File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 97052ms, 88.05% of 110218ms total Dropped 1142 nodes (cum <= 551.09ms) flat flat% sum% cum cum% 0 0% 0% 109782ms 99.60% __libc_start_call_main 0 0% 0% 109782ms 99.60% __libc_start_main_impl 0 0% 0% 109782ms 99.60% _start 0 0% 0% 109762ms 99.59% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 109762ms 99.59% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 109762ms 99.59% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 109762ms 99.59% main 0 0% 0% 109720ms 99.55% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 109720ms 99.55% CxxTest::TestRunner::runTest (inline) 0 0% 0% 109720ms 99.55% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 3ms 0.0027% 0.0027% 109713ms 99.54% AbstractCellBasedSimulation::Solve 18ms 0.016% 0.019% 56815ms 51.55% OffLatticeSimulation::UpdateCellLocationsAndTopology 22ms 0.02% 0.039% 53338ms 48.39% ForwardEulerNumericalMethod::UpdateAllNodePositions 140ms 0.13% 0.17% 51815ms 47.01% AbstractNumericalMethod::ComputeForcesIncludingDamping 351ms 0.32% 0.48% 39766ms 36.08% NagaiHondaForce::AddForceContribution 2ms 0.0018% 0.49% 39667ms 35.99% AbstractCellBasedSimulation::UpdateCellPopulation 5ms 0.0045% 0.49% 24783ms 22.49% VertexBasedCellPopulation::Update 0 0% 0.49% 24657ms 22.37% MutableVertexMesh::ReMesh 14551ms 13.20% 13.69% 22846ms 20.73% Cylindrical2dVertexMesh::GetVectorFromAtoB 127ms 0.12% 13.81% 17588ms 15.96% Cell::ReadyToDivide 56ms 0.051% 13.86% 16292ms 14.78% AbstractPhaseBasedCellCycleModel::ReadyToDivide 378ms 0.34% 14.20% 14820ms 13.45% NagaiHondaForce::GetAdhesionParameter 455ms 0.41% 14.61% 14231ms 12.91% boost::numeric::ublas::c_vector::c_vector (partial-inline) 135ms 0.12% 14.74% 13959ms 12.66% SimpleWntCellCycleModel::UpdateCellCyclePhase 119ms 0.11% 14.85% 13849ms 12.57% CellPropertyCollection::GetPropertiesType (inline) 405ms 0.37% 15.21% 12656ms 11.48% boost::numeric::ublas::vector_assign (inline) 148ms 0.13% 15.35% 12132ms 11.01% MutableVertexMesh::CheckForIntersections 3184ms 2.89% 18.24% 11564ms 10.49% __dynamic_cast 76ms 0.069% 18.30% 11471ms 10.41% VertexBasedCellPopulation::GetDampingConstant 72ms 0.065% 18.37% 11445ms 10.38% AbstractCellProperty::IsSubType (inline) 70ms 0.064% 18.43% 10706ms 9.71% AbstractTargetAreaModifier::UpdateTargetAreas 70ms 0.064% 18.50% 10591ms 9.61% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 22ms 0.02% 18.52% 10310ms 9.35% AbstractCellBasedSimulation::DoCellBirth 1329ms 1.21% 19.72% 10281ms 9.33% std::__new_allocator::allocate (inline) 0 0% 19.72% 9744ms 8.84% std::_Rb_tree::_M_create_node (inline) 0 0% 19.72% 9741ms 8.84% std::allocator_traits::allocate (inline) 2707ms 2.46% 22.18% 9364ms 8.50% boost::numeric::ublas::indexing_vector_assign 1395ms 1.27% 23.44% 9092ms 8.25% std::_Rb_tree::_M_erase 0 0% 23.44% 9076ms 8.23% std::_Rb_tree::_M_get_node (inline) 856ms 0.78% 24.22% 9069ms 8.23% operator new 800ms 0.73% 24.95% 8962ms 8.13% VertexMesh::ElementIncludesPoint 335ms 0.3% 25.25% 8795ms 7.98% VertexMesh::GetNextEdgeGradientOfElementAtNode 30ms 0.027% 25.28% 8734ms 7.92% VertexBasedCellPopulation::GetLocationOfCellCentre 93ms 0.084% 25.36% 8730ms 7.92% Cell::GetMutationState 0 0% 25.36% 8474ms 7.69% std::_Rb_tree::_Alloc_node::operator() (inline) 520ms 0.47% 25.83% 8327ms 7.56% VertexMesh::GetCentroidOfElement 289ms 0.26% 26.10% 8264ms 7.50% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.10% 8187ms 7.43% std::_Rb_tree::_M_drop_node (inline) 16ms 0.015% 26.11% 8151ms 7.40% MutableVertexMesh::RemoveDeletedNodesAndElements 3206ms 2.91% 29.02% 8036ms 7.29% __GI___libc_malloc 224ms 0.2% 29.22% 7999ms 7.26% std::__new_allocator::deallocate (inline) 0 0% 29.22% 7973ms 7.23% std::allocator_traits::deallocate (inline) 3144ms 2.85% 32.08% 7933ms 7.20% __GI___libc_free 0 0% 32.08% 7871ms 7.14% std::_Rb_tree::_M_put_node (inline) 0 0% 32.08% 7748ms 7.03% std::set::~set (inline) 452ms 0.41% 32.49% 7433ms 6.74% std::map::operator[] (partial-inline) 1447ms 1.31% 33.80% 7135ms 6.47% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 170ms 0.15% 33.95% 7105ms 6.45% std::_Rb_tree::_Rb_tree (partial-inline) 6776ms 6.15% 40.10% 6776ms 6.15% __strcmp_avx2 664ms 0.6% 40.70% 6703ms 6.08% std::_Rb_tree::_M_copy (inline) 13ms 0.012% 40.71% 6604ms 5.99% std::set::set (inline) 115ms 0.1% 40.82% 6367ms 5.78% SimpleWntCellCycleModel::GetWntLevel 155ms 0.14% 40.96% 6168ms 5.60% WntConcentration::GetWntLevel 5986ms 5.43% 46.39% 5986ms 5.43% boost::numeric::ublas::c_vector::operator() 2451ms 2.22% 48.61% 5832ms 5.29% std::_Rb_tree::_M_lower_bound (inline) 2700ms 2.45% 51.06% 5830ms 5.29% __cxxabiv1::__si_class_type_info::__do_dyncast 766ms 0.69% 51.76% 5735ms 5.20% std::_Rb_tree::_M_clone_node (inline) 35ms 0.032% 51.79% 5497ms 4.99% MutableVertexMesh::RemoveDeletedNodes 1ms 0.00091% 51.79% 5412ms 4.91% std::set::insert (inline) 42ms 0.038% 51.83% 5307ms 4.82% EdgeHelper::RemoveDeletedEdges 269ms 0.24% 52.07% 5131ms 4.66% MutableElement::ResetIndex 29ms 0.026% 52.10% 5003ms 4.54% EdgeHelper::UpdateEdgesMapKey 4461ms 4.05% 56.15% 4783ms 4.34% _int_free 1498ms 1.36% 57.51% 4782ms 4.34% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 57.51% 4673ms 4.24% std::_Rb_tree::lower_bound (inline) 0 0% 57.51% 4673ms 4.24% std::map::lower_bound (inline) 547ms 0.5% 58.00% 4585ms 4.16% std::_Rb_tree::_M_insert_ (inline) 1ms 0.00091% 58.00% 4558ms 4.14% AbstractCellBasedSimulation::DoCellRemoval (inline) 99ms 0.09% 58.09% 4533ms 4.11% std::set_intersection (inline) 307ms 0.28% 58.37% 4434ms 4.02% std::__set_intersection 139ms 0.13% 58.50% 4144ms 3.76% AbstractCellPopulation::GetCellUsingLocationIndex 3961ms 3.59% 62.09% 3961ms 3.59% boost::numeric::ublas::same_impl_ex 38ms 0.034% 62.13% 3907ms 3.54% Cell::GetCellProliferativeType 69ms 0.063% 62.19% 3817ms 3.46% AbstractCellProperty::IsType (inline) 11ms 0.01% 62.20% 3475ms 3.15% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 37ms 0.034% 62.23% 3355ms 3.04% std::_Rb_tree::erase 2230ms 2.02% 64.26% 3252ms 2.95% _int_malloc 848ms 0.77% 65.03% 3231ms 2.93% AbstractElement::GetNodeLocation 0 0% 65.03% 3201ms 2.90% std::insert_iterator::operator= (inline) 40ms 0.036% 65.06% 3189ms 2.89% Cell::SetCellProliferativeType 2904ms 2.63% 67.70% 2904ms 2.63% std::_Rb_tree::_S_right (inline) 623ms 0.57% 68.26% 2839ms 2.58% boost::numeric::ublas::vector_binary::size (inline) 3ms 0.0027% 68.26% 2807ms 2.55% std::_Rb_tree::_M_insert_unique_ (inline) 425ms 0.39% 68.65% 2765ms 2.51% std::_Rb_tree_const_iterator::operator++ (inline) 781ms 0.71% 69.36% 2746ms 2.49% AbstractCellProperty::IsSame 37ms 0.034% 69.39% 2652ms 2.41% CellPropertyCollection::HasProperty 2ms 0.0018% 69.39% 2604ms 2.36% std::_Rb_tree::_M_insert_unique 23ms 0.021% 69.42% 2567ms 2.33% Cell::GetCellData 0 0% 69.42% 2555ms 2.32% Cell::HasCellProperty (inline) 0 0% 69.42% 2493ms 2.26% AbstractCellPopulation::WriteResultsToFiles 246ms 0.22% 69.64% 2493ms 2.26% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.64% 2438ms 2.21% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.64% 2419ms 2.19% boost::numeric::ublas::c_vector::assign (inline) 1512ms 1.37% 71.01% 2306ms 2.09% std::_Rb_tree::equal_range (inline) 41ms 0.037% 71.05% 2261ms 2.05% std::_Rb_tree::_M_emplace_hint_unique 105ms 0.095% 71.14% 2241ms 2.03% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 92ms 0.083% 71.23% 2225ms 2.02% VertexMesh::GetVolumeOfElement 3ms 0.0027% 71.23% 2200ms 2.00% AbstractCellPopulation::Iterator::operator++ (inline) 244ms 0.22% 71.45% 2194ms 1.99% AbstractCellPopulation::Iterator::IsRealCell (inline) 2152ms 1.95% 73.40% 2152ms 1.95% std::_Rb_tree_increment 0 0% 73.40% 2066ms 1.87% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00091% 73.40% 2054ms 1.86% VertexBasedCellPopulation::WriteCellVtkResultsToFile 2ms 0.0018% 73.41% 1969ms 1.79% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.41% 1969ms 1.79% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 466ms 0.42% 73.83% 1965ms 1.78% std::type_info::operator== (inline) 0 0% 73.83% 1832ms 1.66% VertexMeshWriter::WriteVtkUsingMesh 77ms 0.07% 73.90% 1814ms 1.65% MutableVertexMesh::CheckForSwapsFromShortEdges 20ms 0.018% 73.92% 1673ms 1.52% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 19ms 0.017% 73.93% 1641ms 1.49% VertexMesh::GetSurfaceAreaOfElement 162ms 0.15% 74.08% 1609ms 1.46% CellPropertyCollection::AddProperty 54ms 0.049% 74.13% 1561ms 1.42% Node::RemoveElement 22ms 0.02% 74.15% 1523ms 1.38% std::set::erase (inline) 28ms 0.025% 74.17% 1511ms 1.37% AbstractCellPopulation::GetLocationIndexUsingCell 106ms 0.096% 74.27% 1497ms 1.36% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 108ms 0.098% 74.37% 1417ms 1.29% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 74.37% 1399ms 1.27% tcache_get (inline) 1399ms 1.27% 75.64% 1399ms 1.27% tcache_get_n (inline) 0 0% 75.64% 1368ms 1.24% boost::numeric::ublas::vector_binary::operator() (inline) 3ms 0.0027% 75.64% 1315ms 1.19% OffLatticeSimulation::ApplyBoundaries 0 0% 75.64% 1270ms 1.15% std::_Rb_tree::_Auto_node::_Auto_node (inline) 89ms 0.081% 75.72% 1222ms 1.11% std::less::operator() (inline) 0 0% 75.72% 1221ms 1.11% boost::numeric::ublas::norm_2 (inline) 553ms 0.5% 76.22% 1212ms 1.10% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 72ms 0.065% 76.29% 1199ms 1.09% std::_Rb_tree::_M_erase_aux (partial-inline) 1178ms 1.07% 77.36% 1178ms 1.07% Node::rGetLocation 1156ms 1.05% 78.41% 1156ms 1.05% [libchaste_cell_based.so] 902ms 0.82% 79.22% 1133ms 1.03% std::operator< (inline) 1ms 0.00091% 79.23% 1120ms 1.02% std::_Rb_tree::clear (inline) 1116ms 1.01% 80.24% 1116ms 1.01% std::_Rb_tree_insert_and_rebalance 17ms 0.015% 80.25% 1115ms 1.01% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 22ms 0.02% 80.27% 1113ms 1.01% CellPropertyRegistry::Get 87ms 0.079% 80.35% 1108ms 1.01% std::_Rb_tree::find (inline) 0 0% 80.35% 1106ms 1.00% std::map::clear (inline) 5ms 0.0045% 80.36% 1026ms 0.93% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 487ms 0.44% 80.80% 1004ms 0.91% Edge::GetMapIndex 140ms 0.13% 80.93% 988ms 0.9% boost::detail::shared_count::~shared_count (inline) 0 0% 80.93% 988ms 0.9% boost::shared_ptr::~shared_ptr (inline) 988ms 0.9% 81.82% 988ms 0.9% std::vector::size (inline) 24ms 0.022% 81.84% 977ms 0.89% boost::numeric::ublas::detail::expression_type_check (inline) 151ms 0.14% 81.98% 945ms 0.86% boost::numeric::ublas::detail::equals 943ms 0.86% 82.84% 943ms 0.86% [libchaste_mesh.so] 0 0% 82.84% 913ms 0.83% std::map::find (inline) 0 0% 82.84% 898ms 0.81% boost::numeric::ublas::c_vector::assign_temporary (inline) 10ms 0.0091% 82.85% 898ms 0.81% boost::numeric::ublas::c_vector::swap (inline) 81ms 0.073% 82.92% 888ms 0.81% std::swap_ranges (inline) 2ms 0.0018% 82.92% 847ms 0.77% VertexMeshWriter::MakeVtkMesh 812ms 0.74% 83.66% 820ms 0.74% boost::detail::sp_counted_base::release 0 0% 83.66% 807ms 0.73% std::iter_swap (inline) 807ms 0.73% 84.39% 807ms 0.73% std::swap (inline) 155ms 0.14% 84.53% 784ms 0.71% boost::shared_ptr::shared_ptr (inline) 95ms 0.086% 84.62% 777ms 0.7% MutableElement::GetNodeLocalIndex 19ms 0.017% 84.63% 775ms 0.7% MutableElement::RegisterWithEdges (inline) 29ms 0.026% 84.66% 765ms 0.69% Edge::AddElement 91ms 0.083% 84.74% 748ms 0.68% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 84.74% 748ms 0.68% boost::numeric::ublas::norm_inf (inline) 400ms 0.36% 85.11% 748ms 0.68% boost::numeric::ublas::vector_norm_inf::apply (inline) 112ms 0.1% 85.21% 735ms 0.67% std::__new_allocator::construct (inline) 0 0% 85.21% 735ms 0.67% std::allocator_traits::construct (inline) 0 0% 85.21% 723ms 0.66% CellPropertyCollection::~CellPropertyCollection (inline) 433ms 0.39% 85.60% 714ms 0.65% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 13ms 0.012% 85.61% 695ms 0.63% AbstractNumericalMethod::DetectStepSizeExceptions 90ms 0.082% 85.69% 682ms 0.62% VertexBasedCellPopulation::CheckForStepSizeException 672ms 0.61% 86.30% 672ms 0.61% Node::GetIndex 0 0% 86.30% 668ms 0.61% std::_Rb_tree::_Auto_node::_M_insert (inline) 0 0% 86.30% 668ms 0.61% std::_Rb_tree::_M_construct_node (inline) 25ms 0.023% 86.33% 668ms 0.61% std::_Rb_tree::_M_insert_node (inline) 1ms 0.00091% 86.33% 661ms 0.6% std::_Vector_base::_M_allocate (inline) 592ms 0.54% 86.86% 629ms 0.57% boost::detail::shared_count::shared_count (inline) 0 0% 86.86% 608ms 0.55% vtkPolygon::New 1ms 0.00091% 86.87% 608ms 0.55% vtkPolygon::vtkPolygon 0 0% 86.87% 584ms 0.53% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 581ms 0.53% 87.39% 581ms 0.53% [libstdc++.so.6.0.33] 576ms 0.52% 87.91% 576ms 0.52% operator delete 83ms 0.075% 87.99% 574ms 0.52% std::_Rb_tree::_M_upper_bound (inline) 33ms 0.03% 88.02% 573ms 0.52% MutableElement::RegisterWithNodes (inline) 30ms 0.027% 88.05% 570ms 0.52% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 88.05% 570ms 0.52% boost::numeric::ublas::vector::vector (inline) 8ms 0.0073% 88.05% 552ms 0.5% std::vector::_M_default_append (inline)