13 Jupyter Sessions

13.1 Overview

RStudio Workbench allows you to launch Jupyter sessions from the home page via the Job Launcher, if configured. Users have the option of starting either JupyterLab or Jupyter Notebook sessions that allow them to work with Jupyter while still working within the administrative framework provided by RStudio, such as authentication, PAM session management, etc.

Note: Before Jupyter sessions can be launched, the Job Launcher must be setup correctly. For more information, see the Job Launcher section.

13.2 Configuration

13.2.1 Jupyter configuration

Configuration of the Jupyter feature is handled via the config file /etc/rstudio/jupyter.conf. Note that this file is not automatically created by RStudio, and must be created before being configured, and the Jupyter feature is disabled by default. The following table lists the various configuration options that are available to be specified in the jupyter.conf configuration file:

/etc/rstudio/jupyter.conf

Config Option	Description	Default Value
labs-enabled	Enables launching of JupyterLab sessions.	0 (disabled)
notebooks-enabled	Enabled launching of Jupyter Notebook sessions.	0 (disabled)
jupyter-exe	Path to the Jupyter executable.	/usr/local/bin/jupyter
lab-command	The Jupyter command to run when starting a Lab session.	lab
lab-version	The version of Jupyter Lab being used. If set to `auto`, the version is automatically detected by running the Jupyter Lab version command. If Jupyter is being launched via the Launcher and is not installed locally, you are strongly encouraged to set this to the version in use. Running against multiple different Jupyter versions simultaneously in different Launcher clusters is not supported - they must all be running the same version, or proxying issues will occur.	auto
lab-args	Arguments to be passed to the Jupyter Lab command. Note that this does not override the default value - if you wish to use some of the default arguments, you must contain the default arguments in the configuration value. It is strongly recommended that you do not change this unless you know what you’re doing!	--no-browser --allow-root --ip=0.0.0.0
notebook-command	The Jupyter comman to run when starting a Notebook session.	notebook
notebook-version	The version of Jupyter Notebook being used. If set to `auto`, the version is automatically detected by running the Jupyter Notebook version command. If Jupyter is being launched via the Launcher and is not installed locally, you are strongly encouraged to set this to the version in use. Running against multiple different Jupyter versions simultaneously in different Launcher clusters is not supported - they must all be running the same version, or proxying issues will occur.	auto
notebook-args	Arguments to be passed to the Jupyter Notebook command. Note that this does not override the default value - if you wish to use some of the default arguments, you must contain the default arguments in the configuration value. It is strongly recommended that you do not change this unless you know what you’re doing!	--no-browser --allow-root --ip=0.0.0.0
session-clusters	List of available Job Launcher clusters for launching Jupyter sessions. Leave blank to specify all clusters.
default-session-cluster	The default Job Launcher cluster to use when launching a Jupyter session.
default-session-container-image	The default container image to use when launching a containerized Jupyter session.
session-container-images	Comma-delimited list of images that may be used for running Jupyter sessions.
jupyter-session-path	Path to the Jupyter Session launcher executable/script. It is recommended that you do not change this unless you know what you’re doing, and you need to point to a different script.	/usr/lib/rstudio-server/bin/jupyter-session-run
session-no-profile	Enables/disables running of bash profile scripts when starting Jupyter sessions.	0 (run profile scripts)
session-cull-minutes	The amount of idle time to wait in minutes before a Jupyter session’s kernels and terminals is automatically “culled” (shut down). To disable culling, set the value to `0`. Enabling this sets the following Jupyter arguments: `--MappingKernelManager.cull_interval=60 --MappingKernelManager.cull_idle_timeout=<60 * session-cull-minutes value>`	120
session-shutdown-minutes	The amount of idle time to wait in minutes before a Jupyter session is shut down after its kernels and terminals have been culled. To disable automatic shutdown, set the value to `0`. This setting sets the the following Jupyter arguments: `--NotebookApp.shutdown_no_activity_timeout=<60 * session-shutdown-minutes value> --LapApp.shutdown_no_activity_timeout=<60 * session-shutdown-minutes value>`	5
session-cull-connected	Whether or not to cull sessions that have a browser connected. Regardless of this setting, only idle (unused) sessions are culled. Sets the `--MappingKernelManager.cull_connected` Jupyter setting.	1 (true)

For example, your jupyter.conf file might look like the following:

/etc/rstudio/jupyter.conf

jupyter-exe=/usr/bin/jupyter
labs-enabled=1
notebooks-enabled=1
session-cull-minutes=240
default-session-cluster=Kubernetes
default-session-container-image=rstudio:jupyter-session

13.2.2 Jupyter Versions

Currently, RStudio Workbench supports JupyterLab 2.x and 3.x, as well as Jupyter Notebooks 6.x. Due to differences between Jupyter versions, RStudio Workbench needs to know the versions of Jupyter Notebook and Jupyter Lab that are in use. They can be automatically detected by RStudio Workbench on start up by running the Jupyter command, or can be specified by using the lab-version and notebook-version settings in /etc/rstudio/jupyter.conf. Automatic version detection is done if the default value of auto is used.

If you are running Jupyter in a remote cluster like Kubernetes, you will need to manually specify the version of Jupyter if it is not locally installed or is not running the same version as the remote cluster. Due to differences in routing, running against multiple different versions of Jupyter in different Launcher clusters simultaneously is not supported - the versions must match in all clusters.

You should specify a full Jupyter 3-part version number like so:

/etc/rstudio/jupyter.conf

lab-version=3.0.6
notebook-version=6.2.0

13.2.3 Launcher Configuration

When creating containerized Jupyter sessions via the Job Launcher, you will need to specify mount points as appropriate to mount the users’ home drives and any other desired paths. In order for sessions to run properly within containers, it is required to mount the home directories into the containers.

For more information, see Launcher Mounts. Note that you can specify the Workbench with either JupyterLab or Jupyter Notebook to configure mount entries that should only be mounted for JupyterLab and Jupyter Notebook sessions, respectively.

Note: If you are using NFSv3 for the shared storage for user home directories, you will need to set the local_lock=all NFS setting in /etc/fstab in order for Jupyter sessions to work properly. Failure to do this will cause Jupyter sessions to hang. For this reason, we strongly recommend the use of NFSv4 for Jupyter sessions. See the NFS documentation for information on NFS settings.

Note: Only a user’s home folder is visible within Jupyter sessions. To access other folders, create symbolic links to them within the home folder.

13.2.4 Container Configuration

When running Jupyter sessions in containers, such as by using the Kubernetes Job Launcher plugin, you will need to ensure that the image(s) used to launch Jupyter sessions contain, at minimum, the following:

Python 2.7 or Python 3.x
JupyterLab and/or Jupyter Notebook installation
RStudio session binaries
If creating container users (see Server Configuration), you must have the libuser1-dev or libuser-devel packages, depending on your platform to install the libuser library and development tools.

For ease of use, it is recommended that you use the r-session-complete Docker image as a base for any Jupyter session images you intend to create. This will allow you to use that one base image to provide Jupyter itself and a default version of Python, which you can extend if necessary to add/modify Jupyter versions or add additional versions of Python if desired. See Docker Hub for more information.

13.2.5 Installing the Jupyter Notebook Plugin

RStudio Workbench can further integrate with Jupyter Notebooks by utilizing the rsp-jupyter Jupyter Notebook plugin. This plugin will automatically track and write recently opened notebooks to the Workbench homepage under the Recent Projects section, and also provides an easy way for users to leave their notebooks and return to the homepage.

If running Workbench in containers via the r-session-complete Docker image, you do not need to install the Notebook plugin, as it comes with the container. Otherwise, to install and enable the plugin, run the following commands:

pip install rsp_jupyter
jupyter-nbextension install --sys-prefix --py rsp_jupyter
jupyter-nbextension enable --sys-prefix --py rsp_jupyter

If you need to uninstall the plugin for whatever reason, run the following command:

jupyter-nbextension uninstall --sys-prefix --py rsp_jupyter

To upgrade the plugin, you must first uninstall and then reinstall it.

13.2.6 Adding Python Environments to Jupyter

You can add new Python virtual environments or conda environments to Jupyter as Python Kernels that users can select, allowing them to have flexibility in the Python versions they can use.

The following steps show how to add a new Python virtualenv as a Kernel to Jupyter:

Create the virtualenv or conda environment
Add the environment as an iPython kernel
Verify the kernel is available in Jupyter

# first, create the virtual env in a directory accessible by all users
cd /opt/python-kernels

# then make the virtualenv
virtualenv myenv

# alternatively, you can make a conda environment
# conda create -n myenv

# then, add the virtualenv to the Kernels list globally for all users
sudo ipython kernel install --name "myenv" --display-name "My Python Environment"

# finally, verify that the kernel is registered with Jupyter
sudo jupyter kernelspec list

Once the Kernel is listed in the output of the jupyter kernelspec list command, it will be available for use in both JupyterLab and Jupyter Notebooks.

To remove the kernel, simply run the following command:

sudo jupyter kernelspec remove "myenv"

For more information, see the IPython docs.

13.2.7 Installing JupyterLab Extensions

With the release of JupyterLab 3, it is now easier for system administrator to add extensions to Jupyter by using pip. Simply pip install the extension you want, and it will show up in JupyterLab sessions launched from RStudio Workbench.

For example, to install the jupyterlab-kernelspy extension using pip:

pip install jupyterlab-kernelspy

Note: You will need to install the desired extensions on all Launcher nodes that are running JupyterLab sessions. For containerized sessions, the extension must be installed in the container image(s) that are used.

There is no need to explicitly enable or disable the extension. Once installed, active sessions can see the extension after refreshing the browser. Other extensions can be found on the Pypi.org site.

In previous versions of JupyterLab, you needed to install packages from source and build them with nodejs. This flow is still supported, but installing prebuilt extensions via pip is much simpler. For more information, see the JupyterLab extension docs.

13.3 Troubleshooting

If you experience issues related to running Jupyter sessions, you can use the Launcher verification tool which will attempt to launch both RStudio and Jupyter launcher sessions and provide diagnostic output about what could be going wrong. For more information, see the Troubleshooting section for the Job Launcher integration documentation.