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* Add new H5R API that abstracts object, region and attribute reference typesJerome Soumagne2019-10-081-198/+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
* Added an H5MM_memcpy call that checks for buffer overlap.Dana Robinson2019-03-161-2/+2
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* Switch loc_params to VOL callbacks to pass struct by pointer instead of byQuincey Koziol2018-11-221-1/+1
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* Remove most debugging shims & scaffolding.Quincey Koziol2018-11-041-10/+0
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* Switch driver | plugin => connector.Quincey Koziol2018-11-041-1/+1
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* Refactor and standardize object VOL callbacks.Quincey Koziol2018-11-011-3/+1
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* Squashed commit of private branch changes to support stackable VOL plugins.Quincey Koziol2018-10-251-2/+12
| | | | modified: test/dsets.c
* VOL FEATUREDana Robinson2018-10-101-9/+22
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* Remainder of vol_normalization changes (dataset, attribute, files, objects).Dana Robinson2018-09-241-29/+25
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* Normalization with vol_integration (property lists, file drivers,Dana Robinson2018-09-211-32/+24
| | | | other misc).
* Normalization with vol_integration (misc internal and datatype)Dana Robinson2018-09-201-4/+3
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* Removed 'VOL' versions of FUNC_ENTER macros as well as empty functionsDana Robinson2018-09-181-5/+2
| | | | orginally intended to support the full SWMR feature.
* Fixed HDFFV-10404Binh-Minh Ribler2018-07-131-1/+1
| | | | | | | | | Description: Applied the typo fixes from user's report. The previous pull request couldn't be merged because it was too old, and it was too complicated for me to resolve conflicts. Platform tested: Linux/64 (jelly) - very minor
* Remove redundant 'is_collective' parameter from H5CX_set_loc.Quincey Koziol2018-03-271-1/+1
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* Cleanup API context function usage.Quincey Koziol2018-03-191-10/+3
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* Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Quincey Koziol2018-03-181-6/+24
|\ | | | | | | | | | | merge_func_enter_vol Plus initial steps toward merging API context push into FUNC_ENTER_API* macros
| * Changes made based on code reviews.Vailin Choi2018-01-121-0/+6
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| * (1) Merge branch 'develop' into bugfix/version_boundsVailin Choi2017-11-251-6/+18
| | | | | | | | | | | | (2) Add two new options to h5repack for low and high bounds as in H5Pset_libver_bounds. (3) Modify message pre_copy callbacks so that H5Ocopy can handle version bounds check. (4) Add version bounds check for cache image feature.
* | Add API context interface and use it throughout the library.Quincey Koziol2018-03-151-143/+179
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* Fix for HDFFV-7853 H5Ocopy doesn't work with open identifiersVailin Choi2017-06-111-30/+2
| | | | 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.
* Bring SWMR support in to the main development branch. (Finally!) More testsQuincey Koziol2016-12-021-1/+11
| | | | and the tool and API wrappers will be coming in over the weekend.
* Tentative fix for valgrind issues related to EoC.Dana Robinson2016-11-261-1/+1
| | | | | | | | | 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.
* Code style and warning cleanups, from revise_chunks branch.Quincey Koziol2016-11-061-5/+5
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* [svn-r29626] Description:Quincey Koziol2016-04-041-3/+16
| | | | | | | | Revise method of invoking object flush callback. Tested on: MacOSX/64 10.11.4 (amazon) w/serial & parallel (h5committest forthcoming)
* [svn-r29081] - merge in the phdf5_metadata_opt/ branch with the collective ↵Mohamad Chaarawi2016-02-101-1/+1
|\ | | | | | | | | | | | | | | metadata optimizations. - rename H5AC_dxpl_id to H5AC_ind_read_dxpl_id and update all usage in the library tested on bb-8 with parallel and serial.
| * [svn-r29066] - fixing some of the internal usage of dxpls.Mohamad Chaarawi2016-02-081-3/+4
| | | | | | | | - merge from trunk.
* | [svn-r29076] Description:Quincey Koziol2016-02-101-3/+4
|/ | | | | | | | | Normalize against the phdf5_metadata_opt branch, in preparation for merging it to trunk. Tested on: MacOSX/64 10.11.3 (amazon) w/serial, parallel, and production builds h5committest forthcoming
* [svn-r28950] - remove META_FLUSH_COLLECTIVELY property for delayed sanity ↵Mohamad Chaarawi2016-01-211-2/+2
| | | | | | | | | | 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-r28797] Description:Quincey Koziol2016-01-051-2/+2
| | | | | | | | 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-r28761] Description:Quincey Koziol2016-01-011-18/+6
| | | | | | | | | | | | Clean up many mismatches between malloc/free and H5MM_malloc/H5MM_xfree in the library and tests (and use of H5free_memory and H5Dvlen_reclaim). Also make H5Ocopy use a private version of H5Lexists, which doesn't internally throw (and suppress) errors when an object (or the path to it) isn't found in the destination. Tested on: MacOSX/64 10.11.2 (amazon) w/serial & parallel (h5committest forthcoming)
* [svn-r28606] Description:Quincey Koziol2015-12-131-7/+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-r27811] Description:Quincey Koziol2015-09-161-1/+1
| | | | | | | | | | | 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 Koziol2015-09-141-1/+2
| | | | | | | | | | | | | | | | | | | | | | 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-r27237] Description:Quincey Koziol2015-06-181-1/+1
| | | | | | | | | Merge v3 metadata cache changes to trunk. Yay! :-) Tested on: MacOSX/64 10.10.3 (amazon) w/serial & parallel Linux/32 2.6.x (jam) w/serial & parallel (daily tested on branch)
* [svn-r27133] - Add a new attribute function characterstic for format:Mohamad Chaarawi2015-06-011-3/+3
| | | | | | | | * 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-r26777] - Fix usage of the internal AC global dxplsMohamad Chaarawi2015-04-101-7/+7
| | | | | | - allocate sieve buffer with calloc instead of malloc tested with h5committest
* [svn-r23695] Description:Quincey Koziol2013-05-111-13/+14
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Clean up warnings in H5Tconv.c (down to _only_ 9000 lines of output now!) Merge changes from Coverity branch back to trunk: r20684: Fix for coverity bug #1721 which was due to the fix for coverity bug #943. r20685: Use HDstrncpy. --gh r20761: Purpose: Fix valgrind issues Description: Free image_data and data as appropriate in test_image. r20762: Purpose: Fix coverity issue 600 Description: Add check for return value of H5O_close in H5Ocopy. Also cleaned up various warnings. r20763: Purpose: Fix valgrind issues with h5stat Description: Modified h5stat to free "iter" before exit, and free "hand" before exit if parse_command_line exits directly. r20764: fixed coverity issues: 69, 327, 614, 684, 685, 696, 697, 1681, 967, 826, 660, 80 r20765: Fixed coverity bug 668 Pulled x * y * z multiply out of malloc operand into a separate n_elements variable to quiet integer overflow warning. No actual integer overflow tests are performed since it's just a test program but I did add a check that n_elements is >= 1. I also changed an error condition from doing its own close and returning -1 to "goto out;" like the rest of the program. r20766: Fixed coverity bug 667 Pulled x * y * z multiply out of malloc operand into a separate n_elements variable to quiet integer overflow warning. No actual integer overflow tests are performed since it's just a test program. Tested on: Mac OSX/64 10.8.3 (amazon) w/C++ & FORTRAN (h5committest upcoming)
* [svn-r23313] Description:Quincey Koziol2013-02-251-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring changes from Coverity branch to the trunk: r20612: Changed string functions to versions with string length to fix coverity issues 922, 942 and 943. r20614: Use HDsnprintf. --gh r20675: Fix for coverity #1714 due to the fix for #810. Use HDfree() instead of H5MM_xfree(). r20678: Repaired coverity issue #598 -- failure to check return value from a call to fstat(), or to tidy up in the event of failure. r20679: Use HDstrncpy. --gh r20681: Use HDstrncat and HDstrncpy. --gh Tested on: Mac OSX/64 10.8.2 (amazon) w/Debug, etc. (too minor to require h5committest)
* [svn-r22679] Changed H5O_copy_search_comm_dt_check() to use H5O_obj_class() ↵Vailin Choi2012-08-141-6/+10
| | | | | | to get object type instead of H5O_get_info(...TRUE...) saving time in traversing metadata. (This is part of the checkin to 1.8 branch #22677)
* [svn-r22646] Description:Quincey Koziol2012-08-081-1/+4
| | | | | | | | | Changes resulting from Klocwork static analysis tool, from Mark Miller @ LLNL (miller86@llnl.gov). Tested on: Mac OS X/64 10.7.4 (amazon) w/debug, C++ & FORTRAN, using gcc 4.7.x (too minor to require h5committest)
* [svn-r22608] Description:Quincey Koziol2012-07-261-6/+6
| | | | | | | | | | | | | | | Switch propert list/class iteration from internal to external form of iteration, cleaning up and simplifying the code a bit. Bring other general improvements from plist_encode_decode branch back to trunk. Clean up many warnings. Tested on: Mac OSX/64 10.7.4 (amazon) w/gcc 4.7, debug and C++ & FORTRAN (too minor to require h5committest)
* [svn-r22601] Purpose: Fix HDFFV-5853Neil Fortner2012-07-251-1/+1
| | | | | | | | | | | | | | Description: When jumping out from between H5_BEGIN_TAG and H5_END_TAG macros using HGOTO_ERROR or HGOTO_DONE, the previous metadata tag is not reset on the dxpl. This could cause problems when, for example, calling H5Ocopy within an H5Literate callback. Added new HGOTO_ERROR_TAG and HGOTO_DONE_TAG macros which must be used in place of the above between H5_BEGIN_TAG and H5_END_TAG. Tested: jam, koala, ostrich (h5committest), durandal
* [svn-r22171] Description:Quincey Koziol2012-03-281-45/+733
| | | | | | | | | Bring "merge committed datatypes during H5Ocopy" feature from branch to trunk. (Also has some minor bugfixes with it) Tested on: Mac OSX/64 10.7.3 (amazon) w/debug (h5committest coming up)
* [svn-r22164] Fixed a bug in H5Ocopy(): When copying an opened object, call ↵Vailin Choi2012-03-281-4/+31
| | | | | | | the object's flush class action to ensure that cached data is flushed so that H5Ocopy will get the correct data. (HDFFV-7853)
* [svn-r22058] Description:Quincey Koziol2012-03-131-2/+1
| | | | | | | Better fix for zero-sized dataset error (r22053). Tested on: Mac OSX/64 10.7.3 (amazon) w/debug & parallel
* [svn-r21919] Description:Quincey Koziol2012-02-091-8/+8
| | | | | | | | 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-r21629] Purpose: Update fix committed in r21556Neil Fortner2011-10-201-27/+15
| | | | | | | | Description: An old patch was mistakenly committed in r21556. Replaced this fix with the latest. Tested: jam, koala, heiwa (h5committest)
* [svn-r21610] Purpose: Fix bug 7776Neil Fortner2011-10-191-6/+18
| | | | | | | | | | | Description: When H5Ocopy failed due to attempting to expand an invalid reference in an attribute (or at any point after the destination object header was inserted into the cache), it failed to clean up correctly. Modified H5O_copy_header_real to keep track of whether the object header was inserted and take appropriate action on failure. Tested: fedora (too minor for full commit test)
* [svn-r21603] Purpose: Add generic skip list implementationNeil Fortner2011-10-181-1/+1
| | | | | | | | | | | | | Description: Added new H5SL_TYPE_GENERIC skip list type, which uses void *'s as keys and a client-supplied callback for key comparison. This was added to support the upcoming "merge named datatype" feature for H5Ocopy, but may be used in other places as well. Also added testing. Also fixed a potential bug with the H5SL_TYPE_OBJ implementation, and added testing for that. Tested: jam, koala, heiwa (h5committest), durandal
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