File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20668ms, 89.01% of 23219ms total Dropped 766 nodes (cum <= 116.09ms) flat flat% sum% cum cum% 0 0% 0% 23079ms 99.40% __libc_start_call_main 0 0% 0% 23079ms 99.40% __libc_start_main_impl 0 0% 0% 23079ms 99.40% _start 0 0% 0% 23063ms 99.33% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 23063ms 99.33% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 23063ms 99.33% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 23063ms 99.33% main 0 0% 0% 23025ms 99.16% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 23025ms 99.16% CxxTest::TestRunner::runTest (inline) 0 0% 0% 23025ms 99.16% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0043% 0.0043% 23017ms 99.13% AbstractCellBasedSimulation::Solve 0 0% 0.0043% 13040ms 56.16% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0043% 8807ms 37.93% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.013% 0.017% 8315ms 35.81% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.026% 0.043% 8137ms 35.04% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.0043% 0.047% 7788ms 33.54% NodeBasedCellPopulation::Update 1285ms 5.53% 5.58% 7525ms 32.41% RepulsionForce::AddForceContribution (partial-inline) 8ms 0.034% 5.62% 5742ms 24.73% DistributedBoxCollection::CalculateInteriorNodePairs 2116ms 9.11% 14.73% 4772ms 20.55% std::_Rb_tree::_M_lower_bound (inline) 23ms 0.099% 14.83% 4516ms 19.45% NodeAttributes::RemoveDuplicateNeighbours 0 0% 14.83% 4454ms 19.18% OffLatticeSimulation::ApplyBoundaries 4ms 0.017% 14.85% 4330ms 18.65% std::__sort (inline) 0 0% 14.85% 4330ms 18.65% std::sort (inline) 187ms 0.81% 15.65% 3743ms 16.12% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 7ms 0.03% 15.68% 3414ms 14.70% AbstractCellPopulation::Iterator::operator++ (inline) 206ms 0.89% 16.57% 3382ms 14.57% AbstractCellPopulation::Iterator::IsRealCell 77ms 0.33% 16.90% 3362ms 14.48% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 248ms 1.07% 17.97% 3142ms 13.53% std::_Rb_tree::find (inline) 0 0% 17.97% 3142ms 13.53% std::map::find (inline) 16ms 0.069% 18.04% 2894ms 12.46% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2600ms 11.20% 29.23% 2600ms 11.20% std::_Rb_tree::_S_right (inline) 197ms 0.85% 30.08% 2509ms 10.81% std::__introsort_loop 221ms 0.95% 31.03% 2391ms 10.30% std::map::operator[] (partial-inline) 19ms 0.082% 31.12% 2296ms 9.89% PlaneBoundaryCondition::ImposeBoundaryCondition 25ms 0.11% 31.22% 2267ms 9.76% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 31.22% 2247ms 9.68% std::__unguarded_partition_pivot (inline) 143ms 0.62% 31.84% 2239ms 9.64% AbstractMesh::GetNode 61ms 0.26% 32.10% 2222ms 9.57% NodesOnlyMesh::GetNodeOrHaloNode 16ms 0.069% 32.17% 2158ms 9.29% PlaneBoundaryCondition::VerifyBoundaryCondition 88ms 0.38% 32.55% 2099ms 9.04% NodesOnlyMesh::SolveNodeMapping 1047ms 4.51% 37.06% 2045ms 8.81% std::__unguarded_partition (inline) 0 0% 37.06% 1910ms 8.23% std::_Rb_tree::lower_bound (inline) 0 0% 37.06% 1910ms 8.23% std::map::lower_bound (inline) 178ms 0.77% 37.83% 1884ms 8.11% DistributedBoxCollection::AddPairsFromBox 1ms 0.0043% 37.83% 1816ms 7.82% std::__final_insertion_sort (inline) 104ms 0.45% 38.28% 1597ms 6.88% std::__unguarded_insertion_sort (inline) 592ms 2.55% 40.83% 1543ms 6.65% std::__unguarded_linear_insert (inline) 21ms 0.09% 40.92% 1478ms 6.37% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 24ms 0.1% 41.02% 1452ms 6.25% AbstractCellPopulation::GetCellUsingLocationIndex 1408ms 6.06% 47.09% 1408ms 6.06% __gnu_cxx::__normal_iterator::operator-- (inline) 36ms 0.16% 47.24% 1235ms 5.32% boost::numeric::ublas::c_vector::c_vector (partial-inline) 45ms 0.19% 47.44% 1113ms 4.79% boost::numeric::ublas::vector_assign (inline) 0 0% 47.44% 1112ms 4.79% NodeBasedCellPopulation::UpdateCellProcessLocation 7ms 0.03% 47.47% 1102ms 4.75% DistributedBoxCollection::CalculateBoundaryNodePairs 266ms 1.15% 48.61% 989ms 4.26% boost::numeric::ublas::indexing_vector_assign 230ms 0.99% 49.60% 905ms 3.90% __dynamic_cast 163ms 0.7% 50.30% 805ms 3.47% AbstractMesh::GetVectorFromAtoB 28ms 0.12% 50.42% 794ms 3.42% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 50.42% 781ms 3.36% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 367ms 1.58% 52.00% 772ms 3.32% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 52.00% 754ms 3.25% boost::numeric::ublas::norm_2 (inline) 592ms 2.55% 54.55% 754ms 3.25% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 54.55% 754ms 3.25% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 54.55% 734ms 3.16% AbstractCellPopulation::WriteResultsToFiles 208ms 0.9% 55.45% 721ms 3.11% NodeAttributes::AddNeighbour 26ms 0.11% 55.56% 634ms 2.73% std::_Rb_tree_const_iterator::operator++ (inline) 6ms 0.026% 55.59% 628ms 2.70% boost::numeric::ublas::c_vector::operator= (inline) 611ms 2.63% 58.22% 611ms 2.63% std::_Rb_tree_increment 606ms 2.61% 60.83% 606ms 2.61% boost::numeric::ublas::c_vector::operator() 33ms 0.14% 60.97% 604ms 2.60% std::__copy_move::__copy_m (inline) 0 0% 60.97% 604ms 2.60% std::__copy_move_a (inline) 0 0% 60.97% 604ms 2.60% std::__copy_move_a1 (inline) 0 0% 60.97% 604ms 2.60% std::__copy_move_a2 (inline) 0 0% 60.97% 603ms 2.60% std::copy (inline) 585ms 2.52% 63.49% 585ms 2.52% __memcpy_avx_unaligned_erms 5ms 0.022% 63.51% 578ms 2.49% CellPropertyCollection::GetPropertiesType (inline) 512ms 2.21% 65.72% 577ms 2.49% std::vector::push_back (inline) 265ms 1.14% 66.86% 565ms 2.43% __cxxabiv1::__si_class_type_info::__do_dyncast 3ms 0.013% 66.87% 558ms 2.40% AbstractCentreBasedCellPopulation::GetDampingConstant 4ms 0.017% 66.89% 545ms 2.35% AbstractCellBasedSimulation::DoCellBirth 533ms 2.30% 69.18% 533ms 2.30% boost::numeric::ublas::same_impl_ex 52ms 0.22% 69.41% 510ms 2.20% std::__new_allocator::allocate (inline) 0 0% 69.41% 490ms 2.11% std::allocator_traits::allocate (inline) 2ms 0.0086% 69.42% 476ms 2.05% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 69.42% 474ms 2.04% AbstractCellBasedSimulation::DoCellRemoval (inline) 470ms 2.02% 71.44% 470ms 2.02% __strcmp_avx2 8ms 0.034% 71.48% 458ms 1.97% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 16ms 0.069% 71.54% 457ms 1.97% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 71.54% 455ms 1.96% std::_Rb_tree::_M_create_node (inline) 32ms 0.14% 71.68% 453ms 1.95% boost::detail::shared_count::~shared_count (inline) 0 0% 71.68% 453ms 1.95% boost::shared_ptr::~shared_ptr (inline) 31ms 0.13% 71.82% 441ms 1.90% operator new 39ms 0.17% 71.98% 429ms 1.85% std::_Rb_tree::_M_copy (inline) 139ms 0.6% 72.58% 420ms 1.81% Node::GetRadius 400ms 1.72% 74.31% 411ms 1.77% boost::detail::sp_counted_base::release 0 0% 74.31% 408ms 1.76% std::_Rb_tree::_M_get_node (inline) 138ms 0.59% 74.90% 401ms 1.73% std::_Rb_tree::_M_erase 119ms 0.51% 75.41% 400ms 1.72% __GI___libc_malloc 3ms 0.013% 75.43% 393ms 1.69% Cell::GetMutationState 120ms 0.52% 75.94% 388ms 1.67% std::_Rb_tree::_M_clone_node (inline) 0 0% 75.94% 385ms 1.66% AbstractCellProperty::IsSubType (inline) 2ms 0.0086% 75.95% 373ms 1.61% std::set::set (inline) 25ms 0.11% 76.06% 342ms 1.47% boost::numeric::ublas::vector_binary::size (inline) 325ms 1.40% 77.46% 325ms 1.40% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 77.46% 324ms 1.40% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 77.46% 323ms 1.39% boost::numeric::ublas::inner_prod (inline) 322ms 1.39% 78.84% 322ms 1.39% __gnu_cxx::__normal_iterator::operator++ (inline) 1ms 0.0043% 78.85% 322ms 1.39% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 20ms 0.086% 78.94% 321ms 1.38% boost::numeric::ublas::vector_scalar_binary::evaluate 5ms 0.022% 78.96% 317ms 1.37% NodeBasedCellPopulation::UpdateMapsAfterRemesh 45ms 0.19% 79.15% 311ms 1.34% std::_Rb_tree::~_Rb_tree (inline) 0 0% 79.15% 303ms 1.30% boost::numeric::ublas::c_vector::assign (inline) 0 0% 79.15% 298ms 1.28% NodesOnlyMesh::ReMesh 291ms 1.25% 80.40% 291ms 1.25% Node::CheckForNodeAttributes 6ms 0.026% 80.43% 291ms 1.25% NodesOnlyMesh::UpdateNodeIndices 0 0% 80.43% 261ms 1.12% std::_Rb_tree::_M_drop_node (inline) 5ms 0.022% 80.45% 260ms 1.12% std::_Rb_tree::_M_emplace_hint_unique 3ms 0.013% 80.46% 253ms 1.09% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 80.46% 253ms 1.09% NodesOnlyMesh::UpdateBoxCollection 101ms 0.43% 80.90% 253ms 1.09% boost::numeric::ublas::vector_inner_prod::apply (inline) 6ms 0.026% 80.93% 241ms 1.04% DistributedBoxCollection::GetProcessOwningNode 0 0% 80.93% 233ms 1.00% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 80.93% 232ms 1% VtkMeshWriter::WriteFiles 0 0% 80.93% 231ms 0.99% std::set::~set (inline) 1ms 0.0043% 80.93% 222ms 0.96% NodesOnlyMesh::AddNodesToBoxes 121ms 0.52% 81.45% 220ms 0.95% _int_malloc 29ms 0.12% 81.58% 218ms 0.94% std::__insertion_sort (inline) 0 0% 81.58% 218ms 0.94% std::__new_allocator::deallocate (inline) 0 0% 81.58% 209ms 0.9% vtkCompositeDataPipeline::ExecuteData 0 0% 81.58% 209ms 0.9% vtkDemandDrivenPipeline::ExecuteData 0 0% 81.58% 209ms 0.9% vtkDemandDrivenPipeline::ProcessRequest 0 0% 81.58% 209ms 0.9% vtkExecutive::CallAlgorithm 0 0% 81.58% 209ms 0.9% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 81.58% 209ms 0.9% vtkStreamingDemandDrivenPipeline::Update 0 0% 81.58% 209ms 0.9% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 81.58% 209ms 0.9% vtkXMLWriterBase::Write 105ms 0.45% 82.03% 203ms 0.87% boost::shared_ptr::shared_ptr (inline) 90ms 0.39% 82.42% 202ms 0.87% std::__move_median_to_first (inline) 0 0% 82.42% 201ms 0.87% std::allocator_traits::deallocate (inline) 0 0% 82.42% 200ms 0.86% std::_Rb_tree::_M_put_node (inline) 0 0% 82.42% 198ms 0.85% Cell::HasCellProperty (inline) 3ms 0.013% 82.43% 198ms 0.85% CellPropertyCollection::HasProperty 0 0% 82.43% 191ms 0.82% NodesOnlyMesh::ResizeBoxCollection 70ms 0.3% 82.73% 191ms 0.82% __GI___libc_free 16ms 0.069% 82.80% 189ms 0.81% NodesOnlyMesh::IsANodeCloseToDomainBoundary 189ms 0.81% 83.61% 189ms 0.81% [libchaste_cell_based.so] 186ms 0.8% 84.41% 186ms 0.8% Node::GetIndex 3ms 0.013% 84.43% 180ms 0.78% Cell::ReadyToDivide 0 0% 84.43% 174ms 0.75% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 84.43% 174ms 0.75% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 84.43% 171ms 0.74% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 2ms 0.0086% 84.44% 166ms 0.71% AbstractCellProperty::IsType (inline) 88ms 0.38% 84.81% 160ms 0.69% Node::AddNeighbour 1ms 0.0043% 84.82% 158ms 0.68% std::_Rb_tree::clear (inline) 145ms 0.62% 85.44% 148ms 0.64% std::__adjacent_find (inline) 0 0% 85.44% 148ms 0.64% std::__unique (inline) 0 0% 85.44% 148ms 0.64% std::unique (inline) 145ms 0.62% 86.07% 145ms 0.62% Node::IsDeleted 0 0% 86.07% 144ms 0.62% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 144ms 0.62% 86.69% 144ms 0.62% boost::shared_ptr::operator-> (inline) 0 0% 86.69% 143ms 0.62% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 86.69% 140ms 0.6% vtkXMLWriter::WriteBinaryData 139ms 0.6% 87.29% 139ms 0.6% [libchaste_mesh.so] 16ms 0.069% 87.36% 139ms 0.6% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 87.36% 136ms 0.59% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.36% 136ms 0.59% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.36% 136ms 0.59% vtkXMLWriter::WriteCompressionBlock 8ms 0.034% 87.39% 135ms 0.58% DistributedBoxCollection::GetIsPeriodicAllDims 0 0% 87.39% 131ms 0.56% std::_Rb_tree::_Auto_node::_Auto_node (inline) 130ms 0.56% 87.95% 130ms 0.56% __ieee754_log_fma 0 0% 87.95% 128ms 0.55% std::map::clear (inline) 4ms 0.017% 87.97% 127ms 0.55% AbstractCellPopulation::SetCellUsingLocationIndex 32ms 0.14% 88.10% 123ms 0.53% AbstractCellProperty::IsSame 38ms 0.16% 88.27% 122ms 0.53% AbstractCellCycleModel::GetAge 0 0% 88.27% 122ms 0.53% compress2 62ms 0.27% 88.54% 122ms 0.53% crc32 0 0% 88.54% 122ms 0.53% deflate 0 0% 88.54% 122ms 0.53% vtkDataCompressor::Compress 0 0% 88.54% 122ms 0.53% vtkZLibDataCompressor::CompressBuffer 108ms 0.47% 89.00% 121ms 0.52% _int_free 3ms 0.013% 89.01% 120ms 0.52% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 89.01% 119ms 0.51% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 89.01% 119ms 0.51% vtkXMLWriter::WritePointsAppendedData