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* [svn-r23510] I merged the changes for DESY project from the trunk (r23496) ↵Raymond Lu2013-04-012-1/+69
| | | | | | into this 1.8 DESY branch. Tested with h5committest (duck failed with CMake because I don't know how to change test/CMakeLists.txt. I'll wait for Allen to do it).
* [svn-r23498] Bug fix: HDFFV-8358Albert Cheng2013-03-301-7/+64
| | | | | | | | Change h5redeploy to change all 4 lines, prefix=..., exec_prefix=..., libdir=..., and includedir=... This way, it reset all 4 lines. Should work for both version of h5cc created by configure or by rpm. Tested: hand tested in jam.
* [svn-r23477] HDFFV-8359: correct script function calls.Allen Byrne2013-03-281-5/+5
| | | | Tested: local linux
* [svn-r23464] Purpose: Jonathan Kim2013-03-273-10/+24
| | | | | | | | | | | | | HDFFV-8214 - h5repack failed converting small chunked dataset (size < 1K) to contiguous layout. Description: h5repack failed converting small chunked dataset (size < 1K) to contiguous layout. The first case was when chunk dim is bigger than the dataset dim (at leat one), h5repack failed with displaying error stacks. The other case is when chunk dim is smaller than the dataset dim, h5repack failed to change layout. Merged from HDF5 trunk 23407 Tested: jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), emu (solaris-BE), fred (mac64-LE), Windows (32-LE cmake), cmake (jam)
* [svn-r23460] Add missing infile assignment and error countsAllen Byrne2013-03-261-0/+2
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* [svn-r23459] HDFFV-8355 h5repack.sh was wrong for the two test cases.Peter Cao2013-03-261-3/+17
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* [svn-r23448] HDFFV-8322: valgrind leaksAllen Byrne2013-03-252-38/+29
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* [svn-r23416] Description:Quincey Koziol2013-03-211-2/+2
| | | | | | | | | Bring r23415 from trunk to 1.8 branch: Avoid using fpclassify() for detecting zero/non-zero values. Tested on: Mac OSX/64 10.8.3 (amazon) w/debug
* [svn-r23396] Description:Quincey Koziol2013-03-207-611/+619
| | | | | | | | | | | | | | Bring r23395 from trunk to 1.8 branch: Bring Coverity changes from branch to trunk: r20682: fixed coverity: 76, 77, 635, 636, 1164, 1165, 1166, 1121, 1122, 1117, 1343 Tested on: Mac OSX/64 10.8.3 (amazon) w/C++ & FORTRAN (too minor to require h5committest)
* [svn-r23383] fixed HDFFV-8344 and HDFFV-8346: add info for user registered ↵Peter Cao2013-03-194-7/+17
| | | | filter in h5dump
* [svn-r23355] Correct target nameAllen Byrne2013-03-151-1/+1
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* [svn-r23324] Snapshot version 1.8 release 11 (snap11)HDF Tester2013-03-0411-11/+11
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* [svn-r23318] HDFFV-8311: Improve tools testing and eliminate dependency problemsAllen Byrne2013-02-255-675/+663
| | | | Tested: local linux
* [svn-r23315] Correct typo in DEPENDSAllen Byrne2013-02-251-1/+1
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* [svn-r23309] Purpose:Jonathan Kim2013-02-214-4/+11
| | | | | | | | | | | | | HDFFV-7643 - h5diff - incorrect exit-code returns for extra attribute exist Description: h5diff: Fixed to return correct exit code 1 when detect unique attribute. Prior to this fix, h5diff returned exit code 0 indicating two files are identical. Merged from HDF5 trunk r23304. Tested: jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), fred (mac64-LE), emu (solaris-BE), Windows (32-LE cmake), cmake (jam)
* [svn-r23302] Remove old file namesAllen Byrne2013-02-187-104/+0
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* [svn-r23301] Allen Byrne2013-02-1868-1290/+4705
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* [svn-r23229] Jonathan Kim2013-02-051-1/+1
| | | | | | | | | | | | Purpose: Revert back one of the coverity updates from previous (r23220) checkin. "r20457: Coverity issue 691" in previous svn log. Only revert the change about using "STDOUT_FILENO". Description: Using "STDOUT_FILENO" caused error on Windows. On unix it's defined in <unistd.h>, but not in Windows. After a little discussion with Allen, he remembered how the similar case were handled for h5dump redirecting those streams. (in h5dump.c) However it would requires more attention to apply, so this issue is entered as a separate task in jira HDDFV-8306. Tested: jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), fred (mac64-LE)
* [svn-r23220] Description:Quincey Koziol2013-02-022-118/+99
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring r23219 from trunk to 1.8 branch: Bring reviewed changes from Coverity branch back to trunk (QK & JK): r20457: Coverity issue 691: return of H5duo could be negative. Fixed by using STDOUT_FILENO and redesign parse_command_line and main to cleanup file allocations. The output_file var is null when using stdout. In cleanup do not close output_file if NULL. r20510: Initialize ufid = -1 and predicate HDclose call on ufid != -1 r20511: Purpose: Fix coverity issue 1715 Description: Free "file" and nested data on failure in H5FD_core_open. r20512: Initialize ifid = -1 and predicate HDclose call on ifid != -1 r20514: Initialize h5fid = -1 and predicate HDclose call on h5fid != -1 r20516: Added else branch to the if (ret_value < 0) check. r20522: Addressed coverity issues 930-933, 850, 836, 835, 1307. All minor potential buffer overwrite bugs, or coverity errors. Fixed by replacing strcpy and sprintf with strncpy and snprintf. r20523: fixed coverity issues 68, 1120, 1116i r20524: Check H5Z_SZIP->encoder_present < 1 assuming 0 represents absence. r20601: Purpose: Fix coverity issues 1703-1705 Description: Modified the cleanup code in test_free in accum.c to reset allocated buffers to NULL after they are freed, and modified the error cleanup code to check if these buffers are NULL before freeing them. Also fixed some unrelated warnings in accum.c. r20602: Use HDsnprintf and HDstrncat r20603: Purpose: Fix coverity issues 808-809 Description: Modified test_core in vfd.c to check the returns from malloc, and keep track of whether points and check are allocated by setting them to NULL when they are not. Added code to free points and check on error if they are not NULL. Also fixed unrelated warnings in vfd.c. r20604: Use HDstrncpy. r20605: Use HDstrncpy and HDstrncat. r20606: Purpose: Fix coverity issue 807 Description: Modified long_compact in stab.c to keep track of whether objname is allocated by setting it to NULL when it is not. Added code to free objname on error if it is not NULL. r20607: Changed string function calls to use versions that specify the string length to fix coverity issues 832 and 839. Tested on: Mac OSX/64 10.8.2 (amazon) (Too minor to require h5committest)
* [svn-r23211] Merge trunk CMake changes for minimum cmake version of 2.8.10. ↵Allen Byrne2013-01-3111-11/+11
| | | | | | This was prompted by HDFFV-8227, OS X requires latest version of cmake for proper support. Tested: local linux
* [svn-r23187] HDFFV-8169: Binary output of String types are wrongAllen Byrne2013-01-224-13/+156
| | | | | | Merge from trunk Add testfiles. Tested: local linux
* [svn-r23186] HDFFV-8169: Binary output of String types are wrongAllen Byrne2013-01-221-1/+1
| | | | Merge from trunk
* [svn-r23069] Bug fix: HDFFV-8233Albert Cheng2012-11-301-2/+12
| | | | | | | | | | | | | testh5stat.sh fails in LLNL uDawn. The test actually ran as expected but it did not prepare for the extra error messages from the MPI process. Solution: This sort of problem has been fixed by using the output filters in output_filter.sh. testh5stat.sh is updated to use the output filters. Tested: uDawn.
* [svn-r23000] Description:Quincey Koziol2012-11-012-23/+30
| | | | | | | | | | | | | | | | | | | | | | | | | Bring r22998 from trunk to 1.8 branch: Clean up warnings and bring changes from Coverity branch back to trunk: r20451: Fixed coverity 810 r20454: Purpose: Fix coverity issue 816 Description: Modified various file drivers to always check the return value from H5P_get_driver_info. r20455: Purpose: Cleanup fix for coverity issue 816 Description: Removed redundant check for "fa" in H5FD_core_open. Tested on: Mac OSX/64 10.8.2 (amazon) w/debug (Too minor to require h5committest)
* [svn-r22934] Purpose:Jonathan Kim2012-10-191-0/+18
| | | | | | | | | | | HDFFV-8145 h5diff slowness with version >= 1.8.7 Description: Improved speed when comparing HDF5 files with lots of attributes. Much slower performance was identified with release version from 1.8.7 to 1.8.10 compared to 1.8.6. Merged from HDF5 trunk r22933. Tested: jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), cmake (jam)
* [svn-r22929] Description:Quincey Koziol2012-10-198-263/+192
| | | | | | | | | | | | | | | | | | | | | | | | | | | Bring r22921 from trunk to 1.8 branch: Review Coverity changes and bring them back to trunk. (QK & JK) r20402: Added #includes for h5tools.y or h5tools_utils.h as required to remedy implicit function declarations which caused compiler warnings and coverity issues 703-4 and 708-11. r20414: This is related to the previous checkin r20399. There were incorrect updates which caused incorrect behavior when no file was given. Also possible segfault when handling hyperslab options. Simplify the code changes. r20449: Description: Modified H5E_walk2_cb to check return value of H5I_object_verify. r20450: fixed coverity 813 Tested on: Mac OSX/64 10.8.2 (amazon) w/C++, FORTRAN, debug & threadsafe (too minor to require h5committest)
* [svn-r22916] Description:Quincey Koziol2012-10-171-7/+8
| | | | | | | | | | | | | | | | | | | | | | | | | Bring r22915 from trunk to 1.8 branch: Bring Coverity changes back to trunk: r20399: Change parse_command_line to free hand structure on error and only "leave()" at end of main. r20400: Purpose: Fix coverity issue 592 Description: Added void cast to call to H5F_sfile_assert_num() in H5F_term)interface(). There is no need to check the return value of this function in general, and there would be nothing to do even if it did fail. r20401: Added free(src_sizes) and free(src_offset). --gh Tested on: Mac OSX/64 10.8.2 (amazon) w/C++, FORTRAN, threadsafe (too minor for h5committest)
* [svn-r22814] Purpose:Jonathan Kim2012-09-266-22/+143
| | | | | | | | | | | | | | HDFFV-8012 - h5repack changes max dims and cause failure if only "-f none" is used without changing layout for chunked dataset when a chunk dim is bigger than a dataset dim Description: "h5repack -f <obj>:NONE <file.h5> out.h5" command failed if source file contains chunked dataset and a chunk dim is bigger than a dataset dim. Another issue is that the command changed max dims if chunk dim is smaller than the dataset dim. These issue occurred when dataset size is smaller than 64k (compact size limit) Fixed them. Merged from HDF5 trunk r22805 Tested: jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), cmake (jam)
* [svn-r22788] HDFFV-8153: Pull POSIX_C_SOURCE define out to separate ↵Allen Byrne2012-09-192-0/+10
| | | | | | variable. Use ADD_DEFINITIONS (${HDF5_EXTRA_C_FLAGS}) in non-fortran CMakeLists.txt folders Tested: local
* [svn-r22753] Purpose:Jonathan Kim2012-09-1113-23/+34
| | | | | | | | | | | | | HDFFV-5919 - GMQS: h5diff - The number of object difference is not consistent between dataset and group/type when attribute(s) have differences Description: Object differences are not consistent between dataset and group/datatype when their attribute(s) have differences. This is because attribute(s) differences is not accumulated to group or datatype object’s difference, but accumulated to dataset difference. To fix, do not accumulate attribute difference to dataset difference. This is referred to h5diff’s default behavior and also past report from users that users were confused by the accumulated behavior. (also can’t figure out only for dataset difference , also hard to spot dataset difference when it has lots of attributes or differences) This also lead to fix inconsistent format indicating difference between dataset and group/datatype object. Merged from HDF5 trunk r22751. Tested: jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), cmake (jam)
* [svn-r22740] Correct typo on test commandAllen Byrne2012-09-051-1/+1
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* [svn-r22727] Add other h5 files needed by pbits testsAllen Byrne2012-08-301-0/+2
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* [svn-r22724] Convert tests to *.sh.in.Allen Byrne2012-08-2825-231/+229
| | | | | | | | Convert configure.in to configure.ac. Align TESTS usage with autotools convention. Update all references from configure.in to configure.ac Tested: h5committest
* [svn-r22721] HDFFV-8133: Add usage text to see Reference manual for compact ↵Allen Byrne2012-08-289-153/+162
| | | | subsetting.
* [svn-r22719] Fix RelWithDebInfo packagingAllen Byrne2012-08-289-12/+12
| | | | Tested: windows
* [svn-r22711] Updated autotools: autoconf 2.69, automake 1.12.3, m4 1.4.16, ↵Larry Knox2012-08-2311-479/+1054
| | | | | | libtool 2.4.2 Tested THG machines.
* [svn-r22701] Purpose: Jonathan Kim2012-08-209-19/+99
| | | | | | | | | | | | | Address HDFFV-7942 - h5diff: incorrect result for comparing attribute data with different type size in same class Description: When comparing attribute data values with same type class but different size, the result was incorrect. It was due to the size difference and got truncated. Fixed to match up the smaller type size to big type size like what dataset does. Merged from HDF5 trunk r22684 and r22691. Tested: jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), Windows (32-LE cmake), cmake (jam)
* [svn-r22699] Merge trunk 22674 to 1.8:Allen Byrne2012-08-204-125/+25
| | | | | Remove checks for filters are available because the h5dump tests never used the filters in the tests. "-H" option excludes data. HDFFV-8125
* [svn-r22647] Description:Quincey Koziol2012-08-093-8/+11
| | | | | | | | | | | Bring r22646 from trunk to 1.8 branch: Changes resulting from Klocwork static analysis tool, from Mark Miller @ LLNL (miller86@llnl.gov). Tested on: Mac OS X/64 10.7.4 (amazon) w/debug, C++ & FORTRAN, using gcc 4.7.x (too minor to require h5committest)
* [svn-r22643] Correct check for filters in tools testAllen Byrne2012-08-082-8/+29
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* [svn-r22639] HDFFV-8111: Remove special case shortcut and use normal path ↵Allen Byrne2012-08-072-223/+102
| | | | | | for comparing single objects. Merged from trunk
* [svn-r22632] Merge from trunk revision 22631Allen Byrne2012-08-0630-1153/+2870
| | | | tested: local linux
* [svn-r22621] Purpose:Jonathan Kim2012-08-0210-61/+170
| | | | | | | | | | | | | | | | HDFFV-8107 testh5diff will fail if build/test in HDF5 source tree Description: This is sub-task for "HDFFV-8105 testh5diff.sh uses the wrong operator (-a) in an if statement." From the HDFFV-8105's update, h5diff test failed if build&test is performed in HDF5 source tree because 'cp' try to copy test files to self dir. It's addressed by skipping if cp's src dir and dest dir is same. Also this applied for all other tools under src/tools dir. No change to the CMakeLists.txt files because CMake cautions/demands that in-source builds be avoided. Merged from HDF5 trunk r22617. Tested: jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), some manual tests as well
* [svn-r22619] Jonathan Kim2012-08-022-16/+1
| | | | | | | | | | | | | | | Purpose: HDFFV-8003 - ph5diff (parallel h5diff): daily test failure on ember intermittently during non comparable test file comparison HDFFV-7755 - parallel h5diff : hanging on koala intermittently during non comparable test file comparison Description: non-comparable test intermittently hung on koala and ember, but not on jam. it didn't occur until -np reaches 4 or bigger. it occurred once out of many repeated attempts of the same test. There was a incorrectly (mistakenly?) duplicated code in MPI section which caused such hang in a certain condition. The test used more processes than other tests, which increased chance to trigger more undone processes, and such process could enter the incorrect code section and wait for wrong pair of send. it explains why it occurred intermittently according to machine condition and using a certain feature. Removed incorrect code which blocked correct code. Merged from HDF5 trunk r22618. Tested: jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), some manually repeated test performed in parallel
* [svn-r22595] Bug fix: HDFFV-8105Albert Cheng2012-07-221-4/+2
| | | | | | | | | | | | | | Description: The test command in COPY_TESTFILES_TO_TESTDIR used the wrong operator -a which means and. It is not sufficient to test mere existence as $tstfile could have been a directory or other non-file things. If the file is not readable, the $CP command would fail but its return code was not checked. Solution: Get rid of the test command and go ahead to $CP it and then check its returned code and report errors if detected. Tested; committested.
* [svn-r22578] Windows compilers require declarations at top of routine.Allen Byrne2012-07-161-8/+5
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* [svn-r22572] Re-Merge attr name with slash changes from trunkAllen Byrne2012-07-1310-12/+70
| | | | Tested: localinux with cmake
* [svn-r22571] HDFFV-7784,-8095,7936 merge from trunkAllen Byrne2012-07-1363-753/+2117
| | | | Tested: local linux with cmake
* [svn-r22551] Merge changes from Trunk revision 22550 for:Allen Byrne2012-07-1116-2158/+2756
| | | | | | HDFFV-4206, -7953, -5930, -2687, -5942 Tested: local linux with cmake
* [svn-r22538] Correct error string contentsAllen Byrne2012-07-101-3/+3
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