File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 97703ms, 88.72% of 110127ms total Dropped 1093 nodes (cum <= 550.63ms) flat flat% sum% cum cum% 0 0% 0% 109651ms 99.57% __libc_start_call_main 0 0% 0% 109651ms 99.57% __libc_start_main_impl 0 0% 0% 109651ms 99.57% _start 0 0% 0% 109630ms 99.55% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 109630ms 99.55% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 109630ms 99.55% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 109630ms 99.55% main 0 0% 0% 109593ms 99.52% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 109593ms 99.52% CxxTest::TestRunner::runTest (inline) 0 0% 0% 109593ms 99.52% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 1ms 0.00091% 0.00091% 109585ms 99.51% AbstractCellBasedSimulation::Solve 20ms 0.018% 0.019% 57029ms 51.78% OffLatticeSimulation::UpdateCellLocationsAndTopology 21ms 0.019% 0.038% 53891ms 48.94% ForwardEulerNumericalMethod::UpdateAllNodePositions 139ms 0.13% 0.16% 52362ms 47.55% AbstractNumericalMethod::ComputeForcesIncludingDamping 372ms 0.34% 0.5% 40117ms 36.43% NagaiHondaForce::AddForceContribution 1ms 0.00091% 0.5% 39335ms 35.72% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00091% 0.5% 24361ms 22.12% VertexBasedCellPopulation::Update 1ms 0.00091% 0.5% 24227ms 22.00% MutableVertexMesh::ReMesh 14572ms 13.23% 13.74% 22806ms 20.71% Cylindrical2dVertexMesh::GetVectorFromAtoB 103ms 0.094% 13.83% 17691ms 16.06% Cell::ReadyToDivide 62ms 0.056% 13.89% 16372ms 14.87% AbstractPhaseBasedCellCycleModel::ReadyToDivide 352ms 0.32% 14.21% 15086ms 13.70% NagaiHondaForce::GetAdhesionParameter 133ms 0.12% 14.33% 14227ms 12.92% CellPropertyCollection::GetPropertiesType (inline) 110ms 0.1% 14.43% 14051ms 12.76% SimpleWntCellCycleModel::UpdateCellCyclePhase 408ms 0.37% 14.80% 13997ms 12.71% boost::numeric::ublas::c_vector::c_vector (partial-inline) 408ms 0.37% 15.17% 12463ms 11.32% boost::numeric::ublas::vector_assign (inline) 136ms 0.12% 15.29% 12043ms 10.94% MutableVertexMesh::CheckForIntersections 69ms 0.063% 15.35% 11749ms 10.67% VertexBasedCellPopulation::GetDampingConstant 3650ms 3.31% 18.67% 11688ms 10.61% __dynamic_cast 71ms 0.064% 18.73% 11574ms 10.51% AbstractCellProperty::IsSubType (inline) 93ms 0.084% 18.82% 10771ms 9.78% AbstractTargetAreaModifier::UpdateTargetAreas 67ms 0.061% 18.88% 10650ms 9.67% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 1459ms 1.32% 20.20% 10467ms 9.50% std::__new_allocator::allocate (inline) 27ms 0.025% 20.23% 10375ms 9.42% AbstractCellBasedSimulation::DoCellBirth 0 0% 20.23% 9971ms 9.05% std::allocator_traits::allocate (inline) 0 0% 20.23% 9962ms 9.05% std::_Rb_tree::_M_create_node (inline) 2699ms 2.45% 22.68% 9378ms 8.52% boost::numeric::ublas::indexing_vector_assign 0 0% 22.68% 9334ms 8.48% std::_Rb_tree::_M_get_node (inline) 838ms 0.76% 23.44% 9153ms 8.31% operator new 1391ms 1.26% 24.70% 9113ms 8.27% std::_Rb_tree::_M_erase 67ms 0.061% 24.76% 8921ms 8.10% Cell::GetMutationState 790ms 0.72% 25.48% 8880ms 8.06% VertexMesh::ElementIncludesPoint 30ms 0.027% 25.51% 8817ms 8.01% VertexBasedCellPopulation::GetLocationOfCellCentre 347ms 0.32% 25.82% 8770ms 7.96% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 25.82% 8765ms 7.96% std::_Rb_tree::_Alloc_node::operator() (inline) 242ms 0.22% 26.04% 8313ms 7.55% std::_Rb_tree::~_Rb_tree (inline) 497ms 0.45% 26.49% 8297ms 7.53% VertexMesh::GetCentroidOfElement 3057ms 2.78% 29.27% 8135ms 7.39% __GI___libc_malloc 0 0% 29.27% 8126ms 7.38% std::_Rb_tree::_M_drop_node (inline) 264ms 0.24% 29.51% 7918ms 7.19% std::__new_allocator::deallocate (inline) 0 0% 29.51% 7891ms 7.17% std::allocator_traits::deallocate (inline) 0 0% 29.51% 7853ms 7.13% std::set::~set (inline) 420ms 0.38% 29.89% 7834ms 7.11% std::map::operator[] (partial-inline) 0 0% 29.89% 7816ms 7.10% std::_Rb_tree::_M_put_node (inline) 3003ms 2.73% 32.62% 7662ms 6.96% __GI___libc_free 20ms 0.018% 32.64% 7658ms 6.95% MutableVertexMesh::RemoveDeletedNodesAndElements 111ms 0.1% 32.74% 7152ms 6.49% std::_Rb_tree::_Rb_tree (partial-inline) 1458ms 1.32% 34.06% 7148ms 6.49% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 684ms 0.62% 34.68% 6829ms 6.20% std::_Rb_tree::_M_copy (inline) 16ms 0.015% 34.70% 6775ms 6.15% std::set::set (inline) 6493ms 5.90% 40.59% 6493ms 5.90% __strcmp_avx2 108ms 0.098% 40.69% 6410ms 5.82% SimpleWntCellCycleModel::GetWntLevel 2537ms 2.30% 42.99% 6336ms 5.75% std::_Rb_tree::_M_lower_bound (inline) 143ms 0.13% 43.12% 6207ms 5.64% WntConcentration::GetWntLevel 5909ms 5.37% 48.49% 5909ms 5.37% boost::numeric::ublas::c_vector::operator() 781ms 0.71% 49.20% 5878ms 5.34% std::_Rb_tree::_M_clone_node (inline) 0 0% 49.20% 5584ms 5.07% std::set::insert (inline) 28ms 0.025% 49.22% 5477ms 4.97% MutableVertexMesh::RemoveDeletedNodes 2668ms 2.42% 51.65% 5443ms 4.94% __cxxabiv1::__si_class_type_info::__do_dyncast 30ms 0.027% 51.67% 5297ms 4.81% EdgeHelper::RemoveDeletedEdges 0 0% 51.67% 5175ms 4.70% std::_Rb_tree::lower_bound (inline) 0 0% 51.67% 5175ms 4.70% std::map::lower_bound (inline) 34ms 0.031% 51.70% 5039ms 4.58% EdgeHelper::UpdateEdgesMapKey 207ms 0.19% 51.89% 4760ms 4.32% MutableElement::ResetIndex 1489ms 1.35% 53.24% 4751ms 4.31% boost::numeric::ublas::c_vector::operator[] (inline) 575ms 0.52% 53.77% 4750ms 4.31% std::_Rb_tree::_M_insert_ (inline) 4305ms 3.91% 57.68% 4653ms 4.23% _int_free 3ms 0.0027% 57.68% 4591ms 4.17% AbstractCellBasedSimulation::DoCellRemoval (inline) 51ms 0.046% 57.73% 4476ms 4.06% std::set_intersection (inline) 278ms 0.25% 57.98% 4425ms 4.02% std::__set_intersection 130ms 0.12% 58.10% 4403ms 4.00% AbstractCellPopulation::GetCellUsingLocationIndex 47ms 0.043% 58.14% 4009ms 3.64% Cell::GetCellProliferativeType 3940ms 3.58% 61.72% 3940ms 3.58% boost::numeric::ublas::same_impl_ex 70ms 0.064% 61.78% 3871ms 3.52% AbstractCellProperty::IsType (inline) 6ms 0.0054% 61.79% 3511ms 3.19% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 929ms 0.84% 62.63% 3280ms 2.98% AbstractElement::GetNodeLocation 2353ms 2.14% 64.77% 3237ms 2.94% _int_malloc 0 0% 64.77% 3234ms 2.94% std::insert_iterator::operator= (inline) 52ms 0.047% 64.81% 3219ms 2.92% Cell::SetCellProliferativeType 3188ms 2.89% 67.71% 3188ms 2.89% std::_Rb_tree::_S_right (inline) 39ms 0.035% 67.74% 3025ms 2.75% std::_Rb_tree::erase 4ms 0.0036% 67.75% 2882ms 2.62% std::_Rb_tree::_M_insert_unique_ (inline) 419ms 0.38% 68.13% 2817ms 2.56% std::_Rb_tree_const_iterator::operator++ (inline) 783ms 0.71% 68.84% 2816ms 2.56% AbstractCellProperty::IsSame 48ms 0.044% 68.88% 2765ms 2.51% CellPropertyCollection::HasProperty 593ms 0.54% 69.42% 2748ms 2.50% boost::numeric::ublas::vector_binary::size (inline) 4ms 0.0036% 69.42% 2702ms 2.45% std::_Rb_tree::_M_insert_unique 0 0% 69.42% 2661ms 2.42% Cell::HasCellProperty (inline) 20ms 0.018% 69.44% 2617ms 2.38% Cell::GetCellData 226ms 0.21% 69.65% 2489ms 2.26% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.65% 2464ms 2.24% boost::numeric::ublas::c_vector::assign (inline) 0 0% 69.65% 2432ms 2.21% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.65% 2428ms 2.20% boost::numeric::ublas::c_vector::operator-= (inline) 235ms 0.21% 69.86% 2256ms 2.05% AbstractCellPopulation::Iterator::IsRealCell (inline) 3ms 0.0027% 69.86% 2251ms 2.04% AbstractCellPopulation::Iterator::operator++ (inline) 95ms 0.086% 69.95% 2243ms 2.04% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 2216ms 2.01% 71.96% 2216ms 2.01% std::_Rb_tree_increment 29ms 0.026% 71.99% 2187ms 1.99% std::_Rb_tree::_M_emplace_hint_unique 68ms 0.062% 72.05% 2147ms 1.95% VertexMesh::GetVolumeOfElement 1404ms 1.27% 73.32% 2069ms 1.88% std::_Rb_tree::equal_range (inline) 475ms 0.43% 73.76% 2033ms 1.85% std::type_info::operator== (inline) 0 0% 73.76% 1994ms 1.81% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 73.76% 1980ms 1.80% VertexBasedCellPopulation::WriteCellVtkResultsToFile 79ms 0.072% 73.83% 1872ms 1.70% MutableVertexMesh::CheckForSwapsFromShortEdges 5ms 0.0045% 73.83% 1851ms 1.68% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.83% 1851ms 1.68% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 73.83% 1775ms 1.61% VertexMeshWriter::WriteVtkUsingMesh 31ms 0.028% 73.86% 1760ms 1.60% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 175ms 0.16% 74.02% 1662ms 1.51% CellPropertyCollection::AddProperty 48ms 0.044% 74.06% 1648ms 1.50% Node::RemoveElement 0 0% 74.06% 1634ms 1.48% tcache_get (inline) 1634ms 1.48% 75.55% 1634ms 1.48% tcache_get_n (inline) 22ms 0.02% 75.57% 1628ms 1.48% VertexMesh::GetSurfaceAreaOfElement 24ms 0.022% 75.59% 1612ms 1.46% std::set::erase (inline) 26ms 0.024% 75.61% 1577ms 1.43% AbstractCellPopulation::GetLocationIndexUsingCell 82ms 0.074% 75.69% 1562ms 1.42% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 121ms 0.11% 75.80% 1421ms 1.29% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 75.80% 1393ms 1.26% boost::numeric::ublas::vector_binary::operator() (inline) 93ms 0.084% 75.88% 1296ms 1.18% std::less::operator() (inline) 1ms 0.00091% 75.88% 1259ms 1.14% OffLatticeSimulation::ApplyBoundaries 1020ms 0.93% 76.81% 1203ms 1.09% std::operator< (inline) 0 0% 76.81% 1197ms 1.09% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 76.81% 1193ms 1.08% boost::numeric::ublas::norm_2 (inline) 1183ms 1.07% 77.88% 1183ms 1.07% Node::rGetLocation 523ms 0.47% 78.36% 1182ms 1.07% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 117ms 0.11% 78.46% 1154ms 1.05% std::_Rb_tree::find (inline) 26ms 0.024% 78.49% 1119ms 1.02% CellPropertyRegistry::Get 81ms 0.074% 78.56% 1119ms 1.02% std::_Rb_tree::_M_erase_aux (partial-inline) 1116ms 1.01% 79.57% 1116ms 1.01% [libchaste_cell_based.so] 1100ms 1% 80.57% 1100ms 1% std::_Rb_tree_insert_and_rebalance 16ms 0.015% 80.59% 1067ms 0.97% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 1ms 0.00091% 80.59% 1046ms 0.95% std::_Rb_tree::clear (inline) 0 0% 80.59% 1028ms 0.93% std::map::clear (inline) 6ms 0.0054% 80.59% 1019ms 0.93% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 163ms 0.15% 80.74% 1013ms 0.92% boost::detail::shared_count::~shared_count (inline) 0 0% 80.74% 1013ms 0.92% boost::shared_ptr::~shared_ptr (inline) 950ms 0.86% 81.60% 950ms 0.86% [libchaste_mesh.so] 950ms 0.86% 82.47% 950ms 0.86% std::vector::size (inline) 1ms 0.00091% 82.47% 949ms 0.86% std::map::find (inline) 387ms 0.35% 82.82% 947ms 0.86% Edge::GetMapIndex 0 0% 82.82% 890ms 0.81% boost::numeric::ublas::c_vector::assign_temporary (inline) 3ms 0.0027% 82.82% 890ms 0.81% boost::numeric::ublas::c_vector::swap (inline) 73ms 0.066% 82.89% 887ms 0.81% std::swap_ranges (inline) 20ms 0.018% 82.91% 870ms 0.79% boost::numeric::ublas::detail::expression_type_check (inline) 1ms 0.00091% 82.91% 859ms 0.78% VertexMeshWriter::MakeVtkMesh 150ms 0.14% 83.04% 841ms 0.76% boost::numeric::ublas::detail::equals 85ms 0.077% 83.12% 819ms 0.74% MutableElement::GetNodeLocalIndex 817ms 0.74% 83.86% 817ms 0.74% std::swap (inline) 805ms 0.73% 84.59% 814ms 0.74% boost::detail::sp_counted_base::release 0 0% 84.59% 814ms 0.74% std::iter_swap (inline) 147ms 0.13% 84.73% 759ms 0.69% boost::shared_ptr::shared_ptr (inline) 757ms 0.69% 85.41% 757ms 0.69% Node::GetIndex 26ms 0.024% 85.44% 756ms 0.69% Edge::AddElement 96ms 0.087% 85.52% 752ms 0.68% boost::numeric::ublas::c_vector::operator= (inline) 26ms 0.024% 85.55% 751ms 0.68% MutableElement::RegisterWithEdges (inline) 408ms 0.37% 85.92% 695ms 0.63% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 85.92% 681ms 0.62% CellPropertyCollection::~CellPropertyCollection (inline) 99ms 0.09% 86.01% 680ms 0.62% std::__new_allocator::construct (inline) 0 0% 86.01% 680ms 0.62% std::allocator_traits::construct (inline) 0 0% 86.01% 665ms 0.6% std::_Rb_tree::_Auto_node::_M_insert (inline) 19ms 0.017% 86.03% 665ms 0.6% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.03% 658ms 0.6% boost::numeric::ublas::norm_inf (inline) 363ms 0.33% 86.36% 658ms 0.6% boost::numeric::ublas::vector_norm_inf::apply (inline) 18ms 0.016% 86.37% 654ms 0.59% AbstractNumericalMethod::DetectStepSizeExceptions 44ms 0.04% 86.41% 652ms 0.59% MutableElement::RegisterWithNodes (inline) 643ms 0.58% 87.00% 643ms 0.58% operator delete 3ms 0.0027% 87.00% 637ms 0.58% std::_Vector_base::_M_allocate (inline) 83ms 0.075% 87.07% 636ms 0.58% VertexBasedCellPopulation::CheckForStepSizeException 0 0% 87.07% 628ms 0.57% std::_Rb_tree::_M_construct_node (inline) 587ms 0.53% 87.61% 612ms 0.56% boost::detail::shared_count::shared_count (inline) 35ms 0.032% 87.64% 606ms 0.55% Node::AddElement 602ms 0.55% 88.19% 602ms 0.55% [libstdc++.so.6.0.33] 0 0% 88.19% 598ms 0.54% vtkPolygon::New 1ms 0.00091% 88.19% 598ms 0.54% vtkPolygon::vtkPolygon 0 0% 88.19% 579ms 0.53% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 560ms 0.51% 88.69% 560ms 0.51% boost::shared_ptr::operator-> (inline) 26ms 0.024% 88.72% 551ms 0.5% AbstractNumericalMethod::SafeNodePositionUpdate