13 Jupyter Sessions

13.1 Overview

RStudio Server Pro 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. Additionally, JupyterLab 3.0 was recently released and has not been fully certified as compatible with RSP; we recommend using a 2.x version to ensure compatibility.

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:


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-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=
notebook-command The Jupyter comman to run when starting a Notebook session. notebook
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=
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:



13.2.2 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.

13.2.3 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:

  1. Python 2.7 or Python 3.x
  2. JupyterLab and/or Jupyter Notebook installation
  3. RSP session binaries
  4. 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.

13.2.4 Installing the Jupyter Notebook Plugin

RStudio Server Pro 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 RSP 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 RSP 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.

13.3 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.