Homec4science
Diffusion akantu (bugfixes/detect_mixed_distributed_initialization) Browse

rAKA/src/mesh/mesh_periodic.cc
ba0d478cf0b3bugfixes/detect_mixed_d…

Last Change
Raw File

mesh_periodic.cc
View Options

/**
* @file mesh_pbc.cc
*
* @author Nicolas Richart
*
* @date creation Sat Feb 10 2018
*
* @brief Implementation of the perdiodicity capabilities in the mesh
*
* @section LICENSE
*
* Copyright (©) 2010-2011 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 "communication_tag.hh"
#include "communicator.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
void Mesh::makePeriodic(const SpatialDirection & direction) {
Array<UInt> list_1;
Array<UInt> list_2;
Real tolerance = 1e-10;
auto lower_bound = this->getLowerBounds();
auto upper_bound = this->getUpperBounds();
auto length = upper_bound(direction) - lower_bound(direction);
const auto & positions = *nodes;
std::cout << bbox << std::endl;
for (auto && data : enumerate(make_view(positions, spatial_dimension))) {
UInt node = std::get<0>(data);
const auto & pos = std::get<1>(data);
if (std::abs((pos(direction) - lower_bound(direction)) / length) <
tolerance) {
list_1.push_back(node);
}
if (std::abs((pos(direction) - upper_bound(direction)) / length) <
tolerance) {
list_2.push_back(node);
}
}
this->makePeriodic(direction, list_1, list_2);
}
namespace {
struct NodeInfo {
NodeInfo() {}
NodeInfo(UInt spatial_dimension) : position(spatial_dimension) {}
NodeInfo(UInt node, const Vector<Real> & position,
const SpatialDirection & direction)
: node(node), position(position) {
this->direction_position = position(direction);
this->position(direction) = 0.;
}
NodeInfo(const NodeInfo & other)
: node(other.node), position(other.position),
direction_position(other.direction_position) {}
UInt node{0};
Vector<Real> position;
Real direction_position{0.};
};
// std::ostream & operator<<(std::ostream & stream, const NodeInfo & info) {
// stream << info.node << " " << info.position << " "
// << info.direction_position;
// return stream;
// }
}
/* -------------------------------------------------------------------------- */
// left is for lower values on direction and right for highest values
void Mesh::makePeriodic(const SpatialDirection & direction,
const Array<UInt> & list_left,
const Array<UInt> & list_right) {
Real tolerance = 1e-10;
const auto & positions = *nodes;
auto lower_bound = this->getLowerBounds();
auto upper_bound = this->getUpperBounds();
auto length = upper_bound(direction) - lower_bound(direction);
lower_bound(direction) = 0;
upper_bound(direction) = 0;
auto prank = communicator->whoAmI();
std::cout << prank << " - left:" << list_left.size()
<< " - right:" << list_right.size() << std::endl;
std::vector<NodeInfo> nodes_left(list_left.size());
std::vector<NodeInfo> nodes_right(list_right.size());
BBox bbox(spatial_dimension);
auto to_position = [&](UInt node) {
Vector<Real> pos(spatial_dimension);
for (UInt s : arange(spatial_dimension)) {
pos(s) = positions(node, s);
}
auto && info = NodeInfo(node, pos, direction);
bbox += info.position;
return info;
};
std::transform(list_left.begin(), list_left.end(), nodes_left.begin(),
to_position);
BBox bbox_left = bbox;
bbox.reset();
std::transform(list_right.begin(), list_right.end(), nodes_right.begin(),
to_position);
BBox bbox_right = bbox;
std::vector<UInt> new_nodes;
if (is_distributed) {
/* ---------------------------------------------------------------------- */
auto extract_and_send_nodes = [&](const auto & bbox, const auto & node_list,
auto & send_buffers, auto proc,
auto cnt) {
send_buffers.emplace_back();
auto & buffer = send_buffers.back();
for (auto & info : node_list) {
if (bbox.contains(info.position) and isLocalOrMasterNode(info.node)) {
Vector<Real> pos = info.position;
pos(direction) = info.direction_position;
buffer << getNodeGlobalId(info.node);
buffer << pos;
buffer << ((*nodes_flags)(info.node) & NodeFlag::_periodic_mask);
if (isPeriodicSlave(info.node)) {
buffer << getNodeGlobalId(periodic_slave_master[info.node]);
}
if (isPeriodicMaster(info.node)) {
buffer << periodic_master_slave.count(info.node);
auto slaves = periodic_master_slave.equal_range(info.node);
for (auto it = slaves.first; it != slaves.second; ++it) {
buffer << getNodeGlobalId(it->second);
}
}
}
}
auto tag = Tag::genTag(prank, cnt, Tag::_PERIODIC_NODES);
return communicator->asyncSend(buffer, proc, tag);
};
/* ---------------------------------------------------------------------- */
auto recv_and_extract_nodes = [&](auto & bbox, auto & node_list,
auto & buffer, const auto proc,
auto cnt) {
if (not bbox)
return;
buffer.reset();
auto tag = Tag::genTag(proc, cnt, Tag::_PERIODIC_NODES);
communicator->receive(buffer, proc, tag);
while (not buffer.empty()) {
Vector<Real> pos(spatial_dimension);
UInt global_node;
NodeFlag flag;
buffer >> global_node;
buffer >> pos;
buffer >> flag;
auto local_node = getNodeLocalId(global_node);
if (flag == NodeFlag::_periodic_slave) {
UInt master_node;
buffer >> master_node;
auto local_master_node = getNodeLocalId(master_node);
AKANTU_DEBUG_ASSERT(local_master_node != UInt(-1),
"Should I know the master node " << master_node);
}
if (flag == NodeFlag::_periodic_master) {
UInt nb_slaves;
buffer >> nb_slaves;
for (auto ns[[gnu::unused]] : arange(nb_slaves)) {
UInt gslave_node;
buffer >> gslave_node;
auto lslave_node = getNodeLocalId(gslave_node);
AKANTU_DEBUG_ASSERT(lslave_node != UInt(-1),
"Should I know the slave node " << gslave_node);
}
}
if (local_node != UInt(-1))
continue;
local_node = nodes->size();
NodeInfo info(local_node, pos, direction);
nodes->push_back(pos);
nodes_global_ids->push_back(global_node);
nodes_flags->push_back(flag | NodeFlag::_pure_ghost);
new_nodes.push_back(info.node);
node_list.push_back(info);
nodes_prank[info.node] = proc;
}
};
/* ---------------------------------------------------------------------- */
auto && intersection_right =
bbox_left.intersection(bbox_right, *communicator);
auto && intersection_left =
bbox_right.intersection(bbox_left, *communicator);
auto prank = communicator->whoAmI();
auto nb_proc = communicator->getNbProc();
using buffers_t = std::vector<DynamicCommunicationBuffer>;
std::vector<CommunicationRequest> send_requests;
buffers_t send_buffers;
for (auto && data :
zip(arange(nb_proc), intersection_left, intersection_right)) {
auto proc = std::get<0>(data);
if (proc == prank)
continue;
buffers_t::iterator it;
const auto & bbox_p_send_left = std::get<1>(data);
if (bbox_p_send_left) {
send_requests.push_back(extract_and_send_nodes(
bbox_p_send_left, nodes_left, send_buffers, proc, 0));
}
const auto & bbox_p_send_right = std::get<2>(data);
if (bbox_p_send_right) {
send_requests.push_back(extract_and_send_nodes(
bbox_p_send_right, nodes_right, send_buffers, proc, 1));
}
}
DynamicCommunicationBuffer buffer;
for (auto && data :
zip(arange(nb_proc), intersection_left, intersection_right)) {
auto proc = std::get<0>(data);
if (proc == prank)
continue;
const auto & bbox_p_send_left = std::get<1>(data);
recv_and_extract_nodes(bbox_p_send_left, nodes_left, buffer, proc, 0);
const auto & bbox_p_send_right = std::get<2>(data);
recv_and_extract_nodes(bbox_p_send_right, nodes_right, buffer, proc, 1);
}
communicator->waitAll(send_requests);
communicator->freeCommunicationRequest(send_requests);
}
auto to_sort = [&](auto && info1, auto && info2) -> bool {
return info1.position < info2.position;
};
std::sort(nodes_left.begin(), nodes_left.end(), to_sort);
std::sort(nodes_right.begin(), nodes_right.end(), to_sort);
auto register_pair = [&](auto & master, auto & slave) {
if (master == slave)
return;
// if pair already registered
auto master_slaves = periodic_master_slave.equal_range(master);
auto slave_it =
std::find_if(master_slaves.first, master_slaves.second,
[&](auto & pair) { return pair.second == slave; });
if (slave_it == master_slaves.second) {
// no duplicates
periodic_master_slave.insert(std::make_pair(master, slave));
std::cout << "adding: M " << getNodeGlobalId(master) << " <- S "
<< getNodeGlobalId(slave) << std::endl;
}
periodic_slave_master[slave] = master;
(*nodes_flags)[slave] |= NodeFlag::_periodic_slave;
(*nodes_flags)[master] |= NodeFlag::_periodic_master;
};
auto updating_master = [&](auto & old_master, auto & new_master) {
if (old_master == new_master)
return;
auto slaves = periodic_master_slave.equal_range(old_master);
AKANTU_DEBUG_ASSERT(slaves.first != periodic_master_slave.end(),
"Cannot update master " << old_master
<< ", its not a master node!");
std::cout << "updating: " << getNodeGlobalId(old_master) << " -> "
<< getNodeGlobalId(new_master) << std::endl;
decltype(periodic_master_slave) tmp_master_slave;
for (auto it = slaves.first; it != slaves.second; ++it) {
auto slave = it->second;
tmp_master_slave.insert(std::make_pair(new_master, slave));
std::cout << " - " << getNodeGlobalId(new_master) << " - "
<< getNodeGlobalId(slave) << std::endl;
/* might need the register_pair here */
// \TODO tell processor prank[slave] that master is now node1
// instead of node2
periodic_slave_master[slave] = new_master;
// \TODO tell processor prank[new_master] that it also has a slave on
// prank[slave]
}
for(auto && data : tmp_master_slave) {
periodic_master_slave.insert(data);
}
periodic_master_slave.erase(old_master);
(*nodes_flags)[old_master] |= NodeFlag::_periodic_slave;
(*nodes_flags)[old_master] &= ~NodeFlag::_periodic_master;
slaves = periodic_master_slave.equal_range(new_master);
for (auto it = slaves.first; it != slaves.second; ++it) {
std::cout << " m " << it->first << " - s " << it->second << std::endl;
}
};
auto match_found = [&](auto & info1, auto & info2) {
auto node1 = info1.node;
auto node2 = info2.node;
std::cout << "Found pair: " << node1 << " " << node2 << std::endl;
auto master = node1;
bool node1_side_master = false;
std::cout << "node1: " << node1;
if (isPeriodicMaster(node1)) {
node1_side_master = true;
std::cout << " master" << std::endl;
} else if (isPeriodicSlave(node1)) {
node1_side_master = true;
master = periodic_slave_master[node1];
// register_pair(master, node1);
std::cout << " slave of " << master << std::endl;
} else {
std::cout << " new" << std::endl;
}
auto node2_master = node2;
std::cout << "node2: " << node2;
if (isPeriodicSlave(node2)) {
node2_master = periodic_slave_master[node2];
std::cout << " slave of " << node2_master << std::endl;
} else if (isPeriodicMaster(node2)) {
std::cout << " master" << std::endl;
} else {
std::cout << " new" << std::endl;
}
if (node1_side_master) {
std::cout << "Master on node 1 side: " << master << std::endl;
if (isPeriodicSlave(node2)) {
updating_master(node2_master, master);
return;
}
if (isPeriodicMaster(node2)) {
updating_master(node2, master);
return;
}
register_pair(master, node2);
} else {
if (isPeriodicSlave(node2)) {
std::cout << "Master is node 2's master: " << node2_master << std::endl;
register_pair(node2_master, node1);
return;
}
if (isPeriodicMaster(node2)) {
std::cout << "Master is node 2: " << node2 << std::endl;
register_pair(node2, node1);
return;
}
std::cout << "Master is node 1: " << node1 << std::endl;
register_pair(node1, node2);
}
};
auto match_pairs = [&](auto & nodes_1, auto & nodes_2) {
auto it = nodes_2.begin();
for (auto && info1 : nodes_1) {
// if (not isLocalOrMasterNode(info1.node))
// continue;
auto & pos1 = info1.position;
auto it_cur = it;
for (; it_cur != nodes_2.end(); ++it_cur) {
auto & info2 = *it_cur;
auto & pos2 = info2.position;
auto dist = pos1.distance(pos2) / length;
if (dist < tolerance) {
std::cout << " ---------------------------------- " << std::endl;
match_found(info1, *it_cur);
it = it_cur;
break;
}
}
}
};
std::cout << " --------- left --- right ------------" << std::endl;
match_pairs(nodes_left, nodes_right);
std::cout << " --------- right --- left ------------" << std::endl;
match_pairs(nodes_right, nodes_left);
std::cout << periodic_slave_master.size() << std::endl;
// for (auto & pair : periodic_master_slave) {
// std::cout << prank << " - " << pair.first << " " << pair.second
// << std::endl;
// }
// std::cout << prank << " - Left" << std::endl;
// for (auto && data : nodes_left) {
// std::cout << prank << " - " << data << " -- " << getNodeType(data.node)
// << std::endl;
// }
// std::cout << prank << " - Right" << std::endl;
// for (auto && data : nodes_right) {
// std::cout << prank << " - " << data << " -- " << getNodeType(data.node)
// << std::endl;
//}
this->is_periodic |= 1 < direction;
}
} // akantu
c4science · Help