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* [svn-r20079] Correct Fortran handling in CMake filesAllen Byrne2011-02-1014-252/+218
| | | | Tested: local: linux
* [svn-r20078] updated mpich version for jam and amani. Removed kagiso.Albert Cheng2011-02-101-17/+10
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* [svn-r20075] Updated for the adding of mpicc/mpif90 as default parallel ↵Albert Cheng2011-02-091-0/+3
| | | | | | compiler commands for linux systems.
* [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-r20069] Corrected a typo inAlbert Cheng2011-02-081-1/+1
| | | | | | | | | PROD_CFLAGS= "-O" Shell does not allow any spaces between the "=" and righthand side value. Changed it to PROD_CFLAGS="-O" Tested in jam.
* [svn-r20066] Description:Quincey Koziol2011-02-0811-235/+239
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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 Koziol2011-02-088-394/+290
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r20059] Changed Linux system to use mpicc as the default parallel C ↵Albert Cheng2011-02-071-2/+8
| | | | | | | | | compiler. mpif90 is already the default parallel Fortran if mpicc is the C compiler. Tested: Amani (serial and parallel). No need for committest since this change is limited to Linux system.
* [svn-r20056] Correct comment handling and remove cut/paste oversightsAllen Byrne2011-02-072-27/+25
| | | | Tested: local linux
* [svn-r20055] Corrected extlib option valueAllen Byrne2011-02-071-1/+1
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* [svn-r20053] Description:Quincey Koziol2011-02-0610-555/+588
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r20051] Description:Quincey Koziol2011-02-056-388/+425
| | | | | | | | | | | | Bring r20050 from trunk to 1.8 branch: Bring sec2 and log VFDs back into agreement. Correct several compiler warnings. Also add some additional statistics to the log VFD and promote the parameter for H5Pset_fapl_log from 'unsigned' to 'unsigned long long'. Tested on: Mac OS X/32 10.6.6 (amazon) w/debug & production (h5committested on trunk)
* [svn-r20049] Description:Quincey Koziol2011-02-052-82/+84
| | | | | | | | | | | | | | | | | | Bring r20048 from trunk to 1.8 branch: Bring Coverity changes back to trunk: r19733: Fix memory leak in h5perf_serial. Global buffer "buffer2" was allocated at the beginning of do_sio() but never freed. Added call to free() at end of do_sio(). r19734: Fix memory leak in iopipe. Buffer "the_data" was allocated at the beginning of main() but never freed. Added call to free() at end of main(). Tested on: Coverity branch in daily tests & Mac
* [svn-r20045] Fix bz2127 by dynamically allocating storgae for comments. Allen Byrne2011-02-048-10/+61
| | | | | | Bring 20044 from trunk Tested: local linux
* [svn-r20043] Add option to build static executables on non-windows machinesAllen Byrne2011-02-041-0/+11
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* [svn-r20042] Disable SVN extlibsAllen Byrne2011-02-041-1/+1
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* [svn-r20041] Created valgrind cacheinit file, Corrected ignore list, updated ↵Allen Byrne2011-02-044-34/+96
| | | | memcheck defines
* [svn-r20034] Problem: A typo caused compilation to fail with gfortran 4.6 on ↵Elena Pourmal2011-02-031-3/+3
| | | | | | | | fred (Max OS X) Fixed. Platforms tested: fred and jam (minor change)
* [svn-r20030] Purpose: Fix bug 2131Neil Fortner2011-02-026-226/+1489
| | | | | | | | | | Description: When using the scale-offset filter with floating point data or fill values, big endian machines would save some metadata in the wrong byte order. This caused such datasets to yield incorrect data when read on little endian machines. Fixed the scale-offset filter to always save this metadata in the right byte order (i.e. little endian). Tested: jam, amani, heiwa (h5committedt); fedora, linew
* [svn-r20028] I added some test cases for H5Oset(get)_comment and ↵Raymond Lu2011-01-311-0/+333
| | | | | | H5Oset(get)_comment_by_name. It's related to bug 2130. Tested on jam because I've tested the same change to the trunk with h5committest.
* [svn-r20021] Update cmake file for testpar changes from r19939Allen Byrne2011-01-311-2/+2
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* [svn-r20020] Bug 2019: h5perf or h5perf_serial is removed twice. Some ↵Albert Cheng2011-01-282-20/+30
| | | | | | | | | | | | | | | | | | | | | | | | systems like AIX do not like it as it may get into a racing condition when "gmake -j N" is used-- two "rm" commands were trying to remove the same file. Solution: Rearranged the Makefile.am so that h5perf or h5perf_serial are built only once, that is through bin_PROGRAMS only. Bug 2135: h5perf_serial is not installed in --enable-parallel build. It was because in parallel build, h5perf_serial is not was not in the bin_PROGRAMS list but it was still being built and tested. Solution: Rearranged the Makefile.am code so that h5perf_serial is installed too. (It is easier to make cleaner code to install it than to build and test h5perf_serial but not test it.) Tested: Jam, both serial and parallel. Did not run h5committest because the changes are in perform/ directory only and I think Jam has given the changes in Makefile a complete test already.
* [svn-r20017] Purpose: fix compiler error on BP (AIX) from recent change for ↵Jonathan Kim2011-01-271-0/+1
| | | | h5repack svn r20007.
* [svn-r20014] Change use of variable to allow a SITE name to be defined, to ↵Allen Byrne2011-01-273-3/+295
| | | | using it to extend the build name used in reporting to CDash
* [svn-r20008] I changed the previous commit from FLOAT to DOUBLE again ↵Raymond Lu2011-01-265-18/+20
| | | | | | | | because Neil prefers to it for fill value test. I updated the data files, too. Tested on linew and jam.
* [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-r20003] Add variable to allow a SITE name to be definedAllen Byrne2011-01-261-0/+3
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* [svn-r20000] Correct typo in check for external library TGZ path defineAllen Byrne2011-01-261-2/+2
| | | | Tested: local linux
* [svn-r19996] remove reference to jpegAllen Byrne2011-01-261-2/+2
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* [svn-r19994] Added ability to use compressed file for external librariesAllen Byrne2011-01-253-61/+135
| | | | | | Bring 19993 from trunk Tested: local linux
* [svn-r19992] Purpose:Jonathan Kim2011-01-255-0/+29
| | | | | | | | 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-r19990] Description:Quincey Koziol2011-01-253-132/+254
| | | | | | | | | | | | Bring r19989 from trunk to 1.8 branch: Finish implementing time tracking for read & seek operations in the 'log' VFD. Also clean up code and track total time during all read/write/seek operations. Tested on: Mac OS X/32 10.6.6 (amazon) w/debug & production (too minor to require h5committest)
* [svn-r19987] Update list of memtest exludeAllen Byrne2011-01-251-1/+3
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* [svn-r19986] Added "gmake clean" known problem in AIX.Albert Cheng2011-01-251-7/+6
| | | | Removed AIX memory problem which was fixed in v186.
* [svn-r19983] I added a test case for dataset with scale-offset filter into ↵Raymond Lu2011-01-245-40/+426
| | | | | | cross_read.c and updated the data files from BE, LE, and VMS. This is the test for bug 2131 that dataset of FLOAT with scale-offset filter can't be read across BE and LE. Tested on jam and linew.
* [svn-r19979] Patched in a temporary fix so that:Albert Cheng2011-01-211-8/+11
| | | | | | | | | | | | | | When $HDF5ExpressTest is NOT set or when it is set to 1 or 0, it does not skip test. When $HDF5ExpressTest is set other than values above, it may skip tests. The following message is printed: Test skipped when some tests are really skipped. This is a temporary patch so that v186 can be tested. A more permanent fix is needed, later. Tested: h5commitest.
* [svn-r19970] Update config.sub to the latest available version ↵Larry Knox2011-01-201-32/+91
| | | | | | | | (timestamp='2008-01-16', Rev. 1.361) from http://cvs.savannah.gnu.org/viewvc/config/config/. Tested with h5committest on amani, heiwa, and jam.
* [svn-r19968] Add note on parallel failures to RELEASE.txtNeil Fortner2011-01-191-0/+12
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* [svn-r19964] Purpose:Albert Cheng2011-01-181-14/+59
| | | | | | | | This continues the previous work and this one breaks the checker_board_hyperslab_dr_pio_test() into 4 smaller sub-tests. Tested: h5committest plus jam serial.
* [svn-r19962] Purpose:Albert Cheng2011-01-162-21/+76
| | | | | | | | | | | | The shape same tests ran too long. Break them into smaller subtests so that they can finish sub-test in a shorter time. Easier to tell which one sub-test is taking too much time and/or errors occur in one fo the sub-tests. This one breaks the contig_hyperslab_dr_pio_test() into 4 smaller sub-tests. Tested: h5committest
* [svn-r19960] Bug: the VRFY macro, for some reason, called MPI_Finalize() ↵Albert Cheng2011-01-165-14/+57
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | when it encountered error and wanted to exit the test program. This was not good since if only a subset of processes called MPI_Finalize(), the other processes will likely hang. That happened in AIX that it would waited till the alarm signal to kill the processes. Definitely a waste of time. Solution: Changed it to call MPI_Abort. That showed another problem. HDF5 has setup atexit post-process to try to close unclose objects, release resources, etc. But if the MPI processes have encountered an error and has been aborted, it is not likely any more MPI calls can function properly. E.g., it would attempt to free some communicators in the HDF5 MPIO file handle. It would again hang. Solution: need to call H5dont_atexit() to disable any atexit post-processing. This must be done early, like before calling H5open. This is added to each parallel test main program. testphdf5.h: Changed macros VRFY and MESG. Added comments too. testphdf5.c: t_mpi.c: t_cache.c: t_shapesame.c: Added H5dont_atexit. Tested: h5committest.
* [svn-r19955] Removed since its code has been copied to t_shapesame.c.Albert Cheng2011-01-142-4434/+0
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* [svn-r19950] Correct CPack confusion with the same for two different ↵Allen Byrne2011-01-131-3/+3
| | | | functions (not case-sensitive)
* [svn-r19946] Bug fix: testph5.in failed to run the 't_shapesame -p' by ↵Albert Cheng2011-01-121-3/+2
| | | | | | | | | | | | | | | claiming it could not find t_shapesame in daily test. Turned out the mpiexec launcher is working like real shell and the daily test signon (hdftest) does not have "." in its $PATH. So, it could not automatically look for executables in the current directory. Solution: Change the executable to an explicit ./t_shapesame. Now mpiexec can "find" it. Tested by hand in Amani.
* [svn-r19940] Updated with new file ./testpar/t_shapesame.cAlbert Cheng2011-01-121-1/+2
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* [svn-r19939] Purpose:Albert Cheng2011-01-125-21/+4864
| | | | | | | | | | | | | | | | | | | | | | | Moved the two shape same tests from testphdf5 to a separated executables, named t_shapesame. The shape same tests runs too long for testphdf5. In a separated executalbe, it will be easier to separate any errors in testphdf5 sub-tests from the shape same tests. t_shapesame.c: Contains the shape same tests (cloned from t_rank_projection.c) plus a duplicate of "testphdf5.c" for now. After verifying it is correct, more cleanup is needed. testphdf5.c: Removed the two shape same tests (chsssdrpio & cbhsssdrpio). Makefile.am: Makefile.in: Added t_shapesame as a new test executable. Removed t_rank_projections.c from part of testphdf5. testph5.sh.in: Temporary added the "t_shapesame -p" test for testing shape same tests with MPIO-Posix VFD. Tested: h5committested, plus serial jam.
* [svn-r19935] Add new packed bits tests to legacy test scriptAllen Byrne2011-01-101-31/+75
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* [svn-r19931] Add packed bits tests to MemCheck ignore listAllen Byrne2011-01-071-0/+42
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* [svn-r19928] Remove pragma statement.Allen Byrne2011-01-071-1/+0
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* [svn-r19925] bring BZ1165 solution from trunk.Allen Byrne2011-01-072-2/+3
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