[CIG-SHORT] PETSc error when running Pylith on a cluster

[Hongfeng Yang]

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