File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 21739ms, 88.23% of 24638ms total Dropped 828 nodes (cum <= 123.19ms) flat flat% sum% cum cum% 0 0% 0% 24517ms 99.51% __libc_start_call_main 0 0% 0% 24517ms 99.51% __libc_start_main_impl 0 0% 0% 24517ms 99.51% _start 0 0% 0% 24501ms 99.44% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 24501ms 99.44% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 24501ms 99.44% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 24501ms 99.44% main 0 0% 0% 24456ms 99.26% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 24456ms 99.26% CxxTest::TestRunner::runTest (inline) 0 0% 0% 24456ms 99.26% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0041% 0.0041% 24447ms 99.22% AbstractCellBasedSimulation::Solve 1ms 0.0041% 0.0081% 13976ms 56.73% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0081% 9290ms 37.71% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0081% 0.016% 9094ms 36.91% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.041% 0.057% 8916ms 36.19% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.057% 8217ms 33.35% NodeBasedCellPopulation::Update 1304ms 5.29% 5.35% 8206ms 33.31% RepulsionForce::AddForceContribution (partial-inline) 13ms 0.053% 5.40% 6085ms 24.70% DistributedBoxCollection::CalculateInteriorNodePairs 2148ms 8.72% 14.12% 5033ms 20.43% std::_Rb_tree::_M_lower_bound (inline) 15ms 0.061% 14.18% 4646ms 18.86% NodeAttributes::RemoveDuplicateNeighbours 1ms 0.0041% 14.19% 4558ms 18.50% OffLatticeSimulation::ApplyBoundaries 5ms 0.02% 14.21% 4457ms 18.09% std::__sort (inline) 0 0% 14.21% 4457ms 18.09% std::sort (inline) 205ms 0.83% 15.04% 4106ms 16.67% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 82ms 0.33% 15.37% 3333ms 13.53% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 274ms 1.11% 16.48% 3317ms 13.46% std::_Rb_tree::find (inline) 0 0% 16.48% 3315ms 13.45% std::map::find (inline) 5ms 0.02% 16.50% 3122ms 12.67% AbstractCellPopulation::Iterator::operator++ (inline) 144ms 0.58% 17.09% 3092ms 12.55% AbstractCellPopulation::Iterator::IsRealCell (inline) 2854ms 11.58% 28.67% 2854ms 11.58% std::_Rb_tree::_S_right (inline) 26ms 0.11% 28.78% 2695ms 10.94% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 171ms 0.69% 29.47% 2600ms 10.55% std::__introsort_loop 185ms 0.75% 30.22% 2485ms 10.09% std::map::operator[] (partial-inline) 177ms 0.72% 30.94% 2444ms 9.92% AbstractMesh::GetNode 49ms 0.2% 31.14% 2422ms 9.83% NodesOnlyMesh::GetNodeOrHaloNode 15ms 0.061% 31.20% 2419ms 9.82% PlaneBoundaryCondition::ImposeBoundaryCondition 0 0% 31.20% 2342ms 9.51% std::__unguarded_partition_pivot (inline) 104ms 0.42% 31.62% 2274ms 9.23% NodesOnlyMesh::SolveNodeMapping 58ms 0.24% 31.86% 2235ms 9.07% AbstractCellPopulation::GetLocationIndexUsingCell 12ms 0.049% 31.91% 2138ms 8.68% PlaneBoundaryCondition::VerifyBoundaryCondition 1057ms 4.29% 36.20% 2093ms 8.50% std::__unguarded_partition (inline) 147ms 0.6% 36.79% 2075ms 8.42% DistributedBoxCollection::AddPairsFromBox 0 0% 36.79% 2036ms 8.26% std::_Rb_tree::lower_bound (inline) 0 0% 36.79% 2036ms 8.26% std::map::lower_bound (inline) 0 0% 36.79% 1850ms 7.51% std::__final_insertion_sort (inline) 13ms 0.053% 36.85% 1706ms 6.92% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 21ms 0.085% 36.93% 1688ms 6.85% AbstractCellPopulation::GetCellUsingLocationIndex 121ms 0.49% 37.42% 1674ms 6.79% std::__unguarded_insertion_sort (inline) 587ms 2.38% 39.80% 1571ms 6.38% std::__unguarded_linear_insert (inline) 1380ms 5.60% 45.41% 1380ms 5.60% __gnu_cxx::__normal_iterator::operator-- (inline) 63ms 0.26% 45.66% 1274ms 5.17% boost::numeric::ublas::c_vector::c_vector (partial-inline) 6ms 0.024% 45.69% 1138ms 4.62% DistributedBoxCollection::CalculateBoundaryNodePairs 1ms 0.0041% 45.69% 1126ms 4.57% NodeBasedCellPopulation::UpdateCellProcessLocation 6ms 0.024% 45.71% 1118ms 4.54% boost::numeric::ublas::vector_assign (inline) 195ms 0.79% 46.51% 1030ms 4.18% boost::numeric::ublas::indexing_vector_assign 284ms 1.15% 47.66% 995ms 4.04% __dynamic_cast 25ms 0.1% 47.76% 982ms 3.99% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 182ms 0.74% 48.50% 846ms 3.43% AbstractMesh::GetVectorFromAtoB 0 0% 48.50% 845ms 3.43% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 2ms 0.0081% 48.51% 834ms 3.39% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 48.51% 828ms 3.36% boost::numeric::ublas::norm_2 (inline) 632ms 2.57% 51.07% 828ms 3.36% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 51.07% 828ms 3.36% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 385ms 1.56% 52.63% 827ms 3.36% DistributedBoxCollection::CalculateContainingBox (partial-inline) 25ms 0.1% 52.74% 807ms 3.28% std::__copy_move::__copy_m (inline) 0 0% 52.74% 807ms 3.28% std::__copy_move_a (inline) 0 0% 52.74% 807ms 3.28% std::__copy_move_a1 (inline) 0 0% 52.74% 807ms 3.28% std::__copy_move_a2 (inline) 0 0% 52.74% 807ms 3.28% std::copy (inline) 802ms 3.26% 55.99% 802ms 3.26% __memcpy_avx_unaligned_erms 0 0% 55.99% 752ms 3.05% AbstractCellPopulation::WriteResultsToFiles 180ms 0.73% 56.72% 744ms 3.02% NodeAttributes::AddNeighbour 739ms 3.00% 59.72% 739ms 3.00% boost::numeric::ublas::c_vector::operator() 33ms 0.13% 59.85% 699ms 2.84% std::_Rb_tree_const_iterator::operator++ (inline) 11ms 0.045% 59.90% 663ms 2.69% CellPropertyCollection::GetPropertiesType (inline) 1ms 0.0041% 59.90% 641ms 2.60% AbstractCentreBasedCellPopulation::GetDampingConstant 641ms 2.60% 62.51% 641ms 2.60% std::_Rb_tree_increment 562ms 2.28% 64.79% 637ms 2.59% std::vector::push_back (inline) 279ms 1.13% 65.92% 575ms 2.33% __cxxabiv1::__si_class_type_info::__do_dyncast 7ms 0.028% 65.95% 562ms 2.28% AbstractCellBasedSimulation::DoCellBirth 546ms 2.22% 68.16% 546ms 2.22% boost::numeric::ublas::same_impl_ex 44ms 0.18% 68.34% 534ms 2.17% std::_Rb_tree::_Rb_tree (partial-inline) 79ms 0.32% 68.66% 522ms 2.12% std::__new_allocator::allocate (inline) 0 0% 68.66% 511ms 2.07% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 68.66% 505ms 2.05% std::allocator_traits::allocate (inline) 4ms 0.016% 68.68% 499ms 2.03% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 33ms 0.13% 68.81% 498ms 2.02% boost::detail::shared_count::~shared_count (inline) 0 0% 68.81% 498ms 2.02% boost::shared_ptr::~shared_ptr (inline) 0 0% 68.81% 492ms 2.00% NodeBasedCellPopulation::WriteVtkResultsToFile 490ms 1.99% 70.80% 490ms 1.99% __strcmp_avx2 0 0% 70.80% 478ms 1.94% std::_Rb_tree::_M_create_node (inline) 42ms 0.17% 70.97% 474ms 1.92% std::_Rb_tree::_M_copy (inline) 5ms 0.02% 70.99% 463ms 1.88% Cell::GetMutationState 444ms 1.80% 72.79% 452ms 1.83% boost::detail::sp_counted_base::release 144ms 0.58% 73.38% 449ms 1.82% std::_Rb_tree::_M_erase 3ms 0.012% 73.39% 438ms 1.78% std::set::set (inline) 21ms 0.085% 73.48% 435ms 1.77% operator new 1ms 0.0041% 73.48% 430ms 1.75% AbstractCellProperty::IsSubType (inline) 145ms 0.59% 74.07% 426ms 1.73% std::_Rb_tree::_M_clone_node (inline) 0 0% 74.07% 425ms 1.72% std::_Rb_tree::_M_get_node (inline) 119ms 0.48% 74.55% 404ms 1.64% __GI___libc_malloc 103ms 0.42% 74.97% 391ms 1.59% boost::numeric::ublas::vector_binary::size (inline) 104ms 0.42% 75.39% 374ms 1.52% Node::GetRadius 374ms 1.52% 76.91% 374ms 1.52% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 76.91% 366ms 1.49% boost::numeric::ublas::inner_prod (inline) 2ms 0.0081% 76.92% 366ms 1.49% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 60ms 0.24% 77.16% 365ms 1.48% std::_Rb_tree::~_Rb_tree (inline) 15ms 0.061% 77.22% 364ms 1.48% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 77.22% 337ms 1.37% boost::numeric::ublas::c_vector::assign (inline) 0 0% 77.22% 337ms 1.37% std::_Rb_tree::_Alloc_node::operator() (inline) 323ms 1.31% 78.53% 323ms 1.31% __gnu_cxx::__normal_iterator::operator++ (inline) 2ms 0.0081% 78.54% 310ms 1.26% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 78.54% 307ms 1.25% NodesOnlyMesh::ReMesh 5ms 0.02% 78.56% 302ms 1.23% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 78.56% 299ms 1.21% std::_Rb_tree::_M_drop_node (inline) 2ms 0.0081% 78.57% 290ms 1.18% NodesOnlyMesh::UpdateNodeIndices 0 0% 78.57% 288ms 1.17% NodesOnlyMesh::UpdateBoxCollection 118ms 0.48% 79.05% 287ms 1.16% boost::numeric::ublas::vector_inner_prod::apply (inline) 6ms 0.024% 79.07% 281ms 1.14% DistributedBoxCollection::GetProcessOwningNode 0 0% 79.07% 275ms 1.12% std::set::~set (inline) 274ms 1.11% 80.19% 274ms 1.11% Node::CheckForNodeAttributes 178ms 0.72% 80.91% 266ms 1.08% Node::AddNeighbour 265ms 1.08% 81.98% 265ms 1.08% [libchaste_mesh.so] 12ms 0.049% 82.03% 264ms 1.07% std::_Rb_tree::_M_emplace_hint_unique 0 0% 82.03% 250ms 1.01% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 82.03% 249ms 1.01% VtkMeshWriter::WriteFiles 7ms 0.028% 82.06% 249ms 1.01% std::__new_allocator::deallocate (inline) 102ms 0.41% 82.47% 244ms 0.99% std::__move_median_to_first (inline) 127ms 0.52% 82.99% 240ms 0.97% boost::shared_ptr::shared_ptr (inline) 133ms 0.54% 83.53% 237ms 0.96% _int_malloc 235ms 0.95% 84.48% 235ms 0.95% Node::GetIndex 0 0% 84.48% 233ms 0.95% std::allocator_traits::deallocate (inline) 21ms 0.085% 84.57% 231ms 0.94% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 84.57% 227ms 0.92% std::_Rb_tree::_M_put_node (inline) 0 0% 84.57% 222ms 0.9% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 84.57% 221ms 0.9% Cell::HasCellProperty (inline) 1ms 0.0041% 84.57% 221ms 0.9% CellPropertyCollection::HasProperty 1ms 0.0041% 84.58% 221ms 0.9% NodesOnlyMesh::AddNodesToBoxes 0 0% 84.58% 214ms 0.87% vtkStreamingDemandDrivenPipeline::Update 0 0% 84.58% 214ms 0.87% vtkXMLWriterBase::Write 0 0% 84.58% 213ms 0.86% vtkDemandDrivenPipeline::ProcessRequest 60ms 0.24% 84.82% 212ms 0.86% __GI___libc_free 0 0% 84.82% 211ms 0.86% vtkCompositeDataPipeline::ExecuteData 0 0% 84.82% 211ms 0.86% vtkDemandDrivenPipeline::ExecuteData 0 0% 84.82% 211ms 0.86% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 84.82% 210ms 0.85% vtkExecutive::CallAlgorithm 1ms 0.0041% 84.82% 209ms 0.85% vtkXMLUnstructuredDataWriter::ProcessRequest 5ms 0.02% 84.84% 194ms 0.79% Cell::ReadyToDivide 23ms 0.093% 84.94% 176ms 0.71% std::__insertion_sort (inline) 3ms 0.012% 84.95% 174ms 0.71% AbstractCellProperty::IsType (inline) 174ms 0.71% 85.66% 174ms 0.71% [libchaste_cell_based.so] 0 0% 85.66% 170ms 0.69% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.66% 170ms 0.69% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 85.66% 166ms 0.67% std::_Rb_tree::clear (inline) 0 0% 85.66% 164ms 0.67% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 85.66% 163ms 0.66% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 162ms 0.66% 86.31% 162ms 0.66% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 1ms 0.0041% 86.32% 159ms 0.65% Cell::GetCellId 0 0% 86.32% 157ms 0.64% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 4ms 0.016% 86.33% 155ms 0.63% boost::numeric::ublas::c_vector::operator[] (inline) 155ms 0.63% 86.96% 155ms 0.63% std::__adjacent_find (inline) 0 0% 86.96% 155ms 0.63% std::__unique (inline) 0 0% 86.96% 155ms 0.63% std::unique (inline) 136ms 0.55% 87.52% 153ms 0.62% _int_free 0 0% 87.52% 145ms 0.59% NodesOnlyMesh::ResizeBoxCollection 5ms 0.02% 87.54% 144ms 0.58% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 87.54% 144ms 0.58% vtkXMLWriter::WriteBinaryData 0 0% 87.54% 141ms 0.57% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 87.54% 139ms 0.56% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.54% 139ms 0.56% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.54% 137ms 0.56% vtkXMLWriter::WriteCompressionBlock 0 0% 87.54% 132ms 0.54% vtkXMLWriter::WritePointsAppendedData 129ms 0.52% 88.06% 129ms 0.52% Node::IsDeleted 2ms 0.0081% 88.07% 126ms 0.51% AbstractCellPopulation::SetCellUsingLocationIndex 38ms 0.15% 88.22% 124ms 0.5% AbstractCellProperty::IsSame 3ms 0.012% 88.23% 124ms 0.5% AbstractNumericalMethod::SafeNodePositionUpdate