File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20661ms, 89.26% of 23148ms total Dropped 758 nodes (cum <= 115.74ms) flat flat% sum% cum cum% 0 0% 0% 23002ms 99.37% __libc_start_call_main 0 0% 0% 23002ms 99.37% __libc_start_main_impl 0 0% 0% 23002ms 99.37% _start 0 0% 0% 22987ms 99.30% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 22987ms 99.30% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 22987ms 99.30% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 22987ms 99.30% main 0 0% 0% 22953ms 99.16% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 22953ms 99.16% CxxTest::TestRunner::runTest (inline) 0 0% 0% 22953ms 99.16% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0043% 0.0043% 22945ms 99.12% AbstractCellBasedSimulation::Solve 2ms 0.0086% 0.013% 13030ms 56.29% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.013% 8725ms 37.69% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.017% 0.03% 8194ms 35.40% ForwardEulerNumericalMethod::UpdateAllNodePositions 12ms 0.052% 0.082% 8012ms 34.61% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.082% 7705ms 33.29% NodeBasedCellPopulation::Update 1206ms 5.21% 5.29% 7418ms 32.05% RepulsionForce::AddForceContribution (partial-inline) 4ms 0.017% 5.31% 5568ms 24.05% DistributedBoxCollection::CalculateInteriorNodePairs 2073ms 8.96% 14.26% 5018ms 21.68% std::_Rb_tree::_M_lower_bound (inline) 18ms 0.078% 14.34% 4568ms 19.73% NodeAttributes::RemoveDuplicateNeighbours 0 0% 14.34% 4550ms 19.66% OffLatticeSimulation::ApplyBoundaries 7ms 0.03% 14.37% 4279ms 18.49% std::__sort (inline) 0 0% 14.37% 4279ms 18.49% std::sort (inline) 209ms 0.9% 15.28% 3797ms 16.40% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 71ms 0.31% 15.58% 3436ms 14.84% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 3ms 0.013% 15.60% 3420ms 14.77% AbstractCellPopulation::Iterator::operator++ (inline) 174ms 0.75% 16.35% 3402ms 14.70% AbstractCellPopulation::Iterator::IsRealCell (inline) 257ms 1.11% 17.46% 3255ms 14.06% std::_Rb_tree::find (inline) 0 0% 17.46% 3255ms 14.06% std::map::find (inline) 2916ms 12.60% 30.05% 2916ms 12.60% std::_Rb_tree::_S_right (inline) 21ms 0.091% 30.15% 2914ms 12.59% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 220ms 0.95% 31.10% 2506ms 10.83% std::map::operator[] (partial-inline) 178ms 0.77% 31.86% 2410ms 10.41% std::__introsort_loop 30ms 0.13% 31.99% 2383ms 10.29% PlaneBoundaryCondition::ImposeBoundaryCondition 35ms 0.15% 32.15% 2349ms 10.15% AbstractCellPopulation::GetLocationIndexUsingCell 165ms 0.71% 32.86% 2328ms 10.06% AbstractMesh::GetNode 43ms 0.19% 33.04% 2293ms 9.91% NodesOnlyMesh::GetNodeOrHaloNode 11ms 0.048% 33.09% 2167ms 9.36% PlaneBoundaryCondition::VerifyBoundaryCondition 78ms 0.34% 33.43% 2163ms 9.34% NodesOnlyMesh::SolveNodeMapping 1ms 0.0043% 33.43% 2149ms 9.28% std::__unguarded_partition_pivot (inline) 0 0% 33.43% 2036ms 8.80% std::_Rb_tree::lower_bound (inline) 0 0% 33.43% 2036ms 8.80% std::map::lower_bound (inline) 1016ms 4.39% 37.82% 1930ms 8.34% std::__unguarded_partition (inline) 0 0% 37.82% 1859ms 8.03% std::__final_insertion_sort (inline) 159ms 0.69% 38.51% 1776ms 7.67% DistributedBoxCollection::AddPairsFromBox 94ms 0.41% 38.91% 1656ms 7.15% std::__unguarded_insertion_sort (inline) 560ms 2.42% 41.33% 1615ms 6.98% std::__unguarded_linear_insert (inline) 19ms 0.082% 41.42% 1529ms 6.61% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 25ms 0.11% 41.52% 1503ms 6.49% AbstractCellPopulation::GetCellUsingLocationIndex 1493ms 6.45% 47.97% 1493ms 6.45% __gnu_cxx::__normal_iterator::operator-- (inline) 43ms 0.19% 48.16% 1279ms 5.53% boost::numeric::ublas::c_vector::c_vector (partial-inline) 3ms 0.013% 48.17% 1193ms 5.15% DistributedBoxCollection::CalculateBoundaryNodePairs 42ms 0.18% 48.35% 1161ms 5.02% boost::numeric::ublas::vector_assign (inline) 0 0% 48.35% 1156ms 4.99% NodeBasedCellPopulation::UpdateCellProcessLocation 291ms 1.26% 49.61% 1043ms 4.51% boost::numeric::ublas::indexing_vector_assign 224ms 0.97% 50.58% 893ms 3.86% __dynamic_cast 19ms 0.082% 50.66% 839ms 3.62% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 329ms 1.42% 52.08% 772ms 3.34% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 52.08% 762ms 3.29% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 161ms 0.7% 52.78% 761ms 3.29% AbstractMesh::GetVectorFromAtoB 0 0% 52.78% 745ms 3.22% boost::numeric::ublas::norm_2 (inline) 578ms 2.50% 55.27% 745ms 3.22% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 55.27% 745ms 3.22% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 174ms 0.75% 56.03% 719ms 3.11% NodeAttributes::AddNeighbour 0 0% 56.03% 717ms 3.10% AbstractCellPopulation::WriteResultsToFiles 681ms 2.94% 58.97% 681ms 2.94% boost::numeric::ublas::c_vector::operator() 5ms 0.022% 58.99% 658ms 2.84% boost::numeric::ublas::c_vector::operator= (inline) 38ms 0.16% 59.15% 637ms 2.75% std::__copy_move::__copy_m (inline) 0 0% 59.15% 637ms 2.75% std::__copy_move_a (inline) 0 0% 59.15% 637ms 2.75% std::__copy_move_a1 (inline) 0 0% 59.15% 637ms 2.75% std::__copy_move_a2 (inline) 0 0% 59.15% 637ms 2.75% std::copy (inline) 619ms 2.67% 61.83% 619ms 2.67% __memcpy_avx_unaligned_erms 541ms 2.34% 64.17% 614ms 2.65% std::vector::push_back (inline) 4ms 0.017% 64.18% 582ms 2.51% AbstractCellBasedSimulation::DoCellBirth 249ms 1.08% 65.26% 553ms 2.39% __cxxabiv1::__si_class_type_info::__do_dyncast 46ms 0.2% 65.46% 534ms 2.31% std::_Rb_tree_const_iterator::operator++ (inline) 4ms 0.017% 65.47% 526ms 2.27% AbstractCentreBasedCellPopulation::GetDampingConstant 7ms 0.03% 65.50% 526ms 2.27% CellPropertyCollection::GetPropertiesType (inline) 30ms 0.13% 65.63% 509ms 2.20% boost::detail::shared_count::~shared_count (inline) 0 0% 65.63% 509ms 2.20% boost::shared_ptr::~shared_ptr (inline) 489ms 2.11% 67.75% 489ms 2.11% std::_Rb_tree_increment 479ms 2.07% 69.82% 479ms 2.07% boost::numeric::ublas::same_impl_ex 2ms 0.0086% 69.82% 473ms 2.04% NodeBasedCellPopulation::WriteVtkResultsToFile 464ms 2.00% 71.83% 469ms 2.03% boost::detail::sp_counted_base::release 459ms 1.98% 73.81% 459ms 1.98% __strcmp_avx2 61ms 0.26% 74.08% 459ms 1.98% std::__new_allocator::allocate (inline) 23ms 0.099% 74.17% 455ms 1.97% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 74.17% 444ms 1.92% std::allocator_traits::allocate (inline) 0 0% 74.17% 437ms 1.89% AbstractCellBasedSimulation::DoCellRemoval (inline) 6ms 0.026% 74.20% 425ms 1.84% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 74.20% 425ms 1.84% std::_Rb_tree::_M_create_node (inline) 45ms 0.19% 74.40% 417ms 1.80% std::_Rb_tree::_M_copy (inline) 26ms 0.11% 74.51% 398ms 1.72% operator new 108ms 0.47% 74.97% 383ms 1.65% std::_Rb_tree::_M_erase 0 0% 74.97% 377ms 1.63% std::_Rb_tree::_M_get_node (inline) 4ms 0.017% 74.99% 376ms 1.62% AbstractCellProperty::IsSubType (inline) 0 0% 74.99% 373ms 1.61% boost::numeric::ublas::c_vector::assign (inline) 110ms 0.48% 75.47% 370ms 1.60% __GI___libc_malloc 123ms 0.53% 76.00% 370ms 1.60% std::_Rb_tree::_M_clone_node (inline) 2ms 0.0086% 76.01% 361ms 1.56% std::set::set (inline) 2ms 0.0086% 76.02% 357ms 1.54% Cell::GetMutationState 121ms 0.52% 76.54% 354ms 1.53% Node::GetRadius 331ms 1.43% 77.97% 331ms 1.43% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 8ms 0.035% 78.00% 315ms 1.36% NodeBasedCellPopulation::UpdateMapsAfterRemesh 24ms 0.1% 78.11% 307ms 1.33% boost::numeric::ublas::vector_binary::size (inline) 0 0% 78.11% 300ms 1.30% NodesOnlyMesh::ReMesh 0 0% 78.11% 298ms 1.29% boost::numeric::ublas::inner_prod (inline) 22ms 0.095% 78.20% 298ms 1.29% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 78.20% 298ms 1.29% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 78.20% 293ms 1.27% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 4ms 0.017% 78.22% 293ms 1.27% NodesOnlyMesh::UpdateNodeIndices 0 0% 78.22% 293ms 1.27% std::_Rb_tree::_Alloc_node::operator() (inline) 4ms 0.017% 78.24% 282ms 1.22% DistributedBoxCollection::GetProcessOwningNode 25ms 0.11% 78.34% 268ms 1.16% std::_Rb_tree::~_Rb_tree (inline) 0 0% 78.34% 262ms 1.13% std::_Rb_tree::_M_drop_node (inline) 261ms 1.13% 79.47% 261ms 1.13% std::__adjacent_find (inline) 0 0% 79.47% 261ms 1.13% std::__unique (inline) 0 0% 79.47% 261ms 1.13% std::unique (inline) 0 0% 79.47% 255ms 1.10% NodesOnlyMesh::UpdateBoxCollection 7ms 0.03% 79.50% 250ms 1.08% std::_Rb_tree::_M_emplace_hint_unique 242ms 1.05% 80.55% 242ms 1.05% __gnu_cxx::__normal_iterator::operator++ (inline) 234ms 1.01% 81.56% 234ms 1.01% Node::CheckForNodeAttributes 3ms 0.013% 81.57% 228ms 0.98% std::__new_allocator::deallocate (inline) 0 0% 81.57% 227ms 0.98% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 81.57% 226ms 0.98% VtkMeshWriter::WriteFiles 90ms 0.39% 81.96% 222ms 0.96% boost::numeric::ublas::vector_inner_prod::apply (inline) 98ms 0.42% 82.38% 214ms 0.92% std::__move_median_to_first (inline) 0 0% 82.38% 211ms 0.91% NodesOnlyMesh::ResizeBoxCollection 128ms 0.55% 82.94% 211ms 0.91% _int_malloc 1ms 0.0043% 82.94% 210ms 0.91% NodesOnlyMesh::AddNodesToBoxes 11ms 0.048% 82.99% 210ms 0.91% NodesOnlyMesh::IsANodeCloseToDomainBoundary 20ms 0.086% 83.07% 203ms 0.88% std::__insertion_sort (inline) 75ms 0.32% 83.40% 201ms 0.87% __GI___libc_free 0 0% 83.40% 201ms 0.87% std::allocator_traits::deallocate (inline) 0 0% 83.40% 199ms 0.86% std::_Rb_tree::_M_put_node (inline) 0 0% 83.40% 198ms 0.86% vtkDemandDrivenPipeline::ExecuteData 0 0% 83.40% 198ms 0.86% vtkDemandDrivenPipeline::ProcessRequest 0 0% 83.40% 198ms 0.86% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 83.40% 198ms 0.86% vtkStreamingDemandDrivenPipeline::Update 0 0% 83.40% 198ms 0.86% vtkXMLWriterBase::Write 0 0% 83.40% 197ms 0.85% vtkCompositeDataPipeline::ExecuteData 0 0% 83.40% 197ms 0.85% vtkExecutive::CallAlgorithm 0 0% 83.40% 197ms 0.85% vtkXMLUnstructuredDataWriter::ProcessRequest 109ms 0.47% 83.87% 191ms 0.83% boost::shared_ptr::shared_ptr (inline) 0 0% 83.87% 184ms 0.79% std::set::~set (inline) 180ms 0.78% 84.65% 180ms 0.78% [libchaste_cell_based.so] 0 0% 84.65% 177ms 0.76% Cell::HasCellProperty (inline) 1ms 0.0043% 84.65% 177ms 0.76% CellPropertyCollection::HasProperty 171ms 0.74% 85.39% 171ms 0.74% Node::GetIndex 0 0% 85.39% 170ms 0.73% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.39% 170ms 0.73% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 85.39% 166ms 0.72% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 8ms 0.035% 85.42% 161ms 0.7% Cell::ReadyToDivide 159ms 0.69% 86.11% 159ms 0.69% Node::IsDeleted 0 0% 86.11% 157ms 0.68% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 86.11% 154ms 0.67% std::_Rb_tree::clear (inline) 55ms 0.24% 86.35% 153ms 0.66% Node::AddNeighbour 6ms 0.026% 86.37% 151ms 0.65% AbstractCellProperty::IsType (inline) 145ms 0.63% 87.00% 145ms 0.63% [libchaste_mesh.so] 7ms 0.03% 87.03% 144ms 0.62% DistributedBoxCollection::GetIsPeriodicAllDims 5ms 0.022% 87.05% 143ms 0.62% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 87.05% 140ms 0.6% vtkXMLWriter::WriteBinaryData 1ms 0.0043% 87.06% 137ms 0.59% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 3ms 0.013% 87.07% 136ms 0.59% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 87.07% 136ms 0.59% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.07% 136ms 0.59% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.07% 136ms 0.59% vtkXMLWriter::WriteCompressionBlock 9ms 0.039% 87.11% 134ms 0.58% boost::numeric::ublas::vector_reference::operator() (inline) 132ms 0.57% 87.68% 132ms 0.57% boost::shared_ptr::operator-> (inline) 0 0% 87.68% 132ms 0.57% std::_Rb_tree::_Auto_node::_Auto_node (inline) 127ms 0.55% 88.23% 128ms 0.55% Node::ConstructNodeAttributes (inline) 115ms 0.5% 88.72% 125ms 0.54% _int_free 0 0% 88.72% 124ms 0.54% vtkXMLWriter::WritePointsAppendedData 0 0% 88.72% 123ms 0.53% Cell::GetCellId 6ms 0.026% 88.75% 122ms 0.53% NodeBasedCellPopulation::SetNode 0 0% 88.75% 119ms 0.51% tbb::detail::r1::parallel_pipeline 117ms 0.51% 89.26% 117ms 0.51% Node::rGetLocation 0 0% 89.26% 116ms 0.5% std::map::clear (inline)