TIL: Building Docker Images with Conda and Custom Users (and devcontainers!)


Hampus Londögård


February 18, 2024

When building Docker containers there’s a few things to clarify:

  1. You’re building something layer by layer
  2. Things you do in Docker is not kept in docker run unless you specify it through special commands.
    • That is, it isn’t a stateful operation to run RUN conda activate highlights.
  3. Docker can be run as multiple users, but is built by default as root
  4. The original container X, FROM X, can have an environment with magic enabled

I found a few problems based on all this when trying to deploy my Solara application using Docker.

  1. conda path is not enabled by default, even if I modified .bashrc.
  2. User permissions where not available, i.e. I wasn’t allowed to create folders.
  3. devcontainer as base image added a “default user” called vscode.

Let’s go through each one step-by-step!

Problem 1. Enabling conda in docker run ..

When running docker run no shell is applied by default. Additionally Docker defaults to /bin/sh because bash is not available in all images. This means that .bashrc modifications and similar not applied when starting your container!

There’s a few ways to make the conda env available by default in your shell, I opted for what I found simplest - modifying $PATH.

See the following edit in Dockerfile

ENV PATH /opt/conda/envs/<ENV_NAME>/bin/:$PATH

Through this when my CMD I can call solara run (solara is a python library available in my env).

Problem 2. Enabling permission to do OS changes, e.g. os.mkdir

As mentioned Docker is built using root user. From my understanding it is later run as any user depending on how you can docker run, this can deactivate capabilities to modify os. One such capability that I use is to run mkdir and creating files.

The simplest solution I found was to:

  1. Create a new user
    • For HuggingFace spaces it’s ID should be set as -u 1000
  2. Allow new user to control the folder where you app resides COPY --chown=user
  3. Default to running as user (USER user)

In a Dockerfile it ends up as follows.

RUN useradd -m -u 1000 user
USER user

COPY --chown=user . /app

Voila! That should make it work!

…unless you have a weird base-image that modifies the OS, i.e. devcontainer as base-image. More about this in the section below! 👇

Problem 3. vscode user

I mentioned that my base-image, FROM mcr.microsoft.com/vscode/devcontainers/miniconda:latest, there already is a user on id=1000. This user is apparently called vscode!

I found this by running docker run -it <img_name> /bin/bash and grokking around in the terminal.

This was a huge blocker for me and took a long while to understand. To enable my deployment I instead of creating a custom user hijacked the existing user vscode. See the final Dockerfile.

FROM mcr.microsoft.com/vscode/devcontainers/miniconda:latest

USER vscode

COPY --chown=vscode . /app

RUN conda env create -f env.yml
RUN conda clean -a -y
RUN conda init


ENV PATH /opt/conda/envs/highlights/bin/:$PATH

CMD ["solara", "run", "sol_app.py", "--host="]

And that makes everything work!