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* [svn-r26298] merge 26279 from trunk.Mohamad Chaarawi2015-02-251-3/+0
| | | | | | HDFFV-883: attach callback to terminate HDF5 library when MPI_COMM_SELF is destroyed on MPI_Finalize. tested h5committest.
* [svn-r26224] merge 26180 from trunk:vms_last_support_1_8Mohamad Chaarawi2015-02-1813-13/+4
| | | | | | | | | | configure fixes for HDFFV-9068,9069,9096,9097,9135 from autotools_rework branch: - Remove Infering parallel compilers (C and Fortran) from configure.ac - Remove restriction to build shared with parallel - Cleanup parallel sections in configure.ac - remove large file support checks - MPE fixes.
* [svn-r26064] HDFFV-9018: Install PDB files to bin folder with dlls.Allen Byrne2015-01-281-1/+1
| | | | Tested: windows
* [svn-r25957] Added Perform and io_timer back into build.Allen Byrne2015-01-052-2/+2
| | | | Tested: local linux cmake
* [svn-r25956] [Merge r25954 from trunk]Albert Cheng2015-01-052-7/+13
| | | | | | | | | | | | | | | HDFFV-9046: reorganize hdf5/perform, step 2 Last changes had caused problems with Windows platform: 1. H5private.h in io_timer.h is not accessible in the distributed shared library of tools. Need to move it to io_timer.c. 2. debug_start_stop_time() would not be available outside of h5perf. Some favor of compiler does not like it. Screened it out for now. 3. mere "extern" is not good enough for Windows shared library. Must mark them as DLL. Need to mark them as "H5TOOLS_DLL". 4. STANDALONE mode is broken. Screened out the code for now. Tested: h5committest.
* [svn-r25952] HDFFV-9054: disable io_timer in tools lib and perform ↵Allen Byrne2015-01-052-2/+2
| | | | sub-folder due to SHARED compile issues and other issues.
* [svn-r25948] [Merged r25946 from trunk]Albert Cheng2015-01-043-12/+0
| | | | | | Removed debug statments that use //. Tested: env CFLAGS=-ansi buildhdf5 in jam and parallel platypus.
* [svn-r25947] [merged changes from trunk r25940]Albert Cheng2015-01-048-16/+11
| | | | | | | | | | | | | | | | | | | | | | | HDFFV-9046: reorganize hdf5/perform, step 2 Move timing measurement routines used by h5perf and h5perf_serial to tools/lib so that they can be used by other tools too. tools/lib/io_timer.c tools/lib/io_timer.h tools/perform/io_timer.c tools/perform/io_timer.h renamed perform/io_timer.[ch] to lib/io_timer.[ch] tools/lib/Makefile.am tools/lib/Makefile.in tools/lib/CMakeLists.txt tools/perform/Makefile.in tools/perform/Makefile.am tools/perform/CMakeLists.txt MANIFEST updated due to the move. Tested; h5committest and jam (serial)
* [svn-r25945] [merge changes r25932 and r25933 from Trunk]Albert Cheng2015-01-0314-573/+375
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | HDFFV-8902: merge the source code of h5perf and h5perf_serial, stage 1. tools/perform/sio_timer.h: tools/perform/pio_timer.c: tools/perform/io_timer.h: tools/perform/io_timer.c: Renamed pio_timer.[ch] as io_timer.[ch]; merged content of sio_timer.[ch] into io_timer.[ch] so that both h5perf and h5perf_serial call the combined io_timer.[ch]. Moved the debug printing code segment in set_time() in [sp]io_timer.c to as debug_start_stop_time() in [sp]io_perf.c where it belongs. Screened out set_timer_type() and get_timer_type() which were not used by any code. tools/perform/Makefile.am: tools/perform/Makefile.in: tools/perform/CMakeLists.txt Adjusted to use io_timer.c for both h5perf and h5perf_serial. tools/perform/pio_perf.c: tools/perform/sio_perf.c: tools/perform/pio_perf.h: tools/perform/sio_perf.h: Renamed [sp]io_time_destory() to same io_time_destroy(); Moved the debug printing code segment in set_time() in [sp]io_timer.c to as debug_start_stop_time() in [sp]io_perf.c where it belongs. tools/perform/pio_engine.c: tools/perform/sio_engine.c: Removed #include io_timer.h since it was already #include by [sp]io_perf.h. MANIFEST: Updated the merge of [sp]io_timer.[ch] into io_timer.[ch]. Tested: h5committest and jam in extra.
* [svn-r25937] Remove build and test commands for deleted benchpar.cAllen Byrne2014-12-312-16/+0
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* [svn-r25919] If not testing skip building test only programs.Allen Byrne2014-12-221-10/+12
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* [svn-r25910] HDFFV-8156: perform/benchpar failed to runAlbert Cheng2014-12-191-488/+0
| | | | | | | Benchpar.c is retired/deleted. If it is ever needed, it can be retrieved from the SVN repository or even previous version of HDF5 source code. Tested: jam parallel make passed.
* [svn-r25907] Fix CMP0054 warningAllen Byrne2014-12-191-2/+2
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* [svn-r25901] HDFFV-9046: reorganize hdf5/perform/ directory Albert Cheng2014-12-1932-2/+15544
| | | | | | Moved perform/ to tools/perform. Updated all the configure related files for the new location. Tested: h5committested plus tested in jam and kite.
* [svn-r25772] Bug fix: HDFFV-8954Albert Cheng2014-11-041-6/+1
| | | | | | | | | | | | | | Previously, ph5diff may hang in a test in Linux 32 platform(HDFFV-587). No solution was available and a patch to bypass the test is implemented. Since the company is changing domain name soon, the patch would not be valid any more. Tests were done (repeat 100 mpiexec -np 6 ./ph5diff -v h5diff_hyper1.h5 h5diff_hyper2.h5) and the previous hanging problem did not occur. It is likely the newer versions of mpich no longer have this problem. Therefore, it is decide to remove this patch to make the test script cleaner, if nothing else. Tested: ran build and test in Jam (linux 32) and the repeat 100 command mentioned above. All passed.
* [svn-r25497] Description:Quincey Koziol2014-07-3018-159/+159
| | | | | | | | | | Merge changes that correspond to the 64-bit ID changes (without the actual switch to 64-bit IDs) to the 1.8 release branch. (Plus a few minor cleanups and alignments with the trunk that aren't on the branch) Tested on: Mac OSX/64 10.9.4 (amazon) w/C++ & FORTRAN (h5committested on branch already for a week)
* [svn-r25402] Bring 25397/8 from trunk:Mohamad Chaarawi2014-07-1011-11/+0
| | | | | | | - remove configure checks for MPI_File_get_size and Big MPI_File_set_size as they are supported by MPIO implementations today. - fix bug in t_mpi.c (HDFFV-8856) tested with h5committest.
* [svn-r25251] change test to ignore h5diff warnings (endianess issue)Allen Byrne2014-06-101-1/+1
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* [svn-r25225] Description:Quincey Koziol2014-05-291-130/+163
| | | | | | | | | | | | | | | | Bring r25215 from trunk to 1.8 branch: Bring changes from Coverity branch back to trunk: r20914: Use HDstrncpy and HDstrncat! --gh r20915: Use HDstrncpy and HDstrncat! --gh Tested on: MacOSX/64 10.9.3 (amazon) w/gcc 4.9, FORTRAN, C++, multi-threads & parallel (h5committested on the trunk)
* [svn-r25222] Merge cmake_ext_mod into 1.8Allen Byrne2014-05-2714-62/+47
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* [svn-r25198] Description:Quincey Koziol2014-05-183-16/+8
| | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring r25197 from trunk to 1.8 branch: Bring changes from hdf5_1_8_coverity branch back to trunk: r20878: Issue 76: Check if H5Tget_nmembers(type) fails and simply return(FALSE). Also move printf to after check. r20880: Issue 192: Create ret_val var set to -1. Add out label for failures to jump to, return ret_val at bottom. r20882: Fixes for coverity: 1) bug #1679: remove dead code in test/mf.c 2) bug #1680: remove dead code in tools/lib/h5diff_dset.c r20883: Fix coverity issue 585 Description: Changed variable "c" in processStrData in h5import.c to an int, to match fgetc return value, and removed call to feof, instead checking if c == EOF. Tested on: MacOSX/64 10.9.3 (amazon) w/C++, FORTRAN & parallel (too minor to require h5committest)
* [svn-r25119] Description:Quincey Koziol2014-04-252-13/+16
| | | | | | | | | Make the exit status from ph5diff always be 0, as it is on the trunk. Also a few coding standard cleanups to the test generation code. Tested on: MacOSX/64 10.9.2 (amazon) w/FORTRAN & parallel (h5committest not necessary)
* [svn-r25111] Changed Subeversion EOL and executable properties. No code changes.Dana Robinson2014-04-2513-48/+48
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* [svn-r25106] Removed LT_ADD_LIBHDF5_DEPENDENCY configure conditional to roll ↵Larry Knox2014-04-2511-11/+0
| | | | | | | | back fix for removing rpaths from lib files. The fix also removed dependencies on libhdf5, etc. when the --disable-sharedlib-rpath configure option was invoked. Added instead configure variable hardcode_into_lib=no. This removes rpath from lib files on Linux and solaris machines. Tested with h5committest on jam, koala, ostrich and platypus (cmake), and on emu and kite.
* [svn-r25082] Bug HDFFV-8625, HDFFV-8639, HDFFV-8745:Albert Cheng2014-04-229-8/+60
| | | | | | | | | | | | | | | | | | | h5diff issues "unable to read attribute" error message when comparing two files Description: h5diff did not handle attributes of variable length strings correctly. It created the wrong memory type if one but not both compared attributes are of the variable strings type. It ended in H5Aread() failure. Solution: We decided to treat the case when one type is variable length string and the other is not as incomparable. That bypassed the above error. We still need to figure out the proper way, if possible, to compare variable string with non-variable string types. Tested: h5committested plus tested in Swallow (OS X 10.8).
* [svn-r25044] Correct test DEPENDS format.Allen Byrne2014-04-141-1/+1
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* [svn-r25014] Purpose:Dana Robinson2014-04-115-14/+15
| | | | | | | | | | | | | | | | | Merge of r24937 from the trunk Adds H5free_memory to the API. This function should be used to free memory allocated by the library (e.g., returned values from H5Tget_tag, H5Pget_class_name, etc.). This is mainly to help Windows applications deal with multiple CRT instances, but can also be helpful when a debug memory manager is being used or when the HDF5 API is being wrapped for managed languages like Python and Java. Tested on: 32-bit LE linux (jam) with fortran and C++ 64-bit BE linux (ostrich) 64-bit LE linux (koala)
* [svn-r25000] Bugfix: HDFFV-8639 Albert Cheng2014-04-091-3/+7
| | | | | | | | | | | h5diff segfaults with user's files Solution: Added a variable to indicate if real data are in the buffer and will call H5Dvlen_reclaim() only when real data are in the buffer. Tested: with the user provided data files and no more segmentaion fault. Also h5committ tested.
* [svn-r24980] HDFFV-8290: Merge automake 1.14.1 changes from trunkAllen Byrne2014-04-0723-850/+5016
| | | | Tested: h5committest
* [svn-r24906] Merge latest CMake changes from trunk.Allen Byrne2014-03-2625-1408/+1504
| | | | Tested: local linux
* [svn-r24894] Description:Quincey Koziol2014-03-251-104/+95
| | | | | | | | | | | | | | | | | | | | | | | | | | | Bring r24869 & r24875 from trunk to 1.8 branch: Clean up more compiler warnings, plus merge a few Coverity bug fixes from the hdf5_1_8_coverity branch back to the trunk: r20877: Purpose: Fix coverity issue 1723 Description: Modified test_generate in hl/test_image to close file "f" before exit, even if an error occurs. r20879: Issue 63: change check of return of H5Tget_nmembers to <=0. No need to go futher if call fails as well as empty. r20881: Coverity #659 in Run 46: I changed the Line 442 where it tries to check whether FLAG_PRINTED is TRUE. But it had just been set to FALSE. I took out the condition check in the print statement. Tested on: Mac OSX/64 10.9.2 (amazon) w/C++, FORTRAN & Parallel (daily tested on trunk)
* [svn-r24878] Description:Quincey Koziol2014-03-2413-75/+20
| | | | | | | | | | | | | | | | | | | | | Bring r24864 from trunk to 1.8 branch: Remove all traces of MPI-POSIX VFD and GPFS detection/code. Remove remaining traces of stream VFD. Remove testpar/t_posix_compliant test (it's not actually verifying anything). Clean up H5D__mpio_opt_possible() further. Moved environment variable that disables MPI collective operations into MPI-IO VFD (instead of it being in src/H5S.c). A few other small code cleanups. Tested on: Mac OSX/64 10.9.2 (amazon) w/parallel & serial (daily tested on trunk)
* [svn-r24810] Description:Quincey Koziol2014-03-178-134/+77
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring r24803 & r24804 from trunk to 1.8 branch: r24804: Brought changes from Coverity branch back to trunk, and cleaned up misc. other warnings & formatting issues: r20833: Fixed Coverity 667 and 668 with real integer overflow tests this time. r20834: Use HDstrncpy and HDstrncat. --gh r20835: Change to use strncpy - use base_len + 1 for line 156, use HDstrlen(path) + 1 for line 159 r20836: Fixed coverity 585 by casting output of fgetc() to a char. r20837: Changed sprintf calls to snprintf with size 1 less than the allocated buffer to address coverity issue #967. r24803: Rename GCC_DIAG_OFF/ON macros to H5_GCC_DIAG_OFF/ON and move from src/H5private.h to src/H5public.h. Wrap typedef of hsize_t and hssize_t in DIAG_OFF(long-long) macros. Clean up a bunch of "macro '-' is unused" warnings. Tested on: Mac OSX/64 10.9.2 (amazon) w/C++, FORTRAN & parallel (too minor to require h5committest)
* [svn-r24746] Merge trunk revision 24744 from cmake branch includes;Allen Byrne2014-02-276-142/+299
| | | | | | HDFFV-8505: UD filter changes to remove filters in h5repack. Tested: local linux
* [svn-r24732] Fix for reconfigure, which fails because ↵Larry Knox2014-02-2211-0/+11
| | | | | | LT_ADD_LIBHDF5_DEPENDENCY is used in Makefiles but the declaration in configure.ac is missing. Copied declaration from trunk. Tested with h5committest on jam ostrich koala and platypus(cmake).
* [svn-r24728] Description:Quincey Koziol2014-02-213-68/+83
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring r24726 & r24727 from trunk to 1.8 branch: Description: Revert some earlier usage of strncpy, which was incorrect. Bring Coverity changes from branch back to trunk: r20821: Use HDstrncpy. --gh (Fixed already, with strdup) r20822: (Not merged, incorrect use of HDstrncpy()) r20823: (Not merged, incorrect use of HDstrncpy()) r20824: Maintenance: Bug fix: addressed CID 666. Value stored at *expression_len should be used in the call to HD5packFstring to avoid overflow (and unnecessary arithmetic calculation and casting) r20825: Issue 642: Added check for error and handler with print to stderr and exit. r20826: Undo revision 20818, as that issue has already been fixed in the 1.8 branch and trunk (but not coverity branch) r20827: (Not merged, incorrect use of HDstrncpy()) r20828: Use HDstrncpy. --gh (Corrected use of strncpy()) r20829: Check return of H5Lget_val(print_udata->fid, path, targbuf, linfo->u.val_size + 1, H5P_DEFAULT) and if error set trgbuf[0] to 0. Check if H5Lunpack_elink_val(targbuf, linfo->u.val_size, NULL, &filename, &objname) was successful and allow print. Otherwise filename and objname are not created. (init those to NULL) r20830: resolved coverity issues 939, 940, 941, 944, and 947. all were complaints about use of sprintf, and in all cases, the buffers used were large enough for all eventualities. Resolved issue by replacing calls to sprintf with calls to snprintf. r20831: Maintenance: Addressed CID 852 Replaced sprintf with snprintf r20832: Purpose: Fix valgrind issues with hl/examples/ex_image2 Description: Modified hl/examples/ex_image2 to free global "gbuf" before exit. Tested on: Mac OSX/64 10.9.1 (amaon) w/C++, FORTRAN & Threadsafety (too minor to require h5committest)
* [svn-r24684] Add IF SHARED block around Windows PDB file generation command.Allen Byrne2014-02-041-2/+3
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* [svn-r24680] Remove acknowledgment file from install.Allen Byrne2014-02-036-74/+89
| | | | | | | Remove obsolete CPack.cmake file. Merge h5repack and h5mkgrp test folder changes from trunk. Tested: local linux
* [svn-r24654] HDFFV-8640: Remove XLATE_UTILITYAllen Byrne2014-01-2845-118/+3180
| | | | Update tools testfiles
* [svn-r24479] Description:Quincey Koziol2013-11-303-148/+153
| | | | | | | | Fix ph5diff worker command handling so it can correctly respond to situations where there's no work to perform. Also, a few minor code cleanups. Tested on: Mac OSX/64 10.9.0 (amazon) w/parallel
* [svn-r24468] tfilters.h5 was created and checked in on 21 Feb 05, rev 10060, ↵Allen Byrne2013-11-263-3/+3
| | | | | | | | and never regenerated. The code for scaleoffset continued to change and the number of params for scaleoffset changed from 7 to 20 on the checkin of 23 Mar 05, rev 10384. The h5dump tests only looked at headers and never the data. Data reads would fail with invalid number of params (7 expected 20). Regenerated file and replacement ddls updated. New h5dump test will be added to read the data.
* [svn-r24395] Missed script file for cleanupAllen Byrne2013-11-011-0/+17
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* [svn-r24393] Cleanup testfiles from scripts. Update lists of files to be ↵Allen Byrne2013-11-0114-8/+208
| | | | | | cleaned. CMake update to clean testfiles. Tested: local cmake, autotools
* [svn-r24228] HDFFV-8529: Space separate define stringsAllen Byrne2013-09-303-8/+8
| | | | Tested: local linux
* [svn-r24205] Merge HDFFV-8513/8522 from trunk (via cmake branch), h5repack ↵Allen Byrne2013-09-2631-4442/+5444
| | | | | | | | UD plugins. Also warning session fixes. Tested: CMake local linux
* [svn-r24201] Merged changes from trunk revisions 23431, 23527 and 24077.Larry Knox2013-09-251-14/+29
| | | | | | | | | | Switched default to link to shared lib files when HDF5 is configure with --disable-static. This addressed HDFFV-8141, h5cc failed because it defaulted to link to lib*.a files which aren't built with --disable-static. -help message also updated. Tested in trunk. Merged code tested with h5committest.
* [svn-r24112] Description:Quincey Koziol2013-09-065-33/+43
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring r24101 & 24111 from trunk to 1.8 branch: r24101: ======= Description: Clean up warnings, enable new compiler warning flag(s) and bring back changes from Coverity branch: r20813: Remove the dead code as listed for coverity bug #1722. h5committested. r20814: Issue 69: Check return value and throw error if negative return. Also free datatype id on error r20815: Use HDstrncpy. --gh r20816: Replaced one last HDstrcat call with HDstrncat to resolve coverity issue 832. r20817: Use HDstrncpy and HDstrncat. --gh r20818: Purpose: Fix valgrind issues with h5jam Description: Modified h5jam to free strings strdup'd in parse_command_line before exit. Note that they may still not be freed in case of error, due to the widespread use of exit(). r20819: Issue 80: change loop to use int as loop index. r20820: Maintenance: Fixed the bug found by coverity CID 788 There were two problems with this function: 1) it tried to unnecessary free NULL pointer 2) it tried to allocate c_name buffer that is done by H5Pget_class_name r24111: ======= Description: Restrict GCC diagnostic pragmas to only gcc 4.6+ Tested on: Mac OSX 10.8.4 (amazon) w/gcc 4.8.1, C++ & FORTRAN (too minor to require h5committest)
* [svn-r24108] Remove file from the future.Allen Byrne2013-09-061-158/+0
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* [svn-r24106] Add help text tests for h5dump and h5repack to the linux ↵Allen Byrne2013-09-0610-108/+1079
| | | | | | scripts. HDFFV-8498 merge from trunk. Tested: local linux - cmake and autotools
* [svn-r24072] Merge trunk cmake changes to 1.8 branch. Allen Byrne2013-08-2639-6681/+7118
| | | | | | | Also add default switch blocks to h5import. Merge h5dump any_path option from trunk. Tested: local linux
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