File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 23821ms, 88.94% of 26782ms total Dropped 839 nodes (cum <= 133.91ms) flat flat% sum% cum cum% 0 0% 0% 26701ms 99.70% __libc_start_call_main 0 0% 0% 26701ms 99.70% __libc_start_main_impl 0 0% 0% 26701ms 99.70% _start 0 0% 0% 26683ms 99.63% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 26683ms 99.63% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 26683ms 99.63% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 26683ms 99.63% main 0 0% 0% 26649ms 99.50% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 26649ms 99.50% CxxTest::TestRunner::runTest (inline) 0 0% 0% 26649ms 99.50% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 26641ms 99.47% AbstractCellBasedSimulation::Solve 1ms 0.0037% 0.0037% 14941ms 55.79% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0037% 10464ms 39.07% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.0037% 9143ms 34.14% NodeBasedCellPopulation::Update 4ms 0.015% 0.019% 8616ms 32.17% ForwardEulerNumericalMethod::UpdateAllNodePositions 5ms 0.019% 0.037% 8433ms 31.49% AbstractNumericalMethod::ComputeForcesIncludingDamping 1013ms 3.78% 3.82% 7597ms 28.37% RepulsionForce::AddForceContribution (partial-inline) 7ms 0.026% 3.85% 7002ms 26.14% DistributedBoxCollection::CalculateInteriorNodePairs 1ms 0.0037% 3.85% 5938ms 22.17% OffLatticeSimulation::ApplyBoundaries 2317ms 8.65% 12.50% 5468ms 20.42% std::_Rb_tree::_M_lower_bound (inline) 20ms 0.075% 12.58% 5214ms 19.47% NodeAttributes::RemoveDuplicateNeighbours 3ms 0.011% 12.59% 5014ms 18.72% std::__sort (inline) 0 0% 12.59% 5014ms 18.72% std::sort (inline) 310ms 1.16% 13.74% 4358ms 16.27% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 180ms 0.67% 14.42% 4208ms 15.71% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 4ms 0.015% 14.43% 4134ms 15.44% AbstractCellPopulation::Iterator::operator++ (inline) 191ms 0.71% 15.14% 4125ms 15.40% AbstractCellPopulation::Iterator::IsRealCell (inline) 265ms 0.99% 16.13% 3593ms 13.42% std::_Rb_tree::find (inline) 0 0% 16.13% 3593ms 13.42% std::map::find (inline) 41ms 0.15% 16.29% 3478ms 12.99% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 277ms 1.03% 17.32% 3047ms 11.38% std::__introsort_loop 54ms 0.2% 17.52% 3004ms 11.22% PlaneBoundaryCondition::ImposeBoundaryCondition 115ms 0.43% 17.95% 2999ms 11.20% AbstractMesh::GetNode 52ms 0.19% 18.15% 2976ms 11.11% NodesOnlyMesh::GetNodeOrHaloNode 58ms 0.22% 18.36% 2932ms 10.95% PlaneBoundaryCondition::VerifyBoundaryCondition 266ms 0.99% 19.36% 2893ms 10.80% NodesOnlyMesh::SolveNodeMapping 224ms 0.84% 20.19% 2833ms 10.58% std::map::operator[] (partial-inline) 2781ms 10.38% 30.58% 2781ms 10.38% std::_Rb_tree::_S_right (inline) 4ms 0.015% 30.59% 2675ms 9.99% std::__unguarded_partition_pivot (inline) 831ms 3.10% 33.69% 2425ms 9.05% std::__unguarded_partition (inline) 118ms 0.44% 34.13% 2402ms 8.97% AbstractCellPopulation::GetLocationIndexUsingCell 131ms 0.49% 34.62% 2336ms 8.72% DistributedBoxCollection::AddPairsFromBox 0 0% 34.62% 2194ms 8.19% std::_Rb_tree::lower_bound (inline) 0 0% 34.62% 2194ms 8.19% std::map::lower_bound (inline) 1ms 0.0037% 34.63% 1961ms 7.32% std::__final_insertion_sort (inline) 13ms 0.049% 34.68% 1930ms 7.21% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 24ms 0.09% 34.77% 1905ms 7.11% AbstractCellPopulation::GetCellUsingLocationIndex 138ms 0.52% 35.28% 1745ms 6.52% std::__unguarded_insertion_sort (inline) 798ms 2.98% 38.26% 1511ms 5.64% std::__unguarded_linear_insert (inline) 30ms 0.11% 38.37% 1272ms 4.75% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 38.37% 1238ms 4.62% NodeBasedCellPopulation::UpdateCellProcessLocation 63ms 0.24% 38.61% 1230ms 4.59% boost::numeric::ublas::c_vector::c_vector (partial-inline) 1124ms 4.20% 42.80% 1124ms 4.20% __gnu_cxx::__normal_iterator::operator-- (inline) 27ms 0.1% 42.91% 1116ms 4.17% boost::detail::shared_count::~shared_count (inline) 0 0% 42.91% 1116ms 4.17% boost::shared_ptr::~shared_ptr (inline) 8ms 0.03% 42.94% 1068ms 3.99% DistributedBoxCollection::CalculateBoundaryNodePairs 1043ms 3.89% 46.83% 1056ms 3.94% boost::detail::sp_counted_base::release 9ms 0.034% 46.86% 1024ms 3.82% boost::numeric::ublas::vector_assign (inline) 331ms 1.24% 48.10% 966ms 3.61% __dynamic_cast 573ms 2.14% 50.24% 958ms 3.58% NodeAttributes::AddNeighbour 39ms 0.15% 50.38% 927ms 3.46% std::_Rb_tree_const_iterator::operator++ (inline) 231ms 0.86% 51.25% 881ms 3.29% boost::numeric::ublas::indexing_vector_assign 364ms 1.36% 52.61% 847ms 3.16% DistributedBoxCollection::CalculateContainingBox (partial-inline) 25ms 0.093% 52.70% 815ms 3.04% CellPropertyCollection::GetPropertiesType (inline) 814ms 3.04% 55.74% 814ms 3.04% std::_Rb_tree_increment 107ms 0.4% 56.14% 794ms 2.96% std::__new_allocator::allocate (inline) 5ms 0.019% 56.16% 767ms 2.86% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 56.16% 766ms 2.86% std::allocator_traits::allocate (inline) 50ms 0.19% 56.34% 759ms 2.83% std::_Rb_tree::_Rb_tree (partial-inline) 108ms 0.4% 56.75% 757ms 2.83% AbstractMesh::GetVectorFromAtoB 0 0% 56.75% 750ms 2.80% AbstractCellPopulation::WriteResultsToFiles 0 0% 56.75% 721ms 2.69% std::_Rb_tree::_M_create_node (inline) 46ms 0.17% 56.92% 697ms 2.60% std::_Rb_tree::_M_copy (inline) 689ms 2.57% 59.49% 689ms 2.57% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 59.49% 689ms 2.57% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 23ms 0.086% 59.58% 684ms 2.55% operator new 0 0% 59.58% 680ms 2.54% std::_Rb_tree::_M_get_node (inline) 675ms 2.52% 62.10% 675ms 2.52% __gnu_cxx::__normal_iterator::operator++ (inline) 2ms 0.0075% 62.11% 668ms 2.49% AbstractCellBasedSimulation::DoCellBirth 0 0% 62.11% 663ms 2.48% boost::numeric::ublas::norm_2 (inline) 529ms 1.98% 64.08% 663ms 2.48% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 64.08% 663ms 2.48% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 64.08% 653ms 2.44% AbstractCellBasedSimulation::DoCellRemoval (inline) 3ms 0.011% 64.09% 653ms 2.44% boost::numeric::ublas::c_vector::operator= (inline) 221ms 0.83% 64.92% 646ms 2.41% __GI___libc_malloc 271ms 1.01% 65.93% 646ms 2.41% std::_Rb_tree::_M_clone_node (inline) 636ms 2.37% 68.30% 636ms 2.37% [libchaste_cell_based.so] 11ms 0.041% 68.34% 628ms 2.34% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 35ms 0.13% 68.48% 628ms 2.34% std::__copy_move::__copy_m (inline) 0 0% 68.48% 628ms 2.34% std::__copy_move_a (inline) 0 0% 68.48% 628ms 2.34% std::__copy_move_a1 (inline) 0 0% 68.48% 628ms 2.34% std::__copy_move_a2 (inline) 0 0% 68.48% 628ms 2.34% std::copy (inline) 0 0% 68.48% 622ms 2.32% std::set::set (inline) 1ms 0.0037% 68.48% 595ms 2.22% Cell::GetMutationState 589ms 2.20% 70.68% 589ms 2.20% [libchaste_mesh.so] 575ms 2.15% 72.83% 575ms 2.15% __memcpy_evex_unaligned_erms 521ms 1.95% 74.77% 521ms 1.95% boost::numeric::ublas::c_vector::operator() 225ms 0.84% 75.61% 519ms 1.94% __cxxabiv1::__si_class_type_info::__do_dyncast 82ms 0.31% 75.92% 508ms 1.90% std::_Rb_tree::_M_erase 345ms 1.29% 77.20% 506ms 1.89% std::vector::push_back (inline) 503ms 1.88% 79.08% 503ms 1.88% boost::numeric::ublas::same_impl_ex 3ms 0.011% 79.09% 478ms 1.78% NodeBasedCellPopulation::WriteVtkResultsToFile 5ms 0.019% 79.11% 474ms 1.77% AbstractCellProperty::IsSubType (inline) 90ms 0.34% 79.45% 467ms 1.74% std::_Rb_tree::~_Rb_tree (inline) 0 0% 79.45% 434ms 1.62% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 79.45% 423ms 1.58% std::_Rb_tree::_M_drop_node (inline) 9ms 0.034% 79.48% 415ms 1.55% std::_Rb_tree::_M_emplace_hint_unique 0 0% 79.48% 415ms 1.55% std::set::~set (inline) 406ms 1.52% 81.00% 406ms 1.52% __strcmp_evex 381ms 1.42% 82.42% 381ms 1.42% std::_Rb_tree::_S_left (inline) 0 0% 82.42% 369ms 1.38% NodesOnlyMesh::ReMesh 13ms 0.049% 82.47% 369ms 1.38% boost::numeric::ublas::vector_binary::size (inline) 3ms 0.011% 82.48% 361ms 1.35% NodesOnlyMesh::UpdateNodeIndices 218ms 0.81% 83.29% 355ms 1.33% _int_malloc 5ms 0.019% 83.31% 334ms 1.25% NodeBasedCellPopulation::UpdateMapsAfterRemesh 2ms 0.0075% 83.32% 309ms 1.15% CellPropertyCollection::HasProperty 0 0% 83.32% 307ms 1.15% Cell::HasCellProperty (inline) 2ms 0.0075% 83.33% 299ms 1.12% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 83.33% 299ms 1.12% NodesOnlyMesh::UpdateBoxCollection 2ms 0.0075% 83.34% 288ms 1.08% Node::GetRadius 0 0% 83.34% 287ms 1.07% std::_Rb_tree::_Auto_node::_Auto_node (inline) 13ms 0.049% 83.38% 286ms 1.07% std::__new_allocator::deallocate (inline) 239ms 0.89% 84.28% 280ms 1.05% boost::shared_ptr::shared_ptr (inline) 2ms 0.0075% 84.28% 275ms 1.03% DistributedBoxCollection::GetProcessOwningNode 3ms 0.011% 84.30% 261ms 0.97% Cell::ReadyToDivide 0 0% 84.30% 261ms 0.97% boost::numeric::ublas::c_vector::assign (inline) 260ms 0.97% 85.27% 260ms 0.97% boost::shared_ptr::operator-> (inline) 0 0% 85.27% 251ms 0.94% std::allocator_traits::deallocate (inline) 0 0% 85.27% 244ms 0.91% std::_Rb_tree::_M_put_node (inline) 80ms 0.3% 85.56% 242ms 0.9% std::__move_median_to_first (inline) 0 0% 85.56% 239ms 0.89% NodesOnlyMesh::AddNodesToBoxes 0 0% 85.56% 236ms 0.88% boost::numeric::ublas::inner_prod (inline) 63ms 0.24% 85.80% 235ms 0.88% __GI___libc_free 1ms 0.0037% 85.80% 234ms 0.87% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 14ms 0.052% 85.86% 233ms 0.87% boost::numeric::ublas::vector_scalar_binary::evaluate 221ms 0.83% 86.68% 221ms 0.83% Node::CheckForNodeAttributes 38ms 0.14% 86.82% 215ms 0.8% std::__insertion_sort (inline) 0 0% 86.82% 211ms 0.79% std::iter_swap (inline) 211ms 0.79% 87.61% 211ms 0.79% std::swap (inline) 0 0% 87.61% 208ms 0.78% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 87.61% 206ms 0.77% VtkMeshWriter::WriteFiles 0 0% 87.61% 188ms 0.7% std::__new_allocator::destroy (inline) 0 0% 87.61% 188ms 0.7% std::allocator_traits::destroy (inline) 54ms 0.2% 87.81% 187ms 0.7% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 87.81% 185ms 0.69% NodesOnlyMesh::ResizeBoxCollection 0 0% 87.81% 185ms 0.69% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 87.81% 185ms 0.69% vtkStreamingDemandDrivenPipeline::Update 0 0% 87.81% 185ms 0.69% vtkXMLWriterBase::Write 0 0% 87.81% 184ms 0.69% std::_Rb_tree::_M_destroy_node (inline) 12ms 0.045% 87.86% 183ms 0.68% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 87.86% 183ms 0.68% vtkDemandDrivenPipeline::ProcessRequest 6ms 0.022% 87.88% 182ms 0.68% AbstractCellProperty::IsType (inline) 0 0% 87.88% 182ms 0.68% vtkCompositeDataPipeline::ExecuteData 0 0% 87.88% 182ms 0.68% vtkDemandDrivenPipeline::ExecuteData 0 0% 87.88% 182ms 0.68% vtkExecutive::CallAlgorithm 0 0% 87.88% 181ms 0.68% vtkXMLUnstructuredDataWriter::ProcessRequest 3ms 0.011% 87.89% 177ms 0.66% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 87.89% 175ms 0.65% boost::numeric::ublas::vector_binary::operator() (inline) 142ms 0.53% 88.42% 168ms 0.63% _int_free 2ms 0.0075% 88.43% 166ms 0.62% Cell::GetCellId 0 0% 88.43% 155ms 0.58% std::map::map (inline) 0 0% 88.43% 151ms 0.56% std::_Rb_tree::clear (inline) 67ms 0.25% 88.68% 150ms 0.56% std::__adjacent_find (inline) 0 0% 88.68% 150ms 0.56% std::__unique (inline) 0 0% 88.68% 150ms 0.56% std::unique (inline) 0 0% 88.68% 147ms 0.55% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 88.68% 147ms 0.55% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 3ms 0.011% 88.69% 145ms 0.54% DistributedBoxCollection::GetIsPeriodicAllDims 2ms 0.0075% 88.70% 144ms 0.54% std::_Rb_tree::_M_insert_unique 0 0% 88.70% 144ms 0.54% std::set::insert (inline) 4ms 0.015% 88.71% 143ms 0.53% NodeBasedCellPopulation::AcceptCellWriter 0 0% 88.71% 143ms 0.53% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 61ms 0.23% 88.94% 140ms 0.52% AbstractCellProperty::IsSame 1ms 0.0037% 88.94% 139ms 0.52% AbstractCellPopulation::SetCellUsingLocationIndex 0 0% 88.94% 139ms 0.52% Cell::GetCellProliferativeType