File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 30004ms, 87.06% of 34463ms total Dropped 842 nodes (cum <= 172.31ms) flat flat% sum% cum cum% 0 0% 0% 34351ms 99.68% __libc_start_call_main 0 0% 0% 34351ms 99.68% __libc_start_main_impl 0 0% 0% 34351ms 99.68% _start 0 0% 0% 34332ms 99.62% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 34332ms 99.62% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 34332ms 99.62% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 34332ms 99.62% main 0 0% 0% 34291ms 99.50% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 34291ms 99.50% CxxTest::TestRunner::runTest (inline) 0 0% 0% 34290ms 99.50% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 34281ms 99.47% AbstractCellBasedSimulation::Solve 3ms 0.0087% 0.0087% 23806ms 69.08% OffLatticeSimulation::UpdateCellLocationsAndTopology 4ms 0.012% 0.02% 18763ms 54.44% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.029% 0.049% 18565ms 53.87% AbstractNumericalMethod::ComputeForcesIncludingDamping 162ms 0.47% 0.52% 17764ms 51.55% AbstractTwoBodyInteractionForce::AddForceContribution 1554ms 4.51% 5.03% 14988ms 43.49% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4730ms 13.72% 18.75% 9957ms 28.89% std::_Rb_tree::_M_lower_bound (inline) 0 0% 18.75% 9256ms 26.86% AbstractCellBasedSimulation::UpdateCellPopulation 374ms 1.09% 19.84% 9098ms 26.40% std::_Rb_tree::find (inline) 0 0% 19.84% 9098ms 26.40% std::map::find (inline) 184ms 0.53% 20.37% 8903ms 25.83% NodesOnlyMesh::GetNodeOrHaloNode 513ms 1.49% 21.86% 8650ms 25.10% AbstractMesh::GetNode 0 0% 21.86% 8166ms 23.69% NodeBasedCellPopulation::Update 401ms 1.16% 23.02% 8141ms 23.62% NodesOnlyMesh::SolveNodeMapping 7ms 0.02% 23.05% 6084ms 17.65% DistributedBoxCollection::CalculateInteriorNodePairs 187ms 0.54% 23.59% 5703ms 16.55% boost::numeric::ublas::vector_assign (inline) 140ms 0.41% 23.99% 5557ms 16.12% boost::numeric::ublas::c_vector::c_vector (partial-inline) 5182ms 15.04% 39.03% 5182ms 15.04% std::_Rb_tree::_S_right (inline) 2ms 0.0058% 39.04% 4722ms 13.70% OffLatticeSimulation::ApplyBoundaries 8ms 0.023% 39.06% 4626ms 13.42% NodeAttributes::RemoveDuplicateNeighbours 3ms 0.0087% 39.07% 4454ms 12.92% std::__sort (inline) 0 0% 39.07% 4454ms 12.92% std::sort (inline) 82ms 0.24% 39.31% 3553ms 10.31% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 1186ms 3.44% 42.75% 3441ms 9.98% boost::numeric::ublas::indexing_vector_assign 3ms 0.0087% 42.76% 3339ms 9.69% AbstractCellPopulation::Iterator::operator++ (inline) 133ms 0.39% 43.14% 3307ms 9.60% AbstractCellPopulation::Iterator::IsRealCell (inline) 24ms 0.07% 43.21% 2933ms 8.51% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 187ms 0.54% 43.75% 2621ms 7.61% std::__introsort_loop 23ms 0.067% 43.82% 2528ms 7.34% PlaneBoundaryCondition::ImposeBoundaryCondition 64ms 0.19% 44.01% 2463ms 7.15% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 44.01% 2350ms 6.82% std::__unguarded_partition_pivot (inline) 15ms 0.044% 44.05% 2192ms 6.36% PlaneBoundaryCondition::VerifyBoundaryCondition 135ms 0.39% 44.44% 2096ms 6.08% DistributedBoxCollection::AddPairsFromBox 989ms 2.87% 47.31% 2077ms 6.03% std::__unguarded_partition (inline) 213ms 0.62% 47.93% 1861ms 5.40% std::map::operator[] (partial-inline) 1ms 0.0029% 47.93% 1829ms 5.31% std::__final_insertion_sort (inline) 1727ms 5.01% 52.94% 1727ms 5.01% boost::numeric::ublas::same_impl_ex 134ms 0.39% 53.33% 1617ms 4.69% std::__unguarded_insertion_sort (inline) 163ms 0.47% 53.81% 1552ms 4.50% AbstractMesh::GetVectorFromAtoB 580ms 1.68% 55.49% 1520ms 4.41% std::__unguarded_linear_insert (inline) 0 0% 55.49% 1423ms 4.13% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 55.49% 1404ms 4.07% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1390ms 4.03% 59.52% 1390ms 4.03% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 59.52% 1359ms 3.94% std::_Rb_tree::lower_bound (inline) 0 0% 59.52% 1359ms 3.94% std::map::lower_bound (inline) 0 0% 59.52% 1184ms 3.44% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 59.52% 1160ms 3.37% NodeBasedCellPopulation::UpdateCellProcessLocation 260ms 0.75% 60.28% 1152ms 3.34% boost::numeric::ublas::detail::equals 8ms 0.023% 60.30% 1108ms 3.22% DistributedBoxCollection::CalculateBoundaryNodePairs 1070ms 3.10% 63.40% 1070ms 3.10% boost::numeric::ublas::c_vector::operator() 145ms 0.42% 63.82% 1000ms 2.90% boost::numeric::ublas::vector_binary::size (inline) 22ms 0.064% 63.89% 934ms 2.71% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 224ms 0.65% 64.54% 907ms 2.63% NodeAttributes::AddAppliedForceContribution 243ms 0.71% 65.24% 854ms 2.48% NodeAttributes::AddNeighbour 0 0% 65.24% 817ms 2.37% boost::numeric::ublas::norm_inf (inline) 501ms 1.45% 66.70% 817ms 2.37% boost::numeric::ublas::vector_norm_inf::apply (inline) 373ms 1.08% 67.78% 811ms 2.35% DistributedBoxCollection::CalculateContainingBox (partial-inline) 561ms 1.63% 69.41% 774ms 2.25% __dynamic_cast 8ms 0.023% 69.43% 747ms 2.17% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 69.43% 746ms 2.16% AbstractCellPopulation::WriteResultsToFiles 90ms 0.26% 69.69% 706ms 2.05% std::__new_allocator::allocate (inline) 0 0% 69.69% 683ms 1.98% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 69.69% 683ms 1.98% boost::numeric::ublas::c_vector::plus_assign (inline) 608ms 1.76% 71.46% 681ms 1.98% std::vector::push_back (inline) 32ms 0.093% 71.55% 650ms 1.89% std::_Rb_tree_const_iterator::operator++ (inline) 78ms 0.23% 71.78% 612ms 1.78% operator new 3ms 0.0087% 71.78% 611ms 1.77% AbstractCellBasedSimulation::DoCellBirth 0 0% 71.78% 606ms 1.76% boost::numeric::ublas::norm_2 (inline) 486ms 1.41% 73.19% 606ms 1.76% boost::numeric::ublas::vector_norm_2::apply (inline) 605ms 1.76% 74.95% 605ms 1.76% std::_Rb_tree_increment 9ms 0.026% 74.98% 574ms 1.67% CellPropertyCollection::GetPropertiesType (inline) 181ms 0.53% 75.50% 526ms 1.53% __GI___libc_malloc 3ms 0.0087% 75.51% 504ms 1.46% Cell::GetMutationState 2ms 0.0058% 75.52% 490ms 1.42% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 75.52% 479ms 1.39% AbstractCellBasedSimulation::DoCellRemoval (inline) 1ms 0.0029% 75.52% 466ms 1.35% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 140ms 0.41% 75.92% 437ms 1.27% __GI___libc_free 432ms 1.25% 77.18% 432ms 1.25% Node::GetIndex 0 0% 77.18% 420ms 1.22% std::allocator_traits::allocate (inline) 0 0% 77.18% 395ms 1.15% std::_Rb_tree::_M_create_node (inline) 28ms 0.081% 77.26% 393ms 1.14% boost::detail::shared_count::~shared_count (inline) 0 0% 77.26% 393ms 1.14% boost::shared_ptr::~shared_ptr (inline) 362ms 1.05% 78.31% 362ms 1.05% __gnu_cxx::__normal_iterator::operator++ (inline) 358ms 1.04% 79.35% 362ms 1.05% boost::detail::sp_counted_base::release 355ms 1.03% 80.38% 355ms 1.03% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 80.38% 349ms 1.01% std::_Rb_tree::_M_get_node (inline) 2ms 0.0058% 80.38% 347ms 1.01% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 6ms 0.017% 80.40% 343ms 1% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 80.40% 341ms 0.99% AbstractCellProperty::IsSubType (inline) 0 0% 80.40% 337ms 0.98% boost::numeric::ublas::inner_prod (inline) 1ms 0.0029% 80.41% 336ms 0.97% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 12ms 0.035% 80.44% 335ms 0.97% boost::numeric::ublas::vector_scalar_binary::evaluate 9ms 0.026% 80.47% 322ms 0.93% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 80.47% 319ms 0.93% NodesOnlyMesh::ReMesh 33ms 0.096% 80.56% 319ms 0.93% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 80.56% 319ms 0.93% boost::numeric::ublas::vector::vector (inline) 5ms 0.015% 80.58% 310ms 0.9% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 1ms 0.0029% 80.58% 303ms 0.88% NodesOnlyMesh::UpdateNodeIndices 259ms 0.75% 81.33% 296ms 0.86% _int_free 130ms 0.38% 81.71% 291ms 0.84% boost::numeric::ublas::vector_inner_prod::apply (inline) 8ms 0.023% 81.73% 289ms 0.84% DistributedBoxCollection::GetProcessOwningNode 4ms 0.012% 81.74% 289ms 0.84% std::_Rb_tree::_M_emplace_hint_unique 69ms 0.2% 81.94% 283ms 0.82% Node::GetRadius 0 0% 81.94% 274ms 0.8% NodesOnlyMesh::UpdateBoxCollection 106ms 0.31% 82.25% 269ms 0.78% std::__move_median_to_first (inline) 94ms 0.27% 82.52% 264ms 0.77% std::_Rb_tree::_M_erase (partial-inline) 139ms 0.4% 82.93% 261ms 0.76% _int_malloc 0 0% 82.93% 257ms 0.75% boost::numeric::ublas::c_vector::assign (inline) 14ms 0.041% 82.97% 257ms 0.75% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 82.97% 242ms 0.7% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 215ms 0.62% 83.59% 241ms 0.7% Node::AddNeighbour 0 0% 83.59% 241ms 0.7% VtkMeshWriter::WriteFiles 0 0% 83.59% 235ms 0.68% Cell::HasCellProperty (inline) 1ms 0.0029% 83.59% 235ms 0.68% CellPropertyCollection::HasProperty 3ms 0.0087% 83.60% 232ms 0.67% std::_Rb_tree::_Rb_tree (partial-inline) 231ms 0.67% 84.27% 231ms 0.67% Node::CheckForNodeAttributes 224ms 0.65% 84.92% 224ms 0.65% [libchaste_cell_based.so] 0 0% 84.92% 223ms 0.65% NodesOnlyMesh::AddNodesToBoxes 25ms 0.073% 85.00% 222ms 0.64% std::_Rb_tree::_M_copy (inline) 0 0% 85.00% 218ms 0.63% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 85.00% 213ms 0.62% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 85.00% 213ms 0.62% vtkStreamingDemandDrivenPipeline::Update 0 0% 85.00% 213ms 0.62% vtkXMLWriterBase::Write 23ms 0.067% 85.06% 211ms 0.61% std::__insertion_sort (inline) 0 0% 85.06% 211ms 0.61% vtkDemandDrivenPipeline::ProcessRequest 5ms 0.015% 85.08% 209ms 0.61% Cell::ReadyToDivide 209ms 0.61% 85.68% 209ms 0.61% [libchaste_mesh.so] 0 0% 85.68% 208ms 0.6% vtkExecutive::CallAlgorithm 207ms 0.6% 86.28% 207ms 0.6% NodeBasedCellPopulation::GetNode 0 0% 86.28% 207ms 0.6% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 86.28% 206ms 0.6% vtkCompositeDataPipeline::ExecuteData 0 0% 86.28% 206ms 0.6% vtkDemandDrivenPipeline::ExecuteData 0 0% 86.28% 206ms 0.6% vtkXMLUnstructuredDataWriter::ProcessRequest 53ms 0.15% 86.44% 198ms 0.57% std::__find_if (inline) 0 0% 86.44% 198ms 0.57% std::find_if (inline) 0 0% 86.44% 198ms 0.57% std::none_of (inline) 24ms 0.07% 86.51% 196ms 0.57% std::_Rb_tree::_M_clone_node (inline) 1ms 0.0029% 86.51% 194ms 0.56% AbstractCellProperty::IsType (inline) 190ms 0.55% 87.06% 190ms 0.55% __strcmp_avx2 0 0% 87.06% 177ms 0.51% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 87.06% 174ms 0.5% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 87.06% 174ms 0.5% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData