Homec4science
Diffusion akantu (bugfixes/39-the-python-example-for-phasefield-are-broken-due-to-a-change-to-setintegrationscheme) Browse

rAKA/src/synchronizer/element_synchronizer.cc
cafceb59140ebugfixes/39-the-python…

Last Change
Raw File

element_synchronizer.cc
View Options

/**
* @file element_synchronizer.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Sep 01 2010
* @date last modification: Fri Jan 22 2016
*
* @brief implementation of a communicator using a static_communicator for
* real
* send/receive
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
* Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
* Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_synchronizer.hh"
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <iostream>
#include <map>
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_DEBUG_TOOLS)
#include "aka_debug_tools.hh"
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
ElementSynchronizer::ElementSynchronizer(Mesh & mesh, const ID & id,
MemoryID memory_id,
const bool register_to_event_manager,
StaticCommunicator & comm)
: SynchronizerImpl<Element>(id, memory_id, comm), mesh(mesh),
prank_to_element("prank_to_element", id, memory_id) {
AKANTU_DEBUG_IN();
if (register_to_event_manager)
this->mesh.registerEventHandler(*this);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
ElementSynchronizer::~ElementSynchronizer() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ElementSynchronizer::printself(std::ostream & stream, int indent) const {}
/* -------------------------------------------------------------------------- */
void ElementSynchronizer::substituteElements(
const std::map<Element, Element> & old_to_new_elements) {
// substitute old elements with new ones
auto subsitute =
[&old_to_new_elements](Communications<Element>::scheme_iterator it,
Communications<Element>::scheme_iterator end) {
std::map<Element, Element>::const_iterator found_element_it;
std::map<Element, Element>::const_iterator found_element_end =
old_to_new_elements.end();
for (; it != end; ++it) {
Array<Element> & list = it->second;
for (UInt el = 0; el < list.getSize(); ++el) {
found_element_it = old_to_new_elements.find(list(el));
if (found_element_it != found_element_end)
list(el) = found_element_it->second;
}
}
};
subsitute(communications.begin_recv_scheme(),
communications.end_recv_scheme());
subsitute(communications.begin_send_scheme(),
communications.end_send_scheme());
}
/* -------------------------------------------------------------------------- */
void ElementSynchronizer::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 ElementSynchronizer::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 ElementSynchronizer::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
Communications<Element>::scheme_iterator recv_it =
communications.begin_recv_scheme();
Communications<Element>::scheme_iterator recv_end =
communications.end_recv_scheme();
for (; recv_it != recv_end; ++recv_it) {
Array<Element> & recv = recv_it->second;
UInt proc = recv_it->first;
Array<Element>::const_scalar_iterator it = recv.begin();
Array<Element>::const_scalar_iterator end = recv.end();
for (; it != end; ++it) {
const Element & el = *it;
Array<UInt> & prank_to_el = prank_to_element(el.type, el.ghost_type);
prank_to_el(el.element) = proc;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ElementSynchronizer::filterElementsByKind(
ElementSynchronizer * new_synchronizer, ElementKind kind) {
AKANTU_DEBUG_IN();
auto filter_list = [&kind](Array<Element> & list, Array<Element> & new_list) {
list.resize(0);
new_list.resize(0);
Array<Element> copy = list;
Array<Element>::const_scalar_iterator it = copy.begin();
Array<Element>::const_scalar_iterator end = copy.end();
for (; it != end; ++it) {
const Element & el = *it;
if (el.kind == kind) {
new_list.push_back(el);
} else {
list.push_back(el);
}
}
};
Communications<Element>::scheme_iterator recv_it =
communications.begin_recv_scheme();
Communications<Element>::scheme_iterator recv_end =
communications.end_recv_scheme();
for (; recv_it != recv_end; ++recv_it) {
UInt proc = recv_it->first;
Array<Element> & recv = recv_it->second;
Array<Element> & new_recv =
new_synchronizer->communications.createRecvScheme(proc);
filter_list(recv, new_recv);
}
Communications<Element>::scheme_iterator send_it =
communications.begin_send_scheme();
Communications<Element>::scheme_iterator send_end =
communications.end_send_scheme();
for (; send_it != send_end; ++send_it) {
UInt proc = send_it->first;
Array<Element> & send = send_it->second;
Array<Element> & new_send =
new_synchronizer->communications.createSendScheme(proc);
filter_list(send, new_send);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ElementSynchronizer::reset() {
AKANTU_DEBUG_IN();
communications.resetSchemes();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ElementSynchronizer::removeElements(
const Array<Element> & element_to_remove) {
AKANTU_DEBUG_IN();
std::vector<CommunicationRequest> send_requests;
std::map<UInt, Array<UInt> > list_of_elements_per_proc;
auto filter_list = [](const Array<UInt> & keep, Array<Element> & list) {
Array<Element> new_list;
for (UInt e = 0; e < keep.getSize() - 1; ++e) {
Element & el = list(keep(e));
new_list.push_back(el);
}
list.copy(new_list);
};
// Handling ghost elements
Communications<Element>::scheme_iterator recv_it =
communications.begin_recv_scheme();
Communications<Element>::scheme_iterator recv_end =
communications.end_recv_scheme();
for (; recv_it != recv_end; ++recv_it) {
Array<Element> & recv = recv_it->second;
UInt proc = recv_it->first;
Array<UInt> & keep_list = list_of_elements_per_proc[proc];
Array<Element>::const_iterator<Element> rem_it = element_to_remove.begin();
Array<Element>::const_iterator<Element> rem_end = element_to_remove.end();
Array<Element>::const_scalar_iterator it = recv.begin();
Array<Element>::const_scalar_iterator end = recv.end();
for (UInt e = 0; it != end; ++it, ++e) {
const Element & el = *it;
Array<Element>::const_iterator<Element> pos =
std::find(rem_it, rem_end, el);
if (pos == rem_end) {
keep_list.push_back(e);
}
}
keep_list.push_back(UInt(-1)); // To no send empty arrays
Tag tag = Tag::genTag(proc, 0, Tag::_MODIFY_SCHEME, this->hash_id);
AKANTU_DEBUG_INFO("Sending a message of size "
<< keep_list.getSize() << " to proc " << proc << " TAG("
<< tag << ")");
send_requests.push_back(this->communicator.asyncSend(keep_list, proc, tag));
UInt old_size = recv.getSize();
filter_list(keep_list, recv);
AKANTU_DEBUG_INFO("I had " << old_size << " elements to recv from proc "
<< proc << " and " << keep_list.getSize()
<< " elements to keep. I have " << recv.getSize()
<< " elements left.");
}
Communications<Element>::scheme_iterator send_it =
communications.begin_send_scheme();
Communications<Element>::scheme_iterator send_end =
communications.end_send_scheme();
for (; send_it != send_end; ++send_it) {
UInt proc = send_it->first;
Array<Element> send = send_it->second;
CommunicationStatus status;
Tag tag = Tag::genTag(rank, 0, Tag::_MODIFY_SCHEME, this->hash_id);
AKANTU_DEBUG_INFO("Getting number of elements of proc "
<< proc << " to keep - TAG(" << tag << ")");
this->communicator.probe<UInt>(proc, tag, status);
Array<UInt> keep_list(status.getSize());
AKANTU_DEBUG_INFO("Receiving list of elements ("
<< keep_list.getSize() << " elements) to keep for proc "
<< proc << " TAG(" << tag << ")");
this->communicator.receive(keep_list, proc, tag);
UInt old_size = send.getSize();
filter_list(keep_list, send);
AKANTU_DEBUG_INFO("I had " << old_size << " elements to send to proc "
<< proc << " and " << keep_list.getSize()
<< " elements to keep. I have " << send.getSize()
<< " elements left.");
}
this->communicator.waitAll(send_requests);
this->communicator.freeCommunicationRequest(send_requests);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ElementSynchronizer::renumberElements(
const ElementTypeMapArray<UInt> & new_numbering) {
auto renumber =
[&new_numbering](Communications<Element>::scheme_iterator it,
Communications<Element>::scheme_iterator end) {
for (; it != end; ++it) {
Array<Element> & list = it->second;
Array<Element>::scalar_iterator el_it = list.begin();
Array<Element>::scalar_iterator el_end = list.end();
for (; el_it != el_end; ++el_it) {
Element & el = *el_it;
el.element = new_numbering(el.type, el.ghost_type)(el.element);
}
}
};
renumber(communications.begin_recv_scheme(),
communications.end_recv_scheme());
renumber(communications.begin_send_scheme(),
communications.end_send_scheme());
}
/* -------------------------------------------------------------------------- */
UInt ElementSynchronizer::sanityCheckDataSize(
const Array<Element> & elements, const SynchronizationTag & tag) const {
return (elements.getSize() * mesh.getSpatialDimension() * sizeof(Real) +
sizeof(SynchronizationTag));
}
/* -------------------------------------------------------------------------- */
void ElementSynchronizer::packSanityCheckData(
CommunicationDescriptor<Element> & comm_desc) const {
CommunicationBuffer & buffer = comm_desc.getBuffer();
buffer << comm_desc.getTag();
Communications<Element>::Scheme & send_element = comm_desc.getScheme();
/// pack barycenters in debug mode
Array<Element>::const_iterator<Element> bit = send_element.begin();
Array<Element>::const_iterator<Element> bend = send_element.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;
}
}
/* -------------------------------------------------------------------------- */
void ElementSynchronizer::unpackSanityCheckData(
CommunicationDescriptor<Element> & comm_desc) const {
CommunicationBuffer & buffer = comm_desc.getBuffer();
const SynchronizationTag & tag = comm_desc.getTag();
SynchronizationTag t;
buffer >> t;
AKANTU_DEBUG_ASSERT(
t == tag, "The tag received does not correspond to the tag expected");
Communications<Element>::Scheme & recv_element = comm_desc.getScheme();
Array<Element>::const_iterator<Element> bit = recv_element.begin();
Array<Element>::const_iterator<Element> bend = recv_element.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;
for (UInt i = 0; i < spatial_dimension; ++i) {
if (!Math::are_float_equal(barycenter_loc(i), barycenter(i)))
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))
<< "] - tag: " << tag);
}
}
}
/* -------------------------------------------------------------------------- */
}
c4science · Help