Connect from Windows

SSH access to the clusters on Windows can be achieved by using an application called an SSH client. We recommend using the PuTTY ssh client for Windows operating systems, which will provide secure connection to the cluster via SSH key authentication. We recommend that you do the full install, since you will need at least putty and puttygen.

Install PuTTY

Download PuTTY ssh client and install onto your local machine.

Generate key pair

A key pair is required to connect to a cluster. A key pair consists of a private key and a public key. The private key remains on your desktop/laptop and should never be shared with a anyone. Your public key is installed in ~/.ssh/authorized_keys on the cluster. In order for someone to access your account on the cluster, they must possess your private key and its associated passphrase.

When you install Putty, it should also install the Putty Key Generator. Open this application to create your key pair.

To generate a public and private key pair, you can accept the defaults in the next prompt and select “Generate”:


Move the mouse around the window to generate randomness for the keys:


Enter a secure passphrase/password for your keys and select “Save public key” and “Save private key”. Make a note of where you put the (2) files as you will be using them later. You can name the public key file “” and the private key file as “netid.ppk”. Examples are shown below.




Use the self-serve tool to upload the key to get access (only accessible on campus or through the Yale VPN). It may take up to 15 minutes after uploading for your key to be pushed to the clusters. You should never send the private key file (netid.ppk) to anyone!

Configuring PuTTY to connect to a cluster

When you start the PuTTY client, you should see the following:


In the following example, we will configure PuTTY to use your keys to connect to the Omega cluster. Note that you need to enter “netid@cluster”. In this case netid "ra359" will be connecting to “”:


On the right side of the configuration tool, select “SSH” then “Auth”. Then browse to your privatekey file (netid.ppk) then select Open.


Give the session a name and save it.


To connect to Omega, you can open PuTTY and simply double-click the name “omega” under Saved Sessions. Once you enter your passphrase you will be logged into Omega. Note that you will see the following prompt the very first time you log in:


Select yes to store the server key on your desktop.

Adding connections to PuTTY

To configure PuTTY to connect to another cluster, we can load the Omega sessions and modify it. In this example, we will add a new connection to the Grace cluster.

  1. Start PuTTY
  2. Select “omega”
  3. Select “Load”
  4. Modify the hostname to say “”
  5. enter “grace” in “Saved Sessions”
  6. select “Save”


Now you should see (2) available sessions when you start PuTTY. Simply double-click “omega” or “grace” to connect.


The hostnames of all the login nodes can be found here.

of typing in your passphrase over and over?

PuTTY provides a tool called “Pageant” which stores your passphrase in memory. To use this tool:

Start Menu -> All Programs -> PuTTY -> Pageant


You will see a small icon on the bottom right. Right click on the icon and select “Add Key”:


Browse to your private key (netid.ppk) and add it. After entering your passphrase you will no longer need to enter it for new PuTTY sessions.

Change Your SSH Key Passphrase

If you are using PuTTY, on Microsoft Windows, run PuTTYgen:

Start Menu -> All Programs -> PuTTY -> PuTTYgen -> Generate

Load your existing private key:

After loading the key, enter your new passphrase and save the private key.

If you forget your passphrase, it cannot be recovered. Instead, you will need to generate and upload a new ssh key pair.

How to Get a Graphical Interface (e.g. MATLAB)

The clusters are command line only. However, it is possible to configure Putty to allow specific applications (e.g. MATLAB) to send windows across the ssh connection. To get this functionality, we recommend you download and install XWin32. Then follow our X11 Forwarding Guide here.