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* Fix for HDFFV-7853 H5Ocopy doesn't work with open identifiersVailin Choi2017-06-115-88/+155
| | | | Changes made so that raw data for dataset objects are copied from cached info when possible instead of flushing objects to file and read them back in again.
* Revert "Merge pull request #567 in HDFFV/hdf5 from ↵Dana Robinson2017-06-098-395/+230
| | | | | | | ~DEROBINS/hdf5_der:develop to develop" This reverts commit 4242753848c44ab3b5d226e66225eac2f64db314, reversing changes made to b0e79fe6dd20ec7aa1b3e5f0f8b370639a4ef5bd.
* * Made STATIC free lists EXTERN for H5O_layout_t.Dana Robinson2017-06-077-170/+251
| | | | * Made all non-global instances of H5O_layout_t in H5Pdcpl.c dynamic.
* Updated H5O_layout_t dynamic work to use the H5FL interface.Dana Robinson2017-06-077-28/+79
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* Made some H5O_layout_t stack allocations dynamic (quiets warnings).Dana Robinson2017-06-066-53/+86
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* Merge branch 'develop' into windows_openDana Robinson2017-05-3130-1674/+1755
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| * Merge branch 'develop' into compat_feature_flagDana Robinson2017-05-2611-137/+145
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| | * Merge pull request #538 in HDFFV/hdf5 from ↵Dana Robinson2017-05-267-128/+131
| | |\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~DEROBINS/hdf5_der:may_dev_warnings to develop * commit '57f0a296c0b727e3d86cea312ba46efc98d76227': Minor warning fix. More minor warning fixes. Minor warning fixes in the tools. Minor type fixes to h5watch. A few more warnings fixed. Fixed additional minor warnings. Fixed many minor warnings.
| | | * More minor warning fixes.Dana Robinson2017-05-251-1/+1
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| | | * Fixed many minor warnings.Dana Robinson2017-05-256-127/+130
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| | * | Merge pull request #534 in HDFFV/hdf5 from ↵Frank Willmore2017-05-251-0/+5
| | |\ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~FRANK.WILLMORE/hdf5:fix-set-mpi-err-handler to develop * commit '1ee90786196c10c2c616a9fb4b8b1f92ebefa1f2': updated MPI error handling call for MPICH2 standard cleanup enabled MPI error handling added test file
| | | * | updated MPI error handling call for MPICH2 standardFrank Willmore2017-05-241-1/+1
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| | | * | enabled MPI error handlingFrank Willmore2017-05-231-0/+5
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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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| * | | * Added new public H5FDdriver_query() API call.Dana Robinson2017-05-244-7/+48
| | | | | | | | | | | | | | | | | | | | | | | | * Changed return type of H5FD_driver_query() to herr_t. * Updated swmr.c to use H5FDdriver_query() instead of the private call. * Added some flags tests to vfd.c.
| * | | * Made H5FD_driver_query() a private function instead of static.Dana Robinson2017-05-244-39/+40
| | | | | | | | | | | | | | | | | | | | | | | | | | | | * Moved H5FD_driver_query() to H5FDint.c. * Minor typo fixes in H5I.c. * Updated swmr.c to check the VFD feature flags and skip the retries test when the VFD is not compatible with H5P_DEFAULT.
| * | | Fixed HDFFV-10214:Dana Robinson2017-05-198-17/+28
| |/ / | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Updated comments in the library to accurately reflect the semantics of the H5FD_FEAT_POSIX_COMPAT_HANDLE flag. * Removed the check for the POSIX compatible handle feature flag when determining if a VFD supports SWMR. Partial work for HDFFV-10197: * Added a new H5FD_FEAT_DEFAULT_VFD_COMPATIBLE feature flag that is set when a VFD creates output that is compatible with the default VFD. Will be used in the testing but might also be generally useful to users.
| * | 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
* | | Rework of the POSIX file open permissions and macros to clean upDana Robinson2017-04-287-28/+18
| | | | | | | | | | | | | | | | | | HDopen() calls. Also fixed a minor const warning in the core VFD.
* | | Changed the Windows POSIX open() file permissions to be correctDana Robinson2017-04-287-9/+28
|/ / | | | | | | according to MSDN. Partial fix for HDFFV-9630.
* | 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.
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