File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 94233ms, 91.00% of 103554ms total Dropped 841 nodes (cum <= 517.77ms) flat flat% sum% cum cum% 0 0% 0% 103283ms 99.74% __libc_start_call_main 0 0% 0% 103283ms 99.74% __libc_start_main_impl 0 0% 0% 103283ms 99.74% _start 0 0% 0% 103262ms 99.72% main 0 0% 0% 103229ms 99.69% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0019% 0.0019% 103222ms 99.68% AbstractCellBasedSimulation::Solve 337ms 0.33% 0.33% 54534ms 52.66% OffLatticeSimulation::UpdateCellLocationsAndTopology 74ms 0.071% 0.4% 51086ms 49.33% ForwardEulerNumericalMethod::UpdateAllNodePositions 141ms 0.14% 0.53% 50002ms 48.29% AbstractNumericalMethod::ComputeForcesIncludingDamping 1605ms 1.55% 2.08% 38949ms 37.61% NagaiHondaForce::AddForceContribution 2ms 0.0019% 2.09% 35515ms 34.30% AbstractCellBasedSimulation::UpdateCellPopulation 10ms 0.0097% 2.10% 21201ms 20.47% VertexBasedCellPopulation::Update 1ms 0.00097% 2.10% 21071ms 20.35% MutableVertexMesh::ReMesh 10415ms 10.06% 12.16% 18118ms 17.50% Cylindrical2dVertexMesh::GetVectorFromAtoB 159ms 0.15% 12.31% 17662ms 17.06% Cell::ReadyToDivide 37ms 0.036% 12.34% 16629ms 16.06% AbstractPhaseBasedCellCycleModel::ReadyToDivide 536ms 0.52% 12.86% 16135ms 15.58% NagaiHondaForce::GetAdhesionParameter 223ms 0.22% 13.08% 14138ms 13.65% SimpleWntCellCycleModel::UpdateCellCyclePhase 873ms 0.84% 13.92% 12346ms 11.92% operator new 3866ms 3.73% 17.65% 11134ms 10.75% __GI___libc_malloc 97ms 0.094% 17.75% 10793ms 10.42% AbstractTargetAreaModifier::UpdateTargetAreas 685ms 0.66% 18.41% 10726ms 10.36% VertexBasedCellPopulation::GetDampingConstant 91ms 0.088% 18.50% 10690ms 10.32% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 2870ms 2.77% 21.27% 10578ms 10.21% __dynamic_cast 341ms 0.33% 21.60% 10098ms 9.75% AbstractCellBasedSimulation::DoCellBirth 312ms 0.3% 21.90% 9659ms 9.33% MutableVertexMesh::CheckForIntersections 1646ms 1.59% 23.49% 9159ms 8.84% std::_Rb_tree::_M_erase 222ms 0.21% 23.70% 8405ms 8.12% Cell::GetMutationState 2047ms 1.98% 25.68% 7992ms 7.72% __GI___libc_free 573ms 0.55% 26.23% 7943ms 7.67% VertexMesh::GetNextEdgeGradientOfElementAtNode 509ms 0.49% 26.72% 7878ms 7.61% VertexBasedCellPopulation::GetLocationOfCellCentre 749ms 0.72% 27.45% 7578ms 7.32% VertexMesh::GetCentroidOfElement 19ms 0.018% 27.47% 7333ms 7.08% MutableVertexMesh::RemoveDeletedNodesAndElements 653ms 0.63% 28.10% 7107ms 6.86% VertexMesh::ElementIncludesPoint 3876ms 3.74% 31.84% 7106ms 6.86% boost::numeric::ublas::indexing_vector_assign 1357ms 1.31% 33.15% 6493ms 6.27% std::__set_intersection 1280ms 1.24% 34.39% 6249ms 6.03% AbstractMesh::GetDistanceBetweenNodes 162ms 0.16% 34.54% 6080ms 5.87% SimpleWntCellCycleModel::GetWntLevel 5927ms 5.72% 40.27% 5927ms 5.72% __strcmp_evex 1789ms 1.73% 41.99% 5927ms 5.72% std::_Rb_tree::_M_copy 5116ms 4.94% 46.93% 5892ms 5.69% _int_free 224ms 0.22% 47.15% 5800ms 5.60% WntConcentration::GetWntLevel 5730ms 5.53% 52.68% 5730ms 5.53% boost::numeric::ublas::c_vector::operator() 4526ms 4.37% 57.05% 5343ms 5.16% _int_malloc 2432ms 2.35% 59.40% 5289ms 5.11% __cxxabiv1::__si_class_type_info::__do_dyncast 61ms 0.059% 59.46% 5287ms 5.11% MutableVertexMesh::RemoveDeletedNodes 100ms 0.097% 59.56% 5127ms 4.95% EdgeHelper::RemoveDeletedEdges 1658ms 1.60% 61.16% 4862ms 4.70% EdgeHelper::UpdateEdgesMapKey 89ms 0.086% 61.25% 4521ms 4.37% Cell::GetCellProliferativeType 176ms 0.17% 61.42% 4394ms 4.24% MutableElement::ResetIndex 4341ms 4.19% 65.61% 4341ms 4.19% boost::numeric::ublas::same_impl_ex 389ms 0.38% 65.98% 4070ms 3.93% AbstractCellPopulation::GetCellUsingLocationIndex 3478ms 3.36% 69.34% 3478ms 3.36% [libchaste_cell_based.so] 295ms 0.28% 69.63% 3291ms 3.18% Cell::SetCellProliferativeType 301ms 0.29% 69.92% 3266ms 3.15% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 874ms 0.84% 70.76% 3074ms 2.97% AbstractElement::GetNodeLocation 416ms 0.4% 71.16% 2736ms 2.64% boost::numeric::ublas::vector_assign 2578ms 2.49% 73.65% 2587ms 2.50% std::map::operator[] 145ms 0.14% 73.79% 2432ms 2.35% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 1241ms 1.20% 74.99% 2426ms 2.34% std::_Rb_tree::erase 0 0% 74.99% 2354ms 2.27% AbstractCellPopulation::WriteResultsToFiles 119ms 0.11% 75.11% 2321ms 2.24% Cell::GetCellData 2263ms 2.19% 77.29% 2263ms 2.19% [libchaste_mesh.so] 274ms 0.26% 77.56% 2165ms 2.09% VertexMesh::GetAreaGradientOfElementAtNode 678ms 0.65% 78.21% 1990ms 1.92% AbstractCellProperty::IsSame 2ms 0.0019% 78.21% 1944ms 1.88% VertexBasedCellPopulation::WriteVtkResultsToFile 8ms 0.0077% 78.22% 1930ms 1.86% VertexBasedCellPopulation::WriteCellVtkResultsToFile 362ms 0.35% 78.57% 1921ms 1.86% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 130ms 0.13% 78.70% 1871ms 1.81% VertexMesh::GetVolumeOfElement 0 0% 78.70% 1752ms 1.69% VertexMeshWriter::WriteVtkUsingMesh 967ms 0.93% 79.63% 1703ms 1.64% CellPropertyCollection::AddProperty 76ms 0.073% 79.70% 1663ms 1.61% MutableVertexMesh::CheckForSwapsFromShortEdges 247ms 0.24% 79.94% 1588ms 1.53% std::_Rb_tree::_Rb_tree 1495ms 1.44% 81.38% 1495ms 1.44% std::_Rb_tree_increment 76ms 0.073% 81.46% 1462ms 1.41% VertexMesh::GetSurfaceAreaOfElement 0 0% 81.46% 1460ms 1.41% tcache_get (inline) 1460ms 1.41% 82.87% 1460ms 1.41% tcache_get_n (inline) 2ms 0.0019% 82.87% 1409ms 1.36% OffLatticeSimulation::ApplyBoundaries 464ms 0.45% 83.32% 1406ms 1.36% AbstractCellPopulation::GetLocationIndexUsingCell 294ms 0.28% 83.60% 1232ms 1.19% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 49ms 0.047% 83.65% 1193ms 1.15% Node::RemoveElement 128ms 0.12% 83.77% 1179ms 1.14% Edge::AddElement 225ms 0.22% 83.99% 1137ms 1.10% CellPropertyRegistry::Get 1107ms 1.07% 85.06% 1109ms 1.07% boost::detail::sp_counted_base::release 1054ms 1.02% 86.08% 1054ms 1.02% [libstdc++.so.6.0.33] 971ms 0.94% 87.01% 971ms 0.94% std::_Rb_tree_insert_and_rebalance 920ms 0.89% 87.90% 964ms 0.93% CellPropertyCollection::GetProperty 963ms 0.93% 88.83% 963ms 0.93% Node::rGetLocation 804ms 0.78% 89.61% 924ms 0.89% boost::numeric::ublas::detail::equals 40ms 0.039% 89.65% 918ms 0.89% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 2ms 0.0019% 89.65% 906ms 0.87% VertexMeshWriter::MakeVtkMesh 852ms 0.82% 90.47% 852ms 0.82% tcache_put (inline) 46ms 0.044% 90.52% 747ms 0.72% std::_Rb_tree::_M_emplace_hint_unique 2ms 0.0019% 90.52% 646ms 0.62% vtkPolygon::New 0 0% 90.52% 643ms 0.62% vtkPolygon::vtkPolygon 144ms 0.14% 90.66% 639ms 0.62% MutableElement::GetNodeLocalIndex 156ms 0.15% 90.81% 556ms 0.54% boost::numeric::ublas::c_vector::c_vector 197ms 0.19% 91.00% 531ms 0.51% Node::AddElement