File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 31584ms, 88.22% of 35800ms total Dropped 850 nodes (cum <= 179ms) flat flat% sum% cum cum% 0 0% 0% 35659ms 99.61% __libc_start_call_main 0 0% 0% 35659ms 99.61% __libc_start_main_impl 0 0% 0% 35659ms 99.61% _start 0 0% 0% 35639ms 99.55% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 35639ms 99.55% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 35639ms 99.55% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 35639ms 99.55% main 0 0% 0% 35599ms 99.44% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 35599ms 99.44% CxxTest::TestRunner::runTest (inline) 0 0% 0% 35599ms 99.44% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 35590ms 99.41% AbstractCellBasedSimulation::Solve 3ms 0.0084% 0.0084% 24959ms 69.72% OffLatticeSimulation::UpdateCellLocationsAndTopology 6ms 0.017% 0.025% 20017ms 55.91% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.028% 0.053% 19823ms 55.37% AbstractNumericalMethod::ComputeForcesIncludingDamping 229ms 0.64% 0.69% 18912ms 52.83% AbstractTwoBodyInteractionForce::AddForceContribution 1556ms 4.35% 5.04% 15639ms 43.68% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4416ms 12.34% 17.37% 9894ms 27.64% std::_Rb_tree::_M_lower_bound (inline) 0 0% 17.37% 9410ms 26.28% AbstractCellBasedSimulation::UpdateCellPopulation 349ms 0.97% 18.35% 9061ms 25.31% std::_Rb_tree::find (inline) 0 0% 18.35% 9059ms 25.30% std::map::find (inline) 213ms 0.59% 18.94% 8986ms 25.10% NodesOnlyMesh::GetNodeOrHaloNode 529ms 1.48% 20.42% 8765ms 24.48% AbstractMesh::GetNode 1ms 0.0028% 20.42% 8299ms 23.18% NodeBasedCellPopulation::Update 365ms 1.02% 21.44% 8239ms 23.01% NodesOnlyMesh::SolveNodeMapping 175ms 0.49% 21.93% 6367ms 17.78% boost::numeric::ublas::vector_assign (inline) 10ms 0.028% 21.96% 6179ms 17.26% DistributedBoxCollection::CalculateInteriorNodePairs 152ms 0.42% 22.39% 6081ms 16.99% boost::numeric::ublas::c_vector::c_vector (partial-inline) 5456ms 15.24% 37.63% 5456ms 15.24% std::_Rb_tree::_S_right (inline) 9ms 0.025% 37.65% 4611ms 12.88% NodeAttributes::RemoveDuplicateNeighbours 0 0% 37.65% 4606ms 12.87% OffLatticeSimulation::ApplyBoundaries 3ms 0.0084% 37.66% 4434ms 12.39% std::__sort (inline) 0 0% 37.66% 4434ms 12.39% std::sort (inline) 1007ms 2.81% 40.47% 3506ms 9.79% boost::numeric::ublas::indexing_vector_assign 79ms 0.22% 40.69% 3331ms 9.30% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 3ms 0.0084% 40.70% 3220ms 8.99% AbstractCellPopulation::Iterator::operator++ (inline) 162ms 0.45% 41.15% 3190ms 8.91% AbstractCellPopulation::Iterator::IsRealCell (inline) 29ms 0.081% 41.23% 2773ms 7.75% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 180ms 0.5% 41.74% 2570ms 7.18% std::__introsort_loop 16ms 0.045% 41.78% 2462ms 6.88% PlaneBoundaryCondition::ImposeBoundaryCondition 0 0% 41.78% 2299ms 6.42% std::__unguarded_partition_pivot (inline) 49ms 0.14% 41.92% 2237ms 6.25% AbstractCellPopulation::GetLocationIndexUsingCell 153ms 0.43% 42.35% 2166ms 6.05% DistributedBoxCollection::AddPairsFromBox 15ms 0.042% 42.39% 2144ms 5.99% PlaneBoundaryCondition::VerifyBoundaryCondition 2097ms 5.86% 48.25% 2097ms 5.86% boost::numeric::ublas::same_impl_ex 1054ms 2.94% 51.19% 2068ms 5.78% std::__unguarded_partition (inline) 1ms 0.0028% 51.19% 1855ms 5.18% std::__final_insertion_sort (inline) 0 0% 51.19% 1733ms 4.84% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 152ms 0.42% 51.62% 1720ms 4.80% std::map::operator[] (partial-inline) 0 0% 51.62% 1718ms 4.80% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 132ms 0.37% 51.99% 1664ms 4.65% std::__unguarded_insertion_sort (inline) 0 0% 51.99% 1583ms 4.42% boost::numeric::ublas::detail::expression_type_check (inline) 627ms 1.75% 53.74% 1575ms 4.40% std::__unguarded_linear_insert (inline) 256ms 0.72% 54.45% 1500ms 4.19% boost::numeric::ublas::detail::equals 170ms 0.47% 54.93% 1441ms 4.03% AbstractMesh::GetVectorFromAtoB 1366ms 3.82% 58.74% 1366ms 3.82% __gnu_cxx::__normal_iterator::operator-- (inline) 225ms 0.63% 59.37% 1342ms 3.75% boost::numeric::ublas::vector_binary::size (inline) 0 0% 59.37% 1310ms 3.66% std::_Rb_tree::lower_bound (inline) 0 0% 59.37% 1310ms 3.66% std::map::lower_bound (inline) 1243ms 3.47% 62.84% 1243ms 3.47% boost::numeric::ublas::c_vector::operator() 0 0% 62.84% 1184ms 3.31% boost::numeric::ublas::norm_inf (inline) 486ms 1.36% 64.20% 1184ms 3.31% boost::numeric::ublas::vector_norm_inf::apply (inline) 1ms 0.0028% 64.20% 1162ms 3.25% NodeBasedCellPopulation::UpdateCellProcessLocation 5ms 0.014% 64.22% 1101ms 3.08% DistributedBoxCollection::CalculateBoundaryNodePairs 172ms 0.48% 64.70% 992ms 2.77% NodeAttributes::AddAppliedForceContribution 27ms 0.075% 64.77% 947ms 2.65% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 423ms 1.18% 65.96% 876ms 2.45% DistributedBoxCollection::CalculateContainingBox (partial-inline) 3ms 0.0084% 65.96% 841ms 2.35% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 65.96% 820ms 2.29% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 65.96% 820ms 2.29% boost::numeric::ublas::c_vector::plus_assign (inline) 89ms 0.25% 66.21% 816ms 2.28% std::__new_allocator::allocate (inline) 235ms 0.66% 66.87% 810ms 2.26% NodeAttributes::AddNeighbour 25ms 0.07% 66.94% 780ms 2.18% std::_Rb_tree_const_iterator::operator++ (inline) 556ms 1.55% 68.49% 773ms 2.16% __dynamic_cast 0 0% 68.49% 765ms 2.14% AbstractCellPopulation::WriteResultsToFiles 737ms 2.06% 70.55% 737ms 2.06% std::_Rb_tree_increment 78ms 0.22% 70.77% 732ms 2.04% operator new 574ms 1.60% 72.37% 661ms 1.85% std::vector::push_back (inline) 206ms 0.58% 72.95% 650ms 1.82% __GI___libc_malloc 9ms 0.025% 72.97% 627ms 1.75% CellPropertyCollection::GetPropertiesType (inline) 4ms 0.011% 72.98% 603ms 1.68% AbstractCellBasedSimulation::DoCellBirth 169ms 0.47% 73.46% 583ms 1.63% __GI___libc_free 2ms 0.0056% 73.46% 556ms 1.55% Cell::GetMutationState 0 0% 73.46% 549ms 1.53% boost::numeric::ublas::norm_2 (inline) 427ms 1.19% 74.65% 549ms 1.53% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 74.65% 507ms 1.42% AbstractCellBasedSimulation::DoCellRemoval (inline) 1ms 0.0028% 74.66% 505ms 1.41% NodeBasedCellPopulation::WriteVtkResultsToFile 5ms 0.014% 74.67% 491ms 1.37% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 485ms 1.35% 76.03% 485ms 1.35% Node::GetIndex 32ms 0.089% 76.11% 439ms 1.23% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 76.11% 439ms 1.23% boost::numeric::ublas::vector::vector (inline) 35ms 0.098% 76.21% 418ms 1.17% boost::detail::shared_count::~shared_count (inline) 0 0% 76.21% 418ms 1.17% boost::shared_ptr::~shared_ptr (inline) 381ms 1.06% 77.28% 414ms 1.16% _int_free 0 0% 77.28% 409ms 1.14% std::allocator_traits::allocate (inline) 0 0% 77.28% 379ms 1.06% boost::numeric::ublas::inner_prod (inline) 371ms 1.04% 78.31% 378ms 1.06% boost::detail::sp_counted_base::release 1ms 0.0028% 78.32% 376ms 1.05% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 14ms 0.039% 78.35% 375ms 1.05% boost::numeric::ublas::vector_scalar_binary::evaluate 319ms 0.89% 79.25% 374ms 1.04% Node::AddAppliedForceContribution 2ms 0.0056% 79.25% 373ms 1.04% AbstractCellProperty::IsSubType (inline) 5ms 0.014% 79.27% 372ms 1.04% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 0 0% 79.27% 366ms 1.02% std::_Rb_tree::_M_create_node (inline) 4ms 0.011% 79.28% 365ms 1.02% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 79.28% 337ms 0.94% NodesOnlyMesh::ReMesh 0 0% 79.28% 325ms 0.91% std::_Rb_tree::_M_get_node (inline) 3ms 0.0084% 79.28% 322ms 0.9% NodesOnlyMesh::UpdateNodeIndices 315ms 0.88% 80.16% 315ms 0.88% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 7ms 0.02% 80.18% 313ms 0.87% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 99ms 0.28% 80.46% 312ms 0.87% std::_Rb_tree::_M_erase (partial-inline) 5ms 0.014% 80.47% 309ms 0.86% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 80.47% 304ms 0.85% NodesOnlyMesh::UpdateBoxCollection 9ms 0.025% 80.50% 301ms 0.84% DistributedBoxCollection::GetProcessOwningNode 120ms 0.34% 80.84% 296ms 0.83% boost::numeric::ublas::vector_inner_prod::apply (inline) 89ms 0.25% 81.08% 293ms 0.82% Node::GetRadius 291ms 0.81% 81.90% 291ms 0.81% __gnu_cxx::__normal_iterator::operator++ (inline) 269ms 0.75% 82.65% 269ms 0.75% [libchaste_cell_based.so] 0 0% 82.65% 266ms 0.74% boost::numeric::ublas::c_vector::assign (inline) 0 0% 82.65% 262ms 0.73% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 1ms 0.0028% 82.65% 259ms 0.72% NodesOnlyMesh::AddNodesToBoxes 0 0% 82.65% 258ms 0.72% VtkMeshWriter::WriteFiles 258ms 0.72% 83.37% 258ms 0.72% [libchaste_mesh.so] 12ms 0.034% 83.41% 256ms 0.72% std::_Rb_tree::_M_emplace_hint_unique 122ms 0.34% 83.75% 248ms 0.69% _int_malloc 10ms 0.028% 83.77% 244ms 0.68% boost::numeric::ublas::vector_reference::operator() (inline) 206ms 0.58% 84.35% 234ms 0.65% Node::AddNeighbour 1ms 0.0028% 84.35% 231ms 0.65% CellPropertyCollection::HasProperty 0 0% 84.35% 229ms 0.64% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 84.35% 228ms 0.64% Cell::HasCellProperty (inline) 0 0% 84.35% 227ms 0.63% vtkStreamingDemandDrivenPipeline::Update 0 0% 84.35% 227ms 0.63% vtkXMLWriterBase::Write 0 0% 84.35% 225ms 0.63% vtkDemandDrivenPipeline::ProcessRequest 104ms 0.29% 84.64% 224ms 0.63% std::__move_median_to_first (inline) 0 0% 84.64% 224ms 0.63% vtkExecutive::CallAlgorithm 223ms 0.62% 85.27% 223ms 0.62% Node::CheckForNodeAttributes 3ms 0.0084% 85.27% 223ms 0.62% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 85.27% 223ms 0.62% vtkCompositeDataPipeline::ExecuteData 0 0% 85.27% 223ms 0.62% vtkDemandDrivenPipeline::ExecuteData 0 0% 85.27% 223ms 0.62% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 85.27% 222ms 0.62% vtkXMLUnstructuredDataWriter::ProcessRequest 16ms 0.045% 85.32% 216ms 0.6% std::_Rb_tree::_M_copy (inline) 7ms 0.02% 85.34% 214ms 0.6% Cell::ReadyToDivide 211ms 0.59% 85.93% 211ms 0.59% NodeBasedCellPopulation::GetNode 0 0% 85.93% 209ms 0.58% std::_Rb_tree::_M_drop_node (inline) 0 0% 85.93% 208ms 0.58% boost::numeric::ublas::vector_binary::operator() (inline) 92ms 0.26% 86.18% 208ms 0.58% std::__find_if (inline) 0 0% 86.18% 208ms 0.58% std::find_if (inline) 0 0% 86.18% 208ms 0.58% std::none_of (inline) 205ms 0.57% 86.76% 205ms 0.57% __strcmp_avx2 27ms 0.075% 86.83% 200ms 0.56% std::_Rb_tree::_M_clone_node (inline) 9ms 0.025% 86.86% 197ms 0.55% std::__new_allocator::deallocate (inline) 19ms 0.053% 86.91% 190ms 0.53% std::__insertion_sort (inline) 0 0% 86.91% 188ms 0.53% boost::numeric::ublas::scalar_traits::norm_inf (inline) 0 0% 86.91% 188ms 0.53% boost::numeric::ublas::scalar_traits::type_abs (inline) 0 0% 86.91% 187ms 0.52% boost_numeric_ublas_abs (inline) 187ms 0.52% 87.43% 187ms 0.52% std::abs (inline) 0 0% 87.43% 182ms 0.51% std::allocator_traits::deallocate (inline) 9ms 0.025% 87.46% 181ms 0.51% std::_Rb_tree::~_Rb_tree (inline) 0 0% 87.46% 181ms 0.51% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 87.46% 181ms 0.51% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 95ms 0.27% 87.72% 180ms 0.5% boost::shared_ptr::shared_ptr (inline) 179ms 0.5% 88.22% 179ms 0.5% Node::rGetLocation