Running NAMD Jobs on Lewis
Version 2.6 of the NAMD software package for parallel molecular dynamics computations has been installed on lewis. It was compiled with the Intel compilers, and linked with the MPICH libraries that support the Topspin InfiniBand high-speed interconnect network. NAMD jobs must be submitted to LSF for execution as batch jobs via the bsub command. Please see Submitting Jobs via LSF on Lewis for information.A sample LSF job script file for a NAMD job would contain lines like the following:
# Set job parametersThe "-a mvapich" option is required and crucial for LSF jobs that use MPI over the Topspin InfiniBand network. The -n option tells LSF how many CPUs are to be used to run the job. (For information about other job parameters, please see Submitting Jobs via LSF on Lewis.)
#BSUB -J jobname
#BSUB -oo jobname.o%J
#BSUB -eo jobname.e%J
#BSUB -a mvapich
#BSUB -n nnnn
# Start NAMD job
mpirun.lsf /share/apps/bin/namd2 configfile
The mpirun.lsf script launches the NAMD processes with LSF. Be sure to specify the full pathname for the NAMD module, /share/apps/bin/namd2. The configfile parameter specifies the name of the NAMD configuration file, usually in the form filename.namd. If the configfile is not in the same directory from which you submit the job, then use a relative or absolute pathname as appropriate. Please note that the mpirun.lsf script does not need to be told the number of CPUs, or the names of nodes where the processes are to be run. It gets all of that information from LSF. The NAMD User's Guide is available online in either HTML or PDF format.