NAMD

Software Summary

Mesabi

Default Module:

2.7-ompi

Other Modules Available:

2.12-ibverbs-smp-CUDA, 2.12-multicore-CUDA, 2.13-ibverbs-smp-CUDA, 2.10-ibverbs, 2.11-ibverbs, 2.12-ibverbs, 2.13-ompi, 2.14-libverbs-CUDA, 2.14-ompi, 2.7-ompi, 2.8-ompi, 2.9-impi, 2.9-libverbs-CUDA, 2.9b1-libverbs, 3.0-alpha13-netlrts-smp-CUDA

Last Updated On:

Tuesday, August 29, 2023

Mesabi K40

Default Module:

Other Modules Available:

Last Updated On:

Mangi

Default Module:

2.7-ompi

Other Modules Available:

2.10-ibverbs, 2.11-ibverbs, 2.12-ibverbs, 2.13-ompi, 2.14-libverbs-CUDA, 2.14-ompi, 2.7-ompi, 2.8-ompi, 2.9-impi, 2.9-libverbs-CUDA, 2.9b1-libverbs, 3.0-alpha13-netlrts-smp-CUDA

Last Updated On:

Tuesday, August 29, 2023

Mangi v100

Default Module:

Other Modules Available:

Last Updated On:

NICE

Default Module:

Other Versions Available:

Last Updated On:

Tuesday, August 29, 2023

Support Level:

Primary Support

Software Access Level:

Open Access

Home Page:

Link

Software Categories:

Drug Discovery

Structural Biology

Molecular Modeling and Simulation

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.

Software Documentation

Software Documentation Tabs

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 -N=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 -N=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 of a job script for running NAMD on MSI's k40 GPU nodes can be found in the k40 documentation tab on this page.

Additional Information

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

Mesabi K40

Mesabi k40 Documentation:

Running a NAMD calculation on GPUs currently requires an IBVerbs-based NAMD module. An example job script for running NAMD on our k40 GPU 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 k40
#SBATCH --gres=gpu:k40:2

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