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* Merge pull request #2037 in HDFFV/hdf5 from ~NFORTNE2/hdf5_naf:develop to ↵Neil Fortner2019-11-122-1/+10
|\ | | | | | | | | | | | | develop * commit 'e5fc4889fa4f412056a4672435c96c17a6d1a936': Fix issue where H5R__reopen_file did not make the file "post open" callback.
| * Fix issue where H5R__reopen_file did not make the file "post open"Neil Fortner2019-11-122-1/+10
|/ | | | callback.
* Merge pull request #2036 in HDFFV/hdf5 from ~DYOUNG/netbsd:develop to developDavid Young2019-11-126-5/+6
|\ | | | | | | | | * commit 'f1b39ad80e2fc0d0f4f6ecae2a9fb0ea436c34cc': Apparently, + has no special meaning, and neither does \+, in so-called "obsolete" / POSIX "basic" regular expressions. Also, not every version of `sed` out there supports the `-E` option. So delete the -E flag and use the regex `[^/][^/]*` instead of `[^/]+`.
| * Apparently, + has no special meaning, and neither does \+, in so-calledDavid Young2019-11-126-5/+6
|/ | | | | | | | "obsolete" / POSIX "basic" regular expressions. Also, not every version of `sed` out there supports the `-E` option. So delete the -E flag and use the regex `[^/][^/]*` instead of `[^/]+`. Add config/netbsd to the MANIFEST.
* 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 Young2019-11-0529-41/+275
|\ \ | |/ |/| | | | | | | | | | | | | | | | | | | | | | | * 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 `==`.
| * Make these scripts relocatable again: derive a relative path for theDavid Young2019-11-054-4/+97
| | | | | | | | | | | | | | 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 subdirectoryDavid Young2019-11-051-1/+1
| | | | | | | | c/.
| * Make this script relocatable again: derive a relative path for theDavid Young2019-11-051-2/+25
| | | | | | | | | | | | | | 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.David Young2019-10-0313-18/+40
| | | | | | | | | | | | | | | | | | 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. Place hdf5_examples/ under ${datarootdir} which on most systems will be ${prefix}/share/, anyway.
| * Follow longstanding execv convention for compatibility with NetBSD.David Young2019-10-031-1/+7
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| * Under the examples directories, always find the installed HDF5David Young2019-10-036-6/+6
| | | | | | | | | | | | | | | | | | | | 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. Examples on NetBSD are installed at ${prefix}/share/examples/hdf5/ instead of at ${prefix}/share/hdf5_examples/, by convention. It may be the same on other BSDs, I'm not sure.
| * Make the HDF5 configure script grok NetBSD.David Young2019-10-032-0/+59
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| * For portability, insulate the HDF5 library from some system macros.David Young2019-10-031-1/+18
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| * Not every system has perl installed in /usr/bin/, so change the shebangDavid Young2019-10-0312-12/+26
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | (#!) line to `/usr/bin/env perl` to locate perl on the PATH. Everything after the first pathname in the shebang line is treated as a single argument to the command interpreter (/usr/bin/env "perl -w"), and there is not ordinarily any such program as "perl -w". So if the old shebang line used an option such as `-w`, add a `use warnings;` statement to the script---note that the semantics change slightly. `bin/destdep` uses a trick to pass `-p` to `/usr/bin/env perl`. It couldn't hurt to use the same trick to pass `-w`. With these changes, `sh autogen.sh` runs on NetBSD. It ought to still work on every other system HDF5 supports, too.
| * For portability, use the POSIX sh(1) string-comparison operator `=`David Young2019-10-031-2/+2
| | | | | | | | instead of `==`.
* | Merge pull request #2015 in HDFFV/hdf5 from HDFFV-10943 to developRichard Warren2019-10-254-14/+13
|\ \ | | | | | | | | | | | | | | | * commit '299c9ed5fe19edac37cab27bc04d587fa67568c2': Removed set_bigio_count prototype since it has been added to H5private.h Change API names for get/set bitio_count. Also added H5_mpi_set_bigio_count to H5private.h.
| * | Removed set_bigio_count prototype since it has been added to H5private.hRichard Warren2019-10-251-2/+0
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| * | Change API names for get/set bitio_count. Also added H5_mpi_set_bigio_count ↵Richard Warren2019-10-234-13/+14
| | | | | | | | | | | | to H5private.h.
* | | Merge pull request #2016 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2019-10-234-8/+15
|\ \ \ | |/ / |/| | | | | | | | * commit '9affb7f12ec6084ccaadec9fcdc8d94bccf4dd4f': Fix MPI test depends
| * | Fix MPI test dependsAllen Byrne2019-10-234-8/+15
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* | Merge pull request #2008 in HDFFV/hdf5 from ~BYRN/hdf5_merge_adb:develop to ↵Allen Byrne2019-10-231-185/+112
|\ \ | | | | | | | | | | | | | | | | | | develop * commit '685956cd4c088d38862b36b8138e643b114b2929': Update format and fix missing prefix
| * | Update format and fix missing prefixAllen Byrne2019-10-211-185/+112
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* | 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
* | | Merge pull request #1998 in HDFFV/hdf5 from ↵Jordan Henderson2019-10-1011-27/+131
|\ \ \ | | | | | | | | | | | | | | | | | | | | | | | | ~JHENDERSON/hdf5:bugfix/H5Dvlen_reclaim_ref_fix to develop * commit '93f509a2f2d5143450a0e6753325557b2bb8b707': Fix various Java issues when deprecated symbols are disabled
| * | | Fix various Java issues when deprecated symbols are disabledJordan Henderson2019-10-1011-27/+131
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* | | | Merge pull request #1996 in HDFFV/hdf5 from ↵Jordan Henderson2019-10-102-9/+14
|\ \ \ \ | |/ / / |/| | | | | | | | | | | | | | | | | | | ~JHENDERSON/hdf5:feature/unify_H5Lcopy_H5Lmove to develop * commit '54d149061f36eaadf5308839a3627f9158d24458': Unify code between H5Lcopy and H5Lmove
| * | | Unify code between H5Lcopy and H5LmoveJordan Henderson2019-10-102-9/+14
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* | | Merge pull request #1993 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2019-10-091-9/+15
|\ \ \ | | | | | | | | | | | | | | | | | | | | | | | | * commit '78268762bcf9cb949f711fa0e5290f96957cb60a': Improvements in response to Allen's suggestions. Corrections and improvements to testh5dump.sh.in changes. Fix errors in testh5dump.sh tests that grep for reference error messages.
| * | | Improvements in response to Allen's suggestions.Larry Knox2019-10-091-12/+12
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| * | | Corrections and improvements to testh5dump.sh.in changes.Larry Knox2019-10-091-34/+10
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| * | | Fix errors in testh5dump.sh tests that grep for reference error messages.Larry Knox2019-10-091-3/+33
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* | | Merge pull request #1994 in HDFFV/hdf5 from ~JSOUMAGNE/hdf5:ref_fix to developJerome Soumagne2019-10-091-1/+1
|\ \ \ | |/ / |/| | | | | | | | * commit 'cc1546ea92304e3b8d24ad32aa7252af367d5762': Fix func enter macro in H5T_ref_reclaim()
| * | Fix func enter macro in H5T_ref_reclaim()Jerome Soumagne2019-10-091-1/+1
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* | Merge pull request #1991 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developLarry Knox2019-10-081-3/+3
|\ \ | | | | | | | | | | | | * commit 'd42203b1d44686a0e5309f061c996b959023ce57': Change reference test to grep for specific error
| * \ Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2019-10-08111-3048/+12295
| |\ \ | |/ / |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '4c558700ab33934e7358483c5d20fea4823baf9e': 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. Remove debugging logic from the new t_bigio test Expanded t_bigio.c to include Jordan's test from HDFFV-10539 Another cleanup pass as suggested by the reviewers. Fix some typos and remove an unused prototype from H5Sprivate.h At the suggestion of the PR reviewers, moved the mpio_create_large_type to 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 files that I touched to eliminate compile warnings (on my Linux box). No functional changes, just removed some tab characters Make the initial bug fixes to allow >2GB writes with Independent IO
* | | Merge pull request #1931 in HDFFV/hdf5 from feature/references to developJerome Soumagne2019-10-08104-2854/+11989
|\ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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.
| * | | Update RELEASE.txt for reference changesJerome Soumagne2019-10-081-0/+10
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| * | | Fix reference type comparison in h5dumpJerome Soumagne2019-10-081-1/+5
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| * | | Make wrappers, tests and tools use H5Treclaim() instead of H5Dvlen_reclaim()Jerome Soumagne2019-10-0831-274/+276
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| * | | Add new H5R API that abstracts object, region and attribute reference typesJerome Soumagne2019-10-0854-1953/+10097
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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 Soumagne2019-10-0814-104/+490
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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 Koziol2019-10-0822-468/+1033
| | | | | | | | | | | | | | | | | | | | | | | | | | | | 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.
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