File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 19359ms, 90.00% of 21510ms total Dropped 731 nodes (cum <= 107.55ms) flat flat% sum% cum cum% 0 0% 0% 21421ms 99.59% __libc_start_call_main 0 0% 0% 21421ms 99.59% __libc_start_main_impl 0 0% 0% 21421ms 99.59% _start 0 0% 0% 21406ms 99.52% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 21406ms 99.52% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 21406ms 99.52% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 21406ms 99.52% main 0 0% 0% 21374ms 99.37% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 21374ms 99.37% CxxTest::TestRunner::runTest (inline) 0 0% 0% 21374ms 99.37% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 21367ms 99.34% AbstractCellBasedSimulation::Solve 3ms 0.014% 0.014% 12031ms 55.93% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0046% 0.019% 8305ms 38.61% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.019% 7304ms 33.96% NodeBasedCellPopulation::Update 1ms 0.0046% 0.023% 6797ms 31.60% ForwardEulerNumericalMethod::UpdateAllNodePositions 5ms 0.023% 0.046% 6647ms 30.90% AbstractNumericalMethod::ComputeForcesIncludingDamping 893ms 4.15% 4.20% 6148ms 28.58% RepulsionForce::AddForceContribution (partial-inline) 3ms 0.014% 4.21% 5511ms 25.62% DistributedBoxCollection::CalculateInteriorNodePairs 0 0% 4.21% 4938ms 22.96% OffLatticeSimulation::ApplyBoundaries 2035ms 9.46% 13.67% 4557ms 21.19% std::_Rb_tree::_M_lower_bound (inline) 20ms 0.093% 13.77% 4402ms 20.46% NodeAttributes::RemoveDuplicateNeighbours 0 0% 13.77% 4211ms 19.58% std::__sort (inline) 0 0% 13.77% 4211ms 19.58% std::sort (inline) 238ms 1.11% 14.87% 3608ms 16.77% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 3ms 0.014% 14.89% 3436ms 15.97% AbstractCellPopulation::Iterator::operator++ (inline) 172ms 0.8% 15.69% 3423ms 15.91% AbstractCellPopulation::Iterator::IsRealCell 122ms 0.57% 16.25% 3325ms 15.46% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 210ms 0.98% 17.23% 2882ms 13.40% std::_Rb_tree::find (inline) 0 0% 17.23% 2880ms 13.39% std::map::find (inline) 27ms 0.13% 17.35% 2874ms 13.36% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 233ms 1.08% 18.44% 2565ms 11.92% std::__introsort_loop 62ms 0.29% 18.73% 2511ms 11.67% PlaneBoundaryCondition::ImposeBoundaryCondition 83ms 0.39% 19.11% 2437ms 11.33% AbstractMesh::GetNode 183ms 0.85% 19.96% 2428ms 11.29% std::map::operator[] (partial-inline) 52ms 0.24% 20.20% 2427ms 11.28% PlaneBoundaryCondition::VerifyBoundaryCondition 49ms 0.23% 20.43% 2423ms 11.26% NodesOnlyMesh::GetNodeOrHaloNode 215ms 1% 21.43% 2363ms 10.99% NodesOnlyMesh::SolveNodeMapping 9ms 0.042% 21.47% 2250ms 10.46% std::__unguarded_partition_pivot (inline) 2180ms 10.13% 31.61% 2180ms 10.13% std::_Rb_tree::_S_right (inline) 105ms 0.49% 32.10% 2055ms 9.55% AbstractCellPopulation::GetLocationIndexUsingCell 704ms 3.27% 35.37% 2044ms 9.50% std::__unguarded_partition (inline) 0 0% 35.37% 1921ms 8.93% std::_Rb_tree::lower_bound (inline) 0 0% 35.37% 1921ms 8.93% std::map::lower_bound (inline) 2ms 0.0093% 35.38% 1641ms 7.63% std::__final_insertion_sort (inline) 109ms 0.51% 35.89% 1610ms 7.48% DistributedBoxCollection::AddPairsFromBox 10ms 0.046% 35.93% 1495ms 6.95% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 22ms 0.1% 36.03% 1473ms 6.85% AbstractCellPopulation::GetCellUsingLocationIndex 102ms 0.47% 36.51% 1445ms 6.72% std::__unguarded_insertion_sort (inline) 686ms 3.19% 39.70% 1293ms 6.01% std::__unguarded_linear_insert (inline) 0 0% 39.70% 1057ms 4.91% NodeBasedCellPopulation::UpdateCellProcessLocation 14ms 0.065% 39.76% 1055ms 4.90% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 57ms 0.26% 40.03% 1020ms 4.74% boost::numeric::ublas::c_vector::c_vector (partial-inline) 957ms 4.45% 44.48% 957ms 4.45% __gnu_cxx::__normal_iterator::operator-- (inline) 27ms 0.13% 44.60% 915ms 4.25% boost::detail::shared_count::~shared_count (inline) 0 0% 44.60% 915ms 4.25% boost::shared_ptr::~shared_ptr (inline) 8ms 0.037% 44.64% 907ms 4.22% DistributedBoxCollection::CalculateBoundaryNodePairs 2ms 0.0093% 44.65% 867ms 4.03% boost::numeric::ublas::vector_assign (inline) 850ms 3.95% 48.60% 859ms 3.99% boost::detail::sp_counted_base::release 175ms 0.81% 49.41% 757ms 3.52% boost::numeric::ublas::indexing_vector_assign 199ms 0.93% 50.34% 724ms 3.37% __dynamic_cast 319ms 1.48% 51.82% 719ms 3.34% DistributedBoxCollection::CalculateContainingBox (partial-inline) 90ms 0.42% 52.24% 640ms 2.98% AbstractMesh::GetVectorFromAtoB 0 0% 52.24% 614ms 2.85% AbstractCellPopulation::WriteResultsToFiles 567ms 2.64% 54.88% 567ms 2.64% __gnu_cxx::__normal_iterator::operator++ (inline) 57ms 0.26% 55.14% 566ms 2.63% std::__new_allocator::allocate (inline) 0 0% 55.14% 553ms 2.57% std::allocator_traits::allocate (inline) 25ms 0.12% 55.26% 549ms 2.55% std::_Rb_tree_const_iterator::operator++ (inline) 547ms 2.54% 57.80% 547ms 2.54% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 255ms 1.19% 58.99% 544ms 2.53% NodeAttributes::AddNeighbour 33ms 0.15% 59.14% 542ms 2.52% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 59.14% 524ms 2.44% AbstractCellBasedSimulation::DoCellBirth 7ms 0.033% 59.17% 524ms 2.44% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 59.17% 515ms 2.39% std::_Rb_tree::_M_create_node (inline) 24ms 0.11% 59.28% 507ms 2.36% operator new 28ms 0.13% 59.41% 506ms 2.35% std::__copy_move::__copy_m (inline) 0 0% 59.41% 506ms 2.35% std::__copy_move_a (inline) 0 0% 59.41% 506ms 2.35% std::__copy_move_a1 (inline) 0 0% 59.41% 506ms 2.35% std::__copy_move_a2 (inline) 0 0% 59.41% 506ms 2.35% std::copy (inline) 0 0% 59.41% 505ms 2.35% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 35ms 0.16% 59.58% 494ms 2.30% std::_Rb_tree::_M_copy (inline) 0 0% 59.58% 485ms 2.25% boost::numeric::ublas::norm_2 (inline) 390ms 1.81% 61.39% 485ms 2.25% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 61.39% 485ms 2.25% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 61.39% 483ms 2.25% std::_Rb_tree::_M_get_node (inline) 176ms 0.82% 62.21% 477ms 2.22% __GI___libc_malloc 0 0% 62.21% 476ms 2.21% AbstractCellBasedSimulation::DoCellRemoval (inline) 475ms 2.21% 64.42% 475ms 2.21% __memcpy_avx512_unaligned_erms 8ms 0.037% 64.45% 468ms 2.18% CellPropertyCollection::GetPropertiesType (inline) 13ms 0.06% 64.51% 467ms 2.17% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 466ms 2.17% 66.68% 466ms 2.17% [libchaste_mesh.so] 464ms 2.16% 68.84% 464ms 2.16% std::_Rb_tree_increment 460ms 2.14% 70.98% 460ms 2.14% [libchaste_cell_based.so] 3ms 0.014% 70.99% 460ms 2.14% std::set::set (inline) 457ms 2.12% 73.11% 457ms 2.12% boost::numeric::ublas::c_vector::operator() 2ms 0.0093% 73.12% 455ms 2.12% AbstractCentreBasedCellPopulation::GetDampingConstant 192ms 0.89% 74.02% 449ms 2.09% std::_Rb_tree::_M_clone_node (inline) 441ms 2.05% 76.07% 441ms 2.05% boost::numeric::ublas::same_impl_ex 216ms 1.00% 77.07% 436ms 2.03% __cxxabiv1::__si_class_type_info::__do_dyncast 2ms 0.0093% 77.08% 411ms 1.91% NodeBasedCellPopulation::WriteVtkResultsToFile 96ms 0.45% 77.53% 411ms 1.91% std::_Rb_tree::~_Rb_tree (inline) 54ms 0.25% 77.78% 409ms 1.90% std::_Rb_tree::_M_erase (partial-inline) 272ms 1.26% 79.04% 390ms 1.81% std::vector::push_back (inline) 0 0% 79.04% 351ms 1.63% std::_Rb_tree::_M_drop_node (inline) 0 0% 79.04% 349ms 1.62% std::set::~set (inline) 341ms 1.59% 80.63% 341ms 1.59% std::_Rb_tree::_S_left (inline) 330ms 1.53% 82.16% 330ms 1.53% __strcmp_evex 1ms 0.0046% 82.17% 328ms 1.52% NodesOnlyMesh::ReMesh 1ms 0.0046% 82.17% 324ms 1.51% Cell::GetMutationState 9ms 0.042% 82.21% 323ms 1.50% std::_Rb_tree::_M_emplace_hint_unique 1ms 0.0046% 82.22% 321ms 1.49% NodesOnlyMesh::UpdateNodeIndices 0 0% 82.22% 308ms 1.43% std::_Rb_tree::_Alloc_node::operator() (inline) 9ms 0.042% 82.26% 299ms 1.39% boost::numeric::ublas::vector_binary::size (inline) 3ms 0.014% 82.27% 294ms 1.37% AbstractCellProperty::IsSubType (inline) 5ms 0.023% 82.30% 270ms 1.26% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 82.30% 261ms 1.21% Node::GetRadius 1ms 0.0046% 82.30% 260ms 1.21% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 10ms 0.046% 82.35% 260ms 1.21% std::__new_allocator::deallocate (inline) 224ms 1.04% 83.39% 252ms 1.17% boost::shared_ptr::shared_ptr (inline) 0 0% 83.39% 247ms 1.15% DistributedBoxCollection::GetProcessOwningNode 146ms 0.68% 84.07% 238ms 1.11% _int_malloc 0 0% 84.07% 234ms 1.09% NodesOnlyMesh::UpdateBoxCollection 0 0% 84.07% 230ms 1.07% std::allocator_traits::deallocate (inline) 0 0% 84.07% 227ms 1.06% std::_Rb_tree::_M_put_node (inline) 52ms 0.24% 84.31% 218ms 1.01% __GI___libc_free 0 0% 84.31% 212ms 0.99% boost::numeric::ublas::c_vector::assign (inline) 0 0% 84.31% 207ms 0.96% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 84.31% 199ms 0.93% CellPropertyCollection::HasProperty 198ms 0.92% 85.23% 198ms 0.92% Node::CheckForNodeAttributes 0 0% 85.23% 197ms 0.92% Cell::HasCellProperty (inline) 0 0% 85.23% 194ms 0.9% boost::numeric::ublas::inner_prod (inline) 35ms 0.16% 85.39% 194ms 0.9% std::__insertion_sort (inline) 1ms 0.0046% 85.40% 193ms 0.9% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 1ms 0.0046% 85.40% 192ms 0.89% NodesOnlyMesh::AddNodesToBoxes 13ms 0.06% 85.46% 192ms 0.89% boost::numeric::ublas::vector_scalar_binary::evaluate 71ms 0.33% 85.79% 187ms 0.87% std::__move_median_to_first (inline) 0 0% 85.79% 187ms 0.87% std::iter_swap (inline) 187ms 0.87% 86.66% 187ms 0.87% std::swap (inline) 0 0% 86.66% 176ms 0.82% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 4ms 0.019% 86.68% 176ms 0.82% Cell::ReadyToDivide 0 0% 86.68% 175ms 0.81% VtkMeshWriter::WriteFiles 161ms 0.75% 87.43% 161ms 0.75% boost::shared_ptr::operator-> (inline) 0 0% 87.43% 159ms 0.74% NodesOnlyMesh::ResizeBoxCollection 140ms 0.65% 88.08% 159ms 0.74% _int_free 13ms 0.06% 88.14% 157ms 0.73% NodesOnlyMesh::IsANodeCloseToDomainBoundary 6ms 0.028% 88.17% 155ms 0.72% AbstractCellProperty::IsType (inline) 34ms 0.16% 88.33% 154ms 0.72% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 88.33% 152ms 0.71% vtkDemandDrivenPipeline::ProcessRequest 0 0% 88.33% 152ms 0.71% vtkStreamingDemandDrivenPipeline::Update 0 0% 88.33% 152ms 0.71% vtkXMLWriterBase::Write 0 0% 88.33% 150ms 0.7% vtkDemandDrivenPipeline::ExecuteData 0 0% 88.33% 150ms 0.7% vtkExecutive::CallAlgorithm 0 0% 88.33% 150ms 0.7% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 88.33% 150ms 0.7% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 88.33% 149ms 0.69% vtkCompositeDataPipeline::ExecuteData 0 0% 88.33% 147ms 0.68% boost::numeric::ublas::vector_binary::operator() (inline) 57ms 0.26% 88.59% 139ms 0.65% std::__adjacent_find (inline) 0 0% 88.59% 139ms 0.65% std::__unique (inline) 0 0% 88.59% 139ms 0.65% std::unique (inline) 0 0% 88.59% 134ms 0.62% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 88.59% 134ms 0.62% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 88.59% 133ms 0.62% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 88.59% 132ms 0.61% std::__new_allocator::destroy (inline) 0 0% 88.59% 132ms 0.61% std::allocator_traits::destroy (inline) 0 0% 88.59% 131ms 0.61% std::_Rb_tree::_M_destroy_node (inline) 1ms 0.0046% 88.60% 124ms 0.58% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 115ms 0.53% 89.13% 115ms 0.53% __ieee754_log_fma 4ms 0.019% 89.15% 114ms 0.53% AbstractCellPopulation::SetCellUsingLocationIndex 7ms 0.033% 89.18% 114ms 0.53% boost::numeric::ublas::c_vector::operator[] (inline) 42ms 0.2% 89.38% 113ms 0.53% AbstractCellProperty::IsSame 113ms 0.53% 89.90% 113ms 0.53% Node::GetIndex 2ms 0.0093% 89.91% 112ms 0.52% AbstractNumericalMethod::SafeNodePositionUpdate 4ms 0.019% 89.93% 112ms 0.52% DistributedBoxCollection::GetIsPeriodicAllDims 15ms 0.07% 90.00% 109ms 0.51% Node::AddNeighbour