File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95117ms, 88.12% of 107941ms total Dropped 1049 nodes (cum <= 539.71ms) flat flat% sum% cum cum% 0 0% 0% 107472ms 99.57% __libc_start_call_main 0 0% 0% 107472ms 99.57% __libc_start_main_impl 0 0% 0% 107472ms 99.57% _start 0 0% 0% 107454ms 99.55% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 107454ms 99.55% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 107454ms 99.55% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 107454ms 99.55% main 0 0% 0% 107419ms 99.52% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 107419ms 99.52% CxxTest::TestRunner::runTest (inline) 0 0% 0% 107419ms 99.52% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 4ms 0.0037% 0.0037% 107412ms 99.51% AbstractCellBasedSimulation::Solve 16ms 0.015% 0.019% 56224ms 52.09% OffLatticeSimulation::UpdateCellLocationsAndTopology 14ms 0.013% 0.031% 53135ms 49.23% ForwardEulerNumericalMethod::UpdateAllNodePositions 125ms 0.12% 0.15% 52119ms 48.28% AbstractNumericalMethod::ComputeForcesIncludingDamping 361ms 0.33% 0.48% 40731ms 37.73% NagaiHondaForce::AddForceContribution 2ms 0.0019% 0.48% 38390ms 35.57% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00093% 0.48% 23683ms 21.94% VertexBasedCellPopulation::Update 1ms 0.00093% 0.49% 23567ms 21.83% MutableVertexMesh::ReMesh 14658ms 13.58% 14.07% 23256ms 21.55% Cylindrical2dVertexMesh::GetVectorFromAtoB 68ms 0.063% 14.13% 17357ms 16.08% Cell::ReadyToDivide 67ms 0.062% 14.19% 16124ms 14.94% AbstractPhaseBasedCellCycleModel::ReadyToDivide 294ms 0.27% 14.46% 14865ms 13.77% NagaiHondaForce::GetAdhesionParameter 404ms 0.37% 14.84% 14561ms 13.49% boost::numeric::ublas::c_vector::c_vector (partial-inline) 129ms 0.12% 14.96% 13648ms 12.64% SimpleWntCellCycleModel::UpdateCellCyclePhase 142ms 0.13% 15.09% 13033ms 12.07% CellPropertyCollection::GetPropertiesType (inline) 362ms 0.34% 15.42% 12974ms 12.02% boost::numeric::ublas::vector_assign (inline) 132ms 0.12% 15.55% 12033ms 11.15% MutableVertexMesh::CheckForIntersections 99ms 0.092% 15.64% 10877ms 10.08% VertexBasedCellPopulation::GetDampingConstant 3027ms 2.80% 18.44% 10701ms 9.91% __dynamic_cast 84ms 0.078% 18.52% 10620ms 9.84% AbstractCellProperty::IsSubType (inline) 82ms 0.076% 18.60% 10427ms 9.66% AbstractTargetAreaModifier::UpdateTargetAreas 68ms 0.063% 18.66% 10323ms 9.56% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 19ms 0.018% 18.68% 10183ms 9.43% AbstractCellBasedSimulation::DoCellBirth 2816ms 2.61% 21.28% 9840ms 9.12% boost::numeric::ublas::indexing_vector_assign 1224ms 1.13% 22.42% 9589ms 8.88% std::__new_allocator::allocate (inline) 431ms 0.4% 22.82% 9461ms 8.76% VertexMesh::GetNextEdgeGradientOfElementAtNode 1341ms 1.24% 24.06% 9369ms 8.68% std::_Rb_tree::_M_erase 0 0% 24.06% 9082ms 8.41% std::_Rb_tree::_M_create_node (inline) 0 0% 24.06% 9082ms 8.41% std::allocator_traits::allocate (inline) 776ms 0.72% 24.78% 8925ms 8.27% VertexMesh::ElementIncludesPoint 224ms 0.21% 24.99% 8631ms 8.00% std::_Rb_tree::~_Rb_tree (inline) 822ms 0.76% 25.75% 8471ms 7.85% operator new 0 0% 25.75% 8445ms 7.82% std::_Rb_tree::_M_get_node (inline) 24ms 0.022% 25.77% 8394ms 7.78% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 25.77% 8307ms 7.70% std::_Rb_tree::_M_drop_node (inline) 80ms 0.074% 25.84% 8262ms 7.65% Cell::GetMutationState 0 0% 25.84% 8187ms 7.58% std::set::~set (inline) 287ms 0.27% 26.11% 8111ms 7.51% std::__new_allocator::deallocate (inline) 0 0% 26.11% 8066ms 7.47% std::allocator_traits::deallocate (inline) 505ms 0.47% 26.58% 7997ms 7.41% VertexMesh::GetCentroidOfElement 0 0% 26.58% 7990ms 7.40% std::_Rb_tree::_M_put_node (inline) 0 0% 26.58% 7975ms 7.39% std::_Rb_tree::_Alloc_node::operator() (inline) 3108ms 2.88% 29.46% 7889ms 7.31% __GI___libc_free 1434ms 1.33% 30.79% 7535ms 6.98% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 3160ms 2.93% 33.71% 7465ms 6.92% __GI___libc_malloc 25ms 0.023% 33.74% 7214ms 6.68% MutableVertexMesh::RemoveDeletedNodesAndElements 493ms 0.46% 34.19% 7052ms 6.53% std::map::operator[] (partial-inline) 118ms 0.11% 34.30% 6453ms 5.98% std::_Rb_tree::_Rb_tree (partial-inline) 6270ms 5.81% 40.11% 6270ms 5.81% boost::numeric::ublas::c_vector::operator() 6176ms 5.72% 45.83% 6176ms 5.72% __strcmp_avx2 669ms 0.62% 46.45% 6113ms 5.66% std::_Rb_tree::_M_copy (inline) 107ms 0.099% 46.55% 6036ms 5.59% SimpleWntCellCycleModel::GetWntLevel 10ms 0.0093% 46.56% 6029ms 5.59% std::set::set (inline) 147ms 0.14% 46.70% 5813ms 5.39% WntConcentration::GetWntLevel 2696ms 2.50% 49.20% 5496ms 5.09% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 49.20% 5468ms 5.07% std::set::insert (inline) 2334ms 2.16% 51.36% 5411ms 5.01% std::_Rb_tree::_M_lower_bound (inline) 685ms 0.63% 51.99% 5152ms 4.77% std::_Rb_tree::_M_clone_node (inline) 33ms 0.031% 52.02% 5074ms 4.70% MutableVertexMesh::RemoveDeletedNodes 35ms 0.032% 52.06% 4910ms 4.55% EdgeHelper::RemoveDeletedEdges 1477ms 1.37% 53.42% 4817ms 4.46% boost::numeric::ublas::c_vector::operator[] (inline) 4436ms 4.11% 57.53% 4773ms 4.42% _int_free 53ms 0.049% 57.58% 4743ms 4.39% std::set_intersection (inline) 282ms 0.26% 57.84% 4690ms 4.34% std::__set_intersection 602ms 0.56% 58.40% 4658ms 4.32% std::_Rb_tree::_M_insert_ (inline) 36ms 0.033% 58.43% 4647ms 4.31% EdgeHelper::UpdateEdgesMapKey 179ms 0.17% 58.60% 4521ms 4.19% MutableElement::ResetIndex 1ms 0.00093% 58.60% 4513ms 4.18% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 58.60% 4366ms 4.04% std::_Rb_tree::lower_bound (inline) 0 0% 58.60% 4366ms 4.04% std::map::lower_bound (inline) 4175ms 3.87% 62.47% 4175ms 3.87% boost::numeric::ublas::same_impl_ex 73ms 0.068% 62.54% 4053ms 3.75% AbstractCellProperty::IsType (inline) 42ms 0.039% 62.58% 3785ms 3.51% Cell::GetCellProliferativeType 101ms 0.094% 62.67% 3772ms 3.49% AbstractCellPopulation::GetCellUsingLocationIndex 9ms 0.0083% 62.68% 3494ms 3.24% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1ms 0.00093% 62.68% 3358ms 3.11% std::insert_iterator::operator= (inline) 766ms 0.71% 63.39% 3118ms 2.89% AbstractElement::GetNodeLocation 67ms 0.062% 63.45% 3057ms 2.83% Cell::SetCellProliferativeType 2ms 0.0019% 63.45% 3005ms 2.78% std::_Rb_tree::_M_insert_unique_ (inline) 655ms 0.61% 64.06% 2957ms 2.74% boost::numeric::ublas::vector_binary::size (inline) 469ms 0.43% 64.49% 2886ms 2.67% std::_Rb_tree_const_iterator::operator++ (inline) 2038ms 1.89% 66.38% 2873ms 2.66% _int_malloc 746ms 0.69% 67.07% 2872ms 2.66% AbstractCellProperty::IsSame 40ms 0.037% 67.11% 2864ms 2.65% CellPropertyCollection::HasProperty 38ms 0.035% 67.15% 2827ms 2.62% std::_Rb_tree::erase 0 0% 67.15% 2739ms 2.54% Cell::HasCellProperty (inline) 2583ms 2.39% 69.54% 2583ms 2.39% std::_Rb_tree::_S_right (inline) 251ms 0.23% 69.77% 2532ms 2.35% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.77% 2477ms 2.29% boost::numeric::ublas::c_vector::assign (inline) 2ms 0.0019% 69.77% 2463ms 2.28% std::_Rb_tree::_M_insert_unique 0 0% 69.77% 2430ms 2.25% boost::numeric::ublas::c_vector::operator-= (inline) 146ms 0.14% 69.91% 2379ms 2.20% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 69.91% 2344ms 2.17% AbstractCellPopulation::WriteResultsToFiles 33ms 0.031% 69.94% 2320ms 2.15% Cell::GetCellData 96ms 0.089% 70.03% 2226ms 2.06% VertexMesh::GetVolumeOfElement 2202ms 2.04% 72.07% 2202ms 2.04% std::_Rb_tree_increment 38ms 0.035% 72.10% 2137ms 1.98% std::_Rb_tree::_M_emplace_hint_unique 1ms 0.00093% 72.10% 2130ms 1.97% AbstractCellPopulation::Iterator::operator++ (inline) 498ms 0.46% 72.56% 2126ms 1.97% std::type_info::operator== (inline) 221ms 0.2% 72.77% 2119ms 1.96% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 72.77% 1929ms 1.79% VertexBasedCellPopulation::WriteVtkResultsToFile 2ms 0.0019% 72.77% 1920ms 1.78% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1ms 0.00093% 72.77% 1895ms 1.76% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.77% 1895ms 1.76% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 75ms 0.069% 72.84% 1855ms 1.72% MutableVertexMesh::CheckForSwapsFromShortEdges 1208ms 1.12% 73.96% 1823ms 1.69% std::_Rb_tree::equal_range (inline) 0 0% 73.96% 1727ms 1.60% VertexMeshWriter::WriteVtkUsingMesh 145ms 0.13% 74.10% 1656ms 1.53% boost::numeric::ublas::vector_reference::operator() (inline) 10ms 0.0093% 74.10% 1648ms 1.53% VertexMesh::GetSurfaceAreaOfElement 39ms 0.036% 74.14% 1605ms 1.49% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 74.14% 1540ms 1.43% boost::numeric::ublas::vector_binary::operator() (inline) 63ms 0.058% 74.20% 1531ms 1.42% Node::RemoveElement 194ms 0.18% 74.38% 1529ms 1.42% CellPropertyCollection::AddProperty 28ms 0.026% 74.40% 1488ms 1.38% std::set::erase (inline) 28ms 0.026% 74.43% 1415ms 1.31% AbstractCellPopulation::GetLocationIndexUsingCell 96ms 0.089% 74.52% 1395ms 1.29% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 74.52% 1234ms 1.14% tcache_get (inline) 1234ms 1.14% 75.66% 1234ms 1.14% tcache_get_n (inline) 1ms 0.00093% 75.66% 1216ms 1.13% OffLatticeSimulation::ApplyBoundaries 0 0% 75.66% 1203ms 1.11% boost::numeric::ublas::norm_2 (inline) 557ms 0.52% 76.18% 1191ms 1.10% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 28ms 0.026% 76.21% 1183ms 1.10% CellPropertyRegistry::Get 78ms 0.072% 76.28% 1158ms 1.07% std::_Rb_tree::_M_erase_aux (partial-inline) 88ms 0.082% 76.36% 1143ms 1.06% std::less::operator() (inline) 1135ms 1.05% 77.41% 1135ms 1.05% std::_Rb_tree_insert_and_rebalance 1130ms 1.05% 78.46% 1130ms 1.05% [libchaste_cell_based.so] 0 0% 78.46% 1107ms 1.03% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1078ms 1% 79.46% 1078ms 1% Node::rGetLocation 168ms 0.16% 79.61% 1066ms 0.99% boost::detail::shared_count::~shared_count (inline) 0 0% 79.61% 1066ms 0.99% boost::shared_ptr::~shared_ptr (inline) 20ms 0.019% 79.63% 1056ms 0.98% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 858ms 0.79% 80.43% 1055ms 0.98% std::operator< (inline) 95ms 0.088% 80.51% 1015ms 0.94% std::_Rb_tree::find (inline) 1011ms 0.94% 81.45% 1011ms 0.94% std::vector::size (inline) 12ms 0.011% 81.46% 977ms 0.91% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1ms 0.00093% 81.46% 971ms 0.9% std::_Rb_tree::clear (inline) 136ms 0.13% 81.59% 965ms 0.89% MutableElement::GetNodeLocalIndex 0 0% 81.59% 956ms 0.89% boost::numeric::ublas::c_vector::assign_temporary (inline) 2ms 0.0019% 81.59% 956ms 0.89% boost::numeric::ublas::c_vector::swap (inline) 86ms 0.08% 81.67% 954ms 0.88% std::swap_ranges (inline) 0 0% 81.67% 949ms 0.88% std::map::clear (inline) 933ms 0.86% 82.53% 933ms 0.86% [libchaste_mesh.so] 37ms 0.034% 82.57% 915ms 0.85% boost::numeric::ublas::detail::expression_type_check (inline) 871ms 0.81% 83.38% 874ms 0.81% boost::detail::sp_counted_base::release 869ms 0.81% 84.18% 869ms 0.81% std::swap (inline) 0 0% 84.18% 868ms 0.8% std::iter_swap (inline) 134ms 0.12% 84.30% 867ms 0.8% boost::numeric::ublas::detail::equals 3ms 0.0028% 84.31% 849ms 0.79% VertexMeshWriter::MakeVtkMesh 369ms 0.34% 84.65% 831ms 0.77% Edge::GetMapIndex 0 0% 84.65% 802ms 0.74% std::map::find (inline) 33ms 0.031% 84.68% 778ms 0.72% MutableElement::RegisterWithEdges (inline) 117ms 0.11% 84.79% 777ms 0.72% boost::numeric::ublas::c_vector::operator= (inline) 172ms 0.16% 84.95% 766ms 0.71% boost::shared_ptr::shared_ptr (inline) 22ms 0.02% 84.97% 754ms 0.7% Edge::AddElement 0 0% 84.97% 746ms 0.69% CellPropertyCollection::~CellPropertyCollection (inline) 743ms 0.69% 85.66% 743ms 0.69% Node::GetIndex 431ms 0.4% 86.06% 742ms 0.69% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 86.06% 692ms 0.64% boost::numeric::ublas::norm_inf (inline) 354ms 0.33% 86.38% 692ms 0.64% boost::numeric::ublas::vector_norm_inf::apply (inline) 109ms 0.1% 86.48% 687ms 0.64% std::__new_allocator::construct (inline) 0 0% 86.48% 687ms 0.64% std::allocator_traits::construct (inline) 0 0% 86.48% 684ms 0.63% std::_Rb_tree::_Auto_node::_M_insert (inline) 32ms 0.03% 86.51% 684ms 0.63% std::_Rb_tree::_M_insert_node (inline) 1ms 0.00093% 86.51% 640ms 0.59% vtkPolygon::New 2ms 0.0019% 86.52% 639ms 0.59% vtkPolygon::vtkPolygon 0 0% 86.52% 637ms 0.59% std::_Rb_tree::_M_construct_node (inline) 0 0% 86.52% 633ms 0.59% std::_Vector_base::_M_allocate (inline) 573ms 0.53% 87.05% 594ms 0.55% boost::detail::shared_count::shared_count (inline) 0 0% 87.05% 587ms 0.54% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 575ms 0.53% 87.58% 575ms 0.53% operator delete 568ms 0.53% 88.11% 568ms 0.53% [libstdc++.so.6.0.33] 14ms 0.013% 88.12% 562ms 0.52% MutableElement::RegisterWithNodes (inline)