Running A Jupyter Kernel In Apptainer

Just a quick example of running a Jupyter kernel inside an ~~Singularity~~ Apptainer container.

First define a container with all the required applications, in particular ipykernel.

bootstrap: docker
From: python:3.11-slim-buster

%runscript
    echo "Hello... I am a new Singularity container"

%labels
    AUTHOR andrew@kail.io

%post
    apt-get update && apt-get install -y python-pip python-dev build-essential
    pip install --upgrade pip
    pip install numpy
    pip install ipykernel

Build the container image.

apptainer build ipykernel.sif ipykernel.def

Finally, add the following to kernel specification under /home/<user>/.local/share/jupyter/kernels/<kernelname>/kernel.json

{
 "argv": [
   "singularity",
   "exec",
   "--cleanenv",
   "/home/akail/Projects/singularity/kernel/ipykernel.sif",
   "python",
   "-m",
   "ipykernel",
   "-f",
   "{connection_file}"
 ],
 "language": "python",
 "display_name": "singularity-kernel"
}

Restart Jupyter or Jupyter lab and you're all set.