File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 97059ms, 88.13% of 110126ms total Dropped 1061 nodes (cum <= 550.63ms) flat flat% sum% cum cum% 0 0% 0% 109643ms 99.56% __libc_start_call_main 0 0% 0% 109643ms 99.56% __libc_start_main_impl 0 0% 0% 109643ms 99.56% _start 0 0% 0% 109624ms 99.54% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 109624ms 99.54% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 109624ms 99.54% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 109624ms 99.54% main 0 0% 0% 109588ms 99.51% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 109588ms 99.51% CxxTest::TestRunner::runTest (inline) 0 0% 0% 109588ms 99.51% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 1ms 0.00091% 0.00091% 109581ms 99.51% AbstractCellBasedSimulation::Solve 22ms 0.02% 0.021% 56913ms 51.68% OffLatticeSimulation::UpdateCellLocationsAndTopology 27ms 0.025% 0.045% 53803ms 48.86% ForwardEulerNumericalMethod::UpdateAllNodePositions 134ms 0.12% 0.17% 52617ms 47.78% AbstractNumericalMethod::ComputeForcesIncludingDamping 385ms 0.35% 0.52% 40616ms 36.88% NagaiHondaForce::AddForceContribution 0 0% 0.52% 39251ms 35.64% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00091% 0.52% 24112ms 21.89% VertexBasedCellPopulation::Update 1ms 0.00091% 0.52% 23967ms 21.76% MutableVertexMesh::ReMesh 14381ms 13.06% 13.58% 22858ms 20.76% Cylindrical2dVertexMesh::GetVectorFromAtoB 84ms 0.076% 13.65% 17932ms 16.28% Cell::ReadyToDivide 57ms 0.052% 13.71% 16658ms 15.13% AbstractPhaseBasedCellCycleModel::ReadyToDivide 332ms 0.3% 14.01% 15566ms 14.13% NagaiHondaForce::GetAdhesionParameter 403ms 0.37% 14.37% 14320ms 13.00% boost::numeric::ublas::c_vector::c_vector (partial-inline) 114ms 0.1% 14.48% 14300ms 12.99% SimpleWntCellCycleModel::UpdateCellCyclePhase 136ms 0.12% 14.60% 14008ms 12.72% CellPropertyCollection::GetPropertiesType (inline) 364ms 0.33% 14.93% 12784ms 11.61% boost::numeric::ublas::vector_assign (inline) 114ms 0.1% 15.03% 12037ms 10.93% MutableVertexMesh::CheckForIntersections 98ms 0.089% 15.12% 11467ms 10.41% VertexBasedCellPopulation::GetDampingConstant 3268ms 2.97% 18.09% 11417ms 10.37% __dynamic_cast 70ms 0.064% 18.15% 11308ms 10.27% AbstractCellProperty::IsSubType (inline) 82ms 0.074% 18.23% 10926ms 9.92% AbstractTargetAreaModifier::UpdateTargetAreas 58ms 0.053% 18.28% 10817ms 9.82% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 40ms 0.036% 18.32% 10547ms 9.58% AbstractCellBasedSimulation::DoCellBirth 1334ms 1.21% 19.53% 10399ms 9.44% std::__new_allocator::allocate (inline) 0 0% 19.53% 9901ms 8.99% std::_Rb_tree::_M_create_node (inline) 0 0% 19.53% 9879ms 8.97% std::allocator_traits::allocate (inline) 2710ms 2.46% 21.99% 9571ms 8.69% boost::numeric::ublas::indexing_vector_assign 1425ms 1.29% 23.28% 9526ms 8.65% std::_Rb_tree::_M_erase 0 0% 23.28% 9244ms 8.39% std::_Rb_tree::_M_get_node (inline) 844ms 0.77% 24.05% 9131ms 8.29% operator new 802ms 0.73% 24.78% 9049ms 8.22% VertexMesh::ElementIncludesPoint 95ms 0.086% 24.86% 8938ms 8.12% Cell::GetMutationState 386ms 0.35% 25.21% 8867ms 8.05% VertexMesh::GetNextEdgeGradientOfElementAtNode 22ms 0.02% 25.23% 8819ms 8.01% VertexBasedCellPopulation::GetLocationOfCellCentre 233ms 0.21% 25.45% 8742ms 7.94% std::_Rb_tree::~_Rb_tree (inline) 0 0% 25.45% 8733ms 7.93% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 25.45% 8354ms 7.59% std::set::~set (inline) 0 0% 25.45% 8338ms 7.57% std::_Rb_tree::_M_drop_node (inline) 479ms 0.43% 25.88% 8291ms 7.53% VertexMesh::GetCentroidOfElement 289ms 0.26% 26.14% 8143ms 7.39% std::__new_allocator::deallocate (inline) 0 0% 26.14% 8095ms 7.35% std::allocator_traits::deallocate (inline) 3410ms 3.10% 29.24% 8068ms 7.33% __GI___libc_malloc 0 0% 29.24% 8033ms 7.29% std::_Rb_tree::_M_put_node (inline) 3270ms 2.97% 32.21% 7905ms 7.18% __GI___libc_free 458ms 0.42% 32.63% 7573ms 6.88% std::map::operator[] (partial-inline) 21ms 0.019% 32.64% 7562ms 6.87% MutableVertexMesh::RemoveDeletedNodesAndElements 140ms 0.13% 32.77% 7142ms 6.49% std::_Rb_tree::_Rb_tree (partial-inline) 1414ms 1.28% 34.06% 7071ms 6.42% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 8ms 0.0073% 34.06% 6787ms 6.16% std::set::set (inline) 684ms 0.62% 34.68% 6749ms 6.13% std::_Rb_tree::_M_copy (inline) 6654ms 6.04% 40.73% 6654ms 6.04% __strcmp_avx2 97ms 0.088% 40.81% 6353ms 5.77% SimpleWntCellCycleModel::GetWntLevel 157ms 0.14% 40.96% 6171ms 5.60% WntConcentration::GetWntLevel 6136ms 5.57% 46.53% 6136ms 5.57% boost::numeric::ublas::c_vector::operator() 2578ms 2.34% 48.87% 6038ms 5.48% std::_Rb_tree::_M_lower_bound (inline) 757ms 0.69% 49.56% 5793ms 5.26% std::_Rb_tree::_M_clone_node (inline) 2670ms 2.42% 51.98% 5722ms 5.20% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 51.98% 5631ms 5.11% std::set::insert (inline) 23ms 0.021% 52.00% 5342ms 4.85% MutableVertexMesh::RemoveDeletedNodes 34ms 0.031% 52.03% 5189ms 4.71% EdgeHelper::RemoveDeletedEdges 0 0% 52.03% 4889ms 4.44% std::_Rb_tree::lower_bound (inline) 0 0% 52.03% 4889ms 4.44% std::map::lower_bound (inline) 31ms 0.028% 52.06% 4867ms 4.42% EdgeHelper::UpdateEdgesMapKey 1572ms 1.43% 53.49% 4833ms 4.39% boost::numeric::ublas::c_vector::operator[] (inline) 531ms 0.48% 53.97% 4795ms 4.35% std::_Rb_tree::_M_insert_ (inline) 200ms 0.18% 54.15% 4683ms 4.25% MutableElement::ResetIndex 4303ms 3.91% 58.06% 4626ms 4.20% _int_free 2ms 0.0018% 58.06% 4585ms 4.16% AbstractCellBasedSimulation::DoCellRemoval (inline) 60ms 0.054% 58.12% 4490ms 4.08% std::set_intersection (inline) 257ms 0.23% 58.35% 4430ms 4.02% std::__set_intersection 121ms 0.11% 58.46% 4103ms 3.73% AbstractCellPopulation::GetCellUsingLocationIndex 74ms 0.067% 58.53% 4030ms 3.66% AbstractCellProperty::IsType (inline) 4016ms 3.65% 62.17% 4016ms 3.65% boost::numeric::ublas::same_impl_ex 41ms 0.037% 62.21% 3982ms 3.62% Cell::GetCellProliferativeType 3ms 0.0027% 62.21% 3550ms 3.22% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.21% 3287ms 2.98% std::insert_iterator::operator= (inline) 842ms 0.76% 62.98% 3263ms 2.96% AbstractElement::GetNodeLocation 49ms 0.044% 63.02% 3186ms 2.89% Cell::SetCellProliferativeType 2178ms 1.98% 65.00% 3041ms 2.76% _int_malloc 2929ms 2.66% 67.66% 2929ms 2.66% std::_Rb_tree::_S_right (inline) 40ms 0.036% 67.70% 2924ms 2.66% std::_Rb_tree::erase 660ms 0.6% 68.30% 2909ms 2.64% boost::numeric::ublas::vector_binary::size (inline) 2ms 0.0018% 68.30% 2870ms 2.61% std::_Rb_tree::_M_insert_unique_ (inline) 792ms 0.72% 69.02% 2868ms 2.60% AbstractCellProperty::IsSame 40ms 0.036% 69.05% 2861ms 2.60% CellPropertyCollection::HasProperty 404ms 0.37% 69.42% 2842ms 2.58% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.0018% 69.42% 2761ms 2.51% std::_Rb_tree::_M_insert_unique 0 0% 69.42% 2743ms 2.49% Cell::HasCellProperty (inline) 0 0% 69.42% 2511ms 2.28% boost::numeric::ublas::c_vector::assign (inline) 261ms 0.24% 69.66% 2500ms 2.27% VertexMesh::GetAreaGradientOfElementAtNode 21ms 0.019% 69.68% 2494ms 2.26% Cell::GetCellData 0 0% 69.68% 2472ms 2.24% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.68% 2362ms 2.14% boost::numeric::ublas::c_vector::operator-= (inline) 111ms 0.1% 69.78% 2287ms 2.08% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.0027% 69.78% 2243ms 2.04% AbstractCellPopulation::Iterator::operator++ (inline) 2241ms 2.03% 71.82% 2241ms 2.03% std::_Rb_tree_increment 230ms 0.21% 72.02% 2220ms 2.02% AbstractCellPopulation::Iterator::IsRealCell (inline) 97ms 0.088% 72.11% 2195ms 1.99% VertexMesh::GetVolumeOfElement 36ms 0.033% 72.15% 2179ms 1.98% std::_Rb_tree::_M_emplace_hint_unique 487ms 0.44% 72.59% 2076ms 1.89% std::type_info::operator== (inline) 1393ms 1.26% 73.85% 2032ms 1.85% std::_Rb_tree::equal_range (inline) 0 0% 73.85% 2023ms 1.84% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 73.85% 2015ms 1.83% VertexBasedCellPopulation::WriteCellVtkResultsToFile 67ms 0.061% 73.91% 1835ms 1.67% MutableVertexMesh::CheckForSwapsFromShortEdges 2ms 0.0018% 73.92% 1835ms 1.67% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.92% 1835ms 1.67% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 73.92% 1814ms 1.65% VertexMeshWriter::WriteVtkUsingMesh 204ms 0.19% 74.10% 1730ms 1.57% CellPropertyCollection::AddProperty 28ms 0.025% 74.13% 1711ms 1.55% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 20ms 0.018% 74.14% 1611ms 1.46% VertexMesh::GetSurfaceAreaOfElement 44ms 0.04% 74.18% 1580ms 1.43% Node::RemoveElement 23ms 0.021% 74.21% 1559ms 1.42% AbstractCellPopulation::GetLocationIndexUsingCell 12ms 0.011% 74.22% 1546ms 1.40% std::set::erase (inline) 98ms 0.089% 74.30% 1516ms 1.38% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 131ms 0.12% 74.42% 1469ms 1.33% boost::numeric::ublas::vector_reference::operator() (inline) 1ms 0.00091% 74.42% 1440ms 1.31% tcache_get (inline) 1439ms 1.31% 75.73% 1439ms 1.31% tcache_get_n (inline) 0 0% 75.73% 1347ms 1.22% boost::numeric::ublas::vector_binary::operator() (inline) 3ms 0.0027% 75.73% 1289ms 1.17% OffLatticeSimulation::ApplyBoundaries 47ms 0.043% 75.78% 1221ms 1.11% CellPropertyRegistry::Get 61ms 0.055% 75.83% 1209ms 1.10% std::less::operator() (inline) 1176ms 1.07% 76.90% 1176ms 1.07% [libchaste_cell_based.so] 1175ms 1.07% 77.97% 1175ms 1.07% std::_Rb_tree_insert_and_rebalance 0 0% 77.97% 1168ms 1.06% std::_Rb_tree::_Auto_node::_Auto_node (inline) 937ms 0.85% 78.82% 1148ms 1.04% std::operator< (inline) 0 0% 78.82% 1139ms 1.03% boost::numeric::ublas::norm_2 (inline) 89ms 0.081% 78.90% 1133ms 1.03% std::_Rb_tree::find (inline) 472ms 0.43% 79.33% 1129ms 1.03% boost::numeric::ublas::vector_norm_2::apply 19ms 0.017% 79.34% 1119ms 1.02% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 1112ms 1.01% 80.35% 1112ms 1.01% Node::rGetLocation 68ms 0.062% 80.42% 1078ms 0.98% std::_Rb_tree::_M_erase_aux (partial-inline) 2ms 0.0018% 80.42% 1027ms 0.93% std::_Rb_tree::clear (inline) 0 0% 80.42% 1017ms 0.92% std::map::clear (inline) 1009ms 0.92% 81.33% 1009ms 0.92% [libchaste_mesh.so] 6ms 0.0054% 81.34% 988ms 0.9% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 150ms 0.14% 81.48% 965ms 0.88% boost::detail::shared_count::~shared_count (inline) 0 0% 81.48% 965ms 0.88% boost::shared_ptr::~shared_ptr (inline) 953ms 0.87% 82.34% 953ms 0.87% std::vector::size (inline) 0 0% 82.34% 923ms 0.84% boost::numeric::ublas::c_vector::assign_temporary (inline) 4ms 0.0036% 82.34% 923ms 0.84% boost::numeric::ublas::c_vector::swap (inline) 88ms 0.08% 82.42% 919ms 0.83% std::swap_ranges (inline) 0 0% 82.42% 899ms 0.82% std::map::find (inline) 19ms 0.017% 82.44% 896ms 0.81% boost::numeric::ublas::detail::expression_type_check (inline) 388ms 0.35% 82.79% 895ms 0.81% Edge::GetMapIndex 1ms 0.00091% 82.80% 881ms 0.8% VertexMeshWriter::MakeVtkMesh 137ms 0.12% 82.92% 868ms 0.79% boost::numeric::ublas::detail::equals 125ms 0.11% 83.03% 858ms 0.78% MutableElement::GetNodeLocalIndex 142ms 0.13% 83.16% 854ms 0.78% boost::shared_ptr::shared_ptr (inline) 0 0% 83.16% 831ms 0.75% std::iter_swap (inline) 831ms 0.75% 83.92% 831ms 0.75% std::swap (inline) 118ms 0.11% 84.02% 827ms 0.75% boost::numeric::ublas::c_vector::operator= (inline) 779ms 0.71% 84.73% 788ms 0.72% boost::detail::sp_counted_base::release 25ms 0.023% 84.75% 766ms 0.7% MutableElement::RegisterWithEdges (inline) 764ms 0.69% 85.45% 764ms 0.69% Node::GetIndex 33ms 0.03% 85.48% 751ms 0.68% Edge::AddElement 112ms 0.1% 85.58% 721ms 0.65% std::__new_allocator::construct (inline) 0 0% 85.58% 721ms 0.65% std::allocator_traits::construct (inline) 0 0% 85.58% 717ms 0.65% CellPropertyCollection::~CellPropertyCollection (inline) 683ms 0.62% 86.20% 712ms 0.65% boost::detail::shared_count::shared_count (inline) 416ms 0.38% 86.58% 710ms 0.64% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 86.58% 696ms 0.63% boost::numeric::ublas::norm_inf (inline) 342ms 0.31% 86.89% 696ms 0.63% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 86.89% 689ms 0.63% std::_Rb_tree::_Auto_node::_M_insert (inline) 21ms 0.019% 86.91% 689ms 0.63% std::_Rb_tree::_M_insert_node (inline) 20ms 0.018% 86.92% 666ms 0.6% MutableElement::RegisterWithNodes (inline) 0 0% 86.92% 657ms 0.6% std::_Rb_tree::_M_construct_node (inline) 1ms 0.00091% 86.93% 645ms 0.59% vtkPolygon::New 643ms 0.58% 87.51% 643ms 0.58% [libstdc++.so.6.0.33] 0 0% 87.51% 643ms 0.58% vtkPolygon::vtkPolygon 35ms 0.032% 87.54% 642ms 0.58% Node::AddElement 1ms 0.00091% 87.54% 634ms 0.58% std::_Vector_base::_M_allocate (inline) 591ms 0.54% 88.08% 591ms 0.54% operator delete 28ms 0.025% 88.10% 581ms 0.53% AbstractNumericalMethod::SafeNodePositionUpdate 33ms 0.03% 88.13% 553ms 0.5% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 88.13% 553ms 0.5% boost::numeric::ublas::vector::vector (inline)