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* [svn-r6643] Snapshot version 1.5 release 50HDF Admin2003-04-121-2/+2
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* [svn-r6640] Purpose:Bill Wendling2003-04-111-15/+2
| | | | | | | | | | | | | | | | | | | | | | Fix Description: This is an analogue to the previous bug-fix for filters not being applied to data written but being applied when read. The old way was if the SZlib library couldn't deflate a dataset, then we'd munge along pretending that it was okay. Solution: Trigger it as an error in this situation. The H5Z_pipeline code which calls this function can clear the error stack if need be. Platforms tested: Modi4 (Parallel & Fortran) Burrwhite (Fortran & C++) Baldric (Fortran), but make check didn't work because of "libucb.so" error that I can't fix...) Misc. update:
* [svn-r6632] Purpose:Quincey Koziol2003-04-112-3/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | | Bug fix Description: This fixes a bug in the low-level metadata caching code in the library which could possibly lose metadata during file I/O when a lot of objects are inserted into a group. This also fixes a couple of (similar) fencepost bugs in the B-tree deletion code. Solution: For the metadata bug - call the low-level driver's 'write' routine instead of H5FD_write. For the B-tree bug - include the correct number of keys. Platforms tested: FreeBSD 4.8 (sleipnir) w/C++ Linux 2.4 (burrwhite) w/FORTRAN Solaris 2.7 (arabica) w/FORTRAN IRIX64 6.5 (modi4) w/FORTRAN & parallel (h5committest is still not working for me on burrwhite) Misc. update:
* [svn-r6628] Purpose:Bill Wendling2003-04-101-22/+20
| | | | | | | | | | | | | | | | | | | | | | Buglet Fix Description: When filtering data, those filters which failed and are optional weren't being specified inside of the H5Z_pipeline() function like they're supposed to be. Solution: Modified the code to set the appropriate bit in the "failed" flag to say that the filter failed if it did and was optional. Removed some cases of setting the "failed" flag where it didn't have any effect (like, right before an HGOTO_ERROR() statement). Platforms tested: Burrwhite (Fortran) Arabica (Fortran) Modi4 (Parallel & Fortran) Misc. update:
* [svn-r6611] Purpose:Quincey Koziol2003-04-099-126/+1027
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Code cleanup/new features Description: Switch over to a new style for registering filters with the library - instead passing in an ID, a string and a callback function to H5Zregister, the client should pass in a single pointer to a H5Z_claass_t struct which contains the ID, the description string and all the function callbacks as fields. Added support for a new "can apply" callback for each filter, which is called when a dataset is created to check whether the parameters for that filter apply correctly to the combination of the datatype and the chunk size (i.e. dataspace) for the dataset. Added support for a new "set local" callback for each filter, which is called when a dataset is created (after the "can apply" filter callback) and sets filter parameters that are specific to that particular dataset. Switched the filters we ship over to use the new H5Z_class_t struct for their internal registrations and also added "set local" callbacks to the szip and shuffle filters and a "can apply" callback to the szip filter. Lots of other code cleanups, etc. also Solution: Platforms tested: FreeBSD 4.8 (sleipnir) w/szip Linux 2.4 (sleipnir) w/szip Solaris 2.7 (arabica) w/FORTRAN IRIX64 6.5 (modi4) w/szip, FORTRAN & parallel Misc. update:
* [svn-r6610] Purpose:Quincey Koziol2003-04-092-47/+283
| | | | | | | | | | | | | | | | | | | | | | | | Code cleanup & new features Description: Added three new API functions for working on I/O filters: H5Pmodify_filter, H5Pget_filter_by_id and H5Pall_filters_avail. Documentation on these will be added for the 1.6.0 release, until then, we'll have to use the source code. Also, simplified the H5Pset_szip and H5Pset_shuffle API interfaces, since those filters are using the new "set local" callback facility to set dataset- specific parameters. Probably, some of the changes to internal H5Z routines are captured in these changes also. Solution: Platforms tested: FreeBSD 4.8 (sleipnir) w/szip Linux 2.4 (sleipnir) w/szip Solaris 2.7 (arabica) w/FORTRAN IRIX64 6.5 (modi4) w/szip, FORTRAN & parallel Misc. update:
* [svn-r6609] Purpose:Quincey Koziol2003-04-091-7/+1
| | | | | | | | | | | | | | | | | | Code cleanup Description: Got rid of anonymous inline struct for filter information in a pipeline and replaced with typedef'd type. Solution: Platforms tested: FreeBSD 4.8 (sleipnir) w/szip Linux 2.4 (sleipnir) w/szip Solaris 2.7 (arabica) w/FORTRAN IRIX64 6.5 (modi4) w/szip, FORTRAN & parallel Misc. update:
* [svn-r6608] Purpose:Quincey Koziol2003-04-092-4/+45
| | | | | | | | | | | | | | | | | | New feature Description: Added new internal API function: H5S_create_simple() for creating simple dataspaces inside the library. Solution: Platforms tested: FreeBSD 4.8 (sleipnir) w/szip Linux 2.4 (sleipnir) w/szip Solaris 2.7 (arabica) w/FORTRAN IRIX64 6.5 (modi4) w/szip, FORTRAN & parallel Misc. update:
* [svn-r6607] Purpose:Quincey Koziol2003-04-092-36/+32
| | | | | | | | | | | | | | | | | Code cleanup Description: Chase internal API changes for H5Z_pipeline and H5S_set_extent_simple Solution: Platforms tested: FreeBSD 4.8 (sleipnir) w/szip Linux 2.4 (sleipnir) w/szip Solaris 2.7 (arabica) w/FORTRAN IRIX64 6.5 (modi4) w/szip, FORTRAN & parallel Misc. update:
* [svn-r6606] Purpose:Quincey Koziol2003-04-092-9/+23
| | | | | | | | | | | | | | | | | New feature Description: Added new error descriptions. Solution: Platforms tested: FreeBSD 4.8 (sleipnir) w/szip Linux 2.4 (sleipnir) w/szip Solaris 2.7 (arabica) w/FORTRAN IRIX64 6.5 (modi4) w/szip, FORTRAN & parallel Misc. update:
* [svn-r6605] Purpose:Quincey Koziol2003-04-091-1/+1
| | | | | | | | | | | | | | | | | | | Code cleanup Description: Array declaration was using hard-coded constant for maximum number of dimensions. Solution: Changed to use H5O_LAYOUT_NDIMS. Platforms tested: FreeBSD 4.8 (sleipnir) w/szip Linux 2.4 (sleipnir) w/szip Solaris 2.7 (arabica) w/FORTRAN IRIX64 6.5 (modi4) w/szip, FORTRAN & parallel Misc. update:
* [svn-r6604] Purpose:Quincey Koziol2003-04-091-30/+45
| | | | | | | | | | | | | | | | | | New feature Description: Hooked up internal dataset creation call (H5D_create) to the new "can apply" and "set local" callbacks for filters. Solution: Platforms tested: FreeBSD 4.8 (sleipnir) w/szip Linux 2.4 (sleipnir) w/szip Solaris 2.7 (arabica) w/FORTRAN IRIX64 6.5 (modi4) w/szip, FORTRAN & parallel Misc. update:
* [svn-r6603] Purpose:Quincey Koziol2003-04-091-173/+172
| | | | | | | | | | | | | | | | | Code cleanup Description: Update dependencies. Solution: Platforms tested: FreeBSD 4.8 (sleipnir) w/szip Linux 2.4 (sleipnir) w/szip Solaris 2.7 (arabica) w/FORTRAN IRIX64 6.5 (modi4) w/szip, FORTRAN & parallel Misc. update:
* [svn-r6598] Purpose:Pedro Vicente Nunes2003-04-082-3/+3
| | | | | | | | | | | | | | | | | code warrior port Description: added some type casts (char*) for CW portability Solution: Platforms tested: w2000(CW , MS) linux arabica modi4 Misc. update:
* [svn-r6581] Purpose:Quincey Koziol2003-04-031-84/+128
| | | | | | | | | | | | | | | | | | | Code cleanup & bug fix Description: Cleaned up comments & copyright statement. Blocks which were unable to be compressed were missing the "length" prefix, causing the decompression routine to fail. Solution: Always add "length" prefix to all blocks, even ones the fail to compress. Platforms tested: FreeBSD 4.8 (sleipnir) IRIX64 6.5 (modi4) w/parallel Misc. update:
* [svn-r6580] Purpose:Quincey Koziol2003-04-031-3/+0
| | | | | | | | | | | | | | | Code cleanup Description: Removed 'szlib.h' header, moving it to the H5Zszip.c filter code. Solution: Platforms tested: FreeBSD 4.8 (sleipnir) IRIX64 6.5 (modi4) w/parallel Misc. update:
* [svn-r6579] Purpose:Quincey Koziol2003-04-031-0/+6
| | | | | | | | | | | | | | | Code cleanup Description: Added flags for szip-specific settings Solution: Platforms tested: FreeBSD 4.8 (sleipnir) IRIX64 6.5 (modi4) w/parallel Misc. update:
* [svn-r6578] Purpose:Quincey Koziol2003-04-035-68/+103
| | | | | | | | | | | | | | | | Code cleanup Description: Added lots of comments to existing filters, so they are easier to understand and use as examples for future filters. Cleaned up various bits of code, etc. Solution: Platforms tested: FreeBSD 4.8 (sleipnir) IRIX64 6.5 (modi4) w/parallel Misc. update:
* [svn-r6577] Purpose:Quincey Koziol2003-04-032-12/+18
| | | | | | | | | | | | | | | | | | Code cleanup (sorta) Description: The H5Pset_szip API call was forcing users to pass in their parameters in the same way as the internal representation of the filter parameters used by the library (as an array of unsigned values). Solution: Changed to pass in separate parameters in a more user-friendly format. Platforms tested: FreeBSD 4.8 (sleipnir) IRIX64 6.5 (modi4) w/parallel Misc. update:
* [svn-r6576] Purpose:Quincey Koziol2003-04-031-20/+49
| | | | | | | | | | | | | | Cleanup Description: Update dependencies. Solution: Platforms tested: Linux 2.4 (eirene) Misc. update:
* [svn-r6559] Purpose:Bill Wendling2003-04-011-11/+13
| | | | | | | | | | | | Update Description: Missed this file when updating copyright statements. Platforms tested: None (comment change) Misc. update:
* [svn-r6558] Purpose:Bill Wendling2003-04-011-1/+1
| | | | | | | | | | | | | | | Bug Fix... Description: The previous bug was in the _free function as well Solution: Used the correct structure Platforms tested: Modi4 Misc. update:
* [svn-r6557] Purpose:Bill Wendling2003-04-011-1/+1
| | | | | | | | | | | | | | | Bug Fix Description: Was using the wrong pointer into a structure... Solution: Used the correct pointer to get the file_id... Platforms tested: Modi4 Misc. update:
* [svn-r6556] Purpose:Bill Wendling2003-04-015-72/+160
| | | | | | | | | | | | | | | | | | | Update & Bug Fix Description: The "free" protocol was missing. Added that to the server side. When doing a "create" of a file (with no other data structures created), the freespace in the file wasn't being reclaimed. Solution: After adding the free protocol, we put the burden of running through the FD_free function on the SAP instead of each client. Platforms tested: Linux Misc. update:
* [svn-r6552] Purpose:MuQun Yang2003-04-011-0/+122
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | To support szip compression in HDF5 Description: This is where szip filter function is located. Solution: The filter function composes of "encode" and "decode" part, which is similar as deflate filter. One critical difference is: when szip decompresses the data, it needs to know the buffer size to hold the decompressed data in advance. Currently it's hard for HDF5 lib to give the buffer size easily. So to avoid this problem, in each chunk, we add a small header to hold the buffer size of each chunk. The code will use UINT32 ENCODE and UINT32 DECODE to finish this part of work. Platforms tested: Since there are changes of configure.in and configure,I didn't use h5committest. I tested with four platforms. 1) Linux 2.4 (eirene) 2) Solaris 2.7(arabica) 3) windows 2000(VS 6.0) 4) SGI IRIX6.5-64(modi4) For test 1)-3), only basic C tests were done For modi4 test, I tested 64-bit C,parallel and fortran. All tests passed, except a warning message from szip library when checksum is used in some order, which doesn't e any real problems. Misc. update:
* [svn-r6551] Purpose:MuQun Yang2003-04-016-13/+74
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | To support szip compression in HDF5 Description: szip compression support is required by NASA ESDIS. The compression algorithm is good for scientific data. In HDF5, we add another filter function to make szip as a default compression package as we did for gzip(or zlib). In this check-in, a new function called H5Pset_szip was added into H5Pdcpl.c, this function is very similar to H5Pset_deflate. The only difference is SZIP needs four parameters from the user to get the compression done while gzip needs only one. So we pass a pointer to this function instead of an integer number. The description of the four parameters of szip should be in different documents. H5Z.c and other header files were simply modified to have HDF5 know szip. Solution: See the decription Platforms tested: Since there are changes of configure.in and configure,I didn't use h5committest. I tested with four platforms. 1) Linux 2.4 (eirene) 2) Solaris 2.7(arabica) 3) windows 2000(VS 6.0) 4) SGI IRIX6.5-64(modi4) For test 1)-3), only basic C tests were done For modi4 test, I tested 64-bit C,parallel and fortran. All tests passed, except a warning message from szip library when checksum is used in some order, which doesn't cause any real problems. Misc. update:
* [svn-r6550] Purpose:MuQun Yang2003-04-012-4/+13
| | | | | | | | | | | | | | | | | | | | | | | | | | To support szip compression in HDF5 Description: szip compression support is required by NASA ESDIS. The compression algorithm is a good compression algorithm for scientific data. In HDF5, we add another filter function to make szip as a default compression package as we did for gzip(or zlib). H5config.in needs to be regenerated by autoheader for SZIP flags. Solution: A new file called H5Zszip.c will be added in the Makefile.in Flags like: HAVE_FILTER_SZIP should be auto-generated by autoheader. Platforms tested: Since there are changes of configure.in and configure,I didn't use h5committest. I tested with four platforms. 1) Linux 2.4 (eirene) 2) Solaris 2.7(arabica) 3) windows 2000(VS 6.0) 4) SGI IRIX6.5-64(modi4) For test 1)-3), only basic C tests were done For modi4 test, I tested 64-bit C,parallel and fortran. All tests passed, except a warning message from szip library when checksum is used in some order, which doesn't cause any real problems. Misc. update:
* [svn-r6546] Purpose:Bill Wendling2003-03-3173-398/+1005
| | | | | | | | | | | | Update Description: Updated copyright statement in files which hadn't been updated yet. Platforms tested: Linux (Only comment change) Misc. update:
* [svn-r6527] Purpose:Bill Wendling2003-03-277-107/+58
| | | | | | | | | | | | | | | | | | | | | | | Bug Fix & Update Description: FPHDF5 was creating files which didn't have the EOA field in the superblock set correctly. It turns out that the SAP was keeping this information to itself instead of giving it to the client processes. Naughty SAP! Solution: Have the SAP send this information back to the clients so that they can update the superblock as necessary. This now creates a file (with just the root group) that looks correct! Only problem is that there's extra file space being allocated. Also, at program termination, there's an infinite loop... Platforms tested: H5committests (run by hand on burrwhite, arabica, and modi4) Misc. update:
* [svn-r6519] Purpose:Quincey Koziol2003-03-225-67/+85
| | | | | | | | | | | | | Bug fix/code cleanup/new feature Description: Fix h5debug to work correctly again, with all the changes over the past few months. Improved and cleaned up debugging output available in h5debug. Platforms tested: FreeBSD 4.7 (sleipnir)
* [svn-r6514] Purpose:Bill Wendling2003-03-207-147/+146
| | | | | | | | | | | | | | | | | | | | | | | | | Bug fix and Update Description: From Quincey's comments on the code I checked in last night: - In H5F_close call, the "private" processes should call the H5F_flush with the "CLEAR_ONLY" flag. - There's no need for a special case for FPHDF5 in the FD_real_alloc function since FPHDF5 doesn't define an alloc function. - The return type of H5Pset_fapl_fphdf5 should be herr_t instead of hid_t. I don't know how it got that way in the first place. - The variable names for MPI types and the structure typedefs should be switched: H5FP_request/H5FP_request_t to H5FP_request_t/H5FP_request and so on. - In the H5FP.c module, I was commiting the H5FP_request MPI datatype but using the wrong offset field... Platforms tested: Linux...will test on others, but these are mostly FPHDF5 changes. Misc. update:
* [svn-r6507] Purpose:Bill Wendling2003-03-192-0/+9
| | | | | | | | | | | | | | | bug Fix Description: MPI stuff was getting into the non-parallel headers. Solution: #ifdefed the headers out if H5_HAVE_FPHDF5 isn't defined... Platforms tested: Sol, Modi4 Misc. update:
* [svn-r6506] Purpose:Bill Wendling2003-03-191-7/+43
| | | | | | | | | | | | | Update Description: When doing an allocation, check to see, if it's an FPHDF5 driver, if only the captain should be performing the allocation Platforms tested: Linux, Modi4, Sol Misc. update:
* [svn-r6505] Purpose:Bill Wendling2003-03-193-67/+179
| | | | | | | | | | | | | | | | | Update Description: Have the FPHDF5 module initialized on startup. Have only the captain process perform certain functions (like flushing during an F_close call or allocating the superblock). H5Fistore needed a few checks to see if it was working with an FPHDF5 driver. Done similarly to how MPI and MPIPOSIX drivers are checked.. Platforms tested: Linux, Modi4, Sol Misc. update:
* [svn-r6504] Purpose:Bill Wendling2003-03-193-176/+201
| | | | | | | | | | | | | | | | | | | | | | | | | Why not? Description: Lots of changes. This is basically a "commit because there are a lot of changes" commit. The server now acts more like a metadata caching server. The dumping mechanism finally works (I think). At least in the test I did it seemed to write things back. There's a new MPI TAG to use (H5FP_TAG_DUMP) when dumping things. Changed a lot of the functions from passing a structure around to just passing a pointer to that structure. I have no clue why I did it the previous way... Um...And more synchronization stuff between the client and server. The protocol between the two was being broke in a couple of places. We're getting closer! Platforms tested: Linux (probably Modi4 too) Misc. update:
* [svn-r6503] Purpose:Bill Wendling2003-03-191-24/+41
| | | | | | | | | | | | | | | | | | | | | Bug Fix Description: The MPI datatypes we were committing weren't using the correct structure. Also, we needed to know the rank of the captain process inside of the BARRIER COMM. Solution: Changed to use the correct structure. Got the Captain process's rank and Bcast it to the "privates". Platforms tested: Linux Misc. update:
* [svn-r6502] Purpose:Bill Wendling2003-03-192-58/+154
| | | | | | | | | | | | | | | | | | | Update Description: More changes to the FPHDF5 file driver. Too many to mention here. Some highlights: - Addition of lock/unlock methods to the driver, though they aren't implemented fully just yet. - Extra query functions to determine various things about the file. (If this is the captain process, etc) - Fixes to make things work... Platforms tested: Linux Misc. update:
* [svn-r6501] Purpose:Bill Wendling2003-03-1911-63/+172
| | | | | | | | | | | | | | New Feature Description: Added support for the lock and unlock function calls for file drivers. Only FPHDF5 uses this feature. All of these drivers don't define lock or unlock methods. Platforms tested: Linux, Modi4, Sol Misc. update:
* [svn-r6500] Purpose:Bill Wendling2003-03-191-57/+87
| | | | | | | | | | | | New Feature Description: Added function pointers for the lock and unlock functions. Platforms tested: Linux, Modi4, Sol Misc. update:
* [svn-r6499] Purpose:Bill Wendling2003-03-191-17/+18
| | | | | | | | | | | | | Update Description: Added support for FPHDF5 wherever there was support for MPI/IO and/or MPIPOSIX. Platforms tested: Linux, Modi4, Sol Misc. update:
* [svn-r6498] Purpose:Bill Wendling2003-03-191-8/+0
| | | | | | | | | | | | | | Cleanup Description: The H5O_FPHDF5 object was left in this header file by mistake when the H5Ofphdf5 module was removed Solution: Removed it. Platforms tested: Linux
* [svn-r6497] Purpose:Quincey Koziol2003-03-1912-56/+73
| | | | | | | | | | | | | | | | | | | 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-r6496] Purpose:Bill Wendling2003-03-194-85/+159
| | | | | | | | | | | | | | | | | | | | | | Refactoring of Flush Logic Description: The Flushing logic passed in multiple flags to indicate what type of flush it was: closing, invalidate, alloc only. This made extending the function of the flush logic to handle other flags annoying. Solution: I changed it to be just one bitmasked flag to indicate what type of flushing to do. I also added the CLEAR_ONLY flag, which will be used in the FPHDF5 stuff. Platforms tested: h5committest doesn't work for me (my environment isn't setup on the other machines I guess). I tested it manually: Linux parallel & C++ Sol Fortran Modi4 parallel & Fortran.
* [svn-r6483] Snapshot version 1.5 release 49HDF Admin2003-03-151-2/+2
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* [svn-r6468] Purpose:Quincey Koziol2003-03-062-2/+2
| | | | | | | | | | | | | | Potential bug fix. Description: The code to rotate the metadata writing process may not be compiled correctly in all cases. Solution: Change from using "++mpi_round" to "mpi_round+1" Platforms tested: Eyeballed...
* [svn-r6452] Purpose:Quincey Koziol2003-03-035-12/+70
| | | | | | | | | | Code cleanup Description: Add B-tree node debugging routine for symbol table nodes (i.e. groups) Platforms tested: FreeBSD 4.7 (sleipnir)
* [svn-r6446] Snapshot version 1.5 release 48HDF Admin2003-03-011-2/+2
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* [svn-r6436] Purpose:Quincey Koziol2003-02-243-9/+1014
| | | | | | | | | | | | | New internal feature Description: Add internal API for building and working with heaps (H5HP). This will be used for the LRU algorithm in the new metadata cache code. Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)} FreeBSD 4.7 (sleipnir)
* [svn-r6433] Purpose:Quincey Koziol2003-02-245-63/+157
| | | | | | | | | | | | | | | Code/comment cleanup Description: Made more information about reference-counted strings private to the H5RS package by trimming the typedef used in H5RSprivate.h and switching from using macros for a couple of operations to using functions. Updated copyright information for a few of these files. Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)}
* [svn-r6431] Purpose:Quincey Koziol2003-02-242-12/+0
| | | | | | | Comment cleanup Description: Corrected comment information.
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