The National Institute for Computational Sciences

Software

NAMD

Category: Science Apps-Molecular Dynamics

Description

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 processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet.

Further information on NAMD can be found on NAMD website.

Use

NAMD is available as a module. The modulefile for NAMD sets up the necessary environmental variables for NAMD and updates PATH to include NAMD executables.

An example PBS script to run STMV benchmarkNAMD_example.sh:

#PBS -A your-account-number
#PBS -j oe
#PBS -l nodes=2 
#PBS -l walltime=1:00:00

module load namd

PPN=15
export KMP_AFFINITY=granularity=fine,compact

cat > nodelist <> nodelist
  n=$(($n + 1))
done < $PBS_NODEFILE
NP=$(($n * $PPN))

charmrun +p $NP ++ppn $PPN /usr/local/bin/micmpiexec -env MIC_ENV_PREFIX MIC -env MIC_OMP_NUM_THREADS 236 -env MIC_KMP_AFFINITY granularity=fine,balanced  $NAMD_PATH/namd2 stmv/stmv.namd +pemap 1-$PPN +commap 0 "+devices 0,1,2,3"  2>&1 | tee log 

Support

This package has the following support level : Supported

Available Versions

Version Available Builds
Other
2.10b1
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2.10
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