File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 99985ms, 88.87% of 112504ms total Dropped 1118 nodes (cum <= 562.52ms) flat flat% sum% cum cum% 0 0% 0% 112126ms 99.66% __libc_start_call_main 0 0% 0% 112126ms 99.66% __libc_start_main_impl 0 0% 0% 112126ms 99.66% _start 0 0% 0% 112105ms 99.65% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 112105ms 99.65% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 112105ms 99.65% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 112105ms 99.65% main 0 0% 0% 112060ms 99.61% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 112060ms 99.61% CxxTest::TestRunner::runTest (inline) 0 0% 0% 112060ms 99.61% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 4ms 0.0036% 0.0036% 112052ms 99.60% AbstractCellBasedSimulation::Solve 21ms 0.019% 0.022% 58034ms 51.58% OffLatticeSimulation::UpdateCellLocationsAndTopology 13ms 0.012% 0.034% 54502ms 48.44% ForwardEulerNumericalMethod::UpdateAllNodePositions 181ms 0.16% 0.19% 52950ms 47.06% AbstractNumericalMethod::ComputeForcesIncludingDamping 286ms 0.25% 0.45% 40563ms 36.05% NagaiHondaForce::AddForceContribution 1ms 0.00089% 0.45% 40349ms 35.86% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.0036% 0.45% 24908ms 22.14% VertexBasedCellPopulation::Update 0 0% 0.45% 24749ms 22.00% MutableVertexMesh::ReMesh 14550ms 12.93% 13.39% 23237ms 20.65% Cylindrical2dVertexMesh::GetVectorFromAtoB 118ms 0.1% 13.49% 18049ms 16.04% Cell::ReadyToDivide 72ms 0.064% 13.56% 16590ms 14.75% AbstractPhaseBasedCellCycleModel::ReadyToDivide 354ms 0.31% 13.87% 14859ms 13.21% NagaiHondaForce::GetAdhesionParameter 104ms 0.092% 13.96% 14212ms 12.63% CellPropertyCollection::GetPropertiesType (inline) 152ms 0.14% 14.10% 14166ms 12.59% SimpleWntCellCycleModel::UpdateCellCyclePhase 437ms 0.39% 14.49% 14081ms 12.52% boost::numeric::ublas::c_vector::c_vector (partial-inline) 321ms 0.29% 14.77% 12625ms 11.22% boost::numeric::ublas::vector_assign (inline) 3628ms 3.22% 18.00% 11971ms 10.64% __dynamic_cast 131ms 0.12% 18.11% 11949ms 10.62% MutableVertexMesh::CheckForIntersections 54ms 0.048% 18.16% 11843ms 10.53% AbstractCellProperty::IsSubType (inline) 85ms 0.076% 18.24% 11778ms 10.47% VertexBasedCellPopulation::GetDampingConstant 81ms 0.072% 18.31% 11066ms 9.84% AbstractTargetAreaModifier::UpdateTargetAreas 46ms 0.041% 18.35% 10957ms 9.74% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 1399ms 1.24% 19.59% 10734ms 9.54% std::__new_allocator::allocate (inline) 36ms 0.032% 19.62% 10488ms 9.32% AbstractCellBasedSimulation::DoCellBirth 0 0% 19.62% 10226ms 9.09% std::_Rb_tree::_M_create_node (inline) 0 0% 19.62% 10216ms 9.08% std::allocator_traits::allocate (inline) 3006ms 2.67% 22.30% 9679ms 8.60% boost::numeric::ublas::indexing_vector_assign 795ms 0.71% 23.00% 9426ms 8.38% operator new 324ms 0.29% 23.29% 9374ms 8.33% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 23.29% 9355ms 8.32% std::_Rb_tree::_M_get_node (inline) 0 0% 23.29% 9098ms 8.09% std::_Rb_tree::_Alloc_node::operator() (inline) 1171ms 1.04% 24.33% 9082ms 8.07% std::_Rb_tree::_M_erase 27ms 0.024% 24.36% 8897ms 7.91% VertexBasedCellPopulation::GetLocationOfCellCentre 100ms 0.089% 24.44% 8867ms 7.88% Cell::GetMutationState 859ms 0.76% 25.21% 8774ms 7.80% VertexMesh::ElementIncludesPoint 0 0% 25.21% 8485ms 7.54% std::_Rb_tree::_M_drop_node (inline) 26ms 0.023% 25.23% 8446ms 7.51% MutableVertexMesh::RemoveDeletedNodesAndElements 3220ms 2.86% 28.09% 8417ms 7.48% __GI___libc_malloc 465ms 0.41% 28.51% 8337ms 7.41% VertexMesh::GetCentroidOfElement 235ms 0.21% 28.72% 8253ms 7.34% std::__new_allocator::deallocate (inline) 0 0% 28.72% 8247ms 7.33% std::allocator_traits::deallocate (inline) 0 0% 28.72% 8153ms 7.25% std::_Rb_tree::_M_put_node (inline) 218ms 0.19% 28.91% 8117ms 7.21% std::_Rb_tree::~_Rb_tree (inline) 501ms 0.45% 29.35% 7912ms 7.03% std::map::operator[] (partial-inline) 167ms 0.15% 29.50% 7814ms 6.95% std::_Rb_tree::_Rb_tree (partial-inline) 2418ms 2.15% 31.65% 7686ms 6.83% __GI___libc_free 0 0% 31.65% 7657ms 6.81% std::set::~set (inline) 1591ms 1.41% 33.07% 7483ms 6.65% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 816ms 0.73% 33.79% 7425ms 6.60% std::_Rb_tree::_M_copy (inline) 39ms 0.035% 33.83% 7268ms 6.46% std::set::set (inline) 6731ms 5.98% 39.81% 6731ms 5.98% __strcmp_avx2 2621ms 2.33% 42.14% 6389ms 5.68% std::_Rb_tree::_M_lower_bound (inline) 815ms 0.72% 42.86% 6307ms 5.61% std::_Rb_tree::_M_clone_node (inline) 106ms 0.094% 42.96% 6267ms 5.57% SimpleWntCellCycleModel::GetWntLevel 6114ms 5.43% 48.39% 6114ms 5.43% boost::numeric::ublas::c_vector::operator() 145ms 0.13% 48.52% 6083ms 5.41% WntConcentration::GetWntLevel 2927ms 2.60% 51.12% 5786ms 5.14% __cxxabiv1::__si_class_type_info::__do_dyncast 23ms 0.02% 51.14% 5606ms 4.98% MutableVertexMesh::RemoveDeletedNodes 0 0% 51.14% 5413ms 4.81% std::set::insert (inline) 33ms 0.029% 51.17% 5406ms 4.81% EdgeHelper::RemoveDeletedEdges 256ms 0.23% 51.40% 5270ms 4.68% MutableElement::ResetIndex 4702ms 4.18% 55.58% 5252ms 4.67% _int_free 1899ms 1.69% 57.27% 5197ms 4.62% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 57.27% 5189ms 4.61% std::_Rb_tree::lower_bound (inline) 0 0% 57.27% 5189ms 4.61% std::map::lower_bound (inline) 36ms 0.032% 57.30% 5059ms 4.50% EdgeHelper::UpdateEdgesMapKey 0 0% 57.30% 4937ms 4.39% AbstractCellBasedSimulation::DoCellRemoval (inline) 136ms 0.12% 57.42% 4655ms 4.14% AbstractCellPopulation::GetCellUsingLocationIndex 489ms 0.43% 57.85% 4597ms 4.09% std::_Rb_tree::_M_insert_ (inline) 132ms 0.12% 57.97% 4253ms 3.78% std::set_intersection (inline) 41ms 0.036% 58.01% 4191ms 3.73% Cell::GetCellProliferativeType 231ms 0.21% 58.21% 4121ms 3.66% std::__set_intersection 54ms 0.048% 58.26% 4070ms 3.62% AbstractCellProperty::IsType (inline) 3825ms 3.40% 61.66% 3825ms 3.40% boost::numeric::ublas::same_impl_ex 12ms 0.011% 61.67% 3664ms 3.26% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 57ms 0.051% 61.72% 3465ms 3.08% std::_Rb_tree::erase 2378ms 2.11% 63.84% 3461ms 3.08% _int_malloc 3285ms 2.92% 66.76% 3285ms 2.92% std::_Rb_tree::_S_right (inline) 52ms 0.046% 66.80% 3217ms 2.86% Cell::SetCellProliferativeType 0 0% 66.80% 3209ms 2.85% std::insert_iterator::operator= (inline) 977ms 0.87% 67.67% 3184ms 2.83% AbstractElement::GetNodeLocation 785ms 0.7% 68.37% 2951ms 2.62% AbstractCellProperty::IsSame 39ms 0.035% 68.40% 2950ms 2.62% CellPropertyCollection::HasProperty 0 0% 68.40% 2863ms 2.54% Cell::HasCellProperty (inline) 10ms 0.0089% 68.41% 2797ms 2.49% std::_Rb_tree::_M_insert_unique_ (inline) 0 0% 68.41% 2643ms 2.35% boost::numeric::ublas::c_vector::operator-= (inline) 25ms 0.022% 68.43% 2637ms 2.34% Cell::GetCellData 2ms 0.0018% 68.44% 2616ms 2.33% std::_Rb_tree::_M_insert_unique 187ms 0.17% 68.60% 2609ms 2.32% VertexMesh::GetAreaGradientOfElementAtNode 632ms 0.56% 69.16% 2584ms 2.30% boost::numeric::ublas::vector_binary::size (inline) 250ms 0.22% 69.39% 2567ms 2.28% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 69.39% 2562ms 2.28% boost::numeric::ublas::c_vector::assign (inline) 0 0% 69.39% 2558ms 2.27% AbstractCellPopulation::WriteResultsToFiles 6ms 0.0053% 69.39% 2339ms 2.08% AbstractCellPopulation::Iterator::operator++ (inline) 55ms 0.049% 69.44% 2333ms 2.07% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 208ms 0.18% 69.63% 2329ms 2.07% AbstractCellPopulation::Iterator::IsRealCell (inline) 104ms 0.092% 69.72% 2329ms 2.07% VertexMesh::GetVolumeOfElement 1506ms 1.34% 71.06% 2281ms 2.03% std::_Rb_tree::equal_range (inline) 3ms 0.0027% 71.06% 2222ms 1.98% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 71.06% 2222ms 1.98% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 37ms 0.033% 71.09% 2171ms 1.93% std::_Rb_tree::_M_emplace_hint_unique 560ms 0.5% 71.59% 2166ms 1.93% std::type_info::operator== (inline) 0 0% 71.59% 2095ms 1.86% VertexBasedCellPopulation::WriteVtkResultsToFile 4ms 0.0036% 71.59% 2079ms 1.85% VertexBasedCellPopulation::WriteCellVtkResultsToFile 2021ms 1.80% 73.39% 2021ms 1.80% std::_Rb_tree_increment 1ms 0.00089% 73.39% 1868ms 1.66% VertexMeshWriter::WriteVtkUsingMesh 67ms 0.06% 73.45% 1842ms 1.64% MutableVertexMesh::CheckForSwapsFromShortEdges 23ms 0.02% 73.47% 1837ms 1.63% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 45ms 0.04% 73.51% 1709ms 1.52% Node::RemoveElement 12ms 0.011% 73.52% 1668ms 1.48% std::set::erase (inline) 32ms 0.028% 73.55% 1646ms 1.46% AbstractCellPopulation::GetLocationIndexUsingCell 91ms 0.081% 73.63% 1618ms 1.44% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 73.63% 1560ms 1.39% tcache_get (inline) 1560ms 1.39% 75.02% 1560ms 1.39% tcache_get_n (inline) 31ms 0.028% 75.05% 1550ms 1.38% VertexMesh::GetSurfaceAreaOfElement 123ms 0.11% 75.15% 1512ms 1.34% CellPropertyCollection::AddProperty 1ms 0.00089% 75.16% 1455ms 1.29% OffLatticeSimulation::ApplyBoundaries 0 0% 75.16% 1452ms 1.29% boost::numeric::ublas::norm_2 (inline) 644ms 0.57% 75.73% 1436ms 1.28% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1422ms 1.26% 76.99% 1422ms 1.26% [libchaste_cell_based.so] 66ms 0.059% 77.05% 1413ms 1.26% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 77.05% 1361ms 1.21% boost::numeric::ublas::vector_binary::operator() (inline) 69ms 0.061% 77.11% 1340ms 1.19% std::_Rb_tree::_M_erase_aux (partial-inline) 48ms 0.043% 77.15% 1301ms 1.16% std::less::operator() (inline) 18ms 0.016% 77.17% 1264ms 1.12% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 1022ms 0.91% 78.08% 1253ms 1.11% std::operator< (inline) 10ms 0.0089% 78.09% 1235ms 1.10% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 110ms 0.098% 78.19% 1228ms 1.09% std::_Rb_tree::find (inline) 29ms 0.026% 78.21% 1191ms 1.06% CellPropertyRegistry::Get 0 0% 78.21% 1191ms 1.06% std::_Rb_tree::clear (inline) 0 0% 78.21% 1164ms 1.03% std::map::clear (inline) 0 0% 78.21% 1128ms 1.00% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 78.21% 1100ms 0.98% boost::numeric::ublas::c_vector::assign_temporary (inline) 12ms 0.011% 78.22% 1100ms 0.98% boost::numeric::ublas::c_vector::swap (inline) 79ms 0.07% 78.29% 1088ms 0.97% std::swap_ranges (inline) 1074ms 0.95% 79.25% 1074ms 0.95% std::_Rb_tree_insert_and_rebalance 0 0% 79.25% 1052ms 0.94% std::map::find (inline) 22ms 0.02% 79.27% 1046ms 0.93% boost::numeric::ublas::detail::expression_type_check (inline) 119ms 0.11% 79.37% 1036ms 0.92% boost::detail::shared_count::~shared_count (inline) 0 0% 79.37% 1036ms 0.92% boost::shared_ptr::~shared_ptr (inline) 189ms 0.17% 79.54% 1015ms 0.9% boost::numeric::ublas::detail::equals 1010ms 0.9% 80.44% 1010ms 0.9% Node::rGetLocation 1010ms 0.9% 81.34% 1010ms 0.9% std::swap (inline) 0 0% 81.34% 1009ms 0.9% std::iter_swap (inline) 289ms 0.26% 81.59% 924ms 0.82% std::__new_allocator::construct (inline) 0 0% 81.59% 924ms 0.82% std::allocator_traits::construct (inline) 895ms 0.8% 82.39% 895ms 0.8% std::vector::size (inline) 1ms 0.00089% 82.39% 880ms 0.78% VertexMeshWriter::MakeVtkMesh 851ms 0.76% 83.15% 878ms 0.78% boost::detail::sp_counted_base::release 0 0% 83.15% 871ms 0.77% std::_Rb_tree::_M_construct_node (inline) 0 0% 83.15% 854ms 0.76% std::_Vector_base::_M_allocate (inline) 92ms 0.082% 83.23% 837ms 0.74% boost::numeric::ublas::c_vector::operator= (inline) 183ms 0.16% 83.39% 830ms 0.74% boost::shared_ptr::shared_ptr (inline) 452ms 0.4% 83.79% 818ms 0.73% Edge::GetMapIndex 0 0% 83.79% 796ms 0.71% CellPropertyCollection::~CellPropertyCollection (inline) 796ms 0.71% 84.50% 796ms 0.71% [libchaste_mesh.so] 33ms 0.029% 84.53% 792ms 0.7% Edge::AddElement 10ms 0.0089% 84.54% 791ms 0.7% MutableElement::RegisterWithEdges (inline) 0 0% 84.54% 781ms 0.69% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 84.54% 770ms 0.68% boost::numeric::ublas::norm_inf (inline) 415ms 0.37% 84.91% 770ms 0.68% boost::numeric::ublas::vector_norm_inf::apply (inline) 22ms 0.02% 84.93% 758ms 0.67% AbstractNumericalMethod::DetectStepSizeExceptions 388ms 0.34% 85.27% 747ms 0.66% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 125ms 0.11% 85.38% 736ms 0.65% VertexBasedCellPopulation::CheckForStepSizeException 8ms 0.0071% 85.39% 720ms 0.64% std::vector::_M_default_append (inline) 107ms 0.095% 85.48% 709ms 0.63% MutableElement::GetNodeLocalIndex 709ms 0.63% 86.11% 709ms 0.63% [libstdc++.so.6.0.33] 0 0% 86.11% 652ms 0.58% std::_Rb_tree::_Auto_node::_M_insert (inline) 27ms 0.024% 86.14% 652ms 0.58% std::_Rb_tree::_M_insert_node (inline) 647ms 0.58% 86.71% 647ms 0.58% Node::GetIndex 619ms 0.55% 87.26% 647ms 0.58% boost::detail::shared_count::shared_count (inline) 487ms 0.43% 87.70% 640ms 0.57% malloc_consolidate 0 0% 87.70% 620ms 0.55% vtkPolygon::New 1ms 0.00089% 87.70% 619ms 0.55% vtkPolygon::vtkPolygon 1ms 0.00089% 87.70% 613ms 0.54% VertexElementMap::VertexElementMap 0 0% 87.70% 612ms 0.54% std::vector::resize (inline) 29ms 0.026% 87.72% 605ms 0.54% MutableElement::RegisterWithNodes (inline) 595ms 0.53% 88.25% 595ms 0.53% tcache_put (inline) 84ms 0.075% 88.33% 594ms 0.53% std::_Rb_tree::_M_upper_bound (inline) 0 0% 88.33% 593ms 0.53% std::map::map (inline) 582ms 0.52% 88.84% 582ms 0.52% boost::shared_ptr::operator-> (inline) 31ms 0.028% 88.87% 579ms 0.51% Node::AddElement