Adding missing file

src/Decomposition/Distribution/Distribution_unit_tests.hpp

@@ -149,7 +149,7 @@ BOOST_AUTO_TEST_CASE( Metis_distribution_test)
 	// operator= functions
 	// operator== functions
 
-	BOOST_REQUIRE_EQUAL(sizeof(MetisDistribution<3,float>),680ul);
+	BOOST_REQUIRE_EQUAL(sizeof(MetisDistribution<3,float>),568ul);
 }
 
 BOOST_AUTO_TEST_CASE( Parmetis_distribution_test)
@@ -231,6 +231,8 @@ BOOST_AUTO_TEST_CASE( Parmetis_distribution_test)
 	}
 
 	//! [refine with parmetis the decomposition]
+
+	BOOST_REQUIRE_EQUAL(sizeof(MetisDistribution<3,float>),568ul);
 }
 
 BOOST_AUTO_TEST_CASE( DistPametis_distribution_test)

src/Decomposition/Distribution/parmetis_util.hpp

@@ -207,6 +207,25 @@ public:
 	{
 		// TODO Move into VCluster
 		MPI_Comm_dup(MPI_COMM_WORLD, &comm);
+
+		// Nullify Mg
+		Mg.nvtxs = NULL;
+		Mg.ncon = NULL;
+		Mg.xadj = NULL;
+		Mg.adjncy = NULL;
+		Mg.vwgt = NULL;
+		Mg.vsize = NULL;
+		Mg.adjwgt = NULL;
+		Mg.nparts = NULL;
+		Mg.tpwgts = NULL;
+		Mg.ubvec = NULL;
+		Mg.options = NULL;
+		Mg.objval = NULL;
+		Mg.part = NULL;
+		Mg.edgecut = NULL;
+		Mg.itr = NULL;
+		Mg.numflag = NULL;
+		Mg.wgtflag = NULL;
 	}
 
 	//TODO deconstruct new variables
@@ -302,66 +321,10 @@ public:
 		last = vtxdist.get(p_id+1)-1;
 		nvertex = last.id - first.id + 1;
 
-		// Get the number of vertex
-		Mg.nvtxs = new idx_t[1];
-		Mg.nvtxs[0] =  nvertex;
-
-		// Set the number of constrains
-		Mg.ncon = new idx_t[1];
-		Mg.ncon[0] = 1;
-
-		// Set to null the weight of the vertex (init after in constructAdjList) (can be removed)
-		Mg.vwgt = NULL;
-
-		// Set to null the weight of the edge (init after in constructAdjList) (can be removed)
-		Mg.adjwgt = NULL;
+		setDefaultParameters(w);
 
 		// construct the adjacency list
 		constructAdjList(g, m2g);
-
-		// Set the total number of partitions
-		Mg.nparts = new idx_t[1];
-		Mg.nparts[0] = nc;
-
-		//! Set option for the graph partitioning (set as default)
-
-		Mg.options = new idx_t[4];
-		Mg.options[0] = 0;
-		Mg.options[1] = 0;
-		Mg.options[2] = 0;
-		Mg.options[3] = 0;
-
-		//! is an output vector containing the partition for each vertex
-
-		//! adaptiveRepart itr value
-		Mg.itr = new real_t[1];
-		Mg.itr[0] = 1000.0;
-
-		//! init tpwgts to have balanced vertices and ubvec
-
-		Mg.tpwgts = new real_t[Mg.nparts[0]];
-		Mg.ubvec = new real_t[Mg.nparts[0]];
-
-		for (size_t s = 0; s < (size_t)Mg.nparts[0]; s++)
-		{
-			Mg.tpwgts[s] = 1.0 / Mg.nparts[0];
-			Mg.ubvec[s] = 1.05;
-		}
-
-		Mg.edgecut = new idx_t[1];
-		Mg.edgecut[0] = 0;
-
-		//! This is used to indicate the numbering scheme that is used for the vtxdist, xadj, adjncy, and part arrays. (0 for C-style, start from 0 index)
-		Mg.numflag = new idx_t[1];
-		Mg.numflag[0] = 0;
-
-		//! This is used to indicate if the graph is weighted. wgtflag can take one of four values:
-		Mg.wgtflag = new idx_t[1];
-
-		if(w)
-			Mg.wgtflag[0] = 3;
-		else
-			Mg.wgtflag[0] = 0;
 	}
 
 	/*! \brief Decompose the graph
@@ -444,6 +407,93 @@ public:
 		constructAdjList(g,m2g);
 	}
 
+	/*! \brief Seth the default parameters for parmetis
+	 *
+	 *
+	 */
+	void setDefaultParameters(bool w)
+	{
+		Mg.nvtxs = new idx_t[1];
+
+		// Set the number of constrains
+		Mg.ncon = new idx_t[1];
+		Mg.ncon[0] = 1;
+
+		// Set to null the weight of the vertex (init after in constructAdjList) (can be removed)
+		Mg.vwgt = NULL;
+
+		// Set to null the weight of the edge (init after in constructAdjList) (can be removed)
+		Mg.adjwgt = NULL;
+
+		// Set the total number of partitions
+		Mg.nparts = new idx_t[1];
+		Mg.nparts[0] = nc;
+
+		//! Set option for the graph partitioning (set as default)
+
+		Mg.options = new idx_t[4];
+		Mg.options[0] = 0;
+		Mg.options[1] = 0;
+		Mg.options[2] = 0;
+		Mg.options[3] = 0;
+
+		//! is an output vector containing the partition for each vertex
+
+		//! adaptiveRepart itr value
+		Mg.itr = new real_t[1];
+		Mg.itr[0] = 1000.0;
+
+		//! init tpwgts to have balanced vertices and ubvec
+
+		Mg.tpwgts = new real_t[Mg.nparts[0]];
+		Mg.ubvec = new real_t[Mg.nparts[0]];
+
+		for (size_t s = 0; s < (size_t)Mg.nparts[0]; s++)
+		{
+			Mg.tpwgts[s] = 1.0 / Mg.nparts[0];
+			Mg.ubvec[s] = 1.05;
+		}
+
+		Mg.edgecut = new idx_t[1];
+		Mg.edgecut[0] = 0;
+
+		//! This is used to indicate the numbering scheme that is used for the vtxdist, xadj, adjncy, and part arrays. (0 for C-style, start from 0 index)
+		Mg.numflag = new idx_t[1];
+		Mg.numflag[0] = 0;
+
+		//! This is used to indicate if the graph is weighted. wgtflag can take one of four values:
+		Mg.wgtflag = new idx_t[1];
+
+		if(w)
+			Mg.wgtflag[0] = 3;
+		else
+			Mg.wgtflag[0] = 0;
+	}
+
+	const Parmetis<Graph> & operator=(const Parmetis<Graph> & pm)
+	{
+		comm = pm.comm;
+		v_cl = pm.v_cl;
+		p_id = pm.p_id;
+		nc = pm.nc;
+
+		setDefaultParameters(pm.Mg.wgtflag[0] == 3);
+
+		return *this;
+	}
+
+	const Parmetis<Graph> & operator=(Parmetis<Graph> && pm)
+	{
+		comm = pm.comm;
+		v_cl = pm.v_cl;
+		p_id = pm.p_id;
+		nc = pm.nc;
+
+		setDefaultParameters(pm.Mg.wgtflag[0] == 3);
+
+		return *this;
+	}
+
 };
 
 #endif

src/Graph/ids.hpp

+/*
+ * ids.hpp
+ *
+ *  Created on: Mar 1, 2016
+ *      Author: i-bird
+ */
+
+#ifndef SRC_GRAPH_IDS_HPP_
+#define SRC_GRAPH_IDS_HPP_
+
+/*! Here we define different the remapped-id
+ *
+ * rid, gid and lid are all unsigned long integer, and can be easily interchanged by mistake
+ *  encapsulating avoid that this could happen. The second is readability, from the definition
+ *  of function/structure we see immediately which id parameter accept/store
+ *
+ */
+struct rid
+{
+	idx_t id;
+
+	inline bool operator<=(const rid & r) const
+	{
+		return id <= r.id;
+	}
+
+	inline bool operator<(const rid & r) const
+	{
+		return id < r.id;
+	}
+
+	inline rid operator-(int i) const
+	{
+		struct rid tmp;
+		tmp.id = id - i;
+		return tmp;
+	}
+
+	inline rid operator-(struct rid i) const
+	{
+		struct rid tmp;
+		tmp.id = id - i.id;
+		return tmp;
+	}
+
+	inline rid operator+(int i) const
+	{
+		struct rid tmp;
+		tmp.id = id + i;
+		return tmp;
+	}
+
+	inline rid & operator+=(const rid & i)
+	{
+		id += i.id;
+		return *this;
+	}
+
+	inline rid & operator++()
+	{
+		id++;
+
+		return *this;
+	}
+
+	inline bool operator==(const rid & r) const
+	{
+		return id == r.id;
+	}
+};
+
+/*! Here we define different the remapped-id
+ *
+ * rid, gid and lid are all unsigned long integer, and can be easily interchanged by mistake
+ *  encapsulating avoid that this could happen. The second is readability, from the definition
+ *  of function/structure we see immediately which id parameter accept/store
+ *
+ */
+struct gid
+{
+	size_t id;
+};
+
+/*! Here we define different the remapped-id
+ *
+ * rid, gid and lid are all unsigned long integer, and can be easily interchanged by mistake
+ *  encapsulating avoid that this could happen. The second is readability, from the definition
+ *  of function/structure we see immediately which id parameter accept/store
+ *
+ */
+struct lid
+{
+	size_t id;
+};
+
+// define hash map for gid rid and lid
+
+namespace std
+{
+	template <>
+	struct hash<rid>
+	{
+		inline std::size_t operator()(const rid& k) const
+		{
+			return k.id;
+		}
+	};
+
+	template <>
+	struct hash<gid>
+	{
+		inline std::size_t operator()(const gid& k) const
+		{
+			return k.id;
+		}
+	};
+
+	template <>
+	struct hash<lid>
+	{
+		inline std::size_t operator()(const lid& k) const
+		{
+			return k.id;
+		}
+	};
+
+}
+
+
+#endif /* SRC_GRAPH_IDS_HPP_ */

src/Grid/grid_dist_id.hpp

@@ -491,6 +491,7 @@ class grid_dist_id
 
 		// Create the sub-domains
 		dec.setParameters(div,domain,bc,ghost);
+		dec.decompose();
 
 		// Calculate ghost boxes
 		dec.calculateGhostBoxes();
@@ -506,8 +507,6 @@ class grid_dist_id
 		// fill the global size of the grid
 		for (size_t i = 0 ; i < dim ; i++)	{this->g_sz[i] = g_sz[i];}
 
-		dec.decompose();
-
 		// Create local grid
 		Create();
 	}

src/Grid/grid_dist_id_unit_test_ext_dom.hpp

+/*
+ * grid_dist_id_unit_test_ext_dom.hpp
+ *
+ *  Created on: Feb 24, 2016
+ *      Author: i-bird
+ */
+
+#ifndef SRC_GRID_GRID_DIST_ID_UNIT_TEST_EXT_DOM_HPP_
+#define SRC_GRID_GRID_DIST_ID_UNIT_TEST_EXT_DOM_HPP_
+
+
+// Test duplicated topology
+
+void Test3D_extended_grid(const Box<3,float> & domain, long int k)
+{
+	long int big_step = k / 30;
+	big_step = (big_step == 0)?1:big_step;
+	long int small_step = 21;
+
+	Vcluster & v_cl = *global_v_cluster;
+
+	if ( v_cl.getProcessingUnits() > 32 )
+		return;
+
+	print_test( "Testing 3D extended grid k<=",k);
+
+	// 3D test
+	for ( ; k >= 2 ; k-= (k > 2*big_step)?big_step:small_step )
+	{
+		BOOST_TEST_CHECKPOINT( "Testing 3D extended grid k=" << k );
+
+		// grid size
+		size_t sz[3];
+		sz[0] = k;
+		sz[1] = k;
+		sz[2] = k;
+
+		// factor
+		float factor = pow(global_v_cluster->getProcessingUnits()/2.0f,1.0f/3.0f);
+
+		// Ghost
+		Ghost<3,float> g(0.01 / factor);
+
+		//! [Construct an extended grid]
+
+		// Distributed grid with id decomposition
+		grid_dist_id<3, float, Point_test<float>, CartDecomposition<3,float>> g_dist1(sz,domain,g);
+
+		// Extend the grid by 2 points
+		Box<3,size_t> ext({2,2,2},{2,2,2});
+
+		// another grid perfectly overlapping the previous, extended by 2 points
+		grid_dist_id<3, float, Point_test<float>, CartDecomposition<3,float>> g_dist2(g_dist1,ext);
+
+		//! [Construct an extended grid]
+
+		bool ret = g_dist2.getDecomposition().check_consistency();
+		BOOST_REQUIRE_EQUAL(ret,true);
+
+		// Given an iterator on grid 1
+		auto dom_g1 = g_dist1.getDomainIterator();
+		// And a sub-iterator on grid 2 overlapping grid 1
+		auto dom_g2 = g_dist2.getSubDomainIterator({2,2,2},{k+2-1,k+2-1,k+2-1});
+
+		grid_key_dx<3> kb({2l,2l,2l});
+
+		// the 2 iterator must match
+
+		bool check = true;
+
+		while (dom_g2.isNext())
+		{
+			auto key1 = dom_g1.get();
+			auto key2 = dom_g2.get();
+
+			grid_key_dx<3> g1_k = g_dist1.getGKey(key1);
+			grid_key_dx<3> g2_k = g_dist2.getGKey(key2);
+
+			g2_k = g2_k - kb;
+
+			check &= (g1_k == g2_k)?true:false;
+
+			std::cout << "KEY: " << g1_k.to_string() << "   " << g2_k.to_string() << "\n";
+
+			if (check == false)
+			{
+				std::cout << "ERROR: " << g1_k.to_string() << "   " << g2_k.to_string() << "\n";
+				break;
+			}
+
+			++dom_g1;
+			++dom_g2;
+		}
+
+		BOOST_REQUIRE_EQUAL(check,true);
+	}
+}
+
+
+#endif /* SRC_GRID_GRID_DIST_ID_UNIT_TEST_EXT_DOM_HPP_ */