File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 30611ms, 88.67% of 34523ms total Dropped 821 nodes (cum <= 172.62ms) flat flat% sum% cum cum% 1ms 0.0029% 0.0029% 34378ms 99.58% _start 0 0% 0.0029% 34377ms 99.58% __libc_start_call_main 0 0% 0.0029% 34377ms 99.58% __libc_start_main_impl 0 0% 0.0029% 34360ms 99.53% CxxTest::ErrorFormatter::run (inline) 0 0% 0.0029% 34360ms 99.53% CxxTest::TestRunner::runAllTests (inline) 0 0% 0.0029% 34360ms 99.53% CxxTest::TestRunner::runWorld (inline) 0 0% 0.0029% 34360ms 99.53% main 0 0% 0.0029% 34324ms 99.42% CxxTest::TestRunner::runSuite (inline) 0 0% 0.0029% 34324ms 99.42% CxxTest::TestRunner::runTest (inline) 0 0% 0.0029% 34324ms 99.42% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0.0029% 34317ms 99.40% AbstractCellBasedSimulation::Solve 1ms 0.0029% 0.0058% 24102ms 69.81% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.0058% 0.012% 19264ms 55.80% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.017% 0.029% 19104ms 55.34% AbstractNumericalMethod::ComputeForcesIncludingDamping 166ms 0.48% 0.51% 18324ms 53.08% AbstractTwoBodyInteractionForce::AddForceContribution 1514ms 4.39% 4.90% 15454ms 44.76% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4312ms 12.49% 17.39% 9514ms 27.56% std::_Rb_tree::_M_lower_bound (inline) 0 0% 17.39% 8996ms 26.06% AbstractCellBasedSimulation::UpdateCellPopulation 356ms 1.03% 18.42% 8628ms 24.99% std::_Rb_tree::find (inline) 0 0% 18.42% 8628ms 24.99% std::map::find (inline) 146ms 0.42% 18.84% 8414ms 24.37% NodesOnlyMesh::GetNodeOrHaloNode 484ms 1.40% 20.24% 8264ms 23.94% AbstractMesh::GetNode 0 0% 20.24% 7950ms 23.03% NodeBasedCellPopulation::Update 298ms 0.86% 21.10% 7786ms 22.55% NodesOnlyMesh::SolveNodeMapping 235ms 0.68% 21.79% 6581ms 19.06% boost::numeric::ublas::vector_assign (inline) 209ms 0.61% 22.39% 6439ms 18.65% boost::numeric::ublas::c_vector::c_vector (partial-inline) 3ms 0.0087% 22.40% 5851ms 16.95% DistributedBoxCollection::CalculateInteriorNodePairs 5179ms 15.00% 37.40% 5179ms 15.00% std::_Rb_tree::_S_right (inline) 0 0% 37.40% 4560ms 13.21% OffLatticeSimulation::ApplyBoundaries 12ms 0.035% 37.44% 4510ms 13.06% NodeAttributes::RemoveDuplicateNeighbours 10ms 0.029% 37.46% 4340ms 12.57% std::__sort (inline) 0 0% 37.46% 4340ms 12.57% std::sort (inline) 1192ms 3.45% 40.92% 3698ms 10.71% boost::numeric::ublas::indexing_vector_assign 1ms 0.0029% 40.92% 3457ms 10.01% AbstractCellPopulation::Iterator::operator++ (inline) 254ms 0.74% 41.66% 3434ms 9.95% AbstractCellPopulation::Iterator::IsRealCell (inline) 73ms 0.21% 41.87% 3401ms 9.85% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 26ms 0.075% 41.94% 2849ms 8.25% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 191ms 0.55% 42.50% 2505ms 7.26% std::__introsort_loop 25ms 0.072% 42.57% 2386ms 6.91% PlaneBoundaryCondition::ImposeBoundaryCondition 46ms 0.13% 42.70% 2313ms 6.70% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.0029% 42.70% 2226ms 6.45% std::__unguarded_partition_pivot (inline) 15ms 0.043% 42.75% 2174ms 6.30% PlaneBoundaryCondition::VerifyBoundaryCondition 1037ms 3.00% 45.75% 2013ms 5.83% std::__unguarded_partition (inline) 217ms 0.63% 46.38% 1993ms 5.77% DistributedBoxCollection::AddPairsFromBox 2ms 0.0058% 46.39% 1823ms 5.28% std::__final_insertion_sort (inline) 230ms 0.67% 47.05% 1816ms 5.26% std::map::operator[] (partial-inline) 1682ms 4.87% 51.92% 1682ms 4.87% boost::numeric::ublas::same_impl_ex 117ms 0.34% 52.26% 1632ms 4.73% AbstractMesh::GetVectorFromAtoB 83ms 0.24% 52.50% 1615ms 4.68% std::__unguarded_insertion_sort (inline) 599ms 1.74% 54.24% 1546ms 4.48% std::__unguarded_linear_insert (inline) 1416ms 4.10% 58.34% 1416ms 4.10% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 58.34% 1331ms 3.86% std::_Rb_tree::lower_bound (inline) 0 0% 58.34% 1331ms 3.86% std::map::lower_bound (inline) 0 0% 58.34% 1283ms 3.72% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 58.34% 1257ms 3.64% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 58.34% 1181ms 3.42% NodeBasedCellPopulation::UpdateCellProcessLocation 1151ms 3.33% 61.67% 1151ms 3.33% boost::numeric::ublas::c_vector::operator() 16ms 0.046% 61.72% 1117ms 3.24% boost::numeric::ublas::detail::expression_type_check (inline) 2ms 0.0058% 61.73% 1085ms 3.14% DistributedBoxCollection::CalculateBoundaryNodePairs 211ms 0.61% 62.34% 1068ms 3.09% boost::numeric::ublas::detail::equals 153ms 0.44% 62.78% 1043ms 3.02% boost::numeric::ublas::vector_binary::size (inline) 197ms 0.57% 63.35% 886ms 2.57% NodeAttributes::AddAppliedForceContribution 400ms 1.16% 64.51% 872ms 2.53% __GI___libc_free 77ms 0.22% 64.73% 837ms 2.42% std::__new_allocator::allocate (inline) 15ms 0.043% 64.78% 828ms 2.40% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 64.78% 816ms 2.36% boost::numeric::ublas::norm_inf (inline) 465ms 1.35% 66.12% 816ms 2.36% boost::numeric::ublas::vector_norm_inf::apply (inline) 380ms 1.10% 67.22% 783ms 2.27% DistributedBoxCollection::CalculateContainingBox (partial-inline) 285ms 0.83% 68.05% 770ms 2.23% NodeAttributes::AddNeighbour 76ms 0.22% 68.27% 760ms 2.20% operator new 0 0% 68.27% 739ms 2.14% AbstractCellPopulation::WriteResultsToFiles 523ms 1.51% 69.79% 730ms 2.11% __dynamic_cast 5ms 0.014% 69.80% 718ms 2.08% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 69.80% 689ms 2.00% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 69.80% 689ms 2.00% boost::numeric::ublas::c_vector::plus_assign (inline) 256ms 0.74% 70.54% 681ms 1.97% __GI___libc_malloc 33ms 0.096% 70.64% 657ms 1.90% std::_Rb_tree_const_iterator::operator++ (inline) 617ms 1.79% 72.42% 617ms 1.79% std::_Rb_tree_increment 483ms 1.40% 73.82% 587ms 1.70% std::vector::push_back (inline) 1ms 0.0029% 73.83% 584ms 1.69% AbstractCellBasedSimulation::DoCellBirth 12ms 0.035% 73.86% 553ms 1.60% CellPropertyCollection::GetPropertiesType (inline) 3ms 0.0087% 73.87% 492ms 1.43% Cell::GetMutationState 2ms 0.0058% 73.88% 483ms 1.40% NodeBasedCellPopulation::WriteVtkResultsToFile 12ms 0.035% 73.91% 470ms 1.36% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 73.91% 470ms 1.36% boost::numeric::ublas::vector::vector (inline) 0 0% 73.91% 467ms 1.35% boost::numeric::ublas::norm_2 (inline) 366ms 1.06% 74.97% 467ms 1.35% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 74.97% 462ms 1.34% AbstractCellBasedSimulation::DoCellRemoval (inline) 422ms 1.22% 76.19% 461ms 1.34% _int_free 7ms 0.02% 76.21% 447ms 1.29% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 392ms 1.14% 77.35% 392ms 1.14% Node::GetIndex 0 0% 77.35% 379ms 1.10% std::allocator_traits::allocate (inline) 32ms 0.093% 77.44% 372ms 1.08% boost::detail::shared_count::~shared_count (inline) 0 0% 77.44% 372ms 1.08% boost::shared_ptr::~shared_ptr (inline) 355ms 1.03% 78.47% 355ms 1.03% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 78.47% 340ms 0.98% NodesOnlyMesh::ReMesh 111ms 0.32% 78.79% 339ms 0.98% Node::GetRadius 6ms 0.017% 78.81% 333ms 0.96% NodesOnlyMesh::UpdateNodeIndices 329ms 0.95% 79.76% 333ms 0.96% boost::detail::sp_counted_base::release 0 0% 79.76% 332ms 0.96% std::_Rb_tree::_M_create_node (inline) 2ms 0.0058% 79.77% 328ms 0.95% AbstractCellProperty::IsSubType (inline) 316ms 0.92% 80.68% 316ms 0.92% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 80.68% 314ms 0.91% boost::numeric::ublas::inner_prod (inline) 4ms 0.012% 80.69% 314ms 0.91% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 15ms 0.043% 80.74% 310ms 0.9% boost::numeric::ublas::vector_scalar_binary::evaluate 4ms 0.012% 80.75% 307ms 0.89% NodeBasedCellPopulation::UpdateMapsAfterRemesh 11ms 0.032% 80.78% 305ms 0.88% boost::numeric::ublas::vector_reference::operator() (inline) 1ms 0.0029% 80.78% 304ms 0.88% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 1ms 0.0029% 80.79% 302ms 0.87% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 80.79% 297ms 0.86% NodesOnlyMesh::UpdateBoxCollection 0 0% 80.79% 289ms 0.84% std::_Rb_tree::_M_get_node (inline) 288ms 0.83% 81.62% 288ms 0.83% [libchaste_cell_based.so] 108ms 0.31% 81.93% 285ms 0.83% std::_Rb_tree::_M_erase (partial-inline) 6ms 0.017% 81.95% 271ms 0.78% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 9ms 0.026% 81.98% 255ms 0.74% std::_Rb_tree::_M_emplace_hint_unique 5ms 0.014% 81.99% 251ms 0.73% DistributedBoxCollection::GetProcessOwningNode 0 0% 81.99% 251ms 0.73% NodesOnlyMesh::AddNodesToBoxes 110ms 0.32% 82.31% 251ms 0.73% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 82.31% 246ms 0.71% boost::numeric::ublas::c_vector::assign (inline) 246ms 0.71% 83.02% 246ms 0.71% boost::numeric::ublas::c_vector::size (inline) 115ms 0.33% 83.36% 237ms 0.69% std::__find_if (inline) 0 0% 83.36% 237ms 0.69% std::find_if (inline) 0 0% 83.36% 237ms 0.69% std::none_of (inline) 0 0% 83.36% 235ms 0.68% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 235ms 0.68% 84.04% 235ms 0.68% Node::CheckForNodeAttributes 0 0% 84.04% 235ms 0.68% VtkMeshWriter::WriteFiles 0 0% 84.04% 231ms 0.67% boost::numeric::ublas::vector_reference::size (inline) 142ms 0.41% 84.45% 230ms 0.67% _int_malloc 225ms 0.65% 85.10% 225ms 0.65% Node::rGetLocation 219ms 0.63% 85.73% 219ms 0.63% NodeBasedCellPopulation::GetNode 10ms 0.029% 85.76% 217ms 0.63% std::_Rb_tree::_Rb_tree (partial-inline) 210ms 0.61% 86.37% 210ms 0.61% boost::numeric::ublas::scalar_plus_assign::apply (inline) 92ms 0.27% 86.64% 209ms 0.61% std::__move_median_to_first (inline) 19ms 0.055% 86.69% 206ms 0.6% std::__insertion_sort (inline) 37ms 0.11% 86.80% 205ms 0.59% std::__new_allocator::deallocate (inline) 4ms 0.012% 86.81% 203ms 0.59% CellPropertyCollection::HasProperty 0 0% 86.81% 202ms 0.59% Cell::HasCellProperty (inline) 0 0% 86.81% 202ms 0.59% vtkStreamingDemandDrivenPipeline::Update 0 0% 86.81% 202ms 0.59% vtkXMLWriterBase::Write 24ms 0.07% 86.88% 201ms 0.58% std::_Rb_tree::_M_copy (inline) 0 0% 86.88% 201ms 0.58% vtkDemandDrivenPipeline::ExecuteData 0 0% 86.88% 201ms 0.58% vtkDemandDrivenPipeline::ProcessRequest 0 0% 86.88% 201ms 0.58% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 86.88% 200ms 0.58% NodesOnlyMesh::ResizeBoxCollection 0 0% 86.88% 200ms 0.58% vtkCompositeDataPipeline::ExecuteData 0 0% 86.88% 200ms 0.58% vtkExecutive::CallAlgorithm 0 0% 86.88% 200ms 0.58% vtkXMLUnstructuredDataWriter::ProcessRequest 5ms 0.014% 86.90% 199ms 0.58% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 86.90% 197ms 0.57% std::_Rb_tree::_Alloc_node::operator() (inline) 194ms 0.56% 87.46% 194ms 0.56% [libchaste_mesh.so] 0 0% 87.46% 192ms 0.56% tcache_get (inline) 192ms 0.56% 88.01% 192ms 0.56% tcache_get_n (inline) 190ms 0.55% 88.56% 190ms 0.55% __strcmp_avx2 5ms 0.014% 88.58% 182ms 0.53% Cell::ReadyToDivide 0 0% 88.58% 182ms 0.53% boost::numeric::ublas::vector_binary::operator() (inline) 31ms 0.09% 88.67% 176ms 0.51% std::_Rb_tree::_M_clone_node (inline)