[AMBER] Problem in running parallel

From: hari krishna <haricoolguy111.gmail.com>
Date: Wed, 31 Oct 2012 10:26:22 +0530

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

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


#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"

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*

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Received on Tue Oct 30 2012 - 22:00:03 PDT
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