File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 99250ms, 89.04% of 111473ms total Dropped 885 nodes (cum <= 557.37ms) flat flat% sum% cum cum% 0 0% 0% 111125ms 99.69% __libc_start_call_main 0 0% 0% 111125ms 99.69% __libc_start_main_impl 0 0% 0% 111125ms 99.69% _start 0 0% 0% 111103ms 99.67% main 0 0% 0% 111058ms 99.63% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0018% 0.0018% 111049ms 99.62% AbstractCellBasedSimulation::Solve 408ms 0.37% 0.37% 57603ms 51.67% OffLatticeSimulation::UpdateCellLocationsAndTopology 72ms 0.065% 0.43% 54130ms 48.56% ForwardEulerNumericalMethod::UpdateAllNodePositions 286ms 0.26% 0.69% 53043ms 47.58% AbstractNumericalMethod::ComputeForcesIncludingDamping 1717ms 1.54% 2.23% 40580ms 36.40% NagaiHondaForce::AddForceContribution 2ms 0.0018% 2.23% 40195ms 36.06% AbstractCellBasedSimulation::UpdateCellPopulation 5ms 0.0045% 2.24% 24879ms 22.32% VertexBasedCellPopulation::Update 1ms 0.0009% 2.24% 24757ms 22.21% MutableVertexMesh::ReMesh 17099ms 15.34% 17.58% 23480ms 21.06% Cylindrical2dVertexMesh::GetVectorFromAtoB 146ms 0.13% 17.71% 17936ms 16.09% Cell::ReadyToDivide 75ms 0.067% 17.77% 16620ms 14.91% AbstractPhaseBasedCellCycleModel::ReadyToDivide 919ms 0.82% 18.60% 14546ms 13.05% NagaiHondaForce::GetAdhesionParameter 269ms 0.24% 18.84% 14308ms 12.84% SimpleWntCellCycleModel::UpdateCellCyclePhase 317ms 0.28% 19.12% 11979ms 10.75% MutableVertexMesh::CheckForIntersections 232ms 0.21% 19.33% 11856ms 10.64% VertexBasedCellPopulation::GetDampingConstant 3678ms 3.30% 22.63% 11574ms 10.38% __dynamic_cast 102ms 0.092% 22.72% 10657ms 9.56% AbstractTargetAreaModifier::UpdateTargetAreas 134ms 0.12% 22.84% 10554ms 9.47% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 276ms 0.25% 23.09% 10494ms 9.41% AbstractCellBasedSimulation::DoCellBirth 606ms 0.54% 23.63% 9552ms 8.57% VertexMesh::GetNextEdgeGradientOfElementAtNode 2001ms 1.80% 25.43% 9129ms 8.19% std::_Rb_tree::_M_erase 848ms 0.76% 26.19% 8883ms 7.97% VertexBasedCellPopulation::GetLocationOfCellCentre 593ms 0.53% 26.72% 8742ms 7.84% Cell::GetMutationState 807ms 0.72% 27.45% 8738ms 7.84% operator new 925ms 0.83% 28.28% 8733ms 7.83% VertexMesh::ElementIncludesPoint 25ms 0.022% 28.30% 8363ms 7.50% MutableVertexMesh::RemoveDeletedNodesAndElements 633ms 0.57% 28.87% 8304ms 7.45% VertexMesh::GetCentroidOfElement 2725ms 2.44% 31.31% 7749ms 6.95% __GI___libc_malloc 1818ms 1.63% 32.94% 7621ms 6.84% AbstractMesh::GetDistanceBetweenNodes 4773ms 4.28% 37.22% 7524ms 6.75% boost::numeric::ublas::indexing_vector_assign 2381ms 2.14% 39.36% 7452ms 6.69% __GI___libc_free 3415ms 3.06% 42.42% 6773ms 6.08% std::_Rb_tree::_M_copy 152ms 0.14% 42.56% 6358ms 5.70% SimpleWntCellCycleModel::GetWntLevel 6213ms 5.57% 48.13% 6213ms 5.57% __strcmp_avx2 221ms 0.2% 48.33% 6140ms 5.51% WntConcentration::GetWntLevel 49ms 0.044% 48.37% 5740ms 5.15% MutableVertexMesh::RemoveDeletedNodes 87ms 0.078% 48.45% 5560ms 4.99% EdgeHelper::RemoveDeletedEdges 2891ms 2.59% 51.05% 5322ms 4.77% __cxxabiv1::__si_class_type_info::__do_dyncast 1731ms 1.55% 52.60% 5222ms 4.68% EdgeHelper::UpdateEdgesMapKey 326ms 0.29% 52.89% 5157ms 4.63% MutableElement::ResetIndex 4629ms 4.15% 57.04% 5053ms 4.53% _int_free 349ms 0.31% 57.36% 4825ms 4.33% AbstractCellPopulation::GetCellUsingLocationIndex 4662ms 4.18% 61.54% 4662ms 4.18% boost::numeric::ublas::c_vector::operator() 883ms 0.79% 62.33% 4007ms 3.59% std::__set_intersection 124ms 0.11% 62.44% 3972ms 3.56% Cell::GetCellProliferativeType 3735ms 3.35% 65.79% 3735ms 3.35% boost::numeric::ublas::same_impl_ex 143ms 0.13% 65.92% 3668ms 3.29% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 156ms 0.14% 66.06% 3412ms 3.06% Cell::SetCellProliferativeType 2390ms 2.14% 68.21% 3378ms 3.03% std::_Rb_tree::erase 2341ms 2.10% 70.31% 3337ms 2.99% _int_malloc 3097ms 2.78% 73.08% 3101ms 2.78% std::map::operator[] 1053ms 0.94% 74.03% 3080ms 2.76% AbstractElement::GetNodeLocation 533ms 0.48% 74.51% 3049ms 2.74% boost::numeric::ublas::vector_assign 1383ms 1.24% 75.75% 2703ms 2.42% AbstractCellProperty::IsSame 244ms 0.22% 75.97% 2649ms 2.38% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 75.97% 2559ms 2.30% AbstractCellPopulation::WriteResultsToFiles 186ms 0.17% 76.13% 2481ms 2.23% Cell::GetCellData 126ms 0.11% 76.25% 2288ms 2.05% VertexMesh::GetVolumeOfElement 85ms 0.076% 76.32% 2219ms 1.99% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 288ms 0.26% 76.58% 2095ms 1.88% std::_Rb_tree::_Rb_tree 1ms 0.0009% 76.58% 2080ms 1.87% VertexBasedCellPopulation::WriteVtkResultsToFile 2064ms 1.85% 78.43% 2064ms 1.85% std::_Rb_tree_increment 2ms 0.0018% 78.44% 2061ms 1.85% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1ms 0.0009% 78.44% 1879ms 1.69% VertexMeshWriter::WriteVtkUsingMesh 82ms 0.074% 78.51% 1820ms 1.63% MutableVertexMesh::CheckForSwapsFromShortEdges 159ms 0.14% 78.65% 1773ms 1.59% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 67ms 0.06% 78.71% 1695ms 1.52% Node::RemoveElement 926ms 0.83% 79.54% 1626ms 1.46% CellPropertyCollection::AddProperty 904ms 0.81% 80.35% 1601ms 1.44% AbstractCellPopulation::GetLocationIndexUsingCell 29ms 0.026% 80.38% 1589ms 1.43% VertexMesh::GetSurfaceAreaOfElement 0 0% 80.38% 1498ms 1.34% tcache_get (inline) 1498ms 1.34% 81.72% 1498ms 1.34% tcache_get_n (inline) 4ms 0.0036% 81.73% 1429ms 1.28% OffLatticeSimulation::ApplyBoundaries 1375ms 1.23% 82.96% 1375ms 1.23% [libchaste_cell_based.so] 230ms 0.21% 83.17% 1215ms 1.09% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 157ms 0.14% 83.31% 1154ms 1.04% CellPropertyRegistry::Get 1132ms 1.02% 84.32% 1132ms 1.02% std::_Rb_tree_insert_and_rebalance 3ms 0.0027% 84.33% 1093ms 0.98% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1070ms 0.96% 85.29% 1070ms 0.96% Node::rGetLocation 774ms 0.69% 85.98% 957ms 0.86% boost::numeric::ublas::detail::equals 4ms 0.0036% 85.98% 883ms 0.79% VertexMeshWriter::MakeVtkMesh 625ms 0.56% 86.54% 859ms 0.77% Edge::GetMapIndex 811ms 0.73% 87.27% 811ms 0.73% [libchaste_mesh.so] 185ms 0.17% 87.44% 778ms 0.7% Edge::AddElement 172ms 0.15% 87.59% 731ms 0.66% MutableElement::GetNodeLocalIndex 682ms 0.61% 88.20% 682ms 0.61% Node::GetIndex 1ms 0.0009% 88.21% 624ms 0.56% vtkPolygon::New 2ms 0.0018% 88.21% 623ms 0.56% vtkPolygon::vtkPolygon 618ms 0.55% 88.76% 618ms 0.55% [libstdc++.so.6.0.33] 72ms 0.065% 88.83% 587ms 0.53% std::_Rb_tree::_M_emplace_hint_unique 233ms 0.21% 89.04% 576ms 0.52% Node::AddElement