File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96666ms, 88.62% of 109083ms total Dropped 1115 nodes (cum <= 545.41ms) flat flat% sum% cum cum% 0 0% 0% 108581ms 99.54% __libc_start_call_main 0 0% 0% 108581ms 99.54% __libc_start_main_impl 0 0% 0% 108581ms 99.54% _start 0 0% 0% 108562ms 99.52% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108562ms 99.52% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108562ms 99.52% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108562ms 99.52% main 0 0% 0% 108522ms 99.49% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108522ms 99.49% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108522ms 99.49% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 4ms 0.0037% 0.0037% 108513ms 99.48% AbstractCellBasedSimulation::Solve 28ms 0.026% 0.029% 56178ms 51.50% OffLatticeSimulation::UpdateCellLocationsAndTopology 25ms 0.023% 0.052% 52873ms 48.47% ForwardEulerNumericalMethod::UpdateAllNodePositions 118ms 0.11% 0.16% 51329ms 47.05% AbstractNumericalMethod::ComputeForcesIncludingDamping 394ms 0.36% 0.52% 39686ms 36.38% NagaiHondaForce::AddForceContribution 0 0% 0.52% 39103ms 35.85% AbstractCellBasedSimulation::UpdateCellPopulation 5ms 0.0046% 0.53% 24379ms 22.35% VertexBasedCellPopulation::Update 1ms 0.00092% 0.53% 24231ms 22.21% MutableVertexMesh::ReMesh 14471ms 13.27% 13.79% 22945ms 21.03% Cylindrical2dVertexMesh::GetVectorFromAtoB 126ms 0.12% 13.91% 17619ms 16.15% Cell::ReadyToDivide 82ms 0.075% 13.98% 16287ms 14.93% AbstractPhaseBasedCellCycleModel::ReadyToDivide 349ms 0.32% 14.30% 14654ms 13.43% NagaiHondaForce::GetAdhesionParameter 453ms 0.42% 14.72% 14279ms 13.09% boost::numeric::ublas::c_vector::c_vector (partial-inline) 142ms 0.13% 14.85% 14035ms 12.87% CellPropertyCollection::GetPropertiesType (inline) 101ms 0.093% 14.94% 13774ms 12.63% SimpleWntCellCycleModel::UpdateCellCyclePhase 370ms 0.34% 15.28% 12691ms 11.63% boost::numeric::ublas::vector_assign (inline) 143ms 0.13% 15.41% 12137ms 11.13% MutableVertexMesh::CheckForIntersections 3257ms 2.99% 18.40% 11522ms 10.56% __dynamic_cast 57ms 0.052% 18.45% 11441ms 10.49% AbstractCellProperty::IsSubType (inline) 91ms 0.083% 18.53% 11139ms 10.21% VertexBasedCellPopulation::GetDampingConstant 79ms 0.072% 18.61% 10737ms 9.84% AbstractTargetAreaModifier::UpdateTargetAreas 72ms 0.066% 18.67% 10639ms 9.75% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 1260ms 1.16% 19.83% 10377ms 9.51% std::__new_allocator::allocate (inline) 31ms 0.028% 19.86% 10208ms 9.36% AbstractCellBasedSimulation::DoCellBirth 0 0% 19.86% 9829ms 9.01% std::allocator_traits::allocate (inline) 0 0% 19.86% 9805ms 8.99% std::_Rb_tree::_M_create_node (inline) 2763ms 2.53% 22.39% 9446ms 8.66% boost::numeric::ublas::indexing_vector_assign 841ms 0.77% 23.16% 9268ms 8.50% operator new 0 0% 23.16% 9142ms 8.38% std::_Rb_tree::_M_get_node (inline) 1426ms 1.31% 24.47% 9038ms 8.29% std::_Rb_tree::_M_erase 807ms 0.74% 25.21% 9004ms 8.25% VertexMesh::ElementIncludesPoint 361ms 0.33% 25.54% 8845ms 8.11% VertexMesh::GetNextEdgeGradientOfElementAtNode 24ms 0.022% 25.56% 8671ms 7.95% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 25.56% 8670ms 7.95% std::_Rb_tree::_Alloc_node::operator() (inline) 52ms 0.048% 25.61% 8624ms 7.91% Cell::GetMutationState 503ms 0.46% 26.07% 8261ms 7.57% VertexMesh::GetCentroidOfElement 3113ms 2.85% 28.92% 8251ms 7.56% __GI___libc_malloc 248ms 0.23% 29.15% 8230ms 7.54% std::_Rb_tree::~_Rb_tree (inline) 0 0% 29.15% 8041ms 7.37% std::_Rb_tree::_M_drop_node (inline) 18ms 0.017% 29.17% 7857ms 7.20% MutableVertexMesh::RemoveDeletedNodesAndElements 262ms 0.24% 29.41% 7844ms 7.19% std::__new_allocator::deallocate (inline) 0 0% 29.41% 7821ms 7.17% std::allocator_traits::deallocate (inline) 0 0% 29.41% 7727ms 7.08% std::set::~set (inline) 0 0% 29.41% 7725ms 7.08% std::_Rb_tree::_M_put_node (inline) 2923ms 2.68% 32.09% 7716ms 7.07% __GI___libc_free 1397ms 1.28% 33.37% 7141ms 6.55% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 416ms 0.38% 33.75% 7108ms 6.52% std::map::operator[] (partial-inline) 140ms 0.13% 33.88% 6967ms 6.39% std::_Rb_tree::_Rb_tree (partial-inline) 6645ms 6.09% 39.97% 6645ms 6.09% __strcmp_avx2 648ms 0.59% 40.56% 6616ms 6.07% std::_Rb_tree::_M_copy (inline) 15ms 0.014% 40.58% 6495ms 5.95% std::set::set (inline) 101ms 0.093% 40.67% 6340ms 5.81% SimpleWntCellCycleModel::GetWntLevel 168ms 0.15% 40.82% 6141ms 5.63% WntConcentration::GetWntLevel 6133ms 5.62% 46.44% 6133ms 5.62% boost::numeric::ublas::c_vector::operator() 741ms 0.68% 47.12% 5720ms 5.24% std::_Rb_tree::_M_clone_node (inline) 2669ms 2.45% 49.57% 5646ms 5.18% __cxxabiv1::__si_class_type_info::__do_dyncast 2465ms 2.26% 51.83% 5574ms 5.11% std::_Rb_tree::_M_lower_bound (inline) 0 0% 51.83% 5508ms 5.05% std::set::insert (inline) 25ms 0.023% 51.85% 5211ms 4.78% MutableVertexMesh::RemoveDeletedNodes 34ms 0.031% 51.88% 5078ms 4.66% EdgeHelper::RemoveDeletedEdges 243ms 0.22% 52.11% 4970ms 4.56% MutableElement::ResetIndex 1533ms 1.41% 53.51% 4879ms 4.47% boost::numeric::ublas::c_vector::operator[] (inline) 26ms 0.024% 53.54% 4786ms 4.39% EdgeHelper::UpdateEdgesMapKey 4416ms 4.05% 57.58% 4786ms 4.39% _int_free 515ms 0.47% 58.06% 4734ms 4.34% std::_Rb_tree::_M_insert_ (inline) 0 0% 58.06% 4525ms 4.15% std::_Rb_tree::lower_bound (inline) 0 0% 58.06% 4525ms 4.15% std::map::lower_bound (inline) 0 0% 58.06% 4506ms 4.13% AbstractCellBasedSimulation::DoCellRemoval (inline) 50ms 0.046% 58.10% 4430ms 4.06% std::set_intersection (inline) 261ms 0.24% 58.34% 4380ms 4.02% std::__set_intersection 44ms 0.04% 58.38% 4098ms 3.76% Cell::GetCellProliferativeType 115ms 0.11% 58.49% 3890ms 3.57% AbstractCellPopulation::GetCellUsingLocationIndex 3877ms 3.55% 62.04% 3877ms 3.55% boost::numeric::ublas::same_impl_ex 73ms 0.067% 62.11% 3792ms 3.48% AbstractCellProperty::IsType (inline) 11ms 0.01% 62.12% 3439ms 3.15% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.12% 3277ms 3.00% std::insert_iterator::operator= (inline) 47ms 0.043% 62.16% 3229ms 2.96% std::_Rb_tree::erase 844ms 0.77% 62.94% 3213ms 2.95% AbstractElement::GetNodeLocation 40ms 0.037% 62.97% 3102ms 2.84% Cell::SetCellProliferativeType 2102ms 1.93% 64.90% 3093ms 2.84% _int_malloc 6ms 0.0055% 64.90% 2884ms 2.64% std::_Rb_tree::_M_insert_unique_ (inline) 629ms 0.58% 65.48% 2814ms 2.58% boost::numeric::ublas::vector_binary::size (inline) 52ms 0.048% 65.53% 2741ms 2.51% CellPropertyCollection::HasProperty 2740ms 2.51% 68.04% 2740ms 2.51% std::_Rb_tree::_S_right (inline) 750ms 0.69% 68.73% 2739ms 2.51% AbstractCellProperty::IsSame 416ms 0.38% 69.11% 2731ms 2.50% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 69.11% 2639ms 2.42% Cell::HasCellProperty (inline) 0 0% 69.11% 2624ms 2.41% std::_Rb_tree::_M_insert_unique (inline) 20ms 0.018% 69.13% 2533ms 2.32% Cell::GetCellData 0 0% 69.13% 2467ms 2.26% AbstractCellPopulation::WriteResultsToFiles 252ms 0.23% 69.36% 2461ms 2.26% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.36% 2434ms 2.23% boost::numeric::ublas::c_vector::assign (inline) 0 0% 69.36% 2431ms 2.23% boost::numeric::ublas::c_vector::operator-= (inline) 92ms 0.084% 69.44% 2408ms 2.21% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 85ms 0.078% 69.52% 2293ms 2.10% VertexMesh::GetVolumeOfElement 1451ms 1.33% 70.85% 2189ms 2.01% std::_Rb_tree::equal_range (inline) 218ms 0.2% 71.05% 2134ms 1.96% AbstractCellPopulation::Iterator::IsRealCell (inline) 3ms 0.0028% 71.05% 2132ms 1.95% AbstractCellPopulation::Iterator::operator++ (inline) 2122ms 1.95% 73.00% 2122ms 1.95% std::_Rb_tree_increment 32ms 0.029% 73.03% 2113ms 1.94% std::_Rb_tree::_M_emplace_hint_unique 0 0% 73.03% 2034ms 1.86% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00092% 73.03% 2023ms 1.85% VertexBasedCellPopulation::WriteCellVtkResultsToFile 486ms 0.45% 73.48% 1989ms 1.82% std::type_info::operator== (inline) 3ms 0.0028% 73.48% 1964ms 1.80% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.48% 1964ms 1.80% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 73.48% 1893ms 1.74% tcache_get (inline) 1893ms 1.74% 75.21% 1893ms 1.74% tcache_get_n (inline) 54ms 0.05% 75.26% 1832ms 1.68% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 75.26% 1810ms 1.66% VertexMeshWriter::WriteVtkUsingMesh 30ms 0.028% 75.29% 1651ms 1.51% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 22ms 0.02% 75.31% 1650ms 1.51% VertexMesh::GetSurfaceAreaOfElement 159ms 0.15% 75.46% 1617ms 1.48% CellPropertyCollection::AddProperty 48ms 0.044% 75.50% 1577ms 1.45% Node::RemoveElement 146ms 0.13% 75.63% 1569ms 1.44% boost::numeric::ublas::vector_reference::operator() (inline) 22ms 0.02% 75.65% 1539ms 1.41% std::set::erase (inline) 32ms 0.029% 75.68% 1483ms 1.36% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 75.68% 1461ms 1.34% boost::numeric::ublas::vector_binary::operator() (inline) 73ms 0.067% 75.75% 1455ms 1.33% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 75.75% 1257ms 1.15% boost::numeric::ublas::norm_2 (inline) 554ms 0.51% 76.26% 1247ms 1.14% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 2ms 0.0018% 76.26% 1226ms 1.12% OffLatticeSimulation::ApplyBoundaries 86ms 0.079% 76.34% 1191ms 1.09% std::_Rb_tree::_M_erase_aux (partial-inline) 1136ms 1.04% 77.38% 1136ms 1.04% Node::rGetLocation 0 0% 77.38% 1135ms 1.04% std::_Rb_tree::_Auto_node::_Auto_node (inline) 70ms 0.064% 77.44% 1132ms 1.04% std::less::operator() (inline) 1117ms 1.02% 78.47% 1117ms 1.02% [libchaste_cell_based.so] 1103ms 1.01% 79.48% 1103ms 1.01% std::_Rb_tree_insert_and_rebalance 19ms 0.017% 79.50% 1071ms 0.98% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 26ms 0.024% 79.52% 1070ms 0.98% CellPropertyRegistry::Get 868ms 0.8% 80.32% 1062ms 0.97% std::operator< (inline) 0 0% 80.32% 1061ms 0.97% std::_Rb_tree::clear (inline) 0 0% 80.32% 1034ms 0.95% std::map::clear (inline) 8ms 0.0073% 80.32% 1028ms 0.94% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 82ms 0.075% 80.40% 1008ms 0.92% std::_Rb_tree::find (inline) 128ms 0.12% 80.52% 980ms 0.9% boost::detail::shared_count::~shared_count (inline) 0 0% 80.52% 980ms 0.9% boost::shared_ptr::~shared_ptr (inline) 969ms 0.89% 81.40% 969ms 0.89% std::vector::size (inline) 476ms 0.44% 81.84% 956ms 0.88% Edge::GetMapIndex 13ms 0.012% 81.85% 941ms 0.86% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 81.85% 936ms 0.86% boost::numeric::ublas::c_vector::assign_temporary (inline) 4ms 0.0037% 81.86% 936ms 0.86% boost::numeric::ublas::c_vector::swap (inline) 73ms 0.067% 81.92% 932ms 0.85% std::swap_ranges (inline) 160ms 0.15% 82.07% 914ms 0.84% boost::numeric::ublas::detail::equals 885ms 0.81% 82.88% 885ms 0.81% [libchaste_mesh.so] 860ms 0.79% 83.67% 860ms 0.79% std::swap (inline) 0 0% 83.67% 859ms 0.79% std::iter_swap (inline) 0 0% 83.67% 844ms 0.77% VertexMeshWriter::MakeVtkMesh 831ms 0.76% 84.43% 835ms 0.77% boost::detail::sp_counted_base::release 0 0% 84.43% 814ms 0.75% std::map::find (inline) 111ms 0.1% 84.53% 787ms 0.72% boost::numeric::ublas::c_vector::operator= (inline) 117ms 0.11% 84.64% 772ms 0.71% MutableElement::GetNodeLocalIndex 140ms 0.13% 84.77% 765ms 0.7% boost::shared_ptr::shared_ptr (inline) 29ms 0.027% 84.80% 763ms 0.7% Edge::AddElement 24ms 0.022% 84.82% 758ms 0.69% MutableElement::RegisterWithEdges (inline) 93ms 0.085% 84.90% 734ms 0.67% std::__new_allocator::construct (inline) 0 0% 84.90% 734ms 0.67% std::allocator_traits::construct (inline) 12ms 0.011% 84.91% 729ms 0.67% AbstractNumericalMethod::DetectStepSizeExceptions 116ms 0.11% 85.02% 717ms 0.66% VertexBasedCellPopulation::CheckForStepSizeException 708ms 0.65% 85.67% 708ms 0.65% Node::GetIndex 0 0% 85.67% 707ms 0.65% boost::numeric::ublas::norm_inf (inline) 349ms 0.32% 85.99% 707ms 0.65% boost::numeric::ublas::vector_norm_inf::apply (inline) 2ms 0.0018% 85.99% 685ms 0.63% std::_Vector_base::_M_allocate (inline) 378ms 0.35% 86.34% 670ms 0.61% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 86.34% 668ms 0.61% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 86.34% 663ms 0.61% std::_Rb_tree::_M_construct_node (inline) 0 0% 86.34% 662ms 0.61% std::_Rb_tree::_Auto_node::_M_insert (inline) 29ms 0.027% 86.36% 662ms 0.61% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.36% 633ms 0.58% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 631ms 0.58% 86.94% 631ms 0.58% [libstdc++.so.6.0.33] 607ms 0.56% 87.50% 625ms 0.57% boost::detail::shared_count::shared_count (inline) 1ms 0.00092% 87.50% 612ms 0.56% vtkPolygon::New 3ms 0.0028% 87.50% 611ms 0.56% vtkPolygon::vtkPolygon 26ms 0.024% 87.53% 592ms 0.54% MutableElement::RegisterWithNodes (inline) 8ms 0.0073% 87.53% 581ms 0.53% std::vector::_M_default_append (inline) 573ms 0.53% 88.06% 573ms 0.53% operator delete 18ms 0.017% 88.08% 566ms 0.52% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 88.08% 566ms 0.52% boost::numeric::ublas::vector::vector (inline) 558ms 0.51% 88.59% 558ms 0.51% boost::shared_ptr::operator-> (inline) 32ms 0.029% 88.62% 556ms 0.51% Node::AddElement