File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 22969ms, 89.74% of 25594ms total Dropped 820 nodes (cum <= 127.97ms) flat flat% sum% cum cum% 0 0% 0% 25471ms 99.52% __libc_start_call_main 0 0% 0% 25471ms 99.52% __libc_start_main_impl 0 0% 0% 25471ms 99.52% _start 0 0% 0% 25454ms 99.45% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 25454ms 99.45% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 25454ms 99.45% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 25454ms 99.45% main 0 0% 0% 25411ms 99.28% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 25411ms 99.28% CxxTest::TestRunner::runTest (inline) 0 0% 0% 25410ms 99.28% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 25402ms 99.25% AbstractCellBasedSimulation::Solve 4ms 0.016% 0.016% 14356ms 56.09% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.016% 9772ms 38.18% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0039% 0.02% 9359ms 36.57% ForwardEulerNumericalMethod::UpdateAllNodePositions 14ms 0.055% 0.074% 9164ms 35.81% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.074% 8596ms 33.59% NodeBasedCellPopulation::Update 1308ms 5.11% 5.18% 8331ms 32.55% RepulsionForce::AddForceContribution (partial-inline) 11ms 0.043% 5.23% 6293ms 24.59% DistributedBoxCollection::CalculateInteriorNodePairs 2148ms 8.39% 13.62% 5242ms 20.48% std::_Rb_tree::_M_lower_bound (inline) 11ms 0.043% 13.66% 4830ms 18.87% NodeAttributes::RemoveDuplicateNeighbours 1ms 0.0039% 13.67% 4633ms 18.10% OffLatticeSimulation::ApplyBoundaries 5ms 0.02% 13.69% 4503ms 17.59% std::__sort (inline) 0 0% 13.69% 4503ms 17.59% std::sort (inline) 212ms 0.83% 14.52% 4167ms 16.28% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 306ms 1.20% 15.71% 3480ms 13.60% std::_Rb_tree::find (inline) 0 0% 15.71% 3480ms 13.60% std::map::find (inline) 74ms 0.29% 16.00% 3409ms 13.32% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 5ms 0.02% 16.02% 3166ms 12.37% AbstractCellPopulation::Iterator::operator++ (inline) 145ms 0.57% 16.59% 3139ms 12.26% AbstractCellPopulation::Iterator::IsRealCell 3058ms 11.95% 28.53% 3058ms 11.95% std::_Rb_tree::_S_right (inline) 30ms 0.12% 28.65% 2739ms 10.70% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 213ms 0.83% 29.48% 2712ms 10.60% std::__introsort_loop 190ms 0.74% 30.23% 2620ms 10.24% std::map::operator[] (partial-inline) 167ms 0.65% 30.88% 2550ms 9.96% AbstractMesh::GetNode 55ms 0.21% 31.09% 2515ms 9.83% NodesOnlyMesh::GetNodeOrHaloNode 17ms 0.066% 31.16% 2432ms 9.50% PlaneBoundaryCondition::ImposeBoundaryCondition 0 0% 31.16% 2415ms 9.44% std::__unguarded_partition_pivot (inline) 115ms 0.45% 31.61% 2388ms 9.33% NodesOnlyMesh::SolveNodeMapping 47ms 0.18% 31.79% 2269ms 8.87% AbstractCellPopulation::GetLocationIndexUsingCell 148ms 0.58% 32.37% 2259ms 8.83% DistributedBoxCollection::AddPairsFromBox 19ms 0.074% 32.45% 2199ms 8.59% PlaneBoundaryCondition::VerifyBoundaryCondition 1081ms 4.22% 36.67% 2119ms 8.28% std::__unguarded_partition (inline) 0 0% 36.67% 2099ms 8.20% std::_Rb_tree::lower_bound (inline) 0 0% 36.67% 2099ms 8.20% std::map::lower_bound (inline) 1ms 0.0039% 36.67% 1785ms 6.97% std::__final_insertion_sort (inline) 21ms 0.082% 36.75% 1779ms 6.95% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 26ms 0.1% 36.86% 1750ms 6.84% AbstractCellPopulation::GetCellUsingLocationIndex 97ms 0.38% 37.24% 1604ms 6.27% std::__unguarded_insertion_sort (inline) 589ms 2.30% 39.54% 1554ms 6.07% std::__unguarded_linear_insert (inline) 1440ms 5.63% 45.16% 1440ms 5.63% __gnu_cxx::__normal_iterator::operator-- (inline) 55ms 0.21% 45.38% 1300ms 5.08% boost::numeric::ublas::c_vector::c_vector (partial-inline) 8ms 0.031% 45.41% 1297ms 5.07% DistributedBoxCollection::CalculateBoundaryNodePairs 0 0% 45.41% 1207ms 4.72% NodeBasedCellPopulation::UpdateCellProcessLocation 13ms 0.051% 45.46% 1145ms 4.47% boost::numeric::ublas::vector_assign (inline) 213ms 0.83% 46.29% 1056ms 4.13% boost::numeric::ublas::indexing_vector_assign 13ms 0.051% 46.34% 982ms 3.84% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 302ms 1.18% 47.52% 947ms 3.70% __dynamic_cast 0 0% 47.52% 923ms 3.61% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 47.52% 905ms 3.54% boost::numeric::ublas::norm_2 (inline) 712ms 2.78% 50.30% 905ms 3.54% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 50.30% 905ms 3.54% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 24ms 0.094% 50.40% 883ms 3.45% std::_Rb_tree_const_iterator::operator++ (inline) 394ms 1.54% 51.94% 853ms 3.33% DistributedBoxCollection::CalculateContainingBox (partial-inline) 177ms 0.69% 52.63% 848ms 3.31% AbstractMesh::GetVectorFromAtoB 3ms 0.012% 52.64% 839ms 3.28% boost::numeric::ublas::c_vector::operator= (inline) 831ms 3.25% 55.89% 831ms 3.25% std::_Rb_tree_increment 29ms 0.11% 56.00% 818ms 3.20% std::__copy_move::__copy_m (inline) 0 0% 56.00% 818ms 3.20% std::__copy_move_a (inline) 0 0% 56.00% 818ms 3.20% std::__copy_move_a1 (inline) 0 0% 56.00% 818ms 3.20% std::__copy_move_a2 (inline) 0 0% 56.00% 818ms 3.20% std::copy (inline) 810ms 3.16% 59.17% 810ms 3.16% __memcpy_avx_unaligned_erms 172ms 0.67% 59.84% 797ms 3.11% NodeAttributes::AddNeighbour 0 0% 59.84% 768ms 3.00% AbstractCellPopulation::WriteResultsToFiles 12ms 0.047% 59.89% 750ms 2.93% CellPropertyCollection::GetPropertiesType (inline) 5ms 0.02% 59.90% 729ms 2.85% AbstractCentreBasedCellPopulation::GetDampingConstant 722ms 2.82% 62.73% 722ms 2.82% boost::numeric::ublas::c_vector::operator() 625ms 2.44% 65.17% 717ms 2.80% std::vector::push_back (inline) 2ms 0.0078% 65.18% 704ms 2.75% AbstractCellBasedSimulation::DoCellBirth 90ms 0.35% 65.53% 571ms 2.23% std::__new_allocator::allocate (inline) 60ms 0.23% 65.76% 562ms 2.20% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 65.76% 550ms 2.15% std::allocator_traits::allocate (inline) 543ms 2.12% 67.88% 543ms 2.12% boost::numeric::ublas::same_impl_ex 264ms 1.03% 68.91% 530ms 2.07% __cxxabiv1::__si_class_type_info::__do_dyncast 3ms 0.012% 68.93% 520ms 2.03% Cell::GetMutationState 0 0% 68.93% 513ms 2.00% std::_Rb_tree::_M_create_node (inline) 0 0% 68.93% 512ms 2.00% NodeBasedCellPopulation::WriteVtkResultsToFile 47ms 0.18% 69.11% 502ms 1.96% boost::detail::shared_count::~shared_count (inline) 0 0% 69.11% 502ms 1.96% boost::shared_ptr::~shared_ptr (inline) 47ms 0.18% 69.29% 489ms 1.91% std::_Rb_tree::_M_copy (inline) 21ms 0.082% 69.38% 477ms 1.86% operator new 0 0% 69.38% 471ms 1.84% AbstractCellBasedSimulation::DoCellRemoval (inline) 3ms 0.012% 69.39% 466ms 1.82% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 69.39% 463ms 1.81% std::_Rb_tree::_M_get_node (inline) 6ms 0.023% 69.41% 462ms 1.81% std::set::set (inline) 113ms 0.44% 69.85% 447ms 1.75% __GI___libc_malloc 5ms 0.02% 69.87% 440ms 1.72% AbstractCellProperty::IsSubType (inline) 429ms 1.68% 71.55% 440ms 1.72% boost::detail::sp_counted_base::release 136ms 0.53% 72.08% 435ms 1.70% std::_Rb_tree::_M_erase 148ms 0.58% 72.66% 432ms 1.69% std::_Rb_tree::_M_clone_node (inline) 422ms 1.65% 74.31% 422ms 1.65% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 419ms 1.64% 75.94% 419ms 1.64% __strcmp_avx2 110ms 0.43% 76.37% 402ms 1.57% boost::numeric::ublas::vector_binary::size (inline) 1ms 0.0039% 76.38% 390ms 1.52% NodesOnlyMesh::ReMesh 69ms 0.27% 76.65% 388ms 1.52% Node::GetRadius 1ms 0.0039% 76.65% 381ms 1.49% NodesOnlyMesh::UpdateNodeIndices 0 0% 76.65% 351ms 1.37% boost::numeric::ublas::inner_prod (inline) 1ms 0.0039% 76.65% 350ms 1.37% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 76.65% 349ms 1.36% boost::numeric::ublas::c_vector::assign (inline) 14ms 0.055% 76.71% 349ms 1.36% boost::numeric::ublas::vector_scalar_binary::evaluate 338ms 1.32% 78.03% 338ms 1.32% Node::CheckForNodeAttributes 12ms 0.047% 78.08% 331ms 1.29% std::_Rb_tree::_M_emplace_hint_unique 52ms 0.2% 78.28% 328ms 1.28% std::_Rb_tree::~_Rb_tree (inline) 0 0% 78.28% 322ms 1.26% Cell::HasCellProperty (inline) 1ms 0.0039% 78.28% 322ms 1.26% CellPropertyCollection::HasProperty 11ms 0.043% 78.33% 321ms 1.25% Cell::ReadyToDivide 0 0% 78.33% 320ms 1.25% std::_Rb_tree::_Alloc_node::operator() (inline) 312ms 1.22% 79.55% 312ms 1.22% [libchaste_mesh.so] 8ms 0.031% 79.58% 301ms 1.18% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 6ms 0.023% 79.60% 295ms 1.15% NodeBasedCellPopulation::UpdateMapsAfterRemesh 291ms 1.14% 80.74% 292ms 1.14% std::__adjacent_find (inline) 99ms 0.39% 81.12% 292ms 1.14% std::__move_median_to_first (inline) 0 0% 81.12% 292ms 1.14% std::__unique (inline) 0 0% 81.12% 292ms 1.14% std::unique (inline) 0 0% 81.12% 290ms 1.13% NodesOnlyMesh::UpdateBoxCollection 157ms 0.61% 81.74% 288ms 1.13% _int_malloc 8ms 0.031% 81.77% 284ms 1.11% DistributedBoxCollection::GetProcessOwningNode 0 0% 81.77% 284ms 1.11% std::_Rb_tree::_M_drop_node (inline) 140ms 0.55% 82.32% 281ms 1.10% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 82.32% 253ms 0.99% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 82.32% 251ms 0.98% VtkMeshWriter::WriteFiles 138ms 0.54% 82.86% 244ms 0.95% Node::AddNeighbour 3ms 0.012% 82.87% 239ms 0.93% std::__new_allocator::deallocate (inline) 0 0% 82.87% 238ms 0.93% std::set::~set (inline) 234ms 0.91% 83.78% 234ms 0.91% __gnu_cxx::__normal_iterator::operator++ (inline) 111ms 0.43% 84.22% 232ms 0.91% boost::shared_ptr::shared_ptr (inline) 4ms 0.016% 84.23% 231ms 0.9% NodesOnlyMesh::AddNodesToBoxes 0 0% 84.23% 229ms 0.89% vtkStreamingDemandDrivenPipeline::Update 0 0% 84.23% 229ms 0.89% vtkXMLWriterBase::Write 0 0% 84.23% 226ms 0.88% vtkDemandDrivenPipeline::ProcessRequest 225ms 0.88% 85.11% 225ms 0.88% Node::GetIndex 0 0% 85.11% 225ms 0.88% std::allocator_traits::deallocate (inline) 0 0% 85.11% 225ms 0.88% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 85.11% 224ms 0.88% vtkDemandDrivenPipeline::ExecuteData 0 0% 85.11% 223ms 0.87% std::_Rb_tree::_M_put_node (inline) 0 0% 85.11% 221ms 0.86% vtkCompositeDataPipeline::ExecuteData 0 0% 85.11% 221ms 0.86% vtkExecutive::CallAlgorithm 0 0% 85.11% 221ms 0.86% vtkXMLUnstructuredDataWriter::ProcessRequest 67ms 0.26% 85.37% 208ms 0.81% __GI___libc_free 0 0% 85.37% 197ms 0.77% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 85.37% 193ms 0.75% std::_Rb_tree::_Auto_node::_Auto_node (inline) 10ms 0.039% 85.41% 192ms 0.75% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 85.41% 185ms 0.72% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.41% 185ms 0.72% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 2ms 0.0078% 85.42% 180ms 0.7% AbstractCellProperty::IsType (inline) 16ms 0.063% 85.48% 180ms 0.7% std::__insertion_sort (inline) 0 0% 85.48% 180ms 0.7% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 172ms 0.67% 86.15% 172ms 0.67% boost::shared_ptr::operator-> (inline) 0 0% 86.15% 169ms 0.66% std::_Rb_tree::clear (inline) 0 0% 86.15% 163ms 0.64% NodesOnlyMesh::ResizeBoxCollection 163ms 0.64% 86.79% 163ms 0.64% [libchaste_cell_based.so] 9ms 0.035% 86.83% 162ms 0.63% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 86.83% 158ms 0.62% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 86.83% 153ms 0.6% vtkXMLWriter::WriteBinaryData 6ms 0.023% 86.85% 152ms 0.59% boost::numeric::ublas::c_vector::operator[] (inline) 3ms 0.012% 86.86% 151ms 0.59% Cell::GetCellId 0 0% 86.86% 149ms 0.58% vtkXMLWriter::WriteBinaryDataBlock 0 0% 86.86% 149ms 0.58% vtkXMLWriter::WriteBinaryDataInternal 148ms 0.58% 87.44% 148ms 0.58% __ieee754_log_fma 0 0% 87.44% 148ms 0.58% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 87.44% 148ms 0.58% vtkXMLWriter::WriteCompressionBlock 1ms 0.0039% 87.44% 145ms 0.57% AbstractNumericalMethod::SafeNodePositionUpdate 65ms 0.25% 87.70% 142ms 0.55% AbstractCellProperty::IsSame 0 0% 87.70% 142ms 0.55% vtkXMLWriter::WritePointsAppendedData 127ms 0.5% 88.19% 141ms 0.55% _int_free 3ms 0.012% 88.20% 135ms 0.53% NodeBasedCellPopulation::SetNode 133ms 0.52% 88.72% 133ms 0.52% Node::rGetLocation 132ms 0.52% 89.24% 132ms 0.52% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 129ms 0.5% 89.74% 130ms 0.51% Node::ConstructNodeAttributes (inline)