File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96859ms, 88.53% of 109404ms total Dropped 1171 nodes (cum <= 547.02ms) flat flat% sum% cum cum% 0 0% 0% 108900ms 99.54% __libc_start_call_main 0 0% 0% 108900ms 99.54% __libc_start_main_impl 0 0% 0% 108900ms 99.54% _start 0 0% 0% 108881ms 99.52% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108881ms 99.52% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108881ms 99.52% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108881ms 99.52% main 0 0% 0% 108835ms 99.48% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108835ms 99.48% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108835ms 99.48% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0018% 0.0018% 108828ms 99.47% AbstractCellBasedSimulation::Solve 13ms 0.012% 0.014% 56230ms 51.40% OffLatticeSimulation::UpdateCellLocationsAndTopology 22ms 0.02% 0.034% 52935ms 48.38% ForwardEulerNumericalMethod::UpdateAllNodePositions 140ms 0.13% 0.16% 51857ms 47.40% AbstractNumericalMethod::ComputeForcesIncludingDamping 448ms 0.41% 0.57% 40261ms 36.80% NagaiHondaForce::AddForceContribution 1ms 0.00091% 0.57% 39504ms 36.11% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.0037% 0.58% 24450ms 22.35% VertexBasedCellPopulation::Update 1ms 0.00091% 0.58% 24321ms 22.23% MutableVertexMesh::ReMesh 14394ms 13.16% 13.73% 23042ms 21.06% Cylindrical2dVertexMesh::GetVectorFromAtoB 82ms 0.075% 13.81% 17652ms 16.13% Cell::ReadyToDivide 103ms 0.094% 13.90% 16510ms 15.09% AbstractPhaseBasedCellCycleModel::ReadyToDivide 303ms 0.28% 14.18% 14980ms 13.69% NagaiHondaForce::GetAdhesionParameter 393ms 0.36% 14.54% 14525ms 13.28% boost::numeric::ublas::c_vector::c_vector (partial-inline) 130ms 0.12% 14.66% 13990ms 12.79% SimpleWntCellCycleModel::UpdateCellCyclePhase 138ms 0.13% 14.78% 13509ms 12.35% CellPropertyCollection::GetPropertiesType (inline) 405ms 0.37% 15.15% 12952ms 11.84% boost::numeric::ublas::vector_assign (inline) 119ms 0.11% 15.26% 12023ms 10.99% MutableVertexMesh::CheckForIntersections 3178ms 2.90% 18.17% 11156ms 10.20% __dynamic_cast 72ms 0.066% 18.23% 11092ms 10.14% VertexBasedCellPopulation::GetDampingConstant 68ms 0.062% 18.30% 11043ms 10.09% AbstractCellProperty::IsSubType (inline) 67ms 0.061% 18.36% 10578ms 9.67% AbstractTargetAreaModifier::UpdateTargetAreas 55ms 0.05% 18.41% 10480ms 9.58% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 26ms 0.024% 18.43% 10458ms 9.56% AbstractCellBasedSimulation::DoCellBirth 1293ms 1.18% 19.61% 9991ms 9.13% std::__new_allocator::allocate (inline) 2760ms 2.52% 22.14% 9734ms 8.90% boost::numeric::ublas::indexing_vector_assign 0 0% 22.14% 9493ms 8.68% std::_Rb_tree::_M_create_node (inline) 0 0% 22.14% 9444ms 8.63% std::allocator_traits::allocate (inline) 1464ms 1.34% 23.47% 9415ms 8.61% std::_Rb_tree::_M_erase 378ms 0.35% 23.82% 8967ms 8.20% VertexMesh::GetNextEdgeGradientOfElementAtNode 795ms 0.73% 24.55% 8939ms 8.17% VertexMesh::ElementIncludesPoint 24ms 0.022% 24.57% 8888ms 8.12% VertexBasedCellPopulation::GetLocationOfCellCentre 805ms 0.74% 25.30% 8816ms 8.06% operator new 0 0% 25.30% 8809ms 8.05% std::_Rb_tree::_M_get_node (inline) 218ms 0.2% 25.50% 8536ms 7.80% std::_Rb_tree::~_Rb_tree (inline) 65ms 0.059% 25.56% 8528ms 7.79% Cell::GetMutationState 480ms 0.44% 26.00% 8449ms 7.72% VertexMesh::GetCentroidOfElement 0 0% 26.00% 8326ms 7.61% std::_Rb_tree::_M_drop_node (inline) 0 0% 26.00% 8315ms 7.60% std::_Rb_tree::_Alloc_node::operator() (inline) 258ms 0.24% 26.24% 8111ms 7.41% std::__new_allocator::deallocate (inline) 0 0% 26.24% 8084ms 7.39% std::set::~set (inline) 0 0% 26.24% 8073ms 7.38% std::allocator_traits::deallocate (inline) 0 0% 26.24% 7999ms 7.31% std::_Rb_tree::_M_put_node (inline) 3129ms 2.86% 29.10% 7943ms 7.26% __GI___libc_free 3165ms 2.89% 31.99% 7844ms 7.17% __GI___libc_malloc 19ms 0.017% 32.01% 7792ms 7.12% MutableVertexMesh::RemoveDeletedNodesAndElements 497ms 0.45% 32.46% 7408ms 6.77% std::map::operator[] (partial-inline) 1419ms 1.30% 33.76% 7261ms 6.64% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 151ms 0.14% 33.90% 6826ms 6.24% std::_Rb_tree::_Rb_tree (partial-inline) 140ms 0.13% 34.02% 6477ms 5.92% SimpleWntCellCycleModel::GetWntLevel 694ms 0.63% 34.66% 6472ms 5.92% std::_Rb_tree::_M_copy (inline) 12ms 0.011% 34.67% 6340ms 5.80% std::set::set (inline) 6318ms 5.77% 40.44% 6318ms 5.77% boost::numeric::ublas::c_vector::operator() 6297ms 5.76% 46.20% 6297ms 5.76% __strcmp_avx2 156ms 0.14% 46.34% 6222ms 5.69% WntConcentration::GetWntLevel 2402ms 2.20% 48.54% 5746ms 5.25% std::_Rb_tree::_M_lower_bound (inline) 2698ms 2.47% 51.00% 5579ms 5.10% __cxxabiv1::__si_class_type_info::__do_dyncast 755ms 0.69% 51.69% 5515ms 5.04% std::_Rb_tree::_M_clone_node (inline) 22ms 0.02% 51.71% 5457ms 4.99% MutableVertexMesh::RemoveDeletedNodes 1ms 0.00091% 51.72% 5457ms 4.99% std::set::insert (inline) 29ms 0.027% 51.74% 5277ms 4.82% EdgeHelper::RemoveDeletedEdges 52ms 0.048% 51.79% 4980ms 4.55% EdgeHelper::UpdateEdgesMapKey 1494ms 1.37% 53.16% 4881ms 4.46% boost::numeric::ublas::c_vector::operator[] (inline) 211ms 0.19% 53.35% 4857ms 4.44% MutableElement::ResetIndex 4497ms 4.11% 57.46% 4802ms 4.39% _int_free 0 0% 57.46% 4647ms 4.25% std::_Rb_tree::lower_bound (inline) 0 0% 57.46% 4647ms 4.25% std::map::lower_bound (inline) 536ms 0.49% 57.95% 4633ms 4.23% std::_Rb_tree::_M_insert_ (inline) 76ms 0.069% 58.02% 4627ms 4.23% std::set_intersection (inline) 0 0% 58.02% 4583ms 4.19% AbstractCellBasedSimulation::DoCellRemoval (inline) 287ms 0.26% 58.28% 4551ms 4.16% std::__set_intersection 4080ms 3.73% 62.01% 4080ms 3.73% boost::numeric::ublas::same_impl_ex 49ms 0.045% 62.05% 4000ms 3.66% Cell::GetCellProliferativeType 119ms 0.11% 62.16% 3988ms 3.65% AbstractCellPopulation::GetCellUsingLocationIndex 55ms 0.05% 62.21% 3603ms 3.29% AbstractCellProperty::IsType (inline) 13ms 0.012% 62.23% 3541ms 3.24% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.23% 3308ms 3.02% std::insert_iterator::operator= (inline) 797ms 0.73% 62.95% 3243ms 2.96% AbstractElement::GetNodeLocation 61ms 0.056% 63.01% 3178ms 2.90% Cell::SetCellProliferativeType 32ms 0.029% 63.04% 3164ms 2.89% std::_Rb_tree::erase 2204ms 2.01% 65.05% 3104ms 2.84% _int_malloc 6ms 0.0055% 65.06% 2936ms 2.68% std::_Rb_tree::_M_insert_unique_ (inline) 621ms 0.57% 65.63% 2877ms 2.63% boost::numeric::ublas::vector_binary::size (inline) 2776ms 2.54% 68.16% 2776ms 2.54% std::_Rb_tree::_S_right (inline) 441ms 0.4% 68.57% 2762ms 2.52% std::_Rb_tree_const_iterator::operator++ (inline) 778ms 0.71% 69.28% 2580ms 2.36% AbstractCellProperty::IsSame 0 0% 69.28% 2529ms 2.31% boost::numeric::ublas::c_vector::operator-= (inline) 1ms 0.00091% 69.28% 2520ms 2.30% std::_Rb_tree::_M_insert_unique (inline) 212ms 0.19% 69.47% 2515ms 2.30% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.47% 2487ms 2.27% AbstractCellPopulation::WriteResultsToFiles 42ms 0.038% 69.51% 2458ms 2.25% CellPropertyCollection::HasProperty 58ms 0.053% 69.56% 2422ms 2.21% Cell::GetCellData 0 0% 69.56% 2422ms 2.21% boost::numeric::ublas::c_vector::assign (inline) 117ms 0.11% 69.67% 2384ms 2.18% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 69.67% 2369ms 2.17% Cell::HasCellProperty (inline) 4ms 0.0037% 69.67% 2241ms 2.05% AbstractCellPopulation::Iterator::operator++ (inline) 98ms 0.09% 69.76% 2229ms 2.04% VertexMesh::GetVolumeOfElement 230ms 0.21% 69.97% 2223ms 2.03% AbstractCellPopulation::Iterator::IsRealCell 35ms 0.032% 70.01% 2208ms 2.02% std::_Rb_tree::_M_emplace_hint_unique 1471ms 1.34% 71.35% 2158ms 1.97% std::_Rb_tree::equal_range (inline) 2138ms 1.95% 73.31% 2138ms 1.95% std::_Rb_tree_increment 0 0% 73.31% 2041ms 1.87% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 73.31% 2024ms 1.85% VertexBasedCellPopulation::WriteCellVtkResultsToFile 76ms 0.069% 73.37% 1921ms 1.76% MutableVertexMesh::CheckForSwapsFromShortEdges 1ms 0.00091% 73.38% 1919ms 1.75% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.38% 1919ms 1.75% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1ms 0.00091% 73.38% 1814ms 1.66% VertexMeshWriter::WriteVtkUsingMesh 426ms 0.39% 73.77% 1802ms 1.65% std::type_info::operator== (inline) 29ms 0.027% 73.79% 1713ms 1.57% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 21ms 0.019% 73.81% 1615ms 1.48% VertexMesh::GetSurfaceAreaOfElement 54ms 0.049% 73.86% 1594ms 1.46% Node::RemoveElement 42ms 0.038% 73.90% 1563ms 1.43% AbstractCellPopulation::GetLocationIndexUsingCell 17ms 0.016% 73.92% 1550ms 1.42% std::set::erase (inline) 131ms 0.12% 74.03% 1546ms 1.41% boost::numeric::ublas::vector_reference::operator() (inline) 168ms 0.15% 74.19% 1521ms 1.39% CellPropertyCollection::AddProperty 67ms 0.061% 74.25% 1496ms 1.37% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 74.25% 1444ms 1.32% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 74.25% 1415ms 1.29% tcache_get (inline) 1415ms 1.29% 75.54% 1415ms 1.29% tcache_get_n (inline) 3ms 0.0027% 75.55% 1272ms 1.16% OffLatticeSimulation::ApplyBoundaries 84ms 0.077% 75.62% 1249ms 1.14% std::_Rb_tree::_M_erase_aux (partial-inline) 100ms 0.091% 75.71% 1249ms 1.14% std::less::operator() (inline) 1239ms 1.13% 76.85% 1239ms 1.13% Node::rGetLocation 0 0% 76.85% 1221ms 1.12% boost::numeric::ublas::norm_2 (inline) 547ms 0.5% 77.35% 1214ms 1.11% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 0 0% 77.35% 1178ms 1.08% std::_Rb_tree::_Auto_node::_Auto_node (inline) 899ms 0.82% 78.17% 1149ms 1.05% std::operator< (inline) 1123ms 1.03% 79.19% 1123ms 1.03% std::_Rb_tree_insert_and_rebalance 0 0% 79.19% 1101ms 1.01% std::_Rb_tree::clear (inline) 1082ms 0.99% 80.18% 1082ms 0.99% [libchaste_cell_based.so] 0 0% 80.18% 1081ms 0.99% std::map::clear (inline) 38ms 0.035% 80.22% 1079ms 0.99% CellPropertyRegistry::Get 93ms 0.085% 80.30% 1068ms 0.98% std::_Rb_tree::find (inline) 13ms 0.012% 80.32% 1065ms 0.97% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 164ms 0.15% 80.47% 1001ms 0.91% boost::detail::shared_count::~shared_count (inline) 0 0% 80.47% 1001ms 0.91% boost::shared_ptr::~shared_ptr (inline) 9ms 0.0082% 80.47% 972ms 0.89% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 964ms 0.88% 81.35% 964ms 0.88% std::vector::size (inline) 0 0% 81.35% 953ms 0.87% boost::numeric::ublas::c_vector::assign_temporary (inline) 6ms 0.0055% 81.36% 953ms 0.87% boost::numeric::ublas::c_vector::swap (inline) 87ms 0.08% 81.44% 947ms 0.87% std::swap_ranges (inline) 427ms 0.39% 81.83% 929ms 0.85% Edge::GetMapIndex 11ms 0.01% 81.84% 910ms 0.83% boost::numeric::ublas::detail::expression_type_check (inline) 905ms 0.83% 82.67% 905ms 0.83% [libchaste_mesh.so] 0 0% 82.67% 897ms 0.82% std::map::find (inline) 142ms 0.13% 82.80% 886ms 0.81% boost::numeric::ublas::detail::equals 110ms 0.1% 82.90% 879ms 0.8% MutableElement::GetNodeLocalIndex 2ms 0.0018% 82.90% 867ms 0.79% VertexMeshWriter::MakeVtkMesh 0 0% 82.90% 860ms 0.79% std::iter_swap (inline) 860ms 0.79% 83.69% 860ms 0.79% std::swap (inline) 176ms 0.16% 83.85% 831ms 0.76% boost::shared_ptr::shared_ptr (inline) 802ms 0.73% 84.58% 811ms 0.74% boost::detail::sp_counted_base::release 121ms 0.11% 84.69% 787ms 0.72% boost::numeric::ublas::c_vector::operator= (inline) 785ms 0.72% 85.41% 785ms 0.72% Node::GetIndex 479ms 0.44% 85.85% 785ms 0.72% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 24ms 0.022% 85.87% 757ms 0.69% Edge::AddElement 23ms 0.021% 85.89% 757ms 0.69% MutableElement::RegisterWithEdges (inline) 0 0% 85.89% 732ms 0.67% CellPropertyCollection::~CellPropertyCollection (inline) 92ms 0.084% 85.97% 728ms 0.67% std::__new_allocator::construct (inline) 0 0% 85.97% 728ms 0.67% std::allocator_traits::construct (inline) 0 0% 85.97% 698ms 0.64% boost::numeric::ublas::norm_inf (inline) 363ms 0.33% 86.30% 698ms 0.64% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 86.30% 684ms 0.63% std::_Rb_tree::_M_construct_node (inline) 0 0% 86.30% 672ms 0.61% std::_Rb_tree::_Auto_node::_M_insert (inline) 34ms 0.031% 86.34% 672ms 0.61% std::_Rb_tree::_M_insert_node (inline) 634ms 0.58% 86.91% 655ms 0.6% boost::detail::shared_count::shared_count (inline) 0 0% 86.91% 632ms 0.58% std::_Vector_base::_M_allocate (inline) 0 0% 86.91% 624ms 0.57% vtkPolygon::New 2ms 0.0018% 86.92% 624ms 0.57% vtkPolygon::vtkPolygon 36ms 0.033% 86.95% 583ms 0.53% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 86.95% 583ms 0.53% boost::numeric::ublas::vector::vector (inline) 0 0% 86.95% 582ms 0.53% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 576ms 0.53% 87.48% 576ms 0.53% [libstdc++.so.6.0.33] 21ms 0.019% 87.49% 573ms 0.52% MutableElement::RegisterWithNodes (inline) 573ms 0.52% 88.02% 573ms 0.52% operator delete 563ms 0.51% 88.53% 563ms 0.51% boost::shared_ptr::operator-> (inline)