File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 97926ms, 89.18% of 109805ms total Dropped 1084 nodes (cum <= 549.02ms) flat flat% sum% cum cum% 0 0% 0% 109329ms 99.57% __libc_start_call_main 0 0% 0% 109329ms 99.57% __libc_start_main_impl 0 0% 0% 109329ms 99.57% _start 0 0% 0% 109310ms 99.55% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 109310ms 99.55% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 109310ms 99.55% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 109310ms 99.55% main 0 0% 0% 109272ms 99.51% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 109272ms 99.51% CxxTest::TestRunner::runTest (inline) 0 0% 0% 109272ms 99.51% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0018% 0.0018% 109265ms 99.51% AbstractCellBasedSimulation::Solve 16ms 0.015% 0.016% 56848ms 51.77% OffLatticeSimulation::UpdateCellLocationsAndTopology 15ms 0.014% 0.03% 53549ms 48.77% ForwardEulerNumericalMethod::UpdateAllNodePositions 130ms 0.12% 0.15% 52488ms 47.80% AbstractNumericalMethod::ComputeForcesIncludingDamping 332ms 0.3% 0.45% 40283ms 36.69% NagaiHondaForce::AddForceContribution 1ms 0.00091% 0.45% 39467ms 35.94% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.0027% 0.45% 24458ms 22.27% VertexBasedCellPopulation::Update 1ms 0.00091% 0.46% 24319ms 22.15% MutableVertexMesh::ReMesh 14429ms 13.14% 13.60% 22870ms 20.83% Cylindrical2dVertexMesh::GetVectorFromAtoB 81ms 0.074% 13.67% 17389ms 15.84% Cell::ReadyToDivide 86ms 0.078% 13.75% 16141ms 14.70% AbstractPhaseBasedCellCycleModel::ReadyToDivide 406ms 0.37% 14.12% 14989ms 13.65% NagaiHondaForce::GetAdhesionParameter 399ms 0.36% 14.48% 14388ms 13.10% boost::numeric::ublas::c_vector::c_vector (partial-inline) 134ms 0.12% 14.60% 13806ms 12.57% SimpleWntCellCycleModel::UpdateCellCyclePhase 111ms 0.1% 14.70% 13776ms 12.55% CellPropertyCollection::GetPropertiesType (inline) 385ms 0.35% 15.05% 12883ms 11.73% boost::numeric::ublas::vector_assign (inline) 144ms 0.13% 15.19% 12019ms 10.95% MutableVertexMesh::CheckForIntersections 70ms 0.064% 15.25% 11703ms 10.66% VertexBasedCellPopulation::GetDampingConstant 3650ms 3.32% 18.57% 11295ms 10.29% __dynamic_cast 58ms 0.053% 18.63% 11171ms 10.17% AbstractCellProperty::IsSubType (inline) 101ms 0.092% 18.72% 10467ms 9.53% AbstractTargetAreaModifier::UpdateTargetAreas 1423ms 1.30% 20.01% 10372ms 9.45% std::__new_allocator::allocate (inline) 46ms 0.042% 20.06% 10346ms 9.42% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 28ms 0.025% 20.08% 10247ms 9.33% AbstractCellBasedSimulation::DoCellBirth 0 0% 20.08% 9817ms 8.94% std::_Rb_tree::_M_create_node (inline) 0 0% 20.08% 9797ms 8.92% std::allocator_traits::allocate (inline) 2674ms 2.44% 22.52% 9370ms 8.53% boost::numeric::ublas::indexing_vector_assign 1372ms 1.25% 23.77% 9273ms 8.44% std::_Rb_tree::_M_erase 0 0% 23.77% 9131ms 8.32% std::_Rb_tree::_M_get_node (inline) 949ms 0.86% 24.63% 9035ms 8.23% operator new 784ms 0.71% 25.34% 8980ms 8.18% VertexMesh::ElementIncludesPoint 383ms 0.35% 25.69% 8889ms 8.10% VertexMesh::GetNextEdgeGradientOfElementAtNode 30ms 0.027% 25.72% 8814ms 8.03% VertexBasedCellPopulation::GetLocationOfCellCentre 72ms 0.066% 25.79% 8752ms 7.97% Cell::GetMutationState 0 0% 25.79% 8646ms 7.87% std::_Rb_tree::_Alloc_node::operator() (inline) 235ms 0.21% 26.00% 8508ms 7.75% std::_Rb_tree::~_Rb_tree (inline) 490ms 0.45% 26.45% 8228ms 7.49% VertexMesh::GetCentroidOfElement 0 0% 26.45% 8085ms 7.36% std::_Rb_tree::_M_drop_node (inline) 0 0% 26.45% 8059ms 7.34% std::set::~set (inline) 441ms 0.4% 26.85% 7970ms 7.26% std::map::operator[] (partial-inline) 3090ms 2.81% 29.66% 7931ms 7.22% __GI___libc_malloc 289ms 0.26% 29.93% 7871ms 7.17% std::__new_allocator::deallocate (inline) 0 0% 29.93% 7828ms 7.13% std::allocator_traits::deallocate (inline) 13ms 0.012% 29.94% 7781ms 7.09% MutableVertexMesh::RemoveDeletedNodesAndElements 0 0% 29.94% 7775ms 7.08% std::_Rb_tree::_M_put_node (inline) 2940ms 2.68% 32.62% 7732ms 7.04% __GI___libc_free 1377ms 1.25% 33.87% 7032ms 6.40% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 147ms 0.13% 34.00% 6972ms 6.35% std::_Rb_tree::_Rb_tree (partial-inline) 2555ms 2.33% 36.33% 6713ms 6.11% std::_Rb_tree::_M_lower_bound (inline) 644ms 0.59% 36.92% 6601ms 6.01% std::_Rb_tree::_M_copy (inline) 13ms 0.012% 36.93% 6539ms 5.96% std::set::set (inline) 118ms 0.11% 37.04% 6403ms 5.83% SimpleWntCellCycleModel::GetWntLevel 150ms 0.14% 37.17% 6187ms 5.63% WntConcentration::GetWntLevel 6133ms 5.59% 42.76% 6133ms 5.59% boost::numeric::ublas::c_vector::operator() 5955ms 5.42% 48.18% 5955ms 5.42% __strcmp_avx2 741ms 0.67% 48.86% 5702ms 5.19% std::_Rb_tree::_M_clone_node (inline) 0 0% 48.86% 5510ms 5.02% std::set::insert (inline) 30ms 0.027% 48.88% 5468ms 4.98% MutableVertexMesh::RemoveDeletedNodes 34ms 0.031% 48.91% 5306ms 4.83% EdgeHelper::RemoveDeletedEdges 0 0% 48.91% 5305ms 4.83% std::_Rb_tree::lower_bound (inline) 0 0% 48.91% 5305ms 4.83% std::map::lower_bound (inline) 2642ms 2.41% 51.32% 5298ms 4.82% __cxxabiv1::__si_class_type_info::__do_dyncast 31ms 0.028% 51.35% 5060ms 4.61% EdgeHelper::UpdateEdgesMapKey 224ms 0.2% 51.55% 4901ms 4.46% MutableElement::ResetIndex 1582ms 1.44% 52.99% 4894ms 4.46% boost::numeric::ublas::c_vector::operator[] (inline) 4400ms 4.01% 57.00% 4781ms 4.35% _int_free 0 0% 57.00% 4753ms 4.33% AbstractCellBasedSimulation::DoCellRemoval (inline) 545ms 0.5% 57.50% 4729ms 4.31% std::_Rb_tree::_M_insert_ (inline) 53ms 0.048% 57.54% 4478ms 4.08% std::set_intersection (inline) 97ms 0.088% 57.63% 4458ms 4.06% AbstractCellPopulation::GetCellUsingLocationIndex 264ms 0.24% 57.87% 4425ms 4.03% std::__set_intersection 47ms 0.043% 57.92% 3888ms 3.54% Cell::GetCellProliferativeType 3861ms 3.52% 61.43% 3861ms 3.52% boost::numeric::ublas::same_impl_ex 64ms 0.058% 61.49% 3709ms 3.38% AbstractCellProperty::IsType (inline) 12ms 0.011% 61.50% 3668ms 3.34% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 3490ms 3.18% 64.68% 3490ms 3.18% std::_Rb_tree::_S_right (inline) 0 0% 64.68% 3339ms 3.04% std::insert_iterator::operator= (inline) 2301ms 2.10% 66.78% 3179ms 2.90% _int_malloc 41ms 0.037% 66.81% 3148ms 2.87% std::_Rb_tree::erase 758ms 0.69% 67.50% 3131ms 2.85% AbstractElement::GetNodeLocation 40ms 0.036% 67.54% 3098ms 2.82% Cell::SetCellProliferativeType 9ms 0.0082% 67.55% 2901ms 2.64% std::_Rb_tree::_M_insert_unique_ (inline) 434ms 0.4% 67.94% 2820ms 2.57% std::_Rb_tree_const_iterator::operator++ (inline) 605ms 0.55% 68.49% 2706ms 2.46% boost::numeric::ublas::vector_binary::size (inline) 805ms 0.73% 69.23% 2678ms 2.44% AbstractCellProperty::IsSame 39ms 0.036% 69.26% 2663ms 2.43% CellPropertyCollection::HasProperty 2ms 0.0018% 69.26% 2609ms 2.38% std::_Rb_tree::_M_insert_unique 0 0% 69.26% 2548ms 2.32% Cell::HasCellProperty (inline) 2ms 0.0018% 69.27% 2487ms 2.26% AbstractCellPopulation::Iterator::operator++ (inline) 248ms 0.23% 69.49% 2482ms 2.26% AbstractCellPopulation::Iterator::IsRealCell 0 0% 69.49% 2460ms 2.24% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.49% 2452ms 2.23% AbstractCellPopulation::WriteResultsToFiles 225ms 0.2% 69.70% 2449ms 2.23% VertexMesh::GetAreaGradientOfElementAtNode 22ms 0.02% 69.72% 2439ms 2.22% Cell::GetCellData 0 0% 69.72% 2335ms 2.13% boost::numeric::ublas::c_vector::assign (inline) 107ms 0.097% 69.81% 2279ms 2.08% VertexMesh::GetVolumeOfElement 93ms 0.085% 69.90% 2224ms 2.03% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 1462ms 1.33% 71.23% 2204ms 2.01% std::_Rb_tree::equal_range (inline) 45ms 0.041% 71.27% 2172ms 1.98% std::_Rb_tree::_M_emplace_hint_unique 2170ms 1.98% 73.25% 2170ms 1.98% std::_Rb_tree_increment 0 0% 73.25% 2016ms 1.84% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00091% 73.25% 2015ms 1.84% VertexBasedCellPopulation::WriteCellVtkResultsToFile 28ms 0.025% 73.27% 1955ms 1.78% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2ms 0.0018% 73.28% 1879ms 1.71% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.28% 1879ms 1.71% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 473ms 0.43% 73.71% 1873ms 1.71% std::type_info::operator== (inline) 80ms 0.073% 73.78% 1851ms 1.69% MutableVertexMesh::CheckForSwapsFromShortEdges 36ms 0.033% 73.81% 1834ms 1.67% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 73.81% 1776ms 1.62% VertexMeshWriter::WriteVtkUsingMesh 88ms 0.08% 73.89% 1705ms 1.55% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 53ms 0.048% 73.94% 1657ms 1.51% Node::RemoveElement 23ms 0.021% 73.96% 1624ms 1.48% VertexMesh::GetSurfaceAreaOfElement 188ms 0.17% 74.13% 1614ms 1.47% CellPropertyCollection::AddProperty 19ms 0.017% 74.15% 1613ms 1.47% std::set::erase (inline) 143ms 0.13% 74.28% 1492ms 1.36% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 74.28% 1492ms 1.36% tcache_get (inline) 1492ms 1.36% 75.64% 1492ms 1.36% tcache_get_n (inline) 0 0% 75.64% 1441ms 1.31% OffLatticeSimulation::ApplyBoundaries 0 0% 75.64% 1404ms 1.28% boost::numeric::ublas::vector_binary::operator() (inline) 75ms 0.068% 75.71% 1364ms 1.24% std::less::operator() (inline) 90ms 0.082% 75.79% 1348ms 1.23% std::_Rb_tree::find (inline) 1064ms 0.97% 76.76% 1289ms 1.17% std::operator< (inline) 14ms 0.013% 76.77% 1244ms 1.13% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 76.77% 1171ms 1.07% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1153ms 1.05% 77.82% 1153ms 1.05% Node::rGetLocation 1ms 0.00091% 77.82% 1145ms 1.04% std::map::find (inline) 1125ms 1.02% 78.85% 1125ms 1.02% [libchaste_cell_based.so] 0 0% 78.85% 1119ms 1.02% boost::numeric::ublas::norm_2 (inline) 78ms 0.071% 78.92% 1115ms 1.02% std::_Rb_tree::_M_erase_aux (partial-inline) 484ms 0.44% 79.36% 1110ms 1.01% boost::numeric::ublas::vector_norm_2::apply 1092ms 0.99% 80.35% 1092ms 0.99% std::_Rb_tree_insert_and_rebalance 1083ms 0.99% 81.34% 1083ms 0.99% std::vector::size (inline) 10ms 0.0091% 81.35% 1051ms 0.96% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 22ms 0.02% 81.37% 1051ms 0.96% boost::numeric::ublas::detail::expression_type_check (inline) 33ms 0.03% 81.40% 1050ms 0.96% CellPropertyRegistry::Get 195ms 0.18% 81.58% 1011ms 0.92% boost::numeric::ublas::detail::equals 0 0% 81.58% 1006ms 0.92% std::_Rb_tree::clear (inline) 426ms 0.39% 81.96% 993ms 0.9% Edge::GetMapIndex 122ms 0.11% 82.08% 991ms 0.9% boost::detail::shared_count::~shared_count (inline) 0 0% 82.08% 991ms 0.9% boost::shared_ptr::~shared_ptr (inline) 0 0% 82.08% 989ms 0.9% std::map::clear (inline) 944ms 0.86% 82.94% 944ms 0.86% [libchaste_mesh.so] 0 0% 82.94% 902ms 0.82% boost::numeric::ublas::c_vector::assign_temporary (inline) 6ms 0.0055% 82.94% 902ms 0.82% boost::numeric::ublas::c_vector::swap (inline) 76ms 0.069% 83.01% 896ms 0.82% std::swap_ranges (inline) 1ms 0.00091% 83.01% 865ms 0.79% VertexMeshWriter::MakeVtkMesh 829ms 0.75% 83.77% 834ms 0.76% boost::detail::sp_counted_base::release 821ms 0.75% 84.51% 821ms 0.75% std::swap (inline) 0 0% 84.51% 820ms 0.75% std::iter_swap (inline) 79ms 0.072% 84.59% 816ms 0.74% MutableElement::GetNodeLocalIndex 24ms 0.022% 84.61% 798ms 0.73% MutableElement::RegisterWithEdges (inline) 22ms 0.02% 84.63% 780ms 0.71% Edge::AddElement 101ms 0.092% 84.72% 779ms 0.71% boost::numeric::ublas::c_vector::operator= (inline) 771ms 0.7% 85.42% 771ms 0.7% Node::GetIndex 0 0% 85.42% 760ms 0.69% boost::numeric::ublas::norm_inf (inline) 421ms 0.38% 85.80% 760ms 0.69% boost::numeric::ublas::vector_norm_inf::apply (inline) 163ms 0.15% 85.95% 754ms 0.69% boost::shared_ptr::shared_ptr (inline) 134ms 0.12% 86.08% 742ms 0.68% std::__new_allocator::construct (inline) 0 0% 86.08% 742ms 0.68% std::allocator_traits::construct (inline) 0 0% 86.08% 693ms 0.63% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 86.08% 686ms 0.62% std::_Rb_tree::_M_construct_node (inline) 0 0% 86.08% 683ms 0.62% std::_Rb_tree::_Auto_node::_M_insert (inline) 32ms 0.029% 86.10% 683ms 0.62% std::_Rb_tree::_M_insert_node (inline) 2ms 0.0018% 86.11% 668ms 0.61% std::_Vector_base::_M_allocate (inline) 368ms 0.34% 86.44% 652ms 0.59% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 650ms 0.59% 87.03% 650ms 0.59% operator delete 0 0% 87.03% 616ms 0.56% vtkPolygon::New 2ms 0.0018% 87.04% 615ms 0.56% vtkPolygon::vtkPolygon 22ms 0.02% 87.06% 597ms 0.54% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.06% 597ms 0.54% boost::numeric::ublas::vector::vector (inline) 552ms 0.5% 87.56% 591ms 0.54% boost::detail::shared_count::shared_count (inline) 587ms 0.53% 88.09% 587ms 0.53% [libstdc++.so.6.0.33] 583ms 0.53% 88.62% 583ms 0.53% std::_Rb_tree::_S_left (inline) 581ms 0.53% 89.15% 581ms 0.53% boost::shared_ptr::operator-> (inline) 23ms 0.021% 89.17% 571ms 0.52% MutableElement::RegisterWithNodes (inline) 9ms 0.0082% 89.18% 559ms 0.51% std::vector::_M_default_append (inline)