Integrating RStudio Server Pro with Jupyter Notebooks, Launcher, and Slurm

Info

Launcher is a new feature of RStudio Server Pro 1.2 that is only available under named user licensing. RStudio Server Pro 1.2 without Launcher is available under existing server-based licensing. For questions about using Launcher with RStudio Server Pro, please contact sales@rstudio.com.

Overview

These steps describe how to integrate RStudio Server Pro with Jupyter Notebooks running with Launcher and Slurm.

Prerequisites

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

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.

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 3.6.5 with the version of Python that you are using:

Terminal

$ export PYTHON_VERSION=3.6.5

Install Jupyter Notebooks, JupyterLab, and the notebook extensions for RStudio Server Pro and RStudio Connect:

Terminal

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

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

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/3.6.5/bin/jupyter
notebooks-enabled=1
labs-enabled=1
default-session-cluster=Local

If you installed a version other than Python 3.6.5, then you can replace 3.6.5 in the above jupyter-exe setting with the the version of Python that you installed.

4. Restart RStudio Server Pro and Launcher Services

Terminal

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

5. Test RStudio Server Pro with Launcher and Jupyter Notebooks

In your browser, navigate to the RStudio Server Pro interface and log in.

Select New Session, choose Jupyter Notebooks or JupyterLab as the IDE, then click the Start Session button.

You can then use the Jupyter Notebooks or JupyterLab interfaces.

Troubleshooting RStudio Server Pro and Jupyter

Refer to the support article on troubleshooting Jupyter Notebooks in RStudio Server Pro for additional information on troubleshooting RStudio Server Pro with Jupyter.

Additional Documentation

For more information on RStudio Server Pro and Launcher, refer to the following reference documentation: