[gmx-users] GROMACS with Torque: Job stuck
mark.j.abraham at gmail.com
Fri Aug 25 16:26:43 CEST 2017
Sounds like an issue with some infrastructure being mismatched (e.g.
different MPI at compile and run time). Does it work when you run a
different MPI-used program, compiled and run using the same approach?
On Fri, Aug 25, 2017 at 3:25 PM Souparno Adhikary <souparnoa91 at gmail.com>
> 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
> 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.
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