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* Warnings fixes (#1680)jhendersonHDF2022-04-251-5/+7
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* Removes the STATIC flavor of FUNC_ENTER macros (#1622)Dana Robinson2022-04-081-12/+12
| | | | | * Removes the STATIC flavor of FUNC_ENTER macros
* Merge initial version of selection I/O feature into develop (#1367)Neil Fortner2022-03-261-11/+99
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* Parallel rank0 deadlock fixes (#1183)jhendersonHDF2022-01-221-3/+10
| | | | | | | * Fix several places where rank 0 can skip past collective MPI operations on failure * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Stop lying about H5S_t const-ness (#1209)Dana Robinson2021-11-201-14/+24
| | | | | | Hyperslabs can be reworked inside several H5S callbacks, making H5S_t non-const in some places where it is marked const. This change switches these incorrectly const H5S_t pointer parameters and variables to non-const where appropriate.
* Update license url (#332)Larry Knox2021-02-171-1/+1
| | | | | | * Modify temporary rpath for testing in java example scripts. * Update URL in source file Copyright headers for web copy of COPYING file - src and test directories.
* Replace H5E_ATOM major error category with H5E_ID (#121)Dana Robinson2020-11-301-2/+2
| | | | | | | | | | * Renames H5I_ATOM to H5I_ID, among other related changes * Java has been updated. * Fortran is failing on my VM, even though I don't touch that. * Adds a RELEASE.txt note for H5E_ATOM to H5E_ID changes * Fixes typos in comments
* Clang-format of source filesAllen Byrne2020-09-301-421/+392
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* Clean up private / package / static namespace issues (function naming, whichQuincey Koziol2020-08-061-1/+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.
* Trim trailing whitespaceQuincey Koziol2020-04-201-3/+3
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* Implement H5VLget_file_type() to return a copy of a datatype with theNeil Fortner2019-11-081-1/+1
| | | | | | | | | | | 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.
* Add new H5R API that abstracts object, region and attribute reference typesJerome Soumagne2019-10-081-7/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
* Switch shared file struct name from 'H5F_file_t' to 'H5F_shared_t', to matchQuincey Koziol2019-08-221-6/+6
| | | | naming convention for shared structs in rest of library data structures.
* Begin converting dataset code to use shared file pointer instead of top fileQuincey Koziol2019-08-201-30/+30
| | | | pointer.
* Merge remote-tracking branch 'origin/develop' into env_vol_loadQuincey Koziol2019-04-031-11/+37
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| * - Added H5MMprivate.h #includes where neededDana Robinson2019-03-161-0/+1
| | | | | | | | | | - Added casts to quiet H5MM_memcpy warnings - Removed char * casts from HDmemcpy
| * Added an H5MM_memcpy call that checks for buffer overlap.Dana Robinson2019-03-161-11/+11
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| * Fix issue with direct chunk write not updating the "last chunk" indexNeil Fortner2019-03-061-0/+25
| | | | | | | | | | cache. Fix issues involving datasets being "no allocated" when they contain cached raw data.
* | Specify the default VOL connector to use with an environment variable.Quincey Koziol2019-03-101-20/+0
|/ | | | | | | | This implicitly adds support for changing the VOL connector for command-line tools or any application linked with the library. Also, add 'make check-vol' support for all directories, clearing up necessary issues in testing scripts, etc.
* Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Quincey Koziol2018-04-291-83/+87
|\ | | | | | | merge_hyperslab_updates
| * Add API context interface and use it throughout the library.Quincey Koziol2018-03-151-64/+49
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| * Cleaned up misc warnings in src and test.Dana Robinson2017-11-101-1/+1
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| * Fix for HDFFV-7853 H5Ocopy doesn't work with open identifiersVailin Choi2017-06-111-17/+38
| | | | | | | | Changes made so that raw data for dataset objects are copied from cached info when possible instead of flushing objects to file and read them back in again.
| * 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.
* | Checkpoint normalization against incoming hyperslab / selection / dataspaceQuincey Koziol2017-03-281-1/+1
|/ | | | improvements.
* [svn-r29549] Minor normalization w/ revise_chunks 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-r29057] added dxpl type checking when debug mode is enabled ↵Mohamad Chaarawi2016-02-071-28/+23
| | | | | | (H5_DEBUG_BUILD) tested on bb-8 with Serial and Parallel, debug and production builds.
* [svn-r28972] Removed option to clear file buffers from autotools, CMake, and ↵Dana Robinson2016-01-261-4/+3
| | | | | | | | | | | | library. Buffers that will be written to disk will now always be cleared since not doing this has huge security implications. Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0, x86_64) gcc 5.2.1 serial autotools parallel autotools (MPICH 3.1.4) serial CMake
* [svn-r28950] - remove META_FLUSH_COLLECTIVELY property for delayed sanity ↵Mohamad Chaarawi2016-01-211-1/+1
| | | | | | | | | | checks from metadata dxpls - remove H5AC_ind_dxpl_id and use only H5AC_dxpl_id everywhere instead. - remove flush_me_collectively flag from cache entries - add a collective sanity check (MPI_Barrier) for every HDF5 API routine that could possibly touch the file. This is trigerred when the environment variable H5_COLL_API_SANITY_CHECK is set to a non 0 digit. tested on BB-8 with serial and parallel.
* [svn-r28646] Minor normalization with revise_chunks.Dana Robinson2015-12-141-1/+0
| | | | | | | | | Also purged obsolete /*ARGSUSED*/ from the library. Tested on: Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1 serial only (these changes have been in revise_chunks for a long time)
* [svn-r27811] Description:Quincey Koziol2015-09-161-2/+3
| | | | | | | | | | | Refactor property list code to "deep copy" properties in the correct way, retraining the rest of the library to copy & release things correctly. This cleans up another batch of memory leaks, etc. within the library. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel Linux/32 2.6.x (jam) w/serial & parallel (h5committest forthcoming)
* [svn-r27768] Description:Quincey Koziol2015-09-141-5/+6
| | | | | | | | | | | | | | | | | | | | | | 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-r27613] Description:Quincey Koziol2015-08-291-1/+75
| | | | | | | | | Align w/vds branch: Move code for initializing contiguous datasets into layout 'init' callback. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel (h5committest forthcoming)
* [svn-r27133] - Add a new attribute function characterstic for format:Mohamad Chaarawi2015-06-011-5/+5
| | | | | | | | * H5_ATTR_FORMAT(X,Y,Z) __attribute__((format(X, Y, Z))) - Rename UNUSED attribute characterstic to H5_ATTR_UNUSED. - Rename NORETURN attribute characterstic to H5_ATTR_NORETURN tested with h5committest.
* [svn-r27045] Renamed H5_ASSIGN_OVERFLOW() to H5_CHECKED_ASSIGN() and re-orderedDana Robinson2015-05-101-9/+21
| | | | | | the arguments to be in a more logical order. Tested on: h5committest
* [svn-r26842] Description:Quincey Koziol2015-04-181-9/+4
| | | | | | | | | | Cache the dataset's rank & dimension sizes, instead of querying them frequently, to speed up various checks & algorithms. Also, a few minor cleanups. Tested on: MacOSX/64 10.10.2 (amazon) w/serial & parallel Linux/32 2.6.18 (jam) w/serial & parallel
* [svn-r26777] - Fix usage of the internal AC global dxplsMohamad Chaarawi2015-04-101-2/+2
| | | | | | - allocate sieve buffer with calloc instead of malloc tested with h5committest
* [svn-r25766] Description:Quincey Koziol2014-11-031-1/+1
| | | | | | | | | | 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 Koziol2014-06-131-1/+1
| | | | | | | | | | | 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-r24769] Description:Quincey Koziol2014-03-071-1/+1
| | | | | | | | | Check in Mohamad's changes to support collective I/O on point selections, along with some other minor cleanups. Tested on: Mac OSX/64 10.9.2 (amazon) w/parallel & serial (h5committest forthcoming)
* [svn-r24709] rename H5V to H5VM since H5V is needed in the fastforward ↵Mohamad Chaarawi2014-02-131-17/+17
| | | | | | | | | | | | project for view objects. The addition of view objects in the fastforward project is expected to be brough into the trunk sometimes in the future, which is why we need to make this change. Tested Manually on Jam and Ostrich. Tested with h5commitest - Koala with intel compilers failed, but nothing had to do with those changes. error on Koala: error while loading shared libraries: libirng.so
* [svn-r22287] Description:Quincey Koziol2012-04-161-126/+101
| | | | | | | | Clean up more FUNC_ENTER/FUNC_LEAVE macros and move H5D & H5T code toward the final design (as exemplified by the H5EA & H5FA code). Tested on: Mac OSX/64 10.7.3 (amazon) w/debug & parallel
* [svn-r22242] Issue 7934 - The data sieve buffer size was for all the ↵Raymond Lu2012-04-021-2/+11
| | | | | | | | | | datasets in the file. It could waste memory if any dataset size is smaller than the sieve buffer size. Now the library picks the smaller one between the dataset size and the sieve buffer size from the file access property. Tested on jam, koala, and ostrich.
* [svn-r22058] Description:Quincey Koziol2012-03-131-5/+2
| | | | | | | Better fix for zero-sized dataset error (r22053). Tested on: Mac OSX/64 10.7.3 (amazon) w/debug & parallel
* [svn-r22053] Description:Quincey Koziol2012-03-121-2/+5
| | | | | | | | | | Correct corner case for creating a contiguous dataset with a zero-sized dataspace, when the allocation time is set to early. Also clean up a few compiler warnings in the dataspace code. Tested on: Mac OSX/64 10.7.3 (amazon) w/debug & parallel
* [svn-r21919] Description:Quincey Koziol2012-02-091-18/+18
| | | | | | | | Refactor function name macros and simplify the FUNC_ENTER macros, to clear away the cruft and prepare for further cleanups. Tested on: Mac OSX/64 10.7.3 (amazon) w/debug, production & parallel
* [svn-r20588] Description:Quincey Koziol2011-04-211-1/+1
| | | | | | | | | Clean up code a bit, move new "terminate" VFD callback to new position in H5FD_class_t struct. Tested on: Mac OS X/32 10.6.7 (amazon) w/debug & production (h5committest not required on this branch)
* [svn-r20587] Description:Quincey Koziol2011-04-211-1/+1
| | | | | | | | Initial commit of John Biddescomb's VFD & MPI tweaks. Tested on: None (yet) (h5committest not required for this branch)
* [svn-r19654] Description:Quincey Koziol2010-10-211-5/+5
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring Coverity revisions from branch back to trunk, and clean up some other misc. compiler warnings also. r19500: Fix coverity items 1446 and 1447. Moved up calls to memset in test_cont in ohdr.c so the test never tries to close uninitialized locations. r19501: Fix coverity items 1398-1445. Various uninitialized variable errors in fheap.c. r19502: Fixed coverity issue 579 and some additional warnings in the file as well. r19503: Bug fix: This fix addressed the "RESOURCE_LEAK" problems #789 and 790, run 26 r19504: minor mods to try to keep coverity from flagging false positives. r19505: Fixed coverity issues 566 - 571. Declared variables that are passed to functions that use them as arrays to be arrays of size 1. Tested on: Mac OS X/32 10.6.4 (amazon) w/debug, production & parallel (h5committested on trunk)
* [svn-r19498] Description:Quincey Koziol2010-10-011-457/+516
| | | | | | | | | | | | | | | | | | | | | | | | | | | Optimize the vector-vector memcpy() routine even further, for a total of ~2x speedup. :-) Make a generic vector-vector operation routine and convert other vector-vector read & write routines to use generic routine instead of multiple copies of the basic algorithm. 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, w/threadsafe, in production mode Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug 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 10.6.4 (amazon) in debug mode Mac OS X/32 10.6.4 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode Mac OS X/32 10.6.4 (amazon) w/parallel, in debug mode
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