From 7a85fddc7e4082b17500edb7fc08cf68efcda984 Mon Sep 17 00:00:00 2001
From: Antonin Portelli <antonin.portelli@me.com>
Date: Thu, 22 Dec 2016 00:25:36 +0100
Subject: [PATCH 1/2] Hadrons: modification of registration mechanism to allow
 for persistent caches

---
 extras/Hadrons/Application.cc  |  2 +-
 extras/Hadrons/Environment.cc  | 47 +++++++++++++++++++++++++++++-----
 extras/Hadrons/Environment.hpp |  4 ++-
 3 files changed, 45 insertions(+), 8 deletions(-)

diff --git a/extras/Hadrons/Application.cc b/extras/Hadrons/Application.cc
index cf7906eb..4bb3b383 100644
--- a/extras/Hadrons/Application.cc
+++ b/extras/Hadrons/Application.cc
@@ -306,7 +306,7 @@ void Application::configLoop(void)
                      << " " << BIG_SEP << std::endl;
         env_.setTrajectory(t);
         env_.executeProgram(program_);
-        env_.freeAll();
     }
     LOG(Message) << BIG_SEP << " End of measurement " << BIG_SEP << std::endl;
+    env_.freeAll();
 }
diff --git a/extras/Hadrons/Environment.cc b/extras/Hadrons/Environment.cc
index 4b230e20..68c170b8 100644
--- a/extras/Hadrons/Environment.cc
+++ b/extras/Hadrons/Environment.cc
@@ -410,12 +410,19 @@ Environment::Size Environment::executeProgram(const std::vector<std::string> &p)
 // general memory management ///////////////////////////////////////////////////
 void Environment::addObject(const std::string name, const int moduleAddress)
 {
-    ObjInfo info;
-    
-    info.name   = name;
-    info.module = moduleAddress;
-    object_.push_back(std::move(info));
-    objectAddress_[name] = static_cast<unsigned int>(object_.size() - 1);
+    if (!hasObject(name))
+    {
+        ObjInfo info;
+        
+        info.name   = name;
+        info.module = moduleAddress;
+        object_.push_back(std::move(info));
+        objectAddress_[name] = static_cast<unsigned int>(object_.size() - 1);
+    }
+    else
+    {
+        HADRON_ERROR("object '" + name + "' already exists");
+    }
 }
 
 void Environment::registerObject(const unsigned int address,
@@ -444,6 +451,10 @@ void Environment::registerObject(const unsigned int address,
 void Environment::registerObject(const std::string name,
                                  const unsigned int size, const unsigned int Ls)
 {
+    if (!hasObject(name))
+    {
+        addObject(name);
+    }
     registerObject(getObjectAddress(name), size, Ls);
 }
 
@@ -573,6 +584,30 @@ bool Environment::hasRegisteredObject(const std::string name) const
     }
 }
 
+bool Environment::hasCreatedObject(const unsigned int address) const
+{
+    if (hasObject(address))
+    {
+        return (object_[address].data != nullptr);
+    }
+    else
+    {
+        return false;
+    }
+}
+
+bool Environment::hasCreatedObject(const std::string name) const
+{
+    if (hasObject(name))
+    {
+        return hasCreatedObject(getObjectAddress(name));
+    }
+    else
+    {
+        return false;
+    }
+}
+
 bool Environment::isObject5d(const unsigned int address) const
 {
     return (getObjectLs(address) > 1);
diff --git a/extras/Hadrons/Environment.hpp b/extras/Hadrons/Environment.hpp
index 41a7a008..041bcc0e 100644
--- a/extras/Hadrons/Environment.hpp
+++ b/extras/Hadrons/Environment.hpp
@@ -137,7 +137,7 @@ public:
     Size                    executeProgram(const std::vector<std::string> &p);
     // general memory management
     void                    addObject(const std::string name,
-                                      const int moduleAddress);
+                                      const int moduleAddress = -1);
     void                    registerObject(const unsigned int address,
                                            const unsigned int size,
                                            const unsigned int Ls = 1);
@@ -176,6 +176,8 @@ public:
     bool                    hasObject(const std::string name) const;
     bool                    hasRegisteredObject(const unsigned int address) const;
     bool                    hasRegisteredObject(const std::string name) const;
+    bool                    hasCreatedObject(const unsigned int address) const;
+    bool                    hasCreatedObject(const std::string name) const;
     bool                    isObject5d(const unsigned int address) const;
     bool                    isObject5d(const std::string name) const;
     Environment::Size       getTotalSize(void) const;

From 3215ae6b7e82acb91caa42d2799d63e6a3676461 Mon Sep 17 00:00:00 2001
From: Antonin Portelli <antonin.portelli@me.com>
Date: Thu, 22 Dec 2016 00:26:30 +0100
Subject: [PATCH 2/2] Hadrons: genetic scheduler crashes in multi-thread with 1
 module, multi-threading deactivated for now

---
 extras/Hadrons/GeneticScheduler.hpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/extras/Hadrons/GeneticScheduler.hpp b/extras/Hadrons/GeneticScheduler.hpp
index 7b5fc183..c9256d96 100644
--- a/extras/Hadrons/GeneticScheduler.hpp
+++ b/extras/Hadrons/GeneticScheduler.hpp
@@ -134,7 +134,7 @@ void GeneticScheduler<T>::nextGeneration(void)
     LOG(Debug) << "Starting population:\n" << *this << std::endl;
     
     // random mutations
-    PARALLEL_FOR_LOOP
+    //PARALLEL_FOR_LOOP
     for (unsigned int i = 0; i < par_.popSize; ++i)
     {
         doMutation();
@@ -142,7 +142,7 @@ void GeneticScheduler<T>::nextGeneration(void)
     LOG(Debug) << "After mutations:\n" << *this << std::endl;
     
     // mating
-    PARALLEL_FOR_LOOP
+    //PARALLEL_FOR_LOOP
     for (unsigned int i = 0; i < par_.popSize/2; ++i)
     {
         doCrossover();