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* Merge pull request #405 in HDFFV/hdf5 from ~MAINZER/hdf5_jrm:develop to developJohn Mainzer2017-04-078-26/+293
|\ | | | | | | | | | | * commit 'eb75dc1bb02e13902d73a36caafe763eea585d02': Removed commeted out code from H5C_dump_coll_write_list() Checkin of fix for CGNS bug (https://jira.hdfgroup.org/browse/HDFFV-10055).
| * Removed commeted out code from H5C_dump_coll_write_list()mainzer2017-04-071-5/+0
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| * Merge branch 'develop' of ↵mainzer2017-04-063-6/+17
| |\ | | | | | | | | | | | | | | | https://bitbucket.hdfgroup.org/scm/~mainzer/hdf5_jrm into develop Update to permit push to develop_jrm fork
| * | 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.
* | | Merge pull request #396 in HDFFV/hdf5 from ~VCHOI/my_hdf5_fork:develop to ↵Vailin Choi2017-04-071-301/+368
|\ \ \ | |_|/ |/| | | | | | | | | | | | | | develop * commit 'b3ff39585c3f8e6e9096fc84f02dd049f0d3ae36': 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.
| * | Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Vailin Choi2017-04-073-6/+17
| |\ \ | |/ / |/| | | | | | | | | | | | | | * commit '4a05d27c6fcef81612e005b6f6429ab362247492': HDFFV-10143 add missing javadoc param Add missing test status Fix CMake regex commands
* | | Merge pull request #402 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2017-04-062-0/+11
|\ \ \ | | | | | | | | | | | | | | | | | | | | * commit '4b11c4fd518026667944b50b4cd4cb41bec7e25a': HDFFV-10143 add missing javadoc param Add missing test status
| * | | HDFFV-10143 add missing javadoc paramAllen Byrne2017-04-061-0/+10
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| * | | Add missing test statusAllen Byrne2017-04-061-0/+1
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* | | Merge pull request #397 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developLarry Knox2017-04-061-6/+6
|\ \ \ | |_|/ |/| | | | | | | | * commit 'f1ad2feb0b253302895a0bc9835ade8f2f2484e8': Fix CMake regex commands
| * | Fix CMake regex commandsAllen Byrne2017-04-061-6/+6
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| * Modify test/fheap.c to run with various file space strategies and/or page ↵Vailin Choi2017-04-051-301/+368
|/ | | | | | | | 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.
* Merge pull request #395 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2017-04-0513-394/+1245
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '1e0ecb4481e226239c1fd51bd214bd7e7490805d': 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 HDFFV-10143 Cleanup due to comments HDFFV-10143 remove debugging output HDFFV-10143 change h5PLget to use buffer like H5Iget_name HDFFV-10143 change put to replace and add const Remove redundant code HDFFV-10143 Use Windows A version of ExpandEnvironmentStrings HDFFV-10143 Fix initial issues from review Remove duplicated paths, add new paths HDFFV-10143 add APIs to manipulate plugin path table
| * 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.
* | Merge pull request #394 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:develop to developDana Robinson2017-04-051-2/+4
|\ \ | | | | | | | | | | | | | | | * commit '9876155d3fdb073dd3769f18665c86d04cda4806': 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.
| * Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2017-04-051-8/+13
| |\ | |/ |/| | | | | * commit '60bb3fd1108e2006a79b008d031a0f68a1e6b393': 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.
* | Merge pull request #393 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:develop to developDana Robinson2017-04-051-8/+13
|\ \ | | | | | | | | | | | | * commit 'f060e05999849c1eb3ef653c08977e4b154749d8': 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.
| * | Re-enabled fixed array index testing in the test_random_rank4_vl() testDana Robinson2017-04-051-8/+13
|/ / | | | | | | | | in test/set_extent. This was fixed some time ago, but the test was never re-enabled for that index type.
| * Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2017-04-041-4/+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.
* | Merge pull request #389 in HDFFV/hdf5 from fix_h5watch_signal to developQuincey Koziol2017-04-031-4/+5
|\ \ | | | | | | | | | | | | * commit '1e4b2588b671a2172827bb422aee9ba96c0320b6': 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.
| * | Switch to using flag in signal handler, to trigger dropping out of main loopQuincey Koziol2017-04-031-4/+5
|/ / | | | | | | and shutdown cleanly, instead of calling leave() from the signal handler.
| * Fix typo deletionAllen Byrne2017-04-041-2/+2
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| * HDFFV-10143 Update new feature section.Allen Byrne2017-04-041-0/+4
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| * HDFFV-10143 clean up format and function returnAllen Byrne2017-04-041-348/+306
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| * HDFFV-10143 Add plugin APIs to Java interfaceAllen Byrne2017-04-035-1/+328
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| * Update with checks for index boundsAllen Byrne2017-04-032-12/+24
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| * Update tools issuesAllen Byrne2017-04-031-2/+9
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| * Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2017-04-0311-87/+952
| |\ | |/ |/| | | | | | | | | | | | | | | * 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 Ribler2017-03-286-13/+82
| |\ \ | | | | | | | | | | | | 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)
* | | | Merge pull request #382 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2017-03-301-0/+1
|\ \ \ \ | | | | | | | | | | | | | | | | | | | | * commit '9afc2d1fc05c0ee87cb27ff1f6179e00b5eb6ac2': Add new file COPYING_LBNL_HDF5.
| * \ \ \ Merge branch 'develop' of ↵lrknox2017-03-307-78/+886
| |\ \ \ \ | |/ / / / |/| | | | | | | | | https://bitbucket.hdfgroup.org/scm/~lrknox/hdf5_lrk into develop
* | | | | Merge pull request #376 in HDFFV/hdf5 from ~MAINZER/hdf5_jrm:develop to developJohn Mainzer2017-03-307-78/+886
|\ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | * commit 'afd8f64c29f7cffde895232406a3a388c6d77e77': Omnibus checkin for several relatively minor modifications:
| * | | | | Omnibus checkin for several relatively minor modifications:mainzer2017-03-287-78/+886
| | |_|/ / | |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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 new file COPYING_LBNL_HDF5.lrknox2017-03-301-0/+1
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* | | | Merge pull request #375 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2017-03-302-4/+60
|\ \ \ \ | |/ / / |/| | | | | | | | | | | | | | | | | | | * commit 'c1f95b28caae290a7c0136537daca9004db055b8': Revert "Clear hdf5 1.10 entries from RELEASE.txt in the develop branch. Entries" Add LBNL license file and modify COPYING file accordingly. 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.
| * | | Revert "Clear hdf5 1.10 entries from RELEASE.txt in the develop branch. ↵lrknox2017-03-291-27/+332
| | | | | | | | | | | | | | | | | | | | | | | | Entries" This reverts commit 1a114c191d6366558202522df96c2726c0512cc0.
| * | | Add LBNL license file and modify COPYING file accordingly.lrknox2017-03-292-4/+60
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| * | | Clear hdf5 1.10 entries from RELEASE.txt in the develop branch. Entrieslrknox2017-03-281-332/+27
|/ / / | | | | | | | | | | | | in this branch version of RELEASE.txt should be intended for the future 1.12.0 release.
| | * HDFFV-10143 fix use before setAllen Byrne2017-03-301-1/+1
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| | * HDFFV-10143 surround will fail with try blockAllen Byrne2017-03-301-1/+4
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| | * HDFFV-10143 typo cleanupAllen Byrne2017-03-301-4/+4
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| | * HDFFV-10143 typo removedAllen Byrne2017-03-301-1/+1
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| | * Fix code error and use H5PL_MAX_PATH_NUM in testAllen Byrne2017-03-302-15/+18
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| | * HDFFV-10143 Cleanup due to commentsAllen Byrne2017-03-303-13/+11
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| | * HDFFV-10143 remove debugging outputAllen Byrne2017-03-301-6/+0
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| | * HDFFV-10143 change h5PLget to use buffer like H5Iget_nameAllen Byrne2017-03-303-44/+74
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