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* For portability, insulate the HDF5 library from some system macros.David Young2019-10-031-1/+18
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* Fixed the java assert issue with H5O cache corking calls.Dana Robinson2019-10-031-3/+4
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* fix for statement declare of typeAllen Byrne2019-09-302-57/+59
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* Corrected missing parallel #ifdefs.Dana Robinson2019-09-271-0/+2
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* Merge pull request #1934 in HDFFV/hdf5 from ↵Vailin Choi2019-09-271-36/+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.
| * (1) Address the feedback from the PR reviewVailin Choi2019-09-261-4/+3
| | | | | | | | (2) Add release notes
| * Merge pull request #21 in ~VCHOI/my_third_fork from develop to ↵Vailin Choi2019-09-2620-1716/+1750
| |\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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 Choi2019-09-191-36/+169
| | | | | | | | | | | | | | | | | | | | | 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 Robinson2019-09-276-57/+252
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* | | Marked up H5Fget/set_mpi_atomicity() to use the VOL.Dana Robinson2019-09-274-29/+109
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* | Fix the errors when updating the versions in the new 1.13 develop branch.Vailin Choi2019-09-262-2/+2
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* | add missing version to listAllen Byrne2019-09-261-1/+1
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* | Update N_FSINFO_VERSION_BOUNDS to H5F_LIBVER_NBOUND.Larry Knox2019-09-251-1/+1
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* | Update versioning to next major versionAllen Byrne2019-09-2513-1694/+1710
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* | Update develop branch version to 1.13.0 after creation of hdf5_1_12Larry 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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| * | | Fixed a bug where we incorrectly pass a lock struct to fcntlDana Robinson2019-08-271-1/+1
| |/ / | | | | | | | | | for file locking instead of a pointer.
* | | Merge branch 'develop' into H5Pset_fapl_mpiDana Robinson2019-08-276-6/+10
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| * | Merge pull request #1897 in HDFFV/hdf5 from ~KOZIOL/hdf5:refactor_file to ↵Quincey Koziol2019-08-265-5/+9
| |\ \ | | | | | | | | | | | | | | | | | | | | | | | | develop * commit '3090ac81506094ee510ae89c31749b5c1632aa34': Add a 'closing' flag on the shared file struct, and switch several of the "internal" data structures to use it.
| | * | Add a 'closing' flag on the shared file struct, and switch several of theQuincey Koziol2019-08-265-5/+9
| | | | | | | | | | | | | | | | "internal" data structures to use it.
| * | | Fixed the assertion failure for HDFFV-10873.Vailin Choi2019-08-231-1/+1
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* | | Added H5Pset/get_mpi_params calls and unified them with the MPI-I/ODana Robinson2019-08-268-336/+843
|/ / | | | | | | VFD info in H5FDmpio.c.
* | Fix major error codesQuincey Koziol2019-08-221-4/+4
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* | Switch shared file struct name from 'H5F_file_t' to 'H5F_shared_t', to matchQuincey Koziol2019-08-2220-111/+111
| | | | | | | | naming convention for shared structs in rest of library data structures.
* | Merge branch 'develop' into shared_file_ptrQuincey Koziol2019-08-215-517/+65
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