Welcome to the Mykopat Grid Wiki

What is the Mykopat Computing Grid?

The computing grid has been setup for users to be able to analyse very large genetic data sets, and other analysis requiring long computing times on Linux systems. A grid of computers is essentially a number of computers linked together by a common management software. The management software delegates how the job requests should be handled by the computer resources.

Currently our grid consists of five computers available around the clock for long running high-resource jobs. Four of these have 32 GB RAM, while the last is equipped with 82GB RAM. In addition to this we are also adding normal desktop computers as a part of the grid during non-office hours. Currently this adds somewhat more than 33 extra cores for short-running low-memory tasks.

How to log in: 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.
3. There is also an option to start a Remote Desktop on the grid.

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.

Projects

You should register for a project before running analyses on the grid. This will give you a project directory available for all members, as well as provide a fair sharing of run time on the grid. Without any project assigned, the priority of your grid jobs will be very low.

There are some commands related to projects described on the ProjectCommands page.

In short:

• All project files should go into the project directory (/proj/project-name)
• Before cd:ing into the project directory, use the proj command your role into a member of that project (e.g. once logged in proj my-project-name and the cd proj/my-project-name)

Frequently Asked Questions

Go here to find out information about common problems (for example: installing software in your local folder)

Project Web Services

For each project a number of WebServices are available to use. These include:

• Project web folder
• Subversion for version control of project files
• Trac for project documentation (includes a wiki like this, issue handling and a nice browser for subversion)

Installed Software

Here we have a list of installed Software. On these pages, you are encourage to add comments on how the software works (RAM needed, Runtimes etc.) as well, if you think the program is good for the needs specified in the description (here and the software homepage). You might also want to check the OtherSoftware page for hints about software which is better run from your account.

Technical documentation for Administrators is found in the Admin section of the wiki.