ReturnType SendCouplingMDCommand::executeTransfer ()
{
SteereoStream resultStream;
CouplingInformationType* couplingInfo = (CouplingInformationType*) this->getData(0);
Simulation* theSim = (Simulation*) this->getData(1);
//ParticleContainer* moleculeContainer = theSim->getMolecules();
/*int direction = borderToLook / 2;
int otherdir1 = (direction + 1) % 3;
int otherdir2 = (direction + 2) % 3;
resultStream << moleculeContainer->getBoundingBoxMax(direction);
resultStream << moleculeContainer->getBoundingBoxMax(otherdir1) << moleculeContainer->getBoundingBoxMax(otherdir2);
logger->debug() << "I will now execute the transfer of the SendCouplingMDCommand" << std::endl;
logger->debug() << "borderToLook is " << borderToLook << std::endl;*/
for (int i = 0; i < couplingInfo->numberOfBoundaries; i++)
{
logger->debug() << "For boundary " << i << " I will transfer " << transferContainer[i].size() << " molecules" << std::endl;
std::vector<Molecule>::iterator molIt = transferContainer[i].begin();
resultStream.allocateMemory(7 * transferContainer[i].size() * sizeof(double) + sizeof(int));
resultStream << (int) transferContainer[i].size();
while (molIt != transferContainer[i].end()) {
resultStream << (theSim->getDomain()->getComponents())[molIt->componentid()].m();
resultStream << molIt->r(0) << molIt->r(1) << molIt->r(2) << molIt->v(0) << molIt->v(1) << molIt->v(2);
molIt++;
}
transferContainer[i].clear();
}
this->getCommunicator()->sendStream (this->getConnection()->getDataConnection(), resultStream);
return EXECUTED;
}
ReturnType SnapshotCommand::execute ()
{
#ifdef ENABLE_MPI
int myRank, mySize;
MPI_Comm_size (MPI_COMM_WORLD, &mySize);
MPI_Comm_rank (MPI_COMM_WORLD, &myRank);
#else
logger->debug() << "----------------->Not Parallel snapshot " << std::endl;
//return EXECUTED;
#endif
Domain* dom = sim -> getDomain ();
int numberOfComponents = dom -> getComponents().size();
SteereoStream daStream;
SteereoStream outStream;
int counter = 0;
#ifdef ENABLE_MPI
int* molNumbers = NULL;
int* dataSizes = NULL;
int* displ = NULL;
int baseDispl = 0;
#endif
int factor = 3 + sendForces + sendVelocity + sendV2;
//int offset = sendV2Max;
// at the moment the simulation area extents need 6 floats
int offset = 7;
ParticleContainer* m_molecules = sim -> getMolecules ();
#ifdef ENABLE_MPI
int anzahl_mol = sim -> getDomain () -> getglobalNumMolecules ();
#endif
int local_mol = m_molecules->getNumberOfParticles();
#ifdef ENABLE_MPI
if (myRank == 0)
{
outStream.allocateMemory (factor * anzahl_mol * sizeof(float) + offset * sizeof(float));
}
// The stream will only be used for sending. And we will send maximally 3*sizeof(float) * local_mol at once
daStream.allocateMemory (3 * local_mol * sizeof(float));
#else
daStream.allocateMemory(factor * local_mol * sizeof(float) + offset * sizeof(float));
#endif
//send the extents of the domain
daStream << (float) 0.0 << (float) 0.0 << (float) 0.0;
daStream << (float) dom->getGlobalLength(0) << (float) dom->getGlobalLength(1) << (float) dom->getGlobalLength(2);
daStream << (int) numberOfComponents;
#ifdef ENABLE_MPI
if (myRank == 0)
{
molNumbers = new int [mySize];
dataSizes = new int [mySize];
}
MPI_Gather (&local_mol, 1, MPI_INT, molNumbers, 1, MPI_INT, 0, MPI_COMM_WORLD );
if (myRank == 0)
{
displ = new int[mySize];
displ[0] = 0;
dataSizes[0] = molNumbers[0] * 3 * sizeof(float);
for (int i = 1; i < mySize; i++)
{
displ[i] = displ[i-1] + dataSizes[i-1];
dataSizes[i] = molNumbers[i] * 3 * sizeof(float);
std::cout << "MolNumber ["<< i-1 << "]: " << molNumbers[i-1] << std::endl;
}
std::cout << "MolNumber ["<< mySize-1 << "]: " << molNumbers[mySize-1] << std::endl;
}
#endif
Molecule* pos = NULL;
double crit = 0.0;
for (pos = m_molecules->begin (); pos != m_molecules->end (); pos = m_molecules->next ()) {
//crit = pos->r(0) * pos->r(0) + pos->r(1) * pos->r(1) + pos->r(2) * pos->r(2);
daStream << (float) pos->r(0);
daStream << (float) pos->r(1);
daStream << (float) pos->r(2);
counter++;
}
#ifdef ENABLE_MPI
MPI_Gatherv (daStream.getStream(), local_mol * 3 * sizeof(float), MPI_CHAR, outStream.getStream (), dataSizes, displ, MPI_CHAR, 0, MPI_COMM_WORLD);
daStream.resetActPos();
daStream.resetReadPos();
#endif
float tempF = 0.0;
if (sendForces)
{
for (pos = m_molecules->begin (); pos != m_molecules->end (); pos = m_molecules->next ())
{
tempF = pos->F(0) * pos->F(0) + pos->F(1) * pos->F(1) + pos->F(2) * pos->F(2);
tempF = sqrt(tempF);
/*daStream << (float) pos->F(0);
daStream << (float) pos->F(1);
daStream << (float) pos->F(2);*/
daStream << tempF;
}
#ifdef ENABLE_MPI
if (myRank == 0)
{
baseDispl = displ[mySize-1] + dataSizes[mySize-1];
displ[0] = baseDispl;
dataSizes[0] = molNumbers[0] * sizeof(float);
for (int i = 1; i < mySize; i++)
{
displ[i] = displ[i-1] + dataSizes[i-1];
dataSizes[i] = molNumbers[i] * sizeof(float);
}
}
MPI_Gatherv (daStream.getStream(), local_mol * sizeof(float), MPI_CHAR, outStream.getStream (), dataSizes, displ, MPI_CHAR, 0, MPI_COMM_WORLD);
daStream.resetActPos();
daStream.resetReadPos();
#endif
}
if (sendVelocity)
{
float vel = 0;
for (pos = m_molecules->begin (); pos != m_molecules->end (); pos = m_molecules->next ())
{
vel = sqrt (pos->v2());
/*daStream << (float) pos->v(0);
daStream << (float) pos->v(1);
daStream << (float) pos->v(2);*/
daStream << vel;
}
#ifdef ENABLE_MPI
if (myRank == 0)
{
baseDispl = displ[mySize-1] + dataSizes[mySize-1];
displ[0] = baseDispl;
dataSizes[0] = molNumbers[0] * sizeof(float);
for (int i = 1; i < mySize; i++)
{
displ[i] = displ[i-1] + dataSizes[i-1];
dataSizes[i] = molNumbers[i] * sizeof(float);
}
}
MPI_Gatherv (daStream.getStream(), local_mol * sizeof(float), MPI_CHAR, outStream.getStream(), dataSizes, displ, MPI_CHAR, 0, MPI_COMM_WORLD);
daStream.resetActPos();
daStream.resetReadPos();
#endif
}
float v2max = 0;
if (sendV2)
{
float v2 = 0;
for (pos = m_molecules->begin (); pos != m_molecules->end (); pos = m_molecules->next ())
{
v2 = pos->v2();
v2max = v2 > v2max ? v2 : v2max;
daStream << v2;
}
#ifdef ENABLE_MPI
if (myRank == 0)
{
baseDispl = displ[mySize-1] + dataSizes[mySize-1];
displ[0] = baseDispl;
std::cout << "0: " << displ[0] << std::endl;
dataSizes[0] = molNumbers[0] * sizeof(float);
std::cout << "datasize[0]: " << dataSizes[0] << std::endl;
for (int i = 1; i < mySize; i++)
{
displ[i] = displ[i-1] + dataSizes[i-1];
dataSizes[i] = molNumbers[i] * sizeof(float);
std::cout << "i: " << displ[i] << std::endl;
}
}
MPI_Gatherv (daStream.getStream(), local_mol * sizeof(float), MPI_CHAR, outStream.getStream(), dataSizes, displ, MPI_CHAR, 0, MPI_COMM_WORLD);
#endif
/*if (sendV2Max)
{
daStream << v2max;
}*/
}
#ifdef ENABLE_MPI
if (myRank == 0)
{
// std::cout << "snapshotCommand: assembled the data to be sent in a stream: " << outStream.getStreamSize() << " "<< counter <<std::endl;
this->getCommunicator()->sendStream (this->getConnection()->getDataConnection(), outStream);
// std::cout << "snapshotCommand: sent the stream" << std::endl;
}
#else
// std::cout << "snapshotCommand: assembled the data to be sent in a stream: " << daStream.getStreamSize() << " "<< counter <<std::endl;
this->getCommunicator()->sendStream (this->getConnection()->getDataConnection(), daStream);
// std::cout << "snapshotCommand: sent the stream" << std::endl;
#endif
if (stepInterval > 0)
{
return REPETITION_REQUESTED;
}
else
{
return EXECUTED;
}
}