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* Fixed a bug (HDFFV-10899) where the behavior of the deprecatedDana Robinson2019-10-111-78/+81
| | | | | | | | 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.
* Fixed the java assert issue with H5O cache corking calls.Dana Robinson2019-10-111-3/+4
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* Corrected missing parallel #ifdefs.Dana Robinson2019-10-111-0/+2
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* Converted H5O MD cache cork calls to use the VOL.Dana Robinson2019-10-116-57/+252
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* Marked up H5Fget/set_mpi_atomicity() to use the VOL.Dana Robinson2019-10-114-23/+105
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* Unify code between H5Lcopy and H5LmoveJordan Henderson2019-10-102-9/+14
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* Merge pull request #1990 in HDFFV/hdf5 from ~JSOUMAGNE/hdf5:references_1_12 ↵Larry Knox2019-10-0957-1985/+6295
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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.
| * Fix func enter macro in H5T_ref_reclaim()Jerome Soumagne2019-10-091-1/+1
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| * Make wrappers, tests and tools use H5Treclaim() instead of H5Dvlen_reclaim()Jerome Soumagne2019-10-081-2/+2
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| * Add new H5R API that abstracts object, region and attribute reference typesJerome Soumagne2019-10-0838-1357/+4694
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
| * Remove ability to loc by ref from H5VL layerJerome Soumagne2019-10-083-113/+2
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| * Add support for retrieving object name by tokenJerome Soumagne2019-10-081-0/+12
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| * Add H5VL_OBJECT_GET_TYPE to get object typeJerome Soumagne2019-10-083-1/+63
| | | | | | | | Add H5VL_OBJECT_LOOKUP to lookup objects
| * Add H5VL_MAX_TOKEN_SIZE and H5VL_token_tJerome Soumagne2019-10-081-0/+7
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| * Adapt Jerome's "file info" H5VL 'get' query to retrieve container token info.Quincey Koziol2019-10-088-81/+135
| | | | | | | | Remove "by address" location for VOL operations. (Switching to "by token")
| * Fix H5VL_blob_get to return size of blobJerome Soumagne2019-10-0813-104/+489
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Fix const in blob API Add H5HG_HEAP_ID_SIZE macro to return native blob size Add maximum size for blobs Fix blob API callbacks to pass VOL file object Add public wrappers for blob VOL API Implement passthrough blob callbacks Update H5Tvlen after callback changes Update trace information for H5VL blob routines Fix public header inclusion in native and passthru headers
| * Add 'blob' callbacks to VOL, along with a native implementation to store themQuincey Koziol2019-10-0821-468/+1032
| | | | | | | | | | | | | | in the global heap, and changed the VL datatype conversion code to use blobs. Move encode/decode of sequence lengths into VL datatype callbacks, from native VOL blob routines.
* | Merge pull request #1962 in HDFFV/hdf5 from ↵Vailin Choi2019-10-091-36/+168
|\ \ | |/ |/| | | | | | | | | | | ~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 #1934 in HDFFV/hdf5 from ↵Vailin Choi2019-09-301-36/+168
| | | | | | | | | | | | | | | | ~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.
* | Whitespace and macro semi-colonAllen Byrne2019-10-027-199/+197
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* | More whitespace synchingAllen Byrne2019-10-0213-1695/+1693
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* | Cleanup whitespace and comments compared to developAllen Byrne2019-10-021-4/+4
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* | fix for statement declare variableAllen Byrne2019-09-302-57/+59
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* Set versions in initial hdf5_1_12 revision.hdf5_1_12-initialLarry Knox2019-09-251-3/+3
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* Revert "Moved NDEBUG guards to H5EA_DEBUG in H5EA package."Dana Robinson2019-09-246-16/+36
| | | | This reverts commit 431123503d387bce30b1f6db7dc4ad3a33bc51bb.
* Revert "Fix for H5EA debug package when built in release mode."Dana Robinson2019-09-241-2/+0
| | | | This reverts commit 911b1ca67fdf7c2f3a32dd42c591e4e9b2fa1950.
* Fix for H5EA debug package when built in release mode.Dana Robinson2019-09-181-0/+2
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* Moved NDEBUG guards to H5EA_DEBUG in H5EA package.Dana Robinson2019-09-176-36/+16
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* Added MPICH_SKIP_MPICXX and OMPI_SKIP_CXX to H5public.h to avoid inadvertantDana Robinson2019-09-171-0/+3
| | | | linking to the deprecated MPI C++ wrappers. Fixes HDFFV-10893.
* Fix segfault after H5VL_loc_params_t fix mergeJordan Henderson2019-09-162-4/+4
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* Merge pull request #1922 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2019-09-162-7/+8
|\ | | | | | | | | * commit 'b477f9bcc7bb83d7c06e1d09f428030f51d71897': HDFFV-10901 add missing config options
| * HDFFV-10901 add missing config optionsAllen Byrne2019-09-132-7/+8
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* | Merge pull request #1887 in HDFFV/hdf5 from ~JHENDERSON/hdf5:develop to developJordan Henderson2019-09-163-6/+6
|\ \ | |/ |/| | | | | * commit '0de0965c61823186ac61c0d6876d4d77578e5bcc': Fix issue in H5Lcreate_hard and H5Olink where entire H5VL_loc_params_t structure was passed via varargs
| * Fix issue in H5Lcreate_hard and H5Olink where entire H5VL_loc_params_t ↵Jordan Henderson2019-08-213-6/+6
| | | | | | | | structure was passed via varargs
* | Fix get home dir for windowsAllen Byrne2019-09-121-23/+26
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* | revert windows changeAllen Byrne2019-09-061-4/+4
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* | Windows ssl headers are not in system loacationAllen Byrne2019-09-061-5/+5
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* | Add back missing java implementationAllen Byrne2019-09-051-10/+10
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* | Merge pull request #1908 in HDFFV/hdf5 from ~BMRIBLER/hdf5-bmr:develop to ↵Binh-Minh Ribler2019-09-039-64/+699
|\ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
| * | Fixed error code and error messagesBinh-Minh Ribler2019-09-031-1/+1
| | | | | | | | | | | | Tested on Jelly (very minor)
| * | Changed H5VL_NATIVE_DATASET_GET_CHUNK_INFO_BY_COOR toBinh-Minh Ribler2019-09-033-3/+3
| | | | | | | | | | | | H5VL_NATIVE_DATASET_GET_CHUNK_INFO_BY_COORD per a review comment.
| * | Updated based on reviews and refactored test codeBinh-Minh Ribler2019-09-013-10/+6
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| * | Code cleanup and refactorBinh-Minh Ribler2019-08-291-4/+0
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| * | Merge branch 'develop' of ↵Binh-Minh Ribler2019-08-289-337/+838
| |\ \ | | | | | | | | | | | | https://bitbucket.hdfgroup.org/scm/~bmribler/hdf5-bmr into develop
| * | | HDFFV-10677 and HDFFV-10661Binh-Minh Ribler2019-08-289-64/+707
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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)
* | | | Move ext_path field in H5F_t to H5F_shared_t.Vailin Choi2019-08-314-33/+12
| | | | | | | | | | | | | | | | Remove unused routine H5F_set_coll_md_read().
* | | | Move coll_md_read and coll_md_write fields in H5F_t to H5F_shared_t.Vailin Choi2019-08-315-14/+16
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* | | | Fix EXISTS test syntaxAllen Byrne2019-08-291-1/+1
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* | | Minor tweaks to new H5P MPI code based on code review feedback.Dana Robinson2019-08-272-23/+17
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* | | Merge branch 'develop_minor_pr' into H5Pset_fapl_mpiDana Robinson2019-08-271-1/+1
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