File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 97543ms, 88.44% of 110288ms total Dropped 1105 nodes (cum <= 551.44ms) flat flat% sum% cum cum% 0 0% 0% 109912ms 99.66% __libc_start_call_main 0 0% 0% 109912ms 99.66% __libc_start_main_impl 0 0% 0% 109912ms 99.66% _start 0 0% 0% 109891ms 99.64% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 109891ms 99.64% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 109891ms 99.64% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 109891ms 99.64% main 0 0% 0% 109853ms 99.61% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 109853ms 99.61% CxxTest::TestRunner::runTest (inline) 0 0% 0% 109853ms 99.61% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 5ms 0.0045% 0.0045% 109845ms 99.60% AbstractCellBasedSimulation::Solve 18ms 0.016% 0.021% 56725ms 51.43% OffLatticeSimulation::UpdateCellLocationsAndTopology 11ms 0.01% 0.031% 53480ms 48.49% ForwardEulerNumericalMethod::UpdateAllNodePositions 154ms 0.14% 0.17% 52415ms 47.53% AbstractNumericalMethod::ComputeForcesIncludingDamping 277ms 0.25% 0.42% 39971ms 36.24% NagaiHondaForce::AddForceContribution 0 0% 0.42% 39652ms 35.95% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0018% 0.42% 24361ms 22.09% VertexBasedCellPopulation::Update 0 0% 0.42% 24195ms 21.94% MutableVertexMesh::ReMesh 14679ms 13.31% 13.73% 23250ms 21.08% Cylindrical2dVertexMesh::GetVectorFromAtoB 83ms 0.075% 13.81% 18094ms 16.41% Cell::ReadyToDivide 92ms 0.083% 13.89% 16666ms 15.11% AbstractPhaseBasedCellCycleModel::ReadyToDivide 141ms 0.13% 14.02% 14252ms 12.92% SimpleWntCellCycleModel::UpdateCellCyclePhase 363ms 0.33% 14.35% 14221ms 12.89% NagaiHondaForce::GetAdhesionParameter 121ms 0.11% 14.46% 14071ms 12.76% CellPropertyCollection::GetPropertiesType (inline) 470ms 0.43% 14.88% 13672ms 12.40% boost::numeric::ublas::c_vector::c_vector (partial-inline) 331ms 0.3% 15.18% 12173ms 11.04% boost::numeric::ublas::vector_assign (inline) 3631ms 3.29% 18.48% 12027ms 10.91% __dynamic_cast 46ms 0.042% 18.52% 11884ms 10.78% AbstractCellProperty::IsSubType (inline) 90ms 0.082% 18.60% 11877ms 10.77% VertexBasedCellPopulation::GetDampingConstant 159ms 0.14% 18.74% 11675ms 10.59% MutableVertexMesh::CheckForIntersections 63ms 0.057% 18.80% 10954ms 9.93% AbstractTargetAreaModifier::UpdateTargetAreas 42ms 0.038% 18.84% 10868ms 9.85% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 31ms 0.028% 18.87% 10619ms 9.63% AbstractCellBasedSimulation::DoCellBirth 1407ms 1.28% 20.14% 10062ms 9.12% std::__new_allocator::allocate (inline) 0 0% 20.14% 9544ms 8.65% std::_Rb_tree::_M_create_node (inline) 0 0% 20.14% 9504ms 8.62% std::allocator_traits::allocate (inline) 373ms 0.34% 20.48% 9498ms 8.61% VertexMesh::GetNextEdgeGradientOfElementAtNode 2790ms 2.53% 23.01% 9200ms 8.34% boost::numeric::ublas::indexing_vector_assign 1275ms 1.16% 24.17% 8803ms 7.98% std::_Rb_tree::_M_erase 24ms 0.022% 24.19% 8781ms 7.96% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 24.19% 8774ms 7.96% std::_Rb_tree::_M_get_node (inline) 83ms 0.075% 24.26% 8749ms 7.93% Cell::GetMutationState 744ms 0.67% 24.94% 8703ms 7.89% operator new 844ms 0.77% 25.70% 8619ms 7.81% VertexMesh::ElementIncludesPoint 0 0% 25.70% 8396ms 7.61% std::_Rb_tree::_Alloc_node::operator() (inline) 441ms 0.4% 26.10% 8233ms 7.47% VertexMesh::GetCentroidOfElement 529ms 0.48% 26.58% 8170ms 7.41% std::map::operator[] (partial-inline) 17ms 0.015% 26.60% 7934ms 7.19% MutableVertexMesh::RemoveDeletedNodesAndElements 0 0% 26.60% 7915ms 7.18% std::_Rb_tree::_M_drop_node (inline) 224ms 0.2% 26.80% 7853ms 7.12% std::_Rb_tree::~_Rb_tree (inline) 2842ms 2.58% 29.38% 7714ms 6.99% __GI___libc_malloc 228ms 0.21% 29.59% 7639ms 6.93% std::__new_allocator::deallocate (inline) 0 0% 29.59% 7633ms 6.92% std::allocator_traits::deallocate (inline) 0 0% 29.59% 7570ms 6.86% std::_Rb_tree::_M_put_node (inline) 1544ms 1.40% 30.99% 7546ms 6.84% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 0 0% 30.99% 7422ms 6.73% std::set::~set (inline) 190ms 0.17% 31.16% 7273ms 6.59% std::_Rb_tree::_Rb_tree (partial-inline) 2307ms 2.09% 33.25% 7130ms 6.46% __GI___libc_free 785ms 0.71% 33.96% 6843ms 6.20% std::_Rb_tree::_M_copy (inline) 31ms 0.028% 33.99% 6808ms 6.17% std::set::set (inline) 6692ms 6.07% 40.06% 6692ms 6.07% __strcmp_avx2 2489ms 2.26% 42.31% 6655ms 6.03% std::_Rb_tree::_M_lower_bound (inline) 142ms 0.13% 42.44% 6403ms 5.81% SimpleWntCellCycleModel::GetWntLevel 201ms 0.18% 42.63% 6206ms 5.63% WntConcentration::GetWntLevel 6025ms 5.46% 48.09% 6025ms 5.46% boost::numeric::ublas::c_vector::operator() 842ms 0.76% 48.85% 5808ms 5.27% std::_Rb_tree::_M_clone_node (inline) 20ms 0.018% 48.87% 5712ms 5.18% MutableVertexMesh::RemoveDeletedNodes 3014ms 2.73% 51.60% 5689ms 5.16% __cxxabiv1::__si_class_type_info::__do_dyncast 35ms 0.032% 51.63% 5514ms 5.00% EdgeHelper::RemoveDeletedEdges 0 0% 51.63% 5404ms 4.90% std::_Rb_tree::lower_bound (inline) 0 0% 51.63% 5404ms 4.90% std::map::lower_bound (inline) 1970ms 1.79% 53.42% 5403ms 4.90% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 53.42% 5236ms 4.75% std::set::insert (inline) 42ms 0.038% 53.46% 5165ms 4.68% EdgeHelper::UpdateEdgesMapKey 4369ms 3.96% 57.42% 4799ms 4.35% _int_free 178ms 0.16% 57.58% 4793ms 4.35% MutableElement::ResetIndex 114ms 0.1% 57.69% 4710ms 4.27% AbstractCellPopulation::GetCellUsingLocationIndex 3ms 0.0027% 57.69% 4662ms 4.23% AbstractCellBasedSimulation::DoCellRemoval (inline) 490ms 0.44% 58.13% 4451ms 4.04% std::_Rb_tree::_M_insert_ (inline) 146ms 0.13% 58.26% 4126ms 3.74% std::set_intersection (inline) 33ms 0.03% 58.29% 4069ms 3.69% Cell::GetCellProliferativeType 221ms 0.2% 58.50% 3980ms 3.61% std::__set_intersection 45ms 0.041% 58.54% 3926ms 3.56% AbstractCellProperty::IsType (inline) 3740ms 3.39% 61.93% 3740ms 3.39% boost::numeric::ublas::same_impl_ex 3507ms 3.18% 65.11% 3507ms 3.18% std::_Rb_tree::_S_right (inline) 13ms 0.012% 65.12% 3499ms 3.17% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 84ms 0.076% 65.19% 3404ms 3.09% Cell::SetCellProliferativeType 2254ms 2.04% 67.24% 3236ms 2.93% _int_malloc 887ms 0.8% 68.04% 3088ms 2.80% AbstractElement::GetNodeLocation 0 0% 68.04% 3077ms 2.79% std::insert_iterator::operator= (inline) 56ms 0.051% 68.09% 3061ms 2.78% std::_Rb_tree::erase 27ms 0.024% 68.12% 3008ms 2.73% CellPropertyCollection::HasProperty 0 0% 68.12% 2817ms 2.55% Cell::HasCellProperty (inline) 705ms 0.64% 68.76% 2794ms 2.53% AbstractCellProperty::IsSame 15ms 0.014% 68.77% 2687ms 2.44% std::_Rb_tree::_M_insert_unique_ (inline) 223ms 0.2% 68.97% 2604ms 2.36% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 68.97% 2603ms 2.36% boost::numeric::ublas::c_vector::operator-= (inline) 257ms 0.23% 69.21% 2599ms 2.36% std::_Rb_tree_const_iterator::operator++ (inline) 632ms 0.57% 69.78% 2582ms 2.34% boost::numeric::ublas::vector_binary::size (inline) 3ms 0.0027% 69.78% 2549ms 2.31% std::_Rb_tree::_M_insert_unique 28ms 0.025% 69.81% 2539ms 2.30% Cell::GetCellData 0 0% 69.81% 2526ms 2.29% boost::numeric::ublas::c_vector::assign (inline) 1ms 0.00091% 69.81% 2474ms 2.24% AbstractCellPopulation::WriteResultsToFiles 87ms 0.079% 69.89% 2388ms 2.17% VertexMesh::GetVolumeOfElement 57ms 0.052% 69.94% 2300ms 2.09% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 6ms 0.0054% 69.94% 2277ms 2.06% AbstractCellPopulation::Iterator::operator++ (inline) 171ms 0.16% 70.10% 2259ms 2.05% AbstractCellPopulation::Iterator::IsRealCell (inline) 39ms 0.035% 70.13% 2197ms 1.99% std::_Rb_tree::_M_emplace_hint_unique 2105ms 1.91% 72.04% 2105ms 1.91% std::_Rb_tree_increment 471ms 0.43% 72.47% 2089ms 1.89% std::type_info::operator== (inline) 1ms 0.00091% 72.47% 2086ms 1.89% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.47% 2086ms 1.89% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1318ms 1.20% 73.67% 2055ms 1.86% std::_Rb_tree::equal_range (inline) 0 0% 73.67% 2030ms 1.84% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 73.67% 2014ms 1.83% VertexBasedCellPopulation::WriteCellVtkResultsToFile 82ms 0.074% 73.74% 1942ms 1.76% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 73.74% 1792ms 1.62% VertexMeshWriter::WriteVtkUsingMesh 25ms 0.023% 73.76% 1756ms 1.59% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 41ms 0.037% 73.80% 1596ms 1.45% VertexMesh::GetSurfaceAreaOfElement 44ms 0.04% 73.84% 1567ms 1.42% AbstractCellPopulation::GetLocationIndexUsingCell 57ms 0.052% 73.89% 1559ms 1.41% Node::RemoveElement 65ms 0.059% 73.95% 1548ms 1.40% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 11ms 0.01% 73.96% 1506ms 1.37% std::set::erase (inline) 141ms 0.13% 74.09% 1490ms 1.35% CellPropertyCollection::AddProperty 0 0% 74.09% 1439ms 1.30% tcache_get (inline) 1439ms 1.30% 75.39% 1439ms 1.30% tcache_get_n (inline) 65ms 0.059% 75.45% 1392ms 1.26% std::less::operator() (inline) 1088ms 0.99% 76.44% 1327ms 1.20% std::operator< (inline) 0 0% 76.44% 1315ms 1.19% boost::numeric::ublas::norm_2 (inline) 582ms 0.53% 76.97% 1305ms 1.18% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1294ms 1.17% 78.14% 1294ms 1.17% [libchaste_cell_based.so] 2ms 0.0018% 78.14% 1271ms 1.15% OffLatticeSimulation::ApplyBoundaries 93ms 0.084% 78.23% 1254ms 1.14% std::_Rb_tree::find (inline) 70ms 0.063% 78.29% 1240ms 1.12% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 78.29% 1226ms 1.11% boost::numeric::ublas::vector_binary::operator() (inline) 1ms 0.00091% 78.29% 1181ms 1.07% std::_Rb_tree::clear (inline) 0 0% 78.29% 1163ms 1.05% std::map::clear (inline) 0 0% 78.29% 1148ms 1.04% std::_Rb_tree::_Auto_node::_Auto_node (inline) 67ms 0.061% 78.35% 1141ms 1.03% std::_Rb_tree::_M_erase_aux (partial-inline) 12ms 0.011% 78.36% 1121ms 1.02% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1121ms 1.02% 79.38% 1121ms 1.02% std::_Rb_tree_insert_and_rebalance 0 0% 79.38% 1118ms 1.01% boost::numeric::ublas::c_vector::assign_temporary (inline) 14ms 0.013% 79.39% 1118ms 1.01% boost::numeric::ublas::c_vector::swap (inline) 18ms 0.016% 79.41% 1114ms 1.01% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 29ms 0.026% 79.43% 1107ms 1.00% CellPropertyRegistry::Get 71ms 0.064% 79.50% 1104ms 1.00% std::swap_ranges (inline) 127ms 0.12% 79.61% 1064ms 0.96% boost::detail::shared_count::~shared_count (inline) 0 0% 79.61% 1064ms 0.96% boost::shared_ptr::~shared_ptr (inline) 12ms 0.011% 79.62% 1036ms 0.94% boost::numeric::ublas::detail::expression_type_check (inline) 1034ms 0.94% 80.56% 1034ms 0.94% std::swap (inline) 0 0% 80.56% 1033ms 0.94% std::iter_swap (inline) 1032ms 0.94% 81.50% 1032ms 0.94% Node::rGetLocation 170ms 0.15% 81.65% 1012ms 0.92% boost::numeric::ublas::detail::equals 1ms 0.00091% 81.65% 1002ms 0.91% std::map::find (inline) 873ms 0.79% 82.44% 898ms 0.81% boost::detail::sp_counted_base::release 889ms 0.81% 83.25% 889ms 0.81% std::vector::size (inline) 2ms 0.0018% 83.25% 872ms 0.79% VertexMeshWriter::MakeVtkMesh 409ms 0.37% 83.62% 854ms 0.77% Edge::GetMapIndex 103ms 0.093% 83.72% 836ms 0.76% boost::numeric::ublas::c_vector::operator= (inline) 260ms 0.24% 83.95% 813ms 0.74% std::__new_allocator::construct (inline) 0 0% 83.95% 813ms 0.74% std::allocator_traits::construct (inline) 13ms 0.012% 83.96% 805ms 0.73% MutableElement::RegisterWithEdges (inline) 32ms 0.029% 83.99% 802ms 0.73% Edge::AddElement 780ms 0.71% 84.70% 780ms 0.71% [libchaste_mesh.so] 0 0% 84.70% 771ms 0.7% boost::numeric::ublas::norm_inf (inline) 419ms 0.38% 85.08% 771ms 0.7% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 85.08% 770ms 0.7% std::_Rb_tree::_M_construct_node (inline) 187ms 0.17% 85.25% 749ms 0.68% boost::shared_ptr::shared_ptr (inline) 423ms 0.38% 85.63% 746ms 0.68% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 85.63% 742ms 0.67% CellPropertyCollection::~CellPropertyCollection (inline) 732ms 0.66% 86.30% 732ms 0.66% [libstdc++.so.6.0.33] 0 0% 86.30% 725ms 0.66% std::_Vector_base::_M_allocate (inline) 692ms 0.63% 86.92% 692ms 0.63% Node::GetIndex 86ms 0.078% 87.00% 674ms 0.61% MutableElement::GetNodeLocalIndex 0 0% 87.00% 673ms 0.61% std::_Rb_tree::_Auto_node::_M_insert (inline) 17ms 0.015% 87.02% 673ms 0.61% std::_Rb_tree::_M_insert_node (inline) 0 0% 87.02% 666ms 0.6% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 1ms 0.00091% 87.02% 629ms 0.57% vtkPolygon::New 0 0% 87.02% 627ms 0.57% vtkPolygon::vtkPolygon 6ms 0.0054% 87.02% 616ms 0.56% std::vector::_M_default_append (inline) 25ms 0.023% 87.05% 601ms 0.54% MutableElement::RegisterWithNodes (inline) 38ms 0.034% 87.08% 596ms 0.54% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.08% 596ms 0.54% boost::numeric::ublas::vector::vector (inline) 22ms 0.02% 87.10% 573ms 0.52% Node::AddElement 539ms 0.49% 87.59% 561ms 0.51% boost::detail::shared_count::shared_count (inline) 390ms 0.35% 87.94% 558ms 0.51% malloc_consolidate 552ms 0.5% 88.44% 552ms 0.5% boost::shared_ptr::operator-> (inline)