File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 48526ms, 87.08% of 55725ms total Dropped 848 nodes (cum <= 278.62ms) flat flat% sum% cum cum% 0 0% 0% 55646ms 99.86% __libc_start_call_main 0 0% 0% 55646ms 99.86% __libc_start_main_impl 0 0% 0% 55646ms 99.86% _start 0 0% 0% 55630ms 99.83% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 55630ms 99.83% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 55630ms 99.83% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 55630ms 99.83% main 0 0% 0% 55591ms 99.76% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 55591ms 99.76% CxxTest::TestRunner::runTest (inline) 0 0% 0% 55591ms 99.76% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 1ms 0.0018% 0.0018% 55347ms 99.32% AbstractCellBasedSimulation::Solve 0 0% 0.0018% 46578ms 83.59% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.0018% 46537ms 83.51% MeshBasedCellPopulation::Update 0 0% 0.0018% 26259ms 47.12% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0.0018% 26259ms 47.12% MeshBasedCellPopulation::TessellateIfNeeded 194ms 0.35% 0.35% 23269ms 41.76% VertexMesh::VertexMesh 0 0% 0.35% 16527ms 29.66% MutableMesh::ReMesh 0 0% 0.35% 12814ms 23.00% tetgen::tetrahedralize 1ms 0.0018% 0.35% 12671ms 22.74% tetgen::tetgenmesh::delaunizevertices 7ms 0.013% 0.36% 12667ms 22.73% tetgen::tetgenmesh::incrflipdelaunay 557ms 1% 1.36% 11252ms 20.19% tetgen::tetgenmesh::lawson 580ms 1.04% 2.40% 11248ms 20.18% TetrahedralMesh::EdgeIterator::operator++ 34ms 0.061% 2.47% 9351ms 16.78% std::set::insert (inline) 314ms 0.56% 3.03% 8863ms 15.90% VertexElement::AddFace 174ms 0.31% 3.34% 8836ms 15.86% std::_Rb_tree::_M_insert_unique 3038ms 5.45% 8.79% 8680ms 15.58% std::_Rb_tree::_M_lower_bound (inline) 228ms 0.41% 9.20% 8139ms 14.61% std::_Rb_tree::find (inline) 0 0% 9.20% 7544ms 13.54% std::set::count (inline) 121ms 0.22% 9.42% 5505ms 9.88% std::less::operator() (inline) 5443ms 9.77% 19.19% 5443ms 9.77% std::operator< (inline) 248ms 0.45% 19.63% 5271ms 9.46% std::_Rb_tree::_M_insert_ (inline) 1ms 0.0018% 19.63% 5044ms 9.05% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0018% 19.64% 4923ms 8.83% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.0054% 19.64% 4901ms 8.79% AbstractNumericalMethod::ComputeForcesIncludingDamping 4709ms 8.45% 28.09% 4709ms 8.45% std::_Rb_tree_increment 188ms 0.34% 28.43% 4648ms 8.34% operator new 1095ms 1.97% 30.39% 4390ms 7.88% __GI___libc_malloc 0 0% 30.39% 4092ms 7.34% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.0018% 30.40% 4039ms 7.25% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 55ms 0.099% 30.49% 4020ms 7.21% std::__new_allocator::allocate (inline) 0 0% 30.49% 3998ms 7.17% std::allocator_traits::allocate (inline) 14ms 0.025% 30.52% 3954ms 7.10% MeshBasedCellPopulation::SpringIterator::operator++ 8ms 0.014% 30.53% 3903ms 7.00% std::_Rb_tree::~_Rb_tree (inline) 1434ms 2.57% 33.11% 3892ms 6.98% std::_Rb_tree::_M_erase 0 0% 33.11% 3845ms 6.90% std::set::~set (inline) 1264ms 2.27% 35.38% 3719ms 6.67% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 35.38% 3576ms 6.42% AbstractCellPopulation::WriteResultsToFiles 1040ms 1.87% 37.24% 3469ms 6.23% __GI___libc_free 120ms 0.22% 37.46% 3455ms 6.20% tetgen::tetgenmesh::insphere_sos 3ms 0.0054% 37.46% 3446ms 6.18% std::set_intersection (inline) 257ms 0.46% 37.92% 3443ms 6.18% std::__set_intersection 3031ms 5.44% 43.36% 3322ms 5.96% tetgen::insphere 0 0% 43.36% 3238ms 5.81% std::_Rb_tree::_M_create_node (inline) 0 0% 43.36% 3204ms 5.75% std::_Rb_tree::_M_get_node (inline) 0 0% 43.36% 3197ms 5.74% std::_Rb_tree::_Alloc_node::operator() (inline) 24ms 0.043% 43.41% 3159ms 5.67% Node::AddElement 138ms 0.25% 43.65% 3146ms 5.65% std::__new_allocator::deallocate (inline) 0 0% 43.65% 3128ms 5.61% std::allocator_traits::deallocate (inline) 0 0% 43.65% 3003ms 5.39% VertexMesh::~VertexMesh 2193ms 3.94% 47.59% 2955ms 5.30% _int_malloc 2952ms 5.30% 52.89% 2952ms 5.30% std::_Rb_tree::_S_right (inline) 16ms 0.029% 52.92% 2949ms 5.29% TetrahedralMesh::ImportFromMesher 225ms 0.4% 53.32% 2752ms 4.94% tetgen::tetgenmesh::flip23 180ms 0.32% 53.64% 2716ms 4.87% std::_Rb_tree_const_iterator::operator++ (inline) 63ms 0.11% 53.76% 2508ms 4.50% MutableElement::AddNode 205ms 0.37% 54.12% 2475ms 4.44% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 1145ms 2.05% 56.18% 2425ms 4.35% _int_free 5ms 0.009% 56.19% 2423ms 4.35% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 2ms 0.0036% 56.19% 2281ms 4.09% std::_Rb_tree_iterator::operator++ (inline) 144ms 0.26% 56.45% 2117ms 3.80% Node::~Node 158ms 0.28% 56.73% 1980ms 3.55% VertexMesh::Clear 1894ms 3.40% 60.13% 1894ms 3.40% std::_Rb_tree_insert_and_rebalance 0 0% 60.13% 1850ms 3.32% std::_Rb_tree::_M_drop_node (inline) 141ms 0.25% 60.38% 1841ms 3.30% tetgen::tetgenmesh::flip32 0 0% 60.38% 1838ms 3.30% std::_Rb_tree::_M_put_node (inline) 5ms 0.009% 60.39% 1484ms 2.66% Element::Element 1361ms 2.44% 62.84% 1455ms 2.61% tetgen::orient3d 1370ms 2.46% 65.29% 1370ms 2.46% Node::GetIndex 15ms 0.027% 65.32% 1305ms 2.34% std::_Vector_base::_M_deallocate (inline) 810ms 1.45% 66.77% 1259ms 2.26% malloc_consolidate 217ms 0.39% 67.16% 1250ms 2.24% tetgen::tetgenmesh::enqueueflipface 0 0% 67.16% 1225ms 2.20% std::vector::~vector (inline) 34ms 0.061% 67.22% 1208ms 2.17% tetgen::tetgenmesh::locate 168ms 0.3% 67.53% 1160ms 2.08% TetrahedralMesh::Clear 3ms 0.0054% 67.53% 1130ms 2.03% std::_Vector_base::~_Vector_base (inline) 88ms 0.16% 67.69% 1120ms 2.01% tetgen::tetgenmesh::preciselocate 2ms 0.0036% 67.69% 1106ms 1.98% Element::RegisterWithNodes (inline) 7ms 0.013% 67.71% 1096ms 1.97% _int_free_maybe_consolidate 52ms 0.093% 67.80% 1082ms 1.94% std::map::operator[] 59ms 0.11% 67.90% 1031ms 1.85% std::vector::_M_realloc_insert 0 0% 67.90% 947ms 1.70% std::_Rb_tree::lower_bound (inline) 0 0% 67.90% 947ms 1.70% std::map::lower_bound (inline) 942ms 1.69% 69.60% 942ms 1.69% unlink_chunk 0 0% 69.60% 924ms 1.66% VoronoiDataWriter::Visit 2ms 0.0036% 69.60% 885ms 1.59% VertexMesh::GenerateVerticesFromElementCircumcentres 854ms 1.53% 71.13% 854ms 1.53% tetgen::tetgenmesh::triface::triface 466ms 0.84% 71.97% 823ms 1.48% tetgen::tetgenmesh::fnextself 94ms 0.17% 72.14% 818ms 1.47% std::vector::push_back (inline) 8ms 0.014% 72.15% 802ms 1.44% std::_Vector_base::_M_allocate (inline) 0 0% 72.15% 746ms 1.34% TetrahedralMesh::RefreshJacobianCachedData 602ms 1.08% 73.23% 736ms 1.32% AbstractElement::GetNodeGlobalIndex 0 0% 73.23% 694ms 1.25% AbstractTwoBodyInteractionForce::AddForceContribution 672ms 1.21% 74.44% 672ms 1.21% [libchaste_mesh.so] 12ms 0.022% 74.46% 669ms 1.20% boost::numeric::ublas::vector_assign (inline) 11ms 0.02% 74.48% 664ms 1.19% AbstractTetrahedralElement::CalculateJacobian 6ms 0.011% 74.49% 663ms 1.19% AbstractTetrahedralElement::CalculateInverseJacobian 12ms 0.022% 74.51% 656ms 1.18% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 653ms 1.17% 75.68% 653ms 1.17% tetgen::tetgenmesh::oppo 10ms 0.018% 75.70% 624ms 1.12% boost::numeric::ublas::c_vector::c_vector (inline) 624ms 1.12% 76.82% 624ms 1.12% tetgen::tetgenmesh::triface::operator= 227ms 0.41% 77.23% 600ms 1.08% AbstractElement::GetNodeLocation 46ms 0.083% 77.31% 597ms 1.07% __atan2 0 0% 77.31% 592ms 1.06% std::set::find (inline) 465ms 0.83% 78.14% 551ms 0.99% __ieee754_atan2_fma 43ms 0.077% 78.22% 539ms 0.97% tetgen::tetgenmesh::enextfnext 521ms 0.93% 79.16% 521ms 0.93% Node::rGetLocation 0 0% 79.16% 514ms 0.92% std::insert_iterator::operator= (inline) 345ms 0.62% 79.78% 491ms 0.88% tetgen::tetgenmesh::sym 0 0% 79.78% 474ms 0.85% boost::numeric::ublas::inner_prod (inline) 38ms 0.068% 79.84% 474ms 0.85% tetgen::tetgenmesh::enext2fnext 7ms 0.013% 79.86% 473ms 0.85% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 52ms 0.093% 79.95% 470ms 0.84% AbstractTetrahedralElement::RefreshJacobian 12ms 0.022% 79.97% 468ms 0.84% Element::CalculateCircumsphere 32ms 0.057% 80.03% 466ms 0.84% boost::numeric::ublas::vector_scalar_binary::evaluate 459ms 0.82% 80.85% 459ms 0.82% std::vector::size (inline) 0 0% 80.85% 455ms 0.82% std::_Rb_tree::_M_insert_unique_ (inline) 128ms 0.23% 81.08% 444ms 0.8% boost::numeric::ublas::indexing_vector_assign 424ms 0.76% 81.84% 424ms 0.76% AbstractElement::IsDeleted 5ms 0.009% 81.85% 411ms 0.74% boost::numeric::ublas::c_vector::operator= (inline) 3ms 0.0054% 81.86% 410ms 0.74% CellPropertyCollection::GetPropertiesType (inline) 397ms 0.71% 82.57% 397ms 0.71% tetgen::tetgenmesh::org 1ms 0.0018% 82.57% 390ms 0.7% Cell::GetCellId 25ms 0.045% 82.62% 386ms 0.69% std::_Rb_tree_iterator::operator-- (inline) 385ms 0.69% 83.31% 385ms 0.69% boost::numeric::ublas::c_vector::operator() 82ms 0.15% 83.45% 381ms 0.68% __dynamic_cast 21ms 0.038% 83.49% 379ms 0.68% VertexMesh::CalculateUnitNormalToFaceWithArea 0 0% 83.49% 379ms 0.68% VertexMeshWriter::WriteVtkUsingMesh 3ms 0.0054% 83.50% 374ms 0.67% AbstractTetrahedralElement::AbstractTetrahedralElement 204ms 0.37% 83.86% 372ms 0.67% AbstractTetrahedralMesh::GetElement 174ms 0.31% 84.18% 367ms 0.66% boost::numeric::ublas::vector_inner_prod::apply (inline) 247ms 0.44% 84.62% 356ms 0.64% tetgen::tetgenmesh::bond 23ms 0.041% 84.66% 349ms 0.63% tetgen::tetgenmesh::queue::push 341ms 0.61% 85.27% 341ms 0.61% std::_Rb_tree_decrement 10ms 0.018% 85.29% 332ms 0.6% std::vector::insert (inline) 5ms 0.009% 85.30% 328ms 0.59% VertexElement::~VertexElement 3ms 0.0054% 85.30% 326ms 0.59% AbstractCellProperty::IsSubType (inline) 227ms 0.41% 85.71% 325ms 0.58% tetgen::tetgenmesh::link::add 132ms 0.24% 85.95% 317ms 0.57% Inverse 0 0% 85.95% 307ms 0.55% tcache_get (inline) 307ms 0.55% 86.50% 307ms 0.55% tcache_get_n (inline) 43ms 0.077% 86.58% 291ms 0.52% tetgen::insphereadapt 281ms 0.5% 87.08% 281ms 0.5% tetgen::tetgenmesh::pointmark