Change to skip copying when a dataset is not allocated.
Merged from hdf5 trunk r19818.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE)
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.
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
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)
Improve configure's large-file support control.
Description:
Modified configure to now attempt to add defines necessary for
supporting largefiles on all systems, instead of solely on linux. This
is in response to user requests to enable largefile support on Solaris
by default, as well as to give extra control on AIX (instead of just
jamming the necessary flag into the config files).
The old --enable-linux-lfs flag is being deprecated in favor of the
--enable-largefile flag (enabled by default), which can be used on all
platforms. --disable-linux-lfs can still be used to disable largefile
support (on linux) when the --enable-largefile flag is not specified.
On systems where large files cannot be supported in this manner,
configure will report as such.
Tested:
h5committest
AIX (NCSA's blue_print machine)
duty, liberty, and linew.
Bring r18650 from trunk to 1.8 branch:
Bring back various minor tweaks & cleanups from the revise_chunks
branch.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
(h5committested on trunk)
Autotool Upgrade / Libtool Bug Fix
Description:
Updated autotools referenced in bin/reconfigure as follows:
Autoconf 2.64 --> Autoconf 2.65
Automake 1.11 --> Automake 1.11.1
Libtool 2.2.6a --> Libtool 2.2.6b-mcg
The referenced libtool version is a custom version of 2.2.6b. It
has been tweaked to fix a bug in libtool that occurs
when using PGI 10.0 compilers. A check incorrectly categorizes
the C++ compiler as version 1.0 instead of 10.0, and the link
line is subsequently set up incorrectly and fails to compile.
A patch has been made available and will be included in the next
release of libtool, but in the meantime I've applied the patch to a custom
installation as indicated above. This bin/reconfigure now references
the custom installation, and the resulting configure script will correctly
categorize the PGI 10.0 C++ compiler.
Ran bin/reconfigure to regenerate configure and makefiles.
Tested:
jam and amani with PGI 10.0 compilers.
h5committest
Resolve windows build issue from previous checkin r18427
Description:
The previous checkin was for bug1814 - NPOESS: h5repack doesn't handle
references to the groups as an element of a dataset
Tested:
jam
Fix for bug1814 - NPOESS: h5repack doesn't handle references to the groups
as an element of a dataset
Description:
Merged from hdf5 trunk r18425
handles object reference to named-datatype as well.
Add test cases.
Tested:
jam
The mixed use of RUNTEST (original) and RUNTESTS (new) caused
confusion. E.g., the timings in test/ was still using the old
$RUNTEST. It made more sense to use $RUNTEST which is used
by the dejagnu feature of automake. So, I changed all
$RUNTEST or $RUNTESTS to $RUNEXEC.
config/commence.am & config/conclude.am are the two files
that got changes. Also fixed an error in test/Makefile.am.
The rest are changed by bin/reconfigure.
Tested: h5committested.
Bring r17980 from trunk to 1.8 branch:
Bring Coverity changes into the trunk: (also other minor cleanups)
r17955:
Fix Coverity item 24. Add missing error condition to
H5AC_ext_config_2_int_config.
r17956:
Fix Coverity item 24. Improve error checking in H5A_compact_build_table_cb.
r17957:
Fix Coverity item 150. Fix warning in H5A_compact_build_table_cb.
r17958:
Fix Coverity item 117. Fix error handling in H5B_shared_new.
r17959:
Fix Coverity item 209. Added an assertion for leaf->shared in
H5B2_cache_leaf_dest.
r17960:
Fix Coverity item 208. Added an assertion for internal->shared in
H5B2_cache_internal_dest.
r17961:
Fix Coverity item 89. Reworked the code to avoid array overrun in
H5C__autoadjust__ageout__insert_new_marker.
r17962:
Fix for coverity Resource_leak 195,203,204,205.
r17963:
Fix Coverity item 44. Prevented potential NULL dereference in H5D_btree_debug.
r17964:
Fix Coverity issues #197, 198 & 199: memory not being released. (Also
clean up other resource leaks in nearby and/or similar code).
r17965:
Fix Coverity issue #151: release resources on error
r17966:
Fix Coverity issue #187: Remove leftover code remnant from prior bugfix
which was causing resource leak of open files.
r17967:
Fixed Coverity issues # 193 & 194. Removed unnecessary memory allocation and
added comparison of length of path parameter to the size of the destination
buffer in h5import.h/h5import.c.
r17968:
Fix Coverity item 144. Fixed memory leak on error in H5D_chunk_copy.
r17969:
Fix for coverity Resource_leak #196.
r17970:
Coverity 167-173:
Initialized pointer of buffers.
In error handling, closed types and free memory.
Tested on:
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
(h5committested on trunk)
Bring r17953 from trunk to 1.8 branch:
Bring Coverity changes into the trunk:
r17877:
Error 266: Uninitialized memspace set to -1. Changed malloc and free to HDmalloc and HDfree. Removed unused dtype var.
r17878:
Error 265: Uninitialized mem_space set to -1. Changed malloc and free to HDmalloc and HDfree.
Error 267: Uninitialized smspace set to -1. Changed malloc and free to HDmalloc and HDfree.
r17879:
Error 242: Uninitialized aid set to -1.
Error 243: Uninitialized sid set to -1.
Uninitialized tid set to -1 for consistency
r17880:
Error 242: reinitialized aid to -1 after close to be ready for reuse.
Error 243: reinitialized sid to -1 after close to be ready for reuse.
reinitialized tid to -1 for consistency after close to be ready for reuse.
r17881:
use valgrind to check there is a memory leak. The fix is to free ptrstr in line 5838 at xml_dump_group() of h5dump.c after it is used. run the valgrind after the fix, no memory leak for that part of the code.
r17882:
Fix Coverity items 256 and 269.
r17883:
Error 222-230: initialized hid_t vars to -1 after close to be ready for reuse.
Also added H5Tclose for tid in gent_bigdims
r17884:
Bug fix (Coverity run2, view 23, dead code)
(this is pair-program done by Albert, Elena and Larry).
Confirmed and fixed the deadcode in hyperslab read branch of function
diff_datasetid.
(Discovered other bad code that diff_datasetid() should be recoded.
Bug 1693 is entered for this.)
r17906:
Fix Coverity item 260.
r17907:
262: Initialized hid_t's dtype, dtype_tmp and file to -1. Initialized H5T_t * dt to NULL.
r17908:
Fix Coverity item 261.
r17909:
Fix Coverity item 248.
r17910:
Revise fix for Coverity item 248.
r17911:
Resolved coverity issues #s 263, 162, 163, 164. All issues in dsets.c. Initialized fid and did hid_t's. filter_corrupt function was returning in the middle of an if statement, bypassing free calls. Updated error handling to free buffers and hid_t's appropriately.
r17912:
(done by Larry and Albert)
Cleanup Coverity view warnings (#231-241) about
using uninitialized variables. Initialized all
of them.
r17913:
Resolved issue 251 and 264. Initialized tid2 to -1 and initialized buffers that were freed in case of an error.
r17914:
Resolved coverity issues 66, 220, and 221:
66: Negative Return assignment ignored
220,221: Initialized hid_t's.
r17915:
Fix Coverity item 247.
r17916:
Fix Coverity item 246.
r17917:
Fix Coverity item 245.
r17918:
Fix Coverity item 244.
r17919:
Coverity Issue #84: Moved asserts in H5T_cmp to the top of the function, and converted them to HDassert. Coverity complaining about using potentially NULL pointer without checking it. Want to see if Coverity will accept Assertions as acceptable checking before using the value.
Tested on:
FreeBSD/32 6.3 (duty) w/debug
(h5committested on trunk)
Merge from Trunk
Description:
Merging all of my CFLAGS-related changes from trunk to 1.8
This includes revision #s: 17616, 17625, 17627, 17639, and 17643.
Tested:
h5committest and some additional checks on our FreeBSD as well
as NCSA's machines.
Bring r17553 from trunk to 1.8 branch:
Bring general fixes/improvements from file_free_space branch back to
trunk.
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/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 production 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
Merge from trunk
Description:
Merged revisions 17228 and 17440 from trunk to 1.8
Specifically, this brings support of --enable-static-exec flag into 1.8
Tested:
Manually on jam, linew, smirom, liberty, plus h5committest.
Currently, there is no automatic regression test that exists due to
portability issues. Behavior is both different and undefined on certain
systems (and while 'nm' command seems to exist on all machines, behavior
is confirmed to be different on Mac, possibly others). Solution will be
to set up some sort of framework in daily tests to build statically,
remove shared paths, and verify executables can function.
Updating autotools
Description:
Bring revisions 17345 and 17357 from trunk to 1.8, specifically:
- Automake upgraded to 1.11
- Autoconf upgraded to 2.64
- bin/reconfigure script edited to use new versions (on jam), and
run to generate new configure script and Makefile.in's.
- configure.in script edited to add "_cv_" to all AC_CACHE_VAL strings
(in order to comply with new autoconf standard).
- bin/install-sh script replaced with new version as provided
by automake.
Tested:
- All issues on trunk were resolved, so only tested on jam and linew. Any
other outliers should be caught by daily tests.
Bring r17313 from trunk to 1.8 branch:
Bring back various minor code cleanups from the file free space branch
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 (kagiso) w/PGI compilers, 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 production 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
Clean up various compiler warnings from IRIX64 build
Tested on:
Mac OS X/32 (amazon) debug & production
(yes, I know it's not an IRIX64 system :-)
Too minor to require h5committest
bug fix: h5repack was not applying a requested contiguous layout for a dataset with filters
added a test to the C program test (not to the script), that verifies the layout and filters
tested: linux
Add a run to the h5repack shell script to read a family file
The file used for input is located in the common source tools for testfiles, in tools/testfiles
Modified the h5repack shell script to read files from this location (h5repack reads its input files from a dedicated testfiles location in h5repack/testfiles)
Changed the h5diff open file call to use h5tools_fopen, so that it can open all file drivers
Tested: linux
Adding dependency to h5repack test script.
h5repack.sh needs h5repacktst to run first.
Tested:
Problem only appeared on Glory, but tested the dependence
manually on jam by trying to run only the script and checking
that it first ran the h5repacktst test program.
Description:
h5repack previously would not take named datatypes into consideration when copying
datasets and attributes. This would cause extra anonymous datatypes in the target file
at best, and cause errors halfway through the repacking at worst. h5repack should now
always handle named datatypes correctly. Named datatypes are also now converted to the
native type when -n is given.
Tested: jam, linew, smirom (h5committest)
- Updated bin/reconfigure to use latest version of automake (1.10.2).
Regenerated Makefile.in's by running bin/reconfigure.
- Added libtool version numbers to c++, fortran, hl, hl c++, and hl fortran
libraries.
Tested:
jam, liberty, smirom
