| Commit message (Collapse) | Author | Age | Files | Lines |
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* 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
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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
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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
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* added h5pget_actual_selection_io_mode_f test
* added tests for h5pget_actual_selection_io_mode_f
* fixed int_f type conversion
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* 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
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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
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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.
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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
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* Correct use of set() command with options
* Force filter off if not found
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
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* Adds a config/clang-fflags options file to support Flang
* Corrects missing "-Wl," from linker options in the libtool wrappers
when using Flang, the MPI Fortran compiler wrappers, and building
the shared library. This would often result in unrecognized options
like -soname.
* Enable -nomp w/ Flang to avoid linking to the OpenMPI library.
CMake can build the parallel, shared library w/ Fortran using AOCC
and Flang, so no changes were needed for that build system.
Fixes GitHub issues #3439, #1588, #366, #280
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* added cmake ieee flag for nagfor
* fixes gfortran -O2 and -O3, -fdefault-real-16
* fixed sync
* updated release notes
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* added cmake ieee flag for nagfor
* generalized determining the nag compiler
* fixing some misc. NAG warnings
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* synchronize TGZ naming convention/usage
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The thread-safety feature on Windows requires a hook in DllMain() and
thus is only available when HDF5 is built as a shared library.
This was previously a warning, but has now been elevated to a fatal
error that cannot be overridden with ALLOW_UNSUPPORTED.
Fixes GitHub #3613
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Removed the use of -commons linking option on Darwin as COMMON and EQUIVALENCE is no long used
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* Added new wrappers for
h5get_free_list_sizes_f
H5Sselect_intersect_block_f
H5Sselect_shape_same_f
h5pget_no_selection_io_cause_f
h5pget_mpio_no_collective_cause_f
H5Lvisit_by_name_f
H5Lvisit_f
H5Fget_info_f
h5dwrite_chunk_f
h5dread_chunk_f
* added h5pget_file_space_page_size_f, h5pset_file_space_page_size_f, h5pget_file_space_strategy_f, h5pset_file_space_strategy_f, h5info tests
* added fortran tests
* Update tH5F.F90
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The Autotools were handled in a separate commit
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Since libaec is so prevalent and BSD-licensed for both encode and
decode, we build the szip filter by default when the szip or aec
libraries are found.
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This CVE issue was previously listed as fixed (via HDFFV-9950) back in
2016, but with no confirmation test. Now that test files exist for
the 2016 Talos CVE issues, we found that CVE-2016-4332 can raise an
assert in debug builds.
This fix replaces the assert with pointer checks that don't raise
errors or asserts. Since the function is in cleanup code, we do our
best to close and free things, even when presented with partially-
initialized structs.
Fixes CVE-2016-4332 and HDFFV-9950 (confirmed via the cve_hdf5 repo)
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* Add Fortran ES module to deploy list
* Change fortran mod file export to use a list of names
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A malformed file could result in chunk index memory leaks. Under most
conditions (i.e., when the --enable-using-memchecker option is NOT
used), this would result in a small memory leak and and infinite loop
and abort when shutting down the library. The infinite loop would be
due to the "free list" package not being able to clear its resources
so the library couldn't shut down. When the "using a memory checker"
option is used, the free lists are disabled so there is just a memory
leak with no abort on library shutdown.
The chunk index resources are now correctly cleaned up when reading
misparsed files and valgrind confirms no memory leaks.
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* Option changed but not all references
* remove quotes from binary var
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