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Versions and Availability


Module Names for namd on smic
Machine Version Module Name
smic 2.10 namd/2.10/INTEL-14.0.2-ibverbs(default)
smic 2.10 namd/2.10/INTEL-14.0.2-ibverbs-mic

▶ Module FAQ?

The information here is applicable to LSU HPC and LONI systems.



A user may choose between using /bin/bash and /bin/tcsh. Details about each shell follows.


System resource file: /etc/profile

When one access the shell, the following user files are read in if they exist (in order):

  1. ~/.bash_profile (anything sent to STDOUT or STDERR will cause things like rsync to break)
  2. ~/.bashrc (interactive login only)
  3. ~/.profile

When a user logs out of an interactive session, the file ~/.bash_logout is executed if it exists.

The default value of the environmental variable, PATH, is set automatically using Modules. See below for more information.


The file ~/.cshrc is used to customize the user's environment if his login shell is /bin/tcsh.


Modules is a utility which helps users manage the complex business of setting up their shell environment in the face of potentially conflicting application versions and libraries.

Default Setup

When a user logs in, the system looks for a file named .modules in their home directory. This file contains module commands to set up the initial shell environment.

Viewing Available Modules

The command

$ module avail

displays a list of all the modules available. The list will look something like:

--- some stuff deleted ---

---------------- /usr/local/packages/Modules/modulefiles/admin -----------------
EasyBuild/1.11.1       GCC/4.9.0              INTEL-140-MPICH/3.1.1
EasyBuild/1.13.0       INTEL/14.0.2           INTEL-140-MVAPICH2/2.0
--- some stuff deleted ---

The module names take the form appname/version/compiler, providing the application name, the version, and information about how it was compiled (if needed).

Managing Modules

Besides avail, there are other basic module commands to use for manipulating the environment. These include:

add/load mod1 mod2 ... modn . . . Add modules
rm/unload mod1 mod2 ... modn  . . Remove modules
switch/swap mod . . . . . . . . . Switch or swap one module for another
display/show  . . . . . . . . . . List modules loaded in the environment
avail . . . . . . . . . . . . . . List available module names
whatis mod1 mod2 ... modn . . . . Describe listed modules

The -h option to module will list all available commands.

About the Software

NAMD 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 cores for typical simulations and beyond 200,000 cores for the largest simulations. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR. - Homepage:


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


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):


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

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



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


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

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:


Then run NAMD using scripts similar to this one:


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


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



To run NAMD with GPU support (e.g. on QB2) on clusters using PBS, 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

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


On QB3 with Slurm, please use the below script template as a reference:

#SBATCH -p gpu
#SBATCH -n 96
#SBATCH -t 00:10:00
#SBATCH -A your_allocation_name

module load namd/2.14b2/intel-19.0.5-cuda
srun -n $SLURM_NTASKS $(which namd2) apoa1.namd
echo "took:$SECONDS sec."


Last modified: October 16 2020 14:18:17.