File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 80390ms, 88.45% of 90891ms total Dropped 1012 nodes (cum <= 454.45ms) flat flat% sum% cum cum% 0 0% 0% 90619ms 99.70% __libc_start_call_main 0 0% 0% 90619ms 99.70% __libc_start_main_impl 0 0% 0% 90619ms 99.70% _start 0 0% 0% 90601ms 99.68% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 90601ms 99.68% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 90601ms 99.68% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 90601ms 99.68% main 0 0% 0% 90571ms 99.65% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 90571ms 99.65% CxxTest::TestRunner::runTest (inline) 0 0% 0% 90571ms 99.65% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 1ms 0.0011% 0.0011% 90564ms 99.64% AbstractCellBasedSimulation::Solve 5ms 0.0055% 0.0066% 48055ms 52.87% OffLatticeSimulation::UpdateCellLocationsAndTopology 8ms 0.0088% 0.015% 44911ms 49.41% ForwardEulerNumericalMethod::UpdateAllNodePositions 54ms 0.059% 0.075% 43936ms 48.34% AbstractNumericalMethod::ComputeForcesIncludingDamping 345ms 0.38% 0.45% 34149ms 37.57% NagaiHondaForce::AddForceContribution 1ms 0.0011% 0.46% 31513ms 34.67% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0011% 0.46% 18797ms 20.68% VertexBasedCellPopulation::Update 1ms 0.0011% 0.46% 18701ms 20.58% MutableVertexMesh::ReMesh 7904ms 8.70% 9.15% 15174ms 16.69% Cylindrical2dVertexMesh::GetVectorFromAtoB 96ms 0.11% 9.26% 15023ms 16.53% Cell::ReadyToDivide 74ms 0.081% 9.34% 14130ms 15.55% NagaiHondaForce::GetAdhesionParameter 24ms 0.026% 9.37% 14035ms 15.44% AbstractPhaseBasedCellCycleModel::ReadyToDivide 78ms 0.086% 9.45% 11954ms 13.15% SimpleWntCellCycleModel::UpdateCellCyclePhase 634ms 0.7% 10.15% 11847ms 13.03% std::__new_allocator::allocate (inline) 346ms 0.38% 10.53% 11633ms 12.80% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 10.53% 11421ms 12.57% std::allocator_traits::allocate (inline) 0 0% 10.53% 11170ms 12.29% std::_Rb_tree::_M_create_node (inline) 66ms 0.073% 10.60% 11161ms 12.28% CellPropertyCollection::GetPropertiesType (inline) 820ms 0.9% 11.51% 11094ms 12.21% operator new 0 0% 11.51% 10842ms 11.93% std::_Rb_tree::_M_get_node (inline) 267ms 0.29% 11.80% 10433ms 11.48% boost::numeric::ublas::vector_assign (inline) 3451ms 3.80% 15.60% 9986ms 10.99% __GI___libc_malloc 0 0% 15.60% 9570ms 10.53% std::_Rb_tree::_Alloc_node::operator() (inline) 81ms 0.089% 15.69% 9463ms 10.41% VertexBasedCellPopulation::GetDampingConstant 78ms 0.086% 15.77% 9174ms 10.09% AbstractCellProperty::IsSubType (inline) 2346ms 2.58% 18.35% 9096ms 10.01% __dynamic_cast 60ms 0.066% 18.42% 9034ms 9.94% AbstractTargetAreaModifier::UpdateTargetAreas 14ms 0.015% 18.43% 8955ms 9.85% AbstractCellBasedSimulation::DoCellBirth 37ms 0.041% 18.47% 8944ms 9.84% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 92ms 0.1% 18.58% 8251ms 9.08% MutableVertexMesh::CheckForIntersections 917ms 1.01% 19.58% 7915ms 8.71% std::_Rb_tree::_M_erase 0 0% 19.58% 7872ms 8.66% std::_Rb_tree::_M_drop_node (inline) 421ms 0.46% 20.05% 7691ms 8.46% std::map::operator[] (partial-inline) 2128ms 2.34% 22.39% 7559ms 8.32% boost::numeric::ublas::indexing_vector_assign 288ms 0.32% 22.71% 7469ms 8.22% std::_Rb_tree::~_Rb_tree (inline) 86ms 0.095% 22.80% 7139ms 7.85% std::__new_allocator::deallocate (inline) 0 0% 22.80% 7119ms 7.83% std::allocator_traits::deallocate (inline) 0 0% 22.80% 7109ms 7.82% std::set::~set (inline) 49ms 0.054% 22.85% 7078ms 7.79% Cell::GetMutationState 0 0% 22.85% 7064ms 7.77% std::_Rb_tree::_M_put_node (inline) 0 0% 22.85% 6882ms 7.57% std::set::insert (inline) 2013ms 2.21% 25.07% 6864ms 7.55% __GI___libc_free 7ms 0.0077% 25.08% 6752ms 7.43% MutableVertexMesh::RemoveDeletedNodesAndElements 47ms 0.052% 25.13% 6718ms 7.39% VertexBasedCellPopulation::GetLocationOfCellCentre 369ms 0.41% 25.53% 6699ms 7.37% VertexMesh::GetNextEdgeGradientOfElementAtNode 822ms 0.9% 26.44% 6340ms 6.98% std::_Rb_tree::_M_insert_ (inline) 539ms 0.59% 27.03% 6281ms 6.91% VertexMesh::GetCentroidOfElement 107ms 0.12% 27.15% 6082ms 6.69% std::_Rb_tree::_Rb_tree (partial-inline) 443ms 0.49% 27.64% 6077ms 6.69% VertexMesh::ElementIncludesPoint 565ms 0.62% 28.26% 5812ms 6.39% std::_Rb_tree::_M_copy (inline) 4ms 0.0044% 28.26% 5696ms 6.27% std::set::set (inline) 59ms 0.065% 28.33% 5553ms 6.11% std::set_intersection (inline) 5510ms 6.06% 34.39% 5510ms 6.06% boost::numeric::ublas::c_vector::operator() 211ms 0.23% 34.62% 5494ms 6.04% std::__set_intersection 2018ms 2.22% 36.84% 5365ms 5.90% std::_Rb_tree::_M_lower_bound (inline) 888ms 0.98% 37.82% 5294ms 5.82% AbstractMesh::GetDistanceBetweenNodes 5262ms 5.79% 43.61% 5262ms 5.79% __strcmp_evex 662ms 0.73% 44.34% 5107ms 5.62% std::_Rb_tree::_M_clone_node (inline) 137ms 0.15% 44.49% 5099ms 5.61% SimpleWntCellCycleModel::GetWntLevel 24ms 0.026% 44.51% 4905ms 5.40% MutableVertexMesh::RemoveDeletedNodes 117ms 0.13% 44.64% 4840ms 5.33% WntConcentration::GetWntLevel 4203ms 4.62% 49.27% 4810ms 5.29% _int_free 3954ms 4.35% 53.62% 4808ms 5.29% _int_malloc 55ms 0.061% 53.68% 4785ms 5.26% EdgeHelper::RemoveDeletedEdges 0 0% 53.68% 4625ms 5.09% std::_Rb_tree::lower_bound (inline) 0 0% 53.68% 4625ms 5.09% std::map::lower_bound (inline) 15ms 0.017% 53.70% 4566ms 5.02% EdgeHelper::UpdateEdgesMapKey 0 0% 53.70% 4484ms 4.93% std::insert_iterator::operator= (inline) 503ms 0.55% 54.25% 4466ms 4.91% boost::numeric::ublas::c_vector::operator[] (inline) 2141ms 2.36% 56.60% 4410ms 4.85% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 56.60% 4214ms 4.64% std::_Rb_tree::_M_insert_unique_ (inline) 94ms 0.1% 56.71% 4009ms 4.41% MutableElement::ResetIndex 51ms 0.056% 56.76% 4005ms 4.41% AbstractCellPopulation::GetCellUsingLocationIndex 1ms 0.0011% 56.76% 3752ms 4.13% AbstractCellBasedSimulation::DoCellRemoval (inline) 27ms 0.03% 56.79% 3751ms 4.13% Cell::GetCellProliferativeType 3685ms 4.05% 60.85% 3685ms 4.05% boost::numeric::ublas::same_impl_ex 2946ms 3.24% 64.09% 2946ms 3.24% [libchaste_cell_based.so] 152ms 0.17% 64.26% 2945ms 3.24% AbstractCellProperty::IsType (inline) 35ms 0.039% 64.30% 2889ms 3.18% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 2863ms 3.15% 67.45% 2863ms 3.15% std::_Rb_tree::_S_right (inline) 81ms 0.089% 67.53% 2733ms 3.01% Cell::SetCellProliferativeType 0 0% 67.53% 2668ms 2.94% std::_Rb_tree::_M_insert_unique 109ms 0.12% 67.65% 2633ms 2.90% boost::detail::shared_count::~shared_count (inline) 0 0% 67.65% 2633ms 2.90% boost::shared_ptr::~shared_ptr (inline) 27ms 0.03% 67.68% 2597ms 2.86% std::_Rb_tree::_M_emplace_hint_unique 663ms 0.73% 68.41% 2573ms 2.83% AbstractElement::GetNodeLocation 2461ms 2.71% 71.12% 2467ms 2.71% boost::detail::sp_counted_base::release 197ms 0.22% 71.34% 2462ms 2.71% AbstractCellPopulation::Iterator::IsRealCell (inline) 5ms 0.0055% 71.34% 2462ms 2.71% AbstractCellPopulation::Iterator::operator++ (inline) 55ms 0.061% 71.40% 2357ms 2.59% std::_Rb_tree::erase 0 0% 71.40% 2187ms 2.41% boost::numeric::ublas::c_vector::assign (inline) 116ms 0.13% 71.53% 2158ms 2.37% boost::numeric::ublas::vector_binary::size (inline) 16ms 0.018% 71.55% 2157ms 2.37% Cell::GetCellData 59ms 0.065% 71.61% 2039ms 2.24% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 249ms 0.27% 71.89% 2037ms 2.24% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 71.89% 2010ms 2.21% boost::numeric::ublas::c_vector::operator-= (inline) 42ms 0.046% 71.93% 1998ms 2.20% CellPropertyCollection::HasProperty 1979ms 2.18% 74.11% 1979ms 2.18% [libchaste_mesh.so] 0 0% 74.11% 1951ms 2.15% Cell::HasCellProperty (inline) 0 0% 74.11% 1934ms 2.13% AbstractCellPopulation::WriteResultsToFiles 190ms 0.21% 74.32% 1875ms 2.06% VertexMesh::GetAreaGradientOfElementAtNode 20ms 0.022% 74.34% 1874ms 2.06% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 378ms 0.42% 74.76% 1827ms 2.01% AbstractCellProperty::IsSame 292ms 0.32% 75.08% 1705ms 1.88% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 75.08% 1600ms 1.76% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 75.08% 1597ms 1.76% VertexBasedCellPopulation::WriteVtkResultsToFile 2ms 0.0022% 75.08% 1587ms 1.75% VertexBasedCellPopulation::WriteCellVtkResultsToFile 81ms 0.089% 75.17% 1533ms 1.69% VertexMesh::GetVolumeOfElement 53ms 0.058% 75.23% 1485ms 1.63% MutableVertexMesh::CheckForSwapsFromShortEdges 102ms 0.11% 75.34% 1481ms 1.63% CellPropertyCollection::AddProperty 154ms 0.17% 75.51% 1449ms 1.59% std::type_info::operator== (inline) 0 0% 75.51% 1435ms 1.58% VertexMeshWriter::WriteVtkUsingMesh 2ms 0.0022% 75.51% 1431ms 1.57% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 75.51% 1431ms 1.57% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 75ms 0.083% 75.60% 1417ms 1.56% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 75.60% 1371ms 1.51% boost::numeric::ublas::vector_binary::operator() (inline) 1ms 0.0011% 75.60% 1371ms 1.51% tcache_get (inline) 1370ms 1.51% 77.10% 1370ms 1.51% tcache_get_n (inline) 4ms 0.0044% 77.11% 1333ms 1.47% OffLatticeSimulation::ApplyBoundaries 62ms 0.068% 77.18% 1304ms 1.43% std::_Rb_tree::_M_erase_aux (partial-inline) 69ms 0.076% 77.25% 1292ms 1.42% VertexMesh::GetSurfaceAreaOfElement 1232ms 1.36% 78.61% 1232ms 1.36% std::_Rb_tree_increment 49ms 0.054% 78.66% 1170ms 1.29% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 731ms 0.8% 79.47% 1160ms 1.28% std::_Rb_tree::equal_range (inline) 124ms 0.14% 79.60% 1142ms 1.26% boost::numeric::ublas::vector_reference::operator() (inline) 35ms 0.039% 79.64% 1135ms 1.25% Node::RemoveElement 2ms 0.0022% 79.64% 1102ms 1.21% std::set::erase (inline) 51ms 0.056% 79.70% 995ms 1.09% CellPropertyRegistry::Get 15ms 0.017% 79.72% 957ms 1.05% MutableElement::RegisterWithEdges (inline) 39ms 0.043% 79.76% 949ms 1.04% Edge::AddElement 0 0% 79.76% 925ms 1.02% CellPropertyCollection::~CellPropertyCollection (inline) 924ms 1.02% 80.78% 924ms 1.02% [libstdc++.so.6.0.33] 922ms 1.01% 81.79% 922ms 1.01% std::_Rb_tree_insert_and_rebalance 18ms 0.02% 81.81% 906ms 1% boost::numeric::ublas::detail::expression_type_check (inline) 166ms 0.18% 81.99% 849ms 0.93% boost::numeric::ublas::detail::equals 0 0% 81.99% 849ms 0.93% boost::numeric::ublas::norm_2 (inline) 8ms 0.0088% 82.00% 827ms 0.91% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 303ms 0.33% 82.33% 810ms 0.89% boost::numeric::ublas::vector_norm_2::apply 100ms 0.11% 82.44% 810ms 0.89% std::_Rb_tree::find (inline) 0 0% 82.44% 808ms 0.89% std::_Rb_tree::_M_destroy_node (inline) 0 0% 82.44% 808ms 0.89% std::__new_allocator::destroy (inline) 0 0% 82.44% 808ms 0.89% std::allocator_traits::destroy (inline) 804ms 0.88% 83.33% 804ms 0.88% Node::rGetLocation 1ms 0.0011% 83.33% 780ms 0.86% VertexMeshWriter::MakeVtkMesh 0 0% 83.33% 737ms 0.81% std::_Rb_tree::clear (inline) 731ms 0.8% 84.13% 731ms 0.8% tcache_put (inline) 0 0% 84.13% 721ms 0.79% boost::numeric::ublas::c_vector::assign_temporary (inline) 1ms 0.0011% 84.14% 721ms 0.79% boost::numeric::ublas::c_vector::swap (inline) 143ms 0.16% 84.29% 720ms 0.79% std::swap_ranges (inline) 0 0% 84.29% 717ms 0.79% std::map::clear (inline) 44ms 0.048% 84.34% 715ms 0.79% std::less::operator() (inline) 546ms 0.6% 84.94% 711ms 0.78% CellPropertyCollection::GetProperty 1ms 0.0011% 84.94% 681ms 0.75% std::map::find (inline) 0 0% 84.94% 674ms 0.74% std::_Rb_tree::_Auto_node::_M_insert (inline) 28ms 0.031% 84.97% 674ms 0.74% std::_Rb_tree::_M_insert_node (inline) 523ms 0.58% 85.55% 671ms 0.74% std::operator< (inline) 56ms 0.062% 85.61% 646ms 0.71% boost::numeric::ublas::c_vector::operator= (inline) 311ms 0.34% 85.95% 632ms 0.7% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 623ms 0.69% 86.64% 623ms 0.69% std::vector::size (inline) 49ms 0.054% 86.69% 606ms 0.67% MutableElement::GetNodeLocalIndex 0 0% 86.69% 593ms 0.65% boost::numeric::ublas::norm_inf (inline) 229ms 0.25% 86.94% 593ms 0.65% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 86.94% 582ms 0.64% vtkPolygon::New 0 0% 86.94% 582ms 0.64% vtkPolygon::vtkPolygon 0 0% 86.94% 577ms 0.63% std::iter_swap (inline) 577ms 0.63% 87.58% 577ms 0.63% std::swap (inline) 0 0% 87.58% 575ms 0.63% std::_Vector_base::_M_allocate (inline) 20ms 0.022% 87.60% 516ms 0.57% MutableElement::RegisterWithNodes (inline) 488ms 0.54% 88.14% 488ms 0.54% Node::GetIndex 244ms 0.27% 88.41% 486ms 0.53% Edge::GetMapIndex 36ms 0.04% 88.45% 482ms 0.53% Node::AddElement