File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 29953ms, 87.02% of 34421ms total Dropped 836 nodes (cum <= 172.10ms) flat flat% sum% cum cum% 0 0% 0% 34306ms 99.67% __libc_start_call_main 0 0% 0% 34306ms 99.67% __libc_start_main_impl 0 0% 0% 34306ms 99.67% _start 0 0% 0% 34287ms 99.61% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 34287ms 99.61% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 34287ms 99.61% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 34287ms 99.61% main 0 0% 0% 34249ms 99.50% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 34249ms 99.50% CxxTest::TestRunner::runTest (inline) 0 0% 0% 34249ms 99.50% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 2ms 0.0058% 0.0058% 34241ms 99.48% AbstractCellBasedSimulation::Solve 2ms 0.0058% 0.012% 23746ms 68.99% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0029% 0.015% 18705ms 54.34% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.023% 0.038% 18520ms 53.80% AbstractNumericalMethod::ComputeForcesIncludingDamping 167ms 0.49% 0.52% 17723ms 51.49% AbstractTwoBodyInteractionForce::AddForceContribution 1510ms 4.39% 4.91% 15044ms 43.71% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4523ms 13.14% 18.05% 9761ms 28.36% std::_Rb_tree::_M_lower_bound (inline) 0 0% 18.05% 9264ms 26.91% AbstractCellBasedSimulation::UpdateCellPopulation 369ms 1.07% 19.12% 8944ms 25.98% std::_Rb_tree::find (inline) 0 0% 19.12% 8944ms 25.98% std::map::find (inline) 195ms 0.57% 19.69% 8768ms 25.47% NodesOnlyMesh::GetNodeOrHaloNode 480ms 1.39% 21.08% 8597ms 24.98% AbstractMesh::GetNode 1ms 0.0029% 21.09% 8181ms 23.77% NodeBasedCellPopulation::Update 345ms 1.00% 22.09% 8123ms 23.60% NodesOnlyMesh::SolveNodeMapping 6ms 0.017% 22.11% 6089ms 17.69% DistributedBoxCollection::CalculateInteriorNodePairs 212ms 0.62% 22.72% 5869ms 17.05% boost::numeric::ublas::vector_assign (inline) 169ms 0.49% 23.21% 5749ms 16.70% boost::numeric::ublas::c_vector::c_vector (partial-inline) 5219ms 15.16% 38.37% 5219ms 15.16% std::_Rb_tree::_S_right (inline) 0 0% 38.37% 4712ms 13.69% OffLatticeSimulation::ApplyBoundaries 14ms 0.041% 38.42% 4617ms 13.41% NodeAttributes::RemoveDuplicateNeighbours 4ms 0.012% 38.43% 4436ms 12.89% std::__sort (inline) 0 0% 38.43% 4436ms 12.89% std::sort (inline) 1037ms 3.01% 41.44% 3449ms 10.02% boost::numeric::ublas::indexing_vector_assign 71ms 0.21% 41.65% 3353ms 9.74% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 4ms 0.012% 41.66% 3120ms 9.06% AbstractCellPopulation::Iterator::operator++ (inline) 178ms 0.52% 42.17% 3087ms 8.97% AbstractCellPopulation::Iterator::IsRealCell (inline) 16ms 0.046% 42.22% 2704ms 7.86% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 193ms 0.56% 42.78% 2567ms 7.46% std::__introsort_loop 30ms 0.087% 42.87% 2470ms 7.18% PlaneBoundaryCondition::ImposeBoundaryCondition 56ms 0.16% 43.03% 2312ms 6.72% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 43.03% 2310ms 6.71% std::__unguarded_partition_pivot (inline) 9ms 0.026% 43.06% 2242ms 6.51% PlaneBoundaryCondition::VerifyBoundaryCondition 157ms 0.46% 43.51% 2084ms 6.05% DistributedBoxCollection::AddPairsFromBox 998ms 2.90% 46.41% 2054ms 5.97% std::__unguarded_partition (inline) 2ms 0.0058% 46.42% 1862ms 5.41% std::__final_insertion_sort (inline) 190ms 0.55% 46.97% 1752ms 5.09% std::map::operator[] (partial-inline) 1672ms 4.86% 51.83% 1672ms 4.86% boost::numeric::ublas::same_impl_ex 111ms 0.32% 52.15% 1625ms 4.72% std::__unguarded_insertion_sort (inline) 632ms 1.84% 53.99% 1561ms 4.54% std::__unguarded_linear_insert (inline) 174ms 0.51% 54.49% 1546ms 4.49% AbstractMesh::GetVectorFromAtoB 0 0% 54.49% 1494ms 4.34% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 54.49% 1481ms 4.30% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1404ms 4.08% 58.57% 1404ms 4.08% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 58.57% 1292ms 3.75% std::_Rb_tree::lower_bound (inline) 0 0% 58.57% 1292ms 3.75% std::map::lower_bound (inline) 3ms 0.0087% 58.58% 1227ms 3.56% boost::numeric::ublas::detail::expression_type_check (inline) 1214ms 3.53% 62.11% 1214ms 3.53% boost::numeric::ublas::c_vector::operator() 257ms 0.75% 62.85% 1183ms 3.44% boost::numeric::ublas::detail::equals 0 0% 62.85% 1182ms 3.43% NodeBasedCellPopulation::UpdateCellProcessLocation 7ms 0.02% 62.87% 1100ms 3.20% DistributedBoxCollection::CalculateBoundaryNodePairs 20ms 0.058% 62.93% 997ms 2.90% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 145ms 0.42% 63.35% 922ms 2.68% boost::numeric::ublas::vector_binary::size (inline) 408ms 1.19% 64.54% 896ms 2.60% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 64.54% 864ms 2.51% boost::numeric::ublas::norm_inf (inline) 581ms 1.69% 66.23% 864ms 2.51% boost::numeric::ublas::vector_norm_inf::apply (inline) 206ms 0.6% 66.83% 857ms 2.49% NodeAttributes::AddAppliedForceContribution 558ms 1.62% 68.45% 759ms 2.21% __dynamic_cast 0 0% 68.45% 742ms 2.16% AbstractCellPopulation::WriteResultsToFiles 153ms 0.44% 68.89% 735ms 2.14% NodeAttributes::AddNeighbour 5ms 0.015% 68.91% 727ms 2.11% AbstractCentreBasedCellPopulation::GetDampingConstant 83ms 0.24% 69.15% 727ms 2.11% std::__new_allocator::allocate (inline) 580ms 1.69% 70.83% 665ms 1.93% std::vector::push_back (inline) 26ms 0.076% 70.91% 654ms 1.90% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 70.91% 651ms 1.89% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 70.91% 651ms 1.89% boost::numeric::ublas::c_vector::plus_assign (inline) 69ms 0.2% 71.11% 646ms 1.88% operator new 0 0% 71.11% 630ms 1.83% boost::numeric::ublas::norm_2 (inline) 498ms 1.45% 72.55% 630ms 1.83% boost::numeric::ublas::vector_norm_2::apply (inline) 607ms 1.76% 74.32% 607ms 1.76% std::_Rb_tree_increment 5ms 0.015% 74.33% 596ms 1.73% AbstractCellBasedSimulation::DoCellBirth 20ms 0.058% 74.39% 567ms 1.65% CellPropertyCollection::GetPropertiesType (inline) 199ms 0.58% 74.97% 567ms 1.65% __GI___libc_malloc 1ms 0.0029% 74.97% 493ms 1.43% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 74.97% 487ms 1.41% AbstractCellBasedSimulation::DoCellRemoval (inline) 5ms 0.015% 74.99% 475ms 1.38% Cell::GetMutationState 4ms 0.012% 75.00% 473ms 1.37% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 128ms 0.37% 75.37% 469ms 1.36% __GI___libc_free 43ms 0.12% 75.49% 444ms 1.29% boost::detail::shared_count::~shared_count (inline) 0 0% 75.49% 444ms 1.29% boost::shared_ptr::~shared_ptr (inline) 0 0% 75.49% 412ms 1.20% std::allocator_traits::allocate (inline) 407ms 1.18% 76.68% 407ms 1.18% Node::GetIndex 0 0% 76.68% 399ms 1.16% boost::numeric::ublas::inner_prod (inline) 389ms 1.13% 77.81% 397ms 1.15% boost::detail::sp_counted_base::release 2ms 0.0058% 77.81% 393ms 1.14% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 8ms 0.023% 77.84% 391ms 1.14% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 77.84% 369ms 1.07% std::_Rb_tree::_M_create_node (inline) 2ms 0.0058% 77.84% 358ms 1.04% AbstractCellProperty::IsSubType (inline) 38ms 0.11% 77.95% 353ms 1.03% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 77.95% 353ms 1.03% boost::numeric::ublas::vector::vector (inline) 351ms 1.02% 78.97% 351ms 1.02% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 5ms 0.015% 78.99% 344ms 1% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 6ms 0.017% 79.00% 341ms 0.99% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 296ms 0.86% 79.86% 340ms 0.99% _int_free 7ms 0.02% 79.88% 337ms 0.98% AbstractCellPopulation::GetCellUsingLocationIndex 148ms 0.43% 80.31% 335ms 0.97% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 80.31% 325ms 0.94% std::_Rb_tree::_M_get_node (inline) 0 0% 80.31% 324ms 0.94% NodesOnlyMesh::ReMesh 323ms 0.94% 81.25% 323ms 0.94% __gnu_cxx::__normal_iterator::operator++ (inline) 10ms 0.029% 81.28% 320ms 0.93% DistributedBoxCollection::GetProcessOwningNode 13ms 0.038% 81.32% 314ms 0.91% boost::numeric::ublas::vector_reference::operator() (inline) 2ms 0.0058% 81.33% 311ms 0.9% NodesOnlyMesh::UpdateNodeIndices 115ms 0.33% 81.66% 308ms 0.89% std::_Rb_tree::_M_erase (partial-inline) 6ms 0.017% 81.68% 306ms 0.89% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 81.68% 295ms 0.86% boost::numeric::ublas::vector_binary::operator() (inline) 294ms 0.85% 82.53% 294ms 0.85% [libchaste_mesh.so] 0 0% 82.53% 287ms 0.83% NodesOnlyMesh::UpdateBoxCollection 0 0% 82.53% 283ms 0.82% boost::numeric::ublas::c_vector::assign (inline) 59ms 0.17% 82.70% 272ms 0.79% Node::GetRadius 19ms 0.055% 82.76% 270ms 0.78% std::_Rb_tree::_M_emplace_hint_unique 169ms 0.49% 83.25% 262ms 0.76% Node::AddNeighbour 252ms 0.73% 83.98% 252ms 0.73% [libchaste_cell_based.so] 115ms 0.33% 84.31% 251ms 0.73% std::__move_median_to_first (inline) 0 0% 84.31% 245ms 0.71% Cell::HasCellProperty (inline) 2ms 0.0058% 84.32% 245ms 0.71% CellPropertyCollection::HasProperty 0 0% 84.32% 244ms 0.71% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 84.32% 243ms 0.71% VtkMeshWriter::WriteFiles 122ms 0.35% 84.68% 240ms 0.7% _int_malloc 2ms 0.0058% 84.68% 235ms 0.68% std::_Rb_tree::_Rb_tree (partial-inline) 25ms 0.073% 84.75% 235ms 0.68% std::__insertion_sort (inline) 5ms 0.015% 84.77% 233ms 0.68% Cell::ReadyToDivide 21ms 0.061% 84.83% 232ms 0.67% std::_Rb_tree::_M_copy (inline) 231ms 0.67% 85.50% 231ms 0.67% Node::CheckForNodeAttributes 0 0% 85.50% 230ms 0.67% NodesOnlyMesh::AddNodesToBoxes 230ms 0.67% 86.17% 230ms 0.67% __strcmp_avx2 0 0% 86.17% 215ms 0.62% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 86.17% 212ms 0.62% vtkStreamingDemandDrivenPipeline::Update 0 0% 86.17% 212ms 0.62% vtkXMLWriterBase::Write 0 0% 86.17% 210ms 0.61% AbstractCellProperty::IsType (inline) 30ms 0.087% 86.26% 210ms 0.61% std::_Rb_tree::_M_clone_node (inline) 0 0% 86.26% 209ms 0.61% vtkDemandDrivenPipeline::ProcessRequest 0 0% 86.26% 209ms 0.61% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 86.26% 207ms 0.6% vtkExecutive::CallAlgorithm 0 0% 86.26% 206ms 0.6% vtkCompositeDataPipeline::ExecuteData 0 0% 86.26% 206ms 0.6% vtkDemandDrivenPipeline::ExecuteData 0 0% 86.26% 206ms 0.6% vtkXMLUnstructuredDataWriter::ProcessRequest 198ms 0.58% 86.83% 198ms 0.58% NodeBasedCellPopulation::GetNode 0 0% 86.83% 183ms 0.53% std::_Rb_tree::_M_drop_node (inline) 3ms 0.0087% 86.84% 179ms 0.52% std::__new_allocator::deallocate (inline) 62ms 0.18% 87.02% 178ms 0.52% std::__find_if (inline) 0 0% 87.02% 178ms 0.52% std::find_if (inline) 0 0% 87.02% 178ms 0.52% std::none_of (inline) 0 0% 87.02% 177ms 0.51% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 87.02% 177ms 0.51% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 87.02% 174ms 0.51% std::_Rb_tree::clear (inline) 0 0% 87.02% 174ms 0.51% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData