File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 21965ms, 89.09% of 24655ms total Dropped 795 nodes (cum <= 123.28ms) flat flat% sum% cum cum% 0 0% 0% 24532ms 99.50% __libc_start_call_main 0 0% 0% 24532ms 99.50% __libc_start_main_impl 0 0% 0% 24532ms 99.50% _start 0 0% 0% 24514ms 99.43% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 24514ms 99.43% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 24514ms 99.43% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 24514ms 99.43% main 0 0% 0% 24473ms 99.26% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 24473ms 99.26% CxxTest::TestRunner::runTest (inline) 0 0% 0% 24473ms 99.26% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 24464ms 99.23% AbstractCellBasedSimulation::Solve 1ms 0.0041% 0.0041% 13988ms 56.73% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0041% 9281ms 37.64% AbstractCellBasedSimulation::UpdateCellPopulation 7ms 0.028% 0.032% 9055ms 36.73% ForwardEulerNumericalMethod::UpdateAllNodePositions 15ms 0.061% 0.093% 8878ms 36.01% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.093% 8211ms 33.30% NodeBasedCellPopulation::Update 1328ms 5.39% 5.48% 8188ms 33.21% RepulsionForce::AddForceContribution (partial-inline) 10ms 0.041% 5.52% 5974ms 24.23% DistributedBoxCollection::CalculateInteriorNodePairs 2079ms 8.43% 13.95% 5152ms 20.90% std::_Rb_tree::_M_lower_bound (inline) 15ms 0.061% 14.01% 4720ms 19.14% NodeAttributes::RemoveDuplicateNeighbours 0 0% 14.01% 4609ms 18.69% OffLatticeSimulation::ApplyBoundaries 5ms 0.02% 14.03% 4376ms 17.75% std::__sort (inline) 0 0% 14.03% 4376ms 17.75% std::sort (inline) 186ms 0.75% 14.79% 4108ms 16.66% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 271ms 1.10% 15.89% 3422ms 13.88% std::_Rb_tree::find (inline) 0 0% 15.89% 3420ms 13.87% std::map::find (inline) 89ms 0.36% 16.25% 3419ms 13.87% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 2ms 0.0081% 16.26% 3246ms 13.17% AbstractCellPopulation::Iterator::operator++ (inline) 149ms 0.6% 16.86% 3220ms 13.06% AbstractCellPopulation::Iterator::IsRealCell 3045ms 12.35% 29.21% 3045ms 12.35% std::_Rb_tree::_S_right (inline) 30ms 0.12% 29.33% 2797ms 11.34% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 69ms 0.28% 29.61% 2526ms 10.25% NodesOnlyMesh::GetNodeOrHaloNode 170ms 0.69% 30.30% 2522ms 10.23% AbstractMesh::GetNode 212ms 0.86% 31.16% 2522ms 10.23% std::map::operator[] (partial-inline) 161ms 0.65% 31.82% 2518ms 10.21% std::__introsort_loop 20ms 0.081% 31.90% 2439ms 9.89% PlaneBoundaryCondition::ImposeBoundaryCondition 108ms 0.44% 32.33% 2356ms 9.56% NodesOnlyMesh::SolveNodeMapping 44ms 0.18% 32.51% 2299ms 9.32% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 32.51% 2277ms 9.24% std::__unguarded_partition_pivot (inline) 11ms 0.045% 32.56% 2170ms 8.80% PlaneBoundaryCondition::VerifyBoundaryCondition 1040ms 4.22% 36.78% 2046ms 8.30% std::__unguarded_partition (inline) 0 0% 36.78% 2034ms 8.25% std::_Rb_tree::lower_bound (inline) 0 0% 36.78% 2034ms 8.25% std::map::lower_bound (inline) 129ms 0.52% 37.30% 1999ms 8.11% DistributedBoxCollection::AddPairsFromBox 2ms 0.0081% 37.31% 1852ms 7.51% std::__final_insertion_sort (inline) 23ms 0.093% 37.40% 1719ms 6.97% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 37ms 0.15% 37.55% 1693ms 6.87% AbstractCellPopulation::GetCellUsingLocationIndex 99ms 0.4% 37.95% 1622ms 6.58% std::__unguarded_insertion_sort (inline) 561ms 2.28% 40.23% 1600ms 6.49% std::__unguarded_linear_insert (inline) 1498ms 6.08% 46.30% 1498ms 6.08% __gnu_cxx::__normal_iterator::operator-- (inline) 7ms 0.028% 46.33% 1270ms 5.15% DistributedBoxCollection::CalculateBoundaryNodePairs 53ms 0.21% 46.55% 1246ms 5.05% boost::numeric::ublas::c_vector::c_vector (partial-inline) 1ms 0.0041% 46.55% 1146ms 4.65% NodeBasedCellPopulation::UpdateCellProcessLocation 7ms 0.028% 46.58% 1090ms 4.42% boost::numeric::ublas::vector_assign (inline) 205ms 0.83% 47.41% 1015ms 4.12% boost::numeric::ublas::indexing_vector_assign 17ms 0.069% 47.48% 952ms 3.86% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 273ms 1.11% 48.59% 946ms 3.84% __dynamic_cast 396ms 1.61% 50.19% 890ms 3.61% DistributedBoxCollection::CalculateContainingBox (partial-inline) 213ms 0.86% 51.06% 865ms 3.51% NodeAttributes::AddNeighbour 168ms 0.68% 51.74% 835ms 3.39% AbstractMesh::GetVectorFromAtoB 0 0% 51.74% 817ms 3.31% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 51.74% 804ms 3.26% boost::numeric::ublas::norm_2 (inline) 637ms 2.58% 54.32% 804ms 3.26% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 54.32% 804ms 3.26% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 5ms 0.02% 54.34% 795ms 3.22% boost::numeric::ublas::c_vector::operator= (inline) 31ms 0.13% 54.47% 778ms 3.16% std::__copy_move::__copy_m (inline) 0 0% 54.47% 778ms 3.16% std::__copy_move_a (inline) 0 0% 54.47% 778ms 3.16% std::__copy_move_a1 (inline) 0 0% 54.47% 778ms 3.16% std::__copy_move_a2 (inline) 0 0% 54.47% 778ms 3.16% std::copy (inline) 769ms 3.12% 57.59% 769ms 3.12% __memcpy_avx_unaligned_erms 740ms 3.00% 60.59% 740ms 3.00% boost::numeric::ublas::c_vector::operator() 0 0% 60.59% 733ms 2.97% AbstractCellPopulation::WriteResultsToFiles 651ms 2.64% 63.23% 730ms 2.96% std::vector::push_back (inline) 7ms 0.028% 63.26% 593ms 2.41% CellPropertyCollection::GetPropertiesType (inline) 5ms 0.02% 63.28% 592ms 2.40% AbstractCentreBasedCellPopulation::GetDampingConstant 28ms 0.11% 63.39% 580ms 2.35% std::_Rb_tree_const_iterator::operator++ (inline) 3ms 0.012% 63.40% 573ms 2.32% AbstractCellBasedSimulation::DoCellBirth 97ms 0.39% 63.80% 562ms 2.28% std::__new_allocator::allocate (inline) 261ms 1.06% 64.85% 557ms 2.26% __cxxabiv1::__si_class_type_info::__do_dyncast 33ms 0.13% 64.99% 556ms 2.26% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 64.99% 548ms 2.22% std::allocator_traits::allocate (inline) 539ms 2.19% 67.18% 539ms 2.19% std::_Rb_tree_increment 0 0% 67.18% 525ms 2.13% std::_Rb_tree::_M_create_node (inline) 32ms 0.13% 67.30% 509ms 2.06% std::_Rb_tree::_M_copy (inline) 506ms 2.05% 69.36% 506ms 2.05% boost::numeric::ublas::same_impl_ex 48ms 0.19% 69.55% 497ms 2.02% boost::detail::shared_count::~shared_count (inline) 0 0% 69.55% 497ms 2.02% boost::shared_ptr::~shared_ptr (inline) 0 0% 69.55% 494ms 2.00% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 69.55% 488ms 1.98% NodeBasedCellPopulation::WriteVtkResultsToFile 2ms 0.0081% 69.56% 482ms 1.95% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 69.56% 478ms 1.94% std::_Rb_tree::_M_get_node (inline) 155ms 0.63% 70.19% 474ms 1.92% std::_Rb_tree::_M_clone_node (inline) 462ms 1.87% 72.06% 462ms 1.87% __strcmp_avx2 6ms 0.024% 72.09% 451ms 1.83% std::set::set (inline) 19ms 0.077% 72.16% 447ms 1.81% operator new 122ms 0.49% 72.66% 445ms 1.80% std::_Rb_tree::_M_erase 431ms 1.75% 74.41% 439ms 1.78% boost::detail::sp_counted_base::release 1ms 0.0041% 74.41% 427ms 1.73% AbstractCellProperty::IsSubType (inline) 135ms 0.55% 74.96% 423ms 1.72% __GI___libc_malloc 2ms 0.0081% 74.97% 415ms 1.68% Cell::GetMutationState 113ms 0.46% 75.42% 403ms 1.63% boost::numeric::ublas::vector_binary::size (inline) 0 0% 75.42% 376ms 1.53% std::_Rb_tree::_Alloc_node::operator() (inline) 80ms 0.32% 75.75% 364ms 1.48% Node::GetRadius 56ms 0.23% 75.98% 361ms 1.46% std::_Rb_tree::~_Rb_tree (inline) 0 0% 75.98% 358ms 1.45% boost::numeric::ublas::inner_prod (inline) 1ms 0.0041% 75.98% 358ms 1.45% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 18ms 0.073% 76.05% 357ms 1.45% boost::numeric::ublas::vector_scalar_binary::evaluate 351ms 1.42% 77.48% 351ms 1.42% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 4ms 0.016% 77.49% 325ms 1.32% NodeBasedCellPopulation::UpdateMapsAfterRemesh 4ms 0.016% 77.51% 322ms 1.31% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 77.51% 318ms 1.29% boost::numeric::ublas::c_vector::assign (inline) 314ms 1.27% 78.78% 315ms 1.28% std::__adjacent_find (inline) 0 0% 78.78% 315ms 1.28% std::__unique (inline) 0 0% 78.78% 315ms 1.28% std::unique (inline) 1ms 0.0041% 78.79% 311ms 1.26% NodesOnlyMesh::ReMesh 0 0% 78.79% 311ms 1.26% std::_Rb_tree::_M_drop_node (inline) 5ms 0.02% 78.81% 308ms 1.25% DistributedBoxCollection::GetProcessOwningNode 5ms 0.02% 78.83% 306ms 1.24% NodesOnlyMesh::UpdateNodeIndices 302ms 1.22% 80.05% 302ms 1.22% Node::CheckForNodeAttributes 134ms 0.54% 80.60% 298ms 1.21% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 80.60% 277ms 1.12% NodesOnlyMesh::UpdateBoxCollection 14ms 0.057% 80.65% 276ms 1.12% std::_Rb_tree::_M_emplace_hint_unique 0 0% 80.65% 267ms 1.08% std::set::~set (inline) 7ms 0.028% 80.68% 259ms 1.05% std::__new_allocator::deallocate (inline) 258ms 1.05% 81.73% 258ms 1.05% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 81.73% 245ms 0.99% std::allocator_traits::deallocate (inline) 0 0% 81.73% 243ms 0.99% std::_Rb_tree::_M_put_node (inline) 135ms 0.55% 82.28% 234ms 0.95% _int_malloc 0 0% 82.28% 232ms 0.94% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 1ms 0.0041% 82.28% 232ms 0.94% NodesOnlyMesh::AddNodesToBoxes 0 0% 82.28% 232ms 0.94% VtkMeshWriter::WriteFiles 19ms 0.077% 82.36% 228ms 0.92% std::__insertion_sort (inline) 101ms 0.41% 82.77% 228ms 0.92% std::__move_median_to_first (inline) 118ms 0.48% 83.24% 226ms 0.92% boost::shared_ptr::shared_ptr (inline) 217ms 0.88% 84.12% 217ms 0.88% Node::GetIndex 217ms 0.88% 85.01% 217ms 0.88% [libchaste_mesh.so] 68ms 0.28% 85.28% 217ms 0.88% __GI___libc_free 0 0% 85.28% 209ms 0.85% vtkStreamingDemandDrivenPipeline::Update 0 0% 85.28% 209ms 0.85% vtkXMLWriterBase::Write 0 0% 85.28% 208ms 0.84% vtkDemandDrivenPipeline::ProcessRequest 0 0% 85.28% 207ms 0.84% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 85.28% 207ms 0.84% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 85.28% 206ms 0.84% vtkDemandDrivenPipeline::ExecuteData 0 0% 85.28% 205ms 0.83% Cell::HasCellProperty (inline) 1ms 0.0041% 85.28% 205ms 0.83% vtkExecutive::CallAlgorithm 2ms 0.0081% 85.29% 204ms 0.83% CellPropertyCollection::HasProperty 0 0% 85.29% 203ms 0.82% vtkCompositeDataPipeline::ExecuteData 0 0% 85.29% 202ms 0.82% vtkXMLUnstructuredDataWriter::ProcessRequest 172ms 0.7% 85.99% 197ms 0.8% Node::AddNeighbour 12ms 0.049% 86.04% 196ms 0.79% boost::numeric::ublas::vector_reference::operator() (inline) 190ms 0.77% 86.81% 190ms 0.77% [libchaste_cell_based.so] 9ms 0.037% 86.85% 186ms 0.75% Cell::ReadyToDivide 0 0% 86.85% 175ms 0.71% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 86.85% 175ms 0.71% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 86.85% 167ms 0.68% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 86.85% 160ms 0.65% AbstractCellProperty::IsType (inline) 0 0% 86.85% 157ms 0.64% std::_Rb_tree::clear (inline) 4ms 0.016% 86.86% 151ms 0.61% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 86.86% 149ms 0.6% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 86.86% 147ms 0.6% NodesOnlyMesh::ResizeBoxCollection 129ms 0.52% 87.39% 147ms 0.6% _int_free 14ms 0.057% 87.44% 146ms 0.59% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 87.44% 145ms 0.59% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 87.44% 145ms 0.59% vtkXMLWriter::WriteBinaryData 143ms 0.58% 88.02% 143ms 0.58% Node::rGetLocation 0 0% 88.02% 139ms 0.56% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 88.02% 136ms 0.55% vtkXMLWriter::WriteBinaryDataBlock 0 0% 88.02% 136ms 0.55% vtkXMLWriter::WriteBinaryDataInternal 0 0% 88.02% 136ms 0.55% vtkXMLWriter::WriteCompressionBlock 133ms 0.54% 88.56% 133ms 0.54% __ieee754_log_fma 0 0% 88.56% 127ms 0.52% vtkXMLWriter::WritePointsAppendedData 5ms 0.02% 88.58% 126ms 0.51% AbstractCellPopulation::SetCellUsingLocationIndex 125ms 0.51% 89.09% 125ms 0.51% __gnu_cxx::__ops::_Val_less_iter::operator() (inline)