| Commit message (Collapse) | Author | Age | Files | Lines |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Description:
+ The C++ test failed with the new PGI compilers versions 12.4 and 12.5
+ An exception thrown by an internal function, which was called by
a constructor, was not propagating to the test program during the stack
unwinding, so it couldn't be caught by the test and the program terminated.
+ Various trials and errors indicated that the problem is where an STD string
converted to a char* being passed to the internal function, but confirmation
has not been found yet. It could be a compiler bug.
Solution:
+ Added a try/catch in the constructor around the internal function and
re-throw the exception when it is caught. This is a workaround.
+ Unrelated minor fixes: removed unused variables and MESSAGE's; commented
out tvlstr.cpp/test_read_vl_string_attribute because it may be redundant,
and commented out H5Tpkg.h inclusion because TEST_ALIGNMENT is not added
yet and probably not necessary in the C++ API.
Platforms tested:
Linux/32 2.6 (jam) with PGI compilers
Linux/32 2.6 (jam) with GNU compilers
Linux/64 2.6 (koala)
|
|
|
|
|
|
| |
Change configure to test the result of the CHECK HEADERS call before checking for the library.
Tested: local linux, h5committest
|
| |
|
|
|
|
| |
Tested with h5committest on jam, koala and ostrich.
|
|
|
|
|
|
| |
Changed uint to unsigned so that no hdf5-specific header file is needed.
Platform tested:
Linux/32 2.6 (jam) - very minor
|
|
|
|
|
|
|
|
|
|
| |
Description:
Fixed miscellaneous inconsistencies and typos, which also took
care of the failure in Packet Table test on daily test today.
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 2.6 (koala)
Mac Lion (duck)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Description:
In this bug, H5File doesn't have the ability to create attribute. The
following changes will provide that functionality and several others that
were also missing:
- Added an abstract class H5Location in between IdComponent and H5Object.
- New class structure of IdComponent, H5Location, H5Object, H5File
IdComponent
|
H5Location
/ \
H5Object H5File
- Wrappers in H5Object were moved to H5Location because the related C
functions take either file, group, dataset, or named datatype ID.
- Added wrapper for H5Rget_obj_type2
- Added tests for file attributes and H5Rget_obj_type2 wrapper
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 2.6 (koala)
SunOS 5.10 (linew)
|
|
|
|
|
|
| |
if configured with --disable-static the default for HDF5_USE_SHLIB in the compile scripts will be changed to yes. This is a fix for HDFFV-8141, where the compile scripts try to link to non-existant static hdf5 libraries.
Tested on jam,koala,ostrich(h5committest) and other THG machines.
|
|
|
|
|
|
| |
autotools TESTS var, rename configure.in to configure.ac, convert test scripts from hard *.sh to configure managed *sh.in files.
Tested: h5committest
|
|
|
|
|
|
| |
libtool 2.4.2
Tested THG machines.
|
|
|
|
|
|
|
|
| |
tests to fail with the new/PGI compiler (see HDFFV-
8067).
Tested jam, koala, ostrich.
|
|
|
|
|
|
|
|
|
|
| |
Description:
Closed various HDF5 objects in DataSet::getInMemDataSize and
Attribute::getInMemDataSize to remove some memory leaks.
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 2.6 (amani)
SunOS 5.10 (linew)
|
|
|
|
| |
standard 2.8.6
|
|
|
|
|
|
| |
OPTION command for solution folder and no packaging.
Tested: local linux
|
|
|
|
|
|
| |
Ran bin/reconfigure to update the Makefile.in in directories not part of the fortran directory check=in. Updates Makefile.in due to changes made in configure.in for the Fortran 2003 additions.
Tested on all platforms run under daily tests.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
General shared library improvements for CYGWIN / AIX
Description:
Shared libraries are disabled on both CYGWIN and AIX due
to inability to build them correctly. Part of the problem
in both of these situations is the lack of the libtool
flag -no-undefined, which tells libtool that all needed
symbols are defined at link time (a requirement on these
systems) and that it's okay to build shared libraries.
Another problem are lack of dependencies between wrapper
libraries and core C HDF5 library.
This patch addresses both of these by fixing configure to
add in -no-undefined flag for libtool during linking and
adds automake dependencies in the Makefile.am files.
After testing, both CYGWIN and AIX now generate shared
libraries, but there are still some test failures in each.
(cache_api, dt_arith, and testerror.sh on CYGWIN, and
fortran tests on AIX).
Even though the shared libraries are not quite perfect,
this is a general improvement to what we had before, so
I'm applying the patch anyways. Note that default behavior
of shared libraries on these systems being disabled has
NOT been changed and requires the use of the
--enable-unsupported to attempt to build them.
We will need to address the test failures in each
architecture prior to formally supporting shared
libraries on each.
Tested:
h5committested & CYGWIN tested (on bangan)
(AIX tested by Albert on bp-login2)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Add "silent make" mode configure option.
Description:
Automake 1.11 has a new option available that allows for a
silent make mode. This functionality needs to be explicitly
enabled in configure.in via the use of the automake macro
AM_SILENT_RULES, which is what this commit is adding.
This introduces a new configure option:
--{en|dis}able-silent-rules
This option is on by default, and simplies compile and link
line outputs when building the library. Disabling this option
will print full "verbose" output (i.e., full compile and
linking lines for each target).
Tested:
This was tested on jam & h5committested
|
|
|
|
|
|
|
|
|
|
|
|
| |
unlimited. This is a follow-up checkin for
r20440 and r20469:
1. The dataspace code has another bug - when the maximal dimension isn't passed in for H5Sset_extent_simple, it
is supposed to be same as the dimension. The current library sets NULL to it. I corrected it and added a
test case to it.
2. I corrected the tests of Fortran and C++ for this problem.
Tested on heiwa, jam, and amani.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
- Revise shared Fortran library disabling scenarios in configure
- Improve configure output summary
Description:
Shared Fortran libraries are not supported on Mac, but were being
disabled by configure in a way that also forced the C libraries
to be static-only. This has been fixed, so now only shared Fortran
is disabled while shared C can remain.
This prompted two additional changes:
1. While working on the check that addresses whether or not
shared Fortran libraries are allowed, removed old and no
longer needed check(s) that disable shared Fortran
libraries with HP, Intel 8, PGI, and Absoft compilers.
(Essentially, Mac is the only situation in which Fortran
shared are disabled by configure.)
2. Having two different states of libraries (i.e. shared C
library with static-only Fortran library) was not apparent
in the configure summary, which labeled all libraries as
either shared and/or static. I've added lines to both the
C++ and Fortran output sections to list shared/static-ness
of these libraries specifically.
Additionally, I've made sure that the new --enable-unsupported
configure option correctly overrides configure if it tries to
disable a shared library.
Tested:
jam, fred, & h5committest
|
|
|
|
|
|
| |
This will replace the list of ignore tests in CTestCustom.cmake file.
Tested: local linux
|
|
|
|
|
|
| |
macro. Update HDF5 project to use HDFMacros.cmake file. Add test properties for test ordering.
Tested: local linux, windows
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
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)
|
|
|
|
|
|
| |
macro use for checking libtype.
bring r19906 from 1.8 branch
|
|
|
|
| |
programs. Added BUILT_AS_STATIC_LIBRARY define to set the windows import/export defines correctly for static libraries.
|
|
|
|
| |
Tested with h5committest on amani, heiwa, and jam.
|
|
|
|
| |
Bring r19705 from branch
|
|
|
|
|
|
| |
branches/hdf5_1_8 to trunk. These revisions reorganize the compile scripts using h5cc.in, h5fc.in, and h5c++.in, add checks for installed examples to the scripts that run them after installation, and add DESTDIR for install as needed for RPMs.
Tested on amani, heiwa and jam by h5committest and with CYGWIN.
|
|
|
|
|
|
| |
and m4 to version 1.4.14. Also added m4 directory for m4 macros according to autoconf suggestion.
Tested with h5committest on amani, jam, and heiwa, and on linew.
|
| |
|
|
|
|
|
|
|
| |
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
|
|
|
|
|
|
| |
fortran and c++ compilers in libhdf5.settings file and configure output (r18836), to install examples as part of make install (r18680), and to provide scripts to compile and run the examples after they are installed (r18817).
Tested with new/h5committest on amani, heiwa, and jam.
|
|
|
|
|
|
|
|
| |
/NODEFAULTLIB:MSVCRT
Added VERSION vars for inclusion into auto snapshot version update script
Tested windows
|
|
|
|
| |
Tested: Local 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.
|
|
|
|
|
|
| |
Added #ifndef H5_NO_DEPRECATED_SYMBOLS to getObjTypeByIdx tests.
Platforms tested:
amani - with --disable-deprecated-symbols
|
|
|
|
|
|
|
|
|
| |
Added missing overloaded function getObjTypeByIdx to return type name
as a char*.
Platforms tested:
Linux/32 2.6 (jam)
FreeBSD/64 6.3 (liberty)
SunOS 5.10 (linew)
|
|
|
|
|
|
|
|
|
| |
Purpose: Fix bugzilla 1857
Added missing overloaded function getObjnameByIdx to take char* for name.
Platforms tested:
Linux/32 2.6 (jam)
FreeBSD/64 6.3 (liberty)
SunOS 5.10 (linew)
|
|
|
|
|
|
|
|
| |
Added a null character to terminate a fixed-length string returned
by H5Aread.
Platforms tested:
Linux/32 2.6 (jam)
FreeBSD/64 6.3 (liberty)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
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
|
|
|
|
|
|
|
|
|
| |
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)
|
|
|
|
|
|
|
|
| |
Centralize common code for srcdir lookups.
Tested on:
Mac OS X/32 10.6.2 (amazon) w/debug & prod
Linux/32 2.6 (jam)
|
|
|
|
|
|
|
| |
Fix error with srcdir header file included twice.
Tested on:
Mac OS X/32 10.6.2 (amazon) w/debug & production and C++
|
|
|
|
| |
Add copyright to new files
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
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)
|
|
|
|
|
|
|
|
| |
In the previous revision, dsets.cpp was moved from a standalone
program into testhdf5.cpp to be consistent with the rest of the
tests. Makefiles were left out by mistake.
Platform tested:
Verified on Linux/32 2.6 (jam)
|
|
|
|
|
|
|
|
|
|
| |
Removed header file testhdf5.h from C++ tests to eliminate a non-standard
problem on OpenVMS. It wasn't essential.
Platforms tested:
Linux/32 2.6 (jam)
FreeBSD/64 6.3 (liberty)
Ray agreed to test on OpenVMS.
|
|
|
|
|
|
|
|
|
| |
Trim trailing whitespace from source code files with this command:
find . \( -name "*.[ch]" -or -name "*.cpp" -or -name "*.f90" \) -print |xargs -n 1 sed -i "" 's/[[:blank:]]*$//'
Tested on:
None - eyeballed only
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
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:
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
|