What is Migrate, and how do I use it on Quarry?

Note: Following a system-wide upgrade in December 2012, Quarry now runs Red Hat Enterprise Linux version 6 (RHEL 6) and uses the Modules package (instead of SoftEnv) for manipulating user environments. For more, see Information about the 2012 upgrade to Quarry at IU. If you encounter any problems or have questions, email the High Performance Systems group.

Migrate is genome analysis software that applies maximum likelihood estimation and Bayesian inference to genetic data to estimate populations size and migration parameters. For more, see the Migrate home page and the Migrate documentation (in PDF format).

At Indiana University, Migrate is available in serial and parallel versions on Quarry.

If the Intel Compiler Suite is not already added to your environment on Quarry, you must add it before you can use Migrate; at the command prompt, enter:

To add the serial version to your environment, from the command line, enter:

To make permanent changes to your environment, edit your ~/.modules file. For more, see In Modules, how do I save my environment with a .modules file?

Example data sets are available on Quarry at:

If your job will run for fewer than 20 minutes, run migrate-n from the command line in the directory where your input files are located.

If your job will take longer than 20 minutes, you can run an interactive Migrate program as a batch job by creating a file that contains the options you need to pass. To do so, create a text file that contains your options, one option per line, or combine all the options on the command line and pipe them to Migrate.

For example, if the default option is  Y  , which you need to enter to keep the Migrate program running, your option file would have only one line, containing the letter  Y . If you name the text file optionfile, an example TORQUE script (migrate.job) would be:

To submit your script (migrate.job) to TORQUE, at the command prompt, enter qsub migrate.job

Output that Migrate would normally print to the screen is stored in the outfile-ml and outfile-ml.pdf files.

Alternatively, you can echo the option and pipe it to Migrate:

To pass a series of options, add  \n  (new line) to each option, which separates them onto different lines:

To use the parallel version, you must first add the Open MPI libraries to your environment; from the command line, enter:

Then, load the parallel Migrate module:

For running a Migrate job in parallel, an example TORQUE script (migrate_parallel.job) would be:

Quarry is supported by the UITS High Performance Systems group. If you have system-specific questions about Quarry, email High Performance Systems. If you have questions about compilers, programming, scientific/numerical libraries, or debuggers, email Scientific Applications and Performance Tuning.