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* Updated help desk URLloricooperhdf-patch-1Lori Cooper2023-12-121-1/+1
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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
* Renamed h5fuse.sh to h5fuse (#3834)Scot Breitenfeld2023-11-076-11/+17
| | | * provide an alternative to mapfile for older bash
* Create test for H5Pget_dxpl_mpio (#3825)Glenn Song2023-11-063-0/+138
| | | | * Create test and add to testphdf5
* Fortran Wrappers H5VLnative_addr_to_token_f and ↵Scot Breitenfeld2023-11-034-9/+95
| | | | | | | | | 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 * Added H5VLnative_addr_to_token_f and H5VLnative_token_to_address_f tests
* Removed the use of C wrappers from H5P APIs. (#3824)Scot Breitenfeld2023-11-036-103/+32
| | | | | | | | | | | * 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
* Rework MPI Info FAPL preserve PR to use VFD 'ctl' operations (#3782)jhendersonHDF2023-11-039-29/+95
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* Update some doxygen links to local refs (#3814)Allen Byrne2023-11-025-14/+14
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* Update NVHPC version from 23.7 to 23.9. (#3736)H. Joe Lee2023-11-022-18/+18
| | | Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Set NVHPC maximum optimization level to -O1 for now (#3800)jhendersonHDF2023-11-015-13/+75
| | | | | | | | | | | | | | * 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
* Fix misc. warnings from GCC when compiling with -fsanitize=undefined (#3787)jhendersonHDF2023-11-016-7/+17
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* Use the current toolchain for examples as default (#3810)Allen Byrne2023-11-014-1/+24
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* Add processing of NVHPC flags in linux-gnulibc1 file (#3804)jhendersonHDF2023-11-012-7/+28
| | | * Disable testing as tests are failing the same as in CMake
* Remove H5system.c warning on Windows oneAPI. (#3812)H. Joe Lee2023-11-011-2/+1
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* Fix a couple usages of MPI_Info_get (#3809)jhendersonHDF2023-10-312-4/+4
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* Fix parallel driver check in h5_fixname_real (#3808)jhendersonHDF2023-10-311-5/+3
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* Fix usage of h5_clean_files in t_pflush2.c (#3807)jhendersonHDF2023-10-311-5/+6
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* Fix memory corruption in 'MPI I/O FAPL preserve' test (#3806)jhendersonHDF2023-10-311-22/+22
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* Fix h5py CI failure. (#3805)H. Joe Lee2023-10-311-4/+5
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* Don't build util tests when HDF5_EXTERNALLY_CONFIGURED=ON (#3781)Robert Adam2023-10-306-6/+6
| | | | Fixes #3780
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