File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 21103ms, 88.49% of 23848ms total Dropped 811 nodes (cum <= 119.24ms) flat flat% sum% cum cum% 0 0% 0% 23688ms 99.33% __libc_start_call_main 0 0% 0% 23688ms 99.33% __libc_start_main_impl 0 0% 0% 23688ms 99.33% _start 0 0% 0% 23673ms 99.27% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 23673ms 99.27% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 23673ms 99.27% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 23673ms 99.27% main 0 0% 0% 23634ms 99.10% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 23634ms 99.10% CxxTest::TestRunner::runTest (inline) 0 0% 0% 23633ms 99.10% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0042% 0.0042% 23625ms 99.06% AbstractCellBasedSimulation::Solve 2ms 0.0084% 0.013% 13360ms 56.02% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.013% 9082ms 38.08% AbstractCellBasedSimulation::UpdateCellPopulation 5ms 0.021% 0.034% 8466ms 35.50% ForwardEulerNumericalMethod::UpdateAllNodePositions 14ms 0.059% 0.092% 8291ms 34.77% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.0042% 0.096% 7975ms 33.44% NodeBasedCellPopulation::Update 1283ms 5.38% 5.48% 7547ms 31.65% RepulsionForce::AddForceContribution (partial-inline) 9ms 0.038% 5.51% 5937ms 24.90% DistributedBoxCollection::CalculateInteriorNodePairs 2194ms 9.20% 14.71% 5053ms 21.19% std::_Rb_tree::_M_lower_bound (inline) 0 0% 14.71% 4585ms 19.23% OffLatticeSimulation::ApplyBoundaries 10ms 0.042% 14.76% 4486ms 18.81% NodeAttributes::RemoveDuplicateNeighbours 8ms 0.034% 14.79% 4314ms 18.09% std::__sort (inline) 0 0% 14.79% 4314ms 18.09% std::sort (inline) 187ms 0.78% 15.57% 3860ms 16.19% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 2ms 0.0084% 15.58% 3481ms 14.60% AbstractCellPopulation::Iterator::operator++ (inline) 245ms 1.03% 16.61% 3461ms 14.51% AbstractCellPopulation::Iterator::IsRealCell (inline) 64ms 0.27% 16.88% 3436ms 14.41% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 246ms 1.03% 17.91% 3291ms 13.80% std::_Rb_tree::find (inline) 0 0% 17.91% 3291ms 13.80% std::map::find (inline) 19ms 0.08% 17.99% 2911ms 12.21% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2810ms 11.78% 29.77% 2810ms 11.78% std::_Rb_tree::_S_right (inline) 253ms 1.06% 30.83% 2551ms 10.70% std::map::operator[] (partial-inline) 172ms 0.72% 31.55% 2505ms 10.50% std::__introsort_loop 44ms 0.18% 31.74% 2410ms 10.11% PlaneBoundaryCondition::ImposeBoundaryCondition 29ms 0.12% 31.86% 2385ms 10.00% AbstractCellPopulation::GetLocationIndexUsingCell 158ms 0.66% 32.52% 2339ms 9.81% AbstractMesh::GetNode 47ms 0.2% 32.72% 2321ms 9.73% NodesOnlyMesh::GetNodeOrHaloNode 0 0% 32.72% 2247ms 9.42% std::__unguarded_partition_pivot (inline) 70ms 0.29% 33.01% 2185ms 9.16% NodesOnlyMesh::SolveNodeMapping 12ms 0.05% 33.06% 2174ms 9.12% PlaneBoundaryCondition::VerifyBoundaryCondition 199ms 0.83% 33.90% 2053ms 8.61% DistributedBoxCollection::AddPairsFromBox 0 0% 33.90% 2037ms 8.54% std::_Rb_tree::lower_bound (inline) 0 0% 33.90% 2037ms 8.54% std::map::lower_bound (inline) 1073ms 4.50% 38.40% 2031ms 8.52% std::__unguarded_partition (inline) 1ms 0.0042% 38.40% 1801ms 7.55% std::__final_insertion_sort (inline) 90ms 0.38% 38.78% 1598ms 6.70% std::__unguarded_insertion_sort (inline) 592ms 2.48% 41.26% 1567ms 6.57% std::__unguarded_linear_insert (inline) 19ms 0.08% 41.34% 1540ms 6.46% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 27ms 0.11% 41.45% 1518ms 6.37% AbstractCellPopulation::GetCellUsingLocationIndex 1451ms 6.08% 47.54% 1451ms 6.08% __gnu_cxx::__normal_iterator::operator-- (inline) 42ms 0.18% 47.71% 1257ms 5.27% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 47.71% 1155ms 4.84% NodeBasedCellPopulation::UpdateCellProcessLocation 36ms 0.15% 47.87% 1153ms 4.83% boost::numeric::ublas::vector_assign (inline) 4ms 0.017% 47.88% 1055ms 4.42% DistributedBoxCollection::CalculateBoundaryNodePairs 265ms 1.11% 48.99% 1021ms 4.28% boost::numeric::ublas::indexing_vector_assign 290ms 1.22% 50.21% 940ms 3.94% __dynamic_cast 25ms 0.1% 50.31% 810ms 3.40% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 274ms 1.15% 51.46% 778ms 3.26% NodeAttributes::AddNeighbour 162ms 0.68% 52.14% 772ms 3.24% AbstractMesh::GetVectorFromAtoB 0 0% 52.14% 758ms 3.18% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 338ms 1.42% 53.56% 753ms 3.16% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 53.56% 738ms 3.09% boost::numeric::ublas::norm_2 (inline) 569ms 2.39% 55.95% 738ms 3.09% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 55.95% 738ms 3.09% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 55.95% 736ms 3.09% AbstractCellPopulation::WriteResultsToFiles 31ms 0.13% 56.08% 729ms 3.06% std::_Rb_tree_const_iterator::operator++ (inline) 696ms 2.92% 58.99% 696ms 2.92% std::_Rb_tree_increment 688ms 2.88% 61.88% 688ms 2.88% boost::numeric::ublas::c_vector::operator() 7ms 0.029% 61.91% 662ms 2.78% CellPropertyCollection::GetPropertiesType (inline) 3ms 0.013% 61.92% 646ms 2.71% AbstractCentreBasedCellPopulation::GetDampingConstant 4ms 0.017% 61.94% 628ms 2.63% boost::numeric::ublas::c_vector::operator= (inline) 2ms 0.0084% 61.95% 627ms 2.63% AbstractCellBasedSimulation::DoCellBirth 502ms 2.10% 64.05% 607ms 2.55% std::vector::push_back (inline) 28ms 0.12% 64.17% 606ms 2.54% std::__copy_move::__copy_m (inline) 0 0% 64.17% 606ms 2.54% std::__copy_move_a (inline) 0 0% 64.17% 606ms 2.54% std::__copy_move_a1 (inline) 0 0% 64.17% 606ms 2.54% std::__copy_move_a2 (inline) 0 0% 64.17% 604ms 2.53% std::copy (inline) 593ms 2.49% 66.66% 593ms 2.49% __memcpy_avx_unaligned_erms 254ms 1.07% 67.72% 540ms 2.26% __cxxabiv1::__si_class_type_info::__do_dyncast 93ms 0.39% 68.11% 533ms 2.23% std::__new_allocator::allocate (inline) 0 0% 68.11% 517ms 2.17% std::allocator_traits::allocate (inline) 29ms 0.12% 68.23% 510ms 2.14% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 68.23% 488ms 2.05% NodeBasedCellPopulation::WriteVtkResultsToFile 42ms 0.18% 68.41% 482ms 2.02% boost::detail::shared_count::~shared_count (inline) 0 0% 68.41% 482ms 2.02% boost::shared_ptr::~shared_ptr (inline) 0 0% 68.41% 482ms 2.02% std::_Rb_tree::_M_create_node (inline) 0 0% 68.41% 479ms 2.01% AbstractCellBasedSimulation::DoCellRemoval (inline) 4ms 0.017% 68.43% 475ms 1.99% Cell::GetMutationState 46ms 0.19% 68.62% 468ms 1.96% std::_Rb_tree::_M_copy (inline) 465ms 1.95% 70.57% 465ms 1.95% boost::numeric::ublas::same_impl_ex 6ms 0.025% 70.59% 463ms 1.94% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 437ms 1.83% 72.43% 437ms 1.83% __strcmp_avx2 24ms 0.1% 72.53% 437ms 1.83% operator new 427ms 1.79% 74.32% 434ms 1.82% boost::detail::sp_counted_base::release 0 0% 74.32% 428ms 1.79% std::_Rb_tree::_M_get_node (inline) 2ms 0.0084% 74.32% 423ms 1.77% AbstractCellProperty::IsSubType (inline) 137ms 0.57% 74.90% 420ms 1.76% std::_Rb_tree::_M_clone_node (inline) 4ms 0.017% 74.92% 418ms 1.75% std::set::set (inline) 115ms 0.48% 75.40% 408ms 1.71% __GI___libc_malloc 122ms 0.51% 75.91% 397ms 1.66% std::_Rb_tree::_M_erase 127ms 0.53% 76.44% 382ms 1.60% Node::GetRadius 0 0% 76.44% 337ms 1.41% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 76.44% 334ms 1.40% boost::numeric::ublas::c_vector::assign (inline) 3ms 0.013% 76.46% 330ms 1.38% NodeBasedCellPopulation::UpdateMapsAfterRemesh 313ms 1.31% 77.77% 313ms 1.31% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 29ms 0.12% 77.89% 310ms 1.30% boost::numeric::ublas::vector_binary::size (inline) 36ms 0.15% 78.04% 304ms 1.27% std::_Rb_tree::~_Rb_tree (inline) 0 0% 78.04% 303ms 1.27% NodesOnlyMesh::ReMesh 0 0% 78.04% 299ms 1.25% boost::numeric::ublas::inner_prod (inline) 1ms 0.0042% 78.04% 298ms 1.25% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 16ms 0.067% 78.11% 297ms 1.25% boost::numeric::ublas::vector_scalar_binary::evaluate 1ms 0.0042% 78.12% 292ms 1.22% NodesOnlyMesh::UpdateNodeIndices 285ms 1.20% 79.31% 285ms 1.20% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 79.31% 271ms 1.14% std::_Rb_tree::_M_drop_node (inline) 268ms 1.12% 80.43% 268ms 1.12% Node::CheckForNodeAttributes 0 0% 80.43% 267ms 1.12% NodesOnlyMesh::UpdateBoxCollection 11ms 0.046% 80.48% 261ms 1.09% std::_Rb_tree::_M_emplace_hint_unique 4ms 0.017% 80.50% 246ms 1.03% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 129ms 0.54% 81.04% 246ms 1.03% _int_malloc 6ms 0.025% 81.06% 246ms 1.03% std::__new_allocator::deallocate (inline) 85ms 0.36% 81.42% 240ms 1.01% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 81.42% 233ms 0.98% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 5ms 0.021% 81.44% 230ms 0.96% DistributedBoxCollection::GetProcessOwningNode 0 0% 81.44% 230ms 0.96% VtkMeshWriter::WriteFiles 16ms 0.067% 81.51% 219ms 0.92% Cell::ReadyToDivide 1ms 0.0042% 81.51% 219ms 0.92% CellPropertyCollection::HasProperty 0 0% 81.51% 218ms 0.91% Cell::HasCellProperty (inline) 2ms 0.0084% 81.52% 217ms 0.91% NodesOnlyMesh::AddNodesToBoxes 0 0% 81.52% 216ms 0.91% NodesOnlyMesh::ResizeBoxCollection 11ms 0.046% 81.57% 215ms 0.9% NodesOnlyMesh::IsANodeCloseToDomainBoundary 80ms 0.34% 81.90% 214ms 0.9% __GI___libc_free 0 0% 81.90% 214ms 0.9% std::allocator_traits::deallocate (inline) 0 0% 81.90% 212ms 0.89% std::_Rb_tree::_M_put_node (inline) 82ms 0.34% 82.25% 210ms 0.88% std::__move_median_to_first (inline) 0 0% 82.25% 210ms 0.88% std::set::~set (inline) 27ms 0.11% 82.36% 202ms 0.85% std::__insertion_sort (inline) 1ms 0.0042% 82.36% 202ms 0.85% vtkStreamingDemandDrivenPipeline::Update 0 0% 82.36% 202ms 0.85% vtkXMLWriterBase::Write 0 0% 82.36% 198ms 0.83% vtkDemandDrivenPipeline::ProcessRequest 0 0% 82.36% 197ms 0.83% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 82.36% 196ms 0.82% vtkDemandDrivenPipeline::ExecuteData 0 0% 82.36% 196ms 0.82% vtkExecutive::CallAlgorithm 0 0% 82.36% 195ms 0.82% vtkCompositeDataPipeline::ExecuteData 0 0% 82.36% 194ms 0.81% vtkXMLUnstructuredDataWriter::ProcessRequest 193ms 0.81% 83.17% 193ms 0.81% Node::GetIndex 89ms 0.37% 83.55% 189ms 0.79% boost::shared_ptr::shared_ptr (inline) 174ms 0.73% 84.28% 174ms 0.73% [libchaste_cell_based.so] 1ms 0.0042% 84.28% 169ms 0.71% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 84.28% 168ms 0.7% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 84.28% 168ms 0.7% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 10ms 0.042% 84.32% 163ms 0.68% DistributedBoxCollection::GetIsPeriodicAllDims 0 0% 84.32% 163ms 0.68% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 92ms 0.39% 84.71% 157ms 0.66% Node::AddNeighbour 1ms 0.0042% 84.71% 156ms 0.65% AbstractCellProperty::IsType (inline) 154ms 0.65% 85.36% 154ms 0.65% Node::IsDeleted 12ms 0.05% 85.41% 148ms 0.62% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 85.41% 148ms 0.62% std::_Rb_tree::clear (inline) 0 0% 85.41% 145ms 0.61% std::_Rb_tree::_Auto_node::_Auto_node (inline) 141ms 0.59% 86.00% 144ms 0.6% std::__adjacent_find (inline) 0 0% 86.00% 144ms 0.6% std::__unique (inline) 0 0% 86.00% 144ms 0.6% std::unique (inline) 143ms 0.6% 86.60% 143ms 0.6% boost::shared_ptr::operator-> (inline) 3ms 0.013% 86.61% 138ms 0.58% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 86.61% 138ms 0.58% boost::numeric::ublas::vector_binary::operator() (inline) 3ms 0.013% 86.62% 136ms 0.57% Cell::GetCellId 136ms 0.57% 87.19% 136ms 0.57% [libchaste_mesh.so] 126ms 0.53% 87.72% 134ms 0.56% _int_free 0 0% 87.72% 133ms 0.56% vtkXMLWriter::WriteBinaryData 1ms 0.0042% 87.73% 129ms 0.54% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.73% 128ms 0.54% tbb::detail::r1::parallel_pipeline 0 0% 87.73% 128ms 0.54% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.73% 128ms 0.54% vtkXMLWriter::WriteCompressionBlock 0 0% 87.73% 125ms 0.52% clone3 0 0% 87.73% 125ms 0.52% start_thread 2ms 0.0084% 87.73% 124ms 0.52% AbstractCellPopulation::SetCellUsingLocationIndex 56ms 0.23% 87.97% 124ms 0.52% AbstractCellProperty::IsSame 1ms 0.0042% 87.97% 124ms 0.52% vtkXMLWriter::WritePointsAppendedData 1ms 0.0042% 87.98% 123ms 0.52% tbb::detail::r1::reset 122ms 0.51% 88.49% 122ms 0.51% __ieee754_log_fma