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distributed_synchronizer.cc
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/**
* @file distributed_synchronizer.cc
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @date Thu Aug 26 16:36:21 2010
*
* @brief implementation of a communicator using a static_communicator for real
* send/receive
*
* @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 "aka_common.hh"
#include "distributed_synchronizer.hh"
#include "static_communicator.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
#include <map>
#include <iostream>
/* -------------------------------------------------------------------------- */
__BEGIN_AKANTU__
/* -------------------------------------------------------------------------- */
DistributedSynchronizer::DistributedSynchronizer(Mesh & mesh,
SynchronizerID id,
MemoryID memory_id) :
Synchronizer(id, memory_id),
mesh(mesh), static_communicator(&StaticCommunicator::getStaticCommunicator())
{
AKANTU_DEBUG_IN();
nb_proc = static_communicator->getNbProc();
rank = static_communicator->whoAmI();
send_element = new Vector<Element>[nb_proc];
recv_element = new Vector<Element>[nb_proc];
mesh.registerEventHandler(*this);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
DistributedSynchronizer::~DistributedSynchronizer() {
AKANTU_DEBUG_IN();
for (UInt p = 0; p < nb_proc; ++p) {
// send_buffer[p].resize(0);
// recv_buffer[p].resize(0);
send_element[p].clear();
recv_element[p].clear();
}
// delete [] send_buffer;
// delete [] recv_buffer;
delete [] send_element;
delete [] recv_element;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
DistributedSynchronizer * DistributedSynchronizer::
createDistributedSynchronizerMesh(Mesh & mesh,
const MeshPartition * partition,
UInt root,
SynchronizerID id,
MemoryID memory_id) {
AKANTU_DEBUG_IN();
const UInt TAG_SIZES = 0;
const UInt TAG_CONNECTIVITY = 1;
const UInt TAG_DATA = 2;
const UInt TAG_PARTITIONS = 3;
const UInt TAG_NB_NODES = 4;
const UInt TAG_NODES = 5;
const UInt TAG_COORDINATES = 6;
const UInt TAG_NODES_TYPE = 7;
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
UInt nb_proc = comm.getNbProc();
UInt my_rank = comm.whoAmI();
DistributedSynchronizer & communicator = *(new DistributedSynchronizer(mesh, id, memory_id));
if(nb_proc == 1) return &communicator;
UInt * local_connectivity = NULL;
UInt * local_partitions = NULL;
UInt * local_data = NULL;
Vector<UInt> * old_nodes = mesh.getNodesGlobalIdsPointer();
Vector<Real> * nodes = mesh.getNodesPointer();
UInt spatial_dimension = nodes->getNbComponent();
/* ------------------------------------------------------------------------ */
/* Local (rank == root) */
/* ------------------------------------------------------------------------ */
if(my_rank == root) {
AKANTU_DEBUG_ASSERT(partition->getNbPartition() == nb_proc,
"The number of partition does not match the number of processors");
/**
* connectivity and communications scheme construction
*/
Mesh::type_iterator it = mesh.firstType(mesh.getSpatialDimension());
Mesh::type_iterator end = mesh.lastType(mesh.getSpatialDimension());
UInt count = 0;
for(; it != end; ++it) {
ElementType type = *it;
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_element = mesh.getNbElement(*it);
UInt nb_local_element[nb_proc];
UInt nb_ghost_element[nb_proc];
UInt nb_element_to_send[nb_proc];
memset(nb_local_element, 0, nb_proc*sizeof(UInt));
memset(nb_ghost_element, 0, nb_proc*sizeof(UInt));
memset(nb_element_to_send, 0, nb_proc*sizeof(UInt));
UInt * partition_num = partition->getPartition(type, _not_ghost).values;
UInt * ghost_partition = partition->getGhostPartition(type, _ghost).values;
UInt * ghost_partition_offset = partition->getGhostPartitionOffset(type, _ghost).values;
UIntDataMap & uint_data_map = mesh.getUIntDataMap(type, _not_ghost);
UInt nb_tags = uint_data_map.size();
/* -------------------------------------------------------------------- */
/// constructing the reordering structures
for (UInt el = 0; el < nb_element; ++el) {
nb_local_element[partition_num[el]]++;
for (UInt part = ghost_partition_offset[el];
part < ghost_partition_offset[el + 1];
++part) {
nb_ghost_element[ghost_partition[part]]++;
}
nb_element_to_send[partition_num[el]] +=
ghost_partition_offset[el + 1] - ghost_partition_offset[el] + 1;
}
/// allocating buffers
UInt * buffers[nb_proc];
UInt * buffers_tmp[nb_proc];
for (UInt p = 0; p < nb_proc; ++p) {
UInt size = nb_nodes_per_element * (nb_local_element[p] +
nb_ghost_element[p]);
buffers[p] = new UInt[size];
buffers_tmp[p] = buffers[p];
}
/// copying the local connectivity
UInt * conn_val = mesh.getConnectivity(type, _not_ghost).values;
for (UInt el = 0; el < nb_element; ++el) {
memcpy(buffers_tmp[partition_num[el]],
conn_val + el * nb_nodes_per_element,
nb_nodes_per_element * sizeof(UInt));
buffers_tmp[partition_num[el]] += nb_nodes_per_element;
}
/// copying the connectivity of ghost element
for (UInt el = 0; el < nb_element; ++el) {
for (UInt part = ghost_partition_offset[el];
part < ghost_partition_offset[el + 1];
++part) {
UInt proc = ghost_partition[part];
memcpy(buffers_tmp[proc],
conn_val + el * nb_nodes_per_element,
nb_nodes_per_element * sizeof(UInt));
buffers_tmp[proc] += nb_nodes_per_element;
}
}
UInt names_size = 0;
UIntDataMap::iterator it_data;
for(it_data = uint_data_map.begin(); it_data != uint_data_map.end(); ++it_data) {
names_size += it_data->first.size() + 1;
}
/* -------->>>>-SIZE + CONNECTIVITY------------------------------------ */
/// send all connectivity and ghost information to all processors
std::vector<CommunicationRequest *> requests;
for (UInt p = 0; p < nb_proc; ++p) {
if(p != root) {
UInt size[6];
size[0] = (UInt) type;
size[1] = nb_local_element[p];
size[2] = nb_ghost_element[p];
size[3] = nb_element_to_send[p];
size[4] = nb_tags;
size[5] = names_size;
AKANTU_DEBUG_INFO("Sending connectivities informations to proc " << p << " TAG("<< Tag::genTag(my_rank, count, TAG_SIZES) <<")");
comm.send(size, 6, p, Tag::genTag(my_rank, count, TAG_SIZES));
AKANTU_DEBUG_INFO("Sending connectivities to proc " << p << " TAG("<< Tag::genTag(my_rank, count, TAG_CONNECTIVITY) <<")");
requests.push_back(comm.asyncSend(buffers[p],
nb_nodes_per_element * (nb_local_element[p] +
nb_ghost_element[p]),
p, Tag::genTag(my_rank, count, TAG_CONNECTIVITY)));
} else {
local_connectivity = buffers[p];
}
}
/// create the renumbered connectivity
AKANTU_DEBUG_INFO("Renumbering local connectivities");
MeshUtils::renumberMeshNodes(mesh,
local_connectivity,
nb_local_element[root],
nb_ghost_element[root],
type,
*old_nodes);
comm.waitAll(requests);
comm.freeCommunicationRequest(requests);
requests.clear();
for (UInt p = 0; p < nb_proc; ++p) {
delete [] buffers[p];
}
/* -------------------------------------------------------------------- */
for (UInt p = 0; p < nb_proc; ++p) {
buffers[p] = new UInt[nb_ghost_element[p] + nb_element_to_send[p]];
buffers_tmp[p] = buffers[p];
}
/// splitting the partition information to send them to processors
UInt count_by_proc[nb_proc];
memset(count_by_proc, 0, nb_proc*sizeof(UInt));
for (UInt el = 0; el < nb_element; ++el) {
*(buffers_tmp[partition_num[el]]++) = ghost_partition_offset[el + 1] - ghost_partition_offset[el];
for (UInt part = ghost_partition_offset[el], i = 0;
part < ghost_partition_offset[el + 1];
++part, ++i) {
*(buffers_tmp[partition_num[el]]++) = ghost_partition[part];
}
}
for (UInt el = 0; el < nb_element; ++el) {
for (UInt part = ghost_partition_offset[el], i = 0;
part < ghost_partition_offset[el + 1];
++part, ++i) {
*(buffers_tmp[ghost_partition[part]]++) = partition_num[el];
}
}
/* -------->>>>-PARTITIONS--------------------------------------------- */
/// last data to compute the communication scheme
for (UInt p = 0; p < nb_proc; ++p) {
if(p != root) {
AKANTU_DEBUG_INFO("Sending partition informations to proc " << p << " TAG("<< Tag::genTag(my_rank, count, TAG_PARTITIONS) <<")");
requests.push_back(comm.asyncSend(buffers[p],
nb_element_to_send[p] + nb_ghost_element[p],
p, Tag::genTag(my_rank, count, TAG_PARTITIONS)));
} else {
local_partitions = buffers[p];
}
}
AKANTU_DEBUG_INFO("Creating communications scheme");
communicator.fillCommunicationScheme(local_partitions,
nb_local_element[root],
nb_ghost_element[root],
type);
comm.waitAll(requests);
comm.freeCommunicationRequest(requests);
requests.clear();
for (UInt p = 0; p < nb_proc; ++p) {
delete [] buffers[p];
}
/* -------------------------------------------------------------------- */
/// send int data assossiated to the mesh
if(nb_tags) {
UInt uint_names_size = names_size / sizeof(UInt) + (names_size % sizeof(UInt) ? 1 : 0);
for (UInt p = 0; p < nb_proc; ++p) {
UInt size = nb_tags * (nb_local_element[p] + nb_ghost_element[p])
+ uint_names_size;
buffers[p] = new UInt[size];
std::fill_n(buffers[p], size, 0);
buffers_tmp[p] = buffers[p];
}
char * names = new char[names_size];
char * names_tmp = names;
memset(names, 0, names_size);
for(it_data = uint_data_map.begin(); it_data != uint_data_map.end(); ++it_data) {
UInt * data = it_data->second->values;
memcpy(names_tmp, it_data->first.data(), it_data->first.size());
names_tmp += it_data->first.size() + 1;
/// copying data for the local element
for (UInt el = 0; el < nb_element; ++el) {
UInt proc = partition_num[el];
*(buffers_tmp[proc]) = data[el];
buffers_tmp[proc]++;
}
/// copying the data for the ghost element
for (UInt el = 0; el < nb_element; ++el) {
for (UInt part = ghost_partition_offset[el];
part < ghost_partition_offset[el + 1];
++part) {
UInt proc = ghost_partition[part];
*(buffers_tmp[proc]) = data[el];
buffers_tmp[proc]++;
}
}
}
/* -------->>>>-TAGS------------------------------------------------- */
for (UInt p = 0; p < nb_proc; ++p) {
memcpy((char *)buffers_tmp[p], names, names_size);
if(p != root) {
UInt size = nb_tags * (nb_local_element[p] + nb_ghost_element[p])
+ uint_names_size;
AKANTU_DEBUG_INFO("Sending associated data to proc " << p << " TAG("<< Tag::genTag(my_rank, count, TAG_DATA) <<")");
requests.push_back(comm.asyncSend(buffers[p], size, p, Tag::genTag(my_rank, count, TAG_DATA)));
} else {
local_data = buffers[p];
}
}
MeshUtils::setUIntData(mesh, local_data, nb_tags, type);
comm.waitAll(requests);
comm.freeCommunicationRequest(requests);
requests.clear();
for (UInt p = 0; p < nb_proc; ++p) delete [] buffers[p];
delete [] names;
}
++count;
}
/* -------->>>>-SIZE----------------------------------------------------- */
for (UInt p = 0; p < nb_proc; ++p) {
if(p != root) {
UInt size[6];
size[0] = (UInt) _not_defined;
size[1] = 0;
size[2] = 0;
size[3] = 0;
size[4] = 0;
size[5] = 0;
AKANTU_DEBUG_INFO("Sending empty connectivities informations to proc " << p << " TAG("<< Tag::genTag(my_rank, count, TAG_SIZES) <<")");
comm.send(size, 6, p, Tag::genTag(my_rank, count, TAG_SIZES));
}
}
/* ---------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
/**
* Nodes coordinate construction and synchronization
*/
std::multimap< UInt, std::pair<UInt, UInt> > nodes_to_proc;
/// get the list of nodes to send and send them
Real * local_nodes = NULL;
UInt nb_nodes_per_proc[nb_proc];
UInt * nodes_per_proc[nb_proc];
/* --------<<<<-NB_NODES + NODES----------------------------------------- */
for (UInt p = 0; p < nb_proc; ++p) {
UInt nb_nodes = 0;
// UInt * buffer;
if(p != root) {
AKANTU_DEBUG_INFO("Receiving number of nodes from proc " << p << " TAG("<< Tag::genTag(p, 0, TAG_NB_NODES) <<")");
comm.receive(&nb_nodes, 1, p, Tag::genTag(p, 0, TAG_NB_NODES));
nodes_per_proc[p] = new UInt[nb_nodes];
nb_nodes_per_proc[p] = nb_nodes;
AKANTU_DEBUG_INFO("Receiving list of nodes from proc " << p << " TAG("<< Tag::genTag(p, 0, TAG_NODES) <<")");
comm.receive(nodes_per_proc[p], nb_nodes, p, Tag::genTag(p, 0, TAG_NODES));
} else {
nb_nodes = old_nodes->getSize();
nb_nodes_per_proc[p] = nb_nodes;
nodes_per_proc[p] = old_nodes->values;
}
/// get the coordinates for the selected nodes
Real * nodes_to_send = new Real[nb_nodes * spatial_dimension];
Real * nodes_to_send_tmp = nodes_to_send;
for (UInt n = 0; n < nb_nodes; ++n) {
memcpy(nodes_to_send_tmp,
nodes->values + spatial_dimension * nodes_per_proc[p][n],
spatial_dimension * sizeof(Real));
// nodes_to_proc.insert(std::make_pair(buffer[n], std::make_pair(p, n)));
nodes_to_send_tmp += spatial_dimension;
}
/* -------->>>>-COORDINATES-------------------------------------------- */
if(p != root) { /// send them for distant processors
AKANTU_DEBUG_INFO("Sending coordinates to proc " << p << " TAG("<< Tag::genTag(my_rank, 0, TAG_COORDINATES) <<")");
comm.send(nodes_to_send, nb_nodes * spatial_dimension, p, Tag::genTag(my_rank, 0, TAG_COORDINATES));
delete [] nodes_to_send;
} else { /// save them for local processor
local_nodes = nodes_to_send;
}
}
/// construct the local nodes coordinates
UInt nb_nodes = old_nodes->getSize();
nodes->resize(nb_nodes);
memcpy(nodes->values, local_nodes, nb_nodes * spatial_dimension * sizeof(Real));
delete [] local_nodes;
Vector<Int> * nodes_type_per_proc[nb_proc];
for (UInt p = 0; p < nb_proc; ++p) {
nodes_type_per_proc[p] = new Vector<Int>(nb_nodes_per_proc[p]);
}
communicator.fillNodesType(mesh);
/* --------<<<<-NODES_TYPE-1--------------------------------------------- */
for (UInt p = 0; p < nb_proc; ++p) {
if(p != root) {
AKANTU_DEBUG_INFO("Receiving first nodes types from proc " << p << " TAG("<< Tag::genTag(my_rank, count, TAG_NODES_TYPE) <<")");
comm.receive(nodes_type_per_proc[p]->values,
nb_nodes_per_proc[p], p, Tag::genTag(p, 0, TAG_NODES_TYPE));
} else {
nodes_type_per_proc[p]->copy(mesh.getNodesType());
}
for (UInt n = 0; n < nb_nodes_per_proc[p]; ++n) {
if((*nodes_type_per_proc[p])(n) == -2)
nodes_to_proc.insert(std::make_pair(nodes_per_proc[p][n], std::make_pair(p, n)));
}
}
std::multimap< UInt, std::pair<UInt, UInt> >::iterator it_node;
std::pair< std::multimap< UInt, std::pair<UInt, UInt> >::iterator,
std::multimap< UInt, std::pair<UInt, UInt> >::iterator > it_range;
for (UInt i = 0; i < mesh.nb_global_nodes; ++i) {
it_range = nodes_to_proc.equal_range(i);
if(it_range.first == nodes_to_proc.end() || it_range.first->first != i) continue;
UInt node_type = (it_range.first)->second.first;
for (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 != node_type)
nodes_type_per_proc[proc]->values[node] = node_type;
}
}
/* -------->>>>-NODES_TYPE-2--------------------------------------------- */
std::vector<CommunicationRequest *> requests;
for (UInt p = 0; p < nb_proc; ++p) {
if(p != root) {
AKANTU_DEBUG_INFO("Sending nodes types to proc " << p << " TAG("<< Tag::genTag(my_rank, 0, TAG_NODES_TYPE) <<")");
requests.push_back(comm.asyncSend(nodes_type_per_proc[p]->values,
nb_nodes_per_proc[p], p, Tag::genTag(my_rank, 0, TAG_NODES_TYPE)));
} else {
mesh.getNodesTypePointer()->copy(*nodes_type_per_proc[p]);
}
}
comm.waitAll(requests);
comm.freeCommunicationRequest(requests);
requests.clear();
for (UInt p = 0; p < nb_proc; ++p) {
if(p != root) delete [] nodes_per_proc[p];
delete nodes_type_per_proc[p];
}
/* ---------------------------------------------------------------------- */
/* Distant (rank != root) */
/* ---------------------------------------------------------------------- */
} else {
/**
* connectivity and communications scheme construction on distant processors
*/
ElementType type = _not_defined;
UInt count = 0;
do {
/* --------<<<<-SIZE--------------------------------------------------- */
UInt size[6] = { 0 };
comm.receive(size, 6, root, Tag::genTag(root, count, TAG_SIZES));
type = (ElementType) size[0];
UInt nb_local_element = size[1];
UInt nb_ghost_element = size[2];
UInt nb_element_to_send = size[3];
UInt nb_tags = size[4];
UInt names_size = size[5];
UInt uint_names_size = names_size / sizeof(UInt) + (names_size % sizeof(UInt) ? 1 : 0);
if(type != _not_defined) {
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
/* --------<<<<-CONNECTIVITY----------------------------------------- */
local_connectivity = new UInt[(nb_local_element + nb_ghost_element) *
nb_nodes_per_element];
AKANTU_DEBUG_INFO("Receiving connectivities from proc " << root);
comm.receive(local_connectivity, nb_nodes_per_element * (nb_local_element +
nb_ghost_element),
root, Tag::genTag(root, count, TAG_CONNECTIVITY));
AKANTU_DEBUG_INFO("Renumbering local connectivities");
MeshUtils::renumberMeshNodes(mesh,
local_connectivity,
nb_local_element,
nb_ghost_element,
type,
*old_nodes);
delete [] local_connectivity;
/* --------<<<<-PARTITIONS--------------------------------------------- */
local_partitions = new UInt[nb_element_to_send + nb_ghost_element * 2];
AKANTU_DEBUG_INFO("Receiving partition informations from proc " << root);
comm.receive(local_partitions,
nb_element_to_send + nb_ghost_element * 2,
root, Tag::genTag(root, count, TAG_PARTITIONS));
AKANTU_DEBUG_INFO("Creating communications scheme");
communicator.fillCommunicationScheme(local_partitions,
nb_local_element,
nb_ghost_element,
type);
delete [] local_partitions;
/* --------<<<<-TAGS------------------------------------------------- */
if(nb_tags) {
AKANTU_DEBUG_INFO("Receiving associated data from proc " << root);
UInt size_data = (nb_local_element + nb_ghost_element) * nb_tags
+ uint_names_size;
local_data = new UInt[size_data];
comm.receive(local_data, size_data, root, Tag::genTag(root, count, TAG_DATA));
MeshUtils::setUIntData(mesh, local_data, nb_tags, type);
delete [] local_data;
}
}
++count;
} while(type != _not_defined);
/**
* Nodes coordinate construction and synchronization on distant processors
*/
/* -------->>>>-NB_NODES + NODES----------------------------------------- */
AKANTU_DEBUG_INFO("Sending list of nodes to proc " << root);
UInt nb_nodes = old_nodes->getSize();
comm.send(&nb_nodes, 1, root, Tag::genTag(my_rank, 0, TAG_NB_NODES));
comm.send(old_nodes->values, nb_nodes, root, Tag::genTag(my_rank, 0, TAG_NODES));
/* --------<<<<-COORDINATES---------------------------------------------- */
nodes->resize(nb_nodes);
AKANTU_DEBUG_INFO("Receiving coordinates from proc " << root);
comm.receive(nodes->values, nb_nodes * spatial_dimension, root, Tag::genTag(root, 0, TAG_COORDINATES));
communicator.fillNodesType(mesh);
/* --------<<<<-NODES_TYPE-2--------------------------------------------- */
Int * nodes_types = mesh.getNodesTypePointer()->values;
AKANTU_DEBUG_INFO("Sending first nodes types to proc " << root);
comm.send(nodes_types, nb_nodes,
root, Tag::genTag(my_rank, 0, TAG_NODES_TYPE));
/* --------<<<<-NODES_TYPE-2--------------------------------------------- */
AKANTU_DEBUG_INFO("Receiving nodes types from proc " << root);
comm.receive(nodes_types, nb_nodes,
root, Tag::genTag(root, 0, TAG_NODES_TYPE));
}
comm.broadcast(&(mesh.nb_global_nodes), 1, root);
AKANTU_DEBUG_OUT();
return &communicator;
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::fillNodesType(Mesh & mesh) {
AKANTU_DEBUG_IN();
// StaticCommunicator * comm = StaticCommunicator::getStaticCommunicator();
// UInt my_rank = comm.whoAmI();
UInt nb_nodes = mesh.getNbNodes();
// std::cout << nb_nodes << std::endl;
Int * nodes_type = mesh.getNodesTypePointer()->values;
//memcpy(nodes_type, nodes_type_tmp, nb_nodes * sizeof(Int));
UInt * nodes_set = new UInt[nb_nodes];
std::fill_n(nodes_set, nb_nodes, 0);
// Mesh::ConnectivityTypeList::const_iterator it;
const UInt NORMAL_SET = 1;
const UInt GHOST_SET = 2;
bool * already_seen = new bool[nb_nodes];
for(UInt g = _not_ghost; g <= _ghost; ++g) {
GhostType gt = (GhostType) g;
UInt set = NORMAL_SET;
if (gt == _ghost) set = GHOST_SET;
std::fill_n(already_seen, nb_nodes, false);
Mesh::type_iterator it = mesh.firstType(0, gt);
Mesh::type_iterator end = mesh.lastType(0, gt);
for(; it != end; ++it) {
ElementType type = *it;
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_element = mesh.getNbElement(type, gt);
UInt * conn_val = mesh.getConnectivity(type, gt).values;
for (UInt e = 0; e < nb_element; ++e) {
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
AKANTU_DEBUG_ASSERT(*conn_val < nb_nodes, "Node " << *conn_val
<< " bigger than number of nodes " << nb_nodes);
if(!already_seen[*conn_val]) {
nodes_set[*conn_val] += set;
already_seen[*conn_val] = true;
}
conn_val++;
}
}
}
}
delete [] already_seen;
for (UInt i = 0; i < nb_nodes; ++i) {
if(nodes_set[i] == NORMAL_SET) nodes_type[i] = -1;
else if(nodes_set[i] == GHOST_SET) nodes_type[i] = -3;
else if(nodes_set[i] == (GHOST_SET + NORMAL_SET)) nodes_type[i] = -2;
}
delete [] nodes_set;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::fillCommunicationScheme(UInt * partition,
UInt nb_local_element,
UInt nb_ghost_element,
ElementType type) {
AKANTU_DEBUG_IN();
Element element;
element.type = type;
UInt * part = partition;
part = partition;
for (UInt lel = 0; lel < nb_local_element; ++lel) {
UInt nb_send = *part; part++;
element.element = lel;
element.ghost_type = _not_ghost;
for (UInt p = 0; p < nb_send; ++p) {
UInt proc = *part; part++;
AKANTU_DEBUG(dblAccessory, "Must send : " << element << " to proc " << proc);
(send_element[proc]).push_back(element);
}
}
for (UInt gel = 0; gel < nb_ghost_element; ++gel) {
UInt proc = *part; part++;
element.element = gel;
element.ghost_type = _ghost;
AKANTU_DEBUG(dblAccessory, "Must recv : " << element << " from proc " << proc);
recv_element[proc].push_back(element);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::asynchronousSynchronize(DataAccessor & data_accessor,
SynchronizationTag tag) {
AKANTU_DEBUG_IN();
if (communications.find(tag) == communications.end()) {
communications[tag].resize(nb_proc);
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);
for (UInt p = 0; p < nb_proc; ++p) {
UInt ssize = communication.size_to_send[p];
if(p == rank || ssize == 0) continue;
CommunicationBuffer & buffer = communication.send_buffer[p];
buffer.resize(ssize);
#ifndef AKANTU_NDEBUG
UInt nb_elements = send_element[p].getSize();
AKANTU_DEBUG_INFO("Packing data for proc " << p
<< " (" << ssize << "/" << nb_elements
<<" data to send/elements)");
#endif
data_accessor.packElementData(buffer, send_element[p], tag);
AKANTU_DEBUG_ASSERT(buffer.getPackedSize() == ssize,
"a problem have been introduced with "
<< "false sent sizes declaration "
<< buffer.getPackedSize() << " != " << ssize);
std::cerr << std::dec;
AKANTU_DEBUG_INFO("Posting send to proc " << p);
communication.send_requests.push_back(static_communicator->asyncSend(buffer.storage(),
ssize,
p,
(Int) tag));
}
AKANTU_DEBUG_ASSERT(communication.recv_requests.size() == 0,
"There must be some pending receive communications");
for (UInt p = 0; p < nb_proc; ++p) {
UInt rsize = communication.size_to_receive[p];
if(p == rank || rsize == 0) continue;
CommunicationBuffer & buffer = communication.recv_buffer[p];
buffer.resize(rsize);
AKANTU_DEBUG_INFO("Posting receive from proc " << p << " (" << rsize << " data to receive)");
communication.recv_requests.push_back(static_communicator->asyncReceive(buffer.storage(),
rsize,
p,
(Int) tag));
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::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];
data_accessor.unpackElementData(buffer, recv_element[proc], 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();
}
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();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::computeBufferSize(DataAccessor & data_accessor,
SynchronizationTag tag) {
AKANTU_DEBUG_IN();
for (UInt p = 0; p < nb_proc; ++p) {
UInt ssend = 0;
UInt sreceive = 0;
if(p != rank) {
ssend = data_accessor.getNbDataForElements(send_element[p], tag);
sreceive = data_accessor.getNbDataForElements(recv_element[p], tag);
AKANTU_DEBUG_INFO("I have " << ssend << "(" << ssend / 1024.
<< "kB - "<< send_element[p].getSize() <<" element(s)) data to send to " << p
<< " and " << sreceive << "(" << sreceive / 1024.
<< "kB - "<< recv_element[p].getSize() <<" element(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 DistributedSynchronizer::printself(std::ostream & stream, int indent) const {
std::string space;
for(Int i = 0; i < indent; i++, space += AKANTU_INDENT);
Int prank = StaticCommunicator::getStaticCommunicator().whoAmI();
Int psize = StaticCommunicator::getStaticCommunicator().getNbProc();
stream << "[" << prank << "/" << psize << "]" << space << "DistributedSynchronizer [" << std::endl;
for (UInt p = 0; p < nb_proc; ++p) {
if (p == UInt(prank)) continue;
stream << "[" << prank << "/" << psize << "]" << space << " + Communication to proc " << p << " [" << std::endl;
if(AKANTU_DEBUG_TEST(dblDump)) {
stream << "[" << prank << "/" << psize << "]" << space << " - Element to send to proc " << p << " [" << std::endl;
Vector<Element>::iterator<Element> it_el = send_element[p].begin();
Vector<Element>::iterator<Element> end_el = send_element[p].end();
for(;it_el != end_el; ++it_el)
stream << "[" << prank << "/" << psize << "]" << space << " " << *it_el << std::endl;
stream << "[" << prank << "/" << psize << "]" << space << " ]" << std::endl;
stream << "[" << prank << "/" << psize << "]" << space << " - Element to recv from proc " << p << " [" << std::endl;
it_el = recv_element[p].begin();
end_el = recv_element[p].end();
for(;it_el != end_el; ++it_el)
stream << "[" << prank << "/" << psize << "]" << space << " " << *it_el << std::endl;stream << "[" << prank << "/" << psize << "]" << space << " ]" << std::endl;
}
std::map< SynchronizationTag, Communication>::const_iterator it = communications.begin();
std::map< SynchronizationTag, Communication>::const_iterator end = communications.end();
for (; it != end; ++it) {
const SynchronizationTag & tag = it->first;
const Communication & communication = it->second;
UInt ssend = communication.size_to_send[p];
UInt sreceive = communication.size_to_receive[p];
stream << "[" << prank << "/" << psize << "]" << space << " - Tag " << tag << " -> " << ssend << "byte(s) -- <- " << sreceive << "byte(s)" << std::endl;
}
std::cout << "[" << prank << "/" << psize << "]" << space << " ]" << std::endl;
}
std::cout << "[" << prank << "/" << psize << "]" << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::onElementsRemoved(const Vector<Element> & element_to_remove,
const ByElementTypeUInt & new_numbering) {
AKANTU_DEBUG_IN();
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
UInt psize = comm.getNbProc();
UInt prank = comm.whoAmI();
std::vector<CommunicationRequest *> isend_requests;
Vector<UInt> * list_of_el = new Vector<UInt>[nb_proc];
// Handling ghost elements
for (UInt p = 0; p < psize; ++p) {
if (p == prank) continue;
Vector<Element> & recv = recv_element[p];
if(recv.getSize() == 0) continue;
Vector<Element>::iterator<Element> recv_begin = recv.begin();
Vector<Element>::iterator<Element> recv_end = recv.end();
Vector<Element>::const_iterator<Element> er_it = element_to_remove.begin();
Vector<Element>::const_iterator<Element> er_end = element_to_remove.end();
// for (;it != end; ++it) {
// const Element & el = *it;
// if(el.ghost_type == _ghost) {
// Vector<Element>::iterator<Element> pos = std::find(recv_begin, recv_end, el);
// if(pos != recv_end) {
// UInt i = pos - recv_begin;
// AKANTU_DEBUG_ASSERT(i < recv.getSize(), "The element is out of the list");
// list_of_el_to_remove.push_back(i);
// }
// } else {
// /// \todo handle the removal of element to send from the ghost of other procs
// AKANTU_EXCEPTION("DistributedSynchronizer do not know how to remove _not_ghost element, ask a developer to finish is job");
// }
// }
Vector<UInt> & list = list_of_el[p];
for (UInt i = 0; recv_begin != recv_end; ++i, ++recv_begin) {
const Element & el = *recv_begin;
Vector<Element>::const_iterator<Element> pos = std::find(er_it, er_end, el);
if(pos == er_end) {
list.push_back(i);
}
}
// if (list_of_el_to_remove.getSize() != 0) {
// std::sort(list_of_el_to_remove.begin(), list_of_el_to_remove.end());
// UInt lr = 0;
// for (UInt l = 0; l < recv.getSize(); ++l) {
// if(lr < list_of_el_to_remove.getSize() && list_of_el_to_remove(lr) == l) ++lr;
// else list.push_back(l);
// }
// AKANTU_DEBUG_INFO("Sending list of elements (" << list.getSize() << " elements) of proc " << p << " TAG("<< Tag::genTag(p, 0, 0) <<")");
// list.push_back(UInt(-1));
// } else {
// list.push_back(UInt(0));
// }
if(list.getSize() == recv.getSize())
list.push_back(UInt(0));
else list.push_back(UInt(-1));
isend_requests.push_back(comm.asyncSend(list.storage(), list.getSize(),
p, Tag::genTag(prank, 0, 0)));
list.erase(list.getSize() - 1);
if(list.getSize() == recv.getSize()) continue;
Vector<Element> new_recv;
for (UInt nr = 0; nr < list.getSize(); ++nr) {
Element & el = recv(list(nr));
el.element = new_numbering(el.type, el.ghost_type)(el.element);
new_recv.push_back(el);
}
AKANTU_DEBUG_INFO("I had " << recv.getSize() << " elements to recv from proc " << p << " and "
<< list.getSize() << " elements to keep. I have "
<< new_recv.getSize() << " elements left.");
recv.copy(new_recv);
}
for (UInt p = 0; p < psize; ++p) {
if (p == prank) continue;
Vector<Element> & send = send_element[p];
if(send.getSize() == 0) continue;
CommunicationStatus status;
AKANTU_DEBUG_INFO("Getting number of elements of proc " << p << " not needed anymore TAG("<< Tag::genTag(p, 0, 0) <<")");
comm.probe<UInt>(p, Tag::genTag(p, 0, 0), status);
Vector<UInt> list(status.getSize());
AKANTU_DEBUG_INFO("Receiving list of elements (" << status.getSize() - 1 << " elements) no longer needed by proc " << p << " TAG("<< Tag::genTag(p, 0, 0) <<")");
comm.receive(list.storage(), list.getSize(),
p, Tag::genTag(p, 0, 0));
if(list.getSize() == 1 && list(0) == 0) continue;
list.erase(list.getSize() - 1);
Vector<Element> new_send;
for (UInt ns = 0; ns < list.getSize(); ++ns) {
new_send.push_back(send(list(ns)));
}
AKANTU_DEBUG_INFO("I had " << send.getSize() << " elements to send to proc " << p << " and "
<< list.getSize() << " elements to keep. I have "
<< new_send.getSize() << " elements left.");
send.copy(new_send);
}
comm.waitAll(isend_requests);
comm.freeCommunicationRequest(isend_requests);
delete [] list_of_el;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
__END_AKANTU__
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