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* Merge pull request #1990 in HDFFV/hdf5 from ~JSOUMAGNE/hdf5:references_1_12 ↵Larry Knox2019-10-0920-766/+5371
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | to hdf5_1_12 * commit '5d2545ee26d4b7013ed363545705f16a67087549': Fix func enter macro in H5T_ref_reclaim() Update RELEASE.txt for reference changes Fix reference type comparison in h5dump Make wrappers, tests and tools use H5Treclaim() instead of H5Dvlen_reclaim() Add new H5R API that abstracts object, region and attribute reference types Remove ability to loc by ref from H5VL layer Add support for retrieving object name by token Add H5VL_OBJECT_GET_TYPE to get object type Add H5VL_MAX_TOKEN_SIZE and H5VL_token_t Adapt Jerome's "file info" H5VL 'get' query to retrieve container token info. Fix H5VL_blob_get to return size of blob Add 'blob' callbacks to VOL, along with a native implementation to store them in the global heap, and changed the VL datatype conversion code to use blobs.
| * Make wrappers, tests and tools use H5Treclaim() instead of H5Dvlen_reclaim()Jerome Soumagne2019-10-0813-185/+185
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| * Add new H5R API that abstracts object, region and attribute reference typesJerome Soumagne2019-10-087-581/+5186
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Also support references to external files Add new H5T_REF type and type conversion routines Support conversion from H5T_REF_OBJ/DSET_REG to H5T_REF Add H5Treclaim() API to reclaim memory of vlen/reference types Deprecate H5Dvlen_reclaim() Fix H5T_vlen_reclaim() and H5T_reclaim() to use private callback Add H5T_ref_reclaim() Move previous H5R APIs to H5Rdeprec.c Clean up H5Ocopy Separate H5O_copy_expand_ref() to H5Ocopy_ref() Add support for copying new reference types Clean up deprecated routines to go through VOL and same code path Fix return codes in existing trefer.c test Rename trefer.c to trefer_deprec.c trefer.c is for new references Add performance test for trefer Add additional obj_copy_ref test Make use of tokens and blobs to store references Skip blob encoding for object references Start adding new reference examples
* | Merge pull request #1962 in HDFFV/hdf5 from ↵Vailin Choi2019-10-091-0/+162
|\ \ | |/ |/| | | | | | | | | | | ~VCHOI/my_third_fork:bugfix/112_HDFFV-10585-investigate-slowness-of-regular to hdf5_1_12 * commit 'bffa18b684de83359f4ad25e11f4ad0b15f34040': Merge pull request #1957 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop Merge pull request #1934 in HDFFV/hdf5 from ~VCHOI/my_third_fork:bugfix/HDFFV-10585-investigate-slowness-of-regular to develop
| * Merge pull request #1957 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2019-09-301-1/+1
| | | | | | | | | | * commit '3fb711e0ff2516cba7a0cb34f2d8ca38241b06a7': Number of arguments requires H5Dopen2.
| * Merge pull request #1934 in HDFFV/hdf5 from ↵Vailin Choi2019-09-301-0/+162
| | | | | | | | | | | | | | | | ~VCHOI/my_third_fork:bugfix/HDFFV-10585-investigate-slowness-of-regular to develop * commit '7924eee0e5ee0745b784c635042b8633886fb799': (1) Address the feedback from the PR review (2) Add release notes Fix for HDFFV-10585 investigate hyperslab slowness: 1) Improve hyperslab performance when doing I/O from 1-d disjoint file dataspace to 1-d contiguous memory dataspace. 2) Move coding in H5D__chunk_io_init() that is constructing the chunk mappings to a separate routine.
* | Cleanup whitespace and comments compared to developAllen Byrne2019-10-022-18/+20
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* | fix for statement declare variableAllen Byrne2019-09-301-24/+65
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* add missing version to listAllen Byrne2019-09-261-2/+2
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* Merge Binh-Minh's changes for code improvement to chunk_info.c (PR #1942)Larry Knox2019-09-251-20/+25
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* Merge branch 'develop' of ↵Jacob Smith2019-09-23103-23597/+30790
|\ | | | | | | https://bitbucket.hdfgroup.org/scm/~jake.smith/hdf5 into bugfix/repack_external_storage
| * HDFFV-10740 - skip copying dirs in for loopsAllen Byrne2019-09-184-26/+54
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| * Fixed some exit calls.Dana Robinson2019-09-0728-168/+140
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| * Reworked the previously refactorred code.Binh-Minh Ribler2019-09-051-150/+161
| | | | | | | | | | | | | | Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1011test)
| * Merge branch 'develop' of ↵Binh-Minh Ribler2019-09-043-9/+22
| |\ | | | | | | | | | https://bitbucket.hdfgroup.org/scm/~bmribler/hdf5-bmr into develop
| | * Fix CMake build of test needing compression libsAllen Byrne2019-09-031-1/+14
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| | * Merge pull request #1908 in HDFFV/hdf5 from ~BMRIBLER/hdf5-bmr:develop to ↵Binh-Minh Ribler2019-09-033-3/+1968
| | |\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | develop - Added new chunk query functions: H5Dget_num_chunks(), H5Dget_chunk_info(), and H5Dget_chunk_info_by_coord() - Fixed iterator issue in H5EA_iterate(), H5FA_iterate(), and H5D__none_idx_iterate() * commit '96dab622e3bbe75d85b0cef3ca2bd5288cf4ac32': Fixed error code and error messages Tested on Jelly (very minor) Changed H5VL_NATIVE_DATASET_GET_CHUNK_INFO_BY_COOR to H5VL_NATIVE_DATASET_GET_CHUNK_INFO_BY_COORD per a review comment. Updated comments Updated based on reviews and refactored test code Code cleanup and refactor Re-ordered items w.r.t. date. Fixed typo Added notes about HDFFV-10677 and HDFFV-10661 HDFFV-10677 and HDFFV-10661
| | * | Fix EXISTS test syntaxAllen Byrne2019-08-291-7/+7
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| | * | fix get gethostname for windowsAllen Byrne2019-08-281-1/+1
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| * | | Improvement of test codeBinh-Minh Ribler2019-09-041-10/+21
| | |/ | |/| | | | | | | | | | | | | | | | | | | | | | Description: Fixed tests to handle the case when a requested compression filter is not available. Platform tested Linux/64 (jelly) Darwin (osx1011test)
| * | Fixed error code and error messagesBinh-Minh Ribler2019-09-031-26/+26
| | | | | | | | | | | | Tested on Jelly (very minor)
| * | Updated commentsBinh-Minh Ribler2019-09-011-1/+9
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| * | Updated based on reviews and refactored test codeBinh-Minh Ribler2019-09-011-769/+809
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| * | Code cleanup and refactorBinh-Minh Ribler2019-08-291-68/+47
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| * | HDFFV-10677 and HDFFV-10661Binh-Minh Ribler2019-08-283-3/+1941
| |/ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Description: - Added functions to query chunk information: H5Dget_num_chunks(dset_id, fspace_id, *nchunks) Gets the number of written chunks that intersect with the given dataspace. However, in this version, the intersection is not yet completed. Thus, the number of all written chunks will be returned. H5Dget_chunk_info_by_coord(dset_id, *offset, *filter_mask, *addr, *size) Given a chunk's logical coordinates, returns the chunk's filter, address, and size. H5Dget_chunk_info(dset_id, fspace_id, index, *offset, *filter_mask, *addr, *size) Given a chunk's index, returns the chunk's logical coordinates, filter, address, and size. The chunk belongs to a set of chunks that have nonempty intersection with the specified dataspace. However, in this version, the intersection is not yet completed, and the index is of all the written chunks. These functions comply with VOL. - Fixed some oversights found in the library for the tests in chunk_info.c to work correctly. The returned value from a callback function was not checked in H5EA_iterate(), H5FA_iterate(), and H5D__none_idx_iterate(). This oversight caused a callback function to continue iterating even though it's supposed to stop. Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1011test)
| * OESS-29 Update HD prefix mostlyAllen Byrne2019-08-2412-276/+256
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| * Merge branch 'develop' into shared_file_ptrQuincey Koziol2019-08-2160-17385/+17202
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| | * Untangle #ifdef mess in ROS3 code.Dana Robinson2019-08-203-239/+56
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| | * Add missing HD prefixAllen Byrne2019-08-181-121/+121
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| | * Update HD prefix and reconcile hl/cpp testAllen Byrne2019-08-161-1/+1
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| | * Add HD prefix to testsAllen Byrne2019-08-1559-17141/+17141
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| * | Begin converting the H5MF interface to use shared file pointers insteadQuincey Koziol2019-08-211-21/+18
| | | | | | | | | | | | of top file pointers.
| * | Rest of changes for 'top' file pointer to 'shared' file pointer for H5F__accumQuincey Koziol2019-08-191-1/+1
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| * | Partial H5F__accum_* routines.Quincey Koziol2019-08-191-2/+2
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| * Correct name of folderAllen Byrne2019-08-151-1/+1
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| * Mostly whitespace in testpar, addl changes for tmp dirAllen Byrne2019-08-156-151/+152
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| * Merge pull request #1872 in HDFFV/hdf5 from ↵Jake Smith2019-08-143-461/+367
| |\ | | | | | | | | | | | | | | | | | | ~JAKE.SMITH/hdf5:bugfix/ros3_hdfs_warns_squashed to develop * commit '2e5cd3d2b2d953420252c80ab5e32ac95ac0c5b3': Fix compiler warnings with diabled ROS3 and HDFS VFDs. Fix misuse of [HD]strncpy and [HD]snprintf. Minor formatting changes. Fix test cleanup issue with java groups example.
| | * Fix compiler warnings with diabled ROS3 and HDFS VFDs.Jacob Smith2019-08-143-461/+367
| | | | | | | | | | | | | | | | | | Fix misuse of [HD]strncpy and [HD]snprintf. Minor formatting changes. Fix test cleanup issue with java groups example.
| * | Merge pull request #1871 in HDFFV/hdf5 from ↵Ray Lu2019-08-144-5/+5
| |\ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~SONGYULU/hdf5_ray:bugfix/directory_name_develop to develop * commit '0b868668bac0d268120844adb9ad216a9a8e1395': Changed the directory name left out from the previous commit. Changed the name of the temporary directory from 'tmp' to a special name to avoid possible conflicts.
| | * | Changed the directory name left out from the previous commit.Songyu Lu2019-08-141-1/+1
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| | * | Changed the name of the temporary directory from 'tmp' to a special name to ↵Songyu Lu2019-08-144-4/+4
| | |/ | | | | | | | | | avoid possible conflicts.
| * | HDFFV-10879 fix test varnameAllen Byrne2019-08-141-1/+1
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| * Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2019-08-133-1/+19
| |\ | | | | | | | | | | | | | | | | | | | | | | | | * commit 'aeb145428f5e6bc51742fff031b0cf8cf6fbefbb': Updated h5trav.c to emit output that doesn't require ddl changes for map support. Fixed Map API CMake option Renamed H5Mdelete_key to H5Mdelete and H5Mset to H5Mput. Added ifdef for intel compilers, __GNUC__ has to be defined for header files which use it to work with intel compilers. This gives a warning for intel compiler about fallthrough, so added a check not to include fallthrough if using intel compilers. Added the map (H5M) API
| | * Added the map (H5M) APIDana Robinson2019-08-133-1/+19
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| * | Remove old codeAllen Byrne2019-08-131-5/+0
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| * | Correct error test spelling and useAllen Byrne2019-08-133-103/+136
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| * HDFFV-10879 fix reference fileAllen Byrne2019-08-121-1/+1
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| * Add option to explicitly disable extra testsAllen Byrne2019-08-071-0/+2
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| * Cleanup HD prefixAllen Byrne2019-08-053-909/+557
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| * Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2019-08-053-680/+762
| |\ | | | | | | | | | | | | | | | | | | * commit '5fe1216a4e6af8feef0551f7bece8a0e193310a9': Fix return type for H5Sselect_intersect_block(). Updated H5TRACE macro. Add H5Sselect_shape_same and H5Sselect_intersect_block API routines, along with tests and minor cleanups and refactorings.
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