File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 30075ms, 86.72% of 34682ms total Dropped 847 nodes (cum <= 173.41ms) flat flat% sum% cum cum% 0 0% 0% 34549ms 99.62% __libc_start_call_main 0 0% 0% 34549ms 99.62% __libc_start_main_impl 0 0% 0% 34549ms 99.62% _start 0 0% 0% 34531ms 99.56% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 34531ms 99.56% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 34531ms 99.56% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 34531ms 99.56% main 0 0% 0% 34488ms 99.44% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 34488ms 99.44% CxxTest::TestRunner::runTest (inline) 0 0% 0% 34488ms 99.44% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0029% 0.0029% 34479ms 99.41% AbstractCellBasedSimulation::Solve 3ms 0.0087% 0.012% 23654ms 68.20% OffLatticeSimulation::UpdateCellLocationsAndTopology 6ms 0.017% 0.029% 18644ms 53.76% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.023% 0.052% 18449ms 53.19% AbstractNumericalMethod::ComputeForcesIncludingDamping 186ms 0.54% 0.59% 17403ms 50.18% AbstractTwoBodyInteractionForce::AddForceContribution 1543ms 4.45% 5.04% 14757ms 42.55% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 0 0% 5.04% 9579ms 27.62% AbstractCellBasedSimulation::UpdateCellPopulation 4654ms 13.42% 18.46% 9351ms 26.96% std::_Rb_tree::_M_lower_bound (inline) 0 0% 18.46% 8508ms 24.53% NodeBasedCellPopulation::Update 357ms 1.03% 19.49% 8438ms 24.33% std::_Rb_tree::find (inline) 0 0% 19.49% 8435ms 24.32% std::map::find (inline) 245ms 0.71% 20.19% 8398ms 24.21% NodesOnlyMesh::GetNodeOrHaloNode 488ms 1.41% 21.60% 8161ms 23.53% AbstractMesh::GetNode 387ms 1.12% 22.71% 7676ms 22.13% NodesOnlyMesh::SolveNodeMapping 7ms 0.02% 22.74% 6395ms 18.44% DistributedBoxCollection::CalculateInteriorNodePairs 207ms 0.6% 23.33% 5787ms 16.69% boost::numeric::ublas::vector_assign (inline) 184ms 0.53% 23.86% 5697ms 16.43% boost::numeric::ublas::c_vector::c_vector (partial-inline) 11ms 0.032% 23.89% 4659ms 13.43% NodeAttributes::RemoveDuplicateNeighbours 4659ms 13.43% 37.33% 4659ms 13.43% std::_Rb_tree::_S_right (inline) 0 0% 37.33% 4647ms 13.40% OffLatticeSimulation::ApplyBoundaries 8ms 0.023% 37.35% 4483ms 12.93% std::__sort (inline) 0 0% 37.35% 4483ms 12.93% std::sort (inline) 1053ms 3.04% 40.39% 3361ms 9.69% boost::numeric::ublas::indexing_vector_assign 74ms 0.21% 40.60% 3311ms 9.55% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 2ms 0.0058% 40.61% 3044ms 8.78% AbstractCellPopulation::Iterator::operator++ (inline) 157ms 0.45% 41.06% 3014ms 8.69% AbstractCellPopulation::Iterator::IsRealCell (inline) 180ms 0.52% 41.58% 2644ms 7.62% std::__introsort_loop 20ms 0.058% 41.64% 2607ms 7.52% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 28ms 0.081% 41.72% 2460ms 7.09% PlaneBoundaryCondition::ImposeBoundaryCondition 169ms 0.49% 42.20% 2373ms 6.84% DistributedBoxCollection::AddPairsFromBox 0 0% 42.20% 2362ms 6.81% std::__unguarded_partition_pivot (inline) 60ms 0.17% 42.38% 2331ms 6.72% AbstractCellPopulation::GetLocationIndexUsingCell 12ms 0.035% 42.41% 2187ms 6.31% PlaneBoundaryCondition::VerifyBoundaryCondition 1068ms 3.08% 45.49% 2107ms 6.08% std::__unguarded_partition (inline) 186ms 0.54% 46.03% 1850ms 5.33% std::map::operator[] (partial-inline) 3ms 0.0087% 46.04% 1829ms 5.27% std::__final_insertion_sort (inline) 1668ms 4.81% 50.84% 1668ms 4.81% boost::numeric::ublas::same_impl_ex 117ms 0.34% 51.18% 1634ms 4.71% std::__unguarded_insertion_sort (inline) 591ms 1.70% 52.89% 1540ms 4.44% std::__unguarded_linear_insert (inline) 147ms 0.42% 53.31% 1505ms 4.34% AbstractMesh::GetVectorFromAtoB 1410ms 4.07% 57.38% 1410ms 4.07% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 57.38% 1383ms 3.99% std::_Rb_tree::lower_bound (inline) 0 0% 57.38% 1383ms 3.99% std::map::lower_bound (inline) 0 0% 57.38% 1361ms 3.92% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 57.38% 1345ms 3.88% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1199ms 3.46% 60.83% 1199ms 3.46% boost::numeric::ublas::c_vector::operator() 0 0% 60.83% 1197ms 3.45% NodeBasedCellPopulation::UpdateCellProcessLocation 2ms 0.0058% 60.84% 1190ms 3.43% boost::numeric::ublas::detail::expression_type_check (inline) 269ms 0.78% 61.61% 1145ms 3.30% boost::numeric::ublas::detail::equals 10ms 0.029% 61.64% 1116ms 3.22% DistributedBoxCollection::CalculateBoundaryNodePairs 25ms 0.072% 61.72% 1001ms 2.89% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 143ms 0.41% 62.13% 988ms 2.85% boost::numeric::ublas::vector_binary::size (inline) 8ms 0.023% 62.15% 978ms 2.82% AbstractCentreBasedCellPopulation::GetDampingConstant 40ms 0.12% 62.27% 896ms 2.58% std::_Rb_tree_const_iterator::operator++ (inline) 210ms 0.61% 62.87% 888ms 2.56% NodeAttributes::AddAppliedForceContribution 831ms 2.40% 65.27% 831ms 2.40% std::_Rb_tree_increment 367ms 1.06% 66.33% 824ms 2.38% DistributedBoxCollection::CalculateContainingBox (partial-inline) 596ms 1.72% 68.04% 821ms 2.37% __dynamic_cast 0 0% 68.04% 804ms 2.32% boost::numeric::ublas::norm_inf (inline) 483ms 1.39% 69.44% 804ms 2.32% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 69.44% 766ms 2.21% AbstractCellPopulation::WriteResultsToFiles 155ms 0.45% 69.88% 750ms 2.16% NodeAttributes::AddNeighbour 127ms 0.37% 70.25% 740ms 2.13% std::__new_allocator::allocate (inline) 17ms 0.049% 70.30% 708ms 2.04% CellPropertyCollection::GetPropertiesType (inline) 592ms 1.71% 72.01% 687ms 1.98% std::vector::push_back (inline) 0 0% 72.01% 678ms 1.95% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 72.01% 678ms 1.95% boost::numeric::ublas::c_vector::plus_assign (inline) 5ms 0.014% 72.02% 634ms 1.83% Cell::GetMutationState 79ms 0.23% 72.25% 614ms 1.77% operator new 9ms 0.026% 72.27% 602ms 1.74% AbstractCellBasedSimulation::DoCellBirth 0 0% 72.27% 557ms 1.61% boost::numeric::ublas::norm_2 (inline) 448ms 1.29% 73.57% 557ms 1.61% boost::numeric::ublas::vector_norm_2::apply (inline) 188ms 0.54% 74.11% 551ms 1.59% __GI___libc_free 187ms 0.54% 74.65% 530ms 1.53% __GI___libc_malloc 2ms 0.0058% 74.65% 506ms 1.46% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 74.65% 469ms 1.35% AbstractCellBasedSimulation::DoCellRemoval (inline) 6ms 0.017% 74.67% 458ms 1.32% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 35ms 0.1% 74.77% 440ms 1.27% boost::detail::shared_count::~shared_count (inline) 0 0% 74.77% 440ms 1.27% boost::shared_ptr::~shared_ptr (inline) 4ms 0.012% 74.78% 434ms 1.25% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 0 0% 74.78% 434ms 1.25% std::allocator_traits::allocate (inline) 2ms 0.0058% 74.79% 429ms 1.24% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 74.79% 412ms 1.19% std::_Rb_tree::_M_create_node (inline) 391ms 1.13% 75.92% 403ms 1.16% boost::detail::sp_counted_base::release 387ms 1.12% 77.03% 387ms 1.12% [libchaste_mesh.so] 310ms 0.89% 77.93% 362ms 1.04% _int_free 0 0% 77.93% 361ms 1.04% boost::numeric::ublas::inner_prod (inline) 2ms 0.0058% 77.93% 358ms 1.03% AbstractCellProperty::IsSubType (inline) 1ms 0.0029% 77.93% 358ms 1.03% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 12ms 0.035% 77.97% 357ms 1.03% boost::numeric::ublas::vector_scalar_binary::evaluate 181ms 0.52% 78.49% 355ms 1.02% Node::AddNeighbour 0 0% 78.49% 347ms 1.00% std::_Rb_tree::_M_get_node (inline) 346ms 1% 79.49% 346ms 1% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 79.49% 340ms 0.98% NodesOnlyMesh::ReMesh 99ms 0.29% 79.77% 340ms 0.98% std::_Rb_tree::_M_erase 29ms 0.084% 79.86% 335ms 0.97% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 79.86% 335ms 0.97% boost::numeric::ublas::vector::vector (inline) 327ms 0.94% 80.80% 327ms 0.94% Node::GetIndex 5ms 0.014% 80.81% 326ms 0.94% NodeBasedCellPopulation::UpdateMapsAfterRemesh 2ms 0.0058% 80.82% 324ms 0.93% NodesOnlyMesh::UpdateNodeIndices 21ms 0.061% 80.88% 323ms 0.93% std::_Rb_tree::_Rb_tree (partial-inline) 317ms 0.91% 81.79% 317ms 0.91% __gnu_cxx::__normal_iterator::operator++ (inline) 80ms 0.23% 82.03% 304ms 0.88% Node::GetRadius 3ms 0.0087% 82.03% 304ms 0.88% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 19ms 0.055% 82.09% 298ms 0.86% std::_Rb_tree::_M_copy (inline) 12ms 0.035% 82.12% 296ms 0.85% boost::numeric::ublas::vector_reference::operator() (inline) 124ms 0.36% 82.48% 288ms 0.83% boost::numeric::ublas::vector_inner_prod::apply (inline) 6ms 0.017% 82.50% 287ms 0.83% DistributedBoxCollection::GetProcessOwningNode 9ms 0.026% 82.52% 281ms 0.81% std::_Rb_tree::_M_emplace_hint_unique 44ms 0.13% 82.65% 279ms 0.8% std::_Rb_tree::_M_clone_node (inline) 0 0% 82.65% 270ms 0.78% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 82.65% 268ms 0.77% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 82.65% 266ms 0.77% VtkMeshWriter::WriteFiles 0 0% 82.65% 262ms 0.76% NodesOnlyMesh::UpdateBoxCollection 0 0% 82.65% 260ms 0.75% boost::numeric::ublas::c_vector::assign (inline) 259ms 0.75% 83.40% 259ms 0.75% NodeBasedCellPopulation::GetNode 0 0% 83.40% 249ms 0.72% boost::numeric::ublas::vector_binary::operator() (inline) 96ms 0.28% 83.67% 249ms 0.72% std::__move_median_to_first (inline) 2ms 0.0058% 83.68% 242ms 0.7% CellPropertyCollection::HasProperty 0 0% 83.68% 239ms 0.69% Cell::HasCellProperty (inline) 237ms 0.68% 84.36% 237ms 0.68% Node::CheckForNodeAttributes 0 0% 84.36% 237ms 0.68% std::_Rb_tree::_M_drop_node (inline) 127ms 0.37% 84.73% 235ms 0.68% _int_malloc 233ms 0.67% 85.40% 233ms 0.67% [libchaste_cell_based.so] 0 0% 85.40% 230ms 0.66% vtkStreamingDemandDrivenPipeline::Update 0 0% 85.40% 230ms 0.66% vtkXMLWriterBase::Write 11ms 0.032% 85.43% 228ms 0.66% Cell::ReadyToDivide 1ms 0.0029% 85.44% 227ms 0.65% vtkDemandDrivenPipeline::ProcessRequest 0 0% 85.44% 227ms 0.65% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 85.44% 225ms 0.65% vtkDemandDrivenPipeline::ExecuteData 0 0% 85.44% 224ms 0.65% vtkCompositeDataPipeline::ExecuteData 0 0% 85.44% 224ms 0.65% vtkExecutive::CallAlgorithm 0 0% 85.44% 224ms 0.65% vtkXMLUnstructuredDataWriter::ProcessRequest 5ms 0.014% 85.45% 217ms 0.63% std::__new_allocator::deallocate (inline) 2ms 0.0058% 85.46% 211ms 0.61% NodesOnlyMesh::AddNodesToBoxes 203ms 0.59% 86.04% 203ms 0.59% Node::ConstructNodeAttributes (inline) 0 0% 86.04% 198ms 0.57% std::allocator_traits::deallocate (inline) 197ms 0.57% 86.61% 197ms 0.57% __strcmp_avx2 12ms 0.035% 86.64% 196ms 0.57% std::_Rb_tree::~_Rb_tree (inline) 0 0% 86.64% 194ms 0.56% std::_Rb_tree::_M_put_node (inline) 18ms 0.052% 86.70% 192ms 0.55% std::__insertion_sort (inline) 0 0% 86.70% 188ms 0.54% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 86.70% 188ms 0.54% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 86.70% 186ms 0.54% std::_Rb_tree::clear (inline) 3ms 0.0087% 86.70% 183ms 0.53% AbstractCellProperty::IsType (inline) 4ms 0.012% 86.72% 183ms 0.53% std::set::set (inline) 0 0% 86.72% 181ms 0.52% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData