#!/bin/bash
#BSUB -q mpi              # Queue name for MPI jobs.  Ask sys admin.
#BSUB -n 96               # Request 96 cores.
#BSUB -R 'span[ptile=16]' # Request 16 cores per machine, ie, 6 (=96/16) machines.
#BSUB -o logfile          # stdout. Any file name is ok.
#BSUB -e errfile          # stderr. Any file name is ok.
#BSUB -J mafft-mpi        # Any job name is ok.

# Configure MPI as necessary.
#. /foo/bar/mpivars.sh

# Configuration for the pairwise alignment stage:
export  MAFFT_N_THREADS_PER_PROCESS=8
export  MAFFT_MPIRUN="mpirun -n 12 -npernode 2 -bind-to none"  # for OpenMPI
#export MAFFT_MPIRUN="mpirun -n 12 -perhost  2 -binding none"  # for MPICH?
# 8 threads x 2 processes = 16 threads run on each of 6 machines.
# 16 threads x 6 machines = total 96 threads run.

# Configuration for progressive alignment stage:
/somewhere/bin/mafft --mpi --large --globalpair --threadtb 16 input > output
# 16 threads run on one of the machines assigned by scheduler.
# --globalpair can be replaced by --genafpair, --localpair, --oldgenafpair