diff --git a/src/libaevol/SIMD_Individual.cpp b/src/libaevol/SIMD_Individual.cpp
index a92e9063244aa39448280b0b56899e1a26b3d9ed..080339c6ef8881b3e5ecf6eaaaf38f7141ce2c9f 100644
--- a/src/libaevol/SIMD_Individual.cpp
+++ b/src/libaevol/SIMD_Individual.cpp
@@ -647,9 +647,6 @@ void SIMD_Individual::opt_prom_compute_RNA() {
dna_size[indiv_id] :
cur_pos;
int start_pos = cur_pos;
- if (cur_pos >= dna_size[indiv_id] || cur_pos < 0) {
- printf("-----START LEAD-----> Position %d Length %d -- indiv id %d\n",cur_pos,dna_size[indiv_id],indiv_id);
- }
bool terminator_found = false;
bool no_terminator = false;
@@ -695,10 +692,6 @@ void SIMD_Individual::opt_prom_compute_RNA() {
:
cur_pos + 1;
- if (cur_pos >= dna_size[indiv_id] || cur_pos < 0) {
- printf("-----NEXT LEAD-----> Position %d Length %d\n",cur_pos,dna_size[indiv_id]);
- }
-
// if (indiv_id == 152) printf("Next cur value %d (prev %d)\n",cur_pos,term_dist_leading);
term_dist_leading = 0;
if (cur_pos == start_pos) {
@@ -1085,15 +1078,13 @@ void SIMD_Individual::compute_RNA() {
void SIMD_Individual::start_protein() {
//int x, y;
//#pragma omp parallel for schedule(dynamic)
-#pragma omp parallel
-#pragma omp single
- {
+
for (int indiv_id = 0; indiv_id < (int) exp_m_->nb_indivs(); indiv_id++) {
if (exp_m_->dna_mutator_array_[indiv_id]->hasMutate()) {
//#pragma omp parallel for firstprivate(indiv_id) schedule(dynamic)
for (int rna_idx = 0; rna_idx <
(int) internal_simd_struct[indiv_id]->rna_count_; rna_idx++) {
-#pragma omp task firstprivate(indiv_id, rna_idx)
+#pragma omp task firstprivate(indiv_id, rna_idx) depend(inout: internal_simd_struct[indiv_id])
{
if (internal_simd_struct[indiv_id]->rnas[rna_idx]->is_init_) {
int x = indiv_id / exp_m_->world()->height();
@@ -1216,14 +1207,14 @@ void SIMD_Individual::start_protein() {
}
}
}
- }
+ // }
}
void SIMD_Individual::compute_protein() {
//#pragma omp parallel for schedule(dynamic)
-#pragma omp parallel
+/*#pragma omp parallel
#pragma omp single
- {
+ {*/
for (int indiv_id = 0; indiv_id < (int) exp_m_->nb_indivs(); indiv_id++) {
if (exp_m_->dna_mutator_array_[indiv_id]->hasMutate()) {
int resize_to = 0;
@@ -1244,7 +1235,7 @@ void SIMD_Individual::compute_protein() {
for (int protein_idx = 0;
protein_idx < (int) internal_simd_struct[indiv_id]->
rnas[rna_idx]->start_prot.size(); protein_idx++) {
-#pragma omp task firstprivate(indiv_id, rna_idx, protein_idx)
+#pragma omp task firstprivate(indiv_id, rna_idx, protein_idx) depend(in: internal_simd_struct[indiv_id])
{
int x = indiv_id / exp_m_->world()->height();
int y = indiv_id % exp_m_->world()->height();
@@ -1555,24 +1546,24 @@ void SIMD_Individual::compute_protein() {
}
}
}
- }
+// }
}
void SIMD_Individual::translate_protein(double w_max) {
//#pragma omp parallel for schedule(dynamic)
-#pragma omp parallel
+/*#pragma omp parallel
#pragma omp single
- {
+ {*/
for (int indiv_id = 0; indiv_id < (int) exp_m_->nb_indivs(); indiv_id++) {
if (exp_m_->dna_mutator_array_[indiv_id]->hasMutate()) {
/*printf("Translate protein for indiv %d : %ld (%d) -- %ld (%d)\n",
indiv_id,internal_simd_struct[indiv_id]->proteins.size(),internal_simd_struct[indiv_id]->protein_count_,
internal_simd_struct[indiv_id]->rnas.size(),internal_simd_struct[indiv_id]->rna_count_);*/
-#pragma omp parallel for firstprivate(indiv_id) schedule(dynamic)
+//#pragma omp parallel for firstprivate(indiv_id) schedule(dynamic)
for (int protein_idx = 0; protein_idx <
(int) internal_simd_struct[indiv_id]->protein_count_; protein_idx++) {
-#pragma omp task firstprivate(indiv_id, protein_idx)
+#pragma omp task firstprivate(indiv_id, protein_idx) depend(inout: internal_simd_struct[indiv_id])
{
if (internal_simd_struct[indiv_id]->proteins[protein_idx]->is_init_) {
int x = indiv_id / exp_m_->world()->height();
@@ -1828,7 +1819,7 @@ void SIMD_Individual::translate_protein(double w_max) {
}
}
}
- }
+// }
}
void SIMD_Individual::compute_phenotype() {
@@ -1845,9 +1836,9 @@ void SIMD_Individual::compute_phenotype() {
}
-#pragma omp parallel
+/*#pragma omp parallel
#pragma omp single
- {
+ {*/
for (int indiv_id = 0; indiv_id < (int) exp_m_->nb_indivs(); indiv_id++) {
if (exp_m_->dna_mutator_array_[indiv_id]->hasMutate()) {
//printf("%d -- Protein to phenotype for %ld\n",i,internal_simd_struct[i]->proteins.size());
@@ -1868,7 +1859,7 @@ void SIMD_Individual::compute_phenotype() {
1e-15)
continue;
-#pragma omp task firstprivate(indiv_id, protein_idx)
+#pragma omp task firstprivate(indiv_id, protein_idx) depend(inout: internal_simd_struct[indiv_id])
{
if (internal_simd_struct[indiv_id]->proteins[protein_idx]->is_functional) {
@@ -1967,7 +1958,7 @@ void SIMD_Individual::compute_phenotype() {
}
}
}
- }
+// }
}
@@ -2159,7 +2150,26 @@ void SIMD_Individual::run_a_step(double w_max, double selection_pressure,bool op
} else {
}*/
+ for (int indiv_id = 0; indiv_id < exp_m_->nb_indivs(); indiv_id++) {
+ int x = indiv_id / exp_m_->world()->height();
+ int y = indiv_id % exp_m_->world()->height();
+ delete exp_m_->dna_mutator_array_[indiv_id];
+ exp_m_->dna_mutator_array_[indiv_id] = new DnaMutator(
+ exp_m_->world()->grid(x, y)->mut_prng(),
+ internal_simd_struct[indiv_id]->dna_->length(),
+ exp_m_->exp_s()->mut_params()->duplication_rate(),
+ exp_m_->exp_s()->mut_params()->deletion_rate(),
+ exp_m_->exp_s()->mut_params()->translocation_rate(),
+ exp_m_->exp_s()->mut_params()->inversion_rate(),
+ exp_m_->exp_s()->mut_params()->point_mutation_rate(),
+ exp_m_->exp_s()->mut_params()->small_insertion_rate(),
+ exp_m_->exp_s()->mut_params()->small_deletion_rate(),
+ exp_m_->exp_s()->mut_params()->max_indel_size(),
+ exp_m_->exp_s()->min_genome_length(),
+ exp_m_->exp_s()->max_genome_length());
+ exp_m_->dna_mutator_array_[indiv_id]->setMutate(true);
+ }
//printf("Search RNA start/stop motifs\n");
start_stop_RNA();
//printf("Compute RNAs\n");
@@ -2173,17 +2183,24 @@ void SIMD_Individual::run_a_step(double w_max, double selection_pressure,bool op
}
- //printf("Search Protein start motifs\n");
- start_protein();
- //printf("Compute Proteins\n");
- compute_protein();
- //printf("Translate protein\n");
- translate_protein(w_max);
- //printf("Compute phenotype\n");
- compute_phenotype();
- //printf("Compute fitness\n");
- compute_fitness(selection_pressure);
-
+#pragma omp parallel
+#pragma omp single
+ {
+ //printf("Search Protein start motifs\n");
+ start_protein();
+//#pragma omp taskwait
+ //printf("Compute Proteins\n");
+ compute_protein();
+//#pragma omp taskwait
+ //printf("Translate protein\n");
+ translate_protein(w_max);
+//#pragma omp taskwait
+ //printf("Compute phenotype\n");
+ compute_phenotype();
+//#pragma omp taskwait
+ //printf("Compute fitness\n");
+ compute_fitness(selection_pressure);
+ }
//printf("Check results\n");
//check_result();