Auryn

Auryn is Simulator for recurrent spiking neural networks with synaptic plasticity. It comes with the GPLv3 (please see COPYING).

• For examples and documentation visit https://www.fzenke.net/auryn/
• Please reporte issues here https://github.com/fzenke/auryn/issues

Quick start

Note, Auryn needs a C++ compiler, the Boost libraries (www.boost.org) with MPI support installed. To ensure that the necessary modules are loaded for the compilation process, you can use the following commands before proceeding with the setup:

module load Boost.Python/1.71.0-gompi-2019b
module load Ninja/1.9.0-GCCcore-8.3.0
module load CMake/3.15.3-GCCcore-8.3.0
module load MPC/1.1.0-GCC-8.3.0
module load LLVM/9.0.0-GCCcore-8.3.0
module load Perl/5.30.0-GCCcore-8.3.0

sudo apt-get install cmake git build-essential libboost-all-dev
git clone https://github.com/GenAI0/auryn.git && cd auryn/build/release
./bootstrap.sh
cmake --build . --parallel

Run a first network simulation

cd examples
./sim_coba_benchmark --dir .

will run the Vogels Abbott benchmark, a balanced network model with conductance based synapses. Spiking activity is written to files with the extension 'ras'.

If you have gnuplot installed, you can visualize the output of the simulation follows:

echo "set xlabel 'Time [s]'; plot [1:2] 'coba.0.e.ras' with dots lc rgb 'black'" | gnuplot -p

Here time in seconds is plotted on the x-asis and neuron id on the y-axis.

Install as a library

To install Auryn as a library run:

sudo make install

which will put it under /usr/local/ or for a local install

make DESTDIR=./your/dir/ install

Citing Auryn

If you find Auryn useful and you use it, please cite:

Zenke, F. and Gerstner, W., 2014. Limits to high-speed simulations of spiking neural networks using general-purpose computers. Front Neuroinform 8, 76. doi: 10.3389/fninf.2014.00076

url: http://journal.frontiersin.org/Journal/10.3389/fninf.2014.00076/abstract

Bibtex:

@article{zenke_limits_2014,
	title = {Limits to high-speed simulations of spiking neural networks using general-purpose computers},
	author = {Zenke, Friedemann and Gerstner, Wulfram},
	journal = {Front Neuroinform},
	year = {2014},
	volume = {8},
	url = {http://journal.frontiersin.org/Journal/10.3389/fninf.2014.00076/abstract},
	doi = {10.3389/fninf.2014.00076}
}

License & Copyright

Copyright 2014-2023 Friedemann Zenke

Auryn is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

Auryn is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with Auryn. If not, see http://www.gnu.org/licenses/.