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* Fixed an issue that could occur when combining hyperslab selections (#2122)Neil Fortner2022-09-271-0/+7
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* develop Merge doxygen from 1.12 branch (#2095)Allen Byrne2022-09-141-1/+5
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* Update CMake code to 3.18 minimum version (#2080)Allen Byrne2022-09-031-0/+8
| | | | | * Update CMake code to 3.18 minimum version * Updated release note
* Release updates (#2033)Larry Knox2022-08-181-189/+55
| | | * Update HISTORy-1_13.txt and clean RELEASE.txt entries after 1.13.2 release.
* Add note to RELEASE.txt for GitHub #2016 (#2030)Neil Fortner2022-08-181-0/+9
| | | | | | | | | | | | | | | | | * 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>
* Add note to RELEASE.txt for HDFFV-11308 (#2029)Neil Fortner2022-08-171-0/+10
| | | | | * Add note to RELEASE.txt for HDFFV-11308 * Fix formatting error in RELEASE.txt
* Fix c++ test failure (#2005)bmribler2022-08-121-1/+4
| | | | | | | | | | | | | | | | * Fix test failure Description: - Added two H5File constructors to open file with non-default fapl - Added non-default fapl to test functions - Commented certain renaming attribute tests because of the unexpected behavior in renaming an attribute (HDFFV-11327) Platform tested: Linux/64 (jelly) * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Update version to 1.13.3-1 after creating hdf5_1_13_2 branch for 1.13.2 (#2004)Larry Knox2022-08-121-1/+1
| | | | release. Added new version to exceptions in line 75 of src/H5.c.
* Revert "Increment version to 1.13.3-1 after creating hdf5_1_13_2 branch for ↵Larry Knox2022-08-121-1/+1
| | | | | | | | release" This reverts commit c58558e872d529da6eda327183ca2d14cfa91b95. H5TEST-tcheck_version-release failed.
* Increment version to 1.13.3-1 after creating hdf5_1_13_2 branch for releaseLarry Knox2022-08-121-1/+1
| | | | of HDF5 1.13.2.
* Subfiling VFD - tidying up and fixing a few new testing failures (#1977)jhendersonHDF2022-08-091-1/+18
| | | | | | | | | | | | | | | | | | | * Rename Subfiling IOC "thread_pool_count" field to "thread_pool_size" * Add simple HDF5 example for Subfiling VFD * Subfiling VFD - never cache app topology as it may change * Subfiling VFD - cleanup unused funtionality and tidy up some TODOs * Subfiling VFD - tidy up subfiling error handling in H5subfiling_common.c * Subfiling VFD - show number of failed I/O requests on close * Subfiling VFD - Update file cmp callback after switching to MPI I/O VFD * Amend RELEASE.txt with info about h5fuse.sh and Subfiling limitations * Subfiling VFD - switch to using H5_basename and H5_dirname
* Subfiling updates for release (#1963)jhendersonHDF2022-08-041-1/+22
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Remove generated file h5fuse.sh * Link pthreads library when Subfiling VFD is built * Switch to MPI I/O driver for Subfiling HDF5 stub file * Rough first implementation for Subfiling file deletion * Subfiling VFD - get file dirname for file deletion * Subfiling VFD - set lock callback to NULL for now to avoid performance issues * Committing clang-format changes * Minor tidying up of Subfiling testing * Fixups for Subfiling VFD support in tools * Tidy up Subfiling public interface and add Doxygen * Respect Subfiling configuration settings from application * Add release note for Subfiling VFD * Committing clang-format changes * Committing clang-format changes * Shorten some Subfiling environment variable names Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Implement improved CMake fortran module folder from GH#1411 (#1922)Allen Byrne2022-07-261-0/+16
| | | | | | | | | * Implement improved CMake fortran module folder from GH#1411 * Update docs * Fix whitespace * Fix name case
* Removes the ability to build h5perf and h5perf_serial in standalone mode (#1897)Dana Robinson2022-07-201-0/+15
| | | This feature has been broken for some time and lacks a clear use case.
* Removes the small perf tool (#1896)Dana Robinson2022-07-171-0/+7
| | | | | | | | * Removes the small perf tool This tool doesn't really do anything special and installed, which conflicts with gnu's perf tool. * Adds suggestions from code review
* Add utility JNI function for 1.10 style references (#1888)Allen Byrne2022-07-141-0/+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>
* Develop HDFFV-11310 (#1811)Allen Byrne2022-07-111-3/+38
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Rework java vl check in read/write. Handle old refs in h5dump * Committing clang-format changes * Java changes allow default VL reads * Fix JNI utility for old refs * HDFFV-11310 - implement vlen read/write for atomic types. * format check fix * Mostly format fixes * More format issues * Two format changes * Use JNI names for sizeof * format change * fix size typo * Change to older method to initialize list * remove unused var * format fix * switch writeVL functions to use datatype instead of java type * Add VL option to generic read/write check * Correct function name typo * Add JIRA issue * Correct note to match change in code. * HDFFV-11318 add VL references as byte arrays * Add release note and format changes * Another format update * Fix unreleased allocations * Fix format * format correction Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Convert assertion on (possibly corrupt) file contents to normal error check ↵jhendersonHDF2022-07-081-1/+10
| | | | | | | | | (#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>
* Various warning fixes (#1812)Sean McBride2022-06-221-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Fixed -Wreserved-id-macro warnings from header include guards * Removed all __int64 and LL suffix stuff now that C99 is minimum requirement * Rename `H5FD_CTL__` to `H5FD_CTL_` to fix -Wreserved-id-macro warnings Double underscore is reserved in C++ and this public header should be C++ compatible. * Never define __STDC_FORMAT_MACROS anymore Defining it causes a -Wreserved-id-macro. Happily, according to the C++11 standard: "The macros defined by <stdint> are provided unconditionally. In particular, the symbols __STDC_LIMIT_MACROS and __STDC_CONSTANT_MACROS (mentioned in C99 footnotes 219, 220, and 222) play no role in C++." https://cplusplus.github.io/LWG/issue984 So looks like it's not necessary to define it with reasonably new toolchains. * Fixed some -Wunused-macros warnings, removed dead code * Fixed all -Wdouble-promotion warnings in C++ files * Fixed remaining -Wsuggest-destructor-override warnings * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Develop sync (#1793)Allen Byrne2022-06-091-8/+13
| | | | | * Synch update * Branch sync changes
* Update windows VS2019 and fix comments (#1781)Allen Byrne2022-05-201-1/+1
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* added HDFFV-11306 entry (#1662)Scot Breitenfeld2022-04-191-1/+6
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* Update HISTORY-1_13.txt and clean RELEASE.txt (#1471)Larry Knox2022-03-071-139/+5
| | | | | | | | | | | | | | | | | | | * Committing clang-format changes * Spelling of preceed was corrected to proceed, but should have been corrected to precede. * Correct spelling correction of 'preceed' incorrectly to 'proceed'. It should be 'precede'. * Update version to 1.13.2-1 after 1.13.1 release. Add Makefile.in to MANIFEST for addition of utils/tools and h5dwalk. * Update VERS_RELEASE_EXCEPTIONS with new incompatible release version. * Add HDF5 1.13.1 RELEASE.txt to HISTORY-1_13.txt contents to HISTORY-1_13.txt. Clean entries from RELEASE.txt. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Disable memory alloc sanity checks by default for Autotools debug builds (#1468)jhendersonHDF2022-03-031-0/+19
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* Create HISTORY-1_13.txt and update release.txt (#1466)Larry Knox2022-03-011-1419/+16
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* Update version to 1.13.2-1 after 1.13.1 release; add new Makefile.in files ↵Larry Knox2022-03-011-1/+1
| | | | | | to MANIFEST (#1460)
* Fix metadata cache bug when resizing a pinned/protected entry (v2) (#1463)jhendersonHDF2022-03-011-9/+17
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* Amend RELEASE.txt with note about parallel compression testing assertion ↵jhendersonHDF2022-02-251-0/+9
| | | | failure (#1458)
* Add release note for #1438 (#1457)Allen Byrne2022-02-251-0/+17
| | | | | * Add release note for #1438 * fix typos.
* Parallel Compression improvements (#1302)jhendersonHDF2022-02-241-1/+39
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* Enable creation of RPM/DEB binaries GH#1394 (#1398)Allen Byrne2022-02-221-0/+9
| | | Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Revert "Fix metadata cache bug when resizing a pinned/protected entry ↵Larry Knox2022-02-121-17/+0
| | | | | (#1358)" (#1437) This reverts commit 01092658a3095c31d7dc1ed1beebbd965095c244.
* Add -showconfig to h5cc scripts to dump libhdf5.settings file (#1391)Allen Byrne2022-02-111-0/+7
| | | | | * Add -showconfig to h5cc scripts to dump libhdf5.settings file * Added note
* Fix metadata cache bug when resizing a pinned/protected entry (#1358)jhendersonHDF2022-02-081-0/+17
| | | | | | | | | | | | | | When resizing a pinned/protected cache entry, the metadata cache code previously would wait until after resizing the entry to attempt to log the newly-dirtied entry. This would cause H5C_resize_entry to mark the entry as dirty and make H5AC_resize_entry think that it doesn't need to add the newly-dirtied entry to the dirty entries skiplist. Thus, a subsequent H5AC__log_moved_entry would think it needs to allocate a new entry for insertion into the dirty entry skip list, since the entry doesn't exist on that list. This causes an assertion failure, as the code to allocate a new entry assumes that the entry is not dirty.
* Unify handling of collective metadata reads status (#1206)jhendersonHDF2022-01-291-0/+21
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* Parallel rank0 deadlock fixes (#1183)jhendersonHDF2022-01-221-0/+12
| | | | | | | * Fix several places where rank 0 can skip past collective MPI operations on failure * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Implement H5ESget requests function to retrieve requests from an event set ↵Neil Fortner2022-01-201-0/+7
| | | | | | (#1355) Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Convert vds swmr test script to powershell (#1245)Allen Byrne2021-12-081-0/+10
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Convert SWMR shell scripts to Windows powershell. * Use $LastExitCode instead of $? in script * Prevent execution in a different window * Github #969 Use stdout instead of file for configure check (#1089) * Use stdout instead of file for configure check * Make change requested by #1157 * Change fortran to use stderr for configure * Correct typo * remove obsolete file check * Fortran statement fix * Don't allow H5Pset(get)_all_coll_metadata_ops for DXPLs (#1201) * Fixes const warnings in H5ES package (#1211) * Quiets a 'set but not used' warning in h5diff_array.c (#1210) * Convert vds swmr test script to powershell * Enable vdsswmr powershell test * Add configure vdsswmr statement * Correct powershell script vars * Convert SWMR shell scripts to Windows powershell. * Use $LastExitCode instead of $? in script * Prevent execution in a different window * Github #969 Use stdout instead of file for configure check (#1089) * Use stdout instead of file for configure check * Make change requested by #1157 * Change fortran to use stderr for configure * Correct typo * remove obsolete file check * Fortran statement fix * Convert vds swmr test script to powershell * Enable vdsswmr powershell test * Add configure vdsswmr statement * Correct powershell script vars * Cleanup review issues * Fix variable assignment * Change the wait function to pass in the path * Disable actual test execution until programs fixed * Adjust copyright text * Fix spelling Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Fixed Spelling Errors (#1166)Scot Breitenfeld2021-12-071-4/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 * switched from using MPI_count, to actual bytes written for H5FD_mpio_debug rw debugging * Committing clang-format changes * changed size_i in printf to reflect the I/O. * Committing clang-format changes * Fixed seg fault with xlf on BE with -qintsize=8 * fixed error function string * spelling corrections via codespell, added new spell check github actions * Committing clang-format changes * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * Committing clang-format changes * misc * misc * misc * misc * misc * misc * Committing clang-format changes * misc * work around for https://github.com/codespell-project/codespell/issues/2137 * misc * added missing file * misc * misc. * misc * switch to using Codespell with GitHub Actions * misc. * misc. * fixed more sp errors * Fix new typos found by codespell. * fixed proceed with precede * fixed variable in fortran test * fixed minnum * updated spelling list Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Update version to 1.13.1-1 after creation of branch for 1.13.0 release. (#1236)Larry Knox2021-11-301-1/+1
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* Fix indentation in RELEASE.txt to be consistent. (#1232)Larry Knox2021-11-301-519/+519
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* Add support for parallel tools based on the 3rd party library mpiFileUtils ↵rawarren2021-11-291-0/+19
| | | | | | | | | | (libMFU) … (#1177) Adds tool h5dwalk and configure options to enable building it. Co-authored-by: Richard Warren <Richard.Warren@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Richard.Warren <richard.warren@jelly.ad.hdfgroup.org> Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Fixes an assert in H5Pget_filter_by_id1/2 w/ out-of-range IDs (#1222)Dana Robinson2021-11-241-0/+8
| | | | | | | | | | | | * Fixes an assert in H5Pget_filter_by_id1/2 w/ out-of-range IDs Filter IDs < 0 or > H5Z_FILTER_MAX could trip an assert in the library due to missing ID range checks in H5Pget_filter_by_id1/2. The library now returns a normal error code when filter IDs are out of range. Fixes HDFFV-11286. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Re-enable collective metadata reads after disabling for chunk lookup (#1173)jhendersonHDF2021-11-091-0/+7
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* New references for Dimension Scale APIs (#1139)jhendersonHDF2021-11-051-0/+10
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* H5repack tests should fail if a corrupted file causes h5repack to (#1138)Larry Knox2021-10-261-0/+11
| | | | | | * H5repack tests should fail if a corrupted file causes h5repack to segfault/core dump. * Add release note for HDFV-10590, CVE-2018-17432.
* Add release note for HDFFV-11150 fix. (#1106)Larry Knox2021-10-211-1/+23
| | | | | * Add release note for HDFFV-11150 fix. * Add note about gif tool CVEs.
* Fixed HL_test_packet, incorrect length assignment (#1100)Allen Byrne2021-10-201-1/+5
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* Move test utilities to utils/test folder (#1109)Allen Byrne2021-10-201-2/+10
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Move test utilities to utils/test folder * Fix makefile assignment * Add new dir * add new folder * Correct copied makefile * Fix dir typo * Add missing include dir * Remove unnecessary lib link * Correct dependent dirs * Fix conditional checks * Disable test if not built * fix path to executable * Use fixture for swmr_vfd check * Add release note * Correct shell tests and c++ flag warning * Update autotools c++ warning * Fix typo
* To reduce maintenance effort, delete the `noerror-` variants of the compiler ↵David Young2021-10-061-0/+7
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | flags files (#1033) * Avoid maintenance headaches: delete the `noerror-` variants of the compiler flags files, since they essentially duplicate the `error-` files modulo the replacement of `-Werror=` with `-W` and any changes in comments. (I verified the duplication with a script.) For autoconf, reinstate the use of the `demote_errors` shell function to derive the `noerror-` content from the `error-` content. `demote_errors` replaces `-Werror=` with `-W` when `WARNINGS_AS_ERRORS` is `no`. Slightly reorder `configure.ac` so that the setting of `WARNINGS_AS_ERRORS` takes effect before the `error-` files are sourced. * Take a stab at updating the CMake files to match the changes I made to the autoconf files to remove `noerror-` files. I'm not much of a CMake user so these changes are quite rough. Looks like the duplication can be reduced with the introduction of a new macro. * Delete `noerror-` files from the MANIFEST. * Reduce duplication in the CMake files: perform the HDF5_ENABLE_WARNINGS_AS_ERRORS test once in the ADD_H5_FLAGS macro. * Add a release note.
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