Amber

Amber#

Amber is a suite of biomolecular simulation programs.

Amber homepage: ambermd.org/

Official Amber Tutorials: ambermd.org/tutorials/

See also

For examples and tips on submitting jobs, see our SLURM documentation and Best Practices for Jobs

For compute resources, see HPC Queues

Using Amber on the SuperPod#

Files used in the example are available:

  • on github

  • on the SuperPod at /hpc/mp/examples/amber/

Example submission script#

The following job script can be submitted using sbatch amber_gpu_example.sbatch.

 1#!/bin/bash
 2#SBATCH -J example
 3#SBATCH -o example_%j.out
 4#SBATCH -N 1
 5#SBATCH --ntasks-per-node=1
 6#SBATCH -G 1
 7
 8# Amber
 9module purge
10module load amber/22
11
12# Program Command
13# NOTE: the flag -AllowSmallBox is needed to run this example
14# but you shouldn't need it most of the time
15srun pmemd.cuda.MPI -AllowSmallBox -O -o stdout -i alanine_md.in -c alanine_md.rst -p alanine_md.prmtop -r alanine_md_new.rst -x alanine_md_new.mdcrd

Using Amber on M3#

Files used in the example are available:

Example submission script#

The following job script can be submitted using sbatch amber_cpu_example.sbatch.

This example should run in approximately 90 seconds and use about 600 MB of memory when using 4 cores. Therefore, we request 1 GB of memory and 3 minutes of run time to give ourselves some room for error.

Note, we know this from running the job. It is always a good idea to review the resources your jobs use and adjust future jobs to more accurately request resources.

 1#!/bin/bash
 2#SBATCH -J amber_example          # Job name, display in queue
 3#SBATCH -o amber_example_%j.out   # output file, %j is the job id
 4#SBATCH -p dev                    # partition to use
 5#SBATCH -N 1                      # number of nodes
 6#SBATCH -c 1                      # number of cpu cores per task
 7#SBATCH --ntasks-per-node=4       # number of tasks per node
 8#SBATCH --mem=1G                  # memory per node
 9#SBATCH -t 0-00:03:00             # run time, days-HH:MM:SS
10
11# Amber
12module purge
13module load amber/22
14
15# Program Command
16srun sander.MPI -O -o stdout -i alanine_md.in -c alanine_md.rst -p alanine_md.prmtop -r alanine_md_new.rst -x alanine_md_new.mdcrd