File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 30189ms, 87.12% of 34652ms total Dropped 844 nodes (cum <= 173.26ms) flat flat% sum% cum cum% 0 0% 0% 34512ms 99.60% __libc_start_call_main 0 0% 0% 34512ms 99.60% __libc_start_main_impl 0 0% 0% 34512ms 99.60% _start 0 0% 0% 34492ms 99.54% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 34492ms 99.54% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 34492ms 99.54% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 34492ms 99.54% main 0 0% 0% 34449ms 99.41% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 34449ms 99.41% CxxTest::TestRunner::runTest (inline) 0 0% 0% 34449ms 99.41% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 2ms 0.0058% 0.0058% 34440ms 99.39% AbstractCellBasedSimulation::Solve 3ms 0.0087% 0.014% 23852ms 68.83% OffLatticeSimulation::UpdateCellLocationsAndTopology 3ms 0.0087% 0.023% 18904ms 54.55% ForwardEulerNumericalMethod::UpdateAllNodePositions 14ms 0.04% 0.063% 18706ms 53.98% AbstractNumericalMethod::ComputeForcesIncludingDamping 163ms 0.47% 0.53% 17820ms 51.43% AbstractTwoBodyInteractionForce::AddForceContribution 1513ms 4.37% 4.90% 15055ms 43.45% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4353ms 12.56% 17.46% 9662ms 27.88% std::_Rb_tree::_M_lower_bound (inline) 0 0% 17.46% 9353ms 26.99% AbstractCellBasedSimulation::UpdateCellPopulation 288ms 0.83% 18.29% 8908ms 25.71% NodesOnlyMesh::GetNodeOrHaloNode 345ms 1% 19.29% 8904ms 25.70% std::_Rb_tree::find (inline) 0 0% 19.29% 8904ms 25.70% std::map::find (inline) 530ms 1.53% 20.82% 8639ms 24.93% AbstractMesh::GetNode 0 0% 20.82% 8281ms 23.90% NodeBasedCellPopulation::Update 368ms 1.06% 21.88% 8113ms 23.41% NodesOnlyMesh::SolveNodeMapping 13ms 0.038% 21.92% 6161ms 17.78% DistributedBoxCollection::CalculateInteriorNodePairs 208ms 0.6% 22.52% 5700ms 16.45% boost::numeric::ublas::vector_assign (inline) 156ms 0.45% 22.97% 5607ms 16.18% boost::numeric::ublas::c_vector::c_vector (partial-inline) 5288ms 15.26% 38.23% 5288ms 15.26% std::_Rb_tree::_S_right (inline) 10ms 0.029% 38.26% 4631ms 13.36% NodeAttributes::RemoveDuplicateNeighbours 0 0% 38.26% 4583ms 13.23% OffLatticeSimulation::ApplyBoundaries 5ms 0.014% 38.27% 4460ms 12.87% std::__sort (inline) 0 0% 38.27% 4460ms 12.87% std::sort (inline) 1124ms 3.24% 41.52% 3389ms 9.78% boost::numeric::ublas::indexing_vector_assign 70ms 0.2% 41.72% 3164ms 9.13% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 5ms 0.014% 41.73% 3143ms 9.07% AbstractCellPopulation::Iterator::operator++ (inline) 187ms 0.54% 42.27% 3100ms 8.95% AbstractCellPopulation::Iterator::IsRealCell (inline) 30ms 0.087% 42.36% 2648ms 7.64% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 176ms 0.51% 42.87% 2549ms 7.36% std::__introsort_loop 26ms 0.075% 42.94% 2448ms 7.06% PlaneBoundaryCondition::ImposeBoundaryCondition 0 0% 42.94% 2296ms 6.63% std::__unguarded_partition_pivot (inline) 49ms 0.14% 43.08% 2150ms 6.20% AbstractCellPopulation::GetLocationIndexUsingCell 11ms 0.032% 43.11% 2134ms 6.16% PlaneBoundaryCondition::VerifyBoundaryCondition 161ms 0.46% 43.58% 2116ms 6.11% DistributedBoxCollection::AddPairsFromBox 1027ms 2.96% 46.54% 2035ms 5.87% std::__unguarded_partition (inline) 2ms 0.0058% 46.55% 1905ms 5.50% std::__final_insertion_sort (inline) 125ms 0.36% 46.91% 1717ms 4.95% std::__unguarded_insertion_sort (inline) 164ms 0.47% 47.38% 1669ms 4.82% std::map::operator[] (partial-inline) 1612ms 4.65% 52.03% 1612ms 4.65% boost::numeric::ublas::same_impl_ex 634ms 1.83% 53.86% 1611ms 4.65% std::__unguarded_linear_insert (inline) 171ms 0.49% 54.36% 1473ms 4.25% AbstractMesh::GetVectorFromAtoB 0 0% 54.36% 1385ms 4.00% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 1377ms 3.97% 58.33% 1377ms 3.97% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 58.33% 1367ms 3.94% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1242ms 3.58% 61.92% 1242ms 3.58% boost::numeric::ublas::c_vector::operator() 0 0% 61.92% 1207ms 3.48% std::_Rb_tree::lower_bound (inline) 0 0% 61.92% 1207ms 3.48% std::map::lower_bound (inline) 1ms 0.0029% 61.92% 1184ms 3.42% NodeBasedCellPopulation::UpdateCellProcessLocation 0 0% 61.92% 1152ms 3.32% boost::numeric::ublas::detail::expression_type_check (inline) 250ms 0.72% 62.64% 1115ms 3.22% boost::numeric::ublas::detail::equals 6ms 0.017% 62.66% 1105ms 3.19% DistributedBoxCollection::CalculateBoundaryNodePairs 115ms 0.33% 62.99% 914ms 2.64% boost::numeric::ublas::vector_binary::size (inline) 400ms 1.15% 64.14% 889ms 2.57% DistributedBoxCollection::CalculateContainingBox (partial-inline) 276ms 0.8% 64.94% 881ms 2.54% NodeAttributes::AddNeighbour 23ms 0.066% 65.01% 875ms 2.53% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 207ms 0.6% 65.60% 841ms 2.43% NodeAttributes::AddAppliedForceContribution 0 0% 65.60% 812ms 2.34% boost::numeric::ublas::norm_inf (inline) 508ms 1.47% 67.07% 812ms 2.34% boost::numeric::ublas::vector_norm_inf::apply (inline) 2ms 0.0058% 67.08% 809ms 2.33% AbstractCentreBasedCellPopulation::GetDampingConstant 548ms 1.58% 68.66% 774ms 2.23% __dynamic_cast 0 0% 68.66% 755ms 2.18% AbstractCellPopulation::WriteResultsToFiles 105ms 0.3% 68.96% 721ms 2.08% std::__new_allocator::allocate (inline) 26ms 0.075% 69.03% 703ms 2.03% std::_Rb_tree_const_iterator::operator++ (inline) 605ms 1.75% 70.78% 682ms 1.97% std::vector::push_back (inline) 674ms 1.95% 72.73% 674ms 1.95% std::_Rb_tree_increment 0 0% 72.73% 634ms 1.83% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 72.73% 634ms 1.83% boost::numeric::ublas::c_vector::plus_assign (inline) 88ms 0.25% 72.98% 621ms 1.79% operator new 6ms 0.017% 73.00% 611ms 1.76% AbstractCellBasedSimulation::DoCellBirth 3ms 0.0087% 73.01% 597ms 1.72% CellPropertyCollection::GetPropertiesType (inline) 0 0% 73.01% 573ms 1.65% boost::numeric::ublas::norm_2 (inline) 448ms 1.29% 74.30% 573ms 1.65% boost::numeric::ublas::vector_norm_2::apply (inline) 6ms 0.017% 74.32% 541ms 1.56% Cell::GetMutationState 185ms 0.53% 74.85% 528ms 1.52% __GI___libc_malloc 166ms 0.48% 75.33% 509ms 1.47% __GI___libc_free 0 0% 75.33% 499ms 1.44% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 75.33% 460ms 1.33% AbstractCellBasedSimulation::DoCellRemoval (inline) 1ms 0.0029% 75.33% 441ms 1.27% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 19ms 0.055% 75.39% 439ms 1.27% boost::detail::shared_count::~shared_count (inline) 0 0% 75.39% 439ms 1.27% boost::shared_ptr::~shared_ptr (inline) 0 0% 75.39% 426ms 1.23% std::allocator_traits::allocate (inline) 420ms 1.21% 76.60% 420ms 1.21% Node::GetIndex 403ms 1.16% 77.76% 418ms 1.21% boost::detail::sp_counted_base::release 0 0% 77.76% 416ms 1.20% std::_Rb_tree::_M_create_node (inline) 4ms 0.012% 77.77% 395ms 1.14% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 3ms 0.0087% 77.78% 391ms 1.13% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 77.78% 366ms 1.06% boost::numeric::ublas::inner_prod (inline) 2ms 0.0058% 77.79% 363ms 1.05% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 362ms 1.04% 78.83% 362ms 1.04% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 13ms 0.038% 78.87% 361ms 1.04% boost::numeric::ublas::vector_scalar_binary::evaluate 2ms 0.0058% 78.88% 359ms 1.04% AbstractCellProperty::IsSubType (inline) 0 0% 78.88% 354ms 1.02% std::_Rb_tree::_M_get_node (inline) 0 0% 78.88% 348ms 1.00% NodesOnlyMesh::ReMesh 283ms 0.82% 79.69% 342ms 0.99% _int_free 5ms 0.014% 79.71% 341ms 0.98% NodesOnlyMesh::UpdateNodeIndices 30ms 0.087% 79.79% 325ms 0.94% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 79.79% 325ms 0.94% boost::numeric::ublas::vector::vector (inline) 319ms 0.92% 80.71% 319ms 0.92% __gnu_cxx::__normal_iterator::operator++ (inline) 4ms 0.012% 80.73% 316ms 0.91% NodeBasedCellPopulation::UpdateMapsAfterRemesh 102ms 0.29% 81.02% 308ms 0.89% std::_Rb_tree::_M_erase (partial-inline) 1ms 0.0029% 81.02% 307ms 0.89% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 16ms 0.046% 81.07% 302ms 0.87% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 81.07% 299ms 0.86% NodesOnlyMesh::UpdateBoxCollection 21ms 0.061% 81.13% 298ms 0.86% std::_Rb_tree::_M_emplace_hint_unique 11ms 0.032% 81.16% 296ms 0.85% DistributedBoxCollection::GetProcessOwningNode 128ms 0.37% 81.53% 296ms 0.85% boost::numeric::ublas::vector_inner_prod::apply (inline) 72ms 0.21% 81.74% 290ms 0.84% Node::GetRadius 21ms 0.061% 81.80% 288ms 0.83% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 81.80% 283ms 0.82% boost::numeric::ublas::c_vector::assign (inline) 0 0% 81.80% 283ms 0.82% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 81.80% 272ms 0.78% std::_Rb_tree::_Alloc_node::operator() (inline) 1ms 0.0029% 81.80% 263ms 0.76% NodesOnlyMesh::AddNodesToBoxes 16ms 0.046% 81.85% 262ms 0.76% std::_Rb_tree::_M_copy (inline) 225ms 0.65% 82.50% 257ms 0.74% Node::AddNeighbour 105ms 0.3% 82.80% 257ms 0.74% std::__move_median_to_first (inline) 0 0% 82.80% 254ms 0.73% Cell::HasCellProperty (inline) 4ms 0.012% 82.81% 254ms 0.73% CellPropertyCollection::HasProperty 149ms 0.43% 83.24% 254ms 0.73% _int_malloc 0 0% 83.24% 247ms 0.71% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 12ms 0.035% 83.28% 245ms 0.71% Cell::ReadyToDivide 0 0% 83.28% 245ms 0.71% VtkMeshWriter::WriteFiles 39ms 0.11% 83.39% 244ms 0.7% std::_Rb_tree::_M_clone_node (inline) 233ms 0.67% 84.06% 233ms 0.67% [libchaste_cell_based.so] 230ms 0.66% 84.73% 230ms 0.66% Node::CheckForNodeAttributes 219ms 0.63% 85.36% 220ms 0.63% NodeBasedCellPopulation::GetNode 211ms 0.61% 85.97% 211ms 0.61% [libchaste_mesh.so] 0 0% 85.97% 211ms 0.61% vtkStreamingDemandDrivenPipeline::Update 0 0% 85.97% 211ms 0.61% vtkXMLWriterBase::Write 0 0% 85.97% 210ms 0.61% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 85.97% 209ms 0.6% vtkDemandDrivenPipeline::ProcessRequest 0 0% 85.97% 208ms 0.6% vtkExecutive::CallAlgorithm 0 0% 85.97% 207ms 0.6% vtkCompositeDataPipeline::ExecuteData 0 0% 85.97% 207ms 0.6% vtkDemandDrivenPipeline::ExecuteData 0 0% 85.97% 207ms 0.6% vtkXMLUnstructuredDataWriter::ProcessRequest 206ms 0.59% 86.56% 206ms 0.59% __strcmp_avx2 56ms 0.16% 86.72% 202ms 0.58% std::__find_if (inline) 0 0% 86.72% 202ms 0.58% std::find_if (inline) 0 0% 86.72% 202ms 0.58% std::none_of (inline) 0 0% 86.72% 199ms 0.57% std::_Rb_tree::_M_drop_node (inline) 3ms 0.0087% 86.73% 192ms 0.55% std::__new_allocator::deallocate (inline) 16ms 0.046% 86.78% 187ms 0.54% std::_Rb_tree::~_Rb_tree (inline) 97ms 0.28% 87.06% 186ms 0.54% boost::shared_ptr::shared_ptr (inline) 19ms 0.055% 87.11% 186ms 0.54% std::__insertion_sort (inline) 3ms 0.0087% 87.12% 183ms 0.53% AbstractCellProperty::IsType (inline) 0 0% 87.12% 176ms 0.51% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 87.12% 176ms 0.51% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 87.12% 175ms 0.51% std::allocator_traits::deallocate (inline)