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* Misc missed things from previous merges (#3295)Dana Robinson2023-07-272-3/+3
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* Fix assertion failure when attempting to use IOC VFD directly (#3187) (#3288)jhendersonHDF2023-07-271-0/+11
| | | Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Subfiling VFD source cleanup (#3241) (#3290)jhendersonHDF2023-07-271-1/+6
| | | | | | | | | | | | | | | | | | | | | | | | * 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)jhendersonHDF2023-07-271-3/+31
| | | | | | | | | | | | | | | | | | | | | | | | | * 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 documentation (#3253)Allen Byrne2023-07-201-1/+0
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* merges from develop (#3115)Allen Byrne2023-06-131-1/+9
| | | | | | | | * 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
* Update actions and change defaults of compression (fix vars) (#3042)Allen Byrne2023-06-051-19/+16
| | | | | * Update actions and change defaults of compression (fix vars) * Unique location for branches
* Update version (#2971)Larry Knox2023-05-193-381/+756
| | | | | * Update version Copy RELEASE.txt from 1.14.1-2 release into HISTORY-1_14.txt Clear out RELEASE.txt
* Update name of DT action and install text (#2966)Allen Byrne2023-05-161-2/+2
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* Fix CMake generator expression syntax (#2910)Allen Byrne2023-05-051-0/+13
| | | | | * Fix CMake generator expression syntax * Add missing quotes
* remove obsolete SZIP find module (#2907)Allen Byrne2023-05-051-0/+2
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* Force lowercase Fortran module file names (#2892)Allen Byrne2023-05-041-0/+6
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* Add RELEASE.txt entry for API tests (#2889)jhendersonHDF2023-05-031-0/+42
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* Sync with develop (#2871)Dana Robinson2023-05-023-5/+17
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* Sync with develop (#2849)Dana Robinson2023-04-282-2/+123
| | | | | | | | | Cherry pick of ea7dfcd (Change Powershell to PowerShell in docs) to 4497feb (Update H5Dget_space_status bug note to reference 1.14.0)
* Fix ROS3 VFD anonymous credential usage with h5dump and h5ls (#2798) (#2800)jhendersonHDF2023-04-241-0/+13
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* Correct CMake option defaults - deprecate szip for libaec (#2786)Allen Byrne2023-04-243-64/+100
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* Merge with develop (#2790)Dana Robinson2023-04-229-115/+138
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* Add no subsets option to h5diff like h5dump (#2759)Allen Byrne2023-04-181-0/+7
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* Clean up memory allocated when reading messages in H5Dlayout on error (#2769)glennsong092023-04-181-0/+8
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* Remove author and date from RELEASE.txt entries (#2751)Dana Robinson2023-04-161-23/+7
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* Add buffer overrun checks to H5O__layout_decode and H5O__sdspace_decode ↵jhendersonHDF2023-04-151-0/+28
| | | | (#2679) (#2728)
* Fix a heap buffer overflow during H5D__compact_readvv (GitHub #2606) (#2664) ↵jhendersonHDF2023-04-141-20/+18
| | | | (#2725)
* Fix for github issue #2599: (#2665) (#2706)vchoi-hdfgroup2023-04-131-0/+14
| | | | | | | | | | | | | | | * 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.
* CMake - Match Autotools behavior for library instrumentation (#2648) (#2674)jhendersonHDF2023-04-131-0/+10
| | | Enable library instrumentation by default for parallel debug builds
* Fix #2598 sanitize leak (#2675)Allen Byrne2023-04-131-2/+6
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* Fix improper include of build directory (#2422, #2621) (#2667) (#2713)jhendersonHDF2023-04-131-0/+18
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* Minor cherry-pick merges to 1.14 (#2582)Larry Knox2023-04-041-0/+33
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 ↵jhendersonHDF2023-04-041-0/+20
| | | | | | | | (#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
* Fix a memory corruption issue in H5S__point_project_simple (#2626) (#2631)jhendersonHDF2023-04-041-0/+14
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* Subfiling VFD - add option to specify config file prefix (#2495) (#2570)jhendersonHDF2023-03-151-1/+11
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* Update cross compile checks and files #2497 (#2564)Allen Byrne2023-03-151-0/+81
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* Change libaec URL to actively maintained repo GH#2552 (#2560)Allen Byrne2023-03-151-3/+3
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* 1.14 Merge doxygen plist tables changes #2470 from develop (#2503)Allen Byrne2023-03-011-1/+5
| | | | | * Merge doxygen plist tables changes from develop * Doxy corrections
* 1.14 Add fetchcontent for compression libs and fix cmake config #2487 (#2492)Allen Byrne2023-03-012-6/+67
| | | | | | | | | * 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)jhendersonHDF2023-02-211-1/+14
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* 1.14 Merge Correct pkgconfig variables and libraries #2259 (#2477)Allen Byrne2023-02-171-1/+12
| | | | | | | * Merge Correct pkgconfig variables and libraries #290 * Fix typo * Fix spacing
* Update release_docs HISTORY scheme (#2443)Dana Robinson2023-02-138-23530/+899
| | | | | | | | 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
* Adds RELEASE.txt notes and updates Doxygen (#2377) (#2378)Dana Robinson2022-12-291-0/+32
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* 1.14 Fix some doxygen warnings (#2323)Allen Byrne2022-12-211-0/+8
| | | | | | | | | | | | | | | * 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>
* Brings the following changesets over from develop: (#2328)Dana Robinson2022-12-211-0/+19
| | | | | | | | | | | | b9244a85d9f1cc5e9bbec61ca73c0cbd9c4cf249 Align arg types of H5D_chunk_iter_op_t with H5Dget_chunk_info (#2074) 70cf2c390bc2eef8e57f8fa023341011e2d02d9d Removed idioms and misc. text clean-up (#2320) 8102fa8c972bdc0d8fd8f3dae604e070893150d6 Only document Fortran functions (#2319) 784061b15e176b9919c19a220ce278a9f4cddf0e moved onion VFD to FAPL group (#2321) 6b6bcdead66f0456ac0528683faac6a8e48b6565 Hdffv 11052 (#2315) 10c693a04ff0c4a5219879d7f8900157dcbece66 Update hdf5_header.html 0cb58080875070db09b5ecae92482519d58872bc Hdffv 11052 (#2303) a1c81eda203addced514ef655f7a9079f3f0bb04 added doc. warning for H5Literate_async return value (#2295) 502b32b0f22a4bcf6333c85c256db34162c2764a Updated H5ES documenation (#2293) a9036005c3916e6fda0296026323f00d043300f8 Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC)… (#2291)
* 1.14 Disable hl tools by default #2313 (#2318)Allen Byrne2022-12-172-4/+15
| | | | | | | * Disable hl tools by default #2313 * Only gif tools are deprecated * Update autotools
* Hdf5 1 14 (#2296)Larry Knox2022-12-141-1/+4
| | | | | | | | | | | | | | | | * Update versions for hdf5_1_14 develop branch after creation of hdf5_1-14_0 branch for 1.14.0 release. * Update windows worker compilers (#2286) * Update windows worker compilers * Update bin and test issues * Update script and revert java test * Update scripts and versions in java files. Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
* Update versions for hdf5_1_14 develop branch after creation of (#2294)Larry Knox2022-12-131-1/+1
| | | hdf5_1-14_0 branch for 1.14.0 release.
* Compound datatypes may not have members of size 0 (#2243)Egbert Eich2022-12-071-14/+25
| | | | | | | | | | | | | | | | | | | | | | * Compound datatypes may not have members of size 0 A member size of 0 may lead to an FPE later on as reported in CVE-2021-46244. To avoid this, check for this as soon as the member is decoded. This should probably be done in H5O_dtype_decode_helper() already, however it is not clear whether all sizes are expected to be != 0. This fixes CVE-2021-46244 / Bug #2242. Signed-off-by: Egbert Eich <eich@suse.com> * Rework error recovery code in H5O__dtype_decode_helper() and H5O__dtype_decode(). * Format changes for src/H5Odtype.c. Signed-off-by: Egbert Eich <eich@suse.com> Co-authored-by: Neil Fortner <nfortne2@hdfgroup.org> Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Correct requires setting for pkgconfig files (#2280)Allen Byrne2022-12-071-0/+8
| | | | | * Correct requires setting for pkgconfig files * Add issue number
* CVE 2021 46242 develop (#2255)Egbert Eich2022-12-021-0/+12
| | | | | | | | | | | | | | | | | | | | | | * When evicting driver info block, NULL the corresponding entry Since H5C_expunge_entry() called (from H5AC_expunge_entry()) sets the flag H5C__FLUSH_INVALIDATE_FLAG, the driver info block will be freed. NULLing the pointer in f->shared->drvinfo will prevent use-after-free when it is used in other functions (like H5F__dest()) - as other places will check whether the pointer is initialized before using its value. This fixes CVE-2021-46242 / Bug #2254 Signed-off-by: Egbert Eich <eich@suse.com> * When evicting the superblock, NULL the corresponding entry The call to H5AC_expunge_entry() will free the corresonding structure, to avoid a use-after-free, the corrsponding pointer entry will be NULLed. Signed-off-by: Egbert Eich <eich@suse.com> Signed-off-by: Egbert Eich <eich@suse.com>
* Output should only be printed if verbose. (#2273)Allen Byrne2022-12-021-1/+6
| | | | | * Output should only be printed if verbose. * Add note
* Report error if dimensions of chunked storage in data layout < 2 (#2241)Egbert Eich2022-12-021-1/+14
| | | | | | | | | | | | | | | | For Data Layout Messages version 1 & 2 the specification state that the value stored in the data field is 1 greater than the number of dimensions in the dataspace. For version 3 this is not explicitly stated but the implementation suggests it to be the case. Thus the set value needs to be at least 2. For dimensionality < 2 an out-of-bounds access occurs as in CVE-2021-45833. This fixes CVE-2021-45833 / Bug #2240. Signed-off-by: Egbert Eich <eich@suse.com> Signed-off-by: Egbert Eich <eich@suse.com> Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* H5O_dtype_decode_helper: Parent of enum needs to have same size as enum ↵Egbert Eich2022-11-111-13/+26
| | | | | | | | | | | | | | itself (#2237) The size of the enumeration values is determined by the size of the parent. Functions accessing the enumeration values use the size of the enumeration to determine the size of each element and how much data to copy. Thus the size of the enumeration and its parent need to match. Check here to avoid unpleasant surprises later. This fixes CVE-2018-14031 / Bug #2236. Signed-off-by: Egbert Eich <eich@suse.com>
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