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* [svn-r2634] Purpose:Bill Wendling2000-10-051-22/+36
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bug fix Description: In the h5dump_fixtype function, when users created a COMPOUND datatype, the alignment would be off somewhat. Solution: The alignment was being set after insertion. I changed this code: for (i = 0, offset = 0; i < nmembs; i++) { H5Tinsert_array(m_type, name[i], offset, ndims[i], dims + i * 4, NULL, memb[i]); for (j = 0, nelmts = 1; j < ndims[i]; j++) nelmts *= dims[i * 4 + j]; offset = ALIGN(offset, H5Tget_size(memb[i])) + nelmts * H5Tget_size(memb[i]); } to: for (i = 0, offset = 0; i < nmembs; i++) { if (offset) offset = ALIGN(offset, H5Tget_size(memb[i])); H5Tinsert_array(m_type, name[i], offset, ndims[i], dims + i * 4, NULL, memb[i]); for (j = 0, nelmts = 1; j < ndims[i]; j++) nelmts *= dims[i * 4 + j]; offset += nelmts * H5Tget_size(memb[i]); } The alignment is now calculated before the insertion. Platforms tested: Solaris, Linux
* [svn-r2633] Purpose:Quincey Koziol2000-10-042-20/+20
| | | | | | | | | | | | Bug Fix Description: Use H5FD_get_eoa instead of H5FD_get_eof to check for reading off the end of the allocated file space. Using H5FD_get_eof was causing the Stream VFD to fail. Solution: Switched from using H5FD_get_eof to H5FD_get_eoa Platforms tested: FreeBSD 4.1.1 (hawkwind)
* [svn-r2632] Purpose:Bill Wendling2000-10-042-37/+48
| | | | | | | | | | | | | | Bug Description: The testh5toh4 was removing all .h5 files from the testfiles directory, however, with the addition of testh4toh5, we need some .h5 files in there. Solution: Changed the scripts so that an output directory is created for all of the processed files. This is removed after the test is finished. Platforms tested: Linux
* [svn-r2631] Thomas Radke2000-10-041-8/+9
| | | | | | | | | | | | Purpose: Bugfix Description: The Stream VFD was leaking memory on every opened file. Solution: In H5FD_stream_close(), finally free the file structure used to describe the closed file. Platforms tested: Linux, SGI
* [svn-r2630] Purpose:Bill Wendling2000-10-032-759/+627
| | | | | | | | | | | | | | | | Bug Fix Description: zlib was not being retrieved from the place specified by the user even if the user used the --with-zlib flag. Solution: Removed the automatic inclusion of /usr/ncsa/* into the macros and use the user-defined place to try to pickup the zlib. I'm relying on the order of the -L flags in the compile line to specify which libraries to look into first before going on to look into the system libraries. If some compiler doesn't honor the this order, yikes... Platforms tested: Linux
* [svn-r2629] Purpose:Bill Wendling2000-10-031-0/+2
| | | | | | | | Added site-specific/ subdirectory in config/ directory Description: If a machine needs site-specific configure options but those options don't necessarily apply to all machines of that type, place them there.
* [svn-r2628] Purpose:Bill Wendling2000-10-031-0/+33
| | | | | | | | | | | | | | | Site specific configure files Description: Some machines need to specify things during the configure but they aren't necessary for all machines of that type. Those site-specific changes should go here. The format of the filename is: host-$hostname where $hostname is the output from the `hostname' command. Needless to say, this is optional to those sites which don't need it.
* [svn-r2627] Purpose:Albert Cheng2000-10-021-1/+1
| | | | | | | | | | | | Bug fix Description: Attempted to close rawdatastream even if it has not been used to open a new file. Many systems tolerated the NULL value but not FreeBSD. Solution: Check for the NULL value too. Platforms tested: hawkwind (freeBSD) and modi4 parallel.
* [svn-r2626] Purpose:Albert Cheng2000-09-303-2/+57
| | | | | | | | | | | | | | | | | | | | New Feature Description: Add -o option to h5dumper. It displays the raw data of datasets to a separate output file. Add a feature to h5tools library that it uses the FILE *rawdatastream as the stream for the display of datasets raw data. Solution: Define an "extern FILE *rawdatastream" in h5tools.h and declare it in h5tools.c. This way, it would work even if an application does not explicitely declare it. Tried to initialized it to stdout as FILE *rawdatastream = stdout; but Linux gcc rejected it though all other platforms+compilers accepted it fine. For now, put in a kludge to set it right before it is used. Need a safer way to initialize it. Platforms tested: arabica, eirene, modi4 -64.
* [svn-r2625] Purpose:Albert Cheng2000-09-301-1/+14
| | | | | | | | | | | | | | | | | | | | Bug fix and feature Description: It could not find a working h5dump to process the hdf5 files. This could be because h5dump is not installed in $PATH or a disfunctional one is found. (E.g. arabica:/usr/sdt/bin/h5dump does not work.) Setting it to ./h5dump or $PWD/h5dump does not work because when h5dump is used, it has "cd testfiles", a different place. Solution: Set H5DUMP with the current absolute path (used `pwd` instead of $PWD which is sometimes not set for whatever reason.) Also add a feature to allow H5DUMP to be set to a different value by hand. For example, if the h5dump just built is not working correctly, one can do "H5DUMP=/usr/local/bin/h5dump make check" to bypass the broken h5dump. Platforms tested: arabica
* [svn-r2623] Purpose:Albert Cheng2000-09-302-726/+730
| | | | | | | | | | Reformat the source Description: The tabstop seems to defined different from 8-stops. The source files looked very confusing. Just reformate the files. Not change to source code at all. Platforms tested: modi4 -64.
* [svn-r2622] MuQun Yang2000-09-291-0/+13
| | | | | | | | | | Purpose: add h4toh5 converter into MANIFEST Description: add h4toh5 converter source codes, test files into MANIFEST Solution: Platforms tested: arabica,baldric,eirene
* [svn-r2621] Frank Baker2000-09-291-1/+1
| | | | | | | | | | | | Purpose: Bug fix -- #445 Description: In RM_H5D.html in the H5 Reference Manual, the H5Dget_storage_size entry described the wrong FAILURE return value. Solution: Changed H5Dget_storage_size return value on FAILURE to 0 (zero). Platforms tested: Tested in Internet Explorer 5.
* [svn-r2619] MuQun Yang2000-09-291-1/+1
| | | | | | | | | | Purpose: update testh4toh5 Description: change h5dump path at testh4toh5 Solution: Platforms tested: arabica, baldric, eirene
* [svn-r2616] MuQun Yang2000-09-281-0/+0
| | | | | | | | | | | | | | | | Purpose: add h4toh5 converter source codes under tools directory. Description: this is the expected hdf5 result for h4toh5 converter. 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-r2615] MuQun Yang2000-09-281-0/+0
| | | | | | | | | | | | | | | | Purpose: add h4toh5 converter source codes under tools directory. Description: this is the test file for h4toh5 converter. 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-r2614] MuQun Yang2000-09-2811-0/+7575
| | | | | | | | | | | | | | | | Purpose: add h4toh5 converter source codes under tools directory. 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-r2613] MuQun Yang2000-09-281-5/+15
| | | | | | | | | | | | | | | | | Purpose: add h4toh5 converter tool Description: add flag h4toh5 and testh4toh5 in the Makefile. 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: test on eirene and arabica. [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-r2612] MuQun Yang2000-09-282-378/+386
| | | | | | | | | | | | | | | | | Purpose: h4toh5 converter tool under tools Description: put flag h4toh5 and testh4toh5 into the configure file. 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: at eirene and arabica. [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-r2611] Purpose:Quincey Koziol2000-09-287-254/+700
| | | | | | | | | | | | | Rearrange code Description: The data sieve buffering code for contiguously stored datasets was wedged in the H5F_arr_read/H5F_arr_write routines. Solution: Created a new H5Fcontig.c to hold I/O routines for contiguously stored datasets (like H5Fistore.c for chunked dataset I/O routines) and moved data sieving code into those routines. Platforms tested: Solaris 2.6 (i.e. baldric)
* [svn-r2610] Purpose:Quincey Koziol2000-09-281-28/+325
| | | | | | | | | | | | | | | | | | Code Optimization. Description: The optimized routines for copying regular hyperslabs in memory have been using the same matrix routines to copy their hyperslab pieces as the routines for irregularly shaped hyperslabs. This ends up imposing lots of extra overhead on the optimized routine, since it basically "knows" all the matrix information it needs. Solution: Keep track of the [small] amount of matrix information necessary to perform the regular hyperslab copies in the optimized routines themselves instead of using the matrix routines. This improves the performance for the benchmark I'm running from ~18 seconds to ~12 seconds and should apply to parallel I/O situations also. Platforms tested: Solaris 2.6 (i.e. baldric)
* [svn-r2606] Purpose:Quincey Koziol2000-09-271-32/+243
| | | | | | | | | | | | | | | Code Optimization Description: The matrix operations are currently the hot-spot in the library code for regular hyperslab operations. Solution: Unrolled loops for 3 of the more heavily used functions (H5V_stride_optimize2, H5V_hyper_stride & H5V_hyper_copy) for the common cases (i.e. up to 3-D datasets). This squeezes some more blood out of the stone (turnip? :-) and improves the h5hypers.c benchmark on baldric by another 20-25%. Platforms tested: Solaris 2.6 (i.e. baldric)
* [svn-r2605] Updated with the addition of SWControl.html entry.Albert Cheng2000-09-271-0/+1
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* [svn-r2603] Updated the "last update date".Albert Cheng2000-09-271-1/+1
| | | | Test viewed via IE.
* [svn-r2601] Purpose:Quincey Koziol2000-09-272-5/+3
| | | | | | | | | | | | Bug Fix Description: The core and log VFL drivers were leaking small amounts of memory when they were used. Solution: Free the appropriate memory block (for the core driver) and don't allocate a block (for the log driver). Platforms tested: Solaris 2.6 (i.e. baldric)
* [svn-r2600] Purpose:Quincey Koziol2000-09-2615-27/+580
| | | | | | | | | | | Implemented new feature Description: Added data sieve buffering code to raw I/O data path. This is enabled for all the VFL drivers except the mpio & core drivers. Also added two new API functions to control the sieve buffer size: H5Pset_sieve_buf_size() and H5Pget_sieve_buf_size(). Platforms tested: Solaris 2.6 (i.e. baldric)
* [svn-r2599] Purpose:Quincey Koziol2000-09-261-0/+4
| | | | | | | | Document new feature Description: Mention data sieve buffering for next release. Platforms tested: Solaris 2.6 (i.e. baldric)
* [svn-r2597] Purpose:Quincey Koziol2000-09-261-2/+2
| | | | | | | | | | | Fix compiler warning Description: "HUGE_VAL" (a double value) was being put into a float type and generating a warning during compile time. Solution: Replaced "HUGE_VAL" with "FLT_MAX" Platforms tested: FreeBSD 4.1
* [svn-r2595] Purpose:Albert Cheng2000-09-262-0/+43
| | | | | | | | | | Feature Description: Added a new document of all the controls (compiler macros, environment variables, ...) that affect the functionality of the libraries and tools. Platforms tested: Viewed with MS IE.
* [svn-r2594] Purpose:Quincey Koziol2000-09-261-24/+18
| | | | | | | | | | | | Small Code Cleanup Description: Code to optimize adjacent (i.e. contiguous) hyperslab was ugly and used too many temporary variables. Solution: Computed the optimized hyperslabs slightly differently and got rid of unnecessary temporary variables. Platforms tested: FreeBSD 4.1
* [svn-r2591] Purpose:Bill Wendling2000-09-252-592/+602
| | | | | | | | | | | | Libtool bug Description: The AR macro wasn't being propagated to the libtool file correctly. When libtool was being generated, it wasn't recoginizing the AR that was set in the configure script. Solution: export the AR macro after it's set. Platforms tested: Linux
* [svn-r2590] Purpose:Albert Cheng2000-09-241-96/+111
| | | | | | | | | | | | | | | | | | | Bug fix Description: The old code was using count as the block size. The result was asking for a slab of count blocks, each of 1 element. The recent change in the hyperslab algorithm exposed this problem. (The old algorithm merge the count blocks back into 1 big block of count elements.) (This error was due to that the block argument was not in the very early version of hyperslab. Then it was not updated since it had been "working".) Solution: Added in the block argument to the setup and calculation of slab and its data. Also found a dumb error in the dataset_fill algorithm in which stride was used in the calculation. Not so for the cases of BYROW and BYCOL. Platforms tested: modi4 parallel, both -64 an -n32 modes.
* [svn-r2588] Snapshot version 1.3 release 30HDF Admin2000-09-232-2/+2
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* [svn-r2587] Purpose:Quincey Koziol2000-09-223-4/+69
| | | | | | | | | | | | | | | | | | | Bug fix (sorta) Description: When the stride and block size of a hyperslab selection are equal, the blocks that are selected are contiguous in the dataset. Prior to my hyperslab optimizations, this situation used to be detected and somewhat optimized to improve performance. I've added more code to optimize for this situation and integrated it with the new hyperslab optimization that weren't very efficient for that case as they should have been. Solution: Detect contiguous hyperslab selections (i.e. block size in a dimension is the same as the stride in that dimension) and store the optimized, contiguous version of that hyperslab. We also store the original, un- optimized version of the hyperslab to give back to the user if they query the hyperslab selection they just made. Platforms tested: FreeBSD 4.1
* [svn-r2586] Purpose:Bill Wendling2000-09-221-1/+1
| | | | | | | | | | | | | Bug Fix Description: The prototype for the H5Pregister function has a variable named `class'. This is a reserved word in C++ and causes the C++ compiler to freak. Solution: This variable's name was changed to cls_id in the .c file, so I changed it in the header file to cls_id to match. Platforms tested: Linux
* [svn-r2585] Mentioned the new Stream Virtual File Driver.Thomas Radke2000-09-221-1/+7
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* [svn-r2583] Purpose:Quincey Koziol2000-09-201-0/+13
| | | | | | | | | | | | | Bug Fix. Description: An assertion in the local heap code was mistakenly checking against too large of a value for the size of new local heap created. When used with larger-sized (>10KB) variable-length objects, it was failing the check. Solution: Corrected to check against the actual size of the heap allocated, without the heap header. Platforms tested: FreeBSD 4.1
* [svn-r2582] Purpose:Bill Wendling2000-09-201-0/+129
| | | | | | | Bug fix Description: Didn't regen the MANIFEST when I added the Fortran library...sorry.
* [svn-r2581] Purpose:Quincey Koziol2000-09-191-33/+23
| | | | | | Clean up compiler warnings. Platforms tested: FreeBSD 4.1
* [svn-r2580] Purpose:Quincey Koziol2000-09-191-333/+1952
| | | | | | | | | | | | Restore file Description: It appears that Robb's checkin earlier today erroneously overwrote this file with an older version... *grumble* Solution: Found another copy of newest version, verified that it is operating correctly and re-checked it in. Platforms tested: FreeBSD 4.1
* [svn-r2579] Purpose:Quincey Koziol2000-09-1911-34/+22
| | | | | | Clean up small compiler warnings and add missing function prototypes. Platforms tested: FreeBSD 4.1
* [svn-r2578] Purpose:Bill Wendling2000-09-191-4284/+0
| | | | libtool shouldn't be included in the CVS tree.
* [svn-r2577] Purpose:Bill Wendling2000-09-192-1/+2
| | | | | | Added support for compiling in subdirectories. Platforms tested: Solaris, IRIX (O2K)
* [svn-r2576] Purpose:Bill Wendling2000-09-19112-0/+41358
| | | | | | | | Adding the Fortran interface to the HDF5 library Description: Fortran is now a subdirectory of the HDF5 library tree. Platforms tested: Solaris and IRIX (O2K)
* [svn-r2574] Purpose:Bill Wendling2000-09-191-6/+6
| | | | | | | | | H5FDstream.h needs to be installed. Description: H5FDstream.h is included in the hdf5.h file and needs to be installed with the other public headers. Solution: Added it to the rest of the install headers.
* [svn-r2573] Purpose:Robb Matzke2000-09-1914-2154/+1718
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Fix Irix pmake bugs Description: Build fails on Irix when builddir != srcdir Solution: * acconfig.h * src/H5config.h.in [REGENERATED] Added definition for HAVE_STREAM * config/conclude.in * config/depend1.in * config/depend2.in * config/depend3.in * config/depend4.in The `Dependencies' file is located in the source tree. This fixes bugs for Irix pmake when compiling outside the source tree. Hopefully it still preserves Albert's changes which allow concurrent compilations to not stomp on each other's Dependencies files. * examples/Dependencies [REGENERATED] * src/Dependencies [REGENERATED] * test/Dependencies [REGENERATED] * tools/Dependencies [REGENERATED] Regenerated for testing purposes. Platforms: i686-pc-linux mips-sgi-irix6.5 sparc-sun-solaris2.6
* [svn-r2572] Purpose:Albert Cheng2000-09-191-4/+10
| | | | | | | | | | | | | | | | | | Feature Description: Most tests are done inside a for-loop. Whenever a test exits with error, the for-loop does a "exit 1" to exit the make. "make -i" could not catch and ignore the error status. Solution: Replaced "exit 1" with break. At the end of the for-loop, test if all tests have been run. If not, the for-loop is ended by the break command, thus raise an error. Now, 'make -i' can catch and ignor it. Also added the test of variable HDF5_Make_Ignore inside the for-loop to indicate the desire to ignore errors when the HDF5_Make_Ignore is set to a non-null/blank string. Platforms: Tested on modi4 and eirene.
* [svn-r2569] Purpose:Bill Wendling2000-09-182-360/+389
| | | | | | | | | | | | | | I introduced a small bug when trying to fix the zlib stuff. Description: -lz wouldn't be specified with the compile flags if it was found while checking for the HDF4 library. Solution: Removed my bad check and replaced with a better one. Platforms: Linux, Solaris
* [svn-r2568] Description:Quincey Koziol2000-09-161-2/+1
| | | | Mention the hypeslab speedups
* [svn-r2567] Description:Quincey Koziol2000-09-161-0/+3
| | | | Added Stream VFD modules to the MANIFEST
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