namd

About

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

Versions and Availability

Module Names for namd on smic
Machine Version Module Name
smic 2.10 namd/2.10/INTEL-14.0.2-ibverbs
smic 2.10 namd/2.10/INTEL-14.0.2-ibverbs-mic
▶ **FIX-ME** FAQ?

Usage

Depending on which cluster it is installed, NAMD may or may not need MPI to run.

Non-MPI

On SuperMIC, use "charmrun" to run NAMD. Below is a sample script which runs NAMD with 4 nodes (80 CPU cores and 8 Xeon Phi co-processors):

#!/bin/bash

#PBS -A hpc_smictest3
#PBS -l walltime=2:00:00
#PBS -l nodes=4:ppn=20
#PBS -q checkpt

cd $PBS_O_WORKDIR
module add namd/2.10/INTEL-14.0.2-ibverbs-mic

for node in `cat $PBS_NODEFILE | uniq`; do echo host $node; done > hostfile

charmrun ++p 80 ++nodelist ./hostfile ++remote-shell ssh `which namd2` apoa1.namd

	

MPI

Use "mpirun" to run NAMD (e.g. on QB2). Below is a sample script which runs NAMD with 4 nodes (80 CPU cores):

#!/bin/bash

#PBS -A your_allocation_name
#PBS -l walltime=2:00:00
#PBS -l nodes=4:ppn=20
#PBS -q checkpt

cd $PBS_O_WORKDIR
module add namd/2.10b1/CUDA-65-INTEL-140-MVAPICH2-2.0

mpirun -n 80 -f $PBS_NODEFILE `which namd2` apoa1.namd
	

On Super Mike 2, first make sure that the proper keys are loaded in .soft file:

+fftw-3.3.3-Intel-13.0.0-openmpi-1.6.2
+NAMD-2.9-Intel-13.0.0-openmpi-1.6.2
	

Then run NAMD using scripts similar to this one:

#!/bin/bash

#PBS -A hpc_your_allocation
#PBS -l walltime=2:00:00
#PBS -l nodes=4:ppn=16
#PBS -q checkpt

cd $PBS_O_WORKDIR

mpirun -n 64 -hostfile $PBS_NODEFILE `which namd2` apoa1.namd
	

GPU

To run NAMD with GPU support (e.g. on QB2), please use the below script as a reference, the example data and detailed instructions can be downloaded from the namd tutorial titled "GPU Accelerated Molecular Dynamics Simulation, Visualization, and Analysis" from here.

#PBS -A your_allocation_name
#PBS -l walltime=2:00:00
#PBS -l nodes=4:ppn=20
#PBS -q checkpt

cd $PBS_O_WORKDIR
module add namd/2.10b1/CUDA-65-INTEL-140-MVAPICH2-2.0

nprocs=`wc -l $PBS_NODEFILE | awk '{print $1}'`
mpirun -n $nprocs -f $PBS_NODEFILE /usr/local/packages/namd/2.10b1/CUDA-65-INTEL-140-MVAPICH2-2.0/namd2 apoa1.namd
	

Resources

Last modified: March 03 2017 16:07:19.