void LUResolveMPI(int n,float resolving[][maxN])
{
//First We need to Matrix resolving, for it is common to initailize resolving in One process
array=MPI::FLOAT.Create_contiguous(n);
array.Commit();
//Then we need to Scatter the content of resolving
for(int i=0;i<n;i+=totalProcNum)
MPI::COMM_WORLD.Scatter(resolving+i, 1, array, resolving+i+nowProcID, 1, array, 0);
//This time we just assume that ProcNum can completely divide the Scale, then we finished
//We start the round
for(int nowRound=0;nowRound<n;nowRound++)
{
int master=nowRound%totalProcNum;
if(nowProcID==master)
for(int i=nowRound+1;i<n;i++)
buffer[i]=(resolving[nowRound][i]/=resolving[nowRound][nowRound]);
//Then we use broadcast let this part to all
MPI::COMM_WORLD.Bcast(buffer+nowRound+1,n-nowRound-1,MPI::INT,master);
//Now we can use the buffer Number to be calculate the number
for(int row=n-totalProcNum+nowProcID;row>=nowRound+1;row-=totalProcNum)
for(int column=nowRound+1;column<n;column++)
resolving[row][column]=resolving[row][column]-resolving[row][nowRound]*buffer[column];
}
//We finished calculate process
//Then we gather the whole matrix
for(int i=0;i<n;i+=totalProcNum)
MPI::COMM_WORLD.Gather(resolving+i+nowProcID,1,array,resolving+i,1,array,0);
//We finish gathering matrix
array.Free();
}
/*
* Build and commit a user-defined MPI Struct datatype.
*
* \param mpiType new MPI datatype (on output).
*/
void MpiStructBuilder::commit(MPI::Datatype& mpiType)
{
for (int i = 0; i < nMember_; ++i) {
addresses_[i] = addresses_[i] - base_;
}
mpiType =
MPI::Datatype::Create_struct(nMember_, counts_, addresses_, types_);
mpiType.Commit();
}
void runSimulation()
{
int outputFrequency = 1;
int maxSteps = 200;
double factor = pow(MPILayer().size(), 1.0/3.0);
Coord<3> baseDim(15, 15, 15);
Coord<3> dim(factor * baseDim.x(), factor * baseDim.y(), factor * baseDim.z());
MPI::Aint displacements[] = {0};
MPI::Datatype memberTypes[] = {MPI::CHAR};
int lengths[] = { sizeof(CELL) };
MPI::Datatype objType;
objType =
MPI::Datatype::Create_struct(1, lengths, displacements, memberTypes);
objType.Commit();
NBodyInitializer<CELL> *init = new NBodyInitializer<CELL>(dim, maxSteps);
// HiParSimulator::HiParSimulator<CELL, HiParSimulator::RecursiveBisectionPartition<3> > sim(
// init,
// MPILayer().rank() ? 0 : new TracingBalancer(new NoOpBalancer()),
// maxSteps,
// 1,
// objType);
SerialSimulator<CELL> sim(init);
if (MPILayer().rank() == 0) {
std::cout << "ranks: " << MPILayer().size() << "\n"
<< "dim: " << dim << "\n"
<< "serial1\n";
sim.addWriter(
new TracingWriter<CELL>(outputFrequency, init->maxSteps()));
}
long long tStart = Chronometer::timeUSec();
sim.run();
long long tEnd = Chronometer::timeUSec();
double seconds = 1e-6 * (tEnd - tStart);
double flops =
// time steps * grid size
1.0 * maxSteps * dim.prod() *
// interactions per container update
27 * CELL::SIZE * CELL::SIZE *
// FLOPs per interaction
(3 + 6 + 1 + 6);
double gflops = 1e-9 * flops / seconds;
std::cout << "GFLOPS: " << gflops << "\n"
<< "----------------------------------------------------------------------\n";
}
void
ParaSolverTerminationStateMpi::receive(
ParaComm *comm,
int source,
int tag
)
{
DEF_PARA_COMM( commMpi, comm);
MPI::Datatype datatype;
datatype = createDatatype();
datatype.Commit();
PARA_COMM_CALL(
commMpi->receive(&interrupted, 1, datatype, source, tag)
);
datatype.Free();
}
void
ParaSolverTerminationStateMpi::send(
ParaComm *comm,
int destination,
int tag
)
{
DEF_PARA_COMM( commMpi, comm);
MPI::Datatype datatype;
datatype = createDatatype();
datatype.Commit();
PARA_COMM_CALL(
commMpi->send(&interrupted, 1, datatype, destination, tag)
);
datatype.Free();
}
void
ParaCalculationStateMpi::receive(
ParaComm *comm,
int source,
int tag
)
{
DEF_PARA_COMM( commMpi, comm);
MPI::Datatype datatype;
datatype = createDatatype();
datatype.Commit();
PARA_COMM_CALL(
commMpi->receive(&compTime, 1, datatype, source, tag)
);
datatype.Free();
}
void
ParaCalculationStateMpi::send(
ParaComm *comm,
int destination,
int tag
)
{
DEF_PARA_COMM( commMpi, comm);
MPI::Datatype datatype;
datatype = createDatatype();
datatype.Commit();
PARA_COMM_CALL(
commMpi->send(&compTime, 1, datatype, destination, tag)
);
datatype.Free();
}
int main(int argc, char* argv[]) {
MPI::Init(argc, argv);
rank = MPI::COMM_WORLD.Get_rank();
size = MPI::COMM_WORLD.Get_size();
if (size < 2 || size > 32) MPI::COMM_WORLD.Abort(1);
int brojVrsta = size - 1,
brojKolona;
if (0 == rank) {
// master
pline(); cout << "broj kolona matrice: ";
fflush(stdout); cin >> brojKolona;
for (int i=1; i<brojVrsta+1; i++)
MPI::COMM_WORLD.Send(&brojKolona, 1, MPI::INT, i, 0);
if (brojKolona <= 0 || brojKolona > 100) MPI::COMM_WORLD.Abort(1);
pline(); cout << "ucitaj elemente matrice " << "[" << brojVrsta << "][" << brojKolona << "]" << endl;
MPI::Datatype VRSTA = MPI::DOUBLE.Create_contiguous(brojKolona);
VRSTA.Commit();
double matrica[brojVrsta][brojKolona];
for (int i=0; i<brojVrsta; i++) {
for (int j=0; j<brojKolona; j++) {
fflush(stdout);
cin >> matrica[i][j];
}
}
for (int i=0; i<brojVrsta; i++) {
MPI::COMM_WORLD.Send(matrica[i], 1, VRSTA, i+1, 0);
}
VRSTA.Free();
}
int main(int argc, char **argv)
{
MPI::Init(argc, argv);
QApplication app(argc, argv);
LibGeoDecomp::Typemaps::initializeMaps();
MPI::Aint displacements[] = {0};
MPI::Datatype memberTypes[] = {MPI::CHAR};
int lengths[] = {sizeof(CanvasCell)};
MPI::Datatype objType;
objType =
MPI::Datatype::Create_struct(1, lengths, displacements, memberTypes);
objType.Commit();
MPI::Datatype particleType;
lengths[0] = sizeof(Particle);
particleType =
MPI::Datatype::Create_struct(1, lengths, displacements, memberTypes);
particleType.Commit();
ParticleWidget *widget = 0;
CanvasInitializer *init = getInit1();
HiParSimulator<CanvasCell, RecursiveBisectionPartition<2> > *sim = new HiParSimulator<CanvasCell, RecursiveBisectionPartition<2> >(
init,
MPILayer().rank() ? 0 : new NoOpBalancer(),
1000,
1,
particleType);
std::cout << "Simulator created ...\n";
// HiParSimulator<CanvasCell, RecursiveBisectionPartition<2> > sim(
// new CanvasInitializer(dim.x(), dim.y()),
// MPILayer().rank() ? 0 : new NoOpBalancer(),
// 1000,
// 1,
// particleType);
ForceSteerer *steerer = new ForceSteerer(1);
sim->addSteerer(steerer);
std::cout << "Steerer added ...\n";
Storage * storage = 0;
if (MPILayer().rank() == 0) {
storage = new Storage;
widget = new ParticleWidget(*storage, init->gridDimensions(), Qt::black);
widget->resize(1000, 500);
widget->show();
std::cout << "Widget created ...\n";
}
sim->addWriter(new TracingWriter<CanvasCell>(100, 100000));
sim->addWriter(new ParticleWriter(storage, init->gridDimensions(), 1, particleType));
FakeSimulator fakeSim(sim);
// DebugOutput logger;
QTimer timer;
QTimer timerGL;
QObject::connect(&timer, SIGNAL(timeout()),
&fakeSim, SLOT(step()));
// QObject::connect(&widget, SIGNAL(newFrame()),
// &logger, SLOT(newFrame()));
// QObject::connect(&widget, SIGNAL(forceRecorded(QPoint, QPoint)),
// &logger, SLOT(addForce(QPoint, QPoint)));
QObject::connect(storage, SIGNAL(forceRecorded(QVector2D, QVector2D)),
steerer, SLOT(addForce(QVector2D, QVector2D)));
QObject::connect(&timerGL, SIGNAL(timeout()), widget, SLOT(updateGL()));
timer.start(10);
timerGL.start(10);
app.exec();
delete sim;
MPI::Finalize();
}
static vector<int> kmeans(const vector<string> &dnas, int k) {
int rank = MPI::COMM_WORLD.Get_rank();
int size = MPI::COMM_WORLD.Get_size();
int dnaLength = dnas[0].length();
//Define the string for dna as MPI type
MPI::Datatype dnaType = MPI::CHAR.Create_contiguous(dnaLength + 1);
dnaType.Commit();
//Define the class Bases as MPI type
MPI::Datatype basesType, oldTypes[1];
MPI::Aint offsets[1];
int blockCounts[1];
oldTypes[0] = MPI::INT;
offsets[0] = 0;
blockCounts[0] = 4;
basesType = MPI::Datatype::Create_struct(1, blockCounts, offsets, oldTypes);
basesType.Commit();
vector<pair<int, int> > tasks(devideTasks(size, dnas.size()));
int startIndex = tasks[rank].first;
int endIndex = tasks[rank].second;
vector<string> prevCenters(k, string(dnaLength, 'A'));
vector<string> centers(k);
if (isMaster(rank)) {
centers = select_centers(dnas, k);
}
vector<int> belonging(dnas.size());
char *buffer = new char[dnaLength + 1];
while (true) {
//Send the new centers to all tasks
if (isMaster(rank)) {
for (int i = 0; i < size; i++) {
if (!isMaster(i)) {
for (int j = 0; j < k; j++) {
MPI::COMM_WORLD.Send(centers[j].c_str(), 1, dnaType, i, DEFAULT_TAG);
}
}
}
}
//All tasks update their centers
if (!isMaster(rank)) {
for (int j = 0; j < k; j++) {
MPI::COMM_WORLD.Recv(buffer, 1, dnaType, MASTER_RANK, DEFAULT_TAG);
centers[j] = buffer;
}
}
MPI::COMM_WORLD.Barrier();
if (equal(centers.begin(), centers.end(), prevCenters.begin())) {
break;
}
prevCenters = centers;
vector<vector<Bases> > sumClusters(k, vector<Bases>(dnaLength));
for (int i = startIndex; i < endIndex; i++) {
int min_dis = numeric_limits<int>::max();
int belong;
for (int j = 0; j < k; ++j) {
int dis = cal_dis(dnas[i], centers[j]);
if (dis < min_dis) {
min_dis = dis;
belong = j;
}
}
belonging[i] = belong;
for (int j = 0; j < dnaLength; j++) {
int idx = get_idx(dnas[i][j]);
sumClusters[belong][j].increase(idx);
}
}
if (!isMaster(rank)) {
for (int i = 0; i < k; i++) {
MPI::COMM_WORLD.Send(&(sumClusters[i][0]), dnaLength, basesType, MASTER_RANK, DEFAULT_TAG);
}
}
if (isMaster(rank)) {
vector<vector<Bases> > aggrSumClusters(k, vector<Bases>(dnaLength));
for (int i = 0; i < k; i++) {
for (int j = 0; j < dnaLength; j++) {
aggrSumClusters[i][j] += sumClusters[i][j];
//cout << "cluster " << i << " dna " << j << " count " << aggrSumClusters[i][j].get_max() << endl;
}
}
for (int i = 0; i < size; i++) {
if (isMaster(i)) {
continue;
}
for (int j = 0; j < k; j++) {
MPI::COMM_WORLD.Recv(&(sumClusters[j][0]), dnaLength, basesType, i, DEFAULT_TAG);
}
for (int j = 0; j < k; j++) {
for (int n = 0; n < dnaLength; n++) {
aggrSumClusters[j][n] += sumClusters[j][n];
}
}
}
for (int i = 0; i < centers.size(); ++i) {
string center;
for (int j = 0; j < dnas[0].size(); ++j) {
center += get_base(aggrSumClusters[i][j].get_max());
}
centers[i] = center;
}
}
MPI::COMM_WORLD.Barrier();
}
delete[] buffer;
if (!isMaster(rank)) {
MPI::COMM_WORLD.Send(&belonging[startIndex], endIndex - startIndex, MPI::INT, MASTER_RANK, DEFAULT_TAG);
}
if (isMaster(rank)) {
for (int i = 0; i < size; i++) {
if (isMaster(i)) {
continue;
}
int taskStart = tasks[i].first;
int taskEnd = tasks[i].second;
MPI::COMM_WORLD.Recv(&belonging[taskStart], taskEnd - taskStart, MPI::INT, i, DEFAULT_TAG);
}
}
return belonging;
}
void PPS::start(){
//Define parameters struct for mpi
//Refer to this as an example http://lists.mcs.anl.gov/pipermail/mpich-discuss/2009-April/004880.html
MPI::Datatype MPIPPSTRUCT;
int blockcounts[2];
MPI::Aint offsets[2];
MPI::Datatype datatypes[2];
MPI::Aint extent,lb;
blockcounts[0] = 9; //Number of ints
blockcounts[1] = 13; //number of __fpv
datatypes[0] = MPI::INT;
datatypes[1] = MPIFPV;
offsets[0] = 0;
MPI::INT.Get_extent(lb, extent);
offsets[1] = blockcounts[0] * extent;
MPIPPSTRUCT = MPIPPSTRUCT.Create_struct(2,blockcounts,offsets, datatypes);
MPIPPSTRUCT.Commit();
if(PPS::pid == 0){
struct parameters temp;
int start,i,countdown = PPS::comm_size-1;
bool ready = false;
MPI::Status status;
//Logs
std::ofstream logsfile;
logsfile.open("tslogs.txt", std::fstream::out | std::fstream::trunc);
while(true){
if(countdown == 0) break;
//Check first ready-to-compute process
MPI::COMM_WORLD.Recv(&ready, 1, MPI::BOOL, MPI_ANY_SOURCE, 0, status);
//Logs
logsfile << "Remaining sims: " << PPS::plist.size() << " process countdown: " << countdown << std::endl;
//Send a 0 status to all the process to stop
if(ready){
if(PPS::plist.size() == 0 ){
start = EXIT_PROCESS;
MPI::COMM_WORLD.Send(&start, 1, MPI::INT, status.Get_source(), 0);
countdown = countdown - 1;
}else{
//Prepare him to receive the params and start the sim (an int that contains the simulation number (-1 = exit))
start = PPS::plist.size() - 1;
MPI::COMM_WORLD.Send(&start, 1, MPI::INT, status.Get_source(), 0);
temp = PPS::plist.back();
//temp.N = status.Get_source() * 10;
//Deploy the parameterer struct
MPI::COMM_WORLD.Send(&temp, 1, MPIPPSTRUCT, status.Get_source(), 0);
//Pullout the parameter struct from the list
plist.pop_back();
}
}
ready = false;
}
logsfile.close();
}else{
int status;
bool ready = true;
struct parameters recvparams;
while(true){
status == EXIT_PROCESS;
//Send with a point to point that you are free
MPI::COMM_WORLD.Send(&ready, 1, MPI::BOOL, 0, 0);
//receive status value to exit or to receive a new params struct to start new sim
MPI::COMM_WORLD.Recv(&status, 1, MPI::INT, 0, 0);
if(status != EXIT_PROCESS){
//wait to receive parameters
//std::this_thread::sleep_for(std::chrono::seconds(PPS::pid));
MPI::COMM_WORLD.Recv(&recvparams, 1, MPIPPSTRUCT, 0, 0);
//Start sim
//std::cout << "//////////////////////////////////////////////////////////////////////////////////"<< std::endl;
//std::cout << "SAY HI: "<< PPS::pid << std::endl;
//print_params(recvparams);
//std::cout << "STARTING REAL SIM"<< std::endl;
PottsSim(recvparams,"output/"+ std::to_string(PPS::pid) + "_proc_output.dat", status);
//old_code( PPS::pid );
//std::cout << "//////////////////////////////////////////////////////////////////////////////////"<< std::endl;
}else{
std::cout << "I'm the process "<< PPS::pid << ", ready to die." << std::endl;
break;
}
}
}
MPIPPSTRUCT.Free();
}