From 4a5aecc79ed85540b895ab46a214404e58bc6d41 Mon Sep 17 00:00:00 2001
From: bdemsky <bdemsky>
Date: Fri, 25 Apr 2008 08:58:35 +0000
Subject: [PATCH] changes to the barrier and rearrange atomic statements in the
 run method

---
 .../Prefetch/Moldyn/dsm/JGFMolDynBench.java   | 581 +++++++++---------
 .../Benchmarks/Prefetch/Moldyn/dsm/makefile   |   2 +-
 2 files changed, 291 insertions(+), 292 deletions(-)

diff --git a/Robust/src/Benchmarks/Prefetch/Moldyn/dsm/JGFMolDynBench.java b/Robust/src/Benchmarks/Prefetch/Moldyn/dsm/JGFMolDynBench.java
index 5e2b6921..c72ebab5 100644
--- a/Robust/src/Benchmarks/Prefetch/Moldyn/dsm/JGFMolDynBench.java
+++ b/Robust/src/Benchmarks/Prefetch/Moldyn/dsm/JGFMolDynBench.java
@@ -90,10 +90,10 @@ public class JGFMolDynBench {
 
     // spawn threads 
     mdRunner[] thobjects;
-    TournamentBarrier br;
+    Barrier br;
     atomic {
       thobjects = global new mdRunner[numthreads];
-      br= global new TournamentBarrier(numthreads);
+      br= global new Barrier(numthreads);
     }
 
     int mid = (128<<24)|(195<<16)|(175<<8)|73;
@@ -137,7 +137,7 @@ public class JGFMolDynBench {
 class mdRunner extends Thread {
 
   double count;
-  int id,i,j,k,lg,mdsize,move,mm;
+  int id,i,j,k,lg,mdsize,mm;
   double l,rcoff,rcoffs,side,sideh,hsq,hsq2,vel,velt;
   double a,r,sum,tscale,sc,ekin,ts,sp;
   double den;
@@ -155,17 +155,16 @@ class mdRunner extends Thread {
   int irep;
   int istop;
   int iprint;
-  int movemx;
 
-  TournamentBarrier br;
+  Barrier br;
   random randnum;
   JGFMolDynBench mymd;
   int nthreads;
 
   particle[] one;
 
-  public mdRunner(int id, int mm, double [][] sh_force, double [][][] sh_force2,TournamentBarrier br, 
-      int nthreads, JGFMolDynBench mymd) {
+  public mdRunner(int id, int mm, double [][] sh_force, double [][][] sh_force2,Barrier br, 
+		  int nthreads, JGFMolDynBench mymd) {
     this.id=id;
     this.mm=mm;
     this.sh_force=sh_force;
@@ -180,302 +179,302 @@ class mdRunner extends Thread {
     irep = 10;
     istop = 19;
     iprint = 10;
-    movemx = 50;
   } 
 
   public void run() {
 
-    /* Parameter determination */
-
-    atomic {
-      mdsize = mymd.PARTSIZE;
-      one = global new particle[mdsize];
-      l = mymd.LENGTH;
-    }
-
-    int tmpmdsize;
-    double tmpden;
-    atomic {
-      tmpmdsize = mdsize;
-      tmpden = den;
-    }
-    
-    atomic {
-      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;
-    }
-    atomic {
-      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] = global 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;
-            }
-          }
-        }
-      }
-    }
-
-    atomic {
-      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] = global 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;
-            }
-          }
-        }
-      }
-    }
-
-
-    /* Initialise velocities */
-
-    atomic {
-      iseed = 0;
-      v1 = 0.0;
-      v2 = 0.0;
-      randnum = global 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;
-      }
-
-
-      /* velocity scaling */
-
-      ekin = 0.0;
-      sp = 0.0;
-
-      for(i=0;i<tmpmdsize;i++) {
-        sp = sp + one[i].xvelocity;
-      }
-      sp = sp / tmpmdsize;
-
-      for(i=0;i<tmpmdsize;i++) {
-        one[i].xvelocity = one[i].xvelocity - sp;
-        ekin = ekin + one[i].xvelocity*one[i].xvelocity;
-      }
-
-      sp = 0.0;
-      for(i=0;i<tmpmdsize;i++) {
-        sp = sp + one[i].yvelocity;
-      }
-      sp = sp / tmpmdsize;
-
-      for(i=0;i<tmpmdsize;i++) {
-        one[i].yvelocity = one[i].yvelocity - sp;
-        ekin = ekin + one[i].yvelocity*one[i].yvelocity;
-      }
-
-
-      sp = 0.0;
-      for(i=0;i<tmpmdsize;i++) {
-        sp = sp + one[i].zvelocity;
-      }
-      sp = sp / tmpmdsize;
-
-      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);
-
-
-      for(i=0;i<tmpmdsize;i++) {
-
-        one[i].xvelocity = one[i].xvelocity * sc;     
-        one[i].yvelocity = one[i].yvelocity * sc;     
-        one[i].zvelocity = one[i].zvelocity * sc;     
-
+      /* Parameter determination */
+      
+      int tmpmdsize;
+      double tmpden;
+      int movemx=50;
+      Barrier tmpbr;
+      
+      atomic {
+	  tmpbr=br;
+	  mdsize = mymd.PARTSIZE;
+	  one = global 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] = global 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;
+		      }
+		  }
+	      }
+	  }
+	  
+	  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] = global 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;
+		      }
+		  }
+	      }
+	  }
+	  
+	  /* Initialise velocities */
+	  
+	  iseed = 0;
+	  v1 = 0.0;
+	  v2 = 0.0;
+	  randnum = global 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;
+	  }
+	  
+	  
+	  /* velocity scaling */
+	  
+	  ekin = 0.0;
+	  sp = 0.0;
+	  
+	  for(i=0;i<tmpmdsize;i++) {
+	      sp = sp + one[i].xvelocity;
+	  }
+	  sp = sp / tmpmdsize;
+	  
+	  for(i=0;i<tmpmdsize;i++) {
+	      one[i].xvelocity = one[i].xvelocity - sp;
+	      ekin = ekin + one[i].xvelocity*one[i].xvelocity;
+	  }
+	  
+	  sp = 0.0;
+	  for(i=0;i<tmpmdsize;i++) {
+	      sp = sp + one[i].yvelocity;
+	  }
+	  sp = sp / tmpmdsize;
+	  
+	  for(i=0;i<tmpmdsize;i++) {
+	      one[i].yvelocity = one[i].yvelocity - sp;
+	      ekin = ekin + one[i].yvelocity*one[i].yvelocity;
+	  }
+	  
+	  
+	  sp = 0.0;
+	  for(i=0;i<tmpmdsize;i++) {
+	      sp = sp + one[i].zvelocity;
+	  }
+	  sp = sp / tmpmdsize;
+	  
+	  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);
+	  
+	  
+	  for(i=0;i<tmpmdsize;i++) {
+	      
+	      one[i].xvelocity = one[i].xvelocity * sc;     
+	      one[i].yvelocity = one[i].yvelocity * sc;     
+	      one[i].zvelocity = one[i].zvelocity * sc;     
+	      
+	  }
       }
 
-
       /* Synchronise threads and start timer before MD simulation */
-
-        br.DoBarrier(id);
+      
+      Barrier.enterBarrier(tmpbr);
       //if (id == 0) JGFInstrumentor.startTimer("Section3:MolDyn:Run", instr.timers);
-        br.DoBarrier(id);
-
+      //Barrier.enterBarrier(tmpbr);
+      
       /* MD simulation */
-
-      move = 0;
-      for (move=0;move<movemx;move++) {
-
-        /* move the particles and update velocities */
-
-        for (i=0;i<tmpmdsize;i++) {
-          one[i].domove(side,i);       
-        }
-
-        /* Barrier */
-        br.DoBarrier(id);
-
-        if(id==0) {
-          for(j=0;j<3;j++) {
-            for (i=0;i<tmpmdsize;i++) {
-              sh_force[j][i] = 0.0;
-            }
-          }
-        }
-
-        mymd.epot[id] = 0.0;
-        mymd.vir[id] = 0.0;
-        mymd.interacts[id] = 0;
-
-        /* Barrier */
-        br.DoBarrier(id);
-
-        /* compute forces */
-
-        for (i=0+id;i<tmpmdsize;i+=nthreads) {
-          one[i].force(side,rcoff,tmpmdsize,i,xx,yy,zz,mymd); 
-        }
-
-        /* Barrier */
-        br.DoBarrier(id);
-
-        /* 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];
-              }
-            }
-          }
-        }
-
-        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;
-              }
-            }
-          }
-        }
-
-        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]; 
-          }
-        }
-
-        /* Barrier */
-        br.DoBarrier(id);
-
-        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;
-
-        /* Barrier */
-        br.DoBarrier(id);
-
-        /*scale forces, update velocities */
-
-        for (i=0;i<tmpmdsize;i++) {
-          sum = sum + one[i].mkekin(hsq2,i);  
-        }
-
-        ekin = sum/hsq;
-
-        vel = 0.0;
-        count = 0.0;
-
-        /* average velocity */
-
-        for (i=0;i<tmpmdsize;i++) {
-          velt = one[i].velavg(vaverh,h);
-          if(velt > vaverh) { count = count + 1.0; }
-          vel = vel + velt;                    
-        }
-
-        vel = vel / h;
-
-        /* temperature scale if required */
-
-        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;
-        }
-
-        /* sum to get full potential energy and virial */
-
-        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;
-        }
-
-        br.DoBarrier(id);
+      
+      for (int move=0;move<movemx;move++) {
+	  atomic {
+	      
+	      
+	      /* move the particles and update velocities */
+	      
+	      for (i=0;i<tmpmdsize;i++) {
+		  one[i].domove(side,i);       
+	      }
+	  }
+	      
+	  /* Barrier */
+	  Barrier.enterBarrier(tmpbr);
+	  atomic {
+	      
+	      if(id==0) {
+		  for(j=0;j<3;j++) {
+		      for (i=0;i<tmpmdsize;i++) {
+			  sh_force[j][i] = 0.0;
+		      }
+		  }
+	      }
+	      
+	      mymd.epot[id] = 0.0;
+	      mymd.vir[id] = 0.0;
+	      mymd.interacts[id] = 0;
+	  }
+	  
+	  
+	  /* Barrier */
+	  Barrier.enterBarrier(tmpbr);
+	      
+	  atomic {
+	      /* compute forces */
+	      
+	      for (i=0+id;i<tmpmdsize;i+=nthreads) {
+		  one[i].force(side,rcoff,tmpmdsize,i,xx,yy,zz,mymd); 
+	      }
+	      
+	  }
+	  /* Barrier */
+	  Barrier.enterBarrier(tmpbr);
+	      
+	  /* update force arrays */
+	  atomic {
+
+	      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];
+			  }
+		      }
+		  }
+	      }
+	      
+	      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;
+			  }
+		      }
+		  }
+	      }
+	      
+	      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]; 
+		  }
+	      }
+	  }
+
+	  /* Barrier */
+	  Barrier.enterBarrier(tmpbr);
+	   
+	  atomic {
+	      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;
+	  }
+	      
+	  
+	  /* Barrier */
+	  Barrier.enterBarrier(tmpbr);
+	  
+	  atomic {
+	      /*scale forces, update velocities */
+	      
+	      for (i=0;i<tmpmdsize;i++) {
+		  sum = sum + one[i].mkekin(hsq2,i);  
+	      }
+	      
+	      ekin = sum/hsq;
+	      
+	      vel = 0.0;
+	      count = 0.0;
+	      
+	      /* average velocity */
+	      
+	      for (i=0;i<tmpmdsize;i++) {
+		  velt = one[i].velavg(vaverh,h);
+		  if(velt > vaverh) { count = count + 1.0; }
+		  vel = vel + velt;                    
+	      }
+	      
+	      vel = vel / h;
+	      
+	      /* temperature scale if required */
+	      
+	      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;
+	      }
+	      
+	      /* sum to get full potential energy and virial */
+	      
+	      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;
+	      }
+	  }
+	  Barrier.enterBarrier(tmpbr);
       }
 
-
-      br.DoBarrier(id);
+      Barrier.enterBarrier(tmpbr);
       //if (id == 0) JGFInstrumentor.stopTimer("Section3:MolDyn:Run", instr.timers);
-
-    }
-
   }
 
 }
diff --git a/Robust/src/Benchmarks/Prefetch/Moldyn/dsm/makefile b/Robust/src/Benchmarks/Prefetch/Moldyn/dsm/makefile
index 1d8fed82..59051f96 100644
--- a/Robust/src/Benchmarks/Prefetch/Moldyn/dsm/makefile
+++ b/Robust/src/Benchmarks/Prefetch/Moldyn/dsm/makefile
@@ -3,7 +3,7 @@ SRC=${MAINCLASS}.java \
 JGFInstrumentor.java \
 JGFTimer.java \
 JGFMolDynBench.java \
-TournamentBarrier.java
+Barrier.java
 FLAGS=-dsm -prefetch -excprefetch particle.force -excprefetch particle.domove -excprefetch particle.mkekin -excprefetch TournamentBarrier.DoBarrier -excprefetch JGFMolDynBench.JGFvalidate -excprefetch JGFMolDynBench.JGFapplication -optimize -debug -profile -mainclass ${MAINCLASS} -o ${MAINCLASS} -trueprob 0.8
 FLAGS2=-dsm -optimize -debug -profile -mainclass ${MAINCLASS} -o ${MAINCLASS}NP
 
-- 
2.34.1