// Either going to return a status or ThreadStatus
public static Object Recv(Object buf, int offset, int count, int type, int source, int tag)
throws MPIException, InterruptedException {
if (mpiRun) {
if (source == -1) source = MPI.ANY_SOURCE;
if (tag == -1) tag = MPI.ANY_TAG;
Datatype dtype = getDatatype(type);
return MPI.COMM_WORLD.Recv(buf, offset, count, dtype, source, tag);
} else return threadEle.get(Thread.currentThread()).Recv(buf, offset, count, type, source, tag);
}
public static void main(String[] args) {
String inputPrmFile = args[3];
String inputConfFile = args[4];
String inputTopFile = args[5];
String outputTrajFile = args[6];
String outputEnergyFile = args[7];
String ITSout = args[8];
MdSystem<LJParticle> system =
GromacsImporter.buildLJParticleSystem(
"JOB_NAME", inputPrmFile, inputConfFile, inputTopFile);
MdParameter prm = system.getParam();
final double dt = prm.getDt();
final int nsteps = prm.getNsteps();
final int nstlist = prm.getNstlist();
final int nstxout = prm.getNstxout();
final int nstvout = prm.getNstvout();
final int nstenergy = prm.getNstenergy();
final int nstlog = 10; // prm.getNstlog();
final double T0 = prm.getT0();
final double TRef = prm.getRefT();
final double tauT = prm.getTauT();
final boolean convertHbonds = prm.convertHbonds();
if (convertHbonds) {
system.convertHBondsToConstraints();
}
/** ************ ITS setup *************** */
final int ksize = 12;
final double Tstep = 25.0; // T increment
final int ITSEnergyFreq = nstxout; // frequency of energy storing for ITS
final double[] Temps = new double[ksize];
final double[] p0 = new double[ksize];
for (int i = 0; i < ksize; i++) {
Temps[i] = T0 + i * Tstep;
p0[i] = 1.0 / ksize;
}
/** ************************************* */
final BigDecimal[] n0 = new BigDecimal[ksize];
MathContext mathset = new MathContext(5);
n0[0] = new BigDecimal("5.99880e-03", mathset);
n0[1] = new BigDecimal("3.64660e+209", mathset);
n0[2] = new BigDecimal("1.23850e+391", mathset);
n0[3] = new BigDecimal("2.59790e+548", mathset);
n0[4] = new BigDecimal("1.21530e+686", mathset);
n0[5] = new BigDecimal("2.85080e+807", mathset);
n0[6] = new BigDecimal("2.93170e+915", mathset);
n0[7] = new BigDecimal("1.33400e+1012", mathset);
n0[8] = new BigDecimal("1.18050e+1099", mathset);
n0[9] = new BigDecimal("4.27230e+1177", mathset);
n0[10] = new BigDecimal("1.70190e+1249", mathset);
n0[11] = new BigDecimal("2.87210e+1314", mathset);
// gen valocity
system.genRandomVelocities(T0);
/** MPI preparation * */
MPI.Init(args);
final int rank = MPI.COMM_WORLD.Rank();
final int np = MPI.COMM_WORLD.Size();
Integrator<MdSystem<LJParticle>> integrator = new VelocityVerlet<MdSystem<LJParticle>>(dt);
FastLJC<MdSystem<LJParticle>> nonbond = new FastLJC<MdSystem<LJParticle>>(system);
DomainDecomposition<MdSystem<LJParticle>> decomposition =
new DomainDecomposition<MdSystem<LJParticle>>(system, np);
Thermostat<MdSystem<LJParticle>> thermostat =
new BerendsenThermostat<MdSystem<LJParticle>>(TRef, tauT);
// push initial positions to the new trajectory
system.forwardPosition(integrator);
// get partitions using new positions
system.partition(decomposition);
Domain domain = decomposition.getDomain(rank);
DomainNeighborList<MdSystem<LJParticle>> nblist =
new DomainNeighborList<MdSystem<LJParticle>>(system, domain);
int SUB_CAPACITY = domain.getCapacity();
// head node
if (rank == 0) {
try {
PrintStream ps = new PrintStream(outputTrajFile);
PrintStream psEnergy = new PrintStream(outputEnergyFile);
PrintStream psITS = new PrintStream(ITSout);
ITS<MdSystem<LJParticle>> its = new ITS<MdSystem<LJParticle>>(T0, ksize, Temps, p0, n0);
double Uorg = 0.0;
for (int tstep = 0; tstep < nsteps; tstep++) {
if (tstep % nstlog == 0) {
System.out.println(String.format("Computing t = %5.3f ps", tstep * dt));
}
// integrate forward (apply position constraints if applicable)
if (tstep != 0) {
system.forwardPosition(integrator);
system.applyPositionConstraint();
}
// (I) update domains and send them to slave nodes
if (tstep % nstlist == 0) {
// updates partitions using new positions
system.partition(decomposition);
// send updated partition info to slave nodes
for (int proc = 1; proc < np; proc++) {
int[] partition = decomposition.exportPartition(proc);
MPI.COMM_WORLD.Send(partition, 0, SUB_CAPACITY, MPI.INT, proc, 99);
}
// update local neighbor list
nblist.update(system);
}
// (II) export new positions to slave nodes
for (int proc = 1; proc < np; proc++) {
Domain domainEach = decomposition.getDomain(proc);
double[] positionArray = system.exportNewPositions(domainEach);
MPI.COMM_WORLD.Send(positionArray, 0, 3 * SUB_CAPACITY, MPI.DOUBLE, proc, 99);
}
// (ITS Step 0 ) compute original energy
{
double nonbondEnergy = 0.0;
nonbondEnergy = system.getNonBondEnergy(nonbond, nblist);
// receive partial nonbond energies from slave-nodes and add
for (int proc = 1; proc < np; proc++) {
double[] partialEnergy = new double[1];
MPI.COMM_WORLD.Recv(partialEnergy, 0, 1, MPI.DOUBLE, proc, 99);
nonbondEnergy += partialEnergy[0];
}
double coulombEnergy = 0.0; // temporary.
double bond = system.getBondEnergy();
double angle = system.getAngleEnergy();
double dihedral = system.getDihedralEnergy();
Uorg = nonbondEnergy + bond + angle + dihedral;
if (tstep % ITSEnergyFreq == 0) {
its.printEnergy(psITS, system, Uorg);
}
}
// update non-bonded forces
system.updateNonBondForce(nonbond, nblist);
// update long-ranged forces
// update bonded forces
system.updateBondForce();
// update angle forces
system.updateAngleForce();
// update dihedral forces
system.updateDihedralForce();
// (III) receive computed forces from slaves
for (int proc = 1; proc < np; proc++) {
double[] forceArray = new double[3 * SUB_CAPACITY];
MPI.COMM_WORLD.Recv(forceArray, 0, 3 * SUB_CAPACITY, MPI.DOUBLE, proc, 99);
Domain domainEach = decomposition.getDomain(proc);
system.importNewForces(domainEach, forceArray);
}
// (ITS step 1 ) Apply biasing forces
its.applyBiasForce(system, Uorg);
// forward velocities
system.forwardVelocity(integrator);
// apply velocity constraints
system.correctConstraintVelocity();
// apply temperature coupling
thermostat.apply(system);
// print energy (using information in newTraj )
if (tstep % nstenergy == 0) {
double nonbondEnergy = 0.0;
nonbondEnergy = system.getNonBondEnergy(nonbond, nblist);
// receive partial nonbond energies from slave-nodes and add
for (int proc = 1; proc < np; proc++) {
double[] partialEnergy = new double[1];
MPI.COMM_WORLD.Recv(partialEnergy, 0, 1, MPI.DOUBLE, proc, 99);
nonbondEnergy += partialEnergy[0];
}
double coulombEnergy = 0.0; // temporary.
mymd.MdIO.printEnergy(system, nonbondEnergy, coulombEnergy, psEnergy);
}
// update current trajectories from new trajectories
system.update();
if (tstep % nstxout == 0) {
mymd.MdIO.writeGro(system, ps);
}
}
ps.close();
psEnergy.close();
} catch (java.io.IOException ex) {
}
}
// slave nodes
else {
decomposition = null;
String slaveName = String.format("slave-%d", rank);
/**
* * change subSystem constructor so it accepts a MdSystem object as an input parameter.
* SubSystem is needed only if MdSystem object exists. *
*/
// create a sub-system for slave node
Trajectory subTraj = new Trajectory(system.getSize());
subTraj.setBox(system.getBox());
SubSystem<LJParticle> subsystem =
new SubSystem.Builder<LJParticle>()
.name(slaveName)
.particles(system.getParticles())
.parameters(system.getParam())
.topology(system.getTopology())
.subTrajectory(subTraj)
.build();
// mother system is freed. no longer needed for slave nodes
system = null;
for (int tstep = 0; tstep < nsteps; tstep++) {
// (I) receive updated partition info from head node
if (tstep % nstlist == 0) {
int[] partition = new int[SUB_CAPACITY];
MPI.COMM_WORLD.Recv(partition, 0, SUB_CAPACITY, MPI.INT, 0, 99);
// import received array to its local domain
domain.importArray(partition);
}
// (II) receives new positions
double[] positionArray = new double[3 * SUB_CAPACITY];
MPI.COMM_WORLD.Recv(positionArray, 0, SUB_CAPACITY * 3, MPI.DOUBLE, 0, 99);
// import new positions into the subsystem
subsystem.importNewPositions(domain, positionArray);
if (tstep % nstlist == 0) {
// update local neighbor list
nblist.update(subsystem);
}
// (ITS 0 step)
double[] partialEnergy = new double[1];
partialEnergy[0] = subsystem.getNonBondEnergy(nonbond, nblist);
MPI.COMM_WORLD.Send(partialEnergy, 0, 1, MPI.DOUBLE, 0, 99);
// compute non-bonded forces
subsystem.updateNonBondForce(nonbond, nblist);
// PME
// (III) export forces and send them to head-node
double[] forceArray = subsystem.exportNewForces(domain);
MPI.COMM_WORLD.Send(forceArray, 0, SUB_CAPACITY * 3, MPI.DOUBLE, 0, 99);
if (tstep % nstenergy == 0) {
partialEnergy = new double[1];
partialEnergy[0] = subsystem.getNonBondEnergy(nonbond, nblist);
MPI.COMM_WORLD.Send(partialEnergy, 0, 1, MPI.DOUBLE, 0, 99);
}
// reset force components
subsystem.update();
}
}
MPI.Finalize();
}
public scattervO(String[] args) throws Exception {
final int MAXLEN = 10;
int myself, tasks;
MPI.Init(args);
myself = MPI.COMM_WORLD.Rank();
tasks = MPI.COMM_WORLD.Size();
if (tasks > 8) {
if (myself == 0) System.out.println("scattervO must run with fewer than 8 tasks!");
MPI.Finalize();
return;
}
int root, i = 0, j, k, stride = 15;
test out[] = new test[tasks * stride];
test in[] = new test[MAXLEN];
int dis[] = new int[tasks];
int scount[] = new int[tasks];
for (i = 0; i < MAXLEN; i++) {
in[i] = new test();
in[i].a = 0;
}
for (i = 0; i < tasks; i++) {
dis[i] = i * stride;
scount[i] = 5;
}
scount[0] = 10;
for (i = 0; i < tasks * stride; i++) {
out[i] = new test();
out[i].a = i;
}
MPI.COMM_WORLD.Scatterv(out, 0, scount, dis, MPI.OBJECT, in, 0, scount[myself], MPI.OBJECT, 0);
String[] messbuf = new String[1];
if (myself == 0) {
System.out.println("Original array on root...");
for (i = 0; i < tasks * stride; i++) System.out.print(out[i].a + " ");
System.out.println();
System.out.println();
System.out.println("Result on proc 0...");
System.out.println("Stride = 15 " + "Count = " + scount[0]);
for (i = 0; i < MAXLEN; i++) System.out.print(in[i].a + " ");
System.out.println();
System.out.println();
// Reproduces output of original test case, but deterministically
int nmess = tasks < 3 ? tasks : 3;
for (int t = 1; t < nmess; t++) {
MPI.COMM_WORLD.Recv(messbuf, 0, 1, MPI.OBJECT, t, 0);
System.out.print(messbuf[0]);
}
}
if (myself == 1) {
StringBuffer mess = new StringBuffer();
mess.append("Result on proc 1...\n");
mess.append("Stride = 15 " + "Count = " + scount[1] + "\n");
for (i = 0; i < MAXLEN; i++) mess.append(in[i].a + " ");
mess.append("\n");
mess.append("\n");
messbuf[0] = mess.toString();
MPI.COMM_WORLD.Send(messbuf, 0, 1, MPI.OBJECT, 0, 0);
}
if (myself == 2) {
StringBuffer mess = new StringBuffer();
mess.append("Result on proc 2...\n");
mess.append("Stride = 15 " + "Count = " + scount[2] + "\n");
for (i = 0; i < MAXLEN; i++) mess.append(in[i].a + " ");
mess.append("\n");
messbuf[0] = mess.toString();
MPI.COMM_WORLD.Send(messbuf, 0, 1, MPI.OBJECT, 0, 0);
}
if (myself == 0) System.out.println("ScattervO TEST COMPLETE");
MPI.Finalize();
}