File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 16993ms, 88.44% of 19214ms total Dropped 721 nodes (cum <= 96.07ms) flat flat% sum% cum cum% 0 0% 0% 19121ms 99.52% __libc_start_call_main 0 0% 0% 19121ms 99.52% __libc_start_main_impl 0 0% 0% 19121ms 99.52% _start 0 0% 0% 19107ms 99.44% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19107ms 99.44% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19107ms 99.44% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19107ms 99.44% main 0 0% 0% 19068ms 99.24% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19068ms 99.24% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19068ms 99.24% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 19061ms 99.20% AbstractCellBasedSimulation::Solve 2ms 0.01% 0.01% 10938ms 56.93% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.01% 7171ms 37.32% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.01% 0.021% 7166ms 37.30% ForwardEulerNumericalMethod::UpdateAllNodePositions 9ms 0.047% 0.068% 7029ms 36.58% AbstractNumericalMethod::ComputeForcesIncludingDamping 1037ms 5.40% 5.46% 6456ms 33.60% RepulsionForce::AddForceContribution (partial-inline) 0 0% 5.46% 6346ms 33.03% NodeBasedCellPopulation::Update 4ms 0.021% 5.49% 4715ms 24.54% DistributedBoxCollection::CalculateInteriorNodePairs 1715ms 8.93% 14.41% 3974ms 20.68% std::_Rb_tree::_M_lower_bound (inline) 12ms 0.062% 14.47% 3548ms 18.47% NodeAttributes::RemoveDuplicateNeighbours 0 0% 14.47% 3534ms 18.39% OffLatticeSimulation::ApplyBoundaries 2ms 0.01% 14.48% 3411ms 17.75% std::__sort (inline) 0 0% 14.48% 3411ms 17.75% std::sort (inline) 159ms 0.83% 15.31% 3244ms 16.88% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 187ms 0.97% 16.29% 2605ms 13.56% std::_Rb_tree::find (inline) 0 0% 16.29% 2605ms 13.56% std::map::find (inline) 68ms 0.35% 16.64% 2582ms 13.44% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 2ms 0.01% 16.65% 2417ms 12.58% AbstractCellPopulation::Iterator::operator++ (inline) 115ms 0.6% 17.25% 2393ms 12.45% AbstractCellPopulation::Iterator::IsRealCell 2232ms 11.62% 28.86% 2232ms 11.62% std::_Rb_tree::_S_right (inline) 27ms 0.14% 29.00% 2080ms 10.83% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 145ms 0.75% 29.76% 1958ms 10.19% std::__introsort_loop 152ms 0.79% 30.55% 1951ms 10.15% std::map::operator[] (partial-inline) 54ms 0.28% 30.83% 1931ms 10.05% NodesOnlyMesh::GetNodeOrHaloNode 142ms 0.74% 31.57% 1925ms 10.02% AbstractMesh::GetNode 18ms 0.094% 31.66% 1886ms 9.82% PlaneBoundaryCondition::ImposeBoundaryCondition 91ms 0.47% 32.14% 1786ms 9.30% NodesOnlyMesh::SolveNodeMapping 0 0% 32.14% 1745ms 9.08% std::__unguarded_partition_pivot (inline) 25ms 0.13% 32.27% 1704ms 8.87% AbstractCellPopulation::GetLocationIndexUsingCell 11ms 0.057% 32.33% 1647ms 8.57% PlaneBoundaryCondition::VerifyBoundaryCondition 109ms 0.57% 32.89% 1616ms 8.41% DistributedBoxCollection::AddPairsFromBox 0 0% 32.89% 1587ms 8.26% std::_Rb_tree::lower_bound (inline) 0 0% 32.89% 1587ms 8.26% std::map::lower_bound (inline) 736ms 3.83% 36.72% 1560ms 8.12% std::__unguarded_partition (inline) 0 0% 36.72% 1450ms 7.55% std::__final_insertion_sort (inline) 19ms 0.099% 36.82% 1382ms 7.19% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 36ms 0.19% 37.01% 1360ms 7.08% AbstractCellPopulation::GetCellUsingLocationIndex 90ms 0.47% 37.48% 1308ms 6.81% std::__unguarded_insertion_sort (inline) 464ms 2.41% 39.89% 1232ms 6.41% std::__unguarded_linear_insert (inline) 1132ms 5.89% 45.78% 1132ms 5.89% __gnu_cxx::__normal_iterator::operator-- (inline) 42ms 0.22% 46.00% 1005ms 5.23% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 46.00% 913ms 4.75% NodeBasedCellPopulation::UpdateCellProcessLocation 9ms 0.047% 46.05% 868ms 4.52% boost::numeric::ublas::vector_assign (inline) 2ms 0.01% 46.06% 854ms 4.44% DistributedBoxCollection::CalculateBoundaryNodePairs 250ms 1.30% 47.36% 796ms 4.14% __dynamic_cast 169ms 0.88% 48.24% 790ms 4.11% boost::numeric::ublas::indexing_vector_assign 13ms 0.068% 48.31% 748ms 3.89% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 314ms 1.63% 49.94% 695ms 3.62% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 49.94% 665ms 3.46% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 123ms 0.64% 50.58% 656ms 3.41% AbstractMesh::GetVectorFromAtoB 0 0% 50.58% 652ms 3.39% boost::numeric::ublas::norm_2 (inline) 507ms 2.64% 53.22% 652ms 3.39% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 53.22% 652ms 3.39% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 169ms 0.88% 54.10% 648ms 3.37% NodeAttributes::AddNeighbour 4ms 0.021% 54.12% 624ms 3.25% boost::numeric::ublas::c_vector::operator= (inline) 26ms 0.14% 54.26% 607ms 3.16% std::__copy_move::__copy_m (inline) 0 0% 54.26% 607ms 3.16% std::__copy_move_a (inline) 0 0% 54.26% 607ms 3.16% std::__copy_move_a1 (inline) 0 0% 54.26% 607ms 3.16% std::__copy_move_a2 (inline) 0 0% 54.26% 607ms 3.16% std::copy (inline) 601ms 3.13% 57.39% 601ms 3.13% __memcpy_avx512_unaligned_erms 0 0% 57.39% 585ms 3.04% AbstractCellPopulation::WriteResultsToFiles 568ms 2.96% 60.34% 568ms 2.96% boost::numeric::ublas::c_vector::operator() 478ms 2.49% 62.83% 543ms 2.83% std::vector::push_back (inline) 5ms 0.026% 62.86% 537ms 2.79% CellPropertyCollection::GetPropertiesType (inline) 24ms 0.12% 62.98% 534ms 2.78% std::_Rb_tree_const_iterator::operator++ (inline) 3ms 0.016% 63.00% 505ms 2.63% AbstractCentreBasedCellPopulation::GetDampingConstant 499ms 2.60% 65.59% 499ms 2.60% std::_Rb_tree_increment 446ms 2.32% 67.91% 446ms 2.32% boost::numeric::ublas::same_impl_ex 1ms 0.0052% 67.92% 442ms 2.30% AbstractCellBasedSimulation::DoCellBirth 232ms 1.21% 69.13% 436ms 2.27% __cxxabiv1::__si_class_type_info::__do_dyncast 32ms 0.17% 69.29% 431ms 2.24% std::_Rb_tree::_Rb_tree (partial-inline) 68ms 0.35% 69.65% 407ms 2.12% std::__new_allocator::allocate (inline) 20ms 0.1% 69.75% 390ms 2.03% boost::detail::shared_count::~shared_count (inline) 0 0% 69.75% 390ms 2.03% boost::shared_ptr::~shared_ptr (inline) 43ms 0.22% 69.98% 389ms 2.02% std::_Rb_tree::_M_copy (inline) 0 0% 69.98% 387ms 2.01% std::allocator_traits::allocate (inline) 1ms 0.0052% 69.98% 384ms 2.00% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 69.98% 383ms 1.99% AbstractCellBasedSimulation::DoCellRemoval (inline) 4ms 0.021% 70.00% 368ms 1.92% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1ms 0.0052% 70.01% 357ms 1.86% std::set::set (inline) 0 0% 70.01% 356ms 1.85% std::_Rb_tree::_M_create_node (inline) 2ms 0.01% 70.02% 355ms 1.85% AbstractCellProperty::IsSubType (inline) 3ms 0.016% 70.03% 351ms 1.83% Cell::GetMutationState 344ms 1.79% 71.82% 351ms 1.83% boost::detail::sp_counted_base::release 124ms 0.65% 72.47% 338ms 1.76% std::_Rb_tree::_M_clone_node (inline) 15ms 0.078% 72.55% 335ms 1.74% operator new 334ms 1.74% 74.28% 334ms 1.74% __strcmp_evex 0 0% 74.28% 322ms 1.68% std::_Rb_tree::_M_get_node (inline) 95ms 0.49% 74.78% 318ms 1.66% __GI___libc_malloc 75ms 0.39% 75.17% 318ms 1.66% boost::numeric::ublas::vector_binary::size (inline) 83ms 0.43% 75.60% 313ms 1.63% std::_Rb_tree::_M_erase 0 0% 75.60% 281ms 1.46% boost::numeric::ublas::inner_prod (inline) 2ms 0.01% 75.61% 281ms 1.46% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 16ms 0.083% 75.69% 279ms 1.45% boost::numeric::ublas::vector_scalar_binary::evaluate 52ms 0.27% 75.97% 274ms 1.43% Node::GetRadius 263ms 1.37% 77.33% 263ms 1.37% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 34ms 0.18% 77.51% 257ms 1.34% std::_Rb_tree::~_Rb_tree (inline) 2ms 0.01% 77.52% 256ms 1.33% NodeBasedCellPopulation::UpdateMapsAfterRemesh 2ms 0.01% 77.53% 246ms 1.28% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 77.53% 246ms 1.28% boost::numeric::ublas::c_vector::assign (inline) 0 0% 77.53% 245ms 1.28% NodesOnlyMesh::ReMesh 0 0% 77.53% 242ms 1.26% std::_Rb_tree::_Alloc_node::operator() (inline) 5ms 0.026% 77.56% 240ms 1.25% NodesOnlyMesh::UpdateNodeIndices 239ms 1.24% 78.80% 239ms 1.24% __gnu_cxx::__normal_iterator::operator++ (inline) 236ms 1.23% 80.03% 236ms 1.23% Node::CheckForNodeAttributes 2ms 0.01% 80.04% 235ms 1.22% DistributedBoxCollection::GetProcessOwningNode 0 0% 80.04% 227ms 1.18% std::_Rb_tree::_M_drop_node (inline) 1ms 0.0052% 80.05% 220ms 1.14% NodesOnlyMesh::UpdateBoxCollection 91ms 0.47% 80.52% 217ms 1.13% boost::numeric::ublas::vector_inner_prod::apply (inline) 8ms 0.042% 80.56% 212ms 1.10% std::_Rb_tree::_M_emplace_hint_unique 166ms 0.86% 81.43% 197ms 1.03% Node::AddNeighbour 0 0% 81.43% 192ms 1% NodesOnlyMesh::AddNodesToBoxes 0 0% 81.43% 190ms 0.99% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 1ms 0.0052% 81.43% 190ms 0.99% VtkMeshWriter::WriteFiles 88ms 0.46% 81.89% 190ms 0.99% boost::shared_ptr::shared_ptr (inline) 0 0% 81.89% 190ms 0.99% std::set::~set (inline) 2ms 0.01% 81.90% 186ms 0.97% std::__new_allocator::deallocate (inline) 73ms 0.38% 82.28% 183ms 0.95% std::__move_median_to_first (inline) 96ms 0.5% 82.78% 182ms 0.95% _int_malloc 177ms 0.92% 83.70% 177ms 0.92% Node::GetIndex 0 0% 83.70% 171ms 0.89% std::allocator_traits::deallocate (inline) 0 0% 83.70% 169ms 0.88% vtkStreamingDemandDrivenPipeline::Update 0 0% 83.70% 169ms 0.88% vtkXMLWriterBase::Write 0 0% 83.70% 167ms 0.87% vtkDemandDrivenPipeline::ProcessRequest 0 0% 83.70% 166ms 0.86% std::_Rb_tree::_M_put_node (inline) 0 0% 83.70% 165ms 0.86% vtkStreamingDemandDrivenPipeline::ProcessRequest 55ms 0.29% 83.99% 164ms 0.85% __GI___libc_free 0 0% 83.99% 164ms 0.85% vtkCompositeDataPipeline::ExecuteData 0 0% 83.99% 164ms 0.85% vtkDemandDrivenPipeline::ExecuteData 0 0% 83.99% 164ms 0.85% vtkExecutive::CallAlgorithm 1ms 0.0052% 83.99% 164ms 0.85% vtkXMLUnstructuredDataWriter::ProcessRequest 15ms 0.078% 84.07% 163ms 0.85% boost::numeric::ublas::vector_reference::operator() (inline) 1ms 0.0052% 84.07% 162ms 0.84% CellPropertyCollection::HasProperty 0 0% 84.07% 161ms 0.84% Cell::HasCellProperty (inline) 0 0% 84.07% 155ms 0.81% boost::numeric::ublas::vector_binary::operator() (inline) 151ms 0.79% 84.86% 151ms 0.79% [libchaste_mesh.so] 4ms 0.021% 84.88% 150ms 0.78% Cell::ReadyToDivide 23ms 0.12% 85.00% 142ms 0.74% std::__insertion_sort (inline) 0 0% 85.00% 141ms 0.73% Cell::GetCellId 0 0% 85.00% 138ms 0.72% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.00% 138ms 0.72% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 85.00% 136ms 0.71% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 3ms 0.016% 85.02% 131ms 0.68% boost::numeric::ublas::c_vector::operator[] (inline) 124ms 0.65% 85.66% 124ms 0.65% [libchaste_cell_based.so] 0 0% 85.66% 123ms 0.64% NodesOnlyMesh::ResizeBoxCollection 123ms 0.64% 86.30% 123ms 0.64% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 10ms 0.052% 86.35% 122ms 0.63% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 86.35% 120ms 0.62% vtkXMLWriter::WriteBinaryData 0 0% 86.35% 119ms 0.62% vtkXMLWriter::WriteBinaryDataInternal 1ms 0.0052% 86.36% 118ms 0.61% AbstractCellPopulation::SetCellUsingLocationIndex 0 0% 86.36% 118ms 0.61% vtkXMLWriter::WriteBinaryDataBlock 0 0% 86.36% 118ms 0.61% vtkXMLWriter::WriteCompressionBlock 1ms 0.0052% 86.36% 117ms 0.61% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 1ms 0.0052% 86.37% 116ms 0.6% AbstractCellProperty::IsType (inline) 116ms 0.6% 86.97% 116ms 0.6% std::__adjacent_find (inline) 0 0% 86.97% 116ms 0.6% std::__unique (inline) 0 0% 86.97% 116ms 0.6% std::unique (inline) 0 0% 86.97% 115ms 0.6% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 86.97% 114ms 0.59% std::_Rb_tree::_Auto_node::_Auto_node (inline) 97ms 0.5% 87.48% 109ms 0.57% _int_free 104ms 0.54% 88.02% 104ms 0.54% Node::IsDeleted 0 0% 88.02% 104ms 0.54% std::_Rb_tree::clear (inline) 0 0% 88.02% 103ms 0.54% vtkXMLWriter::WritePointsAppendedData 79ms 0.41% 88.43% 102ms 0.53% boost::detail::shared_count::shared_count (inline) 0 0% 88.43% 99ms 0.52% vtkDataCompressor::Compress 1ms 0.0052% 88.44% 98ms 0.51% AbstractCentreBasedCellPopulation::CreateCellPair 1ms 0.0052% 88.44% 98ms 0.51% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 88.44% 97ms 0.5% compress2 0 0% 88.44% 97ms 0.5% vtkZLibDataCompressor::CompressBuffer