File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 31594ms, 87.47% of 36118ms total Dropped 862 nodes (cum <= 180.59ms) flat flat% sum% cum cum% 0 0% 0% 36007ms 99.69% __libc_start_call_main 0 0% 0% 36007ms 99.69% __libc_start_main_impl 0 0% 0% 36007ms 99.69% _start 0 0% 0% 35988ms 99.64% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 35988ms 99.64% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 35988ms 99.64% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 35988ms 99.64% main 0 0% 0% 35955ms 99.55% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 35955ms 99.55% CxxTest::TestRunner::runTest (inline) 0 0% 0% 35955ms 99.55% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 35947ms 99.53% AbstractCellBasedSimulation::Solve 2ms 0.0055% 0.0055% 24844ms 68.79% OffLatticeSimulation::UpdateCellLocationsAndTopology 3ms 0.0083% 0.014% 18694ms 51.76% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.017% 0.03% 18524ms 51.29% AbstractNumericalMethod::ComputeForcesIncludingDamping 223ms 0.62% 0.65% 17724ms 49.07% AbstractTwoBodyInteractionForce::AddForceContribution 1227ms 3.40% 4.05% 15948ms 44.16% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4899ms 13.56% 17.61% 11212ms 31.04% std::_Rb_tree::_M_lower_bound (inline) 201ms 0.56% 18.17% 10646ms 29.48% NodesOnlyMesh::GetNodeOrHaloNode 261ms 0.72% 18.89% 10441ms 28.91% AbstractMesh::GetNode 453ms 1.25% 20.14% 10206ms 28.26% std::_Rb_tree::find (inline) 0 0% 20.14% 10206ms 28.26% std::map::find (inline) 892ms 2.47% 22.61% 10189ms 28.21% NodesOnlyMesh::SolveNodeMapping 0 0% 22.61% 9916ms 27.45% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 22.61% 8689ms 24.06% NodeBasedCellPopulation::Update 6ms 0.017% 22.63% 6635ms 18.37% DistributedBoxCollection::CalculateInteriorNodePairs 0 0% 22.63% 5837ms 16.16% OffLatticeSimulation::ApplyBoundaries 5329ms 14.75% 37.38% 5329ms 14.75% std::_Rb_tree::_S_right (inline) 13ms 0.036% 37.42% 5127ms 14.20% NodeAttributes::RemoveDuplicateNeighbours 4ms 0.011% 37.43% 4924ms 13.63% std::__sort (inline) 0 0% 37.43% 4924ms 13.63% std::sort (inline) 200ms 0.55% 37.98% 4879ms 13.51% boost::numeric::ublas::vector_assign (inline) 74ms 0.2% 38.19% 4794ms 13.27% boost::numeric::ublas::c_vector::c_vector (partial-inline) 338ms 0.94% 39.12% 4247ms 11.76% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 9ms 0.025% 39.15% 4023ms 11.14% AbstractCellPopulation::Iterator::operator++ (inline) 224ms 0.62% 39.77% 4007ms 11.09% AbstractCellPopulation::Iterator::IsRealCell (inline) 33ms 0.091% 39.86% 3365ms 9.32% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 258ms 0.71% 40.58% 3002ms 8.31% std::__introsort_loop 73ms 0.2% 40.78% 2971ms 8.23% PlaneBoundaryCondition::ImposeBoundaryCondition 59ms 0.16% 40.94% 2866ms 7.94% PlaneBoundaryCondition::VerifyBoundaryCondition 4ms 0.011% 40.95% 2633ms 7.29% std::__unguarded_partition_pivot (inline) 112ms 0.31% 41.26% 2469ms 6.84% AbstractCellPopulation::GetLocationIndexUsingCell 817ms 2.26% 43.52% 2388ms 6.61% std::__unguarded_partition (inline) 560ms 1.55% 45.07% 2136ms 5.91% boost::numeric::ublas::indexing_vector_assign 194ms 0.54% 45.61% 2126ms 5.89% std::map::operator[] (partial-inline) 122ms 0.34% 45.95% 2045ms 5.66% DistributedBoxCollection::AddPairsFromBox 1ms 0.0028% 45.95% 1915ms 5.30% std::__final_insertion_sort (inline) 140ms 0.39% 46.34% 1699ms 4.70% std::__unguarded_insertion_sort (inline) 0 0% 46.34% 1659ms 4.59% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 46.34% 1641ms 4.54% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 46.34% 1573ms 4.36% std::_Rb_tree::lower_bound (inline) 0 0% 46.34% 1573ms 4.36% std::map::lower_bound (inline) 37ms 0.1% 46.44% 1552ms 4.30% boost::numeric::ublas::detail::expression_type_check (inline) 780ms 2.16% 48.60% 1520ms 4.21% std::__unguarded_linear_insert (inline) 242ms 0.67% 49.27% 1480ms 4.10% boost::numeric::ublas::detail::equals 31ms 0.086% 49.36% 1279ms 3.54% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 49.36% 1224ms 3.39% boost::numeric::ublas::norm_inf (inline) 507ms 1.40% 50.76% 1224ms 3.39% boost::numeric::ublas::vector_norm_inf::apply (inline) 1ms 0.0028% 50.76% 1189ms 3.29% NodeBasedCellPopulation::UpdateCellProcessLocation 1159ms 3.21% 53.97% 1159ms 3.21% boost::numeric::ublas::same_impl_ex 205ms 0.57% 54.54% 1150ms 3.18% AbstractMesh::GetVectorFromAtoB 1140ms 3.16% 57.70% 1140ms 3.16% __gnu_cxx::__normal_iterator::operator-- (inline) 7ms 0.019% 57.72% 1039ms 2.88% DistributedBoxCollection::CalculateBoundaryNodePairs 999ms 2.77% 60.48% 999ms 2.77% std::_Rb_tree::_S_left (inline) 79ms 0.22% 60.70% 861ms 2.38% std::__new_allocator::allocate (inline) 316ms 0.87% 61.58% 832ms 2.30% DistributedBoxCollection::CalculateContainingBox (partial-inline) 18ms 0.05% 61.63% 832ms 2.30% boost::detail::shared_count::~shared_count (inline) 0 0% 61.63% 832ms 2.30% boost::shared_ptr::~shared_ptr (inline) 425ms 1.18% 62.80% 813ms 2.25% NodeAttributes::AddNeighbour 789ms 2.18% 64.99% 805ms 2.23% boost::detail::sp_counted_base::release 795ms 2.20% 67.19% 795ms 2.20% [libchaste_cell_based.so] 31ms 0.086% 67.27% 764ms 2.12% std::_Rb_tree_const_iterator::operator++ (inline) 5ms 0.014% 67.29% 761ms 2.11% AbstractCentreBasedCellPopulation::GetDampingConstant 74ms 0.2% 67.49% 750ms 2.08% operator new 741ms 2.05% 69.54% 741ms 2.05% boost::numeric::ublas::c_vector::operator() 730ms 2.02% 71.57% 730ms 2.02% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 1ms 0.0028% 71.57% 724ms 2.00% AbstractCellPopulation::WriteResultsToFiles 512ms 1.42% 72.99% 681ms 1.89% __dynamic_cast 667ms 1.85% 74.83% 667ms 1.85% std::_Rb_tree_increment 242ms 0.67% 75.50% 635ms 1.76% __GI___libc_malloc 628ms 1.74% 77.24% 628ms 1.74% [libchaste_mesh.so] 1ms 0.0028% 77.24% 624ms 1.73% AbstractCellBasedSimulation::DoCellBirth 0 0% 77.24% 602ms 1.67% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 77.24% 588ms 1.63% boost::numeric::ublas::scalar_traits::type_abs (inline) 9ms 0.025% 77.27% 586ms 1.62% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 581ms 1.61% 78.88% 581ms 1.61% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 78.88% 573ms 1.59% boost::numeric::ublas::scalar_traits::norm_inf (inline) 213ms 0.59% 79.47% 572ms 1.58% NodeAttributes::AddAppliedForceContribution 2ms 0.0055% 79.47% 572ms 1.58% boost_numeric_ublas_abs (inline) 48ms 0.13% 79.61% 570ms 1.58% boost::numeric::ublas::vector_binary::size (inline) 570ms 1.58% 81.18% 570ms 1.58% std::abs (inline) 9ms 0.025% 81.21% 553ms 1.53% CellPropertyCollection::GetPropertiesType (inline) 0 0% 81.21% 511ms 1.41% std::allocator_traits::allocate (inline) 358ms 0.99% 82.20% 502ms 1.39% std::vector::push_back (inline) 1ms 0.0028% 82.20% 488ms 1.35% Cell::GetMutationState 146ms 0.4% 82.61% 476ms 1.32% __GI___libc_free 2ms 0.0055% 82.61% 475ms 1.32% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 82.61% 453ms 1.25% std::_Rb_tree::_M_create_node (inline) 0 0% 82.61% 435ms 1.20% boost::numeric::ublas::norm_2 (inline) 345ms 0.96% 83.57% 435ms 1.20% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 83.57% 428ms 1.19% std::_Rb_tree::_M_get_node (inline) 0 0% 83.57% 359ms 0.99% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 83.57% 359ms 0.99% boost::numeric::ublas::c_vector::plus_assign (inline) 8ms 0.022% 83.59% 357ms 0.99% std::_Rb_tree::_M_emplace_hint_unique 2ms 0.0055% 83.60% 352ms 0.97% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 83.60% 352ms 0.97% boost::numeric::ublas::vector::vector (inline) 6ms 0.017% 83.61% 336ms 0.93% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 0 0% 83.61% 335ms 0.93% NodesOnlyMesh::ReMesh 2ms 0.0055% 83.62% 329ms 0.91% AbstractCellPopulation::GetCellUsingLocationIndex 6ms 0.017% 83.63% 328ms 0.91% NodeBasedCellPopulation::UpdateMapsAfterRemesh 252ms 0.7% 84.33% 327ms 0.91% _int_free 1ms 0.0028% 84.33% 326ms 0.9% NodesOnlyMesh::UpdateNodeIndices 3ms 0.0083% 84.34% 321ms 0.89% AbstractCellProperty::IsSubType (inline) 0 0% 84.34% 314ms 0.87% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 84.34% 302ms 0.84% Node::GetRadius 3ms 0.0083% 84.35% 293ms 0.81% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 1ms 0.0028% 84.35% 282ms 0.78% NodesOnlyMesh::UpdateBoxCollection 4ms 0.011% 84.37% 272ms 0.75% DistributedBoxCollection::GetProcessOwningNode 30ms 0.083% 84.45% 267ms 0.74% std::_Rb_tree::_M_erase (partial-inline) 240ms 0.66% 85.11% 266ms 0.74% boost::shared_ptr::shared_ptr (inline) 14ms 0.039% 85.15% 263ms 0.73% std::_Rb_tree::_Rb_tree (partial-inline) 157ms 0.43% 85.59% 262ms 0.73% _int_malloc 255ms 0.71% 86.29% 255ms 0.71% Node::CheckForNodeAttributes 12ms 0.033% 86.33% 243ms 0.67% std::_Rb_tree::_M_copy (inline) 9ms 0.025% 86.35% 240ms 0.66% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 86.35% 237ms 0.66% NodesOnlyMesh::AddNodesToBoxes 12ms 0.033% 86.38% 236ms 0.65% std::__new_allocator::deallocate (inline) 0 0% 86.38% 235ms 0.65% std::_Rb_tree::_M_drop_node (inline) 0 0% 86.38% 231ms 0.64% boost::numeric::ublas::c_vector::assign (inline) 0 0% 86.38% 230ms 0.64% std::_Rb_tree::_Auto_node::_Auto_node (inline) 2ms 0.0055% 86.39% 229ms 0.63% CellPropertyCollection::HasProperty 73ms 0.2% 86.59% 229ms 0.63% std::__move_median_to_first (inline) 0 0% 86.59% 228ms 0.63% Cell::HasCellProperty (inline) 55ms 0.15% 86.74% 228ms 0.63% std::_Rb_tree::_M_clone_node (inline) 0 0% 86.74% 225ms 0.62% boost::numeric::ublas::inner_prod (inline) 1ms 0.0028% 86.75% 223ms 0.62% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 86.75% 223ms 0.62% std::_Rb_tree::_Alloc_node::operator() (inline) 15ms 0.042% 86.79% 222ms 0.61% boost::numeric::ublas::vector_scalar_binary::evaluate 21ms 0.058% 86.85% 215ms 0.6% std::__insertion_sort (inline) 5ms 0.014% 86.86% 213ms 0.59% Cell::ReadyToDivide 0 0% 86.86% 209ms 0.58% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 86.86% 207ms 0.57% VtkMeshWriter::WriteFiles 0 0% 86.86% 202ms 0.56% std::iter_swap (inline) 202ms 0.56% 87.42% 202ms 0.56% std::swap (inline) 0 0% 87.42% 191ms 0.53% std::allocator_traits::deallocate (inline) 0 0% 87.42% 190ms 0.53% std::_Rb_tree::_M_put_node (inline) 20ms 0.055% 87.47% 188ms 0.52% std::_Rb_tree::~_Rb_tree (inline) 0 0% 87.47% 181ms 0.5% NodesOnlyMesh::ResizeBoxCollection