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--- examples:sim_coba_benchmark [2014/09/12 10:46] – Updates tutorial with new syntax for example. zenke
+++ examples:sim_coba_benchmark [2015/11/18 18:04] – Removes the full program section --- too hard to maintain zenke
@@ Line 28: / Line 28: @@
 {{ :examples:coba_ras.png?300 |}}
-This figure shows the rasterplot of the spiking activity of the excitatory population written to ''/tmp/coba.0.e.ras''.
+This figure shows the raster plot of the spiking activity of the excitatory population written to ''/tmp/coba.0.e.ras''.
@@ Line 43: / Line 43: @@
 neurons_i->random_mem(-70e-3,10e-3);
 </code>
-This part instatiates two groups of neurons of type [[TIFGroup]] which corresponds to the conductance based model with exponentially decaying PSCs and an absolute refractoriness of 5ms. The ''random_mem'' methods randomize the initial membrane potentials with a Gaussian (mean=-70mV and standard deviation 10e-3mV).
+This part instatiates two groups of neurons of type [[TIFGroup]] which corresponds to the conductance based model with exponentially decaying PSCs and an absolute refractoriness of 5ms. The ''random_mem'' methods randomize the initial membrane potentials with a Gaussian (mean=-70mV and standard deviation 10mV).
@@ Line 77: / Line 77: @@
 </code>
 The second part of the above code saves the network state if ''prime==true'' and is therefore used to create the initial conditions of the self-sustained activity.
-===== The full program =====
-<code c++>
-/*
-* Copyright 2014 Friedemann Zenke
-*
-* This file is part of Auryn, a simulation package for plastic
-* spiking neural networks.
-*
-* 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/>.
-*/
-#include <iostream>
-#include <iomanip>
-#include <stdlib.h>
-#include <string>
-#include <boost/program_options.hpp>
-#include <boost/mpi/environment.hpp>
-#include <boost/mpi/communicator.hpp>
-#include <boost/mpi.hpp>
-#include "System.h"
-#include "IFGroup.h"
-#include "TIFGroup.h"
-#include "PoissonGroup.h"
-#include "SparseConnection.h"
-#include "SymmetricSTDPConnection.h"
-#include "WeightSumMonitor.h"
-#include "SpikeMonitor.h"
-#include "StateMonitor.h"
-#include "RateChecker.h"
-using namespace std;
-namespace po = boost::program_options;
-namespace mpi = boost::mpi;
-int main(int ac,char *av[]) {
-	string dir = "/tmp";
-	string fwmat_ee = "";
-	string fwmat_ei = "";
-	string fwmat_ie = "";
-	string fwmat_ii = "";
-	stringstream oss;
-	string strbuf ;
-	string msg;
-	double w = 0.4;
-	double wi = 5.1;
-	double sparseness = 0.02;
-	double simtime = 20.;
-	NeuronID ne = 3200;
-	NeuronID ni = 800;
-	bool prime = false;
-	bool fast = false;
-	int errcode = 0;
-    try {
-        po::options_description desc("Allowed options");
-        desc.add_options()
-            ("help", "produce help message")
-            ("simtime", po::value<double>(), "simulation time")
-            ("prime", "switch input modalities")
-            ("fast", "turns off most monitoring to reduce IO")
-            ("dir", po::value<string>(), "load/save directory")
-            ("fee", po::value<string>(), "file with EE connections")
-            ("fei", po::value<string>(), "file with EI connections")
-            ("fie", po::value<string>(), "file with IE connections")
-            ("fii", po::value<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")) {
-            cout << desc << "\n";
-            return 1;
-        }
-        if (vm.count("simtime")) {
-			simtime = vm["simtime"].as<double>();
-        }
-        if (vm.count("prime")) {
-			prime = true;
-        }
-        if (vm.count("fast")) {
-			fast = true;
-        }
-        if (vm.count("dir")) {
-			dir = vm["dir"].as<string>();
-        }
-        if (vm.count("fee")) {
-			fwmat_ee = vm["fee"].as<string>();
-        }
-        if (vm.count("fie")) {
-			fwmat_ie = vm["fie"].as<string>();
-        }
-        if (vm.count("fei")) {
-			fwmat_ei = vm["fei"].as<string>();
-        }
-        if (vm.count("fii")) {
-			fwmat_ii = vm["fii"].as<string>();
-        }
-    }
-    catch(exception& e) {
-        cerr << "error: " << e.what() << "\n";
-        return 1;
-    }
-    catch(...) {
-        cerr << "Exception of unknown type!\n";
-    }
-	// BEGIN Global stuff
-	mpi::environment env(ac, av);
-	mpi::communicator world;
-	communicator = &world;
-	oss << dir  << "/coba." << world.rank() << ".";
-	string outputfile = oss.str();
-	char tmp [255];
-	stringstream logfile;
-	logfile << outputfile << "log";
-	logger = new Logger(logfile.str(),world.rank(),PROGRESS,EVERYTHING);
-	sys = new System(&world);
-	// END Global stuff
-	// double primetime = 10;
-	logger->msg("Setting up neuron groups ...",PROGRESS,true);
-	TIFGroup * neurons_e = new TIFGroup( ne);
-	TIFGroup * neurons_i = new TIFGroup( ni);
-	neurons_e->random_mem(-70e-3,10e-3);
-	neurons_i->random_mem(-70e-3,10e-3);
-	logger->msg("Setting up E connections ...",PROGRESS,true);
-	SparseConnection * con_ee
-		= new SparseConnection( neurons_e,neurons_e, w, sparseness, GLUT);
-	SparseConnection * con_ei
-		= new SparseConnection( neurons_e,neurons_i, w,sparseness,GLUT);
-	logger->msg("Setting up I connections ...",PROGRESS,true);
-	SparseConnection * con_ie
-		= new SparseConnection( neurons_i,neurons_e,wi,sparseness,GABA);
-	SparseConnection * con_ii
-		= new SparseConnection( neurons_i,neurons_i,wi,sparseness,GABA);
-	if ( prime ) {
-		msg = "Setting up external input ...";
-		logger->msg(msg,PROGRESS,true);
-		PoissonGroup * poisson= new PoissonGroup(200,10);
-		poisson->seed(132341);
-		// this will give the same seed on each rank,
-		// but since the group should be locked to a single
-		// rank we do not care.
-		SparseConnection * con_ext_e = new SparseConnection(poisson,neurons_e,1,sparseness/2,GLUT);
-		SparseConnection * con_ext_i = new SparseConnection(poisson,neurons_i,1,sparseness/2,GLUT);
-	} else {
-		oss.str("");
-		oss << dir << "/save";
-		sys->load_network_state(oss.str());
-	}
-	if ( !fwmat_ee.empty() ) con_ee->load_from_file(fwmat_ee);
-	if ( !fwmat_ei.empty() ) con_ei->load_from_file(fwmat_ei);
-	if ( !fwmat_ie.empty() ) con_ie->load_from_file(fwmat_ie);
-	if ( !fwmat_ii.empty() ) con_ii->load_from_file(fwmat_ii);
-	// pruning here impairs performance -- probably due to cache poisoning
-	con_ee->prune();
-	con_ei->prune();
-	con_ie->prune();
-	con_ii->prune();
-	if ( !fast ) {
-		msg = "Setting up monitors ...";
-		logger->msg(msg,PROGRESS,true);
-		stringstream filename;
-		filename << outputfile << "e.ras";
-		SpikeMonitor * smon_e = new SpikeMonitor( neurons_e, filename.str().c_str() );
-		filename.str("");
-		filename.clear();
-		filename << outputfile << "i.ras";
-		SpikeMonitor * smon_i = new SpikeMonitor( neurons_i, filename.str().c_str() );
-		filename.str("");
-		filename << outputfile << "e.mem";
-		StateMonitor * smon_mem = new StateMonitor( neurons_e, 3, "mem", filename.str() );
-		filename.str("");
-		filename << outputfile << "e.ampa";
-		StateMonitor * smon_ampa = new StateMonitor( neurons_e, 3, "g_ampa", filename.str() );
-		filename.str("");
-		filename << outputfile << "e.gaba";
-		StateMonitor * smon_gaba = new StateMonitor( neurons_e, 3, "g_gaba", filename.str() );
-	}
-	RateChecker * chk = new RateChecker( neurons_e , -0.1 , 1000. , 100e-3);
-	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 ( prime ) {
-		oss.str("");
-		oss << dir << "/save";
-		sys->save_network_state(oss.str());
-	}
-	logger->msg("Freeing ..." ,PROGRESS,true);
-	delete sys;
-	if (errcode)
-		env.abort(errcode);
-	return errcode;
-}
-</code>