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* [svn-r27768] Description:Quincey Koziol2015-09-141-1/+1
| | | | | | | | | | | | | | | | | | | | | | Complete revamp of package initialization/shutdown mechanism in the library. Each package now has a single init/term routine. This new way should avoid packages being re-initialized during library shutdown and is also be _much_ more proactive about giving feedback for resource leaks internal to the library. Introduces a new "module" header file for packages in the library (e.g src/H5Fmodule.h) which sets up some necessary package configuration macros for the FUNC_ENTER/LEAVE macros. (The VFL drivers have their own slightly modified version of this header, src/H5FDdrvr_module.h) Also cleaned up a bunch of resources leaks all across the library and tests, along with addressing many warnings, as I encountered them. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel Linux/64 3.10.x (kituo) w/serial & parallel Linux/64 2.6.x (ostrich) w/serial
* [svn-r25921] - wrap MPI 3 usage with MPI_VERSION compile time check.Mohamad Chaarawi2014-12-231-2/+4
| | | | - build out unbuffered stdout/err for windows
* [svn-r25651] Fix for: HDFFV-8715Mohamad Chaarawi2014-10-011-1/+1
| | | | | | HDF5_PARAPREFIX is ignored in parallel dense attribute and performance tests. tested on Jam w/ parallel.
* [svn-r25503] - fix bug in encode/decode plist parallel test when 1 proccess ↵Mohamad Chaarawi2014-08-011-1/+1
| | | | | | is used to run the test. - fix warning in t_chunk_alloc.
* [svn-r25401] add serial and parallel regression tests for zero dset ↵Mohamad Chaarawi2014-07-091-0/+3
| | | | read/write bug.
* [svn-r24864] Description:Quincey Koziol2014-03-211-21/+1
| | | | | | | | | | | | | | | | | | 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
* [svn-r24612] fix bugs in parallel tests exposed in corner cases when running ↵Mohamad Chaarawi2014-01-061-6/+12
| | | | | | | | | | | | | | | | with 1 or 2 processes. First bug is in testpar/t_mdset.c, where the test reports an error in addition to skipping the test if there are less than three procs. Fix to just skip the test. Second bug is in testpar/t_dset.c in actual_io_mode tests, where incorrect expected value for IO mode was set if the number of procs running the test is 1. tested with h5committest.
* [svn-r23529] Description:Quincey Koziol2013-04-031-0/+4
| | | | | | | | Stop aliasing property to indicate internal collective metadata operations with property to perform collective raw data operations from the application. Tested on: Mac OSX/64 10.8.3 (amazon) w/paralllel
* [svn-r22992] Purpose:Jonathan Kim2012-10-301-1/+1
| | | | | | | | | | | HDFFV-8146 - Remove "multi-chunk IO without optimization" sub-feature from MPI I/O optimization for chunked dataset feature Description: The “multi-chunk IO without optimization” feature is removed and made the related xfer property (H5FD_MPIO_CHUNK_MULTI_IO) go directly to “multi-chunk-io” feature. Also update/fix/cleanup testings (chunk collective IO and actual chunk opt mode) accordingly. Tested: jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), fred (mac64-LE), Windows (32-LE cmake), cmake (jam)
* [svn-r22807] Description:Quincey Koziol2012-09-251-0/+3
| | | | | | | | | | | | | | | | | | | | | Add encode/decode API routines for property lists: H5Pencode/H5Pdecode. Tested on: FreeBSD/32 8.2 (loyalty) w/gcc4.6, w/C++ & FORTRAN, in debug mode FreeBSD/64 8.2 (freedom) w/gcc4.6, 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 (koala) 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 (ostrich) w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-ia64 2.6 (ember) w/Intel compilers, w/parallel, C++ & FORTRAN, in production mode Mac OS X/32 10.7.3 (amazon) in debug mode Mac OS X/32 10.7.3 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode Mac OS X/32 10.7.3 (amazon) w/parallel, in debug mode
* [svn-r22735] Purpose:Jonathan Kim2012-09-041-0/+4
| | | | | | | | | | | | | | | | | | | HDFFV-8143 Provide a routine(s) for telling the user why the library broke collective data access Description: Added H5Pget_mpio_no_collective_cause() function that retrive reasons why the collective I/O was broken during Read/Write IO access. Reasons to break collective I/O: - SET_INDEPENDENT - DATATYPE_CONVERSION - DATA_TRANSFORMS - MPIPOSIX - NOT_SIMPLE_OR_SCALAR_DATASPACES (NULL Space) - POINT_SELECTIONS - NOT_CONTIGUOUS_OR_CHUNKED_DATASET (Compact or External-Storage) - FILTERS Tested: jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
* [svn-r22651] fix a bug that would skip or include the parallel atomicity ↵Mohamad Chaarawi2012-08-091-10/+10
| | | | test with cmd arguments -o or -x
* [svn-r22385] Skip tests using sparse file writes on Windows. JIRA issue ↵Allen Byrne2012-05-211-0/+4
| | | | (JIRA HDDFV-8064) created.
* [svn-r22219] Description:Quincey Koziol2012-03-311-0/+7
| | | | | | | | Merge "file image" changes from feature branch back to trunk. Tested on: Mac OSX/64 10.7.3 (amazon) w/debug (h5committest upcoming)
* [svn-r22115] Add 2 new API routines to set/unset file atomicity for files ↵Mohamad Chaarawi2012-03-211-0/+12
| | | | | | | opened with the MPI-IO VFD Add test cases for these two routines Jira issue HDFFV-7961
* [svn-r21442] Description:Quincey Koziol2011-10-011-0/+3
| | | | | | | | | | | | | | | | | | | | | | Check in "actual I/O mode" feature to trunk. Will merge back to 1.8 branch after it bakes over the weekend. Tested on: FreeBSD/32 8.2 (loyalty) w/gcc4.6, w/C++ & FORTRAN, in debug mode FreeBSD/64 8.2 (freedom) w/gcc4.6, 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 (koala) 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-ia64 2.6 (ember) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode Mac OS X/32 10.6.8 (amazon) in debug mode Mac OS X/32 10.6.8 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r21334] HDFFV-7687: add HD macro prefrix to functions and use h5_stat_t ↵Allen Byrne2011-08-301-1/+1
| | | | | | where necessary reviewed
* [svn-r19959] Bug: the VRFY macro, for some reason, called MPI_Finalize() ↵Albert Cheng2011-01-161-0/+9
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r19941] Purpose:Albert Cheng2011-01-121-9/+0
| | | | | | | | | | | | | | | | | | | | | | | 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-r19622] Port of fix for the round robin parallel flush bug caused by ↵John Mainzer2010-10-171-0/+7
| | | | | | | | | | | | | | | | | | | | | | | | | | the failure of the H5Ocache.c code to update its image of the on disk representation of the object header on a call to the clear callback. This wasn't an issue as long as all flushes of the object header were made from the same process, but if an object header is modified, and then flushed on one process and cleared on the rest, the changes were not be reflected in the images of the on disk representation on all processes where the object header was cleared rather than flushed. If one of these processes did the next flush, the changes were lost in the on disk representation. Fixed this by causing all dirty messages and to be written to the copy of the on disk image maintained by the object header code on both flush and clear. Also added associated test code in t_mdset.c. Also checking in some cache debug code developed while chasing this bug. Commit tested and tested (parallel) on phoenix.
* [svn-r19092] Description:Quincey Koziol2010-07-191-1/+20
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring "shape same" changes from LBL branch to trunk. These changes allow shapes that are the same, but projected into dataspaces with different ranks to be detected correctly, and also contains code to project a dataspace into greater/lesser number of dimensions, so the I/O can proceed in a faster way. These changes also contain several bug fixes and _lots_ of code cleanups to the MPI datatype creation code. Many other misc. code cleanup are included as well... 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, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode Mac OS X/32 10.6.3 (amazon) in debug mode Mac OS X/32 10.6.3 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r17376] Description:Quincey Koziol2009-08-181-30/+1
| | | | | | | | | | | Make similar change to windows VFD as sec2 VFD, when converting from a family file to a single file. Tweak file sizes expected for parallel tests. Tested on: tg-login3, w/parallel Windows (post facto)
* [svn-r16770] Modified parallel tests so they can run with arbitrary number ↵Christian Chilan2009-04-171-2/+3
| | | | | | of processors. Tested on jam and abe.
* [svn-r16723] Modified dset and t_chunk_alloc tests to use dataset dimensions ↵Christian Chilan2009-04-091-13/+8
| | | | | | that are multiples of the number of processors. Tested on jam and abe.
* [svn-r16659] Modified dset and t_chunk_alloc tests to use dataset dimensions ↵Christian Chilan2009-04-021-1/+8
| | | | | | that are multiples of the number of processors. Tested on jam and abe.
* [svn-r15628] Description:Quincey Koziol2008-09-161-3/+3
| | | | | | | | | | | | | Remove trailing whitespace from C/C++ source files, with the following script: foreach f (*.[ch] *.cpp) sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f end Tested on: Mac OS X/32 10.5.5 (amazon) No need for h5committest, just whitespace changes...
* [svn-r15183] Purpose: _WIN32 macro cleanupScott Wegner2008-06-091-6/+0
| | | | | | | | | | Description: As part of our Windows cleanup, we try to remove windows-specific tweaks in the source code. There are many instances where Windows code is introduces via ifdef's. We re-evaluate whether they are still required, and found that many of them are not. Others we change to "feature"-specific code, rather than Windows-specific. Tested: VS2005 on WinXP VS.NET on WinXP h5committest (kagisopp, smirom, linew)
* [svn-r14098] Description:Quincey Koziol2007-08-211-1/+1
| | | | | | | | Clean up a few remaining API compatibility issues in the H5E API for parallel configurations Tested on: FreeBSD/64 6.2 (liberty) w/parallel
* [svn-r14096] There're 3 changes in this checkin as below:Raymond Lu2007-08-201-0/+3
| | | | | | | | | | | | | | | | | | 1. In H5Dwrite and H5Dread, let the data buffer point to a fake address if the application passes in an empty buffer. This is mainly for MPIO programs that some processes may not have any data to write or read but still participate the I/O. This solution solves some MPI's problem like the ChaMPIon on tungsten which doesn't support empty buffer. 2. The ChaMPIon on tungsten doesn't support complex derived MPI data type correctly and collective I/O when some processes don't have any data to write or read correctly. Detect the compiler "cmpicc" in the system-specific config file and set the variables for these two cases to false. The PHDF5 library already has set up a way to switch collective chunked I/O to independent under these two cases. 3. A bug fix - During the work of the optimization for compound data I/O, the case for switching collective chunked I/O to independent I/O was leftout. Fixed it by adding I/O caching to it in H5D_multi_chunk_collective_io in H5Dmpio.c. Tested on tungsten, cobalt, and kagiso for parallel; on linew and smirom for serial.
* [svn-r13778] Add test_filter_read to testphdf5.Christian Chilan2007-05-221-0/+2
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* [svn-r13766] In Visual Studio 2005 for 64-bit, _WIN32 is defined, but not ↵Scott Wegner2007-05-181-2/+2
| | | | | | | WIN32, so I've standardized all #ifdef's to use _WIN32. This should not affect any other platform. Tested: Visual Studio (32- and 64-bit) on Win XP
* [svn-r13253] Updated all C and C++ style source code files with the THG ↵Albert Cheng2007-02-071-2/+3
| | | | | | | | | copyright notice. Tested platform: Kagiso only since it is only a comment block change. If it works in one machine, it should work in all, I hope. Still need to check the parallel build on copper.
* [svn-r12967] Cleanup.Albert Cheng2006-11-221-43/+0
| | | | | | | The h5_mpi_get_file_size() is no longer used. The unused code caused some compiling warning messages. Removed the whole routine. Tested in heping pp mode.
* [svn-r12725] Purpose:Albert Cheng2006-10-061-0/+22
| | | | | | | | | | | | | Bug Fix (Bug 544) Description: SGI Altix's MPI_File_get_size overflowed at 2GB and more. Put in a temporary patch to use stat() instead to make Cobalt passing on this test (bigdset). A better fix (like detect if MPI_File_get_size does not work before using this is preferred.) Tested: Cobalt and Heping.
* [svn-r12554] New tests have been added to test the correctness of ↵MuQun Yang2006-08-091-4/+15
| | | | | | | | independent IO with file setview. To activite this test, add the command option -i. For example, at IBM AIX, type "poe testphdf5 -i" will test the library with independent IO with file setview. It simply replaces all the collective IO tests with independent IO with file setview.
* [svn-r12440] Purpose:Quincey Koziol2006-06-271-4/+4
| | | | | | | | | | | Code cleanup Description: Trim trailing whitespace in Makefile.am and C/C++ source files to make diffing changes easier. Platforms tested: None necessary, whitespace only change
* [svn-r12174] Purpose:MuQun Yang2006-03-291-1/+27
| | | | | | | | | | | | | | | | | | | | | | | | | | | | Adding parallel tests for optional collective chunk APIs Description: Three new APIs "H5Pset_dxpl_mpio_chunk_opt_ratio H5Pset_dxpl_mpio_chunk_opt_num H5Pset_dxpl_mpio_chunk_opt" for optional optimization choices from users have been added to the libraries. This check-in adds six tests to verify the funcationality and correctedness of these APIs. These tests need to be verified with 3 or more processors and with MPI-IO driver only. Solution: Using H5Pinsert, H5Pget, H5Pset to verify that the library indeed goes into the branch we hope for. Using H5_HAVE_INSTRUMENT macro to isolate these changes so that it won't affect or be misused by the application. Platforms tested: h5committest(shanti still refused to be connected) Parallel tests on heping somehow are skipped. Manually testing at heping. Have checked 1,2,3,4,5 processes. Misc. update:
* [svn-r11953] Purpose:MuQun Yang2006-02-171-2/+0
| | | | | | | | | | | | | | code cleanup Description: remove two printf lines accidently added for debugging at NCSA cobalt. Solution: Platforms tested: No need to test. Misc. update:
* [svn-r11951] Purpose:MuQun Yang2006-02-161-0/+4
| | | | | | | | | | | | | | | | Enhance collective chunk IO supports Description: Add a new test to check the correctness of the HDF5 library behavior for collective IO mode when one process doesn't have any contribution for IO. Solution: Platforms tested: IBM AIX 5.2(copper) Linux (heping) mpich-1.2.6 Misc. update:
* [svn-r11866] Purpose:Albert Cheng2006-01-061-6/+2
| | | | | | | | | | | | | | | | | | | | bug fix 504 Description: testpar/t_mpi would hang if $HDF5_NOCLEANUP is set. E.g., % env HDF5_NOCLEANUP=yes mpirun -np 3 ./t_mpi This happened because the environment variables are not exported to all mpi processes by the mpirun command. So, some attempted to do cleanup while others don't and some hang waiting for others to act. Solution: Instead individual program checking getenv, they all just called h5_cleanup no matter. h5_cleanup now uses getenv_all to check the $HDF5_NOCLEANUP if it is in parallel mode. Platforms tested: h5committested, tested pp in heping too.
* [svn-r11572] Purpose:MuQun Yang2005-10-171-26/+0
| | | | | | | | | | | | | | | Code clean-up for collective regular chunk IO tests. Description: Add descriptions for each tests for future maintenance. Solution: Platforms tested: Mostly comments, No need to use h5committest. heping(linux 2.4) Misc. update:
* [svn-r11448] Purpose:Pedro Vicente Nunes2005-09-211-2/+8
| | | | | | | | | | | | | | | | | | | new features Description: add support for compiling the library and testphdf5 in Windows Solution: Platforms tested: Linux AIX Solaris Windows VC6 Misc. update:
* [svn-r11340] Purpose:Albert Cheng2005-09-021-3/+1
| | | | | | | | Big data set test was default off and rarely tested. Changed it to default on so that it gets tested. Platforms tested: Heping PP and Copper pp.
* [svn-r11312] Purpose:Albert Cheng2005-08-301-0/+2
| | | | | | | | | | | | | | | | | | Bug #281 Description: A dataset created in serial mode with H5D_ALLOC_TIME_INCR allocation setting was not extendible, either explicitly by H5Dextend or implicitly by writing to unallocated chunks. This was because parallel mode expects the allocation mode be H5D_ALLOC_TIME_INCR only. Solution: Modified library to allocate more space when needed or directed if the file is opened by parallel mode, independent of what the dataset allocation mode is. Platforms tested: Heping pp.
* [svn-r11245] Purpose:Quincey Koziol2005-08-131-29/+29
| | | | | | | | | | | | | | | | | | | | Code cleanup Description: Trim trailing whitespace, which is making 'diff'ing the two branches difficult. Solution: Ran this script in each directory: foreach f (*.[ch] *.cpp) sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f end Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r11232] Purpose:MuQun Yang2005-08-111-0/+2
| | | | | | | | | | | | | | Modified collective chunk Io test Description: One test(collective chunk IO test 4) is no longer needed. Comment out first. The code should be cleaned up later. Solution: Platforms tested: Misc. update:
* [svn-r11067] Purpose:MuQun Yang2005-07-121-3/+35
| | | | | | | | | | | | | | | | | | Updating phase 2 work of collective IO Description: The current collective IO tests cannot test for number of processors bigger than some values, this change will lift those restriction. However, the test may be slower. Solution: Platforms tested: linux 2.4, AIX 5.1, Linux 2.4 IA64 and IRIX 6.5 (I haven't tested big number of processors with the restriction of the machine) Misc. update:
* [svn-r10598] Purpose:Albert Cheng2005-04-121-32/+45
| | | | | | | | | | | | | | | | Bug fix. Description: The irregular chunk IO tests do not work for processes sizes larger than 3. Added a check of number of processes and skip the irregular chunk IO tests if number of processes are larger than 3. Revamped the tests of collective chunk IO tests too. Platforms tested: Tested in mir. Misc. update:
* [svn-r10546] Purpose:MuQun Yang2005-04-051-2/+0
| | | | | | | | | | | | | | | | Support collective IO for irregular selection. Description: Solution: Platforms tested: Linux with MPICH AIX with mpcc_r Linux with ChaMPIO Altix with intel Misc. update:
* [svn-r10122] Purpose:Albert Cheng2005-03-021-3/+4
| | | | | | | | | | | | | | | | typo fix and small improvement. Description: t_coll_chunk.c: ccdataset_vrfy() was using a wrong routine name to identify itself. testphdf5.c: Add a definition of NFILENAME to be the common dimension size of FILENAME[] and filenames[][] since they must have the same first dimension size. Platforms tested: h5committested.
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