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* Merge pull request #2033 in HDFFV/hdf5 from ~NFORTNE2/hdf5_naf:public_spi to ↵Neil Fortner2019-11-137-122/+308
|\ | | | | | | | | | | | | develop * commit 'db6eab893e5f027f0b535316e0e7a9abe9ff8619': Implement public H5Sselect_project_intersection(). Updated internal algorithm to (optionally) avoid sharing selection data structures. Tested internal code (including with valgrind) by setting VDS code to avoid sharing selection, has since been changed to share selection for performance, so this code is not yet tested in regression tests. API has not been tested.
| * Implement public H5Sselect_project_intersection(). Updated internalNeil Fortner2019-11-137-122/+308
| | | | | | | | | | | | | | | | algorithm to (optionally) avoid sharing selection data structures. Tested internal code (including with valgrind) by setting VDS code to avoid sharing selection, has since been changed to share selection for performance, so this code is not yet tested in regression tests. API has not been tested.
* | Fix issue where H5R__reopen_file did not make the file "post open"Neil Fortner2019-11-122-1/+10
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* Merge pull request #2032 in HDFFV/hdf5 from ↵Neil Fortner2019-11-0834-289/+656
|\ | | | | | | | | | | | | ~NFORTNE2/hdf5_naf:vlget_file_type to develop * commit '1dbec40d465072540f8507c524ae7b909a6b1cf0': Implement H5VLget_file_type() to return a copy of a datatype with the location set to be in a file. Only meant to be used by VOL connectors. Implement H5VLpeek_connector_id() to support connectors querying their own IDs. Fix app_ref with connector IDs in a couple places (external VOLs registered as default through ENV should be visible to the application). Modify vlen and reference interfaces to work with arbitrary VOL connectors. Implement file "post open" specific callback, to enable connectors to update their file structs after a wrap context has been set.
| * Implement H5VLget_file_type() to return a copy of a datatype with theNeil Fortner2019-11-0834-289/+656
| | | | | | | | | | | | | | | | | | | | | | location set to be in a file. Only meant to be used by VOL connectors. Implement H5VLpeek_connector_id() to support connectors querying their own IDs. Fix app_ref with connector IDs in a couple places (external VOLs registered as default through ENV should be visible to the application). Modify vlen and reference interfaces to work with arbitrary VOL connectors. Implement file "post open" specific callback, to enable connectors to update their file structs after a wrap context has been set.
* | Merge pull request #1984 in HDFFV/hdf5 from ~DYOUNG/netbsd:develop to developDavid Young2019-11-051-1/+18
|\ \ | |/ |/| | | | | | | | | | | | | | | | | | | | | | | * 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 `==`.
| * For portability, insulate the HDF5 library from some system macros.David Young2019-10-031-1/+18
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* | Change API names for get/set bitio_count. Also added H5_mpi_set_bigio_count ↵Richard Warren2019-10-233-11/+12
| | | | | | | | to H5private.h.
* | Merge pull request #2000 in HDFFV/hdf5 from ↵Jerome Soumagne2019-10-118-158/+226
|\ \ | | | | | | | | | | | | | | | | | | ~JSOUMAGNE/hdf5:fix_endian_develop to develop * commit '294e4faab724c26985867fe8ede684967da8a698': Fix encode and decode of tokens in H5VLnative
| * | Fix encode and decode of tokens in H5VLnativeJerome Soumagne2019-10-118-158/+226
| | | | | | | | | | | | | | | | | | | | | | | | Fix encode and decode of deprecated object reference addresses Make H5Rdeprec.c use tokens instead of haddr_t Fix H5Oopen_by_addr() to serialize addr to token
* | | Unify code between H5Lcopy and H5LmoveJordan Henderson2019-10-102-9/+14
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* | | Fix func enter macro in H5T_ref_reclaim()Jerome Soumagne2019-10-091-1/+1
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* | Merge pull request #1931 in HDFFV/hdf5 from feature/references to developJerome Soumagne2019-10-0857-1985/+6295
|\ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '9ed9762889fcd05dc230d6652b92fddc5ec880a4': 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 Soumagne2019-10-081-2/+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.
* | | Another cleanup pass as suggested by the reviewers.Richard Warren2019-10-073-8/+5
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* | | Fix some typos and remove an unused prototype from H5Sprivate.hRichard Warren2019-10-072-2/+1
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* | | At the suggestion of the PR reviewers, moved the mpio_create_large_type to ↵Richard Warren2019-10-075-159/+197
| | | | | | | | | | | | H5mpi.c and renamed the function appropriately. Also moved some support functions to set and get the vvalue where we transistion to using derived datatypes.
* | | Made code review edit suggested by Jerome, plus various code updates to ↵Richard Warren2019-10-071-4/+4
| | | | | | | | | | | | files that I touched to eliminate compile warnings (on my Linux box).
* | | Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Richard Warren2019-10-071-78/+81
|\ \ \ | |/ / | | | | | | HDFFV-10539-2GB-Write-Independent
| * | Fixed a bug (HDFFV-10899) where the behavior of the deprecatedDana Robinson2019-10-041-78/+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.
* | No functional changes, just removed some tab charactersRichard Warren2019-10-051-4/+4
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* | Make the initial bug fixes to allow >2GB writes with Independent IORichard Warren2019-10-053-24/+46
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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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