From b6da8482e184e98f506343325d045bd362778cc0 Mon Sep 17 00:00:00 2001
From: Jonathan Rouzaud-Cornabas <jonathan.rouzaud-cornabas@inria.fr>
Date: Tue, 10 Jul 2018 08:39:42 +0200
Subject: [PATCH] Fix memory leak + add configure switch for different level of
parallelism (and intel hack)
---
configure.ac | 44 +++++++
src/aevol_run.cpp | 9 +-
src/libaevol/Dna_SIMD.cpp | 11 +-
src/libaevol/ExpManager.cpp | 54 ++++----
src/libaevol/ExpManager.h | 1 +
src/libaevol/SIMD_Individual.cpp | 212 +++++++++++++++++++++++++------
src/libaevol/SIMD_Individual.h | 8 +-
src/libaevol/Stats_SIMD.cpp | 4 +-
8 files changed, 272 insertions(+), 71 deletions(-)
diff --git a/configure.ac b/configure.ac
index 1f938b55f..2d23fc175 100644
--- a/configure.ac
+++ b/configure.ac
@@ -556,6 +556,34 @@ if test "x$bitset" = "xyes" ; then
AC_DEFINE(_DYNAMIC_CUSTOM_BITSET)
fi
+# ************************* --with-l1task option *******************************
+#
+# With this option, pow basal support is enabled and the __POW_BASAL flag is defined
+#
+
+
+AC_MSG_CHECKING([whether to use Task or TaskLoop for first level parallelism])
+AC_ARG_WITH(l1task, [--with-l1task to enable Task as first level parallelism], l1task=$withval, l1task=no)
+AC_MSG_RESULT($l1task)
+AM_CONDITIONAL(WITH_L1TASK, test x"$l1task" != xno)
+if test "x$l1task" = "xyes" ; then
+ AC_DEFINE(WITH_L1TASK)
+fi
+
+# ************************* --with-finetaskloop option *******************************
+#
+# With this option, pow basal support is enabled and the __POW_BASAL flag is defined
+#
+
+
+AC_MSG_CHECKING([whether to use TaskLoop for second level parallelism])
+AC_ARG_WITH(finetaskloop, [--with-finetaskloop to enable TaskLoop as second level parallelism], finetaskloop=$withval, finetaskloop=no)
+AC_MSG_RESULT($finetaskloop)
+AM_CONDITIONAL(WITH_FINETASKLOOP, test x"$finetaskloop" != xno)
+if test "x$finetaskloop" = "xyes" ; then
+ AC_DEFINE(WITH_FINETASKLOOP)
+fi
+
# ************************** --without-cuda option **********************************
#
@@ -578,6 +606,22 @@ else
AC_MSG_NOTICE([Disable CUDA Library])
AM_CONDITIONAL([ENABLE_CUDA], [test x"$with_cuda" == xno])
fi
+
+
+
+# ************************ --without-standalonesimd option *********************
+#
+
+AC_MSG_CHECKING([whether to enable SIMD Standalone])
+AC_ARG_WITH(x, [ --without-standalonesimd to disable SIMD standalone], , with_standalonesimd=yes)
+AC_MSG_RESULT($with_standalonesimd)
+AM_CONDITIONAL(WITH_STANDALONESIMD, test x"$with_standalonesimd" != xno)
+if test "x$with_standalonesimd" != xno ; then
+ AC_DEFINE(WITH_STANDALONE_SIMD)
+else
+ AC_DEFINE(__NO_VANILLA)
+fi
+
# ************************* back to GENERAL stuff *******************************
AC_CONFIG_FILES([Makefile
diff --git a/src/aevol_run.cpp b/src/aevol_run.cpp
index 7edafe167..05e9cb24d 100644
--- a/src/aevol_run.cpp
+++ b/src/aevol_run.cpp
@@ -99,6 +99,7 @@ int main(int argc, char* argv[])
int64_t t0 = -1;
int64_t t_end = -1;
int64_t nb_steps = -1;
+ int grain_size = 1;
#ifndef __NO_X
bool show_display_on_startup = true;
@@ -110,7 +111,7 @@ int main(int argc, char* argv[])
// -------------------------------------------------------------------------
// 2) Define allowed options
// -------------------------------------------------------------------------
- const char * options_list = "he:n:r:vVwxp:";
+ const char * options_list = "he:n:r:vVwxp:g:";
static struct option long_options_list[] = {
// Print help
{ "help", no_argument, NULL, 'h' },
@@ -130,6 +131,7 @@ int main(int argc, char* argv[])
{ "noX", no_argument, NULL, 'x' },
// Run in parallel on x threads (0 or negative value yields system default)
{ "parallel", required_argument, NULL, 'p' },
+ { "grainsize", required_argument, NULL, 'g' },
{ 0, 0, 0, 0 }
};
@@ -197,6 +199,10 @@ int main(int argc, char* argv[])
#endif
break;
}
+ case 'g' : {
+ grain_size = atoi(optarg);
+ break;
+ }
default : {
// An error message is printed in getopt_long, we just need to exit
exit(EXIT_FAILURE);
@@ -234,6 +240,7 @@ int main(int argc, char* argv[])
exp_manager = new ExpManager();
#endif
+ exp_manager->grain_size = grain_size;
exp_manager->load(t0, verbose, true);
exp_manager->set_t_end(t_end);
diff --git a/src/libaevol/Dna_SIMD.cpp b/src/libaevol/Dna_SIMD.cpp
index 2b06bdd2a..78ee2d9ae 100644
--- a/src/libaevol/Dna_SIMD.cpp
+++ b/src/libaevol/Dna_SIMD.cpp
@@ -71,13 +71,16 @@ Dna_SIMD::~Dna_SIMD() {
#ifdef WITH_BITSET
delete bitset_;
#else
- free(data_);
+ if (data_ != nullptr) { free(data_); data_=nullptr;}
#endif
- for (auto repl : mutation_list)
- delete repl;
+if (mutation_list.size() > 0) {
+ for (auto repl : mutation_list)
+ delete repl;
+ mutation_list.clear();
+}
+
- mutation_list.clear();
}
#ifndef WITH_BITSET
diff --git a/src/libaevol/ExpManager.cpp b/src/libaevol/ExpManager.cpp
index 500d05961..baeb62eac 100644
--- a/src/libaevol/ExpManager.cpp
+++ b/src/libaevol/ExpManager.cpp
@@ -380,6 +380,19 @@ auto t1 = high_resolution_clock::now();
+
+
+ if (!simd_individual->standalone()) {
+ t1 = high_resolution_clock::now();
+ // Write statistical data and store phylogenetic data (tree)
+#pragma omp single
+ {
+ output_m_->write_current_generation_outputs();
+ }
+ t2 = high_resolution_clock::now();
+ duration_2 += std::chrono::duration_cast<std::chrono::microseconds>( t2 - t1 ).count();
+ }
+
#ifdef __CUDACC__
std::cout<<"PERFLOG,"<<AeTime::time()<<","<<duration_2<<","<<duration<<","<<duration_A<<","<<duration_B<<","<<duration_C<<std::endl;
@@ -390,14 +403,6 @@ auto t1 = high_resolution_clock::now();
#else
std::cout<<"PERFLOG,"<<AeTime::time()<<","<<duration_2<<","<<duration_simd<<std::endl;
#endif
-
- if (!simd_individual->standalone()) {
- // Write statistical data and store phylogenetic data (tree)
-#pragma omp single
- {
- output_m_->write_current_generation_outputs();
- }
- }
}
/*!
@@ -594,31 +599,36 @@ void ExpManager::run_evolution() {
}
simd_individual = new SIMD_Individual(this);
+ simd_individual->protein_grain_size = grain_size;
+ simd_individual->rna_grain_size = grain_size;
+
simd_individual->run_a_step(best_indiv()->w_max(),selection_pressure(),false);
// For each generation
while (true) { // termination condition is into the loop
- printf(
- "============================== %" PRId64 " ==============================\n",
- AeTime::time());
- if (!first_run) {
- if (SIMD_Individual::standalone_simd) {
- printf(
- " Best individual's (%d) distance to target (metabolic) : %f (clones %d)\n",
- simd_individual->best_indiv->indiv_id,
- simd_individual->best_indiv->metaerror,
- simd_individual->nb_clones_);
+ if (AeTime::time() % 100 == 0) {
+ printf(
+ "============================== %" PRId64 " ==============================\n",
+ AeTime::time());
+ if (!first_run) {
+ if (SIMD_Individual::standalone_simd) {
+ printf(
+ " Best individual's (%d) distance to target (metabolic) : %f (clones %d)\n",
+ simd_individual->best_indiv->indiv_id,
+ simd_individual->best_indiv->metaerror,
+ simd_individual->nb_clones_);
+ } else {
+ printf(" Best individual's (%d) distance to target (metabolic) : %f\n",
+ best_indiv()->id(),
+ best_indiv()->dist_to_target_by_feature(METABOLISM));
+ }
} else {
printf(" Best individual's (%d) distance to target (metabolic) : %f\n",
best_indiv()->id(),
best_indiv()->dist_to_target_by_feature(METABOLISM));
}
- } else {
- printf(" Best individual's (%d) distance to target (metabolic) : %f\n",
- best_indiv()->id(),
- best_indiv()->dist_to_target_by_feature(METABOLISM));
}
first_run = false;
diff --git a/src/libaevol/ExpManager.h b/src/libaevol/ExpManager.h
index 485bad0db..f8545a93e 100644
--- a/src/libaevol/ExpManager.h
+++ b/src/libaevol/ExpManager.h
@@ -167,6 +167,7 @@ class ExpManager : public Observer {
// SIMD Stuff
SIMD_Individual* simd_individual = nullptr;
+ int grain_size = 1;
protected:
// =======================================================================
// Protected Methods
diff --git a/src/libaevol/SIMD_Individual.cpp b/src/libaevol/SIMD_Individual.cpp
index afc2cce60..39e228e70 100644
--- a/src/libaevol/SIMD_Individual.cpp
+++ b/src/libaevol/SIMD_Individual.cpp
@@ -12,7 +12,11 @@
namespace aevol {
+#ifndef WITH_STANDALONE_SIMD
+ bool SIMD_Individual::standalone_simd = false;
+#else
bool SIMD_Individual::standalone_simd = true;
+#endif
SIMD_Individual::SIMD_Individual(ExpManager* exp_m) {
@@ -38,6 +42,7 @@ SIMD_Individual::SIMD_Individual(ExpManager* exp_m) {
internal_simd_struct[indiv_id]->parent_id = indiv_id;
//printf("Set Prev Indiv\n");
prev_internal_simd_struct[indiv_id] = internal_simd_struct[indiv_id];
+ internal_simd_struct[indiv_id]->global_id = AeTime::time()*1024+indiv_id;
}
dna_size = new int[exp_m_->nb_indivs()];
@@ -532,14 +537,18 @@ void SIMD_Individual::selection() {
// printf("DNA BEFORE SIZE of %d is %d (%d)\n",indiv_id,dna_size[indiv_id],internal_simd_struct[indiv_id]->dna_->length());
if (exp_m_->dna_mutator_array_[indiv_id]->hasMutate()) {
+/* if (internal_simd_struct[indiv_id] != nullptr) {
+ printf("Warning will replace something that is not null !!!\n");
+ }*/
- exp_m_->simd_individual->internal_simd_struct[indiv_id] =
+ internal_simd_struct[indiv_id] =
new Internal_SIMD_Struct(exp_m_,prev_internal_simd_struct
[next_generation_reproducer_[indiv_id]],false);
- exp_m_->simd_individual->internal_simd_struct[indiv_id]->indiv_id = indiv_id;
- exp_m_->simd_individual->internal_simd_struct[indiv_id]->parent_id =
+ internal_simd_struct[indiv_id]->global_id = AeTime::time()*1024+indiv_id;
+ internal_simd_struct[indiv_id]->indiv_id = indiv_id;
+ internal_simd_struct[indiv_id]->parent_id =
next_generation_reproducer_[indiv_id];
#ifdef WITH_BITSET
@@ -678,36 +687,110 @@ SIMD_Individual::~SIMD_Individual() {
printf("Destroy SIMD Controller\n");
for (int indiv_id = 0; indiv_id < (int) exp_m_->nb_indivs(); indiv_id++) {
- if (internal_simd_struct[indiv_id] != nullptr) {
- for (auto rn : internal_simd_struct[indiv_id]->rnas) {
- delete rn;
- }
- internal_simd_struct[indiv_id]->rnas.clear();
- for (auto prot : internal_simd_struct[indiv_id]->proteins) {
- delete prot;
+
+/*
+ if (internal_simd_struct[indiv_id] != nullptr) {
+ printf("Internal %d : %d \n", indiv_id, internal_simd_struct[indiv_id]->usage_count_);
}
- internal_simd_struct[indiv_id]->proteins.clear();
+*/
- if (internal_simd_struct[indiv_id]->usage_count_ > 1)
- internal_simd_struct[indiv_id]->usage_count_--;
- else {
- delete internal_simd_struct[indiv_id];
- internal_simd_struct[indiv_id] = nullptr;
+ if (internal_simd_struct[indiv_id] != nullptr) {
+
+
+ if (internal_simd_struct[indiv_id]->usage_count_ > 0)
+ internal_simd_struct[indiv_id]->usage_count_--;
+ else {
+ if (internal_simd_struct[indiv_id]->usage_count_ != -1) {
+ internal_simd_struct[indiv_id]->usage_count_ = -1;
+
+ for (auto rn : internal_simd_struct[indiv_id]->rnas) {
+ delete rn;
+ }
+ internal_simd_struct[indiv_id]->rnas.clear();
+ for (auto prot : internal_simd_struct[indiv_id]->proteins) {
+ delete prot;
+ }
+ internal_simd_struct[indiv_id]->proteins.clear();
+
+ delete internal_simd_struct[indiv_id];
+ internal_simd_struct[indiv_id] = nullptr;
+ }
+ }
}
- }
+ }
+ for (int indiv_id = 0; indiv_id < (int) exp_m_->nb_indivs(); indiv_id++) {
if (prev_internal_simd_struct[indiv_id] != nullptr) {
- if (prev_internal_simd_struct[indiv_id]->usage_count_ > 1)
+ if (prev_internal_simd_struct[indiv_id]->usage_count_ > 0)
prev_internal_simd_struct[indiv_id]->usage_count_--;
else {
- delete prev_internal_simd_struct[indiv_id];
- prev_internal_simd_struct[indiv_id] = nullptr;
+ if (prev_internal_simd_struct[indiv_id]->usage_count_ != -1) {
+ prev_internal_simd_struct[indiv_id]->usage_count_ = -1;
+
+ /*printf("DELETE --- PREV %d (%d) : %d \n", indiv_id, prev_internal_simd_struct[indiv_id]->usage_count_,
+ prev_internal_simd_struct[indiv_id]->global_id);*/
+ for (auto rn : prev_internal_simd_struct[indiv_id]->rnas) {
+ delete rn;
+ }
+ prev_internal_simd_struct[indiv_id]->rnas.clear();
+ for (auto prot : prev_internal_simd_struct[indiv_id]->proteins) {
+ delete prot;
+ }
+ prev_internal_simd_struct[indiv_id]->proteins.clear();
+
+ delete prev_internal_simd_struct[indiv_id];
+ prev_internal_simd_struct[indiv_id] = nullptr;
+ }
}
}
delete exp_m_->dna_mutator_array_[indiv_id];
}
+ for (int indiv_id = 0; indiv_id < (int) exp_m_->nb_indivs(); indiv_id++) {
+ /* if (internal_simd_struct[indiv_id] != nullptr) {
+ printf("Still here %d : %d\n",internal_simd_struct[indiv_id]->global_id,
+ internal_simd_struct[indiv_id]->usage_count_);
+ //}
+ // delete internal_simd_struct[indiv_id];
+ }
+*/
+ if (prev_internal_simd_struct[indiv_id] != nullptr) {
+ if (prev_internal_simd_struct[indiv_id]->usage_count_ != -1) {
+ prev_internal_simd_struct[indiv_id]->usage_count_ = -1;
+ /*printf("Still here %d -- %d : %d\n", indiv_id, prev_internal_simd_struct[indiv_id]->global_id,
+ prev_internal_simd_struct[indiv_id]->usage_count_);*/
+
+ for (auto rn : prev_internal_simd_struct[indiv_id]->rnas) {
+ delete rn;
+ }
+
+ prev_internal_simd_struct[indiv_id]->rnas.clear();
+ for (auto prot : prev_internal_simd_struct[indiv_id]->proteins) {
+ delete prot;
+ }
+ prev_internal_simd_struct[indiv_id]->proteins.clear();
+
+ delete prev_internal_simd_struct[indiv_id];
+ prev_internal_simd_struct[indiv_id] = nullptr;
+ }
+ }
+ }
+
+/* for (int indiv_id = 0; indiv_id < (int) exp_m_->nb_indivs(); indiv_id++) {
+ *//* if (internal_simd_struct[indiv_id] != nullptr) {
+ printf("Still here %d : %d\n",internal_simd_struct[indiv_id]->global_id,
+ internal_simd_struct[indiv_id]->usage_count_);
+ //}
+ // delete internal_simd_struct[indiv_id];
+ }
+ *//*
+ if (prev_internal_simd_struct[indiv_id] != nullptr) {
+ printf("WHAT Still here %d -- %d : %d\n",indiv_id,prev_internal_simd_struct[indiv_id]->global_id,
+ prev_internal_simd_struct[indiv_id]->usage_count_);
+ }
+ }*/
+
delete[] prev_internal_simd_struct;
delete[] internal_simd_struct;
@@ -716,6 +799,15 @@ SIMD_Individual::~SIMD_Individual() {
delete stats_best;
delete stats_mean;
+
+ for (int indiv_id = 0; indiv_id < (int) exp_m_->nb_indivs(); indiv_id++) {
+ int x = indiv_id / exp_m_->world()->height();
+ int y = indiv_id % exp_m_->world()->height();
+
+ exp_m_->world()->grid(x, y)->individual()->clear_everything_except_dna_and_promoters();
+ exp_m_->world()->grid(x, y)->individual()->genetic_unit_list_nonconst().clear();
+ delete exp_m_->world()->grid(x, y)->individual();
+ }
}
@@ -1520,7 +1612,9 @@ void SIMD_Individual::opt_prom_compute_RNA() {
//#pragma omp task firstprivate(indiv_id)
// {
+#ifdef WITH_FINETASKLOOP
#pragma omp taskloop grainsize(rna_grain_size)
+#endif
for (int prom_idx = 0; prom_idx< internal_simd_struct[indiv_id]->promoters.size(); prom_idx++) {
if (internal_simd_struct[indiv_id]->promoters.find(prom_idx) !=
@@ -1984,7 +2078,9 @@ void SIMD_Individual::compute_RNA() {
internal_simd_struct[indiv_id]->rnas.resize(
internal_simd_struct[indiv_id]->promoters.size());
//#pragma omp parallel for firstprivate(indiv_id) schedule(dynamic)
+#ifdef WITH_FINETASKLOOP
#pragma omp taskloop grainsize(rna_grain_size)
+#endif
for (int rna_idx = 0; rna_idx <
(int) internal_simd_struct[indiv_id]->promoters.size(); rna_idx++) {
//#pragma omp task firstprivate(indiv_id, rna_idx)
@@ -2169,7 +2265,9 @@ void SIMD_Individual::compute_RNA() {
}
void SIMD_Individual::start_protein(int indiv_id) {
-#pragma omp taskloop grainsize(rna_grain_size)
+#ifdef WITH_FINETASKLOOP
+ #pragma omp taskloop grainsize(rna_grain_size)
+#endif
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) depend(out: internal_simd_struct[indiv_id])
@@ -2449,7 +2547,9 @@ void SIMD_Individual::compute_protein(int indiv_id) {
proteins.resize(resize_to);
}
//#pragma omp parallel for firstprivate(indiv_id) schedule(dynamic)
+#ifdef WITH_FINETASKLOOP
#pragma omp taskloop grainsize(rna_grain_size)
+#endif
for (int rna_idx = 0; rna_idx <
(int) internal_simd_struct[indiv_id]->rna_count_; rna_idx++) {
if (internal_simd_struct[indiv_id]->rnas[rna_idx]->is_init_) {
@@ -3388,7 +3488,9 @@ void SIMD_Individual::translate_protein(double w_max) {
void SIMD_Individual::translate_protein(int indiv_id, double w_max) {
-#pragma omp taskloop grainsize(protein_grain_size)
+#ifdef WITH_FINETASKLOOP
+ #pragma omp taskloop grainsize(protein_grain_size)
+#endif
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) depend(inout: internal_simd_struct[indiv_id])
@@ -4091,9 +4193,13 @@ void SIMD_Individual::run_a_step(double w_max, double selection_pressure,bool op
#pragma omp single nowait
{
nb_clones_ = 0;
-#pragma omp taskloop
+#ifndef WITH_L1TASK
+ #pragma omp taskloop
+#endif
for (int indiv_id = 0; indiv_id < exp_m_->nb_indivs(); indiv_id++) {
- //#pragma omp task firstprivate(indiv_id)
+#ifdef WITH_L1TASK
+ #pragma omp task firstprivate(indiv_id)
+#endif
{
// if (AeTime::time() > 0 && optim_prom) check_selection(indiv_id);
if (standalone_ && optim_prom) {
@@ -4157,8 +4263,8 @@ void SIMD_Individual::run_a_step(double w_max, double selection_pressure,bool op
}
-//#pragma omp task firstprivate(indiv_id)
- // {
+/*#pragma omp task firstprivate(indiv_id)
+ {*/
if (optim_prom) {
//printf("Clear structures\n");
//clear_struct_before_next_step();
@@ -4297,28 +4403,52 @@ void SIMD_Individual::run_a_step(double w_max, double selection_pressure,bool op
//#pragma omp single
//#pragma omp taskloop
for (int indiv_id = 0; indiv_id < (int) exp_m_->nb_indivs(); indiv_id++) {
+ //if (indiv_id == 0)
+ // printf("%d -- usage %d -- \n", indiv_id, internal_simd_struct[indiv_id]->usage_count_);
int usage_cpt = 0;
- //#pragma omp critical
+#pragma omp critical
{
- usage_cpt = prev_internal_simd_struct[indiv_id]->usage_count_--;
+ if (prev_internal_simd_struct[indiv_id]->usage_count_ == 1) {
+ prev_internal_simd_struct[indiv_id]->usage_count_ = -1;
- if (usage_cpt == 0)
delete prev_internal_simd_struct[indiv_id];
+ } else
+ prev_internal_simd_struct[indiv_id]->usage_count_--;
+ /*else {
+ printf("Still alive %d : %d\n",prev_internal_simd_struct[indiv_id]->global_id,
+ prev_internal_simd_struct[indiv_id]->usage_count_);
+ }*/
+
}
prev_internal_simd_struct[indiv_id] = internal_simd_struct[indiv_id];
internal_simd_struct[indiv_id] = nullptr;
}
- } else {
+ } else if (standalone_ && (!optim_prom)) {
+
+ } else {
// printf("Copy to old generation struct\n");
-#pragma omp parallel
-#pragma omp single
-#pragma omp taskloop
+//#pragma omp parallel
+//#pragma omp single
+//#pragma omp taskloop
for (int indiv_id = 0; indiv_id < (int) exp_m_->nb_indivs(); indiv_id++) {
+ int usage_cpt = 0;
+
+ #pragma omp critical
+ {
+ if (prev_internal_simd_struct[indiv_id]->usage_count_ == 1) {
+ prev_internal_simd_struct[indiv_id]->usage_count_ = -1;
- prev_internal_simd_struct[indiv_id] = internal_simd_struct[indiv_id];
- internal_simd_struct[indiv_id] = nullptr;
+ delete prev_internal_simd_struct[indiv_id];
+ } else
+ prev_internal_simd_struct[indiv_id]->usage_count_--;
+ //usage_cpt = prev_internal_simd_struct[indiv_id]->usage_count_;
+
+ }
+
+ prev_internal_simd_struct[indiv_id] = internal_simd_struct[indiv_id];
+ internal_simd_struct[indiv_id] = nullptr;
}
}
@@ -4331,6 +4461,8 @@ void SIMD_Individual::run_a_step(double w_max, double selection_pressure,bool op
best_fitness = prev_internal_simd_struct[indiv_id]->fitness;
}
}
+/*
+ printf("IDX BEST %d\n",idx_best);*/
best_indiv = prev_internal_simd_struct[idx_best];
@@ -4687,10 +4819,12 @@ Internal_SIMD_Struct::Internal_SIMD_Struct(ExpManager* exp_m, Internal_SIMD_Stru
}
Internal_SIMD_Struct::~Internal_SIMD_Struct() {
- for (auto element = promoters.begin();
- element != promoters.end(); ++element) {
- delete element->second;
- }
+ if (promoters.size() > 0) {
+ for (auto element = promoters.begin();
+ element != promoters.end(); ++element) {
+ if (element->second != nullptr) delete element->second;
+ }
+ }
promoters.clear();
diff --git a/src/libaevol/SIMD_Individual.h b/src/libaevol/SIMD_Individual.h
index b12c7b24f..13c59dcdc 100644
--- a/src/libaevol/SIMD_Individual.h
+++ b/src/libaevol/SIMD_Individual.h
@@ -127,6 +127,8 @@ class Internal_SIMD_Struct {
ExpManager* exp_m_;
+ int global_id = -1;
+
void rebuild_index();
void remove_promoters_around(int32_t pos_1);
@@ -264,7 +266,8 @@ class SIMD_Individual {
int32_t nb_clones_;
static bool standalone_simd;//= true;
-
+ int rna_grain_size = 32;
+ int protein_grain_size = 32;
private:
ExpManager* exp_m_;
int* dna_size;
@@ -280,8 +283,7 @@ class SIMD_Individual {
void check_selection(int indiv_id);
- int rna_grain_size = 32;
- int protein_grain_size = 32;
+
};
}
diff --git a/src/libaevol/Stats_SIMD.cpp b/src/libaevol/Stats_SIMD.cpp
index 409c645ae..90877773a 100644
--- a/src/libaevol/Stats_SIMD.cpp
+++ b/src/libaevol/Stats_SIMD.cpp
@@ -187,7 +187,7 @@ void Stats_SIMD::compute_average() {
amount_of_dna_ += simd_individual_->prev_internal_simd_struct[indiv_id]->dna_->length();
for (int i = 0; i < simd_individual_->prev_internal_simd_struct[indiv_id]->rna_count_; i++) {
- if (simd_individual_->best_indiv->rnas[i] != nullptr) {
+ if (simd_individual_->prev_internal_simd_struct[indiv_id]->rnas[i] != nullptr) {
if (simd_individual_->prev_internal_simd_struct[indiv_id]->rnas[i]->is_coding_)
nb_coding_rnas_++;
else
@@ -196,7 +196,7 @@ void Stats_SIMD::compute_average() {
}
for (int i = 0; i < simd_individual_->prev_internal_simd_struct[indiv_id]->protein_count_; i++) {
- if (simd_individual_->best_indiv->rnas[i] != nullptr) {
+ if (simd_individual_->prev_internal_simd_struct[indiv_id]->rnas[i] != nullptr) {
if (simd_individual_->prev_internal_simd_struct[indiv_id]->proteins[i]->is_functional) {
nb_functional_genes_++;
} else {
--
GitLab