File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 97425ms, 89.15% of 109285ms total Dropped 1137 nodes (cum <= 546.42ms) flat flat% sum% cum cum% 0 0% 0% 108812ms 99.57% __libc_start_call_main 0 0% 0% 108812ms 99.57% __libc_start_main_impl 0 0% 0% 108812ms 99.57% _start 0 0% 0% 108793ms 99.55% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108793ms 99.55% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108793ms 99.55% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108793ms 99.55% main 0 0% 0% 108756ms 99.52% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108756ms 99.52% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108756ms 99.52% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 3ms 0.0027% 0.0027% 108748ms 99.51% AbstractCellBasedSimulation::Solve 16ms 0.015% 0.017% 56713ms 51.89% OffLatticeSimulation::UpdateCellLocationsAndTopology 19ms 0.017% 0.035% 53401ms 48.86% ForwardEulerNumericalMethod::UpdateAllNodePositions 124ms 0.11% 0.15% 52302ms 47.86% AbstractNumericalMethod::ComputeForcesIncludingDamping 330ms 0.3% 0.45% 40390ms 36.96% NagaiHondaForce::AddForceContribution 0 0% 0.45% 39032ms 35.72% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0018% 0.45% 24196ms 22.14% VertexBasedCellPopulation::Update 3ms 0.0027% 0.45% 24077ms 22.03% MutableVertexMesh::ReMesh 14595ms 13.35% 13.81% 23272ms 21.29% Cylindrical2dVertexMesh::GetVectorFromAtoB 89ms 0.081% 13.89% 17556ms 16.06% Cell::ReadyToDivide 59ms 0.054% 13.95% 16385ms 14.99% AbstractPhaseBasedCellCycleModel::ReadyToDivide 321ms 0.29% 14.24% 15288ms 13.99% NagaiHondaForce::GetAdhesionParameter 426ms 0.39% 14.63% 14301ms 13.09% boost::numeric::ublas::c_vector::c_vector (partial-inline) 110ms 0.1% 14.73% 13838ms 12.66% SimpleWntCellCycleModel::UpdateCellCyclePhase 147ms 0.13% 14.86% 13716ms 12.55% CellPropertyCollection::GetPropertiesType (inline) 404ms 0.37% 15.23% 12668ms 11.59% boost::numeric::ublas::vector_assign (inline) 130ms 0.12% 15.35% 12130ms 11.10% MutableVertexMesh::CheckForIntersections 57ms 0.052% 15.40% 11464ms 10.49% VertexBasedCellPopulation::GetDampingConstant 3322ms 3.04% 18.44% 11302ms 10.34% __dynamic_cast 74ms 0.068% 18.51% 11203ms 10.25% AbstractCellProperty::IsSubType (inline) 1329ms 1.22% 19.73% 10528ms 9.63% std::__new_allocator::allocate (inline) 73ms 0.067% 19.80% 10519ms 9.63% AbstractTargetAreaModifier::UpdateTargetAreas 72ms 0.066% 19.86% 10426ms 9.54% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 28ms 0.026% 19.89% 10245ms 9.37% AbstractCellBasedSimulation::DoCellBirth 0 0% 19.89% 9974ms 9.13% std::allocator_traits::allocate (inline) 0 0% 19.89% 9928ms 9.08% std::_Rb_tree::_M_create_node (inline) 0 0% 19.89% 9314ms 8.52% std::_Rb_tree::_M_get_node (inline) 2667ms 2.44% 22.33% 9284ms 8.50% boost::numeric::ublas::indexing_vector_assign 855ms 0.78% 23.11% 9265ms 8.48% operator new 424ms 0.39% 23.50% 9132ms 8.36% VertexMesh::GetNextEdgeGradientOfElementAtNode 1404ms 1.28% 24.78% 9108ms 8.33% std::_Rb_tree::_M_erase 744ms 0.68% 25.46% 8964ms 8.20% VertexMesh::ElementIncludesPoint 26ms 0.024% 25.49% 8873ms 8.12% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 25.49% 8728ms 7.99% std::_Rb_tree::_Alloc_node::operator() (inline) 83ms 0.076% 25.56% 8650ms 7.92% Cell::GetMutationState 485ms 0.44% 26.01% 8399ms 7.69% VertexMesh::GetCentroidOfElement 207ms 0.19% 26.20% 8364ms 7.65% std::_Rb_tree::~_Rb_tree (inline) 3448ms 3.16% 29.35% 8230ms 7.53% __GI___libc_malloc 0 0% 29.35% 8011ms 7.33% std::_Rb_tree::_M_drop_node (inline) 0 0% 29.35% 7891ms 7.22% std::set::~set (inline) 271ms 0.25% 29.60% 7765ms 7.11% std::__new_allocator::deallocate (inline) 0 0% 29.60% 7739ms 7.08% std::allocator_traits::deallocate (inline) 0 0% 29.60% 7682ms 7.03% std::_Rb_tree::_M_put_node (inline) 453ms 0.41% 30.01% 7580ms 6.94% std::map::operator[] (partial-inline) 19ms 0.017% 30.03% 7543ms 6.90% MutableVertexMesh::RemoveDeletedNodesAndElements 3220ms 2.95% 32.98% 7531ms 6.89% __GI___libc_free 1416ms 1.30% 34.27% 7308ms 6.69% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 107ms 0.098% 34.37% 7097ms 6.49% std::_Rb_tree::_Rb_tree (partial-inline) 685ms 0.63% 35.00% 6804ms 6.23% std::_Rb_tree::_M_copy (inline) 24ms 0.022% 35.02% 6681ms 6.11% std::set::set (inline) 109ms 0.1% 35.12% 6394ms 5.85% SimpleWntCellCycleModel::GetWntLevel 6348ms 5.81% 40.93% 6348ms 5.81% __strcmp_avx2 132ms 0.12% 41.05% 6197ms 5.67% WntConcentration::GetWntLevel 6067ms 5.55% 46.60% 6067ms 5.55% boost::numeric::ublas::c_vector::operator() 2425ms 2.22% 48.82% 6044ms 5.53% std::_Rb_tree::_M_lower_bound (inline) 779ms 0.71% 49.53% 5870ms 5.37% std::_Rb_tree::_M_clone_node (inline) 2749ms 2.52% 52.05% 5483ms 5.02% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 52.05% 5445ms 4.98% std::set::insert (inline) 31ms 0.028% 52.08% 5360ms 4.90% MutableVertexMesh::RemoveDeletedNodes 23ms 0.021% 52.10% 5169ms 4.73% EdgeHelper::RemoveDeletedEdges 34ms 0.031% 52.13% 4914ms 4.50% EdgeHelper::UpdateEdgesMapKey 1520ms 1.39% 53.52% 4909ms 4.49% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 53.52% 4909ms 4.49% std::_Rb_tree::lower_bound (inline) 0 0% 53.52% 4909ms 4.49% std::map::lower_bound (inline) 155ms 0.14% 53.66% 4681ms 4.28% std::set_intersection (inline) 532ms 0.49% 54.15% 4680ms 4.28% std::_Rb_tree::_M_insert_ (inline) 206ms 0.19% 54.34% 4656ms 4.26% MutableElement::ResetIndex 0 0% 54.34% 4587ms 4.20% AbstractCellBasedSimulation::DoCellRemoval (inline) 287ms 0.26% 54.60% 4526ms 4.14% std::__set_intersection 3957ms 3.62% 58.22% 4303ms 3.94% _int_free 127ms 0.12% 58.34% 4203ms 3.85% AbstractCellPopulation::GetCellUsingLocationIndex 4166ms 3.81% 62.15% 4166ms 3.81% boost::numeric::ublas::same_impl_ex 38ms 0.035% 62.18% 4144ms 3.79% Cell::GetCellProliferativeType 54ms 0.049% 62.23% 3702ms 3.39% AbstractCellProperty::IsType (inline) 9ms 0.0082% 62.24% 3537ms 3.24% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.24% 3321ms 3.04% std::insert_iterator::operator= (inline) 871ms 0.8% 63.04% 3288ms 3.01% AbstractElement::GetNodeLocation 38ms 0.035% 63.07% 3139ms 2.87% Cell::SetCellProliferativeType 2186ms 2.00% 65.07% 3051ms 2.79% _int_malloc 3039ms 2.78% 67.85% 3039ms 2.78% std::_Rb_tree::_S_right (inline) 7ms 0.0064% 67.86% 2930ms 2.68% std::_Rb_tree::_M_insert_unique_ (inline) 51ms 0.047% 67.91% 2925ms 2.68% std::_Rb_tree::erase 607ms 0.56% 68.46% 2911ms 2.66% boost::numeric::ublas::vector_binary::size (inline) 386ms 0.35% 68.81% 2777ms 2.54% std::_Rb_tree_const_iterator::operator++ (inline) 764ms 0.7% 69.51% 2720ms 2.49% AbstractCellProperty::IsSame 48ms 0.044% 69.56% 2612ms 2.39% CellPropertyCollection::HasProperty 241ms 0.22% 69.78% 2535ms 2.32% VertexMesh::GetAreaGradientOfElementAtNode 2ms 0.0018% 69.78% 2515ms 2.30% std::_Rb_tree::_M_insert_unique 0 0% 69.78% 2513ms 2.30% Cell::HasCellProperty (inline) 131ms 0.12% 69.90% 2472ms 2.26% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 69.90% 2457ms 2.25% AbstractCellPopulation::WriteResultsToFiles 25ms 0.023% 69.92% 2391ms 2.19% Cell::GetCellData 0 0% 69.92% 2385ms 2.18% boost::numeric::ublas::c_vector::assign (inline) 0 0% 69.92% 2300ms 2.10% boost::numeric::ublas::c_vector::operator-= (inline) 106ms 0.097% 70.02% 2284ms 2.09% VertexMesh::GetVolumeOfElement 2192ms 2.01% 72.03% 2192ms 2.01% std::_Rb_tree_increment 6ms 0.0055% 72.03% 2176ms 1.99% AbstractCellPopulation::Iterator::operator++ (inline) 35ms 0.032% 72.06% 2173ms 1.99% std::_Rb_tree::_M_emplace_hint_unique 235ms 0.22% 72.28% 2158ms 1.97% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 72.28% 2014ms 1.84% VertexBasedCellPopulation::WriteVtkResultsToFile 2ms 0.0018% 72.28% 2000ms 1.83% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1356ms 1.24% 73.52% 1992ms 1.82% std::_Rb_tree::equal_range (inline) 4ms 0.0037% 73.52% 1971ms 1.80% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.52% 1971ms 1.80% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 459ms 0.42% 73.94% 1956ms 1.79% std::type_info::operator== (inline) 65ms 0.059% 74.00% 1851ms 1.69% MutableVertexMesh::CheckForSwapsFromShortEdges 1ms 0.00092% 74.00% 1788ms 1.64% VertexMeshWriter::WriteVtkUsingMesh 18ms 0.016% 74.02% 1677ms 1.53% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 15ms 0.014% 74.03% 1646ms 1.51% VertexMesh::GetSurfaceAreaOfElement 48ms 0.044% 74.08% 1579ms 1.44% Node::RemoveElement 0 0% 74.08% 1551ms 1.42% tcache_get (inline) 1551ms 1.42% 75.50% 1551ms 1.42% tcache_get_n (inline) 10ms 0.0092% 75.51% 1535ms 1.40% std::set::erase (inline) 70ms 0.064% 75.57% 1519ms 1.39% boost::numeric::ublas::vector_reference::operator() (inline) 171ms 0.16% 75.73% 1517ms 1.39% CellPropertyCollection::AddProperty 29ms 0.027% 75.75% 1493ms 1.37% AbstractCellPopulation::GetLocationIndexUsingCell 88ms 0.081% 75.83% 1471ms 1.35% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 2ms 0.0018% 75.84% 1400ms 1.28% OffLatticeSimulation::ApplyBoundaries 0 0% 75.84% 1269ms 1.16% boost::numeric::ublas::vector_binary::operator() (inline) 1224ms 1.12% 76.96% 1224ms 1.12% Node::rGetLocation 0 0% 76.96% 1216ms 1.11% boost::numeric::ublas::norm_2 (inline) 543ms 0.5% 77.45% 1201ms 1.10% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 0 0% 77.45% 1200ms 1.10% std::_Rb_tree::_Auto_node::_Auto_node (inline) 67ms 0.061% 77.51% 1195ms 1.09% std::less::operator() (inline) 1185ms 1.08% 78.60% 1185ms 1.08% [libchaste_cell_based.so] 930ms 0.85% 79.45% 1128ms 1.03% std::operator< (inline) 96ms 0.088% 79.54% 1102ms 1.01% std::_Rb_tree::find (inline) 110ms 0.1% 79.64% 1100ms 1.01% std::_Rb_tree::_M_erase_aux (partial-inline) 20ms 0.018% 79.66% 1088ms 1% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 24ms 0.022% 79.68% 1076ms 0.98% CellPropertyRegistry::Get 1068ms 0.98% 80.66% 1068ms 0.98% std::_Rb_tree_insert_and_rebalance 4ms 0.0037% 80.66% 1002ms 0.92% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 142ms 0.13% 80.79% 989ms 0.9% boost::detail::shared_count::~shared_count (inline) 0 0% 80.79% 989ms 0.9% boost::shared_ptr::~shared_ptr (inline) 28ms 0.026% 80.82% 975ms 0.89% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 80.82% 973ms 0.89% boost::numeric::ublas::c_vector::assign_temporary (inline) 5ms 0.0046% 80.82% 973ms 0.89% boost::numeric::ublas::c_vector::swap (inline) 969ms 0.89% 81.71% 969ms 0.89% [libchaste_mesh.so] 82ms 0.075% 81.78% 968ms 0.89% std::swap_ranges (inline) 1ms 0.00092% 81.78% 955ms 0.87% std::_Rb_tree::clear (inline) 951ms 0.87% 82.65% 951ms 0.87% std::vector::size (inline) 410ms 0.38% 83.03% 950ms 0.87% Edge::GetMapIndex 0 0% 83.03% 942ms 0.86% std::map::clear (inline) 139ms 0.13% 83.16% 941ms 0.86% boost::numeric::ublas::detail::equals 0 0% 83.16% 915ms 0.84% std::map::find (inline) 888ms 0.81% 83.97% 888ms 0.81% std::swap (inline) 0 0% 83.97% 886ms 0.81% std::iter_swap (inline) 1ms 0.00092% 83.97% 859ms 0.79% VertexMeshWriter::MakeVtkMesh 824ms 0.75% 84.72% 829ms 0.76% boost::detail::sp_counted_base::release 128ms 0.12% 84.84% 823ms 0.75% boost::numeric::ublas::c_vector::operator= (inline) 96ms 0.088% 84.93% 811ms 0.74% MutableElement::GetNodeLocalIndex 0 0% 84.93% 756ms 0.69% boost::numeric::ublas::norm_inf (inline) 364ms 0.33% 85.26% 756ms 0.69% boost::numeric::ublas::vector_norm_inf::apply (inline) 29ms 0.027% 85.29% 743ms 0.68% MutableElement::RegisterWithEdges (inline) 142ms 0.13% 85.42% 741ms 0.68% boost::shared_ptr::shared_ptr (inline) 34ms 0.031% 85.45% 721ms 0.66% Edge::AddElement 404ms 0.37% 85.82% 709ms 0.65% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 693ms 0.63% 86.45% 693ms 0.63% Node::GetIndex 0 0% 86.45% 676ms 0.62% CellPropertyCollection::~CellPropertyCollection (inline) 1ms 0.00092% 86.45% 660ms 0.6% std::_Vector_base::_M_allocate (inline) 657ms 0.6% 87.05% 657ms 0.6% operator delete 110ms 0.1% 87.15% 655ms 0.6% std::__new_allocator::construct (inline) 0 0% 87.15% 655ms 0.6% std::allocator_traits::construct (inline) 37ms 0.034% 87.19% 651ms 0.6% MutableElement::RegisterWithNodes (inline) 0 0% 87.19% 634ms 0.58% std::_Rb_tree::_Auto_node::_M_insert (inline) 21ms 0.019% 87.21% 634ms 0.58% std::_Rb_tree::_M_insert_node (inline) 0 0% 87.21% 614ms 0.56% std::_Rb_tree::_M_construct_node (inline) 383ms 0.35% 87.56% 611ms 0.56% CellPropertyCollection::GetProperty 0 0% 87.56% 611ms 0.56% vtkPolygon::New 1ms 0.00092% 87.56% 611ms 0.56% vtkPolygon::vtkPolygon 28ms 0.026% 87.58% 605ms 0.55% Node::AddElement 567ms 0.52% 88.10% 599ms 0.55% boost::detail::shared_count::shared_count (inline) 28ms 0.026% 88.13% 582ms 0.53% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 88.13% 582ms 0.53% boost::numeric::ublas::vector::vector (inline) 0 0% 88.13% 577ms 0.53% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 563ms 0.52% 88.64% 563ms 0.52% [libstdc++.so.6.0.33] 550ms 0.5% 89.15% 550ms 0.5% boost::shared_ptr::operator-> (inline)