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Connecting to Cirrus

On the Cirrus system, interactive access can be achieved via SSH, either directly from a command line terminal or using an SSH client. In addition data can be transferred to and from the Cirrus system using scp from the command line or by using a file transfer client.

Before following the process below, we assume you have set up an account on Cirrus through the EPCC SAFE. Documentation on how to do this can be found at:

SAFE Guide for Users

This section covers the basic connection methods.

Access credentials: MFA

To access Cirrus, you need to use two credentials (this is known as multi-factor authentication or MFA): your SSH key pair, protected by a passphrase, and a time-based one-time passcode (sometimes known as a TOTP code). You can find more detailed instructions on how to set up your credentials to access Cirrus from Windows, macOS and Linux below.


The first time you log into a new account you will also need to enter a one-time password from SAFE. This is described in more detail below.

SSH Key Pairs

You will need to generate an SSH key pair protected by a passphrase to access Cirrus.

Using a terminal (the command line), set up a key pair that contains your e-mail address and enter a passphrase you will use to unlock the key:

$ ssh-keygen -t rsa -C ""
-bash-4.1$ ssh-keygen -t rsa -C ""
Generating public/private rsa key pair.
Enter file in which to save the key (/Home/user/.ssh/id_rsa): [Enter]
Enter passphrase (empty for no passphrase): [Passphrase]
Enter same passphrase again: [Passphrase]
Your identification has been saved in /Home/user/.ssh/id_rsa.
Your public key has been saved in /Home/user/.ssh/
The key fingerprint is:
The key's randomart image is:
+--[ RSA 2048]----+
|    . ...+o++++. |
| . . . =o..      |
|+ . . .......o o |
|oE .   .         |
|o =     .   S    |
|.    +.+     .   |
|.  oo            |
|.  .             |
| ..              |

(remember to replace "" with your e-mail address).

Upload public part of key pair to SAFE

You should now upload the public part of your SSH key pair to the SAFE by following the instructions at:

Login to SAFE. Then:

  1. Go to the Menu Login accounts and select the Cirrus account you want to add the SSH key to
  2. On the subsequent Login account details page click the Add Credential button
  3. Select SSH public key as the Credential Type and click Next
  4. Either copy and paste the public part of your SSH key into the SSH Public key box or use the button to select the public key file on your computer.
  5. Click Add to associate the public SSH key part with your account

Once you have done this, your SSH key will be added to your Cirrus account.

Time-based one-time passcode (TOTP code)

Remember, you will need to use both an SSH key and time-based one-time passcode (TOTP code) to log into Cirrus so you will also need to set up a method for generating a TOTP code before you can log into Cirrus.

SSH Clients

Interaction with Cirrus is done remotely, over an encrypted communication channel, Secure Shell version 2 (SSH-2). This allows command-line access to one of the login nodes of a Cirrus, from which you can run commands or use a command-line text editor to edit files. SSH can also be used to run graphical programs such as GUI text editors and debuggers when used in conjunction with an X client.

Logging in from Linux and MacOS

Linux distributions and MacOS each come installed with a terminal application that can be use for SSH access to the login nodes. Linux users will have different terminals depending on their distribution and window manager (e.g. GNOME Terminal in GNOME, Konsole in KDE). Consult your Linux distribution's documentation for details on how to load a terminal.

MacOS users can use the Terminal application, located in the Utilities folder within the Applications folder.

You can use the following command from the terminal window to login into Cirrus:


You will first be prompted for the passphrase associated with your SSH key pair. Once you have entered your passphrase successfully, you will then be prompted for your password. You need to enter both correctly to be able to access Cirrus.


If your SSH key pair is not stored in the default location (usually ~/.ssh/id_rsa) on your local system, you may need to specify the path to the private part of the key with the -i option to ssh. For example, if your key is in a file called keys/id_rsa_cirrus you would use the command ssh -i keys/id_rsa_cirrus to log in.

To allow remote programs, especially graphical applications to control your local display, such as being able to open up a new GUI window (such as for a debugger), use:

ssh -X

Some sites recommend using the -Y flag. While this can fix some compatibility issues, the -X flag is more secure.

Current MacOS systems do not have an X window system. Users should install the XQuartz package to allow for SSH with X11 forwarding on MacOS systems:

Logging in from Windows using MobaXterm

A typical Windows installation will not include a terminal client, though there are various clients available. We recommend all our Windows users to download and install MobaXterm to access Cirrus. It is very easy to use and includes an integrated X server with SSH client to run any graphical applications on Cirrus.

You can download MobaXterm Home Edition (Installer Edition) from the following link:

Double-click the downloaded Microsoft Installer file (.msi), and the Windows wizard will automatically guides you through the installation process. Note, you might need to have administrator rights to install on some Windows OS. Also make sure to check whether Windows Firewall hasn't blocked any features of this program after installation.

Start MobaXterm using, for example, the icon added to the Start menu during the installation process.

If you would like to run any small remote GUI applications, then make sure to use -X option along with the ssh command (see above) to enable X11 forwarding, which allows you to run graphical clients on your local X server.

Host Keys

Adding the host keys to your SSH configuration file provides an extra level of security for your connections to Cirrus. The host keys are checked against the login nodes when you login to Cirrus and if the remote server key does not match the one in the configuration file, the connection will be refused. This provides protection against potential malicious servers masquerading as the Cirrus login nodes. ecdsa-sha2-nistp256 AAAAE2VjZHNhLXNoYTItbmlzdHAyNTYAAAAIbmlzdHAyNTYAAABBBOXYXQEFJfIBZRadNjVU9T0bYVlssht4Qz9Urliqor3L+S8rQojSQtPAjsxxgtD/yeaUWAaBZnXcbPFl2/uFPro= ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABgQC4YJNc0yYfUPtiApGzzkwTYxUhFB1q1G2/vO8biwDL4W0LOcaBFCNTVst1IXQ6tZ9l0GfvlmYTb1LHYoTYLn5CyUL5KKS7X4FkhM9n2EExy/WK+H7kOvOwnWEAWM3GOwPYfhPWdddIHO7cI3CTd1kAL3NVzlt/yvx0CKGtw2QyL9gLGPJ23soDlIJYp/OC/f7E6U+JM6jx8QshQn0PiBPN3gB9MLWNX7ZsYXaSafIw1/txoh7D7CawsTrlKEHgEyNpQIgZFR7pLYlydRijbWEtD40DxlgaF1l/OuJrBfddRXC7VYHNvHq0jv0HCncCjxcHZmr3FW9B3PuRvBeWJpzV6Bv2pLGTPPwd8p7QgkAmTQ1Ews/Q4giUboZyqRcJAkFQtOBCmv43+qxWXKMAB7OdbjJL2oO9UIfPtUmE6oj+rnPxpJMhJuQX2aHIlS0Mev7NzaTUpQqNa4QgsI7Kj/m2JT0ZfQ0I33NO10Z3PLZghKqhTH5yy+2nSYLK6rnxZLU= ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIFk4UnY1DaS+LFSS8AFKbmAmlevxShN4hGpn+gGGX8Io

Host key verification can fail if this key is out of date, a problem which can be fixed by removing the offending entry in ~/.ssh/known_hosts and replacing it with the new key published here. We recommend users should check this page for any key updates and not just accept a new key from the server without confirmation.

Making access more convenient using the SSH configuration file

Typing in the full command to login or transfer data to Cirrus can become tedious as it often has to be repeated many times. You can use the SSH configuration file, usually located on your local machine at .ssh/config to make things a bit more convenient.

Each remote site (or group of sites) can have an entry in this file which may look something like:

Host cirrus
  User username

(remember to replace username with your actual username!).

The Host cirrus line defines a short name for the entry. In this case, instead of typing ssh to access the Cirrus login nodes, you could use ssh cirrus instead. The remaining lines define the options for the cirrus host.

  • Hostname - defines the full address of the host
  • User username - defines the username to use by default for this host (replace username with your own username on the remote host)

Now you can use SSH to access Cirrus without needing to enter your username or the full hostname every time:

-bash-4.1$ ssh cirrus

You can set up as many of these entries as you need in your local configuration file. Other options are available. See the ssh_config man page (or man ssh_config on any machine with SSH installed) for a description of the SSH configuration file. You may find the IdentityFile option useful if you have to manage multiple SSH key pairs for different systems as this allows you to specify which SSH key to use for each system.


There is a known bug with Windows ssh-agent. If you get the error message: Warning: agent returned different signature type ssh-rsa (expected rsa-sha2-512), you will need to either specify the path to your ssh key in the command line (using the -i option as described above) or add the path to your SSH config file by using the IdentityFile option.

Accessing Cirrus from more than 1 machine

It is common for users to want to access Cirrus from more than one local machine (e.g. a desktop linux, and a laptop) - this can be achieved through use of an ~/.ssh/authorized_keys file on Cirrus to hold the additional keys you generate. Note that if you want to access Cirrus via another remote service, see the next section, SSH forwarding.

You need to consider one of your local machines as your primary machine - this is the machine you should connect to Cirrus with using the instructions further up this page, adding your public key to SAFE.

On your second local machine, generate a new SSH key pair. Copy the public key to your primary machine (e.g. by email, USB stick, or cloud storage); the default location for this on a Linux or MacOS machine will be ~/.ssh/ If you are a Windows user using MobaXTerm, you should export the public key it generates to OpenSSH format (Conversions > Export OpenSSH Key). You should never move the private key off the machine on which it was generated.

Once back on your primary machine, you should copy the public key from your secondary machine to Cirrus using:

scp <user>

You should then log into Cirrus, as normal: ssh <user>, and then:

  • check to see if the .ssh directory exists, using ls -la ~
  • if it doesn't, create it, and apply appropriate permissions:
mkdir ~/.ssh
chmod 700 ~/.ssh
  • and then create an authorized_keys file, and add the public key from your secondary machine in one go:
cat ~/ >> ~/.ssh/authorized_keys
chmod 600 ~/.ssh/authorized_keys
rm ~/

You can then repeat this process for any more local machines you want to access Cirrus from, omitting the mkdir and chmod lines as the relevant files and directories will already exist with the correct permissions. You don't need to add the public key from your primary machine in your authorized_keys file, because Cirrus can find this in SAFE.

Note that the permissions on the .ssh directory must be set to 700 (Owner can read, can write and can execute but group and world do not have access) and on the authorized_keys file must be 600 (Owner can read and write but group and world do not have access). Keys will be ignored if this is not the case.

SSH forwarding (to use Cirrus from a second remote machine)

If you want to access Cirrus from a machine you already access remotely (e.g. to copy data from Cirrus onto a different cluster), you can forward your local Cirrus SSH keys so that you don't need to create a new key pair on the intermediate machine.

If your local machine is MacOS or Linus, add your Cirrus SSH key to the SSH Agent:

eval "$(ssh-agent -s)"
ssh-add ~/.ssh/id_rsa

(If you created your key with a different name, replace id_rsa in the command with the name of your private key file). You will be prompted for your SSH key's passphrase.

You can then use the -A flag when connecting to your intermediate cluster:

ssh -A <user>@<host>

Once on the intermediate cluster, you should be able to SSH to Cirrus directly:

ssh <user>

SSH debugging tips

If you find you are unable to connect via SSH there are a number of ways you can try and diagnose the issue. Some of these are collected below - if you are having difficulties connecting we suggest trying these before contacting the Cirrus service desk.

Can you connect to the login node?

Try the command ping -c 3 If you successfully connect to the login node, the output should include:

--- ping statistics ---
3 packets transmitted, 3 received, 0% packet loss, time 38ms

(the ping time '38ms' is not important). If not all packets are received there could be a problem with your internet connection, or the login node could be unavailable.

SSH key

If you get the error message Permission denied (publickey) this can indicate a problem with your SSH key. Some things to check:

  • Have you uploaded the key to SAFE? Please note that if the same key is reuploaded SAFE will not map the "new" key to cirrus. If for some reason this is required, please delete the key first, then reupload.

  • Is ssh using the correct key? You can check which keys are being found and offered by ssh using ssh -vvv. If your private key has a non-default name you can use the -i flag to provide it to ssh, i.e. ssh -i path/to/key

  • Are you entering the passphrase correctly? You will be asked for your private key's passphrase first. If you enter it incorrectly you will usually be asked to enter it again, and usually up to three times in total, after which ssh will fail with Permission denied (publickey). If you would like to confirm your passphrase without attempting to connect, you can use ssh-keygen -y -f /path/to/private/key. If successful, this command will print the corresponding public key. You can also use this to check it is the one uploaded to SAFE.

  • Are permissions correct on the ssh key? One common issue is that the permissions are incorrect on the either the key file, or the directory it's contained in. On Linux/MacOS for example, if your private keys are held in ~/.ssh/ you can check this with ls -al ~/.ssh. This should give something similar to the following output:

    $ ls -al ~/.ssh/
    drwx------.  2 user group    48 Jul 15 20:24 .
    drwx------. 12 user group  4096 Oct 13 12:11 ..
    -rw-------.  1 user group   113 Jul 15 20:23 authorized_keys
    -rw-------.  1 user group 12686 Jul 15 20:23 id_rsa
    -rw-r--r--.  1 user group  2785 Jul 15 20:23
    -rw-r--r--.  1 user group  1967 Oct 13 14:11 known_hosts

The important section here is the string of letters and dashes at the start, for the lines ending in ., id_rsa, and, which indicate permissions on the containing directory, private key, and public key respectively. If your permissions are not correct, they can be set with chmod. Consult the table below for the relevant chmod command. On Windows, permissions are handled differently but can be set by right-clicking on the file and selecting Properties > Security > Advanced. The user, SYSTEM, and Administrators should have Full control, and no other permissions should exist for both public and private key files, and the containing folder.

Target Permissions chmod Code
Directory drwx------ 700
Private Key -rw------- 600
Public Key -rw-r--r-- 644

chmod can be used to set permissions on the target in the following way: chmod <code> <target>. So for example to set correct permissions on the private key file id_rsa_cirrus one would use the command chmod 600 id_rsa_cirrus.


Unix file permissions can be understood in the following way. There are three groups that can have file permissions: (owning) users, (owning) groups, and others. The available permissions are read, write, and execute.

The first character indicates whether the target is a file -, or directory d. The next three characters indicate the owning user's permissions. The first character is r if they have read permission, - if they don't, the second character is w if they have write permission, - if they don't, the third character is x if they have execute permission, - if they don't. This pattern is then repeated for group, and other permissions.

For example the pattern -rw-r--r-- indicates that the owning user can read and write the file, members of the owning group can read it, and anyone else can also read it. The chmod codes are constructed by treating the user, group, and owner permission strings as binary numbers, then converting them to decimal. For example the permission string -rwx------ becomes 111 000 000 -> 700.


If your TOTP passcode is being consistently rejected, you can remove MFA from your account and then re-enable it.

SSH verbose output

Verbose debugging output from ssh can be very useful for diagnosing the issue. In particular, it can be used to distinguish between problems with the SSH key and password - further details are given below. To enable verbose output add the -vvv flag to your SSH command. For example:

ssh -vvv

The output is lengthy, but somewhere in there you should see lines similar to the following:

debug1: Next authentication method: publickey
debug1: Offering public key: RSA SHA256:<key-hash> <path_to_private_key>
debug3: send_pubkey_test
debug3: send packet: type 50
debug2: we sent a publickey packet, wait for reply
debug3: receive packet: type 60
debug1: Server accepts key: pkalg ssh-rsa vlen 2071
debug2: input_userauth_pk_ok: fp SHA256:<key-hash>
debug3: sign_and_send_pubkey: RSA SHA256:<key-hash>
Enter passphrase for key '<path_to_private_key>':
debug3: send packet: type 50
debug3: receive packet: type 51
Authenticated with partial success.

Most importantly, you can see which files ssh has checked for private keys, and you can see if any key is accepted. The line Authenticated with partial success indicates that the SSH key has been accepted, and you will next be asked for your password. By default ssh will go through a list of standard private key files, as well as any you have specified with -i or a config file. This is fine, as long as one of the files mentioned is the one that matches the public key uploaded to SAFE.

If you do not see Authenticated with partial success anywhere in the verbose output, consider the suggestions under SSH key above. If you do, but are unable to connect, consider the suggestions under Password above.

The equivalent information can be obtained in PuTTY or MobaXterm by enabling all logging in settings.

Default shell environment

Usually, when a new login shell is created, the commands on $HOME/.bashrc are executed. This tipically includes setting user-defined alias, changing environment variables, and, in the case of an HPC system, loading modules.

Cirrus does not currently read the $HOME/.bashrc file, but it does read the $HOME/.bash_profile file, so, if you wish to read a $HOME/.bashrc file, you can add the following to your $HOME/.bash_profile file (or create one, if it doesn't exist):

# $HOME/.bash_profile
# load $HOME/.bashrc, if it exists
if [ -f $HOME/.bashrc ]; then
        . $HOME/.bashrc