See https://docs.s3it.uzh.ch/cluster/data/

Preconditions

1. You need to have SSH access to the science cluster and be given access to the relevant Science Cluster project. This is usually set up during onboarding (Getting an account on the Fractal Science Cluster Beta server)
2. Access to the Science Cluster scalable storage is only possible within the UZH network or by using the UZH VPN.
3. Be aware that transfer of many small files (which OME-Zarrs can create) can be slow. So if you have large OME-Zarrs processed on the cluster, be patient in data transfers.

Destination for your files:

You will want to put your files in your project share. For example, if you are part of the BVC project, the share would be /shares/prbvc.biovision.uzh/. Check what your project directory is set to, what’s available to you under /shares on the cluster or ask the Fractal admin which project share you are associated with.

Transferring files via FileZilla

FileZilla provides a simple GUI interface to move data from your local machine to the Science Cluster using the FTP protocol.

• Install: Some UZH departments include FileZilla in the preinstalled “Managed Software Center.” FileZilla offers several installation options if this is not the case; see https://filezilla-project.org/. Be careful that you will only need the FileZilla Client and not the FileZilla Server.
• Setup: Once FileZilla is installed, you must set up the credentials to access your data.
  • A) First connection:
  • Host: cluster.s3it.uzh.ch (or depending on your DNS configurations 130.60.24.69.)
  • Username: <shortname>(your main UZH IT username.)
  • Password: **** (your main UZH IT password.)
  • Port (Optional): Can be left empty or use 22. If the connection could not be made, try it with the port set
  • B) You can connect by clicking on the “Quickconnect” button. Once you open the software again, you can connect using the dropdown menu next to the “Quickconnect” button.

The main authentication bar is on the top part of the UI. A) Credentials, B) Shows all used credentials

• Data Moving: Once the login is completed, you will see your file system on the left and the Science Cluster on the right. Files and directories can be moved to and from the server either by drag and drop.

Data can be dragged and dropped from your local machine (left) to the server (right)

• Data Management: If you right-click on a file or folder, you can rename or delete files on the server. Be careful that editing data information might corrupt fractal workflows.

Transfer data via rsync

To send data to the Science Cluster project share:

rsync -rz --progress /my/local/dir <shortname>@cluster.s3it.uzh.ch:/shares/prbvc.biovision.uzh/users/username/target