New openMP development for test cases
git-svn-id: svn://scm.gforge.inria.fr/svnroot/paradiseo@1489 331e1502-861f-0410-8da2-ba01fb791d7f
This commit is contained in:
wcancino
parent
0369405646
commit
7a8ab5fb50
6 changed files with 118 additions and 253 deletions
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@ -25,6 +25,7 @@
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#include <likelihoodcalculator.h>
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//#include <peo>
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#include <iostream>
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#include <utils.h>
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extern ProbMatrixContainer *probmatrixs_ptr;
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@ -58,4 +59,32 @@ private:
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ParsimonyCalculator &parseval;
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};
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class PhyloLikelihoodTimeEval : public moeoEvalFunc < PhyloMOEO >
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{
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public:
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PhyloLikelihoodTimeEval( LikelihoodCalculator &y): likeval(y) { }
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void operator () (PhyloMOEO & _sol)
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{
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ObjectiveVector objVec;
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likeval.set_tree(_sol.get_tree());
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struct timeval start;
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gettimeofday(&start,NULL);
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objVec[0] = -likeval.calculate_likelihood();
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struct timeval end;
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gettimeofday(&end,NULL);
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print_elapsed_time_short(&start,&end);
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_sol.objectiveVector(objVec);
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cout << endl;
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}
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private:
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LikelihoodCalculator &likeval;
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};
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#endif
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@ -241,55 +241,6 @@ double LikelihoodCalculator::calculate_likelihood_exp(edge focus)
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}
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// double LikelihoodCalculator::calculate_all_likelihoods()
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// {
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// oldroot = invalid_node;
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// graph::edge_iterator it = tree_ptr->TREE.edges_begin();
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// graph::edge_iterator it_end = tree_ptr->TREE.edges_end();
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// while(it != it_end)
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// {
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//
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// // select a new root
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// bfocus = *it;
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// a = tree_ptr->istaxon(bfocus.target()) ? bfocus.source() : bfocus.target();
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// b = bfocus.opposite(a);
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//
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// for(int i=0; i< nrates; i++)
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// {
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// double len = tree_ptr->get_branch_length(bfocus)*rates_prob[i];
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// len = len < BL_MIN ? BL_MIN : len;
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// ProbMatrix &p = (*probmatrixs)[ len];
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// prob[i] = p.p;
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// }
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//
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//
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// // make the new tree
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// tree_ptr->convert_graph_to_tree(a, NULL);
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//
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// if( oldroot!=invalid_node)
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// {
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// update_partials(); //cj( oldroot, a, *it);
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// cout << "likelihood ..." << sum_site_liks() <<endl;
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// }
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// else { //first iteration
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// init_partials();
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// calculate_partials( a, &b);
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// calculate_partials( b, &a);
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// cout << "likelihood ..." << sum_site_liks() << endl;
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// }
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//
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// for(int i=0; i< nrates; i++)
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// {
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// double factor = rates_prob[i];
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// double len = tree_ptr->get_branch_length(bfocus);
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// len = len < BL_MIN ? BL_MIN : len;
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// probmatrixs->change_matrix( len*factor, tree_ptr->get_branch_length(bfocus)*factor);
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// }
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//
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// oldroot = a;
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// ++it;
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// }
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// }
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void LikelihoodCalculator::update_partials() //node *oldroot, node newroot, edge newedge)
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{
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@ -334,7 +285,6 @@ void LikelihoodCalculator::recalculate_cj(node n, node father)
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double LikelihoodCalculator::calculate_likelihood()
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{
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double lik;
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// pthread_t threads[2]; /* holds thread info */
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@ -360,29 +310,16 @@ double LikelihoodCalculator::calculate_likelihood()
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for(int i=0; i<2; i++)
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pthread_join(threads[i],NULL);*/
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//cout << "calculando partials..." << endl;
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struct timeval tempo1, tempo2, result;
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gettimeofday(&tempo1, NULL);
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struct timeval start;
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gettimeofday(&start,NULL);
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calculate_partials( a, &b);
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calculate_partials( b, &a);
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//cout << "somando..." << endl;
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// sum all partials
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lik = sum_site_liks();
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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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long hours = (result.tv_sec - remainder)/3600;
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long seconds = remainder % 60;
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long minutes = (remainder - seconds) / 60;
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cout << "Execution time : ";
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cout.width(3);
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cout.fill(' ');
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cout << hours << ":";
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cout.width(2);
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cout.fill('0');
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cout << minutes << ":";
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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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struct timeval end;
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gettimeofday(&end,NULL);
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print_elapsed_time_short(&start, &end);
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return lik;
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}
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@ -402,12 +339,10 @@ double LikelihoodCalculator::sum_site_liks( )
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prob[i] = p->p;
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}
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//#pragma omp parallel for private(factor_correct) schedule(dynamic) num_threads(2) reduction(+:lik)
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for(int i=0; i < seqlen; i++)
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{
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factor_correct = Factors[a][i] + Factors[b][i] ;
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site_liks[i] = sum_partials(i);
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//#pragma omp critical
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lik += ( log(site_liks[i]) + factor_correct)* SeqData->pattern_count(i);
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}
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return lik;
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@ -487,7 +422,7 @@ void LikelihoodCalculator::calculate_node_partial( node father, node son, edge e
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int r,i,j;
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//unsigned char l;
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register int seqlen = tree_ptr->number_of_positions();
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#pragma omp parallel for
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#pragma omp parallel for
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for(int k=0; k<seqlen;k++)
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{
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long index = k*nrates*4;
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@ -498,7 +433,6 @@ void LikelihoodCalculator::calculate_node_partial( node father, node son, edge e
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for(int r=0; r<nrates; r++)
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{
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double sum = 0;
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//#pragma omp critical
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ProbMatrix *p = edgeprobmatrix[edgeaux][r];
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for(int i=0; i < 4; i++)
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@ -594,7 +528,6 @@ double LikelihoodCalculator::calculate_likelihood_omp()
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init_partials();
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struct timeval tempo1, tempo2, result;
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int seqlen = tree_ptr->number_of_positions();
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@ -608,7 +541,8 @@ double LikelihoodCalculator::calculate_likelihood_omp()
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}
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gettimeofday(&tempo1, NULL);
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struct timeval start;
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gettimeofday(&start,NULL);
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#pragma omp parallel for reduction(+:lik)
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for(int i=0; i< seqlen; i++)
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@ -619,22 +553,10 @@ double LikelihoodCalculator::calculate_likelihood_omp()
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// sum all partials
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lik += sum_site_liks_omp(i);
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}
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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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long hours = (result.tv_sec - remainder)/3600;
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long seconds = remainder % 60;
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long minutes = (remainder - seconds) / 60;
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cout << "Execution time : ";
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cout.width(3);
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cout.fill(' ');
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cout << hours << ":";
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cout.width(2);
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cout.fill('0');
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cout << minutes << ":";
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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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struct timeval end;
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gettimeofday(&end,NULL);
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cout << " !! ";
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print_elapsed_time_short(&start,&end);
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return lik;
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}
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@ -645,7 +567,6 @@ double LikelihoodCalculator::sum_site_liks_omp( int pos )
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register double lik = 0;
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register double factor_correct;
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//#pragma omp parallel for private(factor_correct) schedule(dynamic) num_threads(2) reduction(+:lik)
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factor_correct = Factors[a][pos] + Factors[b][pos] ;
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site_liks[pos] = sum_partials(pos);
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lik = ( log(site_liks[pos]) + factor_correct)* SeqData->pattern_count(pos);
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@ -668,7 +589,6 @@ void LikelihoodCalculator::calculate_node_partial_omp( node father, node son, ed
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{
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register double sum;
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//unsigned char l;
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//#pragma omp parallel for
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long index = pos*nrates*4;
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// accumulatre
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Factors[father][pos]+=Factors[son][pos];
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@ -677,7 +597,6 @@ void LikelihoodCalculator::calculate_node_partial_omp( node father, node son, ed
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for(int r=0; r<nrates; r++)
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{
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double sum = 0;
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//#pragma omp critical
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ProbMatrix *p = edgeprobmatrix[edgeaux][r];
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for(int i=0; i < 4; i++)
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@ -89,8 +89,12 @@ private:
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long total_pos = SeqData->pattern_count();
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int ntaxons = SeqData->num_seqs();
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//int nedges = tree_ptr->TREE.number_of_edges();
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part_memory_internal = new double[ (ntaxons-2) * nrates * total_pos * 4 ];
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part_memory_factors = new double [ (2*ntaxons-2) * total_pos];
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unsigned long tamanho = (ntaxons-2) * nrates * total_pos * 4;
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cout << "tamanho de alocacao:" << tamanho << endl;
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part_memory_internal = new double[ tamanho ];
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tamanho = (2*ntaxons-2) * total_pos;
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cout << "tamanho de alocacao:" << tamanho << endl;
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part_memory_factors = new double [ tamanho ];
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part_memory_probmatrix_ptr = new ProbMatrix* [ (2*ntaxons-3) * nrates ] ;
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site_liks = new double[total_pos];
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cout << "allocating done..." << endl;
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@ -47,180 +47,55 @@ 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 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 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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/* 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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ostringstream os;
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os << datafile << "_results_" << 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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/* 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/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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//
|
||||
// lik_calc3.set_tree(population3[0].get_tree());
|
||||
// cout << lik_calc3.calculate_likelihood() << endl;
|
||||
// cout << lik_calc3.calculate_likelihood_omp() << endl;
|
||||
|
||||
// lik_calc4.set_tree(population4[0].get_tree());
|
||||
// cout << lik_calc4.calculate_likelihood() << endl;
|
||||
// cout << lik_calc4.calculate_likelihood_omp() << endl;
|
||||
//
|
||||
// lik_calc5.set_tree(population5[0].get_tree());
|
||||
// cout << lik_calc5.calculate_likelihood() << endl;
|
||||
// cout << lik_calc5.calculate_likelihood_omp() << endl;
|
||||
|
||||
lik_calc6.set_tree(population6[0].get_tree());
|
||||
cout << lik_calc6.calculate_likelihood() << endl;
|
||||
cout << lik_calc6.calculate_likelihood_omp() << endl;
|
||||
//
|
||||
// lik_calc7.set_tree(population7[0].get_tree());
|
||||
// cout << lik_calc7.calculate_likelihood() << endl;
|
||||
// cout << lik_calc7.calculate_likelihood_omp() << endl;
|
||||
|
||||
|
||||
/*
|
||||
for(int i=0; i < population.size(); i++)
|
||||
omp_set_num_threads(nthreads);
|
||||
for(int i=0; i < nexp; i++)
|
||||
{
|
||||
phylotreeIND templatetree6( rn, seq6, rn2);
|
||||
SubstModel modelHKY6( seq6, SubstModel::HKY85);
|
||||
modelHKY6.init();
|
||||
ProbMatrixContainer probmatrixs6(modelHKY6);
|
||||
LikelihoodCalculator lik_calc6(templatetree6, modelHKY6, probmatrixs6, 4);
|
||||
modelHKY6.init();
|
||||
Phyloraninit initializer6(templatetree6);
|
||||
eoPop<PhyloMOEO> population6(ntrees, initializer6);
|
||||
cout.precision(15);
|
||||
PhyloLikelihoodTimeEval eval( lik_calc6 );
|
||||
|
||||
|
||||
cout << " Number of processors available:" << omp_get_num_procs() << " MAX Number of threads " << omp_get_max_threads() << endl;
|
||||
gettimeofday(&tempo1, NULL);
|
||||
|
||||
lik_calc.set_tree(population[i].get_tree());
|
||||
// gettimeofday(&tempo1, NULL);
|
||||
cout << lik_calc.calculate_likelihood_omp() << 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;*/
|
||||
// }
|
||||
|
||||
|
||||
apply<PhyloMOEO> (eval, population6);
|
||||
|
||||
gettimeofday(&tempo2, NULL);
|
||||
cout << "\n"; print_elapsed_time(&tempo1,&tempo2);
|
||||
print_elapsed_time_short(&tempo1,&tempo2,of);
|
||||
of << endl;
|
||||
}
|
||||
of.close();
|
||||
gsl_rng_free(rn2);
|
||||
// delete probmatrixs;
|
||||
delete rn;
|
||||
|
|
|
|||
|
|
@ -61,6 +61,41 @@ int timeval_subtract (struct timeval *result, struct timeval *x, struct timeva
|
|||
return x->tv_sec < y->tv_sec;
|
||||
}
|
||||
|
||||
|
||||
void print_elapsed_time(struct timeval *x, struct timeval *y)
|
||||
{
|
||||
struct timeval result;
|
||||
timeval_subtract(&result,y,x);
|
||||
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;
|
||||
}
|
||||
|
||||
void print_elapsed_time_short(struct timeval *x, struct timeval *y, ostream &os)
|
||||
{
|
||||
struct timeval result;
|
||||
timeval_subtract(&result,y,x);
|
||||
os << " " << result.tv_sec << "." << result.tv_usec;
|
||||
}
|
||||
|
||||
|
||||
void print_cpu_time(clock_t start, clock_t end)
|
||||
{
|
||||
double cpu_time_used = ((double) (end - start)) / CLOCKS_PER_SEC;
|
||||
cout << " " << cpu_time_used << " ";
|
||||
}
|
||||
|
||||
void welcome_message()
|
||||
{
|
||||
cout << "\nPhyloMOEA, a program for multi-criteria phylogenetic inference\n";
|
||||
|
|
|
|||
|
|
@ -32,5 +32,8 @@ void optimize_solutions( eoPop<PhyloMOEO> &);
|
|||
void optimize_solution( PhyloMOEO &);
|
||||
void readtrees(const char *, eoPop<PhyloMOEO> &);
|
||||
int timeval_subtract (struct timeval *, struct timeval *, struct timeval *);
|
||||
void print_cpu_time(clock_t ,clock_t);
|
||||
void print_elapsed_time(struct timeval *, struct timeval *);
|
||||
void print_elapsed_time_short(struct timeval *, struct timeval *, ostream &os=cout);
|
||||
#endif
|
||||
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue