From fa4b3b880f84e1814b658d57a24da99ab5652945 Mon Sep 17 00:00:00 2001
From: adash <adash>
Date: Tue, 13 Jan 2009 04:54:58 +0000
Subject: [PATCH] changes for javasingle files

---
 .../Moldyn/javasingle/DoubleWrapper.java      |   6 +
 .../Moldyn/javasingle/IntWrapper.java         |   6 +
 .../Moldyn/javasingle/JGFMolDynBench.java     | 879 +++++++++---------
 .../javasingle/JGFMolDynBenchSizeA.java       |  22 +-
 .../Prefetch/Moldyn/javasingle/MDWrap.java    |   9 +
 .../Prefetch/Moldyn/javasingle/makefile       |   6 +-
 6 files changed, 458 insertions(+), 470 deletions(-)
 create mode 100644 Robust/src/Benchmarks/Prefetch/Moldyn/javasingle/DoubleWrapper.java
 create mode 100644 Robust/src/Benchmarks/Prefetch/Moldyn/javasingle/IntWrapper.java
 create mode 100644 Robust/src/Benchmarks/Prefetch/Moldyn/javasingle/MDWrap.java

diff --git a/Robust/src/Benchmarks/Prefetch/Moldyn/javasingle/DoubleWrapper.java b/Robust/src/Benchmarks/Prefetch/Moldyn/javasingle/DoubleWrapper.java
new file mode 100644
index 00000000..c0bd06da
--- /dev/null
+++ b/Robust/src/Benchmarks/Prefetch/Moldyn/javasingle/DoubleWrapper.java
@@ -0,0 +1,6 @@
+public class DoubleWrapper {
+  public DoubleWrapper() {
+
+  }
+  double d;
+}
\ No newline at end of file
diff --git a/Robust/src/Benchmarks/Prefetch/Moldyn/javasingle/IntWrapper.java b/Robust/src/Benchmarks/Prefetch/Moldyn/javasingle/IntWrapper.java
new file mode 100644
index 00000000..8bf875d3
--- /dev/null
+++ b/Robust/src/Benchmarks/Prefetch/Moldyn/javasingle/IntWrapper.java
@@ -0,0 +1,6 @@
+public class IntWrapper {
+  public IntWrapper() {
+
+  }
+  int i;
+}
\ No newline at end of file
diff --git a/Robust/src/Benchmarks/Prefetch/Moldyn/javasingle/JGFMolDynBench.java b/Robust/src/Benchmarks/Prefetch/Moldyn/javasingle/JGFMolDynBench.java
index 0f7b8a77..64c41a08 100644
--- a/Robust/src/Benchmarks/Prefetch/Moldyn/javasingle/JGFMolDynBench.java
+++ b/Robust/src/Benchmarks/Prefetch/Moldyn/javasingle/JGFMolDynBench.java
@@ -28,15 +28,15 @@ public class JGFMolDynBench {
 
   public int PARTSIZE;
 
-  public double[] epot;
-  public double[] vir;
-  public double[] ek;
+  public DoubleWrapper[] epot;
+  public DoubleWrapper[] vir;
+  public DoubleWrapper[] ek;
 
   int size,mm;
   int[] datasizes;
 
   public int interactions;
-  public int[] interacts;
+  public IntWrapper[] interacts;
 
   public int nthreads;
   public JGFInstrumentor instr;
@@ -68,59 +68,66 @@ public class JGFMolDynBench {
 
   public static void JGFapplication(JGFMolDynBench mold) { 
     // Create new arrays 
-      mold.epot = new double [mold.nthreads];
-      mold.vir  = new double [mold.nthreads];
-      mold.ek   = new double [mold.nthreads];
-      mold.interacts = new int [mold.nthreads];
-
-    int partsize, numthreads;
-      partsize = mold.PARTSIZE;
-      numthreads = mold.nthreads;
+    //BarrierServer mybarr;
+    /*
+       int[] mid = new int[8];
+       mid[0] = (128<<24)|(195<<16)|(175<<8)|84;//dw-10
+       mid[1] = (128<<24)|(195<<16)|(175<<8)|85;//dw-11
+       mid[2] = (128<<24)|(195<<16)|(175<<8)|86;//dw-12
+       mid[3] = (128<<24)|(195<<16)|(175<<8)|87;//dw-13
+       mid[4] = (128<<24)|(195<<16)|(175<<8)|88;//dw-14
+       mid[5] = (128<<24)|(195<<16)|(175<<8)|89;//dw-15
+       mid[6] = (128<<24)|(195<<16)|(175<<8)|90;//dw-16
+       mid[7] = (128<<24)|(195<<16)|(175<<8)|91;//dw-17
+       */
 
     double sh_force [][];
     double sh_force2 [][][];
-      sh_force = new double[3][partsize];
-      sh_force2 = new double[3][numthreads][partsize];
+    int partsize, numthreads;
+    partsize = mold.PARTSIZE;
+    numthreads = mold.nthreads;
+    //mybarr = new BarrierServer(numthreads);
+    //mybarr.start(mid[0]);
+
+    sh_force = new double[3][partsize];
+    sh_force2 = new double[3][numthreads][partsize];
+    mold.epot = new DoubleWrapper[numthreads];
+    mold.vir  = new DoubleWrapper[numthreads];
+    mold.ek   = new DoubleWrapper[numthreads];
+    mold.interacts = new IntWrapper[numthreads];
+    for(int i=0;i<numthreads;i++) {
+      mold.epot[i]=new DoubleWrapper();
+      mold.vir[i]=new DoubleWrapper();
+      mold.ek[i]=new DoubleWrapper();
+      mold.interacts[i]=new IntWrapper();
+    }
 
     // spawn threads 
-    mdRunner[] thobjects;
-    Barrier br;
-      thobjects = new mdRunner[numthreads];
-      br= new Barrier(numthreads);
-
-    int[] mid = new int[2];
-    mid[0] = (128<<24)|(195<<16)|(175<<8)|73;
-    mid[1] = (128<<24)|(195<<16)|(175<<8)|69;
-    mdRunner tmp;
-
-    for(int i=1;i<numthreads;i++) {
-        thobjects[i] = new mdRunner(i,mold.mm,sh_force,sh_force2,br,mold.nthreads,mold);
-        tmp = thobjects[i];
-      //System.printString("Starting thread  "+ i + "\n");
-      tmp.start();
-    }
-    //System.printString("Finished starting rest threads\n");
-
-      thobjects[0] = new mdRunner(0,mold.mm,sh_force,sh_force2,br,mold.nthreads,mold);
-      tmp = thobjects[0];
-    //System.printString("Starting thread 0\n");
-    tmp.start();
-    tmp.join();
-    //System.printString("Finishing start\n");
-
-    for(int i=1;i<numthreads;i++) {
-      //System.printString("Joining thread  "+ i + "\n");
-        tmp = thobjects[i];
-      tmp.join();
-    }
-    //System.printString("Finished joining all threads\n");
-  } 
+    MDWrap[] thobjects = new MDWrap[numthreads];
+
+    for(int i=0;i<numthreads;i++) {
+      thobjects[i] = new MDWrap(new mdRunner(i,mold.mm,sh_force,sh_force2,mold.nthreads,mold));
+    }
+
+    /*
+       boolean waitfordone=true;
+       while(waitfordone) {
+       if (mybarr.done)
+       waitfordone=false;
+       }
+       */
+
+    for(int i=0;i<numthreads;i++) {
+      //thobjects[i].md.start(mid[i]);
+      thobjects[i].md.run();
+    }
+  }
 
   public void JGFvalidate(){
     double[] refval = new double[2];
     refval[0] = 1731.4306625334357;
     refval[1] = 7397.392307839352;
-    double dev = Math.fabs(ek[0] - refval[size]);
+    double dev = Math.fabs(ek[0].d - refval[size]);
     if (dev > 1.0e-10 ){
       //System.printString("Validation failed\n");
       //System.printString("Kinetic Energy = " + (long)ek[0] + "  " + (long)dev + "  " + size + "\n");
@@ -128,10 +135,10 @@ public class JGFMolDynBench {
   }
 }
 
-class mdRunner extends Thread {
+class mdRunner {
 
   double count;
-  int id,i,j,k,lg,mdsize,mm;
+  int id,i,j,k,lg,mm;
   double l,rcoff,rcoffs,side,sideh,hsq,hsq2,vel,velt;
   double a,r,sum,tscale,sc,ekin,ts,sp;
   double den;
@@ -139,7 +146,7 @@ class mdRunner extends Thread {
   double h;
   double vaver,vaverh,rand;
   double etot,temp,pres,rp;
-  double u1,u2,v1,v2,s, xx, yy, zz;
+  double u1, u2, s, xx, yy, zz;
   double xvelocity, yvelocity, zvelocity;
 
   double [][] sh_force;
@@ -150,20 +157,15 @@ class mdRunner extends Thread {
   int istop;
   int iprint;
 
-  Barrier br;
-  random randnum;
   JGFMolDynBench mymd;
   int nthreads;
 
-  particle[] one;
-
-  public mdRunner(int id, int mm, double [][] sh_force, double [][][] sh_force2,Barrier br, 
-		  int nthreads, JGFMolDynBench mymd) {
+  public mdRunner(int id, int mm, double [][] sh_force, double [][][] sh_force2, 
+      int nthreads, JGFMolDynBench mymd) {
     this.id=id;
     this.mm=mm;
     this.sh_force=sh_force;
     this.sh_force2=sh_force2;
-    this.br=br;
     this.nthreads = nthreads;
     this.mymd = mymd;
     count = 0.0;
@@ -175,523 +177,492 @@ class mdRunner extends Thread {
     iprint = 10;
   } 
 
-  public void run() {
-
-    //System.printString("Start run method\n");
-
-    /* Parameter determination */
-
-    int tmpmdsize;
-    double tmpden;
-    int movemx=50;
-    Barrier tmpbr;
-
-      tmpbr=br;
-      mdsize = mymd.PARTSIZE;
-      one = new particle[mdsize];
-      l = mymd.LENGTH;
-      tmpmdsize = mdsize;
-      tmpden = den;
-      side = Math.pow((tmpmdsize/tmpden),0.3333333);
-      rcoff = mm/4.0;
-
-      a = side/mm;
-      sideh = side*0.5;
-      hsq = h*h;
-      hsq2 = hsq*0.5;
-      npartm = tmpmdsize - 1;
-      rcoffs = rcoff * rcoff;
-      tscale = 16.0 / (1.0 * tmpmdsize - 1.0);
-      vaver = 1.13 * Math.sqrt(tref / 24.0);
-      vaverh = vaver * h;
-
-      /* Particle Generation */
-
-      xvelocity = 0.0;
-      yvelocity = 0.0;
-      zvelocity = 0.0;
-      ijk = 0;
-
-      for (lg=0; lg<=1; lg++) {
-        for (i=0; i<mm; i++) {
-          for (j=0; j<mm; j++) {
-            for (k=0; k<mm; k++) {
-              one[ijk] = new particle((i*a+lg*a*0.5),(j*a+lg*a*0.5),(k*a),
-                  xvelocity,yvelocity,zvelocity,sh_force,sh_force2,id,this);
-              ijk = ijk + 1;
-            }
+  public void init(particle[] one, int mdsize) {
+    int id=this.id;
+    for (int lg=0; lg<=1; lg++) {
+      for (int i=0; i<mm; i++) {
+        for (int j=0; j<mm; j++) {
+          for (int k=0; k<mm; k++) {
+            one[ijk] = new particle((i*a+lg*a*0.5),(j*a+lg*a*0.5),(k*a),
+                xvelocity,yvelocity,zvelocity,sh_force,sh_force2,id,one);
+            ijk = ijk + 1;
           }
         }
       }
+    }
 
-      for (lg=1; lg<=2; lg++) {
-        for (i=0; i<mm; i++) {
-          for (j=0; j<mm; j++) {
-            for (k=0; k<mm; k++) {
-              one[ijk] = new particle((i*a+(2-lg)*a*0.5),(j*a+(lg-1)*a*0.5),
-                  (k*a+a*0.5),xvelocity,yvelocity,zvelocity,sh_force,sh_force2,id,this);
-              ijk = ijk + 1;
-            }
+    for (int lg=1; lg<=2; lg++) {
+      for (int i=0; i<mm; i++) {
+        for (int j=0; j<mm; j++) {
+          for (int k=0; k<mm; k++) {
+            one[ijk] = new particle((i*a+(2-lg)*a*0.5),(j*a+(lg-1)*a*0.5),
+                (k*a+a*0.5),xvelocity,yvelocity,zvelocity,sh_force,sh_force2,id,one);
+            ijk = ijk + 1;
           }
         }
       }
+    }
 
-      /* Initialise velocities */
+    /* Initialise velocities */
 
-      iseed = 0;
-      v1 = 0.0;
-      v2 = 0.0;
-      randnum = new random(iseed,v1,v2);
+    iseed = 0;
+    double v1 = 0.0;
+    double v2 = 0.0;
+    random randnum = new random(iseed,v1,v2);
 
-      for (i=0; i<tmpmdsize; i+=2) {
-        r  = randnum.seed();
-        one[i].xvelocity = r*randnum.v1;
-        one[i+1].xvelocity  = r*randnum.v2;
-      }
 
-      for (i=0; i<tmpmdsize; i+=2) {
-        r  = randnum.seed();
-        one[i].yvelocity = r*randnum.v1;
-        one[i+1].yvelocity  = r*randnum.v2;
-      }
-
-      for (i=0; i<tmpmdsize; i+=2) {
-        r  = randnum.seed();
-        one[i].zvelocity = r*randnum.v1;
-        one[i+1].zvelocity  = r*randnum.v2;
-      }
+    for (int i=0; i<mdsize; i+=2) {
+      r  = randnum.seed();
+      one[i].xvelocity = r*randnum.v1;
+      one[i+1].xvelocity  = r*randnum.v2;
+    }
 
+    for (int i=0; i<mdsize; i+=2) {
+      r  = randnum.seed();
+      one[i].yvelocity = r*randnum.v1;
+      one[i+1].yvelocity  = r*randnum.v2;
+    }
 
-      /* velocity scaling */
+    for (int i=0; i<mdsize; i+=2) {
+      r  = randnum.seed();
+      one[i].zvelocity = r*randnum.v1;
+      one[i+1].zvelocity  = r*randnum.v2;
+    }
 
-      ekin = 0.0;
-      sp = 0.0;
 
-      for(i=0;i<tmpmdsize;i++) {
-        sp = sp + one[i].xvelocity;
-      }
-      sp = sp / tmpmdsize;
+    /* velocity scaling */
 
-      for(i=0;i<tmpmdsize;i++) {
-        one[i].xvelocity = one[i].xvelocity - sp;
-        ekin = ekin + one[i].xvelocity*one[i].xvelocity;
-      }
+    ekin = 0.0;
+    sp = 0.0;
 
-      sp = 0.0;
-      for(i=0;i<tmpmdsize;i++) {
-        sp = sp + one[i].yvelocity;
-      }
-      sp = sp / tmpmdsize;
+    for(int i=0;i<mdsize;i++) {
+      sp = sp + one[i].xvelocity;
+    }
+    sp = sp / mdsize;
 
-      for(i=0;i<tmpmdsize;i++) {
-        one[i].yvelocity = one[i].yvelocity - sp;
-        ekin = ekin + one[i].yvelocity*one[i].yvelocity;
-      }
+    for(int i=0;i<mdsize;i++) {
+      one[i].xvelocity = one[i].xvelocity - sp;
+      ekin = ekin + one[i].xvelocity*one[i].xvelocity;
+    }
 
+    sp = 0.0;
+    for(int i=0;i<mdsize;i++) {
+      sp = sp + one[i].yvelocity;
+    }
+    sp = sp / mdsize;
 
-      sp = 0.0;
-      for(i=0;i<tmpmdsize;i++) {
-        sp = sp + one[i].zvelocity;
-      }
-      sp = sp / tmpmdsize;
+    for(int i=0;i<mdsize;i++) {
+      one[i].yvelocity = one[i].yvelocity - sp;
+      ekin = ekin + one[i].yvelocity*one[i].yvelocity;
+    }
 
-      for(i=0;i<tmpmdsize;i++) {
-        one[i].zvelocity = one[i].zvelocity - sp;
-        ekin = ekin + one[i].zvelocity*one[i].zvelocity;
-      }
 
-      ts = tscale * ekin;
-      sc = h * Math.sqrt(tref/ts);
+    sp = 0.0;
+    for(int i=0;i<mdsize;i++) {
+      sp = sp + one[i].zvelocity;
+    }
+    sp = sp / mdsize;
 
+    for(int i=0;i<mdsize;i++) {
+      one[i].zvelocity = one[i].zvelocity - sp;
+      ekin = ekin + one[i].zvelocity*one[i].zvelocity;
+    }
 
-      for(i=0;i<tmpmdsize;i++) {
+    ts = tscale * ekin;
+    sc = h * Math.sqrt(tref/ts);
 
-        one[i].xvelocity = one[i].xvelocity * sc;     
-        one[i].yvelocity = one[i].yvelocity * sc;     
-        one[i].zvelocity = one[i].zvelocity * sc;     
 
-      }
+    for(int i=0;i<mdsize;i++) {
 
-    /* Synchronise threads and start timer before MD simulation */
+      one[i].xvelocity = one[i].xvelocity * sc;     
+      one[i].yvelocity = one[i].yvelocity * sc;     
+      one[i].zvelocity = one[i].zvelocity * sc;     
 
-    Barrier.enterBarrier(tmpbr);
-    //System.clearPrefetchCache();
-    //int myid;
-    //atomic {
-    // myid = id;
-    //}
-    //TournamentBarrier.enterBarrier(myid, tmpbr);
-    //if (id == 0) JGFInstrumentor.startTimer("Section3:MolDyn:Run", instr.timers);
-    //Barrier.enterBarrier(tmpbr);
+    }
 
-    /* MD simulation */
+  }
 
-    for (int move=0;move<movemx;move++) {
-        /* move the particles and update velocities */
+  public void doinit(int mdsize) {
+    for(int j=0;j<3;j++) {
+      double[] sh=sh_force[j];
+      for (int i=0;i<mdsize;i++) {
+        sh[i] = 0.0;
+      }
+    }
+  }
 
-        for (i=0;i<tmpmdsize;i++) {
-          one[i].domove(side,i);       
-        }
 
-      /* Barrier */
-      //System.printString("Barrier #2\n");
-      Barrier.enterBarrier(tmpbr);
-      //System.clearPrefetchCache();
-      //TournamentBarrier.enterBarrier(myid, tmpbr);
-
-        if(id==0) {
-          for(j=0;j<3;j++) {
-            for (i=0;i<tmpmdsize;i++) {
-              sh_force[j][i] = 0.0;
-            }
-          }
+  public void doinit2(int mdsize) {
+    for(int k=0;k<3;k++) {
+      double[] sh=sh_force[k];
+      double [][] sha=sh_force2[k];
+      for(int j=0;j<nthreads;j++) {
+        double[] sha2=sha[j];
+        for(int i=0;i<mdsize;i++) {
+          sh[i] += sha2[i];
         }
+      }
+    }
 
-        mymd.epot[id] = 0.0;
-        mymd.vir[id] = 0.0;
-        mymd.interacts[id] = 0;
-
-
-      /* Barrier */
-      //System.printString("Barrier #3\n");
-      Barrier.enterBarrier(tmpbr);
-      //System.clearPrefetchCache();
-      //TournamentBarrier.enterBarrier(myid, tmpbr);
+    for(int k=0;k<3;k++) {
+      double [][] sh1=sh_force2[k];
+      for(int j=0;j<nthreads;j++) {
+        double[] sh2=sh1[j];
+        for(int i=0;i<mdsize;i++) {
 
-        /* compute forces */
 
-        for (i=0+id;i<tmpmdsize;i+=nthreads) {
-          one[i].force(side,rcoff,tmpmdsize,i,xx,yy,zz,mymd); 
+          sh2[i] = 0.0;
         }
+      }
+    }
 
-      /* Barrier */
-      //System.printString("Barrier #4\n");
-      Barrier.enterBarrier(tmpbr);
-      //System.clearPrefetchCache();
-      //TournamentBarrier.enterBarrier(myid, tmpbr);
+    for(int j=1;j<nthreads;j++) {
+      mymd.epot[0].d += mymd.epot[j].d;
+      mymd.vir[0].d += mymd.vir[j].d;
+    }
+    for(int j=1;j<nthreads;j++) {       
+      mymd.epot[j].d = mymd.epot[0].d;
+      mymd.vir[j].d = mymd.vir[0].d;
+    }
+    for(int j=0;j<nthreads;j++) {
+      mymd.interactions += mymd.interacts[j].i; 
+    }
 
-      /* update force arrays */
-        if(id == 0) {
-          for(int k=0;k<3;k++) {
-            for(i=0;i<tmpmdsize;i++) {
-              for(j=0;j<nthreads;j++) {
-                sh_force[k][i] += sh_force2[k][j][i];
-              }
-            }
-          }
-        }
+    for (int j=0;j<3;j++) {
+      double sh[]=sh_force[j];
+      for (int i=0;i<mdsize;i++) {
+        sh[i] = sh[i] * hsq2;
+      }
+    }
+  }
 
-        if(id == 0) {
-          for(int k=0;k<3;k++) {
-            for(i=0;i<tmpmdsize;i++) {
-              for(j=0;j<nthreads;j++) {
-                sh_force2[k][j][i] = 0.0;
-              }
-            }
-          }
-        }
+  public void run() {
+    /* Parameter determination */
 
-        if(id==0) {
-          for(j=1;j<nthreads;j++) {
-            mymd.epot[0] += mymd.epot[j];
-            mymd.vir[0] += mymd.vir[j];
-          }
-          for(j=1;j<nthreads;j++) {       
-            mymd.epot[j] = mymd.epot[0];
-            mymd.vir[j] = mymd.vir[0];
-          }
-          for(j=0;j<nthreads;j++) {
-            mymd.interactions += mymd.interacts[j]; 
-          }
-        }
+    int mdsize;
+    double tmpden;
+    int movemx=50;
+    //Barrier barr=new Barrier("128.195.175.84");
+    particle[] one;
+    int id;
+    id=this.id;
+    mdsize = mymd.PARTSIZE;
+    one=new particle[mdsize];
+    l = mymd.LENGTH;
+    tmpden = den;
+    side = Math.pow((mdsize/tmpden),0.3333333);
+    rcoff = mm/4.0;
+
+    a = side/mm;
+    sideh = side*0.5;
+    hsq = h*h;
+    hsq2 = hsq*0.5;
+    npartm = mdsize - 1;
+    rcoffs = rcoff * rcoff;
+    tscale = 16.0 / (1.0 * mdsize - 1.0);
+    vaver = 1.13 * Math.sqrt(tref / 24.0);
+    vaverh = vaver * h;
+
+    /* Particle Generation */
+
+    xvelocity = 0.0;
+    yvelocity = 0.0;
+    zvelocity = 0.0;
+    ijk = 0;
+    init(one, mdsize);
 
-      /* Barrier */
-      //System.printString("Barrier #5\n");
-      Barrier.enterBarrier(tmpbr);
-      //System.clearPrefetchCache();
-      //TournamentBarrier.enterBarrier(myid, tmpbr);
-
-        if(id == 0) {
-          for (j=0;j<3;j++) {
-            for (i=0;i<tmpmdsize;i++) {
-              sh_force[j][i] = sh_force[j][i] * hsq2;
-            }
-          }
-        }
 
-        sum = 0.0;
+    /* Synchronise threads and start timer before MD simulation */
 
+    //Barrier.enterBarrier(barr);
 
-      /* Barrier */
-      //System.printString("Barrier #6\n");
-      Barrier.enterBarrier(tmpbr);
-      //System.clearPrefetchCache();
-      //TournamentBarrier.enterBarrier(myid, tmpbr);
+    /* MD simulation */
 
-        /*scale forces, update velocities */
+    for (int move=0;move<movemx;move++) {
+      /* move the particles and update velocities */
+      for (int i=0;i<mdsize;i++) {
+        one[i].domove(side,i);       
+      }
 
-        for (i=0;i<tmpmdsize;i++) {
-          sum = sum + one[i].mkekin(hsq2,i);  
-        }
+      /* Barrier */
+      //Barrier.enterBarrier(barr);
 
-        ekin = sum/hsq;
+      if(id==0) {
+        doinit(mdsize);
+      }
 
-        vel = 0.0;
-        count = 0.0;
+      mymd.epot[id].d = 0.0;
+      mymd.vir[id].d = 0.0;
+      mymd.interacts[id].i = 0;
 
-        /* average velocity */
 
-        for (i=0;i<tmpmdsize;i++) {
-          velt = one[i].velavg(vaverh,h);
-          if(velt > vaverh) { count = count + 1.0; }
-          vel = vel + velt;                    
-        }
+      /* Barrier */
+      //Barrier.enterBarrier(barr);
 
-        vel = vel / h;
+      /* compute forces */
 
-        /* temperature scale if required */
+      for (int i=0+id;i<mdsize;i+=nthreads) {
+        one[i].force(side,rcoff,mdsize,i,xx,yy,zz,mymd); 
+      }
 
-        if((move < istop) && (((move+1) % irep) == 0)) {
-          sc = Math.sqrt(tref / (tscale*ekin));
-          for (i=0;i<tmpmdsize;i++) {
-            one[i].dscal(sc,1);
-          }
-          ekin = tref / tscale;
-        }
+      /* Barrier */
+      //Barrier.enterBarrier(barr);
 
-        /* sum to get full potential energy and virial */
+      /* update force arrays */
+      if(id == 0) {
+        doinit2(mdsize);
+      }
 
-        if(((move+1) % iprint) == 0) {
-          mymd.ek[id] = 24.0*ekin;
-          mymd.epot[id] = 4.0*mymd.epot[id];
-          etot = mymd.ek[id] + mymd.epot[id];
-          temp = tscale * ekin;
-          pres = tmpden * 16.0 * (ekin - mymd.vir[id]) / tmpmdsize;
-          vel = vel / tmpmdsize; 
-          rp = (count / tmpmdsize) * 100.0;
-        }
-      //System.printString("Barrier #7\n");
-      Barrier.enterBarrier(tmpbr);
-      //System.clearPrefetchCache();
-      //TournamentBarrier.enterBarrier(myid, tmpbr);
-    }
-
-    //System.printString("Barrier #8\n");
-    Barrier.enterBarrier(tmpbr);
-    //System.clearPrefetchCache();
-    //TournamentBarrier.enterBarrier(myid, tmpbr);
-    //if (id == 0) JGFInstrumentor.stopTimer("Section3:MolDyn:Run", instr.timers);
-    //System.printString("End run method\n");
-  }
+      /* Barrier */
+      //Barrier.enterBarrier(barr);
 
-}
+      /*scale forces, update velocities */
+      sum = 0.0;
+      for (int i=0;i<mdsize;i++) {
+        sum = sum + one[i].mkekin(hsq2,i);  
+      }
 
+      ekin = sum/hsq;
 
+      vel = 0.0;
+      count = 0.0;
 
+      /* average velocity */
 
-class particle {
+      for (int i=0;i<mdsize;i++) {
+        velt = one[i].velavg(vaverh,h);
+        if(velt > vaverh) { count = count + 1.0; }
+        vel = vel + velt;                    
+      }
 
-  public double xcoord, ycoord, zcoord;
-  public double xvelocity,yvelocity,zvelocity;
-  int part_id;
-  int id;
-  double [][] sh_force;
-  double [][][] sh_force2;
-  mdRunner runner;
-
-  public particle(double xcoord, double ycoord, double zcoord, double xvelocity,
-      double yvelocity,double zvelocity,double [][] sh_force, 
-      double [][][] sh_force2,int id,mdRunner runner) {
-
-    this.xcoord = xcoord; 
-    this.ycoord = ycoord; 
-    this.zcoord = zcoord;
-    this.xvelocity = xvelocity;
-    this.yvelocity = yvelocity;
-    this.zvelocity = zvelocity;
-    this.sh_force = sh_force;
-    this.sh_force2 = sh_force2;
-    this.id=id;
-    this.runner=runner;
-  }
+      vel = vel / h;
 
-  public void domove(double side,int part_id) {
+      /* temperature scale if required */
 
-    xcoord = xcoord + xvelocity + sh_force[0][part_id];
-    ycoord = ycoord + yvelocity + sh_force[1][part_id];
-    zcoord = zcoord + zvelocity + sh_force[2][part_id];
+      if((move < istop) && (((move+1) % irep) == 0)) {
+        sc = Math.sqrt(tref / (tscale*ekin));
+        for (int i=0;i<mdsize;i++) {
+          one[i].dscal(sc,1);
+        }
+        ekin = tref / tscale;
+      }
 
-    if(xcoord < 0) { xcoord = xcoord + side; } 
-    if(xcoord > side) { xcoord = xcoord - side; }
-    if(ycoord < 0) { ycoord = ycoord + side; }
-    if(ycoord > side) { ycoord = ycoord - side; }
-    if(zcoord < 0) { zcoord = zcoord + side; }
-    if(zcoord > side) { zcoord = zcoord - side; }
+      /* sum to get full potential energy and virial */
 
-    xvelocity = xvelocity + sh_force[0][part_id];
-    yvelocity = yvelocity + sh_force[1][part_id];
-    zvelocity = zvelocity + sh_force[2][part_id];
+      if(((move+1) % iprint) == 0) {
+        mymd.ek[id].d = 24.0*ekin;
+        mymd.epot[id].d = 4.0*mymd.epot[id].d;
+        etot = mymd.ek[id].d + mymd.epot[id].d;
+        temp = tscale * ekin;
+        pres = tmpden * 16.0 * (ekin - mymd.vir[id].d) / mdsize;
+        vel = vel / mdsize; 
+        rp = (count / mdsize) * 100.0;
+      }
+      //Barrier.enterBarrier(barr);
 
+      //if (id == 0) JGFInstrumentor.stopTimer("Section3:MolDyn:Run", instr.timers);
+    }
   }
+}
 
-  public void force(double side, double rcoff,int mdsize,int x, double xx, double yy, double zz, JGFMolDynBench mymd) {
+  class particle {
+
+    public double xcoord, ycoord, zcoord;
+    public double xvelocity,yvelocity,zvelocity;
+    int part_id;
+    int id;
+    double [][] sh_force;
+    double [][][] sh_force2;
+    particle[] one;
+
+    public particle(double xcoord, double ycoord, double zcoord, double xvelocity,
+        double yvelocity,double zvelocity, double [][] sh_force, 
+        double [][][] sh_force2,int id, particle[] one) {
+
+      this.xcoord = xcoord; 
+      this.ycoord = ycoord; 
+      this.zcoord = zcoord;
+      this.xvelocity = xvelocity;
+      this.yvelocity = yvelocity;
+      this.zvelocity = zvelocity;
+      this.sh_force = sh_force;
+      this.sh_force2 = sh_force2;
+      this.id=id;
+      this.one=one;
+    }
 
-    double sideh;
-    double rcoffs;
+    public void domove(double side,int part_id) {
 
-    double fxi,fyi,fzi;
-    double rd,rrd,rrd2,rrd3,rrd4,rrd6,rrd7,r148;
-    double forcex,forcey,forcez;
+      xcoord = xcoord + xvelocity + sh_force[0][part_id];
+      ycoord = ycoord + yvelocity + sh_force[1][part_id];
+      zcoord = zcoord + zvelocity + sh_force[2][part_id];
 
-    sideh = 0.5*side; 
-    rcoffs = rcoff*rcoff;
+      if(xcoord < 0) { xcoord = xcoord + side; } 
+      if(xcoord > side) { xcoord = xcoord - side; }
+      if(ycoord < 0) { ycoord = ycoord + side; }
+      if(ycoord > side) { ycoord = ycoord - side; }
+      if(zcoord < 0) { zcoord = zcoord + side; }
+      if(zcoord > side) { zcoord = zcoord - side; }
 
-    fxi = 0.0;
-    fyi = 0.0;
-    fzi = 0.0;
+      xvelocity = xvelocity + sh_force[0][part_id];
+      yvelocity = yvelocity + sh_force[1][part_id];
+      zvelocity = zvelocity + sh_force[2][part_id];
 
-    for (int i=x+1;i<mdsize;i++) {
-      xx = this.xcoord - runner.one[i].xcoord;
-      yy = this.ycoord - runner.one[i].ycoord;
-      zz = this.zcoord - runner.one[i].zcoord;
+    }
 
-      if(xx < (-sideh)) { xx = xx + side; }
-      if(xx > (sideh))  { xx = xx - side; }
-      if(yy < (-sideh)) { yy = yy + side; }
-      if(yy > (sideh))  { yy = yy - side; }
-      if(zz < (-sideh)) { zz = zz + side; }
-      if(zz > (sideh))  { zz = zz - side; }
+    public void force(double side, double rcoff,int mdsize,int x, double xx, double yy, double zz, JGFMolDynBench mymd) {
 
+      double sideh;
+      double rcoffs;
 
-      rd = xx*xx + yy*yy + zz*zz;
+      double fxi,fyi,fzi;
+      double rd,rrd,rrd2,rrd3,rrd4,rrd6,rrd7,r148;
+      double forcex,forcey,forcez;
+      int id=this.id;
+      sideh = 0.5*side; 
+      rcoffs = rcoff*rcoff;
 
-      if(rd <= rcoffs) {
-        rrd = 1.0/rd;
-        rrd2 = rrd*rrd;
-        rrd3 = rrd2*rrd;
-        rrd4 = rrd2*rrd2;
-        rrd6 = rrd2*rrd4;
-        rrd7 = rrd6*rrd;
-        mymd.epot[id] = mymd.epot[id] + (rrd6 - rrd3);
-        r148 = rrd7 - 0.5*rrd4;
-        mymd.vir[id] = mymd.vir[id] - rd*r148;
-        forcex = xx * r148;
-        fxi = fxi + forcex;
+      fxi = 0.0;
+      fyi = 0.0;
+      fzi = 0.0;
 
-        sh_force2[0][id][i] = sh_force2[0][id][i] - forcex;
+      for (int i=x+1;i<mdsize;i++) {
+        xx = this.xcoord - one[i].xcoord;
+        yy = this.ycoord - one[i].ycoord;
+        zz = this.zcoord - one[i].zcoord;
 
-        forcey = yy * r148;
-        fyi = fyi + forcey;
+        if(xx < (-sideh)) { xx = xx + side; }
+        if(xx > (sideh))  { xx = xx - side; }
+        if(yy < (-sideh)) { yy = yy + side; }
+        if(yy > (sideh))  { yy = yy - side; }
+        if(zz < (-sideh)) { zz = zz + side; }
+        if(zz > (sideh))  { zz = zz - side; }
 
-        sh_force2[1][id][i] = sh_force2[1][id][i] - forcey;
 
-        forcez = zz * r148;
-        fzi = fzi + forcez;
+        rd = xx*xx + yy*yy + zz*zz;
 
-        sh_force2[2][id][i] = sh_force2[2][id][i] - forcez;
+        if(rd <= rcoffs) {
+          rrd = 1.0/rd;
+          rrd2 = rrd*rrd;
+          rrd3 = rrd2*rrd;
+          rrd4 = rrd2*rrd2;
+          rrd6 = rrd2*rrd4;
+          rrd7 = rrd6*rrd;
+          mymd.epot[id].d += (rrd6 - rrd3);
+          r148 = rrd7 - 0.5*rrd4;
+          mymd.vir[id].d += - rd*r148;
+          forcex = xx * r148;
+          fxi = fxi + forcex;
 
-        mymd.interacts[id]++;
-      }
+          sh_force2[0][id][i] = sh_force2[0][id][i] - forcex;
 
-    }
+          forcey = yy * r148;
+          fyi = fyi + forcey;
 
-    sh_force2[0][id][x] = sh_force2[0][id][x] + fxi;
-    sh_force2[1][id][x] = sh_force2[1][id][x] + fyi;
-    sh_force2[2][id][x] = sh_force2[2][id][x] + fzi;
+          sh_force2[1][id][i] = sh_force2[1][id][i] - forcey;
 
-  }
+          forcez = zz * r148;
+          fzi = fzi + forcez;
 
-  public double mkekin(double hsq2,int part_id) {
+          sh_force2[2][id][i] = sh_force2[2][id][i] - forcez;
 
-    double sumt = 0.0; 
+          mymd.interacts[id].i++;
+        }
 
-    xvelocity = xvelocity + sh_force[0][part_id]; 
-    yvelocity = yvelocity + sh_force[1][part_id]; 
-    zvelocity = zvelocity + sh_force[2][part_id]; 
+      }
 
-    sumt = (xvelocity*xvelocity)+(yvelocity*yvelocity)+(zvelocity*zvelocity);
-    return sumt;
-  }
+      sh_force2[0][id][x] = sh_force2[0][id][x] + fxi;
+      sh_force2[1][id][x] = sh_force2[1][id][x] + fyi;
+      sh_force2[2][id][x] = sh_force2[2][id][x] + fzi;
 
-  public double velavg(double vaverh,double h) {
+    }
 
-    double velt;
-    double sq;
+    public double mkekin(double hsq2,int part_id) {
 
-    sq = Math.sqrt(xvelocity*xvelocity + yvelocity*yvelocity +
-        zvelocity*zvelocity);
+      double sumt = 0.0; 
 
-    velt = sq;
-    return velt;
-  }
+      xvelocity = xvelocity + sh_force[0][part_id]; 
+      yvelocity = yvelocity + sh_force[1][part_id]; 
+      zvelocity = zvelocity + sh_force[2][part_id]; 
 
-  public void dscal(double sc,int incx) {
+      sumt = (xvelocity*xvelocity)+(yvelocity*yvelocity)+(zvelocity*zvelocity);
+      return sumt;
+    }
 
-    xvelocity = xvelocity * sc;
-    yvelocity = yvelocity * sc;   
-    zvelocity = zvelocity * sc;   
+    public double velavg(double vaverh,double h) {
 
+      double velt;
+      double sq;
 
+      sq = Math.sqrt(xvelocity*xvelocity + yvelocity*yvelocity +
+          zvelocity*zvelocity);
 
-  }
+      velt = sq;
+      return velt;
+    }
 
-}
+    public void dscal(double sc,int incx) {
+      xvelocity = xvelocity * sc;
+      yvelocity = yvelocity * sc;   
+      zvelocity = zvelocity * sc;   
+    }
+  }
 
-class random {
+  class random {
 
-  public int iseed;
-  public double v1,v2;
+    public int iseed;
+    public double v1,v2;
 
-  public random(int iseed,double v1,double v2) {
-    this.iseed = iseed;
-    this.v1 = v1;
-    this.v2 = v2;
-  }
+    public random(int iseed,double v1,double v2) {
+      this.iseed = iseed;
+      this.v1 = v1;
+      this.v2 = v2;
+    }
 
-  public double update() {
+    public double update() {
 
-    double rand;
-    double scale= 4.656612875e-10;
+      double rand;
+      double scale= 4.656612875e-10;
 
-    int is1,is2,iss2;
-    int imult=16807;
-    int imod = 2147483647;
+      int is1,is2,iss2;
+      int imult=16807;
+      int imod = 2147483647;
 
-    if (iseed<=0) { iseed = 1; }
+      if (iseed<=0) { iseed = 1; }
 
-    is2 = iseed % 32768;
-    is1 = (iseed-is2)/32768;
-    iss2 = is2 * imult;
-    is2 = iss2 % 32768;
-    is1 = (is1*imult+(iss2-is2)/32768) % (65536);
+      is2 = iseed % 32768;
+      is1 = (iseed-is2)/32768;
+      iss2 = is2 * imult;
+      is2 = iss2 % 32768;
+      is1 = (is1*imult+(iss2-is2)/32768) % (65536);
 
-    iseed = (is1*32768+is2) % imod;
+      iseed = (is1*32768+is2) % imod;
 
-    rand = scale * iseed;
+      rand = scale * iseed;
 
-    return rand;
+      return rand;
 
-  }
+    }
 
-  public double seed() {
+    public double seed() {
 
-    double s,u1,u2,r;
-    s = 1.0;
-    do {
-      u1 = update();
-      u2 = update();
+      double s,u1,u2,r;
+      s = 1.0;
+      do {
+        u1 = update();
+        u2 = update();
 
-      v1 = 2.0 * u1 - 1.0;
-      v2 = 2.0 * u2 - 1.0;
-      s = v1*v1 + v2*v2;
+        v1 = 2.0 * u1 - 1.0;
+        v2 = 2.0 * u2 - 1.0;
+        s = v1*v1 + v2*v2;
 
-    } while (s >= 1.0);
+      } while (s >= 1.0);
 
-    r = Math.sqrt(-2.0*Math.log(s)/s);
+      r = Math.sqrt(-2.0*Math.log(s)/s);
 
-    return r;
+      return r;
 
+    }
   }
-}
 
 
diff --git a/Robust/src/Benchmarks/Prefetch/Moldyn/javasingle/JGFMolDynBenchSizeA.java b/Robust/src/Benchmarks/Prefetch/Moldyn/javasingle/JGFMolDynBenchSizeA.java
index 51b52f24..61437401 100644
--- a/Robust/src/Benchmarks/Prefetch/Moldyn/javasingle/JGFMolDynBenchSizeA.java
+++ b/Robust/src/Benchmarks/Prefetch/Moldyn/javasingle/JGFMolDynBenchSizeA.java
@@ -38,44 +38,38 @@ public class JGFMolDynBenchSizeA {
     JGFInstrumentor.addTimer("Section3:MolDyn:Total", "Solutions",size, instr.timers);
     JGFInstrumentor.addTimer("Section3:MolDyn:Run", "Interactions",size, instr.timers);
 
-      mold.JGFsetsize(size); 
+    mold.JGFsetsize(size); 
 
     JGFInstrumentor.startTimer("Section3:MolDyn:Total", instr.timers);
 
     JGFMolDynBench tmp;
-      mold.JGFinitialise(); 
+    mold.JGFinitialise(); 
     JGFMolDynBench.JGFapplication(mold); 
+
     /* Validate data */
     double[] refval = new double[2];
     refval[0] = 1731.4306625334357;
     refval[1] = 7397.392307839352;
     double dval;
-    //System.printString("Here #1\n");
-      dval = mold.ek[0];
-    //System.printString("Here #2\n");
+    dval = mold.ek[0].d;
     double dev = Math.fabs(dval - refval[size]);
-    //long ldev = (long)dev * 1000000;
-    //System.printString("ldev= "+ldev);
-    //long ltmp = (long)1.0e-10 * 1000000;
-    //System.printString("ltmp= "+ltmp);
-    if (dev > 1.0e-10 ){
-    //if (ldev > ltmp ){
+    long l = (long) refval[size] *1000000;
+    long r = (long) dval * 1000000;
+    if (l != r ){
       System.printString("Validation failed\n");
       System.printString("Kinetic Energy = " + (long)dval + "  " + (long)dev + "  " + size + "\n");
     }
-    System.printString("End of JGFvalidate\n");
 
     JGFInstrumentor.stopTimer("Section3:MolDyn:Total", instr.timers);
     double interactions;
-    System.printString("Here #3\n");
     interactions = mold.interactions;
-    System.printString("Here #4\n");
 
     JGFInstrumentor.addOpsToTimer("Section3:MolDyn:Run", (double) interactions, instr.timers);
     JGFInstrumentor.addOpsToTimer("Section3:MolDyn:Total", 1, instr.timers);
 
     JGFInstrumentor.printTimer("Section3:MolDyn:Run", instr.timers); 
     JGFInstrumentor.printTimer("Section3:MolDyn:Total", instr.timers); 
+    System.printString("Finished\n");
   }
 }
 
diff --git a/Robust/src/Benchmarks/Prefetch/Moldyn/javasingle/MDWrap.java b/Robust/src/Benchmarks/Prefetch/Moldyn/javasingle/MDWrap.java
new file mode 100644
index 00000000..5c4ed746
--- /dev/null
+++ b/Robust/src/Benchmarks/Prefetch/Moldyn/javasingle/MDWrap.java
@@ -0,0 +1,9 @@
+public class MDWrap {
+    public mdRunner md;
+    public MDWrap() {
+    }
+
+    public MDWrap(mdRunner m) {
+	md=m;
+    }
+}
diff --git a/Robust/src/Benchmarks/Prefetch/Moldyn/javasingle/makefile b/Robust/src/Benchmarks/Prefetch/Moldyn/javasingle/makefile
index ba8f95cf..3140b7b0 100644
--- a/Robust/src/Benchmarks/Prefetch/Moldyn/javasingle/makefile
+++ b/Robust/src/Benchmarks/Prefetch/Moldyn/javasingle/makefile
@@ -3,9 +3,11 @@ SRC=${MAINCLASS}.java \
 JGFInstrumentor.java \
 JGFTimer.java \
 JGFMolDynBench.java \
-Barrier.java
+DoubleWrapper.java \
+IntWrapper.java \
+MDWrap.java
 
-FLAGS2= -thread -optimize -mainclass ${MAINCLASS} -o ${MAINCLASS}NP
+FLAGS2= -thread -optimize -mainclass ${MAINCLASS} -o ${MAINCLASS}
 
 default:
 	../../../../buildscript ${FLAGS2} ${SRC}
-- 
2.34.1