File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20491ms, 88.70% of 23101ms total Dropped 728 nodes (cum <= 115.50ms) flat flat% sum% cum cum% 0 0% 0% 22941ms 99.31% __libc_start_call_main 0 0% 0% 22941ms 99.31% __libc_start_main_impl 0 0% 0% 22941ms 99.31% _start 0 0% 0% 22926ms 99.24% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 22926ms 99.24% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 22926ms 99.24% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 22926ms 99.24% main 0 0% 0% 22892ms 99.10% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 22892ms 99.10% CxxTest::TestRunner::runTest (inline) 0 0% 0% 22892ms 99.10% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 22884ms 99.06% AbstractCellBasedSimulation::Solve 1ms 0.0043% 0.0043% 13079ms 56.62% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0043% 8625ms 37.34% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0087% 0.013% 8238ms 35.66% ForwardEulerNumericalMethod::UpdateAllNodePositions 20ms 0.087% 0.1% 8071ms 34.94% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.1% 7600ms 32.90% NodeBasedCellPopulation::Update 1163ms 5.03% 5.13% 7486ms 32.41% RepulsionForce::AddForceContribution (partial-inline) 5ms 0.022% 5.16% 5613ms 24.30% DistributedBoxCollection::CalculateInteriorNodePairs 2017ms 8.73% 13.89% 4857ms 21.03% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.0043% 13.89% 4561ms 19.74% OffLatticeSimulation::ApplyBoundaries 14ms 0.061% 13.95% 4455ms 19.28% NodeAttributes::RemoveDuplicateNeighbours 5ms 0.022% 13.97% 4275ms 18.51% std::__sort (inline) 0 0% 13.97% 4275ms 18.51% std::sort (inline) 198ms 0.86% 14.83% 3876ms 16.78% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 2ms 0.0087% 14.84% 3464ms 15.00% AbstractCellPopulation::Iterator::operator++ (inline) 205ms 0.89% 15.73% 3445ms 14.91% AbstractCellPopulation::Iterator::IsRealCell (inline) 75ms 0.32% 16.05% 3377ms 14.62% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 231ms 1% 17.05% 3229ms 13.98% std::_Rb_tree::find (inline) 0 0% 17.05% 3227ms 13.97% std::map::find (inline) 23ms 0.1% 17.15% 2872ms 12.43% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2816ms 12.19% 29.34% 2816ms 12.19% std::_Rb_tree::_S_right (inline) 178ms 0.77% 30.11% 2459ms 10.64% std::__introsort_loop 286ms 1.24% 31.35% 2426ms 10.50% std::map::operator[] (partial-inline) 34ms 0.15% 31.50% 2398ms 10.38% PlaneBoundaryCondition::ImposeBoundaryCondition 154ms 0.67% 32.16% 2353ms 10.19% AbstractMesh::GetNode 50ms 0.22% 32.38% 2341ms 10.13% NodesOnlyMesh::GetNodeOrHaloNode 38ms 0.16% 32.54% 2242ms 9.71% AbstractCellPopulation::GetLocationIndexUsingCell 87ms 0.38% 32.92% 2206ms 9.55% NodesOnlyMesh::SolveNodeMapping 1ms 0.0043% 32.92% 2201ms 9.53% std::__unguarded_partition_pivot (inline) 21ms 0.091% 33.02% 2162ms 9.36% PlaneBoundaryCondition::VerifyBoundaryCondition 1005ms 4.35% 37.37% 1988ms 8.61% std::__unguarded_partition (inline) 0 0% 37.37% 1881ms 8.14% std::_Rb_tree::lower_bound (inline) 0 0% 37.37% 1881ms 8.14% std::map::lower_bound (inline) 1ms 0.0043% 37.37% 1809ms 7.83% std::__final_insertion_sort (inline) 144ms 0.62% 37.99% 1742ms 7.54% DistributedBoxCollection::AddPairsFromBox 91ms 0.39% 38.39% 1609ms 6.97% std::__unguarded_insertion_sort (inline) 579ms 2.51% 40.89% 1576ms 6.82% std::__unguarded_linear_insert (inline) 17ms 0.074% 40.97% 1471ms 6.37% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 1460ms 6.32% 47.29% 1460ms 6.32% __gnu_cxx::__normal_iterator::operator-- (inline) 25ms 0.11% 47.40% 1448ms 6.27% AbstractCellPopulation::GetCellUsingLocationIndex 53ms 0.23% 47.63% 1299ms 5.62% boost::numeric::ublas::c_vector::c_vector (partial-inline) 34ms 0.15% 47.77% 1158ms 5.01% boost::numeric::ublas::vector_assign (inline) 0 0% 47.77% 1142ms 4.94% NodeBasedCellPopulation::UpdateCellProcessLocation 8ms 0.035% 47.81% 1048ms 4.54% DistributedBoxCollection::CalculateBoundaryNodePairs 277ms 1.20% 49.01% 1027ms 4.45% boost::numeric::ublas::indexing_vector_assign 253ms 1.10% 50.10% 1014ms 4.39% __dynamic_cast 25ms 0.11% 50.21% 824ms 3.57% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 157ms 0.68% 50.89% 806ms 3.49% AbstractMesh::GetVectorFromAtoB 0 0% 50.89% 790ms 3.42% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 362ms 1.57% 52.46% 778ms 3.37% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 52.46% 758ms 3.28% boost::numeric::ublas::norm_2 (inline) 601ms 2.60% 55.06% 758ms 3.28% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 55.06% 758ms 3.28% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 164ms 0.71% 55.77% 712ms 3.08% NodeAttributes::AddNeighbour 0 0% 55.77% 706ms 3.06% AbstractCellPopulation::WriteResultsToFiles 654ms 2.83% 58.60% 654ms 2.83% boost::numeric::ublas::c_vector::operator() 5ms 0.022% 58.62% 646ms 2.80% boost::numeric::ublas::c_vector::operator= (inline) 24ms 0.1% 58.72% 627ms 2.71% std::__copy_move::__copy_m (inline) 0 0% 58.72% 627ms 2.71% std::__copy_move_a (inline) 0 0% 58.72% 627ms 2.71% std::__copy_move_a1 (inline) 0 0% 58.72% 627ms 2.71% std::__copy_move_a2 (inline) 0 0% 58.72% 627ms 2.71% std::copy (inline) 264ms 1.14% 59.87% 626ms 2.71% __cxxabiv1::__si_class_type_info::__do_dyncast 624ms 2.70% 62.57% 624ms 2.70% __memcpy_avx_unaligned_erms 541ms 2.34% 64.91% 610ms 2.64% std::vector::push_back (inline) 10ms 0.043% 64.95% 563ms 2.44% CellPropertyCollection::GetPropertiesType (inline) 1ms 0.0043% 64.96% 555ms 2.40% AbstractCellBasedSimulation::DoCellBirth 555ms 2.40% 67.36% 555ms 2.40% __strcmp_avx2 37ms 0.16% 67.52% 525ms 2.27% boost::detail::shared_count::~shared_count (inline) 0 0% 67.52% 525ms 2.27% boost::shared_ptr::~shared_ptr (inline) 3ms 0.013% 67.53% 519ms 2.25% AbstractCentreBasedCellPopulation::GetDampingConstant 506ms 2.19% 69.72% 506ms 2.19% boost::numeric::ublas::same_impl_ex 35ms 0.15% 69.88% 494ms 2.14% std::_Rb_tree_const_iterator::operator++ (inline) 74ms 0.32% 70.20% 486ms 2.10% std::__new_allocator::allocate (inline) 475ms 2.06% 72.25% 478ms 2.07% boost::detail::sp_counted_base::release 0 0% 72.25% 469ms 2.03% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 72.25% 467ms 2.02% std::allocator_traits::allocate (inline) 3ms 0.013% 72.27% 465ms 2.01% NodeBasedCellPopulation::WriteVtkResultsToFile 461ms 2.00% 74.26% 461ms 2.00% std::_Rb_tree_increment 3ms 0.013% 74.27% 455ms 1.97% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 74.27% 448ms 1.94% std::_Rb_tree::_M_create_node (inline) 23ms 0.1% 74.37% 446ms 1.93% std::_Rb_tree::_Rb_tree (partial-inline) 5ms 0.022% 74.40% 438ms 1.90% AbstractCellProperty::IsSubType (inline) 44ms 0.19% 74.59% 408ms 1.77% std::_Rb_tree::_M_copy (inline) 36ms 0.16% 74.74% 402ms 1.74% operator new 0 0% 74.74% 400ms 1.73% std::_Rb_tree::_M_get_node (inline) 7ms 0.03% 74.77% 384ms 1.66% Cell::GetMutationState 126ms 0.55% 75.32% 369ms 1.60% std::_Rb_tree::_M_erase 4ms 0.017% 75.33% 367ms 1.59% std::set::set (inline) 107ms 0.46% 75.80% 363ms 1.57% __GI___libc_malloc 115ms 0.5% 76.30% 363ms 1.57% std::_Rb_tree::_M_clone_node (inline) 124ms 0.54% 76.83% 360ms 1.56% Node::GetRadius 21ms 0.091% 76.92% 347ms 1.50% boost::numeric::ublas::vector_binary::size (inline) 0 0% 76.92% 341ms 1.48% boost::numeric::ublas::c_vector::assign (inline) 8ms 0.035% 76.96% 321ms 1.39% NodeBasedCellPopulation::UpdateMapsAfterRemesh 305ms 1.32% 78.28% 305ms 1.32% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 78.28% 304ms 1.32% std::_Rb_tree::_Alloc_node::operator() (inline) 293ms 1.27% 79.55% 293ms 1.27% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 79.55% 288ms 1.25% NodesOnlyMesh::ReMesh 0 0% 79.55% 281ms 1.22% boost::numeric::ublas::inner_prod (inline) 2ms 0.0087% 79.55% 281ms 1.22% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 14ms 0.061% 79.62% 279ms 1.21% boost::numeric::ublas::vector_scalar_binary::evaluate 38ms 0.16% 79.78% 279ms 1.21% std::_Rb_tree::~_Rb_tree (inline) 3ms 0.013% 79.79% 277ms 1.20% NodesOnlyMesh::UpdateNodeIndices 3ms 0.013% 79.81% 270ms 1.17% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 79.81% 264ms 1.14% NodesOnlyMesh::UpdateBoxCollection 10ms 0.043% 79.85% 259ms 1.12% std::_Rb_tree::_M_emplace_hint_unique 4ms 0.017% 79.87% 258ms 1.12% DistributedBoxCollection::GetProcessOwningNode 244ms 1.06% 80.92% 244ms 1.06% Node::CheckForNodeAttributes 0 0% 80.92% 236ms 1.02% std::_Rb_tree::_M_drop_node (inline) 0 0% 80.92% 223ms 0.97% NodesOnlyMesh::ResizeBoxCollection 78ms 0.34% 81.26% 221ms 0.96% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 81.26% 220ms 0.95% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 16ms 0.069% 81.33% 220ms 0.95% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 81.33% 220ms 0.95% VtkMeshWriter::WriteFiles 106ms 0.46% 81.79% 220ms 0.95% boost::shared_ptr::shared_ptr (inline) 2ms 0.0087% 81.80% 217ms 0.94% NodesOnlyMesh::AddNodesToBoxes 132ms 0.57% 82.37% 207ms 0.9% _int_malloc 111ms 0.48% 82.85% 206ms 0.89% std::__move_median_to_first (inline) 0 0% 82.85% 206ms 0.89% std::set::~set (inline) 2ms 0.0087% 82.86% 200ms 0.87% std::__new_allocator::deallocate (inline) 20ms 0.087% 82.94% 199ms 0.86% std::__insertion_sort (inline) 0 0% 82.94% 196ms 0.85% vtkStreamingDemandDrivenPipeline::Update 0 0% 82.94% 196ms 0.85% vtkXMLWriterBase::Write 0 0% 82.94% 195ms 0.84% vtkDemandDrivenPipeline::ProcessRequest 0 0% 82.94% 194ms 0.84% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 82.94% 193ms 0.84% vtkCompositeDataPipeline::ExecuteData 0 0% 82.94% 193ms 0.84% vtkDemandDrivenPipeline::ExecuteData 0 0% 82.94% 192ms 0.83% vtkExecutive::CallAlgorithm 0 0% 82.94% 192ms 0.83% vtkXMLUnstructuredDataWriter::ProcessRequest 189ms 0.82% 83.76% 189ms 0.82% [libchaste_cell_based.so] 3ms 0.013% 83.78% 185ms 0.8% CellPropertyCollection::HasProperty 0 0% 83.78% 182ms 0.79% Cell::HasCellProperty (inline) 102ms 0.44% 84.22% 178ms 0.77% Node::AddNeighbour 0 0% 84.22% 178ms 0.77% std::allocator_traits::deallocate (inline) 56ms 0.24% 84.46% 177ms 0.77% __GI___libc_free 0 0% 84.46% 172ms 0.74% std::_Rb_tree::_M_put_node (inline) 0 0% 84.46% 168ms 0.73% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 84.46% 168ms 0.73% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 5ms 0.022% 84.48% 164ms 0.71% AbstractCellProperty::IsType (inline) 2ms 0.0087% 84.49% 163ms 0.71% Cell::ReadyToDivide 0 0% 84.49% 163ms 0.71% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 160ms 0.69% 85.18% 160ms 0.69% Node::GetIndex 5ms 0.022% 85.20% 154ms 0.67% DistributedBoxCollection::GetIsPeriodicAllDims 0 0% 85.20% 148ms 0.64% std::_Rb_tree::clear (inline) 147ms 0.64% 85.84% 148ms 0.64% std::__adjacent_find (inline) 0 0% 85.84% 148ms 0.64% std::__unique (inline) 0 0% 85.84% 148ms 0.64% std::unique (inline) 145ms 0.63% 86.47% 145ms 0.63% Node::IsDeleted 0 0% 86.47% 144ms 0.62% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1ms 0.0043% 86.47% 140ms 0.61% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 140ms 0.61% 87.08% 140ms 0.61% boost::shared_ptr::operator-> (inline) 0 0% 87.08% 138ms 0.6% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 87.08% 137ms 0.59% boost::numeric::ublas::vector_binary::operator() (inline) 2ms 0.0087% 87.09% 131ms 0.57% Cell::GetCellId 12ms 0.052% 87.14% 131ms 0.57% boost::numeric::ublas::c_vector::operator[] (inline) 44ms 0.19% 87.33% 130ms 0.56% AbstractCellProperty::IsSame 129ms 0.56% 87.89% 129ms 0.56% [libchaste_mesh.so] 0 0% 87.89% 128ms 0.55% vtkXMLWriter::WriteBinaryData 14ms 0.061% 87.95% 126ms 0.55% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 87.95% 126ms 0.55% tbb::detail::r1::parallel_pipeline 0 0% 87.95% 125ms 0.54% clone3 0 0% 87.95% 125ms 0.54% start_thread 0 0% 87.95% 125ms 0.54% tbb::detail::r1::reset 0 0% 87.95% 124ms 0.54% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.95% 123ms 0.53% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.95% 123ms 0.53% vtkXMLWriter::WriteCompressionBlock 1ms 0.0043% 87.95% 122ms 0.53% AbstractCellPopulation::SetCellUsingLocationIndex 111ms 0.48% 88.43% 121ms 0.52% _int_free 60ms 0.26% 88.69% 121ms 0.52% tbb::detail::r1::wait_bounded_queue_monitor 2ms 0.0087% 88.70% 119ms 0.52% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 88.70% 116ms 0.5% vtkXMLWriter::WritePointsAppendedData