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* VFD SWMR: Merges from develop (#1670)Dana Robinson2022-04-211-31/+31
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Cleans up SWMR test scripts (both legacy and VFD) * Brings over format source changes for Java * Normalization of HL, Fortran, C++, Java w/ develop * Removes the STATIC flavor of FUNC_ENTER macros (#1622) * Removes the STATIC flavor of FUNC_ENTER macros * Remove H5_NO_ALIGNMENT_RESTRICTIONS (#1426) * Do not conditionally compile code that uses a pointer dereference and assignment to copy a potentially unaligned variable to aligned automatic storage, or vice versa. Instead, always use naked `memcpy(3)`s. Disassembling the generated code reveals that the `memcpy(3)`s optimize (`-O3`) to a single `mov` instruction for x86_64, which is not strict about alignment. This change reduces the size of code and scripts by 143 lines, eases our way to cross-compilation, and avoids invoking undefined behavior. * Committing clang-format changes * Per discussion, use HD and add comments. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Removes unused definitions from module headers (#1624) * Misc stuff from develop (includes some parallel things) * Brings over SWMR test quiet mode changes from develop Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* VFD SWMR: Normalization with develop (#1506)Dana Robinson2022-03-231-6/+6
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Brought over plugin and test script changes * Removes remaining register keywords (#1481) * Fixed warnings in the aux process code * Minor fixes from develop * Minor changes from develop, fixed format warnings * Formatted source * Added HD prefix to timespec_get * Cleanup in new files * Removes the MANIFEST file and unused release files (#1497) * Removes the MANIFEST file and unused release files * Updated tar command * checkposix corrections * More checkposix fixes * Ripped out unused instrumentation functionality * Brought over cache tagging changes from develop * Changes to tagged metadata expulsion iteration * Fixed typo * Brought over H5O__free() changes from develop * Brings (unused) parallel page buffer test in line with develop * Moved the functionality in supervise.subr to test_vfd_swmr.sh * Tools VFD parameter updates * Committing clang-format changes * H5F VFD SWMR refactoring * Committing clang-format changes * Misc changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* VFD SWMR: normalization with develop (#1472)Dana Robinson2022-03-061-1406/+3988
| | | Much normalization with develop. Still needs tools changes wrt VFD plugins.
* Normalization of parallelDana Robinson2021-05-071-12/+20
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* Brings trace changes from developDana Robinson2021-04-061-1/+4
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* Updates license url and history docsDana Robinson2021-03-251-1/+1
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* Formats the source and updates the gcc warning pragmasDana Robinson2021-03-251-869/+957
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* Minor changes from normalization with 1.10Dana Robinson2020-07-091-1/+1
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* Trim trailing whitespaceQuincey Koziol2020-04-201-23/+23
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* squash cast warning fixkmu2020-01-231-20/+16
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* Progress toward moving the dataset routines to using the 'shared' file pointerQuincey Koziol2019-08-211-3/+3
| | | | instead of the 'top' file pointer.
* Fixed some low-hanging fruit from -fsanitize in t_filters_parallel.Dana Robinson2019-06-211-2/+3
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* Merge remote-tracking branch 'origin/develop' into merge_hyperslab_update_01Quincey Koziol2019-04-291-0/+3
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| * HDFFV-10365: Changes as described in the RFC: H5Sencode/H5Sdecode Format Change.Vailin Choi2019-04-061-0/+3
| | | | | | | | This also addresses HDFFV-10255: H5Sencode/decode performance issue.
* | Merge remote-tracking branch 'origin/develop' into merge_hyperslab_update_01Quincey Koziol2019-03-171-10/+10
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| * Added an H5MM_memcpy call that checks for buffer overlap.Dana Robinson2019-03-161-10/+10
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* | Core changes to selection code from the hyperslab_updates branch.Quincey Koziol2019-03-161-11/+11
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* More changes to align with incoming selection improvements.Quincey Koziol2019-02-141-2/+2
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* Align develop with incoming hyperslab_updates branch changes.Quincey Koziol2019-02-131-36/+36
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* Fix some collective metadata read issuesJordan Henderson2019-02-121-1/+5
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* HDFFV-10625 -- Implemented a process-0 read and then broadcast for ↵Quincey Koziol2019-01-071-25/+90
| | | | collective read of full (HS_ALL), contiguous, atomic datasets by all the processes in the file communicator.
* Remainder of vol_normalization changes (dataset, attribute, files, objects).Dana Robinson2018-09-241-2/+1
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* Remove now-unused local variableJordan Henderson2018-08-261-3/+0
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* Add fix for HDFFV-10501Jordan Henderson2018-08-261-14/+1
| | | | | Add test for HDFFV-10501 fix Add release note for HDFFV-10501 fix
* Add configure check for MPI_Mprobe and MPI_Imrecv functionsJordan Henderson2018-07-261-0/+24
| | | | | | | | | | | | | | | Add line to libhdf5settings file for status of Parallel writes to filtered datasets status Surround Parallel Compression code in MPI_VERSION >= 3 checks Add disabled message for Parallel Compression built w/ MPI-2 Modify Parallel Compression tests to only run the parallel filtered read tests when parallel filtered writes are disabled Update big I/O code to handle being built with MPI-2 Add checks to CMakeLists.txt for MPI_Mprobe and MPI_Imrecv
* Merge pull request #1127 in HDFFV/hdf5 from ~JHENDERSON/hdf5:develop to developJordan Henderson2018-07-161-51/+98
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit 'a8d6f100cdddbfc42d0c4abfeb4ceb8788b1b087': Add note about single chunk caching and serial library Add check for actually using the MPI file driver when caching one chunk Fix error message mentioning wrong MPI function used Fix for HDFFV-10509 Revise H5D__mpio_array_gatherv() to not allocate memory needlessly Add test to continually grow and shrink chunks Changes to test with checksum filter as well as deflate filter Eliminate warning about signed to unsigned conversion Remove unused local variable Fix bug in parallel reads of compressed data Add data verification to parallel filtered compound write tests Add seven of fourteen parallel filtered data partial read tests
| * Fix error message mentioning wrong MPI function usedJordan Henderson2018-07-131-1/+1
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| * Revise H5D__mpio_array_gatherv() to not allocate memory needlesslyJordan Henderson2018-06-061-38/+61
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| * Eliminate warning about signed to unsigned conversionJordan Henderson2018-05-171-4/+4
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| * Remove unused local variableJordan Henderson2018-05-171-7/+4
| | | | | | Ensure frees are done in a more heap-fragmentation friendly order
| * Fix bug in parallel reads of compressed dataJordan Henderson2018-05-171-7/+34
| | | | | | Add remaining parallel compound dataset partial read tests
* | Fixed HDFFV-10404Binh-Minh Ribler2018-07-131-2/+2
| | | | | | | | | | | | | | | | | | Description: Applied the typo fixes from user's report. The previous pull request couldn't be merged because it was too old, and it was too complicated for me to resolve conflicts. Platform tested: Linux/64 (jelly) - very minor
* | Revert "Merge pull request #1116 in HDFFV/hdf5 from ↵hdftest2018-06-241-6/+2
| | | | | | | | | | | | | | ~HDFTEST/hdf5_hft:hdf5_1_10 to develop" This reverts commit e9f476dad47ce593f13dacb77b1cc664d1f24e7b, reversing changes made to 2ff00b1b937ebe36ac6ddf590c16a4c27fc0b053.
* | Merge branch 'develop' into hdf5_1_10.syncM. Scot Breitenfeld2018-05-081-356/+145
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| * Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Quincey Koziol2018-04-291-309/+1663
| |\ | | | | | | | | | merge_hyperslab_updates
| | * Corrections for parallel I/O & tests.Quincey Koziol2018-03-211-46/+23
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| | * Add API context interface and use it throughout the library.Quincey Koziol2018-03-151-310/+122
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| * | Checkpoint normalization against incoming hyperslab / selection / dataspaceQuincey Koziol2017-03-281-1/+1
| | | | | | | | | | | | improvements.
* | | Fix for HDFFV-9947 H5SencodeVailin Choi2017-11-281-2/+6
| |/ |/| | | | | Modifications to fix H5Sencode bug when num points selected is > 2^32.
* | Revert malloc's back to using hard-coded type for sizeofJordan Henderson2017-09-011-23/+23
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* | Minor comment refactoringJordan Henderson2017-09-011-3/+4
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* | Update documentationJordan Henderson2017-08-311-39/+158
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* | Fix bug where incorrect amount of data was being read from the fileJordan Henderson2017-08-101-1/+1
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* | Suggested changes from code reviewJordan Henderson2017-07-071-2/+1
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* | Amend header comment errorJordan Henderson2017-07-061-19/+18
| | | | | | Suggested fix for allocating too small of a buffer for the chunk data
* | Clean up remaining warningsJordan Henderson2017-07-061-6/+21
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* | Add prototype for H5D__cmp_filtered_collective_io_info_entry_ownerJordan Henderson2017-07-051-0/+2
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* | Add comment for memory copy possibly not being necessary anymore forJordan Henderson2017-07-051-0/+1
| | | | | | Multi-Chunk I/O
* | Remove use of H5E_CANTDISTRIBUTE errorJordan Henderson2017-07-051-1/+1
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* | Add comment for full overwrite special caseJordan Henderson2017-07-051-0/+8
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