int main(int argc, char const *argv[])
{
std::string FILE="/homes/kgori/scratch/basic_pll/GGPS1.phy";
std::string PART="/homes/kgori/scratch/basic_pll/GGPS1.partitions.txt";
std::string TREE="/homes/kgori/scratch/basic_pll/GGPS1.tree";
auto inst = make_unique<pll>(FILE, PART, TREE, 1, 123);
std::cout << inst->get_likelihood() << std::endl;
std::cout << inst->get_partition_name(0) << std::endl;
std::cout << inst->get_model_name(0) << std::endl;
std::cout << inst->get_epsilon() << std::endl;
std::cout << inst->get_alpha(0) << std::endl;
std::cout << inst->get_number_of_partitions() << std::endl;
std::cout << inst->get_tree() << std::endl;
std::cout << inst->get_frac_change() << std::endl;
inst->set_tree("((Ptro:0.00147084048849247711,Ppan:0.00106294370976534763):0.00444598321816729036,(Cjac:0.05157798212603657839,(Csab:0.00440006365327790666,(Mmul:0.00652936575529242547,Panu:0.00101047194512476272):0.00381049900890796569):0.01359968787254225639):0.01375788728353777995,Hsap:0.00674547067186638278):0.0;");
inst->set_epsilon(0.001);
inst->set_alpha(2, 0, true);
auto ef = inst->get_empirical_frequencies();
inst->optimise(true, true, true, true);
inst->optimise_tree_search(true);
std::cout << inst->get_likelihood() << std::endl;
std::cout << inst->get_tree() << std::endl;
return 0;
}
void run_tsp (int nb_threads, int nb_towns, int seed, int nb_clusters, char* machine) {
int i;
uint64_t start = get_time();
TRACE(start, -1, -1, STARTING_EXECUTION);
int nb_partitions = get_number_of_partitions(nb_clusters);
LOG ("nb_clusters = %3d nb_partitions = %3d nb_threads = %3d nb_towns = %3d seed = %d \n",
nb_clusters, nb_partitions, nb_threads, nb_towns, seed);
min_distance = INT_MAX;
next_partition = 0;
running_count = 0;
tsps = (tsp_t_pointer *)(malloc(sizeof(tsp_t_pointer) * nb_clusters));
assert(tsps != NULL);
pthread_t **tids = (pthread_t **) malloc (sizeof(pthread_t *) * nb_clusters);
assert (tids != NULL);
for (i = 0; i < nb_clusters; i++)
tids[i] = spawn(&tsps[i], i, nb_clusters, nb_partitions, nb_threads, nb_towns, seed, machine);
for (i = 0; i < nb_clusters; i++) {
pthread_join (*(tids[i]), NULL);
free(tids[i]);
}
free (tids);
free(tsps);
uint64_t end = get_time();
uint64_t exec_time = diff_time(start, end);
TRACE(end, -1, -1, ENDING_EXECUTION);
printf ("%" PRIu64 "\t%5d\t%2d\t%2d\t%5d\t%2d\t%8d",
exec_time, min_distance,nb_threads, nb_towns, seed, nb_clusters, nb_partitions);
}