File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 16256ms, 89.37% of 18190ms total Dropped 718 nodes (cum <= 90.95ms) flat flat% sum% cum cum% 0 0% 0% 18127ms 99.65% __libc_start_call_main 0 0% 0% 18127ms 99.65% __libc_start_main_impl 0 0% 0% 18127ms 99.65% _start 0 0% 0% 18113ms 99.58% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 18113ms 99.58% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 18113ms 99.58% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 18113ms 99.58% main 0 0% 0% 18081ms 99.40% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 18081ms 99.40% CxxTest::TestRunner::runTest (inline) 0 0% 0% 18081ms 99.40% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0055% 0.0055% 18074ms 99.36% AbstractCellBasedSimulation::Solve 2ms 0.011% 0.016% 10100ms 55.53% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.016% 7092ms 38.99% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0055% 0.022% 6230ms 34.25% NodeBasedCellPopulation::Update 1ms 0.0055% 0.027% 5830ms 32.05% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.022% 0.049% 5694ms 31.30% AbstractNumericalMethod::ComputeForcesIncludingDamping 723ms 3.97% 4.02% 5255ms 28.89% RepulsionForce::AddForceContribution (partial-inline) 7ms 0.038% 4.06% 4667ms 25.66% DistributedBoxCollection::CalculateInteriorNodePairs 1ms 0.0055% 4.07% 4022ms 22.11% OffLatticeSimulation::ApplyBoundaries 15ms 0.082% 4.15% 3777ms 20.76% NodeAttributes::RemoveDuplicateNeighbours 1414ms 7.77% 11.92% 3739ms 20.56% std::_Rb_tree::_M_lower_bound (inline) 2ms 0.011% 11.94% 3607ms 19.83% std::__sort (inline) 0 0% 11.94% 3607ms 19.83% std::sort (inline) 5ms 0.027% 11.96% 2986ms 16.42% AbstractCellPopulation::Iterator::operator++ (inline) 169ms 0.93% 12.89% 2976ms 16.36% AbstractCellPopulation::Iterator::IsRealCell (inline) 222ms 1.22% 14.11% 2938ms 16.15% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 104ms 0.57% 14.68% 2805ms 15.42% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 23ms 0.13% 14.81% 2449ms 13.46% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 182ms 1.00% 15.81% 2438ms 13.40% std::_Rb_tree::find (inline) 0 0% 15.81% 2438ms 13.40% std::map::find (inline) 173ms 0.95% 16.76% 2229ms 12.25% std::__introsort_loop 54ms 0.3% 17.06% 2077ms 11.42% PlaneBoundaryCondition::ImposeBoundaryCondition 2070ms 11.38% 28.44% 2070ms 11.38% std::_Rb_tree::_S_right (inline) 78ms 0.43% 28.87% 2036ms 11.19% AbstractMesh::GetNode 201ms 1.11% 29.97% 2026ms 11.14% std::map::operator[] (partial-inline) 37ms 0.2% 30.18% 2011ms 11.06% NodesOnlyMesh::GetNodeOrHaloNode 15ms 0.082% 30.26% 1967ms 10.81% std::__unguarded_partition_pivot (inline) 169ms 0.93% 31.19% 1961ms 10.78% NodesOnlyMesh::SolveNodeMapping 35ms 0.19% 31.38% 1944ms 10.69% PlaneBoundaryCondition::VerifyBoundaryCondition 623ms 3.42% 34.80% 1745ms 9.59% std::__unguarded_partition (inline) 68ms 0.37% 35.18% 1678ms 9.22% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 35.18% 1508ms 8.29% std::_Rb_tree::lower_bound (inline) 0 0% 35.18% 1508ms 8.29% std::map::lower_bound (inline) 112ms 0.62% 35.79% 1391ms 7.65% DistributedBoxCollection::AddPairsFromBox 0 0% 35.79% 1370ms 7.53% std::__final_insertion_sort (inline) 8ms 0.044% 35.84% 1244ms 6.84% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 20ms 0.11% 35.95% 1230ms 6.76% AbstractCellPopulation::GetCellUsingLocationIndex 66ms 0.36% 36.31% 1213ms 6.67% std::__unguarded_insertion_sort (inline) 569ms 3.13% 39.44% 1099ms 6.04% std::__unguarded_linear_insert (inline) 0 0% 39.44% 880ms 4.84% NodeBasedCellPopulation::UpdateCellProcessLocation 861ms 4.73% 44.17% 861ms 4.73% __gnu_cxx::__normal_iterator::operator-- (inline) 59ms 0.32% 44.50% 846ms 4.65% boost::numeric::ublas::c_vector::c_vector (partial-inline) 8ms 0.044% 44.54% 825ms 4.54% DistributedBoxCollection::CalculateBoundaryNodePairs 9ms 0.049% 44.59% 764ms 4.20% boost::detail::shared_count::~shared_count (inline) 0 0% 44.59% 764ms 4.20% boost::shared_ptr::~shared_ptr (inline) 15ms 0.082% 44.67% 761ms 4.18% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 733ms 4.03% 48.70% 739ms 4.06% boost::detail::sp_counted_base::release 7ms 0.038% 48.74% 690ms 3.79% boost::numeric::ublas::vector_assign (inline) 154ms 0.85% 49.59% 615ms 3.38% boost::numeric::ublas::indexing_vector_assign 166ms 0.91% 50.50% 559ms 3.07% __dynamic_cast 84ms 0.46% 50.96% 556ms 3.06% AbstractMesh::GetVectorFromAtoB 0 0% 50.96% 538ms 2.96% AbstractCellPopulation::WriteResultsToFiles 232ms 1.28% 52.24% 528ms 2.90% DistributedBoxCollection::CalculateContainingBox (partial-inline) 43ms 0.24% 52.47% 507ms 2.79% std::__new_allocator::allocate (inline) 8ms 0.044% 52.52% 501ms 2.75% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 52.52% 494ms 2.72% std::allocator_traits::allocate (inline) 220ms 1.21% 53.73% 489ms 2.69% NodeAttributes::AddNeighbour 26ms 0.14% 53.87% 480ms 2.64% std::__copy_move::__copy_m (inline) 0 0% 53.87% 480ms 2.64% std::__copy_move_a (inline) 0 0% 53.87% 480ms 2.64% std::__copy_move_a1 (inline) 0 0% 53.87% 480ms 2.64% std::__copy_move_a2 (inline) 0 0% 53.87% 480ms 2.64% std::copy (inline) 14ms 0.077% 53.95% 467ms 2.57% std::_Rb_tree_const_iterator::operator++ (inline) 464ms 2.55% 56.50% 464ms 2.55% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 19ms 0.1% 56.60% 464ms 2.55% operator new 447ms 2.46% 59.06% 447ms 2.46% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 59.06% 446ms 2.45% std::_Rb_tree::_M_create_node (inline) 1ms 0.0055% 59.07% 439ms 2.41% AbstractCellBasedSimulation::DoCellBirth 437ms 2.40% 61.47% 437ms 2.40% [libchaste_cell_based.so] 435ms 2.39% 63.86% 435ms 2.39% __memcpy_avx512_unaligned_erms 131ms 0.72% 64.58% 431ms 2.37% __GI___libc_malloc 0 0% 64.58% 426ms 2.34% std::_Rb_tree::_M_get_node (inline) 17ms 0.093% 64.67% 424ms 2.33% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 64.67% 421ms 2.31% AbstractCellBasedSimulation::DoCellRemoval (inline) 8ms 0.044% 64.72% 415ms 2.28% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 64.72% 411ms 2.26% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 406ms 2.23% 66.95% 406ms 2.23% std::_Rb_tree_increment 7ms 0.038% 66.99% 398ms 2.19% CellPropertyCollection::GetPropertiesType (inline) 0 0% 66.99% 397ms 2.18% boost::numeric::ublas::norm_2 (inline) 331ms 1.82% 68.81% 397ms 2.18% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 68.81% 397ms 2.18% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 21ms 0.12% 68.92% 396ms 2.18% std::_Rb_tree::_M_copy (inline) 5ms 0.027% 68.95% 395ms 2.17% AbstractCentreBasedCellPopulation::GetDampingConstant 395ms 2.17% 71.12% 395ms 2.17% boost::numeric::ublas::same_impl_ex 391ms 2.15% 73.27% 391ms 2.15% [libchaste_mesh.so] 1ms 0.0055% 73.28% 369ms 2.03% std::set::set (inline) 167ms 0.92% 74.19% 367ms 2.02% std::_Rb_tree::_M_clone_node (inline) 2ms 0.011% 74.21% 355ms 1.95% NodeBasedCellPopulation::WriteVtkResultsToFile 49ms 0.27% 74.47% 346ms 1.90% std::_Rb_tree::_M_erase 339ms 1.86% 76.34% 339ms 1.86% boost::numeric::ublas::c_vector::operator() 77ms 0.42% 76.76% 335ms 1.84% std::_Rb_tree::~_Rb_tree (inline) 245ms 1.35% 78.11% 326ms 1.79% std::vector::push_back (inline) 7ms 0.038% 78.15% 317ms 1.74% std::_Rb_tree::_M_emplace_hint_unique 170ms 0.93% 79.08% 308ms 1.69% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 79.08% 295ms 1.62% std::_Rb_tree::_M_drop_node (inline) 0 0% 79.08% 283ms 1.56% std::set::~set (inline) 2ms 0.011% 79.09% 280ms 1.54% AbstractCellProperty::IsSubType (inline) 6ms 0.033% 79.13% 272ms 1.50% boost::numeric::ublas::vector_binary::size (inline) 2ms 0.011% 79.14% 268ms 1.47% NodesOnlyMesh::ReMesh 3ms 0.016% 79.15% 265ms 1.46% Cell::GetMutationState 264ms 1.45% 80.60% 264ms 1.45% std::_Rb_tree::_S_left (inline) 3ms 0.016% 80.62% 261ms 1.43% NodesOnlyMesh::UpdateNodeIndices 2ms 0.011% 80.63% 250ms 1.37% NodeBasedCellPopulation::UpdateMapsAfterRemesh 151ms 0.83% 81.46% 248ms 1.36% _int_malloc 0 0% 81.46% 244ms 1.34% std::_Rb_tree::_Alloc_node::operator() (inline) 241ms 1.32% 82.79% 241ms 1.32% __strcmp_evex 0 0% 82.79% 231ms 1.27% Node::GetRadius 0 0% 82.79% 202ms 1.11% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 82.79% 201ms 1.11% std::__new_allocator::deallocate (inline) 169ms 0.93% 83.72% 194ms 1.07% boost::shared_ptr::shared_ptr (inline) 0 0% 83.72% 191ms 1.05% NodesOnlyMesh::UpdateBoxCollection 55ms 0.3% 84.02% 189ms 1.04% std::__move_median_to_first (inline) 1ms 0.0055% 84.02% 188ms 1.03% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 84.02% 185ms 1.02% std::allocator_traits::deallocate (inline) 59ms 0.32% 84.35% 183ms 1.01% __GI___libc_free 0 0% 84.35% 180ms 0.99% std::_Rb_tree::_M_put_node (inline) 3ms 0.016% 84.37% 177ms 0.97% DistributedBoxCollection::GetProcessOwningNode 174ms 0.96% 85.32% 174ms 0.96% Node::CheckForNodeAttributes 0 0% 85.32% 173ms 0.95% Cell::HasCellProperty (inline) 0 0% 85.32% 173ms 0.95% CellPropertyCollection::HasProperty 0 0% 85.32% 170ms 0.93% std::iter_swap (inline) 170ms 0.93% 86.26% 170ms 0.93% std::swap (inline) 0 0% 86.26% 166ms 0.91% boost::numeric::ublas::c_vector::assign (inline) 0 0% 86.26% 161ms 0.89% NodesOnlyMesh::AddNodesToBoxes 0 0% 86.26% 160ms 0.88% boost::numeric::ublas::inner_prod (inline) 3ms 0.016% 86.27% 159ms 0.87% Cell::ReadyToDivide 5ms 0.027% 86.30% 159ms 0.87% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 86.30% 159ms 0.87% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 19ms 0.1% 86.40% 157ms 0.86% std::__insertion_sort (inline) 1ms 0.0055% 86.41% 154ms 0.85% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 86.41% 153ms 0.84% VtkMeshWriter::WriteFiles 31ms 0.17% 86.58% 131ms 0.72% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 86.58% 128ms 0.7% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 86.58% 127ms 0.7% vtkStreamingDemandDrivenPipeline::Update 0 0% 86.58% 127ms 0.7% vtkXMLWriterBase::Write 0 0% 86.58% 126ms 0.69% vtkExecutive::CallAlgorithm 0 0% 86.58% 125ms 0.69% vtkDemandDrivenPipeline::ProcessRequest 0 0% 86.58% 125ms 0.69% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 86.58% 125ms 0.69% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 86.58% 124ms 0.68% vtkCompositeDataPipeline::ExecuteData 0 0% 86.58% 124ms 0.68% vtkDemandDrivenPipeline::ExecuteData 110ms 0.6% 87.19% 123ms 0.68% _int_free 122ms 0.67% 87.86% 122ms 0.67% boost::shared_ptr::operator-> (inline) 61ms 0.34% 88.19% 122ms 0.67% std::__adjacent_find (inline) 0 0% 88.19% 122ms 0.67% std::__unique (inline) 0 0% 88.19% 122ms 0.67% std::unique (inline) 0 0% 88.19% 120ms 0.66% NodesOnlyMesh::ResizeBoxCollection 11ms 0.06% 88.25% 119ms 0.65% NodesOnlyMesh::IsANodeCloseToDomainBoundary 2ms 0.011% 88.26% 117ms 0.64% AbstractCellPopulation::SetCellUsingLocationIndex 8ms 0.044% 88.31% 116ms 0.64% AbstractCellProperty::IsType (inline) 0 0% 88.31% 116ms 0.64% std::_Rb_tree::_M_destroy_node (inline) 0 0% 88.31% 116ms 0.64% std::__new_allocator::destroy (inline) 0 0% 88.31% 116ms 0.64% std::allocator_traits::destroy (inline) 0 0% 88.31% 108ms 0.59% Cell::GetCellId 0 0% 88.31% 106ms 0.58% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 88.31% 106ms 0.58% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 1ms 0.0055% 88.31% 105ms 0.58% std::_Rb_tree::_M_insert_unique 0 0% 88.31% 105ms 0.58% std::set::insert (inline) 1ms 0.0055% 88.32% 104ms 0.57% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 88.32% 104ms 0.57% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 2ms 0.011% 88.33% 100ms 0.55% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 88.33% 99ms 0.54% std::_Rb_tree::clear (inline) 96ms 0.53% 88.86% 96ms 0.53% std::_Rb_tree_insert_and_rebalance 91ms 0.5% 89.36% 91ms 0.5% Node::GetIndex 1ms 0.0055% 89.36% 91ms 0.5% NodeBasedCellPopulation::SetNode 1ms 0.0055% 89.37% 91ms 0.5% boost::numeric::ublas::c_vector::operator[] (inline)