Diffusion akantu (features/17-create-an-element-group-using-a-node-group-with-python-interface) Browse

17-create-an…

dof_synchronizer.cc
View Options

			/**
			* @file dof_synchronizer.cc
			*
			* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
			* @author Nicolas Richart <nicolas.richart@epfl.ch>
			*
			* @date creation: Fri Jun 17 2011
			* @date last modification: Wed Oct 21 2015
			*
			* @brief DOF synchronizing object implementation
			*
			* @section LICENSE
			*
			* Copyright (©) 2010-2012, 2014, 2015 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 "dof_synchronizer.hh"
			#include "mesh.hh"

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


			__BEGIN_AKANTU__

			/* -------------------------------------------------------------------------- */
			/**
			* A DOFSynchronizer needs a mesh and the number of degrees of freedom
			* per node to be created. In the constructor computes the local and global dof
			* number for each dof. The member
			* proc_informations (std vector) is resized with the number of mpi
			* processes. Each entry in the vector is a PerProcInformations object
			* that contains the interactions of the current mpi process (prank) with the
			* mpi process corresponding to the position of that entry. Every
			* ProcInformations object contains one array with the dofs that have
			* to be sent to prank and a second one with dofs that willl be received form prank.
			* This information is needed for the asychronous communications. The
			* constructor sets up this information.
			* @param mesh mesh discretizing the domain we want to analyze
			* @param nb_degree_of_freedom number of degrees of freedom per node
			*/
			DOFSynchronizer::DOFSynchronizer(const Mesh & mesh, UInt nb_degree_of_freedom) :
			global_dof_equation_numbers(0, 1, "global_equation_number"),
			local_dof_equation_numbers(0, 1, "local_equation_number"),
			dof_global_ids(0, 1, "global_ids"),
			dof_types(0, 1, "types") {

			gather_scatter_scheme_initialized = false;

			prank = static_communicator->whoAmI();
			psize = static_communicator->getNbProc();

			proc_informations.resize(psize);

			UInt nb_nodes = mesh.getNbNodes();

			nb_dofs = nb_nodes * nb_degree_of_freedom;

			dof_global_ids.resize(nb_dofs);
			dof_types.resize(nb_dofs);

			nb_global_dofs = mesh.getNbGlobalNodes() * nb_degree_of_freedom;

			/// compute the global id for each dof and store the dof type (pure ghost, slave, master or local)
			UInt * dof_global_id = dof_global_ids.storage();
			Int * dof_type = dof_types.storage();
			for(UInt n = 0, ld = 0; n < nb_nodes; ++n) {
			UInt node_global_id = mesh.getNodeGlobalId(n);
			UInt node_type = mesh.getNodeType(n);
			for (UInt d = 0; d < nb_degree_of_freedom; ++d, ++ld) {
			dof_global_id = node_global_id nb_degree_of_freedom + d;
			global_dof_to_local[*dof_global_id] = ld;

			*(dof_type++) = node_type;

			dof_global_id++;
			}
			}

			if(psize == 1) return;

			/// creating communication scheme
			dof_global_id = dof_global_ids.storage();
			dof_type = dof_types.storage();

			for (UInt n = 0; n < nb_dofs; ++n) {
			/// check if dof is slave. In that case the value stored in
			/// dof_type corresponds to the process that has the corresponding
			/// master dof
			if(*dof_type >= 0) {
			/// has to receive n from proc[*dof_type]
			proc_informations[*dof_type].master_dofs.push_back(n);
			}
			dof_type++;
			}

			/// at this point the master nodes in PerProcInfo are known
			/// exchanging information
			for (UInt p = 1; p < psize; ++p) {
			UInt sendto = (psize + prank + p) % psize;
			UInt recvfrom = (psize + prank - p) % psize;

			/// send the master nodes
			UInt nb_master_dofs = proc_informations[sendto].master_dofs.getSize();
			UInt * master_dofs = proc_informations[sendto].master_dofs.storage();
			UInt * send_buffer = new UInt[nb_master_dofs];
			for (UInt d = 0; d < nb_master_dofs; ++d) {
			send_buffer[d] = dof_global_id[master_dofs[d]];
			}

			UInt nb_slave_dofs = 0;
			UInt * recv_buffer;
			std::vector<CommunicationRequest *> requests;
			requests.push_back(static_communicator->asyncSend(&nb_master_dofs, 1, sendto, 0));
			if(nb_master_dofs != 0) {
			AKANTU_DEBUG(dblInfo, "Sending "<< nb_master_dofs << " dofs to " << sendto);
			requests.push_back(static_communicator->asyncSend(send_buffer, nb_master_dofs, sendto, 1));
			}

			/// Receive the info and store them as slave nodes
			static_communicator->receive(&nb_slave_dofs, 1, recvfrom, 0);
			if(nb_slave_dofs != 0) {
			AKANTU_DEBUG(dblInfo, "Receiving "<< nb_slave_dofs << " dofs from " << recvfrom);
			proc_informations[recvfrom].slave_dofs.resize(nb_slave_dofs);
			recv_buffer = proc_informations[recvfrom].slave_dofs.storage();
			static_communicator->receive(recv_buffer, nb_slave_dofs, recvfrom, 1);
			}

			for (UInt d = 0; d < nb_slave_dofs; ++d) {
			recv_buffer[d] = global_dof_to_local[recv_buffer[d]];
			}

			static_communicator->waitAll(requests);
			static_communicator->freeCommunicationRequest(requests);
			requests.clear();
			delete [] send_buffer;
			}
			}

			/* -------------------------------------------------------------------------- */
			DOFSynchronizer::~DOFSynchronizer() {

			}


			/* -------------------------------------------------------------------------- */
			void DOFSynchronizer::initLocalDOFEquationNumbers() {
			AKANTU_DEBUG_IN();
			local_dof_equation_numbers.resize(nb_dofs);

			Int * dof_equation_number = local_dof_equation_numbers.storage();
			for (UInt d = 0; d < nb_dofs; ++d) {
			*(dof_equation_number++) = d;
			}

			//local_dof_equation_numbers.resize(nb_dofs);
			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void DOFSynchronizer::asynchronousSynchronize(DataAccessor & data_accessor,
			SynchronizationTag tag) {
			AKANTU_DEBUG_IN();

			if (communications.find(tag) == communications.end())
			computeBufferSize(data_accessor, tag);

			Communication & communication = communications[tag];

			AKANTU_DEBUG_ASSERT(communication.send_requests.size() == 0,
			"There must be some pending sending communications. Tag is " << tag);

			std::map<SynchronizationTag, UInt>::iterator t_it = tag_counter.find(tag);
			UInt counter = 0;
			if(t_it == tag_counter.end()) {
			tag_counter[tag] = 0;
			} else {
			counter = ++(t_it->second);
			}

			for (UInt p = 0; p < psize; ++p) {
			UInt ssize = communication.size_to_send[p];
			if(p == prank \|\| ssize == 0) continue;

			CommunicationBuffer & buffer = communication.send_buffer[p];
			buffer.resize(ssize);
			#ifndef AKANTU_NDEBUG
			UInt nb_dofs = proc_informations[p].slave_dofs.getSize();
			AKANTU_DEBUG_INFO("Packing data for proc " << p
			<< " (" << ssize << "/" << nb_dofs
			<<" data to send/dofs)");

			/// pack global equation numbers in debug mode
			Array<UInt>::const_iterator<UInt> bit = proc_informations[p].slave_dofs.begin();
			Array<UInt>::const_iterator<UInt> bend = proc_informations[p].slave_dofs.end();
			for (; bit != bend; ++bit) {
			buffer << global_dof_equation_numbers[*bit];
			}
			#endif


			/// dof synchronizer needs to send the data corresponding to the
			data_accessor.packDOFData(buffer, proc_informations[p].slave_dofs, tag);

			AKANTU_DEBUG_ASSERT(buffer.getPackedSize() == ssize,
			"a problem has been introduced with "
			<< "false sent sizes declaration "
			<< buffer.getPackedSize() << " != " << ssize);
			AKANTU_DEBUG_INFO("Posting send to proc " << p
			<< " (tag: " << tag << " - " << ssize << " data to send)"
			<< " [" << Tag::genTag(prank, counter, tag) << "]");
			communication.send_requests.push_back(static_communicator->asyncSend(buffer.storage(),
			ssize,
			p,
			Tag::genTag(prank, counter, tag)));
			}

			AKANTU_DEBUG_ASSERT(communication.recv_requests.size() == 0,
			"There must be some pending receive communications");

			for (UInt p = 0; p < psize; ++p) {
			UInt rsize = communication.size_to_receive[p];
			if(p == prank \|\| rsize == 0) continue;
			CommunicationBuffer & buffer = communication.recv_buffer[p];
			buffer.resize(rsize);

			AKANTU_DEBUG_INFO("Posting receive from proc " << p
			<< " (tag: " << tag << " - " << rsize << " data to receive) "
			<< " [" << Tag::genTag(p, counter, tag) << "]");
			communication.recv_requests.push_back(static_communicator->asyncReceive(buffer.storage(),
			rsize,
			p,
			Tag::genTag(p, counter, tag)));
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void DOFSynchronizer::waitEndSynchronize(DataAccessor & data_accessor,
			SynchronizationTag tag) {
			AKANTU_DEBUG_IN();

			AKANTU_DEBUG_ASSERT(communications.find(tag) != communications.end(), "No communication with the tag \""
			<< tag <<"\" started");

			Communication & communication = communications[tag];

			std::vector<CommunicationRequest *> req_not_finished;
			std::vector<CommunicationRequest > req_not_finished_tmp = &req_not_finished;
			std::vector<CommunicationRequest > recv_requests_tmp = &(communication.recv_requests);

			// static_communicator->waitAll(recv_requests);
			while(!recv_requests_tmp->empty()) {
			for (std::vector<CommunicationRequest *>::iterator req_it = recv_requests_tmp->begin();
			req_it != recv_requests_tmp->end() ; ++req_it) {
			CommunicationRequest * req = *req_it;

			if(static_communicator->testRequest(req)) {
			UInt proc = req->getSource();
			AKANTU_DEBUG_INFO("Unpacking data coming from proc " << proc);
			CommunicationBuffer & buffer = communication.recv_buffer[proc];

			#ifndef AKANTU_NDEBUG
			Array<UInt>::const_iterator<UInt> bit = proc_informations[proc].master_dofs.begin();
			Array<UInt>::const_iterator<UInt> bend = proc_informations[proc].master_dofs.end();

			for (; bit != bend; ++bit) {
			Int global_dof_eq_nb_loc = global_dof_equation_numbers[*bit];
			Int global_dof_eq_nb = 0;
			buffer >> global_dof_eq_nb;
			Real tolerance = Math::getTolerance();
			if(std::abs(global_dof_eq_nb - global_dof_eq_nb_loc) <= tolerance) continue;
			AKANTU_DEBUG_ERROR("Unpacking an unknown global dof equation number for dof: "
			<< *bit
			<< "(global dof equation number = " << global_dof_eq_nb
			<< " and buffer = " << global_dof_eq_nb << ") ["
			<< std::abs(global_dof_eq_nb - global_dof_eq_nb_loc)
			<< "] - tag: " << tag);
			}

			#endif

			data_accessor.unpackDOFData(buffer, proc_informations[proc].master_dofs, tag);
			buffer.resize(0);

			AKANTU_DEBUG_ASSERT(buffer.getLeftToUnpack() == 0,
			"all data have not been unpacked: "
			<< buffer.getLeftToUnpack() << " bytes left");
			static_communicator->freeCommunicationRequest(req);
			} else {
			req_not_finished_tmp->push_back(req);
			}
			}

			std::vector<CommunicationRequest > swap = req_not_finished_tmp;
			req_not_finished_tmp = recv_requests_tmp;
			recv_requests_tmp = swap;

			req_not_finished_tmp->clear();
			}


			AKANTU_DEBUG_INFO("Waiting that every send requests are received");
			static_communicator->waitAll(communication.send_requests);
			for (std::vector<CommunicationRequest *>::iterator req_it = communication.send_requests.begin();
			req_it != communication.send_requests.end() ; ++req_it) {
			CommunicationRequest & req = (req_it);

			if(static_communicator->testRequest(&req)) {
			UInt proc = req.getDestination();
			CommunicationBuffer & buffer = communication.send_buffer[proc];
			buffer.resize(0);
			static_communicator->freeCommunicationRequest(&req);
			}
			}
			communication.send_requests.clear();

			AKANTU_DEBUG_OUT();


			}

			/* -------------------------------------------------------------------------- */
			/**
			* This function computes the buffer size needed for in order to send data or receive data.
			* @param data_accessor object of a class that needs to use the DOFSynchronizer. This class has to inherit from the * DataAccessor interface.
			* @param tag synchronization tag: indicates what variable should be sychronized, e.g. mass, nodal residual, etc.
			* for the SolidMechanicsModel
			*/
			void DOFSynchronizer::computeBufferSize(DataAccessor & data_accessor,
			SynchronizationTag tag) {
			AKANTU_DEBUG_IN();

			communications[tag].resize(psize);

			for (UInt p = 0; p < psize; ++p) {
			/// initialize the size of data that we be sent and received
			UInt ssend = 0;
			UInt sreceive = 0;
			if(p != prank) {
			/// check if processor prank has to send dof information to p
			if(proc_informations[p].slave_dofs.getSize() != 0) {


			#ifndef AKANTU_NDEBUG
			/// in debug mode increase buffer size to send the positions
			/// of nodes in the direction that correspond to the dofs
			ssend += proc_informations[p].slave_dofs.getSize() * sizeof(Int);
			#endif
			ssend += data_accessor.getNbDataForDOFs(proc_informations[p].slave_dofs, tag);
			AKANTU_DEBUG_INFO("I have " << ssend << "(" << ssend / 1024.
			<< "kB - "<< proc_informations[p].slave_dofs.getSize() <<" dof(s)) data to send to " << p << " for tag "
			<< tag);
			}

			/// check if processor prank has to receive dof information from p
			if(proc_informations[p].master_dofs.getSize() != 0) {
			#ifndef AKANTU_NDEBUG
			/// in debug mode increase buffer size to receive the
			/// positions of nodes in the direction that correspond to the
			/// dofs
			sreceive += proc_informations[p].master_dofs.getSize() * sizeof(Int);
			#endif
			sreceive += data_accessor.getNbDataForDOFs(proc_informations[p].master_dofs, tag);
			AKANTU_DEBUG_INFO("I have " << sreceive << "(" << sreceive / 1024.
			<< "kB - "<< proc_informations[p].master_dofs.getSize() <<" dof(s)) data to receive for tag "
			<< tag);
			}
			}

			communications[tag].size_to_send [p] = ssend;
			communications[tag].size_to_receive[p] = sreceive;
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void DOFSynchronizer::initGlobalDOFEquationNumbers() {
			AKANTU_DEBUG_IN();
			global_dof_equation_numbers.resize(nb_dofs);

			Int * dof_type = dof_types.storage();
			UInt * dof_global_id = dof_global_ids.storage();
			Int * dof_equation_number = global_dof_equation_numbers.storage();
			for(UInt d = 0; d < nb_dofs; ++d) {
			/// if ghost dof the equation_number is greater than nb_global_dofs
			Int global_eq_num = dof_global_id + (dof_type > -3 ? 0 : nb_global_dofs);
			*(dof_equation_number) = global_eq_num;
			global_dof_equation_number_to_local[global_eq_num] = d;

			dof_equation_number++;
			dof_global_id++;
			dof_type++;
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void DOFSynchronizer::initScatterGatherCommunicationScheme() {
			AKANTU_DEBUG_IN();

			if(psize == 1 \|\| gather_scatter_scheme_initialized) {
			if(psize == 1) gather_scatter_scheme_initialized = true;
			AKANTU_DEBUG_OUT();
			return;
			}

			/// creating communication scheme
			UInt * dof_global_id = dof_global_ids.storage();
			Int * dof_type = dof_types.storage();

			Array<UInt> * local_dofs = new Array<UInt>(0,2);
			UInt local_dof_val[2];
			nb_needed_dofs = 0;
			nb_local_dofs = 0;

			for (UInt n = 0; n < nb_dofs; ++n) {
			if(*dof_type != -3) {
			local_dof_val[0] = *dof_global_id;

			if(dof_type == -1 \|\| dof_type == -2) {
			local_dof_val[1] = 0; // master for this node, shared or not
			nb_local_dofs++;
			} else if (*dof_type >= 0) {
			nb_needed_dofs++;
			local_dof_val[1] = 1; // slave node
			}
			local_dofs->push_back(local_dof_val);
			}
			dof_type++;
			dof_global_id++;
			}

			Int * nb_dof_per_proc = new Int[psize];
			nb_dof_per_proc[prank] = local_dofs->getSize();
			static_communicator->allGather(nb_dof_per_proc, 1);
			AKANTU_DEBUG(dblDebug, "I have " << local_dofs->getSize() << " not ghost dofs ("
			<< nb_local_dofs << " local and " << nb_needed_dofs << " slave)");

			UInt pos = 0;
			for (UInt p = 0; p < prank; ++p) pos += nb_dof_per_proc[p];
			UInt nb_total_dofs = pos;
			for (UInt p = prank; p < psize; ++p) nb_total_dofs += nb_dof_per_proc[p];

			int * nb_values = new int[psize];
			for (unsigned int p = 0; p < psize; ++p) nb_values[p] = nb_dof_per_proc[p] * 2;

			UInt * buffer = new UInt[2*nb_total_dofs];
			memcpy(buffer + 2 * pos, local_dofs->storage(), local_dofs->getSize() * 2 * sizeof(UInt));
			delete local_dofs;

			static_communicator->allGatherV(buffer, nb_values);

			UInt * tmp_buffer = buffer;

			for (UInt p = 0; p < psize; ++p) {
			UInt proc_p_nb_dof = nb_dof_per_proc[p];
			if (p != prank){
			AKANTU_DEBUG(dblDebug, "I get " << proc_p_nb_dof << "(" << nb_values[p] << ") dofs from " << p + 1);
			proc_informations[p].dofs.resize(0);
			for (UInt dd = 0; dd < proc_p_nb_dof; ++dd) {
			UInt dof = tmp_buffer[2*dd];
			if(tmp_buffer[2*dd + 1] == 0)
			proc_informations[p].dofs.push_back(dof);
			else
			proc_informations[p].needed_dofs.push_back(dof);
			}

			AKANTU_DEBUG(dblDebug, "Proc " << p + 1 << " sends me "
			<< proc_informations[p].dofs.getSize() << " local dofs, and "
			<< proc_informations[p].needed_dofs.getSize() << " slave dofs");
			}
			tmp_buffer += 2*proc_p_nb_dof;
			}
			delete [] nb_dof_per_proc;
			delete [] buffer;
			delete [] nb_values;
			gather_scatter_scheme_initialized = true;

			AKANTU_DEBUG_OUT();
			}

			__END_AKANTU__

rAKA/src/synchronizer/dof_synchronizer.cc7dd9648d4655features/17-create-an…

dof_synchronizer.ccView Options

rAKA/src/synchronizer/dof_synchronizer.cc
7dd9648d4655features/17-create-an…

dof_synchronizer.cc
View Options