File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 22077ms, 88.97% of 24813ms total Dropped 774 nodes (cum <= 124.06ms) flat flat% sum% cum cum% 0 0% 0% 24677ms 99.45% __libc_start_call_main 0 0% 0% 24677ms 99.45% __libc_start_main_impl 0 0% 0% 24677ms 99.45% _start 0 0% 0% 24659ms 99.38% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 24659ms 99.38% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 24659ms 99.38% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 24659ms 99.38% main 0 0% 0% 24616ms 99.21% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 24616ms 99.21% CxxTest::TestRunner::runTest (inline) 0 0% 0% 24616ms 99.21% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 24607ms 99.17% AbstractCellBasedSimulation::Solve 2ms 0.0081% 0.0081% 14085ms 56.76% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0081% 9307ms 37.51% AbstractCellBasedSimulation::UpdateCellPopulation 6ms 0.024% 0.032% 9175ms 36.98% ForwardEulerNumericalMethod::UpdateAllNodePositions 5ms 0.02% 0.052% 9003ms 36.28% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.052% 8253ms 33.26% NodeBasedCellPopulation::Update 1359ms 5.48% 5.53% 8241ms 33.21% RepulsionForce::AddForceContribution (partial-inline) 7ms 0.028% 5.56% 6132ms 24.71% DistributedBoxCollection::CalculateInteriorNodePairs 2177ms 8.77% 14.33% 5188ms 20.91% std::_Rb_tree::_M_lower_bound (inline) 6ms 0.024% 14.36% 4629ms 18.66% NodeAttributes::RemoveDuplicateNeighbours 0 0% 14.36% 4605ms 18.56% OffLatticeSimulation::ApplyBoundaries 4ms 0.016% 14.37% 4467ms 18.00% std::__sort (inline) 0 0% 14.37% 4467ms 18.00% std::sort (inline) 166ms 0.67% 15.04% 4110ms 16.56% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 226ms 0.91% 15.95% 3346ms 13.48% std::_Rb_tree::find (inline) 0 0% 15.95% 3346ms 13.48% std::map::find (inline) 77ms 0.31% 16.26% 3268ms 13.17% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 4ms 0.016% 16.28% 3142ms 12.66% AbstractCellPopulation::Iterator::operator++ (inline) 188ms 0.76% 17.04% 3103ms 12.51% AbstractCellPopulation::Iterator::IsRealCell (inline) 2974ms 11.99% 29.02% 2974ms 11.99% std::_Rb_tree::_S_right (inline) 35ms 0.14% 29.16% 2680ms 10.80% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 208ms 0.84% 30.00% 2606ms 10.50% std::map::operator[] (partial-inline) 175ms 0.71% 30.71% 2588ms 10.43% std::__introsort_loop 171ms 0.69% 31.39% 2478ms 9.99% AbstractMesh::GetNode 60ms 0.24% 31.64% 2463ms 9.93% NodesOnlyMesh::GetNodeOrHaloNode 20ms 0.081% 31.72% 2435ms 9.81% PlaneBoundaryCondition::ImposeBoundaryCondition 0 0% 31.72% 2330ms 9.39% std::__unguarded_partition_pivot (inline) 80ms 0.32% 32.04% 2314ms 9.33% NodesOnlyMesh::SolveNodeMapping 37ms 0.15% 32.19% 2230ms 8.99% AbstractCellPopulation::GetLocationIndexUsingCell 12ms 0.048% 32.24% 2170ms 8.75% PlaneBoundaryCondition::VerifyBoundaryCondition 151ms 0.61% 32.85% 2118ms 8.54% DistributedBoxCollection::AddPairsFromBox 0 0% 32.85% 2115ms 8.52% std::_Rb_tree::lower_bound (inline) 0 0% 32.85% 2115ms 8.52% std::map::lower_bound (inline) 979ms 3.95% 36.79% 2071ms 8.35% std::__unguarded_partition (inline) 1ms 0.004% 36.80% 1874ms 7.55% std::__final_insertion_sort (inline) 28ms 0.11% 36.91% 1772ms 7.14% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 35ms 0.14% 37.05% 1739ms 7.01% AbstractCellPopulation::GetCellUsingLocationIndex 114ms 0.46% 37.51% 1649ms 6.65% std::__unguarded_insertion_sort (inline) 574ms 2.31% 39.82% 1548ms 6.24% std::__unguarded_linear_insert (inline) 1401ms 5.65% 45.47% 1401ms 5.65% __gnu_cxx::__normal_iterator::operator-- (inline) 46ms 0.19% 45.65% 1302ms 5.25% boost::numeric::ublas::c_vector::c_vector (partial-inline) 2ms 0.0081% 45.66% 1174ms 4.73% NodeBasedCellPopulation::UpdateCellProcessLocation 9ms 0.036% 45.70% 1170ms 4.72% boost::numeric::ublas::vector_assign (inline) 8ms 0.032% 45.73% 1108ms 4.47% DistributedBoxCollection::CalculateBoundaryNodePairs 203ms 0.82% 46.55% 1073ms 4.32% boost::numeric::ublas::indexing_vector_assign 23ms 0.093% 46.64% 938ms 3.78% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 285ms 1.15% 47.79% 925ms 3.73% __dynamic_cast 168ms 0.68% 48.47% 855ms 3.45% AbstractMesh::GetVectorFromAtoB 0 0% 48.47% 838ms 3.38% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 390ms 1.57% 50.04% 836ms 3.37% DistributedBoxCollection::CalculateContainingBox (partial-inline) 236ms 0.95% 50.99% 835ms 3.37% NodeAttributes::AddNeighbour 0 0% 50.99% 823ms 3.32% boost::numeric::ublas::norm_2 (inline) 656ms 2.64% 53.63% 823ms 3.32% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 53.63% 823ms 3.32% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 3ms 0.012% 53.65% 758ms 3.05% boost::numeric::ublas::c_vector::operator= (inline) 33ms 0.13% 53.78% 749ms 3.02% std::_Rb_tree_const_iterator::operator++ (inline) 747ms 3.01% 56.79% 747ms 3.01% __memcpy_avx_unaligned_erms 1ms 0.004% 56.79% 746ms 3.01% AbstractCellPopulation::WriteResultsToFiles 26ms 0.1% 56.90% 739ms 2.98% std::__copy_move::__copy_m (inline) 0 0% 56.90% 739ms 2.98% std::__copy_move_a (inline) 0 0% 56.90% 739ms 2.98% std::__copy_move_a1 (inline) 0 0% 56.90% 739ms 2.98% std::__copy_move_a2 (inline) 0 0% 56.90% 739ms 2.98% std::copy (inline) 716ms 2.89% 59.78% 716ms 2.89% boost::numeric::ublas::c_vector::operator() 702ms 2.83% 62.61% 702ms 2.83% std::_Rb_tree_increment 599ms 2.41% 65.03% 688ms 2.77% std::vector::push_back (inline) 8ms 0.032% 65.06% 677ms 2.73% AbstractCentreBasedCellPopulation::GetDampingConstant 9ms 0.036% 65.09% 669ms 2.70% CellPropertyCollection::GetPropertiesType (inline) 6ms 0.024% 65.12% 587ms 2.37% AbstractCellBasedSimulation::DoCellBirth 54ms 0.22% 65.34% 551ms 2.22% std::_Rb_tree::_Rb_tree (partial-inline) 98ms 0.39% 65.73% 550ms 2.22% std::__new_allocator::allocate (inline) 548ms 2.21% 67.94% 548ms 2.21% boost::numeric::ublas::same_impl_ex 278ms 1.12% 69.06% 534ms 2.15% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 69.06% 528ms 2.13% std::allocator_traits::allocate (inline) 2ms 0.0081% 69.07% 496ms 2.00% NodeBasedCellPopulation::WriteVtkResultsToFile 53ms 0.21% 69.28% 483ms 1.95% std::_Rb_tree::_M_copy (inline) 0 0% 69.28% 482ms 1.94% std::_Rb_tree::_M_create_node (inline) 1ms 0.004% 69.29% 477ms 1.92% Cell::GetMutationState 0 0% 69.29% 467ms 1.88% AbstractCellBasedSimulation::DoCellRemoval (inline) 30ms 0.12% 69.41% 461ms 1.86% boost::detail::shared_count::~shared_count (inline) 0 0% 69.41% 461ms 1.86% boost::shared_ptr::~shared_ptr (inline) 10ms 0.04% 69.45% 460ms 1.85% std::set::set (inline) 20ms 0.081% 69.53% 448ms 1.81% operator new 8ms 0.032% 69.56% 445ms 1.79% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 69.56% 432ms 1.74% std::_Rb_tree::_M_get_node (inline) 134ms 0.54% 70.10% 425ms 1.71% std::_Rb_tree::_M_clone_node (inline) 398ms 1.60% 71.70% 416ms 1.68% boost::detail::sp_counted_base::release 110ms 0.44% 72.15% 415ms 1.67% __GI___libc_malloc 85ms 0.34% 72.49% 406ms 1.64% Node::GetRadius 406ms 1.64% 74.13% 406ms 1.64% __strcmp_avx2 1ms 0.004% 74.13% 398ms 1.60% AbstractCellProperty::IsSubType (inline) 109ms 0.44% 74.57% 397ms 1.60% boost::numeric::ublas::vector_binary::size (inline) 97ms 0.39% 74.96% 393ms 1.58% std::_Rb_tree::_M_erase 0 0% 74.96% 377ms 1.52% boost::numeric::ublas::inner_prod (inline) 376ms 1.52% 76.48% 376ms 1.52% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 11ms 0.044% 76.52% 376ms 1.52% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 76.52% 376ms 1.52% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 370ms 1.49% 78.01% 370ms 1.49% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 78.01% 340ms 1.37% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 78.01% 339ms 1.37% boost::numeric::ublas::c_vector::assign (inline) 338ms 1.36% 79.37% 338ms 1.36% Node::CheckForNodeAttributes 0 0% 79.37% 334ms 1.35% NodesOnlyMesh::ReMesh 6ms 0.024% 79.40% 322ms 1.30% NodeBasedCellPopulation::UpdateMapsAfterRemesh 3ms 0.012% 79.41% 321ms 1.29% NodesOnlyMesh::UpdateNodeIndices 42ms 0.17% 79.58% 321ms 1.29% std::_Rb_tree::~_Rb_tree (inline) 138ms 0.56% 80.14% 311ms 1.25% boost::numeric::ublas::vector_inner_prod::apply (inline) 3ms 0.012% 80.15% 297ms 1.20% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 80.15% 295ms 1.19% std::_Rb_tree::_M_drop_node (inline) 0 0% 80.15% 289ms 1.16% NodesOnlyMesh::UpdateBoxCollection 14ms 0.056% 80.20% 283ms 1.14% std::_Rb_tree::_M_emplace_hint_unique 4ms 0.016% 80.22% 275ms 1.11% DistributedBoxCollection::GetProcessOwningNode 4ms 0.016% 80.24% 252ms 1.02% std::__new_allocator::deallocate (inline) 93ms 0.37% 80.61% 251ms 1.01% std::__move_median_to_first (inline) 132ms 0.53% 81.14% 250ms 1.01% _int_malloc 2ms 0.0081% 81.15% 248ms 1% NodesOnlyMesh::AddNodesToBoxes 0 0% 81.15% 243ms 0.98% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 81.15% 242ms 0.98% VtkMeshWriter::WriteFiles 0 0% 81.15% 239ms 0.96% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 81.15% 238ms 0.96% std::set::~set (inline) 12ms 0.048% 81.20% 234ms 0.94% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 81.20% 234ms 0.94% std::allocator_traits::deallocate (inline) 232ms 0.93% 82.13% 232ms 0.93% Node::GetIndex 113ms 0.46% 82.59% 231ms 0.93% boost::shared_ptr::shared_ptr (inline) 0 0% 82.59% 230ms 0.93% std::_Rb_tree::_M_put_node (inline) 76ms 0.31% 82.90% 225ms 0.91% __GI___libc_free 23ms 0.093% 82.99% 224ms 0.9% std::__insertion_sort (inline) 0 0% 82.99% 223ms 0.9% Cell::HasCellProperty (inline) 4ms 0.016% 83.00% 223ms 0.9% CellPropertyCollection::HasProperty 199ms 0.8% 83.81% 223ms 0.9% Node::AddNeighbour 215ms 0.87% 84.67% 215ms 0.87% [libchaste_mesh.so] 0 0% 84.67% 211ms 0.85% vtkStreamingDemandDrivenPipeline::Update 0 0% 84.67% 211ms 0.85% vtkXMLWriterBase::Write 0 0% 84.67% 209ms 0.84% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 84.67% 208ms 0.84% vtkDemandDrivenPipeline::ProcessRequest 4ms 0.016% 84.69% 207ms 0.83% Cell::ReadyToDivide 0 0% 84.69% 206ms 0.83% vtkDemandDrivenPipeline::ExecuteData 0 0% 84.69% 206ms 0.83% vtkExecutive::CallAlgorithm 0 0% 84.69% 205ms 0.83% vtkCompositeDataPipeline::ExecuteData 0 0% 84.69% 205ms 0.83% vtkXMLUnstructuredDataWriter::ProcessRequest 189ms 0.76% 85.45% 189ms 0.76% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 0 0% 85.45% 181ms 0.73% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.45% 181ms 0.73% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 85.45% 177ms 0.71% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 171ms 0.69% 86.14% 171ms 0.69% [libchaste_cell_based.so] 2ms 0.0081% 86.15% 163ms 0.66% AbstractCellProperty::IsType (inline) 0 0% 86.15% 160ms 0.64% NodesOnlyMesh::ResizeBoxCollection 14ms 0.056% 86.20% 159ms 0.64% NodesOnlyMesh::IsANodeCloseToDomainBoundary 133ms 0.54% 86.74% 149ms 0.6% _int_free 0 0% 86.74% 144ms 0.58% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 1ms 0.004% 86.74% 143ms 0.58% AbstractCellPopulation::SetCellUsingLocationIndex 0 0% 86.74% 143ms 0.58% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 142ms 0.57% 87.32% 142ms 0.57% Node::IsDeleted 0 0% 87.32% 142ms 0.57% std::_Rb_tree::_Auto_node::_Auto_node (inline) 140ms 0.56% 87.88% 140ms 0.56% std::__adjacent_find (inline) 0 0% 87.88% 140ms 0.56% std::__unique (inline) 0 0% 87.88% 140ms 0.56% std::unique (inline) 0 0% 87.88% 138ms 0.56% vtkXMLWriter::WriteBinaryData 137ms 0.55% 88.43% 137ms 0.55% Node::rGetLocation 0 0% 88.43% 134ms 0.54% std::_Rb_tree::clear (inline) 1ms 0.004% 88.44% 133ms 0.54% Cell::GetCellId 0 0% 88.44% 133ms 0.54% vtkXMLWriter::WriteBinaryDataInternal 0 0% 88.44% 132ms 0.53% vtkXMLWriter::WriteBinaryDataBlock 0 0% 88.44% 132ms 0.53% vtkXMLWriter::WriteCompressionBlock 130ms 0.52% 88.96% 130ms 0.52% boost::shared_ptr::operator-> (inline) 3ms 0.012% 88.97% 129ms 0.52% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 88.97% 126ms 0.51% vtkXMLWriter::WritePointsAppendedData