Re: [AMBER] Running several jobs under one script

From: Jason Swails <>
Date: Thu, 25 Mar 2010 09:27:45 -0700

On Thu, Mar 25, 2010 at 2:47 AM, Nkwe Monama <> wrote:
> Dear Amber_Users
> Is it possible to run several jobs under one script (a single job submission), whereby the output from the first job is used as the input for the next job under the same script.
> My run script is as follows:
> ******************************************************************
> ###These lines are for Moab
> #MSUB -l nodes=4:ppn=8
> #MSUB -l partition=ALL
> #MSUB -l walltime=120:00:00
> #MSUB -m be
> #MSUB -V
> #MSUB -o /export/home/kbisetty/scratch/amber/test/penny/meoh/amber.out
> #MSUB -e /export/home/kbisetty/scratch/amber/test/penny/meoh/amber.err
> #MSUB -d /export/home/kbisetty/scratch/amber/test/penny/meoh
> #MSUB -mb
> ##### Running commands
> nproc=`wc $PBS_NODEFILE | awk '{print $1}'`
> mpirun -nolocal -np $nproc -machinefile $PBS_NODEFILE /export/home/nmonama/amber/bin/sander.MPI -O -i -c 1002.rst -p hiv.tipprmtop -o tmpmd3.out -r 1003.rst  -x crd1000to6000ps -e en1000to6000ps
> ***************************************************************************
> for example running:
> /export/home/nmonama/amber/bin/sander.MPI -O -i -c 1003.rst -p hiv.tipprmtop -o tmpmd4.out -r 1004.rst  -x crd6000to11000ps -e en6000to11000ps

I am inclined to say yes since what you submit is a script that will
be executed. Just don't forget to include the mpirun before the
second sander.MPI as well.

Good luck!

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Thu Mar 25 2010 - 09:30:03 PDT
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