Submitting a Towhee Job to SGE

The force fields are located under /opt/und/towhee/ForceFields directory.

To submit a towhee job (assuming that towhee_input file is in the current directory where the job is submitted):

#!/bin/csh
#$ -N towhee_job_name
#$ -M afs_id@nd.edu
#$ -m ae
#$ -r y

module load towhee
towhee

According to the documentation, to submit a parallel job, you will need first to create a file named towhee_parallel with the following parameters:

  • #number of jobs
    The number of simulations to run.
  • #stdout filename
    The filename for the output that would normally go to stdout. This output is placed in each of the working directories.
  • #working directories
    The list of working directories (one per line) where all of the towhee input files are located for each job that you wish to perform. All of the output will be placed in these directories in a manner identical to if you were running a serial job from that directory. Please note that you should specify the full path name for the ff_filename variable (associated with the force field files) in towhee_input.

The submission script looks like (for an 8 node job):

#!/bin/csh
#$ -N towhee_job_name
#$ -pe mpi-8 8
#$ -M afs_id@nd.edu
#$ -m ae
#$ -r y

module load towhee
mpirun -np $NSLOTS `which towhee`

However Towhee is NOT parallelized. It just uses MPI master/slave scheme to spawn other serial jobs. The same result can be achieved with qsub -t job_array from SGE.

For further information, please consult the Towhee documentation: http://towhee.sourceforge.net/usersmanual.html