AMBER

Amber

Versions Installed

Kay: 16 / 18

Description

Amber (Assisted Model Building with Energy Refinement), is a general purpose molecular mechanics/dynamics suite which uses analytic potential energy functions, derived from experimental and ab initio data, to refine macromolecular conformations.

License

ICHEC has acquired a site license for the Amber 16 (AmberTools 17)  and Amber 18 (AmberTools 18) packages.

Thin Component

A job submission example is as follows.

#!/bin/sh
# All the informations about queues can be obtained by 'sinfo'
# PARTITION AVAIL  TIMELIMIT 
# DevQ         up    1:00:00
# ProdQ*       up 3-00:00:00
# LongQ        up 6-00:00:00
# ShmemQ       up 3-00:00:00
# PhiQ         up 1-00:00:00
# GpuQ         up 2-00:00:00

# Slurm flags
#SBATCH -p ProdQ
#SBATCH -N 2
#SBATCH --job-name=jobname 
#SBATCH -t 60:00:00

# Charge job to myaccount
#SBATCH -A your_project

# Write stdout+stderr to file
#SBATCH -o output.txt

# Mail me on job start & end
#SBATCH --mail-user=your_email
#SBATCH --mail-type=BEGIN,END

cd $SLURM_SUBMIT_DIR

module load amber/16 
module load intel/2019
module load gcc/8.2.0

srun $AMBERHOME/bin/pmemd.MPI -O -i mdin.in -o mdout.out -p prmtop.prm -c inpcrd.rst -ref inpcrd.rst -x trjfile.trj -inf file.info -r file.rst7

Benchmarks

Version: Amber 18

Dataset: Cellulose (408,609 atoms) NPT Ensemble

Merit: ns/day (the higher the better)

 

Performance(ns/day)

Serial

0.15

MPI (2 cores)

0.28

MPI (40 cores)

4.27

MPI (80 cores)

6.99

1 GPU

84.71

2 GPUs

85.94

Performance for CelluloseNPT

Additional Notes

To use Amber 18 load the relevant environment module: module load amber/18. Use pmemd.MPI for MPI-only version, pmemd.cuda for CUDA-only version, pmemd.cuda.MPI for CUDA+MPI version.