File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20159ms, 89.14% of 22615ms total Dropped 773 nodes (cum <= 113.08ms) flat flat% sum% cum cum% 0 0% 0% 22545ms 99.69% __libc_start_call_main 0 0% 0% 22545ms 99.69% __libc_start_main_impl 0 0% 0% 22545ms 99.69% _start 0 0% 0% 22529ms 99.62% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 22529ms 99.62% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 22529ms 99.62% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 22529ms 99.62% main 0 0% 0% 22497ms 99.48% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 22497ms 99.48% CxxTest::TestRunner::runTest (inline) 0 0% 0% 22497ms 99.48% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 22489ms 99.44% AbstractCellBasedSimulation::Solve 0 0% 0% 12771ms 56.47% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0% 8640ms 38.20% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 7571ms 33.48% NodeBasedCellPopulation::Update 5ms 0.022% 0.022% 7271ms 32.15% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.013% 0.035% 7112ms 31.45% AbstractNumericalMethod::ComputeForcesIncludingDamping 917ms 4.05% 4.09% 6558ms 29.00% RepulsionForce::AddForceContribution (partial-inline) 10ms 0.044% 4.13% 5708ms 25.24% DistributedBoxCollection::CalculateInteriorNodePairs 1ms 0.0044% 4.14% 5197ms 22.98% OffLatticeSimulation::ApplyBoundaries 2144ms 9.48% 13.62% 4847ms 21.43% std::_Rb_tree::_M_lower_bound (inline) 14ms 0.062% 13.68% 4531ms 20.04% NodeAttributes::RemoveDuplicateNeighbours 5ms 0.022% 13.70% 4352ms 19.24% std::__sort (inline) 0 0% 13.70% 4352ms 19.24% std::sort (inline) 270ms 1.19% 14.90% 3849ms 17.02% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 3ms 0.013% 14.91% 3656ms 16.17% AbstractCellPopulation::Iterator::operator++ (inline) 183ms 0.81% 15.72% 3641ms 16.10% AbstractCellPopulation::Iterator::IsRealCell 145ms 0.64% 16.36% 3494ms 15.45% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 242ms 1.07% 17.43% 3166ms 14.00% std::_Rb_tree::find (inline) 0 0% 17.43% 3166ms 14.00% std::map::find (inline) 27ms 0.12% 17.55% 3051ms 13.49% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 67ms 0.3% 17.85% 2659ms 11.76% AbstractMesh::GetNode 59ms 0.26% 18.11% 2659ms 11.76% NodesOnlyMesh::GetNodeOrHaloNode 63ms 0.28% 18.39% 2649ms 11.71% PlaneBoundaryCondition::ImposeBoundaryCondition 248ms 1.10% 19.48% 2600ms 11.50% std::__introsort_loop 244ms 1.08% 20.56% 2599ms 11.49% NodesOnlyMesh::SolveNodeMapping 244ms 1.08% 21.64% 2556ms 11.30% std::map::operator[] (partial-inline) 37ms 0.16% 21.80% 2547ms 11.26% PlaneBoundaryCondition::VerifyBoundaryCondition 2364ms 10.45% 32.26% 2364ms 10.45% std::_Rb_tree::_S_right (inline) 5ms 0.022% 32.28% 2263ms 10.01% std::__unguarded_partition_pivot (inline) 76ms 0.34% 32.62% 2207ms 9.76% AbstractCellPopulation::GetLocationIndexUsingCell 694ms 3.07% 35.68% 2046ms 9.05% std::__unguarded_partition (inline) 0 0% 35.68% 1981ms 8.76% std::_Rb_tree::lower_bound (inline) 0 0% 35.68% 1981ms 8.76% std::map::lower_bound (inline) 1ms 0.0044% 35.69% 1741ms 7.70% std::__final_insertion_sort (inline) 147ms 0.65% 36.34% 1687ms 7.46% DistributedBoxCollection::AddPairsFromBox 113ms 0.5% 36.84% 1559ms 6.89% std::__unguarded_insertion_sort (inline) 8ms 0.035% 36.87% 1498ms 6.62% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 25ms 0.11% 36.98% 1482ms 6.55% AbstractCellPopulation::GetCellUsingLocationIndex 743ms 3.29% 40.27% 1392ms 6.16% std::__unguarded_linear_insert (inline) 12ms 0.053% 40.32% 1125ms 4.97% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 48ms 0.21% 40.54% 1115ms 4.93% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 40.54% 1095ms 4.84% NodeBasedCellPopulation::UpdateCellProcessLocation 991ms 4.38% 44.92% 991ms 4.38% __gnu_cxx::__normal_iterator::operator-- (inline) 6ms 0.027% 44.94% 956ms 4.23% boost::numeric::ublas::vector_assign (inline) 6ms 0.027% 44.97% 933ms 4.13% DistributedBoxCollection::CalculateBoundaryNodePairs 19ms 0.084% 45.05% 913ms 4.04% boost::detail::shared_count::~shared_count (inline) 0 0% 45.05% 913ms 4.04% boost::shared_ptr::~shared_ptr (inline) 866ms 3.83% 48.88% 875ms 3.87% boost::detail::sp_counted_base::release 204ms 0.9% 49.79% 811ms 3.59% boost::numeric::ublas::indexing_vector_assign 221ms 0.98% 50.76% 752ms 3.33% __dynamic_cast 316ms 1.40% 52.16% 747ms 3.30% DistributedBoxCollection::CalculateContainingBox (partial-inline) 98ms 0.43% 52.59% 668ms 2.95% AbstractMesh::GetVectorFromAtoB 0 0% 52.59% 637ms 2.82% AbstractCellPopulation::WriteResultsToFiles 2ms 0.0088% 52.60% 623ms 2.75% boost::numeric::ublas::c_vector::operator= (inline) 30ms 0.13% 52.73% 611ms 2.70% std::__copy_move::__copy_m (inline) 0 0% 52.73% 611ms 2.70% std::__copy_move_a (inline) 0 0% 52.73% 611ms 2.70% std::__copy_move_a1 (inline) 0 0% 52.73% 611ms 2.70% std::__copy_move_a2 (inline) 0 0% 52.73% 611ms 2.70% std::copy (inline) 56ms 0.25% 52.98% 602ms 2.66% std::__new_allocator::allocate (inline) 17ms 0.075% 53.06% 586ms 2.59% std::_Rb_tree_const_iterator::operator++ (inline) 585ms 2.59% 55.64% 585ms 2.59% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 55.64% 579ms 2.56% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 55.64% 573ms 2.53% std::allocator_traits::allocate (inline) 570ms 2.52% 58.16% 570ms 2.52% __memcpy_avx512_unaligned_erms 0 0% 58.16% 557ms 2.46% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 58.16% 555ms 2.45% boost::numeric::ublas::norm_2 (inline) 458ms 2.03% 60.19% 555ms 2.45% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 60.19% 555ms 2.45% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 256ms 1.13% 61.32% 546ms 2.41% NodeAttributes::AddNeighbour 11ms 0.049% 61.37% 545ms 2.41% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 34ms 0.15% 61.52% 540ms 2.39% operator new 537ms 2.37% 63.90% 537ms 2.37% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 63.90% 537ms 2.37% std::_Rb_tree::_M_create_node (inline) 4ms 0.018% 63.91% 530ms 2.34% CellPropertyCollection::GetPropertiesType (inline) 518ms 2.29% 66.20% 518ms 2.29% std::_Rb_tree_increment 0 0% 66.20% 512ms 2.26% AbstractCellBasedSimulation::DoCellBirth 3ms 0.013% 66.22% 512ms 2.26% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 66.22% 505ms 2.23% std::_Rb_tree::_M_get_node (inline) 19ms 0.084% 66.30% 502ms 2.22% std::_Rb_tree::_Rb_tree (partial-inline) 496ms 2.19% 68.49% 496ms 2.19% boost::numeric::ublas::c_vector::operator() 493ms 2.18% 70.67% 493ms 2.18% [libchaste_cell_based.so] 170ms 0.75% 71.43% 493ms 2.18% __GI___libc_malloc 488ms 2.16% 73.58% 488ms 2.16% boost::numeric::ublas::same_impl_ex 27ms 0.12% 73.70% 474ms 2.10% std::_Rb_tree::_M_copy (inline) 453ms 2.00% 75.71% 453ms 2.00% [libchaste_mesh.so] 77ms 0.34% 76.05% 451ms 1.99% std::_Rb_tree::_M_erase 230ms 1.02% 77.06% 441ms 1.95% __cxxabiv1::__si_class_type_info::__do_dyncast 179ms 0.79% 77.86% 441ms 1.95% std::_Rb_tree::_M_clone_node (inline) 94ms 0.42% 78.27% 427ms 1.89% std::_Rb_tree::~_Rb_tree (inline) 1ms 0.0044% 78.28% 423ms 1.87% NodeBasedCellPopulation::WriteVtkResultsToFile 3ms 0.013% 78.29% 418ms 1.85% std::set::set (inline) 268ms 1.19% 79.47% 392ms 1.73% std::vector::push_back (inline) 0 0% 79.47% 371ms 1.64% std::_Rb_tree::_M_drop_node (inline) 0 0% 79.47% 365ms 1.61% Cell::GetMutationState 0 0% 79.47% 353ms 1.56% std::set::~set (inline) 6ms 0.027% 79.50% 351ms 1.55% AbstractCellProperty::IsSubType (inline) 350ms 1.55% 81.05% 350ms 1.55% std::_Rb_tree::_S_left (inline) 8ms 0.035% 81.08% 331ms 1.46% std::_Rb_tree::_M_emplace_hint_unique 0 0% 81.08% 321ms 1.42% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 81.08% 319ms 1.41% NodesOnlyMesh::ReMesh 9ms 0.04% 81.12% 313ms 1.38% boost::numeric::ublas::vector_binary::size (inline) 3ms 0.013% 81.14% 308ms 1.36% NodesOnlyMesh::UpdateNodeIndices 9ms 0.04% 81.18% 293ms 1.30% std::__new_allocator::deallocate (inline) 290ms 1.28% 82.46% 290ms 1.28% __strcmp_evex 1ms 0.0044% 82.46% 280ms 1.24% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 2ms 0.0088% 82.47% 269ms 1.19% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 82.47% 267ms 1.18% NodesOnlyMesh::UpdateBoxCollection 63ms 0.28% 82.75% 267ms 1.18% __GI___libc_free 5ms 0.022% 82.77% 265ms 1.17% DistributedBoxCollection::GetProcessOwningNode 2ms 0.0088% 82.78% 265ms 1.17% Node::GetRadius 171ms 0.76% 83.54% 261ms 1.15% _int_malloc 0 0% 83.54% 257ms 1.14% std::allocator_traits::deallocate (inline) 0 0% 83.54% 254ms 1.12% boost::numeric::ublas::c_vector::assign (inline) 0 0% 83.54% 252ms 1.11% std::_Rb_tree::_M_put_node (inline) 213ms 0.94% 84.48% 243ms 1.07% boost::shared_ptr::shared_ptr (inline) 0 0% 84.48% 216ms 0.96% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1ms 0.0044% 84.48% 214ms 0.95% NodesOnlyMesh::AddNodesToBoxes 0 0% 84.48% 213ms 0.94% std::iter_swap (inline) 213ms 0.94% 85.43% 213ms 0.94% std::swap (inline) 63ms 0.28% 85.70% 211ms 0.93% std::__move_median_to_first (inline) 204ms 0.9% 86.61% 204ms 0.9% Node::CheckForNodeAttributes 0 0% 86.61% 201ms 0.89% boost::numeric::ublas::inner_prod (inline) 1ms 0.0044% 86.61% 201ms 0.89% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 7ms 0.031% 86.64% 200ms 0.88% boost::numeric::ublas::vector_scalar_binary::evaluate 174ms 0.77% 87.41% 198ms 0.88% _int_free 2ms 0.0088% 87.42% 185ms 0.82% CellPropertyCollection::HasProperty 0 0% 87.42% 183ms 0.81% Cell::HasCellProperty (inline) 0 0% 87.42% 182ms 0.8% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 18ms 0.08% 87.50% 181ms 0.8% std::__insertion_sort (inline) 0 0% 87.50% 180ms 0.8% VtkMeshWriter::WriteFiles 1ms 0.0044% 87.50% 179ms 0.79% NodesOnlyMesh::ResizeBoxCollection 15ms 0.066% 87.57% 176ms 0.78% NodesOnlyMesh::IsANodeCloseToDomainBoundary 2ms 0.0088% 87.58% 168ms 0.74% Cell::ReadyToDivide 39ms 0.17% 87.75% 162ms 0.72% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 87.75% 156ms 0.69% vtkXMLWriterBase::Write 0 0% 87.75% 155ms 0.69% vtkDemandDrivenPipeline::ProcessRequest 0 0% 87.75% 155ms 0.69% vtkStreamingDemandDrivenPipeline::Update 0 0% 87.75% 154ms 0.68% vtkDemandDrivenPipeline::ExecuteData 0 0% 87.75% 154ms 0.68% vtkExecutive::CallAlgorithm 0 0% 87.75% 154ms 0.68% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 87.75% 153ms 0.68% vtkCompositeDataPipeline::ExecuteData 0 0% 87.75% 153ms 0.68% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 87.75% 150ms 0.66% boost::numeric::ublas::vector_binary::operator() (inline) 6ms 0.027% 87.78% 145ms 0.64% AbstractCellProperty::IsType (inline) 1ms 0.0044% 87.78% 142ms 0.63% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 139ms 0.61% 88.40% 139ms 0.61% boost::shared_ptr::operator-> (inline) 2ms 0.0088% 88.41% 138ms 0.61% DistributedBoxCollection::GetIsPeriodicAllDims 0 0% 88.41% 138ms 0.61% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 88.41% 137ms 0.61% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 88.41% 135ms 0.6% std::_Rb_tree::clear (inline) 1ms 0.0044% 88.41% 134ms 0.59% std::_Rb_tree::_M_insert_unique 0 0% 88.41% 134ms 0.59% std::set::insert (inline) 0 0% 88.41% 134ms 0.59% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 49ms 0.22% 88.63% 129ms 0.57% std::__adjacent_find (inline) 0 0% 88.63% 129ms 0.57% std::__unique (inline) 0 0% 88.63% 129ms 0.57% std::unique (inline) 0 0% 88.63% 126ms 0.56% std::__new_allocator::destroy (inline) 0 0% 88.63% 126ms 0.56% std::allocator_traits::destroy (inline) 0 0% 88.63% 124ms 0.55% Cell::GetCellId 0 0% 88.63% 124ms 0.55% std::_Rb_tree::_M_destroy_node (inline) 116ms 0.51% 89.14% 119ms 0.53% __ieee754_log_fma 0 0% 89.14% 114ms 0.5% vtkXMLWriter::WriteBinaryData