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* Added an H5MM_memcpy call that checks for buffer overlap.Dana Robinson2019-03-161-2/+2
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* Add API context interface and use it throughout the library.Quincey Koziol2018-03-151-84/+78
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* Fixed an uninitialized filter callback struct in H5Dchunk.c andDana Robinson2017-11-211-2/+10
| | | | | | unified the naming and initialization of said struct throughout the library. This was causing a crash on VS2015 in debug mode when the debug heap complained. Fixes HDFFV-10330.
* 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.
* [svn-r29057] added dxpl type checking when debug mode is enabled ↵Mohamad Chaarawi2016-02-071-3/+3
| | | | | | (H5_DEBUG_BUILD) tested on bb-8 with Serial and Parallel, debug and production builds.
* [svn-r28422] Description:Quincey Koziol2015-11-201-29/+29
| | | | | | | | | | Revert most of r27549, since revise_chunks code requires debugging contexts for v2 B-trees. Also, misc. warning cleanups and alignments w/changes on revise_chunks branch. Tested on: MacOSX/64 10.11.1 (amazon) w/serial & parallel (h5committest forthcoming)
* [svn-r27768] Description:Quincey Koziol2015-09-141-2/+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-r27549] Description:Quincey Koziol2015-08-221-0/+87
| | | | | | | | | | Update the file format debugging routines to match the recent changes to the metadata cache, along with a few other cleanups and miscellaneous enhancements. Tested on: MacOSX/64 10.10.5 (amazon) (h5committest forthcoming)
* [svn-r27045] Renamed H5_ASSIGN_OVERFLOW() to H5_CHECKED_ASSIGN() and re-orderedDana Robinson2015-05-101-3/+3
| | | | | | the arguments to be in a more logical order. Tested on: h5committest
* [svn-r22233] Description:Quincey Koziol2012-04-011-2/+2
| | | | | | | | | | | | | | | | | Correct several errors in fractal heap code: root indirect block was getting pinned/protected more than once, "single" free space sections weren't getting "re-parented" correctly when the heap transitioned between having a root indirect block and a root direct block, and several related issues. Also cleaned up some warnings in library/tests. Tested on: FreeBSD/32 8.2 (loyalty) w/gcc4.6, w/C++ & FORTRAN, in debug mode FreeBSD/64 8.2 (freedom) w/gcc4.6, 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 (koala) w/Intel compilers, w/default API=1.6.x, w/C++ & FORTRAN, in production mode Mac OSX/64 10.7.3 (amazon) w/debug
* [svn-r21919] Description:Quincey Koziol2012-02-091-12/+12
| | | | | | | | 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-r18256] Description:Quincey Koziol2010-02-151-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring changes from Coverity fixing branch to trunk: r18235: Fixed coverity 114: if (NULL ==_dest) H5MM_free(dest); r18236: Close Coverity issue #28 (again :-) by working through the logic of the routine more thoroughly to eliminate the goto statements. (LK & QK) r18237: fixed coverity 133: if (NULL==_dest && NULL==ret_value && NULL != dest) H5MM_free(dest); r18238: Fix coverity items 421 and 422. Added assertion that the heap's free list is NULL when entering H5HL_fl_deserialize, guarateeing that the free list will always be linked in even on failure. r18239: Fix coverity item 268. Changed H5MM_xfree(read_buf) to read_buf = H5MM_xfree(read_buf) so that read_buf isn't manipulated after it's been freed. r18241: coverity fix: use correct free functon H5FL_FREE()from the previous fix r18242: Coverity fix 139: Free dst correctly in H5O_sdspace_copy(). r18243: Fix Coverity issue #417 by checking for NULL return value from setup_cache() (LK & QK) r18244: Coverity Fix 132: free dest correctly in H5O_efl_copy() r18245: Issue 121: H5S_hyper_make_spans() cannot deal with counts of 0. However, H5Sselect_hyperslab() API does allow a count of 0. Therefore, simply throw an error if this function encounters a count of 0. r18246: Check file_ptr to address coverity issue # 418 r18247: Fixed coverity 113: if (sequence) H5MM_xfree(sequence); r18248: Coverity issue #414 by checking for NULL return from setup_cache() (LK & QK) r18249: fixed coverity 274: moved H5FL_FREE(H5A_t, attr); to a line above so that if attr is null, it will not free it. r18250: Fix coverity issue #86. Check return of malloc function to ensure non-null before continuing. Tested on: Mac OS X/32 10.6.2 (amazon) w/debug & production) (h5committested in daily tests on branch)
* [svn-r17943] Description:Quincey Koziol2009-12-011-12/+12
| | | | | | | | | | | | | | | | | | | | | | Finish refactoring v2 B-trees so that they can have client callback context provided to the encode/decode callbacks. 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 (smirom) 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-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode Mac OS X/32 10.6.2 (amazon) in debug mode Mac OS X/32 10.6.2 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r17893] Descrption:Quincey Koziol2009-11-151-13/+13
| | | | | | | | | | | | | | | | | | | | | | | | | Remove old shim H5B2 routines from refactoring, rename new routines to old routine names and switch all users of the H5B2 interface back to the old routine names now that the switch to using the more current open -> <operation> -> pattern is used for all the H5B2 code. This is the final change before adding a context to the H5B2 client encode/decode callbacks. 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 (smirom) 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-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode Mac OS X/32 10.6.2 (amazon) in debug mode Mac OS X/32 10.6.2 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r17885] Decription:Quincey Koziol2009-11-131-55/+102
| | | | | | | | | | | | | | | | | | | | | | | | | | | | Convert 'huge' fractal heap object management code to use refactored v2 B-tree routines. Also, switch internal representation of 'sizeof_addr' and 'sizeof_size' in files to be uint8_t's instead of size_t's, since they are stored in single bytes in the file format. Various other minor compiler warning cleanups and error call tweaks. 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 (smirom) 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-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode Mac OS X/32 10.6.2 (amazon) in debug mode Mac OS X/32 10.6.2 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r17842] Description:Quincey Koziol2009-11-051-5/+5
| | | | | | | | | | | | | | | | | | | | | | | | | | Further refactor v2 B-tree code toward being able to pass context info down to encode/decode client callbacks: - Separate H5B2_create call to return H5B2_t structure - Make loading the v2 B-tree header pick up the client class from the ID stored in the file. Simplify some internal API calls as a result. 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 (smirom) 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-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode Mac OS X/32 10.6.1 (amazon) in debug mode Mac OS X/32 10.6.1 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r17740] Description:Quincey Koziol2009-10-241-13/+14
| | | | | | | | | | | | | | | | | | | | | | | Refactor v2 B-tree code to take creation parameters to H5B2_create() as a struct (instead of individual arguments), call the client's class "cls" instead of "type" internally, and add client class name to client class struct. 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 (smirom) 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-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode Mac OS X/32 10.6.1 (amazon) in debug mode Mac OS X/32 10.6.1 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r17313] Description:Quincey Koziol2009-08-101-9/+1
| | | | | | | | | | | | | | | | | | | | | Bring back various minor code cleanups from the file free space branch 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 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) 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-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode Mac OS X/32 10.5.8 (amazon) in debug mode Mac OS X/32 10.5.8 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r16560] Description:Quincey Koziol2009-03-101-7/+7
| | | | | | | | | | Remove another call to H5E_clear_stack() from within the library. Clean up lots of compiler warnings. Tested on: Mac OS X/32 10.5.6 (amazon) (followup on other platforms forthcoming)
* [svn-r15800] Description:Quincey Koziol2008-10-071-5/+5
| | | | | | | | | | | | | | | | | | | | | | | Bring file free space branch changes through r15795 into trunk, which includes a fair bit of code cleanup & rearrangement along with a couple of bug fixes also. Tested on: Mac OS X/32 10.5.5 (amazon) in debug mode Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (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/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-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
* [svn-r13367] Description:Quincey Koziol2007-02-211-0/+75
| | | | | | | | | | Allow "big" attributes to push attribute storage into "dense" form immediately, to accomodate storing the attribute. (This is only allowed in the "latest" version of the format). Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r13253] Updated all C and C++ style source code files with the THG ↵Albert Cheng2007-02-071-2/+3
| | | | | | | | | copyright notice. Tested platform: Kagiso only since it is only a comment block change. If it works in one machine, it should work in all, I hope. Still need to check the parallel build on copper.
* [svn-r13117] Description:Quincey Koziol2007-01-071-2/+2
| | | | | | | Clean up some warnings from Windows. Tested on: FreeBSD/32 6.1 (duty)
* [svn-r13067] Description:Quincey Koziol2006-12-181-3/+3
| | | | | | | | | | | | | | Add [quite] limited ability to update (ie. write) data for objects in fractal heap. Limited to just updating objects in managed heap blocks (i.e. not 'tiny' or 'huge' objects) and must be updated with data of the same length as the object in the heap. Updating objects in compressed heaps does work though [as long as the data isn't 'tiny' or 'huge']. Needed for changing the data value or the name of an attribute that is stored in dense or shared storage. Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r12877] Description:Quincey Koziol2006-11-071-1/+1
| | | | | | | Clean up more compiler warnings. Tested on: Linux/64 2.6 (chicago2)
* [svn-r12655] Description:Quincey Koziol2006-09-111-12/+106
| | | | | | | | | | | | Add "op" routine to perform operation on heap object "in situ", to allow for faster operations on dense links during B-tree traversal & lookup. Refactor the "read" routine to use the internal version of the "op" routine, to keep the code duplication as low as possible. Tested on: Mac OS X.4/PPC (amazon) Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r12592] Description:Quincey Koziol2006-08-171-116/+443
| | | | | | | | | | | | | | | | | | | | | Several changes, all mooshed together: - Add support for "tiny" objects - which can be stored in the heap ID itself, instead of in the heap data blocks. - Flesh out support for compressed direct blocks, but comment it out until John's got some metadata cache changes in place to support it. - Add support for applying I/O pipeline filters to 'huge' objects - Refactor 'huge' object code to store information for 'huge' objects directly in the heap ID, when there are I/O pipeline filters applied to the heap (and the heap ID is large enough to hold the information) - Update h5debug tool to correctly handle 'huge' & 'tiny' objects. - Misc. other code cleanups, etc. Tested on: FreeBSD/32 4.11 (sleipnir) Linux/64 2.4 (mir) Solaris/64 2.9 (shanti)
* [svn-r12575] Description:Quincey Koziol2006-08-141-0/+3
| | | | | | | | | | | | | Allow the heap ID length to be chosen at heap creation time, to allow for making heap IDs long enough to directly embed the file offset & length of 'huge' objects in the heap ID (which allows them to be retrieved directly from disk, instead of requiring them to be looked up in the B-tree that tracks 'huge' objects) Tested on: FreeBSD/32 4.11 (sleipnir) Linux/64 2.4 (mir) Solaris/64 9 (shanti)
* [svn-r12573] Description:Quincey Koziol2006-08-131-2/+2
| | | | | | | | | | | | Clean up a couple of compiler warnings in the 'huge' object code in the library. Add a bunch of 'huge' object regression tests Tested on: FreeBSD 4.11 (sleipnir) Linux/64 2.4 (mir) Solaris/64 2.9 (shanti)
* [svn-r12562] Description:Quincey Koziol2006-08-101-0/+574
Initial revision to add support for "huge" objects in the heap (which are actually stored directly in the file, but are tracked with v2 B-tree that is accessed through heap header). Testing: FreeBSD 4.11 (sleipnir) Linux/64 2.4 (mir) Linux/32 2.4 (heping) Mac OS X.4 (amazon)
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