File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96612ms, 88.73% of 108884ms total Dropped 1074 nodes (cum <= 544.42ms) flat flat% sum% cum cum% 0 0% 0% 108368ms 99.53% __libc_start_call_main 0 0% 0% 108368ms 99.53% __libc_start_main_impl 0 0% 0% 108368ms 99.53% _start 0 0% 0% 108347ms 99.51% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108347ms 99.51% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108347ms 99.51% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108347ms 99.51% main 0 0% 0% 108312ms 99.47% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108312ms 99.47% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108312ms 99.47% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 3ms 0.0028% 0.0028% 108305ms 99.47% AbstractCellBasedSimulation::Solve 11ms 0.01% 0.013% 56318ms 51.72% OffLatticeSimulation::UpdateCellLocationsAndTopology 12ms 0.011% 0.024% 53199ms 48.86% ForwardEulerNumericalMethod::UpdateAllNodePositions 140ms 0.13% 0.15% 51682ms 47.47% AbstractNumericalMethod::ComputeForcesIncludingDamping 390ms 0.36% 0.51% 39546ms 36.32% NagaiHondaForce::AddForceContribution 1ms 0.00092% 0.51% 39001ms 35.82% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.0037% 0.52% 24154ms 22.18% VertexBasedCellPopulation::Update 1ms 0.00092% 0.52% 24015ms 22.06% MutableVertexMesh::ReMesh 14425ms 13.25% 13.76% 22639ms 20.79% Cylindrical2dVertexMesh::GetVectorFromAtoB 131ms 0.12% 13.88% 17541ms 16.11% Cell::ReadyToDivide 76ms 0.07% 13.95% 16191ms 14.87% AbstractPhaseBasedCellCycleModel::ReadyToDivide 386ms 0.35% 14.31% 14714ms 13.51% NagaiHondaForce::GetAdhesionParameter 457ms 0.42% 14.73% 14100ms 12.95% boost::numeric::ublas::c_vector::c_vector (partial-inline) 149ms 0.14% 14.87% 13996ms 12.85% CellPropertyCollection::GetPropertiesType (inline) 125ms 0.11% 14.98% 13814ms 12.69% SimpleWntCellCycleModel::UpdateCellCyclePhase 406ms 0.37% 15.35% 12546ms 11.52% boost::numeric::ublas::vector_assign (inline) 160ms 0.15% 15.50% 12005ms 11.03% MutableVertexMesh::CheckForIntersections 78ms 0.072% 15.57% 11617ms 10.67% VertexBasedCellPopulation::GetDampingConstant 3555ms 3.26% 18.84% 11520ms 10.58% __dynamic_cast 66ms 0.061% 18.90% 11397ms 10.47% AbstractCellProperty::IsSubType (inline) 92ms 0.084% 18.98% 10593ms 9.73% AbstractTargetAreaModifier::UpdateTargetAreas 78ms 0.072% 19.05% 10472ms 9.62% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 21ms 0.019% 19.07% 10286ms 9.45% AbstractCellBasedSimulation::DoCellBirth 1330ms 1.22% 20.29% 10255ms 9.42% std::__new_allocator::allocate (inline) 0 0% 20.29% 9734ms 8.94% std::allocator_traits::allocate (inline) 0 0% 20.29% 9725ms 8.93% std::_Rb_tree::_M_create_node (inline) 2640ms 2.42% 22.72% 9341ms 8.58% boost::numeric::ublas::indexing_vector_assign 868ms 0.8% 23.52% 9079ms 8.34% operator new 0 0% 23.52% 9067ms 8.33% std::_Rb_tree::_M_get_node (inline) 758ms 0.7% 24.21% 8877ms 8.15% VertexMesh::ElementIncludesPoint 1266ms 1.16% 25.37% 8840ms 8.12% std::_Rb_tree::_M_erase 76ms 0.07% 25.44% 8832ms 8.11% Cell::GetMutationState 25ms 0.023% 25.47% 8760ms 8.05% VertexBasedCellPopulation::GetLocationOfCellCentre 382ms 0.35% 25.82% 8707ms 8.00% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 25.82% 8535ms 7.84% std::_Rb_tree::_Alloc_node::operator() (inline) 492ms 0.45% 26.27% 8260ms 7.59% VertexMesh::GetCentroidOfElement 200ms 0.18% 26.45% 8074ms 7.42% std::_Rb_tree::~_Rb_tree (inline) 3199ms 2.94% 29.39% 8018ms 7.36% __GI___libc_malloc 0 0% 29.39% 7992ms 7.34% std::_Rb_tree::_M_drop_node (inline) 251ms 0.23% 29.62% 7763ms 7.13% std::__new_allocator::deallocate (inline) 0 0% 29.62% 7739ms 7.11% std::allocator_traits::deallocate (inline) 0 0% 29.62% 7666ms 7.04% std::_Rb_tree::_M_put_node (inline) 451ms 0.41% 30.04% 7633ms 7.01% std::map::operator[] (partial-inline) 0 0% 30.04% 7624ms 7.00% std::set::~set (inline) 2957ms 2.72% 32.75% 7619ms 7.00% __GI___libc_free 19ms 0.017% 32.77% 7531ms 6.92% MutableVertexMesh::RemoveDeletedNodesAndElements 1446ms 1.33% 34.10% 7011ms 6.44% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 128ms 0.12% 34.22% 7004ms 6.43% std::_Rb_tree::_Rb_tree (partial-inline) 691ms 0.63% 34.85% 6641ms 6.10% std::_Rb_tree::_M_copy (inline) 14ms 0.013% 34.86% 6598ms 6.06% std::set::set (inline) 6439ms 5.91% 40.78% 6439ms 5.91% __strcmp_avx2 108ms 0.099% 40.88% 6348ms 5.83% SimpleWntCellCycleModel::GetWntLevel 134ms 0.12% 41.00% 6149ms 5.65% WntConcentration::GetWntLevel 6077ms 5.58% 46.58% 6077ms 5.58% boost::numeric::ublas::c_vector::operator() 2427ms 2.23% 48.81% 5944ms 5.46% std::_Rb_tree::_M_lower_bound (inline) 774ms 0.71% 49.52% 5674ms 5.21% std::_Rb_tree::_M_clone_node (inline) 0 0% 49.52% 5585ms 5.13% std::set::insert (inline) 2689ms 2.47% 51.99% 5442ms 5.00% __cxxabiv1::__si_class_type_info::__do_dyncast 24ms 0.022% 52.01% 5381ms 4.94% MutableVertexMesh::RemoveDeletedNodes 41ms 0.038% 52.05% 5219ms 4.79% EdgeHelper::RemoveDeletedEdges 48ms 0.044% 52.09% 4934ms 4.53% EdgeHelper::UpdateEdgesMapKey 0 0% 52.09% 4882ms 4.48% std::_Rb_tree::lower_bound (inline) 0 0% 52.09% 4882ms 4.48% std::map::lower_bound (inline) 1449ms 1.33% 53.42% 4771ms 4.38% boost::numeric::ublas::c_vector::operator[] (inline) 599ms 0.55% 53.97% 4732ms 4.35% std::_Rb_tree::_M_insert_ (inline) 201ms 0.18% 54.16% 4700ms 4.32% MutableElement::ResetIndex 4326ms 3.97% 58.13% 4651ms 4.27% _int_free 1ms 0.00092% 58.13% 4548ms 4.18% AbstractCellBasedSimulation::DoCellRemoval (inline) 65ms 0.06% 58.19% 4480ms 4.11% std::set_intersection (inline) 258ms 0.24% 58.43% 4415ms 4.05% std::__set_intersection 97ms 0.089% 58.52% 4149ms 3.81% AbstractCellPopulation::GetCellUsingLocationIndex 3986ms 3.66% 62.18% 3986ms 3.66% boost::numeric::ublas::same_impl_ex 34ms 0.031% 62.21% 3936ms 3.61% Cell::GetCellProliferativeType 63ms 0.058% 62.27% 3816ms 3.50% AbstractCellProperty::IsType (inline) 10ms 0.0092% 62.28% 3513ms 3.23% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1ms 0.00092% 62.28% 3257ms 2.99% std::insert_iterator::operator= (inline) 845ms 0.78% 63.05% 3228ms 2.96% AbstractElement::GetNodeLocation 2267ms 2.08% 65.14% 3155ms 2.90% _int_malloc 43ms 0.039% 65.18% 3091ms 2.84% Cell::SetCellProliferativeType 42ms 0.039% 65.21% 3028ms 2.78% std::_Rb_tree::erase 6ms 0.0055% 65.22% 2898ms 2.66% std::_Rb_tree::_M_insert_unique_ (inline) 2889ms 2.65% 67.87% 2889ms 2.65% std::_Rb_tree::_S_right (inline) 396ms 0.36% 68.24% 2773ms 2.55% std::_Rb_tree_const_iterator::operator++ (inline) 789ms 0.72% 68.96% 2766ms 2.54% AbstractCellProperty::IsSame 565ms 0.52% 69.48% 2744ms 2.52% boost::numeric::ublas::vector_binary::size (inline) 38ms 0.035% 69.52% 2701ms 2.48% CellPropertyCollection::HasProperty 2ms 0.0018% 69.52% 2687ms 2.47% std::_Rb_tree::_M_insert_unique 0 0% 69.52% 2620ms 2.41% Cell::HasCellProperty (inline) 21ms 0.019% 69.54% 2488ms 2.29% Cell::GetCellData 0 0% 69.54% 2454ms 2.25% boost::numeric::ublas::c_vector::operator-= (inline) 211ms 0.19% 69.73% 2433ms 2.23% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.73% 2375ms 2.18% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.73% 2358ms 2.17% boost::numeric::ublas::c_vector::assign (inline) 144ms 0.13% 69.86% 2284ms 2.10% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 69.86% 2261ms 2.08% AbstractCellPopulation::Iterator::operator++ (inline) 261ms 0.24% 70.10% 2255ms 2.07% AbstractCellPopulation::Iterator::IsRealCell (inline) 41ms 0.038% 70.14% 2245ms 2.06% std::_Rb_tree::_M_emplace_hint_unique 2200ms 2.02% 72.16% 2200ms 2.02% std::_Rb_tree_increment 90ms 0.083% 72.24% 2186ms 2.01% VertexMesh::GetVolumeOfElement 1420ms 1.30% 73.55% 2039ms 1.87% std::_Rb_tree::equal_range (inline) 2ms 0.0018% 73.55% 1981ms 1.82% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.55% 1981ms 1.82% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 481ms 0.44% 73.99% 1977ms 1.82% std::type_info::operator== (inline) 0 0% 73.99% 1937ms 1.78% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 73.99% 1924ms 1.77% VertexBasedCellPopulation::WriteCellVtkResultsToFile 68ms 0.062% 74.05% 1868ms 1.72% MutableVertexMesh::CheckForSwapsFromShortEdges 23ms 0.021% 74.07% 1730ms 1.59% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 74.07% 1730ms 1.59% VertexMeshWriter::WriteVtkUsingMesh 22ms 0.02% 74.09% 1674ms 1.54% VertexMesh::GetSurfaceAreaOfElement 149ms 0.14% 74.23% 1664ms 1.53% CellPropertyCollection::AddProperty 49ms 0.045% 74.28% 1588ms 1.46% Node::RemoveElement 18ms 0.017% 74.29% 1548ms 1.42% std::set::erase (inline) 83ms 0.076% 74.37% 1529ms 1.40% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 14ms 0.013% 74.38% 1519ms 1.40% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 74.38% 1482ms 1.36% tcache_get (inline) 1482ms 1.36% 75.74% 1482ms 1.36% tcache_get_n (inline) 112ms 0.1% 75.85% 1474ms 1.35% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 75.85% 1353ms 1.24% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 75.85% 1288ms 1.18% boost::numeric::ublas::norm_2 (inline) 575ms 0.53% 76.37% 1277ms 1.17% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 2ms 0.0018% 76.38% 1244ms 1.14% OffLatticeSimulation::ApplyBoundaries 66ms 0.061% 76.44% 1243ms 1.14% std::less::operator() (inline) 0 0% 76.44% 1190ms 1.09% std::_Rb_tree::_Auto_node::_Auto_node (inline) 983ms 0.9% 77.34% 1177ms 1.08% std::operator< (inline) 1172ms 1.08% 78.42% 1172ms 1.08% Node::rGetLocation 1132ms 1.04% 79.46% 1132ms 1.04% std::_Rb_tree_insert_and_rebalance 83ms 0.076% 79.53% 1128ms 1.04% std::_Rb_tree::_M_erase_aux (partial-inline) 24ms 0.022% 79.55% 1099ms 1.01% CellPropertyRegistry::Get 1088ms 1% 80.55% 1088ms 1% [libchaste_cell_based.so] 22ms 0.02% 80.57% 1085ms 1% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 96ms 0.088% 80.66% 1071ms 0.98% std::_Rb_tree::find (inline) 13ms 0.012% 80.67% 983ms 0.9% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 80.67% 980ms 0.9% boost::numeric::ublas::c_vector::assign_temporary (inline) 8ms 0.0073% 80.68% 980ms 0.9% boost::numeric::ublas::c_vector::swap (inline) 67ms 0.062% 80.74% 972ms 0.89% std::swap_ranges (inline) 1ms 0.00092% 80.74% 969ms 0.89% std::_Rb_tree::clear (inline) 146ms 0.13% 80.88% 953ms 0.88% boost::detail::shared_count::~shared_count (inline) 0 0% 80.88% 953ms 0.88% boost::shared_ptr::~shared_ptr (inline) 949ms 0.87% 81.75% 949ms 0.87% [libchaste_mesh.so] 0 0% 81.75% 944ms 0.87% std::map::clear (inline) 17ms 0.016% 81.76% 927ms 0.85% boost::numeric::ublas::detail::expression_type_check (inline) 383ms 0.35% 82.12% 907ms 0.83% Edge::GetMapIndex 0 0% 82.12% 905ms 0.83% std::iter_swap (inline) 905ms 0.83% 82.95% 905ms 0.83% std::swap (inline) 0 0% 82.95% 890ms 0.82% std::map::find (inline) 155ms 0.14% 83.09% 889ms 0.82% boost::numeric::ublas::detail::equals 874ms 0.8% 83.89% 874ms 0.8% std::vector::size (inline) 107ms 0.098% 83.99% 848ms 0.78% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 83.99% 845ms 0.78% VertexMeshWriter::MakeVtkMesh 771ms 0.71% 84.70% 774ms 0.71% boost::detail::sp_counted_base::release 115ms 0.11% 84.80% 767ms 0.7% boost::shared_ptr::shared_ptr (inline) 464ms 0.43% 85.23% 765ms 0.7% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 96ms 0.088% 85.32% 759ms 0.7% MutableElement::GetNodeLocalIndex 726ms 0.67% 85.99% 726ms 0.67% Node::GetIndex 34ms 0.031% 86.02% 708ms 0.65% Edge::AddElement 13ms 0.012% 86.03% 708ms 0.65% MutableElement::RegisterWithEdges (inline) 0 0% 86.03% 707ms 0.65% std::_Rb_tree::_Auto_node::_M_insert (inline) 23ms 0.021% 86.05% 707ms 0.65% std::_Rb_tree::_M_insert_node (inline) 109ms 0.1% 86.15% 697ms 0.64% std::__new_allocator::construct (inline) 0 0% 86.15% 697ms 0.64% std::allocator_traits::construct (inline) 0 0% 86.15% 693ms 0.64% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 86.15% 693ms 0.64% boost::numeric::ublas::norm_inf (inline) 340ms 0.31% 86.46% 693ms 0.64% boost::numeric::ublas::vector_norm_inf::apply (inline) 11ms 0.01% 86.47% 672ms 0.62% AbstractNumericalMethod::DetectStepSizeExceptions 1ms 0.00092% 86.47% 665ms 0.61% std::_Vector_base::_M_allocate (inline) 97ms 0.089% 86.56% 661ms 0.61% VertexBasedCellPopulation::CheckForStepSizeException 0 0% 86.56% 658ms 0.6% std::_Rb_tree::_M_construct_node (inline) 620ms 0.57% 87.13% 652ms 0.6% boost::detail::shared_count::shared_count (inline) 35ms 0.032% 87.16% 637ms 0.59% MutableElement::RegisterWithNodes (inline) 0 0% 87.16% 621ms 0.57% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 87.16% 612ms 0.56% vtkPolygon::New 0 0% 87.16% 612ms 0.56% vtkPolygon::vtkPolygon 27ms 0.025% 87.19% 602ms 0.55% Node::AddElement 569ms 0.52% 87.71% 569ms 0.52% [libstdc++.so.6.0.33] 557ms 0.51% 88.22% 557ms 0.51% operator delete 552ms 0.51% 88.73% 552ms 0.51% boost::shared_ptr::operator-> (inline)