[AMBER] Running Amber in GPU cluster

From: Soumendranath Bhakat <bhakatsoumendranath.gmail.com>
Date: Tue, 5 Nov 2013 10:25:46 +0200

Hello Amber Community;

We are running our MD jobs in Amber in GPU cluster. For submission of our
jobs we are using ./sub_apv.sh & and vi sub_apv.sh is showing a script like

source /etc/profile.d/modules.sh
module add intel-XE/c8000 mvapich2/c8000 cuda/5.0 amber/k20


time mpirun -np $np $exe -O -i Partial_Mini.in -o Partial_Mini.out -p
com_solvated.top -c com_solvated.crd -ref com_solvated.crd -r
time mpirun -np $np $exe -O -i Full_Mini.in -o Full_Mini.out -p
com_solvated.top -c Partial_Mini.rst -r Full_Mini.rst
time mpirun -np $np $exe -O -i Heating.in -o Heating.out -p
com_solvated.top -c Full_Mini.rst -r Heating.rst -ref Full_Mini.rst -x
time mpirun -np $np $exe -O -i equil.in -o equil.out -p com_solvated.top -c
Heating.rst -r equil.rst -x equil.mdcrd
time mpirun -np $np $exe -O -i md.in -o md.out -p com_solvated.top -c
equil.rst -r md.rst -x md.mdcrd

But this script is taking only one command at a time i.e it only takes the
first line and writing out the "Partial_Mini.out" but it is not taking up
the second line of command that means it is not taking the Full_Mini.in.

We request Amber community and Linux/Unix users to let us know about any
solution so that we can run all the command at one time.
Thanks & Regards;
Soumendranath Bhakat
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Received on Tue Nov 05 2013 - 00:30:02 PST
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