Biocluster Jupyter: Difference between revisions
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| Line 10: | Line 10: | ||
module load Anaconda3 | module load Anaconda3 | ||
</pre> | </pre> | ||
* Create Conda Environment | * Create Conda Environment. Currently this doesn't work with a python version 3.11 or later | ||
<pre> | <pre> | ||
conda create -p $HOME/testenv | conda create -p $HOME/testenv python=3.10 | ||
</pre> | </pre> | ||
* Activate Conda Environment | * Activate Conda Environment | ||
Latest revision as of 15:19, 5 February 2025
Jupyter
- There is an installation of Jupyter which is accessible at https://bioapps3.igb.illinois.edu/jupyter
Custom Conda Environment
- NOTE This must be done from the biologin nodes. It will fail on the compute nodes as they do not have access to the internet
- From Regular Command Line using SSH
- Load Anaconda Module
module load Anaconda3
- Create Conda Environment. Currently this doesn't work with a python version 3.11 or later
conda create -p $HOME/testenv python=3.10
- Activate Conda Environment
conda activate $HOME/testenv
- Install ipython conda package
conda install ipykernel
- Install custom ipykernel module. This will install the kernel file into $HOME/.local/share/jupyter/kernels. This can be seen by jupyterhub
ipython kernel install --user --name='testenv'
- Open Jupyterhub at https://bioapps3.igb.illinois.edu/jupyter and start a server.
- Your testenv kernel should be listed in the list of kernels