On 12/11/12 5:10 PM, John Doe wrote:
I'm not sure if this is the right place to be asking this but I haven't been
able to find an answer.
I'm using a pbs script to submit a parallel job of the water tutorial. So in
my home file I have all of the files from the water tutorial and the output
from grompp. If I submit my simulation on the head node:
mdrun
then I get all of the output files such as the trajectory. However, when I try
to mpiexec with the pbs script I get nothing except stdout. My pbs script is
this:
#PBS -l walltime=1:00:00
#PBS -l nodes=1:ppn=12,mem=10GB:comp
#PBS -N Gromacs_HelloWorld
#PBS -o stdout
#PBS -j oe
module load gromacs-4.5.5
module load openmpi-intel
pbsdcp -s $PBS_O_WORKDIR/* $TMPDIR
cd $TMPDIR
NPROCS=`wc -l < $PBS_NODEFILE`
mpiexec -np $NPROCS mdrun_mpi_d
pbsdcp -g -r '*' $PBS_O_WORKDIR
cd $PBS_O_WORKDIR
this is submitted like:
qsub job.pbs
This runs under 2 seconds and all the output I get is the "stdout". Any help
would be greatly appreciated.
Is there anything in this file? Any useful error messages? If you add 'echo
$PATH' to your job script, does it correctly find the location of the Gromacs
executables?
Hopefully your sysadmins would be able to help troubleshoot, within the context
of any specifics of your cluster.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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