File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 97162ms, 88.88% of 109313ms total Dropped 1077 nodes (cum <= 546.57ms) flat flat% sum% cum cum% 0 0% 0% 108880ms 99.60% __libc_start_call_main 0 0% 0% 108880ms 99.60% __libc_start_main_impl 0 0% 0% 108880ms 99.60% _start 0 0% 0% 108861ms 99.59% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108861ms 99.59% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108861ms 99.59% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108861ms 99.59% main 0 0% 0% 108824ms 99.55% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108824ms 99.55% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108824ms 99.55% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 4ms 0.0037% 0.0037% 108817ms 99.55% AbstractCellBasedSimulation::Solve 18ms 0.016% 0.02% 56513ms 51.70% OffLatticeSimulation::UpdateCellLocationsAndTopology 18ms 0.016% 0.037% 53319ms 48.78% ForwardEulerNumericalMethod::UpdateAllNodePositions 142ms 0.13% 0.17% 52288ms 47.83% AbstractNumericalMethod::ComputeForcesIncludingDamping 455ms 0.42% 0.58% 40372ms 36.93% NagaiHondaForce::AddForceContribution 0 0% 0.58% 39451ms 36.09% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00091% 0.58% 24394ms 22.32% VertexBasedCellPopulation::Update 1ms 0.00091% 0.58% 24264ms 22.20% MutableVertexMesh::ReMesh 14536ms 13.30% 13.88% 23045ms 21.08% Cylindrical2dVertexMesh::GetVectorFromAtoB 76ms 0.07% 13.95% 17513ms 16.02% Cell::ReadyToDivide 89ms 0.081% 14.03% 16348ms 14.96% AbstractPhaseBasedCellCycleModel::ReadyToDivide 318ms 0.29% 14.32% 14884ms 13.62% NagaiHondaForce::GetAdhesionParameter 428ms 0.39% 14.72% 14404ms 13.18% boost::numeric::ublas::c_vector::c_vector (partial-inline) 128ms 0.12% 14.83% 13970ms 12.78% SimpleWntCellCycleModel::UpdateCellCyclePhase 119ms 0.11% 14.94% 13701ms 12.53% CellPropertyCollection::GetPropertiesType (inline) 500ms 0.46% 15.40% 12790ms 11.70% boost::numeric::ublas::vector_assign (inline) 147ms 0.13% 15.53% 12055ms 11.03% MutableVertexMesh::CheckForIntersections 3199ms 2.93% 18.46% 11496ms 10.52% __dynamic_cast 67ms 0.061% 18.52% 11413ms 10.44% VertexBasedCellPopulation::GetDampingConstant 85ms 0.078% 18.60% 11409ms 10.44% AbstractCellProperty::IsSubType (inline) 17ms 0.016% 18.61% 10391ms 9.51% AbstractCellBasedSimulation::DoCellBirth 91ms 0.083% 18.70% 10373ms 9.49% AbstractTargetAreaModifier::UpdateTargetAreas 60ms 0.055% 18.75% 10263ms 9.39% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 1302ms 1.19% 19.94% 10138ms 9.27% std::__new_allocator::allocate (inline) 2678ms 2.45% 22.39% 9583ms 8.77% boost::numeric::ublas::indexing_vector_assign 0 0% 22.39% 9575ms 8.76% std::allocator_traits::allocate (inline) 0 0% 22.39% 9502ms 8.69% std::_Rb_tree::_M_create_node (inline) 1449ms 1.33% 23.72% 9286ms 8.49% std::_Rb_tree::_M_erase 395ms 0.36% 24.08% 9017ms 8.25% VertexMesh::GetNextEdgeGradientOfElementAtNode 817ms 0.75% 24.83% 8930ms 8.17% operator new 0 0% 24.83% 8898ms 8.14% std::_Rb_tree::_M_get_node (inline) 769ms 0.7% 25.53% 8839ms 8.09% VertexMesh::ElementIncludesPoint 30ms 0.027% 25.56% 8803ms 8.05% VertexBasedCellPopulation::GetLocationOfCellCentre 77ms 0.07% 25.63% 8665ms 7.93% Cell::GetMutationState 205ms 0.19% 25.82% 8466ms 7.74% std::_Rb_tree::~_Rb_tree (inline) 466ms 0.43% 26.24% 8257ms 7.55% VertexMesh::GetCentroidOfElement 0 0% 26.24% 8253ms 7.55% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 26.24% 8095ms 7.41% std::_Rb_tree::_M_drop_node (inline) 0 0% 26.24% 7989ms 7.31% std::set::~set (inline) 3078ms 2.82% 29.06% 7905ms 7.23% __GI___libc_malloc 450ms 0.41% 29.47% 7900ms 7.23% std::map::operator[] (partial-inline) 284ms 0.26% 29.73% 7854ms 7.18% std::__new_allocator::deallocate (inline) 0 0% 29.73% 7834ms 7.17% std::allocator_traits::deallocate (inline) 0 0% 29.73% 7784ms 7.12% std::_Rb_tree::_M_put_node (inline) 2985ms 2.73% 32.46% 7683ms 7.03% __GI___libc_free 17ms 0.016% 32.48% 7613ms 6.96% MutableVertexMesh::RemoveDeletedNodesAndElements 1449ms 1.33% 33.80% 7333ms 6.71% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 134ms 0.12% 33.92% 6781ms 6.20% std::_Rb_tree::_Rb_tree (partial-inline) 6622ms 6.06% 39.98% 6622ms 6.06% __strcmp_avx2 121ms 0.11% 40.09% 6466ms 5.92% SimpleWntCellCycleModel::GetWntLevel 666ms 0.61% 40.70% 6425ms 5.88% std::_Rb_tree::_M_copy (inline) 18ms 0.016% 40.72% 6349ms 5.81% std::set::set (inline) 6306ms 5.77% 46.49% 6306ms 5.77% boost::numeric::ublas::c_vector::operator() 2560ms 2.34% 48.83% 6256ms 5.72% std::_Rb_tree::_M_lower_bound (inline) 168ms 0.15% 48.98% 6251ms 5.72% WntConcentration::GetWntLevel 2637ms 2.41% 51.40% 5940ms 5.43% __cxxabiv1::__si_class_type_info::__do_dyncast 36ms 0.033% 51.43% 5549ms 5.08% MutableVertexMesh::RemoveDeletedNodes 791ms 0.72% 52.15% 5502ms 5.03% std::_Rb_tree::_M_clone_node (inline) 0 0% 52.15% 5454ms 4.99% std::set::insert (inline) 23ms 0.021% 52.17% 5391ms 4.93% EdgeHelper::RemoveDeletedEdges 0 0% 52.17% 5148ms 4.71% std::_Rb_tree::lower_bound (inline) 0 0% 52.17% 5148ms 4.71% std::map::lower_bound (inline) 35ms 0.032% 52.21% 5125ms 4.69% EdgeHelper::UpdateEdgesMapKey 1491ms 1.36% 53.57% 4826ms 4.41% boost::numeric::ublas::c_vector::operator[] (inline) 4387ms 4.01% 57.58% 4690ms 4.29% _int_free 194ms 0.18% 57.76% 4665ms 4.27% MutableElement::ResetIndex 1ms 0.00091% 57.76% 4659ms 4.26% AbstractCellBasedSimulation::DoCellRemoval (inline) 553ms 0.51% 58.27% 4603ms 4.21% std::_Rb_tree::_M_insert_ (inline) 44ms 0.04% 58.31% 4571ms 4.18% std::set_intersection (inline) 289ms 0.26% 58.57% 4527ms 4.14% std::__set_intersection 123ms 0.11% 58.68% 4253ms 3.89% AbstractCellPopulation::GetCellUsingLocationIndex 46ms 0.042% 58.73% 3987ms 3.65% Cell::GetCellProliferativeType 3925ms 3.59% 62.32% 3925ms 3.59% boost::numeric::ublas::same_impl_ex 8ms 0.0073% 62.32% 3538ms 3.24% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 52ms 0.048% 62.37% 3521ms 3.22% AbstractCellProperty::IsType (inline) 61ms 0.056% 62.43% 3315ms 3.03% Cell::SetCellProliferativeType 890ms 0.81% 63.24% 3284ms 3.00% AbstractElement::GetNodeLocation 0 0% 63.24% 3273ms 2.99% std::insert_iterator::operator= (inline) 2306ms 2.11% 65.35% 3193ms 2.92% _int_malloc 3172ms 2.90% 68.25% 3172ms 2.90% std::_Rb_tree::_S_right (inline) 32ms 0.029% 68.28% 3011ms 2.75% std::_Rb_tree::erase 2ms 0.0018% 68.28% 2908ms 2.66% std::_Rb_tree::_M_insert_unique_ (inline) 629ms 0.58% 68.86% 2853ms 2.61% boost::numeric::ublas::vector_binary::size (inline) 525ms 0.48% 69.34% 2736ms 2.50% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 69.34% 2546ms 2.33% std::_Rb_tree::_M_insert_unique 227ms 0.21% 69.55% 2511ms 2.30% VertexMesh::GetAreaGradientOfElementAtNode 49ms 0.045% 69.59% 2506ms 2.29% CellPropertyCollection::HasProperty 720ms 0.66% 70.25% 2496ms 2.28% AbstractCellProperty::IsSame 0 0% 70.25% 2477ms 2.27% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 70.25% 2461ms 2.25% AbstractCellPopulation::WriteResultsToFiles 0 0% 70.25% 2405ms 2.20% boost::numeric::ublas::c_vector::assign (inline) 0 0% 70.25% 2397ms 2.19% Cell::HasCellProperty (inline) 2ms 0.0018% 70.25% 2359ms 2.16% AbstractCellPopulation::Iterator::operator++ (inline) 200ms 0.18% 70.44% 2329ms 2.13% AbstractCellPopulation::Iterator::IsRealCell (inline) 30ms 0.027% 70.46% 2320ms 2.12% Cell::GetCellData 99ms 0.091% 70.55% 2275ms 2.08% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 38ms 0.035% 70.59% 2253ms 2.06% std::_Rb_tree::_M_emplace_hint_unique 111ms 0.1% 70.69% 2202ms 2.01% VertexMesh::GetVolumeOfElement 1421ms 1.30% 71.99% 2113ms 1.93% std::_Rb_tree::equal_range (inline) 2025ms 1.85% 73.84% 2025ms 1.85% std::_Rb_tree_increment 0 0% 73.84% 2014ms 1.84% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 73.84% 2002ms 1.83% VertexBasedCellPopulation::WriteCellVtkResultsToFile 63ms 0.058% 73.90% 1915ms 1.75% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 73.90% 1821ms 1.67% VertexMeshWriter::WriteVtkUsingMesh 33ms 0.03% 73.93% 1820ms 1.66% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 425ms 0.39% 74.32% 1776ms 1.62% std::type_info::operator== (inline) 4ms 0.0037% 74.32% 1765ms 1.61% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 74.32% 1765ms 1.61% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 20ms 0.018% 74.34% 1653ms 1.51% VertexMesh::GetSurfaceAreaOfElement 42ms 0.038% 74.38% 1621ms 1.48% Node::RemoveElement 12ms 0.011% 74.39% 1586ms 1.45% std::set::erase (inline) 83ms 0.076% 74.47% 1581ms 1.45% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 24ms 0.022% 74.49% 1579ms 1.44% AbstractCellPopulation::GetLocationIndexUsingCell 167ms 0.15% 74.64% 1536ms 1.41% CellPropertyCollection::AddProperty 126ms 0.12% 74.76% 1520ms 1.39% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 74.76% 1459ms 1.33% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 74.76% 1434ms 1.31% tcache_get (inline) 1434ms 1.31% 76.07% 1434ms 1.31% tcache_get_n (inline) 3ms 0.0027% 76.07% 1265ms 1.16% OffLatticeSimulation::ApplyBoundaries 0 0% 76.07% 1249ms 1.14% std::_Rb_tree::_Auto_node::_Auto_node (inline) 65ms 0.059% 76.13% 1247ms 1.14% std::less::operator() (inline) 969ms 0.89% 77.02% 1182ms 1.08% std::operator< (inline) 1163ms 1.06% 78.08% 1163ms 1.06% Node::rGetLocation 1147ms 1.05% 79.13% 1147ms 1.05% [libchaste_cell_based.so] 0 0% 79.13% 1126ms 1.03% boost::numeric::ublas::norm_2 (inline) 83ms 0.076% 79.21% 1125ms 1.03% std::_Rb_tree::_M_erase_aux (partial-inline) 498ms 0.46% 79.66% 1110ms 1.02% boost::numeric::ublas::vector_norm_2::apply 1097ms 1.00% 80.66% 1097ms 1.00% std::_Rb_tree_insert_and_rebalance 102ms 0.093% 80.76% 1095ms 1.00% std::_Rb_tree::find (inline) 15ms 0.014% 80.77% 1091ms 1% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 4ms 0.0037% 80.78% 1058ms 0.97% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 158ms 0.14% 80.92% 1039ms 0.95% boost::detail::shared_count::~shared_count (inline) 0 0% 80.92% 1039ms 0.95% boost::shared_ptr::~shared_ptr (inline) 2ms 0.0018% 80.92% 1034ms 0.95% std::_Rb_tree::clear (inline) 0 0% 80.92% 1008ms 0.92% std::map::clear (inline) 26ms 0.024% 80.95% 1007ms 0.92% CellPropertyRegistry::Get 1001ms 0.92% 81.86% 1001ms 0.92% std::vector::size (inline) 381ms 0.35% 82.21% 959ms 0.88% Edge::GetMapIndex 919ms 0.84% 83.05% 919ms 0.84% [libchaste_mesh.so] 105ms 0.096% 83.15% 906ms 0.83% MutableElement::GetNodeLocalIndex 0 0% 83.15% 906ms 0.83% std::map::find (inline) 0 0% 83.15% 897ms 0.82% boost::numeric::ublas::c_vector::assign_temporary (inline) 2ms 0.0018% 83.15% 897ms 0.82% boost::numeric::ublas::c_vector::swap 84ms 0.077% 83.23% 895ms 0.82% std::swap_ranges (inline) 0 0% 83.23% 868ms 0.79% VertexMeshWriter::MakeVtkMesh 854ms 0.78% 84.01% 862ms 0.79% boost::detail::sp_counted_base::release 21ms 0.019% 84.03% 824ms 0.75% boost::numeric::ublas::detail::expression_type_check (inline) 813ms 0.74% 84.77% 813ms 0.74% std::swap (inline) 0 0% 84.77% 811ms 0.74% std::iter_swap (inline) 119ms 0.11% 84.88% 807ms 0.74% boost::numeric::ublas::c_vector::operator= (inline) 119ms 0.11% 84.99% 793ms 0.73% boost::numeric::ublas::detail::equals 781ms 0.71% 85.70% 781ms 0.71% Node::GetIndex 474ms 0.43% 86.14% 779ms 0.71% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 26ms 0.024% 86.16% 760ms 0.7% Edge::AddElement 15ms 0.014% 86.17% 755ms 0.69% MutableElement::RegisterWithEdges (inline) 145ms 0.13% 86.31% 696ms 0.64% boost::shared_ptr::shared_ptr (inline) 0 0% 86.31% 694ms 0.63% CellPropertyCollection::~CellPropertyCollection (inline) 2ms 0.0018% 86.31% 674ms 0.62% std::_Vector_base::_M_allocate (inline) 0 0% 86.31% 666ms 0.61% std::_Rb_tree::_Auto_node::_M_insert (inline) 15ms 0.014% 86.32% 666ms 0.61% std::_Rb_tree::_M_insert_node (inline) 90ms 0.082% 86.40% 646ms 0.59% std::__new_allocator::construct (inline) 0 0% 86.40% 646ms 0.59% std::allocator_traits::construct (inline) 0 0% 86.40% 639ms 0.58% boost::numeric::ublas::norm_inf (inline) 331ms 0.3% 86.71% 639ms 0.58% boost::numeric::ublas::vector_norm_inf::apply (inline) 636ms 0.58% 87.29% 636ms 0.58% [libstdc++.so.6.0.33] 29ms 0.027% 87.31% 607ms 0.56% MutableElement::RegisterWithNodes (inline) 0 0% 87.31% 604ms 0.55% std::_Rb_tree::_M_construct_node (inline) 0 0% 87.31% 603ms 0.55% vtkPolygon::New 0 0% 87.31% 603ms 0.55% vtkPolygon::vtkPolygon 22ms 0.02% 87.33% 585ms 0.54% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.33% 585ms 0.54% boost::numeric::ublas::vector::vector (inline) 26ms 0.024% 87.36% 569ms 0.52% Node::AddElement 569ms 0.52% 87.88% 569ms 0.52% operator delete 6ms 0.0055% 87.88% 567ms 0.52% std::vector::_M_default_append (inline) 560ms 0.51% 88.40% 560ms 0.51% boost::shared_ptr::operator-> (inline) 533ms 0.49% 88.88% 551ms 0.5% boost::detail::shared_count::shared_count (inline)