File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 23433ms, 89.72% of 26117ms total Dropped 851 nodes (cum <= 130.59ms) flat flat% sum% cum cum% 0 0% 0% 25984ms 99.49% __libc_start_call_main 0 0% 0% 25984ms 99.49% __libc_start_main_impl 0 0% 0% 25984ms 99.49% _start 0 0% 0% 25966ms 99.42% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 25966ms 99.42% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 25966ms 99.42% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 25966ms 99.42% main 0 0% 0% 25920ms 99.25% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 25919ms 99.24% CxxTest::TestRunner::runTest (inline) 0 0% 0% 25919ms 99.24% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 25910ms 99.21% AbstractCellBasedSimulation::Solve 2ms 0.0077% 0.0077% 14710ms 56.32% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0077% 9920ms 37.98% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0077% 0.015% 9674ms 37.04% ForwardEulerNumericalMethod::UpdateAllNodePositions 9ms 0.034% 0.05% 9463ms 36.23% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.05% 8740ms 33.46% NodeBasedCellPopulation::Update 1382ms 5.29% 5.34% 8490ms 32.51% RepulsionForce::AddForceContribution (partial-inline) 14ms 0.054% 5.39% 6578ms 25.19% DistributedBoxCollection::CalculateInteriorNodePairs 2252ms 8.62% 14.02% 5261ms 20.14% std::_Rb_tree::_M_lower_bound (inline) 17ms 0.065% 14.08% 4685ms 17.94% NodeAttributes::RemoveDuplicateNeighbours 1ms 0.0038% 14.09% 4608ms 17.64% OffLatticeSimulation::ApplyBoundaries 2ms 0.0077% 14.09% 4504ms 17.25% std::__sort (inline) 0 0% 14.09% 4504ms 17.25% std::sort (inline) 197ms 0.75% 14.85% 4316ms 16.53% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 228ms 0.87% 15.72% 3386ms 12.96% std::_Rb_tree::find (inline) 0 0% 15.72% 3386ms 12.96% std::map::find (inline) 71ms 0.27% 15.99% 3312ms 12.68% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 4ms 0.015% 16.01% 3097ms 11.86% AbstractCellPopulation::Iterator::operator++ (inline) 154ms 0.59% 16.60% 3069ms 11.75% AbstractCellPopulation::Iterator::IsRealCell (inline) 2996ms 11.47% 28.07% 2996ms 11.47% std::_Rb_tree::_S_right (inline) 191ms 0.73% 28.80% 2700ms 10.34% std::__introsort_loop 29ms 0.11% 28.91% 2682ms 10.27% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 220ms 0.84% 29.75% 2660ms 10.18% std::map::operator[] (partial-inline) 142ms 0.54% 30.30% 2482ms 9.50% DistributedBoxCollection::AddPairsFromBox 160ms 0.61% 30.91% 2465ms 9.44% AbstractMesh::GetNode 21ms 0.08% 30.99% 2462ms 9.43% PlaneBoundaryCondition::ImposeBoundaryCondition 0 0% 30.99% 2432ms 9.31% std::__unguarded_partition_pivot (inline) 59ms 0.23% 31.22% 2423ms 9.28% NodesOnlyMesh::GetNodeOrHaloNode 48ms 0.18% 31.40% 2308ms 8.84% AbstractCellPopulation::GetLocationIndexUsingCell 106ms 0.41% 31.81% 2306ms 8.83% NodesOnlyMesh::SolveNodeMapping 12ms 0.046% 31.85% 2144ms 8.21% PlaneBoundaryCondition::VerifyBoundaryCondition 1046ms 4.01% 35.86% 2141ms 8.20% std::__unguarded_partition (inline) 0 0% 35.86% 2136ms 8.18% std::_Rb_tree::lower_bound (inline) 0 0% 35.86% 2136ms 8.18% std::map::lower_bound (inline) 22ms 0.084% 35.94% 1934ms 7.41% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 38ms 0.15% 36.09% 1907ms 7.30% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 36.09% 1798ms 6.88% std::__final_insertion_sort (inline) 130ms 0.5% 36.59% 1613ms 6.18% std::__unguarded_insertion_sort (inline) 554ms 2.12% 38.71% 1504ms 5.76% std::__unguarded_linear_insert (inline) 1366ms 5.23% 43.94% 1366ms 5.23% __gnu_cxx::__normal_iterator::operator-- (inline) 39ms 0.15% 44.09% 1315ms 5.04% boost::numeric::ublas::c_vector::c_vector (partial-inline) 1ms 0.0038% 44.09% 1204ms 4.61% NodeBasedCellPopulation::UpdateCellProcessLocation 13ms 0.05% 44.14% 1182ms 4.53% boost::numeric::ublas::vector_assign (inline) 8ms 0.031% 44.17% 1126ms 4.31% DistributedBoxCollection::CalculateBoundaryNodePairs 238ms 0.91% 45.08% 1063ms 4.07% boost::numeric::ublas::indexing_vector_assign 27ms 0.1% 45.19% 990ms 3.79% std::_Rb_tree_const_iterator::operator++ (inline) 13ms 0.05% 45.23% 977ms 3.74% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 299ms 1.14% 46.38% 971ms 3.72% __dynamic_cast 13ms 0.05% 46.43% 924ms 3.54% CellPropertyCollection::GetPropertiesType (inline) 924ms 3.54% 49.97% 924ms 3.54% std::_Rb_tree_increment 4ms 0.015% 49.98% 885ms 3.39% AbstractCentreBasedCellPopulation::GetDampingConstant 395ms 1.51% 51.50% 880ms 3.37% DistributedBoxCollection::CalculateContainingBox (partial-inline) 182ms 0.7% 52.19% 853ms 3.27% AbstractMesh::GetVectorFromAtoB 0 0% 52.19% 824ms 3.16% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 52.19% 812ms 3.11% boost::numeric::ublas::norm_2 (inline) 626ms 2.40% 54.59% 812ms 3.11% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 54.59% 812ms 3.11% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 7ms 0.027% 54.62% 792ms 3.03% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 54.62% 783ms 3.00% AbstractCellPopulation::WriteResultsToFiles 174ms 0.67% 55.28% 781ms 2.99% NodeAttributes::AddNeighbour 44ms 0.17% 55.45% 771ms 2.95% std::__copy_move::__copy_m (inline) 0 0% 55.45% 771ms 2.95% std::__copy_move_a (inline) 0 0% 55.45% 771ms 2.95% std::__copy_move_a1 (inline) 0 0% 55.45% 771ms 2.95% std::__copy_move_a2 (inline) 0 0% 55.45% 771ms 2.95% std::copy (inline) 753ms 2.88% 58.33% 753ms 2.88% __memcpy_avx_unaligned_erms 747ms 2.86% 61.19% 747ms 2.86% boost::numeric::ublas::c_vector::operator() 5ms 0.019% 61.21% 731ms 2.80% AbstractCellBasedSimulation::DoCellBirth 605ms 2.32% 63.53% 706ms 2.70% std::vector::push_back (inline) 29ms 0.11% 63.64% 682ms 2.61% std::_Rb_tree::_Rb_tree (partial-inline) 3ms 0.011% 63.65% 677ms 2.59% Cell::GetMutationState 133ms 0.51% 64.16% 653ms 2.50% std::__new_allocator::allocate (inline) 55ms 0.21% 64.37% 638ms 2.44% std::_Rb_tree::_M_copy (inline) 0 0% 64.37% 629ms 2.41% std::allocator_traits::allocate (inline) 0 0% 64.37% 592ms 2.27% std::_Rb_tree::_M_create_node (inline) 213ms 0.82% 65.19% 578ms 2.21% std::_Rb_tree::_M_clone_node (inline) 556ms 2.13% 67.32% 556ms 2.13% boost::numeric::ublas::same_impl_ex 268ms 1.03% 68.34% 554ms 2.12% __cxxabiv1::__si_class_type_info::__do_dyncast 3ms 0.011% 68.35% 544ms 2.08% std::set::set (inline) 192ms 0.74% 69.09% 534ms 2.04% std::_Rb_tree::_M_erase 0 0% 69.09% 527ms 2.02% std::_Rb_tree::_M_get_node (inline) 28ms 0.11% 69.20% 520ms 1.99% operator new 3ms 0.011% 69.21% 512ms 1.96% NodeBasedCellPopulation::WriteVtkResultsToFile 33ms 0.13% 69.33% 496ms 1.90% boost::detail::shared_count::~shared_count (inline) 0 0% 69.33% 496ms 1.90% boost::shared_ptr::~shared_ptr (inline) 120ms 0.46% 69.79% 481ms 1.84% __GI___libc_malloc 0 0% 69.79% 474ms 1.81% AbstractCellProperty::IsSubType (inline) 455ms 1.74% 71.54% 455ms 1.74% __strcmp_avx2 433ms 1.66% 73.19% 452ms 1.73% boost::detail::sp_counted_base::release 0 0% 73.19% 449ms 1.72% AbstractCellBasedSimulation::DoCellRemoval (inline) 5ms 0.019% 73.21% 436ms 1.67% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 59ms 0.23% 73.44% 424ms 1.62% std::_Rb_tree::~_Rb_tree (inline) 0 0% 73.44% 414ms 1.59% std::_Rb_tree::_Alloc_node::operator() (inline) 410ms 1.57% 75.01% 410ms 1.57% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 401ms 1.54% 76.54% 401ms 1.54% [libchaste_mesh.so] 107ms 0.41% 76.95% 400ms 1.53% boost::numeric::ublas::vector_binary::size (inline) 0 0% 76.95% 394ms 1.51% boost::numeric::ublas::c_vector::assign (inline) 199ms 0.76% 77.72% 387ms 1.48% Node::AddNeighbour 70ms 0.27% 77.98% 373ms 1.43% Node::GetRadius 0 0% 77.98% 361ms 1.38% boost::numeric::ublas::inner_prod (inline) 2ms 0.0077% 77.99% 361ms 1.38% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 20ms 0.077% 78.07% 359ms 1.37% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 78.07% 343ms 1.31% NodesOnlyMesh::ReMesh 5ms 0.019% 78.09% 335ms 1.28% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 78.09% 329ms 1.26% std::_Rb_tree::_M_drop_node (inline) 1ms 0.0038% 78.09% 328ms 1.26% NodesOnlyMesh::UpdateNodeIndices 327ms 1.25% 79.34% 327ms 1.25% __gnu_cxx::__normal_iterator::operator++ (inline) 17ms 0.065% 79.41% 325ms 1.24% Cell::ReadyToDivide 5ms 0.019% 79.43% 325ms 1.24% CellPropertyCollection::HasProperty 0 0% 79.43% 324ms 1.24% Cell::HasCellProperty (inline) 314ms 1.20% 80.63% 314ms 1.20% Node::CheckForNodeAttributes 0 0% 80.63% 310ms 1.19% NodesOnlyMesh::UpdateBoxCollection 149ms 0.57% 81.20% 307ms 1.18% _int_malloc 12ms 0.046% 81.25% 304ms 1.16% std::_Rb_tree::_M_emplace_hint_unique 8ms 0.031% 81.28% 294ms 1.13% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 81.28% 290ms 1.11% std::set::~set (inline) 112ms 0.43% 81.71% 288ms 1.10% std::__move_median_to_first (inline) 118ms 0.45% 82.16% 283ms 1.08% boost::numeric::ublas::vector_inner_prod::apply (inline) 9ms 0.034% 82.19% 272ms 1.04% DistributedBoxCollection::GetProcessOwningNode 4ms 0.015% 82.21% 269ms 1.03% std::__new_allocator::deallocate (inline) 0 0% 82.21% 257ms 0.98% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 82.21% 255ms 0.98% VtkMeshWriter::WriteFiles 0 0% 82.21% 252ms 0.96% std::allocator_traits::deallocate (inline) 0 0% 82.21% 251ms 0.96% std::_Rb_tree::_M_put_node (inline) 1ms 0.0038% 82.21% 248ms 0.95% NodesOnlyMesh::AddNodesToBoxes 75ms 0.29% 82.50% 243ms 0.93% __GI___libc_free 229ms 0.88% 83.37% 229ms 0.88% Node::GetIndex 0 0% 83.37% 221ms 0.85% vtkStreamingDemandDrivenPipeline::Update 0 0% 83.37% 221ms 0.85% vtkXMLWriterBase::Write 0 0% 83.37% 220ms 0.84% vtkDemandDrivenPipeline::ProcessRequest 1ms 0.0038% 83.38% 220ms 0.84% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 83.38% 219ms 0.84% vtkCompositeDataPipeline::ExecuteData 0 0% 83.38% 219ms 0.84% vtkDemandDrivenPipeline::ExecuteData 0 0% 83.38% 219ms 0.84% vtkExecutive::CallAlgorithm 0 0% 83.38% 218ms 0.83% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 83.38% 214ms 0.82% AbstractCellProperty::IsType (inline) 0 0% 83.38% 210ms 0.8% boost::numeric::ublas::vector_binary::operator() (inline) 14ms 0.054% 83.43% 208ms 0.8% boost::numeric::ublas::vector_reference::operator() (inline) 206ms 0.79% 84.22% 207ms 0.79% Node::ConstructNodeAttributes (inline) 207ms 0.79% 85.01% 207ms 0.79% boost::shared_ptr::operator-> (inline) 88ms 0.34% 85.35% 186ms 0.71% boost::shared_ptr::shared_ptr (inline) 0 0% 85.35% 186ms 0.71% std::_Rb_tree::clear (inline) 20ms 0.077% 85.43% 185ms 0.71% std::__insertion_sort (inline) 183ms 0.7% 86.13% 183ms 0.7% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 0 0% 86.13% 180ms 0.69% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 86.13% 180ms 0.69% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 86.13% 178ms 0.68% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 86.13% 174ms 0.67% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 169ms 0.65% 86.77% 169ms 0.65% [libchaste_cell_based.so] 0 0% 86.77% 168ms 0.64% Cell::GetCellId 150ms 0.57% 87.35% 167ms 0.64% _int_free 3ms 0.011% 87.36% 162ms 0.62% AbstractNumericalMethod::SafeNodePositionUpdate 3ms 0.011% 87.37% 162ms 0.62% boost::numeric::ublas::c_vector::operator[] (inline) 83ms 0.32% 87.69% 161ms 0.62% AbstractCellProperty::IsSame 1ms 0.0038% 87.69% 161ms 0.62% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 87.69% 160ms 0.61% NodesOnlyMesh::ResizeBoxCollection 11ms 0.042% 87.74% 159ms 0.61% NodesOnlyMesh::IsANodeCloseToDomainBoundary 157ms 0.6% 88.34% 157ms 0.6% Node::rGetLocation 147ms 0.56% 88.90% 148ms 0.57% std::__adjacent_find (inline) 0 0% 88.90% 148ms 0.57% std::__unique (inline) 0 0% 88.90% 148ms 0.57% std::unique (inline) 0 0% 88.90% 145ms 0.56% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 5ms 0.019% 88.92% 144ms 0.55% NodeBasedCellPopulation::SetNode 0 0% 88.92% 142ms 0.54% vtkXMLWriter::WritePointsAppendedData 0 0% 88.92% 141ms 0.54% std::map::map (inline) 0 0% 88.92% 141ms 0.54% vtkXMLWriter::WriteBinaryData 65ms 0.25% 89.17% 140ms 0.54% AbstractCellCycleModel::GetAge 139ms 0.53% 89.70% 139ms 0.53% Node::IsDeleted 5ms 0.019% 89.72% 137ms 0.52% NodesOnlyMesh::SetNode 0 0% 89.72% 135ms 0.52% std::map::~map (inline) 0 0% 89.72% 135ms 0.52% vtkXMLWriter::WriteBinaryDataBlock 0 0% 89.72% 135ms 0.52% vtkXMLWriter::WriteBinaryDataInternal 0 0% 89.72% 135ms 0.52% vtkXMLWriter::WriteCompressionBlock 1ms 0.0038% 89.72% 133ms 0.51% Cell::GetCellProliferativeType