File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 19146ms, 89.38% of 21420ms total Dropped 695 nodes (cum <= 107.10ms) flat flat% sum% cum cum% 0 0% 0% 21329ms 99.58% __libc_start_call_main 0 0% 0% 21329ms 99.58% __libc_start_main_impl 0 0% 0% 21329ms 99.58% _start 0 0% 0% 21314ms 99.51% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 21314ms 99.51% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 21314ms 99.51% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 21314ms 99.51% main 0 0% 0% 21285ms 99.37% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 21285ms 99.37% CxxTest::TestRunner::runTest (inline) 1ms 0.0047% 0.0047% 21285ms 99.37% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0.0047% 21277ms 99.33% AbstractCellBasedSimulation::Solve 2ms 0.0093% 0.014% 12000ms 56.02% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.014% 8290ms 38.70% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.014% 7256ms 33.87% NodeBasedCellPopulation::Update 3ms 0.014% 0.028% 6777ms 31.64% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.019% 0.047% 6621ms 30.91% AbstractNumericalMethod::ComputeForcesIncludingDamping 839ms 3.92% 3.96% 6095ms 28.45% RepulsionForce::AddForceContribution (partial-inline) 7ms 0.033% 4.00% 5492ms 25.64% DistributedBoxCollection::CalculateInteriorNodePairs 0 0% 4.00% 4918ms 22.96% OffLatticeSimulation::ApplyBoundaries 1968ms 9.19% 13.18% 4501ms 21.01% std::_Rb_tree::_M_lower_bound (inline) 12ms 0.056% 13.24% 4375ms 20.42% NodeAttributes::RemoveDuplicateNeighbours 2ms 0.0093% 13.25% 4211ms 19.66% std::__sort (inline) 0 0% 13.25% 4211ms 19.66% std::sort (inline) 266ms 1.24% 14.49% 3606ms 16.83% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 1ms 0.0047% 14.50% 3459ms 16.15% AbstractCellPopulation::Iterator::operator++ (inline) 179ms 0.84% 15.33% 3449ms 16.10% AbstractCellPopulation::Iterator::IsRealCell 127ms 0.59% 15.92% 3299ms 15.40% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 250ms 1.17% 17.09% 2993ms 13.97% std::_Rb_tree::find (inline) 0 0% 17.09% 2992ms 13.97% std::map::find (inline) 27ms 0.13% 17.22% 2892ms 13.50% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 220ms 1.03% 18.24% 2546ms 11.89% std::__introsort_loop 82ms 0.38% 18.63% 2519ms 11.76% AbstractMesh::GetNode 61ms 0.28% 18.91% 2495ms 11.65% PlaneBoundaryCondition::ImposeBoundaryCondition 51ms 0.24% 19.15% 2491ms 11.63% NodesOnlyMesh::GetNodeOrHaloNode 208ms 0.97% 20.12% 2442ms 11.40% NodesOnlyMesh::SolveNodeMapping 61ms 0.28% 20.41% 2423ms 11.31% PlaneBoundaryCondition::VerifyBoundaryCondition 202ms 0.94% 21.35% 2322ms 10.84% std::map::operator[] (partial-inline) 5ms 0.023% 21.37% 2235ms 10.43% std::__unguarded_partition_pivot (inline) 2228ms 10.40% 31.77% 2228ms 10.40% std::_Rb_tree::_S_right (inline) 688ms 3.21% 34.99% 2053ms 9.58% std::__unguarded_partition (inline) 99ms 0.46% 35.45% 2017ms 9.42% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 35.45% 1799ms 8.40% std::_Rb_tree::lower_bound (inline) 0 0% 35.45% 1799ms 8.40% std::map::lower_bound (inline) 1ms 0.0047% 35.45% 1657ms 7.74% std::__final_insertion_sort (inline) 115ms 0.54% 35.99% 1624ms 7.58% DistributedBoxCollection::AddPairsFromBox 103ms 0.48% 36.47% 1459ms 6.81% std::__unguarded_insertion_sort (inline) 6ms 0.028% 36.50% 1391ms 6.49% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 23ms 0.11% 36.61% 1376ms 6.42% AbstractCellPopulation::GetCellUsingLocationIndex 636ms 2.97% 39.58% 1318ms 6.15% std::__unguarded_linear_insert (inline) 18ms 0.084% 39.66% 1025ms 4.79% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 1024ms 4.78% 44.44% 1024ms 4.78% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 44.44% 1008ms 4.71% NodeBasedCellPopulation::UpdateCellProcessLocation 62ms 0.29% 44.73% 968ms 4.52% boost::numeric::ublas::c_vector::c_vector (partial-inline) 19ms 0.089% 44.82% 913ms 4.26% boost::detail::shared_count::~shared_count (inline) 0 0% 44.82% 913ms 4.26% boost::shared_ptr::~shared_ptr (inline) 6ms 0.028% 44.85% 904ms 4.22% DistributedBoxCollection::CalculateBoundaryNodePairs 859ms 4.01% 48.86% 868ms 4.05% boost::detail::sp_counted_base::release 2ms 0.0093% 48.87% 817ms 3.81% boost::numeric::ublas::vector_assign (inline) 233ms 1.09% 49.95% 759ms 3.54% __dynamic_cast 171ms 0.8% 50.75% 706ms 3.30% boost::numeric::ublas::indexing_vector_assign 278ms 1.30% 52.05% 681ms 3.18% DistributedBoxCollection::CalculateContainingBox (partial-inline) 84ms 0.39% 52.44% 621ms 2.90% AbstractMesh::GetVectorFromAtoB 51ms 0.24% 52.68% 589ms 2.75% std::__new_allocator::allocate (inline) 256ms 1.20% 53.87% 588ms 2.75% NodeAttributes::AddNeighbour 0 0% 53.87% 587ms 2.74% AbstractCellPopulation::WriteResultsToFiles 574ms 2.68% 56.55% 574ms 2.68% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 56.55% 569ms 2.66% std::allocator_traits::allocate (inline) 24ms 0.11% 56.67% 548ms 2.56% std::_Rb_tree_const_iterator::operator++ (inline) 533ms 2.49% 59.15% 533ms 2.49% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 59.15% 531ms 2.48% std::_Rb_tree::_M_create_node (inline) 26ms 0.12% 59.28% 528ms 2.46% operator new 2ms 0.0093% 59.29% 524ms 2.45% AbstractCellBasedSimulation::DoCellBirth 518ms 2.42% 61.70% 518ms 2.42% [libchaste_cell_based.so] 4ms 0.019% 61.72% 512ms 2.39% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 61.72% 509ms 2.38% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 61.72% 506ms 2.36% std::_Rb_tree::_M_get_node (inline) 17ms 0.079% 61.80% 504ms 2.35% std::_Rb_tree::_Rb_tree (partial-inline) 7ms 0.033% 61.83% 501ms 2.34% CellPropertyCollection::GetPropertiesType (inline) 0 0% 61.83% 499ms 2.33% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 26ms 0.12% 61.96% 499ms 2.33% std::__copy_move::__copy_m (inline) 0 0% 61.96% 499ms 2.33% std::__copy_move_a (inline) 0 0% 61.96% 499ms 2.33% std::__copy_move_a1 (inline) 0 0% 61.96% 499ms 2.33% std::__copy_move_a2 (inline) 0 0% 61.96% 499ms 2.33% std::copy (inline) 12ms 0.056% 62.01% 496ms 2.32% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 184ms 0.86% 62.87% 496ms 2.32% __GI___libc_malloc 0 0% 62.87% 485ms 2.26% boost::numeric::ublas::norm_2 (inline) 412ms 1.92% 64.79% 485ms 2.26% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 64.79% 485ms 2.26% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 3ms 0.014% 64.81% 480ms 2.24% AbstractCentreBasedCellPopulation::GetDampingConstant 31ms 0.14% 64.95% 469ms 2.19% std::_Rb_tree::_M_copy (inline) 464ms 2.17% 67.12% 464ms 2.17% boost::numeric::ublas::c_vector::operator() 462ms 2.16% 69.28% 462ms 2.16% std::_Rb_tree_increment 453ms 2.11% 71.39% 453ms 2.11% __memcpy_avx512_unaligned_erms 440ms 2.05% 73.45% 440ms 2.05% boost::numeric::ublas::same_impl_ex 438ms 2.04% 75.49% 438ms 2.04% [libchaste_mesh.so] 171ms 0.8% 76.29% 430ms 2.01% std::_Rb_tree::_M_clone_node (inline) 54ms 0.25% 76.54% 420ms 1.96% std::_Rb_tree::_M_erase 218ms 1.02% 77.56% 416ms 1.94% __cxxabiv1::__si_class_type_info::__do_dyncast 303ms 1.41% 78.97% 413ms 1.93% std::vector::push_back (inline) 0 0% 78.97% 408ms 1.90% std::set::set (inline) 77ms 0.36% 79.33% 398ms 1.86% std::_Rb_tree::~_Rb_tree (inline) 2ms 0.0093% 79.34% 388ms 1.81% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 79.34% 362ms 1.69% std::_Rb_tree::_M_drop_node (inline) 1ms 0.0047% 79.35% 354ms 1.65% Cell::GetMutationState 1ms 0.0047% 79.35% 346ms 1.62% AbstractCellProperty::IsSubType (inline) 0 0% 79.35% 336ms 1.57% std::set::~set (inline) 328ms 1.53% 80.88% 328ms 1.53% __strcmp_evex 2ms 0.0093% 80.89% 321ms 1.50% std::_Rb_tree::_M_emplace_hint_unique 0 0% 80.89% 317ms 1.48% std::_Rb_tree::_Alloc_node::operator() (inline) 317ms 1.48% 82.37% 317ms 1.48% std::_Rb_tree::_S_left (inline) 8ms 0.037% 82.41% 301ms 1.41% boost::numeric::ublas::vector_binary::size (inline) 0 0% 82.41% 290ms 1.35% NodesOnlyMesh::ReMesh 1ms 0.0047% 82.41% 280ms 1.31% NodesOnlyMesh::UpdateNodeIndices 3ms 0.014% 82.43% 279ms 1.30% NodeBasedCellPopulation::UpdateMapsAfterRemesh 3ms 0.014% 82.44% 266ms 1.24% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 2ms 0.0093% 82.45% 260ms 1.21% Node::GetRadius 162ms 0.76% 83.21% 250ms 1.17% _int_malloc 8ms 0.037% 83.24% 250ms 1.17% std::__new_allocator::deallocate (inline) 2ms 0.0093% 83.25% 246ms 1.15% DistributedBoxCollection::GetProcessOwningNode 0 0% 83.25% 246ms 1.15% NodesOnlyMesh::UpdateBoxCollection 204ms 0.95% 84.21% 232ms 1.08% boost::shared_ptr::shared_ptr (inline) 0 0% 84.21% 220ms 1.03% std::allocator_traits::deallocate (inline) 0 0% 84.21% 218ms 1.02% std::_Rb_tree::_M_put_node (inline) 61ms 0.28% 84.49% 217ms 1.01% __GI___libc_free 0 0% 84.49% 214ms 1% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 84.49% 212ms 0.99% NodesOnlyMesh::AddNodesToBoxes 209ms 0.98% 85.47% 209ms 0.98% Node::CheckForNodeAttributes 0 0% 85.47% 205ms 0.96% boost::numeric::ublas::inner_prod (inline) 10ms 0.047% 85.51% 205ms 0.96% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 85.51% 205ms 0.96% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 85.51% 197ms 0.92% boost::numeric::ublas::c_vector::assign (inline) 25ms 0.12% 85.63% 197ms 0.92% std::__insertion_sort (inline) 2ms 0.0093% 85.64% 187ms 0.87% CellPropertyCollection::HasProperty 0 0% 85.64% 186ms 0.87% Cell::HasCellProperty (inline) 0 0% 85.64% 184ms 0.86% std::iter_swap (inline) 184ms 0.86% 86.50% 184ms 0.86% std::swap (inline) 67ms 0.31% 86.81% 173ms 0.81% std::__move_median_to_first (inline) 44ms 0.21% 87.02% 167ms 0.78% boost::numeric::ublas::vector_inner_prod::apply (inline) 5ms 0.023% 87.04% 165ms 0.77% Cell::ReadyToDivide 162ms 0.76% 87.80% 162ms 0.76% boost::shared_ptr::operator-> (inline) 0 0% 87.80% 157ms 0.73% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 87.80% 155ms 0.72% VtkMeshWriter::WriteFiles 0 0% 87.80% 155ms 0.72% std::_Rb_tree::_M_destroy_node (inline) 0 0% 87.80% 155ms 0.72% std::__new_allocator::destroy (inline) 0 0% 87.80% 155ms 0.72% std::allocator_traits::destroy (inline) 129ms 0.6% 88.40% 151ms 0.7% _int_free 0 0% 88.40% 145ms 0.68% NodesOnlyMesh::ResizeBoxCollection 7ms 0.033% 88.43% 144ms 0.67% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 88.43% 143ms 0.67% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 88.43% 140ms 0.65% vtkCompositeDataPipeline::ExecuteData 0 0% 88.43% 140ms 0.65% vtkDemandDrivenPipeline::ExecuteData 0 0% 88.43% 140ms 0.65% vtkDemandDrivenPipeline::ProcessRequest 0 0% 88.43% 140ms 0.65% vtkExecutive::CallAlgorithm 0 0% 88.43% 140ms 0.65% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 88.43% 140ms 0.65% vtkStreamingDemandDrivenPipeline::Update 0 0% 88.43% 140ms 0.65% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 88.43% 140ms 0.65% vtkXMLWriterBase::Write 4ms 0.019% 88.45% 137ms 0.64% AbstractCellProperty::IsType (inline) 0 0% 88.45% 131ms 0.61% std::_Rb_tree::_M_insert_unique 0 0% 88.45% 131ms 0.61% std::set::insert (inline) 127ms 0.59% 89.04% 127ms 0.59% Node::GetIndex 1ms 0.0047% 89.05% 126ms 0.59% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 65ms 0.3% 89.35% 123ms 0.57% std::__adjacent_find (inline) 0 0% 89.35% 123ms 0.57% std::__unique (inline) 0 0% 89.35% 123ms 0.57% std::unique (inline) 0 0% 89.35% 123ms 0.57% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 89.35% 123ms 0.57% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 5ms 0.023% 89.37% 121ms 0.56% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 89.37% 120ms 0.56% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 89.37% 117ms 0.55% std::_Rb_tree::clear (inline) 0 0% 89.37% 116ms 0.54% Cell::GetCellId 2ms 0.0093% 89.38% 110ms 0.51% NodeBasedCellPopulation::SetNode 0 0% 89.38% 109ms 0.51% AbstractCellPopulation::SetCellUsingLocationIndex