File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 30216ms, 87.77% of 34425ms total Dropped 814 nodes (cum <= 172.12ms) flat flat% sum% cum cum% 0 0% 0% 34312ms 99.67% __libc_start_call_main 0 0% 0% 34312ms 99.67% __libc_start_main_impl 0 0% 0% 34312ms 99.67% _start 0 0% 0% 34294ms 99.62% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 34294ms 99.62% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 34294ms 99.62% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 34294ms 99.62% main 0 0% 0% 34259ms 99.52% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 34259ms 99.52% CxxTest::TestRunner::runTest (inline) 0 0% 0% 34258ms 99.51% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 34251ms 99.49% AbstractCellBasedSimulation::Solve 1ms 0.0029% 0.0029% 23833ms 69.23% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0029% 0.0058% 17893ms 51.98% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.012% 0.017% 17728ms 51.50% AbstractNumericalMethod::ComputeForcesIncludingDamping 227ms 0.66% 0.68% 17087ms 49.64% AbstractTwoBodyInteractionForce::AddForceContribution 1166ms 3.39% 4.06% 15451ms 44.88% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4649ms 13.50% 17.57% 10912ms 31.70% std::_Rb_tree::_M_lower_bound (inline) 218ms 0.63% 18.20% 10424ms 30.28% NodesOnlyMesh::GetNodeOrHaloNode 245ms 0.71% 18.91% 10209ms 29.66% AbstractMesh::GetNode 475ms 1.38% 20.29% 10043ms 29.17% std::_Rb_tree::find (inline) 0 0% 20.29% 10043ms 29.17% std::map::find (inline) 816ms 2.37% 22.66% 9968ms 28.96% NodesOnlyMesh::SolveNodeMapping 0 0% 22.66% 9285ms 26.97% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0029% 22.67% 8129ms 23.61% NodeBasedCellPopulation::Update 6ms 0.017% 22.68% 6189ms 17.98% DistributedBoxCollection::CalculateInteriorNodePairs 1ms 0.0029% 22.69% 5632ms 16.36% OffLatticeSimulation::ApplyBoundaries 5363ms 15.58% 38.27% 5363ms 15.58% std::_Rb_tree::_S_right (inline) 19ms 0.055% 38.32% 4880ms 14.18% NodeAttributes::RemoveDuplicateNeighbours 2ms 0.0058% 38.33% 4673ms 13.57% std::__sort (inline) 0 0% 38.33% 4673ms 13.57% std::sort (inline) 177ms 0.51% 38.84% 4658ms 13.53% boost::numeric::ublas::vector_assign (inline) 68ms 0.2% 39.04% 4569ms 13.27% boost::numeric::ublas::c_vector::c_vector (partial-inline) 302ms 0.88% 39.92% 4160ms 12.08% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 4ms 0.012% 39.93% 3918ms 11.38% AbstractCellPopulation::Iterator::operator++ (inline) 196ms 0.57% 40.50% 3906ms 11.35% AbstractCellPopulation::Iterator::IsRealCell 27ms 0.078% 40.58% 3303ms 9.59% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 79ms 0.23% 40.80% 2849ms 8.28% PlaneBoundaryCondition::ImposeBoundaryCondition 242ms 0.7% 41.51% 2815ms 8.18% std::__introsort_loop 62ms 0.18% 41.69% 2782ms 8.08% PlaneBoundaryCondition::VerifyBoundaryCondition 9ms 0.026% 41.71% 2481ms 7.21% std::__unguarded_partition_pivot (inline) 100ms 0.29% 42.00% 2366ms 6.87% AbstractCellPopulation::GetLocationIndexUsingCell 763ms 2.22% 44.22% 2252ms 6.54% std::__unguarded_partition (inline) 569ms 1.65% 45.87% 2035ms 5.91% boost::numeric::ublas::indexing_vector_assign 209ms 0.61% 46.48% 2035ms 5.91% std::map::operator[] (partial-inline) 0 0% 46.48% 1856ms 5.39% std::__final_insertion_sort (inline) 145ms 0.42% 46.90% 1837ms 5.34% DistributedBoxCollection::AddPairsFromBox 128ms 0.37% 47.27% 1665ms 4.84% std::__unguarded_insertion_sort (inline) 0 0% 47.27% 1630ms 4.73% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 47.27% 1612ms 4.68% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 25ms 0.073% 47.35% 1480ms 4.30% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 47.35% 1476ms 4.29% std::_Rb_tree::lower_bound (inline) 0 0% 47.35% 1476ms 4.29% std::map::lower_bound (inline) 762ms 2.21% 49.56% 1459ms 4.24% std::__unguarded_linear_insert (inline) 211ms 0.61% 50.17% 1419ms 4.12% boost::numeric::ublas::detail::equals 27ms 0.078% 50.25% 1221ms 3.55% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 50.25% 1189ms 3.45% boost::numeric::ublas::norm_inf (inline) 445ms 1.29% 51.54% 1189ms 3.45% boost::numeric::ublas::vector_norm_inf::apply (inline) 1ms 0.0029% 51.55% 1150ms 3.34% NodeBasedCellPopulation::UpdateCellProcessLocation 1104ms 3.21% 54.75% 1104ms 3.21% boost::numeric::ublas::same_impl_ex 193ms 0.56% 55.31% 1085ms 3.15% AbstractMesh::GetVectorFromAtoB 1057ms 3.07% 58.38% 1057ms 3.07% __gnu_cxx::__normal_iterator::operator-- (inline) 5ms 0.015% 58.40% 981ms 2.85% DistributedBoxCollection::CalculateBoundaryNodePairs 922ms 2.68% 61.08% 922ms 2.68% std::_Rb_tree::_S_left (inline) 72ms 0.21% 61.29% 873ms 2.54% std::__new_allocator::allocate (inline) 17ms 0.049% 61.34% 807ms 2.34% boost::detail::shared_count::~shared_count (inline) 0 0% 61.34% 807ms 2.34% boost::shared_ptr::~shared_ptr (inline) 761ms 2.21% 63.55% 775ms 2.25% boost::detail::sp_counted_base::release 79ms 0.23% 63.78% 773ms 2.25% operator new 309ms 0.9% 64.67% 771ms 2.24% DistributedBoxCollection::CalculateContainingBox (partial-inline) 715ms 2.08% 66.75% 715ms 2.08% [libchaste_cell_based.so] 0 0% 66.75% 691ms 2.01% AbstractCellPopulation::WriteResultsToFiles 668ms 1.94% 68.69% 668ms 1.94% boost::numeric::ublas::c_vector::operator() 241ms 0.7% 69.39% 667ms 1.94% __GI___libc_malloc 503ms 1.46% 70.85% 664ms 1.93% __dynamic_cast 300ms 0.87% 71.72% 656ms 1.91% NodeAttributes::AddNeighbour 651ms 1.89% 73.62% 651ms 1.89% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 621ms 1.80% 75.42% 621ms 1.80% [libchaste_mesh.so] 32ms 0.093% 75.51% 602ms 1.75% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.0058% 75.52% 598ms 1.74% AbstractCentreBasedCellPopulation::GetDampingConstant 593ms 1.72% 77.24% 593ms 1.72% __gnu_cxx::__normal_iterator::operator++ (inline) 4ms 0.012% 77.25% 580ms 1.68% AbstractCellBasedSimulation::DoCellBirth 0 0% 77.25% 574ms 1.67% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 77.25% 563ms 1.64% boost::numeric::ublas::scalar_traits::type_abs (inline) 11ms 0.032% 77.28% 560ms 1.63% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 38ms 0.11% 77.39% 556ms 1.62% boost::numeric::ublas::vector_binary::size (inline) 0 0% 77.39% 548ms 1.59% boost::numeric::ublas::scalar_traits::norm_inf (inline) 1ms 0.0029% 77.40% 546ms 1.59% boost_numeric_ublas_abs (inline) 545ms 1.58% 78.98% 545ms 1.58% std::abs (inline) 198ms 0.58% 79.56% 534ms 1.55% NodeAttributes::AddAppliedForceContribution 0 0% 79.56% 525ms 1.53% std::allocator_traits::allocate (inline) 509ms 1.48% 81.03% 509ms 1.48% std::_Rb_tree_increment 326ms 0.95% 81.98% 480ms 1.39% std::vector::push_back (inline) 0 0% 81.98% 464ms 1.35% std::_Rb_tree::_M_create_node (inline) 3ms 0.0087% 81.99% 460ms 1.34% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 81.99% 445ms 1.29% std::_Rb_tree::_M_get_node (inline) 0 0% 81.99% 441ms 1.28% boost::numeric::ublas::norm_2 (inline) 345ms 1.00% 82.99% 441ms 1.28% boost::numeric::ublas::vector_norm_2::apply (inline) 135ms 0.39% 83.38% 433ms 1.26% __GI___libc_free 6ms 0.017% 83.40% 414ms 1.20% CellPropertyCollection::GetPropertiesType (inline) 0 0% 83.40% 375ms 1.09% Cell::GetMutationState 3ms 0.0087% 83.41% 351ms 1.02% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 83.41% 351ms 1.02% boost::numeric::ublas::vector::vector (inline) 8ms 0.023% 83.43% 350ms 1.02% std::_Rb_tree::_M_emplace_hint_unique 0 0% 83.43% 336ms 0.98% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 83.43% 336ms 0.98% boost::numeric::ublas::c_vector::plus_assign (inline) 0 0% 83.43% 334ms 0.97% boost::numeric::ublas::vector_binary::operator() (inline) 13ms 0.038% 83.47% 329ms 0.96% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 83.47% 312ms 0.91% NodesOnlyMesh::ReMesh 0 0% 83.47% 305ms 0.89% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 2ms 0.0058% 83.48% 304ms 0.88% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 4ms 0.012% 83.49% 301ms 0.87% AbstractCellPopulation::GetCellUsingLocationIndex 3ms 0.0087% 83.50% 300ms 0.87% NodesOnlyMesh::UpdateNodeIndices 210ms 0.61% 84.11% 296ms 0.86% _int_free 0 0% 84.11% 292ms 0.85% Node::GetRadius 170ms 0.49% 84.60% 291ms 0.85% _int_malloc 1ms 0.0029% 84.60% 281ms 0.82% DistributedBoxCollection::GetProcessOwningNode 2ms 0.0058% 84.61% 265ms 0.77% AbstractCellProperty::IsSubType (inline) 0 0% 84.61% 248ms 0.72% std::_Rb_tree::_Auto_node::_Auto_node (inline) 37ms 0.11% 84.72% 245ms 0.71% std::_Rb_tree::_M_erase (partial-inline) 220ms 0.64% 85.36% 240ms 0.7% boost::shared_ptr::shared_ptr (inline) 0 0% 85.36% 238ms 0.69% NodesOnlyMesh::UpdateBoxCollection 0 0% 85.36% 233ms 0.68% Cell::HasCellProperty (inline) 1ms 0.0029% 85.36% 233ms 0.68% CellPropertyCollection::HasProperty 4ms 0.012% 85.37% 233ms 0.68% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 85.37% 231ms 0.67% std::iter_swap (inline) 231ms 0.67% 86.04% 231ms 0.67% std::swap (inline) 228ms 0.66% 86.70% 228ms 0.66% Node::CheckForNodeAttributes 6ms 0.017% 86.72% 226ms 0.66% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 86.72% 216ms 0.63% std::_Rb_tree::_Alloc_node::operator() (inline) 9ms 0.026% 86.75% 214ms 0.62% std::_Rb_tree::_M_copy (inline) 64ms 0.19% 86.93% 214ms 0.62% std::__move_median_to_first (inline) 0 0% 86.93% 211ms 0.61% boost::numeric::ublas::c_vector::assign (inline) 0 0% 86.93% 207ms 0.6% std::_Rb_tree::_M_drop_node (inline) 12ms 0.035% 86.97% 206ms 0.6% std::__new_allocator::deallocate (inline) 0 0% 86.97% 202ms 0.59% boost::numeric::ublas::inner_prod (inline) 2ms 0.0058% 86.97% 202ms 0.59% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 42ms 0.12% 87.10% 202ms 0.59% std::_Rb_tree::_M_clone_node (inline) 0 0% 87.10% 201ms 0.58% NodesOnlyMesh::AddNodesToBoxes 8ms 0.023% 87.12% 200ms 0.58% Cell::ReadyToDivide 10ms 0.029% 87.15% 200ms 0.58% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 87.15% 194ms 0.56% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 87.15% 194ms 0.56% VtkMeshWriter::WriteFiles 27ms 0.078% 87.23% 191ms 0.55% std::__insertion_sort (inline) 10ms 0.029% 87.26% 180ms 0.52% AbstractCellProperty::IsType (inline) 178ms 0.52% 87.77% 178ms 0.52% NodeBasedCellPopulation::GetNode