Integrating Posit Workbench with Jupyter Notebooks, Launcher, and Slurm#

Overview#

These steps describe how to integrate Posit Workbench with Jupyter Notebooks running with Launcher and Slurm.

Prerequisites#

This integration is intended to be performed on top of an installation of Workbench that has already been configured with Launcher and Slurm.

• RStudio Server Pro 1.2.5+ or Workbench configured with Launcher and Slurm

Step 1. Ensure that Python is available on each node#

• Ensure that Python is available on each node in the Slurm cluster.

  • If needed, you can install Python, pip, and virtualenv on each node following the steps to Install Python.

    Info

    Our recommended installation instructions for Python allow you to make multiple versions of Python available and avoid replacing existing versions of Python when updating system packages.

Step 2. Install Jupyter Notebooks, JupyterLab, and Python packages on each node#

• From the previous step, you should still have the PYTHON_VERSION environment variable defined with the version of Python that you installed.

  • If not, you can define this environment variable before proceed by running the following command and replacing 3.9.14 with the version of Python that you are using:

    Terminal

    $ export PYTHON_VERSION=3.9.14
    

• Install Jupyter Notebooks, JupyterLab, and the notebook extensions for Workbench and Connect:

  Terminal

  $ sudo /opt/python/${PYTHON_VERSION}/bin/pip install jupyter jupyterlab rsp_jupyter rsconnect_jupyter workbench_jupyterlab
  

• Install and enable the Jupyter Notebook extensions:

  Terminal

  $ sudo /opt/python/${PYTHON_VERSION}/bin/jupyter-nbextension install --sys-prefix --py rsp_jupyter
  $ sudo /opt/python/${PYTHON_VERSION}/bin/jupyter-nbextension enable --sys-prefix --py rsp_jupyter
  $ sudo /opt/python/${PYTHON_VERSION}/bin/jupyter-nbextension install --sys-prefix --py rsconnect_jupyter
  $ sudo /opt/python/${PYTHON_VERSION}/bin/jupyter-nbextension enable --sys-prefix --py rsconnect_jupyter
  $ sudo /opt/python/${PYTHON_VERSION}/bin/jupyter-serverextension enable --sys-prefix --py rsconnect_jupyter
  

• (Optional) Install supplemental Python packages:

  Terminal

  $ sudo /opt/python/${PYTHON_VERSION}/bin/pip install altair beautifulsoup4 \
    cloudpickle cython dask gensim keras matplotlib nltk numpy pandas pillow \
    pyarrow requests scipy scikit-image scikit-learn scrapy seaborn spacy \
    sqlalchemy statsmodels tensorflow xgboost
  

Step 3. Configure Launcher with Jupyter Notebooks#

• Add the following lines to the Launcher Jupyter configuration file:

  File: /etc/rstudio/jupyter.conf

  jupyter-exe=/opt/python/3.9.14/bin/jupyter
  notebooks-enabled=1
  labs-enabled=1
  default-session-cluster=Local
  

• If you installed a version other than Python 3.9.14, then you can replace 3.9.14 in the above jupyter-exe setting with the the version of Python that you installed.

Step 4. Restart Workbench and Launcher Services#

• Restart the services:

  Terminal

  $ sudo rstudio-server restart
  $ sudo rstudio-launcher restart
  

Step 5. Test Workbench with Launcher and Jupyter Notebooks#

• From your browser, navigate to the Workbench interface and log in.
• Select New Session and do the following:

1. Give your session a name.
2. In the **Editor** field, select either Jupyter Notebooks or JupyterLab as the IDE.
3. Click Start Session.

Now, you can use the Jupyter Notebooks or JupyterLab interfaces.

(Optional) Configure multiple Python versions or environments#

The Python integration steps described above result in a single Python environment that contains both core packages for Jupyter Notebooks as well as Python packages for end users.

While this is a simple approach, this setup can result in issues if end users want to use different versions of the same package or if some packages conflict with core packages for Jupyter Notebooks.

If you would like to use multiple versions of Python or different Python environments, or if you want to install Jupyter Notebook in a separate environment from Python packages for end users, then you can refer to the documentation for using multiple Python versions and environments with Jupyter.

Troubleshooting Workbench and Jupyter#

Refer to the support article on troubleshooting Jupyter Notebooks in Workbench for additional information on troubleshooting Workbench with Jupyter.

Additional Documentation#

For more information on Workbench and Launcher, refer to the following reference documentation:

• Launcher section in the Workbench Administration Guide
• Jupyter section in the Workbench Administration Guide
• Launcher Administration Guide