File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 21879ms, 89.43% of 24465ms total Dropped 817 nodes (cum <= 122.33ms) flat flat% sum% cum cum% 0 0% 0% 24334ms 99.46% __libc_start_call_main 0 0% 0% 24334ms 99.46% __libc_start_main_impl 0 0% 0% 24334ms 99.46% _start 0 0% 0% 24314ms 99.38% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 24314ms 99.38% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 24314ms 99.38% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 24314ms 99.38% main 0 0% 0% 24273ms 99.22% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 24273ms 99.22% CxxTest::TestRunner::runTest (inline) 0 0% 0% 24273ms 99.22% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 24264ms 99.18% AbstractCellBasedSimulation::Solve 3ms 0.012% 0.012% 14119ms 57.71% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.0082% 0.02% 9093ms 37.17% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 0.02% 8953ms 36.60% AbstractCellBasedSimulation::UpdateCellPopulation 16ms 0.065% 0.086% 8906ms 36.40% AbstractNumericalMethod::ComputeForcesIncludingDamping 1333ms 5.45% 5.53% 8254ms 33.74% RepulsionForce::AddForceContribution (partial-inline) 1ms 0.0041% 5.54% 7881ms 32.21% NodeBasedCellPopulation::Update 14ms 0.057% 5.60% 5834ms 23.85% DistributedBoxCollection::CalculateInteriorNodePairs 2270ms 9.28% 14.87% 5155ms 21.07% std::_Rb_tree::_M_lower_bound (inline) 0 0% 14.87% 4704ms 19.23% OffLatticeSimulation::ApplyBoundaries 12ms 0.049% 14.92% 4445ms 18.17% NodeAttributes::RemoveDuplicateNeighbours 4ms 0.016% 14.94% 4263ms 17.42% std::__sort (inline) 0 0% 14.94% 4263ms 17.42% std::sort (inline) 208ms 0.85% 15.79% 4095ms 16.74% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 72ms 0.29% 16.08% 3411ms 13.94% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 242ms 0.99% 17.07% 3348ms 13.68% std::_Rb_tree::find (inline) 0 0% 17.07% 3348ms 13.68% std::map::find (inline) 4ms 0.016% 17.09% 3192ms 13.05% AbstractCellPopulation::Iterator::operator++ (inline) 136ms 0.56% 17.65% 3153ms 12.89% AbstractCellPopulation::Iterator::IsRealCell (inline) 2866ms 11.71% 29.36% 2866ms 11.71% std::_Rb_tree::_S_right (inline) 19ms 0.078% 29.44% 2783ms 11.38% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 184ms 0.75% 30.19% 2549ms 10.42% std::map::operator[] (partial-inline) 189ms 0.77% 30.96% 2531ms 10.35% std::__introsort_loop 17ms 0.069% 31.03% 2481ms 10.14% PlaneBoundaryCondition::ImposeBoundaryCondition 185ms 0.76% 31.79% 2466ms 10.08% AbstractMesh::GetNode 42ms 0.17% 31.96% 2446ms 10.00% NodesOnlyMesh::GetNodeOrHaloNode 31ms 0.13% 32.09% 2341ms 9.57% AbstractCellPopulation::GetLocationIndexUsingCell 116ms 0.47% 32.56% 2284ms 9.34% NodesOnlyMesh::SolveNodeMapping 0 0% 32.56% 2250ms 9.20% std::__unguarded_partition_pivot (inline) 21ms 0.086% 32.65% 2223ms 9.09% PlaneBoundaryCondition::VerifyBoundaryCondition 0 0% 32.65% 2076ms 8.49% std::_Rb_tree::lower_bound (inline) 0 0% 32.65% 2076ms 8.49% std::map::lower_bound (inline) 982ms 4.01% 36.66% 1999ms 8.17% std::__unguarded_partition (inline) 132ms 0.54% 37.20% 1980ms 8.09% DistributedBoxCollection::AddPairsFromBox 1ms 0.0041% 37.20% 1727ms 7.06% std::__final_insertion_sort (inline) 26ms 0.11% 37.31% 1656ms 6.77% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 31ms 0.13% 37.44% 1620ms 6.62% AbstractCellPopulation::GetCellUsingLocationIndex 102ms 0.42% 37.85% 1526ms 6.24% std::__unguarded_insertion_sort (inline) 487ms 1.99% 39.84% 1457ms 5.96% std::__unguarded_linear_insert (inline) 1405ms 5.74% 45.59% 1405ms 5.74% __gnu_cxx::__normal_iterator::operator-- (inline) 59ms 0.24% 45.83% 1274ms 5.21% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 45.83% 1143ms 4.67% NodeBasedCellPopulation::UpdateCellProcessLocation 9ms 0.037% 45.87% 1143ms 4.67% boost::numeric::ublas::vector_assign (inline) 4ms 0.016% 45.88% 1075ms 4.39% DistributedBoxCollection::CalculateBoundaryNodePairs 182ms 0.74% 46.63% 1057ms 4.32% boost::numeric::ublas::indexing_vector_assign 282ms 1.15% 47.78% 987ms 4.03% __dynamic_cast 18ms 0.074% 47.85% 969ms 3.96% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 7ms 0.029% 47.88% 852ms 3.48% boost::numeric::ublas::c_vector::operator= (inline) 385ms 1.57% 49.45% 833ms 3.40% DistributedBoxCollection::CalculateContainingBox (partial-inline) 34ms 0.14% 49.59% 830ms 3.39% std::__copy_move::__copy_m (inline) 0 0% 49.59% 830ms 3.39% std::__copy_move_a (inline) 0 0% 49.59% 830ms 3.39% std::__copy_move_a1 (inline) 0 0% 49.59% 830ms 3.39% std::__copy_move_a2 (inline) 0 0% 49.59% 830ms 3.39% std::copy (inline) 0 0% 49.59% 826ms 3.38% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 814ms 3.33% 52.92% 814ms 3.33% __memcpy_avx_unaligned_erms 164ms 0.67% 53.59% 810ms 3.31% AbstractMesh::GetVectorFromAtoB 0 0% 53.59% 808ms 3.30% boost::numeric::ublas::norm_2 (inline) 651ms 2.66% 56.25% 808ms 3.30% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 56.25% 808ms 3.30% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 56.25% 744ms 3.04% AbstractCellPopulation::WriteResultsToFiles 186ms 0.76% 57.01% 741ms 3.03% NodeAttributes::AddNeighbour 689ms 2.82% 59.83% 689ms 2.82% boost::numeric::ublas::c_vector::operator() 554ms 2.26% 62.09% 625ms 2.55% std::vector::push_back (inline) 13ms 0.053% 62.15% 612ms 2.50% CellPropertyCollection::GetPropertiesType (inline) 9ms 0.037% 62.18% 591ms 2.42% AbstractCellBasedSimulation::DoCellBirth 28ms 0.11% 62.30% 591ms 2.42% std::_Rb_tree_const_iterator::operator++ (inline) 4ms 0.016% 62.31% 572ms 2.34% AbstractCentreBasedCellPopulation::GetDampingConstant 278ms 1.14% 63.45% 571ms 2.33% __cxxabiv1::__si_class_type_info::__do_dyncast 45ms 0.18% 63.63% 567ms 2.32% boost::detail::shared_count::~shared_count (inline) 0 0% 63.63% 567ms 2.32% boost::shared_ptr::~shared_ptr (inline) 548ms 2.24% 65.87% 548ms 2.24% boost::numeric::ublas::same_impl_ex 547ms 2.24% 68.11% 547ms 2.24% std::_Rb_tree_increment 92ms 0.38% 68.49% 544ms 2.22% std::__new_allocator::allocate (inline) 0 0% 68.49% 526ms 2.15% std::allocator_traits::allocate (inline) 486ms 1.99% 70.47% 509ms 2.08% boost::detail::sp_counted_base::release 41ms 0.17% 70.64% 501ms 2.05% std::_Rb_tree::_Rb_tree (partial-inline) 1ms 0.0041% 70.64% 497ms 2.03% NodeBasedCellPopulation::WriteVtkResultsToFile 1ms 0.0041% 70.65% 481ms 1.97% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 70.65% 476ms 1.95% std::_Rb_tree::_M_create_node (inline) 469ms 1.92% 72.56% 469ms 1.92% __strcmp_avx2 5ms 0.02% 72.59% 466ms 1.90% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 72.59% 447ms 1.83% AbstractCellProperty::IsSubType (inline) 18ms 0.074% 72.66% 445ms 1.82% operator new 0 0% 72.66% 443ms 1.81% std::_Rb_tree::_M_get_node (inline) 38ms 0.16% 72.81% 437ms 1.79% std::_Rb_tree::_M_copy (inline) 122ms 0.5% 73.31% 429ms 1.75% std::_Rb_tree::_M_erase 1ms 0.0041% 73.32% 429ms 1.75% std::set::set (inline) 1ms 0.0041% 73.32% 424ms 1.73% Cell::GetMutationState 126ms 0.52% 73.84% 418ms 1.71% __GI___libc_malloc 90ms 0.37% 74.20% 414ms 1.69% Node::GetRadius 110ms 0.45% 74.65% 409ms 1.67% boost::numeric::ublas::vector_binary::size (inline) 137ms 0.56% 75.21% 391ms 1.60% std::_Rb_tree::_M_clone_node (inline) 0 0% 75.21% 363ms 1.48% boost::numeric::ublas::inner_prod (inline) 1ms 0.0041% 75.22% 362ms 1.48% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 17ms 0.069% 75.29% 361ms 1.48% boost::numeric::ublas::vector_scalar_binary::evaluate 64ms 0.26% 75.55% 360ms 1.47% std::_Rb_tree::~_Rb_tree (inline) 0 0% 75.55% 336ms 1.37% boost::numeric::ublas::c_vector::assign (inline) 334ms 1.37% 76.91% 334ms 1.37% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 329ms 1.34% 78.26% 329ms 1.34% Node::CheckForNodeAttributes 329ms 1.34% 79.60% 329ms 1.34% __gnu_cxx::__normal_iterator::operator++ (inline) 6ms 0.025% 79.63% 327ms 1.34% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 79.63% 305ms 1.25% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 79.63% 304ms 1.24% NodesOnlyMesh::ReMesh 0 0% 79.63% 302ms 1.23% std::_Rb_tree::_M_drop_node (inline) 0 0% 79.63% 293ms 1.20% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 146ms 0.6% 80.22% 291ms 1.19% boost::numeric::ublas::vector_inner_prod::apply (inline) 1ms 0.0041% 80.23% 289ms 1.18% NodesOnlyMesh::UpdateNodeIndices 2ms 0.0082% 80.24% 289ms 1.18% std::_Rb_tree::_M_emplace_hint_unique 12ms 0.049% 80.29% 280ms 1.14% DistributedBoxCollection::GetProcessOwningNode 275ms 1.12% 81.41% 275ms 1.12% Node::GetIndex 0 0% 81.41% 267ms 1.09% std::set::~set (inline) 0 0% 81.41% 266ms 1.09% NodesOnlyMesh::UpdateBoxCollection 9ms 0.037% 81.45% 252ms 1.03% std::__new_allocator::deallocate (inline) 149ms 0.61% 82.06% 250ms 1.02% _int_malloc 106ms 0.43% 82.49% 246ms 1.01% std::__move_median_to_first (inline) 242ms 0.99% 83.48% 242ms 0.99% [libchaste_mesh.so] 0 0% 83.48% 241ms 0.99% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 83.48% 239ms 0.98% VtkMeshWriter::WriteFiles 0 0% 83.48% 235ms 0.96% std::allocator_traits::deallocate (inline) 170ms 0.69% 84.17% 233ms 0.95% Node::AddNeighbour 0 0% 84.17% 233ms 0.95% std::_Rb_tree::_M_put_node (inline) 1ms 0.0041% 84.18% 228ms 0.93% NodesOnlyMesh::AddNodesToBoxes 61ms 0.25% 84.43% 220ms 0.9% __GI___libc_free 0 0% 84.43% 215ms 0.88% vtkStreamingDemandDrivenPipeline::Update 0 0% 84.43% 215ms 0.88% vtkXMLWriterBase::Write 0 0% 84.43% 214ms 0.87% vtkDemandDrivenPipeline::ProcessRequest 1ms 0.0041% 84.43% 213ms 0.87% vtkStreamingDemandDrivenPipeline::ProcessRequest 4ms 0.016% 84.45% 212ms 0.87% CellPropertyCollection::HasProperty 0 0% 84.45% 211ms 0.86% Cell::HasCellProperty (inline) 1ms 0.0041% 84.45% 211ms 0.86% vtkCompositeDataPipeline::ExecuteData 0 0% 84.45% 210ms 0.86% vtkDemandDrivenPipeline::ExecuteData 0 0% 84.45% 210ms 0.86% vtkExecutive::CallAlgorithm 0 0% 84.45% 210ms 0.86% vtkXMLUnstructuredDataWriter::ProcessRequest 89ms 0.36% 84.82% 203ms 0.83% boost::shared_ptr::shared_ptr (inline) 21ms 0.086% 84.90% 200ms 0.82% std::__insertion_sort (inline) 2ms 0.0082% 84.91% 195ms 0.8% Cell::ReadyToDivide 194ms 0.79% 85.70% 194ms 0.79% [libchaste_cell_based.so] 0 0% 85.70% 182ms 0.74% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.70% 182ms 0.74% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 85.70% 175ms 0.72% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 1ms 0.0041% 85.71% 172ms 0.7% AbstractCellProperty::IsType (inline) 0 0% 85.71% 171ms 0.7% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 85.71% 163ms 0.67% NodesOnlyMesh::ResizeBoxCollection 8ms 0.033% 85.74% 163ms 0.67% boost::numeric::ublas::vector_reference::operator() (inline) 3ms 0.012% 85.75% 162ms 0.66% AbstractCellPopulation::SetCellUsingLocationIndex 14ms 0.057% 85.81% 162ms 0.66% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 85.81% 161ms 0.66% boost::numeric::ublas::vector_binary::operator() (inline) 138ms 0.56% 86.37% 158ms 0.65% _int_free 0 0% 86.37% 153ms 0.63% vtkXMLWriter::WriteBinaryData 151ms 0.62% 86.99% 151ms 0.62% std::__adjacent_find (inline) 0 0% 86.99% 151ms 0.62% std::__unique (inline) 0 0% 86.99% 151ms 0.62% std::unique (inline) 150ms 0.61% 87.60% 150ms 0.61% __ieee754_log_fma 0 0% 87.60% 149ms 0.61% std::_Rb_tree::clear (inline) 0 0% 87.60% 149ms 0.61% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.60% 149ms 0.61% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.60% 149ms 0.61% vtkXMLWriter::WriteCompressionBlock 1ms 0.0041% 87.61% 148ms 0.6% Cell::GetCellId 1ms 0.0041% 87.61% 145ms 0.59% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 87.61% 139ms 0.57% vtkXMLWriter::WritePointsAppendedData 137ms 0.56% 88.17% 137ms 0.56% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 1ms 0.0041% 88.17% 136ms 0.56% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 88.17% 136ms 0.56% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 1ms 0.0041% 88.18% 129ms 0.53% AbstractNumericalMethod::SafeNodePositionUpdate 57ms 0.23% 88.41% 128ms 0.52% AbstractCellProperty::IsSame 126ms 0.52% 88.93% 126ms 0.52% Node::IsDeleted 123ms 0.5% 89.43% 123ms 0.5% Node::rGetLocation