File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 14248ms, 89.29% of 15957ms total Dropped 746 nodes (cum <= 79.78ms) flat flat% sum% cum cum% 0 0% 0% 15865ms 99.42% __libc_start_call_main 0 0% 0% 15865ms 99.42% __libc_start_main_impl 0 0% 0% 15865ms 99.42% _start 0 0% 0% 15854ms 99.35% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 15854ms 99.35% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 15854ms 99.35% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 15854ms 99.35% main 0 0% 0% 15815ms 99.11% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 15815ms 99.11% CxxTest::TestRunner::runTest (inline) 0 0% 0% 15815ms 99.11% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 15810ms 99.08% AbstractCellBasedSimulation::Solve 0 0% 0% 8826ms 55.31% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0% 6211ms 38.92% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 5540ms 34.72% NodeBasedCellPopulation::Update 0 0% 0% 5259ms 32.96% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.013% 0.013% 5144ms 32.24% AbstractNumericalMethod::ComputeForcesIncludingDamping 747ms 4.68% 4.69% 4755ms 29.80% RepulsionForce::AddForceContribution (partial-inline) 6ms 0.038% 4.73% 4155ms 26.04% DistributedBoxCollection::CalculateInteriorNodePairs 0 0% 4.73% 3374ms 21.14% OffLatticeSimulation::ApplyBoundaries 24ms 0.15% 4.88% 3341ms 20.94% NodeAttributes::RemoveDuplicateNeighbours 1ms 0.0063% 4.89% 3173ms 19.88% std::__sort (inline) 0 0% 4.89% 3173ms 19.88% std::sort (inline) 1607ms 10.07% 14.96% 3101ms 19.43% std::_Rb_tree::_M_lower_bound (inline) 119ms 0.75% 15.70% 2412ms 15.12% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 3ms 0.019% 15.72% 2388ms 14.97% AbstractCellPopulation::Iterator::operator++ (inline) 138ms 0.86% 16.59% 2387ms 14.96% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 104ms 0.65% 17.24% 2368ms 14.84% AbstractCellPopulation::Iterator::IsRealCell (inline) 199ms 1.25% 18.49% 2004ms 12.56% std::_Rb_tree::find (inline) 0 0% 18.49% 2003ms 12.55% std::map::find (inline) 6ms 0.038% 18.52% 1963ms 12.30% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 108ms 0.68% 19.20% 1830ms 11.47% std::__introsort_loop 45ms 0.28% 19.48% 1760ms 11.03% PlaneBoundaryCondition::ImposeBoundaryCondition 0 0% 19.48% 1665ms 10.43% std::__unguarded_partition_pivot (inline) 176ms 1.10% 20.59% 1664ms 10.43% std::map::operator[] (partial-inline) 89ms 0.56% 21.14% 1648ms 10.33% AbstractMesh::GetNode 32ms 0.2% 21.34% 1614ms 10.11% PlaneBoundaryCondition::VerifyBoundaryCondition 2ms 0.013% 21.36% 1602ms 10.04% NodesOnlyMesh::GetNodeOrHaloNode 91ms 0.57% 21.93% 1560ms 9.78% NodesOnlyMesh::SolveNodeMapping 739ms 4.63% 26.56% 1490ms 9.34% std::__unguarded_partition (inline) 1445ms 9.06% 35.61% 1445ms 9.06% std::_Rb_tree::_S_right (inline) 36ms 0.23% 35.84% 1441ms 9.03% AbstractCellPopulation::GetLocationIndexUsingCell 3ms 0.019% 35.86% 1341ms 8.40% std::__final_insertion_sort (inline) 0 0% 35.86% 1312ms 8.22% std::_Rb_tree::lower_bound (inline) 0 0% 35.86% 1312ms 8.22% std::map::lower_bound (inline) 128ms 0.8% 36.66% 1256ms 7.87% DistributedBoxCollection::AddPairsFromBox 75ms 0.47% 37.13% 1190ms 7.46% std::__unguarded_insertion_sort (inline) 404ms 2.53% 39.66% 1131ms 7.09% std::__unguarded_linear_insert (inline) 1079ms 6.76% 46.42% 1079ms 6.76% __gnu_cxx::__normal_iterator::operator-- (inline) 9ms 0.056% 46.48% 978ms 6.13% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 18ms 0.11% 46.59% 966ms 6.05% AbstractCellPopulation::GetCellUsingLocationIndex 31ms 0.19% 46.79% 783ms 4.91% boost::numeric::ublas::c_vector::c_vector (partial-inline) 24ms 0.15% 46.94% 774ms 4.85% boost::detail::shared_count::~shared_count (inline) 0 0% 46.94% 774ms 4.85% boost::shared_ptr::~shared_ptr (inline) 7ms 0.044% 46.98% 766ms 4.80% DistributedBoxCollection::CalculateBoundaryNodePairs 0 0% 46.98% 749ms 4.69% NodeBasedCellPopulation::UpdateCellProcessLocation 741ms 4.64% 51.63% 746ms 4.68% boost::detail::sp_counted_base::release 36ms 0.23% 51.85% 701ms 4.39% boost::numeric::ublas::vector_assign (inline) 13ms 0.081% 51.93% 674ms 4.22% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 131ms 0.82% 52.75% 636ms 3.99% boost::numeric::ublas::indexing_vector_assign 0 0% 52.75% 583ms 3.65% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 52.75% 572ms 3.58% boost::numeric::ublas::norm_2 (inline) 387ms 2.43% 55.18% 572ms 3.58% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 55.18% 572ms 3.58% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 248ms 1.55% 56.73% 539ms 3.38% DistributedBoxCollection::CalculateContainingBox (partial-inline) 91ms 0.57% 57.30% 515ms 3.23% AbstractMesh::GetVectorFromAtoB 0 0% 57.30% 473ms 2.96% AbstractCellPopulation::WriteResultsToFiles 121ms 0.76% 58.06% 467ms 2.93% __dynamic_cast 39ms 0.24% 58.31% 458ms 2.87% std::_Rb_tree_const_iterator::operator++ (inline) 413ms 2.59% 60.89% 413ms 2.59% std::_Rb_tree_increment 1ms 0.0063% 60.90% 407ms 2.55% boost::numeric::ublas::c_vector::operator= (inline) 29ms 0.18% 61.08% 397ms 2.49% std::__copy_move::__copy_m (inline) 0 0% 61.08% 397ms 2.49% std::__copy_move_a (inline) 0 0% 61.08% 397ms 2.49% std::__copy_move_a1 (inline) 0 0% 61.08% 397ms 2.49% std::__copy_move_a2 (inline) 0 0% 61.08% 397ms 2.49% std::copy (inline) 395ms 2.48% 63.56% 395ms 2.48% boost::numeric::ublas::c_vector::operator() 377ms 2.36% 65.92% 377ms 2.36% __memcpy_avx512_unaligned_erms 2ms 0.013% 65.93% 357ms 2.24% AbstractCentreBasedCellPopulation::GetDampingConstant 2ms 0.013% 65.95% 353ms 2.21% AbstractCellBasedSimulation::DoCellBirth 350ms 2.19% 68.14% 350ms 2.19% boost::numeric::ublas::same_impl_ex 28ms 0.18% 68.31% 346ms 2.17% std::__new_allocator::allocate (inline) 0 0% 68.31% 332ms 2.08% std::allocator_traits::allocate (inline) 2ms 0.013% 68.33% 329ms 2.06% NodeBasedCellPopulation::WriteVtkResultsToFile 20ms 0.13% 68.45% 329ms 2.06% std::_Rb_tree::_Rb_tree (partial-inline) 54ms 0.34% 68.79% 320ms 2.01% std::_Rb_tree::_M_erase 0 0% 68.79% 317ms 1.99% AbstractCellBasedSimulation::DoCellRemoval (inline) 92ms 0.58% 69.37% 317ms 1.99% std::_Rb_tree::~_Rb_tree (inline) 7ms 0.044% 69.41% 316ms 1.98% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 18ms 0.11% 69.52% 311ms 1.95% operator new 33ms 0.21% 69.73% 306ms 1.92% std::_Rb_tree::_M_copy (inline) 2ms 0.013% 69.74% 305ms 1.91% CellPropertyCollection::GetPropertiesType (inline) 0 0% 69.74% 294ms 1.84% std::_Rb_tree::_M_create_node (inline) 164ms 1.03% 70.77% 288ms 1.80% __cxxabiv1::__si_class_type_info::__do_dyncast 105ms 0.66% 71.43% 283ms 1.77% __GI___libc_malloc 0 0% 71.43% 282ms 1.77% std::_Rb_tree::_M_get_node (inline) 102ms 0.64% 72.07% 273ms 1.71% std::_Rb_tree::_M_clone_node (inline) 2ms 0.013% 72.08% 273ms 1.71% std::set::set (inline) 0 0% 72.08% 260ms 1.63% std::_Rb_tree::_M_drop_node (inline) 107ms 0.67% 72.75% 259ms 1.62% NodeAttributes::AddNeighbour 0 0% 72.75% 259ms 1.62% std::set::~set (inline) 0 0% 72.75% 245ms 1.54% NodesOnlyMesh::ReMesh 11ms 0.069% 72.82% 242ms 1.52% boost::numeric::ublas::vector_binary::size (inline) 151ms 0.95% 73.77% 239ms 1.50% std::vector::push_back (inline) 193ms 1.21% 74.98% 237ms 1.49% Node::AddNeighbour 4ms 0.025% 75.00% 234ms 1.47% NodesOnlyMesh::UpdateNodeIndices 1ms 0.0063% 75.01% 231ms 1.45% Cell::GetMutationState 21ms 0.13% 75.14% 226ms 1.42% Node::GetRadius 218ms 1.37% 76.51% 218ms 1.37% __gnu_cxx::__normal_iterator::operator++ (inline) 3ms 0.019% 76.52% 211ms 1.32% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 76.52% 210ms 1.32% boost::numeric::ublas::c_vector::assign (inline) 0 0% 76.52% 204ms 1.28% std::_Rb_tree::_Alloc_node::operator() (inline) 198ms 1.24% 77.77% 198ms 1.24% [libchaste_cell_based.so] 0 0% 77.77% 196ms 1.23% AbstractCellProperty::IsSubType (inline) 194ms 1.22% 78.98% 194ms 1.22% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 187ms 1.17% 80.15% 187ms 1.17% __strcmp_evex 181ms 1.13% 81.29% 181ms 1.13% Node::CheckForNodeAttributes 1ms 0.0063% 81.29% 178ms 1.12% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 7ms 0.044% 81.34% 176ms 1.10% std::_Rb_tree::_M_emplace_hint_unique 154ms 0.97% 82.30% 173ms 1.08% boost::shared_ptr::shared_ptr (inline) 0 0% 82.30% 171ms 1.07% DistributedBoxCollection::GetProcessOwningNode 0 0% 82.30% 170ms 1.07% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 82.30% 170ms 1.07% VtkMeshWriter::WriteFiles 6ms 0.038% 82.34% 167ms 1.05% std::__new_allocator::deallocate (inline) 83ms 0.52% 82.86% 166ms 1.04% std::__move_median_to_first (inline) 0 0% 82.86% 165ms 1.03% NodesOnlyMesh::UpdateBoxCollection 0 0% 82.86% 159ms 1% std::allocator_traits::deallocate (inline) 0 0% 82.86% 157ms 0.98% std::_Rb_tree::_M_put_node (inline) 0 0% 82.86% 150ms 0.94% boost::numeric::ublas::inner_prod (inline) 9ms 0.056% 82.92% 148ms 0.93% std::__insertion_sort (inline) 14ms 0.088% 83.00% 146ms 0.91% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 83.00% 146ms 0.91% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 83.00% 144ms 0.9% vtkStreamingDemandDrivenPipeline::Update 0 0% 83.00% 144ms 0.9% vtkXMLWriterBase::Write 0 0% 83.00% 143ms 0.9% vtkDemandDrivenPipeline::ProcessRequest 0 0% 83.00% 142ms 0.89% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 83.00% 142ms 0.89% vtkExecutive::CallAlgorithm 29ms 0.18% 83.19% 141ms 0.88% __GI___libc_free 0 0% 83.19% 140ms 0.88% vtkCompositeDataPipeline::ExecuteData 0 0% 83.19% 140ms 0.88% vtkDemandDrivenPipeline::ExecuteData 0 0% 83.19% 140ms 0.88% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 83.19% 140ms 0.88% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 83.19% 137ms 0.86% NodesOnlyMesh::AddNodesToBoxes 80ms 0.5% 83.69% 137ms 0.86% _int_malloc 121ms 0.76% 84.45% 131ms 0.82% std::__adjacent_find (inline) 0 0% 84.45% 131ms 0.82% std::__unique (inline) 0 0% 84.45% 131ms 0.82% std::unique (inline) 129ms 0.81% 85.25% 129ms 0.81% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 127ms 0.8% 86.05% 127ms 0.8% boost::shared_ptr::operator-> (inline) 125ms 0.78% 86.83% 125ms 0.78% Node::GetIndex 0 0% 86.83% 119ms 0.75% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 86.83% 119ms 0.75% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 86.83% 113ms 0.71% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 31ms 0.19% 87.03% 111ms 0.7% boost::numeric::ublas::vector_inner_prod::apply (inline) 104ms 0.65% 87.68% 110ms 0.69% _int_free 107ms 0.67% 88.35% 107ms 0.67% [libchaste_mesh.so] 0 0% 88.35% 106ms 0.66% std::_Rb_tree::_M_destroy_node (inline) 0 0% 88.35% 106ms 0.66% std::__new_allocator::destroy (inline) 0 0% 88.35% 106ms 0.66% std::allocator_traits::destroy (inline) 0 0% 88.35% 104ms 0.65% std::_Rb_tree::clear (inline) 2ms 0.013% 88.36% 101ms 0.63% CellPropertyCollection::HasProperty 0 0% 88.36% 100ms 0.63% Cell::HasCellProperty (inline) 3ms 0.019% 88.38% 90ms 0.56% Cell::ReadyToDivide 0 0% 88.38% 90ms 0.56% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 88.38% 89ms 0.56% boost::numeric::ublas::vector_binary::operator() (inline) 58ms 0.36% 88.74% 87ms 0.55% std::vector::emplace_back (inline) 0 0% 88.74% 86ms 0.54% vtkXMLWriter::WriteBinaryData 0 0% 88.74% 83ms 0.52% vtkXMLWriter::WriteBinaryDataBlock 0 0% 88.74% 83ms 0.52% vtkXMLWriter::WriteBinaryDataInternal 0 0% 88.74% 82ms 0.51% NodesOnlyMesh::ResizeBoxCollection 0 0% 88.74% 82ms 0.51% std::map::clear (inline) 0 0% 88.74% 82ms 0.51% vtkXMLWriter::WriteCompressionBlock 5ms 0.031% 88.78% 81ms 0.51% NodesOnlyMesh::IsANodeCloseToDomainBoundary 2ms 0.013% 88.79% 80ms 0.5% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 80ms 0.5% 89.29% 80ms 0.5% __ieee754_log_fma 0 0% 89.29% 80ms 0.5% vtkXMLWriter::WritePointsAppendedData