Welcome to our Computing Grid What is the Mykopat Computing Grid? The computing grid has been setup for users to be able to analyse very large genetic data sets. A grid of computers is essentially a number of computers linked together by a common management software controller. The management software delegates how the job requests should be handled by the computer resources. Currently our grid consists of 50 cores and more than 210 GB of RAM.

How to Login: There are several ways to access the grid:

1. From Macs and other unix-like computers you can login using the ssh-command in the terminal. You will then interact with the grid though commands in the terminal.
2. From Windows computers, you can login using Putty to login to a terminal session. You will then interact with the grid though commands in the terminal.

Login command- click here

Don't forget to run your jobs through the queue system, otherwise they might just be stopped by the system when the default resource limits are exceeded.

How to get into your project folder: To get into to your project folder each time you have login, you must first call the project folders name by using the command:

proj project name

(this enables the project, essentially changing your users group membership to the project and setup environment variables to tell the queue system to access that project)

Your project folder can be found by:

cd proj/project name

Please note: when submitting project names, please keep make sure they are no longer than 7 characters.

Be advised, all project names with have the prefix mykopat-"your project name here"

How to submit jobs using the Queue System: To share the computer resources in a fair manner, all jobs have to be run through a queue system. This ensures that jobs are run on appropriate computers and also that no computer is over-loaded. There are a lot of information available on the net on how to submit jobs using Sun Grid Engine. The introduction found here is very brief, and is only to get you started.

How to load Modules: In our system, we have starte to use Module files for all the programs. Module files allow us to keep older versions of software and use them based on their version names. In order to run a program on the grid you must first load the module for that software. For example:

module load R

• this will load the module for the statistics program R and allow you to run the program by now entering just R at the command prompt. If you wanted to run an earlier version of R the module may look like this:

module load R2.1

For legacy software (like SFFiles you need to load the module mykopat.

module load mykopat

NOTE - You need ot have these module load statements in your scripts as well.

Available Software: Here you will find a list of the current software and links to their homepages for manuals and usage instructions.

Some Basic Linux Commands: Here you will find a list of some basic linux commands to get you started. You will also find some of the basic commands for Sun Grid Engine (our queue system) that maybe helpful.

Some Basic SGE Commands: Here you will find a list of some basic Sun Grid Engine commands (our queue system) that maybe helpful.

Frequently Asked Questions: Here you will find a list of common questions on how to use the grid. You will also find information about common problems (for example: installing software in your local folder)