File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 31431ms, 89.03% of 35304ms total Dropped 805 nodes (cum <= 176.52ms) flat flat% sum% cum cum% 0 0% 0% 35141ms 99.54% __libc_start_call_main 0 0% 0% 35141ms 99.54% __libc_start_main_impl 0 0% 0% 35141ms 99.54% _start 0 0% 0% 35124ms 99.49% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 35124ms 99.49% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 35124ms 99.49% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 35124ms 99.49% main 0 0% 0% 35089ms 99.39% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 35088ms 99.39% CxxTest::TestRunner::runTest (inline) 0 0% 0% 35088ms 99.39% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 35080ms 99.37% AbstractCellBasedSimulation::Solve 2ms 0.0057% 0.0057% 24628ms 69.76% OffLatticeSimulation::UpdateCellLocationsAndTopology 3ms 0.0085% 0.014% 19756ms 55.96% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.0085% 0.023% 19592ms 55.50% AbstractNumericalMethod::ComputeForcesIncludingDamping 188ms 0.53% 0.56% 18601ms 52.69% AbstractTwoBodyInteractionForce::AddForceContribution 1515ms 4.29% 4.85% 15621ms 44.25% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4254ms 12.05% 16.90% 9578ms 27.13% std::_Rb_tree::_M_lower_bound (inline) 0 0% 16.90% 9242ms 26.18% AbstractCellBasedSimulation::UpdateCellPopulation 300ms 0.85% 17.75% 8630ms 24.44% std::_Rb_tree::find (inline) 0 0% 17.75% 8630ms 24.44% std::map::find (inline) 183ms 0.52% 18.26% 8412ms 23.83% NodesOnlyMesh::GetNodeOrHaloNode 478ms 1.35% 19.62% 8201ms 23.23% AbstractMesh::GetNode 0 0% 19.62% 8127ms 23.02% NodeBasedCellPopulation::Update 293ms 0.83% 20.45% 7726ms 21.88% NodesOnlyMesh::SolveNodeMapping 323ms 0.91% 21.36% 6753ms 19.13% boost::numeric::ublas::vector_assign (inline) 218ms 0.62% 21.98% 6565ms 18.60% boost::numeric::ublas::c_vector::c_vector (partial-inline) 7ms 0.02% 22.00% 6073ms 17.20% DistributedBoxCollection::CalculateInteriorNodePairs 5313ms 15.05% 37.05% 5313ms 15.05% std::_Rb_tree::_S_right (inline) 1ms 0.0028% 37.05% 4507ms 12.77% OffLatticeSimulation::ApplyBoundaries 22ms 0.062% 37.11% 4504ms 12.76% NodeAttributes::RemoveDuplicateNeighbours 3ms 0.0085% 37.12% 4316ms 12.23% std::__sort (inline) 0 0% 37.12% 4316ms 12.23% std::sort (inline) 1190ms 3.37% 40.49% 3708ms 10.50% boost::numeric::ublas::indexing_vector_assign 4ms 0.011% 40.51% 3388ms 9.60% AbstractCellPopulation::Iterator::operator++ (inline) 189ms 0.54% 41.04% 3361ms 9.52% AbstractCellPopulation::Iterator::IsRealCell 65ms 0.18% 41.22% 3360ms 9.52% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 20ms 0.057% 41.28% 2829ms 8.01% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 198ms 0.56% 41.84% 2488ms 7.05% std::__introsort_loop 30ms 0.085% 41.93% 2362ms 6.69% PlaneBoundaryCondition::ImposeBoundaryCondition 48ms 0.14% 42.06% 2332ms 6.61% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.0028% 42.07% 2234ms 6.33% std::__unguarded_partition_pivot (inline) 257ms 0.73% 42.79% 2180ms 6.17% DistributedBoxCollection::AddPairsFromBox 17ms 0.048% 42.84% 2143ms 6.07% PlaneBoundaryCondition::VerifyBoundaryCondition 1031ms 2.92% 45.76% 1986ms 5.63% std::__unguarded_partition (inline) 230ms 0.65% 46.41% 1845ms 5.23% std::map::operator[] (partial-inline) 3ms 0.0085% 46.42% 1824ms 5.17% std::__final_insertion_sort (inline) 1739ms 4.93% 51.35% 1739ms 4.93% boost::numeric::ublas::same_impl_ex 78ms 0.22% 51.57% 1641ms 4.65% std::__unguarded_insertion_sort (inline) 132ms 0.37% 51.94% 1609ms 4.56% AbstractMesh::GetVectorFromAtoB 566ms 1.60% 53.55% 1578ms 4.47% std::__unguarded_linear_insert (inline) 1475ms 4.18% 57.72% 1475ms 4.18% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 57.72% 1356ms 3.84% std::_Rb_tree::lower_bound (inline) 0 0% 57.72% 1356ms 3.84% std::map::lower_bound (inline) 0 0% 57.72% 1300ms 3.68% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 57.72% 1289ms 3.65% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 57.72% 1170ms 3.31% NodeBasedCellPopulation::UpdateCellProcessLocation 10ms 0.028% 57.75% 1144ms 3.24% boost::numeric::ublas::detail::expression_type_check (inline) 1107ms 3.14% 60.89% 1107ms 3.14% boost::numeric::ublas::c_vector::operator() 206ms 0.58% 61.47% 1094ms 3.10% boost::numeric::ublas::detail::equals 8ms 0.023% 61.49% 1080ms 3.06% DistributedBoxCollection::CalculateBoundaryNodePairs 152ms 0.43% 61.92% 1019ms 2.89% boost::numeric::ublas::vector_binary::size (inline) 204ms 0.58% 62.50% 955ms 2.71% NodeAttributes::AddAppliedForceContribution 465ms 1.32% 63.82% 933ms 2.64% __GI___libc_free 1ms 0.0028% 63.82% 928ms 2.63% AbstractCentreBasedCellPopulation::GetDampingConstant 134ms 0.38% 64.20% 926ms 2.62% std::__new_allocator::allocate (inline) 344ms 0.97% 65.18% 843ms 2.39% NodeAttributes::AddNeighbour 0 0% 65.18% 840ms 2.38% boost::numeric::ublas::norm_inf (inline) 464ms 1.31% 66.49% 840ms 2.38% boost::numeric::ublas::vector_norm_inf::apply (inline) 17ms 0.048% 66.54% 813ms 2.30% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 382ms 1.08% 67.62% 796ms 2.25% DistributedBoxCollection::CalculateContainingBox (partial-inline) 32ms 0.091% 67.71% 796ms 2.25% std::_Rb_tree_const_iterator::operator++ (inline) 86ms 0.24% 67.96% 791ms 2.24% operator new 760ms 2.15% 70.11% 760ms 2.15% std::_Rb_tree_increment 538ms 1.52% 71.63% 757ms 2.14% __dynamic_cast 0 0% 71.63% 751ms 2.13% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 71.63% 751ms 2.13% boost::numeric::ublas::c_vector::plus_assign (inline) 0 0% 71.63% 733ms 2.08% AbstractCellPopulation::WriteResultsToFiles 265ms 0.75% 72.38% 699ms 1.98% __GI___libc_malloc 15ms 0.042% 72.43% 670ms 1.90% CellPropertyCollection::GetPropertiesType (inline) 2ms 0.0057% 72.43% 665ms 1.88% AbstractCellBasedSimulation::DoCellBirth 497ms 1.41% 73.84% 600ms 1.70% std::vector::push_back (inline) 1ms 0.0028% 73.84% 589ms 1.67% Cell::GetMutationState 14ms 0.04% 73.88% 475ms 1.35% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 73.88% 475ms 1.35% boost::numeric::ublas::vector::vector (inline) 0 0% 73.88% 473ms 1.34% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 73.88% 465ms 1.32% std::allocator_traits::allocate (inline) 0 0% 73.88% 460ms 1.30% boost::numeric::ublas::norm_2 (inline) 358ms 1.01% 74.90% 460ms 1.30% boost::numeric::ublas::vector_norm_2::apply (inline) 429ms 1.22% 76.11% 459ms 1.30% _int_free 0 0% 76.11% 447ms 1.27% AbstractCellBasedSimulation::DoCellRemoval (inline) 3ms 0.0085% 76.12% 439ms 1.24% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 5ms 0.014% 76.13% 436ms 1.23% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 76.13% 435ms 1.23% std::_Rb_tree::_M_create_node (inline) 8ms 0.023% 76.16% 432ms 1.22% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 413ms 1.17% 77.33% 413ms 1.17% Node::GetIndex 33ms 0.093% 77.42% 377ms 1.07% boost::detail::shared_count::~shared_count (inline) 0 0% 77.42% 377ms 1.07% boost::shared_ptr::~shared_ptr (inline) 0 0% 77.42% 370ms 1.05% std::_Rb_tree::_M_get_node (inline) 1ms 0.0028% 77.42% 369ms 1.05% AbstractCellProperty::IsSubType (inline) 116ms 0.33% 77.75% 356ms 1.01% Node::GetRadius 333ms 0.94% 78.69% 337ms 0.95% boost::detail::sp_counted_base::release 330ms 0.93% 79.63% 330ms 0.93% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 4ms 0.011% 79.64% 329ms 0.93% NodeBasedCellPopulation::UpdateMapsAfterRemesh 13ms 0.037% 79.68% 324ms 0.92% std::_Rb_tree::_Rb_tree (partial-inline) 127ms 0.36% 80.04% 317ms 0.9% std::_Rb_tree::_M_erase (partial-inline) 0 0% 80.04% 313ms 0.89% boost::numeric::ublas::inner_prod (inline) 311ms 0.88% 80.92% 311ms 0.88% __gnu_cxx::__normal_iterator::operator++ (inline) 4ms 0.011% 80.93% 310ms 0.88% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 80.93% 306ms 0.87% NodesOnlyMesh::ReMesh 15ms 0.042% 80.97% 306ms 0.87% boost::numeric::ublas::vector_scalar_binary::evaluate 20ms 0.057% 81.03% 305ms 0.86% std::_Rb_tree::_M_copy (inline) 15ms 0.042% 81.07% 302ms 0.86% boost::numeric::ublas::vector_reference::operator() (inline) 4ms 0.011% 81.08% 296ms 0.84% NodesOnlyMesh::UpdateNodeIndices 47ms 0.13% 81.21% 285ms 0.81% std::_Rb_tree::_M_clone_node (inline) 0 0% 81.21% 284ms 0.8% std::_Rb_tree::_Alloc_node::operator() (inline) 281ms 0.8% 82.01% 281ms 0.8% [libchaste_cell_based.so] 121ms 0.34% 82.35% 276ms 0.78% std::__find_if (inline) 0 0% 82.35% 276ms 0.78% std::find_if (inline) 0 0% 82.35% 276ms 0.78% std::none_of (inline) 0 0% 82.35% 274ms 0.78% NodesOnlyMesh::UpdateBoxCollection 3ms 0.0085% 82.36% 269ms 0.76% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 3ms 0.0085% 82.37% 259ms 0.73% DistributedBoxCollection::GetProcessOwningNode 7ms 0.02% 82.39% 259ms 0.73% std::_Rb_tree::_M_emplace_hint_unique 122ms 0.35% 82.74% 250ms 0.71% _int_malloc 0 0% 82.74% 250ms 0.71% boost::numeric::ublas::c_vector::assign (inline) 104ms 0.29% 83.03% 249ms 0.71% boost::numeric::ublas::vector_inner_prod::apply (inline) 247ms 0.7% 83.73% 247ms 0.7% Node::CheckForNodeAttributes 99ms 0.28% 84.01% 246ms 0.7% std::__move_median_to_first (inline) 6ms 0.017% 84.03% 243ms 0.69% CellPropertyCollection::HasProperty 0 0% 84.03% 240ms 0.68% Cell::HasCellProperty (inline) 10ms 0.028% 84.06% 236ms 0.67% Cell::ReadyToDivide 236ms 0.67% 84.72% 236ms 0.67% NodeBasedCellPopulation::GetNode 62ms 0.18% 84.90% 235ms 0.67% std::__new_allocator::deallocate (inline) 232ms 0.66% 85.56% 232ms 0.66% boost::numeric::ublas::scalar_plus_assign::apply (inline) 231ms 0.65% 86.21% 231ms 0.65% Node::rGetLocation 0 0% 86.21% 224ms 0.63% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 86.21% 222ms 0.63% VtkMeshWriter::WriteFiles 0 0% 86.21% 220ms 0.62% NodesOnlyMesh::AddNodesToBoxes 218ms 0.62% 86.83% 218ms 0.62% boost::numeric::ublas::c_vector::size (inline) 0 0% 86.83% 204ms 0.58% vtkExecutive::CallAlgorithm 0 0% 86.83% 204ms 0.58% vtkStreamingDemandDrivenPipeline::Update 0 0% 86.83% 204ms 0.58% vtkXMLWriterBase::Write 0 0% 86.83% 203ms 0.58% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 86.83% 203ms 0.58% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 86.83% 202ms 0.57% vtkDemandDrivenPipeline::ProcessRequest 165ms 0.47% 87.30% 201ms 0.57% Node::AddAppliedForceContribution 0 0% 87.30% 201ms 0.57% NodesOnlyMesh::ResizeBoxCollection 201ms 0.57% 87.87% 201ms 0.57% [libchaste_mesh.so] 0 0% 87.87% 201ms 0.57% vtkCompositeDataPipeline::ExecuteData 0 0% 87.87% 201ms 0.57% vtkDemandDrivenPipeline::ExecuteData 10ms 0.028% 87.89% 199ms 0.56% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 87.89% 197ms 0.56% boost::numeric::ublas::vector_reference::size (inline) 0 0% 87.89% 195ms 0.55% boost::numeric::ublas::vector_binary::operator() (inline) 13ms 0.037% 87.93% 191ms 0.54% std::_Rb_tree::~_Rb_tree (inline) 0 0% 87.93% 191ms 0.54% std::set::set (inline) 189ms 0.54% 88.47% 189ms 0.54% __strcmp_avx2 0 0% 88.47% 183ms 0.52% std::_Rb_tree::_M_drop_node (inline) 19ms 0.054% 88.52% 180ms 0.51% std::__insertion_sort (inline) 0 0% 88.52% 180ms 0.51% tcache_get (inline) 180ms 0.51% 89.03% 180ms 0.51% tcache_get_n (inline)