File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 19365ms, 88.68% of 21837ms total Dropped 747 nodes (cum <= 109.19ms) flat flat% sum% cum cum% 0 0% 0% 21758ms 99.64% __libc_start_call_main 0 0% 0% 21758ms 99.64% __libc_start_main_impl 0 0% 0% 21758ms 99.64% _start 0 0% 0% 21743ms 99.57% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 21743ms 99.57% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 21743ms 99.57% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 21743ms 99.57% main 0 0% 0% 21712ms 99.43% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 21712ms 99.43% CxxTest::TestRunner::runTest (inline) 0 0% 0% 21711ms 99.42% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 21704ms 99.39% AbstractCellBasedSimulation::Solve 0 0% 0% 12279ms 56.23% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0% 8379ms 38.37% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0046% 0.0046% 7368ms 33.74% NodeBasedCellPopulation::Update 4ms 0.018% 0.023% 7040ms 32.24% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.014% 0.037% 6875ms 31.48% AbstractNumericalMethod::ComputeForcesIncludingDamping 840ms 3.85% 3.88% 6328ms 28.98% RepulsionForce::AddForceContribution (partial-inline) 6ms 0.027% 3.91% 5554ms 25.43% DistributedBoxCollection::CalculateInteriorNodePairs 0 0% 3.91% 4996ms 22.88% OffLatticeSimulation::ApplyBoundaries 2035ms 9.32% 13.23% 4607ms 21.10% std::_Rb_tree::_M_lower_bound (inline) 11ms 0.05% 13.28% 4417ms 20.23% NodeAttributes::RemoveDuplicateNeighbours 3ms 0.014% 13.29% 4245ms 19.44% std::__sort (inline) 0 0% 13.29% 4245ms 19.44% std::sort (inline) 273ms 1.25% 14.54% 3642ms 16.68% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 4ms 0.018% 14.56% 3516ms 16.10% AbstractCellPopulation::Iterator::operator++ (inline) 208ms 0.95% 15.51% 3500ms 16.03% AbstractCellPopulation::Iterator::IsRealCell (inline) 118ms 0.54% 16.06% 3469ms 15.89% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 240ms 1.10% 17.15% 3049ms 13.96% std::_Rb_tree::find (inline) 0 0% 17.15% 3049ms 13.96% std::map::find (inline) 25ms 0.11% 17.27% 2897ms 13.27% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 86ms 0.39% 17.66% 2599ms 11.90% AbstractMesh::GetNode 67ms 0.31% 17.97% 2586ms 11.84% NodesOnlyMesh::GetNodeOrHaloNode 235ms 1.08% 19.05% 2567ms 11.76% std::__introsort_loop 76ms 0.35% 19.39% 2525ms 11.56% PlaneBoundaryCondition::ImposeBoundaryCondition 245ms 1.12% 20.52% 2519ms 11.54% NodesOnlyMesh::SolveNodeMapping 43ms 0.2% 20.71% 2471ms 11.32% PlaneBoundaryCondition::VerifyBoundaryCondition 165ms 0.76% 21.47% 2313ms 10.59% std::map::operator[] (partial-inline) 4ms 0.018% 21.49% 2258ms 10.34% std::__unguarded_partition_pivot (inline) 2254ms 10.32% 31.81% 2254ms 10.32% std::_Rb_tree::_S_right (inline) 716ms 3.28% 35.09% 2060ms 9.43% std::__unguarded_partition (inline) 100ms 0.46% 35.55% 1985ms 9.09% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 35.55% 1843ms 8.44% std::_Rb_tree::lower_bound (inline) 0 0% 35.55% 1843ms 8.44% std::map::lower_bound (inline) 0 0% 35.55% 1673ms 7.66% std::__final_insertion_sort (inline) 124ms 0.57% 36.11% 1613ms 7.39% DistributedBoxCollection::AddPairsFromBox 105ms 0.48% 36.59% 1480ms 6.78% std::__unguarded_insertion_sort (inline) 7ms 0.032% 36.63% 1455ms 6.66% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 17ms 0.078% 36.70% 1440ms 6.59% AbstractCellPopulation::GetCellUsingLocationIndex 721ms 3.30% 40.01% 1343ms 6.15% std::__unguarded_linear_insert (inline) 18ms 0.082% 40.09% 1118ms 5.12% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 63ms 0.29% 40.38% 1103ms 5.05% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 40.38% 1060ms 4.85% NodeBasedCellPopulation::UpdateCellProcessLocation 962ms 4.41% 44.78% 962ms 4.41% __gnu_cxx::__normal_iterator::operator-- (inline) 27ms 0.12% 44.91% 924ms 4.23% boost::detail::shared_count::~shared_count (inline) 0 0% 44.91% 924ms 4.23% boost::shared_ptr::~shared_ptr (inline) 6ms 0.027% 44.93% 921ms 4.22% DistributedBoxCollection::CalculateBoundaryNodePairs 6ms 0.027% 44.96% 918ms 4.20% boost::numeric::ublas::vector_assign (inline) 863ms 3.95% 48.91% 869ms 3.98% boost::detail::sp_counted_base::release 217ms 0.99% 49.91% 805ms 3.69% boost::numeric::ublas::indexing_vector_assign 227ms 1.04% 50.95% 789ms 3.61% __dynamic_cast 275ms 1.26% 52.20% 709ms 3.25% DistributedBoxCollection::CalculateContainingBox (partial-inline) 91ms 0.42% 52.62% 693ms 3.17% AbstractMesh::GetVectorFromAtoB 0 0% 52.62% 642ms 2.94% AbstractCellPopulation::WriteResultsToFiles 580ms 2.66% 55.28% 580ms 2.66% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 260ms 1.19% 56.47% 558ms 2.56% NodeAttributes::AddNeighbour 28ms 0.13% 56.60% 552ms 2.53% std::_Rb_tree_const_iterator::operator++ (inline) 547ms 2.50% 59.10% 547ms 2.50% __gnu_cxx::__normal_iterator::operator++ (inline) 64ms 0.29% 59.39% 538ms 2.46% std::__new_allocator::allocate (inline) 0 0% 59.39% 526ms 2.41% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 59.39% 523ms 2.40% AbstractCellBasedSimulation::DoCellRemoval (inline) 6ms 0.027% 59.42% 522ms 2.39% boost::numeric::ublas::c_vector::operator= (inline) 6ms 0.027% 59.45% 518ms 2.37% CellPropertyCollection::GetPropertiesType (inline) 514ms 2.35% 61.80% 514ms 2.35% [libchaste_cell_based.so] 7ms 0.032% 61.84% 512ms 2.34% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 61.84% 512ms 2.34% std::allocator_traits::allocate (inline) 0 0% 61.84% 509ms 2.33% boost::numeric::ublas::norm_2 (inline) 402ms 1.84% 63.68% 509ms 2.33% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 63.68% 509ms 2.33% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 32ms 0.15% 63.82% 508ms 2.33% std::__copy_move::__copy_m (inline) 0 0% 63.82% 508ms 2.33% std::__copy_move_a (inline) 0 0% 63.82% 508ms 2.33% std::__copy_move_a1 (inline) 0 0% 63.82% 508ms 2.33% std::__copy_move_a2 (inline) 0 0% 63.82% 508ms 2.33% std::copy (inline) 2ms 0.0092% 63.83% 502ms 2.30% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 63.83% 488ms 2.23% AbstractCellBasedSimulation::DoCellBirth 0 0% 63.83% 483ms 2.21% std::_Rb_tree::_M_create_node (inline) 16ms 0.073% 63.91% 475ms 2.18% operator new 471ms 2.16% 66.06% 471ms 2.16% boost::numeric::ublas::c_vector::operator() 468ms 2.14% 68.21% 468ms 2.14% [libchaste_mesh.so] 464ms 2.12% 70.33% 464ms 2.12% __memcpy_avx512_unaligned_erms 460ms 2.11% 72.44% 460ms 2.11% std::_Rb_tree_increment 0 0% 72.44% 458ms 2.10% std::_Rb_tree::_M_get_node (inline) 13ms 0.06% 72.50% 456ms 2.09% std::_Rb_tree::_Rb_tree (partial-inline) 191ms 0.87% 73.37% 455ms 2.08% __cxxabiv1::__si_class_type_info::__do_dyncast 155ms 0.71% 74.08% 447ms 2.05% __GI___libc_malloc 447ms 2.05% 76.13% 447ms 2.05% boost::numeric::ublas::same_impl_ex 64ms 0.29% 76.42% 447ms 2.05% std::_Rb_tree::_M_erase 32ms 0.15% 76.57% 435ms 1.99% std::_Rb_tree::_M_copy (inline) 90ms 0.41% 76.98% 428ms 1.96% std::_Rb_tree::~_Rb_tree (inline) 3ms 0.014% 76.99% 427ms 1.96% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 76.99% 398ms 1.82% std::set::set (inline) 166ms 0.76% 77.75% 395ms 1.81% std::_Rb_tree::_M_clone_node (inline) 0 0% 77.75% 382ms 1.75% std::_Rb_tree::_M_drop_node (inline) 269ms 1.23% 78.99% 381ms 1.74% std::vector::push_back (inline) 374ms 1.71% 80.70% 374ms 1.71% __strcmp_evex 0 0% 80.70% 366ms 1.68% std::set::~set (inline) 3ms 0.014% 80.71% 354ms 1.62% AbstractCellProperty::IsSubType (inline) 3ms 0.014% 80.73% 353ms 1.62% Cell::GetMutationState 18ms 0.082% 80.81% 348ms 1.59% boost::numeric::ublas::vector_binary::size (inline) 340ms 1.56% 82.36% 340ms 1.56% std::_Rb_tree::_S_left (inline) 0 0% 82.36% 313ms 1.43% NodesOnlyMesh::ReMesh 10ms 0.046% 82.41% 304ms 1.39% std::_Rb_tree::_M_emplace_hint_unique 7ms 0.032% 82.44% 302ms 1.38% NodeBasedCellPopulation::UpdateMapsAfterRemesh 3ms 0.014% 82.46% 299ms 1.37% NodesOnlyMesh::UpdateNodeIndices 0 0% 82.46% 281ms 1.29% std::_Rb_tree::_Alloc_node::operator() (inline) 2ms 0.0092% 82.47% 270ms 1.24% Node::GetRadius 8ms 0.037% 82.50% 261ms 1.20% std::__new_allocator::deallocate (inline) 1ms 0.0046% 82.51% 258ms 1.18% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 204ms 0.93% 83.44% 248ms 1.14% boost::shared_ptr::shared_ptr (inline) 0 0% 83.44% 237ms 1.09% std::allocator_traits::deallocate (inline) 3ms 0.014% 83.45% 232ms 1.06% DistributedBoxCollection::GetProcessOwningNode 55ms 0.25% 83.71% 232ms 1.06% __GI___libc_free 0 0% 83.71% 232ms 1.06% std::_Rb_tree::_M_put_node (inline) 0 0% 83.71% 228ms 1.04% boost::numeric::ublas::c_vector::assign (inline) 152ms 0.7% 84.40% 226ms 1.03% _int_malloc 0 0% 84.40% 225ms 1.03% NodesOnlyMesh::UpdateBoxCollection 211ms 0.97% 85.37% 211ms 0.97% Node::CheckForNodeAttributes 0 0% 85.37% 202ms 0.93% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 85.37% 197ms 0.9% std::iter_swap (inline) 197ms 0.9% 86.27% 197ms 0.9% std::swap (inline) 18ms 0.082% 86.35% 193ms 0.88% std::__insertion_sort (inline) 61ms 0.28% 86.63% 186ms 0.85% std::__move_median_to_first (inline) 0 0% 86.63% 185ms 0.85% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 1ms 0.0046% 86.64% 185ms 0.85% VtkMeshWriter::WriteFiles 0 0% 86.64% 185ms 0.85% boost::numeric::ublas::inner_prod (inline) 2ms 0.0092% 86.65% 184ms 0.84% CellPropertyCollection::HasProperty 12ms 0.055% 86.70% 184ms 0.84% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 86.70% 184ms 0.84% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 86.70% 183ms 0.84% Cell::HasCellProperty (inline) 1ms 0.0046% 86.71% 182ms 0.83% NodesOnlyMesh::AddNodesToBoxes 150ms 0.69% 87.39% 170ms 0.78% _int_free 163ms 0.75% 88.14% 163ms 0.75% boost::shared_ptr::operator-> (inline) 0 0% 88.14% 160ms 0.73% vtkStreamingDemandDrivenPipeline::Update 0 0% 88.14% 160ms 0.73% vtkXMLWriterBase::Write 0 0% 88.14% 159ms 0.73% NodesOnlyMesh::ResizeBoxCollection 0 0% 88.14% 159ms 0.73% vtkDemandDrivenPipeline::ProcessRequest 0 0% 88.14% 158ms 0.72% std::__new_allocator::destroy (inline) 0 0% 88.14% 158ms 0.72% std::allocator_traits::destroy (inline) 9ms 0.041% 88.18% 157ms 0.72% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 88.18% 157ms 0.72% std::_Rb_tree::_M_destroy_node (inline) 0 0% 88.18% 157ms 0.72% vtkCompositeDataPipeline::ExecuteData 0 0% 88.18% 157ms 0.72% vtkDemandDrivenPipeline::ExecuteData 0 0% 88.18% 157ms 0.72% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 88.18% 156ms 0.71% vtkExecutive::CallAlgorithm 0 0% 88.18% 156ms 0.71% vtkXMLUnstructuredDataWriter::ProcessRequest 1ms 0.0046% 88.19% 154ms 0.71% Cell::ReadyToDivide 1ms 0.0046% 88.19% 153ms 0.7% AbstractCellPopulation::SetCellUsingLocationIndex 34ms 0.16% 88.35% 147ms 0.67% boost::numeric::ublas::vector_inner_prod::apply (inline) 5ms 0.023% 88.37% 139ms 0.64% AbstractCellProperty::IsType (inline) 55ms 0.25% 88.62% 138ms 0.63% std::__adjacent_find (inline) 0 0% 88.62% 138ms 0.63% std::__unique (inline) 0 0% 88.62% 138ms 0.63% std::unique (inline) 0 0% 88.62% 138ms 0.63% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 88.62% 138ms 0.63% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 88.62% 138ms 0.63% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 88.62% 133ms 0.61% boost::numeric::ublas::vector_binary::operator() (inline) 1ms 0.0046% 88.62% 132ms 0.6% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 1ms 0.0046% 88.63% 130ms 0.6% Cell::GetCellId 0 0% 88.63% 129ms 0.59% std::_Rb_tree::clear (inline) 3ms 0.014% 88.64% 128ms 0.59% AbstractNumericalMethod::SafeNodePositionUpdate 2ms 0.0092% 88.65% 118ms 0.54% DistributedBoxCollection::GetIsPeriodicAllDims 1ms 0.0046% 88.66% 116ms 0.53% std::_Rb_tree::_M_insert_unique 0 0% 88.66% 116ms 0.53% std::set::insert (inline) 4ms 0.018% 88.68% 115ms 0.53% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 88.68% 112ms 0.51% vtkXMLWriter::WriteBinaryData 1ms 0.0046% 88.68% 110ms 0.5% vtkXMLWriter::WriteBinaryDataInternal