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* Add support for CMakePresets and fix example download (#2819)Allen Byrne2023-04-302-4/+106
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* Clean up memory allocated when reading messages in H5Dlayout on error (#2811)glennsong092023-04-301-0/+10
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* Fix v1 object header gap bug in H5Ocopy (#2785) (#2833)jhendersonHDF2023-04-301-0/+12
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* Add no subsets option to h5diff like h5dump (#2760)Allen Byrne2023-04-191-0/+7
| | | * reorder argument in alpha order
* Fixed GH-2603, heap-buffer-overflow in H5O__linfo_decode (#2763)bmribler2023-04-181-1/+10
| | | | Verified with valgrind -v --tool=memcheck --leak-check=full h5dump POV-GH-2603 The several invalid reads shown originally are now gone.
* Remove author and date from RELEASE.txt entries (#2752)Dana Robinson2023-04-161-43/+15
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* Add buffer overrun checks to H5O__layout_decode and H5O__sdspace_decode ↵jhendersonHDF2023-04-151-0/+8
| | | | (#2679) (#2729)
* Fix a heap buffer overflow during H5D__compact_readvv (GitHub #2606) (#2664) ↵jhendersonHDF2023-04-151-0/+19
| | | | (#2726)
* H5O__pline_decode() Make more resilient to out-of-bounds read (#2210) (#2733)jhendersonHDF2023-04-151-0/+10
| | | | | | | | | 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-hdfgroup2023-04-141-0/+14
| | | | | | | | | | | | 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.
* CMake - Match Autotools behavior for library instrumentation (#2648) (#2673)jhendersonHDF2023-04-131-0/+10
| | | Enable library instrumentation by default for parallel debug builds
* Fix #2598 sanitize leak (#2676)Allen Byrne2023-04-131-0/+7
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* Fix CMake for version less then 3.18 (#2651)Allen Byrne2023-03-303-6/+11
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* Minor cherry-pick merges to 1.12 (#2581)Larry Knox2023-03-291-0/+13
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* Update cross compile checks and files #2497 (#2565)Allen Byrne2023-03-291-0/+81
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* Revert the removal of HDF5GroupInfo class and deprecate. (#2637)Allen Byrne2023-03-291-0/+8
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* Fix a memory corruption issue in H5S__point_project_simple (#2626) (#2630)jhendersonHDF2023-03-291-0/+14
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* Bring release_docs scheme from develop (#2612)Dana Robinson2023-03-205-21001/+127
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* Change libaec URL to actively maintained repo GH#2552 (#2561)Allen Byrne2023-03-181-3/+3
| | | | | * Change libaec URL to actively maintained repo GH#2552 * Remove duplicated https
* 1.12 Add fetchcontent for compression libs and fix cmake config #2487 (#2493)Allen Byrne2023-03-012-5/+68
| | | | | | | * Add fetchcontent for compression libs and fix cmake config #2487 * Add CI test for FetchContent * Use LINK_COMP_LIBS instead of STATIC_LIBRARY for depends
* Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC)… ↵vchoi-hdfgroup2023-02-261-0/+19
| | | | | | | | | | | | | | | | | | | | | | | | (#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 Byrne2023-02-171-0/+13
| | | | | * Merge Correct pkgconfig variables and libraries #2259 * Fix spacing
* Fix for HDFFV-10840: Instead of using fill->buf for datatype conversi… (#2277)vchoi-hdfgroup2022-12-121-0/+13
| | | | | | | | | | | | | | | * 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 h5repack should only print if verbose (#2274)Allen Byrne2022-12-121-1/+6
| | | | | | | | | * h5repack should only print if verbose Also chage dump test to use long option * Add note * Update yaml workflows
* 1.12 Correct requires setting for pkgconfig files #2280 (#2283)Allen Byrne2022-12-121-0/+8
| | | | | * Correct requires setting for pkgconfig files #2280 * Change macos for CI
* 1.12 Merge HDFGroup#2175 Implement option for using CMake GNUInstallDirs (#2221)Allen Byrne2022-11-042-1/+28
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* Merge #2198 correct CMake MPI linking (#2215)Allen Byrne2022-11-041-1/+7
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* Fix problem with variable length attributes being accessed through multiple ↵Neil Fortner2022-11-041-0/+10
| | | | file handles (#2181) (#2207)
* Fixed an issue that could occur when combining hyperslab selections (#2122) ↵Neil Fortner2022-10-041-0/+7
| | | | (#2138)
* Update examples reference to single-source version 2.0.1 (#2108)Allen Byrne2022-09-242-8/+8
| | | Also fix github URL refs
* Fix bug in attribute type conversion wiith compound types - merge to 1.12 ↵Neil Fortner2022-08-241-0/+9
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | (#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 Fortner2022-08-221-0/+10
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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 Robinson2022-08-184-5/+5
| | | | | | | * Spelling fixes for codespell * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* [1.12 Merge] Hdf5 1 12 develop merges (#2012)jhendersonHDF2022-08-161-1/+10
| | | | | | | | | | | | | | | | | * Fix invalid comment about character encoding in H5Fint.c (#1845) * Convert assertion on (possibly corrupt) file contents to normal error check (#1861) * Convert assertion on (possibly corrupt) file contents to normal error check * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Avoid allocating chunk map for contiguous and compact dataset I/O (#1927) * Add documentation for parallel compression feature (#1981) Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Merge UG from 1.10 and add prelim vol section (#1980)Allen Byrne2022-08-091-1/+5
| | | | | | | * Merge UG from 1.10 and add prelim vol section * Spelling fixes * Merge format and autotools javadoc from 1.10
* fortran module folder from GH#1411 #1922 (#1942)Allen Byrne2022-07-272-1/+27
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* Revert "1.12 eliminate unnecessary errors in the error stack (#1880)" (#1935)Larry Knox2022-07-261-2/+45
| | | This reverts commit f6997681335f0b5fe2e8904f9108a71c5200fb2d.
* 1.12 eliminate unnecessary errors in the error stack (#1880)Allen Byrne2022-07-181-45/+2
| | | | | | | | | | | * Eliminate unnecessary error output * Fix merge typo * fix format * Fix object address to tokens * Fix conflict
* 1 12 Add utility JNI function for 1.10 style references (#1889)Allen Byrne2022-07-181-0/+7
| | | | | | | | | | | * Add utility JNI function for 1.10 style references * Clarify text * Correct signature * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 1.12 HDFFV-11310 implement JNI VL support for primitive types (#1856)Allen Byrne2022-07-121-2/+38
| | | | | | | | | | | | | | | * HDFFV-11310 - implement VL read/write using List of Lists * Fix function name typo * Add JIRA issue * Correct note to match change in code. * HDFFV-11318 add VL references as byte arrays * Fix unreleased allocations * Fix format
* Hdf5 1 12 sync (#1794)Allen Byrne2022-06-122-19/+49
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* Change TestExpress #1722 (#1776)Allen Byrne2022-05-202-2/+2
| | | | | * Change TestExpress #1722 * Update comment
* Update VS2019 compilers (#1782)Allen Byrne2022-05-201-1/+1
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* Update version to 1.12.3-1 after creating hdf5_1_12_2 releaseLarry Knox2022-04-081-388/+10
| | | | | preparation branch. Clean release note entries from RELEASE.txt.
* Hdf5 1 12 (#1625)Larry Knox2022-04-081-223/+153
| | | * Update Platforms tested and standardize indentation in RELEASE.txt.
* Commit one more spelling correction.Larry Knox2022-04-071-1/+1
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* Commit codespell spelling corrections.Larry Knox2022-04-078-100/+100
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* Add option for h5repack timing #1142 (#1575)Allen Byrne2022-04-041-0/+8
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* 1.12 New References for Dimension Scales (#1139) (#1574)Larry Knox2022-04-021-0/+10
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * New references for Dimension Scale APIs (#1139) * Enable usage of new-style references with dimension scale APIs * Add API to check if an object ID represents a native connector object * Modified code to use new function H5DSwith_new_ref to determine if new references should be used with Dimension Scales. The new function return TRUE if non-native connector is used or if H5_DIMENSION_SCALES_WITH_NEW_REF varible is define at configure time (--enable-dimension-scales-with-new-ref). Tested on jelly. ToDo: generate testing file on BE system and enable the test; add flag to CMake; test netCDF-4 with the new references. * Adding new test files generated on BE system (hedgehog) created by 32 and 64-bit library. test_ds chokes on test_ds_le_new_ref.h5 on BE system; test passes for test_ds_be_new_ref-32bit.h5 for the 32-bit library and fails for the 64-bit library, and vice versa. I am checking the files for further investigation; but current implementation of the new references is not portable between LE and BE systems, and 32 and 64-bit systems. * Minor fixes for testing issues * Update test_ds.c Enabled broken test; tests pass now. * Update RELEASE.txt Documented new option to use new references with the HDF5 dimension scales APIs (H5DS*). * Update MANIFEST for new 32-bit new-style references test file for H5DS APIs * Update 'dimension scales w/ new-style refs' feature based on review Co-authored-by: Elena <epourmal@hdfgroup.org> * Fix H5DS warnings related to new H5DSwith_new_ref and H5VLobject_is_native APIs (#1184) Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org> Co-authored-by: Elena <epourmal@hdfgroup.org>
* October 2021 Pull Requests not previously merged to 1.12 (#1570)Larry Knox2022-04-011-58/+91
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