[gmx-users] GROMACS with Torque: Job stuck

[Souparno Adhikary]

Hi,

This is related to running GROMACS through mpirun and Torque. After I
installed Torque in our lab cluster, I went on to test GROMACS using a
simple run. I wrote a Torque script as follows:

#!/bin/sh
#PBS -N asyn
#PBS -q batch
#PBS -l nodes=4:ppn=4
#PBS -l walltime=120:00:00
cd $PBS_O_WORKDIR
cat $PBS_NODEFILE>nodes
mpirun -np 16 gmx_mpi mdrun -deffnm asyn_10ns

After I submit this file using qsub command, the job is properly
showing using pbsnodes command in other mom units.

But, the job stays as R in 00:00:00 in the list. I presume, this might
be an error from my part in setting up GROMACS with Torque. I compiled
GROMACS with -DGMX_MPI=ON

The nodes file is not written and the job stays stuck.

Can anyone familiar with job scheduling help me in this regard???


Souparno Adhikary,
CHPC Lab,
Department of Microbiology,
University of Calcutta.