File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20874ms, 87.91% of 23745ms total Dropped 814 nodes (cum <= 118.72ms) flat flat% sum% cum cum% 0 0% 0% 23591ms 99.35% __libc_start_call_main 0 0% 0% 23591ms 99.35% __libc_start_main_impl 0 0% 0% 23591ms 99.35% _start 0 0% 0% 23576ms 99.29% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 23576ms 99.29% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 23576ms 99.29% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 23576ms 99.29% main 0 0% 0% 23535ms 99.12% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 23535ms 99.12% CxxTest::TestRunner::runTest (inline) 0 0% 0% 23535ms 99.12% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 23526ms 99.08% AbstractCellBasedSimulation::Solve 3ms 0.013% 0.013% 13381ms 56.35% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.013% 8933ms 37.62% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0084% 0.021% 8521ms 35.89% ForwardEulerNumericalMethod::UpdateAllNodePositions 7ms 0.029% 0.051% 8345ms 35.14% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.051% 7856ms 33.08% NodeBasedCellPopulation::Update 1199ms 5.05% 5.10% 7625ms 32.11% RepulsionForce::AddForceContribution (partial-inline) 8ms 0.034% 5.13% 5828ms 24.54% DistributedBoxCollection::CalculateInteriorNodePairs 2199ms 9.26% 14.39% 4978ms 20.96% std::_Rb_tree::_M_lower_bound (inline) 0 0% 14.39% 4566ms 19.23% OffLatticeSimulation::ApplyBoundaries 20ms 0.084% 14.48% 4398ms 18.52% NodeAttributes::RemoveDuplicateNeighbours 6ms 0.025% 14.50% 4223ms 17.78% std::__sort (inline) 0 0% 14.50% 4223ms 17.78% std::sort (inline) 194ms 0.82% 15.32% 3909ms 16.46% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 73ms 0.31% 15.63% 3458ms 14.56% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 2ms 0.0084% 15.64% 3450ms 14.53% AbstractCellPopulation::Iterator::operator++ (inline) 190ms 0.8% 16.44% 3418ms 14.39% AbstractCellPopulation::Iterator::IsRealCell (inline) 240ms 1.01% 17.45% 3264ms 13.75% std::_Rb_tree::find (inline) 0 0% 17.45% 3264ms 13.75% std::map::find (inline) 28ms 0.12% 17.57% 2917ms 12.28% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2740ms 11.54% 29.11% 2740ms 11.54% std::_Rb_tree::_S_right (inline) 234ms 0.99% 30.09% 2471ms 10.41% std::map::operator[] (partial-inline) 157ms 0.66% 30.75% 2428ms 10.23% std::__introsort_loop 27ms 0.11% 30.87% 2371ms 9.99% PlaneBoundaryCondition::ImposeBoundaryCondition 45ms 0.19% 31.05% 2361ms 9.94% AbstractCellPopulation::GetLocationIndexUsingCell 148ms 0.62% 31.68% 2268ms 9.55% AbstractMesh::GetNode 64ms 0.27% 31.95% 2265ms 9.54% NodesOnlyMesh::GetNodeOrHaloNode 19ms 0.08% 32.03% 2195ms 9.24% PlaneBoundaryCondition::VerifyBoundaryCondition 0 0% 32.03% 2185ms 9.20% std::__unguarded_partition_pivot (inline) 74ms 0.31% 32.34% 2128ms 8.96% NodesOnlyMesh::SolveNodeMapping 222ms 0.93% 33.27% 2068ms 8.71% DistributedBoxCollection::AddPairsFromBox 1032ms 4.35% 37.62% 1985ms 8.36% std::__unguarded_partition (inline) 0 0% 37.62% 1971ms 8.30% std::_Rb_tree::lower_bound (inline) 0 0% 37.62% 1971ms 8.30% std::map::lower_bound (inline) 1ms 0.0042% 37.62% 1785ms 7.52% std::__final_insertion_sort (inline) 19ms 0.08% 37.70% 1583ms 6.67% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 97ms 0.41% 38.11% 1564ms 6.59% std::__unguarded_insertion_sort (inline) 26ms 0.11% 38.22% 1557ms 6.56% AbstractCellPopulation::GetCellUsingLocationIndex 553ms 2.33% 40.55% 1524ms 6.42% std::__unguarded_linear_insert (inline) 1410ms 5.94% 46.49% 1410ms 5.94% __gnu_cxx::__normal_iterator::operator-- (inline) 58ms 0.24% 46.73% 1241ms 5.23% boost::numeric::ublas::c_vector::c_vector (partial-inline) 1ms 0.0042% 46.74% 1159ms 4.88% NodeBasedCellPopulation::UpdateCellProcessLocation 38ms 0.16% 46.90% 1092ms 4.60% boost::numeric::ublas::vector_assign (inline) 2ms 0.0084% 46.91% 1091ms 4.59% DistributedBoxCollection::CalculateBoundaryNodePairs 264ms 1.11% 48.02% 1007ms 4.24% boost::numeric::ublas::indexing_vector_assign 270ms 1.14% 49.16% 998ms 4.20% __dynamic_cast 17ms 0.072% 49.23% 843ms 3.55% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 173ms 0.73% 49.96% 822ms 3.46% AbstractMesh::GetVectorFromAtoB 359ms 1.51% 51.47% 776ms 3.27% DistributedBoxCollection::CalculateContainingBox (partial-inline) 276ms 1.16% 52.63% 762ms 3.21% NodeAttributes::AddNeighbour 0 0% 52.63% 740ms 3.12% AbstractCellPopulation::WriteResultsToFiles 0 0% 52.63% 723ms 3.04% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 35ms 0.15% 52.78% 712ms 3.00% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 52.78% 708ms 2.98% boost::numeric::ublas::norm_2 (inline) 545ms 2.30% 55.07% 708ms 2.98% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 55.07% 708ms 2.98% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 672ms 2.83% 57.90% 672ms 2.83% boost::numeric::ublas::c_vector::operator() 665ms 2.80% 60.70% 665ms 2.80% std::_Rb_tree_increment 9ms 0.038% 60.74% 663ms 2.79% CellPropertyCollection::GetPropertiesType (inline) 2ms 0.0084% 60.75% 653ms 2.75% boost::numeric::ublas::c_vector::operator= (inline) 44ms 0.19% 60.93% 643ms 2.71% std::__copy_move::__copy_m (inline) 0 0% 60.93% 643ms 2.71% std::__copy_move_a (inline) 0 0% 60.93% 643ms 2.71% std::__copy_move_a1 (inline) 0 0% 60.93% 643ms 2.71% std::__copy_move_a2 (inline) 0 0% 60.93% 643ms 2.71% std::copy (inline) 4ms 0.017% 60.95% 621ms 2.62% AbstractCellBasedSimulation::DoCellBirth 619ms 2.61% 63.56% 619ms 2.61% __memcpy_avx_unaligned_erms 3ms 0.013% 63.57% 616ms 2.59% AbstractCentreBasedCellPopulation::GetDampingConstant 268ms 1.13% 64.70% 613ms 2.58% __cxxabiv1::__si_class_type_info::__do_dyncast 484ms 2.04% 66.74% 591ms 2.49% std::vector::push_back (inline) 80ms 0.34% 67.08% 534ms 2.25% std::__new_allocator::allocate (inline) 0 0% 67.08% 518ms 2.18% std::allocator_traits::allocate (inline) 31ms 0.13% 67.21% 511ms 2.15% boost::detail::shared_count::~shared_count (inline) 0 0% 67.21% 511ms 2.15% boost::shared_ptr::~shared_ptr (inline) 10ms 0.042% 67.25% 508ms 2.14% std::_Rb_tree::_Rb_tree (partial-inline) 507ms 2.14% 69.38% 507ms 2.14% boost::numeric::ublas::same_impl_ex 505ms 2.13% 71.51% 505ms 2.13% __strcmp_avx2 1ms 0.0042% 71.51% 484ms 2.04% NodeBasedCellPopulation::WriteVtkResultsToFile 2ms 0.0084% 71.52% 483ms 2.03% Cell::GetMutationState 0 0% 71.52% 482ms 2.03% std::_Rb_tree::_M_create_node (inline) 56ms 0.24% 71.76% 481ms 2.03% std::_Rb_tree::_M_copy (inline) 463ms 1.95% 73.71% 470ms 1.98% boost::detail::sp_counted_base::release 0 0% 73.71% 456ms 1.92% AbstractCellBasedSimulation::DoCellRemoval (inline) 21ms 0.088% 73.80% 452ms 1.90% operator new 7ms 0.029% 73.83% 445ms 1.87% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 118ms 0.5% 74.32% 426ms 1.79% __GI___libc_malloc 154ms 0.65% 74.97% 424ms 1.79% std::_Rb_tree::_M_clone_node (inline) 2ms 0.0084% 74.98% 424ms 1.79% std::set::set (inline) 131ms 0.55% 75.53% 422ms 1.78% std::_Rb_tree::_M_erase 4ms 0.017% 75.55% 421ms 1.77% AbstractCellProperty::IsSubType (inline) 139ms 0.59% 76.13% 421ms 1.77% Node::GetRadius 0 0% 76.13% 416ms 1.75% std::_Rb_tree::_M_get_node (inline) 22ms 0.093% 76.23% 337ms 1.42% boost::numeric::ublas::vector_binary::size (inline) 0 0% 76.23% 335ms 1.41% std::_Rb_tree::_Alloc_node::operator() (inline) 1ms 0.0042% 76.23% 325ms 1.37% NodesOnlyMesh::ReMesh 0 0% 76.23% 324ms 1.36% boost::numeric::ublas::inner_prod (inline) 1ms 0.0042% 76.23% 323ms 1.36% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 19ms 0.08% 76.32% 322ms 1.36% boost::numeric::ublas::vector_scalar_binary::evaluate 4ms 0.017% 76.33% 321ms 1.35% NodeBasedCellPopulation::UpdateMapsAfterRemesh 31ms 0.13% 76.46% 320ms 1.35% std::_Rb_tree::~_Rb_tree (inline) 316ms 1.33% 77.79% 316ms 1.33% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 3ms 0.013% 77.81% 307ms 1.29% NodesOnlyMesh::UpdateNodeIndices 300ms 1.26% 79.07% 300ms 1.26% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 79.07% 289ms 1.22% boost::numeric::ublas::c_vector::assign (inline) 286ms 1.20% 80.27% 286ms 1.20% Node::CheckForNodeAttributes 0 0% 80.27% 285ms 1.20% std::_Rb_tree::_M_drop_node (inline) 3ms 0.013% 80.29% 281ms 1.18% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 10ms 0.042% 80.33% 266ms 1.12% std::_Rb_tree::_M_emplace_hint_unique 0 0% 80.33% 265ms 1.12% DistributedBoxCollection::GetProcessOwningNode 140ms 0.59% 80.92% 261ms 1.10% _int_malloc 107ms 0.45% 81.37% 254ms 1.07% boost::numeric::ublas::vector_inner_prod::apply (inline) 7ms 0.029% 81.40% 249ms 1.05% std::__new_allocator::deallocate (inline) 0 0% 81.40% 242ms 1.02% NodesOnlyMesh::UpdateBoxCollection 0 0% 81.40% 234ms 0.99% std::set::~set (inline) 1ms 0.0042% 81.40% 232ms 0.98% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 81.40% 231ms 0.97% VtkMeshWriter::WriteFiles 87ms 0.37% 81.77% 228ms 0.96% __GI___libc_free 0 0% 81.77% 224ms 0.94% std::allocator_traits::deallocate (inline) 0 0% 81.77% 223ms 0.94% Cell::HasCellProperty (inline) 1ms 0.0042% 81.77% 223ms 0.94% CellPropertyCollection::HasProperty 0 0% 81.77% 222ms 0.93% std::_Rb_tree::_M_put_node (inline) 21ms 0.088% 81.86% 220ms 0.93% std::__insertion_sort (inline) 8ms 0.034% 81.90% 218ms 0.92% Cell::ReadyToDivide 104ms 0.44% 82.33% 215ms 0.91% boost::shared_ptr::shared_ptr (inline) 0 0% 82.33% 207ms 0.87% vtkStreamingDemandDrivenPipeline::Update 0 0% 82.33% 207ms 0.87% vtkXMLWriterBase::Write 0 0% 82.33% 206ms 0.87% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 82.33% 205ms 0.86% vtkCompositeDataPipeline::ExecuteData 0 0% 82.33% 205ms 0.86% vtkDemandDrivenPipeline::ExecuteData 0 0% 82.33% 205ms 0.86% vtkDemandDrivenPipeline::ProcessRequest 0 0% 82.33% 205ms 0.86% vtkExecutive::CallAlgorithm 0 0% 82.33% 205ms 0.86% vtkXMLUnstructuredDataWriter::ProcessRequest 2ms 0.0084% 82.34% 203ms 0.85% NodesOnlyMesh::AddNodesToBoxes 84ms 0.35% 82.70% 197ms 0.83% std::__move_median_to_first (inline) 193ms 0.81% 83.51% 193ms 0.81% Node::GetIndex 178ms 0.75% 84.26% 178ms 0.75% [libchaste_cell_based.so] 5ms 0.021% 84.28% 177ms 0.75% AbstractCellProperty::IsType (inline) 0 0% 84.28% 172ms 0.72% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 84.28% 172ms 0.72% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 84.28% 166ms 0.7% NodesOnlyMesh::ResizeBoxCollection 0 0% 84.28% 166ms 0.7% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 15ms 0.063% 84.34% 165ms 0.69% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 84.34% 158ms 0.67% std::_Rb_tree::clear (inline) 81ms 0.34% 84.68% 153ms 0.64% Node::AddNeighbour 153ms 0.64% 85.33% 153ms 0.64% boost::shared_ptr::operator-> (inline) 0 0% 85.33% 147ms 0.62% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 85.33% 144ms 0.61% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 142ms 0.6% 85.93% 144ms 0.61% std::__adjacent_find (inline) 0 0% 85.93% 144ms 0.61% std::__unique (inline) 0 0% 85.93% 144ms 0.61% std::unique (inline) 141ms 0.59% 86.52% 141ms 0.59% [libchaste_mesh.so] 126ms 0.53% 87.05% 141ms 0.59% _int_free 139ms 0.59% 87.64% 139ms 0.59% Node::IsDeleted 12ms 0.051% 87.69% 137ms 0.58% boost::numeric::ublas::vector_reference::operator() (inline) 48ms 0.2% 87.89% 136ms 0.57% AbstractCellProperty::IsSame 0 0% 87.89% 133ms 0.56% vtkXMLWriter::WriteBinaryData 0 0% 87.89% 132ms 0.56% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 2ms 0.0084% 87.90% 129ms 0.54% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 87.90% 129ms 0.54% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.90% 129ms 0.54% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.90% 129ms 0.54% vtkXMLWriter::WriteCompressionBlock 0 0% 87.90% 127ms 0.53% std::map::clear (inline) 2ms 0.0084% 87.90% 124ms 0.52% Cell::GetCellId 0 0% 87.90% 124ms 0.52% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 87.90% 121ms 0.51% vtkXMLWriter::WritePointsAppendedData 1ms 0.0042% 87.91% 120ms 0.51% AbstractCellPopulation::SetCellUsingLocationIndex