File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 34702ms, 88.13% of 39377ms total Dropped 826 nodes (cum <= 196.88ms) flat flat% sum% cum cum% 0 0% 0% 39279ms 99.75% __libc_start_call_main 0 0% 0% 39279ms 99.75% __libc_start_main_impl 0 0% 0% 39279ms 99.75% _start 0 0% 0% 39262ms 99.71% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 39262ms 99.71% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 39262ms 99.71% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 39262ms 99.71% main 0 0% 0% 39231ms 99.63% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 39231ms 99.63% CxxTest::TestRunner::runTest (inline) 0 0% 0% 39231ms 99.63% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 2ms 0.0051% 0.0051% 39223ms 99.61% AbstractCellBasedSimulation::Solve 3ms 0.0076% 0.013% 27431ms 69.66% OffLatticeSimulation::UpdateCellLocationsAndTopology 5ms 0.013% 0.025% 21265ms 54.00% ForwardEulerNumericalMethod::UpdateAllNodePositions 18ms 0.046% 0.071% 21029ms 53.40% AbstractNumericalMethod::ComputeForcesIncludingDamping 227ms 0.58% 0.65% 19755ms 50.17% AbstractTwoBodyInteractionForce::AddForceContribution 1172ms 2.98% 3.62% 16812ms 42.69% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 5205ms 13.22% 16.84% 11467ms 29.12% std::_Rb_tree::_M_lower_bound (inline) 431ms 1.09% 17.94% 11325ms 28.76% NodesOnlyMesh::GetNodeOrHaloNode 431ms 1.09% 19.03% 10899ms 27.68% AbstractMesh::GetNode 621ms 1.58% 20.61% 10814ms 27.46% std::_Rb_tree::find (inline) 0 0% 20.61% 10812ms 27.46% std::map::find (inline) 0 0% 20.61% 10486ms 26.63% AbstractCellBasedSimulation::UpdateCellPopulation 605ms 1.54% 22.14% 10472ms 26.59% NodesOnlyMesh::SolveNodeMapping 0 0% 22.14% 9060ms 23.01% NodeBasedCellPopulation::Update 12ms 0.03% 22.18% 6911ms 17.55% DistributedBoxCollection::CalculateInteriorNodePairs 289ms 0.73% 22.91% 6068ms 15.41% boost::numeric::ublas::vector_assign (inline) 2ms 0.0051% 22.91% 5608ms 14.24% OffLatticeSimulation::ApplyBoundaries 73ms 0.19% 23.10% 5535ms 14.06% boost::numeric::ublas::c_vector::c_vector (partial-inline) 4905ms 12.46% 35.56% 4905ms 12.46% std::_Rb_tree::_S_right (inline) 18ms 0.046% 35.60% 4625ms 11.75% NodeAttributes::RemoveDuplicateNeighbours 9ms 0.023% 35.62% 4410ms 11.20% std::__sort (inline) 0 0% 35.62% 4410ms 11.20% std::sort (inline) 215ms 0.55% 36.17% 4122ms 10.47% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 5ms 0.013% 36.18% 3947ms 10.02% AbstractCellPopulation::Iterator::operator++ (inline) 240ms 0.61% 36.79% 3937ms 10.00% AbstractCellPopulation::Iterator::IsRealCell 29ms 0.074% 36.87% 3242ms 8.23% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 808ms 2.05% 38.92% 3179ms 8.07% boost::numeric::ublas::indexing_vector_assign 60ms 0.15% 39.07% 2846ms 7.23% PlaneBoundaryCondition::ImposeBoundaryCondition 518ms 1.32% 40.39% 2822ms 7.17% DistributedBoxCollection::AddPairsFromBox 242ms 0.61% 41.00% 2793ms 7.09% std::__introsort_loop 55ms 0.14% 41.14% 2759ms 7.01% PlaneBoundaryCondition::VerifyBoundaryCondition 2ms 0.0051% 41.15% 2444ms 6.21% std::__unguarded_partition_pivot (inline) 106ms 0.27% 41.42% 2271ms 5.77% AbstractCellPopulation::GetLocationIndexUsingCell 815ms 2.07% 43.48% 2131ms 5.41% std::__unguarded_partition (inline) 311ms 0.79% 44.27% 2113ms 5.37% std::map::operator[] (partial-inline) 3ms 0.0076% 44.28% 1606ms 4.08% std::__final_insertion_sort (inline) 0 0% 44.28% 1429ms 3.63% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 126ms 0.32% 44.60% 1407ms 3.57% std::__unguarded_insertion_sort (inline) 0 0% 44.60% 1405ms 3.57% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1382ms 3.51% 48.11% 1382ms 3.51% std::_Rb_tree::_S_left (inline) 0 0% 48.11% 1352ms 3.43% std::_Rb_tree::lower_bound (inline) 0 0% 48.11% 1352ms 3.43% std::map::lower_bound (inline) 1325ms 3.36% 51.48% 1325ms 3.36% boost::numeric::ublas::same_impl_ex 0 0% 51.48% 1295ms 3.29% NodeBasedCellPopulation::UpdateCellProcessLocation 61ms 0.15% 51.63% 1275ms 3.24% boost::numeric::ublas::detail::expression_type_check (inline) 100ms 0.25% 51.89% 1232ms 3.13% AbstractMesh::GetVectorFromAtoB 23ms 0.058% 51.94% 1231ms 3.13% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 161ms 0.41% 52.35% 1231ms 3.13% std::__new_allocator::allocate (inline) 3ms 0.0076% 52.36% 1199ms 3.04% AbstractCentreBasedCellPopulation::GetDampingConstant 714ms 1.81% 54.17% 1178ms 2.99% NodeAttributes::AddNeighbour 220ms 0.56% 54.73% 1160ms 2.95% boost::numeric::ublas::detail::equals 658ms 1.67% 56.40% 1158ms 2.94% std::__unguarded_linear_insert (inline) 215ms 0.55% 56.95% 1076ms 2.73% NodeAttributes::AddAppliedForceContribution 77ms 0.2% 57.15% 1036ms 2.63% operator new 1023ms 2.60% 59.74% 1023ms 2.60% boost::numeric::ublas::c_vector::operator() 8ms 0.02% 59.76% 1000ms 2.54% DistributedBoxCollection::CalculateBoundaryNodePairs 51ms 0.13% 59.89% 962ms 2.44% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 59.89% 914ms 2.32% boost::numeric::ublas::norm_inf (inline) 437ms 1.11% 61.00% 914ms 2.32% boost::numeric::ublas::vector_norm_inf::apply (inline) 677ms 1.72% 62.72% 911ms 2.31% __dynamic_cast 259ms 0.66% 63.38% 882ms 2.24% __GI___libc_malloc 18ms 0.046% 63.43% 861ms 2.19% CellPropertyCollection::GetPropertiesType (inline) 0 0% 63.43% 861ms 2.19% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 63.43% 861ms 2.19% boost::numeric::ublas::c_vector::plus_assign (inline) 839ms 2.13% 65.56% 839ms 2.13% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 830ms 2.11% 67.66% 830ms 2.11% std::_Rb_tree_increment 4ms 0.01% 67.67% 817ms 2.07% AbstractCellBasedSimulation::DoCellBirth 0 0% 67.67% 807ms 2.05% AbstractCellPopulation::WriteResultsToFiles 348ms 0.88% 68.56% 799ms 2.03% DistributedBoxCollection::CalculateContainingBox (partial-inline) 31ms 0.079% 68.64% 791ms 2.01% boost::detail::shared_count::~shared_count (inline) 0 0% 68.64% 791ms 2.01% boost::shared_ptr::~shared_ptr (inline) 2ms 0.0051% 68.64% 782ms 1.99% Cell::GetMutationState 0 0% 68.64% 766ms 1.95% std::allocator_traits::allocate (inline) 732ms 1.86% 70.50% 754ms 1.91% boost::detail::sp_counted_base::release 733ms 1.86% 72.36% 733ms 1.86% [libchaste_cell_based.so] 0 0% 72.36% 702ms 1.78% std::_Rb_tree::_M_create_node (inline) 695ms 1.76% 74.13% 695ms 1.76% __gnu_cxx::__normal_iterator::operator-- (inline) 147ms 0.37% 74.50% 677ms 1.72% boost::numeric::ublas::vector_binary::size (inline) 667ms 1.69% 76.19% 667ms 1.69% [libchaste_mesh.so] 0 0% 76.19% 647ms 1.64% std::_Rb_tree::_M_get_node (inline) 203ms 0.52% 76.71% 637ms 1.62% __GI___libc_free 0 0% 76.71% 608ms 1.54% AbstractCellBasedSimulation::DoCellRemoval (inline) 10ms 0.025% 76.74% 587ms 1.49% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 393ms 1% 77.73% 548ms 1.39% std::vector::push_back (inline) 4ms 0.01% 77.74% 530ms 1.35% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 528ms 1.34% 79.08% 528ms 1.34% __gnu_cxx::__normal_iterator::operator++ (inline) 5ms 0.013% 79.10% 523ms 1.33% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 79.10% 515ms 1.31% boost::numeric::ublas::norm_2 (inline) 393ms 1% 80.09% 515ms 1.31% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 80.09% 512ms 1.30% NodeBasedCellPopulation::WriteVtkResultsToFile 47ms 0.12% 80.21% 512ms 1.30% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 80.21% 512ms 1.30% boost::numeric::ublas::vector::vector (inline) 8ms 0.02% 80.23% 463ms 1.18% std::_Rb_tree::_Rb_tree (partial-inline) 5ms 0.013% 80.25% 458ms 1.16% AbstractCellProperty::IsSubType (inline) 18ms 0.046% 80.29% 453ms 1.15% std::_Rb_tree::_M_copy (inline) 10ms 0.025% 80.32% 449ms 1.14% std::_Rb_tree::_M_emplace_hint_unique 112ms 0.28% 80.60% 434ms 1.10% std::_Rb_tree::_M_clone_node (inline) 205ms 0.52% 81.12% 428ms 1.09% _int_malloc 355ms 0.9% 82.03% 427ms 1.08% _int_free 134ms 0.34% 82.37% 426ms 1.08% std::_Rb_tree::_M_erase 0 0% 82.37% 371ms 0.94% NodesOnlyMesh::ReMesh 0 0% 82.37% 369ms 0.94% std::_Rb_tree::_Alloc_node::operator() (inline) 3ms 0.0076% 82.37% 364ms 0.92% NodesOnlyMesh::UpdateNodeIndices 0 0% 82.37% 357ms 0.91% Cell::HasCellProperty (inline) 2ms 0.0051% 82.38% 357ms 0.91% CellPropertyCollection::HasProperty 6ms 0.015% 82.39% 354ms 0.9% NodeBasedCellPopulation::UpdateMapsAfterRemesh 8ms 0.02% 82.41% 348ms 0.88% boost::numeric::ublas::vector_reference::operator() (inline) 15ms 0.038% 82.45% 341ms 0.87% Cell::ReadyToDivide 0 0% 82.45% 333ms 0.85% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 82.45% 329ms 0.84% NodesOnlyMesh::UpdateBoxCollection 321ms 0.82% 83.27% 321ms 0.82% boost::numeric::ublas::scalar_plus_assign::apply (inline) 0 0% 83.27% 315ms 0.8% boost::numeric::ublas::vector_binary::operator() (inline) 77ms 0.2% 83.46% 309ms 0.78% std::__move_median_to_first (inline) 306ms 0.78% 84.24% 306ms 0.78% Node::GetIndex 4ms 0.01% 84.25% 303ms 0.77% Node::GetRadius 2ms 0.0051% 84.25% 293ms 0.74% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 84.25% 282ms 0.72% boost::numeric::ublas::scalar_traits::type_abs (inline) 0 0% 84.25% 281ms 0.71% boost::numeric::ublas::scalar_traits::norm_inf (inline) 4ms 0.01% 84.26% 280ms 0.71% DistributedBoxCollection::GetProcessOwningNode 1ms 0.0025% 84.27% 280ms 0.71% boost_numeric_ublas_abs (inline) 279ms 0.71% 84.98% 279ms 0.71% std::abs (inline) 0 0% 84.98% 278ms 0.71% std::_Rb_tree::_M_drop_node (inline) 2ms 0.0051% 84.98% 274ms 0.7% std::set::set (inline) 9ms 0.023% 85.00% 262ms 0.67% std::_Rb_tree::~_Rb_tree (inline) 1ms 0.0025% 85.01% 259ms 0.66% std::vector::vector (inline) 0 0% 85.01% 249ms 0.63% boost::numeric::ublas::inner_prod (inline) 1ms 0.0025% 85.01% 249ms 0.63% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 15ms 0.038% 85.05% 248ms 0.63% boost::numeric::ublas::vector_scalar_binary::evaluate 9ms 0.023% 85.07% 248ms 0.63% std::__new_allocator::deallocate (inline) 1ms 0.0025% 85.07% 244ms 0.62% NodesOnlyMesh::AddNodesToBoxes 0 0% 85.07% 243ms 0.62% boost::numeric::ublas::c_vector::assign (inline) 234ms 0.59% 85.67% 234ms 0.59% Node::CheckForNodeAttributes 214ms 0.54% 86.21% 232ms 0.59% boost::shared_ptr::shared_ptr (inline) 227ms 0.58% 86.79% 227ms 0.58% boost::shared_ptr::operator-> (inline) 0 0% 86.79% 227ms 0.58% std::allocator_traits::deallocate (inline) 0 0% 86.79% 225ms 0.57% std::_Rb_tree::_M_put_node (inline) 0 0% 86.79% 222ms 0.56% std::__uninitialized_copy::__uninit_copy (inline) 0 0% 86.79% 222ms 0.56% std::__uninitialized_copy_a (inline) 0 0% 86.79% 222ms 0.56% std::uninitialized_copy (inline) 36ms 0.091% 86.88% 221ms 0.56% std::__do_uninit_copy 0 0% 86.88% 213ms 0.54% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 86.88% 211ms 0.54% NodesOnlyMesh::ResizeBoxCollection 15ms 0.038% 86.92% 210ms 0.53% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 86.92% 210ms 0.53% VtkMeshWriter::WriteFiles 203ms 0.52% 87.43% 203ms 0.52% __strcmp_evex 0 0% 87.43% 202ms 0.51% std::iter_swap (inline) 202ms 0.51% 87.94% 202ms 0.51% std::swap (inline) 72ms 0.18% 88.13% 200ms 0.51% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 88.13% 200ms 0.51% std::_Rb_tree::clear (inline)