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* Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Jordan Henderson2017-04-172-3/+13
|\ | | | | | | | | | | | | | | | | | | | | * commit '906c1819188755a04fde6cc0ad7346775a6e61b8': Skip tests for page buffering in test/fheap.c for parallel build Skip the two tests for page buffering in test/fheap.c because this feature is disabled in parallel. Activate full testing when this feature is re-enabled in the future for parallel build. Due to HDFVIEW-19 add read VL as string function Fix URL name updated with README changes DAILYTEST-250 change test props to reduce timeout Combined the README_DEVEL and README, and removed out-dated README material Fix for H5Dset_extent test failure with extensive array indexing (HDFFV-9771) 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.
| * 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.
* | Fix deadlocking issueJordan Henderson2017-04-131-58/+98
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* | Fix link-chunk I/O by tidying up local_info_arrayJordan Henderson2017-04-131-12/+13
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* | Minimize size of H5D_filtered_collective_io_info_t structJordan Henderson2017-04-111-204/+102
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* | Revise first-phase algorithm to only use rank 0 for redistributionJordan Henderson2017-04-101-24/+155
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* | Merge pull request #4 in ~JHENDERSON/hdf5 from feature/parallel_filters to ↵Jordan Henderson2017-04-107-65/+1348
|\ \ | |/ |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | develop * commit '7883c0d01b4eadba84697c7bb3322a304d242ed6': (38 commits) Add comments In current implementation, list must be gathered to all Correct error with usage of array_gather function Make array_gather routine more general Updated comments Add comments to H5D_filtered_collective_io_info_t data structure Remove debugging statements Revert "Merge latest changes from develop" Merge latest changes from develop removed erroneous casts from non-rvalue H5MM_free() calls. Replaced assignment of void return values with explicit value of NULL Fix issue with uninitialized chunk index during chunk re-insertion into index Remove potential infinite loops caused by goto in error label region Remove note about src_type_size vs dst_type_size Trigger error if library tries to break to independent I/O with filters in the pipeline Fix issue in H5D__mpio_array_gather when no one contributes anything Iterator for initial chunk entry IO operation should use source datatype size Fix bug where data doesn't write correctly when MEMSPACE isnt the same as FILESPACE Check return value of H5S_GET_EXTENT_NPOINTS macro Fix macro complaint in H5Dmpio.c Test code for user passing one-chunk-per-process hint to library ...
| * Add commentsJordan Henderson2017-04-101-2/+3
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| * In current implementation, list must be gathered to allJordan Henderson2017-04-091-1/+1
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| * Correct error with usage of array_gather functionJordan Henderson2017-04-091-3/+3
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| * Make array_gather routine more generalJordan Henderson2017-04-091-45/+66
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| * Updated commentsJordan Henderson2017-03-301-20/+17
| | | | | | | | changed variable name for list containing all chunks in the I/O operation
| * Add comments to H5D_filtered_collective_io_info_t data structureJordan Henderson2017-03-301-11/+11
| | | | | | | | Correct comment and error message about retrieving the threshold for performing either Linked-chunk or Multi-chunk I/O
| * Merge branch 'feature/parallel_filters' of ↵Jordan Henderson2017-03-3062-2472/+8793
| |\ | | | | | | | | | ssh://bitbucket.hdfgroup.org:7999/~jhenderson/hdf5.git into feature/parallel_filters
| | * Merge pull request #3 in ~JHENDERSON/hdf5 from develop to ↵Jordan Henderson2017-03-2062-2472/+8793
| | |\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | feature/parallel_filters * commit 'b359e8f1a2349d177e70d34560d0a089ce37c4c8': Description: Removed "#ifndef H5_NO_DEPRECATED_SYMBOLS" in file space tests, because the wrappers only use the latest functions now. Platforms tested: Linux/32 2.6 (jam) Linux/64 (platypus) Darwin (osx1010test) Purpose: Add new C++ wrappers Description: Because H5Pset_file_space and H5Pget_file_space are deprecated, changed to make wrappers for the new functions instead: H5Ps/get_file_space_strategy H5Ps/get_file_space_page_size Description: Fixed typos. Platforms tested: Linux/64 (jelly) Description: Deprecating versions of PropList::setProperty that have arguments that miss "const" Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1010test) Description: Miscellaneous clean-up: format and comments Platforms tested: Linux/64 (jelly) Darwin (osx1010test) Add toolset option to cmake configure Update cmake pubconf to match autotools and add strtoll checks Switch from HDatoll to HDstrtoll, for Windows compatibility. output_filter.sh: Comment added to address HDFFV-8270. The sample ontput in the file's comments are not up-to-date with the scripts in the file that remove output unique to certain systems when running test scripts. This output doesn't match expected output files for the tests, causing them to fail. Ther output_filter.sh file removes such output. Currently we don't have access to these systems to update the comments. Correct double sourcedir name on copied datafiles. HDFFV-10138 Merge app framework to examples Final merge of page buffering branch to develop Purpose: Add new C++ wrappers Description: Added wrappers for H5Iis_valid, H5Ps/get_nlinks, H5Tget_create_plist, H5Oopen, H5Oclose and H5Pset_virtual Bring changes to I/O parameters from page_buffering branch. Merge in reentrency changes to "make space in cache" from page_buffering branch. Minor cleanups and bring over "prefetched dirty" fixes for entries loaded from a cache image. Remove some usage of "prefetched_dirty" flag (which hasn't been merged from the page_buffering branch yet. Also, bring over improvements to flush candidate entries for parallel code. Align with incoming page buffering changes: minor cleanups, centralize removing entries from collective metadata read list
| * | | Remove debugging statementsJordan Henderson2017-03-301-342/+6
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| * | Merge pull request #2 in ~JHENDERSON/hdf5 from HDFFV/hdf5:develop to ↵Jordan Henderson2017-03-1047-1630/+8478
| |\ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | feature/parallel_filters * commit '56e5b4ed05fb3bad51c226ec5b567871a45e0bce': (112 commits) updated AM_SILENT_RULES syntax Added a check for AM_SILENT_RULES before enabling it. Fix alignment Fix vds tests Correct result code for strings test Add extension to filename HDFFV-10128 fix string compare and add tests Description: Only format changes: mostly tabs vs. spaces Platforms tested: Linux/64 (jelly) - very minor Lowercase math and set CMake commands Added "flush" and "refresh" to testflushrefresh.sh error output so it's easier to see where errors in the script occur. Misc. small cleanups to sync against incoming page buffering changes. Update CMake formatting Update CMake files and formatting Normalize against incoming page buffering changes. HDFFV-10120 verify nozlib checking with tools tests cmake non-code typo Correct issues from pull request reviews. Corrected version of 4b5e05c084f93c35dae946c2c9e814d565a613b0: Fix some more signed -> unsigned value issues with cache data structures, also misc. style cleanups. All to align w/incoming page_buffering changes. Revert "Fix some more signed -> unsigned value issues with cache data structures, also" Added virtual to list ...
| * | | Revert "Merge latest changes from develop"Jordan Henderson2017-03-1043-4394/+1627
| | | | | | | | | | | | | | | | This reverts commit 104d63f25a8cb6e156bc901eb85aafc0b67775ee.
| * | | Merge latest changes from developJordan Henderson2017-03-1043-1627/+4394
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| * | | removed erroneous casts from non-rvalue H5MM_free() calls. Replaced ↵Frank T Willmore2017-02-211-6/+12
| | | | | | | | | | | | | | | | assignment of void return values with explicit value of NULL
| * | | Fix issue with uninitialized chunk index during chunk re-insertion intoJordan Henderson2017-02-201-2/+12
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| * | | Remove potential infinite loops caused by goto in error label regionJordan Henderson2017-02-101-3/+3
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| * | | Remove note about src_type_size vs dst_type_sizeJordan Henderson2017-02-091-1/+0
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| * | | Trigger error if library tries to break to independent I/O with filtersJordan Henderson2017-02-082-0/+8
| | | | | | | | | | | | in the pipeline
| * | | Fix issue in H5D__mpio_array_gather when no one contributes anythingJordan Henderson2017-02-031-22/+28
| | | | | | | | | | | | | | | | Fix issue in Multi-chunk IO where IO would crash if no one has a selection
| * | | Iterator for initial chunk entry IO operation should use source datatypeJordan Henderson2017-02-031-1/+1
| | | | | | | | | | | | size
| * | | Fix bug where data doesn't write correctly when MEMSPACE isnt the sameJordan Henderson2017-02-031-7/+33
| | | | | | | | | | | | as FILESPACE
| * | | Check return value of H5S_GET_EXTENT_NPOINTS macroJordan Henderson2017-02-021-13/+31
| | | | | | | | | | | | | | | | | | | | Fix bug where a process with no selection during Multi-chunk IO could cause other processes to copy back incorrect chunk information after chunk re-allocation
| * | | Fix macro complaint in H5Dmpio.cJordan Henderson2017-02-021-3/+15
| | | | | | | | | | | | Fix debugging file output for test suite
| * | | Test code for user passing one-chunk-per-process hint to libraryJordan Henderson2017-01-311-7/+15
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| * | | Implement realloc strategy when receiving data modification messagesJordan Henderson2017-01-311-10/+19
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| * | | Add minor error code for H5D__mpio_array_gather failuresJordan Henderson2017-01-302-25/+23
| | | | | | | | | | | | | | | | | | | | | | | | Catch case where total IO size is greater than chunk size (Overlapping write) Update full chunk overwrite code to not need MPI calls
| * | | Add mechanism for determining if a chunk is being fully overwrittenJordan Henderson2017-01-301-36/+60
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| * | | Add back debugging statementsJordan Henderson2017-01-301-4/+300
| | | | | | | | | | | | | | | | Move conditional check inside while loop in construct_filtered_io_info_list
| * | | Remove Debugging Statements for Code ReviewJordan Henderson2017-01-271-310/+5
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| * | | Remove unnecessary num_chunks_selected_array fromJordan Henderson2017-01-271-29/+20
| | | | | | | | | | | | H5D__construct_filtered_io_info_list
| * | | Multiple Bug FixesJordan Henderson2017-01-261-102/+121
| | | | | | | | | | | | | | | | | | | | Add comments explaining different variables Check more overflow/conversion sign change issues
| * | | Fix bug with chunk data updatingJordan Henderson2017-01-261-67/+68
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| * | | Test code for sending chunk modification data aroundJordan Henderson2017-01-241-10/+190
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| * | | Clean up H5Dmpio.c warningsJordan Henderson2017-01-201-30/+34
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| * | | For sake of complexity, force multi chunk IO for parallel filtered readJordan Henderson2017-01-191-2/+13
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| * | | Code refactoringJordan Henderson2017-01-191-157/+197
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Modify single chunk entry function to handle both read and write cases Store array of MPI derived types in Multi-chunk IO so that all freeing can be done at end instead of during processing Add read support for Multi-chunk IO only currently
| * | | Clean up const and other warningsJordan Henderson2017-01-181-30/+28
| | | | | | | | | | | | Add notes about need for another minor error code
| * | | Update documentation for link and multi chunk IOJordan Henderson2017-01-181-43/+46
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| * | | Major cleanupJordan Henderson2017-01-181-475/+303
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Separate update phase for chunk entry into its own function, since code for multi-chunk IO and link-chunk IO is exactly the same Remove last IO mode code from multi-chunk IO, since filtered collective writes cannot break to independent IO mode Fix collective overlapping IO for multi-chunk IO by iterating equal to the max number of chunks on any process Make hard separation between collective read and write since trying to mix the two into one loop becomes messy Add preliminary code for asynchronous sending of chunk modification data to new owning process when redistributing chunks
| * | | Add chunk redistribution for shared chunksJordan Henderson2017-01-171-190/+248
| | | | | | | | | | | | Remove check for process having a selection as this needs to be reworked
| * | | Eliminate owner fieldJordan Henderson2017-01-131-15/+11
| | | | | | | | | | | | Work on redistributing shared chunks
| * | | Switch working branch from master to developJordan Henderson2017-01-136-35/+1391
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* | | | 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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