Migrate

Migrate estimates effective population sizes and past migration rates between n population assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes. Migrate uses Bayesian inference (or maximum likelihood) to jointly estimate all parameters.

Executables: migrate-n migrate-n-mpi

PBS Submit Scripts

Using OpenMPI

#!/bin/sh  
 #PBS -l nodes=4:ppn=1  
 #PBS -q short
 #PBS -N migrateMPI

 . /usr/modules/init/bash

module load openmpi openmpi-apps/1.6.4/migrate/3.6.9

cd $PBS_O_WORKDIR
mpirun migrate-n-mpi parmfile.ml -nomenu

Seems to be happiest when the number of replicates in the parmfile is at least the number of nodes requested minus one.

Slurm Submit Script

#!/bin/bash  
#SBATCH -N 2
#SBATCH --ntasks-per-node=2
#SBATCH -p primary
#SBATCH --job-name=migrateMPIex

. /usr/modules/init/bash

module load openmpi/1.10.2 openmpi-apps/1.10.2/migrate/3.6.11

cd $SLURM_SUBMIT_DIR/testsuite
ulimit -l unlimited
export OMPI_MCA_btl="openib,self"
mpirun --mca migrate-n-mpi parmfile.ml -nomenu

Download the example dataset here

Website

Migrate