From ad526ef2bc4eb85f3d82a7095d30047af85969e4 Mon Sep 17 00:00:00 2001 From: Matthias Hochsteger Date: Tue, 13 Aug 2019 18:47:35 +0200 Subject: [PATCH] Parallelize CombineImprove --- libsrc/meshing/improve3.cpp | 322 +++++++++++++++++++++++++++++++++- libsrc/meshing/improve3.hpp | 8 + libsrc/meshing/meshclass.cpp | 13 +- libsrc/meshing/smoothing3.cpp | 37 ++-- 4 files changed, 362 insertions(+), 18 deletions(-) diff --git a/libsrc/meshing/improve3.cpp b/libsrc/meshing/improve3.cpp index b8cba78f..4e354f05 100644 --- a/libsrc/meshing/improve3.cpp +++ b/libsrc/meshing/improve3.cpp @@ -1,4 +1,8 @@ #include +#include + +#include +#include #include "meshing.hpp" @@ -10,6 +14,20 @@ namespace netgen { + +// Calc badness of new element where pi1 and pi2 are replaced by pnew +double CalcBadReplacePoints (const Mesh::T_POINTS & points, const MeshingParameters & mp, const Element & elem, double h, PointIndex &pi1, PointIndex &pi2, MeshPoint &pnew) + { + if (elem.GetType() != TET) return 0; + + MeshPoint* p[] = {&points[elem[0]], &points[elem[1]], &points[elem[2]], &points[elem[3]]}; + + for (auto i : Range(4)) + if(elem[i]==pi1 || elem[i]==pi2) p[i] = &pnew; + + return CalcTetBadness (*p[0], *p[1], *p[2], *p[3], h, mp); + } + /* Combine two points to one. Set new point into the center, if both are @@ -17,9 +35,138 @@ namespace netgen Connect inner point to boundary point, if one point is inner point. */ +double MeshOptimize3d :: CombineImproveEdge (Mesh & mesh, + const MeshingParameters & mp, + TABLE & elements_of_point, + Array & elerrs, + PointIndex pi0, PointIndex pi1, + FlatArray is_point_removed, + bool check_only) +{ + if (pi1 < pi0) Swap (pi0, pi1); + if(is_point_removed[pi0] || is_point_removed[pi1]) return false; + MeshPoint p0 = mesh[pi0]; + MeshPoint p1 = mesh[pi1]; -void MeshOptimize3d :: CombineImprove (Mesh & mesh, + if (p1.Type() != INNERPOINT) + return false; + + ArrayMem has_one_point; + ArrayMem has_both_points; + + for (auto ei : elements_of_point[pi0] ) + { + Element & elem = mesh[ei]; + if (elem.IsDeleted()) continue; + + if (elem[0] == pi1 || elem[1] == pi1 || elem[2] == pi1 || elem[3] == pi1) + { + if(!has_both_points.Contains(ei)) + has_both_points.Append (ei); + } + else + { + if(!has_one_point.Contains(ei)) + has_one_point.Append (ei); + } + } + + for (auto ei : elements_of_point[pi1] ) + { + Element & elem = mesh[ei]; + if (elem.IsDeleted()) continue; + + if (elem[0] == pi0 || elem[1] == pi0 || elem[2] == pi0 || elem[3] == pi0) + { + ; + } + else + { + if(!has_one_point.Contains(ei)) + has_one_point.Append (ei); + } + } + + double badness_old = 0.0; + for (auto ei : has_one_point) + badness_old += elerrs[ei]; + for (auto ei : has_both_points) + badness_old += elerrs[ei]; + + MeshPoint pnew = p0; + if (p0.Type() == INNERPOINT) + pnew = Center (p0, p1); + + ArrayMem one_point_badness(has_one_point.Size()); + + double badness_new = 0; + for (auto i : Range(has_one_point)) + { + const Element & elem = mesh[has_one_point[i]]; + double badness = CalcBadReplacePoints (mesh.Points(), mp, elem, 0, pi0, pi1, pnew); + badness_new += badness; + one_point_badness[i] = badness; + } + + // Check if changed tets are topologically legal + if (p0.Type() != INNERPOINT) + { + for (auto ei : has_one_point) + { + Element elem = mesh[ei]; + int l; + for (int l = 0; l < 4; l++) + if (elem[l] == pi1) + { + elem[l] = pi0; + break; + } + + elem.flags.illegal_valid = 0; + if (!mesh.LegalTet(elem)) + badness_new += 1e4; + } + } + + double d_badness = badness_new / has_one_point.Size() - badness_old / (has_one_point.Size()+has_both_points.Size()); + + // Do the actual combine operation + if (d_badness < 0.0 && !check_only) + { + is_point_removed[pi1] = true; + mesh[pi0] = pnew; + + for (auto ei : elements_of_point[pi1]) + { + Element & elem = mesh[ei]; + if (elem.IsDeleted()) continue; + + if(elements_of_point[pi0].Pos(ei)==-1) + elements_of_point.Add (pi0, ei); // todo: only add if not already in there! + for (int l = 0; l < elem.GetNP(); l++) + if (elem[l] == pi1) + elem[l] = pi0; + + elem.flags.illegal_valid = 0; + if (!mesh.LegalTet (elem)) + (*testout) << "illegal tet " << ei << endl; + } + + for (auto i : Range(has_one_point)) + elerrs[has_one_point[i]] = one_point_badness[i]; + + for (auto ei : has_both_points) + { + mesh[ei].flags.illegal_valid = 0; + mesh[ei].Delete(); + } + } + + return d_badness; +} + +void MeshOptimize3d :: CombineImproveSequential (Mesh & mesh, OPTIMIZEGOAL goal) { static Timer t("MeshOptimize3d::CombineImprove"); RegionTimer reg(t); @@ -264,6 +411,179 @@ void MeshOptimize3d :: CombineImprove (Mesh & mesh, multithread.task = savetask; } +void MeshOptimize3d :: CombineImprove (Mesh & mesh, + OPTIMIZEGOAL goal) +{ + static Timer t("MeshOptimize3d::CombineImprove"); RegionTimer reg(t); + static Timer topt("Optimize"); + static Timer tsearch("Search"); + static Timer tbuild_edges("Build edges"); + static Timer tbuild_elements_table("Build elements table"); + static Timer tbad("CalcBad"); + + // return CombineImproveSequential(mesh, goal); + + int np = mesh.GetNP(); + int ne = mesh.GetNE(); + int ntasks = 4*ngcore::TaskManager::GetNumThreads(); + + Array elerrs (ne); + Array is_point_removed (np); + is_point_removed = false; + + PrintMessage (3, "CombineImprove"); + (*testout) << "Start CombineImprove" << "\n"; + + // mesh.CalcSurfacesOfNode (); + const char * savetask = multithread.task; + multithread.task = "Combine Improve"; + + + tbad.Start(); + double totalbad = 0.0; + ParallelForRange(Range(ne), [&] (auto myrange) + { + double totalbad_local = 0.0; + for (ElementIndex ei : myrange) + { + if(mesh.GetDimension()==3 && mp.only3D_domain_nr && mp.only3D_domain_nr != mesh[ei].GetIndex()) + continue; + double elerr = CalcBad (mesh.Points(), mesh[ei], 0); + totalbad_local += elerr; + elerrs[ei] = elerr; + } + AtomicAdd(totalbad, totalbad_local); + }, ntasks); + tbad.Stop(); + + if (goal == OPT_QUALITY) + { + totalbad = CalcTotalBad (mesh.Points(), mesh.VolumeElements()); + (*testout) << "Total badness = " << totalbad << endl; + } + + // TODO: Build table in parallel (using TableCreator) + tbuild_elements_table.Start(); + TABLE elementsonnode(np); + for (ElementIndex ei = 0; ei < ne; ei++) + if (!mesh[ei].IsDeleted()) + for (int j = 0; j < mesh[ei].GetNP(); j++) + elementsonnode.Add (mesh[ei][j], ei); + + tbuild_elements_table.Stop(); + + // Build list of all edges + Array> edges; + Array>> thread_edges(ngcore::TaskManager::GetMaxThreads()); + + static constexpr int tetedges[6][2] = + { { 0, 1 }, { 0, 2 }, { 0, 3 }, + { 1, 2 }, { 1, 3 }, { 2, 3 } }; + + tbuild_edges.Start(); + ParallelForRange(mesh.Points().Range(), [&] (auto myrange) + { + ArrayMem, 100> local_edges; + for (auto pi : myrange) + { + local_edges.SetSize(0); + + for(auto ei : elementsonnode[pi]) + { + Element & elem = mesh[ei]; + if (elem.IsDeleted()) continue; + + for (int j = 0; j < 6; j++) + { + PointIndex pi0 = elem[tetedges[j][0]]; + PointIndex pi1 = elem[tetedges[j][1]]; + if (pi1 < pi0) Swap(pi0, pi1); + if(pi0==pi) + local_edges.Append(std::make_tuple(pi0, pi1)); + } + } + QuickSort(local_edges); + + auto edge_prev = std::make_tuple(-1,-1); + + for(auto edge : local_edges) + if(edge != edge_prev) + { + // TODO: Check for CombineEdge improvement already here and only append edges with improvement + thread_edges[ngcore::TaskManager::GetThreadId()].Append(edge); + edge_prev = edge; + } + } + }, ntasks); + + int num_edges = 0; + for (auto & edg : thread_edges) + num_edges += edg.Size(); + edges.SetAllocSize(num_edges); + for (auto & edg : thread_edges) + edges.Append(edg); + + tbuild_edges.Stop(); + + // Find edges with improvement + Array> combine_candidate_edges(edges.Size()); + std::atomic improvement_counter(0); + + tsearch.Start(); + ParallelForRange(Range(edges), [&] (auto myrange) + { + for(auto i : myrange) + { + auto [p0,p1] = edges[i]; + double d_badness = CombineImproveEdge (mesh, mp, elementsonnode, elerrs, p0, p1, is_point_removed, true); + if(d_badness<0.0) + { + int index = improvement_counter++; + combine_candidate_edges[index] = make_tuple(d_badness, i); + } + } + }, ntasks); + tsearch.Stop(); + + auto edges_with_improvement = combine_candidate_edges.Part(0, improvement_counter.load()); + + QuickSort(edges_with_improvement); + PrintMessage(5, edges.Size(), " edges"); + PrintMessage(5, edges_with_improvement.Size(), " edges with improvement"); + + // Apply actual optimizations + topt.Start(); + int cnt = 0; + for(auto [d_badness, ei] : edges_with_improvement) + { + auto [p0,p1] = edges[ei]; + if (CombineImproveEdge (mesh, mp, elementsonnode, elerrs, p0, p1, is_point_removed, false) < 0.0) + cnt++; + } + topt.Stop(); + + mesh.Compress(); + mesh.MarkIllegalElements(); + + PrintMessage (5, cnt, " elements combined"); + (*testout) << "CombineImprove done" << "\n"; + + if (goal == OPT_QUALITY) + { + totalbad = CalcTotalBad (mesh.Points(), mesh.VolumeElements()); + (*testout) << "Total badness = " << totalbad << endl; + + int cntill = 0; + for (ElementIndex ei = 0; ei < ne; ei++) + if(!(mesh.GetDimension()==3 && mp.only3D_domain_nr && mp.only3D_domain_nr != mesh.VolumeElement(ei).GetIndex())) + if (!mesh.LegalTet (mesh[ei])) + cntill++; + + PrintMessage (5, cntill, " illegal tets"); + } + multithread.task = savetask; +} + diff --git a/libsrc/meshing/improve3.hpp b/libsrc/meshing/improve3.hpp index c3baf251..35ab2ae2 100644 --- a/libsrc/meshing/improve3.hpp +++ b/libsrc/meshing/improve3.hpp @@ -13,7 +13,15 @@ class MeshOptimize3d const MeshingParameters & mp; public: MeshOptimize3d (const MeshingParameters & amp) : mp(amp) { ; } + + double CombineImproveEdge (Mesh & mesh, const MeshingParameters & mp, + TABLE & elements_of_point, + Array & elerrs, PointIndex pi0, PointIndex pi1, + FlatArray is_point_removed, bool check_only=false); + void CombineImprove (Mesh & mesh, OPTIMIZEGOAL goal = OPT_QUALITY); + void CombineImproveSequential (Mesh & mesh, OPTIMIZEGOAL goal = OPT_QUALITY); + void SplitImprove (Mesh & mesh, OPTIMIZEGOAL goal = OPT_QUALITY); void SwapImprove (Mesh & mesh, OPTIMIZEGOAL goal = OPT_QUALITY, const BitArray * working_elements = NULL); diff --git a/libsrc/meshing/meshclass.cpp b/libsrc/meshing/meshclass.cpp index 5ae25122..0e5545dc 100644 --- a/libsrc/meshing/meshclass.cpp +++ b/libsrc/meshing/meshclass.cpp @@ -5759,10 +5759,15 @@ namespace netgen int Mesh :: MarkIllegalElements () { - int cnt = 0; - for (auto & el : VolumeElements()) - if (!LegalTet (el)) - cnt++; + atomic cnt = 0; + ParallelForRange( Range(volelements), [&] (auto myrange) + { + int cnt_local = 0; + for(auto & el : volelements.Range(myrange)) + if (!LegalTet (el)) + cnt_local++; + cnt += cnt_local; + }); return cnt; } diff --git a/libsrc/meshing/smoothing3.cpp b/libsrc/meshing/smoothing3.cpp index cb34b10c..e6e2ab2d 100644 --- a/libsrc/meshing/smoothing3.cpp +++ b/libsrc/meshing/smoothing3.cpp @@ -924,27 +924,38 @@ double CalcTotalBad (const Mesh::T_POINTS & points, const MeshingParameters & mp) { static Timer t("CalcTotalBad"); RegionTimer reg(t); + static constexpr int n_classes = 20; double sum = 0; - double elbad; - tets_in_qualclass.SetSize(20); + tets_in_qualclass.SetSize(n_classes); tets_in_qualclass = 0; - double teterrpow = mp.opterrpow; + ParallelForRange( IntRange(elements.Size()), [&] (auto myrange) { + double local_sum = 0.0; + double teterrpow = mp.opterrpow; - for (int i = 0; i < elements.Size(); i++) - { - elbad = pow (max2(CalcBad (points, elements[i], 0, mp),1e-10), - 1/teterrpow); + std::array classes_local{}; - int qualclass = int (20 / elbad + 1); - if (qualclass < 1) qualclass = 1; - if (qualclass > 20) qualclass = 20; - tets_in_qualclass.Elem(qualclass)++; + for (auto i : myrange) + { + double elbad = pow (max2(CalcBad (points, elements[i], 0, mp),1e-10), + 1/teterrpow); + + int qualclass = int (n_classes / elbad + 1); + if (qualclass < 1) qualclass = 1; + if (qualclass > n_classes) qualclass = n_classes; + classes_local[qualclass-1]++; + + local_sum += elbad; + } + + AtomicAdd(sum, local_sum); + + for (auto i : Range(n_classes)) + AsAtomic(tets_in_qualclass[i]) += classes_local[i]; + }); - sum += elbad; - } return sum; }