File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 24349ms, 88.28% of 27582ms total Dropped 762 nodes (cum <= 137.91ms) flat flat% sum% cum cum% 0 0% 0% 27492ms 99.67% __libc_start_call_main 0 0% 0% 27492ms 99.67% __libc_start_main_impl 0 0% 0% 27492ms 99.67% _start 0 0% 0% 27477ms 99.62% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 27477ms 99.62% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 27477ms 99.62% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 27477ms 99.62% main 0 0% 0% 27441ms 99.49% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 27441ms 99.49% CxxTest::TestRunner::runTest (inline) 0 0% 0% 27441ms 99.49% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 27434ms 99.46% AbstractCellBasedSimulation::Solve 3ms 0.011% 0.011% 18767ms 68.04% OffLatticeSimulation::UpdateCellLocationsAndTopology 3ms 0.011% 0.022% 14829ms 53.76% ForwardEulerNumericalMethod::UpdateAllNodePositions 9ms 0.033% 0.054% 14695ms 53.28% AbstractNumericalMethod::ComputeForcesIncludingDamping 98ms 0.36% 0.41% 13763ms 49.90% AbstractTwoBodyInteractionForce::AddForceContribution 1179ms 4.27% 4.68% 11829ms 42.89% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 3454ms 12.52% 17.21% 7713ms 27.96% std::_Rb_tree::_M_lower_bound (inline) 0 0% 17.21% 7694ms 27.90% AbstractCellBasedSimulation::UpdateCellPopulation 297ms 1.08% 18.28% 7070ms 25.63% std::_Rb_tree::find (inline) 0 0% 18.28% 7069ms 25.63% std::map::find (inline) 138ms 0.5% 18.78% 6911ms 25.06% NodesOnlyMesh::GetNodeOrHaloNode 1ms 0.0036% 18.79% 6788ms 24.61% NodeBasedCellPopulation::Update 407ms 1.48% 20.26% 6784ms 24.60% AbstractMesh::GetNode 293ms 1.06% 21.33% 6380ms 23.13% NodesOnlyMesh::SolveNodeMapping 7ms 0.025% 21.35% 5120ms 18.56% DistributedBoxCollection::CalculateInteriorNodePairs 136ms 0.49% 21.84% 4409ms 15.99% boost::numeric::ublas::c_vector::c_vector (partial-inline) 113ms 0.41% 22.25% 4398ms 15.95% boost::numeric::ublas::vector_assign (inline) 4225ms 15.32% 37.57% 4225ms 15.32% std::_Rb_tree::_S_right (inline) 0 0% 37.57% 3640ms 13.20% OffLatticeSimulation::ApplyBoundaries 13ms 0.047% 37.62% 3605ms 13.07% NodeAttributes::RemoveDuplicateNeighbours 4ms 0.015% 37.63% 3436ms 12.46% std::__sort (inline) 0 0% 37.63% 3436ms 12.46% std::sort (inline) 58ms 0.21% 37.84% 2608ms 9.46% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 836ms 3.03% 40.87% 2504ms 9.08% boost::numeric::ublas::indexing_vector_assign 3ms 0.011% 40.89% 2498ms 9.06% AbstractCellPopulation::Iterator::operator++ (inline) 127ms 0.46% 41.35% 2473ms 8.97% AbstractCellPopulation::Iterator::IsRealCell 29ms 0.11% 41.45% 2158ms 7.82% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 147ms 0.53% 41.98% 2039ms 7.39% std::__introsort_loop 110ms 0.4% 42.38% 2017ms 7.31% DistributedBoxCollection::AddPairsFromBox 28ms 0.1% 42.48% 1955ms 7.09% PlaneBoundaryCondition::ImposeBoundaryCondition 36ms 0.13% 42.61% 1829ms 6.63% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 42.61% 1825ms 6.62% std::__unguarded_partition_pivot (inline) 11ms 0.04% 42.65% 1685ms 6.11% PlaneBoundaryCondition::VerifyBoundaryCondition 774ms 2.81% 45.46% 1625ms 5.89% std::__unguarded_partition (inline) 140ms 0.51% 45.97% 1404ms 5.09% std::map::operator[] (partial-inline) 0 0% 45.97% 1390ms 5.04% std::__final_insertion_sort (inline) 0 0% 45.97% 1372ms 4.97% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 45.97% 1352ms 4.90% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 71ms 0.26% 46.23% 1238ms 4.49% std::__unguarded_insertion_sort (inline) 1212ms 4.39% 50.62% 1212ms 4.39% boost::numeric::ublas::same_impl_ex 459ms 1.66% 52.28% 1188ms 4.31% std::__unguarded_linear_insert (inline) 129ms 0.47% 52.75% 1159ms 4.20% AbstractMesh::GetVectorFromAtoB 1078ms 3.91% 56.66% 1078ms 3.91% __gnu_cxx::__normal_iterator::operator-- (inline) 4ms 0.015% 56.67% 1043ms 3.78% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 56.67% 1030ms 3.73% std::_Rb_tree::lower_bound (inline) 0 0% 56.67% 1030ms 3.73% std::map::lower_bound (inline) 100ms 0.36% 57.04% 1017ms 3.69% boost::numeric::ublas::detail::equals 1ms 0.0036% 57.04% 924ms 3.35% NodeBasedCellPopulation::UpdateCellProcessLocation 0 0% 57.04% 914ms 3.31% boost::numeric::ublas::norm_inf (inline) 424ms 1.54% 58.58% 914ms 3.31% boost::numeric::ublas::vector_norm_inf::apply (inline) 6ms 0.022% 58.60% 877ms 3.18% DistributedBoxCollection::CalculateBoundaryNodePairs 4ms 0.015% 58.61% 876ms 3.18% AbstractCentreBasedCellPopulation::GetDampingConstant 853ms 3.09% 61.71% 853ms 3.09% boost::numeric::ublas::c_vector::operator() 22ms 0.08% 61.79% 807ms 2.93% std::_Rb_tree_const_iterator::operator++ (inline) 767ms 2.78% 64.57% 767ms 2.78% std::_Rb_tree_increment 119ms 0.43% 65.00% 732ms 2.65% boost::numeric::ublas::vector_binary::size (inline) 17ms 0.062% 65.06% 714ms 2.59% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 484ms 1.75% 66.82% 658ms 2.39% __dynamic_cast 17ms 0.062% 66.88% 653ms 2.37% CellPropertyCollection::GetPropertiesType (inline) 301ms 1.09% 67.97% 643ms 2.33% DistributedBoxCollection::CalculateContainingBox (partial-inline) 173ms 0.63% 68.60% 618ms 2.24% NodeAttributes::AddAppliedForceContribution 142ms 0.51% 69.11% 616ms 2.23% NodeAttributes::AddNeighbour 0 0% 69.11% 590ms 2.14% AbstractCellPopulation::WriteResultsToFiles 4ms 0.015% 69.12% 588ms 2.13% Cell::GetMutationState 100ms 0.36% 69.49% 583ms 2.11% std::__new_allocator::allocate (inline) 471ms 1.71% 71.19% 558ms 2.02% std::vector::push_back (inline) 9ms 0.033% 71.23% 529ms 1.92% AbstractCellBasedSimulation::DoCellBirth 54ms 0.2% 71.42% 484ms 1.75% operator new 0 0% 71.42% 458ms 1.66% boost::numeric::ublas::norm_2 (inline) 361ms 1.31% 72.73% 458ms 1.66% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 72.73% 445ms 1.61% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 72.73% 445ms 1.61% boost::numeric::ublas::c_vector::plus_assign (inline) 143ms 0.52% 73.25% 426ms 1.54% __GI___libc_malloc 153ms 0.55% 73.81% 397ms 1.44% __GI___libc_free 1ms 0.0036% 73.81% 382ms 1.38% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 73.81% 376ms 1.36% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 73.81% 374ms 1.36% std::allocator_traits::allocate (inline) 0 0% 73.81% 368ms 1.33% std::_Rb_tree::_M_create_node (inline) 5ms 0.018% 73.83% 363ms 1.32% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1ms 0.0036% 73.83% 358ms 1.30% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 5ms 0.018% 73.85% 357ms 1.29% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 73.85% 353ms 1.28% boost::numeric::ublas::scalar_traits::norm_inf (inline) 0 0% 73.85% 353ms 1.28% boost::numeric::ublas::scalar_traits::type_abs (inline) 0 0% 73.85% 350ms 1.27% boost_numeric_ublas_abs (inline) 350ms 1.27% 75.12% 350ms 1.27% std::abs (inline) 344ms 1.25% 76.37% 344ms 1.25% Node::GetIndex 327ms 1.19% 77.55% 327ms 1.19% [libchaste_mesh.so] 0 0% 77.55% 308ms 1.12% AbstractCellProperty::IsSubType (inline) 0 0% 77.55% 308ms 1.12% std::_Rb_tree::_M_get_node (inline) 25ms 0.091% 77.64% 299ms 1.08% boost::detail::shared_count::~shared_count (inline) 0 0% 77.64% 299ms 1.08% boost::shared_ptr::~shared_ptr (inline) 148ms 0.54% 78.18% 298ms 1.08% Node::AddNeighbour 277ms 1.00% 79.18% 277ms 1.00% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 275ms 1% 80.18% 275ms 1% __gnu_cxx::__normal_iterator::operator++ (inline) 17ms 0.062% 80.24% 274ms 0.99% std::_Rb_tree::_Rb_tree (partial-inline) 259ms 0.94% 81.18% 270ms 0.98% boost::detail::sp_counted_base::release 98ms 0.36% 81.54% 266ms 0.96% std::_Rb_tree::_M_erase 3ms 0.011% 81.55% 260ms 0.94% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 81.55% 259ms 0.94% boost::numeric::ublas::inner_prod (inline) 0 0% 81.55% 258ms 0.94% NodesOnlyMesh::ReMesh 12ms 0.044% 81.59% 257ms 0.93% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 81.59% 257ms 0.93% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 24ms 0.087% 81.68% 253ms 0.92% std::_Rb_tree::_M_copy (inline) 1ms 0.0036% 81.68% 247ms 0.9% NodesOnlyMesh::UpdateNodeIndices 2ms 0.0073% 81.69% 244ms 0.88% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 205ms 0.74% 82.43% 244ms 0.88% _int_free 31ms 0.11% 82.54% 240ms 0.87% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 82.54% 240ms 0.87% boost::numeric::ublas::vector::vector (inline) 0 0% 82.54% 238ms 0.86% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 82.54% 234ms 0.85% NodesOnlyMesh::UpdateBoxCollection 0 0% 82.54% 234ms 0.85% boost::numeric::ublas::c_vector::assign (inline) 5ms 0.018% 82.56% 234ms 0.85% std::_Rb_tree::_M_emplace_hint_unique 51ms 0.18% 82.75% 232ms 0.84% Node::GetRadius 7ms 0.025% 82.77% 228ms 0.83% Cell::ReadyToDivide 3ms 0.011% 82.78% 227ms 0.82% DistributedBoxCollection::GetProcessOwningNode 28ms 0.1% 82.88% 227ms 0.82% std::_Rb_tree::_M_clone_node (inline) 224ms 0.81% 83.70% 224ms 0.81% [libchaste_cell_based.so] 0 0% 83.70% 223ms 0.81% Cell::HasCellProperty (inline) 3ms 0.011% 83.71% 223ms 0.81% CellPropertyCollection::HasProperty 104ms 0.38% 84.08% 215ms 0.78% _int_malloc 89ms 0.32% 84.41% 211ms 0.76% boost::numeric::ublas::vector_inner_prod::apply (inline) 197ms 0.71% 85.12% 197ms 0.71% Node::CheckForNodeAttributes 80ms 0.29% 85.41% 197ms 0.71% std::__move_median_to_first (inline) 11ms 0.04% 85.45% 193ms 0.7% boost::numeric::ublas::vector_reference::operator() (inline) 25ms 0.091% 85.54% 187ms 0.68% std::__new_allocator::deallocate (inline) 0 0% 85.54% 185ms 0.67% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 85.54% 183ms 0.66% VtkMeshWriter::WriteFiles 181ms 0.66% 86.20% 182ms 0.66% Node::ConstructNodeAttributes (inline) 0 0% 86.20% 181ms 0.66% NodesOnlyMesh::AddNodesToBoxes 172ms 0.62% 86.82% 172ms 0.62% NodeBasedCellPopulation::GetNode 0 0% 86.82% 167ms 0.61% std::_Rb_tree::_M_drop_node (inline) 0 0% 86.82% 160ms 0.58% vtkCompositeDataPipeline::ExecuteData 0 0% 86.82% 160ms 0.58% vtkDemandDrivenPipeline::ExecuteData 0 0% 86.82% 160ms 0.58% vtkDemandDrivenPipeline::ProcessRequest 0 0% 86.82% 160ms 0.58% vtkExecutive::CallAlgorithm 0 0% 86.82% 160ms 0.58% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 86.82% 160ms 0.58% vtkStreamingDemandDrivenPipeline::Update 0 0% 86.82% 160ms 0.58% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 86.82% 160ms 0.58% vtkXMLWriterBase::Write 0 0% 86.82% 155ms 0.56% std::_Rb_tree::clear (inline) 3ms 0.011% 86.83% 155ms 0.56% std::set::set (inline) 152ms 0.55% 87.38% 152ms 0.55% __strcmp_evex 20ms 0.073% 87.46% 152ms 0.55% std::__insertion_sort (inline) 0 0% 87.46% 149ms 0.54% std::allocator_traits::deallocate (inline) 0 0% 87.46% 148ms 0.54% boost::numeric::ublas::vector_binary::operator() (inline) 5ms 0.018% 87.47% 146ms 0.53% AbstractCellProperty::IsType (inline) 0 0% 87.47% 146ms 0.53% std::_Rb_tree::_M_put_node (inline) 145ms 0.53% 88.00% 146ms 0.53% std::__adjacent_find (inline) 0 0% 88.00% 146ms 0.53% std::__unique (inline) 0 0% 88.00% 146ms 0.53% std::unique (inline) 68ms 0.25% 88.25% 142ms 0.51% boost::shared_ptr::shared_ptr (inline) 9ms 0.033% 88.28% 139ms 0.5% std::_Rb_tree::~_Rb_tree (inline)