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* 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
* Test scripts now execute in-source with creation of tmp dir (#3723)Allen Byrne2023-10-2039-46/+53
| | | | | | Fixes a few issues created in #3580: * Fixes a problem where committed tools test files were deleted when cleaning after an in-source build * Fixes issues with test file paths in Autotools tools test scripts
* Add new API function H5Pget_actual_select_io_mode() (#2974)Neil Fortner2023-10-2012-798/+1472
| | | This function allows the user to determine if the library performed selection I/O, vector I/O, or scalar (legacy) I/O during the last HDF5 operation performed with the provided DXPL. Expanded existing tests to check this functionality.
* Suppress cast-qual warning in H5TB Fortran wrapper (#3728)Dana Robinson2023-10-201-0/+4
| | | This interface is fundamentally broken, const-wise.
* Organize CMake config features like libsettings (#3725)Allen Byrne2023-10-191-19/+30
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* Fixes and adjustments to t_filters_parallel (#3714)jhendersonHDF2023-10-192-81/+152
| | | | | | | | | | | | | | | | | | | | | | | | | Broadcast number of datasets to create in multi-dataset I/O cases so that interference with random number generation doesn't cause mismatches between ranks Set fill time for datasets to "never" by default and adjust on a per-test basis to avoid writing fill values to chunks when it's unnecessary Reduce number of loops run in some tests when performing multi-dataset I/O Fix an issue in the "fill time never" test where data verification could fill if file space reuse causes application buffers to be filled with chosen fill value when reading from datasets with uninitialized storage Skip multi-chunk I/O test configurations for multi-dataset I/O configurations when the TestExpress level is > 1 since those tests can be more stressful on the file system Disable use of persistent file free space management for now since it occasionally runs into an infinite loop in the library's free space management code
* Develop intel split (#3722)Allen Byrne2023-10-1922-79/+125
| | | | | | * Split intel compiler flags into sub-folders * Update Intel options for warnings * Mostly CMake, Autotools needs additional work
* Fix CMake VOL passthrough tests by copying files to correct directory (#3721)jhendersonHDF2023-10-191-3/+3
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* Add an option to disable doxygen warn as error (#3708)Allen Byrne2023-10-196-1/+47
| | | | | | | | | | | | Add for both CMake and the Autotools * HDF5_ENABLE_DOXY_WARNINGS: ON/OFF (Default: ON) * --enable-doxygen-errors: enable/disable (Default: enable) The default will fail compile if the doxygen parsing generates warnings. The option can be disabled if certain versions of doxygen have parsing issues. i.e. 1.9.5, 1.9.8. Fixes #3398
* Attempt to quiet some warnings with cray compilers. (#3724)Scot Breitenfeld2023-10-1912-64/+15
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* provide an alternative to mapfile for older bash (#3717)Scot Breitenfeld2023-10-191-2/+8
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* Fix issue with unmatched messages in ph5diff (#3719)jhendersonHDF2023-10-193-7/+17
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* Some corrections and fix for plugins (#3712)Allen Byrne2023-10-195-63/+19
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* Work around Theta system issue failure in links test (#3710)jhendersonHDF2023-10-181-35/+21
| | | | | | | | When the Subfiling VFD is enabled, the links test may try to initialize the Subfiling VFD and call MPI_Init_thread. On Theta, this appears to have an issue that will cause the links test to fail. Reworked the test to check for the same conditions in a more roundabout way that doesn't involved initializing the Subfiling VFD
* Cache variables req FORCE to change (#3706)Allen Byrne2023-10-182-3/+3
| | | | | * Cache variables req FORCE to change * Also plugin needs FORCE
* Add NVidia compiler support and CI (#3686)Allen Byrne2023-10-1816-127/+593
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* Clean up comments. (#3695)H. Joe Lee2023-10-181-41/+35
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* Correct ld in format strings in cmpd_dset.c (#3697)H. Joe Lee2023-10-181-2/+4
| | | | Removes clang warnings
* Sync changes that are only in 1.14 branch (#3704)jhendersonHDF2023-10-1810-22/+14
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* Correct use of set() command with options (#3667) (#3703)jhendersonHDF2023-10-184-23/+24
| | | | | | | * Correct use of set() command with options * Force filter off if not found Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
* Restore floating-point suffixes in tests (#3698)Dana Robinson2023-10-172-17/+17
| | | | A prior commit removed too many F suffixes. This restores the suffixes for float variables.
* Fix unused variable warning in H5F_sfile_assert_num (#3700)Dana Robinson2023-10-171-6/+9
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* Fix unused variable in tselect.c (#3701)Dana Robinson2023-10-171-3/+5
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* Suppress format string warnings in subfiling test (#3699)Dana Robinson2023-10-171-0/+4
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* Add test info output to t_filters_parallel (#3696)jhendersonHDF2023-10-171-4/+21
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* Initialize API context MPI types to MPI_BYTE (#3688)jhendersonHDF2023-10-171-0/+5
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* switch to using time function instead of date function (#3690)Scot Breitenfeld2023-10-171-101/+105
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* Add Doxygen for H5Pset_fapl_sec2() (#3685)Dana Robinson2023-10-161-1/+17
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* Fix invalid memory access in S3 comms (#3681)Dana Robinson2023-10-161-1/+2
| | | | | | | | | In the ros3 VFD, passing an empty string parameter to an internal API call could result in accessing the -1th element of a string. This would cause failures on big-endian systems like s390x. This parameter is now checked before writing to the string. Fixes GitHub #1168
* Fix printf warnings in t_mpi (#3679)Dana Robinson2023-10-161-3/+6
| | | | | | | * Fix printf warnings in t_mpi The type of MPI_Offset varies with implementation. In MPICH, it's long, which raises warnings when we attempt to use long long format specifiers. Casting to long long fixes the warnings.
* Fix a possible NULL pointer dereference in tests (#3676)Dana Robinson2023-10-161-126/+92
| | | | | The dtypes test could dereference a NULL pointer if a strdup call failed.
* Suppress MPI_Waitall warnings w/ MPICH (#3680)Dana Robinson2023-10-162-9/+19
| | | | | | | | | MPICH defines MPI_STATUSES_IGNORE (a pointer) to 1, which raises warnings w/ gcc. This is a known issue that the MPICH devs are not going to fix. See here: https://github.com/pmodels/mpich/issues/5687 This fix suppresses those issues w/ gcc
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