File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95594ms, 88.70% of 107778ms total Dropped 1081 nodes (cum <= 538.89ms) flat flat% sum% cum cum% 0 0% 0% 107355ms 99.61% __libc_start_call_main 0 0% 0% 107355ms 99.61% __libc_start_main_impl 0 0% 0% 107355ms 99.61% _start 0 0% 0% 107337ms 99.59% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 107337ms 99.59% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 107337ms 99.59% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 107337ms 99.59% main 0 0% 0% 107298ms 99.55% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 107298ms 99.55% CxxTest::TestRunner::runTest (inline) 0 0% 0% 107298ms 99.55% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 3ms 0.0028% 0.0028% 107290ms 99.55% AbstractCellBasedSimulation::Solve 14ms 0.013% 0.016% 55508ms 51.50% OffLatticeSimulation::UpdateCellLocationsAndTopology 20ms 0.019% 0.034% 52293ms 48.52% ForwardEulerNumericalMethod::UpdateAllNodePositions 122ms 0.11% 0.15% 51266ms 47.57% AbstractNumericalMethod::ComputeForcesIncludingDamping 368ms 0.34% 0.49% 39878ms 37.00% NagaiHondaForce::AddForceContribution 4ms 0.0037% 0.49% 38966ms 36.15% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0019% 0.49% 24279ms 22.53% VertexBasedCellPopulation::Update 1ms 0.00093% 0.5% 24166ms 22.42% MutableVertexMesh::ReMesh 14510ms 13.46% 13.96% 22999ms 21.34% Cylindrical2dVertexMesh::GetVectorFromAtoB 89ms 0.083% 14.04% 17349ms 16.10% Cell::ReadyToDivide 67ms 0.062% 14.10% 16148ms 14.98% AbstractPhaseBasedCellCycleModel::ReadyToDivide 393ms 0.36% 14.47% 14829ms 13.76% NagaiHondaForce::GetAdhesionParameter 416ms 0.39% 14.85% 14463ms 13.42% boost::numeric::ublas::c_vector::c_vector (partial-inline) 129ms 0.12% 14.97% 13709ms 12.72% SimpleWntCellCycleModel::UpdateCellCyclePhase 152ms 0.14% 15.11% 13307ms 12.35% CellPropertyCollection::GetPropertiesType (inline) 368ms 0.34% 15.46% 12954ms 12.02% boost::numeric::ublas::vector_assign (inline) 146ms 0.14% 15.59% 12071ms 11.20% MutableVertexMesh::CheckForIntersections 3078ms 2.86% 18.45% 11042ms 10.25% __dynamic_cast 77ms 0.071% 18.52% 10931ms 10.14% AbstractCellProperty::IsSubType (inline) 69ms 0.064% 18.58% 10869ms 10.08% VertexBasedCellPopulation::GetDampingConstant 64ms 0.059% 18.64% 10352ms 9.60% AbstractTargetAreaModifier::UpdateTargetAreas 69ms 0.064% 18.71% 10268ms 9.53% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 24ms 0.022% 18.73% 10110ms 9.38% AbstractCellBasedSimulation::DoCellBirth 1195ms 1.11% 19.84% 9613ms 8.92% std::__new_allocator::allocate (inline) 2627ms 2.44% 22.27% 9580ms 8.89% boost::numeric::ublas::indexing_vector_assign 1528ms 1.42% 23.69% 9471ms 8.79% std::_Rb_tree::_M_erase 0 0% 23.69% 9128ms 8.47% std::_Rb_tree::_M_create_node (inline) 0 0% 23.69% 9086ms 8.43% std::allocator_traits::allocate (inline) 780ms 0.72% 24.42% 8917ms 8.27% VertexMesh::ElementIncludesPoint 375ms 0.35% 24.76% 8863ms 8.22% VertexMesh::GetNextEdgeGradientOfElementAtNode 207ms 0.19% 24.96% 8602ms 7.98% std::_Rb_tree::~_Rb_tree (inline) 28ms 0.026% 24.98% 8573ms 7.95% VertexBasedCellPopulation::GetLocationOfCellCentre 794ms 0.74% 25.72% 8506ms 7.89% operator new 81ms 0.075% 25.79% 8470ms 7.86% Cell::GetMutationState 0 0% 25.79% 8411ms 7.80% std::_Rb_tree::_M_get_node (inline) 0 0% 25.79% 8323ms 7.72% std::_Rb_tree::_M_drop_node (inline) 494ms 0.46% 26.25% 8183ms 7.59% VertexMesh::GetCentroidOfElement 0 0% 26.25% 8118ms 7.53% std::set::~set (inline) 240ms 0.22% 26.47% 8114ms 7.53% std::__new_allocator::deallocate (inline) 0 0% 26.47% 8078ms 7.50% std::allocator_traits::deallocate (inline) 0 0% 26.47% 8026ms 7.45% std::_Rb_tree::_M_put_node (inline) 0 0% 26.47% 8016ms 7.44% std::_Rb_tree::_Alloc_node::operator() (inline) 3412ms 3.17% 29.64% 8015ms 7.44% __GI___libc_free 15ms 0.014% 29.65% 7761ms 7.20% MutableVertexMesh::RemoveDeletedNodesAndElements 3062ms 2.84% 32.50% 7537ms 6.99% __GI___libc_malloc 1367ms 1.27% 33.76% 7133ms 6.62% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 474ms 0.44% 34.20% 6961ms 6.46% std::map::operator[] (partial-inline) 143ms 0.13% 34.34% 6506ms 6.04% std::_Rb_tree::_Rb_tree (partial-inline) 6358ms 5.90% 40.24% 6358ms 5.90% boost::numeric::ublas::c_vector::operator() 6278ms 5.82% 46.06% 6278ms 5.82% __strcmp_avx2 135ms 0.13% 46.19% 6211ms 5.76% SimpleWntCellCycleModel::GetWntLevel 678ms 0.63% 46.81% 6159ms 5.71% std::_Rb_tree::_M_copy (inline) 19ms 0.018% 46.83% 6028ms 5.59% std::set::set (inline) 117ms 0.11% 46.94% 5965ms 5.53% WntConcentration::GetWntLevel 2680ms 2.49% 49.43% 5527ms 5.13% __cxxabiv1::__si_class_type_info::__do_dyncast 2364ms 2.19% 51.62% 5435ms 5.04% std::_Rb_tree::_M_lower_bound (inline) 0 0% 51.62% 5426ms 5.03% std::set::insert (inline) 25ms 0.023% 51.64% 5286ms 4.90% MutableVertexMesh::RemoveDeletedNodes 653ms 0.61% 52.25% 5181ms 4.81% std::_Rb_tree::_M_clone_node (inline) 30ms 0.028% 52.28% 5117ms 4.75% EdgeHelper::RemoveDeletedEdges 1503ms 1.39% 53.67% 4907ms 4.55% boost::numeric::ublas::c_vector::operator[] (inline) 227ms 0.21% 53.88% 4899ms 4.55% MutableElement::ResetIndex 31ms 0.029% 53.91% 4823ms 4.47% EdgeHelper::UpdateEdgesMapKey 52ms 0.048% 53.96% 4611ms 4.28% std::set_intersection (inline) 4254ms 3.95% 57.91% 4592ms 4.26% _int_free 527ms 0.49% 58.40% 4576ms 4.25% std::_Rb_tree::_M_insert_ (inline) 0 0% 58.40% 4565ms 4.24% AbstractCellBasedSimulation::DoCellRemoval (inline) 288ms 0.27% 58.66% 4559ms 4.23% std::__set_intersection 0 0% 58.66% 4350ms 4.04% std::_Rb_tree::lower_bound (inline) 0 0% 58.66% 4350ms 4.04% std::map::lower_bound (inline) 49ms 0.045% 58.71% 4100ms 3.80% Cell::GetCellProliferativeType 3998ms 3.71% 62.42% 3998ms 3.71% boost::numeric::ublas::same_impl_ex 112ms 0.1% 62.52% 3687ms 3.42% AbstractCellPopulation::GetCellUsingLocationIndex 80ms 0.074% 62.60% 3682ms 3.42% AbstractCellProperty::IsType (inline) 13ms 0.012% 62.61% 3520ms 3.27% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.61% 3239ms 3.01% std::insert_iterator::operator= (inline) 57ms 0.053% 62.66% 3230ms 3.00% Cell::SetCellProliferativeType 40ms 0.037% 62.70% 3117ms 2.89% std::_Rb_tree::erase 769ms 0.71% 63.41% 3015ms 2.80% AbstractElement::GetNodeLocation 2115ms 1.96% 65.37% 3010ms 2.79% _int_malloc 2ms 0.0019% 65.38% 2857ms 2.65% std::_Rb_tree::_M_insert_unique_ (inline) 574ms 0.53% 65.91% 2837ms 2.63% boost::numeric::ublas::vector_binary::size (inline) 451ms 0.42% 66.33% 2708ms 2.51% std::_Rb_tree_const_iterator::operator++ (inline) 785ms 0.73% 67.06% 2646ms 2.46% AbstractCellProperty::IsSame 2ms 0.0019% 67.06% 2569ms 2.38% std::_Rb_tree::_M_insert_unique 252ms 0.23% 67.29% 2567ms 2.38% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 67.29% 2531ms 2.35% boost::numeric::ublas::c_vector::operator-= (inline) 2528ms 2.35% 69.64% 2528ms 2.35% std::_Rb_tree::_S_right (inline) 49ms 0.045% 69.68% 2502ms 2.32% CellPropertyCollection::HasProperty 0 0% 69.68% 2437ms 2.26% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.68% 2384ms 2.21% Cell::HasCellProperty (inline) 0 0% 69.68% 2366ms 2.20% boost::numeric::ublas::c_vector::assign (inline) 130ms 0.12% 69.80% 2355ms 2.19% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 124ms 0.12% 69.92% 2317ms 2.15% VertexMesh::GetVolumeOfElement 29ms 0.027% 69.94% 2240ms 2.08% Cell::GetCellData 4ms 0.0037% 69.95% 2182ms 2.02% AbstractCellPopulation::Iterator::operator++ (inline) 215ms 0.2% 70.15% 2145ms 1.99% AbstractCellPopulation::Iterator::IsRealCell (inline) 39ms 0.036% 70.18% 2092ms 1.94% std::_Rb_tree::_M_emplace_hint_unique 1439ms 1.34% 71.52% 2073ms 1.92% std::_Rb_tree::equal_range (inline) 2047ms 1.90% 73.42% 2047ms 1.90% std::_Rb_tree_increment 0 0% 73.42% 2014ms 1.87% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 73.42% 1997ms 1.85% VertexBasedCellPopulation::WriteCellVtkResultsToFile 7ms 0.0065% 73.43% 1954ms 1.81% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.43% 1954ms 1.81% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 451ms 0.42% 73.84% 1861ms 1.73% std::type_info::operator== (inline) 70ms 0.065% 73.91% 1836ms 1.70% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 73.91% 1801ms 1.67% VertexMeshWriter::WriteVtkUsingMesh 26ms 0.024% 73.93% 1661ms 1.54% VertexMesh::GetSurfaceAreaOfElement 37ms 0.034% 73.97% 1624ms 1.51% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 127ms 0.12% 74.08% 1609ms 1.49% boost::numeric::ublas::vector_reference::operator() (inline) 61ms 0.057% 74.14% 1536ms 1.43% Node::RemoveElement 143ms 0.13% 74.27% 1502ms 1.39% CellPropertyCollection::AddProperty 0 0% 74.27% 1490ms 1.38% boost::numeric::ublas::vector_binary::operator() (inline) 25ms 0.023% 74.30% 1488ms 1.38% std::set::erase (inline) 23ms 0.021% 74.32% 1466ms 1.36% AbstractCellPopulation::GetLocationIndexUsingCell 78ms 0.072% 74.39% 1437ms 1.33% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 74.39% 1299ms 1.21% tcache_get (inline) 1299ms 1.21% 75.60% 1299ms 1.21% tcache_get_n (inline) 3ms 0.0028% 75.60% 1231ms 1.14% OffLatticeSimulation::ApplyBoundaries 0 0% 75.60% 1218ms 1.13% boost::numeric::ublas::norm_2 (inline) 551ms 0.51% 76.11% 1205ms 1.12% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 78ms 0.072% 76.18% 1202ms 1.12% std::less::operator() (inline) 85ms 0.079% 76.26% 1200ms 1.11% std::_Rb_tree::_M_erase_aux (partial-inline) 1177ms 1.09% 77.35% 1177ms 1.09% [libchaste_cell_based.so] 1125ms 1.04% 78.40% 1125ms 1.04% std::_Rb_tree_insert_and_rebalance 902ms 0.84% 79.23% 1124ms 1.04% std::operator< (inline) 0 0% 79.23% 1112ms 1.03% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1089ms 1.01% 80.24% 1089ms 1.01% Node::rGetLocation 0 0% 80.24% 1080ms 1.00% std::_Rb_tree::clear (inline) 101ms 0.094% 80.34% 1068ms 0.99% std::_Rb_tree::find (inline) 0 0% 80.34% 1066ms 0.99% std::map::clear (inline) 28ms 0.026% 80.36% 1048ms 0.97% CellPropertyRegistry::Get 18ms 0.017% 80.38% 1030ms 0.96% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 29ms 0.027% 80.41% 1009ms 0.94% boost::numeric::ublas::detail::expression_type_check (inline) 8ms 0.0074% 80.42% 999ms 0.93% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 992ms 0.92% 81.34% 992ms 0.92% [libchaste_mesh.so] 0 0% 81.34% 985ms 0.91% boost::numeric::ublas::c_vector::assign_temporary (inline) 3ms 0.0028% 81.34% 985ms 0.91% boost::numeric::ublas::c_vector::swap (inline) 83ms 0.077% 81.42% 982ms 0.91% std::swap_ranges (inline) 172ms 0.16% 81.58% 973ms 0.9% boost::numeric::ublas::detail::equals 160ms 0.15% 81.72% 948ms 0.88% boost::detail::shared_count::~shared_count (inline) 0 0% 81.72% 948ms 0.88% boost::shared_ptr::~shared_ptr (inline) 901ms 0.84% 82.56% 901ms 0.84% std::swap (inline) 900ms 0.84% 83.39% 900ms 0.84% std::vector::size (inline) 0 0% 83.39% 899ms 0.83% std::iter_swap (inline) 169ms 0.16% 83.55% 876ms 0.81% boost::shared_ptr::shared_ptr (inline) 0 0% 83.55% 859ms 0.8% std::map::find (inline) 384ms 0.36% 83.91% 858ms 0.8% Edge::GetMapIndex 1ms 0.00093% 83.91% 846ms 0.78% VertexMeshWriter::MakeVtkMesh 0 0% 83.91% 799ms 0.74% CellPropertyCollection::~CellPropertyCollection (inline) 31ms 0.029% 83.94% 799ms 0.74% Edge::AddElement 120ms 0.11% 84.05% 799ms 0.74% MutableElement::GetNodeLocalIndex 16ms 0.015% 84.06% 792ms 0.73% MutableElement::RegisterWithEdges (inline) 115ms 0.11% 84.17% 785ms 0.73% std::__new_allocator::construct (inline) 0 0% 84.17% 785ms 0.73% std::allocator_traits::construct (inline) 765ms 0.71% 84.88% 775ms 0.72% boost::detail::sp_counted_base::release 86ms 0.08% 84.96% 766ms 0.71% boost::numeric::ublas::c_vector::operator= (inline) 448ms 0.42% 85.38% 751ms 0.7% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 85.38% 736ms 0.68% boost::numeric::ublas::norm_inf (inline) 379ms 0.35% 85.73% 736ms 0.68% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 85.73% 717ms 0.67% std::_Rb_tree::_M_construct_node (inline) 714ms 0.66% 86.39% 714ms 0.66% Node::GetIndex 688ms 0.64% 87.03% 707ms 0.66% boost::detail::shared_count::shared_count (inline) 3ms 0.0028% 87.03% 674ms 0.63% std::_Vector_base::_M_allocate (inline) 0 0% 87.03% 648ms 0.6% std::_Rb_tree::_Auto_node::_M_insert (inline) 19ms 0.018% 87.05% 648ms 0.6% std::_Rb_tree::_M_insert_node (inline) 29ms 0.027% 87.08% 597ms 0.55% MutableElement::RegisterWithNodes (inline) 597ms 0.55% 87.63% 597ms 0.55% [libstdc++.so.6.0.33] 0 0% 87.63% 590ms 0.55% vtkPolygon::New 2ms 0.0019% 87.63% 590ms 0.55% vtkPolygon::vtkPolygon 0 0% 87.63% 583ms 0.54% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 35ms 0.032% 87.66% 562ms 0.52% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.66% 562ms 0.52% boost::numeric::ublas::vector::vector (inline) 26ms 0.024% 87.69% 559ms 0.52% Node::AddElement 544ms 0.5% 88.19% 544ms 0.5% operator delete 542ms 0.5% 88.70% 542ms 0.5% boost::shared_ptr::operator-> (inline)