Amber Job Sample Scripts
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Serial Submission Script
The following job script runs sander on a single processor.
#!/bin/bash
#SBATCH --job-name=<job_name>
#SBATCH --mail-user=<user@ufl.edu>
#SBATCH --mail-type=FAIL,END
#SBATCH --output <out.out>
#SBATCH --error <out.err>
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --mem-per-cpu=1G
#SBATCH --time=01:00:00
module load intel/2016.0.109 amber/14
echo $PBS_O_WORKDIR
cd $PBS_O_WORKDIR
sander -O -i amber.in -o amber.log -p amber.prmtop -c amber.inpcrd
MPI Submission Script
The following job script runs sander.MPI on two nodes with four processors each.
#!/bin/bash
#SBATCH --job-name=<job_name>
#SBATCH --mail-user=<user@ufl.edu>
#SBATCH --mail-type=FAIL,END
#SBATCH --output <out.out>
#SBATCH --error <out.err>
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --mem-per-cpu=1G
#SBATCH --time=01:00:00
module load intel/2016.0.109 openmpi/1.10.2 amber/14
echo $PBS_O_WORKDIR
cd $PBS_O_WORKDIR
mpiexec sander.MPI -O -i amber.in -o amber.log -p amber.prmtop -c amber.inpcrd