From HPC

Revision as of 14:35, 17 October 2008

Accessing the cluster

You need to have your LSHTM account added to the list of valid users of the cluster. Firstly join the HPC mailing list and then email Steven Whitbread or Dan Johnson with your username, department and a brief description of what you plan to user the cluster for.

Once you have a valid user account on the cluster

You username and password will be the same as you normal LSHTM network user details. You will have a seperate home directory, you will not be able to directly access your H:\ drive.

Access to the cluster is via SSH (secure shell) and to copy files to and from the cluster you will need to use SFTP or SCP. It is also possible to access GUI applications on the cluster i.e. Editors, Netbeans, Stata. It is important to note that the gui apps are only their to help you make modifications, etc. to your jobs, not to actually run the job.

The server you need to connect to for all the above is head.gecko.lshtm.ac.uk. Please below for more specific instructions.

SSH

Windows

On windows you will use a piece of software called putty. This will provide you remote terminal access to the cluster.

Putty is available under the communications folder in "Novell Delivered Apps" or you can download it from http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html

Start putty

In the box labeled hostname type: head.gecko.lshtm.ac.uk

Make sure the ssh radio button is selected.

Now if you want to save these settings, type a suitable name in Saved sessions box (hcpc, cluster or gecko for example) and click save. From now on it will appear in the list of saved sessions. If you want to amend the saved session, highlight it, click load, make your changes and then click save.

Press connect to start your ssh session.

Note: If this is the first time you have connected to the cluster you will have to confirm that you trust the servers host key. The host key is to unique to each server. You should only have to do this once.

When prompted enter you username and password.

You will now be in your home directory.

Linux and Mac OS X

Open a terminal.

Enter the following (replace username with your actual username)

ssh username@head.gecko.lshtm.ac.uk

Enter your password.

Moving files to and from the cluster

Two methods are available: SFTP and SCP

Windows

I recommend WinSCP for managing your files if you are using windows. It is available in communications folder in "Novell Delivered Apps" window or can be downloaded here http://winscp.net/

Open WinSCP

Enter the hostname: head.gecko.lshtm.ac.uk, username and password.

Click connect.

Note: If this is the first time you have connected to the cluster you will have to confirm that you trust the servers host key. The host key is to unique to each server. You should only have to do this once.

Your local files will be on the left side and your files on the cluster will be on the right side. You can now drag and drop files between the two panels.

Mac OS X

I would recommend you use either CyberDuck ( http://cyberduck.ch/ ) or Fugu ( http://rsug.itd.umich.edu/software/fugu/ ) to access your files on the cluster.

Fugu

Open fugu

Enter the hostname: head.gecko.lshtm.ac.uk

Enter you username and password.

Your local files will be on the left side and your files on the cluster will be on the right side. You can now drag and drop files between the two panels.

Linux

If you are using KDE or GNOME, you can open the file browser and in the address bar type sftp://head.gecko.lshtm.ac.uk

You should then be asked for you username and password.

Click connect.