File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 15960ms, 89.03% of 17926ms total Dropped 691 nodes (cum <= 89.63ms) flat flat% sum% cum cum% 0 0% 0% 17876ms 99.72% __libc_start_call_main 0 0% 0% 17876ms 99.72% __libc_start_main_impl 0 0% 0% 17876ms 99.72% _start 0 0% 0% 17861ms 99.64% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 17861ms 99.64% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 17861ms 99.64% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 17861ms 99.64% main 0 0% 0% 17829ms 99.46% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 17829ms 99.46% CxxTest::TestRunner::runTest (inline) 0 0% 0% 17829ms 99.46% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 17824ms 99.43% AbstractCellBasedSimulation::Solve 1ms 0.0056% 0.0056% 9999ms 55.78% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0056% 6997ms 39.03% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.017% 0.022% 6131ms 34.20% NodeBasedCellPopulation::Update 3ms 0.017% 0.039% 5719ms 31.90% ForwardEulerNumericalMethod::UpdateAllNodePositions 5ms 0.028% 0.067% 5590ms 31.18% AbstractNumericalMethod::ComputeForcesIncludingDamping 694ms 3.87% 3.94% 5182ms 28.91% RepulsionForce::AddForceContribution (partial-inline) 4ms 0.022% 3.96% 4580ms 25.55% DistributedBoxCollection::CalculateInteriorNodePairs 0 0% 3.96% 4018ms 22.41% OffLatticeSimulation::ApplyBoundaries 1381ms 7.70% 11.66% 3806ms 21.23% std::_Rb_tree::_M_lower_bound (inline) 11ms 0.061% 11.73% 3719ms 20.75% NodeAttributes::RemoveDuplicateNeighbours 2ms 0.011% 11.74% 3562ms 19.87% std::__sort (inline) 0 0% 11.74% 3562ms 19.87% std::sort (inline) 215ms 1.20% 12.94% 3005ms 16.76% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 2ms 0.011% 12.95% 2915ms 16.26% AbstractCellPopulation::Iterator::operator++ (inline) 129ms 0.72% 13.67% 2909ms 16.23% AbstractCellPopulation::Iterator::IsRealCell (inline) 103ms 0.57% 14.24% 2810ms 15.68% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 180ms 1.00% 15.25% 2456ms 13.70% std::_Rb_tree::find (inline) 0 0% 15.25% 2456ms 13.70% std::map::find (inline) 15ms 0.084% 15.33% 2432ms 13.57% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2175ms 12.13% 27.46% 2175ms 12.13% std::_Rb_tree::_S_right (inline) 198ms 1.10% 28.57% 2162ms 12.06% std::__introsort_loop 50ms 0.28% 28.85% 2050ms 11.44% NodesOnlyMesh::GetNodeOrHaloNode 57ms 0.32% 29.16% 2049ms 11.43% AbstractMesh::GetNode 42ms 0.23% 29.40% 2034ms 11.35% PlaneBoundaryCondition::ImposeBoundaryCondition 195ms 1.09% 30.49% 1994ms 11.12% NodesOnlyMesh::SolveNodeMapping 188ms 1.05% 31.54% 1985ms 11.07% std::map::operator[] (partial-inline) 42ms 0.23% 31.77% 1984ms 11.07% PlaneBoundaryCondition::VerifyBoundaryCondition 21ms 0.12% 31.89% 1899ms 10.59% std::__unguarded_partition_pivot (inline) 631ms 3.52% 35.41% 1699ms 9.48% std::__unguarded_partition (inline) 68ms 0.38% 35.79% 1678ms 9.36% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 35.79% 1555ms 8.67% std::_Rb_tree::lower_bound (inline) 0 0% 35.79% 1555ms 8.67% std::map::lower_bound (inline) 0 0% 35.79% 1397ms 7.79% std::__final_insertion_sort (inline) 125ms 0.7% 36.48% 1360ms 7.59% DistributedBoxCollection::AddPairsFromBox 7ms 0.039% 36.52% 1280ms 7.14% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 16ms 0.089% 36.61% 1262ms 7.04% AbstractCellPopulation::GetCellUsingLocationIndex 87ms 0.49% 37.10% 1233ms 6.88% std::__unguarded_insertion_sort (inline) 578ms 3.22% 40.32% 1129ms 6.30% std::__unguarded_linear_insert (inline) 49ms 0.27% 40.59% 893ms 4.98% boost::numeric::ublas::c_vector::c_vector (partial-inline) 849ms 4.74% 45.33% 849ms 4.74% __gnu_cxx::__normal_iterator::operator-- (inline) 5ms 0.028% 45.36% 826ms 4.61% DistributedBoxCollection::CalculateBoundaryNodePairs 13ms 0.073% 45.43% 822ms 4.59% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 45.43% 815ms 4.55% NodeBasedCellPopulation::UpdateCellProcessLocation 10ms 0.056% 45.49% 775ms 4.32% boost::detail::shared_count::~shared_count (inline) 0 0% 45.49% 775ms 4.32% boost::shared_ptr::~shared_ptr (inline) 2ms 0.011% 45.50% 751ms 4.19% boost::numeric::ublas::vector_assign (inline) 737ms 4.11% 49.61% 745ms 4.16% boost::detail::sp_counted_base::release 152ms 0.85% 50.46% 670ms 3.74% boost::numeric::ublas::indexing_vector_assign 91ms 0.51% 50.97% 573ms 3.20% AbstractMesh::GetVectorFromAtoB 239ms 1.33% 52.30% 550ms 3.07% DistributedBoxCollection::CalculateContainingBox (partial-inline) 169ms 0.94% 53.24% 537ms 3.00% __dynamic_cast 0 0% 53.24% 524ms 2.92% AbstractCellPopulation::WriteResultsToFiles 219ms 1.22% 54.46% 486ms 2.71% NodeAttributes::AddNeighbour 21ms 0.12% 54.58% 477ms 2.66% std::_Rb_tree_const_iterator::operator++ (inline) 459ms 2.56% 57.14% 459ms 2.56% [libchaste_cell_based.so] 51ms 0.28% 57.42% 452ms 2.52% std::__new_allocator::allocate (inline) 1ms 0.0056% 57.43% 451ms 2.52% AbstractCellBasedSimulation::DoCellBirth 0 0% 57.43% 443ms 2.47% std::allocator_traits::allocate (inline) 0 0% 57.43% 441ms 2.46% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 3ms 0.017% 57.45% 439ms 2.45% boost::numeric::ublas::c_vector::operator= (inline) 433ms 2.42% 59.86% 433ms 2.42% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 19ms 0.11% 59.97% 427ms 2.38% std::_Rb_tree::_Rb_tree (partial-inline) 23ms 0.13% 60.10% 427ms 2.38% std::__copy_move::__copy_m (inline) 0 0% 60.10% 427ms 2.38% std::__copy_move_a (inline) 0 0% 60.10% 427ms 2.38% std::__copy_move_a1 (inline) 0 0% 60.10% 427ms 2.38% std::__copy_move_a2 (inline) 0 0% 60.10% 427ms 2.38% std::copy (inline) 0 0% 60.10% 426ms 2.38% boost::numeric::ublas::norm_2 (inline) 345ms 1.92% 62.02% 426ms 2.38% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 62.02% 426ms 2.38% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1ms 0.0056% 62.03% 415ms 2.32% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 62.03% 409ms 2.28% std::_Rb_tree::_M_create_node (inline) 408ms 2.28% 64.30% 408ms 2.28% __memcpy_avx512_unaligned_erms 406ms 2.26% 66.57% 406ms 2.26% __gnu_cxx::__normal_iterator::operator++ (inline) 11ms 0.061% 66.63% 405ms 2.26% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 21ms 0.12% 66.75% 397ms 2.21% operator new 397ms 2.21% 68.96% 397ms 2.21% std::_Rb_tree_increment 24ms 0.13% 69.10% 396ms 2.21% std::_Rb_tree::_M_copy (inline) 388ms 2.16% 71.26% 388ms 2.16% boost::numeric::ublas::same_impl_ex 0 0% 71.26% 384ms 2.14% std::_Rb_tree::_M_get_node (inline) 0 0% 71.26% 371ms 2.07% AbstractCentreBasedCellPopulation::GetDampingConstant 128ms 0.71% 71.97% 369ms 2.06% __GI___libc_malloc 157ms 0.88% 72.85% 366ms 2.04% std::_Rb_tree::_M_clone_node (inline) 362ms 2.02% 74.87% 362ms 2.02% [libchaste_mesh.so] 4ms 0.022% 74.89% 357ms 1.99% NodeBasedCellPopulation::WriteVtkResultsToFile 99ms 0.55% 75.44% 356ms 1.99% std::_Rb_tree::~_Rb_tree (inline) 6ms 0.033% 75.48% 355ms 1.98% CellPropertyCollection::GetPropertiesType (inline) 0 0% 75.48% 352ms 1.96% std::set::set (inline) 54ms 0.3% 75.78% 329ms 1.84% std::_Rb_tree::_M_erase (partial-inline) 327ms 1.82% 77.60% 327ms 1.82% boost::numeric::ublas::c_vector::operator() 249ms 1.39% 78.99% 320ms 1.79% std::vector::push_back (inline) 175ms 0.98% 79.97% 294ms 1.64% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 79.97% 287ms 1.60% std::set::~set (inline) 0 0% 79.97% 273ms 1.52% std::_Rb_tree::_M_drop_node (inline) 265ms 1.48% 81.45% 265ms 1.48% std::_Rb_tree::_S_left (inline) 8ms 0.045% 81.49% 264ms 1.47% boost::numeric::ublas::vector_binary::size (inline) 0 0% 81.49% 256ms 1.43% std::_Rb_tree::_Alloc_node::operator() (inline) 5ms 0.028% 81.52% 247ms 1.38% AbstractCellProperty::IsSubType (inline) 7ms 0.039% 81.56% 242ms 1.35% std::_Rb_tree::_M_emplace_hint_unique 2ms 0.011% 81.57% 241ms 1.34% Cell::GetMutationState 6ms 0.033% 81.60% 238ms 1.33% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 81.60% 227ms 1.27% NodesOnlyMesh::ReMesh 2ms 0.011% 81.61% 217ms 1.21% NodesOnlyMesh::UpdateNodeIndices 0 0% 81.61% 213ms 1.19% boost::numeric::ublas::c_vector::assign (inline) 188ms 1.05% 82.66% 205ms 1.14% boost::shared_ptr::shared_ptr (inline) 1ms 0.0056% 82.67% 202ms 1.13% Node::GetRadius 121ms 0.67% 83.34% 202ms 1.13% _int_malloc 0 0% 83.34% 201ms 1.12% NodesOnlyMesh::UpdateBoxCollection 201ms 1.12% 84.46% 201ms 1.12% __strcmp_evex 0 0% 84.46% 193ms 1.08% std::__new_allocator::deallocate (inline) 3ms 0.017% 84.48% 191ms 1.07% CellPropertyCollection::HasProperty 0 0% 84.48% 191ms 1.07% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 84.48% 188ms 1.05% Cell::HasCellProperty (inline) 5ms 0.028% 84.51% 182ms 1.02% DistributedBoxCollection::GetProcessOwningNode 52ms 0.29% 84.80% 181ms 1.01% __GI___libc_free 0 0% 84.80% 173ms 0.97% std::allocator_traits::deallocate (inline) 54ms 0.3% 85.10% 171ms 0.95% std::__move_median_to_first (inline) 0 0% 85.10% 170ms 0.95% NodesOnlyMesh::AddNodesToBoxes 0 0% 85.10% 170ms 0.95% std::_Rb_tree::_M_put_node (inline) 1ms 0.0056% 85.11% 168ms 0.94% Cell::ReadyToDivide 27ms 0.15% 85.26% 164ms 0.91% std::__insertion_sort (inline) 0 0% 85.26% 163ms 0.91% std::iter_swap (inline) 163ms 0.91% 86.17% 163ms 0.91% std::swap (inline) 0 0% 86.17% 158ms 0.88% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 86.17% 157ms 0.88% VtkMeshWriter::WriteFiles 0 0% 86.17% 153ms 0.85% std::_Rb_tree::_Auto_node::_Auto_node (inline) 152ms 0.85% 87.01% 152ms 0.85% Node::CheckForNodeAttributes 0 0% 87.01% 140ms 0.78% boost::numeric::ublas::inner_prod (inline) 2ms 0.011% 87.02% 140ms 0.78% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 7ms 0.039% 87.06% 138ms 0.77% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 87.06% 135ms 0.75% vtkDemandDrivenPipeline::ProcessRequest 0 0% 87.06% 135ms 0.75% vtkStreamingDemandDrivenPipeline::Update 0 0% 87.06% 135ms 0.75% vtkXMLWriterBase::Write 0 0% 87.06% 134ms 0.75% vtkCompositeDataPipeline::ExecuteData 0 0% 87.06% 134ms 0.75% vtkDemandDrivenPipeline::ExecuteData 0 0% 87.06% 134ms 0.75% vtkExecutive::CallAlgorithm 0 0% 87.06% 134ms 0.75% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 87.06% 133ms 0.74% vtkXMLUnstructuredDataWriter::ProcessRequest 114ms 0.64% 87.70% 129ms 0.72% _int_free 127ms 0.71% 88.41% 127ms 0.71% boost::shared_ptr::operator-> (inline) 3ms 0.017% 88.42% 123ms 0.69% AbstractCellProperty::IsType (inline) 0 0% 88.42% 119ms 0.66% NodesOnlyMesh::ResizeBoxCollection 17ms 0.095% 88.52% 118ms 0.66% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 88.52% 116ms 0.65% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 88.52% 113ms 0.63% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 88.52% 113ms 0.63% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 88.52% 110ms 0.61% std::__new_allocator::destroy (inline) 0 0% 88.52% 110ms 0.61% std::allocator_traits::destroy (inline) 32ms 0.18% 88.70% 109ms 0.61% boost::numeric::ublas::vector_inner_prod::apply (inline) 50ms 0.28% 88.98% 109ms 0.61% std::__adjacent_find (inline) 0 0% 88.98% 109ms 0.61% std::__unique (inline) 0 0% 88.98% 109ms 0.61% std::unique (inline) 0 0% 88.98% 108ms 0.6% std::_Rb_tree::_M_destroy_node (inline) 0 0% 88.98% 106ms 0.59% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 1ms 0.0056% 88.98% 103ms 0.57% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 2ms 0.011% 88.99% 103ms 0.57% AbstractNumericalMethod::SafeNodePositionUpdate 3ms 0.017% 89.01% 97ms 0.54% std::_Rb_tree::_M_insert_unique 0 0% 89.01% 97ms 0.54% std::set::insert (inline) 0 0% 89.01% 94ms 0.52% vtkXMLWriter::WriteBinaryData 0 0% 89.01% 91ms 0.51% AbstractCellPopulation::SetCellUsingLocationIndex 3ms 0.017% 89.03% 91ms 0.51% NodeBasedCellPopulation::SetNode 1ms 0.0056% 89.03% 90ms 0.5% vtkXMLWriter::WriteBinaryDataInternal