File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 32454ms, 88.96% of 36483ms total Dropped 830 nodes (cum <= 182.41ms) flat flat% sum% cum cum% 0 0% 0% 36382ms 99.72% __libc_start_call_main 0 0% 0% 36382ms 99.72% __libc_start_main_impl 0 0% 0% 36382ms 99.72% _start 0 0% 0% 36363ms 99.67% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 36363ms 99.67% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 36363ms 99.67% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 36363ms 99.67% main 0 0% 0% 36326ms 99.57% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 36326ms 99.57% CxxTest::TestRunner::runTest (inline) 0 0% 0% 36326ms 99.57% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 36317ms 99.54% AbstractCellBasedSimulation::Solve 2ms 0.0055% 0.0055% 25113ms 68.83% OffLatticeSimulation::UpdateCellLocationsAndTopology 3ms 0.0082% 0.014% 18872ms 51.73% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.011% 0.025% 18701ms 51.26% AbstractNumericalMethod::ComputeForcesIncludingDamping 218ms 0.6% 0.62% 17847ms 48.92% AbstractTwoBodyInteractionForce::AddForceContribution 1210ms 3.32% 3.94% 16002ms 43.86% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4951ms 13.57% 17.51% 11379ms 31.19% std::_Rb_tree::_M_lower_bound (inline) 206ms 0.56% 18.07% 10886ms 29.84% NodesOnlyMesh::GetNodeOrHaloNode 342ms 0.94% 19.01% 10677ms 29.27% AbstractMesh::GetNode 481ms 1.32% 20.33% 10361ms 28.40% std::_Rb_tree::find (inline) 0 0% 20.33% 10361ms 28.40% std::map::find (inline) 904ms 2.48% 22.81% 10336ms 28.33% NodesOnlyMesh::SolveNodeMapping 0 0% 22.81% 10021ms 27.47% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 22.81% 8774ms 24.05% NodeBasedCellPopulation::Update 5ms 0.014% 22.82% 6659ms 18.25% DistributedBoxCollection::CalculateInteriorNodePairs 0 0% 22.82% 5892ms 16.15% OffLatticeSimulation::ApplyBoundaries 5546ms 15.20% 38.02% 5546ms 15.20% std::_Rb_tree::_S_right (inline) 17ms 0.047% 38.07% 5120ms 14.03% NodeAttributes::RemoveDuplicateNeighbours 5ms 0.014% 38.08% 4922ms 13.49% std::__sort (inline) 0 0% 38.08% 4922ms 13.49% std::sort (inline) 221ms 0.61% 38.69% 4730ms 12.96% boost::numeric::ublas::vector_assign (inline) 72ms 0.2% 38.89% 4591ms 12.58% boost::numeric::ublas::c_vector::c_vector (partial-inline) 298ms 0.82% 39.70% 4330ms 11.87% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 2ms 0.0055% 39.71% 4104ms 11.25% AbstractCellPopulation::Iterator::operator++ (inline) 197ms 0.54% 40.25% 4094ms 11.22% AbstractCellPopulation::Iterator::IsRealCell 33ms 0.09% 40.34% 3424ms 9.39% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 243ms 0.67% 41.01% 3006ms 8.24% std::__introsort_loop 83ms 0.23% 41.23% 2994ms 8.21% PlaneBoundaryCondition::ImposeBoundaryCondition 56ms 0.15% 41.39% 2898ms 7.94% PlaneBoundaryCondition::VerifyBoundaryCondition 11ms 0.03% 41.42% 2668ms 7.31% std::__unguarded_partition_pivot (inline) 118ms 0.32% 41.74% 2502ms 6.86% AbstractCellPopulation::GetLocationIndexUsingCell 816ms 2.24% 43.98% 2377ms 6.52% std::__unguarded_partition (inline) 208ms 0.57% 44.55% 2195ms 6.02% std::map::operator[] (partial-inline) 150ms 0.41% 44.96% 2151ms 5.90% DistributedBoxCollection::AddPairsFromBox 601ms 1.65% 46.61% 2141ms 5.87% boost::numeric::ublas::indexing_vector_assign 0 0% 46.61% 1905ms 5.22% std::__final_insertion_sort (inline) 150ms 0.41% 47.02% 1706ms 4.68% std::__unguarded_insertion_sort (inline) 0 0% 47.02% 1604ms 4.40% std::_Rb_tree::lower_bound (inline) 0 0% 47.02% 1604ms 4.40% std::map::lower_bound (inline) 814ms 2.23% 49.25% 1510ms 4.14% std::__unguarded_linear_insert (inline) 0 0% 49.25% 1497ms 4.10% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 49.25% 1471ms 4.03% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 7ms 0.019% 49.27% 1386ms 3.80% boost::numeric::ublas::detail::expression_type_check (inline) 235ms 0.64% 49.91% 1328ms 3.64% boost::numeric::ublas::detail::equals 18ms 0.049% 49.96% 1288ms 3.53% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 1ms 0.0027% 49.96% 1220ms 3.34% NodeBasedCellPopulation::UpdateCellProcessLocation 1181ms 3.24% 53.20% 1181ms 3.24% boost::numeric::ublas::same_impl_ex 183ms 0.5% 53.70% 1144ms 3.14% AbstractMesh::GetVectorFromAtoB 1123ms 3.08% 56.78% 1123ms 3.08% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 56.78% 1068ms 2.93% boost::numeric::ublas::norm_inf (inline) 350ms 0.96% 57.74% 1068ms 2.93% boost::numeric::ublas::vector_norm_inf::apply (inline) 6ms 0.016% 57.76% 1041ms 2.85% DistributedBoxCollection::CalculateBoundaryNodePairs 89ms 0.24% 58.00% 957ms 2.62% std::__new_allocator::allocate (inline) 718ms 1.97% 59.97% 905ms 2.48% __dynamic_cast 905ms 2.48% 62.45% 905ms 2.48% std::_Rb_tree::_S_left (inline) 23ms 0.063% 62.51% 879ms 2.41% boost::detail::shared_count::~shared_count (inline) 0 0% 62.51% 879ms 2.41% boost::shared_ptr::~shared_ptr (inline) 829ms 2.27% 64.78% 843ms 2.31% boost::detail::sp_counted_base::release 446ms 1.22% 66.01% 835ms 2.29% NodeAttributes::AddNeighbour 78ms 0.21% 66.22% 832ms 2.28% operator new 3ms 0.0082% 66.23% 822ms 2.25% AbstractCentreBasedCellPopulation::GetDampingConstant 818ms 2.24% 68.47% 818ms 2.24% [libchaste_cell_based.so] 342ms 0.94% 69.41% 796ms 2.18% DistributedBoxCollection::CalculateContainingBox (partial-inline) 34ms 0.093% 69.50% 764ms 2.09% std::_Rb_tree_const_iterator::operator++ (inline) 259ms 0.71% 70.21% 719ms 1.97% __GI___libc_malloc 0 0% 70.21% 715ms 1.96% AbstractCellPopulation::WriteResultsToFiles 711ms 1.95% 72.16% 711ms 1.95% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 684ms 1.87% 74.03% 684ms 1.87% boost::numeric::ublas::c_vector::operator() 674ms 1.85% 75.88% 674ms 1.85% [libchaste_mesh.so] 664ms 1.82% 77.70% 664ms 1.82% std::_Rb_tree_increment 0 0% 77.70% 649ms 1.78% AbstractCellBasedSimulation::DoCellRemoval (inline) 214ms 0.59% 78.29% 635ms 1.74% NodeAttributes::AddAppliedForceContribution 14ms 0.038% 78.33% 633ms 1.74% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 11ms 0.03% 78.36% 607ms 1.66% CellPropertyCollection::GetPropertiesType (inline) 1ms 0.0027% 78.36% 597ms 1.64% AbstractCellBasedSimulation::DoCellBirth 55ms 0.15% 78.51% 575ms 1.58% boost::numeric::ublas::vector_binary::size (inline) 572ms 1.57% 80.08% 572ms 1.57% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 80.08% 558ms 1.53% std::allocator_traits::allocate (inline) 0 0% 80.08% 543ms 1.49% boost::numeric::ublas::scalar_traits::type_abs (inline) 0 0% 80.08% 536ms 1.47% Cell::GetMutationState 2ms 0.0055% 80.08% 536ms 1.47% boost_numeric_ublas_abs (inline) 0 0% 80.08% 535ms 1.47% boost::numeric::ublas::scalar_traits::norm_inf (inline) 534ms 1.46% 81.55% 534ms 1.46% std::abs (inline) 0 0% 81.55% 493ms 1.35% std::_Rb_tree::_M_create_node (inline) 355ms 0.97% 82.52% 486ms 1.33% std::vector::push_back (inline) 141ms 0.39% 82.91% 483ms 1.32% __GI___libc_free 0 0% 82.91% 473ms 1.30% std::_Rb_tree::_M_get_node (inline) 2ms 0.0055% 82.91% 464ms 1.27% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 82.91% 429ms 1.18% boost::numeric::ublas::norm_2 (inline) 326ms 0.89% 83.81% 429ms 1.18% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 83.81% 421ms 1.15% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 83.81% 421ms 1.15% boost::numeric::ublas::c_vector::plus_assign (inline) 1ms 0.0027% 83.81% 400ms 1.10% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 83.81% 400ms 1.10% boost::numeric::ublas::vector::vector (inline) 6ms 0.016% 83.83% 383ms 1.05% std::_Rb_tree::_M_emplace_hint_unique 1ms 0.0027% 83.83% 366ms 1.00% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 5ms 0.014% 83.84% 364ms 1% AbstractCellPopulation::GetCellUsingLocationIndex 4ms 0.011% 83.85% 358ms 0.98% AbstractCellProperty::IsSubType (inline) 256ms 0.7% 84.55% 341ms 0.93% _int_free 11ms 0.03% 84.58% 340ms 0.93% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 84.58% 322ms 0.88% NodesOnlyMesh::ReMesh 193ms 0.53% 85.11% 313ms 0.86% _int_malloc 0 0% 85.11% 312ms 0.86% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 85.11% 309ms 0.85% NodesOnlyMesh::UpdateBoxCollection 2ms 0.0055% 85.12% 307ms 0.84% Node::GetRadius 4ms 0.011% 85.13% 307ms 0.84% NodesOnlyMesh::UpdateNodeIndices 0 0% 85.13% 304ms 0.83% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 85.13% 292ms 0.8% DistributedBoxCollection::GetProcessOwningNode 44ms 0.12% 85.25% 282ms 0.77% std::_Rb_tree::_M_erase (partial-inline) 252ms 0.69% 85.94% 275ms 0.75% boost::shared_ptr::shared_ptr (inline) 92ms 0.25% 86.19% 271ms 0.74% std::__move_median_to_first (inline) 7ms 0.019% 86.21% 268ms 0.73% std::_Rb_tree::_Rb_tree (partial-inline) 18ms 0.049% 86.26% 258ms 0.71% std::_Rb_tree::_M_copy (inline) 253ms 0.69% 86.96% 253ms 0.69% Node::CheckForNodeAttributes 0 0% 86.96% 252ms 0.69% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 86.96% 251ms 0.69% NodesOnlyMesh::AddNodesToBoxes 0 0% 86.96% 241ms 0.66% std::_Rb_tree::_Alloc_node::operator() (inline) 66ms 0.18% 87.14% 239ms 0.66% std::_Rb_tree::_M_clone_node (inline) 0 0% 87.14% 231ms 0.63% std::_Rb_tree::_M_drop_node (inline) 0 0% 87.14% 227ms 0.62% std::iter_swap (inline) 227ms 0.62% 87.76% 227ms 0.62% std::swap (inline) 6ms 0.016% 87.78% 220ms 0.6% boost::numeric::ublas::vector_reference::operator() (inline) 3ms 0.0082% 87.78% 218ms 0.6% std::__new_allocator::deallocate (inline) 1ms 0.0027% 87.79% 215ms 0.59% CellPropertyCollection::HasProperty 0 0% 87.79% 214ms 0.59% Cell::HasCellProperty (inline) 0 0% 87.79% 203ms 0.56% boost::numeric::ublas::c_vector::assign (inline) 0 0% 87.79% 200ms 0.55% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 23ms 0.063% 87.85% 199ms 0.55% std::__insertion_sort (inline) 0 0% 87.85% 198ms 0.54% VtkMeshWriter::WriteFiles 0 0% 87.85% 193ms 0.53% NodesOnlyMesh::ResizeBoxCollection 11ms 0.03% 87.88% 192ms 0.53% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 87.88% 191ms 0.52% boost::numeric::ublas::inner_prod (inline) 0 0% 87.88% 191ms 0.52% std::allocator_traits::deallocate (inline) 1ms 0.0027% 87.88% 188ms 0.52% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 87.88% 188ms 0.52% std::_Rb_tree::_M_put_node (inline) 15ms 0.041% 87.92% 187ms 0.51% boost::numeric::ublas::vector_scalar_binary::evaluate 185ms 0.51% 88.43% 186ms 0.51% Node::ConstructNodeAttributes (inline) 8ms 0.022% 88.45% 184ms 0.5% Cell::ReadyToDivide 184ms 0.5% 88.96% 184ms 0.5% boost::shared_ptr::operator-> (inline)