First parallel version of PhyloMOEA

git-svn-id: svn://scm.gforge.inria.fr/svnroot/paradiseo@1390 331e1502-861f-0410-8da2-ba01fb791d7f

contribution/branches/PhyloMOEA/PhyloMOEA/PhyloMOEA.cpp

@@ -1,11 +1,13 @@
 #include <eo>
 #include <moeo>
+#include <peo>
 #include <PhyloMOEO.h>
 #include <PhyloMOEO_operators.h>
 #include <PhyloMOEO_init.h>
 #include <PhyloMOEO_eval.h>
 #include <PhyloMOEO_archive.h>
 #include <PhyloMOEOProbMatrixContainerUpdater.h>
+#include <PhyloMOEO_packunpack.h>
 #include <moeoNSGAII2.h>
 #include <utils/moeoBestObjVecStat.h>
 #include <utils/moeoAverageObjVecStat.h>
@@ -13,6 +15,7 @@
 #include <eoCountedFileMonitor.h>
 #include <eoSingleFileCountedStateSaver.h>
 #include <vectorSortIndex.h>
+
 #include <utils.h>
 #include <ctime>
 #include <apply.h>
@@ -28,13 +31,17 @@ unsigned int ngenerations,  popsize, ncats;
 ofstream exp_data,evolution_data, best_media_scores, final_trees, final_pareto_trees, clades_pareto, clades_final,final_scores,pareto_scores;
 
 
+
 int main(int argc, char *argv[])
 {
-	welcome_message();
+
+	peo :: init( argc, argv );
+
+
+
 
 	eoParser parser(argc, argv);
 
-
 	seed = parser.createParam((unsigned int)(time(NULL)), "seed", "Random Seed", 's',"Param").value();
 	
 	popsize = parser.createParam((unsigned int)(50), "popSize", "Population size", 'n',"Param").value();
@@ -52,18 +59,22 @@ int main(int argc, char *argv[])
  	convert << seed;
 	expid = parser.createParam(convert.str(), "expid", "Experiment ID", 'e',"Param").value();
 
-
+	if(getNodeRank()==1) welcome_message();
 	if( datafile.size()==0 )
 	{
-	 	parser.printHelp( cout );
+		
+	 	if(getNodeRank()==1) parser.printHelp( cout );
 		return(-1);
 	}
 	
+
+	// all nodes read datafile and prepares likelihood and parsimony calculation
 	string filename = path + datafile;
 	cout << "\n\nReading Sequence Datafile...";
 	Sequences seq(filename.c_str());
 	cout << " done.\n";
 	// calculate datafile
+	cout << "calculating pattersn..." << getNodeRank() << endl;
 	seq.calculate_patterns();
 	seq.calculate_frequences();
 
@@ -73,22 +84,19 @@ int main(int argc, char *argv[])
 	ParsimonyCalculator parsi_calc(templatetree);
  	SubstModel modelHKY( seq, SubstModel::HKY85);
  	modelHKY.init();
- 	modelHKY.set_kappa(kappa); // banco_grande
+ 	modelHKY.set_kappa(kappa); 
  	ProbMatrixContainer probmatrixs(modelHKY);
 	LikelihoodCalculator lik_calc(templatetree, modelHKY, probmatrixs,ncats);
 	lik_calc.set_alpha(alpha);
  	modelHKY.init();
 	PhyloEval byobj( parsi_calc, lik_calc );
-
 	Phyloraninit initializer(templatetree);
-
-	eoState state;
-	
-	//eoPop <PhyloMOEO> &population = state.takeOwnership(eoPop<PhyloMOEO>(popsize, initializer));
-
 	eoPop<PhyloMOEO> population(popsize, initializer);
-	//state.registerObject( population ); 
+	peoMoeoPopEval <PhyloMOEO> eval(byobj);
 
+	// Only the master node read the initial trees and writes ouput files
+	if(getNodeRank()==1)
+	{
 		cout << "\n\nReading Initial Trees...";
 		if( usertree.size() >0)	
 		{
@@ -97,7 +105,6 @@ int main(int argc, char *argv[])
 		}
 		cout << " done.\n";
 
-
 		cout << "\n\nCreating output files...";
 	
 		try{
@@ -118,62 +125,96 @@ int main(int argc, char *argv[])
 		{
 			e.Report();
 		}
-			// create the moea	
+				// create the moea	<	
 		save_exp_params(exp_data);
 		seq.save_seq_data(exp_data); 
 
-	moeoAverageObjVecStat <PhyloMOEO> bestfit;
+	}
-	moeoBestObjVecStat <PhyloMOEO> avgfit;
-	eoPopStat<PhyloMOEO> popstats;
-
-	eoCountedFileMonitor media_scores( 2, path + datafile + "_media_scores_" + expid + ".txt", "\t", true,true );
-	media_scores.add( bestfit);
-	media_scores.add( avgfit) ;
-
-	eoCountedFileMonitor evolution_scores( 2, path + datafile + "_evolution_data_" + expid + ".txt", "\n", true,true );
-	evolution_scores.add( popstats);
-
-
-	//cout << "\n\nRunning NSGA-II ..." << endl;
 
 	eoGenContinue<PhyloMOEO> continuator(ngenerations);
 	eoCheckPoint<PhyloMOEO> cp(continuator);
- 	eoValueParam<unsigned> generationCounter(0, "Gen.");
-	eoIncrementor<unsigned> increment(generationCounter.value()); 
-	cp.add(increment); 
-	eoStdoutMonitor monitor(false);
-	monitor.add(generationCounter); 
-	cp.add(monitor); 
 	Phylomutate mutator;
 	Phylocross crossover;
 	eoSequentialOp<PhyloMOEO> operadores;
 	operadores.add(crossover,pcrossover);
 	operadores.add(mutator,pmutation);
 	PhyloMOEOProbMatrixContainerUpdater probmatrixupdater(probmatrixs);
-	cp.add( bestfit);
-	cp.add( avgfit);
-	cp.add( media_scores);
-	cp.add( evolution_scores );
-	cp.add( popstats);
 	cp.add( probmatrixupdater );
 
-//	apply<PhyloMOEO> ( byobj, population );
+	moeoAverageObjVecStat <PhyloMOEO> *bestfit;
-//	population.printOn(cout);
+	moeoBestObjVecStat <PhyloMOEO> *avgfit;
+	eoPopStat<PhyloMOEO> *popstats;
+	
+	eoCountedFileMonitor *media_scores, *evolution_scores;
+	eoStdoutMonitor *monitor;
+	eoValueParam<unsigned> *generationCounter;
+	eoIncrementor<unsigned> *increment;
+
+
+	// only the master output files
+	if(getNodeRank()==1){
+			
+			generationCounter = new eoValueParam<unsigned> (0, "Gen.");
+			increment = new eoIncrementor<unsigned>(generationCounter->value()); 
+			cp.add(*increment); 
+
+			monitor = new eoStdoutMonitor(false);
+			monitor->add(*generationCounter);
+
+			bestfit = new moeoAverageObjVecStat <PhyloMOEO>();
+			avgfit = new moeoBestObjVecStat <PhyloMOEO>();
+			popstats = new eoPopStat<PhyloMOEO> ();
+
+			media_scores = new eoCountedFileMonitor( 2, path + datafile + "_media_scores_" + expid + ".txt", "\t", true,true );
+			media_scores->add( *avgfit) ;
+			media_scores->add( *bestfit );
+
+			evolution_scores = new eoCountedFileMonitor( 2, path + datafile + "_evolution_data_" + expid + ".txt", "\n", true,true );
+			evolution_scores->add( *popstats);
+			cp.add( *media_scores);
+			cp.add( *evolution_scores );
+			cp.add( *popstats);
+			cp.add( *bestfit);
+			cp.add( *avgfit);
+			cp.add( *monitor); 
+	}
+	
+	
 	if(algotype == "ibea")
 	{
 		moeoAdditiveEpsilonBinaryMetric < ObjectiveVector > metric;
 		moeoIBEA < PhyloMOEO > algo (cp, byobj, operadores, metric);
-		cout << "\n\nRunning IBEA ..." << endl;	
+		if(getNodeRank()==1){
-		algo(population);
+		cout << "\n\nRunning IBEA ..." << endl;	}
+  		peoWrapper parallelEA( algo, population);
+  		eval.setOwner(parallelEA);
+		peo :: run();
+		peo :: finalize();
+		//algo(population);
 	}	
 	else
 	{
 		moeoNSGAII < PhyloMOEO > algo (cp, byobj, operadores);
-		cout << "\n\nRunning NSGA-II ..." << endl;	
+		if(getNodeRank()==1){
-		algo(population);
+		cout << "\n\nRunning NSGA-II ..." << endl;	}
-
+  		peoWrapper parallelEA( algo, population); 
+  		eval.setOwner(parallelEA);
+		peo :: run();
+		peo :: finalize();
+		//algo(population);
 	}
 
+	if (getNodeRank()==1) 
+	{
+		delete media_scores;
+		delete evolution_scores;
+		delete bestfit;
+		delete avgfit;
+		delete popstats;
+		delete monitor;
+		delete generationCounter;
+		delete increment;
+	
 		cout << "\nCalculating Final Solutions...";
 		cout << "  done\n";
 	
@@ -184,7 +225,7 @@ int main(int argc, char *argv[])
 		// optimize remaining solutions
 		cout << "\nOptimizing tree branch lenghts...\n";
 		
-	optimize_solutions( finalsolutions, lik_calc );
+		//optimize_solutions( finalsolutions, lik_calc );
 		cout << "\nReevaluating individuals \n";
 		apply<PhyloMOEO> ( byobj, finalsolutions );
 	
@@ -228,7 +269,7 @@ int main(int argc, char *argv[])
 		paretosplitstatsaver.add(splitstats);
 		paretosplitstatsaver();
 	
-//	save_partitions(splitstats.value(), clades_pareto);
+	//	save_partitions(splitstats.value(), clades_pareto);
 		//split_frequences.clear();
 		cout << " done\n";
 		exp_data.close();
@@ -240,10 +281,11 @@ int main(int argc, char *argv[])
 		final_pareto_trees.close();
 		clades_pareto.close();
 		clades_final.close();
-	gsl_rng_free(rn2);
-//	delete probmatrixs;
-	delete rn;
 		cout << "\nPhyloMOEA execution finishes !\n";
+	}
+	gsl_rng_free(rn2);
+	//	delete probmatrixs;
+	delete rn;
 	return 0;
 }