In the previous post of this series we saw how to configure a basic network for our small cluster. Now it is time to work on the MPI stuff. Our cluster will be a Beowulf cluster. This kind of cluster is composed of commodity computers, connected via network sharing resources and programs. And in the next post, we will see how to include a batch queuing system to control the resource utilization in our cluster.

MPI is not a library. MPI is actually a standard. When you find an RESTful application, REST is only a standard, and you have different libraries that implement this standard (Jersey, JBoss Reast Easy, CodeIgniter+Rest Controllers, and so it goes). With MPI it is not different. There are different implementations of the MPI specification. We suggest you to read this tutorial that, although it was written in 2009, it uses Debian (operational system we are using in BioUno cluster) and is very well written and concise. Basically, you have to install OpenMPI, one of the existing MPI libraries. And if you followed the instructions in part 1 of this series, then you already have SSH correctly configured in your computers.

This is a series of posts with the steps we are using to set up an internal cluster for bioinformatics using MPI and PBS for distributed jobs. Our goal with this series is help other nerds setting up similar environment. This cluster is not public yet, and we are using for development of BioUno. At moment we are writing code to integrate our Jenkins with MrBayes and Structure.

In this first post, we will see how to configure the network for each machine be able to see the other one, and how to configure SSH for connecting to the other nodes in the cluster. If you already know MrBayes and Structure, skip the Introduction and go to the basic network configuration topic. We assume you have a intermediary knowledge of Linux, as many instructions in this series are vague. We always reference the original tutorial that we used. This series may be edited to stay up to date or for improvements.