File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 16491ms, 89.67% of 18391ms total Dropped 757 nodes (cum <= 91.95ms) flat flat% sum% cum cum% 0 0% 0% 18340ms 99.72% __libc_start_call_main 0 0% 0% 18340ms 99.72% __libc_start_main_impl 0 0% 0% 18340ms 99.72% _start 0 0% 0% 18327ms 99.65% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 18327ms 99.65% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 18327ms 99.65% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 18327ms 99.65% main 0 0% 0% 18288ms 99.44% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 18288ms 99.44% CxxTest::TestRunner::runTest (inline) 0 0% 0% 18287ms 99.43% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0054% 0.0054% 18281ms 99.40% AbstractCellBasedSimulation::Solve 0 0% 0.0054% 10230ms 55.63% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0054% 7193ms 39.11% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.0054% 6294ms 34.22% NodeBasedCellPopulation::Update 0 0% 0.0054% 5945ms 32.33% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.033% 0.038% 5784ms 31.45% AbstractNumericalMethod::ComputeForcesIncludingDamping 741ms 4.03% 4.07% 5264ms 28.62% RepulsionForce::AddForceContribution (partial-inline) 6ms 0.033% 4.10% 4668ms 25.38% DistributedBoxCollection::CalculateInteriorNodePairs 1ms 0.0054% 4.11% 4050ms 22.02% OffLatticeSimulation::ApplyBoundaries 20ms 0.11% 4.21% 3828ms 20.81% NodeAttributes::RemoveDuplicateNeighbours 1382ms 7.51% 11.73% 3748ms 20.38% std::_Rb_tree::_M_lower_bound (inline) 6ms 0.033% 11.76% 3653ms 19.86% std::__sort (inline) 0 0% 11.76% 3653ms 19.86% std::sort (inline) 254ms 1.38% 13.14% 3017ms 16.40% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 2ms 0.011% 13.15% 2945ms 16.01% AbstractCellPopulation::Iterator::operator++ (inline) 161ms 0.88% 14.03% 2939ms 15.98% AbstractCellPopulation::Iterator::IsRealCell 97ms 0.53% 14.56% 2831ms 15.39% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 13ms 0.071% 14.63% 2435ms 13.24% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 199ms 1.08% 15.71% 2405ms 13.08% std::_Rb_tree::find (inline) 0 0% 15.71% 2405ms 13.08% std::map::find (inline) 171ms 0.93% 16.64% 2227ms 12.11% std::__introsort_loop 2116ms 11.51% 28.14% 2116ms 11.51% std::_Rb_tree::_S_right (inline) 59ms 0.32% 28.47% 2050ms 11.15% PlaneBoundaryCondition::ImposeBoundaryCondition 180ms 0.98% 29.44% 2033ms 11.05% std::map::operator[] (partial-inline) 74ms 0.4% 29.85% 2012ms 10.94% AbstractMesh::GetNode 34ms 0.18% 30.03% 1999ms 10.87% PlaneBoundaryCondition::VerifyBoundaryCondition 45ms 0.24% 30.28% 1981ms 10.77% NodesOnlyMesh::GetNodeOrHaloNode 17ms 0.092% 30.37% 1977ms 10.75% std::__unguarded_partition_pivot (inline) 167ms 0.91% 31.28% 1947ms 10.59% NodesOnlyMesh::SolveNodeMapping 686ms 3.73% 35.01% 1786ms 9.71% std::__unguarded_partition (inline) 51ms 0.28% 35.28% 1676ms 9.11% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 35.28% 1569ms 8.53% std::_Rb_tree::lower_bound (inline) 0 0% 35.28% 1569ms 8.53% std::map::lower_bound (inline) 0 0% 35.28% 1418ms 7.71% std::__final_insertion_sort (inline) 123ms 0.67% 35.95% 1392ms 7.57% DistributedBoxCollection::AddPairsFromBox 5ms 0.027% 35.98% 1288ms 7.00% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 25ms 0.14% 36.12% 1276ms 6.94% AbstractCellPopulation::GetCellUsingLocationIndex 85ms 0.46% 36.58% 1251ms 6.80% std::__unguarded_insertion_sort (inline) 598ms 3.25% 39.83% 1134ms 6.17% std::__unguarded_linear_insert (inline) 61ms 0.33% 40.16% 920ms 5.00% boost::numeric::ublas::c_vector::c_vector (partial-inline) 5ms 0.027% 40.19% 867ms 4.71% DistributedBoxCollection::CalculateBoundaryNodePairs 0 0% 40.19% 846ms 4.60% NodeBasedCellPopulation::UpdateCellProcessLocation 841ms 4.57% 44.76% 841ms 4.57% __gnu_cxx::__normal_iterator::operator-- (inline) 10ms 0.054% 44.82% 826ms 4.49% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 12ms 0.065% 44.88% 798ms 4.34% boost::detail::shared_count::~shared_count (inline) 0 0% 44.88% 798ms 4.34% boost::shared_ptr::~shared_ptr (inline) 762ms 4.14% 49.02% 772ms 4.20% boost::detail::sp_counted_base::release 3ms 0.016% 49.04% 756ms 4.11% boost::numeric::ublas::vector_assign (inline) 153ms 0.83% 49.87% 653ms 3.55% boost::numeric::ublas::indexing_vector_assign 197ms 1.07% 50.94% 593ms 3.22% __dynamic_cast 96ms 0.52% 51.47% 584ms 3.18% AbstractMesh::GetVectorFromAtoB 0 0% 51.47% 542ms 2.95% AbstractCellPopulation::WriteResultsToFiles 256ms 1.39% 52.86% 510ms 2.77% NodeAttributes::AddNeighbour 204ms 1.11% 53.97% 503ms 2.74% DistributedBoxCollection::CalculateContainingBox (partial-inline) 1ms 0.0054% 53.97% 478ms 2.60% AbstractCentreBasedCellPopulation::GetDampingConstant 57ms 0.31% 54.28% 477ms 2.59% std::__new_allocator::allocate (inline) 1ms 0.0054% 54.29% 476ms 2.59% AbstractCellBasedSimulation::DoCellBirth 470ms 2.56% 56.84% 470ms 2.56% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 35ms 0.19% 57.03% 464ms 2.52% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 57.03% 462ms 2.51% std::allocator_traits::allocate (inline) 8ms 0.043% 57.08% 458ms 2.49% CellPropertyCollection::GetPropertiesType (inline) 15ms 0.082% 57.16% 450ms 2.45% std::_Rb_tree_const_iterator::operator++ (inline) 3ms 0.016% 57.17% 443ms 2.41% boost::numeric::ublas::c_vector::operator= (inline) 442ms 2.40% 59.58% 442ms 2.40% [libchaste_cell_based.so] 0 0% 59.58% 442ms 2.40% std::_Rb_tree::_M_create_node (inline) 31ms 0.17% 59.75% 435ms 2.37% std::__copy_move::__copy_m (inline) 0 0% 59.75% 435ms 2.37% std::__copy_move_a (inline) 0 0% 59.75% 435ms 2.37% std::__copy_move_a1 (inline) 0 0% 59.75% 435ms 2.37% std::__copy_move_a2 (inline) 0 0% 59.75% 435ms 2.37% std::copy (inline) 430ms 2.34% 62.08% 430ms 2.34% __gnu_cxx::__normal_iterator::operator++ (inline) 26ms 0.14% 62.23% 424ms 2.31% std::_Rb_tree::_M_copy (inline) 0 0% 62.23% 423ms 2.30% AbstractCellBasedSimulation::DoCellRemoval (inline) 14ms 0.076% 62.30% 422ms 2.29% operator new 0 0% 62.30% 419ms 2.28% std::_Rb_tree::_M_get_node (inline) 0 0% 62.30% 418ms 2.27% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 11ms 0.06% 62.36% 413ms 2.25% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.36% 403ms 2.19% boost::numeric::ublas::norm_2 (inline) 348ms 1.89% 64.25% 403ms 2.19% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 64.25% 403ms 2.19% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 127ms 0.69% 64.94% 399ms 2.17% __GI___libc_malloc 396ms 2.15% 67.10% 396ms 2.15% boost::numeric::ublas::same_impl_ex 395ms 2.15% 69.25% 395ms 2.15% std::_Rb_tree_increment 393ms 2.14% 71.38% 393ms 2.14% [libchaste_mesh.so] 0 0% 71.38% 391ms 2.13% std::set::set (inline) 385ms 2.09% 73.48% 385ms 2.09% __memcpy_avx512_unaligned_erms 165ms 0.9% 74.37% 385ms 2.09% std::_Rb_tree::_M_clone_node (inline) 60ms 0.33% 74.70% 378ms 2.06% std::_Rb_tree::_M_erase 3ms 0.016% 74.72% 367ms 2.00% NodeBasedCellPopulation::WriteVtkResultsToFile 344ms 1.87% 76.59% 344ms 1.87% boost::numeric::ublas::c_vector::operator() 1ms 0.0054% 76.59% 333ms 1.81% Cell::GetMutationState 230ms 1.25% 77.84% 333ms 1.81% std::vector::push_back (inline) 53ms 0.29% 78.13% 323ms 1.76% std::_Rb_tree::~_Rb_tree (inline) 0 0% 78.13% 316ms 1.72% std::_Rb_tree::_M_drop_node (inline) 172ms 0.94% 79.07% 313ms 1.70% __cxxabiv1::__si_class_type_info::__do_dyncast 2ms 0.011% 79.08% 293ms 1.59% AbstractCellProperty::IsSubType (inline) 8ms 0.043% 79.12% 284ms 1.54% std::_Rb_tree::_M_emplace_hint_unique 0 0% 79.12% 275ms 1.50% std::set::~set (inline) 13ms 0.071% 79.19% 272ms 1.48% boost::numeric::ublas::vector_binary::size (inline) 5ms 0.027% 79.22% 266ms 1.45% NodeBasedCellPopulation::UpdateMapsAfterRemesh 265ms 1.44% 80.66% 265ms 1.44% std::_Rb_tree::_S_left (inline) 0 0% 80.66% 263ms 1.43% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 80.66% 256ms 1.39% NodesOnlyMesh::ReMesh 1ms 0.0054% 80.66% 254ms 1.38% NodesOnlyMesh::UpdateNodeIndices 0 0% 80.66% 231ms 1.26% Node::GetRadius 202ms 1.10% 81.76% 220ms 1.20% boost::shared_ptr::shared_ptr (inline) 1ms 0.0054% 81.77% 219ms 1.19% NodesOnlyMesh::UpdateBoxCollection 213ms 1.16% 82.93% 213ms 1.16% __strcmp_evex 0 0% 82.93% 213ms 1.16% boost::numeric::ublas::c_vector::assign (inline) 5ms 0.027% 82.95% 211ms 1.15% std::__new_allocator::deallocate (inline) 138ms 0.75% 83.70% 210ms 1.14% _int_malloc 4ms 0.022% 83.73% 188ms 1.02% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 51ms 0.28% 84.00% 187ms 1.02% __GI___libc_free 0 0% 84.00% 186ms 1.01% std::allocator_traits::deallocate (inline) 0 0% 84.00% 183ms 1% std::_Rb_tree::_M_put_node (inline) 1ms 0.0054% 84.01% 182ms 0.99% CellPropertyCollection::HasProperty 0 0% 84.01% 181ms 0.98% Cell::HasCellProperty (inline) 0 0% 84.01% 179ms 0.97% std::_Rb_tree::_Auto_node::_Auto_node (inline) 3ms 0.016% 84.02% 177ms 0.96% DistributedBoxCollection::GetProcessOwningNode 174ms 0.95% 84.97% 174ms 0.95% Node::CheckForNodeAttributes 0 0% 84.97% 169ms 0.92% boost::numeric::ublas::inner_prod (inline) 2ms 0.011% 84.98% 169ms 0.92% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 84.98% 168ms 0.91% NodesOnlyMesh::AddNodesToBoxes 3ms 0.016% 85.00% 167ms 0.91% boost::numeric::ublas::vector_scalar_binary::evaluate 23ms 0.13% 85.12% 167ms 0.91% std::__insertion_sort (inline) 66ms 0.36% 85.48% 164ms 0.89% std::__move_median_to_first (inline) 2ms 0.011% 85.49% 162ms 0.88% Cell::ReadyToDivide 0 0% 85.49% 161ms 0.88% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 161ms 0.88% 86.37% 161ms 0.88% boost::shared_ptr::operator-> (inline) 0 0% 86.37% 158ms 0.86% VtkMeshWriter::WriteFiles 0 0% 86.37% 155ms 0.84% std::iter_swap (inline) 155ms 0.84% 87.21% 155ms 0.84% std::swap (inline) 48ms 0.26% 87.47% 144ms 0.78% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 87.47% 141ms 0.77% std::__new_allocator::destroy (inline) 0 0% 87.47% 141ms 0.77% std::allocator_traits::destroy (inline) 0 0% 87.47% 138ms 0.75% std::_Rb_tree::_M_destroy_node (inline) 126ms 0.69% 88.16% 136ms 0.74% _int_free 0 0% 88.16% 129ms 0.7% vtkStreamingDemandDrivenPipeline::Update 0 0% 88.16% 129ms 0.7% vtkXMLWriterBase::Write 0 0% 88.16% 127ms 0.69% vtkDemandDrivenPipeline::ProcessRequest 0 0% 88.16% 126ms 0.69% vtkStreamingDemandDrivenPipeline::ProcessRequest 56ms 0.3% 88.46% 125ms 0.68% std::__adjacent_find (inline) 0 0% 88.46% 125ms 0.68% std::__unique (inline) 0 0% 88.46% 125ms 0.68% std::unique (inline) 0 0% 88.46% 125ms 0.68% vtkDemandDrivenPipeline::ExecuteData 1ms 0.0054% 88.47% 124ms 0.67% AbstractCellPopulation::SetCellUsingLocationIndex 0 0% 88.47% 123ms 0.67% vtkCompositeDataPipeline::ExecuteData 0 0% 88.47% 123ms 0.67% vtkExecutive::CallAlgorithm 0 0% 88.47% 123ms 0.67% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 88.47% 122ms 0.66% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 88.47% 121ms 0.66% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 88.47% 117ms 0.64% NodesOnlyMesh::ResizeBoxCollection 6ms 0.033% 88.50% 116ms 0.63% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 88.50% 116ms 0.63% std::_Rb_tree::clear (inline) 3ms 0.016% 88.52% 114ms 0.62% NodeBasedCellPopulation::SetNode 2ms 0.011% 88.53% 110ms 0.6% AbstractCellProperty::IsType (inline) 1ms 0.0054% 88.53% 108ms 0.59% NodesOnlyMesh::SetNode 1ms 0.0054% 88.54% 107ms 0.58% std::_Rb_tree::_M_insert_unique 0 0% 88.54% 107ms 0.58% std::set::insert (inline) 0 0% 88.54% 107ms 0.58% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 88.54% 107ms 0.58% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 88.54% 106ms 0.58% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 1ms 0.0054% 88.54% 103ms 0.56% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 12ms 0.065% 88.61% 101ms 0.55% Node::AddNeighbour 100ms 0.54% 89.15% 100ms 0.54% Node::GetIndex 95ms 0.52% 89.67% 96ms 0.52% Node::ConstructNodeAttributes (inline)