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* [svn-r6519] Purpose:Quincey Koziol2003-03-221-2/+6
| | | | | | | | | | | | | Bug fix/code cleanup/new feature Description: Fix h5debug to work correctly again, with all the changes over the past few months. Improved and cleaned up debugging output available in h5debug. Platforms tested: FreeBSD 4.7 (sleipnir)
* [svn-r6497] Purpose:Quincey Koziol2003-03-191-1/+1
| | | | | | | | | | | | | | | | | | | Finish code cleanup Description: Wrap up the conversion of H5F_flush's multiple boolean flags into a single bitfield of flags by pushing the flags down into the H5AC_flush and H5F_istore_flush routines. Also, changed the flags from H5_FLUSH_<foo> to H5F_FLUSH_<foo> to be more consistent with rest of library. And reverted the changes to H5FDflush and H5FD_flush routines. Platforms tested: FreeBSD 4.7 (sleipnir) Solaris 5.8 (sol) IRIX64 6.5 (modi4) w/parallel Misc. update:
* [svn-r6452] Purpose:Quincey Koziol2003-03-031-3/+17
| | | | | | | | | | Code cleanup Description: Add B-tree node debugging routine for symbol table nodes (i.e. groups) Platforms tested: FreeBSD 4.7 (sleipnir)
* [svn-r6410] Purpose:Quincey Koziol2003-02-171-11/+21
| | | | | | | | | | Bug fix. Description: Correct compile errors when configured with --enable-debug=all. Platforms tested: FreeBSD 4.7 (sleipnir) serial & parallel
* [svn-r6387] Purpose:Quincey Koziol2003-02-101-111/+140
| | | | | | | | | | | | | | | | | | | | | | | | | | | 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 Koziol2003-01-101-17/+17
| | | | | | | | | | | | 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 Koziol2003-01-091-95/+47
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r6136] Raymond Lu2002-11-251-5/+11
| | | | | | | | | | | Purpose: new functions Description: H5Gget_num_objs, H5Gget_objname_by_idx and H5Gget_objtype_by_idx. Platforms tested: modi4, arabica, eirene Misc. update: RELEASE.txt updated.
* [svn-r6108] Purpose:Quincey Koziol2002-11-201-7/+5
| | | | | | | | | | | | Code cleanup. Description: Cleaned up compiler warnings & updated a few comments. Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)} FreeBSD 4.7 (sleipnir)
* [svn-r5881] Purpose:Albert Cheng2002-08-201-1/+3
| | | | | | | | | | | | | | | bug fix Description: Last change of FUNC_ENTER to FUNC_ENTER_NOAPI did not include definition of variable ret_value and label done. Solution: Added the missing ret_value and label done. Not sure if the logic is correct since the function will abort if some assert fails. This fix only takes care of the syntax error. Platforms tested: eirene(pp). Did not test on other machine since the syntax fix is pretty simple.
* [svn-r5867] Purpose:Quincey Koziol2002-08-091-1/+6
| | | | | | | | | | | | | 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 Koziol2002-08-081-404/+262
| | | | | | | | | | | | | | | | 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-r5814] Purpose:Quincey Koziol2002-07-191-8/+16
| | | | | | | | | | | | | | | | | | Bug Fix Description: It was possible to create corrupted metadata information (either in memory or in the file or both) with a parallel I/O program because of the way metadata writes were being handled for writes out of the metadata cache. Solution: Added a dataset transfer property called "block before metadata write" which is used by the MPI-I/O and MPI-posix drivers to sync up all the processes before attempting a metadata write. This property is currently only for metadata writes from the metadata cache. Platforms tested: IRIX64 6.5 (modi4) w/parallel
* [svn-r5471] Purpose:Quincey Koziol2002-05-291-14/+15
| | | | | | | | | | | | | | | | 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-r5467] Purpose:Quincey Koziol2002-05-281-5/+6
| | | | | | | | | | | | | | | | | | | | | | | | Code cleanup. Description: Took Robb's recent ideas for improving the FUNC_ENTER/FUNC_LEAVE macros equivalents in the SAF library and adapted them to our library. I added an additional macro which is equivalent to FUNC_ENTER: FUNC_ENTER_NOINIT - Has the API tracing code, etc. from FUNC_ENTER but none of the library or interface initialization code. This is to be used _only_ for static functions and those which explicitly cannot have the library or interface initialization code enabled (like the API termination routines, etc.). This allowed many more of the functions in the library [but not all yet :-(] to be wrapped with FUNC_ENTER[_NOINIT]/FUNC_LEAVE pairs. It also reduced the size of the library and executables (by cutting out a bunch of code which was never executed), I'll e-mail the exact results when I've finished editing it. Platforms tested: IRIX64 6.5 (modi4)
* [svn-r5390] Purpose:Quincey Koziol2002-05-101-6/+0
| | | | | | | | | | | | | | | | | | | | | | Code cleanup Description: The parallel I/O file driver is optimized to only write metadata with one process (and broadcast the results to the other processes). This is currently enabled by a separate call to H5FD_mpio_tas_allsame() before each metadata write to the file. This can easily lead to problems where the prelude function call is omitted before the actual write code or, in a threaded environment, lead to race condititions where the value set is reset before being used. Solution: Since we only want to write metadata from one process, key off of the 'type' parameter (which has information about whether the data being written it metadata or raw data) to H5FD_mpio_write() as the method for determining whether to only write from one process or not. Platforms tested: IRIX64 6.5 (modi4)
* [svn-r5230] Purpose:Quincey Koziol2002-04-231-117/+7
| | | | | | | | | | | | | | | | | Code cleanup Description: Clean up the H5B_iterate code to not have a single hard-wired iterator for each interface which uses a B-tree, instead accept a function pointer which determines the callback function. This allows additional iterator callbacks to be defined without requiring additional H5B functions to be created. In that spirit, remove the H5B_prune_by_extent call and convert the H5F_istore callback routine for it into a callback routine for H5B_iterate. Platforms tested: FreeBSD 4.5 (sleipnir)
* [svn-r5203] Purpose:Quincey Koziol2002-04-181-110/+113
| | | | | | | | | | Code cleanup Description: Re-indented new code to match coding style of rest of library. Platforms tested: FreeBSD 4.5 (sleipnir)
* [svn-r5168] Pedro Vicente Nunes2002-04-111-0/+110
| | | | | | | | | | | | | | | | | | | | | | Purpose: H5Dset_extent API function Description: 1 new public function: H5Dset_extent, that allows shrinking a dataset several private functions that free the previously allocated chunks H5F_istore_prune_by_extent, H5B_prune_by_extent : removes the chunks H5F_istore_initialize_by_extent : initializes them with the fill value H5S_select_fill is used to fill the selection in the memory buffer Platforms tested: Windows 2000 SUN( arabica) LINUX (eirene) IRIX64 (modi4)
* [svn-r5108] ./hdf5-devel/src/H5B.cRobb Matzke2002-03-281-1/+1
| | | | | | | | Merge of name component length limit bugfix from 1.4 branch. A couple of very minor typos fixed. 2002-03-18 14:30:58 Robb Matzke <matzke@arborea.spizella.com> * H5B_assert: Fixed typos in comments.
* [svn-r4643] Purpose:Quincey Koziol2001-11-271-3/+3
| | | | | | | | | | | | | | | | | | | | | | 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 Koziol2001-11-201-3/+8
| | | | | | | | | 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-r4600] Purpose:Quincey Koziol2001-11-121-1/+1
| | | | | | | | | | | | Bug fix. Description: The internal B-tree code was dumping core with an assertion failure when flushing data to the file if too many objects were put into the same B-tree (forcing the root node to split, I think). Solution: Fixed the B-tree copy routine to copy the correct number of raw keys. Platforms tested: FreeBSD 4.4 (hawkwind), Solaris 2.6 (baldric)
* [svn-r4548] Purpose:Quincey Koziol2001-10-161-4/+27
| | | | | | | | | | | Code cleanup. Description: Fix a few compiler warnings from the file creation property list -> generic property list conversion. Also change a hard-wired value (8) for the number of B-tree key values to a value that uses the enum's generated by the compiler. Platforms tested: FreeBSD 4.4 (hawkwind)
* [svn-r4543] Raymond Lu2001-10-151-24/+40
| | | | | | | Purpose: Changed the file creation property list to the new generic property list. Platform tested: IRIX64, SunOS5.7, FreeBSD
* [svn-r4355] Purpose:Quincey Koziol2001-08-141-22/+22
| | | | | | | | | | | | | | | | | | | | | | Code cleanup (sorta) Description: When the first versions of the HDF5 library were designed, I remembered vividly the difficulties of porting code from a 32-bit platform to a 16-bit platform and asked that people use intn & uintn instead of int & unsigned int, respectively. However, in hindsight, this was overkill and unnecessary since we weren't going to be porting the HDF5 library to 16-bit architectures. Currently, the extra uintn & intn typedefs are causing problems for users who'd like to include both the HDF5 and HDF4 header files in one source module (like Kent's h4toh5 library). Solution: Changed the uintn & intn's to unsigned and int's respectively. Platforms tested: FreeBSD 4.4 (hawkwind)
* [svn-r4324] Purpose:Quincey Koziol2001-08-101-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | New Features! Description: Start migrating the internal use of property lists in the library from the older implementation to the new generic property lists. Currently, only the dataset transfer property lists are migrated to the new architecture, all the rest of the property list types are still using the older architecture. Also, the backward compatibility features are not implemented yet, so applications which use dataset transfer properties may need to make the following changes: H5Pcreate(H5P_DATASET_XFER) -> H5Pcreate_list(H5P_DATASET_XFER_NEW) and H5Pclose(<a dataset transfer property list>) -> H5Pclose_list(id) This still may have some bugs in it, especially with Fortran, but I should be wrapping up those later today. Platforms tested: FreeBSD 4.4 (hawkwind)
* [svn-r4181] Purpose:Quincey Koziol2001-07-101-27/+23
| | | | | | | | | Bug Fix, Code Cleanup, Code Optimization, etc. Description: Fold in the hyperslab speedups, clean up compile warnings and change a few things from using 'unsigned' or 'hsize_t' to use 'size_t' instead. Platforms tested: FreeBSD 4.3 (hawkwind), Solaris 2.7 (arabica), Irix64 6.5 (modi4)
* [svn-r4038] Purpose:Quincey Koziol2001-06-211-5/+5
| | | | | | | | | | | | | Code clean/bug fix Description: H5FL (free-list manager) code currently is taking an hsize_t as the size of a memory block to allocate. On many machines, the size of an hsize_t is greater than the size of a size_t, potentially leading to incorrect memory allocations in rare circumstances. Solution: Changed hsize_t parameters and variables to size_t. Platforms tested: FreeBSD 4.3 (hawkwind)
* [svn-r4013] Purpose:Bill Wendling2001-06-181-2/+2
| | | | | | | | | | | | POSIX Removal Description: Removed calls to POSIX functions and replaced them with the HD* equivalents. Solution: Did just that. Also had to create two new HD* macros, the gettimeofday() and getrusage() Platforms tested: Linux
* [svn-r3983] Purpose:Quincey Koziol2001-06-111-2/+2
| | | | | | | | | Code cleanups Description: Fixed a small number of warnings and also took out the H5private.h header from H5Ppublic.h Platforms tested: FreeBSD 4.3 (hawkwind)
* [svn-r3877] Purpose:Bill Wendling2001-04-301-1/+1
| | | | | | | | | | | Update Description: On further discussion with Albert and Quncey, it was decided to keep the original "unsignedness" of the nkeys variable. Solution: Changed the type from intn to uintn. Platforms tested: Linux
* [svn-r3875] Purpose:Bill Wendling2001-04-301-1/+1
| | | | | | | | | | | | | | | | Bug Fix Description: The --enable-static-exec flag was failing on Linux systems. The reason: a "long long" type was growing by some obscene amount if you just add 1 to it (tis truth!). In one statement, it prints out the correct value. Add one to it and print it out in the next statement and it gives you a very large number. This would, in turn, cause the resulting memcpy to fail... Solution: Changed the variable from "hsize_t" to "intn" which is what the field it's getting is typed anyway. Platforms tested: Linux
* [svn-r3781] Purpose:Bill Wendling2001-04-051-13/+13
| | | | | | | | | | | | | | | | | | Update Description: Changed #include <hdf_file.h> construct to #include "hdf_file.h" so that the GNU compiler can more easily pick up the dependencies which it places in the .depend and Dependencies files. Also regenerated the Dependencies to go along with this. Platforms tested: Linux
* [svn-r3288] Purpose:Albert Cheng2001-01-121-2/+0
| | | | | | | | | | | | | | | | Bug fix (sort of) (H5FDgass.c: just deleted an old code. Nothing to do with this fix.) Description: When --enable-debug=all was used, couple routine printf warnings to stderr that it is an expensive operation. This messed up the testing of h5ls since it included stderr output in its expected output and did not expect the extra messages. Solution: Changed it such that the extra messages are printed only if the appropriate h5-debug-class setting is on (via environment variables, for example). Platforms tested: eirene (debug=all), modi4(parallel,-64,default configure).
* [svn-r3252] Purpose:Quincey Koziol2001-01-091-14/+17
| | | | | | | | | | | | | Code cleanup. Description: Fixed _lots_ (I mean _tons_) of warnings spit out by the gcc with the extra warnings. Including a few show-stoppers for compression on IRIX machines. Solution: Changed lots of variables' types to more sensible and consistent types, more range-checking, more variable typecasts, etc. Platforms tested: FreeBSD 4.2 (hawkwind), IRIX64-64 (modi4)
* [svn-r3236] Purpose:Quincey Koziol2001-01-041-10/+15
| | | | | | | | Clean up code. Description: Cleaned up various compiler warnings. Platforms tested: FreeBSD 4.2 (hawkwind)
* [svn-r3231] Purpose:Quincey Koziol2001-01-031-2/+3
| | | | | | | | | Improved debugging output Description: Added a little more descriptive information to the output for h5debug when debugging B-trees in the file. Platforms tested: FreeBSD 4.2 (hawkwind)
* [svn-r3209] Purpose:Quincey Koziol2000-12-281-0/+3
| | | | | | | | | | | | | Updating debugging information for new features, etc. Description: Lots of the new features added to the library during the last year or so have been added without updating the debugging routines used by h5debug. Solution: Added more of the new features (although not all of them) to the debugging routines for h5debug. Also included some more information to expand on the information printed from h5debug. Platforms tested: FreeBSD 4.2 (hawkwind)
* [svn-r2722] Purpose:Quincey Koziol2000-10-241-1/+1
| | | | | | | | | | Feature symmetry Description: A while ago I needed to get the 'type' of data being accessed during writes to the VFL driver, so I put in code to get the information down there. Albert asked for the same information during reads, so I've added that in. Tested: FreeBSD 4.1.1 (hawkwind)
* [svn-r2652] Purpose:Quincey Koziol2000-10-101-1/+4
| | | | | | | | | | | | | | | Maintainance & performance enhancements Description: Re-arranged header files to protect private symbols better. Changed optimized regular hyperslab I/O to compute the offsets more efficiently from previous method of using matrix operations. Added sequential I/O operations at a more abstract level (at the same level as H5F_arr_read/write), to support the optimized hyperslab I/O. Platforms tested: Solaris 2.6 (baldric) & FreeBSD 4.1.1 (hawkwind)
* [svn-r2491] Added type of data parameter to H5F_block_write calls.Quincey Koziol2000-08-311-1/+1
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* [svn-r2444] Checkpoint the Generic Property implementation. It's not active ↵Quincey Koziol2000-07-251-1/+1
| | | | | | yet, but it's close. This shouldn't interfere with other development work. (I think.. :-)
* [svn-r2284] Duplicate initialization of variable removed.Bill Wendling2000-05-191-1/+0
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* [svn-r2165] Fixed last batch of problems when using free-lists on the SGI ↵Quincey Koziol2000-04-201-5/+5
| | | | | | machines. They should (hopefully) work on all platforms again now.
* [svn-r2158] Modified B-tree splits so they avoid the redundant metadata I/O ↵Quincey Koziol2000-04-191-34/+112
| | | | | | which was occurring when moving a metadata block in the file.
* [svn-r2147] Corrected a few problems in the free-list code and added more ↵Quincey Koziol2000-04-141-7/+9
| | | | | | | | | assert() macros to double-check things. I've turned them back on again now. I also changed the internal representation of a few struct fields to be float instead of double, since the HP/UX 10.20 compiler was having problems with the alignment of the doubles.
* [svn-r2117] Fixed error which manifested in H5Giterate, causing groups with ↵Quincey Koziol2000-04-121-1/+1
| | | | | | | more than one level of B-tree nodes and callback functions which returned non-zero to not work correctly.
* [svn-r2073] Added free-list code to the library and took out the older ↵Quincey Koziol2000-04-041-28/+44
| | | | | | | "temporary buffer" code, since the functionality was superceded. See the followup document for details on the free-list code.
* [svn-r2057] Purpose:Albert Cheng2000-03-241-1/+2
| | | | | | | | | | | | | | Bug fix for parallel mode. Description: H5FD_mpio_tas_allsame was called for all cases, even when MPIO is not used for access. That corrupted the internal file handle structure. Solution: Define a macro, IS_H5FD_MPIO(f), for testing if f is opened with MPIO access. Will call H5FD_mpio_tas_allsame only if this condition is true. Platform tested: O2K, both -64 and -n32 modes.
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