File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 103344ms, 88.82% of 116349ms total Dropped 1079 nodes (cum <= 581.75ms) flat flat% sum% cum cum% 0 0% 0% 115869ms 99.59% __libc_start_call_main 0 0% 0% 115869ms 99.59% __libc_start_main_impl 0 0% 0% 115869ms 99.59% _start 0 0% 0% 115851ms 99.57% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 115851ms 99.57% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 115851ms 99.57% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 115851ms 99.57% main 0 0% 0% 115808ms 99.54% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 115808ms 99.54% CxxTest::TestRunner::runTest (inline) 0 0% 0% 115808ms 99.54% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 3ms 0.0026% 0.0026% 115801ms 99.53% AbstractCellBasedSimulation::Solve 5ms 0.0043% 0.0069% 63662ms 54.72% OffLatticeSimulation::UpdateCellLocationsAndTopology 21ms 0.018% 0.025% 60515ms 52.01% ForwardEulerNumericalMethod::UpdateAllNodePositions 140ms 0.12% 0.15% 59086ms 50.78% AbstractNumericalMethod::ComputeForcesIncludingDamping 318ms 0.27% 0.42% 47023ms 40.42% NagaiHondaForce::AddForceContribution 1ms 0.00086% 0.42% 38739ms 33.30% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0017% 0.42% 23949ms 20.58% VertexBasedCellPopulation::Update 2ms 0.0017% 0.42% 23846ms 20.50% MutableVertexMesh::ReMesh 14551ms 12.51% 12.93% 22996ms 19.76% Cylindrical2dVertexMesh::GetVectorFromAtoB 622ms 0.53% 13.46% 20905ms 17.97% NagaiHondaForce::GetAdhesionParameter 104ms 0.089% 13.55% 18027ms 15.49% Cell::ReadyToDivide 63ms 0.054% 13.61% 16910ms 14.53% AbstractPhaseBasedCellCycleModel::ReadyToDivide 410ms 0.35% 13.96% 15630ms 13.43% boost::numeric::ublas::c_vector::c_vector (partial-inline) 139ms 0.12% 14.08% 14438ms 12.41% SimpleWntCellCycleModel::UpdateCellCyclePhase 323ms 0.28% 14.36% 14045ms 12.07% boost::numeric::ublas::vector_assign (inline) 88ms 0.076% 14.43% 13654ms 11.74% CellPropertyCollection::GetPropertiesType (inline) 1655ms 1.42% 15.85% 12609ms 10.84% std::_Rb_tree::_M_erase 1039ms 0.89% 16.75% 12392ms 10.65% std::__new_allocator::allocate (inline) 151ms 0.13% 16.88% 12136ms 10.43% MutableVertexMesh::CheckForIntersections 225ms 0.19% 17.07% 11844ms 10.18% std::_Rb_tree::~_Rb_tree (inline) 0 0% 17.07% 11580ms 9.95% std::allocator_traits::allocate (inline) 88ms 0.076% 17.15% 11528ms 9.91% VertexBasedCellPopulation::GetDampingConstant 0 0% 17.15% 11464ms 9.85% std::_Rb_tree::_M_create_node (inline) 1091ms 0.94% 18.08% 11408ms 9.80% operator new 0 0% 18.08% 11386ms 9.79% std::set::~set (inline) 3117ms 2.68% 20.76% 11302ms 9.71% __dynamic_cast 0 0% 20.76% 11241ms 9.66% std::_Rb_tree::_M_drop_node (inline) 78ms 0.067% 20.83% 11221ms 9.64% AbstractCellProperty::IsSubType (inline) 81ms 0.07% 20.90% 10955ms 9.42% AbstractTargetAreaModifier::UpdateTargetAreas 0 0% 20.90% 10945ms 9.41% std::_Rb_tree::_M_get_node (inline) 260ms 0.22% 21.12% 10890ms 9.36% std::__new_allocator::deallocate (inline) 0 0% 21.12% 10861ms 9.33% std::allocator_traits::deallocate (inline) 56ms 0.048% 21.17% 10852ms 9.33% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 0 0% 21.17% 10809ms 9.29% std::_Rb_tree::_M_put_node (inline) 4949ms 4.25% 25.43% 10650ms 9.15% __GI___libc_free 0 0% 25.43% 10299ms 8.85% std::_Rb_tree::_Alloc_node::operator() (inline) 24ms 0.021% 25.45% 10266ms 8.82% AbstractCellBasedSimulation::DoCellBirth 3001ms 2.58% 28.03% 10189ms 8.76% boost::numeric::ublas::indexing_vector_assign 4831ms 4.15% 32.18% 10091ms 8.67% __GI___libc_malloc 136ms 0.12% 32.29% 9160ms 7.87% std::_Rb_tree::_Rb_tree (partial-inline) 36ms 0.031% 32.33% 9078ms 7.80% VertexBasedCellPopulation::GetLocationOfCellCentre 832ms 0.72% 33.04% 8959ms 7.70% VertexMesh::ElementIncludesPoint 408ms 0.35% 33.39% 8780ms 7.55% VertexMesh::GetNextEdgeGradientOfElementAtNode 8ms 0.0069% 33.40% 8774ms 7.54% std::set::set (inline) 504ms 0.43% 33.83% 8652ms 7.44% VertexMesh::GetCentroidOfElement 80ms 0.069% 33.90% 8590ms 7.38% Cell::GetMutationState 896ms 0.77% 34.67% 8247ms 7.09% std::_Rb_tree::_M_copy (inline) 24ms 0.021% 34.69% 7408ms 6.37% MutableVertexMesh::RemoveDeletedNodesAndElements 536ms 0.46% 35.15% 7198ms 6.19% std::map::operator[] (partial-inline) 606ms 0.52% 35.67% 7143ms 6.14% std::_Rb_tree::_M_clone_node (inline) 1313ms 1.13% 36.80% 6945ms 5.97% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 117ms 0.1% 36.90% 6714ms 5.77% SimpleWntCellCycleModel::GetWntLevel 6518ms 5.60% 42.50% 6518ms 5.60% __strcmp_avx2 128ms 0.11% 42.61% 6479ms 5.57% WntConcentration::GetWntLevel 6252ms 5.37% 47.99% 6252ms 5.37% boost::numeric::ublas::c_vector::operator() 0 0% 47.99% 6006ms 5.16% std::set::insert (inline) 5210ms 4.48% 52.46% 5697ms 4.90% _int_free 2708ms 2.33% 54.79% 5566ms 4.78% __cxxabiv1::__si_class_type_info::__do_dyncast 2382ms 2.05% 56.84% 5510ms 4.74% std::_Rb_tree::_M_lower_bound (inline) 31ms 0.027% 56.87% 5234ms 4.50% MutableVertexMesh::RemoveDeletedNodes 671ms 0.58% 57.44% 5141ms 4.42% std::set_intersection (inline) 38ms 0.033% 57.48% 5067ms 4.36% EdgeHelper::RemoveDeletedEdges 1606ms 1.38% 58.86% 4997ms 4.29% boost::numeric::ublas::c_vector::operator[] (inline) 467ms 0.4% 59.26% 4917ms 4.23% std::_Rb_tree::_M_insert_ (inline) 38ms 0.033% 59.29% 4829ms 4.15% EdgeHelper::UpdateEdgesMapKey 4628ms 3.98% 63.27% 4628ms 3.98% boost::numeric::ublas::same_impl_ex 211ms 0.18% 63.45% 4580ms 3.94% MutableElement::ResetIndex 2ms 0.0017% 63.45% 4515ms 3.88% AbstractCellBasedSimulation::DoCellRemoval (inline) 261ms 0.22% 63.67% 4470ms 3.84% std::__set_intersection 0 0% 63.67% 4409ms 3.79% std::_Rb_tree::lower_bound (inline) 0 0% 63.67% 4409ms 3.79% std::map::lower_bound (inline) 134ms 0.12% 63.79% 4391ms 3.77% AbstractCellPopulation::GetCellUsingLocationIndex 61ms 0.052% 63.84% 3922ms 3.37% Cell::GetCellProliferativeType 66ms 0.057% 63.90% 3773ms 3.24% AbstractCellProperty::IsType (inline) 1ms 0.00086% 63.90% 3724ms 3.20% std::insert_iterator::operator= (inline) 8ms 0.0069% 63.91% 3506ms 3.01% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 2265ms 1.95% 65.85% 3335ms 2.87% _int_malloc 0 0% 65.85% 3313ms 2.85% std::_Rb_tree::_M_insert_unique_ (inline) 804ms 0.69% 66.54% 3220ms 2.77% AbstractElement::GetNodeLocation 37ms 0.032% 66.58% 3200ms 2.75% Cell::SetCellProliferativeType 654ms 0.56% 67.14% 3040ms 2.61% boost::numeric::ublas::vector_binary::size (inline) 40ms 0.034% 67.17% 2856ms 2.45% std::_Rb_tree::erase 2ms 0.0017% 67.17% 2693ms 2.31% std::_Rb_tree::_M_insert_unique 755ms 0.65% 67.82% 2690ms 2.31% AbstractCellProperty::IsSame 2612ms 2.24% 70.07% 2612ms 2.24% std::_Rb_tree::_S_right (inline) 50ms 0.043% 70.11% 2557ms 2.20% CellPropertyCollection::HasProperty 0 0% 70.11% 2473ms 2.13% Cell::HasCellProperty (inline) 26ms 0.022% 70.13% 2470ms 2.12% Cell::GetCellData 0 0% 70.13% 2453ms 2.11% boost::numeric::ublas::c_vector::assign (inline) 214ms 0.18% 70.32% 2447ms 2.10% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 70.32% 2417ms 2.08% AbstractCellPopulation::WriteResultsToFiles 172ms 0.15% 70.47% 2386ms 2.05% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 70.47% 2289ms 1.97% boost::numeric::ublas::c_vector::operator-= (inline) 319ms 0.27% 70.74% 2268ms 1.95% std::_Rb_tree_const_iterator::operator++ (inline) 3ms 0.0026% 70.74% 2267ms 1.95% AbstractCellPopulation::Iterator::operator++ (inline) 223ms 0.19% 70.93% 2266ms 1.95% AbstractCellPopulation::Iterator::IsRealCell (inline) 98ms 0.084% 71.02% 2260ms 1.94% VertexMesh::GetVolumeOfElement 36ms 0.031% 71.05% 2209ms 1.90% std::_Rb_tree::_M_emplace_hint_unique 4ms 0.0034% 71.05% 2191ms 1.88% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 71.05% 2191ms 1.88% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 71.05% 1974ms 1.70% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 71.05% 1958ms 1.68% VertexBasedCellPopulation::WriteCellVtkResultsToFile 464ms 0.4% 71.45% 1935ms 1.66% std::type_info::operator== (inline) 1282ms 1.10% 72.55% 1900ms 1.63% std::_Rb_tree::equal_range (inline) 69ms 0.059% 72.61% 1833ms 1.58% MutableVertexMesh::CheckForSwapsFromShortEdges 1822ms 1.57% 74.18% 1822ms 1.57% std::_Rb_tree_increment 0 0% 74.18% 1759ms 1.51% VertexMeshWriter::WriteVtkUsingMesh 39ms 0.034% 74.21% 1753ms 1.51% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 74.21% 1727ms 1.48% tcache_get (inline) 1727ms 1.48% 75.70% 1727ms 1.48% tcache_get_n (inline) 196ms 0.17% 75.86% 1715ms 1.47% CellPropertyCollection::AddProperty 12ms 0.01% 75.88% 1619ms 1.39% VertexMesh::GetSurfaceAreaOfElement 44ms 0.038% 75.91% 1567ms 1.35% Node::RemoveElement 88ms 0.076% 75.99% 1561ms 1.34% boost::numeric::ublas::vector_reference::operator() (inline) 21ms 0.018% 76.01% 1536ms 1.32% std::set::erase (inline) 40ms 0.034% 76.04% 1519ms 1.31% AbstractCellPopulation::GetLocationIndexUsingCell 91ms 0.078% 76.12% 1508ms 1.30% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 76.12% 1333ms 1.15% boost::numeric::ublas::vector_binary::operator() (inline) 1289ms 1.11% 77.23% 1289ms 1.11% std::_Rb_tree_insert_and_rebalance 2ms 0.0017% 77.23% 1273ms 1.09% OffLatticeSimulation::ApplyBoundaries 17ms 0.015% 77.24% 1225ms 1.05% boost::numeric::ublas::detail::expression_type_check (inline) 179ms 0.15% 77.40% 1200ms 1.03% boost::numeric::ublas::detail::equals 0 0% 77.40% 1200ms 1.03% boost::numeric::ublas::norm_2 (inline) 558ms 0.48% 77.88% 1195ms 1.03% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1170ms 1.01% 78.88% 1170ms 1.01% [libchaste_cell_based.so] 0 0% 78.88% 1165ms 1.00% std::_Rb_tree::_Auto_node::_Auto_node (inline) 194ms 0.17% 79.05% 1164ms 1.00% boost::detail::shared_count::~shared_count (inline) 0 0% 79.05% 1164ms 1.00% boost::shared_ptr::~shared_ptr (inline) 94ms 0.081% 79.13% 1142ms 0.98% std::_Rb_tree::_M_erase_aux (partial-inline) 62ms 0.053% 79.18% 1127ms 0.97% std::less::operator() (inline) 43ms 0.037% 79.22% 1099ms 0.94% CellPropertyRegistry::Get 19ms 0.016% 79.24% 1097ms 0.94% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 95ms 0.082% 79.32% 1081ms 0.93% std::_Rb_tree::find (inline) 883ms 0.76% 80.08% 1065ms 0.92% std::operator< (inline) 1022ms 0.88% 80.96% 1022ms 0.88% Node::rGetLocation 1020ms 0.88% 81.83% 1020ms 0.88% [libchaste_mesh.so] 244ms 0.21% 82.04% 1020ms 0.88% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 82.04% 992ms 0.85% std::_Rb_tree::clear (inline) 0 0% 82.04% 991ms 0.85% boost::numeric::ublas::norm_inf (inline) 416ms 0.36% 82.40% 991ms 0.85% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 82.40% 971ms 0.83% std::map::clear (inline) 6ms 0.0052% 82.40% 970ms 0.83% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 940ms 0.81% 83.21% 943ms 0.81% boost::detail::sp_counted_base::release 942ms 0.81% 84.02% 942ms 0.81% std::vector::size (inline) 378ms 0.32% 84.35% 898ms 0.77% Edge::GetMapIndex 2ms 0.0017% 84.35% 895ms 0.77% std::map::find (inline) 0 0% 84.35% 894ms 0.77% boost::numeric::ublas::c_vector::assign_temporary (inline) 4ms 0.0034% 84.35% 894ms 0.77% boost::numeric::ublas::c_vector::swap (inline) 757ms 0.65% 85.00% 892ms 0.77% std::_Rb_tree::_M_get_insert_unique_pos (partial-inline) 95ms 0.082% 85.08% 890ms 0.76% std::swap_ranges (inline) 68ms 0.058% 85.14% 880ms 0.76% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 85.14% 880ms 0.76% boost::numeric::ublas::vector::vector (inline) 1ms 0.00086% 85.14% 861ms 0.74% VertexMeshWriter::MakeVtkMesh 844ms 0.73% 85.87% 844ms 0.73% tcache_put (inline) 0 0% 85.87% 795ms 0.68% std::iter_swap (inline) 795ms 0.68% 86.55% 795ms 0.68% std::swap (inline) 103ms 0.089% 86.64% 793ms 0.68% MutableElement::GetNodeLocalIndex 114ms 0.098% 86.74% 777ms 0.67% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 86.74% 773ms 0.66% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 94ms 0.081% 86.82% 773ms 0.66% std::_Rb_tree_header::_Rb_tree_header (inline) 22ms 0.019% 86.84% 753ms 0.65% MutableElement::RegisterWithEdges (inline) 36ms 0.031% 86.87% 743ms 0.64% Edge::AddElement 0 0% 86.87% 734ms 0.63% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 86.87% 702ms 0.6% std::_Rb_tree::_Auto_node::_M_insert (inline) 26ms 0.022% 86.89% 702ms 0.6% std::_Rb_tree::_M_insert_node (inline) 179ms 0.15% 87.05% 687ms 0.59% boost::shared_ptr::shared_ptr (inline) 680ms 0.58% 87.63% 680ms 0.58% std::_Rb_tree_header::_M_reset (inline) 636ms 0.55% 88.18% 636ms 0.55% Node::GetIndex 632ms 0.54% 88.72% 632ms 0.54% [libstdc++.so.6.0.33] 0 0% 88.72% 632ms 0.54% std::_Vector_base::_M_allocate (inline) 31ms 0.027% 88.75% 625ms 0.54% MutableElement::RegisterWithNodes (inline) 0 0% 88.75% 613ms 0.53% vtkPolygon::New 1ms 0.00086% 88.75% 612ms 0.53% vtkPolygon::vtkPolygon 35ms 0.03% 88.78% 605ms 0.52% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 88.78% 600ms 0.52% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 52ms 0.045% 88.82% 594ms 0.51% Node::AddElement