File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 97189ms, 88.83% of 109409ms total Dropped 1103 nodes (cum <= 547.04ms) flat flat% sum% cum cum% 0 0% 0% 108966ms 99.60% __libc_start_call_main 0 0% 0% 108966ms 99.60% __libc_start_main_impl 0 0% 0% 108966ms 99.60% _start 0 0% 0% 108945ms 99.58% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108945ms 99.58% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108945ms 99.58% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108945ms 99.58% main 0 0% 0% 108908ms 99.54% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108908ms 99.54% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108908ms 99.54% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 0 0% 0% 108900ms 99.53% AbstractCellBasedSimulation::Solve 16ms 0.015% 0.015% 57027ms 52.12% OffLatticeSimulation::UpdateCellLocationsAndTopology 16ms 0.015% 0.029% 53821ms 49.19% ForwardEulerNumericalMethod::UpdateAllNodePositions 129ms 0.12% 0.15% 52830ms 48.29% AbstractNumericalMethod::ComputeForcesIncludingDamping 341ms 0.31% 0.46% 40586ms 37.10% NagaiHondaForce::AddForceContribution 0 0% 0.46% 38825ms 35.49% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.0027% 0.46% 24023ms 21.96% VertexBasedCellPopulation::Update 0 0% 0.46% 23884ms 21.83% MutableVertexMesh::ReMesh 14462ms 13.22% 13.68% 22604ms 20.66% Cylindrical2dVertexMesh::GetVectorFromAtoB 76ms 0.069% 13.75% 17580ms 16.07% Cell::ReadyToDivide 77ms 0.07% 13.82% 16392ms 14.98% AbstractPhaseBasedCellCycleModel::ReadyToDivide 326ms 0.3% 14.12% 15358ms 14.04% NagaiHondaForce::GetAdhesionParameter 462ms 0.42% 14.54% 14384ms 13.15% boost::numeric::ublas::c_vector::c_vector (partial-inline) 125ms 0.11% 14.65% 14231ms 13.01% CellPropertyCollection::GetPropertiesType (inline) 117ms 0.11% 14.76% 13936ms 12.74% SimpleWntCellCycleModel::UpdateCellCyclePhase 389ms 0.36% 15.12% 12825ms 11.72% boost::numeric::ublas::vector_assign (inline) 125ms 0.11% 15.23% 12026ms 10.99% MutableVertexMesh::CheckForIntersections 91ms 0.083% 15.31% 11772ms 10.76% VertexBasedCellPopulation::GetDampingConstant 3242ms 2.96% 18.28% 11766ms 10.75% __dynamic_cast 66ms 0.06% 18.34% 11653ms 10.65% AbstractCellProperty::IsSubType (inline) 82ms 0.075% 18.41% 10600ms 9.69% AbstractTargetAreaModifier::UpdateTargetAreas 81ms 0.074% 18.49% 10491ms 9.59% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 23ms 0.021% 18.51% 10254ms 9.37% AbstractCellBasedSimulation::DoCellBirth 1257ms 1.15% 19.66% 10173ms 9.30% std::__new_allocator::allocate (inline) 0 0% 19.66% 9587ms 8.76% std::_Rb_tree::_M_create_node (inline) 0 0% 19.66% 9565ms 8.74% std::allocator_traits::allocate (inline) 2714ms 2.48% 22.14% 9562ms 8.74% boost::numeric::ublas::indexing_vector_assign 1350ms 1.23% 23.37% 9519ms 8.70% std::_Rb_tree::_M_erase 73ms 0.067% 23.44% 9156ms 8.37% Cell::GetMutationState 803ms 0.73% 24.17% 9012ms 8.24% operator new 0 0% 24.17% 8909ms 8.14% std::_Rb_tree::_M_get_node (inline) 780ms 0.71% 24.88% 8885ms 8.12% VertexMesh::ElementIncludesPoint 374ms 0.34% 25.23% 8846ms 8.09% VertexMesh::GetNextEdgeGradientOfElementAtNode 222ms 0.2% 25.43% 8759ms 8.01% std::_Rb_tree::~_Rb_tree (inline) 23ms 0.021% 25.45% 8629ms 7.89% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 25.45% 8444ms 7.72% std::_Rb_tree::_M_drop_node (inline) 0 0% 25.45% 8437ms 7.71% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 25.45% 8302ms 7.59% std::set::~set (inline) 450ms 0.41% 25.86% 8246ms 7.54% VertexMesh::GetCentroidOfElement 281ms 0.26% 26.12% 8185ms 7.48% std::__new_allocator::deallocate (inline) 0 0% 26.12% 8156ms 7.45% std::allocator_traits::deallocate (inline) 0 0% 26.12% 8105ms 7.41% std::_Rb_tree::_M_put_node (inline) 3298ms 3.01% 29.13% 8006ms 7.32% __GI___libc_malloc 3211ms 2.93% 32.07% 7885ms 7.21% __GI___libc_free 22ms 0.02% 32.09% 7416ms 6.78% MutableVertexMesh::RemoveDeletedNodesAndElements 435ms 0.4% 32.49% 7388ms 6.75% std::map::operator[] (partial-inline) 1416ms 1.29% 33.78% 7122ms 6.51% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 183ms 0.17% 33.95% 6980ms 6.38% std::_Rb_tree::_Rb_tree (partial-inline) 6832ms 6.24% 40.19% 6832ms 6.24% __strcmp_avx2 673ms 0.62% 40.81% 6545ms 5.98% std::_Rb_tree::_M_copy (inline) 15ms 0.014% 40.82% 6532ms 5.97% std::set::set (inline) 109ms 0.1% 40.92% 6267ms 5.73% SimpleWntCellCycleModel::GetWntLevel 6126ms 5.60% 46.52% 6126ms 5.60% boost::numeric::ublas::c_vector::operator() 140ms 0.13% 46.65% 6060ms 5.54% WntConcentration::GetWntLevel 2789ms 2.55% 49.20% 5939ms 5.43% __cxxabiv1::__si_class_type_info::__do_dyncast 2454ms 2.24% 51.44% 5819ms 5.32% std::_Rb_tree::_M_lower_bound (inline) 780ms 0.71% 52.15% 5588ms 5.11% std::_Rb_tree::_M_clone_node (inline) 0 0% 52.15% 5499ms 5.03% std::set::insert (inline) 24ms 0.022% 52.17% 5280ms 4.83% MutableVertexMesh::RemoveDeletedNodes 36ms 0.033% 52.21% 5113ms 4.67% EdgeHelper::RemoveDeletedEdges 36ms 0.033% 52.24% 4846ms 4.43% EdgeHelper::UpdateEdgesMapKey 1503ms 1.37% 53.61% 4800ms 4.39% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 53.61% 4743ms 4.34% std::_Rb_tree::lower_bound (inline) 0 0% 53.61% 4743ms 4.34% std::map::lower_bound (inline) 530ms 0.48% 54.10% 4682ms 4.28% std::_Rb_tree::_M_insert_ (inline) 4321ms 3.95% 58.05% 4668ms 4.27% _int_free 55ms 0.05% 58.10% 4646ms 4.25% std::set_intersection (inline) 200ms 0.18% 58.28% 4631ms 4.23% MutableElement::ResetIndex 248ms 0.23% 58.51% 4591ms 4.20% std::__set_intersection 1ms 0.00091% 58.51% 4542ms 4.15% AbstractCellBasedSimulation::DoCellRemoval (inline) 100ms 0.091% 58.60% 4052ms 3.70% AbstractCellPopulation::GetCellUsingLocationIndex 45ms 0.041% 58.64% 3976ms 3.63% Cell::GetCellProliferativeType 3905ms 3.57% 62.21% 3905ms 3.57% boost::numeric::ublas::same_impl_ex 73ms 0.067% 62.28% 3809ms 3.48% AbstractCellProperty::IsType (inline) 7ms 0.0064% 62.28% 3507ms 3.21% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 784ms 0.72% 63.00% 3280ms 3.00% AbstractElement::GetNodeLocation 0 0% 63.00% 3249ms 2.97% std::insert_iterator::operator= (inline) 45ms 0.041% 63.04% 3219ms 2.94% Cell::SetCellProliferativeType 2228ms 2.04% 65.08% 3104ms 2.84% _int_malloc 428ms 0.39% 65.47% 2958ms 2.70% std::_Rb_tree_const_iterator::operator++ (inline) 48ms 0.044% 65.51% 2938ms 2.69% std::_Rb_tree::erase 2870ms 2.62% 68.14% 2870ms 2.62% std::_Rb_tree::_S_right (inline) 8ms 0.0073% 68.14% 2849ms 2.60% std::_Rb_tree::_M_insert_unique_ (inline) 788ms 0.72% 68.86% 2787ms 2.55% AbstractCellProperty::IsSame 644ms 0.59% 69.45% 2753ms 2.52% boost::numeric::ublas::vector_binary::size (inline) 2ms 0.0018% 69.45% 2650ms 2.42% std::_Rb_tree::_M_insert_unique (inline) 40ms 0.037% 69.49% 2636ms 2.41% CellPropertyCollection::HasProperty 0 0% 69.49% 2609ms 2.38% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.49% 2503ms 2.29% Cell::HasCellProperty (inline) 21ms 0.019% 69.51% 2486ms 2.27% Cell::GetCellData 0 0% 69.51% 2444ms 2.23% boost::numeric::ublas::c_vector::assign (inline) 0 0% 69.51% 2426ms 2.22% AbstractCellPopulation::WriteResultsToFiles 233ms 0.21% 69.72% 2407ms 2.20% VertexMesh::GetAreaGradientOfElementAtNode 2355ms 2.15% 71.87% 2355ms 2.15% std::_Rb_tree_increment 126ms 0.12% 71.99% 2346ms 2.14% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 89ms 0.081% 72.07% 2235ms 2.04% VertexMesh::GetVolumeOfElement 217ms 0.2% 72.27% 2210ms 2.02% AbstractCellPopulation::Iterator::IsRealCell (inline) 3ms 0.0027% 72.27% 2205ms 2.02% AbstractCellPopulation::Iterator::operator++ (inline) 31ms 0.028% 72.30% 2153ms 1.97% std::_Rb_tree::_M_emplace_hint_unique 502ms 0.46% 72.76% 1999ms 1.83% std::type_info::operator== (inline) 1356ms 1.24% 74.00% 1993ms 1.82% std::_Rb_tree::equal_range (inline) 0 0% 74.00% 1991ms 1.82% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00091% 74.00% 1978ms 1.81% VertexBasedCellPopulation::WriteCellVtkResultsToFile 78ms 0.071% 74.07% 1884ms 1.72% MutableVertexMesh::CheckForSwapsFromShortEdges 2ms 0.0018% 74.07% 1820ms 1.66% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 74.07% 1820ms 1.66% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 74.07% 1770ms 1.62% VertexMeshWriter::WriteVtkUsingMesh 25ms 0.023% 74.10% 1722ms 1.57% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 199ms 0.18% 74.28% 1670ms 1.53% CellPropertyCollection::AddProperty 29ms 0.027% 74.30% 1625ms 1.49% VertexMesh::GetSurfaceAreaOfElement 52ms 0.048% 74.35% 1567ms 1.43% Node::RemoveElement 127ms 0.12% 74.47% 1541ms 1.41% boost::numeric::ublas::vector_reference::operator() (inline) 14ms 0.013% 74.48% 1523ms 1.39% std::set::erase (inline) 34ms 0.031% 74.51% 1518ms 1.39% AbstractCellPopulation::GetLocationIndexUsingCell 91ms 0.083% 74.59% 1496ms 1.37% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 74.59% 1455ms 1.33% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 74.59% 1398ms 1.28% tcache_get (inline) 1398ms 1.28% 75.87% 1398ms 1.28% tcache_get_n (inline) 1ms 0.00091% 75.87% 1254ms 1.15% OffLatticeSimulation::ApplyBoundaries 0 0% 75.87% 1162ms 1.06% boost::numeric::ublas::norm_2 (inline) 1161ms 1.06% 76.93% 1161ms 1.06% Node::rGetLocation 77ms 0.07% 77.00% 1160ms 1.06% std::less::operator() (inline) 0 0% 77.00% 1150ms 1.05% std::_Rb_tree::_Auto_node::_Auto_node (inline) 520ms 0.48% 77.48% 1148ms 1.05% boost::numeric::ublas::vector_norm_2::apply 1145ms 1.05% 78.53% 1145ms 1.05% std::_Rb_tree_insert_and_rebalance 85ms 0.078% 78.60% 1119ms 1.02% std::_Rb_tree::_M_erase_aux (partial-inline) 1104ms 1.01% 79.61% 1104ms 1.01% [libchaste_cell_based.so] 104ms 0.095% 79.71% 1099ms 1.00% std::_Rb_tree::find (inline) 18ms 0.016% 79.72% 1097ms 1.00% CellPropertyRegistry::Get 878ms 0.8% 80.53% 1083ms 0.99% std::operator< (inline) 1064ms 0.97% 81.50% 1064ms 0.97% std::vector::size (inline) 23ms 0.021% 81.52% 1052ms 0.96% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 141ms 0.13% 81.65% 1008ms 0.92% boost::detail::shared_count::~shared_count (inline) 0 0% 81.65% 1008ms 0.92% boost::shared_ptr::~shared_ptr (inline) 8ms 0.0073% 81.66% 991ms 0.91% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1ms 0.00091% 81.66% 984ms 0.9% std::_Rb_tree::clear (inline) 400ms 0.37% 82.02% 969ms 0.89% Edge::GetMapIndex 0 0% 82.02% 967ms 0.88% std::map::clear (inline) 0 0% 82.02% 955ms 0.87% boost::numeric::ublas::c_vector::assign_temporary (inline) 4ms 0.0037% 82.03% 955ms 0.87% boost::numeric::ublas::c_vector::swap (inline) 81ms 0.074% 82.10% 951ms 0.87% std::swap_ranges (inline) 908ms 0.83% 82.93% 908ms 0.83% [libchaste_mesh.so] 22ms 0.02% 82.95% 903ms 0.83% boost::numeric::ublas::detail::expression_type_check (inline) 108ms 0.099% 83.05% 876ms 0.8% MutableElement::GetNodeLocalIndex 168ms 0.15% 83.20% 874ms 0.8% boost::numeric::ublas::detail::equals 0 0% 83.20% 870ms 0.8% std::iter_swap (inline) 870ms 0.8% 84.00% 870ms 0.8% std::swap (inline) 849ms 0.78% 84.77% 852ms 0.78% boost::detail::sp_counted_base::release 0 0% 84.77% 846ms 0.77% std::map::find (inline) 1ms 0.00091% 84.78% 843ms 0.77% VertexMeshWriter::MakeVtkMesh 778ms 0.71% 85.49% 778ms 0.71% Node::GetIndex 0 0% 85.49% 776ms 0.71% CellPropertyCollection::~CellPropertyCollection (inline) 122ms 0.11% 85.60% 765ms 0.7% boost::shared_ptr::shared_ptr (inline) 16ms 0.015% 85.61% 752ms 0.69% MutableElement::RegisterWithEdges (inline) 26ms 0.024% 85.64% 744ms 0.68% Edge::AddElement 110ms 0.1% 85.74% 741ms 0.68% boost::numeric::ublas::c_vector::operator= (inline) 108ms 0.099% 85.84% 716ms 0.65% std::__new_allocator::construct (inline) 0 0% 85.84% 716ms 0.65% std::allocator_traits::construct (inline) 0 0% 85.84% 694ms 0.63% std::_Rb_tree::_Auto_node::_M_insert (inline) 26ms 0.024% 85.86% 694ms 0.63% std::_Rb_tree::_M_insert_node (inline) 402ms 0.37% 86.23% 688ms 0.63% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 86.23% 678ms 0.62% std::_Rb_tree::_M_construct_node (inline) 0 0% 86.23% 658ms 0.6% boost::numeric::ublas::norm_inf (inline) 348ms 0.32% 86.54% 658ms 0.6% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 86.54% 653ms 0.6% std::_Vector_base::_M_allocate (inline) 616ms 0.56% 87.11% 643ms 0.59% boost::detail::shared_count::shared_count (inline) 635ms 0.58% 87.69% 635ms 0.58% operator delete 17ms 0.016% 87.70% 625ms 0.57% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.70% 625ms 0.57% boost::numeric::ublas::vector::vector (inline) 617ms 0.56% 88.27% 617ms 0.56% [libstdc++.so.6.0.33] 25ms 0.023% 88.29% 609ms 0.56% MutableElement::RegisterWithNodes (inline) 1ms 0.00091% 88.29% 601ms 0.55% vtkPolygon::New 1ms 0.00091% 88.29% 599ms 0.55% vtkPolygon::vtkPolygon 29ms 0.027% 88.32% 586ms 0.54% Node::AddElement 560ms 0.51% 88.83% 560ms 0.51% boost::shared_ptr::operator-> (inline)