File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 32381ms, 89.54% of 36162ms total Dropped 852 nodes (cum <= 180.81ms) flat flat% sum% cum cum% 0 0% 0% 35995ms 99.54% __libc_start_call_main 0 0% 0% 35995ms 99.54% __libc_start_main_impl 0 0% 0% 35995ms 99.54% _start 0 0% 0% 35978ms 99.49% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 35978ms 99.49% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 35978ms 99.49% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 35978ms 99.49% main 0 0% 0% 35938ms 99.38% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 35938ms 99.38% CxxTest::TestRunner::runTest (inline) 0 0% 0% 35938ms 99.38% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 2ms 0.0055% 0.0055% 35930ms 99.36% AbstractCellBasedSimulation::Solve 1ms 0.0028% 0.0083% 25003ms 69.14% OffLatticeSimulation::UpdateCellLocationsAndTopology 8ms 0.022% 0.03% 19971ms 55.23% ForwardEulerNumericalMethod::UpdateAllNodePositions 11ms 0.03% 0.061% 19777ms 54.69% AbstractNumericalMethod::ComputeForcesIncludingDamping 167ms 0.46% 0.52% 18494ms 51.14% AbstractTwoBodyInteractionForce::AddForceContribution 1884ms 5.21% 5.73% 15739ms 43.52% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4323ms 11.95% 17.69% 9707ms 26.84% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.0028% 17.69% 9654ms 26.70% AbstractCellBasedSimulation::UpdateCellPopulation 329ms 0.91% 18.60% 8704ms 24.07% std::_Rb_tree::find (inline) 0 0% 18.60% 8703ms 24.07% std::map::find (inline) 0 0% 18.60% 8429ms 23.31% NodeBasedCellPopulation::Update 139ms 0.38% 18.98% 8360ms 23.12% NodesOnlyMesh::GetNodeOrHaloNode 459ms 1.27% 20.25% 8212ms 22.71% AbstractMesh::GetNode 320ms 0.88% 21.14% 7757ms 21.45% NodesOnlyMesh::SolveNodeMapping 5ms 0.014% 21.15% 6323ms 17.49% DistributedBoxCollection::CalculateInteriorNodePairs 176ms 0.49% 21.64% 6314ms 17.46% boost::numeric::ublas::vector_assign (inline) 211ms 0.58% 22.22% 6116ms 16.91% boost::numeric::ublas::c_vector::c_vector (partial-inline) 5355ms 14.81% 37.03% 5355ms 14.81% std::_Rb_tree::_S_right (inline) 3ms 0.0083% 37.04% 4601ms 12.72% OffLatticeSimulation::ApplyBoundaries 16ms 0.044% 37.08% 4534ms 12.54% NodeAttributes::RemoveDuplicateNeighbours 12ms 0.033% 37.12% 4362ms 12.06% std::__sort (inline) 0 0% 37.12% 4362ms 12.06% std::sort (inline) 1ms 0.0028% 37.12% 3499ms 9.68% AbstractCellPopulation::Iterator::operator++ (inline) 206ms 0.57% 37.69% 3481ms 9.63% AbstractCellPopulation::Iterator::IsRealCell (inline) 77ms 0.21% 37.90% 3475ms 9.61% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 1138ms 3.15% 41.05% 3396ms 9.39% boost::numeric::ublas::indexing_vector_assign 22ms 0.061% 41.11% 2948ms 8.15% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 199ms 0.55% 41.66% 2542ms 7.03% std::__introsort_loop 32ms 0.088% 41.75% 2419ms 6.69% PlaneBoundaryCondition::ImposeBoundaryCondition 170ms 0.47% 42.22% 2394ms 6.62% DistributedBoxCollection::AddPairsFromBox 40ms 0.11% 42.33% 2360ms 6.53% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 42.33% 2267ms 6.27% std::__unguarded_partition_pivot (inline) 20ms 0.055% 42.38% 2179ms 6.03% PlaneBoundaryCondition::VerifyBoundaryCondition 1045ms 2.89% 45.27% 2044ms 5.65% std::__unguarded_partition (inline) 222ms 0.61% 45.89% 1922ms 5.31% std::map::operator[] (partial-inline) 1ms 0.0028% 45.89% 1802ms 4.98% std::__final_insertion_sort (inline) 1652ms 4.57% 50.46% 1652ms 4.57% boost::numeric::ublas::same_impl_ex 148ms 0.41% 50.87% 1623ms 4.49% AbstractMesh::GetVectorFromAtoB 107ms 0.3% 51.16% 1593ms 4.41% std::__unguarded_insertion_sort (inline) 593ms 1.64% 52.80% 1535ms 4.24% std::__unguarded_linear_insert (inline) 1414ms 3.91% 56.71% 1414ms 3.91% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 56.71% 1408ms 3.89% std::_Rb_tree::lower_bound (inline) 0 0% 56.71% 1408ms 3.89% std::map::lower_bound (inline) 138ms 0.38% 57.10% 1382ms 3.82% std::__new_allocator::allocate (inline) 0 0% 57.10% 1246ms 3.45% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 90ms 0.25% 57.34% 1245ms 3.44% operator new 0 0% 57.34% 1231ms 3.40% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 57.34% 1217ms 3.37% NodeBasedCellPopulation::UpdateCellProcessLocation 4ms 0.011% 57.36% 1196ms 3.31% AbstractCentreBasedCellPopulation::GetDampingConstant 567ms 1.57% 58.92% 1150ms 3.18% __GI___libc_malloc 3ms 0.0083% 58.93% 1069ms 2.96% DistributedBoxCollection::CalculateBoundaryNodePairs 1036ms 2.86% 61.80% 1036ms 2.86% boost::numeric::ublas::c_vector::operator() 12ms 0.033% 61.83% 1011ms 2.80% boost::numeric::ublas::detail::expression_type_check (inline) 255ms 0.71% 62.54% 994ms 2.75% NodeAttributes::AddAppliedForceContribution 59ms 0.16% 62.70% 991ms 2.74% std::_Rb_tree_const_iterator::operator++ (inline) 184ms 0.51% 63.21% 971ms 2.69% boost::numeric::ublas::detail::equals 151ms 0.42% 63.62% 967ms 2.67% boost::numeric::ublas::vector_binary::size (inline) 928ms 2.57% 66.19% 928ms 2.57% std::_Rb_tree_increment 4ms 0.011% 66.20% 862ms 2.38% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 66.20% 862ms 2.38% boost::numeric::ublas::vector::vector (inline) 21ms 0.058% 66.26% 857ms 2.37% CellPropertyCollection::GetPropertiesType (inline) 389ms 1.08% 67.34% 827ms 2.29% DistributedBoxCollection::CalculateContainingBox (partial-inline) 607ms 1.68% 69.01% 826ms 2.28% __dynamic_cast 18ms 0.05% 69.06% 825ms 2.28% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 419ms 1.16% 70.22% 797ms 2.20% __GI___libc_free 1ms 0.0028% 70.23% 771ms 2.13% Cell::GetMutationState 0 0% 70.23% 765ms 2.12% AbstractCellPopulation::WriteResultsToFiles 2ms 0.0055% 70.23% 763ms 2.11% AbstractCellBasedSimulation::DoCellBirth 0 0% 70.23% 746ms 2.06% boost::numeric::ublas::norm_inf (inline) 434ms 1.20% 71.43% 746ms 2.06% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 71.43% 739ms 2.04% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 71.43% 739ms 2.04% boost::numeric::ublas::c_vector::plus_assign (inline) 184ms 0.51% 71.94% 687ms 1.90% NodeAttributes::AddNeighbour 130ms 0.36% 72.30% 597ms 1.65% Node::AddNeighbour 498ms 1.38% 73.68% 593ms 1.64% std::vector::push_back (inline) 535ms 1.48% 75.16% 537ms 1.48% Node::ConstructNodeAttributes (inline) 3ms 0.0083% 75.16% 536ms 1.48% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 5ms 0.014% 75.18% 533ms 1.47% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 75.18% 524ms 1.45% std::allocator_traits::allocate (inline) 0 0% 75.18% 514ms 1.42% std::_Rb_tree::_M_create_node (inline) 0 0% 75.18% 500ms 1.38% boost::numeric::ublas::norm_2 (inline) 401ms 1.11% 76.29% 500ms 1.38% boost::numeric::ublas::vector_norm_2::apply (inline) 2ms 0.0055% 76.29% 495ms 1.37% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 76.29% 459ms 1.27% AbstractCellBasedSimulation::DoCellRemoval (inline) 4ms 0.011% 76.30% 442ms 1.22% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 2ms 0.0055% 76.31% 420ms 1.16% AbstractCellProperty::IsSubType (inline) 0 0% 76.31% 420ms 1.16% std::_Rb_tree::_M_get_node (inline) 34ms 0.094% 76.40% 394ms 1.09% boost::detail::shared_count::~shared_count (inline) 0 0% 76.40% 394ms 1.09% boost::shared_ptr::~shared_ptr (inline) 348ms 0.96% 77.37% 378ms 1.05% _int_free 13ms 0.036% 77.40% 370ms 1.02% std::_Rb_tree::_Rb_tree (partial-inline) 147ms 0.41% 77.81% 360ms 1% std::_Rb_tree::_M_erase 357ms 0.99% 78.80% 358ms 0.99% boost::detail::sp_counted_base::release 26ms 0.072% 78.87% 357ms 0.99% std::_Rb_tree::_M_copy (inline) 0 0% 78.87% 348ms 0.96% Cell::HasCellProperty (inline) 2ms 0.0055% 78.87% 348ms 0.96% CellPropertyCollection::HasProperty 0 0% 78.87% 347ms 0.96% std::_Rb_tree::_Alloc_node::operator() (inline) 107ms 0.3% 79.17% 335ms 0.93% Node::GetRadius 0 0% 79.17% 333ms 0.92% NodesOnlyMesh::ReMesh 47ms 0.13% 79.30% 331ms 0.92% std::_Rb_tree::_M_clone_node (inline) 17ms 0.047% 79.35% 328ms 0.91% Cell::ReadyToDivide 326ms 0.9% 80.25% 326ms 0.9% Node::GetIndex 0 0% 80.25% 326ms 0.9% boost::numeric::ublas::inner_prod (inline) 3ms 0.0083% 80.26% 325ms 0.9% NodesOnlyMesh::UpdateNodeIndices 325ms 0.9% 81.15% 325ms 0.9% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 1ms 0.0028% 81.16% 323ms 0.89% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 20ms 0.055% 81.21% 322ms 0.89% boost::numeric::ublas::vector_scalar_binary::evaluate 5ms 0.014% 81.23% 318ms 0.88% NodeBasedCellPopulation::UpdateMapsAfterRemesh 310ms 0.86% 82.08% 310ms 0.86% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 82.08% 306ms 0.85% NodesOnlyMesh::UpdateBoxCollection 149ms 0.41% 82.50% 299ms 0.83% _int_malloc 2ms 0.0055% 82.50% 296ms 0.82% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 11ms 0.03% 82.53% 292ms 0.81% std::_Rb_tree::_M_emplace_hint_unique 12ms 0.033% 82.56% 287ms 0.79% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 82.56% 284ms 0.79% tcache_get (inline) 284ms 0.79% 83.35% 284ms 0.79% tcache_get_n (inline) 4ms 0.011% 83.36% 281ms 0.78% DistributedBoxCollection::GetProcessOwningNode 260ms 0.72% 84.08% 260ms 0.72% NodeBasedCellPopulation::GetNode 0 0% 84.08% 260ms 0.72% boost::numeric::ublas::c_vector::assign (inline) 259ms 0.72% 84.80% 259ms 0.72% [libchaste_cell_based.so] 109ms 0.3% 85.10% 253ms 0.7% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 85.10% 238ms 0.66% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 238ms 0.66% 85.76% 238ms 0.66% Node::CheckForNodeAttributes 1ms 0.0028% 85.76% 237ms 0.66% NodesOnlyMesh::AddNodesToBoxes 0 0% 85.76% 236ms 0.65% VtkMeshWriter::WriteFiles 229ms 0.63% 86.39% 229ms 0.63% Node::rGetLocation 29ms 0.08% 86.47% 222ms 0.61% std::__new_allocator::deallocate (inline) 96ms 0.27% 86.74% 221ms 0.61% std::__move_median_to_first (inline) 158ms 0.44% 87.17% 219ms 0.61% Node::AddAppliedForceContribution 0 0% 87.17% 216ms 0.6% boost::numeric::ublas::vector_binary::operator() (inline) 212ms 0.59% 87.76% 212ms 0.59% boost::shared_ptr::operator-> (inline) 0 0% 87.76% 209ms 0.58% std::set::set (inline) 208ms 0.58% 88.34% 208ms 0.58% boost::numeric::ublas::c_vector::size (inline) 24ms 0.066% 88.40% 208ms 0.58% std::__insertion_sort (inline) 0 0% 88.40% 203ms 0.56% vtkStreamingDemandDrivenPipeline::Update 0 0% 88.40% 203ms 0.56% vtkXMLWriterBase::Write 4ms 0.011% 88.41% 201ms 0.56% AbstractCellProperty::IsType (inline) 0 0% 88.41% 201ms 0.56% std::_Rb_tree::_M_drop_node (inline) 0 0% 88.41% 200ms 0.55% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 88.41% 199ms 0.55% NodesOnlyMesh::ResizeBoxCollection 0 0% 88.41% 199ms 0.55% vtkDemandDrivenPipeline::ProcessRequest 15ms 0.041% 88.45% 198ms 0.55% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 88.45% 198ms 0.55% std::_Rb_tree::clear (inline) 0 0% 88.45% 198ms 0.55% vtkExecutive::CallAlgorithm 0 0% 88.45% 196ms 0.54% vtkDemandDrivenPipeline::ExecuteData 1ms 0.0028% 88.46% 196ms 0.54% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 88.46% 195ms 0.54% vtkCompositeDataPipeline::ExecuteData 194ms 0.54% 88.99% 194ms 0.54% __strcmp_avx2 12ms 0.033% 89.03% 188ms 0.52% std::_Rb_tree::~_Rb_tree (inline) 187ms 0.52% 89.54% 187ms 0.52% [libchaste_mesh.so] 0 0% 89.54% 185ms 0.51% boost::numeric::ublas::vector_reference::size (inline)