File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 30575ms, 87.95% of 34764ms total Dropped 859 nodes (cum <= 173.82ms) flat flat% sum% cum cum% 0 0% 0% 34633ms 99.62% __libc_start_call_main 0 0% 0% 34633ms 99.62% __libc_start_main_impl 0 0% 0% 34633ms 99.62% _start 0 0% 0% 34614ms 99.57% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 34614ms 99.57% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 34614ms 99.57% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 34614ms 99.57% main 0 0% 0% 34573ms 99.45% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 34573ms 99.45% CxxTest::TestRunner::runTest (inline) 0 0% 0% 34573ms 99.45% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 34564ms 99.42% AbstractCellBasedSimulation::Solve 3ms 0.0086% 0.0086% 23944ms 68.88% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.0058% 0.014% 18864ms 54.26% ForwardEulerNumericalMethod::UpdateAllNodePositions 16ms 0.046% 0.06% 18677ms 53.73% AbstractNumericalMethod::ComputeForcesIncludingDamping 158ms 0.45% 0.51% 17794ms 51.19% AbstractTwoBodyInteractionForce::AddForceContribution 1485ms 4.27% 4.79% 15004ms 43.16% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4567ms 13.14% 17.92% 10067ms 28.96% std::_Rb_tree::_M_lower_bound (inline) 0 0% 17.92% 9378ms 26.98% AbstractCellBasedSimulation::UpdateCellPopulation 350ms 1.01% 18.93% 9168ms 26.37% std::_Rb_tree::find (inline) 0 0% 18.93% 9167ms 26.37% std::map::find (inline) 199ms 0.57% 19.50% 9056ms 26.05% NodesOnlyMesh::GetNodeOrHaloNode 507ms 1.46% 20.96% 8847ms 25.45% AbstractMesh::GetNode 376ms 1.08% 22.04% 8347ms 24.01% NodesOnlyMesh::SolveNodeMapping 0 0% 22.04% 8284ms 23.83% NodeBasedCellPopulation::Update 10ms 0.029% 22.07% 6184ms 17.79% DistributedBoxCollection::CalculateInteriorNodePairs 180ms 0.52% 22.59% 5654ms 16.26% boost::numeric::ublas::vector_assign (inline) 157ms 0.45% 23.04% 5495ms 15.81% boost::numeric::ublas::c_vector::c_vector (partial-inline) 5446ms 15.67% 38.71% 5446ms 15.67% std::_Rb_tree::_S_right (inline) 0 0% 38.71% 4735ms 13.62% OffLatticeSimulation::ApplyBoundaries 4ms 0.012% 38.72% 4626ms 13.31% NodeAttributes::RemoveDuplicateNeighbours 5ms 0.014% 38.73% 4459ms 12.83% std::__sort (inline) 0 0% 38.73% 4459ms 12.83% std::sort (inline) 72ms 0.21% 38.94% 3415ms 9.82% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 1017ms 2.93% 41.87% 3372ms 9.70% boost::numeric::ublas::indexing_vector_assign 6ms 0.017% 41.88% 3230ms 9.29% AbstractCellPopulation::Iterator::operator++ (inline) 154ms 0.44% 42.33% 3193ms 9.18% AbstractCellPopulation::Iterator::IsRealCell (inline) 29ms 0.083% 42.41% 2776ms 7.99% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 177ms 0.51% 42.92% 2582ms 7.43% std::__introsort_loop 23ms 0.066% 42.98% 2501ms 7.19% PlaneBoundaryCondition::ImposeBoundaryCondition 38ms 0.11% 43.09% 2342ms 6.74% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 43.09% 2332ms 6.71% std::__unguarded_partition_pivot (inline) 13ms 0.037% 43.13% 2234ms 6.43% PlaneBoundaryCondition::VerifyBoundaryCondition 134ms 0.39% 43.52% 2171ms 6.24% DistributedBoxCollection::AddPairsFromBox 1000ms 2.88% 46.39% 2111ms 6.07% std::__unguarded_partition (inline) 0 0% 46.39% 1868ms 5.37% std::__final_insertion_sort (inline) 190ms 0.55% 46.94% 1831ms 5.27% std::map::operator[] (partial-inline) 1690ms 4.86% 51.80% 1690ms 4.86% boost::numeric::ublas::same_impl_ex 119ms 0.34% 52.14% 1673ms 4.81% std::__unguarded_insertion_sort (inline) 607ms 1.75% 53.89% 1594ms 4.59% std::__unguarded_linear_insert (inline) 173ms 0.5% 54.39% 1515ms 4.36% AbstractMesh::GetVectorFromAtoB 1409ms 4.05% 58.44% 1409ms 4.05% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 58.44% 1349ms 3.88% std::_Rb_tree::lower_bound (inline) 0 0% 58.44% 1349ms 3.88% std::map::lower_bound (inline) 0 0% 58.44% 1328ms 3.82% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 58.44% 1312ms 3.77% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1206ms 3.47% 61.91% 1206ms 3.47% boost::numeric::ublas::c_vector::operator() 0 0% 61.91% 1177ms 3.39% NodeBasedCellPopulation::UpdateCellProcessLocation 1ms 0.0029% 61.91% 1142ms 3.29% boost::numeric::ublas::detail::expression_type_check (inline) 6ms 0.017% 61.93% 1120ms 3.22% DistributedBoxCollection::CalculateBoundaryNodePairs 241ms 0.69% 62.62% 1095ms 3.15% boost::numeric::ublas::detail::equals 23ms 0.066% 62.69% 1002ms 2.88% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 167ms 0.48% 63.17% 957ms 2.75% boost::numeric::ublas::vector_binary::size (inline) 200ms 0.58% 63.74% 897ms 2.58% NodeAttributes::AddAppliedForceContribution 410ms 1.18% 64.92% 859ms 2.47% DistributedBoxCollection::CalculateContainingBox (partial-inline) 232ms 0.67% 65.59% 846ms 2.43% NodeAttributes::AddNeighbour 4ms 0.012% 65.60% 821ms 2.36% AbstractCentreBasedCellPopulation::GetDampingConstant 613ms 1.76% 67.37% 812ms 2.34% __dynamic_cast 0 0% 67.37% 801ms 2.30% boost::numeric::ublas::norm_inf (inline) 472ms 1.36% 68.72% 801ms 2.30% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 68.72% 764ms 2.20% AbstractCellPopulation::WriteResultsToFiles 97ms 0.28% 69.00% 736ms 2.12% std::__new_allocator::allocate (inline) 29ms 0.083% 69.09% 703ms 2.02% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 69.09% 697ms 2.00% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 69.09% 697ms 2.00% boost::numeric::ublas::c_vector::plus_assign (inline) 613ms 1.76% 70.85% 688ms 1.98% std::vector::push_back (inline) 663ms 1.91% 72.76% 663ms 1.91% std::_Rb_tree_increment 71ms 0.2% 72.96% 636ms 1.83% operator new 17ms 0.049% 73.01% 622ms 1.79% CellPropertyCollection::GetPropertiesType (inline) 7ms 0.02% 73.03% 615ms 1.77% AbstractCellBasedSimulation::DoCellBirth 184ms 0.53% 73.56% 563ms 1.62% __GI___libc_malloc 151ms 0.43% 73.99% 533ms 1.53% __GI___libc_free 2ms 0.0058% 74.00% 529ms 1.52% Cell::GetMutationState 0 0% 74.00% 527ms 1.52% boost::numeric::ublas::norm_2 (inline) 423ms 1.22% 75.22% 527ms 1.52% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 75.22% 505ms 1.45% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 75.22% 478ms 1.37% AbstractCellBasedSimulation::DoCellRemoval (inline) 472ms 1.36% 76.57% 472ms 1.36% Node::GetIndex 2ms 0.0058% 76.58% 463ms 1.33% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 76.58% 459ms 1.32% std::allocator_traits::allocate (inline) 31ms 0.089% 76.67% 444ms 1.28% boost::detail::shared_count::~shared_count (inline) 0 0% 76.67% 444ms 1.28% boost::shared_ptr::~shared_ptr (inline) 0 0% 76.67% 410ms 1.18% std::_Rb_tree::_M_create_node (inline) 400ms 1.15% 77.82% 409ms 1.18% boost::detail::sp_counted_base::release 332ms 0.96% 78.77% 382ms 1.10% _int_free 0 0% 78.77% 378ms 1.09% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 9ms 0.026% 78.80% 377ms 1.08% AbstractCellPopulation::GetCellUsingLocationIndex 1ms 0.0029% 78.80% 376ms 1.08% AbstractCellProperty::IsSubType (inline) 363ms 1.04% 79.85% 363ms 1.04% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 79.85% 359ms 1.03% std::_Rb_tree::_M_get_node (inline) 0 0% 79.85% 355ms 1.02% boost::numeric::ublas::inner_prod (inline) 1ms 0.0029% 79.85% 354ms 1.02% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 16ms 0.046% 79.90% 353ms 1.02% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 79.90% 330ms 0.95% NodesOnlyMesh::ReMesh 318ms 0.91% 80.81% 318ms 0.91% __gnu_cxx::__normal_iterator::operator++ (inline) 2ms 0.0058% 80.82% 317ms 0.91% NodesOnlyMesh::UpdateNodeIndices 11ms 0.032% 80.85% 316ms 0.91% boost::numeric::ublas::vector_reference::operator() (inline) 4ms 0.012% 80.86% 312ms 0.9% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 9ms 0.026% 80.89% 310ms 0.89% NodeBasedCellPopulation::UpdateMapsAfterRemesh 31ms 0.089% 80.97% 308ms 0.89% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 80.97% 308ms 0.89% boost::numeric::ublas::vector::vector (inline) 96ms 0.28% 81.25% 307ms 0.88% std::_Rb_tree::_M_erase (partial-inline) 7ms 0.02% 81.27% 297ms 0.85% DistributedBoxCollection::GetProcessOwningNode 4ms 0.012% 81.28% 292ms 0.84% std::_Rb_tree::_M_emplace_hint_unique 65ms 0.19% 81.47% 286ms 0.82% Node::GetRadius 109ms 0.31% 81.78% 284ms 0.82% boost::numeric::ublas::vector_inner_prod::apply (inline) 152ms 0.44% 82.22% 281ms 0.81% _int_malloc 0 0% 82.22% 271ms 0.78% NodesOnlyMesh::UpdateBoxCollection 10ms 0.029% 82.25% 268ms 0.77% std::_Rb_tree::_Rb_tree (partial-inline) 225ms 0.65% 82.90% 267ms 0.77% Node::AddNeighbour 0 0% 82.90% 259ms 0.75% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 82.90% 258ms 0.74% VtkMeshWriter::WriteFiles 258ms 0.74% 83.64% 258ms 0.74% [libchaste_cell_based.so] 0 0% 83.64% 258ms 0.74% boost::numeric::ublas::c_vector::assign (inline) 0 0% 83.64% 255ms 0.73% boost::numeric::ublas::vector_binary::operator() (inline) 21ms 0.06% 83.70% 253ms 0.73% std::_Rb_tree::_M_copy (inline) 0 0% 83.70% 240ms 0.69% std::_Rb_tree::_Alloc_node::operator() (inline) 237ms 0.68% 84.38% 237ms 0.68% [libchaste_mesh.so] 234ms 0.67% 85.05% 234ms 0.67% Node::CheckForNodeAttributes 41ms 0.12% 85.17% 232ms 0.67% std::_Rb_tree::_M_clone_node (inline) 0 0% 85.17% 221ms 0.64% vtkStreamingDemandDrivenPipeline::Update 0 0% 85.17% 221ms 0.64% vtkXMLWriterBase::Write 3ms 0.0086% 85.18% 220ms 0.63% CellPropertyCollection::HasProperty 0 0% 85.18% 220ms 0.63% vtkDemandDrivenPipeline::ProcessRequest 0 0% 85.18% 219ms 0.63% Cell::HasCellProperty (inline) 0 0% 85.18% 219ms 0.63% vtkExecutive::CallAlgorithm 0 0% 85.18% 219ms 0.63% vtkStreamingDemandDrivenPipeline::ProcessRequest 107ms 0.31% 85.49% 218ms 0.63% std::__move_median_to_first (inline) 0 0% 85.49% 218ms 0.63% vtkCompositeDataPipeline::ExecuteData 0 0% 85.49% 218ms 0.63% vtkDemandDrivenPipeline::ExecuteData 0 0% 85.49% 218ms 0.63% vtkXMLUnstructuredDataWriter::ProcessRequest 2ms 0.0058% 85.49% 216ms 0.62% NodesOnlyMesh::AddNodesToBoxes 16ms 0.046% 85.54% 211ms 0.61% Cell::ReadyToDivide 5ms 0.014% 85.55% 210ms 0.6% std::__new_allocator::deallocate (inline) 0 0% 85.55% 209ms 0.6% std::_Rb_tree::_M_drop_node (inline) 203ms 0.58% 86.14% 203ms 0.58% NodeBasedCellPopulation::GetNode 23ms 0.066% 86.20% 195ms 0.56% std::__insertion_sort (inline) 63ms 0.18% 86.39% 190ms 0.55% std::__find_if (inline) 0 0% 86.39% 190ms 0.55% std::find_if (inline) 0 0% 86.39% 190ms 0.55% std::none_of (inline) 0 0% 86.39% 184ms 0.53% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 86.39% 184ms 0.53% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 86.39% 180ms 0.52% std::allocator_traits::deallocate (inline) 179ms 0.51% 86.90% 179ms 0.51% __strcmp_avx2 0 0% 86.90% 179ms 0.51% std::_Rb_tree::_M_put_node (inline) 0 0% 86.90% 179ms 0.51% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 178ms 0.51% 87.41% 178ms 0.51% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 176ms 0.51% 87.92% 176ms 0.51% Node::rGetLocation 11ms 0.032% 87.95% 176ms 0.51% std::_Rb_tree::~_Rb_tree (inline)