File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 78338ms, 88.02% of 89004ms total Dropped 1013 nodes (cum <= 445.02ms) flat flat% sum% cum cum% 0 0% 0% 88767ms 99.73% __libc_start_call_main 0 0% 0% 88767ms 99.73% __libc_start_main_impl 0 0% 0% 88767ms 99.73% _start 0 0% 0% 88750ms 99.71% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 88750ms 99.71% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 88750ms 99.71% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 88750ms 99.71% main 0 0% 0% 88718ms 99.68% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 88718ms 99.68% CxxTest::TestRunner::runTest (inline) 0 0% 0% 88718ms 99.68% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0022% 0.0022% 88712ms 99.67% AbstractCellBasedSimulation::Solve 8ms 0.009% 0.011% 47065ms 52.88% OffLatticeSimulation::UpdateCellLocationsAndTopology 13ms 0.015% 0.026% 44091ms 49.54% ForwardEulerNumericalMethod::UpdateAllNodePositions 34ms 0.038% 0.064% 43156ms 48.49% AbstractNumericalMethod::ComputeForcesIncludingDamping 322ms 0.36% 0.43% 33956ms 38.15% NagaiHondaForce::AddForceContribution 1ms 0.0011% 0.43% 30665ms 34.45% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.0045% 0.43% 18172ms 20.42% VertexBasedCellPopulation::Update 0 0% 0.43% 18060ms 20.29% MutableVertexMesh::ReMesh 7877ms 8.85% 9.28% 15170ms 17.04% Cylindrical2dVertexMesh::GetVectorFromAtoB 97ms 0.11% 9.39% 15027ms 16.88% Cell::ReadyToDivide 19ms 0.021% 9.41% 14083ms 15.82% AbstractPhaseBasedCellCycleModel::ReadyToDivide 86ms 0.097% 9.51% 14060ms 15.80% NagaiHondaForce::GetAdhesionParameter 60ms 0.067% 9.58% 12024ms 13.51% SimpleWntCellCycleModel::UpdateCellCyclePhase 363ms 0.41% 9.98% 11755ms 13.21% boost::numeric::ublas::c_vector::c_vector (partial-inline) 68ms 0.076% 10.06% 11186ms 12.57% CellPropertyCollection::GetPropertiesType (inline) 473ms 0.53% 10.59% 11160ms 12.54% std::__new_allocator::allocate (inline) 0 0% 10.59% 10671ms 11.99% std::allocator_traits::allocate (inline) 721ms 0.81% 11.40% 10624ms 11.94% operator new 208ms 0.23% 11.64% 10497ms 11.79% boost::numeric::ublas::vector_assign (inline) 0 0% 11.64% 10412ms 11.70% std::_Rb_tree::_M_create_node (inline) 0 0% 11.64% 10167ms 11.42% std::_Rb_tree::_M_get_node (inline) 3353ms 3.77% 15.40% 9628ms 10.82% __GI___libc_malloc 95ms 0.11% 15.51% 9223ms 10.36% AbstractCellProperty::IsSubType (inline) 2121ms 2.38% 17.89% 9105ms 10.23% __dynamic_cast 0 0% 17.89% 9095ms 10.22% std::_Rb_tree::_Alloc_node::operator() (inline) 41ms 0.046% 17.94% 9008ms 10.12% AbstractTargetAreaModifier::UpdateTargetAreas 12ms 0.013% 17.95% 8973ms 10.08% AbstractCellBasedSimulation::DoCellBirth 48ms 0.054% 18.01% 8932ms 10.04% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 97ms 0.11% 18.11% 8885ms 9.98% VertexBasedCellPopulation::GetDampingConstant 131ms 0.15% 18.26% 8357ms 9.39% MutableVertexMesh::CheckForIntersections 0 0% 18.26% 8012ms 9.00% std::_Rb_tree::_M_drop_node (inline) 882ms 0.99% 19.25% 7965ms 8.95% std::_Rb_tree::_M_erase 2190ms 2.46% 21.71% 7608ms 8.55% boost::numeric::ublas::indexing_vector_assign 296ms 0.33% 22.05% 7486ms 8.41% std::_Rb_tree::~_Rb_tree (inline) 89ms 0.1% 22.15% 7262ms 8.16% std::__new_allocator::deallocate (inline) 0 0% 22.15% 7241ms 8.14% std::allocator_traits::deallocate (inline) 0 0% 22.15% 7194ms 8.08% std::_Rb_tree::_M_put_node (inline) 0 0% 22.15% 7091ms 7.97% std::set::~set (inline) 43ms 0.048% 22.19% 7086ms 7.96% Cell::GetMutationState 1892ms 2.13% 24.32% 6968ms 7.83% __GI___libc_free 453ms 0.51% 24.83% 6639ms 7.46% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 24.83% 6586ms 7.40% std::set::insert (inline) 52ms 0.058% 24.89% 6551ms 7.36% VertexBasedCellPopulation::GetLocationOfCellCentre 406ms 0.46% 25.34% 6544ms 7.35% std::map::operator[] (partial-inline) 518ms 0.58% 25.93% 6307ms 7.09% VertexMesh::GetCentroidOfElement 459ms 0.52% 26.44% 6157ms 6.92% VertexMesh::ElementIncludesPoint 8ms 0.009% 26.45% 6155ms 6.92% MutableVertexMesh::RemoveDeletedNodesAndElements 738ms 0.83% 27.28% 6069ms 6.82% std::_Rb_tree::_M_insert_ (inline) 129ms 0.14% 27.42% 5736ms 6.44% std::_Rb_tree::_Rb_tree (partial-inline) 52ms 0.058% 27.48% 5662ms 6.36% std::set_intersection (inline) 287ms 0.32% 27.81% 5610ms 6.30% std::__set_intersection 5603ms 6.30% 34.10% 5603ms 6.30% __strcmp_evex 5585ms 6.27% 40.38% 5585ms 6.27% boost::numeric::ublas::c_vector::operator() 11ms 0.012% 40.39% 5412ms 6.08% std::set::set (inline) 550ms 0.62% 41.01% 5394ms 6.06% std::_Rb_tree::_M_copy (inline) 831ms 0.93% 41.94% 5251ms 5.90% AbstractMesh::GetDistanceBetweenNodes 4409ms 4.95% 46.89% 5018ms 5.64% _int_free 132ms 0.15% 47.04% 5014ms 5.63% SimpleWntCellCycleModel::GetWntLevel 125ms 0.14% 47.18% 4786ms 5.38% WntConcentration::GetWntLevel 513ms 0.58% 47.76% 4690ms 5.27% std::_Rb_tree::_M_clone_node (inline) 2101ms 2.36% 50.12% 4571ms 5.14% __cxxabiv1::__si_class_type_info::__do_dyncast 18ms 0.02% 50.14% 4549ms 5.11% MutableVertexMesh::RemoveDeletedNodes 513ms 0.58% 50.72% 4538ms 5.10% boost::numeric::ublas::c_vector::operator[] (inline) 3742ms 4.20% 54.92% 4506ms 5.06% _int_malloc 1956ms 2.20% 57.12% 4479ms 5.03% std::_Rb_tree::_M_lower_bound (inline) 54ms 0.061% 57.18% 4436ms 4.98% EdgeHelper::RemoveDeletedEdges 0 0% 57.18% 4282ms 4.81% std::insert_iterator::operator= (inline) 21ms 0.024% 57.20% 4221ms 4.74% EdgeHelper::UpdateEdgesMapKey 0 0% 57.20% 4015ms 4.51% std::_Rb_tree::_M_insert_unique_ (inline) 0 0% 57.20% 3881ms 4.36% std::_Rb_tree::lower_bound (inline) 0 0% 57.20% 3881ms 4.36% std::map::lower_bound (inline) 17ms 0.019% 57.22% 3845ms 4.32% Cell::GetCellProliferativeType 3711ms 4.17% 61.39% 3711ms 4.17% boost::numeric::ublas::same_impl_ex 101ms 0.11% 61.50% 3634ms 4.08% MutableElement::ResetIndex 0 0% 61.50% 3513ms 3.95% AbstractCellBasedSimulation::DoCellRemoval (inline) 51ms 0.057% 61.56% 3426ms 3.85% AbstractCellPopulation::GetCellUsingLocationIndex 2997ms 3.37% 64.93% 2997ms 3.37% [libchaste_cell_based.so] 135ms 0.15% 65.08% 2943ms 3.31% AbstractCellProperty::IsType (inline) 107ms 0.12% 65.20% 2828ms 3.18% Cell::SetCellProliferativeType 43ms 0.048% 65.25% 2728ms 3.07% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 136ms 0.15% 65.40% 2634ms 2.96% boost::detail::shared_count::~shared_count (inline) 0 0% 65.40% 2634ms 2.96% boost::shared_ptr::~shared_ptr (inline) 637ms 0.72% 66.12% 2571ms 2.89% AbstractElement::GetNodeLocation 2ms 0.0022% 66.12% 2571ms 2.89% std::_Rb_tree::_M_insert_unique 2442ms 2.74% 68.86% 2448ms 2.75% boost::detail::sp_counted_base::release 7ms 0.0079% 68.87% 2332ms 2.62% AbstractCellPopulation::Iterator::operator++ (inline) 191ms 0.21% 69.09% 2315ms 2.60% AbstractCellPopulation::Iterator::IsRealCell (inline) 29ms 0.033% 69.12% 2212ms 2.49% std::_Rb_tree::_M_emplace_hint_unique 0 0% 69.12% 2211ms 2.48% boost::numeric::ublas::c_vector::assign (inline) 15ms 0.017% 69.14% 2172ms 2.44% Cell::GetCellData 129ms 0.14% 69.28% 2158ms 2.42% boost::numeric::ublas::vector_binary::size (inline) 334ms 0.38% 69.66% 2118ms 2.38% std::_Rb_tree_const_iterator::operator++ (inline) 52ms 0.058% 69.71% 2095ms 2.35% std::_Rb_tree::erase 2024ms 2.27% 71.99% 2024ms 2.27% std::_Rb_tree::_S_right (inline) 44ms 0.049% 72.04% 2018ms 2.27% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 40ms 0.045% 72.08% 1982ms 2.23% CellPropertyCollection::HasProperty 0 0% 72.08% 1979ms 2.22% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 72.08% 1952ms 2.19% AbstractCellPopulation::WriteResultsToFiles 1ms 0.0011% 72.08% 1931ms 2.17% Cell::HasCellProperty (inline) 232ms 0.26% 72.34% 1897ms 2.13% VertexMesh::GetAreaGradientOfElementAtNode 1883ms 2.12% 74.46% 1883ms 2.12% [libchaste_mesh.so] 383ms 0.43% 74.89% 1874ms 2.11% AbstractCellProperty::IsSame 25ms 0.028% 74.92% 1720ms 1.93% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 89ms 0.1% 75.02% 1671ms 1.88% VertexMesh::GetVolumeOfElement 0 0% 75.02% 1614ms 1.81% VertexBasedCellPopulation::WriteVtkResultsToFile 2ms 0.0022% 75.02% 1604ms 1.80% VertexBasedCellPopulation::WriteCellVtkResultsToFile 300ms 0.34% 75.36% 1544ms 1.73% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 115ms 0.13% 75.49% 1494ms 1.68% CellPropertyCollection::AddProperty 153ms 0.17% 75.66% 1491ms 1.68% std::type_info::operator== (inline) 66ms 0.074% 75.73% 1473ms 1.65% MutableVertexMesh::CheckForSwapsFromShortEdges 1ms 0.0011% 75.73% 1473ms 1.65% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 75.73% 1473ms 1.65% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 75.73% 1434ms 1.61% VertexMeshWriter::WriteVtkUsingMesh 0 0% 75.73% 1380ms 1.55% tcache_get (inline) 1380ms 1.55% 77.28% 1380ms 1.55% tcache_get_n (inline) 0 0% 77.28% 1341ms 1.51% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 77.28% 1320ms 1.48% OffLatticeSimulation::ApplyBoundaries 0 0% 77.28% 1317ms 1.48% std::_Rb_tree::_Auto_node::_Auto_node (inline) 70ms 0.079% 77.36% 1309ms 1.47% VertexMesh::GetSurfaceAreaOfElement 44ms 0.049% 77.41% 1264ms 1.42% std::_Rb_tree::_M_erase_aux (partial-inline) 68ms 0.076% 77.49% 1249ms 1.40% AbstractCellPopulation::GetLocationIndexUsingCell 1180ms 1.33% 78.81% 1180ms 1.33% std::_Rb_tree_increment 44ms 0.049% 78.86% 1151ms 1.29% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 112ms 0.13% 78.99% 1071ms 1.20% boost::numeric::ublas::vector_reference::operator() (inline) 30ms 0.034% 79.02% 1033ms 1.16% CellPropertyRegistry::Get 0 0% 79.02% 985ms 1.11% CellPropertyCollection::~CellPropertyCollection (inline) 35ms 0.039% 79.06% 968ms 1.09% Node::RemoveElement 29ms 0.033% 79.10% 966ms 1.09% boost::numeric::ublas::detail::expression_type_check (inline) 591ms 0.66% 79.76% 952ms 1.07% std::_Rb_tree::equal_range (inline) 4ms 0.0045% 79.76% 936ms 1.05% std::set::erase (inline) 12ms 0.013% 79.78% 923ms 1.04% MutableElement::RegisterWithEdges (inline) 30ms 0.034% 79.81% 919ms 1.03% Edge::AddElement 164ms 0.18% 80.00% 903ms 1.01% boost::numeric::ublas::detail::equals 870ms 0.98% 80.97% 870ms 0.98% [libstdc++.so.6.0.33] 0 0% 80.97% 849ms 0.95% boost::numeric::ublas::norm_2 (inline) 838ms 0.94% 81.91% 838ms 0.94% std::_Rb_tree_insert_and_rebalance 441ms 0.5% 82.41% 830ms 0.93% boost::numeric::ublas::vector_norm_2::apply 0 0% 82.41% 825ms 0.93% std::__new_allocator::destroy (inline) 0 0% 82.41% 825ms 0.93% std::allocator_traits::destroy (inline) 0 0% 82.41% 818ms 0.92% std::_Rb_tree::_M_destroy_node (inline) 0 0% 82.41% 804ms 0.9% boost::numeric::ublas::c_vector::assign_temporary (inline) 1ms 0.0011% 82.41% 804ms 0.9% boost::numeric::ublas::c_vector::swap (inline) 161ms 0.18% 82.59% 803ms 0.9% std::swap_ranges (inline) 799ms 0.9% 83.49% 799ms 0.9% Node::rGetLocation 0 0% 83.49% 777ms 0.87% std::_Rb_tree::clear (inline) 6ms 0.0067% 83.50% 767ms 0.86% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 83.50% 766ms 0.86% VertexMeshWriter::MakeVtkMesh 582ms 0.65% 84.15% 763ms 0.86% CellPropertyCollection::GetProperty 0 0% 84.15% 757ms 0.85% std::map::clear (inline) 52ms 0.058% 84.21% 726ms 0.82% boost::numeric::ublas::c_vector::operator= (inline) 706ms 0.79% 85.00% 706ms 0.79% tcache_put (inline) 80ms 0.09% 85.09% 664ms 0.75% std::_Rb_tree::find (inline) 48ms 0.054% 85.15% 653ms 0.73% std::less::operator() (inline) 309ms 0.35% 85.49% 648ms 0.73% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 85.49% 642ms 0.72% std::iter_swap (inline) 642ms 0.72% 86.21% 642ms 0.72% std::swap (inline) 0 0% 86.21% 632ms 0.71% boost::numeric::ublas::norm_inf (inline) 231ms 0.26% 86.47% 632ms 0.71% boost::numeric::ublas::vector_norm_inf::apply (inline) 440ms 0.49% 86.97% 605ms 0.68% std::operator< (inline) 594ms 0.67% 87.64% 594ms 0.67% std::vector::size (inline) 85ms 0.096% 87.73% 560ms 0.63% MutableElement::GetNodeLocalIndex 0 0% 87.73% 552ms 0.62% std::_Rb_tree::_Auto_node::_M_insert (inline) 19ms 0.021% 87.75% 552ms 0.62% std::_Rb_tree::_M_insert_node (inline) 1ms 0.0011% 87.75% 551ms 0.62% vtkPolygon::New 3ms 0.0034% 87.76% 549ms 0.62% std::map::find (inline) 0 0% 87.76% 549ms 0.62% vtkPolygon::vtkPolygon 0 0% 87.76% 504ms 0.57% std::_Vector_base::_M_allocate (inline) 9ms 0.01% 87.77% 498ms 0.56% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.77% 498ms 0.56% boost::numeric::ublas::vector::vector (inline) 222ms 0.25% 88.02% 448ms 0.5% Edge::GetMapIndex