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* [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).
* [svn-r5759] Purpose:Quincey Koziol2002-07-021-5/+9
| | | | | | | | | | | | Bug fix. Description: Correct the previous code for detecting 1-D contiguous hyperslabs to detect an extra case that the development branch has, but the release branch doesn't have. Platforms tested: IRIX64 6.5 (modi4) w/parallel
* [svn-r5740] Purpose:Quincey Koziol2002-07-011-2/+6
| | | | | | | | | | | | | | | Bug fix. Description: 1-D non-contiguous hyperslabs were erroneously being detected as contiguous and were causing incorrect behavior for parallel I/O benchmark (and parallel programs in general). Solution: Modified algorithm to handle 1-D case correctly. Platforms tested: IRIX64 6.5 (modi4)
* [svn-r5726] Snapshot version 1.5 release 30HDF Admin2002-06-291-2/+2
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* [svn-r5723] Raymond Lu2002-06-271-3/+2
| | | | | | | | | | | Purpose: Fix bug Description: In function H5HG_remove, heap object header wasn't included for size. Solution: Added heap object header in. Platforms tested: Linux 2.2(eirene).
* [svn-r5707] Purpose:Quincey Koziol2002-06-251-0/+4
| | | | | | | | | | | | | | Bug Fix. Description: Contiguous types created for "all" and contiguous hyperslab selections was not being committed before using them. Solution: Commit them. :-) This fixes the problems on the LLNL Blue Pacific machine. Platforms tested: LLNL Blue Pacific w/parallel.
* [svn-r5690] Purpose:Quincey Koziol2002-06-241-29/+42
| | | | | | | | | | | | | | | | | | | | | | | | | | Bug Fix Description: When parallel I/O is used, the MPI-I/O VFL driver uses a "lazy" model to call MPI_File_set_view() in order to reduce the number of calls to this function. However, this is unsafe, because if a collective I/O which uses MPI derived types (and thus uses MPI_File_set_view()) is immediately followed by an independent I/O, the code will attempt to call MPI_File_set_view() in order to switch back to the default view of the file. MPI_File_set_view() is a collective call however, and this causes the application to hang. Solution: Removed "lazy" MPI_File_set_view() code, instead set the file view when it is needed (with MPI derived types) and immediately set the file view back to the default view before leaving the I/O routine. Platforms tested: IRIX64 6.5 (modi4) w/parallel. Also, tested with the latest development and release code for the SAF library, which now works correctly with this change. (Although the release branch of the SAF library seems to have a bug, this 1.4.4 release candidate code gets as far as the version the SAF library is released on top of (1.4.2-patch1, I believe)).
* [svn-r5680] Purpose:Quincey Koziol2002-06-194-37/+97
| | | | | | | | | | | | | | | | | | | | New feature. Description: There is some discussion among the SAF team as to whether it is better to use MPI derived types for raw data transfers (thus needing a MPI_File_set_view() call), or whether it is better to use a sequence of low-level MPI types (i.e. MPI_BYTE) for the raw data transfer. Solution: Added an in internal flag to determine whether derived types are preferred (the default), or whether they should be avoided. An environment variable ("HDF5_MPI_PREFER_DERIVED_TYPES") can be set by users to control whether MPI types should be used or not. Set the environment variable to "0" (i.e.: 'setenv HDF5_MPI_PREFER_DERIVED_TYPES 0' to avoid using MPI derived types. Platforms tested: IRIX64 6.5 (modi4) w/parallel
* [svn-r5677] Purpose:Quincey Koziol2002-06-1910-71/+52
| | | | | | | | | | | Code improvement Description: Some small code cleanups and took out the code the was turning off the metadata cache for parallel I/O (!) Platforms tested: IRIX64 6.5 (modi4) w/parallel
* [svn-r5674] Purpose:Quincey Koziol2002-06-194-15/+14
| | | | | | | | | | Code cleanup Description: Removed more compiler warnings, etc. Platforms tested: Linux 2.2.x (eirene) w/parallel
* [svn-r5670] Purpose:Quincey Koziol2002-06-193-26/+0
| | | | | | | | | | | Code cleanup Description: Remove "COALESCE_READS" ifdefs, which were brought in by the DPSS VFL driver and are no longer used. Platforms tested: IRIX64 6.5 (modi4) w/parallel
* [svn-r5667] Purpose:Quincey Koziol2002-06-195-13/+13
| | | | | | | | | | Code cleanup Description: Turn on more warnings in the IRIX builds and clean them up. Platforms tested: IRIX64 6.5 (modi4) w/parallel
* [svn-r5662] Purpose:Quincey Koziol2002-06-184-221/+28
| | | | | | | | | | | | | | | | | 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 Koziol2002-06-183-128/+236
| | | | | | | | | | | | 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-r5652] Purpose:Quincey Koziol2002-06-175-36/+112
| | | | | | | | | | | | Code cleanup Description: Use dataset transfer property list to hold information about the MPI types for the current transfer, instead of setting pseudo-global variables in the file's struct. Platforms tested: Linux 2.2.x (eirene) w/parallel & IRIX64 6.5 (modi4) w/parallel & FORTRAN
* [svn-r5650] Purpose:Quincey Koziol2002-06-173-29/+68
| | | | | | | | | | | | Code cleanup Description: Change MPI-I/O code to use the address of the dataset for the displacement, instead of having a separate displacement value. Removed displacement parameter from H5FD_mpio_setup parameters. Platforms tested: Linux 2.2.x (eirene) w/parallel & IRIX64 6.5 (modi4) w/parallel.
* [svn-r5636] Purpose:Quincey Koziol2002-06-141-2/+2
| | | | | | | | | | 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-r5630] Elena Pourmal2002-06-132-0/+6
| | | | | | | | | | | | | | | | Purpose: [is this a bug fix? feature? ...] Description: [describe the bug, or describe the new feature, etc] Solution: [details about the changes, algorithm, etc...] [Please as detail as you can since your own explanation is better than others guessing it from the code.] Platforms tested: [machines you have tested the changed version. This is absolute important. Test it out on at least two or three different platforms such as Big-endian-32bit (SUN/IRIX), little-endian-32(LINUX) and 64-bit (IRIX64/UNICOS/DEC-ALPHA) would be good.]
* [svn-r5605] Purpose:Quincey Koziol2002-06-121-8/+12
| | | | | | | | | | Code cleanup Description: Clean up some compiler warnings... Platforms tested: FreeBSD 4.5 (sleipnir)
* [svn-r5603] Purpose:Quincey Koziol2002-06-121-8/+32
| | | | | | | | | | | | | | | | 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-r5595] Elena Pourmal2002-06-111-7/+17
| | | | | | | | | | | | | | | Purpose: Bug #774 fix Description: H5Tenum_valueof and H5Tenum_nameof functions did not fail when non-existing name or non-existing value were supplied. This happened because binary search algorithm did not check if value or name found during the search were equal to the supplied one. Solution: Added an appropriate check condition. Platforms tested: Solaris 2.7 and Linux 2.2.18
* [svn-r5589] Purpose:Quincey Koziol2002-06-111-2/+2
| | | | | | | | | | | | | | Bug fix. Description: H5P_get was reading a 'hsize_t' field into a 'size_t' variable, causing problems on the HP's and Windows. Solution: Changed the variable to be an hsize_t Platforms tested: HP/UX 11.0 (kelgia)
* [svn-r5586] Purpose:Quincey Koziol2002-06-113-10/+74
| | | | | | | | | | | | | | | | 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-r5582] Purpose:Quincey Koziol2002-06-101-1/+1
| | | | | | | | | | | Code cleanup Description: Need to change FUNC_ENTER_NOINIT to FUNC_ENTER_API_NOINIT for H5dont_atexit() Platforms tested: FreeBSD 4.5 (sleipnir)
* [svn-r5573] Purpose:Quincey Koziol2002-06-103-1/+3
| | | | | | | | | | | Bug fix (#620) Description: Change slightly misleading error message when creating attribute with same name as existing attribute to something a bit more clear. Platforms tested: FreeBSD 4.5 (sleipnir)
* [svn-r5571] Purpose:Quincey Koziol2002-06-102-8/+10
| | | | | | | | | | | 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-r5567] 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-r5563] Purpose:Quincey Koziol2002-06-102-4/+0
| | | | | | | | | | | New Feature Description: Add H5P[set|get]_small_data_block_size API function, per our discussions at last week's HDF5 meeting. Platforms tested: FreeBSD 4.5 (sleipnir)
* [svn-r5562] Purpose:Quincey Koziol2002-06-102-5/+9
| | | | | | | | | | | Code cleanup Description: Allow H5FD_free to return successfully (but ignore) freeing objects with size 0. Platforms tested: FreeBSD 4.5 (sleipnir)
* [svn-r5560] Purpose:Quincey Koziol2002-06-101-0/+2
| | | | | | | | | | | | | | 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-r5551] Purpose:Quincey Koziol2002-06-072-4/+4
| | | | | | | | | | | | Bug fix. Description: Added extra check to locations where metadata and "small data" blocks were being returned to the file's list of free space to avoid freeing 0-sized blocks. This should fix the problems in last night's daily tests. Platforms tested: FreeBSD 4.5 (sleipnir)
* [svn-r5550] Purpose:Quincey Koziol2002-06-073-39/+67
| | | | | | | | | | | | | | | | | Code Improvement Description: Split the metadata accumulator code into two parts: one for allowing writes of the accumulator buffer during reads (when the buffer is dirty and needs to be flushed to disk in order to hold the new metadata being read in) and another for only allowing writes of the buffer during writes. This allows the MPI-I/O VFL driver to use the metadata accumulator (but only during writes) and benefit from the reduced number of metadata I/O operations that it brings. Platforms tested: IRIX64 6.5 (modi4) w/parallel
* [svn-r5545] Purpose:Quincey Koziol2002-06-061-4/+0
| | | | | | | | | | Code cleanup Description: Back out [apparently] unnecessary include of H5F package include files. Platforms tested: FreeBSD 4.5 (sleipnir)
* [svn-r5543] Purpose:Quincey Koziol2002-06-062-9/+0
| | | | | | | | | | Bug fix. Description: Return H5S_all_opt_possible() prototype to original position in H5Spkg.h, it is not related to parallel I/O. Platforms tested: FreeBSD 4.5 (sleipnir)
* [svn-r5542] Purpose:Quincey Koziol2002-06-062-15/+46
| | | | | | | | | | | | | | | | | Code cleanup/bug fix Description: Unused space in the file was being "dropped on the floor" when the metadata or "small data" block was moved to a new location in the file and there was unused space in the old block. Solution: Put the space left in the allocation block into the free list of space for the file. This allows it to be [potentially] reused and sometimes allows the file to be smaller. Platforms tested: Solaris 2.7 (arabica) w/FORTRAN and FreeBSD 4.5 (sleipnir) w/C++
* [svn-r5538] Purpose:Quincey Koziol2002-06-052-41/+101
| | | | | | | | | | | | | | | Code improvement. Description: Added boot block and driver info block checksumming feature to the shared file information. This prevents these blocks from being written out multiple times when they haven't changed. This reduces the number of I/O operations which hit the disk for my test program from 15 to 14 (i.e. from 393 to 14, overall). Platforms tested: Solaris 2.7 (arabica) w/FORTRAN and FreeBSD 4.5 (sleipnir) w/C++
* [svn-r5536] Purpose:Quincey Koziol2002-06-0515-208/+304
| | | | | | | | | | | | | | | | | 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-r5530] Purpose:Bill Wendling2002-06-0410-18/+39
| | | | | | | | | | | | | | | Code Cleanup Description: Removed some compiler warnings. Solution: In a few cases, NULL was being returned when a FAIL was supposed to be returned instead. There were some header files which needed to be included in a few of the sources. A couple of if-then statements had assignments in the conditional part. The compiler warned that they should have extra "()"s around them. Made the code check the values instead. Platforms tested: Linux (parallel) Modi4 (parallel)
* [svn-r5529] Purpose:Quincey Koziol2002-06-041-4/+36
| | | | | | | | | | | | | | | Code improvement Description: Now that the metadata accumulator is working correctly, the buffer size tends to get rather large and stay there. Solution: Put a throttle on the accumulator buffer to reduce its size back down when it isn't needed. Platforms tested: Solaris 2.7 (arabica) w/FORTRAN & FreeBSD 4.5 (sleipnir) w/C++
* [svn-r5524] Elena Pourmal2002-06-041-7/+13
| | | | | | | | | | | | | 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
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