Getting started

Note

If you don’t know what a closed zone is, or you know that you’re not running in one, skip all red boxes like the one below. Most users on GenomeDK are not in a closed zone.

Closed zone…

Running in a closed zone means running in a restricted environment. In some cases, this means that you must use special commands or follow special instructions for certain things. This will be noted in red boxes like this one throughout the documentation.

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

We have several types of users. In most cases you’ll want a normal user. To request this, fill out the form for normal users.

If you need a special user, e.g. for the iPSYCH part of the cluster, fill out the form for special users instead.

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

Connecting to the cluster

Closed zone…

Follow the instructions here.

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.

Note

Access to GenomeDK is restricted to the internal network at Aarhus University. However, if you need access from abroad or for some other reason can not connect connect from AU, feel free to contact us to get whitelisted.

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:

[fe1]$ 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.

Warning

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

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/id_rsa.pub.
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.+.             |
|.++.             |
+----[SHA256]-----+

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 login.genome.au.dk

Replace PUBLIC-KEY-PATH with the path to your public key. 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 USERNAME@login.genome.au.dk

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:

[fe1]$ ssh-keygen

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

[fe1]$ cat ~/.ssh/id_rsa.pub >> authorized_keys

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