Bring changes from Coverity branch to trunk:
r19975:
Fixed potential mem leak at H5O_attr_open_by_name
r19980:
Fix coverity issue 792.
Free tmp_env_prefix in H5Lexternal.c line 365 if it is not NULL but its contents are 0 when it goes out of scope.
r20039:
Eliminate warnings about nested extern and implicit declarations of parallel_print and address Coverity defects 712-781 by #including h5tools_utils.h in h5diff_array.c, h5diff_attr.c, h5diff_dset.c and h5diff_util.c.
r20046:
Purpose: Address TOCTOU warnings in h5jam and h5unjam
Description: Coverity is afraid that the state of the input file could change
between the call to stat() and the call to open(). This is called a time-of-
check time-of-use (TOCTOU) vulnerability. Modified stat calls to fstat which
uses an open file pointer so it (hopefully) won't complain any more.
r20047:
Addressed coverity issues 135-137, 462-464. Local pointers that needed to be freed in case of error were moved out of a switch statement in src/H5Tnative.c, set to NULL, and checked before freeing.
Tested on:
Mac OS X/32 10.6.6 (amazon) w/debug & production
(h5committested on Coverity branch)
Description:
Implements a cache of files opened through external links. Adds the public
functions H5Pset_elink_file_cache_size(), H5Pget_elink_file_cache_size(), and
H5Frelease_file_cache().
Tested: jam, amani, heiwa (h5committest), fedora 64.
Bring changes from Coverity branch to trunk:
r19930:
Fix memory leaks involving VL attributes in h5repack and h5diff. The buffers in
copy_attr and diff_attr were not checked for the presence of a vlen before being
freed, and vlen storage was never reclaimed. Added checks and calls to
H5D_vlen_reclaim().
r19933:
Purpose: Fix memory leak in H5L_move_cb()
Description: H5L_move_cb copied the source link using H5O_msg_copy() but freed
it manually using H5MM_xfree(). Since H5O_link_copy allocates the link using
H5FL_MALLOC, this causes the link to be allocated from the free list but is
never put back on the free list when it is freed. This prevents the link free
list from shutting down properly. Modified H5L_move_cb() and H5L_move_dest_cb()
to free the link properly using H5O_msg_free().
r19973:
Fix resource leaks by freeing string created by HD5f2string
r19974:
Issue #345: Inialize buf variable to null
Tested on:
Mac OS X/32 10.6.6 (amazon) w/debug & production
(h5committested on Coverity branch)
mpif90 is already the default parallel Fortran if mpicc is the C compiler.
Tested: Jam (serial and parallel). No need for committest since this change is
limited to Linux system.
Clean up Coverity warnings, and fix some style issues:
r19735:
Fix for memory leak in test/mf found by valgrind.
r19736:
Fix memory leak in h5repack. The buffer in copy_objects, when copying the
entire dataset at once, was not checked for the presence of a vlen, and vlen
storage was never reclaimed. Added check and call to H5D_vlen_reclaim().
r19772:
Change H5assert() to
if (H5T_VLEN != src->shared->type || H5T_VLEN != dst->shared->type)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a H5T_VLEN datatype")
r19774:
removed unused priv.
r19775:
removed unused variables
r19778:
Fix memory leak comparing for variable length data types.
r19834:
Fixed memory leaks found by valgrind. Memory errors remain for another day.
Tested on:
Mac OS X/32 10.6.6 (amazon) w/debug & production
(h5committested on branch)
Bring sec2 and log VFDs back into agreement. Correct several compiler
warnings. Also add some additional statistics to the log VFD and promote the
parameter for H5Pset_fapl_log from 'unsigned' to 'unsigned long long'.
Tested on:
Mac OS X/32 10.6.6 (amazon) w/debug & production
FreeBSD/32 8.2 (loyalty) w/debug
FreeBSD/64 8.2 (freedom) w/debug
Bring Coverity changes back to trunk:
r19733:
Fix memory leak in h5perf_serial. Global buffer "buffer2" was allocated at the
beginning of do_sio() but never freed. Added call to free() at end of do_sio().
r19734:
Fix memory leak in iopipe. Buffer "the_data" was allocated at the beginning of
main() but never freed. Added call to free() at end of main().
Tested on:
Coverity branch in daily tests & Mac
Description:
When using the scale-offset filter with floating point data or fill values, big
endian machines would save some metadata in the wrong byte order. This caused
such datasets to yield incorrect data when read on little endian machines.
Fixed the scale-offset filter to always save this metadata in the right byte order (i.e. little endian).
Tested: jam, amani, heiwa (h5committedt); fedora, linew
not like it as it may get into a racing condition when "gmake -j N" is used--
two "rm" commands were trying to remove the same file.
Solution:
Rearranged the Makefile.am so that h5perf or h5perf_serial are built only
once, that is through bin_PROGRAMS only.
Bug 2135: h5perf_serial is not installed in --enable-parallel build.
It was because in parallel build, h5perf_serial is not was not in the
bin_PROGRAMS list but it was still being built and tested.
Solution:
Rearranged the Makefile.am code so that h5perf_serial is installed too.
(It is easier to make cleaner code to install it than to build and test
h5perf_serial but not test it.)
Tested: Jam, both serial and parallel.
Did not run h5committest because the changes are in perform/ directory only
and I think Jam has given the changes in Makefile a complete test already.
Clean up tool code.
Remove "h5test.h" from tool code. Currently only in h5repack.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), linew (solaris-BE)
Finish implementing time tracking for read & seek operations in the 'log'
VFD. Also clean up code and track total time during all read/write/seek
operations.
Tested on:
Mac OS X/32 10.6.6 (amazon) w/debug & production
(too minor to require h5committest)
When $HDF5ExpressTest is NOT set or when it is set to 1 or 0, it does not
skip test.
When $HDF5ExpressTest is set other than values above, it may skip tests.
The following message is printed:
Test skipped
when some tests are really skipped.
This is a temporary patch so that v186 can be tested. A more permanent fix
is needed, later.
Tested: h5committest.
h5dump: add dangling external link test case as part of Chicago project.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
This continues the previous work and this one breaks the
checker_board_hyperslab_dr_pio_test() into 4 smaller
sub-tests.
Tested: h5committest plus jam serial.
The shape same tests ran too long. Break them into smaller subtests
so that they can finish sub-test in a shorter time. Easier to tell
which one sub-test is taking too much time and/or errors occur in
one fo the sub-tests.
This one breaks the contig_hyperslab_dr_pio_test() into 4 smaller
sub-tests.
Tested: h5committest
error and wanted to exit the test program. This was not good since if only a
subset of processes called MPI_Finalize(), the other processes will likely
hang. That happened in AIX that it would waited till the alarm signal to kill
the processes. Definitely a waste of time.
Solution: Changed it to call MPI_Abort.
That showed another problem. HDF5 has setup atexit post-process to try to close
unclose objects, release resources, etc. But if the MPI processes have
encountered an error and has been aborted, it is not likely any more MPI calls
can function properly. E.g., it would attempt to free some communicators in
the HDF5 MPIO file handle. It would again hang.
Solution: need to call H5dont_atexit() to disable any atexit post-processing.
This must be done early, like before calling H5open. This is added to each
parallel test main program.
testphdf5.h:
Changed macros VRFY and MESG. Added comments too.
testphdf5.c:
t_mpi.c:
t_cache.c:
t_shapesame.c:
Added H5dont_atexit.
Tested: h5committest.
not find t_shapesame in daily test. Turned out the mpiexec launcher is
working like real shell and the daily test signon (hdftest) does not have
"." in its $PATH. So, it could not automatically look for executables in
the current directory.
Solution:
Change the executable to an explicit ./t_shapesame. Now mpiexec can "find"
it.
Tested by hand in Amani.
Moved the two shape same tests from testphdf5 to a separated executables,
named t_shapesame. The shape same tests runs too long for testphdf5.
In a separated executalbe, it will be easier to separate any errors in
testphdf5 sub-tests from the shape same tests.
t_shapesame.c:
Contains the shape same tests (cloned from t_rank_projection.c) plus
a duplicate of "testphdf5.c" for now. After verifying it is correct, more
cleanup is needed.
testphdf5.c:
Removed the two shape same tests (chsssdrpio & cbhsssdrpio).
Makefile.am:
Makefile.in:
Added t_shapesame as a new test executable.
Removed t_rank_projections.c from part of testphdf5.
testph5.sh.in:
Temporary added the "t_shapesame -p" test for testing shape same tests
with MPIO-Posix VFD.
Tested: h5committested, plus serial jam.
