diff --git a/src/libaevol/ExpManager.cpp b/src/libaevol/ExpManager.cpp
index 1007ffc87adb383f2639b7df25ff7855cdb9463d..500d05961f771285bb62bd9e6f0e684c9d01a466 100644
--- a/src/libaevol/ExpManager.cpp
+++ b/src/libaevol/ExpManager.cpp
@@ -342,11 +342,10 @@ auto t1 = high_resolution_clock::now();
auto duration = std::chrono::duration_cast<std::chrono::microseconds>( t2 - s_t1 ).count();
#endif
- bool simd_first = false;
+/* bool simd_first = false;
if (simd_individual == nullptr) {
simd_first = true;
- simd_individual = new SIMD_Individual(this);
- }
+ }*/
//}
t1 = high_resolution_clock::now();
@@ -365,12 +364,11 @@ auto t1 = high_resolution_clock::now();
auto ta = high_resolution_clock::now();
- if (simd_first) {
- simd_individual->run_a_step(best_indiv()->w_max(),selection_pressure(),false);
+/* if (simd_first) {
//simd_individual->check_result();
- } else {
+ } else {*/
simd_individual->run_a_step(best_indiv()->w_max(),selection_pressure(),true);
- }
+ //}
auto tb = high_resolution_clock::now();
@@ -595,15 +593,18 @@ void ExpManager::run_evolution() {
dna_mutator_array_[i] = nullptr;
}
+ simd_individual = new SIMD_Individual(this);
+ simd_individual->run_a_step(best_indiv()->w_max(),selection_pressure(),false);
+
- // For each generation
+ // For each generation
while (true) { // termination condition is into the loop
printf(
"============================== %" PRId64 " ==============================\n",
AeTime::time());
if (!first_run) {
- if (simd_individual->standalone()) {
+ if (SIMD_Individual::standalone_simd) {
printf(
" Best individual's (%d) distance to target (metabolic) : %f (clones %d)\n",
simd_individual->best_indiv->indiv_id,
diff --git a/src/libaevol/SIMD_Individual.cpp b/src/libaevol/SIMD_Individual.cpp
index e71d2e9485695b1d1155633a17c6733a0d2794b0..a92e9063244aa39448280b0b56899e1a26b3d9ed 100644
--- a/src/libaevol/SIMD_Individual.cpp
+++ b/src/libaevol/SIMD_Individual.cpp
@@ -12,10 +12,12 @@
namespace aevol {
+ bool SIMD_Individual::standalone_simd = true;
+
SIMD_Individual::SIMD_Individual(ExpManager* exp_m) {
printf("Create SIMD Controller\n");
-
+ standalone_ = standalone_simd;
exp_m_ = exp_m;
nb_indivs_ = exp_m_->nb_indivs();
@@ -345,6 +347,10 @@ SIMD_Individual::~SIMD_Individual() {
delete[] internal_simd_struct;
delete[] dna_size;
+
+
+ delete stats_best;
+ delete stats_mean;
}
void SIMD_Individual::start_stop_RNA() {
@@ -1234,7 +1240,7 @@ void SIMD_Individual::compute_protein() {
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_) {
-///#pragma omp parallel for firstprivate(indiv_id, rna_idx) schedule(dynamic)
+//#pragma omp parallel for firstprivate(indiv_id, rna_idx) schedule(dynamic)
for (int protein_idx = 0;
protein_idx < (int) internal_simd_struct[indiv_id]->
rnas[rna_idx]->start_prot.size(); protein_idx++) {
@@ -2216,13 +2222,17 @@ void SIMD_Individual::run_a_step(double w_max, double selection_pressure,bool op
best_indiv = prev_internal_simd_struct[idx_best];
// Stats
- Stats_SIMD* stats_best = new Stats_SIMD(this, AeTime::time(), true);
- stats_best->write_best();
- delete stats_best;
+ if (!optim_prom) {
+ stats_best = new Stats_SIMD(this, AeTime::time(), true);
+ stats_mean = new Stats_SIMD(this, AeTime::time(), false);
+ } else {
+ stats_best->reinit(AeTime::time());
+ stats_mean->reinit(AeTime::time());
+ }
+
- Stats_SIMD* stats_mean = new Stats_SIMD(this, AeTime::time(), false);
+ stats_best->write_best();
stats_mean->write_average();
- delete stats_mean;
if (standalone_ && AeTime::time() % exp_m_->backup_step() == 0) {
@@ -2279,7 +2289,7 @@ void SIMD_Individual::run_a_step(double w_max, double selection_pressure,bool op
last_gener_file << AeTime::time() << std::endl;
last_gener_file.close();
- //if (AeTime::time() != exp_m_->end_step()) {
+ if (AeTime::time() == exp_m_->end_step()) {
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();
@@ -2288,7 +2298,7 @@ void SIMD_Individual::run_a_step(double w_max, double selection_pressure,bool op
exp_m_->world()->grid(x, y)->individual()->genetic_unit_list_nonconst().clear();
delete exp_m_->world()->grid(x, y)->individual();
}
- //}
+ }
}
diff --git a/src/libaevol/SIMD_Individual.h b/src/libaevol/SIMD_Individual.h
index b483ae36436476b278802be5186ddfc5e3677385..d274e17e403c0fbb96f60ae931af9f1ff90de793 100644
--- a/src/libaevol/SIMD_Individual.h
+++ b/src/libaevol/SIMD_Individual.h
@@ -6,6 +6,7 @@
#define RAEVOL_CUDA_SIMD_INDIVIDUAL_H
#include "ExpManager.h"
+#include "Stats_SIMD.h"
namespace aevol {
@@ -245,11 +246,16 @@ class SIMD_Individual {
int32_t nb_indivs_;
int32_t nb_clones_;
+ static bool standalone_simd;//= true;
+
private:
ExpManager* exp_m_;
int* dna_size;
float target[300];
- bool standalone_ = true;
+ bool standalone_;
+
+ Stats_SIMD* stats_best;
+ Stats_SIMD* stats_mean;
void selection();
diff --git a/src/libaevol/Stats_SIMD.cpp b/src/libaevol/Stats_SIMD.cpp
index 231d8243045053f8f3ba70e7b896a17c55f92543..71a554ace245898e5e902f0387f07e40b2b272e9 100644
--- a/src/libaevol/Stats_SIMD.cpp
+++ b/src/libaevol/Stats_SIMD.cpp
@@ -1,6 +1,10 @@
//
// Created by arrouan on 19/01/18.
//
+#include <iostream>
+#include <fstream>
+#include <string>
+#include <fcntl.h>
#include "Stats_SIMD.h"
#include "Dna_SIMD.h"
@@ -35,30 +39,88 @@ Stats_SIMD::Stats_SIMD(SIMD_Individual* simd_individual, int64_t generation, boo
nb_inv_ = 0;
- if (generation_==1) {
- statfile_best_.open("stats/stats_simd_best.csv",std::ofstream::trunc);
- statfile_mean_.open("stats/stats_simd_mean.csv",std::ofstream::trunc);
- if (is_indiv_)
- statfile_best_<<"Generation"<<","<<"fitness"<<","<<"metabolic_error"<<","<<
- "amount_of_dna"<<","<<"nb_coding_rnas"<<","<<"nb_non_coding_rnas"<<","<<
- "nb_functional_genes"<<","<<"nb_non_functional_genes"<<","<<"nb_mut"
- <<","<<"nb_switch"<<","<<"nb_indels"<<","<<"nb_rear"<<","<<"nb_dupl"<<","<<
- "nb_del"<<","<<"nb_trans"<<","<<"nb_inv"<<","<<"dupl_rate"<<","<<"del_rate"
- <<","<<"trans_rate"<<","<<"inv_rate"
- <<std::endl;
- else
- statfile_mean_<<"Generation"<<","<<"fitness"<<","<<"metabolic_error"<<","<<
- "amount_of_dna"<<","<<"nb_coding_rnas"<<","<<"nb_non_coding_rnas"<<","<<
- "nb_functional_genes"<<","<<"nb_non_functional_genes"<<","<<"nb_mut"
- <<","<<"nb_switch"<<","<<"nb_indels"<<","<<"nb_rear"<<","<<"nb_dupl"<<","<<
- "nb_del"<<","<<"nb_trans"<<","<<"nb_inv"<<","<<"dupl_rate"<<","<<"del_rate"
- <<","<<"trans_rate"<<","<<"inv_rate"
- <<std::endl;
+ if (generation_==0) {
+ if (is_indiv_)
+ statfile_best_.open("stats/stats_simd_best.csv",std::ofstream::trunc);
+ else
+ statfile_mean_.open("stats/stats_simd_mean.csv",std::ofstream::trunc);
+
+ if (is_indiv_) {
+ statfile_best_ << "Generation" << "," << "fitness" << "," << "metabolic_error" << "," <<
+ "amount_of_dna" << "," << "nb_coding_rnas" << "," << "nb_non_coding_rnas" << "," <<
+ "nb_functional_genes" << "," << "nb_non_functional_genes" << "," << "nb_mut"
+ << "," << "nb_switch" << "," << "nb_indels" << "," << "nb_rear" << "," << "nb_dupl" << "," <<
+ "nb_del" << "," << "nb_trans" << "," << "nb_inv" << "," << "dupl_rate" << "," << "del_rate"
+ << "," << "trans_rate" << "," << "inv_rate"
+ << std::endl;
+ statfile_best_.flush();
+ } else {
+ statfile_mean_ << "Generation" << "," << "fitness" << "," << "metabolic_error" << "," <<
+ "amount_of_dna" << "," << "nb_coding_rnas" << "," << "nb_non_coding_rnas" << "," <<
+ "nb_functional_genes" << "," << "nb_non_functional_genes" << "," << "nb_mut"
+ << "," << "nb_switch" << "," << "nb_indels" << "," << "nb_rear" << "," << "nb_dupl" << "," <<
+ "nb_del" << "," << "nb_trans" << "," << "nb_inv" << "," << "dupl_rate" << "," << "del_rate"
+ << "," << "trans_rate" << "," << "inv_rate"
+ << std::endl;
+ statfile_mean_.flush();
+ }
} else {
- statfile_best_.open("stats/stats_simd_best.csv",std::ofstream::app);
- statfile_mean_.open("stats/stats_simd_mean.csv",std::ofstream::app);
- }
+ printf("Resume without rheader\n");
+ std::ifstream tmp_mean;
+ std::ifstream tmp_best;
+
+ if (is_indiv_) {
+ tmp_best.open("stats/stats_simd_best.csv",std::ifstream::in);
+ statfile_best_.open("stats/stats_simd_best.csv.tmp", std::ofstream::trunc);
+ } else {
+ tmp_mean.open("stats/stats_simd_mean.csv",std::ifstream::in);
+ statfile_mean_.open("stats/stats_simd_mean.csv.tmp", std::ofstream::trunc);
+ }
+
+ std::string str;
+ for (int i = 0; i <= generation_; i++) {
+ if (is_indiv_) {
+ std::getline(tmp_best, str);
+ statfile_best_ << str << std::endl;
+ } else {
+ std::getline(tmp_mean, str);
+ statfile_mean_ << str << std::endl;
+ }
+ }
+
+ if (is_indiv_) {
+ statfile_best_.flush();
+ statfile_best_.close();
+ } else {
+ statfile_mean_.flush();
+ statfile_mean_.close();
+ }
+ if (is_indiv_) {
+ statfile_best_.open("stats/stats_simd_best.csv", std::ofstream::trunc);
+ tmp_best.close();
+ tmp_best.open("stats/stats_simd_best.csv.tmp", std::ifstream::in);
+ tmp_best.seekg(0, std::ios::beg);
+ } else {
+ statfile_mean_.open("stats/stats_simd_mean.csv", std::ofstream::trunc);
+ tmp_mean.close();
+ tmp_mean.open("stats/stats_simd_mean.csv.tmp", std::ifstream::in);
+ tmp_mean.seekg(0, std::ios::beg);
+ }
+
+ for (int i = 0; i <= generation_; i++) {
+ if (is_indiv_) {
+ std::getline(tmp_best, str);
+ statfile_best_ << str << std::endl;
+ } else {
+ std::getline(tmp_mean, str);
+ statfile_mean_ << str << std::endl;
+ }
+ }
+
+ tmp_best.close();
+ tmp_mean.close();
+ }
}
void Stats_SIMD::compute_best() {
@@ -219,7 +281,35 @@ void Stats_SIMD::write_average() {
nb_del_<<","<<nb_trans_<<","<<nb_inv_<<","<<dupl_rate_<<","<<del_rate_
<<","<<trans_rate_<<","<<inv_rate_
<<std::endl;
+ statfile_mean_.flush();
}
}
+ void Stats_SIMD::reinit(int64_t generation) {
+ generation_ = generation;
+
+ pop_size_ = 0;
+
+ fitness_ = 0;
+ metabolic_error_ = 0;
+
+ amount_of_dna_ = 0;
+ nb_coding_rnas_ = 0;
+ nb_non_coding_rnas_ = 0;
+
+ nb_functional_genes_ = 0;
+ nb_non_functional_genes_ = 0;
+
+ nb_mut_ = 0;
+ nb_rear_ = 0;
+ nb_switch_ = 0;
+ nb_indels_ = 0;
+ nb_dupl_ = 0;
+ nb_del_ = 0;
+ nb_trans_ = 0;
+ nb_inv_ = 0;
+
+ is_computed_ = false;
+ }
+
}
diff --git a/src/libaevol/Stats_SIMD.h b/src/libaevol/Stats_SIMD.h
index 68208ef2edf666a756a1a5358716e5501ed2bf10..4adb0752768771f9cada24730bc7fc5581449709 100644
--- a/src/libaevol/Stats_SIMD.h
+++ b/src/libaevol/Stats_SIMD.h
@@ -8,11 +8,12 @@
#include <cstdint>
#include <fstream>
-
-#include "SIMD_Individual.h"
+#include <limits>
namespace aevol {
+ class SIMD_Individual;
+
class Stats_SIMD {
public:
Stats_SIMD(SIMD_Individual* simd_individual, int64_t generation,
@@ -34,6 +35,8 @@ class Stats_SIMD {
void write_best();
void write_average();
+ void reinit(int64_t generation);
+
bool is_indiv() { return is_indiv_; }
@@ -86,6 +89,7 @@ class Stats_SIMD {
std::ofstream statfile_best_;
std::ofstream statfile_mean_;
+
};
}