File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 31928ms, 90.19% of 35400ms total Dropped 843 nodes (cum <= 177ms) flat flat% sum% cum cum% 0 0% 0% 35230ms 99.52% __libc_start_call_main 0 0% 0% 35230ms 99.52% __libc_start_main_impl 0 0% 0% 35230ms 99.52% _start 0 0% 0% 35213ms 99.47% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 35213ms 99.47% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 35213ms 99.47% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 35213ms 99.47% main 0 0% 0% 35176ms 99.37% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 35176ms 99.37% CxxTest::TestRunner::runTest (inline) 0 0% 0% 35176ms 99.37% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0028% 0.0028% 35167ms 99.34% AbstractCellBasedSimulation::Solve 0 0% 0.0028% 24557ms 69.37% OffLatticeSimulation::UpdateCellLocationsAndTopology 3ms 0.0085% 0.011% 19691ms 55.62% ForwardEulerNumericalMethod::UpdateAllNodePositions 12ms 0.034% 0.045% 19485ms 55.04% AbstractNumericalMethod::ComputeForcesIncludingDamping 213ms 0.6% 0.65% 18461ms 52.15% AbstractTwoBodyInteractionForce::AddForceContribution 1691ms 4.78% 5.42% 15600ms 44.07% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4238ms 11.97% 17.40% 9526ms 26.91% std::_Rb_tree::_M_lower_bound (inline) 0 0% 17.40% 9391ms 26.53% AbstractCellBasedSimulation::UpdateCellPopulation 328ms 0.93% 18.32% 8628ms 24.37% std::_Rb_tree::find (inline) 0 0% 18.32% 8628ms 24.37% std::map::find (inline) 148ms 0.42% 18.74% 8449ms 23.87% NodesOnlyMesh::GetNodeOrHaloNode 535ms 1.51% 20.25% 8317ms 23.49% AbstractMesh::GetNode 0 0% 20.25% 8252ms 23.31% NodeBasedCellPopulation::Update 321ms 0.91% 21.16% 7789ms 22.00% NodesOnlyMesh::SolveNodeMapping 8ms 0.023% 21.18% 6140ms 17.34% DistributedBoxCollection::CalculateInteriorNodePairs 205ms 0.58% 21.76% 5944ms 16.79% boost::numeric::ublas::vector_assign (inline) 205ms 0.58% 22.34% 5832ms 16.47% boost::numeric::ublas::c_vector::c_vector (partial-inline) 5281ms 14.92% 37.26% 5281ms 14.92% std::_Rb_tree::_S_right (inline) 0 0% 37.26% 4530ms 12.80% OffLatticeSimulation::ApplyBoundaries 18ms 0.051% 37.31% 4514ms 12.75% NodeAttributes::RemoveDuplicateNeighbours 6ms 0.017% 37.32% 4340ms 12.26% std::__sort (inline) 0 0% 37.32% 4340ms 12.26% std::sort (inline) 2ms 0.0056% 37.33% 3474ms 9.81% AbstractCellPopulation::Iterator::operator++ (inline) 1163ms 3.29% 40.62% 3473ms 9.81% boost::numeric::ublas::indexing_vector_assign 253ms 0.71% 41.33% 3447ms 9.74% AbstractCellPopulation::Iterator::IsRealCell 74ms 0.21% 41.54% 3334ms 9.42% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 17ms 0.048% 41.59% 2867ms 8.10% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 193ms 0.55% 42.13% 2599ms 7.34% std::__introsort_loop 31ms 0.088% 42.22% 2381ms 6.73% PlaneBoundaryCondition::ImposeBoundaryCondition 1ms 0.0028% 42.22% 2323ms 6.56% std::__unguarded_partition_pivot (inline) 30ms 0.085% 42.31% 2242ms 6.33% AbstractCellPopulation::GetLocationIndexUsingCell 153ms 0.43% 42.74% 2241ms 6.33% DistributedBoxCollection::AddPairsFromBox 16ms 0.045% 42.79% 2149ms 6.07% PlaneBoundaryCondition::VerifyBoundaryCondition 1094ms 3.09% 45.88% 2077ms 5.87% std::__unguarded_partition (inline) 1ms 0.0028% 45.88% 1734ms 4.90% std::__final_insertion_sort (inline) 191ms 0.54% 46.42% 1730ms 4.89% std::map::operator[] (partial-inline) 145ms 0.41% 46.83% 1693ms 4.78% AbstractMesh::GetVectorFromAtoB 85ms 0.24% 47.07% 1530ms 4.32% std::__unguarded_insertion_sort (inline) 555ms 1.57% 48.64% 1502ms 4.24% std::__unguarded_linear_insert (inline) 1467ms 4.14% 52.78% 1467ms 4.14% boost::numeric::ublas::same_impl_ex 1437ms 4.06% 56.84% 1437ms 4.06% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 56.84% 1307ms 3.69% std::_Rb_tree::lower_bound (inline) 0 0% 56.84% 1307ms 3.69% std::map::lower_bound (inline) 0 0% 56.84% 1177ms 3.32% NodeBasedCellPopulation::UpdateCellProcessLocation 1166ms 3.29% 60.13% 1166ms 3.29% boost::numeric::ublas::c_vector::operator() 0 0% 60.13% 1151ms 3.25% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 60.13% 1128ms 3.19% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 2ms 0.0056% 60.14% 1067ms 3.01% DistributedBoxCollection::CalculateBoundaryNodePairs 11ms 0.031% 60.17% 1028ms 2.90% boost::numeric::ublas::detail::expression_type_check (inline) 202ms 0.57% 60.74% 973ms 2.75% boost::numeric::ublas::detail::equals 160ms 0.45% 61.19% 954ms 2.69% boost::numeric::ublas::vector_binary::size (inline) 4ms 0.011% 61.20% 951ms 2.69% AbstractCentreBasedCellPopulation::GetDampingConstant 190ms 0.54% 61.74% 871ms 2.46% NodeAttributes::AddAppliedForceContribution 377ms 1.06% 62.81% 833ms 2.35% DistributedBoxCollection::CalculateContainingBox (partial-inline) 27ms 0.076% 62.88% 830ms 2.34% std::_Rb_tree_const_iterator::operator++ (inline) 589ms 1.66% 64.55% 800ms 2.26% __dynamic_cast 12ms 0.034% 64.58% 793ms 2.24% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 793ms 2.24% 66.82% 793ms 2.24% std::_Rb_tree_increment 314ms 0.89% 67.71% 778ms 2.20% __GI___libc_free 0 0% 67.71% 752ms 2.12% AbstractCellPopulation::WriteResultsToFiles 97ms 0.27% 67.98% 736ms 2.08% std::__new_allocator::allocate (inline) 0 0% 67.98% 717ms 2.03% boost::numeric::ublas::norm_inf (inline) 466ms 1.32% 69.30% 717ms 2.03% boost::numeric::ublas::vector_norm_inf::apply (inline) 21ms 0.059% 69.36% 714ms 2.02% CellPropertyCollection::GetPropertiesType (inline) 190ms 0.54% 69.89% 694ms 1.96% NodeAttributes::AddNeighbour 0 0% 69.89% 681ms 1.92% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 69.89% 681ms 1.92% boost::numeric::ublas::c_vector::plus_assign (inline) 3ms 0.0085% 69.90% 679ms 1.92% AbstractCellBasedSimulation::DoCellBirth 149ms 0.42% 70.32% 678ms 1.92% Node::GetRadius 2ms 0.0056% 70.33% 646ms 1.82% Cell::GetMutationState 107ms 0.3% 70.63% 642ms 1.81% operator new 502ms 1.42% 72.05% 605ms 1.71% std::vector::push_back (inline) 171ms 0.48% 72.53% 527ms 1.49% __GI___libc_malloc 512ms 1.45% 73.98% 512ms 1.45% Node::CheckForNodeAttributes 0 0% 73.98% 491ms 1.39% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 73.98% 460ms 1.30% AbstractCellBasedSimulation::DoCellRemoval (inline) 402ms 1.14% 75.11% 460ms 1.30% _int_free 118ms 0.33% 75.45% 452ms 1.28% Node::AddNeighbour 5ms 0.014% 75.46% 440ms 1.24% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 75.46% 434ms 1.23% boost::numeric::ublas::norm_2 (inline) 346ms 0.98% 76.44% 434ms 1.23% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 76.44% 422ms 1.19% std::allocator_traits::allocate (inline) 29ms 0.082% 76.52% 404ms 1.14% boost::detail::shared_count::~shared_count (inline) 0 0% 76.52% 404ms 1.14% boost::shared_ptr::~shared_ptr (inline) 2ms 0.0056% 76.53% 399ms 1.13% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 0 0% 76.53% 396ms 1.12% std::_Rb_tree::_M_create_node (inline) 1ms 0.0028% 76.53% 395ms 1.12% AbstractCellPopulation::GetCellUsingLocationIndex 378ms 1.07% 77.60% 379ms 1.07% Node::ConstructNodeAttributes (inline) 375ms 1.06% 78.66% 375ms 1.06% Node::GetIndex 367ms 1.04% 79.69% 373ms 1.05% boost::detail::sp_counted_base::release 1ms 0.0028% 79.69% 367ms 1.04% AbstractCellProperty::IsSubType (inline) 37ms 0.1% 79.80% 351ms 0.99% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 79.80% 351ms 0.99% boost::numeric::ublas::vector::vector (inline) 0 0% 79.80% 335ms 0.95% std::_Rb_tree::_M_get_node (inline) 332ms 0.94% 80.74% 332ms 0.94% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 5ms 0.014% 80.75% 328ms 0.93% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 80.75% 322ms 0.91% NodesOnlyMesh::UpdateBoxCollection 111ms 0.31% 81.06% 307ms 0.87% std::_Rb_tree::_M_erase (partial-inline) 0 0% 81.06% 306ms 0.86% boost::numeric::ublas::inner_prod (inline) 4ms 0.011% 81.08% 306ms 0.86% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 302ms 0.85% 81.93% 302ms 0.85% __gnu_cxx::__normal_iterator::operator++ (inline) 20ms 0.056% 81.99% 302ms 0.85% boost::numeric::ublas::vector_scalar_binary::evaluate 1ms 0.0028% 81.99% 294ms 0.83% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 14ms 0.04% 82.03% 288ms 0.81% std::_Rb_tree::_Rb_tree (partial-inline) 9ms 0.025% 82.05% 285ms 0.81% boost::numeric::ublas::vector_reference::operator() (inline) 4ms 0.011% 82.06% 281ms 0.79% DistributedBoxCollection::GetProcessOwningNode 0 0% 82.06% 268ms 0.76% NodesOnlyMesh::ReMesh 26ms 0.073% 82.14% 268ms 0.76% std::_Rb_tree::_M_copy (inline) 1ms 0.0028% 82.14% 265ms 0.75% NodesOnlyMesh::AddNodesToBoxes 0 0% 82.14% 264ms 0.75% Cell::HasCellProperty (inline) 2ms 0.0056% 82.15% 264ms 0.75% CellPropertyCollection::HasProperty 0 0% 82.15% 264ms 0.75% std::_Rb_tree::_Alloc_node::operator() (inline) 10ms 0.028% 82.18% 257ms 0.73% Cell::ReadyToDivide 6ms 0.017% 82.19% 257ms 0.73% NodesOnlyMesh::UpdateNodeIndices 252ms 0.71% 82.90% 252ms 0.71% [libchaste_mesh.so] 137ms 0.39% 83.29% 250ms 0.71% _int_malloc 244ms 0.69% 83.98% 244ms 0.69% [libchaste_cell_based.so] 40ms 0.11% 84.09% 241ms 0.68% std::_Rb_tree::_M_clone_node (inline) 0 0% 84.09% 238ms 0.67% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 97ms 0.27% 84.37% 238ms 0.67% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 84.37% 237ms 0.67% VtkMeshWriter::WriteFiles 96ms 0.27% 84.64% 235ms 0.66% std::__move_median_to_first (inline) 234ms 0.66% 85.30% 234ms 0.66% Node::rGetLocation 10ms 0.028% 85.33% 232ms 0.66% std::_Rb_tree::_M_emplace_hint_unique 88ms 0.25% 85.58% 228ms 0.64% std::__find_if (inline) 0 0% 85.58% 228ms 0.64% std::find_if (inline) 0 0% 85.58% 228ms 0.64% std::none_of (inline) 219ms 0.62% 86.19% 220ms 0.62% NodeBasedCellPopulation::GetNode 0 0% 86.19% 219ms 0.62% NodesOnlyMesh::ResizeBoxCollection 0 0% 86.19% 219ms 0.62% boost::numeric::ublas::c_vector::assign (inline) 5ms 0.014% 86.21% 217ms 0.61% NodesOnlyMesh::IsANodeCloseToDomainBoundary 44ms 0.12% 86.33% 214ms 0.6% std::__new_allocator::deallocate (inline) 210ms 0.59% 86.93% 210ms 0.59% boost::numeric::ublas::scalar_plus_assign::apply (inline) 0 0% 86.93% 209ms 0.59% vtkXMLWriterBase::Write 1ms 0.0028% 86.93% 208ms 0.59% vtkDemandDrivenPipeline::ProcessRequest 0 0% 86.93% 208ms 0.59% vtkStreamingDemandDrivenPipeline::Update 206ms 0.58% 87.51% 206ms 0.58% NodeAttributes::GetRadius 203ms 0.57% 88.08% 203ms 0.57% boost::shared_ptr::operator-> (inline) 19ms 0.054% 88.14% 203ms 0.57% std::__insertion_sort (inline) 0 0% 88.14% 203ms 0.57% vtkDemandDrivenPipeline::ExecuteData 0 0% 88.14% 203ms 0.57% vtkStreamingDemandDrivenPipeline::ProcessRequest 160ms 0.45% 88.59% 202ms 0.57% Node::AddAppliedForceContribution 0 0% 88.59% 202ms 0.57% vtkCompositeDataPipeline::ExecuteData 201ms 0.57% 89.16% 201ms 0.57% boost::numeric::ublas::c_vector::size (inline) 0 0% 89.16% 201ms 0.57% vtkExecutive::CallAlgorithm 0 0% 89.16% 200ms 0.56% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 89.16% 199ms 0.56% boost::numeric::ublas::vector_reference::size (inline) 0 0% 89.16% 199ms 0.56% vtkXMLUnstructuredDataWriter::ProcessRequest 187ms 0.53% 89.69% 187ms 0.53% __strcmp_avx2 179ms 0.51% 90.19% 179ms 0.51% Node::IsDeleted 0 0% 90.19% 177ms 0.5% std::_Rb_tree::_M_drop_node (inline)