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* [svn-r13153] Added checksum to superblock and driver info block (in latest ↵James Laird2007-01-181-5/+52
| | | | | | | | | | | version of superblock). Tried to standardize sizes and added #defines to H5Fpkg.h so that hopefully the code is a little easier to read. Of course this is a file format change. Tested on Windows, juniper, smirom, kagiso.
* [svn-r13116] Description:Quincey Koziol2007-01-061-0/+6
| | | | | | | | | | | | Add support for deleting all the attributes on an object, when they are dense and possibly shared. Also, add some testing routines, for better error detection. Should fix daily test failures also... Tested on: FreeBSD/32 6.1 (duty)
* [svn-r12935] Added list-to-btree conversion, changed SOHM apis, and pushed ↵James Laird2006-11-171-1/+3
| | | | | | | | | | | SOHM table version and size information into the superblock to eliminate a read when loading it. This is a file format change, and hopefully the last one (knock on wood). Tested on kagiso and Windows (mostly just a SOHM change).
* [svn-r12902] Checkin of Shared Object Header Message work.James Laird2006-11-131-0/+1
| | | | | | | | | | | | This feature is still in progress; Shared Object Header Messages are not complete as a feature and are not thoroughly tested. There are still "TODO" comments in the code (comments with the word "JAMES" in them, so as not to be confused with other TODO comments). Hopefully this checkin will reduce the liklihood of conflicts as I finish implementing this feature. All current tests pass on juniper, copper (parallel), heping, kagiso, and mir.
* [svn-r12866] Description:Quincey Koziol2006-11-061-5/+2
| | | | | | | Clean up initialization of H5F & H5L APIs. Tested on: Linux/64 2.6 (chicago2)
* [svn-r12708] Description:Quincey Koziol2006-10-031-5/+16
| | | | | | | | | | | | | | | | | | | Add the "use the latest version of the format" support to datatype messages. And a regression test to check that it's working. Also, found that we have been over-allocating space for compound datatype messages (when they have array datatypes or can use the latest version of the format) and trimmed the size back. Clean up datatype & dataspace encode/decode routines by having them allocate & release "fake" file structures, which gets them out of needing to "know" about the internals of file structures. Other minor whitespace/formatting cleanups, etc. Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r12705] Description:Quincey Koziol2006-10-021-1/+1
| | | | | | | | | | | | Fix file handle destroy routine to not attempt to flush out partially initialized file handles (when opening a file fails). Tested on: (until they finished testing, this time... :-) FreeBSD/32 4.11 (sleipnir) w/threadsafe Linux/64 2.4 (mir) w/1.6 compat Linux/32 2.4 (heping) w/FORTRAN & C++ Mac OSX/32 10.4.8 (amazon)
* [svn-r12656] Description:Quincey Koziol2006-09-111-0/+1
| | | | | | | | | | | | | | | Add "use the latest version of the file format" flag to the file access property list and internal file data structures. Fix bug where metadata block size was retrieved instead of the small data block size. Categorize property list routine prototypes in the public header file. Tested on: Mac OS/PPC 10.4 (amazon) Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r11712] Purpose:Quincey Koziol2005-11-151-3/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | New feature Description: Check in baseline for compact group revisions, which radically revises the source code for managing groups and object headers. WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! This initiates the "unstable" phase of the 1.7.x branch, leading up to the 1.8.0 release. Please test this code, but do _NOT_ keep files created with it - the format will change again before the release and you will not be able to read your old files!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! Solution: There's too many changes to really describe them all, but some of them include: - Stop abusing the H5G_entry_t structure and split it into two separate structures for non-symbol table node use within the library: H5O_loc_t for object locations in a file and H5G_name_t to store the path to an opened object. H5G_entry_t is now only used for storing symbol table entries on disk. - Retire H5G_namei() in favor of a more general mechanism for traversing group paths and issuing callbacks on objects located. This gets us out of the business of hacking H5G_namei() for new features, generally. - Revised H5O* routines to take a H5O_loc_t instead of H5G_entry_t - Lots more... Platforms tested: h5committested and maybe another dozen configurations.... :-)
* [svn-r11490] Purpose:Quincey Koziol2005-10-031-0/+1
| | | | | | | | | | | | | | | Bug fix Description: Fix "double root open" bug and apply same fix to datasets & named datatypes. Also fix bug in symbol table entry lookup code that would "transfer" an object from one file handle to another file handle when the two file handles were opened on the same actual file. Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r11245] Purpose:Quincey Koziol2005-08-131-1/+1
| | | | | | | | | | | | | | | | | | | | 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-r11215] Purpose:Quincey Koziol2005-08-081-0/+5
| | | | | | | | | | | | | Bug fix & code cleanup Description: Fix another bug in the file mounting code and refactor the unmount code that it is simpler. Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4 Too minor to require h5committest
* [svn-r11093] Purpose:Quincey Koziol2005-07-211-5/+4
| | | | | | | | | | | | Bug fix Description: Rewrite code for mounting files to clean up layers of kludges and implement a much cleaner and more maintainable design. Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4
* [svn-r11022] Purpose:Quincey Koziol2005-07-051-0/+14
| | | | | | | | | | | | | | | | | | | | Bug fix & code cleanup Description: Don't unmount child files from a parent file if the parent file is being held open by an object. Also, moved the mounting routines into their own source file and the superblock routines into their own file also. Solution: Moved the code for unmounting child files down in the H5F_close routine and also add checks to the file and group mounting code to unmount child files when the last object holding open a file closes. Platforms tested: FreeBSD 4.11 (sleipnir) h5committest
* [svn-r10971] Purpose: Bug fixRaymond Lu2005-06-221-1/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Description: See details from Bug #213. Family member file size wasn't saved anywhere in file. When family file is opened, the first member size determine the member size. Solution: Hopefully, this is the last step of checkin for this stage. This step mainly enables h5repart tool to be able to convert file driver from family to sec2. Because the library saves family information in file, in trying to convert to sec2 driver, the library simply change the address of driver information to undefined so that the driver information block can be ignored. This step also updates the reference manual of H5Pset_fapl_family() and h5repart. In the fifth step of checkin, backward compatibility with v1.6 is tested. A family file created was created with the v1.6 library and opened with this version of the library. In the fourth step of checkin, a test suit is added for h5repart, including a program to generate the test files, a script file to run h5repart, and a program to verify repartitioned files can be opened by the library. There's a change from the first step of checkin. Family name template is no longer saved in the superblock because different pathname can make the name different. In the third step of checkin, h5repart has been modified. If h5repart is used to change the size of family member file, the new size(actual member size) is saved in the superblock. In the second step of checkin, multi driver is checked against the driver name saved in superblock. Wrong driver will result in a failure with an error message indicating multi driver should be used. This change includes split driver because it's a special case for multi driver. In the first step of checkin. Family member size and name template(unused at this stage) are saved in file superblock. When file is reopened,the size passed in thrin superblock. A different size will trigger a failure with an error message indicating the right size. Wrong driver to open family file will cause a failure, too. Platforms tested: h5committest and fuss. Misc. update: doc/html/RM_H5P.html and doc/html/Tools.html
* [svn-r10736] Purpose:Quincey Koziol2005-05-071-5/+5
| | | | | | | | | | | Code cleanup Description: Clean up some compiler warnings Platforms tested: FreeBSD 4.11 (sleipnir) h5committest
* [svn-r10688] Purpose:John Mainzer2005-04-281-1/+5
| | | | | | | | | | | | | | | | | | | | | | | | | | Add API calls allowing user control of the metadata cache. Description: Prior to this update, the metadata cache was not configurable from outside the library. Solution: Add API calls allowing the user to configure the metadata cache either at file open time, or for any open file. Also added calls permitting the user to monitor cache size and hit rate. These latter facilities are needed for "manual" cache size control Platforms tested: h5committested Misc. update:
* [svn-r9354] Purpose:Quincey Koziol2004-10-011-17/+0
| | | | | | | | | | | | | | | | Bug fix & code cleanup Description: More dataset cleanups to get to a point where we can fix the chunked I/O bug. Also fix a couple of errors in the recent file object resurrection changes which should hopefully address the recent daily test failres (H5T.c) Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel Solaris 2.7 (arabica) h5committest
* [svn-r8853] Purpose:Quincey Koziol2004-07-101-1/+1
| | | | | | | | | | | | | | | | | | | | Code optimization Description: Refactor B-tree code to extract all common information for a B-tree into a shared structure that is pointed to by all the nodes in tree (instead of being included in each node). Also re-order B-tree node comparison checks for chunked datasets to check for >= the upper node first, since the comparison is a bit "heavy" and this check is more likely to succeed when you are adding records to the dataset. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.10 (sleipnir) w/parallel Too minor to require h5committest (also, recent h5dump commits have broken testing...)
* [svn-r8844] Purpose:Quincey Koziol2004-07-091-1/+2
| | | | | | | | | | | | | | | | | | Bug fix Description: The "shared" raw B-tree node can get freed before all the B-tree nodes had been flushed out to disk and released by the cache. Solution: Implement a simple reference counting wrapper for objects in the library and use it to hold the shared raw B-tree nodes so they aren't freed before all references to them in memory are released. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.10 (sleipnir) IRIX64 6.5 (modei4)
* [svn-r8823] Purpose:Quincey Koziol2004-07-071-0/+1
| | | | | | | | | | | | | | | Code optimization Description: Since the raw B-tree nodes are the same size and only used when reading in or writing out a B-tree node, move raw B-tree node buffer from being per node to a single node that is shared among all B-tree nodes of a particular tree, freeing up a lot of space and eliminating lots of memory copies, etc. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.10 (sleipnir) w/parallel Too minor to require h5committest
* [svn-r8800] Purpose:Quincey Koziol2004-07-031-1/+1
| | | | | | | | | | | | | Code cleanup Description: Fix problems when compiling with C++ compiler. Also clean up some warnings with gcc 3.4.x Platforms tested: FreeBSD 4.10 (sleipnir) Too minor to require h5committest
* [svn-r8613] Purpose:Quincey Koziol2004-06-051-70/+4
| | | | | | | | | | | | | | | | | Refactor code Description: Move chunk and contiguous cached raw data from file information to dataset information. This simplifies a number of internal interfaces, aligns the code with it's purpose better and should allow more optimizations to the chunked data I/O performance. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.10 (sleipnir) h5committest Misc. update:
* [svn-r8600] Purpose:Quincey Koziol2004-05-311-2/+3
| | | | | | | | | | | | | Code optimization Description: Don't recompute the internal index value for looking up the chunk in the hash table, just use the value already computed from iterating through the chunks. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.9 (sleipnir) w/parallel
* [svn-r8158] Purpose:Quincey Koziol2004-02-061-4/+12
| | | | | | | | | | | | | | | | | Code cleanup/optimization Description: Query property list values once, at the beginning of the I/O routines, instead of querying the property list values multiple (lots!) of times in lower level routines. Solution: Create "property list caches" for internal library queries of the property list values. Platforms tested: IBM p690 (copper) w/parallel & fphdf5 h5committest
* [svn-r8126] Purpose:Quincey Koziol2004-01-311-8/+0
| | | | | | | | | | | | | | | | | 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-r7860] Purpose:Quincey Koziol2003-11-201-0/+2
| | | | | | | | | | | | | | | | | Bug fix Description: Our previous "optimization" of metadata writing which only wrote metadata from one process was abusing MPI-I/O and after some consultation with Rob Ross and Rajeev Thakur, Albert & I have come up with a solution... Solution: Instead of only writing from one process, issue a collective write operation with all processes, for metadata writes. Platforms tested: FreeBSD 4.9 (sleipnir) h5committest
* [svn-r7784] *** empty log message ***Raymond Lu2003-10-291-0/+1
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* [svn-r7426] Purpose:Quincey Koziol2003-08-281-1/+1
| | | | | | | | | | | | | | | | | Bug fix Description: When datasets are deleted from a file, they are removed from the sieve buffer, but instead of invalidating only the part of the sieve buffer affected, the sieve buffer code would throw away the entire sieve buffer, potentially including other raw data in the buffer that hadn't been written to disk yet. Solution: Improve the sieve buffer clearing code to handle partial invalidations. Platforms tested: FreeBSD 4.8 (sleipnir) h5committest
* [svn-r7381] Purpose:Quincey Koziol2003-08-181-1/+1
| | | | | | | | | | | Code cleanup Description: Various cleanups resulting from running lint tool over H5F.c source module Platforms tested: FreeBSD 4.8 (sleipnir) too minor to require h5committest
* [svn-r7232] Purpose:Quincey Koziol2003-07-161-5/+6
| | | | | | | | | | | | | | | | | | | | Bug fix Description: When a non-default indexed storage B-tree internal 'K' value is set by the user, the chunked datasets created in that file (until it is closed) use the user's 'K' value and the data can be accessed correctly, but the 'K' value is not stored in the file. However, once the file is closed and re-opened, the non-default 'K' value is lost and the data in the chunked datasets will not be able to be accessed correctly. Solution: Store the indexed storage B-tree internal 'K' value in the superblock. Platforms tested: FreeBSD 4.8 (sleipnir) h5committest
* [svn-r7201] Purpose:Quincey Koziol2003-07-101-1/+1
| | | | | | | | | | | | | Code cleanup Description: Finish converting the B-tree 'K' values to use unsigned integers, rather than signed ones, since negative amounts of entries in a B-tree node aren't meaningful. Platforms tested: FreeBSD 4.8 (sleipnir) h5committest
* [svn-r7189] Purpose:Quincey Koziol2003-07-091-2/+2
| | | | | | | | | | | Code cleanup Description: Break some of the "debugging" routines into their own module, so they aren't pulled into every executable, which certainly isn't going to use them. Platforms tested: h5committested
* [svn-r7172] Purpose:Quincey Koziol2003-07-071-4/+4
| | | | | | | | | | | Code cleanup Description: Remove "UNUSED" keyword from function prototypes in header files. Platforms tested: IA64 Linux cluster (titan) too small to need commit test
* [svn-r7122] Purpose:Quincey Koziol2003-06-301-0/+1
| | | | | | | | | | | | | Code cleanup/Feature removal Description: Remove "round robin" writing of metadata in MPI VFDs (and a couple of other places). This never really worked the way I hoped it would and it causes problems on certain machines. Platforms tested: FreeBSD 4.8 (sleipnir) w/parallel Too small for triple check.
* [svn-r6878] Purpose:Quincey Koziol2003-05-151-4/+8
| | | | | | | | | | | Code cleanup Description: Limit the scope on more function prototypes/macros/typedefs. Platforms tested: FreeBSD 4.8 (sleipnir) h5committest not necessary.
* [svn-r6843] Purpose:Quincey Koziol2003-05-091-1/+1
| | | | | | | | | | | | 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 Koziol2003-05-071-29/+27
| | | | | | | | | | | | | | | | | | | | | | | | | 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-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-r6387] Purpose:Quincey Koziol2003-02-101-16/+10
| | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r6252] Purpose:Quincey Koziol2003-01-091-2/+13
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r5931] MuQun Yang2002-09-201-22/+22
| | | | | | | | | | | | Purpose: __DLL__ is a keyword in some platforms and __DLL__ is also defined as a macro for windows DLL applications. That causes problems. Description: Solution: Use H5_DLL*** to replace __DLL***__ at all header files. Change the macro defination at H5api_adpt.h. Platforms tested: linux2.2.18smp, irix64, solaris 2.7 and windows 2000
* [svn-r5894] Purpose:Quincey Koziol2002-08-271-2/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bug fix/Code cleanup/New Feature Description: Correct problems with writing fill-values to external storage and allocate the data storage at the correct times. Also, mostly straighten out the strange code which allocates and fills raw data storage for datasets. Things are still a bit odd in that the fill-values for chunked datasets are written when the space is allocated, instead of in a separate routine, but there are two reasons for this: it's inefficient (especially in parallel) to iterate through all the chunks twice, and (more importantly) the space needed to store compressed chunks isn't known until we've got a buffer of compressed fill-values ready to write to the chunk. Additionally, add in the H5D_SPACE_ALLOC_INCR and H5D_SPACE_ALLOC_DEFAULT setting for the "space time", which incorporate the previous behavior of the space allocation for chunked datasets. The default settings for the different types of dataset storage are now as follows: Contiguous - Late Chunked - Incremental Compact - Early This checkin also incorporates a change to the behavior of external data storage in two ways - fill-values are _never_ written to external storage (under the assumption that writing fill-values is triggered by allocating space in an HDF5 file, and since space is not allocated in the file, the fill-values should not be written) and external data files are now created if they don't exist when data is written to them. The fill-value will probably need to be revisited at some time in the future, this just seemed like the safer course currently. I think I cleaned up some compiler errors also, before getting bogged down in the fixes for the space allocation and fill-values. Platforms tested: FreeBSD 4.6 (sleipnir) w/serial & parallel. Will be testing on IRIX64 6.5 (modi4) in serial & parallel shortly.
* [svn-r5879] Raymond Lu2002-08-201-0/+9
| | | | | | | | | Purpose: Design for compact dataset Description: Compact dataset is stored in the header message for dataset layout. Platforms tested: arabica, eirene.
* [svn-r5799] Purpose:Quincey Koziol2002-07-151-0/+1
| | | | | | | | | | | | 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-r5667] Purpose:Quincey Koziol2002-06-191-6/+0
| | | | | | | | | | Code cleanup Description: Turn on more warnings in the IRIX builds and clean them up. Platforms tested: IRIX64 6.5 (modi4) w/parallel
* [svn-r5538] Purpose:Quincey Koziol2002-06-051-0/+2
| | | | | | | | | | | | | | | Code improvement. Description: Added boot block and driver info block checksumming feature to the shared file information. This prevents these blocks from being written out multiple times when they haven't changed. This reduces the number of I/O operations which hit the disk for my test program from 15 to 14 (i.e. from 393 to 14, overall). Platforms tested: Solaris 2.7 (arabica) w/FORTRAN and FreeBSD 4.5 (sleipnir) w/C++
* [svn-r5429] Purpose:Quincey Koziol2002-05-171-0/+2
| | | | | | | | | | | | | | | | | | | | | Bug fix/Code improvement. Description: Currently, the chunk data allocation routine invoked to allocate space for the entire dataset is inefficient. It writes out each chunk in the dataset, whether it is already allocated or not. Additionally, this happens not only when it is created, but also anytime it is opened for writing, or the dataset is extended. Worse, there's too much parallel I/O syncronization, which slows things down even more. Solution: Only attempt to write out chunks that don't already exist. Additionally, share the I/O writing between all the nodes, instead of writing everything with process 0. Then, only block with MPI_Barrier if chunks were actually created. Platforms tested: IRIX64 6.5 (modi4)
* [svn-r5325] MuQun Yang2002-05-021-1/+1
| | | | | | | | | | Purpose: minor bugs fixed Description: Typos in H5Fpkg.h and H5TB.c Solution: Platforms tested: linux 2.2.18
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