File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 32408ms, 90.11% of 35964ms total Dropped 861 nodes (cum <= 179.82ms) flat flat% sum% cum cum% 0 0% 0% 35809ms 99.57% __libc_start_call_main 0 0% 0% 35809ms 99.57% __libc_start_main_impl 0 0% 0% 35809ms 99.57% _start 0 0% 0% 35792ms 99.52% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 35792ms 99.52% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 35792ms 99.52% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 35792ms 99.52% main 0 0% 0% 35751ms 99.41% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 35751ms 99.41% CxxTest::TestRunner::runTest (inline) 0 0% 0% 35751ms 99.41% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 35743ms 99.39% AbstractCellBasedSimulation::Solve 2ms 0.0056% 0.0056% 24860ms 69.12% OffLatticeSimulation::UpdateCellLocationsAndTopology 5ms 0.014% 0.019% 19861ms 55.22% ForwardEulerNumericalMethod::UpdateAllNodePositions 13ms 0.036% 0.056% 19691ms 54.75% AbstractNumericalMethod::ComputeForcesIncludingDamping 167ms 0.46% 0.52% 18506ms 51.46% AbstractTwoBodyInteractionForce::AddForceContribution 1613ms 4.49% 5.01% 15619ms 43.43% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 1ms 0.0028% 5.01% 9603ms 26.70% AbstractCellBasedSimulation::UpdateCellPopulation 4227ms 11.75% 16.76% 9554ms 26.57% std::_Rb_tree::_M_lower_bound (inline) 345ms 0.96% 17.72% 8684ms 24.15% std::_Rb_tree::find (inline) 0 0% 17.72% 8684ms 24.15% std::map::find (inline) 184ms 0.51% 18.23% 8469ms 23.55% NodesOnlyMesh::GetNodeOrHaloNode 0 0% 18.23% 8409ms 23.38% NodeBasedCellPopulation::Update 490ms 1.36% 19.59% 8269ms 22.99% AbstractMesh::GetNode 277ms 0.77% 20.36% 7783ms 21.64% NodesOnlyMesh::SolveNodeMapping 208ms 0.58% 20.94% 6552ms 18.22% boost::numeric::ublas::vector_assign (inline) 191ms 0.53% 21.47% 6374ms 17.72% boost::numeric::ublas::c_vector::c_vector (partial-inline) 7ms 0.019% 21.49% 6303ms 17.53% DistributedBoxCollection::CalculateInteriorNodePairs 5294ms 14.72% 36.21% 5294ms 14.72% std::_Rb_tree::_S_right (inline) 2ms 0.0056% 36.22% 4603ms 12.80% OffLatticeSimulation::ApplyBoundaries 18ms 0.05% 36.27% 4581ms 12.74% NodeAttributes::RemoveDuplicateNeighbours 7ms 0.019% 36.29% 4405ms 12.25% std::__sort (inline) 0 0% 36.29% 4405ms 12.25% std::sort (inline) 1176ms 3.27% 39.56% 3681ms 10.24% boost::numeric::ublas::indexing_vector_assign 3ms 0.0083% 39.57% 3623ms 10.07% AbstractCellPopulation::Iterator::operator++ (inline) 205ms 0.57% 40.14% 3594ms 9.99% AbstractCellPopulation::Iterator::IsRealCell (inline) 100ms 0.28% 40.42% 3442ms 9.57% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 23ms 0.064% 40.48% 3061ms 8.51% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 199ms 0.55% 41.03% 2586ms 7.19% std::__introsort_loop 30ms 0.083% 41.12% 2408ms 6.70% PlaneBoundaryCondition::ImposeBoundaryCondition 153ms 0.43% 41.54% 2360ms 6.56% DistributedBoxCollection::AddPairsFromBox 0 0% 41.54% 2296ms 6.38% std::__unguarded_partition_pivot (inline) 40ms 0.11% 41.65% 2257ms 6.28% AbstractCellPopulation::GetLocationIndexUsingCell 29ms 0.081% 41.73% 2193ms 6.10% PlaneBoundaryCondition::VerifyBoundaryCondition 1066ms 2.96% 44.70% 2061ms 5.73% std::__unguarded_partition (inline) 206ms 0.57% 45.27% 1821ms 5.06% std::map::operator[] (partial-inline) 2ms 0.0056% 45.28% 1811ms 5.04% std::__final_insertion_sort (inline) 1679ms 4.67% 49.94% 1679ms 4.67% boost::numeric::ublas::same_impl_ex 116ms 0.32% 50.27% 1638ms 4.55% AbstractMesh::GetVectorFromAtoB 84ms 0.23% 50.50% 1580ms 4.39% std::__unguarded_insertion_sort (inline) 578ms 1.61% 52.11% 1573ms 4.37% std::__unguarded_linear_insert (inline) 1439ms 4.00% 56.11% 1439ms 4.00% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 56.11% 1318ms 3.66% std::_Rb_tree::lower_bound (inline) 0 0% 56.11% 1318ms 3.66% std::map::lower_bound (inline) 0 0% 56.11% 1285ms 3.57% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 56.11% 1258ms 3.50% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1ms 0.0028% 56.11% 1238ms 3.44% NodeBasedCellPopulation::UpdateCellProcessLocation 27ms 0.075% 56.19% 1174ms 3.26% boost::numeric::ublas::detail::expression_type_check (inline) 1139ms 3.17% 59.35% 1139ms 3.17% boost::numeric::ublas::c_vector::operator() 210ms 0.58% 59.94% 1116ms 3.10% boost::numeric::ublas::detail::equals 3ms 0.0083% 59.95% 1103ms 3.07% AbstractCentreBasedCellPopulation::GetDampingConstant 3ms 0.0083% 59.95% 1088ms 3.03% DistributedBoxCollection::CalculateBoundaryNodePairs 176ms 0.49% 60.44% 1057ms 2.94% boost::numeric::ublas::vector_binary::size (inline) 147ms 0.41% 60.85% 940ms 2.61% std::__new_allocator::allocate (inline) 207ms 0.58% 61.43% 913ms 2.54% NodeAttributes::AddAppliedForceContribution 44ms 0.12% 61.55% 911ms 2.53% std::_Rb_tree_const_iterator::operator++ (inline) 393ms 1.09% 62.64% 873ms 2.43% __GI___libc_free 859ms 2.39% 65.03% 859ms 2.39% std::_Rb_tree_increment 0 0% 65.03% 852ms 2.37% boost::numeric::ublas::norm_inf (inline) 472ms 1.31% 66.34% 852ms 2.37% boost::numeric::ublas::vector_norm_inf::apply (inline) 611ms 1.70% 68.04% 829ms 2.31% __dynamic_cast 27ms 0.075% 68.12% 810ms 2.25% CellPropertyCollection::GetPropertiesType (inline) 71ms 0.2% 68.32% 797ms 2.22% operator new 18ms 0.05% 68.37% 770ms 2.14% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 68.37% 766ms 2.13% AbstractCellPopulation::WriteResultsToFiles 348ms 0.97% 69.33% 759ms 2.11% DistributedBoxCollection::CalculateContainingBox (partial-inline) 5ms 0.014% 69.35% 744ms 2.07% AbstractCellBasedSimulation::DoCellBirth 1ms 0.0028% 69.35% 734ms 2.04% Cell::GetMutationState 227ms 0.63% 69.98% 724ms 2.01% __GI___libc_malloc 188ms 0.52% 70.50% 717ms 1.99% NodeAttributes::AddNeighbour 0 0% 70.50% 706ms 1.96% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 70.50% 706ms 1.96% boost::numeric::ublas::c_vector::plus_assign (inline) 525ms 1.46% 71.96% 610ms 1.70% std::vector::push_back (inline) 120ms 0.33% 72.30% 547ms 1.52% Node::AddNeighbour 0 0% 72.30% 513ms 1.43% std::allocator_traits::allocate (inline) 3ms 0.0083% 72.31% 498ms 1.38% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 72.31% 490ms 1.36% std::_Rb_tree::_M_create_node (inline) 483ms 1.34% 73.65% 484ms 1.35% Node::ConstructNodeAttributes (inline) 436ms 1.21% 74.86% 477ms 1.33% _int_free 3ms 0.0083% 74.87% 466ms 1.30% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 3ms 0.0083% 74.88% 462ms 1.28% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 74.88% 449ms 1.25% AbstractCellBasedSimulation::DoCellRemoval (inline) 5ms 0.014% 74.89% 441ms 1.23% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 14ms 0.039% 74.93% 441ms 1.23% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 74.93% 441ms 1.23% boost::numeric::ublas::vector::vector (inline) 0 0% 74.93% 433ms 1.20% boost::numeric::ublas::norm_2 (inline) 331ms 0.92% 75.85% 433ms 1.20% boost::numeric::ublas::vector_norm_2::apply (inline) 432ms 1.20% 77.05% 432ms 1.20% Node::GetIndex 3ms 0.0083% 77.06% 428ms 1.19% AbstractCellProperty::IsSubType (inline) 0 0% 77.06% 416ms 1.16% std::_Rb_tree::_M_get_node (inline) 137ms 0.38% 77.44% 377ms 1.05% Node::GetRadius 27ms 0.075% 77.52% 374ms 1.04% boost::detail::shared_count::~shared_count (inline) 0 0% 77.52% 374ms 1.04% boost::shared_ptr::~shared_ptr (inline) 3ms 0.0083% 77.52% 350ms 0.97% std::_Rb_tree::_Rb_tree (partial-inline) 344ms 0.96% 78.48% 345ms 0.96% boost::detail::sp_counted_base::release 29ms 0.081% 78.56% 341ms 0.95% std::_Rb_tree::_M_copy (inline) 2ms 0.0056% 78.57% 340ms 0.95% NodeBasedCellPopulation::UpdateMapsAfterRemesh 340ms 0.95% 79.51% 340ms 0.95% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 143ms 0.4% 79.91% 340ms 0.95% std::_Rb_tree::_M_erase (partial-inline) 0 0% 79.91% 328ms 0.91% boost::numeric::ublas::inner_prod (inline) 1ms 0.0028% 79.91% 328ms 0.91% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 27ms 0.075% 79.99% 327ms 0.91% boost::numeric::ublas::vector_scalar_binary::evaluate 6ms 0.017% 80.01% 326ms 0.91% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 80.01% 321ms 0.89% NodesOnlyMesh::ReMesh 0 0% 80.01% 320ms 0.89% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 80.01% 315ms 0.88% Cell::HasCellProperty (inline) 3ms 0.0083% 80.01% 315ms 0.88% CellPropertyCollection::HasProperty 315ms 0.88% 80.89% 315ms 0.88% __gnu_cxx::__normal_iterator::operator++ (inline) 50ms 0.14% 81.03% 311ms 0.86% std::_Rb_tree::_M_clone_node (inline) 3ms 0.0083% 81.04% 308ms 0.86% NodesOnlyMesh::UpdateNodeIndices 166ms 0.46% 81.50% 308ms 0.86% _int_malloc 12ms 0.033% 81.53% 297ms 0.83% std::_Rb_tree::_M_emplace_hint_unique 12ms 0.033% 81.56% 293ms 0.81% Cell::ReadyToDivide 293ms 0.81% 82.38% 293ms 0.81% [libchaste_cell_based.so] 2ms 0.0056% 82.39% 277ms 0.77% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 82.39% 271ms 0.75% NodesOnlyMesh::UpdateBoxCollection 9ms 0.025% 82.41% 260ms 0.72% DistributedBoxCollection::GetProcessOwningNode 258ms 0.72% 83.13% 258ms 0.72% Node::CheckForNodeAttributes 256ms 0.71% 83.84% 256ms 0.71% NodeBasedCellPopulation::GetNode 109ms 0.3% 84.14% 251ms 0.7% boost::numeric::ublas::vector_inner_prod::apply (inline) 242ms 0.67% 84.82% 242ms 0.67% Node::IsDeleted 0 0% 84.82% 240ms 0.67% boost::numeric::ublas::c_vector::assign (inline) 0 0% 84.82% 239ms 0.66% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 84.82% 236ms 0.66% VtkMeshWriter::WriteFiles 102ms 0.28% 85.10% 230ms 0.64% std::__move_median_to_first (inline) 19ms 0.053% 85.15% 229ms 0.64% std::__insertion_sort (inline) 39ms 0.11% 85.26% 227ms 0.63% std::__new_allocator::deallocate (inline) 224ms 0.62% 85.88% 224ms 0.62% boost::numeric::ublas::c_vector::size (inline) 0 0% 85.88% 221ms 0.61% NodesOnlyMesh::ResizeBoxCollection 7ms 0.019% 85.90% 219ms 0.61% NodesOnlyMesh::IsANodeCloseToDomainBoundary 219ms 0.61% 86.51% 219ms 0.61% [libchaste_mesh.so] 116ms 0.32% 86.83% 219ms 0.61% std::__find_if (inline) 0 0% 86.83% 219ms 0.61% std::find_if (inline) 0 0% 86.83% 219ms 0.61% std::none_of (inline) 2ms 0.0056% 86.84% 218ms 0.61% NodesOnlyMesh::AddNodesToBoxes 216ms 0.6% 87.44% 216ms 0.6% Node::rGetLocation 208ms 0.58% 88.02% 208ms 0.58% boost::numeric::ublas::scalar_plus_assign::apply (inline) 2ms 0.0056% 88.02% 208ms 0.58% std::set::set (inline) 0 0% 88.02% 208ms 0.58% vtkXMLWriterBase::Write 7ms 0.019% 88.04% 207ms 0.58% AbstractCellProperty::IsType (inline) 0 0% 88.04% 207ms 0.58% vtkDemandDrivenPipeline::ProcessRequest 0 0% 88.04% 207ms 0.58% vtkStreamingDemandDrivenPipeline::Update 205ms 0.57% 88.61% 205ms 0.57% boost::shared_ptr::operator-> (inline) 0 0% 88.61% 205ms 0.57% vtkCompositeDataPipeline::ExecuteData 0 0% 88.61% 205ms 0.57% vtkDemandDrivenPipeline::ExecuteData 0 0% 88.61% 205ms 0.57% vtkExecutive::CallAlgorithm 0 0% 88.61% 205ms 0.57% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 88.61% 204ms 0.57% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 88.61% 203ms 0.56% boost::numeric::ublas::vector_reference::size (inline) 0 0% 88.61% 203ms 0.56% vtkXMLUnstructuredDataWriter::ProcessRequest 12ms 0.033% 88.65% 202ms 0.56% std::_Rb_tree::~_Rb_tree (inline) 147ms 0.41% 89.06% 194ms 0.54% Node::AddAppliedForceContribution 0 0% 89.06% 192ms 0.53% std::_Rb_tree::_M_drop_node (inline) 191ms 0.53% 89.59% 191ms 0.53% __strcmp_avx2 0 0% 89.59% 189ms 0.53% tcache_get (inline) 189ms 0.53% 90.11% 189ms 0.53% tcache_get_n (inline)