[AMBER] checkpoint on Amber within batch job

From: Zhuang, Yu <yu.zhuang.tum.de>
Date: Thu, 23 Jan 2014 13:33:53 +0000

Dear all,
I am wondering how to make a checkpoint on Amber 12 within batch job. I am running Amber on Linux cluster, however, they have a time limit for 48 hours. I would like to continue or restart the simulation after it stopped. The cluster is running under SLURM system. if anyone has a similar experience, it will be highly appreciated if you can share with me.
Thanks and regards, Yu

The following is the command I used for sander.MPI.

#SBATCH -o /home/.../myjob.%j.%N.out
#SBATCH -D /home/.../
#SBATCH -J beta_lg_1
#SBATCH --get-user-env
#SBATCH --clusters=MPP1
#SBATCH --ntasks=32
#SBATCH --partition=myri_large
#SBATCH --time=48:00:00

source /etc/profile.d/modules.sh

module load amber

srun_ps sander.MPI -O -i 2q2m_wat_min1.in -o 2q2m_wat_min1.out -c 2q2m_wat.inpcrd -p 2q2m_wat.prmtop -r 2q2m_wat_min1.restrt -ref 2q2m_wat.inpcrd;
srun_ps sander.MPI -O -i 2q2m_wat_min2.in -o 2q2m_wat_min2.out -c 2q2m_wat_min1.restrt -p 2q2m_wat.prmtop -r 2q2m_wat_min2.restrt;
srun_ps sander.MPI -O -i 2q2m_wat_md1.in -o 2q2m_wat_md1.out -c 2q2m_wat_min2.restrt -p 2q2m_wat.prmtop -r 2q2m_wat_md1.restrt -x 2q2m_wat_md1.mdcrd -ref 2q2m_wat_min2.restrt;
srun_ps sander.MPI -O -i 2q2m_wat_md2.in -o 2q2m_wat_md2.out -c 2q2m_wat_md1.restrt -p 2q2m_wat.prmtop -r 2q2m_wat_md2.restrt -x 2q2m_wat_md2.mdcrd

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Received on Thu Jan 23 2014 - 06:00:02 PST
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