5312c3321e
git-svn-id: svn://scm.gforge.inria.fr/svnroot/paradiseo@1592 331e1502-861f-0410-8da2-ba01fb791d7f
104 lines
No EOL
3 KiB
C++
104 lines
No EOL
3 KiB
C++
//
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// C++ Implementation: testomp
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//
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// Description:
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//
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//
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// Author: <>, (C) 2009
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//
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// Copyright: See COPYING file that comes with this distribution
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//
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//
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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 <moeoNSGAII2.h>
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#include <utils/moeoBestObjVecStat.h>
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#include <utils/moeoAverageObjVecStat.h>
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#include <PhyloMOEOPartitionStat.h>
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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 <omp.h>
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#include <utils.h>
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#include <apply.h>
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gsl_rng *rn2;
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RandomNr *rn;
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//Sequences *seq;
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long seed;
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//vector<phylotreeIND> arbores;
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string datafile,usertree, expid, path, algotype;
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double pcrossover, pmutation, kappa, alpha;
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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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LikelihoodCalculator *lik_calc_ptr;
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phylotreeIND *templatetree_ptr;
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ProbMatrixContainer *probmatrixs_ptr;
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int main(int argc, char *argv[])
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{
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// measures execution time
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struct timeval tempo1, tempo2, result;
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eoParser parser(argc, argv);
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datafile = parser.createParam(string(), "data", "Datafile", 'd',"Param").value();
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int nthreads = parser.createParam(omp_get_max_threads(), "nthreads", "Numthreads", 't',"Param").value();
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int ntrees = parser.createParam(20, "ntrees", "NumTrees", 'n',"Param").value();
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int nexp = parser.createParam(1, "nexps", "NumExps", 'e',"Param").value();
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cout << "\n\nReading Sequence Datafile...";
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Sequences seq6(datafile.c_str());
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// Sequences seq7("/home/wcancino/experimentos/PhyloMOEA_0.2/omp_tests/datasets/TEST.500_5000");
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cout << " done.\n";
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// calculate datafile
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cout << "calculating pattersn..." << endl;
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seq6.calculate_patterns();
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seq6.calculate_frequences();
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ostringstream os;
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os << datafile << "_results_serial_" << nthreads << ".txt";
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ofstream of(os.str().c_str());
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gsl_rng *rn2 = gsl_rng_alloc(gsl_rng_default);
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RandomNr *rn = new RandomNr(time(NULL));
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omp_set_num_threads(nthreads);
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for(int i=0; i < nexp; i++)
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{
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phylotreeIND templatetree6( rn, seq6, rn2);
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SubstModel modelHKY6( seq6, SubstModel::HKY85);
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modelHKY6.init();
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ProbMatrixContainer probmatrixs6(modelHKY6);
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LikelihoodCalculator lik_calc6(templatetree6, modelHKY6, probmatrixs6, 4);
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modelHKY6.init();
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Phyloraninit initializer6(templatetree6);
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eoPop<PhyloMOEO> population6(ntrees, initializer6);
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cout.precision(15);
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PhyloLikelihoodTimeEval eval( lik_calc6 );
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cout << " Number of processors available:" << omp_get_num_procs() << " MAX Number of threads " << omp_get_max_threads() << endl;
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gettimeofday(&tempo1, NULL);
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apply<PhyloMOEO> (eval, population6);
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gettimeofday(&tempo2, NULL);
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cout << "\n"; print_elapsed_time(&tempo1,&tempo2);
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print_elapsed_time_short(&tempo1,&tempo2,of);
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of << endl;
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}
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of.close();
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gsl_rng_free(rn2);
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// delete probmatrixs;
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delete rn;
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return 0;
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}
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