First parallel version of PhyloMOEA
git-svn-id: svn://scm.gforge.inria.fr/svnroot/paradiseo@1390 331e1502-861f-0410-8da2-ba01fb791d7f
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wcancino
parent
4e1826a94c
commit
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1 changed files with 180 additions and 138 deletions
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@ -1,11 +1,13 @@
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#include <eo>
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#include <moeo>
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#include <peo>
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#include <PhyloMOEO.h>
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#include <PhyloMOEO_operators.h>
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#include <PhyloMOEO_init.h>
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#include <PhyloMOEO_eval.h>
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#include <PhyloMOEO_archive.h>
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#include <PhyloMOEOProbMatrixContainerUpdater.h>
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#include <PhyloMOEO_packunpack.h>
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#include <moeoNSGAII2.h>
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#include <utils/moeoBestObjVecStat.h>
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#include <utils/moeoAverageObjVecStat.h>
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@ -13,6 +15,7 @@
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#include <eoCountedFileMonitor.h>
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#include <eoSingleFileCountedStateSaver.h>
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#include <vectorSortIndex.h>
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#include <utils.h>
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#include <ctime>
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#include <apply.h>
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@ -28,13 +31,17 @@ unsigned int ngenerations, popsize, ncats;
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ofstream exp_data,evolution_data, best_media_scores, final_trees, final_pareto_trees, clades_pareto, clades_final,final_scores,pareto_scores;
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int main(int argc, char *argv[])
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{
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welcome_message();
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peo :: init( argc, argv );
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eoParser parser(argc, argv);
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seed = parser.createParam((unsigned int)(time(NULL)), "seed", "Random Seed", 's',"Param").value();
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popsize = parser.createParam((unsigned int)(50), "popSize", "Population size", 'n',"Param").value();
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@ -52,18 +59,22 @@ int main(int argc, char *argv[])
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convert << seed;
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expid = parser.createParam(convert.str(), "expid", "Experiment ID", 'e',"Param").value();
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if(getNodeRank()==1) welcome_message();
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if( datafile.size()==0 )
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{
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parser.printHelp( cout );
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if(getNodeRank()==1) parser.printHelp( cout );
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return(-1);
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}
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// all nodes read datafile and prepares likelihood and parsimony calculation
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string filename = path + datafile;
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cout << "\n\nReading Sequence Datafile...";
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Sequences seq(filename.c_str());
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cout << " done.\n";
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// calculate datafile
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cout << "calculating pattersn..." << getNodeRank() << endl;
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seq.calculate_patterns();
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seq.calculate_frequences();
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@ -73,177 +84,208 @@ int main(int argc, char *argv[])
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ParsimonyCalculator parsi_calc(templatetree);
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SubstModel modelHKY( seq, SubstModel::HKY85);
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modelHKY.init();
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modelHKY.set_kappa(kappa); // banco_grande
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modelHKY.set_kappa(kappa);
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ProbMatrixContainer probmatrixs(modelHKY);
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LikelihoodCalculator lik_calc(templatetree, modelHKY, probmatrixs,ncats);
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lik_calc.set_alpha(alpha);
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modelHKY.init();
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PhyloEval byobj( parsi_calc, lik_calc );
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Phyloraninit initializer(templatetree);
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eoState state;
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//eoPop <PhyloMOEO> &population = state.takeOwnership(eoPop<PhyloMOEO>(popsize, initializer));
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eoPop<PhyloMOEO> population(popsize, initializer);
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//state.registerObject( population );
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peoMoeoPopEval <PhyloMOEO> eval(byobj);
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cout << "\n\nReading Initial Trees...";
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if( usertree.size() >0)
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// Only the master node read the initial trees and writes ouput files
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if(getNodeRank()==1)
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{
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filename = path + usertree;
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readtrees(filename.c_str(), population);
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}
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cout << " done.\n";
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cout << "\n\nCreating output files...";
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try{
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filename = path + datafile + "_exp_param_" + expid + ".txt";
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exp_data.open(filename.c_str());
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exp_data.precision(15);
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exp_data.setf(ios::fixed);
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if( !exp_data.is_open() )
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cout << "\n\nReading Initial Trees...";
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if( usertree.size() >0)
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{
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throw( ExceptionManager(12) );
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filename = path + usertree;
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readtrees(filename.c_str(), population);
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}
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cout << " done.\n";
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cout << "\n\nCreating output files...";
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try{
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filename = path + datafile + "_exp_param_" + expid + ".txt";
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exp_data.open(filename.c_str());
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exp_data.precision(15);
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exp_data.setf(ios::fixed);
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if( !exp_data.is_open() )
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{
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throw( ExceptionManager(12) );
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}
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cout << " done.\n";
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}
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catch ( ExceptionManager e )
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{
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e.Report();
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}
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// create the moea <
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save_exp_params(exp_data);
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seq.save_seq_data(exp_data);
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}
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catch ( ExceptionManager e )
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{
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e.Report();
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}
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// create the moea
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save_exp_params(exp_data);
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seq.save_seq_data(exp_data);
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moeoAverageObjVecStat <PhyloMOEO> bestfit;
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moeoBestObjVecStat <PhyloMOEO> avgfit;
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eoPopStat<PhyloMOEO> popstats;
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eoCountedFileMonitor media_scores( 2, path + datafile + "_media_scores_" + expid + ".txt", "\t", true,true );
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media_scores.add( bestfit);
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media_scores.add( avgfit) ;
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eoCountedFileMonitor evolution_scores( 2, path + datafile + "_evolution_data_" + expid + ".txt", "\n", true,true );
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evolution_scores.add( popstats);
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//cout << "\n\nRunning NSGA-II ..." << endl;
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eoGenContinue<PhyloMOEO> continuator(ngenerations);
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eoCheckPoint<PhyloMOEO> cp(continuator);
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eoValueParam<unsigned> generationCounter(0, "Gen.");
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eoIncrementor<unsigned> increment(generationCounter.value());
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cp.add(increment);
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eoStdoutMonitor monitor(false);
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monitor.add(generationCounter);
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cp.add(monitor);
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Phylomutate mutator;
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Phylocross crossover;
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eoSequentialOp<PhyloMOEO> operadores;
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operadores.add(crossover,pcrossover);
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operadores.add(mutator,pmutation);
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PhyloMOEOProbMatrixContainerUpdater probmatrixupdater(probmatrixs);
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cp.add( bestfit);
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cp.add( avgfit);
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cp.add( media_scores);
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cp.add( evolution_scores );
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cp.add( popstats);
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cp.add( probmatrixupdater );
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moeoAverageObjVecStat <PhyloMOEO> *bestfit;
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moeoBestObjVecStat <PhyloMOEO> *avgfit;
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eoPopStat<PhyloMOEO> *popstats;
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eoCountedFileMonitor *media_scores, *evolution_scores;
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eoStdoutMonitor *monitor;
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eoValueParam<unsigned> *generationCounter;
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eoIncrementor<unsigned> *increment;
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// only the master output files
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if(getNodeRank()==1){
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generationCounter = new eoValueParam<unsigned> (0, "Gen.");
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increment = new eoIncrementor<unsigned>(generationCounter->value());
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cp.add(*increment);
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monitor = new eoStdoutMonitor(false);
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monitor->add(*generationCounter);
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bestfit = new moeoAverageObjVecStat <PhyloMOEO>();
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avgfit = new moeoBestObjVecStat <PhyloMOEO>();
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popstats = new eoPopStat<PhyloMOEO> ();
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media_scores = new eoCountedFileMonitor( 2, path + datafile + "_media_scores_" + expid + ".txt", "\t", true,true );
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media_scores->add( *avgfit) ;
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media_scores->add( *bestfit );
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evolution_scores = new eoCountedFileMonitor( 2, path + datafile + "_evolution_data_" + expid + ".txt", "\n", true,true );
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evolution_scores->add( *popstats);
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cp.add( *media_scores);
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cp.add( *evolution_scores );
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cp.add( *popstats);
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cp.add( *bestfit);
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cp.add( *avgfit);
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cp.add( *monitor);
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}
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// apply<PhyloMOEO> ( byobj, population );
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// population.printOn(cout);
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if(algotype == "ibea")
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{
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moeoAdditiveEpsilonBinaryMetric < ObjectiveVector > metric;
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moeoIBEA < PhyloMOEO > algo (cp, byobj, operadores, metric);
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cout << "\n\nRunning IBEA ..." << endl;
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algo(population);
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if(getNodeRank()==1){
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cout << "\n\nRunning IBEA ..." << endl; }
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peoWrapper parallelEA( algo, population);
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eval.setOwner(parallelEA);
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peo :: run();
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peo :: finalize();
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//algo(population);
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}
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else
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{
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moeoNSGAII < PhyloMOEO > algo (cp, byobj, operadores);
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cout << "\n\nRunning NSGA-II ..." << endl;
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algo(population);
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if(getNodeRank()==1){
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cout << "\n\nRunning NSGA-II ..." << endl; }
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peoWrapper parallelEA( algo, population);
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eval.setOwner(parallelEA);
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peo :: run();
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peo :: finalize();
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//algo(population);
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}
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if (getNodeRank()==1)
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{
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delete media_scores;
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delete evolution_scores;
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delete bestfit;
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delete avgfit;
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delete popstats;
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delete monitor;
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delete generationCounter;
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delete increment;
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cout << "\nCalculating Final Solutions...";
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cout << " done\n";
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PhyloMOEOFinalSolutionsArchive finalsolutions;
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finalsolutions.operator()(population);
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//remove_final_solutions( population );
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// optimize remaining solutions
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cout << "\nOptimizing tree branch lenghts...\n";
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cout << "\nCalculating Final Solutions...";
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cout << " done\n";
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optimize_solutions( finalsolutions, lik_calc );
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cout << "\nReevaluating individuals \n";
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apply<PhyloMOEO> ( byobj, finalsolutions );
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finalsolutions.save_scores(path + datafile + "_final_scores_" + expid + ".txt","#Final Solutions Scores");
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finalsolutions.save_trees(path + datafile + "_final_trees_" + expid + ".txt");
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cout << "\ndone \n";
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PhyloMOEOFinalSolutionsArchive finalsolutions;
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finalsolutions.operator()(population);
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// print the optimized solutions
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//print_scores_pop( -2, population, evolution_data);
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//print_scores_pop( -2, population, final_scores);
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//save_trees(finalsolutions, final_trees);
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cout << "\n\nCalculating Final Solutions clade support...";
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//remove_final_solutions( population );
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// optimize remaining solutions
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cout << "\nOptimizing tree branch lenghts...\n";
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//optimize_solutions( finalsolutions, lik_calc );
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cout << "\nReevaluating individuals \n";
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apply<PhyloMOEO> ( byobj, finalsolutions );
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PhyloMOEOPartitionStat splitstats;
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splitstats(finalsolutions);
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eoFileMonitor finalsplitstatsaver(path+datafile+"_clades_final_"+expid+".txt");
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finalsplitstatsaver.add(splitstats);
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finalsplitstatsaver();
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//cout << splitstats.value() << endl;
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//partition_map split_frequences;
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//calculate_frequence_splits(finalsolutions,split_frequences);
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cout << " done\n";
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//save_partitions(splitstats.value(), clades_final);
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//split_frequences.clear();
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// remove dominate solutions
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cout << "\nCalculating Pareto-optimal Solutions...";
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PhyloMOEOParetoSolutionsArchive paretosolutions;
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paretosolutions.operator()(finalsolutions);
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paretosolutions.save_scores(path + datafile + "_pareto_scores_" + expid + ".txt","#Pareto Solutions Scores");
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paretosolutions.save_trees(path + datafile + "_pareto_trees_" + expid + ".txt");
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cout << " done\n";
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// print final pareto trees
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//save_trees( paretosolutions, final_pareto_trees);
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cout << "\nCalculating Pareto-optimal Solutions clade support...";
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splitstats(paretosolutions);
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//calculate_frequence_splits(paretosolutions,split_frequences);
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eoFileMonitor paretosplitstatsaver(path+datafile+"_clades_pareto_"+expid+".txt");
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paretosplitstatsaver.add(splitstats);
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paretosplitstatsaver();
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// save_partitions(splitstats.value(), clades_pareto);
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//split_frequences.clear();
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cout << " done\n";
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exp_data.close();
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evolution_data.close();
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pareto_scores.close();
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final_scores.close();
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best_media_scores.close();
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final_trees.close();
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final_pareto_trees.close();
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clades_pareto.close();
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clades_final.close();
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finalsolutions.save_scores(path + datafile + "_final_scores_" + expid + ".txt","#Final Solutions Scores");
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finalsolutions.save_trees(path + datafile + "_final_trees_" + expid + ".txt");
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cout << "\ndone \n";
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// print the optimized solutions
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//print_scores_pop( -2, population, evolution_data);
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//print_scores_pop( -2, population, final_scores);
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//save_trees(finalsolutions, final_trees);
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cout << "\n\nCalculating Final Solutions clade support...";
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PhyloMOEOPartitionStat splitstats;
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splitstats(finalsolutions);
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eoFileMonitor finalsplitstatsaver(path+datafile+"_clades_final_"+expid+".txt");
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finalsplitstatsaver.add(splitstats);
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finalsplitstatsaver();
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//cout << splitstats.value() << endl;
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//partition_map split_frequences;
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//calculate_frequence_splits(finalsolutions,split_frequences);
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cout << " done\n";
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//save_partitions(splitstats.value(), clades_final);
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//split_frequences.clear();
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// remove dominate solutions
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cout << "\nCalculating Pareto-optimal Solutions...";
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PhyloMOEOParetoSolutionsArchive paretosolutions;
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paretosolutions.operator()(finalsolutions);
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paretosolutions.save_scores(path + datafile + "_pareto_scores_" + expid + ".txt","#Pareto Solutions Scores");
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paretosolutions.save_trees(path + datafile + "_pareto_trees_" + expid + ".txt");
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cout << " done\n";
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// print final pareto trees
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//save_trees( paretosolutions, final_pareto_trees);
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cout << "\nCalculating Pareto-optimal Solutions clade support...";
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splitstats(paretosolutions);
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//calculate_frequence_splits(paretosolutions,split_frequences);
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eoFileMonitor paretosplitstatsaver(path+datafile+"_clades_pareto_"+expid+".txt");
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paretosplitstatsaver.add(splitstats);
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paretosplitstatsaver();
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// save_partitions(splitstats.value(), clades_pareto);
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//split_frequences.clear();
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cout << " done\n";
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exp_data.close();
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evolution_data.close();
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pareto_scores.close();
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final_scores.close();
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best_media_scores.close();
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final_trees.close();
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final_pareto_trees.close();
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clades_pareto.close();
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clades_final.close();
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cout << "\nPhyloMOEA execution finishes !\n";
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}
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gsl_rng_free(rn2);
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// delete probmatrixs;
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// delete probmatrixs;
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delete rn;
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cout << "\nPhyloMOEA execution finishes !\n";
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return 0;
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}
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