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namd

Versions and Availability

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Module Names for namd on qb3
Machine Version Module Name
qb3 2.14b2 namd/2.14b2/intel-19.0.5
qb3 2.14b2 namd/2.14b2/intel-19.0.5-cuda

▶ Module FAQ?

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

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Shells

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

/bin/bash

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.

/bin/tcsh

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

Modules

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 ---
velvet/1.2.10/INTEL-14.0.2
vmatch/2.2.2

---------------- /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.

▶ Did not find the version you want to use??

If a software package you would like to use for your research is not available on a cluster, you can request it to be installed. The software requests are evaluated by the HPC staff on a case-by-case basis. Before you send in a software request, please go through the information below.

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Types of request

Depending on how many users need to use the software, software requests are divided into three types, each of which corresponds to the location where the software is installed:

  • The user's home directory
    • Software packages installed here will be accessible only to the user.
    • It is suitable for software packages that will be used by a single user.
    • Python, Perl and R modules should be installed here.
  • /project
    • Software packages installed in /project can be accessed by a group of users.
    • It is suitable for software packages that
      • Need to be shared by users from the same research group, or
      • are bigger than the quota on the home file syste.
    • This type of request must be sent by the PI of the research group, who may be asked to apply for a storage allocation.
  • /usr/local/packages
    • Software packages installed under /usr/local/packages can be accessed by all users.
    • It is suitable for software packages that will be used by users from multiple research groups.
    • This type of request must be sent by the PI of a research group.

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How to request

Please send an email to sys-help@loni.org with the following information:

  • Your user name
  • The name of cluster where you want to use the requested software
  • The name, version and download link of the software
  • Specific installation instructions if any (e.g. compiler flags, variants and flavor, etc.)
  • Why the software is needed
  • Where the software should be installed (locally, /project, or /usr/local/packages) and justification explaining how many users are expected.

Please note that, once the software is installed, testing and validation are users' responsibility.

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: http://www.ks.uiuc.edu/Research/namd/

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

PBS

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

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

Slurm

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

#!/bin/bash
#SBATCH -p gpu
#SBATCH -N 2
#SBATCH -n 96
#SBATCH -t 00:10:00
#SBATCH -A your_allocation_name

module load namd/2.14b2/intel-19.0.5-cuda
echo "SLURM_NTASKS=$SLURM_NTASKS"
SECONDS=0
srun -n $SLURM_NTASKS $(which namd2) apoa1.namd
echo "took:$SECONDS sec."

Resources

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