File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 98057ms, 88.13% of 111260ms total Dropped 1138 nodes (cum <= 556.30ms) flat flat% sum% cum cum% 0 0% 0% 110903ms 99.68% __libc_start_call_main 0 0% 0% 110903ms 99.68% __libc_start_main_impl 0 0% 0% 110903ms 99.68% _start 0 0% 0% 110880ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 110880ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 110880ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 110880ms 99.66% main 0 0% 0% 110833ms 99.62% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 110833ms 99.62% CxxTest::TestRunner::runTest (inline) 0 0% 0% 110833ms 99.62% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 5ms 0.0045% 0.0045% 110825ms 99.61% AbstractCellBasedSimulation::Solve 16ms 0.014% 0.019% 57300ms 51.50% OffLatticeSimulation::UpdateCellLocationsAndTopology 9ms 0.0081% 0.027% 53855ms 48.40% ForwardEulerNumericalMethod::UpdateAllNodePositions 164ms 0.15% 0.17% 52331ms 47.03% AbstractNumericalMethod::ComputeForcesIncludingDamping 307ms 0.28% 0.45% 40260ms 36.19% NagaiHondaForce::AddForceContribution 3ms 0.0027% 0.45% 40136ms 36.07% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.45% 24424ms 21.95% VertexBasedCellPopulation::Update 3ms 0.0027% 0.46% 24275ms 21.82% MutableVertexMesh::ReMesh 14424ms 12.96% 13.42% 23114ms 20.77% Cylindrical2dVertexMesh::GetVectorFromAtoB 101ms 0.091% 13.51% 18369ms 16.51% Cell::ReadyToDivide 72ms 0.065% 13.58% 16973ms 15.26% AbstractPhaseBasedCellCycleModel::ReadyToDivide 363ms 0.33% 13.90% 14743ms 13.25% NagaiHondaForce::GetAdhesionParameter 133ms 0.12% 14.02% 14638ms 13.16% SimpleWntCellCycleModel::UpdateCellCyclePhase 120ms 0.11% 14.13% 13888ms 12.48% CellPropertyCollection::GetPropertiesType (inline) 500ms 0.45% 14.58% 13861ms 12.46% boost::numeric::ublas::c_vector::c_vector (partial-inline) 295ms 0.27% 14.84% 12320ms 11.07% boost::numeric::ublas::vector_assign (inline) 142ms 0.13% 14.97% 11865ms 10.66% MutableVertexMesh::CheckForIntersections 3536ms 3.18% 18.15% 11735ms 10.55% __dynamic_cast 64ms 0.058% 18.21% 11616ms 10.44% AbstractCellProperty::IsSubType (inline) 89ms 0.08% 18.29% 11462ms 10.30% VertexBasedCellPopulation::GetDampingConstant 37ms 0.033% 18.32% 10880ms 9.78% AbstractCellBasedSimulation::DoCellBirth 66ms 0.059% 18.38% 10848ms 9.75% AbstractTargetAreaModifier::UpdateTargetAreas 51ms 0.046% 18.43% 10760ms 9.67% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 1385ms 1.24% 19.67% 10467ms 9.41% std::__new_allocator::allocate (inline) 0 0% 19.67% 9972ms 8.96% std::_Rb_tree::_M_create_node (inline) 0 0% 19.67% 9897ms 8.90% std::allocator_traits::allocate (inline) 438ms 0.39% 20.06% 9496ms 8.53% VertexMesh::GetNextEdgeGradientOfElementAtNode 33ms 0.03% 20.09% 9411ms 8.46% VertexBasedCellPopulation::GetLocationOfCellCentre 2840ms 2.55% 22.65% 9265ms 8.33% boost::numeric::ublas::indexing_vector_assign 814ms 0.73% 23.38% 9192ms 8.26% operator new 0 0% 23.38% 9176ms 8.25% std::_Rb_tree::_M_get_node (inline) 1178ms 1.06% 24.44% 8952ms 8.05% std::_Rb_tree::_M_erase 385ms 0.35% 24.78% 8896ms 8.00% VertexMesh::GetCentroidOfElement 0 0% 24.78% 8808ms 7.92% std::_Rb_tree::_Alloc_node::operator() (inline) 814ms 0.73% 25.51% 8637ms 7.76% VertexMesh::ElementIncludesPoint 76ms 0.068% 25.58% 8623ms 7.75% Cell::GetMutationState 2845ms 2.56% 28.14% 8181ms 7.35% __GI___libc_malloc 0 0% 28.14% 8131ms 7.31% std::_Rb_tree::_M_drop_node (inline) 14ms 0.013% 28.15% 8077ms 7.26% MutableVertexMesh::RemoveDeletedNodesAndElements 191ms 0.17% 28.32% 7983ms 7.18% std::_Rb_tree::~_Rb_tree (inline) 197ms 0.18% 28.50% 7933ms 7.13% std::__new_allocator::deallocate (inline) 0 0% 28.50% 7923ms 7.12% std::allocator_traits::deallocate (inline) 0 0% 28.50% 7836ms 7.04% std::_Rb_tree::_M_put_node (inline) 524ms 0.47% 28.97% 7774ms 6.99% std::map::operator[] (partial-inline) 219ms 0.2% 29.17% 7614ms 6.84% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 29.17% 7539ms 6.78% std::set::~set (inline) 1524ms 1.37% 30.54% 7472ms 6.72% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 2469ms 2.22% 32.76% 7402ms 6.65% __GI___libc_free 792ms 0.71% 33.47% 7164ms 6.44% std::_Rb_tree::_M_copy (inline) 16ms 0.014% 33.48% 7090ms 6.37% std::set::set (inline) 129ms 0.12% 33.60% 6936ms 6.23% SimpleWntCellCycleModel::GetWntLevel 166ms 0.15% 33.75% 6739ms 6.06% WntConcentration::GetWntLevel 6621ms 5.95% 39.70% 6621ms 5.95% __strcmp_avx2 2534ms 2.28% 41.98% 6235ms 5.60% std::_Rb_tree::_M_lower_bound (inline) 876ms 0.79% 42.76% 6080ms 5.46% std::_Rb_tree::_M_clone_node (inline) 6078ms 5.46% 48.23% 6078ms 5.46% boost::numeric::ublas::c_vector::operator() 2893ms 2.60% 50.83% 5520ms 4.96% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 50.83% 5432ms 4.88% std::set::insert (inline) 21ms 0.019% 50.85% 5428ms 4.88% MutableVertexMesh::RemoveDeletedNodes 2032ms 1.83% 52.67% 5406ms 4.86% boost::numeric::ublas::c_vector::operator[] (inline) 38ms 0.034% 52.71% 5238ms 4.71% EdgeHelper::RemoveDeletedEdges 0 0% 52.71% 5056ms 4.54% std::_Rb_tree::lower_bound (inline) 0 0% 52.71% 5056ms 4.54% std::map::lower_bound (inline) 204ms 0.18% 52.89% 5034ms 4.52% MutableElement::ResetIndex 4443ms 3.99% 56.88% 4910ms 4.41% _int_free 43ms 0.039% 56.92% 4884ms 4.39% EdgeHelper::UpdateEdgesMapKey 3ms 0.0027% 56.93% 4819ms 4.33% AbstractCellBasedSimulation::DoCellRemoval (inline) 517ms 0.46% 57.39% 4616ms 4.15% std::_Rb_tree::_M_insert_ (inline) 126ms 0.11% 57.50% 4472ms 4.02% AbstractCellPopulation::GetCellUsingLocationIndex 122ms 0.11% 57.61% 4258ms 3.83% std::set_intersection (inline) 212ms 0.19% 57.80% 4136ms 3.72% std::__set_intersection 36ms 0.032% 57.84% 3953ms 3.55% Cell::GetCellProliferativeType 50ms 0.045% 57.88% 3924ms 3.53% AbstractCellProperty::IsType (inline) 3731ms 3.35% 61.23% 3731ms 3.35% boost::numeric::ublas::same_impl_ex 10ms 0.009% 61.24% 3616ms 3.25% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 2400ms 2.16% 63.40% 3385ms 3.04% _int_malloc 68ms 0.061% 63.46% 3298ms 2.96% std::_Rb_tree::erase 0 0% 63.46% 3236ms 2.91% std::insert_iterator::operator= (inline) 3184ms 2.86% 66.32% 3184ms 2.86% std::_Rb_tree::_S_right (inline) 24ms 0.022% 66.34% 3169ms 2.85% Cell::SetCellProliferativeType 39ms 0.035% 66.38% 2873ms 2.58% CellPropertyCollection::HasProperty 861ms 0.77% 67.15% 2872ms 2.58% AbstractElement::GetNodeLocation 763ms 0.69% 67.84% 2826ms 2.54% AbstractCellProperty::IsSame 7ms 0.0063% 67.85% 2816ms 2.53% std::_Rb_tree::_M_insert_unique_ (inline) 0 0% 67.85% 2773ms 2.49% Cell::HasCellProperty (inline) 670ms 0.6% 68.45% 2702ms 2.43% boost::numeric::ublas::vector_binary::size (inline) 200ms 0.18% 68.63% 2630ms 2.36% VertexMesh::GetAreaGradientOfElementAtNode 4ms 0.0036% 68.63% 2616ms 2.35% std::_Rb_tree::_M_insert_unique 24ms 0.022% 68.65% 2600ms 2.34% Cell::GetCellData 0 0% 68.65% 2600ms 2.34% boost::numeric::ublas::c_vector::operator-= (inline) 275ms 0.25% 68.90% 2550ms 2.29% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 68.90% 2511ms 2.26% boost::numeric::ublas::c_vector::assign (inline) 0 0% 68.90% 2496ms 2.24% AbstractCellPopulation::WriteResultsToFiles 171ms 0.15% 69.05% 2278ms 2.05% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 69.05% 2275ms 2.04% AbstractCellPopulation::Iterator::operator++ (inline) 53ms 0.048% 69.10% 2244ms 2.02% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 82ms 0.074% 69.17% 2214ms 1.99% VertexMesh::GetVolumeOfElement 3ms 0.0027% 69.18% 2181ms 1.96% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 69.18% 2181ms 1.96% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 31ms 0.028% 69.21% 2149ms 1.93% std::_Rb_tree::_M_emplace_hint_unique 1424ms 1.28% 70.49% 2145ms 1.93% std::_Rb_tree::equal_range (inline) 488ms 0.44% 70.92% 2063ms 1.85% std::type_info::operator== (inline) 2036ms 1.83% 72.75% 2036ms 1.83% std::_Rb_tree_increment 0 0% 72.75% 2033ms 1.83% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.0009% 72.75% 2013ms 1.81% VertexBasedCellPopulation::WriteCellVtkResultsToFile 62ms 0.056% 72.81% 1864ms 1.68% MutableVertexMesh::CheckForSwapsFromShortEdges 18ms 0.016% 72.83% 1822ms 1.64% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 72.83% 1816ms 1.63% VertexMeshWriter::WriteVtkUsingMesh 0 0% 72.83% 1742ms 1.57% tcache_get (inline) 1742ms 1.57% 74.39% 1742ms 1.57% tcache_get_n (inline) 21ms 0.019% 74.41% 1690ms 1.52% AbstractCellPopulation::GetLocationIndexUsingCell 95ms 0.085% 74.50% 1668ms 1.50% boost::numeric::ublas::c_vector::operator= (inline) 84ms 0.075% 74.57% 1625ms 1.46% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 40ms 0.036% 74.61% 1578ms 1.42% Node::RemoveElement 40ms 0.036% 74.64% 1578ms 1.42% VertexMesh::GetSurfaceAreaOfElement 145ms 0.13% 74.77% 1571ms 1.41% CellPropertyCollection::AddProperty 11ms 0.0099% 74.78% 1542ms 1.39% std::set::erase (inline) 1ms 0.0009% 74.79% 1444ms 1.30% OffLatticeSimulation::ApplyBoundaries 0 0% 74.79% 1412ms 1.27% boost::numeric::ublas::norm_2 (inline) 607ms 0.55% 75.33% 1396ms 1.25% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 72ms 0.065% 75.40% 1387ms 1.25% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 75.40% 1335ms 1.20% boost::numeric::ublas::vector_binary::operator() (inline) 1314ms 1.18% 76.58% 1314ms 1.18% [libchaste_cell_based.so] 71ms 0.064% 76.64% 1280ms 1.15% std::_Rb_tree::_M_erase_aux (partial-inline) 72ms 0.065% 76.71% 1267ms 1.14% std::less::operator() (inline) 18ms 0.016% 76.72% 1228ms 1.10% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 107ms 0.096% 76.82% 1218ms 1.09% std::_Rb_tree::find (inline) 962ms 0.86% 77.68% 1195ms 1.07% std::operator< (inline) 1191ms 1.07% 78.75% 1191ms 1.07% __memcpy_avx_unaligned_erms 0 0% 78.75% 1164ms 1.05% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 78.75% 1163ms 1.05% std::_Rb_tree::clear (inline) 38ms 0.034% 78.79% 1160ms 1.04% std::__copy_move::__copy_m (inline) 0 0% 78.79% 1160ms 1.04% std::__copy_move_a (inline) 0 0% 78.79% 1160ms 1.04% std::__copy_move_a1 (inline) 0 0% 78.79% 1160ms 1.04% std::__copy_move_a2 (inline) 0 0% 78.79% 1160ms 1.04% std::copy (inline) 5ms 0.0045% 78.79% 1157ms 1.04% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 24ms 0.022% 78.81% 1142ms 1.03% CellPropertyRegistry::Get 0 0% 78.81% 1140ms 1.02% std::map::clear (inline) 0 0% 78.81% 1087ms 0.98% boost::numeric::ublas::c_vector::assign_temporary (inline) 12ms 0.011% 78.82% 1087ms 0.98% boost::numeric::ublas::c_vector::swap (inline) 80ms 0.072% 78.90% 1075ms 0.97% std::swap_ranges (inline) 22ms 0.02% 78.92% 1065ms 0.96% boost::numeric::ublas::detail::expression_type_check (inline) 1052ms 0.95% 79.86% 1052ms 0.95% std::_Rb_tree_insert_and_rebalance 0 0% 79.86% 1039ms 0.93% std::map::find (inline) 190ms 0.17% 80.03% 1035ms 0.93% boost::numeric::ublas::detail::equals 0 0% 80.03% 995ms 0.89% std::iter_swap (inline) 995ms 0.89% 80.93% 995ms 0.89% std::swap (inline) 92ms 0.083% 81.01% 981ms 0.88% boost::detail::shared_count::~shared_count (inline) 0 0% 81.01% 981ms 0.88% boost::shared_ptr::~shared_ptr (inline) 916ms 0.82% 81.83% 916ms 0.82% Node::rGetLocation 910ms 0.82% 82.65% 910ms 0.82% std::vector::size (inline) 239ms 0.21% 82.86% 865ms 0.78% std::__new_allocator::construct (inline) 0 0% 82.86% 865ms 0.78% std::allocator_traits::construct (inline) 1ms 0.0009% 82.87% 860ms 0.77% VertexMeshWriter::MakeVtkMesh 836ms 0.75% 83.62% 856ms 0.77% boost::detail::sp_counted_base::release 0 0% 83.62% 796ms 0.72% std::_Rb_tree::_M_construct_node (inline) 197ms 0.18% 83.79% 794ms 0.71% boost::shared_ptr::shared_ptr (inline) 416ms 0.37% 84.17% 776ms 0.7% Edge::GetMapIndex 0 0% 84.17% 773ms 0.69% boost::numeric::ublas::norm_inf (inline) 386ms 0.35% 84.51% 773ms 0.69% boost::numeric::ublas::vector_norm_inf::apply (inline) 23ms 0.021% 84.54% 762ms 0.68% MutableElement::RegisterWithEdges (inline) 23ms 0.021% 84.56% 758ms 0.68% AbstractNumericalMethod::DetectStepSizeExceptions 22ms 0.02% 84.58% 743ms 0.67% Edge::AddElement 0 0% 84.58% 741ms 0.67% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 123ms 0.11% 84.69% 735ms 0.66% VertexBasedCellPopulation::CheckForStepSizeException 735ms 0.66% 85.35% 735ms 0.66% [libchaste_mesh.so] 393ms 0.35% 85.70% 733ms 0.66% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 85.70% 715ms 0.64% CellPropertyCollection::~CellPropertyCollection (inline) 2ms 0.0018% 85.70% 714ms 0.64% std::_Vector_base::_M_allocate (inline) 689ms 0.62% 86.32% 689ms 0.62% [libstdc++.so.6.0.33] 149ms 0.13% 86.46% 684ms 0.61% MutableElement::GetNodeLocalIndex 0 0% 86.46% 644ms 0.58% std::_Rb_tree::_Auto_node::_M_insert (inline) 22ms 0.02% 86.47% 644ms 0.58% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.47% 631ms 0.57% vtkPolygon::New 2ms 0.0018% 86.48% 631ms 0.57% vtkPolygon::vtkPolygon 34ms 0.031% 86.51% 630ms 0.57% MutableElement::RegisterWithNodes (inline) 11ms 0.0099% 86.52% 625ms 0.56% std::vector::_M_default_append (inline) 620ms 0.56% 87.07% 620ms 0.56% Node::GetIndex 28ms 0.025% 87.10% 598ms 0.54% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.10% 598ms 0.54% boost::numeric::ublas::vector::vector (inline) 30ms 0.027% 87.13% 597ms 0.54% Node::AddElement 562ms 0.51% 87.63% 597ms 0.54% boost::detail::shared_count::shared_count (inline) 558ms 0.5% 88.13% 558ms 0.5% tcache_put (inline)