File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95563ms, 88.80% of 107621ms total Dropped 1044 nodes (cum <= 538.11ms) flat flat% sum% cum cum% 0 0% 0% 107159ms 99.57% __libc_start_call_main 0 0% 0% 107159ms 99.57% __libc_start_main_impl 0 0% 0% 107159ms 99.57% _start 0 0% 0% 107138ms 99.55% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 107138ms 99.55% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 107138ms 99.55% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 107138ms 99.55% main 0 0% 0% 107102ms 99.52% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 107102ms 99.52% CxxTest::TestRunner::runTest (inline) 0 0% 0% 107102ms 99.52% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0019% 0.0019% 107095ms 99.51% AbstractCellBasedSimulation::Solve 12ms 0.011% 0.013% 55752ms 51.80% OffLatticeSimulation::UpdateCellLocationsAndTopology 16ms 0.015% 0.028% 52599ms 48.87% ForwardEulerNumericalMethod::UpdateAllNodePositions 123ms 0.11% 0.14% 51587ms 47.93% AbstractNumericalMethod::ComputeForcesIncludingDamping 348ms 0.32% 0.47% 39845ms 37.02% NagaiHondaForce::AddForceContribution 0 0% 0.47% 38710ms 35.97% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.0028% 0.47% 23937ms 22.24% VertexBasedCellPopulation::Update 2ms 0.0019% 0.47% 23818ms 22.13% MutableVertexMesh::ReMesh 14562ms 13.53% 14.00% 22830ms 21.21% Cylindrical2dVertexMesh::GetVectorFromAtoB 89ms 0.083% 14.08% 17269ms 16.05% Cell::ReadyToDivide 64ms 0.059% 14.14% 16128ms 14.99% AbstractPhaseBasedCellCycleModel::ReadyToDivide 416ms 0.39% 14.53% 14882ms 13.83% NagaiHondaForce::GetAdhesionParameter 420ms 0.39% 14.92% 14366ms 13.35% boost::numeric::ublas::c_vector::c_vector (partial-inline) 124ms 0.12% 15.04% 13714ms 12.74% SimpleWntCellCycleModel::UpdateCellCyclePhase 131ms 0.12% 15.16% 13362ms 12.42% CellPropertyCollection::GetPropertiesType (inline) 347ms 0.32% 15.48% 12816ms 11.91% boost::numeric::ublas::vector_assign (inline) 135ms 0.13% 15.60% 11985ms 11.14% MutableVertexMesh::CheckForIntersections 72ms 0.067% 15.67% 11232ms 10.44% VertexBasedCellPopulation::GetDampingConstant 3177ms 2.95% 18.62% 11049ms 10.27% __dynamic_cast 96ms 0.089% 18.71% 10942ms 10.17% AbstractCellProperty::IsSubType (inline) 102ms 0.095% 18.81% 10304ms 9.57% AbstractTargetAreaModifier::UpdateTargetAreas 25ms 0.023% 18.83% 10242ms 9.52% AbstractCellBasedSimulation::DoCellBirth 59ms 0.055% 18.89% 10181ms 9.46% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 1284ms 1.19% 20.08% 9985ms 9.28% std::__new_allocator::allocate (inline) 2609ms 2.42% 22.50% 9452ms 8.78% boost::numeric::ublas::indexing_vector_assign 0 0% 22.50% 9431ms 8.76% std::allocator_traits::allocate (inline) 0 0% 22.50% 9383ms 8.72% std::_Rb_tree::_M_create_node (inline) 1381ms 1.28% 23.79% 9282ms 8.62% std::_Rb_tree::_M_erase 740ms 0.69% 24.47% 8902ms 8.27% VertexMesh::ElementIncludesPoint 0 0% 24.47% 8800ms 8.18% std::_Rb_tree::_M_get_node (inline) 805ms 0.75% 25.22% 8777ms 8.16% operator new 365ms 0.34% 25.56% 8675ms 8.06% VertexMesh::GetNextEdgeGradientOfElementAtNode 24ms 0.022% 25.58% 8632ms 8.02% VertexBasedCellPopulation::GetLocationOfCellCentre 216ms 0.2% 25.78% 8547ms 7.94% std::_Rb_tree::~_Rb_tree (inline) 72ms 0.067% 25.85% 8421ms 7.82% Cell::GetMutationState 0 0% 25.85% 8306ms 7.72% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 25.85% 8199ms 7.62% std::_Rb_tree::_M_drop_node (inline) 492ms 0.46% 26.31% 8110ms 7.54% VertexMesh::GetCentroidOfElement 0 0% 26.31% 8063ms 7.49% std::set::~set (inline) 220ms 0.2% 26.51% 7990ms 7.42% std::__new_allocator::deallocate (inline) 0 0% 26.51% 7957ms 7.39% std::allocator_traits::deallocate (inline) 0 0% 26.51% 7897ms 7.34% std::_Rb_tree::_M_put_node (inline) 3555ms 3.30% 29.82% 7867ms 7.31% __GI___libc_free 3320ms 3.08% 32.90% 7771ms 7.22% __GI___libc_malloc 510ms 0.47% 33.37% 7535ms 7.00% std::map::operator[] (partial-inline) 23ms 0.021% 33.40% 7427ms 6.90% MutableVertexMesh::RemoveDeletedNodesAndElements 1290ms 1.20% 34.59% 7001ms 6.51% AbstractMesh::GetDistanceBetweenNodes 121ms 0.11% 34.71% 6670ms 6.20% std::_Rb_tree::_Rb_tree (partial-inline) 92ms 0.085% 34.79% 6358ms 5.91% SimpleWntCellCycleModel::GetWntLevel 644ms 0.6% 35.39% 6328ms 5.88% std::_Rb_tree::_M_copy (inline) 8ms 0.0074% 35.40% 6265ms 5.82% std::set::set (inline) 6159ms 5.72% 41.12% 6159ms 5.72% boost::numeric::ublas::c_vector::operator() 6128ms 5.69% 46.82% 6128ms 5.69% __strcmp_avx2 166ms 0.15% 46.97% 6115ms 5.68% WntConcentration::GetWntLevel 2494ms 2.32% 49.29% 6109ms 5.68% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.00093% 49.29% 5524ms 5.13% std::set::insert (inline) 2708ms 2.52% 51.80% 5452ms 5.07% __cxxabiv1::__si_class_type_info::__do_dyncast 710ms 0.66% 52.46% 5444ms 5.06% std::_Rb_tree::_M_clone_node (inline) 25ms 0.023% 52.49% 5208ms 4.84% MutableVertexMesh::RemoveDeletedNodes 42ms 0.039% 52.53% 5059ms 4.70% EdgeHelper::RemoveDeletedEdges 0 0% 52.53% 4906ms 4.56% std::_Rb_tree::lower_bound (inline) 0 0% 52.53% 4906ms 4.56% std::map::lower_bound (inline) 42ms 0.039% 52.57% 4790ms 4.45% EdgeHelper::UpdateEdgesMapKey 1416ms 1.32% 53.88% 4751ms 4.41% boost::numeric::ublas::c_vector::operator[] (inline) 534ms 0.5% 54.38% 4641ms 4.31% std::_Rb_tree::_M_insert_ (inline) 175ms 0.16% 54.54% 4639ms 4.31% MutableElement::ResetIndex 55ms 0.051% 54.59% 4601ms 4.28% std::set_intersection (inline) 297ms 0.28% 54.87% 4546ms 4.22% std::__set_intersection 2ms 0.0019% 54.87% 4522ms 4.20% AbstractCellBasedSimulation::DoCellRemoval (inline) 3970ms 3.69% 58.56% 4304ms 4.00% _int_free 107ms 0.099% 58.66% 4190ms 3.89% AbstractCellPopulation::GetCellUsingLocationIndex 4056ms 3.77% 62.43% 4056ms 3.77% boost::numeric::ublas::same_impl_ex 39ms 0.036% 62.46% 4010ms 3.73% Cell::GetCellProliferativeType 67ms 0.062% 62.52% 3579ms 3.33% AbstractCellProperty::IsType (inline) 8ms 0.0074% 62.53% 3503ms 3.25% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.53% 3354ms 3.12% std::insert_iterator::operator= (inline) 49ms 0.046% 62.58% 3161ms 2.94% Cell::SetCellProliferativeType 3043ms 2.83% 65.40% 3043ms 2.83% std::_Rb_tree::_S_right (inline) 720ms 0.67% 66.07% 3034ms 2.82% AbstractElement::GetNodeLocation 6ms 0.0056% 66.08% 2964ms 2.75% std::_Rb_tree::_M_insert_unique_ (inline) 2091ms 1.94% 68.02% 2928ms 2.72% _int_malloc 45ms 0.042% 68.06% 2902ms 2.70% std::_Rb_tree::erase 598ms 0.56% 68.62% 2843ms 2.64% boost::numeric::ublas::vector_binary::size (inline) 461ms 0.43% 69.05% 2724ms 2.53% std::_Rb_tree_const_iterator::operator++ (inline) 246ms 0.23% 69.28% 2568ms 2.39% VertexMesh::GetAreaGradientOfElementAtNode 2ms 0.0019% 69.28% 2559ms 2.38% std::_Rb_tree::_M_insert_unique 0 0% 69.28% 2529ms 2.35% boost::numeric::ublas::c_vector::operator-= (inline) 712ms 0.66% 69.94% 2494ms 2.32% AbstractCellProperty::IsSame 39ms 0.036% 69.98% 2472ms 2.30% CellPropertyCollection::HasProperty 0 0% 69.98% 2382ms 2.21% boost::numeric::ublas::c_vector::assign (inline) 7ms 0.0065% 69.98% 2364ms 2.20% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 69.98% 2360ms 2.19% Cell::HasCellProperty (inline) 24ms 0.022% 70.00% 2338ms 2.17% Cell::GetCellData 105ms 0.098% 70.10% 2334ms 2.17% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 218ms 0.2% 70.31% 2317ms 2.15% AbstractCellPopulation::Iterator::IsRealCell 0 0% 70.31% 2304ms 2.14% AbstractCellPopulation::WriteResultsToFiles 93ms 0.086% 70.39% 2290ms 2.13% VertexMesh::GetVolumeOfElement 45ms 0.042% 70.43% 2074ms 1.93% std::_Rb_tree::_M_emplace_hint_unique 2067ms 1.92% 72.35% 2067ms 1.92% std::_Rb_tree_increment 1337ms 1.24% 73.60% 1988ms 1.85% std::_Rb_tree::equal_range (inline) 2ms 0.0019% 73.60% 1928ms 1.79% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.60% 1928ms 1.79% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 82ms 0.076% 73.67% 1917ms 1.78% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 73.67% 1888ms 1.75% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 73.67% 1880ms 1.75% VertexBasedCellPopulation::WriteCellVtkResultsToFile 39ms 0.036% 73.71% 1830ms 1.70% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 437ms 0.41% 74.12% 1782ms 1.66% std::type_info::operator== (inline) 0 0% 74.12% 1688ms 1.57% VertexMeshWriter::WriteVtkUsingMesh 26ms 0.024% 74.14% 1621ms 1.51% AbstractCellPopulation::GetLocationIndexUsingCell 21ms 0.02% 74.16% 1613ms 1.50% VertexMesh::GetSurfaceAreaOfElement 76ms 0.071% 74.23% 1598ms 1.48% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 37ms 0.034% 74.27% 1553ms 1.44% Node::RemoveElement 21ms 0.02% 74.28% 1527ms 1.42% std::set::erase (inline) 129ms 0.12% 74.40% 1483ms 1.38% boost::numeric::ublas::vector_reference::operator() (inline) 140ms 0.13% 74.53% 1479ms 1.37% CellPropertyCollection::AddProperty 0 0% 74.53% 1397ms 1.30% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 74.53% 1360ms 1.26% tcache_get (inline) 1360ms 1.26% 75.80% 1360ms 1.26% tcache_get_n (inline) 0 0% 75.80% 1256ms 1.17% OffLatticeSimulation::ApplyBoundaries 81ms 0.075% 75.87% 1225ms 1.14% std::less::operator() (inline) 0 0% 75.87% 1193ms 1.11% boost::numeric::ublas::norm_2 (inline) 503ms 0.47% 76.34% 1179ms 1.10% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 89ms 0.083% 76.42% 1160ms 1.08% std::_Rb_tree::find (inline) 953ms 0.89% 77.31% 1144ms 1.06% std::operator< (inline) 1120ms 1.04% 78.35% 1120ms 1.04% std::_Rb_tree_insert_and_rebalance 1115ms 1.04% 79.39% 1115ms 1.04% [libchaste_cell_based.so] 1098ms 1.02% 80.41% 1098ms 1.02% Node::rGetLocation 20ms 0.019% 80.42% 1086ms 1.01% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 80.42% 1077ms 1.00% std::_Rb_tree::_Auto_node::_Auto_node (inline) 77ms 0.072% 80.50% 1058ms 0.98% std::_Rb_tree::_M_erase_aux (partial-inline) 30ms 0.028% 80.52% 1036ms 0.96% CellPropertyRegistry::Get 18ms 0.017% 80.54% 1018ms 0.95% boost::numeric::ublas::detail::expression_type_check (inline) 140ms 0.13% 80.67% 1001ms 0.93% boost::detail::shared_count::~shared_count (inline) 0 0% 80.67% 1001ms 0.93% boost::shared_ptr::~shared_ptr (inline) 184ms 0.17% 80.84% 990ms 0.92% boost::numeric::ublas::detail::equals 6ms 0.0056% 80.85% 976ms 0.91% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 968ms 0.9% 81.75% 968ms 0.9% std::vector::size (inline) 0 0% 81.75% 961ms 0.89% boost::numeric::ublas::c_vector::assign_temporary (inline) 2ms 0.0019% 81.75% 961ms 0.89% boost::numeric::ublas::c_vector::swap (inline) 95ms 0.088% 81.84% 959ms 0.89% std::swap_ranges (inline) 1ms 0.00093% 81.84% 953ms 0.89% std::_Rb_tree::clear (inline) 407ms 0.38% 82.22% 946ms 0.88% Edge::GetMapIndex 944ms 0.88% 83.09% 944ms 0.88% [libchaste_mesh.so] 0 0% 83.09% 941ms 0.87% std::map::find (inline) 0 0% 83.09% 940ms 0.87% std::map::clear (inline) 865ms 0.8% 83.90% 865ms 0.8% std::swap (inline) 0 0% 83.90% 864ms 0.8% std::iter_swap (inline) 832ms 0.77% 84.67% 838ms 0.78% boost::detail::sp_counted_base::release 25ms 0.023% 84.69% 832ms 0.77% MutableElement::RegisterWithEdges (inline) 1ms 0.00093% 84.69% 831ms 0.77% VertexMeshWriter::MakeVtkMesh 33ms 0.031% 84.73% 823ms 0.76% Edge::AddElement 0 0% 84.73% 795ms 0.74% CellPropertyCollection::~CellPropertyCollection (inline) 103ms 0.096% 84.82% 760ms 0.71% boost::numeric::ublas::c_vector::operator= (inline) 168ms 0.16% 84.98% 753ms 0.7% boost::shared_ptr::shared_ptr (inline) 465ms 0.43% 85.41% 753ms 0.7% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 85.41% 735ms 0.68% boost::numeric::ublas::norm_inf (inline) 398ms 0.37% 85.78% 735ms 0.68% boost::numeric::ublas::vector_norm_inf::apply (inline) 74ms 0.069% 85.85% 701ms 0.65% MutableElement::GetNodeLocalIndex 0 0% 85.85% 671ms 0.62% std::_Rb_tree::_Auto_node::_M_insert (inline) 14ms 0.013% 85.86% 671ms 0.62% std::_Rb_tree::_M_insert_node (inline) 667ms 0.62% 86.48% 667ms 0.62% Node::GetIndex 88ms 0.082% 86.56% 636ms 0.59% std::__new_allocator::construct (inline) 0 0% 86.56% 636ms 0.59% std::allocator_traits::construct (inline) 0 0% 86.56% 628ms 0.58% std::_Vector_base::_M_allocate (inline) 612ms 0.57% 87.13% 612ms 0.57% [libstdc++.so.6.0.33] 41ms 0.038% 87.17% 611ms 0.57% MutableElement::RegisterWithNodes (inline) 0 0% 87.17% 605ms 0.56% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 87.17% 597ms 0.55% vtkPolygon::New 0 0% 87.17% 596ms 0.55% vtkPolygon::vtkPolygon 35ms 0.033% 87.20% 589ms 0.55% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.20% 589ms 0.55% boost::numeric::ublas::vector::vector (inline) 554ms 0.51% 87.72% 585ms 0.54% boost::detail::shared_count::shared_count (inline) 0 0% 87.72% 583ms 0.54% std::_Rb_tree::_M_construct_node (inline) 580ms 0.54% 88.26% 580ms 0.54% boost::shared_ptr::operator-> (inline) 32ms 0.03% 88.28% 555ms 0.52% Node::AddElement 550ms 0.51% 88.80% 550ms 0.51% operator delete