File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20694ms, 89.33% of 23167ms total Dropped 735 nodes (cum <= 115.83ms) flat flat% sum% cum cum% 0 0% 0% 23010ms 99.32% __libc_start_call_main 0 0% 0% 23010ms 99.32% __libc_start_main_impl 0 0% 0% 23010ms 99.32% _start 0 0% 0% 22995ms 99.26% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 22995ms 99.26% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 22995ms 99.26% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 22995ms 99.26% main 0 0% 0% 22959ms 99.10% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 22959ms 99.10% CxxTest::TestRunner::runTest (inline) 0 0% 0% 22959ms 99.10% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 22951ms 99.07% AbstractCellBasedSimulation::Solve 2ms 0.0086% 0.0086% 13088ms 56.49% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0086% 8682ms 37.48% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.017% 0.026% 8278ms 35.73% ForwardEulerNumericalMethod::UpdateAllNodePositions 7ms 0.03% 0.056% 8117ms 35.04% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.056% 7674ms 33.12% NodeBasedCellPopulation::Update 1195ms 5.16% 5.21% 7509ms 32.41% RepulsionForce::AddForceContribution (partial-inline) 7ms 0.03% 5.24% 5611ms 24.22% DistributedBoxCollection::CalculateInteriorNodePairs 2097ms 9.05% 14.30% 4937ms 21.31% std::_Rb_tree::_M_lower_bound (inline) 0 0% 14.30% 4556ms 19.67% OffLatticeSimulation::ApplyBoundaries 24ms 0.1% 14.40% 4474ms 19.31% NodeAttributes::RemoveDuplicateNeighbours 6ms 0.026% 14.43% 4283ms 18.49% std::__sort (inline) 0 0% 14.43% 4283ms 18.49% std::sort (inline) 187ms 0.81% 15.23% 3849ms 16.61% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 2ms 0.0086% 15.24% 3480ms 15.02% AbstractCellPopulation::Iterator::operator++ (inline) 169ms 0.73% 15.97% 3455ms 14.91% AbstractCellPopulation::Iterator::IsRealCell (inline) 62ms 0.27% 16.24% 3402ms 14.68% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 248ms 1.07% 17.31% 3206ms 13.84% std::_Rb_tree::find (inline) 0 0% 17.31% 3206ms 13.84% std::map::find (inline) 23ms 0.099% 17.41% 2927ms 12.63% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2788ms 12.03% 29.44% 2788ms 12.03% std::_Rb_tree::_S_right (inline) 263ms 1.14% 30.58% 2509ms 10.83% std::map::operator[] (partial-inline) 177ms 0.76% 31.34% 2471ms 10.67% std::__introsort_loop 14ms 0.06% 31.40% 2369ms 10.23% PlaneBoundaryCondition::ImposeBoundaryCondition 22ms 0.095% 31.50% 2325ms 10.04% AbstractCellPopulation::GetLocationIndexUsingCell 137ms 0.59% 32.09% 2281ms 9.85% AbstractMesh::GetNode 52ms 0.22% 32.31% 2274ms 9.82% NodesOnlyMesh::GetNodeOrHaloNode 2ms 0.0086% 32.32% 2217ms 9.57% std::__unguarded_partition_pivot (inline) 13ms 0.056% 32.38% 2187ms 9.44% PlaneBoundaryCondition::VerifyBoundaryCondition 91ms 0.39% 32.77% 2147ms 9.27% NodesOnlyMesh::SolveNodeMapping 1027ms 4.43% 37.20% 2011ms 8.68% std::__unguarded_partition (inline) 0 0% 37.20% 2004ms 8.65% std::_Rb_tree::lower_bound (inline) 0 0% 37.20% 2004ms 8.65% std::map::lower_bound (inline) 1ms 0.0043% 37.21% 1806ms 7.80% std::__final_insertion_sort (inline) 138ms 0.6% 37.80% 1768ms 7.63% DistributedBoxCollection::AddPairsFromBox 71ms 0.31% 38.11% 1622ms 7.00% std::__unguarded_insertion_sort (inline) 593ms 2.56% 40.67% 1576ms 6.80% std::__unguarded_linear_insert (inline) 23ms 0.099% 40.77% 1546ms 6.67% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 35ms 0.15% 40.92% 1518ms 6.55% AbstractCellPopulation::GetCellUsingLocationIndex 1472ms 6.35% 47.27% 1472ms 6.35% __gnu_cxx::__normal_iterator::operator-- (inline) 44ms 0.19% 47.46% 1274ms 5.50% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 47.46% 1170ms 5.05% NodeBasedCellPopulation::UpdateCellProcessLocation 34ms 0.15% 47.61% 1153ms 4.98% boost::numeric::ublas::vector_assign (inline) 3ms 0.013% 47.62% 1096ms 4.73% DistributedBoxCollection::CalculateBoundaryNodePairs 293ms 1.26% 48.89% 1049ms 4.53% boost::numeric::ublas::indexing_vector_assign 264ms 1.14% 50.03% 1004ms 4.33% __dynamic_cast 187ms 0.81% 50.84% 860ms 3.71% AbstractMesh::GetVectorFromAtoB 395ms 1.71% 52.54% 826ms 3.57% DistributedBoxCollection::CalculateContainingBox (partial-inline) 22ms 0.095% 52.64% 820ms 3.54% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 52.64% 718ms 3.10% AbstractCellPopulation::WriteResultsToFiles 0 0% 52.64% 706ms 3.05% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 52.64% 686ms 2.96% boost::numeric::ublas::norm_2 (inline) 533ms 2.30% 54.94% 686ms 2.96% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 54.94% 686ms 2.96% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 183ms 0.79% 55.73% 685ms 2.96% NodeAttributes::AddNeighbour 678ms 2.93% 58.65% 678ms 2.93% boost::numeric::ublas::c_vector::operator() 7ms 0.03% 58.68% 654ms 2.82% boost::numeric::ublas::c_vector::operator= (inline) 39ms 0.17% 58.85% 629ms 2.72% std::__copy_move::__copy_m (inline) 0 0% 58.85% 629ms 2.72% std::__copy_move_a (inline) 0 0% 58.85% 629ms 2.72% std::__copy_move_a1 (inline) 0 0% 58.85% 629ms 2.72% std::__copy_move_a2 (inline) 0 0% 58.85% 629ms 2.72% std::copy (inline) 249ms 1.07% 59.93% 616ms 2.66% __cxxabiv1::__si_class_type_info::__do_dyncast 604ms 2.61% 62.53% 604ms 2.61% __memcpy_avx_unaligned_erms 5ms 0.022% 62.55% 576ms 2.49% CellPropertyCollection::GetPropertiesType (inline) 502ms 2.17% 64.72% 574ms 2.48% std::vector::push_back (inline) 544ms 2.35% 67.07% 544ms 2.35% __strcmp_avx2 28ms 0.12% 67.19% 544ms 2.35% boost::detail::shared_count::~shared_count (inline) 0 0% 67.19% 544ms 2.35% boost::shared_ptr::~shared_ptr (inline) 3ms 0.013% 67.20% 533ms 2.30% AbstractCentreBasedCellPopulation::GetDampingConstant 3ms 0.013% 67.22% 531ms 2.29% AbstractCellBasedSimulation::DoCellBirth 499ms 2.15% 69.37% 505ms 2.18% boost::detail::sp_counted_base::release 43ms 0.19% 69.56% 499ms 2.15% std::_Rb_tree_const_iterator::operator++ (inline) 487ms 2.10% 71.66% 487ms 2.10% boost::numeric::ublas::same_impl_ex 0 0% 71.66% 476ms 2.05% AbstractCellBasedSimulation::DoCellRemoval (inline) 4ms 0.017% 71.68% 473ms 2.04% NodeBasedCellPopulation::WriteVtkResultsToFile 7ms 0.03% 71.71% 460ms 1.99% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 56ms 0.24% 71.95% 456ms 1.97% std::__new_allocator::allocate (inline) 455ms 1.96% 73.91% 455ms 1.96% std::_Rb_tree_increment 2ms 0.0086% 73.92% 451ms 1.95% AbstractCellProperty::IsSubType (inline) 18ms 0.078% 74.00% 448ms 1.93% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 74.00% 441ms 1.90% std::allocator_traits::allocate (inline) 30ms 0.13% 74.13% 418ms 1.80% std::_Rb_tree::_M_copy (inline) 0 0% 74.13% 411ms 1.77% std::_Rb_tree::_M_create_node (inline) 139ms 0.6% 74.73% 395ms 1.71% Node::GetRadius 27ms 0.12% 74.84% 395ms 1.71% operator new 146ms 0.63% 75.47% 386ms 1.67% std::_Rb_tree::_M_clone_node (inline) 115ms 0.5% 75.97% 376ms 1.62% std::_Rb_tree::_M_erase 3ms 0.013% 75.98% 373ms 1.61% Cell::GetMutationState 4ms 0.017% 76.00% 372ms 1.61% std::set::set (inline) 0 0% 76.00% 365ms 1.58% std::_Rb_tree::_M_get_node (inline) 104ms 0.45% 76.45% 364ms 1.57% __GI___libc_malloc 42ms 0.18% 76.63% 357ms 1.54% boost::numeric::ublas::vector_binary::size (inline) 4ms 0.017% 76.65% 316ms 1.36% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 76.65% 311ms 1.34% boost::numeric::ublas::inner_prod (inline) 0 0% 76.65% 310ms 1.34% NodesOnlyMesh::ReMesh 309ms 1.33% 77.98% 309ms 1.33% __gnu_cxx::__normal_iterator::operator++ (inline) 52ms 0.22% 78.21% 309ms 1.33% std::_Rb_tree::~_Rb_tree (inline) 0 0% 78.21% 308ms 1.33% boost::numeric::ublas::c_vector::assign (inline) 3ms 0.013% 78.22% 307ms 1.33% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 22ms 0.095% 78.31% 304ms 1.31% boost::numeric::ublas::vector_scalar_binary::evaluate 3ms 0.013% 78.33% 299ms 1.29% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 3ms 0.013% 78.34% 296ms 1.28% NodesOnlyMesh::UpdateNodeIndices 284ms 1.23% 79.57% 284ms 1.23% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 79.57% 283ms 1.22% std::_Rb_tree::_Alloc_node::operator() (inline) 8ms 0.035% 79.60% 280ms 1.21% DistributedBoxCollection::GetProcessOwningNode 265ms 1.14% 80.74% 265ms 1.14% Node::CheckForNodeAttributes 0 0% 80.74% 256ms 1.11% NodesOnlyMesh::UpdateBoxCollection 0 0% 80.74% 248ms 1.07% std::_Rb_tree::_M_drop_node (inline) 7ms 0.03% 80.77% 242ms 1.04% std::_Rb_tree::_M_emplace_hint_unique 0 0% 80.77% 240ms 1.04% std::set::~set (inline) 97ms 0.42% 81.19% 227ms 0.98% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 81.19% 224ms 0.97% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 81.19% 222ms 0.96% VtkMeshWriter::WriteFiles 0 0% 81.19% 220ms 0.95% NodesOnlyMesh::AddNodesToBoxes 123ms 0.53% 81.72% 209ms 0.9% _int_malloc 96ms 0.41% 82.14% 202ms 0.87% std::__move_median_to_first (inline) 3ms 0.013% 82.15% 202ms 0.87% std::__new_allocator::deallocate (inline) 0 0% 82.15% 199ms 0.86% vtkDemandDrivenPipeline::ExecuteData 0 0% 82.15% 199ms 0.86% vtkDemandDrivenPipeline::ProcessRequest 0 0% 82.15% 199ms 0.86% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 82.15% 199ms 0.86% vtkStreamingDemandDrivenPipeline::Update 0 0% 82.15% 199ms 0.86% vtkXMLWriterBase::Write 0 0% 82.15% 198ms 0.85% vtkCompositeDataPipeline::ExecuteData 0 0% 82.15% 198ms 0.85% vtkExecutive::CallAlgorithm 0 0% 82.15% 198ms 0.85% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 82.15% 195ms 0.84% NodesOnlyMesh::ResizeBoxCollection 11ms 0.047% 82.20% 193ms 0.83% NodesOnlyMesh::IsANodeCloseToDomainBoundary 3ms 0.013% 82.21% 191ms 0.82% CellPropertyCollection::HasProperty 0 0% 82.21% 190ms 0.82% Cell::HasCellProperty (inline) 83ms 0.36% 82.57% 190ms 0.82% boost::shared_ptr::shared_ptr (inline) 21ms 0.091% 82.66% 183ms 0.79% std::__insertion_sort (inline) 80ms 0.35% 83.01% 180ms 0.78% __GI___libc_free 4ms 0.017% 83.02% 179ms 0.77% Cell::ReadyToDivide 0 0% 83.02% 179ms 0.77% std::allocator_traits::deallocate (inline) 0 0% 83.02% 178ms 0.77% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 83.02% 178ms 0.77% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 177ms 0.76% 83.79% 177ms 0.76% [libchaste_mesh.so] 0 0% 83.79% 177ms 0.76% std::_Rb_tree::_M_put_node (inline) 0 0% 83.79% 175ms 0.76% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 5ms 0.022% 83.81% 172ms 0.74% AbstractCellProperty::IsType (inline) 171ms 0.74% 84.55% 171ms 0.74% [libchaste_cell_based.so] 164ms 0.71% 85.25% 164ms 0.71% Node::GetIndex 82ms 0.35% 85.61% 162ms 0.7% Node::AddNeighbour 152ms 0.66% 86.26% 152ms 0.66% std::__adjacent_find (inline) 0 0% 86.26% 152ms 0.66% std::__unique (inline) 0 0% 86.26% 152ms 0.66% std::unique (inline) 151ms 0.65% 86.92% 151ms 0.65% boost::shared_ptr::operator-> (inline) 0 0% 86.92% 149ms 0.64% vtkXMLWriter::WriteBinaryData 11ms 0.047% 86.96% 146ms 0.63% DistributedBoxCollection::GetIsPeriodicAllDims 18ms 0.078% 87.04% 144ms 0.62% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 87.04% 144ms 0.62% vtkXMLWriter::WriteBinaryDataInternal 1ms 0.0043% 87.05% 143ms 0.62% vtkXMLWriter::WriteBinaryDataBlock 142ms 0.61% 87.66% 142ms 0.61% Node::IsDeleted 0 0% 87.66% 142ms 0.61% vtkXMLWriter::WriteCompressionBlock 0 0% 87.66% 140ms 0.6% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 87.66% 137ms 0.59% std::_Rb_tree::clear (inline) 1ms 0.0043% 87.66% 136ms 0.59% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 39ms 0.17% 87.83% 134ms 0.58% AbstractCellProperty::IsSame 0 0% 87.83% 131ms 0.57% boost::numeric::ublas::vector_binary::operator() (inline) 1ms 0.0043% 87.84% 130ms 0.56% Cell::GetCellId 6ms 0.026% 87.86% 130ms 0.56% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 87.86% 128ms 0.55% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 87.86% 128ms 0.55% vtkXMLWriter::WritePointsAppendedData 1ms 0.0043% 87.87% 126ms 0.54% AbstractCellPopulation::SetCellUsingLocationIndex 0 0% 87.87% 124ms 0.54% clone3 0 0% 87.87% 124ms 0.54% start_thread 1ms 0.0043% 87.87% 123ms 0.53% tbb::detail::r1::parallel_pipeline 0 0% 87.87% 120ms 0.52% tbb::detail::r1::reset 50ms 0.22% 88.09% 120ms 0.52% tbb::detail::r1::wait_bounded_queue_monitor 0 0% 88.09% 119ms 0.51% compress2 0 0% 88.09% 119ms 0.51% vtkDataCompressor::Compress 0 0% 88.09% 119ms 0.51% vtkZLibDataCompressor::CompressBuffer 54ms 0.23% 88.32% 118ms 0.51% crc32 0 0% 88.32% 118ms 0.51% deflate 117ms 0.51% 88.82% 117ms 0.51% __ieee754_log_fma 116ms 0.5% 89.33% 116ms 0.5% Node::ConstructNodeAttributes (inline)