File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20523ms, 89.24% of 22997ms total Dropped 721 nodes (cum <= 114.98ms) flat flat% sum% cum cum% 0 0% 0% 22828ms 99.27% __libc_start_call_main 0 0% 0% 22828ms 99.27% __libc_start_main_impl 0 0% 0% 22828ms 99.27% _start 0 0% 0% 22812ms 99.20% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 22812ms 99.20% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 22812ms 99.20% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 22812ms 99.20% main 0 0% 0% 22779ms 99.05% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 22779ms 99.05% CxxTest::TestRunner::runTest (inline) 0 0% 0% 22779ms 99.05% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 22771ms 99.02% AbstractCellBasedSimulation::Solve 2ms 0.0087% 0.0087% 12940ms 56.27% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0087% 8661ms 37.66% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.017% 0.026% 8200ms 35.66% ForwardEulerNumericalMethod::UpdateAllNodePositions 15ms 0.065% 0.091% 8013ms 34.84% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.091% 7660ms 33.31% NodeBasedCellPopulation::Update 1239ms 5.39% 5.48% 7409ms 32.22% RepulsionForce::AddForceContribution (partial-inline) 11ms 0.048% 5.53% 5542ms 24.10% DistributedBoxCollection::CalculateInteriorNodePairs 2080ms 9.04% 14.57% 4950ms 21.52% std::_Rb_tree::_M_lower_bound (inline) 0 0% 14.57% 4504ms 19.59% OffLatticeSimulation::ApplyBoundaries 19ms 0.083% 14.65% 4490ms 19.52% NodeAttributes::RemoveDuplicateNeighbours 6ms 0.026% 14.68% 4196ms 18.25% std::__sort (inline) 0 0% 14.68% 4196ms 18.25% std::sort (inline) 224ms 0.97% 15.65% 3771ms 16.40% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 4ms 0.017% 15.67% 3462ms 15.05% AbstractCellPopulation::Iterator::operator++ (inline) 160ms 0.7% 16.37% 3429ms 14.91% AbstractCellPopulation::Iterator::IsRealCell (inline) 74ms 0.32% 16.69% 3382ms 14.71% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 226ms 0.98% 17.67% 3125ms 13.59% std::_Rb_tree::find (inline) 0 0% 17.67% 3124ms 13.58% std::map::find (inline) 28ms 0.12% 17.79% 2929ms 12.74% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2812ms 12.23% 30.02% 2812ms 12.23% std::_Rb_tree::_S_right (inline) 201ms 0.87% 30.90% 2509ms 10.91% std::map::operator[] (partial-inline) 31ms 0.13% 31.03% 2370ms 10.31% PlaneBoundaryCondition::ImposeBoundaryCondition 33ms 0.14% 31.17% 2297ms 9.99% AbstractCellPopulation::GetLocationIndexUsingCell 167ms 0.73% 31.90% 2290ms 9.96% std::__introsort_loop 173ms 0.75% 32.65% 2249ms 9.78% AbstractMesh::GetNode 42ms 0.18% 32.83% 2205ms 9.59% NodesOnlyMesh::GetNodeOrHaloNode 22ms 0.096% 32.93% 2134ms 9.28% PlaneBoundaryCondition::VerifyBoundaryCondition 71ms 0.31% 33.24% 2080ms 9.04% NodesOnlyMesh::SolveNodeMapping 0 0% 33.24% 2076ms 9.03% std::_Rb_tree::lower_bound (inline) 0 0% 33.24% 2076ms 9.03% std::map::lower_bound (inline) 1ms 0.0043% 33.24% 2030ms 8.83% std::__unguarded_partition_pivot (inline) 2ms 0.0087% 33.25% 1898ms 8.25% std::__final_insertion_sort (inline) 951ms 4.14% 37.39% 1809ms 7.87% std::__unguarded_partition (inline) 144ms 0.63% 38.01% 1771ms 7.70% DistributedBoxCollection::AddPairsFromBox 106ms 0.46% 38.47% 1667ms 7.25% std::__unguarded_insertion_sort (inline) 597ms 2.60% 41.07% 1613ms 7.01% std::__unguarded_linear_insert (inline) 24ms 0.1% 41.17% 1563ms 6.80% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 22ms 0.096% 41.27% 1535ms 6.67% AbstractCellPopulation::GetCellUsingLocationIndex 1404ms 6.11% 47.38% 1404ms 6.11% __gnu_cxx::__normal_iterator::operator-- (inline) 7ms 0.03% 47.41% 1187ms 5.16% DistributedBoxCollection::CalculateBoundaryNodePairs 62ms 0.27% 47.68% 1181ms 5.14% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 47.68% 1116ms 4.85% NodeBasedCellPopulation::UpdateCellProcessLocation 42ms 0.18% 47.86% 1045ms 4.54% boost::numeric::ublas::vector_assign (inline) 259ms 1.13% 48.98% 955ms 4.15% boost::numeric::ublas::indexing_vector_assign 216ms 0.94% 49.92% 869ms 3.78% __dynamic_cast 398ms 1.73% 51.65% 805ms 3.50% DistributedBoxCollection::CalculateContainingBox (partial-inline) 168ms 0.73% 52.39% 784ms 3.41% AbstractMesh::GetVectorFromAtoB 14ms 0.061% 52.45% 745ms 3.24% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 190ms 0.83% 53.27% 739ms 3.21% NodeAttributes::AddNeighbour 0 0% 53.27% 720ms 3.13% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 53.27% 712ms 3.10% AbstractCellPopulation::WriteResultsToFiles 0 0% 53.27% 708ms 3.08% boost::numeric::ublas::norm_2 (inline) 548ms 2.38% 55.66% 708ms 3.08% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 55.66% 708ms 3.08% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 9ms 0.039% 55.69% 663ms 2.88% boost::numeric::ublas::c_vector::operator= (inline) 656ms 2.85% 58.55% 656ms 2.85% boost::numeric::ublas::c_vector::operator() 43ms 0.19% 58.73% 636ms 2.77% std::__copy_move::__copy_m (inline) 0 0% 58.73% 636ms 2.77% std::__copy_move_a (inline) 0 0% 58.73% 636ms 2.77% std::__copy_move_a1 (inline) 0 0% 58.73% 636ms 2.77% std::__copy_move_a2 (inline) 0 0% 58.73% 636ms 2.77% std::copy (inline) 619ms 2.69% 61.43% 619ms 2.69% __memcpy_avx_unaligned_erms 549ms 2.39% 63.81% 605ms 2.63% std::vector::push_back (inline) 3ms 0.013% 63.83% 574ms 2.50% AbstractCellBasedSimulation::DoCellBirth 268ms 1.17% 64.99% 563ms 2.45% __cxxabiv1::__si_class_type_info::__do_dyncast 10ms 0.043% 65.03% 521ms 2.27% CellPropertyCollection::GetPropertiesType (inline) 1ms 0.0043% 65.04% 520ms 2.26% AbstractCentreBasedCellPopulation::GetDampingConstant 34ms 0.15% 65.19% 508ms 2.21% std::_Rb_tree_const_iterator::operator++ (inline) 31ms 0.13% 65.32% 477ms 2.07% boost::detail::shared_count::~shared_count (inline) 0 0% 65.32% 477ms 2.07% boost::shared_ptr::~shared_ptr (inline) 2ms 0.0087% 65.33% 473ms 2.06% NodeBasedCellPopulation::WriteVtkResultsToFile 78ms 0.34% 65.67% 467ms 2.03% std::__new_allocator::allocate (inline) 462ms 2.01% 67.68% 462ms 2.01% std::_Rb_tree_increment 0 0% 67.68% 448ms 1.95% std::allocator_traits::allocate (inline) 434ms 1.89% 69.57% 439ms 1.91% boost::detail::sp_counted_base::release 22ms 0.096% 69.66% 439ms 1.91% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 69.66% 429ms 1.87% std::_Rb_tree::_M_create_node (inline) 0 0% 69.66% 424ms 1.84% AbstractCellBasedSimulation::DoCellRemoval (inline) 424ms 1.84% 71.50% 424ms 1.84% boost::numeric::ublas::same_impl_ex 421ms 1.83% 73.34% 421ms 1.83% __strcmp_avx2 2ms 0.0087% 73.34% 414ms 1.80% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 44ms 0.19% 73.54% 403ms 1.75% std::_Rb_tree::_M_copy (inline) 24ms 0.1% 73.64% 384ms 1.67% operator new 4ms 0.017% 73.66% 383ms 1.67% std::set::set (inline) 0 0% 73.66% 373ms 1.62% std::_Rb_tree::_M_get_node (inline) 1ms 0.0043% 73.66% 368ms 1.60% AbstractCellProperty::IsSubType (inline) 139ms 0.6% 74.27% 362ms 1.57% Node::GetRadius 118ms 0.51% 74.78% 357ms 1.55% std::_Rb_tree::_M_clone_node (inline) 105ms 0.46% 75.24% 354ms 1.54% __GI___libc_malloc 101ms 0.44% 75.68% 352ms 1.53% std::_Rb_tree::_M_erase 0 0% 75.68% 341ms 1.48% boost::numeric::ublas::inner_prod (inline) 1ms 0.0043% 75.68% 341ms 1.48% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 19ms 0.083% 75.76% 340ms 1.48% boost::numeric::ublas::vector_scalar_binary::evaluate 3ms 0.013% 75.78% 337ms 1.47% Cell::GetMutationState 322ms 1.40% 77.18% 322ms 1.40% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 5ms 0.022% 77.20% 312ms 1.36% NodeBasedCellPopulation::UpdateMapsAfterRemesh 20ms 0.087% 77.28% 308ms 1.34% boost::numeric::ublas::vector_binary::size (inline) 0 0% 77.28% 306ms 1.33% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 77.28% 292ms 1.27% boost::numeric::ublas::c_vector::assign (inline) 3ms 0.013% 77.30% 291ms 1.27% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 35ms 0.15% 77.45% 286ms 1.24% std::_Rb_tree::~_Rb_tree (inline) 0 0% 77.45% 285ms 1.24% NodesOnlyMesh::ReMesh 5ms 0.022% 77.47% 278ms 1.21% NodesOnlyMesh::UpdateNodeIndices 2ms 0.0087% 77.48% 274ms 1.19% DistributedBoxCollection::GetProcessOwningNode 0 0% 77.48% 270ms 1.17% NodesOnlyMesh::UpdateBoxCollection 133ms 0.58% 78.06% 268ms 1.17% boost::numeric::ublas::vector_inner_prod::apply (inline) 265ms 1.15% 79.21% 265ms 1.15% std::__adjacent_find (inline) 0 0% 79.21% 265ms 1.15% std::__unique (inline) 0 0% 79.21% 265ms 1.15% std::unique (inline) 252ms 1.10% 80.31% 252ms 1.10% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 80.31% 250ms 1.09% std::_Rb_tree::_M_drop_node (inline) 3ms 0.013% 80.32% 243ms 1.06% NodesOnlyMesh::AddNodesToBoxes 233ms 1.01% 81.33% 233ms 1.01% Node::CheckForNodeAttributes 7ms 0.03% 81.36% 232ms 1.01% std::_Rb_tree::_M_emplace_hint_unique 0 0% 81.36% 231ms 1.00% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 81.36% 229ms 1% VtkMeshWriter::WriteFiles 21ms 0.091% 81.45% 229ms 1% std::__insertion_sort (inline) 107ms 0.47% 81.92% 219ms 0.95% boost::shared_ptr::shared_ptr (inline) 106ms 0.46% 82.38% 215ms 0.93% std::__move_median_to_first (inline) 6ms 0.026% 82.41% 212ms 0.92% std::__new_allocator::deallocate (inline) 0 0% 82.41% 212ms 0.92% std::set::~set (inline) 1ms 0.0043% 82.41% 201ms 0.87% vtkXMLWriterBase::Write 0 0% 82.41% 200ms 0.87% vtkStreamingDemandDrivenPipeline::Update 0 0% 82.41% 199ms 0.87% vtkDemandDrivenPipeline::ProcessRequest 0 0% 82.41% 197ms 0.86% vtkExecutive::CallAlgorithm 1ms 0.0043% 82.42% 197ms 0.86% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 82.42% 196ms 0.85% vtkDemandDrivenPipeline::ExecuteData 110ms 0.48% 82.89% 195ms 0.85% _int_malloc 0 0% 82.89% 195ms 0.85% vtkCompositeDataPipeline::ExecuteData 0 0% 82.89% 195ms 0.85% vtkXMLUnstructuredDataWriter::ProcessRequest 69ms 0.3% 83.19% 194ms 0.84% __GI___libc_free 187ms 0.81% 84.01% 187ms 0.81% Node::GetIndex 0 0% 84.01% 187ms 0.81% std::allocator_traits::deallocate (inline) 0 0% 84.01% 183ms 0.8% std::_Rb_tree::_M_put_node (inline) 4ms 0.017% 84.02% 178ms 0.77% CellPropertyCollection::HasProperty 0 0% 84.02% 177ms 0.77% Cell::HasCellProperty (inline) 66ms 0.29% 84.31% 176ms 0.77% Node::AddNeighbour 0 0% 84.31% 173ms 0.75% NodesOnlyMesh::ResizeBoxCollection 19ms 0.083% 84.39% 172ms 0.75% NodesOnlyMesh::IsANodeCloseToDomainBoundary 4ms 0.017% 84.41% 171ms 0.74% Cell::ReadyToDivide 0 0% 84.41% 169ms 0.73% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 84.41% 169ms 0.73% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 84.41% 165ms 0.72% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 3ms 0.013% 84.42% 163ms 0.71% AbstractCellProperty::IsType (inline) 163ms 0.71% 85.13% 163ms 0.71% [libchaste_cell_based.so] 145ms 0.63% 85.76% 145ms 0.63% [libchaste_mesh.so] 140ms 0.61% 86.37% 140ms 0.61% boost::shared_ptr::operator-> (inline) 0 0% 86.37% 139ms 0.6% tbb::detail::r1::parallel_pipeline 0 0% 86.37% 137ms 0.6% vtkXMLWriter::WriteBinaryData 58ms 0.25% 86.62% 136ms 0.59% tbb::detail::r1::wait_bounded_queue_monitor 0 0% 86.62% 135ms 0.59% clone3 0 0% 86.62% 135ms 0.59% start_thread 0 0% 86.62% 135ms 0.59% tbb::detail::r1::reset 4ms 0.017% 86.64% 134ms 0.58% AbstractNumericalMethod::SafeNodePositionUpdate 134ms 0.58% 87.22% 134ms 0.58% Node::ConstructNodeAttributes (inline) 0 0% 87.22% 133ms 0.58% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 87.22% 133ms 0.58% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 2ms 0.0087% 87.23% 132ms 0.57% AbstractCellPopulation::SetCellUsingLocationIndex 132ms 0.57% 87.81% 132ms 0.57% __ieee754_log_fma 5ms 0.022% 87.83% 132ms 0.57% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 87.83% 131ms 0.57% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.83% 131ms 0.57% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.83% 130ms 0.57% vtkXMLWriter::WriteCompressionBlock 0 0% 87.83% 126ms 0.55% vtkXMLWriter::WritePointsAppendedData 108ms 0.47% 88.30% 125ms 0.54% _int_free 42ms 0.18% 88.48% 124ms 0.54% AbstractCellProperty::IsSame 0 0% 88.48% 123ms 0.53% std::_Rb_tree::_Auto_node::_Auto_node (inline) 122ms 0.53% 89.01% 122ms 0.53% Node::IsDeleted 36ms 0.16% 89.17% 122ms 0.53% boost::numeric::ublas::vector_reference::operator() (inline) 3ms 0.013% 89.18% 122ms 0.53% std::_Rb_tree::_M_insert_unique 0 0% 89.18% 122ms 0.53% std::_Rb_tree::clear (inline) 0 0% 89.18% 122ms 0.53% std::set::insert (inline) 1ms 0.0043% 89.19% 120ms 0.52% Cell::GetCellId 6ms 0.026% 89.21% 119ms 0.52% NodeBasedCellPopulation::SetNode 7ms 0.03% 89.24% 116ms 0.5% DistributedBoxCollection::GetIsPeriodicAllDims