File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 31326ms, 89.60% of 34963ms total Dropped 832 nodes (cum <= 174.81ms) flat flat% sum% cum cum% 0 0% 0% 34821ms 99.59% __libc_start_call_main 0 0% 0% 34821ms 99.59% __libc_start_main_impl 0 0% 0% 34821ms 99.59% _start 0 0% 0% 34804ms 99.55% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 34804ms 99.55% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 34804ms 99.55% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 34804ms 99.55% main 0 0% 0% 34766ms 99.44% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 34766ms 99.44% CxxTest::TestRunner::runTest (inline) 0 0% 0% 34766ms 99.44% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 34757ms 99.41% AbstractCellBasedSimulation::Solve 4ms 0.011% 0.011% 24355ms 69.66% OffLatticeSimulation::UpdateCellLocationsAndTopology 3ms 0.0086% 0.02% 19477ms 55.71% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.017% 0.037% 19294ms 55.18% AbstractNumericalMethod::ComputeForcesIncludingDamping 193ms 0.55% 0.59% 18351ms 52.49% AbstractTwoBodyInteractionForce::AddForceContribution 1562ms 4.47% 5.06% 15455ms 44.20% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4210ms 12.04% 17.10% 9424ms 26.95% std::_Rb_tree::_M_lower_bound (inline) 0 0% 17.10% 9183ms 26.26% AbstractCellBasedSimulation::UpdateCellPopulation 328ms 0.94% 18.04% 8469ms 24.22% std::_Rb_tree::find (inline) 0 0% 18.04% 8469ms 24.22% std::map::find (inline) 151ms 0.43% 18.47% 8232ms 23.54% NodesOnlyMesh::GetNodeOrHaloNode 3ms 0.0086% 18.48% 8112ms 23.20% NodeBasedCellPopulation::Update 441ms 1.26% 19.74% 8091ms 23.14% AbstractMesh::GetNode 313ms 0.9% 20.63% 7658ms 21.90% NodesOnlyMesh::SolveNodeMapping 203ms 0.58% 21.21% 6592ms 18.85% boost::numeric::ublas::vector_assign (inline) 208ms 0.59% 21.81% 6423ms 18.37% boost::numeric::ublas::c_vector::c_vector (partial-inline) 2ms 0.0057% 21.81% 6020ms 17.22% DistributedBoxCollection::CalculateInteriorNodePairs 5196ms 14.86% 36.68% 5196ms 14.86% std::_Rb_tree::_S_right (inline) 23ms 0.066% 36.74% 4523ms 12.94% NodeAttributes::RemoveDuplicateNeighbours 0 0% 36.74% 4523ms 12.94% OffLatticeSimulation::ApplyBoundaries 8ms 0.023% 36.76% 4343ms 12.42% std::__sort (inline) 0 0% 36.76% 4343ms 12.42% std::sort (inline) 1190ms 3.40% 40.17% 3646ms 10.43% boost::numeric::ublas::indexing_vector_assign 4ms 0.011% 40.18% 3373ms 9.65% AbstractCellPopulation::Iterator::operator++ (inline) 201ms 0.57% 40.75% 3340ms 9.55% AbstractCellPopulation::Iterator::IsRealCell 61ms 0.17% 40.93% 3296ms 9.43% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 32ms 0.092% 41.02% 2842ms 8.13% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 184ms 0.53% 41.55% 2538ms 7.26% std::__introsort_loop 35ms 0.1% 41.65% 2357ms 6.74% PlaneBoundaryCondition::ImposeBoundaryCondition 46ms 0.13% 41.78% 2287ms 6.54% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.0029% 41.78% 2279ms 6.52% std::__unguarded_partition_pivot (inline) 12ms 0.034% 41.82% 2166ms 6.20% PlaneBoundaryCondition::VerifyBoundaryCondition 234ms 0.67% 42.48% 2127ms 6.08% DistributedBoxCollection::AddPairsFromBox 1044ms 2.99% 45.47% 2036ms 5.82% std::__unguarded_partition (inline) 194ms 0.55% 46.03% 1865ms 5.33% std::map::operator[] (partial-inline) 2ms 0.0057% 46.03% 1796ms 5.14% std::__final_insertion_sort (inline) 1705ms 4.88% 50.91% 1705ms 4.88% boost::numeric::ublas::same_impl_ex 85ms 0.24% 51.15% 1603ms 4.58% std::__unguarded_insertion_sort (inline) 557ms 1.59% 52.74% 1590ms 4.55% std::__unguarded_linear_insert (inline) 130ms 0.37% 53.12% 1585ms 4.53% AbstractMesh::GetVectorFromAtoB 1499ms 4.29% 57.40% 1499ms 4.29% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 57.40% 1382ms 3.95% std::_Rb_tree::lower_bound (inline) 0 0% 57.40% 1382ms 3.95% std::map::lower_bound (inline) 0 0% 57.40% 1283ms 3.67% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 57.40% 1270ms 3.63% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1ms 0.0029% 57.41% 1194ms 3.42% NodeBasedCellPopulation::UpdateCellProcessLocation 21ms 0.06% 57.47% 1156ms 3.31% boost::numeric::ublas::detail::expression_type_check (inline) 1136ms 3.25% 60.72% 1136ms 3.25% boost::numeric::ublas::c_vector::operator() 219ms 0.63% 61.34% 1102ms 3.15% boost::numeric::ublas::detail::equals 8ms 0.023% 61.36% 1081ms 3.09% DistributedBoxCollection::CalculateBoundaryNodePairs 177ms 0.51% 61.87% 1034ms 2.96% boost::numeric::ublas::vector_binary::size (inline) 123ms 0.35% 62.22% 964ms 2.76% std::__new_allocator::allocate (inline) 214ms 0.61% 62.83% 940ms 2.69% NodeAttributes::AddAppliedForceContribution 323ms 0.92% 63.76% 888ms 2.54% __GI___libc_free 2ms 0.0057% 63.76% 859ms 2.46% AbstractCentreBasedCellPopulation::GetDampingConstant 89ms 0.25% 64.02% 844ms 2.41% operator new 0 0% 64.02% 841ms 2.41% boost::numeric::ublas::norm_inf (inline) 463ms 1.32% 65.34% 841ms 2.41% boost::numeric::ublas::vector_norm_inf::apply (inline) 316ms 0.9% 66.25% 825ms 2.36% NodeAttributes::AddNeighbour 393ms 1.12% 67.37% 791ms 2.26% DistributedBoxCollection::CalculateContainingBox (partial-inline) 16ms 0.046% 67.42% 786ms 2.25% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 248ms 0.71% 68.13% 753ms 2.15% __GI___libc_malloc 554ms 1.58% 69.71% 745ms 2.13% __dynamic_cast 0 0% 69.71% 743ms 2.13% AbstractCellPopulation::WriteResultsToFiles 33ms 0.094% 69.81% 737ms 2.11% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 69.81% 726ms 2.08% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 69.81% 726ms 2.08% boost::numeric::ublas::c_vector::plus_assign (inline) 700ms 2.00% 71.81% 700ms 2.00% std::_Rb_tree_increment 1ms 0.0029% 71.81% 634ms 1.81% AbstractCellBasedSimulation::DoCellBirth 9ms 0.026% 71.84% 621ms 1.78% CellPropertyCollection::GetPropertiesType (inline) 507ms 1.45% 73.29% 614ms 1.76% std::vector::push_back (inline) 520ms 1.49% 74.77% 561ms 1.60% _int_free 2ms 0.0057% 74.78% 549ms 1.57% Cell::GetMutationState 21ms 0.06% 74.84% 514ms 1.47% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 74.84% 514ms 1.47% boost::numeric::ublas::vector::vector (inline) 2ms 0.0057% 74.84% 476ms 1.36% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 74.84% 471ms 1.35% std::allocator_traits::allocate (inline) 446ms 1.28% 76.12% 446ms 1.28% Node::GetIndex 1ms 0.0029% 76.12% 443ms 1.27% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 0 0% 76.12% 442ms 1.26% boost::numeric::ublas::norm_2 (inline) 358ms 1.02% 77.15% 442ms 1.26% boost::numeric::ublas::vector_norm_2::apply (inline) 4ms 0.011% 77.16% 441ms 1.26% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 77.16% 440ms 1.26% std::_Rb_tree::_M_create_node (inline) 0 0% 77.16% 435ms 1.24% AbstractCellBasedSimulation::DoCellRemoval (inline) 11ms 0.031% 77.19% 423ms 1.21% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 77.19% 376ms 1.08% std::_Rb_tree::_M_get_node (inline) 135ms 0.39% 77.58% 368ms 1.05% Node::GetRadius 26ms 0.074% 77.65% 366ms 1.05% boost::detail::shared_count::~shared_count (inline) 0 0% 77.65% 366ms 1.05% boost::shared_ptr::~shared_ptr (inline) 333ms 0.95% 78.60% 337ms 0.96% boost::detail::sp_counted_base::release 2ms 0.0057% 78.61% 331ms 0.95% AbstractCellProperty::IsSubType (inline) 330ms 0.94% 79.55% 330ms 0.94% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 10ms 0.029% 79.58% 326ms 0.93% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 79.58% 325ms 0.93% boost::numeric::ublas::inner_prod (inline) 1ms 0.0029% 79.58% 323ms 0.92% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 20ms 0.057% 79.64% 322ms 0.92% boost::numeric::ublas::vector_scalar_binary::evaluate 6ms 0.017% 79.66% 315ms 0.9% NodeBasedCellPopulation::UpdateMapsAfterRemesh 11ms 0.031% 79.69% 311ms 0.89% std::_Rb_tree::_M_copy (inline) 0 0% 79.69% 308ms 0.88% NodesOnlyMesh::ReMesh 1ms 0.0029% 79.69% 301ms 0.86% NodesOnlyMesh::UpdateNodeIndices 58ms 0.17% 79.86% 300ms 0.86% std::_Rb_tree::_M_clone_node (inline) 299ms 0.86% 80.71% 299ms 0.86% __gnu_cxx::__normal_iterator::operator++ (inline) 13ms 0.037% 80.75% 289ms 0.83% std::_Rb_tree::_M_emplace_hint_unique 0 0% 80.75% 288ms 0.82% std::_Rb_tree::_Alloc_node::operator() (inline) 146ms 0.42% 81.17% 285ms 0.82% _int_malloc 281ms 0.8% 81.97% 281ms 0.8% [libchaste_cell_based.so] 7ms 0.02% 81.99% 278ms 0.8% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 81.99% 277ms 0.79% NodesOnlyMesh::UpdateBoxCollection 3ms 0.0086% 82.00% 275ms 0.79% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 117ms 0.33% 82.34% 272ms 0.78% std::_Rb_tree::_M_erase (partial-inline) 2ms 0.0057% 82.34% 268ms 0.77% CellPropertyCollection::HasProperty 0 0% 82.34% 266ms 0.76% Cell::HasCellProperty (inline) 3ms 0.0086% 82.35% 261ms 0.75% DistributedBoxCollection::GetProcessOwningNode 106ms 0.3% 82.65% 256ms 0.73% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 82.65% 252ms 0.72% boost::numeric::ublas::c_vector::assign (inline) 4ms 0.011% 82.66% 251ms 0.72% Cell::ReadyToDivide 248ms 0.71% 83.37% 248ms 0.71% Node::rGetLocation 244ms 0.7% 84.07% 244ms 0.7% Node::CheckForNodeAttributes 0 0% 84.07% 240ms 0.69% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 84.07% 240ms 0.69% VtkMeshWriter::WriteFiles 104ms 0.3% 84.37% 237ms 0.68% std::__move_median_to_first (inline) 1ms 0.0029% 84.37% 233ms 0.67% NodesOnlyMesh::AddNodesToBoxes 0 0% 84.37% 222ms 0.63% tcache_get (inline) 222ms 0.63% 85.01% 222ms 0.63% tcache_get_n (inline) 0 0% 85.01% 220ms 0.63% NodesOnlyMesh::ResizeBoxCollection 6ms 0.017% 85.02% 219ms 0.63% NodesOnlyMesh::IsANodeCloseToDomainBoundary 215ms 0.61% 85.64% 215ms 0.61% NodeBasedCellPopulation::GetNode 157ms 0.45% 86.09% 210ms 0.6% Node::AddAppliedForceContribution 99ms 0.28% 86.37% 210ms 0.6% std::__find_if (inline) 0 0% 86.37% 210ms 0.6% std::find_if (inline) 0 0% 86.37% 210ms 0.6% std::none_of (inline) 206ms 0.59% 86.96% 206ms 0.59% boost::numeric::ublas::c_vector::size (inline) 1ms 0.0029% 86.96% 203ms 0.58% vtkXMLWriterBase::Write 0 0% 86.96% 202ms 0.58% vtkStreamingDemandDrivenPipeline::Update 0 0% 86.96% 201ms 0.57% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 86.96% 201ms 0.57% vtkDemandDrivenPipeline::ProcessRequest 200ms 0.57% 87.54% 200ms 0.57% [libchaste_mesh.so] 0 0% 87.54% 200ms 0.57% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 87.54% 199ms 0.57% vtkDemandDrivenPipeline::ExecuteData 0 0% 87.54% 199ms 0.57% vtkExecutive::CallAlgorithm 0 0% 87.54% 198ms 0.57% vtkCompositeDataPipeline::ExecuteData 0 0% 87.54% 198ms 0.57% vtkXMLUnstructuredDataWriter::ProcessRequest 194ms 0.55% 88.09% 194ms 0.55% boost::numeric::ublas::scalar_plus_assign::apply (inline) 10ms 0.029% 88.12% 191ms 0.55% std::__insertion_sort (inline) 190ms 0.54% 88.66% 190ms 0.54% __strcmp_avx2 113ms 0.32% 88.99% 189ms 0.54% Node::AddNeighbour 28ms 0.08% 89.07% 188ms 0.54% std::__new_allocator::deallocate (inline) 0 0% 89.07% 188ms 0.54% std::set::set (inline) 182ms 0.52% 89.59% 182ms 0.52% Node::IsDeleted 0 0% 89.59% 182ms 0.52% boost::numeric::ublas::vector_reference::size (inline) 4ms 0.011% 89.60% 178ms 0.51% AbstractCellProperty::IsType (inline)