File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 30247ms, 87.68% of 34496ms total Dropped 808 nodes (cum <= 172.48ms) flat flat% sum% cum cum% 0 0% 0% 34384ms 99.68% __libc_start_call_main 0 0% 0% 34384ms 99.68% __libc_start_main_impl 0 0% 0% 34384ms 99.68% _start 0 0% 0% 34365ms 99.62% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 34365ms 99.62% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 34365ms 99.62% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 34365ms 99.62% main 0 0% 0% 34328ms 99.51% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 34328ms 99.51% CxxTest::TestRunner::runTest (inline) 0 0% 0% 34328ms 99.51% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 34319ms 99.49% AbstractCellBasedSimulation::Solve 3ms 0.0087% 0.0087% 23861ms 69.17% OffLatticeSimulation::UpdateCellLocationsAndTopology 3ms 0.0087% 0.017% 18781ms 54.44% ForwardEulerNumericalMethod::UpdateAllNodePositions 11ms 0.032% 0.049% 18594ms 53.90% AbstractNumericalMethod::ComputeForcesIncludingDamping 177ms 0.51% 0.56% 17808ms 51.62% AbstractTwoBodyInteractionForce::AddForceContribution 1567ms 4.54% 5.10% 15058ms 43.65% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4509ms 13.07% 18.18% 9936ms 28.80% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.0029% 18.18% 9239ms 26.78% AbstractCellBasedSimulation::UpdateCellPopulation 325ms 0.94% 19.12% 9053ms 26.24% std::_Rb_tree::find (inline) 0 0% 19.12% 9052ms 26.24% std::map::find (inline) 223ms 0.65% 19.77% 8906ms 25.82% NodesOnlyMesh::GetNodeOrHaloNode 491ms 1.42% 21.19% 8687ms 25.18% AbstractMesh::GetNode 358ms 1.04% 22.23% 8198ms 23.77% NodesOnlyMesh::SolveNodeMapping 0 0% 22.23% 8141ms 23.60% NodeBasedCellPopulation::Update 12ms 0.035% 22.26% 6065ms 17.58% DistributedBoxCollection::CalculateInteriorNodePairs 212ms 0.61% 22.88% 5689ms 16.49% boost::numeric::ublas::vector_assign (inline) 158ms 0.46% 23.34% 5524ms 16.01% boost::numeric::ublas::c_vector::c_vector (partial-inline) 5366ms 15.56% 38.89% 5366ms 15.56% std::_Rb_tree::_S_right (inline) 0 0% 38.89% 4733ms 13.72% OffLatticeSimulation::ApplyBoundaries 10ms 0.029% 38.92% 4604ms 13.35% NodeAttributes::RemoveDuplicateNeighbours 4ms 0.012% 38.93% 4412ms 12.79% std::__sort (inline) 0 0% 38.93% 4412ms 12.79% std::sort (inline) 79ms 0.23% 39.16% 3449ms 10.00% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 1007ms 2.92% 42.08% 3309ms 9.59% boost::numeric::ublas::indexing_vector_assign 4ms 0.012% 42.09% 3215ms 9.32% AbstractCellPopulation::Iterator::operator++ (inline) 155ms 0.45% 42.54% 3182ms 9.22% AbstractCellPopulation::Iterator::IsRealCell (inline) 23ms 0.067% 42.61% 2799ms 8.11% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 174ms 0.5% 43.11% 2539ms 7.36% std::__introsort_loop 17ms 0.049% 43.16% 2496ms 7.24% PlaneBoundaryCondition::ImposeBoundaryCondition 56ms 0.16% 43.32% 2406ms 6.97% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 43.32% 2280ms 6.61% std::__unguarded_partition_pivot (inline) 10ms 0.029% 43.35% 2236ms 6.48% PlaneBoundaryCondition::VerifyBoundaryCondition 141ms 0.41% 43.76% 2049ms 5.94% DistributedBoxCollection::AddPairsFromBox 995ms 2.88% 46.65% 2026ms 5.87% std::__unguarded_partition (inline) 1ms 0.0029% 46.65% 1866ms 5.41% std::__final_insertion_sort (inline) 205ms 0.59% 47.24% 1817ms 5.27% std::map::operator[] (partial-inline) 106ms 0.31% 47.55% 1666ms 4.83% std::__unguarded_insertion_sort (inline) 598ms 1.73% 49.28% 1603ms 4.65% std::__unguarded_linear_insert (inline) 1563ms 4.53% 53.81% 1563ms 4.53% boost::numeric::ublas::same_impl_ex 155ms 0.45% 54.26% 1474ms 4.27% AbstractMesh::GetVectorFromAtoB 1388ms 4.02% 58.29% 1388ms 4.02% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 58.29% 1359ms 3.94% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 58.29% 1351ms 3.92% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 58.29% 1314ms 3.81% std::_Rb_tree::lower_bound (inline) 0 0% 58.29% 1314ms 3.81% std::map::lower_bound (inline) 1163ms 3.37% 61.66% 1163ms 3.37% boost::numeric::ublas::c_vector::operator() 1ms 0.0029% 61.66% 1144ms 3.32% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 61.66% 1136ms 3.29% NodeBasedCellPopulation::UpdateCellProcessLocation 3ms 0.0087% 61.67% 1119ms 3.24% DistributedBoxCollection::CalculateBoundaryNodePairs 234ms 0.68% 62.35% 1089ms 3.16% boost::numeric::ublas::detail::equals 19ms 0.055% 62.40% 980ms 2.84% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 177ms 0.51% 62.92% 945ms 2.74% boost::numeric::ublas::vector_binary::size (inline) 219ms 0.63% 63.55% 912ms 2.64% NodeAttributes::AddAppliedForceContribution 432ms 1.25% 64.80% 879ms 2.55% DistributedBoxCollection::CalculateContainingBox (partial-inline) 229ms 0.66% 65.47% 837ms 2.43% NodeAttributes::AddNeighbour 0 0% 65.47% 781ms 2.26% boost::numeric::ublas::norm_inf (inline) 473ms 1.37% 66.84% 781ms 2.26% boost::numeric::ublas::vector_norm_inf::apply (inline) 536ms 1.55% 68.39% 745ms 2.16% __dynamic_cast 0 0% 68.39% 741ms 2.15% AbstractCellPopulation::WriteResultsToFiles 103ms 0.3% 68.69% 741ms 2.15% std::__new_allocator::allocate (inline) 2ms 0.0058% 68.70% 719ms 2.08% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 68.70% 693ms 2.01% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 68.70% 693ms 2.01% boost::numeric::ublas::c_vector::plus_assign (inline) 606ms 1.76% 70.45% 692ms 2.01% std::vector::push_back (inline) 31ms 0.09% 70.54% 655ms 1.90% std::_Rb_tree_const_iterator::operator++ (inline) 3ms 0.0087% 70.55% 648ms 1.88% AbstractCellBasedSimulation::DoCellBirth 91ms 0.26% 70.82% 636ms 1.84% operator new 616ms 1.79% 72.60% 616ms 1.79% std::_Rb_tree_increment 0 0% 72.60% 578ms 1.68% boost::numeric::ublas::norm_2 (inline) 456ms 1.32% 73.92% 578ms 1.68% boost::numeric::ublas::vector_norm_2::apply (inline) 199ms 0.58% 74.50% 538ms 1.56% __GI___libc_malloc 6ms 0.017% 74.52% 530ms 1.54% CellPropertyCollection::GetPropertiesType (inline) 172ms 0.5% 75.02% 516ms 1.50% __GI___libc_free 2ms 0.0058% 75.02% 489ms 1.42% NodeBasedCellPopulation::WriteVtkResultsToFile 3ms 0.0087% 75.03% 468ms 1.36% Cell::GetMutationState 0 0% 75.03% 449ms 1.30% AbstractCellBasedSimulation::DoCellRemoval (inline) 9ms 0.026% 75.06% 442ms 1.28% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 75.06% 427ms 1.24% std::allocator_traits::allocate (inline) 33ms 0.096% 75.15% 423ms 1.23% boost::detail::shared_count::~shared_count (inline) 0 0% 75.15% 423ms 1.23% boost::shared_ptr::~shared_ptr (inline) 410ms 1.19% 76.34% 410ms 1.19% Node::GetIndex 377ms 1.09% 77.44% 388ms 1.12% boost::detail::sp_counted_base::release 0 0% 77.44% 378ms 1.10% std::_Rb_tree::_M_create_node (inline) 356ms 1.03% 78.47% 356ms 1.03% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 78.47% 351ms 1.02% boost::numeric::ublas::inner_prod (inline) 19ms 0.055% 78.52% 349ms 1.01% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 78.52% 349ms 1.01% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 3ms 0.0087% 78.53% 346ms 1.00% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 30ms 0.087% 78.62% 344ms 1% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 78.62% 344ms 1% boost::numeric::ublas::vector::vector (inline) 294ms 0.85% 79.47% 343ms 0.99% _int_free 10ms 0.029% 79.50% 342ms 0.99% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 79.50% 337ms 0.98% std::_Rb_tree::_M_get_node (inline) 1ms 0.0029% 79.50% 336ms 0.97% AbstractCellProperty::IsSubType (inline) 71ms 0.21% 79.71% 316ms 0.92% Node::GetRadius 315ms 0.91% 80.62% 315ms 0.91% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 80.62% 312ms 0.9% NodesOnlyMesh::ReMesh 108ms 0.31% 80.93% 312ms 0.9% std::_Rb_tree::_M_erase (partial-inline) 9ms 0.026% 80.96% 310ms 0.9% NodeBasedCellPopulation::UpdateMapsAfterRemesh 8ms 0.023% 80.98% 306ms 0.89% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 1ms 0.0029% 80.99% 303ms 0.88% NodesOnlyMesh::UpdateNodeIndices 9ms 0.026% 81.01% 298ms 0.86% std::_Rb_tree::_M_emplace_hint_unique 0 0% 81.01% 292ms 0.85% NodesOnlyMesh::UpdateBoxCollection 9ms 0.026% 81.04% 287ms 0.83% DistributedBoxCollection::GetProcessOwningNode 1ms 0.0029% 81.04% 267ms 0.77% CellPropertyCollection::HasProperty 0 0% 81.04% 265ms 0.77% Cell::HasCellProperty (inline) 8ms 0.023% 81.06% 265ms 0.77% boost::numeric::ublas::vector_reference::operator() (inline) 116ms 0.34% 81.40% 262ms 0.76% boost::numeric::ublas::vector_inner_prod::apply (inline) 260ms 0.75% 82.15% 260ms 0.75% Node::CheckForNodeAttributes 259ms 0.75% 82.91% 259ms 0.75% [libchaste_mesh.so] 0 0% 82.91% 259ms 0.75% boost::numeric::ublas::c_vector::assign (inline) 255ms 0.74% 83.64% 255ms 0.74% [libchaste_cell_based.so] 111ms 0.32% 83.97% 251ms 0.73% std::__move_median_to_first (inline) 129ms 0.37% 84.34% 249ms 0.72% _int_malloc 8ms 0.023% 84.36% 245ms 0.71% Cell::ReadyToDivide 0 0% 84.36% 243ms 0.7% boost::numeric::ublas::vector_binary::operator() (inline) 15ms 0.043% 84.41% 240ms 0.7% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 84.41% 237ms 0.69% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 84.41% 237ms 0.69% VtkMeshWriter::WriteFiles 2ms 0.0058% 84.41% 233ms 0.68% NodesOnlyMesh::AddNodesToBoxes 198ms 0.57% 84.99% 231ms 0.67% Node::AddNeighbour 0 0% 84.99% 226ms 0.66% std::_Rb_tree::_Alloc_node::operator() (inline) 17ms 0.049% 85.04% 221ms 0.64% std::_Rb_tree::_M_copy (inline) 220ms 0.64% 85.67% 220ms 0.64% NodeBasedCellPopulation::GetNode 4ms 0.012% 85.69% 217ms 0.63% AbstractCellProperty::IsType (inline) 215ms 0.62% 86.31% 215ms 0.62% __strcmp_avx2 0 0% 86.31% 213ms 0.62% vtkDemandDrivenPipeline::ProcessRequest 0 0% 86.31% 213ms 0.62% vtkStreamingDemandDrivenPipeline::Update 0 0% 86.31% 213ms 0.62% vtkXMLWriterBase::Write 0 0% 86.31% 212ms 0.61% vtkCompositeDataPipeline::ExecuteData 0 0% 86.31% 212ms 0.61% vtkDemandDrivenPipeline::ExecuteData 0 0% 86.31% 212ms 0.61% vtkExecutive::CallAlgorithm 0 0% 86.31% 212ms 0.61% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 86.31% 212ms 0.61% vtkXMLUnstructuredDataWriter::ProcessRequest 26ms 0.075% 86.38% 204ms 0.59% std::_Rb_tree::_M_clone_node (inline) 24ms 0.07% 86.45% 199ms 0.58% std::__insertion_sort (inline) 61ms 0.18% 86.63% 196ms 0.57% std::__find_if (inline) 0 0% 86.63% 196ms 0.57% std::find_if (inline) 0 0% 86.63% 196ms 0.57% std::none_of (inline) 0 0% 86.63% 191ms 0.55% std::_Rb_tree::_M_drop_node (inline) 10ms 0.029% 86.66% 181ms 0.52% std::__new_allocator::deallocate (inline) 180ms 0.52% 87.18% 180ms 0.52% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 0 0% 87.18% 178ms 0.52% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 87.18% 178ms 0.52% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 173ms 0.5% 87.68% 173ms 0.5% Node::rGetLocation