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* Develop clang 13 format (#1933)Allen Byrne2022-07-261-1/+1
| | | | | * Update format source to clang 13 * More format changes
* Fixed many -Wreserved-id-macro warnings by fixing header guard spelling (#361)Sean McBride2021-02-231-3/+3
| | | | | | | | | | | | | | | | * Fixed many -Wreserved-id-macro warnings by fixing header guard spelling Removed leading underscore(s) from header guard spelling. Used 2 regexes: ` _H5(.*)_H` ` __H5(.*)_H` Applied case-insensitively to only .h files. * Modified scripts that generate header files to not use underscore prefix Interestingly, there was already no leading underscore in the trailing comment at the end of the file * Fixed remaining -Wreserved-id-macro warning not caught by regex
* 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.
* Clang-format of source filesAllen Byrne2020-09-301-15/+14
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* Add API context interface and use it throughout the library.Quincey Koziol2018-03-151-1/+1
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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-r17313] Description:Quincey Koziol2009-08-101-1/+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-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-r12452] Purpose:James Laird2006-07-051-1/+1
| | | | | | | | | | | | | | | | | | | | | | Feature Description: Revised Link APIs. Solution: New link APIs use H5L* H5*create_expand do not create links to the objects created; this must be done manually with H5Llink. Added APIs to link an object given its ID (H5Llink), to copy links (H5Lcopy), and changed creation APIs (H5Lcreate_hard and H5Lcreate_soft) and query API (H5Lget_linkinfo instead of H5Gget_objinfo). All old APIs are still supported in H5Gdeprec.c . Platforms tested: sol, mir, copper Misc. update: Forgot to update MANIFEST and release docs. Will do after checkin.
* [svn-r11490] Purpose:Quincey Koziol2005-10-031-0/+5
| | | | | | | | | | | | | | | Bug fix Description: Fix "double root open" bug and apply same fix to datasets & named datatypes. Also fix bug in symbol table entry lookup code that would "transfer" an object from one file handle to another file handle when the two file handles were opened on the same actual file. Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r9596] Purpose:Quincey Koziol2004-11-291-1/+1
| | | | | | | | | | | | | Code optimization Description: Retarget metadata cache code from using TBBT routines to using new skiplist routines, for a reasonable speedup (when dealing with dirty metadata) Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel Solaris 2.7 (arabica) Too minor to require h5committest
* [svn-r9585] Purpose:Quincey Koziol2004-11-271-4/+4
| | | | | | | | | | | | | | Code optimization Description: Begin de-orbital burn of threaded, balanced binary tree code use by switching file open object code over to using them. Initial benchmarks show that skip lists are 5-10x faster than our TBBT code... Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel Solaris 2.7 (arabica) Too minor to require h5committest
* [svn-r9329] James Laird2004-09-281-2/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Purpose: Feature Description: Datatypes and groups now use H5FO "file object" code that was previously only used by datasets. These objects will hold a file open if the file is closed but they have not yet been closed. If these objects are unlinked then relinked, they will not be destroyed. If they are opened twice (even by two different names), both IDs will "see" changes made to the object using the other ID. When an object is opened using two different names (e.g., if a dataset was opened under one name, then mounted and opened under its new name), calling H5Iget_name() on a given hid_t will return the name used to open that hid_t, not the current name of the object (this is a feature, and a change from the previous behavior of datasets). Solution: Used H5FO code that was already in place for datasets. Broke H5D_t's, H5T_t's, and H5G_t's into a "shared" struct and a private struct. The shared structs (H5D_shared_t, etc.) hold the object's information and are used by all IDs that point to a given object in the file. The private structs are pointed to by the hid_t and contain the object's group entry information (including its name) and a pointer to the shared struct for that object. This changed the naming of structs throughout the library (e.g., datatype->size is now datatype->shared->size). I added an updated H5Tinit.c to windows.zip. Platforms tested: Visual Studio 7, sleipnir, arabica, verbena Misc. update:
* [svn-r8874] Purpose:Quincey Koziol2004-07-141-1/+2
| | | | | | | | | | | | | | | | | | | | Bug fix Description: Correct problems with "resurrecting" a dataset in a file. (This occurs when a dataset which is open gets unlinked from the group hierarchy (making it "dead" and marked for deletion in the file) and then is re-linked to the group hierarchy). Note that the current solution applies only to datasets, further work will fix this for groups and named datatypes also. Also, fix the "debug" routines to be a little more helpful in certain situations. Additionally, fix a locking bug in the symbol table node splitting routine which could be [one of] the cause[s] of the file corruption in flexible parallel operation. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel h5committested
* [svn-r7428] Purpose:Quincey Koziol2003-08-281-3/+3
| | | | | | | | | | | Code cleanup Description: De-linted more code Platforms tested: FreeBSD 4.8 (sleipnir) too minor to need h5committest
* [svn-r6652] Purpose:Quincey Koziol2003-04-141-1/+2
| | | | | | | | | | | | | | | | New feature. Description: Update prototypes for recent internal API addition. Platforms tested: FreeBSD 4.8 (sleipnir) w/C++ Linux 2.4 (burrwhite) w/FORTRAN Solaris 2.7 (arabica) w/FORTRAN IRIX64 6.5 (modi4) w/parallel & FORTRAN (h5committest not run due to my ongoing difficulties with C++ on burrwhite).
* [svn-r6546] Purpose:Bill Wendling2003-03-311-11/+13
| | | | | | | | | | | | Update Description: Updated copyright statement in files which hadn't been updated yet. Platforms tested: Linux (Only comment change) Misc. update:
* [svn-r6252] Purpose:Quincey Koziol2003-01-091-0/+42
Lots of performance improvements & a couple new internal API interfaces. Description: Performance Improvements: - Cached file offset & length sizes in shared file struct, to avoid constantly looking them up in the FCPL. - Generic property improvements: - Added "revision" number to generic property classes to speed up comparisons. - Changed method of storing properties from using a hash-table to the TBBT routines in the library. - Share the propery names between classes and the lists derived from them. - Removed redundant 'def_value' buffer from each property. - Switching code to use a "copy on write" strategy for properties in each list, where the properties in each list are shared with the properties in the class, until a property's value is changed in a list. - Fixed error in layout code which was allocating too many buffers. - Redefined public macros of the form (H5open()/H5check, <variable>) internally to only be (<variable>), avoiding innumerable useless calls to H5open() and H5check_version(). - Reuse already zeroed buffers in H5F_contig_fill instead of constantly re-zeroing them. - Don't write fill values if writing entire dataset. - Use gettimeofday() system call instead of time() system when checking the modification time of a dataset. - Added reference counted string API and use it for tracking the names of objects opening in a file (for the ID->name code). - Removed redundant H5P_get() calls in B-tree routines. - Redefine H5T datatype macros internally to the library, to avoid calling H5check redundantly. - Keep dataspace information for dataset locally instead of reading from disk each time. Added new module to track open objects in a file, to allow this (which will be useful eventually for some FPH5 metadata caching issues). - Remove H5AC_find macro which was inlining metadata cache lookups, and call function instead. - Remove redundant memset() calls from H5G_namei() routine. - Remove redundant checking of object type when locating objects in metadata cache and rely on the address only. - Create default dataset object to use when default dataset creation property list is used to create datasets, bypassing querying for all the property list values. - Use default I/O vector size when performing raw data with the default dataset transfer property list, instead of querying for I/O vector size. - Remove H5P_DEFAULT internally to the library, replacing it with more specific default property list based on the type of property list needed. - Remove redundant memset() calls in object header message (H5O*) routines. - Remove redunant memset() calls in data I/O routines. - Split free-list allocation routines into malloc() and calloc()- like routines, instead of one combined routine. - Remove lots of indirection in H5O*() routines. - Simplify metadata cache entry comparison routine (used when flushing entire cache out). - Only enable metadata cache statistics when H5AC_DEBUG is turned on, instead of always tracking them. - Simplify address comparison macro (H5F_addr_eq). - Remove redundant metadata cache entry protections during dataset creation by protecting the object header once and making all the modifications necessary for the dataset creation before unprotecting it. - Reduce # of "number of element in extent" computations performed by computing and storing the value during dataspace creation. - Simplify checking for group location's file information, when file has not been involving in file-mounting operations. - Use binary encoding for modification time, instead of ASCII. - Hoist H5HL_peek calls (to get information in a local heap) out of loops in many group routine. - Use static variable for iterators of selections, instead of dynamically allocation them each time. - Lookup & insert new entries in one step, avoiding traversing group's B-tree twice. - Fixed memory leak in H5Gget_objname_idx() routine (tangential to performance improvements, but fixed along the way). - Use free-list for reference counted strings. - Don't bother copying object names into cached group entries, since they are re-created when an object is opened. The benchmark I used to measure these results created several thousand small (2K) datasets in a file and wrote out the data for them. This is Elena's "regular.c" benchmark. These changes resulted in approximately ~4.3x speedup of the development branch when compared to the previous code in the development branch and ~1.4x speedup compared to the release branch. Additionally, these changes reduce the total memory used (code and data) by the development branch by ~800KB, bringing the development branch back into the same ballpark as the release branch. I'll send out a more detailed description of the benchmark results as a followup note. New internal API routines: Added "reference counted strings" API for tracking strings that get used by multiple owners without duplicating the strings. Added "ternary search tree" API for text->object mappings. Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)} Other platforms/configurations tested? FreeBSD 4.7 (sleipnir) serial & parallel Solaris 2.6 (baldric) serial