File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96599ms, 88.40% of 109273ms total Dropped 1081 nodes (cum <= 546.37ms) flat flat% sum% cum cum% 0 0% 0% 108816ms 99.58% __libc_start_call_main 0 0% 0% 108816ms 99.58% __libc_start_main_impl 0 0% 0% 108816ms 99.58% _start 0 0% 0% 108794ms 99.56% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108794ms 99.56% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108794ms 99.56% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108794ms 99.56% main 0 0% 0% 108752ms 99.52% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108752ms 99.52% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108752ms 99.52% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0018% 0.0018% 108744ms 99.52% AbstractCellBasedSimulation::Solve 24ms 0.022% 0.024% 56487ms 51.69% OffLatticeSimulation::UpdateCellLocationsAndTopology 26ms 0.024% 0.048% 53147ms 48.64% ForwardEulerNumericalMethod::UpdateAllNodePositions 129ms 0.12% 0.17% 52068ms 47.65% AbstractNumericalMethod::ComputeForcesIncludingDamping 393ms 0.36% 0.53% 40243ms 36.83% NagaiHondaForce::AddForceContribution 1ms 0.00092% 0.53% 39278ms 35.94% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.0027% 0.53% 24099ms 22.05% VertexBasedCellPopulation::Update 0 0% 0.53% 23969ms 21.93% MutableVertexMesh::ReMesh 14580ms 13.34% 13.87% 23010ms 21.06% Cylindrical2dVertexMesh::GetVectorFromAtoB 70ms 0.064% 13.94% 17666ms 16.17% Cell::ReadyToDivide 70ms 0.064% 14.00% 16438ms 15.04% AbstractPhaseBasedCellCycleModel::ReadyToDivide 303ms 0.28% 14.28% 14856ms 13.60% NagaiHondaForce::GetAdhesionParameter 409ms 0.37% 14.65% 14381ms 13.16% boost::numeric::ublas::c_vector::c_vector (partial-inline) 127ms 0.12% 14.77% 14047ms 12.85% SimpleWntCellCycleModel::UpdateCellCyclePhase 118ms 0.11% 14.88% 13793ms 12.62% CellPropertyCollection::GetPropertiesType (inline) 386ms 0.35% 15.23% 12895ms 11.80% boost::numeric::ublas::vector_assign (inline) 144ms 0.13% 15.36% 12062ms 11.04% MutableVertexMesh::CheckForIntersections 3549ms 3.25% 18.61% 11513ms 10.54% __dynamic_cast 84ms 0.077% 18.69% 11417ms 10.45% AbstractCellProperty::IsSubType (inline) 82ms 0.075% 18.76% 11340ms 10.38% VertexBasedCellPopulation::GetDampingConstant 82ms 0.075% 18.84% 10529ms 9.64% AbstractTargetAreaModifier::UpdateTargetAreas 47ms 0.043% 18.88% 10452ms 9.57% AbstractCellBasedSimulation::DoCellBirth 42ms 0.038% 18.92% 10425ms 9.54% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 1383ms 1.27% 20.18% 9983ms 9.14% std::__new_allocator::allocate (inline) 2728ms 2.50% 22.68% 9565ms 8.75% boost::numeric::ublas::indexing_vector_assign 0 0% 22.68% 9414ms 8.62% std::_Rb_tree::_M_create_node (inline) 0 0% 22.68% 9398ms 8.60% std::allocator_traits::allocate (inline) 1432ms 1.31% 23.99% 9230ms 8.45% std::_Rb_tree::_M_erase 381ms 0.35% 24.34% 8948ms 8.19% VertexMesh::GetNextEdgeGradientOfElementAtNode 737ms 0.67% 25.01% 8858ms 8.11% VertexMesh::ElementIncludesPoint 0 0% 25.01% 8727ms 7.99% std::_Rb_tree::_M_get_node (inline) 873ms 0.8% 25.81% 8719ms 7.98% operator new 32ms 0.029% 25.84% 8713ms 7.97% VertexBasedCellPopulation::GetLocationOfCellCentre 76ms 0.07% 25.91% 8693ms 7.96% Cell::GetMutationState 208ms 0.19% 26.10% 8395ms 7.68% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.10% 8284ms 7.58% std::_Rb_tree::_Alloc_node::operator() (inline) 454ms 0.42% 26.52% 8207ms 7.51% VertexMesh::GetCentroidOfElement 0 0% 26.52% 8097ms 7.41% std::_Rb_tree::_M_drop_node (inline) 0 0% 26.52% 7945ms 7.27% std::set::~set (inline) 299ms 0.27% 26.79% 7885ms 7.22% std::__new_allocator::deallocate (inline) 0 0% 26.79% 7838ms 7.17% std::allocator_traits::deallocate (inline) 0 0% 26.79% 7787ms 7.13% std::_Rb_tree::_M_put_node (inline) 2908ms 2.66% 29.45% 7674ms 7.02% __GI___libc_free 3117ms 2.85% 32.30% 7633ms 6.99% __GI___libc_malloc 14ms 0.013% 32.32% 7474ms 6.84% MutableVertexMesh::RemoveDeletedNodesAndElements 471ms 0.43% 32.75% 7426ms 6.80% std::map::operator[] (partial-inline) 1261ms 1.15% 33.90% 7066ms 6.47% AbstractMesh::GetDistanceBetweenNodes 159ms 0.15% 34.05% 6811ms 6.23% std::_Rb_tree::_Rb_tree (partial-inline) 6421ms 5.88% 39.92% 6421ms 5.88% __strcmp_avx2 650ms 0.59% 40.52% 6403ms 5.86% std::_Rb_tree::_M_copy (inline) 19ms 0.017% 40.54% 6379ms 5.84% std::set::set (inline) 123ms 0.11% 40.65% 6316ms 5.78% SimpleWntCellCycleModel::GetWntLevel 6189ms 5.66% 46.31% 6189ms 5.66% boost::numeric::ublas::c_vector::operator() 138ms 0.13% 46.44% 6096ms 5.58% WntConcentration::GetWntLevel 2557ms 2.34% 48.78% 5940ms 5.44% std::_Rb_tree::_M_lower_bound (inline) 0 0% 48.78% 5537ms 5.07% std::set::insert (inline) 724ms 0.66% 49.44% 5423ms 4.96% std::_Rb_tree::_M_clone_node (inline) 2630ms 2.41% 51.85% 5410ms 4.95% __cxxabiv1::__si_class_type_info::__do_dyncast 24ms 0.022% 51.87% 5350ms 4.90% MutableVertexMesh::RemoveDeletedNodes 33ms 0.03% 51.90% 5193ms 4.75% EdgeHelper::RemoveDeletedEdges 36ms 0.033% 51.93% 4937ms 4.52% EdgeHelper::UpdateEdgesMapKey 1506ms 1.38% 53.31% 4855ms 4.44% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 53.31% 4772ms 4.37% std::_Rb_tree::lower_bound (inline) 0 0% 53.31% 4772ms 4.37% std::map::lower_bound (inline) 4450ms 4.07% 57.38% 4761ms 4.36% _int_free 1ms 0.00092% 57.38% 4714ms 4.31% AbstractCellBasedSimulation::DoCellRemoval (inline) 579ms 0.53% 57.91% 4663ms 4.27% std::_Rb_tree::_M_insert_ (inline) 227ms 0.21% 58.12% 4644ms 4.25% MutableElement::ResetIndex 46ms 0.042% 58.16% 4553ms 4.17% std::set_intersection (inline) 248ms 0.23% 58.39% 4507ms 4.12% std::__set_intersection 111ms 0.1% 58.49% 4105ms 3.76% AbstractCellPopulation::GetCellUsingLocationIndex 50ms 0.046% 58.54% 4057ms 3.71% Cell::GetCellProliferativeType 3912ms 3.58% 62.12% 3912ms 3.58% boost::numeric::ublas::same_impl_ex 67ms 0.061% 62.18% 3811ms 3.49% AbstractCellProperty::IsType (inline) 11ms 0.01% 62.19% 3661ms 3.35% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 45ms 0.041% 62.23% 3356ms 3.07% Cell::SetCellProliferativeType 0 0% 62.23% 3322ms 3.04% std::insert_iterator::operator= (inline) 824ms 0.75% 62.98% 3311ms 3.03% AbstractElement::GetNodeLocation 2161ms 1.98% 64.96% 3046ms 2.79% _int_malloc 3ms 0.0027% 64.96% 2932ms 2.68% std::_Rb_tree::_M_insert_unique_ (inline) 40ms 0.037% 65.00% 2884ms 2.64% std::_Rb_tree::erase 2857ms 2.61% 67.62% 2857ms 2.61% std::_Rb_tree::_S_right (inline) 745ms 0.68% 68.30% 2726ms 2.49% AbstractCellProperty::IsSame 44ms 0.04% 68.34% 2712ms 2.48% CellPropertyCollection::HasProperty 659ms 0.6% 68.94% 2702ms 2.47% boost::numeric::ublas::vector_binary::size (inline) 373ms 0.34% 69.28% 2638ms 2.41% std::_Rb_tree_const_iterator::operator++ (inline) 238ms 0.22% 69.50% 2611ms 2.39% VertexMesh::GetAreaGradientOfElementAtNode 1ms 0.00092% 69.50% 2605ms 2.38% std::_Rb_tree::_M_insert_unique 0 0% 69.50% 2593ms 2.37% Cell::HasCellProperty (inline) 0 0% 69.50% 2529ms 2.31% boost::numeric::ublas::c_vector::operator-= (inline) 1ms 0.00092% 69.50% 2424ms 2.22% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.50% 2415ms 2.21% boost::numeric::ublas::c_vector::assign (inline) 25ms 0.023% 69.52% 2401ms 2.20% Cell::GetCellData 9ms 0.0082% 69.53% 2343ms 2.14% AbstractCellPopulation::Iterator::operator++ (inline) 210ms 0.19% 69.73% 2302ms 2.11% AbstractCellPopulation::Iterator::IsRealCell (inline) 123ms 0.11% 69.84% 2298ms 2.10% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 89ms 0.081% 69.92% 2239ms 2.05% VertexMesh::GetVolumeOfElement 37ms 0.034% 69.95% 2126ms 1.95% std::_Rb_tree::_M_emplace_hint_unique 2077ms 1.90% 71.85% 2077ms 1.90% std::_Rb_tree_increment 482ms 0.44% 72.30% 1981ms 1.81% std::type_info::operator== (inline) 0 0% 72.30% 1973ms 1.81% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 72.30% 1960ms 1.79% VertexBasedCellPopulation::WriteCellVtkResultsToFile 0 0% 72.30% 1944ms 1.78% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.30% 1944ms 1.78% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1298ms 1.19% 73.48% 1914ms 1.75% std::_Rb_tree::equal_range (inline) 61ms 0.056% 73.54% 1844ms 1.69% MutableVertexMesh::CheckForSwapsFromShortEdges 30ms 0.027% 73.57% 1773ms 1.62% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 73.57% 1773ms 1.62% VertexMeshWriter::WriteVtkUsingMesh 22ms 0.02% 73.59% 1629ms 1.49% VertexMesh::GetSurfaceAreaOfElement 169ms 0.15% 73.74% 1607ms 1.47% CellPropertyCollection::AddProperty 36ms 0.033% 73.77% 1602ms 1.47% AbstractCellPopulation::GetLocationIndexUsingCell 59ms 0.054% 73.83% 1578ms 1.44% Node::RemoveElement 82ms 0.075% 73.90% 1567ms 1.43% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 129ms 0.12% 74.02% 1541ms 1.41% boost::numeric::ublas::vector_reference::operator() (inline) 19ms 0.017% 74.04% 1527ms 1.40% std::set::erase (inline) 3ms 0.0027% 74.04% 1429ms 1.31% OffLatticeSimulation::ApplyBoundaries 0 0% 74.04% 1418ms 1.30% boost::numeric::ublas::vector_binary::operator() (inline) 1ms 0.00092% 74.04% 1294ms 1.18% tcache_get (inline) 1293ms 1.18% 75.23% 1293ms 1.18% tcache_get_n (inline) 0 0% 75.23% 1273ms 1.16% boost::numeric::ublas::norm_2 (inline) 572ms 0.52% 75.75% 1266ms 1.16% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 20ms 0.018% 75.77% 1237ms 1.13% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 1236ms 1.13% 76.90% 1236ms 1.13% Node::rGetLocation 64ms 0.059% 76.96% 1175ms 1.08% std::less::operator() (inline) 107ms 0.098% 77.05% 1168ms 1.07% std::_Rb_tree::find (inline) 60ms 0.055% 77.11% 1147ms 1.05% std::_Rb_tree::_M_erase_aux (partial-inline) 1141ms 1.04% 78.15% 1141ms 1.04% [libchaste_cell_based.so] 0 0% 78.15% 1130ms 1.03% std::_Rb_tree::_Auto_node::_Auto_node (inline) 931ms 0.85% 79.01% 1111ms 1.02% std::operator< (inline) 36ms 0.033% 79.04% 1110ms 1.02% CellPropertyRegistry::Get 1095ms 1.00% 80.04% 1095ms 1.00% std::_Rb_tree_insert_and_rebalance 2ms 0.0018% 80.04% 1048ms 0.96% std::_Rb_tree::clear (inline) 0 0% 80.04% 1024ms 0.94% std::map::clear (inline) 8ms 0.0073% 80.05% 1008ms 0.92% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 999ms 0.91% 80.96% 999ms 0.91% std::vector::size (inline) 961ms 0.88% 81.84% 961ms 0.88% [libchaste_mesh.so] 404ms 0.37% 82.21% 949ms 0.87% Edge::GetMapIndex 2ms 0.0018% 82.22% 949ms 0.87% std::map::find (inline) 149ms 0.14% 82.35% 932ms 0.85% boost::detail::shared_count::~shared_count (inline) 0 0% 82.35% 932ms 0.85% boost::shared_ptr::~shared_ptr (inline) 0 0% 82.35% 923ms 0.84% boost::numeric::ublas::c_vector::assign_temporary (inline) 8ms 0.0073% 82.36% 923ms 0.84% boost::numeric::ublas::c_vector::swap (inline) 20ms 0.018% 82.38% 919ms 0.84% boost::numeric::ublas::detail::expression_type_check (inline) 80ms 0.073% 82.45% 915ms 0.84% std::swap_ranges (inline) 152ms 0.14% 82.59% 882ms 0.81% boost::numeric::ublas::detail::equals 179ms 0.16% 82.75% 881ms 0.81% boost::shared_ptr::shared_ptr (inline) 123ms 0.11% 82.87% 875ms 0.8% MutableElement::GetNodeLocalIndex 2ms 0.0018% 82.87% 841ms 0.77% VertexMeshWriter::MakeVtkMesh 836ms 0.77% 83.63% 836ms 0.77% std::swap (inline) 0 0% 83.63% 835ms 0.76% std::iter_swap (inline) 794ms 0.73% 84.36% 794ms 0.73% Node::GetIndex 477ms 0.44% 84.80% 765ms 0.7% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 753ms 0.69% 85.48% 756ms 0.69% boost::detail::sp_counted_base::release 35ms 0.032% 85.52% 743ms 0.68% Edge::AddElement 18ms 0.016% 85.53% 742ms 0.68% MutableElement::RegisterWithEdges (inline) 99ms 0.091% 85.62% 733ms 0.67% std::__new_allocator::construct (inline) 0 0% 85.62% 733ms 0.67% std::allocator_traits::construct (inline) 105ms 0.096% 85.72% 724ms 0.66% boost::numeric::ublas::c_vector::operator= (inline) 657ms 0.6% 86.32% 702ms 0.64% boost::detail::shared_count::shared_count (inline) 0 0% 86.32% 693ms 0.63% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 86.32% 687ms 0.63% std::_Rb_tree::_M_construct_node (inline) 0 0% 86.32% 671ms 0.61% boost::numeric::ublas::norm_inf (inline) 363ms 0.33% 86.65% 671ms 0.61% boost::numeric::ublas::vector_norm_inf::apply (inline) 1ms 0.00092% 86.65% 668ms 0.61% std::_Vector_base::_M_allocate (inline) 0 0% 86.65% 666ms 0.61% std::_Rb_tree::_Auto_node::_M_insert (inline) 17ms 0.016% 86.67% 666ms 0.61% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.67% 632ms 0.58% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 36ms 0.033% 86.70% 626ms 0.57% MutableElement::RegisterWithNodes (inline) 31ms 0.028% 86.73% 616ms 0.56% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 86.73% 616ms 0.56% boost::numeric::ublas::vector::vector (inline) 599ms 0.55% 87.28% 599ms 0.55% [libstdc++.so.6.0.33] 0 0% 87.28% 598ms 0.55% vtkPolygon::New 2ms 0.0018% 87.28% 598ms 0.55% vtkPolygon::vtkPolygon 596ms 0.55% 87.83% 596ms 0.55% operator delete 591ms 0.54% 88.37% 591ms 0.54% boost::shared_ptr::operator-> (inline) 29ms 0.027% 88.39% 577ms 0.53% Node::AddElement 8ms 0.0073% 88.40% 548ms 0.5% std::vector::_M_default_append (inline)