It’s time to get your feet wet and learn how to use GenomeDK! The documentation is organized such that it can be used in two ways:

• You can read it from beginning to end like a book to familiarize yourself with GenomeDK and learn how to do basic things like submitting a job and working with projects.
• You can use it as a reference to look up the solution for specific questions you may have, such as what is the command for requesting a new project folder? Or, how do I get passwordless authentication working?

If you’re new to GenomeDK you will most likely want to read the documentation as a book. As you become more experienced you will more often use it as a reference.

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

Conventions¶

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.