On Wed, Oct 31, 2012 at 12:56 PM, hari krishna <haricoolguy111.gmail.com>wrote:
> Dear all,
>
> I have successfully installed serial and parallel version of AMBER12 in the
> server (in my user user only) using gnu compiled openmpi. Also the test was
> successfully completed. I used ./configure_openmpi in AmberTools/src for
> openmpi.
>
> while using PBS script to run the program in parallel, in the queue, the
> program is running and processors are allocated and the program is shown
> like running in the server. But no output files are created in the given
> folder even after long time. Please look at the following PBS script. Any
> suggestions.
>
> *#!/bin/bash
>
> #PBS -l nodes=8:ppn=8
> #PBS -l pmem=700mb
> #PBS -l walltime=600:00:00
>
> export AMBERHOME=/home/p_kumar/amber12
> export LD_LIBRARY_PATH=/home/p_kumar/amber12/lib:$LD_LIBRARY_PATH
> export DO_PARALLEL="$AMBERHOME/bin/mpirun -np 64"
>
mpirun is not in $AMBERHOME.
Terry
>
> cd /home/p_kumar/thioflavin/dynamics/parallel
>
> $DO_PARALLEL $AMBERHOME/bin/pmemd.MPI -O -i prod.in -o prod.out -p
> complexsol.prmtop -c equil.rst -r prod.rst -x prod.mdcrd -ref equil.rst*
>
>
> Sincerely
> S.Harikrishna
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Received on Tue Oct 30 2012 - 23:00:05 PDT
