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* [svn-r5662] Purpose:Quincey Koziol2002-06-181-0/+4
| | | | | | | | | | | | | | | | | Bug fix. Description: The chunking code was using internal allocation routines to put blocks on a free list for reuse, instead of using the system allocation routines (ie. malloc, free, etc.). This causes problems when user filters attempt to allocate/free chunks for their algorithm's use. Solution: Switched the chunking code back to using the system allocation routines, we can address performance issues with them if it becomes a real problem. Platforms tested: Linux 2.2.x (eirene) && IRIX64 6.5 (modi4)
* [svn-r5660] Purpose:Quincey Koziol2002-06-181-2/+6
| | | | | | | | | | | | Code optimization Description: Avoid creating MPI types (and thus requiring a MPI_File_set_view() call) when contiguous selections are used for dataset I/O. This should be a performance improvement for those sorts of selections. Platforms tested: Linux 2.2.x (eirene) w/parallel && IRIX64 6.5 (modi4) w/parallel & FORTRAN
* [svn-r5657] Updated.Albert Cheng2002-06-172-4/+31
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* [svn-r5649] Bugs in src/Makefile and test/Makefile have been resolved.Albert Cheng2002-06-171-43/+4
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* [svn-r5636] Purpose:Quincey Koziol2002-06-141-0/+3
| | | | | | | | | | Default change Description: Enable the use of MPI types for collective I/O by default. Platforms tested: Linux 2.2.x (eirene) w/parallel
* [svn-r5603] Purpose:Quincey Koziol2002-06-121-3/+6
| | | | | | | | | | | | | | | | Bug fix Description: I/O on "Regular" hyperslab selections could fail to transfer correctly if the number of elements in the selection's row did now fit "evenly" into the buffer being used for the transfer. Solution: Correct the calculation of the block & count offsets within the optimized "regular" hyperslab routines. Platforms tested: FreeBSD 4.5 (sleipnir)
* [svn-r5591] Purpose:Bill Wendling2002-06-111-1/+4
| | | | | | | | Update Description: Explained that, if the user uses the "make install prefix=NEW_DIR" option, they'll need to modify the installed h5cc file to reflect the change.
* [svn-r5586] Purpose:Quincey Koziol2002-06-111-0/+3
| | | | | | | | | | | | | | | | Bug Fix Description: H5Dcreate and H5Tcommit allow "empty" compound and enumerated types (i.e. ones with no members) to be stored in the file, but this causes an assertion failure and is somewhat vapid. Solution: Check the datatype "makes sense" before using it for H5Dcreate and H5Tcommit. Platforms tested: FreeBSD 4.5 (sleipnir)
* [svn-r5571] Purpose:Quincey Koziol2002-06-101-0/+2
| | | | | | | | | | | Bug Fix (#709)/Code improvement. Description: Allow chunks for chunked datasets to be cached when file is open for read-only access. Platforms tested: IRIX64 6.5 (modi4) w/parallel
* [svn-r5566] Purpose:Quincey Koziol2002-06-101-0/+2
| | | | | | | | | | | | | | Bug fix (bug #777) Description: Current code allows a compound datatype to be inserted into itself. Solution: Check if the ID for the member is the same as the ID for the compound datatype and reject it if so. Platforms tested: FreeBSD 4.5 (sleipnir)
* [svn-r5560] Purpose:Quincey Koziol2002-06-101-4/+6
| | | | | | | | | | | | | | Bug Fix for bug #789 Description: Creating a 1-D dataset region reference caused the library to hang (go into an infinite loop). Solution: Corrected algorithm for serializing hyperslab regions. Platforms tested: FreeBSD 4.5 (sleipnir)
* [svn-r5536] Purpose:Quincey Koziol2002-06-051-0/+2
| | | | | | | | | | | | | | | | | New feature. Description: Added a "small data" block allocation mechanism to the library, similar to the mechanism used for allocating metadata currently. See the RFC for more details: http://hdf.ncsa.uiuc.edu/RFC/SmallData/SmallData.html This reduces the number of I/O operations which hit the disk for my test program from 19 to 15 (i.e. from 393 to 15, overall). Platforms tested: Solaris 2.7 (arabica) w/FORTRAN and FreeBSD 4.5 (sleipnir) w/C++
* [svn-r5534] Purpose:Albert Cheng2002-06-041-18/+30
| | | | | | Updated the instructions for tflops and O2K. Platforms tested: eye balled.
* [svn-r5524] Elena Pourmal2002-06-041-1/+4
| | | | | | | | | | | | | Purpose: Bug fix (#699), fix provided by a user, approved by Quincey Description: When a scalar dataspace was written to the file and then subsequently queried with the H5Sget_simple_extent_type function, type was reported H5S_SIMPLE instead of H5S_SCALAR. Solution: Applied a fix (see bug report 699) Platforms tested: Solaris 2.7 and Linux 2.2.18
* [svn-r5521] Purpose:Quincey Koziol2002-06-041-0/+3
| | | | | | | | | | | | | | | | | | | | | | | Code improvement Description: The metadata aggregation code in the library was not terribly smart about extending contiguous regions of metadata in the file and would not extend them as far as possible. This causes space in the file to be wasted, also. Solution: Be smarter about extending the space used in the file for metadata by checking whether new metadata blocks allocated in the file are at the end of the current metadata aggregation region and append them to the metadata region if so. This has the nice side benefit of reducing the number of bytes we waste in the file and reducing the size of the file by a small amount in some cases. This reduces the number of I/O operations which hit the disk for my test program from 53 to 19 (i.e. from 393 to 19, overall). Platforms tested: Solaris 2.7 (arabica) w/FORTRAN and FreeBSD 4.5 (sleipnir) w/C++
* [svn-r5519] Purpose:Quincey Koziol2002-06-041-0/+2
| | | | | | | | | | | | | | | | | | Bug Fix Description: The "dirty" flag for symbol table entries and symbol table nodes was not being cleared when they were flushed to the file, causing lots of extra metadata I/O. Solution: Reset the symbol table entry & nodes' flags when thy are flushed to disk. This reduces the number of I/O operations which hit the disk for my test program from 83 to 53 (i.e. from 393 to 53, overall). Platforms tested: Solaris 2.7 (arabica) w/FORTRAN & FreeBSD 4.5 (sleipnir) w/C++
* [svn-r5510] Purpose:Quincey Koziol2002-06-031-0/+3
| | | | | | | | | | | | | | | | | | | | | | | | Code cleanup/bug fix Description: The "metadata accumulator" cache in the library (which is designed to catch small metadata writes/reads and bundle them together into larger I/O buffers) was incorrectly detecting the important case of metadata pieces being written sequentially to the file, adjoining but not overlapping. Additionally, the metadata accumulator was not being used to cache data read in from disk, only caching writes. Solution: Fix accumulator to correctly cache adjoining metadata writes and also to cache metadata read from disk. Between these two fixes, the number of I/O requests which resulted in actual reads/writes to the filesystem dropped from 393 requests to 82 for the particular test I was using. :-) Platforms tested: Solaris 2.7 (arabica) w/FORTRAN & FreeBSD 4.5 (sleipnir) w/C++
* [svn-r5506] Snapshot version 1.5 release 29HDF Admin2002-06-021-1/+1
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* [svn-r5500] Purpose:Quincey Koziol2002-06-011-1/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | Document Bug Fix Description: Under certain [obscure] circumstances, an object header would get paged out of the metadata cache, and when it was accessed again and brought back into the cache, and immediately had additional metadata added to it (an attribute, usually, or perhaps adding an object to a group), and needed to be extended with a continuation message, but there was no room in any existing object header chunks for the continuation message and an existing object header message needed to be moved to the new object header chunk (I told you it was obscure :-), the object header message moved to the new chunk (not the new metadata being added) would get corrupted. *whew* :-) Solution: Actually copy the "raw" object header message information of the object header message being moved to the new chunk, instead of relying on the "native" object header message information being re-encoded when the object header is flushed. This is because when an object header is paged out of the metadata cache and subsequently brought back in, the "native" information pointer in memory is reset to NULL and only the "raw" information exists. Platforms tested: Solaris 2.7 (arabica) & FreeBSD 4.5 (sleipnir)
* [svn-r5465] Snapshot version 1.5 release 28HDF Admin2002-05-281-1/+1
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* [svn-r5453] MuQun Yang2002-05-221-313/+21
| | | | | | | | | Purpose: update, remove hdf4-related stuff. Description: hdf4 related tools have been moved out of HDF5 CVS tree, The install doc should reflect this. Solution: Platforms tested:
* [svn-r5442] Purpose:Quincey Koziol2002-05-201-0/+4
| | | | Document VFL "flush" changes.
* [svn-r5435] Purpose:Quincey Koziol2002-05-171-0/+4
| | | | | | | | | | Document Code improvement below: Description: Propagated the "fill time" property into the parallel chunk allocation routine, allowing it to avoid writing fill values to each new chunk allocated. This improves the performance of chunked datasets in parallel I/O to be on par with contiguous datasets again (on modi4).
* [svn-r5430] Purpose:Quincey Koziol2002-05-171-4/+8
| | | | | | | | | | | | | | | | | | Document Bug fix/Code improvement below: 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.
* [svn-r5415] Purpose:Quincey Koziol2002-05-141-0/+2
| | | | Document Bug Fix
* [svn-r5409] Purpose:Quincey Koziol2002-05-131-0/+2
| | | | Document Performance enhancement
* [svn-r5404] Purpose:Quincey Koziol2002-05-131-6/+0
| | | | | | | Back out change Description: Back out description of VFL 'flush' change.
* [svn-r5395] Purpose:Bill Wendling2002-05-101-0/+9
| | | | | | | Update Description: Added documentation on how you can install in a different directory than the one you specified during configuration.
* [svn-r5394] Purpose:Quincey Koziol2002-05-101-1/+7
| | | | Document new VFL flush parameter.
* [svn-r5389] Purpose:Quincey Koziol2002-05-101-0/+2
| | | | Update release notes about rotating metadata writes.
* [svn-r5383] Purpose:Bill Wendling2002-05-091-0/+12
| | | | | | Update Description: Updated how to compile HDF5 with Intel compilers (ecc or icc).
* [svn-r5364] Elena Pourmal2002-05-061-1/+12
| | | | | | | | Purpose: Maintenance Description: Added information about Parallel Fortran Support for HP-UX 11.00 SysV and write/read overloaded subroutines (bug #670)
* [svn-r5286] Purpose:Quincey Koziol2002-04-291-0/+2
| | | | | | | | | | | | | | Bug Fix Description: Selection offsets were not being used correctly when iterating through all hyperslabs selections and point selections. Solution: Use the selection offset appropriately. Platforms tested: FreeBSD 4.5 (sleipnir)
* [svn-r5275] Snapshot version 1.5 release 27HDF Admin2002-04-271-1/+1
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* [svn-r5273] Raymond Lu2002-04-261-0/+3
| | | | | | | | | | | | Purpose: New feature Description: Allow H5Glink and H5Gmove to handle links across different locations. Solution: Added H5Glink2 and H5Gmove2 functions with new parameter of destination location. Platforms tested: Linux 2.2(eirene)
* [svn-r5237] Purpose:Albert Cheng2002-04-231-26/+30
| | | | | | | | Updated the installation instruction for the Tflops machine. Moved the parallel HDF5 building instructions to the front and putting in a NOTE that the sequential version is not supported any more because it has little practical value to build sequential applications for the Tflops machine.
* [svn-r5229] Updated with support for parallel C API.Albert Cheng2002-04-231-1/+1
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* [svn-r5224] Purpose:Albert Cheng2002-04-221-0/+75
| | | | | | | | | Update Description: Added the support platform summary paragraph. Thread safe is supported for solaris 2.8_32bit. Platforms tested: hdfsun8
* [svn-r5213] Snapshot version 1.5 release 26HDF Admin2002-04-201-1/+1
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* [svn-r5199] Snapshot version 1.5 release 25HDF Admin2002-04-181-1/+1
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* [svn-r5193] Purpose:Albert Cheng2002-04-171-2/+12
| | | | | | | | | | | Maintenance Description: The tflops option local modification in bin/config.sub was wiped out during the latest autoconfigure tools upgrade. Instead of adding it in for every autoconfigure tools upgrade, I changed the instruction to use a standard feature in configure. ./configure --host=i386-intel-osf1 This is a bit more typing but no more local modification.
* [svn-r5191] Purpose:Quincey Koziol2002-04-171-0/+3
| | | | | | | | | | | | | | | | | | | Bug fix Description: When several level deep nested compound & VL datatypes are used, the data in the nested compound datatypes is incorrectly sharing the same "background buffer", causing data corruption when the data is written to the file. Solution: Allocate a separate background buffer for each level of the nested types to convert. (Also allocate temporary background buffers for array datatypes, where this sort of problem could occur also) Added more regression tests to check for these errors. Platforms tested: FreeBSD 4.5 (sleipnir) & Solaris 2.6 (baldric)
* [svn-r5188] Updated instruction how to configure the TFLOPS machine.Albert Cheng2002-04-161-2/+2
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* [svn-r5176] Pedro Vicente Nunes2002-04-121-0/+3
| | | | | Purpose: added description of H5Dset_extent
* [svn-r5170] Raymond Lu2002-04-111-0/+4
| | | | | | | | | | | Purpose: New feature Description: Fill-value's behaviors for contiguous dataset have been redefined. Basicly, dataset won't allocate space until it's necessary. Full details are available at http://hdf.ncsa.uiuc.edu/RFC/Fill_Value, at this moment. Platforms tested: Linux 2.2.
* [svn-r5152] Purpose:Quincey Koziol2002-04-091-0/+2
| | | | | | | | | | | | | | | New Feature Description: Added new H5Dfill() routine to fill the elements in a selection for a memory buffer with a fill value. This is a user API wrapper around some internal routines which were needed for the fill-value modifications from Raymond as well as Pedro's code for reducing the size of a chunked dataset. Platforms tested: FreeBSD 4.5 (sleipnir) [and IRIX64 6.5 (modi4) in parallel, in a few minutes]
* [svn-r5148] Snapshot version 1.5 release 24HDF Admin2002-04-061-1/+1
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* [svn-r5147] Raymond Lu2002-04-051-0/+3
| | | | | | | | | | Purpose: New feature Description: Added a query function H5Tget_member_index for compound and enumeration data types, to retrieve member's index by its name. Platforms tested: Linux 2.2
* [svn-r5138] Purpose:Quincey Koziol2002-04-031-0/+2
| | | | | | | | | | | | | | | | | | | | | | Bug Fix & Code Cleanup Description: The MPI-IO optimized transfer routines (H5S_mpio_spaces_read/H5S_mpio_space_write) are not being invoked in all the cases where they could be used. Additionally, the code for determining if an optimized transfer is wrapped into the actual I/O transfer routine in a very confusing way. Solution: Re-enabled MPI-IO optimized transfer routines in all the cases where they should work. Extracted all the pre-conditions for optimized transfers into separate routines from the transfer routines. Platforms tested: FreeBSD 4.5 (sleipnir) & IRIX64 6.5 (modi4)
* [svn-r5130] Purpose:Quincey Koziol2002-04-021-167/+172
| | | | | | | | | | | | | | | | | | | | | | Bug Fix & Feature Description: The selection offset was being ignored for optimized hyperslab selection I/O operations. Additionally, I've found that the restrictions on optimized selection I/O operations were too strict and found a way to allow more hyperslabs to use the optimized I/O routines. Solution: Incorporate the selection offset into the selection location when performing optimized I/O operations. Allow optimized I/O on any single hyperslab selection and also allow hyperslab operations on chunked datasets. Platforms tested: FreeBSD 4.5 (sleipnir)
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