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* Change copyright headers to replace url referring to file to be removedlrknox2017-04-14439-2646/+1764
| | | | | | | | and replace it with new url for COPYING file. Fix 2 lines in java error test expected output file where messages include line numbers changed by reducing the copyright header by 2 lines.
* Fix for H5Dset_extent test failure with extensive array indexing (HDFFV-9771)Vailin Choi2017-04-122-3/+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.
* Merge pull request #408 in HDFFV/hdf5 from develop to hdf5_1_10Larry Knox2017-04-119-28/+297
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit 'ccb4e9ed9a5e0af27db9f1504a628e35d7f4cf92': (27 commits) Removed commeted out code from H5C_dump_coll_write_list() Checkin of fix for CGNS bug (https://jira.hdfgroup.org/browse/HDFFV-10055). HDFFV-10143 add missing javadoc param Add missing test status Fix CMake regex commands Modify test/fheap.c to run with various file space strategies and/or page buffering Modify test/fheap.c to run with different combinations of file space strategies and page buffering only when ExpressMode is 0 (HDF5TestExpress is 0). Tested on ostrich, platypus, mayll, emu, osx1010test, quail, kite, kituo. 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. Re-enabled fixed array index testing in the test_random_rank4_vl() test in test/set_extent. This was fixed some time ago, but the test was never re-enabled for that index type. Fix typo deletion HDFFV-10143 Update new feature section. HDFFV-10143 clean up format and function return HDFFV-10143 Add plugin APIs to Java interface Update with checks for index bounds Update tools issues HDFFV-10143 fix use before set HDFFV-10143 surround will fail with try block HDFFV-10143 typo cleanup HDFFV-10143 typo removed Fix code error and use H5PL_MAX_PATH_NUM in test ...
| * 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)
| * | 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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* | | Merging in latest from upstream (HDFFV/hdf5:refs/heads/hdf5_1_10)Allen Byrne2017-04-041-5/+5
|\ \ \ | | | | | | | | | | | | | | | | | | | | * commit 'd6ea49f5cbcaa852cd0caf34278ec61108667bc3': Switch to using flag in signal handler, to trigger dropping out of main loop and shutdown cleanly, instead of calling leave() from the signal handler. 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 #390 in HDFFV/hdf5 from develop to hdf5_1_10Larry Knox2017-04-031-5/+5
| |\ \ \ | | | |/ | | |/| | | | | | | | | | | | | * commit 'd522632b9e1f1d88db2117e89f3caba0dc4cf38b': Switch to using flag in signal handler, to trigger dropping out of main loop and shutdown cleanly, instead of calling leave() from the signal handler. 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)
* | | | | Update with checks for index boundsAllen Byrne2017-04-031-1/+10
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* | | | | Merging in latest from upstream (HDFFV/hdf5:refs/heads/hdf5_1_10)Allen Byrne2017-04-034-29/+116
|\ \ \ \ \ | |/ / / / | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '6387f7099d22c66dab415c57f9fd547eb86e4ad5': Small corrections to DOPYING file. 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:
| * | | | Merge branch 'develop' into hdf5_1_10lrknox2017-03-314-29/+116
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| | * | | 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.
| | * | Add H5_DLL to H5AC_get_mdc_image_info() prototypeQuincey Koziol2017-03-241-1/+1
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| | * | Add prototype for H5AC_get_mdc_image_infoQuincey Koziol2017-03-221-0/+2
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| | * Minor style cleanupsQuincey Koziol2017-03-223-7/+8
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| | * Revert "Switch h5clear for cache images to use existing ↵Quincey Koziol2017-03-225-0/+97
| | | | | | | | | | | | | | | | | | H5Pget_cache_image_config()" This reverts commit dd5105fc9912c77f6d6074700d83e5e8282e86c9.
| | * Extend h5vers to update version strings in java files and h5repacklrknox2017-03-201-3/+3
| | | | | | | | | | | | | | | | | | | | | | | | version test expected output file. Update version on develop branch to 1.11.0. Please enter the commit message for your changes. Lines starting
* | | 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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* | | HDFFV-10143 Use Windows A version of ExpandEnvironmentStringsAllen Byrne2017-03-301-1/+1
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* | | Remove redundant codeAllen Byrne2017-03-301-13/+9
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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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* | Merge bin/h5vers changes from develop.lrknox2017-03-241-3/+3
| | | | | | | | | | Pull version from configure for version test in h5repack_plugin.sh.in Update version to 1.10.2-snap0 for hdf5_1_10 branch.
* | Add H5_DLL to function prototype.lrknox2017-03-231-1/+1
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* | Merge pull request #361 in HDFFV/hdf5 from merge_h5clear_revert to developQuincey Koziol2017-03-235-0/+98
| | | | | | | | | | | | * commit '46c9ab600de491657520897322b75659c3bdfb5f': Minor style cleanups Revert "Switch h5clear for cache images to use existing H5Pget_cache_image_config()"
* | Add prototype for H5AC_get_mdc_image_infoQuincey Koziol2017-03-231-0/+2
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* | Merge branch 'hdf5_1_10' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 ↵lrknox2017-03-201-4/+4
|\ \ | |/ |/| | | into hdf5_1_10
| * set initial version for HDF5 1.10.1.lrknox2017-03-171-4/+4
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* | Merge pull request #341 in HDFFV/hdf5 from ~MAINZER/hdf5_jrm:develop to developJohn Mainzer2017-03-206-20/+50
|\ \ | | | | | | | | | | | | | | | * commit 'b7c58f7dfca66d4caa26d7f8b318ad3514b8c46f': Minor code changes to address comments in pull request Checkin of additions to cache image parallel test code and associated bug fixes.
| * | Minor code changes to address comments in pull requestmainzer2017-03-173-3/+6
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