File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 33383ms, 88.01% of 37932ms total Dropped 866 nodes (cum <= 189.66ms) flat flat% sum% cum cum% 0 0% 0% 37838ms 99.75% __libc_start_call_main 0 0% 0% 37838ms 99.75% __libc_start_main_impl 0 0% 0% 37838ms 99.75% _start 0 0% 0% 37818ms 99.70% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 37818ms 99.70% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 37818ms 99.70% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 37818ms 99.70% main 0 0% 0% 37786ms 99.62% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 37786ms 99.62% CxxTest::TestRunner::runTest (inline) 0 0% 0% 37786ms 99.62% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 37778ms 99.59% AbstractCellBasedSimulation::Solve 0 0% 0% 25867ms 68.19% OffLatticeSimulation::UpdateCellLocationsAndTopology 4ms 0.011% 0.011% 19482ms 51.36% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.011% 0.021% 19305ms 50.89% AbstractNumericalMethod::ComputeForcesIncludingDamping 249ms 0.66% 0.68% 17990ms 47.43% AbstractTwoBodyInteractionForce::AddForceContribution 1177ms 3.10% 3.78% 16069ms 42.36% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 5077ms 13.38% 17.16% 11568ms 30.50% std::_Rb_tree::_M_lower_bound (inline) 223ms 0.59% 17.75% 10932ms 28.82% NodesOnlyMesh::GetNodeOrHaloNode 262ms 0.69% 18.44% 10733ms 28.30% AbstractMesh::GetNode 0 0% 18.44% 10643ms 28.06% AbstractCellBasedSimulation::UpdateCellPopulation 503ms 1.33% 19.77% 10535ms 27.77% std::_Rb_tree::find (inline) 0 0% 19.77% 10535ms 27.77% std::map::find (inline) 920ms 2.43% 22.19% 10478ms 27.62% NodesOnlyMesh::SolveNodeMapping 0 0% 22.19% 9301ms 24.52% NodeBasedCellPopulation::Update 5ms 0.013% 22.21% 7091ms 18.69% DistributedBoxCollection::CalculateInteriorNodePairs 1ms 0.0026% 22.21% 5975ms 15.75% OffLatticeSimulation::ApplyBoundaries 5641ms 14.87% 37.08% 5641ms 14.87% std::_Rb_tree::_S_right (inline) 17ms 0.045% 37.13% 5171ms 13.63% NodeAttributes::RemoveDuplicateNeighbours 2ms 0.0053% 37.13% 4952ms 13.05% std::__sort (inline) 0 0% 37.13% 4952ms 13.05% std::sort (inline) 239ms 0.63% 37.76% 4764ms 12.56% boost::numeric::ublas::vector_assign (inline) 76ms 0.2% 37.96% 4685ms 12.35% boost::numeric::ublas::c_vector::c_vector (partial-inline) 302ms 0.8% 38.76% 4355ms 11.48% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 7ms 0.018% 38.78% 4115ms 10.85% AbstractCellPopulation::Iterator::operator++ (inline) 237ms 0.62% 39.40% 4101ms 10.81% AbstractCellPopulation::Iterator::IsRealCell 39ms 0.1% 39.50% 3431ms 9.05% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 67ms 0.18% 39.68% 3040ms 8.01% PlaneBoundaryCondition::ImposeBoundaryCondition 267ms 0.7% 40.39% 2959ms 7.80% std::__introsort_loop 61ms 0.16% 40.55% 2933ms 7.73% PlaneBoundaryCondition::VerifyBoundaryCondition 1ms 0.0026% 40.55% 2600ms 6.85% std::__unguarded_partition_pivot (inline) 108ms 0.28% 40.83% 2529ms 6.67% AbstractCellPopulation::GetLocationIndexUsingCell 150ms 0.4% 41.23% 2523ms 6.65% DistributedBoxCollection::AddPairsFromBox 812ms 2.14% 43.37% 2347ms 6.19% std::__unguarded_partition (inline) 239ms 0.63% 44.00% 2321ms 6.12% std::map::operator[] (partial-inline) 609ms 1.61% 45.61% 2204ms 5.81% boost::numeric::ublas::indexing_vector_assign 2ms 0.0053% 45.61% 1985ms 5.23% std::__final_insertion_sort (inline) 154ms 0.41% 46.02% 1769ms 4.66% std::__unguarded_insertion_sort (inline) 0 0% 46.02% 1649ms 4.35% std::_Rb_tree::lower_bound (inline) 0 0% 46.02% 1649ms 4.35% std::map::lower_bound (inline) 819ms 2.16% 48.18% 1549ms 4.08% std::__unguarded_linear_insert (inline) 0 0% 48.18% 1452ms 3.83% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 48.18% 1422ms 3.75% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 23ms 0.061% 48.24% 1329ms 3.50% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 48.24% 1294ms 3.41% NodeBasedCellPopulation::UpdateCellProcessLocation 7ms 0.018% 48.25% 1285ms 3.39% boost::numeric::ublas::detail::expression_type_check (inline) 4ms 0.011% 48.27% 1268ms 3.34% AbstractCentreBasedCellPopulation::GetDampingConstant 195ms 0.51% 48.78% 1240ms 3.27% boost::numeric::ublas::detail::equals 232ms 0.61% 49.39% 1203ms 3.17% AbstractMesh::GetVectorFromAtoB 1186ms 3.13% 52.52% 1186ms 3.13% boost::numeric::ublas::same_impl_ex 742ms 1.96% 54.47% 1134ms 2.99% NodeAttributes::AddNeighbour 163ms 0.43% 54.90% 1116ms 2.94% std::__new_allocator::allocate (inline) 1108ms 2.92% 57.82% 1108ms 2.92% __gnu_cxx::__normal_iterator::operator-- (inline) 4ms 0.011% 57.84% 1076ms 2.84% DistributedBoxCollection::CalculateBoundaryNodePairs 34ms 0.09% 57.92% 1035ms 2.73% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 57.92% 1025ms 2.70% boost::numeric::ublas::norm_inf (inline) 312ms 0.82% 58.75% 1025ms 2.70% boost::numeric::ublas::vector_norm_inf::apply (inline) 934ms 2.46% 61.21% 934ms 2.46% std::_Rb_tree_increment 90ms 0.24% 61.45% 916ms 2.41% operator new 40ms 0.11% 61.55% 915ms 2.41% CellPropertyCollection::GetPropertiesType (inline) 887ms 2.34% 63.89% 887ms 2.34% std::_Rb_tree::_S_left (inline) 690ms 1.82% 65.71% 883ms 2.33% __dynamic_cast 2ms 0.0053% 65.71% 815ms 2.15% Cell::GetMutationState 297ms 0.78% 66.50% 803ms 2.12% __GI___libc_malloc 19ms 0.05% 66.55% 796ms 2.10% boost::detail::shared_count::~shared_count (inline) 0 0% 66.55% 796ms 2.10% boost::shared_ptr::~shared_ptr (inline) 774ms 2.04% 68.59% 774ms 2.04% [libchaste_cell_based.so] 751ms 1.98% 70.57% 770ms 2.03% boost::detail::sp_counted_base::release 318ms 0.84% 71.41% 768ms 2.02% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 71.41% 759ms 2.00% AbstractCellPopulation::WriteResultsToFiles 0 0% 71.41% 729ms 1.92% std::allocator_traits::allocate (inline) 2ms 0.0053% 71.41% 714ms 1.88% AbstractCellBasedSimulation::DoCellBirth 699ms 1.84% 73.25% 699ms 1.84% boost::numeric::ublas::c_vector::operator() 684ms 1.80% 75.06% 684ms 1.80% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 75.06% 651ms 1.72% std::_Rb_tree::_M_create_node (inline) 647ms 1.71% 76.76% 647ms 1.71% [libchaste_mesh.so] 0 0% 76.76% 628ms 1.66% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 76.76% 618ms 1.63% std::_Rb_tree::_M_get_node (inline) 615ms 1.62% 78.39% 615ms 1.62% __gnu_cxx::__normal_iterator::operator++ (inline) 59ms 0.16% 78.54% 610ms 1.61% boost::numeric::ublas::vector_binary::size (inline) 10ms 0.026% 78.57% 605ms 1.59% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 192ms 0.51% 79.07% 563ms 1.48% NodeAttributes::AddAppliedForceContribution 0 0% 79.07% 555ms 1.46% boost::numeric::ublas::scalar_traits::type_abs (inline) 0 0% 79.07% 543ms 1.43% boost::numeric::ublas::scalar_traits::norm_inf (inline) 3ms 0.0079% 79.08% 542ms 1.43% boost_numeric_ublas_abs (inline) 539ms 1.42% 80.50% 539ms 1.42% std::abs (inline) 4ms 0.011% 80.51% 531ms 1.40% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 80.51% 531ms 1.40% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 367ms 0.97% 81.48% 512ms 1.35% std::vector::push_back (inline) 160ms 0.42% 81.90% 511ms 1.35% __GI___libc_free 3ms 0.0079% 81.91% 485ms 1.28% NodeBasedCellPopulation::WriteVtkResultsToFile 8ms 0.021% 81.93% 433ms 1.14% std::_Rb_tree::_M_emplace_hint_unique 3ms 0.0079% 81.94% 430ms 1.13% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 81.94% 427ms 1.13% boost::numeric::ublas::norm_2 (inline) 326ms 0.86% 82.80% 427ms 1.13% boost::numeric::ublas::vector_norm_2::apply (inline) 30ms 0.079% 82.88% 424ms 1.12% std::_Rb_tree::_M_copy (inline) 5ms 0.013% 82.89% 420ms 1.11% AbstractCellProperty::IsSubType (inline) 1ms 0.0026% 82.89% 414ms 1.09% NodesOnlyMesh::ReMesh 6ms 0.016% 82.91% 401ms 1.06% NodesOnlyMesh::UpdateNodeIndices 87ms 0.23% 83.14% 392ms 1.03% std::_Rb_tree::_M_clone_node (inline) 3ms 0.0079% 83.15% 390ms 1.03% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 83.15% 390ms 1.03% boost::numeric::ublas::vector::vector (inline) 210ms 0.55% 83.70% 377ms 0.99% _int_malloc 0 0% 83.70% 371ms 0.98% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 83.70% 371ms 0.98% boost::numeric::ublas::c_vector::plus_assign (inline) 0 0% 83.70% 365ms 0.96% std::_Rb_tree::_Alloc_node::operator() (inline) 6ms 0.016% 83.72% 352ms 0.93% NodeBasedCellPopulation::UpdateMapsAfterRemesh 266ms 0.7% 84.42% 350ms 0.92% _int_free 2ms 0.0053% 84.42% 324ms 0.85% CellPropertyCollection::HasProperty 0 0% 84.42% 323ms 0.85% Cell::HasCellProperty (inline) 0 0% 84.42% 315ms 0.83% NodesOnlyMesh::UpdateBoxCollection 54ms 0.14% 84.56% 313ms 0.83% std::_Rb_tree::_M_erase (partial-inline) 1ms 0.0026% 84.57% 310ms 0.82% Node::GetRadius 10ms 0.026% 84.59% 307ms 0.81% Cell::ReadyToDivide 0 0% 84.59% 303ms 0.8% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 84.59% 288ms 0.76% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 84.59% 286ms 0.75% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 84.59% 263ms 0.69% std::set::set (inline) 4ms 0.011% 84.60% 262ms 0.69% DistributedBoxCollection::GetProcessOwningNode 258ms 0.68% 85.28% 258ms 0.68% Node::CheckForNodeAttributes 232ms 0.61% 85.90% 258ms 0.68% boost::shared_ptr::shared_ptr (inline) 1ms 0.0026% 85.90% 243ms 0.64% NodesOnlyMesh::AddNodesToBoxes 0 0% 85.90% 242ms 0.64% std::_Rb_tree::_M_drop_node (inline) 76ms 0.2% 86.10% 242ms 0.64% std::__move_median_to_first (inline) 4ms 0.011% 86.11% 239ms 0.63% std::__new_allocator::deallocate (inline) 1ms 0.0026% 86.11% 238ms 0.63% std::vector::vector (inline) 5ms 0.013% 86.13% 235ms 0.62% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 86.13% 227ms 0.6% std::iter_swap (inline) 227ms 0.6% 86.72% 227ms 0.6% std::swap (inline) 0 0% 86.72% 222ms 0.59% boost::numeric::ublas::c_vector::assign (inline) 0 0% 86.72% 218ms 0.57% boost::numeric::ublas::inner_prod (inline) 1ms 0.0026% 86.73% 218ms 0.57% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 14ms 0.037% 86.76% 217ms 0.57% boost::numeric::ublas::vector_scalar_binary::evaluate 24ms 0.063% 86.83% 214ms 0.56% std::__insertion_sort (inline) 36ms 0.095% 86.92% 207ms 0.55% std::__do_uninit_copy (inline) 0 0% 86.92% 207ms 0.55% std::__uninitialized_copy::__uninit_copy (inline) 0 0% 86.92% 207ms 0.55% std::__uninitialized_copy_a (inline) 0 0% 86.92% 207ms 0.55% std::uninitialized_copy (inline) 0 0% 86.92% 205ms 0.54% std::allocator_traits::deallocate (inline) 0 0% 86.92% 203ms 0.54% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 86.92% 203ms 0.54% VtkMeshWriter::WriteFiles 203ms 0.54% 87.46% 203ms 0.54% boost::shared_ptr::operator-> (inline) 0 0% 87.46% 201ms 0.53% std::_Rb_tree::_M_put_node (inline) 200ms 0.53% 87.98% 200ms 0.53% Node::GetIndex 9ms 0.024% 88.01% 191ms 0.5% AbstractCellProperty::IsType (inline)