File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 30180ms, 88.05% of 34275ms total Dropped 839 nodes (cum <= 171.38ms) flat flat% sum% cum cum% 0 0% 0% 34136ms 99.59% __libc_start_call_main 0 0% 0% 34136ms 99.59% __libc_start_main_impl 0 0% 0% 34136ms 99.59% _start 0 0% 0% 34116ms 99.54% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 34116ms 99.54% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 34116ms 99.54% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 34116ms 99.54% main 0 0% 0% 34074ms 99.41% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 34074ms 99.41% CxxTest::TestRunner::runTest (inline) 0 0% 0% 34074ms 99.41% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0029% 0.0029% 34065ms 99.39% AbstractCellBasedSimulation::Solve 2ms 0.0058% 0.0088% 23679ms 69.09% OffLatticeSimulation::UpdateCellLocationsAndTopology 5ms 0.015% 0.023% 18674ms 54.48% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.023% 0.047% 18472ms 53.89% AbstractNumericalMethod::ComputeForcesIncludingDamping 152ms 0.44% 0.49% 17763ms 51.82% AbstractTwoBodyInteractionForce::AddForceContribution 1502ms 4.38% 4.87% 14993ms 43.74% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4516ms 13.18% 18.05% 9913ms 28.92% std::_Rb_tree::_M_lower_bound (inline) 0 0% 18.05% 9158ms 26.72% AbstractCellBasedSimulation::UpdateCellPopulation 374ms 1.09% 19.14% 9110ms 26.58% std::_Rb_tree::find (inline) 0 0% 19.14% 9110ms 26.58% std::map::find (inline) 207ms 0.6% 19.74% 8957ms 26.13% NodesOnlyMesh::GetNodeOrHaloNode 500ms 1.46% 21.20% 8776ms 25.60% AbstractMesh::GetNode 376ms 1.10% 22.30% 8277ms 24.15% NodesOnlyMesh::SolveNodeMapping 2ms 0.0058% 22.30% 8080ms 23.57% NodeBasedCellPopulation::Update 10ms 0.029% 22.33% 6024ms 17.58% DistributedBoxCollection::CalculateInteriorNodePairs 163ms 0.48% 22.81% 5680ms 16.57% boost::numeric::ublas::vector_assign (inline) 162ms 0.47% 23.28% 5533ms 16.14% boost::numeric::ublas::c_vector::c_vector (partial-inline) 5336ms 15.57% 38.85% 5336ms 15.57% std::_Rb_tree::_S_right (inline) 2ms 0.0058% 38.86% 4668ms 13.62% OffLatticeSimulation::ApplyBoundaries 6ms 0.018% 38.87% 4566ms 13.32% NodeAttributes::RemoveDuplicateNeighbours 4ms 0.012% 38.89% 4388ms 12.80% std::__sort (inline) 0 0% 38.89% 4388ms 12.80% std::sort (inline) 79ms 0.23% 39.12% 3411ms 9.95% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 1157ms 3.38% 42.49% 3392ms 9.90% boost::numeric::ublas::indexing_vector_assign 1ms 0.0029% 42.49% 3298ms 9.62% AbstractCellPopulation::Iterator::operator++ (inline) 157ms 0.46% 42.95% 3280ms 9.57% AbstractCellPopulation::Iterator::IsRealCell 29ms 0.085% 43.04% 2868ms 8.37% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 186ms 0.54% 43.58% 2528ms 7.38% std::__introsort_loop 27ms 0.079% 43.66% 2477ms 7.23% PlaneBoundaryCondition::ImposeBoundaryCondition 52ms 0.15% 43.81% 2357ms 6.88% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 43.81% 2264ms 6.61% std::__unguarded_partition_pivot (inline) 14ms 0.041% 43.85% 2189ms 6.39% PlaneBoundaryCondition::VerifyBoundaryCondition 152ms 0.44% 44.29% 2043ms 5.96% DistributedBoxCollection::AddPairsFromBox 967ms 2.82% 47.12% 2023ms 5.90% std::__unguarded_partition (inline) 2ms 0.0058% 47.12% 1855ms 5.41% std::__final_insertion_sort (inline) 215ms 0.63% 47.75% 1767ms 5.16% std::map::operator[] (partial-inline) 102ms 0.3% 48.05% 1664ms 4.85% std::__unguarded_insertion_sort (inline) 585ms 1.71% 49.75% 1588ms 4.63% std::__unguarded_linear_insert (inline) 1580ms 4.61% 54.36% 1580ms 4.61% boost::numeric::ublas::same_impl_ex 173ms 0.5% 54.87% 1486ms 4.34% AbstractMesh::GetVectorFromAtoB 1421ms 4.15% 59.01% 1421ms 4.15% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 59.01% 1364ms 3.98% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 59.01% 1346ms 3.93% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 59.01% 1283ms 3.74% std::_Rb_tree::lower_bound (inline) 0 0% 59.01% 1283ms 3.74% std::map::lower_bound (inline) 1156ms 3.37% 62.39% 1156ms 3.37% boost::numeric::ublas::c_vector::operator() 2ms 0.0058% 62.39% 1149ms 3.35% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 62.39% 1144ms 3.34% NodeBasedCellPopulation::UpdateCellProcessLocation 251ms 0.73% 63.12% 1106ms 3.23% boost::numeric::ublas::detail::equals 8ms 0.023% 63.15% 1093ms 3.19% DistributedBoxCollection::CalculateBoundaryNodePairs 161ms 0.47% 63.62% 921ms 2.69% boost::numeric::ublas::vector_binary::size (inline) 22ms 0.064% 63.68% 916ms 2.67% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 223ms 0.65% 64.33% 902ms 2.63% NodeAttributes::AddAppliedForceContribution 399ms 1.16% 65.50% 867ms 2.53% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 65.50% 784ms 2.29% boost::numeric::ublas::norm_inf (inline) 503ms 1.47% 66.96% 784ms 2.29% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 66.96% 754ms 2.20% AbstractCellPopulation::WriteResultsToFiles 173ms 0.5% 67.47% 728ms 2.12% NodeAttributes::AddNeighbour 98ms 0.29% 67.75% 725ms 2.12% std::__new_allocator::allocate (inline) 492ms 1.44% 69.19% 683ms 1.99% __dynamic_cast 0 0% 69.19% 679ms 1.98% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 69.19% 679ms 1.98% boost::numeric::ublas::c_vector::plus_assign (inline) 553ms 1.61% 70.80% 642ms 1.87% std::vector::push_back (inline) 6ms 0.018% 70.82% 639ms 1.86% AbstractCentreBasedCellPopulation::GetDampingConstant 36ms 0.11% 70.93% 627ms 1.83% std::_Rb_tree_const_iterator::operator++ (inline) 88ms 0.26% 71.18% 620ms 1.81% operator new 3ms 0.0088% 71.19% 605ms 1.77% AbstractCellBasedSimulation::DoCellBirth 583ms 1.70% 72.89% 583ms 1.70% std::_Rb_tree_increment 0 0% 72.89% 580ms 1.69% boost::numeric::ublas::norm_2 (inline) 453ms 1.32% 74.21% 580ms 1.69% boost::numeric::ublas::vector_norm_2::apply (inline) 183ms 0.53% 74.75% 528ms 1.54% __GI___libc_malloc 0 0% 74.75% 502ms 1.46% NodeBasedCellPopulation::WriteVtkResultsToFile 155ms 0.45% 75.20% 485ms 1.42% __GI___libc_free 10ms 0.029% 75.23% 478ms 1.39% CellPropertyCollection::GetPropertiesType (inline) 0 0% 75.23% 470ms 1.37% AbstractCellBasedSimulation::DoCellRemoval (inline) 5ms 0.015% 75.24% 453ms 1.32% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 432ms 1.26% 76.50% 432ms 1.26% Node::GetIndex 0 0% 76.50% 420ms 1.23% std::allocator_traits::allocate (inline) 5ms 0.015% 76.52% 408ms 1.19% Cell::GetMutationState 0 0% 76.52% 369ms 1.08% std::_Rb_tree::_M_create_node (inline) 0 0% 76.52% 367ms 1.07% boost::numeric::ublas::inner_prod (inline) 2ms 0.0058% 76.53% 362ms 1.06% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 13ms 0.038% 76.56% 360ms 1.05% boost::numeric::ublas::vector_scalar_binary::evaluate 12ms 0.035% 76.60% 356ms 1.04% boost::detail::shared_count::~shared_count (inline) 0 0% 76.60% 356ms 1.04% boost::shared_ptr::~shared_ptr (inline) 352ms 1.03% 77.63% 352ms 1.03% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 335ms 0.98% 78.60% 342ms 1% boost::detail::sp_counted_base::release 32ms 0.093% 78.70% 337ms 0.98% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 78.70% 337ms 0.98% boost::numeric::ublas::vector::vector (inline) 0 0% 78.70% 332ms 0.97% std::_Rb_tree::_M_get_node (inline) 329ms 0.96% 79.66% 329ms 0.96% __gnu_cxx::__normal_iterator::operator++ (inline) 76ms 0.22% 79.88% 328ms 0.96% Node::GetRadius 284ms 0.83% 80.71% 328ms 0.96% _int_free 2ms 0.0058% 80.71% 326ms 0.95% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 16ms 0.047% 80.76% 323ms 0.94% AbstractCellPopulation::GetCellUsingLocationIndex 2ms 0.0058% 80.76% 312ms 0.91% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 2ms 0.0058% 80.77% 307ms 0.9% AbstractCellProperty::IsSubType (inline) 9ms 0.026% 80.80% 305ms 0.89% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 80.80% 304ms 0.89% NodesOnlyMesh::ReMesh 8ms 0.023% 80.82% 297ms 0.87% DistributedBoxCollection::GetProcessOwningNode 4ms 0.012% 80.83% 289ms 0.84% NodesOnlyMesh::UpdateNodeIndices 287ms 0.84% 81.67% 287ms 0.84% [libchaste_mesh.so] 126ms 0.37% 82.04% 287ms 0.84% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 82.04% 280ms 0.82% NodesOnlyMesh::UpdateBoxCollection 0 0% 82.04% 272ms 0.79% boost::numeric::ublas::c_vector::assign (inline) 6ms 0.018% 82.05% 269ms 0.78% std::_Rb_tree::_M_emplace_hint_unique 263ms 0.77% 82.82% 263ms 0.77% Node::CheckForNodeAttributes 152ms 0.44% 83.26% 260ms 0.76% _int_malloc 87ms 0.25% 83.52% 258ms 0.75% std::_Rb_tree::_M_erase (partial-inline) 0 0% 83.52% 248ms 0.72% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 83.52% 248ms 0.72% VtkMeshWriter::WriteFiles 248ms 0.72% 84.24% 248ms 0.72% [libchaste_cell_based.so] 6ms 0.018% 84.26% 245ms 0.71% std::_Rb_tree::_Rb_tree (partial-inline) 6ms 0.018% 84.28% 244ms 0.71% boost::numeric::ublas::vector_reference::operator() (inline) 100ms 0.29% 84.57% 239ms 0.7% std::__move_median_to_first (inline) 20ms 0.058% 84.63% 235ms 0.69% std::_Rb_tree::_M_copy (inline) 145ms 0.42% 85.05% 232ms 0.68% Node::AddNeighbour 0 0% 85.05% 231ms 0.67% std::_Rb_tree::_Alloc_node::operator() (inline) 230ms 0.67% 85.72% 230ms 0.67% NodeBasedCellPopulation::GetNode 0 0% 85.72% 228ms 0.67% NodesOnlyMesh::AddNodesToBoxes 0 0% 85.72% 217ms 0.63% vtkStreamingDemandDrivenPipeline::Update 0 0% 85.72% 217ms 0.63% vtkXMLWriterBase::Write 0 0% 85.72% 216ms 0.63% Cell::HasCellProperty (inline) 1ms 0.0029% 85.72% 216ms 0.63% CellPropertyCollection::HasProperty 0 0% 85.72% 215ms 0.63% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 85.72% 214ms 0.62% vtkDemandDrivenPipeline::ProcessRequest 0 0% 85.72% 214ms 0.62% vtkExecutive::CallAlgorithm 27ms 0.079% 85.80% 213ms 0.62% std::_Rb_tree::_M_clone_node (inline) 0 0% 85.80% 212ms 0.62% vtkDemandDrivenPipeline::ExecuteData 0 0% 85.80% 212ms 0.62% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 85.80% 211ms 0.62% vtkCompositeDataPipeline::ExecuteData 0 0% 85.80% 205ms 0.6% boost::numeric::ublas::vector_binary::operator() (inline) 6ms 0.018% 85.82% 192ms 0.56% Cell::ReadyToDivide 189ms 0.55% 86.37% 189ms 0.55% __strcmp_avx2 21ms 0.061% 86.43% 189ms 0.55% std::__insertion_sort (inline) 187ms 0.55% 86.98% 187ms 0.55% Node::IsDeleted 139ms 0.41% 87.38% 184ms 0.54% Node::AddAppliedForceContribution 51ms 0.15% 87.53% 181ms 0.53% std::__find_if (inline) 0 0% 87.53% 181ms 0.53% std::find_if (inline) 0 0% 87.53% 181ms 0.53% std::none_of (inline) 177ms 0.52% 88.05% 177ms 0.52% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 0 0% 88.05% 176ms 0.51% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 88.05% 176ms 0.51% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 1ms 0.0029% 88.05% 173ms 0.5% AbstractCellProperty::IsType (inline)