File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 94496ms, 88.04% of 107337ms total Dropped 1069 nodes (cum <= 536.68ms) flat flat% sum% cum cum% 0 0% 0% 106867ms 99.56% __libc_start_call_main 0 0% 0% 106867ms 99.56% __libc_start_main_impl 0 0% 0% 106867ms 99.56% _start 0 0% 0% 106848ms 99.54% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 106848ms 99.54% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 106848ms 99.54% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 106848ms 99.54% main 0 0% 0% 106811ms 99.51% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 106811ms 99.51% CxxTest::TestRunner::runTest (inline) 0 0% 0% 106811ms 99.51% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 1ms 0.00093% 0.00093% 106804ms 99.50% AbstractCellBasedSimulation::Solve 16ms 0.015% 0.016% 55803ms 51.99% OffLatticeSimulation::UpdateCellLocationsAndTopology 20ms 0.019% 0.034% 52544ms 48.95% ForwardEulerNumericalMethod::UpdateAllNodePositions 73ms 0.068% 0.1% 51486ms 47.97% AbstractNumericalMethod::ComputeForcesIncludingDamping 339ms 0.32% 0.42% 40293ms 37.54% NagaiHondaForce::AddForceContribution 0 0% 0.42% 38546ms 35.91% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00093% 0.42% 23882ms 22.25% VertexBasedCellPopulation::Update 0 0% 0.42% 23750ms 22.13% MutableVertexMesh::ReMesh 14764ms 13.75% 14.17% 23232ms 21.64% Cylindrical2dVertexMesh::GetVectorFromAtoB 83ms 0.077% 14.25% 17052ms 15.89% Cell::ReadyToDivide 57ms 0.053% 14.30% 15900ms 14.81% AbstractPhaseBasedCellCycleModel::ReadyToDivide 377ms 0.35% 14.66% 15001ms 13.98% boost::numeric::ublas::c_vector::c_vector (partial-inline) 354ms 0.33% 14.99% 14927ms 13.91% NagaiHondaForce::GetAdhesionParameter 136ms 0.13% 15.11% 13560ms 12.63% SimpleWntCellCycleModel::UpdateCellCyclePhase 372ms 0.35% 15.46% 13474ms 12.55% boost::numeric::ublas::vector_assign (inline) 115ms 0.11% 15.57% 13003ms 12.11% CellPropertyCollection::GetPropertiesType (inline) 148ms 0.14% 15.70% 12069ms 11.24% MutableVertexMesh::CheckForIntersections 2969ms 2.77% 18.47% 10866ms 10.12% __dynamic_cast 69ms 0.064% 18.53% 10739ms 10.00% AbstractCellProperty::IsSubType (inline) 70ms 0.065% 18.60% 10707ms 9.98% VertexBasedCellPopulation::GetDampingConstant 68ms 0.063% 18.66% 10123ms 9.43% AbstractTargetAreaModifier::UpdateTargetAreas 51ms 0.048% 18.71% 10026ms 9.34% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 24ms 0.022% 18.73% 10013ms 9.33% AbstractCellBasedSimulation::DoCellBirth 2829ms 2.64% 21.37% 9898ms 9.22% boost::numeric::ublas::indexing_vector_assign 1154ms 1.08% 22.44% 9629ms 8.97% std::__new_allocator::allocate (inline) 1324ms 1.23% 23.68% 9257ms 8.62% std::_Rb_tree::_M_erase 0 0% 23.68% 9140ms 8.52% std::allocator_traits::allocate (inline) 0 0% 23.68% 9081ms 8.46% std::_Rb_tree::_M_create_node (inline) 331ms 0.31% 23.99% 8985ms 8.37% VertexMesh::GetNextEdgeGradientOfElementAtNode 769ms 0.72% 24.70% 8906ms 8.30% VertexMesh::ElementIncludesPoint 36ms 0.034% 24.74% 8753ms 8.15% VertexBasedCellPopulation::GetLocationOfCellCentre 799ms 0.74% 25.48% 8565ms 7.98% operator new 0 0% 25.48% 8493ms 7.91% std::_Rb_tree::_M_get_node (inline) 220ms 0.2% 25.68% 8491ms 7.91% std::_Rb_tree::~_Rb_tree (inline) 77ms 0.072% 25.76% 8432ms 7.86% Cell::GetMutationState 521ms 0.49% 26.24% 8318ms 7.75% VertexMesh::GetCentroidOfElement 0 0% 26.24% 8256ms 7.69% std::_Rb_tree::_M_drop_node (inline) 0 0% 26.24% 8040ms 7.49% std::set::~set (inline) 246ms 0.23% 26.47% 8027ms 7.48% std::__new_allocator::deallocate (inline) 0 0% 26.47% 8000ms 7.45% std::allocator_traits::deallocate (inline) 0 0% 26.47% 7962ms 7.42% std::_Rb_tree::_M_put_node (inline) 0 0% 26.47% 7924ms 7.38% std::_Rb_tree::_Alloc_node::operator() (inline) 3265ms 3.04% 29.51% 7903ms 7.36% __GI___libc_free 2976ms 2.77% 32.29% 7563ms 7.05% __GI___libc_malloc 17ms 0.016% 32.30% 7325ms 6.82% MutableVertexMesh::RemoveDeletedNodesAndElements 1353ms 1.26% 33.56% 7207ms 6.71% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 474ms 0.44% 34.00% 7117ms 6.63% std::map::operator[] (partial-inline) 142ms 0.13% 34.14% 6498ms 6.05% std::_Rb_tree::_Rb_tree (partial-inline) 97ms 0.09% 34.23% 6261ms 5.83% SimpleWntCellCycleModel::GetWntLevel 6259ms 5.83% 40.06% 6259ms 5.83% boost::numeric::ublas::c_vector::operator() 6242ms 5.82% 45.87% 6242ms 5.82% __strcmp_avx2 663ms 0.62% 46.49% 6123ms 5.70% std::_Rb_tree::_M_copy (inline) 10ms 0.0093% 46.50% 6100ms 5.68% std::set::set (inline) 128ms 0.12% 46.62% 6045ms 5.63% WntConcentration::GetWntLevel 2619ms 2.44% 49.06% 5558ms 5.18% __cxxabiv1::__si_class_type_info::__do_dyncast 2471ms 2.30% 51.36% 5496ms 5.12% std::_Rb_tree::_M_lower_bound (inline) 0 0% 51.36% 5445ms 5.07% std::set::insert (inline) 28ms 0.026% 51.39% 5188ms 4.83% MutableVertexMesh::RemoveDeletedNodes 664ms 0.62% 52.01% 5168ms 4.81% std::_Rb_tree::_M_clone_node (inline) 32ms 0.03% 52.04% 5020ms 4.68% EdgeHelper::RemoveDeletedEdges 1472ms 1.37% 53.41% 4805ms 4.48% boost::numeric::ublas::c_vector::operator[] (inline) 39ms 0.036% 53.44% 4765ms 4.44% EdgeHelper::UpdateEdgesMapKey 54ms 0.05% 53.49% 4699ms 4.38% std::set_intersection (inline) 235ms 0.22% 53.71% 4645ms 4.33% std::__set_intersection 0 0% 53.71% 4641ms 4.32% AbstractCellBasedSimulation::DoCellRemoval (inline) 4317ms 4.02% 57.73% 4629ms 4.31% _int_free 222ms 0.21% 57.94% 4593ms 4.28% MutableElement::ResetIndex 584ms 0.54% 58.48% 4522ms 4.21% std::_Rb_tree::_M_insert_ (inline) 0 0% 58.48% 4447ms 4.14% std::_Rb_tree::lower_bound (inline) 0 0% 58.48% 4447ms 4.14% std::map::lower_bound (inline) 4168ms 3.88% 62.37% 4168ms 3.88% boost::numeric::ublas::same_impl_ex 30ms 0.028% 62.40% 3920ms 3.65% Cell::GetCellProliferativeType 9ms 0.0084% 62.40% 3617ms 3.37% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 80ms 0.075% 62.48% 3567ms 3.32% AbstractCellPopulation::GetCellUsingLocationIndex 69ms 0.064% 62.54% 3540ms 3.30% AbstractCellProperty::IsType (inline) 0 0% 62.54% 3393ms 3.16% std::insert_iterator::operator= (inline) 773ms 0.72% 63.26% 3133ms 2.92% AbstractElement::GetNodeLocation 51ms 0.048% 63.31% 3082ms 2.87% Cell::SetCellProliferativeType 2213ms 2.06% 65.37% 3071ms 2.86% _int_malloc 4ms 0.0037% 65.38% 3005ms 2.80% std::_Rb_tree::_M_insert_unique_ (inline) 635ms 0.59% 65.97% 2888ms 2.69% boost::numeric::ublas::vector_binary::size (inline) 42ms 0.039% 66.01% 2873ms 2.68% std::_Rb_tree::erase 450ms 0.42% 66.43% 2754ms 2.57% std::_Rb_tree_const_iterator::operator++ (inline) 216ms 0.2% 66.63% 2548ms 2.37% VertexMesh::GetAreaGradientOfElementAtNode 698ms 0.65% 67.28% 2494ms 2.32% AbstractCellProperty::IsSame 2486ms 2.32% 69.59% 2486ms 2.32% std::_Rb_tree::_S_right (inline) 0 0% 69.59% 2462ms 2.29% boost::numeric::ublas::c_vector::assign (inline) 109ms 0.1% 69.70% 2445ms 2.28% VertexMesh::GetVolumeOfElement 4ms 0.0037% 69.70% 2440ms 2.27% std::_Rb_tree::_M_insert_unique 49ms 0.046% 69.74% 2419ms 2.25% CellPropertyCollection::HasProperty 0 0% 69.74% 2407ms 2.24% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.74% 2313ms 2.15% Cell::HasCellProperty (inline) 0 0% 69.74% 2307ms 2.15% AbstractCellPopulation::WriteResultsToFiles 118ms 0.11% 69.85% 2271ms 2.12% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.0028% 69.86% 2220ms 2.07% AbstractCellPopulation::Iterator::operator++ (inline) 202ms 0.19% 70.05% 2180ms 2.03% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 70.05% 2161ms 2.01% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 70.05% 2161ms 2.01% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 22ms 0.02% 70.07% 2140ms 1.99% std::_Rb_tree::_M_emplace_hint_unique 2135ms 1.99% 72.06% 2135ms 1.99% std::_Rb_tree_increment 27ms 0.025% 72.08% 2116ms 1.97% Cell::GetCellData 0 0% 72.08% 1891ms 1.76% VertexBasedCellPopulation::WriteVtkResultsToFile 2ms 0.0019% 72.08% 1881ms 1.75% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1252ms 1.17% 73.25% 1875ms 1.75% std::_Rb_tree::equal_range (inline) 62ms 0.058% 73.31% 1844ms 1.72% MutableVertexMesh::CheckForSwapsFromShortEdges 425ms 0.4% 73.70% 1796ms 1.67% std::type_info::operator== (inline) 0 0% 73.70% 1705ms 1.59% VertexMeshWriter::WriteVtkUsingMesh 35ms 0.033% 73.74% 1699ms 1.58% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 21ms 0.02% 73.75% 1635ms 1.52% VertexMesh::GetSurfaceAreaOfElement 150ms 0.14% 73.89% 1626ms 1.51% boost::numeric::ublas::vector_reference::operator() (inline) 51ms 0.048% 73.94% 1536ms 1.43% Node::RemoveElement 30ms 0.028% 73.97% 1522ms 1.42% AbstractCellPopulation::GetLocationIndexUsingCell 76ms 0.071% 74.04% 1498ms 1.40% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 19ms 0.018% 74.06% 1496ms 1.39% std::set::erase (inline) 0 0% 74.06% 1494ms 1.39% boost::numeric::ublas::vector_binary::operator() (inline) 172ms 0.16% 74.22% 1427ms 1.33% CellPropertyCollection::AddProperty 3ms 0.0028% 74.22% 1378ms 1.28% OffLatticeSimulation::ApplyBoundaries 1ms 0.00093% 74.22% 1332ms 1.24% tcache_get (inline) 1331ms 1.24% 75.46% 1331ms 1.24% tcache_get_n (inline) 0 0% 75.46% 1248ms 1.16% boost::numeric::ublas::norm_2 (inline) 521ms 0.49% 75.95% 1239ms 1.15% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 23ms 0.021% 75.97% 1207ms 1.12% boost::numeric::ublas::detail::expression_type_check (inline) 81ms 0.075% 76.04% 1181ms 1.10% std::less::operator() (inline) 186ms 0.17% 76.22% 1174ms 1.09% boost::numeric::ublas::detail::equals 0 0% 76.22% 1157ms 1.08% std::_Rb_tree::_Auto_node::_Auto_node (inline) 90ms 0.084% 76.30% 1140ms 1.06% std::_Rb_tree::_M_erase_aux (partial-inline) 1126ms 1.05% 77.35% 1126ms 1.05% Node::rGetLocation 1114ms 1.04% 78.39% 1114ms 1.04% std::_Rb_tree_insert_and_rebalance 887ms 0.83% 79.21% 1100ms 1.02% std::operator< (inline) 1072ms 1% 80.21% 1072ms 1% [libchaste_cell_based.so] 18ms 0.017% 80.23% 1061ms 0.99% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 101ms 0.094% 80.32% 1038ms 0.97% std::_Rb_tree::find (inline) 0 0% 80.32% 989ms 0.92% std::_Rb_tree::clear (inline) 26ms 0.024% 80.35% 988ms 0.92% CellPropertyRegistry::Get 977ms 0.91% 81.26% 977ms 0.91% std::vector::size (inline) 975ms 0.91% 82.17% 975ms 0.91% [libchaste_mesh.so] 0 0% 82.17% 974ms 0.91% std::map::clear (inline) 9ms 0.0084% 82.18% 968ms 0.9% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 137ms 0.13% 82.30% 933ms 0.87% boost::detail::shared_count::~shared_count (inline) 0 0% 82.30% 933ms 0.87% boost::shared_ptr::~shared_ptr (inline) 0 0% 82.30% 913ms 0.85% boost::numeric::ublas::norm_inf (inline) 494ms 0.46% 82.76% 913ms 0.85% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 82.76% 893ms 0.83% boost::numeric::ublas::c_vector::assign_temporary (inline) 5ms 0.0047% 82.77% 893ms 0.83% boost::numeric::ublas::c_vector::swap (inline) 75ms 0.07% 82.84% 888ms 0.83% std::swap_ranges (inline) 0 0% 82.84% 844ms 0.79% std::map::find (inline) 371ms 0.35% 83.18% 843ms 0.79% Edge::GetMapIndex 531ms 0.49% 83.68% 836ms 0.78% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 1ms 0.00093% 83.68% 823ms 0.77% VertexMeshWriter::MakeVtkMesh 0 0% 83.68% 819ms 0.76% CellPropertyCollection::~CellPropertyCollection (inline) 116ms 0.11% 83.79% 818ms 0.76% MutableElement::GetNodeLocalIndex 0 0% 83.79% 813ms 0.76% std::iter_swap (inline) 813ms 0.76% 84.54% 813ms 0.76% std::swap (inline) 178ms 0.17% 84.71% 802ms 0.75% boost::shared_ptr::shared_ptr (inline) 21ms 0.02% 84.73% 792ms 0.74% MutableElement::RegisterWithEdges (inline) 35ms 0.033% 84.76% 786ms 0.73% Edge::AddElement 772ms 0.72% 85.48% 777ms 0.72% boost::detail::sp_counted_base::release 110ms 0.1% 85.58% 748ms 0.7% boost::numeric::ublas::c_vector::operator= (inline) 701ms 0.65% 86.24% 701ms 0.65% Node::GetIndex 0 0% 86.24% 667ms 0.62% std::_Rb_tree::_Auto_node::_M_insert (inline) 18ms 0.017% 86.25% 667ms 0.62% std::_Rb_tree::_M_insert_node (inline) 1ms 0.00093% 86.26% 645ms 0.6% std::_Vector_base::_M_allocate (inline) 96ms 0.089% 86.34% 636ms 0.59% std::__new_allocator::construct (inline) 0 0% 86.34% 636ms 0.59% std::allocator_traits::construct (inline) 595ms 0.55% 86.90% 624ms 0.58% boost::detail::shared_count::shared_count (inline) 0 0% 86.90% 607ms 0.57% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 602ms 0.56% 87.46% 602ms 0.56% [libstdc++.so.6.0.33] 35ms 0.033% 87.49% 588ms 0.55% MutableElement::RegisterWithNodes (inline) 0 0% 87.49% 588ms 0.55% std::_Rb_tree::_M_construct_node (inline) 0 0% 87.49% 583ms 0.54% vtkPolygon::New 1ms 0.00093% 87.49% 583ms 0.54% vtkPolygon::vtkPolygon 548ms 0.51% 88.00% 548ms 0.51% operator delete 6ms 0.0056% 88.01% 544ms 0.51% std::vector::_M_default_append (inline) 29ms 0.027% 88.04% 543ms 0.51% Node::AddElement