File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 22067ms, 89.16% of 24750ms total Dropped 832 nodes (cum <= 123.75ms) flat flat% sum% cum cum% 0 0% 0% 24635ms 99.54% __libc_start_main_impl 0 0% 0% 24635ms 99.54% _start 0 0% 0% 24634ms 99.53% __libc_start_call_main 0 0% 0% 24616ms 99.46% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 24616ms 99.46% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 24616ms 99.46% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 24616ms 99.46% main 0 0% 0% 24576ms 99.30% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 24576ms 99.30% CxxTest::TestRunner::runTest (inline) 0 0% 0% 24576ms 99.30% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 24567ms 99.26% AbstractCellBasedSimulation::Solve 0 0% 0% 14116ms 57.03% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0% 9248ms 37.37% AbstractCellBasedSimulation::UpdateCellPopulation 6ms 0.024% 0.024% 9109ms 36.80% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.04% 0.065% 8922ms 36.05% AbstractNumericalMethod::ComputeForcesIncludingDamping 1267ms 5.12% 5.18% 8237ms 33.28% RepulsionForce::AddForceContribution (partial-inline) 0 0% 5.18% 8209ms 33.17% NodeBasedCellPopulation::Update 12ms 0.048% 5.23% 5982ms 24.17% DistributedBoxCollection::CalculateInteriorNodePairs 2168ms 8.76% 13.99% 5077ms 20.51% std::_Rb_tree::_M_lower_bound (inline) 14ms 0.057% 14.05% 4714ms 19.05% NodeAttributes::RemoveDuplicateNeighbours 1ms 0.004% 14.05% 4714ms 19.05% OffLatticeSimulation::ApplyBoundaries 2ms 0.0081% 14.06% 4380ms 17.70% std::__sort (inline) 0 0% 14.06% 4380ms 17.70% std::sort (inline) 206ms 0.83% 14.89% 4112ms 16.61% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 269ms 1.09% 15.98% 3381ms 13.66% std::_Rb_tree::find (inline) 0 0% 15.98% 3380ms 13.66% std::map::find (inline) 91ms 0.37% 16.35% 3308ms 13.37% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 2ms 0.0081% 16.36% 3092ms 12.49% AbstractCellPopulation::Iterator::operator++ (inline) 141ms 0.57% 16.93% 3062ms 12.37% AbstractCellPopulation::Iterator::IsRealCell 2880ms 11.64% 28.56% 2880ms 11.64% std::_Rb_tree::_S_right (inline) 16ms 0.065% 28.63% 2660ms 10.75% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 192ms 0.78% 29.40% 2604ms 10.52% std::__introsort_loop 22ms 0.089% 29.49% 2509ms 10.14% PlaneBoundaryCondition::ImposeBoundaryCondition 232ms 0.94% 30.43% 2495ms 10.08% std::map::operator[] (partial-inline) 173ms 0.7% 31.13% 2472ms 9.99% AbstractMesh::GetNode 69ms 0.28% 31.41% 2469ms 9.98% NodesOnlyMesh::GetNodeOrHaloNode 0 0% 31.41% 2329ms 9.41% std::__unguarded_partition_pivot (inline) 91ms 0.37% 31.77% 2305ms 9.31% NodesOnlyMesh::SolveNodeMapping 49ms 0.2% 31.97% 2256ms 9.12% AbstractCellPopulation::GetLocationIndexUsingCell 22ms 0.089% 32.06% 2204ms 8.91% PlaneBoundaryCondition::VerifyBoundaryCondition 1041ms 4.21% 36.27% 2090ms 8.44% std::__unguarded_partition (inline) 0 0% 36.27% 2001ms 8.08% std::_Rb_tree::lower_bound (inline) 0 0% 36.27% 2001ms 8.08% std::map::lower_bound (inline) 155ms 0.63% 36.89% 2000ms 8.08% DistributedBoxCollection::AddPairsFromBox 0 0% 36.89% 1766ms 7.14% std::__final_insertion_sort (inline) 26ms 0.11% 37.00% 1752ms 7.08% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 26ms 0.11% 37.10% 1719ms 6.95% AbstractCellPopulation::GetCellUsingLocationIndex 115ms 0.46% 37.57% 1573ms 6.36% std::__unguarded_insertion_sort (inline) 536ms 2.17% 39.73% 1481ms 5.98% std::__unguarded_linear_insert (inline) 1440ms 5.82% 45.55% 1440ms 5.82% __gnu_cxx::__normal_iterator::operator-- (inline) 34ms 0.14% 45.69% 1382ms 5.58% boost::numeric::ublas::c_vector::c_vector (partial-inline) 5ms 0.02% 45.71% 1254ms 5.07% DistributedBoxCollection::CalculateBoundaryNodePairs 7ms 0.028% 45.74% 1235ms 4.99% boost::numeric::ublas::vector_assign (inline) 0 0% 45.74% 1149ms 4.64% NodeBasedCellPopulation::UpdateCellProcessLocation 265ms 1.07% 46.81% 1139ms 4.60% boost::numeric::ublas::indexing_vector_assign 19ms 0.077% 46.88% 974ms 3.94% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 287ms 1.16% 48.04% 951ms 3.84% __dynamic_cast 173ms 0.7% 48.74% 908ms 3.67% AbstractMesh::GetVectorFromAtoB 383ms 1.55% 50.29% 871ms 3.52% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 50.29% 867ms 3.50% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 50.29% 848ms 3.43% boost::numeric::ublas::norm_2 (inline) 678ms 2.74% 53.03% 848ms 3.43% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 53.03% 848ms 3.43% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 8ms 0.032% 53.06% 797ms 3.22% boost::numeric::ublas::c_vector::operator= (inline) 39ms 0.16% 53.22% 765ms 3.09% std::__copy_move::__copy_m (inline) 0 0% 53.22% 765ms 3.09% std::__copy_move_a (inline) 0 0% 53.22% 765ms 3.09% std::__copy_move_a1 (inline) 0 0% 53.22% 765ms 3.09% std::__copy_move_a2 (inline) 0 0% 53.22% 765ms 3.09% std::copy (inline) 741ms 2.99% 56.21% 741ms 2.99% __memcpy_avx_unaligned_erms 0 0% 56.21% 739ms 2.99% AbstractCellPopulation::WriteResultsToFiles 723ms 2.92% 59.14% 723ms 2.92% boost::numeric::ublas::c_vector::operator() 165ms 0.67% 59.80% 719ms 2.91% NodeAttributes::AddNeighbour 553ms 2.23% 62.04% 632ms 2.55% std::vector::push_back (inline) 32ms 0.13% 62.17% 627ms 2.53% std::_Rb_tree_const_iterator::operator++ (inline) 5ms 0.02% 62.19% 621ms 2.51% CellPropertyCollection::GetPropertiesType (inline) 8ms 0.032% 62.22% 607ms 2.45% AbstractCentreBasedCellPopulation::GetDampingConstant 54ms 0.22% 62.44% 576ms 2.33% boost::detail::shared_count::~shared_count (inline) 0 0% 62.44% 576ms 2.33% boost::shared_ptr::~shared_ptr (inline) 569ms 2.30% 64.74% 569ms 2.30% boost::numeric::ublas::same_impl_ex 569ms 2.30% 67.03% 569ms 2.30% std::_Rb_tree_increment 5ms 0.02% 67.05% 568ms 2.29% AbstractCellBasedSimulation::DoCellBirth 90ms 0.36% 67.42% 564ms 2.28% std::__new_allocator::allocate (inline) 23ms 0.093% 67.51% 558ms 2.25% std::_Rb_tree::_Rb_tree (partial-inline) 293ms 1.18% 68.69% 544ms 2.20% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 68.69% 534ms 2.16% std::allocator_traits::allocate (inline) 33ms 0.13% 68.83% 521ms 2.11% std::_Rb_tree::_M_copy (inline) 0 0% 68.83% 519ms 2.10% std::_Rb_tree::_M_create_node (inline) 494ms 2.00% 70.82% 510ms 2.06% boost::detail::sp_counted_base::release 3ms 0.012% 70.84% 489ms 1.98% NodeBasedCellPopulation::WriteVtkResultsToFile 179ms 0.72% 71.56% 484ms 1.96% std::_Rb_tree::_M_clone_node (inline) 2ms 0.0081% 71.57% 473ms 1.91% std::set::set (inline) 0 0% 71.57% 471ms 1.90% AbstractCellBasedSimulation::DoCellRemoval (inline) 44ms 0.18% 71.75% 470ms 1.90% operator new 0 0% 71.75% 467ms 1.89% std::_Rb_tree::_M_get_node (inline) 5ms 0.02% 71.77% 460ms 1.86% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1ms 0.004% 71.77% 438ms 1.77% AbstractCellProperty::IsSubType (inline) 438ms 1.77% 73.54% 438ms 1.77% __strcmp_avx2 4ms 0.016% 73.56% 436ms 1.76% Cell::GetMutationState 102ms 0.41% 73.97% 436ms 1.76% std::_Rb_tree::_M_erase 153ms 0.62% 74.59% 423ms 1.71% __GI___libc_malloc 0 0% 74.59% 406ms 1.64% boost::numeric::ublas::inner_prod (inline) 26ms 0.11% 74.69% 404ms 1.63% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 74.69% 404ms 1.63% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 81ms 0.33% 75.02% 384ms 1.55% Node::GetRadius 58ms 0.23% 75.25% 377ms 1.52% boost::numeric::ublas::vector_binary::size (inline) 0 0% 75.25% 363ms 1.47% std::_Rb_tree::_Alloc_node::operator() (inline) 355ms 1.43% 76.69% 355ms 1.43% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 67ms 0.27% 76.96% 353ms 1.43% std::_Rb_tree::~_Rb_tree (inline) 0 0% 76.96% 347ms 1.40% boost::numeric::ublas::c_vector::assign (inline) 0 0% 76.96% 331ms 1.34% NodesOnlyMesh::ReMesh 186ms 0.75% 77.71% 331ms 1.34% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 77.71% 327ms 1.32% std::_Rb_tree::_M_drop_node (inline) 3ms 0.012% 77.72% 324ms 1.31% NodesOnlyMesh::UpdateNodeIndices 312ms 1.26% 78.98% 312ms 1.26% Node::CheckForNodeAttributes 307ms 1.24% 80.22% 307ms 1.24% std::__adjacent_find (inline) 0 0% 80.22% 307ms 1.24% std::__unique (inline) 0 0% 80.22% 307ms 1.24% std::unique (inline) 7ms 0.028% 80.25% 306ms 1.24% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 6ms 0.024% 80.27% 305ms 1.23% NodeBasedCellPopulation::UpdateMapsAfterRemesh 290ms 1.17% 81.45% 290ms 1.17% __gnu_cxx::__normal_iterator::operator++ (inline) 9ms 0.036% 81.48% 288ms 1.16% DistributedBoxCollection::GetProcessOwningNode 0 0% 81.48% 281ms 1.14% std::set::~set (inline) 0 0% 81.48% 277ms 1.12% NodesOnlyMesh::UpdateBoxCollection 4ms 0.016% 81.50% 266ms 1.07% std::__new_allocator::deallocate (inline) 8ms 0.032% 81.53% 262ms 1.06% std::_Rb_tree::_M_emplace_hint_unique 183ms 0.74% 82.27% 256ms 1.03% Node::AddNeighbour 256ms 1.03% 83.31% 256ms 1.03% [libchaste_mesh.so] 123ms 0.5% 83.80% 256ms 1.03% boost::shared_ptr::shared_ptr (inline) 0 0% 83.80% 252ms 1.02% std::allocator_traits::deallocate (inline) 0 0% 83.80% 246ms 0.99% std::_Rb_tree::_M_put_node (inline) 1ms 0.004% 83.81% 240ms 0.97% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 83.81% 237ms 0.96% VtkMeshWriter::WriteFiles 104ms 0.42% 84.23% 236ms 0.95% std::__move_median_to_first (inline) 75ms 0.3% 84.53% 235ms 0.95% __GI___libc_free 2ms 0.0081% 84.54% 221ms 0.89% NodesOnlyMesh::AddNodesToBoxes 120ms 0.48% 85.02% 217ms 0.88% _int_malloc 0 0% 85.02% 212ms 0.86% vtkDemandDrivenPipeline::ExecuteData 0 0% 85.02% 212ms 0.86% vtkDemandDrivenPipeline::ProcessRequest 0 0% 85.02% 212ms 0.86% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 85.02% 212ms 0.86% vtkStreamingDemandDrivenPipeline::Update 0 0% 85.02% 212ms 0.86% vtkXMLWriterBase::Write 0 0% 85.02% 210ms 0.85% vtkCompositeDataPipeline::ExecuteData 0 0% 85.02% 210ms 0.85% vtkExecutive::CallAlgorithm 0 0% 85.02% 210ms 0.85% vtkXMLUnstructuredDataWriter::ProcessRequest 4ms 0.016% 85.04% 208ms 0.84% CellPropertyCollection::HasProperty 0 0% 85.04% 207ms 0.84% Cell::HasCellProperty (inline) 6ms 0.024% 85.06% 201ms 0.81% Cell::ReadyToDivide 200ms 0.81% 85.87% 200ms 0.81% Node::GetIndex 18ms 0.073% 85.94% 193ms 0.78% std::__insertion_sort (inline) 0 0% 85.94% 182ms 0.74% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.94% 182ms 0.74% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 1ms 0.004% 85.95% 179ms 0.72% AbstractCellProperty::IsType (inline) 178ms 0.72% 86.67% 178ms 0.72% [libchaste_cell_based.so] 0 0% 86.67% 174ms 0.7% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 86.67% 168ms 0.68% std::_Rb_tree::clear (inline) 0 0% 86.67% 162ms 0.65% NodesOnlyMesh::ResizeBoxCollection 12ms 0.048% 86.72% 161ms 0.65% NodesOnlyMesh::IsANodeCloseToDomainBoundary 137ms 0.55% 87.27% 160ms 0.65% _int_free 0 0% 87.27% 156ms 0.63% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 87.27% 149ms 0.6% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 87.27% 146ms 0.59% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 145ms 0.59% 87.85% 145ms 0.59% __ieee754_log_fma 0 0% 87.85% 145ms 0.59% vtkXMLWriter::WriteBinaryData 1ms 0.004% 87.86% 142ms 0.57% Cell::GetCellId 0 0% 87.86% 142ms 0.57% boost::numeric::ublas::vector_binary::operator() (inline) 32ms 0.13% 87.99% 140ms 0.57% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 87.99% 139ms 0.56% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.99% 139ms 0.56% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.99% 139ms 0.56% vtkXMLWriter::WriteCompressionBlock 106ms 0.43% 88.42% 133ms 0.54% boost::detail::shared_count::shared_count (inline) 43ms 0.17% 88.59% 132ms 0.53% AbstractCellProperty::IsSame 0 0% 88.59% 132ms 0.53% vtkXMLWriter::WritePointsAppendedData 3ms 0.012% 88.60% 131ms 0.53% AbstractCellPopulation::SetCellUsingLocationIndex 131ms 0.53% 89.13% 131ms 0.53% Node::rGetLocation 6ms 0.024% 89.16% 129ms 0.52% boost::numeric::ublas::c_vector::operator[] (inline) 1ms 0.004% 89.16% 127ms 0.51% AbstractNumericalMethod::SafeNodePositionUpdate