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* Fix include to correct memory calls - big-endian issue.Allen Byrne2019-12-182-1/+1
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* Merge pull request #2086 in HDFFV/hdf5 from ↵Vailin Choi2019-12-161-1/+1
|\ | | | | | | | | | | | | ~VCHOI/my_third_fork:bugfix/reference_ver_hyperslab_ver to develop * commit 'b42325e8f5ff3b6bfa2ce446af5b6dc5cbbff666': More fixes for previous committed PR #2079 dated Dec 5 2019. (1) H5O_dtype_ver_bounds[] for V112 should be H5O_DTYPE_VRESION_4 (2) The tests for the new reference types should work for V112 and beyond
| * More fixes for previous committed PR #2079 dated Dec 5 2019.Vailin Choi2019-12-061-1/+1
| | | | | | | | | | (1) H5O_dtype_ver_bounds[] for V112 should be H5O_DTYPE_VRESION_4 (2) The tests for the new reference types should work for V112 and beyond
* | HDFFV-10979 cleanup globalsAllen Byrne2019-12-122-7/+5
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* | HDFFV-10979 fix global name clashAllen Byrne2019-12-114-718/+727
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* Merge pull request #2076 in HDFFV/hdf5 from ~JSOUMAGNE/hdf5:type_fixes to ↵Jerome Soumagne2019-12-053-142/+139
|\ | | | | | | | | | | | | | | develop * commit '7b03a1c03633d695b487642e54f897c715f8622e': Fix H5VL_token_t type and fix H5VL_loc_by_token to use H5VL_token_t * Change hdset_reg_ref_t and H5R_ref_t from arrays of unsigned char to 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.
| * Change hdset_reg_ref_t and H5R_ref_t from arrays of unsigned char toDavid Young2019-12-053-142/+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.
* | Two fixes:Vailin Choi2019-12-051-1/+1
|/ | | | | (1) Set the version for reference datatype messge to H5O_DTYPE_VERSION_4. (2) Verify the decoded version for hyperslab selection.
* Yanked -Wc++-compat from the flags used to build the C library in bothDana Robinson2019-12-0424-112/+112
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* Fixed missing blob callbacks in test VOL connectors.Dana Robinson2019-12-032-0/+12
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* Add OAPL parameter to H5Rcreate_ APIsJordan Henderson2019-12-022-42/+42
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* H5R: fix H5Tconv to check for null referencesJerome Soumagne2019-11-261-4/+4
| | | | | | Valid for both deprecated and non-deprecated references Update test
* Merge pull request #2027 in HDFFV/hdf5 from ~DYOUNG/hdf5:dsets-randomness to ↵David Young2019-11-121-32/+121
|\ | | | | | | | | | | | | | | develop * commit '4d834adba4aeb1a0174bddb83212b7073b64e269': Use HD prefix. Fix HDFFV-10937: use a more reliable (and probably faster) scheme for visiting all elements of a matrix in an arbitrary order.
| * Use HD prefix.David Young2019-11-121-8/+8
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| * Fix HDFFV-10937: use a more reliable (and probably faster) scheme forDavid Young2019-10-281-32/+121
| | | | | | | | visiting all elements of a matrix in an arbitrary order.
* | Merge pull request #1984 in HDFFV/hdf5 from ~DYOUNG/netbsd:develop to developDavid Young2019-11-051-1/+7
|\ \ | |/ |/| | | | | | | | | | | | | | | | | | | | | | | * commit '0b721858e46a317c370a24115032d5be41688f67': Make these scripts relocatable again: derive a relative path for the original installation prefix from the examples prefix. Use that relative path to locate the current installation prefix, always. Fall back to an absolute installation prefix if the relative path cannot be derived. Get the path to prefix right: needs a ../ to back out of subdirectory c/. Make this script relocatable again: derive a relative path for the original installation prefix from the examples prefix. Use that relative path to locate the current installation prefix, always. Fall back to an absolute installation prefix if the relative path cannot be derived. Let us override the examples directory using --with-examplesdir=DIR. This is handy for NetBSD where HDF5 examples are installed by convention in $prefix/share/examples/hdf5/ rather than in ${prefix}/share/hdf5_examples/, which is the HDF5 default. Follow longstanding execv convention for compatibility with NetBSD. Under the examples directories, always find the installed HDF5 executables and scripts using @prefix@ instead of a relative path, because the number of ../ in the relative path will be different on NetBSD than on other systems. Make the HDF5 configure script grok NetBSD. For portability, insulate the HDF5 library from some system macros. Not every system has perl installed in /usr/bin/, so change the shebang (#!) line to `/usr/bin/env perl` to locate perl on the PATH. For portability, use the POSIX sh(1) string-comparison operator `=` instead of `==`.
| * Follow longstanding execv convention for compatibility with NetBSD.David Young2019-10-031-1/+7
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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)
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