File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 94524ms, 88.14% of 107248ms total Dropped 1060 nodes (cum <= 536.24ms) flat flat% sum% cum cum% 0 0% 0% 106761ms 99.55% __libc_start_call_main 0 0% 0% 106761ms 99.55% __libc_start_main_impl 0 0% 0% 106761ms 99.55% _start 0 0% 0% 106742ms 99.53% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 106742ms 99.53% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 106742ms 99.53% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 106742ms 99.53% main 0 0% 0% 106704ms 99.49% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 106704ms 99.49% CxxTest::TestRunner::runTest (inline) 0 0% 0% 106704ms 99.49% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 1ms 0.00093% 0.00093% 106696ms 99.49% AbstractCellBasedSimulation::Solve 19ms 0.018% 0.019% 55280ms 51.54% OffLatticeSimulation::UpdateCellLocationsAndTopology 14ms 0.013% 0.032% 52132ms 48.61% ForwardEulerNumericalMethod::UpdateAllNodePositions 118ms 0.11% 0.14% 51054ms 47.60% AbstractNumericalMethod::ComputeForcesIncludingDamping 318ms 0.3% 0.44% 39824ms 37.13% NagaiHondaForce::AddForceContribution 0 0% 0.44% 38809ms 36.19% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.44% 23931ms 22.31% VertexBasedCellPopulation::Update 0 0% 0.44% 23802ms 22.19% MutableVertexMesh::ReMesh 14478ms 13.50% 13.94% 23122ms 21.56% Cylindrical2dVertexMesh::GetVectorFromAtoB 81ms 0.076% 14.01% 17250ms 16.08% Cell::ReadyToDivide 68ms 0.063% 14.08% 16078ms 14.99% AbstractPhaseBasedCellCycleModel::ReadyToDivide 402ms 0.37% 14.45% 14913ms 13.91% boost::numeric::ublas::c_vector::c_vector (partial-inline) 403ms 0.38% 14.83% 14799ms 13.80% NagaiHondaForce::GetAdhesionParameter 127ms 0.12% 14.95% 13707ms 12.78% SimpleWntCellCycleModel::UpdateCellCyclePhase 335ms 0.31% 15.26% 13335ms 12.43% boost::numeric::ublas::vector_assign (inline) 138ms 0.13% 15.39% 13299ms 12.40% CellPropertyCollection::GetPropertiesType (inline) 141ms 0.13% 15.52% 12078ms 11.26% MutableVertexMesh::CheckForIntersections 2941ms 2.74% 18.26% 11227ms 10.47% __dynamic_cast 61ms 0.057% 18.32% 11101ms 10.35% AbstractCellProperty::IsSubType (inline) 92ms 0.086% 18.40% 10729ms 10.00% VertexBasedCellPopulation::GetDampingConstant 71ms 0.066% 18.47% 10232ms 9.54% AbstractTargetAreaModifier::UpdateTargetAreas 49ms 0.046% 18.52% 10123ms 9.44% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 25ms 0.023% 18.54% 10097ms 9.41% AbstractCellBasedSimulation::DoCellBirth 2694ms 2.51% 21.05% 9871ms 9.20% boost::numeric::ublas::indexing_vector_assign 1224ms 1.14% 22.19% 9726ms 9.07% std::__new_allocator::allocate (inline) 0 0% 22.19% 9215ms 8.59% std::allocator_traits::allocate (inline) 1287ms 1.20% 23.39% 9155ms 8.54% std::_Rb_tree::_M_erase 881ms 0.82% 24.21% 9041ms 8.43% VertexMesh::ElementIncludesPoint 0 0% 24.21% 9040ms 8.43% std::_Rb_tree::_M_create_node (inline) 357ms 0.33% 24.55% 8955ms 8.35% VertexMesh::GetNextEdgeGradientOfElementAtNode 21ms 0.02% 24.57% 8755ms 8.16% VertexBasedCellPopulation::GetLocationOfCellCentre 742ms 0.69% 25.26% 8597ms 8.02% operator new 0 0% 25.26% 8426ms 7.86% std::_Rb_tree::_M_get_node (inline) 67ms 0.062% 25.32% 8397ms 7.83% Cell::GetMutationState 502ms 0.47% 25.79% 8372ms 7.81% VertexMesh::GetCentroidOfElement 205ms 0.19% 25.98% 8315ms 7.75% std::_Rb_tree::~_Rb_tree (inline) 0 0% 25.98% 8296ms 7.74% std::_Rb_tree::_M_drop_node (inline) 220ms 0.21% 26.18% 8082ms 7.54% std::__new_allocator::deallocate (inline) 3232ms 3.01% 29.20% 8069ms 7.52% __GI___libc_free 0 0% 29.20% 8051ms 7.51% std::allocator_traits::deallocate (inline) 0 0% 29.20% 8000ms 7.46% std::_Rb_tree::_M_put_node (inline) 0 0% 29.20% 7904ms 7.37% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 29.20% 7878ms 7.35% std::set::~set (inline) 2983ms 2.78% 31.98% 7643ms 7.13% __GI___libc_malloc 16ms 0.015% 31.99% 7352ms 6.86% MutableVertexMesh::RemoveDeletedNodesAndElements 1287ms 1.20% 33.19% 7214ms 6.73% AbstractMesh::GetDistanceBetweenNodes 435ms 0.41% 33.60% 6978ms 6.51% std::map::operator[] (partial-inline) 6618ms 6.17% 39.77% 6618ms 6.17% __strcmp_avx2 161ms 0.15% 39.92% 6475ms 6.04% std::_Rb_tree::_Rb_tree (partial-inline) 6340ms 5.91% 45.83% 6340ms 5.91% boost::numeric::ublas::c_vector::operator() 100ms 0.093% 45.93% 6270ms 5.85% SimpleWntCellCycleModel::GetWntLevel 663ms 0.62% 46.54% 6082ms 5.67% std::_Rb_tree::_M_copy (inline) 135ms 0.13% 46.67% 6081ms 5.67% WntConcentration::GetWntLevel 20ms 0.019% 46.69% 6002ms 5.60% std::set::set (inline) 2724ms 2.54% 49.23% 5916ms 5.52% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 49.23% 5435ms 5.07% std::set::insert (inline) 2352ms 2.19% 51.42% 5338ms 4.98% std::_Rb_tree::_M_lower_bound (inline) 33ms 0.031% 51.45% 5209ms 4.86% MutableVertexMesh::RemoveDeletedNodes 653ms 0.61% 52.06% 5098ms 4.75% std::_Rb_tree::_M_clone_node (inline) 29ms 0.027% 52.09% 5009ms 4.67% EdgeHelper::RemoveDeletedEdges 1461ms 1.36% 53.45% 4826ms 4.50% boost::numeric::ublas::c_vector::operator[] (inline) 4462ms 4.16% 57.61% 4821ms 4.50% _int_free 31ms 0.029% 57.64% 4785ms 4.46% EdgeHelper::UpdateEdgesMapKey 0 0% 57.64% 4770ms 4.45% AbstractCellBasedSimulation::DoCellRemoval (inline) 62ms 0.058% 57.70% 4756ms 4.43% std::set_intersection (inline) 310ms 0.29% 57.99% 4694ms 4.38% std::__set_intersection 174ms 0.16% 58.15% 4580ms 4.27% MutableElement::ResetIndex 530ms 0.49% 58.64% 4537ms 4.23% std::_Rb_tree::_M_insert_ (inline) 0 0% 58.64% 4372ms 4.08% std::_Rb_tree::lower_bound (inline) 0 0% 58.64% 4372ms 4.08% std::map::lower_bound (inline) 4204ms 3.92% 62.56% 4204ms 3.92% boost::numeric::ublas::same_impl_ex 42ms 0.039% 62.60% 4030ms 3.76% Cell::GetCellProliferativeType 117ms 0.11% 62.71% 3694ms 3.44% AbstractCellPopulation::GetCellUsingLocationIndex 10ms 0.0093% 62.72% 3537ms 3.30% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 57ms 0.053% 62.77% 3502ms 3.27% AbstractCellProperty::IsType (inline) 0 0% 62.77% 3351ms 3.12% std::insert_iterator::operator= (inline) 2386ms 2.22% 65.00% 3235ms 3.02% _int_malloc 49ms 0.046% 65.04% 3165ms 2.95% Cell::SetCellProliferativeType 730ms 0.68% 65.72% 3066ms 2.86% AbstractElement::GetNodeLocation 634ms 0.59% 66.32% 3012ms 2.81% boost::numeric::ublas::vector_binary::size (inline) 7ms 0.0065% 66.32% 2962ms 2.76% std::_Rb_tree::_M_insert_unique_ (inline) 51ms 0.048% 66.37% 2830ms 2.64% std::_Rb_tree::erase 457ms 0.43% 66.80% 2660ms 2.48% std::_Rb_tree_const_iterator::operator++ (inline) 270ms 0.25% 67.05% 2575ms 2.40% VertexMesh::GetAreaGradientOfElementAtNode 658ms 0.61% 67.66% 2506ms 2.34% AbstractCellProperty::IsSame 4ms 0.0037% 67.66% 2473ms 2.31% std::_Rb_tree::_M_insert_unique 0 0% 67.66% 2431ms 2.27% boost::numeric::ublas::c_vector::operator-= (inline) 2427ms 2.26% 69.93% 2427ms 2.26% std::_Rb_tree::_S_right (inline) 49ms 0.046% 69.97% 2426ms 2.26% CellPropertyCollection::HasProperty 0 0% 69.97% 2393ms 2.23% boost::numeric::ublas::c_vector::assign (inline) 0 0% 69.97% 2355ms 2.20% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.97% 2350ms 2.19% Cell::HasCellProperty (inline) 104ms 0.097% 70.07% 2280ms 2.13% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 11ms 0.01% 70.08% 2223ms 2.07% Cell::GetCellData 110ms 0.1% 70.18% 2207ms 2.06% VertexMesh::GetVolumeOfElement 0 0% 70.18% 2197ms 2.05% AbstractCellPopulation::Iterator::operator++ (inline) 185ms 0.17% 70.36% 2157ms 2.01% AbstractCellPopulation::Iterator::IsRealCell (inline) 27ms 0.025% 70.38% 2135ms 1.99% std::_Rb_tree::_M_emplace_hint_unique 2034ms 1.90% 72.28% 2034ms 1.90% std::_Rb_tree_increment 2ms 0.0019% 72.28% 2021ms 1.88% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.28% 2021ms 1.88% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 72.28% 1917ms 1.79% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00093% 72.28% 1913ms 1.78% VertexBasedCellPopulation::WriteCellVtkResultsToFile 61ms 0.057% 72.34% 1889ms 1.76% MutableVertexMesh::CheckForSwapsFromShortEdges 428ms 0.4% 72.74% 1848ms 1.72% std::type_info::operator== (inline) 1233ms 1.15% 73.89% 1777ms 1.66% std::_Rb_tree::equal_range (inline) 0 0% 73.89% 1733ms 1.62% VertexMeshWriter::WriteVtkUsingMesh 31ms 0.029% 73.91% 1670ms 1.56% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 22ms 0.021% 73.94% 1657ms 1.55% VertexMesh::GetSurfaceAreaOfElement 153ms 0.14% 74.08% 1551ms 1.45% boost::numeric::ublas::vector_reference::operator() (inline) 55ms 0.051% 74.13% 1485ms 1.38% Node::RemoveElement 0 0% 74.13% 1457ms 1.36% boost::numeric::ublas::vector_binary::operator() (inline) 93ms 0.087% 74.22% 1451ms 1.35% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 20ms 0.019% 74.23% 1441ms 1.34% std::set::erase (inline) 32ms 0.03% 74.26% 1435ms 1.34% AbstractCellPopulation::GetLocationIndexUsingCell 146ms 0.14% 74.40% 1400ms 1.31% CellPropertyCollection::AddProperty 0 0% 74.40% 1260ms 1.17% tcache_get (inline) 1260ms 1.17% 75.58% 1260ms 1.17% tcache_get_n (inline) 0 0% 75.58% 1240ms 1.16% boost::numeric::ublas::norm_2 (inline) 532ms 0.5% 76.07% 1228ms 1.15% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 0 0% 76.07% 1227ms 1.14% OffLatticeSimulation::ApplyBoundaries 98ms 0.091% 76.16% 1194ms 1.11% std::_Rb_tree::_M_erase_aux (partial-inline) 5ms 0.0047% 76.17% 1184ms 1.10% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1176ms 1.10% 77.26% 1176ms 1.10% std::_Rb_tree_insert_and_rebalance 0 0% 77.26% 1136ms 1.06% std::_Rb_tree::_Auto_node::_Auto_node (inline) 77ms 0.072% 77.34% 1131ms 1.05% std::less::operator() (inline) 1119ms 1.04% 78.38% 1119ms 1.04% Node::rGetLocation 29ms 0.027% 78.41% 1112ms 1.04% boost::numeric::ublas::detail::expression_type_check (inline) 220ms 0.21% 78.61% 1081ms 1.01% boost::numeric::ublas::detail::equals 1067ms 0.99% 79.61% 1067ms 0.99% [libchaste_cell_based.so] 847ms 0.79% 80.40% 1054ms 0.98% std::operator< (inline) 15ms 0.014% 80.41% 1053ms 0.98% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 1ms 0.00093% 80.41% 1051ms 0.98% std::_Rb_tree::clear (inline) 0 0% 80.41% 1037ms 0.97% std::map::clear (inline) 26ms 0.024% 80.44% 1013ms 0.94% CellPropertyRegistry::Get 998ms 0.93% 81.37% 998ms 0.93% std::vector::size (inline) 101ms 0.094% 81.46% 973ms 0.91% std::_Rb_tree::find (inline) 963ms 0.9% 82.36% 963ms 0.9% [libchaste_mesh.so] 0 0% 82.36% 954ms 0.89% boost::numeric::ublas::c_vector::assign_temporary (inline) 8ms 0.0075% 82.37% 954ms 0.89% boost::numeric::ublas::c_vector::swap 150ms 0.14% 82.51% 948ms 0.88% boost::detail::shared_count::~shared_count (inline) 0 0% 82.51% 948ms 0.88% boost::shared_ptr::~shared_ptr (inline) 93ms 0.087% 82.59% 946ms 0.88% std::swap_ranges (inline) 368ms 0.34% 82.93% 859ms 0.8% Edge::GetMapIndex 854ms 0.8% 83.73% 854ms 0.8% std::swap (inline) 0 0% 83.73% 853ms 0.8% std::iter_swap (inline) 128ms 0.12% 83.85% 826ms 0.77% MutableElement::GetNodeLocalIndex 0 0% 83.85% 825ms 0.77% VertexMeshWriter::MakeVtkMesh 0 0% 83.85% 811ms 0.76% std::map::find (inline) 171ms 0.16% 84.01% 805ms 0.75% boost::shared_ptr::shared_ptr (inline) 27ms 0.025% 84.04% 802ms 0.75% MutableElement::RegisterWithEdges (inline) 35ms 0.033% 84.07% 790ms 0.74% Edge::AddElement 1ms 0.00093% 84.07% 790ms 0.74% std::_Vector_base::_M_allocate (inline) 120ms 0.11% 84.18% 789ms 0.74% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 84.18% 781ms 0.73% boost::numeric::ublas::norm_inf (inline) 402ms 0.37% 84.56% 781ms 0.73% boost::numeric::ublas::vector_norm_inf::apply (inline) 773ms 0.72% 85.28% 779ms 0.73% boost::detail::sp_counted_base::release 0 0% 85.28% 772ms 0.72% CellPropertyCollection::~CellPropertyCollection (inline) 481ms 0.45% 85.72% 746ms 0.7% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 85.72% 713ms 0.66% std::_Rb_tree::_Auto_node::_M_insert (inline) 14ms 0.013% 85.74% 713ms 0.66% std::_Rb_tree::_M_insert_node (inline) 8ms 0.0075% 85.75% 698ms 0.65% std::vector::_M_default_append (inline) 99ms 0.092% 85.84% 671ms 0.63% std::__new_allocator::construct (inline) 0 0% 85.84% 671ms 0.63% std::allocator_traits::construct (inline) 634ms 0.59% 86.43% 634ms 0.59% Node::GetIndex 600ms 0.56% 86.99% 634ms 0.59% boost::detail::shared_count::shared_count (inline) 44ms 0.041% 87.03% 622ms 0.58% MutableElement::RegisterWithNodes (inline) 0 0% 87.03% 619ms 0.58% VertexElementMap::VertexElementMap 0 0% 87.03% 619ms 0.58% std::vector::resize (inline) 0 0% 87.03% 614ms 0.57% std::_Rb_tree::_M_construct_node (inline) 0 0% 87.03% 611ms 0.57% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 87.03% 580ms 0.54% vtkPolygon::New 0 0% 87.03% 580ms 0.54% vtkPolygon::vtkPolygon 578ms 0.54% 87.57% 578ms 0.54% [libstdc++.so.6.0.33] 38ms 0.035% 87.60% 567ms 0.53% Node::AddElement 30ms 0.028% 87.63% 541ms 0.5% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.63% 541ms 0.5% boost::numeric::ublas::vector::vector (inline) 541ms 0.5% 88.14% 541ms 0.5% boost::shared_ptr::operator-> (inline)