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* [svn-r6843] Purpose:Quincey Koziol2003-05-091-3/+3
| | | | | | | | | | | | Code cleanup Description: Clean up warnings exposed by compiling on O2K. Also, revert some of Bill and my changes to the H5S_mpi_opt_types_g, etc. and settle them back into their original location. Platforms tested: h5committested.
* [svn-r6825] Purpose:Quincey Koziol2003-05-071-605/+149
| | | | | | | | | | | | | | | | | | | | | | | | | New feature/enhancement Description: Chunked datasets are handled poorly in several circumstances involving certain selections and chunks that are too large for the chunk cache and/or chunks with filters, causing the chunk to be read from disk multiple times. Solution: Rearrange raw data I/O infrastructure to handle chunked datasets in a much more friendly way by creating a selection in memory and on disk for each chunk in a chunked dataset and performing all of the I/O on that chunk at one time. There are still some scalability (the current code attempts to create a selection for all the chunks in the dataset, instead of just the chunks that are accessed, requiring portions of the istore.c and fillval.c tests to be commented out) and performance issues, but checking this in will allow the changes to be tested by a much wider audience while I address the remaining issues. Platforms tested: h5committested, FreeBSD 4.8 (sleipnir) serial & parallel, Linux 2.4 (eirene)
* [svn-r6546] Purpose:Bill Wendling2003-03-311-3/+14
| | | | | | | | | | | | Update Description: Updated copyright statement in files which hadn't been updated yet. Platforms tested: Linux (Only comment change) Misc. update:
* [svn-r6387] Purpose:Quincey Koziol2003-02-101-48/+32
| | | | | | | | | | | | | | | | | | | | | | | | | | | 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 Koziol2003-01-101-4/+4
| | | | | | | | | | | | 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 Koziol2003-01-091-26/+20
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r6047] Purpose:Quincey Koziol2002-11-011-0/+2
| | | | | | | | | | | | | | | | | Bug fix & code cleanup Description: Hyperslab code for collapsing dimensions was incorrectly collapsing selections inappropriately when the fastest changing dimension couldn't be collapsed. Also add some more assertions which will make similar bugs easier to find. Solution: Break out of loop earlier. Platforms tested: modi4 (parallel), too small to triple check.
* [svn-r5883] Raymond Lu2002-08-201-30/+30
| | | | | | | | | | Purpose: Rename variables. Description: In this file, dataset address offset is misnamed as file offset. Changed them back to dset_offset_XXX or dset_offset. Platforms tested: eirene
* [svn-r5879] Raymond Lu2002-08-201-5/+20
| | | | | | | | | Purpose: Design for compact dataset Description: Compact dataset is stored in the header message for dataset layout. Platforms tested: arabica, eirene.
* [svn-r5871] Purpose:Quincey Koziol2002-08-121-2/+0
| | | | | | | | | | | | | | | | 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-r5866] Purpose:Quincey Koziol2002-08-091-2/+4
| | | | | | | | | | Code cleanup Description: Cleaned up a few warnings from compiling with --disable-hsizet on Linux Platforms tested: Linux 2.2.x (eirene)
* [svn-r5842] Purpose:Quincey Koziol2002-08-081-8/+12
| | | | | | | | | | | | | | | | 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-r5799] Purpose:Quincey Koziol2002-07-151-37/+42
| | | | | | | | | | | | New feature. Description: Added MPI-posix VFL driver. This driver uses MPI to coordinate actions, but performs I/O directly with posix sec(2) I/O functions. This driver should _NOT_ be used if the file accessed is not on a parallel filesystem. Platforms tested: FreeBSD 4.6 (sleipnir) w/parallel & IRIX64 6.5 (modi4) w/parallel
* [svn-r5677] Purpose:Quincey Koziol2002-06-191-6/+6
| | | | | | | | | | | Code improvement Description: Some small code cleanups and took out the code the was turning off the metadata cache for parallel I/O (!) Platforms tested: IRIX64 6.5 (modi4) w/parallel
* [svn-r5530] Purpose:Bill Wendling2002-06-041-2/+2
| | | | | | | | | | | | | | | Code Cleanup Description: Removed some compiler warnings. Solution: In a few cases, NULL was being returned when a FAIL was supposed to be returned instead. There were some header files which needed to be included in a few of the sources. A couple of if-then statements had assignments in the conditional part. The compiler warned that they should have extra "()"s around them. Made the code check the values instead. Platforms tested: Linux (parallel) Modi4 (parallel)
* [svn-r5471] Purpose:Quincey Koziol2002-05-291-4/+4
| | | | | | | | | | | | | | | | 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-r5259] Purpose:Quincey Koziol2002-04-251-149/+125
| | | | | | | | | | | | | | | | Code cleanup Description: Previously, the I/O pipeline (pline), external file list (efl) and fill- value (fill) structs were passed down the raw data function call chain, even into and/or through functions which didn't use them. Since all three of these pieces of information are available from the dataset creation property list, just pass the dataset creation property list down the function call chain and query for the information needed in a particular function. Platforms tested: FreeBSD 4.5 (sleipnir)
* [svn-r5130] Purpose:Quincey Koziol2002-04-021-16/+30
| | | | | | | | | | | | | | | | | | | | | | Bug Fix & Feature Description: The selection offset was being ignored for optimized hyperslab selection I/O operations. Additionally, I've found that the restrictions on optimized selection I/O operations were too strict and found a way to allow more hyperslabs to use the optimized I/O routines. Solution: Incorporate the selection offset into the selection location when performing optimized I/O operations. Allow optimized I/O on any single hyperslab selection and also allow hyperslab operations on chunked datasets. Platforms tested: FreeBSD 4.5 (sleipnir)
* [svn-r4664] Purpose:Quincey Koziol2001-12-031-35/+34
| | | | | | | | Code cleanup Description: Check in some small speedups for chunked storage I/O. Platforms tested: Solaris 2.6 (baldric)
* [svn-r4633] Purpose:Quincey Koziol2001-11-211-8/+16
| | | | | | | | | | | Bug fix. Description: Builds for parallel testing exposed some places that I forgot to get rid of using IDs in internal APIs. Solution: Switch sections of code to use proper data structures instead of IDs. Platforms tested: Parallel compiles from daily tests.
* [svn-r4620] Purpose:Quincey Koziol2001-11-201-2/+2
| | | | | | | | | 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-r4508] Purpose:Quincey Koziol2001-10-021-6/+6
| | | | | | | | | | | | | Document bug fix. Description: When reading or writing to chunked datasets and the data needed datatype conversion, and the amount of data was more than one conversion buffer, data in the conversion buffer was getting corrupted. Solution: Corrected error in advancing buffer pointer where it was being advanced by the number of elements instead of the number of bytes. Platforms tested: FreeBSD 4.4 (hawkwind)
* [svn-r4489] Purpose:Quincey Koziol2001-09-281-0/+20
| | | | | | | | | | | | | | | | Bug Fix Description: When writing (or reading) the entire dataset to a chunked dataset, there was a boundary case where the code to generate the description of the piece of the dataset to read into the buffer for data conversion would attempt to read off the boundary of the dataset. This was occuring because the code to detect the edge of the dataset was not propagating the change up through the remaining dimensions when an edge in a fast changing dimension was detected. Solution: Propagate edge detection up through slower changing dimensions properly. Platforms tested: Linux 2.2.18smp (eirene)
* [svn-r4482] Purpose:Quincey Koziol2001-09-261-2/+2
| | | | | | | | | | | | | | | | | | | | | | Kludge Description: Since we're only about halfway through converting the internal use of property lists from the "old way" to the generic property lists, we turned off snapshots to avoid exposing lots of API changes to users, until the APIs settled down. Getting the snapshots rolling again seems to have become a priority, so some changes are going to have to be made now that were going to be postponed until we were completely finished with the conversion. This requires that the old API functions be able to deal with both the old and new property lists smoothly. Solution: Kludge together the property list code so that they can transparently handle dealing with both the old and new property lists Platforms tested: FreeBSD 4.4 (hawkwind)
* [svn-r4355] Purpose:Quincey Koziol2001-08-141-7/+7
| | | | | | | | | | | | | | | | | | | | | | 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-r4326] Purpose:Quincey Koziol2001-08-101-4/+4
| | | | | | | | | | Code cleanups, mostly.. Description: Work on pacifying the SGI compiler to get the generic properties working correctly with --enable-parallel and --enable-fortran. It's not quite fixed yet, but I need to head home and these patches help... :-/ Platforms tested: IRIX64 6.5 (modi4)
* [svn-r4324] Purpose:Quincey Koziol2001-08-101-18/+42
| | | | | | | | | | | | | | | | | | | | | | | | 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 Koziol2001-07-101-610/+544
| | | | | | | | | 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-r4018] Purpose:Quincey Koziol2001-06-191-12/+0
| | | | | | | | Code cleanup Description: Removed some more warnings during compilation on SGI machines.. Platforms tested: Irix64-6.5 (modi4)
* [svn-r3885] Purpose:Quincey Koziol2001-05-021-16/+34
| | | | | | | | | | | | | | | | | | | | | | | | Document bug fix Description: IMPORTANT! IMPORTANT! IMPORTANT! A case where metadata in a file could get corrupted in certain unusual sitations was detected and fixed. In certain circumstances, metadata could get cached in the raw data cache, and if that particular piece of metadata was updated on disk while incorrectly cached, the new metadata would get overwritten with the stale metadata from the raw data cache when it was flushed out. Additionally, I've patched up the raw data cache to be smarter about how much it caches and how much I/O it triggers, leading to some speedups. Solution: Changed the raw data I/O routines which perform caching to require a parameter with the size of the dataset being accessed and limited the cache to no more than that many bytes. Platforms tested: FreeBSD 4.3 (hawkwind)
* [svn-r3781] Purpose:Bill Wendling2001-04-051-14/+14
| | | | | | | | | | | | | | | | | | 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-r3653] Purpose:Quincey Koziol2001-03-171-2/+2
| | | | | | | | | | | | Bug Fix Description: Partial hyperslabs which exactly fit the size of the lowest dimension of a chunked dataset weren't being output correctly. Solution: Forgot to divide the offset (seq_len) by the size of the lower dimension hyperslabs - fixed now. Platforms tested: FreeBSD 4.2 (hawkwind)
* [svn-r3528] Purpose:Quincey Koziol2001-02-281-6/+6
| | | | | | | | | | | | Bug fix. Description: Fencepost error in determining number of elements to include in a partial hyperslab for a chunk. Solution: Changed "<down_size[i]"s into "<=down_size[i]"s in a few places, to allow for exactly one slab being left to output/input. Platforms tested: FreeBSD 4.2 (hawkwind)
* [svn-r3479] Purpose:Quincey Koziol2001-02-211-51/+464
| | | | | | | | | | | | | | | | | | | | | | | | Bug Fixes Description: Fixed a bug in H5Shyper.c where 'contiguous' hyperslabs (i.e. ones which took up an entire dataset) were not being detected correctly and would instead be read a part at a time instead of all at once. Also fixed a bug in the handling of hyperslabs for chunked datasets where hyperslabs from chunks which weren't aligned on exact dimension bounaries were not reading/writing data correctly. Solution: H5Shyper.c was a single line change from a 'block' size to a 'count' size. H5Fseq.c changes we much more significant and involved detecting when non-chunk aligned sequences of data were being written and constructing hyperslab blocks to pass down to the chunking I/O routine (which only understand hyperslab I/O requests, not element sequence requests). This was complicated by the need to align the hyperslabs requested on dimension boundaries... Platforms tested: FreeBSD 4.2. (hawkwind)
* [svn-r3252] Purpose:Quincey Koziol2001-01-091-2/+2
| | | | | | | | | | | | | 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-r2945] Purpose:Quincey Koziol2000-11-161-4/+2
| | | | | | | | Small code optimization Description: Removed some unnecessary buffer assignments. Platforms tested: Solaris 2.6 (baldric)
* [svn-r2736] Purpose:Quincey Koziol2000-10-251-10/+6
| | | | | | | | | | Code optimization Description: Minor tweaks throughout the optimized regular hyperslab code to increase speed. This set of improvements increase the benchmark time from taking ~5.46 seconds to ~4.50 seconds, or around a 20% further speedup. Platforms tested: Solaris 2.6 (baldric)
* [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-r2657] Quincey Koziol2000-10-101-2/+2
| | | | | | | | | | | | Purpose: Parallel Bug Fixes Description: Was out of sync with header file re-arrangements I checked in last night. Solution: Fixed to use new header files, etc. Platforms tested: O2K (modi4)
* [svn-r2652] Purpose:Quincey Koziol2000-10-101-0/+494
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)
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