File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 93348ms, 87.40% of 106808ms total Dropped 1129 nodes (cum <= 534.04ms) flat flat% sum% cum cum% 0 0% 0% 106436ms 99.65% __libc_start_call_main 0 0% 0% 106436ms 99.65% __libc_start_main_impl 0 0% 0% 106436ms 99.65% _start 0 0% 0% 106414ms 99.63% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 106414ms 99.63% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 106414ms 99.63% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 106414ms 99.63% main 0 0% 0% 106370ms 99.59% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 106370ms 99.59% CxxTest::TestRunner::runTest (inline) 0 0% 0% 106370ms 99.59% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 3ms 0.0028% 0.0028% 106362ms 99.58% AbstractCellBasedSimulation::Solve 18ms 0.017% 0.02% 55389ms 51.86% OffLatticeSimulation::UpdateCellLocationsAndTopology 13ms 0.012% 0.032% 52121ms 48.80% ForwardEulerNumericalMethod::UpdateAllNodePositions 112ms 0.1% 0.14% 51000ms 47.75% AbstractNumericalMethod::ComputeForcesIncludingDamping 331ms 0.31% 0.45% 39643ms 37.12% NagaiHondaForce::AddForceContribution 0 0% 0.45% 38271ms 35.83% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.45% 23580ms 22.08% VertexBasedCellPopulation::Update 0 0% 0.45% 23456ms 21.96% MutableVertexMesh::ReMesh 14659ms 13.72% 14.17% 23185ms 21.71% Cylindrical2dVertexMesh::GetVectorFromAtoB 102ms 0.095% 14.27% 17114ms 16.02% Cell::ReadyToDivide 93ms 0.087% 14.35% 15919ms 14.90% AbstractPhaseBasedCellCycleModel::ReadyToDivide 370ms 0.35% 14.70% 14479ms 13.56% NagaiHondaForce::GetAdhesionParameter 460ms 0.43% 15.13% 13912ms 13.03% boost::numeric::ublas::c_vector::c_vector (partial-inline) 146ms 0.14% 15.27% 13617ms 12.75% SimpleWntCellCycleModel::UpdateCellCyclePhase 90ms 0.084% 15.35% 13151ms 12.31% CellPropertyCollection::GetPropertiesType (inline) 320ms 0.3% 15.65% 12459ms 11.66% boost::numeric::ublas::vector_assign (inline) 129ms 0.12% 15.77% 11876ms 11.12% MutableVertexMesh::CheckForIntersections 3186ms 2.98% 18.76% 11163ms 10.45% __dynamic_cast 59ms 0.055% 18.81% 11042ms 10.34% AbstractCellProperty::IsSubType (inline) 76ms 0.071% 18.88% 10853ms 10.16% VertexBasedCellPopulation::GetDampingConstant 53ms 0.05% 18.93% 10249ms 9.60% AbstractTargetAreaModifier::UpdateTargetAreas 46ms 0.043% 18.97% 10179ms 9.53% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 22ms 0.021% 18.99% 9975ms 9.34% AbstractCellBasedSimulation::DoCellBirth 1083ms 1.01% 20.01% 9697ms 9.08% std::__new_allocator::allocate (inline) 2899ms 2.71% 22.72% 9467ms 8.86% boost::numeric::ublas::indexing_vector_assign 336ms 0.31% 23.04% 9434ms 8.83% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 23.04% 9220ms 8.63% std::_Rb_tree::_M_create_node (inline) 0 0% 23.04% 9117ms 8.54% std::allocator_traits::allocate (inline) 1211ms 1.13% 24.17% 8909ms 8.34% std::_Rb_tree::_M_erase 872ms 0.82% 24.99% 8728ms 8.17% VertexMesh::ElementIncludesPoint 790ms 0.74% 25.73% 8620ms 8.07% operator new 37ms 0.035% 25.76% 8603ms 8.05% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 25.76% 8485ms 7.94% std::_Rb_tree::_M_get_node (inline) 431ms 0.4% 26.17% 8300ms 7.77% VertexMesh::GetCentroidOfElement 106ms 0.099% 26.26% 8281ms 7.75% Cell::GetMutationState 0 0% 26.26% 8176ms 7.65% std::_Rb_tree::_Alloc_node::operator() (inline) 251ms 0.24% 26.50% 8119ms 7.60% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.50% 8090ms 7.57% std::_Rb_tree::_M_drop_node (inline) 238ms 0.22% 26.72% 7814ms 7.32% std::__new_allocator::deallocate (inline) 0 0% 26.72% 7811ms 7.31% std::allocator_traits::deallocate (inline) 0 0% 26.72% 7757ms 7.26% std::_Rb_tree::_M_put_node (inline) 0 0% 26.72% 7711ms 7.22% std::set::~set (inline) 3036ms 2.84% 29.57% 7613ms 7.13% __GI___libc_malloc 1360ms 1.27% 30.84% 7493ms 7.02% AbstractMesh::GetDistanceBetweenNodes 16ms 0.015% 30.85% 7456ms 6.98% MutableVertexMesh::RemoveDeletedNodesAndElements 2160ms 2.02% 32.88% 7280ms 6.82% __GI___libc_free 498ms 0.47% 33.34% 7142ms 6.69% std::map::operator[] (partial-inline) 172ms 0.16% 33.50% 7036ms 6.59% std::_Rb_tree::_Rb_tree (partial-inline) 771ms 0.72% 34.22% 6640ms 6.22% std::_Rb_tree::_M_copy (inline) 28ms 0.026% 34.25% 6544ms 6.13% std::set::set (inline) 126ms 0.12% 34.37% 6178ms 5.78% SimpleWntCellCycleModel::GetWntLevel 6108ms 5.72% 40.09% 6108ms 5.72% __strcmp_avx2 6062ms 5.68% 45.76% 6062ms 5.68% boost::numeric::ublas::c_vector::operator() 176ms 0.16% 45.93% 5963ms 5.58% WntConcentration::GetWntLevel 717ms 0.67% 46.60% 5624ms 5.27% std::_Rb_tree::_M_clone_node (inline) 2998ms 2.81% 49.41% 5538ms 5.19% __cxxabiv1::__si_class_type_info::__do_dyncast 2406ms 2.25% 51.66% 5508ms 5.16% std::_Rb_tree::_M_lower_bound (inline) 1952ms 1.83% 53.49% 5235ms 4.90% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 53.49% 5190ms 4.86% std::set::insert (inline) 27ms 0.025% 53.51% 5168ms 4.84% MutableVertexMesh::RemoveDeletedNodes 4764ms 4.46% 57.97% 5104ms 4.78% _int_free 48ms 0.045% 58.02% 4975ms 4.66% EdgeHelper::RemoveDeletedEdges 0 0% 58.02% 4704ms 4.40% AbstractCellBasedSimulation::DoCellRemoval (inline) 29ms 0.027% 58.04% 4629ms 4.33% EdgeHelper::UpdateEdgesMapKey 173ms 0.16% 58.21% 4533ms 4.24% MutableElement::ResetIndex 0 0% 58.21% 4480ms 4.19% std::_Rb_tree::lower_bound (inline) 0 0% 58.21% 4480ms 4.19% std::map::lower_bound (inline) 511ms 0.48% 58.68% 4313ms 4.04% std::_Rb_tree::_M_insert_ (inline) 130ms 0.12% 58.81% 4283ms 4.01% AbstractCellPopulation::GetCellUsingLocationIndex 129ms 0.12% 58.93% 4277ms 4.00% std::set_intersection (inline) 232ms 0.22% 59.14% 4148ms 3.88% std::__set_intersection 58ms 0.054% 59.20% 3856ms 3.61% Cell::GetCellProliferativeType 3779ms 3.54% 62.74% 3779ms 3.54% boost::numeric::ublas::same_impl_ex 22ms 0.021% 62.76% 3632ms 3.40% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 42ms 0.039% 62.80% 3468ms 3.25% AbstractCellProperty::IsType (inline) 0 0% 62.80% 3150ms 2.95% std::insert_iterator::operator= (inline) 2116ms 1.98% 64.78% 3020ms 2.83% _int_malloc 56ms 0.052% 64.83% 2973ms 2.78% Cell::SetCellProliferativeType 855ms 0.8% 65.63% 2955ms 2.77% AbstractElement::GetNodeLocation 59ms 0.055% 65.69% 2841ms 2.66% std::_Rb_tree::erase 12ms 0.011% 65.70% 2717ms 2.54% std::_Rb_tree::_M_insert_unique_ (inline) 597ms 0.56% 66.26% 2587ms 2.42% boost::numeric::ublas::vector_binary::size (inline) 0 0% 66.26% 2586ms 2.42% boost::numeric::ublas::c_vector::operator-= (inline) 261ms 0.24% 66.50% 2567ms 2.40% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 66.50% 2553ms 2.39% boost::numeric::ublas::c_vector::assign (inline) 2550ms 2.39% 68.89% 2550ms 2.39% std::_Rb_tree::_S_right (inline) 270ms 0.25% 69.14% 2496ms 2.34% std::_Rb_tree_const_iterator::operator++ (inline) 636ms 0.6% 69.74% 2478ms 2.32% AbstractCellProperty::IsSame 0 0% 69.74% 2473ms 2.32% std::_Rb_tree::_M_insert_unique (inline) 0 0% 69.74% 2424ms 2.27% AbstractCellPopulation::WriteResultsToFiles 25ms 0.023% 69.76% 2415ms 2.26% CellPropertyCollection::HasProperty 27ms 0.025% 69.79% 2351ms 2.20% Cell::GetCellData 0 0% 69.79% 2311ms 2.16% Cell::HasCellProperty (inline) 77ms 0.072% 69.86% 2224ms 2.08% VertexMesh::GetVolumeOfElement 58ms 0.054% 69.91% 2199ms 2.06% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 69.91% 2199ms 2.06% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 69.91% 2199ms 2.06% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 4ms 0.0037% 69.92% 2168ms 2.03% AbstractCellPopulation::Iterator::operator++ (inline) 175ms 0.16% 70.08% 2152ms 2.01% AbstractCellPopulation::Iterator::IsRealCell (inline) 42ms 0.039% 70.12% 2123ms 1.99% std::_Rb_tree::_M_emplace_hint_unique 1ms 0.00094% 70.12% 1982ms 1.86% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00094% 70.12% 1971ms 1.85% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1942ms 1.82% 71.94% 1942ms 1.82% std::_Rb_tree_increment 421ms 0.39% 72.33% 1842ms 1.72% std::type_info::operator== (inline) 67ms 0.063% 72.40% 1811ms 1.70% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 72.40% 1774ms 1.66% VertexMeshWriter::WriteVtkUsingMesh 1161ms 1.09% 73.48% 1762ms 1.65% std::_Rb_tree::equal_range (inline) 26ms 0.024% 73.51% 1619ms 1.52% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 34ms 0.032% 73.54% 1607ms 1.50% VertexMesh::GetSurfaceAreaOfElement 49ms 0.046% 73.58% 1491ms 1.40% AbstractCellPopulation::GetLocationIndexUsingCell 85ms 0.08% 73.66% 1446ms 1.35% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 52ms 0.049% 73.71% 1445ms 1.35% Node::RemoveElement 0 0% 73.71% 1414ms 1.32% boost::numeric::ublas::norm_2 (inline) 137ms 0.13% 73.84% 1400ms 1.31% CellPropertyCollection::AddProperty 6ms 0.0056% 73.85% 1397ms 1.31% std::set::erase (inline) 642ms 0.6% 74.45% 1396ms 1.31% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1390ms 1.30% 75.75% 1390ms 1.30% [libchaste_cell_based.so] 0 0% 75.75% 1375ms 1.29% tcache_get (inline) 1375ms 1.29% 77.04% 1375ms 1.29% tcache_get_n (inline) 71ms 0.066% 77.10% 1363ms 1.28% boost::numeric::ublas::vector_reference::operator() (inline) 2ms 0.0019% 77.10% 1352ms 1.27% OffLatticeSimulation::ApplyBoundaries 0 0% 77.10% 1295ms 1.21% boost::numeric::ublas::vector_binary::operator() (inline) 96ms 0.09% 77.19% 1227ms 1.15% std::_Rb_tree::_M_erase_aux (partial-inline) 51ms 0.048% 77.24% 1204ms 1.13% std::less::operator() (inline) 20ms 0.019% 77.26% 1156ms 1.08% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 947ms 0.89% 78.15% 1153ms 1.08% std::operator< (inline) 1139ms 1.07% 79.21% 1139ms 1.07% std::_Rb_tree_insert_and_rebalance 21ms 0.02% 79.23% 1133ms 1.06% CellPropertyRegistry::Get 0 0% 79.23% 1115ms 1.04% boost::numeric::ublas::c_vector::assign_temporary (inline) 12ms 0.011% 79.25% 1115ms 1.04% boost::numeric::ublas::c_vector::swap (inline) 74ms 0.069% 79.31% 1103ms 1.03% std::swap_ranges (inline) 150ms 0.14% 79.45% 1080ms 1.01% boost::detail::shared_count::~shared_count (inline) 0 0% 79.45% 1080ms 1.01% boost::shared_ptr::~shared_ptr (inline) 13ms 0.012% 79.47% 1061ms 0.99% boost::numeric::ublas::detail::expression_type_check (inline) 104ms 0.097% 79.56% 1057ms 0.99% std::_Rb_tree::find (inline) 0 0% 79.56% 1047ms 0.98% std::_Rb_tree::clear (inline) 0 0% 79.56% 1044ms 0.98% std::_Rb_tree::_Auto_node::_Auto_node (inline) 175ms 0.16% 79.73% 1037ms 0.97% boost::numeric::ublas::detail::equals 7ms 0.0066% 79.73% 1032ms 0.97% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1031ms 0.97% 80.70% 1031ms 0.97% std::swap (inline) 0 0% 80.70% 1029ms 0.96% std::iter_swap (inline) 0 0% 80.70% 1029ms 0.96% std::map::clear (inline) 981ms 0.92% 81.62% 981ms 0.92% Node::rGetLocation 0 0% 81.62% 892ms 0.84% std::map::find (inline) 860ms 0.81% 82.42% 888ms 0.83% boost::detail::sp_counted_base::release 97ms 0.091% 82.51% 871ms 0.82% boost::numeric::ublas::c_vector::operator= (inline) 1ms 0.00094% 82.52% 848ms 0.79% VertexMeshWriter::MakeVtkMesh 223ms 0.21% 82.72% 801ms 0.75% std::__new_allocator::construct (inline) 0 0% 82.72% 801ms 0.75% std::allocator_traits::construct (inline) 798ms 0.75% 83.47% 798ms 0.75% [libchaste_mesh.so] 21ms 0.02% 83.49% 790ms 0.74% MutableElement::RegisterWithEdges (inline) 0 0% 83.49% 785ms 0.73% boost::numeric::ublas::norm_inf (inline) 432ms 0.4% 83.90% 785ms 0.73% boost::numeric::ublas::vector_norm_inf::apply (inline) 19ms 0.018% 83.91% 784ms 0.73% Edge::AddElement 429ms 0.4% 84.31% 777ms 0.73% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 178ms 0.17% 84.48% 772ms 0.72% boost::shared_ptr::shared_ptr (inline) 748ms 0.7% 85.18% 748ms 0.7% std::vector::size (inline) 0 0% 85.18% 742ms 0.69% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 85.18% 735ms 0.69% std::_Rb_tree::_M_construct_node (inline) 0 0% 85.18% 685ms 0.64% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 85.18% 684ms 0.64% std::_Rb_tree::_Auto_node::_M_insert (inline) 17ms 0.016% 85.20% 684ms 0.64% std::_Rb_tree::_M_insert_node (inline) 665ms 0.62% 85.82% 665ms 0.62% [libstdc++.so.6.0.33] 347ms 0.32% 86.15% 647ms 0.61% Edge::GetMapIndex 144ms 0.13% 86.28% 635ms 0.59% MutableElement::GetNodeLocalIndex 2ms 0.0019% 86.28% 631ms 0.59% std::_Vector_base::_M_allocate (inline) 37ms 0.035% 86.32% 617ms 0.58% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 86.32% 617ms 0.58% boost::numeric::ublas::vector::vector (inline) 0 0% 86.32% 613ms 0.57% vtkPolygon::New 0 0% 86.32% 613ms 0.57% vtkPolygon::vtkPolygon 32ms 0.03% 86.35% 593ms 0.56% MutableElement::RegisterWithNodes (inline) 565ms 0.53% 86.88% 593ms 0.56% boost::detail::shared_count::shared_count (inline) 23ms 0.022% 86.90% 558ms 0.52% Node::AddElement 535ms 0.5% 87.40% 535ms 0.5% Node::GetIndex