File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96261ms, 87.47% of 110055ms total Dropped 1129 nodes (cum <= 550.27ms) flat flat% sum% cum cum% 0 0% 0% 109686ms 99.66% __libc_start_call_main 0 0% 0% 109686ms 99.66% __libc_start_main_impl 0 0% 0% 109686ms 99.66% _start 0 0% 0% 109663ms 99.64% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 109663ms 99.64% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 109663ms 99.64% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 109663ms 99.64% main 0 0% 0% 109622ms 99.61% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 109622ms 99.61% CxxTest::TestRunner::runTest (inline) 0 0% 0% 109622ms 99.61% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 0 0% 0% 109613ms 99.60% AbstractCellBasedSimulation::Solve 16ms 0.015% 0.015% 56661ms 51.48% OffLatticeSimulation::UpdateCellLocationsAndTopology 14ms 0.013% 0.027% 53328ms 48.46% ForwardEulerNumericalMethod::UpdateAllNodePositions 125ms 0.11% 0.14% 52186ms 47.42% AbstractNumericalMethod::ComputeForcesIncludingDamping 310ms 0.28% 0.42% 40052ms 36.39% NagaiHondaForce::AddForceContribution 1ms 0.00091% 0.42% 39455ms 35.85% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.42% 24230ms 22.02% VertexBasedCellPopulation::Update 0 0% 0.42% 24108ms 21.91% MutableVertexMesh::ReMesh 14618ms 13.28% 13.71% 23259ms 21.13% Cylindrical2dVertexMesh::GetVectorFromAtoB 107ms 0.097% 13.80% 18059ms 16.41% Cell::ReadyToDivide 76ms 0.069% 13.87% 16651ms 15.13% AbstractPhaseBasedCellCycleModel::ReadyToDivide 355ms 0.32% 14.19% 14514ms 13.19% NagaiHondaForce::GetAdhesionParameter 169ms 0.15% 14.35% 14284ms 12.98% SimpleWntCellCycleModel::UpdateCellCyclePhase 95ms 0.086% 14.43% 13964ms 12.69% CellPropertyCollection::GetPropertiesType (inline) 468ms 0.43% 14.86% 13629ms 12.38% boost::numeric::ublas::c_vector::c_vector (partial-inline) 297ms 0.27% 15.13% 12104ms 11.00% boost::numeric::ublas::vector_assign (inline) 135ms 0.12% 15.25% 11910ms 10.82% MutableVertexMesh::CheckForIntersections 3612ms 3.28% 18.53% 11814ms 10.73% __dynamic_cast 41ms 0.037% 18.57% 11679ms 10.61% AbstractCellProperty::IsSubType (inline) 108ms 0.098% 18.67% 11577ms 10.52% VertexBasedCellPopulation::GetDampingConstant 56ms 0.051% 18.72% 10964ms 9.96% AbstractTargetAreaModifier::UpdateTargetAreas 34ms 0.031% 18.75% 10893ms 9.90% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 29ms 0.026% 18.78% 10520ms 9.56% AbstractCellBasedSimulation::DoCellBirth 1379ms 1.25% 20.03% 10281ms 9.34% std::__new_allocator::allocate (inline) 0 0% 20.03% 9730ms 8.84% std::allocator_traits::allocate (inline) 0 0% 20.03% 9724ms 8.84% std::_Rb_tree::_M_create_node (inline) 364ms 0.33% 20.36% 9445ms 8.58% VertexMesh::GetNextEdgeGradientOfElementAtNode 2773ms 2.52% 22.88% 9312ms 8.46% boost::numeric::ublas::indexing_vector_assign 1263ms 1.15% 24.03% 9086ms 8.26% std::_Rb_tree::_M_erase 0 0% 24.03% 9010ms 8.19% std::_Rb_tree::_M_get_node (inline) 744ms 0.68% 24.70% 8943ms 8.13% operator new 35ms 0.032% 24.74% 8816ms 8.01% VertexBasedCellPopulation::GetLocationOfCellCentre 883ms 0.8% 25.54% 8718ms 7.92% VertexMesh::ElementIncludesPoint 96ms 0.087% 25.63% 8612ms 7.83% Cell::GetMutationState 0 0% 25.63% 8598ms 7.81% std::_Rb_tree::_Alloc_node::operator() (inline) 457ms 0.42% 26.04% 8312ms 7.55% VertexMesh::GetCentroidOfElement 0 0% 26.04% 8255ms 7.50% std::_Rb_tree::_M_drop_node (inline) 202ms 0.18% 26.23% 8141ms 7.40% std::_Rb_tree::~_Rb_tree (inline) 214ms 0.19% 26.42% 7997ms 7.27% std::__new_allocator::deallocate (inline) 0 0% 26.42% 7993ms 7.26% std::allocator_traits::deallocate (inline) 2964ms 2.69% 29.11% 7953ms 7.23% __GI___libc_malloc 0 0% 29.11% 7934ms 7.21% std::_Rb_tree::_M_put_node (inline) 10ms 0.0091% 29.12% 7923ms 7.20% MutableVertexMesh::RemoveDeletedNodesAndElements 475ms 0.43% 29.55% 7872ms 7.15% std::map::operator[] (partial-inline) 0 0% 29.55% 7719ms 7.01% std::set::~set (inline) 2380ms 2.16% 31.72% 7450ms 6.77% __GI___libc_free 1365ms 1.24% 32.96% 7373ms 6.70% AbstractMesh::GetDistanceBetweenNodes 171ms 0.16% 33.11% 7288ms 6.62% std::_Rb_tree::_Rb_tree (partial-inline) 730ms 0.66% 33.77% 6848ms 6.22% std::_Rb_tree::_M_copy (inline) 32ms 0.029% 33.80% 6840ms 6.22% std::set::set (inline) 6719ms 6.11% 39.91% 6719ms 6.11% __strcmp_avx2 152ms 0.14% 40.05% 6397ms 5.81% SimpleWntCellCycleModel::GetWntLevel 2608ms 2.37% 42.42% 6356ms 5.78% std::_Rb_tree::_M_lower_bound (inline) 6178ms 5.61% 48.03% 6178ms 5.61% boost::numeric::ublas::c_vector::operator() 174ms 0.16% 48.19% 6163ms 5.60% WntConcentration::GetWntLevel 846ms 0.77% 48.96% 5860ms 5.32% std::_Rb_tree::_M_clone_node (inline) 2812ms 2.56% 51.51% 5660ms 5.14% __cxxabiv1::__si_class_type_info::__do_dyncast 26ms 0.024% 51.54% 5501ms 5.00% MutableVertexMesh::RemoveDeletedNodes 0 0% 51.54% 5405ms 4.91% std::set::insert (inline) 1983ms 1.80% 53.34% 5387ms 4.89% boost::numeric::ublas::c_vector::operator[] (inline) 39ms 0.035% 53.37% 5299ms 4.81% EdgeHelper::RemoveDeletedEdges 0 0% 53.37% 5174ms 4.70% std::_Rb_tree::lower_bound (inline) 0 0% 53.37% 5174ms 4.70% std::map::lower_bound (inline) 4610ms 4.19% 57.56% 5057ms 4.59% _int_free 34ms 0.031% 57.59% 4996ms 4.54% EdgeHelper::UpdateEdgesMapKey 194ms 0.18% 57.77% 4814ms 4.37% MutableElement::ResetIndex 1ms 0.00091% 57.77% 4694ms 4.27% AbstractCellBasedSimulation::DoCellRemoval (inline) 505ms 0.46% 58.23% 4608ms 4.19% std::_Rb_tree::_M_insert_ (inline) 143ms 0.13% 58.36% 4603ms 4.18% AbstractCellPopulation::GetCellUsingLocationIndex 120ms 0.11% 58.47% 4197ms 3.81% std::set_intersection (inline) 36ms 0.033% 58.50% 4087ms 3.71% Cell::GetCellProliferativeType 199ms 0.18% 58.68% 4077ms 3.70% std::__set_intersection 78ms 0.071% 58.75% 4019ms 3.65% AbstractCellProperty::IsType (inline) 3789ms 3.44% 62.20% 3789ms 3.44% boost::numeric::ublas::same_impl_ex 9ms 0.0082% 62.20% 3543ms 3.22% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 2377ms 2.16% 64.36% 3366ms 3.06% _int_malloc 35ms 0.032% 64.40% 3322ms 3.02% Cell::SetCellProliferativeType 0 0% 64.40% 3195ms 2.90% std::insert_iterator::operator= (inline) 969ms 0.88% 65.28% 3163ms 2.87% AbstractElement::GetNodeLocation 3120ms 2.83% 68.11% 3120ms 2.83% std::_Rb_tree::_S_right (inline) 72ms 0.065% 68.18% 3087ms 2.80% std::_Rb_tree::erase 41ms 0.037% 68.21% 2957ms 2.69% CellPropertyCollection::HasProperty 0 0% 68.21% 2856ms 2.60% Cell::HasCellProperty (inline) 723ms 0.66% 68.87% 2846ms 2.59% AbstractCellProperty::IsSame 12ms 0.011% 68.88% 2771ms 2.52% std::_Rb_tree::_M_insert_unique_ (inline) 37ms 0.034% 68.91% 2648ms 2.41% Cell::GetCellData 1ms 0.00091% 68.92% 2634ms 2.39% std::_Rb_tree::_M_insert_unique (inline) 242ms 0.22% 69.14% 2592ms 2.36% std::_Rb_tree_const_iterator::operator++ (inline) 222ms 0.2% 69.34% 2590ms 2.35% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.34% 2573ms 2.34% boost::numeric::ublas::c_vector::assign (inline) 626ms 0.57% 69.91% 2564ms 2.33% boost::numeric::ublas::vector_binary::size (inline) 0 0% 69.91% 2495ms 2.27% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.91% 2487ms 2.26% boost::numeric::ublas::c_vector::operator-= (inline) 71ms 0.065% 69.97% 2311ms 2.10% VertexMesh::GetVolumeOfElement 57ms 0.052% 70.02% 2277ms 2.07% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 189ms 0.17% 70.19% 2217ms 2.01% AbstractCellPopulation::Iterator::IsRealCell (inline) 8ms 0.0073% 70.20% 2212ms 2.01% AbstractCellPopulation::Iterator::operator++ (inline) 36ms 0.033% 70.23% 2179ms 1.98% std::_Rb_tree::_M_emplace_hint_unique 489ms 0.44% 70.68% 2123ms 1.93% std::type_info::operator== (inline) 2091ms 1.90% 72.58% 2091ms 1.90% std::_Rb_tree_increment 4ms 0.0036% 72.58% 2033ms 1.85% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.58% 2033ms 1.85% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 72.58% 2025ms 1.84% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00091% 72.58% 2013ms 1.83% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1342ms 1.22% 73.80% 2010ms 1.83% std::_Rb_tree::equal_range (inline) 1ms 0.00091% 73.80% 1815ms 1.65% VertexMeshWriter::WriteVtkUsingMesh 72ms 0.065% 73.87% 1809ms 1.64% MutableVertexMesh::CheckForSwapsFromShortEdges 26ms 0.024% 73.89% 1724ms 1.57% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 20ms 0.018% 73.91% 1580ms 1.44% AbstractCellPopulation::GetLocationIndexUsingCell 52ms 0.047% 73.96% 1573ms 1.43% Node::RemoveElement 155ms 0.14% 74.10% 1563ms 1.42% CellPropertyCollection::AddProperty 32ms 0.029% 74.13% 1551ms 1.41% VertexMesh::GetSurfaceAreaOfElement 85ms 0.077% 74.20% 1531ms 1.39% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 12ms 0.011% 74.22% 1526ms 1.39% std::set::erase (inline) 0 0% 74.22% 1419ms 1.29% tcache_get (inline) 1419ms 1.29% 75.50% 1419ms 1.29% tcache_get_n (inline) 0 0% 75.50% 1395ms 1.27% OffLatticeSimulation::ApplyBoundaries 49ms 0.045% 75.55% 1380ms 1.25% std::less::operator() (inline) 64ms 0.058% 75.61% 1378ms 1.25% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 75.61% 1351ms 1.23% boost::numeric::ublas::norm_2 (inline) 597ms 0.54% 76.15% 1334ms 1.21% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1080ms 0.98% 77.13% 1331ms 1.21% std::operator< (inline) 1300ms 1.18% 78.31% 1300ms 1.18% [libchaste_cell_based.so] 0 0% 78.31% 1293ms 1.17% boost::numeric::ublas::vector_binary::operator() (inline) 102ms 0.093% 78.41% 1198ms 1.09% std::_Rb_tree::find (inline) 18ms 0.016% 78.42% 1193ms 1.08% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 87ms 0.079% 78.50% 1187ms 1.08% std::_Rb_tree::_M_erase_aux (partial-inline) 27ms 0.025% 78.53% 1169ms 1.06% CellPropertyRegistry::Get 1ms 0.00091% 78.53% 1149ms 1.04% std::_Rb_tree::clear (inline) 0 0% 78.53% 1138ms 1.03% std::map::clear (inline) 0 0% 78.53% 1126ms 1.02% std::_Rb_tree::_Auto_node::_Auto_node (inline) 9ms 0.0082% 78.53% 1109ms 1.01% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1085ms 0.99% 79.52% 1085ms 0.99% std::_Rb_tree_insert_and_rebalance 0 0% 79.52% 1057ms 0.96% boost::numeric::ublas::c_vector::assign_temporary (inline) 11ms 0.01% 79.53% 1057ms 0.96% boost::numeric::ublas::c_vector::swap (inline) 86ms 0.078% 79.61% 1046ms 0.95% std::swap_ranges (inline) 1027ms 0.93% 80.54% 1027ms 0.93% Node::rGetLocation 135ms 0.12% 80.66% 1017ms 0.92% boost::detail::shared_count::~shared_count (inline) 0 0% 80.66% 1017ms 0.92% boost::shared_ptr::~shared_ptr (inline) 0 0% 80.66% 1007ms 0.91% std::map::find (inline) 0 0% 80.66% 960ms 0.87% std::iter_swap (inline) 960ms 0.87% 81.54% 960ms 0.87% std::swap (inline) 14ms 0.013% 81.55% 916ms 0.83% boost::numeric::ublas::detail::expression_type_check (inline) 173ms 0.16% 81.71% 898ms 0.82% boost::numeric::ublas::detail::equals 0 0% 81.71% 863ms 0.78% VertexMeshWriter::MakeVtkMesh 828ms 0.75% 82.46% 849ms 0.77% boost::detail::sp_counted_base::release 820ms 0.75% 83.20% 820ms 0.75% std::vector::size (inline) 18ms 0.016% 83.22% 806ms 0.73% MutableElement::RegisterWithEdges (inline) 804ms 0.73% 83.95% 804ms 0.73% [libchaste_mesh.so] 22ms 0.02% 83.97% 803ms 0.73% Edge::AddElement 84ms 0.076% 84.05% 796ms 0.72% boost::numeric::ublas::c_vector::operator= (inline) 232ms 0.21% 84.26% 778ms 0.71% std::__new_allocator::construct (inline) 0 0% 84.26% 778ms 0.71% std::allocator_traits::construct (inline) 149ms 0.14% 84.39% 761ms 0.69% MutableElement::GetNodeLocalIndex 760ms 0.69% 85.08% 760ms 0.69% [libstdc++.so.6.0.33] 400ms 0.36% 85.45% 758ms 0.69% Edge::GetMapIndex 161ms 0.15% 85.59% 743ms 0.68% boost::shared_ptr::shared_ptr (inline) 393ms 0.36% 85.95% 721ms 0.66% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 1ms 0.00091% 85.95% 718ms 0.65% std::_Vector_base::_M_allocate (inline) 0 0% 85.95% 715ms 0.65% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 85.95% 714ms 0.65% std::_Rb_tree::_M_construct_node (inline) 0 0% 85.95% 683ms 0.62% boost::numeric::ublas::norm_inf (inline) 333ms 0.3% 86.25% 683ms 0.62% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 86.25% 682ms 0.62% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 86.25% 669ms 0.61% std::_Rb_tree::_Auto_node::_M_insert (inline) 27ms 0.025% 86.28% 669ms 0.61% std::_Rb_tree::_M_insert_node (inline) 666ms 0.61% 86.88% 666ms 0.61% Node::GetIndex 0 0% 86.88% 607ms 0.55% vtkPolygon::New 2ms 0.0018% 86.89% 605ms 0.55% vtkPolygon::vtkPolygon 7ms 0.0064% 86.89% 602ms 0.55% std::vector::_M_default_append (inline) 29ms 0.026% 86.92% 586ms 0.53% MutableElement::RegisterWithNodes (inline) 558ms 0.51% 87.43% 581ms 0.53% boost::detail::shared_count::shared_count (inline) 21ms 0.019% 87.44% 572ms 0.52% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.44% 572ms 0.52% boost::numeric::ublas::vector::vector (inline) 24ms 0.022% 87.47% 554ms 0.5% Node::AddElement