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* Multi Dataset (#2120)Neil Fortner2022-10-191-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Fix bug with cross platform compatibility of references within vlens. No testing yet. * Merge from multi_rd_wd_coll_io to a more recent branch from develop. Untested, probably does not work yet. * Committing clang-format changes * Committing clang-format changes * Fix many bugs in multi dataset branch. Mostly works, some issues in SWMR tests. * Committing clang-format changes * Disable test in swmr.c that was failing due to bug in HDF5 unrelated to multi dataset. * Committing clang-format changes * Fixed fortran multi-dataset tests * Fixed xlf errors * Added benchmark code for multi-datasets * loops over datasets * added missing error arg. * Added gnuplot formatting * Jonathan Kim original MD benchmarking code * updated MD benchmarking code * code clean-up * Only make files in feature test mode * misc clean-up * removed TEST_MDSET_NO_LAST_DSET_2ND_PROC option * Committing clang-format changes * Change multi dataset API to use arrays of individual parameters instead of the parameter struct. * Committing clang-format changes * Update to new multi dataset Fortran API and tests. (#1724) * Update to new multi dataset Fortran API and tests. * Sync Fortran with develop. * skipping h5pget_mpio_actual_io_mode_f for now * Fixed issue with dxpl_id, changed to variable size dim. (#1770) * Remove "is_coll_broken" field from H5D_io_info_t struct * Committing clang-format changes * Minor cleanup in multi dataset code. * Committing clang-format changes * Clean up in multi dataset code. * Committing clang-format changes * Committing clang-format changes * Fix speeling * Fix bug in parallel compression. Switch base_maddr in io_info to be a union. * Committing clang-format changes * Implement selection I/O support with multi dataset. Will be broken in parallel until PR 1803 is merged to develop then the MDS branch. * Committing clang-format changes * Spelling * Fix bug in multi dataset that could cause errors when only some of the datasets in the multi dataset I/O used type conversion. * Committing clang-format changes * Integrate multi dataset APIs with VOL layer. Add async versions of multi dataset APIs. * Committing clang-format changes * Spelling fixes * Fix bug in non-parallel HDF5 compilation. * Committing clang-format changes * Fix potential memory/free list error. Minor performance fix. Other minor changes. * Committing clang-format changes * Fix memory leak with memory dataspace for I/O. * Committing clang-format changes * Fix stack variables too large. Rename H5D_dset_info_t to H5D_dset_io_info_t. * Committing clang-format changes * Remove mem_space_alloc field from H5D_dset_io_info_t. Each function is now responsible for freeing any spaces it adds to dset_info. * Committing clang-format changes * fixed _multi Fortran declaration * Refactor various things in (mostly) the serial I/O code path to make things more maintainable. * Committing clang-format changes * updated to array based, doxygen, and examples * Reinstate H5D_chunk_map_t, stored (via pointer) inside H5D_dset_io_info_t. * Change from calloc to malloc for H5D_dset_io_info_t and H5D_chunk_map_t. Switch temporary dset_infos to be local stack variables. * Committing clang-format changes * format cleanup * format cleanup * added coll and ind * Modify all parallel I/O paths to take dset_info instead of assuming dset_info[0]. * Committing clang-format changes * fixed output * Rework parallel I/O code to work properly with multi dataset in more cases. Fix bug in parallel compression. * Committing clang-format changes * Prevent H5D__multi_chunk_collective_io() from messing up collective opt property for other datasets in I/O. Other minor cleanup. Add new test case to t_pmulti_dset.c for H5FD_MPIO_INDIVIDUAL_IO, disabled for now due to failures apparently unrelated to multi dataset code. * Fix spelling * Committing clang-format changes * Replace N log N algorithm for finding chunk in H5D__multi_chunk_collective_io() with O(N) algorithm, and remove use of io_info->sel_pieces in that function. * Committing clang-format changes * Replace sel_pieces skiplist in io_info with flat array of pointers, use qsort in I/O routine only when necessary. * Committing clang-format changes * Add new test case to mdset.c * Committing clang-format changes * Fix spelling * Very minor fix in H5VL__native_dataset_read() * Fix bug that could affect filtered parallel multi-dataset I/O. * Add RM entries for H5Dread_multi(), H5Dread_multi_async(), H5Dwrite_multi(), and H5Dwrite_multi_async() * Unskip test in swmr.c * Committing clang-format changes * Eliminate H5D__pre_read and H5D__pre_write * Remove examples/ph5mdsettest.c. Will fix and re-add as a test. * Enable hyperslab combinations in mdset test * Committing clang-format changes * Clarify H5Dread/write_multi documentation. * Fix bugs in multi-dataset I/O. Expand serial multi dataset test. Update macro in parallel multi dataset test. * Committing clang-format changes * Spelling * Remove obsolete entry in bin/trace * Rework type conversion buffer allocation. Only one buffer is shared between datasets in mdset mode, and it is malloced instead of calloced. * Committing clang-format changes * Fix bug in error handling in H5D__read/write * added multi-dataset fortran check with optional dataset creation id (#2150) * removed dup. dll entry * Address comments from code review. * Remove spurious changes in H5Fmpi.c * Fix issue with reading unallocated datasets in multi-dataset mode. Address other comments from code review. * Committing clang-format changes * Delay chunk index lookup from io_init to mdio_init so it doesn't add overhead to single dataset I/O. * Committing clang-format changes * Fix inappropriate use of piece_count * updated copyright on new file, removed benchmark from testing dir. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: M. Scot Breitenfeld <brtnfld@hdfgroup.org> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Subfiling Fortran wrapper work. (#2143)Scot Breitenfeld2022-10-061-3/+41
| | | | | | | | | | | | | | | | | * added C ref. for Fortran constants * added C ref. for Fortran constants * move constant paramters to H5* module listing * added back comment * Fortran subfiling and ioc FD with tests. H5Pset/get_mpi_params wrappers with tests, misc.. parallel test clean-up. * misc. fixes * fixed CMake testpar issues, formatted, misc. updates * updated tests
* Update CMake code to 3.18 minimum version (#2080)Allen Byrne2022-09-031-1/+1
| | | | | * Update CMake code to 3.18 minimum version * Updated release note
* changes parallel tests to .F90 ext. and fixes the CALL check strings (#1725)Scot Breitenfeld2022-05-041-3/+3
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* Flag construction must be after compiler detectionAllen Byrne2020-04-051-7/+5
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* TRILAB-192 add c++ and fortran warnings build systems one fileAllen Byrne2020-04-051-4/+2
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* TRILAB-142 Change minimum CMake version to 3.12Allen Byrne2020-02-211-1/+1
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* HDFFV-11011 - merge include listAllen Byrne2020-01-291-2/+1
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* HDFFV-11011 correct issues with target file extensionAllen Byrne2020-01-281-12/+31
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* HDFFV-11001 Add fine control over testingAllen Byrne2020-01-151-1/+3
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* Add missing module_dir propertyAllen Byrne2018-05-091-0/+1
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* Correct command usageAllen Byrne2018-05-071-1/+1
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* Remove APPENDAllen Byrne2018-05-031-1/+1
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* Revert to old style for LINK_FLAGS gen expr not workingAllen Byrne2018-05-031-6/+9
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* LINK_FLAGS must be separate property setsAllen Byrne2018-05-031-3/+6
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* Fix link flags syntaxAllen Byrne2018-05-031-3/+3
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* Revert refactor link flagsAllen Byrne2018-05-021-3/+3
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* refactor link flags to interfaceAllen Byrne2018-05-021-3/+3
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* TRILABS-19 Link flags need - characterAllen Byrne2018-05-021-1/+1
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* TRILABS-19 Refactor fortran propertiesAllen Byrne2018-04-301-10/+18
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* TRILABS-19 remove add_defintions and use generator expressionsAllen Byrne2018-04-261-1/+1
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* TRILABS-20 set a compiler name on all project commandsAllen Byrne2018-04-201-1/+1
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* Change CMake min to 3.10Allen Byrne2018-03-091-1/+1
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* Inc CMake min, Add new tests, rework test CMake filesAllen Byrne2018-02-271-1/+1
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* HDFFV-10385 rework java namesAllen Byrne2018-01-171-1/+0
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* Correct usage of MPI varsAllen Byrne2017-11-011-2/+2
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* mpich module file is in env varAllen Byrne2017-02-241-1/+1
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* Add MPI_Fortran variablesAllen Byrne2017-02-171-2/+2
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* Update cmake min version and cmake command conventionAllen Byrne2017-01-101-3/+3
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* [svn-r27465] Merge dual-binary CMake changesAllen Byrne2015-08-051-3/+3
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* [svn-r26594] Merge macros and fortran changes from dual_binary feature.Allen Byrne2015-03-251-2/+3
| | | | Tested: local linux
* [svn-r26208] Update cmake minimumsAllen Byrne2015-02-181-1/+1
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* [svn-r24789] Bump up the minimum cmake versionAllen Byrne2014-03-131-1/+1
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* [svn-r24781] HDFFV-8700 -Allen Byrne2014-03-111-8/+8
| | | | | | | KitWare recommendations: Change CMake commands to lower case. Remove INCLUDE_DIRECTORIES in src for target level includes. Change ADD_DEFINITIONS package debug defines into CMake option. Remove -DNDEBUG
* [svn-r24029] Move TESTS to seperate file to allow easier editing by all ↵Allen Byrne2013-08-191-1/+1
| | | | | | developers. Tested: local linux
* [svn-r23745] HDFFV-8461: Add Windows /MT supportAllen Byrne2013-06-101-1/+1
| | | | This adds the UserMacros.cmake support needed.
* [svn-r23160] HDFFV-8227: Mac DARWIN requires CMake 2.8.10Allen Byrne2013-01-141-1/+1
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* [svn-r21804] Update CMake Required version in all folders to match current ↵Allen Byrne2011-12-051-1/+1
| | | | standard 2.8.6
* [svn-r21710] CMake FindMPI module changed to look for fortran libs. Cmake ↵Allen Byrne2011-11-031-0/+1
| | | | | | | | files updated to link with fortran mpi libs. Updated cacheinit.cmake to set num of procs to 3 for hdf testing. Tested: local linux and on windows 7
* [svn-r21667] Update FOLDER solution option for target properties. Added ↵Allen Byrne2011-10-251-0/+1
| | | | | | OPTION command for solution folder and no packaging. Tested: local linux
* [svn-r20153] Move ext lib handling for ext project building to a common ↵Allen Byrne2011-02-241-1/+1
| | | | | | macro. Update HDF5 project to use HDFMacros.cmake file. Add test properties for test ordering. Tested: local linux, windows
* [svn-r20141] Bring 1.8 r20139 cmake and windows changes to trunkAllen Byrne2011-02-221-5/+0
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* [svn-r19909] Change how LINK_FLAGS for fortran are appended on WindowsAllen Byrne2011-01-051-1/+1
| | | | bring r19908 from 1.8 branch
* [svn-r19907] Windows: Correct how fortran links in CRT library. Also correct ↵Allen Byrne2011-01-041-1/+1
| | | | | | macro use for checking libtype. bring r19906 from 1.8 branch
* [svn-r19509] Improve CMake support for CYGWIN.Allen Byrne2010-10-041-5/+3
| | | | | | Correct script comment in testh5diff.sh Tested: Windows Cygwin
* [svn-r19361] Move Windows specific compile and link flags to macrosAllen Byrne2010-09-091-12/+1
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* [svn-r19325] Added parallel build commands.Allen Byrne2010-08-311-0/+49
Corrected use/name of source folder aliases. Duplicated FindMPI.cmake so that non-c++ compiler is found first (recommemded commands did not work). Tested: local linux with mpich
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