File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95302ms, 88.10% of 108175ms total Dropped 1095 nodes (cum <= 540.88ms) flat flat% sum% cum cum% 0 0% 0% 107725ms 99.58% __libc_start_call_main 0 0% 0% 107725ms 99.58% __libc_start_main_impl 0 0% 0% 107725ms 99.58% _start 0 0% 0% 107707ms 99.57% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 107707ms 99.57% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 107707ms 99.57% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 107707ms 99.57% main 0 0% 0% 107669ms 99.53% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 107669ms 99.53% CxxTest::TestRunner::runTest (inline) 0 0% 0% 107669ms 99.53% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 3ms 0.0028% 0.0028% 107661ms 99.52% AbstractCellBasedSimulation::Solve 18ms 0.017% 0.019% 56000ms 51.77% OffLatticeSimulation::UpdateCellLocationsAndTopology 16ms 0.015% 0.034% 52832ms 48.84% ForwardEulerNumericalMethod::UpdateAllNodePositions 117ms 0.11% 0.14% 51805ms 47.89% AbstractNumericalMethod::ComputeForcesIncludingDamping 433ms 0.4% 0.54% 40277ms 37.23% NagaiHondaForce::AddForceContribution 0 0% 0.54% 38895ms 35.96% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00092% 0.54% 23982ms 22.17% VertexBasedCellPopulation::Update 0 0% 0.54% 23874ms 22.07% MutableVertexMesh::ReMesh 14466ms 13.37% 13.92% 22814ms 21.09% Cylindrical2dVertexMesh::GetVectorFromAtoB 86ms 0.08% 14.00% 17488ms 16.17% Cell::ReadyToDivide 120ms 0.11% 14.11% 16318ms 15.08% AbstractPhaseBasedCellCycleModel::ReadyToDivide 305ms 0.28% 14.39% 14937ms 13.81% NagaiHondaForce::GetAdhesionParameter 421ms 0.39% 14.78% 14500ms 13.40% boost::numeric::ublas::c_vector::c_vector (partial-inline) 121ms 0.11% 14.89% 13879ms 12.83% SimpleWntCellCycleModel::UpdateCellCyclePhase 142ms 0.13% 15.02% 13298ms 12.29% CellPropertyCollection::GetPropertiesType (inline) 386ms 0.36% 15.38% 13007ms 12.02% boost::numeric::ublas::vector_assign (inline) 140ms 0.13% 15.51% 12068ms 11.16% MutableVertexMesh::CheckForIntersections 3189ms 2.95% 18.46% 11108ms 10.27% __dynamic_cast 58ms 0.054% 18.51% 11047ms 10.21% VertexBasedCellPopulation::GetDampingConstant 101ms 0.093% 18.60% 11023ms 10.19% AbstractCellProperty::IsSubType (inline) 57ms 0.053% 18.65% 10368ms 9.58% AbstractTargetAreaModifier::UpdateTargetAreas 21ms 0.019% 18.67% 10331ms 9.55% AbstractCellBasedSimulation::DoCellBirth 58ms 0.054% 18.73% 10283ms 9.51% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 1196ms 1.11% 19.83% 10057ms 9.30% std::__new_allocator::allocate (inline) 2642ms 2.44% 22.28% 9590ms 8.87% boost::numeric::ublas::indexing_vector_assign 0 0% 22.28% 9480ms 8.76% std::allocator_traits::allocate (inline) 0 0% 22.28% 9435ms 8.72% std::_Rb_tree::_M_create_node (inline) 1463ms 1.35% 23.63% 9177ms 8.48% std::_Rb_tree::_M_erase 411ms 0.38% 24.01% 9062ms 8.38% VertexMesh::GetNextEdgeGradientOfElementAtNode 746ms 0.69% 24.70% 8977ms 8.30% VertexMesh::ElementIncludesPoint 873ms 0.81% 25.50% 8960ms 8.28% operator new 33ms 0.031% 25.54% 8942ms 8.27% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 25.54% 8820ms 8.15% std::_Rb_tree::_M_get_node (inline) 499ms 0.46% 26.00% 8465ms 7.83% VertexMesh::GetCentroidOfElement 251ms 0.23% 26.23% 8449ms 7.81% std::_Rb_tree::~_Rb_tree (inline) 69ms 0.064% 26.29% 8360ms 7.73% Cell::GetMutationState 0 0% 26.29% 8239ms 7.62% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 26.29% 8089ms 7.48% std::_Rb_tree::_M_drop_node (inline) 0 0% 26.29% 7980ms 7.38% std::set::~set (inline) 3214ms 2.97% 29.26% 7899ms 7.30% __GI___libc_malloc 235ms 0.22% 29.48% 7835ms 7.24% std::__new_allocator::deallocate (inline) 0 0% 29.48% 7806ms 7.22% std::allocator_traits::deallocate (inline) 0 0% 29.48% 7746ms 7.16% std::_Rb_tree::_M_put_node (inline) 2922ms 2.70% 32.18% 7703ms 7.12% __GI___libc_free 20ms 0.018% 32.20% 7416ms 6.86% MutableVertexMesh::RemoveDeletedNodesAndElements 470ms 0.43% 32.64% 7295ms 6.74% std::map::operator[] (partial-inline) 1509ms 1.39% 34.03% 7288ms 6.74% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 129ms 0.12% 34.15% 6843ms 6.33% std::_Rb_tree::_Rb_tree (partial-inline) 111ms 0.1% 34.25% 6518ms 6.03% SimpleWntCellCycleModel::GetWntLevel 697ms 0.64% 34.90% 6504ms 6.01% std::_Rb_tree::_M_copy (inline) 13ms 0.012% 34.91% 6436ms 5.95% std::set::set (inline) 6304ms 5.83% 40.74% 6304ms 5.83% __strcmp_avx2 6292ms 5.82% 46.55% 6292ms 5.82% boost::numeric::ublas::c_vector::operator() 133ms 0.12% 46.68% 6278ms 5.80% WntConcentration::GetWntLevel 2413ms 2.23% 48.91% 5742ms 5.31% std::_Rb_tree::_M_lower_bound (inline) 2668ms 2.47% 51.37% 5595ms 5.17% __cxxabiv1::__si_class_type_info::__do_dyncast 803ms 0.74% 52.11% 5567ms 5.15% std::_Rb_tree::_M_clone_node (inline) 0 0% 52.11% 5349ms 4.94% std::set::insert (inline) 37ms 0.034% 52.15% 5267ms 4.87% MutableVertexMesh::RemoveDeletedNodes 39ms 0.036% 52.18% 5098ms 4.71% EdgeHelper::RemoveDeletedEdges 31ms 0.029% 52.21% 4823ms 4.46% EdgeHelper::UpdateEdgesMapKey 4434ms 4.10% 56.31% 4775ms 4.41% _int_free 1414ms 1.31% 57.62% 4749ms 4.39% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 57.62% 4638ms 4.29% std::_Rb_tree::lower_bound (inline) 0 0% 57.62% 4638ms 4.29% std::map::lower_bound (inline) 47ms 0.043% 57.66% 4602ms 4.25% std::set_intersection (inline) 202ms 0.19% 57.85% 4598ms 4.25% MutableElement::ResetIndex 1ms 0.00092% 57.85% 4574ms 4.23% AbstractCellBasedSimulation::DoCellRemoval (inline) 277ms 0.26% 58.11% 4555ms 4.21% std::__set_intersection 532ms 0.49% 58.60% 4499ms 4.16% std::_Rb_tree::_M_insert_ (inline) 110ms 0.1% 58.70% 4043ms 3.74% AbstractCellPopulation::GetCellUsingLocationIndex 3978ms 3.68% 62.38% 3978ms 3.68% boost::numeric::ublas::same_impl_ex 34ms 0.031% 62.41% 3891ms 3.60% Cell::GetCellProliferativeType 81ms 0.075% 62.48% 3652ms 3.38% AbstractCellProperty::IsType (inline) 6ms 0.0055% 62.49% 3524ms 3.26% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.49% 3283ms 3.03% std::insert_iterator::operator= (inline) 797ms 0.74% 63.23% 3201ms 2.96% AbstractElement::GetNodeLocation 2286ms 2.11% 65.34% 3140ms 2.90% _int_malloc 53ms 0.049% 65.39% 3128ms 2.89% Cell::SetCellProliferativeType 50ms 0.046% 65.43% 2932ms 2.71% std::_Rb_tree::erase 5ms 0.0046% 65.44% 2921ms 2.70% std::_Rb_tree::_M_insert_unique_ (inline) 2760ms 2.55% 67.99% 2760ms 2.55% std::_Rb_tree::_S_right (inline) 576ms 0.53% 68.52% 2721ms 2.52% boost::numeric::ublas::vector_binary::size (inline) 487ms 0.45% 68.97% 2713ms 2.51% std::_Rb_tree_const_iterator::operator++ (inline) 55ms 0.051% 69.02% 2575ms 2.38% CellPropertyCollection::HasProperty 747ms 0.69% 69.71% 2558ms 2.36% AbstractCellProperty::IsSame 0 0% 69.71% 2533ms 2.34% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.71% 2466ms 2.28% Cell::HasCellProperty (inline) 1ms 0.00092% 69.72% 2428ms 2.24% std::_Rb_tree::_M_insert_unique 0 0% 69.72% 2412ms 2.23% boost::numeric::ublas::c_vector::assign (inline) 0 0% 69.72% 2377ms 2.20% AbstractCellPopulation::WriteResultsToFiles 26ms 0.024% 69.74% 2345ms 2.17% Cell::GetCellData 199ms 0.18% 69.92% 2305ms 2.13% VertexMesh::GetAreaGradientOfElementAtNode 107ms 0.099% 70.02% 2303ms 2.13% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 103ms 0.095% 70.12% 2227ms 2.06% VertexMesh::GetVolumeOfElement 4ms 0.0037% 70.12% 2155ms 1.99% AbstractCellPopulation::Iterator::operator++ (inline) 37ms 0.034% 70.16% 2142ms 1.98% std::_Rb_tree::_M_emplace_hint_unique 195ms 0.18% 70.34% 2136ms 1.97% AbstractCellPopulation::Iterator::IsRealCell (inline) 2051ms 1.90% 72.23% 2051ms 1.90% std::_Rb_tree_increment 1295ms 1.20% 73.43% 1955ms 1.81% std::_Rb_tree::equal_range (inline) 0 0% 73.43% 1939ms 1.79% VertexBasedCellPopulation::WriteVtkResultsToFile 3ms 0.0028% 73.43% 1929ms 1.78% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.43% 1929ms 1.78% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 73.43% 1926ms 1.78% VertexBasedCellPopulation::WriteCellVtkResultsToFile 77ms 0.071% 73.50% 1871ms 1.73% MutableVertexMesh::CheckForSwapsFromShortEdges 397ms 0.37% 73.87% 1811ms 1.67% std::type_info::operator== (inline) 0 0% 73.87% 1741ms 1.61% VertexMeshWriter::WriteVtkUsingMesh 26ms 0.024% 73.89% 1683ms 1.56% VertexMesh::GetSurfaceAreaOfElement 33ms 0.031% 73.92% 1668ms 1.54% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 46ms 0.043% 73.97% 1581ms 1.46% Node::RemoveElement 108ms 0.1% 74.07% 1547ms 1.43% boost::numeric::ublas::vector_reference::operator() (inline) 21ms 0.019% 74.09% 1546ms 1.43% std::set::erase (inline) 86ms 0.08% 74.17% 1458ms 1.35% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 162ms 0.15% 74.32% 1455ms 1.35% CellPropertyCollection::AddProperty 18ms 0.017% 74.33% 1452ms 1.34% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 74.33% 1436ms 1.33% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 74.33% 1360ms 1.26% tcache_get (inline) 1360ms 1.26% 75.59% 1360ms 1.26% tcache_get_n (inline) 1ms 0.00092% 75.59% 1266ms 1.17% OffLatticeSimulation::ApplyBoundaries 76ms 0.07% 75.66% 1232ms 1.14% std::less::operator() (inline) 0 0% 75.66% 1196ms 1.11% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 75.66% 1192ms 1.10% boost::numeric::ublas::norm_2 (inline) 1185ms 1.10% 76.76% 1185ms 1.10% Node::rGetLocation 536ms 0.5% 77.25% 1183ms 1.09% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 929ms 0.86% 78.11% 1156ms 1.07% std::operator< (inline) 73ms 0.067% 78.18% 1137ms 1.05% std::_Rb_tree::_M_erase_aux (partial-inline) 1108ms 1.02% 79.20% 1108ms 1.02% [libchaste_cell_based.so] 27ms 0.025% 79.23% 1073ms 0.99% CellPropertyRegistry::Get 76ms 0.07% 79.30% 1050ms 0.97% std::_Rb_tree::find (inline) 1041ms 0.96% 80.26% 1041ms 0.96% std::_Rb_tree_insert_and_rebalance 154ms 0.14% 80.40% 1040ms 0.96% boost::detail::shared_count::~shared_count (inline) 0 0% 80.40% 1040ms 0.96% boost::shared_ptr::~shared_ptr (inline) 24ms 0.022% 80.42% 1032ms 0.95% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 1000ms 0.92% 81.35% 1000ms 0.92% [libchaste_mesh.so] 1000ms 0.92% 82.27% 1000ms 0.92% std::vector::size (inline) 7ms 0.0065% 82.28% 998ms 0.92% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 82.28% 981ms 0.91% std::_Rb_tree::clear (inline) 0 0% 82.28% 959ms 0.89% std::map::clear (inline) 20ms 0.018% 82.30% 953ms 0.88% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 82.30% 929ms 0.86% boost::numeric::ublas::c_vector::assign_temporary (inline) 3ms 0.0028% 82.30% 929ms 0.86% boost::numeric::ublas::c_vector::swap (inline) 394ms 0.36% 82.67% 928ms 0.86% Edge::GetMapIndex 83ms 0.077% 82.74% 926ms 0.86% std::swap_ranges (inline) 142ms 0.13% 82.87% 921ms 0.85% boost::numeric::ublas::detail::equals 129ms 0.12% 82.99% 891ms 0.82% MutableElement::GetNodeLocalIndex 850ms 0.79% 83.78% 860ms 0.8% boost::detail::sp_counted_base::release 121ms 0.11% 83.89% 855ms 0.79% boost::numeric::ublas::c_vector::operator= (inline) 1ms 0.00092% 83.89% 854ms 0.79% VertexMeshWriter::MakeVtkMesh 0 0% 83.89% 852ms 0.79% std::map::find (inline) 0 0% 83.89% 843ms 0.78% std::iter_swap (inline) 843ms 0.78% 84.67% 843ms 0.78% std::swap (inline) 773ms 0.71% 85.38% 773ms 0.71% Node::GetIndex 170ms 0.16% 85.54% 771ms 0.71% boost::shared_ptr::shared_ptr (inline) 23ms 0.021% 85.56% 753ms 0.7% MutableElement::RegisterWithEdges (inline) 454ms 0.42% 85.98% 750ms 0.69% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 29ms 0.027% 86.01% 742ms 0.69% Edge::AddElement 0 0% 86.01% 737ms 0.68% boost::numeric::ublas::norm_inf (inline) 376ms 0.35% 86.36% 737ms 0.68% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 86.36% 712ms 0.66% CellPropertyCollection::~CellPropertyCollection (inline) 98ms 0.091% 86.45% 672ms 0.62% std::__new_allocator::construct (inline) 0 0% 86.45% 672ms 0.62% std::allocator_traits::construct (inline) 0 0% 86.45% 657ms 0.61% std::_Vector_base::_M_allocate (inline) 0 0% 86.45% 615ms 0.57% std::_Rb_tree::_M_construct_node (inline) 34ms 0.031% 86.48% 611ms 0.56% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 86.48% 611ms 0.56% boost::numeric::ublas::vector::vector (inline) 0 0% 86.48% 608ms 0.56% std::_Rb_tree::_Auto_node::_M_insert (inline) 19ms 0.018% 86.50% 608ms 0.56% std::_Rb_tree::_M_insert_node (inline) 576ms 0.53% 87.03% 601ms 0.56% boost::detail::shared_count::shared_count (inline) 0 0% 87.03% 593ms 0.55% vtkPolygon::New 0 0% 87.03% 593ms 0.55% vtkPolygon::vtkPolygon 31ms 0.029% 87.06% 577ms 0.53% MutableElement::RegisterWithNodes (inline) 0 0% 87.06% 567ms 0.52% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 565ms 0.52% 87.58% 565ms 0.52% [libstdc++.so.6.0.33] 562ms 0.52% 88.10% 562ms 0.52% operator delete