File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 19598ms, 88.40% of 22170ms total Dropped 707 nodes (cum <= 110.85ms) flat flat% sum% cum cum% 0 0% 0% 22074ms 99.57% __libc_start_call_main 0 0% 0% 22074ms 99.57% __libc_start_main_impl 0 0% 0% 22074ms 99.57% _start 0 0% 0% 22061ms 99.51% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 22061ms 99.51% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 22061ms 99.51% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 22061ms 99.51% main 0 0% 0% 22027ms 99.35% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 22027ms 99.35% CxxTest::TestRunner::runTest (inline) 0 0% 0% 22027ms 99.35% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 22020ms 99.32% AbstractCellBasedSimulation::Solve 0 0% 0% 15234ms 68.71% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0% 11522ms 51.97% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0045% 0.0045% 11403ms 51.43% AbstractNumericalMethod::ComputeForcesIncludingDamping 87ms 0.39% 0.4% 11038ms 49.79% AbstractTwoBodyInteractionForce::AddForceContribution 1117ms 5.04% 5.44% 9894ms 44.63% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 3475ms 15.67% 21.11% 6399ms 28.86% std::_Rb_tree::_M_lower_bound (inline) 0 0% 21.11% 6043ms 27.26% AbstractCellBasedSimulation::UpdateCellPopulation 26ms 0.12% 21.23% 5939ms 26.79% NodesOnlyMesh::GetNodeOrHaloNode 300ms 1.35% 22.58% 5915ms 26.68% AbstractMesh::GetNode 289ms 1.30% 23.88% 5782ms 26.08% std::_Rb_tree::find (inline) 0 0% 23.88% 5782ms 26.08% std::map::find (inline) 404ms 1.82% 25.71% 5616ms 25.33% NodesOnlyMesh::SolveNodeMapping 0 0% 25.71% 5343ms 24.10% NodeBasedCellPopulation::Update 2ms 0.009% 25.71% 3993ms 18.01% DistributedBoxCollection::CalculateInteriorNodePairs 0 0% 25.71% 3509ms 15.83% OffLatticeSimulation::ApplyBoundaries 21ms 0.095% 25.81% 3303ms 14.90% NodeAttributes::RemoveDuplicateNeighbours 163ms 0.74% 26.54% 3236ms 14.60% boost::numeric::ublas::c_vector::c_vector (partial-inline) 85ms 0.38% 26.93% 3175ms 14.32% boost::numeric::ublas::vector_assign (inline) 5ms 0.023% 26.95% 3171ms 14.30% std::__sort (inline) 0 0% 26.95% 3171ms 14.30% std::sort (inline) 2876ms 12.97% 39.92% 2876ms 12.97% std::_Rb_tree::_S_right (inline) 145ms 0.65% 40.58% 2459ms 11.09% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 6ms 0.027% 40.60% 2398ms 10.82% AbstractCellPopulation::Iterator::operator++ (inline) 103ms 0.46% 41.07% 2383ms 10.75% AbstractCellPopulation::Iterator::IsRealCell (inline) 10ms 0.045% 41.11% 1984ms 8.95% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 59ms 0.27% 41.38% 1820ms 8.21% PlaneBoundaryCondition::ImposeBoundaryCondition 127ms 0.57% 41.95% 1820ms 8.21% std::__introsort_loop 37ms 0.17% 42.12% 1689ms 7.62% PlaneBoundaryCondition::VerifyBoundaryCondition 551ms 2.49% 44.61% 1640ms 7.40% boost::numeric::ublas::indexing_vector_assign 0 0% 44.61% 1609ms 7.26% std::__unguarded_partition_pivot (inline) 54ms 0.24% 44.85% 1503ms 6.78% AbstractCellPopulation::GetLocationIndexUsingCell 700ms 3.16% 48.01% 1447ms 6.53% std::__unguarded_partition (inline) 194ms 0.88% 48.88% 1347ms 6.08% std::map::operator[] (partial-inline) 2ms 0.009% 48.89% 1346ms 6.07% std::__final_insertion_sort (inline) 68ms 0.31% 49.20% 1189ms 5.36% std::__unguarded_insertion_sort (inline) 338ms 1.52% 50.72% 1137ms 5.13% std::__unguarded_linear_insert (inline) 1120ms 5.05% 55.77% 1120ms 5.05% __gnu_cxx::__normal_iterator::operator-- (inline) 120ms 0.54% 56.31% 1105ms 4.98% DistributedBoxCollection::AddPairsFromBox 0 0% 56.31% 974ms 4.39% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 56.31% 974ms 4.39% std::_Rb_tree::lower_bound (inline) 0 0% 56.31% 974ms 4.39% std::map::lower_bound (inline) 0 0% 56.31% 957ms 4.32% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 917ms 4.14% 60.45% 917ms 4.14% boost::numeric::ublas::same_impl_ex 145ms 0.65% 61.11% 902ms 4.07% AbstractMesh::GetVectorFromAtoB 23ms 0.1% 61.21% 774ms 3.49% boost::numeric::ublas::detail::expression_type_check (inline) 48ms 0.22% 61.43% 744ms 3.36% boost::numeric::ublas::detail::equals 12ms 0.054% 61.48% 736ms 3.32% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 5ms 0.023% 61.50% 731ms 3.30% DistributedBoxCollection::CalculateBoundaryNodePairs 0 0% 61.50% 728ms 3.28% NodeBasedCellPopulation::UpdateCellProcessLocation 0 0% 61.50% 655ms 2.95% boost::numeric::ublas::norm_inf (inline) 320ms 1.44% 62.95% 655ms 2.95% boost::numeric::ublas::vector_norm_inf::apply (inline) 30ms 0.14% 63.08% 596ms 2.69% boost::detail::shared_count::~shared_count (inline) 0 0% 63.08% 596ms 2.69% boost::shared_ptr::~shared_ptr (inline) 555ms 2.50% 65.58% 565ms 2.55% boost::detail::sp_counted_base::release 76ms 0.34% 65.93% 559ms 2.52% boost::numeric::ublas::vector_binary::size (inline) 239ms 1.08% 67.00% 530ms 2.39% DistributedBoxCollection::CalculateContainingBox (partial-inline) 508ms 2.29% 69.30% 508ms 2.29% boost::numeric::ublas::c_vector::operator() 45ms 0.2% 69.50% 479ms 2.16% std::__new_allocator::allocate (inline) 0 0% 69.50% 460ms 2.07% AbstractCellPopulation::WriteResultsToFiles 127ms 0.57% 70.07% 446ms 2.01% NodeAttributes::AddAppliedForceContribution 87ms 0.39% 70.46% 431ms 1.94% operator new 39ms 0.18% 70.64% 390ms 1.76% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.009% 70.65% 354ms 1.60% AbstractCellBasedSimulation::DoCellBirth 0 0% 70.65% 346ms 1.56% AbstractCellBasedSimulation::DoCellRemoval (inline) 2ms 0.009% 70.66% 344ms 1.55% AbstractCentreBasedCellPopulation::GetDampingConstant 159ms 0.72% 71.38% 343ms 1.55% __GI___libc_malloc 8ms 0.036% 71.41% 342ms 1.54% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 223ms 1.01% 72.42% 336ms 1.52% __dynamic_cast 336ms 1.52% 73.93% 336ms 1.52% std::_Rb_tree_increment 0 0% 73.93% 319ms 1.44% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 73.93% 319ms 1.44% boost::numeric::ublas::c_vector::plus_assign (inline) 0 0% 73.93% 319ms 1.44% boost::numeric::ublas::norm_2 (inline) 284ms 1.28% 75.21% 319ms 1.44% boost::numeric::ublas::vector_norm_2::apply (inline) 3ms 0.014% 75.23% 314ms 1.42% NodeBasedCellPopulation::WriteVtkResultsToFile 112ms 0.51% 75.73% 309ms 1.39% NodeAttributes::AddNeighbour 109ms 0.49% 76.22% 304ms 1.37% __GI___libc_free 0 0% 76.22% 261ms 1.18% std::allocator_traits::allocate (inline) 197ms 0.89% 77.11% 261ms 1.18% std::vector::push_back (inline) 24ms 0.11% 77.22% 242ms 1.09% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 77.22% 242ms 1.09% boost::numeric::ublas::vector::vector (inline) 4ms 0.018% 77.24% 239ms 1.08% CellPropertyCollection::GetPropertiesType (inline) 237ms 1.07% 78.31% 237ms 1.07% __gnu_cxx::__normal_iterator::operator++ (inline) 56ms 0.25% 78.56% 231ms 1.04% Node::GetRadius 0 0% 78.56% 225ms 1.01% std::_Rb_tree::_M_create_node (inline) 2ms 0.009% 78.57% 224ms 1.01% Cell::GetMutationState 2ms 0.009% 78.58% 217ms 0.98% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 78.58% 217ms 0.98% std::_Rb_tree::_M_get_node (inline) 0 0% 78.58% 203ms 0.92% boost::numeric::ublas::scalar_traits::norm_inf (inline) 0 0% 78.58% 203ms 0.92% boost::numeric::ublas::scalar_traits::type_abs (inline) 0 0% 78.58% 200ms 0.9% NodesOnlyMesh::ReMesh 2ms 0.009% 78.59% 199ms 0.9% boost_numeric_ublas_abs (inline) 33ms 0.15% 78.74% 199ms 0.9% std::_Rb_tree::_M_erase (partial-inline) 197ms 0.89% 79.63% 197ms 0.89% std::abs (inline) 1ms 0.0045% 79.63% 195ms 0.88% NodesOnlyMesh::UpdateNodeIndices 175ms 0.79% 80.42% 195ms 0.88% _int_free 194ms 0.88% 81.29% 194ms 0.88% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 1ms 0.0045% 81.30% 185ms 0.83% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 2ms 0.009% 81.31% 179ms 0.81% std::_Rb_tree::_M_emplace_hint_unique 175ms 0.79% 82.10% 175ms 0.79% NodeBasedCellPopulation::GetNode 158ms 0.71% 82.81% 175ms 0.79% boost::shared_ptr::shared_ptr (inline) 6ms 0.027% 82.84% 174ms 0.78% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 82.84% 174ms 0.78% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 4ms 0.018% 82.86% 173ms 0.78% DistributedBoxCollection::GetProcessOwningNode 0 0% 82.86% 169ms 0.76% AbstractCellProperty::IsSubType (inline) 169ms 0.76% 83.62% 169ms 0.76% Node::GetIndex 0 0% 83.62% 169ms 0.76% NodesOnlyMesh::UpdateBoxCollection 0 0% 83.62% 169ms 0.76% boost::numeric::ublas::c_vector::assign (inline) 0 0% 83.62% 165ms 0.74% boost::numeric::ublas::inner_prod (inline) 15ms 0.068% 83.69% 163ms 0.74% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 83.69% 163ms 0.74% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 83.69% 156ms 0.7% std::_Rb_tree::_M_drop_node (inline) 19ms 0.086% 83.77% 155ms 0.7% std::__insertion_sort (inline) 152ms 0.69% 84.46% 152ms 0.69% Node::CheckForNodeAttributes 0 0% 84.46% 151ms 0.68% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 84.46% 150ms 0.68% VtkMeshWriter::WriteFiles 77ms 0.35% 84.80% 145ms 0.65% std::__move_median_to_first (inline) 144ms 0.65% 85.45% 144ms 0.65% [libchaste_cell_based.so] 0 0% 85.45% 142ms 0.64% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 85.45% 139ms 0.63% vtkStreamingDemandDrivenPipeline::Update 0 0% 85.45% 139ms 0.63% vtkXMLWriterBase::Write 0 0% 85.45% 137ms 0.62% NodesOnlyMesh::AddNodesToBoxes 0 0% 85.45% 137ms 0.62% vtkDemandDrivenPipeline::ProcessRequest 80ms 0.36% 85.81% 136ms 0.61% _int_malloc 0 0% 85.81% 136ms 0.61% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 85.81% 135ms 0.61% vtkDemandDrivenPipeline::ExecuteData 0 0% 85.81% 135ms 0.61% vtkExecutive::CallAlgorithm 0 0% 85.81% 134ms 0.6% vtkCompositeDataPipeline::ExecuteData 1ms 0.0045% 85.82% 134ms 0.6% vtkXMLUnstructuredDataWriter::ProcessRequest 11ms 0.05% 85.87% 129ms 0.58% std::_Rb_tree::~_Rb_tree (inline) 94ms 0.42% 86.29% 128ms 0.58% Node::AddNeighbour 128ms 0.58% 86.87% 128ms 0.58% [libchaste_mesh.so] 128ms 0.58% 87.45% 128ms 0.58% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 4ms 0.018% 87.47% 128ms 0.58% std::__new_allocator::deallocate (inline) 29ms 0.13% 87.60% 127ms 0.57% boost::numeric::ublas::vector_inner_prod::apply (inline) 6ms 0.027% 87.62% 125ms 0.56% std::_Rb_tree::_Rb_tree (partial-inline) 120ms 0.54% 88.16% 120ms 0.54% boost::shared_ptr::operator-> (inline) 4ms 0.018% 88.18% 117ms 0.53% std::_Rb_tree::_M_copy (inline) 0 0% 88.18% 117ms 0.53% std::_Rb_tree::_M_put_node (inline) 0 0% 88.18% 117ms 0.53% std::allocator_traits::deallocate (inline) 0 0% 88.18% 113ms 0.51% std::_Rb_tree::_Alloc_node::operator() (inline) 21ms 0.095% 88.28% 113ms 0.51% std::_Rb_tree::_M_clone_node (inline) 27ms 0.12% 88.40% 112ms 0.51% boost::numeric::ublas::c_vector::clear (inline) 0 0% 88.40% 112ms 0.51% std::_Rb_tree::_Auto_node::_Auto_node (inline)