File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 23136ms, 88.95% of 26011ms total Dropped 813 nodes (cum <= 130.06ms) flat flat% sum% cum cum% 0 0% 0% 25908ms 99.60% __libc_start_call_main 0 0% 0% 25908ms 99.60% __libc_start_main_impl 0 0% 0% 25908ms 99.60% _start 0 0% 0% 25893ms 99.55% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 25893ms 99.55% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 25893ms 99.55% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 25893ms 99.55% main 0 0% 0% 25858ms 99.41% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 25858ms 99.41% CxxTest::TestRunner::runTest (inline) 0 0% 0% 25857ms 99.41% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 25848ms 99.37% AbstractCellBasedSimulation::Solve 2ms 0.0077% 0.0077% 14666ms 56.38% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0077% 9942ms 38.22% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.012% 0.019% 8650ms 33.26% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 0.019% 8629ms 33.17% NodeBasedCellPopulation::Update 5ms 0.019% 0.038% 8452ms 32.49% AbstractNumericalMethod::ComputeForcesIncludingDamping 950ms 3.65% 3.69% 7616ms 29.28% RepulsionForce::AddForceContribution (partial-inline) 12ms 0.046% 3.74% 6582ms 25.30% DistributedBoxCollection::CalculateInteriorNodePairs 1ms 0.0038% 3.74% 5519ms 21.22% OffLatticeSimulation::ApplyBoundaries 2284ms 8.78% 12.52% 5065ms 19.47% std::_Rb_tree::_M_lower_bound (inline) 17ms 0.065% 12.59% 4557ms 17.52% NodeAttributes::RemoveDuplicateNeighbours 2ms 0.0077% 12.59% 4358ms 16.75% std::__sort (inline) 0 0% 12.59% 4358ms 16.75% std::sort (inline) 144ms 0.55% 13.15% 4169ms 16.03% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 212ms 0.82% 13.96% 4031ms 15.50% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 2ms 0.0077% 13.97% 3804ms 14.62% AbstractCellPopulation::Iterator::operator++ (inline) 236ms 0.91% 14.88% 3797ms 14.60% AbstractCellPopulation::Iterator::IsRealCell (inline) 373ms 1.43% 16.31% 3455ms 13.28% std::_Rb_tree::find (inline) 0 0% 16.31% 3455ms 13.28% std::map::find (inline) 25ms 0.096% 16.41% 3149ms 12.11% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 159ms 0.61% 17.02% 2927ms 11.25% AbstractMesh::GetNode 60ms 0.23% 17.25% 2927ms 11.25% NodesOnlyMesh::GetNodeOrHaloNode 65ms 0.25% 17.50% 2809ms 10.80% PlaneBoundaryCondition::ImposeBoundaryCondition 222ms 0.85% 18.35% 2773ms 10.66% NodesOnlyMesh::SolveNodeMapping 317ms 1.22% 19.57% 2739ms 10.53% std::map::operator[] (partial-inline) 55ms 0.21% 19.78% 2709ms 10.41% PlaneBoundaryCondition::VerifyBoundaryCondition 217ms 0.83% 20.62% 2637ms 10.14% std::__introsort_loop 413ms 1.59% 22.21% 2514ms 9.67% DistributedBoxCollection::AddPairsFromBox 4ms 0.015% 22.22% 2317ms 8.91% std::__unguarded_partition_pivot (inline) 118ms 0.45% 22.68% 2298ms 8.83% AbstractCellPopulation::GetLocationIndexUsingCell 2245ms 8.63% 31.31% 2245ms 8.63% std::_Rb_tree::_S_right (inline) 798ms 3.07% 34.37% 2054ms 7.90% std::__unguarded_partition (inline) 0 0% 34.37% 2009ms 7.72% std::_Rb_tree::lower_bound (inline) 0 0% 34.37% 2009ms 7.72% std::map::lower_bound (inline) 22ms 0.085% 34.46% 1816ms 6.98% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 28ms 0.11% 34.57% 1789ms 6.88% AbstractCellPopulation::GetCellUsingLocationIndex 2ms 0.0077% 34.57% 1716ms 6.60% std::__final_insertion_sort (inline) 154ms 0.59% 35.17% 1549ms 5.96% std::__unguarded_insertion_sort (inline) 53ms 0.2% 35.37% 1391ms 5.35% boost::numeric::ublas::c_vector::c_vector (partial-inline) 690ms 2.65% 38.02% 1257ms 4.83% std::__unguarded_linear_insert (inline) 13ms 0.05% 38.07% 1241ms 4.77% boost::numeric::ublas::vector_assign (inline) 0 0% 38.07% 1231ms 4.73% NodeBasedCellPopulation::UpdateCellProcessLocation 18ms 0.069% 38.14% 1218ms 4.68% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 267ms 1.03% 39.17% 1069ms 4.11% boost::numeric::ublas::indexing_vector_assign 515ms 1.98% 41.15% 1038ms 3.99% NodeAttributes::AddNeighbour 9ms 0.035% 41.18% 961ms 3.69% DistributedBoxCollection::CalculateBoundaryNodePairs 28ms 0.11% 41.29% 921ms 3.54% boost::detail::shared_count::~shared_count (inline) 0 0% 41.29% 921ms 3.54% boost::shared_ptr::~shared_ptr (inline) 309ms 1.19% 42.48% 917ms 3.53% __dynamic_cast 120ms 0.46% 42.94% 878ms 3.38% AbstractMesh::GetVectorFromAtoB 865ms 3.33% 46.27% 873ms 3.36% boost::detail::sp_counted_base::release 47ms 0.18% 46.45% 863ms 3.32% std::_Rb_tree_const_iterator::operator++ (inline) 107ms 0.41% 46.86% 818ms 3.14% std::__new_allocator::allocate (inline) 0 0% 46.86% 801ms 3.08% std::allocator_traits::allocate (inline) 365ms 1.40% 48.26% 790ms 3.04% DistributedBoxCollection::CalculateContainingBox (partial-inline) 17ms 0.065% 48.33% 783ms 3.01% CellPropertyCollection::GetPropertiesType (inline) 39ms 0.15% 48.48% 779ms 2.99% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 48.48% 771ms 2.96% std::_Rb_tree::_M_create_node (inline) 4ms 0.015% 48.49% 767ms 2.95% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 48.49% 758ms 2.91% AbstractCellPopulation::WriteResultsToFiles 754ms 2.90% 51.39% 754ms 2.90% __gnu_cxx::__normal_iterator::operator-- (inline) 753ms 2.89% 54.28% 753ms 2.89% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 747ms 2.87% 57.16% 747ms 2.87% std::_Rb_tree_increment 63ms 0.24% 57.40% 730ms 2.81% std::_Rb_tree::_M_copy (inline) 1ms 0.0038% 57.40% 722ms 2.78% AbstractCellBasedSimulation::DoCellBirth 0 0% 57.40% 720ms 2.77% std::_Rb_tree::_M_get_node (inline) 42ms 0.16% 57.56% 714ms 2.74% operator new 0 0% 57.56% 712ms 2.74% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 57.56% 684ms 2.63% boost::numeric::ublas::norm_2 (inline) 506ms 1.95% 59.51% 684ms 2.63% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 59.51% 684ms 2.63% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 223ms 0.86% 60.37% 658ms 2.53% __GI___libc_malloc 232ms 0.89% 61.26% 653ms 2.51% std::_Rb_tree::_M_clone_node (inline) 4ms 0.015% 61.27% 600ms 2.31% std::set::set (inline) 438ms 1.68% 62.96% 596ms 2.29% std::vector::push_back (inline) 0 0% 62.96% 590ms 2.27% AbstractCellBasedSimulation::DoCellRemoval (inline) 579ms 2.23% 65.18% 579ms 2.23% __gnu_cxx::__normal_iterator::operator++ (inline) 6ms 0.023% 65.21% 578ms 2.22% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 30ms 0.12% 65.32% 577ms 2.22% boost::numeric::ublas::c_vector::operator= (inline) 575ms 2.21% 67.53% 575ms 2.21% [libchaste_cell_based.so] 569ms 2.19% 69.72% 569ms 2.19% std::_Rb_tree::_S_left (inline) 568ms 2.18% 71.90% 568ms 2.18% boost::numeric::ublas::c_vector::operator() 5ms 0.019% 71.92% 565ms 2.17% Cell::GetMutationState 114ms 0.44% 72.36% 560ms 2.15% std::_Rb_tree::_M_erase 28ms 0.11% 72.47% 529ms 2.03% std::__copy_move::__copy_m (inline) 0 0% 72.47% 529ms 2.03% std::__copy_move_a (inline) 0 0% 72.47% 529ms 2.03% std::__copy_move_a1 (inline) 0 0% 72.47% 529ms 2.03% std::__copy_move_a2 (inline) 0 0% 72.47% 529ms 2.03% std::copy (inline) 521ms 2.00% 74.47% 521ms 2.00% [libchaste_mesh.so] 513ms 1.97% 76.44% 513ms 1.97% boost::numeric::ublas::same_impl_ex 249ms 0.96% 77.40% 500ms 1.92% __cxxabiv1::__si_class_type_info::__do_dyncast 3ms 0.012% 77.41% 492ms 1.89% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 77.41% 485ms 1.86% std::_Rb_tree::_Alloc_node::operator() (inline) 83ms 0.32% 77.73% 485ms 1.86% std::_Rb_tree::~_Rb_tree (inline) 481ms 1.85% 79.58% 481ms 1.85% __memcpy_evex_unaligned_erms 0 0% 79.58% 442ms 1.70% std::_Rb_tree::_M_drop_node (inline) 7ms 0.027% 79.61% 419ms 1.61% AbstractCellProperty::IsSubType (inline) 14ms 0.054% 79.66% 413ms 1.59% std::_Rb_tree::_M_emplace_hint_unique 120ms 0.46% 80.12% 410ms 1.58% boost::numeric::ublas::vector_binary::size (inline) 0 0% 80.12% 370ms 1.42% std::set::~set (inline) 0 0% 80.12% 359ms 1.38% NodesOnlyMesh::ReMesh 188ms 0.72% 80.85% 356ms 1.37% _int_malloc 4ms 0.015% 80.86% 350ms 1.35% NodesOnlyMesh::UpdateNodeIndices 340ms 1.31% 82.17% 340ms 1.31% __strcmp_evex 9ms 0.035% 82.20% 331ms 1.27% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 82.20% 326ms 1.25% boost::numeric::ublas::c_vector::assign (inline) 12ms 0.046% 82.25% 324ms 1.25% std::__new_allocator::deallocate (inline) 0 0% 82.25% 323ms 1.24% NodesOnlyMesh::UpdateBoxCollection 0 0% 82.25% 306ms 1.18% std::allocator_traits::deallocate (inline) 0 0% 82.25% 301ms 1.16% std::_Rb_tree::_M_put_node (inline) 15ms 0.058% 82.31% 297ms 1.14% Node::GetRadius 0 0% 82.31% 286ms 1.10% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1ms 0.0038% 82.31% 284ms 1.09% CellPropertyCollection::HasProperty 0 0% 82.31% 283ms 1.09% Cell::HasCellProperty (inline) 96ms 0.37% 82.68% 282ms 1.08% __GI___libc_free 4ms 0.015% 82.70% 281ms 1.08% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 11ms 0.042% 82.74% 279ms 1.07% Cell::ReadyToDivide 0 0% 82.74% 272ms 1.05% boost::numeric::ublas::inner_prod (inline) 3ms 0.012% 82.75% 271ms 1.04% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 17ms 0.065% 82.81% 268ms 1.03% boost::numeric::ublas::vector_scalar_binary::evaluate 4ms 0.015% 82.83% 262ms 1.01% DistributedBoxCollection::GetProcessOwningNode 236ms 0.91% 83.74% 262ms 1.01% boost::shared_ptr::shared_ptr (inline) 2ms 0.0077% 83.75% 257ms 0.99% NodesOnlyMesh::AddNodesToBoxes 58ms 0.22% 83.97% 254ms 0.98% std::__move_median_to_first (inline) 238ms 0.91% 84.88% 238ms 0.91% boost::shared_ptr::operator-> (inline) 222ms 0.85% 85.74% 222ms 0.85% Node::CheckForNodeAttributes 66ms 0.25% 85.99% 220ms 0.85% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 85.99% 212ms 0.82% NodesOnlyMesh::ResizeBoxCollection 10ms 0.038% 86.03% 210ms 0.81% NodesOnlyMesh::IsANodeCloseToDomainBoundary 1ms 0.0038% 86.03% 203ms 0.78% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 86.03% 200ms 0.77% VtkMeshWriter::WriteFiles 0 0% 86.03% 188ms 0.72% std::_Rb_tree::clear (inline) 0 0% 86.03% 184ms 0.71% std::iter_swap (inline) 0 0% 86.03% 184ms 0.71% std::map::map (inline) 184ms 0.71% 86.74% 184ms 0.71% std::swap (inline) 0 0% 86.74% 183ms 0.7% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 86.74% 183ms 0.7% boost::numeric::ublas::vector_binary::operator() (inline) 164ms 0.63% 87.37% 178ms 0.68% _int_free 0 0% 87.37% 177ms 0.68% vtkStreamingDemandDrivenPipeline::Update 0 0% 87.37% 177ms 0.68% vtkXMLWriterBase::Write 0 0% 87.37% 176ms 0.68% vtkDemandDrivenPipeline::ProcessRequest 1ms 0.0038% 87.37% 175ms 0.67% vtkExecutive::CallAlgorithm 0 0% 87.37% 173ms 0.67% vtkCompositeDataPipeline::ExecuteData 0 0% 87.37% 173ms 0.67% vtkDemandDrivenPipeline::ExecuteData 0 0% 87.37% 173ms 0.67% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 87.37% 173ms 0.67% vtkXMLUnstructuredDataWriter::ProcessRequest 12ms 0.046% 87.42% 167ms 0.64% AbstractCellProperty::IsType (inline) 1ms 0.0038% 87.42% 166ms 0.64% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 29ms 0.11% 87.54% 165ms 0.63% std::__insertion_sort (inline) 0 0% 87.54% 159ms 0.61% Cell::GetCellId 1ms 0.0038% 87.54% 156ms 0.6% DistributedBoxCollection::GetIsPeriodicAllDims 98ms 0.38% 87.92% 153ms 0.59% std::__adjacent_find (inline) 0 0% 87.92% 153ms 0.59% std::__unique (inline) 0 0% 87.92% 153ms 0.59% std::unique (inline) 0 0% 87.92% 153ms 0.59% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 87.92% 153ms 0.59% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 152ms 0.58% 88.50% 152ms 0.58% Node::GetIndex 0 0% 88.50% 151ms 0.58% std::_Rb_tree::_M_destroy_node (inline) 0 0% 88.50% 151ms 0.58% std::__new_allocator::destroy (inline) 0 0% 88.50% 151ms 0.58% std::allocator_traits::destroy (inline) 0 0% 88.50% 151ms 0.58% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 2ms 0.0077% 88.51% 149ms 0.57% std::set::insert (inline) 0 0% 88.51% 147ms 0.57% std::_Rb_tree::_M_insert_unique 84ms 0.32% 88.83% 142ms 0.55% std::__new_allocator::construct (inline) 0 0% 88.83% 142ms 0.55% std::allocator_traits::construct (inline) 13ms 0.05% 88.88% 139ms 0.53% boost::numeric::ublas::c_vector::operator[] (inline) 2ms 0.0077% 88.89% 137ms 0.53% AbstractCellPopulation::SetCellUsingLocationIndex 2ms 0.0077% 88.90% 137ms 0.53% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 88.90% 137ms 0.53% Cell::GetCellProliferativeType 13ms 0.05% 88.95% 135ms 0.52% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 88.95% 132ms 0.51% std::map::clear (inline)