File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 30054ms, 89.02% of 33762ms total Dropped 744 nodes (cum <= 168.81ms) flat flat% sum% cum cum% 0 0% 0% 33639ms 99.64% __libc_start_call_main 0 0% 0% 33639ms 99.64% __libc_start_main_impl 0 0% 0% 33639ms 99.64% _start 0 0% 0% 33622ms 99.59% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 33622ms 99.59% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 33622ms 99.59% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 33622ms 99.59% main 0 0% 0% 33590ms 99.49% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 33590ms 99.49% CxxTest::TestRunner::runTest (inline) 0 0% 0% 33590ms 99.49% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 33583ms 99.47% AbstractCellBasedSimulation::Solve 1ms 0.003% 0.003% 23625ms 69.98% OffLatticeSimulation::UpdateCellLocationsAndTopology 5ms 0.015% 0.018% 18883ms 55.93% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.03% 0.047% 18665ms 55.28% AbstractNumericalMethod::ComputeForcesIncludingDamping 147ms 0.44% 0.48% 18036ms 53.42% AbstractTwoBodyInteractionForce::AddForceContribution 1431ms 4.24% 4.72% 15110ms 44.75% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4294ms 12.72% 17.44% 9516ms 28.19% std::_Rb_tree::_M_lower_bound (inline) 0 0% 17.44% 8788ms 26.03% AbstractCellBasedSimulation::UpdateCellPopulation 352ms 1.04% 18.48% 8710ms 25.80% std::_Rb_tree::find (inline) 0 0% 18.48% 8709ms 25.80% std::map::find (inline) 155ms 0.46% 18.94% 8551ms 25.33% NodesOnlyMesh::GetNodeOrHaloNode 484ms 1.43% 20.37% 8414ms 24.92% AbstractMesh::GetNode 363ms 1.08% 21.45% 7932ms 23.49% NodesOnlyMesh::SolveNodeMapping 0 0% 21.45% 7759ms 22.98% NodeBasedCellPopulation::Update 214ms 0.63% 22.08% 6122ms 18.13% boost::numeric::ublas::vector_assign (inline) 191ms 0.57% 22.65% 6000ms 17.77% boost::numeric::ublas::c_vector::c_vector (partial-inline) 5ms 0.015% 22.66% 5634ms 16.69% DistributedBoxCollection::CalculateInteriorNodePairs 5210ms 15.43% 38.10% 5210ms 15.43% std::_Rb_tree::_S_right (inline) 28ms 0.083% 38.18% 4621ms 13.69% NodeAttributes::RemoveDuplicateNeighbours 0 0% 38.18% 4482ms 13.28% OffLatticeSimulation::ApplyBoundaries 4ms 0.012% 38.19% 4274ms 12.66% std::__sort (inline) 0 0% 38.19% 4274ms 12.66% std::sort (inline) 3ms 0.0089% 38.20% 3403ms 10.08% AbstractCellPopulation::Iterator::operator++ (inline) 1051ms 3.11% 41.31% 3395ms 10.06% boost::numeric::ublas::indexing_vector_assign 173ms 0.51% 41.83% 3384ms 10.02% AbstractCellPopulation::Iterator::IsRealCell (inline) 65ms 0.19% 42.02% 3330ms 9.86% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 16ms 0.047% 42.07% 2886ms 8.55% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 169ms 0.5% 42.57% 2366ms 7.01% std::__introsort_loop 31ms 0.092% 42.66% 2341ms 6.93% PlaneBoundaryCondition::ImposeBoundaryCondition 33ms 0.098% 42.76% 2251ms 6.67% AbstractCellPopulation::GetLocationIndexUsingCell 23ms 0.068% 42.82% 2141ms 6.34% PlaneBoundaryCondition::VerifyBoundaryCondition 1ms 0.003% 42.83% 2117ms 6.27% std::__unguarded_partition_pivot (inline) 0 0% 42.83% 1902ms 5.63% std::__final_insertion_sort (inline) 1002ms 2.97% 45.79% 1866ms 5.53% std::__unguarded_partition (inline) 147ms 0.44% 46.23% 1801ms 5.33% DistributedBoxCollection::AddPairsFromBox 223ms 0.66% 46.89% 1732ms 5.13% std::map::operator[] (partial-inline) 87ms 0.26% 47.15% 1702ms 5.04% std::__unguarded_insertion_sort (inline) 595ms 1.76% 48.91% 1664ms 4.93% std::__unguarded_linear_insert (inline) 1572ms 4.66% 53.57% 1572ms 4.66% boost::numeric::ublas::same_impl_ex 151ms 0.45% 54.01% 1471ms 4.36% AbstractMesh::GetVectorFromAtoB 1465ms 4.34% 58.35% 1465ms 4.34% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 58.35% 1335ms 3.95% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 58.35% 1321ms 3.91% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 58.35% 1249ms 3.70% std::_Rb_tree::lower_bound (inline) 0 0% 58.35% 1249ms 3.70% std::map::lower_bound (inline) 1219ms 3.61% 61.96% 1219ms 3.61% boost::numeric::ublas::c_vector::operator() 5ms 0.015% 61.98% 1202ms 3.56% DistributedBoxCollection::CalculateBoundaryNodePairs 0 0% 61.98% 1127ms 3.34% NodeBasedCellPopulation::UpdateCellProcessLocation 19ms 0.056% 62.03% 1093ms 3.24% boost::numeric::ublas::detail::expression_type_check (inline) 197ms 0.58% 62.62% 1043ms 3.09% boost::numeric::ublas::detail::equals 330ms 0.98% 63.60% 1030ms 3.05% NodeAttributes::AddAppliedForceContribution 158ms 0.47% 64.06% 973ms 2.88% boost::numeric::ublas::vector_binary::size (inline) 378ms 1.12% 65.18% 839ms 2.49% __GI___libc_free 0 0% 65.18% 805ms 2.38% boost::numeric::ublas::norm_inf (inline) 456ms 1.35% 66.53% 805ms 2.38% boost::numeric::ublas::vector_norm_inf::apply (inline) 366ms 1.08% 67.62% 762ms 2.26% DistributedBoxCollection::CalculateContainingBox (partial-inline) 19ms 0.056% 67.67% 744ms 2.20% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 71ms 0.21% 67.88% 741ms 2.19% std::__new_allocator::allocate (inline) 175ms 0.52% 68.40% 719ms 2.13% NodeAttributes::AddNeighbour 0 0% 68.40% 711ms 2.11% AbstractCellPopulation::WriteResultsToFiles 0 0% 68.40% 700ms 2.07% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 68.40% 700ms 2.07% boost::numeric::ublas::c_vector::plus_assign (inline) 465ms 1.38% 69.78% 678ms 2.01% __dynamic_cast 87ms 0.26% 70.04% 675ms 2.00% operator new 542ms 1.61% 71.64% 609ms 1.80% std::vector::push_back (inline) 221ms 0.65% 72.30% 586ms 1.74% __GI___libc_malloc 4ms 0.012% 72.31% 585ms 1.73% AbstractCellBasedSimulation::DoCellBirth 8ms 0.024% 72.33% 570ms 1.69% AbstractCentreBasedCellPopulation::GetDampingConstant 36ms 0.11% 72.44% 541ms 1.60% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 72.44% 530ms 1.57% boost::numeric::ublas::norm_2 (inline) 428ms 1.27% 73.71% 530ms 1.57% boost::numeric::ublas::vector_norm_2::apply (inline) 507ms 1.50% 75.21% 507ms 1.50% std::_Rb_tree_increment 2ms 0.0059% 75.21% 464ms 1.37% NodeBasedCellPopulation::WriteVtkResultsToFile 6ms 0.018% 75.23% 462ms 1.37% CellPropertyCollection::GetPropertiesType (inline) 408ms 1.21% 76.44% 459ms 1.36% _int_free 0 0% 76.44% 442ms 1.31% AbstractCellBasedSimulation::DoCellRemoval (inline) 6ms 0.018% 76.46% 429ms 1.27% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 38ms 0.11% 76.57% 412ms 1.22% boost::detail::shared_count::~shared_count (inline) 0 0% 76.57% 412ms 1.22% boost::shared_ptr::~shared_ptr (inline) 34ms 0.1% 76.67% 395ms 1.17% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 76.67% 395ms 1.17% boost::numeric::ublas::vector::vector (inline) 0 0% 76.67% 380ms 1.13% std::allocator_traits::allocate (inline) 377ms 1.12% 77.79% 377ms 1.12% Node::GetIndex 4ms 0.012% 77.80% 376ms 1.11% Cell::GetMutationState 370ms 1.10% 78.90% 373ms 1.10% boost::detail::sp_counted_base::release 356ms 1.05% 79.95% 356ms 1.05% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 12ms 0.036% 79.99% 331ms 0.98% boost::numeric::ublas::vector_reference::operator() (inline) 132ms 0.39% 80.38% 329ms 0.97% Node::GetRadius 0 0% 80.38% 328ms 0.97% std::_Rb_tree::_M_create_node (inline) 0 0% 80.38% 324ms 0.96% boost::numeric::ublas::inner_prod (inline) 4ms 0.012% 80.39% 323ms 0.96% AbstractCellProperty::IsSubType (inline) 3ms 0.0089% 80.40% 322ms 0.95% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 12ms 0.036% 80.43% 319ms 0.94% boost::numeric::ublas::vector_scalar_binary::evaluate 4ms 0.012% 80.45% 312ms 0.92% NodeBasedCellPopulation::UpdateMapsAfterRemesh 304ms 0.9% 81.35% 305ms 0.9% std::__adjacent_find (inline) 0 0% 81.35% 305ms 0.9% std::__unique (inline) 0 0% 81.35% 305ms 0.9% std::unique (inline) 0 0% 81.35% 298ms 0.88% NodesOnlyMesh::ReMesh 0 0% 81.35% 298ms 0.88% std::_Rb_tree::_M_get_node (inline) 3ms 0.0089% 81.35% 293ms 0.87% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 6ms 0.018% 81.37% 286ms 0.85% NodesOnlyMesh::UpdateNodeIndices 3ms 0.0089% 81.38% 283ms 0.84% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 5ms 0.015% 81.40% 279ms 0.83% AbstractCellPopulation::GetCellUsingLocationIndex 278ms 0.82% 82.22% 278ms 0.82% [libchaste_cell_based.so] 11ms 0.033% 82.25% 275ms 0.81% DistributedBoxCollection::GetProcessOwningNode 114ms 0.34% 82.59% 262ms 0.78% std::__find_if (inline) 0 0% 82.59% 262ms 0.78% std::find_if (inline) 0 0% 82.59% 262ms 0.78% std::none_of (inline) 8ms 0.024% 82.61% 260ms 0.77% std::_Rb_tree::_M_emplace_hint_unique 259ms 0.77% 83.38% 259ms 0.77% __gnu_cxx::__normal_iterator::operator++ (inline) 100ms 0.3% 83.68% 259ms 0.77% std::_Rb_tree::_M_erase (partial-inline) 0 0% 83.68% 248ms 0.73% NodesOnlyMesh::UpdateBoxCollection 115ms 0.34% 84.02% 247ms 0.73% std::__move_median_to_first (inline) 91ms 0.27% 84.29% 244ms 0.72% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 84.29% 234ms 0.69% boost::numeric::ublas::c_vector::assign (inline) 0 0% 84.29% 233ms 0.69% boost::numeric::ublas::vector_binary::operator() (inline) 113ms 0.33% 84.62% 223ms 0.66% _int_malloc 1ms 0.003% 84.62% 222ms 0.66% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 84.62% 220ms 0.65% VtkMeshWriter::WriteFiles 216ms 0.64% 85.26% 216ms 0.64% __strcmp_avx2 208ms 0.62% 85.88% 208ms 0.62% Node::CheckForNodeAttributes 0 0% 85.88% 206ms 0.61% vtkStreamingDemandDrivenPipeline::Update 0 0% 85.88% 206ms 0.61% vtkXMLWriterBase::Write 0 0% 85.88% 205ms 0.61% vtkDemandDrivenPipeline::ProcessRequest 0 0% 85.88% 205ms 0.61% vtkExecutive::CallAlgorithm 0 0% 85.88% 204ms 0.6% vtkStreamingDemandDrivenPipeline::ProcessRequest 1ms 0.003% 85.88% 204ms 0.6% vtkXMLUnstructuredDataWriter::ProcessRequest 203ms 0.6% 86.48% 203ms 0.6% NodeBasedCellPopulation::GetNode 0 0% 86.48% 203ms 0.6% vtkCompositeDataPipeline::ExecuteData 0 0% 86.48% 203ms 0.6% vtkDemandDrivenPipeline::ExecuteData 0 0% 86.48% 201ms 0.6% NodesOnlyMesh::AddNodesToBoxes 21ms 0.062% 86.55% 200ms 0.59% std::__insertion_sort (inline) 195ms 0.58% 87.12% 195ms 0.58% [libchaste_mesh.so] 0 0% 87.12% 194ms 0.57% CellPropertyCollection::HasProperty 0 0% 87.12% 193ms 0.57% Cell::HasCellProperty (inline) 132ms 0.39% 87.52% 192ms 0.57% Node::AddAppliedForceContribution 191ms 0.57% 88.08% 191ms 0.57% Node::rGetLocation 4ms 0.012% 88.09% 183ms 0.54% Cell::ReadyToDivide 179ms 0.53% 88.62% 179ms 0.53% boost::numeric::ublas::scalar_plus_assign::apply (inline) 7ms 0.021% 88.64% 176ms 0.52% std::_Rb_tree::_Rb_tree (partial-inline) 34ms 0.1% 88.74% 176ms 0.52% std::__new_allocator::deallocate (inline) 91ms 0.27% 89.01% 175ms 0.52% boost::shared_ptr::shared_ptr (inline) 0 0% 89.01% 173ms 0.51% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 89.01% 173ms 0.51% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 89.01% 173ms 0.51% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 89.01% 171ms 0.51% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 1ms 0.003% 89.02% 169ms 0.5% NodesOnlyMesh::ResizeBoxCollection