File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 31270ms, 86.95% of 35962ms total Dropped 862 nodes (cum <= 179.81ms) flat flat% sum% cum cum% 0 0% 0% 35837ms 99.65% __libc_start_call_main 0 0% 0% 35837ms 99.65% __libc_start_main_impl 0 0% 0% 35837ms 99.65% _start 0 0% 0% 35819ms 99.60% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 35819ms 99.60% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 35819ms 99.60% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 35819ms 99.60% main 0 0% 0% 35781ms 99.50% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 35781ms 99.50% CxxTest::TestRunner::runTest (inline) 0 0% 0% 35781ms 99.50% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 35772ms 99.47% AbstractCellBasedSimulation::Solve 2ms 0.0056% 0.0056% 24654ms 68.56% OffLatticeSimulation::UpdateCellLocationsAndTopology 3ms 0.0083% 0.014% 19501ms 54.23% ForwardEulerNumericalMethod::UpdateAllNodePositions 16ms 0.044% 0.058% 19274ms 53.60% AbstractNumericalMethod::ComputeForcesIncludingDamping 165ms 0.46% 0.52% 18198ms 50.60% AbstractTwoBodyInteractionForce::AddForceContribution 1523ms 4.24% 4.75% 15380ms 42.77% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4812ms 13.38% 18.13% 10059ms 27.97% std::_Rb_tree::_M_lower_bound (inline) 0 0% 18.13% 9838ms 27.36% AbstractCellBasedSimulation::UpdateCellPopulation 438ms 1.22% 19.35% 9318ms 25.91% std::_Rb_tree::find (inline) 0 0% 19.35% 9318ms 25.91% std::map::find (inline) 215ms 0.6% 19.95% 9236ms 25.68% NodesOnlyMesh::GetNodeOrHaloNode 537ms 1.49% 21.44% 9005ms 25.04% AbstractMesh::GetNode 0 0% 21.44% 8692ms 24.17% NodeBasedCellPopulation::Update 421ms 1.17% 22.61% 8472ms 23.56% NodesOnlyMesh::SolveNodeMapping 10ms 0.028% 22.64% 6452ms 17.94% DistributedBoxCollection::CalculateInteriorNodePairs 212ms 0.59% 23.23% 5748ms 15.98% boost::numeric::ublas::vector_assign (inline) 172ms 0.48% 23.71% 5621ms 15.63% boost::numeric::ublas::c_vector::c_vector (partial-inline) 5209ms 14.48% 38.19% 5209ms 14.48% std::_Rb_tree::_S_right (inline) 0 0% 38.19% 4776ms 13.28% OffLatticeSimulation::ApplyBoundaries 15ms 0.042% 38.23% 4731ms 13.16% NodeAttributes::RemoveDuplicateNeighbours 3ms 0.0083% 38.24% 4574ms 12.72% std::__sort (inline) 0 0% 38.24% 4574ms 12.72% std::sort (inline) 1079ms 3.00% 41.24% 3552ms 9.88% boost::numeric::ublas::indexing_vector_assign 80ms 0.22% 41.47% 3360ms 9.34% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 2ms 0.0056% 41.47% 3200ms 8.90% AbstractCellPopulation::Iterator::operator++ (inline) 190ms 0.53% 42.00% 3168ms 8.81% AbstractCellPopulation::Iterator::IsRealCell (inline) 28ms 0.078% 42.08% 2720ms 7.56% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 169ms 0.47% 42.55% 2688ms 7.47% std::__introsort_loop 22ms 0.061% 42.61% 2536ms 7.05% PlaneBoundaryCondition::ImposeBoundaryCondition 0 0% 42.61% 2423ms 6.74% std::__unguarded_partition_pivot (inline) 167ms 0.46% 43.07% 2409ms 6.70% DistributedBoxCollection::AddPairsFromBox 57ms 0.16% 43.23% 2295ms 6.38% AbstractCellPopulation::GetLocationIndexUsingCell 10ms 0.028% 43.26% 2239ms 6.23% PlaneBoundaryCondition::VerifyBoundaryCondition 1161ms 3.23% 46.49% 2179ms 6.06% std::__unguarded_partition (inline) 3ms 0.0083% 46.50% 1880ms 5.23% std::__final_insertion_sort (inline) 186ms 0.52% 47.01% 1747ms 4.86% std::map::operator[] (partial-inline) 112ms 0.31% 47.32% 1654ms 4.60% std::__unguarded_insertion_sort (inline) 1641ms 4.56% 51.89% 1641ms 4.56% boost::numeric::ublas::same_impl_ex 152ms 0.42% 52.31% 1599ms 4.45% AbstractMesh::GetVectorFromAtoB 583ms 1.62% 53.93% 1597ms 4.44% std::__unguarded_linear_insert (inline) 1469ms 4.08% 58.02% 1469ms 4.08% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 58.02% 1330ms 3.70% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 58.02% 1316ms 3.66% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 58.02% 1282ms 3.56% std::_Rb_tree::lower_bound (inline) 0 0% 58.02% 1282ms 3.56% std::map::lower_bound (inline) 1256ms 3.49% 61.51% 1256ms 3.49% boost::numeric::ublas::c_vector::operator() 8ms 0.022% 61.53% 1215ms 3.38% DistributedBoxCollection::CalculateBoundaryNodePairs 1ms 0.0028% 61.53% 1203ms 3.35% NodeBasedCellPopulation::UpdateCellProcessLocation 7ms 0.019% 61.55% 1050ms 2.92% boost::numeric::ublas::detail::expression_type_check (inline) 206ms 0.57% 62.13% 1015ms 2.82% boost::numeric::ublas::detail::equals 208ms 0.58% 62.71% 998ms 2.78% boost::numeric::ublas::vector_binary::size (inline) 5ms 0.014% 62.72% 997ms 2.77% AbstractCentreBasedCellPopulation::GetDampingConstant 19ms 0.053% 62.77% 976ms 2.71% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 327ms 0.91% 63.68% 928ms 2.58% NodeAttributes::AddNeighbour 423ms 1.18% 64.86% 924ms 2.57% DistributedBoxCollection::CalculateContainingBox (partial-inline) 31ms 0.086% 64.94% 924ms 2.57% std::_Rb_tree_const_iterator::operator++ (inline) 223ms 0.62% 65.56% 915ms 2.54% NodeAttributes::AddAppliedForceContribution 879ms 2.44% 68.01% 879ms 2.44% std::_Rb_tree_increment 575ms 1.60% 69.61% 775ms 2.16% __dynamic_cast 0 0% 69.61% 773ms 2.15% AbstractCellPopulation::WriteResultsToFiles 117ms 0.33% 69.93% 755ms 2.10% std::__new_allocator::allocate (inline) 11ms 0.031% 69.96% 746ms 2.07% CellPropertyCollection::GetPropertiesType (inline) 0 0% 69.96% 744ms 2.07% boost::numeric::ublas::norm_inf (inline) 497ms 1.38% 71.34% 744ms 2.07% boost::numeric::ublas::vector_norm_inf::apply (inline) 599ms 1.67% 73.01% 702ms 1.95% std::vector::push_back (inline) 0 0% 73.01% 692ms 1.92% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 73.01% 692ms 1.92% boost::numeric::ublas::c_vector::plus_assign (inline) 5ms 0.014% 73.02% 678ms 1.89% AbstractCellBasedSimulation::DoCellBirth 11ms 0.031% 73.05% 664ms 1.85% Cell::GetMutationState 78ms 0.22% 73.27% 638ms 1.77% operator new 0 0% 73.27% 586ms 1.63% boost::numeric::ublas::norm_2 (inline) 457ms 1.27% 74.54% 586ms 1.63% boost::numeric::ublas::vector_norm_2::apply (inline) 199ms 0.55% 75.10% 555ms 1.54% __GI___libc_malloc 2ms 0.0056% 75.10% 515ms 1.43% NodeBasedCellPopulation::WriteVtkResultsToFile 145ms 0.4% 75.50% 488ms 1.36% __GI___libc_free 0 0% 75.50% 467ms 1.30% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 75.50% 448ms 1.25% std::allocator_traits::allocate (inline) 6ms 0.017% 75.52% 446ms 1.24% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 4ms 0.011% 75.53% 424ms 1.18% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 421ms 1.17% 76.70% 421ms 1.17% Node::GetIndex 10ms 0.028% 76.73% 418ms 1.16% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 76.73% 414ms 1.15% std::_Rb_tree::_M_create_node (inline) 38ms 0.11% 76.84% 408ms 1.13% boost::detail::shared_count::~shared_count (inline) 0 0% 76.84% 408ms 1.13% boost::shared_ptr::~shared_ptr (inline) 1ms 0.0028% 76.84% 370ms 1.03% AbstractCellProperty::IsSubType (inline) 0 0% 76.84% 369ms 1.03% boost::numeric::ublas::inner_prod (inline) 353ms 0.98% 77.82% 364ms 1.01% boost::detail::sp_counted_base::release 1ms 0.0028% 77.82% 363ms 1.01% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 17ms 0.047% 77.87% 362ms 1.01% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 77.87% 345ms 0.96% std::_Rb_tree::_M_get_node (inline) 344ms 0.96% 78.83% 344ms 0.96% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 70ms 0.19% 79.02% 342ms 0.95% Node::GetRadius 292ms 0.81% 79.83% 342ms 0.95% _int_free 4ms 0.011% 79.85% 337ms 0.94% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 30ms 0.083% 79.93% 337ms 0.94% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 79.93% 337ms 0.94% boost::numeric::ublas::vector::vector (inline) 1ms 0.0028% 79.93% 335ms 0.93% NodesOnlyMesh::ReMesh 105ms 0.29% 80.22% 335ms 0.93% std::_Rb_tree::_M_erase (partial-inline) 4ms 0.011% 80.23% 322ms 0.9% NodesOnlyMesh::UpdateNodeIndices 11ms 0.031% 80.27% 320ms 0.89% DistributedBoxCollection::GetProcessOwningNode 1ms 0.0028% 80.27% 318ms 0.88% NodesOnlyMesh::UpdateBoxCollection 286ms 0.8% 81.06% 317ms 0.88% Node::AddNeighbour 3ms 0.0083% 81.07% 302ms 0.84% NodeBasedCellPopulation::UpdateMapsAfterRemesh 295ms 0.82% 81.89% 295ms 0.82% Node::CheckForNodeAttributes 115ms 0.32% 82.21% 295ms 0.82% boost::numeric::ublas::vector_inner_prod::apply (inline) 20ms 0.056% 82.27% 295ms 0.82% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 82.27% 288ms 0.8% boost::numeric::ublas::c_vector::assign (inline) 0 0% 82.27% 287ms 0.8% Cell::HasCellProperty (inline) 5ms 0.014% 82.28% 287ms 0.8% CellPropertyCollection::HasProperty 283ms 0.79% 83.07% 283ms 0.79% __gnu_cxx::__normal_iterator::operator++ (inline) 12ms 0.033% 83.10% 281ms 0.78% Cell::ReadyToDivide 6ms 0.017% 83.12% 279ms 0.78% std::_Rb_tree::_M_emplace_hint_unique 23ms 0.064% 83.18% 272ms 0.76% std::_Rb_tree::_M_copy (inline) 12ms 0.033% 83.22% 266ms 0.74% boost::numeric::ublas::vector_reference::operator() (inline) 132ms 0.37% 83.58% 265ms 0.74% _int_malloc 0 0% 83.58% 262ms 0.73% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 83.58% 262ms 0.73% VtkMeshWriter::WriteFiles 0 0% 83.58% 258ms 0.72% std::_Rb_tree::_Alloc_node::operator() (inline) 37ms 0.1% 83.69% 249ms 0.69% std::_Rb_tree::_M_clone_node (inline) 246ms 0.68% 84.37% 246ms 0.68% [libchaste_mesh.so] 4ms 0.011% 84.38% 244ms 0.68% NodesOnlyMesh::AddNodesToBoxes 243ms 0.68% 85.06% 243ms 0.68% [libchaste_cell_based.so] 107ms 0.3% 85.35% 241ms 0.67% std::__move_median_to_first (inline) 1ms 0.0028% 85.36% 232ms 0.65% vtkStreamingDemandDrivenPipeline::Update 0 0% 85.36% 232ms 0.65% vtkXMLWriterBase::Write 0 0% 85.36% 230ms 0.64% vtkDemandDrivenPipeline::ProcessRequest 0 0% 85.36% 228ms 0.63% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 85.36% 226ms 0.63% vtkDemandDrivenPipeline::ExecuteData 0 0% 85.36% 224ms 0.62% vtkCompositeDataPipeline::ExecuteData 12ms 0.033% 85.39% 223ms 0.62% std::__insertion_sort (inline) 0 0% 85.39% 223ms 0.62% vtkExecutive::CallAlgorithm 0 0% 85.39% 223ms 0.62% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 85.39% 210ms 0.58% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 85.39% 209ms 0.58% std::_Rb_tree::_M_drop_node (inline) 3ms 0.0083% 85.40% 207ms 0.58% std::__new_allocator::deallocate (inline) 202ms 0.56% 85.96% 202ms 0.56% NodeBasedCellPopulation::GetNode 0 0% 85.96% 195ms 0.54% std::_Rb_tree::clear (inline) 69ms 0.19% 86.15% 191ms 0.53% std::__find_if (inline) 0 0% 86.15% 191ms 0.53% std::find_if (inline) 0 0% 86.15% 191ms 0.53% std::none_of (inline) 98ms 0.27% 86.42% 188ms 0.52% boost::shared_ptr::shared_ptr (inline) 0 0% 86.42% 188ms 0.52% std::allocator_traits::deallocate (inline) 186ms 0.52% 86.94% 186ms 0.52% __strcmp_avx2 0 0% 86.94% 185ms 0.51% std::_Rb_tree::_M_put_node (inline) 4ms 0.011% 86.95% 182ms 0.51% AbstractCellProperty::IsType (inline) 0 0% 86.95% 180ms 0.5% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 86.95% 180ms 0.5% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData