File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 98103ms, 88.21% of 111219ms total Dropped 1105 nodes (cum <= 556.10ms) flat flat% sum% cum cum% 0 0% 0% 110765ms 99.59% __libc_start_call_main 0 0% 0% 110765ms 99.59% __libc_start_main_impl 0 0% 0% 110765ms 99.59% _start 0 0% 0% 110746ms 99.57% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 110746ms 99.57% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 110746ms 99.57% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 110746ms 99.57% main 0 0% 0% 110712ms 99.54% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 110712ms 99.54% CxxTest::TestRunner::runTest (inline) 1ms 0.0009% 0.0009% 110712ms 99.54% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0018% 0.0027% 110703ms 99.54% AbstractCellBasedSimulation::Solve 17ms 0.015% 0.018% 57326ms 51.54% OffLatticeSimulation::UpdateCellLocationsAndTopology 15ms 0.013% 0.031% 54254ms 48.78% ForwardEulerNumericalMethod::UpdateAllNodePositions 158ms 0.14% 0.17% 52738ms 47.42% AbstractNumericalMethod::ComputeForcesIncludingDamping 382ms 0.34% 0.52% 40654ms 36.55% NagaiHondaForce::AddForceContribution 0 0% 0.52% 40057ms 36.02% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.52% 25041ms 22.52% VertexBasedCellPopulation::Update 0 0% 0.52% 24895ms 22.38% MutableVertexMesh::ReMesh 14419ms 12.96% 13.48% 22653ms 20.37% Cylindrical2dVertexMesh::GetVectorFromAtoB 111ms 0.1% 13.58% 17823ms 16.03% Cell::ReadyToDivide 76ms 0.068% 13.65% 16505ms 14.84% AbstractPhaseBasedCellCycleModel::ReadyToDivide 350ms 0.31% 13.96% 15440ms 13.88% NagaiHondaForce::GetAdhesionParameter 364ms 0.33% 14.29% 14291ms 12.85% boost::numeric::ublas::c_vector::c_vector (partial-inline) 133ms 0.12% 14.41% 14107ms 12.68% SimpleWntCellCycleModel::UpdateCellCyclePhase 103ms 0.093% 14.50% 13938ms 12.53% CellPropertyCollection::GetPropertiesType (inline) 396ms 0.36% 14.86% 12817ms 11.52% boost::numeric::ublas::vector_assign (inline) 117ms 0.11% 14.97% 12776ms 11.49% MutableVertexMesh::CheckForIntersections 61ms 0.055% 15.02% 11521ms 10.36% VertexBasedCellPopulation::GetDampingConstant 3528ms 3.17% 18.19% 11442ms 10.29% __dynamic_cast 78ms 0.07% 18.26% 11373ms 10.23% AbstractCellProperty::IsSubType (inline) 82ms 0.074% 18.34% 10818ms 9.73% AbstractTargetAreaModifier::UpdateTargetAreas 56ms 0.05% 18.39% 10703ms 9.62% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 23ms 0.021% 18.41% 10417ms 9.37% AbstractCellBasedSimulation::DoCellBirth 1342ms 1.21% 19.61% 10356ms 9.31% std::__new_allocator::allocate (inline) 0 0% 19.61% 9838ms 8.85% std::_Rb_tree::_M_create_node (inline) 0 0% 19.61% 9830ms 8.84% std::allocator_traits::allocate (inline) 752ms 0.68% 20.29% 9809ms 8.82% VertexMesh::ElementIncludesPoint 2713ms 2.44% 22.73% 9395ms 8.45% boost::numeric::ublas::indexing_vector_assign 1450ms 1.30% 24.03% 9299ms 8.36% std::_Rb_tree::_M_erase 0 0% 24.03% 9163ms 8.24% std::_Rb_tree::_M_get_node (inline) 787ms 0.71% 24.74% 9155ms 8.23% operator new 30ms 0.027% 24.77% 8881ms 7.99% VertexBasedCellPopulation::GetLocationOfCellCentre 82ms 0.074% 24.84% 8820ms 7.93% Cell::GetMutationState 389ms 0.35% 25.19% 8668ms 7.79% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 25.19% 8668ms 7.79% std::_Rb_tree::_Alloc_node::operator() (inline) 215ms 0.19% 25.38% 8485ms 7.63% std::_Rb_tree::~_Rb_tree (inline) 507ms 0.46% 25.84% 8329ms 7.49% VertexMesh::GetCentroidOfElement 0 0% 25.84% 8224ms 7.39% std::_Rb_tree::_M_drop_node (inline) 3197ms 2.87% 28.71% 8172ms 7.35% __GI___libc_malloc 0 0% 28.71% 8073ms 7.26% std::set::~set (inline) 246ms 0.22% 28.94% 7997ms 7.19% std::__new_allocator::deallocate (inline) 0 0% 28.94% 7963ms 7.16% std::allocator_traits::deallocate (inline) 0 0% 28.94% 7895ms 7.10% std::_Rb_tree::_M_put_node (inline) 3194ms 2.87% 31.81% 7836ms 7.05% __GI___libc_free 478ms 0.43% 32.24% 7625ms 6.86% std::map::operator[] (partial-inline) 19ms 0.017% 32.25% 7588ms 6.82% MutableVertexMesh::RemoveDeletedNodesAndElements 131ms 0.12% 32.37% 7125ms 6.41% std::_Rb_tree::_Rb_tree (partial-inline) 1451ms 1.30% 33.68% 7038ms 6.33% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 682ms 0.61% 34.29% 6723ms 6.04% std::_Rb_tree::_M_copy (inline) 9ms 0.0081% 34.30% 6698ms 6.02% std::set::set (inline) 97ms 0.087% 34.39% 6444ms 5.79% SimpleWntCellCycleModel::GetWntLevel 6386ms 5.74% 40.13% 6386ms 5.74% __strcmp_avx2 135ms 0.12% 40.25% 6234ms 5.61% WntConcentration::GetWntLevel 2427ms 2.18% 42.43% 6079ms 5.47% std::_Rb_tree::_M_lower_bound (inline) 6047ms 5.44% 47.87% 6047ms 5.44% boost::numeric::ublas::c_vector::operator() 726ms 0.65% 48.52% 5758ms 5.18% std::_Rb_tree::_M_clone_node (inline) 0 0% 48.52% 5587ms 5.02% std::set::insert (inline) 21ms 0.019% 48.54% 5510ms 4.95% MutableVertexMesh::RemoveDeletedNodes 2683ms 2.41% 50.95% 5468ms 4.92% __cxxabiv1::__si_class_type_info::__do_dyncast 41ms 0.037% 50.99% 5326ms 4.79% EdgeHelper::RemoveDeletedEdges 41ms 0.037% 51.03% 5034ms 4.53% EdgeHelper::UpdateEdgesMapKey 0 0% 51.03% 4930ms 4.43% std::_Rb_tree::lower_bound (inline) 0 0% 51.03% 4930ms 4.43% std::map::lower_bound (inline) 1445ms 1.30% 52.32% 4789ms 4.31% boost::numeric::ublas::c_vector::operator[] (inline) 530ms 0.48% 52.80% 4682ms 4.21% std::_Rb_tree::_M_insert_ (inline) 63ms 0.057% 52.86% 4646ms 4.18% std::set_intersection (inline) 4298ms 3.86% 56.72% 4636ms 4.17% _int_free 200ms 0.18% 56.90% 4627ms 4.16% MutableElement::ResetIndex 3ms 0.0027% 56.90% 4584ms 4.12% AbstractCellBasedSimulation::DoCellRemoval (inline) 274ms 0.25% 57.15% 4583ms 4.12% std::__set_intersection 103ms 0.093% 57.24% 4179ms 3.76% AbstractCellPopulation::GetCellUsingLocationIndex 47ms 0.042% 57.29% 3993ms 3.59% Cell::GetCellProliferativeType 54ms 0.049% 57.33% 3974ms 3.57% AbstractCellProperty::IsType (inline) 3951ms 3.55% 60.89% 3951ms 3.55% boost::numeric::ublas::same_impl_ex 0 0% 60.89% 3533ms 3.18% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 60.89% 3290ms 2.96% std::insert_iterator::operator= (inline) 833ms 0.75% 61.64% 3222ms 2.90% AbstractElement::GetNodeLocation 39ms 0.035% 61.67% 3190ms 2.87% Cell::SetCellProliferativeType 2288ms 2.06% 63.73% 3184ms 2.86% _int_malloc 3097ms 2.78% 66.51% 3097ms 2.78% std::_Rb_tree::_S_right (inline) 38ms 0.034% 66.55% 2919ms 2.62% std::_Rb_tree::erase 5ms 0.0045% 66.55% 2912ms 2.62% std::_Rb_tree::_M_insert_unique_ (inline) 782ms 0.7% 67.25% 2868ms 2.58% AbstractCellProperty::IsSame 424ms 0.38% 67.64% 2835ms 2.55% std::_Rb_tree_const_iterator::operator++ (inline) 56ms 0.05% 67.69% 2749ms 2.47% CellPropertyCollection::HasProperty 623ms 0.56% 68.25% 2680ms 2.41% boost::numeric::ublas::vector_binary::size (inline) 2ms 0.0018% 68.25% 2675ms 2.41% std::_Rb_tree::_M_insert_unique (inline) 0 0% 68.25% 2638ms 2.37% Cell::HasCellProperty (inline) 248ms 0.22% 68.47% 2543ms 2.29% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 68.47% 2513ms 2.26% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 68.47% 2478ms 2.23% AbstractCellPopulation::WriteResultsToFiles 24ms 0.022% 68.49% 2467ms 2.22% Cell::GetCellData 0 0% 68.49% 2397ms 2.16% boost::numeric::ublas::c_vector::assign (inline) 75ms 0.067% 68.56% 2310ms 2.08% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 5ms 0.0045% 68.56% 2299ms 2.07% AbstractCellPopulation::Iterator::operator++ (inline) 230ms 0.21% 68.77% 2289ms 2.06% AbstractCellPopulation::Iterator::IsRealCell (inline) 105ms 0.094% 68.87% 2278ms 2.05% VertexMesh::GetVolumeOfElement 2239ms 2.01% 70.88% 2239ms 2.01% std::_Rb_tree_increment 45ms 0.04% 70.92% 2168ms 1.95% std::_Rb_tree::_M_emplace_hint_unique 522ms 0.47% 71.39% 2086ms 1.88% std::type_info::operator== (inline) 0 0% 71.39% 2028ms 1.82% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 71.39% 2020ms 1.82% VertexBasedCellPopulation::WriteCellVtkResultsToFile 3ms 0.0027% 71.39% 2011ms 1.81% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 71.39% 2011ms 1.81% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1343ms 1.21% 72.60% 1982ms 1.78% std::_Rb_tree::equal_range (inline) 83ms 0.075% 72.67% 1920ms 1.73% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 72.67% 1807ms 1.62% VertexMeshWriter::WriteVtkUsingMesh 17ms 0.015% 72.69% 1799ms 1.62% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 141ms 0.13% 72.82% 1648ms 1.48% CellPropertyCollection::AddProperty 24ms 0.022% 72.84% 1622ms 1.46% VertexMesh::GetSurfaceAreaOfElement 0 0% 72.84% 1602ms 1.44% tcache_get (inline) 1602ms 1.44% 74.28% 1602ms 1.44% tcache_get_n (inline) 128ms 0.12% 74.39% 1585ms 1.43% boost::numeric::ublas::c_vector::operator= (inline) 82ms 0.074% 74.47% 1545ms 1.39% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 25ms 0.022% 74.49% 1542ms 1.39% AbstractCellPopulation::GetLocationIndexUsingCell 48ms 0.043% 74.53% 1516ms 1.36% Node::RemoveElement 21ms 0.019% 74.55% 1481ms 1.33% std::set::erase (inline) 125ms 0.11% 74.66% 1434ms 1.29% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 74.66% 1332ms 1.20% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 74.66% 1272ms 1.14% boost::numeric::ublas::norm_2 (inline) 592ms 0.53% 75.20% 1262ms 1.13% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 3ms 0.0027% 75.20% 1251ms 1.12% OffLatticeSimulation::ApplyBoundaries 76ms 0.068% 75.27% 1250ms 1.12% std::less::operator() (inline) 1222ms 1.10% 76.37% 1222ms 1.10% Node::rGetLocation 30ms 0.027% 76.39% 1198ms 1.08% CellPropertyRegistry::Get 961ms 0.86% 77.26% 1174ms 1.06% std::operator< (inline) 0 0% 77.26% 1170ms 1.05% std::_Rb_tree::_Auto_node::_Auto_node (inline) 99ms 0.089% 77.35% 1130ms 1.02% std::_Rb_tree::find (inline) 1129ms 1.02% 78.36% 1129ms 1.02% std::_Rb_tree_insert_and_rebalance 1128ms 1.01% 79.37% 1128ms 1.01% __memcpy_avx_unaligned_erms 77ms 0.069% 79.44% 1117ms 1.00% std::_Rb_tree::_M_erase_aux (partial-inline) 1098ms 0.99% 80.43% 1098ms 0.99% [libchaste_cell_based.so] 44ms 0.04% 80.47% 1082ms 0.97% std::__copy_move::__copy_m (inline) 0 0% 80.47% 1082ms 0.97% std::__copy_move_a (inline) 0 0% 80.47% 1082ms 0.97% std::__copy_move_a1 (inline) 0 0% 80.47% 1082ms 0.97% std::__copy_move_a2 (inline) 0 0% 80.47% 1082ms 0.97% std::copy (inline) 19ms 0.017% 80.49% 1051ms 0.94% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 139ms 0.12% 80.61% 1036ms 0.93% boost::detail::shared_count::~shared_count (inline) 0 0% 80.61% 1036ms 0.93% boost::shared_ptr::~shared_ptr (inline) 0 0% 80.61% 1033ms 0.93% std::_Rb_tree::clear (inline) 20ms 0.018% 80.63% 1016ms 0.91% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 80.63% 1016ms 0.91% std::map::clear (inline) 10ms 0.009% 80.64% 990ms 0.89% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 989ms 0.89% 81.53% 989ms 0.89% std::vector::size (inline) 180ms 0.16% 81.69% 985ms 0.89% boost::numeric::ublas::detail::equals 427ms 0.38% 82.08% 982ms 0.88% Edge::GetMapIndex 0 0% 82.08% 954ms 0.86% std::map::find (inline) 0 0% 82.08% 936ms 0.84% boost::numeric::ublas::c_vector::assign_temporary (inline) 10ms 0.009% 82.08% 936ms 0.84% boost::numeric::ublas::c_vector::swap (inline) 931ms 0.84% 82.92% 931ms 0.84% [libchaste_mesh.so] 79ms 0.071% 82.99% 926ms 0.83% std::swap_ranges (inline) 128ms 0.12% 83.11% 888ms 0.8% MutableElement::GetNodeLocalIndex 863ms 0.78% 83.88% 870ms 0.78% boost::detail::sp_counted_base::release 2ms 0.0018% 83.88% 860ms 0.77% VertexMeshWriter::MakeVtkMesh 848ms 0.76% 84.65% 848ms 0.76% std::swap (inline) 0 0% 84.65% 847ms 0.76% std::iter_swap (inline) 820ms 0.74% 85.38% 820ms 0.74% Node::GetIndex 135ms 0.12% 85.51% 768ms 0.69% boost::shared_ptr::shared_ptr (inline) 481ms 0.43% 85.94% 761ms 0.68% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 85.94% 739ms 0.66% boost::numeric::ublas::norm_inf (inline) 375ms 0.34% 86.28% 739ms 0.66% boost::numeric::ublas::vector_norm_inf::apply (inline) 100ms 0.09% 86.37% 723ms 0.65% std::__new_allocator::construct (inline) 0 0% 86.37% 723ms 0.65% std::allocator_traits::construct (inline) 26ms 0.023% 86.39% 722ms 0.65% Edge::AddElement 24ms 0.022% 86.41% 722ms 0.65% MutableElement::RegisterWithEdges (inline) 0 0% 86.41% 711ms 0.64% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 86.41% 699ms 0.63% std::_Rb_tree::_Auto_node::_M_insert (inline) 21ms 0.019% 86.43% 699ms 0.63% std::_Rb_tree::_M_insert_node (inline) 9ms 0.0081% 86.44% 693ms 0.62% AbstractNumericalMethod::DetectStepSizeExceptions 98ms 0.088% 86.53% 684ms 0.62% VertexBasedCellPopulation::CheckForStepSizeException 0 0% 86.53% 675ms 0.61% std::_Rb_tree::_M_construct_node (inline) 0 0% 86.53% 665ms 0.6% std::_Vector_base::_M_allocate (inline) 603ms 0.54% 87.07% 633ms 0.57% boost::detail::shared_count::shared_count (inline) 0 0% 87.07% 631ms 0.57% vtkPolygon::New 1ms 0.0009% 87.07% 631ms 0.57% vtkPolygon::vtkPolygon 34ms 0.031% 87.10% 628ms 0.56% MutableElement::RegisterWithNodes (inline) 0 0% 87.10% 626ms 0.56% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 604ms 0.54% 87.64% 604ms 0.54% [libstdc++.so.6.0.33] 33ms 0.03% 87.67% 591ms 0.53% Node::AddElement 590ms 0.53% 88.20% 590ms 0.53% operator delete 5ms 0.0045% 88.21% 562ms 0.51% std::vector::_M_default_append (inline)