Connecting to ARCHER2

On the ARCHER2 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 ARCHER2 system using scp from the command line or by using a file transfer client.

This section covers the basic connection methods.

Before following the process below, we assume you have setup an account on ARCHER2 through the EPCC SAFE. Documentation on how to do this can be found at:

Access credentials

To access ARCHER2, you need to use two credentials: your password and an SSH key pair protected by a passphrase. You can find more detailed instructions on how to set up your credentials to access ARCHER2 from Windows, macOS and Linux below.

SSH Key Pairs

You will need to generate an SSH key pair protected by a passphrase to access ARCHER2.

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 ARCHER2 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 ARCHER2 account.

Remember, you will need to use both an SSH key and password to log into ARCHER2 so you will also need to collect your initial password before you can log into ARCHER2. We cover this next.

Initial passwords

The SAFE web interface is used to provide your initial password for logging onto ARCHER2 (see the SAFE Documentation for more details on requesting accounts and picking up passwords).

Note: you may now change your password on the ARCHER2 machine itself using the passwd command or when you are prompted the first time you login. This change will not be reflected in the SAFE. If you forget your password, you should use the SAFE to request a new one-shot password.

SSH Clients

Interaction with ARCHER2 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 ARCHER2, 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 ARCHER2:


You will first be prompted for your machine account password. Once you have entered your password successfully, you will then be prompted for the passphrase associated with your SSH key pair. You need to enter both credentials correctly to be able to access ARCHER2.


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 wih the -i option to ssh. For example, if your key is in a file called keys/id_rsa_ARCHER2 you would use the command ssh -i keys/id_rsa_ARCHER2 to log in.


When you first log into ARCHER2, you will be prompted to change your initial password. This is a three step process:

  1. When promoted to enter your ldap password: Re-enter the password you retrieved from SAFE
  2. When prompted to enter your new password: type in a new password
  3. When prompted to re-enter the new password: re-enter the new password

Your password has now been changed

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 ARCHER2. It is very easy to use and includes an integrated X server with SSH client to run any graphical applications on ARCHER2.

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. Use your ARCHER2 username, the login host should be set to

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.

Making access more convenient using the SSH configuration file

Typing in the full command to login or transfer data to ARCHER2 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 archer2
  User username

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

The Host archer2 line defines a short name for the entry. In this case, instead of typing ssh to access the ARCHER2 login nodes, you could use ssh archer2 instead. The remaining lines define the options for the archer2 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 ARCHER2 without needing to enter your username or the full hostname every time:

$ ssh archer2

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.

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 ARCHER2 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.


On ARCHER2 you will be asked to enter your password first, then your SSH key passphrase.


If you are having trouble entering your password consider using a password manager, from which you can copy and paste it. This will also help you generate a secure password. If you need to reset your password, instructions for doing so can be found here.

Windows users please note that Ctrl+V does not work to paste in to PuTTY, MobaXterm, or PowerShell. Instead use Shift+Ins to paste. Alternatively, right-click and select ‘Paste’ in PuTTY and MobaXterm, or simply right-click to paste in PowerShell.

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 ARCHER2. 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_ARCHER2 one would use the command chmod 600 id_rsa_ARCHER2.


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.

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: keyboard-interactive
debug2: userauth_kbdint
debug3: send packet: type 50
debug2: we sent a keyboard-interactive packet, wait for reply
debug3: receive packet: type 60
debug2: input_userauth_info_req
debug2: input_userauth_info_req: num_prompts 1
debug3: send packet: type 61
debug3: receive packet: type 60
debug2: input_userauth_info_req
debug2: input_userauth_info_req: num_prompts 0
debug3: send packet: type 61
debug3: receive packet: type 51
Authenticated with partial success.
debug1: Authentications that can continue: publickey,password

If you do not see the Password: prompt you may have connection issues, or there could be a problem with the ARCHER2 login nodes. If you do not see Authenticated with partial success it means your password was not accepted. You will be asked to re-enter your password, usually two more times before the connection will be rejected. Consider the suggestions under Password above. If you do see Authenticated with partial success, it means your password was accepted, and your SSH key will now be checked.

You should next see something similiar to:

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 rsa-sha2-512 blen 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 52
debug1: Authentication succeeded (publickey).

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 succeeded indicates that the SSH key has been accepted. 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 your SSH key passphrase is incorrect, you will be asked to try again up to three times in total, before being disconnected with Permission denied (publickey). If you enter your passphrase correctly, but still see this error message, please consider the advice under SSH key above.

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