File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 66818ms, 88.39% of 75594ms total Dropped 1094 nodes (cum <= 377.97ms) flat flat% sum% cum cum% 0 0% 0% 75428ms 99.78% __libc_start_call_main 0 0% 0% 75428ms 99.78% __libc_start_main_impl 0 0% 0% 75428ms 99.78% _start 0 0% 0% 75411ms 99.76% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 75411ms 99.76% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 75411ms 99.76% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 75411ms 99.76% main 0 0% 0% 75368ms 99.70% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 75368ms 99.70% CxxTest::TestRunner::runTest (inline) 0 0% 0% 75368ms 99.70% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 4ms 0.0053% 0.0053% 75363ms 99.69% AbstractCellBasedSimulation::Solve 11ms 0.015% 0.02% 39480ms 52.23% OffLatticeSimulation::UpdateCellLocationsAndTopology 16ms 0.021% 0.041% 36848ms 48.74% ForwardEulerNumericalMethod::UpdateAllNodePositions 41ms 0.054% 0.095% 35787ms 47.34% AbstractNumericalMethod::ComputeForcesIncludingDamping 226ms 0.3% 0.39% 27939ms 36.96% NagaiHondaForce::AddForceContribution 0 0% 0.39% 26373ms 34.89% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.004% 0.4% 15844ms 20.96% VertexBasedCellPopulation::Update 2ms 0.0026% 0.4% 15743ms 20.83% MutableVertexMesh::ReMesh 6769ms 8.95% 9.36% 13172ms 17.42% Cylindrical2dVertexMesh::GetVectorFromAtoB 107ms 0.14% 9.50% 12557ms 16.61% Cell::ReadyToDivide 23ms 0.03% 9.53% 11673ms 15.44% AbstractPhaseBasedCellCycleModel::ReadyToDivide 69ms 0.091% 9.62% 11600ms 15.35% NagaiHondaForce::GetAdhesionParameter 36ms 0.048% 9.67% 9976ms 13.20% SimpleWntCellCycleModel::UpdateCellCyclePhase 314ms 0.42% 10.08% 9649ms 12.76% boost::numeric::ublas::c_vector::c_vector (partial-inline) 584ms 0.77% 10.85% 9554ms 12.64% std::__new_allocator::allocate (inline) 147ms 0.19% 11.05% 9237ms 12.22% CellPropertyCollection::GetPropertiesType (inline) 0 0% 11.05% 9157ms 12.11% std::allocator_traits::allocate (inline) 0 0% 11.05% 8980ms 11.88% std::_Rb_tree::_M_create_node (inline) 718ms 0.95% 12.00% 8885ms 11.75% operator new 0 0% 12.00% 8707ms 11.52% std::_Rb_tree::_M_get_node (inline) 190ms 0.25% 12.25% 8625ms 11.41% boost::numeric::ublas::vector_assign (inline) 2689ms 3.56% 15.81% 7921ms 10.48% __GI___libc_malloc 0 0% 15.81% 7778ms 10.29% std::_Rb_tree::_Alloc_node::operator() (inline) 29ms 0.038% 15.85% 7736ms 10.23% AbstractTargetAreaModifier::UpdateTargetAreas 25ms 0.033% 15.88% 7679ms 10.16% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 64ms 0.085% 15.96% 7615ms 10.07% AbstractCellProperty::IsSubType (inline) 1703ms 2.25% 18.22% 7565ms 10.01% __dynamic_cast 64ms 0.085% 18.30% 7556ms 10.00% VertexBasedCellPopulation::GetDampingConstant 4ms 0.0053% 18.31% 7364ms 9.74% AbstractCellBasedSimulation::DoCellBirth 83ms 0.11% 18.42% 7305ms 9.66% MutableVertexMesh::CheckForIntersections 725ms 0.96% 19.37% 6617ms 8.75% std::_Rb_tree::_M_erase 0 0% 19.37% 6555ms 8.67% std::_Rb_tree::_M_drop_node (inline) 301ms 0.4% 19.77% 6284ms 8.31% std::_Rb_tree::~_Rb_tree (inline) 1882ms 2.49% 22.26% 6264ms 8.29% boost::numeric::ublas::indexing_vector_assign 0 0% 22.26% 5998ms 7.93% std::set::~set (inline) 382ms 0.51% 22.77% 5916ms 7.83% std::map::operator[] (partial-inline) 74ms 0.098% 22.87% 5864ms 7.76% std::__new_allocator::deallocate (inline) 0 0% 22.87% 5847ms 7.73% std::allocator_traits::deallocate (inline) 1546ms 2.05% 24.91% 5787ms 7.66% __GI___libc_free 0 0% 24.91% 5783ms 7.65% std::_Rb_tree::_M_put_node (inline) 50ms 0.066% 24.98% 5768ms 7.63% Cell::GetMutationState 29ms 0.038% 25.02% 5669ms 7.50% VertexBasedCellPopulation::GetLocationOfCellCentre 11ms 0.015% 25.03% 5574ms 7.37% MutableVertexMesh::RemoveDeletedNodesAndElements 237ms 0.31% 25.34% 5510ms 7.29% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 25.34% 5488ms 7.26% std::set::insert (inline) 419ms 0.55% 25.90% 5461ms 7.22% VertexMesh::GetCentroidOfElement 359ms 0.47% 26.37% 5450ms 7.21% VertexMesh::ElementIncludesPoint 74ms 0.098% 26.47% 5101ms 6.75% std::_Rb_tree::_Rb_tree (partial-inline) 627ms 0.83% 27.30% 5034ms 6.66% std::_Rb_tree::_M_insert_ (inline) 516ms 0.68% 27.98% 4870ms 6.44% std::_Rb_tree::_M_copy (inline) 12ms 0.016% 28.00% 4768ms 6.31% std::set::set (inline) 4762ms 6.30% 34.30% 4762ms 6.30% boost::numeric::ublas::c_vector::operator() 4741ms 6.27% 40.57% 4741ms 6.27% __strcmp_evex 44ms 0.058% 40.63% 4468ms 5.91% std::set_intersection (inline) 189ms 0.25% 40.88% 4424ms 5.85% std::__set_intersection 100ms 0.13% 41.01% 4260ms 5.64% SimpleWntCellCycleModel::GetWntLevel 528ms 0.7% 41.71% 4238ms 5.61% std::_Rb_tree::_M_clone_node (inline) 3842ms 5.08% 46.79% 4202ms 5.56% _int_free 606ms 0.8% 47.59% 4142ms 5.48% AbstractMesh::GetDistanceBetweenNodes 93ms 0.12% 47.72% 4066ms 5.38% WntConcentration::GetWntLevel 1682ms 2.23% 49.94% 4036ms 5.34% std::_Rb_tree::_M_lower_bound (inline) 458ms 0.61% 50.55% 4003ms 5.30% boost::numeric::ublas::c_vector::operator[] (inline) 19ms 0.025% 50.57% 3879ms 5.13% MutableVertexMesh::RemoveDeletedNodes 26ms 0.034% 50.61% 3795ms 5.02% EdgeHelper::RemoveDeletedEdges 3231ms 4.27% 54.88% 3791ms 5.01% _int_malloc 1777ms 2.35% 57.23% 3785ms 5.01% __cxxabiv1::__si_class_type_info::__do_dyncast 12ms 0.016% 57.25% 3652ms 4.83% EdgeHelper::UpdateEdgesMapKey 0 0% 57.25% 3462ms 4.58% std::_Rb_tree::lower_bound (inline) 0 0% 57.25% 3462ms 4.58% std::map::lower_bound (inline) 76ms 0.1% 57.35% 3455ms 4.57% MutableElement::ResetIndex 0 0% 57.35% 3417ms 4.52% std::insert_iterator::operator= (inline) 50ms 0.066% 57.41% 3211ms 4.25% AbstractCellPopulation::GetCellUsingLocationIndex 3188ms 4.22% 61.63% 3188ms 4.22% boost::numeric::ublas::same_impl_ex 0 0% 61.63% 3174ms 4.20% std::_Rb_tree::_M_insert_unique_ (inline) 1ms 0.0013% 61.63% 3162ms 4.18% AbstractCellBasedSimulation::DoCellRemoval (inline) 22ms 0.029% 61.66% 3072ms 4.06% Cell::GetCellProliferativeType 94ms 0.12% 61.79% 2587ms 3.42% AbstractCellProperty::IsType (inline) 2478ms 3.28% 65.06% 2478ms 3.28% [libchaste_cell_based.so] 30ms 0.04% 65.10% 2432ms 3.22% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 83ms 0.11% 65.21% 2335ms 3.09% boost::detail::shared_count::~shared_count (inline) 0 0% 65.21% 2335ms 3.09% boost::shared_ptr::~shared_ptr (inline) 1ms 0.0013% 65.21% 2314ms 3.06% std::_Rb_tree::_M_insert_unique 73ms 0.097% 65.31% 2306ms 3.05% Cell::SetCellProliferativeType 2198ms 2.91% 68.22% 2209ms 2.92% boost::detail::sp_counted_base::release 562ms 0.74% 68.96% 2164ms 2.86% AbstractElement::GetNodeLocation 26ms 0.034% 69.00% 2038ms 2.70% std::_Rb_tree::_M_emplace_hint_unique 7ms 0.0093% 69.01% 2005ms 2.65% AbstractCellPopulation::Iterator::operator++ (inline) 185ms 0.24% 69.25% 2001ms 2.65% AbstractCellPopulation::Iterator::IsRealCell (inline) 55ms 0.073% 69.32% 1992ms 2.64% std::_Rb_tree::erase 1966ms 2.60% 71.92% 1966ms 2.60% std::_Rb_tree::_S_right (inline) 12ms 0.016% 71.94% 1907ms 2.52% Cell::GetCellData 29ms 0.038% 71.98% 1832ms 2.42% CellPropertyCollection::HasProperty 0 0% 71.98% 1826ms 2.42% boost::numeric::ublas::c_vector::assign (inline) 0 0% 71.98% 1797ms 2.38% Cell::HasCellProperty (inline) 56ms 0.074% 72.05% 1760ms 2.33% boost::numeric::ublas::vector_binary::size (inline) 0 0% 72.05% 1748ms 2.31% AbstractCellPopulation::WriteResultsToFiles 229ms 0.3% 72.35% 1707ms 2.26% std::_Rb_tree_const_iterator::operator++ (inline) 328ms 0.43% 72.79% 1682ms 2.23% AbstractCellProperty::IsSame 1671ms 2.21% 75.00% 1671ms 2.21% [libchaste_mesh.so] 19ms 0.025% 75.02% 1664ms 2.20% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 174ms 0.23% 75.25% 1580ms 2.09% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 75.25% 1498ms 1.98% boost::numeric::ublas::c_vector::operator-= (inline) 9ms 0.012% 75.27% 1444ms 1.91% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 66ms 0.087% 75.35% 1425ms 1.89% VertexMesh::GetVolumeOfElement 0 0% 75.35% 1422ms 1.88% VertexBasedCellPopulation::WriteVtkResultsToFile 3ms 0.004% 75.36% 1415ms 1.87% VertexBasedCellPopulation::WriteCellVtkResultsToFile 115ms 0.15% 75.51% 1354ms 1.79% std::type_info::operator== (inline) 250ms 0.33% 75.84% 1328ms 1.76% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 75.84% 1276ms 1.69% VertexMeshWriter::WriteVtkUsingMesh 73ms 0.097% 75.94% 1224ms 1.62% CellPropertyCollection::AddProperty 2ms 0.0026% 75.94% 1202ms 1.59% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 75.94% 1202ms 1.59% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 75.94% 1202ms 1.59% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 75.94% 1162ms 1.54% tcache_get (inline) 1162ms 1.54% 77.48% 1162ms 1.54% tcache_get_n (inline) 46ms 0.061% 77.54% 1135ms 1.50% AbstractCellPopulation::GetLocationIndexUsingCell 3ms 0.004% 77.54% 1113ms 1.47% OffLatticeSimulation::ApplyBoundaries 68ms 0.09% 77.63% 1062ms 1.40% MutableVertexMesh::CheckForSwapsFromShortEdges 44ms 0.058% 77.69% 1034ms 1.37% std::_Rb_tree::_M_erase_aux (partial-inline) 651ms 0.86% 78.55% 1024ms 1.35% std::_Rb_tree::equal_range (inline) 56ms 0.074% 78.63% 1000ms 1.32% VertexMesh::GetSurfaceAreaOfElement 991ms 1.31% 79.94% 991ms 1.31% std::_Rb_tree_increment 0 0% 79.94% 987ms 1.31% boost::numeric::ublas::vector_binary::operator() (inline) 39ms 0.052% 79.99% 986ms 1.30% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 22ms 0.029% 80.02% 952ms 1.26% Node::RemoveElement 0 0% 80.02% 930ms 1.23% std::set::erase (inline) 64ms 0.085% 80.10% 853ms 1.13% boost::numeric::ublas::vector_reference::operator() (inline) 15ms 0.02% 80.12% 846ms 1.12% MutableElement::RegisterWithEdges (inline) 27ms 0.036% 80.16% 835ms 1.10% Edge::AddElement 39ms 0.052% 80.21% 802ms 1.06% CellPropertyRegistry::Get 802ms 1.06% 81.27% 802ms 1.06% [libstdc++.so.6.0.33] 0 0% 81.27% 777ms 1.03% std::__new_allocator::destroy (inline) 0 0% 81.27% 777ms 1.03% std::allocator_traits::destroy (inline) 0 0% 81.27% 775ms 1.03% std::_Rb_tree::_M_destroy_node (inline) 0 0% 81.27% 772ms 1.02% CellPropertyCollection::~CellPropertyCollection (inline) 769ms 1.02% 82.29% 769ms 1.02% std::_Rb_tree_insert_and_rebalance 0 0% 82.29% 729ms 0.96% boost::numeric::ublas::norm_2 (inline) 6ms 0.0079% 82.29% 723ms 0.96% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 82.29% 716ms 0.95% boost::numeric::ublas::c_vector::assign_temporary (inline) 1ms 0.0013% 82.30% 716ms 0.95% boost::numeric::ublas::c_vector::swap (inline) 96ms 0.13% 82.42% 715ms 0.95% std::swap_ranges (inline) 232ms 0.31% 82.73% 714ms 0.94% boost::numeric::ublas::vector_norm_2::apply 8ms 0.011% 82.74% 708ms 0.94% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 143ms 0.19% 82.93% 694ms 0.92% boost::numeric::ublas::detail::equals 25ms 0.033% 82.96% 662ms 0.88% boost::numeric::ublas::c_vector::operator= (inline) 661ms 0.87% 83.84% 661ms 0.87% Node::rGetLocation 1ms 0.0013% 83.84% 650ms 0.86% VertexMeshWriter::MakeVtkMesh 0 0% 83.84% 641ms 0.85% std::_Rb_tree::clear (inline) 0 0% 83.84% 627ms 0.83% std::map::clear (inline) 0 0% 83.84% 619ms 0.82% std::iter_swap (inline) 619ms 0.82% 84.66% 619ms 0.82% std::swap (inline) 74ms 0.098% 84.76% 601ms 0.8% std::_Rb_tree::find (inline) 471ms 0.62% 85.38% 593ms 0.78% CellPropertyCollection::GetProperty 35ms 0.046% 85.42% 575ms 0.76% std::less::operator() (inline) 0 0% 85.42% 545ms 0.72% std::_Rb_tree::_Auto_node::_M_insert (inline) 17ms 0.022% 85.45% 545ms 0.72% std::_Rb_tree::_M_insert_node (inline) 378ms 0.5% 85.95% 540ms 0.71% std::operator< (inline) 257ms 0.34% 86.29% 520ms 0.69% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 13ms 0.017% 86.30% 517ms 0.68% AbstractNumericalMethod::DetectStepSizeExceptions 76ms 0.1% 86.41% 504ms 0.67% VertexBasedCellPopulation::CheckForStepSizeException 1ms 0.0013% 86.41% 495ms 0.65% std::map::find (inline) 0 0% 86.41% 479ms 0.63% boost::numeric::ublas::norm_inf (inline) 169ms 0.22% 86.63% 479ms 0.63% boost::numeric::ublas::vector_norm_inf::apply (inline) 17ms 0.022% 86.65% 476ms 0.63% MutableElement::RegisterWithNodes (inline) 46ms 0.061% 86.71% 453ms 0.6% Node::AddElement 2ms 0.0026% 86.72% 450ms 0.6% std::_Vector_base::_M_allocate (inline) 0 0% 86.72% 445ms 0.59% vtkPolygon::New 1ms 0.0013% 86.72% 445ms 0.59% vtkPolygon::vtkPolygon 55ms 0.073% 86.79% 444ms 0.59% MutableElement::GetNodeLocalIndex 414ms 0.55% 87.34% 414ms 0.55% std::vector::size (inline) 3ms 0.004% 87.34% 400ms 0.53% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.34% 400ms 0.53% boost::numeric::ublas::vector::vector (inline) 398ms 0.53% 87.87% 398ms 0.53% Node::GetIndex 0 0% 87.87% 397ms 0.53% std::map::map (inline) 395ms 0.52% 88.39% 395ms 0.52% tcache_put (inline)