Using Containers with Brainstorm

Authors: Takfarinas Medani & Malte Höltershinken

Some Brainstorm processes rely on external software distributed using containers (for example: duneuro). Containers allow Brainstorm to run complex tools without requiring manual installation of dependencies.

This page explains how to install a supported container runtime on your system.

Containers for beginners

What is a container?

A container is a packaged version of a software tool that includes everything it needs to run.

With containers:

• You do not need to install additional libraries

• The software runs the same way on different computers
• Brainstorm can automatically download and use the required tools

You do not need prior knowledge of containers to use Brainstorm.

Supported container runtimes

Brainstorm supports the following container runtimes:

• Docker (recommended for most users)

• Podman (Linux alternative to Docker)

• Apptainer / Singularity (recommended on HPC clusters)

Brainstorm automatically detects which runtime is available on your system.

You only need to install one of them.

Note: Docker requires a running daemon (a background service).

Podman and Apptainer do not.

Which runtime should I install?

Windows

Docker Desktop (recommended)

1. Download Docker Desktop:

   • Docker Desktop documentation

2. During installation:

   • Enable WSL 2 if prompted

   • Restart your computer if required

3. Start Docker Desktop and wait until it reports that Docker is running

No additional configuration is required for Brainstorm.

macOS

Docker Desktop (recommended)

1. Download Docker Desktop:

   • Docker Desktop documentation

2. Install and launch Docker Desktop
3. Wait until Docker reports that it is running

On macOS, Docker runs inside a virtual machine. This is normal and fully supported by Brainstorm.

Linux (desktop or workstation)

Option 1: Docker

Install Docker following the official instructions: Docker installation guide

After installation, verify that Docker is running:

docker info

Option 2: Podman

Podman is a Docker-compatible alternative available on many Linux systems: Podman getting started

Podman does not require a background service.

Linux (HPC clusters)

Apptainer / Singularity (recommended)

Most HPC systems provide Apptainer (formerly Singularity) by default.

Check availability:

apptainer version

or

singularity version

If Apptainer is not available, please contact your system administrator or consult: Appt contandoer documentation

Container images in Brainstorm

You do not need to download container images manually.

When a Brainstorm process requires a container:

• Brainstorm checks whether the image is already available
• If not, you will be asked for confirmation
• The image is downloaded automatically

No additional commands are required.

Frequently Asked Questions

Do I need to learn Docker or containers to use Brainstorm?

No.

Brainstorm manages containers automatically. You only need to install a supported runtime.

Docker is installed but Brainstorm says it is not running

Make sure Docker Desktop is started and fully initialized, then retry the Brainstorm process.

I don’t have administrator rights on my computer

If you are working on a shared system or cluster:

• Apptainer / Singularity is usually available
• If not, contact your system administrator

Are containers slower than native installations?

On Linux systems, performance is usually identical.

On Windows and macOS, containers run inside a virtual machine, which may be slightly slower but is generally negligible for most workflows.

Summary

• Brainstorm supports Docker, Podman, and Apptainer / Singularity

• Install one runtime appropriate for your system

• Brainstorm downloads required container images automatically
• No container expertise is required

For additional help, please consult the Brainstorm forum: Brainstorm Forum