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* Committing clang-format changesfeature/select_io_chunk_cachegithub-actions2024-01-023-230/+248
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* Work in progress for chunk cache with selection I/O improvement.vchoi-hdfgroup.org2024-01-024-76/+914
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* Add 'warning density' computation to the warnhist script (#3910)Quincey Koziol2023-12-2918-136/+414
| | | | | | | | | * Add 'warning density' computation to the warnhist script, along with several cleanups to it. Add "--enable-show-all-warnings" configure (and CMake) option to disable compiler diagnostic suppression (and therefore show all the otherwise suppressed compiler diagnostics), disabled by default. Clean up a buncn of misc. warnings. Signed-off-by: Quincey Koziol <qkoziol@amazon.com>
* Implement optimized support for vector I/O in Subfiling VFD (#3896)jhendersonHDF2023-12-278-1060/+2190
| | | | | | | | | | | | Vector I/O requests are now processed within a single set of I/O call batches, rather than each I/O vector entry (tuple constructed from the types, addrs, sizes and bufs arrays) being processed individually. This allows I/O to be more efficiently parallelized among the I/O concentrator processes during large I/O requests. * Fixed some calculations and add test cases for issues spotted from review * Removed a variable that was compensating for previous miscalculations
* Added new H5G Fortran HDF5examples (#3908)Scot Breitenfeld2023-12-2227-94/+768
| | | | | | | * updated traverse example * added H5PAR success statement * skipping H5_f90_h5ex_g_traverse
* Add CMake api checks to test the new Examples folder. (#3907)Allen Byrne2023-12-2222-99/+449
| | | | | | | | | * Fix missing build-mode value * Use 110 version file only for the 1.10 library * Fix H5_LIBVER_DIR variable * Disable 1.6 API tests for now.
* Change Trouble Shooting to Troubleshooting (#3905)H. Joe Lee2023-12-221-1/+1
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* Doc versions (#3903)Gerd Heber2023-12-2112-60/+315
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Added missing \since tags to H5D. * Committing clang-format changes * Fixed H5T version info. * Committing clang-format changes * Added missing version info to H5E. * Committing clang-format changes * Added version info to H5F public APIs. * Committing clang-format changes * Added missing H5Z public API version info. * Added missing version info to H5G public APIs * Added missing version info to H5I public API. * Added missing version info to H5 public APIs * Committing clang-format changes * Added missing version info to H5P public APIs * Added missing version info to H5R public APIs * Fix comment error. * Committing clang-format changes --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Move Glossary to the end of docs navigation menu (#3902)H. Joe Lee2023-12-211-1/+1
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* Add VDS examples and fix non-standalone build (#3898)Allen Byrne2023-12-2160-473/+6433
| | | | | | | | * Choose a size for rdata dimension * Fix platform naming conflicts * Fix doxygen references to point within library repo
* Disable doxygen as errors for netcdf (#3900)Allen Byrne2023-12-201-1/+1
| | | * disable building doxygen for netcdf test
* Remove redundant backslash character from comment. (#3899)H. Joe Lee2023-12-201-1/+1
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* Add period(.) at the end of the sentence for consistency. (#3897)H. Joe Lee2023-12-191-1/+1
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* Add intel binaries to daily-build/release workflows (#3895)Allen Byrne2023-12-184-25/+242
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* Add variable option syncing for examples (#3885)Allen Byrne2023-12-14163-16406/+509
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* Bump the github-actions group with 4 updates (#3894)dependabot[bot]2023-12-1324-46/+46
| | | | | | Bumps the github-actions group with 4 updates: [actions/checkout](https://github.com/actions/checkout), [ossf/scorecard-action](https://github.com/ossf/scorecard-action), [github/codeql-action](https://github.com/github/codeql-action) and [actions/setup-python](https://github.com/actions/setup-python). Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Some changes to portal links when they could be found on docs.hdfgroup.org, ↵Lori Cooper2023-12-133-7/+7
| | | | | | | and changed the helpdesk link to help.hdfgroup.org (#3893) * Updated some portal links to go directly to docs.hdfgroup. * Fixed some portal and help desk links
* Feat: Hashpin sensitive dependencies on GitHub Actions and enable Dependabot ↵Diogo Teles Sant'Anna2023-12-133-14/+24
| | | | | | | | | | | | | | | to update them monthly (#3892) * feat: hashpin sensitive dependencies on GHAs Signed-off-by: Diogo Teles Sant'Anna <diogoteles@google.com> * feat: enable dependabot for monthly updates on GHA Signed-off-by: Diogo Teles Sant'Anna <diogoteles@google.com> --------- Signed-off-by: Diogo Teles Sant'Anna <diogoteles@google.com>
* Correct urls and handling of external git repos (#3890)Allen Byrne2023-12-134-11/+31
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* Correct CMake command and example packaging (#3888)Allen Byrne2023-12-082-3/+3
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* Fix build error on freebsd (#3883)Satish Balay2023-12-071-1/+1
| | | | | | | | | Fixes: checking for config freebsd12.1... no checking for config freebsd... found compiler '/home/svcpetsc/petsc-hash-pkgs/39f577/bin/mpicc' is GNU gcc-9.2.0 compiler '/home/svcpetsc/petsc-hash-pkgs/39f577/bin/mpif90' is GNU gfortran-9.2.0 stdout: .: cannot open ./config/classic-fflags: No such file or directory
* Updated URL in funding.yml (#3882)Lori Cooper2023-12-041-1/+1
| | | Using new shortened URL, might look better.
* Update examples with 1.6 api and static libs (#3874)Allen Byrne2023-11-298-38/+98
| | | | | | | * Update examples with 1.6 api and static libs * Only check for STATIC only builds * Do not calculate version as library has already.
* Fix h5dump segmentation fault when --vfd-value option is used (#3873)H. Joe Lee2023-11-281-1/+1
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* Develop merge examples (#3851)Allen Byrne2023-11-27694-80/+244850
| | | | | | | | | * Merge examples repo into library * Change grepTest to be more fault-tolerant * Update examples macro file * Exclude all Fortran examples from doxygen
* Fix configuration issue due to possibly empty CMake variable (#3869)jhendersonHDF2023-11-241-4/+4
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* Complete the `if command line option` sentence. (#3868)H. Joe Lee2023-11-241-1/+1
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* Fix typo in error message for `MPI_Type_dup`. (#3867)Luc Grosheintz2023-11-221-1/+1
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* Fix segfault on user compound dtype conversion callback (#3842)mattjala2023-11-222-7/+135
| | | | | | * Fix segfault on user compound conversion * Check if lib conversion func is in use
* Add HDF5_DISABLE_TESTS_REGEX option to skip tests (#3859)Allen Byrne2023-11-2243-301/+912
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* Moved the README to markdown and expanded its overview of the files, file ↵Scot Breitenfeld2023-11-214-133/+406
| | | | generation, and other Fortran wrapper development practices as mentioned in the HDF5 architectural document. I added a new figure and included the SVG file and the original xfig file it was generated from. (#3862)
* Fix typo: look -> loop (#3866)H. Joe Lee2023-11-211-1/+1
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* Do not publish compression headers or docs (#3865)Allen Byrne2023-11-213-99/+3
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* Implement selection vector I/O with collective chunk filling (#3826)vchoi-hdfgroup2023-11-164-189/+434
| | | | | | | | | | | | | | | | | * Changes for ECP-344: Implement selection vector I/O with collective chunk filling. Also fix a bug in H5FD__mpio_write_vector() to account for fixed size optimization when computing max address. * Fixes based on PR review comments: For H5Dchunk.c: fix H5MM_xfree() For H5FDmpio.c: 1) Revert the fix to H5FD__mpio_write_vector() 2) Apply the patch from Neil on the proper length of s_sizes reported by H5FD__mpio_vector_build_types() * Put back the logic of dividing up the work among all the mpi ranks similar to the original H5D__chunk_collective_fill() routine. * Add a test to verify the fix for the illegal reference problem in H5FD__mpio_write_vector().
* Change dest for doxygen (#3856)Allen Byrne2023-11-157-9/+10
| | | * Switch doxygen refs to hdf5/develop
* Fixes for CI and presets (#3853)Allen Byrne2023-11-154-11/+13
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* Add GitHub actions for testing VOL connectors (#3849)jhendersonHDF2023-11-1519-122/+1087
| | | | | | | | | | | | | | | | * Fix issue with HDF5_VOL_ALLOW_EXTERNAL CMake variable * Add initial API test workflow * Initialize parallel testing with MPI_THREAD_MULTIPLE when testing API * Add CMake variable to allow specifying a VOL connector's package name * Remove call to MPI_Init in serial API tests While previously necessary, it now interferes with VOL connectors that may need to be initialized with MPI_THREAD_MULTIPLE
* Add CMake long double cross-compile defaults (#3683)Dana Robinson2023-11-152-24/+55
| | | | | | | | | | | | | | | | | | | HDF5 performs a couple of checks at build time to see if long double values can be converted correctly (IBM's Power architecture uses a special format for long doubles). These checks were performed using TRY_RUN, which is a problem when cross-compiling. These checks now use default values appropriate for most non-Power systems when cross-compiling. The cache values can be pre-set if necessary, which will preempt both the TRY_RUN and the default. Affected values: H5_LDOUBLE_TO_LONG_SPECIAL (default no) H5_LONG_TO_LDOUBLE_SPECIAL (default no) H5_LDOUBLE_TO_LLONG_ACCURATE (default yes) H5_LLONG_TO_LDOUBLE_CORRECT (default yes) H5_DISABLE_SOME_LDOUBLE_CONV (default no) Fixes GitHub #3585
* Update Actions badges to link to relevant workflow (#3850)jhendersonHDF2023-11-141-6/+6
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* Add extra space in comments for consistency (#3852)H. Joe Lee2023-11-141-2/+2
| | | | | * Add extra space in comments for consistency * uncomment tfloatsattrs test
* Make filter unregister callbacks safe for VOL connectors (#3629)mattjala2023-11-131-44/+98
| | | | | | | | | | | | * Make filter callbacks use top-level API functions When using VOL connectors, H5I_iterate may not provide valid object pointers to its callback. This change keeps existing functionality in H5Zunregister() without using potentially unsafe pointers. * Filter callbacks use internal API * Skip MPI work on non-native VOL
* cmakedefine macro uses C comments with "#undef" (#3845)Allen Byrne2023-11-133-6/+41
| | | | * Correct CMake macro name * Use ifdef for H5_HAVE_FLOAT128 like elsewhere
* HDF5 API test updates (#3835)jhendersonHDF2023-11-1369-92235/+4626
| | | | | | | | | | | | | | | | | | | | | * HDF5 API test updates Removed test duplication from bringing API tests back into the library from external VOL tests repo Synced changes between API tests and library's tests Updated API tests CMake code to directly use and install testhdf5, testphdf5, etc. instead of creating duplicate binaries Added new h5_using_native_vol() test function to determine whether the VOL connector being used is (or the VOL connector stack being used resolves to) the native VOL connector * Remove duplicate variable
* Remove Autotools sed hack (#3848)Dana Robinson2023-11-132-6/+10
| | | | | | | | | | configure.ac contains a sed line that cleans up incorrect library flags which was added to paper over some bugs in earlier versions of the Autotools. These issues are not a problem with the current versions of the Autootols. The sed line causes problems on MacOS, so it has been removed. Fixes #3843
* Remove 1.12 from README.md (#3847)Dana Robinson2023-11-131-3/+0
| | | Also remove 1.14.3 info since that was already released.
* Correct ENV variables (#3841)Allen Byrne2023-11-111-6/+7
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* Test and document path handling of H5Lcreate_* API (#3829)mattjala2023-11-112-7/+270
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* Remove printf format warning on Windows oneAPI. (#3838)H. Joe Lee2023-11-101-1/+1
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* Add intel oneapi windows build to CI CMake (#3836)Allen Byrne2023-11-1012-98/+282
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* Disable FP exceptions in H5T init code (#3837)Dana Robinson2023-11-074-28/+54
| | | | | | | The H5T floating-point datatype initialization code can raise exceptions when handling signaling NaNs. This change disables FE_INVALID exceptions during initialization. Also removes the -ieee=full change for NAG Fortran as that shouldn't be necessary anymore. Fixes #3831
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