File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20609ms, 88.15% of 23380ms total Dropped 797 nodes (cum <= 116.90ms) flat flat% sum% cum cum% 0 0% 0% 23235ms 99.38% __libc_start_call_main 0 0% 0% 23235ms 99.38% __libc_start_main_impl 0 0% 0% 23235ms 99.38% _start 0 0% 0% 23220ms 99.32% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 23220ms 99.32% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 23220ms 99.32% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 23220ms 99.32% main 0 0% 0% 23183ms 99.16% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 23183ms 99.16% CxxTest::TestRunner::runTest (inline) 0 0% 0% 23183ms 99.16% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0043% 0.0043% 23176ms 99.13% AbstractCellBasedSimulation::Solve 1ms 0.0043% 0.0086% 13146ms 56.23% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0086% 8840ms 37.81% AbstractCellBasedSimulation::UpdateCellPopulation 5ms 0.021% 0.03% 8301ms 35.50% ForwardEulerNumericalMethod::UpdateAllNodePositions 11ms 0.047% 0.077% 8120ms 34.73% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.077% 7820ms 33.45% NodeBasedCellPopulation::Update 1186ms 5.07% 5.15% 7489ms 32.03% RepulsionForce::AddForceContribution (partial-inline) 7ms 0.03% 5.18% 5693ms 24.35% DistributedBoxCollection::CalculateInteriorNodePairs 2106ms 9.01% 14.19% 4940ms 21.13% std::_Rb_tree::_M_lower_bound (inline) 0 0% 14.19% 4568ms 19.54% OffLatticeSimulation::ApplyBoundaries 27ms 0.12% 14.30% 4525ms 19.35% NodeAttributes::RemoveDuplicateNeighbours 3ms 0.013% 14.32% 4226ms 18.08% std::__sort (inline) 0 0% 14.32% 4226ms 18.08% std::sort (inline) 189ms 0.81% 15.12% 3694ms 15.80% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 4ms 0.017% 15.14% 3486ms 14.91% AbstractCellPopulation::Iterator::operator++ (inline) 51ms 0.22% 15.36% 3486ms 14.91% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 185ms 0.79% 16.15% 3462ms 14.81% AbstractCellPopulation::Iterator::IsRealCell (inline) 252ms 1.08% 17.23% 3247ms 13.89% std::_Rb_tree::find (inline) 0 0% 17.23% 3246ms 13.88% std::map::find (inline) 19ms 0.081% 17.31% 2945ms 12.60% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2780ms 11.89% 29.20% 2780ms 11.89% std::_Rb_tree::_S_right (inline) 240ms 1.03% 30.23% 2468ms 10.56% std::map::operator[] (partial-inline) 178ms 0.76% 30.99% 2440ms 10.44% std::__introsort_loop 33ms 0.14% 31.13% 2391ms 10.23% PlaneBoundaryCondition::ImposeBoundaryCondition 19ms 0.081% 31.21% 2362ms 10.10% AbstractCellPopulation::GetLocationIndexUsingCell 141ms 0.6% 31.81% 2262ms 9.67% AbstractMesh::GetNode 51ms 0.22% 32.03% 2243ms 9.59% NodesOnlyMesh::GetNodeOrHaloNode 2ms 0.0086% 32.04% 2182ms 9.33% std::__unguarded_partition_pivot (inline) 13ms 0.056% 32.10% 2177ms 9.31% PlaneBoundaryCondition::VerifyBoundaryCondition 73ms 0.31% 32.41% 2124ms 9.08% NodesOnlyMesh::SolveNodeMapping 0 0% 32.41% 1969ms 8.42% std::_Rb_tree::lower_bound (inline) 0 0% 32.41% 1969ms 8.42% std::map::lower_bound (inline) 1036ms 4.43% 36.84% 1949ms 8.34% std::__unguarded_partition (inline) 203ms 0.87% 37.71% 1902ms 8.14% DistributedBoxCollection::AddPairsFromBox 0 0% 37.71% 1781ms 7.62% std::__final_insertion_sort (inline) 84ms 0.36% 38.07% 1593ms 6.81% std::__unguarded_insertion_sort (inline) 24ms 0.1% 38.17% 1565ms 6.69% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 31ms 0.13% 38.30% 1536ms 6.57% AbstractCellPopulation::GetCellUsingLocationIndex 519ms 2.22% 40.52% 1533ms 6.56% std::__unguarded_linear_insert (inline) 1457ms 6.23% 46.75% 1457ms 6.23% __gnu_cxx::__normal_iterator::operator-- (inline) 38ms 0.16% 46.92% 1325ms 5.67% boost::numeric::ublas::c_vector::c_vector (partial-inline) 43ms 0.18% 47.10% 1205ms 5.15% boost::numeric::ublas::vector_assign (inline) 4ms 0.017% 47.12% 1171ms 5.01% DistributedBoxCollection::CalculateBoundaryNodePairs 1ms 0.0043% 47.12% 1157ms 4.95% NodeBasedCellPopulation::UpdateCellProcessLocation 270ms 1.15% 48.28% 1070ms 4.58% boost::numeric::ublas::indexing_vector_assign 232ms 0.99% 49.27% 877ms 3.75% __dynamic_cast 163ms 0.7% 49.97% 836ms 3.58% AbstractMesh::GetVectorFromAtoB 15ms 0.064% 50.03% 816ms 3.49% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 346ms 1.48% 51.51% 775ms 3.31% DistributedBoxCollection::CalculateContainingBox (partial-inline) 264ms 1.13% 52.64% 764ms 3.27% NodeAttributes::AddNeighbour 0 0% 52.64% 751ms 3.21% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 52.64% 723ms 3.09% AbstractCellPopulation::WriteResultsToFiles 0 0% 52.64% 721ms 3.08% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 52.64% 720ms 3.08% boost::numeric::ublas::norm_2 (inline) 562ms 2.40% 55.04% 720ms 3.08% boost::numeric::ublas::vector_norm_2::apply (inline) 9ms 0.038% 55.08% 683ms 2.92% boost::numeric::ublas::c_vector::operator= (inline) 666ms 2.85% 57.93% 666ms 2.85% boost::numeric::ublas::c_vector::operator() 33ms 0.14% 58.07% 661ms 2.83% std::__copy_move::__copy_m (inline) 0 0% 58.07% 661ms 2.83% std::__copy_move_a (inline) 0 0% 58.07% 661ms 2.83% std::__copy_move_a1 (inline) 0 0% 58.07% 661ms 2.83% std::__copy_move_a2 (inline) 0 0% 58.07% 661ms 2.83% std::copy (inline) 643ms 2.75% 60.82% 643ms 2.75% __memcpy_avx_unaligned_erms 497ms 2.13% 62.95% 593ms 2.54% std::vector::push_back (inline) 6ms 0.026% 62.97% 568ms 2.43% CellPropertyCollection::GetPropertiesType (inline) 40ms 0.17% 63.14% 567ms 2.43% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.0086% 63.15% 561ms 2.40% AbstractCellBasedSimulation::DoCellBirth 1ms 0.0043% 63.16% 552ms 2.36% AbstractCentreBasedCellPopulation::GetDampingConstant 237ms 1.01% 64.17% 545ms 2.33% __cxxabiv1::__si_class_type_info::__do_dyncast 520ms 2.22% 66.39% 520ms 2.22% std::_Rb_tree_increment 37ms 0.16% 66.55% 519ms 2.22% boost::detail::shared_count::~shared_count (inline) 0 0% 66.55% 519ms 2.22% boost::shared_ptr::~shared_ptr (inline) 59ms 0.25% 66.80% 507ms 2.17% std::__new_allocator::allocate (inline) 19ms 0.081% 66.89% 502ms 2.15% std::_Rb_tree::_Rb_tree (partial-inline) 500ms 2.14% 69.02% 500ms 2.14% boost::numeric::ublas::same_impl_ex 0 0% 69.02% 490ms 2.10% std::allocator_traits::allocate (inline) 472ms 2.02% 71.04% 478ms 2.04% boost::detail::sp_counted_base::release 2ms 0.0086% 71.05% 477ms 2.04% NodeBasedCellPopulation::WriteVtkResultsToFile 52ms 0.22% 71.27% 472ms 2.02% std::_Rb_tree::_M_copy (inline) 0 0% 71.27% 467ms 2.00% std::_Rb_tree::_M_create_node (inline) 0 0% 71.27% 458ms 1.96% AbstractCellBasedSimulation::DoCellRemoval (inline) 450ms 1.92% 73.20% 450ms 1.92% __strcmp_avx2 29ms 0.12% 73.32% 438ms 1.87% operator new 6ms 0.026% 73.35% 437ms 1.87% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 162ms 0.69% 74.04% 427ms 1.83% Node::GetRadius 2ms 0.0086% 74.05% 420ms 1.80% std::set::set (inline) 149ms 0.64% 74.69% 416ms 1.78% std::_Rb_tree::_M_clone_node (inline) 0 0% 74.69% 413ms 1.77% std::_Rb_tree::_M_get_node (inline) 1ms 0.0043% 74.69% 403ms 1.72% Cell::GetMutationState 104ms 0.44% 75.14% 397ms 1.70% __GI___libc_malloc 116ms 0.5% 75.63% 384ms 1.64% std::_Rb_tree::_M_erase 1ms 0.0043% 75.64% 380ms 1.63% AbstractCellProperty::IsSubType (inline) 39ms 0.17% 75.80% 366ms 1.57% boost::numeric::ublas::vector_binary::size (inline) 0 0% 75.80% 347ms 1.48% boost::numeric::ublas::c_vector::assign (inline) 0 0% 75.80% 325ms 1.39% std::_Rb_tree::_Alloc_node::operator() (inline) 9ms 0.038% 75.84% 313ms 1.34% NodeBasedCellPopulation::UpdateMapsAfterRemesh 48ms 0.21% 76.05% 313ms 1.34% std::_Rb_tree::~_Rb_tree (inline) 310ms 1.33% 77.37% 310ms 1.33% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 77.37% 298ms 1.27% NodesOnlyMesh::ReMesh 0 0% 77.37% 298ms 1.27% boost::numeric::ublas::inner_prod (inline) 1ms 0.0043% 77.38% 298ms 1.27% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 18ms 0.077% 77.46% 297ms 1.27% boost::numeric::ublas::vector_scalar_binary::evaluate 5ms 0.021% 77.48% 286ms 1.22% NodesOnlyMesh::UpdateNodeIndices 276ms 1.18% 78.66% 276ms 1.18% __gnu_cxx::__normal_iterator::operator++ (inline) 2ms 0.0086% 78.67% 273ms 1.17% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 269ms 1.15% 79.82% 269ms 1.15% Node::CheckForNodeAttributes 0 0% 79.82% 262ms 1.12% std::_Rb_tree::_M_drop_node (inline) 14ms 0.06% 79.88% 259ms 1.11% std::_Rb_tree::_M_emplace_hint_unique 0 0% 79.88% 256ms 1.09% NodesOnlyMesh::UpdateBoxCollection 3ms 0.013% 79.89% 254ms 1.09% DistributedBoxCollection::GetProcessOwningNode 249ms 1.07% 80.95% 250ms 1.07% std::__adjacent_find (inline) 0 0% 80.95% 250ms 1.07% std::__unique (inline) 0 0% 80.95% 250ms 1.07% std::unique (inline) 1ms 0.0043% 80.96% 240ms 1.03% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 80.96% 239ms 1.02% std::set::~set (inline) 0 0% 80.96% 238ms 1.02% VtkMeshWriter::WriteFiles 140ms 0.6% 81.56% 232ms 0.99% _int_malloc 87ms 0.37% 81.93% 231ms 0.99% boost::numeric::ublas::vector_inner_prod::apply (inline) 110ms 0.47% 82.40% 226ms 0.97% std::__move_median_to_first (inline) 0 0% 82.40% 219ms 0.94% NodesOnlyMesh::AddNodesToBoxes 3ms 0.013% 82.41% 219ms 0.94% std::__new_allocator::deallocate (inline) 0 0% 82.41% 213ms 0.91% vtkStreamingDemandDrivenPipeline::Update 0 0% 82.41% 213ms 0.91% vtkXMLWriterBase::Write 0 0% 82.41% 212ms 0.91% vtkDemandDrivenPipeline::ProcessRequest 0 0% 82.41% 209ms 0.89% NodesOnlyMesh::ResizeBoxCollection 123ms 0.53% 82.94% 209ms 0.89% boost::shared_ptr::shared_ptr (inline) 13ms 0.056% 82.99% 208ms 0.89% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 82.99% 208ms 0.89% vtkDemandDrivenPipeline::ExecuteData 0 0% 82.99% 208ms 0.89% vtkExecutive::CallAlgorithm 0 0% 82.99% 208ms 0.89% vtkStreamingDemandDrivenPipeline::ProcessRequest 1ms 0.0043% 83.00% 208ms 0.89% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 83.00% 207ms 0.89% vtkCompositeDataPipeline::ExecuteData 61ms 0.26% 83.26% 200ms 0.86% __GI___libc_free 0 0% 83.26% 197ms 0.84% std::allocator_traits::deallocate (inline) 0 0% 83.26% 195ms 0.83% std::_Rb_tree::_M_put_node (inline) 15ms 0.064% 83.32% 188ms 0.8% std::__insertion_sort (inline) 185ms 0.79% 84.11% 185ms 0.79% [libchaste_cell_based.so] 178ms 0.76% 84.88% 178ms 0.76% Node::GetIndex 0 0% 84.88% 175ms 0.75% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 84.88% 175ms 0.75% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 84.88% 168ms 0.72% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 3ms 0.013% 84.89% 165ms 0.71% CellPropertyCollection::HasProperty 0 0% 84.89% 163ms 0.7% Cell::HasCellProperty (inline) 4ms 0.017% 84.91% 156ms 0.67% Cell::ReadyToDivide 150ms 0.64% 85.55% 150ms 0.64% [libchaste_mesh.so] 71ms 0.3% 85.85% 146ms 0.62% Node::AddNeighbour 3ms 0.013% 85.86% 145ms 0.62% DistributedBoxCollection::GetIsPeriodicAllDims 0 0% 85.86% 142ms 0.61% std::_Rb_tree::_Auto_node::_Auto_node (inline) 123ms 0.53% 86.39% 139ms 0.59% _int_free 0 0% 86.39% 139ms 0.59% vtkXMLWriter::WriteBinaryData 0 0% 86.39% 137ms 0.59% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 2ms 0.0086% 86.40% 136ms 0.58% AbstractCellProperty::IsType (inline) 0 0% 86.40% 136ms 0.58% std::_Rb_tree::clear (inline) 0 0% 86.40% 135ms 0.58% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 135ms 0.58% 86.98% 135ms 0.58% boost::shared_ptr::operator-> (inline) 133ms 0.57% 87.54% 133ms 0.57% Node::IsDeleted 0 0% 87.54% 132ms 0.56% vtkXMLWriter::WriteBinaryDataInternal 12ms 0.051% 87.60% 131ms 0.56% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 87.60% 131ms 0.56% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.60% 131ms 0.56% vtkXMLWriter::WriteCompressionBlock 0 0% 87.60% 129ms 0.55% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 87.60% 128ms 0.55% vtkXMLWriter::WritePointsAppendedData 1ms 0.0043% 87.60% 126ms 0.54% AbstractCellPopulation::SetCellUsingLocationIndex 5ms 0.021% 87.62% 125ms 0.53% AbstractNumericalMethod::SafeNodePositionUpdate 2ms 0.0086% 87.63% 118ms 0.5% Cell::GetCellId 118ms 0.5% 88.14% 118ms 0.5% Node::rGetLocation 3ms 0.013% 88.15% 117ms 0.5% boost::numeric::ublas::c_vector::operator[] (inline)