File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 100602ms, 88.75% of 113357ms total Dropped 1157 nodes (cum <= 566.78ms) flat flat% sum% cum cum% 0 0% 0% 112973ms 99.66% __libc_start_call_main 0 0% 0% 112973ms 99.66% __libc_start_main_impl 0 0% 0% 112973ms 99.66% _start 0 0% 0% 112949ms 99.64% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 112949ms 99.64% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 112949ms 99.64% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 112949ms 99.64% main 0 0% 0% 112908ms 99.60% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 112908ms 99.60% CxxTest::TestRunner::runTest (inline) 0 0% 0% 112907ms 99.60% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 5ms 0.0044% 0.0044% 112898ms 99.60% AbstractCellBasedSimulation::Solve 16ms 0.014% 0.019% 58056ms 51.22% OffLatticeSimulation::UpdateCellLocationsAndTopology 9ms 0.0079% 0.026% 54349ms 47.94% ForwardEulerNumericalMethod::UpdateAllNodePositions 186ms 0.16% 0.19% 53154ms 46.89% AbstractNumericalMethod::ComputeForcesIncludingDamping 5ms 0.0044% 0.19% 40936ms 36.11% AbstractCellBasedSimulation::UpdateCellPopulation 278ms 0.25% 0.44% 40779ms 35.97% NagaiHondaForce::AddForceContribution 4ms 0.0035% 0.44% 25386ms 22.39% VertexBasedCellPopulation::Update 1ms 0.00088% 0.44% 25224ms 22.25% MutableVertexMesh::ReMesh 14863ms 13.11% 13.56% 23662ms 20.87% Cylindrical2dVertexMesh::GetVectorFromAtoB 138ms 0.12% 13.68% 18189ms 16.05% Cell::ReadyToDivide 42ms 0.037% 13.72% 16951ms 14.95% AbstractPhaseBasedCellCycleModel::ReadyToDivide 204ms 0.18% 13.90% 14615ms 12.89% SimpleWntCellCycleModel::UpdateCellCyclePhase 334ms 0.29% 14.19% 14521ms 12.81% NagaiHondaForce::GetAdhesionParameter 117ms 0.1% 14.29% 14342ms 12.65% CellPropertyCollection::GetPropertiesType (inline) 432ms 0.38% 14.67% 14053ms 12.40% boost::numeric::ublas::c_vector::c_vector (partial-inline) 319ms 0.28% 14.96% 12617ms 11.13% boost::numeric::ublas::vector_assign (inline) 3408ms 3.01% 17.96% 12065ms 10.64% __dynamic_cast 155ms 0.14% 18.10% 11954ms 10.55% MutableVertexMesh::CheckForIntersections 87ms 0.077% 18.18% 11933ms 10.53% AbstractCellProperty::IsSubType (inline) 72ms 0.064% 18.24% 11721ms 10.34% VertexBasedCellPopulation::GetDampingConstant 71ms 0.063% 18.30% 11265ms 9.94% AbstractTargetAreaModifier::UpdateTargetAreas 51ms 0.045% 18.35% 11143ms 9.83% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 27ms 0.024% 18.37% 10500ms 9.26% AbstractCellBasedSimulation::DoCellBirth 1410ms 1.24% 19.61% 10402ms 9.18% std::__new_allocator::allocate (inline) 0 0% 19.61% 9833ms 8.67% std::allocator_traits::allocate (inline) 0 0% 19.61% 9827ms 8.67% std::_Rb_tree::_M_create_node (inline) 464ms 0.41% 20.02% 9711ms 8.57% VertexMesh::GetNextEdgeGradientOfElementAtNode 2840ms 2.51% 22.53% 9544ms 8.42% boost::numeric::ublas::indexing_vector_assign 1325ms 1.17% 23.70% 9342ms 8.24% std::_Rb_tree::_M_erase 740ms 0.65% 24.35% 9046ms 7.98% operator new 100ms 0.088% 24.44% 9014ms 7.95% Cell::GetMutationState 14ms 0.012% 24.45% 8990ms 7.93% MutableVertexMesh::RemoveDeletedNodesAndElements 27ms 0.024% 24.47% 8898ms 7.85% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 24.47% 8897ms 7.85% std::_Rb_tree::_M_get_node (inline) 888ms 0.78% 25.26% 8754ms 7.72% VertexMesh::ElementIncludesPoint 0 0% 25.26% 8633ms 7.62% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 25.26% 8525ms 7.52% std::_Rb_tree::_M_drop_node (inline) 457ms 0.4% 25.66% 8502ms 7.50% VertexMesh::GetCentroidOfElement 228ms 0.2% 25.86% 8297ms 7.32% std::__new_allocator::deallocate (inline) 0 0% 25.86% 8288ms 7.31% std::allocator_traits::deallocate (inline) 0 0% 25.86% 8217ms 7.25% std::_Rb_tree::_M_put_node (inline) 211ms 0.19% 26.05% 8190ms 7.22% std::_Rb_tree::~_Rb_tree (inline) 3039ms 2.68% 28.73% 8105ms 7.15% __GI___libc_malloc 2322ms 2.05% 30.78% 7792ms 6.87% __GI___libc_free 0 0% 30.78% 7736ms 6.82% std::set::~set (inline) 1498ms 1.32% 32.10% 7663ms 6.76% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 474ms 0.42% 32.52% 7561ms 6.67% std::map::operator[] (partial-inline) 203ms 0.18% 32.70% 7473ms 6.59% std::_Rb_tree::_Rb_tree (partial-inline) 677ms 0.6% 33.29% 7006ms 6.18% std::_Rb_tree::_M_copy (inline) 6988ms 6.16% 39.46% 6988ms 6.16% __strcmp_avx2 20ms 0.018% 39.48% 6813ms 6.01% std::set::set (inline) 197ms 0.17% 39.65% 6468ms 5.71% SimpleWntCellCycleModel::GetWntLevel 166ms 0.15% 39.80% 6195ms 5.47% WntConcentration::GetWntLevel 6179ms 5.45% 45.25% 6179ms 5.45% boost::numeric::ublas::c_vector::operator() 2850ms 2.51% 47.76% 6148ms 5.42% __cxxabiv1::__si_class_type_info::__do_dyncast 951ms 0.84% 48.60% 6069ms 5.35% std::_Rb_tree::_M_clone_node (inline) 2482ms 2.19% 50.79% 5964ms 5.26% std::_Rb_tree::_M_lower_bound (inline) 25ms 0.022% 50.81% 5711ms 5.04% MutableVertexMesh::RemoveDeletedNodes 255ms 0.22% 51.04% 5674ms 5.01% MutableElement::ResetIndex 33ms 0.029% 51.07% 5513ms 4.86% EdgeHelper::RemoveDeletedEdges 2062ms 1.82% 52.89% 5457ms 4.81% boost::numeric::ublas::c_vector::operator[] (inline) 4501ms 3.97% 56.86% 5453ms 4.81% _int_free 0 0% 56.86% 5360ms 4.73% std::set::insert (inline) 41ms 0.036% 56.89% 5166ms 4.56% EdgeHelper::UpdateEdgesMapKey 3ms 0.0026% 56.89% 5028ms 4.44% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 56.89% 4804ms 4.24% std::_Rb_tree::lower_bound (inline) 0 0% 56.89% 4804ms 4.24% std::map::lower_bound (inline) 548ms 0.48% 57.38% 4523ms 3.99% std::_Rb_tree::_M_insert_ (inline) 140ms 0.12% 57.50% 4390ms 3.87% AbstractCellPopulation::GetCellUsingLocationIndex 121ms 0.11% 57.61% 4327ms 3.82% std::set_intersection (inline) 233ms 0.21% 57.81% 4206ms 3.71% std::__set_intersection 46ms 0.041% 57.85% 3990ms 3.52% Cell::GetCellProliferativeType 3980ms 3.51% 61.37% 3980ms 3.51% boost::numeric::ublas::same_impl_ex 128ms 0.11% 61.48% 3932ms 3.47% AbstractCellProperty::IsType (inline) 12ms 0.011% 61.49% 3691ms 3.26% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 74ms 0.065% 61.55% 3627ms 3.20% std::_Rb_tree::erase 2275ms 2.01% 63.56% 3524ms 3.11% _int_malloc 0 0% 63.56% 3232ms 2.85% std::insert_iterator::operator= (inline) 60ms 0.053% 63.61% 3190ms 2.81% Cell::SetCellProliferativeType 945ms 0.83% 64.45% 3075ms 2.71% AbstractElement::GetNodeLocation 3068ms 2.71% 67.15% 3068ms 2.71% std::_Rb_tree::_S_right (inline) 9ms 0.0079% 67.16% 2831ms 2.50% std::_Rb_tree::_M_insert_unique_ (inline) 38ms 0.034% 67.20% 2795ms 2.47% CellPropertyCollection::HasProperty 244ms 0.22% 67.41% 2774ms 2.45% std::_Rb_tree_const_iterator::operator++ (inline) 840ms 0.74% 68.15% 2750ms 2.43% AbstractCellProperty::IsSame 57ms 0.05% 68.20% 2746ms 2.42% Cell::GetCellData 229ms 0.2% 68.40% 2691ms 2.37% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 68.40% 2690ms 2.37% Cell::HasCellProperty (inline) 0 0% 68.40% 2636ms 2.33% boost::numeric::ublas::c_vector::operator-= (inline) 609ms 0.54% 68.94% 2615ms 2.31% boost::numeric::ublas::vector_binary::size (inline) 0 0% 68.94% 2600ms 2.29% boost::numeric::ublas::c_vector::assign (inline) 0 0% 68.94% 2595ms 2.29% AbstractCellPopulation::WriteResultsToFiles 1ms 0.00088% 68.94% 2529ms 2.23% std::_Rb_tree::_M_insert_unique 1565ms 1.38% 70.32% 2421ms 2.14% std::_Rb_tree::equal_range (inline) 79ms 0.07% 70.39% 2327ms 2.05% VertexMesh::GetVolumeOfElement 5ms 0.0044% 70.40% 2318ms 2.04% AbstractCellPopulation::Iterator::operator++ (inline) 167ms 0.15% 70.54% 2297ms 2.03% AbstractCellPopulation::Iterator::IsRealCell (inline) 41ms 0.036% 70.58% 2277ms 2.01% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 2273ms 2.01% 72.59% 2273ms 2.01% std::_Rb_tree_increment 39ms 0.034% 72.62% 2232ms 1.97% std::_Rb_tree::_M_emplace_hint_unique 2ms 0.0018% 72.62% 2163ms 1.91% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.62% 2163ms 1.91% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1ms 0.00088% 72.62% 2156ms 1.90% VertexBasedCellPopulation::WriteVtkResultsToFile 3ms 0.0026% 72.63% 2139ms 1.89% VertexBasedCellPopulation::WriteCellVtkResultsToFile 0 0% 72.63% 1924ms 1.70% VertexMeshWriter::WriteVtkUsingMesh 439ms 0.39% 73.01% 1910ms 1.68% std::type_info::operator== (inline) 59ms 0.052% 73.06% 1806ms 1.59% MutableVertexMesh::CheckForSwapsFromShortEdges 29ms 0.026% 73.09% 1798ms 1.59% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 50ms 0.044% 73.13% 1658ms 1.46% Node::RemoveElement 14ms 0.012% 73.15% 1613ms 1.42% std::set::erase (inline) 40ms 0.035% 73.18% 1580ms 1.39% AbstractCellPopulation::GetLocationIndexUsingCell 35ms 0.031% 73.21% 1557ms 1.37% VertexMesh::GetSurfaceAreaOfElement 83ms 0.073% 73.29% 1531ms 1.35% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 150ms 0.13% 73.42% 1496ms 1.32% CellPropertyCollection::AddProperty 2ms 0.0018% 73.42% 1451ms 1.28% OffLatticeSimulation::ApplyBoundaries 0 0% 73.42% 1398ms 1.23% boost::numeric::ublas::norm_2 (inline) 46ms 0.041% 73.46% 1384ms 1.22% boost::numeric::ublas::vector_reference::operator() (inline) 620ms 0.55% 74.01% 1382ms 1.22% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 0 0% 74.01% 1370ms 1.21% tcache_get (inline) 1370ms 1.21% 75.22% 1370ms 1.21% tcache_get_n (inline) 0 0% 75.22% 1365ms 1.20% std::_Rb_tree::clear (inline) 1364ms 1.20% 76.42% 1364ms 1.20% [libchaste_cell_based.so] 0 0% 76.42% 1344ms 1.19% std::map::clear (inline) 0 0% 76.42% 1328ms 1.17% boost::numeric::ublas::vector_binary::operator() (inline) 73ms 0.064% 76.48% 1322ms 1.17% std::_Rb_tree::_M_erase_aux (partial-inline) 8ms 0.0071% 76.49% 1292ms 1.14% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 64ms 0.056% 76.55% 1278ms 1.13% std::less::operator() (inline) 20ms 0.018% 76.57% 1241ms 1.09% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 33ms 0.029% 76.59% 1233ms 1.09% CellPropertyRegistry::Get 938ms 0.83% 77.42% 1214ms 1.07% std::operator< (inline) 0 0% 77.42% 1194ms 1.05% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 77.42% 1171ms 1.03% boost::numeric::ublas::c_vector::assign_temporary (inline) 10ms 0.0088% 77.43% 1171ms 1.03% boost::numeric::ublas::c_vector::swap (inline) 110ms 0.097% 77.53% 1166ms 1.03% std::_Rb_tree::find (inline) 83ms 0.073% 77.60% 1161ms 1.02% std::swap_ranges (inline) 1079ms 0.95% 78.55% 1079ms 0.95% std::swap (inline) 0 0% 78.55% 1078ms 0.95% std::iter_swap (inline) 1037ms 0.91% 79.47% 1037ms 0.91% std::_Rb_tree_insert_and_rebalance 146ms 0.13% 79.60% 1031ms 0.91% boost::detail::shared_count::~shared_count (inline) 0 0% 79.60% 1031ms 0.91% boost::shared_ptr::~shared_ptr (inline) 9ms 0.0079% 79.60% 1030ms 0.91% boost::numeric::ublas::detail::expression_type_check (inline) 1023ms 0.9% 80.51% 1023ms 0.9% Node::rGetLocation 1017ms 0.9% 81.40% 1017ms 0.9% tcache_put (inline) 182ms 0.16% 81.56% 1004ms 0.89% boost::numeric::ublas::detail::equals 305ms 0.27% 81.83% 995ms 0.88% std::__new_allocator::construct (inline) 0 0% 81.83% 995ms 0.88% std::allocator_traits::construct (inline) 0 0% 81.83% 970ms 0.86% std::map::find (inline) 0 0% 81.83% 930ms 0.82% std::_Rb_tree::_M_construct_node (inline) 2ms 0.0018% 81.84% 930ms 0.82% std::_Vector_base::_M_allocate (inline) 1ms 0.00088% 81.84% 902ms 0.8% VertexMeshWriter::MakeVtkMesh 43ms 0.038% 81.87% 879ms 0.78% MutableElement::RegisterWithEdges (inline) 876ms 0.77% 82.65% 876ms 0.77% [libchaste_mesh.so] 512ms 0.45% 83.10% 865ms 0.76% Edge::GetMapIndex 857ms 0.76% 83.85% 857ms 0.76% std::vector::size (inline) 129ms 0.11% 83.97% 844ms 0.74% Edge::AddElement 796ms 0.7% 84.67% 831ms 0.73% boost::detail::sp_counted_base::release 90ms 0.079% 84.75% 822ms 0.73% boost::numeric::ublas::c_vector::operator= (inline) 202ms 0.18% 84.93% 810ms 0.71% boost::shared_ptr::shared_ptr (inline) 12ms 0.011% 84.94% 778ms 0.69% std::vector::_M_default_append (inline) 424ms 0.37% 85.31% 774ms 0.68% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 41ms 0.036% 85.35% 769ms 0.68% MutableElement::RegisterWithNodes (inline) 0 0% 85.35% 767ms 0.68% boost::numeric::ublas::norm_inf (inline) 383ms 0.34% 85.69% 767ms 0.68% boost::numeric::ublas::vector_norm_inf::apply (inline) 152ms 0.13% 85.82% 745ms 0.66% MutableElement::GetNodeLocalIndex 0 0% 85.82% 725ms 0.64% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 85.82% 723ms 0.64% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 540ms 0.48% 86.30% 713ms 0.63% malloc_consolidate 147ms 0.13% 86.43% 698ms 0.62% Node::AddElement 0 0% 86.43% 692ms 0.61% VertexElementMap::VertexElementMap 0 0% 86.43% 692ms 0.61% std::vector::resize (inline) 0 0% 86.43% 685ms 0.6% std::map::map (inline) 100ms 0.088% 86.52% 671ms 0.59% std::_Rb_tree::_M_upper_bound (inline) 670ms 0.59% 87.11% 670ms 0.59% [libstdc++.so.6.0.33] 0 0% 87.11% 659ms 0.58% std::_Rb_tree::_Auto_node::_M_insert (inline) 23ms 0.02% 87.13% 659ms 0.58% std::_Rb_tree::_M_insert_node (inline) 1ms 0.00088% 87.13% 631ms 0.56% vtkPolygon::New 629ms 0.55% 87.68% 629ms 0.55% Node::GetIndex 0 0% 87.68% 629ms 0.55% vtkPolygon::vtkPolygon 612ms 0.54% 88.22% 612ms 0.54% boost::shared_ptr::operator-> (inline) 566ms 0.5% 88.72% 607ms 0.54% boost::detail::shared_count::shared_count (inline) 30ms 0.026% 88.75% 599ms 0.53% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 88.75% 599ms 0.53% boost::numeric::ublas::vector::vector (inline)