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* [svn-r15706] make a test generate a LE output for test portabilityPedro Vicente Nunes2008-09-261-0/+1
| | | | tested: linux, solaris
* [svn-r15700] added wb falg to read binary files in WIN32Pedro Vicente Nunes2008-09-251-13/+68
| | | | tested: windows
* [svn-r15698] renamed input text files to have the extension .txtPedro Vicente Nunes2008-09-259-8/+38
| | | | tested: linux
* [svn-r15697] renamed configuration files to have the extension .confPedro Vicente Nunes2008-09-258-6/+6
| | | | tested: linux
* [svn-r15694] 1)Pedro Vicente Nunes2008-09-2413-14/+52
| | | | | | | | | | | | | | Bug fix #1281 The TEXTFPE was described in the usage (read floats in scientific notation) but was not implemeneted. Solution: remove TEXTFPE from the help system and have the TEXTFPE input type do the same thing as TEXTPF currently does to support backwards compatibility (the format read for both TEXTFPE and TEXTPF is %f) added a test 2) renamed configuration files to have the extension .conf tested: windows, linux
* [svn-r15680] Pedro Vicente Nunes2008-09-223-42/+74
| | | | | Formatted code Tested: windows, linux
* [svn-r15677] Description:Quincey Koziol2008-09-221-169/+100
| | | | | | | | | | | | Bring r15676 back from trunk: Centralize all macros for declaring "magic numbers"/signatures for objects in the file into src/H5Fprivate.h, so it's easier to know what values have already been defined, etc. Tested on: Mac OS X/32 10.5.5 (amazon) Too minor to require h5committest
* [svn-r15672] Add missing test file, re-add it to the manifest (sorry).Neil Fortner2008-09-221-0/+12
| | | | Tested: kagiso
* [svn-r15669] Purpose: Add feature requested in bug #1282Neil Fortner2008-09-2112-60/+309
| | | | | | | | | | Description: Adds capability to h5ls to traverse external links when the -r (recursive) option is given. Changes to the way absolute path names are patched in h5trav.c. Changes to the way recursive traversal starting from a non-root group is handled (which also fixes some preexisting issues). Tests added for these cases. Tested: kagiso, smirom, linew (h5committest)
* [svn-r15663] fix commentsPedro Vicente Nunes2008-09-191-8/+15
| | | | tested: linux
* [svn-r15662] Cleaned compiler warnings Pedro Vicente Nunes2008-09-198-299/+285
| | | | | | | | Bug fixes: change the options block size variable from int to hsize_t, to match the H5Pset_userblock call, do not print print compression ratio when the requested filter is NONE Tested: windows, linux
* [svn-r15646] Cleaned compiler warnings Pedro Vicente Nunes2008-09-171-4/+4
| | | | | | Bug fix: change the options block size variable from int to hsize_t, to match the H5Pset_userblock call Tested: windows, linux
* [svn-r15642] Pedro Vicente Nunes2008-09-175-3805/+3889
| | | | | | | | Add a default user block size of 1024 when none is given add a failure condition of writing user block Tested: windows, linux
* [svn-r15629] Description:Quincey Koziol2008-09-1631-1901/+1901
| | | | | | | | | | | | | Remove trailing whitespace from C/C++ source files, with the following script: foreach f (*.[ch] *.cpp) sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f end Tested on: Mac OS X/32 10.5.5 (amazon) No need for h5committest, just whitespace changes...
* [svn-r15558] 1) There are 2 new command line parameters for h5repack. ↵Pedro Vicente Nunes2008-08-297-27/+188
| | | | | | | | | | | | | | Together they allow a call to H5Pset_alignment to be made -t T, --threshold=T Threshold value for H5Pset_alignment -a A, --alignment=A Alignment value for H5Pset_alignment 2) bug fix the printing of the dataset name was not done for references (verbose mode) tested: windows, linux
* [svn-r15533] #1184Pedro Vicente Nunes2008-08-266-33/+323
| | | | | | | | | | | Add a userblock to an HDF5 file during the repack. The user gives give a filename and userblock size as command line parameters to h5repack and the contents of that file are stored in the userblock for the HDF5 file created by h5repack. New flags to handle this -u and -b Tested : windows, linux
* [svn-r15511] bug fixPedro Vicente Nunes2008-08-211-270/+282
| | | | | | | | | when comparing attributes, a type ID was not properly closed solution: close the Id on the iteration and continue instead of goto out of the cycle tested: windows, linux
* [svn-r15463] Description:Quincey Koziol2008-08-122-1/+2
| | | | | | | | Bring revision 15462 (compiler warnings) back from trunk. Tested on: Mac OS X/32 10.5.4 (amazon) w/FORTRAN & C++ (Too minor to require h5committest)
* [svn-r15459] Purpose: Modify the library to take the proper action when ↵Neil Fortner2008-08-1160-3/+14
| | | | | | | | | | | | | | | files with incorrect datatype versions are encountered. Description: The library now recognizes some problems with datatype versions in H5O_decode_helper(), and, if not performing strict format checks, automatically corrects them. Framework added for other message decode routines to automatically correct file errors. Datatype version information added to h5debug. Resolves bz#1236, 1266. Test files with incorrect datatype versions corrected. Tested: kagiso, smirom, linew (h5committest)
* [svn-r15447] Pedro Vicente Nunes2008-08-072-3/+15
| | | | | | | | | | | bug fix http://bugzilla.hdfgroup.uiuc.edu/show_bug.cgi?id=788 don't print array indices for regions tested: windows, linux
* [svn-r15441] Purpose: Backport from trunk: Bring the Windows H5pubconf.h ↵Scott Wegner2008-08-061-1/+1
| | | | | | | | | | | | | | | | up-to-date Description: This commit is a major update to the Windows-maintained H5pubconf.h file. This file is statically-distributed because Windows cannot generate it dynamically as other platforms do. Previously, our Windows version contained a minimal subset of the macro definitions required. To update, I've gone through each macro (based on kagiso's output), and tested for the correct value on Windows. This allows us to better target code based on feature flags. It should also be easier to update in the future as changes are made to the configure script. This commit also contains one small bug fix in h5ls.c. Some Windows-specific code was missing a local variable definition. The bug went unnoticed because Windows didn't define the feature flag correctly. I've also made changes to the h5vers script. Whenever the version string is incremented (automatically by h5test after a snapshot), the strings in H5pubconf.h will also be updated. Tested: VS2005 on WinXP (32- and 64-bit) VS.NET on WinXP 32-bit h5vers tested under Cygwin
* [svn-r15436] bug fixPedro Vicente Nunes2008-08-061-11/+11
| | | | | | | the compression ratio was being printed for cases where a layout was requested and not a filter tested: windows, linux
* [svn-r15433] http://bugzilla.hdfgroup.uiuc.edu/show_bug.cgi?id=1170Pedro Vicente Nunes2008-08-0526-294/+570
| | | | | | | | | | | | | Summary: when using h5diff to compare the results of h5repack (or other tools that copy one HDF5 file to another), a new option is needed to allow h5diff to make an "absolute" comparison of the 2 files. This is the "contents" mode explained in the usage below. If this mode is present, objects in both files must match (must be exactly the same). If this does not happen, the tool returns an error code of 1 (instead of the success code of 0) Changes to the h5repack test script: the call to h5diff was changed to include -c (maintaining the previous -q). tested: windows, linux
* [svn-r15334] Update test files for h5stat.Vailin Choi2008-07-084-10/+10
| | | | h5committested.
* [svn-r15181] Purpose: _WIN32 macro cleanupScott Wegner2008-06-097-68/+1
| | | | | | | | | | Description: As part of our Windows cleanup, we try to remove windows-specific tweaks in the source code. There are many instances where Windows code is introduces via ifdef's. We re-evaluate whether they are still required, and found that many of them are not. Others we change to "feature"-specific code, rather than Windows-specific. Tested: VS2005 on WinXP VS.NET on WinXP h5committest (kagisopp, smirom, linew)
* [svn-r15160] Purpose: Separate Windows function macro definitions to win32defs.hScott Wegner2008-06-058-33/+33
| | | | | | | | | | | | | | Description: In library code, we try not to use system calls directly, but instead use the HD{function} macro instead. This way, we can map special versions of the call on particular systems. Previously, it was all done in H5private.h. However, in an effort to clean up platform-specific definitions, we move all of the Windows macros into a separate file, win32defs.h. This way, we can use the non-Posix versions that Visual Studio sends warnings about. Some macros are set specifically in the platform-specific header files. Then, any macros left unset will be set by the "default" implementation in H5private.h. This checkin also cleans up various source files to use the HD* macros when possible. Tested: VS2005 on WinXP VS.NET on WinXP h5committest (kagiso, linew, smirom)
* [svn-r15151] Pedro Vicente Nunes2008-06-053-8/+16
| | | | | | | | | | Fix for #1169 http://bugzilla.hdfgroup.uiuc.edu/show_bug.cgi?id=1169 don't print attributes to stdout when doing binary output added an attribute to the file run on the binary output test tested: windows, linux
* [svn-r15136] Purpose:Albert Cheng2008-06-042-5/+16
| | | | | | | | | | | | | | bug fixes. Description: Added code to create an empty hdf5 (named h5diff_empty.h5) in order to test if h5diff compares correctly an empty hdf5 vs. a non-empty one. Tested: Tested in kagiso of h5diffgentest itself. Verified by h5dump that h5diff_empty.h5 was indeed empty. Then "h5diff h5diff_empty.h5 h5diff_basic1.h5" returned 0 (should have returned non-zero).
* [svn-r15134] Description:Quincey Koziol2008-06-044-41/+45
| | | | | | | | | | Brought revision 15133 back from trunk: Fixed bug in h5ls that prevented relative group listings (like "h5ls foo.h5/bar") from working correctly. Tested on: Mac OS X/32 10.5.3 (amazon)
* [svn-r15132] Description:Quincey Koziol2008-06-031-1/+1
| | | | | | | | | | | | | | Bring back revision 15131 from trunk: Finish omnibus chunked dataset I/O refactoring, to separate general actions on chunked datasets from actions that are specific to using the v1 B-tree index. Cleaned up a few bugs and added some additional tests also. Tested on: Mac OS X/32 10.5.3 (amazon) Linux/32 2.4 (chicago)
* [svn-r15053] Add a test for the 1.6.7 -i infile -o outifle for backward ↵Pedro Vicente Nunes2008-05-211-0/+37
| | | | | | | | compability Used the function TOOLTEST from 1.6.7 Tested: linux
* [svn-r15048] bug fix regarding change from -i to -d regarding number of ↵Pedro Vicente Nunes2008-05-201-1/+1
| | | | | | links in indexed format tested: windows
* [svn-r15042] Bug fix.Albert Cheng2008-05-2011-44/+44
| | | | | | | | | | | | | | | | | | | Description: The fortran Makefile.am used HDF_FORTRAN to indicate it is part of the Fortran API source so that conclude.am will give fortran api prefix in the test output. The symbox HDF_FORTRAN is also used in configure for a different purpose (indicated --enable-fortran). They conflicted. Similar problem for the symbol HDF_CXX. Solution: Changed all the involved Makefile.am to use "FORTRAN_API" instead. It is a more appropriate name. Same for CXX_API. Along the way, discovered that the Makefile.am of hl/fortran/test and hl/cxx/test did not have those symbols at all. Added them in. Platform tested: Kagiso serial and h5committested (kagisopp, smirom, linew).
* [svn-r15033] Purpose:Albert Cheng2008-05-1911-0/+165
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Improvement. Description: src/libhdf5.settings was the initial configure summary and is installed. Then configure is changed to dump a summary of the configure settings to the output and also append it to src/libhdf5.settings. That created two different output formats and duplicated information. This is the initial attempt to clean up this confusion and unify the output format. It is decided to use the src/libhdf5.settings template as the unified means. This requires more macros symbols be defined. The following symbols are all related to generating the src/libhdf5.settings file. AC_SUBST(EXTERNAL_FILTERS) AC_SUBST(MPE) MPE=no AC_SUBST(STATIC_EXEC) STATIC_EXEC=no AC_SUBST(HDF_FORTRAN) HDF_FORTRAN=no AC_SUBST(FC) HDF_FORTRAN=no AC_SUBST(HDF_CXX) HDF_CXX=no AC_SUBST(CXX) HDF_CXX=no AC_SUBST(HDF5_HL) HDF5_HL=yes AC_SUBST(GPFS) GPFS=no AC_SUBST(LINUX_LFS) LINUX_LFS=no AC_SUBST(INSTRUMENT) INSTRUMENT=no AC_SUBST(CODESTACK) CODESTACK=no AC_SUBST(HAVE_DMALLOC) HAVE_DMALLOC=no AC_SUBST(DIRECT_VFD) DIRECT_VFD=no AC_SUBST(THREADSAFE) THREADSAFE=no AC_SUBST(STATIC_SHARED) AC_SUBST(enable_shared) AC_SUBST(enable_static) AC_SUBST(UNAME_INFO) UNAME_INFO=`uname -a` The src/libhdf5.settings.in has CONDITIONAL's added to it too. The untrue conditions turned into a "#" and these lines are cleaned by the post processing script. Platform tested: h5committest on kagiso, smirom and linew. (smirom had failures not due to my changes.)
* [svn-r15024] backward compatibility for old -i infile -o outfile optionsPedro Vicente Nunes2008-05-162-18/+195
| | | | | | | | | | | | | if these are detected this syntax is used, otherwise the one in usage is used there was another -i option for -i L2, --indexed=L2 Minimum number of links in the indexed format That was changed to -d -d L2, --indexed=L2 Minimum number of links in the indexed format Tested: windows, linux
* [svn-r15006] Purpose: configure cleanupMike McGreevy2008-05-1511-11/+0
| | | | | | | Description: cleaning up configure related to removal of --disable-hsizet flag, which we no longer support. Tested: kagiso
* [svn-r14978] Support for external links follow up. The format is to print ↵Pedro Vicente Nunes2008-05-125-40/+194
| | | | | | | | | | | | | | | | | | | | | | | | | | | | the target object as part of TARGETPATH, noted with some extra indentation The previous printing of LINKCLASS 64 was removed HDF5 "textlinksrc.h5" { GROUP "/" { EXTERNAL_LINK "ext_link1" { TARGETFILE "textlinktar.h5" TARGETPATH "dset" DATASET "dset" { DATATYPE H5T_STD_I32LE DATASPACE SIMPLE { ( 6 ) / ( 6 ) } DATA { (0): 1, 2, 3, 4, 5, 6 } } } } } There is no script test for this behavior so far, because test script uses complete paths that vary from test to test, making not possible to define a valid TARGETFILE in the file tested: windows, linux, solaris
* [svn-r14948] Add a test for the floating point user defined printf formatPedro Vicente Nunes2008-05-066-2/+92
| | | | | | | | | | | | | | | | Usage is -m T, --format=T Where T - is a string containing the floating point format, e.g '%.3f' The test consists of writing a number with 7 fractional digits (default precision display of %f is 6 digits) and have the 7 digits displayed with -m %.7f fpformat.h5 Tested: windows, linux, solaris Note: the output file was generated in linux, it may be possible that platforms other than the ones tested have a different representation of the number
* [svn-r14915] Pedro Vicente Nunes2008-05-011-11/+15
| | | | | | | Introduced a compression ratio = uncompressed size / compressed size in the printing of the compression with 3 digits of precision per hdf-forum NASA developers suggestion tested: windows, linux
* [svn-r14906] Introduced a ratio formula compression ratio = uncompressed ↵Pedro Vicente Nunes2008-05-016-13/+13
| | | | | | | | size / compressed size in the printing of the compression with 3 digits of precision per hdf-forum NASA developers suggestion tested: windows, linux, solaris
* [svn-r14895] RFC display compression ratio in h5dumpPedro Vicente Nunes2008-04-296-8/+77
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Here's the current behavior of h5dump regarding the printing of the dataset creation property list For example ./h5dump -H -p -d filters HDF5 "tfilters.h5" { DATASET "deflate" { DATATYPE H5T_STD_I32LE DATASPACE SIMPLE { ( 20, 10 ) / ( 20, 10 ) } STORAGE_LAYOUT { CHUNKED ( 10, 5 ) SIZE 385 } FILTERS { COMPRESSION DEFLATE { LEVEL 9 } } FILLVALUE { FILL_TIME H5D_FILL_TIME_IFSET VALUE 0 } ALLOCATION_TIME { H5D_ALLOC_TIME_INCR } } } The proposed behavior is to add this information after SIZE SIZE 385 (51.9%COMPRESSION) That percentage is obtained trough Per = (b-a) / a Where a = theoretical size obtained by multiplying datum size times number of elements b = size obtained with H5Dget_storage_size The final print would look like HDF5 "tfilters.h5" { DATASET "deflate" { DATATYPE H5T_STD_I32LE DATASPACE SIMPLE { ( 20, 10 ) / ( 20, 10 ) } STORAGE_LAYOUT { CHUNKED ( 10, 5 ) SIZE 385 (51.9%COMPRESSION) } FILTERS { COMPRESSION DEFLATE { LEVEL 9 } } FILLVALUE { FILL_TIME H5D_FILL_TIME_IFSET VALUE 0 } ALLOCATION_TIME { H5D_ALLOC_TIME_INCR } } } tested: windows, linux, solaris
* [svn-r14824] Purpose: Updating HDF5 1.8 to use automake 1.10.1 and ↵Mike McGreevy2008-04-1011-171/+215
| | | | | | | | | | | | | | | | | | libtool 2.2 Description: Updated bin/reconfigure script to reflect the new versions of libtool and automake in the /home1/packages/ directory. Rearranged configure.in script. For some reason, when using libtool 2.2, the libtool script doesn't generate until later in the configuration process, so I had to move a test that parsed through the libtool script to a point after where it was actually being generated. Ran libtoolize on the project, and ran bin/reconfigure to regenerate configure and Makefile.in's throughout. Tested: kagiso, smirom, linew, tg-login
* [svn-r14802] bug fix: #1106 h5dump -b will dump ASCII values for ↵Pedro Vicente Nunes2008-04-074-32/+9
| | | | | | datasets after the first one. One variable that controls the binary output was incorrectly reset to zero after a binary output was done a first time. The effect was that on cases of several datasets, the ones after the first were not binary written. Eliminated the resetting of that variable and tested a file with several datasets. Modified the test file so that it is easier to test with the tool binread, that reads the binary output of h5dump. tested: windows, linux
* [svn-r14703] 1. H5HFiblock.c: fixed problem for uninitialized "u" for bug ↵Vailin Choi2008-03-043-11/+11
| | | | | | | | | | | | | | #1072 in H5HF_man_iblock_size(). 2. H5HFstat.c: Since H5HF_space_size() zeroed out fs_size, add "meta_size" to store free-space size before adding to "heap_size". 3. h5stat_gentest.c: increase # of groups to get "h5stat_newgrat.h5" that contains indirect block entries in fractal heap. This is for testing the recursive part of the code in H5HF_man_iblock_size(). 4. h5stat_newgrat.h5: the new .h5 file generated by h5stat_gentest.c. 5. h5stat_newgrat.ddl: expected output from new "h5stat_newgrat.h5". Tested on kagiso, smirom, linew.
* [svn-r14691] Description:Quincey Koziol2008-02-2810-91/+460
| | | | | | | Handle comparing datasets & attributes w/variable-length strings properly. Tested on: Linux/64 2.6.9 (chicago)
* [svn-r14470] Purpose: Fixing configure problem on IRIX64.Mike McGreevy2008-01-302-4/+4
| | | | | | | | | | | | | | | Description: IRIX64 failed to build tools/h5import, as well as c++/test with szip. This is because IRIX is very picky when it comes to linking libraries, and must be done in specific order. (other UNIXes are not as such, and thus the problem wasn't present). Solution: Rearrange the order in which the libraries are linked on the compiler line by sorting the line that assigns libraries into the LDADD variable in the Makefile.am's of the two respective directories. Tested: IRIX64, kagiso, smirom
* [svn-r14437] bug fix for h5dump subsetting (deal with blocks)and new test runsPedro Vicente Nunes2008-01-167-79/+166
| | | | | | | | | | | | | | | | | | | | | | | | | add a check for block overlap after the command line parsing * Algorithm * * In a inner loop, the parameters from SSET are translated into temporary * variables so that 1 row is printed at a time (getting the coordinate indices * at each row). * We define the stride, count and block to be 1 in the row dimension to achieve * this and advance until all points are printed. * An outer loop for cases where dimensionality is greater than 2D is made. * In each iteration, the 2D block is displayed in the inner loop. The remaining * slower dimensions above the first 2 are incremented one at a time in the outer loop * * The element position is obtained from the matrix according to: * Given an index I(z,y,x) its position from the beginning of an array * of sizes A(size_z, size_y,size_x) is given by * Position of I(z,y,x) = index_z * size_y * size_x * + index_y * size_x * + index_x * tested: windows, linux
* [svn-r14420] Description:Quincey Koziol2008-01-152-2/+2
| | | | | | | | Correct the prototype for H5Sselect_elements() to take an 'hsize_t *' for the coordinates, instead of 'hsize_t **'. Tested on: Mac OS X/32 10.5.1 (amazon)
* [svn-r14414] revert the subsetting calls of h5dump to 1 size block, still a ↵Pedro Vicente Nunes2008-01-154-27/+15
| | | | | | bug with size > 1 tested: linux
* [svn-r14413] Description:Quincey Koziol2008-01-143-3/+3
| | | | | | | | | | | | | | | | | | | Change H5P[gs]et_format_bounds() => H5P[gs]et_libver_bounds() and also enumerated values H5F_FORMAT_{EARLIEST, LATEST} => H5F_LIBVER_{EARLIEST, LATEST} Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
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