File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 30338ms, 87.63% of 34621ms total Dropped 805 nodes (cum <= 173.10ms) flat flat% sum% cum cum% 0 0% 0% 34479ms 99.59% __libc_start_call_main 0 0% 0% 34479ms 99.59% __libc_start_main_impl 0 0% 0% 34479ms 99.59% _start 0 0% 0% 34462ms 99.54% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 34462ms 99.54% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 34462ms 99.54% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 34462ms 99.54% main 0 0% 0% 34427ms 99.44% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 34427ms 99.44% CxxTest::TestRunner::runTest (inline) 0 0% 0% 34427ms 99.44% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 34419ms 99.42% AbstractCellBasedSimulation::Solve 2ms 0.0058% 0.0058% 23965ms 69.22% OffLatticeSimulation::UpdateCellLocationsAndTopology 5ms 0.014% 0.02% 18966ms 54.78% ForwardEulerNumericalMethod::UpdateAllNodePositions 20ms 0.058% 0.078% 18768ms 54.21% AbstractNumericalMethod::ComputeForcesIncludingDamping 187ms 0.54% 0.62% 17922ms 51.77% AbstractTwoBodyInteractionForce::AddForceContribution 1460ms 4.22% 4.84% 15013ms 43.36% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4377ms 12.64% 17.48% 9755ms 28.18% std::_Rb_tree::_M_lower_bound (inline) 0 0% 17.48% 9223ms 26.64% AbstractCellBasedSimulation::UpdateCellPopulation 354ms 1.02% 18.50% 8924ms 25.78% std::_Rb_tree::find (inline) 0 0% 18.50% 8924ms 25.78% std::map::find (inline) 158ms 0.46% 18.96% 8604ms 24.85% NodesOnlyMesh::GetNodeOrHaloNode 476ms 1.37% 20.33% 8437ms 24.37% AbstractMesh::GetNode 0 0% 20.33% 8103ms 23.40% NodeBasedCellPopulation::Update 315ms 0.91% 21.24% 7961ms 22.99% NodesOnlyMesh::SolveNodeMapping 218ms 0.63% 21.87% 6110ms 17.65% boost::numeric::ublas::vector_assign (inline) 6ms 0.017% 21.89% 6026ms 17.41% DistributedBoxCollection::CalculateInteriorNodePairs 168ms 0.49% 22.37% 5987ms 17.29% boost::numeric::ublas::c_vector::c_vector (partial-inline) 5352ms 15.46% 37.83% 5352ms 15.46% std::_Rb_tree::_S_right (inline) 0 0% 37.83% 4677ms 13.51% OffLatticeSimulation::ApplyBoundaries 19ms 0.055% 37.89% 4565ms 13.19% NodeAttributes::RemoveDuplicateNeighbours 11ms 0.032% 37.92% 4376ms 12.64% std::__sort (inline) 0 0% 37.92% 4376ms 12.64% std::sort (inline) 1133ms 3.27% 41.19% 3570ms 10.31% boost::numeric::ublas::indexing_vector_assign 4ms 0.012% 41.20% 3533ms 10.20% AbstractCellPopulation::Iterator::operator++ (inline) 64ms 0.18% 41.39% 3513ms 10.15% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 197ms 0.57% 41.96% 3506ms 10.13% AbstractCellPopulation::Iterator::IsRealCell (inline) 27ms 0.078% 42.04% 3015ms 8.71% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 214ms 0.62% 42.65% 2539ms 7.33% std::__introsort_loop 32ms 0.092% 42.75% 2461ms 7.11% PlaneBoundaryCondition::ImposeBoundaryCondition 38ms 0.11% 42.86% 2377ms 6.87% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.0029% 42.86% 2238ms 6.46% std::__unguarded_partition_pivot (inline) 13ms 0.038% 42.90% 2216ms 6.40% PlaneBoundaryCondition::VerifyBoundaryCondition 246ms 0.71% 43.61% 2093ms 6.05% DistributedBoxCollection::AddPairsFromBox 1047ms 3.02% 46.63% 2005ms 5.79% std::__unguarded_partition (inline) 2ms 0.0058% 46.64% 1824ms 5.27% std::__final_insertion_sort (inline) 208ms 0.6% 47.24% 1737ms 5.02% std::map::operator[] (partial-inline) 1726ms 4.99% 52.22% 1726ms 4.99% boost::numeric::ublas::same_impl_ex 102ms 0.29% 52.52% 1613ms 4.66% std::__unguarded_insertion_sort (inline) 599ms 1.73% 54.25% 1566ms 4.52% std::__unguarded_linear_insert (inline) 127ms 0.37% 54.61% 1481ms 4.28% AbstractMesh::GetVectorFromAtoB 1441ms 4.16% 58.78% 1441ms 4.16% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 58.78% 1324ms 3.82% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 58.78% 1309ms 3.78% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 58.78% 1275ms 3.68% std::_Rb_tree::lower_bound (inline) 0 0% 58.78% 1275ms 3.68% std::map::lower_bound (inline) 0 0% 58.78% 1165ms 3.37% NodeBasedCellPopulation::UpdateCellProcessLocation 1159ms 3.35% 62.12% 1159ms 3.35% boost::numeric::ublas::c_vector::operator() 7ms 0.02% 62.14% 1109ms 3.20% DistributedBoxCollection::CalculateBoundaryNodePairs 25ms 0.072% 62.22% 1101ms 3.18% boost::numeric::ublas::detail::expression_type_check (inline) 219ms 0.63% 62.85% 1049ms 3.03% boost::numeric::ublas::detail::equals 114ms 0.33% 63.18% 970ms 2.80% boost::numeric::ublas::vector_binary::size (inline) 256ms 0.74% 63.92% 924ms 2.67% NodeAttributes::AddAppliedForceContribution 27ms 0.078% 64.00% 840ms 2.43% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 281ms 0.81% 64.81% 806ms 2.33% NodeAttributes::AddNeighbour 0 0% 64.81% 791ms 2.28% boost::numeric::ublas::norm_inf (inline) 463ms 1.34% 66.14% 791ms 2.28% boost::numeric::ublas::vector_norm_inf::apply (inline) 5ms 0.014% 66.16% 774ms 2.24% AbstractCentreBasedCellPopulation::GetDampingConstant 364ms 1.05% 67.21% 769ms 2.22% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 67.21% 756ms 2.18% AbstractCellPopulation::WriteResultsToFiles 35ms 0.1% 67.31% 750ms 2.17% std::_Rb_tree_const_iterator::operator++ (inline) 305ms 0.88% 68.19% 722ms 2.09% __GI___libc_free 86ms 0.25% 68.44% 718ms 2.07% std::__new_allocator::allocate (inline) 506ms 1.46% 69.90% 709ms 2.05% __dynamic_cast 700ms 2.02% 71.92% 700ms 2.02% std::_Rb_tree_increment 4ms 0.012% 71.94% 668ms 1.93% AbstractCellBasedSimulation::DoCellBirth 0 0% 71.94% 668ms 1.93% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 71.94% 668ms 1.93% boost::numeric::ublas::c_vector::plus_assign (inline) 105ms 0.3% 72.24% 636ms 1.84% operator new 14ms 0.04% 72.28% 621ms 1.79% CellPropertyCollection::GetPropertiesType (inline) 523ms 1.51% 73.79% 601ms 1.74% std::vector::push_back (inline) 0 0% 73.79% 533ms 1.54% boost::numeric::ublas::norm_2 (inline) 412ms 1.19% 74.98% 533ms 1.54% boost::numeric::ublas::vector_norm_2::apply (inline) 2ms 0.0058% 74.99% 531ms 1.53% Cell::GetMutationState 176ms 0.51% 75.49% 527ms 1.52% __GI___libc_malloc 3ms 0.0087% 75.50% 494ms 1.43% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 75.50% 452ms 1.31% AbstractCellBasedSimulation::DoCellRemoval (inline) 5ms 0.014% 75.52% 436ms 1.26% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 361ms 1.04% 76.56% 415ms 1.20% _int_free 0 0% 76.56% 409ms 1.18% std::allocator_traits::allocate (inline) 379ms 1.09% 77.66% 379ms 1.09% Node::GetIndex 39ms 0.11% 77.77% 378ms 1.09% boost::detail::shared_count::~shared_count (inline) 0 0% 77.77% 378ms 1.09% boost::shared_ptr::~shared_ptr (inline) 0 0% 77.77% 370ms 1.07% std::_Rb_tree::_M_create_node (inline) 2ms 0.0058% 77.77% 351ms 1.01% AbstractCellProperty::IsSubType (inline) 38ms 0.11% 77.88% 347ms 1.00% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 77.88% 347ms 1.00% boost::numeric::ublas::vector::vector (inline) 1ms 0.0029% 77.89% 339ms 0.98% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 339ms 0.98% 78.87% 339ms 0.98% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 13ms 0.038% 78.90% 339ms 0.98% boost::numeric::ublas::vector_reference::operator() (inline) 3ms 0.0087% 78.91% 337ms 0.97% NodeBasedCellPopulation::UpdateMapsAfterRemesh 145ms 0.42% 79.33% 336ms 0.97% Node::GetRadius 5ms 0.014% 79.34% 335ms 0.97% AbstractCellPopulation::GetCellUsingLocationIndex 331ms 0.96% 80.30% 334ms 0.96% boost::detail::sp_counted_base::release 0 0% 80.30% 318ms 0.92% boost::numeric::ublas::inner_prod (inline) 17ms 0.049% 80.35% 317ms 0.92% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 80.35% 317ms 0.92% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 80.35% 313ms 0.9% std::_Rb_tree::_M_get_node (inline) 132ms 0.38% 80.73% 312ms 0.9% std::_Rb_tree::_M_erase (partial-inline) 293ms 0.85% 81.58% 293ms 0.85% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 81.58% 291ms 0.84% NodesOnlyMesh::ReMesh 0 0% 81.58% 279ms 0.81% boost::numeric::ublas::c_vector::assign (inline) 1ms 0.0029% 81.58% 276ms 0.8% NodesOnlyMesh::UpdateNodeIndices 0 0% 81.58% 268ms 0.77% NodesOnlyMesh::UpdateBoxCollection 6ms 0.017% 81.60% 264ms 0.76% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 261ms 0.75% 82.35% 261ms 0.75% [libchaste_cell_based.so] 258ms 0.75% 83.10% 258ms 0.75% NodeBasedCellPopulation::GetNode 99ms 0.29% 83.38% 257ms 0.74% boost::numeric::ublas::vector_inner_prod::apply (inline) 3ms 0.0087% 83.39% 254ms 0.73% std::_Rb_tree::_M_emplace_hint_unique 144ms 0.42% 83.81% 250ms 0.72% _int_malloc 6ms 0.017% 83.82% 248ms 0.72% DistributedBoxCollection::GetProcessOwningNode 2ms 0.0058% 83.83% 247ms 0.71% std::_Rb_tree::_Rb_tree (partial-inline) 31ms 0.09% 83.92% 242ms 0.7% std::_Rb_tree::_M_copy (inline) 0 0% 83.92% 240ms 0.69% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 83.92% 239ms 0.69% VtkMeshWriter::WriteFiles 180ms 0.52% 84.44% 237ms 0.68% Node::AddAppliedForceContribution 0 0% 84.44% 232ms 0.67% std::_Rb_tree::_Alloc_node::operator() (inline) 86ms 0.25% 84.69% 228ms 0.66% std::__move_median_to_first (inline) 0 0% 84.69% 227ms 0.66% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 84.69% 222ms 0.64% Cell::HasCellProperty (inline) 2ms 0.0058% 84.69% 222ms 0.64% CellPropertyCollection::HasProperty 16ms 0.046% 84.74% 220ms 0.64% Cell::ReadyToDivide 1ms 0.0029% 84.74% 214ms 0.62% NodesOnlyMesh::AddNodesToBoxes 209ms 0.6% 85.35% 209ms 0.6% Node::rGetLocation 34ms 0.098% 85.45% 209ms 0.6% std::_Rb_tree::_M_clone_node (inline) 18ms 0.052% 85.50% 209ms 0.6% std::__insertion_sort (inline) 207ms 0.6% 86.10% 207ms 0.6% [libchaste_mesh.so] 206ms 0.6% 86.69% 206ms 0.6% Node::CheckForNodeAttributes 0 0% 86.69% 205ms 0.59% vtkStreamingDemandDrivenPipeline::Update 0 0% 86.69% 205ms 0.59% vtkXMLWriterBase::Write 0 0% 86.69% 203ms 0.59% vtkDemandDrivenPipeline::ProcessRequest 0 0% 86.69% 202ms 0.58% NodesOnlyMesh::ResizeBoxCollection 11ms 0.032% 86.72% 201ms 0.58% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 86.72% 201ms 0.58% vtkExecutive::CallAlgorithm 0 0% 86.72% 201ms 0.58% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 86.72% 200ms 0.58% vtkXMLUnstructuredDataWriter::ProcessRequest 26ms 0.075% 86.80% 199ms 0.57% std::__new_allocator::deallocate (inline) 0 0% 86.80% 199ms 0.57% vtkCompositeDataPipeline::ExecuteData 0 0% 86.80% 199ms 0.57% vtkDemandDrivenPipeline::ExecuteData 94ms 0.27% 87.07% 196ms 0.57% std::__find_if (inline) 0 0% 87.07% 196ms 0.57% std::find_if (inline) 0 0% 87.07% 196ms 0.57% std::none_of (inline) 194ms 0.56% 87.63% 194ms 0.56% __strcmp_avx2 0 0% 87.63% 188ms 0.54% std::_Rb_tree::clear (inline) 0 0% 87.63% 174ms 0.5% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 87.63% 174ms 0.5% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData