File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 21288ms, 88.46% of 24065ms total Dropped 830 nodes (cum <= 120.33ms) flat flat% sum% cum cum% 0 0% 0% 23923ms 99.41% __libc_start_call_main 0 0% 0% 23923ms 99.41% __libc_start_main_impl 0 0% 0% 23923ms 99.41% _start 0 0% 0% 23907ms 99.34% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 23907ms 99.34% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 23907ms 99.34% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 23907ms 99.34% main 0 0% 0% 23867ms 99.18% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 23867ms 99.18% CxxTest::TestRunner::runTest (inline) 0 0% 0% 23866ms 99.17% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0042% 0.0042% 23859ms 99.14% AbstractCellBasedSimulation::Solve 0 0% 0.0042% 13481ms 56.02% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0042% 9164ms 38.08% AbstractCellBasedSimulation::UpdateCellPopulation 6ms 0.025% 0.029% 8568ms 35.60% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.033% 0.062% 8375ms 34.80% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.062% 8110ms 33.70% NodeBasedCellPopulation::Update 1154ms 4.80% 4.86% 7647ms 31.78% RepulsionForce::AddForceContribution (partial-inline) 10ms 0.042% 4.90% 6046ms 25.12% DistributedBoxCollection::CalculateInteriorNodePairs 2127ms 8.84% 13.74% 5014ms 20.84% std::_Rb_tree::_M_lower_bound (inline) 0 0% 13.74% 4558ms 18.94% OffLatticeSimulation::ApplyBoundaries 16ms 0.066% 13.80% 4486ms 18.64% NodeAttributes::RemoveDuplicateNeighbours 4ms 0.017% 13.82% 4315ms 17.93% std::__sort (inline) 0 0% 13.82% 4315ms 17.93% std::sort (inline) 176ms 0.73% 14.55% 4027ms 16.73% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 3ms 0.012% 14.56% 3386ms 14.07% AbstractCellPopulation::Iterator::operator++ (inline) 69ms 0.29% 14.85% 3365ms 13.98% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 204ms 0.85% 15.70% 3352ms 13.93% AbstractCellPopulation::Iterator::IsRealCell (inline) 240ms 1% 16.70% 3261ms 13.55% std::_Rb_tree::find (inline) 0 0% 16.70% 3260ms 13.55% std::map::find (inline) 2845ms 11.82% 28.52% 2845ms 11.82% std::_Rb_tree::_S_right (inline) 26ms 0.11% 28.63% 2813ms 11.69% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 269ms 1.12% 29.74% 2543ms 10.57% std::map::operator[] (partial-inline) 171ms 0.71% 30.46% 2451ms 10.18% std::__introsort_loop 32ms 0.13% 30.59% 2412ms 10.02% PlaneBoundaryCondition::ImposeBoundaryCondition 44ms 0.18% 30.77% 2327ms 9.67% AbstractCellPopulation::GetLocationIndexUsingCell 156ms 0.65% 31.42% 2308ms 9.59% AbstractMesh::GetNode 46ms 0.19% 31.61% 2286ms 9.50% NodesOnlyMesh::GetNodeOrHaloNode 1ms 0.0042% 31.61% 2199ms 9.14% std::__unguarded_partition_pivot (inline) 177ms 0.74% 32.35% 2156ms 8.96% DistributedBoxCollection::AddPairsFromBox 79ms 0.33% 32.68% 2155ms 8.95% NodesOnlyMesh::SolveNodeMapping 13ms 0.054% 32.73% 2146ms 8.92% PlaneBoundaryCondition::VerifyBoundaryCondition 0 0% 32.73% 2008ms 8.34% std::_Rb_tree::lower_bound (inline) 0 0% 32.73% 2008ms 8.34% std::map::lower_bound (inline) 1012ms 4.21% 36.94% 1973ms 8.20% std::__unguarded_partition (inline) 2ms 0.0083% 36.95% 1857ms 7.72% std::__final_insertion_sort (inline) 93ms 0.39% 37.33% 1651ms 6.86% std::__unguarded_insertion_sort (inline) 23ms 0.096% 37.43% 1642ms 6.82% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 16ms 0.066% 37.49% 1615ms 6.71% AbstractCellPopulation::GetCellUsingLocationIndex 584ms 2.43% 39.92% 1611ms 6.69% std::__unguarded_linear_insert (inline) 1479ms 6.15% 46.07% 1479ms 6.15% __gnu_cxx::__normal_iterator::operator-- (inline) 52ms 0.22% 46.28% 1341ms 5.57% boost::numeric::ublas::c_vector::c_vector (partial-inline) 42ms 0.17% 46.46% 1208ms 5.02% boost::numeric::ublas::vector_assign (inline) 0 0% 46.46% 1164ms 4.84% NodeBasedCellPopulation::UpdateCellProcessLocation 295ms 1.23% 47.68% 1089ms 4.53% boost::numeric::ublas::indexing_vector_assign 3ms 0.012% 47.70% 1063ms 4.42% DistributedBoxCollection::CalculateBoundaryNodePairs 238ms 0.99% 48.68% 877ms 3.64% __dynamic_cast 20ms 0.083% 48.77% 837ms 3.48% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 159ms 0.66% 49.43% 822ms 3.42% AbstractMesh::GetVectorFromAtoB 395ms 1.64% 51.07% 800ms 3.32% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 51.07% 741ms 3.08% AbstractCellPopulation::WriteResultsToFiles 0 0% 51.07% 731ms 3.04% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 185ms 0.77% 51.84% 730ms 3.03% NodeAttributes::AddNeighbour 721ms 3.00% 54.83% 721ms 3.00% boost::numeric::ublas::c_vector::operator() 0 0% 54.83% 705ms 2.93% boost::numeric::ublas::norm_2 (inline) 558ms 2.32% 57.15% 705ms 2.93% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 57.15% 705ms 2.93% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 5ms 0.021% 57.17% 675ms 2.80% boost::numeric::ublas::c_vector::operator= (inline) 36ms 0.15% 57.32% 673ms 2.80% std::_Rb_tree_const_iterator::operator++ (inline) 30ms 0.12% 57.45% 659ms 2.74% std::__copy_move::__copy_m (inline) 0 0% 57.45% 659ms 2.74% std::__copy_move_a (inline) 0 0% 57.45% 659ms 2.74% std::__copy_move_a1 (inline) 0 0% 57.45% 659ms 2.74% std::__copy_move_a2 (inline) 0 0% 57.45% 658ms 2.73% std::copy (inline) 647ms 2.69% 60.14% 647ms 2.69% __memcpy_avx_unaligned_erms 3ms 0.012% 60.15% 640ms 2.66% AbstractCentreBasedCellPopulation::GetDampingConstant 631ms 2.62% 62.77% 631ms 2.62% std::_Rb_tree_increment 5ms 0.021% 62.79% 630ms 2.62% CellPropertyCollection::GetPropertiesType (inline) 539ms 2.24% 65.03% 623ms 2.59% std::vector::push_back (inline) 1ms 0.0042% 65.04% 622ms 2.58% AbstractCellBasedSimulation::DoCellBirth 9ms 0.037% 65.07% 551ms 2.29% std::_Rb_tree::_Rb_tree (partial-inline) 98ms 0.41% 65.48% 544ms 2.26% std::__new_allocator::allocate (inline) 238ms 0.99% 66.47% 542ms 2.25% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 66.47% 525ms 2.18% std::allocator_traits::allocate (inline) 48ms 0.2% 66.67% 519ms 2.16% std::_Rb_tree::_M_copy (inline) 0 0% 66.67% 509ms 2.12% std::_Rb_tree::_M_create_node (inline) 2ms 0.0083% 66.68% 484ms 2.01% NodeBasedCellPopulation::WriteVtkResultsToFile 30ms 0.12% 66.80% 483ms 2.01% boost::detail::shared_count::~shared_count (inline) 0 0% 66.80% 483ms 2.01% boost::shared_ptr::~shared_ptr (inline) 168ms 0.7% 67.50% 468ms 1.94% std::_Rb_tree::_M_clone_node (inline) 467ms 1.94% 69.44% 467ms 1.94% boost::numeric::ublas::same_impl_ex 453ms 1.88% 71.32% 453ms 1.88% __strcmp_avx2 2ms 0.0083% 71.33% 450ms 1.87% Cell::GetMutationState 434ms 1.80% 73.14% 444ms 1.85% boost::detail::sp_counted_base::release 24ms 0.1% 73.23% 444ms 1.85% operator new 3ms 0.012% 73.25% 443ms 1.84% std::set::set (inline) 133ms 0.55% 73.80% 438ms 1.82% std::_Rb_tree::_M_erase 0 0% 73.80% 435ms 1.81% std::_Rb_tree::_M_get_node (inline) 0 0% 73.80% 432ms 1.80% AbstractCellBasedSimulation::DoCellRemoval (inline) 5ms 0.021% 73.82% 416ms 1.73% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 124ms 0.52% 74.34% 413ms 1.72% __GI___libc_malloc 122ms 0.51% 74.84% 405ms 1.68% Node::GetRadius 119ms 0.49% 75.34% 379ms 1.57% Node::AddNeighbour 2ms 0.0083% 75.35% 365ms 1.52% AbstractCellProperty::IsSubType (inline) 0 0% 75.35% 355ms 1.48% boost::numeric::ublas::c_vector::assign (inline) 0 0% 75.35% 348ms 1.45% std::_Rb_tree::_Alloc_node::operator() (inline) 21ms 0.087% 75.43% 339ms 1.41% boost::numeric::ublas::vector_binary::size (inline) 325ms 1.35% 76.78% 325ms 1.35% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 76.78% 318ms 1.32% NodesOnlyMesh::ReMesh 42ms 0.17% 76.96% 310ms 1.29% std::_Rb_tree::~_Rb_tree (inline) 0 0% 76.96% 309ms 1.28% boost::numeric::ublas::inner_prod (inline) 1ms 0.0042% 76.96% 309ms 1.28% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 6ms 0.025% 76.99% 308ms 1.28% NodeBasedCellPopulation::UpdateMapsAfterRemesh 2ms 0.0083% 77.00% 308ms 1.28% NodesOnlyMesh::UpdateNodeIndices 18ms 0.075% 77.07% 308ms 1.28% boost::numeric::ublas::vector_scalar_binary::evaluate 1ms 0.0042% 77.07% 301ms 1.25% NodesOnlyMesh::UpdateBoxCollection 299ms 1.24% 78.32% 299ms 1.24% __gnu_cxx::__normal_iterator::operator++ (inline) 290ms 1.21% 79.52% 290ms 1.21% Node::CheckForNodeAttributes 290ms 1.21% 80.73% 290ms 1.21% Node::ConstructNodeAttributes (inline) 0 0% 80.73% 286ms 1.19% std::_Rb_tree::_M_drop_node (inline) 4ms 0.017% 80.74% 270ms 1.12% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 2ms 0.0083% 80.75% 266ms 1.11% std::_Rb_tree::_M_emplace_hint_unique 4ms 0.017% 80.77% 258ms 1.07% std::__new_allocator::deallocate (inline) 6ms 0.025% 80.79% 253ms 1.05% DistributedBoxCollection::GetProcessOwningNode 147ms 0.61% 81.40% 250ms 1.04% _int_malloc 0 0% 81.40% 244ms 1.01% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 4ms 0.017% 81.42% 244ms 1.01% NodesOnlyMesh::AddNodesToBoxes 0 0% 81.42% 243ms 1.01% VtkMeshWriter::WriteFiles 0 0% 81.42% 238ms 0.99% Cell::HasCellProperty (inline) 2ms 0.0083% 81.43% 238ms 0.99% CellPropertyCollection::HasProperty 0 0% 81.43% 235ms 0.98% std::allocator_traits::deallocate (inline) 100ms 0.42% 81.85% 234ms 0.97% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 81.85% 230ms 0.96% std::_Rb_tree::_M_put_node (inline) 87ms 0.36% 82.21% 226ms 0.94% __GI___libc_free 10ms 0.042% 82.25% 223ms 0.93% Cell::ReadyToDivide 103ms 0.43% 82.68% 219ms 0.91% std::__move_median_to_first (inline) 0 0% 82.68% 218ms 0.91% std::set::~set (inline) 1ms 0.0042% 82.68% 212ms 0.88% NodesOnlyMesh::ResizeBoxCollection 211ms 0.88% 83.56% 211ms 0.88% Node::GetIndex 16ms 0.066% 83.62% 209ms 0.87% NodesOnlyMesh::IsANodeCloseToDomainBoundary 1ms 0.0042% 83.63% 209ms 0.87% vtkXMLWriterBase::Write 0 0% 83.63% 207ms 0.86% vtkStreamingDemandDrivenPipeline::Update 0 0% 83.63% 206ms 0.86% vtkDemandDrivenPipeline::ProcessRequest 0 0% 83.63% 205ms 0.85% vtkStreamingDemandDrivenPipeline::ProcessRequest 21ms 0.087% 83.71% 204ms 0.85% std::__insertion_sort (inline) 0 0% 83.71% 204ms 0.85% vtkDemandDrivenPipeline::ExecuteData 0 0% 83.71% 203ms 0.84% vtkExecutive::CallAlgorithm 0 0% 83.71% 200ms 0.83% vtkCompositeDataPipeline::ExecuteData 0 0% 83.71% 199ms 0.83% vtkXMLUnstructuredDataWriter::ProcessRequest 107ms 0.44% 84.16% 188ms 0.78% boost::shared_ptr::shared_ptr (inline) 187ms 0.78% 84.94% 187ms 0.78% boost::shared_ptr::operator-> (inline) 0 0% 84.94% 185ms 0.77% std::_Rb_tree::clear (inline) 6ms 0.025% 84.96% 180ms 0.75% AbstractCellProperty::IsType (inline) 0 0% 84.96% 174ms 0.72% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 84.96% 174ms 0.72% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 168ms 0.7% 85.66% 168ms 0.7% [libchaste_cell_based.so] 0 0% 85.66% 167ms 0.69% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 85.66% 161ms 0.67% std::_Rb_tree::_Auto_node::_Auto_node (inline) 12ms 0.05% 85.71% 158ms 0.66% DistributedBoxCollection::GetIsPeriodicAllDims 0 0% 85.71% 150ms 0.62% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 14ms 0.058% 85.77% 146ms 0.61% boost::numeric::ublas::vector_reference::operator() (inline) 50ms 0.21% 85.98% 144ms 0.6% AbstractCellProperty::IsSame 144ms 0.6% 86.57% 144ms 0.6% std::__adjacent_find (inline) 0 0% 86.57% 144ms 0.6% std::__unique (inline) 0 0% 86.57% 144ms 0.6% std::unique (inline) 0 0% 86.57% 142ms 0.59% vtkXMLWriter::WriteBinaryData 3ms 0.012% 86.59% 138ms 0.57% AbstractNumericalMethod::SafeNodePositionUpdate 124ms 0.52% 87.10% 138ms 0.57% _int_free 0 0% 87.10% 136ms 0.57% vtkXMLWriter::WriteBinaryDataInternal 135ms 0.56% 87.66% 135ms 0.56% Node::IsDeleted 0 0% 87.66% 135ms 0.56% std::map::clear (inline) 0 0% 87.66% 135ms 0.56% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.66% 135ms 0.56% vtkXMLWriter::WriteCompressionBlock 134ms 0.56% 88.22% 134ms 0.56% [libchaste_mesh.so] 0 0% 88.22% 131ms 0.54% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 88.22% 129ms 0.54% vtkXMLWriter::WritePointsAppendedData 0 0% 88.22% 128ms 0.53% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 58ms 0.24% 88.46% 126ms 0.52% AbstractCellCycleModel::GetAge 0 0% 88.46% 122ms 0.51% Cell::GetCellId