Biocluster Jupyter: Difference between revisions
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__TOC__ | __TOC__ | ||
= Jupyter = | = Jupyter = | ||
* There is an installation of Jupyter which is accessible at [https:// | * There is an installation of Jupyter which is accessible at [https://bioapps3.igb.illinois.edu/jupyter https://bioapps3.igb.illinois.edu/jupyter] | ||
= Custom Conda Environment = | = Custom Conda Environment = | ||
* From Regular Command Line | * '''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 | * Load Anaconda Module | ||
<pre> | <pre> | ||
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 | conda create -p $HOME/testenv python=3.10 | ||
</pre> | </pre> | ||
* Activate Conda Environment | * Activate Conda Environment | ||
| Line 25: | Line 26: | ||
ipython kernel install --user --name='testenv' | ipython kernel install --user --name='testenv' | ||
</pre> | </pre> | ||
* Open Jupyterhub at [https:// | * Open Jupyterhub at [https://bioapps3.igb.illinois.edu/jupyter https://bioapps3.igb.illinois.edu/jupyter] and start a server. | ||
* Your '''testenv''' kernel should be listed in the list of kernels | * Your '''testenv''' kernel should be listed in the list of kernels | ||
= References = | |||
Latest revision as of 14:19, 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