File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 19371ms, 89.85% of 21560ms total Dropped 748 nodes (cum <= 107.80ms) flat flat% sum% cum cum% 0 0% 0% 21484ms 99.65% __libc_start_call_main 0 0% 0% 21484ms 99.65% __libc_start_main_impl 0 0% 0% 21484ms 99.65% _start 0 0% 0% 21469ms 99.58% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 21469ms 99.58% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 21469ms 99.58% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 21469ms 99.58% main 0 0% 0% 21434ms 99.42% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 21434ms 99.42% CxxTest::TestRunner::runTest (inline) 0 0% 0% 21434ms 99.42% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 21427ms 99.38% AbstractCellBasedSimulation::Solve 0 0% 0% 12124ms 56.23% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0% 8265ms 38.33% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 7259ms 33.67% NodeBasedCellPopulation::Update 0 0% 0% 6871ms 31.87% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.019% 0.019% 6706ms 31.10% AbstractNumericalMethod::ComputeForcesIncludingDamping 889ms 4.12% 4.14% 6195ms 28.73% RepulsionForce::AddForceContribution (partial-inline) 7ms 0.032% 4.17% 5496ms 25.49% DistributedBoxCollection::CalculateInteriorNodePairs 0 0% 4.17% 4984ms 23.12% OffLatticeSimulation::ApplyBoundaries 1999ms 9.27% 13.45% 4676ms 21.69% std::_Rb_tree::_M_lower_bound (inline) 17ms 0.079% 13.53% 4401ms 20.41% NodeAttributes::RemoveDuplicateNeighbours 2ms 0.0093% 13.53% 4186ms 19.42% std::__sort (inline) 0 0% 13.53% 4186ms 19.42% std::sort (inline) 260ms 1.21% 14.74% 3635ms 16.86% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 2ms 0.0093% 14.75% 3426ms 15.89% AbstractCellPopulation::Iterator::operator++ (inline) 194ms 0.9% 15.65% 3422ms 15.87% AbstractCellPopulation::Iterator::IsRealCell (inline) 152ms 0.71% 16.35% 3382ms 15.69% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 233ms 1.08% 17.44% 3043ms 14.11% std::_Rb_tree::find (inline) 0 0% 17.44% 3043ms 14.11% std::map::find (inline) 25ms 0.12% 17.55% 2851ms 13.22% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 59ms 0.27% 17.82% 2574ms 11.94% AbstractMesh::GetNode 47ms 0.22% 18.04% 2559ms 11.87% NodesOnlyMesh::GetNodeOrHaloNode 58ms 0.27% 18.31% 2534ms 11.75% PlaneBoundaryCondition::ImposeBoundaryCondition 250ms 1.16% 19.47% 2520ms 11.69% NodesOnlyMesh::SolveNodeMapping 222ms 1.03% 20.50% 2507ms 11.63% std::__introsort_loop 254ms 1.18% 21.68% 2477ms 11.49% std::map::operator[] (partial-inline) 63ms 0.29% 21.97% 2450ms 11.36% PlaneBoundaryCondition::VerifyBoundaryCondition 2366ms 10.97% 32.95% 2366ms 10.97% std::_Rb_tree::_S_right (inline) 5ms 0.023% 32.97% 2208ms 10.24% std::__unguarded_partition_pivot (inline) 84ms 0.39% 33.36% 2103ms 9.75% AbstractCellPopulation::GetLocationIndexUsingCell 703ms 3.26% 36.62% 1983ms 9.20% std::__unguarded_partition (inline) 0 0% 36.62% 1907ms 8.85% std::_Rb_tree::lower_bound (inline) 0 0% 36.62% 1907ms 8.85% std::map::lower_bound (inline) 1ms 0.0046% 36.62% 1674ms 7.76% std::__final_insertion_sort (inline) 113ms 0.52% 37.15% 1600ms 7.42% DistributedBoxCollection::AddPairsFromBox 113ms 0.52% 37.67% 1500ms 6.96% std::__unguarded_insertion_sort (inline) 9ms 0.042% 37.71% 1436ms 6.66% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 20ms 0.093% 37.81% 1415ms 6.56% AbstractCellPopulation::GetCellUsingLocationIndex 688ms 3.19% 41.00% 1318ms 6.11% std::__unguarded_linear_insert (inline) 15ms 0.07% 41.07% 1121ms 5.20% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 41.07% 1047ms 4.86% NodeBasedCellPopulation::UpdateCellProcessLocation 63ms 0.29% 41.36% 1029ms 4.77% boost::numeric::ublas::c_vector::c_vector (partial-inline) 899ms 4.17% 45.53% 899ms 4.17% __gnu_cxx::__normal_iterator::operator-- (inline) 13ms 0.06% 45.59% 888ms 4.12% DistributedBoxCollection::CalculateBoundaryNodePairs 2ms 0.0093% 45.60% 860ms 3.99% boost::numeric::ublas::vector_assign (inline) 21ms 0.097% 45.70% 851ms 3.95% boost::detail::shared_count::~shared_count (inline) 0 0% 45.70% 851ms 3.95% boost::shared_ptr::~shared_ptr (inline) 793ms 3.68% 49.37% 805ms 3.73% boost::detail::sp_counted_base::release 193ms 0.9% 50.27% 743ms 3.45% boost::numeric::ublas::indexing_vector_assign 215ms 1% 51.27% 740ms 3.43% __dynamic_cast 274ms 1.27% 52.54% 662ms 3.07% DistributedBoxCollection::CalculateContainingBox (partial-inline) 103ms 0.48% 53.01% 645ms 2.99% AbstractMesh::GetVectorFromAtoB 0 0% 53.01% 621ms 2.88% AbstractCellPopulation::WriteResultsToFiles 584ms 2.71% 55.72% 584ms 2.71% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 63ms 0.29% 56.02% 577ms 2.68% std::__new_allocator::allocate (inline) 23ms 0.11% 56.12% 564ms 2.62% std::_Rb_tree_const_iterator::operator++ (inline) 559ms 2.59% 58.72% 559ms 2.59% __gnu_cxx::__normal_iterator::operator++ (inline) 260ms 1.21% 59.92% 550ms 2.55% NodeAttributes::AddNeighbour 0 0% 59.92% 550ms 2.55% std::allocator_traits::allocate (inline) 0 0% 59.92% 531ms 2.46% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 59.92% 530ms 2.46% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 9ms 0.042% 59.96% 526ms 2.44% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 21ms 0.097% 60.06% 520ms 2.41% operator new 513ms 2.38% 62.44% 513ms 2.38% [libchaste_cell_based.so] 0 0% 62.44% 513ms 2.38% boost::numeric::ublas::norm_2 (inline) 399ms 1.85% 64.29% 513ms 2.38% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 64.29% 513ms 2.38% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 2ms 0.0093% 64.30% 501ms 2.32% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 64.30% 498ms 2.31% std::_Rb_tree::_M_create_node (inline) 165ms 0.77% 65.06% 491ms 2.28% __GI___libc_malloc 33ms 0.15% 65.22% 489ms 2.27% std::__copy_move::__copy_m (inline) 0 0% 65.22% 489ms 2.27% std::__copy_move_a (inline) 0 0% 65.22% 489ms 2.27% std::__copy_move_a1 (inline) 0 0% 65.22% 489ms 2.27% std::__copy_move_a2 (inline) 0 0% 65.22% 488ms 2.26% std::copy (inline) 5ms 0.023% 65.24% 481ms 2.23% CellPropertyCollection::GetPropertiesType (inline) 0 0% 65.24% 479ms 2.22% std::_Rb_tree::_M_get_node (inline) 0 0% 65.24% 475ms 2.20% AbstractCellBasedSimulation::DoCellBirth 473ms 2.19% 67.44% 473ms 2.19% [libchaste_mesh.so] 3ms 0.014% 67.45% 460ms 2.13% AbstractCentreBasedCellPopulation::GetDampingConstant 459ms 2.13% 69.58% 459ms 2.13% std::_Rb_tree_increment 446ms 2.07% 71.65% 446ms 2.07% __memcpy_avx512_unaligned_erms 18ms 0.083% 71.73% 445ms 2.06% std::_Rb_tree::_Rb_tree (partial-inline) 214ms 0.99% 72.72% 443ms 2.05% __cxxabiv1::__si_class_type_info::__do_dyncast 441ms 2.05% 74.77% 441ms 2.05% boost::numeric::ublas::c_vector::operator() 421ms 1.95% 76.72% 421ms 1.95% boost::numeric::ublas::same_impl_ex 23ms 0.11% 76.83% 418ms 1.94% std::_Rb_tree::_M_copy (inline) 2ms 0.0093% 76.84% 408ms 1.89% NodeBasedCellPopulation::WriteVtkResultsToFile 50ms 0.23% 77.07% 398ms 1.85% std::_Rb_tree::_M_erase (partial-inline) 86ms 0.4% 77.47% 389ms 1.80% std::_Rb_tree::~_Rb_tree (inline) 154ms 0.71% 78.18% 387ms 1.79% std::_Rb_tree::_M_clone_node (inline) 273ms 1.27% 79.45% 384ms 1.78% std::vector::push_back (inline) 1ms 0.0046% 79.45% 373ms 1.73% std::set::set (inline) 0 0% 79.45% 345ms 1.60% std::_Rb_tree::_M_drop_node (inline) 3ms 0.014% 79.47% 335ms 1.55% AbstractCellProperty::IsSubType (inline) 1ms 0.0046% 79.47% 329ms 1.53% Cell::GetMutationState 0 0% 79.47% 327ms 1.52% std::set::~set (inline) 322ms 1.49% 80.96% 322ms 1.49% std::_Rb_tree::_S_left (inline) 6ms 0.028% 80.99% 315ms 1.46% std::_Rb_tree::_M_emplace_hint_unique 0 0% 80.99% 308ms 1.43% NodesOnlyMesh::ReMesh 14ms 0.065% 81.06% 308ms 1.43% boost::numeric::ublas::vector_binary::size (inline) 4ms 0.019% 81.08% 297ms 1.38% NodesOnlyMesh::UpdateNodeIndices 297ms 1.38% 82.45% 297ms 1.38% __strcmp_evex 0 0% 82.45% 279ms 1.29% std::_Rb_tree::_Alloc_node::operator() (inline) 158ms 0.73% 83.19% 269ms 1.25% _int_malloc 10ms 0.046% 83.23% 267ms 1.24% NodeBasedCellPopulation::UpdateMapsAfterRemesh 6ms 0.028% 83.26% 259ms 1.20% std::__new_allocator::deallocate (inline) 2ms 0.0093% 83.27% 257ms 1.19% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 1ms 0.0046% 83.27% 238ms 1.10% DistributedBoxCollection::GetProcessOwningNode 2ms 0.0093% 83.28% 237ms 1.10% Node::GetRadius 0 0% 83.28% 237ms 1.10% NodesOnlyMesh::UpdateBoxCollection 200ms 0.93% 84.21% 232ms 1.08% boost::shared_ptr::shared_ptr (inline) 0 0% 84.21% 231ms 1.07% std::allocator_traits::deallocate (inline) 0 0% 84.21% 229ms 1.06% std::_Rb_tree::_M_put_node (inline) 49ms 0.23% 84.44% 228ms 1.06% __GI___libc_free 0 0% 84.44% 219ms 1.02% boost::numeric::ublas::c_vector::assign (inline) 0 0% 84.44% 219ms 1.02% std::_Rb_tree::_Auto_node::_Auto_node (inline) 73ms 0.34% 84.78% 213ms 0.99% std::__move_median_to_first (inline) 0 0% 84.78% 206ms 0.96% NodesOnlyMesh::AddNodesToBoxes 188ms 0.87% 85.65% 188ms 0.87% Node::CheckForNodeAttributes 0 0% 85.65% 187ms 0.87% boost::numeric::ublas::inner_prod (inline) 1ms 0.0046% 85.65% 187ms 0.87% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 8ms 0.037% 85.69% 186ms 0.86% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 85.69% 186ms 0.86% std::iter_swap (inline) 186ms 0.86% 86.55% 186ms 0.86% std::swap (inline) 0 0% 86.55% 185ms 0.86% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 86.55% 183ms 0.85% VtkMeshWriter::WriteFiles 151ms 0.7% 87.25% 176ms 0.82% _int_free 20ms 0.093% 87.35% 173ms 0.8% std::__insertion_sort (inline) 0 0% 87.35% 166ms 0.77% NodesOnlyMesh::ResizeBoxCollection 84ms 0.39% 87.74% 166ms 0.77% std::__adjacent_find (inline) 0 0% 87.74% 166ms 0.77% std::__unique (inline) 0 0% 87.74% 166ms 0.77% std::unique (inline) 14ms 0.065% 87.80% 164ms 0.76% NodesOnlyMesh::IsANodeCloseToDomainBoundary 161ms 0.75% 88.55% 161ms 0.75% boost::shared_ptr::operator-> (inline) 0 0% 88.55% 157ms 0.73% vtkDemandDrivenPipeline::ProcessRequest 0 0% 88.55% 157ms 0.73% vtkStreamingDemandDrivenPipeline::Update 0 0% 88.55% 157ms 0.73% vtkXMLWriterBase::Write 0 0% 88.55% 155ms 0.72% vtkExecutive::CallAlgorithm 0 0% 88.55% 154ms 0.71% vtkCompositeDataPipeline::ExecuteData 0 0% 88.55% 154ms 0.71% vtkDemandDrivenPipeline::ExecuteData 0 0% 88.55% 154ms 0.71% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 88.55% 154ms 0.71% vtkXMLUnstructuredDataWriter::ProcessRequest 3ms 0.014% 88.56% 153ms 0.71% CellPropertyCollection::HasProperty 0 0% 88.56% 151ms 0.7% Cell::HasCellProperty (inline) 40ms 0.19% 88.75% 146ms 0.68% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 88.75% 140ms 0.65% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 88.75% 137ms 0.64% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 88.75% 137ms 0.64% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 2ms 0.0093% 88.76% 135ms 0.63% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 88.76% 134ms 0.62% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 2ms 0.0093% 88.77% 127ms 0.59% AbstractCellPopulation::SetCellUsingLocationIndex 1ms 0.0046% 88.77% 126ms 0.58% Cell::ReadyToDivide 0 0% 88.77% 125ms 0.58% std::__new_allocator::destroy (inline) 0 0% 88.77% 125ms 0.58% std::allocator_traits::destroy (inline) 0 0% 88.77% 123ms 0.57% std::_Rb_tree::_M_destroy_node (inline) 5ms 0.023% 88.79% 118ms 0.55% AbstractCellProperty::IsType (inline) 2ms 0.0093% 88.80% 118ms 0.55% DistributedBoxCollection::GetIsPeriodicAllDims 6ms 0.028% 88.83% 116ms 0.54% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 88.83% 115ms 0.53% vtkXMLWriter::WriteBinaryData 112ms 0.52% 89.35% 112ms 0.52% Node::GetIndex 0 0% 89.35% 112ms 0.52% vtkXMLWriter::WriteBinaryDataBlock 0 0% 89.35% 112ms 0.52% vtkXMLWriter::WriteBinaryDataInternal 2ms 0.0093% 89.36% 111ms 0.51% Cell::GetCellId 0 0% 89.36% 111ms 0.51% vtkXMLWriter::WriteCompressionBlock 105ms 0.49% 89.85% 109ms 0.51% __ieee754_log_fma