[gmx-users] GROMACS with Torque: Job stuck

Souparno Adhikary souparnoa91 at gmail.com
Fri Aug 25 15:24:09 CEST 2017


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:

#PBS -N asyn
#PBS -q batch
#PBS -l nodes=4:ppn=4
#PBS -l walltime=120:00:00
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

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

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

Souparno Adhikary,
Department of Microbiology,
University of Calcutta.

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