File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 31126ms, 89.49% of 34781ms total Dropped 806 nodes (cum <= 173.91ms) flat flat% sum% cum cum% 0 0% 0% 34631ms 99.57% __libc_start_call_main 0 0% 0% 34631ms 99.57% __libc_start_main_impl 0 0% 0% 34631ms 99.57% _start 0 0% 0% 34616ms 99.53% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 34616ms 99.53% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 34616ms 99.53% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 34616ms 99.53% main 0 0% 0% 34576ms 99.41% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 34576ms 99.41% CxxTest::TestRunner::runTest (inline) 0 0% 0% 34576ms 99.41% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 34568ms 99.39% AbstractCellBasedSimulation::Solve 5ms 0.014% 0.014% 24159ms 69.46% OffLatticeSimulation::UpdateCellLocationsAndTopology 4ms 0.012% 0.026% 19314ms 55.53% ForwardEulerNumericalMethod::UpdateAllNodePositions 15ms 0.043% 0.069% 19123ms 54.98% AbstractNumericalMethod::ComputeForcesIncludingDamping 180ms 0.52% 0.59% 18209ms 52.35% AbstractTwoBodyInteractionForce::AddForceContribution 1502ms 4.32% 4.90% 15394ms 44.26% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4248ms 12.21% 17.12% 9380ms 26.97% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.0029% 17.12% 9210ms 26.48% AbstractCellBasedSimulation::UpdateCellPopulation 377ms 1.08% 18.21% 8542ms 24.56% std::_Rb_tree::find (inline) 0 0% 18.21% 8542ms 24.56% std::map::find (inline) 312ms 0.9% 19.10% 8464ms 24.34% NodesOnlyMesh::GetNodeOrHaloNode 497ms 1.43% 20.53% 8162ms 23.47% AbstractMesh::GetNode 0 0% 20.53% 8087ms 23.25% NodeBasedCellPopulation::Update 308ms 0.89% 21.42% 7669ms 22.05% NodesOnlyMesh::SolveNodeMapping 183ms 0.53% 21.94% 6435ms 18.50% boost::numeric::ublas::vector_assign (inline) 198ms 0.57% 22.51% 6321ms 18.17% boost::numeric::ublas::c_vector::c_vector (partial-inline) 4ms 0.012% 22.52% 6034ms 17.35% DistributedBoxCollection::CalculateInteriorNodePairs 5103ms 14.67% 37.20% 5103ms 14.67% std::_Rb_tree::_S_right (inline) 23ms 0.066% 37.26% 4534ms 13.04% NodeAttributes::RemoveDuplicateNeighbours 0 0% 37.26% 4511ms 12.97% OffLatticeSimulation::ApplyBoundaries 5ms 0.014% 37.28% 4359ms 12.53% std::__sort (inline) 0 0% 37.28% 4359ms 12.53% std::sort (inline) 1175ms 3.38% 40.65% 3623ms 10.42% boost::numeric::ublas::indexing_vector_assign 1ms 0.0029% 40.66% 3418ms 9.83% AbstractCellPopulation::Iterator::operator++ (inline) 216ms 0.62% 41.28% 3395ms 9.76% AbstractCellPopulation::Iterator::IsRealCell 70ms 0.2% 41.48% 3366ms 9.68% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 23ms 0.066% 41.55% 2864ms 8.23% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 208ms 0.6% 42.14% 2522ms 7.25% std::__introsort_loop 29ms 0.083% 42.23% 2393ms 6.88% PlaneBoundaryCondition::ImposeBoundaryCondition 38ms 0.11% 42.34% 2293ms 6.59% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.0029% 42.34% 2240ms 6.44% std::__unguarded_partition_pivot (inline) 234ms 0.67% 43.01% 2154ms 6.19% DistributedBoxCollection::AddPairsFromBox 15ms 0.043% 43.06% 2118ms 6.09% PlaneBoundaryCondition::VerifyBoundaryCondition 1076ms 3.09% 46.15% 1988ms 5.72% std::__unguarded_partition (inline) 0 0% 46.15% 1831ms 5.26% std::__final_insertion_sort (inline) 218ms 0.63% 46.78% 1763ms 5.07% std::map::operator[] (partial-inline) 1668ms 4.80% 51.57% 1668ms 4.80% boost::numeric::ublas::same_impl_ex 135ms 0.39% 51.96% 1624ms 4.67% AbstractMesh::GetVectorFromAtoB 91ms 0.26% 52.22% 1614ms 4.64% std::__unguarded_insertion_sort (inline) 576ms 1.66% 53.88% 1595ms 4.59% std::__unguarded_linear_insert (inline) 1451ms 4.17% 58.05% 1451ms 4.17% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 58.05% 1298ms 3.73% std::_Rb_tree::lower_bound (inline) 0 0% 58.05% 1298ms 3.73% std::map::lower_bound (inline) 0 0% 58.05% 1251ms 3.60% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 58.05% 1229ms 3.53% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 58.05% 1153ms 3.32% NodeBasedCellPopulation::UpdateCellProcessLocation 1113ms 3.20% 61.25% 1113ms 3.20% boost::numeric::ublas::c_vector::operator() 5ms 0.014% 61.26% 1090ms 3.13% DistributedBoxCollection::CalculateBoundaryNodePairs 17ms 0.049% 61.31% 1070ms 3.08% boost::numeric::ublas::detail::expression_type_check (inline) 160ms 0.46% 61.77% 1033ms 2.97% boost::numeric::ublas::vector_binary::size (inline) 185ms 0.53% 62.30% 1026ms 2.95% boost::numeric::ublas::detail::equals 428ms 1.23% 63.53% 918ms 2.64% __GI___libc_free 225ms 0.65% 64.18% 902ms 2.59% NodeAttributes::AddAppliedForceContribution 106ms 0.3% 64.49% 871ms 2.50% std::__new_allocator::allocate (inline) 1ms 0.0029% 64.49% 849ms 2.44% AbstractCentreBasedCellPopulation::GetDampingConstant 41ms 0.12% 64.61% 819ms 2.35% std::_Rb_tree_const_iterator::operator++ (inline) 20ms 0.058% 64.66% 800ms 2.30% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 312ms 0.9% 65.56% 800ms 2.30% NodeAttributes::AddNeighbour 0 0% 65.56% 785ms 2.26% boost::numeric::ublas::norm_inf (inline) 431ms 1.24% 66.80% 785ms 2.26% boost::numeric::ublas::vector_norm_inf::apply (inline) 355ms 1.02% 67.82% 774ms 2.23% DistributedBoxCollection::CalculateContainingBox (partial-inline) 774ms 2.23% 70.05% 774ms 2.23% std::_Rb_tree_increment 94ms 0.27% 70.32% 765ms 2.20% operator new 563ms 1.62% 71.94% 755ms 2.17% __dynamic_cast 0 0% 71.94% 728ms 2.09% AbstractCellPopulation::WriteResultsToFiles 0 0% 71.94% 677ms 1.95% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 71.94% 677ms 1.95% boost::numeric::ublas::c_vector::plus_assign (inline) 242ms 0.7% 72.63% 666ms 1.91% __GI___libc_malloc 3ms 0.0086% 72.64% 659ms 1.89% AbstractCellBasedSimulation::DoCellBirth 13ms 0.037% 72.68% 655ms 1.88% CellPropertyCollection::GetPropertiesType (inline) 486ms 1.40% 74.07% 585ms 1.68% std::vector::push_back (inline) 4ms 0.012% 74.09% 568ms 1.63% Cell::GetMutationState 18ms 0.052% 74.14% 486ms 1.40% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 74.14% 486ms 1.40% boost::numeric::ublas::vector::vector (inline) 438ms 1.26% 75.40% 485ms 1.39% _int_free 2ms 0.0058% 75.40% 484ms 1.39% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 75.40% 466ms 1.34% boost::numeric::ublas::norm_2 (inline) 373ms 1.07% 76.48% 466ms 1.34% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 76.48% 462ms 1.33% AbstractCellBasedSimulation::DoCellRemoval (inline) 3ms 0.0086% 76.48% 450ms 1.29% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 76.48% 403ms 1.16% std::allocator_traits::allocate (inline) 383ms 1.10% 77.59% 383ms 1.10% Node::GetIndex 32ms 0.092% 77.68% 377ms 1.08% boost::detail::shared_count::~shared_count (inline) 0 0% 77.68% 377ms 1.08% boost::shared_ptr::~shared_ptr (inline) 0 0% 77.68% 374ms 1.08% std::_Rb_tree::_M_create_node (inline) 4ms 0.012% 77.69% 373ms 1.07% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 3ms 0.0086% 77.70% 368ms 1.06% AbstractCellPopulation::GetCellUsingLocationIndex 1ms 0.0029% 77.70% 339ms 0.97% AbstractCellProperty::IsSubType (inline) 334ms 0.96% 78.66% 338ms 0.97% boost::detail::sp_counted_base::release 0 0% 78.66% 335ms 0.96% boost::numeric::ublas::inner_prod (inline) 3ms 0.0086% 78.67% 334ms 0.96% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 5ms 0.014% 78.68% 332ms 0.95% NodeBasedCellPopulation::UpdateMapsAfterRemesh 21ms 0.06% 78.74% 331ms 0.95% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 78.74% 325ms 0.93% std::_Rb_tree::_M_get_node (inline) 112ms 0.32% 79.07% 324ms 0.93% Node::GetRadius 319ms 0.92% 79.98% 319ms 0.92% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 18ms 0.052% 80.04% 313ms 0.9% boost::numeric::ublas::vector_reference::operator() (inline) 295ms 0.85% 80.88% 295ms 0.85% [libchaste_cell_based.so] 110ms 0.32% 81.20% 286ms 0.82% std::_Rb_tree::_M_erase (partial-inline) 6ms 0.017% 81.22% 283ms 0.81% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 282ms 0.81% 82.03% 282ms 0.81% __gnu_cxx::__normal_iterator::operator++ (inline) 1ms 0.0029% 82.03% 275ms 0.79% NodesOnlyMesh::ReMesh 0 0% 82.03% 270ms 0.78% NodesOnlyMesh::UpdateBoxCollection 6ms 0.017% 82.05% 265ms 0.76% DistributedBoxCollection::GetProcessOwningNode 101ms 0.29% 82.34% 263ms 0.76% boost::numeric::ublas::vector_inner_prod::apply (inline) 5ms 0.014% 82.35% 260ms 0.75% NodesOnlyMesh::UpdateNodeIndices 0 0% 82.35% 260ms 0.75% boost::numeric::ublas::c_vector::assign (inline) 2ms 0.0058% 82.36% 259ms 0.74% std::_Rb_tree::_Rb_tree (partial-inline) 27ms 0.078% 82.44% 250ms 0.72% std::_Rb_tree::_M_copy (inline) 4ms 0.012% 82.45% 247ms 0.71% std::_Rb_tree::_M_emplace_hint_unique 103ms 0.3% 82.74% 247ms 0.71% std::__move_median_to_first (inline) 3ms 0.0086% 82.75% 243ms 0.7% CellPropertyCollection::HasProperty 0 0% 82.75% 242ms 0.7% Cell::HasCellProperty (inline) 235ms 0.68% 83.43% 235ms 0.68% [libchaste_mesh.so] 0 0% 83.43% 235ms 0.68% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 83.43% 234ms 0.67% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 83.43% 233ms 0.67% VtkMeshWriter::WriteFiles 10ms 0.029% 83.46% 228ms 0.66% Cell::ReadyToDivide 228ms 0.66% 84.11% 228ms 0.66% Node::CheckForNodeAttributes 112ms 0.32% 84.43% 228ms 0.66% std::__find_if (inline) 0 0% 84.43% 228ms 0.66% std::find_if (inline) 0 0% 84.43% 228ms 0.66% std::none_of (inline) 225ms 0.65% 85.08% 225ms 0.65% boost::numeric::ublas::c_vector::size (inline) 116ms 0.33% 85.41% 222ms 0.64% _int_malloc 29ms 0.083% 85.50% 222ms 0.64% std::_Rb_tree::_M_clone_node (inline) 221ms 0.64% 86.13% 221ms 0.64% NodeBasedCellPopulation::GetNode 17ms 0.049% 86.18% 217ms 0.62% std::__insertion_sort (inline) 0 0% 86.18% 216ms 0.62% NodesOnlyMesh::ResizeBoxCollection 1ms 0.0029% 86.18% 215ms 0.62% NodesOnlyMesh::AddNodesToBoxes 0 0% 86.18% 214ms 0.62% boost::numeric::ublas::vector_binary::operator() (inline) 15ms 0.043% 86.23% 213ms 0.61% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 86.23% 210ms 0.6% vtkStreamingDemandDrivenPipeline::Update 0 0% 86.23% 210ms 0.6% vtkXMLWriterBase::Write 1ms 0.0029% 86.23% 209ms 0.6% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 86.23% 208ms 0.6% vtkDemandDrivenPipeline::ExecuteData 0 0% 86.23% 208ms 0.6% vtkDemandDrivenPipeline::ProcessRequest 0 0% 86.23% 208ms 0.6% vtkExecutive::CallAlgorithm 0 0% 86.23% 207ms 0.6% boost::numeric::ublas::vector_reference::size (inline) 0 0% 86.23% 207ms 0.6% vtkCompositeDataPipeline::ExecuteData 0 0% 86.23% 207ms 0.6% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 86.23% 203ms 0.58% tcache_get (inline) 203ms 0.58% 86.81% 203ms 0.58% tcache_get_n (inline) 202ms 0.58% 87.40% 202ms 0.58% boost::numeric::ublas::scalar_plus_assign::apply (inline) 193ms 0.55% 87.95% 193ms 0.55% Node::rGetLocation 33ms 0.095% 88.05% 192ms 0.55% std::__new_allocator::deallocate (inline) 186ms 0.53% 88.58% 186ms 0.53% __strcmp_avx2 2ms 0.0058% 88.59% 183ms 0.53% AbstractCellProperty::IsType (inline) 139ms 0.4% 88.99% 179ms 0.51% Node::AddAppliedForceContribution 176ms 0.51% 89.49% 176ms 0.51% boost::shared_ptr::operator-> (inline) 0 0% 89.49% 174ms 0.5% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 89.49% 174ms 0.5% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData