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namd

About

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

Version and Availability

Softenv Keys for namd on poseidon
Machine Version Softenv Key
poseidon 2.6 +NAMD-2.6-intel-11.1-mvapich-1.1
poseidon 2.7b2 +NAMD-2.7b2-intel-11.1-mvapich-1.1
poseidon 2.7b4 +NAMD-2.7b4-intel-11.1-mvapich-1.1
poseidon 2.9 +NAMD-2.9-intel-11.1-openmpi-1.3.4
▶ Display Softenv Keys for namd all clusters
Machine Version Softenv Key
eric 2.6 +NAMD-2.6-intel-11.1-mvapich-1.1
eric 2.7b2 +NAMD-2.7b2-intel-11.1-mvapich-1.1
eric 2.7b4 +NAMD-2.7b4-intel-11.1-mvapich-1.1
eric 2.9 +NAMD-2.9-intel-11.1-openmpi-1.3.4
qb 2.6 +NAMD-2.6-intel-11.1-mvapich-1.1
qb 2.7b2 +NAMD-2.7b2-intel-11.1-mvapich-1.1
qb 2.7b4 +NAMD-2.7b4-intel-11.1-mvapich-1.1
qb 2.9 +NAMD-2.9-intel-11.1-openmpi-1.3.4
oliver 2.6 +NAMD-2.6-intel-11.1-mvapich-1.1
oliver 2.7b2 +NAMD-2.7b2-intel-11.1-mvapich-1.1
oliver 2.7b4 +NAMD-2.7b4-intel-11.1-mvapich-1.1
oliver 2.9 +NAMD-2.9-intel-11.1-openmpi-1.3.4
louie 2.6 +NAMD-2.6-intel-11.1-mvapich-1.1
louie 2.7b2 +NAMD-2.7b2-intel-11.1-mvapich-1.1
louie 2.7b4 +NAMD-2.7b4-intel-11.1-mvapich-1.1
louie 2.9 +NAMD-2.9-intel-11.1-openmpi-1.3.4
poseidon 2.6 +NAMD-2.6-intel-11.1-mvapich-1.1
poseidon 2.7b2 +NAMD-2.7b2-intel-11.1-mvapich-1.1
poseidon 2.7b4 +NAMD-2.7b4-intel-11.1-mvapich-1.1
poseidon 2.9 +NAMD-2.9-intel-11.1-openmpi-1.3.4
painter 2.6 +NAMD-2.6-intel-11.1-mvapich-1.1
painter 2.7b2 +NAMD-2.7b2-intel-11.1-mvapich-1.1
painter 2.7b4 +NAMD-2.7b4-intel-11.1-mvapich-1.1
painter 2.9 +NAMD-2.9-intel-11.1-openmpi-1.3.4
philip 2.7 +namd-2.7-intel-11.1-mpich2-1.3.2p1
philip 2.7 +namd-2.7-mpich-1.2.7p1-intel-11.1
philip 2.8 +namd-2.8-intel-11.1-mpich2-1.3.2p1
philip 2.8 +namd-2.8-intel-11.1-mpich2-1.3.2p1-cuda-4.0.17
pandora 2.7 +namd-2.7
pandora 2.8 +namd-2.8
supermike2 2.9 +NAMD-2.9-Intel-13.0.0-openmpi-1.6.2
supermike2 2.9 +NAMD-2.9-Intel-13.0.0-openmpi-1.6.2-CUDA-4.2.9
▶ Softenv FAQ?

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

Softenv

SoftEnv is a utility that is supposed to help users manage complex user environments with potentially conflicting application versions and libraries.

System Default Path

When a user logs in, the system /etc/profile or /etc/csh.cshrc (depending on login shell, and mirrored from csm:/cfmroot/etc/profile) calls /usr/local/packages/softenv-1.6.2/bin/use.softenv.sh to set up the default path via the SoftEnv database.

SoftEnv looks for a user's ~/.soft file and updates the variables and paths accordingly.

Viewing Available Packages

Using the softenv command, a user may view the list of available packages. Currently, it can not be ensured that the packages shown are actually available or working on the particular machine. Every attempt is made to present an identical environment on all of the LONI clusters, but sometimes this is not the case.

Example,

$ softenv
These are the macros available:
*   @default
These are the keywords explicitly available:
+amber-8                       Applications: 'Amber', version: 8 Amber is a
+apache-ant-1.6.5              Ant, Java based XML make system version: 1.6.
+charm-5.9                     Applications: 'Charm++', version: 5.9 Charm++
+default                       this is the default environment...nukes /etc/
+essl-4.2                      Libraries: 'ESSL', version: 4.2 ESSL is a sta
+gaussian-03                   Applications: 'Gaussian', version: 03 Gaussia
....
Listing of Available Packages

See Packages Available via SoftEnv on LSU HPC and LONI.

For a more accurate, up to date list, use the softenv command.

Caveats

Currently there are some caveats to using this tool.

  1. packages might be out of sync between what is listed and what is actually available
  2. resoft and soft utilities are not; to update the environment for now, log out and login after modifying the ~/.soft file.
Availability

softenv is available on all LSU HPC and LONI clusters to all users in both interactive login sessions (i.e., just logging into the machine) and the batch environment created by the PBS job scheduler on Linux clusters and by loadleveler on AIX clusters..

Packages Availability

This information can be viewed using the softenv command:

% softenv
Managing Environment with SoftEnv

The file ~/.soft in the user's home directory is where the different packages are managed. Add the +keyword into your .soft file. For instance, ff one wants to add the Amber Molecular Dynamics package into their environment, the end of the .soft file should look like this:

+amber-8

@default

To update the environment after modifying this file, one simply uses the resoft command:

% resoft

Usage

To use NAMD, make sure the key is inserted at the beginning of your .soft file, along with the appropriate TCL and MVAPICH keys.

▶ Open Example?

This example shows how the keys needed for a NAMD installed with the Intel compiler and MVAPICH-1.1 MPI library may appear. Do not simply copy them, as they are subject to change. Use the softenv command to verify them before use.

+tcl-8.3.4-intel-11.1
+NAMD-2.6-intel-11.1-mvapich-1.1
+mvapich-1.1-intel-11.1

In general, NAMD should only be run as a batch job with PBS.

▶ Open Example?

Example PBS script for running NAMD.

#!/bin/sh
#PBS -A your_allocation
#PBS -q checkpt
#PBS -M your_email
# Change ppn to 8 if running on Queen Bee
#PBS -l nodes=4:ppn=4
#PBS -l walltime=06:00:00
#PBS -V
#PBS -o NAMD_test.out
#PBS -e NAMD_test.err
#PBS -N namdtest
  
export EXEC=namd2
export EXEC_DIR=/usr/local/packages/NAMD/2.6/intel-11.1-mvapich-1.1
export WORKDIR=$PBS_O_WORKDIR
export NPROCS=`wc -l $PBS_NODEFILE | gawk '//{print $1}'`
export CONV_RSH=ssh
cd $WORKDIR
  
mpirun -machinefile $PBS_NODEFILE -np $NPROCS $EXEC_DIR/$EXEC apoa1.namd

Resources

  • The NAMD Home Page contains links to the User Manual, training, and other related support materials.

Last modified: March 07 2013 12:30:04.