File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 74809ms, 87.51% of 85483ms total Dropped 1030 nodes (cum <= 427.42ms) flat flat% sum% cum cum% 0 0% 0% 85176ms 99.64% __libc_start_call_main 0 0% 0% 85176ms 99.64% __libc_start_main_impl 0 0% 0% 85176ms 99.64% _start 0 0% 0% 85158ms 99.62% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 85158ms 99.62% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 85158ms 99.62% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 85158ms 99.62% main 0 0% 0% 85117ms 99.57% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 85117ms 99.57% CxxTest::TestRunner::runTest (inline) 0 0% 0% 85117ms 99.57% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0023% 0.0023% 85110ms 99.56% AbstractCellBasedSimulation::Solve 10ms 0.012% 0.014% 44218ms 51.73% OffLatticeSimulation::UpdateCellLocationsAndTopology 17ms 0.02% 0.034% 41645ms 48.72% ForwardEulerNumericalMethod::UpdateAllNodePositions 121ms 0.14% 0.18% 40859ms 47.80% AbstractNumericalMethod::ComputeForcesIncludingDamping 241ms 0.28% 0.46% 30948ms 36.20% NagaiHondaForce::AddForceContribution 0 0% 0.46% 30513ms 35.69% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.0047% 0.46% 18753ms 21.94% VertexBasedCellPopulation::Update 0 0% 0.46% 18647ms 21.81% MutableVertexMesh::ReMesh 11408ms 13.35% 13.81% 18132ms 21.21% Cylindrical2dVertexMesh::GetVectorFromAtoB 76ms 0.089% 13.90% 13915ms 16.28% Cell::ReadyToDivide 61ms 0.071% 13.97% 12859ms 15.04% AbstractPhaseBasedCellCycleModel::ReadyToDivide 106ms 0.12% 14.09% 11044ms 12.92% SimpleWntCellCycleModel::UpdateCellCyclePhase 224ms 0.26% 14.35% 10969ms 12.83% NagaiHondaForce::GetAdhesionParameter 84ms 0.098% 14.45% 10967ms 12.83% CellPropertyCollection::GetPropertiesType (inline) 348ms 0.41% 14.86% 10650ms 12.46% boost::numeric::ublas::c_vector::c_vector (partial-inline) 236ms 0.28% 15.14% 9487ms 11.10% boost::numeric::ublas::vector_assign (inline) 73ms 0.085% 15.22% 9431ms 11.03% VertexBasedCellPopulation::GetDampingConstant 2842ms 3.32% 18.55% 9333ms 10.92% __dynamic_cast 32ms 0.037% 18.58% 9232ms 10.80% AbstractCellProperty::IsSubType (inline) 96ms 0.11% 18.69% 9227ms 10.79% MutableVertexMesh::CheckForIntersections 60ms 0.07% 18.77% 8386ms 9.81% AbstractTargetAreaModifier::UpdateTargetAreas 34ms 0.04% 18.80% 8313ms 9.72% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 17ms 0.02% 18.82% 8185ms 9.58% AbstractCellBasedSimulation::DoCellBirth 1156ms 1.35% 20.18% 7758ms 9.08% std::__new_allocator::allocate (inline) 0 0% 20.18% 7349ms 8.60% std::_Rb_tree::_M_create_node (inline) 0 0% 20.18% 7331ms 8.58% std::allocator_traits::allocate (inline) 288ms 0.34% 20.51% 7267ms 8.50% VertexMesh::GetNextEdgeGradientOfElementAtNode 2095ms 2.45% 22.96% 7252ms 8.48% boost::numeric::ublas::indexing_vector_assign 80ms 0.094% 23.06% 6901ms 8.07% Cell::GetMutationState 23ms 0.027% 23.09% 6875ms 8.04% VertexBasedCellPopulation::GetLocationOfCellCentre 921ms 1.08% 24.16% 6818ms 7.98% std::_Rb_tree::_M_erase 0 0% 24.16% 6792ms 7.95% std::_Rb_tree::_M_get_node (inline) 661ms 0.77% 24.94% 6764ms 7.91% VertexMesh::ElementIncludesPoint 600ms 0.7% 25.64% 6664ms 7.80% operator new 0 0% 25.64% 6489ms 7.59% std::_Rb_tree::_Alloc_node::operator() (inline) 357ms 0.42% 26.06% 6457ms 7.55% std::map::operator[] (partial-inline) 335ms 0.39% 26.45% 6404ms 7.49% VertexMesh::GetCentroidOfElement 226ms 0.26% 26.71% 6240ms 7.30% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.71% 6151ms 7.20% std::_Rb_tree::_M_drop_node (inline) 6ms 0.007% 26.72% 6030ms 7.05% MutableVertexMesh::RemoveDeletedNodesAndElements 167ms 0.2% 26.91% 5958ms 6.97% std::__new_allocator::deallocate (inline) 0 0% 26.91% 5942ms 6.95% std::allocator_traits::deallocate (inline) 0 0% 26.91% 5930ms 6.94% std::set::~set (inline) 2167ms 2.54% 29.45% 5923ms 6.93% __GI___libc_malloc 0 0% 29.45% 5891ms 6.89% std::_Rb_tree::_M_put_node (inline) 1193ms 1.40% 30.84% 5802ms 6.79% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 150ms 0.18% 31.02% 5622ms 6.58% std::_Rb_tree::_Rb_tree (partial-inline) 1887ms 2.21% 33.23% 5576ms 6.52% __GI___libc_free 2073ms 2.43% 35.65% 5325ms 6.23% std::_Rb_tree::_M_lower_bound (inline) 561ms 0.66% 36.31% 5291ms 6.19% std::_Rb_tree::_M_copy (inline) 5257ms 6.15% 42.46% 5257ms 6.15% __strcmp_evex 19ms 0.022% 42.48% 5236ms 6.13% std::set::set (inline) 105ms 0.12% 42.60% 5078ms 5.94% SimpleWntCellCycleModel::GetWntLevel 137ms 0.16% 42.76% 4879ms 5.71% WntConcentration::GetWntLevel 4658ms 5.45% 48.21% 4658ms 5.45% boost::numeric::ublas::c_vector::operator() 697ms 0.82% 49.03% 4541ms 5.31% std::_Rb_tree::_M_clone_node (inline) 0 0% 49.03% 4397ms 5.14% std::_Rb_tree::lower_bound (inline) 0 0% 49.03% 4397ms 5.14% std::map::lower_bound (inline) 15ms 0.018% 49.05% 4252ms 4.97% MutableVertexMesh::RemoveDeletedNodes 1553ms 1.82% 50.86% 4160ms 4.87% boost::numeric::ublas::c_vector::operator[] (inline) 26ms 0.03% 50.89% 4128ms 4.83% EdgeHelper::RemoveDeletedEdges 0 0% 50.89% 4104ms 4.80% std::set::insert (inline) 2217ms 2.59% 53.49% 3983ms 4.66% __cxxabiv1::__si_class_type_info::__do_dyncast 32ms 0.037% 53.52% 3901ms 4.56% EdgeHelper::UpdateEdgesMapKey 94ms 0.11% 53.63% 3818ms 4.47% AbstractCellPopulation::GetCellUsingLocationIndex 3360ms 3.93% 57.56% 3677ms 4.30% _int_free 163ms 0.19% 57.76% 3664ms 4.29% MutableElement::ResetIndex 1ms 0.0012% 57.76% 3563ms 4.17% AbstractCellBasedSimulation::DoCellRemoval (inline) 440ms 0.51% 58.27% 3524ms 4.12% std::_Rb_tree::_M_insert_ (inline) 99ms 0.12% 58.39% 3197ms 3.74% std::set_intersection (inline) 167ms 0.2% 58.58% 3098ms 3.62% std::__set_intersection 29ms 0.034% 58.62% 3058ms 3.58% Cell::GetCellProliferativeType 40ms 0.047% 58.66% 3001ms 3.51% AbstractCellProperty::IsType (inline) 2944ms 3.44% 62.11% 2944ms 3.44% boost::numeric::ublas::same_impl_ex 10ms 0.012% 62.12% 2706ms 3.17% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 2696ms 3.15% 65.27% 2696ms 3.15% std::_Rb_tree::_S_right (inline) 1768ms 2.07% 67.34% 2504ms 2.93% _int_malloc 685ms 0.8% 68.14% 2446ms 2.86% AbstractElement::GetNodeLocation 0 0% 68.14% 2432ms 2.85% std::insert_iterator::operator= (inline) 30ms 0.035% 68.18% 2394ms 2.80% Cell::SetCellProliferativeType 46ms 0.054% 68.23% 2380ms 2.78% std::_Rb_tree::erase 19ms 0.022% 68.25% 2235ms 2.61% CellPropertyCollection::HasProperty 572ms 0.67% 68.92% 2180ms 2.55% AbstractCellProperty::IsSame 6ms 0.007% 68.93% 2146ms 2.51% std::_Rb_tree::_M_insert_unique_ (inline) 0 0% 68.93% 2144ms 2.51% Cell::HasCellProperty (inline) 0 0% 68.93% 2083ms 2.44% boost::numeric::ublas::c_vector::operator-= (inline) 156ms 0.18% 69.11% 2067ms 2.42% VertexMesh::GetAreaGradientOfElementAtNode 461ms 0.54% 69.65% 2017ms 2.36% boost::numeric::ublas::vector_binary::size (inline) 0 0% 69.65% 1977ms 2.31% AbstractCellPopulation::WriteResultsToFiles 23ms 0.027% 69.68% 1974ms 2.31% Cell::GetCellData 0 0% 69.68% 1958ms 2.29% std::_Rb_tree::_M_insert_unique (inline) 0 0% 69.68% 1946ms 2.28% boost::numeric::ublas::c_vector::assign (inline) 187ms 0.22% 69.90% 1867ms 2.18% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.0012% 69.90% 1763ms 2.06% AbstractCellPopulation::Iterator::operator++ (inline) 65ms 0.076% 69.97% 1762ms 2.06% VertexMesh::GetVolumeOfElement 161ms 0.19% 70.16% 1757ms 2.06% AbstractCellPopulation::Iterator::IsRealCell (inline) 38ms 0.044% 70.21% 1743ms 2.04% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 33ms 0.039% 70.25% 1664ms 1.95% std::_Rb_tree::_M_emplace_hint_unique 2ms 0.0023% 70.25% 1655ms 1.94% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 70.25% 1655ms 1.94% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 70.25% 1617ms 1.89% VertexBasedCellPopulation::WriteVtkResultsToFile 1079ms 1.26% 71.51% 1616ms 1.89% std::_Rb_tree::equal_range (inline) 1ms 0.0012% 71.51% 1612ms 1.89% VertexBasedCellPopulation::WriteCellVtkResultsToFile 385ms 0.45% 71.96% 1608ms 1.88% std::type_info::operator== (inline) 1527ms 1.79% 73.75% 1527ms 1.79% std::_Rb_tree_increment 0 0% 73.75% 1455ms 1.70% VertexMeshWriter::WriteVtkUsingMesh 59ms 0.069% 73.82% 1454ms 1.70% MutableVertexMesh::CheckForSwapsFromShortEdges 11ms 0.013% 73.83% 1341ms 1.57% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 29ms 0.034% 73.86% 1258ms 1.47% VertexMesh::GetSurfaceAreaOfElement 30ms 0.035% 73.90% 1229ms 1.44% AbstractCellPopulation::GetLocationIndexUsingCell 35ms 0.041% 73.94% 1219ms 1.43% Node::RemoveElement 52ms 0.061% 74.00% 1205ms 1.41% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 107ms 0.13% 74.13% 1199ms 1.40% CellPropertyCollection::AddProperty 6ms 0.007% 74.13% 1187ms 1.39% std::set::erase (inline) 38ms 0.044% 74.18% 1134ms 1.33% std::less::operator() (inline) 0 0% 74.18% 1121ms 1.31% tcache_get (inline) 1121ms 1.31% 75.49% 1121ms 1.31% tcache_get_n (inline) 0 0% 75.49% 1099ms 1.29% boost::numeric::ublas::vector_binary::operator() (inline) 906ms 1.06% 76.55% 1096ms 1.28% std::operator< (inline) 1ms 0.0012% 76.55% 1056ms 1.24% OffLatticeSimulation::ApplyBoundaries 59ms 0.069% 76.62% 1053ms 1.23% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 76.62% 1043ms 1.22% boost::numeric::ublas::norm_2 (inline) 461ms 0.54% 77.16% 1032ms 1.21% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 89ms 0.1% 77.26% 966ms 1.13% std::_Rb_tree::find (inline) 963ms 1.13% 78.39% 963ms 1.13% [libchaste_cell_based.so] 14ms 0.016% 78.41% 906ms 1.06% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 21ms 0.025% 78.43% 897ms 1.05% CellPropertyRegistry::Get 0 0% 78.43% 892ms 1.04% boost::numeric::ublas::c_vector::assign_temporary (inline) 11ms 0.013% 78.44% 892ms 1.04% boost::numeric::ublas::c_vector::swap (inline) 76ms 0.089% 78.53% 881ms 1.03% std::swap_ranges (inline) 875ms 1.02% 79.55% 875ms 1.02% std::_Rb_tree_insert_and_rebalance 0 0% 79.55% 860ms 1.01% std::_Rb_tree::_Auto_node::_Auto_node (inline) 57ms 0.067% 79.62% 827ms 0.97% std::_Rb_tree::_M_erase_aux (partial-inline) 3ms 0.0035% 79.63% 818ms 0.96% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 79.63% 809ms 0.95% std::_Rb_tree::clear (inline) 0 0% 79.63% 807ms 0.94% std::map::find (inline) 0 0% 79.63% 805ms 0.94% std::iter_swap (inline) 805ms 0.94% 80.57% 805ms 0.94% std::swap (inline) 94ms 0.11% 80.68% 792ms 0.93% boost::detail::shared_count::~shared_count (inline) 0 0% 80.68% 792ms 0.93% boost::shared_ptr::~shared_ptr (inline) 0 0% 80.68% 791ms 0.93% std::map::clear (inline) 788ms 0.92% 81.60% 788ms 0.92% Node::rGetLocation 5ms 0.0058% 81.60% 758ms 0.89% boost::numeric::ublas::detail::expression_type_check (inline) 128ms 0.15% 81.75% 746ms 0.87% boost::numeric::ublas::detail::equals 0 0% 81.75% 691ms 0.81% VertexMeshWriter::MakeVtkMesh 682ms 0.8% 82.55% 682ms 0.8% std::vector::size (inline) 88ms 0.1% 82.66% 667ms 0.78% boost::numeric::ublas::c_vector::operator= (inline) 639ms 0.75% 83.40% 661ms 0.77% boost::detail::sp_counted_base::release 0 0% 83.40% 612ms 0.72% boost::numeric::ublas::norm_inf (inline) 312ms 0.36% 83.77% 612ms 0.72% boost::numeric::ublas::vector_norm_inf::apply (inline) 601ms 0.7% 84.47% 601ms 0.7% [libchaste_mesh.so] 170ms 0.2% 84.67% 597ms 0.7% std::__new_allocator::construct (inline) 0 0% 84.67% 597ms 0.7% std::allocator_traits::construct (inline) 302ms 0.35% 85.02% 589ms 0.69% Edge::GetMapIndex 0 0% 85.02% 579ms 0.68% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 99ms 0.12% 85.14% 568ms 0.66% MutableElement::GetNodeLocalIndex 20ms 0.023% 85.16% 562ms 0.66% MutableElement::RegisterWithEdges (inline) 19ms 0.022% 85.18% 561ms 0.66% Edge::AddElement 0 0% 85.18% 557ms 0.65% std::_Rb_tree::_M_construct_node (inline) 282ms 0.33% 85.51% 548ms 0.64% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 85.51% 544ms 0.64% CellPropertyCollection::~CellPropertyCollection (inline) 544ms 0.64% 86.15% 544ms 0.64% [libstdc++.so.6.0.33] 120ms 0.14% 86.29% 540ms 0.63% boost::shared_ptr::shared_ptr (inline) 0 0% 86.29% 538ms 0.63% std::_Vector_base::_M_allocate (inline) 0 0% 86.29% 507ms 0.59% std::_Rb_tree::_Auto_node::_M_insert (inline) 18ms 0.021% 86.31% 507ms 0.59% std::_Rb_tree::_M_insert_node (inline) 1ms 0.0012% 86.31% 506ms 0.59% vtkPolygon::New 0 0% 86.31% 505ms 0.59% vtkPolygon::vtkPolygon 504ms 0.59% 86.90% 504ms 0.59% Node::GetIndex 470ms 0.55% 87.45% 470ms 0.55% boost::shared_ptr::operator-> (inline) 29ms 0.034% 87.49% 447ms 0.52% MutableElement::RegisterWithNodes (inline) 6ms 0.007% 87.49% 447ms 0.52% std::vector::_M_default_append (inline) 17ms 0.02% 87.51% 444ms 0.52% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.51% 444ms 0.52% boost::numeric::ublas::vector::vector (inline)