Allow DoFRenumbering::Cuthill_McKee to run with distributed triangulations. Of course...

git-svn-id: https://svn.dealii.org/trunk@32520 0785d39b-7218-0410-832d-ea1e28bc413d

diff --git a/deal.II/doc/news/changes.h b/deal.II/doc/news/changes.h
index dcdfd4082aef8b5dc62b25453bb9d55c47ba4dc0..986abc2d376b209d88487d364f20583174f5d6fa 100644 (file)
--- a/deal.II/doc/news/changes.h
+++ b/deal.II/doc/news/changes.h
@@ -135,6 +135,12 @@ inconvenience this causes.
 <h3>Specific improvements</h3>
 
 <ol>
+  <li>Improved: DoFRenumbering::Cuthill_McKee can now run with distributed
+  triangulations with the renumbering only done within each processor's
+  subdomain.
+  <br>
+  (Martin Kronbichler, 2014/02/20)
+
   <li>Fixed: There was an indexing error in GridIn::read_vtk() that triggered
   for some input files. This is now fixed.
   <br>

diff --git a/deal.II/include/deal.II/dofs/dof_renumbering.h b/deal.II/include/deal.II/dofs/dof_renumbering.h
index 063ed91f78ee099ee5cdc4cc1be04a94f8831e19..5e2e9a27030bb26d69fed5c136550c79de94f194 100644 (file)
--- a/deal.II/include/deal.II/dofs/dof_renumbering.h
+++ b/deal.II/include/deal.II/dofs/dof_renumbering.h
@@ -565,7 +565,7 @@ namespace DoFRenumbering
 
   /**
    * Renumber the degrees of freedom according to the Cuthill-McKee method,
-   * eventually using the reverse numbering scheme.
+   * possibly using the reverse numbering scheme.
    *
    * See the general documentation of this class for details on the different
    * methods.
@@ -573,6 +573,11 @@ namespace DoFRenumbering
    * As an example of the results of this algorithm, take a look at the
    * comparison of various algorithms in the documentation of the
    * DoFRenumbering namespace.
+   *
+   * If the given DoFHandler uses a distributed triangulation (i.e., if
+   * dof_handler.locally_owned() is not the complete index set), the
+   * renumbering is performed on each processor's degrees of freedom
+   * individually.
    */
   template <class DH>
   void

diff --git a/deal.II/source/dofs/dof_renumbering.cc b/deal.II/source/dofs/dof_renumbering.cc
index 60d0453536c80d18afebe979336f15ea8e388988..3714e05e9513cf670ded008a2ea7b8f171bad893 100644 (file)
--- a/deal.II/source/dofs/dof_renumbering.cc
+++ b/deal.II/source/dofs/dof_renumbering.cc
@@ -358,7 +358,7 @@ namespace DoFRenumbering
                  const bool       use_constraints,
                  const std::vector<types::global_dof_index> &starting_indices)
   {
-    std::vector<types::global_dof_index> renumbering(dof_handler.n_dofs(),
+    std::vector<types::global_dof_index> renumbering(dof_handler.locally_owned_dofs().n_elements(),
                                                      DH::invalid_dof_index);
     compute_Cuthill_McKee(renumbering, dof_handler, reversed_numbering,
                           use_constraints, starting_indices);
@@ -379,25 +379,19 @@ namespace DoFRenumbering
                          const bool                 use_constraints,
                          const std::vector<types::global_dof_index> &starting_indices)
   {
-    // make the connection graph. in
-    // more than 2d use an intermediate
-    // compressed sparsity pattern
-    // since the we don't have very
-    // good estimates for
-    // max_couplings_between_dofs() in
-    // 3d and this then leads to
-    // excessive memory consumption
+    // make the connection graph. in 2d/3d use an intermediate compressed
+    // sparsity pattern since the we don't have very good estimates for
+    // max_couplings_between_dofs() in 3d and this then leads to excessive
+    // memory consumption
     //
-    // note that if constraints are not
-    // requested, then the
-    // 'constraints' object will be
-    // empty, and calling condense with
-    // it is a no-op
+    // note that if constraints are not requested, then the 'constraints'
+    // object will be empty and nothing happens
     ConstraintMatrix constraints;
     if (use_constraints)
       DoFTools::make_hanging_node_constraints (dof_handler, constraints);
     constraints.close ();
 
+    IndexSet locally_owned = dof_handler.locally_owned_dofs();
     SparsityPattern sparsity;
     if (DH::dimension < 2)
       {
@@ -410,9 +404,26 @@ namespace DoFRenumbering
     else
       {
         CompressedSimpleSparsityPattern csp (dof_handler.n_dofs(),
-                                             dof_handler.n_dofs());
+                                             dof_handler.n_dofs(),
+                                             dof_handler.locally_owned_dofs());
         DoFTools::make_sparsity_pattern (dof_handler, csp, constraints);
-        sparsity.copy_from (csp);
+
+        // Create sparsity pattern from csp by transferring its indices to
+        // processor-local index space and doing Cuthill-McKee there
+        std::vector<unsigned int> row_lengths(locally_owned.n_elements());
+        for (unsigned int i=0; i<locally_owned.n_elements(); ++i)
+          row_lengths[i] = csp.row_length(locally_owned.nth_index_in_set(i));
+        sparsity.reinit(locally_owned.n_elements(), locally_owned.n_elements(),
+                        row_lengths);
+        for (unsigned int i=0; i<locally_owned.n_elements(); ++i)
+          {
+            const types::global_dof_index row = locally_owned.nth_index_in_set(i);
+            for (CompressedSimpleSparsityPattern::row_iterator it =
+                   csp.row_begin(row); it != csp.row_end(row); ++it)
+              if (*it != row && locally_owned.is_element(*it))
+                sparsity.add(i, locally_owned.index_within_set(*it));
+          }
+        sparsity.compress();
       }
 
     // constraints are not needed anymore
@@ -427,6 +438,10 @@ namespace DoFRenumbering
 
     if (reversed_numbering)
       new_indices = Utilities::reverse_permutation (new_indices);
+
+    // convert indices back to global index space
+    for (std::size_t i=0; i<new_indices.size(); ++i)
+      new_indices[i] = locally_owned.nth_index_in_set(new_indices[i]);
   }
 
 

diff --git a/tests/mpi/renumber_cuthill_mckee.cc b/tests/mpi/renumber_cuthill_mckee.cc
new file mode 100644 (file)
index 0000000..4377845
--- /dev/null
+++ b/tests/mpi/renumber_cuthill_mckee.cc
@@ -0,0 +1,121 @@
+// ---------------------------------------------------------------------
+// $Id$
+//
+// Copyright (C) 2009 - 2013 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.
+//
+// ---------------------------------------------------------------------
+
+
+
+// Test that DofRenumbering::Cuthill_McKee works in parallel (by applying
+// Cuthill-McKee individually on each processor's subdomain).
+
+
+#include "../tests.h"
+#include <deal.II/base/logstream.h>
+#include <deal.II/base/mpi.h>
+#include <deal.II/distributed/tria.h>
+#include <deal.II/grid/grid_generator.h>
+#include <deal.II/dofs/dof_handler.h>
+#include <deal.II/grid/tria_iterator.h>
+#include <deal.II/dofs/dof_accessor.h>
+#include <deal.II/dofs/dof_renumbering.h>
+#include <deal.II/fe/fe_q.h>
+
+#include <fstream>
+
+
+template<int dim>
+void test()
+{
+  unsigned int myid = Utilities::MPI::this_mpi_process (MPI_COMM_WORLD);
+  unsigned int nprocs = Utilities::MPI::n_mpi_processes (MPI_COMM_WORLD);
+
+  parallel::distributed::Triangulation<dim> tr (MPI_COMM_WORLD);
+
+  GridGenerator::hyper_cube (tr, -1.0, 1.0);
+  tr.refine_global (8-2*dim);
+
+  for (typename Triangulation<dim>::active_cell_iterator
+       cell = tr.begin_active();
+       cell != tr.end(); ++cell)
+    if (!cell->is_ghost() && !cell->is_artificial())
+      if (cell->center().norm() < 0.3)
+        {
+          cell->set_refine_flag();
+        }
+
+  tr.execute_coarsening_and_refinement ();
+
+  DoFHandler<dim> dofh (tr);
+
+  static const FE_Q<dim> fe (1);
+  dofh.distribute_dofs (fe);
+  std::vector<types::global_dof_index> renumbering(dofh.locally_owned_dofs().n_elements());
+  DoFRenumbering::compute_Cuthill_McKee (renumbering, dofh);
+
+  // send everything to processor 0 for output
+  std::vector<types::global_dof_index> complete_renumbering(dofh.n_dofs());
+  std::copy(renumbering.begin(), renumbering.end(), complete_renumbering.begin());
+  unsigned int offset = renumbering.size();
+  for (unsigned int i=1; i<nprocs; ++i)
+    {
+      if (myid == i)
+        MPI_Send (&renumbering[0], renumbering.size(),
+                  Utilities::MPI::internal::mpi_type_id(&complete_renumbering[0]), 0, i,
+                  MPI_COMM_WORLD);
+      else if (myid == 0)
+        MPI_Recv (&complete_renumbering[offset],
+                  dofh.locally_owned_dofs_per_processor()[i].n_elements(),
+                  Utilities::MPI::internal::mpi_type_id(&complete_renumbering[0]), i, i,
+                  MPI_COMM_WORLD, MPI_STATUSES_IGNORE);
+      offset += dofh.locally_owned_dofs_per_processor()[i].n_elements();
+    }
+
+  if (myid == 0)
+    {
+      AssertDimension(offset, complete_renumbering.size());
+      for (unsigned int i=0; i<complete_renumbering.size(); ++i)
+        deallog << complete_renumbering[i] << std::endl;
+    }
+}
+
+
+int main (int argc, char *argv[])
+{
+  Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv, 1);
+
+  unsigned int myid = Utilities::MPI::this_mpi_process (MPI_COMM_WORLD);
+
+
+  deallog.push (Utilities::int_to_string (myid));
+
+  if (myid == 0)
+    {
+      std::ofstream logfile ("output");
+      deallog.attach (logfile);
+      deallog.depth_console (0);
+      deallog.threshold_double (1.e-10);
+
+      deallog.push ("2d");
+      test<2>();
+      deallog.pop();
+      deallog.push ("3d");
+      test<3>();
+      deallog.pop();
+    }
+  else
+    {
+      test<2>();
+      test<3>();
+    }
+}

diff --git a/tests/mpi/renumber_cuthill_mckee.mpirun=1.output b/tests/mpi/renumber_cuthill_mckee.mpirun=1.output
new file mode 100644 (file)
index 0000000..e571ed9
--- /dev/null
+++ b/tests/mpi/renumber_cuthill_mckee.mpirun=1.output
@@ -0,0 +1,471 @@
+
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diff --git a/tests/mpi/renumber_cuthill_mckee.mpirun=4.output b/tests/mpi/renumber_cuthill_mckee.mpirun=4.output
new file mode 100644 (file)
index 0000000..77331db
--- /dev/null
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