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* Remove mismerged codeQuincey Koziol2020-01-071-4/+0
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* Cherry pick of 0225e6d5969Quincey Koziol2020-01-0414-357/+478
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* Refactor H5Dvlen_get_buf_size to use optional dataset operation, with ↵Quincey Koziol2020-01-041-3/+3
| | | | generic fallback for VOL connectors that don't implement operation
* Refactor all the 'H5VL_*_optional' callbacks to move the type of operation outQuincey Koziol2020-01-043-12/+32
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | of the va_list, so it's at least possible for another connector to know what the operation is and decide whether to implement it or not. Added a new VOL sub-class called "introspect" where callbacks that report information about the connector or container can be placed. Added an 'opt_query' callback to this sub-class, for a connector to report back to the library whether a particular optional callback operation is supported. Also added a 'get_conn_cls' introspection callback, to retrieve the H5VL_class_t of a connector (either the "current" connector, H5VL_GET_CONN_LVL_CURR, or the terminal connector, H5VL_GET_CONN_LVL_TERM). Moved the "post open" operation from a file 'specific' operation to a file 'optional' operation, now that it's possible to detect (with the 'opt_query' introspection callback) whether a VOL connector implements an optional operation, without just returning an error. Added new internal VOL helper routines: H5VL_object_is_native, to determine if an object is in (or is a) native file, and H5VL_file_is_same, to determine if two objects are in (or are) the same terminal VOL connector's container. (And moved the special handling for FILE_IS_EQUAL operation out of internal VOL callback routine into H5VL_file_is_same) Made new dataset 'get' operation for H5Dvlen_get_buf_size, aligning it better with other 'get' operations in API. Fixed several issues with pass-through connectors, which are now passing the 'make check-passthrough-vol' tests again. A bunch of warning and style cleanups as well.
* Use HD prefix.David Young2019-12-191-8/+8
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* Fix HDFFV-10937: use a more reliable (and probably faster) scheme forDavid Young2019-12-191-32/+121
| | | | visiting all elements of a matrix in an arbitrary order.
* Follow longstanding execv convention for compatibility with NetBSD.David Young2019-12-191-1/+7
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* Adjust cache.c only variables.Allen Byrne2019-12-184-30/+27
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* Fix include to correct memory calls - big-endian issue.Allen Byrne2019-12-182-1/+1
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* Yanked -Wc++-compat from the flags used to build the C library in bothDana Robinson2019-12-1624-112/+112
| | | | the Autotools and CMake.
* Fixed missing blob callbacks in test VOL connectors.Dana Robinson2019-12-162-0/+12
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* HDFFV-10979 cleanup global namesAllen Byrne2019-12-122-7/+5
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* HDFFV-10979 Merge global name fix from developAllen Byrne2019-12-114-718/+727
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* Change hdset_reg_ref_t and H5R_ref_t from arrays of unsigned char toDavid Young2019-12-093-142/+139
| | | | | | | | | | | | | | | | | | | structs containing those arrays. Encapsulating the arrays in this way makes it easier to write and think about pointers to these types, casts to/from these types, etc. An interesting side-effect that we probably should *not* rely on is that the struct-encapsulation changes the alignment so that some GCC warnings about casts that increase the alignment requirement of the operand go away. Warnings like that have to be taken seriously: I will add -Werror=cast-align to the default compiler flags so that they stop the build quickly. GCC warnings led me to some surprising casts in test/trefer.c. I found that it was possible to make many simplifications after introducing the struct-encapsulation that I described, above. In test objcopy_ref `same_file` is assigned but never used. Delete it.
* H5R: fix H5Tconv to check for null referencesJerome Soumagne2019-12-091-4/+4
| | | | | | Valid for both deprecated and non-deprecated references Update test
* Revert "Merge branch 'hdf5_1_12' of ↵Jerome Soumagne2019-12-0923-310/+133
| | | | | | | https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into hdf5_1_12" This reverts commit 9f9336a5bd541752f472bab4c93da8de89f862cd, reversing changes made to 437a1919e7ba60fe75a33a466d264183a0255319.
* Merge branch 'hdf5_1_12' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 ↵Richard Warren2019-12-062-43/+43
|\ | | | | | | into hdf5_1_12
| * Merge pull request #2080 in HDFFV/hdf5 from ↵Vailin Choi2019-12-061-1/+1
| |\ | | | | | | | | | | | | | | | | | | | | | ~VCHOI/my_third_fork:bugfix/112_hyper_ver to hdf5_1_12 * commit '0f1be317c37ca04db263680e6f1fe4d97b937b39': More fixes for the PR: (1) Set the version for reference datatype message to H5O_DTYPE_VERSION_4. (2) The tests for the new reference types should work for V112 and beyond. Verify the decoded version for hyperslab selection.
| | * More fixes for the PR:Vailin Choi2019-12-061-1/+1
| | | | | | | | | | | | | | | (1) Set the version for reference datatype message to H5O_DTYPE_VERSION_4. (2) The tests for the new reference types should work for V112 and beyond.
| * | Add OAPL parameter to H5Rcreate_ APIsJordan Henderson2019-12-062-42/+42
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* | Merged HDFFV-10929_2GB_testing to hdf5_1_12Richard Warren2019-12-0623-133/+310
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* Merge pull request #2001 in HDFFV/hdf5 from ↵Dana Robinson2019-10-111-2/+7
|\ | | | | | | | | | | | | | | | | | | | | ~DEROBINS/hdf5_der:1_12_alpha_merges to hdf5_1_12 * commit '75f2ed6167b094431fce2b4b700b3cf9da564c51': Fixed a bug (HDFFV-10899) where the behavior of the deprecated 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. Corrected missing parallel #ifdefs. Converted H5O MD cache cork calls to use the VOL. Marked up H5Fget/set_mpi_atomicity() to use the VOL.
| * Fixed a bug (HDFFV-10899) where the behavior of the deprecatedDana Robinson2019-10-111-2/+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 from develop to 1.12.Vailin Choi2019-10-111-6/+5
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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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