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* Added missing casts for the return value of H5I_object_verify().Dana Robinson2017-05-243-9/+9
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* Incorporate additional code changes for the H5DOread_chunk patch from GE ↵Vailin Choi2017-05-151-21/+22
| | | | | | | | | | Heathcare (HDFFV-9934) This is the similar set of changes that was checked in to 1.8 branch: Incorporate the code changes that were missing from the original patch: (1) Additional tests in hl/test/test_dset_opt.c (2) Fix in src/H5Dchunk.c for direct access when an entry is in chunk cache but not dirty Tested on platypus, ostrich, kituo, mayll, osx1010test, moohan, quail, emu.
* Merged HDFFV-10187 direct chunk overwrite bugfix to develop from 1.10 branch.Dana Robinson2017-05-121-5/+11
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* HDFFV-10186 Add endianess to bitfield and fix testsAllen Byrne2017-05-101-8/+21
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* Fix for HDFFV-10051Vailin Choi2017-05-091-0/+1
| | | | | Fix missing declaration for H5D__layout_compact_dirty_test(). Tested on mayll and osx1010test.
* Merge pull request #494 in HDFFV/hdf5 from ~VCHOI/my_hdf5_fork:develop to ↵Vailin Choi2017-05-093-4/+55
|\ | | | | | | | | | | | | | | develop * commit 'd436db6c6efdfe7e9dbe06a642715116ef0eb5e3': Fix for the two issues reported in HDFFV-10051 Modifications made based on the review comments from pull request #494 Tested on moohan, mayll, kituo, platypus, ostrich, osx1010test, quail, emu. Fix for the two issues reported in HDFFV-10051: (1) Repeated open/close of a compact dataset fails due to the increment of ndims in the dataset structure for every open. --This is done only for chunked dataset via H5D__chunk_set_sizes(). (2) layout "dirty" flag for a compact dataset is not reset properly after flushing the data at dataset close. --Reset the "dirty" flag before flushing the message to the object header via H5O_msg_write(). Tested on moohan, kituo, platypus, ostrich, osx1010test, quail, emu.
| * Fix for the two issues reported in HDFFV-10051Vailin Choi2017-05-092-1/+44
| | | | | | | | | | Modifications made based on the review comments from pull request #494 Tested on moohan, mayll, kituo, platypus, ostrich, osx1010test, quail, emu.
| * Fix for the two issues reported in HDFFV-10051:Vailin Choi2017-05-072-3/+11
| | | | | | | | | | | | | | | | | | | | | | (1) Repeated open/close of a compact dataset fails due to the increment of ndims in the dataset structure for every open. --This is done only for chunked dataset via H5D__chunk_set_sizes(). (2) layout "dirty" flag for a compact dataset is not reset properly after flushing the data at dataset close. --Reset the "dirty" flag before flushing the message to the object header via H5O_msg_write(). Tested on moohan, kituo, platypus, ostrich, osx1010test, quail, emu.
* | HDFFV-10186 Whitespace changesAllen Byrne2017-05-091-1441/+1389
|/ | | | Mostly replacing tabs with spaces Removed empty mod sections
* Set the HDF5_GENERATE_HEADERS CMake option to default to ON and removedDana Robinson2017-04-271-1/+1
| | | | | | the option from the CMake cache init files. Fixes HDFFV-10184
* Change position of declaration to top of blockAllen Byrne2017-04-271-1/+2
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* Modifications based on pull request review.Vailin Choi2017-04-261-1/+1
| | | | Made couple changes based on the review comments.
* Incorporate patch from GE Healthcare (HDFFV-9934)Vailin Choi2017-04-256-70/+438
| | | | | This is the same patch that had already been integrated to 1.8 branch (pull request #387). Tested on moohan, ostrich, platypus, emu, osx1010test, quail, kituo, mayll.
* HDFFV-10170 revert entire changeAllen Byrne2017-04-251-83/+3
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* Merge pull request #426 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10 to ↵Larry Knox2017-04-25440-2653/+1768
| | | | | | | | | | 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.
* Commit copyright header change for src/H5PLpkg.c which was added after ↵lrknox2017-04-251-6/+4
| | | | running script to make changes.
* Revert HDFFV-9655 by disabling test and not using new function.Allen Byrne2017-04-242-13/+15
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* Merge pull request #447 in HDFFV/hdf5 from ↵Allen Byrne2017-04-211-7/+87
|\ | | | | | | | | | | | | | | | | ~BYRN/hdf5_adb:bugfix/HDFFV-9655-plugin-path-relative to develop * commit 'a995a63085d88e1a633770536efeff5b01569445': HDFFV-9655 fix test and some warnings HDFFV-9655 fix compile and test HDFFV-9655 - Add functions for '@' - untested
| * HDFFV-9655 fix test and some warningsAllen Byrne2017-04-211-3/+3
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| * Merge remote-tracking branch 'origin/develop' intoAllen Byrne2017-04-2121-341/+716
| |\ | | | | | | | | | bugfix/HDFFV-9655-plugin-path-relative
| | * Fix parameter formAllen Byrne2017-04-211-4/+4
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| * | HDFFV-9655 fix compile and testAllen Byrne2017-04-211-35/+47
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| * | HDFFV-9655 - Add functions for '@' - untestedAllen Byrne2017-03-291-0/+68
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* | | Fixed problems that prevent bin/trace from marking up some functions.Dana Robinson2017-04-213-22/+20
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* | The cache_image test shows a skipped message about EoC in parallel.Dana Robinson2017-04-201-1/+0
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* | Added code to disable the evict-on-close feature inDana Robinson2017-04-191-2/+19
| | | | | | | | the parallel library.
* | Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2017-04-171-0/+2
|\ \ | | | | | | | | | | | | * commit '5f7822fac4673cdb9e8ed60d104566c9df43303f': Express test mods to test/cache.c
| * | Express test mods to test/cache.cmainzer2017-04-151-0/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Modified test/cache.c to skip the smoke checks with paged aggregation for all express test levels other than 0 Change to src/H5PL.c seems to be the result of autogen.sh. As it seems to be correct, I am checking it in. Tested serial and parallel (debug only) on jelly.
* | | HDFFV-10173 fix compile on VS2008Allen Byrne2017-04-171-118/+118
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* | Fix for H5Dset_extent test failure with extensive array indexing (HDFFV-9771)Vailin Choi2017-04-112-3/+13
| | | | | | | | | | 1) Calculate chunk index for extensive array index based on swizzled max chunks when unlim_dim > 0 2) Minor fixes to test/fheap.c that somehow were missed from last check in. See pull request #396 review comments.
* | Removed commeted out code from H5C_dump_coll_write_list()mainzer2017-04-071-5/+0
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* | Checkin of fix for CGNS bugmainzer2017-04-068-26/+298
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | (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.
* | Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2017-04-051-2/+4
|\ \ | | | | | | | | | | | | | | | * commit 'b56fb149c9a3c9dca11b406b7a2488f0c93ee187': Updated the H5L.c error message after additional thought. Fix for HDFFV-10141. Updated an error message in H5L.c to be more helpful. Fixes HDFFV-10141.
| * | Updated the H5L.c error message after additional thought.Dana Robinson2017-04-051-1/+1
| | | | | | | | | | | | Fix for HDFFV-10141.
| * | Updated an error message in H5L.c to be more helpful.Dana Robinson2017-04-051-2/+4
| | | | | | | | | | | | Fixes HDFFV-10141.
* | | Update with checks for index boundsAllen Byrne2017-04-031-1/+10
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* | | Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2017-04-035-34/+121
|\ \ \ | |/ / | | | | | | | | | | | | | | | | | | | | | | | | * commit '2412158ed8326a3f3d62fbd947e470667d0b5951': Add new file COPYING_LBNL_HDF5. Revert "Clear hdf5 1.10 entries from RELEASE.txt in the develop branch. Entries" Add LBNL license file and modify COPYING file accordingly. Omnibus checkin for several relatively minor modifications: Clear hdf5 1.10 entries from RELEASE.txt in the develop branch. Entries in this branch version of RELEASE.txt should be intended for the future 1.12.0 release. Fix HDFFV-8089 Description: Some code within an "ifdef H5D_CHUNK_DEBUG" block was using outdated data structure but not caught because the case of H5D_CHUNK_DEBUG being defined was never tested. It was commented out. I defined H5D_CHUNK_DEBUG, tested, and commented out again. Platforms tested: Linux/32 2.6 (jam) Linux/64 (platypus) Darwin (osx1010test)
| * | Merge pull request #374 in HDFFV/hdf5 from ~BMRIBLER/hdf5_bmr_cpp3:develop ↵Binh-Minh Ribler2017-04-031-5/+5
| |\ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | to develop Fix HDFFV-8089 * commit '52f8c2ed494ea1b89374981ecc6901abe8fd5fed': Fix HDFFV-8089 Description: Some code within an "ifdef H5D_CHUNK_DEBUG" block was using outdated data structure but not caught because the case of H5D_CHUNK_DEBUG being defined was never tested. It was commented out. I defined H5D_CHUNK_DEBUG, tested, and commented out again. Platforms tested: Linux/32 2.6 (jam) Linux/64 (platypus) Darwin (osx1010test)
| | * \ Merge branch 'develop' of ↵Binh-Minh Ribler2017-03-281-0/+2
| | |\ \ | | | | | | | | | | | | | | | https://bitbucket.hdfgroup.org/scm/~bmribler/hdf5_bmr_cpp3 into develop
| | * | | Fix HDFFV-8089Binh-Minh Ribler2017-03-281-5/+5
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Description: Some code within an "ifdef H5D_CHUNK_DEBUG" block was using outdated data structure but not caught because the case of H5D_CHUNK_DEBUG being defined was never tested. It was commented out. I defined H5D_CHUNK_DEBUG, tested, and commented out again. Platforms tested: Linux/32 2.6 (jam) Linux/64 (platypus) Darwin (osx1010test)
| * | | | Omnibus checkin for several relatively minor modifications:mainzer2017-03-284-29/+116
| | |/ / | |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 1) Added code test/page_buffer.c to verify that page buffering is disabled in parallel builds. 2) Added code to test/cache_image.c to verify correct interaction between evict on close and cache image -- in particular management of a file containing a cache image containing dirty metadata that has been opened R/O. Also fix for the bug exposed. 3) Added code to testpar/t_cache_image.c to verify expected procedure for reading cache images, and also supporting stats collection code needed for the test. 4) Repair of an overactive sanity check in H5C__reconstruct_cache_contents(). 5) Other minor tidies in passing. Tested serial and parallel, debug and production on Jelly.
* | | | HDFFV-10143 fix use before setAllen Byrne2017-03-301-1/+1
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* | | | Fix code error and use H5PL_MAX_PATH_NUM in testAllen Byrne2017-03-301-2/+1
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* | | | HDFFV-10143 Cleanup due to commentsAllen Byrne2017-03-302-6/+4
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* | | | HDFFV-10143 change h5PLget to use buffer like H5Iget_nameAllen Byrne2017-03-302-32/+33
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* | | | HDFFV-10143 change put to replace and add constAllen Byrne2017-03-302-10/+10
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* | | | Remove redundant codeAllen Byrne2017-03-301-13/+9
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* | | | HDFFV-10143 Use Windows A version of ExpandEnvironmentStringsAllen Byrne2017-03-301-1/+1
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* | | | HDFFV-10143 Fix initial issues from reviewAllen Byrne2017-03-303-100/+88
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* | | HDFFV-10143 add APIs to manipulate plugin path tableAllen Byrne2017-03-282-0/+305
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