File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 27081ms, 87.07% of 31103ms total Dropped 756 nodes (cum <= 155.51ms) flat flat% sum% cum cum% 0 0% 0% 31030ms 99.77% __libc_start_call_main 0 0% 0% 31030ms 99.77% __libc_start_main_impl 0 0% 0% 31030ms 99.77% _start 0 0% 0% 31013ms 99.71% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 31013ms 99.71% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 31013ms 99.71% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 31013ms 99.71% main 0 0% 0% 30983ms 99.61% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 30983ms 99.61% CxxTest::TestRunner::runTest (inline) 0 0% 0% 30983ms 99.61% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 30975ms 99.59% AbstractCellBasedSimulation::Solve 1ms 0.0032% 0.0032% 21551ms 69.29% OffLatticeSimulation::UpdateCellLocationsAndTopology 5ms 0.016% 0.019% 16283ms 52.35% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.0096% 0.029% 16092ms 51.74% AbstractNumericalMethod::ComputeForcesIncludingDamping 189ms 0.61% 0.64% 15510ms 49.87% AbstractTwoBodyInteractionForce::AddForceContribution 1087ms 3.49% 4.13% 13957ms 44.87% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4216ms 13.55% 17.69% 9765ms 31.40% std::_Rb_tree::_M_lower_bound (inline) 213ms 0.68% 18.37% 9369ms 30.12% NodesOnlyMesh::GetNodeOrHaloNode 259ms 0.83% 19.20% 9181ms 29.52% AbstractMesh::GetNode 385ms 1.24% 20.44% 8961ms 28.81% std::_Rb_tree::find (inline) 0 0% 20.44% 8961ms 28.81% std::map::find (inline) 748ms 2.40% 22.85% 8925ms 28.69% NodesOnlyMesh::SolveNodeMapping 1ms 0.0032% 22.85% 8383ms 26.95% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 22.85% 7352ms 23.64% NodeBasedCellPopulation::Update 5ms 0.016% 22.87% 5544ms 17.82% DistributedBoxCollection::CalculateInteriorNodePairs 0 0% 22.87% 5002ms 16.08% OffLatticeSimulation::ApplyBoundaries 4810ms 15.46% 38.33% 4810ms 15.46% std::_Rb_tree::_S_right (inline) 139ms 0.45% 38.78% 4445ms 14.29% boost::numeric::ublas::vector_assign (inline) 12ms 0.039% 38.82% 4408ms 14.17% NodeAttributes::RemoveDuplicateNeighbours 70ms 0.23% 39.04% 4346ms 13.97% boost::numeric::ublas::c_vector::c_vector (partial-inline) 5ms 0.016% 39.06% 4238ms 13.63% std::__sort (inline) 0 0% 39.06% 4238ms 13.63% std::sort (inline) 264ms 0.85% 39.91% 3718ms 11.95% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 6ms 0.019% 39.93% 3524ms 11.33% AbstractCellPopulation::Iterator::operator++ (inline) 178ms 0.57% 40.50% 3509ms 11.28% AbstractCellPopulation::Iterator::IsRealCell (inline) 26ms 0.084% 40.58% 2972ms 9.56% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 57ms 0.18% 40.76% 2553ms 8.21% PlaneBoundaryCondition::ImposeBoundaryCondition 215ms 0.69% 41.46% 2512ms 8.08% std::__introsort_loop 55ms 0.18% 41.63% 2449ms 7.87% PlaneBoundaryCondition::VerifyBoundaryCondition 3ms 0.0096% 41.64% 2226ms 7.16% std::__unguarded_partition_pivot (inline) 95ms 0.31% 41.95% 2031ms 6.53% AbstractCellPopulation::GetLocationIndexUsingCell 715ms 2.30% 44.25% 2019ms 6.49% std::__unguarded_partition (inline) 572ms 1.84% 46.09% 1892ms 6.08% boost::numeric::ublas::indexing_vector_assign 157ms 0.5% 46.59% 1799ms 5.78% std::map::operator[] (partial-inline) 0 0% 46.59% 1717ms 5.52% std::__final_insertion_sort (inline) 125ms 0.4% 46.99% 1643ms 5.28% DistributedBoxCollection::AddPairsFromBox 113ms 0.36% 47.36% 1548ms 4.98% std::__unguarded_insertion_sort (inline) 0 0% 47.36% 1523ms 4.90% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 47.36% 1507ms 4.85% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 28ms 0.09% 47.45% 1426ms 4.58% boost::numeric::ublas::detail::expression_type_check (inline) 698ms 2.24% 49.69% 1362ms 4.38% std::__unguarded_linear_insert (inline) 174ms 0.56% 50.25% 1359ms 4.37% boost::numeric::ublas::detail::equals 0 0% 50.25% 1303ms 4.19% std::_Rb_tree::lower_bound (inline) 0 0% 50.25% 1303ms 4.19% std::map::lower_bound (inline) 0 0% 50.25% 1132ms 3.64% boost::numeric::ublas::norm_inf (inline) 437ms 1.41% 51.65% 1132ms 3.64% boost::numeric::ublas::vector_norm_inf::apply (inline) 1ms 0.0032% 51.66% 1059ms 3.40% NodeBasedCellPopulation::UpdateCellProcessLocation 21ms 0.068% 51.72% 1054ms 3.39% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 174ms 0.56% 52.28% 983ms 3.16% AbstractMesh::GetVectorFromAtoB 978ms 3.14% 55.43% 978ms 3.14% __gnu_cxx::__normal_iterator::operator-- (inline) 945ms 3.04% 58.47% 945ms 3.04% boost::numeric::ublas::same_impl_ex 4ms 0.013% 58.48% 919ms 2.95% DistributedBoxCollection::CalculateBoundaryNodePairs 62ms 0.2% 58.68% 812ms 2.61% std::__new_allocator::allocate (inline) 759ms 2.44% 61.12% 759ms 2.44% std::_Rb_tree::_S_left (inline) 70ms 0.23% 61.34% 722ms 2.32% operator new 20ms 0.064% 61.41% 711ms 2.29% boost::detail::shared_count::~shared_count (inline) 0 0% 61.41% 711ms 2.29% boost::shared_ptr::~shared_ptr (inline) 295ms 0.95% 62.36% 680ms 2.19% DistributedBoxCollection::CalculateContainingBox (partial-inline) 658ms 2.12% 64.47% 674ms 2.17% boost::detail::sp_counted_base::release 644ms 2.07% 66.54% 644ms 2.07% [libchaste_cell_based.so] 0 0% 66.54% 628ms 2.02% AbstractCellPopulation::WriteResultsToFiles 209ms 0.67% 67.22% 620ms 1.99% __GI___libc_malloc 607ms 1.95% 69.17% 607ms 1.95% boost::numeric::ublas::c_vector::operator() 455ms 1.46% 70.63% 590ms 1.90% __dynamic_cast 585ms 1.88% 72.51% 585ms 1.88% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 278ms 0.89% 73.40% 581ms 1.87% NodeAttributes::AddNeighbour 1ms 0.0032% 73.41% 560ms 1.80% AbstractCentreBasedCellPopulation::GetDampingConstant 24ms 0.077% 73.48% 556ms 1.79% std::_Rb_tree_const_iterator::operator++ (inline) 532ms 1.71% 75.20% 532ms 1.71% [libchaste_mesh.so] 197ms 0.63% 75.83% 524ms 1.68% NodeAttributes::AddAppliedForceContribution 0 0% 75.83% 519ms 1.67% AbstractCellBasedSimulation::DoCellRemoval (inline) 1ms 0.0032% 75.83% 511ms 1.64% AbstractCellBasedSimulation::DoCellBirth 7ms 0.023% 75.85% 509ms 1.64% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 509ms 1.64% 77.49% 509ms 1.64% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 77.49% 508ms 1.63% boost::numeric::ublas::scalar_traits::type_abs (inline) 0 0% 77.49% 502ms 1.61% boost::numeric::ublas::scalar_traits::norm_inf (inline) 0 0% 77.49% 500ms 1.61% boost_numeric_ublas_abs (inline) 500ms 1.61% 79.10% 500ms 1.61% std::abs (inline) 42ms 0.14% 79.23% 494ms 1.59% boost::numeric::ublas::vector_binary::size (inline) 478ms 1.54% 80.77% 478ms 1.54% std::_Rb_tree_increment 0 0% 80.77% 436ms 1.40% std::allocator_traits::allocate (inline) 135ms 0.43% 81.20% 414ms 1.33% __GI___libc_free 0 0% 81.20% 413ms 1.33% NodeBasedCellPopulation::WriteVtkResultsToFile 6ms 0.019% 81.22% 412ms 1.32% CellPropertyCollection::GetPropertiesType (inline) 0 0% 81.22% 391ms 1.26% boost::numeric::ublas::norm_2 (inline) 293ms 0.94% 82.17% 391ms 1.26% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 82.17% 388ms 1.25% std::_Rb_tree::_M_create_node (inline) 275ms 0.88% 83.05% 381ms 1.22% std::vector::push_back (inline) 4ms 0.013% 83.06% 380ms 1.22% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 83.06% 380ms 1.22% boost::numeric::ublas::vector::vector (inline) 3ms 0.0096% 83.07% 375ms 1.21% Cell::GetMutationState 0 0% 83.07% 367ms 1.18% std::_Rb_tree::_M_get_node (inline) 11ms 0.035% 83.11% 339ms 1.09% std::_Rb_tree::_M_emplace_hint_unique 0 0% 83.11% 327ms 1.05% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 83.11% 327ms 1.05% boost::numeric::ublas::c_vector::plus_assign (inline) 0 0% 83.11% 323ms 1.04% NodesOnlyMesh::ReMesh 0 0% 83.11% 319ms 1.03% boost::numeric::ublas::vector_binary::operator() (inline) 4ms 0.013% 83.12% 317ms 1.02% NodesOnlyMesh::UpdateNodeIndices 7ms 0.023% 83.14% 291ms 0.94% NodeBasedCellPopulation::UpdateMapsAfterRemesh 1ms 0.0032% 83.15% 277ms 0.89% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 200ms 0.64% 83.79% 277ms 0.89% _int_free 2ms 0.0064% 83.80% 273ms 0.88% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 83.80% 268ms 0.86% Node::GetRadius 4ms 0.013% 83.81% 264ms 0.85% AbstractCellProperty::IsSubType (inline) 151ms 0.49% 84.29% 254ms 0.82% _int_malloc 3ms 0.0096% 84.30% 244ms 0.78% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 84.30% 232ms 0.75% NodesOnlyMesh::UpdateBoxCollection 196ms 0.63% 84.93% 228ms 0.73% boost::shared_ptr::shared_ptr (inline) 224ms 0.72% 85.65% 224ms 0.72% Node::CheckForNodeAttributes 3ms 0.0096% 85.66% 219ms 0.7% DistributedBoxCollection::GetProcessOwningNode 38ms 0.12% 85.79% 217ms 0.7% std::_Rb_tree::_M_erase (partial-inline) 0 0% 85.79% 211ms 0.68% std::_Rb_tree::_Auto_node::_Auto_node (inline) 13ms 0.042% 85.83% 205ms 0.66% std::_Rb_tree::_Rb_tree (partial-inline) 8ms 0.026% 85.85% 204ms 0.66% boost::numeric::ublas::vector_reference::operator() (inline) 71ms 0.23% 86.08% 201ms 0.65% std::__move_median_to_first (inline) 0 0% 86.08% 196ms 0.63% NodesOnlyMesh::AddNodesToBoxes 0 0% 86.08% 194ms 0.62% std::iter_swap (inline) 194ms 0.62% 86.71% 194ms 0.62% std::swap (inline) 16ms 0.051% 86.76% 187ms 0.6% std::__new_allocator::deallocate (inline) 0 0% 86.76% 185ms 0.59% boost::numeric::ublas::inner_prod (inline) 9ms 0.029% 86.79% 185ms 0.59% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 86.79% 185ms 0.59% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 9ms 0.029% 86.81% 185ms 0.59% std::_Rb_tree::_M_copy (inline) 0 0% 86.81% 184ms 0.59% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 86.81% 183ms 0.59% VtkMeshWriter::WriteFiles 0 0% 86.81% 183ms 0.59% boost::numeric::ublas::c_vector::assign (inline) 2ms 0.0064% 86.82% 182ms 0.59% CellPropertyCollection::HasProperty 0 0% 86.82% 181ms 0.58% Cell::HasCellProperty (inline) 0 0% 86.82% 179ms 0.58% std::_Rb_tree::_M_drop_node (inline) 0 0% 86.82% 177ms 0.57% std::_Rb_tree::_Alloc_node::operator() (inline) 45ms 0.14% 86.97% 175ms 0.56% std::_Rb_tree::_M_clone_node (inline) 22ms 0.071% 87.04% 169ms 0.54% std::__insertion_sort (inline) 2ms 0.0064% 87.04% 167ms 0.54% Cell::ReadyToDivide 0 0% 87.04% 166ms 0.53% vtkStreamingDemandDrivenPipeline::Update 0 0% 87.04% 166ms 0.53% vtkXMLWriterBase::Write 0 0% 87.04% 164ms 0.53% vtkDemandDrivenPipeline::ProcessRequest 0 0% 87.04% 164ms 0.53% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 87.04% 163ms 0.52% vtkExecutive::CallAlgorithm 0 0% 87.04% 163ms 0.52% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 87.04% 162ms 0.52% vtkCompositeDataPipeline::ExecuteData 0 0% 87.04% 162ms 0.52% vtkDemandDrivenPipeline::ExecuteData 0 0% 87.04% 160ms 0.51% NodesOnlyMesh::ResizeBoxCollection 8ms 0.026% 87.07% 159ms 0.51% NodesOnlyMesh::IsANodeCloseToDomainBoundary