File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 30880ms, 89.18% of 34626ms total Dropped 812 nodes (cum <= 173.13ms) flat flat% sum% cum cum% 0 0% 0% 34488ms 99.60% __libc_start_call_main 0 0% 0% 34488ms 99.60% __libc_start_main_impl 0 0% 0% 34488ms 99.60% _start 0 0% 0% 34473ms 99.56% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 34473ms 99.56% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 34473ms 99.56% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 34473ms 99.56% main 0 0% 0% 34434ms 99.45% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 34434ms 99.45% CxxTest::TestRunner::runTest (inline) 0 0% 0% 34434ms 99.45% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0029% 0.0029% 34425ms 99.42% AbstractCellBasedSimulation::Solve 2ms 0.0058% 0.0087% 24257ms 70.05% OffLatticeSimulation::UpdateCellLocationsAndTopology 5ms 0.014% 0.023% 19492ms 56.29% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.017% 0.04% 19310ms 55.77% AbstractNumericalMethod::ComputeForcesIncludingDamping 199ms 0.57% 0.62% 18508ms 53.45% AbstractTwoBodyInteractionForce::AddForceContribution 1520ms 4.39% 5.00% 15661ms 45.23% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4324ms 12.49% 17.49% 9217ms 26.62% std::_Rb_tree::_M_lower_bound (inline) 0 0% 17.49% 8970ms 25.91% AbstractCellBasedSimulation::UpdateCellPopulation 363ms 1.05% 18.54% 8345ms 24.10% std::_Rb_tree::find (inline) 0 0% 18.54% 8345ms 24.10% std::map::find (inline) 134ms 0.39% 18.93% 8152ms 23.54% NodesOnlyMesh::GetNodeOrHaloNode 525ms 1.52% 20.44% 7996ms 23.09% AbstractMesh::GetNode 0 0% 20.44% 7919ms 22.87% NodeBasedCellPopulation::Update 310ms 0.9% 21.34% 7471ms 21.58% NodesOnlyMesh::SolveNodeMapping 187ms 0.54% 21.88% 6873ms 19.85% boost::numeric::ublas::vector_assign (inline) 212ms 0.61% 22.49% 6744ms 19.48% boost::numeric::ublas::c_vector::c_vector (partial-inline) 7ms 0.02% 22.51% 5906ms 17.06% DistributedBoxCollection::CalculateInteriorNodePairs 4869ms 14.06% 36.57% 4869ms 14.06% std::_Rb_tree::_S_right (inline) 18ms 0.052% 36.63% 4489ms 12.96% NodeAttributes::RemoveDuplicateNeighbours 0 0% 36.63% 4470ms 12.91% OffLatticeSimulation::ApplyBoundaries 5ms 0.014% 36.64% 4314ms 12.46% std::__sort (inline) 0 0% 36.64% 4314ms 12.46% std::sort (inline) 1175ms 3.39% 40.03% 3630ms 10.48% boost::numeric::ublas::indexing_vector_assign 3ms 0.0087% 40.04% 3374ms 9.74% AbstractCellPopulation::Iterator::operator++ (inline) 210ms 0.61% 40.65% 3352ms 9.68% AbstractCellPopulation::Iterator::IsRealCell (inline) 60ms 0.17% 40.82% 3316ms 9.58% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 19ms 0.055% 40.88% 2815ms 8.13% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 182ms 0.53% 41.40% 2447ms 7.07% std::__introsort_loop 23ms 0.066% 41.47% 2340ms 6.76% PlaneBoundaryCondition::ImposeBoundaryCondition 38ms 0.11% 41.58% 2297ms 6.63% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 41.58% 2184ms 6.31% std::__unguarded_partition_pivot (inline) 15ms 0.043% 41.62% 2130ms 6.15% PlaneBoundaryCondition::VerifyBoundaryCondition 151ms 0.44% 42.06% 2041ms 5.89% DistributedBoxCollection::AddPairsFromBox 1001ms 2.89% 44.95% 1991ms 5.75% std::__unguarded_partition (inline) 2ms 0.0058% 44.95% 1859ms 5.37% std::__final_insertion_sort (inline) 201ms 0.58% 45.54% 1805ms 5.21% std::map::operator[] (partial-inline) 1750ms 5.05% 50.59% 1750ms 5.05% boost::numeric::ublas::same_impl_ex 85ms 0.25% 50.83% 1655ms 4.78% std::__unguarded_insertion_sort (inline) 108ms 0.31% 51.15% 1638ms 4.73% AbstractMesh::GetVectorFromAtoB 588ms 1.70% 52.84% 1603ms 4.63% std::__unguarded_linear_insert (inline) 0 0% 52.84% 1562ms 4.51% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 52.84% 1542ms 4.45% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1511ms 4.36% 57.21% 1511ms 4.36% __gnu_cxx::__normal_iterator::operator-- (inline) 21ms 0.061% 57.27% 1502ms 4.34% boost::numeric::ublas::detail::expression_type_check (inline) 222ms 0.64% 57.91% 1457ms 4.21% boost::numeric::ublas::detail::equals 0 0% 57.91% 1322ms 3.82% std::_Rb_tree::lower_bound (inline) 0 0% 57.91% 1322ms 3.82% std::map::lower_bound (inline) 1ms 0.0029% 57.91% 1158ms 3.34% NodeBasedCellPopulation::UpdateCellProcessLocation 0 0% 57.91% 1104ms 3.19% boost::numeric::ublas::norm_inf (inline) 635ms 1.83% 59.75% 1104ms 3.19% boost::numeric::ublas::vector_norm_inf::apply (inline) 1088ms 3.14% 62.89% 1088ms 3.14% boost::numeric::ublas::c_vector::operator() 170ms 0.49% 63.38% 1083ms 3.13% boost::numeric::ublas::vector_binary::size (inline) 5ms 0.014% 63.39% 1055ms 3.05% DistributedBoxCollection::CalculateBoundaryNodePairs 390ms 1.13% 64.52% 902ms 2.60% __GI___libc_free 193ms 0.56% 65.08% 875ms 2.53% NodeAttributes::AddAppliedForceContribution 58ms 0.17% 65.25% 846ms 2.44% std::__new_allocator::allocate (inline) 91ms 0.26% 65.51% 791ms 2.28% operator new 570ms 1.65% 67.15% 784ms 2.26% __dynamic_cast 26ms 0.075% 67.23% 780ms 2.25% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 369ms 1.07% 68.30% 755ms 2.18% DistributedBoxCollection::CalculateContainingBox (partial-inline) 6ms 0.017% 68.31% 751ms 2.17% AbstractCentreBasedCellPopulation::GetDampingConstant 194ms 0.56% 68.87% 727ms 2.10% NodeAttributes::AddNeighbour 0 0% 68.87% 725ms 2.09% AbstractCellPopulation::WriteResultsToFiles 234ms 0.68% 69.55% 695ms 2.01% __GI___libc_malloc 0 0% 69.55% 682ms 1.97% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 69.55% 682ms 1.97% boost::numeric::ublas::c_vector::plus_assign (inline) 38ms 0.11% 69.66% 652ms 1.88% std::_Rb_tree_const_iterator::operator++ (inline) 532ms 1.54% 71.20% 617ms 1.78% std::vector::push_back (inline) 3ms 0.0087% 71.20% 603ms 1.74% AbstractCellBasedSimulation::DoCellBirth 603ms 1.74% 72.95% 603ms 1.74% std::_Rb_tree_increment 12ms 0.035% 72.98% 594ms 1.72% CellPropertyCollection::GetPropertiesType (inline) 1ms 0.0029% 72.98% 522ms 1.51% Cell::GetMutationState 478ms 1.38% 74.36% 512ms 1.48% _int_free 1ms 0.0029% 74.37% 474ms 1.37% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 74.37% 458ms 1.32% boost::numeric::ublas::norm_2 (inline) 364ms 1.05% 75.42% 458ms 1.32% boost::numeric::ublas::vector_norm_2::apply (inline) 10ms 0.029% 75.45% 455ms 1.31% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 75.45% 455ms 1.31% boost::numeric::ublas::vector::vector (inline) 0 0% 75.45% 445ms 1.29% AbstractCellBasedSimulation::DoCellRemoval (inline) 6ms 0.017% 75.46% 429ms 1.24% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 75.46% 401ms 1.16% std::allocator_traits::allocate (inline) 38ms 0.11% 75.57% 393ms 1.13% boost::detail::shared_count::~shared_count (inline) 0 0% 75.57% 393ms 1.13% boost::shared_ptr::~shared_ptr (inline) 381ms 1.10% 76.67% 381ms 1.10% Node::GetIndex 2ms 0.0058% 76.68% 357ms 1.03% AbstractCellProperty::IsSubType (inline) 0 0% 76.68% 354ms 1.02% boost::numeric::ublas::inner_prod (inline) 3ms 0.0087% 76.69% 351ms 1.01% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 345ms 1% 77.68% 349ms 1.01% boost::detail::sp_counted_base::release 21ms 0.061% 77.75% 348ms 1.01% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 77.75% 348ms 1.01% std::_Rb_tree::_M_create_node (inline) 1ms 0.0029% 77.75% 330ms 0.95% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 5ms 0.014% 77.76% 329ms 0.95% AbstractCellPopulation::GetCellUsingLocationIndex 116ms 0.34% 78.10% 327ms 0.94% Node::GetRadius 7ms 0.02% 78.12% 326ms 0.94% NodeBasedCellPopulation::UpdateMapsAfterRemesh 106ms 0.31% 78.42% 319ms 0.92% Node::AddNeighbour 0 0% 78.42% 314ms 0.91% std::_Rb_tree::_M_get_node (inline) 12ms 0.035% 78.46% 313ms 0.9% boost::numeric::ublas::vector_reference::operator() (inline) 300ms 0.87% 79.32% 300ms 0.87% __gnu_cxx::__normal_iterator::operator++ (inline) 297ms 0.86% 80.18% 297ms 0.86% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 80.18% 288ms 0.83% NodesOnlyMesh::ReMesh 7ms 0.02% 80.20% 282ms 0.81% std::_Rb_tree::_M_emplace_hint_unique 4ms 0.012% 80.21% 281ms 0.81% NodesOnlyMesh::UpdateNodeIndices 281ms 0.81% 81.03% 281ms 0.81% [libchaste_cell_based.so] 103ms 0.3% 81.32% 281ms 0.81% std::_Rb_tree::_M_erase (partial-inline) 4ms 0.012% 81.33% 280ms 0.81% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 106ms 0.31% 81.64% 276ms 0.8% std::__find_if (inline) 0 0% 81.64% 276ms 0.8% std::find_if (inline) 0 0% 81.64% 276ms 0.8% std::none_of (inline) 6ms 0.017% 81.66% 267ms 0.77% DistributedBoxCollection::GetProcessOwningNode 100ms 0.29% 81.95% 267ms 0.77% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 81.95% 261ms 0.75% NodesOnlyMesh::UpdateBoxCollection 0 0% 81.95% 259ms 0.75% boost::numeric::ublas::c_vector::assign (inline) 250ms 0.72% 82.67% 250ms 0.72% Node::ConstructNodeAttributes (inline) 139ms 0.4% 83.07% 250ms 0.72% _int_malloc 236ms 0.68% 83.75% 236ms 0.68% NodeBasedCellPopulation::GetNode 0 0% 83.75% 232ms 0.67% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 83.75% 228ms 0.66% VtkMeshWriter::WriteFiles 226ms 0.65% 84.40% 226ms 0.65% Node::CheckForNodeAttributes 0 0% 84.40% 221ms 0.64% boost::numeric::ublas::vector_binary::operator() (inline) 219ms 0.63% 85.04% 219ms 0.63% Node::rGetLocation 214ms 0.62% 85.66% 214ms 0.62% boost::numeric::ublas::c_vector::size (inline) 175ms 0.51% 86.16% 207ms 0.6% Node::AddAppliedForceContribution 4ms 0.012% 86.17% 207ms 0.6% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 86.17% 206ms 0.59% Cell::HasCellProperty (inline) 1ms 0.0029% 86.18% 206ms 0.59% CellPropertyCollection::HasProperty 0 0% 86.18% 205ms 0.59% tcache_get (inline) 205ms 0.59% 86.77% 205ms 0.59% tcache_get_n (inline) 204ms 0.59% 87.36% 204ms 0.59% __strcmp_avx2 1ms 0.0029% 87.36% 202ms 0.58% NodesOnlyMesh::AddNodesToBoxes 202ms 0.58% 87.94% 202ms 0.58% boost::numeric::ublas::scalar_plus_assign::apply (inline) 20ms 0.058% 88.00% 202ms 0.58% std::__insertion_sort (inline) 0 0% 88.00% 201ms 0.58% vtkStreamingDemandDrivenPipeline::Update 0 0% 88.00% 201ms 0.58% vtkXMLWriterBase::Write 24ms 0.069% 88.07% 200ms 0.58% std::_Rb_tree::_M_copy (inline) 0 0% 88.07% 200ms 0.58% vtkDemandDrivenPipeline::ProcessRequest 0 0% 88.07% 200ms 0.58% vtkExecutive::CallAlgorithm 0 0% 88.07% 199ms 0.57% std::_Rb_tree::_Alloc_node::operator() (inline) 1ms 0.0029% 88.07% 199ms 0.57% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 88.07% 198ms 0.57% vtkCompositeDataPipeline::ExecuteData 0 0% 88.07% 198ms 0.57% vtkDemandDrivenPipeline::ExecuteData 0 0% 88.07% 198ms 0.57% vtkXMLUnstructuredDataWriter::ProcessRequest 39ms 0.11% 88.19% 196ms 0.57% std::__new_allocator::deallocate (inline) 0 0% 88.19% 195ms 0.56% NodesOnlyMesh::ResizeBoxCollection 0 0% 88.19% 195ms 0.56% boost::numeric::ublas::vector_reference::size (inline) 19ms 0.055% 88.24% 194ms 0.56% NodesOnlyMesh::IsANodeCloseToDomainBoundary 10ms 0.029% 88.27% 193ms 0.56% Cell::ReadyToDivide 77ms 0.22% 88.49% 187ms 0.54% std::__move_median_to_first (inline) 181ms 0.52% 89.01% 181ms 0.52% [libchaste_mesh.so] 30ms 0.087% 89.10% 176ms 0.51% std::_Rb_tree::_M_clone_node (inline) 28ms 0.081% 89.18% 175ms 0.51% boost::numeric::ublas::c_vector::clear (inline)