Fixes for CI and presets #3853
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Fixes for CI and presets #3853
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byrnHDF
added
Merge - To 1.14
Priority - 0. Blocker ⛔
byrnHDF
requested review from
lrknox,
derobins,
fortnern,
jhendersonHDF,
qkoziol,
vchoi-hdfgroup,
bmribler,
glennsong09,
mattjala and
brtnfld
as code owners
lrknox
approved these changes
Nov 15, 2023
jhendersonHDF
pushed a commit
to jhendersonHDF/hdf5
that referenced
this pull request
Dec 7, 2023
lrknox
pushed a commit
that referenced
this pull request
Dec 7, 2023
* Preserve MPI-I/O file hints when fapl is closed (#3755) * Fix for issue #3025: Save the MPI info in the file struct so H5Fget_access_plist() can retrieve it from there. * Add compression tests for subfiling (#3769) * Fix typo in comment (#3775) * Fixed a file handle leak in the core VFD (#3779) When opening a file with the core VFD and a file image, if the file already exists, the file check would leak the POSIX file handle. Fixes GitHub issue #635 * Fix a format string warning in the C++ examples (#3776) * Cancel running GitHub workflows on push to same PR (#3772) * Cancel running GitHub workflows on push to same PR * Remove github.sha from workflow concurrency groups * Print some messages in parallel tests on MPI rank 0 only (#3785) Avoids overly verbose output from all processes emitting progress, etc. info. * Avoid attempted use of NULL pointer in parallel compression code (#3786) The parallel compression test code tests for the case where all MPI ranks have no selection in a dataset when writing to it. Add an early exit to the code to avoid attempting to use a NULL pointer due to there being no work to do. * Don't install h5tools_test_utils test program on system (#3793) * Add Doxygen to H5FDsplitter.h (#3794) * H5FD_CURR_SPLITTER_VFD_CONFIG_VERSION * H5FD_SPLITTER_PATH_MAX * H5FD_SPLITTER_MAGIC * H5FD_splitter_vfd_config_t * H5Pset_fapl_splitter() * H5Pget_fapl_splitter() * Update Doxygen initializers & identifiers in VFDs (#3795) * Add Doxygen for all H5FD_<VFD> initializers * Add Doxygen for all H5FD_<VFD>_VALUE values * Mark H5FD_<vfd>_init() calls private in Doxygen * Fix memory corruption in 'MPI I/O FAPL preserve' test (#3806) * Fix usage of h5_clean_files in t_pflush2.c (#3807) * Fix parallel driver check in h5_fixname_real (#3808) * Fix a couple usages of MPI_Info_get (#3809) * Remove H5system.c warning on Windows oneAPI. (#3812) * Add processing of NVHPC flags in linux-gnulibc1 file (#3804) * Disable testing as tests are failing the same as in CMake * Use the current toolchain for examples as default (#3810) * Fix misc. warnings from GCC when compiling with -fsanitize=undefined (#3787) * Set NVHPC maximum optimization level to -O1 for now (#3800) * Set NVHPC maximum optimization level to -O1 for now Compiling HDF5 with NVHPC 23.5 - 23.9 results in test failures in 4 different test files that need to be resolved. Since those tests pass with an optimization level of -O1 (and -O0) and it is currently unclear whether the test failures are due to issues in HDF5 or issues in the 'nvc' compiler, set the maximum optimization level for NVHPC to -O1 until the test failures are resolved. * Disable nvhpc Java testing in CMake and amend known issues * Re-enable testing of Autotools nvhpc * Update some doxygen links to local refs (#3814) * Rework MPI Info FAPL preserve PR to use VFD 'ctl' operations (#3782) * Removed the use of C wrappers from H5P APIs. (#3824) * fix seg fault on frontier/cray * fix seg fault on frontier/cray * fix seg fault on frontier/cray * removed the use of h5pclose_c * removed the use of h5pclose_c * Fortran Wrappers H5VLnative_addr_to_token_f and H5VLnative_token_to_address_f (#3801) * Added H5VLnative_addr_to_token_f and H5VLnative_token_to_address_f * Added H5VLnative_addr_to_token_f and H5VLnative_token_to_address_f tests * Create test for H5Pget_dxpl_mpio (#3825) * Create test and add to testphdf5 * Renamed h5fuse.sh to h5fuse (#3834) * provide an alternative to mapfile for older bash * Disable FP exceptions in H5T init code (#3837) 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 * Add intel oneapi windows build to CI CMake (#3836) * Remove printf format warning on Windows oneAPI. (#3838) * Correct ENV variables (#3841) * Remove Autotools sed hack (#3848) 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 * Make filter unregister callbacks safe for VOL connectors (#3629) * 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 * Add extra space in comments for consistency (#3852) * Add extra space in comments for consistency * uncomment tfloatsattrs test * Update Actions badges to link to relevant workflow (#3850) * Add CMake long double cross-compile defaults (#3683) 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 * Updates for building and testing VOL connectors * Fix issue with HDF5_VOL_ALLOW_EXTERNAL CMake variable * 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 * Fixes for CI and presets (#3853) * Change dest for doxygen (#3856) * Implement selection vector I/O with collective chunk filling (#3826) * 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(). * Do not publish compression headers or docs (#3865) * Fix typo: look -> loop (#3866) * Moved the README to markdown and expanded its overview of the files, file 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) * Add HDF5_DISABLE_TESTS_REGEX option to skip tests (#3859) * Fix typo in error message for `MPI_Type_dup`. (#3867) * Complete the `if command line option` sentence. (#3868) * Fix h5dump segmentation fault when --vfd-value option is used (#3873) * Updated URL in funding.yml (#3882) Using new shortened URL, might look better. * Remove unused variable from unmerged changes * Update src/H5Tinit_float.c
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