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.
Contents
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.
Which runtime should I install?
Operating system |
Recommended runtime |
Windows |
Docker Desktop |
macOS |
Docker Desktop |
Linux (desktop) |
Docker or Podman |
Linux (HPC) |
Apptainer / Singularity |
Windows
Docker Desktop (recommended)
- Download Docker Desktop:
- During installation:
Enable WSL 2 if prompted
- Restart your computer if required
Start Docker Desktop and wait until it reports that Docker is running
No additional configuration is required for Brainstorm.
macOS
Docker Desktop (recommended)
- Download Docker Desktop:
- Install and launch Docker Desktop
- 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