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* [svn-r8920] Elena Pourmal2004-07-211-0/+5
| | | | | | | | | | | | Purpose: Maintenance Description: Documented SZIP change. Solution: Platforms tested: Misc. update:
* [svn-r8916] Elena Pourmal2004-07-211-4/+11
| | | | | | | | | | | | | | | | | | | | | 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. Modified the test according to the new algorithm. Platforms tested: verbena, copper, sol Misc. update:
* [svn-r8915] Elena Pourmal2004-07-211-12/+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-r8913] Purpose:Albert Cheng2004-07-212-8/+38
| | | | | | | | | | | | | | | | | | | | Bug fix and feature. Description: The setenv was done in runtest but it has the effect will linger onto the next test. So, if the first test sets $CXX to a certain value, it lingers on the all following tests of the same host. This is usually not desired. Solution: Move the actual setenv code to snapshot. Runtest now just parses them and pass along the setenv request to snapshot. Platforms tested: no h5comittest which does not really test the change. Hand tested in eirene with Tg-NCSA. Misc. update:
* [svn-r8912] Purpose:Pedro Vicente Nunes2004-07-2118-116/+198
| | | | | | | | | | | | | | | | | | | | | | | | | | bug fixes Description: the return error code for a function was not initialized. in HP-UX it happened that this variable was initialized to -1 causing the function to return with an error condtion solution : initialized the variable to 0 the name of the dataset was printed after the differences in verbose mode and report when differences were found solution : check first if differences were found and then print the name of dataset and differences in verbose mode always print the name first Solution: Platforms tested: linux aix solaris Misc. update:
* [svn-r8910] Purpose:MuQun Yang2004-07-201-0/+1
| | | | | | | | | | | | Add t_coll_chunk.c at testpar for collective chunk IO test. Description: Solution: Platforms tested: Misc. update:
* [svn-r8909] Purpose:Pedro Vicente Nunes2004-07-202-11/+115
| | | | | | | | | | | | | | | | update documentation and usage message Description: updated the html documentation for the new h5diff modes added a section for h5repack Solution: Platforms tested: linux Misc. update:
* [svn-r8907] Purpose:MuQun Yang2004-07-204-3/+484
| | | | | | | | | | | | | | | | | | | | To add collective chunk IO tests. Description: three tests are added. 1. Only one hyperslab for each process, and this hyperslab is fit in exactly one chunk. 2. non-contiguous hyperslabs in each process, these hyperslabs are fit in one chunk. 3. Single hyperslab for each process, smaller chunk is assigned. Number of chunks for every process is equal. Solution: the dataset size is set to be very small, will enlarge later. Platforms tested: AIX 5.1(copper) Misc. update:
* [svn-r8906] Purpose:MuQun Yang2004-07-207-27/+196
| | | | | | | | | | | | | | | | | | | | | | | Adding the first round of patches about supporting collective chunk IO in HDF5 Description: The current HDF5 library doesn't support collective MPIO with chunk storage. When users set collective option in their data transfer with chunk storage, the library silently converted the option to INDEPENDENT and that caused trememdous performance penalty. Some application like WRF-parallel HDF5 IO module has to use contiguous storage for this reason. However, chunking storage has its own advantage(supporting compression filters and extensible dataset), so to make collective MPIO possible inside HDF5 with chunking storage is a very important task. This check-in make collective chunk IO possible for some special cases. The condition is as follows(either case is fine with using collective chunk IO) 1. for each process, the hyperslab selection of the file data space of each dataset is regular and it is fit in one chunk. 2. for each process, the hyperslab selection of the file data space of each dataset is single and the number of chunks for the hyperslab selection should be equal. Solution: Lift up the contiguous storage requirement for collective IO. Use H5D_isstore_get_addr to get the corresponding chunk address. Then the original library routines will take care of getting the correct address to make sure that MPI FILE TYPE is built correctly for collective IO> Platforms tested: arabica(sol), copper(AIX), eirene(Linux) parallel test is checked at copper. Misc. update:
* [svn-r8905] Purpose:MuQun Yang2004-07-201-1/+2
| | | | | | | | | | | | | | | | bug fix for windows testing Description: A function called H5C_stats_reset doesn't have H5_DLL in front of it, it cause windows DLL test failed. Solution: Add H5_DLL in front of it. Platforms tested: windows xp, sol 2.7, linux 2.4, aix 5.1 Misc. update:
* [svn-r8904] Purpose:Pedro Vicente Nunes2004-07-2098-1913/+1757
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | h5diff and h5repack changes Description: h5diff introduced the following four modes of output: Normal mode: print the number of differences found and where they occured Report mode: print the above plus the differences Verbose mode: print the above plus a list of objects and warnings Quiet mode: do not print output (h5diff always returns an exit code of 1 when differences are found) h5repack added an extra parameter for SZIP filter (coding method) the new syntax is -f SZIP=<pixels per block,coding> (pixels per block is a even number in 2-32 and coding method is 'EC' or 'NN') Example of use: ./h5repack -i file1 -o file2 -f SZIP=8,NN -v updated usage messages, test scripts and files accordingly Solution: Platforms tested: linux AIX solaris Misc. update:
* [svn-r8901] Purpose:Quincey Koziol2004-07-203-7/+28
| | | | | | | | | | | | 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-r8899] James Laird2004-07-202-0/+15
| | | | | | | | | | | | | | | | Purpose: Bug Fix Description: Calling H5Sset_extent_simple to change a dataspace's maxdims from nonzero to zero causes errors (infinite loops, seg faults, asserts) because the pointer to the maximum size isn't cleaned up properly Solution: Clean up that pointer. Added a test for this case. Platforms tested: sleipnir (very minor change)
* [svn-r8897] James Laird2004-07-203-4/+31
| | | | | | | | | | | | | | | | | 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) Misc. update:
* [svn-r8896] Purpose:Albert Cheng2004-07-192-0/+28
| | | | | | | | | | | | | | Feature Description: Showed the fortran compiler and FFLAGS and CXX compiler and CXXFLAGS when the corresponding language API is enabled. Platforms tested: No h5committest since it is just a simple shell script change. Tested in Eirene. Misc. update:
* [svn-r8892] Purpose:Quincey Koziol2004-07-1619-276/+326
| | | | | | | | | | | | | | 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-r8889] Purpose:Xuan Bai2004-07-161-0/+0
| | | | | | | | | | | | | | | | | | | | | | | | | Update. Description: Due to source code change, added 2 new projects to the Windows tests and removed some files from a Windows project. Updated h5repack testing batch file in Windows. Did some minor updates for cache project. Solution: 1. Added 2 new projects reserved and reserveddll to the Windows workspace. These two projects include the new source code reserved.c. 2. testh5repack_filters.c and testh5repack_layout.c were removed from HDF5 1.7 branch by Pedro. Removed these 2 files from h5repacktst project. 3. Pedro updated h5repack testings. Updated repacktest.bat batch file to match with new h5repack testings in Unix. 4. cache project settings->Link->Ignore libraries: add libcd.lib for release version and libc.lib for debug version. Platforms tested: Microsoft Visual C++ 6.0/.NET on Windows XP. (Will test on Windows 2000 with Visual C++ 6.0 after this check-in). Misc. update:
* [svn-r8888] Purpose:Quincey Koziol2004-07-166-22/+26
| | | | Bump version # after making snapshot
* [svn-r8886] Purpose:Albert Cheng2004-07-151-24/+24
| | | | | | | | | | | | | | bug fix. Description: The previous patch of -D__GNUC__ was causing failure in the newer compiler. The previous failure could not be repeated any more. So, removed it. Platforms tested: Tested only in TG-NCSA since the change affects only the ia64 platform. Misc. update:
* [svn-r8884] Purpose:Albert Cheng2004-07-151-72/+68
| | | | | | | | | | | | | | | | | | | | | Bug fix Description: It uses the value of $ARCH as a gcc option but the linux clusters at NCSA define $ARCH as environment variable with values that are not a valid compiler option. That caused the configure to fail because it was not able to compile at all. Solution: Change ARCH to lower case $arch (convention dictates environment variables are upper cases.) Also preset $arch to null and do not honor any pass it values. Platforms tested: Attempted to run h5committest but sol was failing due to /tmp filled. Copper and verbena passed. Also passed in TG-NCSA. Misc. update:
* [svn-r8882] Purpose:Pedro Vicente Nunes2004-07-158-64/+161
| | | | | | | | | | | | | | | | | | | | | | | | bug fix, new feature Description: fixed bug in the parse function: cases where we have an already inserted name but there is a new name also example: -f dset1:GZIP=1 -l dset1,dset2:CHUNK=20x20 dset1 is already inserted, but dset2 must also be (it was not) added a CHECK_SZIP symbol to enable/disable checking of library related szip parameters added the print of the filter name in verbose mode (confirms visually that the filter was applied ) Solution: Platforms tested: linux solaris AIX Misc. update:
* [svn-r8881] James Laird2004-07-153-3/+5
| | | | | | | | | | | | Purpose: Bug fix Description: Replaced "unsigned long long" with hsize_t in H5MF Added "return 0" at end of reserved.c test Platforms tested: arabica, sleipnir
* [svn-r8879] Raymond Lu2004-07-1411-21/+424
| | | | | | | | | | | | | | Purpose: New feature Description: New API H5Tencode and H5Tdecode. Given object ID, H5Tencode encodes object information into a binary form. H5Tdecode decode an object information in a binary form, reconstructs the object and return a new object ID. Solution: Use object header functions H5O_dtype_decode and H5O_dtype_encode to facilitate them. The encoded binary is exactly like object header information. This is the first step checkin. Will check in H5Sencode and H5Sdecode later. Platforms tested: h5committed and fuss. Misc. update: will update release.txt after 2nd step checkin.
* [svn-r8878] James Laird2004-07-141-0/+399
| | | | | | | | | | | | | Purpose: Description: Missed adding a test file in previous commit. Solution: Platforms tested: Misc. update:
* [svn-r8877] James Laird2004-07-1417-25/+257
| | | | | | | | | | | | | | | | | | | | | | | | | | | 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) Solution: Platforms tested: Misc. update:
* [svn-r8874] Purpose:Quincey Koziol2004-07-147-26/+151
| | | | | | | | | | | | | | | | | | | | 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-r8869] Purpose:Pedro Vicente Nunes2004-07-1328-711/+1086
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | h5repack changes Description: there were some requests to change some minor h5repack features h5repack only made a warning about a non available filter in verbose mode ( -v ) without -v it kept silent, and users sometimes missed this warning the request was that it should print this warning always. so, the new format, is e.g ./h5repack -i test_szip.h5 -o out.h5 Warning: dataset </dset_szip> cannot be read, SZIP filter is not available due to this, and to avoid a lot of these messages in the shell test script, I modified the script h5repack.sh so that it detects the presence of all filters in the environment (previously it only detected SZIP) the test files were also divided in more files , to make the script code easier to follow Solution: Platforms tested: linux AIX (no szip) solaris (no szip, no gzip ) Misc. update:
* [svn-r8867] Purpose:Quincey Koziol2004-07-135-24/+210
| | | | | | | | | | | | | | | | | | | 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-r8865] Purpose:Quincey Koziol2004-07-134-57/+70
| | | | | | | | | | | | | | | | | 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-r8860] Purpose:Quincey Koziol2004-07-121-12/+41
| | | | | | | | | | | | 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-r8859] Purpose:Quincey Koziol2004-07-121-1/+1
| | | | Correct typo in file format for compact layout information
* [svn-r8858] Snapshot version 1.7 release 30HDF Admin2004-07-116-15/+17
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* [svn-r8855] Purpose:Xuan Bai2004-07-101-0/+0
| | | | | | | | | | | | | | | | Update. Description: Update new files into Windows workspace. Solution: Add H5RC.c and H5RCprivate.h to hdf5 and hdf5dll projects in Windows workspace. Platforms tested: MS Visual C++ 6.0 on Windows 2000. (will test on Windows XP with Visual C++ 6.0 and .NET after this check-in) Misc. update:
* [svn-r8853] Purpose:Quincey Koziol2004-07-109-337/+378
| | | | | | | | | | | | | | | | | | | | 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-r8852] Purpose:Pedro Vicente Nunes2004-07-097-143/+434
| | | | | | | | | | | | | | | | h5dump new tests Description: added new tests for the print of array indices (nested objects, several ranks) Solution: Platforms tested: linux AIX solaris Misc. update:
* [svn-r8850] Purpose: Fixing minor bugBinh-Minh Ribler2004-07-091-3/+1
| | | | | | | | | | | Description: Changed call to H5File::getFileSize according to C library and removed CHECK for this call because failure will be handled by exception. Platforms tested: FreeBSD 4.10 (sleipnir) Linux 2.4 (eirene)
* [svn-r8849] Purpose: Adding documentation with doxygen and fixing minor bugBinh-Minh Ribler2004-07-092-4/+5
| | | | | | | | | | | | Description: Added function headers with doxygen. Changed H5File::getFileSize according to C library. Platforms tested: Linux 2.4 (eirene) FreeBSD 4.10 (sleipnir) Misc. update:
* [svn-r8847] 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-r8844] Purpose:Quincey Koziol2004-07-0914-28/+306
| | | | | | | | | | | | | | | | | | 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-r8840] Purpose:Pedro Vicente Nunes2004-07-0821-889/+672
| | | | | | | | | | | | | | | | bug fix Description: when printing array indices , the calculation of the current column was not done correctly Solution: Platforms tested: linux AIX solaris Misc. update:
* [svn-r8838] Frank Baker2004-07-082-0/+0
| | | | | Purpose: Version 3 of document, from August 2003
* [svn-r8837] Purpose: Update doc and fix minor bugBinh-Minh Ribler2004-07-0810-112/+159
| | | | | | | | | | | Description: H5IdComponent.cpp: initialized a pointer to NULL H5Object.cpp: removed functions being added by mistake Update function headers for the rest. Platforms tested: SunOS 5.7 (arabica) Linux 2.4 (eirene)
* [svn-r8836] Elena Pourmal2004-07-085-0/+197
| | | | | | | | | | | | | | | | | Purpose: Maintenance Description: Added h5fget_name_f and h5fget_filesize_f subroutines and tests. Solution: N/A Platforms tested: arabica (32-bit), sol (64-bit) parallle build on copper failed for the C library with the the following error: ld: 0711-317 ERROR: Undefined symbol: .H5FD_stdio_term Since this change doesn't affect the C library, I am cheking it in and will retest the fresh CVS copy after this check-in. Misc. update:
* [svn-r8834] Purpose:Quincey Koziol2004-07-081-1/+0
| | | | | Revert whitespace commit since CVS seem to be working correctly from sleipnir.
* [svn-r8833] Purpose:Quincey Koziol2004-07-081-0/+1
| | | | | Whitespace commit to double check that the repository is working correctly (esp. from sleipnir)
* [svn-r8832] Purpose:Quincey Koziol2004-07-081-0/+0
| | | | | Remove testing file after verifying that binary adds of *.h5 files are working correctly.
* [svn-r8831] Purpose:Quincey Koziol2004-07-081-0/+0
| | | | | Testing "binary" addition of new *.h5 files. (This file will be removed immediately)
* [svn-r8828] Purpose:Xuan Bai2004-07-081-0/+0
| | | | | | | | | | | | | | | | | Update. Description: Added cache.c to the Windows tests. Updated H5Tinit.c. Solution: 1. Added 2 new projects cache and cachedll to the Windows workspace. These two projects include the new source code cache.c. 2. Updated H5Tinit.c. Platforms tested: MS Visual C++ 6.0 and .NET in Windows XP. Misc. update:
* [svn-r8826] Purpose:Pedro Vicente Nunes2004-07-0721-170/+275
| | | | | | | | | | | | | | | | | | h5dump new tests Description: added more tests for the escape/not escape feature for string data (with vlen, with compound, with char data) Solution: Platforms tested: linux solaris AIX Misc. update:
* [svn-r8823] Purpose:Quincey Koziol2004-07-0710-413/+398
| | | | | | | | | | | | | | | 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
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