File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 30285ms, 87.92% of 34447ms total Dropped 837 nodes (cum <= 172.24ms) flat flat% sum% cum cum% 0 0% 0% 34314ms 99.61% __libc_start_call_main 0 0% 0% 34314ms 99.61% __libc_start_main_impl 0 0% 0% 34314ms 99.61% _start 0 0% 0% 34295ms 99.56% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 34295ms 99.56% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 34295ms 99.56% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 34295ms 99.56% main 0 0% 0% 34259ms 99.45% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 34259ms 99.45% CxxTest::TestRunner::runTest (inline) 0 0% 0% 34259ms 99.45% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 34250ms 99.43% AbstractCellBasedSimulation::Solve 6ms 0.017% 0.017% 23745ms 68.93% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0029% 0.02% 18818ms 54.63% ForwardEulerNumericalMethod::UpdateAllNodePositions 12ms 0.035% 0.055% 18636ms 54.10% AbstractNumericalMethod::ComputeForcesIncludingDamping 150ms 0.44% 0.49% 17829ms 51.76% AbstractTwoBodyInteractionForce::AddForceContribution 1504ms 4.37% 4.86% 15095ms 43.82% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4347ms 12.62% 17.48% 9658ms 28.04% std::_Rb_tree::_M_lower_bound (inline) 0 0% 17.48% 9288ms 26.96% AbstractCellBasedSimulation::UpdateCellPopulation 351ms 1.02% 18.50% 8865ms 25.74% std::_Rb_tree::find (inline) 0 0% 18.50% 8864ms 25.73% std::map::find (inline) 189ms 0.55% 19.04% 8783ms 25.50% NodesOnlyMesh::GetNodeOrHaloNode 480ms 1.39% 20.44% 8585ms 24.92% AbstractMesh::GetNode 0 0% 20.44% 8246ms 23.94% NodeBasedCellPopulation::Update 379ms 1.10% 21.54% 8109ms 23.54% NodesOnlyMesh::SolveNodeMapping 7ms 0.02% 21.56% 6140ms 17.82% DistributedBoxCollection::CalculateInteriorNodePairs 223ms 0.65% 22.21% 5753ms 16.70% boost::numeric::ublas::vector_assign (inline) 148ms 0.43% 22.63% 5639ms 16.37% boost::numeric::ublas::c_vector::c_vector (partial-inline) 5292ms 15.36% 38.00% 5292ms 15.36% std::_Rb_tree::_S_right (inline) 4ms 0.012% 38.01% 4646ms 13.49% NodeAttributes::RemoveDuplicateNeighbours 2ms 0.0058% 38.01% 4580ms 13.30% OffLatticeSimulation::ApplyBoundaries 8ms 0.023% 38.04% 4483ms 13.01% std::__sort (inline) 0 0% 38.04% 4483ms 13.01% std::sort (inline) 1122ms 3.26% 41.30% 3384ms 9.82% boost::numeric::ublas::indexing_vector_assign 68ms 0.2% 41.49% 3303ms 9.59% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 2ms 0.0058% 41.50% 3178ms 9.23% AbstractCellPopulation::Iterator::operator++ (inline) 168ms 0.49% 41.99% 3149ms 9.14% AbstractCellPopulation::Iterator::IsRealCell 37ms 0.11% 42.09% 2741ms 7.96% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 196ms 0.57% 42.66% 2603ms 7.56% std::__introsort_loop 37ms 0.11% 42.77% 2429ms 7.05% PlaneBoundaryCondition::ImposeBoundaryCondition 0 0% 42.77% 2339ms 6.79% std::__unguarded_partition_pivot (inline) 31ms 0.09% 42.86% 2203ms 6.40% AbstractCellPopulation::GetLocationIndexUsingCell 11ms 0.032% 42.89% 2149ms 6.24% PlaneBoundaryCondition::VerifyBoundaryCondition 150ms 0.44% 43.33% 2124ms 6.17% DistributedBoxCollection::AddPairsFromBox 999ms 2.90% 46.23% 2100ms 6.10% std::__unguarded_partition (inline) 2ms 0.0058% 46.23% 1868ms 5.42% std::__final_insertion_sort (inline) 211ms 0.61% 46.85% 1751ms 5.08% std::map::operator[] (partial-inline) 1700ms 4.94% 51.78% 1700ms 4.94% boost::numeric::ublas::same_impl_ex 101ms 0.29% 52.07% 1656ms 4.81% std::__unguarded_insertion_sort (inline) 606ms 1.76% 53.83% 1594ms 4.63% std::__unguarded_linear_insert (inline) 162ms 0.47% 54.30% 1503ms 4.36% AbstractMesh::GetVectorFromAtoB 1438ms 4.17% 58.48% 1438ms 4.17% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 58.48% 1347ms 3.91% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 58.48% 1332ms 3.87% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 58.48% 1247ms 3.62% std::_Rb_tree::lower_bound (inline) 0 0% 58.48% 1247ms 3.62% std::map::lower_bound (inline) 0 0% 58.48% 1188ms 3.45% NodeBasedCellPopulation::UpdateCellProcessLocation 1183ms 3.43% 61.91% 1183ms 3.43% boost::numeric::ublas::c_vector::operator() 2ms 0.0058% 61.92% 1139ms 3.31% boost::numeric::ublas::detail::expression_type_check (inline) 4ms 0.012% 61.93% 1114ms 3.23% DistributedBoxCollection::CalculateBoundaryNodePairs 263ms 0.76% 62.69% 1098ms 3.19% boost::numeric::ublas::detail::equals 93ms 0.27% 62.96% 920ms 2.67% boost::numeric::ublas::vector_binary::size (inline) 13ms 0.038% 63.00% 906ms 2.63% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 190ms 0.55% 63.55% 861ms 2.50% NodeAttributes::AddAppliedForceContribution 376ms 1.09% 64.64% 840ms 2.44% DistributedBoxCollection::CalculateContainingBox (partial-inline) 248ms 0.72% 65.36% 822ms 2.39% NodeAttributes::AddNeighbour 573ms 1.66% 67.03% 782ms 2.27% __dynamic_cast 0 0% 67.03% 780ms 2.26% boost::numeric::ublas::norm_inf (inline) 504ms 1.46% 68.49% 780ms 2.26% boost::numeric::ublas::vector_norm_inf::apply (inline) 88ms 0.26% 68.75% 750ms 2.18% std::__new_allocator::allocate (inline) 2ms 0.0058% 68.75% 740ms 2.15% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 68.75% 738ms 2.14% AbstractCellPopulation::WriteResultsToFiles 0 0% 68.75% 671ms 1.95% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 68.75% 671ms 1.95% boost::numeric::ublas::c_vector::plus_assign (inline) 34ms 0.099% 68.85% 671ms 1.95% std::_Rb_tree_const_iterator::operator++ (inline) 88ms 0.26% 69.11% 660ms 1.92% operator new 572ms 1.66% 70.77% 637ms 1.85% std::vector::push_back (inline) 628ms 1.82% 72.59% 628ms 1.82% std::_Rb_tree_increment 211ms 0.61% 73.20% 572ms 1.66% __GI___libc_malloc 9ms 0.026% 73.23% 567ms 1.65% AbstractCellBasedSimulation::DoCellBirth 0 0% 73.23% 567ms 1.65% boost::numeric::ublas::norm_2 (inline) 455ms 1.32% 74.55% 567ms 1.65% boost::numeric::ublas::vector_norm_2::apply (inline) 13ms 0.038% 74.59% 559ms 1.62% CellPropertyCollection::GetPropertiesType (inline) 184ms 0.53% 75.12% 520ms 1.51% __GI___libc_free 0 0% 75.12% 494ms 1.43% NodeBasedCellPopulation::WriteVtkResultsToFile 493ms 1.43% 76.55% 493ms 1.43% Node::GetIndex 2ms 0.0058% 76.56% 482ms 1.40% Cell::GetMutationState 0 0% 76.56% 474ms 1.38% AbstractCellBasedSimulation::DoCellRemoval (inline) 3ms 0.0087% 76.57% 466ms 1.35% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 76.57% 417ms 1.21% std::allocator_traits::allocate (inline) 49ms 0.14% 76.71% 403ms 1.17% boost::detail::shared_count::~shared_count (inline) 0 0% 76.71% 403ms 1.17% boost::shared_ptr::~shared_ptr (inline) 0 0% 76.71% 395ms 1.15% std::_Rb_tree::_M_create_node (inline) 0 0% 76.71% 386ms 1.12% NodesOnlyMesh::ReMesh 3ms 0.0087% 76.72% 374ms 1.09% NodesOnlyMesh::UpdateNodeIndices 28ms 0.081% 76.80% 361ms 1.05% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 76.80% 361ms 1.05% boost::numeric::ublas::vector::vector (inline) 0 0% 76.80% 357ms 1.04% boost::numeric::ublas::inner_prod (inline) 1ms 0.0029% 76.80% 356ms 1.03% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 14ms 0.041% 76.84% 355ms 1.03% boost::numeric::ublas::vector_scalar_binary::evaluate 340ms 0.99% 77.83% 351ms 1.02% boost::detail::sp_counted_base::release 1ms 0.0029% 77.83% 348ms 1.01% AbstractCellProperty::IsSubType (inline) 342ms 0.99% 78.83% 342ms 0.99% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 78.83% 340ms 0.99% std::_Rb_tree::_M_get_node (inline) 2ms 0.0058% 78.83% 338ms 0.98% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 7ms 0.02% 78.85% 336ms 0.98% AbstractCellPopulation::GetCellUsingLocationIndex 301ms 0.87% 79.73% 335ms 0.97% _int_free 333ms 0.97% 80.69% 333ms 0.97% __gnu_cxx::__normal_iterator::operator++ (inline) 112ms 0.33% 81.02% 324ms 0.94% std::_Rb_tree::_M_erase 72ms 0.21% 81.23% 307ms 0.89% Node::GetRadius 4ms 0.012% 81.24% 306ms 0.89% NodeBasedCellPopulation::UpdateMapsAfterRemesh 4ms 0.012% 81.25% 301ms 0.87% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 14ms 0.041% 81.29% 293ms 0.85% std::_Rb_tree::_M_emplace_hint_unique 7ms 0.02% 81.31% 292ms 0.85% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 81.31% 291ms 0.84% boost::numeric::ublas::c_vector::assign (inline) 13ms 0.038% 81.35% 288ms 0.84% DistributedBoxCollection::GetProcessOwningNode 284ms 0.82% 82.17% 284ms 0.82% NodeBasedCellPopulation::GetNode 123ms 0.36% 82.53% 283ms 0.82% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 82.53% 266ms 0.77% NodesOnlyMesh::UpdateBoxCollection 17ms 0.049% 82.58% 254ms 0.74% std::_Rb_tree::_Rb_tree (partial-inline) 251ms 0.73% 83.31% 251ms 0.73% [libchaste_mesh.so] 216ms 0.63% 83.93% 247ms 0.72% Node::AddNeighbour 246ms 0.71% 84.65% 246ms 0.71% Node::CheckForNodeAttributes 136ms 0.39% 85.04% 246ms 0.71% _int_malloc 0 0% 85.04% 245ms 0.71% boost::numeric::ublas::vector_binary::operator() (inline) 242ms 0.7% 85.75% 242ms 0.7% [libchaste_cell_based.so] 0 0% 85.75% 234ms 0.68% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 124ms 0.36% 86.11% 234ms 0.68% std::__move_median_to_first (inline) 0 0% 86.11% 232ms 0.67% VtkMeshWriter::WriteFiles 0 0% 86.11% 232ms 0.67% std::_Rb_tree::_Alloc_node::operator() (inline) 18ms 0.052% 86.16% 231ms 0.67% std::_Rb_tree::_M_copy (inline) 5ms 0.015% 86.17% 224ms 0.65% CellPropertyCollection::HasProperty 0 0% 86.17% 223ms 0.65% Cell::HasCellProperty (inline) 2ms 0.0058% 86.18% 212ms 0.62% NodesOnlyMesh::AddNodesToBoxes 21ms 0.061% 86.24% 211ms 0.61% std::_Rb_tree::_M_clone_node (inline) 29ms 0.084% 86.32% 210ms 0.61% std::__insertion_sort (inline) 0 0% 86.32% 205ms 0.6% std::_Rb_tree::_M_drop_node (inline) 69ms 0.2% 86.52% 204ms 0.59% std::__find_if (inline) 0 0% 86.52% 204ms 0.59% std::find_if (inline) 0 0% 86.52% 204ms 0.59% std::none_of (inline) 0 0% 86.52% 202ms 0.59% vtkStreamingDemandDrivenPipeline::Update 0 0% 86.52% 202ms 0.59% vtkXMLWriterBase::Write 201ms 0.58% 87.11% 201ms 0.58% __strcmp_avx2 0 0% 87.11% 201ms 0.58% vtkDemandDrivenPipeline::ProcessRequest 0 0% 87.11% 199ms 0.58% vtkCompositeDataPipeline::ExecuteData 0 0% 87.11% 199ms 0.58% vtkDemandDrivenPipeline::ExecuteData 0 0% 87.11% 199ms 0.58% vtkExecutive::CallAlgorithm 0 0% 87.11% 199ms 0.58% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 87.11% 199ms 0.58% vtkXMLUnstructuredDataWriter::ProcessRequest 13ms 0.038% 87.15% 197ms 0.57% Cell::ReadyToDivide 8ms 0.023% 87.17% 195ms 0.57% std::__new_allocator::deallocate (inline) 107ms 0.31% 87.48% 186ms 0.54% boost::shared_ptr::shared_ptr (inline) 11ms 0.032% 87.51% 178ms 0.52% std::_Rb_tree::~_Rb_tree (inline) 1ms 0.0029% 87.51% 177ms 0.51% AbstractCellProperty::IsType (inline) 0 0% 87.51% 177ms 0.51% std::_Rb_tree::clear (inline) 0 0% 87.51% 175ms 0.51% std::allocator_traits::deallocate (inline) 139ms 0.4% 87.92% 174ms 0.51% Node::AddAppliedForceContribution 0 0% 87.92% 173ms 0.5% std::_Rb_tree::_M_put_node (inline) 0 0% 87.92% 173ms 0.5% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 87.92% 173ms 0.5% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData