Software Requirements
The CERES cluster has a Linux operating system so you will need an SSH client in order to access the cluster. Depending on which operating system you are using on your own computer, you may need to download an SSH client:

Linux has an SSH client built-in by default. Open a terminal (Ctrl-Alt-T on most distributions or via the main menu). Different variants of Linux will often refer to terminals as "Gnome Terminal", "KDE Terminal", "Command Terminal" or something similar.

MacOS also has an SSH client built-in. You can access it under Applications=>Utilities=>Terminal.

Windows does not include any SSH clients so you may need to download one. There are a few available including MobaXterm, Cygwin and PuTTY. Of the three, we recommend MobaXterm as it has a built-in X-Manager (needed if you need to run graphical interfaces). There are two versions, installable (requires admin rights on your PC), and Portable (can be run without installing).

If you are using a lab PC or your office workstation at UoE, you should find both MobaXterm and PuTTY either within your systems application menu or via the University Software Hub and shouldn't need to install one. This tutorial assumes Windows users are using MobaXterm as it uses SSH and SCP from the command line just as Linux / MacOS users would.

Note the expression "local workstation" (used from now on) refers to the computer you are using, be that your desktop PC / Workstation, a Lab PC, your own laptop etc.

Throughout this practical / tutorial, you will see three types of boxes containing code:

boxes of this colour are commands you should type on the command line, sometimes they will contain parameters you will need to change, these will be between < & > characters, for example "<username>" means replace that (including the <> characters) with your username (or whatever else the parameter represents.


boxes of this colour contain worked examples, often showing what you should see when you use the commands in the other boxes. The commands typed in the example will be in bold.

and finally

and boxes of this colour contain background or useful information to give what you are doing some context.

Pay particular attention to the Important Aspects of Linux panel below, especially if you are unfamiliar with Linux.

Once you have an SSH client, open a terminal window within that client then proceed to the next step.

Important Aspects of Linux
The cluster uses the Linux operating system (specifically Centos) which has some important differences to other operating systems you may be used to using. Some important things to remember with Linux:
  • all command and file/directory names are case sensitive so a file called GenomeData.dat is not the same as genomedata.dat - the system will treat these as separate files.
  • There is no undelete in Linux so you need to be careful when deleting files and directories, particularly with wildcards.
  • If you specify ".." as part of any path (be it a parameter or file path), this is treated as a reference to the parent directory (e.g. "../pfit.txt" refers to the file pfit.txt located in the parent directory to the current directory).
  • Similarly, "." refers to the current directory (e.g. "./pfit.txt refers to the file pfit.txt in the current directory).
  • Another special character is ~. When used as part of a path, it refers to your home directory, so ~/data refers to the data directory in your home directory.
  • Filenames starting with a "." character are treated as system files and hidden so they will not show up in a normal directory listing.
  • You can recall previous commands using the up and down cursor keys
User Account
Before starting, you need to have an account on CERES. UoE users do not automatically get accounts on the CERES cluster, you will need to register for an account using the registration page if you do not already have a CERES account. If you are unsure whether you have an account or not, contact CERES Admin.