File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 30085ms, 88.92% of 33834ms total Dropped 783 nodes (cum <= 169.17ms) flat flat% sum% cum cum% 0 0% 0% 33691ms 99.58% __libc_start_call_main 0 0% 0% 33691ms 99.58% __libc_start_main_impl 0 0% 0% 33691ms 99.58% _start 0 0% 0% 33674ms 99.53% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 33674ms 99.53% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 33674ms 99.53% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 33674ms 99.53% main 0 0% 0% 33637ms 99.42% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 33637ms 99.42% CxxTest::TestRunner::runTest (inline) 0 0% 0% 33637ms 99.42% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 33629ms 99.39% AbstractCellBasedSimulation::Solve 3ms 0.0089% 0.0089% 23898ms 70.63% OffLatticeSimulation::UpdateCellLocationsAndTopology 3ms 0.0089% 0.018% 19124ms 56.52% ForwardEulerNumericalMethod::UpdateAllNodePositions 12ms 0.035% 0.053% 18964ms 56.05% AbstractNumericalMethod::ComputeForcesIncludingDamping 187ms 0.55% 0.61% 18343ms 54.21% AbstractTwoBodyInteractionForce::AddForceContribution 1436ms 4.24% 4.85% 15468ms 45.72% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4397ms 13.00% 17.85% 9458ms 27.95% std::_Rb_tree::_M_lower_bound (inline) 0 0% 17.85% 8580ms 25.36% AbstractCellBasedSimulation::UpdateCellPopulation 315ms 0.93% 18.78% 8568ms 25.32% std::_Rb_tree::find (inline) 0 0% 18.78% 8568ms 25.32% std::map::find (inline) 159ms 0.47% 19.25% 8312ms 24.57% NodesOnlyMesh::GetNodeOrHaloNode 464ms 1.37% 20.62% 8126ms 24.02% AbstractMesh::GetNode 293ms 0.87% 21.48% 7664ms 22.65% NodesOnlyMesh::SolveNodeMapping 0 0% 21.48% 7570ms 22.37% NodeBasedCellPopulation::Update 212ms 0.63% 22.11% 6485ms 19.17% boost::numeric::ublas::vector_assign (inline) 194ms 0.57% 22.68% 6439ms 19.03% boost::numeric::ublas::c_vector::c_vector (partial-inline) 4ms 0.012% 22.70% 5583ms 16.50% DistributedBoxCollection::CalculateInteriorNodePairs 5021ms 14.84% 37.54% 5021ms 14.84% std::_Rb_tree::_S_right (inline) 0 0% 37.54% 4490ms 13.27% OffLatticeSimulation::ApplyBoundaries 21ms 0.062% 37.60% 4442ms 13.13% NodeAttributes::RemoveDuplicateNeighbours 7ms 0.021% 37.62% 4289ms 12.68% std::__sort (inline) 0 0% 37.62% 4289ms 12.68% std::sort (inline) 1234ms 3.65% 41.27% 3606ms 10.66% boost::numeric::ublas::indexing_vector_assign 1ms 0.003% 41.27% 3431ms 10.14% AbstractCellPopulation::Iterator::operator++ (inline) 195ms 0.58% 41.85% 3413ms 10.09% AbstractCellPopulation::Iterator::IsRealCell (inline) 72ms 0.21% 42.06% 3394ms 10.03% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 34ms 0.1% 42.16% 2914ms 8.61% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 187ms 0.55% 42.71% 2444ms 7.22% std::__introsort_loop 25ms 0.074% 42.79% 2348ms 6.94% PlaneBoundaryCondition::ImposeBoundaryCondition 42ms 0.12% 42.91% 2302ms 6.80% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 42.91% 2174ms 6.43% std::__unguarded_partition_pivot (inline) 19ms 0.056% 42.97% 2142ms 6.33% PlaneBoundaryCondition::VerifyBoundaryCondition 1021ms 3.02% 45.98% 1974ms 5.83% std::__unguarded_partition (inline) 1ms 0.003% 45.99% 1835ms 5.42% std::__final_insertion_sort (inline) 163ms 0.48% 46.47% 1764ms 5.21% DistributedBoxCollection::AddPairsFromBox 149ms 0.44% 46.91% 1738ms 5.14% AbstractMesh::GetVectorFromAtoB 190ms 0.56% 47.47% 1736ms 5.13% std::map::operator[] (partial-inline) 1723ms 5.09% 52.56% 1723ms 5.09% boost::numeric::ublas::same_impl_ex 92ms 0.27% 52.83% 1620ms 4.79% std::__unguarded_insertion_sort (inline) 611ms 1.81% 54.64% 1597ms 4.72% std::__unguarded_linear_insert (inline) 1445ms 4.27% 58.91% 1445ms 4.27% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 58.91% 1311ms 3.87% std::_Rb_tree::lower_bound (inline) 0 0% 58.91% 1311ms 3.87% std::map::lower_bound (inline) 0 0% 58.91% 1257ms 3.72% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 58.91% 1237ms 3.66% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1ms 0.003% 58.91% 1138ms 3.36% NodeBasedCellPopulation::UpdateCellProcessLocation 1098ms 3.25% 62.16% 1098ms 3.25% boost::numeric::ublas::c_vector::operator() 17ms 0.05% 62.21% 1082ms 3.20% boost::numeric::ublas::detail::expression_type_check (inline) 4ms 0.012% 62.22% 1057ms 3.12% DistributedBoxCollection::CalculateBoundaryNodePairs 170ms 0.5% 62.72% 1055ms 3.12% boost::numeric::ublas::vector_binary::size (inline) 220ms 0.65% 63.37% 1038ms 3.07% boost::numeric::ublas::detail::equals 293ms 0.87% 64.24% 946ms 2.80% NodeAttributes::AddAppliedForceContribution 484ms 1.43% 65.67% 934ms 2.76% __GI___libc_free 52ms 0.15% 65.82% 793ms 2.34% std::__new_allocator::allocate (inline) 11ms 0.033% 65.86% 770ms 2.28% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 352ms 1.04% 66.90% 768ms 2.27% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 66.90% 764ms 2.26% boost::numeric::ublas::norm_inf (inline) 451ms 1.33% 68.23% 764ms 2.26% boost::numeric::ublas::vector_norm_inf::apply (inline) 547ms 1.62% 69.85% 758ms 2.24% __dynamic_cast 84ms 0.25% 70.10% 744ms 2.20% operator new 192ms 0.57% 70.66% 695ms 2.05% NodeAttributes::AddNeighbour 0 0% 70.66% 692ms 2.05% AbstractCellPopulation::WriteResultsToFiles 231ms 0.68% 71.35% 657ms 1.94% __GI___libc_malloc 0 0% 71.35% 653ms 1.93% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 71.35% 653ms 1.93% boost::numeric::ublas::c_vector::plus_assign (inline) 500ms 1.48% 72.82% 571ms 1.69% std::vector::push_back (inline) 6ms 0.018% 72.84% 570ms 1.68% AbstractCellBasedSimulation::DoCellBirth 2ms 0.0059% 72.85% 554ms 1.64% AbstractCentreBasedCellPopulation::GetDampingConstant 33ms 0.098% 72.94% 511ms 1.51% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 72.94% 493ms 1.46% boost::numeric::ublas::norm_2 (inline) 407ms 1.20% 74.15% 493ms 1.46% boost::numeric::ublas::vector_norm_2::apply (inline) 19ms 0.056% 74.20% 483ms 1.43% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 74.20% 483ms 1.43% boost::numeric::ublas::vector::vector (inline) 473ms 1.40% 75.60% 473ms 1.40% std::_Rb_tree_increment 10ms 0.03% 75.63% 457ms 1.35% CellPropertyCollection::GetPropertiesType (inline) 0 0% 75.63% 453ms 1.34% NodeBasedCellPopulation::WriteVtkResultsToFile 405ms 1.20% 76.83% 449ms 1.33% _int_free 0 0% 76.83% 439ms 1.30% AbstractCellBasedSimulation::DoCellRemoval (inline) 7ms 0.021% 76.85% 426ms 1.26% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 414ms 1.22% 78.07% 414ms 1.22% Node::GetIndex 1ms 0.003% 78.08% 392ms 1.16% Cell::GetMutationState 40ms 0.12% 78.19% 359ms 1.06% boost::detail::shared_count::~shared_count (inline) 0 0% 78.19% 359ms 1.06% boost::shared_ptr::~shared_ptr (inline) 113ms 0.33% 78.53% 340ms 1.00% Node::GetRadius 0 0% 78.53% 332ms 0.98% boost::numeric::ublas::inner_prod (inline) 1ms 0.003% 78.53% 329ms 0.97% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 78.53% 329ms 0.97% std::allocator_traits::allocate (inline) 16ms 0.047% 78.58% 328ms 0.97% boost::numeric::ublas::vector_scalar_binary::evaluate 3ms 0.0089% 78.59% 323ms 0.95% AbstractCellProperty::IsSubType (inline) 307ms 0.91% 79.49% 310ms 0.92% boost::detail::sp_counted_base::release 8ms 0.024% 79.52% 308ms 0.91% NodeBasedCellPopulation::UpdateMapsAfterRemesh 299ms 0.88% 80.40% 299ms 0.88% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 15ms 0.044% 80.45% 294ms 0.87% boost::numeric::ublas::vector_reference::operator() (inline) 290ms 0.86% 81.30% 290ms 0.86% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 81.30% 282ms 0.83% NodesOnlyMesh::ReMesh 112ms 0.33% 81.63% 278ms 0.82% boost::numeric::ublas::vector_inner_prod::apply (inline) 5ms 0.015% 81.65% 276ms 0.82% NodesOnlyMesh::UpdateNodeIndices 5ms 0.015% 81.66% 274ms 0.81% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 81.66% 266ms 0.79% std::_Rb_tree::_M_create_node (inline) 4ms 0.012% 81.68% 263ms 0.78% DistributedBoxCollection::GetProcessOwningNode 89ms 0.26% 81.94% 256ms 0.76% std::_Rb_tree::_M_erase (partial-inline) 246ms 0.73% 82.67% 246ms 0.73% boost::numeric::ublas::c_vector::size (inline) 0 0% 82.67% 245ms 0.72% boost::numeric::ublas::c_vector::assign (inline) 0 0% 82.67% 242ms 0.72% NodesOnlyMesh::UpdateBoxCollection 115ms 0.34% 83.01% 241ms 0.71% std::__find_if (inline) 0 0% 83.01% 241ms 0.71% std::find_if (inline) 0 0% 83.01% 241ms 0.71% std::none_of (inline) 239ms 0.71% 83.71% 239ms 0.71% [libchaste_cell_based.so] 237ms 0.7% 84.41% 237ms 0.7% Node::CheckForNodeAttributes 134ms 0.4% 84.81% 236ms 0.7% _int_malloc 0 0% 84.81% 236ms 0.7% std::_Rb_tree::_M_get_node (inline) 8ms 0.024% 84.83% 235ms 0.69% std::_Rb_tree::_M_emplace_hint_unique 7ms 0.021% 84.85% 234ms 0.69% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 84.85% 234ms 0.69% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 0 0% 84.85% 232ms 0.69% boost::numeric::ublas::vector_reference::size (inline) 231ms 0.68% 85.54% 231ms 0.68% Node::rGetLocation 219ms 0.65% 86.18% 219ms 0.65% [libchaste_mesh.so] 51ms 0.15% 86.33% 219ms 0.65% std::__new_allocator::deallocate (inline) 0 0% 86.33% 215ms 0.64% boost::numeric::ublas::vector_binary::operator() (inline) 15ms 0.044% 86.38% 214ms 0.63% std::__insertion_sort (inline) 0 0% 86.38% 210ms 0.62% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 86.38% 210ms 0.62% NodesOnlyMesh::ResizeBoxCollection 13ms 0.038% 86.42% 209ms 0.62% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 86.42% 209ms 0.62% VtkMeshWriter::WriteFiles 159ms 0.47% 86.89% 204ms 0.6% Node::AddAppliedForceContribution 0 0% 86.89% 204ms 0.6% NodesOnlyMesh::AddNodesToBoxes 201ms 0.59% 87.48% 201ms 0.59% NodeBasedCellPopulation::GetNode 94ms 0.28% 87.76% 196ms 0.58% std::__move_median_to_first (inline) 192ms 0.57% 88.33% 192ms 0.57% __strcmp_avx2 0 0% 88.33% 192ms 0.57% tcache_get (inline) 192ms 0.57% 88.89% 192ms 0.57% tcache_get_n (inline) 0 0% 88.89% 189ms 0.56% vtkStreamingDemandDrivenPipeline::Update 0 0% 88.89% 189ms 0.56% vtkXMLWriterBase::Write 0 0% 88.89% 188ms 0.56% Cell::HasCellProperty (inline) 0 0% 88.89% 188ms 0.56% CellPropertyCollection::HasProperty 0 0% 88.89% 188ms 0.56% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 88.89% 187ms 0.55% vtkDemandDrivenPipeline::ProcessRequest 0 0% 88.89% 186ms 0.55% vtkExecutive::CallAlgorithm 0 0% 88.89% 184ms 0.54% vtkCompositeDataPipeline::ExecuteData 0 0% 88.89% 184ms 0.54% vtkDemandDrivenPipeline::ExecuteData 0 0% 88.89% 184ms 0.54% vtkXMLUnstructuredDataWriter::ProcessRequest 3ms 0.0089% 88.90% 174ms 0.51% AbstractCellProperty::IsType (inline) 6ms 0.018% 88.92% 173ms 0.51% Cell::ReadyToDivide