File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95660ms, 88.20% of 108455ms total Dropped 1064 nodes (cum <= 542.27ms) flat flat% sum% cum cum% 0 0% 0% 107976ms 99.56% __libc_start_call_main 0 0% 0% 107976ms 99.56% __libc_start_main_impl 0 0% 0% 107976ms 99.56% _start 0 0% 0% 107957ms 99.54% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 107957ms 99.54% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 107957ms 99.54% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 107957ms 99.54% main 0 0% 0% 107924ms 99.51% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 107924ms 99.51% CxxTest::TestRunner::runTest (inline) 0 0% 0% 107924ms 99.51% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 3ms 0.0028% 0.0028% 107917ms 99.50% AbstractCellBasedSimulation::Solve 19ms 0.018% 0.02% 56011ms 51.64% OffLatticeSimulation::UpdateCellLocationsAndTopology 25ms 0.023% 0.043% 52842ms 48.72% ForwardEulerNumericalMethod::UpdateAllNodePositions 133ms 0.12% 0.17% 51775ms 47.74% AbstractNumericalMethod::ComputeForcesIncludingDamping 378ms 0.35% 0.51% 40098ms 36.97% NagaiHondaForce::AddForceContribution 1ms 0.00092% 0.52% 39152ms 36.10% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.52% 24216ms 22.33% VertexBasedCellPopulation::Update 1ms 0.00092% 0.52% 24098ms 22.22% MutableVertexMesh::ReMesh 14588ms 13.45% 13.97% 23036ms 21.24% Cylindrical2dVertexMesh::GetVectorFromAtoB 111ms 0.1% 14.07% 17442ms 16.08% Cell::ReadyToDivide 53ms 0.049% 14.12% 16238ms 14.97% AbstractPhaseBasedCellCycleModel::ReadyToDivide 381ms 0.35% 14.47% 15013ms 13.84% NagaiHondaForce::GetAdhesionParameter 422ms 0.39% 14.86% 14385ms 13.26% boost::numeric::ublas::c_vector::c_vector (partial-inline) 125ms 0.12% 14.97% 13858ms 12.78% SimpleWntCellCycleModel::UpdateCellCyclePhase 138ms 0.13% 15.10% 13285ms 12.25% CellPropertyCollection::GetPropertiesType (inline) 353ms 0.33% 15.43% 12764ms 11.77% boost::numeric::ublas::vector_assign (inline) 141ms 0.13% 15.56% 12027ms 11.09% MutableVertexMesh::CheckForIntersections 86ms 0.079% 15.64% 11184ms 10.31% VertexBasedCellPopulation::GetDampingConstant 3234ms 2.98% 18.62% 11039ms 10.18% __dynamic_cast 91ms 0.084% 18.70% 10955ms 10.10% AbstractCellProperty::IsSubType (inline) 85ms 0.078% 18.78% 10358ms 9.55% AbstractTargetAreaModifier::UpdateTargetAreas 19ms 0.018% 18.80% 10282ms 9.48% AbstractCellBasedSimulation::DoCellBirth 58ms 0.053% 18.85% 10248ms 9.45% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 1328ms 1.22% 20.08% 9839ms 9.07% std::__new_allocator::allocate (inline) 2541ms 2.34% 22.42% 9399ms 8.67% boost::numeric::ublas::indexing_vector_assign 1391ms 1.28% 23.70% 9389ms 8.66% std::_Rb_tree::_M_erase 0 0% 23.70% 9312ms 8.59% std::allocator_traits::allocate (inline) 0 0% 23.70% 9272ms 8.55% std::_Rb_tree::_M_create_node (inline) 787ms 0.73% 24.43% 8970ms 8.27% VertexMesh::ElementIncludesPoint 24ms 0.022% 24.45% 8871ms 8.18% VertexBasedCellPopulation::GetLocationOfCellCentre 337ms 0.31% 24.76% 8869ms 8.18% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 24.76% 8638ms 7.96% std::_Rb_tree::_M_get_node (inline) 804ms 0.74% 25.50% 8602ms 7.93% operator new 227ms 0.21% 25.71% 8564ms 7.90% std::_Rb_tree::~_Rb_tree (inline) 80ms 0.074% 25.78% 8485ms 7.82% Cell::GetMutationState 492ms 0.45% 26.24% 8397ms 7.74% VertexMesh::GetCentroidOfElement 0 0% 26.24% 8309ms 7.66% std::_Rb_tree::_M_drop_node (inline) 0 0% 26.24% 8233ms 7.59% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 26.24% 8091ms 7.46% std::set::~set (inline) 248ms 0.23% 26.47% 8078ms 7.45% std::__new_allocator::deallocate (inline) 0 0% 26.47% 8053ms 7.43% std::allocator_traits::deallocate (inline) 0 0% 26.47% 8005ms 7.38% std::_Rb_tree::_M_put_node (inline) 3286ms 3.03% 29.50% 7906ms 7.29% __GI___libc_free 2926ms 2.70% 32.19% 7603ms 7.01% __GI___libc_malloc 22ms 0.02% 32.21% 7574ms 6.98% MutableVertexMesh::RemoveDeletedNodesAndElements 478ms 0.44% 32.66% 7357ms 6.78% std::map::operator[] (partial-inline) 1325ms 1.22% 33.88% 7092ms 6.54% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 136ms 0.13% 34.00% 6783ms 6.25% std::_Rb_tree::_Rb_tree (partial-inline) 123ms 0.11% 34.12% 6440ms 5.94% SimpleWntCellCycleModel::GetWntLevel 690ms 0.64% 34.75% 6435ms 5.93% std::_Rb_tree::_M_copy (inline) 12ms 0.011% 34.76% 6372ms 5.88% std::set::set (inline) 6225ms 5.74% 40.50% 6225ms 5.74% boost::numeric::ublas::c_vector::operator() 146ms 0.13% 40.64% 6218ms 5.73% WntConcentration::GetWntLevel 6187ms 5.70% 46.34% 6187ms 5.70% __strcmp_avx2 2410ms 2.22% 48.56% 5926ms 5.46% std::_Rb_tree::_M_lower_bound (inline) 733ms 0.68% 49.24% 5478ms 5.05% std::_Rb_tree::_M_clone_node (inline) 0 0% 49.24% 5468ms 5.04% std::set::insert (inline) 2655ms 2.45% 51.69% 5466ms 5.04% __cxxabiv1::__si_class_type_info::__do_dyncast 19ms 0.018% 51.71% 5314ms 4.90% MutableVertexMesh::RemoveDeletedNodes 43ms 0.04% 51.74% 5156ms 4.75% EdgeHelper::RemoveDeletedEdges 1556ms 1.43% 53.18% 4880ms 4.50% boost::numeric::ublas::c_vector::operator[] (inline) 18ms 0.017% 53.20% 4856ms 4.48% EdgeHelper::UpdateEdgesMapKey 0 0% 53.20% 4770ms 4.40% std::_Rb_tree::lower_bound (inline) 0 0% 53.20% 4770ms 4.40% std::map::lower_bound (inline) 209ms 0.19% 53.39% 4748ms 4.38% MutableElement::ResetIndex 1ms 0.00092% 53.39% 4642ms 4.28% AbstractCellBasedSimulation::DoCellRemoval (inline) 41ms 0.038% 53.43% 4613ms 4.25% std::set_intersection (inline) 4282ms 3.95% 57.38% 4609ms 4.25% _int_free 249ms 0.23% 57.61% 4572ms 4.22% std::__set_intersection 556ms 0.51% 58.12% 4567ms 4.21% std::_Rb_tree::_M_insert_ (inline) 122ms 0.11% 58.23% 4051ms 3.74% AbstractCellPopulation::GetCellUsingLocationIndex 4027ms 3.71% 61.94% 4027ms 3.71% boost::numeric::ublas::same_impl_ex 44ms 0.041% 61.98% 3951ms 3.64% Cell::GetCellProliferativeType 62ms 0.057% 62.04% 3775ms 3.48% AbstractCellProperty::IsType (inline) 1ms 0.00092% 62.04% 3574ms 3.30% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.04% 3327ms 3.07% std::insert_iterator::operator= (inline) 797ms 0.73% 62.78% 3224ms 2.97% AbstractElement::GetNodeLocation 68ms 0.063% 62.84% 3145ms 2.90% Cell::SetCellProliferativeType 2212ms 2.04% 64.88% 3054ms 2.82% _int_malloc 2ms 0.0018% 64.88% 2978ms 2.75% std::_Rb_tree::_M_insert_unique_ (inline) 31ms 0.029% 64.91% 2964ms 2.73% std::_Rb_tree::erase 2921ms 2.69% 67.60% 2921ms 2.69% std::_Rb_tree::_S_right (inline) 649ms 0.6% 68.20% 2915ms 2.69% boost::numeric::ublas::vector_binary::size (inline) 451ms 0.42% 68.62% 2721ms 2.51% std::_Rb_tree_const_iterator::operator++ (inline) 781ms 0.72% 69.34% 2664ms 2.46% AbstractCellProperty::IsSame 55ms 0.051% 69.39% 2565ms 2.37% CellPropertyCollection::HasProperty 0 0% 69.39% 2492ms 2.30% boost::numeric::ublas::c_vector::operator-= (inline) 1ms 0.00092% 69.39% 2490ms 2.30% std::_Rb_tree::_M_insert_unique 244ms 0.22% 69.61% 2486ms 2.29% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.61% 2458ms 2.27% Cell::HasCellProperty (inline) 0 0% 69.61% 2377ms 2.19% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.61% 2371ms 2.19% boost::numeric::ublas::c_vector::assign (inline) 103ms 0.095% 69.71% 2363ms 2.18% VertexMesh::GetVolumeOfElement 109ms 0.1% 69.81% 2308ms 2.13% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 69.81% 2279ms 2.10% AbstractCellPopulation::Iterator::operator++ (inline) 20ms 0.018% 69.83% 2254ms 2.08% Cell::GetCellData 220ms 0.2% 70.03% 2233ms 2.06% AbstractCellPopulation::Iterator::IsRealCell (inline) 2104ms 1.94% 71.97% 2104ms 1.94% std::_Rb_tree_increment 33ms 0.03% 72.00% 2065ms 1.90% std::_Rb_tree::_M_emplace_hint_unique 2ms 0.0018% 72.00% 1999ms 1.84% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.00% 1999ms 1.84% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1357ms 1.25% 73.25% 1981ms 1.83% std::_Rb_tree::equal_range (inline) 0 0% 73.25% 1955ms 1.80% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 73.25% 1940ms 1.79% VertexBasedCellPopulation::WriteCellVtkResultsToFile 74ms 0.068% 73.32% 1939ms 1.79% MutableVertexMesh::CheckForSwapsFromShortEdges 479ms 0.44% 73.76% 1883ms 1.74% std::type_info::operator== (inline) 0 0% 73.76% 1748ms 1.61% VertexMeshWriter::WriteVtkUsingMesh 45ms 0.041% 73.81% 1730ms 1.60% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 134ms 0.12% 73.93% 1582ms 1.46% boost::numeric::ublas::vector_reference::operator() (inline) 15ms 0.014% 73.94% 1581ms 1.46% VertexMesh::GetSurfaceAreaOfElement 39ms 0.036% 73.98% 1577ms 1.45% AbstractCellPopulation::GetLocationIndexUsingCell 45ms 0.041% 74.02% 1540ms 1.42% Node::RemoveElement 69ms 0.064% 74.08% 1506ms 1.39% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 19ms 0.018% 74.10% 1504ms 1.39% std::set::erase (inline) 0 0% 74.10% 1440ms 1.33% tcache_get (inline) 1440ms 1.33% 75.43% 1440ms 1.33% tcache_get_n (inline) 165ms 0.15% 75.58% 1422ms 1.31% CellPropertyCollection::AddProperty 0 0% 75.58% 1415ms 1.30% boost::numeric::ublas::vector_binary::operator() (inline) 2ms 0.0018% 75.58% 1285ms 1.18% OffLatticeSimulation::ApplyBoundaries 73ms 0.067% 75.65% 1238ms 1.14% std::less::operator() (inline) 0 0% 75.65% 1222ms 1.13% boost::numeric::ublas::norm_2 (inline) 500ms 0.46% 76.11% 1210ms 1.12% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1198ms 1.10% 77.22% 1198ms 1.10% Node::rGetLocation 970ms 0.89% 78.11% 1165ms 1.07% std::operator< (inline) 108ms 0.1% 78.21% 1152ms 1.06% std::_Rb_tree::find (inline) 92ms 0.085% 78.30% 1144ms 1.05% std::_Rb_tree::_M_erase_aux (partial-inline) 1134ms 1.05% 79.34% 1134ms 1.05% std::_Rb_tree_insert_and_rebalance 14ms 0.013% 79.35% 1114ms 1.03% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 1102ms 1.02% 80.37% 1102ms 1.02% [libchaste_cell_based.so] 0 0% 80.37% 1057ms 0.97% std::_Rb_tree::clear (inline) 26ms 0.024% 80.39% 1050ms 0.97% CellPropertyRegistry::Get 20ms 0.018% 80.41% 1047ms 0.97% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 80.41% 1039ms 0.96% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 80.41% 1039ms 0.96% std::map::clear (inline) 162ms 0.15% 80.56% 1016ms 0.94% boost::numeric::ublas::detail::equals 4ms 0.0037% 80.57% 1011ms 0.93% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 998ms 0.92% 81.49% 998ms 0.92% [libchaste_mesh.so] 996ms 0.92% 82.40% 996ms 0.92% std::vector::size (inline) 0 0% 82.40% 962ms 0.89% boost::numeric::ublas::c_vector::assign_temporary (inline) 4ms 0.0037% 82.41% 962ms 0.89% boost::numeric::ublas::c_vector::swap (inline) 83ms 0.077% 82.48% 958ms 0.88% std::swap_ranges (inline) 0 0% 82.48% 956ms 0.88% std::map::find (inline) 132ms 0.12% 82.61% 946ms 0.87% boost::detail::shared_count::~shared_count (inline) 0 0% 82.61% 946ms 0.87% boost::shared_ptr::~shared_ptr (inline) 360ms 0.33% 82.94% 883ms 0.81% Edge::GetMapIndex 0 0% 82.94% 875ms 0.81% std::iter_swap (inline) 875ms 0.81% 83.74% 875ms 0.81% std::swap (inline) 0 0% 83.74% 839ms 0.77% VertexMeshWriter::MakeVtkMesh 98ms 0.09% 83.83% 820ms 0.76% MutableElement::GetNodeLocalIndex 113ms 0.1% 83.94% 801ms 0.74% boost::numeric::ublas::c_vector::operator= (inline) 23ms 0.021% 83.96% 789ms 0.73% MutableElement::RegisterWithEdges (inline) 780ms 0.72% 84.68% 788ms 0.73% boost::detail::sp_counted_base::release 34ms 0.031% 84.71% 780ms 0.72% Edge::AddElement 0 0% 84.71% 777ms 0.72% boost::numeric::ublas::norm_inf (inline) 407ms 0.38% 85.09% 777ms 0.72% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 85.09% 773ms 0.71% CellPropertyCollection::~CellPropertyCollection (inline) 471ms 0.43% 85.52% 770ms 0.71% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 177ms 0.16% 85.68% 749ms 0.69% boost::shared_ptr::shared_ptr (inline) 738ms 0.68% 86.36% 738ms 0.68% Node::GetIndex 0 0% 86.36% 708ms 0.65% std::_Rb_tree::_Auto_node::_M_insert (inline) 28ms 0.026% 86.39% 708ms 0.65% std::_Rb_tree::_M_insert_node (inline) 107ms 0.099% 86.49% 679ms 0.63% std::__new_allocator::construct (inline) 0 0% 86.49% 679ms 0.63% std::allocator_traits::construct (inline) 0 0% 86.49% 669ms 0.62% std::_Vector_base::_M_allocate (inline) 42ms 0.039% 86.53% 659ms 0.61% MutableElement::RegisterWithNodes (inline) 0 0% 86.53% 634ms 0.58% std::_Rb_tree::_M_construct_node (inline) 610ms 0.56% 87.09% 610ms 0.56% operator delete 0 0% 87.09% 607ms 0.56% vtkPolygon::New 1ms 0.00092% 87.09% 604ms 0.56% vtkPolygon::vtkPolygon 30ms 0.028% 87.12% 602ms 0.56% Node::AddElement 587ms 0.54% 87.66% 587ms 0.54% [libstdc++.so.6.0.33] 549ms 0.51% 88.17% 572ms 0.53% boost::detail::shared_count::shared_count (inline) 40ms 0.037% 88.20% 567ms 0.52% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 88.20% 567ms 0.52% boost::numeric::ublas::vector::vector (inline) 0 0% 88.20% 547ms 0.5% boost::numeric::ublas::scalar_traits::type_sqrt (inline)