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* Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Quincey Koziol2018-03-181-239/+237
|\ | | | | | | | | | | merge_func_enter_vol Plus initial steps toward merging API context push into FUNC_ENTER_API* macros
| * Enhancement to the tool h5clear (HDFFV-10360)Vailin Choi2018-03-121-0/+4
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| * Modifications made based on comments from pull request.Vailin Choi2018-02-071-5/+5
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| * Merge branch develop into bugfix/version_boundsVailin Choi2018-01-121-210/+214
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| | * HDFFV-10361 Correct signaturesAllen Byrne2018-01-091-3/+1
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| | * HDDFV-10361 combine duplicated prefix utility functionsAllen Byrne2018-01-051-0/+6
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| | * HDFFV-9724 Corrected files and verified testsAllen Byrne2017-12-281-210/+210
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| | * Revert "Merge pull request #826 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to ↵lrknox2017-12-221-210/+210
| | | | | | | | | | | | | | | | | | | | | develop" This reverts commit b1223dd653e65e076af92b2dfe236f3704da81c8, reversing changes made to b25f123f5f5e25c1447a6a02861cb7c7265c12f2.
| | * HDFFV-9724 Remove VDS file cache functionalityAllen Byrne2017-12-201-1/+0
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| | * Correct var nameAllen Byrne2017-12-131-4/+4
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| | * Fix VDS file cache var namesAllen Byrne2017-12-131-212/+212
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| | * HDFFV-9724 Initial changes and testAllen Byrne2017-12-111-0/+1
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| * | Changes made based on code reviews.Vailin Choi2018-01-121-0/+1
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| * | Merge branch 'develop' into bugfix/version_boundsVailin Choi2017-12-081-6/+9
| |\ \ | | | | | | | | | | | | Merge from develop.
| | * | Normalization with VOL integration branch.Dana Robinson2017-12-051-2/+2
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| * | (1) Merge branch 'develop' into bugfix/version_boundsVailin Choi2017-11-251-3/+0
| |\ \ | | | | | | | | | | | | | | | | | | | | (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 Choi2017-10-031-20/+8
| |/ / | | | | | | | | | 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 Koziol2018-03-151-26/+12
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* | Normalization with VOL integration branch.Dana Robinson2017-12-011-4/+7
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* Changes made based on RFC review commentsVailin Choi2017-07-181-1/+3
| | | | Test the changes in a branch via daily testing.
* 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.
* Checkin of fix for CGNS bugmainzer2017-04-061-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | (https://jira.hdfgroup.org/browse/HDFFV-10055). Briefly, in H5C_collective_write() in H5Cmpio.c, the metadata cache attempts to perform a collective write of metadata cache entries. This worked fine as long as all processes had at least one entry to write. However, when the process has no entries, the function tries to participate in the collective write by calling MPI_File_set_view(), MPI_File_write_all() and then MPI_File_set_view() again, to match the calls in H5FD_mpio_write(). After pull request 183, the CGNS test benchmark_hdf5 started failing. On investigation, I determined that the failure occurred in the first call to MPI_File_set_view() in the "no data to write" path through H5C_collective_write(). Note that pull request 183 did not create the problem, it only exposed it. The bug can be observed after pull request 182 if one executes the CGNS progam src/ptests/benchmark_hdf5 with 90 processes. The problem appears to have been that the calls to MPI_File_set_view() in H5C_collective_write() and H5FD_mpio_write() were using different values for the info parameter. I patched the problem by adding a MPI specific VFD call allowing me to get the MPI_Info used in H5FD_mpio_write() for use in MPI_File_set_view() calls in H5C_collective_write(). Tested serial & parallel, debug & production on Jelly.
* Final merge of page buffering branch to developQuincey Koziol2017-03-141-3/+78
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* Bring changes to I/O parameters from page_buffering branch.Quincey Koziol2017-03-131-2/+10
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* Cache image feature and testingQuincey Koziol2017-01-291-0/+4
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* Bring file shutdown code from cache image branchQuincey Koziol2017-01-051-0/+1
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* More normalizations against incoming cache image branch.Quincey Koziol2016-12-291-0/+1
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* Bring SWMR support in to the main development branch. (Finally!) More testsQuincey Koziol2016-12-021-1/+4
| | | | and the tool and API wrappers will be coming in over the weekend.
* Merge branch 'develop' into eoc_valgrind_bugfixDana Robinson2016-11-261-0/+18
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| * Merge pull request #166 in HDFFV/hdf5 from ↵Dana Robinson2016-11-211-0/+3
| |\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~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/+18
| | | | | | | | | | | | supporting metadata cache callback changes, etc.
* | | Tentative fix for valgrind issues related to EoC.Dana Robinson2016-11-261-4/+1
| |/ |/| | | | | | | | | | | | | | | 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 Robinson2016-11-201-0/+3
|/ | | | | | | | | | | | * 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.
* Code style and warning cleanups, from revise_chunks branch.Quincey Koziol2016-11-061-2/+2
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* Add cache logging property and file pieces.Quincey Koziol2016-11-041-0/+12
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* Merge branch 'develop' into evict_on_closeDana Robinson2016-09-141-1/+1
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| * [svn-r30303] Fixed unbalanced parentheses in H5F_SAME_SHARED macro. Dana Robinson2016-08-181-1/+1
| | | | | | | | | | | | | | | | This version of the macro isn't used anywhere in the HDF5 source. Tested on: 64-bit Ubuntu Linux 16.04 LTS w/ gcc 5.4.0 Autotools serial
| * [svn-r30219] Description:Quincey Koziol2016-07-221-1/+1
| | | | | | | | | | | | | | | | | | More warning cleaups: down to 770 warnings (from ~940) in 134 files (from 148), with 28 unique kinds of warnings (from 31). Tested on: MacOSX/64 10.11.5 (amazon) w/serial & parallel (h5committest forthcoming)
* | [svn-r30084] First pass at the evict-on-close feature.Dana Robinson2016-06-151-1/+5
|/ | | | | | | | | | 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-r30075] Description:Quincey Koziol2016-06-141-0/+1
| | | | | | | | | | Bring object/dataset/group/named datatype features from revise_chunks branch to trunk. Also CMake support for h5format_convert and a bunch of misc. cleanups. Tested on: MacOSX/64 10.11.5 (amazon) w/serial, parallel & production (h5committest forthcoming)
* [svn-r29924] Description:Quincey Koziol2016-05-121-0/+1
| | | | | | | | Bring h5format_convert tool from revise_chunks branch to trunk. Tested on: MacoSX/64 10.11.4 (amazon) w/serial, parallel & production (h5committest forthcoming)
* [svn-r29850] Description:Quincey Koziol2016-05-011-0/+13
| | | | | | | | | | Bring H5DOappend(), H5P[s|g]et_object_flush_cb, and H5P[s|g]et_append_flush from revise_chunks branch to trunk. Brings along updated metadata cache entry tagging, and the internal object flush routine. Tested on: MacOSX/64 10.11.4 (amazon) w/serial, parallel & production (h5committest forthcoming)
* [svn-r29842] Description:Quincey Koziol2016-04-301-3/+3
| | | | | | | | | Bring [appropriate portions of] r29811, 29813, 29826, 29830, 29831 from revise_chunks branch to the trunk. Tested on: MacOSX/64 10.11.4 (amazon) w/serial, parallel & production (h5committest forthcoming)
* [svn-r29612] Description:Quincey Koziol2016-04-031-3/+19
| | | | | | | | | 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-r29077] Description:Quincey Koziol2016-02-101-0/+13
| | | | | | | | 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-r28959] merge from trunk.Mohamad Chaarawi2016-01-221-1/+1
|\ | | | | | | renaming metadata dxpl properties.
| * [svn-r28950] - remove META_FLUSH_COLLECTIVELY property for delayed sanity ↵Mohamad Chaarawi2016-01-211-1/+1
| | | | | | | | | | | | | | | | | | | | 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-r28851] merge from trunk.Mohamad Chaarawi2016-01-111-2/+1
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| * [svn-r28646] Minor normalization with revise_chunks.Dana Robinson2015-12-141-2/+1
| | | | | | | | | | | | | | | | | | Also purged obsolete /*ARGSUSED*/ from the library. Tested on: Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1 serial only (these changes have been in revise_chunks for a long time)
* | [svn-r28649] - add new API to toggle collective metadata write.Mohamad Chaarawi2015-12-141-0/+1
| | | | | | | | | | - set default to FALSE - fix some bugs.
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