File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 21961ms, 89.09% of 24650ms total Dropped 806 nodes (cum <= 123.25ms) flat flat% sum% cum cum% 0 0% 0% 24521ms 99.48% __libc_start_call_main 0 0% 0% 24521ms 99.48% __libc_start_main_impl 0 0% 0% 24521ms 99.48% _start 0 0% 0% 24503ms 99.40% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 24503ms 99.40% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 24503ms 99.40% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 24503ms 99.40% main 0 0% 0% 24461ms 99.23% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 24461ms 99.23% CxxTest::TestRunner::runTest (inline) 0 0% 0% 24461ms 99.23% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 24451ms 99.19% AbstractCellBasedSimulation::Solve 3ms 0.012% 0.012% 14032ms 56.92% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.012% 9204ms 37.34% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.016% 0.028% 9127ms 37.03% ForwardEulerNumericalMethod::UpdateAllNodePositions 16ms 0.065% 0.093% 8927ms 36.22% AbstractNumericalMethod::ComputeForcesIncludingDamping 1382ms 5.61% 5.70% 8229ms 33.38% RepulsionForce::AddForceContribution (partial-inline) 1ms 0.0041% 5.70% 8135ms 33.00% NodeBasedCellPopulation::Update 6ms 0.024% 5.73% 6047ms 24.53% DistributedBoxCollection::CalculateInteriorNodePairs 2221ms 9.01% 14.74% 5173ms 20.99% std::_Rb_tree::_M_lower_bound (inline) 12ms 0.049% 14.79% 4618ms 18.73% NodeAttributes::RemoveDuplicateNeighbours 1ms 0.0041% 14.79% 4578ms 18.57% OffLatticeSimulation::ApplyBoundaries 6ms 0.024% 14.82% 4432ms 17.98% std::__sort (inline) 0 0% 14.82% 4432ms 17.98% std::sort (inline) 210ms 0.85% 15.67% 4059ms 16.47% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 260ms 1.05% 16.72% 3437ms 13.94% std::_Rb_tree::find (inline) 0 0% 16.72% 3436ms 13.94% std::map::find (inline) 57ms 0.23% 16.95% 3349ms 13.59% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 3ms 0.012% 16.97% 3115ms 12.64% AbstractCellPopulation::Iterator::operator++ (inline) 149ms 0.6% 17.57% 3077ms 12.48% AbstractCellPopulation::Iterator::IsRealCell 2922ms 11.85% 29.42% 2922ms 11.85% std::_Rb_tree::_S_right (inline) 22ms 0.089% 29.51% 2714ms 11.01% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 183ms 0.74% 30.26% 2578ms 10.46% std::__introsort_loop 186ms 0.75% 31.01% 2506ms 10.17% std::map::operator[] (partial-inline) 178ms 0.72% 31.73% 2484ms 10.08% AbstractMesh::GetNode 64ms 0.26% 31.99% 2458ms 9.97% NodesOnlyMesh::GetNodeOrHaloNode 19ms 0.077% 32.07% 2430ms 9.86% PlaneBoundaryCondition::ImposeBoundaryCondition 49ms 0.2% 32.27% 2318ms 9.40% AbstractCellPopulation::GetLocationIndexUsingCell 115ms 0.47% 32.73% 2308ms 9.36% NodesOnlyMesh::SolveNodeMapping 0 0% 32.73% 2306ms 9.35% std::__unguarded_partition_pivot (inline) 7ms 0.028% 32.76% 2147ms 8.71% PlaneBoundaryCondition::VerifyBoundaryCondition 972ms 3.94% 36.71% 2065ms 8.38% std::__unguarded_partition (inline) 176ms 0.71% 37.42% 2039ms 8.27% DistributedBoxCollection::AddPairsFromBox 0 0% 37.42% 2038ms 8.27% std::_Rb_tree::lower_bound (inline) 0 0% 37.42% 2038ms 8.27% std::map::lower_bound (inline) 1ms 0.0041% 37.42% 1843ms 7.48% std::__final_insertion_sort (inline) 23ms 0.093% 37.52% 1677ms 6.80% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 35ms 0.14% 37.66% 1649ms 6.69% AbstractCellPopulation::GetCellUsingLocationIndex 137ms 0.56% 38.22% 1641ms 6.66% std::__unguarded_insertion_sort (inline) 568ms 2.30% 40.52% 1561ms 6.33% std::__unguarded_linear_insert (inline) 1474ms 5.98% 46.50% 1474ms 5.98% __gnu_cxx::__normal_iterator::operator-- (inline) 60ms 0.24% 46.74% 1253ms 5.08% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 46.74% 1150ms 4.67% NodeBasedCellPopulation::UpdateCellProcessLocation 5ms 0.02% 46.76% 1107ms 4.49% DistributedBoxCollection::CalculateBoundaryNodePairs 6ms 0.024% 46.79% 1103ms 4.47% boost::numeric::ublas::vector_assign (inline) 231ms 0.94% 47.72% 1039ms 4.22% boost::numeric::ublas::indexing_vector_assign 17ms 0.069% 47.79% 970ms 3.94% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 287ms 1.16% 48.96% 938ms 3.81% __dynamic_cast 393ms 1.59% 50.55% 865ms 3.51% DistributedBoxCollection::CalculateContainingBox (partial-inline) 198ms 0.8% 51.35% 844ms 3.42% AbstractMesh::GetVectorFromAtoB 0 0% 51.35% 821ms 3.33% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 250ms 1.01% 52.37% 806ms 3.27% NodeAttributes::AddNeighbour 0 0% 52.37% 805ms 3.27% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 52.37% 804ms 3.26% boost::numeric::ublas::norm_2 (inline) 633ms 2.57% 54.94% 804ms 3.26% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 54.94% 757ms 3.07% AbstractCellPopulation::WriteResultsToFiles 5ms 0.02% 54.96% 757ms 3.07% boost::numeric::ublas::c_vector::operator= (inline) 34ms 0.14% 55.10% 732ms 2.97% std::__copy_move::__copy_m (inline) 0 0% 55.10% 732ms 2.97% std::__copy_move_a (inline) 0 0% 55.10% 732ms 2.97% std::__copy_move_a1 (inline) 0 0% 55.10% 732ms 2.97% std::__copy_move_a2 (inline) 0 0% 55.10% 732ms 2.97% std::copy (inline) 716ms 2.90% 58.00% 716ms 2.90% __memcpy_avx_unaligned_erms 706ms 2.86% 60.86% 706ms 2.86% boost::numeric::ublas::c_vector::operator() 26ms 0.11% 60.97% 678ms 2.75% std::_Rb_tree_const_iterator::operator++ (inline) 6ms 0.024% 60.99% 649ms 2.63% CellPropertyCollection::GetPropertiesType (inline) 637ms 2.58% 63.58% 637ms 2.58% std::_Rb_tree_increment 552ms 2.24% 65.82% 633ms 2.57% std::vector::push_back (inline) 7ms 0.028% 65.85% 608ms 2.47% AbstractCellBasedSimulation::DoCellBirth 2ms 0.0081% 65.85% 596ms 2.42% AbstractCentreBasedCellPopulation::GetDampingConstant 555ms 2.25% 68.11% 555ms 2.25% boost::numeric::ublas::same_impl_ex 282ms 1.14% 69.25% 537ms 2.18% __cxxabiv1::__si_class_type_info::__do_dyncast 41ms 0.17% 69.42% 527ms 2.14% std::_Rb_tree::_Rb_tree (partial-inline) 84ms 0.34% 69.76% 509ms 2.06% std::__new_allocator::allocate (inline) 0 0% 69.76% 496ms 2.01% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 69.76% 494ms 2.00% std::allocator_traits::allocate (inline) 35ms 0.14% 69.90% 492ms 2.00% boost::detail::shared_count::~shared_count (inline) 0 0% 69.90% 492ms 2.00% boost::shared_ptr::~shared_ptr (inline) 33ms 0.13% 70.03% 467ms 1.89% std::_Rb_tree::_M_copy (inline) 0 0% 70.03% 465ms 1.89% std::_Rb_tree::_M_create_node (inline) 0 0% 70.03% 461ms 1.87% AbstractCellBasedSimulation::DoCellRemoval (inline) 2ms 0.0081% 70.04% 449ms 1.82% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 437ms 1.77% 71.81% 447ms 1.81% boost::detail::sp_counted_base::release 2ms 0.0081% 71.82% 439ms 1.78% Cell::GetMutationState 3ms 0.012% 71.83% 436ms 1.77% AbstractCellProperty::IsSubType (inline) 6ms 0.024% 71.86% 428ms 1.74% std::set::set (inline) 24ms 0.097% 71.96% 425ms 1.72% operator new 148ms 0.6% 72.56% 422ms 1.71% std::_Rb_tree::_M_clone_node (inline) 0 0% 72.56% 416ms 1.69% std::_Rb_tree::_M_get_node (inline) 411ms 1.67% 74.22% 411ms 1.67% __strcmp_avx2 116ms 0.47% 74.69% 404ms 1.64% std::_Rb_tree::_M_erase 79ms 0.32% 75.01% 397ms 1.61% Node::GetRadius 108ms 0.44% 75.45% 393ms 1.59% __GI___libc_malloc 98ms 0.4% 75.85% 391ms 1.59% boost::numeric::ublas::vector_binary::size (inline) 0 0% 75.85% 385ms 1.56% boost::numeric::ublas::inner_prod (inline) 14ms 0.057% 75.91% 385ms 1.56% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 75.91% 385ms 1.56% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 75.91% 336ms 1.36% boost::numeric::ublas::c_vector::assign (inline) 334ms 1.35% 77.26% 334ms 1.35% __gnu_cxx::__normal_iterator::operator++ (inline) 332ms 1.35% 78.61% 332ms 1.35% Node::CheckForNodeAttributes 7ms 0.028% 78.64% 330ms 1.34% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 78.64% 322ms 1.31% NodesOnlyMesh::ReMesh 3ms 0.012% 78.65% 321ms 1.30% NodesOnlyMesh::UpdateNodeIndices 140ms 0.57% 79.22% 321ms 1.30% boost::numeric::ublas::vector_inner_prod::apply (inline) 41ms 0.17% 79.38% 318ms 1.29% std::_Rb_tree::~_Rb_tree (inline) 7ms 0.028% 79.41% 317ms 1.29% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 313ms 1.27% 80.68% 313ms 1.27% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 80.68% 312ms 1.27% std::_Rb_tree::_Alloc_node::operator() (inline) 3ms 0.012% 80.69% 295ms 1.20% DistributedBoxCollection::GetProcessOwningNode 14ms 0.057% 80.75% 282ms 1.14% std::_Rb_tree::_M_emplace_hint_unique 0 0% 80.75% 275ms 1.12% NodesOnlyMesh::UpdateBoxCollection 0 0% 80.75% 275ms 1.12% std::_Rb_tree::_M_drop_node (inline) 0 0% 80.75% 263ms 1.07% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 80.75% 262ms 1.06% VtkMeshWriter::WriteFiles 113ms 0.46% 81.21% 244ms 0.99% boost::shared_ptr::shared_ptr (inline) 107ms 0.43% 81.64% 238ms 0.97% std::__move_median_to_first (inline) 134ms 0.54% 82.19% 235ms 0.95% _int_malloc 1ms 0.0041% 82.19% 233ms 0.95% vtkStreamingDemandDrivenPipeline::Update 0 0% 82.19% 233ms 0.95% vtkXMLWriterBase::Write 229ms 0.93% 83.12% 229ms 0.93% [libchaste_mesh.so] 0 0% 83.12% 227ms 0.92% vtkDemandDrivenPipeline::ProcessRequest 0 0% 83.12% 227ms 0.92% vtkExecutive::CallAlgorithm 16ms 0.065% 83.18% 226ms 0.92% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 83.18% 226ms 0.92% vtkStreamingDemandDrivenPipeline::ProcessRequest 1ms 0.0041% 83.19% 224ms 0.91% vtkXMLUnstructuredDataWriter::ProcessRequest 6ms 0.024% 83.21% 223ms 0.9% std::__new_allocator::deallocate (inline) 1ms 0.0041% 83.22% 222ms 0.9% NodesOnlyMesh::AddNodesToBoxes 0 0% 83.22% 222ms 0.9% std::set::~set (inline) 0 0% 83.22% 222ms 0.9% vtkCompositeDataPipeline::ExecuteData 0 0% 83.22% 222ms 0.9% vtkDemandDrivenPipeline::ExecuteData 0 0% 83.22% 217ms 0.88% std::allocator_traits::deallocate (inline) 0 0% 83.22% 215ms 0.87% std::_Rb_tree::_M_put_node (inline) 12ms 0.049% 83.27% 213ms 0.86% Cell::ReadyToDivide 3ms 0.012% 83.28% 213ms 0.86% CellPropertyCollection::HasProperty 0 0% 83.28% 213ms 0.86% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 83.28% 212ms 0.86% Cell::HasCellProperty (inline) 211ms 0.86% 84.13% 211ms 0.86% Node::GetIndex 174ms 0.71% 84.84% 208ms 0.84% Node::AddNeighbour 14ms 0.057% 84.90% 201ms 0.82% std::__insertion_sort (inline) 65ms 0.26% 85.16% 196ms 0.8% __GI___libc_free 0 0% 85.16% 185ms 0.75% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.16% 185ms 0.75% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 85.16% 174ms 0.71% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 166ms 0.67% 85.83% 166ms 0.67% [libchaste_cell_based.so] 159ms 0.65% 86.48% 160ms 0.65% std::__adjacent_find (inline) 0 0% 86.48% 160ms 0.65% std::__unique (inline) 0 0% 86.48% 160ms 0.65% std::unique (inline) 1ms 0.0041% 86.48% 155ms 0.63% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 86.48% 153ms 0.62% AbstractCellProperty::IsType (inline) 0 0% 86.48% 153ms 0.62% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1ms 0.0041% 86.49% 145ms 0.59% vtkXMLWriter::WriteBinaryData 144ms 0.58% 87.07% 144ms 0.58% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 0 0% 87.07% 144ms 0.58% std::_Rb_tree::clear (inline) 0 0% 87.07% 143ms 0.58% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 87.07% 142ms 0.58% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 87.07% 140ms 0.57% vtkXMLWriter::WritePointsAppendedData 0 0% 87.07% 138ms 0.56% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.07% 138ms 0.56% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.07% 137ms 0.56% vtkXMLWriter::WriteCompressionBlock 136ms 0.55% 87.62% 136ms 0.55% Node::rGetLocation 1ms 0.0041% 87.63% 136ms 0.55% NodesOnlyMesh::ResizeBoxCollection 1ms 0.0041% 87.63% 135ms 0.55% Cell::GetCellId 5ms 0.02% 87.65% 135ms 0.55% boost::numeric::ublas::c_vector::operator[] (inline) 2ms 0.0081% 87.66% 134ms 0.54% AbstractCellPopulation::SetCellUsingLocationIndex 10ms 0.041% 87.70% 133ms 0.54% NodesOnlyMesh::IsANodeCloseToDomainBoundary 3ms 0.012% 87.71% 132ms 0.54% NodeBasedCellPopulation::SetNode 86ms 0.35% 88.06% 131ms 0.53% boost::detail::shared_count::shared_count (inline) 130ms 0.53% 88.59% 130ms 0.53% __ieee754_log_fma 120ms 0.49% 89.08% 129ms 0.52% _int_free 0 0% 89.08% 124ms 0.5% NodeBasedCellPopulation::AcceptCellWriter 4ms 0.016% 89.09% 124ms 0.5% NodesOnlyMesh::SetNode