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* [svn-r22711] Updated autotools: autoconf 2.69, automake 1.12.3, m4 1.4.16, ↵Larry Knox2012-08-231-51/+104
| | | | | | libtool 2.4.2 Tested THG machines.
* [svn-r22701] Purpose: Jonathan Kim2012-08-204-19/+59
| | | | | | | | | | | | | 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-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 Byrne2012-08-068-822/+645
| | | | tested: local linux
* [svn-r22619] Jonathan Kim2012-08-021-8/+0
| | | | | | | | | | | | | | | 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-r22572] Re-Merge attr name with slash changes from trunkAllen Byrne2012-07-132-0/+51
| | | | Tested: localinux with cmake
* [svn-r22571] HDFFV-7784,-8095,7936 merge from trunkAllen Byrne2012-07-132-7/+112
| | | | Tested: local linux with cmake
* [svn-r22551] Merge changes from Trunk revision 22550 for:Allen Byrne2012-07-112-4/+14
| | | | | | 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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* [svn-r22536] added missing break to end of case statementAllen Byrne2012-07-101-0/+1
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* [svn-r22451] Brought cmake configuration / configure changes from Trunk.Allen Byrne2012-06-111-0/+3
| | | | Tested jam, local linux
* [svn-r22412] reduce compiler warnings by removing unreferenced variables and ↵Allen Byrne2012-05-252-11/+11
| | | | | | adding cast Tested: local linux
* [svn-r22397] Merge trunk changes for HDFFV-7999 and h5dump test script to branchAllen Byrne2012-05-231-21/+64
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* [svn-r22320] Purpose:Jonathan Kim2012-04-271-4/+4
| | | | | | | | | | | | | | | Fix for HDFFV-7998-h5diff: incorrect behavior and output for comparing symbolic dangling links without following-symlinks option Description: Fix not to check and display dangling link status without --follow-symlinks option. Berfor the fix, when comparing symbolic link to symbolic link without follow-symlinks option, h5diff followed to check if those links are dangling or not. It caused to display output incorrectly (dangling link instead of symbolic link). The fix also improved performance when comparing lots of symbolic links without the --follow-symlinks option. Test cases were added and tagged with jira#. This merged from HDF5 trunk r22319. Tested: jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), cmake (jam)
* [svn-r22291] Description:Quincey Koziol2012-04-171-5/+3
| | | | | | | | | | Bring r22287 from trunk to 1.8 branch: Clean up more FUNC_ENTER/FUNC_LEAVE macros and move H5D & H5T code toward the final design (as exemplified by the H5EA & H5FA code). Tested on: Mac OSX/64 10.7.3 (amazon) w/debug & parallel
* [svn-r22188] Purpose:Jonathan Kim2012-03-292-276/+102
| | | | | | | | | | | | | Fix for HDFFV-7644 GMQS: h5diff - incorrect behaviors when comparing HDF5 files with different type of objects (dataset, group, type) as common objects Description: Fixed failure for comparing same named object with different object types in comparing groups. (common object comparison) Prior to the fix, h5diff resulted in error. After the fix, h5diff detects such case as non-comparable and display messages accordingly. Test cases were added and tagged with jira#. Merged from HDF5 trunk 22176. Tested: jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake (jam)
* [svn-r22124] Purpose:Jonathan Kim2012-03-221-7/+12
| | | | | | | | | | | | | | | | Fix for HDFFV-7837 - h5diff: incorrect behavior with exclude-path option when unique object exist only in one file Description: If unique objects exists only in one file and try to exclude the unique objects with --exclude-path option, h5diff missed excluding some objects. Fixed to exclude objects correctly in such case. Test cases were added and tagged with jira#. Merged from HDF5 trunk r22114. Tested: jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), Cmake (jam)
* [svn-r22088] HDFFV-7957(7958): Correct use of ERROR_STACK for h5dump and tools.Allen Byrne2012-03-192-2/+2
| | | | Tested: local linux after week in trunk
* [svn-r22060] Description:Quincey Koziol2012-03-131-1/+1
| | | | | | | | Change to use versioned API call, to avoid problems when defaulting to older AI versions. Tested on: Mac OSX/64 10.7.3 (amazon) w/debug
* [svn-r22057] Purpose:Jonathan Kim2012-03-121-20/+31
| | | | | | | | | | | | | | Fix for HDFFV-7835 h5diff: incorrect result for comparing the two same type symlinks as dangling links. Description: When two symbolic dangling links are compared with --follow-symlinks option, the result should be same. It works for comparing two files, but didn't work for comparing two objects. Test cases were added and tagged with jira#. Merged from HDF5 trunk r22038. Tested: jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), Cmake (jam)
* [svn-r22045] HDFFV-7957-7958:Allen Byrne2012-03-124-29/+51
| | | | | Add tools error stack and check return from H5Dreference call. Tested: trunk
* [svn-r22043] HDFFV-7839: Dangling link should not display errorAllen Byrne2012-03-121-2/+0
| | | | | | | If a link is specified on the command with the -d option, call the handle_links function on error from the H5Dopen command. Updated test file results with error stack when link not found. Tested: trunk
* [svn-r22031] Purpose:Jonathan Kim2012-03-061-2/+2
| | | | | | | | | | | | | | | | Task for HDFFV-7862 - Select data by chunk direction to improve performance in h5repack Description: h5repack sometimes became very slow when handling big chunked datasets in certain cases. (when chunk boundary doesn't match with a hyperslab boundary.) The main issue was from figuring out a hypeslab without considering chunk boundary to read from and write to such datasets. The update was made to figure out a better hyperslab unit with considering chunk boundary to improve performance for such cases prior to the update. Tested: jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows
* [svn-r22025] Cleanup compiler warnings.Allen Byrne2012-03-053-25/+6
| | | | | | Add HD prefix to tools library based tests. Cleaned allocation/free in tests. Tested: local linux/ h5committetest
* [svn-r22013] HDFFV-7560:Allen Byrne2012-03-0217-3388/+4853
| | | | | | | | | | Merge 1.8 and h5dump/tools and tests based on tools library from trunk. Reduced warnings. HDFFV-7949: Remove duplicated functions in h5ls Tested: local linux,h5committest
* [svn-r21892] Purpose:Jonathan Kim2012-01-251-11/+13
| | | | | | | | | | | | | | | | Fix for HDFFV-7836 h5diff: displays error stack message for comparing the two dangling symlink with follow-symlinks option Description: While ago, to improve performance, skipping same object checking (h5tools_is_obj_same()) was added. However the checking function doesn't understand about the dangling link and caused the issue. Since handling dangling link code section already implemented, move the checking function after handling dangling-links to address the problem. Test was added and tagged with jira#. Tested: jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), Cmake (jam)
* [svn-r21805] Update CMake Required version in all folders to match current ↵Allen Byrne2011-12-051-1/+1
| | | | standard 2.8.6
* [svn-r21717] Update cmake configurationAllen Byrne2011-11-041-0/+1
| | | | | | | Update cmake to generate source folders in VS Brought parallel changes from trunk Tested: local linux
* [svn-r21660] Purpose:Jonathan Kim2011-10-242-15/+20
| | | | | | | | | | | | 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. Merged from HDF5 trunk r21658. Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows, Cmake
* [svn-r21646] Port r21603 to 1.8 branchNeil Fortner2011-10-211-1/+1
| | | | | | | | | | | | | | | Purpose: Add generic skip list implementation Description: Added new H5SL_TYPE_GENERIC skip list type, which uses void *'s as keys and a client-supplied callback for key comparison. This was added to support the upcoming "merge named datatype" feature for H5Ocopy, but may be used in other places as well. Also added testing. Also fixed a potential bug with the H5SL_TYPE_OBJ implementation, and added testing for that. Tested: jam, koala, heiwa (h5committest), durandal
* [svn-r21605] Back out r21604 (wait for code freeze to be lifted)Neil Fortner2011-10-181-1/+1
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* [svn-r21604] Port r21603 to 1.8 branchNeil Fortner2011-10-181-1/+1
| | | | | | | | | | | | | | | Purpose: Add generic skip list implementation Description: Added new H5SL_TYPE_GENERIC skip list type, which uses void *'s as keys and a client-supplied callback for key comparison. This was added to support the upcoming "merge named datatype" feature for H5Ocopy, but may be used in other places as well. Also added testing. Also fixed a potential bug with the H5SL_TYPE_OBJ implementation, and added testing for that. Tested: jam, koala, heiwa (h5committest), durandal
* [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-r21404] Purpose:Jonathan Kim2011-09-213-24/+25
| | | | | | | | | | | | | | | | | | | | | | 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-r21379] The tools used "%hhd" to print signed char. But VMS doesn't ↵Raymond Lu2011-09-132-1/+9
| | | | | | know it. So I used H5_VMS to have a different way ("%hd") to print it. Tested on jam and VMS.
* [svn-r21368] Purpose:Jonathan Kim2011-09-061-30/+40
| | | | | | | | | | | 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-r21337] Synchronize cmake files with tested commits from trunk, windows ↵Allen Byrne2011-08-303-37/+37
| | | | parallel diff
* [svn-r21264] Purpose:Jonathan Kim2011-08-192-0/+19
| | | | | | | | | | | | | | | | | | | | | 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-r21165] Remove subfolder in library installAllen Byrne2011-08-011-6/+6
| | | | Tested: local linux
* [svn-r21151] Description:Jonathan Kim2011-07-262-56/+83
| | | | | | | | | | | | | 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-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-r21018] Purpose:Jonathan Kim2011-06-221-3/+24
| | | | | | | | | | | | | | | 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-r20893] Description:Quincey Koziol2011-05-231-2/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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 Tester2011-05-231-0/+1
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* [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-r20802] Bring trunk revision 20798 to 1.8. Trunk changes passed overnight.Allen Byrne2011-05-122-55/+89
| | | | Tested: local linux
* [svn-r20794] Purpose:Jonathan Kim2011-05-105-41/+104
| | | | | | | | | | | | | 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 Robinson2011-05-101-2/+33
| | | | | | 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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