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* [svn-r9135] Snapshot version 1.6 release 3 (snap4)HDF Admin2004-08-231-2/+2
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* [svn-r9118] Purpose: Minor Bug FixRaymond Lu2004-08-191-2/+2
| | | | | | | | | Description: In H5O_fill_new_decode and H5O_fill_new_encode, macros UINT32DECODE and UINT32ENCODE were used to decode and encode message size, which is ssize_t. Solution: Changed to INT32DECODE and INT32ENCODE. Platforms tested: Tested v1.7 on fuss - very simple change.
* [svn-r9107] Purpose: Bug fixRaymond Lu2004-08-181-18/+5
| | | | | | | | | | | Description: In H5O_fill_new_decode, it tries to read message size(-1) when fill value is undefined for version 1. During UINT32DECODE, if the machine is 64-bit, a value 0x00000000ffffffff is returned, which is like a valid value. Solution: Don't decode message size if fill value is undefined, simply assign -1 to message size. Platforms tested: h5committest.
* [svn-r9102] Purpose:Quincey Koziol2004-08-174-308/+278
| | | | | | | | | | | | | | | | | | | | | | | | | | | | Bug fix Description: 1 - Dataset contiguous storage cache information had a bug where it was possible to try to access invalid cache information if the cache wasn't filled the first time it attempted to loop through the list of offset/length vectors. 2 - Additionally, the contiguous storage cache information was being used in certain circumstances from the chunked dataset I/O code path, which was generally fatal since the chunk storage and contiguous storage information were stored together in a union. Solution: 1 - Avoid special case of first trip through loop over offset/length I/O vectors and always check for the contiguous storage sieve buffer buffer being NULL. 2 - Change the union containing the chunk and contiguous storage cache information into a struct, allowing both to be used at the same time. Platforms tested: FreeBSD 4.10 (sleipnir) h5committested
* [svn-r9065] Purpose:Robert E. McGrath2004-08-111-9/+9
| | | | | | | | | | | | | | | Bug fix Description: Wrong value returned for error Solution: Return correct value Platforms tested: verbena Misc. update:
* [svn-r9055] Snapshot version 1.6 release 3 (snap3)HDF Admin2004-08-091-2/+2
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* [svn-r9054] Purpose:Quincey Koziol2004-08-082-27/+45
| | | | | | | | | | | | | | | | | | | Bug fix Description: Correct possible core dump when a datatype conversion function is registered with the library after a compound datatype has been converted (having it's type conversion information cached by the library). The compound datatype must have been created by inserting the fields in non-increasing offset order to see the bug. Solution: Re-sort the fields in the compound datatypes before recalculating the cached information when performing the conversion on them. Platforms tested: FreeBSD 4.10 (sleipnir) h5committested
* [svn-r9038] Purpose:Quincey Koziol2004-08-061-1/+1
| | | | | | | | | | | | Code cleanup/bug fix Description: Check for _O_BINARY being defined instead of O_BINARY, since we actually use _O_BINARY. (Note that this only affects Windows) Platforms tested: FreeBSD 4.10 (sleipnir) Not tested w/h5committest
* [svn-r9030] Purpose:Albert Cheng2004-08-051-4/+273
| | | | | | | | | | | | | | | | | | | | | | | | | | Bug fix (Failures when dataset size >= 1 GB, reported by Bill Loewe.) Description: In the IBM AIX system using 32bit mode, if a dataset size was 1GB or larger, when the "end" of the dataset was selected, MPI would complain it could not keep the Upper bound of a datatype within the range of MPI_Aint. This was because the old algorithm would derive the selection with extent of each row first. After all dimensions were processed, it then calculate the start position and just displace the whole MPI derived type. So, the final MPI type was actually the start position plus the whole dataset. Since the start can be as big as the whole dataset, this made the final derived twice as big as 1GB. That would hit the 2GB MPI_Aint range limit in the 32 bit mode. Solution: Use a different algorithm to include the start position in the defining of MPI type for each dimension. When all dimensions are processed, the MPI type represents the selection exactly. Platforms tested: h5committested Misc. update:
* [svn-r9025] Purpose:Quincey Koziol2004-08-051-1/+2
| | | | | | | | | | | | | Bug fix Description: Correct buffer overrun in "multi" VFL driver that was writing past the end of the "driver name" buffer when encoding the driver info block for the file's superblock. Platforms tested: FreeBSD 4.10 (sleipnir) Too minor to require h5committest
* [svn-r9004] Purpose:Robert E. McGrath2004-08-031-0/+7
| | | | | | | | | | | | | | | | Fix to feature added yesterday Description: Needed additional check on the SZIP bits per pixel parameter Solution: if (precision > 24 && precision < 31) precision = 32 if (precision > 32 && precision < 64) precision = 64 Platforms tested: arabica,verbena,hirdls Misc. update:
* [svn-r8998] Purpose:Quincey Koziol2004-08-031-2/+8
| | | | | | | | | | | | | Bug fix Description: Correct assertion and fix minor bug with encoding of "older" style layout information which is updated by writing data to a previously empty dataset. Platforms tested: FreeBSD 4.10 (sleipnir) Too minor to require h5committest
* [svn-r8995] Purpose:Quincey Koziol2004-08-031-1/+1
| | | | | | | | | | | Bug fix Description: Add H5FDmpi.h to the list of public headers. Platforms tested: FreeBSD 4.10 (sleipnir) w/C++ Not tested by h5committest
* [svn-r8990] Purpose:Robert E. McGrath2004-08-021-2/+19
| | | | | | | | | | | | | | | Add missing feature. Strongly requested by NASA. Description: Add support for 'n-bit' data in SZIP filter. Solution: When precision < (size*8) use precision at the BPP for SZIP. Platforms tested: verbena,arabica,hirdls (SGI 64bit) Misc. update:
* [svn-r8989] Purpose:Quincey Koziol2004-08-0213-365/+366
| | | | | | | | | | | | | | Backport feature Description: Backport Kent's collective chunk I/O work to date into the release branch. Also, minor code cleanups, etc. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel IRIX64 6.5 (modi4) h5committested
* [svn-r8988] This commit was manufactured by cvs2svn to create branch 'hdf5_1_6'.cvs2svn2004-08-021-0/+268
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* [svn-r8985] Purpose:Quincey Koziol2004-08-0246-7294/+2217
| | | | | | | | | | | | | | | | | | | | | Bug fixes & code cleanups Description: Backport MPI-I/O changes from the development branch to the release branch in preparation for bringing Kent's collective chunk I/O changes back. Removed last vestiges of FPHDF5 from this branch, as it was never working here. Various code cleanups & syncrontizations to better align with development branch code and reduce diffs. Regenerate dependencies. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel IRIX64 6.5 (modi4) h5committested
* [svn-r8984] This commit was manufactured by cvs2svn to create branch 'hdf5_1_6'.cvs2svn2004-08-024-0/+406
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* [svn-r8980] Snapshot version 1.6 release 3 (snap2)HDF Admin2004-08-021-2/+2
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* [svn-r8970] Purpose:Quincey Koziol2004-07-302-50/+35
| | | | | | | | | | | | | | | | | | | | | | | | Bug fix. Description: Address two problems: - The computation of the scanline in the szip filter was being performed in the "can apply" callback routine instead of the "set local" routine. - The routine which allocated all the chunks for an entire dataset (which is invoked when the allocation time is early or late, rather than incremental) wasn't recording a failed filter in the information for the chunk, causing the library to believe that the chunk had the filter applied when it really hadn't. Solution: - Move the scanline computation to the "set local" callback. - Record the filter mask with each chunk created when allocating them. Platforms tested: FreeBSD 4.10 (sleipnir) w/szip Too obscure to require h5committest
* [svn-r8963] Purpose:Quincey Koziol2004-07-281-3/+3
| | | | | | | | | | | | | | | Bug fix Description: Allow I/O on extendible chunked datasets with (currently) zero-sized dimensions to proceed harmlessly instead of dumping core on an assertion. Solution: Removed assertion and added checks to avoid problem situation in H5TB_end Platforms tested: FreeBSD 4.10 (sleipnir) w/ & w/o parallel Too minor to require h5committest
* [svn-r8959] Purpose:Quincey Koziol2004-07-271-1/+3
| | | | | | | | | | | | | Bug fix Description: Always write fill values to chunks when initializing entire B-tree and any filters are defined. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel Solaris 2.7 (arabica) Too minor to require h5committest
* [svn-r8954] James Laird2004-07-275-1/+60
| | | | | | | | | | | | | | | | Purpose: Bug fix Description: When a simple dataspace is created, its extent should be set before using it, or it will silently function as a NULL dataspace. Solution: Added checks on user-supplied dataspaces. Now dataspaces without extents set will throw errors; users must explicitly set a dataspace to be NULL. Platforms tested: sleipnir, windows
* [svn-r8948] Purpose:Quincey Koziol2004-07-261-2/+2
| | | | Bump version # after making snapshot
* [svn-r8947] Purpose:Quincey Koziol2004-07-265-16/+49
| | | | | | | | | | | | | | | | | | Code cleanup, sorta Description: Added ifdef sections for "H5_USING_PURIFY" in various places in the code, which are designed to reduce the spurious "uninitialized memory read" warnings from purify which are actually OK. Note that this macro will have to be turned on by adding it to the CFLAGS for the build - I didn't think it was important enough to add a configure flag for. Also, the changes in H5HG.c optimize the walks through the objects in a heap to only look at the 'used' entries instead of all the 'allocated' entries. Platforms tested: Solaris 2.7 (arabica) w/purify Not tested by h5committest
* [svn-r8945] Purpose:Quincey Koziol2004-07-261-2/+4
| | | | | | | | | | | | Code optimization Description: Eliminate duplicated call to H5T_detect_class() Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.10 (sleipnir) w/parallel Too minor to require h5committest
* [svn-r8942] Purpose:Quincey Koziol2004-07-261-2/+6
| | | | | | | | | | | | | | Code optimization Description: Changed calloc() calls to malloc() calls allocating background buffers during dataset writes, since the background buffer information will be read from disk anyway, overwriting any existing values. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.10 (sleipnir) w/parallel Too minor to require h5committest
* [svn-r8940] Snapshot version 1.6 release 3 (snap0)HDF Admin2004-07-261-2/+2
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* [svn-r8939] Purpose:Albert Cheng2004-07-231-3/+3
| | | | Updated the library version to 1.6.3-snap0.
* [svn-r8937] James Laird2004-07-232-4/+10
| | | | | | | | | | | | | | | | | | | Purpose: Bug fix Description: Modification time test (mtime) would die silently on some systems. This is because the code is very system-dependant (it relies on getting the current time and the timezone from the OS). Solution: mtime test now uses TEST_ERROR macro to print "FAILED" and to output where the failure occurred. Configure script is a little smarter about whether gettimeofday() function returns the timezone correctly. Further bugs will need to be addressed on a system-by-system basis. Platforms tested: sleipnir, arabica, verbena, copper, windows (VC7)
* [svn-r8935] Elena Pourmal2004-07-221-6/+6
| | | | | | | | | | | | | | | | Purpose: Bug fix Description: While working on the SZIP documentation with Frank, I realized that when scanline was less than 4k and bigger than pixels_per_block, it was not adjusted if number_of_blocks_per_scanline was bigger than max_number_of_blocks_per_scanline. Solution: Fixed the code. Unfortunately it didn't help with the problem I had using h5repack with DOQGROD.he5 file. Platforms tested: copper Misc. update:
* [svn-r8917] Elena Pourmal2004-07-211-10/+28
| | | | | | | | | | | | | | | | | | Purpose: Improvement Description: HDF5 Library set pixels_per_scanline parameter to the size of the chunk's fastest changing dimension. As a result, fastest changing dimension of the chunk could not be bigger than 4K and smaller than pixels_per_block value and szip compression couldn't be used for many real datasets. Solution: Reworked algorithm how HDF5 sets pixels_per_scanline value; only chunks with the total number of elements less than pixels_per_block value are rejected. There is no restriction on the size of the chunk's fastest changing dimension anymore. Platforms tested: verbena, copper, sol Misc. update:
* [svn-r8902] Purpose:Quincey Koziol2004-07-201-6/+3
| | | | | | | | | | | | Bug fix Description: Allow buffer parameter to H5Dread & H5Dwrite to be NULL if there are no elements to transfer. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel Too minor to require h5committest
* [svn-r8900] James Laird2004-07-201-0/+3
| | | | | | | | | | | | | | Purpose: Bug Fix Description: H5Sset_extent_simple causes errors if used to reduce a space's maxdims to zero. Solution: H5Sset_extent_simple now cleans up the pointer. Added a regression test. Platforms tested: sleipnir (very minor change)
* [svn-r8898] James Laird2004-07-201-0/+7
| | | | | | | | | | | | | | | Purpose: Bug Fix Description: Trying to create the root group or the working group ("/" or ".") fakes out HDF5 so that it neither creates a group nor returns an error. Solution: H5G_namei now throws an error if it was supposed to insert but didn't. Platforms tested: sleipnir, Visual Studio 7 (very minor change)
* [svn-r8893] Purpose:Quincey Koziol2004-07-1613-483/+825
| | | | | | | | | | | | | | Code cleanup Description: Clean up a bunch of warnings and bring new code better inline with current library coding practice. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel Too minor to require h5committest Misc. update:
* [svn-r8880] James Laird2004-07-152-3/+3
| | | | | | | | | | | | Purpose: Bug fix Description: Replaced "unsigned long long" with hsize_t in H5MF Added "return 0" at end of reserved.c test (duh!). Platforms tested: arabica, sleipnir
* [svn-r8876] James Laird2004-07-149-13/+202
| | | | | | | | | | | | | | | | | | | | | | Purpose: Bug Fix Description: If an HDF5 file grows larger than its address space, it dies and is unable to write any data. This is more likely to happen since users are able to change the number of bytes used to store addresses in the file. Solution: HDF5 now throws an error instead of dying. In addition, it "reserves" address space for the local heap and for object headers (which do not allocate space immediately). This ensures that after the error occurs, there is enough address space left to flush the entire file to disk, so no data is lost. A more complete explanation is at /doc/html/TechNotes/ReservedFileSpace.html Platforms tested: sleipnir, copper (parallel), verbena, arabica, Windows (Visual Studio 7) Misc. update:
* [svn-r8875] Purpose:Quincey Koziol2004-07-145-110/+192
| | | | | | | | | | | | | | | | | | | | Bug fix Description: Correct problems with "resurrecting" a dataset in a file. (This occurs when a dataset which is open gets unlinked from the group hierarchy (making it "dead" and marked for deletion in the file) and then is re-linked to the group hierarchy). Note that the current solution applies only to datasets, further work will fix this for groups and named datatypes also. Also, fix the "debug" routines to be a little more helpful in certain situations. Additionally, fix a locking bug in the symbol table node splitting routine which could be [one of] the cause[s] of the file corruption in flexible parallel operation. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel h5committested
* [svn-r8868] Purpose:Quincey Koziol2004-07-131-3/+13
| | | | | | | | | | | | | | | | | | | Bug fix Description: Fix error in chunked dataset I/O where data written out wasn't read correctly from a chunked, extendible dataset after the dataset was extended. Also, fix parallel I/O tests to gather error results from all processes, in order to detect errors that only occur on one process. Solution: Bypass chunk cache for reads as well as writes, if parallel I/O driver is used and file is opened for writing. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel Too minor to require h5committest
* [svn-r8866] Purpose:Quincey Koziol2004-07-134-74/+126
| | | | | | | | | | | | | | | | | Code optimization Description: Re-work the insertion of a new child into an existing node, to exploit some speedups for adding the rightmost child, since this is a very common case when appending records to an unlimited size dataset. Also, hoist the checks for the tree's 'K' value into a field in the shared information about the tree, instead of re-calculating them all the time. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.10 (sleipnir) w/parallel Too minor to require h5committest
* [svn-r8862] Purpose:Quincey Koziol2004-07-121-11/+38
| | | | | | | | | | | | Code optimization Description: Avoid calling vector comparison routine when operating on 1-D chunks. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.10 (sleipnir) w/parallel Too minor to require h5committest
* [svn-r8854] Purpose:Quincey Koziol2004-07-109-341/+375
| | | | | | | | | | | | | | | | | | | | 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-r8848] Purpose:Quincey Koziol2004-07-091-69/+20
| | | | | | | | | | | | Code cleanup & small optimization Description: Eliminate redundant recomputation of native key pointer offsets. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.10 (sleipnir) w/parallel too minor to require h5committest
* [svn-r8846] Purpose:Quincey Koziol2004-07-0911-43/+130
| | | | | | | | | | | | | | | | | | 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-r8845] This commit was manufactured by cvs2svn to create branch 'hdf5_1_6'.cvs2svn2004-07-093-0/+231
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* [svn-r8824] Purpose:Quincey Koziol2004-07-0710-416/+405
| | | | | | | | | | | | | | | 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-r8819] Purpose: Potential bug fixRaymond Lu2004-07-072-9/+12
| | | | | | | | Description: In H5Fget_filesize, file size was returned as haddr_t. Solution: Return file size as hsize_t and parameter for Fortran. Platforms tested: eirene
* [svn-r8808] Purpose:Quincey Koziol2004-07-051-68/+58
| | | | | | | | | | | | Code optimization Description: Don't copy layout information, just point to existing information. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.10 (sleipnir) w/parallel Too minor to require h5committest
* [svn-r8806] Purpose:Quincey Koziol2004-07-051-91/+162
| | | | | | | | | | | | | | | | | | Code optimization & bug fix CVS: [is this a bug fix? feature? ...] Description: Speed up "fast comparison" lookups in trees by a factor of 2-3x Correctly handle "fast comparisons" for unsigned values (esp. hsize_t). Solution: Mostly removing if statements and redundant assigns, etc. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.10 (sleipnir) w/parallel Too minor to require h5committest
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