Using Brian2GeNN

Brian supports generating standalone code for multiple devices. In this mode, running a Brian script generates source code in a project tree for the target device/language. This code can then be compiled and run on the device, and modified if needed. The Brian2GeNN package provides such a ‘device’ to run Brian 2 code on the GeNN (GPU enhanced Neuronal Networks) backend. GeNN is in itself a code-generation based framework to generate and execute code for NVIDIA CUDA. Through Brian2GeNN one can hence generate and run CUDA code on NVIDIA GPUs based solely in Brian 2 input.

Installing the Brian2GeNN interface

In order to use the Brian2GeNN interface, all three Brian 2, GeNN and Brian2GeNN need to be fully installed. The easiest way to do this is by using the conda package provided in the brian-team channel on https://anaconda.org. This will install Brian 2 and its dependencies, and Brian2GeNN with an internal version of GeNN (you can always switch to using an existing GeNN installation by setting the devices.genn.path preference). Note that this will not install the CUDA toolkit and driver necessary to run simulations on a NVIDIA graphics card. These will have to be installed manually, e.g. from NVIDIA’s web site (you can always run simulations in the “CPU-only” mode, but that of course defeats the main purpose of Brian2GeNN...). Depending on the installation method, you might also have to manually set the CUDA_PATH environment variable (or alternatively the devices.genn.cuda_path preference) to point to CUDA’s installation directory.

To install Brian2GeNN via conda use:

conda install -c brian-team brian2genn

If you are not using the conda package manager or if there is no conda package for your architecture, you can always install brian2genn from its source package on http://pypi.python.org/

pip install brian2genn

(might require administrator privileges depending on the configuration of your system; add --user to force an installation with user privileges only). Note that in this case, GeNN needs to be installed manually (see its installation instructions), and either the GENN_PATH environment variable of the devices.genn.path preference have to point to its directory. In addition, the CUDA libraries have to be installed (see above).

Note

The above commands install the necessary packages to run simulations with Brian2/GeNN, but most users would install additional packages, e.g. matplotlib for plotting. This can be done with the same package management tools mentioned above, e.g. use conda install matplotlib or pip install matplotlib.

Using the Brian2GeNN interface

To use the interface one then needs to import the brian2genn interface:

import brian2genn

The you need to choose the ‘genn’ device at the beginning of the Brian 2 script, i.e. after the import statements, add:

set_device('genn')

At the encounter of the first run statement (Brian2GeNN does currently only support a single run statement per script), code for GeNN will be generated, compiled and executed.

The set_device function can also take additional arguments, e.g. to run GeNN in its “CPU-only” mode and to get additional debugging output, use:

set_device('genn', useGPU=False, debug=True)

Not all features of Brian work with Brian2GeNN. The current list of excluded features is detailed in Unsupported features in Brian2GeNN.