File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96269ms, 87.65% of 109832ms total Dropped 1112 nodes (cum <= 549.16ms) flat flat% sum% cum cum% 0 0% 0% 109380ms 99.59% __libc_start_call_main 0 0% 0% 109380ms 99.59% __libc_start_main_impl 0 0% 0% 109380ms 99.59% _start 0 0% 0% 109361ms 99.57% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 109361ms 99.57% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 109361ms 99.57% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 109361ms 99.57% main 0 0% 0% 109323ms 99.54% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 109323ms 99.54% CxxTest::TestRunner::runTest (inline) 0 0% 0% 109323ms 99.54% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 1ms 0.00091% 0.00091% 109315ms 99.53% AbstractCellBasedSimulation::Solve 14ms 0.013% 0.014% 56842ms 51.75% OffLatticeSimulation::UpdateCellLocationsAndTopology 31ms 0.028% 0.042% 53567ms 48.77% ForwardEulerNumericalMethod::UpdateAllNodePositions 115ms 0.1% 0.15% 52521ms 47.82% AbstractNumericalMethod::ComputeForcesIncludingDamping 436ms 0.4% 0.54% 40487ms 36.86% NagaiHondaForce::AddForceContribution 1ms 0.00091% 0.54% 39556ms 36.02% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0018% 0.55% 24585ms 22.38% VertexBasedCellPopulation::Update 1ms 0.00091% 0.55% 24461ms 22.27% MutableVertexMesh::ReMesh 14554ms 13.25% 13.80% 23101ms 21.03% Cylindrical2dVertexMesh::GetVectorFromAtoB 84ms 0.076% 13.87% 17359ms 15.81% Cell::ReadyToDivide 111ms 0.1% 13.98% 16149ms 14.70% AbstractPhaseBasedCellCycleModel::ReadyToDivide 310ms 0.28% 14.26% 15001ms 13.66% NagaiHondaForce::GetAdhesionParameter 422ms 0.38% 14.64% 14277ms 13.00% boost::numeric::ublas::c_vector::c_vector (partial-inline) 138ms 0.13% 14.77% 13772ms 12.54% SimpleWntCellCycleModel::UpdateCellCyclePhase 138ms 0.13% 14.89% 13505ms 12.30% CellPropertyCollection::GetPropertiesType (inline) 379ms 0.35% 15.24% 12731ms 11.59% boost::numeric::ublas::vector_assign (inline) 146ms 0.13% 15.37% 12066ms 10.99% MutableVertexMesh::CheckForIntersections 67ms 0.061% 15.43% 11528ms 10.50% VertexBasedCellPopulation::GetDampingConstant 3379ms 3.08% 18.51% 11251ms 10.24% __dynamic_cast 70ms 0.064% 18.57% 11138ms 10.14% AbstractCellProperty::IsSubType (inline) 96ms 0.087% 18.66% 10411ms 9.48% AbstractTargetAreaModifier::UpdateTargetAreas 49ms 0.045% 18.70% 10286ms 9.37% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 1353ms 1.23% 19.94% 10216ms 9.30% std::__new_allocator::allocate (inline) 21ms 0.019% 19.96% 10192ms 9.28% AbstractCellBasedSimulation::DoCellBirth 0 0% 19.96% 9674ms 8.81% std::allocator_traits::allocate (inline) 0 0% 19.96% 9629ms 8.77% std::_Rb_tree::_M_create_node (inline) 2785ms 2.54% 22.49% 9552ms 8.70% boost::numeric::ublas::indexing_vector_assign 1396ms 1.27% 23.76% 9408ms 8.57% std::_Rb_tree::_M_erase 397ms 0.36% 24.12% 9208ms 8.38% VertexMesh::GetNextEdgeGradientOfElementAtNode 782ms 0.71% 24.84% 9027ms 8.22% VertexMesh::ElementIncludesPoint 0 0% 24.84% 8985ms 8.18% std::_Rb_tree::_M_get_node (inline) 789ms 0.72% 25.55% 8953ms 8.15% operator new 27ms 0.025% 25.58% 8848ms 8.06% VertexBasedCellPopulation::GetLocationOfCellCentre 270ms 0.25% 25.82% 8616ms 7.84% std::_Rb_tree::~_Rb_tree (inline) 67ms 0.061% 25.89% 8606ms 7.84% Cell::GetMutationState 0 0% 25.89% 8453ms 7.70% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 25.89% 8351ms 7.60% std::_Rb_tree::_M_drop_node (inline) 489ms 0.45% 26.33% 8298ms 7.56% VertexMesh::GetCentroidOfElement 0 0% 26.33% 8157ms 7.43% std::set::~set (inline) 270ms 0.25% 26.58% 8125ms 7.40% std::__new_allocator::deallocate (inline) 0 0% 26.58% 8101ms 7.38% std::allocator_traits::deallocate (inline) 0 0% 26.58% 8036ms 7.32% std::_Rb_tree::_M_put_node (inline) 3119ms 2.84% 29.42% 7968ms 7.25% __GI___libc_malloc 3065ms 2.79% 32.21% 7921ms 7.21% __GI___libc_free 23ms 0.021% 32.23% 7810ms 7.11% MutableVertexMesh::RemoveDeletedNodesAndElements 484ms 0.44% 32.67% 7738ms 7.05% std::map::operator[] (partial-inline) 1471ms 1.34% 34.01% 7326ms 6.67% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 182ms 0.17% 34.17% 6982ms 6.36% std::_Rb_tree::_Rb_tree (partial-inline) 693ms 0.63% 34.80% 6578ms 5.99% std::_Rb_tree::_M_copy (inline) 14ms 0.013% 34.82% 6553ms 5.97% std::set::set (inline) 124ms 0.11% 34.93% 6323ms 5.76% SimpleWntCellCycleModel::GetWntLevel 6240ms 5.68% 40.61% 6240ms 5.68% __strcmp_avx2 2450ms 2.23% 42.84% 6192ms 5.64% std::_Rb_tree::_M_lower_bound (inline) 6176ms 5.62% 48.47% 6176ms 5.62% boost::numeric::ublas::c_vector::operator() 135ms 0.12% 48.59% 6111ms 5.56% WntConcentration::GetWntLevel 771ms 0.7% 49.29% 5584ms 5.08% std::_Rb_tree::_M_clone_node (inline) 27ms 0.025% 49.32% 5558ms 5.06% MutableVertexMesh::RemoveDeletedNodes 0 0% 49.32% 5460ms 4.97% std::set::insert (inline) 50ms 0.046% 49.36% 5395ms 4.91% EdgeHelper::RemoveDeletedEdges 2661ms 2.42% 51.78% 5286ms 4.81% __cxxabiv1::__si_class_type_info::__do_dyncast 31ms 0.028% 51.81% 5087ms 4.63% EdgeHelper::UpdateEdgesMapKey 0 0% 51.81% 5031ms 4.58% std::_Rb_tree::lower_bound (inline) 0 0% 51.81% 5031ms 4.58% std::map::lower_bound (inline) 207ms 0.19% 52.00% 4884ms 4.45% MutableElement::ResetIndex 1540ms 1.40% 53.40% 4857ms 4.42% boost::numeric::ublas::c_vector::operator[] (inline) 4517ms 4.11% 57.52% 4848ms 4.41% _int_free 0 0% 57.52% 4766ms 4.34% AbstractCellBasedSimulation::DoCellRemoval (inline) 543ms 0.49% 58.01% 4665ms 4.25% std::_Rb_tree::_M_insert_ (inline) 34ms 0.031% 58.04% 4476ms 4.08% std::set_intersection (inline) 279ms 0.25% 58.29% 4442ms 4.04% std::__set_intersection 119ms 0.11% 58.40% 4332ms 3.94% AbstractCellPopulation::GetCellUsingLocationIndex 3949ms 3.60% 62.00% 3949ms 3.60% boost::numeric::ublas::same_impl_ex 32ms 0.029% 62.03% 3929ms 3.58% Cell::GetCellProliferativeType 66ms 0.06% 62.09% 3729ms 3.40% AbstractCellProperty::IsType (inline) 8ms 0.0073% 62.09% 3651ms 3.32% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.09% 3238ms 2.95% std::insert_iterator::operator= (inline) 791ms 0.72% 62.82% 3229ms 2.94% AbstractElement::GetNodeLocation 65ms 0.059% 62.87% 3197ms 2.91% Cell::SetCellProliferativeType 49ms 0.045% 62.92% 3146ms 2.86% std::_Rb_tree::erase 3141ms 2.86% 65.78% 3141ms 2.86% std::_Rb_tree::_S_right (inline) 2198ms 2.00% 67.78% 3133ms 2.85% _int_malloc 3ms 0.0027% 67.78% 2846ms 2.59% std::_Rb_tree::_M_insert_unique_ (inline) 600ms 0.55% 68.33% 2746ms 2.50% boost::numeric::ublas::vector_binary::size (inline) 400ms 0.36% 68.69% 2681ms 2.44% std::_Rb_tree_const_iterator::operator++ (inline) 773ms 0.7% 69.40% 2672ms 2.43% AbstractCellProperty::IsSame 2ms 0.0018% 69.40% 2614ms 2.38% std::_Rb_tree::_M_insert_unique 51ms 0.046% 69.45% 2613ms 2.38% CellPropertyCollection::HasProperty 0 0% 69.45% 2524ms 2.30% Cell::HasCellProperty (inline) 1ms 0.00091% 69.45% 2475ms 2.25% AbstractCellPopulation::WriteResultsToFiles 231ms 0.21% 69.66% 2429ms 2.21% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.66% 2426ms 2.21% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.66% 2387ms 2.17% boost::numeric::ublas::c_vector::assign (inline) 18ms 0.016% 69.67% 2350ms 2.14% Cell::GetCellData 1ms 0.00091% 69.67% 2306ms 2.10% AbstractCellPopulation::Iterator::operator++ (inline) 220ms 0.2% 69.87% 2304ms 2.10% AbstractCellPopulation::Iterator::IsRealCell (inline) 100ms 0.091% 69.97% 2248ms 2.05% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 90ms 0.082% 70.05% 2199ms 2.00% VertexMesh::GetVolumeOfElement 31ms 0.028% 70.08% 2160ms 1.97% std::_Rb_tree::_M_emplace_hint_unique 1475ms 1.34% 71.42% 2158ms 1.96% std::_Rb_tree::equal_range (inline) 2095ms 1.91% 73.33% 2095ms 1.91% std::_Rb_tree_increment 0 0% 73.33% 2025ms 1.84% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 73.33% 2014ms 1.83% VertexBasedCellPopulation::WriteCellVtkResultsToFile 492ms 0.45% 73.77% 1899ms 1.73% std::type_info::operator== (inline) 61ms 0.056% 73.83% 1890ms 1.72% MutableVertexMesh::CheckForSwapsFromShortEdges 3ms 0.0027% 73.83% 1858ms 1.69% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.83% 1858ms 1.69% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 73.83% 1818ms 1.66% VertexMeshWriter::WriteVtkUsingMesh 30ms 0.027% 73.86% 1793ms 1.63% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 54ms 0.049% 73.91% 1670ms 1.52% Node::RemoveElement 17ms 0.015% 73.92% 1623ms 1.48% std::set::erase (inline) 19ms 0.017% 73.94% 1602ms 1.46% VertexMesh::GetSurfaceAreaOfElement 32ms 0.029% 73.97% 1592ms 1.45% AbstractCellPopulation::GetLocationIndexUsingCell 70ms 0.064% 74.03% 1578ms 1.44% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 149ms 0.14% 74.17% 1563ms 1.42% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 74.17% 1550ms 1.41% tcache_get (inline) 1550ms 1.41% 75.58% 1550ms 1.41% tcache_get_n (inline) 159ms 0.14% 75.73% 1525ms 1.39% CellPropertyCollection::AddProperty 0 0% 75.73% 1455ms 1.32% boost::numeric::ublas::vector_binary::operator() (inline) 2ms 0.0018% 75.73% 1383ms 1.26% OffLatticeSimulation::ApplyBoundaries 73ms 0.066% 75.79% 1295ms 1.18% std::less::operator() (inline) 993ms 0.9% 76.70% 1222ms 1.11% std::operator< (inline) 1202ms 1.09% 77.79% 1202ms 1.09% Node::rGetLocation 0 0% 77.79% 1184ms 1.08% boost::numeric::ublas::norm_2 (inline) 0 0% 77.79% 1176ms 1.07% std::_Rb_tree::_Auto_node::_Auto_node (inline) 497ms 0.45% 78.24% 1170ms 1.07% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 101ms 0.092% 78.34% 1159ms 1.06% std::_Rb_tree::find (inline) 12ms 0.011% 78.35% 1142ms 1.04% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 78ms 0.071% 78.42% 1133ms 1.03% std::_Rb_tree::_M_erase_aux (partial-inline) 1122ms 1.02% 79.44% 1122ms 1.02% [libchaste_cell_based.so] 0 0% 79.44% 1067ms 0.97% std::_Rb_tree::clear (inline) 5ms 0.0046% 79.44% 1057ms 0.96% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1055ms 0.96% 80.41% 1055ms 0.96% std::_Rb_tree_insert_and_rebalance 0 0% 80.41% 1048ms 0.95% std::map::clear (inline) 1025ms 0.93% 81.34% 1025ms 0.93% std::vector::size (inline) 24ms 0.022% 81.36% 1013ms 0.92% CellPropertyRegistry::Get 1002ms 0.91% 82.27% 1002ms 0.91% [libchaste_mesh.so] 146ms 0.13% 82.41% 1002ms 0.91% boost::detail::shared_count::~shared_count (inline) 0 0% 82.41% 1002ms 0.91% boost::shared_ptr::~shared_ptr (inline) 429ms 0.39% 82.80% 994ms 0.91% Edge::GetMapIndex 0 0% 82.80% 967ms 0.88% std::map::find (inline) 0 0% 82.80% 953ms 0.87% boost::numeric::ublas::c_vector::assign_temporary (inline) 7ms 0.0064% 82.80% 953ms 0.87% boost::numeric::ublas::c_vector::swap (inline) 89ms 0.081% 82.88% 946ms 0.86% std::swap_ranges (inline) 100ms 0.091% 82.97% 898ms 0.82% MutableElement::GetNodeLocalIndex 24ms 0.022% 83.00% 889ms 0.81% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 83.00% 871ms 0.79% VertexMeshWriter::MakeVtkMesh 141ms 0.13% 83.13% 857ms 0.78% boost::numeric::ublas::detail::equals 0 0% 83.13% 857ms 0.78% std::iter_swap (inline) 857ms 0.78% 83.91% 857ms 0.78% std::swap (inline) 828ms 0.75% 84.66% 834ms 0.76% boost::detail::sp_counted_base::release 122ms 0.11% 84.77% 801ms 0.73% boost::numeric::ublas::c_vector::operator= (inline) 29ms 0.026% 84.80% 789ms 0.72% Edge::AddElement 14ms 0.013% 84.81% 783ms 0.71% MutableElement::RegisterWithEdges (inline) 176ms 0.16% 84.97% 783ms 0.71% boost::shared_ptr::shared_ptr (inline) 760ms 0.69% 85.66% 760ms 0.69% Node::GetIndex 427ms 0.39% 86.05% 739ms 0.67% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 86.05% 738ms 0.67% CellPropertyCollection::~CellPropertyCollection (inline) 99ms 0.09% 86.14% 692ms 0.63% std::__new_allocator::construct (inline) 0 0% 86.14% 692ms 0.63% std::allocator_traits::construct (inline) 0 0% 86.14% 684ms 0.62% std::_Vector_base::_M_allocate (inline) 0 0% 86.14% 675ms 0.61% boost::numeric::ublas::norm_inf (inline) 352ms 0.32% 86.46% 675ms 0.61% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 86.46% 667ms 0.61% std::_Rb_tree::_Auto_node::_M_insert (inline) 28ms 0.025% 86.49% 667ms 0.61% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.49% 644ms 0.59% std::_Rb_tree::_M_construct_node (inline) 0 0% 86.49% 628ms 0.57% vtkPolygon::New 0 0% 86.49% 628ms 0.57% vtkPolygon::vtkPolygon 612ms 0.56% 87.04% 612ms 0.56% [libstdc++.so.6.0.33] 23ms 0.021% 87.06% 607ms 0.55% MutableElement::RegisterWithNodes (inline) 584ms 0.53% 87.60% 607ms 0.55% boost::detail::shared_count::shared_count (inline) 23ms 0.021% 87.62% 591ms 0.54% Node::AddElement 10ms 0.0091% 87.63% 572ms 0.52% std::vector::_M_default_append (inline) 27ms 0.025% 87.65% 569ms 0.52% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.65% 569ms 0.52% boost::numeric::ublas::vector::vector (inline) 0 0% 87.65% 561ms 0.51% boost::numeric::ublas::scalar_traits::type_sqrt (inline)