File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 23995ms, 88.77% of 27032ms total Dropped 816 nodes (cum <= 135.16ms) flat flat% sum% cum cum% 0 0% 0% 26884ms 99.45% __libc_start_call_main 0 0% 0% 26884ms 99.45% __libc_start_main_impl 0 0% 0% 26884ms 99.45% _start 0 0% 0% 26866ms 99.39% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 26866ms 99.39% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 26866ms 99.39% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 26866ms 99.39% main 0 0% 0% 26820ms 99.22% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 26820ms 99.22% CxxTest::TestRunner::runTest (inline) 0 0% 0% 26820ms 99.22% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 26810ms 99.18% AbstractCellBasedSimulation::Solve 1ms 0.0037% 0.0037% 14988ms 55.45% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0037% 10497ms 38.83% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.015% 0.018% 9916ms 36.68% ForwardEulerNumericalMethod::UpdateAllNodePositions 14ms 0.052% 0.07% 9729ms 35.99% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.0037% 0.074% 9188ms 33.99% NodeBasedCellPopulation::Update 1310ms 4.85% 4.92% 8603ms 31.83% RepulsionForce::AddForceContribution (partial-inline) 11ms 0.041% 4.96% 6875ms 25.43% DistributedBoxCollection::CalculateInteriorNodePairs 2025ms 7.49% 12.45% 5182ms 19.17% std::_Rb_tree::_M_lower_bound (inline) 18ms 0.067% 12.52% 4906ms 18.15% NodeAttributes::RemoveDuplicateNeighbours 2ms 0.0074% 12.53% 4700ms 17.39% std::__sort (inline) 0 0% 12.53% 4700ms 17.39% std::sort (inline) 2ms 0.0074% 12.53% 4660ms 17.24% OffLatticeSimulation::ApplyBoundaries 209ms 0.77% 13.31% 4432ms 16.40% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 235ms 0.87% 14.18% 3419ms 12.65% std::_Rb_tree::find (inline) 0 0% 14.18% 3417ms 12.64% std::map::find (inline) 95ms 0.35% 14.53% 3307ms 12.23% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 5ms 0.018% 14.55% 3210ms 11.87% AbstractCellPopulation::Iterator::operator++ (inline) 234ms 0.87% 15.41% 3187ms 11.79% AbstractCellPopulation::Iterator::IsRealCell 3145ms 11.63% 27.05% 3145ms 11.63% std::_Rb_tree::_S_right (inline) 240ms 0.89% 27.93% 2833ms 10.48% std::__introsort_loop 163ms 0.6% 28.54% 2711ms 10.03% DistributedBoxCollection::AddPairsFromBox 35ms 0.13% 28.67% 2677ms 9.90% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 236ms 0.87% 29.54% 2566ms 9.49% std::map::operator[] (partial-inline) 0 0% 29.54% 2510ms 9.29% std::__unguarded_partition_pivot (inline) 179ms 0.66% 30.20% 2506ms 9.27% AbstractMesh::GetNode 33ms 0.12% 30.32% 2497ms 9.24% PlaneBoundaryCondition::ImposeBoundaryCondition 53ms 0.2% 30.52% 2487ms 9.20% NodesOnlyMesh::GetNodeOrHaloNode 95ms 0.35% 30.87% 2333ms 8.63% NodesOnlyMesh::SolveNodeMapping 53ms 0.2% 31.07% 2235ms 8.27% AbstractCellPopulation::GetLocationIndexUsingCell 17ms 0.063% 31.13% 2160ms 7.99% PlaneBoundaryCondition::VerifyBoundaryCondition 1004ms 3.71% 34.84% 2148ms 7.95% std::__unguarded_partition (inline) 0 0% 34.84% 2025ms 7.49% std::_Rb_tree::lower_bound (inline) 0 0% 34.84% 2025ms 7.49% std::map::lower_bound (inline) 20ms 0.074% 34.92% 1961ms 7.25% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 18ms 0.067% 34.98% 1932ms 7.15% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 34.98% 1864ms 6.90% std::__final_insertion_sort (inline) 113ms 0.42% 35.40% 1671ms 6.18% std::__unguarded_insertion_sort (inline) 655ms 2.42% 37.83% 1593ms 5.89% std::__unguarded_linear_insert (inline) 1458ms 5.39% 43.22% 1458ms 5.39% __gnu_cxx::__normal_iterator::operator-- (inline) 39ms 0.14% 43.36% 1321ms 4.89% boost::numeric::ublas::c_vector::c_vector (partial-inline) 6ms 0.022% 43.39% 1248ms 4.62% DistributedBoxCollection::CalculateBoundaryNodePairs 1ms 0.0037% 43.39% 1240ms 4.59% NodeBasedCellPopulation::UpdateCellProcessLocation 10ms 0.037% 43.43% 1207ms 4.47% boost::numeric::ublas::vector_assign (inline) 34ms 0.13% 43.55% 1191ms 4.41% std::_Rb_tree_const_iterator::operator++ (inline) 1149ms 4.25% 47.80% 1149ms 4.25% std::_Rb_tree_increment 251ms 0.93% 48.73% 1106ms 4.09% boost::numeric::ublas::indexing_vector_assign 23ms 0.085% 48.82% 1019ms 3.77% CellPropertyCollection::GetPropertiesType (inline) 7ms 0.026% 48.84% 1012ms 3.74% AbstractCentreBasedCellPopulation::GetDampingConstant 326ms 1.21% 50.05% 1002ms 3.71% __dynamic_cast 409ms 1.51% 51.56% 995ms 3.68% NodeAttributes::AddNeighbour 26ms 0.096% 51.66% 974ms 3.60% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 185ms 0.68% 52.34% 884ms 3.27% AbstractMesh::GetVectorFromAtoB 412ms 1.52% 53.87% 873ms 3.23% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 53.87% 820ms 3.03% AbstractCellPopulation::WriteResultsToFiles 2ms 0.0074% 53.87% 815ms 3.01% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 53.87% 811ms 3.00% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 45ms 0.17% 54.04% 804ms 2.97% std::__copy_move::__copy_m (inline) 0 0% 54.04% 804ms 2.97% std::__copy_move_a (inline) 0 0% 54.04% 804ms 2.97% std::__copy_move_a1 (inline) 0 0% 54.04% 804ms 2.97% std::__copy_move_a2 (inline) 0 0% 54.04% 804ms 2.97% std::copy (inline) 9ms 0.033% 54.07% 803ms 2.97% AbstractCellBasedSimulation::DoCellBirth 0 0% 54.07% 798ms 2.95% boost::numeric::ublas::norm_2 (inline) 638ms 2.36% 56.43% 798ms 2.95% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 56.43% 798ms 2.95% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 6ms 0.022% 56.46% 794ms 2.94% Cell::GetMutationState 776ms 2.87% 59.33% 776ms 2.87% __memcpy_avx_unaligned_erms 756ms 2.80% 62.12% 756ms 2.80% boost::numeric::ublas::c_vector::operator() 50ms 0.18% 62.31% 754ms 2.79% std::_Rb_tree::_Rb_tree (partial-inline) 156ms 0.58% 62.88% 710ms 2.63% std::__new_allocator::allocate (inline) 582ms 2.15% 65.04% 706ms 2.61% std::vector::push_back (inline) 49ms 0.18% 65.22% 684ms 2.53% std::_Rb_tree::_M_copy (inline) 0 0% 65.22% 683ms 2.53% std::allocator_traits::allocate (inline) 0 0% 65.22% 640ms 2.37% std::_Rb_tree::_M_create_node (inline) 226ms 0.84% 66.06% 631ms 2.33% std::_Rb_tree::_M_clone_node (inline) 5ms 0.018% 66.07% 591ms 2.19% std::set::set (inline) 270ms 1% 67.07% 568ms 2.10% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 67.07% 564ms 2.09% std::_Rb_tree::_M_get_node (inline) 26ms 0.096% 67.17% 547ms 2.02% operator new 2ms 0.0074% 67.18% 542ms 2.01% NodeBasedCellPopulation::WriteVtkResultsToFile 536ms 1.98% 69.16% 536ms 1.98% boost::numeric::ublas::same_impl_ex 46ms 0.17% 69.33% 516ms 1.91% boost::detail::shared_count::~shared_count (inline) 0 0% 69.33% 516ms 1.91% boost::shared_ptr::~shared_ptr (inline) 145ms 0.54% 69.87% 516ms 1.91% std::_Rb_tree::_M_erase 119ms 0.44% 70.31% 511ms 1.89% __GI___libc_malloc 0 0% 70.31% 503ms 1.86% AbstractCellBasedSimulation::DoCellRemoval (inline) 4ms 0.015% 70.32% 496ms 1.83% AbstractCellProperty::IsSubType (inline) 5ms 0.018% 70.34% 487ms 1.80% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 483ms 1.79% 72.13% 483ms 1.79% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 450ms 1.66% 73.79% 460ms 1.70% boost::detail::sp_counted_base::release 0 0% 73.79% 458ms 1.69% std::_Rb_tree::_Alloc_node::operator() (inline) 450ms 1.66% 75.46% 450ms 1.66% __strcmp_avx2 366ms 1.35% 76.81% 407ms 1.51% Node::AddNeighbour 102ms 0.38% 77.19% 405ms 1.50% boost::numeric::ublas::vector_binary::size (inline) 4ms 0.015% 77.20% 396ms 1.46% CellPropertyCollection::HasProperty 0 0% 77.20% 394ms 1.46% Cell::HasCellProperty (inline) 91ms 0.34% 77.54% 379ms 1.40% Node::GetRadius 0 0% 77.54% 379ms 1.40% boost::numeric::ublas::inner_prod (inline) 2ms 0.0074% 77.55% 379ms 1.40% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 11ms 0.041% 77.59% 377ms 1.39% boost::numeric::ublas::vector_scalar_binary::evaluate 35ms 0.13% 77.72% 374ms 1.38% std::_Rb_tree::~_Rb_tree (inline) 10ms 0.037% 77.75% 371ms 1.37% Cell::ReadyToDivide 0 0% 77.75% 359ms 1.33% std::_Rb_tree::_M_drop_node (inline) 102ms 0.38% 78.13% 359ms 1.33% std::__move_median_to_first (inline) 0 0% 78.13% 356ms 1.32% boost::numeric::ublas::c_vector::assign (inline) 0 0% 78.13% 354ms 1.31% NodesOnlyMesh::ReMesh 166ms 0.61% 78.74% 346ms 1.28% _int_malloc 2ms 0.0074% 78.75% 339ms 1.25% NodesOnlyMesh::UpdateNodeIndices 8ms 0.03% 78.78% 324ms 1.20% NodeBasedCellPopulation::UpdateMapsAfterRemesh 3ms 0.011% 78.79% 318ms 1.18% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 315ms 1.17% 79.96% 315ms 1.17% __gnu_cxx::__normal_iterator::operator++ (inline) 131ms 0.48% 80.44% 315ms 1.17% boost::numeric::ublas::vector_inner_prod::apply (inline) 1ms 0.0037% 80.45% 307ms 1.14% std::__new_allocator::deallocate (inline) 6ms 0.022% 80.47% 305ms 1.13% std::_Rb_tree::_M_emplace_hint_unique 0 0% 80.47% 304ms 1.12% NodesOnlyMesh::UpdateBoxCollection 7ms 0.026% 80.49% 299ms 1.11% DistributedBoxCollection::GetProcessOwningNode 297ms 1.10% 81.59% 297ms 1.10% Node::CheckForNodeAttributes 103ms 0.38% 81.97% 287ms 1.06% __GI___libc_free 0 0% 81.97% 284ms 1.05% std::allocator_traits::deallocate (inline) 0 0% 81.97% 278ms 1.03% std::_Rb_tree::_M_put_node (inline) 0 0% 81.97% 259ms 0.96% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 81.97% 257ms 0.95% VtkMeshWriter::WriteFiles 0 0% 81.97% 249ms 0.92% std::set::~set (inline) 107ms 0.4% 82.37% 237ms 0.88% boost::shared_ptr::shared_ptr (inline) 1ms 0.0037% 82.37% 230ms 0.85% NodesOnlyMesh::AddNodesToBoxes 16ms 0.059% 82.43% 229ms 0.85% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 82.43% 227ms 0.84% boost::numeric::ublas::vector_binary::operator() (inline) 222ms 0.82% 83.25% 222ms 0.82% Node::GetIndex 1ms 0.0037% 83.26% 222ms 0.82% vtkDemandDrivenPipeline::ExecuteData 0 0% 83.26% 222ms 0.82% vtkDemandDrivenPipeline::ProcessRequest 0 0% 83.26% 222ms 0.82% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 83.26% 222ms 0.82% vtkStreamingDemandDrivenPipeline::Update 0 0% 83.26% 222ms 0.82% vtkXMLWriterBase::Write 0 0% 83.26% 221ms 0.82% vtkCompositeDataPipeline::ExecuteData 220ms 0.81% 84.07% 220ms 0.81% [libchaste_mesh.so] 0 0% 84.07% 220ms 0.81% vtkExecutive::CallAlgorithm 0 0% 84.07% 220ms 0.81% vtkXMLUnstructuredDataWriter::ProcessRequest 219ms 0.81% 84.88% 219ms 0.81% boost::shared_ptr::operator-> (inline) 0 0% 84.88% 208ms 0.77% AbstractCellProperty::IsType (inline) 193ms 0.71% 85.59% 193ms 0.71% [libchaste_cell_based.so] 20ms 0.074% 85.67% 193ms 0.71% std::__insertion_sort (inline) 0 0% 85.67% 189ms 0.7% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.67% 189ms 0.7% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 85.67% 188ms 0.7% std::_Rb_tree::clear (inline) 162ms 0.6% 86.27% 184ms 0.68% _int_free 0 0% 86.27% 182ms 0.67% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 86.27% 182ms 0.67% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 1ms 0.0037% 86.27% 179ms 0.66% NodesOnlyMesh::ResizeBoxCollection 12ms 0.044% 86.32% 177ms 0.65% NodesOnlyMesh::IsANodeCloseToDomainBoundary 1ms 0.0037% 86.32% 170ms 0.63% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 86.32% 169ms 0.63% std::map::map (inline) 2ms 0.0074% 86.33% 168ms 0.62% boost::numeric::ublas::c_vector::operator[] (inline) 168ms 0.62% 86.95% 168ms 0.62% std::__adjacent_find (inline) 0 0% 86.95% 168ms 0.62% std::__unique (inline) 0 0% 86.95% 168ms 0.62% std::unique (inline) 92ms 0.34% 87.29% 166ms 0.61% AbstractCellProperty::IsSame 155ms 0.57% 87.86% 155ms 0.57% __ieee754_log_fma 3ms 0.011% 87.87% 151ms 0.56% Cell::GetCellId 93ms 0.34% 88.22% 150ms 0.55% AbstractCellCycleModel::GetAge 1ms 0.0037% 88.22% 146ms 0.54% vtkXMLWriter::WriteBinaryData 2ms 0.0074% 88.23% 140ms 0.52% Cell::GetCellProliferativeType 1ms 0.0037% 88.23% 140ms 0.52% NodeBasedCellPopulation::AcceptCellWriter 0 0% 88.23% 140ms 0.52% vtkXMLWriter::WriteBinaryDataBlock 0 0% 88.23% 140ms 0.52% vtkXMLWriter::WriteBinaryDataInternal 0 0% 88.23% 140ms 0.52% vtkXMLWriter::WriteCompressionBlock 139ms 0.51% 88.75% 139ms 0.51% Node::rGetLocation 4ms 0.015% 88.76% 138ms 0.51% AbstractNumericalMethod::SafeNodePositionUpdate 1ms 0.0037% 88.77% 138ms 0.51% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 88.77% 136ms 0.5% vtkXMLWriter::WritePointsAppendedData