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Installing Gurobi

In this step, we are going to install Gurobi into our JupyterHub environment.

Installing Gurobi on the server

For installing Gurobi on the server, first download Gurobi from the Gurobi website at https://www.gurobi.com and unpack the archive in a temporary directory. This will create a folder named gurobi811or similar, depending on the version you downloaded. We will install gurobi into /opt, so issue the following commands from your temporary directory:

$ sudo mv gurobi811 /opt
$ cd /opt
$ ln -s gurobi811 gurobi

Installing Gurobi into the Virtual Environment

To install Gurobi into the virtual environment, change into the directory /opt/gurobi/linux64 and issue the following command

/opt/gurobi/linux64$ /srv/jupyterhub/venv/bin/python setup.py install

This will make sure that the Gurobi modules are installed into the correct environment.

License File

The Gurobi license file should be located at /opt/gurobi/linux64/bin/gurobi.lic. If your license is stored elsewhere, please remember to set the variable GRB_LICENSE_FILE in the next section accordingly. If you plan to use a token server for Gurobi, you should deploy a license file with the following contents, adapted to your situation:

TOKENSERVER=gurobi-license-server.demo.invalid

Configuring Environment Variables for Gurobi

Gurobi needs to set a few environment variables to work properly. We will automate this by setting the appropriate variables in the systemd configuration. Unfortunately, a little more work is required so that these settings actually make their way into the Jupyter Notebook / Lab process and can then be seen by Gurobi.

Step 1: Include Variable Settings into systemd

Change /etc/systemd/system/jupyterhub.service to look like this:

[Unit]
Description=JupyterHub
After=syslog.target network.target

[Service]
User=root
Environment="PATH=/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/srv/jupyterhub/venv/bin/:/opt/gurobi/linux64/bin"
Environment="GUROBI_HOME=/opt/gurobi/linux64"
Environment="GRB_LICENSE_FILE=/opt/gurobi/linux64/bin/gurobi.lic"
Environment="LD_LIBRARY_PATH=/opt/gurobi/linux64/lib"
Environment="GITLAB_HOST=https://gitlab.lrz.de"
PassEnvironment=GUROBI_HOME GRB_LICENSE_FILE LD_LIBRARY_PATH
ExecStart=/srv/jupyterhub/venv/bin/jupyterhub -f /etc/jupyterhub/jupyterhub_config.py

[Install]
WantedBy=multi-user.target

Note that we not only set the variables, we also pass them on using the PassEnvironment directive. This is necessary, because otherwise the variables would only be set for the command in ExecStart and then be unset again.

Step 2: Pass Variable Settings to Jupyter Notebooks

While the variables are now visible for the jupyterhub process, they are not automatically passed on to the separate notebook processes, so the local Python interpreter will still not be able to see them. This is a security measure, but for our purposes, passing the variables is necessary, so we will add the following lines to the file /etc/jupyterhub/jupyterhub_config.py:

# import all variables from os into jupyter processes
import os
for var in os.environ:
    c.Spawner.env_keep.append(var)

Restarting JupyterHub

Do not forget to restart the JupyterHub daemon so that the settings take effect.

$ sudo systemctl daemon-reload
$ sudo service jupyterhub stop
$ sudo service jupyterhub start