NAMD

Description

NAMD is a molecular dynamics package

NAMD implements standard MD capabilities (variety of integrators, thermostats, barostats, force field compatibility, PME electrostatics, timestep integration, replica exchange, free energy calculations, etc.)

A more detailed description can be found in this page.

Licence

NAMD operates under a mixed licence: the code is distributed freely, through registration, to non-commercial users

For more information please visit this page.

Available Versions

The currently available versions of NAMD in our facilities are:

2.6 (prades)
2.7b1 (prades)
2.7 (prades, pirineus)
2.8b2 (prades, pirineus)
2.9 (pirineus, collserola)
2.10b1 (all machines)
2.10 (collserola)
2.11 (pirineus, collserola)
2.12 (pirineus, collserola)

To load a version, call it in a script via

module load namd/2.12

or else

module load namd/2.12

Benchmark

NAMD 2.11 benchmark at Collserola: actual speed-up (green) and ideal speed-up (blue) vs. number of cores for the standard NAMD benchmark, ApoA1.

Please note that employing the Xeon Phi coprocessor for offload acceleration provides 1-3x speed-up when compared with CPU-only runs.

LSF example script (collserola) - CPU-only version

#!/bin/bash
##
# IMPORTANT NOTICE: replace the email address
# and the working directories with your own info
##
# BSUB -J namd
# BSUB -o namd.log # send standard output here
# BSUB -e namd.err # send error output here
#
# Pick a queue
# BSUB -q short
#
# Send an email notice once the job is finished
# BSUB -N -u youremail@wherever
#
# Indicate the number of cores
# BSUB -n 4
#
# Pick the machine
# BSUB -R collserola 
 
date
 
# Set up the environment
. /opt/modules/default/init/bash
module load namd/2.11

# Run NAMD in multithread fashion (+pXX)
namd2 +p4 input.namd > output.out

date

LSF example script (collserola) - Xeon Phi offload acceleration

#!/bin/bash
##
# IMPORTANT NOTICE: replace the email address
# and the working directories with your own info
##
# BSUB -J namd
# BSUB -o namd.log # send standard output here
# BSUB -e namd.err # send error output here
#
# Pick a queue
# BSUB -q short
#
# Send an email notice once the job is finished
# BSUB -N -u youremail@wherever
#
# Indicate the number of cores
# BSUB -n 4
#
# Pick the machine
# BSUB -R collserola 
 
date
 
# Set up the environment
. /opt/modules/default/init/bash
module load namd/2.11-mic
. /prod/intel/composer_xe_2015.2.164/bin/compilervars.sh intel64 namd2 +p12 input.namd

# Run namd2 in multi-thread fashion (+pXX) with offload Phi acceleration
namd2 +p4 +devices 0 input.namd > output.out

date

LSF example script (pirineus) - version A

#!/bin/bash
##
# IMPORTANT NOTICE: replace the email address
# and the working directories with your own info
##
# BSUB -J namd
# BSUB -o namd.log # send standard output here
# BSUB -e namd.err # send error output here
#
# Pick a queue
# BSUB -q short
#
# Send an email notice once the job is finished
# BSUB -N -u youremail@wherever
#
# Indicate the number of cores
# BSUB -n 4
#
# Pick the machine
# BSUB -R pirineus
 
date
 
# Set up the environment
. /opt/modules/default/init/bash
module load namd/2.11

# Run NAMD in multithread fashion (+pXX)
namd2 +p12 input.namd > output.out

date

LSF example script (pirineus) - version B

#!/bin/bash
##
# IMPORTANT NOTICE: replace the email address
# and the working directories with your own info
##
# BSUB -J namd
# BSUB -o namd.log # send standard output here
# BSUB -e namd.err # send error output here
#
# Pick a queue
# BSUB -q short
#
# Send an email notice once the job is finished
# BSUB -N -u youremail@wherever
#
# Indicate the number of cores
# BSUB -n 4
#
# Pick the machine
# BSUB -R pirineus
 
date
 
# Set up the environment
. /opt/modules/default/init/bash
module load namd/2.11

# Run NAMD in multithread fashion (+pXX)
namd2 +p12 input.namd > output.out

date

Place the appropriate LSF script in a file (for instance namd.lsf) and submit the job with the command

bsub < namd.lsf

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