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.
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