File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 30441ms, 88.81% of 34278ms total Dropped 843 nodes (cum <= 171.39ms) flat flat% sum% cum cum% 0 0% 0% 34125ms 99.55% __libc_start_call_main 0 0% 0% 34125ms 99.55% __libc_start_main_impl 0 0% 0% 34125ms 99.55% _start 0 0% 0% 34108ms 99.50% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 34108ms 99.50% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 34108ms 99.50% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 34108ms 99.50% main 0 0% 0% 34071ms 99.40% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 34071ms 99.40% CxxTest::TestRunner::runTest (inline) 0 0% 0% 34071ms 99.40% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 34063ms 99.37% AbstractCellBasedSimulation::Solve 0 0% 0% 23949ms 69.87% OffLatticeSimulation::UpdateCellLocationsAndTopology 5ms 0.015% 0.015% 19168ms 55.92% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.012% 0.026% 18972ms 55.35% AbstractNumericalMethod::ComputeForcesIncludingDamping 177ms 0.52% 0.54% 18297ms 53.38% AbstractTwoBodyInteractionForce::AddForceContribution 1522ms 4.44% 4.98% 15452ms 45.08% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4384ms 12.79% 17.77% 9510ms 27.74% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.0029% 17.78% 8942ms 26.09% AbstractCellBasedSimulation::UpdateCellPopulation 318ms 0.93% 18.70% 8627ms 25.17% std::_Rb_tree::find (inline) 0 0% 18.70% 8627ms 25.17% std::map::find (inline) 146ms 0.43% 19.13% 8339ms 24.33% NodesOnlyMesh::GetNodeOrHaloNode 487ms 1.42% 20.55% 8186ms 23.88% AbstractMesh::GetNode 0 0% 20.55% 7887ms 23.01% NodeBasedCellPopulation::Update 285ms 0.83% 21.38% 7701ms 22.47% NodesOnlyMesh::SolveNodeMapping 226ms 0.66% 22.04% 6526ms 19.04% boost::numeric::ublas::vector_assign (inline) 225ms 0.66% 22.70% 6399ms 18.67% boost::numeric::ublas::c_vector::c_vector (partial-inline) 7ms 0.02% 22.72% 5831ms 17.01% DistributedBoxCollection::CalculateInteriorNodePairs 5093ms 14.86% 37.58% 5093ms 14.86% std::_Rb_tree::_S_right (inline) 20ms 0.058% 37.63% 4532ms 13.22% NodeAttributes::RemoveDuplicateNeighbours 1ms 0.0029% 37.64% 4530ms 13.22% OffLatticeSimulation::ApplyBoundaries 7ms 0.02% 37.66% 4334ms 12.64% std::__sort (inline) 0 0% 37.66% 4334ms 12.64% std::sort (inline) 1164ms 3.40% 41.05% 3651ms 10.65% boost::numeric::ublas::indexing_vector_assign 78ms 0.23% 41.28% 3460ms 10.09% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 4ms 0.012% 41.29% 3436ms 10.02% AbstractCellPopulation::Iterator::operator++ (inline) 162ms 0.47% 41.76% 3424ms 9.99% AbstractCellPopulation::Iterator::IsRealCell 26ms 0.076% 41.84% 2962ms 8.64% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 171ms 0.5% 42.34% 2438ms 7.11% std::__introsort_loop 41ms 0.12% 42.46% 2369ms 6.91% AbstractCellPopulation::GetLocationIndexUsingCell 27ms 0.079% 42.54% 2361ms 6.89% PlaneBoundaryCondition::ImposeBoundaryCondition 1ms 0.0029% 42.54% 2202ms 6.42% std::__unguarded_partition_pivot (inline) 20ms 0.058% 42.60% 2168ms 6.32% PlaneBoundaryCondition::VerifyBoundaryCondition 1049ms 3.06% 45.66% 1995ms 5.82% std::__unguarded_partition (inline) 200ms 0.58% 46.24% 1956ms 5.71% DistributedBoxCollection::AddPairsFromBox 1ms 0.0029% 46.25% 1888ms 5.51% std::__final_insertion_sort (inline) 219ms 0.64% 46.88% 1773ms 5.17% std::map::operator[] (partial-inline) 1689ms 4.93% 51.81% 1689ms 4.93% boost::numeric::ublas::same_impl_ex 94ms 0.27% 52.09% 1669ms 4.87% std::__unguarded_insertion_sort (inline) 109ms 0.32% 52.40% 1644ms 4.80% AbstractMesh::GetVectorFromAtoB 620ms 1.81% 54.21% 1626ms 4.74% std::__unguarded_linear_insert (inline) 1475ms 4.30% 58.52% 1475ms 4.30% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 58.52% 1302ms 3.80% std::_Rb_tree::lower_bound (inline) 0 0% 58.52% 1302ms 3.80% std::map::lower_bound (inline) 0 0% 58.52% 1245ms 3.63% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 58.52% 1227ms 3.58% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1ms 0.0029% 58.52% 1145ms 3.34% NodeBasedCellPopulation::UpdateCellProcessLocation 1135ms 3.31% 61.83% 1135ms 3.31% boost::numeric::ublas::c_vector::operator() 18ms 0.053% 61.88% 1116ms 3.26% boost::numeric::ublas::detail::expression_type_check (inline) 2ms 0.0058% 61.89% 1085ms 3.17% DistributedBoxCollection::CalculateBoundaryNodePairs 217ms 0.63% 62.52% 1072ms 3.13% boost::numeric::ublas::detail::equals 158ms 0.46% 62.98% 1048ms 3.06% boost::numeric::ublas::vector_binary::size (inline) 214ms 0.62% 63.61% 913ms 2.66% NodeAttributes::AddAppliedForceContribution 72ms 0.21% 63.82% 879ms 2.56% std::__new_allocator::allocate (inline) 397ms 1.16% 64.97% 838ms 2.44% __GI___libc_free 0 0% 64.97% 810ms 2.36% boost::numeric::ublas::norm_inf (inline) 453ms 1.32% 66.30% 810ms 2.36% boost::numeric::ublas::vector_norm_inf::apply (inline) 95ms 0.28% 66.57% 804ms 2.35% operator new 18ms 0.053% 66.63% 789ms 2.30% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 233ms 0.68% 67.31% 759ms 2.21% NodeAttributes::AddNeighbour 349ms 1.02% 68.32% 752ms 2.19% DistributedBoxCollection::CalculateContainingBox (partial-inline) 570ms 1.66% 69.99% 747ms 2.18% __dynamic_cast 0 0% 69.99% 719ms 2.10% AbstractCellPopulation::WriteResultsToFiles 243ms 0.71% 70.70% 707ms 2.06% __GI___libc_malloc 0 0% 70.70% 699ms 2.04% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 70.70% 699ms 2.04% boost::numeric::ublas::c_vector::plus_assign (inline) 29ms 0.085% 70.78% 637ms 1.86% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.0029% 70.78% 626ms 1.83% AbstractCentreBasedCellPopulation::GetDampingConstant 606ms 1.77% 72.55% 606ms 1.77% std::_Rb_tree_increment 525ms 1.53% 74.08% 600ms 1.75% std::vector::push_back (inline) 1ms 0.0029% 74.09% 565ms 1.65% AbstractCellBasedSimulation::DoCellBirth 18ms 0.053% 74.14% 520ms 1.52% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 74.14% 520ms 1.52% boost::numeric::ublas::vector::vector (inline) 7ms 0.02% 74.16% 495ms 1.44% CellPropertyCollection::GetPropertiesType (inline) 0 0% 74.16% 486ms 1.42% AbstractCellBasedSimulation::DoCellRemoval (inline) 2ms 0.0058% 74.16% 468ms 1.37% NodeBasedCellPopulation::WriteVtkResultsToFile 6ms 0.018% 74.18% 457ms 1.33% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 408ms 1.19% 75.37% 438ms 1.28% _int_free 0 0% 75.37% 435ms 1.27% boost::numeric::ublas::norm_2 (inline) 343ms 1.00% 76.37% 435ms 1.27% boost::numeric::ublas::vector_norm_2::apply (inline) 2ms 0.0058% 76.38% 430ms 1.25% Cell::GetMutationState 397ms 1.16% 77.54% 397ms 1.16% Node::GetIndex 25ms 0.073% 77.61% 381ms 1.11% boost::detail::shared_count::~shared_count (inline) 0 0% 77.61% 381ms 1.11% boost::shared_ptr::~shared_ptr (inline) 0 0% 77.61% 377ms 1.10% std::allocator_traits::allocate (inline) 341ms 0.99% 78.60% 347ms 1.01% boost::detail::sp_counted_base::release 0 0% 78.60% 345ms 1.01% std::_Rb_tree::_M_create_node (inline) 126ms 0.37% 78.97% 333ms 0.97% Node::GetRadius 332ms 0.97% 79.94% 332ms 0.97% __gnu_cxx::__normal_iterator::operator++ (inline) 2ms 0.0058% 79.95% 321ms 0.94% AbstractCellProperty::IsSubType (inline) 0 0% 79.95% 319ms 0.93% boost::numeric::ublas::inner_prod (inline) 4ms 0.012% 79.96% 317ms 0.92% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 79.96% 317ms 0.92% NodesOnlyMesh::ReMesh 5ms 0.015% 79.97% 317ms 0.92% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 17ms 0.05% 80.02% 312ms 0.91% boost::numeric::ublas::vector_scalar_binary::evaluate 4ms 0.012% 80.03% 307ms 0.9% NodesOnlyMesh::UpdateNodeIndices 0 0% 80.03% 307ms 0.9% std::_Rb_tree::_M_get_node (inline) 11ms 0.032% 80.07% 303ms 0.88% boost::numeric::ublas::vector_reference::operator() (inline) 2ms 0.0058% 80.07% 301ms 0.88% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 80.07% 301ms 0.88% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 123ms 0.36% 80.43% 273ms 0.8% std::_Rb_tree::_M_erase (partial-inline) 0 0% 80.43% 271ms 0.79% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 271ms 0.79% 81.22% 271ms 0.79% [libchaste_cell_based.so] 270ms 0.79% 82.01% 270ms 0.79% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 82.01% 268ms 0.78% NodesOnlyMesh::UpdateBoxCollection 6ms 0.018% 82.03% 254ms 0.74% DistributedBoxCollection::GetProcessOwningNode 113ms 0.33% 82.36% 254ms 0.74% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 82.36% 253ms 0.74% boost::numeric::ublas::c_vector::assign (inline) 5ms 0.015% 82.37% 252ms 0.74% std::_Rb_tree::_M_emplace_hint_unique 0 0% 82.37% 237ms 0.69% tcache_get (inline) 237ms 0.69% 83.06% 237ms 0.69% tcache_get_n (inline) 231ms 0.67% 83.74% 231ms 0.67% NodeBasedCellPopulation::GetNode 231ms 0.67% 84.41% 231ms 0.67% boost::numeric::ublas::c_vector::size (inline) 1ms 0.0029% 84.41% 227ms 0.66% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 84.41% 225ms 0.66% VtkMeshWriter::WriteFiles 11ms 0.032% 84.44% 225ms 0.66% std::_Rb_tree::_Rb_tree (partial-inline) 148ms 0.43% 84.88% 220ms 0.64% _int_malloc 219ms 0.64% 85.52% 219ms 0.64% Node::CheckForNodeAttributes 1ms 0.0029% 85.52% 219ms 0.64% NodesOnlyMesh::AddNodesToBoxes 218ms 0.64% 86.15% 218ms 0.64% Node::rGetLocation 25ms 0.073% 86.23% 218ms 0.64% std::__insertion_sort (inline) 0 0% 86.23% 214ms 0.62% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 86.23% 213ms 0.62% boost::numeric::ublas::vector_reference::size (inline) 18ms 0.053% 86.28% 212ms 0.62% std::_Rb_tree::_M_copy (inline) 98ms 0.29% 86.57% 212ms 0.62% std::__find_if (inline) 0 0% 86.57% 212ms 0.62% std::find_if (inline) 0 0% 86.57% 212ms 0.62% std::none_of (inline) 211ms 0.62% 87.18% 211ms 0.62% [libchaste_mesh.so] 0 0% 87.18% 211ms 0.62% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 87.18% 202ms 0.59% Cell::HasCellProperty (inline) 4ms 0.012% 87.19% 202ms 0.59% CellPropertyCollection::HasProperty 90ms 0.26% 87.46% 200ms 0.58% std::__move_median_to_first (inline) 0 0% 87.46% 200ms 0.58% vtkDemandDrivenPipeline::ProcessRequest 0 0% 87.46% 200ms 0.58% vtkStreamingDemandDrivenPipeline::Update 0 0% 87.46% 200ms 0.58% vtkXMLWriterBase::Write 0 0% 87.46% 199ms 0.58% vtkExecutive::CallAlgorithm 197ms 0.57% 88.03% 197ms 0.57% boost::numeric::ublas::scalar_plus_assign::apply (inline) 0 0% 88.03% 197ms 0.57% vtkCompositeDataPipeline::ExecuteData 0 0% 88.03% 197ms 0.57% vtkDemandDrivenPipeline::ExecuteData 0 0% 88.03% 197ms 0.57% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 88.03% 195ms 0.57% NodesOnlyMesh::ResizeBoxCollection 0 0% 88.03% 195ms 0.57% vtkXMLUnstructuredDataWriter::ProcessRequest 13ms 0.038% 88.07% 194ms 0.57% NodesOnlyMesh::IsANodeCloseToDomainBoundary 38ms 0.11% 88.18% 193ms 0.56% std::__new_allocator::deallocate (inline) 34ms 0.099% 88.28% 192ms 0.56% std::_Rb_tree::_M_clone_node (inline) 5ms 0.015% 88.29% 178ms 0.52% Cell::ReadyToDivide 176ms 0.51% 88.81% 176ms 0.51% __strcmp_avx2