Laboratory for Scientific Computing, University of Cambridge

CSD3

Using CSD3

CSD3 is the University of Cambridge supercomputer/cluster. If you need more computational resources than are available on the CSC network, then you will need to apply to use this.

The main web-pages are at www.csd3.cam.ac.uk

The form you need to fill in for access is at: https://www.csd3.cam.ac.uk/services/applying-for-resources.

Your Principal Investigator is usually your supervisor or head of group, or the Director of the MPhil/CDT if appropriate.

Details on using CSD3 are then at: http://www.csd3.cam.ac.uk/using-clusters.

Virtual desktop access to CSD3

There are various ways to get optimised graphical output from CSD3. The easiest (and slowest) is to use ssh -X.

The next best option is to visualize on your local machine only, copying data across. This is at the expense of data transfer time and storage on your local desktop.

If your visualisation program permits, you may be able to use it to launch a compute server on CSD3 which connects to a visualisation server on your local desktop. Thus, the data but not the 3D graphics is transferred. An example of this is VisIt.

The final option is to use a virtual desktop. This is not completely working at present.

On CSD3, log in to login-gfx1 or login-gfx2 (you may need to request access from support@hpc.cam.ac.uk), and run:

$ vncserver
Desktop 'TurboVNC: login-e-19:5 (pmb39)' started on display login-e-19:5

Starting applications specified in /home/pmb39/.vnc/xstartup.turbovnc
Log file is /home/pmb39/.vnc/login-e-19:5.log

Now set a local display password on CSD3:

$ vncpasswd 
Password: [My Password; different from CSD3 one.]
Verify:   [Type again.]
Would you like to enter a view-only password (y/n)? n

On your local desktop, run:
```
/lsc/opt/TurboVNC-2.1.1/bin/vncviewer -via pmb39@login-e-19.hpc.cam.ac.uk login-e-19:5
```
where the login node and display (login-e-19:5) come from the output of vncserver above. If you are not on an LSC/CSC desktop, you can download TurboVNC from SourceForge.
The previous command will give you a window containing a virtual desktop, which is running on the CSD3 node. The performance is much better than using ssh alone.
In order to run GL-aware applications, you must use vglrun by first loading its module:
```
module load vgl/2.5.1/64
```
and then prefixing it on all graphical programs:
```
vglrun glxgears
```
Once you have finished using the virtual desktop, run
```
vncserver -kill :5
```
on the CSD3 node.
A better explanation may be found at CSD3 help.