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* [svn-r20135] Description:Quincey Koziol2011-02-223-3/+47
| | | | | | | | | | | | | | | | | | | | Bring r20134 from metadata journaling merging branch to trunk: Bring changes from metadata journaling branch to "merging" branch: Unify routine to mark a dataset's metadata as changed. 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
* [svn-r20132] Purpose:Jonathan Kim2011-02-216-5/+1017
| | | | | | | | | | | | | | | | | Fixing Bug 2092 - h5dump does not display index for a dataset Description: improve the test case from previous checkin r20108, which also display dataset via region reference. Previous Log: h5dump skip displaying array indices every certain number when the array type dataset is relatively big. The certain number varies according to the size of each array. This checkin fix the skipping array indices problem. This fix also correct indentation of the dataset data output. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake - jam
* [svn-r20124] Bug fix (ID: 519)Albert Cheng2011-02-182-104/+0
| | | | | | | | The content of bin/config_para_ibm_sp.sh has been added to release_docs/INSTALL_parallel long ago. Just got around to remove it. Tested: no need since nothing refer to config_para_ibm_sp.sh except MANIFEST. Ran bin/chkmanifest.
* [svn-r20121] Bug 1586 - the datatype handler created with H5Tencode/decode ↵Raymond Lu2011-02-183-12/+80
| | | | | | had the reference count 0. I fixed it by changing the APP_REF parameter of H5I_register from FALSE to TRUE and added a test case in dtypes.c. Tested on jam, heiwa, and amani.
* [svn-r20119] Description:Quincey Koziol2011-02-175-280/+282
| | | | | | | | | | | | | | | | | | | | 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-r20116] Description:Frank Baker2011-02-171-1/+1
| | | | Update copyright dates to include 2011.
* [svn-r20113] Add note to RELEASE.txt about external file cache.Neil Fortner2011-02-171-0/+4
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* [svn-r20112] Merge open_file_pool branch into trunk.Neil Fortner2011-02-1717-91/+4872
|\ | | | | | | Tested: jam (branch tested with h5committest)
| * [svn-r20064] Purpose: Implement external file cacheNeil Fortner2011-02-0817-91/+4872
| | | | | | | | | | | | | | | | | | Description: Implements a cache of files opened through external links. Adds the public functions H5Pset_elink_file_cache_size(), H5Pget_elink_file_cache_size(), and H5Frelease_file_cache(). Tested: jam, amani, heiwa (h5committest), fedora 64.
| * [svn-r20063] Merge changes from trunk from revision 19519 to 20062 into ↵Neil Fortner2011-02-08284-7465/+23382
| |\ | | | | | | | | | open_file_pool branch. No testing needed as the branch is currently identical to the trunk.
* | | [svn-r20110] Ignore valgrind memleak test on cmake script for ↵Jonathan Kim2011-02-171-0/+2
| | | | | | | | | | | | H5LS-tgrp_comments and H5DUMP-tarray1_big test cases.
* | | [svn-r20108] Purpose:Jonathan Kim2011-02-1513-46/+2163
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Fixing Bug 2092 - h5dump does not display index for a dataset Description: h5dump skip displaying array indices every certain number when the array type dataset is relatively big. The certain number varies according to the size of each array. This checkin fix the skipping array indices problem. This fix also correct indentation of the dataset data output. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
* | | [svn-r20103] Purpose:Jonathan Kim2011-02-147-87/+66
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Change to use HDxxx macros. Description: Originally this started for fixing incorrect pointer usage. But that got fixed through coverity merge. So this is mainly changing to use HDxxx macros and clean up some related code. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
* | | [svn-r20095] Removed AIX 5.3 and Cray xt3, added AIX 6.1 as supported platforms.Albert Cheng2011-02-131-13/+8
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* | | [svn-r20089] Add note to known problems section of RELEASE.txt about ↵Neil Fortner2011-02-111-0/+2
| | | | | | | | | | | | | | | | | | run-all-ex.sh on Cygwin. Tested: kwrite
* | | [svn-r20076] Updated for the adding of mpicc/mpif90 as default parallel ↵Albert Cheng2011-02-091-0/+3
| | | | | | | | | | | | | | | | | | compiler commands for linux systems.
* | | [svn-r20070] Description:Quincey Koziol2011-02-091-1/+1
| | | | | | | | | | | | | | | | | | | | | Switch order of system includes, to correct error on FreeBSD machines. Tested on: FreeBSD/32 6.3 (duty) w/debug
* | | [svn-r20065] Description:Quincey Koziol2011-02-0811-235/+239
| |/ |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r20061] Description:Quincey Koziol2011-02-088-390/+288
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r20060] Missing null character on return of get_comment - force \0Allen Byrne2011-02-071-2/+2
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* | [svn-r20058] 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: Jam (serial and parallel). No need for committest since this change is limited to Linux system.
* | [svn-r20057] Correct comment handling and remove cut/paste oversightsAllen Byrne2011-02-072-28/+25
| | | | | | | | merge r20056 from 1.8
* | [svn-r20054] Created valgrind cacheinit fileAllen Byrne2011-02-072-0/+59
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* | [svn-r20052] Description:Quincey Koziol2011-02-0610-566/+616
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r20050] Description:Quincey Koziol2011-02-056-388/+425
| | | | | | | | | | | | | | | | | | | | | | 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 FreeBSD/32 8.2 (loyalty) w/debug FreeBSD/64 8.2 (freedom) w/debug
* | [svn-r20048] Description:Quincey Koziol2011-02-052-82/+84
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r20044] Fix bz2127 by dynamically allocating storgae for comments.Allen Byrne2011-02-049-10/+62
| | | | | | | | Tested: local linux
* | [svn-r20033] Porblem: A typo caused compilation failures with gfortran 4.6 ↵Elena Pourmal2011-02-031-3/+3
| | | | | | | | | | | | | | | | on fred. Fixed. Platforms tested: fred and jam (minor change)
* | [svn-r20032] Add bug number to RELEASE.txtNeil Fortner2011-02-021-1/+1
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* | [svn-r20029] Purpose: Fix bug 2131Neil Fortner2011-02-027-226/+1493
| | | | | | | | | | | | | | | | | | | | 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-r20027] 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, amani, and heiwa.
* | [svn-r20025] remove t_rank_projection file from list of sourcesAllen Byrne2011-01-311-2/+2
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* | [svn-r20019] 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-r20013] 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-r20012] Use "if...else" to exclude the use when travt is null.Peter Cao2011-01-271-9/+8
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* | [svn-r20011] make sure that travt is nor nullPeter Cao2011-01-271-1/+1
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* | [svn-r20006] I updated the read buffer from float to double to be more ↵Raymond Lu2011-01-262-6/+8
| | | | | | | | | | | | appropriate. Tested on jam and linew.
* | [svn-r20005] Purpose:Jonathan Kim2011-01-262-2/+0
| | | | | | | | | | | | | | | | 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)
* | [svn-r20002] Add variable to allow a SITE name to be definedAllen Byrne2011-01-261-0/+3
| | | | | | | | Tested: local linux
* | [svn-r19999] Correct typo in check for external library TGZ path defineAllen Byrne2011-01-261-2/+2
| | | | | | | | Tested: local linux
* | [svn-r19998] I changed the previous commit from FLOAT to DOUBLE again ↵Raymond Lu2011-01-265-15/+15
| | | | | | | | | | | | | | | | because Neil prefers to it for fill value test. I updated the data files, too. Tested on linew and jam.
* | [svn-r19995] remove reference to jpegAllen Byrne2011-01-261-2/+2
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* | [svn-r19993] Added ability to use compressed file for external libraries ↵Allen Byrne2011-01-253-6/+15
| | | | | | | | | | | | corrected. Tested: local linux
* | [svn-r19991] Added ability to use compressed file for external librariesAllen Byrne2011-01-253-66/+127
| | | | | | | | Tested: local linux
* | [svn-r19989] Description:Quincey Koziol2011-01-252-132/+253
| | | | | | | | | | | | | | | | | | | | 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-r19988] Update list of memtest exludeAllen Byrne2011-01-251-0/+3
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* | [svn-r19982] I changed the previous commit from DOUBLE to FLOAT because the ↵Raymond Lu2011-01-245-15/+15
| | | | | | | | | | | | | | | | bug (2131) happens to FLOAT only. I updated the data files, too. Tested on linew and jam.
* | [svn-r19978] 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: h5committest.
* | [svn-r19977] Bug 2131 - I added a test case for integer data. I also ↵Raymond Lu2011-01-215-29/+195
| | | | | | | | | | | | skipped the test case for double data because it still fails. Tested on jam and linew.
* | [svn-r19972] I added a test case for dataset with scale-offset filter into ↵Raymond Lu2011-01-215-32/+252
| | | | | | | | | | | | cross_read.c and updated the data files from BE, LE, and VMS. Tested on jam and linew.
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