File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 94918ms, 88.07% of 107772ms total Dropped 1073 nodes (cum <= 538.86ms) flat flat% sum% cum cum% 0 0% 0% 107243ms 99.51% __libc_start_call_main 0 0% 0% 107243ms 99.51% __libc_start_main_impl 0 0% 0% 107243ms 99.51% _start 0 0% 0% 107224ms 99.49% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 107224ms 99.49% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 107224ms 99.49% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 107224ms 99.49% main 0 0% 0% 107184ms 99.45% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 107184ms 99.45% CxxTest::TestRunner::runTest (inline) 0 0% 0% 107184ms 99.45% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 3ms 0.0028% 0.0028% 107176ms 99.45% AbstractCellBasedSimulation::Solve 19ms 0.018% 0.02% 55780ms 51.76% OffLatticeSimulation::UpdateCellLocationsAndTopology 10ms 0.0093% 0.03% 52513ms 48.73% ForwardEulerNumericalMethod::UpdateAllNodePositions 102ms 0.095% 0.12% 51481ms 47.77% AbstractNumericalMethod::ComputeForcesIncludingDamping 414ms 0.38% 0.51% 40289ms 37.38% NagaiHondaForce::AddForceContribution 0 0% 0.51% 38728ms 35.94% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00093% 0.51% 23957ms 22.23% VertexBasedCellPopulation::Update 2ms 0.0019% 0.51% 23836ms 22.12% MutableVertexMesh::ReMesh 14446ms 13.40% 13.92% 23076ms 21.41% Cylindrical2dVertexMesh::GetVectorFromAtoB 74ms 0.069% 13.98% 17256ms 16.01% Cell::ReadyToDivide 79ms 0.073% 14.06% 16057ms 14.90% AbstractPhaseBasedCellCycleModel::ReadyToDivide 351ms 0.33% 14.38% 15373ms 14.26% NagaiHondaForce::GetAdhesionParameter 361ms 0.33% 14.72% 14397ms 13.36% boost::numeric::ublas::c_vector::c_vector (partial-inline) 148ms 0.14% 14.86% 13673ms 12.69% SimpleWntCellCycleModel::UpdateCellCyclePhase 143ms 0.13% 14.99% 13013ms 12.07% CellPropertyCollection::GetPropertiesType (inline) 374ms 0.35% 15.34% 12811ms 11.89% boost::numeric::ublas::vector_assign (inline) 140ms 0.13% 15.47% 12052ms 11.18% MutableVertexMesh::CheckForIntersections 3052ms 2.83% 18.30% 10924ms 10.14% __dynamic_cast 78ms 0.072% 18.37% 10792ms 10.01% AbstractCellProperty::IsSubType (inline) 81ms 0.075% 18.44% 10727ms 9.95% VertexBasedCellPopulation::GetDampingConstant 48ms 0.045% 18.49% 10313ms 9.57% AbstractTargetAreaModifier::UpdateTargetAreas 75ms 0.07% 18.56% 10211ms 9.47% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 22ms 0.02% 18.58% 10112ms 9.38% AbstractCellBasedSimulation::DoCellBirth 1193ms 1.11% 19.69% 9851ms 9.14% std::__new_allocator::allocate (inline) 2697ms 2.50% 22.19% 9594ms 8.90% boost::numeric::ublas::indexing_vector_assign 1339ms 1.24% 23.43% 9385ms 8.71% std::_Rb_tree::_M_erase 0 0% 23.43% 9302ms 8.63% std::_Rb_tree::_M_create_node (inline) 0 0% 23.43% 9295ms 8.62% std::allocator_traits::allocate (inline) 380ms 0.35% 23.78% 8983ms 8.34% VertexMesh::GetNextEdgeGradientOfElementAtNode 781ms 0.72% 24.51% 8957ms 8.31% VertexMesh::ElementIncludesPoint 25ms 0.023% 24.53% 8821ms 8.18% VertexBasedCellPopulation::GetLocationOfCellCentre 828ms 0.77% 25.30% 8779ms 8.15% operator new 0 0% 25.30% 8667ms 8.04% std::_Rb_tree::_M_get_node (inline) 201ms 0.19% 25.49% 8588ms 7.97% std::_Rb_tree::~_Rb_tree (inline) 0 0% 25.49% 8415ms 7.81% std::_Rb_tree::_M_drop_node (inline) 498ms 0.46% 25.95% 8388ms 7.78% VertexMesh::GetCentroidOfElement 87ms 0.081% 26.03% 8272ms 7.68% Cell::GetMutationState 252ms 0.23% 26.26% 8170ms 7.58% std::__new_allocator::deallocate (inline) 0 0% 26.26% 8143ms 7.56% std::allocator_traits::deallocate (inline) 0 0% 26.26% 8127ms 7.54% std::set::~set (inline) 0 0% 26.26% 8125ms 7.54% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 26.26% 8088ms 7.50% std::_Rb_tree::_M_put_node (inline) 2977ms 2.76% 29.03% 7878ms 7.31% __GI___libc_free 3181ms 2.95% 31.98% 7780ms 7.22% __GI___libc_malloc 16ms 0.015% 31.99% 7342ms 6.81% MutableVertexMesh::RemoveDeletedNodesAndElements 1399ms 1.30% 33.29% 7248ms 6.73% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 482ms 0.45% 33.74% 7205ms 6.69% std::map::operator[] (partial-inline) 122ms 0.11% 33.85% 6675ms 6.19% std::_Rb_tree::_Rb_tree (partial-inline) 6358ms 5.90% 39.75% 6358ms 5.90% __strcmp_avx2 690ms 0.64% 40.39% 6309ms 5.85% std::_Rb_tree::_M_copy (inline) 110ms 0.1% 40.49% 6302ms 5.85% SimpleWntCellCycleModel::GetWntLevel 6239ms 5.79% 46.28% 6239ms 5.79% boost::numeric::ublas::c_vector::operator() 14ms 0.013% 46.29% 6232ms 5.78% std::set::set (inline) 136ms 0.13% 46.42% 6086ms 5.65% WntConcentration::GetWntLevel 2384ms 2.21% 48.63% 5501ms 5.10% std::_Rb_tree::_M_lower_bound (inline) 2602ms 2.41% 51.05% 5483ms 5.09% __cxxabiv1::__si_class_type_info::__do_dyncast 675ms 0.63% 51.67% 5323ms 4.94% std::_Rb_tree::_M_clone_node (inline) 0 0% 51.67% 5305ms 4.92% std::set::insert (inline) 39ms 0.036% 51.71% 5292ms 4.91% MutableVertexMesh::RemoveDeletedNodes 36ms 0.033% 51.74% 5089ms 4.72% EdgeHelper::RemoveDeletedEdges 4593ms 4.26% 56.00% 4891ms 4.54% _int_free 1491ms 1.38% 57.39% 4882ms 4.53% boost::numeric::ublas::c_vector::operator[] (inline) 33ms 0.031% 57.42% 4841ms 4.49% EdgeHelper::UpdateEdgesMapKey 53ms 0.049% 57.47% 4837ms 4.49% std::set_intersection (inline) 318ms 0.3% 57.76% 4784ms 4.44% std::__set_intersection 1ms 0.00093% 57.76% 4649ms 4.31% AbstractCellBasedSimulation::DoCellRemoval (inline) 182ms 0.17% 57.93% 4586ms 4.26% MutableElement::ResetIndex 0 0% 57.93% 4470ms 4.15% std::_Rb_tree::lower_bound (inline) 0 0% 57.93% 4470ms 4.15% std::map::lower_bound (inline) 482ms 0.45% 58.38% 4446ms 4.13% std::_Rb_tree::_M_insert_ (inline) 4094ms 3.80% 62.18% 4094ms 3.80% boost::numeric::ublas::same_impl_ex 52ms 0.048% 62.23% 3935ms 3.65% Cell::GetCellProliferativeType 125ms 0.12% 62.34% 3814ms 3.54% AbstractCellPopulation::GetCellUsingLocationIndex 83ms 0.077% 62.42% 3689ms 3.42% AbstractCellProperty::IsType (inline) 19ms 0.018% 62.44% 3630ms 3.37% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.44% 3261ms 3.03% std::insert_iterator::operator= (inline) 791ms 0.73% 63.17% 3146ms 2.92% AbstractElement::GetNodeLocation 55ms 0.051% 63.22% 3103ms 2.88% Cell::SetCellProliferativeType 2245ms 2.08% 65.31% 3094ms 2.87% _int_malloc 486ms 0.45% 65.76% 2915ms 2.70% std::_Rb_tree_const_iterator::operator++ (inline) 6ms 0.0056% 65.76% 2903ms 2.69% std::_Rb_tree::_M_insert_unique_ (inline) 619ms 0.57% 66.34% 2902ms 2.69% boost::numeric::ublas::vector_binary::size (inline) 41ms 0.038% 66.37% 2875ms 2.67% std::_Rb_tree::erase 2617ms 2.43% 68.80% 2617ms 2.43% std::_Rb_tree::_S_right (inline) 713ms 0.66% 69.46% 2599ms 2.41% AbstractCellProperty::IsSame 40ms 0.037% 69.50% 2562ms 2.38% CellPropertyCollection::HasProperty 0 0% 69.50% 2498ms 2.32% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.50% 2462ms 2.28% Cell::HasCellProperty (inline) 225ms 0.21% 69.71% 2417ms 2.24% VertexMesh::GetAreaGradientOfElementAtNode 2ms 0.0019% 69.71% 2402ms 2.23% std::_Rb_tree::_M_insert_unique (inline) 0 0% 69.71% 2391ms 2.22% boost::numeric::ublas::c_vector::assign (inline) 0 0% 69.71% 2336ms 2.17% AbstractCellPopulation::WriteResultsToFiles 116ms 0.11% 69.82% 2289ms 2.12% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 2248ms 2.09% 71.91% 2248ms 2.09% std::_Rb_tree_increment 2ms 0.0019% 71.91% 2207ms 2.05% AbstractCellPopulation::Iterator::operator++ (inline) 114ms 0.11% 72.01% 2205ms 2.05% VertexMesh::GetVolumeOfElement 30ms 0.028% 72.04% 2202ms 2.04% std::_Rb_tree::_M_emplace_hint_unique 194ms 0.18% 72.22% 2185ms 2.03% AbstractCellPopulation::Iterator::IsRealCell (inline) 31ms 0.029% 72.25% 2175ms 2.02% Cell::GetCellData 0 0% 72.25% 1905ms 1.77% VertexBasedCellPopulation::WriteVtkResultsToFile 3ms 0.0028% 72.25% 1895ms 1.76% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.25% 1895ms 1.76% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 2ms 0.0019% 72.25% 1892ms 1.76% VertexBasedCellPopulation::WriteCellVtkResultsToFile 435ms 0.4% 72.66% 1886ms 1.75% std::type_info::operator== (inline) 1234ms 1.15% 73.80% 1874ms 1.74% std::_Rb_tree::equal_range (inline) 69ms 0.064% 73.87% 1854ms 1.72% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 73.87% 1719ms 1.60% VertexMeshWriter::WriteVtkUsingMesh 38ms 0.035% 73.90% 1690ms 1.57% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 25ms 0.023% 73.93% 1592ms 1.48% VertexMesh::GetSurfaceAreaOfElement 153ms 0.14% 74.07% 1577ms 1.46% boost::numeric::ublas::vector_reference::operator() (inline) 60ms 0.056% 74.12% 1562ms 1.45% Node::RemoveElement 18ms 0.017% 74.14% 1516ms 1.41% std::set::erase (inline) 33ms 0.031% 74.17% 1480ms 1.37% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 74.17% 1466ms 1.36% boost::numeric::ublas::vector_binary::operator() (inline) 79ms 0.073% 74.24% 1433ms 1.33% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 148ms 0.14% 74.38% 1354ms 1.26% CellPropertyCollection::AddProperty 1ms 0.00093% 74.38% 1329ms 1.23% OffLatticeSimulation::ApplyBoundaries 0 0% 74.38% 1321ms 1.23% tcache_get (inline) 1321ms 1.23% 75.61% 1321ms 1.23% tcache_get_n (inline) 0 0% 75.61% 1187ms 1.10% boost::numeric::ublas::norm_2 (inline) 96ms 0.089% 75.70% 1181ms 1.10% std::_Rb_tree::_M_erase_aux (partial-inline) 514ms 0.48% 76.17% 1180ms 1.09% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 75ms 0.07% 76.24% 1178ms 1.09% std::less::operator() (inline) 0 0% 76.24% 1177ms 1.09% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1146ms 1.06% 77.31% 1146ms 1.06% Node::rGetLocation 904ms 0.84% 78.15% 1103ms 1.02% std::operator< (inline) 13ms 0.012% 78.16% 1095ms 1.02% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 1083ms 1.00% 79.16% 1083ms 1.00% std::_Rb_tree_insert_and_rebalance 1075ms 1% 80.16% 1075ms 1% [libchaste_cell_based.so] 17ms 0.016% 80.18% 1068ms 0.99% CellPropertyRegistry::Get 144ms 0.13% 80.31% 1050ms 0.97% boost::detail::shared_count::~shared_count (inline) 0 0% 80.31% 1050ms 0.97% boost::shared_ptr::~shared_ptr (inline) 110ms 0.1% 80.41% 1037ms 0.96% std::_Rb_tree::find (inline) 1ms 0.00093% 80.41% 1004ms 0.93% std::_Rb_tree::clear (inline) 0 0% 80.41% 989ms 0.92% std::map::clear (inline) 3ms 0.0028% 80.42% 964ms 0.89% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 80.42% 943ms 0.87% boost::numeric::ublas::c_vector::assign_temporary (inline) 2ms 0.0019% 80.42% 943ms 0.87% boost::numeric::ublas::c_vector::swap (inline) 84ms 0.078% 80.49% 941ms 0.87% std::swap_ranges (inline) 921ms 0.85% 81.35% 921ms 0.85% std::vector::size (inline) 919ms 0.85% 82.20% 919ms 0.85% [libchaste_mesh.so] 18ms 0.017% 82.22% 914ms 0.85% boost::numeric::ublas::detail::expression_type_check (inline) 139ms 0.13% 82.35% 885ms 0.82% boost::numeric::ublas::detail::equals 355ms 0.33% 82.68% 876ms 0.81% Edge::GetMapIndex 871ms 0.81% 83.49% 876ms 0.81% boost::detail::sp_counted_base::release 122ms 0.11% 83.60% 859ms 0.8% MutableElement::GetNodeLocalIndex 1ms 0.00093% 83.60% 858ms 0.8% std::map::find (inline) 0 0% 83.60% 857ms 0.8% std::iter_swap (inline) 857ms 0.8% 84.39% 857ms 0.8% std::swap (inline) 0 0% 84.39% 840ms 0.78% VertexMeshWriter::MakeVtkMesh 179ms 0.17% 84.56% 815ms 0.76% boost::shared_ptr::shared_ptr (inline) 145ms 0.13% 84.70% 811ms 0.75% boost::numeric::ublas::c_vector::operator= (inline) 435ms 0.4% 85.10% 791ms 0.73% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 21ms 0.019% 85.12% 784ms 0.73% MutableElement::RegisterWithEdges (inline) 30ms 0.028% 85.15% 777ms 0.72% Edge::AddElement 768ms 0.71% 85.86% 768ms 0.71% Node::GetIndex 0 0% 85.86% 708ms 0.66% boost::numeric::ublas::norm_inf (inline) 343ms 0.32% 86.18% 708ms 0.66% boost::numeric::ublas::vector_norm_inf::apply (inline) 679ms 0.63% 86.81% 679ms 0.63% operator delete 122ms 0.11% 86.92% 672ms 0.62% std::__new_allocator::construct (inline) 0 0% 86.92% 672ms 0.62% std::allocator_traits::construct (inline) 0 0% 86.92% 666ms 0.62% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 86.92% 659ms 0.61% std::_Rb_tree::_Auto_node::_M_insert (inline) 19ms 0.018% 86.94% 659ms 0.61% std::_Rb_tree::_M_insert_node (inline) 603ms 0.56% 87.50% 636ms 0.59% boost::detail::shared_count::shared_count (inline) 0 0% 87.50% 635ms 0.59% std::_Rb_tree::_M_construct_node (inline) 2ms 0.0019% 87.50% 625ms 0.58% std::_Vector_base::_M_allocate (inline) 0 0% 87.50% 597ms 0.55% vtkPolygon::New 2ms 0.0019% 87.50% 597ms 0.55% vtkPolygon::vtkPolygon 38ms 0.035% 87.54% 592ms 0.55% MutableElement::RegisterWithNodes (inline) 11ms 0.01% 87.55% 567ms 0.53% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.55% 567ms 0.53% boost::numeric::ublas::vector::vector (inline) 0 0% 87.55% 562ms 0.52% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 19ms 0.018% 87.56% 553ms 0.51% Node::AddElement 548ms 0.51% 88.07% 548ms 0.51% [libstdc++.so.6.0.33]