Reference documentation for deal.II version 9.1.0-pre
Public Types | Public Member Functions | Protected Member Functions | Private Member Functions | Private Attributes | List of all members
parallel::shared::Triangulation< dim, spacedim > Class Template Reference
Parallel computing » Parallel computing with multiple processors using distributed memory

#include <deal.II/distributed/shared_tria.h>

Inheritance diagram for parallel::shared::Triangulation< dim, spacedim >:
[legend]

Public Types

- Public Types inherited from Triangulation< dim, spacedim >
using cell_iterator = TriaIterator< CellAccessor< dim, spacedim >>
 
using active_cell_iterator = TriaActiveIterator< CellAccessor< dim, spacedim >>
 
using face_iterator = TriaIterator< TriaAccessor< dim-1, dim, spacedim >>
 
using active_face_iterator = TriaActiveIterator< TriaAccessor< dim-1, dim, spacedim >>
 
using vertex_iterator = TriaIterator<::TriaAccessor< 0, dim, spacedim >>
 
using active_vertex_iterator = TriaActiveIterator<::TriaAccessor< 0, dim, spacedim >>
 

Public Member Functions

 Triangulation (MPI_Comm mpi_communicator, const typename::Triangulation< dim, spacedim >::MeshSmoothing=(::Triangulation< dim, spacedim >::none), const bool allow_artificial_cells=false, const Settings settings=partition_auto)
 
virtual ~Triangulation () override=default
 
virtual void execute_coarsening_and_refinement () override
 
virtual void create_triangulation (const std::vector< Point< spacedim >> &vertices, const std::vector< CellData< dim >> &cells, const SubCellData &subcelldata) override
 
virtual void copy_triangulation (const ::Triangulation< dim, spacedim > &other_tria) override
 
template<class Archive >
void load (Archive &ar, const unsigned int version)
 
const std::vector< types::subdomain_id > & get_true_subdomain_ids_of_cells () const
 
const std::vector< types::subdomain_id > & get_true_level_subdomain_ids_of_cells (const unsigned int level) const
 
bool with_artificial_cells () const
 
- Public Member Functions inherited from parallel::Triangulation< dim, spacedim >
 Triangulation (MPI_Comm mpi_communicator, const typename::Triangulation< dim, spacedim >::MeshSmoothing smooth_grid=(::Triangulation< dim, spacedim >::none), const bool check_for_distorted_cells=false)
 
virtual MPI_Comm get_communicator () const
 
virtual void copy_triangulation (const ::Triangulation< dim, spacedim > &old_tria) override
 
const std::vector< unsigned int > & n_locally_owned_active_cells_per_processor () const
 
unsigned int n_locally_owned_active_cells () const
 
virtual types::global_dof_index n_global_active_cells () const override
 
virtual std::size_t memory_consumption () const override
 
virtual unsigned int n_global_levels () const override
 
types::subdomain_id locally_owned_subdomain () const override
 
const std::set< types::subdomain_id > & ghost_owners () const
 
const std::set< types::subdomain_id > & level_ghost_owners () const
 
virtual std::map< unsigned int, std::set<::types::subdomain_id > > compute_vertices_with_ghost_neighbors () const
 
- Public Member Functions inherited from Triangulation< dim, spacedim >
 Triangulation (const MeshSmoothing smooth_grid=none, const bool check_for_distorted_cells=false)
 
 Triangulation (const Triangulation< dim, spacedim > &)=delete
 
 Triangulation (Triangulation< dim, spacedim > &&tria) noexcept
 
Triangulation & operator= (Triangulation< dim, spacedim > &&tria) noexcept
 
virtual void clear ()
 
virtual void set_mesh_smoothing (const MeshSmoothing mesh_smoothing)
 
virtual const MeshSmoothing & get_mesh_smoothing () const
 
void set_manifold (const types::manifold_id number, const Manifold< dim, spacedim > &manifold_object)
 
void set_manifold (const types::manifold_id number)
 
void reset_manifold (const types::manifold_id manifold_number)
 
void reset_all_manifolds ()
 
void set_all_manifold_ids (const types::manifold_id number)
 
void set_all_manifold_ids_on_boundary (const types::manifold_id number)
 
void set_all_manifold_ids_on_boundary (const types::boundary_id b_id, const types::manifold_id number)
 
const Manifold< dim, spacedim > & get_manifold (const types::manifold_id number) const
 
std::vector< types::boundary_id > get_boundary_ids () const
 
std::vector< types::manifold_id > get_manifold_ids () const
 
virtual void copy_triangulation (const Triangulation< dim, spacedim > &other_tria)
 
virtual void create_triangulation_compatibility (const std::vector< Point< spacedim >> &vertices, const std::vector< CellData< dim >> &cells, const SubCellData &subcelldata)
 
void flip_all_direction_flags ()
 
void set_all_refine_flags ()
 
void refine_global (const unsigned int times=1)
 
virtual bool prepare_coarsening_and_refinement ()
 
void save_refine_flags (std::ostream &out) const
 
void save_refine_flags (std::vector< bool > &v) const
 
void load_refine_flags (std::istream &in)
 
void load_refine_flags (const std::vector< bool > &v)
 
void save_coarsen_flags (std::ostream &out) const
 
void save_coarsen_flags (std::vector< bool > &v) const
 
void load_coarsen_flags (std::istream &out)
 
void load_coarsen_flags (const std::vector< bool > &v)
 
bool get_anisotropic_refinement_flag () const
 
void clear_user_flags ()
 
void save_user_flags (std::ostream &out) const
 
void save_user_flags (std::vector< bool > &v) const
 
void load_user_flags (std::istream &in)
 
void load_user_flags (const std::vector< bool > &v)
 
void clear_user_flags_line ()
 
void save_user_flags_line (std::ostream &out) const
 
void save_user_flags_line (std::vector< bool > &v) const
 
void load_user_flags_line (std::istream &in)
 
void load_user_flags_line (const std::vector< bool > &v)
 
void clear_user_flags_quad ()
 
void save_user_flags_quad (std::ostream &out) const
 
void save_user_flags_quad (std::vector< bool > &v) const
 
void load_user_flags_quad (std::istream &in)
 
void load_user_flags_quad (const std::vector< bool > &v)
 
void clear_user_flags_hex ()
 
void save_user_flags_hex (std::ostream &out) const
 
void save_user_flags_hex (std::vector< bool > &v) const
 
void load_user_flags_hex (std::istream &in)
 
void load_user_flags_hex (const std::vector< bool > &v)
 
void clear_user_data ()
 
void save_user_indices (std::vector< unsigned int > &v) const
 
void load_user_indices (const std::vector< unsigned int > &v)
 
void save_user_pointers (std::vector< void * > &v) const
 
void load_user_pointers (const std::vector< void * > &v)
 
void save_user_indices_line (std::vector< unsigned int > &v) const
 
void load_user_indices_line (const std::vector< unsigned int > &v)
 
void save_user_indices_quad (std::vector< unsigned int > &v) const
 
void load_user_indices_quad (const std::vector< unsigned int > &v)
 
void save_user_indices_hex (std::vector< unsigned int > &v) const
 
void load_user_indices_hex (const std::vector< unsigned int > &v)
 
void save_user_pointers_line (std::vector< void * > &v) const
 
void load_user_pointers_line (const std::vector< void * > &v)
 
void save_user_pointers_quad (std::vector< void * > &v) const
 
void load_user_pointers_quad (const std::vector< void * > &v)
 
void save_user_pointers_hex (std::vector< void * > &v) const
 
void load_user_pointers_hex (const std::vector< void * > &v)
 
cell_iterator begin (const unsigned int level=0) const
 
active_cell_iterator begin_active (const unsigned int level=0) const
 
cell_iterator end () const
 
cell_iterator end (const unsigned int level) const
 
active_cell_iterator end_active (const unsigned int level) const
 
cell_iterator last () const
 
active_cell_iterator last_active () const
 
IteratorRange< cell_iterator > cell_iterators () const
 
IteratorRange< active_cell_iterator > active_cell_iterators () const
 
IteratorRange< cell_iterator > cell_iterators_on_level (const unsigned int level) const
 
IteratorRange< active_cell_iterator > active_cell_iterators_on_level (const unsigned int level) const
 
face_iterator begin_face () const
 
active_face_iterator begin_active_face () const
 
face_iterator end_face () const
 
vertex_iterator begin_vertex () const
 
active_vertex_iterator begin_active_vertex () const
 
vertex_iterator end_vertex () const
 
unsigned int n_lines () const
 
unsigned int n_lines (const unsigned int level) const
 
unsigned int n_active_lines () const
 
unsigned int n_active_lines (const unsigned int level) const
 
unsigned int n_quads () const
 
unsigned int n_quads (const unsigned int level) const
 
unsigned int n_active_quads () const
 
unsigned int n_active_quads (const unsigned int level) const
 
unsigned int n_hexs () const
 
unsigned int n_hexs (const unsigned int level) const
 
unsigned int n_active_hexs () const
 
unsigned int n_active_hexs (const unsigned int level) const
 
unsigned int n_cells () const
 
unsigned int n_cells (const unsigned int level) const
 
unsigned int n_active_cells () const
 
unsigned int n_active_cells (const unsigned int level) const
 
unsigned int n_faces () const
 
unsigned int n_active_faces () const
 
unsigned int n_levels () const
 
virtual bool has_hanging_nodes () const
 
unsigned int n_vertices () const
 
const std::vector< Point< spacedim > > & get_vertices () const
 
unsigned int n_used_vertices () const
 
bool vertex_used (const unsigned int index) const
 
const std::vector< bool > & get_used_vertices () const
 
unsigned int max_adjacent_cells () const
 
Triangulation< dim, spacedim > & get_triangulation ()
 
const Triangulation< dim, spacedim > & get_triangulation () const
 
unsigned int n_raw_lines () const
 
unsigned int n_raw_lines (const unsigned int level) const
 
unsigned int n_raw_quads () const
 
unsigned int n_raw_quads (const unsigned int level) const
 
unsigned int n_raw_hexs (const unsigned int level) const
 
unsigned int n_raw_cells (const unsigned int level) const
 
unsigned int n_raw_faces () const
 
template<class Archive >
void save (Archive &ar, const unsigned int version) const
 
template<class Archive >
void load (Archive &ar, const unsigned int version)
 
virtual void add_periodicity (const std::vector< GridTools::PeriodicFacePair< cell_iterator >> &)
 
const std::map< std::pair< cell_iterator, unsigned int >, std::pair< std::pair< cell_iterator, unsigned int >, std::bitset< 3 > > > & get_periodic_face_map () const
 
- Public Member Functions inherited from Subscriptor
 Subscriptor ()
 
 Subscriptor (const Subscriptor &)
 
 Subscriptor (Subscriptor &&) noexcept
 
virtual ~Subscriptor ()
 
Subscriptor & operator= (const Subscriptor &)
 
Subscriptor & operator= (Subscriptor &&) noexcept
 
void subscribe (const char *identifier=nullptr) const
 
void unsubscribe (const char *identifier=nullptr) const
 
unsigned int n_subscriptions () const
 
template<typename StreamType >
void list_subscribers (StreamType &stream) const
 
void list_subscribers () const
 
template<class Archive >
void serialize (Archive &ar, const unsigned int version)
 

Protected Member Functions

virtual void update_number_cache () override
 
- Protected Member Functions inherited from parallel::Triangulation< dim, spacedim >
void fill_level_ghost_owners ()
 
- Protected Member Functions inherited from Triangulation< dim, spacedim >
void update_periodic_face_map ()
 

Private Member Functions

void partition ()
 

Private Attributes

const Settings settings
 
const bool allow_artificial_cells
 
std::vector< types::subdomain_id > true_subdomain_ids_of_cells
 
std::vector< std::vector< types::subdomain_id > > true_level_subdomain_ids_of_cells
 

Additional Inherited Members

- Static Public Member Functions inherited from Triangulation< dim, spacedim >
static::ExceptionBase & ExcInvalidLevel (int arg1)
 
static::ExceptionBase & ExcTriangulationNotEmpty (int arg1, int arg2)
 
static::ExceptionBase & ExcGridReadError ()
 
static::ExceptionBase & ExcFacesHaveNoLevel ()
 
static::ExceptionBase & ExcEmptyLevel (int arg1)
 
static::ExceptionBase & ExcNonOrientableTriangulation ()
 
static::ExceptionBase & ExcBoundaryIdNotFound (types::boundary_id arg1)
 
- Static Public Member Functions inherited from Subscriptor
static::ExceptionBase & ExcInUse (int arg1, std::string arg2, std::string arg3)
 
static::ExceptionBase & ExcNoSubscriber (std::string arg1, std::string arg2)
 
- Public Attributes inherited from Triangulation< dim, spacedim >
Signals signals
 
- Static Public Attributes inherited from Triangulation< dim, spacedim >
static const unsigned int dimension = dim
 
static const unsigned int space_dimension = spacedim
 
- Static Protected Member Functions inherited from Triangulation< dim, spacedim >
static void write_bool_vector (const unsigned int magic_number1, const std::vector< bool > &v, const unsigned int magic_number2, std::ostream &out)
 
static void read_bool_vector (const unsigned int magic_number1, std::vector< bool > &v, const unsigned int magic_number2, std::istream &in)
 
- Protected Attributes inherited from parallel::Triangulation< dim, spacedim >
MPI_Comm mpi_communicator
 
types::subdomain_id my_subdomain
 
types::subdomain_id n_subdomains
 
- Protected Attributes inherited from Triangulation< dim, spacedim >
MeshSmoothing smooth_grid
 

Detailed Description

template<int dim, int spacedim = dim>
class parallel::shared::Triangulation< dim, spacedim >

This class provides a parallel triangulation for which every processor knows about every cell of the global mesh (unlike for the parallel::distributed::Triangulation class) but in which cells are automatically partitioned when run with MPI so that each processor "owns" a subset of cells. The use of this class is demonstrated in step-18.

Different from the parallel::distributed::Triangulation, this implies that the entire mesh is stored on each processor. While this is clearly a memory bottleneck that limits the use of this class to a few dozen or hundreds of MPI processes, the partitioning of the mesh can be used to partition work such as assembly or postprocessing between participating processors, and it can also be used to partition which processor stores which parts of matrices and vectors. As a consequence, using this class is often a gentler introduction to parallelizing a code than the more involved parallel::distributed::Triangulation class in which processors only know their own part of the mesh, but nothing about cells owned by other processors with the exception of a single layer of ghost cells around their own part of the domain.

The class is also useful in cases where compute time and memory considerations dictate that the program needs to be run in parallel, but where algorithmic concerns require that every processor knows about the entire mesh. An example could be where an application has to have both volume and surface meshes that can then both be partitioned independently, but where it is difficult to ensure that the locally owned set of surface mesh cells is adjacent to the locally owned set of volume mesh cells and the other way around. In such cases, knowing the entirety of both meshes ensures that assembly of coupling terms can be implemented without also implementing overly complicated schemes to transfer information about adjacent cells from processor to processor.

The partitioning of cells between processors is done internally based on a number of different possibilities. By passing appropriate flags to the constructor of this class (see the parallel::shared::Triangulation::Settings enum), it is possible to select different ways of partitioning the mesh, including ways that are dictated by the application and not by the desire to minimize the length of the interface between subdomains owned by processors (as is done by the METIS and Zoltan packages, both of which are options for partitioning). Both the DoFHandler and hp::DoFHandler classes know how to enumerate degrees of freedom in ways appropriate for the partitioned mesh.

Author
Denis Davydov, 2015

Definition at line 102 of file shared_tria.h.

Member Enumeration Documentation

template<int dim, int spacedim = dim>
enum parallel::shared::Triangulation::Settings

Configuration flags for distributed Triangulations to be set in the constructor. Settings can be combined using bitwise OR.

The constructor requires that exactly one of partition_auto, partition_metis, partition_zorder, partition_zoltan and partition_custom_signal is set. If partition_auto is chosen, it will use partition_zoltan (if available), then partition_metis (if available) and finally partition_zorder.

Enumerator
partition_auto 

Choose the partitioner depending on the enabled dependencies that were found when configuring deal.II. In particular, if the Trilinos package Zoltan was found, then use the partition_zoltan strategy. If Zoltan was not found but the METIS package was found, then use the partition_metis strategy. If neither of these were found, then use the partition_zorder partitioning strategy.

partition_metis 

Use METIS partitioner to partition active cells.

partition_zorder 

Partition active cells with the same scheme used in the p4est library.

The term "Z-order" originates in the fact that cells are sorted using a space filling curve which in 2d connects the four children of a cell in the order bottom left, bottom right, top left, top right (i.e., with a curve that looks like a reverse "Z"), and does so recursively on all levels of a triangulation. This is also the order in which children are enumerated by the GeometryInfo class. The "Z-order" is also sometimes called "Morton ordering", see https://en.wikipedia.org/wiki/Z-order_curve .

See also
Z order glossary entry.
partition_zoltan 

Use Zoltan to partition active cells.

partition_custom_signal 

Partition cells using a custom, user defined function. This is accomplished by connecting the post_refinement signal to the triangulation whenever it is first created and passing the user defined function through the signal using std::bind. Here is an example:

template <int dim>
void mypartition(parallel::shared::Triangulation<dim> &tria)
{
// user defined partitioning scheme: assign subdomain_ids
// round-robin in a mostly random way:
std::vector<unsigned int> assignment =
{0,0,1,2,0,0,2,1,0,2,2,1,2,2,0,0};
unsigned int index = 0;
for (const auto &cell : tria.active_cell_iterators())
cell->set_subdomain_id(assignment[(index++)%16]);
}
int main ()
{
parallel::shared::Triangulation<dim> tria(
...,
parallel::shared::Triangulation<dim>::partition_custom_signal);
tria.signals.post_refinement.connect(std::bind(&mypartition<dim>,
std::ref(tria)));
}

An equivalent code using lambda functions would look like this:

int main ()
{
parallel::shared::Triangulation<dim> tria(
...,
parallel::shared::Triangulation<dim>::partition_custom_signal);
tria.signals.post_refinement.connect (
[&tria]()
{
// user defined partitioning scheme as above
...
});
}
Note
If you plan to use a custom partition with geometric multigrid, you must manually partition the level cells in addition to the active cells.
construct_multigrid_hierarchy 

This flag needs to be set to use the geometric multigrid functionality. This option requires additional computation and communication.

Note: This flag should always be set alongside a flag for an active cell partitioning method.

Definition at line 123 of file shared_tria.h.

Constructor & Destructor Documentation

template<int dim, int spacedim>
Triangulation< dim, spacedim >::Triangulation ( MPI_Comm  mpi_communicator,
const typename::Triangulation< dim, spacedim >::MeshSmoothing  smooth_grid = (::Triangulation<dim, spacedim>::none),
const bool  allow_artificial_cells = false,
const Settings  settings = partition_auto 
)

Constructor.

If allow_aritifical_cells is true, this class will behave similar to parallel::distributed::Triangulation in that there will be locally owned, ghost and artificial cells.

Otherwise all non-locally owned cells are considered ghost.

Definition at line 39 of file shared_tria.cc.

template<int dim, int spacedim = dim>
virtual parallel::shared::Triangulation< dim, spacedim >::~Triangulation ( )
overridevirtualdefault

Destructor.

Reimplemented from parallel::Triangulation< dim, spacedim >.

Member Function Documentation

template<int dim, int spacedim>
void Triangulation< dim, spacedim >::execute_coarsening_and_refinement ( )
overridevirtual

Coarsen and refine the mesh according to refinement and coarsening flags set.

This step is equivalent to the Triangulation class with an addition of calling GridTools::partition_triangulation() at the end.

Reimplemented from Triangulation< dim, spacedim >.

Definition at line 344 of file shared_tria.cc.

template<int dim, int spacedim>
void Triangulation< dim, spacedim >::create_triangulation ( const std::vector< Point< spacedim >> &  vertices,
const std::vector< CellData< dim >> &  cells,
const SubCellData &  subcelldata 
)
overridevirtual

Create a triangulation.

This function also partitions triangulation based on the MPI communicator provided to the constructor.

Reimplemented from Triangulation< dim, spacedim >.

Definition at line 355 of file shared_tria.cc.

template<int dim, int spacedim>
void Triangulation< dim, spacedim >::copy_triangulation ( const ::Triangulation< dim, spacedim > &  other_tria)
overridevirtual

Copy other_tria to this triangulation.

This function also partitions triangulation based on the MPI communicator provided to the constructor.

Note
This function can not be used with parallel::distributed::Triangulation, since it only stores those cells that it owns, one layer of ghost cells around the ones it locally owns, and a number of artificial cells.

Definition at line 381 of file shared_tria.cc.

template<int dim, int spacedim>
template<class Archive >
void Triangulation< dim, spacedim >::load ( Archive &  ar,
const unsigned int  version 
)

Read the data of this object from a stream for the purpose of serialization. Throw away the previous content.

This function first does the same work as in Triangulation::load, then partitions the triangulation based on the MPI communicator provided to the constructor.

Definition at line 381 of file shared_tria.h.

template<int dim, int spacedim>
const std::vector< types::subdomain_id > & Triangulation< dim, spacedim >::get_true_subdomain_ids_of_cells ( ) const

Return a vector of length Triangulation::n_active_cells() where each element stores the subdomain id of the owner of this cell. The elements of the vector are obviously the same as the subdomain ids for locally owned and ghost cells, but are also correct for artificial cells that do not store who the owner of the cell is in their subdomain_id field.

Definition at line 325 of file shared_tria.cc.

template<int dim, int spacedim>
const std::vector< types::subdomain_id > & Triangulation< dim, spacedim >::get_true_level_subdomain_ids_of_cells ( const unsigned int  level) const

Return a vector of length Triangulation::n_cells(level) where each element stores the level subdomain id of the owner of this cell. The elements of the vector are obviously the same as the level subdomain ids for locally owned and ghost cells, but are also correct for artificial cells that do not store who the owner of the cell is in their level_subdomain_id field.

Definition at line 334 of file shared_tria.cc.

template<int dim, int spacedim>
bool Triangulation< dim, spacedim >::with_artificial_cells ( ) const

Return allow_artificial_cells , namely true if artificial cells are allowed.

Definition at line 316 of file shared_tria.cc.

template<int dim, int spacedim>
void Triangulation< dim, spacedim >::update_number_cache ( )
overrideprotectedvirtual

Override the function to update the number cache so we can fill data like level_ghost_owners.

Reimplemented from parallel::Triangulation< dim, spacedim >.

Definition at line 401 of file shared_tria.cc.

template<int dim, int spacedim>
void Triangulation< dim, spacedim >::partition ( )
private

This function calls GridTools::partition_triangulation () and if requested in the constructor of the class marks artificial cells.

Definition at line 75 of file shared_tria.cc.

Member Data Documentation

template<int dim, int spacedim = dim>
const Settings parallel::shared::Triangulation< dim, spacedim >::settings
private

Settings

Definition at line 338 of file shared_tria.h.

template<int dim, int spacedim = dim>
const bool parallel::shared::Triangulation< dim, spacedim >::allow_artificial_cells
private

A flag to decide whether or not artificial cells are allowed.

Definition at line 343 of file shared_tria.h.

template<int dim, int spacedim = dim>
std::vector<types::subdomain_id> parallel::shared::Triangulation< dim, spacedim >::true_subdomain_ids_of_cells
private

A vector containing subdomain IDs of cells obtained by partitioning using either zorder, METIS, or a user-defined partitioning scheme. In case allow_artificial_cells is false, this vector is consistent with IDs stored in cell->subdomain_id() of the triangulation class. When allow_artificial_cells is true, cells which are artificial will have cell->subdomain_id() == numbers::artificial;

The original partition information is stored to allow using sequential DoF distribution and partitioning functions with semi-artificial cells.

Definition at line 364 of file shared_tria.h.

template<int dim, int spacedim = dim>
std::vector<std::vector<types::subdomain_id> > parallel::shared::Triangulation< dim, spacedim >::true_level_subdomain_ids_of_cells
private

A vector containing level subdomain IDs of cells obtained by partitioning each level.

The original partition information is stored to allow using sequential DoF distribution and partitioning functions with semi-artificial cells.

Definition at line 375 of file shared_tria.h.

The documentation for this class was generated from the following files:
Generated by   doxygen 1.8.11