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* Modifications to:vchoi2022-04-211-3/+0
| | | | | | | | | | | | A) Allow automatic generation of metadata file names for VDS support B) Allow VFD SWMR reader to open an existing HDF5 file either before the VFD SWMR writer has opened it or after it has closed. C) Remove the usage of H5P_FILE_ACCESS_ANY_VFD. D) Add H5FD_FEAT_SUPPORTS_VFD_SWMR feature flag. E) Do not map H5FD_MEM_GHEAP to H5FD_MEM_DRAW when vfd swmr IS enabled; map H5FD_MEM_GHEAP to H5FD_MEM_DRAW when vfd swmr is NOT enabled. For details regarding #A and #B above, see version 9 of the RFC.
* VFD SWMR: Merges from develop (#1670)Dana Robinson2022-04-211-25/+25
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 (#1472)Dana Robinson2022-03-061-154/+215
| | | Much normalization with develop. Still needs tools changes wrt VFD plugins.
* VFD SWMR: Normalization with develop (#1078)Dana Robinson2021-10-061-1/+2
| | | Brings many changes from develop, particularly VOL changes for async
* Much normalization with develop (#701)Dana Robinson2021-05-281-15/+79
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Brings CMake updates from develop * Brings reduction in pedantic casts from develop * Purges UFAIL from the library (#637) * Committing clang-format changes * Purges UFAIL from the library * H5HL_insert change requested in PR Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Removes gratuitous (double)x.yF casts (#632) * Committing clang-format changes * Removes gratuitous (double)x.yF casts * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Committing clang-format changes * Cleans up a const warning left over from previous constification (#633) * Committing clang-format changes * Adds consts to a few global variables * Cleans up a const warning left over from previous constification Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Formatted source * Bring over some VOL registration changes * VOL cleanup * H5VL_request_status_t substitutions * H5F.c cleanup * Minor API tweaks from develop * Moves H5G package init/teardown to H5Gint.c * H5G cleanup * H5M cleanup * H5SM cleanup * H5T cleanup * H5R cleanup * H5Lpublic.h cleanup * H5L cleanup * H5O cleanup * H5A, H5CS, and H5AC cleanup * Moved H5A init/teardown code to H5Aint.c * Moves H5D I/O functions to H5D.c * H5D cleanup * Misc minor cleanup * H5P close cleanup * H5Tpublic.h cleanup * Fixes err_compat test * H5PLpublic.h cleanup * Updates H5Ppublic.h * H5Fpublic.h updates * H5A.c cleanup * Brings over H5Aexists and related changes * Brings CMake shell testing changes from develop * Close callback changes * H5R and H5Tcommit normalization * err_compat test works now * H5O tweaks * Updates VOL registration code * Brings over H5VL_create_object * H5Tconv.c reformatting * H5T.c tweaks * Brings datatype and reference updates from develop * Brings VOL plugin loading changes from develop * Brings event sets from develop * Brings async functions over * Tools changes * Brings over many tools changes from develop * Brings VOL flags from develop * Fixes h5dump double/float tests * Updates h5repack tests * Brings h5diff test changes from develop * Last h5dump changes * Brings test changes from develop * Committing clang-format changes * Tidied h5_testing() * Brings chunk iteration code + misc from develop * Updates vds test * Enables external link parallel test * Brings updated property lists from develop * H5G changes from develop * H5MF cleanup * Brings vfd_swmr test back into CMake * Updates threadsafe test * Updates plist test * Brings recent changes from develop Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Brings atom-->ID and other ID-related changes from developDana Robinson2021-05-051-11/+11
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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 Robinson2021-03-251-1213/+1164
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* Merge branch 'aug-develop' into aug-merge-attempt/feature/vfd_swmrDavid Young2020-08-041-1/+1
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| * Normalization with hdf5_1_10Dana Robinson2020-06-011-1/+1
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| * Trim trailing whitespaceQuincey Koziol2020-04-201-21/+21
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| * merge and fix conflictkmu2020-01-191-4/+4
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| * | fix unused related warningskmu2020-01-131-8/+7
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| * Add new H5R API that abstracts object, region and attribute reference typesJerome Soumagne2019-10-081-4/+34
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
| * Added the map (H5M) APIDana Robinson2019-08-131-5/+29
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| * H5P: Fix wrong value comparison in assertJerome Soumagne2019-07-161-3/+5
| | | | | | | | Move compile assert of H5P_plist_type to H5P__init_package()
| * Updates to warnhist script, along with a few cleanups, and add some commentsQuincey Koziol2019-07-101-1/+1
| | | | | | | | to warning cleanups that are a bit obscure.
| * Add support for GCC9, update warnhist script, and clean up warnings.Quincey Koziol2019-07-031-1/+1
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| * Put the memcpy overlap check back into H5MM.Dana Robinson2019-06-221-2/+2
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| * Added a VOL initialization property list type.Dana Robinson2019-06-051-37/+68
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| * Merge remote-tracking branch 'origin/develop' into env_vol_loadQuincey Koziol2019-04-031-17/+17
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| | * Added an H5MM_memcpy call that checks for buffer overlap.Dana Robinson2019-03-161-17/+17
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| * | Specify the default VOL connector to use with an environment variable.Quincey Koziol2019-03-101-0/+110
| |/ | | | | | | | | | | | | | | This implicitly adds support for changing the VOL connector for command-line tools or any application linked with the library. Also, add 'make check-vol' support for all directories, clearing up necessary issues in testing scripts, etc.
| * VOL FEATUREDana Robinson2018-10-101-0/+19
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* | Change H5F_open to perform deduplication of open VFDs in a more flexible way,David Young2020-07-301-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | using the new routine H5FDdeduplicate(). Simplify H5F_open() a bit, pushing some of the configuration checks into the SMWR VFD. For example, check that page buffering is enabled in H5FD_vfd_swmr_open() instead of in H5F_open(). Compare VFD SWMR configurations in H5FD_vfd_swmr_dedup() instead of in H5F_open(). Clone the default file-access property list at a new file-access property list ID, H5P_FILE_ACCESS_ANY_VFD. The new ID is used to indicate that if the file that's being opened is already open under an existing virtual file, and if that virtual file would not ordinarily be opened with the default FAPL, then it's ok to use that virtual file. Add a new optional method, `dedup`, to H5FD_class_t, and use it to customize a VFD's deduplication. Customize the SWMR VFD's deduplication. Make it honor H5P_FILE_ACCESS_ANY_VFD Embed the VFD SWMR configuration in the H5FD_vfd_swmr_t to facilitate comparison of configuration between new and old SWMR virtual files. In H5F__sfile_search(), match using a pointer comparison instead of H5FD_cmp(), because we will only ever enter H5F__sfile_search() with a deduplicated H5FD_t *.
* | Repair a bunch of H5_ATTR_SANITY_CHECK uses that should have beenDavid Young2020-05-201-2/+2
| | | | | | | | | | H5_ATTR_NDEBUG_UNUSED. This really makes me wonder what else I have screwed up in this merge....
* | Trim trailing whitespaceQuincey Koziol2020-05-201-21/+21
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* | fix unused related warningskmu2020-05-201-8/+7
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* | Merge all of my changes from merge-back-to-feature-vfd_swmr-attempt-1,David Young2019-12-091-58/+274
|/ | | | | | | | including the merge of `hdffv/hdf5/develop`, back to the branch that Vailin and I share. Now I need to put this branch on a fork with a less confusing name than vchoi_fork!
* Normalization with vol_integration (property lists, file drivers,Dana Robinson2018-09-211-303/+286
| | | | other misc).
* Fixed HDFFV-10404Binh-Minh Ribler2018-07-131-17/+17
| | | | | | | | | 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
* Add API context interface and use it throughout the library.Quincey Koziol2018-03-151-80/+27
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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.
* [svn-r29815] Description:Quincey Koziol2016-04-261-1/+1
| | | | | | | | Change 'value' pointer to H5Pset() from 'void *' to 'const void *'. Tested on: MacOSX/64 10.11.4 (amazon) w/serial (h5committest forthcoming)
* [svn-r29712] Description:Quincey Koziol2016-04-161-1/+1
| | | | | | | | Minor code cleanups to address typos & warnings. Tested on: MaOSX/64 10.11.4 (amazon) w/serial & parallel (Too minor to require h5committest)
* [svn-r29077] Description:Quincey Koziol2016-02-101-4/+12
| | | | | | | | 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)
* [svn-r29066] - fixing some of the internal usage of dxpls.Mohamad Chaarawi2016-02-081-22/+22
|\ | | | | | | - merge from trunk.
* \ [svn-r29059] merge from trunk.Mohamad Chaarawi2016-02-071-1/+1
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| * [svn-r28957] fix non-parallel bug.Mohamad Chaarawi2016-01-221-1/+2
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* | [svn-r28959] merge from trunk.Mohamad Chaarawi2016-01-221-7/+30
|\ \ | |/ | | | | renaming metadata dxpl properties.
| * [svn-r28950] - remove META_FLUSH_COLLECTIVELY property for delayed sanity ↵Mohamad Chaarawi2016-01-211-5/+21
| | | | | | | | | | | | | | | | | | | | checks from metadata dxpls - remove H5AC_ind_dxpl_id and use only H5AC_dxpl_id everywhere instead. - remove flush_me_collectively flag from cache entries - add a collective sanity check (MPI_Barrier) for every HDF5 API routine that could possibly touch the file. This is trigerred when the environment variable H5_COLL_API_SANITY_CHECK is set to a non 0 digit. tested on BB-8 with serial and parallel.
| * [svn-r28916] Description:Quincey Koziol2016-01-151-1/+74
| | | | | | | | | | | | | | | | Normalize against incoming changes from the phdf5_metadata_opt branch. Tested on: MacOSX/64 10.11.2 (amazon) w/serial & parallel (h5committest forthcoming)
| * [svn-r28894] Description:Quincey Koziol2016-01-141-1/+1
| | | | | | | | | | | | | | | | Normalize against changes on phdf5_metadata_opt branch to trunk Tested on: MacoSX/64 10.11.2 (amazon) w/serial & parallel (h5committest forthcoming)
* | [svn-r28915] Description:Quincey Koziol2016-01-151-23/+45
| | | | | | | | | | | | | | | | Review revisions on the way to the trunk. Tested on: MacOSX/64 10.11.2 (amazon) w/serial & parallel (h5committest not required on this branch)
* | [svn-r28636] merge from trunk.Mohamad Chaarawi2015-12-141-7/+7
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| * [svn-r28606] Description:Quincey Koziol2015-12-131-7/+7
| | | | | | | | | | | | | | | | | | | | Revisions to normalize revise chunks vs. trunk, plus push dataset metadata changes into the cache immediately (instead of holding them within the dataset data structures). Tested on: MacOSX/64 10.11.2 (amazon) w/serial & parallel (h5committest not required on this branch)
* | [svn-r27929] merge from trunk.Mohamad Chaarawi2015-10-011-520/+758
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| * [svn-r27811] Description:Quincey Koziol2015-09-161-419/+670
| | | | | | | | | | | | | | | | | | | | | | Refactor property list code to "deep copy" properties in the correct way, retraining the rest of the library to copy & release things correctly. This cleans up another batch of memory leaks, etc. within the library. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel Linux/32 2.6.x (jam) w/serial & parallel (h5committest forthcoming)
| * [svn-r27768] Description:Quincey Koziol2015-09-141-122/+109
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Complete revamp of package initialization/shutdown mechanism in the library. Each package now has a single init/term routine. This new way should avoid packages being re-initialized during library shutdown and is also be _much_ more proactive about giving feedback for resource leaks internal to the library. Introduces a new "module" header file for packages in the library (e.g src/H5Fmodule.h) which sets up some necessary package configuration macros for the FUNC_ENTER/LEAVE macros. (The VFL drivers have their own slightly modified version of this header, src/H5FDdrvr_module.h) Also cleaned up a bunch of resources leaks all across the library and tests, along with addressing many warnings, as I encountered them. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel Linux/64 3.10.x (kituo) w/serial & parallel Linux/64 2.6.x (ostrich) w/serial
* | [svn-r27261] apply metadata enhancement patch that was based on the mdc 3 ↵Mohamad Chaarawi2015-06-211-2/+70
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