File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 98569ms, 89.15% of 110562ms total Dropped 882 nodes (cum <= 552.81ms) flat flat% sum% cum cum% 0 0% 0% 110221ms 99.69% __libc_start_call_main 0 0% 0% 110221ms 99.69% __libc_start_main_impl 0 0% 0% 110221ms 99.69% _start 0 0% 0% 110200ms 99.67% main 0 0% 0% 110160ms 99.64% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0018% 0.0018% 110152ms 99.63% AbstractCellBasedSimulation::Solve 387ms 0.35% 0.35% 57239ms 51.77% OffLatticeSimulation::UpdateCellLocationsAndTopology 64ms 0.058% 0.41% 53836ms 48.69% ForwardEulerNumericalMethod::UpdateAllNodePositions 317ms 0.29% 0.7% 52800ms 47.76% AbstractNumericalMethod::ComputeForcesIncludingDamping 1604ms 1.45% 2.15% 40508ms 36.64% NagaiHondaForce::AddForceContribution 1ms 0.0009% 2.15% 39601ms 35.82% AbstractCellBasedSimulation::UpdateCellPopulation 10ms 0.009% 2.16% 24332ms 22.01% VertexBasedCellPopulation::Update 1ms 0.0009% 2.16% 24175ms 21.87% MutableVertexMesh::ReMesh 16992ms 15.37% 17.53% 23171ms 20.96% Cylindrical2dVertexMesh::GetVectorFromAtoB 193ms 0.17% 17.70% 17922ms 16.21% Cell::ReadyToDivide 67ms 0.061% 17.76% 16533ms 14.95% AbstractPhaseBasedCellCycleModel::ReadyToDivide 918ms 0.83% 18.59% 14579ms 13.19% NagaiHondaForce::GetAdhesionParameter 250ms 0.23% 18.82% 14346ms 12.98% SimpleWntCellCycleModel::UpdateCellCyclePhase 312ms 0.28% 19.10% 11795ms 10.67% MutableVertexMesh::CheckForIntersections 263ms 0.24% 19.34% 11721ms 10.60% VertexBasedCellPopulation::GetDampingConstant 3654ms 3.30% 22.64% 11472ms 10.38% __dynamic_cast 88ms 0.08% 22.72% 10783ms 9.75% AbstractTargetAreaModifier::UpdateTargetAreas 131ms 0.12% 22.84% 10691ms 9.67% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 244ms 0.22% 23.06% 10529ms 9.52% AbstractCellBasedSimulation::DoCellBirth 576ms 0.52% 23.58% 9425ms 8.52% VertexMesh::GetNextEdgeGradientOfElementAtNode 1867ms 1.69% 25.27% 8919ms 8.07% std::_Rb_tree::_M_erase 771ms 0.7% 25.97% 8854ms 8.01% operator new 863ms 0.78% 26.75% 8848ms 8.00% VertexBasedCellPopulation::GetLocationOfCellCentre 900ms 0.81% 27.56% 8620ms 7.80% VertexMesh::ElementIncludesPoint 522ms 0.47% 28.04% 8573ms 7.75% Cell::GetMutationState 614ms 0.56% 28.59% 8265ms 7.48% VertexMesh::GetCentroidOfElement 37ms 0.033% 28.62% 8018ms 7.25% MutableVertexMesh::RemoveDeletedNodesAndElements 2964ms 2.68% 31.31% 7862ms 7.11% __GI___libc_malloc 1787ms 1.62% 32.92% 7441ms 6.73% AbstractMesh::GetDistanceBetweenNodes 4708ms 4.26% 37.18% 7417ms 6.71% boost::numeric::ublas::indexing_vector_assign 2002ms 1.81% 38.99% 7335ms 6.63% __GI___libc_free 3413ms 3.09% 42.08% 6724ms 6.08% std::_Rb_tree::_M_copy 169ms 0.15% 42.23% 6459ms 5.84% SimpleWntCellCycleModel::GetWntLevel 203ms 0.18% 42.41% 6202ms 5.61% WntConcentration::GetWntLevel 6140ms 5.55% 47.97% 6140ms 5.55% __strcmp_avx2 44ms 0.04% 48.01% 5608ms 5.07% MutableVertexMesh::RemoveDeletedNodes 70ms 0.063% 48.07% 5425ms 4.91% EdgeHelper::RemoveDeletedEdges 2912ms 2.63% 50.70% 5399ms 4.88% __cxxabiv1::__si_class_type_info::__do_dyncast 5003ms 4.53% 55.23% 5319ms 4.81% _int_free 1659ms 1.50% 56.73% 5144ms 4.65% EdgeHelper::UpdateEdgesMapKey 313ms 0.28% 57.01% 4852ms 4.39% MutableElement::ResetIndex 371ms 0.34% 57.35% 4801ms 4.34% AbstractCellPopulation::GetCellUsingLocationIndex 4684ms 4.24% 61.59% 4684ms 4.24% boost::numeric::ublas::c_vector::operator() 908ms 0.82% 62.41% 4144ms 3.75% std::__set_intersection 120ms 0.11% 62.52% 3935ms 3.56% Cell::GetCellProliferativeType 3657ms 3.31% 65.82% 3657ms 3.31% boost::numeric::ublas::same_impl_ex 144ms 0.13% 65.95% 3569ms 3.23% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 133ms 0.12% 66.07% 3328ms 3.01% Cell::SetCellProliferativeType 2326ms 2.10% 68.18% 3258ms 2.95% _int_malloc 557ms 0.5% 68.68% 3211ms 2.90% boost::numeric::ublas::vector_assign 2258ms 2.04% 70.72% 3174ms 2.87% std::_Rb_tree::erase 3131ms 2.83% 73.56% 3140ms 2.84% std::map::operator[] 1164ms 1.05% 74.61% 3087ms 2.79% AbstractElement::GetNodeLocation 1384ms 1.25% 75.86% 2769ms 2.50% AbstractCellProperty::IsSame 274ms 0.25% 76.11% 2617ms 2.37% VertexMesh::GetAreaGradientOfElementAtNode 170ms 0.15% 76.26% 2523ms 2.28% Cell::GetCellData 0 0% 76.26% 2493ms 2.25% AbstractCellPopulation::WriteResultsToFiles 104ms 0.094% 76.36% 2348ms 2.12% VertexMesh::GetVolumeOfElement 99ms 0.09% 76.44% 2106ms 1.90% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 2089ms 1.89% 78.33% 2089ms 1.89% std::_Rb_tree_increment 1ms 0.0009% 78.34% 2050ms 1.85% VertexBasedCellPopulation::WriteVtkResultsToFile 282ms 0.26% 78.59% 2042ms 1.85% std::_Rb_tree::_Rb_tree 4ms 0.0036% 78.59% 2032ms 1.84% VertexBasedCellPopulation::WriteCellVtkResultsToFile 107ms 0.097% 78.69% 1851ms 1.67% MutableVertexMesh::CheckForSwapsFromShortEdges 137ms 0.12% 78.81% 1843ms 1.67% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 78.81% 1831ms 1.66% VertexMeshWriter::WriteVtkUsingMesh 965ms 0.87% 79.69% 1729ms 1.56% AbstractCellPopulation::GetLocationIndexUsingCell 64ms 0.058% 79.75% 1597ms 1.44% Node::RemoveElement 36ms 0.033% 79.78% 1567ms 1.42% VertexMesh::GetSurfaceAreaOfElement 868ms 0.79% 80.56% 1564ms 1.41% CellPropertyCollection::AddProperty 1ms 0.0009% 80.56% 1458ms 1.32% tcache_get (inline) 1457ms 1.32% 81.88% 1457ms 1.32% tcache_get_n (inline) 1ms 0.0009% 81.88% 1451ms 1.31% OffLatticeSimulation::ApplyBoundaries 1429ms 1.29% 83.18% 1429ms 1.29% [libchaste_cell_based.so] 250ms 0.23% 83.40% 1266ms 1.15% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 169ms 0.15% 83.55% 1191ms 1.08% CellPropertyRegistry::Get 5ms 0.0045% 83.56% 1108ms 1.00% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1079ms 0.98% 84.53% 1079ms 0.98% std::_Rb_tree_insert_and_rebalance 1009ms 0.91% 85.45% 1009ms 0.91% Node::rGetLocation 792ms 0.72% 86.16% 985ms 0.89% boost::numeric::ublas::detail::equals 3ms 0.0027% 86.17% 900ms 0.81% VertexMeshWriter::MakeVtkMesh 608ms 0.55% 86.72% 839ms 0.76% Edge::GetMapIndex 232ms 0.21% 86.93% 825ms 0.75% MutableElement::GetNodeLocalIndex 792ms 0.72% 87.64% 792ms 0.72% [libchaste_mesh.so] 169ms 0.15% 87.80% 745ms 0.67% Edge::AddElement 731ms 0.66% 88.46% 731ms 0.66% Node::GetIndex 705ms 0.64% 89.09% 705ms 0.64% [libstdc++.so.6.0.33] 1ms 0.0009% 89.09% 656ms 0.59% vtkPolygon::New 1ms 0.0009% 89.10% 655ms 0.59% vtkPolygon::vtkPolygon 63ms 0.057% 89.15% 628ms 0.57% std::_Rb_tree::_M_emplace_hint_unique