File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 22453ms, 89.39% of 25118ms total Dropped 786 nodes (cum <= 125.59ms) flat flat% sum% cum cum% 0 0% 0% 25053ms 99.74% __libc_start_call_main 0 0% 0% 25053ms 99.74% __libc_start_main_impl 0 0% 0% 25053ms 99.74% _start 0 0% 0% 25038ms 99.68% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 25038ms 99.68% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 25038ms 99.68% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 25038ms 99.68% main 0 0% 0% 25006ms 99.55% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 25006ms 99.55% CxxTest::TestRunner::runTest (inline) 0 0% 0% 25006ms 99.55% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 3ms 0.012% 0.012% 24998ms 99.52% AbstractCellBasedSimulation::Solve 0 0% 0.012% 14312ms 56.98% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.012% 9492ms 37.79% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.008% 0.02% 8457ms 33.67% ForwardEulerNumericalMethod::UpdateAllNodePositions 9ms 0.036% 0.056% 8264ms 32.90% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.056% 8244ms 32.82% NodeBasedCellPopulation::Update 957ms 3.81% 3.87% 7484ms 29.80% RepulsionForce::AddForceContribution (partial-inline) 7ms 0.028% 3.89% 6246ms 24.87% DistributedBoxCollection::CalculateInteriorNodePairs 0 0% 3.89% 5515ms 21.96% OffLatticeSimulation::ApplyBoundaries 2223ms 8.85% 12.74% 4943ms 19.68% std::_Rb_tree::_M_lower_bound (inline) 11ms 0.044% 12.79% 4569ms 18.19% NodeAttributes::RemoveDuplicateNeighbours 9ms 0.036% 12.82% 4367ms 17.39% std::__sort (inline) 0 0% 12.82% 4367ms 17.39% std::sort (inline) 235ms 0.94% 13.76% 4052ms 16.13% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 175ms 0.7% 14.46% 4010ms 15.96% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 7ms 0.028% 14.48% 3830ms 15.25% AbstractCellPopulation::Iterator::operator++ (inline) 224ms 0.89% 15.38% 3812ms 15.18% AbstractCellPopulation::Iterator::IsRealCell (inline) 341ms 1.36% 16.73% 3317ms 13.21% std::_Rb_tree::find (inline) 0 0% 16.73% 3316ms 13.20% std::map::find (inline) 44ms 0.18% 16.91% 3208ms 12.77% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 62ms 0.25% 17.16% 2782ms 11.08% PlaneBoundaryCondition::ImposeBoundaryCondition 69ms 0.27% 17.43% 2733ms 10.88% PlaneBoundaryCondition::VerifyBoundaryCondition 217ms 0.86% 18.29% 2731ms 10.87% std::__introsort_loop 144ms 0.57% 18.87% 2727ms 10.86% AbstractMesh::GetNode 58ms 0.23% 19.10% 2705ms 10.77% NodesOnlyMesh::GetNodeOrHaloNode 340ms 1.35% 20.45% 2665ms 10.61% std::map::operator[] (partial-inline) 182ms 0.72% 21.18% 2590ms 10.31% NodesOnlyMesh::SolveNodeMapping 5ms 0.02% 21.20% 2412ms 9.60% std::__unguarded_partition_pivot (inline) 112ms 0.45% 21.64% 2312ms 9.20% AbstractCellPopulation::GetLocationIndexUsingCell 338ms 1.35% 22.99% 2189ms 8.71% DistributedBoxCollection::AddPairsFromBox 807ms 3.21% 26.20% 2186ms 8.70% std::__unguarded_partition (inline) 2148ms 8.55% 34.75% 2148ms 8.55% std::_Rb_tree::_S_right (inline) 0 0% 34.75% 1998ms 7.95% std::_Rb_tree::lower_bound (inline) 0 0% 34.75% 1998ms 7.95% std::map::lower_bound (inline) 12ms 0.048% 34.80% 1716ms 6.83% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 18ms 0.072% 34.87% 1690ms 6.73% AbstractCellPopulation::GetCellUsingLocationIndex 1ms 0.004% 34.88% 1625ms 6.47% std::__final_insertion_sort (inline) 149ms 0.59% 35.47% 1436ms 5.72% std::__unguarded_insertion_sort (inline) 62ms 0.25% 35.72% 1408ms 5.61% boost::numeric::ublas::c_vector::c_vector (partial-inline) 11ms 0.044% 35.76% 1219ms 4.85% boost::numeric::ublas::vector_assign (inline) 22ms 0.088% 35.85% 1213ms 4.83% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 659ms 2.62% 38.47% 1166ms 4.64% std::__unguarded_linear_insert (inline) 1ms 0.004% 38.47% 1164ms 4.63% NodeBasedCellPopulation::UpdateCellProcessLocation 278ms 1.11% 39.58% 1066ms 4.24% boost::numeric::ublas::indexing_vector_assign 332ms 1.32% 40.90% 1031ms 4.10% __dynamic_cast 8ms 0.032% 40.93% 969ms 3.86% DistributedBoxCollection::CalculateBoundaryNodePairs 31ms 0.12% 41.06% 926ms 3.69% boost::detail::shared_count::~shared_count (inline) 0 0% 41.06% 926ms 3.69% boost::shared_ptr::~shared_ptr (inline) 120ms 0.48% 41.54% 906ms 3.61% AbstractMesh::GetVectorFromAtoB 861ms 3.43% 44.96% 871ms 3.47% boost::detail::sp_counted_base::release 357ms 1.42% 46.39% 818ms 3.26% DistributedBoxCollection::CalculateContainingBox (partial-inline) 802ms 3.19% 49.58% 802ms 3.19% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 352ms 1.40% 50.98% 800ms 3.18% NodeAttributes::AddNeighbour 43ms 0.17% 51.15% 791ms 3.15% std::_Rb_tree_const_iterator::operator++ (inline) 10ms 0.04% 51.19% 758ms 3.02% CellPropertyCollection::GetPropertiesType (inline) 754ms 3.00% 54.19% 754ms 3.00% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 54.19% 734ms 2.92% AbstractCellPopulation::WriteResultsToFiles 1ms 0.004% 54.20% 711ms 2.83% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 54.20% 681ms 2.71% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 54.20% 657ms 2.62% boost::numeric::ublas::norm_2 (inline) 498ms 1.98% 56.18% 657ms 2.62% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 56.18% 657ms 2.62% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 98ms 0.39% 56.57% 657ms 2.62% std::__new_allocator::allocate (inline) 654ms 2.60% 59.17% 654ms 2.60% std::_Rb_tree_increment 648ms 2.58% 61.75% 648ms 2.58% [libchaste_cell_based.so] 2ms 0.008% 61.76% 640ms 2.55% AbstractCellBasedSimulation::DoCellBirth 0 0% 61.76% 639ms 2.54% std::allocator_traits::allocate (inline) 33ms 0.13% 61.89% 631ms 2.51% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 61.89% 608ms 2.42% std::_Rb_tree::_M_create_node (inline) 0 0% 61.89% 607ms 2.42% AbstractCellBasedSimulation::DoCellRemoval (inline) 49ms 0.2% 62.09% 592ms 2.36% std::_Rb_tree::_M_copy (inline) 8ms 0.032% 62.12% 586ms 2.33% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 584ms 2.33% 64.44% 584ms 2.33% std::_Rb_tree::_S_left (inline) 228ms 0.91% 65.35% 582ms 2.32% __cxxabiv1::__si_class_type_info::__do_dyncast 574ms 2.29% 67.64% 574ms 2.29% boost::numeric::ublas::c_vector::operator() 0 0% 67.64% 569ms 2.27% std::_Rb_tree::_M_get_node (inline) 557ms 2.22% 69.85% 557ms 2.22% __gnu_cxx::__normal_iterator::operator++ (inline) 21ms 0.084% 69.94% 551ms 2.19% boost::numeric::ublas::c_vector::operator= (inline) 30ms 0.12% 70.06% 550ms 2.19% operator new 0 0% 70.06% 546ms 2.17% Cell::GetMutationState 539ms 2.15% 72.20% 539ms 2.15% boost::numeric::ublas::same_impl_ex 207ms 0.82% 73.03% 537ms 2.14% std::_Rb_tree::_M_clone_node (inline) 389ms 1.55% 74.58% 532ms 2.12% std::vector::push_back (inline) 3ms 0.012% 74.59% 524ms 2.09% std::set::set (inline) 31ms 0.12% 74.71% 514ms 2.05% std::__copy_move::__copy_m (inline) 0 0% 74.71% 514ms 2.05% std::__copy_move_a (inline) 0 0% 74.71% 514ms 2.05% std::__copy_move_a1 (inline) 0 0% 74.71% 514ms 2.05% std::__copy_move_a2 (inline) 0 0% 74.71% 514ms 2.05% std::copy (inline) 95ms 0.38% 75.09% 513ms 2.04% std::_Rb_tree::_M_erase 166ms 0.66% 75.75% 505ms 2.01% __GI___libc_malloc 495ms 1.97% 77.72% 495ms 1.97% [libchaste_mesh.so] 5ms 0.02% 77.74% 479ms 1.91% NodeBasedCellPopulation::WriteVtkResultsToFile 1ms 0.004% 77.75% 462ms 1.84% AbstractCellProperty::IsSubType (inline) 462ms 1.84% 79.58% 462ms 1.84% __memcpy_evex_unaligned_erms 450ms 1.79% 81.38% 450ms 1.79% __strcmp_evex 85ms 0.34% 81.71% 449ms 1.79% std::_Rb_tree::~_Rb_tree (inline) 117ms 0.47% 82.18% 434ms 1.73% boost::numeric::ublas::vector_binary::size (inline) 0 0% 82.18% 416ms 1.66% std::_Rb_tree::_M_drop_node (inline) 0 0% 82.18% 393ms 1.56% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 82.18% 367ms 1.46% std::set::~set (inline) 4ms 0.016% 82.20% 327ms 1.30% std::_Rb_tree::_M_emplace_hint_unique 1ms 0.004% 82.20% 325ms 1.29% NodesOnlyMesh::ReMesh 3ms 0.012% 82.21% 322ms 1.28% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 82.21% 317ms 1.26% NodesOnlyMesh::UpdateNodeIndices 0 0% 82.21% 310ms 1.23% NodesOnlyMesh::UpdateBoxCollection 16ms 0.064% 82.28% 310ms 1.23% std::__new_allocator::deallocate (inline) 13ms 0.052% 82.33% 304ms 1.21% Node::GetRadius 0 0% 82.33% 302ms 1.20% boost::numeric::ublas::c_vector::assign (inline) 2ms 0.008% 82.34% 295ms 1.17% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 82.34% 290ms 1.15% std::allocator_traits::deallocate (inline) 0 0% 82.34% 285ms 1.13% std::_Rb_tree::_M_put_node (inline) 1ms 0.004% 82.34% 281ms 1.12% DistributedBoxCollection::GetProcessOwningNode 0 0% 82.34% 279ms 1.11% boost::numeric::ublas::inner_prod (inline) 4ms 0.016% 82.36% 279ms 1.11% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 245ms 0.98% 83.33% 278ms 1.11% boost::shared_ptr::shared_ptr (inline) 10ms 0.04% 83.37% 275ms 1.09% boost::numeric::ublas::vector_scalar_binary::evaluate 161ms 0.64% 84.01% 272ms 1.08% _int_malloc 56ms 0.22% 84.23% 260ms 1.04% __GI___libc_free 4ms 0.016% 84.25% 249ms 0.99% NodesOnlyMesh::AddNodesToBoxes 2ms 0.008% 84.26% 246ms 0.98% CellPropertyCollection::HasProperty 0 0% 84.26% 245ms 0.98% Cell::HasCellProperty (inline) 238ms 0.95% 85.21% 238ms 0.95% Node::CheckForNodeAttributes 7ms 0.028% 85.23% 236ms 0.94% Cell::ReadyToDivide 59ms 0.23% 85.47% 223ms 0.89% boost::numeric::ublas::vector_inner_prod::apply (inline) 56ms 0.22% 85.69% 217ms 0.86% std::__move_median_to_first (inline) 0 0% 85.69% 215ms 0.86% std::_Rb_tree::_Auto_node::_Auto_node (inline) 205ms 0.82% 86.51% 205ms 0.82% boost::shared_ptr::operator-> (inline) 1ms 0.004% 86.51% 202ms 0.8% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 186ms 0.74% 87.25% 202ms 0.8% _int_free 0 0% 87.25% 199ms 0.79% VtkMeshWriter::WriteFiles 0 0% 87.25% 191ms 0.76% NodesOnlyMesh::ResizeBoxCollection 16ms 0.064% 87.32% 190ms 0.76% NodesOnlyMesh::IsANodeCloseToDomainBoundary 41ms 0.16% 87.48% 188ms 0.75% std::__insertion_sort (inline) 0 0% 87.48% 182ms 0.72% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 87.48% 177ms 0.7% std::iter_swap (inline) 177ms 0.7% 88.18% 177ms 0.7% std::swap (inline) 0 0% 88.18% 174ms 0.69% std::_Rb_tree::clear (inline) 0 0% 88.18% 174ms 0.69% vtkDemandDrivenPipeline::ProcessRequest 0 0% 88.18% 174ms 0.69% vtkStreamingDemandDrivenPipeline::Update 0 0% 88.18% 174ms 0.69% vtkXMLWriterBase::Write 0 0% 88.18% 172ms 0.68% vtkExecutive::CallAlgorithm 0 0% 88.18% 170ms 0.68% vtkCompositeDataPipeline::ExecuteData 0 0% 88.18% 170ms 0.68% vtkDemandDrivenPipeline::ExecuteData 0 0% 88.18% 170ms 0.68% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 88.18% 170ms 0.68% vtkXMLUnstructuredDataWriter::ProcessRequest 3ms 0.012% 88.20% 168ms 0.67% Cell::GetCellId 0 0% 88.20% 157ms 0.63% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 1ms 0.004% 88.20% 156ms 0.62% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 2ms 0.008% 88.21% 154ms 0.61% AbstractCellProperty::IsType (inline) 107ms 0.43% 88.63% 151ms 0.6% std::__adjacent_find (inline) 0 0% 88.63% 151ms 0.6% std::__unique (inline) 0 0% 88.63% 151ms 0.6% std::unique (inline) 16ms 0.064% 88.70% 149ms 0.59% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 88.70% 149ms 0.59% std::__new_allocator::destroy (inline) 0 0% 88.70% 149ms 0.59% std::allocator_traits::destroy (inline) 0 0% 88.70% 144ms 0.57% std::_Rb_tree::_M_destroy_node (inline) 0 0% 88.70% 144ms 0.57% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 88.70% 144ms 0.57% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 143ms 0.57% 89.27% 143ms 0.57% Node::GetIndex 2ms 0.008% 89.27% 142ms 0.57% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 89.27% 142ms 0.57% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 1ms 0.004% 89.28% 138ms 0.55% Cell::GetCellProliferativeType 0 0% 89.28% 137ms 0.55% std::_Rb_tree::_M_insert_unique 0 0% 89.28% 137ms 0.55% std::set::insert (inline) 2ms 0.008% 89.29% 135ms 0.54% AbstractCellPopulation::SetCellUsingLocationIndex 6ms 0.024% 89.31% 133ms 0.53% DistributedBoxCollection::GetIsPeriodicAllDims 3ms 0.012% 89.32% 132ms 0.53% NodeBasedCellPopulation::SetNode 0 0% 89.32% 127ms 0.51% NodeBasedCellPopulation::AcceptCellWriter 17ms 0.068% 89.39% 127ms 0.51% boost::numeric::ublas::c_vector::operator[] (inline)