Container image for Brian 1¶
Brian 1 depends on Python 2.x and other deprecated libraries, so running it on modern systems has become difficult. For convenience, we provide a Docker image that you can use to run existing Brian 1 code. It is based on a Debian image, and provides Brian 1.4.3, as packaged by the NeuroDebian team.
To use these images, you either need to have docker,
podman or singularity
installed – the commands below are shown for the
docker command, but you can
simply replace them by
podman if necessary. For singularity, the basic workflow
is similar but the commands are slightly different, please see the documentation.
To pull the container image with singularity, refer to
Running a graphical interface within the docker container can be complicated, and the details how to make it work depend on the host operating system. We therefore recommend to instead either 1) only use the container image to generate and save the simulation results to disk, and then to create the plots on the host system, or 2) to use the container image to plot files to disk by adding
plt.savefig(...) to the script. The container already sets the matplotlib backend to
Agg by default (by setting the environment variable
MPLBACKEND), necessary to avoid errors when no graphical interface is available.
To download the image and to rename it to
brian1 (for convenience only, the commands below would also work directly with the full name), use:
docker pull docker.io/briansimulator/brian1.4.3 docker tag briansimulator/brian1.4.3 brian1
The following command runs
myscript.py with the container image providing Brian 1 and its dependencies, mapping the current directory to the working directory in the container (this means, the script has access to all files in the current directory and its subdirectories, and can also write files there):
docker run -v "$(pwd):/workdir" brian1 python myscript.py
For Windows users using the Command Prompt (
cmd.exe) instead of the Powershell, the following command will do the same thing:
docker run -v %cd%:/workdir brian1 python myscript.py
To run an interactive ipython prompt, use:
docker run -it -v "$(pwd):/workdir" brian1 ipython
Depending on your operating system, files written by the container might be owned by the user “root”, which can lead to problems later (e.g. you cannot rename/move/delete/overwrite the file on your home system without administrator rights). On Unix-based systems, you can prevent this issue by running scripts with the same user id as the host user:
docker run -u $(id -u):$(id -g) -v "$(pwd):/workdir" brian1 python myscript.py
Please report any issues to the Brian discussion forum.