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* Merges from develop Aug 2-4 (#3354)Larry Knox2023-08-042-0/+15
| | | | | | | | | | | | | | | | | | | | * Fix CVE-2018-11202 (#3330) 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 CVE-2018-13867 (#3336) * Windows runtime items go into the bin folder (#3320)
* Fix assertion failure in H5D__mpio_collective_filtered_vec_io (#3340) (#3350)jhendersonHDF2023-08-041-3/+3
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* Set version to 1.14.3-1. (#3343)Larry Knox2023-08-031-2/+2
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* Merge Fixes the last of the -Wextra-semi-stmt warnings #3326 (#3338)Allen Byrne2023-08-034-29/+29
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* Merge Made HGOTO_ERROR a do-while loop changes from develop (#3334)Allen Byrne2023-08-03319-14832/+14560
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* Fix H5Otoken_to_str call in h5dump and other minor cleanup (#3314) (#3329)jhendersonHDF2023-08-021-6/+10
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* Fix incorrect error check in H5Ofill.c for undefined fill values (#3312) (#3328)jhendersonHDF2023-08-021-1/+1
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* Switch parallel compression to use vector I/O (#3245) (#3327)jhendersonHDF2023-08-022-816/+544
| | | | Updates parallel compression feature to use vector I/O instead of creating and passing down MPI derived types to VFD
* Fix loading plugin fails with missing directory GH issue #3248 (#3323)Allen Byrne2023-08-021-2/+1
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* Sync of src w/ develop (#3307)Dana Robinson2023-07-28279-14539/+12225
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* Bring clang-format changes from develop (#3305)Dana Robinson2023-07-281-3/+3
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* Brings an enum fix from develop (#3304)Dana Robinson2023-07-282-31/+39
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* Sync ros3 VFD w/ develop (#3299)Dana Robinson2023-07-284-87/+522
| | | | | * Sync ros3 VFD w/ develop Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Convert H5F_addr calls to H5_addr (#3297)Dana Robinson2023-07-27135-1137/+1135
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* Misc missed things from previous merges (#3295)Dana Robinson2023-07-271-4/+3
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* Remove "Programmer" lines (#3294)Dana Robinson2023-07-27312-11306/+44
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* Brings over most of the HD prefix removal (#3293)Dana Robinson2023-07-27311-15764/+15712
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* Misc warnings and cross-compile improvements (#3281)Dana Robinson2023-07-275-27/+48
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* Normalizes the public headers (#3292)Dana Robinson2023-07-2741-418/+405
| | | * Also brings over the apostrophe fix
* Fix assertion failure when attempting to use IOC VFD directly (#3187) (#3288)jhendersonHDF2023-07-271-0/+13
| | | Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Fix some warnings in developer builds (#3247) (#3291)jhendersonHDF2023-07-278-196/+185
| | | | | * Fix some warnings in developer builds * Switch approach to Winline flag
* Subfiling VFD source cleanup (#3241) (#3290)jhendersonHDF2023-07-2731-3291/+116
| | | | | | | | | | | | | | | | | | | | | | | | * Subfiling VFD source cleanup (#3241) * 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 CMake builds when Subfiling VFD isn't enabled (#3250) * Fix CMake builds when Subfiling VFD isn't enabled * Add Subfiling VFD entry to hdf5-config.cmake.in
* API test updates (#3018) (#3287)jhendersonHDF2023-07-271-7/+11
| | | | | | | | | | | | | | | | | | | | | | | | | * 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
* Fix release version for some H5Pfapl routines (#3023) (#3286)jhendersonHDF2023-07-271-3/+3
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* Add test for HDstrcasestr macro (#2115) (#3285)jhendersonHDF2023-07-272-1/+24
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* Brings over some H5F changes (#3278)Dana Robinson2023-07-274-48/+21
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* Remove unused files (#3276)Dana Robinson2023-07-274-295/+0
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* Sync fortran src files with develop (#3126)Allen Byrne2023-06-151-1/+0
| | | * Sync fortran src files with develop
* merges from develop (#3115)Allen Byrne2023-06-131-2/+2
| | | | | | | | * Fix release action that allows files to be uploaded. * Add autotools h5copy help test. * Update cmake tools.cmake file for clang-tidy. * CMake build is missing H5FDsubfiling.h * Correct snapshot location * Add note for issue 3056
* Fix doxygen and actions - merge from develop (#3109)Allen Byrne2023-06-131-0/+6
| | | | | | | * Update the workflows to changes in develop * Disable java for error only action * Fix Fortran doxygen * add fortran alias * Merge changes from develop to fix actions
* Update version (#2971)Larry Knox2023-05-191-2/+2
| | | | | * Update version Copy RELEASE.txt from 1.14.1-2 release into HISTORY-1_14.txt Clear out RELEASE.txt
* Warn about changing collections during iteration (#2962)mattjala2023-05-167-15/+37
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* Prevent buffer overrun in H5S_select_deserialize (#2953)mattjala2023-05-1612-104/+233
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* Remove H5TB discussion (#2899)Dana Robinson2023-05-051-10/+0
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* Fix CMake generator expression syntax (#2910)Allen Byrne2023-05-051-11/+11
| | | | | * Fix CMake generator expression syntax * Add missing quotes
* Fix Autotools internal-debug=all builds (#2886)jhendersonHDF2023-05-031-1/+1
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* Sync with develop (#2871)Dana Robinson2023-05-0226-703/+2497
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* Sync with develop (#2849)Dana Robinson2023-04-2829-1055/+1209
| | | | | | | | | Cherry pick of ea7dfcd (Change Powershell to PowerShell in docs) to 4497feb (Update H5Dget_space_status bug note to reference 1.14.0)
* Merge with develop (#2790)Dana Robinson2023-04-22155-4036/+1788
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* H5Spoint.c: Comment fix (#2783)Dave Allured2023-04-201-1/+1
| | | Comment here should be "point", not "hyperslab".
* Clean up memory allocated when reading messages in H5Dlayout on error (#2769)glennsong092023-04-181-4/+15
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* Check for invalid AAPL in H5Aopen (#2712) (#2770)jhendersonHDF2023-04-171-5/+9
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* Add buffer overrun checks to H5O__layout_decode and H5O__sdspace_decode ↵jhendersonHDF2023-04-153-55/+268
| | | | (#2679) (#2728)
* Fix a heap buffer overflow during H5D__compact_readvv (GitHub #2606) (#2664) ↵jhendersonHDF2023-04-141-0/+27
| | | | (#2725)
* Fix for github issue #2599: (#2665) (#2706)vchoi-hdfgroup2023-04-131-1/+6
| | | | | | | | | | | | | | | * Fix for github issue #2599: As indicated in the description, memory leak is detected when running "./h5dump pov". The problem is: when calling H5O__add_cont_msg() from H5O__chunk_deserialize(), memory is allocated for cont_msg_info->msgs. Eventually, when the library tries to load the continuation message via H5AC_protect() in H5O_protect(), error is encountered due to illegal info in the continuation message. Due to the error, H5O_protect() exits but the memory allocated for cont_msg_info->msgs is not freed. When we figure out how to handle fuzzed files that we didn't generate, a test needs to be added to run h5dump with the provided "pov" file. * Add message to release notes for the fix to github issue #2599.
* Avoid suppressing error output for non-tentative file opens (#2632) (#2670)jhendersonHDF2023-04-131-11/+41
| | | | | * Avoid suppressing error output for non-tentative file opens * Update comment about tentative file opens
* Fix memory leaks and aborts in H5O EFL decode (#2656) (#2707)Dana Robinson2023-04-131-48/+61
| | | | | | | | | | | | | | | | | | | | | * Convert asserts to error handling in efl decode The function that decodes external data files object header messages would call assert() when parsing malformed files, causing applications to crash when linked against the debug library. This change converts these assert() calls to HDF5 error checks, so the messages are sanity checked in both release and debug mode and debug mode no longer crashes applications. Also cleaned up some error handling usage and debug checks. * Free memory on H5O efl decode errors * Add buffer size checks to efl msg decode * Add parentheses to math expressions Fixes GitHub #2605
* Minor cherry-pick merges to 1.14 (#2582)Larry Knox2023-04-041-4/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Enclose MESG in do...while loop (#2576) Enclose MSG macro in a do...while loop * Add a clang-format comment about permissions (#2577) * Remove an obsolete comment from the MDS test (#2578) The seed is now broadcast from rank 0, so the warning about multiple machines having different seeds is unnecessary. * Subfiling VFD - fix issues with I/O concentrator selection strategies (#2571) Fix multiple bugs with the SELECT_IOC_EVERY_NTH_RANK and SELECT_IOC_TOTAL I/O concentrator selection strategies and add a regression test for them * Check for overflow when calculating on-disk attribute data size (#2459) * Remove duplicate code Signed-off-by: Egbert Eich <eich@suse.com> * Add test case for CVE-2021-37501 Bogus sizes in this test case causes the on-disk data size calculation in H5O__attr_decode() to overflow so that the calculated size becomes 0. This causes the read to overflow and h5dump to segfault. This test case was crafted, the test file was not directly generated by HDF5. Test case from: https://github.com/ST4RF4LL/Something_Found/blob/main/HDF5_v1.13.0_h5dump_heap_overflow.md --------- Co-authored-by: glennsong09 <43005495+glennsong09@users.noreply.github.com> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org> Co-authored-by: Egbert Eich <eich@suse.com>
* Subfiling VFD - fix issues with I/O concentrator selection strategies ↵jhendersonHDF2023-04-041-39/+71
| | | | | | | | (#2571) (#2618) Fix multiple bugs with the SELECT_IOC_EVERY_NTH_RANK and SELECT_IOC_TOTAL I/O concentrator selection strategies and add a regression test for them
* Make sure that ONLY_SHARED_LIBS option is correctly set (#2545)Allen Byrne2023-04-041-4/+4
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