File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 31518ms, 88.67% of 35546ms total Dropped 821 nodes (cum <= 177.73ms) flat flat% sum% cum cum% 0 0% 0% 35386ms 99.55% __libc_start_call_main 0 0% 0% 35386ms 99.55% __libc_start_main_impl 0 0% 0% 35386ms 99.55% _start 0 0% 0% 35370ms 99.50% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 35370ms 99.50% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 35370ms 99.50% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 35370ms 99.50% main 0 0% 0% 35331ms 99.40% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 35331ms 99.40% CxxTest::TestRunner::runTest (inline) 0 0% 0% 35331ms 99.40% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0028% 0.0028% 35321ms 99.37% AbstractCellBasedSimulation::Solve 1ms 0.0028% 0.0056% 24478ms 68.86% OffLatticeSimulation::UpdateCellLocationsAndTopology 3ms 0.0084% 0.014% 19391ms 54.55% ForwardEulerNumericalMethod::UpdateAllNodePositions 15ms 0.042% 0.056% 19190ms 53.99% AbstractNumericalMethod::ComputeForcesIncludingDamping 205ms 0.58% 0.63% 18002ms 50.64% AbstractTwoBodyInteractionForce::AddForceContribution 1397ms 3.93% 4.56% 15037ms 42.30% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4341ms 12.21% 16.78% 9787ms 27.53% std::_Rb_tree::_M_lower_bound (inline) 0 0% 16.78% 9609ms 27.03% AbstractCellBasedSimulation::UpdateCellPopulation 360ms 1.01% 17.79% 8893ms 25.02% std::_Rb_tree::find (inline) 0 0% 17.79% 8893ms 25.02% std::map::find (inline) 163ms 0.46% 18.25% 8559ms 24.08% NodesOnlyMesh::GetNodeOrHaloNode 495ms 1.39% 19.64% 8405ms 23.65% AbstractMesh::GetNode 1ms 0.0028% 19.64% 8404ms 23.64% NodeBasedCellPopulation::Update 332ms 0.93% 20.58% 7915ms 22.27% NodesOnlyMesh::SolveNodeMapping 220ms 0.62% 21.20% 6325ms 17.79% boost::numeric::ublas::vector_assign (inline) 6ms 0.017% 21.21% 6297ms 17.72% DistributedBoxCollection::CalculateInteriorNodePairs 163ms 0.46% 21.67% 6165ms 17.34% boost::numeric::ublas::c_vector::c_vector (partial-inline) 5406ms 15.21% 36.88% 5406ms 15.21% std::_Rb_tree::_S_right (inline) 1ms 0.0028% 36.88% 4685ms 13.18% OffLatticeSimulation::ApplyBoundaries 21ms 0.059% 36.94% 4560ms 12.83% NodeAttributes::RemoveDuplicateNeighbours 6ms 0.017% 36.96% 4397ms 12.37% std::__sort (inline) 0 0% 36.96% 4397ms 12.37% std::sort (inline) 1178ms 3.31% 40.27% 3713ms 10.45% boost::numeric::ublas::indexing_vector_assign 5ms 0.014% 40.29% 3550ms 9.99% AbstractCellPopulation::Iterator::operator++ (inline) 194ms 0.55% 40.83% 3521ms 9.91% AbstractCellPopulation::Iterator::IsRealCell (inline) 88ms 0.25% 41.08% 3521ms 9.91% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 32ms 0.09% 41.17% 3010ms 8.47% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 203ms 0.57% 41.74% 2559ms 7.20% std::__introsort_loop 23ms 0.065% 41.80% 2485ms 6.99% PlaneBoundaryCondition::ImposeBoundaryCondition 41ms 0.12% 41.92% 2419ms 6.81% AbstractCellPopulation::GetLocationIndexUsingCell 143ms 0.4% 42.32% 2348ms 6.61% DistributedBoxCollection::AddPairsFromBox 1ms 0.0028% 42.33% 2287ms 6.43% std::__unguarded_partition_pivot (inline) 22ms 0.062% 42.39% 2199ms 6.19% PlaneBoundaryCondition::VerifyBoundaryCondition 1095ms 3.08% 45.47% 2039ms 5.74% std::__unguarded_partition (inline) 0 0% 45.47% 1832ms 5.15% std::__final_insertion_sort (inline) 202ms 0.57% 46.04% 1811ms 5.09% std::map::operator[] (partial-inline) 1747ms 4.91% 50.95% 1747ms 4.91% boost::numeric::ublas::same_impl_ex 95ms 0.27% 51.22% 1618ms 4.55% std::__unguarded_insertion_sort (inline) 594ms 1.67% 52.89% 1588ms 4.47% std::__unguarded_linear_insert (inline) 136ms 0.38% 53.27% 1485ms 4.18% AbstractMesh::GetVectorFromAtoB 1457ms 4.10% 57.37% 1457ms 4.10% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 57.37% 1336ms 3.76% std::_Rb_tree::lower_bound (inline) 0 0% 57.37% 1336ms 3.76% std::map::lower_bound (inline) 0 0% 57.37% 1265ms 3.56% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 57.37% 1250ms 3.52% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 57.37% 1222ms 3.44% NodeBasedCellPopulation::UpdateCellProcessLocation 1168ms 3.29% 60.66% 1168ms 3.29% boost::numeric::ublas::c_vector::operator() 4ms 0.011% 60.67% 1103ms 3.10% AbstractCentreBasedCellPopulation::GetDampingConstant 18ms 0.051% 60.72% 1098ms 3.09% boost::numeric::ublas::detail::expression_type_check (inline) 4ms 0.011% 60.73% 1085ms 3.05% DistributedBoxCollection::CalculateBoundaryNodePairs 213ms 0.6% 61.33% 1053ms 2.96% boost::numeric::ublas::detail::equals 146ms 0.41% 61.74% 953ms 2.68% boost::numeric::ublas::vector_binary::size (inline) 53ms 0.15% 61.89% 930ms 2.62% std::_Rb_tree_const_iterator::operator++ (inline) 227ms 0.64% 62.53% 920ms 2.59% NodeAttributes::AddAppliedForceContribution 878ms 2.47% 65.00% 878ms 2.47% std::_Rb_tree_increment 51ms 0.14% 65.14% 850ms 2.39% CellPropertyCollection::GetPropertiesType (inline) 27ms 0.076% 65.22% 825ms 2.32% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 400ms 1.13% 66.34% 811ms 2.28% DistributedBoxCollection::CalculateContainingBox (partial-inline) 136ms 0.38% 66.72% 806ms 2.27% std::__new_allocator::allocate (inline) 0 0% 66.72% 803ms 2.26% boost::numeric::ublas::norm_inf (inline) 474ms 1.33% 68.06% 803ms 2.26% boost::numeric::ublas::vector_norm_inf::apply (inline) 574ms 1.61% 69.67% 782ms 2.20% __dynamic_cast 5ms 0.014% 69.69% 771ms 2.17% Cell::GetMutationState 299ms 0.84% 70.53% 752ms 2.12% __GI___libc_free 0 0% 70.53% 747ms 2.10% AbstractCellPopulation::WriteResultsToFiles 2ms 0.0056% 70.53% 726ms 2.04% AbstractCellBasedSimulation::DoCellBirth 0 0% 70.53% 693ms 1.95% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 70.53% 693ms 1.95% boost::numeric::ublas::c_vector::plus_assign (inline) 194ms 0.55% 71.08% 692ms 1.95% NodeAttributes::AddNeighbour 104ms 0.29% 71.37% 675ms 1.90% operator new 494ms 1.39% 72.76% 596ms 1.68% std::vector::push_back (inline) 162ms 0.46% 73.22% 568ms 1.60% __GI___libc_malloc 115ms 0.32% 73.54% 565ms 1.59% Node::AddNeighbour 514ms 1.45% 74.99% 515ms 1.45% Node::ConstructNodeAttributes (inline) 0 0% 74.99% 492ms 1.38% std::allocator_traits::allocate (inline) 0 0% 74.99% 487ms 1.37% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 74.99% 478ms 1.34% std::_Rb_tree::_M_create_node (inline) 0 0% 74.99% 477ms 1.34% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 74.99% 462ms 1.30% boost::numeric::ublas::norm_2 (inline) 359ms 1.01% 76.00% 462ms 1.30% boost::numeric::ublas::vector_norm_2::apply (inline) 393ms 1.11% 77.10% 454ms 1.28% _int_free 6ms 0.017% 77.12% 450ms 1.27% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1ms 0.0028% 77.12% 438ms 1.23% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 5ms 0.014% 77.14% 434ms 1.22% AbstractCellPopulation::GetCellUsingLocationIndex 1ms 0.0028% 77.14% 409ms 1.15% AbstractCellProperty::IsSubType (inline) 0 0% 77.14% 393ms 1.11% std::_Rb_tree::_M_get_node (inline) 11ms 0.031% 77.17% 380ms 1.07% std::_Rb_tree::_Rb_tree (partial-inline) 379ms 1.07% 78.24% 379ms 1.07% Node::GetIndex 29ms 0.082% 78.32% 376ms 1.06% boost::detail::shared_count::~shared_count (inline) 0 0% 78.32% 376ms 1.06% boost::shared_ptr::~shared_ptr (inline) 24ms 0.068% 78.39% 366ms 1.03% std::_Rb_tree::_M_copy (inline) 178ms 0.5% 78.89% 349ms 0.98% std::_Rb_tree::_M_erase 3ms 0.0084% 78.89% 346ms 0.97% NodeBasedCellPopulation::UpdateMapsAfterRemesh 139ms 0.39% 79.29% 341ms 0.96% Node::GetRadius 341ms 0.96% 80.25% 341ms 0.96% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 65ms 0.18% 80.43% 341ms 0.96% std::_Rb_tree::_M_clone_node (inline) 331ms 0.93% 81.36% 339ms 0.95% boost::detail::sp_counted_base::release 24ms 0.068% 81.43% 338ms 0.95% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 81.43% 338ms 0.95% boost::numeric::ublas::vector::vector (inline) 9ms 0.025% 81.45% 327ms 0.92% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 81.45% 326ms 0.92% NodesOnlyMesh::ReMesh 0 0% 81.45% 325ms 0.91% std::_Rb_tree::_Alloc_node::operator() (inline) 5ms 0.014% 81.47% 309ms 0.87% NodesOnlyMesh::UpdateNodeIndices 0 0% 81.47% 305ms 0.86% boost::numeric::ublas::c_vector::assign (inline) 148ms 0.42% 81.88% 301ms 0.85% _int_malloc 300ms 0.84% 82.73% 300ms 0.84% [libchaste_cell_based.so] 0 0% 82.73% 298ms 0.84% Cell::HasCellProperty (inline) 3ms 0.0084% 82.74% 298ms 0.84% CellPropertyCollection::HasProperty 2ms 0.0056% 82.74% 298ms 0.84% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 13ms 0.037% 82.78% 293ms 0.82% Cell::ReadyToDivide 292ms 0.82% 83.60% 292ms 0.82% __gnu_cxx::__normal_iterator::operator++ (inline) 8ms 0.023% 83.62% 284ms 0.8% DistributedBoxCollection::GetProcessOwningNode 0 0% 83.62% 283ms 0.8% boost::numeric::ublas::inner_prod (inline) 4ms 0.011% 83.63% 282ms 0.79% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 22ms 0.062% 83.69% 278ms 0.78% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 83.69% 273ms 0.77% NodesOnlyMesh::UpdateBoxCollection 9ms 0.025% 83.72% 273ms 0.77% std::_Rb_tree::_M_emplace_hint_unique 96ms 0.27% 83.99% 244ms 0.69% std::__move_median_to_first (inline) 90ms 0.25% 84.24% 232ms 0.65% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 84.24% 230ms 0.65% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 229ms 0.64% 84.89% 229ms 0.64% boost::shared_ptr::operator-> (inline) 0 0% 84.89% 226ms 0.64% VtkMeshWriter::WriteFiles 159ms 0.45% 85.33% 220ms 0.62% Node::AddAppliedForceContribution 0 0% 85.33% 219ms 0.62% boost::numeric::ublas::vector_binary::operator() (inline) 218ms 0.61% 85.95% 218ms 0.61% NodeBasedCellPopulation::GetNode 216ms 0.61% 86.56% 216ms 0.61% Node::CheckForNodeAttributes 23ms 0.065% 86.62% 214ms 0.6% std::__insertion_sort (inline) 1ms 0.0028% 86.62% 204ms 0.57% NodesOnlyMesh::AddNodesToBoxes 0 0% 86.62% 204ms 0.57% std::_Rb_tree::clear (inline) 41ms 0.12% 86.74% 201ms 0.57% std::__new_allocator::deallocate (inline) 200ms 0.56% 87.30% 200ms 0.56% Node::rGetLocation 0 0% 87.30% 199ms 0.56% std::set::set (inline) 1ms 0.0028% 87.30% 195ms 0.55% vtkXMLWriterBase::Write 0 0% 87.30% 194ms 0.55% vtkStreamingDemandDrivenPipeline::Update 0 0% 87.30% 193ms 0.54% vtkDemandDrivenPipeline::ProcessRequest 0 0% 87.30% 192ms 0.54% vtkCompositeDataPipeline::ExecuteData 0 0% 87.30% 192ms 0.54% vtkDemandDrivenPipeline::ExecuteData 0 0% 87.30% 192ms 0.54% vtkExecutive::CallAlgorithm 0 0% 87.30% 192ms 0.54% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 87.30% 192ms 0.54% vtkXMLUnstructuredDataWriter::ProcessRequest 191ms 0.54% 87.84% 191ms 0.54% [libchaste_mesh.so] 0 0% 87.84% 185ms 0.52% NodesOnlyMesh::ResizeBoxCollection 10ms 0.028% 87.87% 184ms 0.52% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 87.87% 182ms 0.51% std::map::map (inline) 180ms 0.51% 88.38% 180ms 0.51% __strcmp_avx2 7ms 0.02% 88.40% 180ms 0.51% std::_Rb_tree::~_Rb_tree (inline) 97ms 0.27% 88.67% 179ms 0.5% boost::shared_ptr::shared_ptr (inline) 0 0% 88.67% 178ms 0.5% boost::numeric::ublas::vector_binary_scalar1::operator() (inline)