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).
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
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 only. It is a trivia change.
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.
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
Description: Applying update to autotools that was applied to 1.8 a couple
of weeks ago to the trunk.
Updated bin/reconfigure script to reflect the new versions of
libtool and automake in the /home1/packages/ directory.
Rearranged configure.in script. When using libtool 2.2.2, 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 (h5committest)
formatted code
bug fix: the 1.6 branch did not have a test for the existence of long double type on print_type (print name of datatype)
tested: windows, linux
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".
renamed the h5import test files to have the extensions
text input files = .txt
binary input files = .bin
configuration files = .conf
hdf5 files = .h5
besides that in very test the files have the same name except extension.
For example
TOOLTEST txtin16.txt -c $srcdir/testfiles/txtin16.conf -o txtin16.h5
The convention for the test name is for example, for "txtin16"
"txt" for text then "in16" means integer 16 size
Tested: linux, solaris
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
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
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)
Add work-around to allow reading files that were produced with a buggy
earlier version of the library, which could create objects with the wrong
object header message count. There is now a configure flag
"--enable-strict-format-checks" which triggers a failure on reading a file
with this sort of corruption (when enabled) and allows the object to be read
(when disabled). The default value for the "strict-format-checks" flag is
yes when the "debug" flag is enabled and no when the "debug" flag is disabled.
Note that if strict format checks are disabled (allowing objects with
this particular kind of corruption to be read) and the file is opened with
write access, the library will re-write the object header for the corrupt
object with the correct # of object header messages.
This closes bugzilla bug #1010.
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
