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* [svn-r2678] MuQun Yang2000-10-121-10/+28
| | | | | | | | | | | Purpose: fixing output format of character array converted from hdf4 vdata. Description: Now one dimensional chactacter array can be outputed as one H5 string instead of string of array before. Solution: modify gen_h5comtype() so that when we detect the datatype is hdf5 string, we will merge hdf4 fieldorder into H5T string size and output the whole character array into hdf5 string(with string size = size of the array length). Platforms tested: eirene(LINUX), arabica(sun 5.6)
* [svn-r2677] MuQun Yang2000-10-121-0/+0
| | | | | | | | | | | | | | | | Purpose: update windows project all.zip for development branch of hdf5 Description: Now it can test h4toh5 and h5toh4 converters, at least for static case(non-dll lib.) Solution: 1. For h4toh5 and h5toh4 converter to work, the platform must have both hdf4 and hdf5 libs. For hdf4 it includes both hdf and mfhdf libs. Besides this, WS2_32.LIB has to be included for recongizing symbols related to networking issues. 2. adding several new source files(h5FDlog.c etc) into all.dsw. 3. modify H5FDstream.c so that it bypasses netdb.h and other socket headers for win 32, instead using winsock.h. Platforms tested: windows 2000
* [svn-r2676] MuQun Yang2000-10-121-0/+0
| | | | | | | | | | Purpose: Update the test file vg.h5 Description: Solution: Platforms tested: eirene(LINUX),arabica,baldric(SUN 5.6),paz(IRIX6.5),gondolin(DEC),opus(HP-UX11)
* [svn-r2675] MuQun Yang2000-10-123-26/+27
| | | | | | | | | | | | Purpose: fix "zero memory" routine and change dimensional scale name size to MAX_DIM_NAME Description: change bzero into h4toh5_ZeroMemory change dimensional scale name size(orginally MAX_NC_NAME) to MAX_DIM_NAME at converter. Solution: see description Platforms tested: arabica,baldric,gondolin(DEC),opus(HP 11),eirene(Linux),paz(IRIX6.5)
* [svn-r2674] MuQun Yang2000-10-123-8/+35
| | | | | | | | | | | | | | | | | Purpose: 1. fix size of dimensional name list so that the size of dimensional name in dumper output will not change because of different versions of hdf library(h4toh5util.h and h4toh5sds.c). 2. fix bzero routine for windows platform(h4toh5util.h,h4toh5util.c,h4toh5anno.c,h4toh5main.c, h4toh5sds.c) Description: 1. change the MAX_DIM_NAME into 276(MAX_NC_NAME +dimension group name) and hopefully we will not expand the size of MAX_NC_NAME(currently 256) for a long time. 2. create a new routine(h4toh5_ZeroMemory) to zero out memory. Use ZeroMemory in windows and bzero at UNIX. Solution: see Description. Platforms tested: LINUX(eirene),WINDOWS 2000, sun 5.6(baldric and arabica),HP-UX11(opus),DEC(gondolin),IRIX 6.5(paz).
* [svn-r2672] Frank Baker2000-10-121-1/+3
| | | | | | | | | Purpose: Clarification of H5Fclose Description: RM_H5F.html / H5Fclose: Added note that all data is flushed to file. Platforms tested: Tested with IE 5.
* [svn-r2671] Purpose:Albert Cheng2000-10-111-30/+30
| | | | | | | | | | | | | | Bug fix Description: The setting does not work for the --srcdir option as source file names are hard set in the action lines. Solution: Changed the dependence targets to the form of *.lo and the action lines would use the *.lo files. This way, *.lo files are created when -srcdir option is used or not. Also added that they all depend on the C hdf5 library. Platforms tested: IRIX64 -64 with --srcdir
* [svn-r2670] Purpose:Albert Cheng2000-10-111-6/+6
| | | | | | | | | | | | | | Bug fix Description: The setting does not work for the --src-dir option as source file names are hard set in the action lines. Solution: Changed the dependence targets to the form of *.lo and the action lines would use the *.lo files. This way, *.lo files are created when -src-dir option is used or not. Platforms tested: IRIX64 -64 (I knows it works for other platforms because "'I know the hammer will drop when i let go'--Mr. Spock")
* [svn-r2669] Purpose:Bill Wendling2000-10-113-9/+19
| | | | | | | | | | | Bug Fix Description: I was relying on the PARALLEL macro to be "yes" or "no" all the time. This isn't the case. Solution: Created the ADD_PARALLEL_FILES macro to do just this. Platforms tested: Modi4
* [svn-r2668] Purpose:Bill Wendling2000-10-113-5/+4
| | | | | | | | | | | | Bug Fix Description: Wasn't picking up the header files from the proper source and build directories. There were some funky things happening in there. Solution: Put the correct path in. Platforms tested: Modi4
* [svn-r2667] Purpose:Bill Wendling2000-10-112-2/+4
| | | | | | | | | | Bug Fix Description: Broke on Arabica trying to export the SEARCH macro. Solution: Assigned to the SEARCH macro and then exported it. Platforms tested: Arabica.
* [svn-r2666] Another typoBill Wendling2000-10-111-1/+1
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* [svn-r2665] Small typo...Bill Wendling2000-10-111-1/+1
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* [svn-r2664] Purpose:Bill Wendling2000-10-113-6/+8
| | | | | | | | | | *sigh* Description: Wasn't picking up a header file which is in the source directory. Solution: Changed some flags so that it does this now. Platforms tested: Modi4
* [svn-r2663] Purpose:Bill Wendling2000-10-113-5/+5
| | | | | | | | | | | | Bug Fix 37 Description: Okay...this is really it now. Sorry for all the other "fixes". This will take care of the top_builddir macro for the Fortran interface. Solution: Hardcoded the path to the build directory. Platforms tested: Modi4.
* [svn-r2662] Purpose:Bill Wendling2000-10-111-2/+2
| | | | | | | | | | Bug Fix Description: Wasn't picking up the correct build directory source files. Solution: Use top_builddir instead of srcdir macro. Platforms tested: Modi4
* [svn-r2661] Purpose:Bill Wendling2000-10-115-5/+5
| | | | | | | | | | | Bug Fix Description: Wasn't finding the Dependencies file when doing a make. Solution: Modified the path to the Dependencies file by prepending a `$(srcdir)/' to it. Platforms tested: Modi4
* [svn-r2660] Purpose:Bill Wendling2000-10-112-6/+10
| | | | | | | | | | | | Bug Fix Description: The "fix" for search paths was wrong. It would try to recompute the SEARCH macro at the end. Solution: Stopped it from doing that if the $SEARCH macro has a value. One question, will fortran always be built from the top directory? Platforms tested: Modi4
* [svn-r2659] Purpose:Bill Wendling2000-10-104-139/+143
| | | | | | | | | | | | Bug Fix Description: When running configure on subdirectories (like fortran/), looking up how make implements SEARCHes failed. Solution: Exporting the SEARCH macro so that subdirectories don't have to look for it. Platforms tested: Modi4.
* [svn-r2658] Elena Pourmal2000-10-101-2/+2
| | | | | | | | | | | | Purpose: Buf fix Description: On DEC, H5Dff.f90 would not compile because of variables declaration order. Other UNIX platforms including J90 did not care. Solution: Change the order of variables declarations. Platforms tested: DEC Unix (gondolin)
* [svn-r2657] Quincey Koziol2000-10-1012-322/+64
| | | | | | | | | | | | Purpose: Parallel Bug Fixes Description: Was out of sync with header file re-arrangements I checked in last night. Solution: Fixed to use new header files, etc. Platforms tested: O2K (modi4)
* [svn-r2656] Purpose:Quincey Koziol2000-10-103-1/+29
| | | | | | | | | | | | | | Bug Fix Description: When parallel I/O is turned on, there were some macros used in the H5D routines which poked around in the H5F_t structure. This breaks the privacy of that structure and ties the H5D code too tightly to the H5F_t struct. Solution: Added a small function to retrieve the the value (driver_id) needed from the H5F_t function. Platforms tested: Eyeballed only, Albert needs this right away...
* [svn-r2655] Purpose:Bill Wendling2000-10-101-0/+5
| | | | | | | Small bug fix (see bug report 528) Description: Added another example us using the h5dumper to dump an attribute from the root group.
* [svn-r2654] Elena Pourmal2000-10-102-5/+10
| | | | | | | | | | Purpose: Updated source code to use new APIs to write/read references Description and Solution: Write/read subrotine has extra parameter - size of the reference array. I modified the source to reflect this change. Platforms tested: Solaris 2.6
* [svn-r2653] Purpose:Quincey Koziol2000-10-102-2/+6
| | | | | | | | | No change. Description: Must've added some debuging printf's and then took them out in a way which triggered CVS. Platforms tested: Solaris 2.6 (baldric) & FreeBSD 4.1.1 (hawkwind)
* [svn-r2652] Purpose:Quincey Koziol2000-10-1059-717/+2023
| | | | | | | | | | | | | | | Maintainance & performance enhancements Description: Re-arranged header files to protect private symbols better. Changed optimized regular hyperslab I/O to compute the offsets more efficiently from previous method of using matrix operations. Added sequential I/O operations at a more abstract level (at the same level as H5F_arr_read/write), to support the optimized hyperslab I/O. Platforms tested: Solaris 2.6 (baldric) & FreeBSD 4.1.1 (hawkwind)
* [svn-r2651] Purpose:Quincey Koziol2000-10-101-0/+4
| | | | | | | | | Maintainance Description: Updated for the new files I'm adding as well as the tools/talign.c file missing from last night's tests. Platforms tested: Solaris 2.6 (baldric) & FreeBSD 4.1.1 (hawkwind)
* [svn-r2650] Purpose:Albert Cheng2000-10-101-2/+2
| | | | | | | | | | | | Bug fix Description: The predefined HDF5_PARAPREFIX has a trailing slash. The parallel testfile names end up with two adjacent slashes that made some system unhappy. Solution: Removed the trailing slash. Platforms tested: Arabica (solaris 2.7).
* [svn-r2649] Elena Pourmal2000-10-101-6/+11
| | | | | | | Purpose: Rewrote test to use new APIs to read and write references. Platforms tested: J90 and Solaris 2.6
* [svn-r2648] Elena Pourmal2000-10-107-103/+408
| | | | | | | | | | | | | | | | | | | | | | Purpose: Reimplemented references to the objects and dataset regions. Description: Previous implementation was not portable. This implementation should work on UNIX workstations and Crays, but is very inefficient since it uses memcpy to repack Fortran buffers with references to C buffers and vice versa. Solution: I used fortran derived datatype with integer fields. h5dwrite_f and h5dread_f have extra parameter when references are written or read. This parameter describes size of the buffer that holds references. Platforms tested: J90 and Solaris 2.6 H5Pf.c Some of the functions do not exist now in the development branch. Commented those out, so one does not need to apply patch in order to build Fortran Library.
* [svn-r2647] Purpose:Albert Cheng2000-10-101-15/+19
| | | | | | | | | | | | | | Bug fiX Description: H5S_hyper_select_valid would report hyperslab invalid if the one of the count values is zero. The verifying algorithm did not take into consideration that block or count can contain zeros to indicate no element is wanted. Solution: Added code to test if block or count is zero. If so, skip the rest of the validity check. Platforms tested: IRIX64 -64.
* [svn-r2646] Purpose:Albert Cheng2000-10-102-6/+28
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bug fix (done by Kim Yates) Description: The optimized mpio code was broken and when read was done, it hanged. Solution: H5FDmpio.c: In H5FD_mpio_write, moved the 16-line block of code in which all procs other than p0 skip the actual write to be just before the call to MPI_File_write_at. Previously, the values of the local vars that controlled "allsame" were not always set correctly when the moved block was reached. H5S.c: Changed default value of H5_mpi_opt_types_g to TRUE, so that the MPI-IO hyperslab code is executed by default in parallel HDF5, rather than executing the serial hyperslab code. H5Smpio.c: In function H5S_mpio_hyper_type, added a call to free an intermediate type. Cures a small memory leak. Added code for cases of empty hyperslab Changed displacements to be MPI_Aint Platforms tested: modi4 -64: worked fine with mpich 1.2.0 but failed with the messages saying it ran out of entries for MPI_Types during the collective_read test. After tracing the code all the way to the collective read, all MPI Types have been freed properly. It aborted with the above message when it executed the line if (MPI_SUCCESS!= MPI_File_read_at_all(file->f, mpi_off, buf, size_i, buf_type, &mpi_stat )) Could not see any problem with this line. It could be a bug in the SGI version of MPI.
* [svn-r2645] Albert Cheng2000-10-101-17/+25
| | | | | | | | | | | | | | | | 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-r2644] Purpose:Bill Wendling2000-10-091-3/+3
| | | | | | | | | | Bug fix Description: ; missing from end of some > macros. Solution: Added Platforms tested: Mosaic^WNetscape
* [svn-r2643] Purpose:Bill Wendling2000-10-092-7/+173
| | | | | | | | | | | | Adding Testing Description: Alignment when putting elements in a compound datatype can be off. Solution: This was a bug which I'd fixed. Here's a program to exercise the bug. Platforms tested: Linux
* [svn-r2642] Purpose:Bill Wendling2000-10-091-0/+19
| | | | | | | | | | | | Bug fix Description: The documentation on how to dump attribute data was not complete enough. Some people got confused on the commandline syntax (you have to specify the "path" from the root group to the attribute to dump it). I put some examples in to show how to correctly dump attributes. Platforms tested: Viewed with Netscrape.
* [svn-r2641] Purpose:Albert Cheng2000-10-094-23/+143
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Added features Description: There were no automatic tests for transfering zero elements. Solution: t_dset.c: Added two new patterns of ZROW (zero rows for process 0) and ZCOL(zero columns for process 0). ZROW test was added but it failed because the current library does not accept it. Not compiled in now. Need to fix the library before turning it back on again and also to add the ZCOL test. t_mdset.c: Added statement to show progress. Also the MPI_Barrier() call get processes synchornoized. It eliminates the racing condition but this is not a permenant solution. The library code needs to be fixed. testphdf5.c: Added a bunch of MPI_Type_XXX debug code. Added the -md option to skip the multiple datasets tests. Changed the cosmitic appearance of the banner messages. testphdf5.h: When an error is detected, the old way was to call MPI_Finalize() before exiting. This sometimes hangs because some processes may be waiting for a message of a different tag. Changed to call MPI_Abort() for now so that the whole MPI job would abort rather than hanging due resource limits exceeded. Added the definition of ZROW and ZCOL. Platforms tested: Modi4 -64.
* [svn-r2639] Purpose:Albert Cheng2000-10-091-0/+2
| | | | | | | | | Update Description: Added the description of the environment variable HDF5_MPI_OPT_TYPES which controls the use of optimized MPIO routines. Platforms tested: Viewed via IE.
* [svn-r2638] Snapshot version 1.3 release 31HDF Admin2000-10-072-2/+2
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* [svn-r2637] Purpose:Bill Wendling2000-10-061-803/+756
| | | | Format changes
* [svn-r2636] Purpose:Quincey Koziol2000-10-051-1/+1
| | | | | | | | | | Bug Fix Description: Test was not detecting hdp tool from HDF 4.1r4 correctly. Solution: Modified test to detect HDF4.1r[3-9] correctly. Platforms tested: FreeBSD 4.1.1 (hawkwind)
* [svn-r2635] Purpose:Quincey Koziol2000-10-051-5/+11
| | | | | | | | | | | Portability fix Description: Non-portable GNU-specific features were used. Solution: Replaced GNU-specific features with more portable (but more difficult to maintain) forms of the features. Platforms tested: FresBSD 4.1.1 (hawkwind)
* [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.
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