File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20575ms, 88.47% of 23257ms total Dropped 778 nodes (cum <= 116.28ms) flat flat% sum% cum cum% 0 0% 0% 23085ms 99.26% __libc_start_call_main 0 0% 0% 23085ms 99.26% __libc_start_main_impl 0 0% 0% 23085ms 99.26% _start 0 0% 0% 23070ms 99.20% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 23070ms 99.20% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 23070ms 99.20% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 23070ms 99.20% main 0 0% 0% 23034ms 99.04% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 23034ms 99.04% CxxTest::TestRunner::runTest (inline) 0 0% 0% 23034ms 99.04% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 23026ms 99.01% AbstractCellBasedSimulation::Solve 2ms 0.0086% 0.0086% 13129ms 56.45% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0086% 8705ms 37.43% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.017% 0.026% 8332ms 35.83% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.043% 0.069% 8148ms 35.03% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.069% 7676ms 33.01% NodeBasedCellPopulation::Update 1175ms 5.05% 5.12% 7543ms 32.43% RepulsionForce::AddForceContribution (partial-inline) 10ms 0.043% 5.16% 5663ms 24.35% DistributedBoxCollection::CalculateInteriorNodePairs 2093ms 9.00% 14.16% 5009ms 21.54% std::_Rb_tree::_M_lower_bound (inline) 0 0% 14.16% 4506ms 19.37% OffLatticeSimulation::ApplyBoundaries 23ms 0.099% 14.26% 4456ms 19.16% NodeAttributes::RemoveDuplicateNeighbours 4ms 0.017% 14.28% 4297ms 18.48% std::__sort (inline) 0 0% 14.28% 4297ms 18.48% std::sort (inline) 202ms 0.87% 15.15% 3908ms 16.80% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 3ms 0.013% 15.16% 3547ms 15.25% AbstractCellPopulation::Iterator::operator++ (inline) 192ms 0.83% 15.99% 3518ms 15.13% AbstractCellPopulation::Iterator::IsRealCell 55ms 0.24% 16.22% 3453ms 14.85% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 224ms 0.96% 17.19% 3198ms 13.75% std::_Rb_tree::find (inline) 0 0% 17.19% 3198ms 13.75% std::map::find (inline) 31ms 0.13% 17.32% 2995ms 12.88% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2882ms 12.39% 29.71% 2882ms 12.39% std::_Rb_tree::_S_right (inline) 235ms 1.01% 30.72% 2578ms 11.08% std::map::operator[] (partial-inline) 167ms 0.72% 31.44% 2438ms 10.48% std::__introsort_loop 27ms 0.12% 31.56% 2357ms 10.13% AbstractCellPopulation::GetLocationIndexUsingCell 27ms 0.12% 31.67% 2349ms 10.10% PlaneBoundaryCondition::ImposeBoundaryCondition 142ms 0.61% 32.28% 2250ms 9.67% AbstractMesh::GetNode 45ms 0.19% 32.48% 2237ms 9.62% NodesOnlyMesh::GetNodeOrHaloNode 1ms 0.0043% 32.48% 2185ms 9.40% std::__unguarded_partition_pivot (inline) 22ms 0.095% 32.58% 2157ms 9.27% PlaneBoundaryCondition::VerifyBoundaryCondition 73ms 0.31% 32.89% 2113ms 9.09% NodesOnlyMesh::SolveNodeMapping 0 0% 32.89% 2063ms 8.87% std::_Rb_tree::lower_bound (inline) 0 0% 32.89% 2063ms 8.87% std::map::lower_bound (inline) 1003ms 4.31% 37.20% 1976ms 8.50% std::__unguarded_partition (inline) 3ms 0.013% 37.21% 1853ms 7.97% std::__final_insertion_sort (inline) 150ms 0.64% 37.86% 1778ms 7.65% DistributedBoxCollection::AddPairsFromBox 84ms 0.36% 38.22% 1657ms 7.12% std::__unguarded_insertion_sort (inline) 588ms 2.53% 40.75% 1607ms 6.91% std::__unguarded_linear_insert (inline) 29ms 0.12% 40.87% 1593ms 6.85% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 38ms 0.16% 41.04% 1563ms 6.72% AbstractCellPopulation::GetCellUsingLocationIndex 1490ms 6.41% 47.44% 1490ms 6.41% __gnu_cxx::__normal_iterator::operator-- (inline) 54ms 0.23% 47.68% 1266ms 5.44% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 47.68% 1167ms 5.02% NodeBasedCellPopulation::UpdateCellProcessLocation 28ms 0.12% 47.80% 1121ms 4.82% boost::numeric::ublas::vector_assign (inline) 4ms 0.017% 47.81% 1060ms 4.56% DistributedBoxCollection::CalculateBoundaryNodePairs 273ms 1.17% 48.99% 1036ms 4.45% __dynamic_cast 275ms 1.18% 50.17% 1015ms 4.36% boost::numeric::ublas::indexing_vector_assign 362ms 1.56% 51.73% 807ms 3.47% DistributedBoxCollection::CalculateContainingBox (partial-inline) 158ms 0.68% 52.41% 804ms 3.46% AbstractMesh::GetVectorFromAtoB 27ms 0.12% 52.52% 765ms 3.29% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 52.52% 718ms 3.09% AbstractCellPopulation::WriteResultsToFiles 186ms 0.8% 53.32% 712ms 3.06% NodeAttributes::AddNeighbour 0 0% 53.32% 708ms 3.04% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 53.32% 694ms 2.98% boost::numeric::ublas::norm_2 (inline) 546ms 2.35% 55.67% 694ms 2.98% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 55.67% 694ms 2.98% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 2ms 0.0086% 55.68% 677ms 2.91% boost::numeric::ublas::c_vector::operator= (inline) 666ms 2.86% 58.54% 666ms 2.86% boost::numeric::ublas::c_vector::operator() 42ms 0.18% 58.72% 658ms 2.83% std::__copy_move::__copy_m (inline) 0 0% 58.72% 658ms 2.83% std::__copy_move_a (inline) 0 0% 58.72% 658ms 2.83% std::__copy_move_a1 (inline) 0 0% 58.72% 658ms 2.83% std::__copy_move_a2 (inline) 0 0% 58.72% 658ms 2.83% std::copy (inline) 633ms 2.72% 61.44% 633ms 2.72% __memcpy_avx_unaligned_erms 248ms 1.07% 62.51% 620ms 2.67% __cxxabiv1::__si_class_type_info::__do_dyncast 523ms 2.25% 64.76% 584ms 2.51% std::vector::push_back (inline) 2ms 0.0086% 64.77% 575ms 2.47% AbstractCellBasedSimulation::DoCellBirth 569ms 2.45% 67.21% 569ms 2.45% __strcmp_avx2 2ms 0.0086% 67.22% 544ms 2.34% AbstractCentreBasedCellPopulation::GetDampingConstant 6ms 0.026% 67.25% 528ms 2.27% CellPropertyCollection::GetPropertiesType (inline) 74ms 0.32% 67.57% 518ms 2.23% std::__new_allocator::allocate (inline) 31ms 0.13% 67.70% 509ms 2.19% std::_Rb_tree_const_iterator::operator++ (inline) 37ms 0.16% 67.86% 507ms 2.18% boost::detail::shared_count::~shared_count (inline) 0 0% 67.86% 507ms 2.18% boost::shared_ptr::~shared_ptr (inline) 0 0% 67.86% 499ms 2.15% std::allocator_traits::allocate (inline) 488ms 2.10% 69.96% 488ms 2.10% boost::numeric::ublas::same_impl_ex 0 0% 69.96% 477ms 2.05% NodeBasedCellPopulation::WriteVtkResultsToFile 471ms 2.03% 71.98% 471ms 2.03% std::_Rb_tree_increment 19ms 0.082% 72.06% 459ms 1.97% std::_Rb_tree::_Rb_tree (partial-inline) 450ms 1.93% 74.00% 455ms 1.96% boost::detail::sp_counted_base::release 0 0% 74.00% 454ms 1.95% std::_Rb_tree::_M_create_node (inline) 0 0% 74.00% 453ms 1.95% AbstractCellBasedSimulation::DoCellRemoval (inline) 30ms 0.13% 74.13% 437ms 1.88% operator new 1ms 0.0043% 74.13% 436ms 1.87% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 46ms 0.2% 74.33% 424ms 1.82% std::_Rb_tree::_M_copy (inline) 0 0% 74.33% 415ms 1.78% std::_Rb_tree::_M_get_node (inline) 132ms 0.57% 74.90% 406ms 1.75% std::_Rb_tree::_M_erase 117ms 0.5% 75.40% 399ms 1.72% __GI___libc_malloc 0 0% 75.40% 396ms 1.70% AbstractCellProperty::IsSubType (inline) 148ms 0.64% 76.04% 386ms 1.66% Node::GetRadius 4ms 0.017% 76.05% 384ms 1.65% std::set::set (inline) 6ms 0.026% 76.08% 379ms 1.63% Cell::GetMutationState 136ms 0.58% 76.67% 377ms 1.62% std::_Rb_tree::_M_clone_node (inline) 26ms 0.11% 76.78% 348ms 1.50% boost::numeric::ublas::vector_binary::size (inline) 42ms 0.18% 76.96% 325ms 1.40% std::_Rb_tree::~_Rb_tree (inline) 0 0% 76.96% 323ms 1.39% NodesOnlyMesh::ReMesh 3ms 0.013% 76.97% 318ms 1.37% NodeBasedCellPopulation::UpdateMapsAfterRemesh 2ms 0.0086% 76.98% 312ms 1.34% NodesOnlyMesh::UpdateNodeIndices 0 0% 76.98% 311ms 1.34% boost::numeric::ublas::c_vector::assign (inline) 0 0% 76.98% 302ms 1.30% boost::numeric::ublas::inner_prod (inline) 2ms 0.0086% 76.99% 302ms 1.30% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 14ms 0.06% 77.05% 300ms 1.29% boost::numeric::ublas::vector_scalar_binary::evaluate 299ms 1.29% 78.33% 299ms 1.29% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 78.33% 299ms 1.29% std::_Rb_tree::_Alloc_node::operator() (inline) 286ms 1.23% 79.56% 286ms 1.23% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 5ms 0.021% 79.58% 280ms 1.20% std::_Rb_tree::_M_emplace_hint_unique 3ms 0.013% 79.60% 267ms 1.15% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 79.60% 258ms 1.11% std::_Rb_tree::_M_drop_node (inline) 0 0% 79.60% 254ms 1.09% NodesOnlyMesh::UpdateBoxCollection 3ms 0.013% 79.61% 253ms 1.09% DistributedBoxCollection::GetProcessOwningNode 247ms 1.06% 80.67% 247ms 1.06% Node::CheckForNodeAttributes 100ms 0.43% 81.10% 244ms 1.05% boost::numeric::ublas::vector_inner_prod::apply (inline) 150ms 0.64% 81.75% 238ms 1.02% _int_malloc 0 0% 81.75% 233ms 1.00% std::set::~set (inline) 4ms 0.017% 81.76% 229ms 0.98% std::__new_allocator::deallocate (inline) 0 0% 81.76% 224ms 0.96% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 81.76% 222ms 0.95% VtkMeshWriter::WriteFiles 0 0% 81.76% 220ms 0.95% NodesOnlyMesh::AddNodesToBoxes 90ms 0.39% 82.15% 204ms 0.88% std::__move_median_to_first (inline) 0 0% 82.15% 203ms 0.87% std::allocator_traits::deallocate (inline) 200ms 0.86% 83.01% 200ms 0.86% [libchaste_cell_based.so] 63ms 0.27% 83.28% 200ms 0.86% __GI___libc_free 0 0% 83.28% 200ms 0.86% std::_Rb_tree::_M_put_node (inline) 0 0% 83.28% 199ms 0.86% NodesOnlyMesh::ResizeBoxCollection 13ms 0.056% 83.34% 197ms 0.85% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 83.34% 196ms 0.84% vtkStreamingDemandDrivenPipeline::Update 0 0% 83.34% 196ms 0.84% vtkXMLWriterBase::Write 26ms 0.11% 83.45% 193ms 0.83% std::__insertion_sort (inline) 0 0% 83.45% 193ms 0.83% vtkDemandDrivenPipeline::ProcessRequest 0 0% 83.45% 192ms 0.83% vtkStreamingDemandDrivenPipeline::ProcessRequest 190ms 0.82% 84.27% 190ms 0.82% Node::GetIndex 0 0% 84.27% 190ms 0.82% vtkDemandDrivenPipeline::ExecuteData 0 0% 84.27% 189ms 0.81% vtkCompositeDataPipeline::ExecuteData 0 0% 84.27% 188ms 0.81% vtkExecutive::CallAlgorithm 0 0% 84.27% 187ms 0.8% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 84.27% 186ms 0.8% Cell::HasCellProperty (inline) 0 0% 84.27% 186ms 0.8% CellPropertyCollection::HasProperty 91ms 0.39% 84.66% 184ms 0.79% boost::shared_ptr::shared_ptr (inline) 4ms 0.017% 84.68% 175ms 0.75% AbstractCellProperty::IsType (inline) 84ms 0.36% 85.04% 171ms 0.74% Node::AddNeighbour 0 0% 85.04% 169ms 0.73% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.04% 169ms 0.73% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 4ms 0.017% 85.05% 163ms 0.7% Cell::ReadyToDivide 0 0% 85.05% 162ms 0.7% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 157ms 0.68% 85.73% 157ms 0.68% [libchaste_mesh.so] 0 0% 85.73% 155ms 0.67% std::_Rb_tree::_Auto_node::_Auto_node (inline) 13ms 0.056% 85.78% 142ms 0.61% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 85.78% 141ms 0.61% std::_Rb_tree::clear (inline) 0 0% 85.78% 139ms 0.6% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 85.78% 139ms 0.6% clone3 0 0% 85.78% 139ms 0.6% start_thread 0 0% 85.78% 139ms 0.6% vtkXMLWriter::WriteBinaryData 0 0% 85.78% 138ms 0.59% tbb::detail::r1::parallel_pipeline 0 0% 85.78% 138ms 0.59% tbb::detail::r1::reset 0 0% 85.78% 137ms 0.59% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 126ms 0.54% 86.33% 137ms 0.59% _int_free 0 0% 86.33% 136ms 0.58% AbstractCellPopulation::SetCellUsingLocationIndex 135ms 0.58% 86.91% 135ms 0.58% Node::IsDeleted 6ms 0.026% 86.93% 134ms 0.58% DistributedBoxCollection::GetIsPeriodicAllDims 5ms 0.021% 86.95% 134ms 0.58% boost::numeric::ublas::c_vector::operator[] (inline) 65ms 0.28% 87.23% 132ms 0.57% tbb::detail::r1::wait_bounded_queue_monitor 35ms 0.15% 87.38% 131ms 0.56% AbstractCellProperty::IsSame 129ms 0.55% 87.94% 129ms 0.55% boost::shared_ptr::operator-> (inline) 1ms 0.0043% 87.94% 129ms 0.55% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.94% 129ms 0.55% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.94% 128ms 0.55% vtkXMLWriter::WriteCompressionBlock 4ms 0.017% 87.96% 123ms 0.53% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 87.96% 123ms 0.53% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 2ms 0.0086% 87.97% 119ms 0.51% Cell::GetCellId 0 0% 87.97% 119ms 0.51% vtkXMLWriter::WritePointsAppendedData 116ms 0.5% 88.47% 118ms 0.51% std::__adjacent_find (inline) 0 0% 88.47% 118ms 0.51% std::__unique (inline) 0 0% 88.47% 118ms 0.51% std::unique (inline)