| Commit message (Collapse) | Author | Age | Files | Lines |
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* Add binary test job
* Correct names of jobs
* Add build mode to binary names
* Limit packaging execution
* Make mac DragNDrop optional
* Format if checks
* fix checks for TS
* Allow examples to be packaged
* Correct if NOT format
* Correct configure and workflow call
* Separate out CMake/Autotools Parallel job
* Correct binary examples path
* Correct dir path for windows test
* Correct paths and add extlibs
* Windows binaries do not have a share folder
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(#3954)
* The issue was that the "allargs" variable was not being used in the final command of the compiler wrapper. Any entries containing an escaped quote (\", \') or other non-matching argument (*) would not be passed to the compile line. I have fixed this problem by ensuring all arguments passed to the compiler wrapper are now included in the compile line.
* added testing for compiler wrappers
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* fixed XL and Gfortran errors
* fixed data type len array
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* revert to using c-stub for _F08 MPI APIs
* use mpi compiler wrappers for cmake and nvhpc
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* Switch warnings as errors to default OFF
* Enable mac docs
* Add doxygen action uses step
* Use html div around snippet
* Allow preset name to be an argument to cmake-ctest.yml
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as well (#3958)
ATM configuration was embedded within the CI workflow but that makes impossible
to use codespell locally since the tool would not find those settings. I moved them
into .codespellrc but then also removed codespell.yml workflow from skips, added .git and
in general makde it look for .dotfiles too
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* update H5Ssel_iter_reset_f test
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Remove cached datatype conversion path table entries on file close
When performing datatype conversions during I/O, the library
checks to see whether it can re-use a cached datatype conversion
pathway by performing comparisons between the source and destination
datatypes of the current operation and the source and destination
datatypes associated with each cached datatype conversion pathway.
For variable-length and reference datatypes, a comparison is made
between the VOL object for the file associated with these datatypes,
which may change as a file is closed and reopened. In workflows
involving a loop that opens a file, performs I/O on an object with a
variable-length or reference datatype and then closes the file, this
can lead to constant memory usage growth as the library compares the
file VOL objects between the datatypes as different and adds a new
cached conversion pathway entry on each iteration during I/O. This is
now fixed by clearing out any cached conversion pathway entries for
variable-length or reference datatypes associated with a particular
file when that file is closed.
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Add the user test program for committed types in HDFFV-9174
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* - Added Fortran APIs:
H5FGET_INTENT_F, H5SSELECT_ITER_CREATE_F, H5SSEL_ITER_GET_SEQ_LIST_F,
H5SSELECT_ITER_CLOSE_F, H5S_mp_H5SSELECT_ITER_RESET_F
- Added Fortran Parameters:
H5S_SEL_ITER_GET_SEQ_LIST_SORTED_F, H5S_SEL_ITER_SHARE_WITH_DATASPACE_F
- Added tests for new APIs
- Removed H5F C wrapper stubs
- Documentation misc. cleanup.
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Co-authored-by: Glenn Song <gsong@hdfgroup.org>
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off_t is a 32-bit signed value on Windows, so we should use HDoff_t
(which is __int64 on Windows) internally instead.
Also defines HDftell on Windows to be _ftelli64().
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not used here] (#3886)
* autogen.sh: check directly for libtoolize instead of libtool [as libtool is not used here]
* autogen.sh: simplify (g)libtoolize check - look for glibtoolize first - and then libtoolize
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* Reorg and update options for doc and cmake config
* Correct subfiling depends
* Add linux S3 binaries to GH published files
* Correct path
* Try reducing parallel jobs in tests
* Change examples jobs for test from 8 to 4
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* Reorg and update options for doc and cmake config
* Correct subfiling depends
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* Update upload- artifact to match download version
* Correct form of action call
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* Document that fileno is same for all handles
* Mention filesystem requirement
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* Add H5Dread/write_multi to API tests
* Remove debug prints, set NULL for safety
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* Merge CMake dir props and compression changes from develop
* Remove unused include
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* Fix build error on freebsd (#3883)
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
* Correct CMake command and example packaging (#3888)
* Feat: Hashpin sensitive dependencies on GitHub Actions and enable Dependabot 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>
* Some changes to portal links when they could be found on docs.hdfgroup.org, 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
* Add variable option syncing for examples (#3885)
* Add period(.) at the end of the sentence for consistency. (#3897)
* Remove redundant backslash character from comment. (#3899)
* Disable doxygen as errors for netcdf (#3900)
* disable building doxygen for netcdf test
* Doc versions (#3903)
* 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>
* Change Trouble Shooting to Troubleshooting (#3905)
* Implement optimized support for vector I/O in Subfiling VFD (#3896)
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
* Add 'warning density' computation to the warnhist script (#3910)
* 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>
* Added H5Fdelete_f with test (#3912)
* New Fortran Examples added (#3916)
* added subfiling example
* Added filtered writes with no selection example
* Version and space corrections.
* Restore H5_VERSION definition in configure.ac.
* renamed defined H5_VERS* to avoid conflicts (#3926)
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* Handle CMake version through override variable
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* 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
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* 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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* Check if lib conversion func is in use
* Use TEST_ERROR macro in user cmpd conv test
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* Sync fixes for CI and presets
* Sync the Fortran build changes
* Update fortran test file
* Sync hl/fortran files
* Merge the nvidia compiler flag changes
* Update link
* Update links to doxygen refs for 1.14
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* Document path handling of H5Lcreate_* API
* Document that link name is last part of path
* Test H5Lcreate path handling behavior
* State that absolute paths require forward slash
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* Deploy branch docs to a subfolder
* Update doxygen links
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Guard test dirs with HDF5_EXTERNALLY_CONFIGURED
Add toolchain support to examples testing
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Clean 1.14.3 entries from RELEASE.txt.
Add hdf5-1.14.3-RELEASE.txt contents to HISTORY-1_14.txt.
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(#3767)
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* Add missing test files to distclean target (#3734)
Cleans up new files in Autotools `make distclean` in the test directory
* Add tools/libtest to Autotools builds (#3735)
This was only added to CMake many years ago and tests the tools
library.
* Clean up onion VFD files in tools `make clean` (#3739)
Cleans up h5dump and h5diff *.onion files in the Autotools when
runing `make clean`.
* Clean Java test files on Autotools (#3740)
Removes generated HDF5 and text output files when running `make clean`.
* Clean the flushrefresh test dir on Autotools (#3741)
The flushrefresh_test directory was not being cleaned up w/
`make clean` under the Autotools
* Fix file names in tfile.c (#3743)
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 Autotools files in parallel tests (#3744)
Adds missing files to `make clean` for parallel, including Fortran.
* Add native VOL checks to deprecated functions (#3647)
* Add native VOL checks to deprecated functions
* Remove unneeded native VOL checks
* Move native checks to top level calls
* Fix buffer overflow in cache debugging code (#3691)
* update stat arg for apple (#3726)
* 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 windows cpack error in WiX package. (#3747)
* Add a simple cache to the ros3 VFD (#3753)
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
* Update Autotools to correctly configure oneAPI (#3751)
* 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 h5pget_actual_selection_io_mode fortran wrapper (#3746)
* added h5pget_actual_selection_io_mode_f test
* added tests for h5pget_actual_selection_io_mode_f
* fixed int_f type conversion
* Update fortran action step (#3748)
* Added missing DLL for H5PGET_ACTUAL_SELECTION_IO_MODE_F (#3760)
* add missing H5PGET_ACTUAL_SELECTION_IO_MODE_F dll
* Bump the ros3 VFD cache to 16 MiB (#3759)
* Fix hangs during collective I/O with independent metadata writes (#3693)
* Fix some issues with collective metadata reads for chunked datasets (#3716)
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 failure in t_select_io_dset when run with more than 10 ranks (#3758)
* Fix H5Pset_evict_on_close failing regardless of actual parallel use (#3761)
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
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- 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.
Fixed GH #3054
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Fixes GitHub #3524 in 1.14
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* Correct ld in format strings in cmpd_dset.c (#3697)
Removes clang warnings
* Clean up comments. (#3695)
* Add NVidia compiler support and CI (#3686)
* Work around Theta system issue failure in links test (#3710)
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
* Fix issue with unmatched messages in ph5diff (#3719)
* provide an alternative to mapfile for older bash (#3717)
* Attempt to quiet some warnings with cray compilers. (#3724)
* Fix CMake VOL passthrough tests by copying files to correct directory (#3721)
* Develop intel split (#3722)
* Split intel compiler flags into sub-folders
* Update Intel options for warnings
* Mostly CMake, Autotools needs additional work
* Fixes and adjustments to t_filters_parallel (#3714)
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
* Suppress cast-qual warning in H5TB Fortran wrapper (#3728)
This interface is fundamentally broken, const-wise.
* Add new API function H5Pget_actual_select_io_mode() (#2974)
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.
* Test scripts now execute in-source with creation of tmp dir (#3723)
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 -h and --help as flags in h5cc & h5fc (#3729)
Adds these common help flags in addition to -help
* Update the library version matrix for H5Pset_libver_bounds() (#3702)
* Fixed #3524
Added 1.12, 1.14, and 1.16 to the table for libver bounds in the H5Pset_libver_bounds docs.
* Remove references to LIBVER_V116
---------
Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Neil Fortner <fortnern@gmail.com>
Co-authored-by: Glenn Song <43005495+glennsong09@users.noreply.github.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
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