File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95587ms, 88.16% of 108429ms total Dropped 1107 nodes (cum <= 542.14ms) flat flat% sum% cum cum% 0 0% 0% 107982ms 99.59% __libc_start_call_main 0 0% 0% 107982ms 99.59% __libc_start_main_impl 0 0% 0% 107982ms 99.59% _start 0 0% 0% 107965ms 99.57% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 107965ms 99.57% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 107965ms 99.57% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 107965ms 99.57% main 0 0% 0% 107928ms 99.54% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 107928ms 99.54% CxxTest::TestRunner::runTest (inline) 0 0% 0% 107928ms 99.54% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 0 0% 0% 107921ms 99.53% AbstractCellBasedSimulation::Solve 22ms 0.02% 0.02% 55919ms 51.57% OffLatticeSimulation::UpdateCellLocationsAndTopology 14ms 0.013% 0.033% 52653ms 48.56% ForwardEulerNumericalMethod::UpdateAllNodePositions 136ms 0.13% 0.16% 51606ms 47.59% AbstractNumericalMethod::ComputeForcesIncludingDamping 492ms 0.45% 0.61% 40077ms 36.96% NagaiHondaForce::AddForceContribution 0 0% 0.61% 39247ms 36.20% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00092% 0.61% 24520ms 22.61% VertexBasedCellPopulation::Update 0 0% 0.61% 24397ms 22.50% MutableVertexMesh::ReMesh 14709ms 13.57% 14.18% 23367ms 21.55% Cylindrical2dVertexMesh::GetVectorFromAtoB 77ms 0.071% 14.25% 17228ms 15.89% Cell::ReadyToDivide 75ms 0.069% 14.32% 16066ms 14.82% AbstractPhaseBasedCellCycleModel::ReadyToDivide 346ms 0.32% 14.64% 14723ms 13.58% NagaiHondaForce::GetAdhesionParameter 449ms 0.41% 15.05% 14292ms 13.18% boost::numeric::ublas::c_vector::c_vector (partial-inline) 131ms 0.12% 15.17% 13643ms 12.58% SimpleWntCellCycleModel::UpdateCellCyclePhase 141ms 0.13% 15.30% 13349ms 12.31% CellPropertyCollection::GetPropertiesType (inline) 420ms 0.39% 15.69% 12633ms 11.65% boost::numeric::ublas::vector_assign (inline) 132ms 0.12% 15.81% 12371ms 11.41% MutableVertexMesh::CheckForIntersections 3160ms 2.91% 18.73% 11103ms 10.24% __dynamic_cast 72ms 0.066% 18.79% 11051ms 10.19% VertexBasedCellPopulation::GetDampingConstant 73ms 0.067% 18.86% 10980ms 10.13% AbstractCellProperty::IsSubType (inline) 77ms 0.071% 18.93% 10303ms 9.50% AbstractTargetAreaModifier::UpdateTargetAreas 73ms 0.067% 19.00% 10189ms 9.40% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 1284ms 1.18% 20.18% 10125ms 9.34% std::__new_allocator::allocate (inline) 20ms 0.018% 20.20% 10100ms 9.31% AbstractCellBasedSimulation::DoCellBirth 0 0% 20.20% 9458ms 8.72% std::_Rb_tree::_M_create_node (inline) 0 0% 20.20% 9441ms 8.71% std::allocator_traits::allocate (inline) 2636ms 2.43% 22.63% 9328ms 8.60% boost::numeric::ublas::indexing_vector_assign 771ms 0.71% 23.34% 9260ms 8.54% VertexMesh::ElementIncludesPoint 1395ms 1.29% 24.63% 9062ms 8.36% std::_Rb_tree::_M_erase 353ms 0.33% 24.96% 8982ms 8.28% VertexMesh::GetNextEdgeGradientOfElementAtNode 986ms 0.91% 25.86% 8934ms 8.24% operator new 39ms 0.036% 25.90% 8817ms 8.13% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 25.90% 8788ms 8.10% std::_Rb_tree::_M_get_node (inline) 67ms 0.062% 25.96% 8390ms 7.74% Cell::GetMutationState 442ms 0.41% 26.37% 8364ms 7.71% VertexMesh::GetCentroidOfElement 0 0% 26.37% 8289ms 7.64% std::_Rb_tree::_Alloc_node::operator() (inline) 238ms 0.22% 26.59% 8278ms 7.63% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.59% 8049ms 7.42% std::_Rb_tree::_M_drop_node (inline) 243ms 0.22% 26.81% 7846ms 7.24% std::__new_allocator::deallocate (inline) 0 0% 26.81% 7825ms 7.22% std::set::~set (inline) 0 0% 26.81% 7821ms 7.21% std::allocator_traits::deallocate (inline) 3106ms 2.86% 29.68% 7771ms 7.17% __GI___libc_malloc 0 0% 29.68% 7768ms 7.16% std::_Rb_tree::_M_put_node (inline) 2994ms 2.76% 32.44% 7608ms 7.02% __GI___libc_free 18ms 0.017% 32.46% 7517ms 6.93% MutableVertexMesh::RemoveDeletedNodesAndElements 486ms 0.45% 32.90% 7513ms 6.93% std::map::operator[] (partial-inline) 1425ms 1.31% 34.22% 7373ms 6.80% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 131ms 0.12% 34.34% 6752ms 6.23% std::_Rb_tree::_Rb_tree (partial-inline) 673ms 0.62% 34.96% 6407ms 5.91% std::_Rb_tree::_M_copy (inline) 101ms 0.093% 35.05% 6346ms 5.85% SimpleWntCellCycleModel::GetWntLevel 14ms 0.013% 35.07% 6294ms 5.80% std::set::set (inline) 6208ms 5.73% 40.79% 6208ms 5.73% __strcmp_avx2 133ms 0.12% 40.91% 6152ms 5.67% WntConcentration::GetWntLevel 6149ms 5.67% 46.59% 6149ms 5.67% boost::numeric::ublas::c_vector::operator() 2431ms 2.24% 48.83% 5880ms 5.42% std::_Rb_tree::_M_lower_bound (inline) 2732ms 2.52% 51.35% 5571ms 5.14% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 51.35% 5464ms 5.04% std::set::insert (inline) 717ms 0.66% 52.01% 5449ms 5.03% std::_Rb_tree::_M_clone_node (inline) 24ms 0.022% 52.03% 5385ms 4.97% MutableVertexMesh::RemoveDeletedNodes 35ms 0.032% 52.06% 5215ms 4.81% EdgeHelper::RemoveDeletedEdges 1672ms 1.54% 53.60% 5042ms 4.65% boost::numeric::ublas::c_vector::operator[] (inline) 37ms 0.034% 53.64% 4948ms 4.56% EdgeHelper::UpdateEdgesMapKey 0 0% 53.64% 4774ms 4.40% std::_Rb_tree::lower_bound (inline) 0 0% 53.64% 4774ms 4.40% std::map::lower_bound (inline) 236ms 0.22% 53.86% 4658ms 4.30% MutableElement::ResetIndex 527ms 0.49% 54.34% 4614ms 4.26% std::_Rb_tree::_M_insert_ (inline) 2ms 0.0018% 54.34% 4608ms 4.25% AbstractCellBasedSimulation::DoCellRemoval (inline) 4299ms 3.96% 58.31% 4606ms 4.25% _int_free 39ms 0.036% 58.35% 4555ms 4.20% std::set_intersection (inline) 259ms 0.24% 58.58% 4516ms 4.16% std::__set_intersection 94ms 0.087% 58.67% 4103ms 3.78% AbstractCellPopulation::GetCellUsingLocationIndex 46ms 0.042% 58.71% 3996ms 3.69% Cell::GetCellProliferativeType 3973ms 3.66% 62.38% 3973ms 3.66% boost::numeric::ublas::same_impl_ex 70ms 0.065% 62.44% 3541ms 3.27% AbstractCellProperty::IsType (inline) 11ms 0.01% 62.45% 3535ms 3.26% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.45% 3317ms 3.06% std::insert_iterator::operator= (inline) 53ms 0.049% 62.50% 3154ms 2.91% Cell::SetCellProliferativeType 2226ms 2.05% 64.55% 3112ms 2.87% _int_malloc 729ms 0.67% 65.23% 3065ms 2.83% AbstractElement::GetNodeLocation 3ms 0.0028% 65.23% 2945ms 2.72% std::_Rb_tree::_M_insert_unique_ (inline) 28ms 0.026% 65.25% 2876ms 2.65% std::_Rb_tree::erase 640ms 0.59% 65.84% 2834ms 2.61% boost::numeric::ublas::vector_binary::size (inline) 2823ms 2.60% 68.45% 2823ms 2.60% std::_Rb_tree::_S_right (inline) 441ms 0.41% 68.86% 2665ms 2.46% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 68.86% 2519ms 2.32% std::_Rb_tree::_M_insert_unique 660ms 0.61% 69.46% 2478ms 2.29% AbstractCellProperty::IsSame 0 0% 69.46% 2466ms 2.27% boost::numeric::ublas::c_vector::operator-= (inline) 242ms 0.22% 69.69% 2441ms 2.25% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.69% 2425ms 2.24% AbstractCellPopulation::WriteResultsToFiles 45ms 0.042% 69.73% 2398ms 2.21% CellPropertyCollection::HasProperty 132ms 0.12% 69.85% 2335ms 2.15% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 69.85% 2325ms 2.14% boost::numeric::ublas::c_vector::assign (inline) 0 0% 69.85% 2322ms 2.14% Cell::HasCellProperty (inline) 31ms 0.029% 69.88% 2309ms 2.13% Cell::GetCellData 5ms 0.0046% 69.88% 2218ms 2.05% AbstractCellPopulation::Iterator::operator++ (inline) 85ms 0.078% 69.96% 2217ms 2.04% VertexMesh::GetVolumeOfElement 35ms 0.032% 69.99% 2204ms 2.03% std::_Rb_tree::_M_emplace_hint_unique 230ms 0.21% 70.21% 2193ms 2.02% AbstractCellPopulation::Iterator::IsRealCell (inline) 2062ms 1.90% 72.11% 2062ms 1.90% std::_Rb_tree_increment 1ms 0.00092% 72.11% 1986ms 1.83% VertexBasedCellPopulation::WriteVtkResultsToFile 4ms 0.0037% 72.11% 1971ms 1.82% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1295ms 1.19% 73.31% 1928ms 1.78% std::_Rb_tree::equal_range (inline) 1ms 0.00092% 73.31% 1919ms 1.77% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.31% 1919ms 1.77% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 86ms 0.079% 73.39% 1917ms 1.77% MutableVertexMesh::CheckForSwapsFromShortEdges 431ms 0.4% 73.78% 1818ms 1.68% std::type_info::operator== (inline) 0 0% 73.78% 1783ms 1.64% VertexMeshWriter::WriteVtkUsingMesh 18ms 0.017% 73.80% 1711ms 1.58% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 21ms 0.019% 73.82% 1692ms 1.56% VertexMesh::GetSurfaceAreaOfElement 44ms 0.041% 73.86% 1611ms 1.49% Node::RemoveElement 22ms 0.02% 73.88% 1579ms 1.46% std::set::erase (inline) 135ms 0.12% 74.01% 1504ms 1.39% boost::numeric::ublas::vector_reference::operator() (inline) 21ms 0.019% 74.03% 1499ms 1.38% AbstractCellPopulation::GetLocationIndexUsingCell 158ms 0.15% 74.17% 1476ms 1.36% CellPropertyCollection::AddProperty 67ms 0.062% 74.23% 1475ms 1.36% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 74.23% 1376ms 1.27% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 74.23% 1362ms 1.26% tcache_get (inline) 1362ms 1.26% 75.49% 1362ms 1.26% tcache_get_n (inline) 1ms 0.00092% 75.49% 1346ms 1.24% OffLatticeSimulation::ApplyBoundaries 93ms 0.086% 75.58% 1276ms 1.18% std::less::operator() (inline) 0 0% 75.58% 1249ms 1.15% boost::numeric::ublas::norm_2 (inline) 535ms 0.49% 76.07% 1245ms 1.15% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1193ms 1.10% 77.17% 1193ms 1.10% Node::rGetLocation 949ms 0.88% 78.04% 1183ms 1.09% std::operator< (inline) 0 0% 78.04% 1169ms 1.08% std::_Rb_tree::_Auto_node::_Auto_node (inline) 91ms 0.084% 78.13% 1135ms 1.05% std::_Rb_tree::_M_erase_aux (partial-inline) 1130ms 1.04% 79.17% 1130ms 1.04% std::_Rb_tree_insert_and_rebalance 23ms 0.021% 79.19% 1113ms 1.03% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 1099ms 1.01% 80.21% 1099ms 1.01% [libchaste_cell_based.so] 90ms 0.083% 80.29% 1086ms 1.00% std::_Rb_tree::find (inline) 1085ms 1.00% 81.29% 1085ms 1.00% std::vector::size (inline) 22ms 0.02% 81.31% 1048ms 0.97% CellPropertyRegistry::Get 0 0% 81.31% 1025ms 0.95% std::_Rb_tree::clear (inline) 11ms 0.01% 81.32% 1018ms 0.94% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 81.32% 1011ms 0.93% std::map::clear (inline) 0 0% 81.32% 967ms 0.89% boost::numeric::ublas::c_vector::assign_temporary (inline) 0 0% 81.32% 967ms 0.89% boost::numeric::ublas::c_vector::swap (inline) 86ms 0.079% 81.40% 967ms 0.89% std::swap_ranges (inline) 959ms 0.88% 82.28% 959ms 0.88% [libchaste_mesh.so] 152ms 0.14% 82.42% 946ms 0.87% boost::detail::shared_count::~shared_count (inline) 0 0% 82.42% 946ms 0.87% boost::shared_ptr::~shared_ptr (inline) 397ms 0.37% 82.79% 918ms 0.85% Edge::GetMapIndex 0 0% 82.79% 897ms 0.83% std::map::find (inline) 121ms 0.11% 82.90% 890ms 0.82% MutableElement::GetNodeLocalIndex 882ms 0.81% 83.71% 882ms 0.81% std::swap (inline) 0 0% 83.71% 881ms 0.81% std::iter_swap (inline) 26ms 0.024% 83.74% 868ms 0.8% boost::numeric::ublas::detail::expression_type_check (inline) 2ms 0.0018% 83.74% 847ms 0.78% VertexMeshWriter::MakeVtkMesh 127ms 0.12% 83.86% 831ms 0.77% boost::numeric::ublas::detail::equals 104ms 0.096% 83.95% 816ms 0.75% boost::numeric::ublas::c_vector::operator= (inline) 141ms 0.13% 84.08% 804ms 0.74% boost::shared_ptr::shared_ptr (inline) 468ms 0.43% 84.52% 774ms 0.71% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 27ms 0.025% 84.54% 771ms 0.71% MutableElement::RegisterWithEdges (inline) 771ms 0.71% 85.25% 771ms 0.71% Node::GetIndex 765ms 0.71% 85.96% 769ms 0.71% boost::detail::sp_counted_base::release 19ms 0.018% 85.97% 751ms 0.69% Edge::AddElement 0 0% 85.97% 727ms 0.67% CellPropertyCollection::~CellPropertyCollection (inline) 92ms 0.085% 86.06% 722ms 0.67% std::__new_allocator::construct (inline) 0 0% 86.06% 722ms 0.67% std::allocator_traits::construct (inline) 36ms 0.033% 86.09% 720ms 0.66% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 86.09% 720ms 0.66% boost::numeric::ublas::vector::vector (inline) 0 0% 86.09% 682ms 0.63% std::_Rb_tree::_Auto_node::_M_insert (inline) 26ms 0.024% 86.12% 682ms 0.63% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.12% 670ms 0.62% boost::numeric::ublas::norm_inf (inline) 309ms 0.28% 86.40% 670ms 0.62% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 86.40% 670ms 0.62% std::_Rb_tree::_M_construct_node (inline) 620ms 0.57% 86.97% 663ms 0.61% boost::detail::shared_count::shared_count (inline) 2ms 0.0018% 86.97% 651ms 0.6% std::_Vector_base::_M_allocate (inline) 0 0% 86.97% 639ms 0.59% vtkPolygon::New 0 0% 86.97% 639ms 0.59% vtkPolygon::vtkPolygon 623ms 0.57% 87.55% 623ms 0.57% operator delete 22ms 0.02% 87.57% 609ms 0.56% MutableElement::RegisterWithNodes (inline) 608ms 0.56% 88.13% 608ms 0.56% [libstdc++.so.6.0.33] 0 0% 88.13% 580ms 0.53% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 28ms 0.026% 88.16% 574ms 0.53% Node::AddElement