Using Migrate-N v 3.4.4 (Jan 14, 2013) on the CCG Ubuntu NGS server

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Table of Contents

Jan. 29, 2013
Installation of Migrate-N for parallel processing (MPI).
    Download the current .tar.gz version into /opt
    Assuming Openmpi has been properly installed and configured (/opt/openmpi) including the creation of a "hosts" file in
    /opt/openmpi/etc. Our "hosts" file has a single line: localhost slots=33
    unpack the migrate3.4.4.src.tar.gz file 

$ tar xfz migrate3.4.4.src.tar.gz

This creates a new directory /opt/migrate3.4.4

$ cd /opt/migrate3.4.4/src $ sudo ./configure $ sudo make mpis

This will create an executable named "migrate-n-mpi" in the /opt/migrate3.4.4/src directory.

Jan. 29, 2013
Running Migrate example file

$ cd /opt/migrate3.4.4/example $ sudo mpirun -np 7 --hostfile /opt/openmpi/etc/hosts ../src/migrate-n-mpi parmfile.testbayes

Jan. 29, 2013
Running real data

    Create a Migrate project directory (/data/Migrate/projectX) where your input data and parameter files will reside
    (myMigrateData.txt, parmfile). "mpirun" will allocate multiple cores to the analysis with the -np option.
    Use one core for each marker plus one for "overhead". The example below is for a data file with 6 markers so I set -np 7.

$ cd /data/Migrate/projectX $ sudo mpirun -np 7 --hostfile /opt/openmpi/etc/hosts /opt/migrate3.4.4/src/migrate-n-mpi parmfile

The output files will be written into this project directory.