From: nivesh Date: Tue, 5 Dec 2017 18:25:24 +0000 (+0100) Subject: color_sparsity_pattern function added in GraphColoring namespace. Test added for... X-Git-Tag: v9.0.0-rc1~685^2 X-Git-Url: https://gitweb.dealii.org/cgi-bin/gitweb.cgi?a=commitdiff_plain;h=93f48664833097fb458901c830dd4643fbbcff0a;p=dealii.git color_sparsity_pattern function added in GraphColoring namespace. Test added for the same. Added assertion --- diff --git a/include/deal.II/base/graph_coloring.h b/include/deal.II/base/graph_coloring.h index 7513dbc9bb..c8d1f6cdf0 100644 --- a/include/deal.II/base/graph_coloring.h +++ b/include/deal.II/base/graph_coloring.h @@ -22,6 +22,7 @@ #include #include #include +#include #include #include @@ -542,6 +543,15 @@ namespace GraphColoring return internal::gather_colors(partition_coloring); } + /** + * GraphColoring::color_sparsity_pattern, a wrapper function for + * SparsityTools::color_sparsity_pattern, is an alternate method for + * coloring using graph connections represented by SparsityPattern. + * For further details, refer to SparsityTools::color_sparsity_pattern. + */ + unsigned int color_sparsity_pattern (const SparsityPattern &sparsity_pattern, + std::vector &color_indices); + } // End graph_coloring namespace DEAL_II_NAMESPACE_CLOSE diff --git a/include/deal.II/lac/sparsity_tools.h b/include/deal.II/lac/sparsity_tools.h index 0a2ee7cc23..811bd2620c 100644 --- a/include/deal.II/lac/sparsity_tools.h +++ b/include/deal.II/lac/sparsity_tools.h @@ -112,19 +112,22 @@ namespace SparsityTools * an edge between two nodes. The goal is to assign each node a color index * such that no two directly connected nodes have the same color. * The assigned colors are listed in @p color_indices indexed from one and - * the function returns total number of colors used. Note that this function - * requires that SparsityPattern be symmetric (and hence square) i.e an - * undirected graph representation. We do not check for symmetry of the - * sparsity pattern, since this is an expensive operation, but rather leave - * this as the responsibility of caller of this function. + * the function returns total number of colors used. ZOLTAN coloring + * algorithm is run in serial by each processor. Hence all processors have + * coloring information of all the nodes. A wrapper function to this + * function is available in GraphColoring namespace as well. * - * ZOLTAN coloring algorithm is run in serial by each processor. Hence all - * processors have coloring information of all the nodes. + * Note that this function requires that SparsityPattern be symmetric + * (and hence square) i.e an undirected graph representation. We do not + * check for symmetry of the sparsity pattern, since this is an expensive + * operation, but rather leave this as the responsibility of caller of + * this function. * * @image html color_undirected_graph.png - * For example, the above image shows 5 nodes numbered from 0 to 4. - * The connections shown are bidirectional. After coloring, no two connected - * nodes have the same color. + * The usage of the function is illustrated by the image above, showing five + * nodes numbered from 0 to 4. The connections shown are bidirectional. + * After coloring, it is clear that no two directly connected nodes are + * assigned the same color. * * If deal.II was not installed with package ZOLTAN, this function will * generate an error. diff --git a/source/base/CMakeLists.txt b/source/base/CMakeLists.txt index c140d4c722..5361e2a66d 100644 --- a/source/base/CMakeLists.txt +++ b/source/base/CMakeLists.txt @@ -39,6 +39,7 @@ SET(_unity_include_src function_time.cc geometry_info.cc geometric_utilities.cc + graph_coloring.cc index_set.cc job_identifier.cc logstream.cc diff --git a/source/base/graph_coloring.cc b/source/base/graph_coloring.cc new file mode 100644 index 0000000000..41cea44093 --- /dev/null +++ b/source/base/graph_coloring.cc @@ -0,0 +1,30 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 1998 - 2015 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. +// +// --------------------------------------------------------------------- + +#include + + +DEAL_II_NAMESPACE_OPEN + +namespace GraphColoring +{ + unsigned int color_sparsity_pattern (const SparsityPattern &sparsity_pattern, + std::vector &color_indices) + { + return SparsityTools::color_sparsity_pattern (sparsity_pattern, color_indices); + } +} + +DEAL_II_NAMESPACE_CLOSE diff --git a/source/lac/sparsity_tools.cc b/source/lac/sparsity_tools.cc index ea3d33bd0e..5733b4b061 100644 --- a/source/lac/sparsity_tools.cc +++ b/source/lac/sparsity_tools.cc @@ -381,9 +381,14 @@ namespace SparsityTools color_exp.data()); //Check for error code - Assert (rc == ZOLTAN_OK , ExcInternalError()); + Assert (rc == ZOLTAN_OK , + ExcInternalError()); + + //Allocate and assign color indices + color_indices.resize(num_objects); + Assert (color_exp.size() == color_indices.size(), + ExcDimensionMismatch (color_exp.size(),color_indices.size())); - //Allocate and assign color std::copy (color_exp.begin(), color_exp.end(), color_indices.begin()); unsigned int n_colors = *(std::max_element (color_indices.begin(), diff --git a/tests/zoltan/zoltan_02.cc b/tests/zoltan/zoltan_02.cc index 585b5840da..d3630b3ec2 100644 --- a/tests/zoltan/zoltan_02.cc +++ b/tests/zoltan/zoltan_02.cc @@ -18,17 +18,7 @@ #include "../tests.h" -#include -#include -#include -#include -#include #include -#include - -#include -#include - void fill_graph (DynamicSparsityPattern &graph) { diff --git a/tests/zoltan/zoltan_03.cc b/tests/zoltan/zoltan_03.cc new file mode 100644 index 0000000000..fd44a9b082 --- /dev/null +++ b/tests/zoltan/zoltan_03.cc @@ -0,0 +1,81 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2004 - 2015 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. +// +// --------------------------------------------------------------------- + + +// check wrapper function GraphColoring::color_sparsity_pattern + + +#include "../tests.h" +#include + + +void fill_graph (DynamicSparsityPattern &graph) +{ + //Edges in only one direction + graph.add(0,1); + graph.add(0,2); + graph.add(1,2); + graph.add(1,4); + graph.add(4,3); + graph.add(2,4); + graph.add(3,2); + + //Edges in opposite direction + graph.add(1,0); + graph.add(2,0); + graph.add(2,1); + graph.add(4,1); + graph.add(3,4); + graph.add(4,2); + graph.add(2,3); +} + + +int main (int argc, char **argv) +{ + //Initialize MPI and Zoltan + Utilities::MPI::MPI_InitFinalize mpi_initialization (argc, argv); + MPILogInitAll all; + + //Number of nodes + unsigned int num_indices = 5; + + //Create temporary object to hold graph connection info. + DynamicSparsityPattern dynamic_sparse_graph; + dynamic_sparse_graph.reinit(num_indices,num_indices); + + //fill dynamic sparsity pattern + fill_graph(dynamic_sparse_graph); + + //Create sparity pattern to hold graph connection info. + SparsityPattern sp_graph; + sp_graph.copy_from(dynamic_sparse_graph); + + Assert( num_indices == sp_graph.n_rows() , ExcInternalError() ); + + std::vector color_indices; + unsigned int num_colors; + + color_indices.resize(num_indices); + num_colors = GraphColoring::color_sparsity_pattern (sp_graph, color_indices); + + //color + deallog << "Coloring" << std::endl; + deallog << "Number of colors used: " << num_colors << std::endl; + for (unsigned int i=0; i