24
| | | | | | macro use for checking libtype. Tested: Windows
* [svn-r19905] Corrected typo of offset in comment at top of reference filesAllen Byrne2011-01-044-4/+4
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* [svn-r19904] Add missing .ddl extension onto packed bits command line in ↵Allen Byrne2011-01-041-36/+36
| | | | test script.
* [svn-r19903] Need to check if the length of mask is equal to the size of the ↵Allen Byrne2011-01-041-2/+6
| | | | | | mask and skip the shift. Tested: local linux
* [svn-r19902] Use an unsigned long long variable to generate the mask instead ↵Allen Byrne2011-01-031-4/+4
| | | | | | of a constant. Tested: windows where it had failed.
* [svn-r19900] Correct typo in commentAllen Byrne2010-12-311-1/+1
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* [svn-r19898] Remove use of /MT compile flag for building static libs and ↵Allen Byrne2010-12-308-22/+0
| | | | programs. Added BUILT_AS_STATIC_LIBRARY define to set the windows import/export defines correctly for static libraries.
* [svn-r19897] Extend packed bits and testing to 64 bit integers.Allen Byrne2010-12-3050-66/+3469
| | | | Tested: local Linux
* [svn-r19893] Purpose:Jonathan Kim2010-12-285-315/+734
| | | | | | | | | | | | | | | | | | | | Bug 2089 - GMQS: h5diff segfault on a compound dataset with fixed length + vlen string type order Description: Merged from HDF5 trunk r19892. This is fix for the segfault when h5diff compares a compound dataset with combination of fixed length string types and vlen string types in certain orders. Optimized vlariable length string handling codes. The fix is referred from h5dump handling vlen strings. For testing, several compound datasets were added with various combinations. Previous failed cases: - Vlen string, Fixed length string, Vlen string, Fixed length string - Fixed length string, Fixed length string, Vlen string, Vlen string - Fixed length string, Vlen string, Fixed length string, Vlen string Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), linew (solaris-BE)
* [svn-r19862] Updated libtool to version 2.4, autoconf to version 2.68, and ↵Larry Knox2010-12-0111-0/+33
| | | | | | m4 to version 1.4.15. Tested with h5committest on amani, jam and heiwa.
* [svn-r19851] Problem: AIX prints some error messages when MPI_Abort is ↵Albert Cheng2010-11-261-1/+9
| | | | | | | | | | called. That caused the output matching some problems. Solution: Add stderr filtering for AIX ERROR: messages. Tested: NCSA BP.
* [svn-r19819] Purpose:Jonathan Kim2010-11-181-3/+9
| | | | | | | | Change to skip copying when a dataset is not allocated. Merged from hdf5 trunk r19818. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE)
* [svn-r19802] Update valgrind ignore tests.Allen Byrne2010-11-171-0/+6
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* [svn-r19793] Revised the valgrind ignore list, added simple execute command ↵Allen Byrne2010-11-164-0/+38
| | | | tests for when doing a valgrind test of tools that only use a cmake script for testing.
* [svn-r19760] Purpose:Jonathan Kim2010-11-111-4/+12
| | | | | | | | | | | | | | | | | | Fix compile error for Windows from previous checkin r19758. Description: Previous log: Improve h5diff performance. The following changes for improving h5diff performance: 1) use HDmemcmp() before comparing each elements (memcmp() is very fast at both linew and jam) 2) replace the expensive H5Tequals() calls 3) retrieve datatype information at dataset level not each element level for compound datasets Tested: jam (linux32-LE), Windows
* [svn-r19758] Purpose:Jonathan Kim2010-11-112-36/+132
| | | | | | | | | | | | | | | | | Improve h5diff performance. Description: The following changes for improving h5diff performance: 1) use HDmemcmp() before comparing each elements (memcmp() is very fast at both linew and jam) 2) replace the expensive H5Tequals() calls 3) retrieve datatype information at dataset level not each element level for compound datasets Merged from hdf5 trunk r19757. Tested: jam (linux32-LE)
* [svn-r19752] Purpose:Jonathan Kim2010-11-096-2/+89
| | | | | | | | | | | | | | | Fixed Bug# 1979 Output from h5ls -rdlS on nested compound datatypes is difficult to parse. Description: Update to add curly brackets for the nested compound members, when S (--simple) option is used with -l (--label), so user can tell which members blong to which compound type. Merged from hdf5 trunk r19751. Tested: jam (linux32-LE), amani (linux64-LE)
* [svn-r19732] Purpose:Jonathan Kim2010-11-051-1/+1
| | | | | | | | | | | Fix the test script from the previous checkin r19730. expect output is under misc/testfiles/ in srcdir. Previous Log: [BZ2072]Add compare output to expected test for help and version options of mkgrp. Tested: jam (linux32-LE)
* [svn-r19730] Purpose:Jonathan Kim2010-11-041-3/+3
| | | | | | | | | | | Fix the test script from the previous checkin r19727 due to contiguous build system failure. Previous Log: [BZ2072]Add compare output to expected test for help and version options of mkgrp. Tested: jam (linux32-LE)
* [svn-r19728] Description:Quincey Koziol2010-11-041-1/+1
| | | | | | | | | | | | Bring r19725 from trunk to 1.8 branch: Add a little bit of extra info to the output from h5debug when displaying global heaps, and make it dump the file's superblock again when an address is not given on the command line. Tested on: FreeBSD/32 6.3 (duty) w/debug (too minor to require h5committest)
* [svn-r19727] [BZ2072]Add compare output to expected test for help and ↵Allen Byrne2010-11-044-5/+76
| | | | | | | | version options of mkgrp. bring r19726 back from trunk Tested: local linux
* [svn-r19713] Purpose:Jonathan Kim2010-11-025-30/+396
| | | | | | | | | | | | | | | | Fixed h5diff to handle variable-length strings in a compound dataset correctly. Also variable-length string array in a compound dataset. Bug #1989. Description: Garbage values were displayed when h5diff compared variable-length strings (or string array) in a compound type dataset. Merged from hdf5 trunk r19712. Tested: jam (linux32-LE), heiwa (linuxppc64-BE)
* [svn-r19705] Added VFD test options.Allen Byrne2010-11-011-0/+36
| | | | Tested: local linux
* [svn-r19690] Added new h5copy testAllen Byrne2010-10-281-7/+44
| | | | Tested: local linux
* [svn-r19678] Remove duplicate files in reference list for copyingAllen Byrne2010-10-271-10/+0
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* [svn-r19677] Added h5mkgrp testsAllen Byrne2010-10-271-0/+91
| | | | | | Added valgrind test variables and increased Tested: Local linux
* [svn-r19655] Description:Quincey Koziol2010-10-211-34/+34
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring r19654 from trunk to 1.8 branch: Bring Coverity revisions from branch back to trunk, and clean up some other misc. compiler warnings also. r19500: Fix coverity items 1446 and 1447. Moved up calls to memset in test_cont in ohdr.c so the test never tries to close uninitialized locations. r19501: Fix coverity items 1398-1445. Various uninitialized variable errors in fheap.c. r19502: Fixed coverity issue 579 and some additional warnings in the file as well. r19503: Bug fix: This fix addressed the "RESOURCE_LEAK" problems #789 and 790, run 26 r19504: minor mods to try to keep coverity from flagging false positives. r19505: Fixed coverity issues 566 - 571. Declared variables that are passed to functions that use them as arrays to be arrays of size 1. Tested on: Mac OS X/32 10.6.4 (amazon) w/debug, production & parallel (h5committested on coverity branch)
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