NAMD¶

NAMD is a molecular dynamics (MD) program designed for parallel computation.

Example run script¶

This script requires that ${INPUT_FILE} be specified. The script is written such that only the number of nodes needs to be changed.

Cori KNL

#!/bin/bash
#SBATCH --qos=regular
#SBATCH --time=02:00:00
#SBATCH --nodes=8
#SBATCH --constraint=knl
#SBATCH --ntasks-per-node=68
#SBATCH --cpus-per-task=4

# make sure KNL environment is loaded
module swap craype-${CRAY_CPU_TARGET} craype-mic-knl
module load namd
srun namd2 ${INPUT_FILE}

Cori Haswell

#!/bin/bash
#SBATCH --qos=regular
#SBATCH --time=02:00:00
#SBATCH --nodes=4
#SBATCH --constraint=haswell
#SBATCH --ntasks-per-node=32
#SBATCH --cpus-per-task=2

# make sure Haswell environment is loaded
module swap craype-${CRAY_CPU_TARGET} craype-haswell
module load namd
srun namd2 ${INPUT_FILE}

SMP¶

An SMP build is also provided with the namd/$version-smp module for some versions. The primary use of the SMP builds is to reduce memory usage.

Tip

It is recommended to use the non-SMP builds where possible as those typically provide the best performance.

Cori KNL SMP

#!/bin/bash
#SBATCH --qos=regular
#SBATCH --time=02:00:00
#SBATCH --nodes=8
#SBATCH --constraint=knl
#SBATCH --ntasks-per-node=34
#SBATCH --cpus-per-task=8

# make sure KNL environment is loaded
module swap craype-${CRAY_CPU_TARGET} craype-mic-knl
module load namd/2.13-smp
srun --cpu-bind=cores namd2 ++ppn 2 ${INPUT_FILE}

Support¶

Tip

If after the checking the above you believe there is an issue with the NERSC module file a ticket with our help desk