File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 22083ms, 90.04% of 24527ms total Dropped 797 nodes (cum <= 122.64ms) flat flat% sum% cum cum% 0 0% 0% 24399ms 99.48% __libc_start_call_main 0 0% 0% 24399ms 99.48% __libc_start_main_impl 0 0% 0% 24399ms 99.48% _start 0 0% 0% 24381ms 99.40% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 24381ms 99.40% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 24381ms 99.40% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 24381ms 99.40% main 0 0% 0% 24341ms 99.24% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 24341ms 99.24% CxxTest::TestRunner::runTest (inline) 0 0% 0% 24341ms 99.24% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 24332ms 99.20% AbstractCellBasedSimulation::Solve 2ms 0.0082% 0.0082% 13991ms 57.04% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0082% 9132ms 37.23% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.012% 0.02% 9071ms 36.98% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.033% 0.053% 8908ms 36.32% AbstractNumericalMethod::ComputeForcesIncludingDamping 1304ms 5.32% 5.37% 8228ms 33.55% RepulsionForce::AddForceContribution (partial-inline) 0 0% 5.37% 8075ms 32.92% NodeBasedCellPopulation::Update 11ms 0.045% 5.41% 5997ms 24.45% DistributedBoxCollection::CalculateInteriorNodePairs 2112ms 8.61% 14.03% 5099ms 20.79% std::_Rb_tree::_M_lower_bound (inline) 12ms 0.049% 14.07% 4583ms 18.69% NodeAttributes::RemoveDuplicateNeighbours 0 0% 14.07% 4559ms 18.59% OffLatticeSimulation::ApplyBoundaries 7ms 0.029% 14.10% 4426ms 18.05% std::__sort (inline) 0 0% 14.10% 4426ms 18.05% std::sort (inline) 190ms 0.77% 14.88% 4126ms 16.82% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 257ms 1.05% 15.93% 3365ms 13.72% std::_Rb_tree::find (inline) 0 0% 15.93% 3363ms 13.71% std::map::find (inline) 74ms 0.3% 16.23% 3308ms 13.49% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 2ms 0.0082% 16.24% 3226ms 13.15% AbstractCellPopulation::Iterator::operator++ (inline) 151ms 0.62% 16.85% 3203ms 13.06% AbstractCellPopulation::Iterator::IsRealCell (inline) 2954ms 12.04% 28.89% 2954ms 12.04% std::_Rb_tree::_S_right (inline) 38ms 0.15% 29.05% 2800ms 11.42% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 163ms 0.66% 29.71% 2609ms 10.64% std::__introsort_loop 185ms 0.75% 30.47% 2505ms 10.21% std::map::operator[] (partial-inline) 168ms 0.68% 31.15% 2429ms 9.90% AbstractMesh::GetNode 26ms 0.11% 31.26% 2429ms 9.90% PlaneBoundaryCondition::ImposeBoundaryCondition 48ms 0.2% 31.46% 2406ms 9.81% NodesOnlyMesh::GetNodeOrHaloNode 0 0% 31.46% 2343ms 9.55% std::__unguarded_partition_pivot (inline) 84ms 0.34% 31.80% 2267ms 9.24% NodesOnlyMesh::SolveNodeMapping 55ms 0.22% 32.02% 2262ms 9.22% AbstractCellPopulation::GetLocationIndexUsingCell 11ms 0.045% 32.07% 2129ms 8.68% PlaneBoundaryCondition::VerifyBoundaryCondition 1034ms 4.22% 36.28% 2087ms 8.51% std::__unguarded_partition (inline) 0 0% 36.28% 2044ms 8.33% std::_Rb_tree::lower_bound (inline) 0 0% 36.28% 2044ms 8.33% std::map::lower_bound (inline) 144ms 0.59% 36.87% 2001ms 8.16% DistributedBoxCollection::AddPairsFromBox 2ms 0.0082% 36.88% 1806ms 7.36% std::__final_insertion_sort (inline) 15ms 0.061% 36.94% 1697ms 6.92% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 33ms 0.13% 37.07% 1672ms 6.82% AbstractCellPopulation::GetCellUsingLocationIndex 135ms 0.55% 37.62% 1616ms 6.59% std::__unguarded_insertion_sort (inline) 563ms 2.30% 39.92% 1519ms 6.19% std::__unguarded_linear_insert (inline) 1379ms 5.62% 45.54% 1379ms 5.62% __gnu_cxx::__normal_iterator::operator-- (inline) 38ms 0.15% 45.70% 1277ms 5.21% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 45.70% 1153ms 4.70% NodeBasedCellPopulation::UpdateCellProcessLocation 12ms 0.049% 45.75% 1143ms 4.66% boost::numeric::ublas::vector_assign (inline) 4ms 0.016% 45.76% 1111ms 4.53% DistributedBoxCollection::CalculateBoundaryNodePairs 205ms 0.84% 46.60% 1057ms 4.31% boost::numeric::ublas::indexing_vector_assign 265ms 1.08% 47.68% 910ms 3.71% __dynamic_cast 0 0% 47.68% 904ms 3.69% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 26ms 0.11% 47.78% 892ms 3.64% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 47.78% 891ms 3.63% boost::numeric::ublas::norm_2 (inline) 709ms 2.89% 50.67% 891ms 3.63% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 50.67% 891ms 3.63% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 179ms 0.73% 51.40% 855ms 3.49% AbstractMesh::GetVectorFromAtoB 378ms 1.54% 52.95% 852ms 3.47% DistributedBoxCollection::CalculateContainingBox (partial-inline) 2ms 0.0082% 52.95% 811ms 3.31% boost::numeric::ublas::c_vector::operator= (inline) 28ms 0.11% 53.07% 788ms 3.21% std::__copy_move::__copy_m (inline) 0 0% 53.07% 788ms 3.21% std::__copy_move_a (inline) 0 0% 53.07% 788ms 3.21% std::__copy_move_a1 (inline) 0 0% 53.07% 788ms 3.21% std::__copy_move_a2 (inline) 0 0% 53.07% 787ms 3.21% std::copy (inline) 775ms 3.16% 56.23% 775ms 3.16% __memcpy_avx_unaligned_erms 0 0% 56.23% 739ms 3.01% AbstractCellPopulation::WriteResultsToFiles 724ms 2.95% 59.18% 724ms 2.95% boost::numeric::ublas::c_vector::operator() 148ms 0.6% 59.78% 718ms 2.93% NodeAttributes::AddNeighbour 570ms 2.32% 62.11% 639ms 2.61% std::vector::push_back (inline) 21ms 0.086% 62.19% 616ms 2.51% std::_Rb_tree_const_iterator::operator++ (inline) 4ms 0.016% 62.21% 610ms 2.49% AbstractCellBasedSimulation::DoCellBirth 9ms 0.037% 62.25% 599ms 2.44% CellPropertyCollection::GetPropertiesType (inline) 4ms 0.016% 62.26% 591ms 2.41% AbstractCentreBasedCellPopulation::GetDampingConstant 570ms 2.32% 64.59% 570ms 2.32% std::_Rb_tree_increment 557ms 2.27% 66.86% 557ms 2.27% boost::numeric::ublas::same_impl_ex 250ms 1.02% 67.88% 543ms 2.21% __cxxabiv1::__si_class_type_info::__do_dyncast 44ms 0.18% 68.06% 543ms 2.21% std::_Rb_tree::_Rb_tree (partial-inline) 45ms 0.18% 68.24% 531ms 2.16% boost::detail::shared_count::~shared_count (inline) 0 0% 68.24% 531ms 2.16% boost::shared_ptr::~shared_ptr (inline) 84ms 0.34% 68.58% 526ms 2.14% std::__new_allocator::allocate (inline) 0 0% 68.58% 504ms 2.05% std::allocator_traits::allocate (inline) 0 0% 68.58% 497ms 2.03% std::_Rb_tree::_M_create_node (inline) 0 0% 68.58% 491ms 2.00% NodeBasedCellPopulation::WriteVtkResultsToFile 33ms 0.13% 68.72% 482ms 1.97% std::_Rb_tree::_M_copy (inline) 460ms 1.88% 70.59% 474ms 1.93% boost::detail::sp_counted_base::release 451ms 1.84% 72.43% 451ms 1.84% __strcmp_avx2 0 0% 72.43% 445ms 1.81% AbstractCellBasedSimulation::DoCellRemoval (inline) 156ms 0.64% 73.07% 445ms 1.81% std::_Rb_tree::_M_clone_node (inline) 0 0% 73.07% 441ms 1.80% std::_Rb_tree::_M_get_node (inline) 20ms 0.082% 73.15% 440ms 1.79% operator new 4ms 0.016% 73.16% 433ms 1.77% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 112ms 0.46% 73.62% 424ms 1.73% std::_Rb_tree::_M_erase 2ms 0.0082% 73.63% 424ms 1.73% std::set::set (inline) 2ms 0.0082% 73.64% 413ms 1.68% Cell::GetMutationState 109ms 0.44% 74.08% 410ms 1.67% boost::numeric::ublas::vector_binary::size (inline) 130ms 0.53% 74.61% 408ms 1.66% __GI___libc_malloc 4ms 0.016% 74.63% 398ms 1.62% AbstractCellProperty::IsSubType (inline) 0 0% 74.63% 367ms 1.50% boost::numeric::ublas::inner_prod (inline) 3ms 0.012% 74.64% 367ms 1.50% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 14ms 0.057% 74.70% 364ms 1.48% boost::numeric::ublas::vector_scalar_binary::evaluate 73ms 0.3% 74.99% 355ms 1.45% Node::GetRadius 0 0% 74.99% 344ms 1.40% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 74.99% 330ms 1.35% boost::numeric::ublas::c_vector::assign (inline) 329ms 1.34% 76.34% 329ms 1.34% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 76.34% 328ms 1.34% NodesOnlyMesh::ReMesh 49ms 0.2% 76.54% 326ms 1.33% std::_Rb_tree::~_Rb_tree (inline) 9ms 0.037% 76.57% 325ms 1.33% NodeBasedCellPopulation::UpdateMapsAfterRemesh 318ms 1.30% 77.87% 318ms 1.30% __gnu_cxx::__normal_iterator::operator++ (inline) 4ms 0.016% 77.89% 315ms 1.28% NodesOnlyMesh::UpdateNodeIndices 112ms 0.46% 78.34% 308ms 1.26% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 78.34% 306ms 1.25% std::_Rb_tree::_M_drop_node (inline) 2ms 0.0082% 78.35% 300ms 1.22% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 294ms 1.20% 79.55% 294ms 1.20% Node::CheckForNodeAttributes 3ms 0.012% 79.56% 286ms 1.17% DistributedBoxCollection::GetProcessOwningNode 10ms 0.041% 79.60% 276ms 1.13% std::_Rb_tree::_M_emplace_hint_unique 0 0% 79.60% 269ms 1.10% NodesOnlyMesh::UpdateBoxCollection 184ms 0.75% 80.35% 259ms 1.06% Node::AddNeighbour 2ms 0.0082% 80.36% 257ms 1.05% std::__new_allocator::deallocate (inline) 252ms 1.03% 81.39% 252ms 1.03% [libchaste_mesh.so] 117ms 0.48% 81.86% 248ms 1.01% std::__move_median_to_first (inline) 241ms 0.98% 82.85% 241ms 0.98% Node::GetIndex 0 0% 82.85% 237ms 0.97% std::allocator_traits::deallocate (inline) 0 0% 82.85% 236ms 0.96% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 86ms 0.35% 83.20% 236ms 0.96% __GI___libc_free 0 0% 83.20% 234ms 0.95% VtkMeshWriter::WriteFiles 0 0% 83.20% 234ms 0.95% std::_Rb_tree::_M_put_node (inline) 0 0% 83.20% 232ms 0.95% std::set::~set (inline) 99ms 0.4% 83.60% 223ms 0.91% boost::shared_ptr::shared_ptr (inline) 0 0% 83.60% 222ms 0.91% CellPropertyCollection::HasProperty 0 0% 83.60% 219ms 0.89% Cell::HasCellProperty (inline) 126ms 0.51% 84.12% 219ms 0.89% _int_malloc 1ms 0.0041% 84.12% 212ms 0.86% NodesOnlyMesh::AddNodesToBoxes 14ms 0.057% 84.18% 212ms 0.86% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 84.18% 209ms 0.85% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 84.18% 208ms 0.85% vtkDemandDrivenPipeline::ProcessRequest 0 0% 84.18% 208ms 0.85% vtkStreamingDemandDrivenPipeline::Update 0 0% 84.18% 208ms 0.85% vtkXMLWriterBase::Write 0 0% 84.18% 207ms 0.84% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 84.18% 206ms 0.84% vtkCompositeDataPipeline::ExecuteData 0 0% 84.18% 206ms 0.84% vtkDemandDrivenPipeline::ExecuteData 0 0% 84.18% 205ms 0.84% vtkExecutive::CallAlgorithm 0 0% 84.18% 205ms 0.84% vtkXMLUnstructuredDataWriter::ProcessRequest 3ms 0.012% 84.19% 204ms 0.83% Cell::ReadyToDivide 23ms 0.094% 84.28% 188ms 0.77% std::__insertion_sort (inline) 186ms 0.76% 85.04% 186ms 0.76% Node::IsDeleted 3ms 0.012% 85.05% 181ms 0.74% AbstractCellProperty::IsType (inline) 0 0% 85.05% 178ms 0.73% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.05% 178ms 0.73% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 175ms 0.71% 85.77% 175ms 0.71% [libchaste_cell_based.so] 0 0% 85.77% 175ms 0.71% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 170ms 0.69% 86.46% 170ms 0.69% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 0 0% 86.46% 168ms 0.68% std::_Rb_tree::clear (inline) 2ms 0.0082% 86.47% 161ms 0.66% NodesOnlyMesh::ResizeBoxCollection 7ms 0.029% 86.50% 157ms 0.64% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 86.50% 156ms 0.64% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 86.50% 153ms 0.62% std::_Rb_tree::_Auto_node::_Auto_node (inline) 134ms 0.55% 87.04% 150ms 0.61% _int_free 0 0% 87.04% 146ms 0.6% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 87.04% 145ms 0.59% Cell::GetCellId 4ms 0.016% 87.06% 145ms 0.59% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 87.06% 143ms 0.58% vtkXMLWriter::WriteBinaryData 2ms 0.0082% 87.07% 141ms 0.57% AbstractCellPopulation::SetCellUsingLocationIndex 141ms 0.57% 87.64% 141ms 0.57% __ieee754_log_fma 0 0% 87.64% 141ms 0.57% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.64% 141ms 0.57% vtkXMLWriter::WriteBinaryDataInternal 1ms 0.0041% 87.65% 141ms 0.57% vtkXMLWriter::WriteCompressionBlock 136ms 0.55% 88.20% 136ms 0.55% Node::rGetLocation 47ms 0.19% 88.39% 133ms 0.54% AbstractCellProperty::IsSame 130ms 0.53% 88.92% 131ms 0.53% std::__adjacent_find (inline) 0 0% 88.92% 131ms 0.53% std::__unique (inline) 0 0% 88.92% 131ms 0.53% std::unique (inline) 0 0% 88.92% 131ms 0.53% vtkXMLWriter::WritePointsAppendedData 55ms 0.22% 89.15% 129ms 0.53% AbstractCellCycleModel::GetAge 0 0% 89.15% 125ms 0.51% std::map::map (inline) 124ms 0.51% 89.65% 124ms 0.51% boost::shared_ptr::operator-> (inline) 94ms 0.38% 90.04% 123ms 0.5% boost::detail::shared_count::shared_count (inline)