File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 23138ms, 88.72% of 26080ms total Dropped 781 nodes (cum <= 130.40ms) flat flat% sum% cum cum% 0 0% 0% 26022ms 99.78% __libc_start_call_main 0 0% 0% 26022ms 99.78% __libc_start_main_impl 0 0% 0% 26022ms 99.78% _start 0 0% 0% 26007ms 99.72% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 26007ms 99.72% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 26007ms 99.72% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 26007ms 99.72% main 0 0% 0% 25969ms 99.57% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 25969ms 99.57% CxxTest::TestRunner::runTest (inline) 0 0% 0% 25969ms 99.57% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0038% 0.0038% 25962ms 99.55% AbstractCellBasedSimulation::Solve 1ms 0.0038% 0.0077% 17795ms 68.23% OffLatticeSimulation::UpdateCellLocationsAndTopology 6ms 0.023% 0.031% 13445ms 51.55% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.012% 0.042% 13317ms 51.06% AbstractNumericalMethod::ComputeForcesIncludingDamping 228ms 0.87% 0.92% 12821ms 49.16% AbstractTwoBodyInteractionForce::AddForceContribution 820ms 3.14% 4.06% 11479ms 44.01% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 3161ms 12.12% 16.18% 8102ms 31.07% std::_Rb_tree::_M_lower_bound (inline) 162ms 0.62% 16.80% 7727ms 29.63% NodesOnlyMesh::GetNodeOrHaloNode 219ms 0.84% 17.64% 7554ms 28.96% AbstractMesh::GetNode 589ms 2.26% 19.90% 7342ms 28.15% NodesOnlyMesh::SolveNodeMapping 260ms 1% 20.90% 7327ms 28.09% std::_Rb_tree::find (inline) 0 0% 20.90% 7327ms 28.09% std::map::find (inline) 0 0% 20.90% 7286ms 27.94% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 20.90% 6385ms 24.48% NodeBasedCellPopulation::Update 8ms 0.031% 20.93% 4773ms 18.30% DistributedBoxCollection::CalculateInteriorNodePairs 4316ms 16.55% 37.48% 4316ms 16.55% std::_Rb_tree::_S_right (inline) 1ms 0.0038% 37.48% 4091ms 15.69% OffLatticeSimulation::ApplyBoundaries 12ms 0.046% 37.53% 3804ms 14.59% NodeAttributes::RemoveDuplicateNeighbours 2ms 0.0077% 37.53% 3651ms 14.00% std::__sort (inline) 0 0% 37.53% 3651ms 14.00% std::sort (inline) 123ms 0.47% 38.01% 3554ms 13.63% boost::numeric::ublas::vector_assign (inline) 39ms 0.15% 38.16% 3493ms 13.39% boost::numeric::ublas::c_vector::c_vector (partial-inline) 238ms 0.91% 39.07% 3000ms 11.50% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 3ms 0.012% 39.08% 2934ms 11.25% AbstractCellPopulation::Iterator::operator++ (inline) 171ms 0.66% 39.74% 2929ms 11.23% AbstractCellPopulation::Iterator::IsRealCell (inline) 12ms 0.046% 39.78% 2435ms 9.34% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 193ms 0.74% 40.52% 2188ms 8.39% std::__introsort_loop 53ms 0.2% 40.72% 2068ms 7.93% PlaneBoundaryCondition::ImposeBoundaryCondition 57ms 0.22% 40.94% 2022ms 7.75% PlaneBoundaryCondition::VerifyBoundaryCondition 12ms 0.046% 40.99% 1904ms 7.30% std::__unguarded_partition_pivot (inline) 619ms 2.37% 43.36% 1709ms 6.55% std::__unguarded_partition (inline) 77ms 0.3% 43.66% 1671ms 6.41% AbstractCellPopulation::GetLocationIndexUsingCell 445ms 1.71% 45.36% 1549ms 5.94% boost::numeric::ublas::indexing_vector_assign 156ms 0.6% 45.96% 1544ms 5.92% std::map::operator[] (partial-inline) 86ms 0.33% 46.29% 1502ms 5.76% DistributedBoxCollection::AddPairsFromBox 0 0% 46.29% 1460ms 5.60% std::__final_insertion_sort (inline) 85ms 0.33% 46.62% 1298ms 4.98% std::__unguarded_insertion_sort (inline) 0 0% 46.62% 1249ms 4.79% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 46.62% 1233ms 4.73% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 598ms 2.29% 48.91% 1170ms 4.49% std::__unguarded_linear_insert (inline) 20ms 0.077% 48.99% 1146ms 4.39% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 48.99% 1122ms 4.30% std::_Rb_tree::lower_bound (inline) 0 0% 48.99% 1122ms 4.30% std::map::lower_bound (inline) 150ms 0.58% 49.56% 1088ms 4.17% boost::numeric::ublas::detail::equals 0 0% 49.56% 933ms 3.58% boost::numeric::ublas::norm_inf (inline) 361ms 1.38% 50.95% 933ms 3.58% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 50.95% 872ms 3.34% NodeBasedCellPopulation::UpdateCellProcessLocation 5ms 0.019% 50.97% 867ms 3.32% DistributedBoxCollection::CalculateBoundaryNodePairs 860ms 3.30% 54.26% 860ms 3.30% boost::numeric::ublas::same_impl_ex 854ms 3.27% 57.54% 854ms 3.27% __gnu_cxx::__normal_iterator::operator-- (inline) 16ms 0.061% 57.60% 818ms 3.14% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 82ms 0.31% 57.91% 747ms 2.86% AbstractMesh::GetVectorFromAtoB 67ms 0.26% 58.17% 672ms 2.58% std::__new_allocator::allocate (inline) 637ms 2.44% 60.61% 637ms 2.44% std::_Rb_tree::_S_left (inline) 7ms 0.027% 60.64% 598ms 2.29% boost::detail::shared_count::~shared_count (inline) 0 0% 60.64% 598ms 2.29% boost::shared_ptr::~shared_ptr (inline) 299ms 1.15% 61.79% 597ms 2.29% NodeAttributes::AddNeighbour 575ms 2.20% 63.99% 583ms 2.24% boost::detail::sp_counted_base::release 61ms 0.23% 64.23% 580ms 2.22% operator new 563ms 2.16% 66.38% 563ms 2.16% [libchaste_cell_based.so] 0 0% 66.38% 554ms 2.12% AbstractCellPopulation::WriteResultsToFiles 235ms 0.9% 67.29% 539ms 2.07% DistributedBoxCollection::CalculateContainingBox (partial-inline) 14ms 0.054% 67.34% 498ms 1.91% std::_Rb_tree_const_iterator::operator++ (inline) 166ms 0.64% 67.98% 496ms 1.90% __GI___libc_malloc 1ms 0.0038% 67.98% 491ms 1.88% AbstractCellBasedSimulation::DoCellBirth 480ms 1.84% 69.82% 480ms 1.84% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 478ms 1.83% 71.65% 478ms 1.83% [libchaste_mesh.so] 337ms 1.29% 72.94% 466ms 1.79% __dynamic_cast 0 0% 72.94% 456ms 1.75% boost::numeric::ublas::scalar_traits::type_abs (inline) 1ms 0.0038% 72.95% 450ms 1.73% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 72.95% 444ms 1.70% boost::numeric::ublas::scalar_traits::norm_inf (inline) 1ms 0.0038% 72.95% 443ms 1.70% boost_numeric_ublas_abs (inline) 442ms 1.69% 74.65% 442ms 1.69% std::abs (inline) 441ms 1.69% 76.34% 441ms 1.69% boost::numeric::ublas::c_vector::operator() 19ms 0.073% 76.41% 438ms 1.68% boost::numeric::ublas::vector_binary::size (inline) 429ms 1.64% 78.06% 429ms 1.64% std::_Rb_tree_increment 425ms 1.63% 79.69% 425ms 1.63% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 79.69% 409ms 1.57% AbstractCellBasedSimulation::DoCellRemoval (inline) 150ms 0.58% 80.26% 404ms 1.55% NodeAttributes::AddAppliedForceContribution 9ms 0.035% 80.30% 399ms 1.53% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 80.30% 387ms 1.48% std::allocator_traits::allocate (inline) 278ms 1.07% 81.36% 373ms 1.43% std::vector::push_back (inline) 1ms 0.0038% 81.37% 372ms 1.43% NodeBasedCellPopulation::WriteVtkResultsToFile 104ms 0.4% 81.76% 357ms 1.37% __GI___libc_free 0 0% 81.76% 357ms 1.37% std::_Rb_tree::_M_create_node (inline) 0 0% 81.76% 335ms 1.28% std::_Rb_tree::_M_get_node (inline) 9ms 0.035% 81.80% 329ms 1.26% CellPropertyCollection::GetPropertiesType (inline) 0 0% 81.80% 316ms 1.21% boost::numeric::ublas::norm_2 (inline) 232ms 0.89% 82.69% 316ms 1.21% boost::numeric::ublas::vector_norm_2::apply (inline) 4ms 0.015% 82.70% 289ms 1.11% Cell::GetMutationState 4ms 0.015% 82.72% 289ms 1.11% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 82.72% 289ms 1.11% boost::numeric::ublas::vector::vector (inline) 10ms 0.038% 82.76% 266ms 1.02% std::_Rb_tree::_M_emplace_hint_unique 4ms 0.015% 82.77% 261ms 1.00% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 82.77% 260ms 1% NodesOnlyMesh::ReMesh 1ms 0.0038% 82.78% 257ms 0.99% NodesOnlyMesh::UpdateNodeIndices 0 0% 82.78% 254ms 0.97% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 82.78% 254ms 0.97% boost::numeric::ublas::c_vector::plus_assign (inline) 219ms 0.84% 83.62% 252ms 0.97% _int_free 2ms 0.0077% 83.62% 235ms 0.9% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 1ms 0.0038% 83.63% 231ms 0.89% AbstractCellPopulation::GetCellUsingLocationIndex 32ms 0.12% 83.75% 227ms 0.87% std::_Rb_tree::_M_erase (partial-inline) 1ms 0.0038% 83.75% 223ms 0.86% Node::GetRadius 0 0% 83.75% 217ms 0.83% boost::numeric::ublas::vector_binary::operator() (inline) 137ms 0.53% 84.28% 215ms 0.82% _int_malloc 4ms 0.015% 84.29% 203ms 0.78% AbstractCellProperty::IsSubType (inline) 0 0% 84.29% 195ms 0.75% NodesOnlyMesh::UpdateBoxCollection 177ms 0.68% 84.97% 192ms 0.74% boost::shared_ptr::shared_ptr (inline) 0 0% 84.97% 190ms 0.73% std::_Rb_tree::_M_drop_node (inline) 0 0% 84.97% 188ms 0.72% std::_Rb_tree::_Alloc_node::operator() (inline) 1ms 0.0038% 84.98% 186ms 0.71% std::_Rb_tree::_Rb_tree (partial-inline) 1ms 0.0038% 84.98% 184ms 0.71% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 9ms 0.035% 85.02% 184ms 0.71% std::_Rb_tree::_M_copy (inline) 0 0% 85.02% 182ms 0.7% boost::numeric::ublas::inner_prod (inline) 3ms 0.012% 85.03% 182ms 0.7% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 85.03% 179ms 0.69% Cell::HasCellProperty (inline) 0 0% 85.03% 179ms 0.69% CellPropertyCollection::HasProperty 10ms 0.038% 85.07% 179ms 0.69% boost::numeric::ublas::vector_scalar_binary::evaluate 3ms 0.012% 85.08% 178ms 0.68% DistributedBoxCollection::GetProcessOwningNode 178ms 0.68% 85.76% 178ms 0.68% Node::CheckForNodeAttributes 34ms 0.13% 85.89% 173ms 0.66% std::_Rb_tree::_M_clone_node (inline) 64ms 0.25% 86.13% 173ms 0.66% std::__move_median_to_first (inline) 11ms 0.042% 86.18% 171ms 0.66% std::__new_allocator::deallocate (inline) 0 0% 86.18% 170ms 0.65% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 5ms 0.019% 86.20% 170ms 0.65% Cell::ReadyToDivide 0 0% 86.20% 169ms 0.65% VtkMeshWriter::WriteFiles 0 0% 86.20% 169ms 0.65% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 86.20% 166ms 0.64% std::iter_swap (inline) 166ms 0.64% 86.83% 166ms 0.64% std::swap (inline) 0 0% 86.83% 164ms 0.63% NodesOnlyMesh::AddNodesToBoxes 20ms 0.077% 86.91% 162ms 0.62% std::__insertion_sort (inline) 0 0% 86.91% 158ms 0.61% boost::numeric::ublas::c_vector::assign (inline) 4ms 0.015% 86.92% 157ms 0.6% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 86.92% 150ms 0.58% std::allocator_traits::deallocate (inline) 144ms 0.55% 87.48% 144ms 0.55% boost::shared_ptr::operator-> (inline) 0 0% 87.48% 144ms 0.55% std::_Rb_tree::_M_put_node (inline) 11ms 0.042% 87.52% 144ms 0.55% std::_Rb_tree::~_Rb_tree (inline) 138ms 0.53% 88.05% 138ms 0.53% Node::GetIndex 0 0% 88.05% 138ms 0.53% vtkStreamingDemandDrivenPipeline::Update 0 0% 88.05% 138ms 0.53% vtkXMLWriterBase::Write 43ms 0.16% 88.21% 136ms 0.52% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 88.21% 136ms 0.52% vtkDemandDrivenPipeline::ProcessRequest 0 0% 88.21% 136ms 0.52% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 88.21% 134ms 0.51% vtkExecutive::CallAlgorithm 1ms 0.0038% 88.22% 133ms 0.51% vtkCompositeDataPipeline::ExecuteData 0 0% 88.22% 133ms 0.51% vtkDemandDrivenPipeline::ExecuteData 0 0% 88.22% 132ms 0.51% vtkXMLUnstructuredDataWriter::ProcessRequest 131ms 0.5% 88.72% 131ms 0.5% Node::ConstructNodeAttributes (inline) 0 0% 88.72% 131ms 0.5% NodesOnlyMesh::ResizeBoxCollection