File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95564ms, 87.37% of 109380ms total Dropped 1117 nodes (cum <= 546.90ms) flat flat% sum% cum cum% 0 0% 0% 109026ms 99.68% __libc_start_call_main 0 0% 0% 109026ms 99.68% __libc_start_main_impl 0 0% 0% 109026ms 99.68% _start 0 0% 0% 109002ms 99.65% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 109002ms 99.65% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 109002ms 99.65% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 109002ms 99.65% main 0 0% 0% 108958ms 99.61% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108958ms 99.61% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108958ms 99.61% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 3ms 0.0027% 0.0027% 108950ms 99.61% AbstractCellBasedSimulation::Solve 16ms 0.015% 0.017% 56559ms 51.71% OffLatticeSimulation::UpdateCellLocationsAndTopology 22ms 0.02% 0.037% 53372ms 48.80% ForwardEulerNumericalMethod::UpdateAllNodePositions 153ms 0.14% 0.18% 52243ms 47.76% AbstractNumericalMethod::ComputeForcesIncludingDamping 346ms 0.32% 0.49% 40167ms 36.72% NagaiHondaForce::AddForceContribution 3ms 0.0027% 0.5% 39122ms 35.77% AbstractCellBasedSimulation::UpdateCellPopulation 5ms 0.0046% 0.5% 23925ms 21.87% VertexBasedCellPopulation::Update 2ms 0.0018% 0.5% 23772ms 21.73% MutableVertexMesh::ReMesh 14557ms 13.31% 13.81% 23078ms 21.10% Cylindrical2dVertexMesh::GetVectorFromAtoB 87ms 0.08% 13.89% 18031ms 16.48% Cell::ReadyToDivide 55ms 0.05% 13.94% 16735ms 15.30% AbstractPhaseBasedCellCycleModel::ReadyToDivide 353ms 0.32% 14.26% 14516ms 13.27% NagaiHondaForce::GetAdhesionParameter 160ms 0.15% 14.41% 14297ms 13.07% SimpleWntCellCycleModel::UpdateCellCyclePhase 474ms 0.43% 14.84% 13883ms 12.69% boost::numeric::ublas::c_vector::c_vector (partial-inline) 96ms 0.088% 14.93% 13687ms 12.51% CellPropertyCollection::GetPropertiesType (inline) 298ms 0.27% 15.20% 12340ms 11.28% boost::numeric::ublas::vector_assign (inline) 124ms 0.11% 15.32% 11875ms 10.86% MutableVertexMesh::CheckForIntersections 3613ms 3.30% 18.62% 11721ms 10.72% __dynamic_cast 45ms 0.041% 18.66% 11572ms 10.58% AbstractCellProperty::IsSubType (inline) 78ms 0.071% 18.73% 11471ms 10.49% VertexBasedCellPopulation::GetDampingConstant 77ms 0.07% 18.80% 10794ms 9.87% AbstractTargetAreaModifier::UpdateTargetAreas 33ms 0.03% 18.83% 10697ms 9.78% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 36ms 0.033% 18.87% 10446ms 9.55% AbstractCellBasedSimulation::DoCellBirth 1305ms 1.19% 20.06% 10012ms 9.15% std::__new_allocator::allocate (inline) 0 0% 20.06% 9491ms 8.68% std::_Rb_tree::_M_create_node (inline) 362ms 0.33% 20.39% 9483ms 8.67% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 20.39% 9436ms 8.63% std::allocator_traits::allocate (inline) 2746ms 2.51% 22.90% 9302ms 8.50% boost::numeric::ublas::indexing_vector_assign 1280ms 1.17% 24.07% 9116ms 8.33% std::_Rb_tree::_M_erase 34ms 0.031% 24.10% 8875ms 8.11% VertexBasedCellPopulation::GetLocationOfCellCentre 801ms 0.73% 24.83% 8777ms 8.02% operator new 90ms 0.082% 24.92% 8736ms 7.99% Cell::GetMutationState 0 0% 24.92% 8725ms 7.98% std::_Rb_tree::_M_get_node (inline) 813ms 0.74% 25.66% 8652ms 7.91% VertexMesh::ElementIncludesPoint 471ms 0.43% 26.09% 8405ms 7.68% VertexMesh::GetCentroidOfElement 0 0% 26.09% 8357ms 7.64% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 26.09% 8212ms 7.51% std::_Rb_tree::_M_drop_node (inline) 190ms 0.17% 26.26% 8191ms 7.49% std::_Rb_tree::~_Rb_tree (inline) 240ms 0.22% 26.48% 7953ms 7.27% std::__new_allocator::deallocate (inline) 0 0% 26.48% 7947ms 7.27% std::allocator_traits::deallocate (inline) 0 0% 26.48% 7878ms 7.20% std::_Rb_tree::_M_put_node (inline) 0 0% 26.48% 7773ms 7.11% std::set::~set (inline) 3000ms 2.74% 29.23% 7746ms 7.08% __GI___libc_malloc 14ms 0.013% 29.24% 7659ms 7.00% MutableVertexMesh::RemoveDeletedNodesAndElements 1707ms 1.56% 30.80% 7581ms 6.93% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 464ms 0.42% 31.22% 7562ms 6.91% std::map::operator[] (partial-inline) 2594ms 2.37% 33.60% 7505ms 6.86% __GI___libc_free 170ms 0.16% 33.75% 7081ms 6.47% std::_Rb_tree::_Rb_tree (partial-inline) 732ms 0.67% 34.42% 6641ms 6.07% std::_Rb_tree::_M_copy (inline) 16ms 0.015% 34.43% 6619ms 6.05% std::set::set (inline) 6473ms 5.92% 40.35% 6473ms 5.92% __strcmp_avx2 115ms 0.11% 40.46% 6424ms 5.87% SimpleWntCellCycleModel::GetWntLevel 159ms 0.15% 40.60% 6212ms 5.68% WntConcentration::GetWntLevel 5993ms 5.48% 46.08% 5993ms 5.48% boost::numeric::ublas::c_vector::operator() 2388ms 2.18% 48.27% 5889ms 5.38% std::_Rb_tree::_M_lower_bound (inline) 799ms 0.73% 49.00% 5670ms 5.18% std::_Rb_tree::_M_clone_node (inline) 2920ms 2.67% 51.67% 5569ms 5.09% __cxxabiv1::__si_class_type_info::__do_dyncast 13ms 0.012% 51.68% 5378ms 4.92% MutableVertexMesh::RemoveDeletedNodes 2027ms 1.85% 53.53% 5295ms 4.84% boost::numeric::ublas::c_vector::operator[] (inline) 30ms 0.027% 53.56% 5196ms 4.75% EdgeHelper::RemoveDeletedEdges 0 0% 53.56% 5187ms 4.74% std::set::insert (inline) 4521ms 4.13% 57.69% 4902ms 4.48% _int_free 39ms 0.036% 57.73% 4890ms 4.47% EdgeHelper::UpdateEdgesMapKey 0 0% 57.73% 4854ms 4.44% std::_Rb_tree::lower_bound (inline) 0 0% 57.73% 4854ms 4.44% std::map::lower_bound (inline) 1ms 0.00091% 57.73% 4735ms 4.33% AbstractCellBasedSimulation::DoCellRemoval (inline) 195ms 0.18% 57.91% 4635ms 4.24% MutableElement::ResetIndex 496ms 0.45% 58.36% 4493ms 4.11% std::_Rb_tree::_M_insert_ (inline) 122ms 0.11% 58.47% 4304ms 3.93% AbstractCellPopulation::GetCellUsingLocationIndex 122ms 0.11% 58.58% 4180ms 3.82% std::set_intersection (inline) 207ms 0.19% 58.77% 4058ms 3.71% std::__set_intersection 47ms 0.043% 58.82% 3995ms 3.65% Cell::GetCellProliferativeType 73ms 0.067% 58.88% 3992ms 3.65% AbstractCellProperty::IsType (inline) 3876ms 3.54% 62.43% 3876ms 3.54% boost::numeric::ublas::same_impl_ex 16ms 0.015% 62.44% 3570ms 3.26% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 70ms 0.064% 62.50% 3268ms 2.99% Cell::SetCellProliferativeType 2208ms 2.02% 64.52% 3158ms 2.89% _int_malloc 978ms 0.89% 65.42% 3146ms 2.88% AbstractElement::GetNodeLocation 0 0% 65.42% 3131ms 2.86% std::insert_iterator::operator= (inline) 57ms 0.052% 65.47% 2928ms 2.68% std::_Rb_tree::erase 2880ms 2.63% 68.10% 2880ms 2.63% std::_Rb_tree::_S_right (inline) 789ms 0.72% 68.82% 2840ms 2.60% AbstractCellProperty::IsSame 28ms 0.026% 68.85% 2785ms 2.55% CellPropertyCollection::HasProperty 11ms 0.01% 68.86% 2711ms 2.48% std::_Rb_tree::_M_insert_unique_ (inline) 0 0% 68.86% 2700ms 2.47% Cell::HasCellProperty (inline) 187ms 0.17% 69.03% 2622ms 2.40% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.03% 2598ms 2.38% boost::numeric::ublas::c_vector::operator-= (inline) 624ms 0.57% 69.60% 2579ms 2.36% boost::numeric::ublas::vector_binary::size (inline) 0 0% 69.60% 2574ms 2.35% boost::numeric::ublas::c_vector::assign (inline) 238ms 0.22% 69.82% 2538ms 2.32% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.00091% 69.82% 2476ms 2.26% std::_Rb_tree::_M_insert_unique 0 0% 69.82% 2437ms 2.23% AbstractCellPopulation::WriteResultsToFiles 29ms 0.027% 69.85% 2388ms 2.18% Cell::GetCellData 85ms 0.078% 69.92% 2363ms 2.16% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 70ms 0.064% 69.99% 2325ms 2.13% VertexMesh::GetVolumeOfElement 46ms 0.042% 70.03% 2205ms 2.02% std::_Rb_tree::_M_emplace_hint_unique 2ms 0.0018% 70.03% 2116ms 1.93% AbstractCellPopulation::Iterator::operator++ (inline) 146ms 0.13% 70.16% 2110ms 1.93% AbstractCellPopulation::Iterator::IsRealCell (inline) 2ms 0.0018% 70.17% 2090ms 1.91% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 70.17% 2090ms 1.91% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 488ms 0.45% 70.61% 2051ms 1.88% std::type_info::operator== (inline) 2046ms 1.87% 72.48% 2046ms 1.87% std::_Rb_tree_increment 0 0% 72.48% 1996ms 1.82% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00091% 72.48% 1982ms 1.81% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1279ms 1.17% 73.65% 1905ms 1.74% std::_Rb_tree::equal_range (inline) 69ms 0.063% 73.72% 1811ms 1.66% MutableVertexMesh::CheckForSwapsFromShortEdges 1ms 0.00091% 73.72% 1781ms 1.63% VertexMeshWriter::WriteVtkUsingMesh 20ms 0.018% 73.74% 1703ms 1.56% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 36ms 0.033% 73.77% 1659ms 1.52% VertexMesh::GetSurfaceAreaOfElement 47ms 0.043% 73.81% 1551ms 1.42% Node::RemoveElement 79ms 0.072% 73.88% 1514ms 1.38% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 12ms 0.011% 73.89% 1506ms 1.38% std::set::erase (inline) 37ms 0.034% 73.93% 1494ms 1.37% AbstractCellPopulation::GetLocationIndexUsingCell 147ms 0.13% 74.06% 1415ms 1.29% CellPropertyCollection::AddProperty 0 0% 74.06% 1369ms 1.25% tcache_get (inline) 1369ms 1.25% 75.31% 1369ms 1.25% tcache_get_n (inline) 67ms 0.061% 75.38% 1358ms 1.24% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 75.38% 1356ms 1.24% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 75.38% 1308ms 1.20% boost::numeric::ublas::norm_2 (inline) 1ms 0.00091% 75.38% 1298ms 1.19% OffLatticeSimulation::ApplyBoundaries 581ms 0.53% 75.91% 1295ms 1.18% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1284ms 1.17% 77.08% 1284ms 1.17% [libchaste_cell_based.so] 97ms 0.089% 77.17% 1270ms 1.16% std::less::operator() (inline) 33ms 0.03% 77.20% 1231ms 1.13% CellPropertyRegistry::Get 938ms 0.86% 78.06% 1173ms 1.07% std::operator< (inline) 1160ms 1.06% 79.12% 1160ms 1.06% [libchaste_mesh.so] 62ms 0.057% 79.18% 1146ms 1.05% std::_Rb_tree::_M_erase_aux (partial-inline) 0 0% 79.18% 1134ms 1.04% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 79.18% 1129ms 1.03% boost::numeric::ublas::c_vector::assign_temporary (inline) 10ms 0.0091% 79.18% 1129ms 1.03% boost::numeric::ublas::c_vector::swap (inline) 1120ms 1.02% 80.21% 1120ms 1.02% std::_Rb_tree_insert_and_rebalance 86ms 0.079% 80.29% 1119ms 1.02% std::swap_ranges (inline) 0 0% 80.29% 1118ms 1.02% std::_Rb_tree::clear (inline) 3ms 0.0027% 80.29% 1117ms 1.02% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 21ms 0.019% 80.31% 1115ms 1.02% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 80.31% 1104ms 1.01% std::map::clear (inline) 99ms 0.091% 80.40% 1069ms 0.98% std::_Rb_tree::find (inline) 8ms 0.0073% 80.41% 1064ms 0.97% boost::numeric::ublas::detail::expression_type_check (inline) 132ms 0.12% 80.53% 1053ms 0.96% boost::detail::shared_count::~shared_count (inline) 0 0% 80.53% 1053ms 0.96% boost::shared_ptr::~shared_ptr (inline) 200ms 0.18% 80.71% 1044ms 0.95% boost::numeric::ublas::detail::equals 0 0% 80.71% 1033ms 0.94% std::iter_swap (inline) 1033ms 0.94% 81.65% 1033ms 0.94% std::swap (inline) 0 0% 81.65% 908ms 0.83% std::map::find (inline) 857ms 0.78% 82.44% 888ms 0.81% boost::detail::sp_counted_base::release 0 0% 82.44% 867ms 0.79% VertexMeshWriter::MakeVtkMesh 839ms 0.77% 83.21% 839ms 0.77% std::vector::size (inline) 115ms 0.11% 83.31% 831ms 0.76% boost::numeric::ublas::c_vector::operator= (inline) 825ms 0.75% 84.06% 825ms 0.75% Node::rGetLocation 240ms 0.22% 84.28% 818ms 0.75% std::__new_allocator::construct (inline) 0 0% 84.28% 818ms 0.75% std::allocator_traits::construct (inline) 168ms 0.15% 84.44% 811ms 0.74% boost::shared_ptr::shared_ptr (inline) 17ms 0.016% 84.45% 805ms 0.74% MutableElement::RegisterWithEdges (inline) 18ms 0.016% 84.47% 800ms 0.73% Edge::AddElement 0 0% 84.47% 782ms 0.71% boost::numeric::ublas::norm_inf (inline) 411ms 0.38% 84.85% 782ms 0.71% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 84.85% 766ms 0.7% std::_Rb_tree::_M_construct_node (inline) 370ms 0.34% 85.18% 748ms 0.68% Edge::GetMapIndex 0 0% 85.18% 720ms 0.66% CellPropertyCollection::~CellPropertyCollection (inline) 1ms 0.00091% 85.18% 705ms 0.64% std::_Vector_base::_M_allocate (inline) 0 0% 85.18% 690ms 0.63% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 85.18% 686ms 0.63% std::_Rb_tree::_Auto_node::_M_insert (inline) 21ms 0.019% 85.20% 686ms 0.63% std::_Rb_tree::_M_insert_node (inline) 370ms 0.34% 85.54% 685ms 0.63% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 643ms 0.59% 86.13% 643ms 0.59% [libstdc++.so.6.0.33] 606ms 0.55% 86.68% 643ms 0.59% boost::detail::shared_count::shared_count (inline) 120ms 0.11% 86.79% 641ms 0.59% MutableElement::GetNodeLocalIndex 0 0% 86.79% 617ms 0.56% vtkPolygon::New 1ms 0.00091% 86.79% 615ms 0.56% vtkPolygon::vtkPolygon 22ms 0.02% 86.81% 598ms 0.55% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 86.81% 598ms 0.55% boost::numeric::ublas::vector::vector (inline) 8ms 0.0073% 86.82% 585ms 0.53% std::vector::_M_default_append (inline) 27ms 0.025% 86.85% 579ms 0.53% MutableElement::RegisterWithNodes (inline) 571ms 0.52% 87.37% 571ms 0.52% Node::GetIndex