SSH setup (Windows)

Secure Shell (SSH) is a way to login to remote computers securely as all data is encrypted in both directions between the local computer (your laptop) and the remote computer (Abacus 2.0).

Using SSH keys is an even more secure way to use SSH to access a remote compute as there is no password exchange between the local and remote computer. An SSH key pair is generated on the local computer. The key pair consists of a private key which stays on your local computer and a public key which must be uploaded to the remote computer.

SSH using SSH keys is the only way to get remote access to Abacus 2.0. The steps below walk you through how to generate your own SSH key for access to the cluster.

This is our guide for Windows users. Linux and Mac users should instead look at our SSH guide for Linux/Mac users.


For Windows users, we recommend using either MobaXterm or PuTTY to access Abacus 2.0.

  • MobaXterm: MobaXterm includes a lot of extra features compared to PuTTY, including easy GUI file transfers and X11 forwarding.

    The free version of MobaXterm is enough for most users.

  • PuTTY: PuTTY is probably the most popular Windows SSH program. PuTTY consists of several smaller binaries, including in particular putty.exe (used to actually do ssh), and PuTTYgen (used to generate SSH keys).

    We suggest to use the PuTTY Windows MSI installer. which includes all programs.

Before continuing to the next step, you should download and install either MobaXterm or PuTTY.

For data transfers to Abacus 2.0, see the Data Transfer Section.

Creating a SSH key pair

The first step is to create a SSH Key pair.

  • MobaXterm: Launch MobaXterm, and select Tools / MobaKeyGen (SSH key generator) in the menu.

  • PuTTY: Launch the PuTTYgen key generation program.

In both cases you get a window similar to the following:

PuTTYgen default

To create a new key suitable for Abacus 2.0, you should leave the default parameters at SSH-2 RSA and a keylength of 2048 bits. Click Generate to generate a new key. After they key has been generated the screen is updated with information on the new key:

PuTTYgen after key generation

Add a key comment, e.g., Office PC, and write a strong passphrase to guard the key. Finally, save the two parts of the key. For both parts of the key pair, we suggest saving them in a folder you can easily find again, e.g., a subfolder of your main Documents folder.

  • Public key: This is the public part of the key which you must upload the Abacus admin home page.

    The easiest way to get a the public key in the format suitable for Abacus 2.0 is to copy+paste the content of the frame titled Public key for pasting into OpenSSH authorized_keys file. Highlight+copy everything in the frame to the clipboard. Next, open Notepad and paste the contents. Everything must be in one (very long) line. Save the contents in a file with the extension .txt for easy access later, e.g., id_rsa_pub.txt.

    NOTE: Clicking Save public key will not save the public key in a format suitable for Abacus 2.0.

  • Private key: This is the private part of the key which stays on your own computer.

    Click Save private key to save the private key in "PuTTY format". For easy access later, save this in a file with the extension .ppk, e.g., id_rsa.ppk.

  • Private key (OpenSSH format): If you plan later to use MATLAB over ssh (as explained here), you must also save the private key in OpenSSH format as MATLAB cannot use a private key in ppk format. To do this, select Conversions / Export OpenSSH key in the menu, and export+save the key.

Note that you can use the same private+public key pair on multiple computers and to access many other clusters apart from Abacus 2.0.

Add the public SSH key to your Abacus account

Sign in to our admin home page

Go to your User's page and select Add SSH key. Open the public key file you created earlier in e.g. Notepad and copy the contents of the file using Ctrl-C. Next, paste the key to the public key box on the Add SSH Key page in your browser, and click Add key.

It is very important to copy the public key exactly as it appears. This is something along the lines of the following (with everything appearing in one very long line).

unw== Office PC

You should expect up to 15 minutes delay for the new key to be effective on the cluster, i.e., wait a few minutes before trying whether everything works as expected.

Connecting to Abacus 2.0

After uploading the key and waiting some minutes (up to 15 minutes), you are now ready to login using your new ssh key.

Connecting to Abacus 2.0 using MobaXterm

Start the main MobaXterm program. A window similar to this appears. Note that you can skip the first many steps after you have completed this the first time.


  • In the top left corner, click Session, and a new window appears. Fill out a few details:

    • Remote Host:
    • Username: Your username on Abacus, e.g., testuser
    • Use private key: Select the private key you generated earlier, e.g., id_rsa.ppk.

    Finally, click ✓ OK.


  • You have now connected to Abacus.

    If you get the error: Disconnected: No supported authentication methods available (server sent: publickey, hostbased), you did probably not wait the required 15 minutes before trying to login. Try again in a few minutes.

    Note that you have a file browser to the left side which can be used to copy files to and from Abacus.


Next time, you can open a connection to by simply using the link to on the first page of MobaXterm.

Connecting to Abacus 2.0 using PuTTY

Start the main PuTTY program. A window similar to this appears. Note that you can skip the first many steps after you have completed this the first time.

Putty start

  • Select Connection / SSH / Auth in the menu on the left, and select Browse... to locate the private SSH key you saved earlier.

Putty SSH key

  • Next, go to the submenu Connection / Data, and set the user name you selected to use on our system in Auto-login username:

Putty username

  • Finally, return to the main Session submenu, and write the ssh host name
  • Save this as a PuTTY Saved session to skip the previous steps at future logins, by writing e.g., Abacus in the Saved sessions box, and clicking Save.

Putty hostname

  • In the future, you can simply double click Abacus to load all the settings.
  • Now to login, click Open. You will be asked for the passphrase for your SSH key before you are allowed to login.
Using username "testuser".
Authenticating with public key "Office PC"
Passphrase for key "Office PC":
    _    _                            ____    ___
   / \  | |__   __ _  ___ _   _ ___  |___ \  / _ \
  / _ \ | '_ \ / _` |/ __| | | / __|   __) || | | |
 / ___ \| |_) | (_| | (__| |_| \__ \  / __/ | |_| |
/_/   \_\_.__/ \__,_|\___|\__,_|___/ |_____(_)___/

Welcome to DeIC National HPC Centre, SDU

If you get the error: Disconnected: No supported authentication methods available (server sent: publickey, hostbased), you did probably not wait the required 15 minutes before trying to login. Try again in a few minutes.

Data transfer

To copy files to and from Abacus we suggest using either MobaXterm, pscp (command-line, part of the PuTTY package) or WinSCP.

In all cases must use the SSH key you uploaded earlier.

SSH Tips

Putty key agent: Pageant

For ease of use, you can use the Putty key agent Pageant to store the passphrase of your private key. Then you only have to write the passphrase once every time your computer is booted.

After installing Pageant via the (PuTTY MSI installer you simply double-click on the private key, and enter the passphrase for the key.