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* Sync with develop (#2871)Dana Robinson2023-05-021-0/+27
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* Update copyright headers (#2184)Larry Knox2022-11-011-1/+0
| | | | | * Updated source file copyright headers to remove "Copyright by the Board of Trustees of the University of Illinois", which is kept in the top-level COPYING file.
* Support for UnifyFS with MPI_File_sync (#1801)Houjun Tang2022-07-111-0/+31
| | | | | | | | | | | | | | | | | | | | | | | | | * Initial implementation for supporting UnifyFS in HDF5 with MPI_File_sync after write * Committing clang-format changes * Fix format * Fix env variable and return value check * Fix flag retrieve * Fix issues with getting/setting the flag * Fix merge conflicts * Update * Committing clang-format changes * Update based on suggestions * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Update compact dataset I/O routines to handle driver-level memory copy (#1054)jhendersonHDF2021-09-301-0/+23
| | | | | | | | | | * Update compact dataset I/O routines to handle driver-level memory copy * Combine compact I/O read/write struct into single I/O struct Rename CTL memory copy flag and H5Fquery routine to get file driver structure * Add RELEASE.txt entry for new "ctl" memory copy operation
* Update license url (#332)Larry Knox2021-02-171-1/+1
| | | | | | * Modify temporary rpath for testing in java example scripts. * Update URL in source file Copyright headers for web copy of COPYING file - src and test directories.
* Fix VFD h5repacktest (#20)Allen Byrne2020-10-061-6/+6
| | | | | | | | | | | | | | * h5repacktest VFD fix and formatting changes * Fix memory leak in H5PL__find_plugin_in_path When encountering a directory, the current loop iteration was skipped without freeing the memory allocated for the path. * Refactor parser GCC diagnostic statements * genparser on jelly with default bison/flex Co-authored-by: Michael Kuhn <michael.kuhn@ovgu.de>
* Clang-format of source filesAllen Byrne2020-09-301-88/+23
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* Moves lock flag to H5F_shared_t and adds test.Dana Robinson2020-08-171-0/+21
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* Clean up private / package / static namespace issues (function naming, whichQuincey Koziol2020-08-061-2/+1
| | | | | | header file, FUNC_ENTER / LEAVE, etc). Removed remaining personal email addresses from library source code (still needs cleaned from other directories). Misc. warning, style, and whitespace cleanup.
* Minor normalizations with HDF5 1.10.Dana Robinson2020-06-071-0/+1
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* Normalization with hdf5_1_10Dana Robinson2020-06-011-0/+1
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* Implement H5VLget_file_type() to return a copy of a datatype with theNeil Fortner2019-11-081-0/+20
| | | | | | | | | | | location set to be in a file. Only meant to be used by VOL connectors. Implement H5VLpeek_connector_id() to support connectors querying their own IDs. Fix app_ref with connector IDs in a couple places (external VOLs registered as default through ENV should be visible to the application). Modify vlen and reference interfaces to work with arbitrary VOL connectors. Implement file "post open" specific callback, to enable connectors to update their file structs after a wrap context has been set.
* Adapt Jerome's "file info" H5VL 'get' query to retrieve container token info.Quincey Koziol2019-10-081-0/+38
| | | | Remove "by address" location for VOL operations. (Switching to "by token")
* Add 'blob' callbacks to VOL, along with a native implementation to store themQuincey Koziol2019-10-081-0/+25
| | | | | | | in the global heap, and changed the VL datatype conversion code to use blobs. Move encode/decode of sequence lengths into VL datatype callbacks, from native VOL blob routines.
* Move ext_path field in H5F_t to H5F_shared_t.Vailin Choi2019-08-311-2/+2
| | | | Remove unused routine H5F_set_coll_md_read().
* Move coll_md_read and coll_md_write fields in H5F_t to H5F_shared_t.Vailin Choi2019-08-311-1/+1
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* Switch shared file struct name from 'H5F_file_t' to 'H5F_shared_t', to matchQuincey Koziol2019-08-221-5/+5
| | | | naming convention for shared structs in rest of library data structures.
* First pass of converting H5PB_* routines to use shared file pointers.Quincey Koziol2019-08-191-0/+69
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* Checkin for new shutting down free-space manager.Vailin Choi2019-06-201-30/+6
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* Merge branch 'develop' into dset_ohdr_minimizeJacob Smith2018-12-121-8/+8
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| * Squashed commit of private branch changes to support stackable VOL plugins.Quincey Koziol2018-10-251-1/+1
| | | | | | | | modified: test/dsets.c
| * VOL FEATUREDana Robinson2018-10-101-7/+7
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| * Normalization with vol_integration (misc internal and datatype)Dana Robinson2018-09-201-3/+3
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* | Change H5F internals accessJacob Smith2018-09-141-0/+19
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* Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Quincey Koziol2018-03-181-30/+62
|\ | | | | | | | | | | merge_func_enter_vol Plus initial steps toward merging API context push into FUNC_ENTER_API* macros
| * Modifications made based on comments from pull request.Vailin Choi2018-02-071-2/+2
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| * Merge branch develop into bugfix/version_boundsVailin Choi2018-01-121-1/+1
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| | * HDFFV-9724 Corrected files and verified testsAllen Byrne2017-12-281-1/+1
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| | * Revert "Merge pull request #826 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to ↵lrknox2017-12-221-1/+1
| | | | | | | | | | | | | | | | | | | | | develop" This reverts commit b1223dd653e65e076af92b2dfe236f3704da81c8, reversing changes made to b25f123f5f5e25c1447a6a02861cb7c7265c12f2.
| | * HDFFV-9724 combine efc and vds into one functionAllen Byrne2017-12-131-1/+1
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| * | Changes made based on code reviews.Vailin Choi2018-01-121-3/+8
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| * | Merge branch 'develop' into bugfix/version_boundsVailin Choi2017-12-081-4/+4
| |\ \ | | |/ | | | | | | Merge from develop.
| | * Normalization with VOL integration branch.Dana Robinson2017-12-051-4/+4
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| * | (1) Merge branch 'develop' into bugfix/version_boundsVailin Choi2017-11-251-410/+218
| |\ \ | | |/ | | | | | | | | | | | | (2) Add two new options to h5repack for low and high bounds as in H5Pset_libver_bounds. (3) Modify message pre_copy callbacks so that H5Ocopy can handle version bounds check. (4) Add version bounds check for cache image feature.
| * | Initial checkin for library version boundsVailin Choi2017-10-031-28/+50
| | | | | | | | | | | | Code changes to provide versioning support when adding to the enumerated defines for H5F_libver_t.
* | | Add API context interface and use it throughout the library.Quincey Koziol2018-03-151-1/+1
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* | Remove tabsAllen Byrne2017-11-081-411/+214
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* Merge pull request #426 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10 to ↵Larry Knox2017-04-251-6/+4
| | | | | | | | | | hdf5_1_10 * commit '54957d37f5aa73912763dbb6e308555e863c43f4': Commit copyright header change for src/H5PLpkg.c which was added after running script to make changes. Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh. Merge pull request #407 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_1 to hdf5_1_10_1 Change copyright headers to replace url referring to file to be removed and replace it with new url for COPYING file.
* Final merge of page buffering branch to developQuincey Koziol2017-03-141-0/+147
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* Merge branch 'develop' into eoc_valgrind_bugfixDana Robinson2016-11-261-0/+23
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| * Merge pull request #166 in HDFFV/hdf5 from ↵Dana Robinson2016-11-211-1/+27
| |\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~DEROBINS/hdf5_der:eoc_valgrind_bugfix to develop Two minor evict-on-close changes: * Fix for a valgrind-reported issue where invoking EoC behavior when the file is closing leads to garbage file data being passed to downstream calls. The solution is to ignore EoC when the file is closing anyway. * Added brackets so an infinite loop that arises when evicting tagged entries (due to pinned entries preventing progress) raises an error instead. * commit '4e7b19f8260a7adb0e3b3df30e2d8289fccdcca6': Two minor cache changes:
| * | Bring over support for retrying metadata cache entry loads, along with all theQuincey Koziol2016-11-201-0/+23
| | | | | | | | | | | | supporting metadata cache callback changes, etc.
* | | Tentative fix for valgrind issues related to EoC.Dana Robinson2016-11-261-25/+0
| |/ |/| | | | | | | | | | | | | | | Adds /*out*/ parameters to H5O_close() and H5F_try_close() so that H5D/G_close() will know when H5O_close() has triggered a file close and thus the file struct is not reliable. Also removes the H5F_CLOSING() macro and related which were formerly used to check if the file was closing.
* | Two minor cache changes:Dana Robinson2016-11-201-1/+27
|/ | | | | | | | | | | | * Evict-on-close behavior is now skipped when the file is closing. This fixes a potential issue discovered by Valgind on Windows where potentially garbage data would be availble for manipulation. * Added brackets to some code in the tagged entry evict iterators so that the flag that determines if progress was made only gets set if things are actually evicted. This prevents an infinite loop (and emits an error) when pinned entries prevent eviction and thus progress.
* Add cache logging property and file pieces.Quincey Koziol2016-11-041-0/+84
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* [svn-r30084] First pass at the evict-on-close feature.Dana Robinson2016-06-151-0/+27
| | | | | | | | | | The features is controlled via H5Pset/get_evict_on_close() and is currently enabled by default (it will be disabled by default in the final implementation). There is a bug in the code where the eviction of tagged metadata fails due to some of the metadata being dirty, resulting in error return values and test failures.
* [svn-r29612] Description:Quincey Koziol2016-04-031-9/+8
| | | | | | | | | Bring updated layout and EFL property comparisons and new "latest format" flags from revise_chunks branch. Tested on: MacOSX/64 10.11.4 (amazon) w/serial, parallel & production (h5committest forthcoming)
* [svn-r29182] Re-commit of HDFFV-8740 fix, which adds the ability to configureDana Robinson2016-02-221-1/+1
| | | | | | | | | | | | external dataset storage path behavior. This check-in fixes a bug in the original check-in where the external path stored in the file struct was not copied on reopen causing subsequent dataset operations to fail. Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1 autotools serial w/ fortran and C++ autotools parallel (MPICH 3.1.4) w/ fortran
* [svn-r29084] Revert of:Dana Robinson2016-02-111-1/+1
| | | | | | | | | | | | | | | r29069 and 72 (gheap cleanup) r29041 and 43 (HDFFV-8740 external storage) These cause problems in the daily tests. They will be re-introduced when their respective problems have been addressed. Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1 autotools serial (check-vfd) w/ Fortran and C++ autotools parallel w/ Fortran CMake serial
* [svn-r29077] Description:Quincey Koziol2016-02-101-0/+28
| | | | | | | | Normalize against the trunk, in preparation for final merge. Tested on: MacOSX/64 10.11.3 (amazon) w/serial & parallel (h5committest not required on this branch)
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