File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 98859ms, 89.05% of 111011ms total Dropped 1071 nodes (cum <= 555.05ms) flat flat% sum% cum cum% 0 0% 0% 110592ms 99.62% __libc_start_call_main 0 0% 0% 110592ms 99.62% __libc_start_main_impl 0 0% 0% 110592ms 99.62% _start 0 0% 0% 110573ms 99.61% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 110573ms 99.61% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 110573ms 99.61% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 110573ms 99.61% main 0 0% 0% 110536ms 99.57% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 110536ms 99.57% CxxTest::TestRunner::runTest (inline) 0 0% 0% 110536ms 99.57% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 1ms 0.0009% 0.0009% 110528ms 99.56% AbstractCellBasedSimulation::Solve 16ms 0.014% 0.015% 57679ms 51.96% OffLatticeSimulation::UpdateCellLocationsAndTopology 18ms 0.016% 0.032% 54518ms 49.11% ForwardEulerNumericalMethod::UpdateAllNodePositions 139ms 0.13% 0.16% 53500ms 48.19% AbstractNumericalMethod::ComputeForcesIncludingDamping 366ms 0.33% 0.49% 40723ms 36.68% NagaiHondaForce::AddForceContribution 0 0% 0.49% 39538ms 35.62% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.0036% 0.49% 24365ms 21.95% VertexBasedCellPopulation::Update 1ms 0.0009% 0.49% 24221ms 21.82% MutableVertexMesh::ReMesh 14607ms 13.16% 13.65% 23064ms 20.78% Cylindrical2dVertexMesh::GetVectorFromAtoB 76ms 0.068% 13.72% 18208ms 16.40% Cell::ReadyToDivide 104ms 0.094% 13.81% 16992ms 15.31% AbstractPhaseBasedCellCycleModel::ReadyToDivide 366ms 0.33% 14.14% 15514ms 13.98% NagaiHondaForce::GetAdhesionParameter 126ms 0.11% 14.25% 14554ms 13.11% SimpleWntCellCycleModel::UpdateCellCyclePhase 415ms 0.37% 14.63% 14395ms 12.97% boost::numeric::ublas::c_vector::c_vector (partial-inline) 150ms 0.14% 14.76% 14333ms 12.91% CellPropertyCollection::GetPropertiesType (inline) 391ms 0.35% 15.12% 12896ms 11.62% boost::numeric::ublas::vector_assign (inline) 113ms 0.1% 15.22% 12278ms 11.06% VertexBasedCellPopulation::GetDampingConstant 138ms 0.12% 15.34% 12107ms 10.91% MutableVertexMesh::CheckForIntersections 3475ms 3.13% 18.47% 11772ms 10.60% __dynamic_cast 74ms 0.067% 18.54% 11646ms 10.49% AbstractCellProperty::IsSubType (inline) 81ms 0.073% 18.61% 10855ms 9.78% AbstractTargetAreaModifier::UpdateTargetAreas 47ms 0.042% 18.65% 10743ms 9.68% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 1331ms 1.20% 19.85% 10638ms 9.58% std::__new_allocator::allocate (inline) 23ms 0.021% 19.87% 10549ms 9.50% AbstractCellBasedSimulation::DoCellBirth 0 0% 19.87% 10117ms 9.11% std::allocator_traits::allocate (inline) 0 0% 19.87% 10068ms 9.07% std::_Rb_tree::_M_create_node (inline) 2616ms 2.36% 22.23% 9680ms 8.72% boost::numeric::ublas::indexing_vector_assign 65ms 0.059% 22.29% 9534ms 8.59% Cell::GetMutationState 865ms 0.78% 23.07% 9413ms 8.48% operator new 0 0% 23.07% 9397ms 8.46% std::_Rb_tree::_M_get_node (inline) 1433ms 1.29% 24.36% 9265ms 8.35% std::_Rb_tree::_M_erase 784ms 0.71% 25.07% 8991ms 8.10% VertexMesh::ElementIncludesPoint 29ms 0.026% 25.09% 8979ms 8.09% VertexBasedCellPopulation::GetLocationOfCellCentre 357ms 0.32% 25.41% 8860ms 7.98% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 25.41% 8854ms 7.98% std::_Rb_tree::_Alloc_node::operator() (inline) 515ms 0.46% 25.88% 8535ms 7.69% VertexMesh::GetCentroidOfElement 215ms 0.19% 26.07% 8437ms 7.60% std::_Rb_tree::~_Rb_tree (inline) 3321ms 2.99% 29.06% 8340ms 7.51% __GI___libc_malloc 0 0% 29.06% 8129ms 7.32% std::_Rb_tree::_M_drop_node (inline) 0 0% 29.06% 7973ms 7.18% std::set::~set (inline) 265ms 0.24% 29.30% 7919ms 7.13% std::__new_allocator::deallocate (inline) 0 0% 29.30% 7897ms 7.11% std::allocator_traits::deallocate (inline) 0 0% 29.30% 7834ms 7.06% std::_Rb_tree::_M_put_node (inline) 445ms 0.4% 29.70% 7722ms 6.96% std::map::operator[] (partial-inline) 3038ms 2.74% 32.44% 7698ms 6.93% __GI___libc_free 22ms 0.02% 32.46% 7669ms 6.91% MutableVertexMesh::RemoveDeletedNodesAndElements 131ms 0.12% 32.58% 7373ms 6.64% std::_Rb_tree::_Rb_tree (partial-inline) 1376ms 1.24% 33.82% 7086ms 6.38% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 14ms 0.013% 33.83% 6985ms 6.29% std::set::set (inline) 638ms 0.57% 34.40% 6933ms 6.25% std::_Rb_tree::_M_copy (inline) 6717ms 6.05% 40.45% 6717ms 6.05% __strcmp_avx2 114ms 0.1% 40.56% 6594ms 5.94% SimpleWntCellCycleModel::GetWntLevel 156ms 0.14% 40.70% 6405ms 5.77% WntConcentration::GetWntLevel 6204ms 5.59% 46.29% 6204ms 5.59% boost::numeric::ublas::c_vector::operator() 2436ms 2.19% 48.48% 6169ms 5.56% std::_Rb_tree::_M_lower_bound (inline) 811ms 0.73% 49.21% 5978ms 5.39% std::_Rb_tree::_M_clone_node (inline) 2696ms 2.43% 51.64% 5845ms 5.27% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 51.64% 5631ms 5.07% std::set::insert (inline) 36ms 0.032% 51.67% 5517ms 4.97% MutableVertexMesh::RemoveDeletedNodes 30ms 0.027% 51.70% 5319ms 4.79% EdgeHelper::RemoveDeletedEdges 51ms 0.046% 51.74% 5083ms 4.58% EdgeHelper::UpdateEdgesMapKey 0 0% 51.74% 5044ms 4.54% std::_Rb_tree::lower_bound (inline) 0 0% 51.74% 5044ms 4.54% std::map::lower_bound (inline) 1568ms 1.41% 53.16% 4782ms 4.31% boost::numeric::ublas::c_vector::operator[] (inline) 541ms 0.49% 53.64% 4765ms 4.29% std::_Rb_tree::_M_insert_ (inline) 183ms 0.16% 53.81% 4719ms 4.25% MutableElement::ResetIndex 4363ms 3.93% 57.74% 4646ms 4.19% _int_free 100ms 0.09% 57.83% 4615ms 4.16% std::set_intersection (inline) 0 0% 57.83% 4609ms 4.15% AbstractCellBasedSimulation::DoCellRemoval (inline) 300ms 0.27% 58.10% 4515ms 4.07% std::__set_intersection 106ms 0.095% 58.20% 4258ms 3.84% AbstractCellPopulation::GetCellUsingLocationIndex 4059ms 3.66% 61.85% 4059ms 3.66% boost::numeric::ublas::same_impl_ex 46ms 0.041% 61.89% 3968ms 3.57% Cell::GetCellProliferativeType 64ms 0.058% 61.95% 3933ms 3.54% AbstractCellProperty::IsType (inline) 8ms 0.0072% 61.96% 3529ms 3.18% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 803ms 0.72% 62.68% 3326ms 3.00% AbstractElement::GetNodeLocation 2400ms 2.16% 64.84% 3290ms 2.96% _int_malloc 0 0% 64.84% 3290ms 2.96% std::insert_iterator::operator= (inline) 42ms 0.038% 64.88% 3198ms 2.88% Cell::SetCellProliferativeType 3137ms 2.83% 67.71% 3137ms 2.83% std::_Rb_tree::_S_right (inline) 46ms 0.041% 67.75% 3015ms 2.72% std::_Rb_tree::erase 9ms 0.0081% 67.76% 2913ms 2.62% std::_Rb_tree::_M_insert_unique_ (inline) 461ms 0.42% 68.17% 2913ms 2.62% std::_Rb_tree_const_iterator::operator++ (inline) 678ms 0.61% 68.78% 2825ms 2.54% boost::numeric::ublas::vector_binary::size (inline) 45ms 0.041% 68.82% 2763ms 2.49% CellPropertyCollection::HasProperty 773ms 0.7% 69.52% 2759ms 2.49% AbstractCellProperty::IsSame 4ms 0.0036% 69.52% 2718ms 2.45% std::_Rb_tree::_M_insert_unique 0 0% 69.52% 2654ms 2.39% Cell::HasCellProperty (inline) 0 0% 69.52% 2520ms 2.27% boost::numeric::ublas::c_vector::assign (inline) 221ms 0.2% 69.72% 2485ms 2.24% VertexMesh::GetAreaGradientOfElementAtNode 1ms 0.0009% 69.72% 2438ms 2.20% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.72% 2382ms 2.15% boost::numeric::ublas::c_vector::operator-= (inline) 25ms 0.023% 69.75% 2341ms 2.11% Cell::GetCellData 95ms 0.086% 69.83% 2315ms 2.09% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 2298ms 2.07% 71.90% 2298ms 2.07% std::_Rb_tree_increment 7ms 0.0063% 71.91% 2295ms 2.07% AbstractCellPopulation::Iterator::operator++ (inline) 230ms 0.21% 72.11% 2289ms 2.06% AbstractCellPopulation::Iterator::IsRealCell (inline) 108ms 0.097% 72.21% 2256ms 2.03% VertexMesh::GetVolumeOfElement 32ms 0.029% 72.24% 2187ms 1.97% std::_Rb_tree::_M_emplace_hint_unique 1422ms 1.28% 73.52% 2096ms 1.89% std::_Rb_tree::equal_range (inline) 448ms 0.4% 73.93% 1986ms 1.79% std::type_info::operator== (inline) 0 0% 73.93% 1983ms 1.79% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 73.93% 1961ms 1.77% VertexBasedCellPopulation::WriteCellVtkResultsToFile 76ms 0.068% 73.99% 1813ms 1.63% MutableVertexMesh::CheckForSwapsFromShortEdges 32ms 0.029% 74.02% 1787ms 1.61% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 74.02% 1773ms 1.60% VertexMeshWriter::WriteVtkUsingMesh 1ms 0.0009% 74.02% 1769ms 1.59% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 74.02% 1769ms 1.59% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 172ms 0.15% 74.18% 1677ms 1.51% CellPropertyCollection::AddProperty 22ms 0.02% 74.20% 1633ms 1.47% VertexMesh::GetSurfaceAreaOfElement 46ms 0.041% 74.24% 1578ms 1.42% Node::RemoveElement 92ms 0.083% 74.32% 1566ms 1.41% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 74.32% 1557ms 1.40% tcache_get (inline) 1557ms 1.40% 75.72% 1557ms 1.40% tcache_get_n (inline) 17ms 0.015% 75.74% 1539ms 1.39% std::set::erase (inline) 20ms 0.018% 75.76% 1522ms 1.37% AbstractCellPopulation::GetLocationIndexUsingCell 103ms 0.093% 75.85% 1517ms 1.37% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 75.85% 1376ms 1.24% boost::numeric::ublas::vector_binary::operator() (inline) 68ms 0.061% 75.91% 1275ms 1.15% std::less::operator() (inline) 0 0% 75.91% 1264ms 1.14% OffLatticeSimulation::ApplyBoundaries 1242ms 1.12% 77.03% 1242ms 1.12% Node::rGetLocation 0 0% 77.03% 1214ms 1.09% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1016ms 0.92% 77.95% 1207ms 1.09% std::operator< (inline) 93ms 0.084% 78.03% 1149ms 1.04% std::_Rb_tree::_M_erase_aux (partial-inline) 0 0% 78.03% 1123ms 1.01% boost::numeric::ublas::norm_2 (inline) 1117ms 1.01% 79.04% 1117ms 1.01% std::_Rb_tree_insert_and_rebalance 35ms 0.032% 79.07% 1116ms 1.01% CellPropertyRegistry::Get 490ms 0.44% 79.51% 1114ms 1.00% boost::numeric::ublas::vector_norm_2::apply 99ms 0.089% 79.60% 1107ms 1% std::_Rb_tree::find (inline) 1095ms 0.99% 80.58% 1095ms 0.99% [libchaste_cell_based.so] 26ms 0.023% 80.61% 1070ms 0.96% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 2ms 0.0018% 80.61% 1050ms 0.95% std::_Rb_tree::clear (inline) 0 0% 80.61% 1038ms 0.94% std::map::clear (inline) 9ms 0.0081% 80.62% 1029ms 0.93% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 192ms 0.17% 80.79% 1028ms 0.93% boost::detail::shared_count::~shared_count (inline) 0 0% 80.79% 1028ms 0.93% boost::shared_ptr::~shared_ptr (inline) 383ms 0.35% 81.14% 979ms 0.88% Edge::GetMapIndex 960ms 0.86% 82.00% 960ms 0.86% std::vector::size (inline) 922ms 0.83% 82.83% 922ms 0.83% [libchaste_mesh.so] 0 0% 82.83% 910ms 0.82% boost::numeric::ublas::c_vector::assign_temporary (inline) 10ms 0.009% 82.84% 910ms 0.82% boost::numeric::ublas::c_vector::swap (inline) 85ms 0.077% 82.92% 900ms 0.81% std::swap_ranges (inline) 0 0% 82.92% 899ms 0.81% std::map::find (inline) 159ms 0.14% 83.06% 897ms 0.81% boost::shared_ptr::shared_ptr (inline) 93ms 0.084% 83.14% 886ms 0.8% MutableElement::GetNodeLocalIndex 29ms 0.026% 83.17% 868ms 0.78% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 83.17% 864ms 0.78% VertexMeshWriter::MakeVtkMesh 146ms 0.13% 83.30% 828ms 0.75% boost::numeric::ublas::detail::equals 0 0% 83.30% 815ms 0.73% std::iter_swap (inline) 815ms 0.73% 84.04% 815ms 0.73% std::swap (inline) 799ms 0.72% 84.76% 807ms 0.73% boost::detail::sp_counted_base::release 132ms 0.12% 84.87% 781ms 0.7% boost::numeric::ublas::c_vector::operator= (inline) 20ms 0.018% 84.89% 771ms 0.69% MutableElement::RegisterWithEdges (inline) 765ms 0.69% 85.58% 765ms 0.69% Node::GetIndex 34ms 0.031% 85.61% 764ms 0.69% Edge::AddElement 709ms 0.64% 86.25% 738ms 0.66% boost::detail::shared_count::shared_count (inline) 0 0% 86.25% 732ms 0.66% CellPropertyCollection::~CellPropertyCollection (inline) 120ms 0.11% 86.36% 716ms 0.64% std::__new_allocator::construct (inline) 0 0% 86.36% 716ms 0.64% std::allocator_traits::construct (inline) 0 0% 86.36% 711ms 0.64% std::_Vector_base::_M_allocate (inline) 407ms 0.37% 86.73% 692ms 0.62% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 86.73% 671ms 0.6% std::_Rb_tree::_M_construct_node (inline) 0 0% 86.73% 666ms 0.6% std::_Rb_tree::_Auto_node::_M_insert (inline) 29ms 0.026% 86.75% 666ms 0.6% std::_Rb_tree::_M_insert_node (inline) 651ms 0.59% 87.34% 651ms 0.59% [libstdc++.so.6.0.33] 0 0% 87.34% 646ms 0.58% boost::numeric::ublas::norm_inf (inline) 310ms 0.28% 87.62% 646ms 0.58% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 87.62% 638ms 0.57% vtkPolygon::New 0 0% 87.62% 638ms 0.57% vtkPolygon::vtkPolygon 26ms 0.023% 87.64% 628ms 0.57% MutableElement::RegisterWithNodes (inline) 621ms 0.56% 88.20% 621ms 0.56% operator delete 324ms 0.29% 88.49% 619ms 0.56% CellPropertyCollection::GetProperty 28ms 0.025% 88.52% 597ms 0.54% Node::AddElement 12ms 0.011% 88.53% 586ms 0.53% std::vector::_M_default_append (inline) 583ms 0.53% 89.05% 583ms 0.53% boost::shared_ptr::operator-> (inline)