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* [svn-r29903] merge from trunk.Mohamad Chaarawi2016-05-091-9/+9
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| * [svn-r29081] - merge in the phdf5_metadata_opt/ branch with the collective ↵Mohamad Chaarawi2016-02-101-5/+5
| | | | | | | | | | | | | | | | 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-r28950] - remove META_FLUSH_COLLECTIVELY property for delayed sanity ↵Mohamad Chaarawi2016-01-211-4/+4
| | | | | | | | | | | | | | | | | | | | 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-r27777] merge from trunk.Mohamad Chaarawi2015-09-141-50/+2
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| * [svn-r27768] Description:Quincey Koziol2015-09-141-50/+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-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-r25721] The return type of H5A_create was changed from hid_t to H5A_t *Albert Cheng2014-10-201-1/+1
| | | | | | | | | | | | | | but the test was not changed (still doing H5A_create(...) < 0). Fixed the error by changing to compare against NULL. Tested: ADA AIX machine where the old code was flagged as an error by the AIX compiler.
| * [svn-r25468] some code refactoring to align trunk with VOL branch.Mohamad Chaarawi2014-07-221-1/+6
| | | | | | | | tested with h5committest.
| * [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-r25575] cleanup H5I usage in VOL by removing the use of the aux pointer andMohamad Chaarawi2014-09-051-57/+43
| | | | | | | | | | make a higher level wrapper object around all VOL objects that includes the VOL information.
* | [svn-r25555] - rework the public H5VL wrappers to not use H5VL_t* and use a ↵Mohamad Chaarawi2014-08-261-16/+16
| | | | | | | | | | | | | | plugin hid_t instead - rework the private VL layer to use the class structure directly - some bug fixes
* | [svn-r25537] VOL framework changes.Mohamad Chaarawi2014-08-191-8/+10
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* | [svn-r25482] - update is_accessible implementation to use fapl and pass it ↵Mohamad Chaarawi2014-07-241-3/+3
| | | | | | | | | | | | | | | | | | | | down to H5Fint.c - move is_HDF5 inside deprecated macros in H5Fpublic.h - move H5ES_status_t outside of H5VLpublic.h to H5ESpublic.h - rename public properties in H5VLpublic.h to H5VL_PROP_* to add more scoping - no need to include private if pkg is included in H5VLnative.c - rename plist_id to lapl_id in loc_params structs
* | [svn-r25254] merge from trunk.Mohamad Chaarawi2014-06-111-0/+24
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| * [svn-r24998] Description:Quincey Koziol2014-04-091-0/+24
| | | | | | | | | | | | | | | | Check in Neil's changes for correctly handling case where library is reinitialized through a deprecated routine. Tested on: Linux 2.4.x/32 (jam)
* | [svn-r24311] change event queue to event stack (just variable names)Mohamad Chaarawi2013-10-171-7/+7
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* | [svn-r23473] Update the VOL plugin callbacks with better async I/O support:Mohamad Chaarawi2013-03-281-7/+7
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - change hid_t req in callbacks to void **req - change all callbacks to accept dxpl_ids (except dataset write and read which already do) - update all the private and public VL routines to accept a dxpl_id and event queue id - Add an async class for the VOL plugin with cancel, test, and wait request operations - add the external VOL log plugin test to the examples directory NOTE that async operations are still not provided by the HDF5 API, so all event queue IDs and requests passed to all plugins are NULL for now. Tested on jam.
* | [svn-r22584] merge from trunk and resolve type ID registrationMohamad Chaarawi2012-07-161-6/+6
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| * [svn-r22582] Description:Quincey Koziol2012-07-161-6/+6
| | | | | | | | | | | | | | | | | | Refactor ID class registration to be more like how other "class"s in the library are registered, and clean up compiler warnings. Tested on: Mac OSX/64 10.7.4 (amazon) w/debug (Too minor to require h5comittest)
* | [svn-r22549] Mohamad Chaarawi2012-07-101-3/+0
| | | | | | | | | | | | | | | | | | | | move ref count management on the VOL struct inside the VLint code - H5Freopen still needs to be handled create the public interface for VOL callbacks: - unresolved issue with var_args update and create new API fapl calls to support stacking drivers: - need to add fapl copy callback fix a memory leak with registration of external plugins
* | [svn-r22523] - rework how IDs for VOL objects are createdMohamad Chaarawi2012-07-061-23/+8
| | | | | | | | | | - change how the vlose routine is registered with VOL IDs - some bug fixes
* | [svn-r22511] - remove the internal file type and use the file ID created at ↵Mohamad Chaarawi2012-07-031-4/+4
| | | | | | | | | | | | | | the API level for the native implementation - work on fixing the named datatype issue.. still not resolved - branch still not stable and tests do not pass at this point
* | [svn-r22501] change the interface callbacks for the VOL to use objects ↵Mohamad Chaarawi2012-06-281-15/+107
| | | | | | | | | | | | pointers and public VL structure instead of IDs. tests will fail now because of named datatypes.
* | [svn-r22457] rename location types for objects at the VOL levelMohamad Chaarawi2012-06-121-2/+2
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* | [svn-r22452] - remove nrefs paramMohamad Chaarawi2012-06-111-4/+11
| | | | | | | | | | | | | | | | - create a struct to hold parameters for object locations instead of calling into VOL to lookup and free object: * update the implementation for H5Oopen(_by_name/idx/ref) * H5Rderefence * H5Aopen(_by_name), H5Arename(_by_name) * other routines coming later
* | [svn-r22417] rename the properties used for the VOL callbacks.Mohamad Chaarawi2012-05-291-3/+3
| | | | | | | | move them to the VOL public header.
* | [svn-r22404] split the generic callback into a misc and optional callback ↵Mohamad Chaarawi2012-05-241-1/+1
| | | | | | | | for objects and files
* | [svn-r22395] remove the high level ID implementation that wraps the actual ↵Mohamad Chaarawi2012-05-231-3/+3
| | | | | | | | | | | | ID, and store the VOL plugin in an auxilary structure in the ID pointer.
* | [svn-r22306] add a request id to each of the VOL callbacks and update the nativeMohamad Chaarawi2012-04-201-4/+4
| | | | | | | | plugin to pass a NULL request
* | [svn-r22283] H5Lget routines through VOLMohamad Chaarawi2012-04-121-69/+11
| | | | | | | | | | | | | | | | H5G and H5A deprecated routines through VOL H5A exists(_by_name), delete_by_idx, rename through attr generic callbacks H5O incr/decr_ref_count set_comment(_by_name) exists(by_name) through a generic Object cb remove the attr generic callback and use the object generic callback instead add the usual workarounds for named datatypes in test code
* | [svn-r22258] links and attributes VOL routinesMohamad Chaarawi2012-04-081-49/+30
| | | | | | | | | | change native location token to be of type H5O_loc_t several bug fixes and issues resolved
* | [svn-r22250] - fix most of issues from code reviewMohamad Chaarawi2012-04-041-3/+3
| | | | | | | | | | | | | | - object open routines fall back to the generic VL object open in case the specific call back is not impemented - H5L VOL create/copy/move routines - make VOL create routines have similar interface and stuff parameters in creation plist - some bug fixes
* | [svn-r22153] renaming some VL public variables and wrapper ID typeMohamad Chaarawi2012-03-261-3/+4
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* | [svn-r22151] - object lookup returns the haddr_tMohamad Chaarawi2012-03-261-2/+21
|/ | | | - make the VL implementation for all variations of H5Oopen, H5Oget_info, H5Gget_info common, by looking up the object location first.
* [svn-r21919] Description:Quincey Koziol2012-02-091-6/+6
| | | | | | | | 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-r20885] Description:Quincey Koziol2011-05-201-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring Coverity changes back to trunk: r20340: Address coverity issue 248. Set freed pointer to NULL if realloc fails, then check for NULL before attempting to close array of handles stored in memory addressed by pointer. r20341: Added initialization udata.path = NULL; udata.visited = NULL; to prevent unintialized use after done: label. Do C-style initialization AFTER all variable definitions. r20342: Fix valgrind error in H5DUMP-XML-tall.h5 r20343: Addressed Coverity issue 591 - check the return value of H5S_SELECT_ITER_RELEASE. r20344: Added initialization udata.path = NULL; to prevent uninitialized used after done: label r20347: Purpose: Fix memory leak in overhead.c Description: Fixed leak in test() in overhead.c where array "had" was never freed. r20348: Addressed Coverity issue 705 - added prototype for resize_configs_are_equal to cache_common.h. r20392: Purpose: Fix coverity issues 1677 and 1678 Description: Added return value checking for 4 funciton calls in H5tools_get_symlink_info(). r20394: Purpose: Fix coverity issues 1674 and 1675 Description: Modified H5Epush2() and H5E_printf_stack() to keep track of whether va_start() has been called, and to call va_end() at the end if so. r20395: Should be H5MM_calloc(count * sizeof(void*)). Fixed --gh r20396: Should be H5MM_calloc(count * sizeof(void*)). Fixed. --gh Tested on: Mac OSX/32 10.6.7 (amazon) w/debug & production (h5committested on branch)
* [svn-r18564] Description:Quincey Koziol2010-04-151-0/+13
| | | | | | | | Clean up compiler warnings. Tested on: Mac OS X/32 10.6.3 (amazon) w/debug (too simple to require h5committest)
* [svn-r15485] Purpose: Allow library to shut down properly when objects have ↵Neil Fortner2008-08-191-2/+2
| | | | | | | | | | | | | | | | reference count > 1. Description: Added a new field 'app_count' to H5I_id_info_t struct, to track the reference count on an id due to the application. the old 'count' field tracks the total. Generally any id visible to the application gets placed in app_count. Added app_ref boolean parameter to H5I_inc_ref, H5I_dec_ref, H5I_register, H5I_clear_type, and a few other functions, to specify whether the operation(s) being performed on the id(s) are due to the application (TRUE) or not (FALSE). Test added for this case. Tested: kagiso, smirom, linew (h5committest)
* [svn-r14903] Undoing change committed in r14902.Scot Breitenfeld2008-04-301-0/+2
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* [svn-r14902] Merged fortran_1_8 branch changes r14505:14901 into the trunk. ↵Scot Breitenfeld2008-04-301-2/+0
| | | | New fortran wrappers added.
* [svn-r14720] Description:Quincey Koziol2008-03-111-0/+2
| | | | | | | | | Minor bug fix to H5Aget_num_attrs() to return error when an invalid location ID is passed in. Tested on: Mac OS X/32 (amazon) Too minor to require h5committest
* [svn-r14222] Description:Quincey Koziol2007-10-301-42/+0
| | | | | | | | | | | | | | | | | | Change H5Adelete2 -> H5Adelete_by_name and un-deprecate H5Adelete1 back to H5Adelete, for better consistency with new other API routiens. 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
* [svn-r14219] Description:Quincey Koziol2007-10-301-43/+0
| | | | | | | | | | | | | | | | | | Change H5Arename2 -> H5Arename_by_name and un-deprecate H5Arename1 back to H5Arename. 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
* [svn-r14187] Description:Quincey Koziol2007-10-041-6/+11
| | | | | | | | | | | | | | | | | | | | Put H5Acreate() under API versioning, with all internal usage shifted to H5Acreate2(). Add regression tests for H5Acreate1(). 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
* [svn-r14185] Description:Quincey Koziol2007-10-041-1/+1
| | | | | | | | | | | | | | | | | | | | | Move H5Aopen_name() routine to deprecated symbol section and replace internal usage with H5Aopen(). Add simple regression test for H5Aopen_name() to deprecated routine test. 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
* [svn-r14184] Description:Quincey Koziol2007-10-041-1/+5
| | | | | | | | | | | | | | | | | | | | Move H5Aopen_idx() into deprecated symbols section, replacing all internal usage with H5Aopen_by_idx(). Add simple regression test for H5Aopen_idx(). 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
* [svn-r14183] Description:Quincey Koziol2007-10-041-1/+1
| | | | | | | | | | | | | | | | | | Move H5Aget_num_attrs() into deprecated routines section, replacing all internal usage with H5Oget_info(). 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
* [svn-r14180] Description:Quincey Koziol2007-10-041-8/+8
| | | | | | | | | | | | | | | | | | | Make H5Aiterate() versioned and change all internal use to H5Aiterate2() Leave some regression tests that exercise H5Aiterate1() Fix attribute display in h5dump & h5ls to be "by name" by default 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 2.6 (smirom) 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 Mac OS X/32 10.4.10 (amazon) in debug mode
* [svn-r14163] Description:Quincey Koziol2007-09-271-4/+8
| | | | | | | | | | | | | | | | | | | Make H5Arename() versioned and switch internal usage to use H5Arename2() Add regression test for H5Arename1() 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 2.6 (smirom) 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 AIX/32 5.3 (copper) w/FORTRAN, w/parallel, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode
* [svn-r14162] Description:Quincey Koziol2007-09-271-5/+9
| | | | | | | | | | | | | | | | | | Make H5Adelete versioned and switch internal library use to H5Adelete2. Add regression test for H5Adelete1 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 2.6 (smirom) 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 AIX/32 5.3 (copper) w/FORTRAN, w/parallel, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode
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