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* Update copyright headers (#2184)Larry Knox2022-11-011-1/+0
| | | | | * Updated source file copyright headers to remove "Copyright by the Board of Trustees of the University of Illinois", which is kept in the top-level COPYING file.
* Fix typos found in the rest of the hdf5 code-base (#1985)luzpaz2022-08-101-1/+1
| | | | | | | | | | | * Fix typos found in the rest of the hdf5 code-base * Typo in tool.cmake * Revert "Typo in tool.cmake" This reverts commit 06b8403d99757c7d20f1eed530cf317c3d84de4b. * Fix clang-format styling
* Develop clang 13 format (#1933)Allen Byrne2022-07-261-2/+2
| | | | | * Update format source to clang 13 * More format changes
* Merge initial version of selection I/O feature into develop (#1367)Neil Fortner2022-03-261-1/+4
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* Fixed Spelling Errors (#1166)Scot Breitenfeld2021-12-071-8/+8
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * fixed missed closing of a dataset * fixed missed closing of a dataset * fixed typo in error return * Committing clang-format changes * minor edits * code format * Committing clang-format changes * code format * minor edit * switched from using MPI_count, to actual bytes written for H5FD_mpio_debug rw debugging * Committing clang-format changes * changed size_i in printf to reflect the I/O. * Committing clang-format changes * Fixed seg fault with xlf on BE with -qintsize=8 * fixed error function string * spelling corrections via codespell, added new spell check github actions * Committing clang-format changes * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * Committing clang-format changes * misc * misc * misc * misc * misc * misc * Committing clang-format changes * misc * work around for https://github.com/codespell-project/codespell/issues/2137 * misc * added missing file * misc * misc. * misc * switch to using Codespell with GitHub Actions * misc. * misc. * fixed more sp errors * Fix new typos found by codespell. * fixed proceed with precede * fixed variable in fortran test * fixed minnum * updated spelling list Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* 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.
* Clang-format of source filesAllen Byrne2020-09-301-607/+584
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* Trim trailing whitespaceQuincey Koziol2020-04-201-1/+1
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* squash cast warning fixkmu2020-01-231-15/+15
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* remove unsed var,function,macro, etckmu2019-12-061-1/+0
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* OESS-29 Update HD prefix mostlyAllen Byrne2019-08-241-15/+15
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* 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.
* [svn-r25573] fix error output when dataset verify detects wrong data.Mohamad Chaarawi2014-09-051-1/+1
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* [svn-r24864] Description:Quincey Koziol2014-03-211-3/+2
| | | | | | | | | | | | | | | | | | 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-r24772] Description:Quincey Koziol2014-03-101-6/+6
| | | | | | | Correct some dynamically sized arrays that fail on Windows. Tested on: Mac OSX/64 10.9.2 (amazon) w/parallel
* [svn-r24769] Description:Quincey Koziol2014-03-071-84/+317
| | | | | | | | | Check in Mohamad's changes to support collective I/O on point selections, along with some other minor cleanups. Tested on: Mac OSX/64 10.9.2 (amazon) w/parallel & serial (h5committest forthcoming)
* [svn-r24380] The parallel test code now uses HDfree, HDmalloc, and HDcallocDana Robinson2013-10-311-5/+5
| | | | | | | | | | | exclusively. Part of the preparation for a fix for HDFFV-8551. Tested on: 32-bit LE linux (jam) w/ parallel and Fortran. There are no behavior changes, so testing was minimal.
* [svn-r22992] Purpose:Jonathan Kim2012-10-301-23/+13
| | | | | | | | | | | 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-r16560] Description:Quincey Koziol2009-03-101-77/+24
| | | | | | | | | | Remove another call to H5E_clear_stack() from within the library. Clean up lots of compiler warnings. Tested on: Mac OS X/32 10.5.6 (amazon) (followup on other platforms forthcoming)
* [svn-r15800] Description:Quincey Koziol2008-10-071-2/+2
| | | | | | | | | | | | | | | | | | | | | | | Bring file free space branch changes through r15795 into trunk, which includes a fair bit of code cleanup & rearrangement along with a couple of bug fixes also. Tested on: Mac OS X/32 10.5.5 (amazon) in debug mode Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) 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-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
* [svn-r15628] Description:Quincey Koziol2008-09-161-52/+52
| | | | | | | | | | | | | 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-r15627] This check-in fixes a bug inside parallel HDF5 testsuite.MuQun Yang2008-09-161-2/+22
| | | | | | | | | When enable-debug is turned on, a special macro block H5_HAVE_INSTRUMENTED_LIBRARY inside HDF5 will be executed to check if some collective chunk IO test cases are being run with the correct settings(one link, multiple chunk etc.). However,when complicated derived datatype in some mpi-io packages are not supported, the library has to switch one link IO with/without the optimization to multiple chunk IO with/without the optimization. The current testsuite doesn't know this and generates a false assertion failure message. This check-in fix this problem by providing a second property to avoid the false faiure message. Tested at abe(NCSA linux cluster) and kagiso.
* [svn-r14204] Description:Quincey Koziol2007-10-121-17/+20
| | | | | | | | | | | | | | | | | | | | | | Move H5Pinsert() out of old "compat v1.6" section and into API versioning, switching internal usage to H5Pinsert2(). Add regression test for H5Pinsert1() Clean up some other minor warnings. Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode
* [svn-r14199] Description:Quincey Koziol2007-10-111-9/+9
| | | | | | | | | | | | | | | | | | | | | Add H5Dcreate to API versioned routines, replacing internal usage with H5Dcreate2 Fix thread-safe error stack initialization for API versioned error stack printing routines. Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode
* [svn-r14193] Description:Quincey Koziol2007-10-081-1/+1
| | | | | | | | | | | | | | | | | | | Make H5Dopen versioned and change all internal usage to use H5Dopen2 Add simple regression test for H5Dopen1 Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode
* [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-r12844] Description:Quincey Koziol2006-11-021-77/+77
| | | | | | | Fix parallel build failure for property list class initialization refactor. Tested on: AIX (copper) w/parallel
* [svn-r12554] New tests have been added to test the correctness of ↵MuQun Yang2006-08-091-55/+64
| | | | | | | | 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 Koziol2006-06-271-55/+55
| | | | | | | | | | | 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-r12401] Purpose:MuQun Yang2006-06-031-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | Some collective chunk IO macro names are confusing, change them to more meaningful names. Description: H5Pset_dxpl_mpio_chunk_opt will set a flag so that the library can do one linked IO or mul ti-chunk IO with collective in chunking storage directly. That is, the library won't do an alyses to determine this. The flags for the enum type we used before are: H5FD_MPIO_OPT_ONE_IO H5FD_MPIO_OPT_MULTI_IO They are not good names because of the following two reasons: 1. It doesn't reflect chunking storage 2. OPT is kind of redundant and misleading, Solution: We change the names to H5FD_MPIO_CHUNK_ONE_IO H5FD_MPIO_CHUNK_MULTI_IO Platforms tested: Since only macro names are changed, no need to test with h5committest. Misc. update:
* [svn-r12174] Purpose:MuQun Yang2006-03-291-7/+433
| | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r12148] Purpose:MuQun Yang2006-03-231-1/+31
| | | | | | | | | | | | | | | | | | | | | | | | | | | Add tests for optional APIs to support collective chunk IO Description: In order to test whether library picks up the user's options, The number of chunks need to be varied for different processes, Selection of the number of processes selected in one chunk also need to be varied. Solution: Create two cases, 1. Each chunk only selected by one unique process, this case library should use independent for collective call. 2. One-third of the processes occupies the top half of the whole domain, The rest of the processes occupies the lower half of the domain. The total number of chunk is a fixed number 8. Platforms tested: Linux 2.4 with mpich 1.2.6(only) Since I only checked in the code that handles the selection, haven't added any new tests yet. So it won't affect any platforms. Misc. update:
* [svn-r12142] Purpose:MuQun Yang2006-03-231-27/+26
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | change the array size of collective chunking features of parallel tests. Description: Previously array size for collective optimization tests including cchunk1, cchunk2, cchunk3, cchunk4, ccontw, ccontr, cschunkw, cschunkr, ccchunkw, ccchunkr are fixed, They are only valid for some good number of processors(1,2,3,4,6,8,12,16,24,32,48 etc). Recently there are more requests for parallel tests to be valid on some odd number of processes such as 5,7,11,13 etc. Solution: I change the array size to be dynamic rather than static. Now the fastest change array size is a function of mpi_size. dim2 = constant *mpi_size. After some tunings, theoretically the above tests should be valid for any number of processors. However, other parallel tests still need to be tuned. To verify the correctness of these tests, using mpirun -np 5 ./testphdf5 -b cchunk1 at heping. Platforms tested: h5committest(shanti is refused to be connected) at heping, 5 and 7 processes are used to verify the correctness. Misc. update:
* [svn-r12044] Purpose:MuQun Yang2006-03-091-1/+1
| | | | | | | | | | | | | | | Add new tests Description: Collective IO doesn't work for some platforms/mpio packages when more than one process has no contributions to IO. Solution: 1. Add a collective IO test to verify the correctness of the library when more than one process has no contributions to IO. 2. Add the similar MPI-IO test in t_mpi to help us maintain in more platforms. Platforms tested: heping, mir, copper Misc. update:
* [svn-r11951] Purpose:MuQun Yang2006-02-161-4/+66
| | | | | | | | | | | | | | | | 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-r11572] Purpose:MuQun Yang2005-10-171-182/+294
| | | | | | | | | | | | | | | 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-r11294] Purpose:MuQun Yang2005-08-251-52/+3
| | | | | | | | | | | | | | | bug fix Description: The previous version always tests with mpi-IO driver even when mpi-posix driver is set. Solution: Add the option to test mpi-posix driver for the first round collective chunk IO test. Platforms tested: IRIX64, AIX 5.1, Linux 2.4 Misc. update:
* [svn-r11245] Purpose:Quincey Koziol2005-08-131-24/+24
| | | | | | | | | | | | | | | | | | | | 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-r11067] Purpose:MuQun Yang2005-07-121-1/+5
| | | | | | | | | | | | | | | | | | 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-r10122] Purpose:Albert Cheng2005-03-021-1/+1
| | | | | | | | | | | | | | | | 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.
* [svn-r9727] Purpose:Quincey Koziol2004-12-291-27/+27
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bug Fix/Code Cleanup/Doc Cleanup/Optimization/Branch Sync :-) Description: Generally speaking, this is the "signed->unsigned" change to selections. However, in the process of merging code back, things got stickier and stickier until I ended up doing a big "sync the two branches up" operation. So... I brought back all the "infrastructure" fixes from the development branch to the release branch (which I think were actually making some improvement in performance) as well as fixed several bugs which had been fixed in one branch, but not the other. I've also tagged the repository before making this checkin with the label "before_signed_unsigned_changes". Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel & fphdf5 FreeBSD 4.10 (sleipnir) w/threadsafe FreeBSD 4.10 (sleipnir) w/backward compatibility Solaris 2.7 (arabica) w/"purify options" Solaris 2.8 (sol) w/FORTRAN & C++ AIX 5.x (copper) w/parallel & FORTRAN IRIX64 6.5 (modi4) w/FORTRAN Linux 2.4 (heping) w/FORTRAN & C++ Misc. update:
* [svn-r9358] Purpose:Quincey Koziol2004-10-041-9/+2
| | | | | | | | | | | | | | | Bug fix Description: Relax restrictions on parallel I/O to allow compressed, chunked datasets to be read in parallel (collective access will be degraded to independent access, but will retrieve the information still). Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel Solaris 2.7 (arabica) IRIX64 6.5 (modi4) h5committest
* [svn-r9071] Purpose:MuQun Yang2004-08-121-6/+19
| | | | | | | | | | | | | | | | Make collective chunk IO test more general Description: Previously collective chunk IO test is only fit for processor =4 with the dimension size to be set small; sometimes people would like to test with more than 4 processors(5,6 or more), the test therefore failed. Solution: To make the test case more general, dimensional size of the data is set to be large(right now 288 for each dimension), the disjoint hyperslab selection is re-calculated. Now the test cases should pass with 5,6 or 12 processors. Note, there is nothing wrong with the implementation of the library, it is the test case that causes the failure with the number of processor greater than 4. Platforms tested: Only at eirene, since only the test code is modified a little and it is very slow to test the parallel case. Misc. update:
* [svn-r8932] Purpose:Quincey Koziol2004-07-221-65/+72
| | | | | | | | | | | | | | | | | | | | Code cleanup Description: Clean up collective chunking code a bit. Also, add '--enable-instrument' configure flag to have a mechanism for determining that optimized operations happened correctly in the library (instead of just the "normal" way) by allowing 'flag' properties to be set outside the library and set when the "right" thing happens. This is mainly for debugging and regression checks, so we make certain we don't break optimized I/O by accident. It's enabled by default when --enable-debug is on (which is on by default in the development branch and off by default in the release branch), but can also be independently controlled with its own configure flag. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel IBM p690 (copper) w/parallel
* [svn-r8924] Purpose:MuQun Yang2004-07-211-19/+52
| | | | | | | | | | | | | | To test collective chunk IO properly. Description: See the previous message. Solution: See the previous message. Platforms tested: arabica(Sol 2.7), eirene(Linux), copper(AIX) Misc. update:
* [svn-r8907] Purpose:MuQun Yang2004-07-201-0/+449
To add collective chunk IO tests. Description: three tests are added. 1. Only one hyperslab for each process, and this hyperslab is fit in exactly one chunk. 2. non-contiguous hyperslabs in each process, these hyperslabs are fit in one chunk. 3. Single hyperslab for each process, smaller chunk is assigned. Number of chunks for every process is equal. Solution: the dataset size is set to be very small, will enlarge later. Platforms tested: AIX 5.1(copper) Misc. update:
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