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* Removes the STATIC flavor of FUNC_ENTER macros (#1622)Dana Robinson2022-04-081-1/+1
| | | | | * Removes the STATIC flavor of FUNC_ENTER macros
* Stop lying about H5S_t const-ness (#1209)Dana Robinson2021-11-201-1/+1
| | | | | | 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.
* Move API routines for VOL objects to main source file. (#133)Quincey Koziol2020-11-301-52/+0
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* Clang-format of source filesAllen Byrne2020-09-301-156/+149
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* Clean up private / package / static namespace issues (function naming, whichQuincey Koziol2020-08-061-2/+2
| | | | | | 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 Koziol2020-04-201-1/+1
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* squash cast warning fixkmu2020-01-231-3/+2
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* Merge remote-tracking branch 'origin/develop' into merge_hyperslab_update_01Quincey Koziol2019-03-171-3/+4
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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 Robinson2019-03-161-3/+3
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* | Core changes to selection code from the hyperslab_updates branch.Quincey Koziol2019-03-161-2/+2
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* Remainder of vol_normalization changes (dataset, attribute, files, objects).Dana Robinson2018-09-241-1/+1
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* Cleanup API context function usage.Quincey Koziol2018-03-191-6/+0
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* Add API context interface and use it throughout the library.Quincey Koziol2018-03-151-23/+24
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* 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-r30189] Description:Quincey Koziol2016-07-181-9/+16
| | | | | | | | | Clean up more warnings: drop the warning count from ~1310 down to ~940, with only 31 types of warnings in 148 files (down from 38 types in 167 files). Tested on: MacOSX/64 10.11.5 (amazon) w/serial & parallel (h5committest forthcoming)
* [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-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-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-r26777] - Fix usage of the internal AC global dxplsMohamad Chaarawi2015-04-101-1/+1
| | | | | | - allocate sieve buffer with calloc instead of malloc tested with h5committest
* [svn-r24709] rename H5V to H5VM since H5V is needed in the fastforward ↵Mohamad Chaarawi2014-02-131-4/+4
| | | | | | | | | | | | 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-r22582] Description:Quincey Koziol2012-07-161-2/+2
| | | | | | | | | 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-r22287] Description:Quincey Koziol2012-04-161-27/+29
| | | | | | | | 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-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-r19398] Descriptino:Quincey Koziol2010-09-161-3/+3
| | | | | | | | | | | | | | | | | | | | | | | Clean up the internal usage H5I_dec_ref() to eliminate the sequence of flags that has been creeping in. 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
* [svn-r19363] When mandatory filter failed to write data chunks, the datasetRaymond Lu2010-09-091-3/+3
| | | | | | | couldn't close (bug 1260). The fix releases all resources and closes the dataset but returns a failure. Tested with h5committest - jam, heiwa, amani.
* [svn-r19297] Description:Quincey Koziol2010-08-251-2/+4
| | | | | | | | | | Whack a few more memory errors exposed by valgrind. Make the debugging dump output a little bit prettier. Tested on: Mac OS X/32 10.6.4 (amazon) w/debug (h5committest forthcoming)
* [svn-r19278] Description:Quincey Koziol2010-08-231-1/+2
| | | | | | | | | | | | | | | | | | | | | | More fixes to memory allocation, etc. exposed by valgrind. 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
* [svn-r19273] Description:Quincey Koziol2010-08-201-1/+1
| | | | | | | | | | | | | | | | | | Correct an off-by-one oversight with the valgrind changes in r19272. 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
* [svn-r19272] Description:Quincey Koziol2010-08-201-5/+7
| | | | | | | | | | | | Close out various resource leaks and usages of uninitialized memory that were flagged by valgrind. [There's still some more valgrind warnings, but it's better now... :-/ ] Also clean up warnings and code formatting. Tested on: Mac OS X/32 10.6.4 (amazon) w/debug & valgrind (h5committest forthcoming)
* [svn-r19156] Description:Quincey Koziol2010-07-301-0/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring revisions from Coverity branch back to trunk: r19044: Coverity #449 - Line 1560 called function H5O_chunk_protect for 2 pointers to allocate. But when there's failure on the second one, the first wasn't freed (H5O_chunk_unprotect). We fixed it by freeing the pointers when an error happens. r19045: Fixed coverity issue # 319. Free sec_node in done if it is not NULL. r19046: Add intended but missing assignments to initialize pointers to NULL (coverity issue fixes). r19049: Hdf5_1_8_coverity branch was recreated from hdf5_1_8 branch in revision 18839 without fix for Coverity issue #84 having been propagated to the hdf5_1_8 branch. This revision adds the fix again. r19060: added parentheses to see if they will keep subversion from getting confused r19061: Fix coverity item 139. Fixed incorrect condition for freeing buffer on error. Fix coverity items 20 and 21. Removed unused NTESTS facility from dtypes.c. Cleanup in H5Shyper.c. r19062: Fix coverity item 450. Check to see if chk_proxy has been allocated before attempting to free it. Fix coverity item 454. Check to see if allocation of buf failed in H5D_fill_refill_vl. Fix coverity items 455-457. Initilize hid_t's to -1, check their value before attempting to close them, and check if the close failed. r19063: New fix to address coverity issue #84. Check that pointers in H5Z_xform_find_type are not NULL before passing them to H5T_cmp. Tested on: Mac OS X/32 10.6.4 (amazon) w/debug & production (Too minor to require h5committest)
* [svn-r18894] Purpose: Improve allocation performance of filtered datasets ↵Neil Fortner2010-05-251-22/+7
| | | | | | | | | | | | | with non-default VL fill values. Description: Previously, H5D_chunk_allocate would, if a dataset were filtered and had a non-default VL fill value, allocate a new buffer for every chunk. Changed H5D_chunk_allocate to reuse the existing buffer if possible. Also other miscellaneous cleanup. Tested: jam, linew, amani (h5committest)
* [svn-r18804] Purpose:Mike McGreevy2010-05-141-0/+22
| | | | | | | | | | | | | Fix memory leaks Description Added a routine to free memory which addresses a memory leak when variable length strings are used as fill values. Tested: h5committest and valgrind (on jam/amani) to confirm freed memory.
* [svn-r18650] Description:Quincey Koziol2010-04-271-1/+0
| | | | | | | | | | | | | | | | | | | Bring back various minor tweaks & cleanups from the revise_chunks 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 (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-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
* [svn-r18595] Description:Quincey Koziol2010-04-201-5/+5
| | | | | | | | Clean up compiler warnings Tested on: Mac OS X/32 10.6.3 (amazon) w/debug (too minor to require h5committest)
* [svn-r18357] Description:Quincey Koziol2010-03-021-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | Bring r18356 from metadata journaling merge branch to trunk: Converge metadata journaling branch with trunk with a bunch of v1 B-tree changes: - Remove H5ACprivate.h header from H5Bprivate.h header - Revise v1 B-tree client callbacks - Get rid of H5B_serialize() by bringing it into H5B_flush() 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-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
* [svn-r17977] Bug fix for 1584. H5Tdetect_class said a VL string is a string ↵Raymond Lu2009-12-091-2/+2
| | | | | | | | | | | | type. But when it's in a compound type, it says it's a VL type. We want to tell user a VL string is a string. But internally we treat it as a VL type. I added a flag as a parameter of H5T_detect_class. It tells whether the caller is the public function H5Tdetect_class. I also added a detection for VL string in the private function for the compound case (or array or nested VL type). Tested on jam and amani - I tested the same change for 1.8 with h5committest.
* [svn-r16279] Description:Quincey Koziol2009-01-081-2/+7
| | | | | | | | | | | | | | Bring revision 16278 back from revise_chunks branch: Update layout information in DCPL to unify all information in one underlying property and switch to using H5O_layout_t for storing it, which simplifies things considerably. Also, fix many compiler warnings. Tested on: FreeBSD/32 6.3 (duty) in debug mode (Original patch tested on many machines)
* [svn-r15628] Description:Quincey Koziol2008-09-161-4/+4
| | | | | | | | | | | | | 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-r15609] Description:Quincey Koziol2008-09-101-6/+6
| | | | | | | | Omnibus compiler warning cleanup & some reformatting also. Tested on: Mac OS X/32 10.5.4 (amazon) Too minor to require h5committest
* [svn-r15485] Purpose: Allow library to shut down properly when objects have ↵Neil Fortner2008-08-191-6/+6
| | | | | | | | | | | | | | | | 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 Breitenfeld2008-04-301-6/+6
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* [svn-r14902] Merged fortran_1_8 branch changes r14505:14901 into the trunk. ↵Scot Breitenfeld2008-04-301-6/+6
| | | | New fortran wrappers added.
* [svn-r14860] Description:Quincey Koziol2008-04-241-6/+6
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Omnibus raw data I/O revisions, with wide-ranging changes and refactoring, in order to prepare for implementing "fast append" feature. These changes remove the majority of the code duplication for raw data I/O which has crept in over the last ten years and introduces a more object- oriented design for operating on different types of dataset storage. Chunked storage no longer has it's own I/O routines, it is now handled as either contiguous (if chunk is not pulled into the cache) or compact (if the chunk is cached in memory). No bug or feature changes, at least intentionally... :-) 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 10.5.2 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r14203] Description:Quincey Koziol2007-10-111-1/+1
| | | | | | | | | | | | | | | | | | | Break up H5D source file into H5D/H5Dint/H5Ddeprec Attempt fix for "szip noencoder" build failure. 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-r13942] Description:Quincey Koziol2007-07-051-2/+1
| | | | | | | | | Minor code & comment cleanups Tested on: Mac OS X/32 10.4.10 (amazon) Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r13926] Description:Quincey Koziol2007-06-291-25/+44
| | | | | | | | | | | | Add small interface to "wrap" a static buffer (usually on the stack), but still allow for buffers larger than the static buffer to be allocated. This can eliminate _many_ short-lived buffer allocations in situations where the buffer is a predictable size (or at least a "very likely" size). Also, some minor code cleanups, particularly in the SOHM caching code. Tested on: Mac OS X/32 10.4.10 (amazon)
* [svn-r13918] Description:Quincey Koziol2007-06-261-0/+667
Refactor fill value buffer code into one location, for better long-term maintenance. Tested on: Mac OS X/32 10.4.10 (amazon) Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
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