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* removed the use of encoded single apostrophe (#3261)Scot Breitenfeld2023-07-2011-44/+44
| | | | | | * removed the use of encoded single apostrophe, and fix H5Dread_chunk from write to read * updated sanitizer paragraph * fixed brief description for H5Fget_info
* changed the scope of #ifdef DOXYGEN to now include H5D multi-functions (#3254)Scot Breitenfeld2023-07-181-2/+3
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* Fixed more warnings about extra semicolons (#3249)Sean McBride2023-07-187-56/+56
| | | | | | | * Require semi-colon after H5_CHECK_OVERFLOW calls Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* addresses compilation fortran warnings on Frontier (#3236)Scot Breitenfeld2023-07-1216-20/+12
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* Remove programmer/date from comments (#3210)Dana Robinson2023-06-2930-1774/+6
| | | | * Removes Programmer: and Date: fields * Fixes a few Modifications: fields leftover from previous work
* Remove HD/hbool_t from fortran (#3182)Dana Robinson2023-06-2818-254/+254
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* Fixed check for a VOL's async compatibility (#3164)Scot Breitenfeld2023-06-221-4/+6
| | | | | * cap flag fix in test * added async comp. output
* Print out the VOL connector being used in the ASYNC test (#3016)Scot Breitenfeld2023-06-058-97/+386
| | | | | * Print out the VOL connector being used in the ASYNC test * Add h5pget_vol_cap_flags_f with test
* Convert H5F haddr_t macros to H5 (#3039)Dana Robinson2023-06-051-1/+1
| | | | | | | | | | | | | | | | | | | | | | Several macros for handling haddr_t values exist in H5Fprivate.h and have H5F prefixes, even though they have nothing to do with a particular file (e.g., H5F_addr_lt()). These macros have been moved to H5private.h and renamed to have an H5 prefix. Affected macros: H5F_addr_overflow H5F_addr_defined H5F_addr_eq H5F_addr_ne H5F_addr_lt H5F_addr_le H5F_addr_gt H5F_addr_ge H5F_addr_cmp H5F_addr_overlap H5F_addr_pow2 was unused and removed instead of converted.
* Fixed Fortran Doxygen warnings (#3017)Scot Breitenfeld2023-05-268-94/+104
| | | | Fixes Fortran doxygen warnings, #2998
* fixed GNU 4.8.5 compilation issue with C_LOC and strings (#2996)Scot Breitenfeld2023-05-231-2/+2
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* Updated H5Ovisit_f and H5Ovisit_by_name_f wrappers internals. (#2987)Scot Breitenfeld2023-05-227-171/+72
| | | | | | | | | * * Removed C wrappers for H5Ovisit_f and H5Ovist_by_name_f, modifying the Fortran source accordingly. * The intent for op_data was declared INOUT, even though the pointer address INTENT is, in actuality, IN. gfortran was optimizing out op_data in tests where the values were repeatedly reset to the same value. The values were reset in the test because the data the pointer targeted was updated in the callback. * Made use of the 'verify' function to check value correctness. * changed to useing INTEGER(C_INT) instead of C_BOOL, updated the documentation
* Fix 'datatype' misspellings ('dataype') (#2984)Dana Robinson2023-05-191-1/+1
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* Fixes failures with gfortran 4.8 (#2979)Scot Breitenfeld2023-05-183-19/+25
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* Updated INTENT to IN for C_PTR types dummy args. (#2961)Scot Breitenfeld2023-05-178-133/+133
| | | | * Changed to INTENT(IN) for C_PTR dummy args since it refers to whether C_PTR can be changed and does not relate to the INTENT state of the target.
* added missing H5ES function DLLs (#2969)Scot Breitenfeld2023-05-172-0/+21
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* addresses gfortran issue https://gcc.gnu.org/bugzilla/show_bug.cgi?id=109861 ↵Scot Breitenfeld2023-05-152-9/+9
| | | | (#2957)
* Fix CMake generator expression syntax (#2909)Allen Byrne2023-05-053-16/+16
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* Remove references to old MANIFEST file (#2890)jhendersonHDF2023-05-031-1/+0
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* Fixed test failure for when REAL is promoted via a compiler flag (#2873)Scot Breitenfeld2023-05-022-13/+14
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* Add Fortran Selection IO APIs (#2864)Scot Breitenfeld2023-05-018-50/+407
| | | new selection IO fortran APIs with tests
* Remove "the the" from comments and docs (#2865)Dana Robinson2023-05-015-13/+13
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* Remove unused variable warning (#2828)H. Joe Lee2023-04-281-1/+1
| | | Polaris FORTRAN compiler reported the unused variable warning.
* Added Fortran Async APIs (#2715)Scot Breitenfeld2023-04-2139-2666/+6146
| | | H5A, H5D, H5ES, H5G, H5F, H5L and H5O async APIs were added.
* Comment cleanup (#2689)Quincey Koziol2023-04-118-34/+0
| | | * Clean up content and redundant logging in comments.
* Make sure that ONLY_SHARED_LIBS option is correctly set (#2544)Allen Byrne2023-03-132-14/+14
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* Fix new codespell issues (#2521)Mark Kittisopikul2023-03-082-2/+2
| | | | | * Fix new codespell issues * Have codespell ignore ./config/sanitizer/sanitizers.cmake
* CMake generated pkg-config file is incorrect #2259 (#2476)Allen Byrne2023-02-171-2/+6
| | | | | | | | | | | | | * CMake generated pkg-config file is incorrect #2259 * Fix fortran pc template * hdf5.pc is incorrect for debug builds #1546 * Correct pkg name and lib name * Fix typo * Fix missing space
* Pass-through connector testing flexibility (#2399)Quincey Koziol2023-01-091-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | * Correct concurrency bugs when running tests, along with a bugfix & small warning cleanup. * Committing clang-format changes * Allow spaces (and tabs) in VOL connector info string from environment variable. * Parse connector name from HDF5_PLUGIN_PATH environment variable better * Correct H5VLquery_optional to use H5VL routine instead of H5I. Also add an error message to the failure return value from not finding a plugin. * Play nice with existing plugin paths * Use API routine to determine if native connector is terminal. * Committing clang-format changes * Make string size larger, to allow for connectors with longer names. * Be more flexible about testing external pass through connectors, especially if they have registered new optional operations. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: AWS ParallelCluster user <ec2-user@ip-10-0-0-65.us-east-2.compute.internal> Co-authored-by: Koziol <qkoziol@88665a374c70.ant.amazon.com>
* Update FORTRAN VOL connector test for external pass-through testing (#2393)Quincey Koziol2023-01-051-1/+3
| | | | | | | | | | | | | | | | | * Correct concurrency bugs when running tests, along with a bugfix & small warning cleanup. * Committing clang-format changes * Allow spaces (and tabs) in VOL connector info string from environment variable. * Parse connector name from HDF5_PLUGIN_PATH environment variable better * Correct H5VLquery_optional to use H5VL routine instead of H5I. Also add an error message to the failure return value from not finding a plugin. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: AWS ParallelCluster user <ec2-user@ip-10-0-0-65.us-east-2.compute.internal> Co-authored-by: Koziol <qkoziol@88665a374c70.ant.amazon.com>
* Fix doxygen warnings and remove javadocs (#2324)Allen Byrne2022-12-201-25/+0
| | | | | * Fix doxygen warnings and remove javadocs * fix typo
* 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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