Amber is a suite of biomolecular simulation programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules. The Amber software suite is divided into two parts: AmberTools22, a collection of freely available and Amber22, which is centered around the pmemd simulation program.
Official website : https://ambermd.org/index.php
updated : 5 May 2023
Available version
Amber22 is available on Lanta which can be accessed by module load Amber/2022-cpeGNU-CUDA-11.7. Running MD simulations in Amber22 is also supported by GPU acceleration.
Version | Module name |
|---|---|
22 | Amber/2022-cpeGNU-CUDA-11.7 |
1. Input files
The input files for running Amber22 can be studied from https://ambermd.org/tutorials/. The example input file for Amber can be found at /project/common/Amber/Example/
2. Job submission script
create a script using vi submit.sh command and specify the following details depending on computational resources you want to use.
2.1 Run Amber on CPU node
#!/bin/bash -l #SBATCH -p compute # specific partition #SBATCH -N 1 # specific no. of nodes #SBATCH --ntasks-per-node=128 # specific MPI tasks #SBATCH --time=24:00:00 # job time limit <hr:min:sec> #SBATCH -A ltXXXXXX # project account #SBATCH -J Amber-run # job name module purge #purge all module module load Amber/2022-cpeGNU-CUDA-11.7 WORKDIR=$SLURM_SUBMIT_DIR ###################################################### cd $WORKDIR srun pmemd.MPI -O -i mdin -o mdout -p prmtop -c inpcrd
The script above using compute partition (-p compute), 1 node (-N 1) with 128 tasks per node (--ntasks-per-node=128). The account is set to ltXXXXXX (-A ltXXXXXX) that is subjected to change to your own account. The wall-time limit is set to 2 hours 24:00:00 (the maximum time limit is 5 days -t 5-00:00:00).
2.2 Run Amber on GPU node
2.2.1 Single gpu
#!/bin/bash -l #SBATCH -p gpu # specific partition #SBATCH -N 1 # specific no. of nodes #SBATCH --ntasks-per-node=1 # specific MPI tasks #SBATCH -G 1 # specific no. of GPUs #SBATCH --time=24:00:00 # job time limit <hr:min:sec> #SBATCH -A thaisc # project account #SBATCH -J Amber-run # job name module purge #purge all module module load Amber/2022-cpeGNU-CUDA-11.7 WORKDIR=$SLURM_SUBMIT_DIR ###################################################### cd $WORKDIR srun pmemd.cuda -O -i mdin -o mdout -p prmtop -c inpcrd
The script above request for GPU partition (-p gpu), 1 node (-N 1), 1 tasks (--ntasks-per-node=1) and 1 GPU cards -G 1.
2.2.2 Multiple gpus
#!/bin/bash -l #SBATCH -p gpu # specific partition #SBATCH -N 1 # specific no. of nodes #SBATCH --ntasks-per-node=2 # specific MPI tasks #SBATCH -G 2 # specific no. of GPUs #SBATCH --time=24:00:00 # job time limit <hr:min:sec> #SBATCH -A thaisc # project account #SBATCH -J Amber-run # job name module purge #purge all module module load Amber/2022-cpeGNU-CUDA-11.7 WORKDIR=$SLURM_SUBMIT_DIR ###################################################### cd $WORKDIR srun pmemd.cuda.MPI -O -i mdin -o mdout -p prmtop -c inpcrd
Please make sure that the number of tasks ( --ntasks-per-node ) must match the number of GPU cards ( -G ).
There is no significant scaling for running Amber on multiple GPUs over single GPU.
3. Job submission
using sbatch submit.sh command to submit the job to the queuing system.