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* Multi Dataset (#2120)Neil Fortner2022-10-191-0/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* renamed H5_FORTRAN_C_LONG_DOUBLE_IS_UNIQUE DLL (#2158)Scot Breitenfeld2022-10-131-1/+1
| | | * changed DLL define to a unique name
* Fix for missing h5dfill_c_long_double in dll (#2155)Scot Breitenfeld2022-10-121-1/+1
| | | * added conditionally include h5dfill_c_long_double in dll
* Implemented C matching (and general) H5Dfill Fortran wrappers (#2152)Scot Breitenfeld2022-10-111-1/+5
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* Subfiling Fortran wrapper work. (#2143)Scot Breitenfeld2022-10-061-0/+6
| | | | | | | | | | | | | | | | | * 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
* removed H5R interface definition (#2090)Scot Breitenfeld2022-09-141-1/+1
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* removed h5rget_object_type_f module interface (#2057)Scot Breitenfeld2022-08-231-1/+1
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* Squash merge of file locking fixesDana Robinson2020-08-031-0/+2
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* HDFFV-11018 Add Fortran H5F_LIBVER_V*_F definitionsM. Scot Breitenfeld2020-02-101-0/+1
| | | | | | | | | | | | | | | | | | | Added ------ New Definitions: INTEGER :: H5F_LIBVER_ERROR_F INTEGER :: H5F_LIBVER_NBOUNDS_F INTEGER :: H5F_LIBVER_V18_F INTEGER :: H5F_LIBVER_V110_F INTEGER :: H5F_LIBVER_V112_F INTEGER :: H5F_LIBVER_V114_F New API: h5pget_libver_bounds_f(fapl_id, low, high, hdferr) Removed: call to C wrapper h5pset_libver_bounds_c in h5pset_libver_bounds_f
* Introduce new H5VL _by_value routinesJordan Henderson2020-01-291-1/+3
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* Squashed commit of the token_refactoring branch:Dana Robinson2020-01-161-1/+3
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* added H5Pset_volM. Scot Breitenfeld2019-05-221-0/+2
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* removed VOLL NULL connector and replaced it with native VOLM. Scot Breitenfeld2019-05-161-1/+0
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* Merge branch 'develop' into H10621M. Scot Breitenfeld2019-04-241-0/+1
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| * Fix fortran omissionAllen Byrne2019-04-151-0/+1
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* | Merge branch 'develop' into H10621M. Scot Breitenfeld2019-03-071-0/+5
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| * Merge pull request #1409 in HDFFV/hdf5 from ~BRTNFLD/hdf5_msb:J10443 to developScot Breitenfeld2019-01-081-0/+1
| |\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit 'b4d4d371a03158c39f120b1bde6c4bd51f1b2eb6': HDFFV-10443: Add "field" parameter to H5Oinfo* and H5Ovisit* APIs. Added chunked dataset, H5S_ALL test typo typo updated defined constants Documented HDFFV-10652 HDFFV-10652 Implemented a process-0 read and then broadcast for collective read of full datasets (H5S_ALL) by all the processes in the file communicator. Removed reason for breaking read-proc0-and-bcast switched to using CX instead of a global var. HDFFV-10652 Implemented a process-0 read and then broadcast for collective read of full datasets (H5S_ALL) by all the processes in the file communicator.
| | * HDFFV-10443: Add "field" parameter to H5Oinfo* and H5Ovisit* APIs.Scot Breitenfeld2019-01-081-0/+1
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| * | Fortran wrappers for dataset obj header minimization API calls.Dana Robinson2019-01-081-0/+4
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* | Implemented VOL APIs and C constants, no testsScot Breitenfeld2018-12-071-3/+7
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* | initial API impl.Scot Breitenfeld2018-12-071-0/+5
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* VOL FEATUREDana Robinson2018-10-101-0/+1
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* [svn-r29155] HDFFV-9652: Add fortran wrappers/test for collective metadata ↵Scot Breitenfeld2016-02-191-0/+4
| | | | | | functions Tested: h5committest.new
* [svn-r29062] HDFFV-9564: Implement VDS Fortran wrappers.Scot Breitenfeld2016-02-081-0/+12
| | | | Tested: h5committest.new
* [svn-r27592] Added dll for H5DGET_OFFSET_FScot Breitenfeld2015-08-271-0/+1
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* [svn-r27525] Added missing H5A_mp_H5AREAD_PTR and H5A_mp_H5AWRITE_PTR ↵Scot Breitenfeld2015-08-191-0/+2
| | | | definitions.
* [svn-r27493] Trying again to merge the F2003_v1.10 branch to the trunk.Scot Breitenfeld2015-08-111-207/+65
| | | | Tested: h5committest --PASSED--
* [svn-r27489] reverted merge of branchScot Breitenfeld2015-08-111-65/+207
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* [svn-r27385] H5Dwrite,H5Dread,H5Awrite,H5Dread for INTEGERs and Characters ↵Scot Breitenfeld2015-07-141-44/+0
| | | | are now generated code
* [svn-r27384] H5Dwrite and H5Awrite for INTEGERs are now generated codeScot Breitenfeld2015-07-141-16/+0
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* [svn-r26968] Removed H5A,H5D and H5P declarations which now use the KIND ↵Scot Breitenfeld2015-04-291-117/+0
| | | | findings.
* [svn-r26915] Added missing long_double APIs.Scot Breitenfeld2015-04-231-1/+0
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* [svn-r26895] Added missing interfaces for c_double_long.Scot Breitenfeld2015-04-231-53/+59
| | | | Added DLLs.
* [svn-r26893] added c_long_double interfaces and updated DLLsScot Breitenfeld2015-04-221-140/+236
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* [svn-r26866] Removed the default REAL and DOUBLE PRECESION dependency.Scot Breitenfeld2015-04-211-66/+0
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* [svn-r26512] Reverted changed 26488 and 26477Scot Breitenfeld2015-03-201-280/+0
| | | | Tested: h5committest
* [svn-r26477] Removed COMMON and EQUIVALENCE usage from Fortran Source. Scot Breitenfeld2015-03-191-0/+280
| | | | | | | | | Also removed disabling shared when building Fortran on the Mac. These fixes should fix all the building shared with Fortran problems. HDF5-247 Also fixes array bounds starting from zero in H5Pff.f90 routines. Tested: h5committest
* [svn-r26233] Disable h5tenum_insert_f if F2003 is enabled.Scot Breitenfeld2015-02-191-1/+1
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* [svn-r26217] Added H5T_PROVISIONAL_mp_H5TENUM_INSERT_FScot Breitenfeld2015-02-181-1/+1
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* [svn-r26214] Fix for HDFFV-8908:Scot Breitenfeld2015-02-181-0/+2
| | | | h5tenum_insert_f does not work with default 8 byte integers (xlf compiler)
* [svn-r25113] Fixed Subversion EOL and executable attributes. No code changes.Dana Robinson2014-04-251-572/+572
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* [svn-r24939] Fix for HDFFV-8309 Fortran wrappers for H5Pget/set_file_image ↵Scot Breitenfeld2014-04-011-0/+2
| | | | | | | functions Tested: jam (gnu, intel, pgi)
* [svn-r24864] Description:Quincey Koziol2014-03-211-2/+0
| | | | | | | | | | | | | | | | | | 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-r23462] Added definition for h5kind_to_typeScot Breitenfeld2013-03-271-0/+1
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* [svn-r23293] Fix for HDFFV-8268: Fortran wrapper for H5Fget_file_image function.Scot Breitenfeld2013-02-181-0/+1
| | | | Tested: (jam, gnu,intel compilers)
* [svn-r23066] HDFFV-8265: create .def file during configure, added F2003 ↵Allen Byrne2012-11-291-8/+26
| | | | | | optional functions and refactor ISO_C_BINDING usage in cmake files Tested: local cmake
* [svn-r23057] HDFFV-8265: create .def file during configureAllen Byrne2012-11-271-0/+552
Tested: windows
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