Amber Job Sample Scripts

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