File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95284ms, 88.61% of 107530ms total Dropped 1096 nodes (cum <= 537.65ms) flat flat% sum% cum cum% 0 0% 0% 107283ms 99.77% __libc_start_call_main 0 0% 0% 107283ms 99.77% __libc_start_main_impl 0 0% 0% 107283ms 99.77% _start 0 0% 0% 107261ms 99.75% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 107261ms 99.75% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 107261ms 99.75% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 107261ms 99.75% main 0 0% 0% 107228ms 99.72% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 107228ms 99.72% CxxTest::TestRunner::runTest (inline) 0 0% 0% 107228ms 99.72% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0019% 0.0019% 107219ms 99.71% AbstractCellBasedSimulation::Solve 7ms 0.0065% 0.0084% 55656ms 51.76% OffLatticeSimulation::UpdateCellLocationsAndTopology 21ms 0.02% 0.028% 52082ms 48.43% ForwardEulerNumericalMethod::UpdateAllNodePositions 82ms 0.076% 0.1% 50981ms 47.41% AbstractNumericalMethod::ComputeForcesIncludingDamping 344ms 0.32% 0.42% 39151ms 36.41% NagaiHondaForce::AddForceContribution 0 0% 0.42% 37702ms 35.06% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.0028% 0.43% 22230ms 20.67% VertexBasedCellPopulation::Update 1ms 0.00093% 0.43% 22105ms 20.56% MutableVertexMesh::ReMesh 85ms 0.079% 0.51% 18742ms 17.43% Cell::ReadyToDivide 9426ms 8.77% 9.27% 17973ms 16.71% Cylindrical2dVertexMesh::GetVectorFromAtoB 32ms 0.03% 9.30% 17599ms 16.37% AbstractPhaseBasedCellCycleModel::ReadyToDivide 77ms 0.072% 9.37% 16192ms 15.06% NagaiHondaForce::GetAdhesionParameter 108ms 0.1% 9.47% 15135ms 14.08% SimpleWntCellCycleModel::UpdateCellCyclePhase 66ms 0.061% 9.54% 13921ms 12.95% CellPropertyCollection::GetPropertiesType (inline) 849ms 0.79% 10.33% 13763ms 12.80% std::__new_allocator::allocate (inline) 418ms 0.39% 10.71% 13619ms 12.67% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 10.71% 13230ms 12.30% std::allocator_traits::allocate (inline) 0 0% 10.71% 12993ms 12.08% std::_Rb_tree::_M_create_node (inline) 970ms 0.9% 11.62% 12841ms 11.94% operator new 0 0% 11.62% 12602ms 11.72% std::_Rb_tree::_M_get_node (inline) 248ms 0.23% 11.85% 12083ms 11.24% boost::numeric::ublas::vector_assign (inline) 3954ms 3.68% 15.52% 11549ms 10.74% __GI___libc_malloc 89ms 0.083% 15.61% 11514ms 10.71% AbstractCellProperty::IsSubType (inline) 2905ms 2.70% 18.31% 11440ms 10.64% __dynamic_cast 95ms 0.088% 18.40% 11437ms 10.64% VertexBasedCellPopulation::GetDampingConstant 60ms 0.056% 18.45% 11411ms 10.61% AbstractTargetAreaModifier::UpdateTargetAreas 41ms 0.038% 18.49% 11320ms 10.53% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 0 0% 18.49% 11187ms 10.40% std::_Rb_tree::_Alloc_node::operator() (inline) 12ms 0.011% 18.50% 10957ms 10.19% AbstractCellBasedSimulation::DoCellBirth 152ms 0.14% 18.64% 9867ms 9.18% MutableVertexMesh::CheckForIntersections 0 0% 18.64% 9414ms 8.75% std::_Rb_tree::_M_drop_node (inline) 1045ms 0.97% 19.61% 9389ms 8.73% std::_Rb_tree::_M_erase 556ms 0.52% 20.13% 9057ms 8.42% std::map::operator[] (partial-inline) 359ms 0.33% 20.47% 8859ms 8.24% std::_Rb_tree::~_Rb_tree (inline) 69ms 0.064% 20.53% 8842ms 8.22% Cell::GetMutationState 2640ms 2.46% 22.99% 8689ms 8.08% boost::numeric::ublas::indexing_vector_assign 61ms 0.057% 23.04% 8590ms 7.99% VertexBasedCellPopulation::GetLocationOfCellCentre 102ms 0.095% 23.14% 8481ms 7.89% std::__new_allocator::deallocate (inline) 0 0% 23.14% 8475ms 7.88% std::set::~set (inline) 0 0% 23.14% 8467ms 7.87% std::allocator_traits::deallocate (inline) 0 0% 23.14% 8396ms 7.81% std::_Rb_tree::_M_put_node (inline) 2181ms 2.03% 25.17% 8255ms 7.68% __GI___libc_free 0 0% 25.17% 8142ms 7.57% std::set::insert (inline) 754ms 0.7% 25.87% 8050ms 7.49% VertexMesh::GetCentroidOfElement 15ms 0.014% 25.88% 7963ms 7.41% MutableVertexMesh::RemoveDeletedNodesAndElements 434ms 0.4% 26.28% 7823ms 7.28% VertexMesh::GetNextEdgeGradientOfElementAtNode 843ms 0.78% 27.07% 7519ms 6.99% std::_Rb_tree::_M_insert_ (inline) 541ms 0.5% 27.57% 7277ms 6.77% VertexMesh::ElementIncludesPoint 6976ms 6.49% 34.06% 6976ms 6.49% __strcmp_evex 136ms 0.13% 34.18% 6968ms 6.48% std::_Rb_tree::_Rb_tree (partial-inline) 155ms 0.14% 34.33% 6692ms 6.22% SimpleWntCellCycleModel::GetWntLevel 673ms 0.63% 34.95% 6635ms 6.17% std::_Rb_tree::_M_copy (inline) 7ms 0.0065% 34.96% 6509ms 6.05% std::set::set (inline) 2492ms 2.32% 37.28% 6409ms 5.96% std::_Rb_tree::_M_lower_bound (inline) 150ms 0.14% 37.42% 6380ms 5.93% WntConcentration::GetWntLevel 6332ms 5.89% 43.31% 6332ms 5.89% boost::numeric::ublas::c_vector::operator() 64ms 0.06% 43.37% 6318ms 5.88% std::set_intersection (inline) 268ms 0.25% 43.62% 6254ms 5.82% std::__set_intersection 1017ms 0.95% 44.56% 6170ms 5.74% AbstractMesh::GetDistanceBetweenNodes 5237ms 4.87% 49.43% 6016ms 5.59% _int_free 749ms 0.7% 50.13% 5794ms 5.39% std::_Rb_tree::_M_clone_node (inline) 4809ms 4.47% 54.60% 5720ms 5.32% _int_malloc 31ms 0.029% 54.63% 5658ms 5.26% MutableVertexMesh::RemoveDeletedNodes 2387ms 2.22% 56.85% 5568ms 5.18% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 56.85% 5529ms 5.14% std::_Rb_tree::lower_bound (inline) 0 0% 56.85% 5529ms 5.14% std::map::lower_bound (inline) 64ms 0.06% 56.91% 5516ms 5.13% EdgeHelper::RemoveDeletedEdges 571ms 0.53% 57.44% 5271ms 4.90% boost::numeric::ublas::c_vector::operator[] (inline) 14ms 0.013% 57.45% 5241ms 4.87% EdgeHelper::UpdateEdgesMapKey 0 0% 57.45% 5083ms 4.73% std::insert_iterator::operator= (inline) 112ms 0.1% 57.56% 4870ms 4.53% MutableElement::ResetIndex 57ms 0.053% 57.61% 4776ms 4.44% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 57.61% 4737ms 4.41% std::_Rb_tree::_M_insert_unique_ (inline) 32ms 0.03% 57.64% 4702ms 4.37% Cell::GetCellProliferativeType 0 0% 57.64% 4506ms 4.19% AbstractCellBasedSimulation::DoCellRemoval (inline) 4438ms 4.13% 61.77% 4438ms 4.13% boost::numeric::ublas::same_impl_ex 50ms 0.046% 61.81% 3486ms 3.24% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 96ms 0.089% 61.90% 3451ms 3.21% Cell::SetCellProliferativeType 149ms 0.14% 62.04% 3409ms 3.17% AbstractCellProperty::IsType (inline) 0 0% 62.04% 3405ms 3.17% std::_Rb_tree::_M_insert_unique 3334ms 3.10% 65.14% 3334ms 3.10% std::_Rb_tree::_S_right (inline) 3251ms 3.02% 68.17% 3251ms 3.02% [libchaste_cell_based.so] 794ms 0.74% 68.90% 3168ms 2.95% AbstractElement::GetNodeLocation 151ms 0.14% 69.04% 3154ms 2.93% boost::detail::shared_count::~shared_count (inline) 0 0% 69.04% 3154ms 2.93% boost::shared_ptr::~shared_ptr (inline) 2936ms 2.73% 71.77% 2949ms 2.74% boost::detail::sp_counted_base::release 45ms 0.042% 71.82% 2931ms 2.73% std::_Rb_tree::_M_emplace_hint_unique 6ms 0.0056% 71.82% 2890ms 2.69% AbstractCellPopulation::Iterator::operator++ (inline) 199ms 0.19% 72.01% 2877ms 2.68% AbstractCellPopulation::Iterator::IsRealCell (inline) 66ms 0.061% 72.07% 2731ms 2.54% std::_Rb_tree::erase 143ms 0.13% 72.20% 2673ms 2.49% boost::numeric::ublas::vector_binary::size (inline) 23ms 0.021% 72.22% 2641ms 2.46% Cell::GetCellData 0 0% 72.22% 2593ms 2.41% boost::numeric::ublas::c_vector::assign (inline) 44ms 0.041% 72.26% 2416ms 2.25% CellPropertyCollection::HasProperty 0 0% 72.26% 2415ms 2.25% AbstractCellPopulation::WriteResultsToFiles 43ms 0.04% 72.30% 2405ms 2.24% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 72.30% 2344ms 2.18% Cell::HasCellProperty (inline) 2327ms 2.16% 74.47% 2327ms 2.16% [libchaste_mesh.so] 277ms 0.26% 74.73% 2322ms 2.16% std::_Rb_tree_const_iterator::operator++ (inline) 36ms 0.033% 74.76% 2281ms 2.12% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 74.76% 2279ms 2.12% boost::numeric::ublas::c_vector::operator-= (inline) 437ms 0.41% 75.17% 2182ms 2.03% AbstractCellProperty::IsSame 254ms 0.24% 75.40% 2158ms 2.01% VertexMesh::GetAreaGradientOfElementAtNode 325ms 0.3% 75.70% 2053ms 1.91% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 75.70% 2001ms 1.86% VertexBasedCellPopulation::WriteVtkResultsToFile 2ms 0.0019% 75.71% 1987ms 1.85% VertexBasedCellPopulation::WriteCellVtkResultsToFile 87ms 0.081% 75.79% 1884ms 1.75% VertexMesh::GetVolumeOfElement 123ms 0.11% 75.90% 1820ms 1.69% CellPropertyCollection::AddProperty 0 0% 75.90% 1806ms 1.68% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1ms 0.00093% 75.90% 1793ms 1.67% VertexMeshWriter::WriteVtkUsingMesh 3ms 0.0028% 75.90% 1754ms 1.63% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 75.90% 1754ms 1.63% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 76ms 0.071% 75.98% 1750ms 1.63% AbstractCellPopulation::GetLocationIndexUsingCell 143ms 0.13% 76.11% 1745ms 1.62% std::type_info::operator== (inline) 69ms 0.064% 76.17% 1646ms 1.53% MutableVertexMesh::CheckForSwapsFromShortEdges 53ms 0.049% 76.22% 1572ms 1.46% std::_Rb_tree::_M_erase_aux (partial-inline) 0 0% 76.22% 1524ms 1.42% OffLatticeSimulation::ApplyBoundaries 85ms 0.079% 76.30% 1499ms 1.39% VertexMesh::GetSurfaceAreaOfElement 0 0% 76.30% 1455ms 1.35% tcache_get (inline) 1455ms 1.35% 77.65% 1455ms 1.35% tcache_get_n (inline) 1413ms 1.31% 78.97% 1413ms 1.31% std::_Rb_tree_increment 38ms 0.035% 79.00% 1345ms 1.25% Node::RemoveElement 50ms 0.046% 79.05% 1321ms 1.23% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 79.05% 1319ms 1.23% boost::numeric::ublas::vector_binary::operator() (inline) 2ms 0.0019% 79.05% 1309ms 1.22% std::set::erase (inline) 748ms 0.7% 79.75% 1285ms 1.20% std::_Rb_tree::equal_range (inline) 12ms 0.011% 79.76% 1254ms 1.17% MutableElement::RegisterWithEdges (inline) 39ms 0.036% 79.79% 1253ms 1.17% Edge::AddElement 0 0% 79.79% 1167ms 1.09% CellPropertyCollection::~CellPropertyCollection (inline) 85ms 0.079% 79.87% 1137ms 1.06% boost::numeric::ublas::vector_reference::operator() (inline) 66ms 0.061% 79.93% 1098ms 1.02% CellPropertyRegistry::Get 1093ms 1.02% 80.95% 1093ms 1.02% Node::rGetLocation 1088ms 1.01% 81.96% 1088ms 1.01% [libstdc++.so.6.0.33] 15ms 0.014% 81.98% 1072ms 1% boost::numeric::ublas::detail::expression_type_check (inline) 1070ms 1% 82.97% 1070ms 1% std::_Rb_tree_insert_and_rebalance 0 0% 82.97% 1028ms 0.96% boost::numeric::ublas::norm_2 (inline) 164ms 0.15% 83.12% 1026ms 0.95% boost::numeric::ublas::detail::equals 0 0% 83.12% 1021ms 0.95% std::__new_allocator::destroy (inline) 0 0% 83.12% 1021ms 0.95% std::allocator_traits::destroy (inline) 0 0% 83.12% 1018ms 0.95% std::_Rb_tree::_M_destroy_node (inline) 512ms 0.48% 83.60% 1000ms 0.93% boost::numeric::ublas::vector_norm_2::apply 12ms 0.011% 83.61% 989ms 0.92% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 83.61% 942ms 0.88% boost::numeric::ublas::c_vector::assign_temporary (inline) 4ms 0.0037% 83.62% 942ms 0.88% boost::numeric::ublas::c_vector::swap (inline) 148ms 0.14% 83.75% 938ms 0.87% std::swap_ranges (inline) 104ms 0.097% 83.85% 935ms 0.87% std::_Rb_tree::find (inline) 1ms 0.00093% 83.85% 925ms 0.86% VertexMeshWriter::MakeVtkMesh 1ms 0.00093% 83.85% 897ms 0.83% std::_Rb_tree::clear (inline) 702ms 0.65% 84.50% 884ms 0.82% CellPropertyCollection::GetProperty 0 0% 84.50% 877ms 0.82% std::map::clear (inline) 856ms 0.8% 85.30% 856ms 0.8% tcache_put (inline) 72ms 0.067% 85.37% 829ms 0.77% boost::numeric::ublas::c_vector::operator= (inline) 57ms 0.053% 85.42% 822ms 0.76% std::less::operator() (inline) 1ms 0.00093% 85.42% 802ms 0.75% std::map::find (inline) 0 0% 85.42% 790ms 0.73% std::iter_swap (inline) 790ms 0.73% 86.16% 790ms 0.73% std::swap (inline) 585ms 0.54% 86.70% 765ms 0.71% std::operator< (inline) 0 0% 86.70% 735ms 0.68% boost::numeric::ublas::norm_inf (inline) 287ms 0.27% 86.97% 735ms 0.68% boost::numeric::ublas::vector_norm_inf::apply (inline) 362ms 0.34% 87.30% 732ms 0.68% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 87.30% 716ms 0.67% std::_Rb_tree::_Auto_node::_M_insert (inline) 24ms 0.022% 87.33% 716ms 0.67% std::_Rb_tree::_M_insert_node (inline) 680ms 0.63% 87.96% 680ms 0.63% std::vector::size (inline) 21ms 0.02% 87.98% 671ms 0.62% MutableElement::RegisterWithNodes (inline) 3ms 0.0028% 87.98% 661ms 0.61% vtkPolygon::New 1ms 0.00093% 87.98% 658ms 0.61% vtkPolygon::vtkPolygon 71ms 0.066% 88.05% 656ms 0.61% MutableElement::GetNodeLocalIndex 41ms 0.038% 88.09% 634ms 0.59% Node::AddElement 0 0% 88.09% 623ms 0.58% std::_Vector_base::_M_allocate (inline) 551ms 0.51% 88.60% 551ms 0.51% Node::GetIndex 14ms 0.013% 88.61% 547ms 0.51% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 88.61% 547ms 0.51% boost::numeric::ublas::vector::vector (inline)