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* Brings the native implementation of H5Fdelete() from Bitbucket (#524)Dana Robinson2021-04-161-0/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Committing clang-format changes * Brings the native VFD H5Fdelete() implementation from Bitbucket Only brings the 'del' callbacks, not the 'open/close' scheme. * Formatter changes * Committing clang-format changes * Fixes direct VFD callback name * Removes UNUSED macro from family API call * Adds barrier and rank 0 check to MPI-I/O VFD delete * Revert "Adds barrier and rank 0 check to MPI-I/O VFD delete" This reverts commit 909765f759d9d96e84f4b8b1cc14f7d2b3ac8143. * Revert "Revert "Adds barrier and rank 0 check to MPI-I/O VFD delete"" This reverts commit 9b04bef1157853fc79fcb8fcc3e8ba1371091702. * Adds a second barrier after the delete in MPI-I/O VFD * Only delete files in the core VFD when the backing store flag is set * Fixes string issues in multi VFD Also, h5test.c cleanup code now uses H5Fdelete(). * Formatted source * Rework fapl checks for MPI-I/O VFD delete callback Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Minor parallel improvements (#519)Quincey Koziol2021-03-261-3/+0
| | | | | | | * Improve MPI error reporting, handled failed operations in parallel tests more nicely, and clean up MPI_Allreduce for determining whether to break collective I/O * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Update license url part2 (#333)Larry Knox2021-02-171-1/+1
| | | | | | * Modify temporary rpath for testing in java example scripts. * Update URL in source file Copyright headers for web copy of COPYING file - files not in src or test.
* Fix for HDFFV-11109 - Copy MPI comm and info object into output FAPL from ↵jhendersonHDF2021-02-171-0/+2
| | | | | | | H5F_get_access_plist (#342) * Avoid freeing MPI_COMM_WORLD in H5_mpi_comm_free * Copy MPI Comm and Info to new FAPL in H5F_get_access_plist
* Clang-format of source filesAllen Byrne2020-09-301-288/+226
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* Mostly whitespace in testpar, addl changes for tmp dirAllen Byrne2019-08-151-183/+183
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* Combine "collective group and dataset write" and "independent group andLarry Knox2019-05-031-4/+4
| | | | | dataset read" tests into one test. The second test is dependent on the file created by the first test, and will not pass when run by itself.
* Add final list of single testphdf5 testsAllen Byrne2019-05-021-208/+208
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* Fix some collective metadata read issuesJordan Henderson2019-02-121-1/+4
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* Add fix for HDFFV-10501Jordan Henderson2018-08-261-0/+3
| | | | | Add test for HDFFV-10501 fix Add release note for HDFFV-10501 fix
* Merge pull request #426 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10 to ↵Larry Knox2017-04-251-6/+4
| | | | | | | | | | hdf5_1_10 * commit '54957d37f5aa73912763dbb6e308555e863c43f4': Commit copyright header change for src/H5PLpkg.c which was added after running script to make changes. Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh. Merge pull request #407 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_1 to hdf5_1_10_1 Change copyright headers to replace url referring to file to be removed and replace it with new url for COPYING file.
* Final merge of page buffering branch to developQuincey Koziol2017-03-141-0/+5
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* [svn-r30270] Fix an issue that could occur when allocating a chunked dataset ↵Neil Fortner2016-08-081-0/+5
| | | | | | | | | in parallel, with an alignment threshold set to be larger than the chunk size but smaller than the size of the small data aggregator. Tested: koala, ostrich (h5committest); jelly, ummon
* [svn-r30201] Description:Quincey Koziol2016-07-181-0/+4
| | | | | | | | | Switch test framework to dynamically allocate the testing array, and expand the length of the description field. Tested on: MacOSX/64 10.11.5 (amazon) w/serial & parallel (h5committest forthcoming)
* [svn-r30112] Description:Quincey Koziol2016-06-281-1/+1
| | | | | | | | | | Move updated flush dependency code in metadata cache from revise_chunks branch to trunk. Also many of the cleanups from r30111 in the revise_chunks branch. Tested on: MacOSX/64 10.11.5 (amazon) w/serial, parallel & production (h5committest forthcoming)
* [svn-r29880] Add HD to sleep function callsAllen Byrne2016-05-041-1/+1
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* [svn-r29088] - Add a test for retrieving the property values for the new ↵Mohamad Chaarawi2016-02-111-0/+3
| | | | | | | | | coll md functions. - ifdef some code that don't need to be built in parallel - more minor enhancements tested on bb-8 with parallel and serial
* [svn-r29079] rename the coll read requirement function.Mohamad Chaarawi2016-02-101-1/+1
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* [svn-r29077] Description:Quincey Koziol2016-02-101-2/+3
| | | | | | | | Normalize against the trunk, in preparation for final merge. Tested on: MacOSX/64 10.11.3 (amazon) w/serial & parallel (h5committest not required on this branch)
* [svn-r28959] merge from trunk.Mohamad Chaarawi2016-01-221-1/+0
|\ | | | | | | renaming metadata dxpl properties.
* | [svn-r28649] - add new API to toggle collective metadata write.Mohamad Chaarawi2015-12-141-1/+3
| | | | | | | | | | - set default to FALSE - fix some bugs.
* | [svn-r27929] merge from trunk.Mohamad Chaarawi2015-10-011-1/+1
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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-r27261] apply metadata enhancement patch that was based on the mdc 3 ↵Mohamad Chaarawi2015-06-211-0/+2
|/ | | | branch.
* [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)
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