Running NAMD on ARCHIE-WeSt
This is a simple example of NAMD which should run on ARCHIE-WeSt and take 12 minutes. The input files and job script are downloadable below.
1. Load the appropriate environment modules
To run NAMD load the appropriate modules:
module load mpi/gcc/openmpi/1.4.5
module load libs/gcc/fftw2/float-mpi/2.1.5
module load apps/gcc/namd/mpi/2.8
2. Prepare input files
The following files are required to be present in the working directory (input files):
- par_all.inp
- protein_SC.pdb and protein_SC.psf
- protein_D1.coor, protein_D1.vel, protein_D1.xsc
- protein_D2.inp(the input file for the calculations)
- job script namd_run.sh
These can be downloaded as a tar file from here.
The sample input file (protein_D2.inp):
structure protein_SC.psf coordinates protein_SC.pdb bincoordinates protein_D1.coor paratypecharmm on parameters par_all.inp exclude scaled1-4 1-4scaling 1.0 switching on switchdist 8 cutoff 12 pairlistdist 14 margin 0 stepspercycle 20 wrapWater on rigidBonds water timestep 2.0 outputenergies 100 outputtiming 100 binaryoutput yes outputname protein_D2 dcdfreq 2000 restartfreq 100000 restartname rest_protein_D2 binvelocities protein_D1.vel PME yes fullElectFrequency 2 PMEGridsizex 87 PMEGridsizey 93 PMEGridsizez 100 langevin on langevinDamping 5 langevinTemp 300 langevinHydrogen no extendedSystem protein_D1.xsc run 50000 |
The job script (run_namd.sh) will use 10 nodes (120 cores):
# export PROCS_ON_EACH_NODE=12 # ************* SGE qsub options **************** #Export env variables and keep current working directory #$ -V -cwd #Specify the project ID #$ -P project.prj #Select parallel environment and number of parallel queue slots (nodes) #$ -pe mpi-verbose 10 #Combine STDOUT/STDERR #$ -j y #Specify output file #$ -o out.$JOB_ID #Request resource reservation (reserve slots on each scheduler run until enough have been gathered to run the job #$ -R y #Request exclusivity of each node #Indicate runtime #$ -l h_rt=12:00:00 # ************** END SGE qsub options ************ export NCORES=`expr $PROCS_ON_EACH_NODE \* $NSLOTS` export OMPI_MCA_btl=openib,self # Execute NAMD2 with configuration script with output to log file charmrun +p$NCORES -v namd2 protein_D2.inp > protein_D2.out #to launch jobs one after the other: charmrun +p$NCORES -v namd2 protein_D3.inp > protein_D3.out charmrun +p$NCORES -v namd2 protein_D4.inp > protein_D4.out |
3. Job submission
To submit the job, type:
qsub run_namd.sh
As a result, the following files will be produced (output files):
- protein_D2.coor, protein_D2.vel, protein_D2.xsc, protein_D2.dcd
- protein_D2.out
- out.$jobID$
The output files can be downloaded as a tar file from here for comparison.