Using Docker containers in R

Docker containers are everywhere nowadays, and there are many use cases for containerizing R code. In this deck, I go over the benefits of using containers based on examples from the R universe, and share a few tips and tricks for efficient Docker based workflows.

Transcript

1. Using Docker containers in R @tudosgar | tamaszilagyi.com
2. 2 whoami @tudosgar | tamaszilagyi.com • EX - Sr. Analyst ING • blog: http:/ /tamaszilagyi.com/ • love hiking!
3. 3 • Docker Basics • Our first Docker container: 2 usecases • Best practices, tools and resources Agenda @tudosgar | tamaszilagyi.com
4. 4 @tudosgar | tamaszilagyi.com Your program you not you
5. 5 @tudosgar | tamaszilagyi.com Your program dev prod
6. 6 @tudosgar | tamaszilagyi.com Common problems • Different OS • Missing system-level dependencies • Missing packages • Different versions • Missing keys • …
7. The solution? @tudosgar | tamaszilagyi.com
8. The solution? @tudosgar | tamaszilagyi.com
9. @tudosgar | tamaszilagyi.com Infrastructure Host OS Docker engine app B bin / lib bin / lib app A Infrastructure Host OS Hypervisor guest OS guest OS bin / lib bin / lib app A app B Containers Virtual Machines Unlike VM’s, containers are not “real computers”, just a combination of Linux kernel features that isolate what the processes inside can see and use.
10. Benefits @tudosgar | tamaszilagyi.com • OS independent • Your code is all of a sudden portable • Your analysis is reproducible • Consistency in production • Prototype -> deployment is faster • Relatively lightweight footprint
11. 11 Your first Docker container. @tudosgar | tamaszilagyi.com
12. 12 @tudosgar | tamaszilagyi.com Dockerfile Image Container
13. 13 @tudosgar | tamaszilagyi.com Dockerfile Image Container write command command
14. 14 Usecase #1: Shiny App @tudosgar | tamaszilagyi.com
15. 15 @tudosgar | tamaszilagyi.com A shiny app consists of two components: 1. A ui.R that defines the frontend logic. Shiny App assets
16. 16 @tudosgar | tamaszilagyi.com A shiny app consists of two components: 1. A ui.R that defines the frontend logic. 2. And a server.R for the backend. Shiny App assets
17. 17 How do we package this up? @tudosgar | tamaszilagyi.com
18. 18 @tudosgar | tamaszilagyi.com The Dockerfile is a text file that contains all the instructions on how to build and assemble the image. Each is instruction is a layer. We start with a (larger) read-only layers, this is our base image. Everything ]after are (small) read-write layers. read-only base layers read-write layers Write a Dockerfile!
19. 19 @tudosgar | tamaszilagyi.com The base image contains the read-only layers and is preceded by FROM. Specifically for R, the rocker project (https:/ /www.rocker- project.org/images/) maintains many useful images, for example for shiny apps. The read-write layers are what we add, and here we simply COPY our app into the relevant folder inside the container. Dockerfile
20. 20 @tudosgar | tamaszilagyi.com Dockerfile Image Container write command command
21. 21 @tudosgar | tamaszilagyi.com If your app is large, use volumes!
22. 22 Interlude: docker commands @tudosgar | tamaszilagyi.com • docker build builds a docker image from our Dockerfile. • docker run instantiates the container from our image. • docker ps list (running) containers • docker kill terminates a container. • docker rm deletes a container. • docker login login to Dockerhub (to upload our image). • docker push uploads the image back to Dockerhub. • docker pull pulls an image from the registry (Dockerhub).
23. 23 Usecase #2: Web API @tudosgar | tamaszilagyi.com
24. 24 @tudosgar | tamaszilagyi.com We can create Web API’s by creating a plumber.R file by “merely decorating your existing R source code with special comments” Using Plumber
25. 25 @tudosgar | tamaszilagyi.com We can then plumb our function and expose it to the outside world (in this case only locally). Using Plumber
26. 26 @tudosgar | tamaszilagyi.com We don’t always have everything we need for our application to run. In this case we need to install additional packages and its system level dependencies. We can also EXPOSE ports from within the Dockerfie and run commands using CMD. Dockerfile
27. 27 @tudosgar | tamaszilagyi.com Dockerfile Image Container write command command
28. 28 @tudosgar | tamaszilagyi.com Tips & Tricks
29. 29 @tudosgar | tamaszilagyi.com Use shared base layer images
30. 30 @tudosgar | tamaszilagyi.com Less layers is better
31. 31 @tudosgar | tamaszilagyi.com Use volumes
32. 32 @tudosgar | tamaszilagyi.com Push down layers that invalidate the cache
33. 33 Tools & resources @tudosgar | tamaszilagyi.com • R-specific base images: https:/ /hub.docker.com/r/rocker/ • Free interactive tutorials: https:/ /katacoda.com/courses/docker • Packages containerit and liftr to automatically containerize your R-code • Follow @jessfraz and @abbyfuller
34. http:/ /tamaszilagyi.com/ @tudosgar @tudosgar | tamaszilagyi.com Keep in touch!