File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 30952ms, 87.45% of 35392ms total Dropped 881 nodes (cum <= 176.96ms) flat flat% sum% cum cum% 0 0% 0% 35274ms 99.67% __libc_start_call_main 0 0% 0% 35274ms 99.67% __libc_start_main_impl 0 0% 0% 35274ms 99.67% _start 0 0% 0% 35257ms 99.62% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 35257ms 99.62% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 35257ms 99.62% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 35257ms 99.62% main 0 0% 0% 35215ms 99.50% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 35215ms 99.50% CxxTest::TestRunner::runTest (inline) 0 0% 0% 35215ms 99.50% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 2ms 0.0057% 0.0057% 35206ms 99.47% AbstractCellBasedSimulation::Solve 2ms 0.0057% 0.011% 24037ms 67.92% OffLatticeSimulation::UpdateCellLocationsAndTopology 5ms 0.014% 0.025% 19019ms 53.74% ForwardEulerNumericalMethod::UpdateAllNodePositions 13ms 0.037% 0.062% 18817ms 53.17% AbstractNumericalMethod::ComputeForcesIncludingDamping 153ms 0.43% 0.49% 17615ms 49.77% AbstractTwoBodyInteractionForce::AddForceContribution 1516ms 4.28% 4.78% 14837ms 41.92% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 0 0% 4.78% 9919ms 28.03% AbstractCellBasedSimulation::UpdateCellPopulation 4540ms 12.83% 17.61% 9576ms 27.06% std::_Rb_tree::_M_lower_bound (inline) 0 0% 17.61% 8777ms 24.80% NodeBasedCellPopulation::Update 340ms 0.96% 18.57% 8714ms 24.62% std::_Rb_tree::find (inline) 0 0% 18.57% 8714ms 24.62% std::map::find (inline) 218ms 0.62% 19.18% 8566ms 24.20% NodesOnlyMesh::GetNodeOrHaloNode 504ms 1.42% 20.61% 8345ms 23.58% AbstractMesh::GetNode 371ms 1.05% 21.65% 7841ms 22.15% NodesOnlyMesh::SolveNodeMapping 9ms 0.025% 21.68% 6626ms 18.72% DistributedBoxCollection::CalculateInteriorNodePairs 238ms 0.67% 22.35% 5854ms 16.54% boost::numeric::ublas::vector_assign (inline) 175ms 0.49% 22.85% 5725ms 16.18% boost::numeric::ublas::c_vector::c_vector (partial-inline) 5025ms 14.20% 37.05% 5025ms 14.20% std::_Rb_tree::_S_right (inline) 13ms 0.037% 37.08% 4646ms 13.13% NodeAttributes::RemoveDuplicateNeighbours 0 0% 37.08% 4629ms 13.08% OffLatticeSimulation::ApplyBoundaries 3ms 0.0085% 37.09% 4461ms 12.60% std::__sort (inline) 0 0% 37.09% 4461ms 12.60% std::sort (inline) 1047ms 2.96% 40.05% 3514ms 9.93% boost::numeric::ublas::indexing_vector_assign 74ms 0.21% 40.26% 3360ms 9.49% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 4ms 0.011% 40.27% 3162ms 8.93% AbstractCellPopulation::Iterator::operator++ (inline) 172ms 0.49% 40.75% 3139ms 8.87% AbstractCellPopulation::Iterator::IsRealCell 26ms 0.073% 40.83% 2720ms 7.69% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 185ms 0.52% 41.35% 2616ms 7.39% std::__introsort_loop 172ms 0.49% 41.84% 2597ms 7.34% DistributedBoxCollection::AddPairsFromBox 19ms 0.054% 41.89% 2474ms 6.99% PlaneBoundaryCondition::ImposeBoundaryCondition 0 0% 41.89% 2327ms 6.57% std::__unguarded_partition_pivot (inline) 37ms 0.1% 42.00% 2284ms 6.45% AbstractCellPopulation::GetLocationIndexUsingCell 15ms 0.042% 42.04% 2155ms 6.09% PlaneBoundaryCondition::VerifyBoundaryCondition 1005ms 2.84% 44.88% 2063ms 5.83% std::__unguarded_partition (inline) 1ms 0.0028% 44.88% 1838ms 5.19% std::__final_insertion_sort (inline) 188ms 0.53% 45.41% 1739ms 4.91% std::map::operator[] (partial-inline) 1656ms 4.68% 50.09% 1656ms 4.68% boost::numeric::ublas::same_impl_ex 117ms 0.33% 50.42% 1637ms 4.63% std::__unguarded_insertion_sort (inline) 133ms 0.38% 50.80% 1584ms 4.48% AbstractMesh::GetVectorFromAtoB 615ms 1.74% 52.53% 1574ms 4.45% std::__unguarded_linear_insert (inline) 1388ms 3.92% 56.46% 1388ms 3.92% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 56.46% 1340ms 3.79% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 56.46% 1317ms 3.72% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 56.46% 1293ms 3.65% std::_Rb_tree::lower_bound (inline) 0 0% 56.46% 1293ms 3.65% std::map::lower_bound (inline) 1200ms 3.39% 59.85% 1200ms 3.39% boost::numeric::ublas::c_vector::operator() 1ms 0.0028% 59.85% 1170ms 3.31% NodeBasedCellPopulation::UpdateCellProcessLocation 5ms 0.014% 59.86% 1140ms 3.22% DistributedBoxCollection::CalculateBoundaryNodePairs 2ms 0.0057% 59.87% 1126ms 3.18% AbstractCentreBasedCellPopulation::GetDampingConstant 1ms 0.0028% 59.87% 1109ms 3.13% boost::numeric::ublas::detail::expression_type_check (inline) 234ms 0.66% 60.53% 1081ms 3.05% boost::numeric::ublas::detail::equals 40ms 0.11% 60.65% 1036ms 2.93% std::_Rb_tree_const_iterator::operator++ (inline) 400ms 1.13% 61.78% 1008ms 2.85% NodeAttributes::AddNeighbour 983ms 2.78% 64.55% 983ms 2.78% std::_Rb_tree_increment 15ms 0.042% 64.60% 974ms 2.75% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 224ms 0.63% 65.23% 970ms 2.74% boost::numeric::ublas::vector_binary::size (inline) 216ms 0.61% 65.84% 909ms 2.57% NodeAttributes::AddAppliedForceContribution 402ms 1.14% 66.98% 889ms 2.51% DistributedBoxCollection::CalculateContainingBox (partial-inline) 629ms 1.78% 68.75% 837ms 2.36% __dynamic_cast 21ms 0.059% 68.81% 818ms 2.31% CellPropertyCollection::GetPropertiesType (inline) 0 0% 68.81% 768ms 2.17% AbstractCellPopulation::WriteResultsToFiles 0 0% 68.81% 765ms 2.16% boost::numeric::ublas::norm_inf (inline) 492ms 1.39% 70.20% 765ms 2.16% boost::numeric::ublas::vector_norm_inf::apply (inline) 129ms 0.36% 70.57% 765ms 2.16% std::__new_allocator::allocate (inline) 0 0% 70.57% 731ms 2.07% Cell::GetMutationState 604ms 1.71% 72.27% 714ms 2.02% std::vector::push_back (inline) 0 0% 72.27% 693ms 1.96% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 72.27% 693ms 1.96% boost::numeric::ublas::c_vector::plus_assign (inline) 14ms 0.04% 72.31% 682ms 1.93% AbstractCellBasedSimulation::DoCellBirth 87ms 0.25% 72.56% 637ms 1.80% operator new 0 0% 72.56% 575ms 1.62% boost::numeric::ublas::norm_2 (inline) 445ms 1.26% 73.82% 575ms 1.62% boost::numeric::ublas::vector_norm_2::apply (inline) 217ms 0.61% 74.43% 547ms 1.55% __GI___libc_malloc 1ms 0.0028% 74.43% 506ms 1.43% NodeBasedCellPopulation::WriteVtkResultsToFile 160ms 0.45% 74.88% 489ms 1.38% __GI___libc_free 6ms 0.017% 74.90% 480ms 1.36% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 16ms 0.045% 74.95% 473ms 1.34% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 74.95% 459ms 1.30% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 74.95% 454ms 1.28% std::allocator_traits::allocate (inline) 0 0% 74.95% 448ms 1.27% std::_Rb_tree::_M_create_node (inline) 6ms 0.017% 74.96% 441ms 1.25% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1ms 0.0028% 74.97% 403ms 1.14% AbstractCellProperty::IsSubType (inline) 29ms 0.082% 75.05% 398ms 1.12% boost::detail::shared_count::~shared_count (inline) 0 0% 75.05% 398ms 1.12% boost::shared_ptr::~shared_ptr (inline) 343ms 0.97% 76.02% 372ms 1.05% Node::AddNeighbour 372ms 1.05% 77.07% 372ms 1.05% Node::GetIndex 0 0% 77.07% 371ms 1.05% std::_Rb_tree::_M_get_node (inline) 7ms 0.02% 77.09% 371ms 1.05% std::_Rb_tree::_Rb_tree (partial-inline) 353ms 1% 78.09% 366ms 1.03% boost::detail::sp_counted_base::release 363ms 1.03% 79.11% 363ms 1.03% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 37ms 0.1% 79.22% 359ms 1.01% std::_Rb_tree::_M_copy (inline) 43ms 0.12% 79.34% 354ms 1.00% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 79.34% 354ms 1.00% boost::numeric::ublas::vector::vector (inline) 0 0% 79.34% 349ms 0.99% boost::numeric::ublas::inner_prod (inline) 2ms 0.0057% 79.34% 346ms 0.98% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 18ms 0.051% 79.39% 344ms 0.97% boost::numeric::ublas::vector_scalar_binary::evaluate 284ms 0.8% 80.20% 330ms 0.93% _int_free 115ms 0.32% 80.52% 327ms 0.92% std::_Rb_tree::_M_erase 48ms 0.14% 80.66% 321ms 0.91% std::_Rb_tree::_M_clone_node (inline) 0 0% 80.66% 319ms 0.9% NodesOnlyMesh::ReMesh 5ms 0.014% 80.67% 317ms 0.9% NodeBasedCellPopulation::UpdateMapsAfterRemesh 5ms 0.014% 80.68% 311ms 0.88% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 80.68% 308ms 0.87% std::_Rb_tree::_Alloc_node::operator() (inline) 1ms 0.0028% 80.69% 305ms 0.86% NodesOnlyMesh::UpdateNodeIndices 67ms 0.19% 80.88% 303ms 0.86% Node::GetRadius 0 0% 80.88% 302ms 0.85% NodesOnlyMesh::UpdateBoxCollection 6ms 0.017% 80.89% 300ms 0.85% DistributedBoxCollection::GetProcessOwningNode 16ms 0.045% 80.94% 299ms 0.84% Cell::ReadyToDivide 2ms 0.0057% 80.94% 295ms 0.83% CellPropertyCollection::HasProperty 0 0% 80.94% 294ms 0.83% Cell::HasCellProperty (inline) 134ms 0.38% 81.32% 278ms 0.79% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 81.32% 276ms 0.78% boost::numeric::ublas::c_vector::assign (inline) 267ms 0.75% 82.08% 267ms 0.75% __gnu_cxx::__normal_iterator::operator++ (inline) 14ms 0.04% 82.12% 267ms 0.75% boost::numeric::ublas::vector_reference::operator() (inline) 114ms 0.32% 82.44% 259ms 0.73% std::__move_median_to_first (inline) 7ms 0.02% 82.46% 258ms 0.73% std::_Rb_tree::_M_emplace_hint_unique 0 0% 82.46% 257ms 0.73% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 82.46% 257ms 0.73% VtkMeshWriter::WriteFiles 254ms 0.72% 83.18% 254ms 0.72% [libchaste_mesh.so] 248ms 0.7% 83.88% 248ms 0.7% Node::CheckForNodeAttributes 132ms 0.37% 84.25% 239ms 0.68% _int_malloc 4ms 0.011% 84.26% 232ms 0.66% NodesOnlyMesh::AddNodesToBoxes 0 0% 84.26% 229ms 0.65% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 84.26% 228ms 0.64% vtkStreamingDemandDrivenPipeline::Update 0 0% 84.26% 228ms 0.64% vtkXMLWriterBase::Write 0 0% 84.26% 227ms 0.64% vtkDemandDrivenPipeline::ProcessRequest 0 0% 84.26% 227ms 0.64% vtkExecutive::CallAlgorithm 0 0% 84.26% 226ms 0.64% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 84.26% 225ms 0.64% vtkCompositeDataPipeline::ExecuteData 0 0% 84.26% 225ms 0.64% vtkDemandDrivenPipeline::ExecuteData 0 0% 84.26% 225ms 0.64% vtkXMLUnstructuredDataWriter::ProcessRequest 219ms 0.62% 84.88% 219ms 0.62% NodeBasedCellPopulation::GetNode 215ms 0.61% 85.49% 215ms 0.61% [libchaste_cell_based.so] 2ms 0.0057% 85.49% 204ms 0.58% std::set::set (inline) 2ms 0.0057% 85.50% 203ms 0.57% AbstractCellProperty::IsType (inline) 68ms 0.19% 85.69% 201ms 0.57% std::__find_if (inline) 0 0% 85.69% 201ms 0.57% std::find_if (inline) 0 0% 85.69% 201ms 0.57% std::none_of (inline) 200ms 0.57% 86.26% 200ms 0.57% Node::rGetLocation 0 0% 86.26% 200ms 0.57% std::_Rb_tree::_M_drop_node (inline) 22ms 0.062% 86.32% 200ms 0.57% std::__insertion_sort (inline) 10ms 0.028% 86.35% 196ms 0.55% std::__new_allocator::deallocate (inline) 195ms 0.55% 86.90% 195ms 0.55% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 184ms 0.52% 87.42% 184ms 0.52% __strcmp_avx2 12ms 0.034% 87.45% 181ms 0.51% std::_Rb_tree::~_Rb_tree (inline) 0 0% 87.45% 180ms 0.51% std::_Rb_tree::clear (inline) 1ms 0.0028% 87.45% 178ms 0.5% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 87.45% 177ms 0.5% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData