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* [svn-r6395] Purpose:Quincey Koziol2003-02-1222-4153/+5072
| | | | | | | | | | | | | | | | | | | | | | | Code cleanup. Description: Break up the ~9350 line H5T.c module into smaller pieces, which contain code for a particular feature or support for a datatype class. This should make the "main" H5T code (still in H5T.c) easier to support, as well as removing some of the "minor" routines from the user applications which don't use them (my rough estimates show about 4% reduction (~30K on a FreeBSD machine) in optimized, staticly-linked binaries for very simple programs) Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)} FreeBSD 4.7 (sleipnir) Misc. update: Update MANIFEST
* [svn-r6394] Purpose:Quincey Koziol2003-02-121-6/+2
| | | | | | | | | | | | | | Bug fix. Description: Missed adding the dxpl to the 'flush' VFL callback in the stream driver, causing the C++ compiles to fail. Solution: Added the dxpl parameter. Platforms tested: FreeBSD 4.7 (sleipnir) w/CC=g++
* [svn-r6392] Purpose:Bill Wendling2003-02-103-580/+874
| | | | | | | | | | | | | | | | | | | | | | | | Update Description: Folded in Quincey's changes to the caching stuff. (Stole the code from the H5FDmpio driver). Roughed in some code for doing a read from the SAP. Also roughed in code for doing a write. However, the write requires an OID, which I'm not sure how to pass down into the driver (maybe via the dxpl_id?...but then it has always to be set before calling one of these routines...). Removed some of the global variables which were there because of the FPHDF5 stuff... Removed the H5Ofphdf5.* stuff from the Makefile.in, since I'm pretty sure it's going away and I don't want to waste time updating that module if that's the case...so just don't compile it. Platforms tested: Linux
* [svn-r6391] Purpose:Bill Wendling2003-02-101-3/+0
| | | | | | | | | | Fix Description: The extra field I put in this structure wasn't needed. Solution: Placed it in the file driver's structure instead. Platforms tested: Linux
* [svn-r6390] Purpose:Bill Wendling2003-02-104-76/+105
| | | | | | | | | | | | | | | | Update Description: Removed some obsolete fields - such as the AC_subst_t object ID - which isn't needed. Fixed so that there are fewer global variables. There are still some left, however. Modified the client and server code so that it handles read requests better. There were some flaws in how this was done before (it was calling H5FD_read() instead of just returning the status that it couldn't find the metadata in the cache). Platforms tested: Linux
* [svn-r6388] Purpose:Quincey Koziol2003-02-106-18/+18
| | | | | | | | | | | | | Update feature Description: Relax collective constraint for API functions which only read metadata from a file. Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)} FreeBSD 4.7 w/parallel
* [svn-r6387] Purpose:Quincey Koziol2003-02-1069-2086/+2798
| | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r6386] Purpose:Quincey Koziol2003-02-101-0/+4
| | | | | | | | | | | | | | Bug fix Description: The "system scope" for threads isn't supported on all platforms. Solution: Add detection of this feature to the configure script and check for "H5_HAVE_SYSTEM_SCOPE_THREADS" in the appropriate places. Platforms tested: modi4 w/threadsafe
* [svn-r6383] Purpose:Quincey Koziol2003-02-079-54/+625
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | New feature for developers. Description: Added "function stack" tracing to library. This allows developers (there is no public API) to call H5FS_print within the library and get a listing of the functions traversed to reach that point in the library. Eventually, I may add support for reporting the parameters to each function also... Mainly for debugging parallel I/O programs, but I think it will come in handy in other cases also. The function stack tracking is controlled with a configure switch: --enable-funcstack, which defaults to enabled currently. When we branch for 1.6, we should change the default setting on the branch to be disabled. Also, added a destructor to the thread-specific keys when thread-safety is turned on in the library. Otherwise, they were leaking memory and causing difficult to debug errors in threaded programs (like the test/ttsafe test). Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)} FreeBSD 4.7 (sleipnir) w/thread-safety enabled. Misc. update: Updated MANIFEST with new files added (src/H5FS.c & src/H5FDprivate.h) Update release_docs/RELEASE with thread-safety bug fix.
* [svn-r6381] Purpose:Bill Wendling2003-02-061-0/+3
| | | | | | | | | | | | | Field Addition Description: Added a File ID field to the H5FD_t structure so that, way deep down in the H5FD_* functions, I'll know what ID the SAP wants for this particular file. This is #ifdef'd out so that if you don't have FPHDF5 enabled, then it won't be there... Platforms tested: Linux
* [svn-r6380] Purpose:Bill Wendling2003-02-061-15/+16
| | | | | | | | Update Description: Added support for the H5FDfphdf5.[ch] file driver. Platforms tested: Linux
* [svn-r6379] Purpose:Bill Wendling2003-02-066-100/+1747
| | | | | | | | | | | | | | Update Description: H5FP.c, H5FPclient.c, H5FPprivate.h, H5FPserver.c: Update. More progression towards the SAP as metadata cache. It only lacks the ability to take care of metadata allocations. H5FDfphdf5.[ch]: Start of a new driver for FPHDF5. Not fully implemented just yet... Platforms tested: Linux
* [svn-r6375] Raymond Lu2003-02-0417-105/+577
| | | | | | | | | | | Purpose: New feature Description: Added Adler32 checksum as a filter in pipeline Platforms tested: arabica (fortran), eirene (, C++), modi4 (parallel, fortran) Misc. update: Update release_docs/RELEASE.
* [svn-r6374] Purpose:Bill Wendling2003-02-031-7/+7
| | | | | | | | | | | | | Update Description: Converted the "FUNC_LEAVE" macros to "FUNC_LEAVE_NOAPI" to be consistent with the rest of the library. Note: This is probably completely useless as the file is going to go away with the new model of the SAP as metadata cache...But it helps me compile... Platforms tested: Linux (FPHDF5)
* [svn-r6373] Purpose:Bill Wendling2003-02-031-10/+25
| | | | | | | | | | | Update Description: Added support for defining what the haddr type is in terms of MPI types. Solution: Include some #defines when we typedef haddr... Platforms tested: Linux (For FPHDF5 stuff)...
* [svn-r6372] Purpose:Bill Wendling2003-02-031-1/+1
| | | | | | | | | | Buglet Description: The title of the function in FUNC_ENTER_* was wrong. Solution: Changed to correct title. Platforms tested: Linux (small change).
* [svn-r6371] Purpose:Bill Wendling2003-02-034-280/+597
| | | | | | | | | | | | | | Update Description: Changes: - Added support for the server dumping metadata writes to a client. - Some of the code wasn't handling allocated buffers correctly (freeing twice). - Modified server so that it handles metadata only. Platforms tested: Linux
* [svn-r6358] Snapshot version 1.5 release 46HDF Admin2003-02-011-2/+2
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* [svn-r6336] Purpose:Bill Wendling2003-01-276-816/+596
| | | | | | | | | | | | | | | Update Description: This is the first conversion of the FPHDF5 code to be a metadata cache. There's an extra error message. I rewrote the sync/change code to be read metadata/write metadata instead. I still need to hook these changes into the HDF5 code so that it looks at the SAP first before checking the file for metadata. Platforms tested: Linux
* [svn-r6330] Purpose:Quincey Koziol2003-01-241-0/+2
| | | | | | | | | | | | | | | Bug Fix Description: When calling H5Fopen with the core VFL driver, but without the H5F_ACC_CREAT flag goes ahead and creates a memory file. Solution: Check for the H5F_ACC_CREAT flag before allowing the memory file to be created. Platforms tested: FreeBSD 4.7 (sleipnir)
* [svn-r6313] Purpose:Albert Cheng2003-01-221-8/+23
| | | | | | | | | | | Updated Description: Updated Copyright notice. Replaced HGOTO_ERROR calls involving MPI calls with HMPI_GOTO_ERROR. Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)}? Tested on Eirene (PP) only since the code is in the MPIO module only.
* [svn-r6308] Purpose:Quincey Koziol2003-01-215-11/+375
| | | | | | | | | | | | | | | | | Bug fix Description: Currently, when the library encounters an object header message that isn't know, it fails to open that object in the file. Solution: Allow the library to skip over the unknown object header message and continue to process the remaining messages, in the hope that the skipped message isn't important later. If it is important, it will be caught at a higher level of the library. Platforms tested: FreeBSD 4.7 (sleipnir)
* [svn-r6302] Added the testing of libmpe.Albert Cheng2003-01-181-0/+3
| | | | | | | | This is generated by autoheader. Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)}? YES Other platforms/configurations tested? eirene with --enable-mpe
* [svn-r6301] Purpose:Quincey Koziol2003-01-185-9/+10
| | | | | | | | | | | Code cleanup & bug fix Description: Cleanup another set of warnings on Windows and also fix mis-placed assertion that caused the daily tests to fail. Platforms tested: IRIX64 6.5 (modi4) w/-n32
* [svn-r6296] Purpose:Quincey Koziol2003-01-179-41/+68
| | | | | | | | | | Code cleanup Description: Reduce warnings on Windows Platforms tested: FreeBSD 4.7 (sleipnir)
* [svn-r6283] MuQun Yang2003-01-142-1/+15
| | | | | | | | | | | | | | | | | Purpose: Change some macros to make windows happy Description: Currently no srandom and random functions on windows, Function gethostname cannot be resolved when DLL turned on Solution: use srand and rand to replace srandom and random turn off the option to check gethostname Platforms tested: windows 2000, linux 2.2.18smp Misc. update: Update MANIFEST if you add or remove any file. Update release_docs/RELEASE for bug fixes, new features, etc. Update applicable document files too.
* [svn-r6278] Purpose:Quincey Koziol2003-01-141-30/+51
| | | | | | | | | | | | Code cleanup Description: Add 'H5_DLL' macro to H5FL macros, in order to allow Windows builds to work. Platforms tested: FreeBSD 4.7 (sleipnir) Visual Studio 6.0
* [svn-r6275] Purpose:Quincey Koziol2003-01-131-1/+1
| | | | | | | | | | Code cleanup Description: Added "UNUSED" flag to an inlinable function Platforms tested: FreeBSD 4.7 (sleipnir) w/gcc 3.2.1
* [svn-r6272] Purpose:Quincey Koziol2003-01-131-4/+4
| | | | | | | | | | Code cleanup Description: Fix preprocessor macros to declare variables correctly. Platforms tested: MS Visual Studio
* [svn-r6269] Purpose:Quincey Koziol2003-01-138-26/+66
| | | | | | | | | | | | | Code cleanup Description: Various code cleanups to allow the development branch to be compiled with a C++ compiler (i.e. CC=g++ ) Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)} FreeBSD 4.7 (sleipnir) C++
* [svn-r6268] Purpose:Quincey Koziol2003-01-111-4/+4
| | | | | | | | | | | Code improvement Description: Add extra pair of braces to API versions of FUNC_ENTER/FUNC_LEAVE macros, to make API <-> non-API mismatches obvious. Platforms tested: FreeBSD 4.7 (sleipnir)
* [svn-r6267] Snapshot version 1.5 release 45HDF Admin2003-01-112-3/+4
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* [svn-r6266] Purpose:Quincey Koziol2003-01-1084-1526/+1505
| | | | | | | | | | | | 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-r6255] Purpose:Quincey Koziol2003-01-0910-179/+724
| | | | | | | | | | Code cleanup Description: Clean up a few more warnings and update dependencies. Platforms tested: Linux 2.2.18smp (eirene) serial & parallel
* [svn-r6252] Purpose:Quincey Koziol2003-01-0987-3062/+6559
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r6232] Purpose:Albert Cheng2003-01-035-5/+467
| | | | | | | | | | | | | | | | new feature Description: Added MPICH/MPE instrumentation support. All source code are bracketed by the macro H5_HAVE_MPE. Use "--enable-mpe" to configure it in. Currently only worked in Eirene because the MPE library is not installed in all machines yet. The added file, H5MPprivate.h, holds HDF5/MPE related defintions. Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)}? Yep. Other platforms/configurations tested? --enable-mpe feature tested in Eirene.
* [svn-r6229] Purpose:Albert Cheng2003-01-031-1/+2
| | | | | | | | | | | Minor fix Description: By mistake, the MPI_Error handling macros were inserted outside the overall macro bracket. Moved them back inside the bracket. Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)}? Yep.
* [svn-r6228] Description:Albert Cheng2003-01-031-3/+0
| | | | | | | | When I removed the option (--enable-parallel=mpich), which did not work, I failed to run autoheader to update this file. I am checking in the updated version now. Platforms tested: No need to test since it just removed a #undefine and comments.
* [svn-r6223] Purpose:Binh-Minh Ribler2002-12-222-8/+8
| | | | | | | | | | | | | | | | | | | | | | Bug fix - informed by Kent Description: Some identifiers were flagged as unresolved symbols when building with c++ on Windows. The reason is the name of these identifiers were changed by the c++ compiler, also called name mangling. Solution: Moved #ifdef __cplusplus extern "C" { #endif to include the offending identifiers so the c++ compiler will take them as is. Platforms: SunOS 5.7 (arabica) Linux 6.2 (eirene) Windows 2000
* [svn-r6221] Snapshot version 1.5 release 44HDF Admin2002-12-211-2/+2
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* [svn-r6220] Purpose:Bill Wendling2002-12-194-156/+299
| | | | | | | | | | Update Description: A few generic changes to the FPHDF5 code. Some error messages reworked a bit. Cleaning up in case of failure improved in some cases. Added another field to the synchronization messages... Platforms tested: Linux
* [svn-r6219] Purpose:Bill Wendling2002-12-191-1/+0
| | | | | | | | | Update Description: Removed the EFL field from the FPHDF5 structure as the property list already has this info. Platforms tested: Linux
* [svn-r6218] Purpose:Bill Wendling2002-12-191-47/+17
| | | | | | | | | | Bug Fix Description: Was encoding a value as DTYPE instead of MTIME, which would cause a couple of errors. Also, got rid of the EFL field as it's encoded in the PLIST already... Platforms tested: Linux...Modest test, FPHDF5 not fully implemented just yet.
* [svn-r6206] Raymond Lu2002-12-131-2/+2
| | | | | | | | | Purpose: Improve error handling Description: make error handling better for VL string null pointer. Platform tested: arabica
* [svn-r6202] MuQun Yang2002-12-133-4/+12
| | | | | | | | | | | | | | | | Purpose: Fix bugs for windows platform. Description: 1. Update HDlseek for windows 2. Update H5Otime.c for normal time(non-daylight time) 3. Add H5_DLL in front of two functions so that windows DLL can work. Solution: Platforms tested: windows 2000, eirene(since most updates have WIN32 around it, not need to test other platforms) Misc. update: Update MANIFEST if you add or remove any file. Update release_docs/RELEASE for bug fixes, new features, etc. Update applicable document files too.
* [svn-r6199] Raymond Lu2002-12-121-2/+3
| | | | | | | Purpose: error-detection improvement Description: verify string parameter in function H5T_vlen_str_mem_getlen isn't nil.
* [svn-r6195] Raymond Lu2002-12-114-105/+249
| | | | | | | | | | Purpose: Cleanup H5Tget_native_type code Description: improve code cosmetics. Solution: Platforms tested: modi4, eirene, arabica
* [svn-r6193] Snapshot version 1.5 release 43HDF Admin2002-12-071-2/+2
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* [svn-r6178] ./hdf5-devel/src/H5Epublic.hRobb Matzke2002-12-041-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Purpose: New Feature; Optimization; Clean-up (Merged from 1.4 branch) Description: There is no symbolic constant to pass to functions that take an optional object ID for when the caller wants to indicate no object ID. In the past the caller always passed a negative integer. GPFS performs poorly. The h5ls tool decides whether to list the file name in the output based on a compile-time choice, which isn't always optimal at run time. Solution: Added a symbolic constant H5I_INVALID_HID. Added code to tell the mmfsd of GPFS to forego byte range token prefetching. h5ls decides whether to print the file name at runtime based on the number of objects being listed. Platforms tested: SuSE Linux (arborea), gcc and mpich-1.2.4 SunOS (baldric), gcc 2002-12-03 22:51:43 Robb Matzke <matzke@arborea.spizella.com> *: Added H5E_FCNTL minor error number.
* [svn-r6177] ./hdf5-devel/src/H5E.cRobb Matzke2002-12-041-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Purpose: New Feature; Optimization; Clean-up (Merged from 1.4 branch) Description: There is no symbolic constant to pass to functions that take an optional object ID for when the caller wants to indicate no object ID. In the past the caller always passed a negative integer. GPFS performs poorly. The h5ls tool decides whether to list the file name in the output based on a compile-time choice, which isn't always optimal at run time. Solution: Added a symbolic constant H5I_INVALID_HID. Added code to tell the mmfsd of GPFS to forego byte range token prefetching. h5ls decides whether to print the file name at runtime based on the number of objects being listed. Platforms tested: SuSE Linux (arborea), gcc and mpich-1.2.4 SunOS (baldric), gcc 2002-12-03 22:50:23 Robb Matzke <matzke@arborea.spizella.com> *: Added H5E_FCNTL minor error number.
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