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* Add new H5R API that abstracts object, region and attribute reference typesJerome Soumagne2019-10-081-5/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
* Add 'blob' callbacks to VOL, along with a native implementation to store themQuincey Koziol2019-10-081-18/+18
| | | | | | | 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.
* Begin converting dataset code to use shared file pointer instead of top fileQuincey Koziol2019-08-201-0/+1
| | | | pointer.
* Add H5Sselect_shape_same and H5Sselect_intersect_block API routines, alongQuincey Koziol2019-07-301-2/+2
| | | | with tests and minor cleanups and refactorings.
* Fix issue with direct chunk write not updating the "last chunk" indexNeil Fortner2019-03-061-1/+3
| | | | | cache. Fix issues involving datasets being "no allocated" when they contain cached raw data.
* Updated H5Dio.c comment.Dana Robinson2019-02-011-5/+2
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* Fixed a bug revealed by the dtransform test. A datatype transformDana Robinson2019-01-311-1/+1
| | | | buffer needed to be calloc'd.
* Fix for parallel filters tests with new read-proc0-broadcast featureJordan Henderson2019-01-081-4/+8
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* HDFFV-10625 -- Implemented a process-0 read and then broadcast for ↵Quincey Koziol2019-01-071-14/+4
| | | | collective read of full (HS_ALL), contiguous, atomic datasets by all the processes in the file communicator.
* Moved private native VOL connector functions to H5VLnative_private.h.Dana Robinson2018-12-201-1/+2
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* Moved the optional enums to H5VLnative.h and converted to an intDana Robinson2018-12-181-0/+1
| | | | typedef and a set of #defines.
* Moved the native VOL connector's optional enums to theDana Robinson2018-12-151-2/+2
| | | | | public headers and renamed to include native/NATIVE in the name.
* Refactor and standarize file object callbacks, including some fixes on theQuincey Koziol2018-10-311-2/+2
| | | | dataset callbacks.
* Convert dataset callbacks to standard form, for wrapping object IDs, etc.Quincey Koziol2018-10-291-8/+4
| | | | Also, fix a few attribute issues that I missed.
* Squashed commit of private branch changes to support stackable VOL plugins.Quincey Koziol2018-10-251-4/+4
| | | | modified: test/dsets.c
* VOL FEATUREDana Robinson2018-10-101-55/+29
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* Remainder of vol_normalization changes (dataset, attribute, files, objects).Dana Robinson2018-09-241-30/+29
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* Removed 'VOL' versions of FUNC_ENTER macros as well as empty functionsDana Robinson2018-09-181-2/+2
| | | | orginally intended to support the full SWMR feature.
* Add configure check for MPI_Mprobe and MPI_Imrecv functionsJordan Henderson2018-07-261-1/+2
| | | | | | | | | | | | | | | Add line to libhdf5settings file for status of Parallel writes to filtered datasets status Surround Parallel Compression code in MPI_VERSION >= 3 checks Add disabled message for Parallel Compression built w/ MPI-2 Modify Parallel Compression tests to only run the parallel filtered read tests when parallel filtered writes are disabled Update big I/O code to handle being built with MPI-2 Add checks to CMakeLists.txt for MPI_Mprobe and MPI_Imrecv
* * Added H5DO compatibility functions.Dana Robinson2018-05-041-56/+51
| | | | | * Changed the offset copy to use an array on the stack. * Yanked some unused #defines.
* * Fixed the error testsDana Robinson2018-05-021-88/+83
| | | | * Moved common functionality into helper functions
* Merge branch 'develop' into h5do_direct_chunk_hl_to_srcDana Robinson2018-04-301-12/+12
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| * Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Quincey Koziol2018-04-291-340/+277
| |\ | | | | | | | | | merge_hyperslab_updates
| * | Checkpoint normalization against incoming hyperslab / selection / dataspaceQuincey Koziol2017-03-281-18/+18
| | | | | | | | | | | | improvements.
* | | Normalize with trunk prior to update mergeDana Robinson2018-04-301-16/+16
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* | | Fixed a warning.Dana Robinson2018-04-301-1/+1
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* | | Finished move of H5DOread/write_chunk calls to H5D.Dana Robinson2018-04-301-246/+142
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* | | First stage of moving H5DOread/write_chunk() to src/ and makingDana Robinson2018-04-301-5/+150
| |/ |/| | | | | | | | | | | | | | | | | them H5D calls. * Moved H5DOread/write_chunk() to H5Dio.c and renamed to H5D*. * Moved the hl/test/test_dset_opt test to test/ and renamed to direct_chunk. * Moved the hl/test/dectris_hl_perf test to tools/test/perform and renamed to direct_write_perf. * Updated autotools and CMake files.
* | Corrections for parallel I/O & tests.Quincey Koziol2018-03-211-5/+4
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* | Cleanup API context function usage.Quincey Koziol2018-03-191-20/+4
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* | Add API context interface and use it throughout the library.Quincey Koziol2018-03-151-313/+168
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* | Normalization with VOL integration branch.Dana Robinson2017-12-011-1/+1
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* | Normalization with VOL integration branch.Dana Robinson2017-11-301-11/+4
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* | Fixed misc Warnings flagged by VS2017.Dana Robinson2017-11-271-1/+3
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* | Add test file to build processJordan Henderson2017-08-031-1/+1
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* | Suggested changes from code reviewJordan Henderson2017-07-071-3/+57
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* | Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Jordan Henderson2017-07-051-55/+103
|\ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '6428a637752753cc8a9007c0c3c38b9ea9cc97fd': (165 commits) Skip HDFFV-10160 filenotclosed test for split/multi driver Temporary skip this test for split/multi driver. Further investigation to resolve the failure is needed. Please enter the commit message for your changes. Lines starting More minor whitespace cleanup Fixed a minor comment typo in H5R.c * Reverted removal of H5I_REFERENCE to avoid breaking binary compatibility. * Added a quick H5I_REFERENCE smoke check to test_misc19() in tmisc.c. Added missing free() call to test_misc19(). Purged the unused H5I_REFERENCE from the library. Added a test for VFD IDs to testhdf5. Revert "Partial removal of NDEBUG ifdefs from the library." Partial removal of NDEBUG ifdefs from the library. Removed compiler flag cleanup since Solaris chokes on it. Fix for HDFFV-10160 Modifications to fix the assertion/abort failure when the application does not close the file. Fixed a bug in autotools Fortran processing where a test for the presence of a C long double type always returned true. Updated the --enable-debug/production handling in configure.ac so that it more reliably indicates that the configure option can no longer be used. Previously, using --enable-debug="", etc. would not trigger an error (even though such usage is unlikely). Added awk processing to remove extraneous whitespace from H5_ flags in configure. Fixed a comment in configure.ac HDFFV-10219 another mode change HDFFV-10219 change subset to use BINARY mode for h5dump HDFFV-10219 default input binary to NATIVE Set default of var to NATIVE HDFFV-10219 - disable h5dump tests until h5import NATIVE is fixed ...
| * | Fixed many minor warnings.Dana Robinson2017-05-251-1/+0
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| * | Incorporate patch from GE Healthcare (HDFFV-9934)Vailin Choi2017-04-251-49/+100
| | | | | | | | | | | | | | | This is the same patch that had already been integrated to 1.8 branch (pull request #387). Tested on moohan, ostrich, platypus, emu, osx1010test, quail, kituo, mayll.
| * | Merge pull request #426 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10 to ↵Larry Knox2017-04-251-6/+4
| |/ | | | | | | | | | | | | | | | | | | hdf5_1_10 * commit '54957d37f5aa73912763dbb6e308555e863c43f4': Commit copyright header change for src/H5PLpkg.c which was added after running script to make changes. Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh. Merge pull request #407 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_1 to hdf5_1_10_1 Change copyright headers to replace url referring to file to be removed and replace it with new url for COPYING file.
* | Trigger error if library tries to break to independent I/O with filtersJordan Henderson2017-02-081-0/+7
| | | | | | in the pipeline
* | Switch working branch from master to developJordan Henderson2017-01-131-5/+0
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* [svn-r30189] Description:Quincey Koziol2016-07-181-12/+25
| | | | | | | | | Clean up more warnings: drop the warning count from ~1310 down to ~940, with only 31 types of warnings in 148 files (down from 38 types in 167 files). Tested on: MacOSX/64 10.11.5 (amazon) w/serial & parallel (h5committest forthcoming)
* [svn-r29776] Description:Quincey Koziol2016-04-241-0/+4
| | | | | | | | Bring "file pointer patching" code & test from revise_chunks to trunk. Tested on: MacOSX/64 10.11.4 (amazon) w/serial, parallel & production (h5committest forthcoming)
* [svn-r29548] Minor normalization w/ trunk in preparation for big merge.Dana Robinson2016-03-241-1/+1
| | | | | | Tested on: 64-bit Ubuntu 15.10 w/ gcc 5.2.1 autotools serial autotools parallel (MPICH 3.1.4)
* [svn-r29245] use HDONE_ERROR instead of HGOTO after done.Mohamad Chaarawi2016-03-011-2/+2
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* [svn-r29057] added dxpl type checking when debug mode is enabled ↵Mohamad Chaarawi2016-02-071-27/+99
| | | | | | (H5_DEBUG_BUILD) tested on bb-8 with Serial and Parallel, debug and production builds.
* [svn-r27835] Description:Quincey Koziol2015-09-211-1/+1
|\ | | | | | | | | | | | | | | Sync w/trunk. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel (h5committest not required on this branch)
| * [svn-r27768] Description:Quincey Koziol2015-09-141-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Complete revamp of package initialization/shutdown mechanism in the library. Each package now has a single init/term routine. This new way should avoid packages being re-initialized during library shutdown and is also be _much_ more proactive about giving feedback for resource leaks internal to the library. Introduces a new "module" header file for packages in the library (e.g src/H5Fmodule.h) which sets up some necessary package configuration macros for the FUNC_ENTER/LEAVE macros. (The VFL drivers have their own slightly modified version of this header, src/H5FDdrvr_module.h) Also cleaned up a bunch of resources leaks all across the library and tests, along with addressing many warnings, as I encountered them. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel Linux/64 3.10.x (kituo) w/serial & parallel Linux/64 2.6.x (ostrich) w/serial
* | [svn-r27103] Merge revisions 26780 through 27102 from trunk to vds branch.Neil Fortner2015-05-211-10/+5
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