--- trunk/gadget/ecosystem.cc	2014/02/10 17:09:07	1
+++ trunk/gadget/ecosystem.cc	2016/05/25 16:36:33	19
@@ -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();
@@ -101,7 +115,19 @@
 void Ecosystem::Optimise() {
   int i;
   for (i = 0; i < optvec.Size(); i++) {
-    optvec[i]->OptimiseLikelihood();
+	  time(&starttime);
+#ifdef _OPENMP
+	  int j, numThr = omp_get_max_threads ( );
+	  DoubleVector v = this->getValues();
+	  for (j = 0; j < numThr; j++)
+		  EcoSystems[j]->Update(v);
+#endif
+#ifdef SPECULATIVE
+	  optvec[i]->OptimiseLikelihoodOMP();
+#else
+	  optvec[i]->OptimiseLikelihood();
+#endif
+	  time(&stoptime);
     this->writeOptValues();
   }
 }
@@ -148,7 +174,13 @@
   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
+  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 +188,8 @@
     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 +202,11 @@
 }
 
 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);
 }