File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 31584ms, 89.13% of 35434ms total Dropped 823 nodes (cum <= 177.17ms) flat flat% sum% cum cum% 0 0% 0% 35280ms 99.57% __libc_start_call_main 0 0% 0% 35280ms 99.57% __libc_start_main_impl 0 0% 0% 35280ms 99.57% _start 0 0% 0% 35265ms 99.52% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 35265ms 99.52% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 35265ms 99.52% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 35265ms 99.52% main 0 0% 0% 35226ms 99.41% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 35226ms 99.41% CxxTest::TestRunner::runTest (inline) 0 0% 0% 35226ms 99.41% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0028% 0.0028% 35218ms 99.39% AbstractCellBasedSimulation::Solve 0 0% 0.0028% 24608ms 69.45% OffLatticeSimulation::UpdateCellLocationsAndTopology 4ms 0.011% 0.014% 19718ms 55.65% ForwardEulerNumericalMethod::UpdateAllNodePositions 5ms 0.014% 0.028% 19524ms 55.10% AbstractNumericalMethod::ComputeForcesIncludingDamping 196ms 0.55% 0.58% 18394ms 51.91% AbstractTwoBodyInteractionForce::AddForceContribution 1531ms 4.32% 4.90% 15543ms 43.86% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4365ms 12.32% 17.22% 9713ms 27.41% std::_Rb_tree::_M_lower_bound (inline) 0 0% 17.22% 9381ms 26.47% AbstractCellBasedSimulation::UpdateCellPopulation 337ms 0.95% 18.17% 8859ms 25.00% std::_Rb_tree::find (inline) 0 0% 18.17% 8859ms 25.00% std::map::find (inline) 128ms 0.36% 18.53% 8570ms 24.19% NodesOnlyMesh::GetNodeOrHaloNode 465ms 1.31% 19.85% 8443ms 23.83% AbstractMesh::GetNode 1ms 0.0028% 19.85% 8241ms 23.26% NodeBasedCellPopulation::Update 301ms 0.85% 20.70% 7984ms 22.53% NodesOnlyMesh::SolveNodeMapping 223ms 0.63% 21.33% 6543ms 18.47% boost::numeric::ublas::vector_assign (inline) 192ms 0.54% 21.87% 6401ms 18.06% boost::numeric::ublas::c_vector::c_vector (partial-inline) 10ms 0.028% 21.90% 6180ms 17.44% DistributedBoxCollection::CalculateInteriorNodePairs 5319ms 15.01% 36.91% 5319ms 15.01% std::_Rb_tree::_S_right (inline) 0 0% 36.91% 4534ms 12.80% OffLatticeSimulation::ApplyBoundaries 14ms 0.04% 36.95% 4517ms 12.75% NodeAttributes::RemoveDuplicateNeighbours 5ms 0.014% 36.96% 4353ms 12.28% std::__sort (inline) 0 0% 36.96% 4353ms 12.28% std::sort (inline) 1178ms 3.32% 40.29% 3564ms 10.06% boost::numeric::ublas::indexing_vector_assign 1ms 0.0028% 40.29% 3461ms 9.77% AbstractCellPopulation::Iterator::operator++ (inline) 176ms 0.5% 40.79% 3452ms 9.74% AbstractCellPopulation::Iterator::IsRealCell (inline) 76ms 0.21% 41.00% 3393ms 9.58% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 27ms 0.076% 41.08% 2952ms 8.33% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 196ms 0.55% 41.63% 2546ms 7.19% std::__introsort_loop 25ms 0.071% 41.70% 2402ms 6.78% PlaneBoundaryCondition::ImposeBoundaryCondition 266ms 0.75% 42.45% 2292ms 6.47% DistributedBoxCollection::AddPairsFromBox 0 0% 42.45% 2281ms 6.44% std::__unguarded_partition_pivot (inline) 44ms 0.12% 42.57% 2255ms 6.36% AbstractCellPopulation::GetLocationIndexUsingCell 18ms 0.051% 42.63% 2132ms 6.02% PlaneBoundaryCondition::VerifyBoundaryCondition 1050ms 2.96% 45.59% 2047ms 5.78% std::__unguarded_partition (inline) 1ms 0.0028% 45.59% 1797ms 5.07% std::__final_insertion_sort (inline) 222ms 0.63% 46.22% 1775ms 5.01% std::map::operator[] (partial-inline) 1640ms 4.63% 50.85% 1640ms 4.63% boost::numeric::ublas::same_impl_ex 94ms 0.27% 51.11% 1609ms 4.54% std::__unguarded_insertion_sort (inline) 97ms 0.27% 51.39% 1561ms 4.41% AbstractMesh::GetVectorFromAtoB 580ms 1.64% 53.02% 1549ms 4.37% std::__unguarded_linear_insert (inline) 1488ms 4.20% 57.22% 1488ms 4.20% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 57.22% 1282ms 3.62% std::_Rb_tree::lower_bound (inline) 0 0% 57.22% 1282ms 3.62% std::map::lower_bound (inline) 0 0% 57.22% 1263ms 3.56% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 57.22% 1238ms 3.49% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 28ms 0.079% 57.30% 1178ms 3.32% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 57.30% 1165ms 3.29% NodeBasedCellPopulation::UpdateCellProcessLocation 198ms 0.56% 57.86% 1115ms 3.15% boost::numeric::ublas::detail::equals 6ms 0.017% 57.88% 1077ms 3.04% DistributedBoxCollection::CalculateBoundaryNodePairs 1072ms 3.03% 60.90% 1072ms 3.03% boost::numeric::ublas::c_vector::operator() 3ms 0.0085% 60.91% 1059ms 2.99% AbstractCentreBasedCellPopulation::GetDampingConstant 172ms 0.49% 61.40% 1040ms 2.94% boost::numeric::ublas::vector_binary::size (inline) 157ms 0.44% 61.84% 949ms 2.68% std::__new_allocator::allocate (inline) 482ms 1.36% 63.20% 913ms 2.58% __GI___libc_free 34ms 0.096% 63.30% 908ms 2.56% std::_Rb_tree_const_iterator::operator++ (inline) 201ms 0.57% 63.86% 881ms 2.49% NodeAttributes::AddAppliedForceContribution 369ms 1.04% 64.90% 877ms 2.48% NodeAttributes::AddNeighbour 873ms 2.46% 67.37% 873ms 2.46% std::_Rb_tree_increment 0 0% 67.37% 854ms 2.41% boost::numeric::ublas::norm_inf (inline) 487ms 1.37% 68.74% 854ms 2.41% boost::numeric::ublas::vector_norm_inf::apply (inline) 90ms 0.25% 69.00% 798ms 2.25% operator new 576ms 1.63% 70.62% 786ms 2.22% __dynamic_cast 375ms 1.06% 71.68% 767ms 2.16% DistributedBoxCollection::CalculateContainingBox (partial-inline) 18ms 0.051% 71.73% 759ms 2.14% CellPropertyCollection::GetPropertiesType (inline) 17ms 0.048% 71.78% 756ms 2.13% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 71.78% 746ms 2.11% AbstractCellPopulation::WriteResultsToFiles 230ms 0.65% 72.43% 702ms 1.98% __GI___libc_malloc 1ms 0.0028% 72.43% 694ms 1.96% Cell::GetMutationState 3ms 0.0085% 72.44% 691ms 1.95% AbstractCellBasedSimulation::DoCellBirth 0 0% 72.44% 680ms 1.92% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 72.44% 680ms 1.92% boost::numeric::ublas::c_vector::plus_assign (inline) 504ms 1.42% 73.86% 644ms 1.82% std::vector::push_back (inline) 0 0% 73.86% 486ms 1.37% std::allocator_traits::allocate (inline) 20ms 0.056% 73.92% 483ms 1.36% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 73.92% 483ms 1.36% boost::numeric::ublas::vector::vector (inline) 0 0% 73.92% 482ms 1.36% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 73.92% 462ms 1.30% std::_Rb_tree::_M_create_node (inline) 3ms 0.0085% 73.93% 450ms 1.27% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 0 0% 73.93% 446ms 1.26% AbstractCellBasedSimulation::DoCellRemoval (inline) 6ms 0.017% 73.94% 446ms 1.26% AbstractCellPopulation::GetCellUsingLocationIndex 380ms 1.07% 75.02% 430ms 1.21% _int_free 7ms 0.02% 75.04% 425ms 1.20% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 75.04% 409ms 1.15% boost::numeric::ublas::norm_2 (inline) 326ms 0.92% 75.96% 409ms 1.15% boost::numeric::ublas::vector_norm_2::apply (inline) 32ms 0.09% 76.05% 406ms 1.15% boost::detail::shared_count::~shared_count (inline) 0 0% 76.05% 406ms 1.15% boost::shared_ptr::~shared_ptr (inline) 0 0% 76.05% 404ms 1.14% std::_Rb_tree::_M_get_node (inline) 398ms 1.12% 77.17% 398ms 1.12% Node::GetIndex 3ms 0.0085% 77.18% 376ms 1.06% AbstractCellProperty::IsSubType (inline) 362ms 1.02% 78.20% 367ms 1.04% boost::detail::sp_counted_base::release 135ms 0.38% 78.58% 344ms 0.97% std::_Rb_tree::_M_erase 113ms 0.32% 78.90% 337ms 0.95% Node::GetRadius 1ms 0.0028% 78.90% 323ms 0.91% NodesOnlyMesh::ReMesh 0 0% 78.90% 318ms 0.9% boost::numeric::ublas::inner_prod (inline) 2ms 0.0056% 78.91% 316ms 0.89% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 1ms 0.0028% 78.91% 316ms 0.89% std::_Rb_tree::_Rb_tree (partial-inline) 21ms 0.059% 78.97% 314ms 0.89% boost::numeric::ublas::vector_scalar_binary::evaluate 32ms 0.09% 79.06% 314ms 0.89% std::_Rb_tree::_M_copy (inline) 312ms 0.88% 79.94% 312ms 0.88% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 1ms 0.0028% 79.94% 311ms 0.88% NodesOnlyMesh::UpdateNodeIndices 8ms 0.023% 79.97% 310ms 0.87% NodeBasedCellPopulation::UpdateMapsAfterRemesh 10ms 0.028% 79.99% 300ms 0.85% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 79.99% 299ms 0.84% std::_Rb_tree::_Alloc_node::operator() (inline) 298ms 0.84% 80.83% 298ms 0.84% __gnu_cxx::__normal_iterator::operator++ (inline) 292ms 0.82% 81.66% 292ms 0.82% [libchaste_cell_based.so] 0 0% 81.66% 290ms 0.82% NodesOnlyMesh::UpdateBoxCollection 33ms 0.093% 81.75% 282ms 0.8% std::_Rb_tree::_M_clone_node (inline) 0 0% 81.75% 280ms 0.79% Cell::HasCellProperty (inline) 1ms 0.0028% 81.75% 280ms 0.79% CellPropertyCollection::HasProperty 9ms 0.025% 81.78% 271ms 0.76% std::_Rb_tree::_M_emplace_hint_unique 15ms 0.042% 81.82% 269ms 0.76% Cell::ReadyToDivide 5ms 0.014% 81.84% 267ms 0.75% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 81.84% 259ms 0.73% boost::numeric::ublas::c_vector::assign (inline) 130ms 0.37% 82.20% 259ms 0.73% std::__find_if (inline) 0 0% 82.20% 259ms 0.73% std::find_if (inline) 0 0% 82.20% 259ms 0.73% std::none_of (inline) 140ms 0.4% 82.60% 257ms 0.73% _int_malloc 5ms 0.014% 82.61% 251ms 0.71% DistributedBoxCollection::GetProcessOwningNode 87ms 0.25% 82.86% 243ms 0.69% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 82.86% 238ms 0.67% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 82.86% 236ms 0.67% VtkMeshWriter::WriteFiles 52ms 0.15% 83.01% 234ms 0.66% std::__new_allocator::deallocate (inline) 233ms 0.66% 83.66% 233ms 0.66% Node::CheckForNodeAttributes 233ms 0.66% 84.32% 233ms 0.66% NodeBasedCellPopulation::GetNode 102ms 0.29% 84.61% 228ms 0.64% std::__move_median_to_first (inline) 1ms 0.0028% 84.61% 225ms 0.63% NodesOnlyMesh::AddNodesToBoxes 0 0% 84.61% 212ms 0.6% tcache_get (inline) 212ms 0.6% 85.21% 212ms 0.6% tcache_get_n (inline) 211ms 0.6% 85.80% 211ms 0.6% boost::numeric::ublas::c_vector::size (inline) 206ms 0.58% 86.39% 206ms 0.58% boost::numeric::ublas::scalar_plus_assign::apply (inline) 0 0% 86.39% 204ms 0.58% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 86.39% 202ms 0.57% vtkStreamingDemandDrivenPipeline::Update 0 0% 86.39% 202ms 0.57% vtkXMLWriterBase::Write 0 0% 86.39% 201ms 0.57% NodesOnlyMesh::ResizeBoxCollection 1ms 0.0028% 86.39% 201ms 0.57% vtkDemandDrivenPipeline::ProcessRequest 0 0% 86.39% 201ms 0.57% vtkStreamingDemandDrivenPipeline::ProcessRequest 16ms 0.045% 86.43% 200ms 0.56% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 86.43% 200ms 0.56% vtkDemandDrivenPipeline::ExecuteData 199ms 0.56% 87.00% 199ms 0.56% Node::rGetLocation 14ms 0.04% 87.04% 199ms 0.56% std::_Rb_tree::~_Rb_tree (inline) 0 0% 87.04% 199ms 0.56% vtkCompositeDataPipeline::ExecuteData 0 0% 87.04% 199ms 0.56% vtkExecutive::CallAlgorithm 0 0% 87.04% 199ms 0.56% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 87.04% 194ms 0.55% std::_Rb_tree::_M_drop_node (inline) 193ms 0.54% 87.58% 193ms 0.54% __strcmp_avx2 0 0% 87.58% 193ms 0.54% boost::numeric::ublas::vector_reference::size (inline) 8ms 0.023% 87.60% 192ms 0.54% AbstractCellProperty::IsType (inline) 192ms 0.54% 88.14% 192ms 0.54% boost::shared_ptr::operator-> (inline) 0 0% 88.14% 188ms 0.53% std::set::set (inline) 29ms 0.082% 88.23% 187ms 0.53% std::__insertion_sort (inline) 182ms 0.51% 88.74% 182ms 0.51% [libchaste_mesh.so] 140ms 0.4% 89.13% 178ms 0.5% Node::AddAppliedForceContribution 0 0% 89.13% 178ms 0.5% std::_Rb_tree::clear (inline)