File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96760ms, 87.42% of 110685ms total Dropped 1141 nodes (cum <= 553.42ms) flat flat% sum% cum cum% 0 0% 0% 110303ms 99.65% __libc_start_call_main 0 0% 0% 110303ms 99.65% __libc_start_main_impl 0 0% 0% 110303ms 99.65% _start 0 0% 0% 110282ms 99.64% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 110282ms 99.64% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 110282ms 99.64% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 110282ms 99.64% main 0 0% 0% 110237ms 99.60% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 110237ms 99.60% CxxTest::TestRunner::runTest (inline) 0 0% 0% 110237ms 99.60% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 0 0% 0% 110229ms 99.59% AbstractCellBasedSimulation::Solve 21ms 0.019% 0.019% 57780ms 52.20% OffLatticeSimulation::UpdateCellLocationsAndTopology 6ms 0.0054% 0.024% 54440ms 49.18% ForwardEulerNumericalMethod::UpdateAllNodePositions 156ms 0.14% 0.17% 52898ms 47.79% AbstractNumericalMethod::ComputeForcesIncludingDamping 327ms 0.3% 0.46% 40713ms 36.78% NagaiHondaForce::AddForceContribution 5ms 0.0045% 0.47% 39125ms 35.35% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0009% 0.47% 24127ms 21.80% VertexBasedCellPopulation::Update 1ms 0.0009% 0.47% 23969ms 21.66% MutableVertexMesh::ReMesh 14794ms 13.37% 13.83% 23400ms 21.14% Cylindrical2dVertexMesh::GetVectorFromAtoB 105ms 0.095% 13.93% 17712ms 16.00% Cell::ReadyToDivide 83ms 0.075% 14.00% 16315ms 14.74% AbstractPhaseBasedCellCycleModel::ReadyToDivide 354ms 0.32% 14.32% 14891ms 13.45% NagaiHondaForce::GetAdhesionParameter 156ms 0.14% 14.46% 14014ms 12.66% SimpleWntCellCycleModel::UpdateCellCyclePhase 114ms 0.1% 14.57% 13784ms 12.45% CellPropertyCollection::GetPropertiesType (inline) 460ms 0.42% 14.98% 13771ms 12.44% boost::numeric::ublas::c_vector::c_vector (partial-inline) 285ms 0.26% 15.24% 12275ms 11.09% boost::numeric::ublas::vector_assign (inline) 141ms 0.13% 15.37% 11813ms 10.67% MutableVertexMesh::CheckForIntersections 3520ms 3.18% 18.55% 11677ms 10.55% __dynamic_cast 91ms 0.082% 18.63% 11614ms 10.49% VertexBasedCellPopulation::GetDampingConstant 36ms 0.033% 18.66% 11516ms 10.40% AbstractCellProperty::IsSubType (inline) 78ms 0.07% 18.73% 10809ms 9.77% AbstractTargetAreaModifier::UpdateTargetAreas 38ms 0.034% 18.77% 10690ms 9.66% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 1334ms 1.21% 19.97% 10375ms 9.37% std::__new_allocator::allocate (inline) 24ms 0.022% 19.99% 10232ms 9.24% AbstractCellBasedSimulation::DoCellBirth 0 0% 19.99% 9931ms 8.97% std::_Rb_tree::_M_create_node (inline) 0 0% 19.99% 9854ms 8.90% std::allocator_traits::allocate (inline) 384ms 0.35% 20.34% 9520ms 8.60% VertexMesh::GetNextEdgeGradientOfElementAtNode 2842ms 2.57% 22.91% 9417ms 8.51% boost::numeric::ublas::indexing_vector_assign 0 0% 22.91% 9164ms 8.28% std::_Rb_tree::_M_get_node (inline) 733ms 0.66% 23.57% 9130ms 8.25% operator new 1268ms 1.15% 24.72% 8978ms 8.11% std::_Rb_tree::_M_erase 0 0% 24.72% 8777ms 7.93% std::_Rb_tree::_Alloc_node::operator() (inline) 862ms 0.78% 25.49% 8711ms 7.87% VertexMesh::ElementIncludesPoint 29ms 0.026% 25.52% 8686ms 7.85% VertexBasedCellPopulation::GetLocationOfCellCentre 95ms 0.086% 25.61% 8545ms 7.72% Cell::GetMutationState 464ms 0.42% 26.03% 8217ms 7.42% VertexMesh::GetCentroidOfElement 0 0% 26.03% 8156ms 7.37% std::_Rb_tree::_M_drop_node (inline) 3145ms 2.84% 28.87% 8150ms 7.36% __GI___libc_malloc 234ms 0.21% 29.08% 8063ms 7.28% std::_Rb_tree::~_Rb_tree (inline) 582ms 0.53% 29.60% 7920ms 7.16% std::map::operator[] (partial-inline) 198ms 0.18% 29.78% 7905ms 7.14% std::__new_allocator::deallocate (inline) 0 0% 29.78% 7904ms 7.14% std::allocator_traits::deallocate (inline) 16ms 0.014% 29.80% 7856ms 7.10% MutableVertexMesh::RemoveDeletedNodesAndElements 0 0% 29.80% 7824ms 7.07% std::_Rb_tree::_M_put_node (inline) 0 0% 29.80% 7635ms 6.90% std::set::~set (inline) 1509ms 1.36% 31.16% 7529ms 6.80% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 2562ms 2.31% 33.48% 7439ms 6.72% __GI___libc_free 193ms 0.17% 33.65% 7437ms 6.72% std::_Rb_tree::_Rb_tree (partial-inline) 744ms 0.67% 34.32% 6978ms 6.30% std::_Rb_tree::_M_copy (inline) 22ms 0.02% 34.34% 6973ms 6.30% std::set::set (inline) 6604ms 5.97% 40.31% 6604ms 5.97% __strcmp_avx2 119ms 0.11% 40.42% 6293ms 5.69% SimpleWntCellCycleModel::GetWntLevel 6204ms 5.61% 46.02% 6204ms 5.61% boost::numeric::ublas::c_vector::operator() 2558ms 2.31% 48.33% 6132ms 5.54% std::_Rb_tree::_M_lower_bound (inline) 188ms 0.17% 48.50% 6085ms 5.50% WntConcentration::GetWntLevel 854ms 0.77% 49.27% 6001ms 5.42% std::_Rb_tree::_M_clone_node (inline) 2883ms 2.60% 51.88% 5506ms 4.97% __cxxabiv1::__si_class_type_info::__do_dyncast 20ms 0.018% 51.90% 5486ms 4.96% MutableVertexMesh::RemoveDeletedNodes 0 0% 51.90% 5411ms 4.89% std::set::insert (inline) 33ms 0.03% 51.93% 5303ms 4.79% EdgeHelper::RemoveDeletedEdges 1832ms 1.66% 53.58% 5252ms 4.74% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 53.58% 5064ms 4.58% std::_Rb_tree::lower_bound (inline) 0 0% 53.58% 5064ms 4.58% std::map::lower_bound (inline) 34ms 0.031% 53.61% 4977ms 4.50% EdgeHelper::UpdateEdgesMapKey 4423ms 4.00% 57.61% 4847ms 4.38% _int_free 151ms 0.14% 57.74% 4788ms 4.33% MutableElement::ResetIndex 1ms 0.0009% 57.75% 4754ms 4.30% AbstractCellBasedSimulation::DoCellRemoval (inline) 161ms 0.15% 57.89% 4646ms 4.20% AbstractCellPopulation::GetCellUsingLocationIndex 455ms 0.41% 58.30% 4582ms 4.14% std::_Rb_tree::_M_insert_ (inline) 211ms 0.19% 58.49% 4488ms 4.05% std::set_intersection (inline) 221ms 0.2% 58.69% 4277ms 3.86% std::__set_intersection 40ms 0.036% 58.73% 4077ms 3.68% Cell::GetCellProliferativeType 41ms 0.037% 58.77% 3927ms 3.55% AbstractCellProperty::IsType (inline) 3765ms 3.40% 62.17% 3765ms 3.40% boost::numeric::ublas::same_impl_ex 13ms 0.012% 62.18% 3579ms 3.23% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.18% 3334ms 3.01% std::insert_iterator::operator= (inline) 2308ms 2.09% 64.26% 3269ms 2.95% _int_malloc 38ms 0.034% 64.30% 3174ms 2.87% Cell::SetCellProliferativeType 72ms 0.065% 64.36% 3125ms 2.82% std::_Rb_tree::erase 926ms 0.84% 65.20% 3092ms 2.79% AbstractElement::GetNodeLocation 3030ms 2.74% 67.94% 3030ms 2.74% std::_Rb_tree::_S_right (inline) 18ms 0.016% 67.95% 2921ms 2.64% std::_Rb_tree::_M_insert_unique_ (inline) 35ms 0.032% 67.99% 2894ms 2.61% CellPropertyCollection::HasProperty 758ms 0.68% 68.67% 2863ms 2.59% AbstractCellProperty::IsSame 0 0% 68.67% 2805ms 2.53% Cell::HasCellProperty (inline) 211ms 0.19% 68.86% 2643ms 2.39% VertexMesh::GetAreaGradientOfElementAtNode 274ms 0.25% 69.11% 2623ms 2.37% std::_Rb_tree_const_iterator::operator++ (inline) 623ms 0.56% 69.67% 2603ms 2.35% boost::numeric::ublas::vector_binary::size (inline) 0 0% 69.67% 2602ms 2.35% boost::numeric::ublas::c_vector::operator-= (inline) 28ms 0.025% 69.70% 2577ms 2.33% Cell::GetCellData 0 0% 69.70% 2518ms 2.27% boost::numeric::ublas::c_vector::assign (inline) 2ms 0.0018% 69.70% 2490ms 2.25% std::_Rb_tree::_M_insert_unique 0 0% 69.70% 2485ms 2.25% AbstractCellPopulation::WriteResultsToFiles 90ms 0.081% 69.78% 2329ms 2.10% VertexMesh::GetVolumeOfElement 48ms 0.043% 69.82% 2218ms 2.00% std::_Rb_tree::_M_emplace_hint_unique 4ms 0.0036% 69.83% 2199ms 1.99% AbstractCellPopulation::Iterator::operator++ (inline) 60ms 0.054% 69.88% 2195ms 1.98% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 164ms 0.15% 70.03% 2185ms 1.97% AbstractCellPopulation::Iterator::IsRealCell (inline) 2105ms 1.90% 71.93% 2105ms 1.90% std::_Rb_tree_increment 491ms 0.44% 72.37% 2105ms 1.90% std::type_info::operator== (inline) 1ms 0.0009% 72.38% 2086ms 1.88% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.38% 2086ms 1.88% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 72.38% 2025ms 1.83% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 72.38% 2018ms 1.82% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1338ms 1.21% 73.58% 2007ms 1.81% std::_Rb_tree::equal_range (inline) 0 0% 73.58% 1826ms 1.65% VertexMeshWriter::WriteVtkUsingMesh 71ms 0.064% 73.65% 1812ms 1.64% MutableVertexMesh::CheckForSwapsFromShortEdges 21ms 0.019% 73.67% 1701ms 1.54% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 41ms 0.037% 73.70% 1611ms 1.46% VertexMesh::GetSurfaceAreaOfElement 58ms 0.052% 73.76% 1594ms 1.44% Node::RemoveElement 0 0% 73.76% 1559ms 1.41% tcache_get (inline) 1559ms 1.41% 75.17% 1559ms 1.41% tcache_get_n (inline) 37ms 0.033% 75.20% 1558ms 1.41% AbstractCellPopulation::GetLocationIndexUsingCell 3ms 0.0027% 75.20% 1537ms 1.39% std::set::erase (inline) 90ms 0.081% 75.28% 1516ms 1.37% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 129ms 0.12% 75.40% 1451ms 1.31% CellPropertyCollection::AddProperty 64ms 0.058% 75.46% 1435ms 1.30% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 75.46% 1403ms 1.27% boost::numeric::ublas::norm_2 (inline) 0 0% 75.46% 1402ms 1.27% boost::numeric::ublas::vector_binary::operator() (inline) 609ms 0.55% 76.01% 1394ms 1.26% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1ms 0.0009% 76.01% 1361ms 1.23% OffLatticeSimulation::ApplyBoundaries 45ms 0.041% 76.05% 1278ms 1.15% std::less::operator() (inline) 1249ms 1.13% 77.18% 1249ms 1.13% [libchaste_cell_based.so] 77ms 0.07% 77.25% 1235ms 1.12% std::_Rb_tree::_M_erase_aux (partial-inline) 1013ms 0.92% 78.16% 1233ms 1.11% std::operator< (inline) 21ms 0.019% 78.18% 1170ms 1.06% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 78.18% 1154ms 1.04% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 78.18% 1151ms 1.04% std::_Rb_tree::clear (inline) 35ms 0.032% 78.21% 1143ms 1.03% CellPropertyRegistry::Get 6ms 0.0054% 78.22% 1139ms 1.03% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 78.22% 1129ms 1.02% std::map::clear (inline) 85ms 0.077% 78.30% 1080ms 0.98% std::_Rb_tree::find (inline) 1072ms 0.97% 79.26% 1072ms 0.97% std::_Rb_tree_insert_and_rebalance 0 0% 79.26% 1065ms 0.96% boost::numeric::ublas::c_vector::assign_temporary (inline) 17ms 0.015% 79.28% 1065ms 0.96% boost::numeric::ublas::c_vector::swap (inline) 68ms 0.061% 79.34% 1048ms 0.95% std::swap_ranges (inline) 111ms 0.1% 79.44% 1014ms 0.92% boost::detail::shared_count::~shared_count (inline) 0 0% 79.44% 1014ms 0.92% boost::shared_ptr::~shared_ptr (inline) 981ms 0.89% 80.33% 981ms 0.89% std::swap (inline) 0 0% 80.33% 980ms 0.89% std::iter_swap (inline) 973ms 0.88% 81.21% 973ms 0.88% Node::rGetLocation 10ms 0.009% 81.22% 953ms 0.86% boost::numeric::ublas::detail::expression_type_check (inline) 194ms 0.18% 81.39% 932ms 0.84% boost::numeric::ublas::detail::equals 3ms 0.0027% 81.39% 913ms 0.82% std::map::find (inline) 1ms 0.0009% 81.39% 877ms 0.79% VertexMeshWriter::MakeVtkMesh 870ms 0.79% 82.18% 870ms 0.79% std::vector::size (inline) 843ms 0.76% 82.94% 869ms 0.79% boost::detail::sp_counted_base::release 179ms 0.16% 83.10% 831ms 0.75% boost::shared_ptr::shared_ptr (inline) 107ms 0.097% 83.20% 828ms 0.75% boost::numeric::ublas::c_vector::operator= (inline) 224ms 0.2% 83.40% 806ms 0.73% std::__new_allocator::construct (inline) 0 0% 83.40% 806ms 0.73% std::allocator_traits::construct (inline) 434ms 0.39% 83.79% 784ms 0.71% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 773ms 0.7% 84.49% 773ms 0.7% [libchaste_mesh.so] 401ms 0.36% 84.86% 770ms 0.7% Edge::GetMapIndex 23ms 0.021% 84.88% 767ms 0.69% AbstractNumericalMethod::DetectStepSizeExceptions 0 0% 84.88% 767ms 0.69% std::_Rb_tree::_M_construct_node (inline) 23ms 0.021% 84.90% 761ms 0.69% MutableElement::RegisterWithEdges (inline) 752ms 0.68% 85.58% 752ms 0.68% [libstdc++.so.6.0.33] 0 0% 85.58% 749ms 0.68% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 16ms 0.014% 85.59% 744ms 0.67% Edge::AddElement 136ms 0.12% 85.71% 744ms 0.67% VertexBasedCellPopulation::CheckForStepSizeException 147ms 0.13% 85.85% 738ms 0.67% MutableElement::GetNodeLocalIndex 0 0% 85.85% 721ms 0.65% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 85.85% 687ms 0.62% std::_Vector_base::_M_allocate (inline) 0 0% 85.85% 684ms 0.62% boost::numeric::ublas::norm_inf (inline) 361ms 0.33% 86.17% 684ms 0.62% boost::numeric::ublas::vector_norm_inf::apply (inline) 666ms 0.6% 86.77% 666ms 0.6% Node::GetIndex 0 0% 86.77% 653ms 0.59% std::_Rb_tree::_Auto_node::_M_insert (inline) 16ms 0.014% 86.79% 653ms 0.59% std::_Rb_tree::_M_insert_node (inline) 622ms 0.56% 87.35% 652ms 0.59% boost::detail::shared_count::shared_count (inline) 0 0% 87.35% 628ms 0.57% vtkPolygon::New 2ms 0.0018% 87.35% 627ms 0.57% vtkPolygon::vtkPolygon 37ms 0.033% 87.39% 609ms 0.55% MutableElement::RegisterWithNodes (inline) 9ms 0.0081% 87.39% 602ms 0.54% std::vector::_M_default_append (inline) 28ms 0.025% 87.42% 560ms 0.51% Node::AddElement