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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}
Edison
#!/bin/bash
#SBATCH --qos=regular
#SBATCH --time=02:00:00
#SBATCH --nodes=10
#SBATCH --ntasks-per-node=24
#SBATCH --cpus-per-task=2

# make sure correct hugepages module is loaded
module unload $(module -l list 2>&1 | grep craype-hugepages | awk '{print $1}')
module load craype-hugepages8M
module load rca
module load namd
export HUGETLB_DEFAULT_PAGE_SIZE=8M
export HUGETLB_MORECORE=no

srun namd2 ${INPUT_FILE}

Support

Tip

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