[CIG-SHORT] PETSc error when running Pylith on a cluster
Hongfeng Yang
hyang at whoi.edu
Thu Feb 16 07:26:57 PST 2012
Hi All,
The cluster is running CentOS 5.7. Options to build Pylith are
$HOME/src57/pylith/pylith-installer-1.6.2-0/configure \
--enable-python --with-make-threads=2 \
--with-petsc-options="--download-chaco=1 --download-ml=1 --download-f-blas-lapack=1 --with-debugging=yes" \
--prefix=$HOME/pylith
However, the following error message appears when running an example on
the cluster.
[30]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
So, we have successfully built debugging into petsc, but it is not enabled.
Here is the full run command:
/usr/mpi/gcc/openmpi-1.4.3/bin/mpirun --hostfile $PBS_NODEFILE -np $NPROCS /home/username/pylith57/bin/mpinemesis --pyre-start /home/username/pylith57/bin:/home/username/pylith57/lib/python2.6/site-packages/pythia-0.8.1.12-py2.6.egg:/home/username/pylith57/lib/python2.6/site-packages/setuptools-0.6c9-py2.6.egg:/home/username/pylith57/lib/python2.6/site-packages/merlin-1.7.egg:/home/username/pylith57/lib/python2.6/site-packages:/home/username/pylith57/lib/python/site-packages:/home/username/pylith57/lib64/python/site-packages:/home/username/pylith57/lib/python/site-packages:/home/username/pylith57/lib64/python/site-packages:/home/username/pylith57/lib/python/site-packages:/home/username/pylith57/lib64/python/site-packages:/home/username/pylith57/src/pylith/examples/3d/hex8:/home/username/pylith57/lib/python26.zip:/home/username/pylith57/lib/python2.6/lib-dynload:/home/username/pylith57/lib/python2.6:/home/username/pylith57/lib/python2.6/plat-linux2:/home/username/pylith57/lib/python2.6/lib-tk:/home/username/pylith57/lib/python2.6/lib-old:/home/username/pylith57/lib64/python/site-packages:/home/username/pylith57/lib/python/site-packages:/home/username/pylith57/lib64/python/site-packages:/home/username/pylith57/lib/python/site-packages::/home/username/pylith57/lib/python/site-packages:/home/username/pylith57/lib64/python/site-packages:/home/username/pylith57/src/pylith/examples/3d/hex8:/home/username/pylith57/lib/python26.zip:/home/username/pylith57/lib/python2.6/plat-linux2:/home/username/pylith57/lib/python2.6/lib-tk:/home/username/pylith57/lib/python2.6/lib-old pythia mpi:mpistart pylith.apps.PyLithApp:PyLithApp step14.cfg --nodes=$NPROCS --petsc.start_in_debugger --launcher.dry --nodes=$NPROCS --macros.nodes=$NPROCS --macros.job.name= --macros.job.id=8403>& ./$PBS_JOBID.log
Here is the full error message which states that we are not in debugging mode:
[35]PETSC ERROR: --------------------- Stack Frames ------------------------------------
[30]PETSC ERROR: ------------------------------------------------------------------------
[30]PETSC ERROR: Caught signal number 15 Terminate: Somet process (or the batch system) has told this process to end
[30]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[30]PETSC ERROR: or seehttp://www.mcs.anl.gov/petsc/petsc-as/documentation/faq.html#valgrind[30]PETSC ERROR: or tryhttp://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
[30]PETSC ERROR: likely location of problem given in stack below
[30]PETSC ERROR: --------------------- Stack Frames ------------------------------------
Anyone could help? Thanks!
Hongfeng Yang
--
Postdoc Investigator
Woods Hole Oceanographic Institution
Dept. Geology and Geophysics
360 Woods Hole Rd, MS 24
Woods Hole, MA 02543
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