Jupyter

Example

To use system Jupyter, select "Jupyter 3.5.0"

To use Jupyter with a Python virtualenv
- On the login node, select a python version to use, activate your virtualenv and install the jupyter and jupyterlab modules using pip - e.g.

module load foss/2022a Python/3.10.4
source ~/venvs/3.10.4/bin/activate
pip install jupyterlab notebook
- In Open OnDemand, select the "Modules" to "Virtual Python 3.10.4", and put source ~/venvs/3.10.4/bin/activate to the "Commands to run before Jupyter"

To use Jupyter with Anaconda
- On the login node, load the Anaconda module, activate your conda env, and install the Jupyter and Jupyterlab modules using pip - e.g. 

module load Anaconda3/2022.10
eval "$(conda shell.bash hook)"
conda activate Your_Conda_Environment
pip install jupyterlab notebook
- Select "Anaconda 2022.10" in the Modules section in OnDemand - Put conda activate Your_Conda_Environment in "Commands to run before Jupyter" section.

To use Jupyter with GPU, select "Jupyter/3.5.0" in the Modules section, put "module load CUDA/11.7.0" in "Commands to run before Jupyter" section, and change the "Number of GPUs" to be 1 or more

Login to spartan via ssh and activate your existing virtual env (venv-3.10.4)

Install ipykernel pip package 

$ pip install ipykernel

Now integrate that with jupyter notebook. You can choose a different kernel name, but I just went with the same name "venv" 

$ python -m ipykernel install --user --name=spartan-venv

NOTE: some users may end up needing to install ipyparallel package as well in their venv

Check the list of kernels. We now have "venv" also listed 

$ ls ~/.local/share/jupyter/kernels/

The ~/.local/share/jupyter/kernels/spartan-venv/kernel.json points to the python executable inside your vitual environment. Jupyter will automatically pick this up when you select the "spartan-venv" option. 

$ cat ~/.local/share/jupyter/kernels/spartan-venv/kernel.json

In opendemand, create a jupyter notebooks session with the following input values:

Add the dependency "Modules" field to ensure that the right python modules are loaded.

Remove the activate command from "Commands to run before Jupyter"

Start the jupyter session and select the spartan-venv from the available kernels and start a new notebook. You may select "spartan-venv" by clicking the drop-down-box (labeled as "New") near the top left corner to open a new notebook. For existing notebooks, you may change the kernel by selecting "Kernel -> > Change Kernel -> spartan-venv"