File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 97590ms, 88.92% of 109745ms total Dropped 1080 nodes (cum <= 548.73ms) flat flat% sum% cum cum% 0 0% 0% 109310ms 99.60% __libc_start_call_main 0 0% 0% 109310ms 99.60% __libc_start_main_impl 0 0% 0% 109310ms 99.60% _start 0 0% 0% 109292ms 99.59% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 109292ms 99.59% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 109292ms 99.59% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 109292ms 99.59% main 0 0% 0% 109259ms 99.56% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 109259ms 99.56% CxxTest::TestRunner::runTest (inline) 0 0% 0% 109259ms 99.56% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 0 0% 0% 109252ms 99.55% AbstractCellBasedSimulation::Solve 20ms 0.018% 0.018% 56916ms 51.86% OffLatticeSimulation::UpdateCellLocationsAndTopology 13ms 0.012% 0.03% 53677ms 48.91% ForwardEulerNumericalMethod::UpdateAllNodePositions 121ms 0.11% 0.14% 52641ms 47.97% AbstractNumericalMethod::ComputeForcesIncludingDamping 480ms 0.44% 0.58% 40670ms 37.06% NagaiHondaForce::AddForceContribution 1ms 0.00091% 0.58% 39355ms 35.86% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.58% 24317ms 22.16% VertexBasedCellPopulation::Update 1ms 0.00091% 0.58% 24202ms 22.05% MutableVertexMesh::ReMesh 14555ms 13.26% 13.84% 23159ms 21.10% Cylindrical2dVertexMesh::GetVectorFromAtoB 99ms 0.09% 13.93% 17613ms 16.05% Cell::ReadyToDivide 79ms 0.072% 14.00% 16418ms 14.96% AbstractPhaseBasedCellCycleModel::ReadyToDivide 332ms 0.3% 14.31% 15324ms 13.96% NagaiHondaForce::GetAdhesionParameter 400ms 0.36% 14.67% 14295ms 13.03% boost::numeric::ublas::c_vector::c_vector (partial-inline) 115ms 0.1% 14.78% 14032ms 12.79% SimpleWntCellCycleModel::UpdateCellCyclePhase 128ms 0.12% 14.89% 13565ms 12.36% CellPropertyCollection::GetPropertiesType (inline) 405ms 0.37% 15.26% 12709ms 11.58% boost::numeric::ublas::vector_assign (inline) 119ms 0.11% 15.37% 11999ms 10.93% MutableVertexMesh::CheckForIntersections 76ms 0.069% 15.44% 11474ms 10.46% VertexBasedCellPopulation::GetDampingConstant 3406ms 3.10% 18.54% 11234ms 10.24% __dynamic_cast 79ms 0.072% 18.61% 11134ms 10.15% AbstractCellProperty::IsSubType (inline) 86ms 0.078% 18.69% 10539ms 9.60% AbstractTargetAreaModifier::UpdateTargetAreas 47ms 0.043% 18.74% 10425ms 9.50% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 21ms 0.019% 18.76% 10353ms 9.43% AbstractCellBasedSimulation::DoCellBirth 1296ms 1.18% 19.94% 10276ms 9.36% std::__new_allocator::allocate (inline) 1407ms 1.28% 21.22% 9750ms 8.88% std::_Rb_tree::_M_erase 0 0% 21.22% 9745ms 8.88% std::allocator_traits::allocate (inline) 0 0% 21.22% 9710ms 8.85% std::_Rb_tree::_M_create_node (inline) 2637ms 2.40% 23.62% 9569ms 8.72% boost::numeric::ublas::indexing_vector_assign 0 0% 23.62% 9109ms 8.30% std::_Rb_tree::_M_get_node (inline) 840ms 0.77% 24.39% 9078ms 8.27% operator new 382ms 0.35% 24.73% 8989ms 8.19% VertexMesh::GetNextEdgeGradientOfElementAtNode 739ms 0.67% 25.41% 8942ms 8.15% VertexMesh::ElementIncludesPoint 249ms 0.23% 25.63% 8939ms 8.15% std::_Rb_tree::~_Rb_tree (inline) 27ms 0.025% 25.66% 8909ms 8.12% VertexBasedCellPopulation::GetLocationOfCellCentre 87ms 0.079% 25.74% 8726ms 7.95% Cell::GetMutationState 0 0% 25.74% 8635ms 7.87% std::_Rb_tree::_M_drop_node (inline) 0 0% 25.74% 8505ms 7.75% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 25.74% 8435ms 7.69% std::set::~set (inline) 262ms 0.24% 25.98% 8406ms 7.66% std::__new_allocator::deallocate (inline) 0 0% 25.98% 8381ms 7.64% std::allocator_traits::deallocate (inline) 493ms 0.45% 26.43% 8360ms 7.62% VertexMesh::GetCentroidOfElement 0 0% 26.43% 8314ms 7.58% std::_Rb_tree::_M_put_node (inline) 3089ms 2.81% 29.24% 8129ms 7.41% __GI___libc_free 2938ms 2.68% 31.92% 8048ms 7.33% __GI___libc_malloc 509ms 0.46% 32.38% 7808ms 7.11% std::map::operator[] (partial-inline) 13ms 0.012% 32.39% 7596ms 6.92% MutableVertexMesh::RemoveDeletedNodesAndElements 1417ms 1.29% 33.69% 7240ms 6.60% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 139ms 0.13% 33.81% 6918ms 6.30% std::_Rb_tree::_Rb_tree (partial-inline) 634ms 0.58% 34.39% 6592ms 6.01% std::_Rb_tree::_M_copy (inline) 10ms 0.0091% 34.40% 6489ms 5.91% std::set::set (inline) 99ms 0.09% 34.49% 6415ms 5.85% SimpleWntCellCycleModel::GetWntLevel 6256ms 5.70% 40.19% 6256ms 5.70% boost::numeric::ublas::c_vector::operator() 2492ms 2.27% 42.46% 6222ms 5.67% std::_Rb_tree::_M_lower_bound (inline) 148ms 0.13% 42.60% 6219ms 5.67% WntConcentration::GetWntLevel 6150ms 5.60% 48.20% 6150ms 5.60% __strcmp_avx2 785ms 0.72% 48.91% 5738ms 5.23% std::_Rb_tree::_M_clone_node (inline) 33ms 0.03% 48.94% 5518ms 5.03% MutableVertexMesh::RemoveDeletedNodes 0 0% 48.94% 5471ms 4.99% std::set::insert (inline) 34ms 0.031% 48.98% 5336ms 4.86% EdgeHelper::RemoveDeletedEdges 2736ms 2.49% 51.47% 5315ms 4.84% __cxxabiv1::__si_class_type_info::__do_dyncast 40ms 0.036% 51.50% 5065ms 4.62% EdgeHelper::UpdateEdgesMapKey 4642ms 4.23% 55.73% 5029ms 4.58% _int_free 0 0% 55.73% 5024ms 4.58% std::_Rb_tree::lower_bound (inline) 0 0% 55.73% 5024ms 4.58% std::map::lower_bound (inline) 1541ms 1.40% 57.14% 4862ms 4.43% boost::numeric::ublas::c_vector::operator[] (inline) 240ms 0.22% 57.36% 4694ms 4.28% MutableElement::ResetIndex 0 0% 57.36% 4673ms 4.26% AbstractCellBasedSimulation::DoCellRemoval (inline) 560ms 0.51% 57.87% 4644ms 4.23% std::_Rb_tree::_M_insert_ (inline) 51ms 0.046% 57.91% 4603ms 4.19% std::set_intersection (inline) 296ms 0.27% 58.18% 4552ms 4.15% std::__set_intersection 104ms 0.095% 58.28% 4242ms 3.87% AbstractCellPopulation::GetCellUsingLocationIndex 4057ms 3.70% 61.98% 4057ms 3.70% boost::numeric::ublas::same_impl_ex 41ms 0.037% 62.01% 3966ms 3.61% Cell::GetCellProliferativeType 61ms 0.056% 62.07% 3749ms 3.42% AbstractCellProperty::IsType (inline) 8ms 0.0073% 62.08% 3623ms 3.30% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.08% 3340ms 3.04% std::insert_iterator::operator= (inline) 52ms 0.047% 62.12% 3225ms 2.94% Cell::SetCellProliferativeType 2354ms 2.14% 64.27% 3184ms 2.90% _int_malloc 781ms 0.71% 64.98% 3174ms 2.89% AbstractElement::GetNodeLocation 3125ms 2.85% 67.83% 3125ms 2.85% std::_Rb_tree::_S_right (inline) 7ms 0.0064% 67.83% 3011ms 2.74% std::_Rb_tree::_M_insert_unique_ (inline) 39ms 0.036% 67.87% 2968ms 2.70% std::_Rb_tree::erase 596ms 0.54% 68.41% 2885ms 2.63% boost::numeric::ublas::vector_binary::size (inline) 483ms 0.44% 68.85% 2693ms 2.45% std::_Rb_tree_const_iterator::operator++ (inline) 765ms 0.7% 69.55% 2639ms 2.40% AbstractCellProperty::IsSame 48ms 0.044% 69.59% 2579ms 2.35% CellPropertyCollection::HasProperty 223ms 0.2% 69.80% 2519ms 2.30% VertexMesh::GetAreaGradientOfElementAtNode 39ms 0.036% 69.83% 2461ms 2.24% Cell::GetCellData 2ms 0.0018% 69.83% 2460ms 2.24% std::_Rb_tree::_M_insert_unique 0 0% 69.83% 2459ms 2.24% Cell::HasCellProperty (inline) 0 0% 69.83% 2419ms 2.20% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.83% 2369ms 2.16% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.83% 2357ms 2.15% boost::numeric::ublas::c_vector::assign (inline) 114ms 0.1% 69.94% 2291ms 2.09% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 69.94% 2269ms 2.07% AbstractCellPopulation::Iterator::operator++ (inline) 214ms 0.19% 70.13% 2250ms 2.05% AbstractCellPopulation::Iterator::IsRealCell (inline) 44ms 0.04% 70.17% 2235ms 2.04% std::_Rb_tree::_M_emplace_hint_unique 90ms 0.082% 70.25% 2202ms 2.01% VertexMesh::GetVolumeOfElement 2034ms 1.85% 72.11% 2034ms 1.85% std::_Rb_tree_increment 1346ms 1.23% 73.33% 2030ms 1.85% std::_Rb_tree::equal_range (inline) 0 0% 73.33% 1987ms 1.81% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00091% 73.34% 1974ms 1.80% VertexBasedCellPopulation::WriteCellVtkResultsToFile 71ms 0.065% 73.40% 1915ms 1.74% MutableVertexMesh::CheckForSwapsFromShortEdges 453ms 0.41% 73.81% 1874ms 1.71% std::type_info::operator== (inline) 2ms 0.0018% 73.81% 1867ms 1.70% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.81% 1867ms 1.70% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 73.81% 1771ms 1.61% tcache_get (inline) 1771ms 1.61% 75.43% 1771ms 1.61% tcache_get_n (inline) 0 0% 75.43% 1768ms 1.61% VertexMeshWriter::WriteVtkUsingMesh 30ms 0.027% 75.46% 1729ms 1.58% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 14ms 0.013% 75.47% 1631ms 1.49% VertexMesh::GetSurfaceAreaOfElement 53ms 0.048% 75.52% 1628ms 1.48% Node::RemoveElement 26ms 0.024% 75.54% 1590ms 1.45% AbstractCellPopulation::GetLocationIndexUsingCell 26ms 0.024% 75.56% 1589ms 1.45% std::set::erase (inline) 79ms 0.072% 75.64% 1536ms 1.40% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 108ms 0.098% 75.73% 1510ms 1.38% boost::numeric::ublas::vector_reference::operator() (inline) 143ms 0.13% 75.86% 1444ms 1.32% CellPropertyCollection::AddProperty 0 0% 75.86% 1420ms 1.29% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 75.86% 1275ms 1.16% OffLatticeSimulation::ApplyBoundaries 85ms 0.077% 75.94% 1274ms 1.16% std::less::operator() (inline) 1215ms 1.11% 77.05% 1215ms 1.11% Node::rGetLocation 0 0% 77.05% 1205ms 1.10% std::_Rb_tree::_Auto_node::_Auto_node (inline) 984ms 0.9% 77.95% 1189ms 1.08% std::operator< (inline) 0 0% 77.95% 1174ms 1.07% boost::numeric::ublas::norm_2 (inline) 509ms 0.46% 78.41% 1166ms 1.06% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 119ms 0.11% 78.52% 1166ms 1.06% std::_Rb_tree::find (inline) 1161ms 1.06% 79.58% 1161ms 1.06% [libchaste_cell_based.so] 1143ms 1.04% 80.62% 1143ms 1.04% std::_Rb_tree_insert_and_rebalance 77ms 0.07% 80.69% 1106ms 1.01% std::_Rb_tree::_M_erase_aux (partial-inline) 22ms 0.02% 80.71% 1103ms 1.01% CellPropertyRegistry::Get 19ms 0.017% 80.73% 1086ms 0.99% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 80.73% 1064ms 0.97% std::_Rb_tree::clear (inline) 0 0% 80.73% 1047ms 0.95% std::map::clear (inline) 1023ms 0.93% 81.66% 1023ms 0.93% std::vector::size (inline) 11ms 0.01% 81.67% 998ms 0.91% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 145ms 0.13% 81.80% 980ms 0.89% boost::detail::shared_count::~shared_count (inline) 0 0% 81.80% 980ms 0.89% boost::shared_ptr::~shared_ptr (inline) 0 0% 81.80% 965ms 0.88% std::map::find (inline) 951ms 0.87% 82.67% 951ms 0.87% [libchaste_mesh.so] 0 0% 82.67% 907ms 0.83% CellPropertyCollection::~CellPropertyCollection (inline) 389ms 0.35% 83.02% 906ms 0.83% Edge::GetMapIndex 22ms 0.02% 83.04% 905ms 0.82% boost::numeric::ublas::detail::expression_type_check (inline) 152ms 0.14% 83.18% 871ms 0.79% boost::numeric::ublas::detail::equals 0 0% 83.18% 869ms 0.79% boost::numeric::ublas::c_vector::assign_temporary (inline) 0 0% 83.18% 869ms 0.79% boost::numeric::ublas::c_vector::swap (inline) 92ms 0.084% 83.26% 869ms 0.79% std::swap_ranges (inline) 0 0% 83.26% 859ms 0.78% VertexMeshWriter::MakeVtkMesh 148ms 0.13% 83.40% 821ms 0.75% boost::numeric::ublas::c_vector::operator= (inline) 100ms 0.091% 83.49% 819ms 0.75% MutableElement::GetNodeLocalIndex 813ms 0.74% 84.23% 815ms 0.74% boost::detail::sp_counted_base::release 0 0% 84.23% 777ms 0.71% std::iter_swap (inline) 777ms 0.71% 84.94% 777ms 0.71% std::swap (inline) 142ms 0.13% 85.07% 773ms 0.7% boost::shared_ptr::shared_ptr (inline) 748ms 0.68% 85.75% 748ms 0.68% Node::GetIndex 28ms 0.026% 85.77% 736ms 0.67% Edge::AddElement 22ms 0.02% 85.79% 736ms 0.67% MutableElement::RegisterWithEdges (inline) 441ms 0.4% 86.20% 731ms 0.67% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 86.20% 704ms 0.64% std::_Rb_tree::_Auto_node::_M_insert (inline) 23ms 0.021% 86.22% 704ms 0.64% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.22% 693ms 0.63% boost::numeric::ublas::norm_inf (inline) 385ms 0.35% 86.57% 693ms 0.63% boost::numeric::ublas::vector_norm_inf::apply (inline) 93ms 0.085% 86.65% 645ms 0.59% std::__new_allocator::construct (inline) 0 0% 86.65% 645ms 0.59% std::allocator_traits::construct (inline) 0 0% 86.65% 633ms 0.58% std::_Vector_base::_M_allocate (inline) 600ms 0.55% 87.20% 631ms 0.57% boost::detail::shared_count::shared_count (inline) 621ms 0.57% 87.77% 621ms 0.57% operator delete 2ms 0.0018% 87.77% 621ms 0.57% vtkPolygon::New 0 0% 87.77% 619ms 0.56% vtkPolygon::vtkPolygon 610ms 0.56% 88.32% 610ms 0.56% boost::shared_ptr::operator-> (inline) 0 0% 88.32% 601ms 0.55% std::_Rb_tree::_M_construct_node (inline) 25ms 0.023% 88.35% 584ms 0.53% MutableElement::RegisterWithNodes (inline) 582ms 0.53% 88.88% 582ms 0.53% [libstdc++.so.6.0.33] 0 0% 88.88% 566ms 0.52% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 27ms 0.025% 88.90% 557ms 0.51% Node::AddElement 26ms 0.024% 88.92% 557ms 0.51% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 88.92% 557ms 0.51% boost::numeric::ublas::vector::vector (inline)