--- trunk/gadget/ecosystem.cc	2014/02/10 17:09:07	1
+++ trunk/gadget/ecosystem.cc	2017/04/26 09:06:03	24
@@ -1,11 +1,23 @@
 #include "ecosystem.h"
 #include "runid.h"
 #include "global.h"
+#include <ctime>
+#ifdef _OPENMP
+#include <omp.h>
+#endif
+
+#ifdef _OPENMP
+extern Ecosystem** EcoSystems;
+//extern StochasticData* data;
+#endif
+extern volatile int interrupted_print;
+
+time_t starttime, stoptime;
 
 Ecosystem::Ecosystem(const MainInfo& main) : printinfo(main.getPI()) {
 
   funceval = 0;
-  interrupted = 0;
+  //interrupted = 0;
   likelihood = 0.0;
   keeper = new Keeper;
 
@@ -32,7 +44,9 @@
       infile.open(filename, ios::in);
       handle.checkIfFailure(infile, filename);
       handle.Open(filename);
-      this->readOptimisation(commin);
+      unsigned seed;
+      main.getForcePrint();
+      this->readOptimisation(commin, main.getSeed());
       handle.Close();
       infile.close();
       infile.clear();
@@ -41,12 +55,33 @@
       optvec.resize(new OptInfoHooke());
     }
   }
-
+#ifdef _OPENMP
+  runParallel=main.runParallel();
+  if (!omp_in_parallel()){
+  	if (main.runOptimise())
+	{
+    		switch(runParallel){
+			case SPECULATIVE: 
+				handle.logMessage(LOGINFO, "\nFinished reading model data files, starting to run parallel speculative optimisation with ", omp_get_max_threads(), " threads");
+				break;
+			case REPRODUCIBLE:
+				handle.logMessage(LOGINFO, "\nFinished reading model data files, starting to run parallel reproducible optimisation with ", omp_get_max_threads(), " threads");
+				break;
+			default:
+				handle.logMessage(LOGINFO, "\nFinished reading model data files, starting to serial optimisation with ", omp_get_num_threads() , "threads");
+		}
+	}
+  	else
+    		handle.logMessage(LOGINFO, "\nFinished reading model data files, starting to run simulation ", omp_get_num_threads(), " threads");
+  	handle.logMessage(LOGMESSAGE, "");  //write blank line to log file
+  }
+#else
   if (main.runOptimise())
     handle.logMessage(LOGINFO, "\nFinished reading model data files, starting to run optimisation");
   else
     handle.logMessage(LOGINFO, "\nFinished reading model data files, starting to run simulation");
   handle.logMessage(LOGMESSAGE, "");  //write blank line to log file
+#endif
 }
 
 Ecosystem::~Ecosystem() {
@@ -101,7 +136,36 @@
 void Ecosystem::Optimise() {
   int i;
   for (i = 0; i < optvec.Size(); i++) {
-    optvec[i]->OptimiseLikelihood();
+	  time(&starttime);
+#ifdef _OPENMP
+          if (runParallel){
+	  	int j, numThr = omp_get_max_threads ( ); //AGT REMOVED
+	  	DoubleVector v = this->getValues();
+	  	for (j = 0; j < numThr; j++)
+		  	EcoSystems[j]->Update(v);
+	  	if(runParallel==SPECULATIVE)
+		{
+    			handle.logMessage(LOGINFO, "\nCalling Speculative Optimization");
+         	  	optvec[i]->OptimiseLikelihoodOMP();
+		}
+	  	else
+		{
+    			handle.logMessage(LOGINFO, "\nCalling Reproducible parallel Optimization");
+			optvec[i]->OptimiseLikelihoodREP();
+		}
+	  }
+	  else
+	  {
+    			handle.logMessage(LOGINFO, "\nCalling Reproducible serial Optimization");
+		 optvec[i]->OptimiseLikelihood();
+	}
+#else
+//#ifdef SPECULATIVE
+//	  optvec[i]->OptimiseLikelihoodOMP();
+//#else
+	  optvec[i]->OptimiseLikelihood();
+#endif
+	  time(&stoptime);
     this->writeOptValues();
   }
 }
@@ -115,6 +179,7 @@
     currentval.resize(keeper->numVariables(), 0.0);
     optflag.resize(keeper->numVariables(), 0);
     keeper->getOptFlags(optflag);
+    
   }
 
   j = 0;
@@ -148,7 +213,15 @@
   for (i = 0; i < likevec.Size(); i++)
     tmpvec[i] = likevec[i]->getUnweightedLikelihood();
 
-  handle.logMessage(LOGINFO, "\nAfter a total of", funceval, "function evaluations the best point found is");
+  int iters = 0;
+#ifdef _OPENMP
+  if (runParallel){
+  	int numThr = omp_get_max_threads ( );
+    	for (i = 0; i < numThr; i++)
+  	  iters += EcoSystems[i]->getFuncEval();
+  }
+#endif
+  handle.logMessage(LOGINFO, "\nAfter a total of", funceval+iters, "function evaluations the best point found is");
   keeper->writeBestValues();
   handle.logMessage(LOGINFO, "\nThe scores from each likelihood component are");
   handle.logMessage(LOGINFO, tmpvec);
@@ -156,6 +229,8 @@
     handle.logMessage(LOGINFO, "\nThe overall likelihood score is", keeper->getBestLikelihoodScore());
   else
     handle.logMessage(LOGINFO, "\nThe overall likelihood score is", this->getLikelihood());
+
+  handle.logMessage(LOGINFO, "\n Runtime for the algorithm was ", difftime(stoptime, starttime)," seconds\n");
 }
 
 void Ecosystem::writeInitialInformation(const char* const filename) {
@@ -168,11 +243,11 @@
 }
 
 void Ecosystem::writeParams(const char* const filename, int prec) const {
-  if ((funceval > 0) && (interrupted == 0)) {
+  if ((funceval > 0) && (interrupted_print == 0)) {
     //JMB - print the final values to any output files specified
     //in case they have been missed by the -print value
     if (printinfo.getPrint())
       keeper->writeValues(likevec, printinfo.getPrecision());
   }
-  keeper->writeParams(optvec, filename, prec, interrupted);
+  keeper->writeParams(optvec, filename, prec, interrupted_print);
 }