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Launching Jupyter on the FMRIB Cluster

The Jupyter Interactive App allows you to launch a Jupyter session on the FMRIB cluster, which you can then interact with using a web browser.

First select the session type (Advanced will allow you to specify cores and memory), duration and whether you need a GPU - see Remote Desktop for details.

Before you can launch Jupyter you need to prepare a script that will provide the jupyter command. Typically this would be achieved using a conda environment. As a basic example, create a conda environment `jupyter` using a desktop, shell or SSH session:

conda create -y -n jupyter jupyter

create a text file in your home folder called `jupyter.sh` containing:

#!/bin/bash
. $HOME/.bashrc
conda activate jupyter

In the Jupyter form, enter the full path to this file, /home/fs0/<username>/jupyter.sh in the first text field (first red arrow below)

Now choose from Jupyter Notebook, the classic view, or Jupyter Lab, which offers an Integrated Development Environment (IDE) interface.

Specify the startup folder, for example /vols/Scratch/<username>/<myanalysis> in the next field (second red arrow).

Open OnDemand JupyterOpen OnDemand Jupyter

Click Launch to request your session.

If you receive a red error box mentioning QOS, then you have requested a second Jupyter session - we do not allow this for fair-share reasons.

Error box you will see at the top of the page if you already have a session running

 

You will now be taken to the My Interactive Sessions page where you can wait for the job to launch.

Once the card heading turns green (from blue), your session has started and you will find a button 'Connect to Jupyter' that will launch your web session.

NB At present, unlike other interactive apps this will not launch a new tab/window - we do not currently understand why this occurs.