From 4975f4b31816fcd423d714df84f83977fb7a2015 Mon Sep 17 00:00:00 2001 From: Giovanni Alzetta Date: Wed, 9 Jan 2019 22:13:56 +0100 Subject: [PATCH] Added covering rtree and flag to GridTools::Cache --- .../changes/minor/20190111GiovanniAlzetta | 5 + include/deal.II/grid/grid_tools_cache.h | 33 + .../grid/grid_tools_cache_update_flags.h | 12 + source/grid/grid_tools_cache.cc | 41 + tests/grid/grid_tools_cache_04.cc | 120 ++ ...h_mpi=true.with_p4est=true.mpirun=1.output | 238 ++++ ...h_mpi=true.with_p4est=true.mpirun=4.output | 1007 +++++++++++++++++ 7 files changed, 1456 insertions(+) create mode 100644 doc/news/changes/minor/20190111GiovanniAlzetta create mode 100644 tests/grid/grid_tools_cache_04.cc create mode 100644 tests/grid/grid_tools_cache_04.with_mpi=true.with_p4est=true.mpirun=1.output create mode 100644 tests/grid/grid_tools_cache_04.with_mpi=true.with_p4est=true.mpirun=4.output diff --git a/doc/news/changes/minor/20190111GiovanniAlzetta b/doc/news/changes/minor/20190111GiovanniAlzetta new file mode 100644 index 0000000000..868aee927f --- /dev/null +++ b/doc/news/changes/minor/20190111GiovanniAlzetta @@ -0,0 +1,5 @@ +New: GridTools::Cache::get_covering_rtree() automatically stores and generates +a rtree of bounding boxes covering the whole triangulation. In a distributed setting +it can identify which processes have locally owned cells in any part of the mesh. +
+(Giovanni Alzetta, 2019/01/11) diff --git a/include/deal.II/grid/grid_tools_cache.h b/include/deal.II/grid/grid_tools_cache.h index ddbfc8444d..e348103f6d 100644 --- a/include/deal.II/grid/grid_tools_cache.h +++ b/include/deal.II/grid/grid_tools_cache.h @@ -150,6 +150,33 @@ namespace GridTools const Mapping & get_mapping() const; + + /** + * This function returns an object that allows identifying + * which process(es) in a parallel computation may own the + * cell that surrounds a given point. The elements of this + * object -- an Rtree -- are pairs of bounding boxes denoting + * areas that cover all or parts of the local portion of a + * parallel triangulation, and an unsigned int representing + * the process or subdomain that owns these cells. + * Given a point on a parallel::Triangulation, this tree + * allows to identify one, or few candidate processes, for + * which the point lies on a locally owned cell. + * + * Constructing or updating the rtree requires a call to + * GridTools::build_global_description_tree(), which exchanges + * bounding boxes between all processes using + * Utilities::MPI::all_gather(), a collective operation. + * Therefore this function must be called by all processes + * at the same time. + * + * While each box may only cover part of a process's locally + * owned part of the triangulation, the boxes associated with + * each process jointly cover the entire local portion. + */ + const RTree, unsigned int>> & + get_covering_rtree() const; + #ifdef DEAL_II_WITH_NANOFLANN /** * Return the cached vertex_kdtree object, constructed with the vertices of @@ -191,6 +218,12 @@ namespace GridTools mutable std::vector>> vertex_to_cell_centers; + /** + * An rtree object covering the whole mesh. + */ + mutable RTree, unsigned int>> + covering_rtree; + #ifdef DEAL_II_WITH_NANOFLANN /** * A KDTree object constructed with the vertices of the triangulation. diff --git a/include/deal.II/grid/grid_tools_cache_update_flags.h b/include/deal.II/grid/grid_tools_cache_update_flags.h index a119af38ab..9ae073b7d1 100644 --- a/include/deal.II/grid/grid_tools_cache_update_flags.h +++ b/include/deal.II/grid/grid_tools_cache_update_flags.h @@ -73,6 +73,16 @@ namespace GridTools */ update_cell_bounding_boxes_rtree = 0x020, + /** + * Update the covering rtree object, initialized with pairs + * of a bounding box and an unsigned int. The bounding + * boxes are used to describe approximately which portion + * of the mesh contains locally owned cells by the + * process of rank the second element of the pair. + * + */ + update_covering_rtree = 0x040, + /** * Update all objects. */ @@ -94,6 +104,8 @@ namespace GridTools s << "|vertex_to_cell_map"; if (u & update_vertex_to_cell_centers_directions) s << "|vertex_to_cells_centers_directions"; + if (u & update_covering_rtree) + s << "|covering_rtree"; #ifdef DEAL_II_WITH_NANOFLANN if (u & update_vertex_kdtree) s << "|vertex_kdtree"; diff --git a/source/grid/grid_tools_cache.cc b/source/grid/grid_tools_cache.cc index 96219c9996..6c8b6af8a1 100644 --- a/source/grid/grid_tools_cache.cc +++ b/source/grid/grid_tools_cache.cc @@ -13,9 +13,15 @@ // // --------------------------------------------------------------------- +#include +#include + +#include #include #include +#include + DEAL_II_NAMESPACE_OPEN namespace GridTools @@ -146,6 +152,41 @@ namespace GridTools } return vertex_kdtree; } + + + + template + const RTree, unsigned int>> & + Cache::get_covering_rtree() const + { + if (update_flags & update_covering_rtree) + { + // TO DO: the locally owned portion of the domain + // might consists of more separate pieces: a single + // bounding box might not always be the best choice. + IteratorFilters::LocallyOwnedCell locally_owned_cell_predicate; + const BoundingBox bbox = + GridTools::compute_bounding_box(*tria, locally_owned_cell_predicate); + + + std::vector> bbox_v(1, bbox); + if (const auto tria_mpi = + dynamic_cast *>( + &(*tria))) + { + covering_rtree = GridTools::build_global_description_tree( + bbox_v, tria_mpi->get_communicator()); + } + else + { + covering_rtree = + GridTools::build_global_description_tree(bbox_v, MPI_COMM_SELF); + } + update_flags = update_flags & ~update_covering_rtree; + } + + return covering_rtree; + } #endif #include "grid_tools_cache.inst" diff --git a/tests/grid/grid_tools_cache_04.cc b/tests/grid/grid_tools_cache_04.cc new file mode 100644 index 0000000000..42116eca17 --- /dev/null +++ b/tests/grid/grid_tools_cache_04.cc @@ -0,0 +1,120 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2001 - 2019 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.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + +// Validate grid_tools_cache for the creation of build global rtree + + +#include +#include +#include + +#include +#include +#include +#include +#include + +#include +#include +#include + +#include "../tests.h" + +using namespace dealii; + +namespace bg = boost::geometry; +namespace bgi = boost::geometry::index; + + +template +void +test(unsigned int n_points) +{ + deallog << "Testing for dim = " << dim << std::endl; + + // Creating a grid in the square [0,1]x[0,1] + parallel::shared::Triangulation tria(MPI_COMM_WORLD); + GridGenerator::hyper_cube(tria); + tria.refine_global(std::max(8 - dim, 3)); + + + GridTools::Cache cache(tria); + + const auto &global_description = cache.get_covering_rtree(); + + // Creating the random points + std::vector> points; + + for (size_t i = 0; i < n_points; ++i) + points.push_back(random_point()); + + + + const auto cell_qpoint_map = + GridTools::compute_point_locations(cache, points); + const auto & cells = std::get<0>(cell_qpoint_map); + const auto & maps = std::get<2>(cell_qpoint_map); + unsigned int n_cells = cells.size(); + + for (unsigned int c = 0; c < n_cells; ++c) + { + // We know the owner as we're working on a shared triangulation + unsigned int cell_owner = cells[c]->subdomain_id(); + for (unsigned int idx : maps[c]) + { + std::vector, unsigned int>> test_results; + global_description.query(bgi::intersects(points[idx]), + std::back_inserter(test_results)); + bool found = false; + + // Printing and checking function output + for (const auto &ans : test_results) + { + const auto &bd_points = ans.first.get_boundary_points(); + deallog << "Bounding box: p1 " << bd_points.first << " p2 " + << bd_points.second << " rank owner: " << ans.second + << std::endl; + // Check if the guess made from the tree contains the answer + if (ans.second == cell_owner) + found = true; + } + + if (!found) + deallog << "Error point " << points[idx] << " was not found." + << std::endl; + } + } + deallog << "Test for dim " << dim << " finished." << std::endl; +} + + + +int +main(int argc, char **argv) +{ + Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv, 1); +#ifdef DEAL_II_WITH_MPI + MPILogInitAll log; +#else + initlog(); + deallog.push("0"); +#endif + + test<1>(50); + test<2>(80); + test<3>(101); + + return 0; +} diff --git a/tests/grid/grid_tools_cache_04.with_mpi=true.with_p4est=true.mpirun=1.output b/tests/grid/grid_tools_cache_04.with_mpi=true.with_p4est=true.mpirun=1.output new file mode 100644 index 0000000000..2c5df042b4 --- /dev/null +++ b/tests/grid/grid_tools_cache_04.with_mpi=true.with_p4est=true.mpirun=1.output @@ -0,0 +1,238 @@ + +DEAL:0::Testing for dim = 1 +DEAL:0::Bounding box: p1 0.00000 p2 1.00000 rank owner: 0 +DEAL:0::Bounding box: p1 0.00000 p2 1.00000 rank owner: 0 +DEAL:0::Bounding box: p1 0.00000 p2 1.00000 rank owner: 0 +DEAL:0::Bounding box: p1 0.00000 p2 1.00000 rank owner: 0 +DEAL:0::Bounding box: p1 0.00000 p2 1.00000 rank owner: 0 +DEAL:0::Bounding box: p1 0.00000 p2 1.00000 rank owner: 0 +DEAL:0::Bounding box: p1 0.00000 p2 1.00000 rank owner: 0 +DEAL:0::Bounding box: p1 0.00000 p2 1.00000 rank owner: 0 +DEAL:0::Bounding box: p1 0.00000 p2 1.00000 rank owner: 0 +DEAL:0::Bounding box: p1 0.00000 p2 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