--- /dev/null
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2009 - 2016 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, 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 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE at
+// the top level of the deal.II distribution.
+//
+// ---------------------------------------------------------------------
+
+
+// A lightly adapted version of the step-40 tutorial program
+//
+// like the step-40 test, but using a Cuthill-McKee renumbering
+// algorithm for DoFs that includes starting indices that are not
+// locally owned but only locally active
+
+#include "../tests.h"
+#include <deal.II/base/quadrature_lib.h>
+#include <deal.II/base/function.h>
+#include <deal.II/base/mpi.h>
+#include <deal.II/lac/vector.h>
+#include <deal.II/lac/full_matrix.h>
+#include <deal.II/lac/solver_cg.h>
+#include <deal.II/lac/constraint_matrix.h>
+#include <deal.II/lac/dynamic_sparsity_pattern.h>
+
+#include <deal.II/lac/petsc_parallel_sparse_matrix.h>
+#include <deal.II/lac/petsc_parallel_vector.h>
+#include <deal.II/lac/petsc_solver.h>
+#include <deal.II/lac/petsc_precondition.h>
+
+#include <deal.II/grid/grid_generator.h>
+#include <deal.II/grid/tria_accessor.h>
+#include <deal.II/grid/tria_iterator.h>
+#include <deal.II/dofs/dof_handler.h>
+#include <deal.II/dofs/dof_accessor.h>
+#include <deal.II/dofs/dof_tools.h>
+#include <deal.II/dofs/dof_renumbering.h>
+#include <deal.II/fe/fe_values.h>
+#include <deal.II/fe/fe_q.h>
+#include <deal.II/numerics/vector_tools.h>
+#include <deal.II/numerics/data_out.h>
+#include <deal.II/numerics/error_estimator.h>
+
+#include <deal.II/base/utilities.h>
+#include <deal.II/base/conditional_ostream.h>
+#include <deal.II/base/index_set.h>
+#include <deal.II/lac/sparsity_tools.h>
+#include <deal.II/distributed/tria.h>
+#include <deal.II/distributed/grid_refinement.h>
+
+#include <iostream>
+
+namespace Step40
+{
+ using namespace dealii;
+
+
+ template <int dim>
+ class LaplaceProblem
+ {
+ public:
+ LaplaceProblem ();
+ ~LaplaceProblem ();
+
+ void run ();
+
+ private:
+ void setup_system ();
+ void assemble_system ();
+ void solve ();
+ void refine_grid ();
+
+ MPI_Comm mpi_communicator;
+
+ parallel::distributed::Triangulation<dim> triangulation;
+
+ DoFHandler<dim> dof_handler;
+ FE_Q<dim> fe;
+
+ IndexSet locally_owned_dofs;
+ IndexSet locally_relevant_dofs;
+
+ ConstraintMatrix constraints;
+
+ PETScWrappers::MPI::SparseMatrix system_matrix;
+ PETScWrappers::MPI::Vector locally_relevant_solution;
+ PETScWrappers::MPI::Vector system_rhs;
+
+ ConditionalOStream pcout;
+ };
+
+
+
+
+ template <int dim>
+ LaplaceProblem<dim>::LaplaceProblem ()
+ :
+ mpi_communicator (MPI_COMM_WORLD),
+ triangulation (mpi_communicator,
+ typename Triangulation<dim>::MeshSmoothing
+ (Triangulation<dim>::smoothing_on_refinement |
+ Triangulation<dim>::smoothing_on_coarsening)),
+ dof_handler (triangulation),
+ fe (2),
+ pcout (Utilities::MPI::this_mpi_process(mpi_communicator)
+ == 0
+ ?
+ deallog.get_file_stream()
+ :
+ std::cout,
+ (Utilities::MPI::this_mpi_process(mpi_communicator)
+ == 0))
+ {}
+
+
+
+ template <int dim>
+ LaplaceProblem<dim>::~LaplaceProblem ()
+ {
+ dof_handler.clear ();
+ }
+
+
+
+ template <int dim>
+ void LaplaceProblem<dim>::setup_system ()
+ {
+ dof_handler.distribute_dofs (fe);
+ locally_owned_dofs = dof_handler.locally_owned_dofs();
+ DoFTools::extract_locally_relevant_dofs(dof_handler, locally_relevant_dofs);
+
+ {
+ std::vector<types::global_dof_index> starting_indices;
+
+
+ const QGauss<dim - 1> face_quadrature_formula(fe.degree + 1);
+ FEFaceValues<dim> fe_face_values(fe, face_quadrature_formula,
+ update_values | update_quadrature_points | update_normal_vectors |
+ update_JxW_values);
+
+ Tensor<1, dim> u;
+ Point<dim> down {0,-1};
+ std::vector< types::global_dof_index >dof_indices (fe.n_dofs_per_face(), 0);
+
+
+ for (const auto &cell: dof_handler.active_cell_iterators())
+ {
+ if (cell->is_locally_owned())
+ {
+
+ for (unsigned int face = 0; face < GeometryInfo<dim>::faces_per_cell; ++face)
+ {
+ if ((cell->face(face)->at_boundary())
+ || (cell->neighbor(face)->active() && cell->neighbor(face)->is_ghost()))
+ {
+ fe_face_values.reinit(cell, face);
+ //for Q_2 this is in middle of face, dim=2 or what quadrature point to give?
+ u=fe_face_values.normal_vector(1);
+ if (u*down< 0)
+ {
+ cell->face(face)->get_dof_indices(dof_indices);
+ starting_indices.insert(std::end(starting_indices),
+ std::begin(dof_indices), std::end(dof_indices));
+ }
+ }
+ }
+ }
+ }
+
+ // remove duplicates by creating a set
+ std::set<types::global_dof_index> no_duplicates_please (starting_indices.begin(),
+ starting_indices.end());
+ // back to vector for the DoFRenumbering function
+ starting_indices.clear();
+ starting_indices.assign(no_duplicates_please.begin(), no_duplicates_please.end());
+
+ DoFRenumbering::Cuthill_McKee(dof_handler,false, true, starting_indices);
+
+ locally_owned_dofs = dof_handler.locally_owned_dofs();
+ DoFTools::extract_locally_relevant_dofs(dof_handler, locally_relevant_dofs);
+ }
+
+ locally_relevant_solution.reinit (locally_owned_dofs,
+ locally_relevant_dofs,
+ mpi_communicator);
+ system_rhs.reinit (locally_owned_dofs, mpi_communicator);
+ system_rhs = PetscScalar();
+
+ constraints.clear ();
+ constraints.reinit (locally_relevant_dofs);
+ DoFTools::make_hanging_node_constraints (dof_handler, constraints);
+ VectorTools::interpolate_boundary_values (dof_handler,
+ 0,
+ Functions::ZeroFunction<dim>(),
+ constraints);
+ constraints.close ();
+
+ DynamicSparsityPattern csp (dof_handler.n_dofs(),
+ dof_handler.n_dofs(),
+ locally_relevant_dofs);
+ DoFTools::make_sparsity_pattern (dof_handler,
+ csp,
+ constraints, false);
+ SparsityTools::distribute_sparsity_pattern (csp,
+ dof_handler.n_locally_owned_dofs_per_processor(),
+ mpi_communicator,
+ locally_relevant_dofs);
+ system_matrix.reinit (mpi_communicator,
+ csp,
+ dof_handler.n_locally_owned_dofs_per_processor(),
+ dof_handler.n_locally_owned_dofs_per_processor(),
+ Utilities::MPI::this_mpi_process(mpi_communicator));
+ }
+
+
+
+
+ template <int dim>
+ void LaplaceProblem<dim>::assemble_system ()
+ {
+ const QGauss<dim> quadrature_formula(3);
+
+ FEValues<dim> fe_values (fe, quadrature_formula,
+ update_values | update_gradients |
+ update_quadrature_points |
+ update_JxW_values);
+
+ const unsigned int dofs_per_cell = fe.dofs_per_cell;
+ const unsigned int n_q_points = quadrature_formula.size();
+
+ FullMatrix<PetscScalar> cell_matrix (dofs_per_cell, dofs_per_cell);
+ Vector<PetscScalar> cell_rhs (dofs_per_cell);
+
+ std::vector<types::global_dof_index> local_dof_indices (dofs_per_cell);
+
+ typename DoFHandler<dim>::active_cell_iterator
+ cell = dof_handler.begin_active(),
+ endc = dof_handler.end();
+ for (; cell!=endc; ++cell)
+ if (cell->is_locally_owned())
+ {
+ cell_matrix = PetscScalar();
+ cell_rhs = PetscScalar();
+
+ fe_values.reinit (cell);
+
+ for (unsigned int q_point=0; q_point<n_q_points; ++q_point)
+ {
+ const double
+ rhs_value
+ = (fe_values.quadrature_point(q_point)[1]
+ >
+ 0.5+0.25*std::sin(4.0 * numbers::PI *
+ fe_values.quadrature_point(q_point)[0])
+ ? 1 : -1);
+
+ for (unsigned int i=0; i<dofs_per_cell; ++i)
+ {
+ for (unsigned int j=0; j<dofs_per_cell; ++j)
+ cell_matrix(i,j) += (fe_values.shape_grad(i,q_point) *
+ fe_values.shape_grad(j,q_point) *
+ fe_values.JxW(q_point));
+
+ cell_rhs(i) += (rhs_value *
+ fe_values.shape_value(i,q_point) *
+ fe_values.JxW(q_point));
+ }
+ }
+
+ cell->get_dof_indices (local_dof_indices);
+ constraints.distribute_local_to_global (cell_matrix,
+ cell_rhs,
+ local_dof_indices,
+ system_matrix,
+ system_rhs);
+ }
+
+ system_matrix.compress (VectorOperation::add);
+ system_rhs.compress (VectorOperation::add);
+ }
+
+
+
+
+ template <int dim>
+ void LaplaceProblem<dim>::solve ()
+ {
+ PETScWrappers::MPI::Vector
+ completely_distributed_solution (mpi_communicator,
+ dof_handler.n_dofs(),
+ dof_handler.n_locally_owned_dofs());
+
+ SolverControl solver_control (dof_handler.n_dofs(), 1e-12);
+
+ PETScWrappers::SolverCG solver(solver_control, mpi_communicator);
+
+#ifndef PETSC_USE_COMPLEX
+ PETScWrappers::PreconditionBoomerAMG
+ preconditioner(system_matrix,
+ PETScWrappers::PreconditionBoomerAMG::AdditionalData(true));
+
+ check_solver_within_range(
+ solver.solve (system_matrix, completely_distributed_solution, system_rhs,
+ preconditioner),
+ solver_control.last_step(), 11, 11);
+#else
+ check_solver_within_range(
+ solver.solve (system_matrix, completely_distributed_solution, system_rhs,
+ PETScWrappers::PreconditionJacobi(system_matrix)),
+ solver_control.last_step(), 120, 260);
+#endif
+
+ pcout << " Solved in " << solver_control.last_step()
+ << " iterations." << std::endl;
+
+ constraints.distribute (completely_distributed_solution);
+
+ locally_relevant_solution = completely_distributed_solution;
+ }
+
+
+
+
+ template <int dim>
+ void LaplaceProblem<dim>::refine_grid ()
+ {
+ triangulation.refine_global (1);
+ }
+
+
+
+
+ template <int dim>
+ void LaplaceProblem<dim>::run ()
+ {
+ const unsigned int n_cycles = 2;
+ for (unsigned int cycle=0; cycle<n_cycles; ++cycle)
+ {
+ pcout << "Cycle " << cycle << ':' << std::endl;
+
+ if (cycle == 0)
+ {
+ GridGenerator::hyper_cube (triangulation);
+ triangulation.refine_global (5);
+ }
+ else
+ refine_grid ();
+
+ setup_system ();
+
+ pcout << " Number of active cells: "
+ << triangulation.n_global_active_cells()
+ << std::endl
+ << " ";
+ for (unsigned int i=0; i<Utilities::MPI::n_mpi_processes(mpi_communicator); ++i)
+ pcout << triangulation.n_locally_owned_active_cells_per_processor()[i]
+ << '+';
+ pcout << std::endl;
+
+ pcout << " Number of degrees of freedom: "
+ << dof_handler.n_dofs()
+ << std::endl
+ << " ";
+ for (unsigned int i=0; i<Utilities::MPI::n_mpi_processes(mpi_communicator); ++i)
+ pcout << dof_handler.n_locally_owned_dofs_per_processor()[i]
+ << '+';
+ pcout << std::endl;
+
+ assemble_system ();
+ solve ();
+
+ pcout << std::endl;
+ }
+ }
+}
+
+
+int test_mpi ()
+{
+
+ try
+ {
+ using namespace dealii;
+ using namespace Step40;
+
+
+ {
+ LaplaceProblem<2> laplace_problem_2d;
+ laplace_problem_2d.run ();
+ }
+ }
+ catch (std::exception &exc)
+ {
+ std::cerr << std::endl << std::endl
+ << "----------------------------------------------------"
+ << std::endl;
+ std::cerr << "Exception on processing: " << std::endl
+ << exc.what() << std::endl
+ << "Aborting!" << std::endl
+ << "----------------------------------------------------"
+ << std::endl;
+
+ return 1;
+ }
+ catch (...)
+ {
+ std::cerr << std::endl << std::endl
+ << "----------------------------------------------------"
+ << std::endl;
+ std::cerr << "Unknown exception!" << std::endl
+ << "Aborting!" << std::endl
+ << "----------------------------------------------------"
+ << std::endl;
+ return 1;
+ }
+
+ return 0;
+}
+
+
+
+
+int main(int argc, char *argv[])
+{
+ Utilities::MPI::MPI_InitFinalize mpi_initialization (argc, argv, 1);
+
+ if (Utilities::MPI::this_mpi_process (MPI_COMM_WORLD) == 0)
+ {
+ initlog();
+
+ deallog.push("mpi");
+ test_mpi();
+ deallog.pop();
+ }
+ else
+ test_mpi();
+}
projects / dealii.git / commitdiff