File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 23124ms, 91.57% of 25254ms total Dropped 628 nodes (cum <= 126.27ms) flat flat% sum% cum cum% 0 0% 0% 25122ms 99.48% __libc_start_call_main 0 0% 0% 25122ms 99.48% __libc_start_main_impl 0 0% 0% 25122ms 99.48% _start 0 0% 0% 25104ms 99.41% main 0 0% 0% 25064ms 99.25% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.004% 0.004% 25055ms 99.21% AbstractCellBasedSimulation::Solve 60ms 0.24% 0.24% 14211ms 56.27% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.0079% 0.25% 9573ms 37.91% AbstractCellBasedSimulation::UpdateCellPopulation 10ms 0.04% 0.29% 9354ms 37.04% ForwardEulerNumericalMethod::UpdateAllNodePositions 34ms 0.13% 0.42% 9159ms 36.27% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.004% 0.43% 8480ms 33.58% NodeBasedCellPopulation::Update 2010ms 7.96% 8.39% 8322ms 32.95% RepulsionForce::AddForceContribution 19ms 0.075% 8.46% 6387ms 25.29% DistributedBoxCollection::CalculateInteriorNodePairs 2025ms 8.02% 16.48% 4651ms 18.42% NodeAttributes::RemoveDuplicateNeighbours 0 0% 16.48% 4507ms 17.85% OffLatticeSimulation::ApplyBoundaries 268ms 1.06% 17.54% 4194ms 16.61% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 281ms 1.11% 18.65% 2692ms 10.66% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2614ms 10.35% 29.01% 2614ms 10.35% std::__introsort_loop 152ms 0.6% 29.61% 2443ms 9.67% AbstractMesh::GetNode 54ms 0.21% 29.82% 2417ms 9.57% NodesOnlyMesh::GetNodeOrHaloNode 180ms 0.71% 30.53% 2417ms 9.57% PlaneBoundaryCondition::ImposeBoundaryCondition 369ms 1.46% 31.99% 2325ms 9.21% DistributedBoxCollection::AddPairsFromBox 2293ms 9.08% 41.07% 2293ms 9.08% NodesOnlyMesh::SolveNodeMapping 1249ms 4.95% 46.02% 2261ms 8.95% AbstractCellPopulation::GetLocationIndexUsingCell 2065ms 8.18% 54.20% 2113ms 8.37% std::map::operator[] 159ms 0.63% 54.83% 2090ms 8.28% PlaneBoundaryCondition::VerifyBoundaryCondition 140ms 0.55% 55.38% 1750ms 6.93% AbstractCellPopulation::GetCellUsingLocationIndex 20ms 0.079% 55.46% 1727ms 6.84% NodeBasedCellPopulation::GetCellUsingLocationIndex 0 0% 55.46% 1202ms 4.76% NodeBasedCellPopulation::UpdateCellProcessLocation 6ms 0.024% 55.48% 1106ms 4.38% DistributedBoxCollection::CalculateBoundaryNodePairs 318ms 1.26% 56.74% 994ms 3.94% __dynamic_cast 98ms 0.39% 57.13% 884ms 3.50% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 181ms 0.72% 57.85% 846ms 3.35% AbstractMesh::GetVectorFromAtoB 842ms 3.33% 61.18% 842ms 3.33% std::_Rb_tree_increment 827ms 3.27% 64.46% 829ms 3.28% NodeAttributes::AddNeighbour 455ms 1.80% 66.26% 818ms 3.24% DistributedBoxCollection::CalculateContainingBox 0 0% 66.26% 758ms 3.00% AbstractCellPopulation::WriteResultsToFiles 6ms 0.024% 66.28% 736ms 2.91% AbstractCentreBasedCellPopulation::GetDampingConstant 736ms 2.91% 69.20% 736ms 2.91% __memcpy_avx_unaligned_erms 465ms 1.84% 71.04% 701ms 2.78% boost::numeric::ublas::indexing_vector_assign 58ms 0.23% 71.27% 653ms 2.59% AbstractCellBasedSimulation::DoCellBirth 275ms 1.09% 72.36% 550ms 2.18% __cxxabiv1::__si_class_type_info::__do_dyncast 544ms 2.15% 74.51% 544ms 2.15% boost::numeric::ublas::same_impl_ex 63ms 0.25% 74.76% 536ms 2.12% Cell::GetMutationState 514ms 2.04% 76.80% 514ms 2.04% boost::numeric::ublas::c_vector::operator() 12ms 0.048% 76.84% 506ms 2.00% NodeBasedCellPopulation::WriteVtkResultsToFile 316ms 1.25% 78.09% 491ms 1.94% std::_Rb_tree::_M_copy 25ms 0.099% 78.19% 452ms 1.79% operator new 451ms 1.79% 79.98% 451ms 1.79% __strcmp_avx2 80ms 0.32% 80.30% 448ms 1.77% std::_Rb_tree::_Rb_tree 136ms 0.54% 80.83% 421ms 1.67% std::_Rb_tree::_M_erase 31ms 0.12% 80.96% 419ms 1.66% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 123ms 0.49% 81.44% 414ms 1.64% __GI___libc_malloc 80ms 0.32% 81.76% 373ms 1.48% Node::GetRadius 237ms 0.94% 82.70% 352ms 1.39% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 82.70% 327ms 1.29% NodesOnlyMesh::ReMesh 42ms 0.17% 82.87% 322ms 1.28% NodeBasedCellPopulation::UpdateMapsAfterRemesh 95ms 0.38% 83.24% 315ms 1.25% NodesOnlyMesh::UpdateNodeIndices 11ms 0.044% 83.29% 313ms 1.24% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 298ms 1.18% 84.47% 298ms 1.18% Node::CheckForNodeAttributes 9ms 0.036% 84.50% 296ms 1.17% DistributedBoxCollection::GetProcessOwningNode 0 0% 84.50% 278ms 1.10% NodesOnlyMesh::UpdateBoxCollection 34ms 0.13% 84.64% 274ms 1.08% Cell::ReadyToDivide 21ms 0.083% 84.72% 272ms 1.08% std::_Rb_tree::_M_emplace_hint_unique 264ms 1.05% 85.76% 264ms 1.05% Node::AddNeighbour 262ms 1.04% 86.80% 262ms 1.04% Node::GetIndex 0 0% 86.80% 258ms 1.02% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 86.80% 256ms 1.01% VtkMeshWriter::WriteFiles 76ms 0.3% 87.10% 249ms 0.99% __GI___libc_free 120ms 0.48% 87.58% 248ms 0.98% _int_malloc 59ms 0.23% 87.81% 239ms 0.95% boost::numeric::ublas::c_vector::c_vector 5ms 0.02% 87.83% 218ms 0.86% NodesOnlyMesh::AddNodesToBoxes 0 0% 87.83% 218ms 0.86% vtkStreamingDemandDrivenPipeline::Update 0 0% 87.83% 218ms 0.86% vtkXMLWriterBase::Write 0 0% 87.83% 217ms 0.86% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 87.83% 216ms 0.86% vtkDemandDrivenPipeline::ProcessRequest 0 0% 87.83% 215ms 0.85% vtkDemandDrivenPipeline::ExecuteData 0 0% 87.83% 214ms 0.85% vtkCompositeDataPipeline::ExecuteData 0 0% 87.83% 214ms 0.85% vtkExecutive::CallAlgorithm 0 0% 87.83% 214ms 0.85% vtkXMLUnstructuredDataWriter::ProcessRequest 208ms 0.82% 88.66% 208ms 0.82% [libchaste_mesh.so] 0 0% 88.66% 187ms 0.74% NodesOnlyMesh::ResizeBoxCollection 26ms 0.1% 88.76% 186ms 0.74% NodesOnlyMesh::IsANodeCloseToDomainBoundary 185ms 0.73% 89.49% 185ms 0.73% [libchaste_cell_based.so] 0 0% 89.49% 185ms 0.73% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 89.49% 185ms 0.73% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 89.49% 179ms 0.71% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 159ms 0.63% 90.12% 172ms 0.68% _int_free 164ms 0.65% 90.77% 164ms 0.65% boost::detail::sp_counted_base::release 13ms 0.051% 90.82% 160ms 0.63% Cell::GetCellId 1ms 0.004% 90.83% 155ms 0.61% vtkXMLWriter::WriteBinaryData 87ms 0.34% 91.17% 154ms 0.61% AbstractCellProperty::IsSame 0 0% 91.17% 151ms 0.6% vtkXMLWriter::WriteBinaryDataBlock 0 0% 91.17% 151ms 0.6% vtkXMLWriter::WriteBinaryDataInternal 0 0% 91.17% 149ms 0.59% vtkXMLWriter::WriteCompressionBlock 6ms 0.024% 91.19% 148ms 0.59% AbstractCellPopulation::SetCellUsingLocationIndex 6ms 0.024% 91.22% 148ms 0.59% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 1ms 0.004% 91.22% 143ms 0.57% vtkXMLWriter::WritePointsAppendedData 4ms 0.016% 91.24% 137ms 0.54% AbstractNumericalMethod::SafeNodePositionUpdate 12ms 0.048% 91.28% 130ms 0.51% DistributedBoxCollection::GetIsPeriodicAllDims 71ms 0.28% 91.57% 129ms 0.51% AbstractCellCycleModel::GetAge