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* Merge/update CMake, presets,java and tools (#3393)Allen Byrne2023-08-211-27/+84
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* Fix CMake generator expression syntax (#2940)Allen Byrne2023-05-121-3/+3
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* Make sure that ONLY_SHARED_LIBS option is correctly set (#2546)Allen Byrne2023-03-141-2/+2
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* Change TestExpress #1722 (#1776)Allen Byrne2022-05-201-1/+7
| | | | | * Change TestExpress #1722 * Update comment
* Removes unused H5HP and H5MP packages (#1610)Dana Robinson2022-04-071-2/+0
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* 1.12 Merge Consolidate VFD create list macro #1132 (#1133)Allen Byrne2021-10-311-20/+22
| | | | | | | * Merge Consolidate VFD create list macro #1132 * Split dir create into separate macro * fix VFD settings
* 1.12 Merge Move test utilities to utils/test folder #1109 (#1110)Allen Byrne2021-10-211-16/+20
| | | | | | | * Merge Move test utilities to utils/test folder #1109 * Merge Correct shell tests and c++ flag warning * Fix typo
* Brings the thread-safety recursive writer locks to 1.12 (#466)Dana Robinson2021-05-141-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * First cut at replaceing the existing mutex with a recursive R/W lock. This implementation has the following issues: 1) pthreads implementation only -- we still need a windows version. 2) must investigate thread cancelation issues 3) Error reporting is very poor. I followed the error reporting on the existing thread safe code, but this should be re-visited and improved. Code is currently setup to use the new recursive R/W lock instead of the global mutex to control entry to the library in threadsafe builds. To revert to the global mutex, set H5TS__USE_REC_RW_LOCK_FOR_GLOBAL_MUTEX in H5TSprivate.h to FALSE. Added a reasonably robust regression test for the reursive R/W lock in test/ttsafe_rec_rw_lock.c Note that the change to hl/src/H5LTanalyse.c is an artifact of clang-format. Tested serial threadsafe debug and production on jelly, and also regular serial / debug. On Windows builds, the new recursive R/W lock should not be built and we should use the existing global mutex -- however this is not tested at this time. * Updates CMake to build recursive RW lock test * Updates to allow building on Windows * Moves #if statements to better protect non-RW lock code * Adds configure and CMake options for the recursive RW locks * Committing clang-format changes * Updates RELEASE.txt and the build options * Renames H5TS RW lock things * Makes struct members platform independent Also removes _ptr from identifiers * Partial thread-safety RW locks platform independence * Committing clang-format changes * Pthreads side of things is platform-independent now * Formatted source * Added Windows equivalents for some Pthreads calls * Rename H5TS takedown call to destroy * Reorg of RW lock code * Committing clang-format changes * Changes to Pthreads code after development on Visual Studio * Moves stats macros to static inline functions and tidies memory allocs * Converts RW lock print stats call to use C99 formatting * Fixes typos * Formatted source * Updates the RELEASE.txt note to indicate no Win32 threads support Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Merge PRs #143, 144 to hdf5_1_12 (#630)Larry Knox2021-05-061-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Snapshot version 1.12 release 1-3. Update version to 1.12.1-4. * First cut of the H5 public API documentation. (#80) * First cut of the H5 public API documentation. * Added H5Z "bonus track." * Applied Quincey's patch. * Added the missing patches from Quincey's original patch. * H5PL (complete) and basic H5VL API documentation. * Added H5I API docs. * Added H5L API docs. * First installment from Elena's H5T batch. * Second installment of Elena's H5T batch. * Final installment of Elena's H5T batch. * Full set of current H5F documentation. (#105) * First cut of the H5 public API documentation. * Added H5Z "bonus track." * Applied Quincey's patch. * Added the missing patches from Quincey's original patch. * H5PL (complete) and basic H5VL API documentation. * Added H5I API docs. * Added H5L API docs. * First installment from Elena's H5T batch. * Second installment of Elena's H5T batch. * Final installment of Elena's H5T batch. * Migrated documentation for SWMR functions. * Catching up on MDC functions. * Integrated the H5F MDC function documentation. * Added MDC and parallel H5F functions. * Slightly updated main page. * Added doxygen/dox/H5AC_cache_config_t.dox to MANIFEST. * Doxygen - added (mostly) beginner functions (#112) * Doxygen - added (mostly) beginner functions * Removed duplicate H5Pset_szip function * Add src/H5module.h to MANIFEST. * close #195. (#196) * Update HDF5PluginMacros.cmake * Update HDF5PluginMacros.cmake * Avoid aligned access for references by decoding into temporary buffer and then copying the result into the actual buffer. Update test to be more thorough with using compound datatype fields everywhere. (#206) * Modify temporary rpath for testing in java example scripts. (#230) * Fix undefined left shifting of negative numbers (#338) Undefined Bahavior Sanitizer errored here about left shifting negative numbers. * Fixes various warnings noticed on Windows (#425) * Fixes various warnings noticed on Windows - Adds a prototype for our implementation of vasprintf - Return type of H5_get_utf16_str() is now non-const - Fixes possible uninitialized return type in Wremove_utf8 - Better isolation of fork() code in accum.c:test_swmr_write_big() - Better isolation of non-zlib code in dsets.c:test_filter_delete() - Removed unused variable in trefer.c:test_reference_cmpnd_obj() * Fixes clang-format issues * Applied clang-tidy readability-non-const-parameter warning fixes auto… (#429) * Automatically applied clang-tidy readability-avoid-const-params-in-decls fixes Removes useless const declarations. * Fixed most readability-non-const-parameter warnings These changes were made automatically by clang-tidy, but I manually reverted the changes related to the H5Z_func_t signature. * Reformat source with clang v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * Added C++11 override keyword where appropriate (#433) Added H5_OVERRIDE macro for compatibility with both C++11 and older. * Various clang tidy warning fixes (#448) * Fixed clang-tidy bugprone-reserved-identifier warnings * Fixed clang-tidy bugprone-assert-side-effect warnings * Fixed clang-tidy bugprone-copy-constructor-init warning * Fixed clang-tidy readability-redundant-preprocessor warning For error_test.c the removed code was already dead, because it was in the else of an `#if H5_USE_16_API` block. Based on H5Location.h, I think p_get_ref_obj_type was meant to be in `#ifndef DOXYGEN_SHOULD_SKIP_THIS` and an `#endif` was missing. Similarly, in the header, getObjTypeByIdx is only in H5_NO_DEPRECATED_SYMBOLS, not DOXYGEN_SHOULD_SKIP_THIS. * Fixed clang-tidy readability-redundant-string-init warnings * Fixed some clang-tidy performance-type-promotion-in-math-fn warnings * Fixed clang-tidy performance-unnecessary-value-param warnings * Reformat source with clang v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * Removed checks/workarounds for pre-C++89 compatibility (#449) After 30+ years, just assume that the following exist: - extension-less includes - namespaces - std:: - static_cast - bool * Fixed all clang-tidy bugprone-suspicious-string-compare warnings (#451) * Fixed all clang-tidy bugprone-suspicious-string-compare warnings This change was generated entirely by clang-tidy itself. * Reformat code with clang v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * Remove 2 functions incorrectly merged from develop in a cherry-pick merge of PR #451. * Minor parallel improvements (#519) * Improve MPI error reporting, handled failed operations in parallel tests more nicely, and clean up MPI_Allreduce for determining whether to break collective I/O * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Clean up MPI-IO VFD tracing support (#520) * Clean up tracing support * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Brings the native implementation of H5Fdelete() from Bitbucket (#524) * Committing clang-format changes * Brings the native VFD H5Fdelete() implementation from Bitbucket Only brings the 'del' callbacks, not the 'open/close' scheme. * Formatter changes * Committing clang-format changes * Fixes direct VFD callback name * Removes UNUSED macro from family API call * Adds barrier and rank 0 check to MPI-I/O VFD delete * Revert "Adds barrier and rank 0 check to MPI-I/O VFD delete" This reverts commit 909765f759d9d96e84f4b8b1cc14f7d2b3ac8143. * Revert "Revert "Adds barrier and rank 0 check to MPI-I/O VFD delete"" This reverts commit 9b04bef1157853fc79fcb8fcc3e8ba1371091702. * Adds a second barrier after the delete in MPI-I/O VFD * Only delete files in the core VFD when the backing store flag is set * Fixes string issues in multi VFD Also, h5test.c cleanup code now uses H5Fdelete(). * Formatted source * Rework fapl checks for MPI-I/O VFD delete callback Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Minor warning fixes in develop (#526) * Committing clang-format changes * Minor warning fixes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Removes implementation of my_strdup() from the multi VFD (#527) * Committing clang-format changes * Removes my_strdup() from the multi VFD * Use strdup directly when memory sanity checks are off Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Removes dead H5ST package from the library (#528) * Committing clang-format changes * Removes the unused H5ST package from the library Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix HDFFV-11232 (#530) * fixed missed closing of a dataset * fixed missed closing of a dataset * fixed typo in error return * Committing clang-format changes * minor edits * code format * Committing clang-format changes * code format * minor edit * added H5fortkit dependency for H5VLff.F90, HDFFV-11232 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fixes incorrect usage of H5I_BADID (#554) * Committing clang-format changes * Fixes incorrect use of H5I_BADID Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fixes a segfault when H5Pset_mdc_log_options is called multiple times on a fapl (#601) * Committing clang-format changes * Fixes a segfault when H5Pset_mdc_log_options() is called multiple times An internal string is incorrectly freed when the API call is invoked multiple times on a property list, which will usually cause a segfault to occur. On the first call the log location is NULL so the problem doesn't occur. Fixes HDFFV-11239 * Fixes typos Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix for a segfault when H5Pset_fapl_log is passed an invalid fapl ID (#607) * Committing clang-format changes * Fixes an issue where H5Pset_fapl_log sefaults when passed an invalid fapl ID This was due to a pointer-containing struct being memset after the first internal API call. If the first call failed, the error condition would check if the pointer was not NULL and then attempt to free it if not. This would lead to the freeing of a wild pointer if an invalid fapl ID were passed in. This was fixed by reordering the memset and adding a test to ensure the problem stays fixed. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fixes crashes when size_hint > UINT32_MAX is passed to H5Gcreate1 (#611) * Committing clang-format changes * Fixes incorrect size_hint handling in H5Gcreate1 * Updates the size hint type for group creation * Updates the RELEASE.txt note * Revert "Updates the RELEASE.txt note" This reverts commit 3df386acca806d652bbe2209f7c4503b30f068ff. * Reverts previous behavior to use a uint32_t struct field * Updates RELEASE.txt Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Revert "Brings the native implementation of H5Fdelete() from Bitbucket (#524)" This reverts commit 38d1b121ae428138b8863c2a319518c7363c2d94. * Removed mentions of Wdeclaration-after-statement now that C99 is requ… (#447) * Removed mentions of Wdeclaration-after-statement now that C99 is required * Remove -Werror=declaration-after-statement from error-general file. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * Made private my_yyinput function static (#618) This prevents it being exported as a public symbol. * Adds const to a few global variables (#623) * Committing clang-format changes * Adds consts to a few global variables Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * (fix) Segmentation fault when using a compound type. (#143) * (fix) Segmentation fault when using a compound type. In the case when a compounded attribute is written to dataset followed by writing the data with a data transform function to the dataset will result in a segmentation fault. It turns out the data is classified as compounded while it is not. Now, the state is always reset first to not compounded followed by the existing check if the variable is compounded. * (fix) Removed undesired comment lines. * (fix) Segmentation fault when using a compound type: added test. * (fix) Added the missing cmpd_transform.c file to MANIFEST. * (fix) cmpd_dtransform test: autotools and source header. Added the cmp_dtransform test to the autotools configuration and updated the HDF Group copyright header. Co-authored-by: Jan-Willem Blokland <Jan-Willem.Blokland@Shell.com> * (fix) H5Z_xform_create function and scientific notation (#144) * (fix) H5Z_xform_create function and scientific notation Implemented a more sophisticated check to support scientific notation in the expression of the H5Zset_data_transform function. * (fix) H5Z_xform_create and scientific notation: Added test. Added a test to demonstrate that the parsing of expression which includes scientific notation works correctly. Improved inline comment. Co-authored-by: Jan-Willem Blokland <Jan-Willem.Blokland@Shell.com> * Committing clang-format changes Co-authored-by: Gerd Heber <gheber@hdfgroup.org> Co-authored-by: bljhdf <58825073+bljhdf@users.noreply.github.com> Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: Quincey Koziol <quincey@koziol.cc> Co-authored-by: Sean McBride <sean@rogue-research.com> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: Quincey Koziol <koziol@lbl.gov> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org> Co-authored-by: Jan-Willem Blokland <J.W.S.Blokland@XS4All.nl> Co-authored-by: Jan-Willem Blokland <Jan-Willem.Blokland@Shell.com>
* Cherry-pick 12 develop branch PRs to hdf5_1_12 (#622)Larry Knox2021-05-051-1/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Snapshot version 1.12 release 1-3. Update version to 1.12.1-4. * First cut of the H5 public API documentation. (#80) * First cut of the H5 public API documentation. * Added H5Z "bonus track." * Applied Quincey's patch. * Added the missing patches from Quincey's original patch. * H5PL (complete) and basic H5VL API documentation. * Added H5I API docs. * Added H5L API docs. * First installment from Elena's H5T batch. * Second installment of Elena's H5T batch. * Final installment of Elena's H5T batch. * Full set of current H5F documentation. (#105) * First cut of the H5 public API documentation. * Added H5Z "bonus track." * Applied Quincey's patch. * Added the missing patches from Quincey's original patch. * H5PL (complete) and basic H5VL API documentation. * Added H5I API docs. * Added H5L API docs. * First installment from Elena's H5T batch. * Second installment of Elena's H5T batch. * Final installment of Elena's H5T batch. * Migrated documentation for SWMR functions. * Catching up on MDC functions. * Integrated the H5F MDC function documentation. * Added MDC and parallel H5F functions. * Slightly updated main page. * Added doxygen/dox/H5AC_cache_config_t.dox to MANIFEST. * Doxygen - added (mostly) beginner functions (#112) * Doxygen - added (mostly) beginner functions * Removed duplicate H5Pset_szip function * Add src/H5module.h to MANIFEST. * close #195. (#196) * Update HDF5PluginMacros.cmake * Update HDF5PluginMacros.cmake * Avoid aligned access for references by decoding into temporary buffer and then copying the result into the actual buffer. Update test to be more thorough with using compound datatype fields everywhere. (#206) * Modify temporary rpath for testing in java example scripts. (#230) * Fix undefined left shifting of negative numbers (#338) Undefined Bahavior Sanitizer errored here about left shifting negative numbers. * Fixes various warnings noticed on Windows (#425) * Fixes various warnings noticed on Windows - Adds a prototype for our implementation of vasprintf - Return type of H5_get_utf16_str() is now non-const - Fixes possible uninitialized return type in Wremove_utf8 - Better isolation of fork() code in accum.c:test_swmr_write_big() - Better isolation of non-zlib code in dsets.c:test_filter_delete() - Removed unused variable in trefer.c:test_reference_cmpnd_obj() * Fixes clang-format issues * Applied clang-tidy readability-non-const-parameter warning fixes auto… (#429) * Automatically applied clang-tidy readability-avoid-const-params-in-decls fixes Removes useless const declarations. * Fixed most readability-non-const-parameter warnings These changes were made automatically by clang-tidy, but I manually reverted the changes related to the H5Z_func_t signature. * Reformat source with clang v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * Added C++11 override keyword where appropriate (#433) Added H5_OVERRIDE macro for compatibility with both C++11 and older. * Various clang tidy warning fixes (#448) * Fixed clang-tidy bugprone-reserved-identifier warnings * Fixed clang-tidy bugprone-assert-side-effect warnings * Fixed clang-tidy bugprone-copy-constructor-init warning * Fixed clang-tidy readability-redundant-preprocessor warning For error_test.c the removed code was already dead, because it was in the else of an `#if H5_USE_16_API` block. Based on H5Location.h, I think p_get_ref_obj_type was meant to be in `#ifndef DOXYGEN_SHOULD_SKIP_THIS` and an `#endif` was missing. Similarly, in the header, getObjTypeByIdx is only in H5_NO_DEPRECATED_SYMBOLS, not DOXYGEN_SHOULD_SKIP_THIS. * Fixed clang-tidy readability-redundant-string-init warnings * Fixed some clang-tidy performance-type-promotion-in-math-fn warnings * Fixed clang-tidy performance-unnecessary-value-param warnings * Reformat source with clang v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * Removed checks/workarounds for pre-C++89 compatibility (#449) After 30+ years, just assume that the following exist: - extension-less includes - namespaces - std:: - static_cast - bool * Fixed all clang-tidy bugprone-suspicious-string-compare warnings (#451) * Fixed all clang-tidy bugprone-suspicious-string-compare warnings This change was generated entirely by clang-tidy itself. * Reformat code with clang v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * Remove 2 functions incorrectly merged from develop in a cherry-pick merge of PR #451. * Minor parallel improvements (#519) * Improve MPI error reporting, handled failed operations in parallel tests more nicely, and clean up MPI_Allreduce for determining whether to break collective I/O * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Clean up MPI-IO VFD tracing support (#520) * Clean up tracing support * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Brings the native implementation of H5Fdelete() from Bitbucket (#524) * Committing clang-format changes * Brings the native VFD H5Fdelete() implementation from Bitbucket Only brings the 'del' callbacks, not the 'open/close' scheme. * Formatter changes * Committing clang-format changes * Fixes direct VFD callback name * Removes UNUSED macro from family API call * Adds barrier and rank 0 check to MPI-I/O VFD delete * Revert "Adds barrier and rank 0 check to MPI-I/O VFD delete" This reverts commit 909765f759d9d96e84f4b8b1cc14f7d2b3ac8143. * Revert "Revert "Adds barrier and rank 0 check to MPI-I/O VFD delete"" This reverts commit 9b04bef1157853fc79fcb8fcc3e8ba1371091702. * Adds a second barrier after the delete in MPI-I/O VFD * Only delete files in the core VFD when the backing store flag is set * Fixes string issues in multi VFD Also, h5test.c cleanup code now uses H5Fdelete(). * Formatted source * Rework fapl checks for MPI-I/O VFD delete callback Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Minor warning fixes in develop (#526) * Committing clang-format changes * Minor warning fixes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Removes implementation of my_strdup() from the multi VFD (#527) * Committing clang-format changes * Removes my_strdup() from the multi VFD * Use strdup directly when memory sanity checks are off Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Removes dead H5ST package from the library (#528) * Committing clang-format changes * Removes the unused H5ST package from the library Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix HDFFV-11232 (#530) * fixed missed closing of a dataset * fixed missed closing of a dataset * fixed typo in error return * Committing clang-format changes * minor edits * code format * Committing clang-format changes * code format * minor edit * added H5fortkit dependency for H5VLff.F90, HDFFV-11232 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fixes incorrect usage of H5I_BADID (#554) * Committing clang-format changes * Fixes incorrect use of H5I_BADID Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fixes a segfault when H5Pset_mdc_log_options is called multiple times on a fapl (#601) * Committing clang-format changes * Fixes a segfault when H5Pset_mdc_log_options() is called multiple times An internal string is incorrectly freed when the API call is invoked multiple times on a property list, which will usually cause a segfault to occur. On the first call the log location is NULL so the problem doesn't occur. Fixes HDFFV-11239 * Fixes typos Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix for a segfault when H5Pset_fapl_log is passed an invalid fapl ID (#607) * Committing clang-format changes * Fixes an issue where H5Pset_fapl_log sefaults when passed an invalid fapl ID This was due to a pointer-containing struct being memset after the first internal API call. If the first call failed, the error condition would check if the pointer was not NULL and then attempt to free it if not. This would lead to the freeing of a wild pointer if an invalid fapl ID were passed in. This was fixed by reordering the memset and adding a test to ensure the problem stays fixed. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fixes crashes when size_hint > UINT32_MAX is passed to H5Gcreate1 (#611) * Committing clang-format changes * Fixes incorrect size_hint handling in H5Gcreate1 * Updates the size hint type for group creation * Updates the RELEASE.txt note * Revert "Updates the RELEASE.txt note" This reverts commit 3df386acca806d652bbe2209f7c4503b30f068ff. * Reverts previous behavior to use a uint32_t struct field * Updates RELEASE.txt Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Revert "Brings the native implementation of H5Fdelete() from Bitbucket (#524)" This reverts commit 38d1b121ae428138b8863c2a319518c7363c2d94. Co-authored-by: Gerd Heber <gheber@hdfgroup.org> Co-authored-by: bljhdf <58825073+bljhdf@users.noreply.github.com> Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: Quincey Koziol <quincey@koziol.cc> Co-authored-by: Sean McBride <sean@rogue-research.com> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: Quincey Koziol <koziol@lbl.gov> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
* Manual sync with develop (#95)Dana Robinson2020-11-171-0/+20
| | | | Brings all features from develop. Note that RELEASE.txt has not been updated (will be done in a future PR).
* OESS-98 add CMake option to build plugins project within hdf5Allen Byrne2020-10-161-19/+19
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* Add clang-format changes from develop.Allen Byrne2020-09-281-3/+156
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* Sync with developDana Robinson2020-08-011-1/+41
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* Merge pull request #2693 in HDFFV/hdf5 from ↵Vailin Choi2020-07-211-0/+1
| | | | | | | | ~VCHOI/my_third_fork:bugfix/HDFFV-11080-heap-use-after-free-by-the-call to develop * commit '3023b34272cc6ada84aebfa7441a6a55afa3621c': Update MANIFEST. Add new test to Cmake. Fix for jira issue HDFFV-11080: (1) Patch up the file pointer when reading attribute of variable length datatype (2) Test to verify the fix when doing multiple threads
* Add thread_id.c to the MANIFEST and the CMakeLists.txt per Allen'sDavid Young2020-05-061-0/+1
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* TRILAB-192 - merge changes from developAllen Byrne2020-04-071-3/+13
| | | | Single source, config files, for warnings for both autotools and CMake. Update CMake libraries, tools, tests to use correct flags.
* Merge changes from develop mostly cmake 3.12 minimum versionAllen Byrne2020-02-231-1/+1
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* Improved CMake options for testsAllen Byrne2020-01-191-1/+3
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* Revert "Merge branch 'hdf5_1_12' of ↵Jerome Soumagne2019-12-091-2/+0
| | | | | | | https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into hdf5_1_12" This reverts commit 9f9336a5bd541752f472bab4c93da8de89f862cd, reversing changes made to 437a1919e7ba60fe75a33a466d264183a0255319.
* Merged HDFFV-10929_2GB_testing to hdf5_1_12Richard Warren2019-12-061-0/+2
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* Add new H5R API that abstracts object, region and attribute reference typesJerome Soumagne2019-10-081-0/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Also support references to external files Add new H5T_REF type and type conversion routines Support conversion from H5T_REF_OBJ/DSET_REG to H5T_REF Add H5Treclaim() API to reclaim memory of vlen/reference types Deprecate H5Dvlen_reclaim() Fix H5T_vlen_reclaim() and H5T_reclaim() to use private callback Add H5T_ref_reclaim() Move previous H5R APIs to H5Rdeprec.c Clean up H5Ocopy Separate H5O_copy_expand_ref() to H5Ocopy_ref() Add support for copying new reference types Clean up deprecated routines to go through VOL and same code path Fix return codes in existing trefer.c test Rename trefer.c to trefer_deprec.c trefer.c is for new references Add performance test for trefer Add additional obj_copy_ref test Make use of tokens and blobs to store references Skip blob encoding for object references Start adding new reference examples
* Fix CMake build of test needing compression libsAllen Byrne2019-09-031-1/+14
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* HDFFV-10677 and HDFFV-10661Binh-Minh Ribler2019-08-281-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Description: - Added functions to query chunk information: H5Dget_num_chunks(dset_id, fspace_id, *nchunks) Gets the number of written chunks that intersect with the given dataspace. However, in this version, the intersection is not yet completed. Thus, the number of all written chunks will be returned. H5Dget_chunk_info_by_coord(dset_id, *offset, *filter_mask, *addr, *size) Given a chunk's logical coordinates, returns the chunk's filter, address, and size. H5Dget_chunk_info(dset_id, fspace_id, index, *offset, *filter_mask, *addr, *size) Given a chunk's index, returns the chunk's logical coordinates, filter, address, and size. The chunk belongs to a set of chunks that have nonempty intersection with the specified dataspace. However, in this version, the intersection is not yet completed, and the index is of all the written chunks. These functions comply with VOL. - Fixed some oversights found in the library for the tests in chunk_info.c to work correctly. The returned value from a callback function was not checked in H5EA_iterate(), H5FA_iterate(), and H5D__none_idx_iterate(). This oversight caused a callback function to continue iterating even though it's supposed to stop. Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1011test)
* Squashed commit of the following:Larry Knox2019-07-251-0/+3
| | | | | | | | | | | Merge changes from update_merged_S3_HDFS branch into develop. commit d5034315aea88629929ac0c9c59ebfafd5f21a31 Merge: 9c48823 d3fdcd8 Author: Larry Knox <lrknox@hdfgroup.org> Date: Thu Jul 25 08:24:53 2019 -0500 Merge branch 'develop' into update_merged_S3_HDFS
* HDFFV-8631 mingw is different platformAllen Byrne2019-07-171-2/+2
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* Add support for GCC9, update warnhist script, and clean up warnings.Quincey Koziol2019-07-031-0/+1
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* HDFFV-10805 Add option to only build shared targetsAllen Byrne2019-06-181-126/+103
| | | | | HDFFV-10805 Add ONLY_SHARED_LIBS option and prefer shared over static HDFFV-10803 Update FindSZIP.cmake find module Remove unneeded modules and update java modules
* ESE-97 add vol_plugin test to CMake buildsAllen Byrne2019-04-251-2/+19
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* Fix CMake errorsAllen Byrne2019-04-181-1/+1
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* Forgot to add external_common.c and external_common.h.Songyu Lu2019-04-101-0/+2
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* Updated CMake for the splitting of external.c and vds.c.Songyu Lu2019-04-101-0/+2
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* CMake: fix pthread linking to only be privateJerome Soumagne2019-03-131-1/+6
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* Fix CMake H5_HAVE_THREADSAFE to set value in H5pubconf.hJerome Soumagne2019-02-211-1/+1
| | | | | | Add REQUIRED to find_package(Threads) Link against thread library if static and not WIN32 platform
* HDFFV-10703 Update CMake commands to latest standardAllen Byrne2019-02-151-10/+10
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* Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Vailin Choi2019-01-021-1/+1
|\ | | | | | | | | | | | | | | develop Resolve conflicts: Conflicts: test/Makefile.am
| * Fixed a CMake build issue (CMake still doesn't run the VOL pluginDana Robinson2018-12-281-1/+1
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* | Fix for HDFFV-10659: The library abort with "infinite loop closing library"Vailin Choi2018-12-281-0/+1
|/ | | | | | | | after deleting attributes in densed storage. The fix: When deleting attribute nodes from the name index v2 B-tree, if an attribute is found in the intermediate B-tree nodes, which may be merged/redistributed in the process, we need to free the dynamically allocated spaces for the intermediate decoded attribute.
* HDFFV-10605 Only test plugins if SHARED enabledAllen Byrne2018-11-061-0/+2
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* VOL FEATUREDana Robinson2018-10-101-0/+33
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* CMake changes for SKIPPED and flush testsAllen Byrne2018-09-241-1/+1
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* Fix usage of compression lib in shared testsAllen Byrne2018-06-011-1/+18
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* Merge pull request #1043 in HDFFV/hdf5 from ↵Dana Robinson2018-05-311-0/+1
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~DEROBINS/hdf5_der:h5do_direct_chunk_hl_to_src to develop * commit '1da9c5545c013ebc540ba3044810889d4acfa5be': Restored some unused #defines to the deprecated section of H5Dpublic.h. Added deprecated symbol wrappers for the H5DOwrite/read_chunk wrappers. Updated commenting in the H5DO compat test. Stripped out most of the duplicated functionality in the H5DO compat test. * Added H5DO compatibility functions. * Changed the offset copy to use an array on the stack. * Yanked some unused #defines. * Fixed the error tests * Moved common functionality into helper functions Normalize with trunk prior to update merge Fixed a warning. Finished move of H5DOread/write_chunk calls to H5D. First stage of moving H5DOread/write_chunk() to src/ and making them H5D calls. * Moved H5DOread/write_chunk() to H5Dio.c and renamed to H5D*. * Moved the hl/test/test_dset_opt test to test/ and renamed to direct_chunk. * Moved the hl/test/dectris_hl_perf test to tools/test/perform and renamed to direct_write_perf. * Updated autotools and CMake files.
| * Merge branch 'develop' into h5do_direct_chunk_hl_to_srcDana Robinson2018-05-151-96/+77
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| * \ Merge branch 'develop' into h5do_direct_chunk_hl_to_srcDana Robinson2018-04-301-7/+23
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| * | | First stage of moving H5DOread/write_chunk() to src/ and makingDana Robinson2018-04-301-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | them H5D calls. * Moved H5DOread/write_chunk() to H5Dio.c and renamed to H5D*. * Moved the hl/test/test_dset_opt test to test/ and renamed to direct_chunk. * Moved the hl/test/dectris_hl_perf test to tools/test/perform and renamed to direct_write_perf. * Updated autotools and CMake files.
* | | | Fix MPI on Windows by adding MPI include folderAllen Byrne2018-05-091-21/+21
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* | | Correct COMPILE defs usageAllen Byrne2018-05-091-1/+1
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* | | TRILABS-19 remove add_defintions and use generator expressionsAllen Byrne2018-04-261-96/+77
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* | TRILABS-20 set a compiler name on all project commandsAllen Byrne2018-04-201-1/+1
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