Bring changes from Coverity branch back to trunk:
r19079 & 19080:
[BZ1942] h5dump -u to generate XML, it does not respect the -m option
xml version of dump_data function didn't check for use of fp_format variable.
Added new test expected file for committed bug 1942
r19103, 19104 & 19105:
[BZ1821] h5repack -v did not display correct output for a selected compression. Needed new test for comparing output of -v option.
Added new test file for solution to BZ1821
BZ1821 - Bring test changes from the shell script actually used.
Tested on:
Mac OS X/32 10.6.4 (amazon) debug & production
(h5committested on branch)
Add --no-dangling-links option to h5ls.
Description:
Related to "Bug 1830 - Following an dangling external link in h5ls should set non-zero return code."
If --no-dangling-links option is specified and any dangling link is found, return exit code 1 (error).
Tested:
jam, amani and heiwa
Support follow symbolic links.
Description:
Add '--follow-symlinks' option to follow symbolic links (soft and external).
Update help page according to RM.
Remove some warning messages from compiler.
Tested:
jam, amani and linew
*sigh* Bring along another updated file after recent object header
message info update.
Tested on:
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/default API=1.8.x,
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 debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.6.2 (amazon) in debug mode
Mac OS X/32 10.6.2 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Bring changes from file free space branch back to the trunk. *yay!*
Tested on:
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/default API=1.8.x,
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 debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.5.8 (amazon) in debug mode
Mac OS X/32 10.5.8 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
#1585). I changed it to undefined and let the caller functions decide the location
of the datatype. For H5Tdecode, it should mark the datatype as in memory. For other
callers like H5Dopen or H5Aopen, they should makr it as on disk.
Tested it on jam, smirom, linew.
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 :-) )
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
Description: When attempting to copy an object with a message shared in its own
object header, the library attempts to protect the same object header twice.
Previously, it was possible for the object header to be protected with write
access in one or both of these protects, which would be illegal. The library
should now always protect with read only access in this case. The conditions
for fixing incorrect datatype versions have been made weaker to support this
change. The version will only be corrected if the object header the datatype
is in is modified.
Tested: jam, smirom (h5committest)
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
Introduced a new feature in the tools library regarding command line parsing
In the definition of arguments, an "*" means that the switch can or can not have an optional argument. This "*" is put in the code regarding the letter definition, and it is transparent to the user (e.g b* instead of the previous b: ), where ":" notes a required argument after the letter (and no ":" or "*" notes no argument, mandatory)
Used for the h5dump binary option -b
It can be now
1) -b (defaults to NATIVE)
2) - b NATIVE
3) - b FILE
4) -b LE
5) -b BE
Note: the keyword NATIVE replaces MEMORY
This feature (-b with no argument) was tested with the sequence of h5dump to binary (NATIVE) then h5import to generate an HDF5 file from the binary file and h5diff to compare the 2 HDF5 files
Tested: linux
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)
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)
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)
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.
Tested: kagiso, smirom, linew (h5committest)
for now, the test script just calls the tool binary with the command line parameters, with no special
checking of the accuracy of the output contents (jpeg files)
tested: linux
Fixed bug in h5ls that prevented relative group listings (like
"h5ls foo.h5/bar") from working correctly.
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 10.5.3 (amazon) in debug mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
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).
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
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
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
- Add hash value for skip list string types, to reduce # of string
comparisons.
- Fixed bug with metadata/small data block aggregator adding size == 0
block into file free space list.
- Refactored metadata/small data block aggregator code into single set of
common routines.
- Changed block aggregator code to be smarter about releasing space in the
'other' block when the 'other' block has aggregated enough data.
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
