File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 21666ms, 88.12% of 24586ms total Dropped 793 nodes (cum <= 122.93ms) flat flat% sum% cum cum% 0 0% 0% 24433ms 99.38% __libc_start_call_main 0 0% 0% 24433ms 99.38% __libc_start_main_impl 0 0% 0% 24433ms 99.38% _start 0 0% 0% 24418ms 99.32% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 24418ms 99.32% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 24418ms 99.32% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 24418ms 99.32% main 0 0% 0% 24378ms 99.15% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 24378ms 99.15% CxxTest::TestRunner::runTest (inline) 0 0% 0% 24378ms 99.15% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 24370ms 99.12% AbstractCellBasedSimulation::Solve 2ms 0.0081% 0.0081% 13636ms 55.46% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0081% 9472ms 38.53% AbstractCellBasedSimulation::UpdateCellPopulation 6ms 0.024% 0.033% 8727ms 35.50% ForwardEulerNumericalMethod::UpdateAllNodePositions 7ms 0.028% 0.061% 8540ms 34.74% AbstractNumericalMethod::ComputeForcesIncludingDamping 2ms 0.0081% 0.069% 8342ms 33.93% NodeBasedCellPopulation::Update 1113ms 4.53% 4.60% 7690ms 31.28% RepulsionForce::AddForceContribution (partial-inline) 8ms 0.033% 4.63% 6095ms 24.79% DistributedBoxCollection::CalculateInteriorNodePairs 2119ms 8.62% 13.25% 5019ms 20.41% std::_Rb_tree::_M_lower_bound (inline) 20ms 0.081% 13.33% 4657ms 18.94% NodeAttributes::RemoveDuplicateNeighbours 0 0% 13.33% 4572ms 18.60% OffLatticeSimulation::ApplyBoundaries 6ms 0.024% 13.35% 4313ms 17.54% std::__sort (inline) 0 0% 13.35% 4313ms 17.54% std::sort (inline) 208ms 0.85% 14.20% 4090ms 16.64% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 4ms 0.016% 14.22% 3474ms 14.13% AbstractCellPopulation::Iterator::operator++ (inline) 169ms 0.69% 14.90% 3441ms 14.00% AbstractCellPopulation::Iterator::IsRealCell (inline) 91ms 0.37% 15.27% 3422ms 13.92% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 249ms 1.01% 16.29% 3246ms 13.20% std::_Rb_tree::find (inline) 0 0% 16.29% 3245ms 13.20% std::map::find (inline) 23ms 0.094% 16.38% 2939ms 11.95% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2866ms 11.66% 28.04% 2866ms 11.66% std::_Rb_tree::_S_right (inline) 239ms 0.97% 29.01% 2545ms 10.35% std::map::operator[] (partial-inline) 208ms 0.85% 29.85% 2541ms 10.34% std::__introsort_loop 40ms 0.16% 30.02% 2412ms 9.81% PlaneBoundaryCondition::ImposeBoundaryCondition 154ms 0.63% 30.64% 2323ms 9.45% AbstractMesh::GetNode 35ms 0.14% 30.79% 2293ms 9.33% NodesOnlyMesh::GetNodeOrHaloNode 42ms 0.17% 30.96% 2291ms 9.32% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 30.96% 2233ms 9.08% std::__unguarded_partition_pivot (inline) 152ms 0.62% 31.57% 2223ms 9.04% DistributedBoxCollection::AddPairsFromBox 76ms 0.31% 31.88% 2171ms 8.83% NodesOnlyMesh::SolveNodeMapping 15ms 0.061% 31.95% 2160ms 8.79% PlaneBoundaryCondition::VerifyBoundaryCondition 0 0% 31.95% 2040ms 8.30% std::_Rb_tree::lower_bound (inline) 0 0% 31.95% 2040ms 8.30% std::map::lower_bound (inline) 997ms 4.06% 36.00% 1945ms 7.91% std::__unguarded_partition (inline) 2ms 0.0081% 36.01% 1763ms 7.17% std::__final_insertion_sort (inline) 23ms 0.094% 36.10% 1684ms 6.85% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 28ms 0.11% 36.22% 1655ms 6.73% AbstractCellPopulation::GetCellUsingLocationIndex 90ms 0.37% 36.58% 1562ms 6.35% std::__unguarded_insertion_sort (inline) 534ms 2.17% 38.75% 1516ms 6.17% std::__unguarded_linear_insert (inline) 1441ms 5.86% 44.61% 1441ms 5.86% __gnu_cxx::__normal_iterator::operator-- (inline) 41ms 0.17% 44.78% 1334ms 5.43% boost::numeric::ublas::c_vector::c_vector (partial-inline) 3ms 0.012% 44.79% 1246ms 5.07% DistributedBoxCollection::CalculateBoundaryNodePairs 54ms 0.22% 45.01% 1212ms 4.93% boost::numeric::ublas::vector_assign (inline) 0 0% 45.01% 1199ms 4.88% NodeBasedCellPopulation::UpdateCellProcessLocation 299ms 1.22% 46.23% 1062ms 4.32% boost::numeric::ublas::indexing_vector_assign 346ms 1.41% 47.64% 1039ms 4.23% __dynamic_cast 38ms 0.15% 47.79% 866ms 3.52% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.0081% 47.80% 832ms 3.38% CellPropertyCollection::GetPropertiesType (inline) 826ms 3.36% 51.16% 826ms 3.36% std::_Rb_tree_increment 367ms 1.49% 52.65% 823ms 3.35% DistributedBoxCollection::CalculateContainingBox (partial-inline) 168ms 0.68% 53.34% 798ms 3.25% AbstractMesh::GetVectorFromAtoB 21ms 0.085% 53.42% 790ms 3.21% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 53.42% 768ms 3.12% AbstractCellPopulation::WriteResultsToFiles 2ms 0.0081% 53.43% 766ms 3.12% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 53.43% 752ms 3.06% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 53.43% 719ms 2.92% boost::numeric::ublas::norm_2 (inline) 557ms 2.27% 55.69% 719ms 2.92% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 55.69% 719ms 2.92% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 715ms 2.91% 58.60% 715ms 2.91% boost::numeric::ublas::c_vector::operator() 0 0% 58.60% 682ms 2.77% AbstractCellBasedSimulation::DoCellBirth 180ms 0.73% 59.33% 679ms 2.76% NodeAttributes::AddNeighbour 5ms 0.02% 59.35% 664ms 2.70% boost::numeric::ublas::c_vector::operator= (inline) 31ms 0.13% 59.48% 646ms 2.63% std::__copy_move::__copy_m (inline) 0 0% 59.48% 646ms 2.63% std::__copy_move_a (inline) 0 0% 59.48% 646ms 2.63% std::__copy_move_a1 (inline) 0 0% 59.48% 646ms 2.63% std::__copy_move_a2 (inline) 0 0% 59.48% 646ms 2.63% std::copy (inline) 635ms 2.58% 62.06% 635ms 2.58% __memcpy_avx_unaligned_erms 278ms 1.13% 63.19% 598ms 2.43% __cxxabiv1::__si_class_type_info::__do_dyncast 497ms 2.02% 65.22% 596ms 2.42% std::vector::push_back (inline) 2ms 0.0081% 65.22% 585ms 2.38% Cell::GetMutationState 96ms 0.39% 65.61% 562ms 2.29% std::__new_allocator::allocate (inline) 13ms 0.053% 65.67% 553ms 2.25% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 65.67% 537ms 2.18% std::allocator_traits::allocate (inline) 57ms 0.23% 65.90% 533ms 2.17% std::_Rb_tree::_M_copy (inline) 37ms 0.15% 66.05% 523ms 2.13% boost::detail::shared_count::~shared_count (inline) 0 0% 66.05% 523ms 2.13% boost::shared_ptr::~shared_ptr (inline) 518ms 2.11% 68.16% 518ms 2.11% boost::numeric::ublas::same_impl_ex 0 0% 68.16% 504ms 2.05% std::_Rb_tree::_M_create_node (inline) 5ms 0.02% 68.18% 502ms 2.04% AbstractCellProperty::IsSubType (inline) 3ms 0.012% 68.19% 493ms 2.01% NodeBasedCellPopulation::WriteVtkResultsToFile 466ms 1.90% 70.08% 478ms 1.94% boost::detail::sp_counted_base::release 183ms 0.74% 70.83% 475ms 1.93% std::_Rb_tree::_M_clone_node (inline) 22ms 0.089% 70.92% 461ms 1.88% operator new 457ms 1.86% 72.78% 457ms 1.86% __strcmp_avx2 106ms 0.43% 73.21% 451ms 1.83% Node::AddNeighbour 3ms 0.012% 73.22% 451ms 1.83% std::set::set (inline) 0 0% 73.22% 447ms 1.82% AbstractCellBasedSimulation::DoCellRemoval (inline) 149ms 0.61% 73.83% 440ms 1.79% std::_Rb_tree::_M_erase 0 0% 73.83% 439ms 1.79% std::_Rb_tree::_M_get_node (inline) 101ms 0.41% 74.24% 432ms 1.76% __GI___libc_malloc 3ms 0.012% 74.25% 428ms 1.74% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 125ms 0.51% 74.76% 382ms 1.55% Node::GetRadius 382ms 1.55% 76.31% 382ms 1.55% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 76.31% 382ms 1.55% boost::numeric::ublas::c_vector::assign (inline) 370ms 1.50% 77.82% 370ms 1.50% Node::ConstructNodeAttributes (inline) 49ms 0.2% 78.02% 356ms 1.45% std::_Rb_tree::~_Rb_tree (inline) 0 0% 78.02% 344ms 1.40% std::_Rb_tree::_Alloc_node::operator() (inline) 20ms 0.081% 78.10% 327ms 1.33% boost::numeric::ublas::vector_binary::size (inline) 1ms 0.0041% 78.10% 316ms 1.29% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 78.10% 307ms 1.25% NodesOnlyMesh::ReMesh 0 0% 78.10% 305ms 1.24% boost::numeric::ublas::inner_prod (inline) 19ms 0.077% 78.18% 305ms 1.24% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 78.18% 305ms 1.24% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 301ms 1.22% 79.40% 301ms 1.22% std::__adjacent_find (inline) 0 0% 79.40% 301ms 1.22% std::__unique (inline) 0 0% 79.40% 301ms 1.22% std::unique (inline) 5ms 0.02% 79.42% 293ms 1.19% NodesOnlyMesh::UpdateNodeIndices 0 0% 79.42% 286ms 1.16% Cell::HasCellProperty (inline) 3ms 0.012% 79.44% 286ms 1.16% CellPropertyCollection::HasProperty 0 0% 79.44% 283ms 1.15% NodesOnlyMesh::UpdateBoxCollection 113ms 0.46% 79.90% 283ms 1.15% std::__move_median_to_first (inline) 1ms 0.0041% 79.90% 279ms 1.13% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 79.90% 279ms 1.13% std::_Rb_tree::_M_drop_node (inline) 149ms 0.61% 80.51% 272ms 1.11% _int_malloc 6ms 0.024% 80.53% 271ms 1.10% Cell::ReadyToDivide 266ms 1.08% 81.61% 266ms 1.08% __gnu_cxx::__normal_iterator::operator++ (inline) 3ms 0.012% 81.62% 266ms 1.08% std::_Rb_tree::_M_emplace_hint_unique 4ms 0.016% 81.64% 265ms 1.08% DistributedBoxCollection::GetProcessOwningNode 263ms 1.07% 82.71% 263ms 1.07% Node::CheckForNodeAttributes 0 0% 82.71% 254ms 1.03% std::set::~set (inline) 95ms 0.39% 83.10% 235ms 0.96% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 83.10% 232ms 0.94% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 83.10% 231ms 0.94% VtkMeshWriter::WriteFiles 1ms 0.0041% 83.10% 229ms 0.93% NodesOnlyMesh::AddNodesToBoxes 0 0% 83.10% 228ms 0.93% NodesOnlyMesh::ResizeBoxCollection 11ms 0.045% 83.14% 227ms 0.92% NodesOnlyMesh::IsANodeCloseToDomainBoundary 3ms 0.012% 83.16% 226ms 0.92% std::__new_allocator::deallocate (inline) 212ms 0.86% 84.02% 212ms 0.86% [libchaste_cell_based.so] 88ms 0.36% 84.38% 208ms 0.85% __GI___libc_free 208ms 0.85% 85.22% 208ms 0.85% boost::shared_ptr::operator-> (inline) 98ms 0.4% 85.62% 208ms 0.85% boost::shared_ptr::shared_ptr (inline) 0 0% 85.62% 208ms 0.85% std::allocator_traits::deallocate (inline) 0 0% 85.62% 206ms 0.84% vtkDemandDrivenPipeline::ProcessRequest 0 0% 85.62% 206ms 0.84% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 85.62% 206ms 0.84% vtkStreamingDemandDrivenPipeline::Update 0 0% 85.62% 206ms 0.84% vtkXMLWriterBase::Write 0 0% 85.62% 205ms 0.83% std::_Rb_tree::_M_put_node (inline) 0 0% 85.62% 205ms 0.83% vtkCompositeDataPipeline::ExecuteData 0 0% 85.62% 205ms 0.83% vtkDemandDrivenPipeline::ExecuteData 0 0% 85.62% 205ms 0.83% vtkExecutive::CallAlgorithm 0 0% 85.62% 205ms 0.83% vtkXMLUnstructuredDataWriter::ProcessRequest 16ms 0.065% 85.69% 199ms 0.81% std::__insertion_sort (inline) 0 0% 85.69% 183ms 0.74% Cell::GetCellId 6ms 0.024% 85.71% 182ms 0.74% AbstractCellProperty::IsType (inline) 179ms 0.73% 86.44% 179ms 0.73% Node::GetIndex 0 0% 86.44% 179ms 0.73% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 86.44% 179ms 0.73% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 86.44% 176ms 0.72% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 3ms 0.012% 86.45% 160ms 0.65% DistributedBoxCollection::GetIsPeriodicAllDims 0 0% 86.45% 160ms 0.65% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 86.45% 159ms 0.65% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 61ms 0.25% 86.70% 150ms 0.61% AbstractCellCycleModel::GetAge 0 0% 86.70% 149ms 0.61% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 86.70% 149ms 0.61% std::_Rb_tree::clear (inline) 0 0% 86.70% 145ms 0.59% vtkXMLWriter::WriteBinaryData 0 0% 86.70% 139ms 0.57% vtkXMLWriter::WriteBinaryDataInternal 19ms 0.077% 86.78% 138ms 0.56% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 86.78% 138ms 0.56% vtkXMLWriter::WriteBinaryDataBlock 0 0% 86.78% 138ms 0.56% vtkXMLWriter::WriteCompressionBlock 136ms 0.55% 87.33% 136ms 0.55% Node::IsDeleted 4ms 0.016% 87.35% 134ms 0.55% boost::numeric::ublas::c_vector::operator[] (inline) 61ms 0.25% 87.59% 132ms 0.54% AbstractCellProperty::IsSame 129ms 0.52% 88.12% 129ms 0.52% [libchaste_mesh.so] 0 0% 88.12% 128ms 0.52% vtkXMLWriter::WritePointsAppendedData 1ms 0.0041% 88.12% 125ms 0.51% AbstractCentreBasedCellPopulation::CreateCellPair