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* [svn-r14863] Checking in code supporting metadata journaling in the serial case.John Mainzer2008-04-251-2/+3
| | | | | | | | | | | | | | | While this code doesn't break any of the existing tests, it HAS NOT been tested beyond that. Also mods needed to integrate the journaling code with Quincey's latest mods, and to adapt existing test code to slight changes caused by the addition of journaling. Finally, fixed an undefined variable bug in the HL code exposed by the journaling mods. Tested serial under Linux (Phoenix) and parallel under Linux (Kagiso).
* [svn-r14811] Description:Quincey Koziol2008-04-081-4/+4
| | | | | | | | | | Add "_META" suffix to FUNC_ENTER/FUNC_LEAVE API routines that can modify metadata in the file. This will give us a single place to change to recording the beginning & ending of transactions. Tested on: FreeBSD/32 6.2 (duty) Too simple to require h5committest
* [svn-r14796] Description:Quincey Koziol2008-04-051-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | Switch v1 B-tree nodes from using previous cache to use the new journaling cache code. This is a major switch for the cache callbacks. Switched the metadata caching code from having a pointer to the file it's in to receiving a pointer to the file, when needed. This was necessary in order to avoid crashing when two files IDs were open on the same underlying file and one of those files was closed with cache entries using the file pointers. Also took out the check in the caching code for reading off the end of the file, which didn't play nicely with the multi-file VFD. Switching the cache from having a pointer internally to requiring one externally meant tweaking almost all the test code. :-/ Added correct exit codes to cache2 tests that didn't have them already, so the 'make check' will stop when they fail. Use the path to the h5diff in this build in the tools/h5recover testing script, since we can't guarantee a user has HDF5 already installed. Assorted minor tweaks to get everything to compile more cleanly and pass all the tests (on my Mac :-). Tested on: Mac OS X (10.5.2) w/C++ (more testing coming up shortly, I just didn't have my "rsync testbed" set up for this branch when I started making changes to the code)
* [svn-r14224] Description:Quincey Koziol2007-10-301-1/+1
| | | | | | | | | | | | | | | | | | | 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-r13465] Description:Quincey Koziol2007-03-061-8/+4
| | | | | | | | | | | | Fix bug in external links when "strong" file close degree is used. Make external link callbacks use standard error reporting mechanisms. Other minor code cleanups... Tested on: Mac OS X/32 10.4.8 (amazon) FreeBSD/32 6.2 (duty)
* [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 Laird2006-12-181-8/+8
| | | | | | | | | 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-r12858] Description:Quincey Koziol2006-11-041-1/+1
| | | | | | | | Clean up code to build name for ID with no name tracked - get rid of global variable, unused routines, etc. Tested on: FreeBSD/32 4.11 (sleipnir)
* [svn-r12849] Purpose: FeatureLeon Arber2006-11-021-2/+1
| | | | | | | | Description: Add ability for H5Iget_name to figure out the path name given an object reference. Tested: kagiso, sol
* [svn-r12004] Purpose:Quincey Koziol2006-03-041-1/+0
| | | | | | | | | | | | | | | | | New feature & code cleanup Description: Update fractal heap to be able to insert objects into a direct block hanging off the header. Extract "octal dump" code into separate routine so that both the local heaps & fractal heaps can use it. Other code cleanups & support to get this far. Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4
* [svn-r11838] Purpose:Quincey Koziol2005-12-261-32/+12
| | | | | | | | | | | | | | | | 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 Koziol2005-11-151-106/+105
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r11245] Purpose:Quincey Koziol2005-08-131-40/+40
| | | | | | | | | | | | | | | | | | | | 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-r11093] Purpose:Quincey Koziol2005-07-211-31/+20
| | | | | | | | | | | | 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-r10216] James Laird2005-03-141-10/+15
| | | | | | | | | | | | | | | | Purpose: Bug fix Description: Calling H5Iobject_verify on an invalid type of ID (e.g., H5I_BADID) triggers an assert. Solution: Test for this condition and return an error instead of an assert. Added tests for this case. Platforms tested: sleipnir (minor change)
* [svn-r9857] Purpose: MaintenanceElena Pourmal2005-01-221-3/+0
| | | | | | | | | | | | | | Description: Removed PABLO from the source Solution: Platforms tested: arabica with 64-bit, copper with parallel, heping with GNU C and C++ and PGI fortran (but I disabled hl, there is some weird problem only on heping: F9XMODFLAG is not propagated to the Makefile files Misc. update:
* [svn-r9727] Purpose:Quincey Koziol2004-12-291-89/+86
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bug Fix/Code Cleanup/Doc Cleanup/Optimization/Branch Sync :-) Description: Generally speaking, this is the "signed->unsigned" change to selections. However, in the process of merging code back, things got stickier and stickier until I ended up doing a big "sync the two branches up" operation. So... I brought back all the "infrastructure" fixes from the development branch to the release branch (which I think were actually making some improvement in performance) as well as fixed several bugs which had been fixed in one branch, but not the other. I've also tagged the repository before making this checkin with the label "before_signed_unsigned_changes". Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel & fphdf5 FreeBSD 4.10 (sleipnir) w/threadsafe FreeBSD 4.10 (sleipnir) w/backward compatibility Solaris 2.7 (arabica) w/"purify options" Solaris 2.8 (sol) w/FORTRAN & C++ AIX 5.x (copper) w/parallel & FORTRAN IRIX64 6.5 (modi4) w/FORTRAN Linux 2.4 (heping) w/FORTRAN & C++ Misc. update:
* [svn-r9183] Purpose: New featureRaymond Lu2004-09-011-1/+1
| | | | | | | | | | | | Description: Restore 6 old error API functions back to the library to be backward compatible with v1.6. They are H5Epush, H5Eprint, H5Ewalk, H5Eclear, H5Eset_auto, H5Eget_auto. These functions do not have error stack as parameter. Solution: Internally, these functions use default error stack. Platforms tested: h5committest and fuss. Misc. update: RELEASE.txt
* [svn-r8800] Purpose:Quincey Koziol2004-07-031-5/+5
| | | | | | | | | | | | | Code cleanup Description: Fix problems when compiling with C++ compiler. Also clean up some warnings with gcc 3.4.x Platforms tested: FreeBSD 4.10 (sleipnir) Too minor to require h5committest
* [svn-r8767] Nat Furrer2004-06-301-1/+1
| | | | | | | | | | | | | | Purpose: Forgot to change H5Inmembers's return type in last commit... Description: Changed the number H5Inmembers returns by reference from int to hsize_t. Solution: Platforms tested: Misc. update:
* [svn-r8766] Nat Furrer2004-06-301-13/+67
| | | | | | | | | | | | | | | | | | | Purpose: Small H5I API changes. Description: Changed public version of H5Inmembers to return the number of IDs in a type by reference. This allows the user to differentiate between the case when H5Inmembers has an error and when the ID type is just empty. Added a new API function, H5Itype_exists, which allows the user to find out whether an ID type exists or not, without throwing an error. Solution: Platforms tested: Copper Misc. update:
* [svn-r8765] Purpose: New feature and its test.Raymond Lu2004-06-301-1/+3
| | | | | | | | | | | Description: Added new API H5Fget_name and new test program called filename.c. This function returns the name of the file by object ID(file, group, dataset, named datatype, and attribute) which belongs to the file. Platforms tested: h5committest and fuss. Misc. update: MANIFEST and RELEASE.txt
* [svn-r8732] Purpose:Quincey Koziol2004-06-231-2/+2
| | | | | | | | | | | | Code cleanup Description: Reduce compiler warnings on SGI IRIX Platforms tested: FreeBSD 4.10 (sleipnir) SGI IRIX6 (Cheryl's machine) Too minor to require full h5committest
* [svn-r8731] Purpose:Quincey Koziol2004-06-231-34/+48
| | | | | | | | | | | | | | | Code cleanup & minor optimization Description: Re-work the way interface initialization routines are specified in the library to avoid the overhead of checking for them in routines where there is no interface initialization routine. This cleans up warnings with gcc 3.4, reduces the library binary size a bit (about 2-3%) and should speedup the library's execution slightly. Platforms tested: FreeBSD 4.10 (sleipnir) w/gcc34 h5committest
* [svn-r8712] Fixed bugs in H5I codeJames Laird2004-06-211-1/+1
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* [svn-r8711] Fixed bugs in H5I code, updated manifest.James Laird2004-06-211-2/+1
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* [svn-r8707] Changed the way HDF5 handles hid_t's and added API functions to ↵James Laird2004-06-181-315/+943
| | | | allow users to register IDs and ID types at runtime.
* [svn-r8139] Purpose:Quincey Koziol2004-01-311-5/+4
| | | | | | | | | | Code cleanup Description: Clean up compiler warnings. Platforms tested: h5committested
* [svn-r8135] Purpose:Quincey Koziol2004-01-311-15/+11
| | | | | | | | | | | | Optimization Description: Speed up core ID lookup routine (H5I_find_id) by re-structuring the logic to reduce the number of 'if' statements. Platforms tested: IBM p690 (copper) too minor to require h5committest
* [svn-r7988] Purpose:Quincey Koziol2003-12-291-5/+4
| | | | | | | | | | | Bug fixes & code cleanup Description: Back out some of the debugging that was inadvertently checked in recently. Platforms tested: FreeBSD 4.9 (sleipnir) too minor to require h5committest
* [svn-r7984] Purpose: bug fixRaymond Lu2003-12-291-4/+5
| | | | | | | Description: VL datatype fails in certain way(hard to describe) Platforms tested: h5committest
* [svn-r7932] Purpose:Quincey Koziol2003-12-111-32/+201
| | | | | | | | | | | Add new feature Description: Add new H5I{dec|get|inc}_ref() routines and tests for them. Platforms tested: FreeBSD 4.9 (sleipnir) h5committest
* [svn-r7917] Purpose:Quincey Koziol2003-12-061-4/+4
| | | | | | | | | | | | | | | | | | | Code cleanup Description: Clean up compiler warnings, especially the 'FUNC' variable not used which comes out in production mode. Solution: Had to add a new FUNC_ENTER_NOAPI_NOINIT_NOFUNC macro for those non-API functions which don't need the 'FUNC' variable defined. (This will be _so_ much easier when C99 is standard on all our supposed platforms, since it has a __FUNC__ macro... ) Platforms tested: FreeBSD 4.9 (sleipnir) too minor for h5committest (although there were lots of files changed, the change was minor in each one)
* [svn-r7871] Purpose:Quincey Koziol2003-11-211-5/+3
| | | | | | | | | | | Code cleanup Description: Make some functions static and remove unused variables, etc. Platforms tested: FreeBSD 4.9 (sleipnir) too minor to require h5committest
* [svn-r7868] Purpose: new featureRaymond Lu2003-11-211-3/+5
| | | | | | | | | | Description: data type conversion between integers and float numbers. (Cover your ears. It's going to explode.:) Solution: covers all native type conversion. Mainly uses hardware conversion but handles overflow more gracefully. Platforms tested: h5committest
* [svn-r7803] Purpose:Quincey Koziol2003-10-311-1/+2
| | | | | | | | | | | | Minor code cleanup Description: Fixed up comments, made the H5I_get_file_id() routine static, removed H5Gprivate from including itself... Platforms tested: FreeBSD 4.9 (sleipnir) too minor to require h5committest
* [svn-r7801] Purpose: added featureRaymond Lu2003-10-311-6/+6
| | | | | | | | Description: more feature to H5Iget_file_id(). If file ID is closed, it can still return an ID given object ID. Platforms tested: h5committest
* [svn-r7786] Purpose:Quincey Koziol2003-10-291-18/+22
| | | | | | | | | | | | Code cleanup & add a feature Description: Added support for querying the file ID of named datatypes to new H5Iget_file_id function. Platforms tested: FreeBSD 4.9 (sleipnir) too minor to require h5committest
* [svn-r7784] *** empty log message ***Raymond Lu2003-10-291-0/+88
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* [svn-r7553] Purpose:Quincey Koziol2003-10-061-79/+15
| | | | | | | | | | | | | | | | | | | | | | | | | | | Improved algorithm (bug fix, sorta) Description: The internal algorithm for adding new IDs in the ID manager code (H5I) was adding new IDs to the front of the linked list and never adjusting the order of the items on the list (unless an ID was deleted). If many new objects were created, they would push earlier ones _way_ down the list (especially if the objects were being leaked in the application, as they appear to be in the current HDF-EOS5 library) and would cause O(n) search time for items on the list. The ID caching code in the ID manager was avoiding this behavior sometimes, but it was adding IDs that were looked up to the very tail of the cache and they would frequently leave the cache before helping. Solution: Implemented a "move to front" scheme for the linked list of IDs, which improves the lookup situation for frequently accessed objects. Removed ID caching code now, as the "move to front" algorithm actually works better. Platforms tested: FreeBSD 4.9 (sleipnir) too minor to require h5committest
* [svn-r7303] Purpose:Quincey Koziol2003-08-081-2/+4
| | | | | | | | | | | | | | Code cleanup Description: Chase new error API usage Protect against the current ID getting deleted during iteration over an ID group. Platforms tested: h5committested
* [svn-r7265] *** empty log message ***Raymond Lu2003-07-261-1/+1
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* [svn-r7186] Purpose:Quincey Koziol2003-07-091-8/+8
| | | | | | | | | | | Code cleanup Description: More tweaks to clean up warnings from lint. Platforms tested: FreeBSD 4.8 (sleipnir) not major enough to h5committest
* [svn-r7071] Purpose:Quincey Koziol2003-06-201-1/+1
| | | | | | | | | | | Code cleanup Description: Tweak internal iterator over IDs to not require constant "operator" data. Platforms tested: FreeBSD 4.8 (sleipnir) h5committest
* [svn-r6878] Purpose:Quincey Koziol2003-05-151-11/+70
| | | | | | | | | | | Code cleanup Description: Limit the scope on more function prototypes/macros/typedefs. Platforms tested: FreeBSD 4.8 (sleipnir) h5committest not necessary.
* [svn-r6433] Purpose:Quincey Koziol2003-02-241-15/+16
| | | | | | | | | | | | | | | Code/comment cleanup Description: Made more information about reference-counted strings private to the H5RS package by trimming the typedef used in H5RSprivate.h and switching from using macros for a couple of operations to using functions. Updated copyright information for a few of these files. Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)}
* [svn-r6266] Purpose:Quincey Koziol2003-01-101-19/+19
| | | | | | | | | | | | Code cleanup/new feature. Description: Split FUNC_LEAVE into API and non-API specific versions. This allows a solution to compiling this branch with C++, as well as reducing the size of the binaries produced. Platforms tested: FreeBSD 4.7 (sleipnir) w/serial, parallel (including MPE) & thread-safe
* [svn-r6252] Purpose:Quincey Koziol2003-01-091-5/+7
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
* [svn-r6131] Purpose:Quincey Koziol2002-11-211-1/+1
| | | | | | | | | | Code cleanup Description: Clean up compiler warnings from IRIX64 builds. Platforms tested: IRIX64 6.5 (modi4)
* [svn-r5995] Purpose:Quincey Koziol2002-10-141-3/+3
| | | | | | | | | | | | | | | Code cleanup/Bug Fix Description: Re-do the ID->name code again, taking into account many more weird and wonderful special cases stumbled across during the last set of test writing. Platforms tested: FreeBSD 4.6 (sleipnir) w and w/o parallel Linux 2.2.x (eirene) w/FORTRAN & C++ Solaris 2.7 (arabica) w/FORTRAN IRIX64 6.5 (modi4) w/FORTRAN & parallel
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