Docker2Singularity

A simple utility to convert local docker image to remote singularity image suitable for running on HPC environments.

Generally speaking there is a straightforward way to do this if you create and make your docker image available in a repository. In such case, you can pull the docker image and directly convert it to a singularity using

singularity pull docker://repo/image:tag

However, this utility is useful when you want to stay offline and directly convert your local docker image to a singularity container.

Before You Start

• Local is where you configure/debug/create your docker image. Most probably this will be your local machine with docker setup.
  • In docker/Dockerfile, image can be customized based on requirements e.g. packages and dependencies etc. Please note that the same environment will be available in singularity
• Remote is any environment with singularity already setup. Usually this will be an HPC head/login node.

How To Run?

This is a three step process.

1. [Local] Run d2s_local.sh to create local docker image tarball
   • [Optional] Customize image name in config.env
2. Upload following to Remote environment. (Any file transfer utility e.g. scp etc.)
   • config.env
   • d2s_image.tar (locally generated docker image tarball)
   • d2s_remote.sh
3. [Remote] Run d2s_remote.sh to generate singularity image (d2s_image.sif)

What's Next?

Once you successfully create a singularity image, you can launch and get a shell in it using

singularity shell d2s_image

Alternatively, you can submit a job to HPC with the singularity container by creating the following sbatch script

[NOTE] Please change CMD to desired command or script to be executed for the job.

# Script file name: sbatch_run.sh
#!/bin/bash
#SBATCH --job-name=bone_sim
#SBATCH --cpus-per-task=4
#SBATCH --mem-per-cpu=1G
#SBATCH --partition=high
#SBATCH -o %x-%j.out # File to which STDOUT will be written
#SBATCH -e %x-%j.err # File to which STDERR will be written

singularity run d2s_image.sif CMD

Then submit the job by

sbatch sbatch_run.sh