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* [svn-r21421] Merged the Fortran 2003 changes from the trunk into the 1.8 ↵Scot Breitenfeld2011-09-271-0/+3
| | | | | | | | | | | branch, used: svn merge -r 20506:21414 https://svn.hdfgroup.uiuc.edu/hdf5/trunk/fortran Tested: jam (gnu, intel, pgi compilers) Also merged effected non-Fortran files: svn merge -r21247:r21248 https://svn.hdfgroup.uiuc.edu/hdf5/trunk/src/libhdf5.settings.in
* [svn-r21414] Description:Jonathan Kim2011-09-231-2/+8
| | | | | | | | | | | Skip parallel diff test "-c non_comparables1.h5 non_comparables2.h5" due to hanging issue occurring on koala (linux64-LE) intermittently. Plan to put back when resolved. The test was related to J7693. Merged from HDF5 trunk r21413. Tested: jam (linux32-LE), koala (linux64-LE)
* [svn-r21404] Purpose:Jonathan Kim2011-09-2124-16/+281
| | | | | | | | | | | | | | | | | | | | | | HDFFV-7693 - h5diff produces different behavior between versions: 1.8.3 and 1.8.6 Description: There were two issues on this. One was not displaying all the comparable objects if non-comparable object/attribute exist and compared before comparables ones. This issue occurred after 1.8.4 release. This is the issue from user. The other issue was not displaying all the comparable attributes, if non-comparable object/attribute exist and compared ahead. This issue were exist even before 1.8.4 release. So it's possible some attribute comparison may have not displayed correctly in the past, if non-comparable data were exist in common object. Fixed h5diff to display all the comparable object and attribute regardless of non-comparables. Merged from HDF5 trunk r21396 and r21397. Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake (jam, Windows)
* [svn-r21368] Purpose:Jonathan Kim2011-09-066-5/+670
| | | | | | | | | | | HDFFV-7712 - h5diff: segfault over combinations of complex container types (compound, array, vlen) Description: - Fixed segfault over dataset with container types (array,lven) with multiple nested compound types. (ex: compound->array->compound, compound->vlen->compound) - Merged from HDF5 trunk r21358. Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake (jam)
* [svn-r21337] Synchronize cmake files with tested commits from trunk, windows ↵Allen Byrne2011-08-305-69/+134
| | | | parallel diff
* [svn-r21239] Description:Jonathan Kim2011-08-174-6/+57
| | | | | | | | | Merged from HDF5 trunk r21237. Add test cases for HDFFV-7656 - "--delta=something" considers two NaN of the same type are different. The fix was added (r21105) before but test cases were incorrectly added and missing for cmake script. Tested: jam (linux32-LE), koala (linux64-LE), tejeda (mac32-LE), cmake (jam)
* [svn-r21151] Description:Jonathan Kim2011-07-264-38/+44
| | | | | | | | | | | | | Merged from HDF5 trunk r21105 Fixed two bugs: - h5repack: h5repack failed to copy dataset if the layout is changed from c hunked with unlimited dims to contiguous. (PC -- 2011/07/15) - h5diff: "--delta" option considers two NaN of the same type are different , which is wrong based on http://www.hdfgroup.org/HDF5/doc/RM/Tools.html#Tools-Diff. (PC -- 2011/07/15) Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
* [svn-r21114] Description:Jonathan Kim2011-07-182-2/+2
| | | | | | | | | | | | | | | | Revert the previous makefile change as release snapshot test failed with MANIFEST check. Don't clean 'testfiles' dir via 'make distclean' for the case of build&test in source dir. In regular daily testings, we build&test in seperate dir from source dir, so no issues occurred. However for the release snapshot test, it seems that we build&test in source dir. The previous change can remove testfiles in source dir if build&test is done in source dir becasue currently the dir name 'testfiles' is same in source dir and test dir. Other task (7602) may need to change to use different name for the test directory, so 'make distclean' can do its job without interrupting MANIFEST.
* [svn-r21077] Purpose:Jonathan Kim2011-07-0824-965/+1083
| | | | | | | | | | | | | Work for HDFFV-7600 - GMQS: h5diff - argument options -d, -p and --use-system-epsilon should be mutually exclusive. Description: Merge from HDF5 trunk r21072. Fixed h5diff to display instructive error message and exit with 1 when mutually exclusive options (-d, -p and --use-system-epsilon) are used together. Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake (jam)
* [svn-r21064] Purpose:Jonathan Kim2011-07-011-203/+399
| | | | | | | | | | | Work for HDFFV-7602 - HDF5 command tools: Provide framework for reusable test files among tools Description: Merged from HDF5 trunk r21057 Provide framework to share test files among tools for tools test. Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
* [svn-r21044] Purpose:Mike McGreevy2011-06-281-1/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Fix HDFFV-7592 "Remove PACKEDBITS option from autotools files" Description: The code for h5dump's packed bits feature was conditionally compiled in via this option during its 'beta' release in 1.8.5. Now that the feature is fully supported, h5dump has since been changed to always compile the packed bits code (having removed the #ifdef H5_HAVE_H5DUMP_PACKED_BITS checks), so this option in configure is no longer needed. This commit removes the --enable-h5dump-packed-bits configure option, including the help summary from './configure --help' and the libhdf5.settings output summary, the PACKED_BITS Makefile variable, and the definition of H5_HAVE_H5DUMP_PACKED_BITS define in appropriate pubconf header files (which has already been removed from use in source code as of r20722). Note that this option was never added to the trunk, thus this commit only need occur on the 1.8 branch. Tested: - Configure output, help, & summary verified on jam - h5committested
* [svn-r20889] Snapshot version 1.8 release 8 (snap1)HDF Tester2011-05-231-0/+1
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* [svn-r20794] Purpose:Jonathan Kim2011-05-101-2/+2
| | | | | | | | | | | | | HDFFV-5928 - GMQS: h5diff problem and improvement on comparsing the same objects Description: Merged from HDF5 trunk r20767. Improved performance by eliminating duplicated action for getting object information in half from the previous fixe when comparing group vs group. This is addition to the previous commit r20706. Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE)
* [svn-r20789] Merged 20724 and 20756 from the trunk to fix HDFFV-7527 concerningDana Robinson2011-05-104-0/+110
| | | | | | invalid enum value comparisons. Tested on: h5committest
* [svn-r20772] Problem:Albert Cheng2011-05-071-83/+2
| | | | | | | | | | | | | | | | | Test scripts sometimes need to filter some system-specific messages from the actual output so that it can match the correct expected output. These filtering functions, ususally called "STDOUT_FILTER()" and "STDERR_FILTER()" were being repeated in individual test scripts. This becomes a maintenance problem and is error prone. Solution: Extract the two filter functions code to bin/output_filter.sh and then each test script sources it in. This allows reuse of coding and is much easier to maintain and to add new filtering. Tested: LLNL Zeus (linux64 cluster) and Dawndev (Blue-Gene cluster), both for serial mode only.
* [svn-r20722] Refactor ext lib import and install.Allen Byrne2011-05-041-1/+0
| | | | | | | | Change case of tools subtests to not conflict with tools tests. Add SOVERSION for linux Remove PACKED BITS define/idef blocks Bring r20721 from trunk
* [svn-r20706] Purpose:Jonathan Kim2011-05-0210-44/+70
| | | | | | | | | | | | | | | | | - HDFFV-5928 - GMQS: h5diff problem and improvement on comparsing the same objects Description: Merged from HDF5 trunk r20676. Fixed: 1) adding h5tools_is_obj_same() function to check if two given IDs or paths point to the same object. This function can be very useful for other tools and applications. 2) using h5tools_is_obj_same() at h5diff() and diff() in h5diff.c. If two paths point to the same object, there is no need to check the details of the object since we know there is no difference. The fix will increase the performance by skipping the content comparison. It also fixed the problem of reporting difference for some cases of comparing the same file, e.g. empty files or files with incomparable objects the same file. Test update: Updat prvious test cases (171, 172, 530) affected by this fix, so they still perfrom originally intended testing without bypassing. Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), cmake
* [svn-r20582] Bug 1386 - allowing dimension size to be zero. I forgot to ↵Raymond Lu2011-04-202-0/+0
| | | | | | check in these 2 data files for the test. Now test is needed.
* [svn-r20579] Bug 1386 - allowing dimension size to be zero. I added test ↵Raymond Lu2011-04-204-2/+89
| | | | | | | | cases in the tests for h5dump and h5diff. I also added the test cases in the CMAKE script. Tested on jam. But I tested the same change in the trunk with h5committest.
* [svn-r20527] Blue-Gene port:Albert Cheng2011-04-151-0/+9
| | | | | | | | dawndev mpirun issued diagnose messages to stderr if program exit non-zero. The messages messed up the matching with expected output. Added a filter to screen out the messages. Tested: LLNL dawndev
* [svn-r20525] Description:Mike McGreevy2011-04-151-19/+44
| | | | | | | | Merge revisions 20475, 20502, and 20504 from trunk to 1.8 branch. Tested: Tested on jam, fred, bangan (CYGWIN), and h5committested.
* [svn-r20428] Purpose:Jonathan Kim2011-04-0611-33/+33
| | | | | | | | | | | | Fixed Bug 2184 - GMQS: h5diff - incorrect calculation code for --use-system-epsilon option Description: Additional check in from the previous checkin r20425. Updated help page again. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE)
* [svn-r20425] Purpose:Jonathan Kim2011-04-0611-11/+22
| | | | | | | | | | | | Fixed Bug 2184 - GMQS: h5diff - incorrect calculation code for --use-system-epsilon option Description: Additional check in from the previous checkin r20369. Updated help page. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE)
* [svn-r20369] Purpose:Jonathan Kim2011-03-2923-122/+142
| | | | | | | | | | | | | | | | | Fixed Bug 2184 - GMQS: h5diff - incorrect calculation code for --use-system-epsilon option Description: Fixed h5diff for --use-system-epsilon option: the calculation changed from ( |a - b| / b ) to ( |a - b| ). This was decided for better performance and was corrected only in HDF5 trunk, so 1.8 got updated. Also comments for equal_XXX() function were updated correctly. Also help page and RM got updated correctly. Also add test cases for testing the differences w/wo the option. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE)
* [svn-r20350] Purpose:Jonathan Kim2011-03-2511-11/+110
| | | | | | | | | | | | | | | | Fixed CHICAGO: Bug 2121 - h5diff - incorrect and lack of output for the different set of attributes (different number and names) Description: Merged from HDF5 trunk r20334. This is related to previous checkin r20299. Add help page update for verbose option level feature, which displays useful information about attribute difference with -v1, --verbose=1 -v2 or --verbose=2 option. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE)
* [svn-r20299] Purpose:Jonathan Kim2011-03-2318-1174/+10180
| | | | | | | | | | | | | | | | | Fixed CHICAGO: Bug 2121 - h5diff - incorrect and lack of output for the different set of attributes (different number and names) Description: Merged from HDF5 trunk r20294 Previously h5diff compared attributes correctly only when two objects have the same number of attributes and attribute names are identical. Also didn't display useful information about attribute difference. This fix covers all other cases. This fixes both issues. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE)
* [svn-r20230] Change MEMCHECK condition for test result from if "1" to if NOT ↵Allen Byrne2011-03-111-2/+2
| | | | "0" to account for type "2" exit codes.
* [svn-r20199] Add expected fail condition to memcheck alternate tests.Allen Byrne2011-03-081-0/+3
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* [svn-r20183] Add HDF5_USING_MEMCHECKER guards around script mode ADD_TEST. ↵Allen Byrne2011-03-041-18/+17
| | | | | | | | This will replace the list of ignore tests in CTestCustom.cmake file. Bring back from trunk Tested: local linux
* [svn-r20157] Bring CMake changes to branch up to r20156 from trunkAllen Byrne2011-02-251-2/+2
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* [svn-r20130] Add test dependencies to order testsAllen Byrne2011-02-211-0/+8
| | | | Tested: local linux
* [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-r19906] Windows: Correct how fortran links in CRT library. Also correct ↵Allen Byrne2011-01-041-2/+2
| | | | | | macro use for checking libtype. Tested: Windows
* [svn-r19898] Remove use of /MT compile flag for building static libs and ↵Allen Byrne2010-12-301-2/+0
| | | | programs. Added BUILT_AS_STATIC_LIBRARY define to set the windows import/export defines correctly for static libraries.
* [svn-r19893] Purpose:Jonathan Kim2010-12-284-131/+569
| | | | | | | | | | | | | | | | | | | | 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 Knox2010-12-011-0/+3
| | | | | | 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-r19793] Revised the valgrind ignore list, added simple execute command ↵Allen Byrne2010-11-161-0/+6
| | | | tests for when doing a valgrind test of tools that only use a cmake script for testing.
* [svn-r19713] Purpose:Jonathan Kim2010-11-024-0/+320
| | | | | | | | | | | | | | | | 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-r19528] Add clear generated objects commands to test blocks.Allen Byrne2010-10-061-34/+308
| | | | | | | | Add configurefile command to copy CTestCustom to build folder. Bring r19527 back from trunk Tested: local linux
* [svn-r19510] Improve CMake support for CYGWIN.Allen Byrne2010-10-042-5/+5
| | | | | | | | Correct script comment in testh5diff.sh Bring r19509 back from trunk Tested: Windows Cygwin
* [svn-r19492] Purpose:Jonathan Kim2010-09-2911-0/+264
| | | | | | | | | | | Update help page for exclude-path feature. Description: Merged from hdf5 trunk (r19491). Related to "1890: h5diff excluding object for file comparison via command line" checkins. (r19406) Tested: jam, linew
* [svn-r19444] Purpose:Jonathan Kim2010-09-203-0/+17
| | | | | | | | | | | Fix for group comparison with exclude-path case. Use relative path. Description: Merge from hdf5 trunk (r19443) Related to "1890: h5diff excluding object for file comparison via command line" checkins. (r19407) Tested: jam, amani
* [svn-r19438] Correct use of lib, include, bin in INSTALL commands to use ↵Allen Byrne2010-09-201-1/+1
| | | | | | proper variables. Tested: local linux
* [svn-r19416] Fix for Cmake test. Merged from hdf5 trunk (r19415).Jonathan Kim2010-09-171-22/+28
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* [svn-r19411] Purpose: Jonathan Kim2010-09-1711-1/+468
| | | | | | | | | | | | Add extra test cases for Bug1975 h5diff - support recursive comparison on group when specified as an object Description: Merged from hdf5 trunk (r19409) Additional tests for combination of group recursive and --follow-symlinks with multi-linked external links with several files (same name/strucure). Tested: jam, amani, heiwa
* [svn-r19408] In this revision the '/' after ${DESTDIR} wherever it occursLarry Knox2010-09-161-5/+15
| | | | | | | | | | | | | | | | | | | | has been removed. According to the official description of DESTDIR by Gnu at http://www.gnu.org/prep/standards/html_node/DESTDIR.html, DESTDIR is prepended to the normal and complete install path that it precedes for the purpose of installing in a temporary directory which is useful for building rpms and other packages. The '/' after ${DESTDIR} will be followed by another '/' at the beginning of the normal install path. When DESTDIR is empty the path then begins with '//', which is incorrect and causes problems at least for Cygwin. The change made in config/commence.am affects many Makefile.*s when bin/reconfigure is run. EXAMPLEDIRs had to be corrected individually. Also the scripts to run examples after they are installed have checks added to see that the fortran and c++ directories are present before trying to run the scripts in them. Tested with h5committest on amani, heiwa and jam.
* [svn-r19407] Purpose:Jonathan Kim2010-09-1612-0/+474
| | | | | | | | | | | | Add --exclude-path option Description: Merged from hdf5 trunk (r19406). Specified path to an object will be excluded from comparing the two files or two groups. If group is specified all the member objects will be excluded. Related to "1890: h5diff excluding object for file comparison via command line" Tested: jam, amani
* [svn-r19401] Purpose:Jonathan Kim2010-09-1643-186/+1422
| | | | | | | | | | | Fix for Bug1975 h5diff - support recursive comparison on group when specified as an object Description: Merged from hdf5 trunk (r19400). Compare member objects and groups recursively when two files or groups are specified to be compared. Support parallel diff and handling symbolic links accordingly. Tested: jam, amani
* [svn-r19371] Updated autoconf to version 2.6.7, libtool to version 2.2.10, ↵Larry Knox2010-09-101-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | and m4 to version 1.4.14. Also added m4 directory for m4 macros according to autoconf suggestion. Tested with h5committest on amani, jam, and heiwa, and on linew. -This line, and those below, will be ignored-- M hdf5_1_8/test/Makefile.in A hdf5_1_8/m4 AM hdf5_1_8/m4/ltsugar.m4 AM hdf5_1_8/m4/libtool.m4 AM hdf5_1_8/m4/ltversion.m4 AM hdf5_1_8/m4/lt~obsolete.m4 AM hdf5_1_8/m4/ltoptions.m4 M hdf5_1_8/configure M hdf5_1_8/Makefile.in M hdf5_1_8/testpar/Makefile.in M hdf5_1_8/configure.in M hdf5_1_8/src/Makefile.in M hdf5_1_8/tools/Makefile.in M hdf5_1_8/tools/misc/Makefile.in M hdf5_1_8/tools/h5dump/Makefile.in M hdf5_1_8/tools/h5repack/Makefile.in M hdf5_1_8/tools/h5jam/Makefile.in M hdf5_1_8/tools/h5diff/Makefile.in M hdf5_1_8/tools/lib/Makefile.in M hdf5_1_8/tools/h5copy/Makefile.in M hdf5_1_8/tools/h5import/Makefile.in M hdf5_1_8/tools/h5stat/Makefile.in M hdf5_1_8/tools/h5ls/Makefile.in M hdf5_1_8/hl/test/Makefile.in M hdf5_1_8/hl/tools/Makefile.in M hdf5_1_8/hl/tools/gif2h5/Makefile.in M hdf5_1_8/hl/Makefile.in M hdf5_1_8/hl/src/Makefile.in M hdf5_1_8/hl/c++/test/Makefile.in M hdf5_1_8/hl/c++/Makefile.in M hdf5_1_8/hl/c++/src/Makefile.in M hdf5_1_8/hl/c++/examples/Makefile.in M hdf5_1_8/hl/fortran/test/Makefile.in M hdf5_1_8/hl/fortran/Makefile.in M hdf5_1_8/hl/fortran/src/Makefile.in M hdf5_1_8/hl/fortran/examples/Makefile.in M hdf5_1_8/hl/examples/Makefile.in M hdf5_1_8/config/commence.am M hdf5_1_8/MANIFEST M hdf5_1_8/c++/test/Makefile.in M hdf5_1_8/c++/Makefile.in M hdf5_1_8/c++/src/Makefile.in M hdf5_1_8/c++/examples/Makefile.in M hdf5_1_8/bin/ltmain.sh M hdf5_1_8/bin/reconfigure M hdf5_1_8/perform/Makefile.in M hdf5_1_8/fortran/test/Makefile.in M hdf5_1_8/fortran/testpar/Makefile.in M hdf5_1_8/fortran/Makefile.in M hdf5_1_8/fortran/src/Makefile.in M hdf5_1_8/fortran/examples/Makefile.in M hdf5_1_8/aclocal.m4 M hdf5_1_8/examples/Makefile.in
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