File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 22062ms, 88.65% of 24887ms total Dropped 784 nodes (cum <= 124.44ms) flat flat% sum% cum cum% 0 0% 0% 24755ms 99.47% __libc_start_call_main 0 0% 0% 24755ms 99.47% __libc_start_main_impl 0 0% 0% 24755ms 99.47% _start 0 0% 0% 24737ms 99.40% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 24737ms 99.40% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 24737ms 99.40% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 24737ms 99.40% main 0 0% 0% 24693ms 99.22% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 24693ms 99.22% CxxTest::TestRunner::runTest (inline) 0 0% 0% 24693ms 99.22% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 24684ms 99.18% AbstractCellBasedSimulation::Solve 1ms 0.004% 0.004% 14082ms 56.58% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.004% 9409ms 37.81% AbstractCellBasedSimulation::UpdateCellPopulation 5ms 0.02% 0.024% 9162ms 36.81% ForwardEulerNumericalMethod::UpdateAllNodePositions 21ms 0.084% 0.11% 8962ms 36.01% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.004% 0.11% 8299ms 33.35% NodeBasedCellPopulation::Update 1333ms 5.36% 5.47% 8255ms 33.17% RepulsionForce::AddForceContribution (partial-inline) 6ms 0.024% 5.49% 6185ms 24.85% DistributedBoxCollection::CalculateInteriorNodePairs 2110ms 8.48% 13.97% 5144ms 20.67% std::_Rb_tree::_M_lower_bound (inline) 13ms 0.052% 14.02% 4668ms 18.76% NodeAttributes::RemoveDuplicateNeighbours 1ms 0.004% 14.03% 4555ms 18.30% OffLatticeSimulation::ApplyBoundaries 2ms 0.008% 14.04% 4474ms 17.98% std::__sort (inline) 0 0% 14.04% 4474ms 17.98% std::sort (inline) 212ms 0.85% 14.89% 4157ms 16.70% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 244ms 0.98% 15.87% 3403ms 13.67% std::_Rb_tree::find (inline) 0 0% 15.87% 3402ms 13.67% std::map::find (inline) 75ms 0.3% 16.17% 3348ms 13.45% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 4ms 0.016% 16.19% 3132ms 12.58% AbstractCellPopulation::Iterator::operator++ (inline) 171ms 0.69% 16.87% 3109ms 12.49% AbstractCellPopulation::Iterator::IsRealCell (inline) 3004ms 12.07% 28.94% 3004ms 12.07% std::_Rb_tree::_S_right (inline) 38ms 0.15% 29.10% 2698ms 10.84% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 188ms 0.76% 29.85% 2600ms 10.45% std::__introsort_loop 195ms 0.78% 30.63% 2546ms 10.23% std::map::operator[] (partial-inline) 178ms 0.72% 31.35% 2515ms 10.11% AbstractMesh::GetNode 64ms 0.26% 31.61% 2496ms 10.03% NodesOnlyMesh::GetNodeOrHaloNode 22ms 0.088% 31.70% 2421ms 9.73% PlaneBoundaryCondition::ImposeBoundaryCondition 0 0% 31.70% 2344ms 9.42% std::__unguarded_partition_pivot (inline) 118ms 0.47% 32.17% 2342ms 9.41% NodesOnlyMesh::SolveNodeMapping 43ms 0.17% 32.34% 2247ms 9.03% AbstractCellPopulation::GetLocationIndexUsingCell 145ms 0.58% 32.92% 2147ms 8.63% DistributedBoxCollection::AddPairsFromBox 16ms 0.064% 32.99% 2133ms 8.57% PlaneBoundaryCondition::VerifyBoundaryCondition 972ms 3.91% 36.89% 2070ms 8.32% std::__unguarded_partition (inline) 0 0% 36.89% 2032ms 8.16% std::_Rb_tree::lower_bound (inline) 0 0% 36.89% 2032ms 8.16% std::map::lower_bound (inline) 1ms 0.004% 36.90% 1867ms 7.50% std::__final_insertion_sort (inline) 24ms 0.096% 37.00% 1706ms 6.85% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 25ms 0.1% 37.10% 1671ms 6.71% AbstractCellPopulation::GetCellUsingLocationIndex 111ms 0.45% 37.54% 1654ms 6.65% std::__unguarded_insertion_sort (inline) 564ms 2.27% 39.81% 1599ms 6.43% std::__unguarded_linear_insert (inline) 1496ms 6.01% 45.82% 1496ms 6.01% __gnu_cxx::__normal_iterator::operator-- (inline) 52ms 0.21% 46.03% 1304ms 5.24% boost::numeric::ublas::c_vector::c_vector (partial-inline) 8ms 0.032% 46.06% 1167ms 4.69% boost::numeric::ublas::vector_assign (inline) 0 0% 46.06% 1145ms 4.60% NodeBasedCellPopulation::UpdateCellProcessLocation 6ms 0.024% 46.08% 1116ms 4.48% DistributedBoxCollection::CalculateBoundaryNodePairs 220ms 0.88% 46.97% 1073ms 4.31% boost::numeric::ublas::indexing_vector_assign 13ms 0.052% 47.02% 975ms 3.92% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 295ms 1.19% 48.21% 973ms 3.91% __dynamic_cast 211ms 0.85% 49.05% 912ms 3.66% AbstractMesh::GetVectorFromAtoB 376ms 1.51% 50.56% 846ms 3.40% DistributedBoxCollection::CalculateContainingBox (partial-inline) 5ms 0.02% 50.58% 822ms 3.30% boost::numeric::ublas::c_vector::operator= (inline) 43ms 0.17% 50.76% 801ms 3.22% std::__copy_move::__copy_m (inline) 0 0% 50.76% 801ms 3.22% std::__copy_move_a (inline) 0 0% 50.76% 801ms 3.22% std::__copy_move_a1 (inline) 0 0% 50.76% 801ms 3.22% std::__copy_move_a2 (inline) 0 0% 50.76% 801ms 3.22% std::copy (inline) 0 0% 50.76% 794ms 3.19% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 223ms 0.9% 51.65% 791ms 3.18% NodeAttributes::AddNeighbour 34ms 0.14% 51.79% 777ms 3.12% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 51.79% 776ms 3.12% boost::numeric::ublas::norm_2 (inline) 595ms 2.39% 54.18% 776ms 3.12% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 54.18% 776ms 3.12% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 773ms 3.11% 57.29% 773ms 3.11% __memcpy_avx_unaligned_erms 0 0% 57.29% 749ms 3.01% AbstractCellPopulation::WriteResultsToFiles 722ms 2.90% 60.19% 722ms 2.90% std::_Rb_tree_increment 705ms 2.83% 63.02% 705ms 2.83% boost::numeric::ublas::c_vector::operator() 6ms 0.024% 63.04% 680ms 2.73% CellPropertyCollection::GetPropertiesType (inline) 565ms 2.27% 65.32% 661ms 2.66% std::vector::push_back (inline) 9ms 0.036% 65.35% 626ms 2.52% AbstractCentreBasedCellPopulation::GetDampingConstant 12ms 0.048% 65.40% 624ms 2.51% AbstractCellBasedSimulation::DoCellBirth 37ms 0.15% 65.55% 575ms 2.31% std::_Rb_tree::_Rb_tree (partial-inline) 289ms 1.16% 66.71% 556ms 2.23% __cxxabiv1::__si_class_type_info::__do_dyncast 544ms 2.19% 68.90% 544ms 2.19% boost::numeric::ublas::same_impl_ex 78ms 0.31% 69.21% 539ms 2.17% std::__new_allocator::allocate (inline) 0 0% 69.21% 521ms 2.09% std::allocator_traits::allocate (inline) 54ms 0.22% 69.43% 519ms 2.09% std::_Rb_tree::_M_copy (inline) 0 0% 69.43% 513ms 2.06% std::_Rb_tree::_M_create_node (inline) 0 0% 69.43% 504ms 2.03% NodeBasedCellPopulation::WriteVtkResultsToFile 44ms 0.18% 69.60% 488ms 1.96% boost::detail::shared_count::~shared_count (inline) 0 0% 69.60% 488ms 1.96% boost::shared_ptr::~shared_ptr (inline) 0 0% 69.60% 482ms 1.94% AbstractCellBasedSimulation::DoCellRemoval (inline) 6ms 0.024% 69.63% 474ms 1.90% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 3ms 0.012% 69.64% 462ms 1.86% Cell::GetMutationState 24ms 0.096% 69.74% 458ms 1.84% operator new 165ms 0.66% 70.40% 457ms 1.84% std::_Rb_tree::_M_clone_node (inline) 4ms 0.016% 70.41% 456ms 1.83% std::set::set (inline) 0 0% 70.41% 455ms 1.83% std::_Rb_tree::_M_get_node (inline) 0 0% 70.41% 433ms 1.74% AbstractCellProperty::IsSubType (inline) 413ms 1.66% 72.07% 426ms 1.71% boost::detail::sp_counted_base::release 424ms 1.70% 73.78% 424ms 1.70% __strcmp_avx2 116ms 0.47% 74.24% 423ms 1.70% __GI___libc_malloc 106ms 0.43% 74.67% 411ms 1.65% std::_Rb_tree::_M_erase 98ms 0.39% 75.06% 389ms 1.56% boost::numeric::ublas::vector_binary::size (inline) 384ms 1.54% 76.61% 384ms 1.54% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 93ms 0.37% 76.98% 368ms 1.48% Node::GetRadius 0 0% 76.98% 346ms 1.39% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 76.98% 341ms 1.37% boost::numeric::ublas::inner_prod (inline) 0 0% 76.98% 340ms 1.37% NodesOnlyMesh::ReMesh 1ms 0.004% 76.98% 339ms 1.36% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 18ms 0.072% 77.06% 338ms 1.36% boost::numeric::ublas::vector_scalar_binary::evaluate 2ms 0.008% 77.06% 334ms 1.34% NodesOnlyMesh::UpdateNodeIndices 45ms 0.18% 77.25% 328ms 1.32% std::_Rb_tree::~_Rb_tree (inline) 0 0% 77.25% 325ms 1.31% boost::numeric::ublas::c_vector::assign (inline) 15ms 0.06% 77.31% 318ms 1.28% std::_Rb_tree::_M_emplace_hint_unique 4ms 0.016% 77.32% 315ms 1.27% NodeBasedCellPopulation::UpdateMapsAfterRemesh 2ms 0.008% 77.33% 306ms 1.23% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 77.33% 303ms 1.22% std::_Rb_tree::_M_drop_node (inline) 295ms 1.19% 78.51% 295ms 1.19% __gnu_cxx::__normal_iterator::operator++ (inline) 6ms 0.024% 78.54% 292ms 1.17% DistributedBoxCollection::GetProcessOwningNode 1ms 0.004% 78.54% 284ms 1.14% NodesOnlyMesh::UpdateBoxCollection 280ms 1.13% 79.67% 280ms 1.13% Node::CheckForNodeAttributes 120ms 0.48% 80.15% 276ms 1.11% boost::numeric::ublas::vector_inner_prod::apply (inline) 103ms 0.41% 80.56% 270ms 1.08% std::__move_median_to_first (inline) 227ms 0.91% 81.48% 259ms 1.04% Node::AddNeighbour 127ms 0.51% 81.99% 258ms 1.04% boost::shared_ptr::shared_ptr (inline) 5ms 0.02% 82.01% 252ms 1.01% std::__new_allocator::deallocate (inline) 0 0% 82.01% 248ms 1% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 140ms 0.56% 82.57% 248ms 1% _int_malloc 3ms 0.012% 82.58% 246ms 0.99% CellPropertyCollection::HasProperty 0 0% 82.58% 245ms 0.98% Cell::HasCellProperty (inline) 0 0% 82.58% 245ms 0.98% VtkMeshWriter::WriteFiles 4ms 0.016% 82.60% 242ms 0.97% Cell::ReadyToDivide 0 0% 82.60% 233ms 0.94% std::allocator_traits::deallocate (inline) 0 0% 82.60% 231ms 0.93% std::_Rb_tree::_M_put_node (inline) 2ms 0.008% 82.61% 227ms 0.91% NodesOnlyMesh::AddNodesToBoxes 0 0% 82.61% 225ms 0.9% std::set::~set (inline) 223ms 0.9% 83.50% 223ms 0.9% [libchaste_mesh.so] 67ms 0.27% 83.77% 216ms 0.87% __GI___libc_free 215ms 0.86% 84.63% 215ms 0.86% Node::GetIndex 0 0% 84.63% 214ms 0.86% vtkStreamingDemandDrivenPipeline::Update 0 0% 84.63% 214ms 0.86% vtkXMLWriterBase::Write 0 0% 84.63% 213ms 0.86% vtkDemandDrivenPipeline::ProcessRequest 0 0% 84.63% 212ms 0.85% boost::numeric::ublas::vector_binary::operator() (inline) 30ms 0.12% 84.76% 212ms 0.85% std::__insertion_sort (inline) 0 0% 84.76% 210ms 0.84% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 84.76% 209ms 0.84% vtkDemandDrivenPipeline::ExecuteData 0 0% 84.76% 208ms 0.84% vtkCompositeDataPipeline::ExecuteData 0 0% 84.76% 207ms 0.83% vtkExecutive::CallAlgorithm 0 0% 84.76% 207ms 0.83% vtkXMLUnstructuredDataWriter::ProcessRequest 11ms 0.044% 84.80% 203ms 0.82% boost::numeric::ublas::vector_reference::operator() (inline) 181ms 0.73% 85.53% 181ms 0.73% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 177ms 0.71% 86.24% 177ms 0.71% [libchaste_cell_based.so] 0 0% 86.24% 176ms 0.71% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 86.24% 176ms 0.71% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 86.24% 174ms 0.7% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 86.24% 167ms 0.67% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1ms 0.004% 86.24% 163ms 0.65% AbstractCellProperty::IsType (inline) 158ms 0.63% 86.88% 158ms 0.63% std::__adjacent_find (inline) 0 0% 86.88% 158ms 0.63% std::__unique (inline) 0 0% 86.88% 158ms 0.63% std::unique (inline) 0 0% 86.88% 150ms 0.6% vtkXMLWriter::WriteBinaryData 140ms 0.56% 87.44% 149ms 0.6% _int_free 5ms 0.02% 87.46% 149ms 0.6% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 87.46% 147ms 0.59% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 87.46% 146ms 0.59% std::_Rb_tree::clear (inline) 0 0% 87.46% 146ms 0.59% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.46% 146ms 0.59% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.46% 146ms 0.59% vtkXMLWriter::WriteCompressionBlock 0 0% 87.46% 145ms 0.58% NodesOnlyMesh::ResizeBoxCollection 0 0% 87.46% 144ms 0.58% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 18ms 0.072% 87.53% 144ms 0.58% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 87.53% 142ms 0.57% Cell::GetCellId 1ms 0.004% 87.54% 140ms 0.56% AbstractNumericalMethod::SafeNodePositionUpdate 1ms 0.004% 87.54% 136ms 0.55% AbstractCellPopulation::SetCellUsingLocationIndex 50ms 0.2% 87.74% 133ms 0.53% AbstractCellProperty::IsSame 131ms 0.53% 88.27% 131ms 0.53% __ieee754_log_fma 94ms 0.38% 88.64% 131ms 0.53% boost::detail::shared_count::shared_count (inline) 1ms 0.004% 88.65% 131ms 0.53% vtkXMLWriter::WritePointsAppendedData