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.

What ho lads!

Few days ago I was talking with Olivier Renault [1] about few things that he needs to deploy JinFeng [1] using a non-interactive command line. JinFeng is an integration and testing platform built on top of many Open Source tools, like TestLink [2] and Jenkins [3]. One of the features he needs is Test Steps in TestLink XML-RPC API (I’m working on this, and hopefully will be able to provide a patch for TestLink 1.9.4).

Tell me about writing a specific title. This is my first entry here in TupiLabs. Today I will show you how to configure Jenkins Git Plug-in, to retrieve sources from a private repository hosted at BitBucket. Phew. Ah, and all this using a Windows server.

TL;DR: ssh -vT <host> displays where it is looking for your .ssh directory. Probably you will want check permissions and the %HOME% environment variable too. In case your job is getting stuck, click here to skip the introduction text.

Motivation

• At TupiLabs, we have repositories hosted at GitHub (public repositories) and BitBucket (mix of public and private repositories).
• We use Jenkins for many activities. Not only as a build server, but as a function in our development environment. We will talk about that later ;-)
• We use Jenkins, Mac and Windows for development.
• We have jobs running at Linode with Ubuntu+Jenkins+Git Plug-in+BitBucket.
• There aren’t many resources for configuring Jenkins and BitBucket in Windows.
• I have a good friend of mine who would like to read about it. Heck! That’s enough to write about it :-D