[gmx-users] pbs not returning gromacs files

Justin Lemkul jalemkul at vt.edu
Tue Dec 11 23:23:53 CET 2012

On 12/11/12 5:10 PM, John Doe wrote:
> 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.

Is there anything in this file?  Any useful error messages?  If you add 'echo 
$PATH' to your job script, does it correctly find the location of the Gromacs 

Hopefully your sysadmins would be able to help troubleshoot, within the context 
of any specifics of your cluster.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list