File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 23784ms, 89.20% of 26663ms total Dropped 766 nodes (cum <= 133.31ms) flat flat% sum% cum cum% 0 0% 0% 26533ms 99.51% __libc_start_call_main 0 0% 0% 26533ms 99.51% __libc_start_main_impl 0 0% 0% 26533ms 99.51% _start 0 0% 0% 26514ms 99.44% main 0 0% 0% 26513ms 99.44% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 26513ms 99.44% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 26513ms 99.44% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 26479ms 99.31% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 26479ms 99.31% CxxTest::TestRunner::runTest (inline) 0 0% 0% 26479ms 99.31% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 26470ms 99.28% AbstractCellBasedSimulation::Solve 0 0% 0% 15031ms 56.37% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0% 10168ms 38.14% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.011% 0.011% 9777ms 36.67% ForwardEulerNumericalMethod::UpdateAllNodePositions 18ms 0.068% 0.079% 9574ms 35.91% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.0038% 0.083% 8887ms 33.33% NodeBasedCellPopulation::Update 1350ms 5.06% 5.15% 8568ms 32.13% RepulsionForce::AddForceContribution (partial-inline) 13ms 0.049% 5.19% 6529ms 24.49% DistributedBoxCollection::CalculateInteriorNodePairs 2195ms 8.23% 13.43% 5327ms 19.98% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.0038% 13.43% 4852ms 18.20% OffLatticeSimulation::ApplyBoundaries 11ms 0.041% 13.47% 4816ms 18.06% NodeAttributes::RemoveDuplicateNeighbours 4ms 0.015% 13.49% 4500ms 16.88% std::__sort (inline) 0 0% 13.49% 4500ms 16.88% std::sort (inline) 211ms 0.79% 14.28% 4413ms 16.55% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 78ms 0.29% 14.57% 3552ms 13.32% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 274ms 1.03% 15.60% 3508ms 13.16% std::_Rb_tree::find (inline) 0 0% 15.60% 3508ms 13.16% std::map::find (inline) 4ms 0.015% 15.61% 3422ms 12.83% AbstractCellPopulation::Iterator::operator++ (inline) 190ms 0.71% 16.33% 3389ms 12.71% AbstractCellPopulation::Iterator::IsRealCell (inline) 3122ms 11.71% 28.04% 3122ms 11.71% std::_Rb_tree::_S_right (inline) 30ms 0.11% 28.15% 2934ms 11.00% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 219ms 0.82% 28.97% 2652ms 9.95% std::map::operator[] (partial-inline) 206ms 0.77% 29.74% 2598ms 9.74% std::__introsort_loop 174ms 0.65% 30.39% 2579ms 9.67% AbstractMesh::GetNode 23ms 0.086% 30.48% 2577ms 9.67% PlaneBoundaryCondition::ImposeBoundaryCondition 72ms 0.27% 30.75% 2576ms 9.66% NodesOnlyMesh::GetNodeOrHaloNode 154ms 0.58% 31.33% 2501ms 9.38% DistributedBoxCollection::AddPairsFromBox 121ms 0.45% 31.78% 2406ms 9.02% NodesOnlyMesh::SolveNodeMapping 38ms 0.14% 31.92% 2332ms 8.75% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 31.92% 2310ms 8.66% std::__unguarded_partition_pivot (inline) 11ms 0.041% 31.97% 2274ms 8.53% PlaneBoundaryCondition::VerifyBoundaryCondition 0 0% 31.97% 2139ms 8.02% std::_Rb_tree::lower_bound (inline) 0 0% 31.97% 2139ms 8.02% std::map::lower_bound (inline) 1046ms 3.92% 35.89% 2040ms 7.65% std::__unguarded_partition (inline) 1ms 0.0038% 35.89% 1894ms 7.10% std::__final_insertion_sort (inline) 22ms 0.083% 35.97% 1891ms 7.09% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 31ms 0.12% 36.09% 1864ms 6.99% AbstractCellPopulation::GetCellUsingLocationIndex 119ms 0.45% 36.54% 1696ms 6.36% std::__unguarded_insertion_sort (inline) 571ms 2.14% 38.68% 1615ms 6.06% std::__unguarded_linear_insert (inline) 1503ms 5.64% 44.32% 1503ms 5.64% __gnu_cxx::__normal_iterator::operator-- (inline) 75ms 0.28% 44.60% 1337ms 5.01% boost::numeric::ublas::c_vector::c_vector (partial-inline) 7ms 0.026% 44.62% 1295ms 4.86% DistributedBoxCollection::CalculateBoundaryNodePairs 0 0% 44.62% 1221ms 4.58% NodeBasedCellPopulation::UpdateCellProcessLocation 7ms 0.026% 44.65% 1165ms 4.37% boost::numeric::ublas::vector_assign (inline) 208ms 0.78% 45.43% 1066ms 4.00% boost::numeric::ublas::indexing_vector_assign 357ms 1.34% 46.77% 1064ms 3.99% __dynamic_cast 38ms 0.14% 46.91% 996ms 3.74% std::_Rb_tree_const_iterator::operator++ (inline) 361ms 1.35% 48.27% 988ms 3.71% NodeAttributes::AddNeighbour 12ms 0.045% 48.31% 974ms 3.65% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 943ms 3.54% 51.85% 943ms 3.54% std::_Rb_tree_increment 18ms 0.068% 51.91% 920ms 3.45% CellPropertyCollection::GetPropertiesType (inline) 4ms 0.015% 51.93% 885ms 3.32% AbstractCentreBasedCellPopulation::GetDampingConstant 398ms 1.49% 53.42% 868ms 3.26% DistributedBoxCollection::CalculateContainingBox (partial-inline) 11ms 0.041% 53.46% 860ms 3.23% boost::numeric::ublas::c_vector::operator= (inline) 179ms 0.67% 54.13% 858ms 3.22% AbstractMesh::GetVectorFromAtoB 35ms 0.13% 54.27% 823ms 3.09% std::__copy_move::__copy_m (inline) 0 0% 54.27% 823ms 3.09% std::__copy_move_a (inline) 0 0% 54.27% 823ms 3.09% std::__copy_move_a1 (inline) 0 0% 54.27% 823ms 3.09% std::__copy_move_a2 (inline) 0 0% 54.27% 823ms 3.09% std::copy (inline) 799ms 3.00% 57.26% 799ms 3.00% __memcpy_avx_unaligned_erms 0 0% 57.26% 779ms 2.92% AbstractCellPopulation::WriteResultsToFiles 0 0% 57.26% 779ms 2.92% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 57.26% 767ms 2.88% boost::numeric::ublas::norm_2 (inline) 609ms 2.28% 59.55% 767ms 2.88% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 59.55% 767ms 2.88% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 7ms 0.026% 59.57% 759ms 2.85% AbstractCellBasedSimulation::DoCellBirth 624ms 2.34% 61.91% 729ms 2.73% std::vector::push_back (inline) 727ms 2.73% 64.64% 727ms 2.73% boost::numeric::ublas::c_vector::operator() 52ms 0.2% 64.84% 683ms 2.56% std::_Rb_tree::_Rb_tree (partial-inline) 3ms 0.011% 64.85% 677ms 2.54% Cell::GetMutationState 148ms 0.56% 65.40% 662ms 2.48% std::__new_allocator::allocate (inline) 0 0% 65.40% 640ms 2.40% std::allocator_traits::allocate (inline) 41ms 0.15% 65.56% 617ms 2.31% std::_Rb_tree::_M_copy (inline) 250ms 0.94% 66.49% 600ms 2.25% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 66.49% 594ms 2.23% std::_Rb_tree::_M_create_node (inline) 213ms 0.8% 67.29% 573ms 2.15% std::_Rb_tree::_M_clone_node (inline) 563ms 2.11% 69.40% 563ms 2.11% boost::numeric::ublas::same_impl_ex 22ms 0.083% 69.49% 562ms 2.11% boost::detail::shared_count::~shared_count (inline) 0 0% 69.49% 562ms 2.11% boost::shared_ptr::~shared_ptr (inline) 7ms 0.026% 69.51% 558ms 2.09% std::set::set (inline) 0 0% 69.51% 528ms 1.98% std::_Rb_tree::_M_get_node (inline) 504ms 1.89% 71.40% 519ms 1.95% boost::detail::sp_counted_base::release 0 0% 71.40% 518ms 1.94% AbstractCellBasedSimulation::DoCellRemoval (inline) 2ms 0.0075% 71.41% 512ms 1.92% NodeBasedCellPopulation::WriteVtkResultsToFile 29ms 0.11% 71.52% 508ms 1.91% operator new 7ms 0.026% 71.54% 505ms 1.89% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 495ms 1.86% 73.40% 495ms 1.86% __strcmp_avx2 1ms 0.0038% 73.41% 490ms 1.84% AbstractCellProperty::IsSubType (inline) 163ms 0.61% 74.02% 484ms 1.82% std::_Rb_tree::_M_erase 104ms 0.39% 74.41% 472ms 1.77% __GI___libc_malloc 100ms 0.38% 74.78% 415ms 1.56% boost::numeric::ublas::vector_binary::size (inline) 0 0% 74.78% 408ms 1.53% std::_Rb_tree::_Alloc_node::operator() (inline) 91ms 0.34% 75.12% 389ms 1.46% Node::GetRadius 378ms 1.42% 76.54% 378ms 1.42% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 2ms 0.0075% 76.55% 367ms 1.38% CellPropertyCollection::HasProperty 0 0% 76.55% 366ms 1.37% Cell::HasCellProperty (inline) 10ms 0.038% 76.59% 363ms 1.36% Cell::ReadyToDivide 0 0% 76.59% 354ms 1.33% boost::numeric::ublas::inner_prod (inline) 2ms 0.0075% 76.59% 353ms 1.32% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 76.59% 351ms 1.32% boost::numeric::ublas::c_vector::assign (inline) 16ms 0.06% 76.65% 351ms 1.32% boost::numeric::ublas::vector_scalar_binary::evaluate 317ms 1.19% 77.84% 342ms 1.28% Node::AddNeighbour 5ms 0.019% 77.86% 332ms 1.25% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 46ms 0.17% 78.03% 330ms 1.24% std::_Rb_tree::~_Rb_tree (inline) 0 0% 78.03% 329ms 1.23% NodesOnlyMesh::ReMesh 5ms 0.019% 78.05% 320ms 1.20% NodesOnlyMesh::UpdateNodeIndices 0 0% 78.05% 319ms 1.20% NodesOnlyMesh::UpdateBoxCollection 4ms 0.015% 78.07% 317ms 1.19% NodeBasedCellPopulation::UpdateMapsAfterRemesh 312ms 1.17% 79.24% 312ms 1.17% Node::CheckForNodeAttributes 7ms 0.026% 79.26% 308ms 1.16% DistributedBoxCollection::GetProcessOwningNode 141ms 0.53% 79.79% 308ms 1.16% _int_malloc 0 0% 79.79% 299ms 1.12% std::_Rb_tree::_M_drop_node (inline) 4ms 0.015% 79.81% 294ms 1.10% std::_Rb_tree::_M_emplace_hint_unique 289ms 1.08% 80.89% 290ms 1.09% std::__adjacent_find (inline) 0 0% 80.89% 290ms 1.09% std::__unique (inline) 0 0% 80.89% 290ms 1.09% std::unique (inline) 125ms 0.47% 81.36% 287ms 1.08% boost::numeric::ublas::vector_inner_prod::apply (inline) 278ms 1.04% 82.40% 278ms 1.04% __gnu_cxx::__normal_iterator::operator++ (inline) 4ms 0.015% 82.42% 271ms 1.02% std::__new_allocator::deallocate (inline) 93ms 0.35% 82.77% 268ms 1.01% std::__move_median_to_first (inline) 255ms 0.96% 83.72% 255ms 0.96% [libchaste_mesh.so] 94ms 0.35% 84.08% 247ms 0.93% __GI___libc_free 0 0% 84.08% 244ms 0.92% std::allocator_traits::deallocate (inline) 0 0% 84.08% 242ms 0.91% std::_Rb_tree::_M_put_node (inline) 0 0% 84.08% 233ms 0.87% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 84.08% 231ms 0.87% VtkMeshWriter::WriteFiles 6ms 0.023% 84.10% 229ms 0.86% NodesOnlyMesh::AddNodesToBoxes 114ms 0.43% 84.53% 225ms 0.84% boost::shared_ptr::shared_ptr (inline) 223ms 0.84% 85.36% 223ms 0.84% Node::GetIndex 0 0% 85.36% 219ms 0.82% std::_Rb_tree::clear (inline) 0 0% 85.36% 217ms 0.81% std::set::~set (inline) 0 0% 85.36% 213ms 0.8% vtkDemandDrivenPipeline::ProcessRequest 0 0% 85.36% 213ms 0.8% vtkStreamingDemandDrivenPipeline::Update 0 0% 85.36% 213ms 0.8% vtkXMLWriterBase::Write 0 0% 85.36% 211ms 0.79% vtkCompositeDataPipeline::ExecuteData 0 0% 85.36% 211ms 0.79% vtkDemandDrivenPipeline::ExecuteData 0 0% 85.36% 211ms 0.79% vtkExecutive::CallAlgorithm 0 0% 85.36% 211ms 0.79% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 85.36% 211ms 0.79% vtkXMLUnstructuredDataWriter::ProcessRequest 204ms 0.77% 86.13% 204ms 0.77% [libchaste_cell_based.so] 200ms 0.75% 86.88% 200ms 0.75% boost::shared_ptr::operator-> (inline) 2ms 0.0075% 86.88% 198ms 0.74% AbstractCellProperty::IsType (inline) 10ms 0.038% 86.92% 198ms 0.74% boost::numeric::ublas::vector_reference::operator() (inline) 12ms 0.045% 86.97% 197ms 0.74% std::__insertion_sort (inline) 0 0% 86.97% 195ms 0.73% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 86.97% 186ms 0.7% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 86.97% 183ms 0.69% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 86.97% 183ms 0.69% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 86.97% 179ms 0.67% NodesOnlyMesh::ResizeBoxCollection 11ms 0.041% 87.01% 178ms 0.67% NodesOnlyMesh::IsANodeCloseToDomainBoundary 1ms 0.0038% 87.01% 176ms 0.66% Cell::GetCellId 0 0% 87.01% 176ms 0.66% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 83ms 0.31% 87.32% 159ms 0.6% AbstractCellCycleModel::GetAge 0 0% 87.32% 159ms 0.6% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 79ms 0.3% 87.62% 153ms 0.57% AbstractCellProperty::IsSame 137ms 0.51% 88.13% 153ms 0.57% _int_free 6ms 0.023% 88.16% 149ms 0.56% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 88.16% 149ms 0.56% vtkXMLWriter::WriteBinaryData 0 0% 88.16% 145ms 0.54% vtkXMLWriter::WriteBinaryDataInternal 1ms 0.0038% 88.16% 144ms 0.54% vtkXMLWriter::WriteBinaryDataBlock 143ms 0.54% 88.70% 143ms 0.54% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 0 0% 88.70% 143ms 0.54% vtkXMLWriter::WriteCompressionBlock 1ms 0.0038% 88.70% 142ms 0.53% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 88.70% 137ms 0.51% std::map::clear (inline) 0 0% 88.70% 135ms 0.51% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 134ms 0.5% 89.20% 134ms 0.5% Node::rGetLocation