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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).
Created presets can be selected when starting a new Jupyter instance:
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Create presets here: https://jh.pc2.uni-paderborn.de/services/presets/ (or JupyterHub home → services → presets)
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Spawner
Local spawner (on JupyterHub)
Spawning the Jupyter notebook environment on the JupyterHub host. Slurm job flags not needed.
Slurm tools, Modules, Remote desktop environment are available.
Noctua 2 (via Slurm)
Spawning the Jupyter environment inside a Slurm job (on a compute/gpu/fpga node) on Noctua 2. Note: You need to specifiy Slurm job flags.
Preset scopes
Select who can use your preset. You or one of your compute time projects.
Default URL
The URL to which JupyterHub redirects when the server is started.
Example:
/lab -> Spawning JupyterLab environment
/xprahtml5 -> Spawning Remote desktop environment
Notebook directory
The working directory. Used for JupyterLab, the remote desktop environment and the classic Jupyter view.
Apptainer container
Your self-built Apptainer/Singularity container. Have a look here for creating your own container: https://upb-pc2.atlassian.net/wiki/spaces/PC2DOK/pages/1903131/JupyterHub#Create-my-own-Apptainer%2FSingularity-container
Environment variables
Extra environment variables.
Format:
| Code Block |
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MY_ENV_VAR=”Hello World”
FOO=BAR |
Modules
Extra Lmod modules to load on start time. All system modules and Jupyter specific kernels are available.
Slurm job flags
Slurm job flags in Slurm batch format. Example:
| Code Block |
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#SBATCH --partition=normal
#SBATCH --time=01:00:00 |
Create custom IPython kernel inside custom conda environment
Create a conda environment as described here:
conda activate <your_conda_env>conda install ipykernelOr:
python3 -m pip install ipykernel
python3 -m ipykernel install --user --name <KERNELNAME> --display-name "<DISPLAY NAME>"Make sure, that python3 is called from the environment
Create my own Apptainer/Singularity container
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| Code Block |
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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
Create an acccess token in the JupyterHub web interface:
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Follow following instructions described here: https://marketplace.visualstudio.com/items?itemName=ms-toolsai.jupyter-hub
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: $HOME/.jupyter/last_jh_noctua2.log
PC² Support
If you have any other problems that won’t be solved, please contact the pc2-support@uni-paderborn.de
Troubleshooting
JupyterLab
“A Jupyter server is running.” message
This message appears because user settings managed by JupyterLab do not match the new JupyterLab version.
Try deleting
~/.jupyter/in your$HOMEdirectory as follows:rm -r ~/.jupyter/
If you want to keep your custom user settings, write an email to pc2-support@uni-paderborn.de