File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 17227ms, 89.44% of 19262ms total Dropped 742 nodes (cum <= 96.31ms) flat flat% sum% cum cum% 0 0% 0% 19167ms 99.51% __libc_start_call_main 0 0% 0% 19167ms 99.51% __libc_start_main_impl 0 0% 0% 19167ms 99.51% _start 0 0% 0% 19153ms 99.43% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19153ms 99.43% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19153ms 99.43% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19153ms 99.43% main 0 0% 0% 19114ms 99.23% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19114ms 99.23% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19114ms 99.23% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 19107ms 99.20% AbstractCellBasedSimulation::Solve 1ms 0.0052% 0.0052% 10928ms 56.73% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0052% 7215ms 37.46% AbstractCellBasedSimulation::UpdateCellPopulation 5ms 0.026% 0.031% 7099ms 36.85% ForwardEulerNumericalMethod::UpdateAllNodePositions 16ms 0.083% 0.11% 6950ms 36.08% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.11% 6408ms 33.27% NodeBasedCellPopulation::Update 1031ms 5.35% 5.47% 6375ms 33.10% RepulsionForce::AddForceContribution (partial-inline) 11ms 0.057% 5.52% 4780ms 24.82% DistributedBoxCollection::CalculateInteriorNodePairs 1710ms 8.88% 14.40% 3979ms 20.66% std::_Rb_tree::_M_lower_bound (inline) 10ms 0.052% 14.45% 3579ms 18.58% NodeAttributes::RemoveDuplicateNeighbours 0 0% 14.45% 3575ms 18.56% OffLatticeSimulation::ApplyBoundaries 2ms 0.01% 14.46% 3433ms 17.82% std::__sort (inline) 0 0% 14.46% 3433ms 17.82% std::sort (inline) 168ms 0.87% 15.34% 3248ms 16.86% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 62ms 0.32% 15.66% 2586ms 13.43% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 163ms 0.85% 16.50% 2545ms 13.21% std::_Rb_tree::find (inline) 0 0% 16.50% 2543ms 13.20% std::map::find (inline) 3ms 0.016% 16.52% 2428ms 12.61% AbstractCellPopulation::Iterator::operator++ (inline) 111ms 0.58% 17.10% 2405ms 12.49% AbstractCellPopulation::Iterator::IsRealCell (inline) 2260ms 11.73% 28.83% 2260ms 11.73% std::_Rb_tree::_S_right (inline) 21ms 0.11% 28.94% 2098ms 10.89% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 172ms 0.89% 29.83% 2029ms 10.53% std::map::operator[] (partial-inline) 126ms 0.65% 30.48% 2004ms 10.40% std::__introsort_loop 15ms 0.078% 30.56% 1902ms 9.87% PlaneBoundaryCondition::ImposeBoundaryCondition 145ms 0.75% 31.32% 1880ms 9.76% AbstractMesh::GetNode 49ms 0.25% 31.57% 1879ms 9.75% NodesOnlyMesh::GetNodeOrHaloNode 0 0% 31.57% 1804ms 9.37% std::__unguarded_partition_pivot (inline) 42ms 0.22% 31.79% 1784ms 9.26% AbstractCellPopulation::GetLocationIndexUsingCell 88ms 0.46% 32.24% 1739ms 9.03% NodesOnlyMesh::SolveNodeMapping 10ms 0.052% 32.30% 1673ms 8.69% PlaneBoundaryCondition::VerifyBoundaryCondition 115ms 0.6% 32.89% 1650ms 8.57% DistributedBoxCollection::AddPairsFromBox 0 0% 32.89% 1632ms 8.47% std::_Rb_tree::lower_bound (inline) 0 0% 32.89% 1632ms 8.47% std::map::lower_bound (inline) 781ms 4.05% 36.95% 1617ms 8.39% std::__unguarded_partition (inline) 0 0% 36.95% 1426ms 7.40% std::__final_insertion_sort (inline) 15ms 0.078% 37.03% 1350ms 7.01% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 24ms 0.12% 37.15% 1330ms 6.90% AbstractCellPopulation::GetCellUsingLocationIndex 78ms 0.4% 37.56% 1288ms 6.69% std::__unguarded_insertion_sort (inline) 462ms 2.40% 39.95% 1224ms 6.35% std::__unguarded_linear_insert (inline) 1102ms 5.72% 45.68% 1102ms 5.72% __gnu_cxx::__normal_iterator::operator-- (inline) 37ms 0.19% 45.87% 1036ms 5.38% boost::numeric::ublas::c_vector::c_vector (partial-inline) 8ms 0.042% 45.91% 925ms 4.80% boost::numeric::ublas::vector_assign (inline) 0 0% 45.91% 902ms 4.68% NodeBasedCellPopulation::UpdateCellProcessLocation 4ms 0.021% 45.93% 853ms 4.43% DistributedBoxCollection::CalculateBoundaryNodePairs 201ms 1.04% 46.97% 843ms 4.38% boost::numeric::ublas::indexing_vector_assign 260ms 1.35% 48.32% 787ms 4.09% __dynamic_cast 15ms 0.078% 48.40% 760ms 3.95% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 122ms 0.63% 49.03% 673ms 3.49% AbstractMesh::GetVectorFromAtoB 307ms 1.59% 50.63% 661ms 3.43% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 50.63% 642ms 3.33% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 50.63% 628ms 3.26% boost::numeric::ublas::norm_2 (inline) 486ms 2.52% 53.15% 628ms 3.26% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 53.15% 628ms 3.26% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 4ms 0.021% 53.17% 612ms 3.18% boost::numeric::ublas::c_vector::operator= (inline) 32ms 0.17% 53.34% 596ms 3.09% std::__copy_move::__copy_m (inline) 0 0% 53.34% 596ms 3.09% std::__copy_move_a (inline) 0 0% 53.34% 596ms 3.09% std::__copy_move_a1 (inline) 0 0% 53.34% 596ms 3.09% std::__copy_move_a2 (inline) 0 0% 53.34% 596ms 3.09% std::copy (inline) 0 0% 53.34% 587ms 3.05% AbstractCellPopulation::WriteResultsToFiles 576ms 2.99% 56.33% 576ms 2.99% __memcpy_avx512_unaligned_erms 21ms 0.11% 56.44% 571ms 2.96% std::_Rb_tree_const_iterator::operator++ (inline) 105ms 0.55% 56.98% 559ms 2.90% NodeAttributes::AddNeighbour 533ms 2.77% 59.75% 533ms 2.77% std::_Rb_tree_increment 530ms 2.75% 62.50% 530ms 2.75% boost::numeric::ublas::c_vector::operator() 7ms 0.036% 62.54% 523ms 2.72% CellPropertyCollection::GetPropertiesType (inline) 454ms 2.36% 64.89% 520ms 2.70% std::vector::push_back (inline) 4ms 0.021% 64.92% 516ms 2.68% AbstractCentreBasedCellPopulation::GetDampingConstant 4ms 0.021% 64.94% 454ms 2.36% AbstractCellBasedSimulation::DoCellBirth 69ms 0.36% 65.29% 454ms 2.36% std::__new_allocator::allocate (inline) 0 0% 65.29% 434ms 2.25% std::allocator_traits::allocate (inline) 430ms 2.23% 67.53% 430ms 2.23% boost::numeric::ublas::same_impl_ex 217ms 1.13% 68.65% 423ms 2.20% __cxxabiv1::__si_class_type_info::__do_dyncast 19ms 0.099% 68.75% 397ms 2.06% std::_Rb_tree::_Rb_tree (partial-inline) 25ms 0.13% 68.88% 396ms 2.06% boost::detail::shared_count::~shared_count (inline) 0 0% 68.88% 396ms 2.06% boost::shared_ptr::~shared_ptr (inline) 1ms 0.0052% 68.89% 393ms 2.04% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 68.89% 391ms 2.03% std::_Rb_tree::_M_create_node (inline) 20ms 0.1% 68.99% 383ms 1.99% operator new 1ms 0.0052% 69.00% 370ms 1.92% Cell::GetMutationState 29ms 0.15% 69.15% 368ms 1.91% std::_Rb_tree::_M_copy (inline) 347ms 1.80% 70.95% 362ms 1.88% boost::detail::sp_counted_base::release 0 0% 70.95% 362ms 1.88% std::_Rb_tree::_M_get_node (inline) 86ms 0.45% 71.39% 360ms 1.87% std::_Rb_tree::_M_erase 0 0% 71.39% 353ms 1.83% AbstractCellBasedSimulation::DoCellRemoval (inline) 102ms 0.53% 71.92% 353ms 1.83% __GI___libc_malloc 1ms 0.0052% 71.93% 348ms 1.81% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 344ms 1.79% 73.72% 344ms 1.79% __strcmp_evex 3ms 0.016% 73.73% 338ms 1.75% AbstractCellProperty::IsSubType (inline) 4ms 0.021% 73.75% 337ms 1.75% std::set::set (inline) 106ms 0.55% 74.30% 334ms 1.73% std::_Rb_tree::_M_clone_node (inline) 83ms 0.43% 74.73% 306ms 1.59% boost::numeric::ublas::vector_binary::size (inline) 63ms 0.33% 75.06% 297ms 1.54% Node::GetRadius 38ms 0.2% 75.26% 278ms 1.44% std::_Rb_tree::~_Rb_tree (inline) 273ms 1.42% 76.67% 273ms 1.42% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 76.67% 272ms 1.41% NodesOnlyMesh::ReMesh 1ms 0.0052% 76.68% 269ms 1.40% NodesOnlyMesh::UpdateNodeIndices 0 0% 76.68% 268ms 1.39% boost::numeric::ublas::c_vector::assign (inline) 0 0% 76.68% 263ms 1.37% boost::numeric::ublas::inner_prod (inline) 9ms 0.047% 76.73% 263ms 1.37% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 76.73% 263ms 1.37% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 262ms 1.36% 78.09% 262ms 1.36% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 78.09% 257ms 1.33% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 78.09% 255ms 1.32% std::_Rb_tree::_M_drop_node (inline) 239ms 1.24% 79.33% 239ms 1.24% Node::CheckForNodeAttributes 0 0% 79.33% 237ms 1.23% NodesOnlyMesh::UpdateBoxCollection 12ms 0.062% 79.39% 225ms 1.17% std::_Rb_tree::_M_emplace_hint_unique 4ms 0.021% 79.41% 224ms 1.16% NodeBasedCellPopulation::UpdateMapsAfterRemesh 4ms 0.021% 79.43% 221ms 1.15% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 134ms 0.7% 80.13% 212ms 1.10% Node::AddNeighbour 7ms 0.036% 80.16% 211ms 1.10% std::__new_allocator::deallocate (inline) 2ms 0.01% 80.17% 210ms 1.09% DistributedBoxCollection::GetProcessOwningNode 0 0% 80.17% 207ms 1.07% std::set::~set (inline) 100ms 0.52% 80.69% 205ms 1.06% boost::numeric::ublas::vector_inner_prod::apply (inline) 199ms 1.03% 81.73% 199ms 1.03% [libchaste_mesh.so] 0 0% 81.73% 199ms 1.03% std::allocator_traits::deallocate (inline) 110ms 0.57% 82.30% 198ms 1.03% _int_malloc 0 0% 82.30% 196ms 1.02% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 3ms 0.016% 82.31% 196ms 1.02% NodesOnlyMesh::AddNodesToBoxes 0 0% 82.31% 196ms 1.02% std::_Rb_tree::_M_put_node (inline) 0 0% 82.31% 195ms 1.01% VtkMeshWriter::WriteFiles 2ms 0.01% 82.32% 187ms 0.97% CellPropertyCollection::HasProperty 54ms 0.28% 82.60% 187ms 0.97% __GI___libc_free 0 0% 82.60% 185ms 0.96% Cell::HasCellProperty (inline) 72ms 0.37% 82.98% 185ms 0.96% std::__move_median_to_first (inline) 173ms 0.9% 83.87% 173ms 0.9% Node::GetIndex 0 0% 83.87% 173ms 0.9% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 83.87% 173ms 0.9% vtkStreamingDemandDrivenPipeline::Update 0 0% 83.87% 173ms 0.9% vtkXMLWriterBase::Write 0 0% 83.87% 172ms 0.89% vtkDemandDrivenPipeline::ExecuteData 0 0% 83.87% 172ms 0.89% vtkDemandDrivenPipeline::ProcessRequest 0 0% 83.87% 170ms 0.88% vtkCompositeDataPipeline::ExecuteData 0 0% 83.87% 170ms 0.88% vtkExecutive::CallAlgorithm 1ms 0.0052% 83.88% 170ms 0.88% vtkXMLUnstructuredDataWriter::ProcessRequest 16ms 0.083% 83.96% 168ms 0.87% boost::numeric::ublas::vector_reference::operator() (inline) 4ms 0.021% 83.98% 165ms 0.86% Cell::ReadyToDivide 79ms 0.41% 84.39% 163ms 0.85% boost::shared_ptr::shared_ptr (inline) 0 0% 84.39% 161ms 0.84% boost::numeric::ublas::vector_binary::operator() (inline) 1ms 0.0052% 84.40% 155ms 0.8% AbstractCellProperty::IsType (inline) 0 0% 84.40% 144ms 0.75% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 84.40% 144ms 0.75% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 84.40% 142ms 0.74% NodesOnlyMesh::ResizeBoxCollection 0 0% 84.40% 142ms 0.74% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 13ms 0.067% 84.47% 141ms 0.73% NodesOnlyMesh::IsANodeCloseToDomainBoundary 10ms 0.052% 84.52% 138ms 0.72% std::__insertion_sort (inline) 135ms 0.7% 85.22% 135ms 0.7% [libchaste_cell_based.so] 121ms 0.63% 85.85% 134ms 0.7% _int_free 0 0% 85.85% 134ms 0.7% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 85.85% 133ms 0.69% std::_Rb_tree::clear (inline) 126ms 0.65% 86.50% 126ms 0.65% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 122ms 0.63% 87.14% 122ms 0.63% std::__adjacent_find (inline) 0 0% 87.14% 122ms 0.63% std::__unique (inline) 0 0% 87.14% 122ms 0.63% std::unique (inline) 0 0% 87.14% 118ms 0.61% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 37ms 0.19% 87.33% 114ms 0.59% AbstractCellProperty::IsSame 0 0% 87.33% 112ms 0.58% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 87.33% 111ms 0.58% Cell::GetCellId 0 0% 87.33% 108ms 0.56% vtkXMLWriter::WriteBinaryData 3ms 0.016% 87.34% 106ms 0.55% AbstractNumericalMethod::SafeNodePositionUpdate 4ms 0.021% 87.36% 106ms 0.55% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 87.36% 106ms 0.55% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.36% 106ms 0.55% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.36% 105ms 0.55% vtkXMLWriter::WriteCompressionBlock 103ms 0.53% 87.90% 103ms 0.53% Node::IsDeleted 0 0% 87.90% 103ms 0.53% vtkXMLWriter::WritePointsAppendedData 102ms 0.53% 88.43% 102ms 0.53% boost::shared_ptr::operator-> (inline) 0 0% 88.43% 98ms 0.51% AbstractCellPopulation::SetCellUsingLocationIndex 96ms 0.5% 88.93% 98ms 0.51% Node::ConstructNodeAttributes (inline) 98ms 0.51% 89.44% 98ms 0.51% __ieee754_log_fma