File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 66539ms, 88.35% of 75316ms total Dropped 1069 nodes (cum <= 376.58ms) flat flat% sum% cum cum% 0 0% 0% 75135ms 99.76% __libc_start_call_main 0 0% 0% 75135ms 99.76% __libc_start_main_impl 0 0% 0% 75135ms 99.76% _start 0 0% 0% 75116ms 99.73% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 75116ms 99.73% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 75116ms 99.73% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 75116ms 99.73% main 0 0% 0% 75078ms 99.68% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 75078ms 99.68% CxxTest::TestRunner::runTest (inline) 0 0% 0% 75078ms 99.68% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0027% 0.0027% 75072ms 99.68% AbstractCellBasedSimulation::Solve 9ms 0.012% 0.015% 39349ms 52.25% OffLatticeSimulation::UpdateCellLocationsAndTopology 8ms 0.011% 0.025% 36663ms 48.68% ForwardEulerNumericalMethod::UpdateAllNodePositions 42ms 0.056% 0.081% 35907ms 47.68% AbstractNumericalMethod::ComputeForcesIncludingDamping 252ms 0.33% 0.42% 28060ms 37.26% NagaiHondaForce::AddForceContribution 1ms 0.0013% 0.42% 26579ms 35.29% AbstractCellBasedSimulation::UpdateCellPopulation 5ms 0.0066% 0.42% 15801ms 20.98% VertexBasedCellPopulation::Update 2ms 0.0027% 0.43% 15689ms 20.83% MutableVertexMesh::ReMesh 6744ms 8.95% 9.38% 12926ms 17.16% Cylindrical2dVertexMesh::GetVectorFromAtoB 76ms 0.1% 9.48% 12531ms 16.64% Cell::ReadyToDivide 17ms 0.023% 9.50% 11718ms 15.56% AbstractPhaseBasedCellCycleModel::ReadyToDivide 86ms 0.11% 9.62% 11489ms 15.25% NagaiHondaForce::GetAdhesionParameter 33ms 0.044% 9.66% 10078ms 13.38% SimpleWntCellCycleModel::UpdateCellCyclePhase 281ms 0.37% 10.04% 9780ms 12.99% boost::numeric::ublas::c_vector::c_vector (partial-inline) 599ms 0.8% 10.83% 9616ms 12.77% std::__new_allocator::allocate (inline) 0 0% 10.83% 9234ms 12.26% std::allocator_traits::allocate (inline) 138ms 0.18% 11.01% 9130ms 12.12% CellPropertyCollection::GetPropertiesType (inline) 0 0% 11.01% 9040ms 12.00% std::_Rb_tree::_M_create_node (inline) 681ms 0.9% 11.92% 8935ms 11.86% operator new 0 0% 11.92% 8799ms 11.68% std::_Rb_tree::_M_get_node (inline) 194ms 0.26% 12.18% 8767ms 11.64% boost::numeric::ublas::vector_assign (inline) 2639ms 3.50% 15.68% 7966ms 10.58% __GI___libc_malloc 0 0% 15.68% 7719ms 10.25% std::_Rb_tree::_Alloc_node::operator() (inline) 6ms 0.008% 15.69% 7546ms 10.02% AbstractCellBasedSimulation::DoCellBirth 81ms 0.11% 15.79% 7545ms 10.02% VertexBasedCellPopulation::GetDampingConstant 48ms 0.064% 15.86% 7414ms 9.84% AbstractCellProperty::IsSubType (inline) 2006ms 2.66% 18.52% 7370ms 9.79% __dynamic_cast 32ms 0.042% 18.56% 7367ms 9.78% AbstractTargetAreaModifier::UpdateTargetAreas 24ms 0.032% 18.60% 7304ms 9.70% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 85ms 0.11% 18.71% 7144ms 9.49% MutableVertexMesh::CheckForIntersections 0 0% 18.71% 6504ms 8.64% std::_Rb_tree::_M_drop_node (inline) 681ms 0.9% 19.61% 6484ms 8.61% std::_Rb_tree::_M_erase 1812ms 2.41% 22.02% 6292ms 8.35% boost::numeric::ublas::indexing_vector_assign 287ms 0.38% 22.40% 6131ms 8.14% std::_Rb_tree::~_Rb_tree (inline) 361ms 0.48% 22.88% 6013ms 7.98% std::map::operator[] (partial-inline) 27ms 0.036% 22.92% 5864ms 7.79% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 22.92% 5828ms 7.74% std::set::~set (inline) 75ms 0.1% 23.02% 5752ms 7.64% std::__new_allocator::deallocate (inline) 0 0% 23.02% 5741ms 7.62% std::allocator_traits::deallocate (inline) 43ms 0.057% 23.07% 5739ms 7.62% Cell::GetMutationState 0 0% 23.07% 5701ms 7.57% std::_Rb_tree::_M_put_node (inline) 8ms 0.011% 23.08% 5692ms 7.56% MutableVertexMesh::RemoveDeletedNodesAndElements 292ms 0.39% 23.47% 5636ms 7.48% VertexMesh::GetNextEdgeGradientOfElementAtNode 1510ms 2.00% 25.48% 5628ms 7.47% __GI___libc_free 442ms 0.59% 26.06% 5621ms 7.46% VertexMesh::GetCentroidOfElement 0 0% 26.06% 5492ms 7.29% std::set::insert (inline) 364ms 0.48% 26.55% 5290ms 7.02% VertexMesh::ElementIncludesPoint 112ms 0.15% 26.69% 5112ms 6.79% std::_Rb_tree::_Rb_tree (partial-inline) 635ms 0.84% 27.54% 5054ms 6.71% std::_Rb_tree::_M_insert_ (inline) 536ms 0.71% 28.25% 4858ms 6.45% std::_Rb_tree::_M_copy (inline) 9ms 0.012% 28.26% 4757ms 6.32% std::set::set (inline) 4669ms 6.20% 34.46% 4669ms 6.20% boost::numeric::ublas::c_vector::operator() 38ms 0.05% 34.51% 4556ms 6.05% std::set_intersection (inline) 179ms 0.24% 34.75% 4518ms 6.00% std::__set_intersection 115ms 0.15% 34.90% 4380ms 5.82% SimpleWntCellCycleModel::GetWntLevel 575ms 0.76% 35.66% 4187ms 5.56% std::_Rb_tree::_M_clone_node (inline) 90ms 0.12% 35.78% 4186ms 5.56% WntConcentration::GetWntLevel 641ms 0.85% 36.63% 4136ms 5.49% AbstractMesh::GetDistanceBetweenNodes 4115ms 5.46% 42.10% 4115ms 5.46% __strcmp_evex 3691ms 4.90% 47.00% 4067ms 5.40% _int_free 1598ms 2.12% 49.12% 4021ms 5.34% std::_Rb_tree::_M_lower_bound (inline) 15ms 0.02% 49.14% 3950ms 5.24% MutableVertexMesh::RemoveDeletedNodes 3322ms 4.41% 53.55% 3925ms 5.21% _int_malloc 412ms 0.55% 54.10% 3878ms 5.15% boost::numeric::ublas::c_vector::operator[] (inline) 34ms 0.045% 54.14% 3857ms 5.12% EdgeHelper::RemoveDeletedEdges 11ms 0.015% 54.16% 3735ms 4.96% EdgeHelper::UpdateEdgesMapKey 1799ms 2.39% 56.55% 3672ms 4.88% __cxxabiv1::__si_class_type_info::__do_dyncast 77ms 0.1% 56.65% 3488ms 4.63% MutableElement::ResetIndex 0 0% 56.65% 3483ms 4.62% std::insert_iterator::operator= (inline) 0 0% 56.65% 3448ms 4.58% std::_Rb_tree::lower_bound (inline) 0 0% 56.65% 3448ms 4.58% std::map::lower_bound (inline) 0 0% 56.65% 3272ms 4.34% std::_Rb_tree::_M_insert_unique_ (inline) 0 0% 56.65% 3221ms 4.28% AbstractCellBasedSimulation::DoCellRemoval (inline) 3218ms 4.27% 60.92% 3218ms 4.27% boost::numeric::ublas::same_impl_ex 45ms 0.06% 60.98% 3131ms 4.16% AbstractCellPopulation::GetCellUsingLocationIndex 15ms 0.02% 61.00% 3128ms 4.15% Cell::GetCellProliferativeType 33ms 0.044% 61.05% 2532ms 3.36% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 2511ms 3.33% 64.38% 2511ms 3.33% [libchaste_cell_based.so] 98ms 0.13% 64.51% 2445ms 3.25% AbstractCellProperty::IsType (inline) 65ms 0.086% 64.60% 2342ms 3.11% Cell::SetCellProliferativeType 80ms 0.11% 64.70% 2312ms 3.07% boost::detail::shared_count::~shared_count (inline) 0 0% 64.70% 2312ms 3.07% boost::shared_ptr::~shared_ptr (inline) 2ms 0.0027% 64.70% 2220ms 2.95% std::_Rb_tree::_M_insert_unique (inline) 614ms 0.82% 65.52% 2218ms 2.94% AbstractElement::GetNodeLocation 2177ms 2.89% 68.41% 2183ms 2.90% boost::detail::sp_counted_base::release 37ms 0.049% 68.46% 2148ms 2.85% std::_Rb_tree::_M_emplace_hint_unique 2055ms 2.73% 71.19% 2055ms 2.73% std::_Rb_tree::_S_right (inline) 39ms 0.052% 71.24% 2039ms 2.71% std::_Rb_tree::erase 141ms 0.19% 71.43% 2015ms 2.68% AbstractCellPopulation::Iterator::IsRealCell 8ms 0.011% 71.44% 2010ms 2.67% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 71.44% 1934ms 2.57% boost::numeric::ublas::c_vector::assign (inline) 234ms 0.31% 71.75% 1803ms 2.39% std::_Rb_tree_const_iterator::operator++ (inline) 45ms 0.06% 71.81% 1780ms 2.36% boost::numeric::ublas::vector_binary::size (inline) 0 0% 71.81% 1750ms 2.32% AbstractCellPopulation::WriteResultsToFiles 14ms 0.019% 71.83% 1747ms 2.32% Cell::GetCellData 1747ms 2.32% 74.15% 1747ms 2.32% [libchaste_mesh.so] 30ms 0.04% 74.19% 1608ms 2.14% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 196ms 0.26% 74.45% 1601ms 2.13% VertexMesh::GetAreaGradientOfElementAtNode 29ms 0.039% 74.48% 1586ms 2.11% CellPropertyCollection::HasProperty 0 0% 74.48% 1550ms 2.06% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 74.48% 1545ms 2.05% Cell::HasCellProperty (inline) 6ms 0.008% 74.49% 1504ms 2.00% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 290ms 0.39% 74.88% 1483ms 1.97% AbstractCellProperty::IsSame 0 0% 74.88% 1433ms 1.90% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.0013% 74.88% 1426ms 1.89% VertexBasedCellPopulation::WriteCellVtkResultsToFile 63ms 0.084% 74.96% 1371ms 1.82% VertexMesh::GetVolumeOfElement 249ms 0.33% 75.29% 1365ms 1.81% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 75.29% 1321ms 1.75% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 75.29% 1288ms 1.71% VertexMeshWriter::WriteVtkUsingMesh 2ms 0.0027% 75.30% 1235ms 1.64% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 75.30% 1235ms 1.64% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 112ms 0.15% 75.44% 1193ms 1.58% std::type_info::operator== (inline) 69ms 0.092% 75.54% 1161ms 1.54% CellPropertyCollection::AddProperty 45ms 0.06% 75.60% 1159ms 1.54% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 75.60% 1121ms 1.49% tcache_get (inline) 1121ms 1.49% 77.08% 1121ms 1.49% tcache_get_n (inline) 3ms 0.004% 77.09% 1094ms 1.45% OffLatticeSimulation::ApplyBoundaries 48ms 0.064% 77.15% 1087ms 1.44% std::_Rb_tree::_M_erase_aux (partial-inline) 1076ms 1.43% 78.58% 1076ms 1.43% std::_Rb_tree_increment 65ms 0.086% 78.67% 1062ms 1.41% MutableVertexMesh::CheckForSwapsFromShortEdges 63ms 0.084% 78.75% 1050ms 1.39% VertexMesh::GetSurfaceAreaOfElement 653ms 0.87% 79.62% 1033ms 1.37% std::_Rb_tree::equal_range (inline) 33ms 0.044% 79.66% 960ms 1.27% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 79.66% 951ms 1.26% boost::numeric::ublas::vector_binary::operator() (inline) 31ms 0.041% 79.70% 924ms 1.23% Node::RemoveElement 0 0% 79.70% 893ms 1.19% std::set::erase (inline) 27ms 0.036% 79.74% 848ms 1.13% Edge::AddElement 9ms 0.012% 79.75% 847ms 1.12% MutableElement::RegisterWithEdges (inline) 36ms 0.048% 79.80% 834ms 1.11% CellPropertyRegistry::Get 62ms 0.082% 79.88% 824ms 1.09% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 79.88% 808ms 1.07% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 79.88% 805ms 1.07% std::__new_allocator::destroy (inline) 0 0% 79.88% 805ms 1.07% std::allocator_traits::destroy (inline) 0 0% 79.88% 803ms 1.07% std::_Rb_tree::_M_destroy_node (inline) 777ms 1.03% 80.91% 777ms 1.03% [libstdc++.so.6.0.33] 25ms 0.033% 80.95% 774ms 1.03% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 80.95% 731ms 0.97% boost::numeric::ublas::norm_2 (inline) 141ms 0.19% 81.13% 719ms 0.95% boost::numeric::ublas::detail::equals 257ms 0.34% 81.47% 712ms 0.95% boost::numeric::ublas::vector_norm_2::apply 703ms 0.93% 82.41% 703ms 0.93% std::_Rb_tree_insert_and_rebalance 0 0% 82.41% 697ms 0.93% boost::numeric::ublas::c_vector::assign_temporary (inline) 4ms 0.0053% 82.41% 697ms 0.93% boost::numeric::ublas::c_vector::swap (inline) 97ms 0.13% 82.54% 693ms 0.92% std::swap_ranges (inline) 5ms 0.0066% 82.55% 667ms 0.89% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 2ms 0.0027% 82.55% 662ms 0.88% VertexMeshWriter::MakeVtkMesh 647ms 0.86% 83.41% 647ms 0.86% Node::rGetLocation 1ms 0.0013% 83.41% 645ms 0.86% std::_Rb_tree::clear (inline) 80ms 0.11% 83.52% 628ms 0.83% std::_Rb_tree::find (inline) 0 0% 83.52% 627ms 0.83% std::map::clear (inline) 37ms 0.049% 83.57% 606ms 0.8% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 83.57% 596ms 0.79% std::iter_swap (inline) 44ms 0.058% 83.62% 596ms 0.79% std::less::operator() (inline) 596ms 0.79% 84.42% 596ms 0.79% std::swap (inline) 431ms 0.57% 84.99% 555ms 0.74% CellPropertyCollection::GetProperty 393ms 0.52% 85.51% 552ms 0.73% std::operator< (inline) 266ms 0.35% 85.86% 551ms 0.73% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 58ms 0.077% 85.94% 548ms 0.73% MutableElement::GetNodeLocalIndex 0 0% 85.94% 520ms 0.69% std::map::find (inline) 0 0% 85.94% 512ms 0.68% std::_Rb_tree::_Auto_node::_M_insert (inline) 21ms 0.028% 85.97% 512ms 0.68% std::_Rb_tree::_M_insert_node (inline) 0 0% 85.97% 508ms 0.67% boost::numeric::ublas::norm_inf (inline) 178ms 0.24% 86.20% 508ms 0.67% boost::numeric::ublas::vector_norm_inf::apply (inline) 489ms 0.65% 86.85% 489ms 0.65% std::vector::size (inline) 2ms 0.0027% 86.86% 470ms 0.62% vtkPolygon::New 1ms 0.0013% 86.86% 468ms 0.62% vtkPolygon::vtkPolygon 16ms 0.021% 86.88% 437ms 0.58% MutableElement::RegisterWithNodes (inline) 1ms 0.0013% 86.88% 435ms 0.58% std::_Vector_base::_M_allocate (inline) 430ms 0.57% 87.45% 430ms 0.57% Node::GetIndex 46ms 0.061% 87.51% 410ms 0.54% Node::AddElement 410ms 0.54% 88.06% 410ms 0.54% tcache_put (inline) 0 0% 88.06% 406ms 0.54% std::map::map (inline) 212ms 0.28% 88.34% 389ms 0.52% Edge::GetMapIndex 6ms 0.008% 88.35% 388ms 0.52% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 88.35% 388ms 0.52% boost::numeric::ublas::vector::vector (inline)