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* [svn-r16800] Purpose: Fix bug 1516Neil Fortner2009-04-201-0/+1
| | | | | | | | | | | Description: h5repack previously would not take named datatypes into consideration when copying datasets and attributes. This would cause extra anonymous datatypes in the target file at best, and cause errors halfway through the repacking at worst. h5repack should now always handle named datatypes correctly. Named datatypes are also now converted to the native type when -n is given. Tested: jam, linew, smirom (h5committest)
* [svn-r16710] Purpose: Fix bug 1423Neil Fortner2009-04-081-0/+1
| | | | | | | | | | | | | | Description: Versions of the library between 1.3.0 and 1.6.3 have a bug which prevents them from opening any file that does not have the root group's symbol table information cached in the root group's entry in the superblock. Prior to 1.8 this was not an issue as this information was always cached. However, 1.8.0 stopped writing this information (which is not required by the file format specification), and these older versions can therefore not read files created or last written by versions 1.8.0 to 1.8.2. This fix modifies the library to once again add this information to the superblock (when using the old file format). Tested: jam, linew, smirom (h5committest)
* [svn-r16629] removed a h5dump test (array type) that has a different bogus ↵Pedro Vicente Nunes2009-03-301-2/+0
| | | | | | | | | output in frebsd (liberty) removed the call to the file generation in the test generation program removed the binary h5 and ddl from svn tested: linux
* [svn-r16614] 3. #1501 (B1) tools bug if dataset is larger than ↵Pedro Vicente Nunes2009-03-251-0/+3
| | | | | | | | | | | | H5TOOLS_BUFSIZE limit. ISSUE : the tools use the following formula to read by hyperslabs: hyperslab_size[i] = MIN( dim_size[i], H5TOOLS_BUFSIZE / datum_size) where H5TOOLS_BUFSIZE is a constant defined of 1024K. This is OK as long as the datum_size does not exceed 1024K, otherwise we have a hyperslab size of 0 (since 1024K/(greater than 1024K) = 0). This affects h5dump. h5repack, h5diff SOLUTION: add a check for a 0 size and define as 1 if so. TEST FOR H5DUMP: Defined a case in the h5dump test generator program of such a type (an array type of doubles with a large array dimension, that was the case the user reported). Since the written file commited in svn would be around 1024K, opted for not writing the data (the part of the code where the hyperslab is defined is executed, since h5dump always reads the files). Defined a macro WRITE_ARRAY to enable such writing if needed. Added a run on the h5dump shell script. Added 2 new files to svn: tools/testfiles/tarray8.ddl, tools/testfiles/tarray8.h5. NOTE: while doing this I thought of adding this dataset case to an existing file, but that would add the large array output to those files (the ddls). The issue is that the file list is increasing. TEST FOR H5DIFF: for h5diff the check for reading by hyperslabs is H5TOOLS_MALLOCSIZE (128 * H5TOOLS_BUFSIZE) or 128 Mb. This makes it not possible to add such a file to svn, so used the same method as h5dump (only write the dataset if WRITE_ARRAY is defined). As opposed to h5dump, the hyperslab code is NOT executed when the dataset is empty (dataset is not read). Added the new dataset to existing files and shell run (tools/h5diff/testfiles/h5diff_dset1.h5 and tools/h5diff/testfiles/h5diff_dset2.h5 and output in tools/h5diff/testfiles/h5diff_80.txt). TEST FOR H5REPACK: similar issue as h5diff with the difference that the hyperslab code is run. Added a run to the shell script (with a filter, otherwise the code uses H5Ocopy). tested: linux (h5commitest failed , apparently it did not detect the code changes in /tools/lib that fix the bug: the error in an assertion in the hyperslab of 0. I am sure that making h5ccomitest --distclean will detect the new code , but don't want to wait more 3 hours :-) )
* [svn-r16594] Purpose: fix bug 1189Neil Fortner2009-03-231-0/+1
| | | | | | | | | | | Description: Some files apparently exist in the wild which have corrupt symbol table messages on the root group. These files can be opened by 1.6 (which uses the cached information in the superblock) but not by 1.8. This patch fixes 1.8 and 1.9 so they can now open these files, and will correct them if necessary. Also fix some potential (rare) problems with array datatype versions. Tested: jam (parallel; h5committest not working on linew or smirom)
* [svn-r16552] Correct typo.Larry Knox2009-03-061-1/+1
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* [svn-r16548] Updated MANIFEST for new files in vms/tools.Larry Knox2009-03-051-0/+2
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* [svn-r16518] have 2 expected outputs for 2 h5ls runs depending if run on a ↵Pedro Vicente Nunes2009-02-261-3/+5
| | | | | | | big or little endian machine. Configure.in was modified to export a variable carrying endianess information to testh5ls.sh. This script then compares the current run with 2 expected outputs, one for a big-endian machine (linew was used to generate the output), other for little endian (jam was used to generate the output) the way h5ls prints types, it starts searching for NATIVE types first. One solution would be h5ls not to detect these native types, using for example the same print datatype function that h5dump does, that would make the output look the same on all platforms ("32-bit little-endian integer" would be printed instead). Drawback, this "native" information would not be available. Other solution is to have not one but 2 expected outputs and make the shell script detect the endianess and compare with one output or other tested: h5committest
* [svn-r16461] Bug fix: for compound types, the not comparable test for ↵Pedro Vicente Nunes2009-02-111-0/+2
| | | | | | | | | | | | | | | | | | | | members was not done Solution: for compound types, recursively apply that check Two new cases are added 1) the compound type has a different number of members. Message printed is <obj1> has X members <obj2> has Y members Where X and Y are the number of members of each compound type being compared 2) the compound type has not comparable types (for example a double and an int at the same index) In this case the message Comparison not possible: object1 is of class1 and object2 is of class2 Is replaced with Comparison not possible: object1 has a class1 and object2 has a class2 Modified the test generator program to have these 2 cases Added a shell run for these 2 cases Tested: windows, h5committest
* [svn-r16401] Description:Quincey Koziol2009-02-031-0/+1
| | | | | | | | | Correct error introduced in r16353 with layout version, and add test so it gets caught earlier. Tested on: FreeBSD/32 6.3 (duty) Too minor to require h5committest
* [svn-r16349] new h5diff output filesPedro Vicente Nunes2009-01-261-0/+6
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* [svn-r16299] Print a message ofPedro Vicente Nunes2009-01-131-2/+3
| | | | | | | | | Storage: information not available When displaying storage information for VL and dataset region types Added 2 shell runs that display this information #818 Tested: windows, linux
* [svn-r16204] Description:Quincey Koziol2008-12-181-0/+1
| | | | | | | | | | | | | | | | | | | | | Moved v1 B-tree debugging routines into separate module and thinned out header files a bit. Tested on: Mac OS X/32 10.5.5 (amazon) in debug mode Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r16180] Description:Quincey Koziol2008-12-111-1/+1
| | | | | | | | | | Rename the current chunk indexing routines module for B-tree indices to better reflect their purpose, and to make the upcoming extensible array index module fit in better. Tested: FreeBSD/32 6.3 Too minor to require h5committest
* [svn-r16137] Description:Quincey Koziol2008-11-281-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | Add support for paging large data blocks to extensible arrays Clean up allocation/destroy code for extensible array index, super and data blocks Add a couple of routines to set/get bit values in memory buffers Tested on: Mac OS X/32 10.5.5 (amazon) in debug mode Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
* [svn-r16062] Purpose: Allow per-dataset rdcc configurationNeil Fortner2008-11-121-0/+1
| | | | | | | | Description: Adds 3 new public functions: H5Pset_chunk_cache, H5Pget_chunk_cache, and H5Dget_access_list. First implementation of dataset access properties. See RFC_chunk_cache_functions for details. Tested: kagiso, linew, smirom (h5committest)
* [svn-r15913] Bug fix: #933Albert Cheng2008-10-211-1/+0
| | | | | | | The information of libhdf5_fortran.settings are all included in libhdf5.settings now. Remove it from the source. Tested: kagiso with fortran and C++.
* [svn-r15886] Purpose: Close bug 1332Neil Fortner2008-10-161-0/+3
| | | | | | | | | Description: Improved external link traversal of h5dump. h5dump will now properly avoid all cycles, even those spanning multiple files. Improvement to the output of committed datatypes. Committed datatypes are now checked for uniqueness (like other objects). Tests added for these cases. Tested: kagiso, linew, smirom (h5committest)
* [svn-r15880] Description:Scot Breitenfeld2008-10-151-1/+0
| | | | Moved the H5E fortran flags contained in H5fortran_flags.f90 to the H5E fortran Module (H5Eff.f90), so H5fortran_flags.f90 is no longer needed.
* [svn-r15815] Purpose: Add new source code and tests to WindowsScott Wegner2008-10-081-0/+4
| | | | | | | | | | Description: Many new source files were added from the freespace branch. This checkin adds the code to Windows as well. Note: Some tests are still failing on Windows, but this checkin brings us closer to fixing them. In particular, freespace test fails on compile (Quincey is working on it), and the DLL links test fails at runtime (I'll look into it) Tested: VS2005 on WinXP
* [svn-r15804] Purpose: Add option to h5ls to enable external link traversal.Neil Fortner2008-10-071-0/+4
| | | | | | | | Description: Added -E option to h5ls. When set, this alows h5ls to enter external files (currently only through an external link). The -r option by itself will no longer allow h5ls to traverse external links. Tested: kagiso, linew, smirom (h5committest)
* [svn-r15800] Description:Quincey Koziol2008-10-071-0/+16
| | | | | | | | | | | | | | | | | | | | | | | Bring file free space branch changes through r15795 into trunk, which includes a fair bit of code cleanup & rearrangement along with a couple of bug fixes also. Tested on: Mac OS X/32 10.5.5 (amazon) in debug mode Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (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/Intel compilers w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
* [svn-r15746] Description:Quincey Koziol2008-10-011-0/+1
| | | | | | | | | | | | | | | | | | | | | Add support for extensible array "super block". Tested on: Mac OS X/32 10.5.5 (amazon) in debug mode Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (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/Intel compilers w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
* [svn-r15721] Added a file with user block data to be used by the h5repack ↵Pedro Vicente Nunes2008-09-291-1/+1
| | | | windows shell script only Note: for the unix shell script this file is not used
* [svn-r15699] Bug fix #1281Pedro Vicente Nunes2008-09-251-25/+3
| | | | | | | | | | 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 tested: windows, linux
* [svn-r15674] Description:Quincey Koziol2008-09-221-0/+1
| | | | | | | | | | | | | | | | | | | | | | Add base support for extensible array "data blocks" to code, tests and h5debug. Tested on: Mac OS X/32 10.5.4 (amazon) in debug mode Mac OS X/32 10.5.4 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (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/Intel compilers w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
* [svn-r15668] Purpose: Add feature requested in bug #1282Neil Fortner2008-09-211-0/+5
| | | | | | | | | | 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-r15617] Description:Quincey Koziol2008-09-111-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | Clean up how v2 B-tree (and extensible array) classes are determined in h5debug. Add support for extensible array headers and index blocks to h5debug Tested on: Mac OS X/32 10.5.4 (amazon) in debug mode Mac OS X/32 10.5.4 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (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/Intel compilers w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
* [svn-r15614] Description:Quincey Koziol2008-09-111-0/+2
| | | | | | | | | | | | | | | | | | | | | | More extensible array features: add support for setting/getting elements in the array's index block. Tested on: Mac OS X/32 10.5.4 (amazon) in debug mode Mac OS X/32 10.5.4 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (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/Intel compilers w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
* [svn-r15601] Description:Scot Breitenfeld2008-09-081-0/+1
| | | | Added windows fortran DLL function file, hdf5_fortrandll.def
* [svn-r15584] Purpose: Add new extensible array source code and test project ↵Scott Wegner2008-09-031-0/+4
| | | | | | | | | for Windows Description: In revision 15549, new source code was added for the extensible array interface. This checkin adds the source code to Windows, along with the new test project, earray. Note: The new H5EA interface causes compilation errors on Windows, and will need to be fixed in the source.
* [svn-r15582] Added script to build h5perf_serial in standalone mode.Christian Chilan2008-09-021-0/+1
| | | | Tested on kagiso, smirom, and linew.
* [svn-r15576] Decription:Scot Breitenfeld2008-09-021-0/+1
| | | | | | Added the file: ./fortran/src/H5test_kind_SIZEOF.f90
* [svn-r15549] Description:Quincey Koziol2008-08-281-0/+8
| | | | | | | | | | | | | | | | | | | | | | | | | | | Initial checkin of extensible array data structure prototype code and regression tests. Initial definitions for revised FUNC_ENTER/LEAVE and error reporting macros, which are being vetted in the extensible array code. Minor warning and formatting cleanups in other sections of code. Tested on: Mac OS X/32 10.5.4 (amazon) in debug mode Mac OS X/32 10.5.4 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (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/Intel compilers w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
* [svn-r15535] Description:Scot Breitenfeld2008-08-261-0/+2
| | | | | | | | | Added files: ./fortran/src/H5_DBLE_InterfaceInclude.f90 ./fortran/src/H5_DBLE_InterfaceExclude.f90 Contains the DOUBLE PRECSION interfaces depending on the state of FORTRAN_DEFAULT_REALisDBLE_F.
* [svn-r15504] Purpose: Update MANIFESTScott Wegner2008-08-211-0/+4
| | | | | | | | Description: Add new Windows project files to MANIFEST Tested: none
* [svn-r15485] Purpose: Allow library to shut down properly when objects have ↵Neil Fortner2008-08-191-0/+1
| | | | | | | | | | | | | | | | reference count > 1. Description: Added a new field 'app_count' to H5I_id_info_t struct, to track the reference count on an id due to the application. the old 'count' field tracks the total. Generally any id visible to the application gets placed in app_count. Added app_ref boolean parameter to H5I_inc_ref, H5I_dec_ref, H5I_register, H5I_clear_type, and a few other functions, to specify whether the operation(s) being performed on the id(s) are due to the application (TRUE) or not (FALSE). Test added for this case. Tested: kagiso, smirom, linew (h5committest)
* [svn-r15465] remove h52jpegPedro Vicente Nunes2008-08-121-10/+0
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* [svn-r15429] new test for h5diffPedro Vicente Nunes2008-08-041-0/+1
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* [svn-r15316] added one more palette to the test generator filePedro Vicente Nunes2008-07-031-3/+3
| | | | tested: windows, linux
* [svn-r15314] moved h5jam test files to tools/h5jam/testfilesPedro Vicente Nunes2008-07-031-6/+9
| | | | tested: linux
* [svn-r15307] moved testfiles from hl/tools/testfiles to ↵Pedro Vicente Nunes2008-07-021-3/+4
| | | | | | hl/tools/gif2h5/testfiles tested: linux
* [svn-r15292] moved h52jpeg to /hl/tools/h52jpegPedro Vicente Nunes2008-06-281-8/+8
| | | | tested: linux
* [svn-r15260] new location for h5copy filesPedro Vicente Nunes2008-06-231-2/+2
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* [svn-r15248] new location for h5repack filesPedro Vicente Nunes2008-06-201-16/+16
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* [svn-r15246] Changed the shell script to avoid doing a cd $srcdirPedro Vicente Nunes2008-06-201-3/+0
| | | | | | | | | | | | The name of the files are now given by its full name relative to $srcdir To avoid the printing of the complete full path of the test file, that hides all the other parameters for long paths, the printing of the command line is done first in TESTING with the name only of the test file, not its full path the printing in the expected output that had the file name was removed as well as 3 tests that tested error messages in which the file name was present tested: linux (in 2 different build directories relative to $srcdir), solaris
* [svn-r15238] Pedro Vicente Nunes2008-06-191-77/+77
| | | | | | Moved all h5diff testfiles from /tools/testfiles to tools/h5diff/testfiles Tested: linux, solaris
* [svn-r15223] new testfile location for h52jpegPedro Vicente Nunes2008-06-171-1/+2
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* [svn-r15220] new files for h52jpegPedro Vicente Nunes2008-06-161-1/+2
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* [svn-r15218] new test files for h52jpegPedro Vicente Nunes2008-06-161-0/+3
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