File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 21122ms, 89.08% of 23711ms total Dropped 741 nodes (cum <= 118.56ms) flat flat% sum% cum cum% 0 0% 0% 23610ms 99.57% __libc_start_call_main 0 0% 0% 23610ms 99.57% __libc_start_main_impl 0 0% 0% 23610ms 99.57% _start 0 0% 0% 23594ms 99.51% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 23594ms 99.51% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 23594ms 99.51% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 23594ms 99.51% main 0 0% 0% 23561ms 99.37% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 23561ms 99.37% CxxTest::TestRunner::runTest (inline) 0 0% 0% 23561ms 99.37% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 23553ms 99.33% AbstractCellBasedSimulation::Solve 3ms 0.013% 0.013% 13330ms 56.22% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.013% 9091ms 38.34% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0042% 0.017% 7990ms 33.70% NodeBasedCellPopulation::Update 2ms 0.0084% 0.025% 7530ms 31.76% ForwardEulerNumericalMethod::UpdateAllNodePositions 7ms 0.03% 0.055% 7355ms 31.02% AbstractNumericalMethod::ComputeForcesIncludingDamping 969ms 4.09% 4.14% 6808ms 28.71% RepulsionForce::AddForceContribution (partial-inline) 6ms 0.025% 4.17% 6010ms 25.35% DistributedBoxCollection::CalculateInteriorNodePairs 1ms 0.0042% 4.17% 5491ms 23.16% OffLatticeSimulation::ApplyBoundaries 2148ms 9.06% 13.23% 4957ms 20.91% std::_Rb_tree::_M_lower_bound (inline) 10ms 0.042% 13.27% 4835ms 20.39% NodeAttributes::RemoveDuplicateNeighbours 3ms 0.013% 13.28% 4643ms 19.58% std::__sort (inline) 0 0% 13.28% 4643ms 19.58% std::sort (inline) 292ms 1.23% 14.52% 4055ms 17.10% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 8ms 0.034% 14.55% 3847ms 16.22% AbstractCellPopulation::Iterator::operator++ (inline) 196ms 0.83% 15.38% 3833ms 16.17% AbstractCellPopulation::Iterator::IsRealCell (inline) 135ms 0.57% 15.95% 3601ms 15.19% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 258ms 1.09% 17.03% 3270ms 13.79% std::_Rb_tree::find (inline) 0 0% 17.03% 3270ms 13.79% std::map::find (inline) 24ms 0.1% 17.14% 3209ms 13.53% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 109ms 0.46% 17.60% 2792ms 11.78% AbstractMesh::GetNode 70ms 0.3% 17.89% 2792ms 11.78% PlaneBoundaryCondition::ImposeBoundaryCondition 235ms 0.99% 18.88% 2787ms 11.75% std::__introsort_loop 57ms 0.24% 19.12% 2769ms 11.68% NodesOnlyMesh::GetNodeOrHaloNode 38ms 0.16% 19.28% 2697ms 11.37% PlaneBoundaryCondition::VerifyBoundaryCondition 275ms 1.16% 20.44% 2688ms 11.34% NodesOnlyMesh::SolveNodeMapping 221ms 0.93% 21.37% 2559ms 10.79% std::map::operator[] (partial-inline) 2474ms 10.43% 31.81% 2474ms 10.43% std::_Rb_tree::_S_right (inline) 6ms 0.025% 31.83% 2458ms 10.37% std::__unguarded_partition_pivot (inline) 89ms 0.38% 32.21% 2237ms 9.43% AbstractCellPopulation::GetLocationIndexUsingCell 764ms 3.22% 35.43% 2218ms 9.35% std::__unguarded_partition (inline) 0 0% 35.43% 2000ms 8.43% std::_Rb_tree::lower_bound (inline) 0 0% 35.43% 2000ms 8.43% std::map::lower_bound (inline) 1ms 0.0042% 35.44% 1842ms 7.77% std::__final_insertion_sort (inline) 128ms 0.54% 35.97% 1745ms 7.36% DistributedBoxCollection::AddPairsFromBox 129ms 0.54% 36.52% 1635ms 6.90% std::__unguarded_insertion_sort (inline) 14ms 0.059% 36.58% 1522ms 6.42% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 20ms 0.084% 36.66% 1497ms 6.31% AbstractCellPopulation::GetCellUsingLocationIndex 721ms 3.04% 39.70% 1443ms 6.09% std::__unguarded_linear_insert (inline) 14ms 0.059% 39.76% 1215ms 5.12% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 71ms 0.3% 40.06% 1195ms 5.04% boost::numeric::ublas::c_vector::c_vector (partial-inline) 1ms 0.0042% 40.07% 1150ms 4.85% NodeBasedCellPopulation::UpdateCellProcessLocation 1087ms 4.58% 44.65% 1087ms 4.58% __gnu_cxx::__normal_iterator::operator-- (inline) 5ms 0.021% 44.67% 1008ms 4.25% DistributedBoxCollection::CalculateBoundaryNodePairs 2ms 0.0084% 44.68% 999ms 4.21% boost::numeric::ublas::vector_assign (inline) 24ms 0.1% 44.78% 970ms 4.09% boost::detail::shared_count::~shared_count (inline) 0 0% 44.78% 970ms 4.09% boost::shared_ptr::~shared_ptr (inline) 915ms 3.86% 48.64% 926ms 3.91% boost::detail::sp_counted_base::release 194ms 0.82% 49.46% 877ms 3.70% boost::numeric::ublas::indexing_vector_assign 260ms 1.10% 50.55% 804ms 3.39% __dynamic_cast 131ms 0.55% 51.11% 763ms 3.22% AbstractMesh::GetVectorFromAtoB 311ms 1.31% 52.42% 761ms 3.21% DistributedBoxCollection::CalculateContainingBox (partial-inline) 676ms 2.85% 55.27% 676ms 2.85% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 55.27% 674ms 2.84% AbstractCellPopulation::WriteResultsToFiles 0 0% 55.27% 607ms 2.56% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 21ms 0.089% 55.36% 602ms 2.54% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 55.36% 592ms 2.50% boost::numeric::ublas::norm_2 (inline) 487ms 2.05% 57.41% 592ms 2.50% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 57.41% 592ms 2.50% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 5ms 0.021% 57.43% 585ms 2.47% boost::numeric::ublas::c_vector::operator= (inline) 262ms 1.10% 58.54% 583ms 2.46% NodeAttributes::AddNeighbour 28ms 0.12% 58.66% 571ms 2.41% std::__copy_move::__copy_m (inline) 0 0% 58.66% 571ms 2.41% std::__copy_move_a (inline) 0 0% 58.66% 571ms 2.41% std::__copy_move_a1 (inline) 0 0% 58.66% 571ms 2.41% std::__copy_move_a2 (inline) 48ms 0.2% 58.86% 571ms 2.41% std::__new_allocator::allocate (inline) 0 0% 58.86% 571ms 2.41% std::copy (inline) 561ms 2.37% 61.22% 561ms 2.37% [libchaste_cell_based.so] 0 0% 61.22% 556ms 2.34% AbstractCellBasedSimulation::DoCellRemoval (inline) 549ms 2.32% 63.54% 549ms 2.32% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 63.54% 546ms 2.30% std::allocator_traits::allocate (inline) 2ms 0.0084% 63.55% 544ms 2.29% AbstractCellBasedSimulation::DoCellBirth 6ms 0.025% 63.57% 544ms 2.29% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 535ms 2.26% 65.83% 535ms 2.26% __memcpy_avx512_unaligned_erms 34ms 0.14% 65.97% 518ms 2.18% operator new 517ms 2.18% 68.15% 517ms 2.18% boost::numeric::ublas::same_impl_ex 0 0% 68.15% 514ms 2.17% std::_Rb_tree::_M_create_node (inline) 504ms 2.13% 70.28% 504ms 2.13% boost::numeric::ublas::c_vector::operator() 31ms 0.13% 70.41% 502ms 2.12% std::_Rb_tree::_Rb_tree (partial-inline) 501ms 2.11% 72.52% 501ms 2.11% std::_Rb_tree_increment 494ms 2.08% 74.61% 494ms 2.08% [libchaste_mesh.so] 3ms 0.013% 74.62% 493ms 2.08% CellPropertyCollection::GetPropertiesType (inline) 4ms 0.017% 74.64% 490ms 2.07% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 74.64% 484ms 2.04% std::_Rb_tree::_M_get_node (inline) 169ms 0.71% 75.35% 478ms 2.02% __GI___libc_malloc 70ms 0.3% 75.64% 461ms 1.94% std::_Rb_tree::_M_erase 41ms 0.17% 75.82% 456ms 1.92% std::_Rb_tree::_M_copy (inline) 111ms 0.47% 76.29% 456ms 1.92% std::_Rb_tree::~_Rb_tree (inline) 6ms 0.025% 76.31% 449ms 1.89% NodeBasedCellPopulation::WriteVtkResultsToFile 217ms 0.92% 77.23% 449ms 1.89% __cxxabiv1::__si_class_type_info::__do_dyncast 288ms 1.21% 78.44% 428ms 1.81% std::vector::push_back (inline) 1ms 0.0042% 78.44% 417ms 1.76% std::set::set (inline) 170ms 0.72% 79.16% 404ms 1.70% std::_Rb_tree::_M_clone_node (inline) 0 0% 79.16% 389ms 1.64% std::_Rb_tree::_M_drop_node (inline) 0 0% 79.16% 383ms 1.62% std::set::~set (inline) 5ms 0.021% 79.18% 372ms 1.57% boost::numeric::ublas::vector_binary::size (inline) 1ms 0.0042% 79.19% 352ms 1.48% Cell::GetMutationState 6ms 0.025% 79.21% 351ms 1.48% AbstractCellProperty::IsSubType (inline) 0 0% 79.21% 348ms 1.47% NodesOnlyMesh::ReMesh 347ms 1.46% 80.68% 347ms 1.46% std::_Rb_tree::_S_left (inline) 12ms 0.051% 80.73% 338ms 1.43% std::_Rb_tree::_M_emplace_hint_unique 3ms 0.013% 80.74% 337ms 1.42% NodesOnlyMesh::UpdateNodeIndices 316ms 1.33% 82.07% 316ms 1.33% __strcmp_evex 9ms 0.038% 82.11% 302ms 1.27% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 82.11% 298ms 1.26% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 82.11% 291ms 1.23% std::_Rb_tree::_Alloc_node::operator() (inline) 2ms 0.0084% 82.12% 290ms 1.22% Node::GetRadius 11ms 0.046% 82.16% 284ms 1.20% std::__new_allocator::deallocate (inline) 1ms 0.0042% 82.17% 274ms 1.16% DistributedBoxCollection::GetProcessOwningNode 248ms 1.05% 83.21% 274ms 1.16% boost::shared_ptr::shared_ptr (inline) 0 0% 83.21% 268ms 1.13% NodesOnlyMesh::UpdateBoxCollection 0 0% 83.21% 262ms 1.10% boost::numeric::ublas::c_vector::assign (inline) 0 0% 83.21% 258ms 1.09% std::allocator_traits::deallocate (inline) 0 0% 83.21% 254ms 1.07% std::_Rb_tree::_M_put_node (inline) 167ms 0.7% 83.92% 250ms 1.05% _int_malloc 59ms 0.25% 84.17% 248ms 1.05% __GI___libc_free 223ms 0.94% 85.11% 223ms 0.94% Node::CheckForNodeAttributes 0 0% 85.11% 223ms 0.94% NodesOnlyMesh::AddNodesToBoxes 0 0% 85.11% 223ms 0.94% std::_Rb_tree::_Auto_node::_Auto_node (inline) 69ms 0.29% 85.40% 222ms 0.94% std::__move_median_to_first (inline) 0 0% 85.40% 216ms 0.91% std::iter_swap (inline) 216ms 0.91% 86.31% 216ms 0.91% std::swap (inline) 0 0% 86.31% 211ms 0.89% boost::numeric::ublas::inner_prod (inline) 2ms 0.0084% 86.32% 211ms 0.89% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 10ms 0.042% 86.36% 209ms 0.88% boost::numeric::ublas::vector_scalar_binary::evaluate 27ms 0.11% 86.47% 206ms 0.87% std::__insertion_sort (inline) 0 0% 86.47% 190ms 0.8% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 86.47% 188ms 0.79% VtkMeshWriter::WriteFiles 151ms 0.64% 87.11% 182ms 0.77% _int_free 1ms 0.0042% 87.12% 181ms 0.76% CellPropertyCollection::HasProperty 0 0% 87.12% 180ms 0.76% Cell::HasCellProperty (inline) 0 0% 87.12% 178ms 0.75% NodesOnlyMesh::ResizeBoxCollection 10ms 0.042% 87.16% 177ms 0.75% NodesOnlyMesh::IsANodeCloseToDomainBoundary 172ms 0.73% 87.88% 172ms 0.73% boost::shared_ptr::operator-> (inline) 40ms 0.17% 88.05% 169ms 0.71% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 88.05% 168ms 0.71% vtkDemandDrivenPipeline::ProcessRequest 0 0% 88.05% 168ms 0.71% vtkStreamingDemandDrivenPipeline::Update 0 0% 88.05% 168ms 0.71% vtkXMLWriterBase::Write 0 0% 88.05% 166ms 0.7% vtkCompositeDataPipeline::ExecuteData 0 0% 88.05% 166ms 0.7% vtkDemandDrivenPipeline::ExecuteData 0 0% 88.05% 166ms 0.7% vtkExecutive::CallAlgorithm 0 0% 88.05% 166ms 0.7% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 88.05% 166ms 0.7% vtkXMLUnstructuredDataWriter::ProcessRequest 4ms 0.017% 88.07% 159ms 0.67% Cell::ReadyToDivide 0 0% 88.07% 149ms 0.63% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 88.07% 148ms 0.62% std::_Rb_tree::_M_destroy_node (inline) 0 0% 88.07% 148ms 0.62% std::__new_allocator::destroy (inline) 0 0% 88.07% 148ms 0.62% std::allocator_traits::destroy (inline) 70ms 0.3% 88.36% 145ms 0.61% std::__adjacent_find (inline) 0 0% 88.36% 145ms 0.61% std::__unique (inline) 0 0% 88.36% 145ms 0.61% std::unique (inline) 0 0% 88.36% 142ms 0.6% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 88.36% 142ms 0.6% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 88.36% 140ms 0.59% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 88.36% 139ms 0.59% std::_Rb_tree::clear (inline) 1ms 0.0042% 88.37% 135ms 0.57% std::_Rb_tree::_M_insert_unique 0 0% 88.37% 135ms 0.57% std::set::insert (inline) 6ms 0.025% 88.39% 131ms 0.55% AbstractCellPopulation::SetCellUsingLocationIndex 5ms 0.021% 88.41% 131ms 0.55% AbstractCellProperty::IsType (inline) 3ms 0.013% 88.43% 130ms 0.55% AbstractNumericalMethod::SafeNodePositionUpdate 1ms 0.0042% 88.43% 129ms 0.54% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 88.43% 129ms 0.54% DistributedBoxCollection::GetIsPeriodicAllDims 1ms 0.0042% 88.44% 125ms 0.53% Cell::GetCellId 22ms 0.093% 88.53% 121ms 0.51% Node::AddNeighbour 120ms 0.51% 89.03% 120ms 0.51% Node::GetIndex 5ms 0.021% 89.06% 120ms 0.51% NodeBasedCellPopulation::SetNode 6ms 0.025% 89.08% 120ms 0.51% boost::numeric::ublas::c_vector::operator[] (inline)