Accessing the HPC cluster(s)


Users are allowed to access the cluster only through the login node. No direct access to the computation nodes is allowed. There are two ways to access to the cluster:

ssh-access using a terminal requires a basic knowledge of UNIX commands.  An advantage of ssh-access is that it does not require much bandwidth.

The ThinLinc client gives access to the HPC, and your data, through a Graphical User Interface. It requires a larger bandwidth.

 Note:

  • both methods provide a secure authentication mechanism, so they are both “safe”
  • both act as interfaces to the server-side, so there is no difference in the resources that one can access, the software installed, and the data one gets access to.

 

Command line: SSH access

Once you have a terminal emulator and a ssh-client installed on your own computer you have all you need to login to the system. It is installed by default on GNU-linux and macOS, or through third party software like PuTTY, KiTTY, Cygwin, or similar on Windows. In the following we assume that you have are using a terminal. At the prompt, type:

ssh userid@login.gbar.dtu.dk

or

ssh userid@login.hpc.dtu.dk

where userid is your DTU username, and login.gbar.dtu.dk and login.hpc.dtu.dk are two of our login-nodes. When prompted write your password (some more information can be read here). This way you get access to the login node. Notice that this is a special node, meant only for logging-in, and NOT for running any application. Most of the applications are not even installed on the login node.

You can then switch to another node (dynamically assigned by the system) typing
qrsh
to have access to the hpc_intact queue, that is meant for interactive jobs, or
linuxsh
that gives you access to the nodes of the app queue. From here, you can always access your data, via unix commands, start all the program installed on the system, prepare and submit jobs.

You can also run graphical application, and export the graphical interface to your private computer, if you add the -X option to your command line before logging in, i.e

ssh -X userid@login.gbar.dtu.dk

and then, once logged in:

qrsh -X

or

linuxsh -X

However, using graphical programs remotely usually requires a fast internet access, and it is in any case slow.

Note: after issuing the qrsh or the linuxsh command, you end up on one of the available nodes. Be aware that there could be other users on that specific node.

 

Graphical Interface: ThinLinc

Start the application, and when prompted fill the three required fields:

ThinLinc Access prompt

ThinLinc Access prompt

Server:            thinlinc.gbar.dtu.dk
Username:     DTU userid
Password:      DTU password

Remember that the userid and password are case-sensitive. You can also have a look at the options to customize the program behaviour.
After the log-in, ThinLinc provides you with a traditional desktop interface. The default is the Xfce window manager. Click on the Applications menu button (top left corner) or right-click on the desktop to activate menus from where you can choose the application you need, and the terminal.

ThinLinc xfce screenshot

ThinLinc xfce screenshot

Note: You are on a local terminal if your prompt starts with th, followed by a number and by your username. This does not grant you access to the HPC nodes, and you should not logon or run programs here.

If you want to access one of the HPC nodes, you need to open a special terminal, that you can find under Applications Menu -> DTU-> xterm (application node), as shown in the screenshot. In this way you are assigned a slot in one of the application nodes (same as issuing the linuxsh command). If you want to switch to one of the interactive nodes, type qrsh.

You can also access an application node or an interactive node by typing the command linuxsh or qrsh respectively in a local terminal.