File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 80806ms, 88.35% of 91465ms total Dropped 1063 nodes (cum <= 457.32ms) flat flat% sum% cum cum% 0 0% 0% 91238ms 99.75% __libc_start_call_main 0 0% 0% 91238ms 99.75% __libc_start_main_impl 0 0% 0% 91238ms 99.75% _start 0 0% 0% 91220ms 99.73% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 91220ms 99.73% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 91220ms 99.73% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 91220ms 99.73% main 0 0% 0% 91187ms 99.70% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 91187ms 99.70% CxxTest::TestRunner::runTest (inline) 0 0% 0% 91187ms 99.70% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 3ms 0.0033% 0.0033% 91180ms 99.69% AbstractCellBasedSimulation::Solve 8ms 0.0087% 0.012% 47800ms 52.26% OffLatticeSimulation::UpdateCellLocationsAndTopology 16ms 0.017% 0.03% 44779ms 48.96% ForwardEulerNumericalMethod::UpdateAllNodePositions 36ms 0.039% 0.069% 43775ms 47.86% AbstractNumericalMethod::ComputeForcesIncludingDamping 286ms 0.31% 0.38% 34088ms 37.27% NagaiHondaForce::AddForceContribution 0 0% 0.38% 31634ms 34.59% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0022% 0.38% 18518ms 20.25% VertexBasedCellPopulation::Update 1ms 0.0011% 0.38% 18419ms 20.14% MutableVertexMesh::ReMesh 68ms 0.074% 0.46% 16244ms 17.76% Cell::ReadyToDivide 8063ms 8.82% 9.27% 15558ms 17.01% Cylindrical2dVertexMesh::GetVectorFromAtoB 39ms 0.043% 9.32% 15250ms 16.67% AbstractPhaseBasedCellCycleModel::ReadyToDivide 89ms 0.097% 9.41% 14100ms 15.42% NagaiHondaForce::GetAdhesionParameter 79ms 0.086% 9.50% 13111ms 14.33% SimpleWntCellCycleModel::UpdateCellCyclePhase 378ms 0.41% 9.91% 12170ms 13.31% boost::numeric::ublas::c_vector::c_vector (partial-inline) 84ms 0.092% 10.01% 11718ms 12.81% CellPropertyCollection::GetPropertiesType (inline) 513ms 0.56% 10.57% 11545ms 12.62% std::__new_allocator::allocate (inline) 0 0% 10.57% 11052ms 12.08% std::allocator_traits::allocate (inline) 240ms 0.26% 10.83% 10985ms 12.01% boost::numeric::ublas::vector_assign (inline) 798ms 0.87% 11.70% 10980ms 12.00% operator new 0 0% 11.70% 10809ms 11.82% std::_Rb_tree::_M_create_node (inline) 0 0% 11.70% 10525ms 11.51% std::_Rb_tree::_M_get_node (inline) 3511ms 3.84% 15.54% 9914ms 10.84% __GI___libc_malloc 81ms 0.089% 15.63% 9771ms 10.68% AbstractCellProperty::IsSubType (inline) 2258ms 2.47% 18.10% 9682ms 10.59% __dynamic_cast 44ms 0.048% 18.15% 9641ms 10.54% AbstractTargetAreaModifier::UpdateTargetAreas 38ms 0.042% 18.19% 9559ms 10.45% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 6ms 0.0066% 18.19% 9465ms 10.35% AbstractCellBasedSimulation::DoCellBirth 106ms 0.12% 18.31% 9365ms 10.24% VertexBasedCellPopulation::GetDampingConstant 0 0% 18.31% 9287ms 10.15% std::_Rb_tree::_Alloc_node::operator() (inline) 119ms 0.13% 18.44% 8433ms 9.22% MutableVertexMesh::CheckForIntersections 0 0% 18.44% 8143ms 8.90% std::_Rb_tree::_M_drop_node (inline) 872ms 0.95% 19.39% 8135ms 8.89% std::_Rb_tree::_M_erase 2266ms 2.48% 21.87% 7923ms 8.66% boost::numeric::ublas::indexing_vector_assign 322ms 0.35% 22.22% 7666ms 8.38% std::_Rb_tree::~_Rb_tree (inline) 69ms 0.075% 22.30% 7521ms 8.22% Cell::GetMutationState 100ms 0.11% 22.41% 7388ms 8.08% std::__new_allocator::deallocate (inline) 0 0% 22.41% 7363ms 8.05% std::allocator_traits::deallocate (inline) 0 0% 22.41% 7315ms 8.00% std::set::~set (inline) 0 0% 22.41% 7313ms 8.00% std::_Rb_tree::_M_put_node (inline) 28ms 0.031% 22.44% 7221ms 7.89% VertexBasedCellPopulation::GetLocationOfCellCentre 1897ms 2.07% 24.51% 7136ms 7.80% __GI___libc_free 630ms 0.69% 25.20% 6938ms 7.59% VertexMesh::GetCentroidOfElement 400ms 0.44% 25.64% 6773ms 7.41% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 25.64% 6722ms 7.35% std::set::insert (inline) 440ms 0.48% 26.12% 6700ms 7.33% std::map::operator[] (partial-inline) 9ms 0.0098% 26.13% 6472ms 7.08% MutableVertexMesh::RemoveDeletedNodesAndElements 463ms 0.51% 26.64% 6302ms 6.89% VertexMesh::ElementIncludesPoint 737ms 0.81% 27.44% 6145ms 6.72% std::_Rb_tree::_M_insert_ (inline) 6064ms 6.63% 34.07% 6064ms 6.63% __strcmp_evex 103ms 0.11% 34.18% 5811ms 6.35% std::_Rb_tree::_Rb_tree (partial-inline) 142ms 0.16% 34.34% 5656ms 6.18% SimpleWntCellCycleModel::GetWntLevel 5628ms 6.15% 40.49% 5628ms 6.15% boost::numeric::ublas::c_vector::operator() 51ms 0.056% 40.55% 5539ms 6.06% std::set_intersection (inline) 582ms 0.64% 41.18% 5538ms 6.05% std::_Rb_tree::_M_copy (inline) 289ms 0.32% 41.50% 5488ms 6.00% std::__set_intersection 5ms 0.0055% 41.51% 5419ms 5.92% std::set::set (inline) 129ms 0.14% 41.65% 5391ms 5.89% WntConcentration::GetWntLevel 842ms 0.92% 42.57% 5197ms 5.68% AbstractMesh::GetDistanceBetweenNodes 4535ms 4.96% 47.53% 5190ms 5.67% _int_free 2149ms 2.35% 49.87% 4823ms 5.27% __cxxabiv1::__si_class_type_info::__do_dyncast 496ms 0.54% 50.42% 4794ms 5.24% std::_Rb_tree::_M_clone_node (inline) 19ms 0.021% 50.44% 4672ms 5.11% MutableVertexMesh::RemoveDeletedNodes 3821ms 4.18% 54.62% 4619ms 5.05% _int_malloc 63ms 0.069% 54.68% 4556ms 4.98% EdgeHelper::RemoveDeletedEdges 486ms 0.53% 55.22% 4555ms 4.98% boost::numeric::ublas::c_vector::operator[] (inline) 1930ms 2.11% 57.33% 4370ms 4.78% std::_Rb_tree::_M_lower_bound (inline) 6ms 0.0066% 57.33% 4305ms 4.71% EdgeHelper::UpdateEdgesMapKey 0 0% 57.33% 4274ms 4.67% std::insert_iterator::operator= (inline) 30ms 0.033% 57.37% 4001ms 4.37% Cell::GetCellProliferativeType 0 0% 57.37% 3988ms 4.36% std::_Rb_tree::_M_insert_unique_ (inline) 3953ms 4.32% 61.69% 3953ms 4.32% boost::numeric::ublas::same_impl_ex 95ms 0.1% 61.79% 3840ms 4.20% MutableElement::ResetIndex 0 0% 61.79% 3784ms 4.14% std::_Rb_tree::lower_bound (inline) 0 0% 61.79% 3784ms 4.14% std::map::lower_bound (inline) 0 0% 61.79% 3646ms 3.99% AbstractCellBasedSimulation::DoCellRemoval (inline) 45ms 0.049% 61.84% 3486ms 3.81% AbstractCellPopulation::GetCellUsingLocationIndex 120ms 0.13% 61.97% 3146ms 3.44% AbstractCellProperty::IsType (inline) 85ms 0.093% 62.06% 3018ms 3.30% Cell::SetCellProliferativeType 2949ms 3.22% 65.29% 2949ms 3.22% [libchaste_cell_based.so] 47ms 0.051% 65.34% 2817ms 3.08% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1ms 0.0011% 65.34% 2734ms 2.99% std::_Rb_tree::_M_insert_unique 124ms 0.14% 65.48% 2646ms 2.89% boost::detail::shared_count::~shared_count (inline) 0 0% 65.48% 2646ms 2.89% boost::shared_ptr::~shared_ptr (inline) 656ms 0.72% 66.19% 2589ms 2.83% AbstractElement::GetNodeLocation 2467ms 2.70% 68.89% 2476ms 2.71% boost::detail::sp_counted_base::release 29ms 0.032% 68.92% 2441ms 2.67% std::_Rb_tree::_M_emplace_hint_unique 146ms 0.16% 69.08% 2281ms 2.49% boost::numeric::ublas::vector_binary::size (inline) 0 0% 69.08% 2237ms 2.45% boost::numeric::ublas::c_vector::assign (inline) 2ms 0.0022% 69.08% 2209ms 2.42% AbstractCellPopulation::Iterator::operator++ (inline) 182ms 0.2% 69.28% 2199ms 2.40% AbstractCellPopulation::Iterator::IsRealCell (inline) 44ms 0.048% 69.33% 2168ms 2.37% CellPropertyCollection::HasProperty 11ms 0.012% 69.34% 2161ms 2.36% Cell::GetCellData 56ms 0.061% 69.40% 2140ms 2.34% std::_Rb_tree::erase 251ms 0.27% 69.68% 2131ms 2.33% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 69.68% 2124ms 2.32% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.68% 2113ms 2.31% Cell::HasCellProperty (inline) 0 0% 69.68% 2076ms 2.27% AbstractCellPopulation::WriteResultsToFiles 41ms 0.045% 69.72% 2076ms 2.27% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 270ms 0.3% 70.02% 2024ms 2.21% VertexMesh::GetAreaGradientOfElementAtNode 376ms 0.41% 70.43% 2014ms 2.20% AbstractCellProperty::IsSame 1940ms 2.12% 72.55% 1940ms 2.12% std::_Rb_tree::_S_right (inline) 1914ms 2.09% 74.64% 1914ms 2.09% [libchaste_mesh.so] 0 0% 74.64% 1707ms 1.87% VertexBasedCellPopulation::WriteVtkResultsToFile 3ms 0.0033% 74.65% 1693ms 1.85% VertexBasedCellPopulation::WriteCellVtkResultsToFile 201ms 0.22% 74.87% 1638ms 1.79% std::type_info::operator== (inline) 31ms 0.034% 74.90% 1623ms 1.77% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 103ms 0.11% 75.01% 1550ms 1.69% VertexMesh::GetVolumeOfElement 4ms 0.0044% 75.02% 1537ms 1.68% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 75.02% 1537ms 1.68% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 75.02% 1523ms 1.67% VertexMeshWriter::WriteVtkUsingMesh 0 0% 75.02% 1522ms 1.66% std::_Rb_tree::_Auto_node::_Auto_node (inline) 111ms 0.12% 75.14% 1508ms 1.65% CellPropertyCollection::AddProperty 275ms 0.3% 75.44% 1436ms 1.57% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 48ms 0.052% 75.49% 1419ms 1.55% MutableVertexMesh::CheckForSwapsFromShortEdges 1ms 0.0011% 75.49% 1369ms 1.50% tcache_get (inline) 1368ms 1.50% 76.99% 1368ms 1.50% tcache_get_n (inline) 1295ms 1.42% 78.40% 1295ms 1.42% std::_Rb_tree_increment 57ms 0.062% 78.47% 1266ms 1.38% std::_Rb_tree::_M_erase_aux (partial-inline) 1ms 0.0011% 78.47% 1249ms 1.37% OffLatticeSimulation::ApplyBoundaries 0 0% 78.47% 1249ms 1.37% boost::numeric::ublas::vector_binary::operator() (inline) 64ms 0.07% 78.54% 1230ms 1.34% VertexMesh::GetSurfaceAreaOfElement 57ms 0.062% 78.60% 1194ms 1.31% AbstractCellPopulation::GetLocationIndexUsingCell 37ms 0.04% 78.64% 1098ms 1.20% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 79ms 0.086% 78.73% 1084ms 1.19% boost::numeric::ublas::vector_reference::operator() (inline) 48ms 0.052% 78.78% 1047ms 1.14% CellPropertyRegistry::Get 48ms 0.052% 78.83% 1028ms 1.12% Edge::AddElement 10ms 0.011% 78.84% 1021ms 1.12% MutableElement::RegisterWithEdges (inline) 21ms 0.023% 78.87% 1013ms 1.11% boost::numeric::ublas::detail::expression_type_check (inline) 612ms 0.67% 79.54% 989ms 1.08% std::_Rb_tree::equal_range (inline) 31ms 0.034% 79.57% 981ms 1.07% Node::RemoveElement 139ms 0.15% 79.72% 968ms 1.06% boost::numeric::ublas::detail::equals 0 0% 79.72% 950ms 1.04% std::set::erase (inline) 0 0% 79.72% 925ms 1.01% CellPropertyCollection::~CellPropertyCollection (inline) 887ms 0.97% 80.69% 887ms 0.97% [libstdc++.so.6.0.33] 0 0% 80.69% 878ms 0.96% boost::numeric::ublas::norm_2 (inline) 876ms 0.96% 81.65% 876ms 0.96% std::_Rb_tree_insert_and_rebalance 471ms 0.51% 82.16% 852ms 0.93% boost::numeric::ublas::vector_norm_2::apply 646ms 0.71% 82.87% 838ms 0.92% CellPropertyCollection::GetProperty 0 0% 82.87% 834ms 0.91% std::__new_allocator::destroy (inline) 0 0% 82.87% 834ms 0.91% std::allocator_traits::destroy (inline) 0 0% 82.87% 830ms 0.91% std::_Rb_tree::_M_destroy_node (inline) 0 0% 82.87% 807ms 0.88% boost::numeric::ublas::c_vector::assign_temporary (inline) 4ms 0.0044% 82.87% 807ms 0.88% boost::numeric::ublas::c_vector::swap (inline) 12ms 0.013% 82.89% 803ms 0.88% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 127ms 0.14% 83.03% 803ms 0.88% std::swap_ranges (inline) 0 0% 83.03% 800ms 0.87% std::_Rb_tree::clear (inline) 0 0% 83.03% 786ms 0.86% VertexMeshWriter::MakeVtkMesh 0 0% 83.03% 785ms 0.86% std::map::clear (inline) 777ms 0.85% 83.88% 777ms 0.85% Node::rGetLocation 729ms 0.8% 84.67% 729ms 0.8% tcache_put (inline) 0 0% 84.67% 676ms 0.74% std::iter_swap (inline) 676ms 0.74% 85.41% 676ms 0.74% std::swap (inline) 336ms 0.37% 85.78% 674ms 0.74% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 44ms 0.048% 85.83% 672ms 0.73% boost::numeric::ublas::c_vector::operator= (inline) 94ms 0.1% 85.93% 668ms 0.73% std::_Rb_tree::find (inline) 0 0% 85.93% 667ms 0.73% boost::numeric::ublas::norm_inf (inline) 234ms 0.26% 86.19% 667ms 0.73% boost::numeric::ublas::vector_norm_inf::apply (inline) 48ms 0.052% 86.24% 650ms 0.71% std::less::operator() (inline) 440ms 0.48% 86.72% 602ms 0.66% std::operator< (inline) 0 0% 86.72% 594ms 0.65% std::_Rb_tree::_Auto_node::_M_insert (inline) 22ms 0.024% 86.74% 594ms 0.65% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.74% 585ms 0.64% vtkPolygon::New 0 0% 86.74% 584ms 0.64% vtkPolygon::vtkPolygon 72ms 0.079% 86.82% 578ms 0.63% MutableElement::GetNodeLocalIndex 554ms 0.61% 87.43% 554ms 0.61% std::vector::size (inline) 0 0% 87.43% 536ms 0.59% std::map::find (inline) 1ms 0.0011% 87.43% 522ms 0.57% std::_Vector_base::_M_allocate (inline) 17ms 0.019% 87.45% 519ms 0.57% MutableElement::RegisterWithNodes (inline) 7ms 0.0077% 87.46% 500ms 0.55% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.46% 500ms 0.55% boost::numeric::ublas::vector::vector (inline) 59ms 0.065% 87.52% 491ms 0.54% Node::AddElement 490ms 0.54% 88.06% 490ms 0.54% Node::GetIndex 32ms 0.035% 88.09% 463ms 0.51% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 88.09% 460ms 0.5% std::map::map (inline) 234ms 0.26% 88.35% 458ms 0.5% Edge::GetMapIndex