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

[Brad Aagaard]

Hongfeng,

Please send everything that was written to stdout. Also please indicate 
what NPROCS is (how many processes you are using). It also helps when 
you state what command you entered on the command line so that we can 
see if we can reproduce what you did.

The error message you list only indicates that one of the processes 
aborted because another process already aborted due to an error. The 
message associated with the real error should have been written earlier.

Brad


On 02/16/2012 07:26 AM, Hongfeng Yang wrote:
> 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 $NPROCS  /home/username/pylith57/bin/mpinemesis --pyre-start /home/username/pylith57/bin:/home/username/pylith57/lib/python2.6/site-packages/pythia-0.8.1.12-py2.6.egg:/home/username/pylith57/lib/python2.6/site-packages/setuptools-0.6c9-py2.6.egg:/home/username/pylith57/lib/python2.6/site-packages/merlin-1.7.egg:/home/username/pylith57/lib/python2.6/site-packages:/home/username/pylith57/lib/python/site-packages:/home/username/pylith57/lib64/python/site-packages:/home/username/pylith57/lib/python/site-packages:/home/username/pylith57/lib64/python/site-packages:/home/username/pylith57/lib/python/site-packages:/home/username/pylith57/lib64/python/site-packages:/home/username/pylith57/src/pylith/examples/3d/hex8:/home/username/pylith57/lib/python26.zip:/home/username/pylith57/lib/python2.6/lib-dynload:/home/username/pylith57/lib/python2.6:/home/username/pylith57/lib/python2.6/plat-linux2:/home/username/pylith57/l
ib
>   /python2.6/lib-tk:/home/username/pylith57/lib/python2.6/lib-old:/home/username/pylith57/lib64/python/site-packages:/home/username/pylith57/lib/python/site-packages:/home/username/pylith57/lib64/python/site-packages:/home/username/pylith57/lib/python/site-packages::/home/username/pylith57/lib/python/site-packages:/home/username/pylith57/lib64/python/site-packages:/home/username/pylith57/src/pylith/examples/3d/hex8:/home/username/pylith57/lib/python26.zip:/home/username/pylith57/lib/python2.6/plat-linux2:/home/username/pylith57/lib/python2.6/lib-tk:/home/username/pylith57/lib/python2.6/lib-old pythia mpi:mpistart pylith.apps.PyLithApp:PyLithApp step14.cfg --nodes=$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
>