File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 23231ms, 88.98% of 26107ms total Dropped 753 nodes (cum <= 130.53ms) flat flat% sum% cum cum% 0 0% 0% 26023ms 99.68% __libc_start_call_main 0 0% 0% 26023ms 99.68% __libc_start_main_impl 0 0% 0% 26023ms 99.68% _start 0 0% 0% 26008ms 99.62% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 26008ms 99.62% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 26008ms 99.62% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 26008ms 99.62% main 0 0% 0% 25974ms 99.49% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 25974ms 99.49% CxxTest::TestRunner::runTest (inline) 0 0% 0% 25974ms 99.49% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 2ms 0.0077% 0.0077% 25966ms 99.46% AbstractCellBasedSimulation::Solve 3ms 0.011% 0.019% 14713ms 56.36% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0038% 0.023% 10015ms 38.36% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.015% 0.038% 8713ms 33.37% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.0077% 0.046% 8681ms 33.25% NodeBasedCellPopulation::Update 12ms 0.046% 0.092% 8503ms 32.57% AbstractNumericalMethod::ComputeForcesIncludingDamping 961ms 3.68% 3.77% 7651ms 29.31% RepulsionForce::AddForceContribution (partial-inline) 12ms 0.046% 3.82% 6673ms 25.56% DistributedBoxCollection::CalculateInteriorNodePairs 0 0% 3.82% 5570ms 21.34% OffLatticeSimulation::ApplyBoundaries 2276ms 8.72% 12.54% 5117ms 19.60% std::_Rb_tree::_M_lower_bound (inline) 16ms 0.061% 12.60% 4527ms 17.34% NodeAttributes::RemoveDuplicateNeighbours 6ms 0.023% 12.62% 4344ms 16.64% std::__sort (inline) 0 0% 12.62% 4344ms 16.64% std::sort (inline) 163ms 0.62% 13.25% 4260ms 16.32% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 242ms 0.93% 14.17% 4115ms 15.76% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 6ms 0.023% 14.20% 3837ms 14.70% AbstractCellPopulation::Iterator::operator++ (inline) 197ms 0.75% 14.95% 3813ms 14.61% AbstractCellPopulation::Iterator::IsRealCell (inline) 378ms 1.45% 16.40% 3474ms 13.31% std::_Rb_tree::find (inline) 0 0% 16.40% 3474ms 13.31% std::map::find (inline) 24ms 0.092% 16.49% 3202ms 12.26% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 173ms 0.66% 17.15% 2916ms 11.17% AbstractMesh::GetNode 50ms 0.19% 17.34% 2882ms 11.04% NodesOnlyMesh::GetNodeOrHaloNode 69ms 0.26% 17.61% 2826ms 10.82% PlaneBoundaryCondition::ImposeBoundaryCondition 351ms 1.34% 18.95% 2761ms 10.58% std::map::operator[] (partial-inline) 184ms 0.7% 19.66% 2747ms 10.52% NodesOnlyMesh::SolveNodeMapping 52ms 0.2% 19.86% 2744ms 10.51% PlaneBoundaryCondition::VerifyBoundaryCondition 212ms 0.81% 20.67% 2728ms 10.45% std::__introsort_loop 506ms 1.94% 22.61% 2622ms 10.04% DistributedBoxCollection::AddPairsFromBox 2ms 0.0077% 22.61% 2426ms 9.29% std::__unguarded_partition_pivot (inline) 113ms 0.43% 23.05% 2329ms 8.92% AbstractCellPopulation::GetLocationIndexUsingCell 2198ms 8.42% 31.47% 2198ms 8.42% std::_Rb_tree::_S_right (inline) 824ms 3.16% 34.62% 2167ms 8.30% std::__unguarded_partition (inline) 0 0% 34.62% 2048ms 7.84% std::_Rb_tree::lower_bound (inline) 0 0% 34.62% 2048ms 7.84% std::map::lower_bound (inline) 19ms 0.073% 34.70% 1849ms 7.08% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 22ms 0.084% 34.78% 1823ms 6.98% AbstractCellPopulation::GetCellUsingLocationIndex 1ms 0.0038% 34.78% 1608ms 6.16% std::__final_insertion_sort (inline) 129ms 0.49% 35.28% 1417ms 5.43% std::__unguarded_insertion_sort (inline) 38ms 0.15% 35.42% 1340ms 5.13% boost::numeric::ublas::c_vector::c_vector (partial-inline) 18ms 0.069% 35.49% 1240ms 4.75% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 35.49% 1208ms 4.63% NodeBasedCellPopulation::UpdateCellProcessLocation 8ms 0.031% 35.52% 1192ms 4.57% boost::numeric::ublas::vector_assign (inline) 651ms 2.49% 38.02% 1159ms 4.44% std::__unguarded_linear_insert (inline) 333ms 1.28% 39.29% 1048ms 4.01% __dynamic_cast 517ms 1.98% 41.27% 1041ms 3.99% NodeAttributes::AddNeighbour 213ms 0.82% 42.09% 1025ms 3.93% boost::numeric::ublas::indexing_vector_assign 35ms 0.13% 42.22% 1020ms 3.91% boost::detail::shared_count::~shared_count (inline) 0 0% 42.22% 1020ms 3.91% boost::shared_ptr::~shared_ptr (inline) 10ms 0.038% 42.26% 958ms 3.67% DistributedBoxCollection::CalculateBoundaryNodePairs 944ms 3.62% 45.88% 954ms 3.65% boost::detail::sp_counted_base::release 124ms 0.47% 46.35% 874ms 3.35% AbstractMesh::GetVectorFromAtoB 43ms 0.16% 46.52% 862ms 3.30% std::_Rb_tree_const_iterator::operator++ (inline) 379ms 1.45% 47.97% 816ms 3.13% DistributedBoxCollection::CalculateContainingBox (partial-inline) 809ms 3.10% 51.07% 809ms 3.10% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 13ms 0.05% 51.12% 768ms 2.94% CellPropertyCollection::GetPropertiesType (inline) 9ms 0.034% 51.15% 762ms 2.92% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 51.15% 759ms 2.91% AbstractCellPopulation::WriteResultsToFiles 106ms 0.41% 51.56% 758ms 2.90% std::__new_allocator::allocate (inline) 0 0% 51.56% 740ms 2.83% std::allocator_traits::allocate (inline) 2ms 0.0077% 51.56% 738ms 2.83% AbstractCellBasedSimulation::DoCellBirth 737ms 2.82% 54.39% 737ms 2.82% __gnu_cxx::__normal_iterator::operator-- (inline) 728ms 2.79% 57.18% 728ms 2.79% std::_Rb_tree_increment 17ms 0.065% 57.24% 716ms 2.74% std::_Rb_tree::_Rb_tree (partial-inline) 51ms 0.2% 57.44% 687ms 2.63% std::_Rb_tree::_M_copy (inline) 0 0% 57.44% 684ms 2.62% std::_Rb_tree::_M_create_node (inline) 661ms 2.53% 59.97% 661ms 2.53% std::_Rb_tree::_S_left (inline) 0 0% 59.97% 654ms 2.51% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 59.97% 646ms 2.47% std::_Rb_tree::_M_get_node (inline) 24ms 0.092% 60.06% 641ms 2.46% operator new 0 0% 60.06% 631ms 2.42% boost::numeric::ublas::norm_2 (inline) 462ms 1.77% 61.83% 631ms 2.42% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 61.83% 631ms 2.42% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 244ms 0.93% 62.76% 626ms 2.40% std::_Rb_tree::_M_clone_node (inline) 625ms 2.39% 65.16% 625ms 2.39% [libchaste_cell_based.so] 441ms 1.69% 66.85% 617ms 2.36% std::vector::push_back (inline) 233ms 0.89% 67.74% 603ms 2.31% __cxxabiv1::__si_class_type_info::__do_dyncast 208ms 0.8% 68.54% 596ms 2.28% __GI___libc_malloc 0 0% 68.54% 592ms 2.27% AbstractCellBasedSimulation::DoCellRemoval (inline) 12ms 0.046% 68.58% 578ms 2.21% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 36ms 0.14% 68.72% 578ms 2.21% boost::numeric::ublas::c_vector::operator= (inline) 3ms 0.011% 68.73% 573ms 2.19% std::set::set (inline) 561ms 2.15% 70.88% 561ms 2.15% __gnu_cxx::__normal_iterator::operator++ (inline) 2ms 0.0077% 70.89% 547ms 2.10% Cell::GetMutationState 546ms 2.09% 72.98% 546ms 2.09% boost::numeric::ublas::c_vector::operator() 540ms 2.07% 75.05% 540ms 2.07% [libchaste_mesh.so] 97ms 0.37% 75.42% 540ms 2.07% std::_Rb_tree::_M_erase 31ms 0.12% 75.54% 526ms 2.01% std::__copy_move::__copy_m (inline) 0 0% 75.54% 526ms 2.01% std::__copy_move_a (inline) 0 0% 75.54% 526ms 2.01% std::__copy_move_a1 (inline) 0 0% 75.54% 526ms 2.01% std::__copy_move_a2 (inline) 0 0% 75.54% 526ms 2.01% std::copy (inline) 518ms 1.98% 77.52% 518ms 1.98% boost::numeric::ublas::same_impl_ex 103ms 0.39% 77.92% 488ms 1.87% std::_Rb_tree::~_Rb_tree (inline) 1ms 0.0038% 77.92% 485ms 1.86% NodeBasedCellPopulation::WriteVtkResultsToFile 479ms 1.83% 79.76% 479ms 1.83% __memcpy_evex_unaligned_erms 470ms 1.80% 81.56% 470ms 1.80% __strcmp_evex 4ms 0.015% 81.57% 449ms 1.72% AbstractCellProperty::IsSubType (inline) 0 0% 81.57% 446ms 1.71% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 81.57% 429ms 1.64% std::_Rb_tree::_M_drop_node (inline) 112ms 0.43% 82.00% 424ms 1.62% boost::numeric::ublas::vector_binary::size (inline) 0 0% 82.00% 376ms 1.44% std::set::~set (inline) 12ms 0.046% 82.05% 362ms 1.39% std::_Rb_tree::_M_emplace_hint_unique 10ms 0.038% 82.09% 344ms 1.32% NodeBasedCellPopulation::UpdateMapsAfterRemesh 2ms 0.0077% 82.09% 340ms 1.30% NodesOnlyMesh::ReMesh 5ms 0.019% 82.11% 334ms 1.28% NodesOnlyMesh::UpdateNodeIndices 186ms 0.71% 82.82% 322ms 1.23% _int_malloc 0 0% 82.82% 313ms 1.20% boost::numeric::ublas::c_vector::assign (inline) 1ms 0.0038% 82.83% 307ms 1.18% NodesOnlyMesh::UpdateBoxCollection 8ms 0.031% 82.86% 306ms 1.17% std::__new_allocator::deallocate (inline) 9ms 0.034% 82.89% 305ms 1.17% Node::GetRadius 0 0% 82.89% 300ms 1.15% Cell::HasCellProperty (inline) 1ms 0.0038% 82.90% 300ms 1.15% CellPropertyCollection::HasProperty 1ms 0.0038% 82.90% 300ms 1.15% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 82.90% 285ms 1.09% std::allocator_traits::deallocate (inline) 4ms 0.015% 82.92% 284ms 1.09% DistributedBoxCollection::GetProcessOwningNode 5ms 0.019% 82.94% 279ms 1.07% Cell::ReadyToDivide 0 0% 82.94% 279ms 1.07% std::_Rb_tree::_M_put_node (inline) 73ms 0.28% 83.22% 273ms 1.05% __GI___libc_free 0 0% 83.22% 270ms 1.03% boost::numeric::ublas::inner_prod (inline) 3ms 0.011% 83.23% 267ms 1.02% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 14ms 0.054% 83.28% 264ms 1.01% boost::numeric::ublas::vector_scalar_binary::evaluate 232ms 0.89% 84.17% 260ms 1% boost::shared_ptr::shared_ptr (inline) 55ms 0.21% 84.38% 256ms 0.98% std::__move_median_to_first (inline) 239ms 0.92% 85.30% 239ms 0.92% Node::CheckForNodeAttributes 0 0% 85.30% 238ms 0.91% std::_Rb_tree::_Auto_node::_Auto_node (inline) 5ms 0.019% 85.31% 235ms 0.9% NodesOnlyMesh::AddNodesToBoxes 1ms 0.0038% 85.32% 205ms 0.79% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 85.32% 204ms 0.78% VtkMeshWriter::WriteFiles 67ms 0.26% 85.57% 203ms 0.78% boost::numeric::ublas::vector_inner_prod::apply (inline) 187ms 0.72% 86.29% 197ms 0.75% _int_free 190ms 0.73% 87.02% 190ms 0.73% boost::shared_ptr::operator-> (inline) 50ms 0.19% 87.21% 189ms 0.72% std::__insertion_sort (inline) 0 0% 87.21% 187ms 0.72% std::iter_swap (inline) 187ms 0.72% 87.93% 187ms 0.72% std::swap (inline) 0 0% 87.93% 181ms 0.69% std::_Rb_tree::clear (inline) 0 0% 87.93% 181ms 0.69% vtkStreamingDemandDrivenPipeline::Update 0 0% 87.93% 181ms 0.69% vtkXMLWriterBase::Write 0 0% 87.93% 179ms 0.69% vtkCompositeDataPipeline::ExecuteData 0 0% 87.93% 179ms 0.69% vtkDemandDrivenPipeline::ExecuteData 0 0% 87.93% 179ms 0.69% vtkDemandDrivenPipeline::ProcessRequest 0 0% 87.93% 179ms 0.69% vtkExecutive::CallAlgorithm 0 0% 87.93% 179ms 0.69% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 87.93% 179ms 0.69% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 87.93% 176ms 0.67% boost::numeric::ublas::vector_binary::operator() (inline) 7ms 0.027% 87.95% 173ms 0.66% AbstractCellProperty::IsType (inline) 0 0% 87.95% 170ms 0.65% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 87.95% 170ms 0.65% NodesOnlyMesh::ResizeBoxCollection 8ms 0.031% 87.98% 169ms 0.65% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 87.98% 167ms 0.64% std::__new_allocator::destroy (inline) 0 0% 87.98% 167ms 0.64% std::allocator_traits::destroy (inline) 0 0% 87.98% 165ms 0.63% std::_Rb_tree::_M_destroy_node (inline) 1ms 0.0038% 87.99% 159ms 0.61% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 87.99% 157ms 0.6% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 87.99% 154ms 0.59% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 87.99% 154ms 0.59% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 1ms 0.0038% 87.99% 152ms 0.58% Cell::GetCellId 0 0% 87.99% 152ms 0.58% std::map::map (inline) 0 0% 87.99% 151ms 0.58% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 3ms 0.011% 88.00% 146ms 0.56% AbstractCellPopulation::SetCellUsingLocationIndex 144ms 0.55% 88.55% 144ms 0.55% Node::GetIndex 2ms 0.0077% 88.56% 144ms 0.55% NodeBasedCellPopulation::SetNode 1ms 0.0038% 88.57% 140ms 0.54% Cell::GetCellProliferativeType 0 0% 88.57% 138ms 0.53% NodesOnlyMesh::SetNode 84ms 0.32% 88.89% 137ms 0.52% std::__adjacent_find (inline) 0 0% 88.89% 137ms 0.52% std::__unique (inline) 0 0% 88.89% 137ms 0.52% std::unique (inline) 2ms 0.0077% 88.90% 133ms 0.51% NodeBasedCellPopulation::AcceptCellWriter 0 0% 88.90% 133ms 0.51% vtkXMLWriter::WriteBinaryData 5ms 0.019% 88.91% 132ms 0.51% DistributedBoxCollection::GetIsPeriodicAllDims 18ms 0.069% 88.98% 132ms 0.51% boost::numeric::ublas::vector_reference::operator() (inline)