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grid_synchronizer.cc
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			/**
			* @file grid_synchronizer.cc
			*
			* @author Nicolas Richart <nicolas.richart@epfl.ch>
			*
			* @date creation: Mon Oct 03 2011
			* @date last modification: Thu Jun 05 2014
			*
			* @brief implementation of the grid synchronizer
			*
			* @section LICENSE
			*
			* Copyright (©) 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
			* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
			*
			* Akantu is free software: you can redistribute it and/or modify it under the
			* terms of the GNU Lesser General Public License as published by the Free
			* Software Foundation, either version 3 of the License, or (at your option) any
			* later version.
			*
			* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
			* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
			* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
			* details.
			*
			* You should have received a copy of the GNU Lesser General Public License
			* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
			*
			*/

			/* -------------------------------------------------------------------------- */
			#include "grid_synchronizer.hh"
			#include "aka_grid_dynamic.hh"
			#include "mesh.hh"
			#include "fe_engine.hh"
			#include "static_communicator.hh"
			#include "mesh_io.hh"
			#include <iostream>

			/* -------------------------------------------------------------------------- */


			__BEGIN_AKANTU__

			/* -------------------------------------------------------------------------- */
			GridSynchronizer::GridSynchronizer(Mesh & mesh,
			const ID & id,
			MemoryID memory_id,
			const bool register_to_event_manager) :
			DistributedSynchronizer(mesh, id, memory_id, register_to_event_manager) {
			AKANTU_DEBUG_IN();

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			template <class E>
			GridSynchronizer * GridSynchronizer::createGridSynchronizer(Mesh & mesh,
			const SpatialGrid<E> & grid,
			SynchronizerID id,
			SynchronizerRegistry * synchronizer_registry,
			const std::set<SynchronizationTag> & tags_to_register,
			MemoryID memory_id,
			const bool register_to_event_manager) {
			AKANTU_DEBUG_IN();

			StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
			UInt nb_proc = comm.getNbProc();
			UInt my_rank = comm.whoAmI();

			GridSynchronizer & communicator = *(new GridSynchronizer(mesh, id, memory_id,
			register_to_event_manager));
			if(nb_proc == 1) return &communicator;

			UInt spatial_dimension = mesh.getSpatialDimension();

			Real * bounding_boxes = new Real[2 * spatial_dimension * nb_proc];
			Real * my_bounding_box = bounding_boxes + 2 * spatial_dimension * my_rank;

			// mesh.getLocalLowerBounds(my_bounding_box);
			// mesh.getLocalUpperBounds(my_bounding_box + spatial_dimension);

			const Vector<Real> & lower = grid.getLowerBounds();
			const Vector<Real> & upper = grid.getUpperBounds();
			const Vector<Real> & spacing = grid.getSpacing();

			for (UInt i = 0; i < spatial_dimension; ++i) {
			my_bounding_box[i ] = lower(i) - spacing(i);
			my_bounding_box[spatial_dimension + i] = upper(i) + spacing(i);
			}

			AKANTU_DEBUG_INFO("Exchange of bounding box to detect the overlapping regions.");

			comm.allGather(bounding_boxes, spatial_dimension * 2);

			bool * intersects_proc = new bool[nb_proc];
			std::fill_n(intersects_proc, nb_proc, true);

			Int * first_cells = new Int[3 * nb_proc];
			Int * last_cells = new Int[3 * nb_proc];
			std::fill_n(first_cells, 3 * nb_proc, 0);
			std::fill_n(first_cells, 3 * nb_proc, 0);

			ElementTypeMapArray<UInt> ** element_per_proc = new ElementTypeMapArray<UInt>* [nb_proc];
			for (UInt p = 0; p < nb_proc; ++p) element_per_proc[p] = NULL;

			// check the overlapping between my box and the one from other processors
			for (UInt p = 0; p < nb_proc; ++p) {
			if(p == my_rank) continue;

			Real * proc_bounding_box = bounding_boxes + 2 * spatial_dimension * p;

			bool intersects = false;
			Int * first_cell_p = first_cells + p * spatial_dimension;
			Int * last_cell_p = last_cells + p * spatial_dimension;
			for (UInt s = 0; s < spatial_dimension; ++s) {

			// check overlapping of grid
			intersects = Math::intersects(my_bounding_box[s],
			my_bounding_box[spatial_dimension + s],
			proc_bounding_box[s],
			proc_bounding_box[spatial_dimension + s]);

			intersects_proc[p] &= intersects;

			if(intersects) {
			AKANTU_DEBUG_INFO("I intersects with processor " << p << " in direction " << s);

			// is point 1 of proc p in the dimension s in the range ?
			bool point1 = Math::is_in_range(proc_bounding_box[s],
			my_bounding_box[s],
			my_bounding_box[s+spatial_dimension]);

			// is point 2 of proc p in the dimension s in the range ?
			bool point2 = Math::is_in_range(proc_bounding_box[s+spatial_dimension],
			my_bounding_box[s],
			my_bounding_box[s+spatial_dimension]);

			Real start = 0.;
			Real end = 0.;

			if(point1 && !point2) {
			/* \|-----------\| my_bounding_box(i)
			* \|-----------\| proc_bounding_box(i)
			* 1 2
			*/
			start = proc_bounding_box[s];
			end = my_bounding_box[s+spatial_dimension];

			AKANTU_DEBUG_INFO("Intersection scheme 1 in direction " << s << " with processor " << p << " [" << start << ", " << end <<"]");
			} else if(point1 && point2) {
			/* \|-----------------\| my_bounding_box(i)
			* \|-----------\| proc_bounding_box(i)
			* 1 2
			*/
			start = proc_bounding_box[s];
			end = proc_bounding_box[s+spatial_dimension];

			AKANTU_DEBUG_INFO("Intersection scheme 2 in direction " << s << " with processor " << p << " [" << start << ", " << end << "]");
			} else if(!point1 && point2) {
			/* \|-----------\| my_bounding_box(i)
			* \|-----------\| proc_bounding_box(i)
			* 1 2
			*/
			start = my_bounding_box[s];
			end = proc_bounding_box[s+spatial_dimension];

			AKANTU_DEBUG_INFO("Intersection scheme 3 in direction " << s << " with processor " << p << " [" << start << ", " << end <<"]");
			} else {
			/* \|-----------\| my_bounding_box(i)
			* \|-----------------\| proc_bounding_box(i)
			* 1 2
			*/
			start = my_bounding_box[s];
			end = my_bounding_box[s+spatial_dimension];

			AKANTU_DEBUG_INFO("Intersection scheme 4 in direction " << s << " with processor " << p << " [" << start << ", " << end <<"]");
			}


			first_cell_p[s] = grid.getCellID(start, s);
			last_cell_p [s] = grid.getCellID(end, s);
			}
			}


			//create the list of cells in the overlapping
			typedef typename SpatialGrid<E>::CellID CellID;

			std::vector<CellID> * cell_ids = new std::vector<CellID>;

			if(intersects_proc[p]) {
			AKANTU_DEBUG_INFO("I intersects with processor " << p);

			CellID cell_id(spatial_dimension);

			// for (UInt i = 0; i < spatial_dimension; ++i) {
			// if(first_cell_p[i] != 0) --first_cell_p[i];
			// if(last_cell_p[i] != 0) ++last_cell_p[i];
			// }

			for (Int fd = first_cell_p[0]; fd <= last_cell_p[0]; ++fd) {
			cell_id.setID(0, fd);
			if(spatial_dimension == 1) {
			cell_ids->push_back(cell_id);
			}
			else {
			for (Int sd = first_cell_p[1]; sd <= last_cell_p[1] ; ++sd) {
			cell_id.setID(1, sd);
			if(spatial_dimension == 2) {
			cell_ids->push_back(cell_id);
			} else {
			for (Int ld = first_cell_p[2]; ld <= last_cell_p[2] ; ++ld) {
			cell_id.setID(2, ld);
			cell_ids->push_back(cell_id);
			}
			}
			}
			}
			}

			// get the list of elements in the cells of the overlapping
			typename std::vector<CellID>::iterator cur_cell_id = cell_ids->begin();
			typename std::vector<CellID>::iterator last_cell_id = cell_ids->end();
			std::set<Element> * to_send = new std::set<Element>();

			for (; cur_cell_id != last_cell_id; ++cur_cell_id) {
			typename SpatialGrid<E>::Cell::const_iterator cur_elem = grid.beginCell(*cur_cell_id);
			typename SpatialGrid<E>::Cell::const_iterator last_elem = grid.endCell(*cur_cell_id);

			for (; cur_elem != last_elem; ++cur_elem) {
			to_send->insert(*cur_elem);
			}
			}

			AKANTU_DEBUG_INFO("I have prepared " << to_send->size() << " elements to send to processor " << p);

			std::stringstream sstr; sstr << "element_per_proc_" << p;
			element_per_proc[p] = new ElementTypeMapArray<UInt>(sstr.str(), id);
			ElementTypeMapArray<UInt> & elempproc = *(element_per_proc[p]);

			typename std::set<Element>::iterator elem = to_send->begin();
			typename std::set<Element>::iterator last_elem = to_send->end();
			for (; elem != last_elem; ++elem) {
			ElementType type = elem->type;
			UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);

			// /!\ this part must be slow due to the access in the ElementTypeMapArray<UInt>
			if(!elempproc.exists(type, _not_ghost))
			elempproc.alloc(0, nb_nodes_per_element, type, _not_ghost);

			UInt global_connect[nb_nodes_per_element];
			UInt * local_connect = mesh.getConnectivity(type).storage() + elem->element * nb_nodes_per_element;
			for (UInt i = 0; i < nb_nodes_per_element; ++i) {
			global_connect[i] = mesh.getNodeGlobalId(local_connect[i]);
			AKANTU_DEBUG_ASSERT(global_connect[i] < mesh.getNbGlobalNodes(),
			"This global node send in the connectivity does not seem correct "
			<< global_connect[i] << " corresponding to "
			<< local_connect[i] << " from element " << elem->element);
			}

			elempproc(type).push_back(global_connect);
			communicator.send_element[p].push_back(*elem);
			}

			delete to_send;
			}

			delete cell_ids;
			}


			delete [] first_cells;
			delete [] last_cells;
			delete [] bounding_boxes;

			AKANTU_DEBUG_INFO("I have finished to compute intersection,"
			<< " no it's time to communicate with my neighbors");

			/**
			* Sending loop, sends the connectivity asynchronously to all concerned proc
			*/
			std::vector<CommunicationRequest *> isend_requests;
			for (UInt p = 0; p < nb_proc; ++p) {
			if(p == my_rank) continue;
			if(intersects_proc[p]) {
			ElementTypeMapArray<UInt> & elempproc = *(element_per_proc[p]);

			ElementTypeMapArray<UInt>::type_iterator it_type = elempproc.firstType(_all_dimensions, _not_ghost);
			ElementTypeMapArray<UInt>::type_iterator last_type = elempproc.lastType (_all_dimensions, _not_ghost);

			UInt count = 0;
			for (; it_type != last_type; ++it_type) {
			Array<UInt> & conn = elempproc(*it_type, _not_ghost);
			UInt info[2];
			info[0] = (UInt) *it_type;
			info[1] = conn.getSize() * conn.getNbComponent();

			AKANTU_DEBUG_INFO("I have " << conn.getSize() << " elements of type " << *it_type
			<< " to send to processor " << p
			<< " (communication tag : " << Tag::genTag(my_rank, count, DATA_TAG) << ")");

			isend_requests.push_back(comm.asyncSend(info, 2, p, Tag::genTag(my_rank, count, SIZE_TAG)));
			if(info[1] != 0)
			isend_requests.push_back(comm.asyncSend<UInt>(conn.storage(),
			info[1],
			p, Tag::genTag(my_rank, count, DATA_TAG)));

			++count;
			}

			UInt info[2];
			info[0] = (UInt) _not_defined;
			info[1] = 0;
			isend_requests.push_back(comm.asyncSend(info, 2, p, Tag::genTag(my_rank, count, SIZE_TAG)));
			}
			}

			/**
			* Receives the connectivity and store them in the ghosts elements
			*/
			Array<UInt> & global_nodes_ids = const_cast<Array<UInt> &>(mesh.getGlobalNodesIds());
			Array<Int> & nodes_type = const_cast<Array<Int> &>(const_cast<const Mesh &>(mesh).getNodesType());
			std::vector<CommunicationRequest *> isend_nodes_requests;
			UInt nb_nodes_to_recv[nb_proc];
			UInt nb_total_nodes_to_recv = 0;
			UInt nb_current_nodes = global_nodes_ids.getSize();

			NewNodesEvent new_nodes;
			NewElementsEvent new_elements;

			Array<UInt> * ask_nodes_per_proc = new Array<UInt>[nb_proc];

			for (UInt p = 0; p < nb_proc; ++p) {
			nb_nodes_to_recv[p] = 0;
			if(p == my_rank) continue;

			Array<UInt> & ask_nodes = ask_nodes_per_proc[p];
			UInt count = 0;
			if(intersects_proc[p]) {
			ElementType type = _not_defined;
			do {
			UInt info[2] = { 0 };
			comm.receive(info, 2, p, Tag::genTag(p, count, SIZE_TAG));

			type = (ElementType) info[0];
			if(type != _not_defined) {
			UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);;
			UInt nb_element = info[1] / nb_nodes_per_element;

			Array<UInt> tmp_conn(nb_element, nb_nodes_per_element);
			tmp_conn.clear();
			if(info[1] != 0)
			comm.receive<UInt>(tmp_conn.storage(), info[1], p, Tag::genTag(p, count, DATA_TAG));

			AKANTU_DEBUG_INFO("I will receive " << nb_element << " elements of type " << ElementType(info[0])
			<< " from processor " << p
			<< " (communication tag : " << Tag::genTag(p, count, DATA_TAG) << ")");


			Array<UInt> & ghost_connectivity = const_cast<Array<UInt> &>(mesh.getConnectivity(type, _ghost));

			UInt nb_ghost_element = ghost_connectivity.getSize();
			Element element(type, 0, _ghost);

			UInt conn[nb_nodes_per_element];
			for (UInt el = 0; el < nb_element; ++el) {
			UInt nb_node_to_ask_for_elem = 0;

			for (UInt n = 0; n < nb_nodes_per_element; ++n) {
			UInt gn = tmp_conn(el, n);
			UInt ln = global_nodes_ids.find(gn);

			AKANTU_DEBUG_ASSERT(gn < mesh.getNbGlobalNodes(), "This global node seems not correct " << gn << " from element " << el << " node " << n);

			if(ln == UInt(-1)) {
			global_nodes_ids.push_back(gn);
			nodes_type.push_back(-3); // pure ghost node
			ln = nb_current_nodes;

			new_nodes.getList().push_back(ln);
			++nb_current_nodes;
			ask_nodes.push_back(gn);
			++nb_node_to_ask_for_elem;
			}

			conn[n] = ln;
			}

			// all the nodes are already known locally, the element should already exists
			UInt c = UInt(-1);
			if(nb_node_to_ask_for_elem == 0) {
			c = ghost_connectivity.find(conn);
			element.element = c;
			}

			if(c == UInt(-1)) {
			element.element = nb_ghost_element;
			++nb_ghost_element;
			ghost_connectivity.push_back(conn);
			new_elements.getList().push_back(element);
			}

			communicator.recv_element[p].push_back(element);
			}
			}
			count++;
			} while(type != _not_defined);

			AKANTU_DEBUG_INFO("I have " << ask_nodes.getSize()
			<< " missing nodes for elements coming from processor " << p
			<< " (communication tag : " << Tag::genTag(my_rank, 0, ASK_NODES_TAG) << ")");

			ask_nodes.push_back(UInt(-1));

			isend_nodes_requests.push_back(comm.asyncSend(ask_nodes.storage(), ask_nodes.getSize(),
			p, Tag::genTag(my_rank, 0, ASK_NODES_TAG)));
			nb_nodes_to_recv[p] = ask_nodes.getSize() - 1;
			nb_total_nodes_to_recv += nb_nodes_to_recv[p];
			}
			}

			comm.waitAll(isend_requests);
			comm.freeCommunicationRequest(isend_requests);

			for (UInt p = 0; p < nb_proc; ++p) {
			if(element_per_proc[p]) delete element_per_proc[p];
			}
			delete [] element_per_proc;

			/**
			* Sends requested nodes to proc
			*/
			Array<Real> & nodes = const_cast<Array<Real> &>(mesh.getNodes());
			UInt nb_nodes = nodes.getSize();

			std::vector<CommunicationRequest *> isend_coordinates_requests;
			Array<Real> * nodes_to_send_per_proc = new Array<Real>[nb_proc];
			for (UInt p = 0; p < nb_proc; ++p) {
			if(p == my_rank \|\| !intersects_proc[p]) continue;

			Array<UInt> asked_nodes;
			CommunicationStatus status;
			AKANTU_DEBUG_INFO("Waiting list of nodes to send to processor " << p
			<< "(communication tag : " << Tag::genTag(p, 0, ASK_NODES_TAG) << ")");

			comm.probe<UInt>(p, Tag::genTag(p, 0, ASK_NODES_TAG), status);
			UInt nb_nodes_to_send = status.getSize();
			asked_nodes.resize(nb_nodes_to_send);

			AKANTU_DEBUG_INFO("I have " << nb_nodes_to_send - 1
			<< " nodes to send to processor " << p
			<< " (communication tag : " << Tag::genTag(p, 0, ASK_NODES_TAG) << ")");

			AKANTU_DEBUG_INFO("Getting list of nodes to send to processor " << p
			<< " (communication tag : " << Tag::genTag(p, 0, ASK_NODES_TAG) << ")");

			comm.receive(asked_nodes.storage(), nb_nodes_to_send, p, Tag::genTag(p, 0, ASK_NODES_TAG));

			nb_nodes_to_send--;
			asked_nodes.resize(nb_nodes_to_send);

			Array<Real> & nodes_to_send = nodes_to_send_per_proc[p];
			nodes_to_send.extendComponentsInterlaced(spatial_dimension, 1);
			for (UInt n = 0; n < nb_nodes_to_send; ++n) {
			UInt ln = global_nodes_ids.find(asked_nodes(n));
			AKANTU_DEBUG_ASSERT(ln != UInt(-1), "The node [" << asked_nodes(n) << "] requested by proc " << p << " was not found locally!");
			nodes_to_send.push_back(nodes.storage() + ln * spatial_dimension);
			}

			if(nb_nodes_to_send != 0) {
			AKANTU_DEBUG_INFO("Sending the " << nb_nodes_to_send << " nodes to processor " << p
			<< " (communication tag : " << Tag::genTag(p, 0, SEND_NODES_TAG) << ")");

			isend_coordinates_requests.push_back(comm.asyncSend(nodes_to_send.storage(), nb_nodes_to_send * spatial_dimension, p, Tag::genTag(my_rank, 0, SEND_NODES_TAG)));
			}
			#if not defined (AKANTU_NDEBUG)
			else {
			AKANTU_DEBUG_INFO("No nodes to send to processor " << p);
			}
			#endif
			}

			comm.waitAll(isend_nodes_requests);
			comm.freeCommunicationRequest(isend_nodes_requests);
			delete [] ask_nodes_per_proc;

			nodes.resize(nb_total_nodes_to_recv + nb_nodes);
			for (UInt p = 0; p < nb_proc; ++p) {
			if((p != my_rank) && (nb_nodes_to_recv[p] > 0)) {
			AKANTU_DEBUG_INFO("Receiving the " << nb_nodes_to_recv[p] << " nodes from processor " << p
			<< " (communication tag : " << Tag::genTag(p, 0, SEND_NODES_TAG) << ")");

			comm.receive(nodes.storage() + nb_nodes * spatial_dimension,
			nb_nodes_to_recv[p] * spatial_dimension,
			p, Tag::genTag(p, 0, SEND_NODES_TAG));
			nb_nodes += nb_nodes_to_recv[p];
			}
			#if not defined (AKANTU_NDEBUG)
			else {
			if(p != my_rank) {
			AKANTU_DEBUG_INFO("No nodes to receive from processor " << p);
			}
			}
			#endif

			}

			comm.waitAll(isend_coordinates_requests);
			comm.freeCommunicationRequest(isend_coordinates_requests);
			delete [] nodes_to_send_per_proc;

			// Register the tags if any
			if(synchronizer_registry) {
			std::set<SynchronizationTag>::const_iterator it = tags_to_register.begin();
			std::set<SynchronizationTag>::const_iterator end = tags_to_register.end();
			for (; it != end; ++it) {
			synchronizer_registry->registerSynchronizer(communicator, *it);
			}
			}

			mesh.sendEvent(new_nodes);
			mesh.sendEvent(new_elements);

			delete [] intersects_proc;

			AKANTU_DEBUG_OUT();
			return &communicator;
			}

			/* -------------------------------------------------------------------------- */
			template GridSynchronizer *
			GridSynchronizer::createGridSynchronizer<IntegrationPoint>(Mesh & mesh,
			const SpatialGrid<IntegrationPoint> & grid,
			SynchronizerID id,
			SynchronizerRegistry * synchronizer_registry,
			const std::set<SynchronizationTag> & tags_to_register,
			MemoryID memory_id,
			const bool register_to_event_manager = true);
			template GridSynchronizer *
			GridSynchronizer::createGridSynchronizer<Element>(Mesh & mesh,
			const SpatialGrid<Element> & grid,
			SynchronizerID id,
			SynchronizerRegistry * synchronizer_registry,
			const std::set<SynchronizationTag> & tags_to_register,
			MemoryID memory_id,
			const bool register_to_event_manager = true);

			__END_AKANTU__

rAKA/src/synchronizer/grid_synchronizer.cc54e599859086bugfixes/32-python…

grid_synchronizer.ccView Options

rAKA/src/synchronizer/grid_synchronizer.cc
54e599859086bugfixes/32-python…

grid_synchronizer.cc
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