File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 31002ms, 89.62% of 34591ms total Dropped 828 nodes (cum <= 172.96ms) flat flat% sum% cum cum% 0 0% 0% 34437ms 99.55% __libc_start_call_main 0 0% 0% 34437ms 99.55% __libc_start_main_impl 0 0% 0% 34437ms 99.55% _start 0 0% 0% 34420ms 99.51% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 34420ms 99.51% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 34420ms 99.51% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 34420ms 99.51% main 0 0% 0% 34382ms 99.40% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 34382ms 99.40% CxxTest::TestRunner::runTest (inline) 0 0% 0% 34382ms 99.40% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 34374ms 99.37% AbstractCellBasedSimulation::Solve 1ms 0.0029% 0.0029% 24058ms 69.55% OffLatticeSimulation::UpdateCellLocationsAndTopology 4ms 0.012% 0.014% 19210ms 55.53% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.012% 0.026% 19040ms 55.04% AbstractNumericalMethod::ComputeForcesIncludingDamping 175ms 0.51% 0.53% 18216ms 52.66% AbstractTwoBodyInteractionForce::AddForceContribution 1535ms 4.44% 4.97% 15369ms 44.43% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4315ms 12.47% 17.44% 9528ms 27.54% std::_Rb_tree::_M_lower_bound (inline) 0 0% 17.44% 9092ms 26.28% AbstractCellBasedSimulation::UpdateCellPopulation 331ms 0.96% 18.40% 8586ms 24.82% std::_Rb_tree::find (inline) 0 0% 18.40% 8586ms 24.82% std::map::find (inline) 143ms 0.41% 18.81% 8382ms 24.23% NodesOnlyMesh::GetNodeOrHaloNode 465ms 1.34% 20.16% 8223ms 23.77% AbstractMesh::GetNode 0 0% 20.16% 8000ms 23.13% NodeBasedCellPopulation::Update 337ms 0.97% 21.13% 7761ms 22.44% NodesOnlyMesh::SolveNodeMapping 282ms 0.82% 21.95% 6445ms 18.63% boost::numeric::ublas::vector_assign (inline) 226ms 0.65% 22.60% 6332ms 18.31% boost::numeric::ublas::c_vector::c_vector (partial-inline) 7ms 0.02% 22.62% 5910ms 17.09% DistributedBoxCollection::CalculateInteriorNodePairs 5186ms 14.99% 37.61% 5186ms 14.99% std::_Rb_tree::_S_right (inline) 19ms 0.055% 37.67% 4532ms 13.10% NodeAttributes::RemoveDuplicateNeighbours 0 0% 37.67% 4526ms 13.08% OffLatticeSimulation::ApplyBoundaries 5ms 0.014% 37.68% 4384ms 12.67% std::__sort (inline) 0 0% 37.68% 4384ms 12.67% std::sort (inline) 1203ms 3.48% 41.16% 3603ms 10.42% boost::numeric::ublas::indexing_vector_assign 0 0% 41.16% 3457ms 9.99% AbstractCellPopulation::Iterator::operator++ (inline) 192ms 0.56% 41.72% 3432ms 9.92% AbstractCellPopulation::Iterator::IsRealCell (inline) 91ms 0.26% 41.98% 3401ms 9.83% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 18ms 0.052% 42.03% 2903ms 8.39% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 189ms 0.55% 42.58% 2568ms 7.42% std::__introsort_loop 33ms 0.095% 42.67% 2365ms 6.84% PlaneBoundaryCondition::ImposeBoundaryCondition 42ms 0.12% 42.79% 2353ms 6.80% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 42.79% 2306ms 6.67% std::__unguarded_partition_pivot (inline) 14ms 0.04% 42.83% 2161ms 6.25% PlaneBoundaryCondition::VerifyBoundaryCondition 1045ms 3.02% 45.86% 2043ms 5.91% std::__unguarded_partition (inline) 205ms 0.59% 46.45% 2026ms 5.86% DistributedBoxCollection::AddPairsFromBox 219ms 0.63% 47.08% 1846ms 5.34% std::map::operator[] (partial-inline) 0 0% 47.08% 1809ms 5.23% std::__final_insertion_sort (inline) 1652ms 4.78% 51.86% 1652ms 4.78% boost::numeric::ublas::same_impl_ex 106ms 0.31% 52.16% 1611ms 4.66% std::__unguarded_insertion_sort (inline) 110ms 0.32% 52.48% 1565ms 4.52% AbstractMesh::GetVectorFromAtoB 601ms 1.74% 54.22% 1556ms 4.50% std::__unguarded_linear_insert (inline) 1407ms 4.07% 58.29% 1407ms 4.07% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 58.29% 1373ms 3.97% std::_Rb_tree::lower_bound (inline) 0 0% 58.29% 1373ms 3.97% std::map::lower_bound (inline) 0 0% 58.29% 1209ms 3.50% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 58.29% 1182ms 3.42% NodeBasedCellPopulation::UpdateCellProcessLocation 0 0% 58.29% 1174ms 3.39% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 8ms 0.023% 58.31% 1100ms 3.18% DistributedBoxCollection::CalculateBoundaryNodePairs 1052ms 3.04% 61.35% 1052ms 3.04% boost::numeric::ublas::c_vector::operator() 14ms 0.04% 61.39% 1042ms 3.01% boost::numeric::ublas::detail::expression_type_check (inline) 202ms 0.58% 61.98% 991ms 2.86% boost::numeric::ublas::detail::equals 147ms 0.42% 62.40% 945ms 2.73% boost::numeric::ublas::vector_binary::size (inline) 234ms 0.68% 63.08% 922ms 2.67% NodeAttributes::AddAppliedForceContribution 403ms 1.17% 64.24% 893ms 2.58% __GI___libc_free 84ms 0.24% 64.48% 850ms 2.46% std::__new_allocator::allocate (inline) 371ms 1.07% 65.56% 812ms 2.35% DistributedBoxCollection::CalculateContainingBox (partial-inline) 24ms 0.069% 65.63% 786ms 2.27% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 274ms 0.79% 66.42% 780ms 2.25% NodeAttributes::AddNeighbour 82ms 0.24% 66.66% 768ms 2.22% operator new 0 0% 66.66% 752ms 2.17% boost::numeric::ublas::norm_inf (inline) 484ms 1.40% 68.06% 752ms 2.17% boost::numeric::ublas::vector_norm_inf::apply (inline) 3ms 0.0087% 68.06% 750ms 2.17% AbstractCentreBasedCellPopulation::GetDampingConstant 33ms 0.095% 68.16% 750ms 2.17% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 68.16% 741ms 2.14% AbstractCellPopulation::WriteResultsToFiles 522ms 1.51% 69.67% 729ms 2.11% __dynamic_cast 706ms 2.04% 71.71% 706ms 2.04% std::_Rb_tree_increment 0 0% 71.71% 688ms 1.99% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 71.71% 688ms 1.99% boost::numeric::ublas::c_vector::plus_assign (inline) 246ms 0.71% 72.42% 679ms 1.96% __GI___libc_malloc 3ms 0.0087% 72.43% 636ms 1.84% AbstractCellBasedSimulation::DoCellBirth 505ms 1.46% 73.89% 605ms 1.75% std::vector::push_back (inline) 8ms 0.023% 73.91% 603ms 1.74% CellPropertyCollection::GetPropertiesType (inline) 2ms 0.0058% 73.92% 519ms 1.50% Cell::GetMutationState 0 0% 73.92% 485ms 1.40% NodeBasedCellPopulation::WriteVtkResultsToFile 446ms 1.29% 75.21% 484ms 1.40% _int_free 15ms 0.043% 75.25% 468ms 1.35% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 75.25% 468ms 1.35% boost::numeric::ublas::vector::vector (inline) 0 0% 75.25% 457ms 1.32% boost::numeric::ublas::norm_2 (inline) 375ms 1.08% 76.33% 457ms 1.32% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 76.33% 455ms 1.32% AbstractCellBasedSimulation::DoCellRemoval (inline) 4ms 0.012% 76.35% 439ms 1.27% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 35ms 0.1% 76.45% 420ms 1.21% boost::detail::shared_count::~shared_count (inline) 0 0% 76.45% 420ms 1.21% boost::shared_ptr::~shared_ptr (inline) 0 0% 76.45% 397ms 1.15% std::allocator_traits::allocate (inline) 396ms 1.14% 77.59% 396ms 1.14% Node::GetIndex 371ms 1.07% 78.66% 375ms 1.08% boost::detail::sp_counted_base::release 0 0% 78.66% 365ms 1.06% std::_Rb_tree::_M_create_node (inline) 108ms 0.31% 78.98% 343ms 0.99% Node::GetRadius 2ms 0.0058% 78.98% 341ms 0.99% AbstractCellProperty::IsSubType (inline) 336ms 0.97% 79.95% 336ms 0.97% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 5ms 0.014% 79.97% 320ms 0.93% NodeBasedCellPopulation::UpdateMapsAfterRemesh 317ms 0.92% 80.89% 317ms 0.92% __gnu_cxx::__normal_iterator::operator++ (inline) 3ms 0.0087% 80.89% 315ms 0.91% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 0 0% 80.89% 314ms 0.91% std::_Rb_tree::_M_get_node (inline) 2ms 0.0058% 80.90% 312ms 0.9% AbstractCellPopulation::GetCellUsingLocationIndex 4ms 0.012% 80.91% 307ms 0.89% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 132ms 0.38% 81.29% 306ms 0.88% std::_Rb_tree::_M_erase (partial-inline) 0 0% 81.29% 305ms 0.88% boost::numeric::ublas::inner_prod (inline) 1ms 0.0029% 81.30% 305ms 0.88% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 23ms 0.066% 81.36% 304ms 0.88% boost::numeric::ublas::vector_scalar_binary::evaluate 10ms 0.029% 81.39% 296ms 0.86% boost::numeric::ublas::vector_reference::operator() (inline) 9ms 0.026% 81.42% 290ms 0.84% DistributedBoxCollection::GetProcessOwningNode 0 0% 81.42% 283ms 0.82% NodesOnlyMesh::ReMesh 280ms 0.81% 82.23% 280ms 0.81% [libchaste_cell_based.so] 0 0% 82.23% 279ms 0.81% NodesOnlyMesh::UpdateBoxCollection 4ms 0.012% 82.24% 277ms 0.8% NodesOnlyMesh::UpdateNodeIndices 102ms 0.29% 82.53% 258ms 0.75% std::__move_median_to_first (inline) 0 0% 82.53% 257ms 0.74% boost::numeric::ublas::c_vector::assign (inline) 0 0% 82.53% 256ms 0.74% Cell::HasCellProperty (inline) 1ms 0.0029% 82.54% 256ms 0.74% CellPropertyCollection::HasProperty 6ms 0.017% 82.55% 254ms 0.73% std::_Rb_tree::_M_emplace_hint_unique 247ms 0.71% 83.27% 247ms 0.71% Node::CheckForNodeAttributes 3ms 0.0087% 83.28% 238ms 0.69% Cell::ReadyToDivide 133ms 0.38% 83.66% 238ms 0.69% _int_malloc 111ms 0.32% 83.98% 237ms 0.69% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 83.98% 233ms 0.67% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 83.98% 230ms 0.66% VtkMeshWriter::WriteFiles 111ms 0.32% 84.30% 229ms 0.66% std::__find_if (inline) 0 0% 84.30% 229ms 0.66% std::find_if (inline) 0 0% 84.30% 229ms 0.66% std::none_of (inline) 0 0% 84.30% 226ms 0.65% std::_Rb_tree::_Alloc_node::operator() (inline) 222ms 0.64% 84.94% 222ms 0.64% Node::rGetLocation 2ms 0.0058% 84.95% 222ms 0.64% NodesOnlyMesh::AddNodesToBoxes 9ms 0.026% 84.98% 216ms 0.62% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 84.98% 208ms 0.6% NodesOnlyMesh::ResizeBoxCollection 14ms 0.04% 85.02% 207ms 0.6% NodesOnlyMesh::IsANodeCloseToDomainBoundary 207ms 0.6% 85.61% 207ms 0.6% __strcmp_avx2 202ms 0.58% 86.20% 202ms 0.58% [libchaste_mesh.so] 15ms 0.043% 86.24% 202ms 0.58% std::_Rb_tree::_M_copy (inline) 199ms 0.58% 86.82% 199ms 0.58% NodeBasedCellPopulation::GetNode 14ms 0.04% 86.86% 198ms 0.57% std::__insertion_sort (inline) 0 0% 86.86% 197ms 0.57% vtkDemandDrivenPipeline::ExecuteData 0 0% 86.86% 197ms 0.57% vtkDemandDrivenPipeline::ProcessRequest 0 0% 86.86% 197ms 0.57% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 86.86% 197ms 0.57% vtkStreamingDemandDrivenPipeline::Update 0 0% 86.86% 197ms 0.57% vtkXMLWriterBase::Write 0 0% 86.86% 196ms 0.57% vtkCompositeDataPipeline::ExecuteData 0 0% 86.86% 196ms 0.57% vtkExecutive::CallAlgorithm 0 0% 86.86% 196ms 0.57% vtkXMLUnstructuredDataWriter::ProcessRequest 33ms 0.095% 86.95% 195ms 0.56% std::__new_allocator::deallocate (inline) 193ms 0.56% 87.51% 193ms 0.56% boost::numeric::ublas::scalar_plus_assign::apply (inline) 0 0% 87.51% 192ms 0.56% tcache_get (inline) 192ms 0.56% 88.07% 192ms 0.56% tcache_get_n (inline) 141ms 0.41% 88.47% 189ms 0.55% Node::AddAppliedForceContribution 24ms 0.069% 88.54% 186ms 0.54% std::_Rb_tree::_M_clone_node (inline) 185ms 0.53% 89.08% 185ms 0.53% boost::numeric::ublas::c_vector::size (inline) 0 0% 89.08% 185ms 0.53% boost::numeric::ublas::vector_binary::operator() (inline) 176ms 0.51% 89.59% 176ms 0.51% boost::shared_ptr::operator-> (inline) 3ms 0.0087% 89.60% 175ms 0.51% AbstractCellProperty::IsType (inline) 10ms 0.029% 89.62% 173ms 0.5% std::_Rb_tree::~_Rb_tree (inline)