File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 30894ms, 88.77% of 34801ms total Dropped 808 nodes (cum <= 174ms) flat flat% sum% cum cum% 0 0% 0% 34645ms 99.55% __libc_start_call_main 0 0% 0% 34645ms 99.55% __libc_start_main_impl 0 0% 0% 34645ms 99.55% _start 0 0% 0% 34628ms 99.50% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 34628ms 99.50% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 34628ms 99.50% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 34628ms 99.50% main 0 0% 0% 34590ms 99.39% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 34590ms 99.39% CxxTest::TestRunner::runTest (inline) 0 0% 0% 34590ms 99.39% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 34581ms 99.37% AbstractCellBasedSimulation::Solve 2ms 0.0057% 0.0057% 24248ms 69.68% OffLatticeSimulation::UpdateCellLocationsAndTopology 4ms 0.011% 0.017% 19376ms 55.68% ForwardEulerNumericalMethod::UpdateAllNodePositions 11ms 0.032% 0.049% 19177ms 55.10% AbstractNumericalMethod::ComputeForcesIncludingDamping 213ms 0.61% 0.66% 18285ms 52.54% AbstractTwoBodyInteractionForce::AddForceContribution 1454ms 4.18% 4.84% 15442ms 44.37% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4435ms 12.74% 17.58% 9844ms 28.29% std::_Rb_tree::_M_lower_bound (inline) 0 0% 17.58% 9134ms 26.25% AbstractCellBasedSimulation::UpdateCellPopulation 312ms 0.9% 18.48% 8878ms 25.51% std::_Rb_tree::find (inline) 0 0% 18.48% 8878ms 25.51% std::map::find (inline) 121ms 0.35% 18.83% 8599ms 24.71% NodesOnlyMesh::GetNodeOrHaloNode 495ms 1.42% 20.25% 8450ms 24.28% AbstractMesh::GetNode 2ms 0.0057% 20.26% 8039ms 23.10% NodeBasedCellPopulation::Update 321ms 0.92% 21.18% 7958ms 22.87% NodesOnlyMesh::SolveNodeMapping 245ms 0.7% 21.88% 6415ms 18.43% boost::numeric::ublas::vector_assign (inline) 178ms 0.51% 22.39% 6218ms 17.87% boost::numeric::ublas::c_vector::c_vector (partial-inline) 10ms 0.029% 22.42% 5986ms 17.20% DistributedBoxCollection::CalculateInteriorNodePairs 5386ms 15.48% 37.90% 5386ms 15.48% std::_Rb_tree::_S_right (inline) 1ms 0.0029% 37.90% 4534ms 13.03% OffLatticeSimulation::ApplyBoundaries 29ms 0.083% 37.98% 4471ms 12.85% NodeAttributes::RemoveDuplicateNeighbours 10ms 0.029% 38.01% 4297ms 12.35% std::__sort (inline) 0 0% 38.01% 4297ms 12.35% std::sort (inline) 1147ms 3.30% 41.31% 3586ms 10.30% boost::numeric::ublas::indexing_vector_assign 1ms 0.0029% 41.31% 3446ms 9.90% AbstractCellPopulation::Iterator::operator++ (inline) 221ms 0.64% 41.95% 3423ms 9.84% AbstractCellPopulation::Iterator::IsRealCell 79ms 0.23% 42.17% 3421ms 9.83% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 26ms 0.075% 42.25% 2874ms 8.26% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 193ms 0.55% 42.80% 2423ms 6.96% std::__introsort_loop 29ms 0.083% 42.89% 2377ms 6.83% PlaneBoundaryCondition::ImposeBoundaryCondition 40ms 0.11% 43.00% 2350ms 6.75% AbstractCellPopulation::GetLocationIndexUsingCell 12ms 0.034% 43.04% 2156ms 6.20% PlaneBoundaryCondition::VerifyBoundaryCondition 0 0% 43.04% 2156ms 6.20% std::__unguarded_partition_pivot (inline) 220ms 0.63% 43.67% 2087ms 6.00% DistributedBoxCollection::AddPairsFromBox 988ms 2.84% 46.51% 1929ms 5.54% std::__unguarded_partition (inline) 1ms 0.0029% 46.51% 1862ms 5.35% std::__final_insertion_sort (inline) 228ms 0.66% 47.17% 1831ms 5.26% std::map::operator[] (partial-inline) 99ms 0.28% 47.45% 1645ms 4.73% std::__unguarded_insertion_sort (inline) 581ms 1.67% 49.12% 1609ms 4.62% std::__unguarded_linear_insert (inline) 118ms 0.34% 49.46% 1569ms 4.51% AbstractMesh::GetVectorFromAtoB 1560ms 4.48% 53.94% 1560ms 4.48% boost::numeric::ublas::same_impl_ex 1505ms 4.32% 58.27% 1505ms 4.32% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 58.27% 1350ms 3.88% std::_Rb_tree::lower_bound (inline) 0 0% 58.27% 1350ms 3.88% std::map::lower_bound (inline) 0 0% 58.27% 1202ms 3.45% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 58.27% 1182ms 3.40% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 58.27% 1175ms 3.38% NodeBasedCellPopulation::UpdateCellProcessLocation 1164ms 3.34% 61.61% 1164ms 3.34% boost::numeric::ublas::c_vector::operator() 5ms 0.014% 61.62% 1059ms 3.04% DistributedBoxCollection::CalculateBoundaryNodePairs 19ms 0.055% 61.68% 1028ms 2.95% boost::numeric::ublas::detail::expression_type_check (inline) 184ms 0.53% 62.21% 970ms 2.79% boost::numeric::ublas::detail::equals 152ms 0.44% 62.64% 945ms 2.72% boost::numeric::ublas::vector_binary::size (inline) 224ms 0.64% 63.29% 927ms 2.66% NodeAttributes::AddAppliedForceContribution 97ms 0.28% 63.57% 922ms 2.65% std::__new_allocator::allocate (inline) 305ms 0.88% 64.44% 844ms 2.43% __GI___libc_free 19ms 0.055% 64.50% 826ms 2.37% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 96ms 0.28% 64.77% 821ms 2.36% operator new 294ms 0.84% 65.62% 819ms 2.35% NodeAttributes::AddNeighbour 3ms 0.0086% 65.63% 817ms 2.35% AbstractCentreBasedCellPopulation::GetDampingConstant 376ms 1.08% 66.71% 808ms 2.32% DistributedBoxCollection::CalculateContainingBox (partial-inline) 585ms 1.68% 68.39% 777ms 2.23% __dynamic_cast 38ms 0.11% 68.50% 760ms 2.18% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 68.50% 745ms 2.14% boost::numeric::ublas::norm_inf (inline) 459ms 1.32% 69.82% 745ms 2.14% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 69.82% 738ms 2.12% AbstractCellPopulation::WriteResultsToFiles 262ms 0.75% 70.57% 721ms 2.07% __GI___libc_malloc 715ms 2.05% 72.62% 715ms 2.05% std::_Rb_tree_increment 0 0% 72.62% 703ms 2.02% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 72.62% 703ms 2.02% boost::numeric::ublas::c_vector::plus_assign (inline) 522ms 1.50% 74.12% 630ms 1.81% std::vector::push_back (inline) 1ms 0.0029% 74.13% 616ms 1.77% AbstractCellBasedSimulation::DoCellBirth 12ms 0.034% 74.16% 605ms 1.74% CellPropertyCollection::GetPropertiesType (inline) 16ms 0.046% 74.21% 540ms 1.55% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 74.21% 540ms 1.55% boost::numeric::ublas::vector::vector (inline) 1ms 0.0029% 74.21% 539ms 1.55% Cell::GetMutationState 483ms 1.39% 75.60% 536ms 1.54% _int_free 1ms 0.0029% 75.60% 484ms 1.39% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 75.60% 479ms 1.38% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 75.60% 457ms 1.31% boost::numeric::ublas::norm_2 (inline) 370ms 1.06% 76.66% 457ms 1.31% boost::numeric::ublas::vector_norm_2::apply (inline) 2ms 0.0057% 76.67% 455ms 1.31% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 76.67% 398ms 1.14% std::allocator_traits::allocate (inline) 34ms 0.098% 76.77% 393ms 1.13% boost::detail::shared_count::~shared_count (inline) 0 0% 76.77% 393ms 1.13% boost::shared_ptr::~shared_ptr (inline) 391ms 1.12% 77.89% 391ms 1.12% Node::GetIndex 2ms 0.0057% 77.90% 380ms 1.09% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 4ms 0.011% 77.91% 378ms 1.09% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 77.91% 376ms 1.08% std::_Rb_tree::_M_create_node (inline) 351ms 1.01% 78.92% 356ms 1.02% boost::detail::sp_counted_base::release 126ms 0.36% 79.28% 355ms 1.02% Node::GetRadius 1ms 0.0029% 79.28% 348ms 1% AbstractCellProperty::IsSubType (inline) 0 0% 79.28% 322ms 0.93% std::_Rb_tree::_M_get_node (inline) 0 0% 79.28% 316ms 0.91% boost::numeric::ublas::inner_prod (inline) 1ms 0.0029% 79.29% 314ms 0.9% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 79.29% 313ms 0.9% NodesOnlyMesh::ReMesh 16ms 0.046% 79.33% 313ms 0.9% boost::numeric::ublas::vector_scalar_binary::evaluate 6ms 0.017% 79.35% 305ms 0.88% NodeBasedCellPopulation::UpdateMapsAfterRemesh 3ms 0.0086% 79.36% 303ms 0.87% NodesOnlyMesh::UpdateNodeIndices 124ms 0.36% 79.71% 296ms 0.85% std::_Rb_tree::_M_erase (partial-inline) 295ms 0.85% 80.56% 295ms 0.85% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 1ms 0.0029% 80.56% 292ms 0.84% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 292ms 0.84% 81.40% 292ms 0.84% __gnu_cxx::__normal_iterator::operator++ (inline) 5ms 0.014% 81.42% 279ms 0.8% DistributedBoxCollection::GetProcessOwningNode 17ms 0.049% 81.47% 273ms 0.78% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 81.47% 269ms 0.77% NodesOnlyMesh::UpdateBoxCollection 0 0% 81.47% 256ms 0.74% boost::numeric::ublas::c_vector::assign (inline) 10ms 0.029% 81.49% 256ms 0.74% std::_Rb_tree::_Rb_tree (partial-inline) 114ms 0.33% 81.82% 254ms 0.73% boost::numeric::ublas::vector_inner_prod::apply (inline) 11ms 0.032% 81.85% 253ms 0.73% std::_Rb_tree::_M_emplace_hint_unique 251ms 0.72% 82.58% 251ms 0.72% Node::rGetLocation 248ms 0.71% 83.29% 248ms 0.71% [libchaste_cell_based.so] 246ms 0.71% 83.99% 246ms 0.71% Node::CheckForNodeAttributes 24ms 0.069% 84.06% 244ms 0.7% std::_Rb_tree::_M_copy (inline) 0 0% 84.06% 239ms 0.69% std::_Rb_tree::_Alloc_node::operator() (inline) 129ms 0.37% 84.43% 230ms 0.66% _int_malloc 0 0% 84.43% 228ms 0.66% tcache_get (inline) 228ms 0.66% 85.09% 228ms 0.66% tcache_get_n (inline) 0 0% 85.09% 227ms 0.65% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 85.09% 227ms 0.65% VtkMeshWriter::WriteFiles 0 0% 85.09% 226ms 0.65% NodesOnlyMesh::ResizeBoxCollection 8ms 0.023% 85.11% 224ms 0.64% NodesOnlyMesh::IsANodeCloseToDomainBoundary 12ms 0.034% 85.15% 222ms 0.64% Cell::ReadyToDivide 222ms 0.64% 85.78% 222ms 0.64% NodeBasedCellPopulation::GetNode 101ms 0.29% 86.08% 221ms 0.64% std::__move_median_to_first (inline) 36ms 0.1% 86.18% 220ms 0.63% std::_Rb_tree::_M_clone_node (inline) 1ms 0.0029% 86.18% 219ms 0.63% NodesOnlyMesh::AddNodesToBoxes 0 0% 86.18% 218ms 0.63% Cell::HasCellProperty (inline) 0 0% 86.18% 218ms 0.63% CellPropertyCollection::HasProperty 18ms 0.052% 86.23% 216ms 0.62% std::__insertion_sort (inline) 155ms 0.45% 86.68% 206ms 0.59% Node::AddAppliedForceContribution 33ms 0.095% 86.77% 204ms 0.59% std::__new_allocator::deallocate (inline) 0 0% 86.77% 203ms 0.58% vtkDemandDrivenPipeline::ProcessRequest 0 0% 86.77% 203ms 0.58% vtkStreamingDemandDrivenPipeline::Update 0 0% 86.77% 203ms 0.58% vtkXMLWriterBase::Write 201ms 0.58% 87.35% 201ms 0.58% [libchaste_mesh.so] 201ms 0.58% 87.93% 201ms 0.58% boost::numeric::ublas::c_vector::size (inline) 96ms 0.28% 88.20% 200ms 0.57% std::__find_if (inline) 0 0% 88.20% 200ms 0.57% std::find_if (inline) 0 0% 88.20% 200ms 0.57% std::none_of (inline) 0 0% 88.20% 199ms 0.57% vtkDemandDrivenPipeline::ExecuteData 0 0% 88.20% 199ms 0.57% vtkStreamingDemandDrivenPipeline::ProcessRequest 198ms 0.57% 88.77% 198ms 0.57% boost::numeric::ublas::scalar_plus_assign::apply (inline) 0 0% 88.77% 197ms 0.57% vtkCompositeDataPipeline::ExecuteData 0 0% 88.77% 197ms 0.57% vtkExecutive::CallAlgorithm 0 0% 88.77% 196ms 0.56% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 88.77% 187ms 0.54% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 88.77% 176ms 0.51% boost::numeric::ublas::vector_reference::size (inline)