File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 29433ms, 88.83% of 33135ms total Dropped 810 nodes (cum <= 165.68ms) flat flat% sum% cum cum% 0 0% 0% 32981ms 99.54% __libc_start_call_main 0 0% 0% 32981ms 99.54% __libc_start_main_impl 0 0% 0% 32981ms 99.54% _start 0 0% 0% 32964ms 99.48% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 32964ms 99.48% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 32964ms 99.48% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 32964ms 99.48% main 0 0% 0% 32927ms 99.37% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 32927ms 99.37% CxxTest::TestRunner::runTest (inline) 0 0% 0% 32927ms 99.37% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 32919ms 99.35% AbstractCellBasedSimulation::Solve 1ms 0.003% 0.003% 22928ms 69.20% OffLatticeSimulation::UpdateCellLocationsAndTopology 4ms 0.012% 0.015% 18100ms 54.63% ForwardEulerNumericalMethod::UpdateAllNodePositions 9ms 0.027% 0.042% 17923ms 54.09% AbstractNumericalMethod::ComputeForcesIncludingDamping 201ms 0.61% 0.65% 17250ms 52.06% AbstractTwoBodyInteractionForce::AddForceContribution 1442ms 4.35% 5.00% 14385ms 43.41% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4306ms 13.00% 18.00% 9500ms 28.67% std::_Rb_tree::_M_lower_bound (inline) 0 0% 18.00% 8786ms 26.52% AbstractCellBasedSimulation::UpdateCellPopulation 326ms 0.98% 18.98% 8613ms 25.99% std::_Rb_tree::find (inline) 0 0% 18.98% 8613ms 25.99% std::map::find (inline) 132ms 0.4% 19.38% 8350ms 25.20% NodesOnlyMesh::GetNodeOrHaloNode 472ms 1.42% 20.80% 8210ms 24.78% AbstractMesh::GetNode 0 0% 20.80% 7744ms 23.37% NodeBasedCellPopulation::Update 302ms 0.91% 21.71% 7743ms 23.37% NodesOnlyMesh::SolveNodeMapping 7ms 0.021% 21.74% 5721ms 17.27% DistributedBoxCollection::CalculateInteriorNodePairs 241ms 0.73% 22.46% 5661ms 17.08% boost::numeric::ublas::vector_assign (inline) 176ms 0.53% 22.99% 5491ms 16.57% boost::numeric::ublas::c_vector::c_vector (partial-inline) 5177ms 15.62% 38.62% 5177ms 15.62% std::_Rb_tree::_S_right (inline) 1ms 0.003% 38.62% 4547ms 13.72% OffLatticeSimulation::ApplyBoundaries 12ms 0.036% 38.66% 4482ms 13.53% NodeAttributes::RemoveDuplicateNeighbours 13ms 0.039% 38.70% 4329ms 13.06% std::__sort (inline) 0 0% 38.70% 4329ms 13.06% std::sort (inline) 73ms 0.22% 38.92% 3440ms 10.38% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 5ms 0.015% 38.93% 3435ms 10.37% AbstractCellPopulation::Iterator::operator++ (inline) 182ms 0.55% 39.48% 3404ms 10.27% AbstractCellPopulation::Iterator::IsRealCell 1055ms 3.18% 42.66% 3252ms 9.81% boost::numeric::ublas::indexing_vector_assign 17ms 0.051% 42.72% 2891ms 8.72% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 168ms 0.51% 43.22% 2435ms 7.35% std::__introsort_loop 39ms 0.12% 43.34% 2363ms 7.13% PlaneBoundaryCondition::ImposeBoundaryCondition 42ms 0.13% 43.47% 2334ms 7.04% AbstractCellPopulation::GetLocationIndexUsingCell 17ms 0.051% 43.52% 2183ms 6.59% PlaneBoundaryCondition::VerifyBoundaryCondition 0 0% 43.52% 2182ms 6.59% std::__unguarded_partition_pivot (inline) 999ms 3.01% 46.53% 1969ms 5.94% std::__unguarded_partition (inline) 1ms 0.003% 46.54% 1880ms 5.67% std::__final_insertion_sort (inline) 145ms 0.44% 46.97% 1840ms 5.55% DistributedBoxCollection::AddPairsFromBox 232ms 0.7% 47.67% 1799ms 5.43% std::map::operator[] (partial-inline) 102ms 0.31% 47.98% 1671ms 5.04% std::__unguarded_insertion_sort (inline) 649ms 1.96% 49.94% 1642ms 4.96% std::__unguarded_linear_insert (inline) 1513ms 4.57% 54.51% 1513ms 4.57% boost::numeric::ublas::same_impl_ex 1457ms 4.40% 58.90% 1457ms 4.40% __gnu_cxx::__normal_iterator::operator-- (inline) 130ms 0.39% 59.30% 1382ms 4.17% AbstractMesh::GetVectorFromAtoB 0 0% 59.30% 1283ms 3.87% std::_Rb_tree::lower_bound (inline) 0 0% 59.30% 1283ms 3.87% std::map::lower_bound (inline) 0 0% 59.30% 1270ms 3.83% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 59.30% 1255ms 3.79% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 59.30% 1156ms 3.49% NodeBasedCellPopulation::UpdateCellProcessLocation 1146ms 3.46% 62.76% 1146ms 3.46% boost::numeric::ublas::c_vector::operator() 5ms 0.015% 62.77% 1072ms 3.24% DistributedBoxCollection::CalculateBoundaryNodePairs 18ms 0.054% 62.82% 1019ms 3.08% boost::numeric::ublas::detail::expression_type_check (inline) 169ms 0.51% 63.33% 973ms 2.94% boost::numeric::ublas::detail::equals 232ms 0.7% 64.04% 889ms 2.68% NodeAttributes::AddAppliedForceContribution 124ms 0.37% 64.41% 866ms 2.61% boost::numeric::ublas::vector_binary::size (inline) 14ms 0.042% 64.45% 821ms 2.48% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 383ms 1.16% 65.61% 804ms 2.43% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 65.61% 762ms 2.30% boost::numeric::ublas::norm_inf (inline) 452ms 1.36% 66.97% 762ms 2.30% boost::numeric::ublas::vector_norm_inf::apply (inline) 52ms 0.16% 67.13% 735ms 2.22% std::__new_allocator::allocate (inline) 190ms 0.57% 67.70% 731ms 2.21% NodeAttributes::AddNeighbour 0 0% 67.70% 730ms 2.20% AbstractCellPopulation::WriteResultsToFiles 502ms 1.52% 69.22% 717ms 2.16% __dynamic_cast 115ms 0.35% 69.56% 687ms 2.07% operator new 0 0% 69.56% 657ms 1.98% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 69.56% 657ms 1.98% boost::numeric::ublas::c_vector::plus_assign (inline) 250ms 0.75% 70.32% 651ms 1.96% __GI___libc_free 4ms 0.012% 70.33% 616ms 1.86% AbstractCentreBasedCellPopulation::GetDampingConstant 539ms 1.63% 71.96% 601ms 1.81% std::vector::push_back (inline) 4ms 0.012% 71.97% 578ms 1.74% AbstractCellBasedSimulation::DoCellBirth 218ms 0.66% 72.63% 567ms 1.71% __GI___libc_malloc 33ms 0.1% 72.73% 561ms 1.69% std::_Rb_tree_const_iterator::operator++ (inline) 516ms 1.56% 74.28% 516ms 1.56% std::_Rb_tree_increment 0 0% 74.28% 508ms 1.53% boost::numeric::ublas::norm_2 (inline) 411ms 1.24% 75.52% 508ms 1.53% boost::numeric::ublas::vector_norm_2::apply (inline) 7ms 0.021% 75.55% 500ms 1.51% CellPropertyCollection::GetPropertiesType (inline) 2ms 0.006% 75.55% 481ms 1.45% NodeBasedCellPopulation::WriteVtkResultsToFile 1ms 0.003% 75.55% 463ms 1.40% AbstractCellBasedSimulation::DoCellRemoval (inline) 7ms 0.021% 75.58% 445ms 1.34% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 5ms 0.015% 75.59% 437ms 1.32% Cell::GetMutationState 0 0% 75.59% 413ms 1.25% std::allocator_traits::allocate (inline) 358ms 1.08% 76.67% 399ms 1.20% _int_free 40ms 0.12% 76.79% 396ms 1.20% boost::detail::shared_count::~shared_count (inline) 0 0% 76.79% 396ms 1.20% boost::shared_ptr::~shared_ptr (inline) 390ms 1.18% 77.97% 390ms 1.18% Node::GetIndex 47ms 0.14% 78.11% 369ms 1.11% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 78.11% 369ms 1.11% boost::numeric::ublas::vector::vector (inline) 0 0% 78.11% 360ms 1.09% boost::numeric::ublas::inner_prod (inline) 4ms 0.012% 78.12% 358ms 1.08% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 25ms 0.075% 78.20% 354ms 1.07% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 78.20% 353ms 1.07% std::_Rb_tree::_M_create_node (inline) 10ms 0.03% 78.23% 352ms 1.06% boost::numeric::ublas::vector_reference::operator() (inline) 344ms 1.04% 79.27% 349ms 1.05% boost::detail::sp_counted_base::release 3ms 0.0091% 79.28% 329ms 0.99% AbstractCellProperty::IsSubType (inline) 0 0% 79.28% 318ms 0.96% NodesOnlyMesh::ReMesh 0 0% 79.28% 316ms 0.95% std::_Rb_tree::_M_get_node (inline) 2ms 0.006% 79.28% 308ms 0.93% NodesOnlyMesh::UpdateNodeIndices 306ms 0.92% 80.21% 306ms 0.92% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 116ms 0.35% 80.56% 300ms 0.91% Node::GetRadius 293ms 0.88% 81.44% 293ms 0.88% __gnu_cxx::__normal_iterator::operator++ (inline) 4ms 0.012% 81.45% 292ms 0.88% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 2ms 0.006% 81.46% 290ms 0.88% NodeBasedCellPopulation::UpdateMapsAfterRemesh 3ms 0.0091% 81.47% 285ms 0.86% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 8ms 0.024% 81.49% 284ms 0.86% std::_Rb_tree::_M_emplace_hint_unique 120ms 0.36% 81.85% 281ms 0.85% boost::numeric::ublas::vector_inner_prod::apply (inline) 5ms 0.015% 81.87% 280ms 0.85% AbstractCellPopulation::GetCellUsingLocationIndex 116ms 0.35% 82.22% 280ms 0.85% std::_Rb_tree::_M_erase (partial-inline) 8ms 0.024% 82.24% 273ms 0.82% DistributedBoxCollection::GetProcessOwningNode 0 0% 82.24% 263ms 0.79% NodesOnlyMesh::UpdateBoxCollection 0 0% 82.24% 261ms 0.79% boost::numeric::ublas::vector_binary::operator() (inline) 258ms 0.78% 83.02% 258ms 0.78% [libchaste_cell_based.so] 145ms 0.44% 83.46% 254ms 0.77% _int_malloc 0 0% 83.46% 232ms 0.7% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 1ms 0.003% 83.46% 231ms 0.7% VtkMeshWriter::WriteFiles 0 0% 83.46% 230ms 0.69% boost::numeric::ublas::c_vector::assign (inline) 104ms 0.31% 83.78% 230ms 0.69% std::__find_if (inline) 0 0% 83.78% 230ms 0.69% std::find_if (inline) 0 0% 83.78% 230ms 0.69% std::none_of (inline) 217ms 0.65% 84.43% 217ms 0.65% NodeBasedCellPopulation::GetNode 1ms 0.003% 84.43% 217ms 0.65% NodesOnlyMesh::AddNodesToBoxes 215ms 0.65% 85.08% 215ms 0.65% Node::rGetLocation 138ms 0.42% 85.50% 211ms 0.64% Node::AddAppliedForceContribution 98ms 0.3% 85.79% 211ms 0.64% std::__move_median_to_first (inline) 15ms 0.045% 85.84% 208ms 0.63% std::__insertion_sort (inline) 88ms 0.27% 86.11% 201ms 0.61% Node::AddNeighbour 0 0% 86.11% 200ms 0.6% vtkXMLWriterBase::Write 0 0% 86.11% 199ms 0.6% vtkStreamingDemandDrivenPipeline::Update 198ms 0.6% 86.70% 198ms 0.6% Node::CheckForNodeAttributes 0 0% 86.70% 197ms 0.59% vtkDemandDrivenPipeline::ProcessRequest 0 0% 86.70% 194ms 0.59% vtkDemandDrivenPipeline::ExecuteData 0 0% 86.70% 194ms 0.59% vtkExecutive::CallAlgorithm 0 0% 86.70% 194ms 0.59% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 86.70% 193ms 0.58% vtkCompositeDataPipeline::ExecuteData 1ms 0.003% 86.71% 193ms 0.58% vtkXMLUnstructuredDataWriter::ProcessRequest 189ms 0.57% 87.28% 190ms 0.57% Node::ConstructNodeAttributes (inline) 1ms 0.003% 87.28% 187ms 0.56% NodesOnlyMesh::ResizeBoxCollection 187ms 0.56% 87.84% 187ms 0.56% __strcmp_avx2 33ms 0.1% 87.94% 186ms 0.56% std::__new_allocator::deallocate (inline) 12ms 0.036% 87.98% 184ms 0.56% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 87.98% 183ms 0.55% std::_Rb_tree::_Alloc_node::operator() (inline) 92ms 0.28% 88.26% 181ms 0.55% boost::shared_ptr::shared_ptr (inline) 174ms 0.53% 88.78% 174ms 0.53% [libchaste_mesh.so] 11ms 0.033% 88.82% 173ms 0.52% Cell::ReadyToDivide 4ms 0.012% 88.83% 172ms 0.52% CellPropertyCollection::HasProperty 0 0% 88.83% 171ms 0.52% Cell::HasCellProperty (inline) 0 0% 88.83% 170ms 0.51% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 88.83% 167ms 0.5% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 88.83% 167ms 0.5% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 88.83% 166ms 0.5% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData