This guide provides step-by-step instructions for users migrating their data from the Bonna to Marvin.
⚠️ Please read carefully to ensure a smooth transition.
The cluster Bonna will remain accessible until December 31, 2025.
After this date, access will be discontinued.
We therefore strongly recommend that you begin the migration process as soon as possible.
If your Bonna access would time out before December 31, you do not need to renew it, all accounts will remain valid until the final shutdown.
There is no automatic migration of user accounts or data between the two clusters. Therefore, you will need to apply for access to Marvin.
After your Marvin account has been created, you can begin transferring your data. There are several methods available depending on the size and amount of your data.
scp (Secure Copy)The scp command allows you to securely copy files between the two clusters via SSH.
Example:
# Copy a single file
scp username@bonna.hpc.uni-bonn.de:/path/to/file.txt username@marvin.hpc.uni-bonn.de:/path/to/destination/
# Copy an entire directory (recursively)
scp -r username@bonna.hpc.uni-bonn.de:/path/to/directory/ username@marvin.hpc.uni-bonn.de:/path/to/destination/
rsync (Remote Synchronization)rsync is recommended for larger transfers or when you need to resume interrupted transfers. It efficiently synchronizes directories between system by copying only changed or missing files.
Note that rsync cannot copy between two remote locations. The easiest way around that is run the copying process on Marvin, as in the following example:
Example:
First, generate a key pair on the Marvin login node. When asked to specify a filename, pick a new name. We describe key generation here.
The following examples will assume the user is named tmuster and the key is in /home/tmuster/.ssh/rsync_bonna_key.
$ ssh-keygen -t ed25519
(...) # Follow the instructions.
Remember the filename that you gave the key.
Then, add an SSH config entry on the Marvin login node.
Example:
host your_bonna_config
Hostname bonna.hpc.uni-bonn.de
User tmuster
IdentityFile ~/.ssh/rsync_bonna_key
Then, add the public key to the ~/.ssh/authorized_keys file on Bonna.
From that point on, you can run the following rsync command on Marvin.
# Basic rsync usage, run this command on the Marvin login node.
rsync -avz your_bonna_config:/path/to/data/ /path/to/destination/
# Resume or update an existing transfer
rsync -avz --progress --partial your_bonna_config:/path/to/data/ /path/to/destination/
Tip:
Add the--dry-runflag to preview the files that would be transferred without actually copying them.
sftp (Secure File Transfer Protocol)sftp provides an interactive command-line interface for file transfers. It’s useful when you want to browse directories and transfer files manually.
Example:
# Connect to the old cluster
sftp username@bonna.hpc.uni-bonn.de
# Inside the SFTP prompt:
sftp> cd /path/to/source/
sftp> get file.txt
sftp> lcd /path/to/local/destination/
sftp> put file.txt
sftp> exit
Tip:
You need to script SFTP commands using a slurm job script file for repetitive transfers.
FileZilla or any SFTP client offers a graphical interface for transferring files between clusters. This method is user-friendly and suitable for users who prefer not to use the command line.
Steps:
Open FileZilla.
Connect to the Bonna cluster using your username, password (or SSH key), and hostname.
Connect to the Marvin cluster in another tab or window.
Drag and drop files or directories from the old cluster to the new one.
For very large data, we offer a workspace storage system on Marvin.
Important Note:
All options mentioned above apply when working within your own workspace.