File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20683ms, 89.12% of 23207ms total Dropped 739 nodes (cum <= 116.03ms) flat flat% sum% cum cum% 0 0% 0% 23057ms 99.35% __libc_start_call_main 0 0% 0% 23057ms 99.35% __libc_start_main_impl 0 0% 0% 23057ms 99.35% _start 0 0% 0% 23042ms 99.29% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 23042ms 99.29% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 23042ms 99.29% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 23042ms 99.29% main 0 0% 0% 23008ms 99.14% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 23008ms 99.14% CxxTest::TestRunner::runTest (inline) 0 0% 0% 23007ms 99.14% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 23000ms 99.11% AbstractCellBasedSimulation::Solve 1ms 0.0043% 0.0043% 13082ms 56.37% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0043% 8741ms 37.67% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0086% 0.013% 8253ms 35.56% ForwardEulerNumericalMethod::UpdateAllNodePositions 12ms 0.052% 0.065% 8067ms 34.76% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.065% 7713ms 33.24% NodeBasedCellPopulation::Update 1238ms 5.33% 5.40% 7444ms 32.08% RepulsionForce::AddForceContribution (partial-inline) 10ms 0.043% 5.44% 5597ms 24.12% DistributedBoxCollection::CalculateInteriorNodePairs 2035ms 8.77% 14.21% 4879ms 21.02% std::_Rb_tree::_M_lower_bound (inline) 17ms 0.073% 14.28% 4540ms 19.56% NodeAttributes::RemoveDuplicateNeighbours 0 0% 14.28% 4533ms 19.53% OffLatticeSimulation::ApplyBoundaries 6ms 0.026% 14.31% 4220ms 18.18% std::__sort (inline) 0 0% 14.31% 4220ms 18.18% std::sort (inline) 195ms 0.84% 15.15% 3722ms 16.04% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 4ms 0.017% 15.17% 3396ms 14.63% AbstractCellPopulation::Iterator::operator++ (inline) 166ms 0.72% 15.88% 3372ms 14.53% AbstractCellPopulation::Iterator::IsRealCell (inline) 66ms 0.28% 16.17% 3364ms 14.50% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 253ms 1.09% 17.26% 3170ms 13.66% std::_Rb_tree::find (inline) 0 0% 17.26% 3170ms 13.66% std::map::find (inline) 20ms 0.086% 17.34% 2894ms 12.47% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2799ms 12.06% 29.40% 2799ms 12.06% std::_Rb_tree::_S_right (inline) 256ms 1.10% 30.51% 2511ms 10.82% std::map::operator[] (partial-inline) 182ms 0.78% 31.29% 2400ms 10.34% std::__introsort_loop 25ms 0.11% 31.40% 2378ms 10.25% PlaneBoundaryCondition::ImposeBoundaryCondition 30ms 0.13% 31.53% 2335ms 10.06% AbstractCellPopulation::GetLocationIndexUsingCell 133ms 0.57% 32.10% 2210ms 9.52% AbstractMesh::GetNode 50ms 0.22% 32.32% 2192ms 9.45% NodesOnlyMesh::GetNodeOrHaloNode 21ms 0.09% 32.41% 2155ms 9.29% PlaneBoundaryCondition::VerifyBoundaryCondition 1ms 0.0043% 32.41% 2127ms 9.17% std::__unguarded_partition_pivot (inline) 88ms 0.38% 32.79% 2077ms 8.95% NodesOnlyMesh::SolveNodeMapping 0 0% 32.79% 1991ms 8.58% std::_Rb_tree::lower_bound (inline) 0 0% 32.79% 1991ms 8.58% std::map::lower_bound (inline) 1002ms 4.32% 37.11% 1919ms 8.27% std::__unguarded_partition (inline) 0 0% 37.11% 1814ms 7.82% std::__final_insertion_sort (inline) 148ms 0.64% 37.75% 1790ms 7.71% DistributedBoxCollection::AddPairsFromBox 98ms 0.42% 38.17% 1645ms 7.09% std::__unguarded_insertion_sort (inline) 535ms 2.31% 40.47% 1568ms 6.76% std::__unguarded_linear_insert (inline) 23ms 0.099% 40.57% 1549ms 6.67% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 27ms 0.12% 40.69% 1520ms 6.55% AbstractCellPopulation::GetCellUsingLocationIndex 1426ms 6.14% 46.84% 1426ms 6.14% __gnu_cxx::__normal_iterator::operator-- (inline) 72ms 0.31% 47.15% 1292ms 5.57% boost::numeric::ublas::c_vector::c_vector (partial-inline) 9ms 0.039% 47.18% 1183ms 5.10% DistributedBoxCollection::CalculateBoundaryNodePairs 3ms 0.013% 47.20% 1126ms 4.85% NodeBasedCellPopulation::UpdateCellProcessLocation 35ms 0.15% 47.35% 1113ms 4.80% boost::numeric::ublas::vector_assign (inline) 257ms 1.11% 48.46% 1015ms 4.37% boost::numeric::ublas::indexing_vector_assign 233ms 1.00% 49.46% 918ms 3.96% __dynamic_cast 20ms 0.086% 49.55% 808ms 3.48% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 159ms 0.69% 50.23% 792ms 3.41% AbstractMesh::GetVectorFromAtoB 351ms 1.51% 51.74% 752ms 3.24% DistributedBoxCollection::CalculateContainingBox (partial-inline) 216ms 0.93% 52.67% 749ms 3.23% NodeAttributes::AddNeighbour 0 0% 52.67% 731ms 3.15% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 52.67% 724ms 3.12% AbstractCellPopulation::WriteResultsToFiles 0 0% 52.67% 720ms 3.10% boost::numeric::ublas::norm_2 (inline) 551ms 2.37% 55.05% 720ms 3.10% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 55.05% 720ms 3.10% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 681ms 2.93% 57.98% 681ms 2.93% boost::numeric::ublas::c_vector::operator() 5ms 0.022% 58.00% 662ms 2.85% boost::numeric::ublas::c_vector::operator= (inline) 38ms 0.16% 58.17% 637ms 2.74% std::__copy_move::__copy_m (inline) 0 0% 58.17% 637ms 2.74% std::__copy_move_a (inline) 0 0% 58.17% 637ms 2.74% std::__copy_move_a1 (inline) 0 0% 58.17% 637ms 2.74% std::__copy_move_a2 (inline) 0 0% 58.17% 637ms 2.74% std::copy (inline) 614ms 2.65% 60.81% 614ms 2.65% __memcpy_avx_unaligned_erms 532ms 2.29% 63.11% 591ms 2.55% std::vector::push_back (inline) 2ms 0.0086% 63.11% 582ms 2.51% AbstractCellBasedSimulation::DoCellBirth 297ms 1.28% 64.39% 577ms 2.49% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 64.39% 559ms 2.41% AbstractCentreBasedCellPopulation::GetDampingConstant 7ms 0.03% 64.42% 532ms 2.29% CellPropertyCollection::GetPropertiesType (inline) 45ms 0.19% 64.62% 532ms 2.29% boost::detail::shared_count::~shared_count (inline) 0 0% 64.62% 532ms 2.29% boost::shared_ptr::~shared_ptr (inline) 519ms 2.24% 66.85% 519ms 2.24% boost::numeric::ublas::same_impl_ex 67ms 0.29% 67.14% 519ms 2.24% std::__new_allocator::allocate (inline) 35ms 0.15% 67.29% 503ms 2.17% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 67.29% 501ms 2.16% std::allocator_traits::allocate (inline) 0 0% 67.29% 478ms 2.06% NodeBasedCellPopulation::WriteVtkResultsToFile 463ms 2.00% 69.29% 471ms 2.03% boost::detail::sp_counted_base::release 0 0% 69.29% 461ms 1.99% std::_Rb_tree::_M_create_node (inline) 461ms 1.99% 71.28% 461ms 1.99% std::_Rb_tree_increment 31ms 0.13% 71.41% 449ms 1.93% operator new 446ms 1.92% 73.33% 446ms 1.92% __strcmp_avx2 0 0% 73.33% 444ms 1.91% AbstractCellBasedSimulation::DoCellRemoval (inline) 18ms 0.078% 73.41% 439ms 1.89% std::_Rb_tree::_Rb_tree (partial-inline) 6ms 0.026% 73.43% 431ms 1.86% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 160ms 0.69% 74.12% 426ms 1.84% Node::GetRadius 0 0% 74.12% 425ms 1.83% std::_Rb_tree::_M_get_node (inline) 129ms 0.56% 74.68% 412ms 1.78% __GI___libc_malloc 41ms 0.18% 74.86% 408ms 1.76% std::_Rb_tree::_M_copy (inline) 4ms 0.017% 74.87% 398ms 1.71% AbstractCellProperty::IsSubType (inline) 121ms 0.52% 75.40% 390ms 1.68% std::_Rb_tree::_M_erase 1ms 0.0043% 75.40% 372ms 1.60% Cell::GetMutationState 104ms 0.45% 75.85% 366ms 1.58% std::_Rb_tree::_M_clone_node (inline) 0 0% 75.85% 352ms 1.52% boost::numeric::ublas::c_vector::assign (inline) 0 0% 75.85% 347ms 1.50% std::set::set (inline) 22ms 0.095% 75.94% 342ms 1.47% boost::numeric::ublas::vector_binary::size (inline) 7ms 0.03% 75.97% 322ms 1.39% NodeBasedCellPopulation::UpdateMapsAfterRemesh 319ms 1.37% 77.35% 319ms 1.37% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 77.35% 315ms 1.36% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 77.35% 314ms 1.35% boost::numeric::ublas::inner_prod (inline) 6ms 0.026% 77.37% 313ms 1.35% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 31ms 0.13% 77.51% 312ms 1.34% std::_Rb_tree::~_Rb_tree (inline) 17ms 0.073% 77.58% 307ms 1.32% boost::numeric::ublas::vector_scalar_binary::evaluate 1ms 0.0043% 77.58% 279ms 1.20% NodesOnlyMesh::ReMesh 277ms 1.19% 78.78% 278ms 1.20% std::__adjacent_find (inline) 0 0% 78.78% 278ms 1.20% std::__unique (inline) 0 0% 78.78% 278ms 1.20% std::unique (inline) 276ms 1.19% 79.97% 276ms 1.19% Node::CheckForNodeAttributes 2ms 0.0086% 79.98% 267ms 1.15% NodesOnlyMesh::UpdateNodeIndices 3ms 0.013% 79.99% 265ms 1.14% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 10ms 0.043% 80.03% 264ms 1.14% std::_Rb_tree::_M_emplace_hint_unique 0 0% 80.03% 260ms 1.12% std::_Rb_tree::_M_drop_node (inline) 254ms 1.09% 81.13% 254ms 1.09% __gnu_cxx::__normal_iterator::operator++ (inline) 5ms 0.022% 81.15% 252ms 1.09% DistributedBoxCollection::GetProcessOwningNode 0 0% 81.15% 251ms 1.08% NodesOnlyMesh::UpdateBoxCollection 91ms 0.39% 81.54% 245ms 1.06% boost::numeric::ublas::vector_inner_prod::apply (inline) 144ms 0.62% 82.16% 239ms 1.03% _int_malloc 0 0% 82.16% 237ms 1.02% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 82.16% 234ms 1.01% VtkMeshWriter::WriteFiles 0 0% 82.16% 220ms 0.95% std::set::~set (inline) 0 0% 82.16% 214ms 0.92% NodesOnlyMesh::AddNodesToBoxes 0 0% 82.16% 211ms 0.91% Cell::HasCellProperty (inline) 5ms 0.022% 82.18% 211ms 0.91% CellPropertyCollection::HasProperty 0 0% 82.18% 208ms 0.9% NodesOnlyMesh::ResizeBoxCollection 2ms 0.0086% 82.19% 208ms 0.9% std::__new_allocator::deallocate (inline) 7ms 0.03% 82.22% 207ms 0.89% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 82.22% 206ms 0.89% vtkStreamingDemandDrivenPipeline::Update 0 0% 82.22% 206ms 0.89% vtkXMLWriterBase::Write 0 0% 82.22% 205ms 0.88% vtkDemandDrivenPipeline::ProcessRequest 0 0% 82.22% 205ms 0.88% vtkExecutive::CallAlgorithm 0 0% 82.22% 205ms 0.88% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 82.22% 204ms 0.88% vtkCompositeDataPipeline::ExecuteData 0 0% 82.22% 204ms 0.88% vtkDemandDrivenPipeline::ExecuteData 0 0% 82.22% 204ms 0.88% vtkXMLUnstructuredDataWriter::ProcessRequest 111ms 0.48% 82.70% 202ms 0.87% std::__move_median_to_first (inline) 93ms 0.4% 83.10% 191ms 0.82% boost::shared_ptr::shared_ptr (inline) 0 0% 83.10% 190ms 0.82% std::allocator_traits::deallocate (inline) 189ms 0.81% 83.91% 189ms 0.81% Node::GetIndex 0 0% 83.91% 189ms 0.81% std::_Rb_tree::_M_put_node (inline) 3ms 0.013% 83.93% 185ms 0.8% AbstractCellProperty::IsType (inline) 5ms 0.022% 83.95% 185ms 0.8% Cell::ReadyToDivide 69ms 0.3% 84.25% 183ms 0.79% Node::AddNeighbour 180ms 0.78% 85.02% 180ms 0.78% [libchaste_cell_based.so] 60ms 0.26% 85.28% 179ms 0.77% __GI___libc_free 0 0% 85.28% 170ms 0.73% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.28% 170ms 0.73% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 23ms 0.099% 85.38% 169ms 0.73% std::__insertion_sort (inline) 163ms 0.7% 86.08% 163ms 0.7% Node::IsDeleted 0 0% 86.08% 162ms 0.7% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 86.08% 160ms 0.69% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 49ms 0.21% 86.29% 148ms 0.64% AbstractCellProperty::IsSame 0 0% 86.29% 146ms 0.63% std::_Rb_tree::_Auto_node::_Auto_node (inline) 18ms 0.078% 86.37% 145ms 0.62% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 86.37% 141ms 0.61% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 139ms 0.6% 86.97% 139ms 0.6% [libchaste_mesh.so] 0 0% 86.97% 137ms 0.59% vtkXMLWriter::WriteBinaryData 8ms 0.034% 87.00% 135ms 0.58% DistributedBoxCollection::GetIsPeriodicAllDims 2ms 0.0086% 87.01% 134ms 0.58% AbstractNumericalMethod::SafeNodePositionUpdate 5ms 0.022% 87.03% 134ms 0.58% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 87.03% 132ms 0.57% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.03% 132ms 0.57% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.03% 132ms 0.57% vtkXMLWriter::WriteCompressionBlock 129ms 0.56% 87.59% 129ms 0.56% boost::shared_ptr::operator-> (inline) 0 0% 87.59% 129ms 0.56% std::_Rb_tree::clear (inline) 2ms 0.0086% 87.60% 127ms 0.55% AbstractCellPopulation::SetCellUsingLocationIndex 126ms 0.54% 88.14% 126ms 0.54% Node::ConstructNodeAttributes (inline) 0 0% 88.14% 125ms 0.54% vtkXMLWriter::WritePointsAppendedData 0 0% 88.14% 124ms 0.53% boost::numeric::ublas::vector_binary::operator() (inline) 111ms 0.48% 88.62% 119ms 0.51% _int_free 0 0% 88.62% 118ms 0.51% tbb::detail::r1::parallel_pipeline 117ms 0.5% 89.12% 117ms 0.5% __ieee754_log_fma