How to: GPU-Accelerated R/Keras on NixOS (via Docker)

I spent a weekend trying to get R, Keras, and CUDA to play nice together on NixOS. I suspect this’ll be the task I’m assigned on my first day in Hell.

I’ve given up on managing it natively with a shell.nix and am now using a Docker image combined with nVidia’s docker wrapper.

Before now, I’d dismissed Docker as “probable fad, soon irrelevant,”1 so this is my first experience with it.

Enabling Docker with the nvidia wrapper took adding this to my configuration .nix:

virtualisation.docker.enable = true;
virtualisation.docker.enableNvidia = true;
hardware.opengl.driSupport32Bit = true;

I ended up cycling through a few different Docker images before rocker/ml-gpu finally worked.

sudo nvidia-docker run --gpus all --rm -v ~/:/home/rps -ti rocker/ml-gpu /bin/bash

The bit here, ~-v /:/home/rps, mounts my home directory into the Docker container, making it the least painful Linux file-sharing experience I’ve ever had, excepting maybe sshfs. I’m impressed; maybe this containerization thing isn’t so bad. This feature allowed me to easily access my training data / emacs config from inside the container.

Fixing Pillow PNG errors

Unfortunately even the Dockerized setup isn’t quite right out the box; it ships an older version of Pillow that produces errors like StopIteration: 'PngStream' object has no attribute 'chunk_bBPn'.

To fix, just install an up-to-date version into the Docker container using:

pip --upgrade pillow

How to check if Keras & R are using the GPU

Your environment ought to be working now. You can confirm that R/Keras is picking up your GPU via


sess = k$get_session()

You can also use nvidia-smi to check the GPU’s load when you’re, say, training a model. It’s sorta like top.

  1. Also in this category: everything that comes out of the JavaScript community, all AWS technologies beside EC2, Kubernetes and whatever new meaning “devOps” has this week and, finally, PulseAudio, whose decade-plus reign of terror can be understood only as divine trial. Just as the Lord tested Jonah with the whale, he tests me with PulseAudio, and just as the Lord commanded the whale to vomit Jonah onto land, he will command the Linux community to vomit PulseAudio onto /dev/null. Amen. [return]

You've read this far⁠—want more?

Subscribe and I'll e-mail you updates along with the ideas that I don't share anywhere else.

This site is protected by reCAPTCHA and the Google Privacy Policy and Terms of Service apply.