File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95270ms, 89.37% of 106605ms total Dropped 1000 nodes (cum <= 533.02ms) flat flat% sum% cum cum% 0 0% 0% 106264ms 99.68% __libc_start_call_main 0 0% 0% 106264ms 99.68% __libc_start_main_impl 0 0% 0% 106264ms 99.68% _start 0 0% 0% 106245ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 106245ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 106245ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 106245ms 99.66% main 0 0% 0% 106210ms 99.63% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 106210ms 99.63% CxxTest::TestRunner::runTest (inline) 0 0% 0% 106210ms 99.63% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 1ms 0.00094% 0.00094% 106202ms 99.62% AbstractCellBasedSimulation::Solve 14ms 0.013% 0.014% 55925ms 52.46% OffLatticeSimulation::UpdateCellLocationsAndTopology 14ms 0.013% 0.027% 52525ms 49.27% ForwardEulerNumericalMethod::UpdateAllNodePositions 140ms 0.13% 0.16% 51492ms 48.30% AbstractNumericalMethod::ComputeForcesIncludingDamping 375ms 0.35% 0.51% 39764ms 37.30% NagaiHondaForce::AddForceContribution 2ms 0.0019% 0.51% 38721ms 36.32% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.0038% 0.52% 24072ms 22.58% VertexBasedCellPopulation::Update 1ms 0.00094% 0.52% 23954ms 22.47% MutableVertexMesh::ReMesh 14281ms 13.40% 13.91% 22721ms 21.31% Cylindrical2dVertexMesh::GetVectorFromAtoB 75ms 0.07% 13.98% 17290ms 16.22% Cell::ReadyToDivide 75ms 0.07% 14.05% 16167ms 15.17% AbstractPhaseBasedCellCycleModel::ReadyToDivide 338ms 0.32% 14.37% 15193ms 14.25% NagaiHondaForce::GetAdhesionParameter 398ms 0.37% 14.74% 14157ms 13.28% boost::numeric::ublas::c_vector::c_vector (partial-inline) 116ms 0.11% 14.85% 13802ms 12.95% SimpleWntCellCycleModel::UpdateCellCyclePhase 128ms 0.12% 14.97% 13544ms 12.70% CellPropertyCollection::GetPropertiesType (inline) 312ms 0.29% 15.27% 12671ms 11.89% boost::numeric::ublas::vector_assign (inline) 147ms 0.14% 15.40% 12022ms 11.28% MutableVertexMesh::CheckForIntersections 3319ms 3.11% 18.52% 11253ms 10.56% __dynamic_cast 91ms 0.085% 18.60% 11237ms 10.54% VertexBasedCellPopulation::GetDampingConstant 76ms 0.071% 18.67% 11161ms 10.47% AbstractCellProperty::IsSubType (inline) 69ms 0.065% 18.74% 10332ms 9.69% AbstractTargetAreaModifier::UpdateTargetAreas 1278ms 1.20% 19.94% 10258ms 9.62% std::__new_allocator::allocate (inline) 47ms 0.044% 19.98% 10247ms 9.61% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 22ms 0.021% 20.00% 10088ms 9.46% AbstractCellBasedSimulation::DoCellBirth 0 0% 20.00% 9758ms 9.15% std::allocator_traits::allocate (inline) 0 0% 20.00% 9744ms 9.14% std::_Rb_tree::_M_create_node (inline) 2623ms 2.46% 22.46% 9497ms 8.91% boost::numeric::ublas::indexing_vector_assign 1311ms 1.23% 23.69% 9138ms 8.57% std::_Rb_tree::_M_erase 0 0% 23.69% 9117ms 8.55% std::_Rb_tree::_M_get_node (inline) 872ms 0.82% 24.51% 8891ms 8.34% operator new 789ms 0.74% 25.25% 8849ms 8.30% VertexMesh::ElementIncludesPoint 360ms 0.34% 25.59% 8762ms 8.22% VertexMesh::GetNextEdgeGradientOfElementAtNode 83ms 0.078% 25.67% 8629ms 8.09% Cell::GetMutationState 25ms 0.023% 25.69% 8619ms 8.08% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 25.69% 8535ms 8.01% std::_Rb_tree::_Alloc_node::operator() (inline) 223ms 0.21% 25.90% 8346ms 7.83% std::_Rb_tree::~_Rb_tree (inline) 0 0% 25.90% 8181ms 7.67% std::_Rb_tree::_M_drop_node (inline) 493ms 0.46% 26.36% 8179ms 7.67% VertexMesh::GetCentroidOfElement 268ms 0.25% 26.61% 7930ms 7.44% std::__new_allocator::deallocate (inline) 0 0% 26.61% 7906ms 7.42% std::allocator_traits::deallocate (inline) 0 0% 26.61% 7881ms 7.39% std::set::~set (inline) 0 0% 26.61% 7860ms 7.37% std::_Rb_tree::_M_put_node (inline) 3116ms 2.92% 29.54% 7792ms 7.31% __GI___libc_malloc 2982ms 2.80% 32.33% 7582ms 7.11% __GI___libc_free 16ms 0.015% 32.35% 7470ms 7.01% MutableVertexMesh::RemoveDeletedNodesAndElements 469ms 0.44% 32.79% 7355ms 6.90% std::map::operator[] (partial-inline) 125ms 0.12% 32.90% 7133ms 6.69% std::_Rb_tree::_Rb_tree (partial-inline) 1429ms 1.34% 34.25% 7077ms 6.64% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 768ms 0.72% 34.97% 6737ms 6.32% std::_Rb_tree::_M_copy (inline) 13ms 0.012% 34.98% 6699ms 6.28% std::set::set (inline) 6295ms 5.90% 40.88% 6295ms 5.90% boost::numeric::ublas::c_vector::operator() 6280ms 5.89% 46.77% 6280ms 5.89% __strcmp_avx2 88ms 0.083% 46.86% 6174ms 5.79% SimpleWntCellCycleModel::GetWntLevel 141ms 0.13% 46.99% 6000ms 5.63% WntConcentration::GetWntLevel 2331ms 2.19% 49.17% 5720ms 5.37% std::_Rb_tree::_M_lower_bound (inline) 745ms 0.7% 49.87% 5649ms 5.30% std::_Rb_tree::_M_clone_node (inline) 0 0% 49.87% 5505ms 5.16% std::set::insert (inline) 35ms 0.033% 49.91% 5405ms 5.07% MutableVertexMesh::RemoveDeletedNodes 2592ms 2.43% 52.34% 5398ms 5.06% __cxxabiv1::__si_class_type_info::__do_dyncast 42ms 0.039% 52.38% 5233ms 4.91% EdgeHelper::RemoveDeletedEdges 36ms 0.034% 52.41% 4963ms 4.66% EdgeHelper::UpdateEdgesMapKey 1542ms 1.45% 53.86% 4940ms 4.63% boost::numeric::ublas::c_vector::operator[] (inline) 580ms 0.54% 54.40% 4682ms 4.39% std::_Rb_tree::_M_insert_ (inline) 0 0% 54.40% 4627ms 4.34% std::_Rb_tree::lower_bound (inline) 0 0% 54.40% 4627ms 4.34% std::map::lower_bound (inline) 4279ms 4.01% 58.42% 4594ms 4.31% _int_free 179ms 0.17% 58.58% 4565ms 4.28% MutableElement::ResetIndex 3ms 0.0028% 58.59% 4552ms 4.27% AbstractCellBasedSimulation::DoCellRemoval (inline) 49ms 0.046% 58.63% 4505ms 4.23% std::set_intersection (inline) 250ms 0.23% 58.87% 4456ms 4.18% std::__set_intersection 44ms 0.041% 58.91% 3977ms 3.73% Cell::GetCellProliferativeType 103ms 0.097% 59.00% 3973ms 3.73% AbstractCellPopulation::GetCellUsingLocationIndex 3935ms 3.69% 62.70% 3935ms 3.69% boost::numeric::ublas::same_impl_ex 78ms 0.073% 62.77% 3630ms 3.41% AbstractCellProperty::IsType (inline) 9ms 0.0084% 62.78% 3493ms 3.28% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.78% 3413ms 3.20% std::insert_iterator::operator= (inline) 49ms 0.046% 62.82% 3207ms 3.01% Cell::SetCellProliferativeType 2206ms 2.07% 64.89% 3053ms 2.86% _int_malloc 777ms 0.73% 65.62% 3037ms 2.85% AbstractElement::GetNodeLocation 2ms 0.0019% 65.62% 2979ms 2.79% std::_Rb_tree::_M_insert_unique_ (inline) 51ms 0.048% 65.67% 2874ms 2.70% std::_Rb_tree::erase 2785ms 2.61% 68.28% 2785ms 2.61% std::_Rb_tree::_S_right (inline) 613ms 0.58% 68.86% 2765ms 2.59% boost::numeric::ublas::vector_binary::size (inline) 404ms 0.38% 69.24% 2678ms 2.51% std::_Rb_tree_const_iterator::operator++ (inline) 772ms 0.72% 69.96% 2614ms 2.45% AbstractCellProperty::IsSame 1ms 0.00094% 69.96% 2526ms 2.37% std::_Rb_tree::_M_insert_unique 42ms 0.039% 70.00% 2474ms 2.32% CellPropertyCollection::HasProperty 0 0% 70.00% 2450ms 2.30% boost::numeric::ublas::c_vector::operator-= (inline) 212ms 0.2% 70.20% 2378ms 2.23% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 70.20% 2377ms 2.23% Cell::HasCellProperty (inline) 0 0% 70.20% 2355ms 2.21% boost::numeric::ublas::c_vector::assign (inline) 23ms 0.022% 70.22% 2281ms 2.14% Cell::GetCellData 110ms 0.1% 70.33% 2275ms 2.13% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 88ms 0.083% 70.41% 2212ms 2.07% VertexMesh::GetVolumeOfElement 29ms 0.027% 70.44% 2205ms 2.07% std::_Rb_tree::_M_emplace_hint_unique 4ms 0.0038% 70.44% 2187ms 2.05% AbstractCellPopulation::Iterator::operator++ (inline) 211ms 0.2% 70.64% 2179ms 2.04% AbstractCellPopulation::Iterator::IsRealCell (inline) 2103ms 1.97% 72.61% 2103ms 1.97% std::_Rb_tree_increment 85ms 0.08% 72.69% 1897ms 1.78% MutableVertexMesh::CheckForSwapsFromShortEdges 1296ms 1.22% 73.91% 1883ms 1.77% std::_Rb_tree::equal_range (inline) 433ms 0.41% 74.31% 1842ms 1.73% std::type_info::operator== (inline) 3ms 0.0028% 74.31% 1802ms 1.69% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 74.31% 1802ms 1.69% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 27ms 0.025% 74.34% 1671ms 1.57% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 17ms 0.016% 74.36% 1585ms 1.49% VertexMesh::GetSurfaceAreaOfElement 128ms 0.12% 74.48% 1546ms 1.45% boost::numeric::ublas::vector_reference::operator() (inline) 45ms 0.042% 74.52% 1530ms 1.44% Node::RemoveElement 179ms 0.17% 74.69% 1517ms 1.42% CellPropertyCollection::AddProperty 14ms 0.013% 74.70% 1496ms 1.40% std::set::erase (inline) 86ms 0.081% 74.78% 1495ms 1.40% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 39ms 0.037% 74.82% 1480ms 1.39% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 74.82% 1451ms 1.36% tcache_get (inline) 1451ms 1.36% 76.18% 1451ms 1.36% tcache_get_n (inline) 0 0% 76.18% 1425ms 1.34% OffLatticeSimulation::ApplyBoundaries 0 0% 76.18% 1418ms 1.33% boost::numeric::ublas::vector_binary::operator() (inline) 77ms 0.072% 76.25% 1263ms 1.18% std::less::operator() (inline) 0 0% 76.25% 1209ms 1.13% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 76.25% 1200ms 1.13% AbstractCellPopulation::WriteResultsToFiles 990ms 0.93% 77.18% 1186ms 1.11% std::operator< (inline) 27ms 0.025% 77.20% 1157ms 1.09% CellPropertyRegistry::Get 0 0% 77.20% 1157ms 1.09% boost::numeric::ublas::norm_2 (inline) 74ms 0.069% 77.27% 1152ms 1.08% std::_Rb_tree::_M_erase_aux (partial-inline) 505ms 0.47% 77.75% 1145ms 1.07% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1144ms 1.07% 78.82% 1144ms 1.07% [libchaste_cell_based.so] 1119ms 1.05% 79.87% 1119ms 1.05% Node::rGetLocation 76ms 0.071% 79.94% 1079ms 1.01% std::_Rb_tree::find (inline) 20ms 0.019% 79.96% 1068ms 1.00% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 1034ms 0.97% 80.93% 1034ms 0.97% std::_Rb_tree_insert_and_rebalance 0 0% 80.93% 1020ms 0.96% std::_Rb_tree::clear (inline) 1015ms 0.95% 81.88% 1015ms 0.95% std::vector::size (inline) 0 0% 81.88% 1014ms 0.95% std::map::clear (inline) 150ms 0.14% 82.02% 1012ms 0.95% boost::detail::shared_count::~shared_count (inline) 0 0% 82.02% 1012ms 0.95% boost::shared_ptr::~shared_ptr (inline) 6ms 0.0056% 82.03% 1011ms 0.95% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 413ms 0.39% 82.42% 982ms 0.92% Edge::GetMapIndex 887ms 0.83% 83.25% 887ms 0.83% [libchaste_mesh.so] 17ms 0.016% 83.26% 885ms 0.83% boost::numeric::ublas::detail::expression_type_check (inline) 1ms 0.00094% 83.26% 877ms 0.82% std::map::find (inline) 0 0% 83.26% 868ms 0.81% boost::numeric::ublas::c_vector::assign_temporary (inline) 6ms 0.0056% 83.27% 868ms 0.81% boost::numeric::ublas::c_vector::swap (inline) 67ms 0.063% 83.33% 862ms 0.81% std::swap_ranges (inline) 157ms 0.15% 83.48% 853ms 0.8% boost::numeric::ublas::detail::equals 0 0% 83.48% 852ms 0.8% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00094% 83.48% 846ms 0.79% VertexBasedCellPopulation::WriteCellVtkResultsToFile 827ms 0.78% 84.26% 832ms 0.78% boost::detail::sp_counted_base::release 121ms 0.11% 84.37% 815ms 0.76% MutableElement::GetNodeLocalIndex 796ms 0.75% 85.12% 796ms 0.75% std::swap (inline) 0 0% 85.12% 795ms 0.75% std::iter_swap (inline) 123ms 0.12% 85.23% 787ms 0.74% boost::numeric::ublas::c_vector::operator= (inline) 26ms 0.024% 85.26% 771ms 0.72% MutableElement::RegisterWithEdges (inline) 28ms 0.026% 85.28% 762ms 0.71% Edge::AddElement 460ms 0.43% 85.71% 760ms 0.71% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 133ms 0.12% 85.84% 740ms 0.69% boost::shared_ptr::shared_ptr (inline) 724ms 0.68% 86.52% 724ms 0.68% Node::GetIndex 0 0% 86.52% 703ms 0.66% CellPropertyCollection::~CellPropertyCollection (inline) 694ms 0.65% 87.17% 694ms 0.65% [libstdc++.so.6.0.33] 113ms 0.11% 87.28% 673ms 0.63% std::__new_allocator::construct (inline) 0 0% 87.28% 673ms 0.63% std::allocator_traits::construct (inline) 0 0% 87.28% 660ms 0.62% VertexMeshWriter::WriteVtkUsingMesh 0 0% 87.28% 649ms 0.61% std::_Rb_tree::_Auto_node::_M_insert (inline) 28ms 0.026% 87.30% 649ms 0.61% std::_Rb_tree::_M_insert_node (inline) 0 0% 87.30% 645ms 0.61% boost::numeric::ublas::norm_inf (inline) 382ms 0.36% 87.66% 645ms 0.61% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 87.66% 639ms 0.6% std::_Vector_base::_M_allocate (inline) 0 0% 87.66% 627ms 0.59% std::_Rb_tree::_M_construct_node (inline) 613ms 0.58% 88.24% 613ms 0.58% operator delete 25ms 0.023% 88.26% 609ms 0.57% MutableElement::RegisterWithNodes (inline) 581ms 0.55% 88.80% 607ms 0.57% boost::detail::shared_count::shared_count (inline) 575ms 0.54% 89.34% 575ms 0.54% boost::shared_ptr::operator-> (inline) 26ms 0.024% 89.37% 570ms 0.53% Node::AddElement 0 0% 89.37% 561ms 0.53% boost::numeric::ublas::scalar_traits::type_sqrt (inline)