File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20846ms, 89.90% of 23187ms total Dropped 726 nodes (cum <= 115.94ms) flat flat% sum% cum cum% 0 0% 0% 23044ms 99.38% __libc_start_call_main 0 0% 0% 23044ms 99.38% __libc_start_main_impl 0 0% 0% 23044ms 99.38% _start 0 0% 0% 23029ms 99.32% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 23029ms 99.32% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 23029ms 99.32% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 23029ms 99.32% main 0 0% 0% 22987ms 99.14% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 22987ms 99.14% CxxTest::TestRunner::runTest (inline) 0 0% 0% 22987ms 99.14% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0043% 0.0043% 22979ms 99.10% AbstractCellBasedSimulation::Solve 2ms 0.0086% 0.013% 13107ms 56.53% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.013% 8681ms 37.44% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0043% 0.017% 8327ms 35.91% ForwardEulerNumericalMethod::UpdateAllNodePositions 7ms 0.03% 0.047% 8142ms 35.11% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.047% 7659ms 33.03% NodeBasedCellPopulation::Update 1233ms 5.32% 5.37% 7536ms 32.50% RepulsionForce::AddForceContribution (partial-inline) 8ms 0.035% 5.40% 5654ms 24.38% DistributedBoxCollection::CalculateInteriorNodePairs 1970ms 8.50% 13.90% 4810ms 20.74% std::_Rb_tree::_M_lower_bound (inline) 0 0% 13.90% 4511ms 19.45% OffLatticeSimulation::ApplyBoundaries 21ms 0.091% 13.99% 4442ms 19.16% NodeAttributes::RemoveDuplicateNeighbours 4ms 0.017% 14.00% 4273ms 18.43% std::__sort (inline) 0 0% 14.00% 4273ms 18.43% std::sort (inline) 177ms 0.76% 14.77% 3808ms 16.42% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 3ms 0.013% 14.78% 3522ms 15.19% AbstractCellPopulation::Iterator::operator++ (inline) 193ms 0.83% 15.61% 3498ms 15.09% AbstractCellPopulation::Iterator::IsRealCell (inline) 73ms 0.31% 15.93% 3334ms 14.38% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 213ms 0.92% 16.85% 3150ms 13.59% std::_Rb_tree::find (inline) 0 0% 16.85% 3148ms 13.58% std::map::find (inline) 22ms 0.095% 16.94% 2950ms 12.72% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2804ms 12.09% 29.03% 2804ms 12.09% std::_Rb_tree::_S_right (inline) 184ms 0.79% 29.83% 2486ms 10.72% std::__introsort_loop 223ms 0.96% 30.79% 2398ms 10.34% std::map::operator[] (partial-inline) 31ms 0.13% 30.92% 2331ms 10.05% PlaneBoundaryCondition::ImposeBoundaryCondition 145ms 0.63% 31.55% 2271ms 9.79% AbstractMesh::GetNode 39ms 0.17% 31.72% 2233ms 9.63% NodesOnlyMesh::GetNodeOrHaloNode 2ms 0.0086% 31.72% 2224ms 9.59% std::__unguarded_partition_pivot (inline) 17ms 0.073% 31.80% 2180ms 9.40% PlaneBoundaryCondition::VerifyBoundaryCondition 31ms 0.13% 31.93% 2142ms 9.24% AbstractCellPopulation::GetLocationIndexUsingCell 74ms 0.32% 32.25% 2131ms 9.19% NodesOnlyMesh::SolveNodeMapping 1040ms 4.49% 36.74% 1993ms 8.60% std::__unguarded_partition (inline) 0 0% 36.74% 1900ms 8.19% std::_Rb_tree::lower_bound (inline) 0 0% 36.74% 1900ms 8.19% std::map::lower_bound (inline) 147ms 0.63% 37.37% 1793ms 7.73% DistributedBoxCollection::AddPairsFromBox 2ms 0.0086% 37.38% 1780ms 7.68% std::__final_insertion_sort (inline) 80ms 0.35% 37.72% 1578ms 6.81% std::__unguarded_insertion_sort (inline) 19ms 0.082% 37.81% 1576ms 6.80% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 558ms 2.41% 40.21% 1557ms 6.71% std::__unguarded_linear_insert (inline) 38ms 0.16% 40.38% 1550ms 6.68% AbstractCellPopulation::GetCellUsingLocationIndex 1437ms 6.20% 46.57% 1437ms 6.20% __gnu_cxx::__normal_iterator::operator-- (inline) 47ms 0.2% 46.78% 1250ms 5.39% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 46.78% 1146ms 4.94% NodeBasedCellPopulation::UpdateCellProcessLocation 39ms 0.17% 46.94% 1145ms 4.94% boost::numeric::ublas::vector_assign (inline) 9ms 0.039% 46.98% 1067ms 4.60% DistributedBoxCollection::CalculateBoundaryNodePairs 300ms 1.29% 48.28% 1038ms 4.48% boost::numeric::ublas::indexing_vector_assign 259ms 1.12% 49.39% 886ms 3.82% __dynamic_cast 168ms 0.72% 50.12% 815ms 3.51% AbstractMesh::GetVectorFromAtoB 360ms 1.55% 51.67% 794ms 3.42% DistributedBoxCollection::CalculateContainingBox (partial-inline) 18ms 0.078% 51.75% 781ms 3.37% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 165ms 0.71% 52.46% 721ms 3.11% NodeAttributes::AddNeighbour 0 0% 52.46% 709ms 3.06% AbstractCellPopulation::WriteResultsToFiles 0 0% 52.46% 706ms 3.04% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 52.46% 697ms 3.01% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 52.46% 696ms 3.00% boost::numeric::ublas::norm_2 (inline) 533ms 2.30% 54.76% 696ms 3.00% boost::numeric::ublas::vector_norm_2::apply (inline) 677ms 2.92% 57.68% 677ms 2.92% boost::numeric::ublas::c_vector::operator() 8ms 0.035% 57.71% 645ms 2.78% boost::numeric::ublas::c_vector::operator= (inline) 27ms 0.12% 57.83% 622ms 2.68% std::__copy_move::__copy_m (inline) 0 0% 57.83% 622ms 2.68% std::__copy_move_a (inline) 0 0% 57.83% 622ms 2.68% std::__copy_move_a1 (inline) 0 0% 57.83% 622ms 2.68% std::__copy_move_a2 (inline) 0 0% 57.83% 622ms 2.68% std::copy (inline) 618ms 2.67% 60.50% 618ms 2.67% __memcpy_avx_unaligned_erms 556ms 2.40% 62.89% 609ms 2.63% std::vector::push_back (inline) 1ms 0.0043% 62.90% 592ms 2.55% AbstractCellBasedSimulation::DoCellBirth 74ms 0.32% 63.22% 548ms 2.36% std::__new_allocator::allocate (inline) 7ms 0.03% 63.25% 545ms 2.35% AbstractCentreBasedCellPopulation::GetDampingConstant 45ms 0.19% 63.44% 543ms 2.34% boost::detail::shared_count::~shared_count (inline) 0 0% 63.44% 543ms 2.34% boost::shared_ptr::~shared_ptr (inline) 0 0% 63.44% 525ms 2.26% std::allocator_traits::allocate (inline) 4ms 0.017% 63.46% 516ms 2.23% CellPropertyCollection::GetPropertiesType (inline) 247ms 1.07% 64.52% 515ms 2.22% __cxxabiv1::__si_class_type_info::__do_dyncast 505ms 2.18% 66.70% 505ms 2.18% boost::numeric::ublas::same_impl_ex 33ms 0.14% 66.84% 504ms 2.17% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 66.84% 490ms 2.11% std::_Rb_tree::_M_create_node (inline) 481ms 2.07% 68.92% 488ms 2.10% boost::detail::sp_counted_base::release 2ms 0.0086% 68.93% 473ms 2.04% NodeBasedCellPopulation::WriteVtkResultsToFile 34ms 0.15% 69.07% 472ms 2.04% operator new 462ms 1.99% 71.07% 462ms 1.99% std::_Rb_tree_increment 14ms 0.06% 71.13% 451ms 1.95% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 71.13% 436ms 1.88% std::_Rb_tree::_M_get_node (inline) 434ms 1.87% 73.00% 434ms 1.87% __strcmp_avx2 129ms 0.56% 73.55% 433ms 1.87% __GI___libc_malloc 0 0% 73.55% 430ms 1.85% AbstractCellBasedSimulation::DoCellRemoval (inline) 39ms 0.17% 73.72% 427ms 1.84% std::_Rb_tree::_M_copy (inline) 4ms 0.017% 73.74% 414ms 1.79% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 127ms 0.55% 74.29% 401ms 1.73% Node::GetRadius 122ms 0.53% 74.81% 387ms 1.67% std::_Rb_tree::_M_clone_node (inline) 111ms 0.48% 75.29% 385ms 1.66% std::_Rb_tree::_M_erase 3ms 0.013% 75.31% 381ms 1.64% std::set::set (inline) 3ms 0.013% 75.32% 367ms 1.58% AbstractCellProperty::IsSubType (inline) 7ms 0.03% 75.35% 357ms 1.54% Cell::GetMutationState 24ms 0.1% 75.45% 339ms 1.46% boost::numeric::ublas::vector_binary::size (inline) 0 0% 75.45% 331ms 1.43% std::_Rb_tree::_Alloc_node::operator() (inline) 323ms 1.39% 76.84% 323ms 1.39% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 76.84% 322ms 1.39% boost::numeric::ublas::inner_prod (inline) 19ms 0.082% 76.93% 320ms 1.38% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 76.93% 320ms 1.38% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 5ms 0.022% 76.95% 312ms 1.35% NodeBasedCellPopulation::UpdateMapsAfterRemesh 31ms 0.13% 77.08% 303ms 1.31% std::_Rb_tree::~_Rb_tree (inline) 0 0% 77.08% 297ms 1.28% boost::numeric::ublas::c_vector::assign (inline) 0 0% 77.08% 293ms 1.26% NodesOnlyMesh::ReMesh 289ms 1.25% 78.33% 289ms 1.25% __gnu_cxx::__normal_iterator::operator++ (inline) 287ms 1.24% 79.57% 287ms 1.24% Node::CheckForNodeAttributes 3ms 0.013% 79.58% 287ms 1.24% NodesOnlyMesh::UpdateNodeIndices 8ms 0.035% 79.61% 281ms 1.21% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 9ms 0.039% 79.65% 275ms 1.19% std::_Rb_tree::_M_emplace_hint_unique 0 0% 79.65% 264ms 1.14% std::_Rb_tree::_M_drop_node (inline) 0 0% 79.65% 261ms 1.13% NodesOnlyMesh::UpdateBoxCollection 5ms 0.022% 79.67% 260ms 1.12% DistributedBoxCollection::GetProcessOwningNode 101ms 0.44% 80.11% 253ms 1.09% boost::numeric::ublas::vector_inner_prod::apply (inline) 149ms 0.64% 80.75% 238ms 1.03% _int_malloc 0 0% 80.75% 229ms 0.99% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 80.75% 228ms 0.98% VtkMeshWriter::WriteFiles 0 0% 80.75% 228ms 0.98% std::set::~set (inline) 97ms 0.42% 81.17% 226ms 0.97% std::__move_median_to_first (inline) 3ms 0.013% 81.18% 224ms 0.97% std::__new_allocator::deallocate (inline) 0 0% 81.18% 222ms 0.96% NodesOnlyMesh::AddNodesToBoxes 214ms 0.92% 82.11% 214ms 0.92% Node::IsDeleted 117ms 0.5% 82.61% 212ms 0.91% boost::shared_ptr::shared_ptr (inline) 210ms 0.91% 83.52% 210ms 0.91% Node::GetIndex 66ms 0.28% 83.80% 206ms 0.89% __GI___libc_free 0 0% 83.80% 202ms 0.87% NodesOnlyMesh::ResizeBoxCollection 24ms 0.1% 83.90% 201ms 0.87% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 83.90% 201ms 0.87% vtkStreamingDemandDrivenPipeline::Update 0 0% 83.90% 201ms 0.87% vtkXMLWriterBase::Write 19ms 0.082% 83.99% 200ms 0.86% std::__insertion_sort (inline) 0 0% 83.99% 200ms 0.86% vtkDemandDrivenPipeline::ProcessRequest 0 0% 83.99% 199ms 0.86% vtkExecutive::CallAlgorithm 0 0% 83.99% 199ms 0.86% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 83.99% 198ms 0.85% vtkDemandDrivenPipeline::ExecuteData 0 0% 83.99% 197ms 0.85% std::allocator_traits::deallocate (inline) 0 0% 83.99% 197ms 0.85% vtkCompositeDataPipeline::ExecuteData 0 0% 83.99% 197ms 0.85% vtkXMLUnstructuredDataWriter::ProcessRequest 194ms 0.84% 84.82% 194ms 0.84% [libchaste_cell_based.so] 0 0% 84.82% 194ms 0.84% std::_Rb_tree::_M_put_node (inline) 4ms 0.017% 84.84% 191ms 0.82% CellPropertyCollection::HasProperty 0 0% 84.84% 188ms 0.81% Cell::HasCellProperty (inline) 79ms 0.34% 85.18% 183ms 0.79% Node::AddNeighbour 4ms 0.017% 85.20% 170ms 0.73% Cell::ReadyToDivide 0 0% 85.20% 165ms 0.71% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.20% 165ms 0.71% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 85.20% 164ms 0.71% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 3ms 0.013% 85.21% 163ms 0.7% AbstractCellProperty::IsType (inline) 0 0% 85.21% 159ms 0.69% std::_Rb_tree::_Auto_node::_Auto_node (inline) 158ms 0.68% 85.89% 158ms 0.68% boost::shared_ptr::operator-> (inline) 21ms 0.091% 85.98% 146ms 0.63% boost::numeric::ublas::vector_reference::operator() (inline) 143ms 0.62% 86.60% 144ms 0.62% Node::ConstructNodeAttributes (inline) 0 0% 86.60% 140ms 0.6% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 124ms 0.53% 87.14% 139ms 0.6% _int_free 9ms 0.039% 87.17% 138ms 0.6% DistributedBoxCollection::GetIsPeriodicAllDims 0 0% 87.17% 138ms 0.6% std::_Rb_tree::clear (inline) 136ms 0.59% 87.76% 136ms 0.59% [libchaste_mesh.so] 0 0% 87.76% 132ms 0.57% vtkXMLWriter::WriteBinaryData 0 0% 87.76% 131ms 0.56% vtkXMLWriter::WriteBinaryDataInternal 130ms 0.56% 88.32% 130ms 0.56% Node::rGetLocation 0 0% 88.32% 130ms 0.56% vtkXMLWriter::WriteBinaryDataBlock 0 0% 88.32% 130ms 0.56% vtkXMLWriter::WriteCompressionBlock 0 0% 88.32% 129ms 0.56% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 3ms 0.013% 88.33% 129ms 0.56% AbstractNumericalMethod::SafeNodePositionUpdate 3ms 0.013% 88.35% 129ms 0.56% Cell::GetCellId 129ms 0.56% 88.90% 129ms 0.56% __ieee754_log_fma 124ms 0.53% 89.44% 126ms 0.54% std::__adjacent_find (inline) 0 0% 89.44% 126ms 0.54% std::__unique (inline) 0 0% 89.44% 126ms 0.54% std::unique (inline) 4ms 0.017% 89.46% 125ms 0.54% AbstractCellPopulation::SetCellUsingLocationIndex 37ms 0.16% 89.61% 125ms 0.54% AbstractCellProperty::IsSame 56ms 0.24% 89.86% 125ms 0.54% NodeAttributes::AddAppliedForceContribution 0 0% 89.86% 125ms 0.54% vtkXMLWriter::WritePointsAppendedData 4ms 0.017% 89.87% 124ms 0.53% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 89.87% 123ms 0.53% boost::numeric::ublas::vector_binary::operator() (inline) 7ms 0.03% 89.90% 116ms 0.5% NodeBasedCellPopulation::SetNode