File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20258ms, 88.23% of 22960ms total Dropped 751 nodes (cum <= 114.80ms) flat flat% sum% cum cum% 0 0% 0% 22828ms 99.43% __libc_start_call_main 0 0% 0% 22828ms 99.43% __libc_start_main_impl 0 0% 0% 22828ms 99.43% _start 0 0% 0% 22814ms 99.36% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 22814ms 99.36% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 22814ms 99.36% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 22814ms 99.36% main 0 0% 0% 22780ms 99.22% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 22780ms 99.22% CxxTest::TestRunner::runTest (inline) 0 0% 0% 22780ms 99.22% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 22773ms 99.19% AbstractCellBasedSimulation::Solve 1ms 0.0044% 0.0044% 12964ms 56.46% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0044% 8644ms 37.65% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0087% 0.013% 8179ms 35.62% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.017% 0.03% 7986ms 34.78% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.03% 7648ms 33.31% NodeBasedCellPopulation::Update 1185ms 5.16% 5.19% 7379ms 32.14% RepulsionForce::AddForceContribution (partial-inline) 4ms 0.017% 5.21% 5535ms 24.11% DistributedBoxCollection::CalculateInteriorNodePairs 2125ms 9.26% 14.46% 4900ms 21.34% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.0044% 14.47% 4530ms 19.73% OffLatticeSimulation::ApplyBoundaries 13ms 0.057% 14.53% 4524ms 19.70% NodeAttributes::RemoveDuplicateNeighbours 7ms 0.03% 14.56% 4252ms 18.52% std::__sort (inline) 0 0% 14.56% 4252ms 18.52% std::sort (inline) 202ms 0.88% 15.44% 3784ms 16.48% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 7ms 0.03% 15.47% 3372ms 14.69% AbstractCellPopulation::Iterator::operator++ (inline) 62ms 0.27% 15.74% 3367ms 14.66% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 170ms 0.74% 16.48% 3337ms 14.53% AbstractCellPopulation::Iterator::IsRealCell (inline) 254ms 1.11% 17.58% 3222ms 14.03% std::_Rb_tree::find (inline) 0 0% 17.58% 3221ms 14.03% std::map::find (inline) 30ms 0.13% 17.71% 2850ms 12.41% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2729ms 11.89% 29.60% 2729ms 11.89% std::_Rb_tree::_S_right (inline) 267ms 1.16% 30.76% 2480ms 10.80% std::map::operator[] (partial-inline) 179ms 0.78% 31.54% 2449ms 10.67% std::__introsort_loop 32ms 0.14% 31.68% 2393ms 10.42% PlaneBoundaryCondition::ImposeBoundaryCondition 37ms 0.16% 31.84% 2364ms 10.30% AbstractCellPopulation::GetLocationIndexUsingCell 131ms 0.57% 32.41% 2241ms 9.76% AbstractMesh::GetNode 38ms 0.17% 32.58% 2200ms 9.58% NodesOnlyMesh::GetNodeOrHaloNode 0 0% 32.58% 2179ms 9.49% std::__unguarded_partition_pivot (inline) 18ms 0.078% 32.66% 2136ms 9.30% PlaneBoundaryCondition::VerifyBoundaryCondition 77ms 0.34% 32.99% 2113ms 9.20% NodesOnlyMesh::SolveNodeMapping 0 0% 32.99% 1954ms 8.51% std::_Rb_tree::lower_bound (inline) 0 0% 32.99% 1954ms 8.51% std::map::lower_bound (inline) 1053ms 4.59% 37.58% 1939ms 8.45% std::__unguarded_partition (inline) 1ms 0.0044% 37.58% 1794ms 7.81% std::__final_insertion_sort (inline) 126ms 0.55% 38.13% 1744ms 7.60% DistributedBoxCollection::AddPairsFromBox 103ms 0.45% 38.58% 1618ms 7.05% std::__unguarded_insertion_sort (inline) 536ms 2.33% 40.91% 1540ms 6.71% std::__unguarded_linear_insert (inline) 24ms 0.1% 41.02% 1527ms 6.65% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 24ms 0.1% 41.12% 1500ms 6.53% AbstractCellPopulation::GetCellUsingLocationIndex 1428ms 6.22% 47.34% 1428ms 6.22% __gnu_cxx::__normal_iterator::operator-- (inline) 35ms 0.15% 47.50% 1250ms 5.44% boost::numeric::ublas::c_vector::c_vector (partial-inline) 4ms 0.017% 47.51% 1188ms 5.17% DistributedBoxCollection::CalculateBoundaryNodePairs 0 0% 47.51% 1143ms 4.98% NodeBasedCellPopulation::UpdateCellProcessLocation 39ms 0.17% 47.68% 1132ms 4.93% boost::numeric::ublas::vector_assign (inline) 248ms 1.08% 48.76% 1006ms 4.38% boost::numeric::ublas::indexing_vector_assign 271ms 1.18% 49.94% 948ms 4.13% __dynamic_cast 16ms 0.07% 50.01% 811ms 3.53% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 352ms 1.53% 51.55% 779ms 3.39% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 51.55% 753ms 3.28% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 154ms 0.67% 52.22% 744ms 3.24% AbstractMesh::GetVectorFromAtoB 0 0% 52.22% 722ms 3.14% boost::numeric::ublas::norm_2 (inline) 563ms 2.45% 54.67% 722ms 3.14% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 54.67% 722ms 3.14% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 180ms 0.78% 55.45% 704ms 3.07% NodeAttributes::AddNeighbour 699ms 3.04% 58.50% 699ms 3.04% boost::numeric::ublas::c_vector::operator() 0 0% 58.50% 695ms 3.03% AbstractCellPopulation::WriteResultsToFiles 3ms 0.013% 58.51% 675ms 2.94% boost::numeric::ublas::c_vector::operator= (inline) 37ms 0.16% 58.67% 654ms 2.85% std::__copy_move::__copy_m (inline) 0 0% 58.67% 654ms 2.85% std::__copy_move_a (inline) 0 0% 58.67% 654ms 2.85% std::__copy_move_a1 (inline) 0 0% 58.67% 654ms 2.85% std::__copy_move_a2 (inline) 0 0% 58.67% 653ms 2.84% std::copy (inline) 641ms 2.79% 61.46% 641ms 2.79% __memcpy_avx_unaligned_erms 520ms 2.26% 63.73% 594ms 2.59% std::vector::push_back (inline) 6ms 0.026% 63.75% 563ms 2.45% AbstractCellBasedSimulation::DoCellBirth 245ms 1.07% 64.82% 555ms 2.42% __cxxabiv1::__si_class_type_info::__do_dyncast 3ms 0.013% 64.83% 542ms 2.36% AbstractCentreBasedCellPopulation::GetDampingConstant 3ms 0.013% 64.85% 536ms 2.33% CellPropertyCollection::GetPropertiesType (inline) 65ms 0.28% 65.13% 535ms 2.33% std::__new_allocator::allocate (inline) 0 0% 65.13% 516ms 2.25% std::allocator_traits::allocate (inline) 33ms 0.14% 65.27% 515ms 2.24% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 65.27% 487ms 2.12% std::_Rb_tree::_M_create_node (inline) 30ms 0.13% 65.41% 478ms 2.08% boost::detail::shared_count::~shared_count (inline) 0 0% 65.41% 478ms 2.08% boost::shared_ptr::~shared_ptr (inline) 477ms 2.08% 67.48% 477ms 2.08% boost::numeric::ublas::same_impl_ex 476ms 2.07% 69.56% 476ms 2.07% std::_Rb_tree_increment 468ms 2.04% 71.59% 468ms 2.04% __strcmp_avx2 18ms 0.078% 71.67% 459ms 2.00% operator new 1ms 0.0044% 71.68% 454ms 1.98% NodeBasedCellPopulation::WriteVtkResultsToFile 17ms 0.074% 71.75% 445ms 1.94% std::_Rb_tree::_Rb_tree (partial-inline) 435ms 1.89% 73.65% 438ms 1.91% boost::detail::sp_counted_base::release 1ms 0.0044% 73.65% 432ms 1.88% AbstractCellBasedSimulation::DoCellRemoval (inline) 135ms 0.59% 74.24% 432ms 1.88% __GI___libc_malloc 0 0% 74.24% 432ms 1.88% std::_Rb_tree::_M_get_node (inline) 6ms 0.026% 74.26% 417ms 1.82% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 47ms 0.2% 74.47% 414ms 1.80% std::_Rb_tree::_M_copy (inline) 4ms 0.017% 74.49% 395ms 1.72% AbstractCellProperty::IsSubType (inline) 8ms 0.035% 74.52% 385ms 1.68% std::set::set (inline) 152ms 0.66% 75.18% 384ms 1.67% Node::GetRadius 1ms 0.0044% 75.19% 371ms 1.62% Cell::GetMutationState 120ms 0.52% 75.71% 368ms 1.60% std::_Rb_tree::_M_erase 106ms 0.46% 76.17% 367ms 1.60% std::_Rb_tree::_M_clone_node (inline) 0 0% 76.17% 353ms 1.54% boost::numeric::ublas::c_vector::assign (inline) 0 0% 76.17% 331ms 1.44% boost::numeric::ublas::inner_prod (inline) 24ms 0.1% 76.28% 330ms 1.44% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 76.28% 330ms 1.44% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 76.28% 328ms 1.43% std::_Rb_tree::_Alloc_node::operator() (inline) 25ms 0.11% 76.39% 315ms 1.37% boost::numeric::ublas::vector_binary::size (inline) 4ms 0.017% 76.40% 313ms 1.36% NodeBasedCellPopulation::UpdateMapsAfterRemesh 307ms 1.34% 77.74% 307ms 1.34% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 35ms 0.15% 77.89% 294ms 1.28% std::_Rb_tree::~_Rb_tree (inline) 0 0% 77.89% 279ms 1.22% NodesOnlyMesh::ReMesh 3ms 0.013% 77.91% 273ms 1.19% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 3ms 0.013% 77.92% 263ms 1.15% NodesOnlyMesh::UpdateNodeIndices 99ms 0.43% 78.35% 263ms 1.15% boost::numeric::ublas::vector_inner_prod::apply (inline) 8ms 0.035% 78.38% 259ms 1.13% std::_Rb_tree::_M_emplace_hint_unique 3ms 0.013% 78.40% 257ms 1.12% DistributedBoxCollection::GetProcessOwningNode 250ms 1.09% 79.49% 250ms 1.09% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 79.49% 245ms 1.07% NodesOnlyMesh::UpdateBoxCollection 242ms 1.05% 80.54% 242ms 1.05% std::__adjacent_find (inline) 0 0% 80.54% 242ms 1.05% std::__unique (inline) 0 0% 80.54% 242ms 1.05% std::unique (inline) 142ms 0.62% 81.16% 238ms 1.04% _int_malloc 0 0% 81.16% 238ms 1.04% std::_Rb_tree::_M_drop_node (inline) 125ms 0.54% 81.70% 236ms 1.03% std::__move_median_to_first (inline) 235ms 1.02% 82.73% 235ms 1.02% Node::CheckForNodeAttributes 0 0% 82.73% 221ms 0.96% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 82.73% 221ms 0.96% VtkMeshWriter::WriteFiles 0 0% 82.73% 220ms 0.96% std::set::~set (inline) 0 0% 82.73% 218ms 0.95% NodesOnlyMesh::ResizeBoxCollection 8ms 0.035% 82.76% 217ms 0.95% NodesOnlyMesh::IsANodeCloseToDomainBoundary 3ms 0.013% 82.77% 212ms 0.92% std::__new_allocator::deallocate (inline) 0 0% 82.77% 204ms 0.89% NodesOnlyMesh::AddNodesToBoxes 108ms 0.47% 83.24% 197ms 0.86% boost::shared_ptr::shared_ptr (inline) 50ms 0.22% 83.46% 191ms 0.83% __GI___libc_free 0 0% 83.46% 191ms 0.83% vtkDemandDrivenPipeline::ProcessRequest 0 0% 83.46% 191ms 0.83% vtkStreamingDemandDrivenPipeline::Update 0 0% 83.46% 191ms 0.83% vtkXMLWriterBase::Write 0 0% 83.46% 189ms 0.82% vtkCompositeDataPipeline::ExecuteData 0 0% 83.46% 189ms 0.82% vtkDemandDrivenPipeline::ExecuteData 0 0% 83.46% 189ms 0.82% vtkExecutive::CallAlgorithm 0 0% 83.46% 189ms 0.82% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 83.46% 189ms 0.82% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 83.46% 188ms 0.82% std::allocator_traits::deallocate (inline) 187ms 0.81% 84.28% 187ms 0.81% [libchaste_cell_based.so] 0 0% 84.28% 181ms 0.79% std::_Rb_tree::_M_put_node (inline) 0 0% 84.28% 179ms 0.78% Cell::HasCellProperty (inline) 5ms 0.022% 84.30% 179ms 0.78% CellPropertyCollection::HasProperty 178ms 0.78% 85.07% 178ms 0.78% Node::GetIndex 9ms 0.039% 85.11% 177ms 0.77% Cell::ReadyToDivide 22ms 0.096% 85.21% 175ms 0.76% std::__insertion_sort (inline) 71ms 0.31% 85.52% 166ms 0.72% Node::AddNeighbour 0 0% 85.52% 163ms 0.71% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.52% 163ms 0.71% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 4ms 0.017% 85.54% 161ms 0.7% AbstractCellProperty::IsType (inline) 0 0% 85.54% 159ms 0.69% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 85.54% 159ms 0.69% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 7ms 0.03% 85.57% 152ms 0.66% DistributedBoxCollection::GetIsPeriodicAllDims 0 0% 85.57% 148ms 0.64% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 146ms 0.64% 86.20% 146ms 0.64% [libchaste_mesh.so] 124ms 0.54% 86.74% 141ms 0.61% _int_free 24ms 0.1% 86.85% 139ms 0.61% boost::numeric::ublas::vector_reference::operator() (inline) 2ms 0.0087% 86.86% 137ms 0.6% AbstractCellPopulation::SetCellUsingLocationIndex 1ms 0.0044% 86.86% 137ms 0.6% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 86.86% 137ms 0.6% boost::numeric::ublas::vector_binary::operator() (inline) 137ms 0.6% 87.46% 137ms 0.6% boost::shared_ptr::operator-> (inline) 2ms 0.0087% 87.47% 136ms 0.59% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 87.47% 131ms 0.57% vtkXMLWriter::WriteBinaryData 3ms 0.013% 87.48% 127ms 0.55% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 87.48% 126ms 0.55% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.48% 126ms 0.55% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.48% 126ms 0.55% vtkXMLWriter::WriteCompressionBlock 1ms 0.0044% 87.48% 125ms 0.54% std::_Rb_tree::clear (inline) 0 0% 87.48% 124ms 0.54% vtkXMLWriter::WritePointsAppendedData 123ms 0.54% 88.02% 123ms 0.54% Node::IsDeleted 5ms 0.022% 88.04% 123ms 0.54% NodeBasedCellPopulation::SetNode 43ms 0.19% 88.23% 119ms 0.52% AbstractCellProperty::IsSame 0 0% 88.23% 115ms 0.5% NodesOnlyMesh::SetNode 1ms 0.0044% 88.23% 115ms 0.5% std::set::insert (inline)