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* [svn-r5900] Purpose:Quincey Koziol2002-08-271-11/+115
| | | | | | | | | | | Code cleanup/New Feature Description: Improve the space allocation in the file by re-using freed space more effectively. Platforms tested: FreeBSD 4.6 (sleipnir) w/serial & parallel
* [svn-r5897] Purpose:Bill Wendling2002-08-271-35/+52
| | | | | | Cleaned up the documentation Description: There were some small errors in the documentation in the source file.
* [svn-r5894] Purpose:Quincey Koziol2002-08-2720-410/+857
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r5886] Purpose:Quincey Koziol2002-08-232-0/+28
| | | | | | | | | | | | | | Bug fix Description: Correctly apply filters (like compression) to fill values in chunks that are pre-allocated. This is OK in parallel also, since all the chunks are identical at this point and any chunk may be written by any process. Platforms tested: FreeBSD 4.6 (sleipnir) w/parallel
* [svn-r5884] Purpose:Quincey Koziol2002-08-211-48/+53
| | | | | | | | | | | | Bug fix/Code cleanup Description: Clean up memory leak in fill value code Also rearrange logic of code a bit Platforms tested: FreeBSD 4.6 (sleipnir)
* [svn-r5883] Raymond Lu2002-08-202-60/+60
| | | | | | | | | | Purpose: Rename variables. Description: In this file, dataset address offset is misnamed as file offset. Changed them back to dset_offset_XXX or dset_offset. Platforms tested: eirene
* [svn-r5882] Raymond Lu2002-08-201-74/+72
| | | | | | | | | | Purpose: Bug fix. Description: In H5D_init_storage, contiguous dataset is not initialized properly when fill value is library default. Platforms tested: eirene
* [svn-r5881] Purpose:Albert Cheng2002-08-201-1/+3
| | | | | | | | | | | | | | | bug fix Description: Last change of FUNC_ENTER to FUNC_ENTER_NOAPI did not include definition of variable ret_value and label done. Solution: Added the missing ret_value and label done. Not sure if the logic is correct since the function will abort if some assert fails. This fix only takes care of the syntax error. Platforms tested: eirene(pp). Did not test on other machine since the syntax fix is pretty simple.
* [svn-r5879] Raymond Lu2002-08-2015-100/+601
| | | | | | | | | Purpose: Design for compact dataset Description: Compact dataset is stored in the header message for dataset layout. Platforms tested: arabica, eirene.
* [svn-r5875] Purpose:Quincey Koziol2002-08-144-67/+120
| | | | | | | | | | | | | | Additional regression tests & bug fixes Description: There was no testing for the H5Dget_storage_size function and it seemed to be having problems with compressed, chunked datasets, so write some tests to verify that its working correctly. Also, fix case for allocating storage early for chunked datasets Platforms tested: FreeBSD 4.6 (sleipnir) serial & parallel
* [svn-r5872] Purpose:Quincey Koziol2002-08-126-3679/+3822
| | | | | | | | | | | | Code cleanup Description: Move get/set routines for each type of property list (file creation, dataset creation, file access and dataset transfer) into their own source code module. Platforms tested: FreeBSD 4.6 (sleipnir)
* [svn-r5871] Purpose:Quincey Koziol2002-08-1222-371/+183
| | | | | | | | | | | | | | | | Code cleanup Description: Combined H5P_isa_class and H5I_object functionality into a new internal H5P API function: H5P_object_verify, which checks that a property list is the appropriate class and then returns the property list object associated with the property list ID. This reduces the source code by about 200 LOC and trims the library binary some more. Platforms tested: FreeBSD 4.6 (sleipnir)
* [svn-r5869] Snapshot version 1.5 release 33HDF Admin2002-08-101-2/+2
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* [svn-r5868] Purpose:Quincey Koziol2002-08-091-1/+1
| | | | | | | | | | Code cleanup Description: Cleanup up a few compiler warnings... Platforms tested: IRIX64 6.5 (modi4) w/parallel
* [svn-r5867] Purpose:Quincey Koziol2002-08-0951-294/+1042
| | | | | | | | | | | | | Code cleanup Description: Changed the last HRETURN* statements in the FUNC_ENTER macros into HGOTO* macros, which reduces the size of the library binary in certain configurations by another 10% Platforms tested: FreeBSD 4.6 (sleipnir) serial & parallel, IRIX64 6.5 (modi4) serial & parallel
* [svn-r5866] Purpose:Quincey Koziol2002-08-095-12/+18
| | | | | | | | | | Code cleanup Description: Cleaned up a few warnings from compiling with --disable-hsizet on Linux Platforms tested: Linux 2.2.x (eirene)
* [svn-r5865] Purpose:Quincey Koziol2002-08-092-4/+4
| | | | | | | | | | | | | | Bug fix Description: hsize_t comparisons for selection boundaries (in H5Sget_select_bounds) were failing on Linux with --disable-hsizet. Solution: Changed comparisons to use use unsigned values instead of signed ones. Platforms tested: Linux 2.2.x (eirene)
* [svn-r5864] ./hdf5-devel/src/H5private.hRobb Matzke2002-08-091-37/+33
| | | | | | | | | | | | | | | | | Purpose: Merged from 1.4 branch Description: API tracing improvements Platforms tested: Linux (--disable-hsizet didn't work before my changes and still doesn't work, but --enable-hsizet is fine). Note: This checkin includes temporary code in H5FDmpiposix.c to turn off GPFS byte range token prefetches on ASCI/Blue. Once the HDF5 API supports the necessary prerequisite functionality this temporary code can be migraged up above HDF5.
* [svn-r5863] ./hdf5-devel/src/H5T.cRobb Matzke2002-08-091-1/+1
| | | | | | | | | | | | | | | | | Purpose: Merged from 1.4 branch Description: API tracing improvements Platforms tested: Linux (--disable-hsizet didn't work before my changes and still doesn't work, but --enable-hsizet is fine). Note: This checkin includes temporary code in H5FDmpiposix.c to turn off GPFS byte range token prefetches on ASCI/Blue. Once the HDF5 API supports the necessary prerequisite functionality this temporary code can be migraged up above HDF5.
* [svn-r5862] ./hdf5-devel/src/H5O.cRobb Matzke2002-08-091-3/+3
| | | | | | | | | | | | | | | | | Purpose: Merged from 1.4 branch Description: API tracing improvements Platforms tested: Linux (--disable-hsizet didn't work before my changes and still doesn't work, but --enable-hsizet is fine). Note: This checkin includes temporary code in H5FDmpiposix.c to turn off GPFS byte range token prefetches on ASCI/Blue. Once the HDF5 API supports the necessary prerequisite functionality this temporary code can be migraged up above HDF5.
* [svn-r5861] ./hdf5-devel/src/H5FDmpiposix.cRobb Matzke2002-08-091-0/+35
| | | | | | | | | | | | | | | | | Purpose: Merged from 1.4 branch Description: API tracing improvements Platforms tested: Linux (--disable-hsizet didn't work before my changes and still doesn't work, but --enable-hsizet is fine). Note: This checkin includes temporary code in H5FDmpiposix.c to turn off GPFS byte range token prefetches on ASCI/Blue. Once the HDF5 API supports the necessary prerequisite functionality this temporary code can be migraged up above HDF5.
* [svn-r5860] ./hdf5-devel/src/H5.cRobb Matzke2002-08-091-14/+89
| | | | | | | | | | | | | | | | | Purpose: Merged from 1.4 branch Description: API tracing improvements Platforms tested: Linux (--disable-hsizet didn't work before my changes and still doesn't work, but --enable-hsizet is fine). Note: This checkin includes temporary code in H5FDmpiposix.c to turn off GPFS byte range token prefetches on ASCI/Blue. Once the HDF5 API supports the necessary prerequisite functionality this temporary code can be migraged up above HDF5.
* [svn-r5843] Purpose:Quincey Koziol2002-08-086-18/+18
| | | | | | | | | | | Code cleanup Description: Clean up a few warnings which were showing up with --enable-production turned on. Platforms tested: FreeBSD 4.6 (sleipnir) serial & parallel
* [svn-r5842] Purpose:Quincey Koziol2002-08-0864-8376/+7713
| | | | | | | | | | | | | | | | Code cleanup Description: Change most (all?) HRETURN_ERROR macros to HGOTO_ERROR macros, along with HRETURN macros to HGOTO_DONE macros. This unifies the error return path from functions and reduces the size of the library by up to 10% on some platforms. Additionally, I improved a lot of the error cleanup code in many routines. Platforms tested: FreeBSD 4.6 (sleipnir) serial & parallel and IRIX64 6.5 (modi4) serial & parallel.
* [svn-r5841] Snapshot version 1.5 release 32HDF Admin2002-08-032-3/+3
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* [svn-r5840] Purpose:Quincey Koziol2002-07-3120-790/+556
| | | | | | | | | | | | | | Code cleanup Description: Created a new H5I function which combined the some of the functionality of H5I_get_type and H5I_object: H5I_object_verify. Using this new function in the library trims another ~200 lines of code off the library and makes the resulting binaries smaller and faster also. Platforms tested: FreeBSD 4.6 (sleipnir)
* [svn-r5839] Purpose:Quincey Koziol2002-07-3116-1962/+1829
| | | | | | | | | | | | | | | Code cleanup Description: Move operations on each type of selection into the source code file for each selection type (all->H5Sall.c, hyperslab->H5Shyper.c, etc.) Remove central H5S_select_<foo> operations, instead calling the operations through function pointers in each selection (a much more object-oriented approach). Platforms tested: FreeBSD 4.6 (sleipnir)
* [svn-r5835] Purpose:Quincey Koziol2002-07-241-1/+1
| | | | | | | | | | Bug fix. Description: Correct erroneous assertion. Platforms tested: IRIX64 6.5 (modi4) w/parallel
* [svn-r5834] Purpose:Quincey Koziol2002-07-249-6141/+2735
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Large code cleanup/re-write Description: This is phase 1 of the data I/O re-architecture, with the following changes: - Changed the selection drivers to not actually do any I/O, they only generate the sequences of offset/length pairs needed for the I/O (or memory access, in the case of iterating or filling a selection in a memory buffer) - Wrote more abstract I/O routines which get the sequence of offset/ length pairs for each selection and access perform the I/O or memory access. Benefits of this change include: - Removed ~3400 lines of quite redundant code, with corresponding reduction in the size of library binary. - Any selection can now directly access memory when performing I/O, if no type conversions are required, instead of just "regular" hyperslab and 'all' selections, which speeds up I/O. - Sped up I/O for hyperslab selections which have contiguous lower dimensions by "flattening" them out into lesser dimensional objects for the I/O. No file format or API changes were necessary for this change. The next phase will be to create a "selection driver" for each type of selection, allowing each type of selection to directly call certain methods that only apply to that type of selection, instead of passing through dozens of functions which have switch statements to call the appropriate method for each selection type. This will also reduce the amount of code in the library and speed things up a bit more. Phase 3 will involve generating an MPI datatype for all types of selections, instead of only "regular" hyperslab and 'all' selections. This will allow collective parallel I/O for all I/O operations which don't require type conversions. It will also open up the door for allowing collective I/O on datasets which require type conversion. Phase 4 will involve changing the access pattern to deal with chunked datasets in a more optimal way (in serial). Phase 5 will deal with accessing chunked datasets more optimally for collective parallel I/O operations. Platforms tested: FreeBSD 4.6 (sleipnir) w/ parallel & C++ and IRIX64 6.5 (modi4) w/parallel
* [svn-r5832] Purpose:Quincey Koziol2002-07-241-7/+7
| | | | | | | | | | Code cleanup Description: Re-alphabetized header includes. Platforms tested: FreeBSD 4.6 (sleipnir) w/parallel & C++
* [svn-r5829] MuQun Yang2002-07-231-1/+1
| | | | | | | | | | Purpose: correct a typo in the H5FD_sec2_flush. Description: fd is not defined. It should be file->fd Solution: Platforms tested: windows 2000, linux 2.2.18smp
* [svn-r5828] Purpose:Quincey Koziol2002-07-233-7/+16
| | | | | | | | | | Code cleanup Description: Make the sieve buffer managed by the free-list code. Platforms tested: FreeBSD 4.6 (sleipnir)
* [svn-r5826] Purpose:Quincey Koziol2002-07-231-14/+19
| | | | | | | | | | | | | | Bug Fix Description: Dynamically allocated H5S_t structure was not being freed under certain error conditions. Solution: Free it. Platforms tested: FreeBSD 4.6 (sleipnir)
* [svn-r5819] Purpose:Quincey Koziol2002-07-211-6/+2
| | | | | | | | | | | | | | Bug Fix Description: non-parallel case for new metadata cache flushing property wasn't set up correctly. Solution: Initialize variables correctly. Platforms tested: FreeBSD 4.6 (sleipnir)
* [svn-r5814] Purpose:Quincey Koziol2002-07-1911-108/+304
| | | | | | | | | | | | | | | | | | Bug Fix Description: It was possible to create corrupted metadata information (either in memory or in the file or both) with a parallel I/O program because of the way metadata writes were being handled for writes out of the metadata cache. Solution: Added a dataset transfer property called "block before metadata write" which is used by the MPI-I/O and MPI-posix drivers to sync up all the processes before attempting a metadata write. This property is currently only for metadata writes from the metadata cache. Platforms tested: IRIX64 6.5 (modi4) w/parallel
* [svn-r5812] Raymond Lu2002-07-172-15/+44
| | | | | | | | | Purpose: Bug fix. Description: This should fix the nested VL datatype bug. Platforms tested: modi4, eirene, impact
* [svn-r5809] Purpose:Quincey Koziol2002-07-171-1/+1
| | | | | | | | | | | | | | Bug fix Description: Deleting objects from a global heap was incorrectly setting the free space in the heap chunk. Solution: Encode correct amount of free space. Platforms tested: IRIX64 6.5 (modi4)
* [svn-r5807] Purpose:Bill Wendling2002-07-172-9/+12
| | | | | | | | | | | | | | | | | | | | | | | | | Update, Bug Fix, and Feature Add Description: - Updated how AC_{ENABLE,WITH} help messages were being generated. Autoconf now gives you an AC_HELP_STRING macro to use to create them. - Fixed the problem with Linux LFS on RedHat 7.3 machines. It wasn't finding getdents64(), so we can't rely on that being present anymore... - Added GPFS detection and setting. - Updated how compression is specified. It's no longer necessary to test for HAVE_ZLIB_H, HAVE_LIBZ, and HAVE_COMPRESS2. The one macro {H5_}HAVE_COMPRESSION takes care of all of these. Solution: Changed the check for Linux LFS from looking for getdents() to looking at the version number of the kernel (using the uname -r command). You can still override with the --enable-linux-lfs switch if you really believe that your <2.4 kernel has LFS support. Platforms tested: Linux (2.2 and 2.4)
* [svn-r5799] Purpose:Quincey Koziol2002-07-1514-167/+1427
| | | | | | | | | | | | 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-r5793] Purpose:Quincey Koziol2002-07-152-19/+37
| | | | | | | | | | | | Code cleanup Description: Changed a few direct calls to posix functions to use proper wrapper macros. Also, changed method of extending file to use ftruncate(). Platforms tested: FreeBSD 4.6 (sleipnir) && IRIX64 6.5 (modi4)
* [svn-r5789] Purpose:Quincey Koziol2002-07-152-2/+2
| | | | | | | | | | Code cleanup Description: Make a "H5T_t *" parameter into a "const H5T_t *" parameter. Platforms tested: FreeBSD 4.6 (sleipnir)
* [svn-r5787] Purpose:Quincey Koziol2002-07-121-1/+1
| | | | | | | | | | Update code Description: Re-enable free-lists, which were accidentally disabled from last checkin. Platforms tested: FreeBSD 4.6 (sleipnir)
* [svn-r5785] Purpose:Quincey Koziol2002-07-122-51/+37
| | | | | | | | | | Code update Description: Re-arrange to disable free-list code in a more transparent way. Platforms tested: FreeBSD 4.6 (sleipnir)
* [svn-r5784] Purpose:Quincey Koziol2002-07-121-91/+100
| | | | | | | | | | | | | | | Bug fix. Description: "strong" file closing feature was re-using free'd memory for objects which were still open in the file. Solution: Used the "dmalloc" tools to determine where the memory was being re-used and re-arranged the code to avoid these cases. Platforms tested: FreeBSD 4.6 (sleipnir)
* [svn-r5783] Purpose:Quincey Koziol2002-07-122-2/+6
| | | | | | | | | | New code Description: Add a few new error messages. Platforms tested: FreeBSD 4.6 (sleipnir)
* [svn-r5782] Purpose:Quincey Koziol2002-07-122-3/+13
| | | | | | | | | | | New feature Description: Add support in for "dmalloc" debugging malloc library to configure script and library headers. Platforms tested: IRIX64 6.5 (modi4) and FreeBSD 4.6 (sleipnir)
* [svn-r5779] Raymond Lu2002-07-111-3/+4
| | | | | | | | | | | Purpose: Bug fix Description: Nested VL datatype test fails on 64-bit machines Solution: bug fixed. Platforms tested: IRIX64 6.5(modi4) 64-bit
* [svn-r5776] Raymond Lu2002-07-101-2/+19
| | | | | | | | | | | | | Purpose: Bug fix. Description: For nested VL datatype, the heap object of VL elements lower than top level weren't freed. Solution: Read in the content of heap object for VL elements and free them in function H5T_conv_vlen. Platforms tested: eirene
* [svn-r5774] Snapshot version 1.5 release 31HDF Admin2002-07-061-2/+2
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* [svn-r5764] Raymond Lu2002-07-034-30/+83
| | | | | | | | | | | Purpose: Bug Fix. Description: VL type memory leak when data is overwritten. Solution: Free heap objects holding old data. Platforms tested: Linux 2.2(eirene), IRIX 6.5(paz).
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