File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 16807ms, 88.90% of 18905ms total Dropped 733 nodes (cum <= 94.53ms) flat flat% sum% cum cum% 0 0% 0% 18794ms 99.41% __libc_start_call_main 0 0% 0% 18794ms 99.41% __libc_start_main_impl 0 0% 0% 18794ms 99.41% _start 0 0% 0% 18780ms 99.34% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 18780ms 99.34% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 18780ms 99.34% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 18780ms 99.34% main 0 0% 0% 18740ms 99.13% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 18740ms 99.13% CxxTest::TestRunner::runTest (inline) 0 0% 0% 18740ms 99.13% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 18734ms 99.10% AbstractCellBasedSimulation::Solve 0 0% 0% 10757ms 56.90% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0% 7045ms 37.27% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0053% 0.0053% 6987ms 36.96% ForwardEulerNumericalMethod::UpdateAllNodePositions 5ms 0.026% 0.032% 6845ms 36.21% AbstractNumericalMethod::ComputeForcesIncludingDamping 1110ms 5.87% 5.90% 6313ms 33.39% RepulsionForce::AddForceContribution (partial-inline) 1ms 0.0053% 5.91% 6239ms 33.00% NodeBasedCellPopulation::Update 8ms 0.042% 5.95% 4623ms 24.45% DistributedBoxCollection::CalculateInteriorNodePairs 1722ms 9.11% 15.06% 3972ms 21.01% std::_Rb_tree::_M_lower_bound (inline) 4ms 0.021% 15.08% 3544ms 18.75% NodeAttributes::RemoveDuplicateNeighbours 0 0% 15.08% 3532ms 18.68% OffLatticeSimulation::ApplyBoundaries 2ms 0.011% 15.09% 3416ms 18.07% std::__sort (inline) 0 0% 15.09% 3416ms 18.07% std::sort (inline) 155ms 0.82% 15.91% 3064ms 16.21% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 178ms 0.94% 16.85% 2661ms 14.08% std::_Rb_tree::find (inline) 0 0% 16.85% 2661ms 14.08% std::map::find (inline) 52ms 0.28% 17.13% 2602ms 13.76% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 3ms 0.016% 17.14% 2407ms 12.73% AbstractCellPopulation::Iterator::operator++ (inline) 108ms 0.57% 17.71% 2381ms 12.59% AbstractCellPopulation::Iterator::IsRealCell (inline) 2227ms 11.78% 29.49% 2227ms 11.78% std::_Rb_tree::_S_right (inline) 21ms 0.11% 29.61% 2104ms 11.13% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 128ms 0.68% 30.28% 1962ms 10.38% AbstractMesh::GetNode 142ms 0.75% 31.03% 1941ms 10.27% std::__introsort_loop 36ms 0.19% 31.22% 1937ms 10.25% NodesOnlyMesh::GetNodeOrHaloNode 21ms 0.11% 31.34% 1909ms 10.10% PlaneBoundaryCondition::ImposeBoundaryCondition 174ms 0.92% 32.26% 1885ms 9.97% std::map::operator[] (partial-inline) 85ms 0.45% 32.71% 1839ms 9.73% NodesOnlyMesh::SolveNodeMapping 29ms 0.15% 32.86% 1773ms 9.38% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 32.86% 1748ms 9.25% std::__unguarded_partition_pivot (inline) 7ms 0.037% 32.90% 1623ms 8.59% PlaneBoundaryCondition::VerifyBoundaryCondition 727ms 3.85% 36.74% 1555ms 8.23% std::__unguarded_partition (inline) 105ms 0.56% 37.30% 1544ms 8.17% DistributedBoxCollection::AddPairsFromBox 0 0% 37.30% 1523ms 8.06% std::_Rb_tree::lower_bound (inline) 0 0% 37.30% 1523ms 8.06% std::map::lower_bound (inline) 0 0% 37.30% 1471ms 7.78% std::__final_insertion_sort (inline) 93ms 0.49% 37.79% 1308ms 6.92% std::__unguarded_insertion_sort (inline) 491ms 2.60% 40.39% 1283ms 6.79% std::__unguarded_linear_insert (inline) 17ms 0.09% 40.48% 1232ms 6.52% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 23ms 0.12% 40.60% 1212ms 6.41% AbstractCellPopulation::GetCellUsingLocationIndex 1133ms 5.99% 46.59% 1133ms 5.99% __gnu_cxx::__normal_iterator::operator-- (inline) 52ms 0.28% 46.87% 996ms 5.27% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 46.87% 922ms 4.88% NodeBasedCellPopulation::UpdateCellProcessLocation 7ms 0.037% 46.90% 891ms 4.71% boost::numeric::ublas::vector_assign (inline) 6ms 0.032% 46.93% 842ms 4.45% DistributedBoxCollection::CalculateBoundaryNodePairs 195ms 1.03% 47.97% 809ms 4.28% boost::numeric::ublas::indexing_vector_assign 203ms 1.07% 49.04% 734ms 3.88% __dynamic_cast 13ms 0.069% 49.11% 726ms 3.84% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 49.11% 683ms 3.61% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 49.11% 663ms 3.51% boost::numeric::ublas::norm_2 (inline) 533ms 2.82% 51.93% 663ms 3.51% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 51.93% 663ms 3.51% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 286ms 1.51% 53.44% 650ms 3.44% DistributedBoxCollection::CalculateContainingBox (partial-inline) 134ms 0.71% 54.15% 645ms 3.41% AbstractMesh::GetVectorFromAtoB 6ms 0.032% 54.18% 607ms 3.21% boost::numeric::ublas::c_vector::operator= (inline) 120ms 0.63% 54.82% 592ms 3.13% NodeAttributes::AddNeighbour 25ms 0.13% 54.95% 588ms 3.11% std::__copy_move::__copy_m (inline) 0 0% 54.95% 588ms 3.11% std::__copy_move_a (inline) 0 0% 54.95% 588ms 3.11% std::__copy_move_a1 (inline) 0 0% 54.95% 588ms 3.11% std::__copy_move_a2 (inline) 0 0% 54.95% 588ms 3.11% std::copy (inline) 0 0% 54.95% 575ms 3.04% AbstractCellPopulation::WriteResultsToFiles 570ms 3.02% 57.96% 570ms 3.02% __memcpy_avx512_unaligned_erms 547ms 2.89% 60.86% 547ms 2.89% boost::numeric::ublas::c_vector::operator() 471ms 2.49% 63.35% 526ms 2.78% std::vector::push_back (inline) 28ms 0.15% 63.50% 492ms 2.60% std::_Rb_tree_const_iterator::operator++ (inline) 5ms 0.026% 63.52% 466ms 2.46% CellPropertyCollection::GetPropertiesType (inline) 9ms 0.048% 63.57% 463ms 2.45% AbstractCentreBasedCellPopulation::GetDampingConstant 452ms 2.39% 65.96% 452ms 2.39% std::_Rb_tree_increment 2ms 0.011% 65.97% 447ms 2.36% AbstractCellBasedSimulation::DoCellBirth 214ms 1.13% 67.10% 437ms 2.31% __cxxabiv1::__si_class_type_info::__do_dyncast 64ms 0.34% 67.44% 415ms 2.20% std::__new_allocator::allocate (inline) 23ms 0.12% 67.56% 404ms 2.14% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 67.56% 399ms 2.11% std::allocator_traits::allocate (inline) 393ms 2.08% 69.64% 393ms 2.08% boost::numeric::ublas::same_impl_ex 0 0% 69.64% 385ms 2.04% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 69.64% 373ms 1.97% std::_Rb_tree::_M_create_node (inline) 23ms 0.12% 69.76% 367ms 1.94% std::_Rb_tree::_M_copy (inline) 0 0% 69.76% 357ms 1.89% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 69.76% 349ms 1.85% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 26ms 0.14% 69.90% 349ms 1.85% operator new 345ms 1.82% 71.73% 345ms 1.82% __strcmp_evex 28ms 0.15% 71.88% 343ms 1.81% boost::detail::shared_count::~shared_count (inline) 0 0% 71.88% 343ms 1.81% boost::shared_ptr::~shared_ptr (inline) 118ms 0.62% 72.50% 340ms 1.80% std::_Rb_tree::_M_clone_node (inline) 0 0% 72.50% 334ms 1.77% std::_Rb_tree::_M_get_node (inline) 3ms 0.016% 72.52% 326ms 1.72% std::set::set (inline) 4ms 0.021% 72.54% 324ms 1.71% Cell::GetMutationState 2ms 0.011% 72.55% 322ms 1.70% AbstractCellProperty::IsSubType (inline) 100ms 0.53% 73.08% 319ms 1.69% __GI___libc_malloc 84ms 0.44% 73.52% 314ms 1.66% std::_Rb_tree::_M_erase 297ms 1.57% 75.09% 309ms 1.63% boost::detail::sp_counted_base::release 74ms 0.39% 75.48% 295ms 1.56% Node::GetRadius 75ms 0.4% 75.88% 284ms 1.50% boost::numeric::ublas::vector_binary::size (inline) 0 0% 75.88% 278ms 1.47% boost::numeric::ublas::inner_prod (inline) 23ms 0.12% 76.00% 277ms 1.47% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 76.00% 277ms 1.47% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 76.00% 267ms 1.41% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 76.00% 264ms 1.40% boost::numeric::ublas::c_vector::assign (inline) 262ms 1.39% 77.39% 262ms 1.39% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 77.39% 247ms 1.31% NodesOnlyMesh::ReMesh 3ms 0.016% 77.40% 245ms 1.30% NodeBasedCellPopulation::UpdateMapsAfterRemesh 2ms 0.011% 77.41% 239ms 1.26% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 35ms 0.19% 77.60% 239ms 1.26% std::_Rb_tree::~_Rb_tree (inline) 3ms 0.016% 77.61% 237ms 1.25% NodesOnlyMesh::UpdateNodeIndices 229ms 1.21% 78.83% 229ms 1.21% __gnu_cxx::__normal_iterator::operator++ (inline) 96ms 0.51% 79.33% 224ms 1.18% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 79.33% 224ms 1.18% std::_Rb_tree::_M_drop_node (inline) 223ms 1.18% 80.51% 223ms 1.18% Node::CheckForNodeAttributes 5ms 0.026% 80.54% 222ms 1.17% DistributedBoxCollection::GetProcessOwningNode 0 0% 80.54% 204ms 1.08% NodesOnlyMesh::UpdateBoxCollection 190ms 1.01% 81.54% 190ms 1.01% [libchaste_mesh.so] 0 0% 81.54% 189ms 1% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 3ms 0.016% 81.56% 189ms 1% std::__new_allocator::deallocate (inline) 0 0% 81.56% 188ms 0.99% VtkMeshWriter::WriteFiles 6ms 0.032% 81.59% 188ms 0.99% std::_Rb_tree::_M_emplace_hint_unique 83ms 0.44% 82.03% 188ms 0.99% std::__move_median_to_first (inline) 106ms 0.56% 82.59% 179ms 0.95% _int_malloc 0 0% 82.59% 178ms 0.94% std::allocator_traits::deallocate (inline) 1ms 0.0053% 82.60% 176ms 0.93% NodesOnlyMesh::AddNodesToBoxes 0 0% 82.60% 176ms 0.93% std::_Rb_tree::_M_put_node (inline) 0 0% 82.60% 175ms 0.93% vtkStreamingDemandDrivenPipeline::Update 0 0% 82.60% 175ms 0.93% vtkXMLWriterBase::Write 0 0% 82.60% 174ms 0.92% std::set::~set (inline) 0 0% 82.60% 174ms 0.92% vtkDemandDrivenPipeline::ProcessRequest 173ms 0.92% 83.51% 173ms 0.92% Node::GetIndex 0 0% 83.51% 172ms 0.91% vtkExecutive::CallAlgorithm 0 0% 83.51% 172ms 0.91% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 83.51% 171ms 0.9% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 83.51% 170ms 0.9% vtkCompositeDataPipeline::ExecuteData 0 0% 83.51% 170ms 0.9% vtkDemandDrivenPipeline::ExecuteData 3ms 0.016% 83.53% 169ms 0.89% CellPropertyCollection::HasProperty 55ms 0.29% 83.82% 169ms 0.89% __GI___libc_free 0 0% 83.82% 168ms 0.89% Cell::HasCellProperty (inline) 103ms 0.54% 84.36% 168ms 0.89% Node::AddNeighbour 92ms 0.49% 84.85% 165ms 0.87% boost::shared_ptr::shared_ptr (inline) 0 0% 84.85% 163ms 0.86% boost::numeric::ublas::vector_binary::operator() (inline) 14ms 0.074% 84.92% 163ms 0.86% std::__insertion_sort (inline) 8ms 0.042% 84.97% 157ms 0.83% Cell::ReadyToDivide 11ms 0.058% 85.03% 156ms 0.83% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 85.03% 155ms 0.82% NodesOnlyMesh::ResizeBoxCollection 10ms 0.053% 85.08% 154ms 0.81% NodesOnlyMesh::IsANodeCloseToDomainBoundary 143ms 0.76% 85.83% 143ms 0.76% [libchaste_cell_based.so] 0 0% 85.83% 141ms 0.75% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.83% 141ms 0.75% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 85.83% 140ms 0.74% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 2ms 0.011% 85.85% 138ms 0.73% AbstractCellProperty::IsType (inline) 136ms 0.72% 86.56% 136ms 0.72% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 4ms 0.021% 86.59% 133ms 0.7% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 86.59% 120ms 0.63% std::_Rb_tree::clear (inline) 0 0% 86.59% 116ms 0.61% vtkXMLWriter::WriteBinaryData 101ms 0.53% 87.12% 114ms 0.6% _int_free 0 0% 87.12% 113ms 0.6% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.12% 113ms 0.6% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.12% 113ms 0.6% vtkXMLWriter::WriteCompressionBlock 109ms 0.58% 87.70% 109ms 0.58% std::__adjacent_find (inline) 0 0% 87.70% 109ms 0.58% std::__unique (inline) 0 0% 87.70% 109ms 0.58% std::unique (inline) 2ms 0.011% 87.71% 107ms 0.57% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 87.71% 107ms 0.57% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 87.71% 106ms 0.56% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1ms 0.0053% 87.71% 105ms 0.56% Cell::GetCellId 1ms 0.0053% 87.72% 104ms 0.55% AbstractCellPopulation::SetCellUsingLocationIndex 2ms 0.011% 87.73% 102ms 0.54% DistributedBoxCollection::GetIsPeriodicAllDims 0 0% 87.73% 100ms 0.53% vtkXMLWriter::WritePointsAppendedData 26ms 0.14% 87.87% 99ms 0.52% AbstractCellProperty::IsSame 2ms 0.011% 87.88% 98ms 0.52% AbstractNumericalMethod::SafeNodePositionUpdate 97ms 0.51% 88.39% 97ms 0.51% Node::IsDeleted 97ms 0.51% 88.90% 97ms 0.51% __ieee754_log_fma 0 0% 88.90% 96ms 0.51% std::map::clear (inline)