libMesh::PetscPreconditioner< T > Class Template Reference

#include <petsc_preconditioner.h>

Inheritance diagram for libMesh::PetscPreconditioner< T >:

Public Member Functions
	PetscPreconditioner (const libMesh::Parallel::Communicator &comm_in)
virtual	~PetscPreconditioner ()
virtual void	apply (const NumericVector< T > &x, NumericVector< T > &y) override
virtual void	clear () override
virtual void	init () override
PC	pc ()
bool	initialized () const
virtual void	setup ()
void	set_matrix (SparseMatrix< Number > &mat)
PreconditionerType	type () const
void	set_type (const PreconditionerType pct)
const Parallel::Communicator &	comm () const
processor_id_type	n_processors () const
processor_id_type	processor_id () const

Static Public Member Functions
static void	set_petsc_preconditioner_type (const PreconditionerType &preconditioner_type, PC &pc)
static std::unique_ptr< Preconditioner< T > >	build_preconditioner (const libMesh::Parallel::Communicator &comm, const SolverPackage solver_package=libMesh::default_solver_package())
static Preconditioner< T > *	build (const libMesh::Parallel::Communicator &comm, const SolverPackage solver_package=libMesh::default_solver_package())
static std::string	get_info ()
static void	print_info (std::ostream &out=libMesh::out)
static unsigned int	n_objects ()
static void	enable_print_counter_info ()
static void	disable_print_counter_info ()

Protected Types
typedef std::map< std::string, std::pair< unsigned int, unsigned int > >	Counts

Protected Member Functions
void	increment_constructor_count (const std::string &name)
void	increment_destructor_count (const std::string &name)

Protected Attributes
PC	_pc
Mat	_mat
SparseMatrix< T > *	_matrix
PreconditionerType	_preconditioner_type
bool	_is_initialized
const Parallel::Communicator &	_communicator

Static Protected Attributes
static Counts	_counts
static Threads::atomic< unsigned int >	_n_objects
static Threads::spin_mutex	_mutex
static bool	_enable_print_counter = true

Static Private Member Functions
static void	set_petsc_subpreconditioner_type (PCType type, PC &pc)
static void	set_petsc_subpreconditioner_type (const PCType type, PC &pc)

Detailed Description

template<typename T>
class libMesh::PetscPreconditioner< T >

This class provides an interface to the suite of preconditioners available from PETSc. All overridden virtual functions are documented in preconditioner.h.

Author

Derek Gaston

Date

2009

Definition at line 63 of file petsc_preconditioner.h.

Member Typedef Documentation

Counts

typedef std::map<std::string, std::pair<unsigned int, unsigned int> > libMesh::ReferenceCounter::Counts

protectedinherited

Data structure to log the information. The log is identified by the class name.

Definition at line 117 of file reference_counter.h.

Constructor & Destructor Documentation

PetscPreconditioner()

template<typename T >

libMesh::PetscPreconditioner< T >::PetscPreconditioner ( const libMesh::Parallel::Communicator &  comm_in )

inline

Constructor. Initializes PetscPreconditioner data structures

Definition at line 129 of file petsc_preconditioner.h.

                                                                                        :
  Preconditioner<T>(comm_in),
  _pc(PETSC_NULL)
{
}

~PetscPreconditioner()

template<typename T >

libMesh::PetscPreconditioner< T >::~PetscPreconditioner ( )

inlinevirtual

Destructor.

Definition at line 139 of file petsc_preconditioner.h.

{
  this->clear ();
}

Member Function Documentation

apply()

template<typename T >

void libMesh::PetscPreconditioner< T >::apply ( const NumericVector< T > &  x, NumericVector< T > &  y  )

overridevirtual

Computes the preconditioned vector y based on input vector x. This is usually done by solving to get the action of .

Implements libMesh::Preconditioner< T >.

Definition at line 41 of file petsc_preconditioner.C.

References ierr, and libMesh::PetscVector< T >::vec().

{
  PetscVector<T> & x_pvec = cast_ref<PetscVector<T> &>(const_cast<NumericVector<T> &>(x));
  PetscVector<T> & y_pvec = cast_ref<PetscVector<T> &>(const_cast<NumericVector<T> &>(y));

  Vec x_vec = x_pvec.vec();
  Vec y_vec = y_pvec.vec();

  int ierr = PCApply(_pc,x_vec,y_vec);
  LIBMESH_CHKERR(ierr);
}

build()

template<typename T >

Preconditioner< T > * libMesh::Preconditioner< T >::build ( const libMesh::Parallel::Communicator &  comm, const SolverPackage  solver_package = libMesh::default_solver_package()  )

staticinherited

Builds a Preconditioner using the linear solver package specified by solver_package

Deprecated:

Use build_preconditioner() instead.

Definition at line 84 of file preconditioner.C.

{
  // You should be calling build_preconditioner() instead.
  libmesh_deprecated();

  // Call the non-deprecated method
  std::unique_ptr<Preconditioner<T>> ptr =
    Preconditioner<T>::build_preconditioner(comm, solver_package);

  // Vaya con dios
  return ptr.release();
}

build_preconditioner()

template<typename T >

std::unique_ptr< Preconditioner< T > > libMesh::Preconditioner< T >::build_preconditioner ( const libMesh::Parallel::Communicator &  comm, const SolverPackage  solver_package = libMesh::default_solver_package()  )

staticinherited

Builds a Preconditioner using the linear solver package specified by solver_package, returning the result wrapped in a std::unique_ptr for safety.

Definition at line 46 of file preconditioner.C.

{
  // Avoid unused parameter warnings when no solver packages are enabled.
  libmesh_ignore(comm);

  // Build and return the appropriate Preconditioner object.
  switch (solver_package)
    {

#ifdef LIBMESH_HAVE_PETSC
    case PETSC_SOLVERS:
      {
        return libmesh_make_unique<PetscPreconditioner<T>>(comm);
      }
#endif

#ifdef LIBMESH_TRILINOS_HAVE_EPETRA
    case TRILINOS_SOLVERS:
      return libmesh_make_unique<TrilinosPreconditioner<T>>(comm);
#endif

#ifdef LIBMESH_HAVE_EIGEN
    case EIGEN_SOLVERS:
      return libmesh_make_unique<EigenPreconditioner<T>>(comm);
#endif

    default:
      libmesh_error_msg("ERROR:  Unrecognized solver package: " << solver_package);
    }
}

clear()

template<typename T >

void libMesh::PetscPreconditioner< T >::clear ( )

overridevirtual

Release all memory and clear data structures.

Reimplemented from libMesh::Preconditioner< T >.

Definition at line 102 of file petsc_preconditioner.C.

References ierr.

{
  if (_pc)
    {
      int ierr = LibMeshPCDestroy(&_pc);
      LIBMESH_CHKERR(ierr);
    }
}

comm()

const Parallel::Communicator& libMesh::ParallelObject::comm ( ) const

inlineinherited

Returns

A reference to the Parallel::Communicator object used by this mesh.

Definition at line 89 of file parallel_object.h.

References libMesh::ParallelObject::_communicator.

Referenced by libMesh::__libmesh_petsc_diff_solver_jacobian(), libMesh::__libmesh_petsc_diff_solver_monitor(), libMesh::__libmesh_petsc_diff_solver_residual(), libMesh::__libmesh_tao_equality_constraints(), libMesh::__libmesh_tao_equality_constraints_jacobian(), libMesh::__libmesh_tao_gradient(), libMesh::__libmesh_tao_hessian(), libMesh::__libmesh_tao_inequality_constraints(), libMesh::__libmesh_tao_inequality_constraints_jacobian(), libMesh::__libmesh_tao_objective(), libMesh::MeshRefinement::_coarsen_elements(), libMesh::ExactSolution::_compute_error(), libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::BoundaryInfo::_find_id_maps(), libMesh::SlepcEigenSolver< T >::_petsc_shell_matrix_get_diagonal(), libMesh::PetscLinearSolver< T >::_petsc_shell_matrix_get_diagonal(), libMesh::SlepcEigenSolver< T >::_petsc_shell_matrix_mult(), libMesh::PetscLinearSolver< T >::_petsc_shell_matrix_mult(), libMesh::PetscLinearSolver< T >::_petsc_shell_matrix_mult_add(), libMesh::EquationSystems::_read_impl(), libMesh::MeshRefinement::_refine_elements(), libMesh::MeshRefinement::_smooth_flags(), libMesh::PetscDMWrapper::add_dofs_helper(), libMesh::PetscDMWrapper::add_dofs_to_section(), libMesh::ImplicitSystem::add_matrix(), libMesh::System::add_vector(), libMesh::UnstructuredMesh::all_second_order(), libMesh::MeshTools::Modification::all_tri(), libMesh::LaplaceMeshSmoother::allgather_graph(), libMesh::FEMSystem::assemble_qoi(), libMesh::MeshCommunication::assign_global_indices(), libMesh::DofMap::attach_matrix(), libMesh::MeshTools::Generation::build_extrusion(), libMesh::BoundaryInfo::build_node_list_from_side_list(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::PetscDMWrapper::build_section(), libMesh::PetscDMWrapper::build_sf(), libMesh::MeshBase::cache_elem_dims(), libMesh::System::calculate_norm(), libMesh::DofMap::check_dirichlet_bcid_consistency(), libMesh::PetscDMWrapper::check_section_n_dofs(), libMesh::Nemesis_IO_Helper::compute_num_global_elem_blocks(), libMesh::Nemesis_IO_Helper::compute_num_global_nodesets(), libMesh::Nemesis_IO_Helper::compute_num_global_sidesets(), libMesh::Problem_Interface::computeF(), libMesh::Problem_Interface::computeJacobian(), libMesh::Problem_Interface::computePreconditioner(), libMesh::ExodusII_IO::copy_elemental_solution(), libMesh::MeshTools::correct_node_proc_ids(), libMesh::MeshTools::create_bounding_box(), libMesh::MeshTools::create_nodal_bounding_box(), libMesh::MeshRefinement::create_parent_error_vector(), libMesh::MeshTools::create_processor_bounding_box(), libMesh::MeshTools::create_subdomain_bounding_box(), libMesh::MeshCommunication::delete_remote_elements(), libMesh::DofMap::distribute_dofs(), DMlibMeshFunction(), DMlibMeshJacobian(), DMlibMeshSetSystem_libMesh(), DMVariableBounds_libMesh(), libMesh::MeshRefinement::eliminate_unrefined_patches(), libMesh::EpetraVector< T >::EpetraVector(), libMesh::WeightedPatchRecoveryErrorEstimator::estimate_error(), libMesh::PatchRecoveryErrorEstimator::estimate_error(), libMesh::JumpErrorEstimator::estimate_error(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::MeshRefinement::flag_elements_by_elem_fraction(), libMesh::MeshRefinement::flag_elements_by_error_fraction(), libMesh::MeshRefinement::flag_elements_by_nelem_target(), libMesh::CondensedEigenSystem::get_eigenpair(), libMesh::DofMap::get_info(), libMesh::ImplicitSystem::get_linear_solver(), libMesh::LocationMap< T >::init(), libMesh::TimeSolver::init(), libMesh::SystemSubsetBySubdomain::init(), libMesh::PetscDMWrapper::init_and_attach_petscdm(), libMesh::EigenSystem::init_data(), libMesh::EigenSystem::init_matrices(), libMesh::OptimizationSystem::initialize_equality_constraints_storage(), libMesh::OptimizationSystem::initialize_inequality_constraints_storage(), libMesh::MeshTools::libmesh_assert_consistent_distributed(), libMesh::MeshTools::libmesh_assert_consistent_distributed_nodes(), libMesh::MeshTools::libmesh_assert_contiguous_dof_ids(), libMesh::MeshTools::libmesh_assert_parallel_consistent_new_node_procids(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Elem >(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_topology_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_valid_boundary_ids(), libMesh::MeshTools::libmesh_assert_valid_dof_ids(), libMesh::MeshTools::libmesh_assert_valid_neighbors(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_flags(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_object_ids(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_p_levels(), libMesh::MeshTools::libmesh_assert_valid_refinement_flags(), libMesh::MeshTools::libmesh_assert_valid_unique_ids(), libMesh::libmesh_petsc_snes_fd_residual(), libMesh::libmesh_petsc_snes_jacobian(), libMesh::libmesh_petsc_snes_mffd_residual(), libMesh::libmesh_petsc_snes_postcheck(), libMesh::libmesh_petsc_snes_residual(), libMesh::libmesh_petsc_snes_residual_helper(), libMesh::MeshRefinement::limit_level_mismatch_at_edge(), libMesh::MeshRefinement::limit_level_mismatch_at_node(), libMesh::MeshRefinement::limit_overrefined_boundary(), libMesh::MeshRefinement::limit_underrefined_boundary(), libMesh::MeshRefinement::make_coarsening_compatible(), libMesh::MeshCommunication::make_elems_parallel_consistent(), libMesh::MeshRefinement::make_flags_parallel_consistent(), libMesh::MeshCommunication::make_new_node_proc_ids_parallel_consistent(), libMesh::MeshCommunication::make_new_nodes_parallel_consistent(), libMesh::MeshCommunication::make_node_ids_parallel_consistent(), libMesh::MeshCommunication::make_node_proc_ids_parallel_consistent(), libMesh::MeshCommunication::make_node_unique_ids_parallel_consistent(), libMesh::MeshCommunication::make_nodes_parallel_consistent(), libMesh::MeshCommunication::make_p_levels_parallel_consistent(), libMesh::MeshRefinement::make_refinement_compatible(), libMesh::FEMSystem::mesh_position_set(), libMesh::DistributedMesh::n_active_elem(), libMesh::MeshTools::n_active_levels(), libMesh::BoundaryInfo::n_boundary_conds(), libMesh::BoundaryInfo::n_edge_conds(), libMesh::CondensedEigenSystem::n_global_non_condensed_dofs(), libMesh::MeshTools::n_levels(), libMesh::BoundaryInfo::n_nodeset_conds(), libMesh::MeshTools::n_p_levels(), libMesh::BoundaryInfo::n_shellface_conds(), libMesh::DistributedMesh::parallel_max_elem_id(), libMesh::DistributedMesh::parallel_max_node_id(), libMesh::ReplicatedMesh::parallel_max_unique_id(), libMesh::DistributedMesh::parallel_max_unique_id(), libMesh::DistributedMesh::parallel_n_elem(), libMesh::DistributedMesh::parallel_n_nodes(), libMesh::SparsityPattern::Build::parallel_sync(), libMesh::MeshTools::paranoid_n_levels(), libMesh::petsc_auto_fieldsplit(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::MeshBase::prepare_for_use(), libMesh::Nemesis_IO::read(), libMesh::XdrIO::read(), libMesh::CheckpointIO::read_header(), libMesh::XdrIO::read_header(), libMesh::System::read_header(), libMesh::System::read_legacy_data(), libMesh::System::read_SCALAR_dofs(), libMesh::XdrIO::read_serialized_bc_names(), libMesh::XdrIO::read_serialized_bcs_helper(), libMesh::System::read_serialized_blocked_dof_objects(), libMesh::XdrIO::read_serialized_connectivity(), libMesh::XdrIO::read_serialized_nodes(), libMesh::XdrIO::read_serialized_nodesets(), libMesh::XdrIO::read_serialized_subdomain_names(), libMesh::System::read_serialized_vector(), libMesh::MeshBase::recalculate_n_partitions(), libMesh::MeshRefinement::refine_and_coarsen_elements(), libMesh::DistributedMesh::renumber_dof_objects(), libMesh::CheckpointIO::select_split_config(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::PetscDMWrapper::set_point_range_in_section(), libMesh::PetscDiffSolver::setup_petsc_data(), libMesh::LaplaceMeshSmoother::smooth(), libMesh::split_mesh(), libMesh::MeshBase::subdomain_ids(), libMesh::BoundaryInfo::sync(), libMesh::MeshRefinement::test_level_one(), libMesh::MeshRefinement::test_unflagged(), libMesh::MeshTools::total_weight(), libMesh::MeshRefinement::uniformly_coarsen(), libMesh::NameBasedIO::write(), libMesh::XdrIO::write(), libMesh::System::write_SCALAR_dofs(), libMesh::XdrIO::write_serialized_bcs_helper(), libMesh::System::write_serialized_blocked_dof_objects(), libMesh::XdrIO::write_serialized_connectivity(), libMesh::XdrIO::write_serialized_nodes(), and libMesh::XdrIO::write_serialized_nodesets().

  { return _communicator; }

disable_print_counter_info()

void libMesh::ReferenceCounter::disable_print_counter_info ( )

staticinherited

Definition at line 106 of file reference_counter.C.

References libMesh::ReferenceCounter::_enable_print_counter.

Referenced by libMesh::LibMeshInit::LibMeshInit().

{
  _enable_print_counter = false;
  return;
}

enable_print_counter_info()

void libMesh::ReferenceCounter::enable_print_counter_info ( )

staticinherited

Methods to enable/disable the reference counter output from print_info()

Definition at line 100 of file reference_counter.C.

References libMesh::ReferenceCounter::_enable_print_counter.

{
  _enable_print_counter = true;
  return;
}

get_info()

std::string libMesh::ReferenceCounter::get_info ( )

staticinherited

Gets a string containing the reference information.

Definition at line 47 of file reference_counter.C.

References libMesh::ReferenceCounter::_counts, and libMesh::Quality::name().

Referenced by libMesh::ReferenceCounter::print_info().

{
#if defined(LIBMESH_ENABLE_REFERENCE_COUNTING) && defined(DEBUG)

  std::ostringstream oss;

  oss << '\n'
      << " ---------------------------------------------------------------------------- \n"
      << "| Reference count information                                                |\n"
      << " ---------------------------------------------------------------------------- \n";

  for (const auto & pr : _counts)
    {
      const std::string name(pr.first);
      const unsigned int creations    = pr.second.first;
      const unsigned int destructions = pr.second.second;

      oss << "| " << name << " reference count information:\n"
          << "|  Creations:    " << creations    << '\n'
          << "|  Destructions: " << destructions << '\n';
    }

  oss << " ---------------------------------------------------------------------------- \n";

  return oss.str();

#else

  return "";

#endif
}

increment_constructor_count()

void libMesh::ReferenceCounter::increment_constructor_count ( const std::string &  name )

inlineprotectedinherited

Increments the construction counter. Should be called in the constructor of any derived class that will be reference counted.

Definition at line 181 of file reference_counter.h.

References libMesh::ReferenceCounter::_counts, libMesh::Quality::name(), and libMesh::Threads::spin_mtx.

Referenced by libMesh::ReferenceCountedObject< RBParametrized >::ReferenceCountedObject().

{
  Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
  std::pair<unsigned int, unsigned int> & p = _counts[name];

  p.first++;
}

increment_destructor_count()

void libMesh::ReferenceCounter::increment_destructor_count ( const std::string &  name )

inlineprotectedinherited

Increments the destruction counter. Should be called in the destructor of any derived class that will be reference counted.

Definition at line 194 of file reference_counter.h.

References libMesh::ReferenceCounter::_counts, libMesh::Quality::name(), and libMesh::Threads::spin_mtx.

Referenced by libMesh::ReferenceCountedObject< RBParametrized >::~ReferenceCountedObject().

{
  Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
  std::pair<unsigned int, unsigned int> & p = _counts[name];

  p.second++;
}

init()

template<typename T >

void libMesh::PetscPreconditioner< T >::init ( )

overridevirtual

Initialize data structures if not done so already.

Note

This MUST be called before the preconditioning object is used.

Reimplemented from libMesh::Preconditioner< T >.

Definition at line 57 of file petsc_preconditioner.C.

References libMesh::libMeshPrivateData::_is_initialized, ierr, and libMesh::PetscMatrix< T >::mat().

{
  if (!this->_matrix)
    libmesh_error_msg("ERROR: No matrix set for PetscPreconditioner, but init() called");

  // Clear the preconditioner in case it has been created in the past
  if (!this->_is_initialized)
    {
      // Should probably use PCReset(), but it's not working at the moment so we'll destroy instead
      if (_pc)
        {
          int ierr = LibMeshPCDestroy(&_pc);
          LIBMESH_CHKERR(ierr);
        }

      int ierr = PCCreate(this->comm().get(),&_pc);
      LIBMESH_CHKERR(ierr);

      PetscMatrix<T> * pmatrix = cast_ptr<PetscMatrix<T> *, SparseMatrix<T>>(this->_matrix);

      _mat = pmatrix->mat();
    }

#if PETSC_RELEASE_LESS_THAN(3,5,0)
  int ierr = PCSetOperators(_pc,_mat,_mat,SAME_NONZERO_PATTERN);
#else
  int ierr = PCSetOperators(_pc,_mat,_mat);
#endif
  LIBMESH_CHKERR(ierr);

  // Set the PCType.  Note: this used to be done *before* the call to
  // PCSetOperators(), and only when !_is_initialized, but
  // 1.) Some preconditioners (those employing sub-preconditioners,
  // for example) have to call PCSetUp(), and can only do this after
  // the operators have been set.
  // 2.) It should be safe to call set_petsc_preconditioner_type()
  // multiple times.
  set_petsc_preconditioner_type(this->_preconditioner_type, _pc);

  this->_is_initialized = true;
}

initialized()

template<typename T>

bool libMesh::Preconditioner< T >::initialized ( ) const

inlineinherited

Returns

true if the data structures are initialized, false otherwise.

Definition at line 106 of file preconditioner.h.

{ return _is_initialized; }

n_objects()

static unsigned int libMesh::ReferenceCounter::n_objects ( )

inlinestaticinherited

Prints the number of outstanding (created, but not yet destroyed) objects.

Definition at line 83 of file reference_counter.h.

References libMesh::ReferenceCounter::_n_objects.

  { return _n_objects; }

n_processors()

processor_id_type libMesh::ParallelObject::n_processors ( ) const

inlineinherited

Returns

The number of processors in the group.

Definition at line 95 of file parallel_object.h.

References libMesh::ParallelObject::_communicator, and libMesh::Parallel::Communicator::size().

Referenced by libMesh::BoundaryInfo::_find_id_maps(), libMesh::PetscDMWrapper::add_dofs_to_section(), libMesh::DistributedMesh::add_elem(), libMesh::DistributedMesh::add_node(), libMesh::LaplaceMeshSmoother::allgather_graph(), libMesh::FEMSystem::assembly(), libMesh::AztecLinearSolver< T >::AztecLinearSolver(), libMesh::BoundaryInfo::build_node_list_from_side_list(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::DistributedMesh::clear(), libMesh::Nemesis_IO_Helper::compute_border_node_ids(), libMesh::Nemesis_IO_Helper::construct_nemesis_filename(), libMesh::UnstructuredMesh::create_pid_mesh(), libMesh::MeshTools::create_processor_bounding_box(), libMesh::DofMap::distribute_dofs(), libMesh::DofMap::distribute_local_dofs_node_major(), libMesh::DofMap::distribute_local_dofs_var_major(), libMesh::EnsightIO::EnsightIO(), libMesh::MeshBase::get_info(), libMesh::SystemSubsetBySubdomain::init(), libMesh::PetscDMWrapper::init_and_attach_petscdm(), libMesh::Nemesis_IO_Helper::initialize(), libMesh::DistributedMesh::insert_elem(), libMesh::MeshTools::libmesh_assert_contiguous_dof_ids(), libMesh::MeshTools::libmesh_assert_parallel_consistent_new_node_procids(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Elem >(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_topology_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_valid_boundary_ids(), libMesh::MeshTools::libmesh_assert_valid_dof_ids(), libMesh::MeshTools::libmesh_assert_valid_neighbors(), libMesh::MeshTools::libmesh_assert_valid_refinement_flags(), libMesh::DofMap::local_variable_indices(), libMesh::MeshRefinement::make_coarsening_compatible(), libMesh::MeshBase::n_active_elem_on_proc(), libMesh::MeshBase::n_elem_on_proc(), libMesh::MeshBase::n_nodes_on_proc(), libMesh::MeshBase::partition(), libMesh::PetscLinearSolver< T >::PetscLinearSolver(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::NameBasedIO::read(), libMesh::Nemesis_IO::read(), libMesh::CheckpointIO::read(), libMesh::CheckpointIO::read_connectivity(), libMesh::XdrIO::read_header(), libMesh::CheckpointIO::read_nodes(), libMesh::System::read_parallel_data(), libMesh::System::read_SCALAR_dofs(), libMesh::System::read_serialized_blocked_dof_objects(), libMesh::System::read_serialized_vector(), libMesh::DistributedMesh::renumber_dof_objects(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::PetscDMWrapper::set_point_range_in_section(), libMesh::MeshRefinement::uniformly_coarsen(), libMesh::DistributedMesh::update_parallel_id_counts(), libMesh::GMVIO::write_binary(), libMesh::GMVIO::write_discontinuous_gmv(), libMesh::System::write_parallel_data(), libMesh::System::write_SCALAR_dofs(), libMesh::XdrIO::write_serialized_bcs_helper(), libMesh::System::write_serialized_blocked_dof_objects(), libMesh::XdrIO::write_serialized_connectivity(), libMesh::XdrIO::write_serialized_nodes(), and libMesh::XdrIO::write_serialized_nodesets().

  { return cast_int<processor_id_type>(_communicator.size()); }

pc()

template<typename T >

PC libMesh::PetscPreconditioner< T >::pc ( )

inline

Returns

The PETSc PC object. Can be useful for implementing more advanced algorithms.

Definition at line 87 of file petsc_preconditioner.h.

References libMesh::PetscPreconditioner< T >::_pc.

{ return _pc; }

print_info()

void libMesh::ReferenceCounter::print_info ( std::ostream &  out = libMesh::out )

staticinherited

Prints the reference information, by default to libMesh::out.

Definition at line 87 of file reference_counter.C.

References libMesh::ReferenceCounter::_enable_print_counter, and libMesh::ReferenceCounter::get_info().

{
  if (_enable_print_counter)
    out_stream << ReferenceCounter::get_info();
}

processor_id()

processor_id_type libMesh::ParallelObject::processor_id ( ) const

inlineinherited

Returns

The rank of this processor in the group.

Definition at line 101 of file parallel_object.h.

References libMesh::ParallelObject::_communicator, and libMesh::Parallel::Communicator::rank().

Referenced by libMesh::BoundaryInfo::_find_id_maps(), libMesh::EquationSystems::_read_impl(), libMesh::PetscDMWrapper::add_dofs_to_section(), libMesh::DistributedMesh::add_elem(), libMesh::BoundaryInfo::add_elements(), libMesh::DofMap::add_neighbors_to_send_list(), libMesh::DistributedMesh::add_node(), libMesh::UnstructuredMesh::all_second_order(), libMesh::MeshTools::Modification::all_tri(), libMesh::FEMSystem::assembly(), libMesh::EquationSystems::build_discontinuous_solution_vector(), libMesh::Nemesis_IO_Helper::build_element_and_node_maps(), libMesh::InfElemBuilder::build_inf_elem(), libMesh::BoundaryInfo::build_node_list_from_side_list(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::DistributedMesh::clear(), libMesh::ExodusII_IO_Helper::close(), libMesh::Nemesis_IO_Helper::compute_border_node_ids(), libMesh::Nemesis_IO_Helper::compute_communication_map_parameters(), libMesh::Nemesis_IO_Helper::compute_internal_and_border_elems_and_internal_nodes(), libMesh::Nemesis_IO_Helper::compute_node_communication_maps(), libMesh::Nemesis_IO_Helper::compute_num_global_elem_blocks(), libMesh::Nemesis_IO_Helper::compute_num_global_nodesets(), libMesh::Nemesis_IO_Helper::compute_num_global_sidesets(), libMesh::Nemesis_IO_Helper::construct_nemesis_filename(), libMesh::MeshTools::correct_node_proc_ids(), libMesh::ExodusII_IO_Helper::create(), libMesh::DistributedMesh::delete_elem(), libMesh::DistributedMesh::delete_node(), libMesh::MeshCommunication::delete_remote_elements(), libMesh::DofMap::distribute_dofs(), libMesh::DofMap::distribute_local_dofs_node_major(), libMesh::DofMap::distribute_local_dofs_var_major(), libMesh::DistributedMesh::DistributedMesh(), libMesh::DofMap::end_dof(), libMesh::DofMap::end_old_dof(), libMesh::EnsightIO::EnsightIO(), libMesh::MeshFunction::find_element(), libMesh::MeshFunction::find_elements(), libMesh::UnstructuredMesh::find_neighbors(), libMesh::DofMap::first_dof(), libMesh::DofMap::first_old_dof(), libMesh::Nemesis_IO_Helper::get_cmap_params(), libMesh::Nemesis_IO_Helper::get_eb_info_global(), libMesh::Nemesis_IO_Helper::get_elem_cmap(), libMesh::Nemesis_IO_Helper::get_elem_map(), libMesh::MeshBase::get_info(), libMesh::DofMap::get_info(), libMesh::Nemesis_IO_Helper::get_init_global(), libMesh::Nemesis_IO_Helper::get_init_info(), libMesh::Nemesis_IO_Helper::get_loadbal_param(), libMesh::Nemesis_IO_Helper::get_node_cmap(), libMesh::Nemesis_IO_Helper::get_node_map(), libMesh::Nemesis_IO_Helper::get_ns_param_global(), libMesh::Nemesis_IO_Helper::get_ss_param_global(), libMesh::SparsityPattern::Build::handle_vi_vj(), libMesh::SystemSubsetBySubdomain::init(), libMesh::ExodusII_IO_Helper::initialize(), libMesh::ExodusII_IO_Helper::initialize_element_variables(), libMesh::ExodusII_IO_Helper::initialize_global_variables(), libMesh::ExodusII_IO_Helper::initialize_nodal_variables(), libMesh::DistributedMesh::insert_elem(), libMesh::DofMap::is_evaluable(), libMesh::SparsityPattern::Build::join(), libMesh::DofMap::last_dof(), libMesh::MeshTools::libmesh_assert_consistent_distributed(), libMesh::MeshTools::libmesh_assert_consistent_distributed_nodes(), libMesh::MeshTools::libmesh_assert_contiguous_dof_ids(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Elem >(), libMesh::MeshTools::libmesh_assert_valid_neighbors(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_object_ids(), libMesh::DofMap::local_variable_indices(), libMesh::MeshRefinement::make_coarsening_compatible(), libMesh::MeshBase::n_active_local_elem(), libMesh::BoundaryInfo::n_boundary_conds(), libMesh::BoundaryInfo::n_edge_conds(), libMesh::DofMap::n_local_dofs(), libMesh::System::n_local_dofs(), libMesh::MeshBase::n_local_elem(), libMesh::MeshBase::n_local_nodes(), libMesh::BoundaryInfo::n_nodeset_conds(), libMesh::BoundaryInfo::n_shellface_conds(), libMesh::SparsityPattern::Build::operator()(), libMesh::DistributedMesh::own_node(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::Nemesis_IO_Helper::put_cmap_params(), libMesh::Nemesis_IO_Helper::put_elem_cmap(), libMesh::Nemesis_IO_Helper::put_elem_map(), libMesh::Nemesis_IO_Helper::put_loadbal_param(), libMesh::Nemesis_IO_Helper::put_node_cmap(), libMesh::Nemesis_IO_Helper::put_node_map(), libMesh::NameBasedIO::read(), libMesh::Nemesis_IO::read(), libMesh::XdrIO::read(), libMesh::CheckpointIO::read(), libMesh::ExodusII_IO_Helper::read_elem_num_map(), libMesh::ExodusII_IO_Helper::read_global_values(), libMesh::CheckpointIO::read_header(), libMesh::XdrIO::read_header(), libMesh::System::read_header(), libMesh::System::read_legacy_data(), libMesh::ExodusII_IO_Helper::read_node_num_map(), libMesh::System::read_parallel_data(), libMesh::System::read_SCALAR_dofs(), libMesh::XdrIO::read_serialized_bc_names(), libMesh::XdrIO::read_serialized_bcs_helper(), libMesh::System::read_serialized_blocked_dof_objects(), libMesh::XdrIO::read_serialized_connectivity(), libMesh::System::read_serialized_data(), libMesh::XdrIO::read_serialized_nodes(), libMesh::XdrIO::read_serialized_nodesets(), libMesh::XdrIO::read_serialized_subdomain_names(), libMesh::System::read_serialized_vector(), libMesh::System::read_serialized_vectors(), libMesh::DistributedMesh::renumber_dof_objects(), libMesh::CheckpointIO::select_split_config(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::PetscDMWrapper::set_point_range_in_section(), libMesh::LaplaceMeshSmoother::smooth(), libMesh::MeshTools::total_weight(), libMesh::MeshRefinement::uniformly_coarsen(), libMesh::Parallel::Packing< T >::unpack(), libMesh::DistributedMesh::update_parallel_id_counts(), libMesh::NameBasedIO::write(), libMesh::XdrIO::write(), libMesh::CheckpointIO::write(), libMesh::EquationSystems::write(), libMesh::GMVIO::write_discontinuous_gmv(), libMesh::ExodusII_IO::write_element_data(), libMesh::ExodusII_IO_Helper::write_element_values(), libMesh::ExodusII_IO_Helper::write_elements(), libMesh::ExodusII_IO::write_global_data(), libMesh::ExodusII_IO_Helper::write_global_values(), libMesh::System::write_header(), libMesh::ExodusII_IO::write_information_records(), libMesh::ExodusII_IO_Helper::write_information_records(), libMesh::ExodusII_IO_Helper::write_nodal_coordinates(), libMesh::UCDIO::write_nodal_data(), libMesh::ExodusII_IO::write_nodal_data(), libMesh::ExodusII_IO::write_nodal_data_discontinuous(), libMesh::ExodusII_IO_Helper::write_nodal_values(), libMesh::Nemesis_IO_Helper::write_nodesets(), libMesh::ExodusII_IO_Helper::write_nodesets(), libMesh::System::write_parallel_data(), libMesh::System::write_SCALAR_dofs(), libMesh::XdrIO::write_serialized_bc_names(), libMesh::XdrIO::write_serialized_bcs_helper(), libMesh::System::write_serialized_blocked_dof_objects(), libMesh::XdrIO::write_serialized_connectivity(), libMesh::System::write_serialized_data(), libMesh::XdrIO::write_serialized_nodes(), libMesh::XdrIO::write_serialized_nodesets(), libMesh::XdrIO::write_serialized_subdomain_names(), libMesh::System::write_serialized_vector(), libMesh::System::write_serialized_vectors(), libMesh::Nemesis_IO_Helper::write_sidesets(), libMesh::ExodusII_IO_Helper::write_sidesets(), libMesh::ExodusII_IO::write_timestep(), libMesh::ExodusII_IO_Helper::write_timestep(), and libMesh::ExodusII_IO::write_timestep_discontinuous().

  { return cast_int<processor_id_type>(_communicator.rank()); }

set_matrix()

template<typename T >

void libMesh::Preconditioner< T >::set_matrix ( SparseMatrix< Number > &  mat )

inherited

Sets the matrix to be preconditioned.

Definition at line 181 of file preconditioner.h.

{
  //If the matrix is changing then we (probably) need to reinitialize.
  _is_initialized = false;
  _matrix = &mat;
}

set_petsc_preconditioner_type()

template<typename T >

void libMesh::PetscPreconditioner< T >::set_petsc_preconditioner_type ( const PreconditionerType &  preconditioner_type, PC &  pc  )

static

Tells PETSc to use the user-specified preconditioner.

Definition at line 115 of file petsc_preconditioner.C.

References libMesh::AMG_PRECOND, libMesh::ASM_PRECOND, libMesh::BLOCK_JACOBI_PRECOND, libMesh::CHOLESKY_PRECOND, libMesh::EISENSTAT_PRECOND, libMesh::err, libMesh::ICC_PRECOND, libMesh::IDENTITY_PRECOND, ierr, libMesh::ILU_PRECOND, libMesh::JACOBI_PRECOND, libMesh::LU_PRECOND, libMesh::SHELL_PRECOND, libMesh::SOR_PRECOND, and libMesh::USER_PRECOND.

Referenced by libMesh::PetscLinearSolver< T >::init().

{
  int ierr = 0;

  // get the communicator from the PETSc object
  Parallel::communicator comm;
  PetscObjectGetComm((PetscObject)pc, & comm);
  Parallel::Communicator communicator(comm);

  switch (preconditioner_type)
    {
    case IDENTITY_PRECOND:
      ierr = PCSetType (pc, const_cast<KSPType>(PCNONE));
      CHKERRABORT(comm,ierr);
      break;

    case CHOLESKY_PRECOND:
      ierr = PCSetType (pc, const_cast<KSPType>(PCCHOLESKY));
      CHKERRABORT(comm,ierr);
      break;

    case ICC_PRECOND:
      ierr = PCSetType (pc, const_cast<KSPType>(PCICC));
      CHKERRABORT(comm,ierr);
      break;

    case ILU_PRECOND:
      {
        // In serial, just set the ILU preconditioner type
        if (communicator.size())
          {
            ierr = PCSetType (pc, const_cast<KSPType>(PCILU));
            CHKERRABORT(comm,ierr);
          }
        else
          {
            // But PETSc has no truly parallel ILU, instead you have to set
            // an actual parallel preconditioner (e.g. block Jacobi) and then
            // assign ILU sub-preconditioners.
            ierr = PCSetType (pc, const_cast<KSPType>(PCBJACOBI));
            CHKERRABORT(comm,ierr);

            // Set ILU as the sub preconditioner type
            set_petsc_subpreconditioner_type(PCILU, pc);
          }
        break;
      }

    case LU_PRECOND:
      {
        // In serial, just set the LU preconditioner type
        if (communicator.size())
          {
            ierr = PCSetType (pc, const_cast<KSPType>(PCLU));
            CHKERRABORT(comm,ierr);
          }
        else
          {
            // But PETSc has no truly parallel LU, instead you have to set
            // an actual parallel preconditioner (e.g. block Jacobi) and then
            // assign LU sub-preconditioners.
            ierr = PCSetType (pc, const_cast<KSPType>(PCBJACOBI));
            CHKERRABORT(comm,ierr);

            // Set ILU as the sub preconditioner type
            set_petsc_subpreconditioner_type(PCLU, pc);
          }
        break;
      }

    case ASM_PRECOND:
      {
        // In parallel, I think ASM uses ILU by default as the sub-preconditioner...
        // I tried setting a different sub-preconditioner here, but apparently the matrix
        // is not in the correct state (at this point) to call PCSetUp().
        ierr = PCSetType (pc, const_cast<KSPType>(PCASM));
        CHKERRABORT(comm,ierr);
        break;
      }

    case JACOBI_PRECOND:
      ierr = PCSetType (pc, const_cast<KSPType>(PCJACOBI));
      CHKERRABORT(comm,ierr);
      break;

    case BLOCK_JACOBI_PRECOND:
      ierr = PCSetType (pc, const_cast<KSPType>(PCBJACOBI));
      CHKERRABORT(comm,ierr);
      break;

    case SOR_PRECOND:
      ierr = PCSetType (pc, const_cast<KSPType>(PCSOR));
      CHKERRABORT(comm,ierr);
      break;

    case EISENSTAT_PRECOND:
      ierr = PCSetType (pc, const_cast<KSPType>(PCEISENSTAT));
      CHKERRABORT(comm,ierr);
      break;

    case AMG_PRECOND:
      ierr = PCSetType (pc, const_cast<KSPType>(PCHYPRE));
      CHKERRABORT(comm,ierr);
      break;

    case USER_PRECOND:
      ierr = PCSetType (pc, const_cast<KSPType>(PCMAT));
      CHKERRABORT(comm,ierr);
      break;

    case SHELL_PRECOND:
      ierr = PCSetType (pc, const_cast<KSPType>(PCSHELL));
      CHKERRABORT(comm,ierr);
      break;

    default:
      libMesh::err << "ERROR:  Unsupported PETSC Preconditioner: "
                   << preconditioner_type       << std::endl
                   << "Continuing with PETSC defaults" << std::endl;
    }

  // Set additional options if we are doing AMG and
  // HYPRE is available
#ifdef LIBMESH_HAVE_PETSC_HYPRE
  if (preconditioner_type == AMG_PRECOND)
    {
      ierr = PCHYPRESetType(pc, "boomeramg");
      CHKERRABORT(comm,ierr);
    }
#endif

  // Let the commandline override stuff
  ierr = PCSetFromOptions(pc);
  CHKERRABORT(comm,ierr);
}

set_petsc_subpreconditioner_type() [1/2]

template<typename T >

static void libMesh::PetscPreconditioner< T >::set_petsc_subpreconditioner_type ( PCType  type, PC &  pc  )

staticprivate

Some PETSc preconditioners (ILU, LU) don't work in parallel. This function is called from set_petsc_preconditioner_type() to set additional options for those so-called sub-preconditioners. This method ends up being static so that it can be called from set_petsc_preconditioner_type(). Not sure why set_petsc_preconditioner_type() needs to be static though...

set_petsc_subpreconditioner_type() [2/2]

template<typename T >

static void libMesh::PetscPreconditioner< T >::set_petsc_subpreconditioner_type ( const PCType  type, PC &  pc  )

staticprivate

set_type()

template<typename T >

void libMesh::Preconditioner< T >::set_type ( const PreconditionerType  pct )

inherited

Sets the type of preconditioner to use.

Definition at line 190 of file preconditioner.h.

{
  //If the preconditioner type changes we (probably) need to reinitialize.
  _is_initialized = false;
  _preconditioner_type = pct;
}

setup()

template<typename T>

virtual void libMesh::Preconditioner< T >::setup ( )

inlinevirtualinherited

This is called every time the "operator might have changed".

This is where you need to fill in your preconditioning matrix.

Definition at line 132 of file preconditioner.h.

{}

type()

template<typename T>

PreconditionerType libMesh::Preconditioner< T >::type ( ) const

inlineinherited

Returns

The type of preconditioner to use.

Definition at line 142 of file preconditioner.h.

{ return _preconditioner_type; }

Member Data Documentation

_communicator

const Parallel::Communicator& libMesh::ParallelObject::_communicator

protectedinherited

Definition at line 107 of file parallel_object.h.

Referenced by libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::ParallelObject::comm(), libMesh::ParallelObject::n_processors(), libMesh::ParallelObject::operator=(), and libMesh::ParallelObject::processor_id().

_counts

ReferenceCounter::Counts libMesh::ReferenceCounter::_counts

staticprotectedinherited

Actually holds the data.

Definition at line 122 of file reference_counter.h.

Referenced by libMesh::ReferenceCounter::get_info(), libMesh::ReferenceCounter::increment_constructor_count(), and libMesh::ReferenceCounter::increment_destructor_count().

_enable_print_counter

bool libMesh::ReferenceCounter::_enable_print_counter = true

staticprotectedinherited

Flag to control whether reference count information is printed when print_info is called.

Definition at line 141 of file reference_counter.h.

Referenced by libMesh::ReferenceCounter::disable_print_counter_info(), libMesh::ReferenceCounter::enable_print_counter_info(), and libMesh::ReferenceCounter::print_info().

_is_initialized

template<typename T>

bool libMesh::Preconditioner< T >::_is_initialized

protectedinherited

Flag indicating if the data structures have been initialized.

Definition at line 165 of file preconditioner.h.

Referenced by libMesh::Preconditioner< Number >::initialized().

_mat

template<typename T >

Mat libMesh::PetscPreconditioner< T >::_mat

protected

PETSc Mat pulled out of the _matrix object during init().

Definition at line 104 of file petsc_preconditioner.h.

_matrix

template<typename T>

SparseMatrix<T>* libMesh::Preconditioner< T >::_matrix

protectedinherited

The matrix P... ie the matrix to be preconditioned. This is often the actual system matrix of a linear system.

Definition at line 155 of file preconditioner.h.

_mutex

Threads::spin_mutex libMesh::ReferenceCounter::_mutex

staticprotectedinherited

Mutual exclusion object to enable thread-safe reference counting.

Definition at line 135 of file reference_counter.h.

_n_objects

Threads::atomic< unsigned int > libMesh::ReferenceCounter::_n_objects

staticprotectedinherited

The number of objects. Print the reference count information when the number returns to 0.

Definition at line 130 of file reference_counter.h.

Referenced by libMesh::ReferenceCounter::n_objects(), libMesh::ReferenceCounter::ReferenceCounter(), and libMesh::ReferenceCounter::~ReferenceCounter().

_pc

template<typename T >

PC libMesh::PetscPreconditioner< T >::_pc

protected

Preconditioner context

Definition at line 99 of file petsc_preconditioner.h.

Referenced by libMesh::PetscPreconditioner< T >::pc().

_preconditioner_type

template<typename T>

PreconditionerType libMesh::Preconditioner< T >::_preconditioner_type

protectedinherited

Enum stating with type of preconditioner to use.

Definition at line 160 of file preconditioner.h.

Referenced by libMesh::Preconditioner< Number >::type().

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The documentation for this class was generated from the following files:

• petsc_preconditioner.h
• petsc_preconditioner.C