File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20219ms, 88.02% of 22971ms total Dropped 770 nodes (cum <= 114.86ms) flat flat% sum% cum cum% 0 0% 0% 22824ms 99.36% __libc_start_call_main 0 0% 0% 22824ms 99.36% __libc_start_main_impl 0 0% 0% 22824ms 99.36% _start 0 0% 0% 22809ms 99.29% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 22809ms 99.29% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 22809ms 99.29% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 22809ms 99.29% main 0 0% 0% 22771ms 99.13% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 22771ms 99.13% CxxTest::TestRunner::runTest (inline) 0 0% 0% 22771ms 99.13% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 2ms 0.0087% 0.0087% 22763ms 99.09% AbstractCellBasedSimulation::Solve 2ms 0.0087% 0.017% 13018ms 56.67% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.017% 8619ms 37.52% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.013% 0.03% 8144ms 35.45% ForwardEulerNumericalMethod::UpdateAllNodePositions 12ms 0.052% 0.083% 7971ms 34.70% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.083% 7623ms 33.19% NodeBasedCellPopulation::Update 1197ms 5.21% 5.29% 7396ms 32.20% RepulsionForce::AddForceContribution (partial-inline) 9ms 0.039% 5.33% 5514ms 24.00% DistributedBoxCollection::CalculateInteriorNodePairs 2166ms 9.43% 14.76% 4907ms 21.36% std::_Rb_tree::_M_lower_bound (inline) 0 0% 14.76% 4552ms 19.82% OffLatticeSimulation::ApplyBoundaries 19ms 0.083% 14.84% 4491ms 19.55% NodeAttributes::RemoveDuplicateNeighbours 9ms 0.039% 14.88% 4203ms 18.30% std::__sort (inline) 0 0% 14.88% 4203ms 18.30% std::sort (inline) 210ms 0.91% 15.80% 3774ms 16.43% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 4ms 0.017% 15.82% 3409ms 14.84% AbstractCellPopulation::Iterator::operator++ (inline) 258ms 1.12% 16.94% 3387ms 14.74% AbstractCellPopulation::Iterator::IsRealCell (inline) 68ms 0.3% 17.23% 3328ms 14.49% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 204ms 0.89% 18.12% 3139ms 13.67% std::_Rb_tree::find (inline) 0 0% 18.12% 3139ms 13.67% std::map::find (inline) 18ms 0.078% 18.20% 2815ms 12.25% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2693ms 11.72% 29.92% 2693ms 11.72% std::_Rb_tree::_S_right (inline) 238ms 1.04% 30.96% 2504ms 10.90% std::map::operator[] (partial-inline) 35ms 0.15% 31.11% 2370ms 10.32% PlaneBoundaryCondition::ImposeBoundaryCondition 183ms 0.8% 31.91% 2336ms 10.17% std::__introsort_loop 56ms 0.24% 32.15% 2238ms 9.74% NodesOnlyMesh::GetNodeOrHaloNode 138ms 0.6% 32.75% 2237ms 9.74% AbstractMesh::GetNode 31ms 0.13% 32.89% 2230ms 9.71% AbstractCellPopulation::GetLocationIndexUsingCell 17ms 0.074% 32.96% 2182ms 9.50% PlaneBoundaryCondition::VerifyBoundaryCondition 74ms 0.32% 33.29% 2100ms 9.14% NodesOnlyMesh::SolveNodeMapping 0 0% 33.29% 2061ms 8.97% std::__unguarded_partition_pivot (inline) 0 0% 33.29% 1992ms 8.67% std::_Rb_tree::lower_bound (inline) 0 0% 33.29% 1992ms 8.67% std::map::lower_bound (inline) 1ms 0.0044% 33.29% 1855ms 8.08% std::__final_insertion_sort (inline) 946ms 4.12% 37.41% 1844ms 8.03% std::__unguarded_partition (inline) 160ms 0.7% 38.10% 1750ms 7.62% DistributedBoxCollection::AddPairsFromBox 84ms 0.37% 38.47% 1663ms 7.24% std::__unguarded_insertion_sort (inline) 555ms 2.42% 40.89% 1612ms 7.02% std::__unguarded_linear_insert (inline) 25ms 0.11% 41.00% 1488ms 6.48% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 1465ms 6.38% 47.37% 1465ms 6.38% __gnu_cxx::__normal_iterator::operator-- (inline) 18ms 0.078% 47.45% 1459ms 6.35% AbstractCellPopulation::GetCellUsingLocationIndex 65ms 0.28% 47.73% 1297ms 5.65% boost::numeric::ublas::c_vector::c_vector (partial-inline) 36ms 0.16% 47.89% 1173ms 5.11% boost::numeric::ublas::vector_assign (inline) 7ms 0.03% 47.92% 1161ms 5.05% DistributedBoxCollection::CalculateBoundaryNodePairs 0 0% 47.92% 1110ms 4.83% NodeBasedCellPopulation::UpdateCellProcessLocation 293ms 1.28% 49.20% 1071ms 4.66% boost::numeric::ublas::indexing_vector_assign 231ms 1.01% 50.20% 907ms 3.95% __dynamic_cast 191ms 0.83% 51.03% 827ms 3.60% AbstractMesh::GetVectorFromAtoB 17ms 0.074% 51.11% 788ms 3.43% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 333ms 1.45% 52.56% 729ms 3.17% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 52.56% 723ms 3.15% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 52.56% 708ms 3.08% boost::numeric::ublas::norm_2 (inline) 556ms 2.42% 54.98% 708ms 3.08% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 54.98% 708ms 3.08% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 188ms 0.82% 55.80% 700ms 3.05% NodeAttributes::AddNeighbour 0 0% 55.80% 695ms 3.03% AbstractCellPopulation::WriteResultsToFiles 680ms 2.96% 58.76% 680ms 2.96% boost::numeric::ublas::c_vector::operator() 7ms 0.03% 58.79% 672ms 2.93% boost::numeric::ublas::c_vector::operator= (inline) 44ms 0.19% 58.98% 648ms 2.82% std::__copy_move::__copy_m (inline) 0 0% 58.98% 648ms 2.82% std::__copy_move_a (inline) 0 0% 58.98% 648ms 2.82% std::__copy_move_a1 (inline) 0 0% 58.98% 648ms 2.82% std::__copy_move_a2 (inline) 0 0% 58.98% 647ms 2.82% std::copy (inline) 624ms 2.72% 61.70% 624ms 2.72% __memcpy_avx_unaligned_erms 510ms 2.22% 63.92% 585ms 2.55% std::vector::push_back (inline) 269ms 1.17% 65.09% 568ms 2.47% __cxxabiv1::__si_class_type_info::__do_dyncast 3ms 0.013% 65.10% 527ms 2.29% AbstractCellBasedSimulation::DoCellBirth 2ms 0.0087% 65.11% 505ms 2.20% AbstractCentreBasedCellPopulation::GetDampingConstant 4ms 0.017% 65.13% 491ms 2.14% CellPropertyCollection::GetPropertiesType (inline) 489ms 2.13% 67.25% 489ms 2.13% boost::numeric::ublas::same_impl_ex 29ms 0.13% 67.38% 477ms 2.08% boost::detail::shared_count::~shared_count (inline) 0 0% 67.38% 477ms 2.08% boost::shared_ptr::~shared_ptr (inline) 68ms 0.3% 67.68% 476ms 2.07% std::__new_allocator::allocate (inline) 30ms 0.13% 67.81% 472ms 2.05% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 67.81% 469ms 2.04% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 67.81% 468ms 2.04% std::allocator_traits::allocate (inline) 1ms 0.0044% 67.81% 458ms 1.99% NodeBasedCellPopulation::WriteVtkResultsToFile 1ms 0.0044% 67.82% 452ms 1.97% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 450ms 1.96% 69.77% 450ms 1.96% __strcmp_avx2 0 0% 69.77% 449ms 1.95% std::_Rb_tree::_M_create_node (inline) 434ms 1.89% 71.66% 443ms 1.93% boost::detail::sp_counted_base::release 17ms 0.074% 71.74% 440ms 1.92% std::_Rb_tree::_Rb_tree (partial-inline) 429ms 1.87% 73.61% 429ms 1.87% std::_Rb_tree_increment 39ms 0.17% 73.78% 410ms 1.78% std::_Rb_tree::_M_copy (inline) 0 0% 73.78% 406ms 1.77% std::_Rb_tree::_M_get_node (inline) 34ms 0.15% 73.92% 404ms 1.76% operator new 117ms 0.51% 74.43% 394ms 1.72% std::_Rb_tree::_M_erase 1ms 0.0044% 74.44% 375ms 1.63% AbstractCellProperty::IsSubType (inline) 118ms 0.51% 74.95% 368ms 1.60% std::_Rb_tree::_M_clone_node (inline) 110ms 0.48% 75.43% 364ms 1.58% __GI___libc_malloc 130ms 0.57% 76.00% 353ms 1.54% Node::GetRadius 0 0% 76.00% 347ms 1.51% boost::numeric::ublas::inner_prod (inline) 2ms 0.0087% 76.00% 346ms 1.51% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 17ms 0.074% 76.08% 344ms 1.50% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 76.08% 341ms 1.48% boost::numeric::ublas::c_vector::assign (inline) 0 0% 76.08% 341ms 1.48% std::set::set (inline) 3ms 0.013% 76.09% 323ms 1.41% Cell::GetMutationState 5ms 0.022% 76.11% 321ms 1.40% NodeBasedCellPopulation::UpdateMapsAfterRemesh 25ms 0.11% 76.22% 318ms 1.38% boost::numeric::ublas::vector_binary::size (inline) 0 0% 76.22% 316ms 1.38% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 76.22% 309ms 1.35% NodesOnlyMesh::ReMesh 37ms 0.16% 76.38% 305ms 1.33% std::_Rb_tree::~_Rb_tree (inline) 304ms 1.32% 77.71% 304ms 1.32% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 2ms 0.0087% 77.72% 303ms 1.32% NodesOnlyMesh::UpdateNodeIndices 103ms 0.45% 78.16% 275ms 1.20% boost::numeric::ublas::vector_inner_prod::apply (inline) 8ms 0.035% 78.20% 274ms 1.19% std::_Rb_tree::_M_emplace_hint_unique 269ms 1.17% 79.37% 269ms 1.17% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 79.37% 265ms 1.15% std::_Rb_tree::_M_drop_node (inline) 0 0% 79.37% 261ms 1.14% NodesOnlyMesh::UpdateBoxCollection 259ms 1.13% 80.50% 259ms 1.13% std::__adjacent_find (inline) 0 0% 80.50% 259ms 1.13% std::__unique (inline) 0 0% 80.50% 259ms 1.13% std::unique (inline) 4ms 0.017% 80.51% 245ms 1.07% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 228ms 0.99% 81.51% 228ms 0.99% Node::CheckForNodeAttributes 2ms 0.0087% 81.52% 226ms 0.98% DistributedBoxCollection::GetProcessOwningNode 0 0% 81.52% 225ms 0.98% std::__new_allocator::deallocate (inline) 1ms 0.0044% 81.52% 224ms 0.98% NodesOnlyMesh::AddNodesToBoxes 0 0% 81.52% 224ms 0.98% std::set::~set (inline) 147ms 0.64% 82.16% 219ms 0.95% _int_malloc 0 0% 82.16% 217ms 0.94% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 82.16% 215ms 0.94% VtkMeshWriter::WriteFiles 110ms 0.48% 82.64% 215ms 0.94% std::__move_median_to_first (inline) 0 0% 82.64% 201ms 0.88% std::allocator_traits::deallocate (inline) 106ms 0.46% 83.10% 200ms 0.87% boost::shared_ptr::shared_ptr (inline) 71ms 0.31% 83.41% 198ms 0.86% __GI___libc_free 0 0% 83.41% 197ms 0.86% NodesOnlyMesh::ResizeBoxCollection 0 0% 83.41% 197ms 0.86% std::_Rb_tree::_M_put_node (inline) 13ms 0.057% 83.47% 196ms 0.85% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 83.47% 196ms 0.85% vtkStreamingDemandDrivenPipeline::Update 0 0% 83.47% 196ms 0.85% vtkXMLWriterBase::Write 0 0% 83.47% 194ms 0.84% vtkDemandDrivenPipeline::ProcessRequest 0 0% 83.47% 194ms 0.84% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 83.47% 193ms 0.84% vtkCompositeDataPipeline::ExecuteData 0 0% 83.47% 193ms 0.84% vtkDemandDrivenPipeline::ExecuteData 0 0% 83.47% 193ms 0.84% vtkExecutive::CallAlgorithm 0 0% 83.47% 192ms 0.84% vtkXMLUnstructuredDataWriter::ProcessRequest 15ms 0.065% 83.53% 191ms 0.83% std::__insertion_sort (inline) 188ms 0.82% 84.35% 188ms 0.82% Node::GetIndex 0 0% 84.35% 172ms 0.75% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 84.35% 172ms 0.75% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 1ms 0.0044% 84.35% 171ms 0.74% CellPropertyCollection::HasProperty 0 0% 84.35% 170ms 0.74% Cell::HasCellProperty (inline) 170ms 0.74% 85.09% 170ms 0.74% [libchaste_cell_based.so] 0 0% 85.09% 170ms 0.74% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 3ms 0.013% 85.11% 161ms 0.7% Cell::ReadyToDivide 88ms 0.38% 85.49% 158ms 0.69% Node::AddNeighbour 15ms 0.065% 85.56% 156ms 0.68% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 85.56% 154ms 0.67% AbstractCellProperty::IsType (inline) 149ms 0.65% 86.20% 149ms 0.65% [libchaste_mesh.so] 0 0% 86.20% 143ms 0.62% std::_Rb_tree::clear (inline) 0 0% 86.20% 141ms 0.61% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 86.20% 141ms 0.61% vtkXMLWriter::WriteBinaryData 0 0% 86.20% 139ms 0.61% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 86.20% 137ms 0.6% vtkXMLWriter::WriteBinaryDataBlock 0 0% 86.20% 137ms 0.6% vtkXMLWriter::WriteBinaryDataInternal 0 0% 86.20% 137ms 0.6% vtkXMLWriter::WriteCompressionBlock 1ms 0.0044% 86.21% 134ms 0.58% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 86.21% 133ms 0.58% std::_Rb_tree::_Auto_node::_Auto_node (inline) 3ms 0.013% 86.22% 129ms 0.56% boost::numeric::ublas::c_vector::operator[] (inline) 2ms 0.0087% 86.23% 128ms 0.56% AbstractCellPopulation::SetCellUsingLocationIndex 3ms 0.013% 86.24% 128ms 0.56% DistributedBoxCollection::GetIsPeriodicAllDims 113ms 0.49% 86.74% 126ms 0.55% _int_free 0 0% 86.74% 126ms 0.55% vtkXMLWriter::WritePointsAppendedData 124ms 0.54% 87.28% 124ms 0.54% Node::IsDeleted 1ms 0.0044% 87.28% 119ms 0.52% std::_Rb_tree::_M_insert_unique 0 0% 87.28% 119ms 0.52% std::set::insert (inline) 117ms 0.51% 87.79% 117ms 0.51% boost::shared_ptr::operator-> (inline) 45ms 0.2% 87.98% 116ms 0.5% AbstractCellProperty::IsSame 8ms 0.035% 88.02% 115ms 0.5% AbstractNumericalMethod::SafeNodePositionUpdate