[gmx-users] pbs not returning gromacs files

John Doe helstreak at hotmail.com
Tue Dec 11 23:10:05 CET 2012

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:

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

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.  

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