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* Removed the use of -commons linking option on Darwin (#3581) (#3616)Larry Knox2023-09-291-2/+0
| | | Removed the use of -commons linking option on Darwin as COMMON and EQUIVALENCE is no long used
* Sync CMake and doxygen (#3593)Allen Byrne2023-09-261-1/+1
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* Add Fortran H5ES module to deploy list (#3342)Allen Byrne2023-08-051-44/+30
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* Sync Fortran w/ develop (#3296)Dana Robinson2023-07-2729-141/+134
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* Remove "Programmer" lines (#3294)Dana Robinson2023-07-2730-1774/+6
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* Brings over most of the HD prefix removal (#3293)Dana Robinson2023-07-2714-191/+191
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* Normalizes the public headers (#3292)Dana Robinson2023-07-2711-44/+44
| | | * Also brings over the apostrophe fix
* Fixed check for a VOL's async compatibility (#3164) (#3224)Larry Knox2023-07-061-4/+6
| | | | | | | * cap flag fix in test * added async comp. output Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
* Sync fortran src files with develop (#3126)Allen Byrne2023-06-1512-214/+384
| | | * Sync fortran src files with develop
* Fix doxygen and actions - merge from develop (#3109)Allen Byrne2023-06-1310-292/+349
| | | | | | | * Update the workflows to changes in develop * Disable java for error only action * Fix Fortran doxygen * add fortran alias * Merge changes from develop to fix actions
* Fix CMake generator expression syntax (#2910)Allen Byrne2023-05-053-16/+16
| | | | | * Fix CMake generator expression syntax * Add missing quotes
* Remove references to old MANIFEST file (#2890)jhendersonHDF2023-05-031-1/+0
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* Sync 2 new develop prs to hdf5_1_14 (#2879)Larry Knox2023-05-022-13/+14
| | | | | | | | | | | | * Add bin directory to make distclean (#2872) This allows h5cc to be cleaned up * Fixed test failure for when REAL is promoted via a compiler flag (#2873) --------- Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
* Sync with develop (#2871)Dana Robinson2023-05-0213-63/+420
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* Sync with develop (#2849)Dana Robinson2023-04-281-1/+1
| | | | | | | | | Cherry pick of ea7dfcd (Change Powershell to PowerShell in docs) to 4497feb (Update H5Dget_space_status bug note to reference 1.14.0)
* Merge with develop (#2790)Dana Robinson2023-04-2247-2702/+6150
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* Make sure that ONLY_SHARED_LIBS option is correctly set (#2545)Allen Byrne2023-04-042-14/+14
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* Fix new codespell issues (#2521) (#2533)Larry Knox2023-03-102-2/+2
| | | | | | | * Fix new codespell issues * Have codespell ignore ./config/sanitizer/sanitizers.cmake Co-authored-by: Mark Kittisopikul <mkitti@users.noreply.github.com>
* 1.14 Merge Correct pkgconfig variables and libraries #2259 (#2477)Allen Byrne2023-02-171-2/+6
| | | | | | | * Merge Correct pkgconfig variables and libraries #290 * Fix typo * Fix spacing
* 1.14 Fix some doxygen warnings (#2323)Allen Byrne2022-12-211-25/+0
| | | | | | | | | | | | | | | * Fix some doxygen warnings * Remove javadocs * Fix spelling * Fix section format * Correct doxygen function name * Remove duplicate Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* fixed unclosed objects in test (#2290)Scot Breitenfeld2022-12-101-6/+10
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* Correct requires setting for pkgconfig files (#2280)Allen Byrne2022-12-071-2/+2
| | | | | * Correct requires setting for pkgconfig files * Add issue number
* Update copyright headers (#2184)Larry Knox2022-11-01106-149/+43
| | | | | * 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.
* Removed the file, func, line args in the _async APIs fpr doxygen (#2179)Scot Breitenfeld2022-10-257-24/+24
| | | | | | | | | | | | | | | | | | | | | | | | | * Removed the: file, func, line args in the _async APIs from the doxygen arguments. Documented H5ESclean. * format fixes * fixed DOXYGEN_PREDEFINED * Fixed the #ifdet logic for doxygen, added missing multi-dataset va_args * format fixes * Use H5_DOXYGEN instead of H5_DOXYGEN_FORTRAN * reordered multidataset declarations * alt. for H5Aclose_async and H5Acreate_async * made doxgyen API into seperate blocks * updated codespell * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Implement option for using CMake GNUInstallDirs (#2175)Allen Byrne2022-10-251-3/+3
| | | | | * Implement option for using CMake GNUInstallDirs * Add release notes
* Multi Dataset (#2120)Neil Fortner2022-10-1910-18/+630
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* address test failing when default real and integers are 8 bytes (#2173)Scot Breitenfeld2022-10-191-6/+17
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* changed to referencing C APIs by empty brackets (Fortran) (#2167)Scot Breitenfeld2022-10-1714-396/+396
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* Fix H5Dfill_f test (#2162)Scot Breitenfeld2022-10-144-126/+188
| | | | | | | * change to integer for legacy H5Dfill_f testing * fixed H5Dfill testing issues with promoted real and integer * updated build fortran dependencies
* renamed H5_FORTRAN_C_LONG_DOUBLE_IS_UNIQUE DLL (#2158)Scot Breitenfeld2022-10-132-2/+2
| | | * changed DLL define to a unique name
* Fix for missing h5dfill_c_long_double in dll (#2155)Scot Breitenfeld2022-10-122-1/+4
| | | * added conditionally include h5dfill_c_long_double in dll
* Implemented C matching (and general) H5Dfill Fortran wrappers (#2152)Scot Breitenfeld2022-10-116-70/+393
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* Avoid calling H5FD_subfiling_init from h5open_f. (#2149)Scot Breitenfeld2022-10-071-1/+23
| | | | | * Only call H5FD_SUBFILING if subfiling conditions are met * clang format
* Subfiling Fortran wrapper work. (#2143)Scot Breitenfeld2022-10-0616-34/+868
| | | | | | | | | | | | | | | | | * 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
* Grouped the Fortran constants in Doxygen (#2136)Scot Breitenfeld2022-10-036-67/+104
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* Misc. Fortran Doxygen updates (#2129)Scot Breitenfeld2022-09-288-283/+271
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* Added C references to Fortran constants. (#2126)Scot Breitenfeld2022-09-2716-425/+1077
| | | * added C references for Fortran APIs
* develop Merge doxygen from 1.12 branch (#2095)Allen Byrne2022-09-1413-68/+82
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* removed H5R interface definition (#2090)Scot Breitenfeld2022-09-141-1/+1
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* Doxygen Fortran (#2062)Scot Breitenfeld2022-09-0715-13813/+6865
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* Update CMake code to 3.18 minimum version (#2080)Allen Byrne2022-09-035-5/+5
| | | | | * Update CMake code to 3.18 minimum version * Updated release note
* Fortran module directory improvements (#2060)Dana Robinson2022-08-231-1/+1
| | | | | | * Removes the module directory from the Automake flags as this generated a large number of "missing include directory" warnings and is unecessary * Adds the module path to libhdf5.settings
* removed h5rget_object_type_f module interface (#2057)Scot Breitenfeld2022-08-232-12/+5
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* Corrects more Fortran warnings (#2059)Dana Robinson2022-08-232-3/+8
| | | | | | | | | * Moves -Wunused-dummy-arguments to the developer warnings since this generates a lot of spurious, unfixable noise due to things like callback wrappers * Changes the return cast in h5fget_fileno_c, fixes a comment, and comment on potential badness * Initializes a variable in tH5L_F03.F90 to quiet a 'maybe uninitialized' warning
* Quiets Fortran warnings about large arrays (#2053)Dana Robinson2022-08-221-2/+4
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* Removes cmake_ext_mod (files moved to cmake) (#2041)Dana Robinson2022-08-192-6/+6
| | | | At one time this content was a git submodule shared between several projects but that time has long passed.
* Fixes codespell issues (#2032)Dana Robinson2022-08-172-2/+2
| | | | | * Fixes codespell issues * Fixed another typo
* Fix typos found in the rest of the hdf5 code-base (#1985)luzpaz2022-08-108-60/+60
| | | | | | | | | | | * 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 cmake clean (#1971)Allen Byrne2022-08-073-5/+40
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* Develop clang 13 format (#1933)Allen Byrne2022-07-2612-66/+66
| | | | | * Update format source to clang 13 * More format changes
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