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.

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.

There are three ways to connect to GenomeDK:

• Connecting with SSH (open zone only)
• Connecting with GenomeDK Desktop (open and closed zones)

In any case, you must first prepare for two-factor authentication.

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 via SSH (open zone only)¶

On Linux, open the terminal of your choice. On macOS, you may use Terminal.app 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 USERNAME@login.genome.au.dk

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

[local]$ ssh.exe USERNAME@login.genome.au.dk

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:

gdk-auth-show-qr

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

Connecting via the GenomeDK Desktop (any zone)¶

GenomeDK Desktop provides access to a graphical desktop environment (virtual desktop) directly in your browser. For closed zones, this is the only way to connect to GenomeDK.

• Go to the GenomeDK Desktop and log in with your usual GenomeDK credentials.
• If this is your first login, you will be guided through the process of setting up two-factor authentication.
• Choose the service you wish to connect to (for example “Frontend - Open”, to access the frontend in the open zone) or launch a desktop with dedicated resources by choosing “Start a new desktop…”.

Please note that desktops launched on a frontend should not be used for heavy computations.

You can learn more about using the Desktop here.

I forgot my password¶

If you forgot your password, send an e-mail to support to request a password reset. You will receive a password reset mail with a new, temporary password.

You should change the temporary password immediately after logging in (see the next section).

Change your password¶

You may change your password at any time using the gdk-auth-change-password 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.

Public-key authentication¶

A public-key setup is a way to be able to access one computer from another computer with SSH, but without typing a password every time you want to log in.

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

[local]$ ssh-keygen -t ed25519 -q -N ""

This will generate a private/public key-pair with no password. If you have a key already, you can just use that (the command will warn you if you do).

Now copy the public key to GenomeDK:

[local]$ ssh-copy-id -i ~/.ssh/id_ed25519 <username>@login.genome.au.dk

You will be asked to enter your password for the cluster to transfer the public key.

You should now be able to log in to the cluster without typing your password. Test this by runnning:

[local]$ ssh <username>@login.genome.au.dk

You should not be prompted for a password this time.

Using a terminal multiplexer¶

Using a terminal multiplexer allows you to keep your SSH session open, even when you disconnect from the cluster. You can even reconnect from a different computer and get your session back. This is especially useful when downloading large amounts of data, as you can keep the download running even if your connection to GenomeDK is lost, or if intentionally logging out.

We recommend that you use either tmux or screen.

• tmux
• screen.

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.