Final modifications to serial version

git-svn-id: svn://scm.gforge.inria.fr/svnroot/paradiseo@1556 331e1502-861f-0410-8da2-ba01fb791d7f

contribution/branches/PhyloMOEA/PhyloMOEA-serial/PhyloMOEA/CMakeLists.txt

@@ -32,6 +32,6 @@ SET( PHYLOMOEA_SOURCES	eigensolver.cpp
 
 ADD_EXECUTABLE( PhyloMOEA-serial ${PHYLOMOEA_SOURCES} )
 
-TARGET_LINK_LIBRARIES(PhyloMOEA gsl gslcblas GTL eo eoutils ga moeo cma)
+TARGET_LINK_LIBRARIES(PhyloMOEA-serial gsl gslcblas GTL eo eoutils ga moeo cma)
 
-INSTALL( TARGETS PhyloMOEA RUNTIME DESTINATION bin)
+INSTALL( TARGETS PhyloMOEA-serial RUNTIME DESTINATION bin)

contribution/branches/PhyloMOEA/PhyloMOEA-serial/PhyloMOEA/PhyloMOEA.cpp

@@ -22,7 +22,7 @@ RandomNr *rn;
 //Sequences *seq;
 long seed;
 //vector<phylotreeIND> arbores;
-string datafile,usertree, expid, path, algotype;
+string datafile,usertree, expid, path, algotype, optimize_branch;
 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;
@@ -30,6 +30,9 @@ ofstream exp_data,evolution_data, best_media_scores, final_trees, final_pareto_t
 
 int main(int argc, char *argv[])
 {
+	struct timeval tempo1, tempo2, result;
+	gettimeofday(&tempo1, NULL);
+
 	welcome_message();
 
 	eoParser parser(argc, argv);
@@ -48,6 +51,7 @@ int main(int argc, char *argv[])
 	usertree = parser.createParam(string(), "treef", "Treefile", 't',"Param").value();
 	path = parser.createParam(string(), "path", "Treefile", 'p',"Param").value();
 	algotype = parser.createParam(string("nsgaii"), "algo", "Algorith, Type", 'b',"Param").value();
+	optimize_branch = parser.createParam(string("yes"), "opt", "Optimize Branch Lenght", 'o',"Param").value();
  	ostringstream convert;
  	convert << seed;
 	expid = parser.createParam(convert.str(), "expid", "Experiment ID", 'e',"Param").value();
@@ -184,7 +188,7 @@ int main(int argc, char *argv[])
 	// optimize remaining solutions
 	cout << "\nOptimizing tree branch lenghts...\n";
 	
-	optimize_solutions( finalsolutions, lik_calc );
+	if(optimize_branch=="yes")optimize_solutions( finalsolutions, lik_calc );
 	cout << "\nReevaluating individuals \n";
 	apply<PhyloMOEO> ( byobj, finalsolutions );
 
@@ -214,8 +218,8 @@ int main(int argc, char *argv[])
 	// remove dominate solutions
 	cout << "\nCalculating Pareto-optimal Solutions...";
 
-    PhyloMOEOParetoSolutionsArchive paretosolutions;
-    paretosolutions.operator()(finalsolutions);
+      PhyloMOEOParetoSolutionsArchive paretosolutions;
+      paretosolutions.operator()(finalsolutions);
 	paretosolutions.save_scores(path + datafile + "_pareto_scores_" + expid + ".txt","#Pareto Solutions Scores");
 	paretosolutions.save_trees(path + datafile + "_pareto_trees_" + expid + ".txt");
 	cout << " done\n";
@@ -244,6 +248,8 @@ int main(int argc, char *argv[])
 //	delete probmatrixs;
 	delete rn;
 	cout << "\nPhyloMOEA execution finishes !\n";
+	gettimeofday(&tempo2, NULL);
+	print_elapsed_time(&tempo1,&tempo2);
 	return 0;
 } 
 

contribution/branches/PhyloMOEA/PhyloMOEA-serial/PhyloMOEA/utils.cpp

@@ -34,6 +34,66 @@ extern string datafile,usertree, expid, path;
 extern double pcrossover, pmutation, kappa, alpha;
 extern unsigned int ngenerations,  popsize, ncats;
 
+int   timeval_subtract (struct timeval *result, struct timeval *x, struct timeval *y)
+{
+/* Perform the carry for the later subtraction by updating y. */
+	if (x->tv_usec < y->tv_usec) {
+		int nsec = (y->tv_usec - x->tv_usec) / 1000000 + 1;
+		y->tv_usec -= 1000000 * nsec;
+		y->tv_sec += nsec;
+	}
+
+	if (x->tv_usec - y->tv_usec > 1000000) {
+		int nsec = (x->tv_usec - y->tv_usec) / 1000000;
+		y->tv_usec += 1000000 * nsec;
+		y->tv_sec -= nsec;
+	}
+
+	/* Compute the time remaining to wait.
+	tv_usec is certainly positive. */
+	result->tv_sec = x->tv_sec - y->tv_sec;
+	result->tv_usec = x->tv_usec - y->tv_usec;
+	
+	/* Return 1 if result is negative. */
+	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";

contribution/branches/PhyloMOEA/PhyloMOEA-serial/PhyloMOEA/utils.h

@@ -30,5 +30,9 @@ void welcome_message();
 void save_exp_params(ostream &);
 void optimize_solutions( eoPop<PhyloMOEO> &, LikelihoodCalculator &);
 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