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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/aiida.pub), 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 remote 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):

Host YOURCLUSTERADDRESS
      User YOURUSERNAME
      IdentityFile ~/.ssh/aiida

Note

If your cluster needs you to connect to another computer PROXY first, you can use the ProxyJump or ProxyCommand feature of SSH, see :ref:`how-to:ssh:proxy`.

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

$ ssh YOURCLUSTERADDRESS
# this connection is used to copy files
$ sftp YOURCLUSTERADDRESS

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:

$ ssh YOURCLUSTERADDRESS QUEUE_VISUALIZATION_COMMAND

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

or:

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

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:

$ ssh YOURCLUSTERADDRESS 'echo $PATH'

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 :ref:`how-to:ssh:passwordless`, 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.

Note

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 :download:`load-singlesshagent.sh <include/load-singlesshagent.sh>` and place it e.g. in ~/bin. Then add the following lines to your ~/.bashrc file:

if [ -f ~/bin/load-singlesshagent.sh ]; then
   . ~/bin/load-singlesshagent.sh
fi

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 :ref:`configuring the computer in AiiDA <how-to:run-codes💻configuration>`, 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 ProxyJump or ProxyCommand feature of ssh in order to make this jump automatically.

Tip

This method can also be used to avoid having to start a virtual private network (VPN) client if you have an SSH account on a proxy/jumphost server which is accessible from your current network and from which you can access the TARGET machine directly.

SSH configuration

To decide whether to use the ProxyJump (recommended) or the ProxyCommand directive, please check the version of your SSH client first with ssh -V. The ProxyJump directive has been added in version 7.3 of OpenSSH, hence if you are using an older version of SSH (on your machine or the PROXY) you have to use the older ProxyCommand.

To setup the proxy configuration with ProxyJump, edit the ~/.ssh/config file on the computer on which you installed AiiDA (or create it if missing) and add the following lines:

Host SHORTNAME_TARGET
    Hostname FULLHOSTNAME_TARGET
    User USER_TARGET
    IdentityFile ~/.ssh/aiida
    ProxyJump USER_PROXY@FULLHOSTNAME_PROXY

Host FULLHOSTNAME_PROXY
    IdentityFile ~/.ssh/aiida

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

.. dropdown:: :fa:`plus-circle` Alternative setup with ``ProxyCommand``

   To setup the proxy configuration with ``ProxyCommand`` **instead**, edit the ``~/.ssh/config`` file on the computer on which you installed AiiDA (or create it if missing)
   and add the following lines::

    Host SHORTNAME_TARGET
        Hostname FULLHOSTNAME_TARGET
        User USER_TARGET
        IdentityFile ~/.ssh/aiida
        ProxyCommand ssh -W %h:%p USER_PROXY@FULLHOSTNAME_PROXY

    Host FULLHOSTNAME_PROXY
        IdentityFile ~/.ssh/aiida

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

In both cases, this should allow you to directly connect to the TARGET server using

$ ssh SHORTNAME_TARGET

Note

If the user directory is not shared between the PROXY and the TARGET (in most supercomputing facilities your user directory is shared between the machines), you need to follow the :ref:`instructions for a passwordless connection <how-to:ssh:passwordless>` 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 (e.g. the public key must be listed in the ~/.ssh/authorized_keys file of both the PROXY and the TARGET server).

AiiDA configuration

When :ref:`configuring the computer in AiiDA <how-to:run-codes💻configuration>`, AiiDA will automatically parse most of required information from your ~/.ssh/config file. A notable exception to this is the proxy_jump directive, which must be specified manually.

Simply copy & paste the same instructions as you have used for ProxyJump in your ~/.ssh/config to the input for proxy_jump:

$ verdi computer configure core.ssh SHORTNAME_TARGET
...
Allow ssh agent [True]:
SSH proxy jump []: USER_PROXY@FULLHOSTNAME_PROXY

Note

A chain of proxies can be specified as a comma-separated list. If you need to specify a different username, you can so with USER_PROXY@.... If no username is specified for the proxy the same username as for the TARGET is used.

Important

Specifying the proxy_command manually

When specifying or updating the proxy_command option via verdi computer configure ssh, please do not use placeholders %h and %p but provide the actual hostname and port. AiiDA replaces them only when parsing from the ~/.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

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.