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Small program to test OpenMP bnechmark of likelihood function

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git-svn-id: svn://scm.gforge.inria.fr/svnroot/paradiseo@1472 331e1502-861f-0410-8da2-ba01fb791d7f
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wcancino 2009-03-04 14:31:45 +00:00
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//
// C++ Implementation: testomp
//
// Description:
//
//
// Author: <>, (C) 2009
//
// Copyright: See COPYING file that comes with this distribution
//
//
#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 <moeoNSGAII2.h>
#include <utils/moeoBestObjVecStat.h>
#include <utils/moeoAverageObjVecStat.h>
#include <PhyloMOEOPartitionStat.h>
#include <eoCountedFileMonitor.h>
#include <eoSingleFileCountedStateSaver.h>
#include <vectorSortIndex.h>
#include <utils.h>
#include <apply.h>
gsl_rng *rn2;
RandomNr *rn;
//Sequences *seq;
long seed;
//vector<phylotreeIND> arbores;
string datafile,usertree, expid, path, algotype;
double pcrossover, pmutation, kappa, alpha;
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;
LikelihoodCalculator *lik_calc_ptr;
phylotreeIND *templatetree_ptr;
ProbMatrixContainer *probmatrixs_ptr;
int main(int argc, char *argv[])
{
// measures execution time
struct timeval tempo1, tempo2, result;
gettimeofday(&tempo1, NULL);
cout << "\n\nReading Sequence Datafile...";
Sequences seq("/home/wcancino/experimentos/PhyloMOEA_0.2/500/500_ZILLA.plain");
cout << " done.\n";
// calculate datafile
cout << "calculating pattersn..." << endl;
seq.calculate_patterns();
seq.calculate_frequences();
gsl_rng *rn2 = gsl_rng_alloc(gsl_rng_default);
RandomNr *rn = new RandomNr(time(NULL));
phylotreeIND templatetree( rn, seq, rn2);
SubstModel modelHKY( seq, SubstModel::HKY85);
modelHKY.init();
modelHKY.set_kappa(3.890);
ProbMatrixContainer probmatrixs(modelHKY);
probmatrixs_ptr = &probmatrixs;
LikelihoodCalculator lik_calc(templatetree, modelHKY, probmatrixs, 4);
lik_calc.set_alpha(0.950);
modelHKY.init();
Phyloraninit initializer(templatetree);
eoPop<PhyloMOEO> population(100, initializer);
cout << "Reading trees..." << endl;
readtrees("/home/wcancino/experimentos/PhyloMOEA_0.2/500/init_trees.dat", population);
gettimeofday(&tempo1, NULL);
//cout << " Number of processors available:" << omp_get_num_procs() << " MAX Number of threads " << omp_get_max_threads() << endl;
for(int i=0; i < population.size(); i++)
{
lik_calc.set_tree(population[i].get_tree());
cout << lik_calc.calculate_likelihood() << endl;
}
gettimeofday(&tempo2, NULL);
timeval_subtract(&result,&tempo2,&tempo1);
long remainder = result.tv_sec % 3600;
long hours = (result.tv_sec - remainder)/3600;
long seconds = remainder % 60;
long minutes = (remainder - seconds) / 60;
cout << "Execution time : ";
cout.width(3);
cout.fill(' ');
cout << hours << ":";
cout.width(2);
cout.fill('0');
cout << minutes << ":";
cout.width(2);
cout.fill('0');
cout << seconds << "." << result.tv_usec << "(" << result.tv_sec << ")" << endl;
gsl_rng_free(rn2);
// delete probmatrixs;
delete rn;
return 0;
}