File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 22752ms, 89.92% of 25302ms total Dropped 800 nodes (cum <= 126.51ms) flat flat% sum% cum cum% 0 0% 0% 25165ms 99.46% __libc_start_call_main 0 0% 0% 25165ms 99.46% __libc_start_main_impl 0 0% 0% 25165ms 99.46% _start 0 0% 0% 25147ms 99.39% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 25147ms 99.39% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 25147ms 99.39% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 25147ms 99.39% main 0 0% 0% 25104ms 99.22% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 25104ms 99.22% CxxTest::TestRunner::runTest (inline) 0 0% 0% 25104ms 99.22% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 25095ms 99.18% AbstractCellBasedSimulation::Solve 1ms 0.004% 0.004% 14300ms 56.52% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.004% 9532ms 37.67% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.016% 0.02% 9349ms 36.95% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.04% 0.059% 9156ms 36.19% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.059% 8418ms 33.27% NodeBasedCellPopulation::Update 1360ms 5.38% 5.43% 8347ms 32.99% RepulsionForce::AddForceContribution (partial-inline) 7ms 0.028% 5.46% 6314ms 24.95% DistributedBoxCollection::CalculateInteriorNodePairs 2140ms 8.46% 13.92% 5091ms 20.12% std::_Rb_tree::_M_lower_bound (inline) 12ms 0.047% 13.97% 4667ms 18.45% NodeAttributes::RemoveDuplicateNeighbours 0 0% 13.97% 4607ms 18.21% OffLatticeSimulation::ApplyBoundaries 6ms 0.024% 13.99% 4491ms 17.75% std::__sort (inline) 0 0% 13.99% 4491ms 17.75% std::sort (inline) 192ms 0.76% 14.75% 4158ms 16.43% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 218ms 0.86% 15.61% 3351ms 13.24% std::_Rb_tree::find (inline) 0 0% 15.61% 3348ms 13.23% std::map::find (inline) 110ms 0.43% 16.05% 3315ms 13.10% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 2ms 0.0079% 16.05% 3150ms 12.45% AbstractCellPopulation::Iterator::operator++ (inline) 150ms 0.59% 16.65% 3111ms 12.30% AbstractCellPopulation::Iterator::IsRealCell 2942ms 11.63% 28.27% 2942ms 11.63% std::_Rb_tree::_S_right (inline) 33ms 0.13% 28.40% 2675ms 10.57% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 172ms 0.68% 29.08% 2591ms 10.24% std::__introsort_loop 223ms 0.88% 29.97% 2488ms 9.83% std::map::operator[] (partial-inline) 23ms 0.091% 30.06% 2467ms 9.75% PlaneBoundaryCondition::ImposeBoundaryCondition 184ms 0.73% 30.78% 2428ms 9.60% AbstractMesh::GetNode 59ms 0.23% 31.02% 2400ms 9.49% NodesOnlyMesh::GetNodeOrHaloNode 0 0% 31.02% 2339ms 9.24% std::__unguarded_partition_pivot (inline) 157ms 0.62% 31.64% 2287ms 9.04% DistributedBoxCollection::AddPairsFromBox 92ms 0.36% 32.00% 2250ms 8.89% NodesOnlyMesh::SolveNodeMapping 58ms 0.23% 32.23% 2248ms 8.88% AbstractCellPopulation::GetLocationIndexUsingCell 15ms 0.059% 32.29% 2140ms 8.46% PlaneBoundaryCondition::VerifyBoundaryCondition 1020ms 4.03% 36.32% 2087ms 8.25% std::__unguarded_partition (inline) 0 0% 36.32% 1992ms 7.87% std::_Rb_tree::lower_bound (inline) 0 0% 36.32% 1992ms 7.87% std::map::lower_bound (inline) 0 0% 36.32% 1892ms 7.48% std::__final_insertion_sort (inline) 13ms 0.051% 36.37% 1742ms 6.88% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 38ms 0.15% 36.52% 1725ms 6.82% AbstractCellPopulation::GetCellUsingLocationIndex 139ms 0.55% 37.07% 1687ms 6.67% std::__unguarded_insertion_sort (inline) 599ms 2.37% 39.44% 1595ms 6.30% std::__unguarded_linear_insert (inline) 1452ms 5.74% 45.18% 1452ms 5.74% __gnu_cxx::__normal_iterator::operator-- (inline) 36ms 0.14% 45.32% 1295ms 5.12% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 45.32% 1220ms 4.82% NodeBasedCellPopulation::UpdateCellProcessLocation 6ms 0.024% 45.34% 1147ms 4.53% boost::numeric::ublas::vector_assign (inline) 4ms 0.016% 45.36% 1123ms 4.44% DistributedBoxCollection::CalculateBoundaryNodePairs 211ms 0.83% 46.19% 1055ms 4.17% boost::numeric::ublas::indexing_vector_assign 279ms 1.10% 47.30% 1033ms 4.08% __dynamic_cast 18ms 0.071% 47.37% 975ms 3.85% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 176ms 0.7% 48.06% 875ms 3.46% AbstractMesh::GetVectorFromAtoB 0 0% 48.06% 871ms 3.44% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 48.06% 856ms 3.38% boost::numeric::ublas::norm_2 (inline) 667ms 2.64% 50.70% 856ms 3.38% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 50.70% 856ms 3.38% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 281ms 1.11% 51.81% 851ms 3.36% NodeAttributes::AddNeighbour 412ms 1.63% 53.44% 844ms 3.34% DistributedBoxCollection::CalculateContainingBox (partial-inline) 3ms 0.012% 53.45% 829ms 3.28% boost::numeric::ublas::c_vector::operator= (inline) 35ms 0.14% 53.59% 829ms 3.28% std::_Rb_tree_const_iterator::operator++ (inline) 21ms 0.083% 53.67% 814ms 3.22% std::__copy_move::__copy_m (inline) 0 0% 53.67% 814ms 3.22% std::__copy_move_a (inline) 0 0% 53.67% 814ms 3.22% std::__copy_move_a1 (inline) 0 0% 53.67% 814ms 3.22% std::__copy_move_a2 (inline) 0 0% 53.67% 814ms 3.22% std::copy (inline) 807ms 3.19% 56.86% 807ms 3.19% __memcpy_avx_unaligned_erms 781ms 3.09% 59.95% 781ms 3.09% std::_Rb_tree_increment 0 0% 59.95% 758ms 3.00% AbstractCellPopulation::WriteResultsToFiles 12ms 0.047% 60.00% 750ms 2.96% CellPropertyCollection::GetPropertiesType (inline) 2ms 0.0079% 60.00% 723ms 2.86% AbstractCentreBasedCellPopulation::GetDampingConstant 705ms 2.79% 62.79% 705ms 2.79% boost::numeric::ublas::c_vector::operator() 568ms 2.24% 65.03% 659ms 2.60% std::vector::push_back (inline) 12ms 0.047% 65.08% 657ms 2.60% AbstractCellBasedSimulation::DoCellBirth 262ms 1.04% 66.12% 600ms 2.37% __cxxabiv1::__si_class_type_info::__do_dyncast 28ms 0.11% 66.23% 587ms 2.32% std::_Rb_tree::_Rb_tree (partial-inline) 580ms 2.29% 68.52% 580ms 2.29% boost::numeric::ublas::same_impl_ex 103ms 0.41% 68.93% 580ms 2.29% std::__new_allocator::allocate (inline) 0 0% 68.93% 558ms 2.21% std::allocator_traits::allocate (inline) 2ms 0.0079% 68.94% 554ms 2.19% Cell::GetMutationState 38ms 0.15% 69.09% 540ms 2.13% std::_Rb_tree::_M_copy (inline) 539ms 2.13% 71.22% 539ms 2.13% __strcmp_avx2 0 0% 71.22% 526ms 2.08% std::_Rb_tree::_M_create_node (inline) 36ms 0.14% 71.36% 519ms 2.05% boost::detail::shared_count::~shared_count (inline) 0 0% 71.36% 519ms 2.05% boost::shared_ptr::~shared_ptr (inline) 1ms 0.004% 71.36% 501ms 1.98% NodeBasedCellPopulation::WriteVtkResultsToFile 165ms 0.65% 72.01% 495ms 1.96% std::_Rb_tree::_M_clone_node (inline) 5ms 0.02% 72.03% 490ms 1.94% std::set::set (inline) 455ms 1.80% 73.83% 471ms 1.86% boost::detail::sp_counted_base::release 18ms 0.071% 73.90% 471ms 1.86% operator new 0 0% 73.90% 462ms 1.83% std::_Rb_tree::_M_get_node (inline) 137ms 0.54% 74.44% 461ms 1.82% std::_Rb_tree::_M_erase 0 0% 74.44% 456ms 1.80% AbstractCellBasedSimulation::DoCellRemoval (inline) 1ms 0.004% 74.45% 454ms 1.79% AbstractCellProperty::IsSubType (inline) 9ms 0.036% 74.48% 445ms 1.76% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 140ms 0.55% 75.04% 438ms 1.73% __GI___libc_malloc 86ms 0.34% 75.38% 407ms 1.61% boost::numeric::ublas::vector_binary::size (inline) 77ms 0.3% 75.68% 382ms 1.51% Node::GetRadius 0 0% 75.68% 369ms 1.46% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 75.68% 356ms 1.41% boost::numeric::ublas::inner_prod (inline) 1ms 0.004% 75.69% 356ms 1.41% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 12ms 0.047% 75.73% 355ms 1.40% boost::numeric::ublas::vector_scalar_binary::evaluate 43ms 0.17% 75.90% 346ms 1.37% std::_Rb_tree::~_Rb_tree (inline) 5ms 0.02% 75.92% 341ms 1.35% NodeBasedCellPopulation::UpdateMapsAfterRemesh 341ms 1.35% 77.27% 341ms 1.35% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 3ms 0.012% 77.28% 327ms 1.29% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 1ms 0.004% 77.29% 327ms 1.29% NodesOnlyMesh::ReMesh 0 0% 77.29% 326ms 1.29% boost::numeric::ublas::c_vector::assign (inline) 2ms 0.0079% 77.29% 318ms 1.26% NodesOnlyMesh::UpdateNodeIndices 313ms 1.24% 78.53% 313ms 1.24% Node::CheckForNodeAttributes 7ms 0.028% 78.56% 311ms 1.23% DistributedBoxCollection::GetProcessOwningNode 0 0% 78.56% 309ms 1.22% std::_Rb_tree::_M_drop_node (inline) 306ms 1.21% 79.77% 306ms 1.21% __gnu_cxx::__normal_iterator::operator++ (inline) 128ms 0.51% 80.27% 299ms 1.18% boost::numeric::ublas::vector_inner_prod::apply (inline) 265ms 1.05% 81.32% 293ms 1.16% Node::AddNeighbour 1ms 0.004% 81.33% 284ms 1.12% CellPropertyCollection::HasProperty 0 0% 81.33% 280ms 1.11% Cell::HasCellProperty (inline) 11ms 0.043% 81.37% 273ms 1.08% std::_Rb_tree::_M_emplace_hint_unique 8ms 0.032% 81.40% 258ms 1.02% Cell::ReadyToDivide 126ms 0.5% 81.90% 254ms 1.00% boost::shared_ptr::shared_ptr (inline) 0 0% 81.90% 252ms 1% NodesOnlyMesh::UpdateBoxCollection 7ms 0.028% 81.93% 251ms 0.99% std::__new_allocator::deallocate (inline) 0 0% 81.93% 249ms 0.98% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 128ms 0.51% 82.43% 249ms 0.98% _int_malloc 118ms 0.47% 82.90% 249ms 0.98% std::__move_median_to_first (inline) 0 0% 82.90% 246ms 0.97% VtkMeshWriter::WriteFiles 0 0% 82.90% 246ms 0.97% std::set::~set (inline) 239ms 0.94% 83.84% 239ms 0.94% Node::GetIndex 0 0% 83.84% 236ms 0.93% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 83.84% 236ms 0.93% std::allocator_traits::deallocate (inline) 9ms 0.036% 83.88% 233ms 0.92% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 83.88% 231ms 0.91% std::_Rb_tree::_M_put_node (inline) 68ms 0.27% 84.15% 225ms 0.89% __GI___libc_free 213ms 0.84% 84.99% 213ms 0.84% [libchaste_mesh.so] 0 0% 84.99% 208ms 0.82% vtkDemandDrivenPipeline::ProcessRequest 0 0% 84.99% 208ms 0.82% vtkStreamingDemandDrivenPipeline::Update 0 0% 84.99% 208ms 0.82% vtkXMLWriterBase::Write 0 0% 84.99% 206ms 0.81% vtkDemandDrivenPipeline::ExecuteData 0 0% 84.99% 206ms 0.81% vtkStreamingDemandDrivenPipeline::ProcessRequest 24ms 0.095% 85.08% 205ms 0.81% std::__insertion_sort (inline) 0 0% 85.08% 205ms 0.81% vtkCompositeDataPipeline::ExecuteData 0 0% 85.08% 205ms 0.81% vtkExecutive::CallAlgorithm 0 0% 85.08% 205ms 0.81% vtkXMLUnstructuredDataWriter::ProcessRequest 1ms 0.004% 85.09% 201ms 0.79% NodesOnlyMesh::AddNodesToBoxes 5ms 0.02% 85.11% 200ms 0.79% AbstractCellProperty::IsType (inline) 0 0% 85.11% 180ms 0.71% std::_Rb_tree::clear (inline) 179ms 0.71% 85.82% 179ms 0.71% [libchaste_cell_based.so] 0 0% 85.82% 174ms 0.69% vtkXMLUnstructuredDataWriter::WriteAPiece 1ms 0.004% 85.82% 174ms 0.69% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 85.82% 170ms 0.67% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 85.82% 161ms 0.64% Cell::GetCellId 2ms 0.0079% 85.83% 161ms 0.64% NodesOnlyMesh::ResizeBoxCollection 9ms 0.036% 85.86% 157ms 0.62% NodesOnlyMesh::IsANodeCloseToDomainBoundary 139ms 0.55% 86.41% 157ms 0.62% _int_free 0 0% 86.41% 157ms 0.62% std::_Rb_tree::_Auto_node::_Auto_node (inline) 156ms 0.62% 87.03% 156ms 0.62% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 63ms 0.25% 87.28% 155ms 0.61% AbstractCellProperty::IsSame 1ms 0.004% 87.28% 153ms 0.6% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 87.28% 149ms 0.59% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 146ms 0.58% 87.86% 146ms 0.58% boost::shared_ptr::operator-> (inline) 146ms 0.58% 88.44% 146ms 0.58% std::__adjacent_find (inline) 0 0% 88.44% 146ms 0.58% std::__unique (inline) 0 0% 88.44% 146ms 0.58% std::unique (inline) 139ms 0.55% 88.99% 139ms 0.55% Node::rGetLocation 0 0% 88.99% 138ms 0.55% vtkXMLWriter::WriteBinaryData 5ms 0.02% 89.00% 136ms 0.54% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 89.00% 136ms 0.54% std::map::clear (inline) 0 0% 89.00% 135ms 0.53% vtkXMLWriter::WriteBinaryDataBlock 0 0% 89.00% 135ms 0.53% vtkXMLWriter::WriteBinaryDataInternal 0 0% 89.00% 134ms 0.53% vtkXMLWriter::WriteCompressionBlock 9ms 0.036% 89.04% 132ms 0.52% boost::numeric::ublas::c_vector::operator[] (inline) 130ms 0.51% 89.55% 130ms 0.51% __ieee754_log_fma 0 0% 89.55% 129ms 0.51% vtkXMLWriter::WritePointsAppendedData 93ms 0.37% 89.92% 128ms 0.51% boost::detail::shared_count::shared_count (inline)