From 49fc07433e4aee7641fe512448dc7e96c6f7b70e Mon Sep 17 00:00:00 2001
From: Emily Dolson <EmilyLDolson@gmail.com>
Date: Wed, 26 Sep 2018 01:31:48 -0400
Subject: [PATCH] Drastic reduction in memory use

---
 avida-core/source/main/cPopulation.cc |  6 +++---
 avida-core/source/main/cWorld.cc      | 20 +++++++++++++-------
 avida-core/source/main/cWorld.h       |  8 ++++----
 3 files changed, 20 insertions(+), 14 deletions(-)

diff --git a/avida-core/source/main/cPopulation.cc b/avida-core/source/main/cPopulation.cc
index 89a78630f..f019df98a 100644
--- a/avida-core/source/main/cPopulation.cc
+++ b/avida-core/source/main/cPopulation.cc
@@ -6136,9 +6136,9 @@ void cPopulation::ProcessPostUpdate(cAvidaContext& ctx)
   }
 
   for (int i = 0; i < deme_array.GetSize(); i++) deme_array[i].ProcessUpdate(ctx);
-  if (m_world->fit_fun.size() > 100000) {
-      m_world->fit_fun.Clear();
-  }
+  // if (m_world->fit_fun.size() > 10) {
+  //     m_world->fit_fun.Clear();
+  // }
   // if (m_world->skel_fun.size() > 100000) {
   //     m_world->skel_fun.Clear();
   // }
diff --git a/avida-core/source/main/cWorld.cc b/avida-core/source/main/cWorld.cc
index 4a572f6df..4d989e0fb 100644
--- a/avida-core/source/main/cWorld.cc
+++ b/avida-core/source/main/cWorld.cc
@@ -66,6 +66,7 @@ cWorld::cWorld(cAvidaConfig* cfg, const cString& wd)
       cTestCPU* test_cpu = GetHardwareManager().CreateTestCPU(*m_ctx);
       // test_info.UseManualInputs(curr_target_cell.GetInputs()); // Test using what the environment will be
       test_cpu->TestGenome(*m_ctx, test_info, gen);  // Use the true genome
+      delete test_cpu;
       return test_info.GetGenotypeFitness();
    };
   
@@ -230,15 +231,20 @@ bool cWorld::setup(World* new_world, cUserFeedback* feedback, const Apto::Map<Ap
   // std::cout << "test" << std::endl;
 
   // std::cout << "Got hardware manager" << std::endl;
-  
+  // emp_assert(false);
   skel_fun = [this, null_inst](const Avida::InstructionSequence & seq){
-    // std::cout << std::endl; for (auto inst : emp::Skeletonize(seq, null_inst, fit_fun.to_function())){std::cout << inst.AsString() << std::endl;}; std::cout << std::endl;
-    return emp::Skeletonize(seq, null_inst, fit_fun.to_function());
+    // std::cout << "Skeletonizing" <<std::endl;
+    std::stringstream ss;
+    emp::vector<Avida::Instruction> skel = emp::Skeletonize(seq, null_inst, fit_fun);
+    for (auto inst : skel) {
+      ss << inst.GetSymbol();
+    }
+    return ss.str();
   };
 
   systematics_manager.New([](const Avida::InstructionSequence & seq){return Avida::InstructionSequence(seq);});
   // systematics_manager->PrintStatus();
-  OEE_stats.New(systematics_manager, skel_fun, [null_inst](const emp::vector<Instruction> & org){return org.size();});
+  OEE_stats.New(systematics_manager, skel_fun, [null_inst](const std::string & org){return org.size();}, m_conf->WORLD_X.Get() * m_conf->WORLD_Y.Get() * 200000);
   OEE_stats->SetGenerationInterval(m_conf->FILTER_TIME.Get());
   OEE_stats->SetResolution(m_conf->OEE_RES.Get());
 
@@ -248,9 +254,9 @@ bool cWorld::setup(World* new_world, cUserFeedback* feedback, const Apto::Map<Ap
     //   std::cout << systematics_manager->GetTaxonAt(pos)->GetID();
     // } 
     systematics_manager->SetNextParent(pos);});
-  OnOffspringReady([this](Avida::InstructionSequence seq){ systematics_manager->AddOrg(seq, next_cell_id, GetStats().GetGeneration(), false);});
-  OnOrgDeath([this](int pos){ systematics_manager->RemoveOrgAfterRepro(pos, GetStats().GetGeneration());});
-  OnUpdate([this](int ud){if (std::round(GetStats().GetGeneration()) > latest_gen) { latest_gen = std::round(GetStats().GetGeneration()); OEE_stats->Update(latest_gen); oee_file.Update(latest_gen);}});
+  OnOffspringReady([this](Avida::InstructionSequence seq){ systematics_manager->AddOrg(seq, next_cell_id, GetStats().GetUpdate(), false);});
+  OnOrgDeath([this](int pos){ systematics_manager->RemoveOrgAfterRepro(pos, GetStats().GetUpdate());});
+  OnUpdate([this](int ud){if (std::round(GetStats().GetGeneration()) > latest_gen) { latest_gen = std::round(GetStats().GetGeneration()); OEE_stats->Update(latest_gen, GetStats().GetUpdate()); oee_file.Update(latest_gen);}});
 
   std::function<int()> update_fun = [this](){return std::round(GetStats().GetGeneration());};
 
diff --git a/avida-core/source/main/cWorld.h b/avida-core/source/main/cWorld.h
index c220ce84b..c5270471f 100644
--- a/avida-core/source/main/cWorld.h
+++ b/avida-core/source/main/cWorld.h
@@ -153,8 +153,8 @@ class cWorld
   int next_cell_id = -1;
   emp::DataFile oee_file;
 
-  emp::memo_function<double(const Avida::InstructionSequence&)> fit_fun;
-  std::function<emp::vector<Avida::Instruction>(const Avida::InstructionSequence&)> skel_fun;
+  std::function<double(const Avida::InstructionSequence&)> fit_fun;
+  std::function<std::string(const Avida::InstructionSequence&)> skel_fun;
 
   emp::SignalKey OnBeforeRepro(const std::function<void(int)> & fun) { return before_repro_sig.AddAction(fun); }
   emp::SignalKey OnOffspringReady(const std::function<void(Avida::InstructionSequence)> & fun) { return offspring_ready_sig.AddAction(fun); }
@@ -184,9 +184,9 @@ class cWorld
   bool all_tasks = false;
   int latest_gen = -1; // Force time to go forward
 
-  emp::Ptr<emp::Systematics<Avida::InstructionSequence, Avida::InstructionSequence, emp::datastruct::oee_data<emp::vector<Avida::Instruction> > > > systematics_manager;
+  emp::Ptr<emp::Systematics<Avida::InstructionSequence, Avida::InstructionSequence, emp::datastruct::oee_data<std::string > > > systematics_manager;
   // // If there are multiple instruction ets this could be a problem
-  emp::Ptr<emp::OEETracker<Avida::InstructionSequence, Avida::InstructionSequence, emp::vector<Instruction>, emp::datastruct::oee_data<emp::vector<Avida::Instruction> > > > OEE_stats;
+  emp::Ptr<emp::OEETracker<Avida::InstructionSequence, Avida::InstructionSequence, std::string, emp::datastruct::oee_data<std::string > > > OEE_stats;
   Genome curr_genome;
 
   Data::ManagerPtr& GetDataManager() { return m_data_mgr; }