File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 29395ms, 88.48% of 33221ms total Dropped 801 nodes (cum <= 166.10ms) flat flat% sum% cum cum% 0 0% 0% 33053ms 99.49% __libc_start_call_main 0 0% 0% 33053ms 99.49% __libc_start_main_impl 0 0% 0% 33053ms 99.49% _start 0 0% 0% 33037ms 99.45% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 33037ms 99.45% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 33037ms 99.45% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 33037ms 99.45% main 0 0% 0% 33000ms 99.33% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 33000ms 99.33% CxxTest::TestRunner::runTest (inline) 0 0% 0% 33000ms 99.33% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 32992ms 99.31% AbstractCellBasedSimulation::Solve 1ms 0.003% 0.003% 22832ms 68.73% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.006% 0.009% 17983ms 54.13% ForwardEulerNumericalMethod::UpdateAllNodePositions 15ms 0.045% 0.054% 17824ms 53.65% AbstractNumericalMethod::ComputeForcesIncludingDamping 255ms 0.77% 0.82% 17210ms 51.80% AbstractTwoBodyInteractionForce::AddForceContribution 1519ms 4.57% 5.39% 14417ms 43.40% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4473ms 13.46% 18.86% 9623ms 28.97% std::_Rb_tree::_M_lower_bound (inline) 0 0% 18.86% 8952ms 26.95% AbstractCellBasedSimulation::UpdateCellPopulation 300ms 0.9% 19.76% 8739ms 26.31% std::_Rb_tree::find (inline) 0 0% 19.76% 8739ms 26.31% std::map::find (inline) 162ms 0.49% 20.25% 8518ms 25.64% NodesOnlyMesh::GetNodeOrHaloNode 472ms 1.42% 21.67% 8298ms 24.98% AbstractMesh::GetNode 0 0% 21.67% 7908ms 23.80% NodeBasedCellPopulation::Update 303ms 0.91% 22.58% 7829ms 23.57% NodesOnlyMesh::SolveNodeMapping 9ms 0.027% 22.61% 5741ms 17.28% DistributedBoxCollection::CalculateInteriorNodePairs 214ms 0.64% 23.25% 5550ms 16.71% boost::numeric::ublas::vector_assign (inline) 180ms 0.54% 23.80% 5399ms 16.25% boost::numeric::ublas::c_vector::c_vector (partial-inline) 5120ms 15.41% 39.21% 5120ms 15.41% std::_Rb_tree::_S_right (inline) 1ms 0.003% 39.21% 4568ms 13.75% OffLatticeSimulation::ApplyBoundaries 17ms 0.051% 39.26% 4544ms 13.68% NodeAttributes::RemoveDuplicateNeighbours 9ms 0.027% 39.29% 4351ms 13.10% std::__sort (inline) 0 0% 39.29% 4351ms 13.10% std::sort (inline) 2ms 0.006% 39.29% 3505ms 10.55% AbstractCellPopulation::Iterator::operator++ (inline) 207ms 0.62% 39.92% 3490ms 10.51% AbstractCellPopulation::Iterator::IsRealCell 70ms 0.21% 40.13% 3456ms 10.40% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 1076ms 3.24% 43.37% 3169ms 9.54% boost::numeric::ublas::indexing_vector_assign 24ms 0.072% 43.44% 2966ms 8.93% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 172ms 0.52% 43.96% 2461ms 7.41% std::__introsort_loop 29ms 0.087% 44.04% 2381ms 7.17% PlaneBoundaryCondition::ImposeBoundaryCondition 50ms 0.15% 44.19% 2324ms 7.00% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 44.19% 2213ms 6.66% std::__unguarded_partition_pivot (inline) 14ms 0.042% 44.24% 2186ms 6.58% PlaneBoundaryCondition::VerifyBoundaryCondition 1017ms 3.06% 47.30% 1998ms 6.01% std::__unguarded_partition (inline) 2ms 0.006% 47.30% 1879ms 5.66% std::__final_insertion_sort (inline) 191ms 0.57% 47.88% 1854ms 5.58% DistributedBoxCollection::AddPairsFromBox 227ms 0.68% 48.56% 1755ms 5.28% std::map::operator[] (partial-inline) 87ms 0.26% 48.82% 1670ms 5.03% std::__unguarded_insertion_sort (inline) 581ms 1.75% 50.57% 1637ms 4.93% std::__unguarded_linear_insert (inline) 1527ms 4.60% 55.17% 1527ms 4.60% __gnu_cxx::__normal_iterator::operator-- (inline) 1421ms 4.28% 59.45% 1421ms 4.28% boost::numeric::ublas::same_impl_ex 0 0% 59.45% 1350ms 4.06% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 59.45% 1319ms 3.97% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 131ms 0.39% 59.84% 1296ms 3.90% AbstractMesh::GetVectorFromAtoB 0 0% 59.84% 1268ms 3.82% std::_Rb_tree::lower_bound (inline) 0 0% 59.84% 1268ms 3.82% std::map::lower_bound (inline) 1208ms 3.64% 63.48% 1208ms 3.64% boost::numeric::ublas::c_vector::operator() 7ms 0.021% 63.50% 1168ms 3.52% DistributedBoxCollection::CalculateBoundaryNodePairs 0 0% 63.50% 1151ms 3.46% NodeBasedCellPopulation::UpdateCellProcessLocation 19ms 0.057% 63.56% 1055ms 3.18% boost::numeric::ublas::detail::expression_type_check (inline) 159ms 0.48% 64.03% 1008ms 3.03% boost::numeric::ublas::detail::equals 365ms 1.10% 65.13% 894ms 2.69% DistributedBoxCollection::CalculateContainingBox (partial-inline) 248ms 0.75% 65.88% 874ms 2.63% NodeAttributes::AddAppliedForceContribution 23ms 0.069% 65.95% 836ms 2.52% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 99ms 0.3% 66.25% 822ms 2.47% boost::numeric::ublas::vector_binary::size (inline) 0 0% 66.25% 803ms 2.42% boost::numeric::ublas::norm_inf (inline) 507ms 1.53% 67.77% 803ms 2.42% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 67.77% 755ms 2.27% AbstractCellPopulation::WriteResultsToFiles 519ms 1.56% 69.34% 716ms 2.16% __dynamic_cast 75ms 0.23% 69.56% 661ms 1.99% std::__new_allocator::allocate (inline) 0 0% 69.56% 626ms 1.88% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 69.56% 626ms 1.88% boost::numeric::ublas::c_vector::plus_assign (inline) 237ms 0.71% 70.27% 597ms 1.80% __GI___libc_free 56ms 0.17% 70.44% 597ms 1.80% std::_Rb_tree_const_iterator::operator++ (inline) 98ms 0.29% 70.74% 587ms 1.77% operator new 2ms 0.006% 70.74% 570ms 1.72% AbstractCellBasedSimulation::DoCellBirth 211ms 0.64% 71.38% 557ms 1.68% NodeAttributes::AddNeighbour 2ms 0.006% 71.39% 553ms 1.66% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 71.39% 547ms 1.65% boost::numeric::ublas::norm_2 (inline) 429ms 1.29% 72.68% 547ms 1.65% boost::numeric::ublas::vector_norm_2::apply (inline) 529ms 1.59% 74.27% 529ms 1.59% std::_Rb_tree_increment 3ms 0.009% 74.28% 492ms 1.48% NodeBasedCellPopulation::WriteVtkResultsToFile 180ms 0.54% 74.82% 483ms 1.45% __GI___libc_malloc 0 0% 74.82% 472ms 1.42% AbstractCellBasedSimulation::DoCellRemoval (inline) 5ms 0.015% 74.84% 464ms 1.40% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 455ms 1.37% 76.20% 455ms 1.37% Node::GetIndex 9ms 0.027% 76.23% 450ms 1.35% CellPropertyCollection::GetPropertiesType (inline) 342ms 1.03% 77.26% 417ms 1.26% std::vector::push_back (inline) 25ms 0.075% 77.34% 411ms 1.24% boost::detail::shared_count::~shared_count (inline) 0 0% 77.34% 411ms 1.24% boost::shared_ptr::~shared_ptr (inline) 5ms 0.015% 77.35% 392ms 1.18% Cell::GetMutationState 376ms 1.13% 78.48% 378ms 1.14% boost::detail::sp_counted_base::release 328ms 0.99% 79.47% 360ms 1.08% _int_free 0 0% 79.47% 348ms 1.05% std::allocator_traits::allocate (inline) 26ms 0.078% 79.55% 339ms 1.02% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 79.55% 339ms 1.02% boost::numeric::ublas::vector::vector (inline) 2ms 0.006% 79.56% 331ms 1% AbstractCellProperty::IsSubType (inline) 129ms 0.39% 79.94% 325ms 0.98% Node::GetRadius 317ms 0.95% 80.90% 317ms 0.95% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 80.90% 315ms 0.95% NodesOnlyMesh::ReMesh 0 0% 80.90% 315ms 0.95% std::_Rb_tree::_M_create_node (inline) 3ms 0.009% 80.91% 313ms 0.94% NodeBasedCellPopulation::UpdateMapsAfterRemesh 2ms 0.006% 80.91% 313ms 0.94% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 80.91% 308ms 0.93% boost::numeric::ublas::inner_prod (inline) 12ms 0.036% 80.95% 308ms 0.93% boost::numeric::ublas::vector_reference::operator() (inline) 20ms 0.06% 81.01% 307ms 0.92% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 81.01% 307ms 0.92% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 5ms 0.015% 81.02% 303ms 0.91% NodesOnlyMesh::UpdateNodeIndices 8ms 0.024% 81.05% 297ms 0.89% DistributedBoxCollection::GetProcessOwningNode 294ms 0.88% 81.93% 294ms 0.88% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 81.93% 293ms 0.88% NodesOnlyMesh::UpdateBoxCollection 128ms 0.39% 82.32% 288ms 0.87% std::_Rb_tree::_M_erase (partial-inline) 284ms 0.85% 83.17% 284ms 0.85% [libchaste_cell_based.so] 0 0% 83.17% 283ms 0.85% std::_Rb_tree::_M_get_node (inline) 3ms 0.009% 83.18% 265ms 0.8% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 4ms 0.012% 83.19% 261ms 0.79% AbstractCellPopulation::GetCellUsingLocationIndex 11ms 0.033% 83.23% 260ms 0.78% std::_Rb_tree::_M_emplace_hint_unique 0 0% 83.23% 250ms 0.75% NodesOnlyMesh::AddNodesToBoxes 0 0% 83.23% 250ms 0.75% boost::numeric::ublas::c_vector::assign (inline) 0 0% 83.23% 239ms 0.72% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 83.23% 238ms 0.72% VtkMeshWriter::WriteFiles 0 0% 83.23% 235ms 0.71% boost::numeric::ublas::vector_binary::operator() (inline) 105ms 0.32% 83.54% 232ms 0.7% boost::numeric::ublas::vector_inner_prod::apply (inline) 170ms 0.51% 84.06% 221ms 0.67% Node::AddNeighbour 0 0% 84.06% 211ms 0.64% vtkDemandDrivenPipeline::ProcessRequest 0 0% 84.06% 211ms 0.64% vtkStreamingDemandDrivenPipeline::Update 0 0% 84.06% 211ms 0.64% vtkXMLWriterBase::Write 210ms 0.63% 84.69% 210ms 0.63% Node::CheckForNodeAttributes 0 0% 84.69% 210ms 0.63% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 84.69% 209ms 0.63% vtkExecutive::CallAlgorithm 139ms 0.42% 85.11% 208ms 0.63% _int_malloc 0 0% 85.11% 208ms 0.63% vtkCompositeDataPipeline::ExecuteData 0 0% 85.11% 208ms 0.63% vtkDemandDrivenPipeline::ExecuteData 0 0% 85.11% 208ms 0.63% vtkXMLUnstructuredDataWriter::ProcessRequest 23ms 0.069% 85.18% 207ms 0.62% std::__insertion_sort (inline) 89ms 0.27% 85.44% 207ms 0.62% std::__move_median_to_first (inline) 198ms 0.6% 86.04% 199ms 0.6% NodeBasedCellPopulation::GetNode 75ms 0.23% 86.26% 196ms 0.59% std::__find_if (inline) 0 0% 86.26% 195ms 0.59% std::find_if (inline) 0 0% 86.26% 195ms 0.59% std::none_of (inline) 40ms 0.12% 86.39% 193ms 0.58% std::__new_allocator::deallocate (inline) 188ms 0.57% 86.95% 188ms 0.57% __strcmp_avx2 0 0% 86.95% 185ms 0.56% std::_Rb_tree::_Alloc_node::operator() (inline) 7ms 0.021% 86.97% 184ms 0.55% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 86.97% 183ms 0.55% NodesOnlyMesh::ResizeBoxCollection 7ms 0.021% 86.99% 181ms 0.54% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 86.99% 181ms 0.54% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 86.99% 181ms 0.54% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 86.99% 176ms 0.53% Cell::HasCellProperty (inline) 2ms 0.006% 87.00% 176ms 0.53% CellPropertyCollection::HasProperty 126ms 0.38% 87.38% 176ms 0.53% Node::AddAppliedForceContribution 176ms 0.53% 87.91% 176ms 0.53% [libchaste_mesh.so] 0 0% 87.91% 175ms 0.53% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 20ms 0.06% 87.97% 172ms 0.52% std::_Rb_tree::_M_copy (inline) 171ms 0.51% 88.48% 171ms 0.51% Node::rGetLocation