# namd

## Summary

+ **Module Name:** namd
+ **Support Level:** Primary Support
+ **Software Access Level:** Open Access
+ **Home Page:** [http://www.ks.uiuc.edu/Research/namd/](http://www.ks.uiuc.edu/Research/namd/)

## Software Description

NAMD, recipient of a 2002 Gordon Bell Award, is a parallel molecular
dynamics code designed for high-performance simulation of large
biomolecular systems. Based on Charm++ parallel objects, NAMD scales to
hundreds of processors on high-end parallel platforms. NAMD is best run
on the high performance systems where it has been compiled with the
latest Intel compilers and recent MPI parallel libraries. There are
different compiled versions of NAMD, which use different parallelization
methods.
## General Linux

**OpenMPI NAMD version**

The following is an example job script for running an OpenMPI-based NAMD module under SLURM:

	!/bin/bash -l
	#SBATCH -t 24:00:00
	#SBATCH --mem-per-cpu=2gb
	#SBATCH --nodes==8
	#SBATCH --ntasks-per-node=32
	cd $SLURM_SUBMIT_DIR

	module load namd/2.14-ompi
	mpirun namd2 stmv.namd > stmv.out

**IBVerbs NAMD version**

The following is an example of a SLURM script for running an IBVerbs version of NAMD. This script is more complex because using IBVerbs, we are responsible for telling charmrun about the topology and environment under which we want the NAMD calculation to run.

	#!/bin/bash -l
	#SBATCH -t 24:00:00
	#SBATCH --mem-per-cpu=2gb
	#SBATCH --nodes==4
	#SBATCH --ntasks-per-node=8

	module load namd/2.12-ibverbs
	cd $SLURM_SUBMIT_DIR

	# Create a formatted list of nodes
	rm namd.hostfile
	HOSTNAMES=$(scontrol show hostnames)
	while IFS= read -r HOST;
	do
	 echo "host ${HOST}" >> namd.hostfile;
	done <<< "$HOSTNAMES"

	# Create a runscript for loading the namd module
	# on each node
	cat > runscript << EOL
	#!/bin/bash
	module load namd/2.12-ibverbs
	\$*
	EOL
	chmod +x runscript

	# Please note there is no line break
	# in the following command.
	`which charmrun` ++runscript ./runscript `which namd2` \
	++nodelist namd.hostfile ++p $SLURM_NPROCS stmv.namd > stmv.out

One of the things that using IBVerbs allows us to do is to run NAMD on GPUs, which can offer significant performance improvements over purely-CPU-based calculations in many cases. An example job script for running NAMD on our msigpu partition follows:

	#!/bin/bash -l
	#SBATCH --time=2:00:00
	#SBATCH --nodes=2
	#SBATCH --ntasks-per-node=24
	#SBATCH --mem-per-cpu=2gb
	#SBATCH -p mspigpu
	#SBATCH --gres=gpu:v100:2

	module load namd/2.14-libverbs-CUDA

	# Create a formatted list of nodes
	HOSTNAMES=$(scontrol show hostnames)
	while IFS= read -r HOST;
	do
	 echo "host ${HOST}" >> namd.hostfile;
	done <<< "$HOSTNAMES"

	# Create a runscript for loading the namd module
	# on each node
	cat > runscript << EOL
	#!/bin/bash
	module load namd/2.12-ibverbs
	\$*
	EOL

	chmod +x runscript
	let NCPUS=$SLURM_CPUS_ON_NODE-1
	# Please note there is no line break
	# in the following command.
	`which charmrun` ++runscript ./runscript `which namd2` \
	++nodelist namd.hostfile ++n $SLURM_JOB_NUM_NODES ++ppn $NCPUS \
	+idlepoll +devices 0,1 stmv.namd > stmv.out

Additional information may be found at: <http://www.ks.uiuc.edu/Research/namd>
Performance hints are found at: <http://www.ks.uiuc.edu/Research/namd/wiki/?NamdPerformanceTuning>