File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 30700ms, 89.70% of 34225ms total Dropped 817 nodes (cum <= 171.12ms) flat flat% sum% cum cum% 0 0% 0% 34073ms 99.56% __libc_start_call_main 0 0% 0% 34073ms 99.56% __libc_start_main_impl 0 0% 0% 34073ms 99.56% _start 0 0% 0% 34056ms 99.51% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 34056ms 99.51% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 34056ms 99.51% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 34056ms 99.51% main 0 0% 0% 34018ms 99.40% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 34018ms 99.40% CxxTest::TestRunner::runTest (inline) 0 0% 0% 34018ms 99.40% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 34010ms 99.37% AbstractCellBasedSimulation::Solve 3ms 0.0088% 0.0088% 23969ms 70.03% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.0058% 0.015% 19180ms 56.04% ForwardEulerNumericalMethod::UpdateAllNodePositions 7ms 0.02% 0.035% 18981ms 55.46% AbstractNumericalMethod::ComputeForcesIncludingDamping 176ms 0.51% 0.55% 18259ms 53.35% AbstractTwoBodyInteractionForce::AddForceContribution 1495ms 4.37% 4.92% 15517ms 45.34% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4307ms 12.58% 17.50% 9628ms 28.13% std::_Rb_tree::_M_lower_bound (inline) 0 0% 17.50% 8851ms 25.86% AbstractCellBasedSimulation::UpdateCellPopulation 318ms 0.93% 18.43% 8709ms 25.45% std::_Rb_tree::find (inline) 0 0% 18.43% 8709ms 25.45% std::map::find (inline) 156ms 0.46% 18.89% 8564ms 25.02% NodesOnlyMesh::GetNodeOrHaloNode 487ms 1.42% 20.31% 8381ms 24.49% AbstractMesh::GetNode 343ms 1.00% 21.31% 7901ms 23.09% NodesOnlyMesh::SolveNodeMapping 0 0% 21.31% 7794ms 22.77% NodeBasedCellPopulation::Update 210ms 0.61% 21.93% 6442ms 18.82% boost::numeric::ublas::vector_assign (inline) 234ms 0.68% 22.61% 6361ms 18.59% boost::numeric::ublas::c_vector::c_vector (partial-inline) 7ms 0.02% 22.63% 5753ms 16.81% DistributedBoxCollection::CalculateInteriorNodePairs 5283ms 15.44% 38.07% 5283ms 15.44% std::_Rb_tree::_S_right (inline) 0 0% 38.07% 4515ms 13.19% OffLatticeSimulation::ApplyBoundaries 18ms 0.053% 38.12% 4481ms 13.09% NodeAttributes::RemoveDuplicateNeighbours 2ms 0.0058% 38.12% 4319ms 12.62% std::__sort (inline) 0 0% 38.12% 4319ms 12.62% std::sort (inline) 1215ms 3.55% 41.67% 3589ms 10.49% boost::numeric::ublas::indexing_vector_assign 3ms 0.0088% 41.68% 3373ms 9.86% AbstractCellPopulation::Iterator::operator++ (inline) 209ms 0.61% 42.29% 3338ms 9.75% AbstractCellPopulation::Iterator::IsRealCell (inline) 81ms 0.24% 42.53% 3337ms 9.75% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 21ms 0.061% 42.59% 2802ms 8.19% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 206ms 0.6% 43.19% 2487ms 7.27% std::__introsort_loop 24ms 0.07% 43.26% 2369ms 6.92% PlaneBoundaryCondition::ImposeBoundaryCondition 34ms 0.099% 43.36% 2286ms 6.68% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.0029% 43.37% 2213ms 6.47% std::__unguarded_partition_pivot (inline) 22ms 0.064% 43.43% 2146ms 6.27% PlaneBoundaryCondition::VerifyBoundaryCondition 1020ms 2.98% 46.41% 2005ms 5.86% std::__unguarded_partition (inline) 140ms 0.41% 46.82% 1885ms 5.51% DistributedBoxCollection::AddPairsFromBox 1ms 0.0029% 46.82% 1827ms 5.34% std::__final_insertion_sort (inline) 213ms 0.62% 47.44% 1797ms 5.25% std::map::operator[] (partial-inline) 1633ms 4.77% 52.22% 1633ms 4.77% boost::numeric::ublas::same_impl_ex 87ms 0.25% 52.47% 1630ms 4.76% std::__unguarded_insertion_sort (inline) 130ms 0.38% 52.85% 1611ms 4.71% AbstractMesh::GetVectorFromAtoB 607ms 1.77% 54.62% 1584ms 4.63% std::__unguarded_linear_insert (inline) 1479ms 4.32% 58.95% 1479ms 4.32% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 58.95% 1320ms 3.86% std::_Rb_tree::lower_bound (inline) 0 0% 58.95% 1320ms 3.86% std::map::lower_bound (inline) 0 0% 58.95% 1297ms 3.79% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 58.95% 1271ms 3.71% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1ms 0.0029% 58.95% 1143ms 3.34% NodeBasedCellPopulation::UpdateCellProcessLocation 16ms 0.047% 58.99% 1112ms 3.25% boost::numeric::ublas::detail::expression_type_check (inline) 1094ms 3.20% 62.19% 1094ms 3.20% boost::numeric::ublas::c_vector::operator() 5ms 0.015% 62.21% 1085ms 3.17% DistributedBoxCollection::CalculateBoundaryNodePairs 218ms 0.64% 62.84% 1073ms 3.14% boost::numeric::ublas::detail::equals 154ms 0.45% 63.29% 1032ms 3.02% boost::numeric::ublas::vector_binary::size (inline) 181ms 0.53% 63.82% 849ms 2.48% NodeAttributes::AddAppliedForceContribution 19ms 0.056% 63.88% 843ms 2.46% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 71ms 0.21% 64.08% 836ms 2.44% std::__new_allocator::allocate (inline) 376ms 1.10% 65.18% 823ms 2.40% __GI___libc_free 0 0% 65.18% 815ms 2.38% boost::numeric::ublas::norm_inf (inline) 466ms 1.36% 66.54% 815ms 2.38% boost::numeric::ublas::vector_norm_inf::apply (inline) 357ms 1.04% 67.59% 778ms 2.27% DistributedBoxCollection::CalculateContainingBox (partial-inline) 77ms 0.22% 67.81% 762ms 2.23% operator new 547ms 1.60% 69.41% 745ms 2.18% __dynamic_cast 0 0% 69.41% 726ms 2.12% AbstractCellPopulation::WriteResultsToFiles 178ms 0.52% 69.93% 701ms 2.05% NodeAttributes::AddNeighbour 262ms 0.77% 70.70% 683ms 2.00% __GI___libc_malloc 0 0% 70.70% 668ms 1.95% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 70.70% 668ms 1.95% boost::numeric::ublas::c_vector::plus_assign (inline) 4ms 0.012% 70.71% 656ms 1.92% AbstractCentreBasedCellPopulation::GetDampingConstant 3ms 0.0088% 70.72% 606ms 1.77% AbstractCellBasedSimulation::DoCellBirth 31ms 0.091% 70.81% 597ms 1.74% std::_Rb_tree_const_iterator::operator++ (inline) 519ms 1.52% 72.32% 593ms 1.73% std::vector::push_back (inline) 562ms 1.64% 73.97% 562ms 1.64% std::_Rb_tree_increment 9ms 0.026% 73.99% 524ms 1.53% CellPropertyCollection::GetPropertiesType (inline) 0 0% 73.99% 482ms 1.41% boost::numeric::ublas::norm_2 (inline) 378ms 1.10% 75.10% 482ms 1.41% boost::numeric::ublas::vector_norm_2::apply (inline) 10ms 0.029% 75.13% 475ms 1.39% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 75.13% 475ms 1.39% boost::numeric::ublas::vector::vector (inline) 3ms 0.0088% 75.14% 470ms 1.37% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 75.14% 450ms 1.31% AbstractCellBasedSimulation::DoCellRemoval (inline) 407ms 1.19% 76.32% 443ms 1.29% _int_free 3ms 0.0088% 76.33% 439ms 1.28% Cell::GetMutationState 7ms 0.02% 76.35% 432ms 1.26% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 24ms 0.07% 76.42% 390ms 1.14% boost::detail::shared_count::~shared_count (inline) 0 0% 76.42% 390ms 1.14% boost::shared_ptr::~shared_ptr (inline) 380ms 1.11% 77.53% 380ms 1.11% Node::GetIndex 0 0% 77.53% 371ms 1.08% std::allocator_traits::allocate (inline) 355ms 1.04% 78.57% 359ms 1.05% boost::detail::sp_counted_base::release 120ms 0.35% 78.92% 350ms 1.02% Node::GetRadius 5ms 0.015% 78.94% 338ms 0.99% AbstractCellProperty::IsSubType (inline) 7ms 0.02% 78.96% 326ms 0.95% NodeBasedCellPopulation::UpdateMapsAfterRemesh 320ms 0.93% 79.89% 320ms 0.93% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 1ms 0.0029% 79.89% 311ms 0.91% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 0 0% 79.89% 310ms 0.91% std::_Rb_tree::_M_create_node (inline) 5ms 0.015% 79.91% 309ms 0.9% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 79.91% 300ms 0.88% boost::numeric::ublas::inner_prod (inline) 18ms 0.053% 79.96% 299ms 0.87% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 79.96% 299ms 0.87% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 294ms 0.86% 80.82% 294ms 0.86% [libchaste_cell_based.so] 5ms 0.015% 80.84% 293ms 0.86% boost::numeric::ublas::vector_reference::operator() (inline) 290ms 0.85% 81.68% 290ms 0.85% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 81.68% 288ms 0.84% NodesOnlyMesh::ReMesh 0 0% 81.68% 280ms 0.82% std::_Rb_tree::_M_get_node (inline) 4ms 0.012% 81.69% 278ms 0.81% NodesOnlyMesh::UpdateNodeIndices 0 0% 81.69% 267ms 0.78% NodesOnlyMesh::UpdateBoxCollection 112ms 0.33% 82.02% 266ms 0.78% std::_Rb_tree::_M_erase (partial-inline) 5ms 0.015% 82.04% 264ms 0.77% std::_Rb_tree::_M_emplace_hint_unique 3ms 0.0088% 82.05% 253ms 0.74% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 240ms 0.7% 82.75% 240ms 0.7% Node::CheckForNodeAttributes 0 0% 82.75% 239ms 0.7% boost::numeric::ublas::c_vector::assign (inline) 239ms 0.7% 83.44% 239ms 0.7% boost::numeric::ublas::c_vector::size (inline) 99ms 0.29% 83.73% 238ms 0.7% Node::AddNeighbour 0 0% 83.73% 237ms 0.69% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 95ms 0.28% 84.01% 237ms 0.69% boost::numeric::ublas::vector_inner_prod::apply (inline) 3ms 0.0088% 84.02% 235ms 0.69% DistributedBoxCollection::GetProcessOwningNode 0 0% 84.02% 235ms 0.69% VtkMeshWriter::WriteFiles 1ms 0.0029% 84.02% 232ms 0.68% NodesOnlyMesh::AddNodesToBoxes 124ms 0.36% 84.39% 221ms 0.65% _int_malloc 219ms 0.64% 85.03% 219ms 0.64% Node::rGetLocation 0 0% 85.03% 214ms 0.63% boost::numeric::ublas::vector_reference::size (inline) 100ms 0.29% 85.32% 213ms 0.62% std::__find_if (inline) 0 0% 85.32% 213ms 0.62% std::find_if (inline) 0 0% 85.32% 213ms 0.62% std::none_of (inline) 0 0% 85.32% 210ms 0.61% Cell::HasCellProperty (inline) 1ms 0.0029% 85.32% 210ms 0.61% CellPropertyCollection::HasProperty 0 0% 85.32% 209ms 0.61% NodesOnlyMesh::ResizeBoxCollection 7ms 0.02% 85.34% 208ms 0.61% NodesOnlyMesh::IsANodeCloseToDomainBoundary 92ms 0.27% 85.61% 202ms 0.59% std::__move_median_to_first (inline) 0 0% 85.61% 202ms 0.59% vtkStreamingDemandDrivenPipeline::Update 0 0% 85.61% 202ms 0.59% vtkXMLWriterBase::Write 201ms 0.59% 86.20% 201ms 0.59% [libchaste_mesh.so] 0 0% 86.20% 201ms 0.59% vtkCompositeDataPipeline::ExecuteData 0 0% 86.20% 201ms 0.59% vtkDemandDrivenPipeline::ExecuteData 0 0% 86.20% 201ms 0.59% vtkDemandDrivenPipeline::ProcessRequest 0 0% 86.20% 201ms 0.59% vtkExecutive::CallAlgorithm 0 0% 86.20% 201ms 0.59% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 86.20% 201ms 0.59% vtkXMLUnstructuredDataWriter::ProcessRequest 7ms 0.02% 86.22% 200ms 0.58% Cell::ReadyToDivide 41ms 0.12% 86.34% 200ms 0.58% std::__new_allocator::deallocate (inline) 0 0% 86.34% 198ms 0.58% boost::numeric::ublas::vector_binary::operator() (inline) 196ms 0.57% 86.91% 196ms 0.57% NodeBasedCellPopulation::GetNode 12ms 0.035% 86.95% 196ms 0.57% std::__insertion_sort (inline) 192ms 0.56% 87.51% 192ms 0.56% boost::numeric::ublas::scalar_plus_assign::apply (inline) 0 0% 87.51% 192ms 0.56% tcache_get (inline) 192ms 0.56% 88.07% 192ms 0.56% tcache_get_n (inline) 144ms 0.42% 88.49% 189ms 0.55% Node::AddAppliedForceContribution 187ms 0.55% 89.03% 189ms 0.55% Node::ConstructNodeAttributes (inline) 35ms 0.1% 89.14% 189ms 0.55% boost::numeric::ublas::c_vector::clear (inline) 12ms 0.035% 89.17% 179ms 0.52% std::_Rb_tree::_Rb_tree (partial-inline) 178ms 0.52% 89.69% 178ms 0.52% __strcmp_avx2 3ms 0.0088% 89.70% 176ms 0.51% AbstractCellProperty::IsType (inline) 0 0% 89.70% 172ms 0.5% std::_Rb_tree::_Alloc_node::operator() (inline)