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* [svn-r21421] Merged the Fortran 2003 changes from the trunk into the 1.8 ↵Scot Breitenfeld2011-09-2711-0/+33
| | | | | | | | | | | 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 Kim2011-09-2127-40/+306
| | | | | | | | | | | | | | | | | | | | | | 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-r21400] Purpose:Jonathan Kim2011-09-204-164/+333
| | | | | | | | | | | | | HDFFV-5932 - h5repack breaks files with dimension scales Description: - Fixed h5repack to update values of references(object and region) of attributes in h5repack for 1) references, 2) ARRAY of references, 3) VLEN of references, and 4) COMPOUND of references. - Merged from HDF5 trunk 21393, 21382, 21386, 21389. (support Peter) Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE)
* [svn-r21379] The tools used "%hhd" to print signed char. But VMS doesn't ↵Raymond Lu2011-09-133-3/+19
| | | | | | know it. So I used H5_VMS to have a different way ("%hd") to print it. Tested on jam and VMS.
* [svn-r21376] JIRA-HDFFV-2748: Relplace WIN32 macros in source. New ↵Allen Byrne2011-09-122-3/+3
| | | | | | | | H5_HAVE_WIN32_API and H5_HAVE_VISUAL_STUDIO defines only need to be set on windows. Autotools configure is not affected. Trunk passed for a week and cmake branch has been in place > 3 weeks. Tested: local linux
* [svn-r21368] Purpose:Jonathan Kim2011-09-067-35/+710
| | | | | | | | | | | 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-r21356] Issue 7674 - CLANG compiler complained about the line (about 800):Raymond Lu2011-09-021-10/+48
| | | | | | | | | | tempint = (tempint >> packed_data_offset) & packed_data_mask; The right shift may cause undefined behavior if PACKED_DATA_OFFSET is 32-bit or more. For every kind of native integers, I changed the code to make it zero if PACKED_DATA_OFFSET is greater than or equal to the size of integer. Tested on jam and on MacOS with CLANG compiler.
* [svn-r21355] Purpose:Jonathan Kim2011-09-021-6/+3
| | | | | | | | | | | | | | HDFFV-2511 - GMQS: h5repack: some tests failed in -q32 AIX Description: - Need to be Merged from HDF5 trunk r21283 also, which was missed from previous checkin. - Previously Merged from HDF5 trunk r21265 - Added macro to handle failure in H5Dread/write when memory allocation failed inside the library. Add graceful error message when lack of memory error occurs from HDF5 lib. (XCAO) Tested: jam (linux32-LE), koala (linux64-LE)
* [svn-r21344] Purpose:Jonathan Kim2011-08-311-11/+37
| | | | | | | | | | | | HDFFV-2511 - GMQS: h5repack: some tests failed in -q32 AIX Description: - Merged from HDF5 trunk r21265 - Added macro to handle failure in H5Dread/write when memory allocation failed inside the library (XCAO) Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE)
* [svn-r21337] Synchronize cmake files with tested commits from trunk, windows ↵Allen Byrne2011-08-308-106/+171
| | | | parallel diff
* [svn-r21297] Move all tests into DEPENDS structure so that clear-all-objects ↵Allen Byrne2011-08-231-310/+317
| | | | | | is first. Also preface all tests with H5REPACK.
* [svn-r21281] Correct IF/ENDIF argumentsAllen Byrne2011-08-221-2/+2
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* [svn-r21264] Purpose:Jonathan Kim2011-08-199-61/+299
| | | | | | | | | | | | | | | | | | | | | Work for: HDFFV-7515 - GMQS: h5unjam - incorrect help page and should display when no file is given. and HDFFV-5941 - h5jam: specifying a user block file with a proper HDF5 magic number will result in a corrupted HDF5 file. Description: - Merged from HDF5 trunk r21236, - Revised command help pages of h5jam and h5unjam. The descriptions were not up to date and some were missing. (HDFFV-7515) - Fixed h5jam not to allow specifying an HDF5 formatted file as input file for -u (user block file) option, because the original HDF5 file will not be accessible if allows. (HDFFV-5941) Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), cmake (jam, win)
* [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-r21216] Alter clear-objects tests to mate with test that generates ↵Allen Byrne2011-08-103-60/+128
| | | | | | object file. Tested: local linux
* [svn-r21211] Correct location of xml schema files. JIRA HDFFV-7688Allen Byrne2011-08-1062-66/+66
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* [svn-r21165] Remove subfolder in library installAllen Byrne2011-08-011-6/+6
| | | | Tested: local linux
* [svn-r21151] Description:Jonathan Kim2011-07-268-94/+132
| | | | | | | | | | | | | 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-r21129] Description:Quincey Koziol2011-07-201-6/+6
| | | | | | | | | | Bring half of r21125 from trunk to 1.8 branch: Correct char arrays that were too small for strings defined. Tested on: FreeBSD/32 8.2 (loyalty) w/debug (h5committested on trunk)
* [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-r21111] Renamed test files to more descriptive nameAllen Byrne2011-07-1837-263/+251
| | | | Tested: local linux
* [svn-r21089] Add dependicies for tests to address issues when run in parallelAllen Byrne2011-07-111-0/+10
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* [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 Kim2011-07-0110-522/+1631
| | | | | | | | | | | 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-r21048] Add configure check for endianess and adjust test depending on ↵Allen Byrne2011-06-291-3/+3
| | | | | | status of check. Bring r21026 from trunk
* [svn-r21044] Purpose:Mike McGreevy2011-06-2811-11/+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-r21018] Purpose:Jonathan Kim2011-06-226-47/+128
| | | | | | | | | | | | | | | HDFFV-5878 - GMQS: h5dump - incorrect output format for array type with multiple elements in an index Description: Merged from HDF5 trunk r21014. Fixed h5dump to display the first line of each element into correct position for multiple dimention array type. Before this fix, the first line of each element in array were displayed after the last line of previous element without moving to the next line (+indentation) Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
* [svn-r20997] Get comment section did not add null terminator.Allen Byrne2011-06-191-7/+8
| | | | Tested: Debug windows
* [svn-r20936] Issue 4278 - When reading data fails, the error message should ↵Raymond Lu2011-06-061-1/+1
| | | | | | say which filter isn't registered. The fix is simple. Most of the effort is on the test. The file with filter enabled is created in gen_filter.c. The verification of the error message is in test_error.c. The output is compared against the standard output. Tested on jam, koala, and heiwa.
* [svn-r20928] Purpose:Jonathan Kim2011-06-0355-175/+15
| | | | | | | | | | | | HDFFV-7607: h5ls - improve efficiency of test scripts - removing top 3 extra lines from expected output files Description: Merged from hdf5 trunk r20927. This is a subtask from 'HDFFV-7514 - gmqs: h5dump - improve effectiveness of testing scripts for handling expected output files'. This is prerequisite for 'HDFFV-7602 tools - upgrade tools' test scripts to share test files among tools, providing framework for test file re-usability.' Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
* [svn-r20904] Bring r20871, 20875, 20901, 20903 from trunk.Allen Byrne2011-05-256-2875/+2827
| | | | Tested: local linux
* [svn-r20893] Description:Quincey Koziol2011-05-232-5/+7
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring r20885 from trunk to 1.8 branch: r20340: Address coverity issue 248. Set freed pointer to NULL if realloc fails, then check for NULL before attempting to close array of handles stored in memory addressed by pointer. r20341: Added initialization udata.path = NULL; udata.visited = NULL; to prevent unintialized use after done: label. Do C-style initialization AFTER all variable definitions. r20342: Fix valgrind error in H5DUMP-XML-tall.h5 r20343: Addressed Coverity issue 591 - check the return value of H5S_SELECT_ITER_RELEASE. r20344: Added initialization udata.path = NULL; to prevent uninitialized used after done: label r20347: Purpose: Fix memory leak in overhead.c Description: Fixed leak in test() in overhead.c where array "had" was never freed. r20348: Addressed Coverity issue 705 - added prototype for resize_configs_are_equal to cache_common.h. r20392: Purpose: Fix coverity issues 1677 and 1678 Description: Added return value checking for 4 funciton calls in H5tools_get_symlink_info(). r20394: Purpose: Fix coverity issues 1674 and 1675 Description: Modified H5Epush2() and H5E_printf_stack() to keep track of whether va_start() has been called, and to call va_end() at the end if so. r20395: Should be H5MM_calloc(count * sizeof(void*)). Fixed --gh r20396: Should be H5MM_calloc(count * sizeof(void*)). Fixed. --gh Tested on: Mac OSX/32 10.6.7 (amazon) w/debug & production (h5committested on branch)
* [svn-r20889] Snapshot version 1.8 release 8 (snap1)HDF Tester2011-05-238-0/+8
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* [svn-r20886] purpose:Jonathan Kim2011-05-20228-761/+31
| | | | | | | | | | | | | hdffv-7514 - GMQS: h5dump - improve effectiveness of testing scripts for handling expected output files description: Removed top 3 lines from expected output file and update testing scripts accordingly. These lines started to become maintainence headaches. First phase for h5dump test update. Next phase will be for h5ls. this is prerequisite for 'hdffv-7602 tools - upgrade tools' test scripts to share test files among tools, providing framework for test file re-usability.' Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), cmake (jam)
* [svn-r20811] Purpose:Jonathan Kim2011-05-131-1/+1
| | | | | | | | | | | | | HDFFV-7594 - GMQS: h5dump shows wrong values for H5T_STD_I8LE dataset on Blue-gene (ppc64 linux BE +@) Description: Merged from HDF5 trunk r20804. For the STD_I8 type data, updated to use 'signed char' instead of 'char' as 'char' could be defined as unsigned on a certain system, which cause h5dump to display data values incorrectly. Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), cmake
* [svn-r20806] references files for jam tests are in sub-folder - testfilesAllen Byrne2011-05-131-502/+502
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* [svn-r20802] Bring trunk revision 20798 to 1.8. Trunk changes passed overnight.Allen Byrne2011-05-1212-365/+688
| | | | Tested: local linux
* [svn-r20794] Purpose:Jonathan Kim2011-05-106-43/+106
| | | | | | | | | | | | | 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 Robinson2011-05-105-2/+143
| | | | | | invalid enum value comparisons. Tested on: h5committest
* [svn-r20786] Revert region data print changes from yesterdayAllen Byrne2011-05-101-60/+50
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* [svn-r20784] correct type of variable for blkindx, indx and jndxAllen Byrne2011-05-091-6/+6
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* [svn-r20780] Corrected export test to use parameters passed in from ADD_TEST()Allen Byrne2011-05-091-1/+1
| | | | Tested: local linux
* [svn-r20777] Refactor print_data_region_blocks/ponts to remove context ↵Allen Byrne2011-05-091-44/+54
| | | | | | passed in by value. The print functions needed an independent context with only the current indent level passed in by argument. Also synched the two routines logical flows and corrected a mem_space error. Tested: local linux
* [svn-r20772] Problem:Albert Cheng2011-05-075-171/+55
| | | | | | | | | | | | | | | | | 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-r20753] Windows does not have snprintf, need to use HDsnprintf.Allen Byrne2011-05-051-3/+3
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* [svn-r20727] bring r20725 from trunkAllen Byrne2011-05-042-8/+15
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* [svn-r20722] Refactor ext lib import and install.Allen Byrne2011-05-0426-3015/+3044
| | | | | | | | 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 Kim2011-05-0213-51/+186
| | | | | | | | | | | | | | | | | - 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-r20624] Albert's test on bp reveals that the dumper had assertion ↵Raymond Lu2011-04-252-38/+46
| | | | | | | | failure when it tried to display empty attribute data. I added a check for empty attribute in h5dump.c. I also added a check for empty dataset in tools/lib/h5tools.c. Tested on jam, linew, and amani.
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