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* 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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* Remove H5detect and H5make_libsettings (#3104)Dana Robinson2023-06-133-28/+18
| | | | | | | | Removes H5detect and H5make_libsettings from the build and replaces their functionality with things that don't affect cross-compiling. H5detect --> floating-point types are now detected on library load H5make_libsettings --> Moved functionality to a new H5build_settings.c template file
* Remove long double conversion work-arounds (#3097)Dana Robinson2023-06-122-1/+22
| | | | | | | | | | | | | | | | | | | | | Several options and public symbols that were provided to paper over non-standard long double conversions between signed/unsigned long and long long values were removed from the Autotools and CMake. These were added twenty years ago, when C99 and 64-bit platforms were less common and are no longer needed. Autotools: --enable-dconv-accuracy CMake: HDF5_WANT_DATA_ACCURACY H5pubconf.h symbols: H5_WANT_DATA_ACCURACY H5_LDOUBLE_TO_LONG_SPECIAL H5_LONG_TO_LDOUBLE_SPECIAL H5_LDOUBLE_TO_LLONG_ACCURATE H5_LLONG_TO_LDOUBLE_CORRECT H5_DISABLE_SOME_LDOUBLE_CONV
* Address memory issues when copying empty enums (#3088)Dana Robinson2023-06-121-0/+11
| | | | | | | | | | When copying an empty enum type (including implicitly, as when an enum is contained in a compound type), the library would allocate 0-size blocks of memory and attempt to memcpy 0 bytes from NULL pointers, which are undefined behavior. In debug mode, the library would raise an assert in H5MM. The library now avoid undefined memory operations when copying empty enum types and a test that copies empty enums has been added.
* Print out the VOL connector being used in the ASYNC test (#3016)Scot Breitenfeld2023-06-051-0/+3
| | | | | * Print out the VOL connector being used in the ASYNC test * Add h5pget_vol_cap_flags_f with test
* API test updates (#3018)jhendersonHDF2023-05-261-1/+33
| | | | | | | | | | | | | | | | | | | | | | | | | * Remove macros from api tests (#2929) * Remove macros and undefined callbacks (#2959) * Remove remaining macros from H5_api_tests_disabled.h (#2968) * Put some vol capability checks in testpar tests and remove remaining warnings (#2995) * API tests datatype generation cleanup * Clean up API tests' random datatype generation and fix bug with enum datatype generation * Init parallel API tests with MPI_THREAD_MULTIPLE * HDF5 API tests - Check VOL connector registration * Determine whether a VOL connector failed to load before running API tests * Cleanup some usages of H5VL_CAP_FLAG_CREATION_ORDER in API tests * Remove some now-unused macros from H5_api_tests_disabled.h * Enable HDF5 API tests by default * Implement CMake option to install HDF5 API tests * Check for invalid AAPL from H5Acreate * Enable building of VOL connectors alongside HDF5 in CMake * Prepend CMake VOL URL option indices with 0s so they come in order * Don't turn on API tests by default yet * Document VOL connector FetchContent functionality * Add release note for API test updates * Only install testing library if API tests are installed * Fix grammar
* Add release note for #2999 (#3009)Dana Robinson2023-05-251-0/+8
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* Fix plugin cache variable name (#2988)Allen Byrne2023-05-222-10/+16
| | | | * Fix plugin cache variable name * Prefix plugin project local variables
* Fix 'datatype' misspellings ('dataype') (#2984)Dana Robinson2023-05-191-2/+2
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* Change defaults of standard filters. (#2927)Allen Byrne2023-05-182-9/+16
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* Remove version specific examples from README_HPC. (#2613) (#2975)Larry Knox2023-05-171-14/+12
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* Fix CMake generator expression syntax (#2909)Allen Byrne2023-05-051-0/+13
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* remove obsolete SZIP find module (#2901)metadata_cache_macro_cleanupAllen Byrne2023-05-051-0/+2
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* Force lowercase Fortran module file names (#2891)Scot Breitenfeld2023-05-041-0/+6
| | | | | * fixed args in execvp for h5fuse * Force lowercase Fortran module file names for Cray compilers
* Add RELEASE.txt entry for API tests (#2889)jhendersonHDF2023-05-031-0/+42
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* Add Fortran Selection IO APIs (#2864)Scot Breitenfeld2023-05-011-2/+4
| | | new selection IO fortran APIs with tests
* Remove "the the" from comments and docs (#2865)Dana Robinson2023-05-012-3/+3
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* Implement selection I/O with type conversion (#2823)Neil Fortner2023-04-281-0/+10
| | | | | Initial implementation of selection I/O with type conversion. Allows Parallel collective I/O with type conversion, as long as selection I/O is enabled.
* Fix v1 object header gap bug in H5Ocopy (#2785)jhendersonHDF2023-04-261-0/+12
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* Add support for CMakePresets and fix example download (#2817)Allen Byrne2023-04-262-2/+105
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