File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 31230ms, 86.57% of 36074ms total Dropped 892 nodes (cum <= 180.37ms) flat flat% sum% cum cum% 0 0% 0% 35947ms 99.65% __libc_start_call_main 0 0% 0% 35947ms 99.65% __libc_start_main_impl 0 0% 0% 35947ms 99.65% _start 0 0% 0% 35927ms 99.59% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 35927ms 99.59% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 35927ms 99.59% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 35927ms 99.59% main 0 0% 0% 35881ms 99.46% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 35881ms 99.46% CxxTest::TestRunner::runTest (inline) 0 0% 0% 35881ms 99.46% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 35872ms 99.44% AbstractCellBasedSimulation::Solve 5ms 0.014% 0.014% 24471ms 67.84% OffLatticeSimulation::UpdateCellLocationsAndTopology 3ms 0.0083% 0.022% 19275ms 53.43% ForwardEulerNumericalMethod::UpdateAllNodePositions 9ms 0.025% 0.047% 19060ms 52.84% AbstractNumericalMethod::ComputeForcesIncludingDamping 151ms 0.42% 0.47% 17808ms 49.37% AbstractTwoBodyInteractionForce::AddForceContribution 1494ms 4.14% 4.61% 15053ms 41.73% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 0 0% 4.61% 10117ms 28.05% AbstractCellBasedSimulation::UpdateCellPopulation 4563ms 12.65% 17.26% 9971ms 27.64% std::_Rb_tree::_M_lower_bound (inline) 375ms 1.04% 18.30% 9084ms 25.18% std::_Rb_tree::find (inline) 0 0% 18.30% 9083ms 25.18% std::map::find (inline) 164ms 0.45% 18.75% 8887ms 24.64% NodesOnlyMesh::GetNodeOrHaloNode 1ms 0.0028% 18.75% 8858ms 24.56% NodeBasedCellPopulation::Update 523ms 1.45% 20.20% 8750ms 24.26% AbstractMesh::GetNode 343ms 0.95% 21.15% 8233ms 22.82% NodesOnlyMesh::SolveNodeMapping 8ms 0.022% 21.18% 6668ms 18.48% DistributedBoxCollection::CalculateInteriorNodePairs 177ms 0.49% 21.67% 5843ms 16.20% boost::numeric::ublas::vector_assign (inline) 137ms 0.38% 22.05% 5710ms 15.83% boost::numeric::ublas::c_vector::c_vector (partial-inline) 5364ms 14.87% 36.92% 5364ms 14.87% std::_Rb_tree::_S_right (inline) 1ms 0.0028% 36.92% 4774ms 13.23% OffLatticeSimulation::ApplyBoundaries 10ms 0.028% 36.95% 4752ms 13.17% NodeAttributes::RemoveDuplicateNeighbours 4ms 0.011% 36.96% 4546ms 12.60% std::__sort (inline) 0 0% 36.96% 4546ms 12.60% std::sort (inline) 1178ms 3.27% 40.22% 3488ms 9.67% boost::numeric::ublas::indexing_vector_assign 98ms 0.27% 40.49% 3349ms 9.28% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 4ms 0.011% 40.51% 3245ms 9.00% AbstractCellPopulation::Iterator::operator++ (inline) 199ms 0.55% 41.06% 3217ms 8.92% AbstractCellPopulation::Iterator::IsRealCell (inline) 31ms 0.086% 41.14% 2762ms 7.66% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 201ms 0.56% 41.70% 2672ms 7.41% std::__introsort_loop 28ms 0.078% 41.78% 2544ms 7.05% PlaneBoundaryCondition::ImposeBoundaryCondition 164ms 0.45% 42.23% 2528ms 7.01% DistributedBoxCollection::AddPairsFromBox 0 0% 42.23% 2373ms 6.58% std::__unguarded_partition_pivot (inline) 54ms 0.15% 42.38% 2363ms 6.55% AbstractCellPopulation::GetLocationIndexUsingCell 18ms 0.05% 42.43% 2228ms 6.18% PlaneBoundaryCondition::VerifyBoundaryCondition 1013ms 2.81% 45.24% 2095ms 5.81% std::__unguarded_partition (inline) 197ms 0.55% 45.79% 1875ms 5.20% std::map::operator[] (partial-inline) 1ms 0.0028% 45.79% 1866ms 5.17% std::__final_insertion_sort (inline) 1739ms 4.82% 50.61% 1739ms 4.82% boost::numeric::ublas::same_impl_ex 110ms 0.3% 50.91% 1650ms 4.57% std::__unguarded_insertion_sort (inline) 594ms 1.65% 52.56% 1572ms 4.36% std::__unguarded_linear_insert (inline) 150ms 0.42% 52.98% 1540ms 4.27% AbstractMesh::GetVectorFromAtoB 1408ms 3.90% 56.88% 1408ms 3.90% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 56.88% 1377ms 3.82% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 56.88% 1369ms 3.79% std::_Rb_tree::lower_bound (inline) 0 0% 56.88% 1369ms 3.79% std::map::lower_bound (inline) 0 0% 56.88% 1357ms 3.76% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 56.88% 1206ms 3.34% NodeBasedCellPopulation::UpdateCellProcessLocation 0 0% 56.88% 1184ms 3.28% boost::numeric::ublas::detail::expression_type_check (inline) 6ms 0.017% 56.90% 1164ms 3.23% DistributedBoxCollection::CalculateBoundaryNodePairs 3ms 0.0083% 56.91% 1157ms 3.21% AbstractCentreBasedCellPopulation::GetDampingConstant 249ms 0.69% 57.60% 1141ms 3.16% boost::numeric::ublas::detail::equals 1081ms 3.00% 60.59% 1081ms 3.00% boost::numeric::ublas::c_vector::operator() 31ms 0.086% 60.68% 1063ms 2.95% std::_Rb_tree_const_iterator::operator++ (inline) 173ms 0.48% 61.16% 999ms 2.77% boost::numeric::ublas::vector_binary::size (inline) 999ms 2.77% 63.93% 999ms 2.77% std::_Rb_tree_increment 25ms 0.069% 64.00% 948ms 2.63% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 176ms 0.49% 64.48% 892ms 2.47% std::__new_allocator::allocate (inline) 197ms 0.55% 65.03% 890ms 2.47% NodeAttributes::AddAppliedForceContribution 399ms 1.11% 66.14% 859ms 2.38% DistributedBoxCollection::CalculateContainingBox (partial-inline) 19ms 0.053% 66.19% 849ms 2.35% CellPropertyCollection::GetPropertiesType (inline) 0 0% 66.19% 824ms 2.28% boost::numeric::ublas::norm_inf (inline) 520ms 1.44% 67.63% 824ms 2.28% boost::numeric::ublas::vector_norm_inf::apply (inline) 579ms 1.61% 69.24% 798ms 2.21% __dynamic_cast 0 0% 69.24% 793ms 2.20% AbstractCellPopulation::WriteResultsToFiles 5ms 0.014% 69.25% 781ms 2.16% AbstractCellBasedSimulation::DoCellBirth 0 0% 69.25% 754ms 2.09% Cell::GetMutationState 163ms 0.45% 69.70% 743ms 2.06% NodeAttributes::AddNeighbour 72ms 0.2% 69.90% 722ms 2.00% operator new 580ms 1.61% 71.51% 699ms 1.94% std::vector::push_back (inline) 0 0% 71.51% 693ms 1.92% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 71.51% 693ms 1.92% boost::numeric::ublas::c_vector::plus_assign (inline) 231ms 0.64% 72.15% 640ms 1.77% __GI___libc_malloc 0 0% 72.15% 553ms 1.53% boost::numeric::ublas::norm_2 (inline) 438ms 1.21% 73.36% 553ms 1.53% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 73.36% 552ms 1.53% std::allocator_traits::allocate (inline) 1ms 0.0028% 73.37% 528ms 1.46% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 17ms 0.047% 73.41% 526ms 1.46% AbstractCellPopulation::GetCellUsingLocationIndex 6ms 0.017% 73.43% 522ms 1.45% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 73.43% 515ms 1.43% std::_Rb_tree::_M_create_node (inline) 156ms 0.43% 73.86% 482ms 1.34% __GI___libc_free 0 0% 73.86% 476ms 1.32% AbstractCellBasedSimulation::DoCellRemoval (inline) 3ms 0.0083% 73.87% 463ms 1.28% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 463ms 1.28% 75.15% 463ms 1.28% [libchaste_mesh.so] 0 0% 75.15% 444ms 1.23% std::_Rb_tree::_M_get_node (inline) 1ms 0.0028% 75.16% 407ms 1.13% AbstractCellProperty::IsSubType (inline) 193ms 0.54% 75.69% 404ms 1.12% Node::AddNeighbour 29ms 0.08% 75.77% 404ms 1.12% std::_Rb_tree::_Rb_tree (partial-inline) 400ms 1.11% 76.88% 400ms 1.11% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 76.88% 400ms 1.11% boost::numeric::ublas::inner_prod (inline) 399ms 1.11% 77.99% 399ms 1.11% Node::GetIndex 21ms 0.058% 78.05% 399ms 1.11% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 78.05% 399ms 1.11% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 19ms 0.053% 78.10% 387ms 1.07% boost::detail::shared_count::~shared_count (inline) 0 0% 78.10% 387ms 1.07% boost::shared_ptr::~shared_ptr (inline) 38ms 0.11% 78.20% 378ms 1.05% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 78.20% 378ms 1.05% boost::numeric::ublas::vector::vector (inline) 39ms 0.11% 78.31% 371ms 1.03% std::_Rb_tree::_M_copy (inline) 180ms 0.5% 78.81% 366ms 1.01% std::_Rb_tree::_M_erase 353ms 0.98% 79.79% 365ms 1.01% boost::detail::sp_counted_base::release 348ms 0.96% 80.75% 348ms 0.96% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 80.75% 338ms 0.94% Cell::HasCellProperty (inline) 2ms 0.0055% 80.76% 338ms 0.94% CellPropertyCollection::HasProperty 0 0% 80.76% 337ms 0.93% NodesOnlyMesh::ReMesh 5ms 0.014% 80.77% 336ms 0.93% NodeBasedCellPopulation::UpdateMapsAfterRemesh 138ms 0.38% 81.16% 336ms 0.93% boost::numeric::ublas::vector_inner_prod::apply (inline) 51ms 0.14% 81.30% 332ms 0.92% std::_Rb_tree::_M_clone_node (inline) 0 0% 81.30% 331ms 0.92% boost::numeric::ublas::c_vector::assign (inline) 0 0% 81.30% 331ms 0.92% std::_Rb_tree::_Alloc_node::operator() (inline) 14ms 0.039% 81.34% 328ms 0.91% Cell::ReadyToDivide 4ms 0.011% 81.35% 327ms 0.91% NodesOnlyMesh::UpdateNodeIndices 274ms 0.76% 82.11% 326ms 0.9% _int_free 9ms 0.025% 82.13% 309ms 0.86% std::_Rb_tree::_M_emplace_hint_unique 78ms 0.22% 82.35% 304ms 0.84% Node::GetRadius 0 0% 82.35% 294ms 0.81% NodesOnlyMesh::UpdateBoxCollection 18ms 0.05% 82.40% 291ms 0.81% boost::numeric::ublas::vector_reference::operator() (inline) 134ms 0.37% 82.77% 290ms 0.8% _int_malloc 1ms 0.0028% 82.77% 289ms 0.8% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 9ms 0.025% 82.80% 275ms 0.76% DistributedBoxCollection::GetProcessOwningNode 91ms 0.25% 83.05% 271ms 0.75% std::__move_median_to_first (inline) 0 0% 83.05% 261ms 0.72% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 83.05% 260ms 0.72% VtkMeshWriter::WriteFiles 253ms 0.7% 83.75% 256ms 0.71% Node::ConstructNodeAttributes (inline) 245ms 0.68% 84.43% 245ms 0.68% [libchaste_cell_based.so] 0 0% 84.43% 243ms 0.67% std::set::set (inline) 239ms 0.66% 85.09% 239ms 0.66% Node::CheckForNodeAttributes 0 0% 85.09% 239ms 0.66% boost::numeric::ublas::vector_binary::operator() (inline) 230ms 0.64% 85.73% 230ms 0.64% NodeBasedCellPopulation::GetNode 0 0% 85.73% 227ms 0.63% vtkStreamingDemandDrivenPipeline::Update 0 0% 85.73% 227ms 0.63% vtkXMLWriterBase::Write 3ms 0.0083% 85.74% 226ms 0.63% NodesOnlyMesh::AddNodesToBoxes 0 0% 85.74% 224ms 0.62% vtkDemandDrivenPipeline::ProcessRequest 0 0% 85.74% 224ms 0.62% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 85.74% 223ms 0.62% vtkCompositeDataPipeline::ExecuteData 0 0% 85.74% 223ms 0.62% vtkExecutive::CallAlgorithm 0 0% 85.74% 222ms 0.62% vtkDemandDrivenPipeline::ExecuteData 0 0% 85.74% 221ms 0.61% vtkXMLUnstructuredDataWriter::ProcessRequest 18ms 0.05% 85.79% 215ms 0.6% std::__insertion_sort (inline) 18ms 0.05% 85.84% 206ms 0.57% std::_Rb_tree::~_Rb_tree (inline) 0 0% 85.84% 201ms 0.56% std::_Rb_tree::clear (inline) 199ms 0.55% 86.39% 199ms 0.55% __strcmp_avx2 3ms 0.0083% 86.40% 193ms 0.54% AbstractCellProperty::IsType (inline) 0 0% 86.40% 184ms 0.51% std::_Rb_tree::_Auto_node::_Auto_node (inline) 63ms 0.17% 86.57% 182ms 0.5% std::__find_if (inline) 0 0% 86.57% 182ms 0.5% std::find_if (inline) 0 0% 86.57% 182ms 0.5% std::none_of (inline) 0 0% 86.57% 182ms 0.5% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 86.57% 182ms 0.5% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData