File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20378ms, 87.85% of 23197ms total Dropped 728 nodes (cum <= 115.98ms) flat flat% sum% cum cum% 0 0% 0% 23047ms 99.35% __libc_start_call_main 0 0% 0% 23047ms 99.35% __libc_start_main_impl 0 0% 0% 23047ms 99.35% _start 0 0% 0% 23031ms 99.28% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 23031ms 99.28% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 23031ms 99.28% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 23031ms 99.28% main 0 0% 0% 22993ms 99.12% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 22993ms 99.12% CxxTest::TestRunner::runTest (inline) 0 0% 0% 22993ms 99.12% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 22985ms 99.09% AbstractCellBasedSimulation::Solve 2ms 0.0086% 0.0086% 13067ms 56.33% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0086% 8723ms 37.60% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.017% 0.026% 8248ms 35.56% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.043% 0.069% 8059ms 34.74% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.069% 7696ms 33.18% NodeBasedCellPopulation::Update 1214ms 5.23% 5.30% 7479ms 32.24% RepulsionForce::AddForceContribution (partial-inline) 7ms 0.03% 5.33% 5554ms 23.94% DistributedBoxCollection::CalculateInteriorNodePairs 2137ms 9.21% 14.54% 4984ms 21.49% std::_Rb_tree::_M_lower_bound (inline) 0 0% 14.54% 4566ms 19.68% OffLatticeSimulation::ApplyBoundaries 24ms 0.1% 14.65% 4538ms 19.56% NodeAttributes::RemoveDuplicateNeighbours 6ms 0.026% 14.67% 4250ms 18.32% std::__sort (inline) 0 0% 14.67% 4250ms 18.32% std::sort (inline) 189ms 0.81% 15.49% 3777ms 16.28% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 5ms 0.022% 15.51% 3504ms 15.11% AbstractCellPopulation::Iterator::operator++ (inline) 233ms 1.00% 16.52% 3479ms 15.00% AbstractCellPopulation::Iterator::IsRealCell (inline) 71ms 0.31% 16.82% 3420ms 14.74% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 264ms 1.14% 17.96% 3235ms 13.95% std::_Rb_tree::find (inline) 0 0% 17.96% 3235ms 13.95% std::map::find (inline) 21ms 0.091% 18.05% 2927ms 12.62% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2800ms 12.07% 30.12% 2800ms 12.07% std::_Rb_tree::_S_right (inline) 214ms 0.92% 31.04% 2515ms 10.84% std::map::operator[] (partial-inline) 170ms 0.73% 31.78% 2461ms 10.61% std::__introsort_loop 27ms 0.12% 31.89% 2403ms 10.36% PlaneBoundaryCondition::ImposeBoundaryCondition 41ms 0.18% 32.07% 2339ms 10.08% AbstractCellPopulation::GetLocationIndexUsingCell 154ms 0.66% 32.73% 2306ms 9.94% AbstractMesh::GetNode 64ms 0.28% 33.01% 2291ms 9.88% NodesOnlyMesh::GetNodeOrHaloNode 0 0% 33.01% 2206ms 9.51% std::__unguarded_partition_pivot (inline) 10ms 0.043% 33.05% 2163ms 9.32% PlaneBoundaryCondition::VerifyBoundaryCondition 74ms 0.32% 33.37% 2158ms 9.30% NodesOnlyMesh::SolveNodeMapping 0 0% 33.37% 2037ms 8.78% std::_Rb_tree::lower_bound (inline) 0 0% 33.37% 2037ms 8.78% std::map::lower_bound (inline) 1079ms 4.65% 38.02% 1979ms 8.53% std::__unguarded_partition (inline) 151ms 0.65% 38.67% 1806ms 7.79% DistributedBoxCollection::AddPairsFromBox 0 0% 38.67% 1781ms 7.68% std::__final_insertion_sort (inline) 88ms 0.38% 39.05% 1590ms 6.85% std::__unguarded_insertion_sort (inline) 531ms 2.29% 41.34% 1546ms 6.66% std::__unguarded_linear_insert (inline) 24ms 0.1% 41.45% 1504ms 6.48% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 31ms 0.13% 41.58% 1471ms 6.34% AbstractCellPopulation::GetCellUsingLocationIndex 1449ms 6.25% 47.83% 1449ms 6.25% __gnu_cxx::__normal_iterator::operator-- (inline) 45ms 0.19% 48.02% 1319ms 5.69% boost::numeric::ublas::c_vector::c_vector (partial-inline) 4ms 0.017% 48.04% 1190ms 5.13% DistributedBoxCollection::CalculateBoundaryNodePairs 45ms 0.19% 48.23% 1180ms 5.09% boost::numeric::ublas::vector_assign (inline) 0 0% 48.23% 1168ms 5.04% NodeBasedCellPopulation::UpdateCellProcessLocation 290ms 1.25% 49.48% 1053ms 4.54% boost::numeric::ublas::indexing_vector_assign 254ms 1.09% 50.58% 897ms 3.87% __dynamic_cast 136ms 0.59% 51.16% 806ms 3.47% AbstractMesh::GetVectorFromAtoB 21ms 0.091% 51.25% 783ms 3.38% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 191ms 0.82% 52.08% 733ms 3.16% NodeAttributes::AddNeighbour 0 0% 52.08% 727ms 3.13% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 52.08% 721ms 3.11% AbstractCellPopulation::WriteResultsToFiles 0 0% 52.08% 712ms 3.07% boost::numeric::ublas::norm_2 (inline) 574ms 2.47% 54.55% 712ms 3.07% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 54.55% 712ms 3.07% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 343ms 1.48% 56.03% 710ms 3.06% DistributedBoxCollection::CalculateContainingBox (partial-inline) 2ms 0.0086% 56.04% 667ms 2.88% boost::numeric::ublas::c_vector::operator= (inline) 647ms 2.79% 58.83% 647ms 2.79% boost::numeric::ublas::c_vector::operator() 33ms 0.14% 58.97% 642ms 2.77% std::__copy_move::__copy_m (inline) 0 0% 58.97% 642ms 2.77% std::__copy_move_a (inline) 0 0% 58.97% 642ms 2.77% std::__copy_move_a1 (inline) 0 0% 58.97% 642ms 2.77% std::__copy_move_a2 (inline) 0 0% 58.97% 642ms 2.77% std::copy (inline) 622ms 2.68% 61.65% 622ms 2.68% __memcpy_avx_unaligned_erms 541ms 2.33% 63.98% 619ms 2.67% std::vector::push_back (inline) 2ms 0.0086% 63.99% 585ms 2.52% AbstractCellBasedSimulation::DoCellBirth 264ms 1.14% 65.13% 542ms 2.34% __cxxabiv1::__si_class_type_info::__do_dyncast 6ms 0.026% 65.15% 538ms 2.32% CellPropertyCollection::GetPropertiesType (inline) 39ms 0.17% 65.32% 516ms 2.22% std::_Rb_tree_const_iterator::operator++ (inline) 510ms 2.20% 67.52% 510ms 2.20% boost::numeric::ublas::same_impl_ex 4ms 0.017% 67.54% 507ms 2.19% AbstractCentreBasedCellPopulation::GetDampingConstant 54ms 0.23% 67.77% 501ms 2.16% std::__new_allocator::allocate (inline) 0 0% 67.77% 481ms 2.07% std::allocator_traits::allocate (inline) 477ms 2.06% 69.83% 477ms 2.06% std::_Rb_tree_increment 1ms 0.0043% 69.83% 475ms 2.05% NodeBasedCellPopulation::WriteVtkResultsToFile 31ms 0.13% 69.97% 451ms 1.94% boost::detail::shared_count::~shared_count (inline) 0 0% 69.97% 451ms 1.94% boost::shared_ptr::~shared_ptr (inline) 0 0% 69.97% 446ms 1.92% std::_Rb_tree::_M_create_node (inline) 0 0% 69.97% 441ms 1.90% AbstractCellBasedSimulation::DoCellRemoval (inline) 29ms 0.13% 70.09% 435ms 1.88% operator new 2ms 0.0086% 70.10% 422ms 1.82% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 417ms 1.80% 71.90% 417ms 1.80% __strcmp_avx2 405ms 1.75% 73.64% 415ms 1.79% boost::detail::sp_counted_base::release 9ms 0.039% 73.68% 409ms 1.76% std::_Rb_tree::_Rb_tree (partial-inline) 123ms 0.53% 74.21% 399ms 1.72% __GI___libc_malloc 0 0% 74.21% 394ms 1.70% std::_Rb_tree::_M_get_node (inline) 27ms 0.12% 74.33% 392ms 1.69% std::_Rb_tree::_M_copy (inline) 6ms 0.026% 74.35% 390ms 1.68% AbstractCellProperty::IsSubType (inline) 144ms 0.62% 74.98% 381ms 1.64% Node::GetRadius 127ms 0.55% 75.52% 374ms 1.61% std::_Rb_tree::_M_erase 127ms 0.55% 76.07% 364ms 1.57% std::_Rb_tree::_M_clone_node (inline) 3ms 0.013% 76.08% 360ms 1.55% Cell::GetMutationState 5ms 0.022% 76.10% 352ms 1.52% std::set::set (inline) 0 0% 76.10% 335ms 1.44% boost::numeric::ublas::c_vector::assign (inline) 15ms 0.065% 76.17% 331ms 1.43% boost::numeric::ublas::vector_binary::size (inline) 6ms 0.026% 76.20% 327ms 1.41% NodeBasedCellPopulation::UpdateMapsAfterRemesh 326ms 1.41% 77.60% 326ms 1.41% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 43ms 0.19% 77.79% 306ms 1.32% std::_Rb_tree::~_Rb_tree (inline) 0 0% 77.79% 300ms 1.29% NodesOnlyMesh::ReMesh 0 0% 77.79% 300ms 1.29% boost::numeric::ublas::inner_prod (inline) 0 0% 77.79% 300ms 1.29% std::_Rb_tree::_Alloc_node::operator() (inline) 1ms 0.0043% 77.79% 299ms 1.29% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 13ms 0.056% 77.85% 298ms 1.28% boost::numeric::ublas::vector_scalar_binary::evaluate 1ms 0.0043% 77.85% 293ms 1.26% NodesOnlyMesh::UpdateNodeIndices 1ms 0.0043% 77.85% 264ms 1.14% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 7ms 0.03% 77.89% 264ms 1.14% std::_Rb_tree::_M_emplace_hint_unique 257ms 1.11% 78.99% 257ms 1.11% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 78.99% 253ms 1.09% NodesOnlyMesh::UpdateBoxCollection 248ms 1.07% 80.06% 248ms 1.07% std::__adjacent_find (inline) 0 0% 80.06% 248ms 1.07% std::__unique (inline) 0 0% 80.06% 248ms 1.07% std::unique (inline) 246ms 1.06% 81.12% 246ms 1.06% Node::CheckForNodeAttributes 109ms 0.47% 81.59% 245ms 1.06% boost::numeric::ublas::vector_inner_prod::apply (inline) 3ms 0.013% 81.61% 243ms 1.05% DistributedBoxCollection::GetProcessOwningNode 0 0% 81.61% 243ms 1.05% std::_Rb_tree::_M_drop_node (inline) 0 0% 81.61% 234ms 1.01% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 81.61% 232ms 1.00% VtkMeshWriter::WriteFiles 0 0% 81.61% 230ms 0.99% std::set::~set (inline) 96ms 0.41% 82.02% 222ms 0.96% std::__move_median_to_first (inline) 0 0% 82.02% 220ms 0.95% std::__new_allocator::deallocate (inline) 1ms 0.0043% 82.02% 219ms 0.94% NodesOnlyMesh::ResizeBoxCollection 134ms 0.58% 82.60% 219ms 0.94% _int_malloc 11ms 0.047% 82.65% 217ms 0.94% NodesOnlyMesh::IsANodeCloseToDomainBoundary 1ms 0.0043% 82.65% 216ms 0.93% NodesOnlyMesh::AddNodesToBoxes 0 0% 82.65% 207ms 0.89% vtkCompositeDataPipeline::ExecuteData 0 0% 82.65% 207ms 0.89% vtkDemandDrivenPipeline::ExecuteData 0 0% 82.65% 207ms 0.89% vtkDemandDrivenPipeline::ProcessRequest 0 0% 82.65% 207ms 0.89% vtkExecutive::CallAlgorithm 0 0% 82.65% 207ms 0.89% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 82.65% 207ms 0.89% vtkStreamingDemandDrivenPipeline::Update 0 0% 82.65% 207ms 0.89% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 82.65% 207ms 0.89% vtkXMLWriterBase::Write 71ms 0.31% 82.96% 203ms 0.88% __GI___libc_free 9ms 0.039% 83.00% 191ms 0.82% std::__insertion_sort (inline) 98ms 0.42% 83.42% 189ms 0.81% boost::shared_ptr::shared_ptr (inline) 0 0% 83.42% 188ms 0.81% std::allocator_traits::deallocate (inline) 183ms 0.79% 84.21% 183ms 0.79% [libchaste_cell_based.so] 0 0% 84.21% 181ms 0.78% std::_Rb_tree::_M_put_node (inline) 0 0% 84.21% 179ms 0.77% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 84.21% 179ms 0.77% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 177ms 0.76% 84.97% 177ms 0.76% Node::GetIndex 0 0% 84.97% 170ms 0.73% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 3ms 0.013% 84.99% 166ms 0.72% CellPropertyCollection::HasProperty 81ms 0.35% 85.33% 166ms 0.72% Node::AddNeighbour 0 0% 85.33% 165ms 0.71% Cell::HasCellProperty (inline) 6ms 0.026% 85.36% 159ms 0.69% DistributedBoxCollection::GetIsPeriodicAllDims 157ms 0.68% 86.04% 157ms 0.68% Node::IsDeleted 3ms 0.013% 86.05% 152ms 0.66% Cell::ReadyToDivide 2ms 0.0086% 86.06% 147ms 0.63% AbstractCellProperty::IsType (inline) 0 0% 86.06% 146ms 0.63% std::_Rb_tree::_Auto_node::_Auto_node (inline) 3ms 0.013% 86.07% 145ms 0.63% AbstractCellPopulation::SetCellUsingLocationIndex 145ms 0.63% 86.70% 145ms 0.63% boost::shared_ptr::operator-> (inline) 0 0% 86.70% 144ms 0.62% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 86.70% 137ms 0.59% vtkXMLWriter::WriteBinaryData 135ms 0.58% 87.28% 135ms 0.58% [libchaste_mesh.so] 3ms 0.013% 87.29% 134ms 0.58% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 87.29% 133ms 0.57% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 1ms 0.0043% 87.30% 132ms 0.57% Cell::GetCellId 110ms 0.47% 87.77% 132ms 0.57% _int_free 0 0% 87.77% 131ms 0.56% std::_Rb_tree::clear (inline) 0 0% 87.77% 131ms 0.56% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.77% 131ms 0.56% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.77% 131ms 0.56% vtkXMLWriter::WriteCompressionBlock 0 0% 87.77% 126ms 0.54% vtkXMLWriter::WritePointsAppendedData 0 0% 87.77% 125ms 0.54% boost::numeric::ublas::vector_binary::operator() (inline) 7ms 0.03% 87.80% 124ms 0.53% NodeBasedCellPopulation::SetNode 11ms 0.047% 87.85% 123ms 0.53% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 87.85% 121ms 0.52% tbb::detail::r1::parallel_pipeline