Add extra test cases for Bug1975 h5diff - support recursive comparison on group when specified as an object
Description:
Merged from hdf5 trunk (r19409)
Additional tests for combination of group recursive and --follow-symlinks
with multi-linked external links with several files (same name/strucure).
Tested:
jam, amani, heiwa
has been removed. According to the official description of DESTDIR by Gnu at
http://www.gnu.org/prep/standards/html_node/DESTDIR.html, DESTDIR is
prepended to the normal and complete install path that it precedes for the
purpose of installing in a temporary directory which is useful for building
rpms and other packages. The '/' after ${DESTDIR} will be followed by another
'/' at the beginning of the normal install path. When DESTDIR is empty the
path then begins with '//', which is incorrect and causes problems at least for
Cygwin.
The change made in config/commence.am affects many Makefile.*s when bin/reconfigure
is run. EXAMPLEDIRs had to be corrected individually.
Also the scripts to run examples after they are installed have checks added to see
that the fortran and c++ directories are present before trying to run the scripts
in them.
Tested with h5committest on amani, heiwa and jam.
Add --exclude-path option
Description:
Merged from hdf5 trunk (r19406).
Specified path to an object will be excluded from comparing the two files or two groups. If group is specified all the member objects will be excluded.
Related to "1890: h5diff excluding object for file comparison via command line"
Tested:
jam, amani
Fix for Bug1975 h5diff - support recursive comparison on group when specified as an object
Description:
Merged from hdf5 trunk (r19400).
Compare member objects and groups recursively when two files or groups are specified to be compared. Support parallel diff and handling symbolic links accordingly.
Tested:
jam, amani
Bring r19396 from trunk to 1.8 branch:
Bring back various modifications to the v2 B-trees that were introduced
in the revise_chunks branch but aren't dependent on any file format or API
changes.
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 (amani) 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, w/threadsafe, in production mode
Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
Mac OS X/32 10.6.4 (amazon) in debug mode
Mac OS X/32 10.6.4 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Mac OS X/32 10.6.4 (amazon) w/parallel, in debug mode
Additional fix for Bug 1821 - h5repack outputs compression information where it is not supposed to
Description:
Merged from hdf5 trunk (r19392)
Remove unnecessary lopping code, which only lowers performance.
Tested:
jam, amani
Fix for Bug1896 h5repack - changing layout to COMPACT does not work
Description:
Merged from hdf5 trunk (r19389)
Make h5repack be able to convert a layout to COMPACT for small size dataset as default. Also add verifying layout changes in our test script.
Tested:
jam, amani
Tested with h5committest on amani, jam, and heiwa, and on linew.
-This line, and those below, will be ignored--
M hdf5_1_8/test/Makefile.in
A hdf5_1_8/m4
AM hdf5_1_8/m4/ltsugar.m4
AM hdf5_1_8/m4/libtool.m4
AM hdf5_1_8/m4/ltversion.m4
AM hdf5_1_8/m4/lt~obsolete.m4
AM hdf5_1_8/m4/ltoptions.m4
M hdf5_1_8/configure
M hdf5_1_8/Makefile.in
M hdf5_1_8/testpar/Makefile.in
M hdf5_1_8/configure.in
M hdf5_1_8/src/Makefile.in
M hdf5_1_8/tools/Makefile.in
M hdf5_1_8/tools/misc/Makefile.in
M hdf5_1_8/tools/h5dump/Makefile.in
M hdf5_1_8/tools/h5repack/Makefile.in
M hdf5_1_8/tools/h5jam/Makefile.in
M hdf5_1_8/tools/h5diff/Makefile.in
M hdf5_1_8/tools/lib/Makefile.in
M hdf5_1_8/tools/h5copy/Makefile.in
M hdf5_1_8/tools/h5import/Makefile.in
M hdf5_1_8/tools/h5stat/Makefile.in
M hdf5_1_8/tools/h5ls/Makefile.in
M hdf5_1_8/hl/test/Makefile.in
M hdf5_1_8/hl/tools/Makefile.in
M hdf5_1_8/hl/tools/gif2h5/Makefile.in
M hdf5_1_8/hl/Makefile.in
M hdf5_1_8/hl/src/Makefile.in
M hdf5_1_8/hl/c++/test/Makefile.in
M hdf5_1_8/hl/c++/Makefile.in
M hdf5_1_8/hl/c++/src/Makefile.in
M hdf5_1_8/hl/c++/examples/Makefile.in
M hdf5_1_8/hl/fortran/test/Makefile.in
M hdf5_1_8/hl/fortran/Makefile.in
M hdf5_1_8/hl/fortran/src/Makefile.in
M hdf5_1_8/hl/fortran/examples/Makefile.in
M hdf5_1_8/hl/examples/Makefile.in
M hdf5_1_8/config/commence.am
M hdf5_1_8/MANIFEST
M hdf5_1_8/c++/test/Makefile.in
M hdf5_1_8/c++/Makefile.in
M hdf5_1_8/c++/src/Makefile.in
M hdf5_1_8/c++/examples/Makefile.in
M hdf5_1_8/bin/ltmain.sh
M hdf5_1_8/bin/reconfigure
M hdf5_1_8/perform/Makefile.in
M hdf5_1_8/fortran/test/Makefile.in
M hdf5_1_8/fortran/testpar/Makefile.in
M hdf5_1_8/fortran/Makefile.in
M hdf5_1_8/fortran/src/Makefile.in
M hdf5_1_8/fortran/examples/Makefile.in
M hdf5_1_8/aclocal.m4
M hdf5_1_8/examples/Makefile.in
Corrected use/name of source folder aliases.
Duplicated FindMPI.cmake so that non-c++ compiler is found first (recommemded commands did not work).
Bring r19325 from trunk
Tested: local linux with mpich
Avoid getting object information for soft/external links if we aren't
going to traverse across the link itself.
Tested on:
Linux/64 2.6 (chicago) w/debug & production
(h5committest coming up)
Corrected use of "SKIP" message in cmake.
Corrections to cmake configuration files (for cmake external projects).
Community suggested changes.
Tested: local linux
Bring r19252 & 19253 from trunk to 1.8 branch:
Bring Coverity changes from branch to trunk:
r19161:
Fixed the part for matching the subset info with dataset
r19189:
BZ1646: h5dump does not check number of dimensions for subsetting parameters against the dataset
Changed subset_t structure from holding hsize_t pointers to holding new subset_d pointers, which hold the original hsize_t pointer + len. this len is then checked against dataset ndims in the handle_dataset function of h5dump.
Changed all references to use new data structure.
Added tests for each subset parameter.
r19190:
Added new h5dump ddl files
Tested on:
Mac OS X/32 10.6.4 (amazon) w/debug & production
(h5committested on Coverity branch)
Bring r19237 from trunk to 1.8 branch:
Clean up misc. compiler warnings.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
Mac OS X/32 10.6.4 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Mac OS X/32 10.6.4 (amazon) w/parallel, in debug mode
Bring r19179 from trunk to 1.8 branch:
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)
Bring r19156 from trunk to 1.8 branch:
Bring revisions from Coverity branch back to trunk:
r19044:
Coverity #449 - Line 1560 called function H5O_chunk_protect for 2 pointers to allocate. But when there's failure on the second one, the first wasn't freed
(H5O_chunk_unprotect). We fixed it by freeing the pointers when an error happens.
r19045:
Fixed coverity issue # 319. Free sec_node in done if it is not NULL.
r19046:
Add intended but missing assignments to initialize pointers to NULL (coverity issue fixes).
r19049:
Hdf5_1_8_coverity branch was recreated from hdf5_1_8 branch in revision 18839 without fix for Coverity issue #84 having been propagated to the hdf5_1_8 branch. This revision adds the fix again.
r19060:
added parentheses to see if they will keep subversion from getting confused
r19061:
Fix coverity item 139. Fixed incorrect condition for freeing buffer on error.
Fix coverity items 20 and 21. Removed unused NTESTS facility from dtypes.c.
Cleanup in H5Shyper.c.
r19062:
Fix coverity item 450. Check to see if chk_proxy has been allocated before
attempting to free it.
Fix coverity item 454. Check to see if allocation of buf failed in
H5D_fill_refill_vl.
Fix coverity items 455-457. Initilize hid_t's to -1, check their value before
attempting to close them, and check if the close failed.
r19063:
New fix to address coverity issue #84. Check that pointers in H5Z_xform_find_type are not NULL before passing them to H5T_cmp.
Tested on:
Mac OS X/32 10.6.4 (amazon) w/debug & production
(h5committested on Coverity branch)
Bring r19153 from trunk to 1.8 branch:
Bring changes on Coverity branch back to trunk:
r19040:
Fixed coverity #440 - NULL check after dereference. We moved the NULL check up
into the IF block and changed it to assertion.
r19041:
Maintenance: Addressed Coverity issues 441 and 449 by initializing proper
variables
r19042:
In function H5O_chunk_protect (H5Ochunk.c):
- Initialize H5O_chunk_proxy_t pointers chk_proxy and ret_value.
- Free chk_proxy on error.
r19043:
Addressed coverity issues 442 - 448 by initializing pointers to NULL.
Tested on:
Mac OS X/32 10.6.4 (amazon) w/debug & production
(Too minor to require h5committest)
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).
Merged from hdf5 trunk r19051
Tested:
jam, amani, heiwa
Change h5ls not to manipulate special characters in object name or attribute name for smart display.
Description:
Merged from hdf5 trunk r19034.
Related to "But1784 h5ls has input and output issues with links that have '\' characters in them."
Tested:
jam, amani
Problem:
some launching command like yod (and sometimes mpirun), do not pass
back the exit code of the executables back to the shell. It always returns 0
if it can launch the executable. This cause tests that expect non-zero exit
code to fail incorrectly.
Short term Solution:
Added the feature that if $RUNSERIAL_NOEXITCODE is defined, do not
test conditions that rely on non-zero exit code.
Tests:
dove-linux using RUNSERIAL=thgyod to see the failures and using
$RUNSERIAL_NOEXITCODE=yes to bypass the errors.
Also h5committested.
Fixed Windows compile error. Renamed to use 'gid1' and 'gid2' instead of
'grp1' and 'grp2'.
Description:
This is related SVN r18946.
There is variable name confliction with 'grp1' ~ 'grp9' in Windows system.
It occurs if H5private.h is included in the code.
Support follow symbolic links.
Description:
Merged from hdf5 trunk r18943.
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
Revised the online help page of h5dump to explain the packed bits feature and
added an example too.
Tested: h5committest plus jam tested with --disable-h5dump-packedbits.
Rename '--follow-links' to '--follow-symlinks'
Description:
The '--follow-links' option is to follow symbolic links (soft and external).
Make the name more intuitive and specific to the feature.
Merged from hdf5 trunk r18873.
Tested:
jam
