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* Clean up private / package / static namespace issues (function naming, whichQuincey Koziol2020-08-221-1/+1
| | | | | | header file, FUNC_ENTER / LEAVE, etc). Removed remaining personal email addresses from library source code (still needs cleaned from other directories). Misc. warning, style, and whitespace cleanup.
* Sync with developDana Robinson2020-08-011-4/+2
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* Merge pull request #2451 in HDFFV/hdf5 from ↵Vailin Choi2020-03-161-4/+7
| | | | | | | ~VCHOI/my_third_fork:bugfix/develop_seg_fault_sel_compat to develop * commit '81b1ed4e1724b8a6a731ab2b8fb03234a8b49d15': Fix issues when deserializing point/all/none selection with version beyond the library's supported version: (1) Verify the decoded version before proceeding further with deserialization (2) Close the dataspace if errors occurred after opening the dataspace
* Replace H5Sselect_adjust_u() and H5Shyper_adjust_s() withNeil Fortner2019-12-061-0/+3
| | | | | H5Sselect_adjust. Implement "adjust_s" callback for all selection types. Add range checking to H5Sselect_adjust().
* Implement public H5Sselect_project_intersection(). Updated internalNeil Fortner2019-12-061-11/+20
| | | | | | | | 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.
* Verify the decoded version for hyperslab selection.Vailin Choi2019-12-051-3/+4
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* Add H5Sselect_shape_same and H5Sselect_intersect_block API routines, alongQuincey Koziol2019-07-301-1/+12
| | | | with tests and minor cleanups and refactorings.
* New hyperslab selection routines and new public selection iterator routines.Quincey Koziol2019-06-161-0/+3
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* Merge remote-tracking branch 'origin/develop' into merge_hyperslab_update_01Quincey Koziol2019-04-291-2/+29
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| * HDFFV-10365: Changes as described in the RFC: H5Sencode/H5Sdecode Format Change.Vailin Choi2019-04-061-2/+29
| | | | | | | | This also addresses HDFFV-10255: H5Sencode/decode performance issue.
* | Merge remote-tracking branch 'origin/develop' into merge_hyperslab_update_01Quincey Koziol2019-04-061-2/+1
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| * Move dataspace selection-specific coding to the callbacks as preparation for ↵Vailin Choi2019-04-051-2/+1
| | | | | | | | the H5Sencode changes.
* | Core changes to selection code from the hyperslab_updates branch.Quincey Koziol2019-03-161-36/+93
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* More changes to align with incoming selection improvements.Quincey Koziol2019-02-141-2/+2
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* Align develop with incoming hyperslab_updates branch changes.Quincey Koziol2019-02-131-8/+15
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* Delta reduction against hyperslab_updates branch.Quincey Koziol2019-01-111-3/+2
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* H5S adjust callbacks now return an herr_t instead of void.Dana Robinson2018-09-241-1/+1
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* Revert "Merge pull request #1116 in HDFFV/hdf5 from ↵hdftest2018-06-241-27/+6
| | | | | | | ~HDFTEST/hdf5_hft:hdf5_1_10 to develop" This reverts commit e9f476dad47ce593f13dacb77b1cc664d1f24e7b, reversing changes made to 2ff00b1b937ebe36ac6ddf590c16a4c27fc0b053.
* Merge branch 'develop' into hdf5_1_10.syncM. Scot Breitenfeld2018-05-081-9/+12
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| * Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Quincey Koziol2018-04-291-6/+7
| |\ | | | | | | | | | merge_hyperslab_updates
| | * Fix for daily test failuresVailin Choi2018-02-141-0/+3
| | | | | | | | | | | | | | | | | | | | | | | | Move the declarations for the three arrays of versions from H5Opkg.h: (1) H5O_layout_vers_bounds to H5Dpkg.h (2) H5O_dtype_ver_bounds to H5Tpkg.h (3) H5O_sdspace_ver_bounds to H5Spkg.h This is to fix Windows' complaint for unresolved symbols.
| | * 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.
| * | Further minor cleanupsQuincey Koziol2017-03-281-3/+3
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| * | Checkpoint normalization against incoming hyperslab / selection / dataspaceQuincey Koziol2017-03-281-6/+9
| |/ | | | | | | improvements.
* | Re-factor coding for H5P/Sencode with libver bounds.Vailin Choi2018-03-121-1/+2
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* | Needs to sync with lib version and Sencode.M. Scot Breitenfeld2018-03-071-0/+3
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* | Fix for HDFFV-9947 H5SencodeVailin Choi2017-11-281-5/+25
| | | | | | | | Modifications to fix H5Sencode bug when num points selected is > 2^32.
* | Change copyright headers to replace url referring to file to be removedlrknox2017-04-141-6/+4
|/ | | | | | | | and replace it with new url for COPYING file. Fix 2 lines in java error test expected output file where messages include line numbers changed by reducing the copyright header by 2 lines.
* [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-r26302] Description:Quincey Koziol2015-02-251-2/+2
| | | | | | | | | | | | | | | | | | Revise dataspace encode/decode routines to make them work better with future virtual dataset feature. Tested on: Mac OSX/64 10.10.2 (amazon) w/serial (h5committest forthcoming)
* | [svn-r27632] Description:Quincey Koziol2015-08-311-5/+4
| | | | | | | | | | | | | | | | | | | | Revert changes to pass file pointer to selection serialize/deserialize routines. Also patch back in some changes that were merged out in the previous merge w/trunk. Tested on: MacOSX/64 10.10.5 (amazon) w/serial (h5committest not required on this branch)
* | [svn-r27479] Add checking for invalid inputs to H5Dset_virtual: point ↵Neil Fortner2015-08-071-2/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | 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-r27246] Remove "clipped" status from unlimited selections, decoupling ↵Neil Fortner2015-06-181-6/+2
| | | | | | | | | | | | | | | | | | | | | | 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-r27153] Implement fill value support for VDS.Neil Fortner2015-06-051-0/+1
| | | | | | | | | | | | | | | | | | Add testing for this. Fix bug in printf string parsing. Add test for this. Other minor fixes/cleanup. Tested: ummon
* | [svn-r26984] Add support for unlimited selection being clipped in the middle ↵Neil Fortner2015-04-301-1/+5
| | | | | | | | | | | | | | | | | | of a block. Add tests for this (pure selection tests, needs testing with VDS). Various bug fixes. Tested: ummon
* | [svn-r26962] Add support for unlimited selections to VDS code.Neil Fortner2015-04-291-1/+4
| | | | | | | | | | | | | | | | Not tested (except for percival-unlim example) Fix percival-unlim example Other bug fixes/cleanup Tested: Fedora 64
* | [svn-r26878] Fix errors in unlimited selection serialize/deserializeNeil Fortner2015-04-211-1/+3
| | | | | | | | | | | | Other minor fixes Tested: jam
* | [svn-r26828] Implement support for unlimited selections (not supported by ↵Neil Fortner2015-04-161-4/+16
| | | | | | | | | | | | | | | | | | VDS code yet). Add tests for unlimited selections. Various other minor changes. Tested: ummon
* | [svn-r26476] Add support for I/O in all cases with fixed size datasets and ↵Neil Fortner2015-03-181-0/+6
| | | | | | | | | | | | | | | | | | | | | | | | | | 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-r26293] Implement patching of virtual dataspace extent in mapping ↵Neil Fortner2015-02-241-1/+1
| | | | | | | | | | | | | | | | dataspaces when opening virtual dataset. Add tests for this. Tested: ummon
* | [svn-r26198] INCOMPLETE, UNWORKING CODENeil Fortner2015-02-171-2/+2
| | | | | | | | Commit progress through 1610 CST 2/17/15
* | [svn-r26153] INCOMPLETE, UNWORKING CODENeil Fortner2015-02-101-1/+1
|/ | | | Commit progress through 2/10/15 at 1500 CST
* [svn-r25766] Description:Quincey Koziol2014-11-031-25/+6
| | | | | | | | | | Revert r25273, 25283 & 25439 (the hyperslab improvement changes). They are buggy and it's taking me a long time to correct the problem. I'll check in a revised form of the changes when I've got them straightened out. Tested on: Mac OSX 10.10.0 (amazon) w/gcc 4.9.x, C++, FORTRAN Linux 2.6.x (jam) w/parallel
* [svn-r25273] Description:Quincey Koziol2014-06-131-6/+25
| | | | | | | | | | | Bring in Chao/Neil/my changes to optimize hyperslab selection operations further, along with 3 new public API routines: H5Scombine_hyperslab(), H5Sselect_select() and H5Scombine_select(), along with many minor cleanups to the code and fixing a few compiler warnings. Tested on: Mac OSX/64 10.9.3 w/gcc 4.9.x and parallel w/OpenMPI (h5commttest forthcoming)
* [svn-r19092] Description:Quincey Koziol2010-07-191-0/+6
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring "shape same" changes from LBL branch to trunk. These changes allow shapes that are the same, but projected into dataspaces with different ranks to be detected correctly, and also contains code to project a dataspace into greater/lesser number of dimensions, so the I/O can proceed in a faster way. These changes also contain several bug fixes and _lots_ of code cleanups to the MPI datatype creation code. Many other misc. code cleanup are included as well... Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (amani) w/Intel compilers, w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode Mac OS X/32 10.6.3 (amazon) in debug mode Mac OS X/32 10.6.3 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r15628] Description:Quincey Koziol2008-09-161-1/+1
| | | | | | | | | | | | | Remove trailing whitespace from C/C++ source files, with the following script: foreach f (*.[ch] *.cpp) sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f end Tested on: Mac OS X/32 10.5.5 (amazon) No need for h5committest, just whitespace changes...
* [svn-r14326] Description:Quincey Koziol2007-12-061-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | - Keep skip list for tracking chunks with dataset (instead of creating/ destroying it for each I/O operation) and just delete the skip list nodes. - Avoid computations for normalizing selection offset when offset not set. - Avoid updating object modification time twice during dataset creation. - Avoid updating dataset layout message (and object modification time) until dataset is closed. Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r14307] Description:Quincey Koziol2007-11-291-1/+4
| | | | | | | | | | | | | | | | | | | | | | | | - Extracted common code from H5D_select_read/H5D_select_write into single routine (H5D_select_io) and made H5D_select_read/H5D_select_write "gateway" routines, passing I/O buffer to operate on in "op" struct. - Create optimized pathway in H5D_select_io for I/O operations on single elements. - Make "get linear offset of first element" callback for each type of selection (used in "optimized pathway", above) Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r14278] Description:Quincey Koziol2007-11-201-0/+3
| | | | | | | | | | | | | | | | | | | | - Remember # of elements in file selection, instead of querying more than once - Handle building chunk map for single element as special case Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
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