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* [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-r13139] Fixed the MULTI problem (Bug #731) that corrupted the data. ↵Raymond Lu2007-01-121-4/+10
| | | | | | | The problem came from the EOA for the whole MULTI file. It's taken out because it's meaningless for MULTI file. Instead, each individual file has its EOA.
* [svn-r13125] Description:Quincey Koziol2007-01-091-2/+4
| | | | | | | Add extra protection for sanity checks, when assertions are enabled. Tested on: Linux/32 2.6 (chicago)
* [svn-r13068] Ran bin/reconfigure. Some of the scripts have been changed or ↵James Laird2006-12-181-1/+1
| | | | | | | | | 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-r12803] Description:Quincey Koziol2006-10-231-1/+1
| | | | | | | | | | | | | | Finish new version of the I/O pipeline message, which is much smaller than the previous version. This version is used with the "use the latest version of the format" flag. Closed several memory leaks/overruns (found with valgrind). Also, lots of compiler & formatting cleanups. Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r12706] Description:Quincey Koziol2006-10-021-3/+3
| | | | | | | | | Clean up some of the warnings on 64-bit Linux... Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2) Too minor to require h5committest
* [svn-r11886] Purpose:Quincey Koziol2006-01-231-2/+2
| | | | | | | | | | | | | Code cleanup Description: Check in some of the code cleanups from working on the external link support. (This doesn't include any of the external link features) Platforms tested: FreeBSD 4.11 (sleipnir) Mac OSX.4 (amazon) Linux 2.4
* [svn-r11245] Purpose:Quincey Koziol2005-08-131-26/+26
| | | | | | | | | | | | | | | | | | | | 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-r10628] Purpose:Quincey Koziol2005-04-181-6/+6
| | | | | | | | | | | Code cleanup Description: Clean up various warnings reported by the Windows team. Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [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 Koziol2004-12-291-5/+5
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r9654] Purpose:Raymond Lu2004-12-101-1/+1
| | | | | | | | | | | | | Description: In file H5FDsec2.c and H5FDlog.c, there's statements like H5_ASSIGN_OVERFLOW(file->eof,sb.st_size,off_t,haddr_t); It assumes sb.st_size from h5_stat_t is of type off_t. But on Windows, it has type __int64. So the H5_ASSIGN_OVERFLOW statement may cause problem. Instead of trying to do switch between Windows and other systems in H5FDsec2.c and H5FDlog.c, define a substituting type in H5private.h to fix the problem. On Windows, this type is __int64; on other systems, it is off_t. Platforms tested: fuss. Simple fix. Already did h5committest for v1.6.
* [svn-r8731] Purpose:Quincey Koziol2004-06-231-3/+24
| | | | | | | | | | | | | | | 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-r8287] Purpose:Quincey Koziol2004-03-301-1/+1
| | | | | | | | | | | | | | Bug fix/code cleanup Description: Copy Robb's feature in SSlib that checks that the name of the function used in the FUNC_ENTER macro is actually the name of function. Fixed a bunch of typos & copy-n-pasto's for functions with incorrect names. Platforms tested: FreeBSD 4.9 (sleipnir) w/parallel too minor to require h5committest
* [svn-r8134] Purpose:Quincey Koziol2004-01-311-1/+27
| | | | | | | | | | | | | | | | Code cleanup Description: Add destructor to match constructor fr VFLs when they are shut down by the library. Solution: Added H5FD_*_term() routines to "undo" changes made in H5FD_*_init() routines. Platforms tested: IBM p690 (copper) too minor to require h5committest
* [svn-r8126] Purpose:Quincey Koziol2004-01-311-1/+1
| | | | | | | | | | | | | | | | | Bug fix/optimization Description: Address slowdown in MPI-I/O file metadata operations that was introduced mid-stream. We now _require_ a POSIX compliant parallel file system for the MPI-I/O file driver (as well as for the MPI-POSIX file driver). Also optimized file open operation when the file is being created by reducing the number of collective & syncronizing calls. Additionally, refactor the MPI routines into a common place, eliminating duplicated code. Platforms tested: FreeBSD 4.9 (sleipnir) w/parallel h5committest
* [svn-r7398] Purpose:Quincey Koziol2003-08-251-0/+4
| | | | | | | | | | | Code cleanup Description: De-linted more code Platforms tested: FreeBSD 4.8 (sleipnir) too minor to require h5committest
* [svn-r7387] Purpose:Quincey Koziol2003-08-211-84/+91
| | | | | | | | | | | Code cleanup Description: More de-linting Platforms tested: FreeBSD 4.8 (sleipnir) too small to need h5committest
* [svn-r7181] Purpose:Quincey Koziol2003-07-071-49/+0
| | | | | | | | | | | Version update Description: Removed 1.4 compatibility code in the library. Platforms tested: FreeBSD 4.8 (sleipnir) h5committest
* [svn-r6598] Purpose:Pedro Vicente Nunes2003-04-081-2/+2
| | | | | | | | | | | | | | | | | code warrior port Description: added some type casts (char*) for CW portability Solution: Platforms tested: w2000(CW , MS) linux arabica modi4 Misc. update:
* [svn-r6501] Purpose:Bill Wendling2003-03-191-4/+17
| | | | | | | | | | | | | | New Feature Description: Added support for the lock and unlock function calls for file drivers. Only FPHDF5 uses this feature. All of these drivers don't define lock or unlock methods. Platforms tested: Linux, Modi4, Sol Misc. update:
* [svn-r6398] Purpose:Quincey Koziol2003-02-121-2/+2
| | | | | | | | | | Code cleanup Description: Clean up some compiler warnings Platforms tested: FreeBSD 4.7 (sleipnir)
* [svn-r6387] Purpose:Quincey Koziol2003-02-101-7/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | Bug Fix Description: Metadata cache in parallel I/O can cause hangs in applications which perform independent I/O on chunked datasets, because the metadata cache can attempt to flush out dirty metadata from only a single process, instead of collectively from all processes. Solution: Pass a dataset transfer property list down from every API function which could possibly trigger metadata I/O. Then, split the metadata cache into two sets of entries to allow dirty metadata to be set aside when a hash table collision occurs during independent I/O. Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)} FreeBSD 4.7 (sleipnir) serial & parallel Misc. update: Updated release_docs/RELEASE
* [svn-r6266] Purpose:Quincey Koziol2003-01-101-18/+18
| | | | | | | | | | | | 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 Koziol2003-01-091-3/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r5951] Raymond Lu2002-09-301-0/+34
| | | | | | | | | | | Purpose: New API functions Description: Added API functions to return pointer to low-level file handle (H5Fget_vfd_handle and H5FDget_vfd_handle) and related property list setting functions(H5Pset_family_offset and H5Pset_multi_type). Platforms tested: Linux 2.2(eirene), Solaris 2.7(arabica), IRIX64 6.5(modi4)
* [svn-r5918] Purpose:Quincey Koziol2002-09-111-1/+1
| | | | | | | | | | | | Bug fix. Description/Solution: Fix bug in log file driver where the size of the buffer for recording the log information was being set incorrectly. Platforms tested: FreeBSD 4.6 (sleipnir) - no additional testing on other machines neceessary, due to scope of fix.
* [svn-r5871] Purpose:Quincey Koziol2002-08-121-3/+3
| | | | | | | | | | | | | | | | Code cleanup Description: Combined H5P_isa_class and H5I_object functionality into a new internal H5P API function: H5P_object_verify, which checks that a property list is the appropriate class and then returns the property list object associated with the property list ID. This reduces the source code by about 200 LOC and trims the library binary some more. Platforms tested: FreeBSD 4.6 (sleipnir)
* [svn-r5867] Purpose:Quincey Koziol2002-08-091-7/+38
| | | | | | | | | | | | | Code cleanup Description: Changed the last HRETURN* statements in the FUNC_ENTER macros into HGOTO* macros, which reduces the size of the library binary in certain configurations by another 10% Platforms tested: FreeBSD 4.6 (sleipnir) serial & parallel, IRIX64 6.5 (modi4) serial & parallel
* [svn-r5842] Purpose:Quincey Koziol2002-08-081-48/+71
| | | | | | | | | | | | | | | | Code cleanup Description: Change most (all?) HRETURN_ERROR macros to HGOTO_ERROR macros, along with HRETURN macros to HGOTO_DONE macros. This unifies the error return path from functions and reduces the size of the library by up to 10% on some platforms. Additionally, I improved a lot of the error cleanup code in many routines. Platforms tested: FreeBSD 4.6 (sleipnir) serial & parallel and IRIX64 6.5 (modi4) serial & parallel.
* [svn-r5536] Purpose:Quincey Koziol2002-06-051-0/+1
| | | | | | | | | | | | | | | | | New feature. Description: Added a "small data" block allocation mechanism to the library, similar to the mechanism used for allocating metadata currently. See the RFC for more details: http://hdf.ncsa.uiuc.edu/RFC/SmallData/SmallData.html This reduces the number of I/O operations which hit the disk for my test program from 19 to 15 (i.e. from 393 to 15, overall). Platforms tested: Solaris 2.7 (arabica) w/FORTRAN and FreeBSD 4.5 (sleipnir) w/C++
* [svn-r5471] Purpose:Quincey Koziol2002-05-291-17/+17
| | | | | | | | | | | | | | | | Code cleanup Description: Broke the FUNC_ENTER macro into several macros, with more specialized uses (which followup mail will describe). This was designed to move most/all of the checks which could be done at compile time to that point, instead of needlessly performing them (over & over :-) at run-time. This reduces the library's size (and thus staticly linked binaries) and has a minor speedup effect also. Platforms tested: IRIX64 6.5 (modi4) with parallel & FORTRAN enabled, and additional testing on FreeBSD and Solaris immediately after the checkin.
* [svn-r5440] Purpose:Quincey Koziol2002-05-201-3/+3
| | | | | | | | | | | New feature Description: Add 'closing' parameter to H5FDflush and VFL "flush" functions, per http://hdf.ncsa.uiuc.edu/RFC/VFLFlush/VFLFlush.html Platforms tested: IRIX64 6.5 (modi4)
* [svn-r5436] Pedro Vicente Nunes2002-05-181-1/+0
| | | | | | | | | Purpose: code clean up Description: removed some debugging comments regading the code warrior port Platforms tested: w2000
* [svn-r5422] Description:Albert Cheng2002-05-141-1/+1
| | | | | | | Corrected typos in the FUNC_ENTER macros of H5FD_sec2_flush and H5FD_log_flush. Platforms tested: modi4 (just tested it compiled fine.)
* [svn-r5403] Purpose:Quincey Koziol2002-05-131-3/+3
| | | | | | | | | | Back out changes. Description: Back out changes to VFL 'flush' API function, pending review. Platforms tested: IRIX64 6.5 (modi4)
* [svn-r5393] Purpose:Quincey Koziol2002-05-101-3/+3
| | | | | | | | | | | | | | | | | | | | | | New Feature Description: The VFL flush function is called immediately before a file is closed. This can cause duplicate syncronization actions to occur, if the VFL close function also performs them. Solution: Added 'closing' parameter to VFL 'flush' operation. This allows the VFL flush function to bypass operations that will be duplicated within the VFL close function. Additionally, use the 'closing' parameter to bypass calls to MPI_File_sync() when set. Since MPI_File_close() also syncronizes the file, this avoids the terrible performance hit taken when calling MPI_File_sync() as the file is closing. Platforms tested: IRIX64 6.5 (modi4)
* [svn-r5261] Purpose:Quincey Koziol2002-04-251-3/+0
| | | | | | | | | | Code cleanup Description: Remove more debugging printf's that were ifdef'd out. Platforms tested: FreeBSD 4.5 (sleipnir)
* [svn-r5219] Purpose:Quincey Koziol2002-04-221-1/+1
| | | | | | | | | | Code cleanup Description: Clean up warnings from gcc 3.1 Platforms tested: FreeBSD 4.5 (sleipnir)
* [svn-r5205] Purpose:Albert Cheng2002-04-191-3/+1
| | | | | | | | | | | | | | Code cleanup Description: Platform dependent code related to the struct stat and fstat calls polluted source codes. Hard to maintain. Solution: Platform dependent code are moved to H5private.h and then internal code can #include H5private.h. Repeat those macro definition for the stdio and multi drivers since they area examples for writing a virtual file driver. They must not use any internal code. Platforms tested: eirene (parallel), modi4 (serial including gass driver.)
* [svn-r5101] MuQun Yang2002-03-271-1/+3
| | | | | | | | | | | | | | | Purpose: fix a windows bug Description: 1. To create a >4GB file, fstati64 has to be used instead of fstat. change fstat to fstati64 for WIN32 macroes. Some discussions are going on the general issue on how to better handle with WIN32 or other similar platform. This check-in is just a reminder not to forget the windows bug. 2. erase a WIN32 macro(include winsock2.h) at h5detect.c. It is not a problem now. Solution: use fstati64 instead of fstat for win32. Platforms tested: windows2000(confirmed at linux machine eirene)
* [svn-r4696] Raymond Lu2001-12-111-0/+1
| | | | | | | | | | | | | | | | | Purpose: Modify H5Fclose behavior Description: The HDF5 actual file close behaves in several ways in terms of if there are still objects(dataset, group, datatype) opened in file. Solution: Added a new file access property, file close degree. It has four values, H5F_CLOSE_DEFAULT H5F_CLOSE_WEAK H5F_CLOSE_SEMI H5F_CLOSE_STRONG The way a file is closed is decided by these values. Platforms tested: IRIX64 6.5, SunOS 5.6, FreeBSD 4.4
* [svn-r4679] Snapshot version 1.5 release 16Albert Cheng2001-12-061-1/+1
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* [svn-r4673] Purpose:Quincey Koziol2001-12-051-0/+48
| | | | | | | | | | | | | | Backward Compatibility Fix Description: H5Pset_fapl_log's parameters have changed from a simple "verbosity" level to bit-masked flags to enable various behaviors. Solution: Added in v1.4 compat stuff, on the unlikely chance that others are actually using this code in some production way. There are no C++ or FORTRAN wrappers for this call. Platforms tested: FreeBSD 4.4 (hawkwind)
* [svn-r4666] Purpose:Quincey Koziol2001-12-041-3/+5
| | | | | | | | | | | Bug fix Description: Missing a statement for an else branch when HAVE_GETTIMEOFDAY was defined, which caused most machines to fail compiling. Solution: Re-arranged if/else statement to eliminate problem. Platforms tested: FreeBSD 4.4 (sleipnir)
* [svn-r4665] Purpose:Quincey Koziol2001-12-031-112/+161
| | | | | | | | | Code cleanup Description: Changed the logging file driver to use bitmasked flags for features to enable, instead of using a verbosity level. Platforms tested: Solaris 2.6 (baldric)
* [svn-r4643] Purpose:Quincey Koziol2001-11-271-1/+1
| | | | | | | | | | | | | | | | | | | | | | Code cleanup Description: Windows is generating hundreds of warnings from some of the practices in the library. Mostly, they are because size_t is 32-bit and hsize_t is 64-bit on Windows and we were carelessly casting the larger values down to the smaller ones without checking for overflow. Also, some other small code cleanups,etc. Solution: Re-worked some algorithms to eliminate the casts and also added more overflow checking for assignments and function parameters which needed casts. Kent did most of the work, I just went over his changes and fit them into the the library code a bit better. Platforms tested: FreeBSD 4.4 (hawkwind)
* [svn-r4620] Purpose:Quincey Koziol2001-11-201-11/+12
| | | | | | | | | Code cleanup Description: Get rid of IDs from internal function calls and some small cleanups from the old-stype => generic property list conversion. Platforms tested: FreeBSD 4.4 (hawkwind)
* [svn-r4589] Purpose:Quincey Koziol2001-11-031-2/+3
| | | | | | | | Code cleanup Description: Clean up various compiler warnings from generic property updates. Platforms tested: FreeBSD 4.4 (hawkwind)
* [svn-r4572] Raymond Lu2001-10-251-2/+8
| | | | | | | Purpose: Followup file access property list changes. Platforms tested: IRIX64, SunOS 5.7, FreeBSD.
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