File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 18331ms, 88.36% of 20745ms total Dropped 660 nodes (cum <= 103.72ms) flat flat% sum% cum cum% 0 0% 0% 20667ms 99.62% __libc_start_call_main 0 0% 0% 20667ms 99.62% __libc_start_main_impl 0 0% 0% 20667ms 99.62% _start 0 0% 0% 20656ms 99.57% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 20656ms 99.57% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 20656ms 99.57% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 20656ms 99.57% main 0 0% 0% 20627ms 99.43% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 20627ms 99.43% CxxTest::TestRunner::runTest (inline) 0 0% 0% 20627ms 99.43% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 20623ms 99.41% AbstractCellBasedSimulation::Solve 2ms 0.0096% 0.0096% 14284ms 68.86% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.0096% 0.019% 10819ms 52.15% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0048% 0.024% 10695ms 51.55% AbstractNumericalMethod::ComputeForcesIncludingDamping 65ms 0.31% 0.34% 10387ms 50.07% AbstractTwoBodyInteractionForce::AddForceContribution 1060ms 5.11% 5.45% 9420ms 45.41% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 3645ms 17.57% 23.02% 6131ms 29.55% std::_Rb_tree::_M_lower_bound (inline) 21ms 0.1% 23.12% 5700ms 27.48% NodesOnlyMesh::GetNodeOrHaloNode 0 0% 23.12% 5679ms 27.38% AbstractCellBasedSimulation::UpdateCellPopulation 288ms 1.39% 24.51% 5663ms 27.30% AbstractMesh::GetNode 283ms 1.36% 25.87% 5550ms 26.75% std::_Rb_tree::find (inline) 0 0% 25.87% 5550ms 26.75% std::map::find (inline) 411ms 1.98% 27.85% 5382ms 25.94% NodesOnlyMesh::SolveNodeMapping 0 0% 27.85% 5038ms 24.29% NodeBasedCellPopulation::Update 2ms 0.0096% 27.86% 3774ms 18.19% DistributedBoxCollection::CalculateInteriorNodePairs 0 0% 27.86% 3303ms 15.92% OffLatticeSimulation::ApplyBoundaries 19ms 0.092% 27.95% 3180ms 15.33% NodeAttributes::RemoveDuplicateNeighbours 1ms 0.0048% 27.96% 3031ms 14.61% std::__sort (inline) 0 0% 27.96% 3031ms 14.61% std::sort (inline) 142ms 0.68% 28.64% 2979ms 14.36% boost::numeric::ublas::c_vector::c_vector (partial-inline) 65ms 0.31% 28.96% 2928ms 14.11% boost::numeric::ublas::vector_assign (inline) 2438ms 11.75% 40.71% 2438ms 11.75% std::_Rb_tree::_S_right (inline) 127ms 0.61% 41.32% 2367ms 11.41% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 2ms 0.0096% 41.33% 2254ms 10.87% AbstractCellPopulation::Iterator::operator++ (inline) 101ms 0.49% 41.82% 2239ms 10.79% AbstractCellPopulation::Iterator::IsRealCell (inline) 9ms 0.043% 41.86% 1875ms 9.04% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 153ms 0.74% 42.60% 1776ms 8.56% std::__introsort_loop 45ms 0.22% 42.82% 1703ms 8.21% PlaneBoundaryCondition::ImposeBoundaryCondition 45ms 0.22% 43.03% 1600ms 7.71% PlaneBoundaryCondition::VerifyBoundaryCondition 0 0% 43.03% 1546ms 7.45% std::__unguarded_partition_pivot (inline) 39ms 0.19% 43.22% 1435ms 6.92% AbstractCellPopulation::GetLocationIndexUsingCell 465ms 2.24% 45.46% 1406ms 6.78% boost::numeric::ublas::indexing_vector_assign 702ms 3.38% 48.85% 1395ms 6.72% std::__unguarded_partition (inline) 4ms 0.019% 48.86% 1254ms 6.04% std::__final_insertion_sort (inline) 162ms 0.78% 49.65% 1249ms 6.02% std::map::operator[] (partial-inline) 61ms 0.29% 49.94% 1094ms 5.27% std::__unguarded_insertion_sort (inline) 359ms 1.73% 51.67% 1035ms 4.99% std::__unguarded_linear_insert (inline) 1017ms 4.90% 56.57% 1017ms 4.90% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 56.57% 1004ms 4.84% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 108ms 0.52% 57.09% 991ms 4.78% DistributedBoxCollection::AddPairsFromBox 0 0% 57.09% 990ms 4.77% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 57.09% 916ms 4.42% std::_Rb_tree::lower_bound (inline) 0 0% 57.09% 916ms 4.42% std::map::lower_bound (inline) 829ms 4.00% 61.09% 829ms 4.00% boost::numeric::ublas::same_impl_ex 16ms 0.077% 61.17% 793ms 3.82% boost::numeric::ublas::detail::expression_type_check (inline) 46ms 0.22% 61.39% 770ms 3.71% boost::numeric::ublas::detail::equals 145ms 0.7% 62.09% 766ms 3.69% AbstractMesh::GetVectorFromAtoB 21ms 0.1% 62.19% 746ms 3.60% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 62.19% 706ms 3.40% DistributedBoxCollection::CalculateBoundaryNodePairs 0 0% 62.19% 691ms 3.33% boost::numeric::ublas::norm_inf (inline) 318ms 1.53% 63.72% 691ms 3.33% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 63.72% 670ms 3.23% NodeBasedCellPopulation::UpdateCellProcessLocation 17ms 0.082% 63.80% 535ms 2.58% boost::detail::shared_count::~shared_count (inline) 0 0% 63.80% 535ms 2.58% boost::shared_ptr::~shared_ptr (inline) 228ms 1.10% 64.90% 517ms 2.49% DistributedBoxCollection::CalculateContainingBox (partial-inline) 513ms 2.47% 67.38% 515ms 2.48% boost::detail::sp_counted_base::release 54ms 0.26% 67.64% 479ms 2.31% boost::numeric::ublas::vector_binary::size (inline) 447ms 2.15% 69.79% 447ms 2.15% boost::numeric::ublas::c_vector::operator() 30ms 0.14% 69.93% 424ms 2.04% std::__new_allocator::allocate (inline) 107ms 0.52% 70.45% 397ms 1.91% NodeAttributes::AddAppliedForceContribution 86ms 0.41% 70.87% 393ms 1.89% operator new 0 0% 70.87% 390ms 1.88% AbstractCellPopulation::WriteResultsToFiles 0 0% 70.87% 345ms 1.66% AbstractCellBasedSimulation::DoCellRemoval (inline) 10ms 0.048% 70.91% 337ms 1.62% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 37ms 0.18% 71.09% 330ms 1.59% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 71.09% 313ms 1.51% boost::numeric::ublas::norm_2 (inline) 283ms 1.36% 72.46% 313ms 1.51% boost::numeric::ublas::vector_norm_2::apply (inline) 146ms 0.7% 73.16% 308ms 1.48% __GI___libc_malloc 101ms 0.49% 73.65% 303ms 1.46% __GI___libc_free 199ms 0.96% 74.61% 296ms 1.43% __dynamic_cast 1ms 0.0048% 74.61% 295ms 1.42% AbstractCellBasedSimulation::DoCellBirth 0 0% 74.61% 290ms 1.40% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 74.61% 290ms 1.40% boost::numeric::ublas::c_vector::plus_assign (inline) 286ms 1.38% 75.99% 286ms 1.38% std::_Rb_tree_increment 1ms 0.0048% 75.99% 278ms 1.34% AbstractCentreBasedCellPopulation::GetDampingConstant 112ms 0.54% 76.53% 274ms 1.32% NodeAttributes::AddNeighbour 1ms 0.0048% 76.54% 263ms 1.27% NodeBasedCellPopulation::WriteVtkResultsToFile 21ms 0.1% 76.64% 250ms 1.21% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 76.64% 250ms 1.21% boost::numeric::ublas::vector::vector (inline) 0 0% 76.64% 223ms 1.07% boost::numeric::ublas::scalar_traits::norm_inf (inline) 0 0% 76.64% 223ms 1.07% boost::numeric::ublas::scalar_traits::type_abs (inline) 2ms 0.0096% 76.65% 222ms 1.07% boost_numeric_ublas_abs (inline) 220ms 1.06% 77.71% 220ms 1.06% std::abs (inline) 217ms 1.05% 78.76% 217ms 1.05% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 214ms 1.03% 79.79% 214ms 1.03% __gnu_cxx::__normal_iterator::operator++ (inline) 41ms 0.2% 79.99% 205ms 0.99% Node::GetRadius 0 0% 79.99% 203ms 0.98% NodesOnlyMesh::ReMesh 188ms 0.91% 80.89% 202ms 0.97% _int_free 199ms 0.96% 81.85% 199ms 0.96% NodeBasedCellPopulation::GetNode 160ms 0.77% 82.62% 198ms 0.95% std::vector::push_back (inline) 3ms 0.014% 82.64% 197ms 0.95% NodesOnlyMesh::UpdateNodeIndices 0 0% 82.64% 195ms 0.94% std::allocator_traits::allocate (inline) 3ms 0.014% 82.65% 191ms 0.92% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 82.65% 189ms 0.91% CellPropertyCollection::GetPropertiesType (inline) 1ms 0.0048% 82.66% 179ms 0.86% Cell::GetMutationState 166ms 0.8% 83.46% 174ms 0.84% boost::shared_ptr::shared_ptr (inline) 5ms 0.024% 83.48% 171ms 0.82% std::_Rb_tree::_M_emplace_hint_unique 3ms 0.014% 83.49% 169ms 0.81% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 31ms 0.15% 83.64% 169ms 0.81% std::_Rb_tree::_M_erase (partial-inline) 0 0% 83.64% 167ms 0.81% std::_Rb_tree::_M_create_node (inline) 0 0% 83.64% 160ms 0.77% std::_Rb_tree::_M_get_node (inline) 159ms 0.77% 84.41% 159ms 0.77% [libchaste_cell_based.so] 157ms 0.76% 85.17% 157ms 0.76% Node::CheckForNodeAttributes 0 0% 85.17% 156ms 0.75% NodesOnlyMesh::UpdateBoxCollection 0 0% 85.17% 156ms 0.75% boost::numeric::ublas::c_vector::assign (inline) 17ms 0.082% 85.25% 156ms 0.75% std::__insertion_sort (inline) 1ms 0.0048% 85.25% 155ms 0.75% DistributedBoxCollection::GetProcessOwningNode 0 0% 85.25% 155ms 0.75% boost::numeric::ublas::vector_binary::operator() (inline) 1ms 0.0048% 85.26% 148ms 0.71% AbstractCellProperty::IsSubType (inline) 147ms 0.71% 85.97% 147ms 0.71% Node::GetIndex 0 0% 85.97% 146ms 0.7% boost::numeric::ublas::inner_prod (inline) 10ms 0.048% 86.02% 146ms 0.7% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 86.02% 146ms 0.7% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 75ms 0.36% 86.38% 143ms 0.69% std::__move_median_to_first (inline) 4ms 0.019% 86.40% 136ms 0.66% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 86.40% 136ms 0.66% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 0 0% 86.40% 133ms 0.64% std::_Rb_tree::_M_drop_node (inline) 87ms 0.42% 86.82% 125ms 0.6% Node::AddNeighbour 0 0% 86.82% 124ms 0.6% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 86.82% 124ms 0.6% VtkMeshWriter::WriteFiles 0 0% 86.82% 122ms 0.59% NodesOnlyMesh::AddNodesToBoxes 122ms 0.59% 87.40% 122ms 0.59% [libchaste_mesh.so] 6ms 0.029% 87.43% 122ms 0.59% std::__new_allocator::deallocate (inline) 103ms 0.5% 87.93% 120ms 0.58% std::__adjacent_find (inline) 0 0% 87.93% 120ms 0.58% std::__unique (inline) 0 0% 87.93% 120ms 0.58% std::unique (inline) 0 0% 87.93% 115ms 0.55% std::allocator_traits::deallocate (inline) 23ms 0.11% 88.04% 113ms 0.54% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 88.04% 113ms 0.54% std::_Rb_tree::_M_put_node (inline) 0 0% 88.04% 111ms 0.54% vtkStreamingDemandDrivenPipeline::Update 0 0% 88.04% 111ms 0.54% vtkXMLWriterBase::Write 0 0% 88.04% 110ms 0.53% vtkDemandDrivenPipeline::ProcessRequest 0 0% 88.04% 110ms 0.53% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 88.04% 109ms 0.53% vtkCompositeDataPipeline::ExecuteData 0 0% 88.04% 109ms 0.53% vtkDemandDrivenPipeline::ExecuteData 0 0% 88.04% 109ms 0.53% vtkExecutive::CallAlgorithm 0 0% 88.04% 108ms 0.52% vtkXMLUnstructuredDataWriter::ProcessRequest 67ms 0.32% 88.36% 107ms 0.52% _int_malloc 0 0% 88.36% 106ms 0.51% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 88.36% 105ms 0.51% std::_Rb_tree::clear (inline)