Before you start reading the documentation and using GenomeDK, there’s a few things that you should know.


You will be jumping a lot between different computers. This includes your own computer, the frontend node, and various compute nodes.

Commands that need to be run on your own computer will look like this:

[local]$ echo hello

Note that the prompt says local in square brackets. When you need to run a command on the frontend node, the prompt will instead say:

[fe-open-01]$ echo hello

Here, fe-open-01 is the name of the frontend node. If you need to run a command on a compute node that you started an interactive job on (more about this later), it will be shown like this:

[s03n11]$ echo hello

In this case the compute node is s03n11, but anything that has the format sXXnYY is a compute node.

Learning to use the shell

When interacting with the cluster you will be using a shell on a Linux/UNIX system. If you are not familiar with these concepts we recommend the Shell novice tutorial from Software Carpentry.