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* Update URL in source file Copyright headers for web copy of COPYINGLarry Knox2021-02-201-1/+1
| | | | file - src and test directories.
* Basic alignment with async branch (#115) (#137)Quincey Koziol2020-11-301-44/+3
| | | | | | | * Basic alignment with async branch - trivial changes to reduce clutter in overall diff. * Update minor error code to reflect change within library * Update the error output to match library
* Source formattedAllen Byrne2020-10-011-305/+280
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* Clean up private / package / static namespace issues (function naming, whichQuincey Koziol2020-08-221-39/+39
| | | | | | 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.
* Sync with developDana Robinson2020-08-011-14/+9
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* Squashed commit of the token_refactoring branch:Dana Robinson2020-01-191-27/+37
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* Cherry pick of 0225e6d5969Quincey Koziol2020-01-041-3/+3
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* Added the map (H5M) APIDana Robinson2019-08-131-0/+6
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* Add support for GCC 7.x warnings, update warnhist script to account for them,Quincey Koziol2019-06-211-0/+1
| | | | clean up warnings.
* Added an H5MM_memcpy call that checks for buffer overlap.Dana Robinson2019-03-161-1/+1
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* Removed H5I_REFERENCE from the library. It has always been unusedDana Robinson2018-12-081-1/+0
| | | | and has been marked 'deprecated' since 1.10.0. Fixes HDFFV-10252.
* Squashed commit of private branch changes to support stackable VOL plugins.Quincey Koziol2018-10-251-17/+4
| | | | modified: test/dsets.c
* VOL FEATUREDana Robinson2018-10-101-0/+1
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* Remainder of vol_normalization changes (dataset, attribute, files, objects).Dana Robinson2018-09-241-1/+1
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* Normalization with vol_integration (property lists, file drivers,Dana Robinson2018-09-211-22/+24
| | | | other misc).
* 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
* Add API context interface and use it throughout the library.Quincey Koziol2018-03-151-12/+7
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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-r27768] Description:Quincey Koziol2015-09-141-6/+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-r24285] Eliminate several "passing argument ... with different width ↵Larry Knox2013-10-101-2/+2
| | | | | | due to prototype" warnings by casting constants to size_t where expected by string functions. Tested on jam, koala,ostrich and platypus with h5committest.
* [svn-r23713] Description:Quincey Koziol2013-05-211-7/+7
| | | | | | | | | | Clean up warnings, switch library code to use Standard C/POSIX wrapper macros, remove internal calls to API routines, update checkapi and checkposix scripts. Tested on: Mac OSX/64 10.8.3 (amazon) w/C++ & FORTRAN Big-Endian Linux/64 (ostrich)
* [svn-r23238] Description:Quincey Koziol2013-02-081-1/+1
| | | | | | | | | | | | | | | | | | | | | | Bring changes from Coverity branch to trunk: r20528: Purpose: Fix coverity issue 1372 Description: Rewrite file open secition of H5FD_stdio_open to avoid TOCTUO condition. No longer calls access, and uses a tentative open in "rb" or "rb+" mode to check for existence of the file. r20609: Use HDstrncpy and HDstrncat. --gh r20611: Use HDstrncpy. --gh Tested on: Mac OSX/64 10.8.2 (amazon) w/debug, C++ & FORTRAN (h5committest not required, already tested on branch)
* [svn-r23219] Description:Quincey Koziol2013-02-021-20/+33
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring reviewed changes from Coverity branch back to trunk (QK & JK): r20457: Coverity issue 691: return of H5duo could be negative. Fixed by using STDOUT_FILENO and redesign parse_command_line and main to cleanup file allocations. The output_file var is null when using stdout. In cleanup do not close output_file if NULL. r20510: Initialize ufid = -1 and predicate HDclose call on ufid != -1 r20511: Purpose: Fix coverity issue 1715 Description: Free "file" and nested data on failure in H5FD_core_open. r20512: Initialize ifid = -1 and predicate HDclose call on ifid != -1 r20514: Initialize h5fid = -1 and predicate HDclose call on h5fid != -1 r20516: Added else branch to the if (ret_value < 0) check. r20522: Addressed coverity issues 930-933, 850, 836, 835, 1307. All minor potential buffer overwrite bugs, or coverity errors. Fixed by replacing strcpy and sprintf with strncpy and snprintf. r20523: fixed coverity issues 68, 1120, 1116i r20524: Check H5Z_SZIP->encoder_present < 1 assuming 0 represents absence. r20601: Purpose: Fix coverity issues 1703-1705 Description: Modified the cleanup code in test_free in accum.c to reset allocated buffers to NULL after they are freed, and modified the error cleanup code to check if these buffers are NULL before freeing them. Also fixed some unrelated warnings in accum.c. r20602: Use HDsnprintf and HDstrncat r20603: Purpose: Fix coverity issues 808-809 Description: Modified test_core in vfd.c to check the returns from malloc, and keep track of whether points and check are allocated by setting them to NULL when they are not. Added code to free points and check on error if they are not NULL. Also fixed unrelated warnings in vfd.c. r20604: Use HDstrncpy. r20605: Use HDstrncpy and HDstrncat. r20606: Purpose: Fix coverity issue 807 Description: Modified long_compact in stab.c to keep track of whether objname is allocated by setting it to NULL when it is not. Added code to free objname on error if it is not NULL. r20607: Changed string function calls to use versions that specify the string length to fix coverity issues 832 and 839. Tested on: Mac OSX/64 10.8.2 (amazon) (Too minor to require h5committest)
* [svn-r22219] Description:Quincey Koziol2012-03-311-4/+7
| | | | | | | | Merge "file image" changes from feature branch back to trunk. Tested on: Mac OSX/64 10.7.3 (amazon) w/debug (h5committest upcoming)
* [svn-r21923] Description:Quincey Koziol2012-02-101-9/+107
| | | | | | | | | Add FUNC_ENTER macros for package-private routines and begin process of switching package routines to use them. All H5G routines are currently finished. Tested on: Mac OSX/64 10.7.3 (amazon) w/debug, production & parallel
* [svn-r21919] Description:Quincey Koziol2012-02-091-15/+15
| | | | | | | | 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-r21126] Description:Quincey Koziol2011-07-191-19/+53
| | | | | | | | | | | | | Clean up some compiler warnings, but mainly an interim checkin on the path of reducing code coupling in the library by removing most of the places which were accessing H5F package definitions. Tested on: Mac OS X/32 10.6.8 (amazon) w/debug FreeBSD/32 8.2 (loyalty) w/debug FreeBSD/64 8.2 (freedom) w/debug Linux/64 2.6 (heiwa) w/debug Linux/64 2.6 (ember) w/parallel
* [svn-r20885] Description:Quincey Koziol2011-05-201-2/+7
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r19398] Descriptino:Quincey Koziol2010-09-161-2/+2
| | | | | | | | | | | | | | | | | | | | | | | 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 Lu2010-09-091-2/+2
| | | | | | | 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-r19133] Description:Quincey Koziol2010-07-281-32/+40
| | | | | | | | | | | | | | | | | | | | | | | | | | | | Correct traversal of user-defined links (including external links) to retain path information of object, allowing H5Iget_name() queries to work quickly (without searching entire destination file). This required some refactoring and addition of a mechanism to detect if a "fast" query was performed (for the tests). Minor code cleanups, etc. 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-r18616] Description:Quincey Koziol2010-04-221-0/+19
| | | | | | | | Clean up compiler warnings. Tested on: Mac OS X/32 10.6.3 (amazon) w/debug (too minor to require h5committest)
* [svn-r16560] Description:Quincey Koziol2009-03-101-2/+0
| | | | | | | | | | 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-r16279] Description:Quincey Koziol2009-01-081-3/+1
| | | | | | | | | | | | | | 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-r15796] Purpose: Close bug #1322Neil Fortner2008-10-071-3/+3
| | | | | | | | | Description: Fixes a possible datatype id leak that could occur during compound datatype conversion, or more precisely, when unregistering those conversions. Datatype ids normally registered by the library are no longer visible to the application via H5Fget_obj_ids and H5Fget_obj_count. Tested: kagiso, linew, smirom (h5committest)
* [svn-r15628] Description:Quincey Koziol2008-09-161-8/+8
| | | | | | | | | | | | | 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-r15485] Purpose: Allow library to shut down properly when objects have ↵Neil Fortner2008-08-191-3/+3
| | | | | | | | | | | | | | | | 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-r15451] Purpose: Fix various problems that were occurring when using ↵Neil Fortner2008-08-071-6/+6
| | | | | | | | | | | | | | | | mounted files. Description: Moved mount table from top file structure to shared file structure. Moved parent out of mount table and back into top file structure. Mounted files can now be accessed from any handle of the parent file. Changes to how files are closed. Stricter cycle checking on mounted files. Removed unused function H5F_has_mount(). Tested: committest in 1.8 branch. Committing now due to the urgency of the fix. No changes here are specific to the trunk, but I will keep an eye on the daily tests.
* [svn-r15290] H5Tpack didn't act correctly with nested compound datatype. ↵Raymond Lu2008-06-271-1/+0
| | | | | | | | The new size of the type in the inner nest wasn't passed to the outer nest. This has been fixed. Tested on kagiso, linew, smirom.
* [svn-r15131] Description:Quincey Koziol2008-06-031-3/+0
| | | | | | | | | | | | | | | | | | | | | | Finish omnibus chunked dataset I/O refactoring, to separate general actions on chunked datasets from actions that are specific to using the v1 B-tree index. Cleaned up a few bugs and added some additional tests also. 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-r14973] Purpose: Fix bug in H5G_get_name_by_addr where buffer size is ↵Scott Wegner2008-05-121-1/+1
| | | | | | | | | | | less than size of name Description: In the new tests merged from the fortran_1_8 branch, there is a test that fetches a dataset name in a small buffer. The call to H5G_get_name_by_addr wrote an extra byte off the end of the buffer. A simple and sufficient fix is to decrease the buffer size passed to strncmp by 1. This bug was only caught by Visual Studio 2005 with extra debug checks on. Tested: VS2005 on WinXP kagiso
* [svn-r14284] Description:Quincey Koziol2007-11-241-188/+94
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Add H5Lvisit_by_name() API routine to library. Eliminated all (five!) other group traversal routines and changed them all to use the new API routine. Cleaned up output of h5ls & h5stat: - Issue error when requesting recursive traversal of a file with the "group info" flag, but no group given - Print info about root group in all(?) appropriate situations - Don't print "verbose" information about root group until the root group is in the list of objects to display (mostly because h5ls & h5stat had a different twist on traversing the groups in a file that the other utilities) 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 Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r14224] Description:Quincey Koziol2007-10-301-4/+7
| | | | | | | | | | | | | | | | | | | Change H5Literate -> H5Literate_by_name and add simpler form of H5Literate, to bring this routine into alignment with the other new API routines. 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-r14175] Description:Quincey Koziol2007-10-021-2/+8
| | | | | | | | Minor fixes to avoid memory leaks when 'realloc' fails. Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r14154] Description:Quincey Koziol2007-09-251-87/+92
| | | | | | | | | | | | | | | | | | | | Finish deprecating last H5G symbol (H5G_obj_t) - yay! Lots of misc. library fixes to remove confusion between links and objects. The tools could still use another pass, to remove h5trav_type_t type and make the correct distinction between links & objects. 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-r14122] Description:Quincey Koziol2007-08-281-1/+1
| | | | | | | | | | | | | Move H5Gmove() to deprecated code section, replacing with H5Lmove() in source files. Tested on: FreeBSD/32 6.2 (duty) FreeBSD/64 6.2 (liberty) Linux/32 2.6 (kagiso) Linux/64 2.6 (smirom) Solaris/32 5.10 (linew) Mac OS X/32 10.4.10 (amazon)
* [svn-r13986] Description:Quincey Koziol2007-07-171-1/+1
| | | | | | | | | Add flag to bypass (expensive) B-tree & heap size retrieval for internal calls to H5O_get_info(). Teted on: Mac OS X/32 10.4.10 (amazon) FreeBSD/32 6.2 (duty)
* [svn-r13814] Description:Quincey Koziol2007-05-291-2/+2
| | | | | | | | | | | | | | Change back to clearing memory buffers by default, but give users option to disable this, for performance reasons (--disable-clear-file-buffers). Also, add configure option (--enable-using-memchecker) to conveniently control making the library "play nice" with memory checking tools like valgrind and purify. Tested on: Mac OS X/32 10.4.9 (amazon) FreeBSD/32 6.2 (duty) Linux/32 2.6 (kagiso)
* [svn-r13704] Change to H5G_get_refobj_name so that H5I_get_name returns the ↵Christian Chilan2007-04-271-1/+1
| | | | length of the name of a dereferenced object without counting the null terminator. Tested on smirom, copper, and cobalt.
* [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.
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