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* Port VOL User Guide to doxygen (#2165)Allen Byrne2022-10-253-12/+1200
| | | | | | | | | * Port VOL User Guide to doxygen * Fix spelling * 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 Byrne2022-10-2518-40/+129
| | | | | * Implement option for using CMake GNUInstallDirs * Add release notes
* Added a test case to verify the VOL capacity flags work correctly. (#2178)raylu-hdf2022-10-251-10/+112
| | | | | | | * Added a test case to verify the VOL capacity flags work correctly. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* fixed error code returned for H5Aexits (#2180)Scot Breitenfeld2022-10-251-2/+2
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* Fix problem with variable length attributes being accessed through multiple ↵Neil Fortner2022-10-253-1/+92
| | | | | | | | | | | file handles (#2181) * Fix bug with variable length attributes being accessed through multiple file handles. * Committing clang-format changes Co-authored-by: Neil Fortner <nfortne2@localhost.localdomain> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Multi Dataset (#2120)Neil Fortner2022-10-1940-2984/+6502
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* make sure to match the debug library postfix with external cmake projects ↵Pierce Brooks2022-10-191-1/+9
| | | | and allow for zlib link name to be manually overridden (#2166)
* 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 Breitenfeld2022-10-1718-463/+463
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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
* Fix for HDFFV-10840: Instead of using fill->buf for datatype conversion (#2153)vchoi-hdfgroup2022-10-142-14/+24
| | | | | | | | | | * Fix for HDFFV-10840: Instead of using fill->buf for datatype conversion if it is large enough, a buffer is allocated regardless so that the element in fill->buf can later be reclaimed. Valgrind is run on test/set_extent.c and there is no memory leak. * Add information of this fix to release notes. Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org>
* Cleans final production mode warnings from H5Shyper.c (#2163)Dana Robinson2022-10-142-161/+249
| | | | | | | | | | | | | | | | | | | * H5S__hyper_free_span_info() returns herr_t (not checked) * Set up H5S__hyper_free_span_info() error handling * Set up H5S__hyper_free_span() error handling * Added error handling to H5S_HYPER_ADVANCE_SPAN * Handled errors in H5S__hyper_iter_get_seq_list_gen() * Added a production mode build target for -Werror * Committing clang-format changes * Updated names for -Werror checks Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 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 Breitenfeld2022-10-117-72/+398
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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 Breitenfeld2022-10-0618-34/+870
| | | | | | | | | | | | | | | | | * 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
* Fix static-cast format (#2141)Allen Byrne2022-10-041-3/+3
| | | | | * Fix static-cast format * clang format fix
* Fix mostly java warnings, and cpp cast (#2134)Allen Byrne2022-10-039-185/+204
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* Grouped the Fortran constants in Doxygen (#2136)Scot Breitenfeld2022-10-036-67/+104
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* Adds a first cut at a "getting started with HDF5 development" guide (#2137)Dana Robinson2022-10-011-0/+866
| | | | | | | | | | | | | | | | | * Added empty "getting started" markdown file * Added title and brief tour of source code * Moved platform-independence text to markdown * Added anatomy of a function documentation * Adds information on public/private/package calls and macros * Adds much getting started guide text * Fixed typos * Fixed codespell issues
* Subfiling testing fix and documentation (#2132)jhendersonHDF2022-09-305-29/+157
| | | | | | | | | * Fix a sporadic failure in Subfiling VFD tests * Subfiling VFD - add note to H5Pget_fapl_subfiling documentation Adds note about how H5Pget_fapl_subfiling only returns the original settings on a FAPL and those settings could have been modified by the Subfiling VFD's environment variables
* Misc. Fortran Doxygen updates (#2129)Scot Breitenfeld2022-09-2812-287/+377
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* Fixed an issue that could occur when combining hyperslab selections (#2122)Neil Fortner2022-09-273-2/+61
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* Added C references to Fortran constants. (#2126)Scot Breitenfeld2022-09-2716-425/+1077
| | | * added C references for Fortran APIs
* Restructure ref manual presentation (#2123)Allen Byrne2022-09-2712-167/+902
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* Add missing windows include/lib configure for StrStrIA (#2114)Allen Byrne2022-09-221-0/+7
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* Use case-insensitive comparison for headers fix #2100 (#2101)Frank Berghaus2022-09-218-2/+80
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Use case-inseneitive comparison for headers HTTP headers should be case-insensitive. Use case-insensitive string comparisons when working with HTTP header responses to ensure compatibility. * Revert "Use case-inseneitive comparison for headers" This reverts commit a02f591723506b62b7208449be6eef7122120398 * Ignore case when searching HTTP header responses Looking up the Content-Length in the header returned by S3 storage endpoints should ignore case. To guarantee portability implement a function for case-insensitive string search, because it is non-standard. * Add an _ after H5 for the strcasestr implementation It is a private function and should sport that underscore. * Remove author comment from the doc comment * Use search function defined by system if available Check whether the system provides a function implementing case insensitive string searches. Only use the custom implementation if the system does not provide the functionality. * Add tests for case-insensitive search Basic tests: - Search for empty string - Search with exact match - Search with case-insensitive match - search with no match * Enforce clang-format style Some variable definitions in the th5_system tests did not conform to clang-format's expectations. Updated the offending lines. * Correct comment describing test case * Added some spaces to please clang-format * Ignore discarding const Ask the compiler to ignore discarding the const when retunring a match from H5_strcasestr Co-authored-by: Frank Berghaus <frank.berghaus@mpcdf.mpg.de>
* Update examples reference to single-source version 2.0.1 (#2107)Allen Byrne2022-09-205-7/+7
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* Updates VOL capabilities flags (#2105)Dana Robinson2022-09-1713-56/+103
| | | | | | | | | | | | | | | * Added feature/vol_cap_flags branch to GitHub actions * Convert unsigned cap flag field to uint64_t and add flags * Committing clang-format changes * Convert unsigned cap flag field to uint64_t and add flags * Committing clang-format changes * Updates the VOL struct version number Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Use doxygen snippets for common tables (#2104)Allen Byrne2022-09-167-743/+1069
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* Subfiling VFD updates (#2106)jhendersonHDF2022-09-1618-2356/+5432
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* develop Merge doxygen from 1.12 branch (#2095)Allen Byrne2022-09-14322-14783/+38360
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* removed H5R interface definition (#2090)Scot Breitenfeld2022-09-141-1/+1
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* Fix memory bug in selection I/O (#2096)Neil Fortner2022-09-141-14/+18
| | | | | | * Fix memory bug in selection I/O * Change error messages for calls to H5I_remove() in H5FD_read/write_selection()
* Adds file locking documentation (#2084)Dana Robinson2022-09-141-0/+366
| | | | | | | | | | | | | | | * Added initial (partial) file locking document * Almost done with file locking document * Fix intro * Cleaned up text * Updated environment variable verion info * Fix typo * Fix typos
* Remove bitbucket.hdfgroup.org dependency. #2082 (#2086)Allen Byrne2022-09-072-12/+12
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* Change `test` to `example`. (#2087)H. Joe Lee2022-09-071-2/+0
| | | | | * Remove the commented line.
* Fix grammar and spelling in comment block. (#2089)H. Joe Lee2022-09-071-1/+1
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* Doxygen Fortran (#2062)Scot Breitenfeld2022-09-0720-15614/+8610
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* Updates release schedule for 2023 (#2085)Dana Robinson2022-09-043-22/+21
| | | | | * Updates release schedule for 2023 * Updates figure to put 1.13 and 1.14 on the same line
* Update CMake code to 3.18 minimum version (#2080)Allen Byrne2022-09-03105-498/+243
| | | | | * Update CMake code to 3.18 minimum version * Updated release note
* Minor changes to CMake comments, etc. (#2078)Dana Robinson2022-08-317-56/+57
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* Updates onion VFD major error codes (#2076)Dana Robinson2022-08-314-49/+49
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* Address review comments from downstream merge of #2016 (#2073)Neil Fortner2022-08-312-4/+6
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* Fix Java tests for Developer build modes (#2079)jhendersonHDF2022-08-295-5/+5
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* Tidying of configure check C code (#2077)Dana Robinson2022-08-292-172/+200
| | | | | * Tidying of configure check C code * Fixed missing endif removal
* Adds documentation for config directory (#2065)Dana Robinson2022-08-251-0/+88
| | | | | * Adds documentation for config directory * Fix spelling error
* Added VOL connector feature flag RFC. (#2064)Gerd Heber2022-08-242-0/+2
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* Fortran module directory improvements (#2060)Dana Robinson2022-08-234-2/+4
| | | | | | * 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
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