[AMBER] Running several jobs under one script

From: Nkwe Monama <nmonama.csir.co.za>
Date: Thu, 25 Mar 2010 11:47:57 +0200

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 -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 boxeq.in -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 boxeq.in -c 1003.rst -p hiv.tipprmtop -o tmpmd4.out -r 1004.rst -x crd6000to11000ps -e en6000to11000ps


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Received on Thu Mar 25 2010 - 03:00:03 PDT
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