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Global optimizers: better parallel performance 

- We used to have a thread-local variable for cell::TDS_data to make
  incident_cells concurrently callable but it was slow and memory-consuming
  => new incident_cells function which do not use cell::TDS_data
  => faster and lighter
- update_restricted_delaunay now uses parallel_for instead of parallel_do
  (it was quite slow with the implicit oracle)
  => faster (but requires to fill a temporary vector)
This commit is contained in:
Clement Jamin 2012-11-27 19:35:04 +01:00
parent 2b67ae0bed
commit 9c5cddbbc3
3 changed files with 367 additions and 154 deletions
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405
Mesh_3/include/CGAL/Mesh_3/C3T3_helpers.h
View File

@ -409,7 +409,7 @@ protected:
return true;
}
void unlock_all_elements() {}
void unlock_all_elements() const {}
};
#ifdef CGAL_LINKED_WITH_TBB
@ -494,7 +494,7 @@ protected:
return locked;
}
void unlock_all_elements()
void unlock_all_elements() const
{
if (m_lock_ds)
{
@ -615,7 +615,7 @@ public:
*
* Same as update_mesh, but with the precondition that
* Th().no_topological_change(tr_, old_vertex, new_position,
* incident_cells) return false.
* incident_cells_) return false.
*/
template <typename SliverCriterion, typename OutputIterator>
std::pair<bool,Vertex_handle>
@ -698,6 +698,23 @@ public:
Outdated_cell_set& outdated_cells_set,
Moving_vertices_set& moving_vertices,
bool *p_could_lock_zone);
/**
* Try to lock the incident cells and return them in \c cells
* Return value:
* - false: everything is unlocked and \c cells is empty
* - true: incident cells are locked and \c cells contains all of them
*/
bool
try_lock_and_get_incident_cells(const Vertex_handle& v,
Cell_vector &cells) const;
/**
* Get the incident cells and return them in \c cells
*/
void
get_incident_cells_without_using_tds_data(const Vertex_handle& v,
Cell_vector &cells) const;
/**
* Outputs to out the sliver (wrt \c criterion and \c sliver_bound) incident
@ -1556,6 +1573,114 @@ private:
}
}
}
// Used by the parallel version
template <typename FacetUpdater>
void update_facets(std::vector<Cell_handle>& outdated_cells_vector, FacetUpdater updater)
{
#ifdef CGAL_LINKED_WITH_TBB
// Parallel
if (boost::is_base_of<Parallel_tag, Concurrency_tag>::value)
{
tbb::parallel_for(tbb::blocked_range<size_t>(0, outdated_cells_vector.size()),
[&]( const tbb::blocked_range<size_t>& r ) // CJTODO: lambdas ok?
{
for( size_t i = r.begin() ; i != r.end() ; ++i)
{
const Cell_handle cell = outdated_cells_vector[i];
Cell_handle null_cell;
bool inf = false;
for (int i=0 ; i<4 && (!inf) ; ++i ){
if ( tr_.is_infinite(cell->vertex(i)) ){
inf = true;
Cell_handle n = cell->neighbor(i);
if(n->next_intrusive() != null_cell){// the neighbor is also outdated
if(cell < n){ // otherwise n will report it later
Facet f(cell,i);
updater(f);
}
} else { // report it now or never
if(cell < n){
Facet f(cell,i);
updater(f);
}else {
Facet f(n,n->index(cell));
updater(f);
}
}
}
}
if(! inf){
for ( int i=0 ; i<4 ; ++i ){
Cell_handle n = cell->neighbor(i);
if(n->next_intrusive() != null_cell){// the neighbor is also outdated
if(cell < n){ // otherwise n will report it later
Facet f(cell,i);
updater(f);
}
} else { // report it now or never
if(cell < n){
Facet f(cell,i);
updater(f);
}else {
Facet f(n,n->index(cell));
updater(f);
}
}
}
}
}
});
}
// Sequential
else
#endif // CGAL_LINKED_WITH_TBB
{
std::vector<Cell_handle>::iterator it;
for(it = outdated_cells_vector.begin();
it != outdated_cells_vector.end();
++it)
{
Cell_handle cell = *it;
int i=0;
bool inf = false;
for ( ; i<4 && (!inf) ; ++i ){
if ( tr_.is_infinite(cell->vertex(i)) ){
inf = true;
Cell_handle n = cell->neighbor(i);
if(n->next_intrusive() != Cell_handle()){// the neighbor is also outdated
if(cell < n){ // otherwise n will report it later
updater(Facet(cell,i));
}
} else { // report it now or never
if(cell < n){
updater(Facet(cell,i));
}else {
updater(Facet(n,n->index(cell)));
}
}
}
}
if(! inf){
for ( i=0 ; i<4 ; ++i ){
Cell_handle n = cell->neighbor(i);
if(n->next_intrusive() != Cell_handle()){// the neighbor is also outdated
if(cell < n){ // otherwise n will report it later
updater(Facet(cell,i));
}
} else { // report it now or never
if(cell < n){
updater(Facet(cell,i));
}else {
updater(Facet(n,n->index(cell)));
}
}
}
}
}
}
}
#endif //CGAL_INTRUSIVE_LIST
@ -1740,13 +1865,13 @@ update_mesh(const Point_3& new_position,
// << " " << (void*)(&*old_vertex) << "=" << old_vertex->point()
// << ")\n";
Cell_vector incident_cells;
incident_cells.reserve(64);
tr_.incident_cells(old_vertex, std::back_inserter(incident_cells));
if ( Th().no_topological_change(tr_, old_vertex, new_position, incident_cells) )
Cell_vector incident_cells_;
incident_cells_.reserve(64);
tr_.incident_cells(old_vertex, std::back_inserter(incident_cells_));
if ( Th().no_topological_change(tr_, old_vertex, new_position, incident_cells_) )
{
BOOST_FOREACH(Cell_handle& ch, std::make_pair(incident_cells.begin(),
incident_cells.end()))
BOOST_FOREACH(Cell_handle& ch, std::make_pair(incident_cells_.begin(),
incident_cells_.end()))
{
ch->invalidate_circumcenter();
}
@ -1754,7 +1879,7 @@ update_mesh(const Point_3& new_position,
old_vertex,
criterion,
modified_vertices,
incident_cells);
incident_cells_);
}
else
{
@ -1947,16 +2072,53 @@ rebuild_restricted_delaunay(OutdatedCells& outdated_cells,
// Updates cells
// Note: ~58% of rebuild_restricted_delaunay time
std::set<Vertex_handle> vertex_to_proj;
#ifdef CGAL_LINKED_WITH_TBB
// Parallel
if (boost::is_base_of<Parallel_tag, Concurrency_tag>::value)
{
tbb::parallel_do(first_cell, last_cell,
std::vector<Cell_handle> outdated_cells_vector;
outdated_cells_vector.reserve(outdated_cells.size());
for ( ; first_cell != last_cell ; ++first_cell)
{
outdated_cells_vector.push_back(*first_cell);
}
tbb::parallel_for(tbb::blocked_range<size_t>(0, outdated_cells_vector.size()),
[&]( const tbb::blocked_range<size_t>& r ) // CJTODO: lambdas ok?
{
for( size_t i = r.begin() ; i != r.end() ; ++i)
{
c3t3_.remove_from_complex(outdated_cells_vector[i]);
updater(outdated_cells_vector[i]);
}
});
/*tbb::parallel_do(first_cell, last_cell,
[&]( OutdatedCells::const_reference cell ) // CJTODO: lambdas ok?
{
c3t3_.remove_from_complex(cell);
updater(cell);
});
});*/
#ifdef MESH_3_PROFILING
std::cerr << " done in " << t.elapsed() << " seconds (#cells from "
<< num_cells << " to " << c3t3_.number_of_cells_in_complex() << ")."
<< std::endl;
std::cerr << " Updating facets...";
t.reset();
#endif
// Get facets (returns each canonical facet only once)
// Note: ~42% of rebuild_restricted_delaunay time
// Facet_vector facets;
Facet_updater facet_updater(c3t3_,vertex_to_proj, updater);
update_facets(outdated_cells_vector, facet_updater);
// now we can clear
outdated_cells.clear();
}
// Sequential
else
@ -1968,25 +2130,25 @@ rebuild_restricted_delaunay(OutdatedCells& outdated_cells,
c3t3_.remove_from_complex(cell);
updater(cell);
}
}
#ifdef MESH_3_PROFILING
std::cerr << " done in " << t.elapsed() << " seconds (#cells from "
<< num_cells << " to " << c3t3_.number_of_cells_in_complex() << ")."
<< std::endl;
std::cerr << " Updating facets...";
t.reset();
std::cerr << " done in " << t.elapsed() << " seconds (#cells from "
<< num_cells << " to " << c3t3_.number_of_cells_in_complex() << ")."
<< std::endl;
std::cerr << " Updating facets...";
t.reset();
#endif
// Get facets (returns each canonical facet only once)
// Note: ~42% of rebuild_restricted_delaunay time
// Facet_vector facets;
std::set<Vertex_handle> vertex_to_proj;
Facet_updater facet_updater(c3t3_,vertex_to_proj, updater);
update_facets(outdated_cells, facet_updater);
// Get facets (returns each canonical facet only once)
// Note: ~42% of rebuild_restricted_delaunay time
// Facet_vector facets;
Facet_updater facet_updater(c3t3_,vertex_to_proj, updater);
update_facets(outdated_cells, facet_updater);
// now we can clear
outdated_cells.clear();
}
// now we can clear
outdated_cells.clear();
#ifdef MESH_3_PROFILING
std::cerr << " done in " << t.elapsed() << " seconds ("
@ -2163,17 +2325,17 @@ move_point(const Vertex_handle& old_vertex,
// std::cerr << "C3T3_helpers::move_point[v2]("
// << (void*)(&*old_vertex) << " = " << old_vertex->point()
// << " , " << new_position << ")\n";
Cell_vector incident_cells;
incident_cells.reserve(64);
tr_.incident_cells(old_vertex, std::back_inserter(incident_cells));
if ( Th().no_topological_change(tr_, old_vertex, new_position, incident_cells) )
Cell_vector incident_cells_;
incident_cells_.reserve(64);
tr_.incident_cells(old_vertex, std::back_inserter(incident_cells_));
if ( Th().no_topological_change(tr_, old_vertex, new_position, incident_cells_) )
{
BOOST_FOREACH(Cell_handle& ch, std::make_pair(incident_cells.begin(),
incident_cells.end()))
BOOST_FOREACH(Cell_handle& ch, std::make_pair(incident_cells_.begin(),
incident_cells_.end()))
{
ch->invalidate_circumcenter();
}
std::copy(incident_cells.begin(),incident_cells.end(), outdated_cells);
std::copy(incident_cells_.begin(),incident_cells_.end(), outdated_cells);
return move_point_no_topo_change(old_vertex,
new_position);
}
@ -2195,17 +2357,17 @@ move_point(const Vertex_handle& old_vertex,
Outdated_cell_set& outdated_cells_set,
Moving_vertices_set& moving_vertices)
{
Cell_vector incident_cells;
incident_cells.reserve(64);
tr_.incident_cells(old_vertex, std::back_inserter(incident_cells));
if ( Th().no_topological_change(tr_, old_vertex, new_position, incident_cells) )
Cell_vector incident_cells_;
incident_cells_.reserve(64);
tr_.incident_cells(old_vertex, std::back_inserter(incident_cells_));
if ( Th().no_topological_change(tr_, old_vertex, new_position, incident_cells_) )
{
BOOST_FOREACH(Cell_handle& ch, std::make_pair(incident_cells.begin(),
incident_cells.end()))
BOOST_FOREACH(Cell_handle& ch, std::make_pair(incident_cells_.begin(),
incident_cells_.end()))
{
ch->invalidate_circumcenter();
}
std::copy(incident_cells.begin(),incident_cells.end(),
std::copy(incident_cells_.begin(),incident_cells_.end(),
std::inserter(outdated_cells_set, outdated_cells_set.end()));
return move_point_no_topo_change(old_vertex, new_position);
}
@ -2236,8 +2398,8 @@ move_point(const Vertex_handle& old_vertex,
CGAL_assertion(p_could_lock_zone != 0);
*p_could_lock_zone = true;
Cell_vector incident_cells;
incident_cells.reserve(64);
Cell_vector incident_cells_;
incident_cells_.reserve(64);
if (!try_lock_vertex(old_vertex)) // LOCK
{
*p_could_lock_zone = false;
@ -2246,54 +2408,11 @@ move_point(const Vertex_handle& old_vertex,
}
//======= Get incident cells ==========
//tr_.incident_cells(old_vertex, std::back_inserter(incident_cells));
Cell_handle d = old_vertex->cell();
if (!try_lock_element(d)) // LOCK
if (try_lock_and_get_incident_cells(old_vertex, incident_cells_) == false)
{
BOOST_FOREACH(Cell_handle& ch,
std::make_pair(incident_cells.begin(), incident_cells.end()))
{
ch->tds_data().clear();
}
*p_could_lock_zone = false;
unlock_all_elements();
return Vertex_handle();
}
incident_cells.push_back(d);
d->tds_data().mark_in_conflict();
int head=0;
int tail=1;
do {
Cell_handle c = incident_cells[head];
for (int i=0; i<4; ++i) {
if (c->vertex(i) == old_vertex)
continue;
Cell_handle next = c->neighbor(i);
if (!try_lock_element(next)) // LOCK
{
BOOST_FOREACH(Cell_handle& ch,
std::make_pair(incident_cells.begin(), incident_cells.end()))
{
ch->tds_data().clear();
}
*p_could_lock_zone = false;
unlock_all_elements();
return Vertex_handle();
}
if (! next->tds_data().is_clear())
continue;
incident_cells.push_back(next);
++tail;
next->tds_data().mark_in_conflict();
}
++head;
} while(head != tail);
BOOST_FOREACH(Cell_handle& ch,
std::make_pair(incident_cells.begin(), incident_cells.end()))
{
ch->tds_data().clear();
}
//======= /Get incident cells ==========
if (!try_lock_point(new_position)) // LOCK
@ -2302,16 +2421,16 @@ move_point(const Vertex_handle& old_vertex,
unlock_all_elements();
return Vertex_handle();
}
if ( Th().no_topological_change(tr_, old_vertex, new_position, incident_cells) )
if ( Th().no_topological_change(tr_, old_vertex, new_position, incident_cells_) )
{
BOOST_FOREACH(Cell_handle& ch, std::make_pair(incident_cells.begin(),
incident_cells.end()))
BOOST_FOREACH(Cell_handle& ch, std::make_pair(incident_cells_.begin(),
incident_cells_.end()))
{
ch->invalidate_circumcenter();
}
tbb::mutex::scoped_lock lock(mut_outdated_cells); // CJTODO LOCK
std::copy(incident_cells.begin(),incident_cells.end(),
std::copy(incident_cells_.begin(),incident_cells_.end(),
std::inserter(outdated_cells_set, outdated_cells_set.end()));
lock.release(); // CJTODO LOCK
@ -2759,10 +2878,10 @@ C3T3_helpers<C3T3,MD>::
min_incident_value(const Vertex_handle& vh,
const SliverCriterion& criterion) const
{
Cell_vector incident_cells;
tr_.finite_incident_cells(vh,std::back_inserter(incident_cells));
Cell_vector incident_cells_;
tr_.finite_incident_cells(vh,std::back_inserter(incident_cells_));
return min_sliver_in_c3t3_value(incident_cells, criterion);
return min_sliver_in_c3t3_value(incident_cells_, criterion);
}
template <typename OutputIterator, typename CH, typename Fct>
@ -2804,6 +2923,86 @@ struct Counter {
};
template <typename C3T3, typename MD>
void
C3T3_helpers<C3T3,MD>::
get_incident_cells_without_using_tds_data(const Vertex_handle& v,
Cell_vector &cells) const
{
std::set<Cell_handle> found_cells;
Cell_handle d = v->cell();
cells.push_back(d);
found_cells.insert(d);
int head=0;
int tail=1;
do {
Cell_handle c = cells[head];
for (int i=0; i<4; ++i) {
if (c->vertex(i) == v)
continue;
Cell_handle next = c->neighbor(i);
if (! found_cells.insert(next).second )
continue;
cells.push_back(next);
++tail;
}
++head;
} while(head != tail);
}
template <typename C3T3, typename MD>
bool
C3T3_helpers<C3T3,MD>::
try_lock_and_get_incident_cells(const Vertex_handle& v,
Cell_vector &cells) const
{
Cell_handle d = v->cell();
if (!try_lock_element(d)) // LOCK
{
unlock_all_elements();
return false;
}
cells.push_back(d);
d->tds_data().mark_in_conflict();
int head=0;
int tail=1;
do {
Cell_handle c = cells[head];
for (int i=0; i<4; ++i) {
if (c->vertex(i) == v)
continue;
Cell_handle next = c->neighbor(i);
if (!try_lock_element(next)) // LOCK
{
BOOST_FOREACH(Cell_handle& ch,
std::make_pair(cells.begin(), cells.end()))
{
ch->tds_data().clear();
}
cells.clear();
unlock_all_elements();
return false;
}
if (! next->tds_data().is_clear())
continue;
cells.push_back(next);
++tail;
next->tds_data().mark_in_conflict();
}
++head;
} while(head != tail);
BOOST_FOREACH(Cell_handle& ch, std::make_pair(cells.begin(), cells.end()))
{
ch->tds_data().clear();
}
return true;
}
template <typename C3T3, typename MD>
template <typename SliverCriterion, typename OutputIterator>
OutputIterator
@ -2815,11 +3014,11 @@ incident_slivers(const Vertex_handle& v,
{
typedef SliverCriterion Sc;
std::vector<Cell_handle> incident_cells;
tr_.incident_cells(v, std::back_inserter(incident_cells));
std::vector<Cell_handle> incident_cells_;
tr_.incident_cells(v, std::back_inserter(incident_cells_));
std::remove_copy_if(incident_cells.begin(),
incident_cells.end(),
std::remove_copy_if(incident_cells_.begin(),
incident_cells_.end(),
out,
std::not1(Is_sliver<Sc>(c3t3_,criterion,sliver_bound)));
@ -2989,9 +3188,9 @@ get_conflict_zone_topo_change(const Vertex_handle& vertex,
OutputIterator conflict_cells) const
{
// Get triangulation_vertex incident cells
Cell_vector incident_cells;
incident_cells.reserve(64);
tr_.incident_cells(vertex, std::back_inserter(incident_cells));
Cell_vector incident_cells_;
incident_cells_.reserve(64);
tr_.incident_cells(vertex, std::back_inserter(incident_cells_));
// Get conflict_point conflict zone
Cell_vector deleted_cells;
@ -3020,10 +3219,10 @@ get_conflict_zone_topo_change(const Vertex_handle& vertex,
// Compute union of conflict_point conflict zone and triangulation_vertex
// incident cells
std::sort(deleted_cells.begin(),deleted_cells.end());
std::sort(incident_cells.begin(),incident_cells.end());
std::sort(incident_cells_.begin(),incident_cells_.end());
std::set_union(deleted_cells.begin(), deleted_cells.end(),
incident_cells.begin(), incident_cells.end(),
incident_cells_.begin(), incident_cells_.end(),
conflict_cells);
return conflict_cells;

69
Mesh_3/include/CGAL/Mesh_3/Mesh_global_optimizer.h
View File

@ -665,8 +665,18 @@ compute_move(const Vertex_handle& v)
Gt().construct_translated_point_3_object();
Cell_vector incident_cells;
incident_cells.reserve(64);
tr_.incident_cells(v, std::back_inserter(incident_cells));
incident_cells.reserve(64);
#ifdef CGAL_LINKED_WITH_TBB
// Parallel
if (boost::is_base_of<Parallel_tag, Concurrency_tag>::value)
{
helper_.get_incident_cells_without_using_tds_data(v, incident_cells);
}
else
#endif //CGAL_LINKED_WITH_TBB
{
tr_.incident_cells(v, std::back_inserter(incident_cells));
}
// Get move from move function
Vector_3 move = move_function_(v, incident_cells, c3t3_, sizing_field_);
@ -839,14 +849,43 @@ Mesh_global_optimizer<C3T3,Md,Mf,V_>::
fill_sizing_field()
{
std::map<Point_3,FT> value_map;
// Fill map with local size
for(typename Tr::Finite_vertices_iterator vit = tr_.finite_vertices_begin();
vit != tr_.finite_vertices_end();
++vit)
#ifdef CGAL_LINKED_WITH_TBB
// Parallel
if (boost::is_base_of<Parallel_tag, Concurrency_tag>::value)
{
value_map.insert(std::make_pair(vit->point(),
average_circumradius_length(vit)));
typedef tbb::enumerable_thread_specific<
std::vector< std::pair<Point_3, FT> > > Local_list;
Local_list local_lists;
tbb::parallel_do(tr_.finite_vertices_begin(), tr_.finite_vertices_end(),
[&]( Vertex& v ) // CJTODO: lambdas ok?
{
// CJTODO: should use Compact_container::s_iterator_to,
// but we don't know the exact Compact_container type here
Vertex_handle vh(&v);
local_lists.local().push_back(
std::make_pair(v.point(), average_circumradius_length(vh)));
});
for(typename Local_list::iterator it_list = local_lists.begin() ;
it_list != local_lists.end() ;
++it_list )
{
value_map.insert(it_list->begin(), it_list->end());
}
}
else
#endif //CGAL_LINKED_WITH_TBB
{
// Fill map with local size
for(typename Tr::Finite_vertices_iterator vit = tr_.finite_vertices_begin();
vit != tr_.finite_vertices_end();
++vit)
{
value_map.insert(std::make_pair(vit->point(),
average_circumradius_length(vit)));
}
}
// fill sizing field
@ -885,7 +924,17 @@ average_circumradius_length(const Vertex_handle& v) const
{
Cell_vector incident_cells;
incident_cells.reserve(64);
tr_.incident_cells(v, std::back_inserter(incident_cells));
#ifdef CGAL_LINKED_WITH_TBB
// Parallel
if (boost::is_base_of<Parallel_tag, Concurrency_tag>::value)
{
helper_.get_incident_cells_without_using_tds_data(v, incident_cells);
}
else
#endif //CGAL_LINKED_WITH_TBB
{
tr_.incident_cells(v, std::back_inserter(incident_cells));
}
FT sum_len (0);
unsigned int nb = 0;

47
Triangulation_3/include/CGAL/Triangulation_ds_cell_base_3.h
View File

@ -27,50 +27,10 @@
#include <CGAL/triangulation_assertions.h>
#include <CGAL/internal/Dummy_tds_3.h>
#ifdef CGAL_LINKED_WITH_TBB
# include <tbb/enumerable_thread_specific.h>
#endif
namespace CGAL {
/************************************************
// Class Triangulation_ds_cell_base_3_base
// Two versions: sequential / parallel
************************************************/
// Sequential
template <typename TDS_data, bool used_by_parallel_mesh_3>
class Triangulation_ds_cell_base_3_base
{
public:
// TDS internal data access functions.
TDS_data& tds_data() { return _tds_data; }
const TDS_data& tds_data() const { return _tds_data; }
protected:
TDS_data _tds_data;
};
#ifdef CGAL_LINKED_WITH_TBB
// Parallel
template <typename TDS_data>
class Triangulation_ds_cell_base_3_base<TDS_data, true>
{
public:
// TDS internal data access functions.
TDS_data& tds_data() { return _tds_data.local(); }
const TDS_data& tds_data() const { return _tds_data.local(); }
protected:
tbb::enumerable_thread_specific<TDS_data> _tds_data;
};
#endif // CGAL_LINKED_WITH_TBB
template < typename TDS = void >
class Triangulation_ds_cell_base_3
: public Triangulation_ds_cell_base_3_base<typename TDS::Cell_data,
TDS::Is_for_parallel_mesh_3>
{
public:
typedef TDS Triangulation_data_structure;
@ -238,10 +198,15 @@ public:
void * for_compact_container() const { return N[0].for_compact_container(); }
void * & for_compact_container() { return N[0].for_compact_container(); }
// TDS internal data access functions.
TDS_data& tds_data() { return _tds_data; }
const TDS_data& tds_data() const { return _tds_data; }
private:
Cell_handle N[4];
Vertex_handle V[4];
TDS_data _tds_data;
};
template < class TDS >
@ -276,4 +241,4 @@ public:
} //namespace CGAL
#endif // CGAL_TRIANGULATION_DS_CELL_BASE_3_H
#endif // CGAL_TRIANGULATION_DS_CELL_BASE_3_H