How to setup an open source Data Science environment with Python and R. Part 2/2

VirtualBox 6 on Windows host machine. Ubuntu Desktop 18.04.2 LTS under VirtualBox. Docker container with Jupyter image. Python and R Jupyter kernels.

Navigate to Part 1

Table of Contents

• VirtualBox (part 1)
• Ubuntu under VirtualBox (part 1)
• Ubuntu settings in VirtualBox (part 1)
• Ubuntu configuration
• Docker CE for Ubuntu
• Jupyter

Ubuntu configuration

Click Install Now button:

Click Restart Now:

Log in to Ubuntu. Open terminal. Update and upgrade Ubuntu packages:

$ sudo apt update
$ sudo apt upgrade

Select Devices VirtualBox menu. Click Insert Guest Additions CD image…:

Click Run button. Press Return in terminal.

Select again Devices VirtualBox menu. Select Optical Drives. Click Remove disk from virtual drive:

How to share directory between host machine and Ubuntu? Open terminal in Ubuntu and create new host directory:

$ mkdir host

Add your user (e.g., medium) to vboxsf group:

$ sudo usermod -aG vboxsf <username>

Example:

$ sudo usermod -aG vboxsf medium

Shut down the system:

$ sudo shutdown -h now

Open VirtialBox. Select Ubuntu Desktop 18.04.2 LTS virtual machine and click Settings button. Select Shared Folders tab. Click Add new shared folder icon:

Create shared directory on Windows host machine. Enter path to Folder Path field. Select Auto-mount option. Enter host directory path on Ubuntu (e.g., /home/medium/host). Click OK:

Click OK:

Select Ubuntu Desktop 18.04.2 LTS in VirtualBox and Click Start button:

How to mount shared directory permanently? Add line below to /etc/fstab file and save:

share /home/<username>/host vboxsf defaults 0 0

Example:

share /home/medium/host vboxsf defaults 0 0

Check result:

$ sudo mount -a

Docker CE for Ubuntu

Install Docker CE for Ubuntu. If you would like to use Docker as a non-root user, add your user (e.g., medium) to the “docker” group with something like:

$ sudo usermod -aG docker <username>

Example:

$ sudo usermod -aG docker medium

Note: Remember to log out and back in for this to take effect!

Jupyter

Download Jupyter Docker image (~6.23 GB):

$ docker pull jupyter/datascience-notebook

Run Jupyter in Docker:

$ docker run -d -p 8888:8888 --name jupyter \
jupyter/datascience-notebook

Where:

• -d or --detach — run container in background;
• -p or --publish — publish a container’s port(s) to the host;
• --name — assign a name to the container.

Verify result:

$ docker ps

Get Jupyter token:

$ docker exec jupyter jupyter-notebook list

Save your token (e.g., 1fe440bef0c2973ab63d464a93ea8124ab5a93f598f5f9cb).

Open browser and navigate to http://localhost:8888/login. Copy token to Token field. Enter password and click Log in and set new password:

Final result looks like below:

Restart jupyter Docker container from terminal in Ubuntu:

$ docker restart jupyter

Add Jupyter to Ubuntu startup. Create rc.local file:

$ sudo touch /etc/rc.local

Add code below to rc.local file and save:

Make rc.local file executable:

$ sudo chmod +x /etc/rc.local

Jupyter runs on startup. Restart Ubuntu and verify result:

$ sudo reboot

Ho to execute sudo in Jupyter without password? Run 3 commands below in Ubuntu terminal:

$ docker exec -u root jupyter chmod 640 /etc/sudoers
$ docker exec -u root jupyter sh -c \
"echo 'jovyan ALL=(ALL) NOPASSWD: ALL' >> /etc/sudoers"
$ docker exec -u root jupyter chmod 440 /etc/sudoers

Verify result in Jupyter terminal: