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* 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
* Fixed a bug (HDFFV-10899) where the behavior of the deprecatedDana Robinson2019-10-041-2/+7
| | | | | | | | H5Gget_objinfo() call had changed and passing in a non-existing soft link with a statbuf of NULL passed instead of failed (as it should as per the RM). The HDF5 1.8 and 1.10 behavior was restored and H5Gget_objinfo() will now fail and return -1 as before.
* Merge pull request #1959 in HDFFV/hdf5 from ↵Vailin Choi2019-10-011-6/+5
|\ | | | | | | | | | | | | ~VCHOI/my_third_fork:bugfix/iteration_error_in_test_versionbounds to develop * commit '9ea386b6a660bd29225e96a246439db0c7f73da2': Fixed the iteration error in test_versionbounds() in test/dtypes.c.
| * Fixed the iteration error in test_versionbounds() in test/dtypes.c.Vailin Choi2019-09-301-6/+5
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* | Move function-scope macro definition to file-scope.Jacob Smith2019-09-301-5/+6
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* | Refactor external file addition loop to static function.Jacob Smith2019-09-291-18/+57
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* | fix declaring variable in for statementJacob Smith2019-09-281-9/+10
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* Number of arguments requires H5Dopen2.Larry Knox2019-09-281-1/+1
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* Merge pull request #1934 in HDFFV/hdf5 from ↵Vailin Choi2019-09-271-0/+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.
| * (1) Address the feedback from the PR reviewVailin Choi2019-09-261-11/+11
| | | | | | | | (2) Add release notes
| * Merge pull request #21 in ~VCHOI/my_third_fork from develop to ↵Vailin Choi2019-09-2610-231/+420
| |\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | bugfix/HDFFV-10585-investigate-slowness-of-regular * commit '0ea77179d507bd2c29f3b9b357a0c35d4077b29c': (39 commits) Fix the errors when updating the versions in the new 1.13 develop branch. add missing version to list Add new versioned filename to list Update N_FSINFO_VERSION_BOUNDS to H5F_LIBVER_NBOUND. Remove file script Update versioning to next major version Update develop branch version to 1.13.0 after creation of hdf5_1_12 branch. Merge Binh-Minh's changes for code improvement to chunk_info.c (PR #1942) to develop branch. Update to current external file population. Revert else-if to single line. Fix missing option and incorrect close Revert "Moved NDEBUG guards to H5EA_DEBUG in H5EA package." Revert "Fix for H5EA debug package when built in release mode." Change print calls to HD-wrapped. Minor formatting tweaks (inc. regressions and in-file style-matching). Refactor h5repackgentest to have more modular internals, for easier addition of new tests. Update manifest and test script for new hdf5 external-storage .h5 files. Remove obsolete symbol small syntax changes Renamed get/set_time() calls in the tools library to avoid name clash when building static parallel HDF5 w/ static linking to OpenMPI. Change unused variable to generic form Whitespace cleanup ...
| * | Fix for HDFFV-10585 investigate hyperslab slowness:Vailin Choi2019-09-191-0/+162
| | | | | | | | | | | | | | | | | | | | | 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.
* | | Converted H5O MD cache cork calls to use the VOL.Dana Robinson2019-09-271-5/+7
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* | add missing version to listAllen Byrne2019-09-261-2/+2
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* | Add new versioned filename to listAllen Byrne2019-09-261-13/+14
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* | Update versioning to next major versionAllen Byrne2019-09-252-1/+3
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* | Merge Binh-Minh's changes for code improvement to chunk_info.c (PR #1942)Larry Knox2019-09-251-20/+25
| | | | | | | | to develop branch.
* | 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
| | | | | | | | | | | | routines.
| * | 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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