}
}
-
for (int i = 0; i < iteration; i++) {
/* for eNodes */
- System.clearPrefetchCache();
-
atomic {
Node n = enodebase;
for(int j = lowerlimit; j<upperlimit; j++) {
}
Barrier.enterBarrier(barr);
-
System.clearPrefetchCache();
-
-
+
/* for hNodes */
atomic {
Node n = hnodebase;
}
}
Barrier.enterBarrier(barr);
+ System.clearPrefetchCache();
}
}
Em3d em = new Em3d();
Em3d.parseCmdLine(args, em);
if (em.printMsgs)
- System.printString("Initializing em3d random graph...");
+ System.printString("Initializing em3d random graph...\n");
long start0 = System.currentTimeMillis();
- int numThreads = 1;
- System.printString("DEBUG -> numThreads = " + numThreads);
+ int numThreads = 4;
+ int[] mid = new int[numThreads];
+ mid[0] = (128<<24)|(195<<16)|(175<<8)|69;
+ mid[1] = (128<<24)|(195<<16)|(175<<8)|78;
+ mid[2] = (128<<24)|(195<<16)|(175<<8)|73;
+ mid[3] = (128<<24)|(195<<16)|(175<<8)|79;
+ System.printString("DEBUG -> numThreads = " + numThreads+"\n");
Barrier mybarr;
atomic {
mybarr = global new Barrier(numThreads);
// compute a single iteration of electro-magnetic propagation
if (em.printMsgs)
System.printString("Propagating field values for " + em.numIter +
- " iteration(s)...");
+ " iteration(s)...\n");
long start1 = System.currentTimeMillis();
Em3d[] em3d;
atomic {
em3d = global new Em3d[numThreads];
- em3d[0] = global new Em3d(graph, 0, em.numNodes, em.numIter, mybarr);
+ em3d[0] = global new Em3d(graph, 0, em.numNodes/4, em.numIter, mybarr);
+ em3d[1] = global new Em3d(graph, (em.numNodes/4) + 1, em.numNodes/2, em.numIter, mybarr);
+ em3d[2] = global new Em3d(graph, (em.numNodes/2) + 1, (3*em.numNodes)/4, em.numIter, mybarr);
+ em3d[3] = global new Em3d(graph, (3*em.numNodes)/4 + 1, em.numNodes, em.numIter, mybarr);
}
- int mid = (128<<24)|(195<<16)|(175<<8)|73;
Em3d tmp;
for(int i = 0; i<numThreads; i++) {
atomic {
tmp = em3d[i];
}
- tmp.start(mid);
+ tmp.start(mid[i]);
}
for(int i = 0; i<numThreads; i++) {
StringBuffer retval = new StringBuffer();
double dvalue;
atomic {
- dvalue = graph.eNodes.value;
+ dvalue = graph.hNodes.value;
}
int intvalue = (int)dvalue;
- System.printString("Value = " + intvalue + "\n");
}
if (em.printMsgs) {
- System.printString("EM3D build time "+ (long)((end0 - start0)/1000.0));
- System.printString("EM3D compute time " + (long)((end1 - start1)/1000.0));
- System.printString("EM3D total time " + (long)((end1 - start0)/1000.0));
+ System.printString("EM3D build time "+ (long)((end0 - start0)/1000.0) + "\n");
+ System.printString("EM3D compute time " + (long)((end1 - start1)/1000.0) + "\n");
+ System.printString("EM3D total time " + (long)((end1 - start0)/1000.0) + "\n");
}
- System.printString("Done!");
+ System.printString("Done!"+ "\n");
}
**/
public void usage()
{
- System.printString("usage: java Em3d -n <nodes> -d <degree> [-p] [-m] [-h]");
- System.printString(" -n the number of nodes");
- System.printString(" -d the out-degree of each node");
- System.printString(" -i the number of iterations");
- System.printString(" -p (print detailed results)");
- System.printString(" -m (print informative messages)");
- System.printString(" -h (this message)");
+ System.printString("usage: java Em3d -n <nodes> -d <degree> [-p] [-m] [-h]\n");
+ System.printString(" -n the number of nodes\n");
+ System.printString(" -d the out-degree of each node\n");
+ System.printString(" -i the number of iterations\n");
+ System.printString(" -p (print detailed results\n)");
+ System.printString(" -m (print informative messages)\n");
+ System.printString(" -h (this message)\n");
}
}
br= global new Barrier(numthreads);
}
- int mid = (128<<24)|(195<<16)|(175<<8)|73;
+ int[] mid = new int[4];
+ mid[0] = (128<<24)|(195<<16)|(175<<8)|73;
+ mid[1] = (128<<24)|(195<<16)|(175<<8)|69;
+ mid[2] = (128<<24)|(195<<16)|(175<<8)|79;
+ mid[3] = (128<<24)|(195<<16)|(175<<8)|78;
mdRunner tmp;
for(int i=1;i<numthreads;i++) {
thobjects[i] = global new mdRunner(i,mold.mm,sh_force,sh_force2,br,mold.nthreads,mold);
tmp = thobjects[i];
}
- tmp.start(mid);
+ tmp.start(mid[i]);
}
atomic {
thobjects[0] = global new mdRunner(0,mold.mm,sh_force,sh_force2,br,mold.nthreads,mold);
tmp = thobjects[0];
}
- tmp.start(mid);
+ tmp.start(mid[0]);
tmp.join();
for(int i=1;i<numthreads;i++) {
public void run() {
- /* Parameter determination */
-
- int tmpmdsize;
- double tmpden;
- int movemx=50;
- Barrier tmpbr;
-
+ /* 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 */
+
+ Barrier.enterBarrier(tmpbr);
+ System.clearPrefetchCache();
+
+ /* MD simulation */
+
+ for (int move=0;move<movemx;move++) {
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;
-
- }
+ /* move the particles and update velocities */
+
+ for (i=0;i<tmpmdsize;i++) {
+ one[i].domove(side,i);
+ }
}
- /* Synchronise threads and start timer before MD simulation */
-
+ /* Barrier */
Barrier.enterBarrier(tmpbr);
- //if (id == 0) JGFInstrumentor.startTimer("Section3:MolDyn:Run", instr.timers);
- //Barrier.enterBarrier(tmpbr);
-
- /* MD simulation */
-
- 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);
+ System.clearPrefetchCache();
+
+ 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);
- //if (id == 0) JGFInstrumentor.stopTimer("Section3:MolDyn:Run", instr.timers);
- }
+ System.clearPrefetchCache();
-}
+ 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);
+ System.clearPrefetchCache();
+
+ /* 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);
+ System.clearPrefetchCache();
+
+ 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);
+ System.clearPrefetchCache();
+
+ 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);
+ System.clearPrefetchCache();
+ }
+
+ Barrier.enterBarrier(tmpbr);
+ System.clearPrefetchCache();
+ //if (id == 0) JGFInstrumentor.stopTimer("Section3:MolDyn:Run", instr.timers);
+ }
+
+}
class particle {
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