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* 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
* Remove CDASH_LOCAL variable reference (#3796)Allen Byrne2023-10-305-27/+11
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* Update Doxygen initializers & identifiers in VFDs (#3795)Dana Robinson2023-10-3014-52/+163
| | | | | * Add Doxygen for all H5FD_<VFD> initializers * Add Doxygen for all H5FD_<VFD>_VALUE values * Mark H5FD_<vfd>_init() calls private in Doxygen
* Add Doxygen to H5FDsplitter.h (#3794)Dana Robinson2023-10-301-55/+54
| | | | | | | | | * H5FD_CURR_SPLITTER_VFD_CONFIG_VERSION * H5FD_SPLITTER_PATH_MAX * H5FD_SPLITTER_MAGIC * H5FD_splitter_vfd_config_t * H5Pset_fapl_splitter() * H5Pget_fapl_splitter()
* Don't install h5tools_test_utils test program on system (#3793)jhendersonHDF2023-10-302-1/+11
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* Avoid attempted use of NULL pointer in parallel compression code (#3786)jhendersonHDF2023-10-281-0/+4
| | | 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.
* Print some messages in parallel tests on MPI rank 0 only (#3785)jhendersonHDF2023-10-285-82/+99
| | | Avoids overly verbose output from all processes emitting progress, etc. info.
* Cancel running GitHub workflows on push to same PR (#3772)jhendersonHDF2023-10-265-5/+5
| | | | | * Cancel running GitHub workflows on push to same PR * Remove github.sha from workflow concurrency groups
* Fix a format string warning in the C++ examples (#3776)Dana Robinson2023-10-261-1/+1
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* Fixed a file handle leak in the core VFD (#3779)Dana Robinson2023-10-262-1/+10
| | | | | | 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 typo in comment (#3775)tbeu2023-10-261-1/+1
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* Cache installation of OpenMPI for AOCC action (#3774)jhendersonHDF2023-10-251-9/+16
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* Add compression tests for subfiling (#3769)Scot Breitenfeld2023-10-251-17/+125
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* Preserve MPI-I/O file hints when fapl is closed (#3755)vchoi-hdfgroup2023-10-255-5/+124
| | | * Fix for issue #3025: Save the MPI info in the file struct so H5Fget_access_plist() can retrieve it from there.
* Add release note for H5Pset_evict_on_close change for parallel HDF5 (#3765)jhendersonHDF2023-10-241-0/+12
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* Fix H5Pset_evict_on_close failing regardless of actual parallel use (#3761)Glenn Song2023-10-246-100/+80
| | | | | Allow H5Pset_evict_on_close to be called regardless of whether a parallel build of HDF5 is being used Fail during file opens if H5Pset_evict_on_close has been set to true on the given File Access Property List and the size of the MPI communicator being used is greater than 1
* Fix failure in t_select_io_dset when run with more than 10 ranks (#3758)Neil Fortner2023-10-241-2/+28
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* Fix some issues with collective metadata reads for chunked datasets (#3716)jhendersonHDF2023-10-2410-624/+1292
| | | | | | | | | | Add functions/callbacks for explicit control over chunk index open/close Add functions/callbacks to check if chunk index is open or not so that it can be opened if necessary before temporarily disabling collective metadata reads in the library Add functions/callbacks for requesting loading of additional chunk index metadata beyond the chunk index itself
* Fix hangs during collective I/O with independent metadata writes (#3693)jhendersonHDF2023-10-246-5/+160
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* Bump the ros3 VFD cache to 16 MiB (#3759)Dana Robinson2023-10-242-3/+3
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* Added missing DLL for H5PGET_ACTUAL_SELECTION_IO_MODE_F (#3760)Scot Breitenfeld2023-10-241-0/+1
| | | * add missing H5PGET_ACTUAL_SELECTION_IO_MODE_F dll
* Update fortran action step (#3748)Allen Byrne2023-10-231-2/+6
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* Add h5pget_actual_selection_io_mode fortran wrapper (#3746)Scot Breitenfeld2023-10-237-3/+77
| | | | | | | * added h5pget_actual_selection_io_mode_f test * added tests for h5pget_actual_selection_io_mode_f * fixed int_f type conversion
* Update Autotools to correctly configure oneAPI (#3751)Dana Robinson2023-10-238-24/+539
| | | | | | | | | | | | | | | | | | | * Update Autotools to correctly configure oneAPI Splits the Intel config files under the Autotools into 'classic' Intel and oneAPI versions, fixing 'unsupported option' messages. Also turns off `-check uninit` (new in 2023) in Fortran, which kills the H5_buildiface program due to false positives. * Enable Fortran in oneAPI CI workflow * Turn on Fortran in CMake, update LD_LIBRARY_PATH * Go back to disabling Fortran w/ Intel For some reason there's a linking problem w/ Fortran error while loading shared libraries: libifport.so.5: cannot open shared object file: No such file or directory
* Add helpful text to h5clear (#3754)bmribler2023-10-233-6/+27
| | | | | | | Added text to the usage of h5clear to explain that this tool is not for fixing corrupted files but simply for helping in the inspection of the damage.. Fixed expected output for testing the modified usage.
* Add a simple cache to the ros3 VFD (#3753)Dana Robinson2023-10-232-22/+61
| | | | | | | | | Adds a small cache of the first N bytes of a file opened with the read-only S3 (ros3) VFD, where N is 4kiB or the size of the file, whichever is smaller. This avoids a lot of small I/O operations on file open. Addresses GitHub issue #3381
* Fix windows cpack error in WiX package. (#3747)Allen Byrne2023-10-231-1/+1
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* update stat arg for apple (#3726)Scot Breitenfeld2023-10-237-16/+25
| | | | | | | | | | | * update stat arg for apple * use H5_HAVE_DARWIN for Apple ifdef * fix typo * removed duplicate H5_ih_info_t * added fortran async test to cmake
* Fix buffer overflow in cache debugging code (#3691)jhendersonHDF2023-10-231-20/+84
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* Add native VOL checks to deprecated functions (#3647)mattjala2023-10-232-58/+145
| | | | | | | * Add native VOL checks to deprecated functions * Remove unneeded native VOL checks * Move native checks to top level calls
* Clean Autotools files in parallel tests (#3744)Dana Robinson2023-10-232-2/+3
| | | Adds missing files to `make clean` for parallel, including Fortran.
* Additional update to the library version matrix for H5Pset_libver_bounds() ↵bmribler2023-10-221-145/+87
| | | | | (#3742) This is the follow-up of PR #3702.
* Fix file names in tfile.c (#3743)Dana Robinson2023-10-222-5/+18
| | | | | | | | | | | Some tests in tfile.c use h5_fileaccess to get a VFD-dependent file name but use the scheme from testhdf5, reusing the FILE1 and FILE8 names. This leads to files like test1.h5.h5 which are unintended and not cleaned up. This changes the filename scheme for a few tests to work with h5test, resulting in more informative names and allowing the files to be cleaned up at the end of the test. The test files have also been added to the `make clean` target for the Autotools.
* Clean the flushrefresh test dir on Autotools (#3741)Dana Robinson2023-10-211-1/+1
| | | | The flushrefresh_test directory was not being cleaned up w/ `make clean` under the Autotools
* Clean Java test files on Autotools (#3740)Dana Robinson2023-10-211-1/+2
| | | Removes generated HDF5 and text output files when running `make clean`.
* Clean up onion VFD files in tools `make clean` (#3739)Dana Robinson2023-10-212-3/+2
| | | | Cleans up h5dump and h5diff *.onion files in the Autotools when runing `make clean`.
* Add tools/libtest to Autotools builds (#3735)Dana Robinson2023-10-203-6/+6
| | | | | This was only added to CMake many years ago and tests the tools library.
* Add missing test files to distclean target (#3734)Dana Robinson2023-10-201-2/+5
| | | Cleans up new files in Autotools `make distclean` in the test directory
* Update the library version matrix for H5Pset_libver_bounds() (#3702)bmribler2023-10-201-20/+288
| | | | | | | * Fixed #3524 Added 1.12, 1.14, and 1.16 to the table for libver bounds in the H5Pset_libver_bounds docs.
* Add -h and --help as flags in h5cc & h5fc (#3729)Glenn Song2023-10-202-16/+28
| | | Adds these common help flags in addition to -help
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