File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96842ms, 87.63% of 110516ms total Dropped 1131 nodes (cum <= 552.58ms) flat flat% sum% cum cum% 0 0% 0% 110122ms 99.64% __libc_start_call_main 0 0% 0% 110122ms 99.64% __libc_start_main_impl 0 0% 0% 110122ms 99.64% _start 0 0% 0% 110099ms 99.62% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 110099ms 99.62% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 110099ms 99.62% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 110099ms 99.62% main 0 0% 0% 110056ms 99.58% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 110056ms 99.58% CxxTest::TestRunner::runTest (inline) 0 0% 0% 110056ms 99.58% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 5ms 0.0045% 0.0045% 110048ms 99.58% AbstractCellBasedSimulation::Solve 28ms 0.025% 0.03% 57285ms 51.83% OffLatticeSimulation::UpdateCellLocationsAndTopology 12ms 0.011% 0.041% 53936ms 48.80% ForwardEulerNumericalMethod::UpdateAllNodePositions 165ms 0.15% 0.19% 52448ms 47.46% AbstractNumericalMethod::ComputeForcesIncludingDamping 299ms 0.27% 0.46% 40101ms 36.29% NagaiHondaForce::AddForceContribution 3ms 0.0027% 0.46% 39283ms 35.55% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0018% 0.47% 24069ms 21.78% VertexBasedCellPopulation::Update 2ms 0.0018% 0.47% 23950ms 21.67% MutableVertexMesh::ReMesh 14711ms 13.31% 13.78% 23351ms 21.13% Cylindrical2dVertexMesh::GetVectorFromAtoB 81ms 0.073% 13.85% 18049ms 16.33% Cell::ReadyToDivide 78ms 0.071% 13.92% 16637ms 15.05% AbstractPhaseBasedCellCycleModel::ReadyToDivide 142ms 0.13% 14.05% 14332ms 12.97% SimpleWntCellCycleModel::UpdateCellCyclePhase 328ms 0.3% 14.35% 14221ms 12.87% NagaiHondaForce::GetAdhesionParameter 132ms 0.12% 14.47% 14199ms 12.85% CellPropertyCollection::GetPropertiesType (inline) 454ms 0.41% 14.88% 13718ms 12.41% boost::numeric::ublas::c_vector::c_vector (partial-inline) 281ms 0.25% 15.13% 12278ms 11.11% boost::numeric::ublas::vector_assign (inline) 3535ms 3.20% 18.33% 12106ms 10.95% __dynamic_cast 44ms 0.04% 18.37% 11975ms 10.84% AbstractCellProperty::IsSubType (inline) 146ms 0.13% 18.50% 11887ms 10.76% MutableVertexMesh::CheckForIntersections 85ms 0.077% 18.58% 11733ms 10.62% VertexBasedCellPopulation::GetDampingConstant 83ms 0.075% 18.65% 10964ms 9.92% AbstractTargetAreaModifier::UpdateTargetAreas 44ms 0.04% 18.69% 10851ms 9.82% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 23ms 0.021% 18.71% 10559ms 9.55% AbstractCellBasedSimulation::DoCellBirth 1496ms 1.35% 20.07% 10145ms 9.18% std::__new_allocator::allocate (inline) 399ms 0.36% 20.43% 9649ms 8.73% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 20.43% 9574ms 8.66% std::allocator_traits::allocate (inline) 0 0% 20.43% 9539ms 8.63% std::_Rb_tree::_M_create_node (inline) 2830ms 2.56% 22.99% 9310ms 8.42% boost::numeric::ublas::indexing_vector_assign 1266ms 1.15% 24.14% 8854ms 8.01% std::_Rb_tree::_M_erase 96ms 0.087% 24.22% 8844ms 8.00% Cell::GetMutationState 0 0% 24.22% 8842ms 8.00% std::_Rb_tree::_M_get_node (inline) 14ms 0.013% 24.24% 8786ms 7.95% VertexBasedCellPopulation::GetLocationOfCellCentre 816ms 0.74% 24.97% 8774ms 7.94% VertexMesh::ElementIncludesPoint 784ms 0.71% 25.68% 8731ms 7.90% operator new 0 0% 25.68% 8404ms 7.60% std::_Rb_tree::_Alloc_node::operator() (inline) 464ms 0.42% 26.10% 8208ms 7.43% VertexMesh::GetCentroidOfElement 499ms 0.45% 26.55% 8069ms 7.30% std::map::operator[] (partial-inline) 0 0% 26.55% 7986ms 7.23% std::_Rb_tree::_M_drop_node (inline) 214ms 0.19% 26.75% 7951ms 7.19% std::_Rb_tree::~_Rb_tree (inline) 12ms 0.011% 26.76% 7780ms 7.04% MutableVertexMesh::RemoveDeletedNodesAndElements 2942ms 2.66% 29.42% 7742ms 7.01% __GI___libc_malloc 232ms 0.21% 29.63% 7735ms 7.00% std::__new_allocator::deallocate (inline) 0 0% 29.63% 7729ms 6.99% std::allocator_traits::deallocate (inline) 0 0% 29.63% 7656ms 6.93% std::_Rb_tree::_M_put_node (inline) 1544ms 1.40% 31.03% 7537ms 6.82% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 0 0% 31.03% 7503ms 6.79% std::set::~set (inline) 186ms 0.17% 31.20% 7320ms 6.62% std::_Rb_tree::_Rb_tree (partial-inline) 2415ms 2.19% 33.38% 7275ms 6.58% __GI___libc_free 6907ms 6.25% 39.63% 6907ms 6.25% __strcmp_avx2 29ms 0.026% 39.66% 6885ms 6.23% std::set::set (inline) 773ms 0.7% 40.36% 6873ms 6.22% std::_Rb_tree::_M_copy (inline) 2602ms 2.35% 42.71% 6432ms 5.82% std::_Rb_tree::_M_lower_bound (inline) 139ms 0.13% 42.84% 6424ms 5.81% SimpleWntCellCycleModel::GetWntLevel 153ms 0.14% 42.98% 6209ms 5.62% WntConcentration::GetWntLevel 6169ms 5.58% 48.56% 6169ms 5.58% boost::numeric::ublas::c_vector::operator() 866ms 0.78% 49.34% 5872ms 5.31% std::_Rb_tree::_M_clone_node (inline) 2993ms 2.71% 52.05% 5863ms 5.31% __cxxabiv1::__si_class_type_info::__do_dyncast 25ms 0.023% 52.07% 5457ms 4.94% MutableVertexMesh::RemoveDeletedNodes 1950ms 1.76% 53.84% 5380ms 4.87% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 53.84% 5338ms 4.83% std::_Rb_tree::lower_bound (inline) 0 0% 53.84% 5338ms 4.83% std::map::lower_bound (inline) 40ms 0.036% 53.87% 5280ms 4.78% EdgeHelper::RemoveDeletedEdges 0 0% 53.87% 5199ms 4.70% std::set::insert (inline) 37ms 0.033% 53.91% 4930ms 4.46% EdgeHelper::UpdateEdgesMapKey 4408ms 3.99% 57.89% 4842ms 4.38% _int_free 212ms 0.19% 58.09% 4726ms 4.28% MutableElement::ResetIndex 130ms 0.12% 58.20% 4658ms 4.21% AbstractCellPopulation::GetCellUsingLocationIndex 2ms 0.0018% 58.21% 4639ms 4.20% AbstractCellBasedSimulation::DoCellRemoval (inline) 494ms 0.45% 58.65% 4401ms 3.98% std::_Rb_tree::_M_insert_ (inline) 41ms 0.037% 58.69% 4135ms 3.74% Cell::GetCellProliferativeType 121ms 0.11% 58.80% 4112ms 3.72% std::set_intersection (inline) 225ms 0.2% 59.00% 3991ms 3.61% std::__set_intersection 55ms 0.05% 59.05% 3968ms 3.59% AbstractCellProperty::IsType (inline) 3699ms 3.35% 62.40% 3699ms 3.35% boost::numeric::ublas::same_impl_ex 21ms 0.019% 62.42% 3484ms 3.15% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 33ms 0.03% 62.45% 3294ms 2.98% Cell::SetCellProliferativeType 3187ms 2.88% 65.33% 3187ms 2.88% std::_Rb_tree::_S_right (inline) 2260ms 2.04% 67.38% 3178ms 2.88% _int_malloc 899ms 0.81% 68.19% 3118ms 2.82% AbstractElement::GetNodeLocation 0 0% 68.19% 3062ms 2.77% std::insert_iterator::operator= (inline) 60ms 0.054% 68.25% 3028ms 2.74% std::_Rb_tree::erase 812ms 0.73% 68.98% 2897ms 2.62% AbstractCellProperty::IsSame 31ms 0.028% 69.01% 2895ms 2.62% CellPropertyCollection::HasProperty 0 0% 69.01% 2822ms 2.55% Cell::HasCellProperty (inline) 9ms 0.0081% 69.02% 2670ms 2.42% std::_Rb_tree::_M_insert_unique_ (inline) 196ms 0.18% 69.19% 2650ms 2.40% VertexMesh::GetAreaGradientOfElementAtNode 245ms 0.22% 69.42% 2571ms 2.33% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 69.42% 2559ms 2.32% boost::numeric::ublas::c_vector::operator-= (inline) 17ms 0.015% 69.43% 2546ms 2.30% Cell::GetCellData 0 0% 69.43% 2546ms 2.30% boost::numeric::ublas::c_vector::assign (inline) 648ms 0.59% 70.02% 2540ms 2.30% boost::numeric::ublas::vector_binary::size (inline) 1ms 0.0009% 70.02% 2529ms 2.29% std::_Rb_tree::_M_insert_unique 0 0% 70.02% 2475ms 2.24% AbstractCellPopulation::WriteResultsToFiles 93ms 0.084% 70.10% 2365ms 2.14% VertexMesh::GetVolumeOfElement 5ms 0.0045% 70.11% 2219ms 2.01% AbstractCellPopulation::Iterator::operator++ (inline) 205ms 0.19% 70.29% 2214ms 2.00% AbstractCellPopulation::Iterator::IsRealCell (inline) 42ms 0.038% 70.33% 2207ms 2.00% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 38ms 0.034% 70.36% 2191ms 1.98% std::_Rb_tree::_M_emplace_hint_unique 2ms 0.0018% 70.37% 2123ms 1.92% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 70.37% 2123ms 1.92% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 479ms 0.43% 70.80% 2085ms 1.89% std::type_info::operator== (inline) 2047ms 1.85% 72.65% 2047ms 1.85% std::_Rb_tree_increment 0 0% 72.65% 2019ms 1.83% VertexBasedCellPopulation::WriteVtkResultsToFile 2ms 0.0018% 72.65% 2003ms 1.81% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1305ms 1.18% 73.83% 1972ms 1.78% std::_Rb_tree::equal_range (inline) 70ms 0.063% 73.90% 1814ms 1.64% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 73.90% 1799ms 1.63% VertexMeshWriter::WriteVtkUsingMesh 16ms 0.014% 73.91% 1715ms 1.55% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 20ms 0.018% 73.93% 1580ms 1.43% AbstractCellPopulation::GetLocationIndexUsingCell 26ms 0.024% 73.95% 1577ms 1.43% VertexMesh::GetSurfaceAreaOfElement 73ms 0.066% 74.02% 1527ms 1.38% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 40ms 0.036% 74.06% 1524ms 1.38% Node::RemoveElement 6ms 0.0054% 74.06% 1487ms 1.35% std::set::erase (inline) 0 0% 74.06% 1455ms 1.32% tcache_get (inline) 1455ms 1.32% 75.38% 1455ms 1.32% tcache_get_n (inline) 113ms 0.1% 75.48% 1446ms 1.31% CellPropertyCollection::AddProperty 0 0% 75.48% 1395ms 1.26% boost::numeric::ublas::norm_2 (inline) 581ms 0.53% 76.01% 1379ms 1.25% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1ms 0.0009% 76.01% 1361ms 1.23% OffLatticeSimulation::ApplyBoundaries 64ms 0.058% 76.07% 1338ms 1.21% boost::numeric::ublas::vector_reference::operator() (inline) 57ms 0.052% 76.12% 1334ms 1.21% std::less::operator() (inline) 1296ms 1.17% 77.29% 1296ms 1.17% [libchaste_cell_based.so] 0 0% 77.29% 1283ms 1.16% boost::numeric::ublas::vector_binary::operator() (inline) 1034ms 0.94% 78.22% 1277ms 1.16% std::operator< (inline) 58ms 0.052% 78.28% 1211ms 1.10% std::_Rb_tree::_M_erase_aux (partial-inline) 29ms 0.026% 78.30% 1195ms 1.08% CellPropertyRegistry::Get 22ms 0.02% 78.32% 1147ms 1.04% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 78.32% 1135ms 1.03% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 78.32% 1120ms 1.01% std::_Rb_tree::clear (inline) 1114ms 1.01% 79.33% 1114ms 1.01% std::_Rb_tree_insert_and_rebalance 89ms 0.081% 79.41% 1110ms 1.00% std::_Rb_tree::find (inline) 0 0% 79.41% 1104ms 1% std::map::clear (inline) 3ms 0.0027% 79.41% 1100ms 1% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1077ms 0.97% 80.39% 1077ms 0.97% Node::rGetLocation 0 0% 80.39% 1064ms 0.96% boost::numeric::ublas::c_vector::assign_temporary (inline) 6ms 0.0054% 80.39% 1064ms 0.96% boost::numeric::ublas::c_vector::swap 132ms 0.12% 80.51% 1059ms 0.96% boost::detail::shared_count::~shared_count (inline) 0 0% 80.51% 1059ms 0.96% boost::shared_ptr::~shared_ptr (inline) 73ms 0.066% 80.58% 1058ms 0.96% std::swap_ranges (inline) 17ms 0.015% 80.60% 1015ms 0.92% boost::numeric::ublas::detail::expression_type_check (inline) 200ms 0.18% 80.78% 991ms 0.9% boost::numeric::ublas::detail::equals 0 0% 80.78% 985ms 0.89% std::iter_swap (inline) 985ms 0.89% 81.67% 985ms 0.89% std::swap (inline) 0 0% 81.67% 971ms 0.88% std::map::find (inline) 949ms 0.86% 82.53% 949ms 0.86% std::vector::size (inline) 868ms 0.79% 83.31% 892ms 0.81% boost::detail::sp_counted_base::release 2ms 0.0018% 83.31% 869ms 0.79% VertexMeshWriter::MakeVtkMesh 110ms 0.1% 83.41% 804ms 0.73% boost::numeric::ublas::c_vector::operator= (inline) 414ms 0.37% 83.79% 770ms 0.7% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 83.79% 767ms 0.69% CellPropertyCollection::~CellPropertyCollection (inline) 370ms 0.33% 84.12% 767ms 0.69% Edge::GetMapIndex 766ms 0.69% 84.82% 766ms 0.69% [libchaste_mesh.so] 25ms 0.023% 84.84% 759ms 0.69% Edge::AddElement 227ms 0.21% 85.04% 753ms 0.68% std::__new_allocator::construct (inline) 0 0% 85.04% 753ms 0.68% std::allocator_traits::construct (inline) 12ms 0.011% 85.05% 752ms 0.68% MutableElement::RegisterWithEdges (inline) 0 0% 85.05% 734ms 0.66% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 12ms 0.011% 85.07% 730ms 0.66% AbstractNumericalMethod::DetectStepSizeExceptions 0 0% 85.07% 728ms 0.66% boost::numeric::ublas::norm_inf (inline) 378ms 0.34% 85.41% 728ms 0.66% boost::numeric::ublas::vector_norm_inf::apply (inline) 1ms 0.0009% 85.41% 728ms 0.66% std::_Vector_base::_M_allocate (inline) 130ms 0.12% 85.53% 718ms 0.65% VertexBasedCellPopulation::CheckForStepSizeException 176ms 0.16% 85.69% 708ms 0.64% boost::shared_ptr::shared_ptr (inline) 121ms 0.11% 85.79% 703ms 0.64% MutableElement::GetNodeLocalIndex 0 0% 85.79% 697ms 0.63% std::_Rb_tree::_M_construct_node (inline) 0 0% 85.79% 685ms 0.62% std::_Rb_tree::_Auto_node::_M_insert (inline) 22ms 0.02% 85.81% 685ms 0.62% std::_Rb_tree::_M_insert_node (inline) 657ms 0.59% 86.41% 657ms 0.59% Node::GetIndex 657ms 0.59% 87.00% 657ms 0.59% [libstdc++.so.6.0.33] 0 0% 87.00% 624ms 0.56% vtkPolygon::New 3ms 0.0027% 87.01% 624ms 0.56% vtkPolygon::vtkPolygon 10ms 0.009% 87.02% 611ms 0.55% std::vector::_M_default_append (inline) 29ms 0.026% 87.04% 607ms 0.55% MutableElement::RegisterWithNodes (inline) 32ms 0.029% 87.07% 603ms 0.55% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.07% 603ms 0.55% boost::numeric::ublas::vector::vector (inline) 583ms 0.53% 87.60% 583ms 0.53% boost::shared_ptr::operator-> (inline) 32ms 0.029% 87.63% 574ms 0.52% Node::AddElement