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rAKA/src/synchronizer/distributed_synchronizer.cc
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distributed_synchronizer.cc
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/**
* @file distributed_synchronizer.cc
*
* @author Dana Christen <dana.christen@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Jun 16 2011
* @date last modification: Fri Sep 05 2014
*
* @brief implementation of a communicator using a static_communicator for real
* send/receive
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 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 "aka_common.hh"
#include "distributed_synchronizer.hh"
#include "static_communicator.hh"
#include "mesh_utils.hh"
#include "mesh_data.hh"
#include "element_group.hh"
/* -------------------------------------------------------------------------- */
#include <map>
#include <iostream>
#include <algorithm>
#if defined(AKANTU_DEBUG_TOOLS)
# include "aka_debug_tools.hh"
#endif
/* -------------------------------------------------------------------------- */
__BEGIN_AKANTU__
/* -------------------------------------------------------------------------- */
DistributedSynchronizer::DistributedSynchronizer(Mesh & mesh,
SynchronizerID id,
MemoryID memory_id,
const bool register_to_event_manager) :
Synchronizer(id, memory_id),
mesh(mesh),
prank_to_element("prank_to_element", id)
{
AKANTU_DEBUG_IN();
nb_proc = static_communicator->getNbProc();
rank = static_communicator->whoAmI();
send_element = new Array<Element>[nb_proc];
recv_element = new Array<Element>[nb_proc];
for (UInt p = 0; p < nb_proc; ++p) {
std::stringstream sstr; sstr << p;
send_element[p].setID(id+":send_elements_"+sstr.str());
recv_element[p].setID(id+":recv_elements_"+sstr.str());
}
if (register_to_event_manager)
mesh.registerEventHandler(*this);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
DistributedSynchronizer::~DistributedSynchronizer() {
AKANTU_DEBUG_IN();
for (UInt p = 0; p < nb_proc; ++p) {
send_element[p].clear();
recv_element[p].clear();
}
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();
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;
Array<UInt> * old_nodes = mesh.getNodesGlobalIdsPointer();
old_nodes->resize(0);
Array<Real> * nodes = mesh.getNodesPointer();
UInt spatial_dimension = nodes->getNbComponent();
mesh.synchronizeGroupNames();
/* ------------------------------------------------------------------------ */
/* 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: " <<
partition->getNbPartition() << " != " << nb_proc);
/**
* connectivity and communications scheme construction
*/
Mesh::type_iterator it = mesh.firstType(_all_dimensions,
_not_ghost,
_ek_not_defined);
Mesh::type_iterator end = mesh.lastType(_all_dimensions,
_not_ghost,
_ek_not_defined);
UInt count = 0;
/* --- MAIN LOOP ON TYPES --- */
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));
/// \todo change this ugly way to avoid a problem if an element
/// type is present in the mesh but not in the partitions
const Array<UInt> * tmp_partition_num = NULL;
try {
tmp_partition_num = &partition->getPartition(type, _not_ghost);
} catch(...) {
continue;
}
const Array<UInt> & partition_num = *tmp_partition_num;
const CSR<UInt> & ghost_partition = partition->getGhostPartitionCSR()(type, _not_ghost);
/* -------------------------------------------------------------------- */
/// constructing the reordering structures
for (UInt el = 0; el < nb_element; ++el) {
nb_local_element[partition_num(el)]++;
for (CSR<UInt>::const_iterator part = ghost_partition.begin(el);
part != ghost_partition.end(el);
++part) {
nb_ghost_element[*part]++;
}
nb_element_to_send[partition_num(el)] += ghost_partition.getNbCols(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).storage();
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 (CSR<UInt>::const_iterator part = ghost_partition.begin(el);
part != ghost_partition.end(el);
++part) {
UInt proc = *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;
}
}
/// tag info
std::vector<std::string> tag_names;
mesh.getMeshData().getTagNames(tag_names, type);
UInt nb_tags = tag_names.size();
/* -------->>>>-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[5];
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;
AKANTU_DEBUG_INFO("Sending connectivities informations to proc " << p << " TAG("<< Tag::genTag(my_rank, count, TAG_SIZES) <<")");
comm.send(size, 5, 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.getNbCols(el);
UInt i(0);
for (CSR<UInt>::const_iterator part = ghost_partition.begin(el);
part != ghost_partition.end(el);
++part, ++i) {
*(buffers_tmp[partition_num(el)]++) = *part;
}
}
for (UInt el = 0; el < nb_element; ++el) {
UInt i(0);
for (CSR<UInt>::const_iterator part = ghost_partition.begin(el);
part != ghost_partition.end(el);
++part, ++i) {
*(buffers_tmp[*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];
}
}
if(Mesh::getSpatialDimension(type) == mesh.getSpatialDimension()) {
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 data assossiated to the mesh
/* -------->>>>-TAGS--------------------------------------------------- */
synchronizeTagsSend(communicator, root, mesh, nb_tags, type,
partition_num,
ghost_partition,
nb_local_element[root],
nb_ghost_element[root]);
/* -------------------------------------------------------------------- */
/// send data assossiated to groups
/* -------->>>>-GROUPS------------------------------------------------- */
synchronizeElementGroups(communicator, root, mesh, type,
partition_num,
ghost_partition,
nb_element);
++count;
}
/* -------->>>>-SIZE----------------------------------------------------- */
for (UInt p = 0; p < nb_proc; ++p) {
if(p != root) {
UInt size[5];
size[0] = (UInt) _not_defined;
size[1] = 0;
size[2] = 0;
size[3] = 0;
size[4] = 0;
AKANTU_DEBUG_INFO("Sending empty connectivities informations to proc " << p << " TAG("<< Tag::genTag(my_rank, count, TAG_SIZES) <<")");
comm.send(size, 5, 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];
comm.broadcast(&(mesh.nb_global_nodes), 1, root);
/* --------<<<<-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->storage();
}
/// 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->storage() + 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->storage(), local_nodes, nb_nodes * spatial_dimension * sizeof(Real));
delete [] local_nodes;
Array<Int> * nodes_type_per_proc[nb_proc];
for (UInt p = 0; p < nb_proc; ++p) {
nodes_type_per_proc[p] = new Array<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]->storage(),
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]->storage()[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]->storage(),
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];
}
/* -------->>>>-NODE GROUPS --------------------------------------------- */
synchronizeNodeGroupsMaster(communicator, root, mesh);
/* ---------------------------------------------------------------------- */
/* Distant (rank != root) */
/* ---------------------------------------------------------------------- */
} else {
/**
* connectivity and communications scheme construction on distant processors
*/
ElementType type = _not_defined;
UInt count = 0;
do {
/* --------<<<<-SIZE--------------------------------------------------- */
UInt size[5] = { 0 };
comm.receive(size, 5, 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];
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));
if(Mesh::getSpatialDimension(type) == mesh.getSpatialDimension()) {
AKANTU_DEBUG_INFO("Creating communications scheme");
communicator.fillCommunicationScheme(local_partitions,
nb_local_element,
nb_ghost_element,
type);
}
delete [] local_partitions;
/* --------<<<<-TAGS------------------------------------------------- */
synchronizeTagsRecv(communicator, root, mesh, nb_tags, type,
nb_local_element,
nb_ghost_element);
/* --------<<<<-GROUPS----------------------------------------------- */
synchronizeElementGroups(communicator, root, mesh, type);
}
++count;
} while(type != _not_defined);
/**
* Nodes coordinate construction and synchronization on distant processors
*/
comm.broadcast(&(mesh.nb_global_nodes), 1, root);
/* -------->>>>-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->storage(), 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->storage(), nb_nodes * spatial_dimension, root, Tag::genTag(root, 0, TAG_COORDINATES));
communicator.fillNodesType(mesh);
/* -------->>>>-NODES_TYPE-1--------------------------------------------- */
Int * nodes_types = mesh.getNodesTypePointer()->storage();
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));
/* --------<<<<-NODE GROUPS --------------------------------------------- */
synchronizeNodeGroupsSlaves(communicator, root, mesh);
}
MeshUtils::fillElementToSubElementsData(mesh);
mesh.is_distributed = true;
AKANTU_DEBUG_OUT();
return &communicator;
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::fillTagBuffer(const MeshData & mesh_data,
DynamicCommunicationBuffer * buffers,
const std::string & tag_name,
const ElementType & el_type,
const Array<UInt> & partition_num,
const CSR<UInt> & ghost_partition) {
#define AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA(r, extra_param, elem) \
case BOOST_PP_TUPLE_ELEM(2, 0, elem) : { \
fillTagBufferTemplated<BOOST_PP_TUPLE_ELEM(2, 1, elem)>(mesh_data, buffers, tag_name, el_type, partition_num, ghost_partition); \
break; \
} \
MeshDataTypeCode data_type_code = mesh_data.getTypeCode(tag_name);
switch(data_type_code) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA, , AKANTU_MESH_DATA_TYPES)
default : AKANTU_DEBUG_ERROR("Could not obtain the type of tag" << tag_name << "!"); break;
}
#undef AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::fillNodesType(Mesh & mesh) {
AKANTU_DEBUG_IN();
UInt nb_nodes = mesh.getNbNodes();
Int * nodes_type = mesh.getNodesTypePointer()->storage();
UInt * nodes_set = new UInt[nb_nodes];
std::fill_n(nodes_set, nb_nodes, 0);
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(_all_dimensions, gt, _ek_not_defined);
Mesh::type_iterator end = mesh.lastType(_all_dimensions, gt, _ek_not_defined);
for(; it != end; ++it) {
ElementType type = *it;
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_element = mesh.getNbElement(type, gt);
Array<UInt>::iterator< Vector<UInt> > conn_it = mesh.getConnectivity(type, gt).begin(nb_nodes_per_element);
for (UInt e = 0; e < nb_element; ++e, ++conn_it) {
Vector<UInt> & conn = *conn_it;
for (UInt n = 0; n < nb_nodes_per_element; ++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;
}
}
}
}
}
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(const UInt * partition,
UInt nb_local_element,
UInt nb_ghost_element,
ElementType type) {
AKANTU_DEBUG_IN();
Element element;
element.type = type;
element.kind = Mesh::getKind(type);
const 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())
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 < 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);
Tag comm_tag = Tag::genTag(rank, counter, tag);
buffer << int(comm_tag);
#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)");
/// pack barycenters in debug mode
Array<Element>::const_iterator<Element> bit = send_element[p].begin();
Array<Element>::const_iterator<Element> bend = send_element[p].end();
for (; bit != bend; ++bit) {
const Element & element = *bit;
Vector<Real> barycenter(mesh.getSpatialDimension());
mesh.getBarycenter(element.element, element.type, barycenter.storage(), element.ghost_type);
buffer << barycenter;
}
#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);
AKANTU_DEBUG_INFO("Posting send to proc " << p
<< " (tag: " << tag << " - " << ssize << " data to send)"
<< " [ " << comm_tag << ":" << std::hex << int(this->genTagFromID(tag)) << " ]");
communication.send_requests.push_back(static_communicator->asyncSend(buffer.storage(),
ssize,
p,
this->genTagFromID(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);
Tag comm_tag = Tag::genTag(rank, counter, tag);
buffer << int(comm_tag);
AKANTU_DEBUG_INFO("Posting receive from proc " << p
<< " (tag: " << tag << " - " << rsize << " data to receive) "
<< " [ " << comm_tag << ":" << std::hex << int(this->genTagFromID(tag)) << " ]");
communication.recv_requests.push_back(static_communicator->asyncReceive(buffer.storage(),
rsize,
p,
this->genTagFromID(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];
int _tag; buffer >> _tag;
Tag comm_tag(_tag);
#ifndef AKANTU_NDEBUG
Array<Element>::const_iterator<Element> bit = recv_element[proc].begin();
Array<Element>::const_iterator<Element> bend = recv_element[proc].end();
UInt spatial_dimension = mesh.getSpatialDimension();
for (; bit != bend; ++bit) {
const Element & element = *bit;
Vector<Real> barycenter_loc(spatial_dimension);
mesh.getBarycenter(element.element,
element.type,
barycenter_loc.storage(),
element.ghost_type);
Vector<Real> barycenter(spatial_dimension);
buffer >> barycenter;
Real tolerance = Math::getTolerance();
Real bary_norm = barycenter.norm();
for (UInt i = 0; i < spatial_dimension; ++i) {
if((std::abs(barycenter_loc(i)) <= tolerance && std::abs(barycenter(i)) <= tolerance) ||
(std::abs((barycenter(i) - barycenter_loc(i))/bary_norm) <= tolerance)) continue;
AKANTU_DEBUG_ERROR("Unpacking an unknown value for the element: "
<< element
<< "(barycenter[" << i << "] = " << barycenter_loc(i)
<< " and buffer[" << i << "] = " << barycenter(i) << ") ["
<< std::abs((barycenter(i) - barycenter_loc(i))/bary_norm)
<< "] - tag: " << tag
<< " comm_tag[ " << comm_tag << " ]");
}
}
#endif
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"
<< " [ " << comm_tag << " ]");
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();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::computeBufferSize(DataAccessor & data_accessor,
SynchronizationTag tag) {
AKANTU_DEBUG_IN();
communications[tag].resize(nb_proc);
for (UInt p = 0; p < nb_proc; ++p) {
UInt ssend = 0;
UInt sreceive = 0;
if(p != rank) {
if(send_element[p].getSize() != 0) {
ssend += sizeof(int); // sizeof(int) is for the communication tag
#ifndef AKANTU_NDEBUG
ssend += send_element[p].getSize() * mesh.getSpatialDimension() * sizeof(Real);
#endif
ssend += data_accessor.getNbDataForElements(send_element[p], tag);
AKANTU_DEBUG_INFO("I have " << ssend << "(" << ssend / 1024.
<< "kB - "<< send_element[p].getSize() <<" element(s)) data to send to " << p << " for tag "
<< tag);
}
if(recv_element[p].getSize() != 0) {
sreceive += sizeof(int); // sizeof(int) is for the communication tag
#ifndef AKANTU_NDEBUG
sreceive += recv_element[p].getSize() * mesh.getSpatialDimension() * sizeof(Real);
#endif
sreceive += data_accessor.getNbDataForElements(recv_element[p], tag);
AKANTU_DEBUG_INFO("I have " << 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::computeAllBufferSizes(DataAccessor & data_accessor) {
std::map<SynchronizationTag, Communication>::iterator it = this->communications.begin();
std::map<SynchronizationTag, Communication>::iterator end = this->communications.end();
for (; it != end; ++it) {
SynchronizationTag tag = it->first;
this->computeBufferSize(data_accessor, tag);
}
}
/* -------------------------------------------------------------------------- */
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;
Array<Element>::iterator<Element> it_el = send_element[p].begin();
Array<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;
}
}
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::substituteElements(const std::map<Element, Element> & old_to_new_elements) {
// substitute old elements with new ones
std::map<Element, Element>::const_iterator found_element_it;
std::map<Element, Element>::const_iterator found_element_end = old_to_new_elements.end();
for (UInt p = 0; p < nb_proc; ++p) {
if (p == rank) continue;
Array<Element> & recv = recv_element[p];
for (UInt el = 0; el < recv.getSize(); ++el) {
found_element_it = old_to_new_elements.find(recv(el));
if (found_element_it != found_element_end)
recv(el) = found_element_it->second;
}
Array<Element> & send = send_element[p];
for (UInt el = 0; el < send.getSize(); ++el) {
found_element_it = old_to_new_elements.find(send(el));
if (found_element_it != found_element_end)
send(el) = found_element_it->second;
}
}
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::onElementsChanged(const Array<Element> & old_elements_list,
const Array<Element> & new_elements_list,
__attribute__((unused)) const ElementTypeMapArray<UInt> & new_numbering,
__attribute__((unused)) const ChangedElementsEvent & event) {
// create a map to link old elements to new ones
std::map<Element, Element> old_to_new_elements;
for (UInt el = 0; el < old_elements_list.getSize(); ++el) {
AKANTU_DEBUG_ASSERT(old_to_new_elements.find(old_elements_list(el)) == old_to_new_elements.end(),
"The same element cannot appear twice in the list");
old_to_new_elements[old_elements_list(el)] = new_elements_list(el);
}
substituteElements(old_to_new_elements);
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::onElementsRemoved(const Array<Element> & element_to_remove,
const ElementTypeMapArray<UInt> & new_numbering,
__attribute__((unused)) const RemovedElementsEvent & event) {
AKANTU_DEBUG_IN();
this->removeElements(element_to_remove);
this->renumberElements(new_numbering);
AKANTU_DEBUG_OUT();
}
// void DistributedSynchronizer::checkCommunicationScheme() {
// for (UInt p = 0; p < psize; ++p) {
// if (p == prank) continue;
// for(UInt e(0), e < recv_element.getSize())
// }
// }
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::buildPrankToElement() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
mesh.initElementTypeMapArray(prank_to_element,
1,
spatial_dimension,
false,
_ek_not_defined,
true);
Mesh::type_iterator it = mesh.firstType(spatial_dimension,
_not_ghost,
_ek_not_defined);
Mesh::type_iterator end = mesh.lastType(spatial_dimension,
_not_ghost,
_ek_not_defined);
/// assign prank to all not ghost elements
for (; it != end; ++it) {
UInt nb_element = mesh.getNbElement(*it);
Array<UInt> & prank_to_el = prank_to_element(*it);
for (UInt el = 0; el < nb_element; ++el) {
prank_to_el(el) = rank;
}
}
/// assign prank to all ghost elements
for (UInt p = 0; p < nb_proc; ++p) {
UInt nb_ghost_element = recv_element[p].getSize();
for (UInt el = 0; el < nb_ghost_element; ++el) {
UInt element = recv_element[p](el).element;
ElementType type = recv_element[p](el).type;
GhostType ghost_type = recv_element[p](el).ghost_type;
Array<UInt> & prank_to_el = prank_to_element(type, ghost_type);
prank_to_el(element) = p;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::filterElementsByKind(DistributedSynchronizer * new_synchronizer,
ElementKind kind) {
AKANTU_DEBUG_IN();
Array<Element> * newsy_send_element = new_synchronizer->send_element;
Array<Element> * newsy_recv_element = new_synchronizer->recv_element;
Array<Element> * new_send_element = new Array<Element>[nb_proc];
Array<Element> * new_recv_element = new Array<Element>[nb_proc];
for (UInt p = 0; p < nb_proc; ++p) {
/// send element copying part
new_send_element[p].resize(0);
for (UInt el = 0; el < send_element[p].getSize(); ++el) {
Element & element = send_element[p](el);
if (element.kind == kind)
newsy_send_element[p].push_back(element);
else
new_send_element[p].push_back(element);
}
/// recv element copying part
new_recv_element[p].resize(0);
for (UInt el = 0; el < recv_element[p].getSize(); ++el) {
Element & element = recv_element[p](el);
if (element.kind == kind)
newsy_recv_element[p].push_back(element);
else
new_recv_element[p].push_back(element);
}
}
/// deleting and reassigning old pointers
delete [] send_element;
delete [] recv_element;
send_element = new_send_element;
recv_element = new_recv_element;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::reset() {
AKANTU_DEBUG_IN();
for (UInt p = 0; p < nb_proc; ++p) {
send_element[p].resize(0);
recv_element[p].resize(0);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::synchronizeTagsSend(DistributedSynchronizer & communicator,
UInt root,
Mesh & mesh,
UInt nb_tags,
const ElementType & type,
const Array<UInt> & partition_num,
const CSR<UInt> & ghost_partition,
UInt nb_local_element,
UInt nb_ghost_element) {
AKANTU_DEBUG_IN();
static UInt count = 0;
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
UInt nb_proc = comm.getNbProc();
UInt my_rank = comm.whoAmI();
if(nb_tags == 0) {
AKANTU_DEBUG_OUT();
return;
}
UInt mesh_data_sizes_buffer_length;
MeshData & mesh_data = mesh.getMeshData();
/// tag info
std::vector<std::string> tag_names;
mesh.getMeshData().getTagNames(tag_names, type);
// Make sure the tags are sorted (or at least not in random order),
// because they come from a map !!
std::sort(tag_names.begin(), tag_names.end());
// Sending information about the tags in mesh_data: name, data type and
// number of components of the underlying array associated to the current type
DynamicCommunicationBuffer mesh_data_sizes_buffer;
std::vector<std::string>::const_iterator names_it = tag_names.begin();
std::vector<std::string>::const_iterator names_end = tag_names.end();
for(;names_it != names_end; ++names_it) {
mesh_data_sizes_buffer << *names_it;
mesh_data_sizes_buffer << mesh_data.getTypeCode(*names_it);
mesh_data_sizes_buffer << mesh_data.getNbComponent(*names_it, type);
}
mesh_data_sizes_buffer_length = mesh_data_sizes_buffer.getSize();
AKANTU_DEBUG_INFO("Broadcasting the size of the information about the mesh data tags: (" << mesh_data_sizes_buffer_length << ")." );
comm.broadcast(&mesh_data_sizes_buffer_length, 1, root);
AKANTU_DEBUG_INFO("Broadcasting the information about the mesh data tags, addr " << (void*)mesh_data_sizes_buffer.storage());
if(mesh_data_sizes_buffer_length !=0)
comm.broadcast(mesh_data_sizes_buffer.storage(), mesh_data_sizes_buffer.getSize(), root);
if(mesh_data_sizes_buffer_length !=0) {
//Sending the actual data to each processor
DynamicCommunicationBuffer * buffers = new DynamicCommunicationBuffer[nb_proc];
std::vector<std::string>::const_iterator names_it = tag_names.begin();
std::vector<std::string>::const_iterator names_end = tag_names.end();
// Loop over each tag for the current type
for(;names_it != names_end; ++names_it) {
// Type code of the current tag (i.e. the tag named *names_it)
communicator.fillTagBuffer(mesh_data,
buffers,
*names_it,
type,
partition_num,
ghost_partition);
}
std::vector<CommunicationRequest *> requests;
for (UInt p = 0; p < nb_proc; ++p) {
if(p != root) {
AKANTU_DEBUG_INFO("Sending " << buffers[p].getSize() << " bytes of mesh data to proc " << p << " TAG("<< Tag::genTag(my_rank, count, TAG_MESH_DATA) <<")");
requests.push_back(comm.asyncSend(buffers[p].storage(),
buffers[p].getSize(), p, Tag::genTag(my_rank, count, TAG_MESH_DATA)));
}
}
names_it = tag_names.begin();
// Loop over each tag for the current type
for(;names_it != names_end; ++names_it) {
// Reinitializing the mesh data on the master
communicator.populateMeshData(mesh_data,
buffers[root],
*names_it,
type,
mesh_data.getTypeCode(*names_it),
mesh_data.getNbComponent(*names_it, type),
nb_local_element,
nb_ghost_element);
}
comm.waitAll(requests);
comm.freeCommunicationRequest(requests);
requests.clear();
delete [] buffers;
}
++count;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::synchronizeTagsRecv(DistributedSynchronizer & communicator,
UInt root,
Mesh & mesh,
UInt nb_tags,
const ElementType & type,
UInt nb_local_element,
UInt nb_ghost_element) {
AKANTU_DEBUG_IN();
static UInt count = 0;
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
if(nb_tags == 0) {
AKANTU_DEBUG_OUT();
return;
}
/* --------<<<<-TAGS------------------------------------------------- */
UInt mesh_data_sizes_buffer_length = 0;
CommunicationBuffer mesh_data_sizes_buffer;
MeshData & mesh_data = mesh.getMeshData();
AKANTU_DEBUG_INFO("Receiving the size of the information about the mesh data tags.");
comm.broadcast(&mesh_data_sizes_buffer_length, 1, root);
if(mesh_data_sizes_buffer_length != 0) {
mesh_data_sizes_buffer.resize(mesh_data_sizes_buffer_length);
AKANTU_DEBUG_INFO("Receiving the information about the mesh data tags, addr " << (void*)mesh_data_sizes_buffer.storage());
comm.broadcast(mesh_data_sizes_buffer.storage(), mesh_data_sizes_buffer_length, root);
AKANTU_DEBUG_INFO("Size of the information about the mesh data: " << mesh_data_sizes_buffer_length);
std::vector<std::string> tag_names;
std::vector<MeshDataTypeCode> tag_type_codes;
std::vector<UInt> tag_nb_component;
tag_names.resize(nb_tags);
tag_type_codes.resize(nb_tags);
tag_nb_component.resize(nb_tags);
CommunicationBuffer mesh_data_buffer;
UInt type_code_int;
for(UInt i(0); i < nb_tags; ++i) {
mesh_data_sizes_buffer >> tag_names[i];
mesh_data_sizes_buffer >> type_code_int;
tag_type_codes[i] = static_cast<MeshDataTypeCode>(type_code_int);
mesh_data_sizes_buffer >> tag_nb_component[i];
}
std::vector<std::string>::const_iterator names_it = tag_names.begin();
std::vector<std::string>::const_iterator names_end = tag_names.end();
CommunicationStatus mesh_data_comm_status;
AKANTU_DEBUG_INFO("Checking size of data to receive for mesh data TAG("
<< Tag::genTag(root, count, TAG_MESH_DATA) << ")");
comm.probe<char>(root, Tag::genTag(root, count, TAG_MESH_DATA), mesh_data_comm_status);
UInt mesh_data_buffer_size(mesh_data_comm_status.getSize());
AKANTU_DEBUG_INFO("Receiving " << mesh_data_buffer_size
<< " bytes of mesh data TAG("
<< Tag::genTag(root, count, TAG_MESH_DATA) << ")");
mesh_data_buffer.resize(mesh_data_buffer_size);
comm.receive(mesh_data_buffer.storage(),
mesh_data_buffer_size,
root,
Tag::genTag(root, count, TAG_MESH_DATA));
// Loop over each tag for the current type
UInt k(0);
for(; names_it != names_end; ++names_it, ++k) {
communicator.populateMeshData(mesh_data, mesh_data_buffer,
*names_it, type,
tag_type_codes[k],
tag_nb_component[k],
nb_local_element, nb_ghost_element);
}
}
++count;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<class CommunicationBuffer>
void DistributedSynchronizer::fillElementGroupsFromBuffer(DistributedSynchronizer & communicator,
Mesh & mesh,
const ElementType & type,
CommunicationBuffer & buffer) {
AKANTU_DEBUG_IN();
Element el;
el.type = type;
for (ghost_type_t::iterator gt = ghost_type_t::begin(); gt != ghost_type_t::end(); ++gt) {
UInt nb_element = mesh.getNbElement(type, *gt);
el.ghost_type = *gt;
for (UInt e = 0; e < nb_element; ++e) {
el.element = e;
std::vector<std::string> element_to_group;
buffer >> element_to_group;
AKANTU_DEBUG_ASSERT(e < mesh.getNbElement(type, *gt), "The mesh does not have the element " << e);
std::vector<std::string>::iterator it = element_to_group.begin();
std::vector<std::string>::iterator end = element_to_group.end();
for (; it != end; ++it) {
mesh.getElementGroup(*it).add(el, false, false);
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::synchronizeElementGroups(DistributedSynchronizer & communicator,
UInt root,
Mesh & mesh,
const ElementType & type,
const Array<UInt> & partition_num,
const CSR<UInt> & ghost_partition,
UInt nb_element) {
AKANTU_DEBUG_IN();
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
UInt nb_proc = comm.getNbProc();
UInt my_rank = comm.whoAmI();
DynamicCommunicationBuffer * buffers = new DynamicCommunicationBuffer[nb_proc];
typedef std::vector< std::vector<std::string> > ElementToGroup;
ElementToGroup element_to_group;
element_to_group.resize(nb_element);
GroupManager::const_element_group_iterator egi = mesh.element_group_begin();
GroupManager::const_element_group_iterator ege = mesh.element_group_end();
for (; egi != ege; ++egi) {
ElementGroup & eg = *(egi->second);
std::string name = egi->first;
ElementGroup::const_element_iterator eit = eg.element_begin(type, _not_ghost);
ElementGroup::const_element_iterator eend = eg.element_end(type, _not_ghost);
for (; eit != eend; ++eit) {
element_to_group[*eit].push_back(name);
}
eit = eg.element_begin(type, _not_ghost);
if(eit != eend)
const_cast<Array<UInt> &>(eg.getElements(type)).empty();
}
/// preparing the buffers
const UInt * part = partition_num.storage();
/// copying the data, element by element
ElementToGroup::const_iterator data_it = element_to_group.begin();
ElementToGroup::const_iterator data_end = element_to_group.end();
for (; data_it != data_end; ++part, ++data_it) {
buffers[*part] << *data_it;
}
data_it = element_to_group.begin();
/// copying the data for the ghost element
for (UInt el(0); data_it != data_end; ++data_it, ++el) {
CSR<UInt>::const_iterator it = ghost_partition.begin(el);
CSR<UInt>::const_iterator end = ghost_partition.end(el);
for (;it != end; ++it) {
UInt proc = *it;
buffers[proc] << *data_it;
}
}
std::vector<CommunicationRequest *> requests;
for (UInt p = 0; p < nb_proc; ++p) {
if(p == my_rank) continue;
AKANTU_DEBUG_INFO("Sending element groups to proc " << p
<< " TAG("<< Tag::genTag(my_rank, p, TAG_ELEMENT_GROUP) <<")");
requests.push_back(comm.asyncSend(buffers[p].storage(),
buffers[p].getSize(),
p,
Tag::genTag(my_rank, p, TAG_ELEMENT_GROUP)));
}
fillElementGroupsFromBuffer(communicator, mesh, type, buffers[my_rank]);
comm.waitAll(requests);
comm.freeCommunicationRequest(requests);
requests.clear();
delete [] buffers;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::synchronizeElementGroups(DistributedSynchronizer & communicator,
UInt root,
Mesh & mesh,
const ElementType & type) {
AKANTU_DEBUG_IN();
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
UInt my_rank = comm.whoAmI();
AKANTU_DEBUG_INFO("Receiving element groups from proc " << root
<< " TAG("<< Tag::genTag(root, my_rank, TAG_ELEMENT_GROUP) <<")");
CommunicationStatus status;
comm.probe<char>(root, Tag::genTag(root, my_rank, TAG_ELEMENT_GROUP), status);
CommunicationBuffer buffer(status.getSize());
comm.receive(buffer.storage(), buffer.getSize(), root, Tag::genTag(root, my_rank, TAG_ELEMENT_GROUP));
fillElementGroupsFromBuffer(communicator, mesh, type, buffer);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<class CommunicationBuffer>
void DistributedSynchronizer::fillNodeGroupsFromBuffer(DistributedSynchronizer & communicator,
Mesh & mesh,
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 Array<UInt> & global_nodes = mesh.getGlobalNodesIds();
Array<UInt>::const_scalar_iterator nbegin = global_nodes.begin();
Array<UInt>::const_scalar_iterator nit = global_nodes.begin();
Array<UInt>::const_scalar_iterator nend = global_nodes.end();
for (; nit != nend; ++nit) {
std::vector<std::string>::iterator it = node_to_group[*nit].begin();
std::vector<std::string>::iterator 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 DistributedSynchronizer::synchronizeNodeGroupsMaster(DistributedSynchronizer & communicator,
UInt root,
Mesh & mesh) {
AKANTU_DEBUG_IN();
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
UInt nb_proc = comm.getNbProc();
UInt my_rank = comm.whoAmI();
UInt nb_total_nodes = mesh.getNbGlobalNodes();
DynamicCommunicationBuffer buffer;
typedef std::vector< std::vector<std::string> > NodeToGroup;
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 == my_rank) continue;
AKANTU_DEBUG_INFO("Sending node groups to proc " << p
<< " TAG("<< Tag::genTag(my_rank, p, TAG_NODE_GROUP) <<")");
requests.push_back(comm.asyncSend(buffer.storage(),
buffer.getSize(),
p,
Tag::genTag(my_rank, p, TAG_NODE_GROUP)));
}
fillNodeGroupsFromBuffer(communicator, mesh, buffer);
comm.waitAll(requests);
comm.freeCommunicationRequest(requests);
requests.clear();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::synchronizeNodeGroupsSlaves(DistributedSynchronizer & communicator,
UInt root,
Mesh & mesh) {
AKANTU_DEBUG_IN();
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
UInt my_rank = comm.whoAmI();
AKANTU_DEBUG_INFO("Receiving node groups from proc " << root
<< " TAG("<< Tag::genTag(root, my_rank, TAG_NODE_GROUP) <<")");
CommunicationStatus status;
comm.probe<char>(root, Tag::genTag(root, my_rank, TAG_NODE_GROUP), status);
CommunicationBuffer buffer(status.getSize());
comm.receive(buffer.storage(), buffer.getSize(), root, Tag::genTag(root, my_rank, TAG_NODE_GROUP));
fillNodeGroupsFromBuffer(communicator, mesh, buffer);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::removeElements(const Array<Element> & element_to_remove) {
AKANTU_DEBUG_IN();
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
std::vector<CommunicationRequest *> isend_requests;
Array<UInt> * list_of_el = new Array<UInt>[nb_proc];
// Handling ghost elements
for (UInt p = 0; p < nb_proc; ++p) {
if (p == rank) continue;
Array<Element> & recv = recv_element[p];
if(recv.getSize() == 0) continue;
Array<Element>::iterator<Element> recv_begin = recv.begin();
Array<Element>::iterator<Element> recv_end = recv.end();
Array<Element>::const_iterator<Element> er_it = element_to_remove.begin();
Array<Element>::const_iterator<Element> er_end = element_to_remove.end();
Array<UInt> & list = list_of_el[p];
for (UInt i = 0; recv_begin != recv_end; ++i, ++recv_begin) {
const Element & el = *recv_begin;
Array<Element>::const_iterator<Element> pos = std::find(er_it, er_end, el);
if(pos == er_end) {
list.push_back(i);
}
}
if(list.getSize() == recv.getSize())
list.push_back(UInt(0));
else list.push_back(UInt(-1));
AKANTU_DEBUG_INFO("Sending a message of size " << list.getSize() << " to proc " << p << " TAG(" << this->genTagFromID(0) << ")");
isend_requests.push_back(comm.asyncSend(list.storage(), list.getSize(),
p, this->genTagFromID(0)));
list.erase(list.getSize() - 1);
if (list.getSize() == recv.getSize()) continue;
Array<Element> new_recv;
for (UInt nr = 0; nr < list.getSize(); ++nr) {
Element & el = recv(list(nr));
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 < nb_proc; ++p) {
if (p == rank) continue;
Array<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("<< this->genTagFromID(0) <<")");
comm.probe<UInt>(p, this->genTagFromID(0), status);
Array<UInt> list(status.getSize());
AKANTU_DEBUG_INFO("Receiving list of elements (" << status.getSize() - 1
<< " elements) no longer needed by proc " << p
<< " TAG("<< this->genTagFromID(0) <<")");
comm.receive(list.storage(), list.getSize(),
p, this->genTagFromID(0));
if(list.getSize() == 1 && list(0) == 0) continue;
list.erase(list.getSize() - 1);
if (list.getSize() == send.getSize()) continue;
Array<Element> new_send;
for (UInt ns = 0; ns < list.getSize(); ++ns) {
Element & el = send(list(ns));
new_send.push_back(el);
}
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();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::renumberElements(const ElementTypeMapArray<UInt> & new_numbering) {
// Handling ghost elements
for (UInt p = 0; p < nb_proc; ++p) {
if (p == rank) continue;
Array<Element> & recv = recv_element[p];
for (UInt i = 0; i < recv.getSize(); ++i) {
Element & el = recv(i);
el.element = new_numbering(el.type, el.ghost_type)(el.element);
}
Array<Element> & send = send_element[p];
for (UInt i = 0; i < send.getSize(); ++i) {
Element & el = send(i);
el.element = new_numbering(el.type, el.ghost_type)(el.element);
}
}
}
__END_AKANTU__
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