#!/bin/sh 

####### Manually edit the variables below

n_machines="6"
# Number of machines to use

n_processes_per_machine="2"
# Number of processes per machine

n_threads_per_process="8"
# Number of threads per process

# n_processes_per_machine x n_threads_per_process 
# must be less than or equal to the number of physical cores in a machine

n_processes=`expr $n_machines \* $n_processes_per_machine`
n_threads=`expr $n_processes \* $n_threads_per_process`
n_threads_per_machine=`expr $n_threads_per_process \* $n_processes_per_machine `
                                          
command="/somewhere/bin/mafft --mpi --large --globalpair"
input="input"
output="output"
# Command, input file, output file

machinefileopt=""                          # system default is used?
#machinefileopt="--machinefile $PWD/hosts" # for OpenMPI/MPICH
# Machine list file. Absolute path is necessary.
# Use $PWD if the file is in the current directory.

export  MAFFT_N_THREADS_PER_PROCESS=$n_threads_per_process

export  MAFFT_MPIRUN="mpirun $machinefileopt -n $n_processes -npernode $n_processes_per_machine -bind-to none"  # for OpenMPI
#export MAFFT_MPIRUN="mpirun $machinefileopt -n $n_processes -perhost  $n_processes_per_machine -binding none"  # for MPICH?
# mpirun or mpiexec and options
# Add environment-specific options as necessary.

#export LD_LIBRARY_PATH="/foo/bar/lib/${LD_LIBRARY_PATH:+:$LD_LIBRARY_PATH}"
# . /foo/bar/mpivars.sh
# Configure MPI if necessary

#export  MAFFT_TMPDIR="/fast/filesystem/"
# Directory for temporary data, in fast shared filesystem
# If not set, "$HOME/maffttmp"

####### Manually edit the variables above

w=`expr $n_threads_per_process \* $n_processes - 1`

echo $n_machines " machines"       1>&2
echo $n_processes " processes"     1>&2
echo $n_threads " threads"         1>&2
echo $w " workers"                 1>&2
echo ''                            1>&2

$command --threadtb $n_threads_per_machine $input > $output