File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96482ms, 88.76% of 108705ms total Dropped 1091 nodes (cum <= 543.52ms) flat flat% sum% cum cum% 0 0% 0% 108221ms 99.55% __libc_start_call_main 0 0% 0% 108221ms 99.55% __libc_start_main_impl 0 0% 0% 108221ms 99.55% _start 0 0% 0% 108203ms 99.54% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108203ms 99.54% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108203ms 99.54% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108203ms 99.54% main 0 0% 0% 108164ms 99.50% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108164ms 99.50% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108164ms 99.50% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 5ms 0.0046% 0.0046% 108157ms 99.50% AbstractCellBasedSimulation::Solve 20ms 0.018% 0.023% 56001ms 51.52% OffLatticeSimulation::UpdateCellLocationsAndTopology 18ms 0.017% 0.04% 52830ms 48.60% ForwardEulerNumericalMethod::UpdateAllNodePositions 138ms 0.13% 0.17% 51840ms 47.69% AbstractNumericalMethod::ComputeForcesIncludingDamping 330ms 0.3% 0.47% 39582ms 36.41% NagaiHondaForce::AddForceContribution 1ms 0.00092% 0.47% 39083ms 35.95% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00092% 0.47% 24127ms 22.19% VertexBasedCellPopulation::Update 1ms 0.00092% 0.47% 23999ms 22.08% MutableVertexMesh::ReMesh 14570ms 13.40% 13.88% 23043ms 21.20% Cylindrical2dVertexMesh::GetVectorFromAtoB 80ms 0.074% 13.95% 17584ms 16.18% Cell::ReadyToDivide 54ms 0.05% 14.00% 16506ms 15.18% AbstractPhaseBasedCellCycleModel::ReadyToDivide 337ms 0.31% 14.31% 14692ms 13.52% NagaiHondaForce::GetAdhesionParameter 126ms 0.12% 14.43% 14204ms 13.07% CellPropertyCollection::GetPropertiesType (inline) 126ms 0.12% 14.54% 14026ms 12.90% SimpleWntCellCycleModel::UpdateCellCyclePhase 433ms 0.4% 14.94% 14014ms 12.89% boost::numeric::ublas::c_vector::c_vector (partial-inline) 457ms 0.42% 15.36% 12457ms 11.46% boost::numeric::ublas::vector_assign (inline) 129ms 0.12% 15.48% 12079ms 11.11% MutableVertexMesh::CheckForIntersections 3561ms 3.28% 18.75% 11906ms 10.95% __dynamic_cast 64ms 0.059% 18.81% 11784ms 10.84% AbstractCellProperty::IsSubType (inline) 93ms 0.086% 18.90% 11761ms 10.82% VertexBasedCellPopulation::GetDampingConstant 72ms 0.066% 18.97% 10634ms 9.78% AbstractTargetAreaModifier::UpdateTargetAreas 51ms 0.047% 19.01% 10540ms 9.70% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 22ms 0.02% 19.03% 10296ms 9.47% AbstractCellBasedSimulation::DoCellBirth 1369ms 1.26% 20.29% 9906ms 9.11% std::__new_allocator::allocate (inline) 0 0% 20.29% 9399ms 8.65% std::_Rb_tree::_M_create_node (inline) 0 0% 20.29% 9339ms 8.59% std::allocator_traits::allocate (inline) 2538ms 2.33% 22.63% 9119ms 8.39% boost::numeric::ublas::indexing_vector_assign 1387ms 1.28% 23.90% 9094ms 8.37% std::_Rb_tree::_M_erase 373ms 0.34% 24.25% 9010ms 8.29% VertexMesh::GetNextEdgeGradientOfElementAtNode 809ms 0.74% 24.99% 8999ms 8.28% VertexMesh::ElementIncludesPoint 69ms 0.063% 25.05% 8958ms 8.24% Cell::GetMutationState 24ms 0.022% 25.08% 8935ms 8.22% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 25.08% 8741ms 8.04% std::_Rb_tree::_M_get_node (inline) 817ms 0.75% 25.83% 8651ms 7.96% operator new 494ms 0.45% 26.28% 8454ms 7.78% VertexMesh::GetCentroidOfElement 241ms 0.22% 26.50% 8336ms 7.67% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.50% 8247ms 7.59% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 26.50% 8057ms 7.41% std::_Rb_tree::_M_drop_node (inline) 0 0% 26.50% 7875ms 7.24% std::set::~set (inline) 281ms 0.26% 26.76% 7851ms 7.22% std::__new_allocator::deallocate (inline) 0 0% 26.76% 7821ms 7.19% std::allocator_traits::deallocate (inline) 0 0% 26.76% 7767ms 7.15% std::_Rb_tree::_M_put_node (inline) 3083ms 2.84% 29.60% 7683ms 7.07% __GI___libc_malloc 2982ms 2.74% 32.34% 7622ms 7.01% __GI___libc_free 18ms 0.017% 32.36% 7479ms 6.88% MutableVertexMesh::RemoveDeletedNodesAndElements 468ms 0.43% 32.79% 7408ms 6.81% std::map::operator[] (partial-inline) 1345ms 1.24% 34.03% 7273ms 6.69% AbstractMesh::GetDistanceBetweenNodes 145ms 0.13% 34.16% 6714ms 6.18% std::_Rb_tree::_Rb_tree (partial-inline) 6603ms 6.07% 40.23% 6603ms 6.07% __strcmp_avx2 99ms 0.091% 40.32% 6516ms 5.99% SimpleWntCellCycleModel::GetWntLevel 649ms 0.6% 40.92% 6375ms 5.86% std::_Rb_tree::_M_copy (inline) 167ms 0.15% 41.07% 6338ms 5.83% WntConcentration::GetWntLevel 18ms 0.017% 41.09% 6269ms 5.77% std::set::set (inline) 6020ms 5.54% 46.63% 6020ms 5.54% boost::numeric::ublas::c_vector::operator() 2335ms 2.15% 48.78% 5918ms 5.44% std::_Rb_tree::_M_lower_bound (inline) 2658ms 2.45% 51.22% 5688ms 5.23% __cxxabiv1::__si_class_type_info::__do_dyncast 718ms 0.66% 51.88% 5483ms 5.04% std::_Rb_tree::_M_clone_node (inline) 0 0% 51.88% 5340ms 4.91% std::set::insert (inline) 36ms 0.033% 51.92% 5237ms 4.82% MutableVertexMesh::RemoveDeletedNodes 40ms 0.037% 51.95% 5080ms 4.67% EdgeHelper::RemoveDeletedEdges 1524ms 1.40% 53.35% 4898ms 4.51% boost::numeric::ublas::c_vector::operator[] (inline) 39ms 0.036% 53.39% 4824ms 4.44% EdgeHelper::UpdateEdgesMapKey 0 0% 53.39% 4741ms 4.36% std::_Rb_tree::lower_bound (inline) 0 0% 53.39% 4741ms 4.36% std::map::lower_bound (inline) 223ms 0.21% 53.60% 4730ms 4.35% MutableElement::ResetIndex 3ms 0.0028% 53.60% 4653ms 4.28% AbstractCellBasedSimulation::DoCellRemoval (inline) 4316ms 3.97% 57.57% 4627ms 4.26% _int_free 81ms 0.075% 57.64% 4505ms 4.14% std::set_intersection (inline) 500ms 0.46% 58.10% 4479ms 4.12% std::_Rb_tree::_M_insert_ (inline) 289ms 0.27% 58.37% 4424ms 4.07% std::__set_intersection 113ms 0.1% 58.47% 4259ms 3.92% AbstractCellPopulation::GetCellUsingLocationIndex 35ms 0.032% 58.51% 4102ms 3.77% Cell::GetCellProliferativeType 3987ms 3.67% 62.17% 3987ms 3.67% boost::numeric::ublas::same_impl_ex 10ms 0.0092% 62.18% 3600ms 3.31% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 60ms 0.055% 62.24% 3551ms 3.27% AbstractCellProperty::IsType (inline) 875ms 0.8% 63.04% 3292ms 3.03% AbstractElement::GetNodeLocation 47ms 0.043% 63.09% 3185ms 2.93% Cell::SetCellProliferativeType 1ms 0.00092% 63.09% 3180ms 2.93% std::insert_iterator::operator= (inline) 3029ms 2.79% 65.87% 3029ms 2.79% std::_Rb_tree::_S_right (inline) 2172ms 2.00% 67.87% 3007ms 2.77% _int_malloc 36ms 0.033% 67.90% 2974ms 2.74% std::_Rb_tree::erase 3ms 0.0028% 67.91% 2822ms 2.60% std::_Rb_tree::_M_insert_unique_ (inline) 610ms 0.56% 68.47% 2776ms 2.55% boost::numeric::ublas::vector_binary::size (inline) 456ms 0.42% 68.89% 2740ms 2.52% std::_Rb_tree_const_iterator::operator++ (inline) 792ms 0.73% 69.62% 2550ms 2.35% AbstractCellProperty::IsSame 235ms 0.22% 69.83% 2526ms 2.32% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.83% 2518ms 2.32% std::_Rb_tree::_M_insert_unique 42ms 0.039% 69.87% 2481ms 2.28% CellPropertyCollection::HasProperty 131ms 0.12% 69.99% 2415ms 2.22% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 29ms 0.027% 70.02% 2412ms 2.22% Cell::GetCellData 0 0% 70.02% 2400ms 2.21% AbstractCellPopulation::WriteResultsToFiles 0 0% 70.02% 2400ms 2.21% boost::numeric::ublas::c_vector::assign (inline) 0 0% 70.02% 2392ms 2.20% Cell::HasCellProperty (inline) 0 0% 70.02% 2325ms 2.14% AbstractCellPopulation::Iterator::operator++ (inline) 256ms 0.24% 70.25% 2316ms 2.13% AbstractCellPopulation::Iterator::IsRealCell (inline) 78ms 0.072% 70.33% 2273ms 2.09% VertexMesh::GetVolumeOfElement 0 0% 70.33% 2193ms 2.02% boost::numeric::ublas::c_vector::operator-= (inline) 37ms 0.034% 70.36% 2164ms 1.99% std::_Rb_tree::_M_emplace_hint_unique 2110ms 1.94% 72.30% 2110ms 1.94% std::_Rb_tree_increment 1370ms 1.26% 73.56% 2025ms 1.86% std::_Rb_tree::equal_range (inline) 0 0% 73.56% 1974ms 1.82% VertexBasedCellPopulation::WriteVtkResultsToFile 2ms 0.0018% 73.56% 1960ms 1.80% VertexBasedCellPopulation::WriteCellVtkResultsToFile 67ms 0.062% 73.62% 1896ms 1.74% MutableVertexMesh::CheckForSwapsFromShortEdges 1ms 0.00092% 73.62% 1862ms 1.71% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.62% 1862ms 1.71% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 32ms 0.029% 73.65% 1770ms 1.63% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 449ms 0.41% 74.07% 1758ms 1.62% std::type_info::operator== (inline) 0 0% 74.07% 1748ms 1.61% VertexMeshWriter::WriteVtkUsingMesh 20ms 0.018% 74.09% 1697ms 1.56% VertexMesh::GetSurfaceAreaOfElement 51ms 0.047% 74.13% 1624ms 1.49% Node::RemoveElement 17ms 0.016% 74.15% 1579ms 1.45% std::set::erase (inline) 82ms 0.075% 74.22% 1561ms 1.44% boost::numeric::ublas::vector_reference::operator() (inline) 40ms 0.037% 74.26% 1558ms 1.43% AbstractCellPopulation::GetLocationIndexUsingCell 86ms 0.079% 74.34% 1554ms 1.43% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 161ms 0.15% 74.49% 1493ms 1.37% CellPropertyCollection::AddProperty 0 0% 74.49% 1439ms 1.32% tcache_get (inline) 1439ms 1.32% 75.81% 1439ms 1.32% tcache_get_n (inline) 0 0% 75.81% 1327ms 1.22% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 75.81% 1288ms 1.18% OffLatticeSimulation::ApplyBoundaries 1229ms 1.13% 76.94% 1229ms 1.13% Node::rGetLocation 76ms 0.07% 77.01% 1202ms 1.11% std::less::operator() (inline) 102ms 0.094% 77.11% 1168ms 1.07% std::_Rb_tree::find (inline) 0 0% 77.11% 1152ms 1.06% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 77.11% 1144ms 1.05% boost::numeric::ublas::norm_2 (inline) 500ms 0.46% 77.57% 1136ms 1.05% boost::numeric::ublas::vector_norm_2::apply 110ms 0.1% 77.67% 1127ms 1.04% std::_Rb_tree::_M_erase_aux (partial-inline) 907ms 0.83% 78.50% 1126ms 1.04% std::operator< (inline) 1098ms 1.01% 79.51% 1098ms 1.01% std::_Rb_tree_insert_and_rebalance 19ms 0.017% 79.53% 1094ms 1.01% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 33ms 0.03% 79.56% 1034ms 0.95% CellPropertyRegistry::Get 1020ms 0.94% 80.50% 1020ms 0.94% std::vector::size (inline) 1005ms 0.92% 81.42% 1005ms 0.92% [libchaste_cell_based.so] 0 0% 81.42% 1002ms 0.92% std::_Rb_tree::clear (inline) 9ms 0.0083% 81.43% 997ms 0.92% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 81.43% 988ms 0.91% std::map::clear (inline) 0 0% 81.43% 984ms 0.91% std::map::find (inline) 0 0% 81.43% 944ms 0.87% boost::numeric::ublas::c_vector::assign_temporary (inline) 6ms 0.0055% 81.44% 944ms 0.87% boost::numeric::ublas::c_vector::swap (inline) 942ms 0.87% 82.30% 942ms 0.87% [libchaste_mesh.so] 84ms 0.077% 82.38% 938ms 0.86% std::swap_ranges (inline) 25ms 0.023% 82.40% 934ms 0.86% boost::numeric::ublas::detail::expression_type_check (inline) 373ms 0.34% 82.75% 914ms 0.84% Edge::GetMapIndex 140ms 0.13% 82.87% 909ms 0.84% boost::detail::shared_count::~shared_count (inline) 0 0% 82.87% 909ms 0.84% boost::shared_ptr::~shared_ptr (inline) 143ms 0.13% 83.01% 900ms 0.83% boost::numeric::ublas::detail::equals 0 0% 83.01% 862ms 0.79% VertexMeshWriter::MakeVtkMesh 855ms 0.79% 83.79% 855ms 0.79% std::swap (inline) 0 0% 83.79% 854ms 0.79% std::iter_swap (inline) 111ms 0.1% 83.89% 831ms 0.76% boost::numeric::ublas::c_vector::operator= (inline) 123ms 0.11% 84.01% 826ms 0.76% MutableElement::GetNodeLocalIndex 794ms 0.73% 84.74% 794ms 0.73% Node::GetIndex 162ms 0.15% 84.89% 792ms 0.73% boost::shared_ptr::shared_ptr (inline) 19ms 0.017% 84.91% 787ms 0.72% MutableElement::RegisterWithEdges (inline) 34ms 0.031% 84.94% 784ms 0.72% Edge::AddElement 465ms 0.43% 85.36% 779ms 0.72% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 739ms 0.68% 86.04% 746ms 0.69% boost::detail::sp_counted_base::release 0 0% 86.04% 718ms 0.66% boost::numeric::ublas::norm_inf (inline) 372ms 0.34% 86.39% 718ms 0.66% boost::numeric::ublas::vector_norm_inf::apply (inline) 107ms 0.098% 86.48% 701ms 0.64% std::__new_allocator::construct (inline) 0 0% 86.48% 701ms 0.64% std::allocator_traits::construct (inline) 0 0% 86.48% 691ms 0.64% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 86.48% 669ms 0.62% std::_Rb_tree::_Auto_node::_M_insert (inline) 18ms 0.017% 86.50% 669ms 0.62% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.50% 658ms 0.61% std::_Rb_tree::_M_construct_node (inline) 605ms 0.56% 87.06% 630ms 0.58% boost::detail::shared_count::shared_count (inline) 617ms 0.57% 87.63% 617ms 0.57% boost::shared_ptr::operator-> (inline) 0 0% 87.63% 614ms 0.56% vtkPolygon::New 1ms 0.00092% 87.63% 614ms 0.56% vtkPolygon::vtkPolygon 28ms 0.026% 87.65% 595ms 0.55% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.65% 595ms 0.55% boost::numeric::ublas::vector::vector (inline) 1ms 0.00092% 87.65% 593ms 0.55% std::_Vector_base::_M_allocate (inline) 591ms 0.54% 88.20% 591ms 0.54% operator delete 42ms 0.039% 88.24% 588ms 0.54% MutableElement::RegisterWithNodes (inline) 566ms 0.52% 88.76% 566ms 0.52% [libstdc++.so.6.0.33]