File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96315ms, 88.33% of 109044ms total Dropped 1104 nodes (cum <= 545.22ms) flat flat% sum% cum cum% 0 0% 0% 108685ms 99.67% __libc_start_call_main 0 0% 0% 108685ms 99.67% __libc_start_main_impl 0 0% 0% 108685ms 99.67% _start 0 0% 0% 108664ms 99.65% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108664ms 99.65% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108664ms 99.65% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108664ms 99.65% main 0 0% 0% 108619ms 99.61% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108619ms 99.61% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108619ms 99.61% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 1ms 0.00092% 0.00092% 108612ms 99.60% AbstractCellBasedSimulation::Solve 19ms 0.017% 0.018% 56441ms 51.76% OffLatticeSimulation::UpdateCellLocationsAndTopology 20ms 0.018% 0.037% 53133ms 48.73% ForwardEulerNumericalMethod::UpdateAllNodePositions 132ms 0.12% 0.16% 52029ms 47.71% AbstractNumericalMethod::ComputeForcesIncludingDamping 343ms 0.31% 0.47% 40253ms 36.91% NagaiHondaForce::AddForceContribution 3ms 0.0028% 0.48% 39166ms 35.92% AbstractCellBasedSimulation::UpdateCellPopulation 5ms 0.0046% 0.48% 24117ms 22.12% VertexBasedCellPopulation::Update 2ms 0.0018% 0.48% 23981ms 21.99% MutableVertexMesh::ReMesh 14631ms 13.42% 13.90% 23337ms 21.40% Cylindrical2dVertexMesh::GetVectorFromAtoB 93ms 0.085% 13.98% 17606ms 16.15% Cell::ReadyToDivide 41ms 0.038% 14.02% 16303ms 14.95% AbstractPhaseBasedCellCycleModel::ReadyToDivide 308ms 0.28% 14.30% 14221ms 13.04% NagaiHondaForce::GetAdhesionParameter 161ms 0.15% 14.45% 14003ms 12.84% SimpleWntCellCycleModel::UpdateCellCyclePhase 413ms 0.38% 14.83% 13971ms 12.81% boost::numeric::ublas::c_vector::c_vector (partial-inline) 113ms 0.1% 14.93% 13304ms 12.20% CellPropertyCollection::GetPropertiesType (inline) 331ms 0.3% 15.24% 12574ms 11.53% boost::numeric::ublas::vector_assign (inline) 127ms 0.12% 15.35% 11885ms 10.90% MutableVertexMesh::CheckForIntersections 3365ms 3.09% 18.44% 11341ms 10.40% __dynamic_cast 84ms 0.077% 18.52% 11226ms 10.29% AbstractCellProperty::IsSubType (inline) 80ms 0.073% 18.59% 11190ms 10.26% VertexBasedCellPopulation::GetDampingConstant 73ms 0.067% 18.66% 10524ms 9.65% AbstractTargetAreaModifier::UpdateTargetAreas 41ms 0.038% 18.70% 10435ms 9.57% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 27ms 0.025% 18.72% 10304ms 9.45% AbstractCellBasedSimulation::DoCellBirth 1215ms 1.11% 19.83% 9673ms 8.87% std::__new_allocator::allocate (inline) 2910ms 2.67% 22.50% 9593ms 8.80% boost::numeric::ublas::indexing_vector_assign 0 0% 22.50% 9286ms 8.52% std::_Rb_tree::_M_create_node (inline) 385ms 0.35% 22.86% 9285ms 8.51% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 22.86% 9160ms 8.40% std::allocator_traits::allocate (inline) 1292ms 1.18% 24.04% 8972ms 8.23% std::_Rb_tree::_M_erase 23ms 0.021% 24.06% 8792ms 8.06% VertexBasedCellPopulation::GetLocationOfCellCentre 860ms 0.79% 24.85% 8675ms 7.96% VertexMesh::ElementIncludesPoint 0 0% 24.85% 8485ms 7.78% std::_Rb_tree::_M_get_node (inline) 741ms 0.68% 25.53% 8473ms 7.77% operator new 93ms 0.085% 25.62% 8422ms 7.72% Cell::GetMutationState 469ms 0.43% 26.05% 8338ms 7.65% VertexMesh::GetCentroidOfElement 0 0% 26.05% 8190ms 7.51% std::_Rb_tree::_Alloc_node::operator() (inline) 194ms 0.18% 26.22% 8096ms 7.42% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.22% 7939ms 7.28% std::_Rb_tree::_M_drop_node (inline) 15ms 0.014% 26.24% 7806ms 7.16% MutableVertexMesh::RemoveDeletedNodesAndElements 215ms 0.2% 26.43% 7683ms 7.05% std::__new_allocator::deallocate (inline) 0 0% 26.43% 7677ms 7.04% std::allocator_traits::deallocate (inline) 0 0% 26.43% 7668ms 7.03% std::set::~set (inline) 0 0% 26.43% 7604ms 6.97% std::_Rb_tree::_M_put_node (inline) 2895ms 2.65% 29.09% 7549ms 6.92% __GI___libc_malloc 495ms 0.45% 29.54% 7536ms 6.91% std::map::operator[] (partial-inline) 1478ms 1.36% 30.90% 7450ms 6.83% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 2123ms 1.95% 32.85% 7213ms 6.61% __GI___libc_free 189ms 0.17% 33.02% 6963ms 6.39% std::_Rb_tree::_Rb_tree (partial-inline) 661ms 0.61% 33.62% 6529ms 5.99% std::_Rb_tree::_M_copy (inline) 27ms 0.025% 33.65% 6459ms 5.92% std::set::set (inline) 162ms 0.15% 33.80% 6313ms 5.79% SimpleWntCellCycleModel::GetWntLevel 6306ms 5.78% 39.58% 6306ms 5.78% boost::numeric::ublas::c_vector::operator() 6185ms 5.67% 45.25% 6185ms 5.67% __strcmp_avx2 168ms 0.15% 45.41% 6070ms 5.57% WntConcentration::GetWntLevel 2487ms 2.28% 47.69% 5945ms 5.45% std::_Rb_tree::_M_lower_bound (inline) 815ms 0.75% 48.44% 5609ms 5.14% std::_Rb_tree::_M_clone_node (inline) 2002ms 1.84% 50.27% 5466ms 5.01% boost::numeric::ublas::c_vector::operator[] (inline) 2942ms 2.70% 52.97% 5415ms 4.97% __cxxabiv1::__si_class_type_info::__do_dyncast 25ms 0.023% 52.99% 5344ms 4.90% MutableVertexMesh::RemoveDeletedNodes 0 0% 52.99% 5222ms 4.79% std::set::insert (inline) 37ms 0.034% 53.03% 5154ms 4.73% EdgeHelper::RemoveDeletedEdges 4573ms 4.19% 57.22% 5070ms 4.65% _int_free 0 0% 57.22% 4871ms 4.47% std::_Rb_tree::lower_bound (inline) 0 0% 57.22% 4871ms 4.47% std::map::lower_bound (inline) 31ms 0.028% 57.25% 4810ms 4.41% EdgeHelper::UpdateEdgesMapKey 213ms 0.2% 57.44% 4809ms 4.41% MutableElement::ResetIndex 1ms 0.00092% 57.44% 4733ms 4.34% AbstractCellBasedSimulation::DoCellRemoval (inline) 477ms 0.44% 57.88% 4372ms 4.01% std::_Rb_tree::_M_insert_ (inline) 132ms 0.12% 58.00% 4360ms 4.00% AbstractCellPopulation::GetCellUsingLocationIndex 115ms 0.11% 58.11% 4306ms 3.95% std::set_intersection (inline) 235ms 0.22% 58.32% 4191ms 3.84% std::__set_intersection 38ms 0.035% 58.36% 4027ms 3.69% Cell::GetCellProliferativeType 3737ms 3.43% 61.79% 3737ms 3.43% boost::numeric::ublas::same_impl_ex 51ms 0.047% 61.83% 3707ms 3.40% AbstractCellProperty::IsType (inline) 20ms 0.018% 61.85% 3620ms 3.32% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 79ms 0.072% 61.92% 3293ms 3.02% Cell::SetCellProliferativeType 0 0% 61.92% 3197ms 2.93% std::insert_iterator::operator= (inline) 0 0% 61.92% 3138ms 2.88% boost::numeric::ublas::c_vector::operator-= (inline) 2177ms 2.00% 63.92% 3113ms 2.85% _int_malloc 71ms 0.065% 63.99% 3094ms 2.84% std::_Rb_tree::erase 897ms 0.82% 64.81% 3039ms 2.79% AbstractElement::GetNodeLocation 2862ms 2.62% 67.43% 2862ms 2.62% std::_Rb_tree::_S_right (inline) 8ms 0.0073% 67.44% 2788ms 2.56% std::_Rb_tree::_M_insert_unique_ (inline) 226ms 0.21% 67.65% 2769ms 2.54% VertexMesh::GetAreaGradientOfElementAtNode 25ms 0.023% 67.67% 2655ms 2.43% CellPropertyCollection::HasProperty 751ms 0.69% 68.36% 2648ms 2.43% AbstractCellProperty::IsSame 0 0% 68.36% 2593ms 2.38% boost::numeric::ublas::c_vector::assign (inline) 0 0% 68.36% 2565ms 2.35% Cell::HasCellProperty (inline) 275ms 0.25% 68.61% 2557ms 2.34% std::_Rb_tree_const_iterator::operator++ (inline) 601ms 0.55% 69.16% 2546ms 2.33% boost::numeric::ublas::vector_binary::size (inline) 1ms 0.00092% 69.16% 2434ms 2.23% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.16% 2434ms 2.23% std::_Rb_tree::_M_insert_unique 83ms 0.076% 69.24% 2369ms 2.17% VertexMesh::GetVolumeOfElement 20ms 0.018% 69.26% 2319ms 2.13% Cell::GetCellData 61ms 0.056% 69.31% 2240ms 2.05% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.0028% 69.32% 2161ms 1.98% AbstractCellPopulation::Iterator::operator++ (inline) 193ms 0.18% 69.49% 2142ms 1.96% AbstractCellPopulation::Iterator::IsRealCell (inline) 32ms 0.029% 69.52% 2124ms 1.95% std::_Rb_tree::_M_emplace_hint_unique 1ms 0.00092% 69.52% 2093ms 1.92% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 69.52% 2093ms 1.92% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1329ms 1.22% 70.74% 2035ms 1.87% std::_Rb_tree::equal_range (inline) 2020ms 1.85% 72.59% 2020ms 1.85% std::_Rb_tree_increment 0 0% 72.59% 2000ms 1.83% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00092% 72.60% 1989ms 1.82% VertexBasedCellPopulation::WriteCellVtkResultsToFile 458ms 0.42% 73.02% 1897ms 1.74% std::type_info::operator== (inline) 69ms 0.063% 73.08% 1885ms 1.73% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 73.08% 1787ms 1.64% VertexMeshWriter::WriteVtkUsingMesh 35ms 0.032% 73.11% 1663ms 1.53% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 73.11% 1607ms 1.47% boost::numeric::ublas::c_vector::assign_temporary (inline) 7ms 0.0064% 73.12% 1607ms 1.47% boost::numeric::ublas::c_vector::swap 516ms 0.47% 73.59% 1600ms 1.47% std::swap_ranges (inline) 39ms 0.036% 73.63% 1592ms 1.46% VertexMesh::GetSurfaceAreaOfElement 47ms 0.043% 73.67% 1528ms 1.40% Node::RemoveElement 39ms 0.036% 73.71% 1525ms 1.40% AbstractCellPopulation::GetLocationIndexUsingCell 8ms 0.0073% 73.71% 1486ms 1.36% std::set::erase (inline) 80ms 0.073% 73.79% 1478ms 1.36% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 78ms 0.072% 73.86% 1422ms 1.30% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 73.86% 1402ms 1.29% boost::numeric::ublas::vector_binary::operator() (inline) 140ms 0.13% 73.99% 1401ms 1.28% CellPropertyCollection::AddProperty 1371ms 1.26% 75.24% 1371ms 1.26% [libchaste_cell_based.so] 1ms 0.00092% 75.24% 1359ms 1.25% tcache_get (inline) 1358ms 1.25% 76.49% 1358ms 1.25% tcache_get_n (inline) 0 0% 76.49% 1341ms 1.23% boost::numeric::ublas::norm_2 (inline) 1ms 0.00092% 76.49% 1330ms 1.22% OffLatticeSimulation::ApplyBoundaries 65ms 0.06% 76.55% 1327ms 1.22% std::less::operator() (inline) 612ms 0.56% 77.11% 1325ms 1.22% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1050ms 0.96% 78.07% 1262ms 1.16% std::operator< (inline) 79ms 0.072% 78.15% 1161ms 1.06% std::_Rb_tree::_M_erase_aux (partial-inline) 12ms 0.011% 78.16% 1131ms 1.04% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 18ms 0.017% 78.17% 1120ms 1.03% CellPropertyRegistry::Get 1104ms 1.01% 79.19% 1104ms 1.01% std::_Rb_tree_insert_and_rebalance 0 0% 79.19% 1096ms 1.01% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1086ms 1% 80.18% 1086ms 1% std::swap (inline) 0 0% 80.18% 1084ms 0.99% std::iter_swap (inline) 4ms 0.0037% 80.19% 1076ms 0.99% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1ms 0.00092% 80.19% 1074ms 0.98% std::_Rb_tree::clear (inline) 0 0% 80.19% 1056ms 0.97% std::map::clear (inline) 82ms 0.075% 80.26% 1054ms 0.97% std::_Rb_tree::find (inline) 10ms 0.0092% 80.27% 1052ms 0.96% boost::numeric::ublas::detail::expression_type_check (inline) 197ms 0.18% 80.45% 1027ms 0.94% boost::numeric::ublas::detail::equals 1022ms 0.94% 81.39% 1022ms 0.94% Node::rGetLocation 107ms 0.098% 81.49% 996ms 0.91% boost::detail::shared_count::~shared_count (inline) 0 0% 81.49% 996ms 0.91% boost::shared_ptr::~shared_ptr (inline) 0 0% 81.49% 902ms 0.83% std::map::find (inline) 285ms 0.26% 81.75% 876ms 0.8% std::__new_allocator::construct (inline) 0 0% 81.75% 876ms 0.8% std::allocator_traits::construct (inline) 863ms 0.79% 82.54% 863ms 0.79% std::vector::size (inline) 98ms 0.09% 82.63% 856ms 0.79% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 82.63% 854ms 0.78% VertexMeshWriter::MakeVtkMesh 818ms 0.75% 83.38% 853ms 0.78% boost::detail::sp_counted_base::release 818ms 0.75% 84.13% 818ms 0.75% [libchaste_mesh.so] 0 0% 84.13% 801ms 0.73% std::_Rb_tree::_M_construct_node (inline) 0 0% 84.13% 789ms 0.72% CellPropertyCollection::~CellPropertyCollection (inline) 25ms 0.023% 84.15% 787ms 0.72% MutableElement::RegisterWithEdges (inline) 27ms 0.025% 84.18% 772ms 0.71% Edge::AddElement 159ms 0.15% 84.32% 757ms 0.69% boost::shared_ptr::shared_ptr (inline) 0 0% 84.32% 752ms 0.69% boost::numeric::ublas::norm_inf (inline) 385ms 0.35% 84.68% 752ms 0.69% boost::numeric::ublas::vector_norm_inf::apply (inline) 152ms 0.14% 84.82% 747ms 0.69% MutableElement::GetNodeLocalIndex 413ms 0.38% 85.19% 741ms 0.68% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 381ms 0.35% 85.54% 735ms 0.67% Edge::GetMapIndex 0 0% 85.54% 723ms 0.66% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 85.54% 681ms 0.62% std::_Rb_tree::_Auto_node::_M_insert (inline) 28ms 0.026% 85.57% 681ms 0.62% std::_Rb_tree::_M_insert_node (inline) 0 0% 85.57% 673ms 0.62% std::_Vector_base::_M_allocate (inline) 638ms 0.59% 86.16% 638ms 0.59% [libstdc++.so.6.0.33] 0 0% 86.16% 615ms 0.56% vtkPolygon::New 1ms 0.00092% 86.16% 615ms 0.56% vtkPolygon::vtkPolygon 605ms 0.55% 86.71% 605ms 0.55% Node::GetIndex 576ms 0.53% 87.24% 598ms 0.55% boost::detail::shared_count::shared_count (inline) 36ms 0.033% 87.27% 582ms 0.53% MutableElement::RegisterWithNodes (inline) 557ms 0.51% 87.78% 557ms 0.51% tcache_put (inline) 554ms 0.51% 88.29% 554ms 0.51% boost::shared_ptr::operator-> (inline) 11ms 0.01% 88.30% 553ms 0.51% std::vector::_M_default_append (inline) 28ms 0.026% 88.33% 546ms 0.5% Node::AddElement