[gmx-users] GROMACS with Torque: Job stuck
vytautas1987 at yahoo.com
Fri Aug 25 15:49:17 CEST 2017
Check log files in server_logs and mom_logs folders in the TORQUE_HOME. You can find there what is going on in more detail.
On Friday, August 25, 2017, 4:25:03 PM GMT+3, Souparno Adhikary <souparnoa91 at gmail.com> wrote:
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
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???
Department of Microbiology,
University of Calcutta.
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