This is an old revision of the document!
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) |
Available Versions and Combinations
| Version | Compiler | MPI | Path |
|---|---|---|---|
| 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/ |
Usage
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.lsf $PATH/namd2 <configfile>
Notes
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.