Fixing Bug 2092 - h5dump does not display index for a dataset
Description:
improve the test case from previous checkin r20108, which also display
dataset via region reference.
Previous Log:
h5dump skip displaying array indices every certain number when the
array type dataset is relatively big. The certain number varies
according to the size of each array.
This checkin fix the skipping array indices problem. This fix also
correct indentation of the dataset data output.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake - jam
Clean up MPI resource leaks in parallel tests, along with a bunch of
compiler warnings.
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-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
Mac OS X/32 10.6.6 (amazon) in debug mode
Mac OS X/32 10.6.6 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Fixing Bug 2092 - h5dump does not display index for a dataset
Description:
h5dump skip displaying array indices every certain number when the
array type dataset is relatively big. The certain number varies
according to the size of each array.
This checkin fix the skipping array indices problem. This fix also
correct indentation of the dataset data output.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
Change to use HDxxx macros.
Description:
Originally this started for fixing incorrect pointer usage. But that got
fixed through coverity merge. So this is mainly changing to use HDxxx
macros and clean up some related code.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
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)
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)
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)
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)
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)
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.
Bug 2089 - GMQS: h5diff segfault on a compound dataset with fixed length +
vlen string type order
Description:
This is fix for the segfault when h5diff compares a compound dataset with
combination of fixed length string types and vlen string types in certain
orders. Optimized vlariable length string handling codes. The fix is
referred from h5dump handling vlen strings.
For testing, several compound datasets were added with various combinations.
Previous failed cases:
- Vlen string, Fixed length string, Vlen string, Fixed length string
- Fixed length string, Fixed length string, Vlen string, Vlen string
- Fixed length string, Vlen string, Fixed length string, Vlen string
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
Fix compile error for Windows from previous checkin r19757.
Description:
Previous log:
Improve h5diff performance.
The following changes for improving h5diff performance:
1) use HDmemcmp() before comparing each elements
(memcmp() is very fast at both linew and jam)
2) replace the expensive H5Tequals() calls
3) retrieve datatype information at dataset level not each element level
for compound datasets
Tested:
jam (linux32-LE), Windows
Improve h5diff performance.
Description:
The following changes for improving h5diff performance:
1) use HDmemcmp() before comparing each elements
(memcmp() is very fast at both linew and jam)
2) replace the expensive H5Tequals() calls
3) retrieve datatype information at dataset level not each element level
for compound datasets
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
Fixed Bug# 1979 Output from h5ls -rdlS on nested compound datatypes is
difficult to parse.
Description:
Update to add curly brackets for the nested compound members, when
S (--simple) option is used with -l (--label), so user can tell
which members blong to which compound type.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32)
Fix the test script from the previous checkin r19729. expect output is
under misc/testfiles/ in srcdir.
Previous Log:
[BZ2072]Add compare output to expected test for help and version options
of mkgrp.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE)
Fix the test script from the previous checkin r19726 due to contiguous
build system failure.
Previous Log:
[BZ2072]Add compare output to expected test for help and version options
of mkgrp.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE)
Add a little bit of extra info to the output from h5debug when
displaying global heaps, and make it dump the file's superblock again when
an address is not given on the command line.
Tested on:
FreeBSD/32 6.3 (duty) w/debug
(too minor to require h5committest)
Fixed h5diff to handle variable-length strings in a compound dataset
correctly. Also variable-length string array in a compound dataset.
Bug #1989.
Description:
Garbage values were displayed when h5diff compared variable-length
strings (or string array) in a compound type dataset.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (Mac32)
Bring Coverity revisions from branch back to trunk, and clean up some other
misc. compiler warnings also.
r19500:
Fix coverity items 1446 and 1447. Moved up calls to memset in test_cont in
ohdr.c so the test never tries to close uninitialized locations.
r19501:
Fix coverity items 1398-1445. Various uninitialized variable errors in fheap.c.
r19502:
Fixed coverity issue 579 and some additional warnings in the file as well.
r19503:
Bug fix: This fix addressed the "RESOURCE_LEAK" problems #789 and 790, run 26
r19504:
minor mods to try to keep coverity from flagging false positives.
r19505:
Fixed coverity issues 566 - 571. Declared variables that are passed to functions that use them as arrays to be arrays of size 1.
Tested on:
Mac OS X/32 10.6.4 (amazon) w/debug, production & parallel
(h5committested on trunk)
Fix nightly build error on non-linux platforms related to
the Fix for bug# 2040 - h5copy should fail gracefully for expected failure copying to non-exist nested group without -p option. (r19633)
Description:
- Updated to use standard C functions instead of strndup() due to failure on non-linux platforms.
- Changed to Use HDxxx macros for future reference.
- Correct indentation.
Tested:
jam, amani, heiwa, linew
Fix for bug# 2040 - h5copy should fail gracefully for expected failure copying to non-exist nested group without -p option.
Description:
Fixed h5copy to fail gracefully when copying object to non-exist group without -p option. This is expected to be failed.
Tested:
jam, amani, heiwa
Backout the previous changes (r19598):
(Fix for bug# 2040 - h5copy should fail gracefully for expected failure copying to non-exist nested group without -p option.)
Description:
Some failure occurred on talwit, so backout the changes and will put it back
after the fix.
(Fixed h5copy to fail gracefully when copying object to non-exist group without -p option. This is expected to be failed.
Merged from hdf5 trunk r19598.)
Fix for bug# 2040 - h5copy should fail gracefully for expected failure copying to non-exist nested group without -p option.
Description:
Fixed h5copy to fail gracefully when copying object to non-exist group without -p option. Expected to be failed.
Tested:
jam, amani, heiwa
Address issue with object headers being created getting evicted from
the metadata cache cache before they are completely initialized. This is
done by pinning the object header in the cache until it is completely
initialized and attached to a group.
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
Update help page for exclude-path feature.
Description:
Related to "1890: h5diff excluding object for file comparison via command line" checkins. (r19406)
Tested:
jam, amani, heiwa
