File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 22254ms, 89.86% of 24765ms total Dropped 794 nodes (cum <= 123.83ms) flat flat% sum% cum cum% 0 0% 0% 24636ms 99.48% __libc_start_call_main 0 0% 0% 24636ms 99.48% __libc_start_main_impl 0 0% 0% 24636ms 99.48% _start 0 0% 0% 24618ms 99.41% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 24618ms 99.41% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 24618ms 99.41% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 24618ms 99.41% main 0 0% 0% 24579ms 99.25% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 24579ms 99.25% CxxTest::TestRunner::runTest (inline) 0 0% 0% 24579ms 99.25% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.004% 0.004% 24570ms 99.21% AbstractCellBasedSimulation::Solve 3ms 0.012% 0.016% 14069ms 56.81% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.004% 0.02% 9302ms 37.56% AbstractCellBasedSimulation::UpdateCellPopulation 5ms 0.02% 0.04% 9132ms 36.87% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.032% 0.073% 8923ms 36.03% AbstractNumericalMethod::ComputeForcesIncludingDamping 2ms 0.0081% 0.081% 8225ms 33.21% NodeBasedCellPopulation::Update 1342ms 5.42% 5.50% 8217ms 33.18% RepulsionForce::AddForceContribution (partial-inline) 8ms 0.032% 5.53% 5973ms 24.12% DistributedBoxCollection::CalculateInteriorNodePairs 2139ms 8.64% 14.17% 5162ms 20.84% std::_Rb_tree::_M_lower_bound (inline) 11ms 0.044% 14.21% 4737ms 19.13% NodeAttributes::RemoveDuplicateNeighbours 2ms 0.0081% 14.22% 4626ms 18.68% OffLatticeSimulation::ApplyBoundaries 10ms 0.04% 14.26% 4397ms 17.75% std::__sort (inline) 0 0% 14.26% 4397ms 17.75% std::sort (inline) 194ms 0.78% 15.05% 4071ms 16.44% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 283ms 1.14% 16.19% 3492ms 14.10% std::_Rb_tree::find (inline) 0 0% 16.19% 3491ms 14.10% std::map::find (inline) 69ms 0.28% 16.47% 3372ms 13.62% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 0 0% 16.47% 3092ms 12.49% AbstractCellPopulation::Iterator::operator++ (inline) 161ms 0.65% 17.12% 3067ms 12.38% AbstractCellPopulation::Iterator::IsRealCell 3007ms 12.14% 29.26% 3007ms 12.14% std::_Rb_tree::_S_right (inline) 23ms 0.093% 29.35% 2681ms 10.83% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 163ms 0.66% 30.01% 2553ms 10.31% AbstractMesh::GetNode 174ms 0.7% 30.71% 2553ms 10.31% std::__introsort_loop 45ms 0.18% 30.89% 2510ms 10.14% NodesOnlyMesh::GetNodeOrHaloNode 19ms 0.077% 30.97% 2451ms 9.90% PlaneBoundaryCondition::ImposeBoundaryCondition 183ms 0.74% 31.71% 2444ms 9.87% std::map::operator[] (partial-inline) 102ms 0.41% 32.12% 2394ms 9.67% NodesOnlyMesh::SolveNodeMapping 0 0% 32.12% 2290ms 9.25% std::__unguarded_partition_pivot (inline) 50ms 0.2% 32.32% 2246ms 9.07% AbstractCellPopulation::GetLocationIndexUsingCell 14ms 0.057% 32.38% 2173ms 8.77% PlaneBoundaryCondition::VerifyBoundaryCondition 1024ms 4.13% 36.52% 2022ms 8.16% std::__unguarded_partition (inline) 0 0% 36.52% 1986ms 8.02% std::_Rb_tree::lower_bound (inline) 0 0% 36.52% 1986ms 8.02% std::map::lower_bound (inline) 130ms 0.52% 37.04% 1966ms 7.94% DistributedBoxCollection::AddPairsFromBox 0 0% 37.04% 1834ms 7.41% std::__final_insertion_sort (inline) 22ms 0.089% 37.13% 1707ms 6.89% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 33ms 0.13% 37.26% 1676ms 6.77% AbstractCellPopulation::GetCellUsingLocationIndex 105ms 0.42% 37.69% 1637ms 6.61% std::__unguarded_insertion_sort (inline) 548ms 2.21% 39.90% 1553ms 6.27% std::__unguarded_linear_insert (inline) 1442ms 5.82% 45.72% 1442ms 5.82% __gnu_cxx::__normal_iterator::operator-- (inline) 52ms 0.21% 45.93% 1309ms 5.29% boost::numeric::ublas::c_vector::c_vector (partial-inline) 3ms 0.012% 45.94% 1249ms 5.04% DistributedBoxCollection::CalculateBoundaryNodePairs 7ms 0.028% 45.97% 1170ms 4.72% boost::numeric::ublas::vector_assign (inline) 0 0% 45.97% 1155ms 4.66% NodeBasedCellPopulation::UpdateCellProcessLocation 225ms 0.91% 46.88% 1080ms 4.36% boost::numeric::ublas::indexing_vector_assign 17ms 0.069% 46.95% 1043ms 4.21% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 297ms 1.20% 48.15% 998ms 4.03% __dynamic_cast 394ms 1.59% 49.74% 886ms 3.58% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 49.74% 829ms 3.35% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 167ms 0.67% 50.41% 826ms 3.34% AbstractMesh::GetVectorFromAtoB 0 0% 50.41% 806ms 3.25% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 50.41% 805ms 3.25% boost::numeric::ublas::norm_2 (inline) 651ms 2.63% 53.04% 805ms 3.25% boost::numeric::ublas::vector_norm_2::apply (inline) 217ms 0.88% 53.92% 804ms 3.25% NodeAttributes::AddNeighbour 4ms 0.016% 53.93% 803ms 3.24% boost::numeric::ublas::c_vector::operator= (inline) 33ms 0.13% 54.07% 779ms 3.15% std::__copy_move::__copy_m (inline) 0 0% 54.07% 779ms 3.15% std::__copy_move_a (inline) 0 0% 54.07% 779ms 3.15% std::__copy_move_a1 (inline) 0 0% 54.07% 779ms 3.15% std::__copy_move_a2 (inline) 0 0% 54.07% 779ms 3.15% std::copy (inline) 762ms 3.08% 57.15% 762ms 3.08% __memcpy_avx_unaligned_erms 744ms 3.00% 60.15% 744ms 3.00% boost::numeric::ublas::c_vector::operator() 0 0% 60.15% 739ms 2.98% AbstractCellPopulation::WriteResultsToFiles 8ms 0.032% 60.18% 691ms 2.79% CellPropertyCollection::GetPropertiesType (inline) 40ms 0.16% 60.34% 683ms 2.76% std::_Rb_tree_const_iterator::operator++ (inline) 588ms 2.37% 62.72% 662ms 2.67% std::vector::push_back (inline) 5ms 0.02% 62.74% 640ms 2.58% AbstractCentreBasedCellPopulation::GetDampingConstant 628ms 2.54% 65.27% 628ms 2.54% std::_Rb_tree_increment 290ms 1.17% 66.44% 586ms 2.37% __cxxabiv1::__si_class_type_info::__do_dyncast 5ms 0.02% 66.46% 572ms 2.31% AbstractCellBasedSimulation::DoCellBirth 46ms 0.19% 66.65% 572ms 2.31% std::_Rb_tree::_Rb_tree (partial-inline) 552ms 2.23% 68.88% 552ms 2.23% boost::numeric::ublas::same_impl_ex 90ms 0.36% 69.24% 522ms 2.11% std::__new_allocator::allocate (inline) 47ms 0.19% 69.43% 512ms 2.07% std::_Rb_tree::_M_copy (inline) 0 0% 69.43% 502ms 2.03% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 69.43% 502ms 2.03% std::allocator_traits::allocate (inline) 1ms 0.004% 69.44% 490ms 1.98% NodeBasedCellPopulation::WriteVtkResultsToFile 39ms 0.16% 69.59% 487ms 1.97% boost::detail::shared_count::~shared_count (inline) 0 0% 69.59% 487ms 1.97% boost::shared_ptr::~shared_ptr (inline) 10ms 0.04% 69.63% 487ms 1.97% std::set::set (inline) 2ms 0.0081% 69.64% 486ms 1.96% Cell::GetMutationState 0 0% 69.64% 483ms 1.95% std::_Rb_tree::_M_create_node (inline) 4ms 0.016% 69.66% 481ms 1.94% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 167ms 0.67% 70.33% 459ms 1.85% std::_Rb_tree::_M_clone_node (inline) 2ms 0.0081% 70.34% 455ms 1.84% AbstractCellProperty::IsSubType (inline) 453ms 1.83% 72.17% 453ms 1.83% __strcmp_avx2 0 0% 72.17% 436ms 1.76% std::_Rb_tree::_M_get_node (inline) 88ms 0.36% 72.53% 434ms 1.75% Node::GetRadius 418ms 1.69% 74.21% 434ms 1.75% boost::detail::sp_counted_base::release 24ms 0.097% 74.31% 429ms 1.73% operator new 138ms 0.56% 74.87% 424ms 1.71% std::_Rb_tree::_M_erase 120ms 0.48% 75.35% 404ms 1.63% __GI___libc_malloc 101ms 0.41% 75.76% 390ms 1.57% boost::numeric::ublas::vector_binary::size (inline) 382ms 1.54% 77.30% 382ms 1.54% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 77.30% 368ms 1.49% boost::numeric::ublas::c_vector::assign (inline) 0 0% 77.30% 361ms 1.46% boost::numeric::ublas::inner_prod (inline) 2ms 0.0081% 77.31% 361ms 1.46% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 19ms 0.077% 77.39% 359ms 1.45% boost::numeric::ublas::vector_scalar_binary::evaluate 347ms 1.40% 78.79% 347ms 1.40% Node::CheckForNodeAttributes 0 0% 78.79% 342ms 1.38% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 78.79% 337ms 1.36% NodesOnlyMesh::ReMesh 41ms 0.17% 78.95% 327ms 1.32% std::_Rb_tree::~_Rb_tree (inline) 3ms 0.012% 78.97% 325ms 1.31% NodesOnlyMesh::UpdateNodeIndices 316ms 1.28% 80.24% 318ms 1.28% std::__adjacent_find (inline) 0 0% 80.24% 318ms 1.28% std::__unique (inline) 0 0% 80.24% 318ms 1.28% std::unique (inline) 0 0% 80.24% 308ms 1.24% NodeBasedCellPopulation::UpdateMapsAfterRemesh 2ms 0.0081% 80.25% 307ms 1.24% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 80.25% 299ms 1.21% NodesOnlyMesh::UpdateBoxCollection 122ms 0.49% 80.74% 296ms 1.20% boost::numeric::ublas::vector_inner_prod::apply (inline) 6ms 0.024% 80.77% 290ms 1.17% DistributedBoxCollection::GetProcessOwningNode 278ms 1.12% 81.89% 278ms 1.12% __gnu_cxx::__normal_iterator::operator++ (inline) 12ms 0.048% 81.94% 275ms 1.11% std::_Rb_tree::_M_emplace_hint_unique 0 0% 81.94% 267ms 1.08% std::_Rb_tree::_M_drop_node (inline) 103ms 0.42% 82.35% 263ms 1.06% std::__move_median_to_first (inline) 3ms 0.012% 82.37% 237ms 0.96% NodesOnlyMesh::AddNodesToBoxes 107ms 0.43% 82.80% 237ms 0.96% boost::shared_ptr::shared_ptr (inline) 0 0% 82.80% 235ms 0.95% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 82.80% 235ms 0.95% VtkMeshWriter::WriteFiles 2ms 0.0081% 82.81% 235ms 0.95% std::__new_allocator::deallocate (inline) 145ms 0.59% 83.39% 233ms 0.94% _int_malloc 0 0% 83.39% 232ms 0.94% std::set::~set (inline) 2ms 0.0081% 83.40% 220ms 0.89% CellPropertyCollection::HasProperty 0 0% 83.40% 220ms 0.89% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 83.40% 219ms 0.88% Cell::HasCellProperty (inline) 60ms 0.24% 83.64% 217ms 0.88% __GI___libc_free 0 0% 83.64% 216ms 0.87% std::allocator_traits::deallocate (inline) 0 0% 83.64% 213ms 0.86% std::_Rb_tree::_M_put_node (inline) 212ms 0.86% 84.50% 212ms 0.86% [libchaste_mesh.so] 23ms 0.093% 84.59% 212ms 0.86% boost::numeric::ublas::vector_reference::operator() (inline) 3ms 0.012% 84.60% 210ms 0.85% Cell::ReadyToDivide 0 0% 84.60% 209ms 0.84% vtkStreamingDemandDrivenPipeline::Update 0 0% 84.60% 209ms 0.84% vtkXMLWriterBase::Write 0 0% 84.60% 208ms 0.84% vtkDemandDrivenPipeline::ProcessRequest 0 0% 84.60% 208ms 0.84% vtkStreamingDemandDrivenPipeline::ProcessRequest 182ms 0.73% 85.34% 207ms 0.84% Node::AddNeighbour 0 0% 85.34% 207ms 0.84% vtkDemandDrivenPipeline::ExecuteData 0 0% 85.34% 205ms 0.83% vtkCompositeDataPipeline::ExecuteData 0 0% 85.34% 205ms 0.83% vtkExecutive::CallAlgorithm 0 0% 85.34% 205ms 0.83% vtkXMLUnstructuredDataWriter::ProcessRequest 203ms 0.82% 86.16% 203ms 0.82% Node::GetIndex 11ms 0.044% 86.20% 197ms 0.8% std::__insertion_sort (inline) 188ms 0.76% 86.96% 188ms 0.76% [libchaste_cell_based.so] 0 0% 86.96% 168ms 0.68% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 86.96% 168ms 0.68% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 86.96% 164ms 0.66% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 1ms 0.004% 86.97% 163ms 0.66% AbstractCellProperty::IsType (inline) 0 0% 86.97% 161ms 0.65% NodesOnlyMesh::ResizeBoxCollection 0 0% 86.97% 161ms 0.65% std::_Rb_tree::clear (inline) 9ms 0.036% 87.00% 159ms 0.64% NodesOnlyMesh::IsANodeCloseToDomainBoundary 141ms 0.57% 87.57% 157ms 0.63% _int_free 3ms 0.012% 87.58% 154ms 0.62% boost::numeric::ublas::c_vector::operator[] (inline) 1ms 0.004% 87.59% 150ms 0.61% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 1ms 0.004% 87.59% 150ms 0.61% Cell::GetCellId 142ms 0.57% 88.16% 142ms 0.57% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 0 0% 88.16% 141ms 0.57% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1ms 0.004% 88.17% 137ms 0.55% AbstractNumericalMethod::SafeNodePositionUpdate 137ms 0.55% 88.72% 137ms 0.55% __ieee754_log_fma 0 0% 88.72% 136ms 0.55% vtkXMLWriter::WriteBinaryData 0 0% 88.72% 133ms 0.54% vtkXMLWriter::WriteBinaryDataBlock 0 0% 88.72% 133ms 0.54% vtkXMLWriter::WriteBinaryDataInternal 0 0% 88.72% 132ms 0.53% vtkXMLWriter::WriteCompressionBlock 100ms 0.4% 89.13% 130ms 0.52% boost::detail::shared_count::shared_count (inline) 0 0% 89.13% 128ms 0.52% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 56ms 0.23% 89.35% 126ms 0.51% AbstractCellProperty::IsSame 126ms 0.51% 89.86% 126ms 0.51% Node::rGetLocation 0 0% 89.86% 126ms 0.51% NodeBasedCellPopulation::SetNode 0 0% 89.86% 125ms 0.5% vtkXMLWriter::WritePointsAppendedData