Merge accum_tests branch back to the trunk.
Description:
Changes consist of addition of tests for H5Faccum.c source code,
as well as some fixes that address some discovered bugs in the
metadata accumulator on several corner cases.
Tested:
h5committested
Description:
In an AIX 6.1 system, configure --enable-shared could not build a shared
HDF5 library. The problem was because the version of config.guess was too
old to recongnize AIX 6.X and also configure.in had a local fix which did
not recognize AIX 6.X.
Solution:
1. Mike McGreevy updated bin/config.guess to handle AIX 6.X.
2 Albert fixed configure.in to recognize AIX 6.X.
Note that though HDF5 can build shared lib for AIX 6.X systems
but it still could not install the proper library as in AIX 5.X
systems. Also, bin/config.sub should be updated too.
Tested: BP which is the AIX 6.1 system that exposed this problem.
fseek64 was used to support large file access for the STDIO driver back in
version 1.2.2 in year 2000. Some how it was not included in version 1.4.0.
Now, fseeko64 is used to support large file. There is no more need for fseek64
which is not a standard call. Removed its presence from configure and related
files.
Tested: jam for configure only.
In some machine (Linux), when --disable-largefile is used, it claims it has
fseeko64 but off64_t is NOT supported. Moved the test of fseeko64 and ftello64
to where fseek64 is so that they are tested only if off64_t is supported.
Tested: h5committested.
Description:
A bug introduced in 1.8.5 causes local heap data blocks to be mis-aligned when
sizeof_offsets + 2*sizeof_lengths is not a multiple of 8. In this case, the
address of the data block as stored in the heap prefix is aligned but the actual
data block is not. This causes files created with these sizes to be corrupted,
and prevents uncorrupted files with these sizes to be unreadable. Modified
local heap code to account for alignment.
Tested: jam, amani, linew (h5committest)
Removed the recognition of parallel compilers of LAM (hcc) and ChMPIon (cmpicc)
since we have no access to these two MPI implementations and decided not to
support them any more.
Test: Jam using parallel tests:
1. use CC=mpicc and confirmed it is recognized as a parallel compiler;
2. use CC=hcc and confirmed it is NOT recognized as a parallel compiler
any more.
PHDF5 changed to use "mpiexec", instead of mpirun, as the default MPI
applications startup command as defined in the MPI-2 definition, section
4.1. Note that only mpich related (using mpicc command) definitions are
changed to mpiexec. Other favors like hcc, AIX, champion, are not changed
since I don't have a way to verify them yet.
Tested:
jam and amani, using both current and new mpich.
Did not h5committested since this affects PHDF5 configure only.
Bring r18724 from metadata journaling 'merging' branch to trunk:
Rename H5[A]C_rename to H5[A]C_move_entry.
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, in production 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 production mode
Mac OS X/32 10.6.3 (amazon) in debug mode
Mac OS X/32 10.6.3 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
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.
Description:
longjmp do not necessary restore signal that is blocked during the signal
handling. This caused the Alignment test to fail quietly, resulting in wrong
alignment information which will cause failures later.
Solution:
One can use sigsetjmp/siglongjmp to restore signal handling but not all systems
such as Cray XT or VMS supports sigsetjmp. Backup solution is to use
sigprocmask to reset the signal. Again, some systems may not support it either.
Added code to try the first and then the second solution. Also added tests
to verify if the signal_handler routines are working properly. Finally, added
code to print results of the verification (in form of comments) to H5Tinit.c
for inspection in case of failure.
(Note that many platforms do not have alignment limits at all and ALIGNMNET
code never raise the SIGBUS or SIGSEGV errors. In those cases, it does not
matter whether the signal handlers work or not. Again, this can be deduced
from the results comments near the end of the H5Tinit.c. If the sum of signal
handlers called equals the total of verify, it means ALIGNMENT does not raise
any signals.)
For configure.in and configure:
Added the test for setjmp, sigsetjmp, sigprocmask which are used by the
H5detec.c.
Tested:
htcommittested, jam(serial).
size of nested compound type are calculated by using H5T_cmp_offset. The old way had a bug
in it (see bug #1850).
Tested on jam. I tested the same change for 1.8 on amani, linew, and jam.
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
recent changes to the embedded library generation code does not quite work
for the AIX system. The strings command of AIX does not display the embedded
library information be default.
Solution:
Changed the H5libhhdf5_setting[] to be an extern variable. Also removed the
const qualifier so that strings can see the variable data.
Tested:
Blue-print (with embedded-libinfo enabled and disabled).
Also tested in Jam.
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)
Move the libhdf5.settings information out of src/H5Tinit.c and into a
separate header file (src/H5lib_settings.h), which is generated at build time
(not configure time) with the src/H5make_libsettings generator program.
Tested on:
Linux/32 2.6 (jam)
Mac OS X/32 10.6.2 (amazon)
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)
a bug report (#1608) saying h5repack failed to do that sometimes. But I couldn't reproduce it.
So I added this test and closed the report. The test is in the function test_copy_dcpl in dsets.c.
Tested on jam. But I tested the same change in 1.8 on jam, amani, and linew.
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 r18071 from metadata journaling merge branch:
Refactor local heap routines with changes from metadata journaling
branch, along with other misc. changes as the changes on the metadata journaling
branch are being converged with the current state of the 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/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, 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
