Persistent SSH and Terminal configs

Your SSH keys and configuration files (like .ssh or .gitconfig) are typically saved in the home directory. However, since the home directory is ephemeral, any changes you make to these files disappear when your container restarts.

The most common use case for this is Git integration, and the remote access via SSH. By persisting your SSH keys, you can upload a single public key to GitHub (or similar hosting) and maintain access across container restarts or when launching new containers. Since your cloned projects are already stored in your personal storage folders, persisting your identity allows you to push and pull changes seamlessly without re-authenticating every session.

To maintain persistent changes, we rely on the persistence pattern: store the actual data in your persistent volume and link it to the system.

The Problem: Ephemeral `.ssh`

The system expects your SSH keys to be in ~/.ssh. If you create them there, they are lost on restart. This is important if you are working for example with git repositories, and you want to use a consistent ssh key for your work in SciServer.

The Solution: The Symlink Pattern

The most efficient way to handle this is to store your .ssh directory in persistent storage and create a symbolic link (symlink) that points the system to that location.

1. Create your keys normally

If you don’t have SSH keys yet, generate them in your home directory first. This ensures that the ~/.ssh folder is created with the correct system permissions automatically.

ssh-keygen -t ed25519 -C "$SCISERVER_USER_NAME@sciserver_container"

You can already use this key ~/.ssh/id_ed25519.pub your git hosting provider (e.g. Github, MPCDF Gitlab, Codeberg.org, etc)

2. Move keys to Persistent Storage

Now that the folder exists with the correct permissions (or if you already had existing keys), move it to your persistent storage:

mv ~/.ssh ~/workspace/Storage/$SCISERVER_USER_NAME/persistent/.ssh

2. Manually Link Them (Temporary Fix)

You can link them manually for your current session:

ln -s ~/workspace/Storage/$SCISERVER_USER_NAME/persistent/.ssh ~/.ssh

3. Automate the Link (Permanent Fix)

To avoid doing this every time you launch a container, add the linking logic to your Automation Engine ( See Shell Automation ).

Add this to your $HOME/workspace/Storage/$SCISERVER_USER_NAME/persistent/.bashrc file:

# Automatically restore SSH symlink if persistent storage exists
if [ -d "$HOME/workspace/Storage/$SCISERVER_USER_NAME/persistent/.ssh" ]; then
    ln -s "$HOME/workspace/Storage/$SCISERVER_USER_NAME/persistent/.ssh" "$HOME/.ssh" 2>/dev/null
fi

Now, every time you start a new container, your SSH keys will be automatically “restored” to the expected location.

Other Identity Files

You can use this same pattern for other configuration files:

Git Config: Move .gitconfig to ~/workspace/Storage/$SCISERVER_USER/persistent/ and link it in your .bashrc.