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* HDF5 with MPI2 build fix (#3641)Scot Breitenfeld2023-10-061-4/+19
| | | | | * fixed fortran parallel testing with cmake * mpich2 compiler fix
* Fix spelling (#3633)Dana Robinson2023-10-0423-36/+36
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* Cherry-pick of CVE fixes from 1.10 (#3490)Dana Robinson2023-09-036-82/+147
| | | | | | | | | * CVE-2016-4332 * CVE-2018-11202 * CVE-2018-11205 * CVE-2018-13866 * CVE-2018-13867 * CVE-2018-13871 * CVE-2018-15671
* [1.12 Merge] Fix serial to parallel chunked dataset file space allocation ↵jhendersonHDF2023-09-011-10/+24
| | | | bug (#3394) (#3476)
* [1.12 Merge] Fix assertion failure during file close on error (#3461)jhendersonHDF2023-09-014-41/+62
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* Fix valgrind warning about write of uninitialized bytes in ScaleOffset ↵jhendersonHDF2023-09-011-1/+7
| | | | filter (#3390) (#3462)
* Merge/update CMake, presets,java and tools (#3393)Allen Byrne2023-08-214-24/+60
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* Fix loading plugin fails with missing directory GH issue #3248 (#3324)Allen Byrne2023-08-024-19/+44
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* Merges from develop/1.14 (#3118)Allen Byrne2023-06-153-34/+38
| | | | | | | | | | | | * 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 macros improved for configure output capture. Remove obsolete files * Revert parallel config with TS * Fix doxygen warnings
* Bring MD cache uthash tag list from develop (#3099)Dana Robinson2023-06-123-216/+75
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* Update uthash and move to H5private.h (#3074)Dana Robinson2023-06-074-86/+57
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* Bring gcc/clang attribute and warning macros over (#3063)Dana Robinson2023-06-072-47/+89
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* Bring key changesets from develop (#3052)Dana Robinson2023-06-062-8/+22
| | | | | | | | | * Bump GitHub action macOS version to 13 (#2999, #3009) * Bump GitHub action gcc/g++/gfortran version to 12 (#3015) * Bump Autoconf version to 2.71 (#2944) * Fix missing h5_reset() calls in accum test (#3001) * Only run ttsafe in GitHub thread-safe actions (#2777) * Fix Java debug asserts on Windows (#3012) * Fix long double dt_arith bug on macOS (#3038)
* Prevent buffer overrun in H5S_select_deserialize (#2956)mattjala2023-05-1812-213/+560
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* Fix CMake generator expression syntax (#2940)Allen Byrne2023-05-121-9/+10
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* Add configure_file commands for batch (#2882)Allen Byrne2023-05-031-0/+8
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* Add bug note to H5Dget_space_status documentation (#2788) (#2836)jhendersonHDF2023-04-301-0/+14
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* Clean up memory allocated when reading messages in H5Dlayout on error (#2811)glennsong092023-04-301-5/+16
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* Fix v1 object header gap bug in H5Ocopy (#2785) (#2833)jhendersonHDF2023-04-301-2/+7
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* H5Spoint.c: Comment fix (#2782)Dave Allured2023-04-201-1/+1
| | | Comment should be "point", not "hyperslab".
* Fixed GH-2603, heap-buffer-overflow in H5O__linfo_decode (#2763)bmribler2023-04-181-7/+23
| | | | Verified with valgrind -v --tool=memcheck --leak-check=full h5dump POV-GH-2603 The several invalid reads shown originally are now gone.
* Check for invalid AAPL in H5Aopen (#2712) (#2771)jhendersonHDF2023-04-181-5/+9
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* Add buffer overrun checks to H5O__layout_decode and H5O__sdspace_decode ↵jhendersonHDF2023-04-153-53/+270
| | | | (#2679) (#2729)
* Fix a heap buffer overflow during H5D__compact_readvv (GitHub #2606) (#2664) ↵jhendersonHDF2023-04-151-0/+27
| | | | (#2726)
* H5O__pline_decode() Make more resilient to out-of-bounds read (#2210) (#2733)jhendersonHDF2023-04-152-2/+18
| | | | | | | | | Malformed hdf5 files may have trunkated content which does not match the expected size. When this function attempts to decode these it may read past the end of the allocated space leading to heap overflows as bounds checking is incomplete. Make sure each element is within bounds before reading. This fixes CVE-2019-8396 / HDFFV-10712 / github bug #2209.
* Fix for github issue #2599: (#2665) (#2735)vchoi-hdfgroup2023-04-141-1/+6
| | | | | | | | | | | | 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.
* Avoid suppressing error output for non-tentative file opens (#2632) (#2669)jhendersonHDF2023-04-131-7/+43
| | | | | * Avoid suppressing error output for non-tentative file opens * Update comment about tentative file opens
* * Convert asserts to error handling in efl decode (#2709)Dana Robinson2023-04-131-48/+61
| | | | | | | | | | | | | | | | | | | 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
* Port h5dchunk_iter_hsizet_size #2074 to hdf5_1_12 branch (#2329)Mark Kittisopikul2023-03-293-29/+3
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* Minor cherry-pick merges to 1.12 (#2581)Larry Knox2023-03-292-8/+10
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* Fix a memory corruption issue in H5S__point_project_simple (#2626) (#2630)jhendersonHDF2023-03-291-1/+1
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* Make sure that ONLY_SHARED_LIBS option is correctly set (#2546)Allen Byrne2023-03-141-4/+4
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* Update Copyright headers. (#2534)Larry Knox2023-03-13405-410/+0
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* Fix new codespell issues (#2521) (#2530)Larry Knox2023-03-103-3/+3
| | | | | | | | | | | | | * Fix new codespell issues (#2521) * Fix new codespell issues * Have codespell ignore ./config/sanitizer/sanitizers.cmake * Fix typo in genparser. --------- Co-authored-by: Mark Kittisopikul <mkitti@users.noreply.github.com>
* 1.12 Merge doxygen plist tables changes #2470 from develop (#2505)Allen Byrne2023-03-0121-826/+219
| | | | | | | | | * Merge doxygen plist tables changes #2470 from develop * Add new/moved files * More add new/moved files * Doxy corrections
* Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC)… ↵vchoi-hdfgroup2023-02-262-24/+32
| | | | | | | | | | | | | | | | | | | | | | | | (#2291) (#2496) * Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC) producing a core dump. When h5debug closes the corrupted file, the library calls H5F__dest() which performs all the closing operations for the file "f" (H5F_t *) but just keeping note of errors in "ret_value" all the way till the end of the routine. The user-provided corrupted file has an illegal file size causing failure when reading the image during the closing process. At the end of this routine it sets f->shared to NULL and then frees "f". This is done whether there is error or not in "ret_value". Due to the failure in reading the file earlier, the routine then returns error. The error return from H5F__dest() causes the file object "f" not being removed from the ID node table. When the library finally exits, it will try to close the file objects in the table. This causes assert failure when H5F_ID_EXISTS(f) or H5F_NREFS(f). Fix: a) H5F_dest(): free the f only when there is no error in "ret_value" at the end of the routine. b) H5VL__native_file_close(): if f->shared is NULL, free "f"; otherwise, perform closing on "f" as before. c) h5debug.c main(): track error return from H5Fclose(). * Committing clang-format changes Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 1.12 Merge Correct pkgconfig variables and libraries #2259 (#2478)Allen Byrne2023-02-171-4/+14
| | | | | * Merge Correct pkgconfig variables and libraries #2259 * Fix spacing
* Brings mirror VFD test fixes from develop (#2392)Dana Robinson2023-01-051-36/+36
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* Minor change to H5private.h to bring in line with develop (#2391)Dana Robinson2023-01-051-20/+5
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* Fix for HDFFV-10840: Instead of using fill->buf for datatype conversi… (#2277)vchoi-hdfgroup2022-12-121-14/+11
| | | | | | | | | | | | | | | * Fix for HDFFV-10840: Instead of using fill->buf for datatype conversion (#2153) * Fix for HDFFV-10840: Instead of using fill->buf for datatype conversion if it is large enough, a buffer is allocated regardless so that the element in fill->buf can later be reclaimed. Valgrind is run on test/set_extent.c and there is no memory leak. * Add information of this fix to release notes. * Change macos version for CI to macos-11 until accum test failure is fixed for macos 12. Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* 1.12 Merge HDFGroup#2175 Implement option for using CMake GNUInstallDirs (#2221)Allen Byrne2022-11-042-6/+6
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* Merge #2198 correct CMake MPI linking (#2215)Allen Byrne2022-11-041-6/+6
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* Fix problem with variable length attributes being accessed through multiple ↵Neil Fortner2022-11-041-0/+4
| | | | file handles (#2181) (#2207)
* Fixed an issue that could occur when combining hyperslab selections (#2122) ↵Neil Fortner2022-10-041-2/+2
| | | | (#2138)
* 1 12 doxygen merge from 1.10 (#2094)Allen Byrne2022-09-1312-17/+41
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* Address review comments from downstream merge of #2016 (#2073) (#2081)Neil Fortner2022-09-011-3/+5
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* Fix bug in attribute type conversion wiith compound types - merge to 1.12 ↵Neil Fortner2022-08-241-9/+44
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | (#2061) * Fix bug in attribute type conversion wiith compound types (#2016) * Fix bug in attribute type conversion where the background buffer would not be initialized with the destination contents when necessary. Other minor simplification. * Committing clang-format changes * Fix warnings. * Address review comments. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Add note to RELEASE.txt for GitHub #2016 (#2030) * Fix bug in attribute type conversion where the background buffer would not be initialized with the destination contents when necessary. Other minor simplification. * Committing clang-format changes * Fix warnings. * Address review comments. * Add RELEASE.txt note for PR #2016 * Add GitHub number to release note 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>
* Persist dataset access properties when using H5Fstart_swmr_write - merge to ↵Neil Fortner2022-08-224-31/+121
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 1.12 branch (#2031) * Merge GitHub #1862 (HDFFV-11308) to 1.12 branch Persist dataset access properties when using H5Fstart_swmr_write (#1862) * Fix HDFFV-11308 - dataset access properties disappear when using H5Fstart_swmr_write. * Committing clang-format changes * Add test for H5Fstart_swmr_write() persisting DAPL settings. Fix bugs in the library exposed by this test. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix bug in swmr.c introduced with recent merge (double_t) (#1913) * Fix HDFFV-11308 - dataset access properties disappear when using H5Fstart_swmr_write. * Committing clang-format changes * Add test for H5Fstart_swmr_write() persisting DAPL settings. Fix bugs in the library exposed by this test. * Committing clang-format changes * Replace accidental use of double_t in swmr.c with double. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Add note to RELEASE.txt for HDFFV-11308 (#2029) * Add note to RELEASE.txt for HDFFV-11308 * Fix formatting error in RELEASE.txt * Committing clang-format changes * Fix inappropriate use of HGOTO_ERROR (#2055) Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Spelling fixes for codespell (#2038)Dana Robinson2022-08-1842-62/+62
| | | | | | | * Spelling fixes for codespell * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Backport H5Dchunk_iter to 1.12 branch (#1970)Mark Kittisopikul2022-08-166-16/+269
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Revert "Revert H5Dchunk_iter changes in hdf5_1_12_1 (#733)" This reverts commit 10abe9a8b4985a18a0c88615686184d233d7b845. * Apply clang-format * Reincorporate spelling fix from #1166 * Incorporate H5Dchunk_iter changes from #161 * Backport to 1.12: Adds a quick for for some egregious chunk_info badness (#722) * Backport to 1.12: Converts testhdf5 macros to h5test macros in chunk_info.c (#1820) The two macro schemes were not designed to work together. Also quiets some MSVC warnings about comparing pointers and integers. * Backport to 1.12: H5Dchunk_iter now passes offsets in units of dataset elements, fix #1419 (#1969) * H5Dchunk_iter now passes chunk dimension scaled offsets, fix #1419 * Update docs for H5Dchunk_iter, H5Dget_chunk_info* Modified description for `H5Dchunk_iter`, `H5Dget_chunk_info`, and `H5Dget_chunk_info_by_coord` to the following * offset Logical position of the chunk’s first element in units of dataset elements * filter_mask Bitmask indicating the filters used when the chunk was written * size Chunk size in bytes, 0 if the chunk does not exist * Sync H5Dchunk_iter documentation with develop * Remove H5VL_DATASET_WAIT references from 1.12 * Backport to 1.12 #161, #1474, review comments Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
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