Getting started

This page will tell you everything you need to know to get up and running on GenomeDK. However, we assume that you have some experience with the command line/terminal.

Get access to the cluster

You should check out our terms of service.

To request a user, fill out the user request form.

Once you’ve been granted access, you’ll receive an e-mail. You’ll then be able to connect to the cluster.

Cite us!

We provide GenomeDK as a resource to research. If you publish results from computations performed on GenomeDK, it is important that you acknowledge/cite GenomeDK in your publications. We recommend phrasing it like this:

Some/all of the computing for this project was performed on the GenomeDK cluster. We would like to thank GenomeDK and Aarhus University for providing computational resources and support that contributed to these research results.

Connecting to the cluster

GenomeDK is divided into multiple zones. Most users belong to the open zone. If you’re in doubt about which zone you belong to, check your account confirmation e-mail. If it doesn’t mention a specific zone, you belong to the open zone. If still in doubt, please contact support.

Prepare for two-factor authentication

You must first install an authenticator app on your phone (if you don’t already have one). Popular authenticator apps include:

  • Microsoft Authenticator
  • Google Authenticator
  • FreeOTP

All of these apps will allow you to scan a QR code and generate tokens for future logins.

Connecting to the open zone

On your first login, you must set up two-factor authentication. If you do not set up two-factor on the first login, you will not be able to access your account. Read the instructions to the end before logging in for the first time.

On Linux, open the terminal of your choice. On macOS, you may use which can be found in the /Applications/Utilities folder. In both cases, you should now be able to log in to the frontend by typing this command:

[local]$ ssh

On Windows, you have multiple options. On Windows 10, open PowerShell. You should then be able to type:

[local]$ ssh.exe

Older versions of Windows do not include the ssh command and thus you will need to install an alternative yourself. We recommend MobaXterm.

Set up two-factor

You must now set up two-factor authentication. Run the following command on GenomeDK:


This will show a QR code in your terminal. Open the the authenticator app on your phone and scan the QR code.

Connecting to a closed zone

On your first login, you must set up two-factor authentication. If you do not set up two-factor on the first login, you will not be able to access your account. Read the instructions to the end before logging in for the first time.

Download and install the remote desktop client for your operating system on your local machine.

Download the connection file for the zone you wish to connect to:

Using the login information received in your mailbox. Login by entering your username and password.

Assuming you entered correctly you will get access to the virtual desktop.

Set up two-factor

Open the the authenticator app on your phone and scan the QRCode.png located on your NoMachine desktop. From now on you will need to generate a one-time password with the authenticator app every time you log in.

Changing your password

This is important! Since e-mail is not secure, someone may get access to the password that we sent to you. Thus, you should change it immediately after logging in. Run the command:

[fe-open-01]$ gdk-auth-change-password

It will ask you for your current password, then ask what your new password should be. Finally, it will ask you to confirm your new password by typing it again.

Do not use passwd, yppasswd or ipsych-passwd to change your password. These commands won’t work in all cases or at all.

I forgot my password

Send an e-mail to support to request a password reset.

Public-key authentication

A public-key setup is a way to be able to access one computer from another computer securely, but without typing a password every time you want to log in. This is practical if you often log in to the frontend of the cluster. However, we can also use a public-key setup to allow you to access any compute node on the cluster from the frontend without typing your password every time. This is especially handy when you’re debugging a problem on the compute nodes.

Here, we will first set up a public key for accessing the frontend. Then, we’ll set up a key for accessing compute nodes from the frontend.

On your own computer, open the terminal of your choice and type:

[local]$ ssh-keygen

You’ll be asked several questions. The defaults are just fine, so just press the Enter for all of them. Make sure to leave the passphrase empty!

The output should look similar to this:

Generating public/private rsa key pair.
Enter file in which to save the key (/Users/das/.ssh/id_rsa):
Enter passphrase (empty for no passphrase):
Enter same passphrase again:
Your identification has been saved in /Users/das/.ssh/id_rsa.
Your public key has been saved in /Users/das/.ssh/
The key fingerprint is:
SHA256:XxSd35yPd1bUoIJQDBCAvxDu+pB25ipYpcmp+VEh5JE das@jorn
The key's randomart image is:
+---[RSA 2048]----+
| .+oooo+.   ...o.|
|ooE.   ...   oo o|
|.oo .   . . o  +o|
|......     o   .=|
|.o *.   S   .  .o|
| oB.     . .  . =|
|==.o      .    o.|
|B.+.             |
|.++.             |

Note the path of the public key (on the highlighted line). To copy the public key to the cluster, run:

[local]$ ssh-copy-id -i PUBLIC-KEY-PATH

Replace PUBLIC-KEY-PATH with the path to your public key and USERNAME with your cluster username. You will be asked to enter your password for the cluster. You should now be able to log in to the cluster without typing your password. Test this by runnning:

[local]$ ssh

You should not be prompted for a password.

Now, set up public-key access to all compute nodes. On the frontend, run the same ssh-keygen command as before:

[fe-open-01]$ ssh-keygen

Again, just press Enter to use the default values (and do not type in a password). Then run:

[fe-open-01]$ cat ~/.ssh/ >> authorized_keys

You will now be able to SSH between compute nodes without typing a password.

Using a terminal multiplexer

Using a terminal multiplexer allows you to keep your session open, even when you disconnect from the cluster. You can even reconnect from a different computer and get your session back.

We recommend that you use either tmux or screen.