NAMD on Sulis

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

Accessing NAMD

List the available NAMD modules:

[user@login01(sulis) ~]$ module spider NAMD

List the details and requirements for a particular NAMD module from that list:

[user@login01(sulis) ~]$ module spider NAMD/2.14-mpi

Load the module, after loading the requirements:

[user@login01(sulis) ~]$ module load GCC/10.2.0 OpenMPI/4.0.5 NAMD/2.14-mpi

Running NAMD on CPUs

#!/bin/bash
#SBATCH --time=10:00:00
#SBATCH --job-name=NAMD
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=128
#SBATCH --account=suXXX-somebudget

module purge
module load GCC/10.2.0
module load OpenMPI/4.0.5
module load NAMD/2.14-mpi

charmrun +p$SLURM_NTASKS namd2 +setcpuaffinity stmv.namd

The +setcpuaffinity flag significantly improves performance.

Running NAMD on GPUs

This example is for a single GPU job, using 20 CPU cores in support:

#!/bin/bash
#SBATCH --time=10:00:00
#SBATCH --job-name=NAMD
#SBATCH --partition=gpu
#SBATCH --gres=gpu:ampere_a100:1
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=42
#SBATCH --account=suXXX-somebudget

module purge
module load GCC/10.2.0
module load CUDA/11.1.1
module load OpenMPI/4.0.5
module load NAMD/2.14

charmrun +p20 namd2 +devices $CUDA_VISIBLE_DEVICES +setcpuaffinity stmv.namd

Performance will vary with the number of host cores used per-GPU. Allowing 20 host cores per-GPU is typically a good starting point.

Performance

The STMV and ApoA1 test cases were downloaded from the NAMD benchmarking web page. Please note that these are the basic test cases and not the customised cases used for most of the graphs on that page.

These NAMD 2.14 results are provided as a guide to scaling and to CPU / GPU selection.

CPU runs

STMV 1M atoms

Number of nodes	1	2	3	4
Performance (ns/day)	1.43	2.72	3.90	4.80

ApoA1 92k atoms

Number of nodes	1	2	3	4
Performance (ns/day)	13.4	19.6	28.3	27.3

GPU runs

STMV 1M atoms

Number of GPUs	1	2	3
ns/day	3.25	4.96	5.62

ApoA1 92k atoms

Number of GPUs	1	2	3
ns/day	35.3	45.7	54.4