File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 24399ms, 88.67% of 27517ms total Dropped 815 nodes (cum <= 137.59ms) flat flat% sum% cum cum% 0 0% 0% 27430ms 99.68% __libc_start_call_main 0 0% 0% 27430ms 99.68% __libc_start_main_impl 0 0% 0% 27430ms 99.68% _start 0 0% 0% 27415ms 99.63% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 27415ms 99.63% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 27415ms 99.63% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 27415ms 99.63% main 0 0% 0% 27380ms 99.50% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 27380ms 99.50% CxxTest::TestRunner::runTest (inline) 0 0% 0% 27379ms 99.50% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0036% 0.0036% 27370ms 99.47% AbstractCellBasedSimulation::Solve 2ms 0.0073% 0.011% 15833ms 57.54% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.011% 10248ms 37.24% AbstractCellBasedSimulation::UpdateCellPopulation 9ms 0.033% 0.044% 9833ms 35.73% ForwardEulerNumericalMethod::UpdateAllNodePositions 12ms 0.044% 0.087% 9611ms 34.93% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.087% 8884ms 32.29% NodeBasedCellPopulation::Update 955ms 3.47% 3.56% 8638ms 31.39% RepulsionForce::AddForceContribution (partial-inline) 9ms 0.033% 3.59% 6783ms 24.65% DistributedBoxCollection::CalculateInteriorNodePairs 0 0% 3.59% 5441ms 19.77% OffLatticeSimulation::ApplyBoundaries 2226ms 8.09% 11.68% 5128ms 18.64% std::_Rb_tree::_M_lower_bound (inline) 190ms 0.69% 12.37% 4980ms 18.10% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 16ms 0.058% 12.43% 4597ms 16.71% NodeAttributes::RemoveDuplicateNeighbours 4ms 0.015% 12.44% 4401ms 15.99% std::__sort (inline) 0 0% 12.44% 4401ms 15.99% std::sort (inline) 209ms 0.76% 13.20% 3982ms 14.47% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 4ms 0.015% 13.22% 3834ms 13.93% AbstractCellPopulation::Iterator::operator++ (inline) 234ms 0.85% 14.07% 3814ms 13.86% AbstractCellPopulation::Iterator::IsRealCell 343ms 1.25% 15.31% 3460ms 12.57% std::_Rb_tree::find (inline) 0 0% 15.31% 3459ms 12.57% std::map::find (inline) 32ms 0.12% 15.43% 3170ms 11.52% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 66ms 0.24% 15.67% 2908ms 10.57% NodesOnlyMesh::GetNodeOrHaloNode 157ms 0.57% 16.24% 2906ms 10.56% AbstractMesh::GetNode 328ms 1.19% 17.43% 2812ms 10.22% std::map::operator[] (partial-inline) 68ms 0.25% 17.68% 2796ms 10.16% PlaneBoundaryCondition::ImposeBoundaryCondition 251ms 0.91% 18.59% 2769ms 10.06% std::__introsort_loop 181ms 0.66% 19.25% 2758ms 10.02% NodesOnlyMesh::SolveNodeMapping 504ms 1.83% 21.08% 2667ms 9.69% DistributedBoxCollection::AddPairsFromBox 58ms 0.21% 21.29% 2645ms 9.61% PlaneBoundaryCondition::VerifyBoundaryCondition 5ms 0.018% 21.31% 2441ms 8.87% std::__unguarded_partition_pivot (inline) 2286ms 8.31% 29.62% 2286ms 8.31% std::_Rb_tree::_S_right (inline) 108ms 0.39% 30.01% 2186ms 7.94% AbstractCellPopulation::GetLocationIndexUsingCell 778ms 2.83% 32.84% 2174ms 7.90% std::__unguarded_partition (inline) 21ms 0.076% 32.91% 2123ms 7.72% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 50ms 0.18% 33.10% 2071ms 7.53% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 33.10% 2039ms 7.41% std::_Rb_tree::lower_bound (inline) 0 0% 33.10% 2039ms 7.41% std::map::lower_bound (inline) 1ms 0.0036% 33.10% 1625ms 5.91% std::__final_insertion_sort (inline) 63ms 0.23% 33.33% 1581ms 5.75% boost::numeric::ublas::c_vector::c_vector (partial-inline) 166ms 0.6% 33.93% 1432ms 5.20% std::__unguarded_insertion_sort (inline) 12ms 0.044% 33.98% 1393ms 5.06% boost::numeric::ublas::vector_assign (inline) 2ms 0.0073% 33.98% 1290ms 4.69% NodeBasedCellPopulation::UpdateCellProcessLocation 241ms 0.88% 34.86% 1229ms 4.47% boost::numeric::ublas::indexing_vector_assign 663ms 2.41% 37.27% 1184ms 4.30% std::__unguarded_linear_insert (inline) 20ms 0.073% 37.34% 1181ms 4.29% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 389ms 1.41% 38.75% 1152ms 4.19% __dynamic_cast 554ms 2.01% 40.77% 1035ms 3.76% NodeAttributes::AddNeighbour 135ms 0.49% 41.26% 1009ms 3.67% AbstractMesh::GetVectorFromAtoB 4ms 0.015% 41.27% 988ms 3.59% DistributedBoxCollection::CalculateBoundaryNodePairs 43ms 0.16% 41.43% 947ms 3.44% std::_Rb_tree_const_iterator::operator++ (inline) 21ms 0.076% 41.51% 945ms 3.43% boost::detail::shared_count::~shared_count (inline) 0 0% 41.51% 945ms 3.43% boost::shared_ptr::~shared_ptr (inline) 25ms 0.091% 41.60% 927ms 3.37% CellPropertyCollection::GetPropertiesType (inline) 892ms 3.24% 44.84% 911ms 3.31% boost::detail::sp_counted_base::release 146ms 0.53% 45.37% 901ms 3.27% std::__new_allocator::allocate (inline) 29ms 0.11% 45.47% 890ms 3.23% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 45.47% 880ms 3.20% std::allocator_traits::allocate (inline) 2ms 0.0073% 45.48% 858ms 3.12% AbstractCentreBasedCellPopulation::GetDampingConstant 32ms 0.12% 45.60% 847ms 3.08% std::_Rb_tree::_M_copy (inline) 0 0% 45.60% 831ms 3.02% std::_Rb_tree::_M_create_node (inline) 374ms 1.36% 46.96% 824ms 2.99% DistributedBoxCollection::CalculateContainingBox (partial-inline) 804ms 2.92% 49.88% 804ms 2.92% std::_Rb_tree_increment 332ms 1.21% 51.08% 801ms 2.91% std::_Rb_tree::_M_clone_node (inline) 0 0% 51.08% 797ms 2.90% AbstractCellPopulation::WriteResultsToFiles 3ms 0.011% 51.10% 777ms 2.82% AbstractCellBasedSimulation::DoCellBirth 0 0% 51.10% 774ms 2.81% std::_Rb_tree::_M_get_node (inline) 761ms 2.77% 53.86% 761ms 2.77% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 28ms 0.1% 53.96% 751ms 2.73% operator new 749ms 2.72% 56.68% 749ms 2.72% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 56.68% 739ms 2.69% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 2ms 0.0073% 56.69% 731ms 2.66% std::set::set (inline) 0 0% 56.69% 713ms 2.59% boost::numeric::ublas::norm_2 (inline) 541ms 1.97% 58.66% 713ms 2.59% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 58.66% 713ms 2.59% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 239ms 0.87% 59.53% 702ms 2.55% __GI___libc_malloc 688ms 2.50% 62.03% 688ms 2.50% boost::numeric::ublas::c_vector::operator() 680ms 2.47% 64.50% 680ms 2.47% [libchaste_cell_based.so] 2ms 0.0073% 64.51% 649ms 2.36% Cell::GetMutationState 641ms 2.33% 66.84% 641ms 2.33% std::_Rb_tree::_S_left (inline) 244ms 0.89% 67.72% 628ms 2.28% __cxxabiv1::__si_class_type_info::__do_dyncast 147ms 0.53% 68.26% 603ms 2.19% std::_Rb_tree::_M_erase 0 0% 68.26% 586ms 2.13% AbstractCellBasedSimulation::DoCellRemoval (inline) 582ms 2.12% 70.37% 582ms 2.12% boost::numeric::ublas::same_impl_ex 575ms 2.09% 72.46% 575ms 2.09% __gnu_cxx::__normal_iterator::operator++ (inline) 16ms 0.058% 72.52% 573ms 2.08% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 570ms 2.07% 74.59% 570ms 2.07% [libchaste_mesh.so] 402ms 1.46% 76.05% 568ms 2.06% std::vector::push_back (inline) 28ms 0.1% 76.15% 562ms 2.04% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 76.15% 525ms 1.91% std::_Rb_tree::_Alloc_node::operator() (inline) 30ms 0.11% 76.26% 522ms 1.90% std::__copy_move::__copy_m (inline) 0 0% 76.26% 522ms 1.90% std::__copy_move_a (inline) 0 0% 76.26% 522ms 1.90% std::__copy_move_a1 (inline) 0 0% 76.26% 522ms 1.90% std::__copy_move_a2 (inline) 0 0% 76.26% 521ms 1.89% std::copy (inline) 1ms 0.0036% 76.27% 506ms 1.84% NodeBasedCellPopulation::WriteVtkResultsToFile 89ms 0.32% 76.59% 506ms 1.84% std::_Rb_tree::~_Rb_tree (inline) 505ms 1.84% 78.42% 505ms 1.84% __strcmp_evex 4ms 0.015% 78.44% 493ms 1.79% AbstractCellProperty::IsSubType (inline) 476ms 1.73% 80.17% 476ms 1.73% __memcpy_evex_unaligned_erms 117ms 0.43% 80.59% 471ms 1.71% boost::numeric::ublas::vector_binary::size (inline) 0 0% 80.59% 452ms 1.64% std::_Rb_tree::_M_drop_node (inline) 6ms 0.022% 80.62% 444ms 1.61% std::_Rb_tree::_M_emplace_hint_unique 207ms 0.75% 81.37% 401ms 1.46% _int_malloc 0 0% 81.37% 390ms 1.42% boost::numeric::ublas::c_vector::assign (inline) 0 0% 81.37% 383ms 1.39% NodesOnlyMesh::ReMesh 0 0% 81.37% 371ms 1.35% std::set::~set (inline) 7ms 0.025% 81.39% 369ms 1.34% NodesOnlyMesh::UpdateNodeIndices 32ms 0.12% 81.51% 358ms 1.30% Node::GetRadius 6ms 0.022% 81.53% 351ms 1.28% NodeBasedCellPopulation::UpdateMapsAfterRemesh 2ms 0.0073% 81.54% 317ms 1.15% CellPropertyCollection::HasProperty 0 0% 81.54% 315ms 1.14% Cell::HasCellProperty (inline) 8ms 0.029% 81.57% 311ms 1.13% std::__new_allocator::deallocate (inline) 12ms 0.044% 81.61% 309ms 1.12% Cell::ReadyToDivide 0 0% 81.61% 306ms 1.11% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 81.61% 298ms 1.08% NodesOnlyMesh::UpdateBoxCollection 2ms 0.0073% 81.62% 295ms 1.07% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 81.62% 294ms 1.07% std::allocator_traits::deallocate (inline) 248ms 0.9% 82.52% 293ms 1.06% boost::shared_ptr::shared_ptr (inline) 0 0% 82.52% 289ms 1.05% std::_Rb_tree::_M_put_node (inline) 5ms 0.018% 82.54% 277ms 1.01% DistributedBoxCollection::GetProcessOwningNode 76ms 0.28% 82.81% 275ms 1% __GI___libc_free 0 0% 82.81% 273ms 0.99% boost::numeric::ublas::inner_prod (inline) 5ms 0.018% 82.83% 269ms 0.98% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 265ms 0.96% 83.80% 265ms 0.96% Node::CheckForNodeAttributes 9ms 0.033% 83.83% 264ms 0.96% boost::numeric::ublas::vector_scalar_binary::evaluate 64ms 0.23% 84.06% 258ms 0.94% std::__move_median_to_first (inline) 140ms 0.51% 84.57% 224ms 0.81% AbstractCellCycleModel::GetAge 0 0% 84.57% 222ms 0.81% std::_Rb_tree::clear (inline) 73ms 0.27% 84.83% 221ms 0.8% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 84.83% 220ms 0.8% std::iter_swap (inline) 220ms 0.8% 85.63% 220ms 0.8% std::swap (inline) 4ms 0.015% 85.65% 219ms 0.8% NodesOnlyMesh::AddNodesToBoxes 216ms 0.78% 86.43% 216ms 0.78% boost::shared_ptr::operator-> (inline) 0 0% 86.43% 205ms 0.74% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 86.43% 203ms 0.74% VtkMeshWriter::WriteFiles 2ms 0.0073% 86.44% 198ms 0.72% Cell::GetCellId 181ms 0.66% 87.10% 197ms 0.72% _int_free 2ms 0.0073% 87.11% 193ms 0.7% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 49ms 0.18% 87.28% 192ms 0.7% std::__insertion_sort (inline) 0 0% 87.28% 192ms 0.7% std::map::map (inline) 0 0% 87.28% 191ms 0.69% NodesOnlyMesh::ResizeBoxCollection 11ms 0.04% 87.32% 188ms 0.68% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 87.32% 188ms 0.68% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 87.32% 182ms 0.66% vtkStreamingDemandDrivenPipeline::Update 0 0% 87.32% 182ms 0.66% vtkXMLWriterBase::Write 0 0% 87.32% 179ms 0.65% vtkDemandDrivenPipeline::ProcessRequest 0 0% 87.32% 179ms 0.65% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 87.32% 178ms 0.65% std::__new_allocator::destroy (inline) 0 0% 87.32% 178ms 0.65% std::allocator_traits::destroy (inline) 1ms 0.0036% 87.33% 177ms 0.64% vtkCompositeDataPipeline::ExecuteData 0 0% 87.33% 177ms 0.64% vtkExecutive::CallAlgorithm 0 0% 87.33% 176ms 0.64% vtkDemandDrivenPipeline::ExecuteData 0 0% 87.33% 176ms 0.64% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 87.33% 173ms 0.63% std::_Rb_tree::_M_destroy_node (inline) 5ms 0.018% 87.35% 171ms 0.62% AbstractCellProperty::IsType (inline) 0 0% 87.35% 162ms 0.59% Cell::GetCellProliferativeType 162ms 0.59% 87.93% 162ms 0.59% Node::GetIndex 0 0% 87.93% 159ms 0.58% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 1ms 0.0036% 87.94% 158ms 0.57% AbstractCentreBasedCellPopulation::CreateCellPair 14ms 0.051% 87.99% 158ms 0.57% boost::numeric::ublas::vector_reference::operator() (inline) 1ms 0.0036% 87.99% 156ms 0.57% NodeBasedCellPopulation::AcceptCellWriter 4ms 0.015% 88.01% 153ms 0.56% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 88.01% 153ms 0.56% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 88.01% 153ms 0.56% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 79ms 0.29% 88.29% 152ms 0.55% std::__new_allocator::construct (inline) 0 0% 88.29% 152ms 0.55% std::allocator_traits::construct (inline) 0 0% 88.29% 150ms 0.55% std::map::clear (inline) 0 0% 88.29% 147ms 0.53% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 3ms 0.011% 88.31% 142ms 0.52% AbstractCellPopulation::SetCellUsingLocationIndex 12ms 0.044% 88.35% 141ms 0.51% boost::numeric::ublas::c_vector::operator[] (inline) 4ms 0.015% 88.36% 140ms 0.51% NodeBasedCellPopulation::SetNode 6ms 0.022% 88.39% 139ms 0.51% DistributedBoxCollection::GetIsPeriodicAllDims 78ms 0.28% 88.67% 139ms 0.51% std::__adjacent_find (inline) 0 0% 88.67% 139ms 0.51% std::__unique (inline) 0 0% 88.67% 139ms 0.51% std::unique (inline)