File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 22253ms, 89.89% of 24755ms total Dropped 764 nodes (cum <= 123.78ms) flat flat% sum% cum cum% 0 0% 0% 24624ms 99.47% __libc_start_call_main 0 0% 0% 24624ms 99.47% __libc_start_main_impl 0 0% 0% 24624ms 99.47% _start 0 0% 0% 24606ms 99.40% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 24606ms 99.40% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 24606ms 99.40% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 24606ms 99.40% main 0 0% 0% 24569ms 99.25% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 24569ms 99.25% CxxTest::TestRunner::runTest (inline) 0 0% 0% 24569ms 99.25% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 24560ms 99.21% AbstractCellBasedSimulation::Solve 0 0% 0% 14004ms 56.57% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0% 9320ms 37.65% AbstractCellBasedSimulation::UpdateCellPopulation 6ms 0.024% 0.024% 9143ms 36.93% ForwardEulerNumericalMethod::UpdateAllNodePositions 11ms 0.044% 0.069% 8946ms 36.14% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.004% 0.073% 8242ms 33.29% NodeBasedCellPopulation::Update 1358ms 5.49% 5.56% 8231ms 33.25% RepulsionForce::AddForceContribution (partial-inline) 13ms 0.053% 5.61% 5984ms 24.17% DistributedBoxCollection::CalculateInteriorNodePairs 2036ms 8.22% 13.84% 5002ms 20.21% std::_Rb_tree::_M_lower_bound (inline) 9ms 0.036% 13.87% 4733ms 19.12% NodeAttributes::RemoveDuplicateNeighbours 0 0% 13.87% 4584ms 18.52% OffLatticeSimulation::ApplyBoundaries 5ms 0.02% 13.89% 4405ms 17.79% std::__sort (inline) 0 0% 13.89% 4405ms 17.79% std::sort (inline) 203ms 0.82% 14.71% 4086ms 16.51% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 290ms 1.17% 15.88% 3358ms 13.56% std::_Rb_tree::find (inline) 0 0% 15.88% 3357ms 13.56% std::map::find (inline) 80ms 0.32% 16.21% 3355ms 13.55% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 3ms 0.012% 16.22% 3219ms 13.00% AbstractCellPopulation::Iterator::operator++ (inline) 158ms 0.64% 16.86% 3165ms 12.79% AbstractCellPopulation::Iterator::IsRealCell (inline) 2945ms 11.90% 28.75% 2945ms 11.90% std::_Rb_tree::_S_right (inline) 38ms 0.15% 28.91% 2778ms 11.22% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 178ms 0.72% 29.63% 2570ms 10.38% std::__introsort_loop 63ms 0.25% 29.88% 2470ms 9.98% NodesOnlyMesh::GetNodeOrHaloNode 196ms 0.79% 30.67% 2466ms 9.96% AbstractMesh::GetNode 17ms 0.069% 30.74% 2449ms 9.89% PlaneBoundaryCondition::ImposeBoundaryCondition 191ms 0.77% 31.51% 2403ms 9.71% std::map::operator[] (partial-inline) 0 0% 31.51% 2310ms 9.33% std::__unguarded_partition_pivot (inline) 49ms 0.2% 31.71% 2274ms 9.19% AbstractCellPopulation::GetLocationIndexUsingCell 104ms 0.42% 32.13% 2274ms 9.19% NodesOnlyMesh::SolveNodeMapping 17ms 0.069% 32.20% 2135ms 8.62% PlaneBoundaryCondition::VerifyBoundaryCondition 1061ms 4.29% 36.49% 2069ms 8.36% std::__unguarded_partition (inline) 154ms 0.62% 37.11% 2019ms 8.16% DistributedBoxCollection::AddPairsFromBox 0 0% 37.11% 1961ms 7.92% std::_Rb_tree::lower_bound (inline) 0 0% 37.11% 1961ms 7.92% std::map::lower_bound (inline) 0 0% 37.11% 1826ms 7.38% std::__final_insertion_sort (inline) 51ms 0.21% 37.31% 1682ms 6.79% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 35ms 0.14% 37.46% 1631ms 6.59% AbstractCellPopulation::GetCellUsingLocationIndex 92ms 0.37% 37.83% 1625ms 6.56% std::__unguarded_insertion_sort (inline) 562ms 2.27% 40.10% 1561ms 6.31% std::__unguarded_linear_insert (inline) 1447ms 5.85% 45.94% 1447ms 5.85% __gnu_cxx::__normal_iterator::operator-- (inline) 57ms 0.23% 46.17% 1373ms 5.55% boost::numeric::ublas::c_vector::c_vector (partial-inline) 5ms 0.02% 46.19% 1286ms 5.19% DistributedBoxCollection::CalculateBoundaryNodePairs 5ms 0.02% 46.21% 1199ms 4.84% boost::numeric::ublas::vector_assign (inline) 0 0% 46.21% 1186ms 4.79% NodeBasedCellPopulation::UpdateCellProcessLocation 230ms 0.93% 47.14% 1087ms 4.39% boost::numeric::ublas::indexing_vector_assign 18ms 0.073% 47.21% 948ms 3.83% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 281ms 1.14% 48.35% 947ms 3.83% __dynamic_cast 166ms 0.67% 49.02% 871ms 3.52% AbstractMesh::GetVectorFromAtoB 392ms 1.58% 50.60% 865ms 3.49% DistributedBoxCollection::CalculateContainingBox (partial-inline) 6ms 0.024% 50.63% 849ms 3.43% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 50.63% 826ms 3.34% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 33ms 0.13% 50.76% 822ms 3.32% std::__copy_move::__copy_m (inline) 0 0% 50.76% 822ms 3.32% std::__copy_move_a (inline) 0 0% 50.76% 822ms 3.32% std::__copy_move_a1 (inline) 0 0% 50.76% 822ms 3.32% std::__copy_move_a2 (inline) 0 0% 50.76% 822ms 3.32% std::copy (inline) 810ms 3.27% 54.03% 810ms 3.27% __memcpy_avx_unaligned_erms 0 0% 54.03% 805ms 3.25% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 54.03% 804ms 3.25% boost::numeric::ublas::norm_2 (inline) 621ms 2.51% 56.54% 804ms 3.25% boost::numeric::ublas::vector_norm_2::apply (inline) 209ms 0.84% 57.39% 796ms 3.22% NodeAttributes::AddNeighbour 0 0% 57.39% 742ms 3.00% AbstractCellPopulation::WriteResultsToFiles 726ms 2.93% 60.32% 726ms 2.93% boost::numeric::ublas::c_vector::operator() 31ms 0.13% 60.44% 665ms 2.69% std::_Rb_tree_const_iterator::operator++ (inline) 586ms 2.37% 62.81% 664ms 2.68% std::vector::push_back (inline) 5ms 0.02% 62.83% 638ms 2.58% AbstractCentreBasedCellPopulation::GetDampingConstant 8ms 0.032% 62.86% 632ms 2.55% CellPropertyCollection::GetPropertiesType (inline) 7ms 0.028% 62.89% 623ms 2.52% AbstractCellBasedSimulation::DoCellBirth 620ms 2.50% 65.40% 620ms 2.50% std::_Rb_tree_increment 245ms 0.99% 66.39% 548ms 2.21% __cxxabiv1::__si_class_type_info::__do_dyncast 534ms 2.16% 68.54% 534ms 2.16% boost::numeric::ublas::same_impl_ex 32ms 0.13% 68.67% 521ms 2.10% std::_Rb_tree::_Rb_tree (partial-inline) 78ms 0.32% 68.99% 518ms 2.09% std::__new_allocator::allocate (inline) 0 0% 68.99% 496ms 2.00% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 68.99% 494ms 2.00% std::allocator_traits::allocate (inline) 35ms 0.14% 69.13% 493ms 1.99% boost::detail::shared_count::~shared_count (inline) 0 0% 69.13% 493ms 1.99% boost::shared_ptr::~shared_ptr (inline) 48ms 0.19% 69.32% 478ms 1.93% std::_Rb_tree::_M_copy (inline) 467ms 1.89% 71.21% 467ms 1.89% __strcmp_avx2 0 0% 71.21% 458ms 1.85% std::_Rb_tree::_M_create_node (inline) 0 0% 71.21% 454ms 1.83% AbstractCellBasedSimulation::DoCellRemoval (inline) 3ms 0.012% 71.22% 451ms 1.82% Cell::GetMutationState 428ms 1.73% 72.95% 448ms 1.81% boost::detail::sp_counted_base::release 128ms 0.52% 73.47% 444ms 1.79% std::_Rb_tree::_M_erase 8ms 0.032% 73.50% 441ms 1.78% std::set::set (inline) 2ms 0.0081% 73.51% 439ms 1.77% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 29ms 0.12% 73.63% 438ms 1.77% operator new 168ms 0.68% 74.30% 427ms 1.72% std::_Rb_tree::_M_clone_node (inline) 2ms 0.0081% 74.31% 420ms 1.70% AbstractCellProperty::IsSubType (inline) 0 0% 74.31% 420ms 1.70% std::_Rb_tree::_M_get_node (inline) 112ms 0.45% 74.76% 410ms 1.66% boost::numeric::ublas::vector_binary::size (inline) 116ms 0.47% 75.23% 399ms 1.61% __GI___libc_malloc 79ms 0.32% 75.55% 384ms 1.55% Node::GetRadius 0 0% 75.55% 379ms 1.53% boost::numeric::ublas::c_vector::assign (inline) 373ms 1.51% 77.06% 373ms 1.51% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 47ms 0.19% 77.25% 349ms 1.41% std::_Rb_tree::~_Rb_tree (inline) 0 0% 77.25% 339ms 1.37% boost::numeric::ublas::inner_prod (inline) 2ms 0.0081% 77.26% 339ms 1.37% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 17ms 0.069% 77.33% 337ms 1.36% boost::numeric::ublas::vector_scalar_binary::evaluate 5ms 0.02% 77.35% 329ms 1.33% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 323ms 1.30% 78.65% 323ms 1.30% Node::CheckForNodeAttributes 0 0% 78.65% 322ms 1.30% NodesOnlyMesh::ReMesh 9ms 0.036% 78.69% 318ms 1.28% NodeBasedCellPopulation::UpdateMapsAfterRemesh 2ms 0.0081% 78.70% 314ms 1.27% NodesOnlyMesh::UpdateNodeIndices 0 0% 78.70% 310ms 1.25% std::_Rb_tree::_M_drop_node (inline) 0 0% 78.70% 309ms 1.25% std::_Rb_tree::_Alloc_node::operator() (inline) 8ms 0.032% 78.73% 303ms 1.22% DistributedBoxCollection::GetProcessOwningNode 296ms 1.20% 79.92% 296ms 1.20% std::__adjacent_find (inline) 0 0% 79.92% 296ms 1.20% std::__unique (inline) 0 0% 79.92% 296ms 1.20% std::unique (inline) 275ms 1.11% 81.03% 275ms 1.11% __gnu_cxx::__normal_iterator::operator++ (inline) 122ms 0.49% 81.53% 273ms 1.10% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 81.53% 263ms 1.06% NodesOnlyMesh::UpdateBoxCollection 8ms 0.032% 81.56% 258ms 1.04% std::__new_allocator::deallocate (inline) 0 0% 81.56% 254ms 1.03% std::set::~set (inline) 7ms 0.028% 81.59% 251ms 1.01% std::_Rb_tree::_M_emplace_hint_unique 216ms 0.87% 82.46% 245ms 0.99% Node::AddNeighbour 0 0% 82.46% 244ms 0.99% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 82.46% 243ms 0.98% VtkMeshWriter::WriteFiles 126ms 0.51% 82.97% 242ms 0.98% boost::shared_ptr::shared_ptr (inline) 98ms 0.4% 83.36% 241ms 0.97% std::__move_median_to_first (inline) 142ms 0.57% 83.94% 235ms 0.95% _int_malloc 0 0% 83.94% 234ms 0.95% std::_Rb_tree::_M_put_node (inline) 0 0% 83.94% 234ms 0.95% std::allocator_traits::deallocate (inline) 2ms 0.0081% 83.95% 222ms 0.9% CellPropertyCollection::HasProperty 0 0% 83.95% 221ms 0.89% Cell::HasCellProperty (inline) 69ms 0.28% 84.23% 219ms 0.88% __GI___libc_free 0 0% 84.23% 219ms 0.88% boost::numeric::ublas::vector_binary::operator() (inline) 217ms 0.88% 85.10% 217ms 0.88% Node::GetIndex 0 0% 85.10% 217ms 0.88% vtkDemandDrivenPipeline::ProcessRequest 0 0% 85.10% 217ms 0.88% vtkStreamingDemandDrivenPipeline::Update 0 0% 85.10% 217ms 0.88% vtkXMLWriterBase::Write 0 0% 85.10% 215ms 0.87% vtkDemandDrivenPipeline::ExecuteData 0 0% 85.10% 215ms 0.87% vtkExecutive::CallAlgorithm 0 0% 85.10% 215ms 0.87% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 85.10% 214ms 0.86% vtkCompositeDataPipeline::ExecuteData 0 0% 85.10% 214ms 0.86% vtkXMLUnstructuredDataWriter::ProcessRequest 8ms 0.032% 85.13% 212ms 0.86% Cell::ReadyToDivide 3ms 0.012% 85.15% 211ms 0.85% NodesOnlyMesh::AddNodesToBoxes 206ms 0.83% 85.98% 206ms 0.83% [libchaste_mesh.so] 17ms 0.069% 86.05% 204ms 0.82% boost::numeric::ublas::vector_reference::operator() (inline) 19ms 0.077% 86.12% 201ms 0.81% std::__insertion_sort (inline) 0 0% 86.12% 186ms 0.75% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 86.12% 186ms 0.75% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 86.12% 182ms 0.74% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 86.12% 175ms 0.71% NodesOnlyMesh::ResizeBoxCollection 12ms 0.048% 86.17% 173ms 0.7% NodesOnlyMesh::IsANodeCloseToDomainBoundary 171ms 0.69% 86.86% 171ms 0.69% [libchaste_cell_based.so] 0 0% 86.86% 163ms 0.66% AbstractCellProperty::IsType (inline) 0 0% 86.86% 161ms 0.65% std::_Rb_tree::clear (inline) 0 0% 86.86% 152ms 0.61% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 138ms 0.56% 87.42% 150ms 0.61% _int_free 1ms 0.004% 87.42% 150ms 0.61% vtkXMLWriter::WriteBinaryData 0 0% 87.42% 149ms 0.6% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1ms 0.004% 87.43% 146ms 0.59% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.43% 146ms 0.59% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.43% 143ms 0.58% vtkXMLWriter::WriteCompressionBlock 0 0% 87.43% 142ms 0.57% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 138ms 0.56% 87.99% 138ms 0.56% Node::IsDeleted 137ms 0.55% 88.54% 137ms 0.55% Node::rGetLocation 4ms 0.016% 88.56% 135ms 0.55% AbstractNumericalMethod::SafeNodePositionUpdate 135ms 0.55% 89.10% 135ms 0.55% __ieee754_log_fma 3ms 0.012% 89.11% 134ms 0.54% Cell::GetCellId 3ms 0.012% 89.13% 134ms 0.54% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 89.13% 134ms 0.54% vtkXMLWriter::WritePointsAppendedData 132ms 0.53% 89.66% 132ms 0.53% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 5ms 0.02% 89.68% 129ms 0.52% DistributedBoxCollection::GetIsPeriodicAllDims 2ms 0.0081% 89.69% 126ms 0.51% AbstractCellPopulation::SetCellUsingLocationIndex 51ms 0.21% 89.89% 125ms 0.5% AbstractCellProperty::IsSame