File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96503ms, 87.89% of 109804ms total Dropped 1138 nodes (cum <= 549.02ms) flat flat% sum% cum cum% 0 0% 0% 109402ms 99.63% __libc_start_call_main 0 0% 0% 109402ms 99.63% __libc_start_main_impl 0 0% 0% 109402ms 99.63% _start 0 0% 0% 109380ms 99.61% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 109380ms 99.61% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 109380ms 99.61% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 109380ms 99.61% main 0 0% 0% 109337ms 99.57% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 109337ms 99.57% CxxTest::TestRunner::runTest (inline) 0 0% 0% 109337ms 99.57% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 5ms 0.0046% 0.0046% 109329ms 99.57% AbstractCellBasedSimulation::Solve 18ms 0.016% 0.021% 57266ms 52.15% OffLatticeSimulation::UpdateCellLocationsAndTopology 9ms 0.0082% 0.029% 53983ms 49.16% ForwardEulerNumericalMethod::UpdateAllNodePositions 133ms 0.12% 0.15% 52843ms 48.12% AbstractNumericalMethod::ComputeForcesIncludingDamping 283ms 0.26% 0.41% 40815ms 37.17% NagaiHondaForce::AddForceContribution 2ms 0.0018% 0.41% 38895ms 35.42% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00091% 0.41% 24006ms 21.86% VertexBasedCellPopulation::Update 14756ms 13.44% 13.85% 23873ms 21.74% Cylindrical2dVertexMesh::GetVectorFromAtoB 2ms 0.0018% 13.85% 23853ms 21.72% MutableVertexMesh::ReMesh 113ms 0.1% 13.95% 17626ms 16.05% Cell::ReadyToDivide 73ms 0.066% 14.02% 16314ms 14.86% AbstractPhaseBasedCellCycleModel::ReadyToDivide 380ms 0.35% 14.37% 15021ms 13.68% NagaiHondaForce::GetAdhesionParameter 453ms 0.41% 14.78% 14167ms 12.90% boost::numeric::ublas::c_vector::c_vector (partial-inline) 178ms 0.16% 14.94% 14078ms 12.82% SimpleWntCellCycleModel::UpdateCellCyclePhase 112ms 0.1% 15.04% 13722ms 12.50% CellPropertyCollection::GetPropertiesType (inline) 223ms 0.2% 15.25% 12497ms 11.38% boost::numeric::ublas::vector_assign (inline) 139ms 0.13% 15.37% 11831ms 10.77% MutableVertexMesh::CheckForIntersections 3427ms 3.12% 18.49% 11695ms 10.65% __dynamic_cast 40ms 0.036% 18.53% 11552ms 10.52% AbstractCellProperty::IsSubType (inline) 79ms 0.072% 18.60% 11497ms 10.47% VertexBasedCellPopulation::GetDampingConstant 66ms 0.06% 18.66% 10628ms 9.68% AbstractTargetAreaModifier::UpdateTargetAreas 46ms 0.042% 18.70% 10544ms 9.60% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 30ms 0.027% 18.73% 10180ms 9.27% AbstractCellBasedSimulation::DoCellBirth 1295ms 1.18% 19.91% 10124ms 9.22% std::__new_allocator::allocate (inline) 318ms 0.29% 20.20% 9650ms 8.79% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 20.20% 9577ms 8.72% std::_Rb_tree::_M_create_node (inline) 2843ms 2.59% 22.79% 9542ms 8.69% boost::numeric::ublas::indexing_vector_assign 0 0% 22.79% 9515ms 8.67% std::allocator_traits::allocate (inline) 1335ms 1.22% 24.01% 9485ms 8.64% std::_Rb_tree::_M_erase 746ms 0.68% 24.68% 8861ms 8.07% operator new 85ms 0.077% 24.76% 8807ms 8.02% Cell::GetMutationState 38ms 0.035% 24.80% 8805ms 8.02% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 24.80% 8773ms 7.99% std::_Rb_tree::_M_get_node (inline) 847ms 0.77% 25.57% 8619ms 7.85% VertexMesh::ElementIncludesPoint 225ms 0.2% 25.77% 8606ms 7.84% std::_Rb_tree::~_Rb_tree (inline) 0 0% 25.77% 8519ms 7.76% std::_Rb_tree::_M_drop_node (inline) 0 0% 25.77% 8501ms 7.74% std::_Rb_tree::_Alloc_node::operator() (inline) 451ms 0.41% 26.18% 8354ms 7.61% VertexMesh::GetCentroidOfElement 171ms 0.16% 26.34% 8259ms 7.52% std::__new_allocator::deallocate (inline) 0 0% 26.34% 8252ms 7.52% std::allocator_traits::deallocate (inline) 0 0% 26.34% 8189ms 7.46% std::_Rb_tree::_M_put_node (inline) 0 0% 26.34% 8159ms 7.43% std::set::~set (inline) 1535ms 1.40% 27.74% 7972ms 7.26% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 3071ms 2.80% 30.53% 7897ms 7.19% __GI___libc_malloc 3136ms 2.86% 33.39% 7880ms 7.18% __GI___libc_free 13ms 0.012% 33.40% 7718ms 7.03% MutableVertexMesh::RemoveDeletedNodesAndElements 442ms 0.4% 33.80% 7476ms 6.81% std::map::operator[] (partial-inline) 177ms 0.16% 33.97% 7240ms 6.59% std::_Rb_tree::_Rb_tree (partial-inline) 25ms 0.023% 33.99% 6795ms 6.19% std::set::set (inline) 726ms 0.66% 34.65% 6789ms 6.18% std::_Rb_tree::_M_copy (inline) 6579ms 5.99% 40.64% 6579ms 5.99% __strcmp_avx2 136ms 0.12% 40.77% 6392ms 5.82% SimpleWntCellCycleModel::GetWntLevel 6225ms 5.67% 46.43% 6225ms 5.67% boost::numeric::ublas::c_vector::operator() 147ms 0.13% 46.57% 6168ms 5.62% WntConcentration::GetWntLevel 2484ms 2.26% 48.83% 5869ms 5.34% std::_Rb_tree::_M_lower_bound (inline) 803ms 0.73% 49.56% 5785ms 5.27% std::_Rb_tree::_M_clone_node (inline) 2895ms 2.64% 52.20% 5568ms 5.07% __cxxabiv1::__si_class_type_info::__do_dyncast 1963ms 1.79% 53.99% 5391ms 4.91% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 53.99% 5360ms 4.88% std::set::insert (inline) 21ms 0.019% 54.01% 5354ms 4.88% MutableVertexMesh::RemoveDeletedNodes 33ms 0.03% 54.04% 5163ms 4.70% EdgeHelper::RemoveDeletedEdges 0 0% 54.04% 4862ms 4.43% std::_Rb_tree::lower_bound (inline) 0 0% 54.04% 4862ms 4.43% std::map::lower_bound (inline) 35ms 0.032% 54.07% 4826ms 4.40% EdgeHelper::UpdateEdgesMapKey 211ms 0.19% 54.26% 4743ms 4.32% MutableElement::ResetIndex 4233ms 3.86% 58.11% 4731ms 4.31% _int_free 1ms 0.00091% 58.12% 4693ms 4.27% AbstractCellBasedSimulation::DoCellRemoval (inline) 468ms 0.43% 58.54% 4504ms 4.10% std::_Rb_tree::_M_insert_ (inline) 133ms 0.12% 58.66% 4313ms 3.93% AbstractCellPopulation::GetCellUsingLocationIndex 129ms 0.12% 58.78% 4287ms 3.90% std::set_intersection (inline) 206ms 0.19% 58.97% 4158ms 3.79% std::__set_intersection 3875ms 3.53% 62.50% 3875ms 3.53% boost::numeric::ublas::same_impl_ex 39ms 0.036% 62.53% 3855ms 3.51% Cell::GetCellProliferativeType 59ms 0.054% 62.59% 3779ms 3.44% AbstractCellProperty::IsType (inline) 19ms 0.017% 62.60% 3521ms 3.21% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.60% 3181ms 2.90% std::insert_iterator::operator= (inline) 2203ms 2.01% 64.61% 3161ms 2.88% _int_malloc 48ms 0.044% 64.65% 3124ms 2.85% Cell::SetCellProliferativeType 71ms 0.065% 64.72% 3033ms 2.76% std::_Rb_tree::erase 836ms 0.76% 65.48% 2943ms 2.68% AbstractElement::GetNodeLocation 2899ms 2.64% 68.12% 2899ms 2.64% std::_Rb_tree::_S_right (inline) 795ms 0.72% 68.84% 2870ms 2.61% boost::numeric::ublas::vector_binary::size (inline) 4ms 0.0036% 68.85% 2799ms 2.55% std::_Rb_tree::_M_insert_unique_ (inline) 30ms 0.027% 68.87% 2719ms 2.48% CellPropertyCollection::HasProperty 217ms 0.2% 69.07% 2705ms 2.46% VertexMesh::GetAreaGradientOfElementAtNode 690ms 0.63% 69.70% 2667ms 2.43% AbstractCellProperty::IsSame 0 0% 69.70% 2617ms 2.38% Cell::HasCellProperty (inline) 0 0% 69.70% 2607ms 2.37% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.70% 2561ms 2.33% std::_Rb_tree::_M_insert_unique 244ms 0.22% 69.92% 2528ms 2.30% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.00091% 69.92% 2498ms 2.27% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.92% 2477ms 2.26% boost::numeric::ublas::c_vector::assign (inline) 47ms 0.043% 69.97% 2444ms 2.23% Cell::GetCellData 84ms 0.076% 70.04% 2278ms 2.07% VertexMesh::GetVolumeOfElement 11ms 0.01% 70.05% 2153ms 1.96% AbstractCellPopulation::Iterator::operator++ (inline) 46ms 0.042% 70.09% 2152ms 1.96% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 180ms 0.16% 70.26% 2145ms 1.95% AbstractCellPopulation::Iterator::IsRealCell (inline) 4ms 0.0036% 70.26% 2123ms 1.93% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 70.26% 2123ms 1.93% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 39ms 0.036% 70.30% 2113ms 1.92% std::_Rb_tree::_M_emplace_hint_unique 0 0% 70.30% 2041ms 1.86% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00091% 70.30% 2033ms 1.85% VertexBasedCellPopulation::WriteCellVtkResultsToFile 2007ms 1.83% 72.13% 2007ms 1.83% std::_Rb_tree_increment 498ms 0.45% 72.58% 1977ms 1.80% std::type_info::operator== (inline) 1300ms 1.18% 73.76% 1970ms 1.79% std::_Rb_tree::equal_range (inline) 68ms 0.062% 73.83% 1862ms 1.70% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 73.83% 1824ms 1.66% VertexMeshWriter::WriteVtkUsingMesh 29ms 0.026% 73.85% 1683ms 1.53% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 43ms 0.039% 73.89% 1652ms 1.50% VertexMesh::GetSurfaceAreaOfElement 42ms 0.038% 73.93% 1496ms 1.36% Node::RemoveElement 145ms 0.13% 74.06% 1487ms 1.35% CellPropertyCollection::AddProperty 42ms 0.038% 74.10% 1484ms 1.35% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 74.10% 1473ms 1.34% tcache_get (inline) 1473ms 1.34% 75.44% 1473ms 1.34% tcache_get_n (inline) 79ms 0.072% 75.51% 1464ms 1.33% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 10ms 0.0091% 75.52% 1458ms 1.33% std::set::erase (inline) 71ms 0.065% 75.59% 1412ms 1.29% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 75.59% 1381ms 1.26% boost::numeric::ublas::vector_binary::operator() (inline) 1369ms 1.25% 76.83% 1369ms 1.25% [libchaste_cell_based.so] 0 0% 76.83% 1363ms 1.24% boost::numeric::ublas::norm_2 (inline) 588ms 0.54% 77.37% 1349ms 1.23% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 2ms 0.0018% 77.37% 1314ms 1.20% OffLatticeSimulation::ApplyBoundaries 44ms 0.04% 77.41% 1209ms 1.10% std::less::operator() (inline) 61ms 0.056% 77.47% 1181ms 1.08% std::_Rb_tree::_M_erase_aux (partial-inline) 960ms 0.87% 78.34% 1165ms 1.06% std::operator< (inline) 28ms 0.025% 78.37% 1129ms 1.03% CellPropertyRegistry::Get 6ms 0.0055% 78.37% 1127ms 1.03% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 78.37% 1115ms 1.02% boost::numeric::ublas::c_vector::assign_temporary (inline) 12ms 0.011% 78.38% 1115ms 1.02% boost::numeric::ublas::c_vector::swap (inline) 19ms 0.017% 78.40% 1112ms 1.01% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 78.40% 1112ms 1.01% std::_Rb_tree::clear (inline) 1109ms 1.01% 79.41% 1109ms 1.01% std::_Rb_tree_insert_and_rebalance 60ms 0.055% 79.47% 1103ms 1.00% std::swap_ranges (inline) 0 0% 79.47% 1097ms 1% std::map::clear (inline) 0 0% 79.47% 1076ms 0.98% std::_Rb_tree::_Auto_node::_Auto_node (inline) 136ms 0.12% 79.59% 1054ms 0.96% boost::detail::shared_count::~shared_count (inline) 0 0% 79.59% 1054ms 0.96% boost::shared_ptr::~shared_ptr (inline) 0 0% 79.59% 1043ms 0.95% std::iter_swap (inline) 1043ms 0.95% 80.54% 1043ms 0.95% std::swap (inline) 14ms 0.013% 80.55% 1023ms 0.93% boost::numeric::ublas::detail::expression_type_check (inline) 94ms 0.086% 80.64% 1015ms 0.92% std::_Rb_tree::find (inline) 187ms 0.17% 80.81% 998ms 0.91% boost::numeric::ublas::detail::equals 950ms 0.87% 81.67% 950ms 0.87% Node::rGetLocation 843ms 0.77% 82.44% 881ms 0.8% boost::detail::sp_counted_base::release 878ms 0.8% 83.24% 878ms 0.8% std::vector::size (inline) 1ms 0.00091% 83.24% 873ms 0.8% VertexMeshWriter::MakeVtkMesh 236ms 0.21% 83.46% 865ms 0.79% std::__new_allocator::construct (inline) 0 0% 83.46% 865ms 0.79% std::allocator_traits::construct (inline) 0 0% 83.46% 863ms 0.79% std::map::find (inline) 95ms 0.087% 83.54% 831ms 0.76% boost::numeric::ublas::c_vector::operator= (inline) 807ms 0.73% 84.28% 807ms 0.73% [libchaste_mesh.so] 0 0% 84.28% 804ms 0.73% std::_Rb_tree::_M_construct_node (inline) 19ms 0.017% 84.29% 802ms 0.73% Edge::AddElement 23ms 0.021% 84.32% 800ms 0.73% MutableElement::RegisterWithEdges (inline) 178ms 0.16% 84.48% 787ms 0.72% boost::shared_ptr::shared_ptr (inline) 442ms 0.4% 84.88% 763ms 0.69% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 84.88% 761ms 0.69% boost::numeric::ublas::norm_inf (inline) 382ms 0.35% 85.23% 761ms 0.69% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 85.23% 759ms 0.69% CellPropertyCollection::~CellPropertyCollection (inline) 384ms 0.35% 85.58% 749ms 0.68% Edge::GetMapIndex 0 0% 85.58% 740ms 0.67% std::_Vector_base::_M_allocate (inline) 0 0% 85.58% 693ms 0.63% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 85.58% 668ms 0.61% std::_Rb_tree::_Auto_node::_M_insert (inline) 14ms 0.013% 85.59% 668ms 0.61% std::_Rb_tree::_M_insert_node (inline) 127ms 0.12% 85.71% 661ms 0.6% MutableElement::GetNodeLocalIndex 31ms 0.028% 85.73% 640ms 0.58% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 85.73% 640ms 0.58% boost::numeric::ublas::vector::vector (inline) 0 0% 85.73% 621ms 0.57% vtkPolygon::New 0 0% 85.73% 621ms 0.57% vtkPolygon::vtkPolygon 7ms 0.0064% 85.74% 614ms 0.56% std::vector::_M_default_append (inline) 579ms 0.53% 86.27% 609ms 0.55% boost::detail::shared_count::shared_count (inline) 583ms 0.53% 86.80% 583ms 0.53% tcache_put (inline) 42ms 0.038% 86.84% 580ms 0.53% MutableElement::RegisterWithNodes (inline) 579ms 0.53% 87.36% 579ms 0.53% [libstdc++.so.6.0.33] 573ms 0.52% 87.89% 573ms 0.52% Node::GetIndex