File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 30033ms, 89.30% of 33630ms total Dropped 728 nodes (cum <= 168.15ms) flat flat% sum% cum cum% 0 0% 0% 33488ms 99.58% __libc_start_call_main 0 0% 0% 33488ms 99.58% __libc_start_main_impl 0 0% 0% 33488ms 99.58% _start 0 0% 0% 33471ms 99.53% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 33471ms 99.53% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 33471ms 99.53% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 33471ms 99.53% main 0 0% 0% 33435ms 99.42% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 33435ms 99.42% CxxTest::TestRunner::runTest (inline) 0 0% 0% 33435ms 99.42% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 33427ms 99.40% AbstractCellBasedSimulation::Solve 0 0% 0% 23687ms 70.43% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.0059% 0.0059% 18966ms 56.40% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.03% 0.036% 18786ms 55.86% AbstractNumericalMethod::ComputeForcesIncludingDamping 204ms 0.61% 0.64% 18208ms 54.14% AbstractTwoBodyInteractionForce::AddForceContribution 1479ms 4.40% 5.04% 15345ms 45.63% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4285ms 12.74% 17.78% 9349ms 27.80% std::_Rb_tree::_M_lower_bound (inline) 0 0% 17.78% 8580ms 25.51% AbstractCellBasedSimulation::UpdateCellPopulation 342ms 1.02% 18.80% 8499ms 25.27% std::_Rb_tree::find (inline) 0 0% 18.80% 8499ms 25.27% std::map::find (inline) 153ms 0.45% 19.25% 8358ms 24.85% NodesOnlyMesh::GetNodeOrHaloNode 515ms 1.53% 20.79% 8202ms 24.39% AbstractMesh::GetNode 307ms 0.91% 21.70% 7690ms 22.87% NodesOnlyMesh::SolveNodeMapping 0 0% 21.70% 7580ms 22.54% NodeBasedCellPopulation::Update 196ms 0.58% 22.28% 6481ms 19.27% boost::numeric::ublas::vector_assign (inline) 210ms 0.62% 22.91% 6316ms 18.78% boost::numeric::ublas::c_vector::c_vector (partial-inline) 5ms 0.015% 22.92% 5577ms 16.58% DistributedBoxCollection::CalculateInteriorNodePairs 5037ms 14.98% 37.90% 5037ms 14.98% std::_Rb_tree::_S_right (inline) 23ms 0.068% 37.97% 4463ms 13.27% NodeAttributes::RemoveDuplicateNeighbours 1ms 0.003% 37.97% 4452ms 13.24% OffLatticeSimulation::ApplyBoundaries 8ms 0.024% 37.99% 4276ms 12.71% std::__sort (inline) 0 0% 37.99% 4276ms 12.71% std::sort (inline) 1186ms 3.53% 41.52% 3699ms 11.00% boost::numeric::ublas::indexing_vector_assign 2ms 0.0059% 41.53% 3364ms 10.00% AbstractCellPopulation::Iterator::operator++ (inline) 181ms 0.54% 42.06% 3344ms 9.94% AbstractCellPopulation::Iterator::IsRealCell (inline) 71ms 0.21% 42.27% 3339ms 9.93% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 27ms 0.08% 42.36% 2835ms 8.43% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 197ms 0.59% 42.94% 2390ms 7.11% std::__introsort_loop 24ms 0.071% 43.01% 2321ms 6.90% PlaneBoundaryCondition::ImposeBoundaryCondition 36ms 0.11% 43.12% 2266ms 6.74% AbstractCellPopulation::GetLocationIndexUsingCell 12ms 0.036% 43.15% 2130ms 6.33% PlaneBoundaryCondition::VerifyBoundaryCondition 0 0% 43.15% 2125ms 6.32% std::__unguarded_partition_pivot (inline) 965ms 2.87% 46.02% 1938ms 5.76% std::__unguarded_partition (inline) 1ms 0.003% 46.03% 1877ms 5.58% std::__final_insertion_sort (inline) 226ms 0.67% 46.70% 1738ms 5.17% std::map::operator[] (partial-inline) 146ms 0.43% 47.13% 1734ms 5.16% DistributedBoxCollection::AddPairsFromBox 103ms 0.31% 47.44% 1686ms 5.01% std::__unguarded_insertion_sort (inline) 146ms 0.43% 47.87% 1665ms 4.95% AbstractMesh::GetVectorFromAtoB 1663ms 4.94% 52.82% 1663ms 4.94% boost::numeric::ublas::same_impl_ex 620ms 1.84% 54.66% 1608ms 4.78% std::__unguarded_linear_insert (inline) 1418ms 4.22% 58.88% 1418ms 4.22% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 58.88% 1279ms 3.80% std::_Rb_tree::lower_bound (inline) 0 0% 58.88% 1279ms 3.80% std::map::lower_bound (inline) 0 0% 58.88% 1257ms 3.74% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 58.88% 1247ms 3.71% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1142ms 3.40% 62.27% 1142ms 3.40% boost::numeric::ublas::c_vector::operator() 0 0% 62.27% 1129ms 3.36% NodeBasedCellPopulation::UpdateCellProcessLocation 22ms 0.065% 62.34% 1093ms 3.25% boost::numeric::ublas::detail::expression_type_check (inline) 5ms 0.015% 62.36% 1060ms 3.15% DistributedBoxCollection::CalculateBoundaryNodePairs 212ms 0.63% 62.99% 1046ms 3.11% boost::numeric::ublas::detail::equals 167ms 0.5% 63.48% 1024ms 3.04% boost::numeric::ublas::vector_binary::size (inline) 201ms 0.6% 64.08% 926ms 2.75% NodeAttributes::AddAppliedForceContribution 402ms 1.20% 65.28% 852ms 2.53% __GI___libc_free 24ms 0.071% 65.35% 825ms 2.45% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 71ms 0.21% 65.56% 800ms 2.38% std::__new_allocator::allocate (inline) 369ms 1.10% 66.65% 795ms 2.36% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 66.65% 786ms 2.34% boost::numeric::ublas::norm_inf (inline) 442ms 1.31% 67.97% 786ms 2.34% boost::numeric::ublas::vector_norm_inf::apply (inline) 86ms 0.26% 68.22% 732ms 2.18% operator new 512ms 1.52% 69.75% 727ms 2.16% __dynamic_cast 0 0% 69.75% 725ms 2.16% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 69.75% 725ms 2.16% boost::numeric::ublas::c_vector::plus_assign (inline) 178ms 0.53% 70.28% 709ms 2.11% NodeAttributes::AddNeighbour 0 0% 70.28% 682ms 2.03% AbstractCellPopulation::WriteResultsToFiles 250ms 0.74% 71.02% 643ms 1.91% __GI___libc_malloc 531ms 1.58% 72.60% 589ms 1.75% std::vector::push_back (inline) 3ms 0.0089% 72.61% 579ms 1.72% AbstractCellBasedSimulation::DoCellBirth 5ms 0.015% 72.62% 512ms 1.52% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 72.62% 471ms 1.40% boost::numeric::ublas::norm_2 (inline) 357ms 1.06% 73.68% 471ms 1.40% boost::numeric::ublas::vector_norm_2::apply (inline) 13ms 0.039% 73.72% 466ms 1.39% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 73.72% 466ms 1.39% boost::numeric::ublas::vector::vector (inline) 47ms 0.14% 73.86% 460ms 1.37% std::_Rb_tree_const_iterator::operator++ (inline) 406ms 1.21% 75.07% 450ms 1.34% _int_free 1ms 0.003% 75.07% 449ms 1.34% NodeBasedCellPopulation::WriteVtkResultsToFile 426ms 1.27% 76.34% 426ms 1.27% Node::GetIndex 0 0% 76.34% 420ms 1.25% AbstractCellBasedSimulation::DoCellRemoval (inline) 4ms 0.012% 76.35% 410ms 1.22% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 408ms 1.21% 77.56% 408ms 1.21% std::_Rb_tree_increment 3ms 0.0089% 77.57% 406ms 1.21% CellPropertyCollection::GetPropertiesType (inline) 26ms 0.077% 77.65% 385ms 1.14% boost::detail::shared_count::~shared_count (inline) 0 0% 77.65% 385ms 1.14% boost::shared_ptr::~shared_ptr (inline) 123ms 0.37% 78.02% 361ms 1.07% Node::GetRadius 360ms 1.07% 79.09% 360ms 1.07% __gnu_cxx::__normal_iterator::operator++ (inline) 352ms 1.05% 80.13% 353ms 1.05% boost::detail::sp_counted_base::release 3ms 0.0089% 80.14% 348ms 1.03% Cell::GetMutationState 0 0% 80.14% 347ms 1.03% std::allocator_traits::allocate (inline) 22ms 0.065% 80.21% 327ms 0.97% boost::numeric::ublas::vector_reference::operator() (inline) 2ms 0.0059% 80.21% 313ms 0.93% AbstractCellProperty::IsSubType (inline) 0 0% 80.21% 311ms 0.92% std::_Rb_tree::_M_create_node (inline) 0 0% 80.21% 299ms 0.89% NodesOnlyMesh::ReMesh 0 0% 80.21% 297ms 0.88% boost::numeric::ublas::inner_prod (inline) 3ms 0.0089% 80.22% 297ms 0.88% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 1ms 0.003% 80.23% 294ms 0.87% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 18ms 0.054% 80.28% 294ms 0.87% boost::numeric::ublas::vector_scalar_binary::evaluate 4ms 0.012% 80.29% 291ms 0.87% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 80.29% 286ms 0.85% NodesOnlyMesh::UpdateBoxCollection 3ms 0.0089% 80.30% 285ms 0.85% NodesOnlyMesh::UpdateNodeIndices 281ms 0.84% 81.14% 281ms 0.84% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 5ms 0.015% 81.15% 273ms 0.81% DistributedBoxCollection::GetProcessOwningNode 0 0% 81.15% 269ms 0.8% std::_Rb_tree::_M_get_node (inline) 112ms 0.33% 81.48% 266ms 0.79% std::_Rb_tree::_M_erase (partial-inline) 0 0% 81.48% 258ms 0.77% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 3ms 0.0089% 81.49% 257ms 0.76% AbstractCellPopulation::GetCellUsingLocationIndex 247ms 0.73% 82.23% 247ms 0.73% Node::CheckForNodeAttributes 244ms 0.73% 82.95% 244ms 0.73% Node::rGetLocation 96ms 0.29% 83.24% 242ms 0.72% boost::numeric::ublas::vector_inner_prod::apply (inline) 237ms 0.7% 83.94% 237ms 0.7% [libchaste_cell_based.so] 2ms 0.0059% 83.95% 236ms 0.7% NodesOnlyMesh::AddNodesToBoxes 233ms 0.69% 84.64% 233ms 0.69% boost::numeric::ublas::c_vector::size (inline) 8ms 0.024% 84.67% 233ms 0.69% std::_Rb_tree::_M_emplace_hint_unique 0 0% 84.67% 228ms 0.68% boost::numeric::ublas::c_vector::assign (inline) 108ms 0.32% 84.99% 226ms 0.67% std::__find_if (inline) 0 0% 84.99% 226ms 0.67% std::find_if (inline) 0 0% 84.99% 226ms 0.67% std::none_of (inline) 224ms 0.67% 85.65% 224ms 0.67% NodeBasedCellPopulation::GetNode 0 0% 85.65% 222ms 0.66% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 85.65% 217ms 0.65% boost::numeric::ublas::vector_reference::size (inline) 0 0% 85.65% 213ms 0.63% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 85.65% 212ms 0.63% VtkMeshWriter::WriteFiles 210ms 0.62% 86.28% 210ms 0.62% [libchaste_mesh.so] 210ms 0.62% 86.90% 210ms 0.62% boost::numeric::ublas::scalar_plus_assign::apply (inline) 208ms 0.62% 87.52% 208ms 0.62% __strcmp_avx2 3ms 0.0089% 87.53% 199ms 0.59% CellPropertyCollection::HasProperty 0 0% 87.53% 198ms 0.59% Cell::HasCellProperty (inline) 0 0% 87.53% 195ms 0.58% tcache_get (inline) 195ms 0.58% 88.11% 195ms 0.58% tcache_get_n (inline) 0 0% 88.11% 193ms 0.57% NodesOnlyMesh::ResizeBoxCollection 110ms 0.33% 88.44% 193ms 0.57% _int_malloc 20ms 0.059% 88.50% 192ms 0.57% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 88.50% 192ms 0.57% std::_Rb_tree::_Alloc_node::operator() (inline) 19ms 0.056% 88.55% 190ms 0.56% std::__insertion_sort (inline) 95ms 0.28% 88.83% 186ms 0.55% std::__move_median_to_first (inline) 0 0% 88.83% 184ms 0.55% vtkDemandDrivenPipeline::ProcessRequest 0 0% 88.83% 184ms 0.55% vtkExecutive::CallAlgorithm 0 0% 88.83% 184ms 0.55% vtkStreamingDemandDrivenPipeline::Update 0 0% 88.83% 184ms 0.55% vtkXMLWriterBase::Write 0 0% 88.83% 183ms 0.54% vtkCompositeDataPipeline::ExecuteData 0 0% 88.83% 183ms 0.54% vtkDemandDrivenPipeline::ExecuteData 0 0% 88.83% 183ms 0.54% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 88.83% 183ms 0.54% vtkXMLUnstructuredDataWriter::ProcessRequest 4ms 0.012% 88.85% 180ms 0.54% Cell::ReadyToDivide 26ms 0.077% 88.92% 178ms 0.53% std::__new_allocator::deallocate (inline) 5ms 0.015% 88.94% 174ms 0.52% std::_Rb_tree::_Rb_tree (partial-inline) 4ms 0.012% 88.95% 173ms 0.51% AbstractCellProperty::IsType (inline) 119ms 0.35% 89.30% 173ms 0.51% Node::AddAppliedForceContribution