File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 31834ms, 88.93% of 35797ms total Dropped 839 nodes (cum <= 178.99ms) flat flat% sum% cum cum% 0 0% 0% 35642ms 99.57% __libc_start_call_main 0 0% 0% 35642ms 99.57% __libc_start_main_impl 0 0% 0% 35642ms 99.57% _start 0 0% 0% 35627ms 99.53% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 35627ms 99.53% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 35627ms 99.53% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 35627ms 99.53% main 0 0% 0% 35590ms 99.42% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 35590ms 99.42% CxxTest::TestRunner::runTest (inline) 0 0% 0% 35590ms 99.42% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0028% 0.0028% 35581ms 99.40% AbstractCellBasedSimulation::Solve 2ms 0.0056% 0.0084% 24711ms 69.03% OffLatticeSimulation::UpdateCellLocationsAndTopology 4ms 0.011% 0.02% 19770ms 55.23% ForwardEulerNumericalMethod::UpdateAllNodePositions 11ms 0.031% 0.05% 19544ms 54.60% AbstractNumericalMethod::ComputeForcesIncludingDamping 211ms 0.59% 0.64% 18317ms 51.17% AbstractTwoBodyInteractionForce::AddForceContribution 1541ms 4.30% 4.94% 15359ms 42.91% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 0 0% 4.94% 9649ms 26.95% AbstractCellBasedSimulation::UpdateCellPopulation 4321ms 12.07% 17.02% 9440ms 26.37% std::_Rb_tree::_M_lower_bound (inline) 0 0% 17.02% 8456ms 23.62% NodeBasedCellPopulation::Update 350ms 0.98% 17.99% 8438ms 23.57% std::_Rb_tree::find (inline) 0 0% 17.99% 8438ms 23.57% std::map::find (inline) 188ms 0.53% 18.52% 8232ms 23.00% NodesOnlyMesh::GetNodeOrHaloNode 450ms 1.26% 19.78% 8059ms 22.51% AbstractMesh::GetNode 336ms 0.94% 20.71% 7614ms 21.27% NodesOnlyMesh::SolveNodeMapping 205ms 0.57% 21.29% 6664ms 18.62% boost::numeric::ublas::vector_assign (inline) 212ms 0.59% 21.88% 6517ms 18.21% boost::numeric::ublas::c_vector::c_vector (partial-inline) 4ms 0.011% 21.89% 6327ms 17.67% DistributedBoxCollection::CalculateInteriorNodePairs 5097ms 14.24% 36.13% 5097ms 14.24% std::_Rb_tree::_S_right (inline) 13ms 0.036% 36.17% 4595ms 12.84% NodeAttributes::RemoveDuplicateNeighbours 1ms 0.0028% 36.17% 4557ms 12.73% OffLatticeSimulation::ApplyBoundaries 9ms 0.025% 36.19% 4420ms 12.35% std::__sort (inline) 0 0% 36.19% 4420ms 12.35% std::sort (inline) 1161ms 3.24% 39.44% 3759ms 10.50% boost::numeric::ublas::indexing_vector_assign 4ms 0.011% 39.45% 3467ms 9.69% AbstractCellPopulation::Iterator::operator++ (inline) 207ms 0.58% 40.03% 3438ms 9.60% AbstractCellPopulation::Iterator::IsRealCell (inline) 78ms 0.22% 40.24% 3435ms 9.60% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 27ms 0.075% 40.32% 2918ms 8.15% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 220ms 0.61% 40.93% 2616ms 7.31% std::__introsort_loop 25ms 0.07% 41.00% 2406ms 6.72% PlaneBoundaryCondition::ImposeBoundaryCondition 42ms 0.12% 41.12% 2371ms 6.62% AbstractCellPopulation::GetLocationIndexUsingCell 332ms 0.93% 42.05% 2361ms 6.60% DistributedBoxCollection::AddPairsFromBox 1ms 0.0028% 42.05% 2310ms 6.45% std::__unguarded_partition_pivot (inline) 22ms 0.061% 42.11% 2150ms 6.01% PlaneBoundaryCondition::VerifyBoundaryCondition 1035ms 2.89% 45.00% 2069ms 5.78% std::__unguarded_partition (inline) 234ms 0.65% 45.66% 1938ms 5.41% std::map::operator[] (partial-inline) 1ms 0.0028% 45.66% 1793ms 5.01% std::__final_insertion_sort (inline) 1759ms 4.91% 50.57% 1759ms 4.91% boost::numeric::ublas::same_impl_ex 121ms 0.34% 50.91% 1722ms 4.81% AbstractMesh::GetVectorFromAtoB 93ms 0.26% 51.17% 1600ms 4.47% std::__unguarded_insertion_sort (inline) 610ms 1.70% 52.88% 1560ms 4.36% std::__unguarded_linear_insert (inline) 1467ms 4.10% 56.97% 1467ms 4.10% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 56.97% 1441ms 4.03% std::_Rb_tree::lower_bound (inline) 0 0% 56.97% 1441ms 4.03% std::map::lower_bound (inline) 0 0% 56.97% 1335ms 3.73% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 56.97% 1317ms 3.68% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 56.97% 1196ms 3.34% NodeBasedCellPopulation::UpdateCellProcessLocation 4ms 0.011% 56.99% 1157ms 3.23% AbstractCentreBasedCellPopulation::GetDampingConstant 1151ms 3.22% 60.20% 1151ms 3.22% boost::numeric::ublas::c_vector::operator() 24ms 0.067% 60.27% 1151ms 3.22% boost::numeric::ublas::detail::expression_type_check (inline) 177ms 0.49% 60.76% 1104ms 3.08% boost::numeric::ublas::vector_binary::size (inline) 6ms 0.017% 60.78% 1102ms 3.08% DistributedBoxCollection::CalculateBoundaryNodePairs 208ms 0.58% 61.36% 1102ms 3.08% boost::numeric::ublas::detail::equals 35ms 0.098% 61.46% 1000ms 2.79% std::_Rb_tree_const_iterator::operator++ (inline) 965ms 2.70% 64.15% 965ms 2.70% std::_Rb_tree_increment 216ms 0.6% 64.76% 964ms 2.69% NodeAttributes::AddAppliedForceContribution 145ms 0.41% 65.16% 928ms 2.59% std::__new_allocator::allocate (inline) 418ms 1.17% 66.33% 908ms 2.54% NodeAttributes::AddNeighbour 406ms 1.13% 67.46% 900ms 2.51% __GI___libc_free 0 0% 67.46% 849ms 2.37% boost::numeric::ublas::norm_inf (inline) 473ms 1.32% 68.79% 849ms 2.37% boost::numeric::ublas::vector_norm_inf::apply (inline) 395ms 1.10% 69.89% 834ms 2.33% DistributedBoxCollection::CalculateContainingBox (partial-inline) 13ms 0.036% 69.92% 831ms 2.32% CellPropertyCollection::GetPropertiesType (inline) 19ms 0.053% 69.98% 826ms 2.31% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 79ms 0.22% 70.20% 790ms 2.21% operator new 567ms 1.58% 71.78% 762ms 2.13% __dynamic_cast 0 0% 71.78% 756ms 2.11% AbstractCellPopulation::WriteResultsToFiles 2ms 0.0056% 71.79% 749ms 2.09% Cell::GetMutationState 0 0% 71.79% 748ms 2.09% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 71.79% 748ms 2.09% boost::numeric::ublas::c_vector::plus_assign (inline) 3ms 0.0084% 71.80% 710ms 1.98% AbstractCellBasedSimulation::DoCellBirth 235ms 0.66% 72.45% 707ms 1.98% __GI___libc_malloc 487ms 1.36% 73.81% 612ms 1.71% std::vector::push_back (inline) 1ms 0.0028% 73.82% 494ms 1.38% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 4ms 0.011% 73.83% 492ms 1.37% AbstractCellPopulation::GetCellUsingLocationIndex 3ms 0.0084% 73.84% 491ms 1.37% NodeBasedCellPopulation::WriteVtkResultsToFile 445ms 1.24% 75.08% 488ms 1.36% _int_free 0 0% 75.08% 486ms 1.36% boost::numeric::ublas::norm_2 (inline) 394ms 1.10% 76.18% 486ms 1.36% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 76.18% 486ms 1.36% std::allocator_traits::allocate (inline) 0 0% 76.18% 482ms 1.35% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 76.18% 475ms 1.33% std::_Rb_tree::_M_create_node (inline) 8ms 0.022% 76.20% 467ms 1.30% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 17ms 0.047% 76.25% 459ms 1.28% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 76.25% 459ms 1.28% boost::numeric::ublas::vector::vector (inline) 398ms 1.11% 77.36% 398ms 1.11% Node::GetIndex 0 0% 77.36% 394ms 1.10% std::_Rb_tree::_M_get_node (inline) 30ms 0.084% 77.45% 375ms 1.05% boost::detail::shared_count::~shared_count (inline) 0 0% 77.45% 375ms 1.05% boost::shared_ptr::~shared_ptr (inline) 1ms 0.0028% 77.45% 368ms 1.03% AbstractCellProperty::IsSubType (inline) 161ms 0.45% 77.90% 355ms 0.99% std::_Rb_tree::_M_erase 336ms 0.94% 78.84% 341ms 0.95% boost::detail::sp_counted_base::release 340ms 0.95% 79.79% 340ms 0.95% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 4ms 0.011% 79.80% 338ms 0.94% std::_Rb_tree::_Rb_tree (partial-inline) 3ms 0.0084% 79.81% 331ms 0.92% CellPropertyCollection::HasProperty 0 0% 79.81% 329ms 0.92% Cell::HasCellProperty (inline) 0 0% 79.81% 328ms 0.92% NodesOnlyMesh::ReMesh 9ms 0.025% 79.83% 326ms 0.91% NodeBasedCellPopulation::UpdateMapsAfterRemesh 16ms 0.045% 79.88% 325ms 0.91% std::_Rb_tree::_M_copy (inline) 116ms 0.32% 80.20% 318ms 0.89% Node::GetRadius 8ms 0.022% 80.22% 316ms 0.88% Cell::ReadyToDivide 0 0% 80.22% 315ms 0.88% std::_Rb_tree::_Alloc_node::operator() (inline) 17ms 0.047% 80.27% 314ms 0.88% boost::numeric::ublas::vector_reference::operator() (inline) 1ms 0.0028% 80.27% 312ms 0.87% NodesOnlyMesh::UpdateNodeIndices 44ms 0.12% 80.40% 308ms 0.86% std::_Rb_tree::_M_clone_node (inline) 0 0% 80.40% 304ms 0.85% boost::numeric::ublas::inner_prod (inline) 2ms 0.0056% 80.40% 301ms 0.84% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 18ms 0.05% 80.45% 299ms 0.84% boost::numeric::ublas::vector_scalar_binary::evaluate 5ms 0.014% 80.46% 294ms 0.82% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 286ms 0.8% 81.26% 286ms 0.8% __gnu_cxx::__normal_iterator::operator++ (inline) 144ms 0.4% 81.67% 284ms 0.79% _int_malloc 281ms 0.78% 82.45% 281ms 0.78% [libchaste_cell_based.so] 3ms 0.0084% 82.46% 280ms 0.78% DistributedBoxCollection::GetProcessOwningNode 0 0% 82.46% 276ms 0.77% boost::numeric::ublas::c_vector::assign (inline) 0 0% 82.46% 275ms 0.77% NodesOnlyMesh::UpdateBoxCollection 6ms 0.017% 82.48% 263ms 0.73% std::_Rb_tree::_M_emplace_hint_unique 89ms 0.25% 82.72% 244ms 0.68% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 82.72% 238ms 0.66% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 237ms 0.66% 83.39% 237ms 0.66% boost::numeric::ublas::c_vector::size (inline) 90ms 0.25% 83.64% 236ms 0.66% std::__move_median_to_first (inline) 0 0% 83.64% 235ms 0.66% VtkMeshWriter::WriteFiles 232ms 0.65% 84.29% 232ms 0.65% boost::numeric::ublas::scalar_plus_assign::apply (inline) 230ms 0.64% 84.93% 230ms 0.64% boost::shared_ptr::operator-> (inline) 106ms 0.3% 85.23% 229ms 0.64% std::__find_if (inline) 0 0% 85.23% 229ms 0.64% std::find_if (inline) 0 0% 85.23% 229ms 0.64% std::none_of (inline) 41ms 0.11% 85.34% 227ms 0.63% std::__new_allocator::deallocate (inline) 226ms 0.63% 85.97% 226ms 0.63% [libchaste_mesh.so] 0 0% 85.97% 224ms 0.63% boost::numeric::ublas::vector_reference::size (inline) 216ms 0.6% 86.57% 216ms 0.6% Node::CheckForNodeAttributes 2ms 0.0056% 86.58% 216ms 0.6% NodesOnlyMesh::AddNodesToBoxes 0 0% 86.58% 213ms 0.6% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 86.58% 211ms 0.59% vtkStreamingDemandDrivenPipeline::Update 0 0% 86.58% 211ms 0.59% vtkXMLWriterBase::Write 210ms 0.59% 87.17% 210ms 0.59% NodeBasedCellPopulation::GetNode 0 0% 87.17% 210ms 0.59% vtkDemandDrivenPipeline::ProcessRequest 0 0% 87.17% 209ms 0.58% vtkDemandDrivenPipeline::ExecuteData 0 0% 87.17% 209ms 0.58% vtkExecutive::CallAlgorithm 0 0% 87.17% 209ms 0.58% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 87.17% 208ms 0.58% vtkCompositeDataPipeline::ExecuteData 0 0% 87.17% 208ms 0.58% vtkXMLUnstructuredDataWriter::ProcessRequest 204ms 0.57% 87.74% 204ms 0.57% Node::rGetLocation 0 0% 87.74% 202ms 0.56% std::_Rb_tree::clear (inline) 0 0% 87.74% 197ms 0.55% std::set::set (inline) 194ms 0.54% 88.28% 194ms 0.54% __strcmp_avx2 20ms 0.056% 88.33% 192ms 0.54% std::__insertion_sort (inline) 0 0% 88.33% 187ms 0.52% tcache_get (inline) 187ms 0.52% 88.86% 187ms 0.52% tcache_get_n (inline) 11ms 0.031% 88.89% 186ms 0.52% std::_Rb_tree::~_Rb_tree (inline) 5ms 0.014% 88.90% 184ms 0.51% AbstractCellProperty::IsType (inline) 0 0% 88.90% 184ms 0.51% NodesOnlyMesh::ResizeBoxCollection 10ms 0.028% 88.93% 182ms 0.51% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 88.93% 182ms 0.51% std::_Rb_tree::_M_drop_node (inline) 0 0% 88.93% 182ms 0.51% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 88.93% 182ms 0.51% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData