File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 97132ms, 88.43% of 109839ms total Dropped 1111 nodes (cum <= 549.20ms) flat flat% sum% cum cum% 0 0% 0% 109392ms 99.59% __libc_start_call_main 0 0% 0% 109392ms 99.59% __libc_start_main_impl 0 0% 0% 109392ms 99.59% _start 0 0% 0% 109373ms 99.58% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 109373ms 99.58% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 109373ms 99.58% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 109373ms 99.58% main 0 0% 0% 109336ms 99.54% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 109336ms 99.54% CxxTest::TestRunner::runTest (inline) 0 0% 0% 109336ms 99.54% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0018% 0.0018% 109329ms 99.54% AbstractCellBasedSimulation::Solve 22ms 0.02% 0.022% 57022ms 51.91% OffLatticeSimulation::UpdateCellLocationsAndTopology 20ms 0.018% 0.04% 53819ms 49.00% ForwardEulerNumericalMethod::UpdateAllNodePositions 139ms 0.13% 0.17% 52278ms 47.60% AbstractNumericalMethod::ComputeForcesIncludingDamping 337ms 0.31% 0.47% 39788ms 36.22% NagaiHondaForce::AddForceContribution 0 0% 0.47% 39207ms 35.69% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.47% 24249ms 22.08% VertexBasedCellPopulation::Update 1ms 0.00091% 0.47% 24126ms 21.96% MutableVertexMesh::ReMesh 14434ms 13.14% 13.62% 22767ms 20.73% Cylindrical2dVertexMesh::GetVectorFromAtoB 95ms 0.086% 13.70% 17493ms 15.93% Cell::ReadyToDivide 80ms 0.073% 13.77% 16255ms 14.80% AbstractPhaseBasedCellCycleModel::ReadyToDivide 375ms 0.34% 14.12% 14746ms 13.43% NagaiHondaForce::GetAdhesionParameter 138ms 0.13% 14.24% 14509ms 13.21% CellPropertyCollection::GetPropertiesType (inline) 464ms 0.42% 14.66% 14244ms 12.97% boost::numeric::ublas::c_vector::c_vector (partial-inline) 112ms 0.1% 14.77% 13927ms 12.68% SimpleWntCellCycleModel::UpdateCellCyclePhase 368ms 0.34% 15.10% 12694ms 11.56% boost::numeric::ublas::vector_assign (inline) 3424ms 3.12% 18.22% 12070ms 10.99% __dynamic_cast 59ms 0.054% 18.27% 12010ms 10.93% VertexBasedCellPopulation::GetDampingConstant 112ms 0.1% 18.37% 12007ms 10.93% MutableVertexMesh::CheckForIntersections 77ms 0.07% 18.44% 11983ms 10.91% AbstractCellProperty::IsSubType (inline) 81ms 0.074% 18.52% 10640ms 9.69% AbstractTargetAreaModifier::UpdateTargetAreas 50ms 0.046% 18.56% 10527ms 9.58% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 21ms 0.019% 18.58% 10299ms 9.38% AbstractCellBasedSimulation::DoCellBirth 1393ms 1.27% 19.85% 10128ms 9.22% std::__new_allocator::allocate (inline) 0 0% 19.85% 9707ms 8.84% std::_Rb_tree::_M_create_node (inline) 0 0% 19.85% 9647ms 8.78% std::allocator_traits::allocate (inline) 2732ms 2.49% 22.34% 9496ms 8.65% boost::numeric::ublas::indexing_vector_assign 84ms 0.076% 22.41% 9253ms 8.42% Cell::GetMutationState 1375ms 1.25% 23.67% 9085ms 8.27% std::_Rb_tree::_M_erase 0 0% 23.67% 9007ms 8.20% std::_Rb_tree::_M_get_node (inline) 834ms 0.76% 24.43% 8966ms 8.16% VertexMesh::ElementIncludesPoint 813ms 0.74% 25.17% 8866ms 8.07% operator new 403ms 0.37% 25.53% 8814ms 8.02% VertexMesh::GetNextEdgeGradientOfElementAtNode 31ms 0.028% 25.56% 8791ms 8.00% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 25.56% 8542ms 7.78% std::_Rb_tree::_Alloc_node::operator() (inline) 228ms 0.21% 25.77% 8232ms 7.49% std::_Rb_tree::~_Rb_tree (inline) 446ms 0.41% 26.17% 8185ms 7.45% VertexMesh::GetCentroidOfElement 0 0% 26.17% 8125ms 7.40% std::_Rb_tree::_M_drop_node (inline) 241ms 0.22% 26.39% 7953ms 7.24% std::__new_allocator::deallocate (inline) 0 0% 26.39% 7930ms 7.22% std::allocator_traits::deallocate (inline) 2981ms 2.71% 29.11% 7857ms 7.15% __GI___libc_free 3145ms 2.86% 31.97% 7855ms 7.15% __GI___libc_malloc 0 0% 31.97% 7833ms 7.13% std::_Rb_tree::_M_put_node (inline) 460ms 0.42% 32.39% 7757ms 7.06% std::map::operator[] (partial-inline) 0 0% 32.39% 7751ms 7.06% std::set::~set (inline) 19ms 0.017% 32.41% 7690ms 7.00% MutableVertexMesh::RemoveDeletedNodesAndElements 1344ms 1.22% 33.63% 7112ms 6.47% AbstractMesh::GetDistanceBetweenNodes 144ms 0.13% 33.76% 7041ms 6.41% std::_Rb_tree::_Rb_tree (partial-inline) 6864ms 6.25% 40.01% 6864ms 6.25% __strcmp_avx2 645ms 0.59% 40.60% 6673ms 6.08% std::_Rb_tree::_M_copy (inline) 16ms 0.015% 40.61% 6637ms 6.04% std::set::set (inline) 100ms 0.091% 40.70% 6362ms 5.79% SimpleWntCellCycleModel::GetWntLevel 156ms 0.14% 40.85% 6188ms 5.63% WntConcentration::GetWntLevel 2534ms 2.31% 43.15% 6181ms 5.63% std::_Rb_tree::_M_lower_bound (inline) 2833ms 2.58% 45.73% 6137ms 5.59% __cxxabiv1::__si_class_type_info::__do_dyncast 6031ms 5.49% 51.22% 6031ms 5.49% boost::numeric::ublas::c_vector::operator() 795ms 0.72% 51.95% 5781ms 5.26% std::_Rb_tree::_M_clone_node (inline) 27ms 0.025% 51.97% 5479ms 4.99% MutableVertexMesh::RemoveDeletedNodes 0 0% 51.97% 5468ms 4.98% std::set::insert (inline) 37ms 0.034% 52.01% 5320ms 4.84% EdgeHelper::RemoveDeletedEdges 0 0% 52.01% 5050ms 4.60% std::_Rb_tree::lower_bound (inline) 0 0% 52.01% 5050ms 4.60% std::map::lower_bound (inline) 23ms 0.021% 52.03% 5046ms 4.59% EdgeHelper::UpdateEdgesMapKey 4520ms 4.12% 56.14% 4867ms 4.43% _int_free 1509ms 1.37% 57.52% 4828ms 4.40% boost::numeric::ublas::c_vector::operator[] (inline) 188ms 0.17% 57.69% 4752ms 4.33% MutableElement::ResetIndex 1ms 0.00091% 57.69% 4650ms 4.23% AbstractCellBasedSimulation::DoCellRemoval (inline) 520ms 0.47% 58.16% 4619ms 4.21% std::_Rb_tree::_M_insert_ (inline) 67ms 0.061% 58.22% 4433ms 4.04% std::set_intersection (inline) 261ms 0.24% 58.46% 4366ms 3.97% std::__set_intersection 111ms 0.1% 58.56% 4260ms 3.88% AbstractCellPopulation::GetCellUsingLocationIndex 3925ms 3.57% 62.13% 3925ms 3.57% boost::numeric::ublas::same_impl_ex 54ms 0.049% 62.18% 3903ms 3.55% Cell::GetCellProliferativeType 53ms 0.048% 62.23% 3772ms 3.43% AbstractCellProperty::IsType (inline) 9ms 0.0082% 62.24% 3584ms 3.26% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.24% 3231ms 2.94% std::insert_iterator::operator= (inline) 784ms 0.71% 62.95% 3139ms 2.86% AbstractElement::GetNodeLocation 46ms 0.042% 62.99% 3096ms 2.82% Cell::SetCellProliferativeType 3094ms 2.82% 65.81% 3094ms 2.82% std::_Rb_tree::_S_right (inline) 2148ms 1.96% 67.77% 3067ms 2.79% _int_malloc 52ms 0.047% 67.81% 3065ms 2.79% std::_Rb_tree::erase 2ms 0.0018% 67.82% 2847ms 2.59% std::_Rb_tree::_M_insert_unique_ (inline) 628ms 0.57% 68.39% 2823ms 2.57% boost::numeric::ublas::vector_binary::size (inline) 807ms 0.73% 69.12% 2746ms 2.50% AbstractCellProperty::IsSame 448ms 0.41% 69.53% 2670ms 2.43% std::_Rb_tree_const_iterator::operator++ (inline) 53ms 0.048% 69.58% 2659ms 2.42% CellPropertyCollection::HasProperty 2ms 0.0018% 69.58% 2621ms 2.39% std::_Rb_tree::_M_insert_unique 12ms 0.011% 69.59% 2611ms 2.38% Cell::GetCellData 0 0% 69.59% 2548ms 2.32% Cell::HasCellProperty (inline) 200ms 0.18% 69.77% 2473ms 2.25% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.77% 2432ms 2.21% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.77% 2424ms 2.21% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.77% 2413ms 2.20% boost::numeric::ublas::c_vector::assign (inline) 2ms 0.0018% 69.78% 2310ms 2.10% AbstractCellPopulation::Iterator::operator++ (inline) 221ms 0.2% 69.98% 2297ms 2.09% AbstractCellPopulation::Iterator::IsRealCell (inline) 101ms 0.092% 70.07% 2240ms 2.04% VertexMesh::GetVolumeOfElement 104ms 0.095% 70.16% 2221ms 2.02% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 44ms 0.04% 70.20% 2198ms 2.00% std::_Rb_tree::_M_emplace_hint_unique 1449ms 1.32% 71.52% 2082ms 1.90% std::_Rb_tree::equal_range (inline) 2050ms 1.87% 73.39% 2050ms 1.87% std::_Rb_tree_increment 0 0% 73.39% 1985ms 1.81% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 73.39% 1972ms 1.80% VertexBasedCellPopulation::WriteCellVtkResultsToFile 493ms 0.45% 73.84% 1939ms 1.77% std::type_info::operator== (inline) 1ms 0.00091% 73.84% 1889ms 1.72% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.84% 1889ms 1.72% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 52ms 0.047% 73.89% 1824ms 1.66% MutableVertexMesh::CheckForSwapsFromShortEdges 24ms 0.022% 73.91% 1801ms 1.64% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 73.91% 1772ms 1.61% VertexMeshWriter::WriteVtkUsingMesh 24ms 0.022% 73.93% 1675ms 1.52% VertexMesh::GetSurfaceAreaOfElement 45ms 0.041% 73.97% 1621ms 1.48% Node::RemoveElement 167ms 0.15% 74.12% 1612ms 1.47% CellPropertyCollection::AddProperty 17ms 0.015% 74.14% 1587ms 1.44% std::set::erase (inline) 82ms 0.075% 74.21% 1565ms 1.42% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 25ms 0.023% 74.24% 1532ms 1.39% AbstractCellPopulation::GetLocationIndexUsingCell 131ms 0.12% 74.36% 1503ms 1.37% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 74.36% 1426ms 1.30% tcache_get (inline) 1426ms 1.30% 75.65% 1426ms 1.30% tcache_get_n (inline) 0 0% 75.65% 1393ms 1.27% boost::numeric::ublas::vector_binary::operator() (inline) 1ms 0.00091% 75.65% 1269ms 1.16% OffLatticeSimulation::ApplyBoundaries 72ms 0.066% 75.72% 1248ms 1.14% std::less::operator() (inline) 0 0% 75.72% 1197ms 1.09% boost::numeric::ublas::norm_2 (inline) 491ms 0.45% 76.17% 1189ms 1.08% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1182ms 1.08% 77.24% 1182ms 1.08% Node::rGetLocation 959ms 0.87% 78.12% 1176ms 1.07% std::operator< (inline) 0 0% 78.12% 1165ms 1.06% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1148ms 1.05% 79.16% 1148ms 1.05% std::_Rb_tree_insert_and_rebalance 71ms 0.065% 79.23% 1123ms 1.02% std::_Rb_tree::_M_erase_aux (partial-inline) 89ms 0.081% 79.31% 1113ms 1.01% std::_Rb_tree::find (inline) 21ms 0.019% 79.33% 1090ms 0.99% CellPropertyRegistry::Get 1ms 0.00091% 79.33% 1087ms 0.99% std::_Rb_tree::clear (inline) 0 0% 79.33% 1072ms 0.98% std::map::clear (inline) 1055ms 0.96% 80.29% 1055ms 0.96% [libchaste_cell_based.so] 19ms 0.017% 80.30% 1049ms 0.96% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 6ms 0.0055% 80.31% 1018ms 0.93% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 130ms 0.12% 80.43% 987ms 0.9% boost::detail::shared_count::~shared_count (inline) 0 0% 80.43% 987ms 0.9% boost::shared_ptr::~shared_ptr (inline) 418ms 0.38% 80.81% 975ms 0.89% Edge::GetMapIndex 967ms 0.88% 81.69% 967ms 0.88% std::vector::size (inline) 925ms 0.84% 82.53% 925ms 0.84% [libchaste_mesh.so] 20ms 0.018% 82.55% 922ms 0.84% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 82.55% 893ms 0.81% boost::numeric::ublas::c_vector::assign_temporary (inline) 3ms 0.0027% 82.55% 893ms 0.81% boost::numeric::ublas::c_vector::swap (inline) 0 0% 82.55% 892ms 0.81% std::map::find (inline) 73ms 0.066% 82.62% 890ms 0.81% std::swap_ranges (inline) 147ms 0.13% 82.75% 889ms 0.81% boost::numeric::ublas::detail::equals 0 0% 82.75% 861ms 0.78% VertexMeshWriter::MakeVtkMesh 113ms 0.1% 82.86% 837ms 0.76% MutableElement::GetNodeLocalIndex 828ms 0.75% 83.61% 830ms 0.76% boost::detail::sp_counted_base::release 818ms 0.74% 84.35% 818ms 0.74% std::swap (inline) 0 0% 84.35% 817ms 0.74% std::iter_swap (inline) 102ms 0.093% 84.45% 768ms 0.7% boost::numeric::ublas::c_vector::operator= (inline) 130ms 0.12% 84.57% 751ms 0.68% std::__new_allocator::construct (inline) 0 0% 84.57% 751ms 0.68% std::allocator_traits::construct (inline) 137ms 0.12% 84.69% 743ms 0.68% boost::shared_ptr::shared_ptr (inline) 17ms 0.015% 84.71% 737ms 0.67% MutableElement::RegisterWithEdges (inline) 17ms 0.015% 84.72% 732ms 0.67% Edge::AddElement 731ms 0.67% 85.39% 731ms 0.67% Node::GetIndex 15ms 0.014% 85.40% 723ms 0.66% AbstractNumericalMethod::DetectStepSizeExceptions 432ms 0.39% 85.79% 715ms 0.65% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 82ms 0.075% 85.87% 708ms 0.64% VertexBasedCellPopulation::CheckForStepSizeException 0 0% 85.87% 700ms 0.64% std::_Rb_tree::_M_construct_node (inline) 0 0% 85.87% 692ms 0.63% boost::numeric::ublas::norm_inf (inline) 390ms 0.36% 86.22% 692ms 0.63% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 86.22% 689ms 0.63% std::_Rb_tree::_Auto_node::_M_insert (inline) 31ms 0.028% 86.25% 689ms 0.63% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.25% 669ms 0.61% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 86.25% 649ms 0.59% vtkPolygon::New 2ms 0.0018% 86.25% 649ms 0.59% vtkPolygon::vtkPolygon 1ms 0.00091% 86.25% 638ms 0.58% std::_Vector_base::_M_allocate (inline) 32ms 0.029% 86.28% 615ms 0.56% MutableElement::RegisterWithNodes (inline) 577ms 0.53% 86.81% 606ms 0.55% boost::detail::shared_count::shared_count (inline) 590ms 0.54% 87.35% 590ms 0.54% operator delete 582ms 0.53% 87.88% 582ms 0.53% boost::shared_ptr::operator-> (inline) 0 0% 87.88% 580ms 0.53% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 35ms 0.032% 87.91% 579ms 0.53% Node::AddElement 575ms 0.52% 88.43% 575ms 0.52% [libstdc++.so.6.0.33]