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* [svn-r13495] Description:Quincey Koziol2007-03-111-4/+7
| | | | | | | Cleanup handling of file consistency/status flags a bit. Tested on: FreeBSD/32 6.2 (duty)
* [svn-r13477] Description:Quincey Koziol2007-03-081-1/+2
| | | | | | | | | | | | | | | | | | | | The main purpose of this checkin was to eliminate the space used for tracking creation time indices when there is no way they can be used (i.e. attributes can't be shared in the file and the user hasn't turned on attribute creation tracking), however there were some other minor changes which crept in: - Fix a cache locking deadlock when a shared attribute and one of its components end up in the same fractal heap direct block. (This is fixed the "slow" way for right now, until John has time to add support for readers/writer locking to the cache. - Optimize attribute copying when a copy will be kept during a v2 B-tree search. - When freeing a block on disk, attempt to merge it with the metadata and "small data" aggregators. Tested on: Mac OS X/32 10.4.8 (amazon) FreeBSD/32 6.2 (duty)
* [svn-r13465] Description:Quincey Koziol2007-03-061-1/+0
| | | | | | | | | | | | Fix bug in external links when "strong" file close degree is used. Make external link callbacks use standard error reporting mechanisms. Other minor code cleanups... Tested on: Mac OS X/32 10.4.8 (amazon) FreeBSD/32 6.2 (duty)
* [svn-r13440] Description:Quincey Koziol2007-03-011-4/+4
| | | | | | | | | | | | | | | | | | | Revise latest form of superblock format pretty drastically, to eliminate unused fields and move rarely used fields into superblock extension. Finished removing last vestiges of references to (never used) i"shared" object header message ID. Added object header messages for non-default v1 B-tree 'K' values and for driver info. Updated testfiles to reflect size changes, etc. Various minor cleanups, etc. Tested on: FreeBSD/32 6.2 (duty) Mac OS X/32 10.4.8 (amazon)
* [svn-r13413] Description:Quincey Koziol2007-02-271-1/+0
| | | | | | | | | | | | | Further cleanups to superblock code: - Move most of the ISOHM-specific code into the H5SM module - Make only one checksum, for combined superblock & driver info block Minor other cleanups, etc. Tested on: Mac OS X/32 10.4.8 (amazon) FreeBSD/32 6.2 (duty)
* [svn-r13375] Description:Quincey Koziol2007-02-221-66/+2
| | | | | | | | | | Straighten out some of the code for handling superblocks, in preparation for revising the format of the latest version of the superblock before the beta release. Tested on: Mac OS X/32 10.4.8 (amazon) FreeBSD/32 6.2 (duty)
* [svn-r13253] Updated all C and C++ style source code files with the THG ↵Albert Cheng2007-02-071-2/+3
| | | | | | | | | copyright notice. Tested platform: Kagiso only since it is only a comment block change. If it works in one machine, it should work in all, I hope. Still need to check the parallel build on copper.
* [svn-r13250] Description:Quincey Koziol2007-02-071-2/+2
| | | | | | | | | | Add support for inserting attributes into creation order index. Also, update support for dense link & attribute storage in h5debug. Tested on: FreeBSD/32 6.2 (duty) Mac OS X/32 10.4.8 (amazon)
* [svn-r13245] Added "superblock extension" object header to hold shared ↵James Laird2007-02-061-3/+5
| | | | | | | | | object header information, rather than storing it directly in the superblock. This should make future updates to the superblock much less painful. Tested on Windows, kagiso, and smirom.
* [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
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