File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 17251ms, 89.24% of 19330ms total Dropped 730 nodes (cum <= 96.65ms) flat flat% sum% cum cum% 0 0% 0% 19227ms 99.47% __libc_start_call_main 0 0% 0% 19227ms 99.47% __libc_start_main_impl 0 0% 0% 19227ms 99.47% _start 0 0% 0% 19213ms 99.39% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19213ms 99.39% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19213ms 99.39% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19213ms 99.39% main 0 0% 0% 19175ms 99.20% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19175ms 99.20% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19175ms 99.20% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 19168ms 99.16% AbstractCellBasedSimulation::Solve 1ms 0.0052% 0.0052% 11018ms 57.00% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0052% 7204ms 37.27% AbstractCellBasedSimulation::UpdateCellPopulation 7ms 0.036% 0.041% 7021ms 36.32% ForwardEulerNumericalMethod::UpdateAllNodePositions 5ms 0.026% 0.067% 6866ms 35.52% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.067% 6349ms 32.85% NodeBasedCellPopulation::Update 1047ms 5.42% 5.48% 6295ms 32.57% RepulsionForce::AddForceContribution (partial-inline) 6ms 0.031% 5.51% 4753ms 24.59% DistributedBoxCollection::CalculateInteriorNodePairs 1829ms 9.46% 14.98% 4188ms 21.67% std::_Rb_tree::_M_lower_bound (inline) 0 0% 14.98% 3761ms 19.46% OffLatticeSimulation::ApplyBoundaries 12ms 0.062% 15.04% 3562ms 18.43% NodeAttributes::RemoveDuplicateNeighbours 2ms 0.01% 15.05% 3417ms 17.68% std::__sort (inline) 0 0% 15.05% 3417ms 17.68% std::sort (inline) 139ms 0.72% 15.77% 3138ms 16.23% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 170ms 0.88% 16.65% 2732ms 14.13% std::_Rb_tree::find (inline) 0 0% 16.65% 2732ms 14.13% std::map::find (inline) 51ms 0.26% 16.91% 2673ms 13.83% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 3ms 0.016% 16.93% 2499ms 12.93% AbstractCellPopulation::Iterator::operator++ (inline) 145ms 0.75% 17.68% 2479ms 12.82% AbstractCellPopulation::Iterator::IsRealCell (inline) 2310ms 11.95% 29.63% 2310ms 11.95% std::_Rb_tree::_S_right (inline) 18ms 0.093% 29.72% 2164ms 11.20% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 180ms 0.93% 30.65% 2061ms 10.66% std::map::operator[] (partial-inline) 28ms 0.14% 30.80% 2032ms 10.51% PlaneBoundaryCondition::ImposeBoundaryCondition 139ms 0.72% 31.52% 2010ms 10.40% std::__introsort_loop 124ms 0.64% 32.16% 1983ms 10.26% AbstractMesh::GetNode 37ms 0.19% 32.35% 1971ms 10.20% NodesOnlyMesh::GetNodeOrHaloNode 43ms 0.22% 32.57% 1864ms 9.64% AbstractCellPopulation::GetLocationIndexUsingCell 73ms 0.38% 32.95% 1863ms 9.64% NodesOnlyMesh::SolveNodeMapping 0 0% 32.95% 1818ms 9.41% std::__unguarded_partition_pivot (inline) 6ms 0.031% 32.98% 1729ms 8.94% PlaneBoundaryCondition::VerifyBoundaryCondition 0 0% 32.98% 1651ms 8.54% std::_Rb_tree::lower_bound (inline) 0 0% 32.98% 1651ms 8.54% std::map::lower_bound (inline) 113ms 0.58% 33.56% 1627ms 8.42% DistributedBoxCollection::AddPairsFromBox 769ms 3.98% 37.54% 1600ms 8.28% std::__unguarded_partition (inline) 2ms 0.01% 37.55% 1404ms 7.26% std::__final_insertion_sort (inline) 15ms 0.078% 37.63% 1335ms 6.91% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 21ms 0.11% 37.74% 1316ms 6.81% AbstractCellPopulation::GetCellUsingLocationIndex 87ms 0.45% 38.19% 1255ms 6.49% std::__unguarded_insertion_sort (inline) 458ms 2.37% 40.56% 1182ms 6.11% std::__unguarded_linear_insert (inline) 1095ms 5.66% 46.22% 1095ms 5.66% __gnu_cxx::__normal_iterator::operator-- (inline) 43ms 0.22% 46.45% 1006ms 5.20% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 46.45% 913ms 4.72% NodeBasedCellPopulation::UpdateCellProcessLocation 7ms 0.036% 46.48% 851ms 4.40% boost::numeric::ublas::vector_assign (inline) 6ms 0.031% 46.51% 831ms 4.30% DistributedBoxCollection::CalculateBoundaryNodePairs 15ms 0.078% 46.59% 780ms 4.04% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 151ms 0.78% 47.37% 771ms 3.99% boost::numeric::ublas::indexing_vector_assign 222ms 1.15% 48.52% 724ms 3.75% __dynamic_cast 305ms 1.58% 50.10% 670ms 3.47% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 50.10% 667ms 3.45% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 135ms 0.7% 50.80% 646ms 3.34% AbstractMesh::GetVectorFromAtoB 0 0% 50.80% 646ms 3.34% boost::numeric::ublas::norm_2 (inline) 511ms 2.64% 53.44% 646ms 3.34% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 53.44% 646ms 3.34% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 162ms 0.84% 54.28% 619ms 3.20% NodeAttributes::AddNeighbour 3ms 0.016% 54.29% 607ms 3.14% boost::numeric::ublas::c_vector::operator= (inline) 24ms 0.12% 54.42% 588ms 3.04% std::__copy_move::__copy_m (inline) 0 0% 54.42% 588ms 3.04% std::__copy_move_a (inline) 0 0% 54.42% 588ms 3.04% std::__copy_move_a1 (inline) 0 0% 54.42% 588ms 3.04% std::__copy_move_a2 (inline) 0 0% 54.42% 588ms 3.04% std::copy (inline) 0 0% 54.42% 582ms 3.01% AbstractCellPopulation::WriteResultsToFiles 575ms 2.97% 57.39% 575ms 2.97% __memcpy_avx512_unaligned_erms 17ms 0.088% 57.48% 554ms 2.87% std::_Rb_tree_const_iterator::operator++ (inline) 455ms 2.35% 59.83% 549ms 2.84% std::vector::push_back (inline) 548ms 2.83% 62.67% 548ms 2.83% boost::numeric::ublas::c_vector::operator() 516ms 2.67% 65.34% 516ms 2.67% std::_Rb_tree_increment 10ms 0.052% 65.39% 512ms 2.65% AbstractCentreBasedCellPopulation::GetDampingConstant 8ms 0.041% 65.43% 502ms 2.60% CellPropertyCollection::GetPropertiesType (inline) 2ms 0.01% 65.44% 458ms 2.37% AbstractCellBasedSimulation::DoCellBirth 81ms 0.42% 65.86% 443ms 2.29% std::__new_allocator::allocate (inline) 433ms 2.24% 68.10% 433ms 2.24% boost::numeric::ublas::same_impl_ex 0 0% 68.10% 429ms 2.22% std::allocator_traits::allocate (inline) 33ms 0.17% 68.27% 405ms 2.10% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 68.27% 395ms 2.04% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 68.27% 393ms 2.03% std::_Rb_tree::_M_create_node (inline) 208ms 1.08% 69.35% 392ms 2.03% __cxxabiv1::__si_class_type_info::__do_dyncast 1ms 0.0052% 69.35% 388ms 2.01% NodeBasedCellPopulation::WriteVtkResultsToFile 2ms 0.01% 69.36% 387ms 2.00% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 32ms 0.17% 69.53% 364ms 1.88% std::_Rb_tree::_M_copy (inline) 2ms 0.01% 69.54% 361ms 1.87% Cell::GetMutationState 0 0% 69.54% 361ms 1.87% std::_Rb_tree::_M_get_node (inline) 11ms 0.057% 69.60% 359ms 1.86% operator new 37ms 0.19% 69.79% 358ms 1.85% boost::detail::shared_count::~shared_count (inline) 0 0% 69.79% 358ms 1.85% boost::shared_ptr::~shared_ptr (inline) 105ms 0.54% 70.33% 341ms 1.76% __GI___libc_malloc 337ms 1.74% 72.07% 337ms 1.74% __strcmp_evex 3ms 0.016% 72.09% 337ms 1.74% std::set::set (inline) 106ms 0.55% 72.64% 328ms 1.70% std::_Rb_tree::_M_clone_node (inline) 1ms 0.0052% 72.64% 322ms 1.67% AbstractCellProperty::IsSubType (inline) 306ms 1.58% 74.23% 316ms 1.63% boost::detail::sp_counted_base::release 75ms 0.39% 74.61% 316ms 1.63% boost::numeric::ublas::vector_binary::size (inline) 0 0% 74.61% 298ms 1.54% boost::numeric::ublas::inner_prod (inline) 21ms 0.11% 74.72% 295ms 1.53% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 74.72% 295ms 1.53% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 86ms 0.44% 75.17% 292ms 1.51% std::_Rb_tree::_M_erase 58ms 0.3% 75.47% 279ms 1.44% Node::GetRadius 278ms 1.44% 76.91% 278ms 1.44% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 76.91% 272ms 1.41% boost::numeric::ublas::c_vector::assign (inline) 7ms 0.036% 76.94% 251ms 1.30% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 76.94% 251ms 1.30% std::_Rb_tree::_Alloc_node::operator() (inline) 3ms 0.016% 76.96% 250ms 1.29% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 249ms 1.29% 78.25% 249ms 1.29% __gnu_cxx::__normal_iterator::operator++ (inline) 1ms 0.0052% 78.25% 245ms 1.27% NodesOnlyMesh::ReMesh 3ms 0.016% 78.27% 237ms 1.23% DistributedBoxCollection::GetProcessOwningNode 3ms 0.016% 78.28% 236ms 1.22% NodesOnlyMesh::UpdateNodeIndices 128ms 0.66% 78.94% 235ms 1.22% boost::numeric::ublas::vector_inner_prod::apply (inline) 231ms 1.20% 80.14% 231ms 1.20% Node::CheckForNodeAttributes 6ms 0.031% 80.17% 230ms 1.19% std::_Rb_tree::_M_emplace_hint_unique 35ms 0.18% 80.35% 230ms 1.19% std::_Rb_tree::~_Rb_tree (inline) 99ms 0.51% 80.86% 212ms 1.10% std::__move_median_to_first (inline) 0 0% 80.86% 208ms 1.08% NodesOnlyMesh::UpdateBoxCollection 0 0% 80.86% 205ms 1.06% std::_Rb_tree::_M_drop_node (inline) 109ms 0.56% 81.43% 193ms 1% _int_malloc 0 0% 81.43% 190ms 0.98% Cell::HasCellProperty (inline) 1ms 0.0052% 81.43% 190ms 0.98% CellPropertyCollection::HasProperty 0 0% 81.43% 189ms 0.98% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 81.43% 189ms 0.98% VtkMeshWriter::WriteFiles 166ms 0.86% 82.29% 188ms 0.97% Node::AddNeighbour 0 0% 82.29% 181ms 0.94% std::set::~set (inline) 3ms 0.016% 82.31% 174ms 0.9% std::__new_allocator::deallocate (inline) 0 0% 82.31% 170ms 0.88% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 82.31% 170ms 0.88% vtkStreamingDemandDrivenPipeline::Update 0 0% 82.31% 170ms 0.88% vtkXMLWriterBase::Write 7ms 0.036% 82.34% 169ms 0.87% Cell::ReadyToDivide 2ms 0.01% 82.35% 169ms 0.87% NodesOnlyMesh::AddNodesToBoxes 0 0% 82.35% 169ms 0.87% vtkDemandDrivenPipeline::ProcessRequest 168ms 0.87% 83.22% 168ms 0.87% Node::GetIndex 0 0% 83.22% 168ms 0.87% vtkExecutive::CallAlgorithm 0 0% 83.22% 168ms 0.87% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 83.22% 167ms 0.86% vtkCompositeDataPipeline::ExecuteData 0 0% 83.22% 167ms 0.86% vtkDemandDrivenPipeline::ExecuteData 82ms 0.42% 83.65% 166ms 0.86% boost::shared_ptr::shared_ptr (inline) 0 0% 83.65% 163ms 0.84% std::allocator_traits::deallocate (inline) 159ms 0.82% 84.47% 159ms 0.82% [libchaste_mesh.so] 0 0% 84.47% 158ms 0.82% std::_Rb_tree::_M_put_node (inline) 49ms 0.25% 84.72% 156ms 0.81% __GI___libc_free 21ms 0.11% 84.83% 147ms 0.76% std::__insertion_sort (inline) 24ms 0.12% 84.96% 145ms 0.75% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 84.96% 144ms 0.74% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 84.96% 144ms 0.74% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 84.96% 142ms 0.73% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 84.96% 140ms 0.72% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 84.96% 136ms 0.7% AbstractCellProperty::IsType (inline) 133ms 0.69% 85.64% 133ms 0.69% [libchaste_cell_based.so] 3ms 0.016% 85.66% 132ms 0.68% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 85.66% 129ms 0.67% NodesOnlyMesh::ResizeBoxCollection 10ms 0.052% 85.71% 128ms 0.66% NodesOnlyMesh::IsANodeCloseToDomainBoundary 123ms 0.64% 86.35% 123ms 0.64% std::__adjacent_find (inline) 0 0% 86.35% 123ms 0.64% std::__unique (inline) 0 0% 86.35% 123ms 0.64% std::unique (inline) 0 0% 86.35% 119ms 0.62% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 86.35% 116ms 0.6% vtkXMLWriter::WriteBinaryData 0 0% 86.35% 112ms 0.58% boost::numeric::ublas::vector_binary::operator() (inline) 1ms 0.0052% 86.35% 110ms 0.57% vtkXMLWriter::WriteBinaryDataInternal 109ms 0.56% 86.92% 109ms 0.56% Node::IsDeleted 0 0% 86.92% 109ms 0.56% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 86.92% 109ms 0.56% vtkXMLWriter::WriteBinaryDataBlock 0 0% 86.92% 109ms 0.56% vtkXMLWriter::WriteCompressionBlock 2ms 0.01% 86.93% 108ms 0.56% AbstractCellPopulation::SetCellUsingLocationIndex 108ms 0.56% 87.49% 108ms 0.56% Node::rGetLocation 95ms 0.49% 87.98% 107ms 0.55% _int_free 1ms 0.0052% 87.98% 107ms 0.55% std::_Rb_tree::clear (inline) 105ms 0.54% 88.53% 105ms 0.54% __ieee754_log_fma 104ms 0.54% 89.06% 104ms 0.54% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 35ms 0.18% 89.24% 103ms 0.53% AbstractCellProperty::IsSame 0 0% 89.24% 101ms 0.52% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 89.24% 101ms 0.52% vtkXMLWriter::WritePointsAppendedData 0 0% 89.24% 97ms 0.5% NodeBasedCellPopulation::AcceptCellWriter