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* Fix memory leaks and aborts in H5O EFL decode (#2656)Dana Robinson2023-04-031-48/+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
* Avoid suppressing error output for non-tentative file opens (#2632)jhendersonHDF2023-04-011-11/+41
| | | | | * Avoid suppressing error output for non-tentative file opens * Update comment about tentative file opens
* Fix a memory corruption issue in H5S__point_project_simple (#2626)jhendersonHDF2023-03-241-1/+1
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* Fix minor things noted when doing 1.10 merges (#2610)Dana Robinson2023-03-241-1/+1
| | | | * Duplicated HDF_RESOURCES_DIR from cmake_ext_mod merge * Typos in comments
* Subfiling VFD - fix issues with I/O concentrator selection strategies (#2571)jhendersonHDF2023-03-171-39/+71
| | | | | 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 (#2544)Allen Byrne2023-03-131-4/+4
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* Addressed various Doxygen grammar issues. (#2524)Scot Breitenfeld2023-03-1339-203/+203
| | | | | | | | | | * reviewed H5A * Addressed various grammar issues. * remove double words, spelling fixes * replace the use of rawdata with raw data
* Elaborate how cd_values get stored (#2522)Mark (he/his) C. Miller2023-03-081-4/+7
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* docs: in -> out (#2514) (#2516)H. Joe Lee2023-03-081-1/+1
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* Remove redundant and flawed documentation of H5D_chunk_iter_op_t from H5D.c ↵Mark Kittisopikul2023-03-081-26/+0
| | | | | (#2512) Forward port of 9f252f1 from #2329
* Fix new codespell issues (#2521)Mark Kittisopikul2023-03-083-3/+3
| | | | | * Fix new codespell issues * Have codespell ignore ./config/sanitizer/sanitizers.cmake
* Check for overflow when calculating on-disk attribute data size (#2459)Egbert Eich2023-03-021-4/+3
| | | | | | | | | | | | | | | | | * 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
* Missing or misplaced entries in API reference tables #2470 (#2472)Allen Byrne2023-03-011-0/+2
| | | | | * Missing or misplaced entries in API reference tables #2470 * Doxy corrections
* Subfiling VFD - add option to specify config file prefix (#2495)jhendersonHDF2023-02-265-18/+165
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* HDFFV-10368 (OESS-319): Making two useful macros (H5L_EXT_FLAGS_ALL and ↵raylu-hdf2023-02-212-6/+10
| | | | | | | | | | | | | | | | | | | | | H5L_EXT_VERSION) public (#2386) * HDFFV-10368 (OESS-319): Move two useful macros (H5L_EXT_FLAGS_ALL and H5L_EXT_VERSION) from H5Lpkg.h to H5Lpublic.h for public usage. The test in vol.c only envokes H5Lcreate_external using the passthru VOL. To test if the macros are public, one can use them in the link creation of the passthru VOL, such as printing out their values. * Committing clang-format changes * Moved the test for the external link public macros (H5L_EXT_FLAGS_ALL and H5L_EXT_VERSION) from vol.c to links.c. * Committing clang-format changes * Minor change: changed a pointer variable to an integer. * Committing clang-format changes * Moved two macros (H5L_EXT_VERSION and H5L_EXT_FLAGS_ALL) to H5Ldevelop.h for only developers to use. --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* OESS-330/HDFFV-11282: Improve failure message when a VOL connector can't be ↵raylu-hdf2023-02-202-3/+8
| | | | | | | | | | | loaded (#2481) * OESS-330/HDFFV-11282: Improve failure message when a VOL connector can't be loaded. Made the error message clearer when the library can't find a plugin in the path table that contains the paths set by HDF5_PLUGIN_PATH and the default location and maybe set by H5PLxxx functions. * Committing clang-format changes --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix issue with collective metadata writes of global heap data (#2480)jhendersonHDF2023-02-201-0/+8
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* CMake generated pkg-config file is incorrect #2259 (#2476)Allen Byrne2023-02-171-4/+14
| | | | | | | | | | | | | * CMake generated pkg-config file is incorrect #2259 * Fix fortran pc template * hdf5.pc is incorrect for debug builds #1546 * Correct pkg name and lib name * Fix typo * Fix missing space
* GitHub #2417: to avoid the pass-through VOL failing in unexpected places, ↵raylu-hdf2023-02-171-0/+31
| | | | | | | | | | | make sure the underneath VOL ID is specified. (#2475) * GitHub #2417: to avoid the pass-through VOL failing in unexpected places, make sure the underneath VOL ID is specified. * Committing clang-format changes --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix parallel warnings in H5Dmpio.c (#2457)Dana Robinson2023-02-131-2/+8
| | | | | | | * Mark a parameter as unused when not using a special debug define * Check for a chunk_entry NULL pointer after using HASH_FIND These should be the last parallel warnings so we can start building parallel with -Werror.
* corrected/added note about closing creation property list identifier (#2425)Scot Breitenfeld2023-02-115-19/+20
| | | | | | | * corrected/added note about closing creation property list identifier * removed immaterial \see APIs * added details to H5Literate
* Remove duplicated "help@hdfgroup.org" lines in file headers. (#2441)Larry Knox2023-02-111-1/+0
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* Add szip/libaec to GitHub CI and fix warnings (#2438)Dana Robinson2023-02-092-10/+16
| | | | | | | | szip (or libaec) is currently not tested in CI. This adds szip to the the Autotools GitHub CI actions on Linux when building with the Autotools. This PR also cleans up a few warnings that remained in the szip- related code so the -Werror check will pass.
* Include shlwapi.h explicitly on Windows (#2407)Mark Kittisopikul2023-01-171-0/+1
| | | | | | | | * Include shlwapi.h explicitly * Add shlwapi library to LINK_LIB when header is detected Looking for StrStrIA in the shlwapi library is not reliable due to stdcall on mingw32.
* Update FORTRAN VOL connector test for external pass-through testing (#2393)Quincey Koziol2023-01-052-1/+3
| | | | | | | | | | | | | | | | | * Correct concurrency bugs when running tests, along with a bugfix & small warning cleanup. * Committing clang-format changes * Allow spaces (and tabs) in VOL connector info string from environment variable. * Parse connector name from HDF5_PLUGIN_PATH environment variable better * Correct H5VLquery_optional to use H5VL routine instead of H5I. Also add an error message to the failure return value from not finding a plugin. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: AWS ParallelCluster user <ec2-user@ip-10-0-0-65.us-east-2.compute.internal> Co-authored-by: Koziol <qkoziol@88665a374c70.ant.amazon.com>
* Correct VOL connector env string parsing issue (#2350)Quincey Koziol2023-01-041-1/+1
| | | | | | | | | | | | * Correct concurrency bugs when running tests, along with a bugfix & small warning cleanup. * Committing clang-format changes * Allow spaces (and tabs) in VOL connector info string from environment variable. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: AWS ParallelCluster user <ec2-user@ip-10-0-0-65.us-east-2.compute.internal> Co-authored-by: Koziol <qkoziol@88665a374c70.ant.amazon.com>
* Adds RELEASE.txt notes and updates Doxygen (#2377) (#2379)Dana Robinson2022-12-292-8/+10
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* Adds Doxygen markup for H5FDdriver_query() (#2376)Dana Robinson2022-12-282-4/+23
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* Purged references to HDF5 1.13.x from the Doxygen documentation (#2365)Dana Robinson2022-12-2710-38/+30
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* Adds missing Doxygen for H5ESpublic.h (#2364)Dana Robinson2022-12-271-16/+77
| | | | | | | * Adds missing Doxygen for H5ESpublic.h * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* HL GIF tools changes (#2360)Dana Robinson2022-12-241-0/+1
| | | | * Fixes the broken Autotools option * Removes the "build HL tools" option
* Adds Doxygen VOL flag markup (#2340)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>
* Onion VFD header cleanup (#2337)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>
* H5F_LIBVER_LATEST changes for move to 1.15 (#2288)Allen Byrne2022-12-2115-13/+30
| | | | | | | | | | | | | | | * H5F_LIBVER_LATEST changes for move to 1.15 * Add new default api check * Format fixes * Fix default configure * fix lib version tests * Fix another version variable * Add 1.14 doc link
* Fix doxygen warnings and remove javadocs (#2324)Allen Byrne2022-12-205-6/+6
| | | | | * Fix doxygen warnings and remove javadocs * fix typo
* Align arg types of H5D_chunk_iter_op_t with H5Dget_chunk_info (#2074)Mark Kittisopikul2022-12-193-11/+11
| | | | | | | * Align arg types of H5D_chunk_iter_op_t with H5Dget_chunk_info * Modify chunk_info test to for unsigned / hsize_t types * Fix types in test
* moved onion VFD to FAPL group (#2321)Scot Breitenfeld2022-12-171-4/+4
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* Adds 'unused' hints for MDS io_info parameters (#2301)Dana Robinson2022-12-143-18/+17
| | | | | | | | | | | | | | | * Adds 'unused' hints for MDS io_info parameters * Committing clang-format changes * Fix issue with formatter * Committing clang-format changes * Final fix for formatter * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* added doc. warning for H5Literate_async return value (#2295)Scot Breitenfeld2022-12-141-0/+5
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* Updated H5ES documenation (#2293)Scot Breitenfeld2022-12-131-5/+5
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* Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC)… (#2291)vchoi-hdfgroup2022-12-132-24/+32
| | | | | | | | | | | | | | | | | | | | | | * 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>
* added doc. warning for H5Oflush in parallel (#2289)Scot Breitenfeld2022-12-101-0/+3
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* Check for size==0 for all datatypes read from disk, not just compound (#2287)Neil Fortner2022-12-081-9/+5
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* Compound datatypes may not have members of size 0 (#2243)Egbert Eich2022-12-071-55/+100
| | | | | | | | | | | | | | | | | | | | | | * 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>
* Fixes warnings in H5Opline.c error messages (#2281)Dana Robinson2022-12-061-3/+5
| | | | | | | * Fixes warnings in H5Opline.c error messages * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* H5E_ERR_CLS_g symbol missing when compiling C++ plugins (#2269)V. Armando Solé2022-12-061-0/+7
| | | | C++ HDF5 filter plugin SZ3 fails to build under windows with failure at linking time unless that extern "C" block is added.
* return error message related to calling API (#2276)Scot Breitenfeld2022-12-021-2/+2
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* CVE 2021 46242 develop (#2255)Egbert Eich2022-12-021-2/+6
| | | | | | | | | | | | | | | | | | | | | | * 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>
* Report error if dimensions of chunked storage in data layout < 2 (#2241)Egbert Eich2022-12-021-0/+4
| | | | | | | | | | | | | | | | 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>
* Bug Fix: Segfault in H5CX_get_vol_wrap_ctx when H5VLwrap_register is called ↵raylu-hdf2022-11-172-2/+35
| | | | | | | | | | | | | | | | from an application (#2248) * Jira HDFFV-10881: Segfault in H5CX_get_vol_wrap_ctx when H5VLwrap_register is called from an application. A quick and simple fix to make it fail with a relevant error message. * Format changes. * Committing clang-format changes * Minor change: split one condition check into two for clarity. * Adding doxygen comment for H5VLwrap_register. * Minor change: adding a little more detail to the Doxygen comment for H5VLwrap_register.
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