Homec4science
Diffusion akantu (bugfixes/installation-instructions) Browse

rAKA/src/synchronizer/node_info_per_processor.cc
ba0d478cf0b3bugfixes/installation…

Last Change
Raw File

node_info_per_processor.cc
View Options

/**
* @file node_info_per_processor.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Mar 16 2016
* @date last modification: Wed Nov 08 2017
*
* @brief Please type the brief for file: Helper classes to create the
* distributed synchronizer and distribute a mesh
*
* @section LICENSE
*
* Copyright (©) 2016-2018 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 "node_info_per_processor.hh"
#include "communicator.hh"
#include "node_group.hh"
#include "node_synchronizer.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
NodeInfoPerProc::NodeInfoPerProc(NodeSynchronizer & synchronizer,
UInt message_cnt, UInt root)
: MeshAccessor(synchronizer.getMesh()), synchronizer(synchronizer),
comm(synchronizer.getCommunicator()), rank(comm.whoAmI()),
nb_proc(comm.getNbProc()), root(root), mesh(synchronizer.getMesh()),
spatial_dimension(synchronizer.getMesh().getSpatialDimension()),
message_count(message_cnt) {}
/* -------------------------------------------------------------------------- */
template <class CommunicationBuffer>
void NodeInfoPerProc::fillNodeGroupsFromBuffer(CommunicationBuffer & buffer) {
AKANTU_DEBUG_IN();
std::vector<std::vector<std::string>> node_to_group;
buffer >> node_to_group;
AKANTU_DEBUG_ASSERT(node_to_group.size() == mesh.getNbGlobalNodes(),
"Not the good amount of nodes where transmitted");
const auto & global_nodes = mesh.getGlobalNodesIds();
auto nbegin = global_nodes.begin();
auto nit = global_nodes.begin();
auto nend = global_nodes.end();
for (; nit != nend; ++nit) {
auto it = node_to_group[*nit].begin();
auto end = node_to_group[*nit].end();
for (; it != end; ++it) {
mesh.getNodeGroup(*it).add(nit - nbegin, false);
}
}
GroupManager::const_node_group_iterator ngi = mesh.node_group_begin();
GroupManager::const_node_group_iterator nge = mesh.node_group_end();
for (; ngi != nge; ++ngi) {
NodeGroup & ng = *(ngi->second);
ng.optimize();
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NodeInfoPerProc::fillNodesType() {
AKANTU_DEBUG_IN();
UInt nb_nodes = mesh.getNbNodes();
auto & nodes_flags = this->getNodesFlags();
Array<UInt> nodes_set(nb_nodes);
nodes_set.set(0);
enum NodeSet {
NORMAL_SET = 1,
GHOST_SET = 2,
};
Array<bool> already_seen(nb_nodes, 1, false);
for (auto gt : ghost_types) {
UInt set = NORMAL_SET;
if (gt == _ghost)
set = GHOST_SET;
already_seen.set(false);
for (auto && type :
mesh.elementTypes(_all_dimensions, gt, _ek_not_defined)) {
const auto & connectivity = mesh.getConnectivity(type, gt);
for (auto & conn :
make_view(connectivity, connectivity.getNbComponent())) {
for (UInt n = 0; n < conn.size(); ++n) {
AKANTU_DEBUG_ASSERT(conn(n) < nb_nodes,
"Node " << conn(n)
<< " bigger than number of nodes "
<< nb_nodes);
if (!already_seen(conn(n))) {
nodes_set(conn(n)) += set;
already_seen(conn(n)) = true;
}
}
}
}
}
nodes_flags.resize(nb_nodes);
for (UInt i = 0; i < nb_nodes; ++i) {
if (nodes_set(i) == NORMAL_SET)
nodes_flags(i) = NodeFlag::_normal;
else if (nodes_set(i) == GHOST_SET)
nodes_flags(i) = NodeFlag::_pure_ghost;
else if (nodes_set(i) == (GHOST_SET + NORMAL_SET))
nodes_flags(i) = NodeFlag::_master;
}
AKANTU_DEBUG_OUT();
}
/* --------------------------------------------------------------------------
*/
void NodeInfoPerProc::fillCommunicationScheme(const Array<UInt> & master_info) {
AKANTU_DEBUG_IN();
Communications<UInt> & communications =
this->synchronizer.getCommunications();
{ // send schemes
auto it = master_info.begin_reinterpret(2, master_info.size() / 2);
auto end = master_info.end_reinterpret(2, master_info.size() / 2);
std::map<UInt, Array<UInt>> send_array_per_proc;
for (; it != end; ++it) {
const Vector<UInt> & send_info = *it;
send_array_per_proc[send_info(0)].push_back(send_info(1));
}
for (auto & send_schemes : send_array_per_proc) {
auto & scheme = communications.createSendScheme(send_schemes.first);
auto & sends = send_schemes.second;
std::sort(sends.begin(), sends.end());
std::transform(sends.begin(), sends.end(), sends.begin(),
[this](UInt g) -> UInt { return mesh.getNodeLocalId(g); });
scheme.copy(sends);
}
}
{ // receive schemes
std::map<UInt, Array<UInt>> recv_array_per_proc;
for (auto node : arange(mesh.getNbNodes())) {
if (mesh.isSlaveNode(node)) {
recv_array_per_proc[mesh.getNodePrank(node)].push_back(
mesh.getNodeGlobalId(node));
}
}
for (auto & recv_schemes : recv_array_per_proc) {
auto & scheme = communications.createRecvScheme(recv_schemes.first);
auto & recvs = recv_schemes.second;
std::sort(recvs.begin(), recvs.end());
std::transform(recvs.begin(), recvs.end(), recvs.begin(),
[this](UInt g) -> UInt { return mesh.getNodeLocalId(g); });
scheme.copy(recvs);
}
}
AKANTU_DEBUG_OUT();
}
/* --------------------------------------------------------------------------
*/
/* --------------------------------------------------------------------------
*/
/* --------------------------------------------------------------------------
*/
MasterNodeInfoPerProc::MasterNodeInfoPerProc(NodeSynchronizer & synchronizer,
UInt message_cnt, UInt root)
: NodeInfoPerProc(synchronizer, message_cnt, root) {
UInt nb_global_nodes = this->mesh.getNbGlobalNodes();
this->comm.broadcast(nb_global_nodes, this->root);
}
/* --------------------------------------------------------------------------
*/
void MasterNodeInfoPerProc::synchronizeNodes() {
this->nodes_per_proc.resize(nb_proc);
this->nb_nodes_per_proc.resize(nb_proc);
Array<Real> local_nodes(0, spatial_dimension);
Array<Real> & nodes = this->getNodes();
for (UInt p = 0; p < nb_proc; ++p) {
UInt nb_nodes = 0;
// UInt * buffer;
Array<Real> * nodes_to_send;
Array<UInt> & nodespp = nodes_per_proc[p];
if (p != root) {
nodes_to_send = new Array<Real>(0, spatial_dimension);
AKANTU_DEBUG_INFO("Receiving number of nodes from proc "
<< p << " " << Tag::genTag(p, 0, Tag::_NB_NODES));
comm.receive(nb_nodes, p, Tag::genTag(p, 0, Tag::_NB_NODES));
nodespp.resize(nb_nodes);
this->nb_nodes_per_proc(p) = nb_nodes;
AKANTU_DEBUG_INFO("Receiving list of nodes from proc "
<< p << " " << Tag::genTag(p, 0, Tag::_NODES));
comm.receive(nodespp, p, Tag::genTag(p, 0, Tag::_NODES));
} else {
Array<UInt> & local_ids = this->getNodesGlobalIds();
this->nb_nodes_per_proc(p) = local_ids.size();
nodespp.copy(local_ids);
nodes_to_send = &local_nodes;
}
Array<UInt>::const_scalar_iterator it = nodespp.begin();
Array<UInt>::const_scalar_iterator end = nodespp.end();
/// get the coordinates for the selected nodes
for (; it != end; ++it) {
Vector<Real> coord(nodes.storage() + spatial_dimension * *it,
spatial_dimension);
nodes_to_send->push_back(coord);
}
if (p != root) { /// send them for distant processors
AKANTU_DEBUG_INFO("Sending coordinates to proc "
<< p << " "
<< Tag::genTag(this->rank, 0, Tag::_COORDINATES));
comm.send(*nodes_to_send, p,
Tag::genTag(this->rank, 0, Tag::_COORDINATES));
delete nodes_to_send;
}
}
/// construct the local nodes coordinates
nodes.copy(local_nodes);
}
/* --------------------------------------------------------------------------
*/
void MasterNodeInfoPerProc::synchronizeTypes() {
// <global_id, <proc, local_id> >
std::multimap<UInt, std::pair<UInt, UInt>> nodes_to_proc;
std::vector<Array<NodeFlag>> nodes_flags_per_proc(nb_proc);
std::vector<Array<Int>> nodes_prank_per_proc(nb_proc);
// arrays containing pairs of (proc, node)
std::vector<Array<UInt>> nodes_to_send_per_proc(nb_proc);
for (UInt p = 0; p < nb_proc; ++p) {
nodes_flags_per_proc[p].resize(nb_nodes_per_proc(p));
nodes_prank_per_proc[p].resize(nb_nodes_per_proc(p));
}
this->fillNodesType();
for (UInt p = 0; p < nb_proc; ++p) {
auto & nodes_flags = nodes_flags_per_proc[p];
if (p != root) {
AKANTU_DEBUG_INFO(
"Receiving first nodes types from proc "
<< p << " "
<< Tag::genTag(this->rank, this->message_count, Tag::_NODES_TYPE));
comm.receive(nodes_flags, p, Tag::genTag(p, 0, Tag::_NODES_TYPE));
} else {
nodes_flags.copy(this->getNodesFlags());
}
// stack all processors claiming to be master for a node
for (UInt local_node = 0; local_node < nb_nodes_per_proc(p); ++local_node) {
if ((nodes_flags(local_node) & NodeFlag::_shared_mask) == NodeFlag::_master) {
UInt global_node = nodes_per_proc[p](local_node);
nodes_to_proc.insert(
std::make_pair(global_node, std::make_pair(p, local_node)));
}
}
}
for (UInt i = 0; i < mesh.getNbGlobalNodes(); ++i) {
auto it_range = nodes_to_proc.equal_range(i);
if (it_range.first == nodes_to_proc.end() || it_range.first->first != i)
continue;
// pick the first processor out of the multi-map as the actual master
UInt master_proc = (it_range.first)->second.first;
for (auto it_node = it_range.first; it_node != it_range.second; ++it_node) {
UInt proc = it_node->second.first;
UInt node = it_node->second.second;
if (proc != master_proc) {
// store the info on all the slaves for a given master
nodes_prank_per_proc[proc](node) = master_proc;
nodes_to_send_per_proc[master_proc].push_back(proc);
nodes_to_send_per_proc[master_proc].push_back(i);
}
}
}
std::vector<CommunicationRequest> requests_send_type;
std::vector<CommunicationRequest> requests_send_master_info;
for (UInt p = 0; p < nb_proc; ++p) {
if (p != root) {
AKANTU_DEBUG_INFO("Sending nodes types to proc "
<< p << " "
<< Tag::genTag(this->rank, 0, Tag::_NODES_TYPE));
requests_send_type.push_back(
comm.asyncSend(nodes_flags_per_proc[p], p,
Tag::genTag(this->rank, 0, Tag::_NODES_TYPE)));
requests_send_type.push_back(
comm.asyncSend(nodes_prank_per_proc[p], p,
Tag::genTag(this->rank, 2, Tag::_NODES_TYPE)));
auto & nodes_to_send = nodes_to_send_per_proc[p];
AKANTU_DEBUG_INFO("Sending nodes master info to proc "
<< p << " "
<< Tag::genTag(this->rank, 1, Tag::_NODES_TYPE));
requests_send_master_info.push_back(comm.asyncSend(
nodes_to_send, p, Tag::genTag(this->rank, 1, Tag::_NODES_TYPE)));
} else {
this->getNodesFlags().copy(nodes_flags_per_proc[p]);
for(auto && data : enumerate(nodes_prank_per_proc[p])) {
auto node = std::get<0>(data);
if(mesh.isSlaveNode(node)) {
this->setNodePrank(node, std::get<1>(data));
}
}
this->fillCommunicationScheme(nodes_to_send_per_proc[root]);
}
}
comm.waitAll(requests_send_type);
comm.freeCommunicationRequest(requests_send_type);
requests_send_type.clear();
comm.waitAll(requests_send_master_info);
comm.freeCommunicationRequest(requests_send_master_info);
}
/* --------------------------------------------------------------------------
*/
void MasterNodeInfoPerProc::synchronizeGroups() {
AKANTU_DEBUG_IN();
UInt nb_total_nodes = mesh.getNbGlobalNodes();
DynamicCommunicationBuffer buffer;
using NodeToGroup = std::vector<std::vector<std::string>>;
NodeToGroup node_to_group;
node_to_group.resize(nb_total_nodes);
GroupManager::const_node_group_iterator ngi = mesh.node_group_begin();
GroupManager::const_node_group_iterator nge = mesh.node_group_end();
for (; ngi != nge; ++ngi) {
NodeGroup & ng = *(ngi->second);
std::string name = ngi->first;
NodeGroup::const_node_iterator nit = ng.begin();
NodeGroup::const_node_iterator nend = ng.end();
for (; nit != nend; ++nit) {
node_to_group[*nit].push_back(name);
}
nit = ng.begin();
if (nit != nend)
ng.empty();
}
buffer << node_to_group;
std::vector<CommunicationRequest> requests;
for (UInt p = 0; p < nb_proc; ++p) {
if (p == this->rank)
continue;
AKANTU_DEBUG_INFO("Sending node groups to proc "
<< p << " "
<< Tag::genTag(this->rank, p, Tag::_NODE_GROUP));
requests.push_back(comm.asyncSend(
buffer, p, Tag::genTag(this->rank, p, Tag::_NODE_GROUP)));
}
this->fillNodeGroupsFromBuffer(buffer);
comm.waitAll(requests);
comm.freeCommunicationRequest(requests);
requests.clear();
AKANTU_DEBUG_OUT();
}
/* --------------------------------------------------------------------------
*/
/* --------------------------------------------------------------------------
*/
/* --------------------------------------------------------------------------
*/
SlaveNodeInfoPerProc::SlaveNodeInfoPerProc(NodeSynchronizer & synchronizer,
UInt message_cnt, UInt root)
: NodeInfoPerProc(synchronizer, message_cnt, root) {
UInt nb_global_nodes = 0;
comm.broadcast(nb_global_nodes, root);
this->setNbGlobalNodes(nb_global_nodes);
}
/* --------------------------------------------------------------------------
*/
void SlaveNodeInfoPerProc::synchronizeNodes() {
AKANTU_DEBUG_INFO("Sending list of nodes to proc "
<< root << " " << Tag::genTag(this->rank, 0, Tag::_NB_NODES)
<< " " << Tag::genTag(this->rank, 0, Tag::_NODES));
Array<UInt> & local_ids = this->getNodesGlobalIds();
Array<Real> & nodes = this->getNodes();
UInt nb_nodes = local_ids.size();
comm.send(nb_nodes, root, Tag::genTag(this->rank, 0, Tag::_NB_NODES));
comm.send(local_ids, root, Tag::genTag(this->rank, 0, Tag::_NODES));
/* --------<<<<-COORDINATES---------------------------------------------- */
nodes.resize(nb_nodes);
AKANTU_DEBUG_INFO("Receiving coordinates from proc "
<< root << " " << Tag::genTag(root, 0, Tag::_COORDINATES));
comm.receive(nodes, root, Tag::genTag(root, 0, Tag::_COORDINATES));
}
/* --------------------------------------------------------------------------
*/
void SlaveNodeInfoPerProc::synchronizeTypes() {
this->fillNodesType();
auto & nodes_types = this->getNodesFlags();
AKANTU_DEBUG_INFO("Sending first nodes types to proc "
<< root << ""
<< Tag::genTag(this->rank, 0, Tag::_NODES_TYPE));
comm.send(nodes_types, root, Tag::genTag(this->rank, 0, Tag::_NODES_TYPE));
AKANTU_DEBUG_INFO("Receiving nodes types from proc "
<< root << " " << Tag::genTag(root, 0, Tag::_NODES_TYPE));
comm.receive(nodes_types, root, Tag::genTag(root, 0, Tag::_NODES_TYPE));
Array<Int> nodes_prank(nodes_types.size());
comm.receive(nodes_prank, root, Tag::genTag(root, 2, Tag::_NODES_TYPE));
for(auto && data : enumerate(nodes_prank)) {
auto node = std::get<0>(data);
if(mesh.isSlaveNode(node)) {
this->setNodePrank(node, std::get<1>(data));
}
}
AKANTU_DEBUG_INFO("Receiving nodes master info from proc "
<< root << " " << Tag::genTag(root, 1, Tag::_NODES_TYPE));
CommunicationStatus status;
comm.probe<UInt>(root, Tag::genTag(root, 1, Tag::_NODES_TYPE), status);
Array<UInt> nodes_master_info(status.size());
if(nodes_master_info.size()>0)
comm.receive(nodes_master_info, root, Tag::genTag(root, 1, Tag::_NODES_TYPE));
this->fillCommunicationScheme(nodes_master_info);
}
/* --------------------------------------------------------------------------
*/
void SlaveNodeInfoPerProc::synchronizeGroups() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Receiving node groups from proc "
<< root << " "
<< Tag::genTag(root, this->rank, Tag::_NODE_GROUP));
CommunicationStatus status;
comm.probe<char>(root, Tag::genTag(root, this->rank, Tag::_NODE_GROUP),
status);
CommunicationBuffer buffer(status.size());
comm.receive(buffer, root, Tag::genTag(root, this->rank, Tag::_NODE_GROUP));
this->fillNodeGroupsFromBuffer(buffer);
AKANTU_DEBUG_OUT();
}
} // akantu
c4science · Help