Additional fix for Bug 1821 - h5repack outputs compression information where it is not supposed to
Description:
Remove unnecessary lopping code, which only lowers performance.
Tested:
jam, amani, heiwa
Fix for Bug1896 h5repack - changing layout to COMPACT does not work
Description:
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, heiwa
Corrected use/name of source folder aliases.
Duplicated FindMPI.cmake so that non-c++ compiler is found first (recommemded commands did not work).
Tested: local linux with mpich
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 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)
Enable tools lib to be built as a dll on windows. Added two get/set functions for progname and d_status.
Also add windows import/export declarations to functions.
Updated error_mesg() and warn_mesg() to remove progname argument and use get functions
Tested:
Windows, linux
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 has been removed in favor of the
--enable-largefile flag (enabled by default), which can be used on all
platforms.
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.
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
Add test cases for bug1797 - h5repack doesn't handle references in
compound and vlen datatypes for attributes
Description:
Add test cases ahead as waiting for H5Acopy to complete the fix.
1. obj references in attr of compound type
2. region references in attr of compound type
3. obj references in attr of vlen type
4. region references in attr of vlen type
NOTE:
This test is skipped now and will be included when code part is completed.
( H5Acopy() replaces copy_attr() )
The file&code can be used for lib portion test.
Tested:
jam, amani, linew
Fix for the bug1726 - NPOESS: h5repack loses attributes for datasets of
type H5T_REFERENCE.
Description:
include test cases.
also test cases for attribute with object and region reference.
Tested:
jam, amani, linew
Resolve windows build issue from previous checkin r18425
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:
handles object reference to named-datatype as well.
Add test cases.
Tested:
jam, amani, linew
Re-run bin/reconfigure to catch up with recent rearrangements, remove some
unused srcdir headers and duplicated code in main test header.
Tested on:
Mac OS X/32 10.6.2 (amazon) w/debug & prod
Linux/32 2.6 (jam)
Clean up srcdir querying code more, extracting it into single header file,
to avoid compiler warnings.
Tested on:
Mac OS X/32 10.6.2 (amazon) w/debug & prod
Linux/32 2.6 (jam)
Unify srcdir handling for test executables and allow them to use the srcdir
setting from configure time without requiring the 'srcdir' environment variable
be set (although you still can, to override the built in setting). Attempted
to get this right for Windows builds also.
Also add dependency between src/H5Tinit.c and src/libhdf5.settings, so
that the test/testcheck_version.sh script works correctly.
Tested on:
Linux/32 2.6 (jam)
Mac OS X/32 10.6.2 (amazon)
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 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/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 (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 debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.6.2 (amazon) in debug mode
Mac OS X/32 10.6.2 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
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) 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 (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 debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.6.2 (amazon) in debug mode
Mac OS X/32 10.6.2 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
2. tools/h5stat/h5stat.c: clean up and activate options as stated in usage
3. tools/h5stat/testfiles/*.ddl: modified according to the latest output
-This line, and those below, will be ignored--
M tools/h5repack/h5repack_main.c
M tools/h5stat/testfiles/h5stat_newgrat.ddl
M tools/h5stat/testfiles/h5stat_filters.ddl
M tools/h5stat/testfiles/h5stat_help1.ddl
M tools/h5stat/testfiles/h5stat_help2.ddl
M tools/h5stat/testfiles/h5stat_tsohm.ddl
M tools/h5stat/testfiles/h5stat_filters-F.ddl
M tools/h5stat/h5stat.c
CFLAGS overhaul
Description:
Modified the way configure handles CFLAGS.
(note: all changes also apply to FCFLAGS, CXXFLAGS, CPPFLAGS, and LDFLAGS).
1. The configure process will now always preserve a user's CFLAGS
environment variable setup. Any additional flags necessary for compilation
added at configure time will be passed into the Makefiles as AM_CFLAGS,
which is an automake construct to be used in addition to CFLAGS.
This will allow a user to have the final say, as CFLAGS will always appear
later in the compile line than AM_CFLAGS. Additionally, setting CFLAGS
during make will no longer completely erase all flags set by configure,
since they're maintained in AM_CFLAGS.
2. Additionally, where possible, flags previously being assigned directly
into CFLAGS (and thus propagating into h5cc) have now been redirected into
H5_CFLAGS, so they're used ONLY for compiling hdf5, and not embedded into
the h5cc wrapper script as well.
*Note that H5_CFLAGS ultimately is assigned into AM_CFLAGS for use in the
Makefiles. Complete description of changes and build process will be
included in a Configure Document that Elena and I are working on.
3. Removed unsupported config files. This includes:
config/dec-osf*
config/hpux11.00
config/irix5.x
config/powerpc-ibm-aix4.x
config/rs6000-ibm-aix5.x
config/unicos*
4. Modified configure summary to display additional values. Specifically,
appropriate AM_* variables are being shown, as well as H5_FCFLAGS and
H5_CXXFLAGS, which were for some reason not already present.
Tested:
- H5committest
- Tested on all THG / NCSA machines, using several combinations of the more
prominent configure options (c++, fortran, szip, threadsafe, parallel,
et cetera). (Thanks to Quincey for rysnc testing setup!)
- With regards to new automated testing, anything *necessary* for
compilation will be caught by the daily tests as it stands now. (i.e.,
if LDFLAGS is not properly set when szip is used, linking will fail).
Additionally, with regards to which flags get into h5cc, if any
*necessary* flags have been improperly removed, then daily tests should
fail during make installcheck. Additional machine-specific desired
behaviors and/or checks may have to be set up separately within the
daily tests, so this is something to work on.
Bring changes from file free space branch back to the trunk. *yay!*
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 (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 debug 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
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
Updating autotools
Description:
Installed new autotools and used them to reconfigure HDF5.
- 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).
Tested:
Tested on machines jam, smirom, liberty, linew.
Tested w/ features c++, fortran, parallel.
Tested w/ compilers gcc, pgcc, icc.
Further testing via Daily Tests should catch any other outliers. Upon
passing DT's, I'll propogate the new tools into 1.8, hdf4, et cetera.
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
