File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 94671ms, 87.61% of 108063ms total Dropped 1104 nodes (cum <= 540.32ms) flat flat% sum% cum cum% 0 0% 0% 107734ms 99.70% __libc_start_call_main 0 0% 0% 107734ms 99.70% __libc_start_main_impl 0 0% 0% 107734ms 99.70% _start 0 0% 0% 107711ms 99.67% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 107711ms 99.67% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 107711ms 99.67% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 107711ms 99.67% main 0 0% 0% 107675ms 99.64% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 107675ms 99.64% CxxTest::TestRunner::runTest (inline) 0 0% 0% 107675ms 99.64% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0019% 0.0019% 107666ms 99.63% AbstractCellBasedSimulation::Solve 28ms 0.026% 0.028% 55868ms 51.70% OffLatticeSimulation::UpdateCellLocationsAndTopology 12ms 0.011% 0.039% 52498ms 48.58% ForwardEulerNumericalMethod::UpdateAllNodePositions 136ms 0.13% 0.16% 51380ms 47.55% AbstractNumericalMethod::ComputeForcesIncludingDamping 314ms 0.29% 0.46% 39557ms 36.61% NagaiHondaForce::AddForceContribution 0 0% 0.46% 38616ms 35.73% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.0028% 0.46% 23658ms 21.89% VertexBasedCellPopulation::Update 1ms 0.00093% 0.46% 23519ms 21.76% MutableVertexMesh::ReMesh 14467ms 13.39% 13.85% 23139ms 21.41% Cylindrical2dVertexMesh::GetVectorFromAtoB 118ms 0.11% 13.96% 17704ms 16.38% Cell::ReadyToDivide 82ms 0.076% 14.03% 16322ms 15.10% AbstractPhaseBasedCellCycleModel::ReadyToDivide 472ms 0.44% 14.47% 14214ms 13.15% boost::numeric::ublas::c_vector::c_vector (partial-inline) 319ms 0.3% 14.76% 14084ms 13.03% NagaiHondaForce::GetAdhesionParameter 170ms 0.16% 14.92% 13913ms 12.87% SimpleWntCellCycleModel::UpdateCellCyclePhase 102ms 0.094% 15.02% 13636ms 12.62% CellPropertyCollection::GetPropertiesType (inline) 281ms 0.26% 15.28% 12685ms 11.74% boost::numeric::ublas::vector_assign (inline) 124ms 0.11% 15.39% 11803ms 10.92% MutableVertexMesh::CheckForIntersections 3458ms 3.20% 18.59% 11704ms 10.83% __dynamic_cast 42ms 0.039% 18.63% 11570ms 10.71% AbstractCellProperty::IsSubType (inline) 104ms 0.096% 18.73% 11271ms 10.43% VertexBasedCellPopulation::GetDampingConstant 67ms 0.062% 18.79% 10691ms 9.89% AbstractTargetAreaModifier::UpdateTargetAreas 51ms 0.047% 18.83% 10598ms 9.81% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 31ms 0.029% 18.86% 10250ms 9.49% AbstractCellBasedSimulation::DoCellBirth 2897ms 2.68% 21.54% 9696ms 8.97% boost::numeric::ublas::indexing_vector_assign 1185ms 1.10% 22.64% 9637ms 8.92% std::__new_allocator::allocate (inline) 379ms 0.35% 22.99% 9461ms 8.76% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 22.99% 9190ms 8.50% std::_Rb_tree::_M_create_node (inline) 0 0% 22.99% 9114ms 8.43% std::allocator_traits::allocate (inline) 1195ms 1.11% 24.10% 8821ms 8.16% std::_Rb_tree::_M_erase 97ms 0.09% 24.19% 8663ms 8.02% Cell::GetMutationState 838ms 0.78% 24.96% 8659ms 8.01% VertexMesh::ElementIncludesPoint 42ms 0.039% 25.00% 8600ms 7.96% VertexBasedCellPopulation::GetLocationOfCellCentre 749ms 0.69% 25.69% 8481ms 7.85% operator new 0 0% 25.69% 8438ms 7.81% std::_Rb_tree::_M_get_node (inline) 432ms 0.4% 26.09% 8123ms 7.52% VertexMesh::GetCentroidOfElement 0 0% 26.09% 8116ms 7.51% std::_Rb_tree::_Alloc_node::operator() (inline) 242ms 0.22% 26.32% 7964ms 7.37% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.32% 7948ms 7.35% std::_Rb_tree::_M_drop_node (inline) 210ms 0.19% 26.51% 7687ms 7.11% std::__new_allocator::deallocate (inline) 0 0% 26.51% 7678ms 7.11% std::allocator_traits::deallocate (inline) 0 0% 26.51% 7621ms 7.05% std::_Rb_tree::_M_put_node (inline) 0 0% 26.51% 7572ms 7.01% std::set::~set (inline) 487ms 0.45% 26.96% 7520ms 6.96% std::map::operator[] (partial-inline) 2949ms 2.73% 29.69% 7500ms 6.94% __GI___libc_malloc 18ms 0.017% 29.71% 7464ms 6.91% MutableVertexMesh::RemoveDeletedNodesAndElements 1434ms 1.33% 31.04% 7368ms 6.82% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 2346ms 2.17% 33.21% 7197ms 6.66% __GI___libc_free 179ms 0.17% 33.37% 6950ms 6.43% std::_Rb_tree::_Rb_tree (partial-inline) 6620ms 6.13% 39.50% 6620ms 6.13% __strcmp_avx2 778ms 0.72% 40.22% 6519ms 6.03% std::_Rb_tree::_M_copy (inline) 21ms 0.019% 40.24% 6475ms 5.99% std::set::set (inline) 6247ms 5.78% 46.02% 6247ms 5.78% boost::numeric::ublas::c_vector::operator() 107ms 0.099% 46.12% 6165ms 5.71% SimpleWntCellCycleModel::GetWntLevel 2641ms 2.44% 48.56% 5989ms 5.54% std::_Rb_tree::_M_lower_bound (inline) 154ms 0.14% 48.70% 5968ms 5.52% WntConcentration::GetWntLevel 2960ms 2.74% 51.44% 5699ms 5.27% __cxxabiv1::__si_class_type_info::__do_dyncast 718ms 0.66% 52.11% 5460ms 5.05% std::_Rb_tree::_M_clone_node (inline) 1967ms 1.82% 53.93% 5381ms 4.98% boost::numeric::ublas::c_vector::operator[] (inline) 17ms 0.016% 53.94% 5228ms 4.84% MutableVertexMesh::RemoveDeletedNodes 0 0% 53.94% 5218ms 4.83% std::set::insert (inline) 34ms 0.031% 53.97% 5057ms 4.68% EdgeHelper::RemoveDeletedEdges 0 0% 53.97% 4896ms 4.53% std::_Rb_tree::lower_bound (inline) 0 0% 53.97% 4896ms 4.53% std::map::lower_bound (inline) 4392ms 4.06% 58.04% 4834ms 4.47% _int_free 33ms 0.031% 58.07% 4738ms 4.38% EdgeHelper::UpdateEdgesMapKey 1ms 0.00093% 58.07% 4698ms 4.35% AbstractCellBasedSimulation::DoCellRemoval (inline) 194ms 0.18% 58.25% 4551ms 4.21% MutableElement::ResetIndex 502ms 0.46% 58.71% 4412ms 4.08% std::_Rb_tree::_M_insert_ (inline) 183ms 0.17% 58.88% 4356ms 4.03% AbstractCellPopulation::GetCellUsingLocationIndex 113ms 0.1% 58.99% 4203ms 3.89% std::set_intersection (inline) 220ms 0.2% 59.19% 4090ms 3.78% std::__set_intersection 44ms 0.041% 59.23% 3944ms 3.65% Cell::GetCellProliferativeType 3920ms 3.63% 62.86% 3920ms 3.63% boost::numeric::ublas::same_impl_ex 56ms 0.052% 62.91% 3833ms 3.55% AbstractCellProperty::IsType (inline) 8ms 0.0074% 62.92% 3600ms 3.33% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.92% 3138ms 2.90% std::insert_iterator::operator= (inline) 52ms 0.048% 62.97% 3116ms 2.88% Cell::SetCellProliferativeType 882ms 0.82% 63.78% 3050ms 2.82% AbstractElement::GetNodeLocation 2126ms 1.97% 65.75% 3043ms 2.82% _int_malloc 27ms 0.025% 65.78% 2897ms 2.68% CellPropertyCollection::HasProperty 68ms 0.063% 65.84% 2883ms 2.67% std::_Rb_tree::erase 0 0% 65.84% 2768ms 2.56% Cell::HasCellProperty (inline) 3ms 0.0028% 65.84% 2756ms 2.55% std::_Rb_tree::_M_insert_unique_ (inline) 2740ms 2.54% 68.38% 2740ms 2.54% std::_Rb_tree::_S_right (inline) 659ms 0.61% 68.99% 2733ms 2.53% AbstractCellProperty::IsSame 0 0% 68.99% 2714ms 2.51% boost::numeric::ublas::c_vector::operator-= (inline) 612ms 0.57% 69.55% 2652ms 2.45% boost::numeric::ublas::vector_binary::size (inline) 0 0% 69.55% 2618ms 2.42% boost::numeric::ublas::c_vector::assign (inline) 234ms 0.22% 69.77% 2610ms 2.42% VertexMesh::GetAreaGradientOfElementAtNode 252ms 0.23% 70.00% 2548ms 2.36% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 70.00% 2462ms 2.28% std::_Rb_tree::_M_insert_unique 0 0% 70.00% 2457ms 2.27% AbstractCellPopulation::WriteResultsToFiles 28ms 0.026% 70.03% 2435ms 2.25% Cell::GetCellData 3ms 0.0028% 70.03% 2315ms 2.14% AbstractCellPopulation::Iterator::operator++ (inline) 156ms 0.14% 70.18% 2307ms 2.13% AbstractCellPopulation::Iterator::IsRealCell (inline) 52ms 0.048% 70.22% 2306ms 2.13% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 101ms 0.093% 70.32% 2270ms 2.10% VertexMesh::GetVolumeOfElement 48ms 0.044% 70.36% 2090ms 1.93% std::_Rb_tree::_M_emplace_hint_unique 518ms 0.48% 70.84% 2074ms 1.92% std::type_info::operator== (inline) 2039ms 1.89% 72.73% 2039ms 1.89% std::_Rb_tree_increment 2ms 0.0019% 72.73% 2026ms 1.87% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.73% 2026ms 1.87% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 72.73% 2001ms 1.85% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 72.73% 1991ms 1.84% VertexBasedCellPopulation::WriteCellVtkResultsToFile 73ms 0.068% 72.80% 1876ms 1.74% MutableVertexMesh::CheckForSwapsFromShortEdges 1237ms 1.14% 73.94% 1842ms 1.70% std::_Rb_tree::equal_range (inline) 13ms 0.012% 73.96% 1829ms 1.69% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 73.96% 1776ms 1.64% VertexMeshWriter::WriteVtkUsingMesh 41ms 0.038% 73.99% 1592ms 1.47% VertexMesh::GetSurfaceAreaOfElement 27ms 0.025% 74.02% 1556ms 1.44% AbstractCellPopulation::GetLocationIndexUsingCell 83ms 0.077% 74.09% 1534ms 1.42% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 35ms 0.032% 74.13% 1494ms 1.38% Node::RemoveElement 4ms 0.0037% 74.13% 1460ms 1.35% std::set::erase (inline) 91ms 0.084% 74.22% 1428ms 1.32% boost::numeric::ublas::vector_reference::operator() (inline) 130ms 0.12% 74.34% 1425ms 1.32% CellPropertyCollection::AddProperty 0 0% 74.34% 1411ms 1.31% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 74.34% 1379ms 1.28% OffLatticeSimulation::ApplyBoundaries 1336ms 1.24% 75.57% 1336ms 1.24% [libchaste_cell_based.so] 0 0% 75.57% 1315ms 1.22% boost::numeric::ublas::norm_2 (inline) 0 0% 75.57% 1304ms 1.21% tcache_get (inline) 1304ms 1.21% 76.78% 1304ms 1.21% tcache_get_n (inline) 570ms 0.53% 77.31% 1301ms 1.20% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 66ms 0.061% 77.37% 1272ms 1.18% std::less::operator() (inline) 1006ms 0.93% 78.30% 1206ms 1.12% std::operator< (inline) 16ms 0.015% 78.31% 1195ms 1.11% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 78.31% 1148ms 1.06% boost::numeric::ublas::c_vector::assign_temporary (inline) 12ms 0.011% 78.32% 1148ms 1.06% boost::numeric::ublas::c_vector::swap (inline) 75ms 0.069% 78.39% 1142ms 1.06% std::_Rb_tree::_M_erase_aux (partial-inline) 77ms 0.071% 78.46% 1136ms 1.05% std::swap_ranges (inline) 19ms 0.018% 78.48% 1131ms 1.05% CellPropertyRegistry::Get 93ms 0.086% 78.57% 1131ms 1.05% std::_Rb_tree::find (inline) 1114ms 1.03% 79.60% 1114ms 1.03% std::_Rb_tree_insert_and_rebalance 0 0% 79.60% 1104ms 1.02% std::_Rb_tree::clear (inline) 0 0% 79.60% 1088ms 1.01% std::map::clear (inline) 0 0% 79.60% 1074ms 0.99% std::_Rb_tree::_Auto_node::_Auto_node (inline) 7ms 0.0065% 79.61% 1062ms 0.98% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1060ms 0.98% 80.59% 1060ms 0.98% std::swap (inline) 0 0% 80.59% 1059ms 0.98% std::iter_swap (inline) 131ms 0.12% 80.71% 1044ms 0.97% boost::detail::shared_count::~shared_count (inline) 0 0% 80.71% 1044ms 0.97% boost::shared_ptr::~shared_ptr (inline) 21ms 0.019% 80.73% 1043ms 0.97% boost::numeric::ublas::detail::expression_type_check (inline) 247ms 0.23% 80.96% 1010ms 0.93% boost::numeric::ublas::detail::equals 936ms 0.87% 81.82% 936ms 0.87% Node::rGetLocation 0 0% 81.82% 930ms 0.86% std::map::find (inline) 874ms 0.81% 82.63% 874ms 0.81% std::vector::size (inline) 840ms 0.78% 83.41% 868ms 0.8% boost::detail::sp_counted_base::release 1ms 0.00093% 83.41% 862ms 0.8% VertexMeshWriter::MakeVtkMesh 103ms 0.095% 83.50% 823ms 0.76% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 83.50% 812ms 0.75% CellPropertyCollection::~CellPropertyCollection (inline) 219ms 0.2% 83.71% 808ms 0.75% std::__new_allocator::construct (inline) 0 0% 83.71% 808ms 0.75% std::allocator_traits::construct (inline) 767ms 0.71% 84.42% 767ms 0.71% [libchaste_mesh.so] 0 0% 84.42% 752ms 0.7% std::_Rb_tree::_M_construct_node (inline) 23ms 0.021% 84.44% 746ms 0.69% Edge::AddElement 17ms 0.016% 84.45% 740ms 0.68% MutableElement::RegisterWithEdges (inline) 191ms 0.18% 84.63% 730ms 0.68% boost::shared_ptr::shared_ptr (inline) 393ms 0.36% 84.99% 715ms 0.66% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 369ms 0.34% 85.34% 714ms 0.66% Edge::GetMapIndex 0 0% 85.34% 711ms 0.66% boost::numeric::ublas::norm_inf (inline) 359ms 0.33% 85.67% 711ms 0.66% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 85.67% 706ms 0.65% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 705ms 0.65% 86.32% 705ms 0.65% [libstdc++.so.6.0.33] 146ms 0.14% 86.46% 676ms 0.63% MutableElement::GetNodeLocalIndex 0 0% 86.46% 673ms 0.62% std::_Vector_base::_M_allocate (inline) 0 0% 86.46% 663ms 0.61% std::_Rb_tree::_Auto_node::_M_insert (inline) 19ms 0.018% 86.47% 663ms 0.61% std::_Rb_tree::_M_insert_node (inline) 1ms 0.00093% 86.47% 638ms 0.59% vtkPolygon::New 3ms 0.0028% 86.48% 636ms 0.59% vtkPolygon::vtkPolygon 38ms 0.035% 86.51% 627ms 0.58% MutableElement::RegisterWithNodes (inline) 25ms 0.023% 86.53% 577ms 0.53% Node::AddElement 564ms 0.52% 87.06% 564ms 0.52% Node::GetIndex 559ms 0.52% 87.57% 559ms 0.52% boost::shared_ptr::operator-> (inline) 30ms 0.028% 87.60% 553ms 0.51% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.60% 553ms 0.51% boost::numeric::ublas::vector::vector (inline) 6ms 0.0056% 87.61% 552ms 0.51% std::vector::_M_default_append (inline)