File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 99733ms, 89.77% of 111102ms total Dropped 1131 nodes (cum <= 555.51ms) flat flat% sum% cum cum% 0 0% 0% 110623ms 99.57% __libc_start_call_main 0 0% 0% 110623ms 99.57% __libc_start_main_impl 0 0% 0% 110623ms 99.57% _start 0 0% 0% 110604ms 99.55% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 110604ms 99.55% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 110604ms 99.55% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 110604ms 99.55% main 0 0% 0% 110564ms 99.52% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 110564ms 99.52% CxxTest::TestRunner::runTest (inline) 0 0% 0% 110564ms 99.52% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0018% 0.0018% 110556ms 99.51% AbstractCellBasedSimulation::Solve 16ms 0.014% 0.016% 57895ms 52.11% OffLatticeSimulation::UpdateCellLocationsAndTopology 19ms 0.017% 0.033% 54746ms 49.28% ForwardEulerNumericalMethod::UpdateAllNodePositions 160ms 0.14% 0.18% 53655ms 48.29% AbstractNumericalMethod::ComputeForcesIncludingDamping 304ms 0.27% 0.45% 40404ms 36.37% NagaiHondaForce::AddForceContribution 0 0% 0.45% 39491ms 35.54% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0018% 0.45% 24468ms 22.02% VertexBasedCellPopulation::Update 1ms 0.0009% 0.45% 24331ms 21.90% MutableVertexMesh::ReMesh 14381ms 12.94% 13.40% 22919ms 20.63% Cylindrical2dVertexMesh::GetVectorFromAtoB 75ms 0.068% 13.47% 17645ms 15.88% Cell::ReadyToDivide 157ms 0.14% 13.61% 17388ms 15.65% CellPropertyCollection::GetPropertiesType (inline) 53ms 0.048% 13.65% 16651ms 14.99% AbstractPhaseBasedCellCycleModel::ReadyToDivide 371ms 0.33% 13.99% 15031ms 13.53% NagaiHondaForce::GetAdhesionParameter 3569ms 3.21% 17.20% 14955ms 13.46% __dynamic_cast 76ms 0.068% 17.27% 14812ms 13.33% AbstractCellProperty::IsSubType (inline) 423ms 0.38% 17.65% 14468ms 13.02% boost::numeric::ublas::c_vector::c_vector (partial-inline) 124ms 0.11% 17.76% 13805ms 12.43% SimpleWntCellCycleModel::UpdateCellCyclePhase 370ms 0.33% 18.09% 12819ms 11.54% boost::numeric::ublas::vector_assign (inline) 77ms 0.069% 18.16% 12718ms 11.45% VertexBasedCellPopulation::GetDampingConstant 116ms 0.1% 18.27% 12120ms 10.91% MutableVertexMesh::CheckForIntersections 97ms 0.087% 18.36% 10944ms 9.85% Cell::GetMutationState 75ms 0.068% 18.42% 10637ms 9.57% AbstractTargetAreaModifier::UpdateTargetAreas 37ms 0.033% 18.46% 10544ms 9.49% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 36ms 0.032% 18.49% 10387ms 9.35% AbstractCellBasedSimulation::DoCellBirth 1312ms 1.18% 19.67% 10018ms 9.02% std::__new_allocator::allocate (inline) 2817ms 2.54% 22.20% 9671ms 8.70% boost::numeric::ublas::indexing_vector_assign 0 0% 22.20% 9527ms 8.58% std::allocator_traits::allocate (inline) 0 0% 22.20% 9524ms 8.57% std::_Rb_tree::_M_create_node (inline) 1417ms 1.28% 23.48% 9521ms 8.57% std::_Rb_tree::_M_erase 785ms 0.71% 24.19% 9042ms 8.14% VertexMesh::ElementIncludesPoint 4043ms 3.64% 27.83% 8918ms 8.03% __cxxabiv1::__si_class_type_info::__do_dyncast 399ms 0.36% 28.18% 8831ms 7.95% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 28.18% 8828ms 7.95% std::_Rb_tree::_M_get_node (inline) 825ms 0.74% 28.93% 8799ms 7.92% operator new 227ms 0.2% 29.13% 8688ms 7.82% std::_Rb_tree::~_Rb_tree (inline) 27ms 0.024% 29.16% 8642ms 7.78% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 29.16% 8454ms 7.61% std::_Rb_tree::_M_drop_node (inline) 0 0% 29.16% 8384ms 7.55% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 29.16% 8268ms 7.44% std::set::~set (inline) 228ms 0.21% 29.36% 8170ms 7.35% std::__new_allocator::deallocate (inline) 0 0% 29.36% 8129ms 7.32% std::allocator_traits::deallocate (inline) 515ms 0.46% 29.82% 8115ms 7.30% VertexMesh::GetCentroidOfElement 0 0% 29.82% 8075ms 7.27% std::_Rb_tree::_M_put_node (inline) 3033ms 2.73% 32.55% 7976ms 7.18% __GI___libc_free 22ms 0.02% 32.57% 7804ms 7.02% MutableVertexMesh::RemoveDeletedNodesAndElements 3164ms 2.85% 35.42% 7774ms 7.00% __GI___libc_malloc 461ms 0.41% 35.84% 7491ms 6.74% std::map::operator[] (partial-inline) 1400ms 1.26% 37.10% 7109ms 6.40% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 7076ms 6.37% 43.47% 7076ms 6.37% __strcmp_avx2 148ms 0.13% 43.60% 6944ms 6.25% std::_Rb_tree::_Rb_tree (partial-inline) 698ms 0.63% 44.23% 6554ms 5.90% std::_Rb_tree::_M_copy (inline) 8ms 0.0072% 44.24% 6494ms 5.85% std::set::set (inline) 114ms 0.1% 44.34% 6319ms 5.69% SimpleWntCellCycleModel::GetWntLevel 6267ms 5.64% 49.98% 6267ms 5.64% boost::numeric::ublas::c_vector::operator() 168ms 0.15% 50.13% 6066ms 5.46% WntConcentration::GetWntLevel 2384ms 2.15% 52.28% 5921ms 5.33% std::_Rb_tree::_M_lower_bound (inline) 783ms 0.7% 52.98% 5583ms 5.03% std::_Rb_tree::_M_clone_node (inline) 23ms 0.021% 53.00% 5496ms 4.95% MutableVertexMesh::RemoveDeletedNodes 0 0% 53.00% 5479ms 4.93% std::set::insert (inline) 38ms 0.034% 53.04% 5334ms 4.80% EdgeHelper::RemoveDeletedEdges 42ms 0.038% 53.07% 5113ms 4.60% Cell::GetCellProliferativeType 36ms 0.032% 53.11% 5029ms 4.53% EdgeHelper::UpdateEdgesMapKey 4578ms 4.12% 57.23% 4929ms 4.44% _int_free 0 0% 57.23% 4841ms 4.36% std::_Rb_tree::lower_bound (inline) 0 0% 57.23% 4841ms 4.36% std::map::lower_bound (inline) 232ms 0.21% 57.43% 4797ms 4.32% MutableElement::ResetIndex 1480ms 1.33% 58.77% 4784ms 4.31% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 58.77% 4629ms 4.17% AbstractCellBasedSimulation::DoCellRemoval (inline) 500ms 0.45% 59.22% 4625ms 4.16% std::_Rb_tree::_M_insert_ (inline) 62ms 0.056% 59.27% 4503ms 4.05% std::set_intersection (inline) 223ms 0.2% 59.47% 4441ms 4.00% std::__set_intersection 116ms 0.1% 59.58% 4164ms 3.75% AbstractCellPopulation::GetCellUsingLocationIndex 3931ms 3.54% 63.12% 3931ms 3.54% boost::numeric::ublas::same_impl_ex 50ms 0.045% 63.16% 3705ms 3.33% Cell::SetCellProliferativeType 5ms 0.0045% 63.17% 3556ms 3.20% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 63.17% 3316ms 2.98% std::insert_iterator::operator= (inline) 734ms 0.66% 63.83% 3128ms 2.82% AbstractElement::GetNodeLocation 34ms 0.031% 63.86% 3103ms 2.79% std::_Rb_tree::erase 433ms 0.39% 64.25% 3083ms 2.77% std::_Rb_tree_const_iterator::operator++ (inline) 2140ms 1.93% 66.17% 3039ms 2.74% _int_malloc 2988ms 2.69% 68.86% 2988ms 2.69% std::_Rb_tree::_S_right (inline) 32ms 0.029% 68.89% 2955ms 2.66% Cell::GetCellData 6ms 0.0054% 68.90% 2902ms 2.61% std::_Rb_tree::_M_insert_unique_ (inline) 667ms 0.6% 69.50% 2804ms 2.52% boost::numeric::ublas::vector_binary::size (inline) 97ms 0.087% 69.58% 2781ms 2.50% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.0027% 69.59% 2577ms 2.32% std::_Rb_tree::_M_insert_unique 0 0% 69.59% 2495ms 2.25% AbstractCellPopulation::WriteResultsToFiles 2483ms 2.23% 71.82% 2483ms 2.23% std::_Rb_tree_increment 0 0% 71.82% 2473ms 2.23% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 71.82% 2420ms 2.18% boost::numeric::ublas::c_vector::assign (inline) 241ms 0.22% 72.04% 2385ms 2.15% VertexMesh::GetAreaGradientOfElementAtNode 1ms 0.0009% 72.04% 2326ms 2.09% AbstractCellPopulation::Iterator::operator++ (inline) 305ms 0.27% 72.31% 2302ms 2.07% AbstractCellPopulation::Iterator::IsRealCell (inline) 91ms 0.082% 72.40% 2266ms 2.04% VertexMesh::GetVolumeOfElement 34ms 0.031% 72.43% 2138ms 1.92% std::_Rb_tree::_M_emplace_hint_unique 1360ms 1.22% 73.65% 2090ms 1.88% std::_Rb_tree::equal_range (inline) 0 0% 73.65% 2038ms 1.83% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 73.65% 2033ms 1.83% VertexBasedCellPopulation::WriteCellVtkResultsToFile 85ms 0.077% 73.73% 1926ms 1.73% CellPropertyCollection::HasProperty 1ms 0.0009% 73.73% 1862ms 1.68% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.73% 1862ms 1.68% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 67ms 0.06% 73.79% 1849ms 1.66% MutableVertexMesh::CheckForSwapsFromShortEdges 2ms 0.0018% 73.79% 1822ms 1.64% VertexMeshWriter::WriteVtkUsingMesh 0 0% 73.79% 1819ms 1.64% Cell::HasCellProperty (inline) 22ms 0.02% 73.81% 1710ms 1.54% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 29ms 0.026% 73.84% 1660ms 1.49% VertexMesh::GetSurfaceAreaOfElement 122ms 0.11% 73.95% 1601ms 1.44% boost::numeric::ublas::vector_reference::operator() (inline) 48ms 0.043% 73.99% 1568ms 1.41% Node::RemoveElement 153ms 0.14% 74.13% 1561ms 1.41% CellPropertyCollection::AddProperty 20ms 0.018% 74.14% 1534ms 1.38% std::set::erase (inline) 27ms 0.024% 74.17% 1531ms 1.38% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 74.17% 1512ms 1.36% boost::numeric::ublas::vector_binary::operator() (inline) 93ms 0.084% 74.25% 1503ms 1.35% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 828ms 0.75% 75.00% 1440ms 1.30% AbstractCellProperty::IsType (inline) 0 0% 75.00% 1377ms 1.24% tcache_get (inline) 1377ms 1.24% 76.24% 1377ms 1.24% tcache_get_n (inline) 3ms 0.0027% 76.24% 1312ms 1.18% OffLatticeSimulation::ApplyBoundaries 58ms 0.052% 76.29% 1260ms 1.13% std::less::operator() (inline) 0 0% 76.29% 1207ms 1.09% boost::numeric::ublas::norm_2 (inline) 995ms 0.9% 77.19% 1202ms 1.08% std::operator< (inline) 521ms 0.47% 77.66% 1200ms 1.08% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1155ms 1.04% 78.70% 1155ms 1.04% Node::rGetLocation 74ms 0.067% 78.76% 1152ms 1.04% std::_Rb_tree::_M_erase_aux (partial-inline) 0 0% 78.76% 1140ms 1.03% std::_Rb_tree::_Auto_node::_Auto_node (inline) 20ms 0.018% 78.78% 1122ms 1.01% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 1120ms 1.01% 79.79% 1120ms 1.01% std::_Rb_tree_insert_and_rebalance 205ms 0.18% 79.97% 1096ms 0.99% boost::detail::shared_count::~shared_count (inline) 0 0% 79.97% 1096ms 0.99% boost::shared_ptr::~shared_ptr (inline) 116ms 0.1% 80.08% 1078ms 0.97% std::_Rb_tree::find (inline) 0 0% 80.08% 1069ms 0.96% std::_Rb_tree::clear (inline) 0 0% 80.08% 1057ms 0.95% std::map::clear (inline) 5ms 0.0045% 80.08% 1018ms 0.92% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 976ms 0.88% 80.96% 976ms 0.88% [libchaste_mesh.so] 424ms 0.38% 81.34% 966ms 0.87% Edge::GetMapIndex 0 0% 81.34% 965ms 0.87% boost::numeric::ublas::c_vector::assign_temporary (inline) 3ms 0.0027% 81.35% 965ms 0.87% boost::numeric::ublas::c_vector::swap (inline) 90ms 0.081% 81.43% 962ms 0.87% std::swap_ranges (inline) 912ms 0.82% 82.25% 912ms 0.82% std::vector::size (inline) 30ms 0.027% 82.27% 907ms 0.82% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 82.27% 878ms 0.79% std::map::find (inline) 873ms 0.79% 83.06% 873ms 0.79% std::swap (inline) 0 0% 83.06% 872ms 0.78% VertexMeshWriter::MakeVtkMesh 0 0% 83.06% 872ms 0.78% std::iter_swap (inline) 861ms 0.77% 83.83% 869ms 0.78% boost::detail::sp_counted_base::release 159ms 0.14% 83.98% 861ms 0.77% boost::numeric::ublas::detail::equals 119ms 0.11% 84.08% 834ms 0.75% boost::numeric::ublas::c_vector::operator= (inline) 104ms 0.094% 84.18% 809ms 0.73% MutableElement::GetNodeLocalIndex 798ms 0.72% 84.90% 798ms 0.72% [libchaste_cell_based.so] 150ms 0.14% 85.03% 776ms 0.7% boost::shared_ptr::shared_ptr (inline) 441ms 0.4% 85.43% 764ms 0.69% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 85.43% 763ms 0.69% CellPropertyCollection::~CellPropertyCollection (inline) 24ms 0.022% 85.45% 763ms 0.69% MutableElement::RegisterWithEdges (inline) 128ms 0.12% 85.57% 753ms 0.68% std::__new_allocator::construct (inline) 0 0% 85.57% 753ms 0.68% std::allocator_traits::construct (inline) 34ms 0.031% 85.60% 751ms 0.68% Edge::AddElement 710ms 0.64% 86.24% 710ms 0.64% Node::GetIndex 1ms 0.0009% 86.24% 698ms 0.63% std::_Vector_base::_M_allocate (inline) 0 0% 86.24% 696ms 0.63% std::_Rb_tree::_M_construct_node (inline) 445ms 0.4% 86.64% 665ms 0.6% CellPropertyCollection::GetProperty 0 0% 86.64% 655ms 0.59% boost::numeric::ublas::norm_inf (inline) 375ms 0.34% 86.97% 655ms 0.59% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 86.97% 655ms 0.59% std::_Rb_tree::_Auto_node::_M_insert (inline) 19ms 0.017% 86.99% 655ms 0.59% std::_Rb_tree::_M_insert_node (inline) 2ms 0.0018% 86.99% 628ms 0.57% vtkPolygon::New 605ms 0.54% 87.54% 626ms 0.56% boost::detail::shared_count::shared_count (inline) 1ms 0.0009% 87.54% 626ms 0.56% vtkPolygon::vtkPolygon 623ms 0.56% 88.10% 623ms 0.56% boost::shared_ptr::operator-> (inline) 612ms 0.55% 88.65% 612ms 0.55% CellProperty::GetTypeId 612ms 0.55% 89.20% 612ms 0.55% [libstdc++.so.6.0.33] 588ms 0.53% 89.73% 588ms 0.53% operator delete 10ms 0.009% 89.74% 585ms 0.53% std::vector::_M_default_append (inline) 31ms 0.028% 89.77% 572ms 0.51% MutableElement::RegisterWithNodes (inline) 0 0% 89.77% 567ms 0.51% boost::numeric::ublas::scalar_traits::type_sqrt (inline)