software:namd2

NAMD

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

NAMD (Not (just) Another Molecular Dynamics program) 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
Version:2.9
Release:April 2012
Lizenz:University of Illinois license
Developer:Theoretical and Computational Biophysics Group (TCB) and the Parallel Programming Laboratory (PPL)
Version Compiler MPI Path Environment
2.9 GCC 4.7.0 intelmpi 4.0.3.008 /cluster/Apps/NAMD/gcc_4.7.0/impi_4.0.3.008/
OpenMPI 1.6.1 /cluster/Apps/NAMD/gcc_4.7.0/openmpi_1.6.1/
/cluster/Apps/NAMD/gcc_4.7.0/ibverbs/
Intel Composer 2011 SP1 10.319 intelmpi 4.0.3.008 /cluster/Apps/NAMD/intel-studio-2011-sp1-10/impi_4.0.3.008/ I_MPI_FABRICS=shm:ofa1)

To use NAMD, you first need to load the corresponding modulefiles.

For single-cpu usage:

$ $PATH/namd2 <configfile>

For parallel usage with LSF:

$ bsub -a <mpi> -q <queuename> -o <outputfile> -e <errorfile> -n <amount of cores> -app Reserve1900M -R 'span[ptile=32]' mpirun $PATH/namd2 <configfile>

For computations with up to around 256 cores the version gcc_4.7.0/impi_4.0.3.008/ will be faster than intel-studio-2011-sp1-10/impi_4.0.3.008/. With a higher number of cores it will be reversed.


1)
This version of NAMD will be faster, if you set the Intel-MPI runtime environment variable I_MPI_FABRICS to shm:ofa. Just type export I_MPI_FABRICS=shm:ofa in your console and then run Namd
  • software/namd2.txt
  • Last modified: 2014/03/13 14:59
  • by schlarbm