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* Add new API function H5Pget_actual_select_io_mode() (#2974)Neil Fortner2023-10-201-0/+6
| | | 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.
* Add an option to disable doxygen warn as error (#3708)Allen Byrne2023-10-192-0/+13
| | | | | | | | | | | | 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
* Fix issue with unmatched messages in ph5diff (#3719)jhendersonHDF2023-10-191-0/+13
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* Some corrections and fix for plugins (#3712)Allen Byrne2023-10-191-6/+5
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* Correct use of set() command with options (#3667) (#3703)jhendersonHDF2023-10-181-9/+9
| | | | | | | * Correct use of set() command with options * Force filter off if not found Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
* Add support for AOCC & Flang w/ the Autotools (#3674)Dana Robinson2023-10-151-0/+14
| | | | | | | | | | | | | * 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
* Fixes test failure for gfortran -O2 and -O3, -fdefault-real-16 (#3662)Scot Breitenfeld2023-10-131-1/+6
| | | | | | | | | * added cmake ieee flag for nagfor * fixes gfortran -O2 and -O3, -fdefault-real-16 * fixed sync * updated release notes
* Address nagfor exceptions stoppage. (#3658)Scot Breitenfeld2023-10-111-0/+6
| | | | | | | * added cmake ieee flag for nagfor * generalized determining the nag compiler * fixing some misc. NAG warnings
* Update parallel compression feature to support multi-dataset I/O (#3591)jhendersonHDF2023-10-101-1/+10
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* Use real URLs and updated names for plugins (#3651)Allen Byrne2023-10-101-48/+58
| | | * synchronize TGZ naming convention/usage
* Fixes GH#1027 compilation error (#3654)Scot Breitenfeld2023-10-101-1/+8
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* Drop MPI-2 support (#3643)Scot Breitenfeld2023-10-081-0/+6
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* Improve consistency in past tense usage (#3638)H. Joe Lee2023-10-061-1/+1
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* Remove old EXTERNALPROJECT_ADD in favor of FETCH_CONTENT (#3624)Allen Byrne2023-10-042-19/+28
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* Disable static + thread-safe on Windows w/ CMake (#3622)Dana Robinson2023-10-031-0/+11
| | | | | | | | | 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
* Fix several spelling/grammar issues (#3621)jhendersonHDF2023-10-034-5/+5
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* Removed the use of -commons linking option on Darwin (#3581)Scot Breitenfeld2023-09-251-0/+5
| | | | Removed the use of -commons linking option on Darwin as COMMON and EQUIVALENCE is no long used
* Fix ifx unused variable hdferr warning. (#3568)H. Joe Lee2023-09-221-0/+4
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* Added new Fortran API wrappers (#3511)Scot Breitenfeld2023-09-071-1/+9
| | | | | | | | | | | | | | | | | | | * 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
* Fix Subfiling VFD IOC assignment bug (#3456)jhendersonHDF2023-09-011-0/+13
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* Remove extraneous "33" in RELEASE.txt (#3425)Neil Fortner2023-08-241-1/+1
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* Skip atomicity tests for OpenMPI major versions < 5 (#3421)jhendersonHDF2023-08-241-0/+9
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* Add RELEASE.txt entry for compound performance regression fix (#3376) (#3416)Neil Fortner2023-08-231-0/+10
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* Fix Heap-buffer-overflow WRITE in H5MM_memcpy (#3368)Alex2023-08-231-0/+4
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* Re-enable SZIP default to ON in CMake (#3414)Allen Byrne2023-08-232-1/+4
| | | The Autotools were handled in a separate commit
* Enable szip by default in Autotools (#3412)Dana Robinson2023-08-231-0/+6
| | | | | 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.
* Fix for CVE-2016-4332 (#3406)Dana Robinson2023-08-221-0/+12
| | | | | | | | | | | | | 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)
* Fix serial to parallel chunked dataset file space allocation bug (#3394)jhendersonHDF2023-08-221-0/+11
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* Update presets, examples uncompress, szip cache (#3391)Allen Byrne2023-08-181-1/+1
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* Fix assertion failure during file close on error (#3387)jhendersonHDF2023-08-181-0/+11
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* Add RELEASE.txt notes for recent selection I/O work. (#3374)Neil Fortner2023-08-101-0/+23
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* Work around a testphdf5 failure on Cray MPICH machines (#3361)jhendersonHDF2023-08-081-0/+11
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* Add Fortran ES module to deploy list (#3341)Allen Byrne2023-08-041-1/+4
| | | | | * Add Fortran ES module to deploy list * Change fortran mod file export to use a list of names
* Fix a typo in RELEASE.txtAleksandar Jelenak2023-08-031-1/+1
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* Fix CVE-2018-13867 (#3336)Dana Robinson2023-08-021-0/+9
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* Fix CVE-2018-11202 (#3330)Dana Robinson2023-08-021-0/+14
| | | | | | | | | | | | | 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.
* Fix h5repack for variable-length datatyped datasets (#3331)jhendersonHDF2023-08-021-0/+16
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* Fix loading plugin fails with missing directory GH issue #3248 (#3315)Allen Byrne2023-08-021-1/+8
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* Fix incorrect error check in H5Ofill.c for undefined fill values (#3312)jhendersonHDF2023-08-021-0/+8
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* Option changed but not all references (#3252)Allen Byrne2023-07-182-3/+2
| | | | | * Option changed but not all references * remove quotes from binary var
* Update DEFAULT_API_VERSION documentation for CMake (#3255)Allen Byrne2023-07-181-1/+1
| | | | | | | | | * Update DEFAULT_API_VERSION documentation for CMake * Fix hint --------- Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Avoid truncating at null byte when copying to std::string (#3083)Mark Kittisopikul2023-07-161-0/+7
| | | | | --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* ROS3: (feature) Temporary security credentials (#3030)Jan-Willem Blokland2023-07-141-0/+9
| | | | | | | | | | - Implemented support for AWS temporary security credentials. For this kind of credentials also a session/security token should be included in the request by adding the x-amz-security-token header. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> Co-authored-by: Jordan Henderson <jhenderson@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Subfiling VFD source cleanup (#3241)jhendersonHDF2023-07-131-0/+7
| | | | | | | | | | | | | | | | * Subfiling VFD source cleanup Modularize Subfiling CMake code into separate CMakeLists.txt file Update Mercury util code to latest version and update Copyright Generate mercury_util_config.h header file instead of using pre-generated file Remove unnecessary Mercury functionality Fix minor warning in Subfiling VFD code * Remove Mercury headers from Autotools publicly-distributed header list
* Fix assertion failure when attempting to use IOC VFD directly (#3187)jhendersonHDF2023-06-281-0/+11
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* Fix #1978 h5vers usage message. (#3162)Larry Knox2023-06-201-36/+26
| | | Update Platforms Tested in RELEASE.txt.
* chore: fix grammar (#3150)H. Joe Lee2023-06-161-2/+2
| | | * chore: fix grammar
* CMake: (feature) ROS3 and cmake config file. (#3146)Jan-Willem Blokland2023-06-161-0/+3
| | | | | - Added a cmake variable to the hdf5-config.cmake file which indicate if the library has been build with or without the read-only S3 functionality.
* Revert long double checks (#3133)Dana Robinson2023-06-152-22/+1
| | | | | | | * Revert "Remove long double conversion work-arounds (#3097)" This reverts commit 1e1dac1dac58fa18f6b7788346d1ba7d3315b0f9. * Update comments to reflect newer systems
* Add note for issue 3056 (#3117)Allen Byrne2023-06-131-1/+9
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