File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 30618ms, 87.63% of 34940ms total Dropped 840 nodes (cum <= 174.70ms) flat flat% sum% cum cum% 0 0% 0% 34820ms 99.66% __libc_start_call_main 0 0% 0% 34820ms 99.66% __libc_start_main_impl 0 0% 0% 34820ms 99.66% _start 0 0% 0% 34802ms 99.61% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 34802ms 99.61% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 34802ms 99.61% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 34802ms 99.61% main 0 0% 0% 34761ms 99.49% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 34761ms 99.49% CxxTest::TestRunner::runTest (inline) 0 0% 0% 34761ms 99.49% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 34752ms 99.46% AbstractCellBasedSimulation::Solve 2ms 0.0057% 0.0057% 23970ms 68.60% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0029% 0.0086% 18942ms 54.21% ForwardEulerNumericalMethod::UpdateAllNodePositions 25ms 0.072% 0.08% 18737ms 53.63% AbstractNumericalMethod::ComputeForcesIncludingDamping 146ms 0.42% 0.5% 17732ms 50.75% AbstractTwoBodyInteractionForce::AddForceContribution 1580ms 4.52% 5.02% 15096ms 43.21% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4497ms 12.87% 17.89% 9907ms 28.35% std::_Rb_tree::_M_lower_bound (inline) 0 0% 17.89% 9538ms 27.30% AbstractCellBasedSimulation::UpdateCellPopulation 372ms 1.06% 18.96% 9045ms 25.89% std::_Rb_tree::find (inline) 0 0% 18.96% 9044ms 25.88% std::map::find (inline) 207ms 0.59% 19.55% 8907ms 25.49% NodesOnlyMesh::GetNodeOrHaloNode 519ms 1.49% 21.03% 8723ms 24.97% AbstractMesh::GetNode 0 0% 21.03% 8413ms 24.08% NodeBasedCellPopulation::Update 382ms 1.09% 22.13% 8207ms 23.49% NodesOnlyMesh::SolveNodeMapping 10ms 0.029% 22.16% 6271ms 17.95% DistributedBoxCollection::CalculateInteriorNodePairs 213ms 0.61% 22.76% 5693ms 16.29% boost::numeric::ublas::vector_assign (inline) 137ms 0.39% 23.16% 5575ms 15.96% boost::numeric::ublas::c_vector::c_vector (partial-inline) 5338ms 15.28% 38.43% 5338ms 15.28% std::_Rb_tree::_S_right (inline) 0 0% 38.43% 4695ms 13.44% OffLatticeSimulation::ApplyBoundaries 10ms 0.029% 38.46% 4640ms 13.28% NodeAttributes::RemoveDuplicateNeighbours 3ms 0.0086% 38.47% 4427ms 12.67% std::__sort (inline) 0 0% 38.47% 4427ms 12.67% std::sort (inline) 91ms 0.26% 38.73% 3397ms 9.72% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 1057ms 3.03% 41.76% 3307ms 9.46% boost::numeric::ublas::indexing_vector_assign 1ms 0.0029% 41.76% 3199ms 9.16% AbstractCellPopulation::Iterator::operator++ (inline) 170ms 0.49% 42.25% 3168ms 9.07% AbstractCellPopulation::Iterator::IsRealCell 34ms 0.097% 42.34% 2747ms 7.86% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 187ms 0.54% 42.88% 2665ms 7.63% std::__introsort_loop 30ms 0.086% 42.97% 2498ms 7.15% PlaneBoundaryCondition::ImposeBoundaryCondition 0 0% 42.97% 2399ms 6.87% std::__unguarded_partition_pivot (inline) 59ms 0.17% 43.13% 2362ms 6.76% AbstractCellPopulation::GetLocationIndexUsingCell 132ms 0.38% 43.51% 2246ms 6.43% DistributedBoxCollection::AddPairsFromBox 13ms 0.037% 43.55% 2197ms 6.29% PlaneBoundaryCondition::VerifyBoundaryCondition 1042ms 2.98% 46.53% 2132ms 6.10% std::__unguarded_partition (inline) 174ms 0.5% 47.03% 1812ms 5.19% std::map::operator[] (partial-inline) 0 0% 47.03% 1757ms 5.03% std::__final_insertion_sort (inline) 1647ms 4.71% 51.74% 1647ms 4.71% boost::numeric::ublas::same_impl_ex 120ms 0.34% 52.09% 1566ms 4.48% std::__unguarded_insertion_sort (inline) 156ms 0.45% 52.53% 1501ms 4.30% AbstractMesh::GetVectorFromAtoB 590ms 1.69% 54.22% 1494ms 4.28% std::__unguarded_linear_insert (inline) 1386ms 3.97% 58.19% 1386ms 3.97% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 58.19% 1357ms 3.88% std::_Rb_tree::lower_bound (inline) 0 0% 58.19% 1357ms 3.88% std::map::lower_bound (inline) 0 0% 58.19% 1356ms 3.88% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 58.19% 1340ms 3.84% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 3ms 0.0086% 58.20% 1205ms 3.45% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 58.20% 1193ms 3.41% NodeBasedCellPopulation::UpdateCellProcessLocation 277ms 0.79% 58.99% 1152ms 3.30% boost::numeric::ublas::detail::equals 8ms 0.023% 59.01% 1128ms 3.23% DistributedBoxCollection::CalculateBoundaryNodePairs 1125ms 3.22% 62.23% 1125ms 3.22% boost::numeric::ublas::c_vector::operator() 17ms 0.049% 62.28% 968ms 2.77% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 141ms 0.4% 62.68% 962ms 2.75% boost::numeric::ublas::vector_binary::size (inline) 5ms 0.014% 62.70% 919ms 2.63% AbstractCentreBasedCellPopulation::GetDampingConstant 269ms 0.77% 63.47% 892ms 2.55% NodeAttributes::AddNeighbour 224ms 0.64% 64.11% 858ms 2.46% NodeAttributes::AddAppliedForceContribution 409ms 1.17% 65.28% 855ms 2.45% DistributedBoxCollection::CalculateContainingBox (partial-inline) 27ms 0.077% 65.36% 855ms 2.45% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 65.36% 817ms 2.34% boost::numeric::ublas::norm_inf (inline) 496ms 1.42% 66.78% 817ms 2.34% boost::numeric::ublas::vector_norm_inf::apply (inline) 810ms 2.32% 69.10% 810ms 2.32% std::_Rb_tree_increment 586ms 1.68% 70.77% 801ms 2.29% __dynamic_cast 0 0% 70.77% 756ms 2.16% AbstractCellPopulation::WriteResultsToFiles 107ms 0.31% 71.08% 751ms 2.15% std::__new_allocator::allocate (inline) 619ms 1.77% 72.85% 706ms 2.02% std::vector::push_back (inline) 24ms 0.069% 72.92% 702ms 2.01% CellPropertyCollection::GetPropertiesType (inline) 2ms 0.0057% 72.93% 651ms 1.86% AbstractCellBasedSimulation::DoCellBirth 107ms 0.31% 73.23% 645ms 1.85% operator new 0 0% 73.23% 634ms 1.81% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 73.23% 634ms 1.81% boost::numeric::ublas::c_vector::plus_assign (inline) 0 0% 73.23% 621ms 1.78% Cell::GetMutationState 0 0% 73.23% 539ms 1.54% boost::numeric::ublas::norm_2 (inline) 427ms 1.22% 74.45% 539ms 1.54% boost::numeric::ublas::vector_norm_2::apply (inline) 187ms 0.54% 74.99% 533ms 1.53% __GI___libc_malloc 1ms 0.0029% 74.99% 502ms 1.44% NodeBasedCellPopulation::WriteVtkResultsToFile 155ms 0.44% 75.44% 493ms 1.41% __GI___libc_free 0 0% 75.44% 472ms 1.35% AbstractCellBasedSimulation::DoCellRemoval (inline) 3ms 0.0086% 75.44% 461ms 1.32% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 75.44% 447ms 1.28% std::allocator_traits::allocate (inline) 39ms 0.11% 75.56% 445ms 1.27% boost::detail::shared_count::~shared_count (inline) 0 0% 75.56% 445ms 1.27% boost::shared_ptr::~shared_ptr (inline) 412ms 1.18% 76.73% 412ms 1.18% Node::GetIndex 0 0% 76.73% 409ms 1.17% std::_Rb_tree::_M_create_node (inline) 395ms 1.13% 77.86% 405ms 1.16% boost::detail::sp_counted_base::release 1ms 0.0029% 77.87% 401ms 1.15% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 12ms 0.034% 77.90% 399ms 1.14% AbstractCellPopulation::GetCellUsingLocationIndex 1ms 0.0029% 77.90% 383ms 1.10% AbstractCellProperty::IsSubType (inline) 378ms 1.08% 78.99% 378ms 1.08% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 78.99% 363ms 1.04% NodesOnlyMesh::ReMesh 0 0% 78.99% 357ms 1.02% std::_Rb_tree::_M_get_node (inline) 1ms 0.0029% 78.99% 345ms 0.99% NodesOnlyMesh::UpdateNodeIndices 34ms 0.097% 79.09% 338ms 0.97% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 79.09% 338ms 0.97% boost::numeric::ublas::vector::vector (inline) 276ms 0.79% 79.88% 337ms 0.96% _int_free 0 0% 79.88% 337ms 0.96% boost::numeric::ublas::inner_prod (inline) 13ms 0.037% 79.91% 336ms 0.96% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 79.91% 336ms 0.96% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 114ms 0.33% 80.24% 308ms 0.88% std::_Rb_tree::_M_erase (partial-inline) 8ms 0.023% 80.26% 307ms 0.88% NodeBasedCellPopulation::UpdateMapsAfterRemesh 299ms 0.86% 81.12% 299ms 0.86% __gnu_cxx::__normal_iterator::operator++ (inline) 65ms 0.19% 81.31% 297ms 0.85% Node::GetRadius 0 0% 81.31% 292ms 0.84% NodesOnlyMesh::UpdateBoxCollection 4ms 0.011% 81.32% 290ms 0.83% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 245ms 0.7% 82.02% 285ms 0.82% Node::AddNeighbour 8ms 0.023% 82.04% 281ms 0.8% std::_Rb_tree::_M_emplace_hint_unique 4ms 0.011% 82.05% 276ms 0.79% CellPropertyCollection::HasProperty 0 0% 82.05% 275ms 0.79% Cell::HasCellProperty (inline) 5ms 0.014% 82.07% 275ms 0.79% DistributedBoxCollection::GetProcessOwningNode 117ms 0.33% 82.40% 273ms 0.78% boost::numeric::ublas::vector_inner_prod::apply (inline) 7ms 0.02% 82.42% 273ms 0.78% boost::numeric::ublas::vector_reference::operator() (inline) 10ms 0.029% 82.45% 270ms 0.77% std::_Rb_tree::_Rb_tree (partial-inline) 7ms 0.02% 82.47% 264ms 0.76% Cell::ReadyToDivide 0 0% 82.47% 262ms 0.75% boost::numeric::ublas::c_vector::assign (inline) 106ms 0.3% 82.77% 262ms 0.75% std::__move_median_to_first (inline) 261ms 0.75% 83.52% 261ms 0.75% [libchaste_cell_based.so] 0 0% 83.52% 256ms 0.73% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 83.52% 255ms 0.73% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 83.52% 253ms 0.72% VtkMeshWriter::WriteFiles 23ms 0.066% 83.59% 253ms 0.72% std::_Rb_tree::_M_copy (inline) 1ms 0.0029% 83.59% 242ms 0.69% NodesOnlyMesh::AddNodesToBoxes 241ms 0.69% 84.28% 241ms 0.69% Node::CheckForNodeAttributes 133ms 0.38% 84.66% 235ms 0.67% _int_malloc 234ms 0.67% 85.33% 234ms 0.67% [libchaste_mesh.so] 0 0% 85.33% 228ms 0.65% boost::numeric::ublas::vector_binary::operator() (inline) 38ms 0.11% 85.44% 227ms 0.65% std::_Rb_tree::_M_clone_node (inline) 222ms 0.64% 86.07% 222ms 0.64% __strcmp_avx2 0 0% 86.07% 222ms 0.64% vtkStreamingDemandDrivenPipeline::Update 0 0% 86.07% 222ms 0.64% vtkXMLWriterBase::Write 0 0% 86.07% 220ms 0.63% vtkDemandDrivenPipeline::ProcessRequest 0 0% 86.07% 218ms 0.62% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 86.07% 217ms 0.62% vtkCompositeDataPipeline::ExecuteData 0 0% 86.07% 217ms 0.62% vtkDemandDrivenPipeline::ExecuteData 0 0% 86.07% 217ms 0.62% vtkExecutive::CallAlgorithm 0 0% 86.07% 217ms 0.62% vtkXMLUnstructuredDataWriter::ProcessRequest 196ms 0.56% 86.63% 196ms 0.56% NodeBasedCellPopulation::GetNode 17ms 0.049% 86.68% 191ms 0.55% std::__insertion_sort (inline) 91ms 0.26% 86.94% 188ms 0.54% boost::shared_ptr::shared_ptr (inline) 0 0% 86.94% 187ms 0.54% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 86.94% 187ms 0.54% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 86.94% 186ms 0.53% AbstractCellProperty::IsType (inline) 186ms 0.53% 87.48% 186ms 0.53% std::__adjacent_find (inline) 0 0% 87.48% 186ms 0.53% std::__unique (inline) 0 0% 87.48% 186ms 0.53% std::unique (inline) 0 0% 87.48% 179ms 0.51% std::_Rb_tree::_M_drop_node (inline) 53ms 0.15% 87.63% 178ms 0.51% std::__find_if (inline) 0 0% 87.63% 178ms 0.51% std::find_if (inline) 0 0% 87.63% 178ms 0.51% std::none_of (inline) 0 0% 87.63% 178ms 0.51% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 1ms 0.0029% 87.63% 175ms 0.5% NodesOnlyMesh::ResizeBoxCollection