File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 101122ms, 88.04% of 114860ms total Dropped 1089 nodes (cum <= 574.30ms) flat flat% sum% cum cum% 0 0% 0% 114570ms 99.75% __libc_start_call_main 0 0% 0% 114570ms 99.75% __libc_start_main_impl 0 0% 0% 114570ms 99.75% _start 0 0% 0% 114552ms 99.73% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 114552ms 99.73% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 114552ms 99.73% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 114552ms 99.73% main 0 0% 0% 114516ms 99.70% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 114516ms 99.70% CxxTest::TestRunner::runTest (inline) 0 0% 0% 114516ms 99.70% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 3ms 0.0026% 0.0026% 114508ms 99.69% AbstractCellBasedSimulation::Solve 19ms 0.017% 0.019% 61296ms 53.37% OffLatticeSimulation::UpdateCellLocationsAndTopology 30ms 0.026% 0.045% 57933ms 50.44% ForwardEulerNumericalMethod::UpdateAllNodePositions 105ms 0.091% 0.14% 56994ms 49.62% AbstractNumericalMethod::ComputeForcesIncludingDamping 622ms 0.54% 0.68% 45421ms 39.54% NagaiHondaForce::AddForceContribution 1ms 0.00087% 0.68% 38790ms 33.77% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00087% 0.68% 22517ms 19.60% VertexBasedCellPopulation::Update 2ms 0.0017% 0.68% 22401ms 19.50% MutableVertexMesh::ReMesh 10117ms 8.81% 9.49% 20578ms 17.92% Cylindrical2dVertexMesh::GetVectorFromAtoB 70ms 0.061% 9.55% 20008ms 17.42% Cell::ReadyToDivide 70ms 0.061% 9.61% 18853ms 16.41% AbstractPhaseBasedCellCycleModel::ReadyToDivide 394ms 0.34% 9.95% 17912ms 15.59% boost::numeric::ublas::c_vector::c_vector (partial-inline) 92ms 0.08% 10.03% 17409ms 15.16% NagaiHondaForce::GetAdhesionParameter 88ms 0.077% 10.11% 16278ms 14.17% SimpleWntCellCycleModel::UpdateCellCyclePhase 488ms 0.42% 10.54% 15994ms 13.92% boost::numeric::ublas::vector_assign (inline) 1169ms 1.02% 11.55% 14747ms 12.84% std::__new_allocator::allocate (inline) 0 0% 11.55% 14047ms 12.23% std::allocator_traits::allocate (inline) 65ms 0.057% 11.61% 13830ms 12.04% CellPropertyCollection::GetPropertiesType (inline) 0 0% 11.61% 13754ms 11.97% std::_Rb_tree::_M_create_node (inline) 826ms 0.72% 12.33% 13502ms 11.76% operator new 0 0% 12.33% 13283ms 11.56% std::_Rb_tree::_M_get_node (inline) 0 0% 12.33% 12080ms 10.52% std::_Rb_tree::_Alloc_node::operator() (inline) 4525ms 3.94% 16.27% 12070ms 10.51% __GI___libc_malloc 52ms 0.045% 16.31% 11868ms 10.33% AbstractTargetAreaModifier::UpdateTargetAreas 13ms 0.011% 16.33% 11770ms 10.25% AbstractCellBasedSimulation::DoCellBirth 59ms 0.051% 16.38% 11741ms 10.22% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 2787ms 2.43% 18.80% 11702ms 10.19% boost::numeric::ublas::indexing_vector_assign 85ms 0.074% 18.88% 11126ms 9.69% VertexBasedCellPopulation::GetDampingConstant 127ms 0.11% 18.99% 11004ms 9.58% AbstractCellProperty::IsSubType (inline) 3492ms 3.04% 22.03% 10891ms 9.48% __dynamic_cast 164ms 0.14% 22.17% 10597ms 9.23% MutableVertexMesh::CheckForIntersections 508ms 0.44% 22.61% 9608ms 8.36% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 22.61% 9570ms 8.33% std::_Rb_tree::_M_drop_node (inline) 1054ms 0.92% 23.53% 9491ms 8.26% std::_Rb_tree::_M_erase 68ms 0.059% 23.59% 9359ms 8.15% VertexBasedCellPopulation::GetLocationOfCellCentre 853ms 0.74% 24.33% 9036ms 7.87% VertexMesh::GetCentroidOfElement 335ms 0.29% 24.62% 8987ms 7.82% std::_Rb_tree::~_Rb_tree (inline) 168ms 0.15% 24.77% 8728ms 7.60% std::__new_allocator::deallocate (inline) 0 0% 24.77% 8726ms 7.60% std::allocator_traits::deallocate (inline) 0 0% 24.77% 8650ms 7.53% std::_Rb_tree::_M_put_node (inline) 2708ms 2.36% 27.13% 8643ms 7.52% __GI___libc_free 0 0% 27.13% 8611ms 7.50% std::set::~set (inline) 53ms 0.046% 27.17% 8526ms 7.42% Cell::GetMutationState 73ms 0.064% 27.24% 8182ms 7.12% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 27.24% 8182ms 7.12% std::set::insert (inline) 641ms 0.56% 27.80% 7945ms 6.92% std::_Rb_tree::_M_copy (inline) 693ms 0.6% 28.40% 7935ms 6.91% VertexMesh::ElementIncludesPoint 663ms 0.58% 28.98% 7903ms 6.88% std::map::operator[] (partial-inline) 7825ms 6.81% 35.79% 7825ms 6.81% boost::numeric::ublas::c_vector::operator() 18ms 0.016% 35.81% 7805ms 6.80% MutableVertexMesh::RemoveDeletedNodesAndElements 25ms 0.022% 35.83% 7679ms 6.69% std::set::set (inline) 853ms 0.74% 36.57% 7360ms 6.41% std::_Rb_tree::_M_insert_ (inline) 154ms 0.13% 36.70% 7283ms 6.34% SimpleWntCellCycleModel::GetWntLevel 914ms 0.8% 37.50% 7010ms 6.10% std::_Rb_tree::_M_clone_node (inline) 133ms 0.12% 37.62% 6991ms 6.09% WntConcentration::GetWntLevel 36ms 0.031% 37.65% 6262ms 5.45% std::set_intersection (inline) 880ms 0.77% 38.41% 6232ms 5.43% AbstractMesh::GetDistanceBetweenNodes 186ms 0.16% 38.57% 6226ms 5.42% std::__set_intersection 5058ms 4.40% 42.98% 5741ms 5.00% _int_free 1008ms 0.88% 43.86% 5551ms 4.83% boost::numeric::ublas::c_vector::operator[] (inline) 5440ms 4.74% 48.59% 5440ms 4.74% __strcmp_evex 4256ms 3.71% 52.30% 5314ms 4.63% _int_malloc 2020ms 1.76% 54.06% 5232ms 4.56% std::_Rb_tree::_M_lower_bound (inline) 20ms 0.017% 54.07% 5226ms 4.55% MutableVertexMesh::RemoveDeletedNodes 2503ms 2.18% 56.25% 5189ms 4.52% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 56.25% 5099ms 4.44% std::insert_iterator::operator= (inline) 68ms 0.059% 56.31% 5089ms 4.43% EdgeHelper::RemoveDeletedEdges 4948ms 4.31% 60.62% 4948ms 4.31% boost::numeric::ublas::same_impl_ex 147ms 0.13% 60.75% 4889ms 4.26% MutableElement::ResetIndex 12ms 0.01% 60.76% 4819ms 4.20% EdgeHelper::UpdateEdgesMapKey 0 0% 60.76% 4784ms 4.17% std::_Rb_tree::_M_insert_unique_ (inline) 23ms 0.02% 60.78% 4626ms 4.03% Cell::GetCellProliferativeType 96ms 0.084% 60.86% 4573ms 3.98% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 60.86% 4494ms 3.91% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 60.86% 4439ms 3.86% std::_Rb_tree::lower_bound (inline) 0 0% 60.86% 4439ms 3.86% std::map::lower_bound (inline) 197ms 0.17% 61.03% 3935ms 3.43% AbstractCellProperty::IsType (inline) 90ms 0.078% 61.11% 3737ms 3.25% Cell::SetCellProliferativeType 818ms 0.71% 61.82% 3602ms 3.14% AbstractElement::GetNodeLocation 3601ms 3.14% 64.96% 3601ms 3.14% [libchaste_cell_based.so] 868ms 0.76% 65.71% 3434ms 2.99% boost::numeric::ublas::vector_binary::size (inline) 0 0% 65.71% 3398ms 2.96% std::_Rb_tree::_M_insert_unique (inline) 38ms 0.033% 65.75% 3379ms 2.94% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 65.75% 3190ms 2.78% boost::numeric::ublas::c_vector::assign (inline) 397ms 0.35% 66.09% 2960ms 2.58% std::_Rb_tree_const_iterator::operator++ (inline) 344ms 0.3% 66.39% 2881ms 2.51% VertexMesh::GetAreaGradientOfElementAtNode 172ms 0.15% 66.54% 2860ms 2.49% boost::detail::shared_count::~shared_count (inline) 0 0% 66.54% 2860ms 2.49% boost::shared_ptr::~shared_ptr (inline) 52ms 0.045% 66.59% 2853ms 2.48% std::_Rb_tree::erase 38ms 0.033% 66.62% 2749ms 2.39% std::_Rb_tree::_M_emplace_hint_unique 2593ms 2.26% 68.88% 2631ms 2.29% boost::detail::sp_counted_base::release 17ms 0.015% 68.89% 2628ms 2.29% Cell::GetCellData 2619ms 2.28% 71.17% 2619ms 2.28% std::_Rb_tree::_S_right (inline) 0 0% 71.17% 2579ms 2.25% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 71.17% 2520ms 2.19% AbstractCellPopulation::WriteResultsToFiles 33ms 0.029% 71.20% 2514ms 2.19% CellPropertyCollection::HasProperty 12ms 0.01% 71.21% 2507ms 2.18% AbstractCellPopulation::Iterator::operator++ (inline) 677ms 0.59% 71.80% 2506ms 2.18% AbstractCellProperty::IsSame 41ms 0.036% 71.84% 2479ms 2.16% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 199ms 0.17% 72.01% 2473ms 2.15% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 72.01% 2434ms 2.12% Cell::HasCellProperty (inline) 2402ms 2.09% 74.10% 2402ms 2.09% [libchaste_mesh.so] 147ms 0.13% 74.23% 2194ms 1.91% VertexMesh::GetVolumeOfElement 1ms 0.00087% 74.23% 2075ms 1.81% VertexBasedCellPopulation::WriteVtkResultsToFile 2ms 0.0017% 74.23% 2060ms 1.79% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1ms 0.00087% 74.23% 1958ms 1.70% tcache_get (inline) 1957ms 1.70% 75.94% 1957ms 1.70% tcache_get_n (inline) 142ms 0.12% 76.06% 1921ms 1.67% CellPropertyCollection::AddProperty 0 0% 76.06% 1900ms 1.65% boost::numeric::ublas::vector_binary::operator() (inline) 29ms 0.025% 76.09% 1894ms 1.65% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 15ms 0.013% 76.10% 1892ms 1.65% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 76.10% 1892ms 1.65% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 171ms 0.15% 76.25% 1888ms 1.64% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 76.25% 1886ms 1.64% VertexMeshWriter::WriteVtkUsingMesh 1838ms 1.60% 77.85% 1838ms 1.60% std::_Rb_tree_increment 445ms 0.39% 78.24% 1829ms 1.59% std::type_info::operator== (inline) 80ms 0.07% 78.31% 1682ms 1.46% std::_Rb_tree::_M_erase_aux (partial-inline) 0 0% 78.31% 1674ms 1.46% std::_Rb_tree::_Auto_node::_Auto_node (inline) 219ms 0.19% 78.50% 1662ms 1.45% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 94ms 0.082% 78.58% 1627ms 1.42% MutableVertexMesh::CheckForSwapsFromShortEdges 68ms 0.059% 78.64% 1494ms 1.30% VertexMesh::GetSurfaceAreaOfElement 813ms 0.71% 79.35% 1433ms 1.25% std::_Rb_tree::equal_range (inline) 72ms 0.063% 79.41% 1389ms 1.21% AbstractCellPopulation::GetLocationIndexUsingCell 1376ms 1.20% 80.61% 1376ms 1.20% [libstdc++.so.6.0.33] 30ms 0.026% 80.63% 1348ms 1.17% Node::RemoveElement 9ms 0.0078% 80.64% 1318ms 1.15% std::set::erase (inline) 1ms 0.00087% 80.64% 1304ms 1.14% OffLatticeSimulation::ApplyBoundaries 66ms 0.057% 80.70% 1288ms 1.12% CellPropertyRegistry::Get 37ms 0.032% 80.73% 1196ms 1.04% boost::numeric::ublas::detail::expression_type_check (inline) 18ms 0.016% 80.75% 1172ms 1.02% MutableElement::RegisterWithEdges (inline) 33ms 0.029% 80.77% 1161ms 1.01% Edge::AddElement 52ms 0.045% 80.82% 1151ms 1.00% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 1136ms 0.99% 81.81% 1136ms 0.99% Node::rGetLocation 265ms 0.23% 82.04% 1136ms 0.99% boost::numeric::ublas::detail::equals 8ms 0.007% 82.05% 1091ms 0.95% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 82.05% 1064ms 0.93% boost::numeric::ublas::norm_2 (inline) 253ms 0.22% 82.27% 1035ms 0.9% boost::numeric::ublas::vector_norm_2::apply 1032ms 0.9% 83.17% 1032ms 0.9% std::_Rb_tree_insert_and_rebalance 0 0% 83.17% 999ms 0.87% CellPropertyCollection::~CellPropertyCollection (inline) 2ms 0.0017% 83.17% 979ms 0.85% VertexMeshWriter::MakeVtkMesh 0 0% 83.17% 925ms 0.81% std::__new_allocator::destroy (inline) 0 0% 83.17% 925ms 0.81% std::allocator_traits::destroy (inline) 0 0% 83.17% 922ms 0.8% std::_Rb_tree::_M_destroy_node (inline) 0 0% 83.17% 918ms 0.8% boost::numeric::ublas::c_vector::assign_temporary (inline) 120ms 0.1% 83.27% 918ms 0.8% boost::numeric::ublas::c_vector::swap (inline) 80ms 0.07% 83.34% 879ms 0.77% boost::numeric::ublas::c_vector::operator= (inline) 490ms 0.43% 83.77% 871ms 0.76% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 99ms 0.086% 83.85% 852ms 0.74% std::_Rb_tree::find (inline) 2ms 0.0017% 83.86% 851ms 0.74% std::_Rb_tree::clear (inline) 0 0% 83.86% 834ms 0.73% std::map::clear (inline) 0 0% 83.86% 829ms 0.72% boost::numeric::ublas::norm_inf (inline) 419ms 0.36% 84.22% 829ms 0.72% boost::numeric::ublas::vector_norm_inf::apply (inline) 58ms 0.05% 84.27% 827ms 0.72% std::less::operator() (inline) 81ms 0.071% 84.34% 798ms 0.69% std::swap_ranges (inline) 609ms 0.53% 84.87% 778ms 0.68% CellPropertyCollection::GetProperty 778ms 0.68% 85.55% 778ms 0.68% tcache_put (inline) 582ms 0.51% 86.06% 769ms 0.67% std::operator< (inline) 762ms 0.66% 86.72% 762ms 0.66% std::vector::size (inline) 94ms 0.082% 86.80% 755ms 0.66% MutableElement::GetNodeLocalIndex 0 0% 86.80% 755ms 0.66% std::_Vector_base::_M_allocate (inline) 40ms 0.035% 86.84% 740ms 0.64% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 86.84% 740ms 0.64% boost::numeric::ublas::vector::vector (inline) 0 0% 86.84% 717ms 0.62% std::iter_swap (inline) 717ms 0.62% 87.46% 717ms 0.62% std::swap (inline) 0 0% 87.46% 675ms 0.59% vtkPolygon::New 0 0% 87.46% 673ms 0.59% std::_Rb_tree::_Auto_node::_M_insert (inline) 28ms 0.024% 87.48% 673ms 0.59% std::_Rb_tree::_M_insert_node (inline) 4ms 0.0035% 87.49% 672ms 0.59% vtkPolygon::vtkPolygon 2ms 0.0017% 87.49% 668ms 0.58% std::map::find (inline) 26ms 0.023% 87.51% 634ms 0.55% MutableElement::RegisterWithNodes (inline) 21ms 0.018% 87.53% 606ms 0.53% Node::AddElement 7ms 0.0061% 87.54% 597ms 0.52% std::vector::_M_default_append (inline) 577ms 0.5% 88.04% 577ms 0.5% Node::GetIndex