File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 17953ms, 88.74% of 20232ms total Dropped 820 nodes (cum <= 101.16ms) flat flat% sum% cum cum% 0 0% 0% 20075ms 99.22% __libc_start_call_main 0 0% 0% 20075ms 99.22% __libc_start_main_impl 0 0% 0% 20075ms 99.22% _start 0 0% 0% 20059ms 99.14% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 20059ms 99.14% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 20059ms 99.14% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 20059ms 99.14% main 0 0% 0% 20019ms 98.95% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 20019ms 98.95% CxxTest::TestRunner::runTest (inline) 0 0% 0% 20019ms 98.95% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0049% 0.0049% 20012ms 98.91% AbstractCellBasedSimulation::Solve 2ms 0.0099% 0.015% 11410ms 56.40% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.015% 7689ms 38.00% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.02% 0.035% 7638ms 37.75% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.049% 0.084% 7540ms 37.27% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.084% 6806ms 33.64% NodeBasedCellPopulation::Update 1195ms 5.91% 5.99% 6742ms 33.32% RepulsionForce::AddForceContribution (partial-inline) 6ms 0.03% 6.02% 5966ms 29.49% DistributedBoxCollection::CalculateInteriorNodePairs 23ms 0.11% 6.13% 3537ms 17.48% NodeAttributes::RemoveDuplicateNeighbours 1ms 0.0049% 6.14% 3517ms 17.38% OffLatticeSimulation::ApplyBoundaries 5ms 0.025% 6.16% 3385ms 16.73% std::__sort (inline) 0 0% 6.16% 3385ms 16.73% std::sort (inline) 195ms 0.96% 7.13% 3122ms 15.43% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 1313ms 6.49% 13.62% 2884ms 14.25% std::_Rb_tree::_M_lower_bound (inline) 2ms 0.0099% 13.63% 2333ms 11.53% AbstractCellPopulation::Iterator::operator++ (inline) 59ms 0.29% 13.92% 2320ms 11.47% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 237ms 1.17% 15.09% 2309ms 11.41% AbstractCellPopulation::Iterator::IsRealCell (inline) 41ms 0.2% 15.29% 2277ms 11.25% AbstractCellPopulation::GetLocationIndexUsingCell 226ms 1.12% 16.41% 2227ms 11.01% std::map::operator[] (partial-inline) 198ms 0.98% 17.39% 2180ms 10.78% DistributedBoxCollection::AddPairsFromBox 131ms 0.65% 18.04% 1976ms 9.77% std::__introsort_loop 27ms 0.13% 18.17% 1857ms 9.18% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 18.17% 1848ms 9.13% std::_Rb_tree::lower_bound (inline) 0 0% 18.17% 1848ms 9.13% std::map::lower_bound (inline) 24ms 0.12% 18.29% 1839ms 9.09% PlaneBoundaryCondition::ImposeBoundaryCondition 0 0% 18.29% 1771ms 8.75% std::__unguarded_partition_pivot (inline) 7ms 0.035% 18.32% 1677ms 8.29% PlaneBoundaryCondition::VerifyBoundaryCondition 801ms 3.96% 22.28% 1612ms 7.97% std::__unguarded_partition (inline) 15ms 0.074% 22.36% 1580ms 7.81% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 25ms 0.12% 22.48% 1557ms 7.70% AbstractCellPopulation::GetCellUsingLocationIndex 1529ms 7.56% 30.04% 1529ms 7.56% std::_Rb_tree::_S_right (inline) 0 0% 30.04% 1404ms 6.94% std::__final_insertion_sort (inline) 585ms 2.89% 32.93% 1280ms 6.33% std::__unguarded_linear_insert (inline) 75ms 0.37% 33.30% 1227ms 6.06% std::__unguarded_insertion_sort (inline) 134ms 0.66% 33.96% 1170ms 5.78% std::_Rb_tree::find (inline) 0 0% 33.96% 1170ms 5.78% std::map::find (inline) 74ms 0.37% 34.33% 1145ms 5.66% boost::numeric::ublas::c_vector::c_vector (partial-inline) 1084ms 5.36% 39.68% 1084ms 5.36% __gnu_cxx::__normal_iterator::operator-- (inline) 42ms 0.21% 39.89% 962ms 4.75% boost::numeric::ublas::vector_assign (inline) 285ms 1.41% 41.30% 943ms 4.66% __dynamic_cast 255ms 1.26% 42.56% 873ms 4.31% boost::numeric::ublas::indexing_vector_assign 237ms 1.17% 43.73% 778ms 3.85% NodeAttributes::AddNeighbour 42ms 0.21% 43.94% 769ms 3.80% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 43.94% 753ms 3.72% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 131ms 0.65% 44.59% 750ms 3.71% AbstractMesh::GetVectorFromAtoB 8ms 0.04% 44.63% 746ms 3.69% CellPropertyCollection::GetPropertiesType (inline) 0 0% 44.63% 743ms 3.67% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 44.63% 742ms 3.67% boost::numeric::ublas::norm_2 (inline) 589ms 2.91% 47.54% 742ms 3.67% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 47.54% 730ms 3.61% NodeBasedCellPopulation::UpdateCellProcessLocation 22ms 0.11% 47.65% 717ms 3.54% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 4ms 0.02% 47.67% 704ms 3.48% AbstractCentreBasedCellPopulation::GetDampingConstant 700ms 3.46% 51.13% 700ms 3.46% std::_Rb_tree_increment 4ms 0.02% 51.15% 691ms 3.42% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 51.15% 687ms 3.40% AbstractCellPopulation::WriteResultsToFiles 34ms 0.17% 51.31% 674ms 3.33% std::__copy_move::__copy_m (inline) 0 0% 51.31% 674ms 3.33% std::__copy_move_a (inline) 0 0% 51.31% 674ms 3.33% std::__copy_move_a1 (inline) 0 0% 51.31% 674ms 3.33% std::__copy_move_a2 (inline) 0 0% 51.31% 674ms 3.33% std::copy (inline) 664ms 3.28% 54.60% 664ms 3.28% __memcpy_avx_unaligned_erms 538ms 2.66% 57.26% 627ms 3.10% std::vector::push_back (inline) 342ms 1.69% 58.95% 593ms 2.93% DistributedBoxCollection::CalculateContainingBox (partial-inline) 256ms 1.27% 60.21% 567ms 2.80% __cxxabiv1::__si_class_type_info::__do_dyncast 2ms 0.0099% 60.22% 548ms 2.71% Cell::GetMutationState 2ms 0.0099% 60.23% 502ms 2.48% AbstractCellBasedSimulation::DoCellBirth 489ms 2.42% 62.65% 489ms 2.42% boost::numeric::ublas::c_vector::operator() 469ms 2.32% 64.97% 469ms 2.32% boost::numeric::ublas::same_impl_ex 34ms 0.17% 65.13% 456ms 2.25% std::_Rb_tree::_Rb_tree (partial-inline) 446ms 2.20% 67.34% 446ms 2.20% __strcmp_avx2 2ms 0.0099% 67.35% 441ms 2.18% std::set::set (inline) 1ms 0.0049% 67.35% 437ms 2.16% AbstractCellProperty::IsSubType (inline) 6ms 0.03% 67.38% 432ms 2.14% NodeBasedCellPopulation::WriteVtkResultsToFile 42ms 0.21% 67.59% 413ms 2.04% NodesOnlyMesh::GetNodeOrHaloNode 46ms 0.23% 67.82% 410ms 2.03% std::_Rb_tree::_M_copy (inline) 89ms 0.44% 68.26% 402ms 1.99% std::__new_allocator::allocate (inline) 134ms 0.66% 68.92% 390ms 1.93% Node::GetRadius 0 0% 68.92% 386ms 1.91% std::allocator_traits::allocate (inline) 0 0% 68.92% 380ms 1.88% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 68.92% 367ms 1.81% std::_Rb_tree::_M_create_node (inline) 30ms 0.15% 69.07% 362ms 1.79% boost::detail::shared_count::~shared_count (inline) 0 0% 69.07% 362ms 1.79% boost::shared_ptr::~shared_ptr (inline) 151ms 0.75% 69.82% 362ms 1.79% std::_Rb_tree::_M_clone_node (inline) 4ms 0.02% 69.83% 360ms 1.78% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 201ms 0.99% 70.83% 355ms 1.75% AbstractMesh::GetNode 124ms 0.61% 71.44% 348ms 1.72% std::_Rb_tree::_M_erase (partial-inline) 0 0% 71.44% 342ms 1.69% std::_Rb_tree::_M_get_node (inline) 319ms 1.58% 73.02% 325ms 1.61% boost::detail::sp_counted_base::release 26ms 0.13% 73.15% 325ms 1.61% boost::numeric::ublas::vector_binary::size (inline) 0 0% 73.15% 321ms 1.59% boost::numeric::ublas::inner_prod (inline) 16ms 0.079% 73.23% 319ms 1.58% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 73.23% 319ms 1.58% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 40ms 0.2% 73.42% 315ms 1.56% std::_Rb_tree::~_Rb_tree (inline) 20ms 0.099% 73.52% 312ms 1.54% operator new 305ms 1.51% 75.03% 305ms 1.51% [libchaste_mesh.so] 8ms 0.04% 75.07% 303ms 1.50% NodeBasedCellPopulation::UpdateMapsAfterRemesh 97ms 0.48% 75.55% 292ms 1.44% __GI___libc_malloc 0 0% 75.55% 275ms 1.36% boost::numeric::ublas::c_vector::assign (inline) 269ms 1.33% 76.88% 269ms 1.33% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 76.88% 268ms 1.32% std::_Rb_tree::_Alloc_node::operator() (inline) 261ms 1.29% 78.17% 261ms 1.29% Node::CheckForNodeAttributes 88ms 0.43% 78.60% 248ms 1.23% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 78.60% 242ms 1.20% std::set::~set (inline) 4ms 0.02% 78.62% 237ms 1.17% CellPropertyCollection::HasProperty 0 0% 78.62% 236ms 1.17% Cell::HasCellProperty (inline) 0 0% 78.62% 229ms 1.13% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 78.62% 228ms 1.13% VtkMeshWriter::WriteFiles 0 0% 78.62% 226ms 1.12% NodesOnlyMesh::UpdateBoxCollection 8ms 0.04% 78.66% 225ms 1.11% Cell::ReadyToDivide 0 0% 78.66% 218ms 1.08% std::_Rb_tree::_M_drop_node (inline) 5ms 0.025% 78.69% 208ms 1.03% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 95ms 0.47% 79.16% 207ms 1.02% boost::shared_ptr::shared_ptr (inline) 0 0% 79.16% 201ms 0.99% vtkStreamingDemandDrivenPipeline::Update 0 0% 79.16% 201ms 0.99% vtkXMLWriterBase::Write 0 0% 79.16% 199ms 0.98% vtkDemandDrivenPipeline::ProcessRequest 1ms 0.0049% 79.16% 199ms 0.98% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 79.16% 198ms 0.98% vtkDemandDrivenPipeline::ExecuteData 5ms 0.025% 79.19% 197ms 0.97% DistributedBoxCollection::GetProcessOwningNode 0 0% 79.19% 197ms 0.97% vtkCompositeDataPipeline::ExecuteData 0 0% 79.19% 197ms 0.97% vtkExecutive::CallAlgorithm 1ms 0.0049% 79.19% 196ms 0.97% vtkXMLUnstructuredDataWriter::ProcessRequest 186ms 0.92% 80.11% 186ms 0.92% Node::GetIndex 11ms 0.054% 80.17% 177ms 0.87% std::__insertion_sort (inline) 175ms 0.86% 81.03% 175ms 0.86% [libchaste_cell_based.so] 6ms 0.03% 81.06% 175ms 0.86% std::__new_allocator::deallocate (inline) 92ms 0.45% 81.51% 169ms 0.84% Node::AddNeighbour 0 0% 81.51% 168ms 0.83% NodesOnlyMesh::AddNodesToBoxes 0 0% 81.51% 166ms 0.82% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 81.51% 166ms 0.82% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 4ms 0.02% 81.53% 165ms 0.82% AbstractCellProperty::IsType (inline) 165ms 0.82% 82.35% 165ms 0.82% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 82.35% 164ms 0.81% NodesOnlyMesh::ResizeBoxCollection 8ms 0.04% 82.39% 163ms 0.81% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 82.39% 160ms 0.79% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 76ms 0.38% 82.76% 159ms 0.79% std::__move_median_to_first (inline) 133ms 0.66% 83.42% 156ms 0.77% NodesOnlyMesh::SolveNodeMapping 54ms 0.27% 83.69% 156ms 0.77% __GI___libc_free 93ms 0.46% 84.15% 153ms 0.76% _int_malloc 1ms 0.0049% 84.15% 153ms 0.76% std::_Rb_tree::_M_emplace_hint_unique 149ms 0.74% 84.89% 149ms 0.74% boost::shared_ptr::operator-> (inline) 0 0% 84.89% 146ms 0.72% std::allocator_traits::deallocate (inline) 15ms 0.074% 84.96% 143ms 0.71% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 84.96% 143ms 0.71% std::_Rb_tree::_M_put_node (inline) 1ms 0.0049% 84.97% 141ms 0.7% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 84.97% 135ms 0.67% vtkXMLWriter::WriteBinaryData 0 0% 84.97% 134ms 0.66% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 84.97% 132ms 0.65% Cell::GetCellId 132ms 0.65% 85.62% 132ms 0.65% Node::IsDeleted 0 0% 85.62% 130ms 0.64% vtkXMLWriter::WriteBinaryDataInternal 0 0% 85.62% 129ms 0.64% vtkXMLWriter::WriteBinaryDataBlock 54ms 0.27% 85.89% 128ms 0.63% AbstractCellProperty::IsSame 0 0% 85.89% 128ms 0.63% vtkXMLWriter::WriteCompressionBlock 126ms 0.62% 86.51% 126ms 0.62% std::__adjacent_find (inline) 0 0% 86.51% 126ms 0.62% std::__unique (inline) 0 0% 86.51% 126ms 0.62% std::unique (inline) 123ms 0.61% 87.12% 123ms 0.61% __ieee754_log_fma 0 0% 87.12% 123ms 0.61% tbb::detail::r1::parallel_pipeline 0 0% 87.12% 119ms 0.59% clone3 0 0% 87.12% 119ms 0.59% start_thread 0 0% 87.12% 118ms 0.58% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 87.12% 118ms 0.58% tbb::detail::r1::reset 7ms 0.035% 87.15% 117ms 0.58% DistributedBoxCollection::GetIsPeriodicAllDims 1ms 0.0049% 87.16% 116ms 0.57% NodeBasedCellPopulation::AcceptCellWriter 0 0% 87.16% 116ms 0.57% vtkDataCompressor::Compress 0 0% 87.16% 114ms 0.56% compress2 0 0% 87.16% 114ms 0.56% vtkZLibDataCompressor::CompressBuffer 0 0% 87.16% 113ms 0.56% Cell::GetCellProliferativeType 54ms 0.27% 87.43% 113ms 0.56% crc32 0 0% 87.43% 113ms 0.56% deflate 53ms 0.26% 87.69% 113ms 0.56% tbb::detail::r1::wait_bounded_queue_monitor 0 0% 87.69% 113ms 0.56% vtkXMLWriter::WritePointsAppendedData 52ms 0.26% 87.94% 112ms 0.55% AbstractCellCycleModel::GetAge 69ms 0.34% 88.29% 112ms 0.55% boost::detail::shared_count::shared_count (inline) 1ms 0.0049% 88.29% 110ms 0.54% AbstractCellPopulation::SetCellUsingLocationIndex 0 0% 88.29% 109ms 0.54% std::_Rb_tree::_M_insert_unique 0 0% 88.29% 109ms 0.54% std::set::insert (inline) 90ms 0.44% 88.74% 102ms 0.5% _int_free