* All rights reserved. *
* *
**************************************************************************/
-
-import java.io.*;
-
public class JGFMolDynBench {
public int ITERS;
public double LENGTH;
public int nthreads;
public JGFInstrumentor instr;
- public JGFMolDynBench(int nthreads, JGFInstrumentor instr) {
+ public JGFMolDynBench(int nthreads) {
this.nthreads=nthreads;
- this.instr = instr;
}
public void JGFsetsize(int size){
kb = 1.38066e-23;
TSIM = 50;
deltat = 5e-16;
-
- //initialise();
}
- public void JGFapplication() {
+ public static void JGFapplication(JGFMolDynBench mold) {
// Create new arrays
- epot = new double [nthreads];
- vir = new double [nthreads];
- ek = new double [nthreads];
+ mold.epot = new double [mold.nthreads];
+ mold.vir = new double [mold.nthreads];
+ mold.ek = new double [mold.nthreads];
+ mold.interacts = new int [mold.nthreads];
- interacts = new int [nthreads];
+ int partsize, numthreads;
+ partsize = mold.PARTSIZE;
+ numthreads = mold.nthreads;
- double sh_force [][] = new double[3][PARTSIZE];
- double sh_force2 [][][] = new double[3][nthreads][PARTSIZE];
+ double sh_force [][];
+ double sh_force2 [][][];
+ sh_force = new double[3][partsize];
+ sh_force2 = new double[3][numthreads][partsize];
// spawn threads
- Thread thobjects[] = new Thread [nthreads];
- TournamentBarrier br= new TournamentBarrier(nthreads);
- //Barrier br = new Barrier(nthreads);
-
- for(int i=1;i<nthreads;i++) {
- thobjects[i] = new mdRunner(i,mm,sh_force,sh_force2,br,instr,nthreads,this);
- thobjects[i].start();
+ 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();
}
-
- thobjects[0] = new mdRunner(0,mm,sh_force,sh_force2,br,instr,nthreads,this);
- thobjects[0].run();
-
- for(int i=1;i<nthreads;i++) {
- try {
- thobjects[i].join();
- }
- catch (InterruptedException e) {}
+ //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");
}
public void JGFvalidate(){
double[] refval = new double[2];
refval[0] = 1731.4306625334357;
refval[1] = 7397.392307839352;
- double dev = Math.abs(ek[0] - refval[size]);
+ double dev = Math.fabs(ek[0] - refval[size]);
if (dev > 1.0e-10 ){
- System.out.println("Validation failed");
- System.out.println("Kinetic Energy = " + ek[0] + " " + dev + " " + size);
+ //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,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;
int irep;
int istop;
int iprint;
- int movemx;
- TournamentBarrier br;
- //Barrier br;
+ Barrier br;
random randnum;
- JGFInstrumentor instr;
JGFMolDynBench mymd;
int nthreads;
particle[] one;
- public mdRunner(int id, int mm, double [][] sh_force, double [][][] sh_force2,TournamentBarrier br,
- //public mdRunner(int id, int mm, double [][] sh_force, double [][][] sh_force2,Barrier br,
- JGFInstrumentor instr, 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;
this.sh_force2=sh_force2;
this.br=br;
- this.instr = instr;
this.nthreads = nthreads;
this.mymd = mymd;
count = 0.0;
irep = 10;
istop = 19;
iprint = 10;
- movemx = 50;
}
public void run() {
+ //System.printString("Start run method\n");
+
/* Parameter determination */
- mdsize = mymd.PARTSIZE;
- one = new particle [mdsize];
- l = mymd.LENGTH;
-
- side = Math.pow((mdsize/den),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;
- 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;
+ 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;
+ }
}
}
}
- }
- 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 (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;
+ }
}
}
}
- }
-
- /* Initialise velocities */
+ /* Initialise velocities */
- iseed = 0;
- v1 = 0.0;
- v2 = 0.0;
+ iseed = 0;
+ v1 = 0.0;
+ v2 = 0.0;
+ randnum = new random(iseed,v1,v2);
- randnum = new random(iseed,v1,v2);
-
- for (i=0; i<mdsize; i+=2) {
- r = randnum.seed();
- one[i].xvelocity = r*randnum.v1;
- one[i+1].xvelocity = r*randnum.v2;
- }
-
- for (i=0; i<mdsize; 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].xvelocity = r*randnum.v1;
+ one[i+1].xvelocity = r*randnum.v2;
+ }
- for (i=0; i<mdsize; i+=2) {
- r = randnum.seed();
- one[i].zvelocity = r*randnum.v1;
- one[i+1].zvelocity = 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;
+ /* velocity scaling */
- for(i=0;i<mdsize;i++) {
- sp = sp + one[i].xvelocity;
- }
- sp = sp / mdsize;
+ ekin = 0.0;
+ sp = 0.0;
- for(i=0;i<mdsize;i++) {
- one[i].xvelocity = one[i].xvelocity - sp;
- ekin = ekin + one[i].xvelocity*one[i].xvelocity;
- }
+ for(i=0;i<tmpmdsize;i++) {
+ sp = sp + one[i].xvelocity;
+ }
+ sp = sp / tmpmdsize;
- sp = 0.0;
- for(i=0;i<mdsize;i++) {
- sp = sp + one[i].yvelocity;
- }
- sp = sp / mdsize;
+ for(i=0;i<tmpmdsize;i++) {
+ one[i].xvelocity = one[i].xvelocity - sp;
+ ekin = ekin + one[i].xvelocity*one[i].xvelocity;
+ }
- for(i=0;i<mdsize;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].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<mdsize;i++) {
- sp = sp + one[i].zvelocity;
- }
- sp = sp / mdsize;
- for(i=0;i<mdsize;i++) {
- one[i].zvelocity = one[i].zvelocity - sp;
- ekin = ekin + one[i].zvelocity*one[i].zvelocity;
- }
+ sp = 0.0;
+ for(i=0;i<tmpmdsize;i++) {
+ sp = sp + one[i].zvelocity;
+ }
+ sp = sp / tmpmdsize;
- ts = tscale * ekin;
- sc = h * Math.sqrt(tref/ts);
+ 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<mdsize;i++) {
- one[i].xvelocity = one[i].xvelocity * sc;
- one[i].yvelocity = one[i].yvelocity * sc;
- one[i].zvelocity = one[i].zvelocity * sc;
+ 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(br);
- if (id == 0) JGFInstrumentor.startTimer("Section3:MolDyn:Run", instr.timers);
- // Barrier.enterBarrier(br);
- br.DoBarrier(id);
-
+ 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 */
- move = 0;
- for (move=0;move<movemx;move++) {
-
- /* move the particles and update velocities */
+ for (int move=0;move<movemx;move++) {
+ /* move the particles and update velocities */
- for (i=0;i<mdsize;i++) {
- one[i].domove(side,i);
- }
+ for (i=0;i<tmpmdsize;i++) {
+ one[i].domove(side,i);
+ }
/* Barrier */
- br.DoBarrier(id);
- //Barrier.enterBarrier(br);
-
- if(id==0) {
- for(j=0;j<3;j++) {
- for (i=0;i<mdsize;i++) {
- sh_force[j][i] = 0.0;
+ //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;
+ }
}
}
- }
- mymd.epot[id] = 0.0;
- mymd.vir[id] = 0.0;
- mymd.interacts[id] = 0;
-
- /* Barrier */
- //Barrier.enterBarrier(br);
- br.DoBarrier(id);
+ 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);
- /* compute forces */
+ /* compute forces */
- for (i=0+id;i<mdsize;i+=nthreads) {
- one[i].force(side,rcoff,mdsize,i,xx,yy,zz,mymd);
- }
+ for (i=0+id;i<tmpmdsize;i+=nthreads) {
+ one[i].force(side,rcoff,tmpmdsize,i,xx,yy,zz,mymd);
+ }
/* Barrier */
- //Barrier.enterBarrier(br);
- br.DoBarrier(id);
+ //System.printString("Barrier #4\n");
+ Barrier.enterBarrier(tmpbr);
+ //System.clearPrefetchCache();
+ //TournamentBarrier.enterBarrier(myid, tmpbr);
/* update force arrays */
-
- if(id == 0) {
- for(int k=0;k<3;k++) {
- for(i=0;i<mdsize;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_force[k][i] += sh_force2[k][j][i];
+ }
}
}
}
- }
- if(id == 0) {
- for(int k=0;k<3;k++) {
- for(i=0;i<mdsize;i++) {
- for(j=0;j<nthreads;j++) {
- sh_force2[k][j][i] = 0.0;
+ 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];
+ 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(br);
- br.DoBarrier(id);
-
- if(id == 0) {
- for (j=0;j<3;j++) {
- for (i=0;i<mdsize;i++) {
- sh_force[j][i] = sh_force[j][i] * hsq2;
+ //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;
+ sum = 0.0;
+
/* Barrier */
- //Barrier.enterBarrier(br);
- br.DoBarrier(id);
+ //System.printString("Barrier #6\n");
+ Barrier.enterBarrier(tmpbr);
+ //System.clearPrefetchCache();
+ //TournamentBarrier.enterBarrier(myid, tmpbr);
- /*scale forces, update velocities */
+ /*scale forces, update velocities */
- for (i=0;i<mdsize;i++) {
- sum = sum + one[i].mkekin(hsq2,i);
- }
+ for (i=0;i<tmpmdsize;i++) {
+ sum = sum + one[i].mkekin(hsq2,i);
+ }
- ekin = sum/hsq;
+ ekin = sum/hsq;
- vel = 0.0;
- count = 0.0;
+ vel = 0.0;
+ count = 0.0;
- /* average velocity */
+ /* average velocity */
- for (i=0;i<mdsize;i++) {
- velt = one[i].velavg(vaverh,h);
- if(velt > vaverh) { count = count + 1.0; }
- vel = vel + velt;
- }
+ 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;
+ vel = vel / h;
- /* temperature scale if required */
+ /* temperature scale if required */
- if((move < istop) && (((move+1) % irep) == 0)) {
- sc = Math.sqrt(tref / (tscale*ekin));
- for (i=0;i<mdsize;i++) {
- one[i].dscal(sc,1);
+ 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;
}
- ekin = tref / tscale;
- }
- /* sum to get full potential energy and virial */
+ /* 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 = den * 16.0 * (ekin - mymd.vir[id]) / mdsize;
- vel = vel / mdsize;
- rp = (count / mdsize) * 100.0;
- }
-
- //Barrier.enterBarrier(br);
- br.DoBarrier(id);
+ 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);
}
-
- //Barrier.enterBarrier(br);
- br.DoBarrier(id);
- if (id == 0) JGFInstrumentor.stopTimer("Section3:MolDyn:Run", instr.timers);
-
+ //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");
}
}
projects / IRC.git / blobdiff