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* Change copyright headers to replace url referring to file to be removedlrknox2017-04-061-6/+4
| | | | | | | | and replace it with new url for COPYING file. Fix 2 lines in java error test expected output file where messages include line numbers changed by reducing the copyright header by 2 lines.
* Bring changes to I/O parameters from page_buffering branch.Quincey Koziol2017-03-131-5/+5
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* Tentative fix for valgrind issues related to EoC.Dana Robinson2016-11-261-2/+2
| | | | | | | | | 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.
* [svn-r29081] - merge in the phdf5_metadata_opt/ branch with the collective ↵Mohamad Chaarawi2016-02-101-2/+2
| | | | | | | | 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-r27768] Description:Quincey Koziol2015-09-141-27/+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-r27133] - Add a new attribute function characterstic for format:Mohamad Chaarawi2015-06-011-1/+1
| | | | | | | | * 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-r21919] Description:Quincey Koziol2012-02-091-16/+13
| | | | | | | | 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 Koziol2011-07-191-0/+80
| | | | | | | | | | | | | 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-r20219] Description:Quincey Koziol2011-03-101-1/+1
| | | | | | | | | | | | | | | | | Tell the VFL flush call that the file will be closing, allowing the VFDs to avoid sync'ing the file (particularly valuable in parallel). 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-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
* [svn-r18702] Description:Quincey Koziol2010-05-051-0/+1
| | | | | | | | | | | | | | | | | | | | | | | Bring r18672 from metadata journaling "merging" branch to trunk: Mostly changes to move to only using one 'user data' parameter for calls to H5AC_protect(), along with some minor reformatting code cleanups. 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-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode Mac OS X/32 10.6.3 (amazon) in debug mode Mac OS X/32 10.6.3 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r17413] Description:Quincey Koziol2009-08-241-1/+1
| | | | | | | | | | | | | | | | | | | | | | | Remove vestigial intermediate routine for flushing file and move it into API routine. Also, remove private, unused (now) 'H5F_FLUSH_DOWN' symbol from public header file. 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-r17412] Description:Quincey Koziol2009-08-241-1/+1
| | | | | | | | | | | | | | | | | | | | | | Seperate 'flush' functionality from 'destroy' functionality at the H5F level also. 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-r17408] Description:Quincey Koziol2009-08-211-0/+77
| | | | | | | | | | | | | | | | | | | | | Move flush operation on mounted file hierarchy into H5Fmount module. 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-r16279] Description:Quincey Koziol2009-01-081-4/+4
| | | | | | | | | | | | | | 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-r16082] Purpose: Fix a problem in the file unmounting codeNeil Fortner2008-11-171-5/+13
| | | | | | | | | Description: Fixes a problem in H5F_close_mounts where it wouldn't correctly reshape the "child" array when unmounting files. Test added for this case. Also fixed a potential bug in H5F_unmount where that routine reshapes the child array. Tested: kagiso linew smirom (h5committest)
* [svn-r15628] Description:Quincey Koziol2008-09-161-1/+1
| | | | | | | | | | | | | 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-r15510] Description:Quincey Koziol2008-08-211-4/+4
| | | | | | | | Clean up warnings & formatting Tested on: Mac OS X/32 10.5.4 (amazon) More tests forthcoming
* [svn-r15451] Purpose: Fix various problems that were occurring when using ↵Neil Fortner2008-08-071-82/+64
| | | | | | | | | | | | | | | | 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-r15367] Description:Quincey Koziol2008-07-151-1/+5
| | | | | | | | | | | | | | | | Add check to avoid mounting the a file on a group twice, then the mounts are done on the same HDF5 file, but opened with separate H5Fopen calls. Also add new 'mounted' flag to the H5G_info_t struct, queried with the H5Gget_info() API call, to allow applications to detect and avoid this situation. This probably fixes Bz#1070 also, I'll check with Dan Anov (who reported a different sort of behavior, but seems to have the same underlying problem). Tested on: Mac OS X/32 10.5.4 (amazon) Linux/64 2.6 (chicago)
* [svn-r14154] Description:Quincey Koziol2007-09-251-7/+9
| | | | | | | | | | | | | | | | | | | | 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-r13475] There's a configure issue linking szip's shared libraries when ↵Mike McGreevy2007-03-081-2/+2
| | | | | | | | | | | | running on kagiso. The static szip libraries are working as intended, but when shared szip libraries are present and intended for use they cannot be opened. A check has been implemented to test if shared szip libraries are functional on current platform. If they are not, and the user is trying to use them, szip is now disbaled and the user is informed. This issue occurs on kagiso, and the resolution was tested on kagiso.
* [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-r13068] Ran bin/reconfigure. Some of the scripts have been changed or ↵James Laird2006-12-181-2/+2
| | | | | | | | | haven't been run in a while, so many of the source files were updated with tracing macros, etc. No code changes by me. Tested on kagiso and smirom.
* [svn-r12907] Description:Quincey Koziol2006-11-141-5/+7
| | | | | | | | | Finish refactoring internal link deletion code, to make it possible to wrap up the H5Ldelete_by_idx() coding. Tested on: Linxu/32 2.6 (chicago) Linxu/64 2.6 (chicago2)
* [svn-r12866] Description:Quincey Koziol2006-11-061-1/+1
| | | | | | | Clean up initialization of H5F & H5L APIs. Tested on: Linux/64 2.6 (chicago2)
* [svn-r12842] Description:Quincey Koziol2006-11-021-3/+3
| | | | | | | | | | | | | | | | Refactor generic property list initialization code to put property list specific routines in property list modules, instead of scattered to the four winds. Also, introduce property list class initialization objects, to make adding new property list classes in the library easier. Fix daily test failure by using H5Pget_elink_prefix() API routine instead of looking at the "raw" generic property list information. Tested on: Mac OS X/32 10.4.8 (amazon) FreeBSD/32 4.11 (sleipnir) w/threadsafe Linux/32 2.4 (heping) w/C++ & FORTRAN Linux/64 2.4 (mir) w/build-all & 1.6 compat
* [svn-r12596] Refactored how external files are opened and closed.James Laird2006-08-181-3/+19
| | | | | | | | Object header locations (H5O_loc_t's) can now "hold open" a file and decrement its open object count when they close. This means that locations (H5O_loc_t's and H5G_loc_t's) should always be freed. Added more thorough tests to ensure that external files are closed.
* [svn-r12528] Added User-Defined links to the library.James Laird2006-08-021-2/+2
| | | | | | | | | | | | | | Users can create external links using H5L_create_external(). These links point to an object in another HDF5 file. Users can alter the behavior of external links or create new kinds of links by registering callbacks using the H5L interface. Added tests, tools support, etc. Also a number of other, minor changes have been made (some restructuring of the H5L interface, for instance). Additional documentation and examples are forthcoming.
* [svn-r11838] Purpose:Quincey Koziol2005-12-261-17/+33
| | | | | | | | | | | | | | | | Bug fix Description: Retrieving an object's name could fail (in various ways) under certain circumstances (mostly having to do with mounted files). Solution: Re-write & simplify "get object name" code to fix error in a better way than adding yet another hack to the previous pile of hacks... :-) Platforms tested: FreeBSD 4.11 (sleipnir) h5committest
* [svn-r11712] Purpose:Quincey Koziol2005-11-151-217/+128
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | New feature Description: Check in baseline for compact group revisions, which radically revises the source code for managing groups and object headers. WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! This initiates the "unstable" phase of the 1.7.x branch, leading up to the 1.8.0 release. Please test this code, but do _NOT_ keep files created with it - the format will change again before the release and you will not be able to read your old files!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! Solution: There's too many changes to really describe them all, but some of them include: - Stop abusing the H5G_entry_t structure and split it into two separate structures for non-symbol table node use within the library: H5O_loc_t for object locations in a file and H5G_name_t to store the path to an opened object. H5G_entry_t is now only used for storing symbol table entries on disk. - Retire H5G_namei() in favor of a more general mechanism for traversing group paths and issuing callbacks on objects located. This gets us out of the business of hacking H5G_namei() for new features, generally. - Revised H5O* routines to take a H5O_loc_t instead of H5G_entry_t - Lots more... Platforms tested: h5committested and maybe another dozen configurations.... :-)
* [svn-r11386] Purpose:Quincey Koziol2005-09-121-2/+2
| | | | | | | | | | | | | | Code cleanup/reorganization Description: Merge back some more changes extracted from the "compact group" set. This bunch cleans up and prepares the H5G_* routines for eventual import of new features. Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4 Mac OS X.4
* [svn-r11245] Purpose:Quincey Koziol2005-08-131-17/+17
| | | | | | | | | | | | | | | | | | | | Code cleanup Description: Trim trailing whitespace, which is making 'diff'ing the two branches difficult. Solution: Ran this script in each directory: foreach f (*.[ch] *.cpp) sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f end Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r11215] Purpose:Quincey Koziol2005-08-081-42/+47
| | | | | | | | | | | | | Bug fix & code cleanup Description: Fix another bug in the file mounting code and refactor the unmount code that it is simpler. Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4 Too minor to require h5committest
* [svn-r11093] Purpose:Quincey Koziol2005-07-211-112/+74
| | | | | | | | | | | | Bug fix Description: Rewrite code for mounting files to clean up layers of kludges and implement a much cleaner and more maintainable design. Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4
* [svn-r11077] Purpose:Quincey Koziol2005-07-161-5/+12
| | | | | | | | | | | | Bug fix Description: Further progress on fixing file mounting to work properly. Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4 Too minor to require h5committest
* [svn-r11022] Purpose:Quincey Koziol2005-07-051-0/+713
Bug fix & code cleanup Description: Don't unmount child files from a parent file if the parent file is being held open by an object. Also, moved the mounting routines into their own source file and the superblock routines into their own file also. Solution: Moved the code for unmounting child files down in the H5F_close routine and also add checks to the file and group mounting code to unmount child files when the last object holding open a file closes. Platforms tested: FreeBSD 4.11 (sleipnir) h5committest
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