File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 23799ms, 87.58% of 27175ms total Dropped 799 nodes (cum <= 135.88ms) flat flat% sum% cum cum% 0 0% 0% 27065ms 99.60% __libc_start_call_main 0 0% 0% 27065ms 99.60% __libc_start_main_impl 0 0% 0% 27065ms 99.60% _start 0 0% 0% 27050ms 99.54% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 27050ms 99.54% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 27050ms 99.54% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 27050ms 99.54% main 0 0% 0% 27014ms 99.41% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 27014ms 99.41% CxxTest::TestRunner::runTest (inline) 0 0% 0% 27014ms 99.41% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 27008ms 99.39% AbstractCellBasedSimulation::Solve 2ms 0.0074% 0.0074% 18746ms 68.98% OffLatticeSimulation::UpdateCellLocationsAndTopology 3ms 0.011% 0.018% 14765ms 54.33% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.011% 0.029% 14610ms 53.76% AbstractNumericalMethod::ComputeForcesIncludingDamping 110ms 0.4% 0.43% 13909ms 51.18% AbstractTwoBodyInteractionForce::AddForceContribution 1214ms 4.47% 4.90% 11947ms 43.96% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 3490ms 12.84% 17.74% 7747ms 28.51% std::_Rb_tree::_M_lower_bound (inline) 0 0% 17.74% 7313ms 26.91% AbstractCellBasedSimulation::UpdateCellPopulation 316ms 1.16% 18.91% 7092ms 26.10% std::_Rb_tree::find (inline) 0 0% 18.91% 7092ms 26.10% std::map::find (inline) 165ms 0.61% 19.51% 6950ms 25.57% NodesOnlyMesh::GetNodeOrHaloNode 399ms 1.47% 20.98% 6795ms 25.00% AbstractMesh::GetNode 2ms 0.0074% 20.99% 6444ms 23.71% NodeBasedCellPopulation::Update 263ms 0.97% 21.96% 6397ms 23.54% NodesOnlyMesh::SolveNodeMapping 2ms 0.0074% 21.97% 4833ms 17.78% DistributedBoxCollection::CalculateInteriorNodePairs 157ms 0.58% 22.54% 4593ms 16.90% boost::numeric::ublas::vector_assign (inline) 128ms 0.47% 23.01% 4552ms 16.75% boost::numeric::ublas::c_vector::c_vector (partial-inline) 4216ms 15.51% 38.53% 4216ms 15.51% std::_Rb_tree::_S_right (inline) 0 0% 38.53% 3674ms 13.52% OffLatticeSimulation::ApplyBoundaries 10ms 0.037% 38.56% 3577ms 13.16% NodeAttributes::RemoveDuplicateNeighbours 1ms 0.0037% 38.57% 3446ms 12.68% std::__sort (inline) 0 0% 38.57% 3446ms 12.68% std::sort (inline) 55ms 0.2% 38.77% 2714ms 9.99% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 0 0% 38.77% 2550ms 9.38% AbstractCellPopulation::Iterator::operator++ (inline) 840ms 3.09% 41.86% 2539ms 9.34% boost::numeric::ublas::indexing_vector_assign 128ms 0.47% 42.33% 2532ms 9.32% AbstractCellPopulation::Iterator::IsRealCell 17ms 0.063% 42.40% 2226ms 8.19% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 134ms 0.49% 42.89% 2043ms 7.52% std::__introsort_loop 16ms 0.059% 42.95% 1950ms 7.18% PlaneBoundaryCondition::ImposeBoundaryCondition 42ms 0.15% 43.10% 1864ms 6.86% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 43.10% 1854ms 6.82% std::__unguarded_partition_pivot (inline) 14ms 0.052% 43.15% 1724ms 6.34% PlaneBoundaryCondition::VerifyBoundaryCondition 135ms 0.5% 43.65% 1717ms 6.32% DistributedBoxCollection::AddPairsFromBox 825ms 3.04% 46.69% 1647ms 6.06% std::__unguarded_partition (inline) 162ms 0.6% 47.28% 1425ms 5.24% std::map::operator[] (partial-inline) 0 0% 47.28% 1416ms 5.21% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 2ms 0.0074% 47.29% 1402ms 5.16% std::__final_insertion_sort (inline) 0 0% 47.29% 1396ms 5.14% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 83ms 0.31% 47.60% 1251ms 4.60% std::__unguarded_insertion_sort (inline) 447ms 1.64% 49.24% 1185ms 4.36% std::__unguarded_linear_insert (inline) 1180ms 4.34% 53.58% 1180ms 4.34% boost::numeric::ublas::same_impl_ex 132ms 0.49% 54.07% 1178ms 4.33% AbstractMesh::GetVectorFromAtoB 15ms 0.055% 54.12% 1105ms 4.07% boost::numeric::ublas::detail::expression_type_check (inline) 1085ms 3.99% 58.12% 1085ms 3.99% __gnu_cxx::__normal_iterator::operator-- (inline) 94ms 0.35% 58.46% 1078ms 3.97% boost::numeric::ublas::detail::equals 0 0% 58.46% 1052ms 3.87% std::_Rb_tree::lower_bound (inline) 0 0% 58.46% 1052ms 3.87% std::map::lower_bound (inline) 0 0% 58.46% 957ms 3.52% boost::numeric::ublas::norm_inf (inline) 446ms 1.64% 60.10% 957ms 3.52% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 60.10% 899ms 3.31% NodeBasedCellPopulation::UpdateCellProcessLocation 880ms 3.24% 63.34% 880ms 3.24% boost::numeric::ublas::c_vector::operator() 6ms 0.022% 63.36% 855ms 3.15% DistributedBoxCollection::CalculateBoundaryNodePairs 162ms 0.6% 63.96% 772ms 2.84% boost::numeric::ublas::vector_binary::size (inline) 17ms 0.063% 64.02% 742ms 2.73% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 312ms 1.15% 65.17% 679ms 2.50% DistributedBoxCollection::CalculateContainingBox (partial-inline) 203ms 0.75% 65.92% 679ms 2.50% NodeAttributes::AddNeighbour 3ms 0.011% 65.93% 645ms 2.37% AbstractCentreBasedCellPopulation::GetDampingConstant 147ms 0.54% 66.47% 604ms 2.22% NodeAttributes::AddAppliedForceContribution 81ms 0.3% 66.77% 593ms 2.18% std::__new_allocator::allocate (inline) 0 0% 66.77% 582ms 2.14% AbstractCellPopulation::WriteResultsToFiles 406ms 1.49% 68.26% 579ms 2.13% __dynamic_cast 27ms 0.099% 68.36% 557ms 2.05% std::_Rb_tree_const_iterator::operator++ (inline) 471ms 1.73% 70.09% 534ms 1.97% std::vector::push_back (inline) 514ms 1.89% 71.99% 514ms 1.89% std::_Rb_tree_increment 71ms 0.26% 72.25% 510ms 1.88% operator new 4ms 0.015% 72.26% 491ms 1.81% AbstractCellBasedSimulation::DoCellBirth 8ms 0.029% 72.29% 467ms 1.72% CellPropertyCollection::GetPropertiesType (inline) 0 0% 72.29% 459ms 1.69% boost::numeric::ublas::norm_2 (inline) 361ms 1.33% 73.62% 459ms 1.69% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 73.62% 457ms 1.68% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 73.62% 457ms 1.68% boost::numeric::ublas::c_vector::plus_assign (inline) 155ms 0.57% 74.19% 438ms 1.61% __GI___libc_malloc 0 0% 74.19% 426ms 1.57% Cell::GetMutationState 0 0% 74.19% 385ms 1.42% NodeBasedCellPopulation::WriteVtkResultsToFile 116ms 0.43% 74.62% 378ms 1.39% __GI___libc_free 0 0% 74.62% 377ms 1.39% AbstractCellBasedSimulation::DoCellRemoval (inline) 6ms 0.022% 74.64% 370ms 1.36% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 74.64% 350ms 1.29% boost::numeric::ublas::scalar_traits::norm_inf (inline) 0 0% 74.64% 350ms 1.29% boost::numeric::ublas::scalar_traits::type_abs (inline) 0 0% 74.64% 349ms 1.28% boost_numeric_ublas_abs (inline) 349ms 1.28% 75.92% 349ms 1.28% std::abs (inline) 0 0% 75.92% 344ms 1.27% std::allocator_traits::allocate (inline) 332ms 1.22% 77.14% 332ms 1.22% Node::GetIndex 18ms 0.066% 77.21% 326ms 1.20% boost::detail::shared_count::~shared_count (inline) 0 0% 77.21% 326ms 1.20% boost::shared_ptr::~shared_ptr (inline) 0 0% 77.21% 320ms 1.18% std::_Rb_tree::_M_create_node (inline) 5ms 0.018% 77.23% 307ms 1.13% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 302ms 1.11% 78.34% 306ms 1.13% boost::detail::sp_counted_base::release 7ms 0.026% 78.37% 299ms 1.10% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 78.37% 290ms 1.07% boost::numeric::ublas::inner_prod (inline) 11ms 0.04% 78.41% 288ms 1.06% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 78.41% 288ms 1.06% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 29ms 0.11% 78.51% 278ms 1.02% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 78.51% 278ms 1.02% boost::numeric::ublas::vector::vector (inline) 3ms 0.011% 78.52% 276ms 1.02% AbstractCellProperty::IsSubType (inline) 0 0% 78.52% 273ms 1.00% std::_Rb_tree::_M_get_node (inline) 266ms 0.98% 79.50% 266ms 0.98% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 230ms 0.85% 80.35% 261ms 0.96% _int_free 3ms 0.011% 80.36% 247ms 0.91% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 86ms 0.32% 80.68% 247ms 0.91% std::_Rb_tree::_M_erase (partial-inline) 243ms 0.89% 81.57% 243ms 0.89% __gnu_cxx::__normal_iterator::operator++ (inline) 6ms 0.022% 81.59% 241ms 0.89% NodeBasedCellPopulation::UpdateMapsAfterRemesh 49ms 0.18% 81.77% 236ms 0.87% Node::GetRadius 0 0% 81.77% 236ms 0.87% NodesOnlyMesh::ReMesh 111ms 0.41% 82.18% 235ms 0.86% boost::numeric::ublas::vector_inner_prod::apply (inline) 4ms 0.015% 82.20% 231ms 0.85% DistributedBoxCollection::GetProcessOwningNode 12ms 0.044% 82.24% 231ms 0.85% boost::numeric::ublas::vector_reference::operator() (inline) 3ms 0.011% 82.25% 226ms 0.83% NodesOnlyMesh::UpdateNodeIndices 187ms 0.69% 82.94% 221ms 0.81% Node::AddNeighbour 1ms 0.0037% 82.94% 215ms 0.79% NodesOnlyMesh::UpdateBoxCollection 9ms 0.033% 82.98% 211ms 0.78% std::_Rb_tree::_M_emplace_hint_unique 3ms 0.011% 82.99% 211ms 0.78% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 82.99% 207ms 0.76% boost::numeric::ublas::c_vector::assign (inline) 0 0% 82.99% 206ms 0.76% std::_Rb_tree::_Alloc_node::operator() (inline) 102ms 0.38% 83.36% 205ms 0.75% std::__move_median_to_first (inline) 16ms 0.059% 83.42% 204ms 0.75% std::_Rb_tree::_M_copy (inline) 196ms 0.72% 84.14% 196ms 0.72% Node::CheckForNodeAttributes 105ms 0.39% 84.53% 195ms 0.72% _int_malloc 0 0% 84.53% 186ms 0.68% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 24ms 0.088% 84.62% 186ms 0.68% std::_Rb_tree::_M_clone_node (inline) 4ms 0.015% 84.63% 185ms 0.68% CellPropertyCollection::HasProperty 0 0% 84.63% 184ms 0.68% Cell::HasCellProperty (inline) 0 0% 84.63% 184ms 0.68% VtkMeshWriter::WriteFiles 184ms 0.68% 85.31% 184ms 0.68% [libchaste_cell_based.so] 0 0% 85.31% 183ms 0.67% boost::numeric::ublas::vector_binary::operator() (inline) 2ms 0.0074% 85.32% 180ms 0.66% NodesOnlyMesh::AddNodesToBoxes 7ms 0.026% 85.34% 176ms 0.65% Cell::ReadyToDivide 170ms 0.63% 85.97% 170ms 0.63% [libchaste_mesh.so] 166ms 0.61% 86.58% 166ms 0.61% __strcmp_evex 24ms 0.088% 86.67% 166ms 0.61% std::__new_allocator::deallocate (inline) 0 0% 86.67% 153ms 0.56% std::_Rb_tree::_M_drop_node (inline) 0 0% 86.67% 153ms 0.56% vtkDemandDrivenPipeline::ProcessRequest 0 0% 86.67% 153ms 0.56% vtkStreamingDemandDrivenPipeline::Update 0 0% 86.67% 153ms 0.56% vtkXMLWriterBase::Write 0 0% 86.67% 150ms 0.55% vtkCompositeDataPipeline::ExecuteData 0 0% 86.67% 150ms 0.55% vtkDemandDrivenPipeline::ExecuteData 0 0% 86.67% 150ms 0.55% vtkExecutive::CallAlgorithm 0 0% 86.67% 150ms 0.55% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 86.67% 150ms 0.55% vtkXMLUnstructuredDataWriter::ProcessRequest 18ms 0.066% 86.73% 149ms 0.55% std::__insertion_sort (inline) 148ms 0.54% 87.28% 148ms 0.54% NodeBasedCellPopulation::GetNode 74ms 0.27% 87.55% 146ms 0.54% boost::shared_ptr::shared_ptr (inline) 7ms 0.026% 87.58% 146ms 0.54% std::_Rb_tree::~_Rb_tree (inline)