more OMP test with larges datasets
git-svn-id: svn://scm.gforge.inria.fr/svnroot/paradiseo@1481 331e1502-861f-0410-8da2-ba01fb791d7f
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wcancino
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2664403459
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1 changed files with 136 additions and 17 deletions
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@ -50,40 +50,158 @@ int main(int argc, char *argv[])
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cout << "\n\nReading Sequence Datafile...";
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Sequences seq("/home/wcancino/experimentos/PhyloMOEA_0.2/500/500_ZILLA.plain");
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// Sequences seq("/home/wcancino/experimentos/PhyloMOEA_0.2/omp_tests/datasets/TEST.50_5000");
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// Sequences seq2("/home/wcancino/experimentos/PhyloMOEA_0.2/omp_tests/datasets/TEST.50_50000");
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// Sequences seq3("/home/wcancino/experimentos/PhyloMOEA_0.2/omp_tests/datasets/TEST.50_500000");
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/* Sequences seq4("/home/wcancino/experimentos/PhyloMOEA_0.2/omp_tests/datasets/TEST.250_5000");
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Sequences seq5("/home/wcancino/experimentos/PhyloMOEA_0.2/omp_tests/datasets/TEST.250_50000");*/
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Sequences seq6("/home/wcancino/experimentos/PhyloMOEA_0.2/omp_tests/datasets/TEST.250_500000");
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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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seq.calculate_patterns();
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/* seq.calculate_patterns();
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seq.calculate_frequences();
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seq2.calculate_patterns();
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seq2.calculate_frequences();
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seq3.calculate_patterns();
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seq3.calculate_frequences();*/
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/* seq4.calculate_patterns();
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seq4.calculate_frequences();
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seq5.calculate_patterns();
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seq5.calculate_frequences();*/
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seq6.calculate_patterns();
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seq6.calculate_frequences();
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// seq7.calculate_patterns();
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// seq7.calculate_frequences();
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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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phylotreeIND templatetree( rn, seq, rn2);
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SubstModel modelHKY( seq, SubstModel::HKY85);
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modelHKY.init();
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modelHKY.set_kappa(3.890);
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ProbMatrixContainer probmatrixs(modelHKY);
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probmatrixs_ptr = &probmatrixs;
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LikelihoodCalculator lik_calc(templatetree, modelHKY, probmatrixs, 4);
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lik_calc.set_alpha(0.950);
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modelHKY.init();
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Phyloraninit initializer(templatetree);
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eoPop<PhyloMOEO> population(100, initializer);
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/* phylotreeIND templatetree( rn, seq, rn2);
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phylotreeIND templatetree2( rn, seq2, rn2);
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phylotreeIND templatetree3( rn, seq3, rn2);*/
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/* phylotreeIND templatetree4( rn, seq4, rn2);
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phylotreeIND templatetree5( rn, seq5, rn2);*/
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phylotreeIND templatetree6( rn, seq6, rn2);
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// phylotreeIND templatetree7( rn, seq7, rn2);
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/* SubstModel modelHKY( seq, SubstModel::HKY85);
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SubstModel modelHKY2( seq2, SubstModel::HKY85);
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SubstModel modelHKY3( seq3, SubstModel::HKY85);*/
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/* SubstModel modelHKY4( seq4, SubstModel::HKY85);
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SubstModel modelHKY5( seq5, SubstModel::HKY85);*/
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SubstModel modelHKY6( seq6, SubstModel::HKY85);
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// SubstModel modelHKY7( seq7, SubstModel::HKY85);
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/* modelHKY.init();
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modelHKY2.init();
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modelHKY3.init();*/
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/* modelHKY4.init();
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modelHKY5.init();*/
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modelHKY6.init();
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// modelHKY7.init();
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//modelHKY.set_kappa(3.890);
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/* ProbMatrixContainer probmatrixs(modelHKY);
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ProbMatrixContainer probmatrixs2(modelHKY2);
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ProbMatrixContainer probmatrixs3(modelHKY3);*/
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/* ProbMatrixContainer probmatrixs4(modelHKY4);
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ProbMatrixContainer probmatrixs5(modelHKY5);*/
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ProbMatrixContainer probmatrixs6(modelHKY6);
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// ProbMatrixContainer probmatrixs7(modelHKY7);
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//probmatrixs_ptr = &probmatrixs;
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/* LikelihoodCalculator lik_calc(templatetree, modelHKY, probmatrixs, 4);
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LikelihoodCalculator lik_calc2(templatetree2, modelHKY2, probmatrixs2, 4);
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LikelihoodCalculator lik_calc3(templatetree3, modelHKY3, probmatrixs3, 4);*/
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/* LikelihoodCalculator lik_calc4(templatetree4, modelHKY4, probmatrixs4, 4);
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LikelihoodCalculator lik_calc5(templatetree5, modelHKY5, probmatrixs5, 4); */
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LikelihoodCalculator lik_calc6(templatetree6, modelHKY6, probmatrixs6, 4);
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// LikelihoodCalculator lik_calc7(templatetree7, modelHKY7, probmatrixs7, 4);
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//lik_calc.set_alpha(0.950);
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/* modelHKY.init();
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modelHKY2.init();
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modelHKY3.init();*/
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/* modelHKY4.init();
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modelHKY5.init();*/
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modelHKY6.init();
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// modelHKY7.init();
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/* Phyloraninit initializer(templatetree);
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Phyloraninit initializer2(templatetree2);
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Phyloraninit initializer3(templatetree3);*/
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/* Phyloraninit initializer4(templatetree4);
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Phyloraninit initializer5(templatetree5);*/
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Phyloraninit initializer6(templatetree6);
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// Phyloraninit initializer7(templatetree7);
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/* eoPop<PhyloMOEO> population(1, initializer);
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eoPop<PhyloMOEO> population2(1, initializer2);
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eoPop<PhyloMOEO> population3(1, initializer3);*/
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/* eoPop<PhyloMOEO> population4(1, initializer4);
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eoPop<PhyloMOEO> population5(1, initializer5);*/
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eoPop<PhyloMOEO> population6(1, initializer6);
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// eoPop<PhyloMOEO> population7(1, initializer7);
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cout << "Reading trees..." << endl;
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readtrees("/home/wcancino/experimentos/PhyloMOEA_0.2/500/init_trees.dat", population);
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/* readtrees("/home/wcancino/experimentos/PhyloMOEA_0.2/omp_tests/datasets/start.TEST.50_5000", population);
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readtrees("/home/wcancino/experimentos/PhyloMOEA_0.2/omp_tests/datasets/start.TEST.50_50000", population2);
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readtrees("/home/wcancino/experimentos/PhyloMOEA_0.2/omp_tests/datasets/start.TEST.50_500000", population3);*/
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/* readtrees("/home/wcancino/experimentos/PhyloMOEA_0.2/omp_tests/datasets/start.TEST.250_5000", population4);
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readtrees("/home/wcancino/experimentos/PhyloMOEA_0.2/omp_tests/datasets/start.TEST.250_50000", population5);*/
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readtrees("/home/wcancino/experimentos/PhyloMOEA_0.2/omp_tests/datasets/start.TEST.250_500000", population6);
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// readtrees("/home/wcancino/experimentos/PhyloMOEA_0.2/omp_tests/datasets/start.TEST.500_5000", population7);
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gettimeofday(&tempo1, NULL);
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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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cout.precision(15);
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// lik_calc.set_tree(population[0].get_tree());
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// cout << lik_calc.calculate_likelihood() << endl;
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// cout << lik_calc.calculate_likelihood_omp() << endl;
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//
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// lik_calc2.set_tree(population2[0].get_tree());
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// cout << lik_calc2.calculate_likelihood() << endl;
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// cout << lik_calc2.calculate_likelihood_omp() << endl;
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//
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// lik_calc3.set_tree(population3[0].get_tree());
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// cout << lik_calc3.calculate_likelihood() << endl;
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// cout << lik_calc3.calculate_likelihood_omp() << endl;
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// lik_calc4.set_tree(population4[0].get_tree());
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// cout << lik_calc4.calculate_likelihood() << endl;
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// cout << lik_calc4.calculate_likelihood_omp() << endl;
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//
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// lik_calc5.set_tree(population5[0].get_tree());
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// cout << lik_calc5.calculate_likelihood() << endl;
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// cout << lik_calc5.calculate_likelihood_omp() << endl;
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lik_calc6.set_tree(population6[0].get_tree());
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cout << lik_calc6.calculate_likelihood() << endl;
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cout << lik_calc6.calculate_likelihood_omp() << endl;
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//
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// lik_calc7.set_tree(population7[0].get_tree());
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// cout << lik_calc7.calculate_likelihood() << endl;
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// cout << lik_calc7.calculate_likelihood_omp() << endl;
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/*
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for(int i=0; i < population.size(); i++)
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{
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lik_calc.set_tree(population[i].get_tree());
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// gettimeofday(&tempo1, NULL);
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cout << lik_calc.calculate_likelihood() << endl;
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cout << lik_calc.calculate_likelihood_omp() << endl;
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/* gettimeofday(&tempo2, NULL);
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timeval_subtract(&result,&tempo2,&tempo1);
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long remainder = result.tv_sec % 3600;
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@ -100,7 +218,8 @@ int main(int argc, char *argv[])
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cout.width(2);
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cout.fill('0');
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cout << seconds << "." << result.tv_usec << "(" << result.tv_sec << ")" << endl;*/
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}
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// }
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gsl_rng_free(rn2);
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// delete probmatrixs;
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