File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 98446ms, 89.72% of 109720ms total Dropped 852 nodes (cum <= 548.60ms) flat flat% sum% cum cum% 0 0% 0% 109278ms 99.60% __libc_start_call_main 0 0% 0% 109278ms 99.60% __libc_start_main_impl 0 0% 0% 109278ms 99.60% _start 0 0% 0% 109259ms 99.58% main 0 0% 0% 109222ms 99.55% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 6ms 0.0055% 0.0055% 109214ms 99.54% AbstractCellBasedSimulation::Solve 342ms 0.31% 0.32% 56732ms 51.71% OffLatticeSimulation::UpdateCellLocationsAndTopology 63ms 0.057% 0.37% 53488ms 48.75% ForwardEulerNumericalMethod::UpdateAllNodePositions 282ms 0.26% 0.63% 52478ms 47.83% AbstractNumericalMethod::ComputeForcesIncludingDamping 1611ms 1.47% 2.10% 40541ms 36.95% NagaiHondaForce::AddForceContribution 3ms 0.0027% 2.10% 39564ms 36.06% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00091% 2.10% 24521ms 22.35% VertexBasedCellPopulation::Update 1ms 0.00091% 2.10% 24391ms 22.23% MutableVertexMesh::ReMesh 16332ms 14.89% 16.99% 23207ms 21.15% Cylindrical2dVertexMesh::GetVectorFromAtoB 150ms 0.14% 17.13% 17464ms 15.92% Cell::ReadyToDivide 115ms 0.1% 17.23% 16298ms 14.85% AbstractPhaseBasedCellCycleModel::ReadyToDivide 832ms 0.76% 17.99% 14778ms 13.47% NagaiHondaForce::GetAdhesionParameter 284ms 0.26% 18.25% 13849ms 12.62% SimpleWntCellCycleModel::UpdateCellCyclePhase 303ms 0.28% 18.52% 12106ms 11.03% MutableVertexMesh::CheckForIntersections 219ms 0.2% 18.72% 11439ms 10.43% VertexBasedCellPopulation::GetDampingConstant 3292ms 3.00% 21.72% 11153ms 10.16% __dynamic_cast 113ms 0.1% 21.83% 10430ms 9.51% AbstractTargetAreaModifier::UpdateTargetAreas 308ms 0.28% 22.11% 10331ms 9.42% AbstractCellBasedSimulation::DoCellBirth 145ms 0.13% 22.24% 10315ms 9.40% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 2092ms 1.91% 24.15% 9361ms 8.53% std::_Rb_tree::_M_erase 667ms 0.61% 24.75% 9119ms 8.31% VertexMesh::GetNextEdgeGradientOfElementAtNode 870ms 0.79% 25.55% 8988ms 8.19% VertexMesh::ElementIncludesPoint 810ms 0.74% 26.29% 8901ms 8.11% VertexBasedCellPopulation::GetLocationOfCellCentre 776ms 0.71% 26.99% 8824ms 8.04% operator new 590ms 0.54% 27.53% 8702ms 7.93% Cell::GetMutationState 653ms 0.6% 28.13% 8364ms 7.62% VertexMesh::GetCentroidOfElement 3407ms 3.11% 31.23% 7939ms 7.24% __GI___libc_free 3066ms 2.79% 34.03% 7870ms 7.17% __GI___libc_malloc 35ms 0.032% 34.06% 7838ms 7.14% MutableVertexMesh::RemoveDeletedNodesAndElements 4906ms 4.47% 38.53% 7697ms 7.02% boost::numeric::ublas::indexing_vector_assign 1617ms 1.47% 40.00% 7189ms 6.55% AbstractMesh::GetDistanceBetweenNodes 116ms 0.11% 40.11% 6485ms 5.91% SimpleWntCellCycleModel::GetWntLevel 181ms 0.16% 40.27% 6275ms 5.72% WntConcentration::GetWntLevel 2964ms 2.70% 42.97% 6229ms 5.68% std::_Rb_tree::_M_copy 6064ms 5.53% 48.50% 6064ms 5.53% __strcmp_avx2 47ms 0.043% 48.54% 5520ms 5.03% MutableVertexMesh::RemoveDeletedNodes 2714ms 2.47% 51.02% 5396ms 4.92% __cxxabiv1::__si_class_type_info::__do_dyncast 79ms 0.072% 51.09% 5356ms 4.88% EdgeHelper::RemoveDeletedEdges 1629ms 1.48% 52.57% 5088ms 4.64% EdgeHelper::UpdateEdgesMapKey 340ms 0.31% 52.88% 4860ms 4.43% MutableElement::ResetIndex 4693ms 4.28% 57.16% 4693ms 4.28% boost::numeric::ublas::c_vector::operator() 4182ms 3.81% 60.97% 4522ms 4.12% _int_free 1200ms 1.09% 62.07% 4427ms 4.03% std::__set_intersection 295ms 0.27% 62.34% 4309ms 3.93% AbstractCellPopulation::GetCellUsingLocationIndex 4030ms 3.67% 66.01% 4030ms 3.67% boost::numeric::ublas::same_impl_ex 174ms 0.16% 66.17% 3951ms 3.60% Cell::GetCellProliferativeType 176ms 0.16% 66.33% 3604ms 3.28% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1049ms 0.96% 67.28% 3238ms 2.95% AbstractElement::GetNodeLocation 105ms 0.096% 67.38% 3172ms 2.89% Cell::SetCellProliferativeType 2223ms 2.03% 69.41% 3168ms 2.89% _int_malloc 2333ms 2.13% 71.53% 3156ms 2.88% std::_Rb_tree::erase 621ms 0.57% 72.10% 3141ms 2.86% boost::numeric::ublas::vector_assign 2875ms 2.62% 74.72% 2883ms 2.63% std::map::operator[] 261ms 0.24% 74.96% 2561ms 2.33% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 74.96% 2461ms 2.24% AbstractCellPopulation::WriteResultsToFiles 1215ms 1.11% 76.06% 2419ms 2.20% AbstractCellProperty::IsSame 150ms 0.14% 76.20% 2332ms 2.13% Cell::GetCellData 146ms 0.13% 76.33% 2328ms 2.12% VertexMesh::GetVolumeOfElement 154ms 0.14% 76.47% 2322ms 2.12% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 2137ms 1.95% 78.42% 2137ms 1.95% std::_Rb_tree_increment 4ms 0.0036% 78.43% 2033ms 1.85% VertexBasedCellPopulation::WriteVtkResultsToFile 7ms 0.0064% 78.43% 2018ms 1.84% VertexBasedCellPopulation::WriteCellVtkResultsToFile 212ms 0.19% 78.62% 1848ms 1.68% std::_Rb_tree::_Rb_tree 79ms 0.072% 78.70% 1846ms 1.68% MutableVertexMesh::CheckForSwapsFromShortEdges 153ms 0.14% 78.84% 1827ms 1.67% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 78.84% 1821ms 1.66% VertexMeshWriter::WriteVtkUsingMesh 33ms 0.03% 78.87% 1650ms 1.50% VertexMesh::GetSurfaceAreaOfElement 35ms 0.032% 78.90% 1634ms 1.49% Node::RemoveElement 864ms 0.79% 79.69% 1603ms 1.46% AbstractCellPopulation::GetLocationIndexUsingCell 871ms 0.79% 80.48% 1513ms 1.38% CellPropertyCollection::AddProperty 0 0% 80.48% 1459ms 1.33% tcache_get (inline) 1459ms 1.33% 81.81% 1459ms 1.33% tcache_get_n (inline) 3ms 0.0027% 81.81% 1297ms 1.18% OffLatticeSimulation::ApplyBoundaries 1205ms 1.10% 82.91% 1205ms 1.10% Node::rGetLocation 1083ms 0.99% 83.90% 1083ms 0.99% [libchaste_cell_based.so] 223ms 0.2% 84.10% 1077ms 0.98% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 1066ms 0.97% 85.07% 1066ms 0.97% std::_Rb_tree_insert_and_rebalance 11ms 0.01% 85.08% 1059ms 0.97% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 161ms 0.15% 85.23% 975ms 0.89% CellPropertyRegistry::Get 698ms 0.64% 85.86% 958ms 0.87% Edge::GetMapIndex 915ms 0.83% 86.70% 915ms 0.83% [libchaste_mesh.so] 708ms 0.65% 87.34% 885ms 0.81% boost::numeric::ublas::detail::equals 4ms 0.0036% 87.35% 862ms 0.79% VertexMeshWriter::MakeVtkMesh 194ms 0.18% 87.52% 839ms 0.76% MutableElement::GetNodeLocalIndex 762ms 0.69% 88.22% 762ms 0.69% Node::GetIndex 187ms 0.17% 88.39% 745ms 0.68% Edge::AddElement 0 0% 88.39% 611ms 0.56% vtkPolygon::New 0 0% 88.39% 611ms 0.56% vtkPolygon::vtkPolygon 43ms 0.039% 88.43% 597ms 0.54% std::_Rb_tree::_M_emplace_hint_unique 590ms 0.54% 88.97% 590ms 0.54% [libstdc++.so.6.0.33] 587ms 0.53% 89.50% 587ms 0.53% operator delete 245ms 0.22% 89.72% 554ms 0.5% Node::AddElement