diff --git a/CMakeLists.txt b/CMakeLists.txt
index 2498d19a2871e7dce30001849b3e247c7588f069..ebd530d98e79f505c9ca16a647e444d8d3263a0d 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -13,11 +13,12 @@ add_definitions(-DVERSION="${PROJECT_VERSION}")
set(AUTHORIZED_MTPERIOD 607 1279 2281 4253 11213 19937 44497 86243 132049 216091)
-set(with-x ON CACHE BOOL "Whether to enable graphical outputs")
+set(with-x OFF CACHE BOOL "Whether to enable graphical outputs")
set(with-omp OFF CACHE BOOL "Whether to enable OpenMP parallelization")
set(with-tbb OFF CACHE BOOL "Whether to enable TBB parallelization")
set(enable-profiling OFF CACHE BOOL "Whether to enable profiling")
set(with-tracing OFF CACHE BOOL "Whether to use tracing")
+set(enable-perflog OFF CACHE BOOL "Whether to active performance log")
set(enable-normalized-fitness OFF CACHE BOOL "With this option, the NORMALIZED_FITNESS flag is defined, allowing a different fitness calculation")
set(enable-mtperiod 607 CACHE STRING "Period of the Mersen Twister. Autorized values are : 607 1279 2281 4253 11213 19937 44497 86243 132049 216091")
set(enable-trivialjumps OFF CACHE STRING "When this option is set, a trivial jump algorithm will be used instead of the polynomial-based method")
@@ -59,6 +60,12 @@ if ( ${with-tracing} )
add_definitions(-D__TRACING__)
endif ()
+if ( ${enable-perflog} )
+ add_definitions(-D__PERF_LOG__)
+endif ()
+
+
+
if ( ${enable-normalized-fitness} )
add_definitions(-DNORMALIZED_FITNESS)
endif ()
diff --git a/examples/basic/param.in b/examples/basic/param.in
deleted file mode 100644
index dd7d25aba4ec34f9c51cb9920c00c64f1518ca00..0000000000000000000000000000000000000000
--- a/examples/basic/param.in
+++ /dev/null
@@ -1,61 +0,0 @@
-###################################
-# AEVOL PARAMATERS #
-###################################
-
-##### 1. Initial setup ############
-STRAIN_NAME basic_example
-SEED 7250909
-INIT_POP_SIZE 1024
-WORLD_SIZE 32 32
-INIT_METHOD ONE_GOOD_GENE CLONE
-CHROMOSOME_INITIAL_LENGTH 5000
-FUZZY_FLAVOR 1
-
-##### 2. Selection ################
-SELECTION_SCHEME fitness_proportionate 1000
-
-##### 3. Mutation rates ###########
-POINT_MUTATION_RATE 1e-6
-SMALL_INSERTION_RATE 1e-6
-SMALL_DELETION_RATE 1e-6
-MAX_INDEL_SIZE 6
-
-##### 4. Rearrangement rates (w/o alignements)
-WITH_ALIGNMENTS false
-DUPLICATION_RATE 1e-5
-DELETION_RATE 1e-5
-TRANSLOCATION_RATE 1e-5
-INVERSION_RATE 1e-5
-
-
-##### 5. Population Structure #####
-
-
-##### 6. Target function ##########
-ENV_SAMPLING 300
-ENV_ADD_GAUSSIAN 1.2 0.52 0.12
-ENV_ADD_GAUSSIAN -1.4 0.5 0.07
-ENV_ADD_GAUSSIAN 0.3 0.8 0.03
-MAX_TRIANGLE_WIDTH 0.033333333
-
-##### 7. Recording ################
-BACKUP_STEP 100
-RECORD_TREE false
-MORE_STATS false
-
-
-##### 8. Environment variation ####
-ENV_VARIATION none
-
-##### 9. Phenotypic axis ##########
-ENV_AXIS_FEATURES METABOLISM
-
-##### 10. Secretion ###############
-
-##### 11. Plasmids ################
-ALLOW_PLASMIDS false
-WITH_TRANSFER false
-
-
-
-
diff --git a/src/aevol_create.cpp b/src/aevol_create.cpp
index 6e4aa1647c162217bdc479fc335990552dc6cf44..89af64d0abbd3ed5410a7e38ee1d6b0cb871a96d 100644
--- a/src/aevol_create.cpp
+++ b/src/aevol_create.cpp
@@ -151,7 +151,7 @@ int main(int argc, char* argv[]) {
// 8) Save the experiment
- exp_manager->Save();
+ exp_manager->Save(true);
delete exp_manager;
}
diff --git a/src/libaevol/Dump.cpp b/src/libaevol/Dump.cpp
index 51db080be8636048a72fbdf9e1398222b4f38c69..9779acb591574e34517f1bcd24f75ceba469d896 100644
--- a/src/libaevol/Dump.cpp
+++ b/src/libaevol/Dump.cpp
@@ -218,7 +218,7 @@ void Dump::write_individual_probes()
{
for(int16_t y = 0 ; y < exp_m_->grid_height() ; y++)
{
- fprintf(current_file, "%" PRId32,
+ fprintf(current_file, "%llu",
exp_m_->world()->indiv_at(x,y)->id());
int32_t* int_probes =
exp_m_->world()->indiv_at(x,y)->int_probes();
diff --git a/src/libaevol/ExpManager.cpp b/src/libaevol/ExpManager.cpp
index facf4a55525e719d6821dcdd23b3f35b80a1723a..c31673c01f2fb5c650e2518197ceb4d6d9acd719 100644
--- a/src/libaevol/ExpManager.cpp
+++ b/src/libaevol/ExpManager.cpp
@@ -321,10 +321,11 @@ void ExpManager::step_to_next_generation() {
//if (AeTime::time() == 14) {
// Create the corresponding new generation
-
+#ifdef __PERF_LOG__
auto t1 = high_resolution_clock::now();
auto s_t1 = high_resolution_clock::now();
+#endif
#ifdef __CUDACC__
if (first_gen) {
@@ -366,7 +367,9 @@ auto t1 = high_resolution_clock::now();
}*/
//}
- t1 = high_resolution_clock::now();
+#ifdef __PERF_LOG__
+ t1 = high_resolution_clock::now();
+#endif
if (!simd_individual->standalone())
exp_s_->step_to_next_generation();
@@ -375,12 +378,16 @@ auto t1 = high_resolution_clock::now();
#ifdef __CUDACC__
t2 = high_resolution_clock::now();
#else
+#ifdef __PERF_LOG__
auto t2 = high_resolution_clock::now();
#endif
+#endif
- auto duration_2 = std::chrono::duration_cast<std::chrono::microseconds>( t2 - t1 ).count();
+#ifdef __PERF_LOG__
+ auto duration_2 = std::chrono::duration_cast<std::chrono::microseconds>( t2 - t1 ).count();
auto ta = high_resolution_clock::now();
+#endif
/* if (simd_first) {
//simd_individual->check_result();
@@ -388,28 +395,26 @@ auto t1 = high_resolution_clock::now();
if (simd_individual->standalone())
simd_individual->run_a_step(best_indiv()->w_max(),selection_pressure(),true);
//}
- auto tb = high_resolution_clock::now();
-
-
+#ifdef __PERF_LOG__
+ auto tb = high_resolution_clock::now();
auto duration_simd = std::chrono::duration_cast<std::chrono::microseconds>( tb - ta ).count();
-
-
-
-
-
-
-
+#endif
if (!simd_individual->standalone()) {
- t1 = high_resolution_clock::now();
+#ifdef __PERF_LOG__
+ t1 = high_resolution_clock::now();
+#endif
// Write statistical data and store phylogenetic data (tree)
#pragma omp single
{
output_m_->write_current_generation_outputs();
}
- t2 = high_resolution_clock::now();
+
+#ifdef __PERF_LOG__
+ t2 = high_resolution_clock::now();
duration_2 += std::chrono::duration_cast<std::chrono::microseconds>( t2 - t1 ).count();
+#endif
}
#ifdef __CUDACC__
@@ -420,8 +425,12 @@ auto t1 = high_resolution_clock::now();
first_gen = false;
}
#else
+
+#ifdef __PERF_LOG__
std::cout<<"PERFLOG,"<<AeTime::time()<<","<<duration_2<<","<<duration_simd<<std::endl;
#endif
+
+#endif
}
/*!
diff --git a/src/libaevol/Individual.cpp b/src/libaevol/Individual.cpp
index e8dda27af4bc58d7d411739298d7323ef2013029..9f9ae3935f5c12a3a10df1ce5c02f557ad1e643b 100644
--- a/src/libaevol/Individual.cpp
+++ b/src/libaevol/Individual.cpp
@@ -641,7 +641,6 @@ double Individual::dist_to_target_by_feature(
/// TODO
double Individual::fitness() const {
- if (!fitness_computed_) printf("Error !!! %d\n",id_);
assert(fitness_computed_);
return fitness_;
diff --git a/src/libaevol/LightTree.cpp b/src/libaevol/LightTree.cpp
index 88e79fe4f3073afe91777d6ae6f7fc498af5038d..e2e4854b5b6cbae638eb0f340a46a172ce2c6fe7 100644
--- a/src/libaevol/LightTree.cpp
+++ b/src/libaevol/LightTree.cpp
@@ -114,7 +114,7 @@ void LightTree::init_tree(int64_t time, std::list<Individual*> root_indiv) {
}
}
-void LightTree::update_tree(int64_t gen, Internal_SIMD_Struct* simd_indiv){
+void LightTree::update_tree(int64_t gen, Internal_SIMD_Struct** prev_internal_simd_struct){
parentsNodes_.clear();
// debug std::cout << "New generation : " << gen << '\n';
std::unordered_map<int32_t, Node*> previous = allNodes_[gen-1];
@@ -138,6 +138,7 @@ void LightTree::update_tree(int64_t gen, Internal_SIMD_Struct* simd_indiv){
if(prev_mrca == 0) {
Individual* to_set;
if (SIMD_Individual::standalone_simd) {
+ Internal_SIMD_Struct* simd_indiv = prev_internal_simd_struct[allNodes_[0].begin()->second->id_];
int x = simd_indiv->indiv_id / exp_m_->world()->height();
int y = simd_indiv->indiv_id % exp_m_->world()->height();
diff --git a/src/libaevol/LightTree.h b/src/libaevol/LightTree.h
index 8037480380551e0e7eeb9deb2c77369a4b9c3a3d..0d3c02e5b43c2674be97fcfefe184ac0e35c6a7c 100644
--- a/src/libaevol/LightTree.h
+++ b/src/libaevol/LightTree.h
@@ -106,7 +106,7 @@ class LightTree : public Observer
// by creating the link parent/children
// it also prune the tree
// if ask it perform ancestor_stat
- void update_tree(int64_t gen, Internal_SIMD_Struct* simd_indiv = nullptr);
+ void update_tree(int64_t gen, Internal_SIMD_Struct** prev_internal_simd_struct = nullptr);
// write the Newick format tree
void write_tree(int64_t t = -1);
diff --git a/src/libaevol/OutputManager.cpp b/src/libaevol/OutputManager.cpp
index 0fce5756c91594fa5a9fbce2525bb1e840af0f01..e3d0033dd94f41449311397ffd3df80d1f8cd8ed 100644
--- a/src/libaevol/OutputManager.cpp
+++ b/src/libaevol/OutputManager.cpp
@@ -220,7 +220,7 @@ void OutputManager::write_current_generation_outputs(bool create) const
stats_->add_indivs(AeTime::time(), indivs);
SaveWorld* backup_world;
- JumpingMT* backup_prng;
+ //JumpingMT* backup_prng;
if (t % backup_step_ == 0) {
backup_world = exp_m_->world()->make_save(exp_m_, indivs);
}
@@ -232,7 +232,7 @@ void OutputManager::write_current_generation_outputs(bool create) const
if (record_light_tree_ && t > 0) {
light_tree_->update_tree(t, nullptr);
if(t % backup_step_ == 0) {
- std::cout << "writing light tree for gen : " << t << '\n';
+ //std::cout << "writing light tree for gen : " << t << '\n';
write_light_tree(t);
}
}
@@ -249,7 +249,7 @@ void OutputManager::write_current_generation_outputs(bool create) const
if (record_tree_ &&
t > 0 &&
(t % tree_->tree_step() == 0)) {
- std::cout << "writing tree for gen : " << t << '\n';
+ //std::cout << "writing tree for gen : " << t << '\n';
write_tree(t);
}
@@ -275,7 +275,7 @@ void OutputManager::write_current_generation_outputs(bool create) const
exp_m_->WriteDynamicFiles(t, backup_world, create);
WriteLastGenerFile(".", t);
- delete backup_prng;
+ //delete backup_prng;
delete backup_world;
}
#ifdef __OPENMP_TASK
diff --git a/src/libaevol/SIMD_Individual.cpp b/src/libaevol/SIMD_Individual.cpp
index 858a32d50d2882593b701187db7e0058168148d9..32a89bf08fa544de6efc659b2b0838a7fa833473 100644
--- a/src/libaevol/SIMD_Individual.cpp
+++ b/src/libaevol/SIMD_Individual.cpp
@@ -4672,7 +4672,7 @@ void SIMD_Individual::run_a_step(double w_max, double selection_pressure,bool op
}
if (standalone_ && exp_m_->record_light_tree() && AeTime::time() > 0) {
- exp_m_->output_m()->light_tree()->update_tree(AeTime::time(), nullptr);
+ exp_m_->output_m()->light_tree()->update_tree(AeTime::time(), prev_internal_simd_struct);
if (AeTime::time() % exp_m_->backup_step() == 0) {
std::cout << "writing light tree for gen : " << AeTime::time() << '\n';
@@ -4806,7 +4806,7 @@ void SIMD_Individual::check_dna() {
if (exp_m_->world()->grid(x, y)->individual()->genetic_unit(
0).dna()->data()[dna_pos] != internal_simd_struct[i]->dna_->data_[dna_pos]) {
- printf("Check DNA indiv %d %ld %ld --- NB Mutation %ld\n",i,dna_size[i],exp_m_->world()->grid(x, y)->individual()->genetic_unit(
+ printf("Check DNA indiv %d %d %d --- NB Mutation %ld\n",i,dna_size[i],exp_m_->world()->grid(x, y)->individual()->genetic_unit(
0).dna()->length(),exp_m_->dna_mutator_array_[i]->mutation_list_.size());
printf("Divergence between classic DNA and SIMD DNA %d %d at pos %d\n",
diff --git a/src/libaevol/Tree.cpp b/src/libaevol/Tree.cpp
index 1408082439f473eb3c7f9b53853d5dd51c71a8af..1713c203b0a20425a5bf74ce27cab2fefbbfd0b2 100644
--- a/src/libaevol/Tree.cpp
+++ b/src/libaevol/Tree.cpp
@@ -187,7 +187,7 @@ void Tree::signal_end_of_generation() {
void Tree::write_to_tree_file(int64_t gen, gzFile tree_file) {
// Write the tree in the backup
- std::cout << "writing tree from : " << replics_.begin()->first << " to " << gen << '\n';
+ //std::cout << "writing tree from : " << replics_.begin()->first << " to " << gen << '\n';
for (int64_t t = replics_.begin()->first ; t <= gen ; t++) {
for (int32_t indiv_i = 0 ; indiv_i < exp_m_->nb_indivs() ; indiv_i++) {
assert(replics_[t][indiv_i] != NULL);
diff --git a/src/libaevol/World.cpp b/src/libaevol/World.cpp
index 6bb6407e668fc6d996fe16b44a3ec7c69019a482..36708a3c8259d249140bfb0cda7babdd9c39cca0 100644
--- a/src/libaevol/World.cpp
+++ b/src/libaevol/World.cpp
@@ -72,7 +72,7 @@ namespace aevol {
// =================================================================
World::~World()
{
- for (int16_t x = 0 ; x < width_ ; x++)
+/* for (int16_t x = 0 ; x < width_ ; x++)
for (int16_t y = 0 ; y < height_ ; y++) {
for (int16_t x2 = x ; x2 < width_ ; x2++)
for (int16_t y2 = 0 ; y2 < height_ ; y2++) {
@@ -80,7 +80,7 @@ World::~World()
if (grid_[x][y]->individual_->id() == grid_[x2][y2]->individual_->id())
grid_[x2][y2]->individual_ = nullptr;
}
- }
+ }*/
for (int16_t x = 0 ; x < width_ ; x++)
for (int16_t y = 0 ; y < height_ ; y++)
diff --git a/src/post_treatments/CMakeLists.txt b/src/post_treatments/CMakeLists.txt
index 70f9cbd1919f64c535e407f370a5a19082d14ddd..0d6df0b4d110535005633b3af8ec4adb833de8fc 100644
--- a/src/post_treatments/CMakeLists.txt
+++ b/src/post_treatments/CMakeLists.txt
@@ -45,6 +45,9 @@ target_link_libraries(aevol_misc_lineage PUBLIC aevol)
add_executable(aevol_misc_mutagenesis mutagenesis.cpp)
target_link_libraries(aevol_misc_mutagenesis PUBLIC aevol)
+add_executable(aevol_misc_soft_lineage soft_lineage.cpp)
+target_link_libraries(aevol_misc_soft_lineage PUBLIC aevol)
+
add_executable(aevol_misc_robustness robustness.cpp IndivAnalysis.cpp)
target_link_libraries(aevol_misc_robustness PUBLIC aevol)
diff --git a/src/post_treatments/ancestor_stats.cpp b/src/post_treatments/ancestor_stats.cpp
index d80a6f8139d662b11687c006c866944063248f81..12cad904ff40e91eda2c263650cef149aa5754a9 100644
--- a/src/post_treatments/ancestor_stats.cpp
+++ b/src/post_treatments/ancestor_stats.cpp
@@ -482,9 +482,6 @@ int main(int argc, char* argv[]) {
composed_fitness/=number_of_phenotypic_target_models;
fitmeta<<t0<<","<<"-1"<<","<<"1"<<","<<composed_fitness<<std::endl;
}
-#else
- printf("Fitness local sum is not supported for Aevol (only R-Aevol)\n");
- exit(-1);
#endif
indiv->Reevaluate();