File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 21828ms, 89.13% of 24491ms total Dropped 812 nodes (cum <= 122.45ms) flat flat% sum% cum cum% 0 0% 0% 24385ms 99.57% __libc_start_call_main 0 0% 0% 24385ms 99.57% __libc_start_main_impl 0 0% 0% 24385ms 99.57% _start 0 0% 0% 24367ms 99.49% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 24367ms 99.49% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 24367ms 99.49% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 24367ms 99.49% main 0 0% 0% 24326ms 99.33% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 24326ms 99.33% CxxTest::TestRunner::runTest (inline) 0 0% 0% 24326ms 99.33% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 24317ms 99.29% AbstractCellBasedSimulation::Solve 0 0% 0% 13963ms 57.01% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0% 9132ms 37.29% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.016% 0.016% 9032ms 36.88% ForwardEulerNumericalMethod::UpdateAllNodePositions 11ms 0.045% 0.061% 8831ms 36.06% AbstractNumericalMethod::ComputeForcesIncludingDamping 1354ms 5.53% 5.59% 8154ms 33.29% RepulsionForce::AddForceContribution (partial-inline) 0 0% 5.59% 8060ms 32.91% NodeBasedCellPopulation::Update 13ms 0.053% 5.64% 5975ms 24.40% DistributedBoxCollection::CalculateInteriorNodePairs 2265ms 9.25% 14.89% 5175ms 21.13% std::_Rb_tree::_M_lower_bound (inline) 0 0% 14.89% 4599ms 18.78% OffLatticeSimulation::ApplyBoundaries 7ms 0.029% 14.92% 4577ms 18.69% NodeAttributes::RemoveDuplicateNeighbours 2ms 0.0082% 14.93% 4398ms 17.96% std::__sort (inline) 0 0% 14.93% 4398ms 17.96% std::sort (inline) 219ms 0.89% 15.82% 4123ms 16.83% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 243ms 0.99% 16.81% 3449ms 14.08% std::_Rb_tree::find (inline) 0 0% 16.81% 3447ms 14.07% std::map::find (inline) 64ms 0.26% 17.08% 3285ms 13.41% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 3ms 0.012% 17.09% 3153ms 12.87% AbstractCellPopulation::Iterator::operator++ (inline) 169ms 0.69% 17.78% 3119ms 12.74% AbstractCellPopulation::Iterator::IsRealCell 2878ms 11.75% 29.53% 2878ms 11.75% std::_Rb_tree::_S_right (inline) 30ms 0.12% 29.65% 2692ms 10.99% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 179ms 0.73% 30.38% 2548ms 10.40% std::__introsort_loop 179ms 0.73% 31.11% 2518ms 10.28% AbstractMesh::GetNode 228ms 0.93% 32.04% 2501ms 10.21% std::map::operator[] (partial-inline) 44ms 0.18% 32.22% 2477ms 10.11% NodesOnlyMesh::GetNodeOrHaloNode 18ms 0.073% 32.30% 2449ms 10.00% PlaneBoundaryCondition::ImposeBoundaryCondition 109ms 0.45% 32.74% 2344ms 9.57% NodesOnlyMesh::SolveNodeMapping 0 0% 32.74% 2300ms 9.39% std::__unguarded_partition_pivot (inline) 46ms 0.19% 32.93% 2266ms 9.25% AbstractCellPopulation::GetLocationIndexUsingCell 15ms 0.061% 32.99% 2150ms 8.78% PlaneBoundaryCondition::VerifyBoundaryCondition 1007ms 4.11% 37.10% 2045ms 8.35% std::__unguarded_partition (inline) 0 0% 37.10% 1997ms 8.15% std::_Rb_tree::lower_bound (inline) 0 0% 37.10% 1997ms 8.15% std::map::lower_bound (inline) 134ms 0.55% 37.65% 1980ms 8.08% DistributedBoxCollection::AddPairsFromBox 1ms 0.0041% 37.65% 1847ms 7.54% std::__final_insertion_sort (inline) 17ms 0.069% 37.72% 1719ms 7.02% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 33ms 0.13% 37.86% 1697ms 6.93% AbstractCellPopulation::GetCellUsingLocationIndex 115ms 0.47% 38.33% 1656ms 6.76% std::__unguarded_insertion_sort (inline) 603ms 2.46% 40.79% 1574ms 6.43% std::__unguarded_linear_insert (inline) 1411ms 5.76% 46.55% 1411ms 5.76% __gnu_cxx::__normal_iterator::operator-- (inline) 49ms 0.2% 46.75% 1261ms 5.15% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 46.75% 1164ms 4.75% NodeBasedCellPopulation::UpdateCellProcessLocation 7ms 0.029% 46.78% 1124ms 4.59% boost::numeric::ublas::vector_assign (inline) 7ms 0.029% 46.81% 1119ms 4.57% DistributedBoxCollection::CalculateBoundaryNodePairs 226ms 0.92% 47.73% 1040ms 4.25% boost::numeric::ublas::indexing_vector_assign 270ms 1.10% 48.83% 931ms 3.80% __dynamic_cast 14ms 0.057% 48.89% 925ms 3.78% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 450ms 1.84% 50.73% 878ms 3.58% DistributedBoxCollection::CalculateContainingBox (partial-inline) 196ms 0.8% 51.53% 832ms 3.40% AbstractMesh::GetVectorFromAtoB 6ms 0.024% 51.55% 819ms 3.34% boost::numeric::ublas::c_vector::operator= (inline) 37ms 0.15% 51.70% 797ms 3.25% std::__copy_move::__copy_m (inline) 0 0% 51.70% 797ms 3.25% std::__copy_move_a (inline) 0 0% 51.70% 797ms 3.25% std::__copy_move_a1 (inline) 0 0% 51.70% 797ms 3.25% std::__copy_move_a2 (inline) 0 0% 51.70% 797ms 3.25% std::copy (inline) 0 0% 51.70% 791ms 3.23% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 779ms 3.18% 54.89% 779ms 3.18% __memcpy_avx_unaligned_erms 0 0% 54.89% 770ms 3.14% boost::numeric::ublas::norm_2 (inline) 603ms 2.46% 57.35% 770ms 3.14% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 57.35% 770ms 3.14% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 57.35% 741ms 3.03% AbstractCellPopulation::WriteResultsToFiles 177ms 0.72% 58.07% 735ms 3.00% NodeAttributes::AddNeighbour 698ms 2.85% 60.92% 698ms 2.85% boost::numeric::ublas::c_vector::operator() 553ms 2.26% 63.18% 639ms 2.61% std::vector::push_back (inline) 12ms 0.049% 63.23% 634ms 2.59% CellPropertyCollection::GetPropertiesType (inline) 27ms 0.11% 63.34% 630ms 2.57% std::_Rb_tree_const_iterator::operator++ (inline) 4ms 0.016% 63.35% 604ms 2.47% AbstractCellBasedSimulation::DoCellBirth 8ms 0.033% 63.39% 599ms 2.45% AbstractCentreBasedCellPopulation::GetDampingConstant 584ms 2.38% 65.77% 584ms 2.38% std::_Rb_tree_increment 37ms 0.15% 65.92% 565ms 2.31% std::_Rb_tree::_Rb_tree (partial-inline) 99ms 0.4% 66.33% 561ms 2.29% std::__new_allocator::allocate (inline) 289ms 1.18% 67.51% 542ms 2.21% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 67.51% 541ms 2.21% std::allocator_traits::allocate (inline) 58ms 0.24% 67.74% 518ms 2.12% std::_Rb_tree::_M_copy (inline) 513ms 2.09% 69.84% 513ms 2.09% boost::numeric::ublas::same_impl_ex 0 0% 69.84% 511ms 2.09% std::_Rb_tree::_M_create_node (inline) 44ms 0.18% 70.02% 499ms 2.04% boost::detail::shared_count::~shared_count (inline) 0 0% 70.02% 499ms 2.04% boost::shared_ptr::~shared_ptr (inline) 1ms 0.0041% 70.02% 492ms 2.01% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 70.02% 468ms 1.91% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 70.02% 463ms 1.89% std::_Rb_tree::_M_get_node (inline) 34ms 0.14% 70.16% 459ms 1.87% operator new 5ms 0.02% 70.18% 455ms 1.86% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 156ms 0.64% 70.82% 454ms 1.85% std::_Rb_tree::_M_clone_node (inline) 3ms 0.012% 70.83% 454ms 1.85% std::set::set (inline) 418ms 1.71% 72.54% 439ms 1.79% boost::detail::sp_counted_base::release 430ms 1.76% 74.29% 430ms 1.76% __strcmp_avx2 1ms 0.0041% 74.30% 427ms 1.74% Cell::GetMutationState 6ms 0.024% 74.32% 419ms 1.71% AbstractCellProperty::IsSubType (inline) 120ms 0.49% 74.81% 417ms 1.70% __GI___libc_malloc 104ms 0.42% 75.24% 403ms 1.65% std::_Rb_tree::_M_erase 99ms 0.4% 75.64% 385ms 1.57% boost::numeric::ublas::vector_binary::size (inline) 80ms 0.33% 75.97% 383ms 1.56% Node::GetRadius 0 0% 75.97% 352ms 1.44% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 75.97% 350ms 1.43% boost::numeric::ublas::inner_prod (inline) 15ms 0.061% 76.03% 350ms 1.43% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 76.03% 350ms 1.43% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 76.03% 345ms 1.41% boost::numeric::ublas::c_vector::assign (inline) 331ms 1.35% 77.38% 331ms 1.35% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 77.38% 326ms 1.33% NodesOnlyMesh::ReMesh 8ms 0.033% 77.41% 317ms 1.29% NodeBasedCellPopulation::UpdateMapsAfterRemesh 315ms 1.29% 78.70% 315ms 1.29% Node::CheckForNodeAttributes 2ms 0.0082% 78.71% 312ms 1.27% NodesOnlyMesh::UpdateNodeIndices 9ms 0.037% 78.74% 308ms 1.26% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 308ms 1.26% 80.00% 308ms 1.26% __gnu_cxx::__normal_iterator::operator++ (inline) 45ms 0.18% 80.18% 308ms 1.26% std::_Rb_tree::~_Rb_tree (inline) 128ms 0.52% 80.71% 289ms 1.18% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 80.71% 285ms 1.16% std::_Rb_tree::_M_drop_node (inline) 7ms 0.029% 80.74% 284ms 1.16% DistributedBoxCollection::GetProcessOwningNode 0 0% 80.74% 277ms 1.13% NodesOnlyMesh::UpdateBoxCollection 6ms 0.024% 80.76% 276ms 1.13% std::_Rb_tree::_M_emplace_hint_unique 112ms 0.46% 81.22% 255ms 1.04% std::__move_median_to_first (inline) 249ms 1.02% 82.23% 249ms 1.02% [libchaste_mesh.so] 0 0% 82.23% 240ms 0.98% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 82.23% 239ms 0.98% VtkMeshWriter::WriteFiles 174ms 0.71% 82.94% 238ms 0.97% Node::AddNeighbour 8ms 0.033% 82.98% 235ms 0.96% std::__new_allocator::deallocate (inline) 231ms 0.94% 83.92% 231ms 0.94% Node::GetIndex 119ms 0.49% 84.41% 231ms 0.94% _int_malloc 106ms 0.43% 84.84% 228ms 0.93% boost::shared_ptr::shared_ptr (inline) 3ms 0.012% 84.85% 226ms 0.92% CellPropertyCollection::HasProperty 3ms 0.012% 84.86% 226ms 0.92% NodesOnlyMesh::AddNodesToBoxes 0 0% 84.86% 224ms 0.91% Cell::HasCellProperty (inline) 8ms 0.033% 84.90% 219ms 0.89% Cell::ReadyToDivide 0 0% 84.90% 218ms 0.89% std::allocator_traits::deallocate (inline) 0 0% 84.90% 218ms 0.89% std::set::~set (inline) 0 0% 84.90% 216ms 0.88% std::_Rb_tree::_M_put_node (inline) 1ms 0.0041% 84.90% 211ms 0.86% vtkXMLWriterBase::Write 0 0% 84.90% 210ms 0.86% vtkStreamingDemandDrivenPipeline::Update 0 0% 84.90% 209ms 0.85% vtkDemandDrivenPipeline::ProcessRequest 0 0% 84.90% 208ms 0.85% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 84.90% 206ms 0.84% vtkStreamingDemandDrivenPipeline::ProcessRequest 63ms 0.26% 85.16% 205ms 0.84% __GI___libc_free 17ms 0.069% 85.23% 205ms 0.84% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 85.23% 205ms 0.84% vtkExecutive::CallAlgorithm 0 0% 85.23% 204ms 0.83% vtkCompositeDataPipeline::ExecuteData 0 0% 85.23% 204ms 0.83% vtkDemandDrivenPipeline::ExecuteData 0 0% 85.23% 204ms 0.83% vtkXMLUnstructuredDataWriter::ProcessRequest 21ms 0.086% 85.31% 190ms 0.78% std::__insertion_sort (inline) 0 0% 85.31% 176ms 0.72% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.31% 176ms 0.72% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 85.31% 172ms 0.7% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 4ms 0.016% 85.33% 171ms 0.7% AbstractCellProperty::IsType (inline) 0 0% 85.33% 159ms 0.65% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 85.33% 159ms 0.65% std::_Rb_tree::clear (inline) 159ms 0.65% 85.98% 159ms 0.65% std::__adjacent_find (inline) 0 0% 85.98% 159ms 0.65% std::__unique (inline) 0 0% 85.98% 159ms 0.65% std::unique (inline) 158ms 0.65% 86.62% 158ms 0.65% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 1ms 0.0041% 86.63% 157ms 0.64% NodesOnlyMesh::ResizeBoxCollection 157ms 0.64% 87.27% 157ms 0.64% [libchaste_cell_based.so] 1ms 0.0041% 87.27% 155ms 0.63% Cell::GetCellId 11ms 0.045% 87.32% 155ms 0.63% NodesOnlyMesh::IsANodeCloseToDomainBoundary 1ms 0.0041% 87.32% 148ms 0.6% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 87.32% 147ms 0.6% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 1ms 0.0041% 87.33% 142ms 0.58% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 130ms 0.53% 87.86% 141ms 0.58% _int_free 0 0% 87.86% 140ms 0.57% vtkXMLWriter::WriteBinaryData 138ms 0.56% 88.42% 138ms 0.56% __ieee754_log_fma 2ms 0.0082% 88.43% 138ms 0.56% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 88.43% 135ms 0.55% vtkXMLWriter::WritePointsAppendedData 0 0% 88.43% 134ms 0.55% vtkXMLWriter::WriteBinaryDataInternal 0 0% 88.43% 133ms 0.54% vtkXMLWriter::WriteBinaryDataBlock 0 0% 88.43% 133ms 0.54% vtkXMLWriter::WriteCompressionBlock 130ms 0.53% 88.96% 130ms 0.53% Node::IsDeleted 3ms 0.012% 88.97% 130ms 0.53% NodeBasedCellPopulation::SetNode 38ms 0.16% 89.13% 127ms 0.52% AbstractCellProperty::IsSame