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* 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.
* Bring SWMR support in to the main development branch. (Finally!) More testsQuincey Koziol2016-12-021-1/+1
| | | | and the tool and API wrappers will be coming in over the weekend.
* Tentative fix for valgrind issues related to EoC.Dana Robinson2016-11-261-2/+2
| | | | | | | | | Adds /*out*/ parameters to H5O_close() and H5F_try_close() so that H5D/G_close() will know when H5O_close() has triggered a file close and thus the file struct is not reliable. Also removes the H5F_CLOSING() macro and related which were formerly used to check if the file was closing.
* [svn-r30075] Description:Quincey Koziol2016-06-141-0/+220
| | | | | | | | | | Bring object/dataset/group/named datatype features from revise_chunks branch to trunk. Also CMake support for h5format_convert and a bunch of misc. cleanups. Tested on: MacOSX/64 10.11.5 (amazon) w/serial, parallel & production (h5committest forthcoming)
* [svn-r29057] added dxpl type checking when debug mode is enabled ↵Mohamad Chaarawi2016-02-071-7/+8
| | | | | | (H5_DEBUG_BUILD) tested on bb-8 with Serial and Parallel, debug and production builds.
* [svn-r28797] Description:Quincey Koziol2016-01-051-5/+5
| | | | | | | | Clean up another round of memory allocation mis-matches. Tested on: Linux/32 2.6.x (jam) w/serial MacOSX/64 10.11.2 (amazon) w/serial & parallel
* [svn-r28606] Description:Quincey Koziol2015-12-131-4/+5
| | | | | | | | | | Revisions to normalize revise chunks vs. trunk, plus push dataset metadata changes into the cache immediately (instead of holding them within the dataset data structures). Tested on: MacOSX/64 10.11.2 (amazon) w/serial & parallel (h5committest not required on this branch)
* [svn-r28533] Fix loops in H5Dvirtual.c to only loop over used entries in VDS ↵Neil Fortner2015-12-071-3/+3
| | | | | | | | mapping list, instead of all allocated entries. Tested: ummon (too minor for full h5committest)
* [svn-r28452] Description:Quincey Koziol2015-11-231-1/+1
| | | | | | | | Normalization changes against revise_chunks branch. Tested on: MacOSX/64 10.11.1 (amazon) w/serial & parallel (h5committest forthcoming)
* [svn-r28311] Description:Quincey Koziol2015-11-091-0/+1
| | | | | | | | Add missing callback to virtual layout "class" structure. Tested on: MacOSX/64 10.11.1 (amazon) w/serial & parallel (Too minor to require h5committest)
* [svn-r27957] Description:Quincey Koziol2015-10-051-23/+12
| | | | | | | | Minor whitespace cleanups. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel (h5committest not required on this branch)
* [svn-r27944] Description:Quincey Koziol2015-10-041-6/+12
| | | | | | | | Avoid duplicating source FAPL & DAPL if they are already available. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel (h5committest not required on this branch)
* [svn-r27835] Description:Quincey Koziol2015-09-211-4/+6
| | | | | | | | Sync w/trunk. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel (h5committest not required on this branch)
* [svn-r27646] Add version number to VDS global heap object encoding.Neil Fortner2015-09-011-1/+1
| | | | | | | | | Fix handling of layout version number. Other minor fixes/cleanup. NOTE: This commit changes the file format for VDS, all files must be re-generated. Tested: ummon
* [svn-r27538] Add tests to cover remaining code coverage assertions in src ↵Neil Fortner2015-08-201-7/+2
| | | | | | | | directory except for those in H5Doh.c and H5Shyper.c. Tested: ummon
* [svn-r27528] Modify printf implementation to not open source datasets that ↵Neil Fortner2015-08-191-4/+12
| | | | | | | | were previously opened when calculating the VDS extent, instead assuming they still exist. Tested: ummon
* [svn-r27527] Add tests to hit code coverage assertions in H5Olayout.c.Neil Fortner2015-08-191-8/+10
| | | | | | Fix issue in VDS delete routine. Tested: ummon
* [svn-r27520] Add new test for all 3 selection types in the same VDS.Neil Fortner2015-08-181-7/+2
| | | | | | Minor cleanup in the tests. Tested: ummon
* [svn-r27506] H5Dset_extent no longer holds all printf source datasets open.Neil Fortner2015-08-141-4/+9
| | | | | | Other items identified during reviews. Tested: ummon
* [svn-r27505] Add support for H5Dset_extent for VDS.Neil Fortner2015-08-141-48/+151
| | | | | | | Add tests for this. Other bug fixes/cleanup Tested: Kubuntu 64 (home computer)
* [svn-r27504] Change comments/code around to reflect decision to have virtual ↵Neil Fortner2015-08-131-2/+6
| | | | | | | | datasets always return TRUE when their is_alloc function is called. Tested: ummon
* [svn-r27501] Add mapping validity checking to VDS open.Neil Fortner2015-08-121-0/+138
| | | | | | Other minor fixes/cleanup. Tested: ummon
* [svn-r27498] Add support for I/O after reopening a VDS with unlimited and/or ↵Neil Fortner2015-08-121-73/+296
| | | | | | | | | | printf mappings without calling H5Dget_space first. Add tests for this. Other minor fixes/cleanup. Tested: ummon
* [svn-r27481] Add support for offset selections passed to H5Pset_virtual.Neil Fortner2015-08-071-2/+14
| | | | | | Add test for this. Tested: ummon
* [svn-r27479] Add checking for invalid inputs to H5Dset_virtual: point ↵Neil Fortner2015-08-071-15/+29
| | | | | | | | | | | | | selections, incorrect numbers of elements selected, incorrect "slice" through limited dimensions, incorrect number of printf substitutions. Patch source selection space extent with bounds of selection if extent is unknown before returning via H5Pget_virtual_srcspace. Write updated VDS dataspace to file when it changes due to unlimited selections. Other minor fixes/cleanup. Tested: ummon
* [svn-r27450] Add descriptions for all non-public functions.Neil Fortner2015-07-311-2/+19
| | | | | | | Other comments. Add some input checking. Tested: ummon
* [svn-r27424] Implement support for h5debug for VDS.Neil Fortner2015-07-221-7/+7
| | | | | | | | | | Implement support for H5Pencode/decode with VDS properties. Testing for H5Pencode/decode with VDS. Relax assertion check for number of elements written to buffer as we do not check for overlaps in mappings. Other minor fixes/cleanup. Tested: ummon
* [svn-r27323] Implement support for H5Dflush for VDS.Neil Fortner2015-07-021-40/+88
| | | | | | | | | | Implement support for H5Ocopy on VDS. Testing for H5Ocopy on VDS. Fix check-vfd failure. Other minor fixes/cleanup. Note there is a preexisting failure in h5repack testing. Tested: ummon
* [svn-r27284] Modify VDS implementation to always use FAPL and DAPL from VDS ↵Neil Fortner2015-06-251-51/+108
| | | | | | | | | | | | file and dataset to open source files and datasets, instead of using the default property lists. Modify VDS to reject attempts at parallel I/O, fix parallel compile error. Modify VDS to not write fill value to memory buffer if the fill value is undefined. Other minor fixes/cleanup. Tested: ummon
* [svn-r27246] Remove "clipped" status from unlimited selections, decoupling ↵Neil Fortner2015-06-181-27/+5
| | | | | | | | | | | them from the extent. Improve algorithm for calculation of VDS extent by removing the need for a temporary copy of a dataspace. Other minor fixes/cleanup. Tested: ummon
* [svn-r27224] Fix bug that prevented reading from datasets with unlimited ↵Neil Fortner2015-06-171-31/+41
| | | | | | | | | | mappings with missing source datasets. Decided not to attempt to open the source dataset in this case, as doing so could create issues related to the sizing of the VDS. Users should call H5Dget_space to open these datasets. No regression test yet. Tested: ummon
* [svn-r27215] Fix issue where % characters could not be used in non-printf ↵Neil Fortner2015-06-161-28/+90
| | | | | | | | mappings. Other minor fixes/cleanup. Tested: ummon
* [svn-r27197] Improve performance of "printf" VDS with selections in the file ↵Neil Fortner2015-06-121-9/+49
| | | | | | | | | | space - the library no longer iterates over all source datasets in the printf mapping, it now only looks at the ones that could be involved in I/O (the ones whose bounds overlap with the selection in the unlimited dimension). Tested: ummon
* [svn-r27192] Improve support for printf selections (support partial blocks withNeil Fortner2015-06-121-236/+328
| | | | | | | | | | H5_VDS_FIRST_MISSING) Add test for this Rework VDS code to not depend on unlimited selections having a "clipped" state in preparation for removing the clipped state from unlimited selections. Other bug fixes/cleanup Tested: Kubuntu 64 (home computer)
* [svn-r27191] Merged r26781 to r27185 from trunkDana Robinson2015-06-111-9/+12
| | | | | Tested on: 64-bit Ubuntu Linux VM w/ gcc 4.8.2 (C++ and Fortran 2003 also tested)
* [svn-r27153] Implement fill value support for VDS.Neil Fortner2015-06-051-131/+356
| | | | | | | | | Add testing for this. Fix bug in printf string parsing. Add test for this. Other minor fixes/cleanup. Tested: ummon
* [svn-r27145] Add some testing for printf-style source dataset name resolution.Neil Fortner2015-06-031-128/+173
| | | | | | | Various bug fixes, including a temporary fix for printf with FIRST_MISSING view. Other cleanup. Tested: ummon
* [svn-r27104] Add support for printf-style source dataset name resolution.Neil Fortner2015-05-221-323/+1025
| | | | | | | | Passes use case test, no regression tests yet. Add functions H5Pset/get_virtual_printf_gap (not tested yet). Other minor fixes/cleanup. Tested: ummon
* [svn-r27053] Add more tests for unlimited selections.Neil Fortner2015-05-121-4/+4
| | | | | | | Fix off by 1 error involving minimum extent of VDS. Other minor fixes/cleanup. Tested: ummon
* [svn-r27049] Rename H5Pset/get_virtual_dataspace_bounds to ↵Neil Fortner2015-05-111-91/+42
| | | | | | | | | | | | | | H5Pset/get_virtual_view and rename enum argument. Add support for AND and NOTA/NOTB operations with unlimited selections. Add some tests for unlimited selections. Other minor fixes/cleanup. Note: "clipped" status of unlimited selections is not properly updated with H5Sselect_copy. This is a deliberate omission since fixing it would take work and we are planning to eliminate the clipped status anyways. Tested: ummon
* [svn-r27022] Add new functions H5Pset_virtual_dataspace_bounds andNeil Fortner2015-05-051-33/+36
| | | | | | | | | H5Pget_virtual_dataspace_bounds. Minor refactor of dataset initialization code to make this cleaner. Update h5_vds-percival-unlim-maxmin.c Other minor fixes/cleanup. Tested: ummon
* [svn-r26967] Refactor VDS unlimited dimension code to correctly handle case ↵Neil Fortner2015-04-291-45/+92
| | | | | | | | | where selections have discrete blocks and the extent is set by the minimum (untested, and there is still no way to set that preference). Tested: ummon
* [svn-r26962] Add support for unlimited selections to VDS code.Neil Fortner2015-04-291-5/+266
| | | | | | | | Not tested (except for percival-unlim example) Fix percival-unlim example Other bug fixes/cleanup Tested: Fedora 64
* [svn-r26680] Implement minor suggestions from 3/26/15 code review.Neil Fortner2015-03-311-20/+19
| | | | | | Note make check still fails in h5dump test (unrelated to this checkin). Tested: ummon
* [svn-r26668] Fix error in H5D__virtual_read/write that prevented short circuit.Neil Fortner2015-03-301-4/+5
| | | | | | | | Fix off by 1 error in H5S__hyper_project_intersection algorithm. Add many tests for fixed size hyperslab I/O. Note make check still fails in h5dump test (unrelated to this checkin). Tested: ummon
* [svn-r26482] Opening source files now reuses the flags from the virtual file.Neil Fortner2015-03-191-1/+1
| | | | | | | | | Added tests for I/O on virtual dataset with source datasets in unopened files. Note there are still some code coverage assertions in the selection matching algorithm - if you hit these try taking them out. Note make check still fails in h5dump test (unrelated to this checkin). Tested: ummon
* [svn-r26476] Add support for I/O in all cases with fixed size datasets and ↵Neil Fortner2015-03-181-28/+41
| | | | | | | | | | | | | no point selections. Add source dataspace extent patching (should allow closing the source file). Note fill values and various other features are not yet supported. Note there are still some code coverage assertions in the selection matching algorithm - if you hit these try taking them out. Note make check still fails in h5dump test (unrelated to this checkin). Tested: ummon
* [svn-r26469] INCOMPLETE, UNWORKING CODENeil Fortner2015-03-171-7/+37
| | | | Commit progress through 3/17/15
* [svn-r26411] Add support for I/O in very simple cases (virtual mapping and ↵Neil Fortner2015-03-091-14/+221
| | | | | | | | | file space are both H5S_ALL). Note make check fails in h5dump test (unrelated to this checkin). Tested: ummon
* [svn-r26346] Add more test cases, refactor test code to reduce code ↵Neil Fortner2015-03-031-1/+1
| | | | | | | | | duplication. Minor fixes in src. Note make check still fails in h5ls test. Tested: ummon
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