File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95842ms, 87.95% of 108970ms total Dropped 1124 nodes (cum <= 544.85ms) flat flat% sum% cum cum% 0 0% 0% 108671ms 99.73% __libc_start_call_main 0 0% 0% 108671ms 99.73% __libc_start_main_impl 0 0% 0% 108671ms 99.73% _start 0 0% 0% 108649ms 99.71% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108649ms 99.71% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108649ms 99.71% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108649ms 99.71% main 0 0% 0% 108616ms 99.68% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108616ms 99.68% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108616ms 99.68% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 3ms 0.0028% 0.0028% 108608ms 99.67% AbstractCellBasedSimulation::Solve 14ms 0.013% 0.016% 56760ms 52.09% OffLatticeSimulation::UpdateCellLocationsAndTopology 15ms 0.014% 0.029% 53042ms 48.68% ForwardEulerNumericalMethod::UpdateAllNodePositions 73ms 0.067% 0.096% 51918ms 47.64% AbstractNumericalMethod::ComputeForcesIncludingDamping 420ms 0.39% 0.48% 40537ms 37.20% NagaiHondaForce::AddForceContribution 1ms 0.00092% 0.48% 38025ms 34.89% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00092% 0.48% 22383ms 20.54% VertexBasedCellPopulation::Update 0 0% 0.48% 22250ms 20.42% MutableVertexMesh::ReMesh 9902ms 9.09% 9.57% 18816ms 17.27% Cylindrical2dVertexMesh::GetVectorFromAtoB 106ms 0.097% 9.67% 18539ms 17.01% Cell::ReadyToDivide 21ms 0.019% 9.69% 17455ms 16.02% AbstractPhaseBasedCellCycleModel::ReadyToDivide 131ms 0.12% 9.81% 17021ms 15.62% NagaiHondaForce::GetAdhesionParameter 83ms 0.076% 9.88% 15051ms 13.81% SimpleWntCellCycleModel::UpdateCellCyclePhase 811ms 0.74% 10.63% 14062ms 12.90% std::__new_allocator::allocate (inline) 426ms 0.39% 11.02% 13883ms 12.74% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 11.02% 13485ms 12.37% std::allocator_traits::allocate (inline) 0 0% 11.02% 13198ms 12.11% std::_Rb_tree::_M_create_node (inline) 899ms 0.82% 11.84% 13189ms 12.10% operator new 68ms 0.062% 11.91% 12998ms 11.93% CellPropertyCollection::GetPropertiesType (inline) 0 0% 11.91% 12812ms 11.76% std::_Rb_tree::_M_get_node (inline) 254ms 0.23% 12.14% 12395ms 11.37% boost::numeric::ublas::vector_assign (inline) 4087ms 3.75% 15.89% 11928ms 10.95% __GI___libc_malloc 0 0% 15.89% 11417ms 10.48% std::_Rb_tree::_Alloc_node::operator() (inline) 48ms 0.044% 15.93% 11311ms 10.38% AbstractTargetAreaModifier::UpdateTargetAreas 42ms 0.039% 15.97% 11215ms 10.29% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 113ms 0.1% 16.08% 10970ms 10.07% VertexBasedCellPopulation::GetDampingConstant 10ms 0.0092% 16.09% 10912ms 10.01% AbstractCellBasedSimulation::DoCellBirth 87ms 0.08% 16.16% 10748ms 9.86% AbstractCellProperty::IsSubType (inline) 2832ms 2.60% 18.76% 10686ms 9.81% __dynamic_cast 135ms 0.12% 18.89% 9983ms 9.16% MutableVertexMesh::CheckForIntersections 0 0% 18.89% 9582ms 8.79% std::_Rb_tree::_M_drop_node (inline) 1070ms 0.98% 19.87% 9559ms 8.77% std::_Rb_tree::_M_erase 515ms 0.47% 20.34% 9052ms 8.31% std::map::operator[] (partial-inline) 380ms 0.35% 20.69% 9043ms 8.30% std::_Rb_tree::~_Rb_tree (inline) 2700ms 2.48% 23.17% 9031ms 8.29% boost::numeric::ublas::indexing_vector_assign 56ms 0.051% 23.22% 8760ms 8.04% VertexBasedCellPopulation::GetLocationOfCellCentre 106ms 0.097% 23.32% 8740ms 8.02% std::__new_allocator::deallocate (inline) 0 0% 23.32% 8714ms 8.00% std::allocator_traits::deallocate (inline) 0 0% 23.32% 8644ms 7.93% std::_Rb_tree::_M_put_node (inline) 0 0% 23.32% 8640ms 7.93% std::set::~set (inline) 2262ms 2.08% 25.39% 8479ms 7.78% __GI___libc_free 416ms 0.38% 25.77% 8280ms 7.60% VertexMesh::GetNextEdgeGradientOfElementAtNode 746ms 0.68% 26.46% 8231ms 7.55% VertexMesh::GetCentroidOfElement 0 0% 26.46% 8203ms 7.53% std::set::insert (inline) 12ms 0.011% 26.47% 7978ms 7.32% MutableVertexMesh::RemoveDeletedNodesAndElements 55ms 0.05% 26.52% 7932ms 7.28% Cell::GetMutationState 891ms 0.82% 27.34% 7516ms 6.90% std::_Rb_tree::_M_insert_ (inline) 551ms 0.51% 27.84% 7389ms 6.78% VertexMesh::ElementIncludesPoint 165ms 0.15% 28.00% 7287ms 6.69% std::_Rb_tree::_Rb_tree (partial-inline) 695ms 0.64% 28.63% 6913ms 6.34% std::_Rb_tree::_M_copy (inline) 8ms 0.0073% 28.64% 6772ms 6.21% std::set::set (inline) 6642ms 6.10% 34.74% 6642ms 6.10% boost::numeric::ublas::c_vector::operator() 145ms 0.13% 34.87% 6608ms 6.06% SimpleWntCellCycleModel::GetWntLevel 66ms 0.061% 34.93% 6528ms 5.99% std::set_intersection (inline) 2517ms 2.31% 37.24% 6521ms 5.98% std::_Rb_tree::_M_lower_bound (inline) 1036ms 0.95% 38.19% 6509ms 5.97% AbstractMesh::GetDistanceBetweenNodes 317ms 0.29% 38.48% 6462ms 5.93% std::__set_intersection 130ms 0.12% 38.60% 6330ms 5.81% WntConcentration::GetWntLevel 6223ms 5.71% 44.31% 6223ms 5.71% __strcmp_evex 5326ms 4.89% 49.20% 6151ms 5.64% _int_free 703ms 0.65% 49.84% 6044ms 5.55% std::_Rb_tree::_M_clone_node (inline) 4718ms 4.33% 54.17% 5718ms 5.25% _int_malloc 24ms 0.022% 54.20% 5577ms 5.12% MutableVertexMesh::RemoveDeletedNodes 0 0% 54.20% 5564ms 5.11% std::_Rb_tree::lower_bound (inline) 0 0% 54.20% 5564ms 5.11% std::map::lower_bound (inline) 635ms 0.58% 54.78% 5512ms 5.06% boost::numeric::ublas::c_vector::operator[] (inline) 64ms 0.059% 54.84% 5430ms 4.98% EdgeHelper::RemoveDeletedEdges 22ms 0.02% 54.86% 5162ms 4.74% EdgeHelper::UpdateEdgesMapKey 0 0% 54.86% 5127ms 4.70% std::insert_iterator::operator= (inline) 2375ms 2.18% 57.04% 5018ms 4.60% __cxxabiv1::__si_class_type_info::__do_dyncast 133ms 0.12% 57.16% 4933ms 4.53% MutableElement::ResetIndex 69ms 0.063% 57.22% 4825ms 4.43% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 57.22% 4798ms 4.40% std::_Rb_tree::_M_insert_unique_ (inline) 0 0% 57.22% 4717ms 4.33% AbstractCellBasedSimulation::DoCellRemoval (inline) 29ms 0.027% 57.25% 4656ms 4.27% Cell::GetCellProliferativeType 4432ms 4.07% 61.32% 4432ms 4.07% boost::numeric::ublas::same_impl_ex 47ms 0.043% 61.36% 3650ms 3.35% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 119ms 0.11% 61.47% 3604ms 3.31% Cell::SetCellProliferativeType 155ms 0.14% 61.61% 3541ms 3.25% AbstractCellProperty::IsType (inline) 3435ms 3.15% 64.76% 3435ms 3.15% std::_Rb_tree::_S_right (inline) 2ms 0.0018% 64.76% 3405ms 3.12% std::_Rb_tree::_M_insert_unique 3396ms 3.12% 67.88% 3396ms 3.12% [libchaste_cell_based.so] 799ms 0.73% 68.61% 3200ms 2.94% AbstractElement::GetNodeLocation 141ms 0.13% 68.74% 3043ms 2.79% boost::detail::shared_count::~shared_count (inline) 0 0% 68.74% 3043ms 2.79% boost::shared_ptr::~shared_ptr (inline) 4ms 0.0037% 68.75% 2961ms 2.72% AbstractCellPopulation::Iterator::operator++ (inline) 230ms 0.21% 68.96% 2955ms 2.71% AbstractCellPopulation::Iterator::IsRealCell (inline) 35ms 0.032% 68.99% 2920ms 2.68% std::_Rb_tree::_M_emplace_hint_unique 2842ms 2.61% 71.60% 2859ms 2.62% boost::detail::sp_counted_base::release 69ms 0.063% 71.66% 2833ms 2.60% std::_Rb_tree::erase 159ms 0.15% 71.81% 2629ms 2.41% boost::numeric::ublas::vector_binary::size (inline) 0 0% 71.81% 2574ms 2.36% boost::numeric::ublas::c_vector::assign (inline) 20ms 0.018% 71.83% 2555ms 2.34% Cell::GetCellData 0 0% 71.83% 2480ms 2.28% AbstractCellPopulation::WriteResultsToFiles 41ms 0.038% 71.86% 2474ms 2.27% CellPropertyCollection::HasProperty 0 0% 71.86% 2404ms 2.21% Cell::HasCellProperty (inline) 301ms 0.28% 72.14% 2373ms 2.18% std::_Rb_tree_const_iterator::operator++ (inline) 42ms 0.039% 72.18% 2359ms 2.16% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 72.18% 2275ms 2.09% boost::numeric::ublas::c_vector::operator-= (inline) 42ms 0.039% 72.22% 2252ms 2.07% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2241ms 2.06% 74.27% 2241ms 2.06% [libchaste_mesh.so] 460ms 0.42% 74.70% 2236ms 2.05% AbstractCellProperty::IsSame 270ms 0.25% 74.94% 2174ms 2.00% VertexMesh::GetAreaGradientOfElementAtNode 317ms 0.29% 75.23% 2054ms 1.88% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 75.23% 2041ms 1.87% VertexBasedCellPopulation::WriteVtkResultsToFile 3ms 0.0028% 75.24% 2026ms 1.86% VertexBasedCellPopulation::WriteCellVtkResultsToFile 81ms 0.074% 75.31% 1892ms 1.74% VertexMesh::GetVolumeOfElement 141ms 0.13% 75.44% 1839ms 1.69% CellPropertyCollection::AddProperty 0 0% 75.44% 1831ms 1.68% VertexMeshWriter::WriteVtkUsingMesh 0 0% 75.44% 1781ms 1.63% std::_Rb_tree::_Auto_node::_Auto_node (inline) 205ms 0.19% 75.63% 1776ms 1.63% std::type_info::operator== (inline) 84ms 0.077% 75.71% 1741ms 1.60% AbstractCellPopulation::GetLocationIndexUsingCell 4ms 0.0037% 75.71% 1713ms 1.57% tcache_get (inline) 1709ms 1.57% 77.28% 1709ms 1.57% tcache_get_n (inline) 69ms 0.063% 77.34% 1699ms 1.56% MutableVertexMesh::CheckForSwapsFromShortEdges 75ms 0.069% 77.41% 1643ms 1.51% std::_Rb_tree::_M_erase_aux (partial-inline) 1ms 0.00092% 77.41% 1621ms 1.49% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 77.41% 1621ms 1.49% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 4ms 0.0037% 77.41% 1553ms 1.43% OffLatticeSimulation::ApplyBoundaries 73ms 0.067% 77.48% 1495ms 1.37% VertexMesh::GetSurfaceAreaOfElement 0 0% 77.48% 1486ms 1.36% boost::numeric::ublas::vector_binary::operator() (inline) 1426ms 1.31% 78.79% 1426ms 1.31% std::_Rb_tree_increment 41ms 0.038% 78.83% 1359ms 1.25% Node::RemoveElement 817ms 0.75% 79.58% 1342ms 1.23% std::_Rb_tree::equal_range (inline) 52ms 0.048% 79.63% 1334ms 1.22% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 2ms 0.0018% 79.63% 1320ms 1.21% std::set::erase (inline) 87ms 0.08% 79.71% 1298ms 1.19% boost::numeric::ublas::vector_reference::operator() (inline) 32ms 0.029% 79.74% 1276ms 1.17% Edge::AddElement 12ms 0.011% 79.75% 1274ms 1.17% MutableElement::RegisterWithEdges (inline) 1162ms 1.07% 80.81% 1162ms 1.07% [libstdc++.so.6.0.33] 1139ms 1.05% 81.86% 1139ms 1.05% std::_Rb_tree_insert_and_rebalance 60ms 0.055% 81.91% 1132ms 1.04% CellPropertyRegistry::Get 1119ms 1.03% 82.94% 1119ms 1.03% Node::rGetLocation 0 0% 82.94% 1075ms 0.99% CellPropertyCollection::~CellPropertyCollection (inline) 20ms 0.018% 82.96% 1025ms 0.94% boost::numeric::ublas::detail::expression_type_check (inline) 14ms 0.013% 82.97% 1022ms 0.94% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 89ms 0.082% 83.05% 1004ms 0.92% std::_Rb_tree::find (inline) 0 0% 83.05% 979ms 0.9% boost::numeric::ublas::norm_2 (inline) 521ms 0.48% 83.53% 959ms 0.88% boost::numeric::ublas::vector_norm_2::apply 149ms 0.14% 83.67% 958ms 0.88% boost::numeric::ublas::detail::equals 0 0% 83.67% 939ms 0.86% std::__new_allocator::destroy (inline) 0 0% 83.67% 939ms 0.86% std::allocator_traits::destroy (inline) 0 0% 83.67% 938ms 0.86% std::_Rb_tree::_M_destroy_node (inline) 3ms 0.0028% 83.67% 933ms 0.86% VertexMeshWriter::MakeVtkMesh 927ms 0.85% 84.52% 927ms 0.85% tcache_put (inline) 1ms 0.00092% 84.52% 903ms 0.83% std::_Rb_tree::clear (inline) 0 0% 84.52% 889ms 0.82% boost::numeric::ublas::c_vector::assign_temporary (inline) 6ms 0.0055% 84.53% 889ms 0.82% boost::numeric::ublas::c_vector::swap (inline) 197ms 0.18% 84.71% 883ms 0.81% std::swap_ranges (inline) 0 0% 84.71% 879ms 0.81% std::map::clear (inline) 61ms 0.056% 84.77% 867ms 0.8% std::less::operator() (inline) 682ms 0.63% 85.39% 849ms 0.78% CellPropertyCollection::GetProperty 0 0% 85.39% 837ms 0.77% std::map::find (inline) 45ms 0.041% 85.43% 823ms 0.76% boost::numeric::ublas::c_vector::operator= (inline) 595ms 0.55% 85.98% 806ms 0.74% std::operator< (inline) 382ms 0.35% 86.33% 778ms 0.71% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 86.33% 767ms 0.7% std::_Rb_tree::_Auto_node::_M_insert (inline) 24ms 0.022% 86.35% 767ms 0.7% std::_Rb_tree::_M_insert_node (inline) 721ms 0.66% 87.01% 721ms 0.66% std::vector::size (inline) 0 0% 87.01% 693ms 0.64% vtkPolygon::New 0 0% 87.01% 693ms 0.64% vtkPolygon::vtkPolygon 687ms 0.63% 87.64% 687ms 0.63% std::swap (inline) 0 0% 87.64% 686ms 0.63% std::iter_swap (inline) 1ms 0.00092% 87.64% 668ms 0.61% std::_Vector_base::_M_allocate (inline) 64ms 0.059% 87.70% 661ms 0.61% MutableElement::GetNodeLocalIndex 0 0% 87.70% 645ms 0.59% boost::numeric::ublas::norm_inf (inline) 207ms 0.19% 87.89% 645ms 0.59% boost::numeric::ublas::vector_norm_inf::apply (inline) 5ms 0.0046% 87.90% 607ms 0.56% MutableElement::RegisterWithNodes (inline) 0 0% 87.90% 599ms 0.55% std::map::map (inline) 49ms 0.045% 87.94% 594ms 0.55% Node::AddElement 11ms 0.01% 87.95% 588ms 0.54% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.95% 588ms 0.54% boost::numeric::ublas::vector::vector (inline)