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* Merge "Use additional CPUs" and related fixes (#2742)Dana Robinson2023-04-146-6/+28
| | | | * 2720 Fix java depends and pdb lib install * 2695 Use additional CPUs in GitHub actions
* Remove 1.14 release schedule (#2743)Dana Robinson2023-04-143-63/+0
| | | | | | There is no need to maintain the release schedule in each branch, so it's being removed from all branches aside from develop. Also removes the badges that don't pertain to 1.14
* Add Elena to CODEOWNERS for FortranDana Robinson2023-04-141-1/+1
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* Fix a heap buffer overflow during H5D__compact_readvv (GitHub #2606) (#2664) ↵jhendersonHDF2023-04-142-20/+45
| | | | (#2725)
* Fix for github issue #2599: (#2665) (#2706)vchoi-hdfgroup2023-04-132-1/+20
| | | | | | | | | | | | | | | * 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.
* Change name of test file to avoid conflict (#2703)Allen Byrne2023-04-131-2/+2
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* CMake - Match Autotools behavior for library instrumentation (#2648) (#2674)jhendersonHDF2023-04-132-1/+17
| | | Enable library instrumentation by default for parallel debug builds
* Minor fixes for Subfiling VFD tests (#2633) (#2671)jhendersonHDF2023-04-132-26/+109
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* 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 #2598 sanitize leak (#2675)Allen Byrne2023-04-132-6/+10
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* Fix improper include of build directory (#2422, #2621) (#2667) (#2713)jhendersonHDF2023-04-132-4/+20
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* 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 Knox2023-04-048-10/+60
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 ↵jhendersonHDF2023-04-043-39/+286
| | | | | | | | (#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 Byrne2023-04-0437-125/+117
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* Fix a memory corruption issue in H5S__point_project_simple (#2626) (#2631)jhendersonHDF2023-04-042-1/+15
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* Update java logger version (#2644)Allen Byrne2023-04-0422-31/+34
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* Cherry-pick merges from develop to hdf5_1_14 (#2572)Larry Knox2023-03-164-9/+12
| | | | Co-authored-by: Mark (he/his) C. Miller <miller86@llnl.gov> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* 1.14 Fix H5Dchunk_iter doxygen example, cherry-pick of 04682f2 (#2519) (#2548)Larry Knox2023-03-161-3/+3
| | | | | * Fix H5Dchunk_iter doxygen example, cherry-pick of ef3bed6 (#2519) Co-authored-by: Mark Kittisopikul <mkitti@users.noreply.github.com>
* Subfiling VFD - add option to specify config file prefix (#2495) (#2570)jhendersonHDF2023-03-157-25/+272
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* Update ReferenceManual.dox (#2517) (#2569)Larry Knox2023-03-151-1/+1
| | | Co-authored-by: mattjala <124107509+mattjala@users.noreply.github.com>
* docs: in -> out (#2514) (#2516) (#2568)Larry Knox2023-03-151-1/+1
| | | Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
* Remove redundant and flawed documentation of H5D_chunk_iter_op_t from H5D.c ↵Larry Knox2023-03-151-26/+0
| | | | | | | (#2512) (#2566) Forward port of 9f252f1 from #2329 Co-authored-by: Mark Kittisopikul <mkitti@users.noreply.github.com>
* Update cross compile checks and files #2497 (#2564)Allen Byrne2023-03-153-54/+138
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* Change libaec URL to actively maintained repo GH#2552 (#2560)Allen Byrne2023-03-153-6/+6
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* GH issue #2538, print must have verbose on first (#2541)Allen Byrne2023-03-151-4/+6
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* Add concurrency option to cancel in-progress jobs (#2539) (#2558)Larry Knox2023-03-151-1/+6
| | | Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
* Fix new codespell issues (#2521) (#2533)Larry Knox2023-03-1012-12/+12
| | | | | | | * Fix new codespell issues * Have codespell ignore ./config/sanitizer/sanitizers.cmake Co-authored-by: Mark Kittisopikul <mkitti@users.noreply.github.com>
* 1.14 Merge doxygen plist tables changes #2470 from develop (#2503)Allen Byrne2023-03-0112-83/+5143
| | | | | * Merge doxygen plist tables changes from develop * Doxy corrections
* 1.14 Add fetchcontent for compression libs and fix cmake config #2487 (#2492)Allen Byrne2023-03-0121-153/+2149
| | | | | | | | | * Add fetchcontent for compression libs and fix cmake config #2487 * Update cmake doc for FetchContent * Add CI test for FetchContent * Use LINK_COMP_LIBS instead of STATIC_LIBRARY for depends
* Fix issue with collective metadata writes of global heap data (#2480) (#2486)jhendersonHDF2023-02-217-5/+104
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* Remove space from toolchain name #2482 (#2483)Allen Byrne2023-02-211-0/+0
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* Merge toolchain lowercase names and updates #2426 (#2467)Allen Byrne2023-02-179-24/+39
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* 1.14 Merge Correct pkgconfig variables and libraries #2259 (#2477)Allen Byrne2023-02-179-17/+58
| | | | | | | * Merge Correct pkgconfig variables and libraries #290 * Fix typo * Fix spacing
* Merge Add build options for CMake packaging #2347 (#2464)Allen Byrne2023-02-171-24/+30
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* 1.14 Correct VERS compatible (#2460)Allen Byrne2023-02-172-3/+2
| | | | | | | | | * Correct VERS compatible * Remove FAIL check in CMake test * Remove unnecessary value in vers array * revert empty list
* Update release_docs HISTORY scheme (#2443)Dana Robinson2023-02-1310-23560/+1007
| | | | | | | | We will no longer maintain HISTORY files for other maintenance branches, so those have been removed. Adds a README.md explaining the purpose and procedures of HDF5 HISTORY. Also adds a newsletter template and updates the RELEASE.txt note part of CONTRIBUTING.md. Also cleans out RELEASE.txt post-HDF5-1.14.0
* Drop non-1.14 branches in main.yml (#2448)Dana Robinson2023-02-121-1/+1
| | | | | There's no reason to list develop, etc. in the list of branches where this flavor of main.yml applies. Those branches have their own main.yml files.
* Update CODEOWNERS given personnel changes (#2456)Dana Robinson2023-02-111-2/+2
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* CMake: Find MPI in HDF5 CMake config (#2400) (#2410)Larry Knox2023-01-191-0/+2
| | | Co-authored-by: kwryankrattiger <80296582+kwryankrattiger@users.noreply.github.com>
* Brings README.md changes from develop (#2388)Dana Robinson2023-01-053-25/+26
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* Adds RELEASE.txt notes and updates Doxygen (#2377) (#2378)Dana Robinson2022-12-293-8/+42
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* Adds Doxygen markup for H5FDdriver_query() (#2375)Dana Robinson2022-12-282-4/+23
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* Brings Doxygen changes from develop (#2366)Dana Robinson2022-12-2710-51/+104
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* Brings HL GIF tools configure changes from develop (#2361)Dana Robinson2022-12-247-56/+32
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* Fixed version info. (#2344)Gerd Heber2022-12-221-2/+2
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* Adds Doxygen VOL flag markup (#2340) (#2341)Dana Robinson2022-12-211-55/+63
| | | | | | | | | | | | | * Initial doxygen markup * Committing clang-format changes * Adds Doxygen comments to VOL flags * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Onion VFD header cleanup (#2337) (#2338)Dana Robinson2022-12-213-112/+85
| | | | | | | | | | | * Partial work towards cleaning up the onion VFD code * Committing clang-format changes * A few minor tweaks to the onion VFD public header Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix up the H5Pencode2 test for virtual layout. (#2325) (#2335)Dana Robinson2022-12-211-91/+87
| | | | | | | | | | | | | * Fix up the H5Pencode2 test for virtual layout. * Committing clang-format changes * Remove VERIFY and use TEST_ERROR. Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 1.14 Fix some doxygen warnings (#2323)Allen Byrne2022-12-2117-62/+29
| | | | | | | | | | | | | | | * Fix some doxygen warnings * Remove javadocs * Fix spelling * Fix section format * Correct doxygen function name * Remove duplicate Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
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