sim_brunel2k.cpp File Reference

Implementation of the Brunel (2000) network as implemented in NEST. More...

#include "auryn.h"

Include dependency graph for sim_brunel2k.cpp:

Functions
int	main (int ac, char *av[])

Detailed Description

Implementation of the Brunel (2000) network as implemented in NEST.

This simulates the network from Brunel, N. (2000). Dynamics of sparsely connected networks of excitatory and inhibitory spiking neurons. J Comput Neurosci 8, 183–208. as implemented in the NEST examples (https://github.com/nest/nest-simulator/tree/master/examples/nest).

This file contains the network without plasticity. However, the same network was implemented with and without weight-dependent STDP for performance comparison with NEST. The results are published in Zenke, F., and Gerstner, W. (2014). Limits to high-speed simulations of spiking neural networks using general-purpose computers. Front Neuroinform 8, 76.

Function Documentation

main()

int main	(	int	ac,
		char *	av[]
	)

                            {
        std::string dir = ".";

        std::stringstream oss;
        std::string strbuf ;
        std::string msg;

        NeuronID ne = 8000;
        NeuronID ni = 2000;

        NeuronID nrec = 50;

        double w = 0.1e-3; // 0.1mV PSC size
        double wext = 0.1e-3; 
        double sparseness = 0.1;
        double simtime = 1.;

        double gamma = 5.0;
        double poisson_rate = 20.0e3;

        std::string load = "";
        std::string save = "";

        std::string fwmat_ee = "";
        std::string fwmat_ei = "";
        std::string fwmat_ie = "";
        std::string fwmat_ii = "";

        int errcode = 0;

        

    try {

        po::options_description desc("Allowed options");
        desc.add_options()
            ("help", "produce help message")
            ("simtime", po::value<double>(), "duration of simulation")
            ("gamma", po::value<double>(), "gamma factor for inhibitory weight")
            ("nu", po::value<double>(), "the external firing rate nu")
            ("dir", po::value<std::string>(), "dir from file")
            ("load", po::value<std::string>(), "load from file")
            ("save", po::value<std::string>(), "save to file")
            ("fee", po::value<std::string>(), "file with EE connections")
            ("fei", po::value<std::string>(), "file with EI connections")
            ("fie", po::value<std::string>(), "file with IE connections")
            ("fii", po::value<std::string>(), "file with II connections")
        ;

        po::variables_map vm;        
        po::store(po::parse_command_line(ac, av, desc), vm);
        po::notify(vm);    

        if (vm.count("help")) {
            std::cout << desc << "\n";
            return 1;
        }

        if (vm.count("simtime")) {
                        simtime = vm["simtime"].as<double>();
        } 

        if (vm.count("gamma")) {
                        gamma = vm["gamma"].as<double>();
        } 

        if (vm.count("nu")) {
                        poisson_rate = vm["nu"].as<double>();
        } 

        if (vm.count("dir")) {
                        dir = vm["dir"].as<std::string>();
        } 

        if (vm.count("load")) {
                        load = vm["load"].as<std::string>();
        } 

        if (vm.count("save")) {
                        save = vm["save"].as<std::string>();
        } 

        if (vm.count("fee")) {
                        fwmat_ee = vm["fee"].as<std::string>();
        } 

        if (vm.count("fie")) {
                        fwmat_ie = vm["fie"].as<std::string>();
        } 

        if (vm.count("fei")) {
                        fwmat_ei = vm["fei"].as<std::string>();
        } 

        if (vm.count("fii")) {
                        fwmat_ii = vm["fii"].as<std::string>();
        } 
    }
    catch(std::exception& e) {
                std::cerr << "error: " << e.what() << "\n";
        return 1;
    }
    catch(...) {
                std::cerr << "Exception of unknown type!\n";
    }

        auryn_init(ac, av);

        oss << dir  << "/brunel." << sys->mpi_rank() << ".";
        std::string outputfile = oss.str();

        //
        logger->msg("Setting up neuron groups ...",PROGRESS,true);
        IafPscDeltaGroup * neurons_e = new IafPscDeltaGroup( ne );
        neurons_e->set_tau_mem(20.0e-3);
        neurons_e->set_tau_ref(2.0e-3);
        neurons_e->e_rest = 0e-3;
        neurons_e->e_reset = 10e-3;
        neurons_e->thr = 20e-3;

        IafPscDeltaGroup * neurons_i = new IafPscDeltaGroup( ni );
        neurons_i->set_tau_mem(20.0e-3);
        neurons_i->set_tau_ref(2.0e-3);
        neurons_i->e_rest = 0e-3;
        neurons_i->e_reset = 10e-3;
        neurons_i->thr = 20e-3;

        logger->msg("Setting up Poisson input ...",PROGRESS,true);
        // The traditional way to implement the network is with 
        // independent Poisson noise.
        PoissonStimulator * pstim_e
                = new PoissonStimulator( neurons_e, poisson_rate, wext );
        PoissonStimulator * pstim_i
                = new PoissonStimulator( neurons_i, poisson_rate, wext );

        // The following would give correlated poisson noise from a single
        // population of Poisson Neurons.
        // PoissonGroup * poisson 
        //      = new PoissonGroup( ne, poisson_rate );
        // SparseConnection * cone 
        //      = new SparseConnection(poisson,neurons_e, w, sparseness, MEM );
        // SparseConnection * coni 
        //      = new SparseConnection(poisson,neurons_i, w, sparseness, MEM );

        // This would be a solution where independend Poisson spikes
        // are used from two PoissonGroups.
        // PoissonGroup * pstim_e 
        //      = new PoissonGroup( ne, poisson_rate*ne*sparseness );
        // IdentityConnection * ide 
        //      = new IdentityConnection(pstim_e,neurons_e, w, MEM );
        // PoissonGroup * pstim_i  
        //      = new PoissonGroup( ni, poisson_rate*ne*sparseness );
        // IdentityConnection * idi
        //      = new IdentityConnection(pstim_i,neurons_i, w, MEM );
        

        SparseConnection * con_ee 
                = new SparseConnection( neurons_e,neurons_e,w,sparseness,MEM);

        SparseConnection * con_ei 
                = new SparseConnection( neurons_e,neurons_i,w,sparseness,MEM);

        logger->msg("Setting up I connections ...",PROGRESS,true);
        SparseConnection * con_ii 
                = new SparseConnection( neurons_i,neurons_i,-gamma*w,sparseness,MEM);
        SparseConnection * con_ie 
                = new SparseConnection( neurons_i,neurons_e,-gamma*w,sparseness,MEM);

        msg = "Setting up monitors ...";
        logger->msg(msg,PROGRESS,true);

        std::stringstream filename;
        filename << outputfile << "e.ras";
        SpikeMonitor * smon_e = new SpikeMonitor( neurons_e, filename.str().c_str(), nrec);

        filename.str("");
        filename.clear();
        filename << outputfile << "i.ras";
        SpikeMonitor * smon_i = new SpikeMonitor( neurons_i, filename.str().c_str(), nrec);

        // filename.str("");
        // filename.clear();
        // filename << outputfile << "syn";
        // WeightMonitor * wmon = new WeightMonitor( con_ee, filename.str() );
        // wmon->add_equally_spaced(1000);

        // filename.str("");
        // filename.clear();
        // filename << outputfile << "mem";
        // StateMonitor * smon = new StateMonitor( neurons_e, 13, "mem", filename.str() );

        RateChecker * chk = new RateChecker( neurons_e , 0.1 , 1000. , 100e-3);

        if ( !load.empty() ) {
                sys->load_network_state(load);
        }

        if ( !fwmat_ee.empty() ) con_ee->load_from_complete_file(fwmat_ee);
        if ( !fwmat_ei.empty() ) con_ei->load_from_complete_file(fwmat_ei);
        if ( !fwmat_ie.empty() ) con_ie->load_from_complete_file(fwmat_ie);
        if ( !fwmat_ii.empty() ) con_ii->load_from_complete_file(fwmat_ii);

        logger->msg("Running sanity check ...",PROGRESS,true);
        con_ee->sanity_check();
        con_ei->sanity_check();
        con_ie->sanity_check();
        con_ii->sanity_check();

        logger->msg("Simulating ..." ,PROGRESS,true);
        if (!sys->run(simtime,true)) 
                        errcode = 1;

        if ( !save.empty() ) {
                sys->save_network_state(save);
        }


        if (errcode)
                auryn_abort(errcode);


        logger->msg("Freeing ..." ,PROGRESS,true);
        auryn_free();
        return errcode;
}

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