File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20372ms, 88.82% of 22936ms total Dropped 752 nodes (cum <= 114.68ms) flat flat% sum% cum cum% 0 0% 0% 22788ms 99.35% __libc_start_call_main 0 0% 0% 22788ms 99.35% __libc_start_main_impl 0 0% 0% 22788ms 99.35% _start 0 0% 0% 22773ms 99.29% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 22773ms 99.29% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 22773ms 99.29% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 22773ms 99.29% main 0 0% 0% 22738ms 99.14% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 22738ms 99.14% CxxTest::TestRunner::runTest (inline) 0 0% 0% 22737ms 99.13% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 22730ms 99.10% AbstractCellBasedSimulation::Solve 0 0% 0% 12976ms 56.57% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0% 8610ms 37.54% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0044% 0.0044% 8224ms 35.86% ForwardEulerNumericalMethod::UpdateAllNodePositions 7ms 0.031% 0.035% 8047ms 35.08% AbstractNumericalMethod::ComputeForcesIncludingDamping 2ms 0.0087% 0.044% 7613ms 33.19% NodeBasedCellPopulation::Update 1226ms 5.35% 5.39% 7442ms 32.45% RepulsionForce::AddForceContribution (partial-inline) 6ms 0.026% 5.42% 5572ms 24.29% DistributedBoxCollection::CalculateInteriorNodePairs 2069ms 9.02% 14.44% 4843ms 21.12% std::_Rb_tree::_M_lower_bound (inline) 0 0% 14.44% 4481ms 19.54% OffLatticeSimulation::ApplyBoundaries 10ms 0.044% 14.48% 4442ms 19.37% NodeAttributes::RemoveDuplicateNeighbours 4ms 0.017% 14.50% 4258ms 18.56% std::__sort (inline) 0 0% 14.50% 4258ms 18.56% std::sort (inline) 188ms 0.82% 15.32% 3753ms 16.36% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 2ms 0.0087% 15.33% 3439ms 14.99% AbstractCellPopulation::Iterator::operator++ (inline) 175ms 0.76% 16.09% 3418ms 14.90% AbstractCellPopulation::Iterator::IsRealCell (inline) 56ms 0.24% 16.33% 3340ms 14.56% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 225ms 0.98% 17.31% 3148ms 13.73% std::_Rb_tree::find (inline) 0 0% 17.31% 3147ms 13.72% std::map::find (inline) 23ms 0.1% 17.41% 2881ms 12.56% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2734ms 11.92% 29.33% 2734ms 11.92% std::_Rb_tree::_S_right (inline) 180ms 0.78% 30.12% 2440ms 10.64% std::__introsort_loop 225ms 0.98% 31.10% 2419ms 10.55% std::map::operator[] (partial-inline) 25ms 0.11% 31.21% 2340ms 10.20% PlaneBoundaryCondition::ImposeBoundaryCondition 38ms 0.17% 31.37% 2257ms 9.84% AbstractCellPopulation::GetLocationIndexUsingCell 128ms 0.56% 31.93% 2226ms 9.71% AbstractMesh::GetNode 48ms 0.21% 32.14% 2211ms 9.64% NodesOnlyMesh::GetNodeOrHaloNode 0 0% 32.14% 2184ms 9.52% std::__unguarded_partition_pivot (inline) 17ms 0.074% 32.22% 2141ms 9.33% PlaneBoundaryCondition::VerifyBoundaryCondition 88ms 0.38% 32.60% 2101ms 9.16% NodesOnlyMesh::SolveNodeMapping 1010ms 4.40% 37.00% 1977ms 8.62% std::__unguarded_partition (inline) 0 0% 37.00% 1943ms 8.47% std::_Rb_tree::lower_bound (inline) 0 0% 37.00% 1943ms 8.47% std::map::lower_bound (inline) 0 0% 37.00% 1814ms 7.91% std::__final_insertion_sort (inline) 165ms 0.72% 37.72% 1720ms 7.50% DistributedBoxCollection::AddPairsFromBox 81ms 0.35% 38.08% 1599ms 6.97% std::__unguarded_insertion_sort (inline) 582ms 2.54% 40.61% 1580ms 6.89% std::__unguarded_linear_insert (inline) 26ms 0.11% 40.73% 1538ms 6.71% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 36ms 0.16% 40.88% 1509ms 6.58% AbstractCellPopulation::GetCellUsingLocationIndex 1486ms 6.48% 47.36% 1486ms 6.48% __gnu_cxx::__normal_iterator::operator-- (inline) 32ms 0.14% 47.50% 1308ms 5.70% boost::numeric::ublas::c_vector::c_vector (partial-inline) 51ms 0.22% 47.72% 1201ms 5.24% boost::numeric::ublas::vector_assign (inline) 0 0% 47.72% 1141ms 4.97% NodeBasedCellPopulation::UpdateCellProcessLocation 4ms 0.017% 47.74% 1069ms 4.66% DistributedBoxCollection::CalculateBoundaryNodePairs 343ms 1.50% 49.24% 1061ms 4.63% boost::numeric::ublas::indexing_vector_assign 259ms 1.13% 50.37% 970ms 4.23% __dynamic_cast 164ms 0.72% 51.08% 849ms 3.70% AbstractMesh::GetVectorFromAtoB 363ms 1.58% 52.66% 827ms 3.61% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 52.66% 771ms 3.36% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 15ms 0.065% 52.73% 758ms 3.30% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 52.73% 742ms 3.24% boost::numeric::ublas::norm_2 (inline) 587ms 2.56% 55.29% 742ms 3.24% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 55.29% 742ms 3.24% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 203ms 0.89% 56.17% 704ms 3.07% NodeAttributes::AddNeighbour 0 0% 56.17% 689ms 3.00% AbstractCellPopulation::WriteResultsToFiles 681ms 2.97% 59.14% 681ms 2.97% boost::numeric::ublas::c_vector::operator() 10ms 0.044% 59.19% 617ms 2.69% boost::numeric::ublas::c_vector::operator= (inline) 258ms 1.12% 60.31% 605ms 2.64% __cxxabiv1::__si_class_type_info::__do_dyncast 27ms 0.12% 60.43% 601ms 2.62% std::__copy_move::__copy_m (inline) 0 0% 60.43% 601ms 2.62% std::__copy_move_a (inline) 0 0% 60.43% 601ms 2.62% std::__copy_move_a1 (inline) 0 0% 60.43% 601ms 2.62% std::__copy_move_a2 (inline) 0 0% 60.43% 601ms 2.62% std::copy (inline) 598ms 2.61% 63.04% 598ms 2.61% __memcpy_avx_unaligned_erms 501ms 2.18% 65.22% 569ms 2.48% std::vector::push_back (inline) 0 0% 65.22% 552ms 2.41% AbstractCellBasedSimulation::DoCellBirth 7ms 0.031% 65.25% 548ms 2.39% CellPropertyCollection::GetPropertiesType (inline) 4ms 0.017% 65.27% 543ms 2.37% AbstractCentreBasedCellPopulation::GetDampingConstant 39ms 0.17% 65.44% 531ms 2.32% boost::detail::shared_count::~shared_count (inline) 0 0% 65.44% 531ms 2.32% boost::shared_ptr::~shared_ptr (inline) 501ms 2.18% 67.62% 501ms 2.18% __strcmp_avx2 67ms 0.29% 67.92% 500ms 2.18% std::__new_allocator::allocate (inline) 485ms 2.11% 70.03% 488ms 2.13% boost::detail::sp_counted_base::release 0 0% 70.03% 484ms 2.11% std::allocator_traits::allocate (inline) 26ms 0.11% 70.14% 477ms 2.08% std::_Rb_tree_const_iterator::operator++ (inline) 472ms 2.06% 72.20% 472ms 2.06% boost::numeric::ublas::same_impl_ex 0 0% 72.20% 457ms 1.99% NodeBasedCellPopulation::WriteVtkResultsToFile 446ms 1.94% 74.15% 446ms 1.94% std::_Rb_tree_increment 0 0% 74.15% 444ms 1.94% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 74.15% 440ms 1.92% std::_Rb_tree::_M_create_node (inline) 10ms 0.044% 74.19% 438ms 1.91% std::_Rb_tree::_Rb_tree (partial-inline) 3ms 0.013% 74.20% 433ms 1.89% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 25ms 0.11% 74.31% 428ms 1.87% operator new 52ms 0.23% 74.54% 415ms 1.81% std::_Rb_tree::_M_copy (inline) 4ms 0.017% 74.56% 413ms 1.80% AbstractCellProperty::IsSubType (inline) 112ms 0.49% 75.04% 397ms 1.73% __GI___libc_malloc 0 0% 75.04% 393ms 1.71% std::_Rb_tree::_M_get_node (inline) 4ms 0.017% 75.06% 376ms 1.64% Cell::GetMutationState 115ms 0.5% 75.56% 373ms 1.63% std::_Rb_tree::_M_erase 130ms 0.57% 76.13% 369ms 1.61% Node::GetRadius 120ms 0.52% 76.65% 360ms 1.57% std::_Rb_tree::_M_clone_node (inline) 5ms 0.022% 76.67% 357ms 1.56% std::set::set (inline) 0 0% 76.67% 356ms 1.55% boost::numeric::ublas::c_vector::assign (inline) 0 0% 76.67% 345ms 1.50% boost::numeric::ublas::inner_prod (inline) 14ms 0.061% 76.74% 344ms 1.50% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 76.74% 344ms 1.50% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 29ms 0.13% 76.86% 312ms 1.36% boost::numeric::ublas::vector_binary::size (inline) 6ms 0.026% 76.89% 308ms 1.34% NodeBasedCellPopulation::UpdateMapsAfterRemesh 37ms 0.16% 77.05% 303ms 1.32% std::_Rb_tree::~_Rb_tree (inline) 0 0% 77.05% 300ms 1.31% std::_Rb_tree::_Alloc_node::operator() (inline) 293ms 1.28% 78.33% 293ms 1.28% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 112ms 0.49% 78.81% 286ms 1.25% boost::numeric::ublas::vector_inner_prod::apply (inline) 283ms 1.23% 80.05% 283ms 1.23% __gnu_cxx::__normal_iterator::operator++ (inline) 3ms 0.013% 80.06% 277ms 1.21% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 80.06% 275ms 1.20% NodesOnlyMesh::UpdateBoxCollection 0 0% 80.06% 269ms 1.17% NodesOnlyMesh::ReMesh 9ms 0.039% 80.10% 266ms 1.16% DistributedBoxCollection::GetProcessOwningNode 5ms 0.022% 80.12% 262ms 1.14% NodesOnlyMesh::UpdateNodeIndices 0 0% 80.12% 253ms 1.10% std::_Rb_tree::_M_drop_node (inline) 7ms 0.031% 80.15% 251ms 1.09% std::_Rb_tree::_M_emplace_hint_unique 246ms 1.07% 81.23% 246ms 1.07% Node::CheckForNodeAttributes 0 0% 81.23% 244ms 1.06% NodesOnlyMesh::AddNodesToBoxes 126ms 0.55% 81.78% 234ms 1.02% _int_malloc 0 0% 81.78% 228ms 0.99% std::set::~set (inline) 22ms 0.096% 81.87% 215ms 0.94% std::__insertion_sort (inline) 0 0% 81.87% 211ms 0.92% NodesOnlyMesh::ResizeBoxCollection 0 0% 81.87% 210ms 0.92% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 20ms 0.087% 81.96% 210ms 0.92% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 81.96% 209ms 0.91% VtkMeshWriter::WriteFiles 106ms 0.46% 82.42% 207ms 0.9% boost::shared_ptr::shared_ptr (inline) 99ms 0.43% 82.85% 206ms 0.9% std::__move_median_to_first (inline) 6ms 0.026% 82.88% 196ms 0.85% std::__new_allocator::deallocate (inline) 0 0% 82.88% 191ms 0.83% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 82.88% 191ms 0.83% vtkStreamingDemandDrivenPipeline::Update 0 0% 82.88% 191ms 0.83% vtkXMLWriterBase::Write 1ms 0.0044% 82.88% 190ms 0.83% vtkDemandDrivenPipeline::ProcessRequest 0 0% 82.88% 190ms 0.83% vtkExecutive::CallAlgorithm 0 0% 82.88% 190ms 0.83% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 82.88% 189ms 0.82% vtkCompositeDataPipeline::ExecuteData 0 0% 82.88% 189ms 0.82% vtkDemandDrivenPipeline::ExecuteData 185ms 0.81% 83.69% 185ms 0.81% [libchaste_cell_based.so] 0 0% 83.69% 176ms 0.77% std::allocator_traits::deallocate (inline) 2ms 0.0087% 83.70% 175ms 0.76% CellPropertyCollection::HasProperty 0 0% 83.70% 175ms 0.76% std::_Rb_tree::_M_put_node (inline) 0 0% 83.70% 174ms 0.76% Cell::HasCellProperty (inline) 67ms 0.29% 83.99% 172ms 0.75% __GI___libc_free 9ms 0.039% 84.03% 170ms 0.74% Cell::ReadyToDivide 169ms 0.74% 84.77% 169ms 0.74% Node::GetIndex 0 0% 84.77% 167ms 0.73% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 84.77% 167ms 0.73% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 163ms 0.71% 85.48% 166ms 0.72% std::__adjacent_find (inline) 0 0% 85.48% 166ms 0.72% std::__unique (inline) 0 0% 85.48% 166ms 0.72% std::unique (inline) 0 0% 85.48% 162ms 0.71% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 161ms 0.7% 86.18% 161ms 0.7% boost::shared_ptr::operator-> (inline) 22ms 0.096% 86.27% 157ms 0.68% boost::numeric::ublas::vector_reference::operator() (inline) 6ms 0.026% 86.30% 153ms 0.67% DistributedBoxCollection::GetIsPeriodicAllDims 72ms 0.31% 86.61% 147ms 0.64% Node::AddNeighbour 0 0% 86.61% 142ms 0.62% boost::numeric::ublas::vector_binary::operator() (inline) 6ms 0.026% 86.64% 140ms 0.61% AbstractCellProperty::IsType (inline) 0 0% 86.64% 140ms 0.61% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 86.64% 138ms 0.6% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 86.64% 137ms 0.6% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 86.64% 136ms 0.59% vtkXMLWriter::WriteBinaryData 134ms 0.58% 87.23% 134ms 0.58% [libchaste_mesh.so] 0 0% 87.23% 129ms 0.56% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.23% 128ms 0.56% Cell::GetCellId 0 0% 87.23% 127ms 0.55% std::_Rb_tree::clear (inline) 0 0% 87.23% 127ms 0.55% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.23% 127ms 0.55% vtkXMLWriter::WriteCompressionBlock 3ms 0.013% 87.24% 125ms 0.54% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 87.24% 123ms 0.54% vtkXMLWriter::WritePointsAppendedData 5ms 0.022% 87.26% 122ms 0.53% boost::numeric::ublas::c_vector::operator[] (inline) 3ms 0.013% 87.27% 121ms 0.53% AbstractCellPopulation::SetCellUsingLocationIndex 120ms 0.52% 87.80% 120ms 0.52% __ieee754_log_fma 1ms 0.0044% 87.80% 119ms 0.52% std::set::insert (inline) 118ms 0.51% 88.32% 118ms 0.51% Node::IsDeleted 1ms 0.0044% 88.32% 118ms 0.51% std::_Rb_tree::_M_insert_unique 0 0% 88.32% 116ms 0.51% tbb::detail::r1::parallel_pipeline 115ms 0.5% 88.82% 115ms 0.5% Node::rGetLocation