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// (c) 2018 Bruno Chareyre <bruno.chareyre@grenoble-inp.fr>
// (c) 2019 Deepak Kunhappan, <deepak.kunhappan@3sr-grenoble.fr> <deepak.kn1990@gmail.com>
#ifdef YADE_MPI
#include "Subdomain.hpp"
#include <lib/serialization/ObjectIO.hpp>
#include <core/BodyContainer.hpp>
#include <core/Interaction.hpp>
#include <core/InteractionContainer.hpp>
#include <core/InteractionLoop.hpp>
#include <core/MPIBodyContainer.hpp>
#include <core/State.hpp>
#include <pkg/common/Sphere.hpp>
#include <boost/iostreams/device/array.hpp>
#include <boost/iostreams/device/back_inserter.hpp>
#include <boost/iostreams/stream.hpp>
#include <boost/iostreams/stream_buffer.hpp>
#include <preprocessing/dem/Shop.hpp>
namespace yade { // Cannot have #include directive inside.
YADE_PLUGIN((Subdomain));
CREATE_LOGGER(Subdomain);
YADE_PLUGIN((Bo1_Subdomain_Aabb) /*(Bo1_Facet_Aabb)(Bo1_Box_Aabb)*/);
CREATE_LOGGER(Bo1_Subdomain_Aabb);
void Subdomain::setMinMax()
{
Scene* scene(Omega::instance().getScene().get()); // get scene
// Vector3r min, max;
Real inf = std::numeric_limits<Real>::infinity();
boundsMin = Vector3r(inf, inf, inf);
boundsMax = Vector3r(-inf, -inf, -inf);
if (ids.size() == 0) LOG_WARN("empty subdomain!");
if (ids.size() > 0 and Body::byId(ids[0], scene)->subdomain != scene->subdomain)
LOG_WARN("setMinMax executed with deprecated data (body->subdomain != scene->subdomain)");
for (const auto& id : ids) {
const shared_ptr<Body>& b = Body::byId(id, scene);
if (!b or !b->bound) continue;
if (!scene->isPeriodic) {
boundsMax = boundsMax.cwiseMax(b->bound->max);
boundsMin = boundsMin.cwiseMin(b->bound->min);
} else {
// if periodic, find the period of minbound, find size, wrap minbound based on period and add size to get maxbound (of body)
Vector3r inVsz = Vector3r(1. / scene->cell->getSize()[0], 1. / scene->cell->getSize()[1], 1. / scene->cell->getSize()[2]);
Vector3i period(Vector3i::Zero());
for (int i = 0; i != 3; ++i) {
period[i] = (int)(math::floor(b->state->pos[i] * inVsz[i]));
}
Vector3r wMax;
Vector3r wMin;
for (int i = 0; i != 3; ++i) {
wMin[i] = (period[i]) != 0 ? (b->bound->min[i] / period[i]) : (b->bound->min[i]);
wMax[i] = (period[i]) != 0 ? (b->bound->max[i] / period[i]) : (b->bound->max[i]);
}
boundsMax = boundsMax.cwiseMax(wMax);
boundsMin = boundsMin.cwiseMin(wMin);
}
}
}
// inspired by Integrator::slaves_set (Integrator.hpp)
void Subdomain::intrs_set(const boost::python::list& source)
{
int len = boost::python::len(source);
intersections.clear();
for (int i = 0; i < len; i++) {
boost::python::extract<std::vector<Body::id_t>> serialGroup(source[i]);
if (serialGroup.check()) {
intersections.push_back(serialGroup());
continue;
}
cerr << " ... failed" << endl;
PyErr_SetString(PyExc_TypeError, "intersections should be provided as a list of list of ids");
boost::python::throw_error_already_set();
}
}
void Subdomain::mIntrs_set(const boost::python::list& source)
{
int len = boost::python::len(source);
mirrorIntersections.clear();
for (int i = 0; i < len; i++) {
boost::python::extract<std::vector<Body::id_t>> serialGroup(source[i]);
if (serialGroup.check()) {
mirrorIntersections.push_back(serialGroup());
continue;
}
cerr << " ... failed" << endl;
PyErr_SetString(PyExc_TypeError, "intersections should be provided as a list of list of ids");
boost::python::throw_error_already_set();
}
}
boost::python::list Subdomain::intrs_get()
{
boost::python::list ret;
for (const auto& grp : intersections) {
ret.append(boost::python::list(grp));
}
return ret;
}
boost::python::list Subdomain::mIntrs_get()
{
boost::python::list ret;
for (const auto& grp : mirrorIntersections) {
ret.append(boost::python::list(grp));
}
return ret;
}
void Subdomain::setSubdomainIds(std::vector<Body::id_t> subdIds) { subdomains = subdIds; }
std::vector<Body::id_t> Subdomain::getSubdomainIds() const { return subdomains; }
void Subdomain::append(Body::id_t bId) { subdomains.push_back(bId); }
void Subdomain::appendList(const boost::python::list& lst)
{
unsigned sz = boost::python::len(lst);
for (unsigned i = 0; i != sz; ++i) {
subdomains.push_back(boost::python::extract<int>(lst[i]));
}
}
void Bo1_Subdomain_Aabb::go(const shared_ptr<Shape>& cm, shared_ptr<Bound>& bv, const Se3r& /*se3*/, const Body* /*b*/)
{
// LOG_WARN("Bo1_Subdomain_Aabb::go()")
scene = Omega::instance().getScene().get();
Subdomain* domain = static_cast<Subdomain*>(cm.get());
if (!bv) { bv = shared_ptr<Bound>(new Aabb); }
Aabb* aabb = static_cast<Aabb*>(bv.get());
aabb->min = domain->boundsMin;
aabb->max = domain->boundsMax;
return;
}
/********************dpk********************/
std::string Subdomain::serializeMPIBodyContainer(const shared_ptr<MPIBodyContainer>& container)
{
std::string strContainer;
boost::iostreams::back_insert_device<std::string> inserter(strContainer);
boost::iostreams::stream<boost::iostreams::back_insert_device<std::string>> s(inserter);
yade::ObjectIO::save<decltype(container), boost::archive::binary_oarchive>(s, "container", container);
s.flush();
return strContainer;
}
shared_ptr<MPIBodyContainer> Subdomain::deSerializeMPIBodyContainer(const char* strContainer, int sizeC)
{
shared_ptr<MPIBodyContainer> container(shared_ptr<MPIBodyContainer>(new MPIBodyContainer()));
boost::iostreams::basic_array_source<char> device(strContainer, sizeC);
boost::iostreams::stream<boost::iostreams::basic_array_source<char>> s(device);
yade::ObjectIO::load<decltype(container), boost::archive::binary_iarchive>(s, "container", container);
return container;
}
string Subdomain::fillContainerGetString(shared_ptr<MPIBodyContainer>& container, const std::vector<Body::id_t>& ids2)
{
container->insertBodyList(ids2);
std::string containerString = serializeMPIBodyContainer(container);
return containerString;
}
string Subdomain::idsToSerializedMPIBodyContainer(const std::vector<Body::id_t>& ids2)
{
shared_ptr<MPIBodyContainer> container(shared_ptr<MPIBodyContainer>(new MPIBodyContainer()));
container->insertBodyList(ids2);
return serializeMPIBodyContainer(container);
}
void Subdomain::clearSubdomainIds() { ids.clear(); }
void Subdomain::setIDstoSubdomain(boost::python::list& idList)
{ //Remark: probably no need for a function to assign a python list to vector<int>, boost::python does this very well.
unsigned int listSize = boost::python::len(idList);
for (unsigned int i = 0; i != listSize; ++i) {
int b_id = boost::python::extract<int>(idList[i]);
ids.push_back(b_id); // So it's not reset before filling?
}
}
void Subdomain::getRankSize()
{
if (!ranksSet) {
MPI_Comm_rank(selfComm(), &subdomainRank);
MPI_Comm_size(selfComm(), &commSize);
ranksSet = true;
} else {
return;
}
}
// driver function for merge operation // workers send bodies, master recieves, sets the bodies into bodycontainer, sets interactions in interactionContainer.
void Subdomain::mergeOp()
{
getRankSize();
sendAllBodiesToMaster();
recvBodyContainersFromWorkers();
if (subdomainRank == master) {
Scene* scene = Omega::instance().getScene().get();
bool ifMerge = true;
bool overWriteBodies = true;
processContainerStrings();
setBodiesToBodyContainer(scene, recvdBodyContainers, ifMerge, overWriteBodies);
recvdBodyContainers.clear();
bodiesSet = false; // reset flag for next merge op.
containersRecvd = false;
}
}
//unused at the moment, can be used to send and recv bodies between subdomains.
void Subdomain::setCommunicationContainers()
{
//here, we setup the serialized MPIBodyContainer (MPIBodyContainer to string). it is std::vector<std::pair<container(string), sendRank/recvRank> >
// fill the send container based on the ids from the intersection(local) map
//Send container
if (subdomainRank == master) { return; }
recvRanks.clear();
sendContainer.clear();
unsigned int zero = 0;
for (unsigned int i = 1; i != intersections.size(); ++i) {
if ((intersections[i].size() == zero) || (i == (unsigned)subdomainRank)) { continue; } // exclude self or if no intersections with others)
shared_ptr<MPIBodyContainer> container(shared_ptr<MPIBodyContainer>(new MPIBodyContainer()));
container->subdomainRank = subdomainRank; // used to identify the origin rank at the reciever side. (maybe not needed?)
std::string containerString = fillContainerGetString(container, intersections[i]);
sendContainer.push_back(std::make_pair(containerString, i));
}
//Recv container, here we just need the ranks for now.
for (unsigned int i = 1; i != remoteCount.size(); ++i) {
if ((static_cast<unsigned int>(subdomainRank) == i) || (!remoteCount[i])) { continue; }
recvRanks.push_back(i);
}
commContainer = true; //flag to check if the communicationContainers are set.
}
void Subdomain::sendContainerString()
{
//send the containers.
if (subdomainRank == master) { return; }
if (!commContainer) {
LOG_ERROR("communication containers are not set!");
return;
}
for (unsigned int i = 0; i != sendContainer.size(); ++i) {
MPI_Request request;
sendString(sendContainer[i].first, sendContainer[i].second, TAG_STRING + sendContainer[i].second, request);
mpiReqs.push_back(request); //FIXME will not work since we access by index...
}
}
void Subdomain::processContainerStrings()
{
//convert the recieved string buffers to MPIBodyContainer.
recvdBodyContainers.clear();
if (!containersRecvd) {
LOG_ERROR("containerStrings not recvd. Fail!");
return;
}
for (unsigned int i = 0; i != recvdStringSizes.size(); ++i) {
char* cbuf = recvdCharBuff[i];
int sz = recvdStringSizes[i];
cbuf[sz] = '\0';
shared_ptr<MPIBodyContainer> cntr(deSerializeMPIBodyContainer(cbuf, sz));
recvdBodyContainers.push_back(cntr);
}
//free the pointers
clearRecvdCharBuff(recvdCharBuff);
}
void Subdomain::sendAllBodiesToMaster()
{
// send all bodies from this subdomain to the master. Can be used for merge.
// (note to self: this can be improved based on the bisection decomposition.)
if (subdomainRank == master) { return; }
shared_ptr<MPIBodyContainer> container(shared_ptr<MPIBodyContainer>(new MPIBodyContainer()));
std::string s = fillContainerGetString(container, ids);
sendStringBlocking(s, master, TAG_BODY + master);
}
void Subdomain::sendBodies(const int receiver, const vector<Body::id_t>& idsToSend)
{
shared_ptr<MPIBodyContainer> container(shared_ptr<MPIBodyContainer>(new MPIBodyContainer()));
std::string s = idsToSerializedMPIBodyContainer(idsToSend);
stringBuff[receiver] = s;
MPI_Request req;
MPI_Isend(stringBuff[receiver].data(), s.size(), MPI_CHAR, receiver, TAG_BODY, selfComm(), &req);
sendBodyReqs.push_back(req);
}
void Subdomain::receiveBodies(const int sender)
{
// cout<<"receiving in "<<subdomainRank<<" from "<<sender<<" ";
int recv_size = probeIncomingBlocking(sender, TAG_BODY);
char* cbuf = new char[recv_size + 1];
recvBuffBlocking(cbuf, recv_size, TAG_BODY, sender);
cbuf[recv_size] = '\0';
shared_ptr<MPIBodyContainer> mpiBC(deSerializeMPIBodyContainer(cbuf, recv_size));
// cout<<mpiBC->bContainer.size()<<" bodies"<<endl;
std::vector<shared_ptr<MPIBodyContainer>> mpiBCVect(1, mpiBC); //setBodiesToBodyContainer needs a vector of MPIBodyContainer, so create one of size 1.
Scene* scene = Omega::instance().getScene().get();
setBodiesToBodyContainer(scene, mpiBCVect, false, /*overwriteBodies?*/ true);
delete[] cbuf;
}
void Subdomain::completeSendBodies()
{
processReqs(sendBodyReqs); // calls MPI_Wait on the reqs, cleans the vect of mpi Reqs
}
/********Functions exclusive to the master*************/
void Subdomain::initMasterContainer()
{
if (subdomainRank != master) { return; }
recvRanks.resize(commSize - 1);
for (unsigned i = 0; i != recvRanks.size(); ++i) {
recvRanks[i] = i + 1;
}
recvdStringSizes.resize(commSize - 1);
recvdCharBuff.resize(commSize - 1);
allocContainerMaster = true;
}
void Subdomain::recvBodyContainersFromWorkers()
{
if (subdomainRank != master) {
return;
} else if (subdomainRank == master) {
//if (! allocContainerMaster){ initMasterContainer(); std::cout << "init Done in MASTER " << subdomainRank << std::endl;}
for (int sourceRank = 1; sourceRank != commSize; ++sourceRank) {
int sz = probeIncomingBlocking(sourceRank, TAG_BODY + subdomainRank);
recvdStringSizes[sourceRank - 1] = sz;
int sztmp = sz + 1;
char* cbuf = new char[sztmp];
recvBuffBlocking(cbuf, sz, TAG_BODY + subdomainRank, sourceRank);
recvdCharBuff[sourceRank - 1] = cbuf;
}
containersRecvd = true;
}
}
//
// set all body properties from the recvd MPIBodyContainer
void Subdomain::setBodiesToBodyContainer(Scene* scene, std::vector<shared_ptr<MPIBodyContainer>>& containers, bool ifMerge, bool overwriteBodies)
{
// to be used when deserializing a recieved container.
shared_ptr<BodyContainer>& bodyContainer = scene->bodies;
for (unsigned int i = 0; i != containers.size(); ++i) {
shared_ptr<MPIBodyContainer>& mpiContainer = containers[i];
std::vector<shared_ptr<Body>>& bContainer = mpiContainer->bContainer;
for (auto bIter = bContainer.begin(); bIter != bContainer.end(); ++bIter) {
const shared_ptr<Body>& newBody = *(bIter);
// check if the body already exists in the existing bodycontainer
const Body::id_t& idx = newBody->id;
std::map<Body::id_t, shared_ptr<Interaction>> intrsToSet = newBody->intrs;
shared_ptr<Body>& b = (*bodyContainer)[idx];
if (!b) newBody->intrs.clear(); //we can clear here, interactions are stored in intrsToSet and will be reinserted
else
newBody->intrs = b->intrs; //keep interactions generated in current subdomain as they may not exist on the sender's side
if (ifMerge) newBody->material = scene->materials[newBody->material->id];
if (!b) bodyContainer->insertAtId(newBody, newBody->id);
else if (overwriteBodies) {
b = newBody;
bodyContainer->dirty = true;
bodyContainer->checkedByCollider = false;
}
for (auto mapIter = intrsToSet.begin(); mapIter != intrsToSet.end(); ++mapIter) {
const Body::id_t& id1 = mapIter->second->id1;
const Body::id_t& id2 = mapIter->second->id2;
if (ifMerge) {
if ((*bodyContainer)[id1] and (*bodyContainer)[id2]) { // we will insert interactions only when both bodies are inserted
/* FIXME: we should make really sure that we are not overwriting a live interaction with a deprecated one (possible solution: make all interactions between remote bodies virtual)*/
scene->interactions->insertInteractionMPI(mapIter->second);
}
} else {
if ((*bodyContainer)[id1] and (*bodyContainer)[id2]
and ((*bodyContainer)[id1]->subdomain == scene->subdomain
or (*bodyContainer)[id2]->subdomain == scene->subdomain)) {
// we will insert interactions only when both bodies are inserted
/* FIXME: we should make really sure that we are not overwriting a live interaction with a deprecated one (possible solution: make all interactions between remote bodies virtual)*/
scene->interactions->insertInteractionMPI(mapIter->second);
}
}
}
}
}
containers.clear();
bodiesSet = true;
}
void Subdomain::splitBodiesToWorkers(const bool& eraseWorkerIds)
{
if (!eraseWorkerIds) { return; }
shared_ptr<Scene> scene = Omega::instance().getScene();
shared_ptr<BodyContainer> bodyContainer = scene->bodies;
std::vector<std::vector<Body::id_t>> idsToSend;
if (subdomainRank == 0) {
idsToSend.resize(commSize - 1);
for (const auto& b : bodyContainer->body) {
if (!b->getIsSubdomain()) {
if (b->subdomain != master) { idsToSend[b->subdomain - 1].push_back(b->id); }
for (const auto& bIntrs : b->intrs) {
Body::id_t otherId;
shared_ptr<Interaction> I = bIntrs.second;
if (b->id == I->getId1()) {
otherId = I->getId2();
} else {
otherId = I->getId1();
}
const shared_ptr<Body>& otherBody = (*bodyContainer)[otherId];
if (otherBody->getIsSubdomain()) { idsToSend[otherBody->subdomain - 1].push_back(b->id); }
}
}
}
}
if ((subdomainRank != master) && (eraseWorkerIds)) {
for (const auto& b : bodyContainer->body) {
if (!b) { continue; }
if (b->subdomain == 0) { continue; }
if (!b->getIsSubdomain()) { bodyContainer->erase(b->id, true); }
}
clearSubdomainIds();
}
if (subdomainRank == master) {
for (unsigned rnk = 0; rnk != idsToSend.size(); ++rnk) {
const std::vector<Body::id_t>& workerIds = idsToSend[rnk];
shared_ptr<MPIBodyContainer> container(shared_ptr<MPIBodyContainer>(new MPIBodyContainer()));
std::string s = fillContainerGetString(container, workerIds);
sendStringBlocking(s, rnk + 1, TAG_BODY);
}
}
if (subdomainRank != master) {
receiveBodies(master);
for (const auto& b : bodyContainer->body) {
if (!b) { continue; }
if (!b->getIsSubdomain()) {
if (b->subdomain == subdomainRank) { ids.push_back(b->id); }
}
}
}
}
/*********************communication functions**************/
//blocking send and recv
void Subdomain::sendStringBlocking(std::string& s, int destRank, int tag) { MPI_Send(s.data(), s.size(), MPI_CHAR, destRank, tag, selfComm()); }
int Subdomain::probeIncomingBlocking(int sourceRank, int tag)
{
MPI_Status status;
MPI_Probe(sourceRank, tag, selfComm(), &status);
int sz;
MPI_Get_count(&status, MPI_CHAR, &sz);
return sz;
}
void Subdomain::recvBuffBlocking(char* cbuf, int cbufSz, int tag, int sourceRank)
{
MPI_Status status;
MPI_Recv(cbuf, cbufSz, MPI_CHAR, sourceRank, tag, selfComm(), &status);
}
//non-blocking calls --> Isend, Iprobe, Irecv, Waitall(); (we will use mpi_isend + mpi_wait and then mpi_probe followed by mpi_recv)
void Subdomain::sendString(std::string& s, int destRank, int tag, MPI_Request& request)
{
int len = s.size();
MPI_Isend(s.data(), len, MPI_CHAR, destRank, tag, selfComm(), &request); //
}
int Subdomain::probeIncoming(int sourceRank, int tag)
{
int flag = 0;
MPI_Status status;
while (!flag) {
MPI_Iprobe(sourceRank, tag, selfComm(), &flag, &status);
}
int sz;
MPI_Get_count(&status, MPI_CHAR, &sz);
return sz;
}
void Subdomain::recvBuff(char* cbuf, int cbufsZ, int sourceRank, MPI_Request& request)
{
MPI_Irecv(cbuf, cbufsZ, MPI_CHAR, sourceRank, TAG_STRING + subdomainRank, selfComm(), &request);
}
void Subdomain::processReqs(std::vector<MPI_Request>& mpiReqs2)
{
// mpiReqs shadows a member yade::Subdomain::mpiReqs
if (!mpiReqs2.size()) { return; }
for (unsigned int i = 0; i != mpiReqs2.size(); ++i) {
MPI_Status status;
MPI_Wait(&mpiReqs2[i], &status);
}
resetReqs(mpiReqs2);
}
void Subdomain::resetReqs(std::vector<MPI_Request>& mpiReqs2) { mpiReqs2.clear(); }
void Subdomain::processReqsAll(std::vector<MPI_Request>& mpiReqs2, std::vector<MPI_Status>& mpiStats)
{
for (unsigned int i = 0; i != mpiReqs2.size(); ++i) {
//MPI_Status status;
MPI_Waitall(1, &mpiReqs2[i], &mpiStats[i]);
}
mpiStats.clear();
resetReqs(mpiReqs2);
}
void Subdomain::clearRecvdCharBuff(std::vector<char*>& rcharBuff)
{
for (std::vector<char*>::iterator cIter = rcharBuff.begin(); cIter != rcharBuff.end(); ++cIter) {
delete[](*cIter);
}
if (subdomainRank != master) { rcharBuff.clear(); } // assuming master alwasy recieves from workers, hence the size of this vector for master is fixed.
}
void Subdomain::getMirrorIntersections()
{
/* warning : local intersections have to be generated first. */
std::vector<MPI_Request> interReqs;
mirrorIntersections.clear();
mirrorIntersections.resize(commSize);
//workers exchange their intersections.
if (subdomainRank != master) {
assert(intersections[subdomainRank].size());
//get procs to communicate.
const auto& interProcs = intersections[subdomainRank];
for (const auto& proc : interProcs) {
if (proc == master) continue;
const auto& interVec = intersections[proc];
MPI_Request req;
//send the intersections
MPI_Isend(&interVec.front(), (int)interVec.size(), MPI_INT, proc, TAG_INTERSECTIONS, selfComm(), &req);
interReqs.push_back(req);
}
// probe size of incoming intersections :
for (const auto& proc : interProcs) {
if (proc == master) continue;
MPI_Status status;
MPI_Probe(proc, TAG_INTERSECTIONS, selfComm(), &status);
int sz;
MPI_Get_count(&status, MPI_INT, &sz);
auto& mirrorVec = mirrorIntersections[proc];
mirrorVec.resize(sz);
}
// recv intersections..
for (const auto& proc : interProcs) {
if (proc == master) continue;
auto& mirrorVec = mirrorIntersections[proc];
MPI_Status stat;
MPI_Recv(&mirrorVec.front(), (int)mirrorVec.size(), MPI_INT, proc, TAG_INTERSECTIONS, selfComm(), &stat);
}
//complete the interactive send.
processReqs(interReqs);
}
//get intesections from master
std::vector<int> intrSzMaster;
if (subdomainRank == master) {
for (const auto& vec : intersections) {
intrSzMaster.push_back((int)vec.size());
}
} else {
intrSzMaster.resize(commSize);
}
//master bcasts it's size of intersections
MPI_Bcast(&intrSzMaster.front(), commSize, MPI_INT, master, selfComm());
// master sends intersections to those procs with size
if (subdomainRank == master) {
interReqs.clear();
int prc = 0;
for (auto& inters : intersections) {
if (inters.size() and prc != subdomainRank) {
MPI_Request req;
MPI_Isend(&inters.front(), (int)inters.size(), MPI_INT, prc, TAG_INTERSECTIONS, selfComm(), &req);
interReqs.push_back(req);
}
++prc;
}
}
// workers with intersection with master receives.
if (subdomainRank != master) {
if (intrSzMaster[subdomainRank] > 0) {
const auto& it = std::find(intersections[subdomainRank].begin(), intersections[subdomainRank].end(), master);
if (it == intersections[subdomainRank].end()) intersections[subdomainRank].push_back(master);
auto& vecMaster = mirrorIntersections[0];
vecMaster.clear();
vecMaster.resize(intrSzMaster[subdomainRank]);
// recv
MPI_Status stat;
MPI_Recv(&vecMaster.front(), (int)vecMaster.size(), MPI_INT, master, TAG_INTERSECTIONS, selfComm(), &stat);
}
}
//complete the interactive send in master's side.
if (subdomainRank == master) { processReqs(interReqs); }
}
/* Migrate bodies, translation of python functions */
Real Subdomain::boundOnAxis(Bound& b, const Vector3r& direction, bool min)
const //return projected extremum of an AABB in a particular direction (in the the '+' or '-' sign depending on 'min' )
{
Vector3r size = b.max - b.min;
Real extremum = 0;
for (unsigned k = 0; k < 3; k++)
extremum += math::abs(size[k] * direction[k]); // this is equivalent to taking the vertex maximizing projected length
if (min) extremum = -extremum;
extremum
+= (b.max + b.min)
.dot(direction); // should be *0.5 to be center of the box, but since we use 'size' instead of half-size everything is doubled, neutral in terms of ordering the boxes
return 0.5 * extremum;
}
std::vector<projectedBoundElem> Subdomain::projectedBoundsCPP(int otherSD, const Vector3r& otherSubDCM, const Vector3r& subDCM, bool useAABB)
{
std::vector<projectedBoundElem> pos;
const shared_ptr<Scene>& scene = Omega::instance().getScene();
const shared_ptr<Body>& otherSubdomainBody = (*scene->bodies)[subdomains[otherSD - 1]];
if (!otherSubdomainBody) {
LOG_ERROR("invalid subdomain id, perhaps not in intersection?, other subd = " << otherSD);
return pos;
}
//const shared_ptr<Subdomain>& otherSubD = YADE_PTR_CAST<Subdomain>(otherSubdomainBody->shape);
Vector3r pt1, pt2, axis;
if (useAABB) {
const auto& otherSubDBound = otherSubdomainBody->bound;
const auto& thisSubDBound = (*scene->bodies)[subdomains[subdomainRank - 1]]->bound;
pt1 = 0.5 * (thisSubDBound->min + thisSubDBound->max);
pt2 = 0.5 * (otherSubDBound->min + otherSubDBound->max);
} else {
pt1 = subDCM;
pt2 = otherSubDCM;
}
axis = pt2 - pt1;
axis.normalize();
// from intersections (bodies in this subdomain which has intersections with the other sd)
for (const auto& bId : intersections[otherSD]) {
const shared_ptr<Body>& b = (*scene->bodies)[bId];
if (!b or b->getIsSubdomain()) { continue; }
Real ps = boundOnAxis((*b->bound), axis, true);
projectedBoundElem pElem(ps, std::make_pair(subdomainRank, bId));
pos.push_back(pElem);
}
// from mirror intersections (bodies from other subdomain which has intersections with this sd)
for (const auto& bId : mirrorIntersections[otherSD]) {
const shared_ptr<Body>& b = (*scene->bodies)[bId];
if (!b or b->getIsSubdomain()) { continue; }
Real ps = boundOnAxis((*b->bound), axis, false);
projectedBoundElem pElem(ps, std::make_pair(otherSD, bId));
pos.push_back(pElem);
}
// sort
std::sort(pos.begin(), pos.end(), [](const auto& p1, const auto& p2) { return p1.first < p2.first; });
return pos;
}
std::vector<Body::id_t> Subdomain::medianFilterCPP(int otherSD, const Vector3r& otherSubDCM, const Vector3r& subDCM, int giveAway, bool useAABB)
{
std::vector<Body::id_t> idsToSend;
std::vector<projectedBoundElem> pos = projectedBoundsCPP(otherSD, otherSubDCM, subDCM, useAABB);
if (!pos.size()) LOG_ERROR("ERROR IN CALCULATING PROJECTED BOUNDS WITH SUBDOMAIN = " << otherSD << " from Subdomain = " << subdomainRank);
int firstJ = pos.size();
int lastI = 0;
for (int n = 0; n < (int)pos.size(); n++) {
if (pos[n].second.first != subdomainRank and n < firstJ) firstJ = n;
if (pos[n].second.first == subdomainRank) lastI = n;
}
int finalSize = std::max(0, (int)intersections[otherSD].size() - giveAway); // The desired final number on this side
if (finalSize > lastI) finalSize = lastI + 1;
if (finalSize < firstJ) finalSize = firstJ + 1;
for (int x = finalSize; x < (int)pos.size(); x++) // whatever is on the other side is given away
if (pos[x].second.first == subdomainRank) idsToSend.push_back(pos[x].second.second);
return idsToSend;
}
void Subdomain::migrateBodiesSend(const std::vector<Body::id_t>& sendIds, int destination)
{
const shared_ptr<Scene>& scene = Omega::instance().getScene();
const auto& thisSubd = subdomains[subdomainRank - 1];
for (const auto& bId : sendIds) {
const shared_ptr<Body>& bdy = (*scene->bodies)[bId];
if (!bdy) { LOG_ERROR("reassignBodies failed " << bId << " is not in subdomain " << subdomainRank << std::endl); }
bdy->subdomain = destination;
InteractionLoop::createExplicitInteraction(thisSubd, bId, false, true);
}
sendBodies(destination, sendIds);
}
// void Subdomain::migrateBodiesRecv()
void Subdomain::updateLocalIds(bool eraseRemoteMaster)
{
/* in case of the master proc and not eraseRemoteMaster the worker ids are updated */
if (subdomainRank != master) {
const shared_ptr<Scene>& scene = Omega::instance().getScene();
ids.clear();
for (const auto& b : (*scene->bodies)) {
if (!b) { continue; }
if ((b->subdomain == subdomainRank) && (!(b->getIsSubdomain()))) { ids.push_back(b->id); }
}
}
if (!eraseRemoteMaster) {
MPI_Status iSendstat;
MPI_Request iSendReq;
if (subdomainRank != master) { MPI_Isend(&ids.front(), (int)ids.size(), MPI_INT, master, 500, selfComm(), &iSendReq); }
if (subdomainRank == master) {
std::vector<std::vector<Body::id_t>> workerIdsVec;
workerIdsVec.resize(commSize - 1);
int worker = 1;
for (auto& workerId : workerIdsVec) {
MPI_Status status;
MPI_Probe(worker, 500, selfComm(), &status);
int sz;
MPI_Get_count(&status, MPI_INT, &sz);
workerId.resize(sz);
MPI_Recv(&workerId.front(), sz, MPI_INT, worker, 500, selfComm(), &status);
++worker;
}
// in master
const shared_ptr<Scene>& scene = Omega::instance().getScene();
worker = 1;
for (const auto& workerIds : workerIdsVec) {
for (const auto& bId : workerIds) {
(*scene->bodies)[bId]->subdomain = worker;
}
const auto& workerSubD = YADE_PTR_CAST<Subdomain>((*scene->bodies)[subdomains[worker - 1]]->shape);
workerSubD->ids = workerIds;
++worker;
}
}
if (subdomainRank != master) { MPI_Wait(&iSendReq, &iSendstat); }
}
}
void Subdomain::cleanIntersections(int otherDomain)
{
std::vector<Body::id_t> ints;
const shared_ptr<Scene>& scene = Omega::instance().getScene();
for (const auto& bId : intersections[otherDomain]) {
const shared_ptr<Body>& b = (*scene->bodies)[bId];
if (b && (b->subdomain == subdomainRank)) ints.push_back(bId);
}
intersections[otherDomain] = ints;
}
void Subdomain::updateNewMirrorIntrs(int otherDomain, const std::vector<Body::id_t>& newMirror) { mirrorIntersections[otherDomain] = newMirror; }
// Count interactions of a body with given subdomain
unsigned Subdomain::countIntsWith(Body::id_t body, Body::id_t someSubD, const shared_ptr<Scene>& scene) const
{
if (not Body::byId(body, scene)) {
LOG_WARN("invalid body id: " << body << " vs. sd " << someSubD << ", compared in " << subdomainRank);
return 0;
}
const auto& intrs = Body::byId(body, scene)->intrs;
return std::count_if(intrs.begin(), intrs.end(), [&](auto i) {
assert(scene->bodies->exists(i.first));
return (Body::byId(i.first, scene)->subdomain == someSubD and not Body::byId(i.first, scene)->getIsSubdomain());
});
}
vector<Body::id_t> Subdomain::filteredInts(Body::id_t someSubD, bool mirror) const
{
auto& intrs = mirror ? mirrorIntersections[someSubD] : intersections[someSubD];
std::vector<Body::id_t> filtered;
const shared_ptr<Scene>& scene = Omega::instance().getScene();
std::copy_if(intrs.begin(), intrs.end(), std::back_inserter(filtered), [&](auto i) {
return (this->countIntsWith(i, mirror ? scene->subdomain : someSubD, scene) > 0);
});
return filtered;
}
double Subdomain::filterIntersections()
{
// we don't touch intersections with zero yet, unsure it would work directly as it's a bit special
assert(intersections.size() == mirrorIntersections.size());
const shared_ptr<Scene>& scene = Omega::instance().getScene();
assert(scene->subdomain > 0); // this function should not be called by master
unsigned oldNum(0), newNum(0);
for (Body::id_t subd = 1; unsigned(subd) < intersections.size(); subd++)
if (subd != scene->subdomain) {
// PLEASE DON'T REMOVE THOSE COMMENTED DEBUG MESSAGES
// unsigned oldI(intersections[subd].size()), oldM(mirrorIntersections[subd].size());
oldNum += intersections[subd].size();
if (mirrorIntersections[subd].size() > 0) mirrorIntersections[subd] = filteredInts(subd, true);
if (intersections[subd].size() > 0) intersections[subd] = filteredInts(subd, false);
newNum += intersections[subd].size();
// LOG_WARN("SubD "<<scene->subdomain<<" suppressed "<<(oldI-intersections[subd].size())<<" / "<<oldI<<" vs. "<<subd);
// LOG_WARN("SubD "<<scene->subdomain<<" suppressed "<<(oldM-mirrorIntersections[subd].size())<<" / "<<oldM<<" from "<<subd);
}
// LOG_WARN("SubD "<<scene->subdomain<<" suppressed "<<oldNum-newNum<<" / "<<oldNum);
return (oldNum ? (oldNum - newNum) / double(oldNum) : 0); //return overall ratio of removed elements (low means useless)
}
} // namespace yade
#endif
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