From c2f70e1e44693f84d117d9c4e9376db9713dc1a0 Mon Sep 17 00:00:00 2001
From: adash <adash>
Date: Tue, 10 Mar 2009 08:04:58 +0000
Subject: [PATCH] Manual prefetch version of Moldyn

---
 .../ManualPrefetch/Moldyn/DoubleWrapper.java  |   6 +
 .../ManualPrefetch/Moldyn/IntWrapper.java     |   6 +
 .../Moldyn/JGFInstrumentor.java               | 199 +++++
 .../ManualPrefetch/Moldyn/JGFMolDynBench.java | 779 ++++++++++++++++++
 .../Moldyn/JGFMolDynBenchSizeB.java           |  85 ++
 .../ManualPrefetch/Moldyn/JGFTimer.java       | 123 +++
 .../ManualPrefetch/Moldyn/MDWrap.java         |   9 +
 .../Prefetch/ManualPrefetch/Moldyn/makefile   |  17 +
 8 files changed, 1224 insertions(+)
 create mode 100644 Robust/src/Benchmarks/Prefetch/ManualPrefetch/Moldyn/DoubleWrapper.java
 create mode 100644 Robust/src/Benchmarks/Prefetch/ManualPrefetch/Moldyn/IntWrapper.java
 create mode 100644 Robust/src/Benchmarks/Prefetch/ManualPrefetch/Moldyn/JGFInstrumentor.java
 create mode 100644 Robust/src/Benchmarks/Prefetch/ManualPrefetch/Moldyn/JGFMolDynBench.java
 create mode 100644 Robust/src/Benchmarks/Prefetch/ManualPrefetch/Moldyn/JGFMolDynBenchSizeB.java
 create mode 100644 Robust/src/Benchmarks/Prefetch/ManualPrefetch/Moldyn/JGFTimer.java
 create mode 100644 Robust/src/Benchmarks/Prefetch/ManualPrefetch/Moldyn/MDWrap.java
 create mode 100644 Robust/src/Benchmarks/Prefetch/ManualPrefetch/Moldyn/makefile

diff --git a/Robust/src/Benchmarks/Prefetch/ManualPrefetch/Moldyn/DoubleWrapper.java b/Robust/src/Benchmarks/Prefetch/ManualPrefetch/Moldyn/DoubleWrapper.java
new file mode 100644
index 00000000..c0bd06da
--- /dev/null
+++ b/Robust/src/Benchmarks/Prefetch/ManualPrefetch/Moldyn/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/ManualPrefetch/Moldyn/IntWrapper.java b/Robust/src/Benchmarks/Prefetch/ManualPrefetch/Moldyn/IntWrapper.java
new file mode 100644
index 00000000..8bf875d3
--- /dev/null
+++ b/Robust/src/Benchmarks/Prefetch/ManualPrefetch/Moldyn/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/ManualPrefetch/Moldyn/JGFInstrumentor.java b/Robust/src/Benchmarks/Prefetch/ManualPrefetch/Moldyn/JGFInstrumentor.java
new file mode 100644
index 00000000..3f9f580c
--- /dev/null
+++ b/Robust/src/Benchmarks/Prefetch/ManualPrefetch/Moldyn/JGFInstrumentor.java
@@ -0,0 +1,199 @@
+/**************************************************************************
+ *                                                                         *
+ *         Java Grande Forum Benchmark Suite - Thread Version 1.0          *
+ *                                                                         *
+ *                            produced by                                  *
+ *                                                                         *
+ *                  Java Grande Benchmarking Project                       *
+ *                                                                         *
+ *                                at                                       *
+ *                                                                         *
+ *                Edinburgh Parallel Computing Centre                      *
+ *                                                                         * 
+ *                email: epcc-javagrande@epcc.ed.ac.uk                     *
+ *                                                                         *
+ *                                                                         *
+ *      This version copyright (c) The University of Edinburgh, 1999.      *
+ *                         All rights reserved.                            *
+ *                                                                         *
+ **************************************************************************/
+public class JGFInstrumentor{
+
+  protected HashMap timers;
+  protected HashMap data; 
+
+  public JGFInstrumentor() {
+    timers = new HashMap();
+    data = new HashMap(); 
+  }
+
+  public static void addTimer (String name, HashMap timers){
+
+    if (timers.containsKey(name)) {
+      System.printString("JGFInstrumentor.addTimer: warning -  timer " + name + 
+          " already exists\n");
+    }
+    else {
+      timers.put(name, new JGFTimer(name));
+    }
+  }
+
+  public static void addTimer (String name, String opname, HashMap timers){
+
+    if (timers.containsKey(name)) {
+      System.printString("JGFInstrumentor.addTimer: warning -  timer " + name + 
+          " already exists\n");
+    }
+    else {
+      timers.put(name, new JGFTimer(name,opname));
+    }
+
+  }
+
+  public static void addTimer (String name, String opname, int size, HashMap timers){
+
+    if (timers.containsKey(name)) {
+      System.printString("JGFInstrumentor.addTimer: warning -  timer " + name +
+          " already exists\n");
+    }
+    else {
+      timers.put(name, new JGFTimer(name,opname,size));
+    }
+
+  }
+
+  public static void startTimer(String name, HashMap timers){
+    if (timers.containsKey(name)) {
+      ((JGFTimer) timers.get(name)).start();
+    }
+    else {
+      System.printString("JGFInstrumentor.startTimer: failed -  timer " + name + 
+          " does not exist\n");
+    }
+
+  }
+
+  public static void stopTimer(String name, HashMap timers){
+    if (timers.containsKey(name)) {
+      ((JGFTimer) timers.get(name)).stop();
+    }
+    else {
+      System.printString("JGFInstrumentor.stopTimer: failed -  timer " + name + 
+          " does not exist\n");
+    }
+  }
+
+  public static void addOpsToTimer(String name, double count, HashMap timers){
+    if (timers.containsKey(name)) {
+      ((JGFTimer) timers.get(name)).addops(count);
+    }
+    else {
+      System.printString("JGFInstrumentor.addOpsToTimer: failed -  timer " + name + 
+          " does not exist\n");
+    }
+  }  
+
+  public static void addTimeToTimer(String name, double added_time, HashMap timers){
+    if (timers.containsKey(name)) {
+      ((JGFTimer) timers.get(name)).addtime(added_time);
+    }
+    else {
+      System.printString("JGFInstrumentor.addTimeToTimer: failed -  timer " + name +
+          " does not exist\n");
+    }
+
+
+
+  }
+
+  public static double readTimer(String name, HashMap timers){
+    double time; 
+    if (timers.containsKey(name)) {
+      time = ((JGFTimer) timers.get(name)).time;
+    }
+    else {
+      System.printString("JGFInstrumentor.readTimer: failed -  timer " + name + 
+          " does not exist\n");
+      time = 0.0; 
+    }
+    return time; 
+  }  
+
+  public static void resetTimer(String name, HashMap timers){
+    if (timers.containsKey(name)) {
+      ((JGFTimer) timers.get(name)).reset();
+    }
+    else {
+      System.printString("JGFInstrumentor.resetTimer: failed -  timer " + name +
+          " does not exist\n");
+    }
+  }
+
+  public static void printTimer(String name, HashMap timers){
+    if (timers.containsKey(name)) {
+      ((JGFTimer) timers.get(name)).print();
+    }
+    else {
+      System.printString("JGFInstrumentor.printTimer: failed -  timer " + name +
+          " does not exist\n");
+    }
+  }
+
+  public static void printperfTimer(String name, HashMap timers){
+    if (timers.containsKey(name)) {
+      ((JGFTimer) timers.get(name)).printperf();
+    }
+    else {
+      System.printString("JGFInstrumentor.printTimer: failed -  timer " + name +
+          " does not exist\n");
+    }
+  }
+
+  public static void storeData(String name, Object obj, HashMap data){
+    data.put(name,obj); 
+  }
+
+  public static void retrieveData(String name, Object obj, HashMap data){
+    obj = data.get(name); 
+  }
+
+  public static void printHeader(int section, int size,int nthreads) {
+
+    String header, base; 
+
+    header = "";
+    base = "Java Grande Forum Thread Benchmark Suite - Version 1.0 - Section "; 
+
+    if (section == 1)
+    {
+      header = base + "1";
+    }
+    else if (section == 2)
+    {
+      if (size == 0)
+        header = base + "2 - Size A";
+      else if (size == 1)
+        header = base + "2 - Size B";
+      else if (size == 2)
+        header = base + "2 - Size C";
+    }
+    else if (section == 3)
+    {
+      if (size == 0)
+        header = base + "3 - Size A";
+      else if (size == 1)
+        header = base + "3 - Size B";
+    }
+
+    System.printString(header + "\n"); 
+
+    if (nthreads == 1) {
+      System.printString("Executing on " + nthreads + " thread\n");
+    }
+    else {
+      System.printString("Executing on " + nthreads + " threads\n");
+    }
+
+    System.printString(" \n");
+  } 
+}
diff --git a/Robust/src/Benchmarks/Prefetch/ManualPrefetch/Moldyn/JGFMolDynBench.java b/Robust/src/Benchmarks/Prefetch/ManualPrefetch/Moldyn/JGFMolDynBench.java
new file mode 100644
index 00000000..42471686
--- /dev/null
+++ b/Robust/src/Benchmarks/Prefetch/ManualPrefetch/Moldyn/JGFMolDynBench.java
@@ -0,0 +1,779 @@
+/**************************************************************************
+ *                                                                         *
+ *         Java Grande Forum Benchmark Suite - Thread Version 1.0          *
+ *                                                                         *
+ *                            produced by                                  *
+ *                                                                         *
+ *                  Java Grande Benchmarking Project                       *
+ *                                                                         *
+ *                                at                                       *
+ *                                                                         *
+ *                Edinburgh Parallel Computing Centre                      *
+ *                                                                         * 
+ *                email: epcc-javagrande@epcc.ed.ac.uk                     *
+ *                                                                         *
+ *                                                                         *
+ *      This version copyright (c) The University of Edinburgh, 2001.      *
+ *                         All rights reserved.                            *
+ *                                                                         *
+ **************************************************************************/
+public class JGFMolDynBench {
+  public int ITERS;
+  public double LENGTH;
+  public double m;
+  public double mu;
+  public double kb;
+  public double TSIM;
+  public double deltat;
+
+  public int PARTSIZE;
+
+  public DoubleWrapper[] epot;
+  public DoubleWrapper[] vir;
+  public DoubleWrapper[] ek;
+
+  int size,mm;
+  int[] datasizes;
+
+  public int interactions;
+  public IntWrapper[] interacts;
+
+  public int nthreads;
+  public JGFInstrumentor instr;
+
+  public JGFMolDynBench(int nthreads) {
+    this.nthreads=nthreads;
+  }
+
+  public void JGFsetsize(int size){
+    this.size = size;
+  }
+
+  public void JGFinitialise(){
+    interactions = 0;
+    datasizes = global new int[3];
+    datasizes[0] = 8;
+    datasizes[1] = 13;
+    datasizes[2] = 18;
+
+    mm = datasizes[size];
+    PARTSIZE = mm*mm*mm*4;
+    ITERS = 100;
+    LENGTH = 50e-10;
+    m = 4.0026;
+    mu = 1.66056e-27;
+    kb = 1.38066e-23;
+    TSIM = 50;
+    deltat = 5e-16;
+  }
+
+  public static void JGFapplication(JGFMolDynBench mold) { 
+    // Create new arrays 
+    BarrierServer mybarr;
+    int[] mid = new int[8];
+    mid[0] = (128<<24)|(195<<16)|(136<<8)|162; //dw-10
+    mid[1] = (128<<24)|(195<<16)|(136<<8)|163; //dw-11
+    mid[2] = (128<<24)|(195<<16)|(136<<8)|164; //dw-12
+    mid[3] = (128<<24)|(195<<16)|(136<<8)|165; //dw-13
+    mid[4] = (128<<24)|(195<<16)|(136<<8)|166; //dw-14
+    mid[5] = (128<<24)|(195<<16)|(136<<8)|167; //dw-15
+    mid[6] = (128<<24)|(195<<16)|(136<<8)|168; //dw-16
+    mid[7] = (128<<24)|(195<<16)|(136<<8)|169; //dw-17
+
+    double sh_force [][];
+    double sh_force2 [][][];
+    int partsize, numthreads;
+    atomic {
+      partsize = mold.PARTSIZE;
+      numthreads = mold.nthreads;
+      mybarr = global new BarrierServer(numthreads);
+    }
+    mybarr.start(mid[0]);
+    
+    atomic {
+      sh_force = global new double[3][partsize];
+      sh_force2 = global new double[3][numthreads][partsize];
+      mold.epot = global new DoubleWrapper[numthreads];
+      mold.vir  = global new DoubleWrapper[numthreads];
+      mold.ek   = global new DoubleWrapper[numthreads];
+      mold.interacts = global new IntWrapper[numthreads];
+      for(int i=0;i<numthreads;i++) {
+        mold.epot[i]=global new DoubleWrapper();
+        mold.vir[i]=global new DoubleWrapper();
+        mold.ek[i]=global new DoubleWrapper();
+        mold.interacts[i]=global new IntWrapper();
+      }
+    }
+    
+    // spawn threads 
+    MDWrap[] thobjects = new MDWrap[numthreads];
+    
+    atomic {
+      for(int i=0;i<numthreads;i++) {
+        thobjects[i] = new MDWrap(global new mdRunner(i,mold.mm,sh_force,sh_force2,mold.nthreads,mold));
+      }
+    }
+    
+    boolean waitfordone=true;
+    while(waitfordone) {
+      atomic{
+        if (mybarr.done)
+          waitfordone=false;
+      }
+    }
+    
+    for(int i=0;i<numthreads;i++) {
+      thobjects[i].md.start(mid[i]);
+    }
+    
+    for(int i=0;i<numthreads;i++) {
+      thobjects[i].md.join();
+    }
+  }
+
+  public void JGFvalidate(){
+    double[] refval = new double[2];
+    refval[0] = 1731.4306625334357;
+    refval[1] = 7397.392307839352;
+    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");
+    }
+  }
+}
+
+class mdRunner extends Thread {
+
+  double count;
+  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;
+  double tref;
+  double h;
+  double vaver,vaverh,rand;
+  double etot,temp,pres,rp;
+  double u1, u2, s, xx, yy, zz;
+  double xvelocity, yvelocity, zvelocity;
+
+  double [][] sh_force;
+  double [][][] sh_force2;
+
+  int ijk,npartm,iseed,tint;
+  int irep;
+  int istop;
+  int iprint;
+
+  JGFMolDynBench mymd;
+  int nthreads;
+
+  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.nthreads = nthreads;
+    this.mymd = mymd;
+    count = 0.0;
+    den = 0.83134;
+    tref = 0.722;
+    h = 0.064;
+    irep = 10;
+    istop = 19;
+    iprint = 10;
+  } 
+
+    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 (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 */
+
+      iseed = 0;
+      double v1 = 0.0;
+      double v2 = 0.0;
+      random randnum = new random(iseed,v1,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;
+      }
+
+      for (int i=0; i<mdsize; i+=2) {
+        r  = randnum.seed();
+        one[i].zvelocity = r*randnum.v1;
+        one[i+1].zvelocity  = r*randnum.v2;
+      }
+
+
+      /* velocity scaling */
+
+      ekin = 0.0;
+      sp = 0.0;
+
+      for(int i=0;i<mdsize;i++) {
+        sp = sp + one[i].xvelocity;
+      }
+      sp = sp / mdsize;
+
+      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;
+
+      for(int i=0;i<mdsize;i++) {
+        one[i].yvelocity = one[i].yvelocity - sp;
+        ekin = ekin + one[i].yvelocity*one[i].yvelocity;
+      }
+
+
+      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;
+      }
+
+      ts = tscale * ekin;
+      sc = h * Math.sqrt(tref/ts);
+
+
+      for(int i=0;i<mdsize;i++) {
+
+        one[i].xvelocity = one[i].xvelocity * sc;     
+        one[i].yvelocity = one[i].yvelocity * sc;     
+        one[i].zvelocity = one[i].zvelocity * sc;     
+
+      }
+
+    }
+
+    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;
+            }
+	}
+    }
+
+
+    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];
+              }
+            }
+          }
+	  
+          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++) {
+		
+
+                sh2[i] = 0.0;
+              }
+            }
+          }
+
+          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; 
+          }
+
+	  for (int j=0;j<3;j++) {
+	      double sh[]=sh_force[j];
+	    for (int i=0;i<mdsize;i++) {
+	      sh[i] = sh[i] * hsq2;
+	    }
+	  }
+}
+
+  public void run() {
+    /* Parameter determination */
+    
+    int mdsize;
+    double tmpden;
+    int movemx=50;
+    Barrier barr=new Barrier("128.195.136.162");
+    particle[] one;
+    int id;
+    atomic {
+	id=this.id;
+      //
+      //Add manual prefetch for this.mymd.epot[id]
+      //
+      Object o = this;
+      short[] offsets = new short[6];
+      offsets[0] = getoffset{mdRunner, mymd};
+      offsets[1] = (short) 0;
+      offsets[2] = getoffset{JGFMolDynBench, epot};
+      offsets[3] = (short) 0;
+      offsets[4] = (short) id;
+      offsets[5] = (short)  0;
+      System.rangePrefetch(o, offsets);
+
+      // this.mymd.interacts[id]
+      Object o1 = mymd;
+      short[] offsets1 = new short[4];
+      offsets1[0] = getoffset{JGFMolDynBench, interacts};
+      offsets1[1] = (short) 0;
+      offsets1[2] = (short) id;
+      offsets1[3] = (short)  0;
+      System.rangePrefetch(o1, offsets1);
+
+      // this.mymd.vir[id], 
+      offsets1[0] = getoffset{JGFMolDynBench, vir};
+      offsets1[1] = (short) 0;
+      offsets1[2] = (short) id;
+      offsets1[3] = (short)  0;
+      System.rangePrefetch(o1, offsets1);
+
+      /////////////////////
+
+      mdsize = mymd.PARTSIZE;
+      one=new particle[mdsize]; // Do not prefetch "one[]" because its local
+      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);
+
+    }
+
+    /* Synchronise threads and start timer before MD simulation */
+
+    Barrier.enterBarrier(barr);
+
+    /* MD simulation */
+
+    for (int move=0;move<movemx;move++) {
+      atomic {
+        /* move the particles and update velocities */
+        for (int i=0;i<mdsize;i++) {
+          one[i].domove(side,i);       
+        }
+      }
+
+      /* Barrier */
+      Barrier.enterBarrier(barr);
+
+      atomic {
+        if(id==0) {
+          //
+          // Add manual prefetch for this.sh_force[]
+          //
+          Object o = this;
+          short[] offsets = new short[4];
+          offsets[0] = getoffset{mdRunner, sh_force};
+          offsets[1] = (short) 0;
+          offsets[2] = (short) 0;
+          offsets[3] = (short) 2; // loop accesses 3 elements
+          System.rangePrefetch(o, offsets);
+
+          doinit(mdsize);
+        }
+	
+        mymd.epot[id].d = 0.0;
+        mymd.vir[id].d = 0.0;
+        mymd.interacts[id].i = 0;
+      }
+
+
+      /* Barrier */
+      Barrier.enterBarrier(barr);
+      
+      atomic {
+        /* compute forces */
+	
+        for (int i=0+id;i<mdsize;i+=nthreads) {
+          one[i].force(side,rcoff,mdsize,i,xx,yy,zz,mymd); 
+        }
+      }
+
+      /* Barrier */
+      Barrier.enterBarrier(barr);
+
+      /* update force arrays */
+      atomic {
+        if(id == 0) {
+          //
+          // Add manual prefetch for this.sh_force[]
+          //
+          Object o = this;
+          short[] offsets = new short[4];
+          offsets[0] = getoffset{mdRunner, sh_force};
+          offsets[1] = (short) 0;
+          offsets[2] = (short) 0;
+          offsets[3] = (short) 2; // loop accesses 3 elements
+          System.rangePrefetch(o, offsets);
+
+          // Add manual prefetch for this.sh_force2[][]
+          short[] offsets1 = new short[6];
+          offsets1[0] = getoffset{mdRunner, sh_force2};
+          offsets1[1] = (short) 0;
+          offsets1[2] = (short) 0;
+          offsets1[3] = (short) 2; //max is 3 elements
+          offsets1[4] = (short) 0;
+          offsets1[5] = (short) (nthreads - 1); //max is nthreads
+          System.rangePrefetch(o, offsets1);
+
+          // Add manual prefetch for this.mymd.epot[]
+          offsets1[0] = getoffset{mdRunner, mymd};
+          offsets1[1] = (short) 0;
+          offsets1[2] = getoffset{JGFMolDynBench, epot};
+          offsets1[3] = (short) 0;
+          offsets1[4] = (short) 0;
+          offsets1[5] = (short) (nthreads-1);
+          System.rangePrefetch(o, offsets1);
+
+          // Add manual prefetch for this.mymd.vir[]
+          offsets1[0] = getoffset{mdRunner, mymd};
+          offsets1[1] = (short) 0;
+          offsets1[2] = getoffset{JGFMolDynBench, vir};
+          offsets1[3] = (short) 0;
+          offsets1[4] = (short) 0;
+          offsets1[5] = (short) (nthreads-1);
+          System.rangePrefetch(o, offsets1);
+
+          // Add manual prefetch for this.mymd.interacts[]
+          offsets1[0] = getoffset{mdRunner, mymd};
+          offsets1[1] = (short) 0;
+          offsets1[2] = getoffset{JGFMolDynBench, interacts};
+          offsets1[3] = (short) 0;
+          offsets1[4] = (short) 0;
+          offsets1[5] = (short) (nthreads-1);
+          System.rangePrefetch(o, offsets1);
+          ////////////////////////////
+          doinit2(mdsize);
+        }
+      }
+
+      /* Barrier */
+      Barrier.enterBarrier(barr);
+
+      atomic {
+        /*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 */
+
+        for (int i=0;i<mdsize;i++) {
+          velt = one[i].velavg(vaverh,h);
+          if(velt > vaverh) { count = count + 1.0; }
+          vel = vel + velt;                    
+        }
+
+        vel = vel / h;
+
+        /* temperature scale if required */
+
+        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;
+        }
+
+        /* sum to get full potential energy and virial */
+
+        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);
+  }
+
+}
+
+class particle {
+
+  public double xcoord, ycoord, zcoord;
+  public double xvelocity,yvelocity,zvelocity;
+  int part_id;
+  int id;
+  global double [][] sh_force;
+  global 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;
+  }
+
+  public void domove(double side,int part_id) {
+
+    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(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; }
+
+    xvelocity = xvelocity + sh_force[0][part_id];
+    yvelocity = yvelocity + sh_force[1][part_id];
+    zvelocity = zvelocity + sh_force[2][part_id];
+
+  }
+
+  public void force(double side, double rcoff,int mdsize,int x, double xx, double yy, double zz, JGFMolDynBench mymd) {
+
+    double sideh;
+    double rcoffs;
+
+    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;
+
+    fxi = 0.0;
+    fyi = 0.0;
+    fzi = 0.0;
+
+    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;
+
+      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; }
+
+
+      rd = xx*xx + yy*yy + zz*zz;
+
+      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;
+
+        sh_force2[0][id][i] = sh_force2[0][id][i] - forcex;
+
+        forcey = yy * r148;
+        fyi = fyi + forcey;
+
+        sh_force2[1][id][i] = sh_force2[1][id][i] - forcey;
+
+        forcez = zz * r148;
+        fzi = fzi + forcez;
+
+        sh_force2[2][id][i] = sh_force2[2][id][i] - forcez;
+
+        mymd.interacts[id].i++;
+      }
+
+    }
+
+    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 mkekin(double hsq2,int part_id) {
+
+    double sumt = 0.0; 
+
+    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;
+  }
+
+  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 {
+
+  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 double update() {
+
+    double rand;
+    double scale= 4.656612875e-10;
+
+    int is1,is2,iss2;
+    int imult=16807;
+    int imod = 2147483647;
+
+    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);
+
+    iseed = (is1*32768+is2) % imod;
+
+    rand = scale * iseed;
+
+    return rand;
+
+  }
+
+  public double seed() {
+
+    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;
+
+    } while (s >= 1.0);
+
+    r = Math.sqrt(-2.0*Math.log(s)/s);
+
+    return r;
+
+  }
+}
+
+
diff --git a/Robust/src/Benchmarks/Prefetch/ManualPrefetch/Moldyn/JGFMolDynBenchSizeB.java b/Robust/src/Benchmarks/Prefetch/ManualPrefetch/Moldyn/JGFMolDynBenchSizeB.java
new file mode 100644
index 00000000..716f31b5
--- /dev/null
+++ b/Robust/src/Benchmarks/Prefetch/ManualPrefetch/Moldyn/JGFMolDynBenchSizeB.java
@@ -0,0 +1,85 @@
+/**************************************************************************
+ *                                                                         *
+ *         Java Grande Forum Benchmark Suite - Thread Version 1.0          *
+ *                                                                         *
+ *                            produced by                                  *
+ *                                                                         *
+ *                  Java Grande Benchmarking Project                       *
+ *                                                                         *
+ *                                at                                       *
+ *                                                                         *
+ *                Edinburgh Parallel Computing Centre                      *
+ *                                                                         * 
+ *                email: epcc-javagrande@epcc.ed.ac.uk                     *
+ *                                                                         *
+ *                                                                         *
+ *      This version copyright (c) The University of Edinburgh, 2001.      *
+ *                         All rights reserved.                            *
+ *                                                                         *
+ **************************************************************************/
+public class JGFMolDynBenchSizeB { 
+
+    public static void main(String argv[]){
+    int nthreads;
+    if(argv.length != 0 ) {
+      nthreads = Integer.parseInt(argv[0]);
+    } else {
+      System.printString("The no of threads has not been specified, defaulting to 1\n");
+      System.printString("  " + "\n");
+      nthreads = 1;
+    }
+
+    JGFInstrumentor instr = new JGFInstrumentor();
+    JGFInstrumentor.printHeader(3,0,nthreads);
+
+    JGFMolDynBench mold;
+    atomic {
+      mold = global new JGFMolDynBench(nthreads); 
+    }
+    int size = 1;
+    JGFInstrumentor.addTimer("Section3:MolDyn:Total", "Solutions",size, instr.timers);
+    JGFInstrumentor.addTimer("Section3:MolDyn:Run", "Interactions",size, instr.timers);
+
+    atomic {
+      mold.JGFsetsize(size); 
+    }
+
+    JGFInstrumentor.startTimer("Section3:MolDyn:Total", instr.timers);
+
+    JGFMolDynBench tmp;
+    atomic {
+      mold.JGFinitialise(); 
+    }
+    JGFMolDynBench.JGFapplication(mold); 
+
+    /* Validate data */
+    double[] refval = new double[2];
+    refval[0] = 1731.4306625334357;
+    refval[1] = 7397.392307839352;
+    double dval;
+    atomic {
+      dval = mold.ek[0].d;
+    }
+    double dev = Math.fabs(dval - refval[size]);
+    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");
+    }
+
+    JGFInstrumentor.stopTimer("Section3:MolDyn:Total", instr.timers);
+    double interactions;
+    atomic {
+      interactions = mold.interactions;
+    }
+
+    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/ManualPrefetch/Moldyn/JGFTimer.java b/Robust/src/Benchmarks/Prefetch/ManualPrefetch/Moldyn/JGFTimer.java
new file mode 100644
index 00000000..4e1d168f
--- /dev/null
+++ b/Robust/src/Benchmarks/Prefetch/ManualPrefetch/Moldyn/JGFTimer.java
@@ -0,0 +1,123 @@
+/**************************************************************************
+ *                                                                         *
+ *         Java Grande Forum Benchmark Suite - Thread Version 1.0          *
+ *                                                                         *
+ *                            produced by                                  *
+ *                                                                         *
+ *                  Java Grande Benchmarking Project                       *
+ *                                                                         *
+ *                                at                                       *
+ *                                                                         *
+ *                Edinburgh Parallel Computing Centre                      *
+ *                                                                         * 
+ *                email: epcc-javagrande@epcc.ed.ac.uk                     *
+ *                                                                         *
+ *                                                                         *
+ *      This version copyright (c) The University of Edinburgh, 1999.      *
+ *                         All rights reserved.                            *
+ *                                                                         *
+ **************************************************************************/
+
+public class JGFTimer {
+
+  public String name; 
+  public String opname; 
+  public double time; 
+  public double opcount; 
+  public long calls; 
+  public int size;
+
+  private long start_time;
+  private boolean on; 
+
+  public JGFTimer(String name, String opname){
+    this.size = -1;
+    this.name = name;
+    this.opname = opname;
+    reset(); 
+  }
+
+  public JGFTimer(String name, String opname, int size){
+    this.name = name;
+    this.opname = opname;
+    this.size = size;
+    reset();
+  }
+
+  public JGFTimer(String name){
+    this.name = name;
+    this.opname = "";
+    reset();
+  }
+
+
+
+  public void start(){
+    if (on) System.printString("Warning timer " + " was already turned on\n");
+    on = true; 
+    start_time = System.currentTimeMillis();
+  }
+
+
+  public void stop(){
+    time += (double) (System.currentTimeMillis()-start_time) / 1000.;
+    if (!on) System.printString("Warning timer " + " wasn't turned on\n");
+    calls++;
+    on = false;  
+  }
+
+  public void addops(double count){
+    opcount += count;
+  } 
+
+  public void addtime(double added_time){
+    time += added_time;
+  }
+
+  public void reset(){
+    time = 0.0; 
+    calls = 0; 
+    opcount = 0; 
+    on = false;
+  }
+
+  public double perf(){
+    return opcount / time; 
+  }
+
+  public void longprint(){
+    System.printString("Timer            Calls         Time(s)       Performance("+opname+"/s)\n");   
+    System.printString(name + "           " + calls +    "           "  +  (long)time + "        " + (long)this.perf() + "\n");
+  }
+
+  public void print(){
+    if (opname.equals("")) {
+      System.printString(name + "   " + (long)time + " (s)\n");
+    }
+    else {
+      if(size == 0) {
+        System.printString(name + ":SizeA" + "\t" + (long)time + " (s) \t " + (long)this.perf() + "\t" + " ("+opname+"/s)\n");
+      } else if (size == 1) {
+        System.printString(name + ":SizeB" + "\t" + (long)time + " (s) \t " + (long)this.perf() + "\t" + " ("+opname+"/s)\n");
+      } else if (size == 2) {
+        System.printString(name + ":SizeC" + "\t" + (long)time + " (s) \t " + (long)this.perf() + "\t" + " ("+opname+"/s)\n");
+      } else{
+        System.printString(name + "\t" + (long)time + " (s) \t " + (long)this.perf() + "\t" + " ("+opname+"/s)\n");
+      }
+    }
+  }
+
+
+  public void printperf(){
+
+    String name;
+    name = this.name; 
+
+    // pad name to 40 characters
+    while ( name.length() < 40 ) name = name + " "; 
+
+    System.printString(name + "\t" + (long)this.perf() + "\t"
+        + " ("+opname+"/s)\n");  
+  }
+
+}
diff --git a/Robust/src/Benchmarks/Prefetch/ManualPrefetch/Moldyn/MDWrap.java b/Robust/src/Benchmarks/Prefetch/ManualPrefetch/Moldyn/MDWrap.java
new file mode 100644
index 00000000..317ba061
--- /dev/null
+++ b/Robust/src/Benchmarks/Prefetch/ManualPrefetch/Moldyn/MDWrap.java
@@ -0,0 +1,9 @@
+public class MDWrap {
+    public global mdRunner md;
+    public MDWrap() {
+    }
+
+    public MDWrap(mdRunner m) {
+	md=m;
+    }
+}
\ No newline at end of file
diff --git a/Robust/src/Benchmarks/Prefetch/ManualPrefetch/Moldyn/makefile b/Robust/src/Benchmarks/Prefetch/ManualPrefetch/Moldyn/makefile
new file mode 100644
index 00000000..0a6c03c8
--- /dev/null
+++ b/Robust/src/Benchmarks/Prefetch/ManualPrefetch/Moldyn/makefile
@@ -0,0 +1,17 @@
+MAINCLASS=JGFMolDynBenchSizeB
+SRC=${MAINCLASS}.java \
+	JGFInstrumentor.java \
+	JGFTimer.java \
+	JGFMolDynBench.java \
+	DoubleWrapper.java \
+	IntWrapper.java \
+	MDWrap.java \
+	../../../../ClassLibrary/JavaDSM/Barrier.java
+FLAGS=-dsm -dsmcaching -rangeprefetch -optimize -mainclass ${MAINCLASS} -trueprob 0.75
+
+default:
+	../../../../buildscript ${FLAGS} -o ${MAINCLASS}RangeN  ${SRC}
+
+clean:
+	rm -rf tmpbuilddirectory/
+	rm *.bin
-- 
2.34.1