File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96684ms, 88.31% of 109480ms total Dropped 1086 nodes (cum <= 547.40ms) flat flat% sum% cum cum% 0 0% 0% 109021ms 99.58% __libc_start_call_main 0 0% 0% 109021ms 99.58% __libc_start_main_impl 0 0% 0% 109021ms 99.58% _start 0 0% 0% 109004ms 99.57% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 109004ms 99.57% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 109004ms 99.57% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 109004ms 99.57% main 0 0% 0% 108969ms 99.53% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108969ms 99.53% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108969ms 99.53% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 3ms 0.0027% 0.0027% 108961ms 99.53% AbstractCellBasedSimulation::Solve 18ms 0.016% 0.019% 56816ms 51.90% OffLatticeSimulation::UpdateCellLocationsAndTopology 33ms 0.03% 0.049% 53728ms 49.08% ForwardEulerNumericalMethod::UpdateAllNodePositions 130ms 0.12% 0.17% 52680ms 48.12% AbstractNumericalMethod::ComputeForcesIncludingDamping 342ms 0.31% 0.48% 40753ms 37.22% NagaiHondaForce::AddForceContribution 1ms 0.00091% 0.48% 39228ms 35.83% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00091% 0.48% 23990ms 21.91% VertexBasedCellPopulation::Update 2ms 0.0018% 0.48% 23867ms 21.80% MutableVertexMesh::ReMesh 14515ms 13.26% 13.74% 23162ms 21.16% Cylindrical2dVertexMesh::GetVectorFromAtoB 81ms 0.074% 13.82% 17995ms 16.44% Cell::ReadyToDivide 93ms 0.085% 13.90% 16824ms 15.37% AbstractPhaseBasedCellCycleModel::ReadyToDivide 355ms 0.32% 14.23% 15744ms 14.38% NagaiHondaForce::GetAdhesionParameter 410ms 0.37% 14.60% 14548ms 13.29% boost::numeric::ublas::c_vector::c_vector (partial-inline) 155ms 0.14% 14.74% 14380ms 13.13% SimpleWntCellCycleModel::UpdateCellCyclePhase 127ms 0.12% 14.86% 14298ms 13.06% CellPropertyCollection::GetPropertiesType (inline) 424ms 0.39% 15.24% 12983ms 11.86% boost::numeric::ublas::vector_assign (inline) 147ms 0.13% 15.38% 12120ms 11.07% MutableVertexMesh::CheckForIntersections 3300ms 3.01% 18.39% 12044ms 11.00% __dynamic_cast 77ms 0.07% 18.46% 11938ms 10.90% AbstractCellProperty::IsSubType (inline) 128ms 0.12% 18.58% 11441ms 10.45% VertexBasedCellPopulation::GetDampingConstant 1553ms 1.42% 20.00% 10796ms 9.86% std::__new_allocator::allocate (inline) 28ms 0.026% 20.02% 10713ms 9.79% AbstractCellBasedSimulation::DoCellBirth 74ms 0.068% 20.09% 10524ms 9.61% AbstractTargetAreaModifier::UpdateTargetAreas 75ms 0.069% 20.16% 10430ms 9.53% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 0 0% 20.16% 10222ms 9.34% std::allocator_traits::allocate (inline) 0 0% 20.16% 10209ms 9.32% std::_Rb_tree::_M_create_node (inline) 2692ms 2.46% 22.62% 9643ms 8.81% boost::numeric::ublas::indexing_vector_assign 0 0% 22.62% 9561ms 8.73% std::_Rb_tree::_M_get_node (inline) 1205ms 1.10% 23.72% 9395ms 8.58% std::_Rb_tree::_M_erase 1033ms 0.94% 24.66% 9326ms 8.52% operator new 84ms 0.077% 24.74% 9218ms 8.42% Cell::GetMutationState 0 0% 24.74% 9053ms 8.27% std::_Rb_tree::_Alloc_node::operator() (inline) 778ms 0.71% 25.45% 8971ms 8.19% VertexMesh::ElementIncludesPoint 379ms 0.35% 25.80% 8893ms 8.12% VertexMesh::GetNextEdgeGradientOfElementAtNode 26ms 0.024% 25.82% 8713ms 7.96% VertexBasedCellPopulation::GetLocationOfCellCentre 214ms 0.2% 26.02% 8607ms 7.86% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.02% 8557ms 7.82% std::_Rb_tree::_M_drop_node (inline) 246ms 0.22% 26.24% 8307ms 7.59% std::__new_allocator::deallocate (inline) 476ms 0.43% 26.68% 8287ms 7.57% VertexMesh::GetCentroidOfElement 0 0% 26.68% 8281ms 7.56% std::allocator_traits::deallocate (inline) 0 0% 26.68% 8238ms 7.52% std::_Rb_tree::_M_put_node (inline) 0 0% 26.68% 8165ms 7.46% std::set::~set (inline) 3121ms 2.85% 29.53% 8103ms 7.40% __GI___libc_malloc 2622ms 2.39% 31.92% 8083ms 7.38% __GI___libc_free 16ms 0.015% 31.94% 7397ms 6.76% MutableVertexMesh::RemoveDeletedNodesAndElements 1455ms 1.33% 33.27% 7163ms 6.54% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 478ms 0.44% 33.70% 7154ms 6.53% std::map::operator[] (partial-inline) 7148ms 6.53% 40.23% 7148ms 6.53% __strcmp_avx2 167ms 0.15% 40.38% 7059ms 6.45% std::_Rb_tree::_Rb_tree (partial-inline) 11ms 0.01% 40.39% 6637ms 6.06% std::set::set (inline) 593ms 0.54% 40.94% 6634ms 6.06% std::_Rb_tree::_M_copy (inline) 96ms 0.088% 41.02% 6268ms 5.73% SimpleWntCellCycleModel::GetWntLevel 6211ms 5.67% 46.70% 6211ms 5.67% boost::numeric::ublas::c_vector::operator() 2714ms 2.48% 49.18% 6187ms 5.65% __cxxabiv1::__si_class_type_info::__do_dyncast 131ms 0.12% 49.29% 6104ms 5.58% WntConcentration::GetWntLevel 0 0% 49.29% 5816ms 5.31% std::set::insert (inline) 756ms 0.69% 49.99% 5766ms 5.27% std::_Rb_tree::_M_clone_node (inline) 2360ms 2.16% 52.14% 5577ms 5.09% std::_Rb_tree::_M_lower_bound (inline) 5062ms 4.62% 56.76% 5440ms 4.97% _int_free 34ms 0.031% 56.80% 5197ms 4.75% MutableVertexMesh::RemoveDeletedNodes 46ms 0.042% 56.84% 5022ms 4.59% EdgeHelper::RemoveDeletedEdges 463ms 0.42% 57.26% 4999ms 4.57% std::_Rb_tree::_M_insert_ (inline) 51ms 0.047% 57.31% 4967ms 4.54% std::set_intersection (inline) 336ms 0.31% 57.61% 4916ms 4.49% std::__set_intersection 1507ms 1.38% 58.99% 4897ms 4.47% boost::numeric::ublas::c_vector::operator[] (inline) 33ms 0.03% 59.02% 4774ms 4.36% EdgeHelper::UpdateEdgesMapKey 201ms 0.18% 59.20% 4602ms 4.20% MutableElement::ResetIndex 1ms 0.00091% 59.21% 4517ms 4.13% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 59.21% 4500ms 4.11% std::_Rb_tree::lower_bound (inline) 0 0% 59.21% 4500ms 4.11% std::map::lower_bound (inline) 43ms 0.039% 59.24% 4111ms 3.76% Cell::GetCellProliferativeType 4019ms 3.67% 62.92% 4019ms 3.67% boost::numeric::ublas::same_impl_ex 106ms 0.097% 63.01% 3910ms 3.57% AbstractCellPopulation::GetCellUsingLocationIndex 62ms 0.057% 63.07% 3899ms 3.56% AbstractCellProperty::IsType (inline) 0 0% 63.07% 3672ms 3.35% std::insert_iterator::operator= (inline) 7ms 0.0064% 63.08% 3502ms 3.20% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 2592ms 2.37% 65.44% 3477ms 3.18% _int_malloc 4ms 0.0037% 65.45% 3297ms 3.01% std::_Rb_tree::_M_insert_unique_ (inline) 43ms 0.039% 65.49% 3233ms 2.95% Cell::SetCellProliferativeType 732ms 0.67% 66.15% 3094ms 2.83% AbstractElement::GetNodeLocation 676ms 0.62% 66.77% 2913ms 2.66% boost::numeric::ublas::vector_binary::size (inline) 36ms 0.033% 66.80% 2877ms 2.63% std::_Rb_tree::erase 751ms 0.69% 67.49% 2814ms 2.57% AbstractCellProperty::IsSame 414ms 0.38% 67.87% 2764ms 2.52% std::_Rb_tree_const_iterator::operator++ (inline) 2714ms 2.48% 70.35% 2714ms 2.48% std::_Rb_tree::_S_right (inline) 32ms 0.029% 70.38% 2695ms 2.46% CellPropertyCollection::HasProperty 0 0% 70.38% 2616ms 2.39% Cell::HasCellProperty (inline) 1ms 0.00091% 70.38% 2519ms 2.30% std::_Rb_tree::_M_insert_unique (inline) 0 0% 70.38% 2437ms 2.23% boost::numeric::ublas::c_vector::assign (inline) 0 0% 70.38% 2420ms 2.21% boost::numeric::ublas::c_vector::operator-= (inline) 24ms 0.022% 70.40% 2400ms 2.19% Cell::GetCellData 217ms 0.2% 70.60% 2391ms 2.18% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 70.60% 2366ms 2.16% AbstractCellPopulation::WriteResultsToFiles 105ms 0.096% 70.69% 2330ms 2.13% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 110ms 0.1% 70.79% 2328ms 2.13% VertexMesh::GetVolumeOfElement 2176ms 1.99% 72.78% 2176ms 1.99% std::_Rb_tree_increment 9ms 0.0082% 72.79% 2135ms 1.95% AbstractCellPopulation::Iterator::operator++ (inline) 43ms 0.039% 72.83% 2135ms 1.95% std::_Rb_tree::_M_emplace_hint_unique 192ms 0.18% 73.01% 2123ms 1.94% AbstractCellPopulation::Iterator::IsRealCell 508ms 0.46% 73.47% 2063ms 1.88% std::type_info::operator== (inline) 0 0% 73.47% 1930ms 1.76% VertexBasedCellPopulation::WriteVtkResultsToFile 2ms 0.0018% 73.47% 1921ms 1.75% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1267ms 1.16% 74.63% 1898ms 1.73% std::_Rb_tree::equal_range (inline) 62ms 0.057% 74.68% 1879ms 1.72% MutableVertexMesh::CheckForSwapsFromShortEdges 3ms 0.0027% 74.69% 1808ms 1.65% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 74.69% 1808ms 1.65% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 74.69% 1724ms 1.57% VertexMeshWriter::WriteVtkUsingMesh 24ms 0.022% 74.71% 1651ms 1.51% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 25ms 0.023% 74.73% 1634ms 1.49% VertexMesh::GetSurfaceAreaOfElement 53ms 0.048% 74.78% 1527ms 1.39% Node::RemoveElement 29ms 0.026% 74.81% 1496ms 1.37% AbstractCellPopulation::GetLocationIndexUsingCell 104ms 0.095% 74.90% 1491ms 1.36% boost::numeric::ublas::vector_reference::operator() (inline) 15ms 0.014% 74.92% 1482ms 1.35% std::set::erase (inline) 142ms 0.13% 75.05% 1451ms 1.33% CellPropertyCollection::AddProperty 88ms 0.08% 75.13% 1439ms 1.31% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 75.13% 1418ms 1.30% boost::numeric::ublas::vector_binary::operator() (inline) 1ms 0.00091% 75.13% 1309ms 1.20% tcache_get (inline) 1308ms 1.19% 76.32% 1308ms 1.19% tcache_get_n (inline) 3ms 0.0027% 76.32% 1236ms 1.13% OffLatticeSimulation::ApplyBoundaries 0 0% 76.32% 1156ms 1.06% std::_Rb_tree::_Auto_node::_Auto_node (inline) 60ms 0.055% 76.38% 1131ms 1.03% std::less::operator() (inline) 79ms 0.072% 76.45% 1115ms 1.02% std::_Rb_tree::_M_erase_aux (partial-inline) 1109ms 1.01% 77.46% 1109ms 1.01% Node::rGetLocation 0 0% 77.46% 1102ms 1.01% boost::numeric::ublas::norm_2 (inline) 453ms 0.41% 77.88% 1093ms 1% boost::numeric::ublas::vector_norm_2::apply 1088ms 0.99% 78.87% 1088ms 0.99% [libchaste_cell_based.so] 97ms 0.089% 78.96% 1076ms 0.98% std::_Rb_tree::find (inline) 857ms 0.78% 79.74% 1071ms 0.98% std::operator< (inline) 180ms 0.16% 79.91% 1070ms 0.98% boost::detail::shared_count::~shared_count (inline) 0 0% 79.91% 1070ms 0.98% boost::shared_ptr::~shared_ptr (inline) 19ms 0.017% 79.93% 1064ms 0.97% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 25ms 0.023% 79.95% 1059ms 0.97% CellPropertyRegistry::Get 1054ms 0.96% 80.91% 1054ms 0.96% std::_Rb_tree_insert_and_rebalance 1ms 0.00091% 80.91% 1005ms 0.92% std::_Rb_tree::clear (inline) 0 0% 80.91% 988ms 0.9% std::map::clear (inline) 8ms 0.0073% 80.92% 975ms 0.89% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 954ms 0.87% 81.79% 954ms 0.87% [libchaste_mesh.so] 19ms 0.017% 81.81% 935ms 0.85% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 81.81% 916ms 0.84% boost::numeric::ublas::c_vector::assign_temporary (inline) 9ms 0.0082% 81.82% 916ms 0.84% boost::numeric::ublas::c_vector::swap (inline) 913ms 0.83% 82.65% 913ms 0.83% std::vector::size (inline) 157ms 0.14% 82.79% 907ms 0.83% boost::numeric::ublas::detail::equals 71ms 0.065% 82.86% 907ms 0.83% std::swap_ranges (inline) 0 0% 82.86% 894ms 0.82% std::map::find (inline) 108ms 0.099% 82.96% 891ms 0.81% MutableElement::GetNodeLocalIndex 369ms 0.34% 83.29% 878ms 0.8% Edge::GetMapIndex 864ms 0.79% 84.08% 870ms 0.79% boost::detail::sp_counted_base::release 0 0% 84.08% 853ms 0.78% VertexMeshWriter::MakeVtkMesh 0 0% 84.08% 836ms 0.76% std::iter_swap (inline) 836ms 0.76% 84.85% 836ms 0.76% std::swap (inline) 19ms 0.017% 84.86% 812ms 0.74% MutableElement::RegisterWithEdges (inline) 25ms 0.023% 84.89% 798ms 0.73% Edge::AddElement 141ms 0.13% 85.02% 777ms 0.71% boost::shared_ptr::shared_ptr (inline) 0 0% 85.02% 754ms 0.69% CellPropertyCollection::~CellPropertyCollection (inline) 454ms 0.41% 85.43% 746ms 0.68% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 110ms 0.1% 85.53% 726ms 0.66% boost::numeric::ublas::c_vector::operator= (inline) 719ms 0.66% 86.19% 719ms 0.66% Node::GetIndex 0 0% 86.19% 706ms 0.64% boost::numeric::ublas::norm_inf (inline) 368ms 0.34% 86.52% 706ms 0.64% boost::numeric::ublas::vector_norm_inf::apply (inline) 79ms 0.072% 86.60% 694ms 0.63% std::__new_allocator::construct (inline) 0 0% 86.60% 694ms 0.63% std::allocator_traits::construct (inline) 0 0% 86.60% 660ms 0.6% std::_Vector_base::_M_allocate (inline) 0 0% 86.60% 648ms 0.59% std::_Rb_tree::_M_construct_node (inline) 0 0% 86.60% 644ms 0.59% std::_Rb_tree::_Auto_node::_M_insert (inline) 24ms 0.022% 86.62% 644ms 0.59% std::_Rb_tree::_M_insert_node (inline) 616ms 0.56% 87.18% 636ms 0.58% boost::detail::shared_count::shared_count (inline) 629ms 0.57% 87.75% 629ms 0.57% operator delete 0 0% 87.75% 616ms 0.56% vtkPolygon::New 0 0% 87.75% 616ms 0.56% vtkPolygon::vtkPolygon 24ms 0.022% 87.78% 598ms 0.55% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.78% 598ms 0.55% boost::numeric::ublas::vector::vector (inline) 24ms 0.022% 87.80% 571ms 0.52% MutableElement::RegisterWithNodes (inline) 554ms 0.51% 88.30% 554ms 0.51% [libstdc++.so.6.0.33] 8ms 0.0073% 88.31% 550ms 0.5% std::vector::_M_default_append (inline)