SURFSARA@WUR

Welcome to the portal for large scale computing at WUR. We have free facilities for computing in the life sciences!

Harm Nijveen, Jan van Haarst en Pjotr Prins.

What is it?

The Life Science Grid is a network of computer clusters at different dutch universities maintained by SARA. The Wageningen UR node of consists of two machines (running Centos 5.8) with each 64 cores, 256 GB memory and 6 TB scratch disk.

Using the grid

Using the grid is not as easy as using your own linux server: things like creating the right software environment (libraries etc.), starting jobs, splitting up the work and collecting the output require some or a lot of work. To get an idea, have a look at this wiki.

If you want to use only the 2 local machines (128 cores), jobs can be submitted locally using PBS (qsub).In this way, you will use them as a small cluster, without the overhead of the grid software, and using the shared local HDD scratch space.

A limited number of applications are available via a web interface, they can be used through the webinterface. Preferably you do not use them via a webbrowser but with command line tools like 'curl'. It is possible to add applications for yourself and others to use! Contact gridsupport for more information on how that works

Access

The use of this cluster and similar clusters at other universities in the Netherlands is free for life science researchers. To get access you need a grid certificate which can be requested here (using jGridStart). Then you should become a member of the lsgrid VO (virtual organisation, see wiki), and get a user account on the local cluster.