File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 47415ms, 86.54% of 54790ms total Dropped 847 nodes (cum <= 273.95ms) flat flat% sum% cum cum% 0 0% 0% 54735ms 99.90% __libc_start_call_main 0 0% 0% 54735ms 99.90% __libc_start_main_impl 0 0% 0% 54735ms 99.90% _start 0 0% 0% 54720ms 99.87% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 54720ms 99.87% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 54720ms 99.87% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 54720ms 99.87% main 0 0% 0% 54685ms 99.81% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 54685ms 99.81% CxxTest::TestRunner::runTest (inline) 0 0% 0% 54685ms 99.81% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 54424ms 99.33% AbstractCellBasedSimulation::Solve 0 0% 0% 45907ms 83.79% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 45864ms 83.71% MeshBasedCellPopulation::Update 0 0% 0% 25378ms 46.32% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 25378ms 46.32% MeshBasedCellPopulation::TessellateIfNeeded 165ms 0.3% 0.3% 22518ms 41.10% VertexMesh::VertexMesh 0 0% 0.3% 16723ms 30.52% MutableMesh::ReMesh 0 0% 0.3% 12886ms 23.52% tetgen::tetrahedralize 1ms 0.0018% 0.3% 12750ms 23.27% tetgen::tetgenmesh::delaunizevertices 10ms 0.018% 0.32% 12745ms 23.26% tetgen::tetgenmesh::incrflipdelaunay 498ms 0.91% 1.23% 11327ms 20.67% tetgen::tetgenmesh::lawson 614ms 1.12% 2.35% 10960ms 20.00% TetrahedralMesh::EdgeIterator::operator++ 28ms 0.051% 2.40% 9313ms 17.00% std::set::insert (inline) 243ms 0.44% 2.85% 8815ms 16.09% std::_Rb_tree::_M_insert_unique 350ms 0.64% 3.48% 8772ms 16.01% VertexElement::AddFace 3014ms 5.50% 8.99% 8341ms 15.22% std::_Rb_tree::_M_lower_bound (inline) 255ms 0.47% 9.45% 7849ms 14.33% std::_Rb_tree::find (inline) 0 0% 9.45% 7265ms 13.26% std::set::count (inline) 293ms 0.53% 9.99% 5348ms 9.76% std::_Rb_tree::_M_insert_ (inline) 110ms 0.2% 10.19% 5238ms 9.56% std::less::operator() (inline) 5183ms 9.46% 19.65% 5183ms 9.46% std::operator< (inline) 0 0% 19.65% 5006ms 9.14% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 19.65% 4895ms 8.93% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.0037% 19.65% 4867ms 8.88% AbstractNumericalMethod::ComputeForcesIncludingDamping 181ms 0.33% 19.98% 4514ms 8.24% operator new 4278ms 7.81% 27.79% 4278ms 7.81% std::_Rb_tree_increment 1089ms 1.99% 29.78% 4257ms 7.77% __GI___libc_malloc 1ms 0.0018% 29.78% 4113ms 7.51% MeshBasedCellPopulation::UpdateNodePairs 2ms 0.0037% 29.78% 4005ms 7.31% MeshBasedCellPopulation::SpringIterator::operator++ 45ms 0.082% 29.86% 3955ms 7.22% std::__new_allocator::allocate (inline) 6ms 0.011% 29.87% 3933ms 7.18% std::_Rb_tree::~_Rb_tree (inline) 1461ms 2.67% 32.54% 3927ms 7.17% std::_Rb_tree::_M_erase 0 0% 32.54% 3927ms 7.17% std::allocator_traits::allocate (inline) 8ms 0.015% 32.56% 3926ms 7.17% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 0 0% 32.56% 3902ms 7.12% std::set::~set (inline) 1272ms 2.32% 34.88% 3548ms 6.48% std::_Rb_tree::_M_get_insert_unique_pos 1089ms 1.99% 36.86% 3486ms 6.36% __GI___libc_free 113ms 0.21% 37.07% 3394ms 6.19% tetgen::tetgenmesh::insphere_sos 0 0% 37.07% 3347ms 6.11% AbstractCellPopulation::WriteResultsToFiles 2949ms 5.38% 42.45% 3257ms 5.94% tetgen::insphere 0 0% 42.45% 3213ms 5.86% std::_Rb_tree::_M_create_node (inline) 0 0% 42.45% 3187ms 5.82% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 42.45% 3186ms 5.81% std::_Rb_tree::_M_get_node (inline) 1ms 0.0018% 42.45% 3152ms 5.75% std::set_intersection (inline) 226ms 0.41% 42.87% 3151ms 5.75% std::__set_intersection 145ms 0.26% 43.13% 3134ms 5.72% std::__new_allocator::deallocate (inline) 0 0% 43.13% 3111ms 5.68% std::allocator_traits::deallocate (inline) 7ms 0.013% 43.14% 3096ms 5.65% TetrahedralMesh::ImportFromMesher 23ms 0.042% 43.19% 3064ms 5.59% Node::AddElement 2ms 0.0037% 43.19% 2883ms 5.26% VertexMesh::~VertexMesh 2190ms 4.00% 47.19% 2862ms 5.22% _int_malloc 216ms 0.39% 47.58% 2761ms 5.04% tetgen::tetgenmesh::flip23 2670ms 4.87% 52.45% 2670ms 4.87% std::_Rb_tree::_S_right (inline) 171ms 0.31% 52.77% 2489ms 4.54% std::_Rb_tree_const_iterator::operator++ (inline) 1185ms 2.16% 54.93% 2394ms 4.37% _int_free 195ms 0.36% 55.29% 2258ms 4.12% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 4ms 0.0073% 55.29% 2252ms 4.11% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 69ms 0.13% 55.42% 2252ms 4.11% MutableElement::AddNode 151ms 0.28% 55.69% 2162ms 3.95% Node::~Node 4ms 0.0073% 55.70% 2073ms 3.78% std::_Rb_tree_iterator::operator++ (inline) 162ms 0.3% 56.00% 1962ms 3.58% VertexMesh::Clear 1940ms 3.54% 59.54% 1940ms 3.54% std::_Rb_tree_insert_and_rebalance 0 0% 59.54% 1925ms 3.51% std::_Rb_tree::_M_drop_node (inline) 0 0% 59.54% 1916ms 3.50% std::_Rb_tree::_M_put_node (inline) 177ms 0.32% 59.86% 1874ms 3.42% tetgen::tetgenmesh::flip32 2ms 0.0037% 59.86% 1547ms 2.82% Element::Element 1313ms 2.40% 62.26% 1399ms 2.55% tetgen::orient3d 171ms 0.31% 62.57% 1322ms 2.41% tetgen::tetgenmesh::enqueueflipface 181ms 0.33% 62.90% 1268ms 2.31% TetrahedralMesh::Clear 4ms 0.0073% 62.91% 1242ms 2.27% Element::RegisterWithNodes (inline) 14ms 0.026% 62.94% 1209ms 2.21% std::_Vector_base::_M_deallocate (inline) 40ms 0.073% 63.01% 1186ms 2.16% tetgen::tetgenmesh::locate 1176ms 2.15% 65.16% 1176ms 2.15% Node::GetIndex 778ms 1.42% 66.58% 1174ms 2.14% malloc_consolidate 0 0% 66.58% 1113ms 2.03% std::vector::~vector (inline) 91ms 0.17% 66.74% 1097ms 2.00% tetgen::tetgenmesh::preciselocate 0 0% 66.74% 1029ms 1.88% std::_Vector_base::~_Vector_base (inline) 56ms 0.1% 66.84% 1018ms 1.86% std::map::operator[] 6ms 0.011% 66.86% 1009ms 1.84% _int_free_maybe_consolidate 46ms 0.084% 66.94% 978ms 1.78% std::vector::_M_realloc_insert 0 0% 66.94% 905ms 1.65% std::_Rb_tree::lower_bound (inline) 0 0% 66.94% 905ms 1.65% std::map::lower_bound (inline) 1ms 0.0018% 66.94% 867ms 1.58% VoronoiDataWriter::Visit 833ms 1.52% 68.46% 833ms 1.52% tetgen::tetgenmesh::triface::triface 824ms 1.50% 69.97% 824ms 1.50% unlink_chunk 2ms 0.0037% 69.97% 819ms 1.49% VertexMesh::GenerateVerticesFromElementCircumcentres 2ms 0.0037% 69.97% 797ms 1.45% AbstractTwoBodyInteractionForce::AddForceContribution 87ms 0.16% 70.13% 790ms 1.44% std::vector::push_back (inline) 784ms 1.43% 71.56% 784ms 1.43% tetgen::tetgenmesh::triface::operator= 488ms 0.89% 72.45% 780ms 1.42% tetgen::tetgenmesh::fnextself 20ms 0.037% 72.49% 754ms 1.38% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 11ms 0.02% 72.51% 752ms 1.37% std::_Vector_base::_M_allocate (inline) 744ms 1.36% 73.87% 744ms 1.36% tetgen::tetgenmesh::oppo 597ms 1.09% 74.96% 735ms 1.34% AbstractElement::GetNodeGlobalIndex 0 0% 74.96% 724ms 1.32% TetrahedralMesh::RefreshJacobianCachedData 17ms 0.031% 74.99% 674ms 1.23% boost::numeric::ublas::vector_assign (inline) 8ms 0.015% 75.00% 669ms 1.22% AbstractTetrahedralElement::CalculateInverseJacobian 10ms 0.018% 75.02% 656ms 1.20% boost::numeric::ublas::c_vector::c_vector (inline) 615ms 1.12% 76.14% 615ms 1.12% [libchaste_mesh.so] 61ms 0.11% 76.25% 601ms 1.10% __atan2 0 0% 76.25% 581ms 1.06% std::set::find (inline) 10ms 0.018% 76.27% 577ms 1.05% AbstractTetrahedralElement::CalculateJacobian 236ms 0.43% 76.70% 552ms 1.01% AbstractElement::GetNodeLocation 442ms 0.81% 77.51% 540ms 0.99% __ieee754_atan2_fma 38ms 0.069% 77.58% 507ms 0.93% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 77.58% 507ms 0.93% std::insert_iterator::operator= (inline) 54ms 0.099% 77.68% 495ms 0.9% tetgen::tetgenmesh::enextfnext 485ms 0.89% 78.56% 485ms 0.89% Node::rGetLocation 40ms 0.073% 78.64% 484ms 0.88% tetgen::tetgenmesh::enext2fnext 18ms 0.033% 78.67% 482ms 0.88% Element::CalculateCircumsphere 0 0% 78.67% 477ms 0.87% boost::numeric::ublas::inner_prod (inline) 7ms 0.013% 78.68% 472ms 0.86% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 101ms 0.18% 78.87% 466ms 0.85% __dynamic_cast 28ms 0.051% 78.92% 465ms 0.85% boost::numeric::ublas::vector_scalar_binary::evaluate 290ms 0.53% 79.45% 462ms 0.84% tetgen::tetgenmesh::sym 0 0% 79.45% 449ms 0.82% std::_Rb_tree::_M_insert_unique_ (inline) 39ms 0.071% 79.52% 429ms 0.78% AbstractTetrahedralElement::RefreshJacobian 425ms 0.78% 80.29% 425ms 0.78% std::vector::size (inline) 118ms 0.22% 80.51% 405ms 0.74% boost::numeric::ublas::indexing_vector_assign 3ms 0.0055% 80.51% 404ms 0.74% CellPropertyCollection::GetPropertiesType (inline) 6ms 0.011% 80.53% 400ms 0.73% Cell::GetCellId 392ms 0.72% 81.24% 392ms 0.72% boost::numeric::ublas::c_vector::operator() 374ms 0.68% 81.92% 391ms 0.71% AbstractTetrahedralMesh::GetNumAllElements 0 0% 81.92% 390ms 0.71% VertexMeshWriter::WriteVtkUsingMesh 91ms 0.17% 82.09% 386ms 0.7% TetrahedralMesh::EdgeIterator::EdgeIterator 3ms 0.0055% 82.10% 382ms 0.7% boost::numeric::ublas::c_vector::operator= (inline) 215ms 0.39% 82.49% 380ms 0.69% AbstractTetrahedralMesh::GetElement 162ms 0.3% 82.78% 380ms 0.69% boost::numeric::ublas::vector_inner_prod::apply (inline) 16ms 0.029% 82.81% 370ms 0.68% tetgen::tetgenmesh::queue::push 362ms 0.66% 83.47% 362ms 0.66% AbstractElement::IsDeleted 359ms 0.66% 84.13% 359ms 0.66% tetgen::tetgenmesh::org 15ms 0.027% 84.16% 358ms 0.65% VertexMesh::CalculateUnitNormalToFaceWithArea 262ms 0.48% 84.63% 350ms 0.64% tetgen::tetgenmesh::link::add 133ms 0.24% 84.88% 344ms 0.63% Inverse 21ms 0.038% 84.92% 344ms 0.63% std::_Rb_tree_iterator::operator-- (inline) 3ms 0.0055% 84.92% 328ms 0.6% AbstractCellProperty::IsSubType (inline) 230ms 0.42% 85.34% 319ms 0.58% tetgen::tetgenmesh::bond 15ms 0.027% 85.37% 309ms 0.56% VertexElement::~VertexElement 31ms 0.057% 85.42% 308ms 0.56% tetgen::insphereadapt 306ms 0.56% 85.98% 306ms 0.56% std::_Rb_tree_decrement 4ms 0.0073% 85.99% 305ms 0.56% AbstractTetrahedralElement::AbstractTetrahedralElement 56ms 0.1% 86.09% 305ms 0.56% boost::numeric::ublas::vector_reference::operator() (inline) 10ms 0.018% 86.11% 297ms 0.54% std::vector::insert (inline) 164ms 0.3% 86.41% 295ms 0.54% __cxxabiv1::__si_class_type_info::__do_dyncast 61ms 0.11% 86.52% 294ms 0.54% tetgen::tetgenmesh::queue::pop 10ms 0.018% 86.54% 279ms 0.51% MeshBasedCellPopulation::SpringsEnd (inline)