Lab 3: Docker

Biostat 203B

Author

Dr. Hua Zhou @ UCLA

Published

January 23, 2024

A customized Docker container provides a self-contained Linux Ubuntu environment for reproducing materials in this course. This tutorial shows how to install Docker Desktop on your computer, run the Docker container, build your own Docker image, and push the image to Docker Hub.

This tutorial assumes that you have already installed R, RStudio, and Git on your computer. If not, please refer to the Lab 1.

1 Install Docker Desktop

Download and install the Docker Desktop https://www.docker.com/products/docker-desktop/.

2 Run a Docker container

  • Open Terminal (Mac Terminal, Windows Git Bash, or Windows WSL) at the /Docker folder of the course material.

  • To run a Docker container, we first modify the volumes section of the docker-compose.yml file to map the 203b-lecture, 203-hw, and mimic folders on your computer to the home directory in the Ubuntu system in Docker container. Then type

docker-compose up

to run the Docker container. This can take up to 10 minutes for Docker to pull the image, depending on internet connection.

  • Point your browser to localhost:8787 to connect to the RStudio Server running on the Ubuntu system in the container.

3 Build your own Docker image

  • Modify the Dockerfile.amd64 (Intel or AMD CPU) or Dockerfile.arm64 (ARM CPU e.g. Apple M1/M2/M3 CPU) according to your computer architecture.

  • Open Terminal (Mac Terminal, Windows Git Bash, or Windows WSL) at the /Docker folder of course material. Type

docker build -f Dockerfile.amd64 . -t [DOCKERHUB_USERNAME]/ucla_biostat_203b_2024w

to build the new Docker image.

4 Push the Docker image to Docker Hub

docker push [DOCKERHUB_USERNAME]/ucla_biostat_203b_2024w

to push the new Docker image to Docker Hub.

5 Run Docker container on Hoffman2 (TODO)

Follow the instructions here to run the Docker container on Hoffman2.

To pull the image:

apptainer pull docker://huazhou/ucla_biostat_203b_2024w

Run the container:

apptainer shell ucla-biostat-203b-2024w_latest.sif

Not worked out yet.

6 Run Docker container on cloud (TODO)

6.1 Initial set up to push Docker image to GCR (Google Cloud Registry)

  • Install Google Cloud CLI on local machine (laptop or desktop).

  • Initialize the gcloud CLI:

gcloud init
  • GCP authentication:
gcloud auth configure-docker -q
  • List existing Docker images and tag for gcr:
docker image list
docker tag huazhou/ucla-biostat-203b-2024w gcr.io/biostat-203b-2024-winter/ubuntu-rstudio-server
  • Push the image to gcr:
docker push gcr.io/biostat-203b-2024-winter/ubuntu-rstudio-server

6.2 Run Docker container on GCP

  • Create a GCE (Google Compute Engine) instance

  • Create a firewall rule rstudio-server that opens the 8787 port and add Network tag rstudio-server to the GCE instance.

  • Paste the GCR image name gcr.io/biostat-203b-2024-winter/ubuntu-rstudio-server to the Container image field of the GCE instance.

  • Input Environment Variables: PASSWORD: 203b, ROOT: true, and DISABLE_AUTH: true to the GCE instance.

  • Add volume and disks to the GCE instance. I haven’t got the permissions right yet. The /mnt/mimic and /home/studio/203b-lecture appear to be owned by root and not writable by rstudio. (TODO)