Diffusion akantu (bugfixes/64-building-akantu) Browse

64-building…

mesh_partition_scotch.cc
View Options

			/**
			* @file mesh_partition_scotch.cc
			*
			* @author David Simon Kammer <david.kammer@epfl.ch>
			* @author Nicolas Richart <nicolas.richart@epfl.ch>
			*
			* @date creation: Fri Jun 18 2010
			* @date last modification: Tue Feb 20 2018
			*
			* @brief implementation of the MeshPartitionScotch class
			*
			* @section LICENSE
			*
			* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
			* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
			*
			* Akantu is free software: you can 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 3 of the License, or (at your option) any
			* later version.
			*
			* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
			* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
			* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
			* details.
			*
			* You should have received a copy of the GNU Lesser General Public License
			* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
			*
			*/

			/* -------------------------------------------------------------------------- */
			#include "mesh_partition_scotch.hh"
			#include "aka_common.hh"
			#include "aka_random_generator.hh"
			#include "aka_static_if.hh"
			#include "mesh_utils.hh"
			/* -------------------------------------------------------------------------- */
			#include <cstdio>
			#include <fstream>
			/* -------------------------------------------------------------------------- */

			#if !defined(AKANTU_USE_PTSCOTCH)
			#ifndef AKANTU_SCOTCH_NO_EXTERN
			extern "C" {
			#endif // AKANTU_SCOTCH_NO_EXTERN
			#include <scotch.h>
			#ifndef AKANTU_SCOTCH_NO_EXTERN
			}
			#endif // AKANTU_SCOTCH_NO_EXTERN
			#else // AKANTU_USE_PTSCOTCH
			#include <ptscotch.h>
			#endif // AKANTU_USE_PTSCOTCH

			namespace akantu {

			namespace {
			constexpr int scotch_version = int(SCOTCH_VERSION);
			}

			/* -------------------------------------------------------------------------- */
			MeshPartitionScotch::MeshPartitionScotch(const Mesh & mesh,
			UInt spatial_dimension, const ID & id,
			const MemoryID & memory_id)
			: MeshPartition(mesh, spatial_dimension, id, memory_id) {
			AKANTU_DEBUG_IN();

			// check if the akantu types and Scotch one are consistent
			static_assert(
			sizeof(Int) == sizeof(SCOTCH_Num),
			"The integer type of Akantu does not match the one from Scotch");

			static_if(aka::bool_constant<scotch_version >= 6>{})
			.then([](auto && y) { SCOTCH_randomSeed(y); })
			.else_([](auto && y) { srandom(y); })(
			std::forward<UInt>(RandomGenerator<UInt>::seed()));

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			static SCOTCH_Mesh * createMesh(const Mesh & mesh) {
			AKANTU_DEBUG_IN();

			UInt spatial_dimension = mesh.getSpatialDimension();
			UInt nb_nodes = mesh.getNbNodes();

			UInt total_nb_element = 0;
			UInt nb_edge = 0;

			for (auto & type : mesh.elementTypes(spatial_dimension)) {
			UInt nb_element = mesh.getNbElement(type);
			UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);

			total_nb_element += nb_element;
			nb_edge += nb_element * nb_nodes_per_element;
			}

			SCOTCH_Num vnodbas = 0;
			SCOTCH_Num vnodnbr = nb_nodes;

			SCOTCH_Num velmbas = vnodnbr;
			SCOTCH_Num velmnbr = total_nb_element;

			auto * verttab = new SCOTCH_Num[vnodnbr + velmnbr + 1];
			SCOTCH_Num * vendtab = verttab + 1;

			SCOTCH_Num * velotab = nullptr;
			SCOTCH_Num * vnlotab = nullptr;
			SCOTCH_Num * vlbltab = nullptr;

			memset(verttab, 0, (vnodnbr + velmnbr + 1) * sizeof(SCOTCH_Num));

			for (auto & type : mesh.elementTypes(spatial_dimension)) {
			if (Mesh::getSpatialDimension(type) != spatial_dimension)
			continue;

			UInt nb_element = mesh.getNbElement(type);
			UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
			const Array<UInt> & connectivity = mesh.getConnectivity(type, _not_ghost);

			/// count number of occurrence of each node
			for (UInt el = 0; el < nb_element; ++el) {
			UInt * conn_val = connectivity.storage() + el * nb_nodes_per_element;
			for (UInt n = 0; n < nb_nodes_per_element; ++n) {
			verttab[*(conn_val++)]++;
			}
			}
			}

			/// convert the occurrence array in a csr one
			for (UInt i = 1; i < nb_nodes; ++i)
			verttab[i] += verttab[i - 1];
			for (UInt i = nb_nodes; i > 0; --i)
			verttab[i] = verttab[i - 1];
			verttab[0] = 0;

			/// rearrange element to get the node-element list
			SCOTCH_Num edgenbr = verttab[vnodnbr] + nb_edge;
			auto * edgetab = new SCOTCH_Num[edgenbr];

			UInt linearized_el = 0;

			for (auto & type : mesh.elementTypes(spatial_dimension)) {
			UInt nb_element = mesh.getNbElement(type);
			UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
			const Array<UInt> & connectivity = mesh.getConnectivity(type, _not_ghost);

			for (UInt el = 0; el < nb_element; ++el, ++linearized_el) {
			UInt * conn_val = connectivity.storage() + el * nb_nodes_per_element;
			for (UInt n = 0; n < nb_nodes_per_element; ++n)
			edgetab[verttab[*(conn_val++)]++] = linearized_el + velmbas;
			}
			}

			for (UInt i = nb_nodes; i > 0; --i)
			verttab[i] = verttab[i - 1];
			verttab[0] = 0;

			SCOTCH_Num * verttab_tmp = verttab + vnodnbr + 1;
			SCOTCH_Num * edgetab_tmp = edgetab + verttab[vnodnbr];

			for (auto & type : mesh.elementTypes(spatial_dimension)) {
			UInt nb_element = mesh.getNbElement(type);
			UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);

			const Array<UInt> & connectivity = mesh.getConnectivity(type, _not_ghost);

			for (UInt el = 0; el < nb_element; ++el) {
			verttab_tmp = (verttab_tmp - 1) + nb_nodes_per_element;
			verttab_tmp++;
			UInt * conn = connectivity.storage() + el * nb_nodes_per_element;
			for (UInt i = 0; i < nb_nodes_per_element; ++i) {
			(edgetab_tmp++) = (conn++) + vnodbas;
			}
			}
			}

			auto * meshptr = new SCOTCH_Mesh;

			SCOTCH_meshInit(meshptr);

			SCOTCH_meshBuild(meshptr, velmbas, vnodbas, velmnbr, vnodnbr, verttab,
			vendtab, velotab, vnlotab, vlbltab, edgenbr, edgetab);

			/// Check the mesh
			AKANTU_DEBUG_ASSERT(SCOTCH_meshCheck(meshptr) == 0,
			"Scotch mesh is not consistent");

			#ifndef AKANTU_NDEBUG
			if (AKANTU_DEBUG_TEST(dblDump)) {
			/// save initial graph
			FILE * fmesh = fopen("ScotchMesh.msh", "w");
			SCOTCH_meshSave(meshptr, fmesh);
			fclose(fmesh);

			/// write geometry file
			std::ofstream fgeominit;
			fgeominit.open("ScotchMesh.xyz");
			fgeominit << spatial_dimension << std::endl << nb_nodes << std::endl;

			const Array<Real> & nodes = mesh.getNodes();
			Real * nodes_val = nodes.storage();
			for (UInt i = 0; i < nb_nodes; ++i) {
			fgeominit << i << " ";
			for (UInt s = 0; s < spatial_dimension; ++s)
			fgeominit << *(nodes_val++) << " ";
			fgeominit << std::endl;
			;
			}
			fgeominit.close();
			}
			#endif

			AKANTU_DEBUG_OUT();
			return meshptr;
			}

			/* -------------------------------------------------------------------------- */
			static void destroyMesh(SCOTCH_Mesh * meshptr) {
			AKANTU_DEBUG_IN();

			SCOTCH_Num velmbas, vnodbas, vnodnbr, velmnbr, verttab, vendtab, *velotab,
			vnlotab, vlbltab, edgenbr, *edgetab, degrptr;

			SCOTCH_meshData(meshptr, &velmbas, &vnodbas, &velmnbr, &vnodnbr, &verttab,
			&vendtab, &velotab, &vnlotab, &vlbltab, &edgenbr, &edgetab,
			&degrptr);

			delete[] verttab;
			delete[] edgetab;

			SCOTCH_meshExit(meshptr);

			delete meshptr;

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void MeshPartitionScotch::partitionate(
			UInt nb_part,
			std::function<Int(const Element &, const Element &)> edge_load_func,
			std::function<Int(const Element &)> vertex_load_func) {
			AKANTU_DEBUG_IN();

			nb_partitions = nb_part;

			if (mesh.isPeriodic()) {
			tweakConnectivity();
			}

			AKANTU_DEBUG_INFO("Partitioning the mesh " << mesh.getID() << " in "
			<< nb_part << " parts.");

			Array<Int> dxadj;
			Array<Int> dadjncy;
			Array<Int> edge_loads;
			Array<Int> vertex_loads;
			buildDualGraph(dxadj, dadjncy, edge_loads, edge_load_func, vertex_loads,
			vertex_load_func);

			/// variables that will hold our structures in scotch format
			SCOTCH_Graph scotch_graph;
			SCOTCH_Strat scotch_strat;

			/// description number and arrays for struct mesh for scotch
			SCOTCH_Num baseval = 0; // base numbering for element and
			// nodes (0 -> C , 1 -> fortran)
			SCOTCH_Num vertnbr = dxadj.size() - 1; // number of vertexes
			SCOTCH_Num * parttab; // array of partitions
			SCOTCH_Num edgenbr = dxadj(vertnbr); // twice the number of "edges"
			//(an "edge" bounds two nodes)
			SCOTCH_Num * verttab = dxadj.storage(); // array of start indices in edgetab
			SCOTCH_Num * vendtab = nullptr; // array of after-last indices in edgetab
			SCOTCH_Num * velotab =
			vertex_loads.storage(); // integer load associated with
			// every vertex ( optional )
			SCOTCH_Num * edlotab = edge_loads.storage(); // integer load associated with
			// every edge ( optional )
			SCOTCH_Num * edgetab = dadjncy.storage(); // adjacency array of every vertex
			SCOTCH_Num * vlbltab = nullptr; // vertex label array (optional)

			/// Allocate space for Scotch arrays
			parttab = new SCOTCH_Num[vertnbr];

			/// Initialize the strategy structure
			SCOTCH_stratInit(&scotch_strat);

			/// Initialize the graph structure
			SCOTCH_graphInit(&scotch_graph);

			/// Build the graph from the adjacency arrays
			SCOTCH_graphBuild(&scotch_graph, baseval, vertnbr, verttab, vendtab, velotab,
			vlbltab, edgenbr, edgetab, edlotab);

			#ifndef AKANTU_NDEBUG
			if (AKANTU_DEBUG_TEST(dblDump)) {
			/// save initial graph
			FILE * fgraphinit = fopen("GraphIniFile.grf", "w");
			SCOTCH_graphSave(&scotch_graph, fgraphinit);
			fclose(fgraphinit);

			/// write geometry file
			std::ofstream fgeominit;
			fgeominit.open("GeomIniFile.xyz");
			fgeominit << spatial_dimension << std::endl << vertnbr << std::endl;

			const Array<Real> & nodes = mesh.getNodes();

			auto nodes_it = nodes.begin(spatial_dimension);

			UInt out_linerized_el = 0;
			for (auto & type :
			mesh.elementTypes(spatial_dimension, _not_ghost, _ek_not_defined)) {
			UInt nb_element = mesh.getNbElement(type);
			UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
			const Array<UInt> & connectivity = mesh.getConnectivity(type);

			Vector<Real> mid(spatial_dimension);
			for (UInt el = 0; el < nb_element; ++el) {
			mid.set(0.);
			for (UInt n = 0; n < nb_nodes_per_element; ++n) {
			UInt node = connectivity.storage()[nb_nodes_per_element * el + n];
			mid += Vector<Real>(nodes_it[node]);
			}
			mid /= nb_nodes_per_element;

			fgeominit << out_linerized_el++ << " ";
			for (UInt s = 0; s < spatial_dimension; ++s)
			fgeominit << mid[s] << " ";

			fgeominit << std::endl;
			;
			}
			}
			fgeominit.close();
			}
			#endif

			/// Check the graph
			AKANTU_DEBUG_ASSERT(SCOTCH_graphCheck(&scotch_graph) == 0,
			"Graph to partition is not consistent");

			/// Partition the mesh
			SCOTCH_graphPart(&scotch_graph, nb_part, &scotch_strat, parttab);

			/// Check the graph
			AKANTU_DEBUG_ASSERT(SCOTCH_graphCheck(&scotch_graph) == 0,
			"Partitioned graph is not consistent");

			#ifndef AKANTU_NDEBUG
			if (AKANTU_DEBUG_TEST(dblDump)) {
			/// save the partitioned graph
			FILE * fgraph = fopen("GraphFile.grf", "w");
			SCOTCH_graphSave(&scotch_graph, fgraph);
			fclose(fgraph);

			/// save the partition map
			std::ofstream fmap;
			fmap.open("MapFile.map");
			fmap << vertnbr << std::endl;
			for (Int i = 0; i < vertnbr; i++)
			fmap << i << " " << parttab[i] << std::endl;
			fmap.close();
			}
			#endif

			/// free the scotch data structures
			SCOTCH_stratExit(&scotch_strat);
			SCOTCH_graphFree(&scotch_graph);
			SCOTCH_graphExit(&scotch_graph);

			fillPartitionInformation(mesh, parttab);

			delete[] parttab;

			if (mesh.isPeriodic()) {
			restoreConnectivity();
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void MeshPartitionScotch::reorder() {
			AKANTU_DEBUG_IN();

			AKANTU_DEBUG_INFO("Reordering the mesh " << mesh.getID());
			SCOTCH_Mesh * scotch_mesh = createMesh(mesh);

			UInt nb_nodes = mesh.getNbNodes();

			SCOTCH_Strat scotch_strat;
			// SCOTCH_Ordering scotch_order;

			auto * permtab = new SCOTCH_Num[nb_nodes];
			SCOTCH_Num * peritab = nullptr;
			SCOTCH_Num cblknbr = 0;
			SCOTCH_Num * rangtab = nullptr;
			SCOTCH_Num * treetab = nullptr;

			/// Initialize the strategy structure
			SCOTCH_stratInit(&scotch_strat);

			SCOTCH_Graph scotch_graph;

			SCOTCH_graphInit(&scotch_graph);
			SCOTCH_meshGraph(scotch_mesh, &scotch_graph);

			#ifndef AKANTU_NDEBUG
			if (AKANTU_DEBUG_TEST(dblDump)) {
			FILE * fgraphinit = fopen("ScotchMesh.grf", "w");
			SCOTCH_graphSave(&scotch_graph, fgraphinit);
			fclose(fgraphinit);
			}
			#endif

			/// Check the graph
			// AKANTU_DEBUG_ASSERT(SCOTCH_graphCheck(&scotch_graph) == 0,
			// "Mesh to Graph is not consistent");

			SCOTCH_graphOrder(&scotch_graph, &scotch_strat, permtab, peritab, &cblknbr,
			rangtab, treetab);

			SCOTCH_graphExit(&scotch_graph);
			SCOTCH_stratExit(&scotch_strat);
			destroyMesh(scotch_mesh);

			/// Renumbering
			UInt spatial_dimension = mesh.getSpatialDimension();

			for (auto gt : ghost_types) {
			for (auto & type : mesh.elementTypes(_ghost_type = gt)) {
			UInt nb_element = mesh.getNbElement(type, gt);
			UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);

			const Array<UInt> & connectivity = mesh.getConnectivity(type, gt);

			UInt * conn = connectivity.storage();
			for (UInt el = 0; el < nb_element * nb_nodes_per_element; ++el, ++conn) {
			conn = permtab[conn];
			}
			}
			}

			/// \todo think of a in-place way to do it
			auto * new_coordinates = new Real[spatial_dimension * nb_nodes];
			Real * old_coordinates = mesh.getNodes().storage();
			for (UInt i = 0; i < nb_nodes; ++i) {
			memcpy(new_coordinates + permtab[i] * spatial_dimension,
			old_coordinates + i * spatial_dimension,
			spatial_dimension * sizeof(Real));
			}
			memcpy(old_coordinates, new_coordinates,
			nb_nodes * spatial_dimension * sizeof(Real));
			delete[] new_coordinates;

			delete[] permtab;

			AKANTU_DEBUG_OUT();
			}

			} // namespace akantu

rAKA/src/mesh_utils/mesh_partition/mesh_partition_scotch.cc47c3bed53838bugfixes/64-building…

mesh_partition_scotch.ccView Options

rAKA/src/mesh_utils/mesh_partition/mesh_partition_scotch.cc
47c3bed53838bugfixes/64-building…

mesh_partition_scotch.cc
View Options