File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 21999ms, 88.68% of 24806ms total Dropped 830 nodes (cum <= 124.03ms) flat flat% sum% cum cum% 0 0% 0% 24689ms 99.53% __libc_start_call_main 0 0% 0% 24689ms 99.53% __libc_start_main_impl 0 0% 0% 24689ms 99.53% _start 0 0% 0% 24671ms 99.46% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 24671ms 99.46% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 24671ms 99.46% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 24671ms 99.46% main 0 0% 0% 24632ms 99.30% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 24632ms 99.30% CxxTest::TestRunner::runTest (inline) 0 0% 0% 24632ms 99.30% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.004% 0.004% 24623ms 99.26% AbstractCellBasedSimulation::Solve 4ms 0.016% 0.02% 14092ms 56.81% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.004% 0.024% 9282ms 37.42% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0081% 0.032% 9150ms 36.89% ForwardEulerNumericalMethod::UpdateAllNodePositions 14ms 0.056% 0.089% 8973ms 36.17% AbstractNumericalMethod::ComputeForcesIncludingDamping 1306ms 5.26% 5.35% 8233ms 33.19% RepulsionForce::AddForceContribution (partial-inline) 1ms 0.004% 5.36% 8215ms 33.12% NodeBasedCellPopulation::Update 12ms 0.048% 5.41% 6098ms 24.58% DistributedBoxCollection::CalculateInteriorNodePairs 2116ms 8.53% 13.94% 5088ms 20.51% std::_Rb_tree::_M_lower_bound (inline) 10ms 0.04% 13.98% 4629ms 18.66% NodeAttributes::RemoveDuplicateNeighbours 0 0% 13.98% 4629ms 18.66% OffLatticeSimulation::ApplyBoundaries 7ms 0.028% 14.00% 4440ms 17.90% std::__sort (inline) 0 0% 14.00% 4440ms 17.90% std::sort (inline) 221ms 0.89% 14.90% 4067ms 16.40% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 67ms 0.27% 15.17% 3336ms 13.45% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 257ms 1.04% 16.20% 3336ms 13.45% std::_Rb_tree::find (inline) 0 0% 16.20% 3336ms 13.45% std::map::find (inline) 8ms 0.032% 16.23% 3222ms 12.99% AbstractCellPopulation::Iterator::operator++ (inline) 174ms 0.7% 16.94% 3175ms 12.80% AbstractCellPopulation::Iterator::IsRealCell (inline) 2941ms 11.86% 28.79% 2941ms 11.86% std::_Rb_tree::_S_right (inline) 21ms 0.085% 28.88% 2750ms 11.09% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 185ms 0.75% 29.62% 2581ms 10.40% std::__introsort_loop 190ms 0.77% 30.39% 2547ms 10.27% std::map::operator[] (partial-inline) 186ms 0.75% 31.14% 2478ms 9.99% AbstractMesh::GetNode 58ms 0.23% 31.37% 2466ms 9.94% NodesOnlyMesh::GetNodeOrHaloNode 14ms 0.056% 31.43% 2451ms 9.88% PlaneBoundaryCondition::ImposeBoundaryCondition 0 0% 31.43% 2301ms 9.28% std::__unguarded_partition_pivot (inline) 110ms 0.44% 31.87% 2298ms 9.26% NodesOnlyMesh::SolveNodeMapping 50ms 0.2% 32.07% 2228ms 8.98% AbstractCellPopulation::GetLocationIndexUsingCell 10ms 0.04% 32.11% 2178ms 8.78% PlaneBoundaryCondition::VerifyBoundaryCondition 144ms 0.58% 32.69% 2102ms 8.47% DistributedBoxCollection::AddPairsFromBox 983ms 3.96% 36.66% 2081ms 8.39% std::__unguarded_partition (inline) 0 0% 36.66% 2050ms 8.26% std::_Rb_tree::lower_bound (inline) 0 0% 36.66% 2050ms 8.26% std::map::lower_bound (inline) 1ms 0.004% 36.66% 1849ms 7.45% std::__final_insertion_sort (inline) 18ms 0.073% 36.73% 1724ms 6.95% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 24ms 0.097% 36.83% 1701ms 6.86% AbstractCellPopulation::GetCellUsingLocationIndex 103ms 0.42% 37.25% 1650ms 6.65% std::__unguarded_insertion_sort (inline) 601ms 2.42% 39.67% 1580ms 6.37% std::__unguarded_linear_insert (inline) 1426ms 5.75% 45.42% 1426ms 5.75% __gnu_cxx::__normal_iterator::operator-- (inline) 44ms 0.18% 45.59% 1317ms 5.31% boost::numeric::ublas::c_vector::c_vector (partial-inline) 1ms 0.004% 45.60% 1212ms 4.89% NodeBasedCellPopulation::UpdateCellProcessLocation 8ms 0.032% 45.63% 1174ms 4.73% boost::numeric::ublas::vector_assign (inline) 5ms 0.02% 45.65% 1126ms 4.54% DistributedBoxCollection::CalculateBoundaryNodePairs 227ms 0.92% 46.57% 1075ms 4.33% boost::numeric::ublas::indexing_vector_assign 21ms 0.085% 46.65% 945ms 3.81% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 268ms 1.08% 47.73% 900ms 3.63% __dynamic_cast 0 0% 47.73% 868ms 3.50% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 165ms 0.67% 48.40% 866ms 3.49% AbstractMesh::GetVectorFromAtoB 0 0% 48.40% 858ms 3.46% boost::numeric::ublas::norm_2 (inline) 675ms 2.72% 51.12% 858ms 3.46% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 51.12% 858ms 3.46% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 367ms 1.48% 52.60% 819ms 3.30% DistributedBoxCollection::CalculateContainingBox (partial-inline) 7ms 0.028% 52.62% 802ms 3.23% boost::numeric::ublas::c_vector::operator= (inline) 223ms 0.9% 53.52% 787ms 3.17% NodeAttributes::AddNeighbour 41ms 0.17% 53.69% 785ms 3.16% std::__copy_move::__copy_m (inline) 0 0% 53.69% 785ms 3.16% std::__copy_move_a (inline) 0 0% 53.69% 785ms 3.16% std::__copy_move_a1 (inline) 0 0% 53.69% 785ms 3.16% std::__copy_move_a2 (inline) 0 0% 53.69% 785ms 3.16% std::copy (inline) 772ms 3.11% 56.80% 772ms 3.11% __memcpy_avx_unaligned_erms 1ms 0.004% 56.80% 745ms 3.00% AbstractCellPopulation::WriteResultsToFiles 26ms 0.1% 56.91% 703ms 2.83% std::_Rb_tree_const_iterator::operator++ (inline) 702ms 2.83% 59.74% 702ms 2.83% boost::numeric::ublas::c_vector::operator() 6ms 0.024% 59.76% 665ms 2.68% AbstractCentreBasedCellPopulation::GetDampingConstant 660ms 2.66% 62.42% 660ms 2.66% std::_Rb_tree_increment 12ms 0.048% 62.47% 656ms 2.64% CellPropertyCollection::GetPropertiesType (inline) 561ms 2.26% 64.73% 650ms 2.62% std::vector::push_back (inline) 3ms 0.012% 64.75% 586ms 2.36% AbstractCellBasedSimulation::DoCellBirth 104ms 0.42% 65.17% 566ms 2.28% std::__new_allocator::allocate (inline) 561ms 2.26% 67.43% 561ms 2.26% boost::numeric::ublas::same_impl_ex 46ms 0.19% 67.61% 551ms 2.22% boost::detail::shared_count::~shared_count (inline) 0 0% 67.61% 551ms 2.22% boost::shared_ptr::~shared_ptr (inline) 0 0% 67.61% 542ms 2.18% std::allocator_traits::allocate (inline) 41ms 0.17% 67.78% 540ms 2.18% std::_Rb_tree::_Rb_tree (partial-inline) 247ms 1% 68.77% 511ms 2.06% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 68.77% 497ms 2.00% std::_Rb_tree::_M_create_node (inline) 0 0% 68.77% 496ms 2.00% NodeBasedCellPopulation::WriteVtkResultsToFile 467ms 1.88% 70.66% 490ms 1.98% boost::detail::sp_counted_base::release 46ms 0.19% 70.84% 483ms 1.95% std::_Rb_tree::_M_copy (inline) 0 0% 70.84% 476ms 1.92% AbstractCellBasedSimulation::DoCellRemoval (inline) 24ms 0.097% 70.94% 464ms 1.87% operator new 6ms 0.024% 70.96% 463ms 1.87% Cell::GetMutationState 1ms 0.004% 70.97% 462ms 1.86% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1ms 0.004% 70.97% 459ms 1.85% std::set::set (inline) 0 0% 70.97% 457ms 1.84% std::_Rb_tree::_M_get_node (inline) 120ms 0.48% 71.45% 448ms 1.81% std::_Rb_tree::_M_erase 441ms 1.78% 73.23% 441ms 1.78% __strcmp_avx2 108ms 0.44% 73.67% 427ms 1.72% __GI___libc_malloc 5ms 0.02% 73.69% 426ms 1.72% AbstractCellProperty::IsSubType (inline) 143ms 0.58% 74.26% 426ms 1.72% std::_Rb_tree::_M_clone_node (inline) 104ms 0.42% 74.68% 414ms 1.67% boost::numeric::ublas::vector_binary::size (inline) 79ms 0.32% 75.00% 392ms 1.58% Node::GetRadius 0 0% 75.00% 386ms 1.56% NodesOnlyMesh::ReMesh 2ms 0.0081% 75.01% 367ms 1.48% NodesOnlyMesh::UpdateNodeIndices 0 0% 75.01% 357ms 1.44% boost::numeric::ublas::c_vector::assign (inline) 0 0% 75.01% 353ms 1.42% boost::numeric::ublas::inner_prod (inline) 17ms 0.069% 75.08% 352ms 1.42% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 75.08% 352ms 1.42% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 349ms 1.41% 76.49% 349ms 1.41% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 347ms 1.40% 77.88% 347ms 1.40% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 77.88% 334ms 1.35% std::_Rb_tree::_Alloc_node::operator() (inline) 52ms 0.21% 78.09% 325ms 1.31% std::_Rb_tree::~_Rb_tree (inline) 320ms 1.29% 79.38% 320ms 1.29% Node::CheckForNodeAttributes 0 0% 79.38% 316ms 1.27% std::_Rb_tree::_M_drop_node (inline) 8ms 0.032% 79.42% 310ms 1.25% NodeBasedCellPopulation::UpdateMapsAfterRemesh 14ms 0.056% 79.47% 307ms 1.24% std::_Rb_tree::_M_emplace_hint_unique 130ms 0.52% 80.00% 304ms 1.23% boost::numeric::ublas::vector_inner_prod::apply (inline) 8ms 0.032% 80.03% 299ms 1.21% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 4ms 0.016% 80.05% 280ms 1.13% DistributedBoxCollection::GetProcessOwningNode 10ms 0.04% 80.09% 271ms 1.09% std::__new_allocator::deallocate (inline) 0 0% 80.09% 270ms 1.09% NodesOnlyMesh::UpdateBoxCollection 130ms 0.52% 80.61% 265ms 1.07% boost::shared_ptr::shared_ptr (inline) 230ms 0.93% 81.54% 263ms 1.06% Node::AddNeighbour 152ms 0.61% 82.15% 260ms 1.05% _int_malloc 0 0% 82.15% 253ms 1.02% std::allocator_traits::deallocate (inline) 0 0% 82.15% 250ms 1.01% std::_Rb_tree::_M_put_node (inline) 78ms 0.31% 82.46% 243ms 0.98% __GI___libc_free 0 0% 82.46% 242ms 0.98% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 82.46% 240ms 0.97% VtkMeshWriter::WriteFiles 0 0% 82.46% 237ms 0.96% std::set::~set (inline) 233ms 0.94% 83.40% 233ms 0.94% Node::GetIndex 3ms 0.012% 83.42% 231ms 0.93% CellPropertyCollection::HasProperty 0 0% 83.42% 230ms 0.93% Cell::HasCellProperty (inline) 217ms 0.87% 84.29% 217ms 0.87% [libchaste_mesh.so] 1ms 0.004% 84.29% 217ms 0.87% vtkStreamingDemandDrivenPipeline::Update 0 0% 84.29% 217ms 0.87% vtkXMLWriterBase::Write 0 0% 84.29% 214ms 0.86% vtkStreamingDemandDrivenPipeline::ProcessRequest 4ms 0.016% 84.31% 213ms 0.86% NodesOnlyMesh::AddNodesToBoxes 0 0% 84.31% 213ms 0.86% vtkDemandDrivenPipeline::ProcessRequest 99ms 0.4% 84.71% 212ms 0.85% std::__move_median_to_first (inline) 0 0% 84.71% 212ms 0.85% vtkDemandDrivenPipeline::ExecuteData 0 0% 84.71% 212ms 0.85% vtkExecutive::CallAlgorithm 0 0% 84.71% 212ms 0.85% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 84.71% 211ms 0.85% vtkCompositeDataPipeline::ExecuteData 0 0% 84.71% 203ms 0.82% boost::numeric::ublas::vector_binary::operator() (inline) 19ms 0.077% 84.79% 203ms 0.82% boost::numeric::ublas::vector_reference::operator() (inline) 3ms 0.012% 84.80% 202ms 0.81% Cell::ReadyToDivide 17ms 0.069% 84.87% 198ms 0.8% std::__insertion_sort (inline) 0 0% 84.87% 190ms 0.77% std::_Rb_tree::clear (inline) 6ms 0.024% 84.89% 184ms 0.74% AbstractCellProperty::IsType (inline) 0 0% 84.89% 180ms 0.73% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 84.89% 180ms 0.73% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 84.89% 172ms 0.69% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 166ms 0.67% 85.56% 166ms 0.67% std::__adjacent_find (inline) 0 0% 85.56% 166ms 0.67% std::__unique (inline) 0 0% 85.56% 166ms 0.67% std::unique (inline) 154ms 0.62% 86.18% 165ms 0.67% _int_free 0 0% 86.18% 163ms 0.66% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 86.18% 161ms 0.65% NodesOnlyMesh::ResizeBoxCollection 14ms 0.056% 86.24% 160ms 0.65% NodesOnlyMesh::IsANodeCloseToDomainBoundary 156ms 0.63% 86.87% 156ms 0.63% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 1ms 0.004% 86.87% 153ms 0.62% vtkXMLWriter::WriteBinaryData 0 0% 86.87% 150ms 0.6% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 150ms 0.6% 87.47% 150ms 0.6% Node::rGetLocation 149ms 0.6% 88.08% 149ms 0.6% [libchaste_cell_based.so] 0 0% 88.08% 147ms 0.59% vtkXMLWriter::WriteBinaryDataBlock 0 0% 88.08% 147ms 0.59% vtkXMLWriter::WriteBinaryDataInternal 0 0% 88.08% 146ms 0.59% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 88.08% 146ms 0.59% vtkXMLWriter::WriteCompressionBlock 0 0% 88.08% 144ms 0.58% Cell::GetCellId 52ms 0.21% 88.29% 141ms 0.57% AbstractCellProperty::IsSame 1ms 0.004% 88.29% 137ms 0.55% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 88.29% 137ms 0.55% std::map::clear (inline) 98ms 0.4% 88.68% 135ms 0.54% boost::detail::shared_count::shared_count (inline) 0 0% 88.68% 132ms 0.53% vtkXMLWriter::WritePointsAppendedData