Metis support for vertex distribution

CMakeLists.txt

@@ -2,6 +2,18 @@ project(genericCommunicator)
 cmake_minimum_required(VERSION 2.8.5)
 
 
+###############################################################################
+# CMAKE module path in utils/cmake/modules/
+###############################################################################
+set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/utils/cmake/modules/" ${CMAKE_MODULE_PATH})
+
+###############################################################################
+# METIS
+###############################################################################
+find_package(METIS 5.1.0 REQUIRED)
+include_directories(SYSTEM ${METIS_INCLUDE_DIRS})
+set(LIBS ${LIBS} ${METIS_LIBRARIES})
+
 ###############################################################################
 # Boost
 ###############################################################################
@@ -10,7 +22,7 @@ include_directories(SYSTEM ${Boost_INCLUDE_DIRS})
 set(LIBS ${LIBS} ${Boost_LIBRARIES})
 
 ################################################################################
-# Find MPI
+# MPI
 ################################################################################
 find_package(MPI REQUIRED)
   include_directories(SYSTEM ${MPI_C_INCLUDE_PATH})

README.md

@@ -34,8 +34,7 @@ GrayBat  is licensed under the **GPLv3+**. Please refer to our [LICENSE.md](LICE
  * Boost 1.57.0
  * OpenMPI 1.8.0
  * g++ 4.9.2
- * Doxygen 1.8.8
-
+ * metis 5.1
 
 ##Compiling##
 

include/Cave.hpp

@@ -259,6 +259,15 @@ namespace graybat {
 
 	}
 
+	/**
+	 * @breif Returns the number of hosts
+	 *        of the current **graph**.
+	 *
+	 */
+	unsigned nHosts(){
+	    return getGraphContext(graph).size();
+	}
+
 
 	/**
 	 * @brief Returns true if the *vertex* is hosted by the

include/mapping.hpp

@@ -4,6 +4,7 @@
 #include <vector>    /* std::vector */
 #include <assert.h>  /* assert */
 #include <stdlib.h>  /* srand, rand */
+#include <metis.h>   /* idx_t, METIS_PartGraphKway */
 
 /*******************************************************************************
  *
@@ -16,6 +17,107 @@ namespace graybat {
     namespace mapping {
 
 
+	/**
+	 * Partitioning of the communication graph
+	 * into k parts. k is set either to the 
+	 * number of peers that want to take
+	 * part in communication or is given
+	 * as an input parameter.
+	 *
+	 * @param  nParts number of parts to partition
+	 * @return set of vertices that belong "together"
+	 */
+	struct GraphPartition {
+
+	    GraphPartition() : GraphPartition(0){
+
+	    }
+
+	    GraphPartition(unsigned nParts)
+		: nParts(nParts){
+
+	    }
+
+	    /**
+	     * @Brief Translates the graph into the compressed row storage
+	     *        format (CSR) which can be parsed by Metis.
+	     *
+	     * @See http://en.wikipedia.org/wiki/Sparse_matrix#Compressed_row_Storage_.28CRS_or_CSR.29
+	     *
+	     */
+	    template<typename T_Graph>
+	    std::pair<std::vector<idx_t>, std::vector<idx_t> > toCompressedRowStorage(T_Graph &graph) {
+
+		typedef typename T_Graph::Vertex Vertex;
+		typedef typename T_Graph::Edge   Edge;
+
+		unsigned i = 0;
+
+		std::vector<idx_t> xadj(1,i);
+		std::vector<idx_t> adjncy;
+
+
+		for(Vertex v : graph.getVertices()){
+		    for(auto link : graph.getOutEdges(v)){
+			Vertex destVertex = link.first;
+			Edge   destEdge   = link.second;
+
+			adjncy.push_back(destVertex.id);
+			i++;
+
+		    }
+		    xadj.push_back(i);
+
+		}
+
+		return std::make_pair(xadj, adjncy);
+	    }
+
+	    template<typename T_Graph>
+	    std::vector<typename T_Graph::Vertex> operator()(const unsigned processID, const unsigned processCount, T_Graph &graph){
+
+		typedef typename T_Graph::Vertex Vertex;
+		std::vector<Vertex> myVertices;
+		auto csr = toCompressedRowStorage(graph);
+
+		if(nParts == 0){
+		    nParts = processCount;
+		}
+
+		if(nParts == 1){
+		    return graph.getVertices();
+		}
+
+		idx_t nVertices = graph.getVertices().size();
+		idx_t nWeights  = 1;
+		idx_t objval;
+		std::vector<idx_t> part(nVertices, 0);
+
+		METIS_PartGraphKway(&nVertices, &nWeights,
+				    csr.first.data(), csr.second.data(),
+				    NULL, NULL, NULL, &nParts, NULL,
+				    NULL, NULL,
+				    &objval,
+				    part.data());
+
+
+		for(unsigned part_i = 0; part_i < part.size(); part_i++){
+		    if(part[part_i] == (int)processID){
+			myVertices.push_back(graph.getVertices().at(part_i));
+		    }
+
+		} 
+
+		return myVertices;
+	    }
+
+	private:
+	    idx_t nParts;
+
+	};
+
+
+
 	/**
 	 * Random distribution of vertices of the *graph* to the
 	 * the peers. All peers need to set the same random *seed*.

src/gol.cc

@@ -111,7 +111,7 @@ int gol(const unsigned nCells, const unsigned nTimeSteps ) {
     MyCave cave(graybat::pattern::GridDiagonal(height, width));
 
     // Distribute vertices
-    cave.distribute(graybat::mapping::Consecutive());
+    cave.distribute(graybat::mapping::GraphPartition());
 
     /***************************************************************************
      * Run Simulation

utils/cmake/modules/FindMETIS.cmake

@@ -0,0 +1,33 @@
+  #
+  # Find the METIS includes and libraries
+  #
+  # ParMETIS is an MPI-based parallel library that implements a variety of algorithms for 
+  # partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of 
+  # sparse matrices. It can be found at:
+  # 	http://www-users.cs.umn.edu/~karypis/metis/parmetis/index.html
+  #
+  # METIS_INCLUDE_DIR - where to find autopack.h
+  # METIS_LIBRARIES   - List of fully qualified libraries to link against.
+  # METIS_FOUND       - Do not attempt to use if "no" or undefined.
+
+  FIND_PATH(METIS_INCLUDE_DIR metis.h
+    /usr/local/include
+    /usr/include
+  )
+
+  FIND_LIBRARY(METIS_LIBRARY metis
+    /usr/local/lib
+    /usr/lib
+  )
+
+  FIND_LIBRARY(METIS_LIBRARY metis
+    /usr/local/lib
+    /usr/lib
+  )
+
+  IF(METIS_INCLUDE_DIR)
+    IF(METIS_LIBRARY)
+      SET( METIS_LIBRARIES ${METIS_LIBRARY} ${METIS_LIBRARY})
+      SET( METIS_FOUND "YES" )
+    ENDIF(METIS_LIBRARY)
+  ENDIF(METIS_INCLUDE_DIR)