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rAKA/src/mesh_utils/mesh_partition/mesh_partition_scotch.cc
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mesh_partition_scotch.cc
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/**
* @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: Fri Jul 24 2020
*
* @brief implementation of the MeshPartitionScotch class
*
*
* @section LICENSE
*
* Copyright (©) 2010-2021 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_accessor.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(Mesh & mesh, Int spatial_dimension,
const ID & id)
: MeshPartition(mesh, spatial_dimension, 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();
auto spatial_dimension = mesh.getSpatialDimension();
auto nb_nodes = mesh.getNbNodes();
Int total_nb_element = 0;
Int nb_edge = 0;
for (const auto & type : mesh.elementTypes(spatial_dimension)) {
auto nb_element = mesh.getNbElement(type);
auto 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 (const auto & type : mesh.elementTypes(spatial_dimension)) {
if (Mesh::getSpatialDimension(type) != spatial_dimension) {
continue;
}
const auto & connectivity = mesh.getConnectivity(type, _not_ghost);
/// count number of occurrence of each node
for (auto && conn : make_view(connectivity, connectivity.getNbComponent()))
for (auto && node : conn)
verttab[node]++;
}
/// convert the occurrence array in a csr one
for (Int i = 1; i < nb_nodes; ++i) {
verttab[i] += verttab[i - 1];
}
for (Int 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];
Idx linearized_el = 0;
for (const auto & type : mesh.elementTypes(spatial_dimension)) {
auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const auto & connectivity = mesh.getConnectivity(type, _not_ghost);
for (auto && conn : make_view(connectivity, nb_nodes_per_element)) {
for (auto c : conn) {
edgetab[verttab[c]++] = linearized_el + velmbas;
}
++linearized_el;
}
}
for (Int i = nb_nodes; i > 0; --i) {
verttab[i] = verttab[i - 1];
}
verttab[0] = 0;
auto * verttab_tmp = verttab + vnodnbr + 1;
auto * edgetab_tmp = edgetab + verttab[vnodnbr];
for (const auto & type : mesh.elementTypes(spatial_dimension)) {
auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const auto & connectivity = mesh.getConnectivity(type, _not_ghost);
for (auto && conn : make_view(connectivity, nb_nodes_per_element)) {
*verttab_tmp = *(verttab_tmp - 1) + nb_nodes_per_element;
verttab_tmp++;
for (auto c : conn) {
*(edgetab_tmp++) = c + 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.data();
for (Int i = 0; i < nb_nodes; ++i) {
fgeominit << i << " ";
for (Int 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;
SCOTCH_Num vnodbas;
SCOTCH_Num vnodnbr;
SCOTCH_Num velmnbr;
SCOTCH_Num * verttab;
SCOTCH_Num * vendtab;
SCOTCH_Num * velotab;
SCOTCH_Num * vnlotab;
SCOTCH_Num * vlbltab;
SCOTCH_Num edgenbr;
SCOTCH_Num * edgetab;
SCOTCH_Num 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(
Int nb_part,
const std::function<Int(const Element &, const Element &)> & edge_load_func,
const 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.data(); // array of start indices in edgetab
SCOTCH_Num * vendtab = nullptr; // array of after-last indices in edgetab
SCOTCH_Num * velotab = vertex_loads.data(); // integer load associated with
// every vertex ( optional )
SCOTCH_Num * edlotab = edge_loads.data(); // integer load associated with
// every edge ( optional )
SCOTCH_Num * edgetab = dadjncy.data(); // adjacency array of every vertex
SCOTCH_Num * vlbltab = nullptr; // vertex label array (optional)
/// Allocate space for Scotch arrays
Array<SCOTCH_Num> parttab_array(vertnbr);
parttab = parttab_array.data();
/// 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 auto & nodes = mesh.getNodes();
auto nodes_it = nodes.begin(spatial_dimension);
Int out_linerized_el = 0;
for (const auto & type :
mesh.elementTypes(spatial_dimension, _not_ghost, _ek_not_defined)) {
auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const auto & connectivity = mesh.getConnectivity(type);
Vector<Real> mid(spatial_dimension);
for (auto && conn : make_view(connectivity, nb_nodes_per_element)) {
mid.set(0.);
for (auto node : conn) {
mid += nodes_it[node];
}
mid /= conn.size();
fgeominit << out_linerized_el++ << " ";
for (Int 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);
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);
auto nb_nodes = mesh.getNbNodes();
SCOTCH_Strat scotch_strat;
// SCOTCH_Ordering scotch_order;
Array<SCOTCH_Num> permtab(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.data(), peritab,
&cblknbr, rangtab, treetab);
SCOTCH_graphExit(&scotch_graph);
SCOTCH_stratExit(&scotch_strat);
destroyMesh(scotch_mesh);
/// Renumbering
auto spatial_dimension = mesh.getSpatialDimension();
MeshAccessor mesh_accessor(mesh);
for (auto gt : ghost_types) {
for (const auto & type : mesh.elementTypes(_ghost_type = gt)) {
auto & connectivity = mesh_accessor.getConnectivity(type, gt);
for (auto && c : make_view(connectivity)) {
c = permtab[c];
}
}
}
/// \todo think of a in-place way to do it
Array<Real> new_coordinates(nb_nodes, spatial_dimension);
auto new_nodes_it = make_view(new_coordinates, spatial_dimension).begin();
for (auto && data :
zip(make_view(mesh.getNodes(), spatial_dimension), permtab)) {
new_nodes_it[std::get<1>(data)] = std::get<0>(data);
}
mesh_accessor.getNodes().copy(new_coordinates);
AKANTU_DEBUG_OUT();
}
} // namespace akantu
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