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You have the possibility of creating a preset with predefined start options for yourself or your project group.

Note: The preset functionality is currently only available on Noctua 2.

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Click here to list your presets: https://jh.pc2.uni-paderborn.de/services/presets/

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When you click on the tile ‘Xpra Desktop’, a remote desktop environment is set up in the background. Graphical applications (e.g. loaded via modules) can be started from the started graphical terminal.

How-To

Creating presets

Note: The preset functionality is currently only available on Noctua 2.

To save time when configuring your Jupyter environenment you have the possibilty to create preset environments for yourself or your compute time group(s).

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Your self-built Apptainer/Singularity container. Have a look here for creating your own container: <LINK>: https://upb-pc2.atlassian.net/wiki/spaces/PC2DOK/pages/1903131/JupyterHub#Create-my-own-Apptainer%2FSingularity-container

Environment variables

Extra environment variables.

Format:

MY_ENV_VAR=”Hello World”

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FOO=BAR

Modules

Extra Lmod modules to load on start time. All system modules and Jupyter specific kernels are available.

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1. Create a conda environment as described here:

   1. Python & Python Package Management

2. conda activate <your_conda_env>

3. conda install ipykernel

   1. Or: python3 -m pip install ipykernel

4. python3 -m ipykernel install --user --name <KERNELNAME> --display-name "<DISPLAY NAME>"

   1. Make sure, that python3 is called from the environment

Create my own Apptainer/Singularity container

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ln -s /scratch/hpc-prf-project/jupyter_container.sif $HOME/.jupyter/pc2-jupyterhub/

Access remote JupyterHub server with the local Visual Studio Code instance

You need following extensions for Visual Studio Code:

• https://marketplace.visualstudio.com/items?itemName=ms-toolsai.jupyter

• https://marketplace.visualstudio.com/items?itemName=ms-toolsai.jupyter-hub

1. Create an acccess token in the JupyterHub web interface:

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2. Follow following instructions described here: https://marketplace.visualstudio.com/items?itemName=ms-toolsai.jupyter-hub

   1. You need to start a Jupyter session using our JupyterHub web interface. After successful start, you can copy the URL starting with https://jh.pc2.uni-paderborn.de/user/.../...

View Slurm job logs

If the path of the Slurm Job output has not been changed explicity, it can be found here by default:

Noctua 1: $HOME/.jupyter/last_jh_noctua1.log

Noctua 2: $HOME/.jupyter/last_jh_noctua2.log

PC² Support

If you have any other problems that won’t be solved, please contact the pc2-support@uni-paderborn.de

Troubleshooting

JupyterLab

“A Jupyter server is running.” message

• This message appears because user settings managed by JupyterLab do not match the new JupyterLab version.

  • Try deleting ~/.jupyter/ in your $HOME directory as follows:

    • rm -r ~/.jupyter/

  • If you want to keep your custom user settings, write an email to pc2-support@uni-paderborn.de