How to setup SSH connections

AiiDA communicates with remote computers via the SSH protocol. There are two ways of setting up an SSH connection for AiiDA:

  1. Using a passwordless SSH key (easier, less safe)

  2. Using a password-protected SSH key through ssh-agent (one more step, safer)

Using a passwordless SSH key

There are numerous tutorials on the web, see e.g. here. Very briefly, first create a new private/public keypair (aiida/, leaving passphrase emtpy:

$ ssh-keygen -t rsa -b 4096 -f ~/.ssh/aiida

Copy the public key to the remote machine, normally this will add the public key to the rmote machine’s ~/.ssh/authorized_keys:

$ ssh-copy-id -i ~/.ssh/aiida YOURUSERNAME@YOURCLUSTERADDRESS

Add the following lines to your ~/.ssh/config file (or create it, if it does not exist):

      IdentityFile ~/.ssh/aiida


If your cluster needs you to connect to another computer PROXY first, you can use the proxy_command feature of ssh, see Connecting to a remote computer via a proxy server.

You should now be able to access the remote computer (without the need to type a password) via:

# this connection is used to copy files

Connection closed failures

If the ssh command works, but the sftp command prints Connection closed, there may be a line in the ~/.bashrc file on the cluster that either produces text output or an error. Remove/comment lines from this file until no output or error is produced: this should make sftp work again.

Finally, if you are planning to use a batch scheduler on the remote computer, try also:


replacing QUEUE_VISUALIZATION_COMMAND by squeue (SLURM), qstat (PBSpro) or the equivalent command of your scheduler and check that it prints a list of the job queue without errors.

Scheduler errors?

If the previous command errors with command not found, while the same QUEUE_VISUALIZATION_COMMAND works fine after you’ve logged in via SSH, it may be that a guard in the .bashrc file on the cluster prevents necessary modules from being loaded.

Look for lines like:

[ -z "$PS1" ] && return


case $- in
    *i*) ;;
    *) return;;

which will prevent any instructions that follow from being executed.

You can either move relevant instructions before these lines or delete the guards entirely. If you are wondering whether the PATH environment variable is set correctly, you can check its value using:


Using passphrase-protected keys via an ssh-agent

Tools like ssh-agent (available on most Linux distros and MacOS) allow you to enter the passphrase of a protected key once and provide access to the decrypted key for as long as the agent is running. This allows you to use a passphrase-protected key (required by some HPC centres), while making the decrypted key available to AiiDA for automatic SSH operations.

Creating the key

Start by following the instructions above for Using a passwordless SSH key, the only difference being that you enter a passphrase when creating the key (and when logging in to the remote computer).

Adding the key to the agent

Now provide the passphrase for your private key to the agent:

ssh-add ~/.ssh/aiida

The private key and the relative passphrase are now recorded in an instance of the agent.


The passphase is stored in the agent only until the next reboot. If you shut down or restart the AiiDA machine, before starting the AiiDA deamon remember to run the ssh-add command again.

Starting the ssh-agent

On most modern Linux installations, the ssh-agent starts automatically at login (e.g. Ubuntu 16.04 and later or MacOS 10.5 and later). If you received an error Could not open a connection to your authentication agent, you will need to start the agent manually instead.

Check whether you can start an ssh-agent in your current shell:

eval `ssh-agent`

In order to reuse the same agent instance everywhere (including the AiiDA daemon), the environment variables of ssh-agent need to be reused by all shells. Download the script and place it e.g. in ~/bin. Then add the following lines to your ~/.bashrc file:

if [ -f ~/bin/ ]; then
   . ~/bin/

To check that it works:

  • Open a new shell (~/.bashrc file is sourced).

  • Run ssh-add.

  • Close the shell.

  • Open a new shell and try logging in to the remote computer.

Try logging in to the remote computer; it should no longer require a passphrase.

The key and its corresponding passphrase are now stored by the agent until it is stopped. After a reboot, remember to run ssh-add ~/.ssh/aiida again before starting the AiiDA daemon.

Integrating the ssh-agent with keychain on OSX

On OSX Sierra and later, the native ssh-add client allows passphrases to be stored persistently in the OSX keychain. Store the passphrase in the keychain using the OSX-specific -k argument:

ssh-add -k ~/.ssh/aiida

To instruct ssh to look in the OSX keychain for key passphrases, add the following lines to ~/.ssh/config:

Host *
   UseKeychain yes

AiiDA configuration

When configuring the computer in AiiDA, simply make sure that Allow ssh agent is set to true (default).

Connecting to a remote computer via a proxy server

Some compute clusters require you to connect to an intermediate server PROXY, from which you can then connect to the cluster TARGET on which you run your calculations. This section explains how to use the proxy_command feature of ssh in order to make this jump automatically.


This method can also be used to automatically tunnel into virtual private networks, if you have an account on a proxy/jumphost server with access to the network.

SSH configuration

Edit the ~/.ssh/config file on the computer on which you installed AiiDA (or create it if missing) and add the following lines:

    IdentityFile ~/.ssh/aiida
    ProxyCommand ssh -W %h:%p USER_PROXY@FULLHOSTNAME_PROXY

replacing the ..._TARGET and ..._PROXY variables with the host/user names of the respective servers.

This should allow you to directly connect to the TARGET server using


For a passwordless connection, you need to follow the instructions Using a passwordless SSH key twice: once for the connection from your computer to the PROXY server, and once for the connection from the PROXY server to the TARGET server.

AiiDA configuration

When configuring the computer in AiiDA, AiiDA will automatically parse the required information from your ~/.ssh/config file.

Using kerberos tokens

If the remote machine requires authentication through a Kerberos token (that you need to obtain before using ssh), you typically need to

  • install libffi (sudo apt-get install libffi-dev under Ubuntu)

  • install the ssh_kerberos extra during the installation of aiida-core (see Setup).

If you provide all necessary GSSAPI options in your ~/.ssh/config file, verdi computer configure should already pick up the appropriate values for all the gss-related options.