Aleksandra Pawlik · Mar 5, 2019

Learning Docker through Dockter

This is a short summary of my, somewhat painful, route to discovering that what I thought I knew about Docker was in fact just the tip of the iceberg. Fortunately, I was able to upgrade my understanding through testing and using a new tool we have been developing: Dockter , a container image builder for researchers.

I used Docker for the first time several years ago when it entered the world of computational research. Working with computational research communities I was well aware of the problems with reproducibility due to dependency hell. Docker images appeared to be (and are!) a great solution. However, not actually doing computational research myself, I only used Docker a couple of times following a tutorial to build an image just to see how it would go. It all went fine, as usually well prepared tutorials present the user with a typical and uncomplicated case. I have run several Docker images that I pulled from the Docker hub. That has also worked fine for me. And that was it, as far as it came to my hands-on experience with Docker.


Hence I was convinced that Docker is the silver bullet for the reproducibility problems in computational research. I happily recommended Docker to a number of researchers that I talked to and even to some developers who were struggling with dependency hell. It was only after I started helping with Stencila’s Dockter that I understood how naive I was.

Firstly, I didn’t realize that rebuilding images with Docker can take a long time even if you only changed a tiny bit in your Dockerfile. In most cases, it is a recommended practice to create Docker images with as few layers as possible. That means that making even small changes in the list of required packages in a Dockerfile can results in Docker reinstalling all the packages.

Really excited about a feature in Dockter which helps deal with that, I started trying it out with a few examples that I was hoping to publish as a part of a Stencila Dockter tutorial. Everything was working fine until one morning my Linux just refused to boot up. After a frustrating few hours of trying to fix the problem using fdisk (suspecting segmentation fault), I booted into Windows on my dual-boot machine to do actual work. The following day using Ubuntu Live USB I got into the Linux partition and discovered that it was pretty much full. My experiments with fast rebuilding Docker images with Dockter resulted in a massive pile of Docker images that filled up the disk and stopped it being able to boot.

That’s the second lesson I learnt about Docker. Clean up your images regularly. They can take a lot of space. While obviously I suppose it wasn’t much of an issue when I was trying out Docker writing Dockerfiles manually. Rebuilding images involved more effort and it made me think about deleting the old image before I built the new one. However, Dockter “exacerbated” the problem as all I had to do to rebuild images was to change the example code in R or Python and mindlessly re-run dockter build, resulting in even more Docker images.

Conscious of the problem I nuked all Docker images which I created with Dockter and successfully logged back into Linux. Still working on the Dockter tutorial, I wanted to be smarter and sometimes would just halt the building process through the ever convenient “Ctrl+C”. Due to the previous image disaster, I was monitoring how much the free space on my drive was shrinking and rather nervously listing the images on the disk. That’s how I discovered Docker dangling images. I’m not sure if it was me hitting “Ctrl+C” too much that caused but now I know how to purge all Docker images effectively . It will bite me back one day but so far so good.

Would I still recommend Docker for reproducible research? Yes.

Docker makes reproducibility a lot easier if you can get the hang of installing the right packages. Using Dockter makes this a lot easier by automatically detecting the right packages to use, eliminating dependency hell. Just make sure to keep track of your disk space if you’re building a lot of images!