File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20523ms, 89.09% of 23036ms total Dropped 792 nodes (cum <= 115.18ms) flat flat% sum% cum cum% 0 0% 0% 22900ms 99.41% __libc_start_call_main 0 0% 0% 22900ms 99.41% __libc_start_main_impl 0 0% 0% 22900ms 99.41% _start 0 0% 0% 22885ms 99.34% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 22885ms 99.34% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 22885ms 99.34% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 22885ms 99.34% main 0 0% 0% 22849ms 99.19% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 22849ms 99.19% CxxTest::TestRunner::runTest (inline) 0 0% 0% 22849ms 99.19% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 22842ms 99.16% AbstractCellBasedSimulation::Solve 2ms 0.0087% 0.0087% 13007ms 56.46% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0087% 8644ms 37.52% AbstractCellBasedSimulation::UpdateCellPopulation 7ms 0.03% 0.039% 8235ms 35.75% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.043% 0.082% 8073ms 35.05% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.082% 7635ms 33.14% NodeBasedCellPopulation::Update 1196ms 5.19% 5.27% 7448ms 32.33% RepulsionForce::AddForceContribution (partial-inline) 5ms 0.022% 5.30% 5635ms 24.46% DistributedBoxCollection::CalculateInteriorNodePairs 2068ms 8.98% 14.27% 4915ms 21.34% std::_Rb_tree::_M_lower_bound (inline) 18ms 0.078% 14.35% 4512ms 19.59% NodeAttributes::RemoveDuplicateNeighbours 0 0% 14.35% 4493ms 19.50% OffLatticeSimulation::ApplyBoundaries 7ms 0.03% 14.38% 4331ms 18.80% std::__sort (inline) 0 0% 14.38% 4331ms 18.80% std::sort (inline) 186ms 0.81% 15.19% 3800ms 16.50% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 2ms 0.0087% 15.20% 3497ms 15.18% AbstractCellPopulation::Iterator::operator++ (inline) 213ms 0.92% 16.12% 3472ms 15.07% AbstractCellPopulation::Iterator::IsRealCell 63ms 0.27% 16.40% 3358ms 14.58% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 244ms 1.06% 17.46% 3152ms 13.68% std::_Rb_tree::find (inline) 0 0% 17.46% 3151ms 13.68% std::map::find (inline) 25ms 0.11% 17.56% 2900ms 12.59% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2805ms 12.18% 29.74% 2805ms 12.18% std::_Rb_tree::_S_right (inline) 228ms 0.99% 30.73% 2521ms 10.94% std::map::operator[] (partial-inline) 208ms 0.9% 31.63% 2487ms 10.80% std::__introsort_loop 30ms 0.13% 31.76% 2334ms 10.13% PlaneBoundaryCondition::ImposeBoundaryCondition 36ms 0.16% 31.92% 2263ms 9.82% AbstractCellPopulation::GetLocationIndexUsingCell 48ms 0.21% 32.13% 2245ms 9.75% NodesOnlyMesh::GetNodeOrHaloNode 141ms 0.61% 32.74% 2244ms 9.74% AbstractMesh::GetNode 1ms 0.0043% 32.74% 2204ms 9.57% std::__unguarded_partition_pivot (inline) 23ms 0.1% 32.84% 2159ms 9.37% PlaneBoundaryCondition::VerifyBoundaryCondition 73ms 0.32% 33.16% 2106ms 9.14% NodesOnlyMesh::SolveNodeMapping 0 0% 33.16% 2027ms 8.80% std::_Rb_tree::lower_bound (inline) 0 0% 33.16% 2027ms 8.80% std::map::lower_bound (inline) 1031ms 4.48% 37.64% 2006ms 8.71% std::__unguarded_partition (inline) 2ms 0.0087% 37.65% 1837ms 7.97% std::__final_insertion_sort (inline) 157ms 0.68% 38.33% 1777ms 7.71% DistributedBoxCollection::AddPairsFromBox 88ms 0.38% 38.71% 1613ms 7.00% std::__unguarded_insertion_sort (inline) 579ms 2.51% 41.22% 1574ms 6.83% std::__unguarded_linear_insert (inline) 23ms 0.1% 41.32% 1565ms 6.79% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 25ms 0.11% 41.43% 1540ms 6.69% AbstractCellPopulation::GetCellUsingLocationIndex 1430ms 6.21% 47.64% 1430ms 6.21% __gnu_cxx::__normal_iterator::operator-- (inline) 49ms 0.21% 47.85% 1216ms 5.28% boost::numeric::ublas::c_vector::c_vector (partial-inline) 1ms 0.0043% 47.86% 1162ms 5.04% NodeBasedCellPopulation::UpdateCellProcessLocation 35ms 0.15% 48.01% 1090ms 4.73% boost::numeric::ublas::vector_assign (inline) 5ms 0.022% 48.03% 1047ms 4.55% DistributedBoxCollection::CalculateBoundaryNodePairs 274ms 1.19% 49.22% 968ms 4.20% boost::numeric::ublas::indexing_vector_assign 241ms 1.05% 50.26% 939ms 4.08% __dynamic_cast 165ms 0.72% 50.98% 799ms 3.47% AbstractMesh::GetVectorFromAtoB 0 0% 50.98% 789ms 3.43% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 23ms 0.1% 51.08% 787ms 3.42% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 51.08% 775ms 3.36% boost::numeric::ublas::norm_2 (inline) 615ms 2.67% 53.75% 775ms 3.36% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 53.75% 775ms 3.36% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 193ms 0.84% 54.59% 728ms 3.16% NodeAttributes::AddNeighbour 328ms 1.42% 56.01% 724ms 3.14% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 56.01% 720ms 3.13% AbstractCellPopulation::WriteResultsToFiles 7ms 0.03% 56.04% 633ms 2.75% boost::numeric::ublas::c_vector::operator= (inline) 617ms 2.68% 58.72% 617ms 2.68% boost::numeric::ublas::c_vector::operator() 28ms 0.12% 58.84% 614ms 2.67% std::__copy_move::__copy_m (inline) 0 0% 58.84% 614ms 2.67% std::__copy_move_a (inline) 0 0% 58.84% 614ms 2.67% std::__copy_move_a1 (inline) 0 0% 58.84% 614ms 2.67% std::__copy_move_a2 (inline) 0 0% 58.84% 614ms 2.67% std::copy (inline) 601ms 2.61% 61.45% 601ms 2.61% __memcpy_avx_unaligned_erms 535ms 2.32% 63.77% 601ms 2.61% std::vector::push_back (inline) 271ms 1.18% 64.95% 577ms 2.50% __cxxabiv1::__si_class_type_info::__do_dyncast 3ms 0.013% 64.96% 573ms 2.49% AbstractCellBasedSimulation::DoCellBirth 3ms 0.013% 64.98% 557ms 2.42% AbstractCentreBasedCellPopulation::GetDampingConstant 4ms 0.017% 64.99% 556ms 2.41% CellPropertyCollection::GetPropertiesType (inline) 66ms 0.29% 65.28% 503ms 2.18% std::__new_allocator::allocate (inline) 29ms 0.13% 65.41% 501ms 2.17% std::_Rb_tree_const_iterator::operator++ (inline) 34ms 0.15% 65.55% 487ms 2.11% boost::detail::shared_count::~shared_count (inline) 0 0% 65.55% 487ms 2.11% boost::shared_ptr::~shared_ptr (inline) 480ms 2.08% 67.64% 480ms 2.08% boost::numeric::ublas::same_impl_ex 0 0% 67.64% 476ms 2.07% std::allocator_traits::allocate (inline) 1ms 0.0043% 67.64% 473ms 2.05% NodeBasedCellPopulation::WriteVtkResultsToFile 470ms 2.04% 69.68% 470ms 2.04% __strcmp_avx2 468ms 2.03% 71.71% 468ms 2.03% std::_Rb_tree_increment 0 0% 71.71% 448ms 1.94% std::_Rb_tree::_M_create_node (inline) 437ms 1.90% 73.61% 442ms 1.92% boost::detail::sp_counted_base::release 0 0% 73.61% 434ms 1.88% AbstractCellBasedSimulation::DoCellRemoval (inline) 35ms 0.15% 73.76% 433ms 1.88% operator new 11ms 0.048% 73.81% 431ms 1.87% std::_Rb_tree::_Rb_tree (partial-inline) 2ms 0.0087% 73.82% 420ms 1.82% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 129ms 0.56% 74.38% 418ms 1.81% std::_Rb_tree::_M_erase 3ms 0.013% 74.39% 412ms 1.79% AbstractCellProperty::IsSubType (inline) 33ms 0.14% 74.54% 402ms 1.75% std::_Rb_tree::_M_copy (inline) 110ms 0.48% 75.01% 396ms 1.72% __GI___libc_malloc 0 0% 75.01% 396ms 1.72% std::_Rb_tree::_M_get_node (inline) 135ms 0.59% 75.60% 395ms 1.71% Node::GetRadius 3ms 0.013% 75.61% 381ms 1.65% Cell::GetMutationState 107ms 0.46% 76.08% 367ms 1.59% std::_Rb_tree::_M_clone_node (inline) 1ms 0.0043% 76.08% 348ms 1.51% std::set::set (inline) 45ms 0.2% 76.28% 335ms 1.45% std::_Rb_tree::~_Rb_tree (inline) 334ms 1.45% 77.73% 334ms 1.45% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 7ms 0.03% 77.76% 333ms 1.45% NodeBasedCellPopulation::UpdateMapsAfterRemesh 316ms 1.37% 79.13% 316ms 1.37% __gnu_cxx::__normal_iterator::operator++ (inline) 23ms 0.1% 79.23% 312ms 1.35% boost::numeric::ublas::vector_binary::size (inline) 0 0% 79.23% 311ms 1.35% NodesOnlyMesh::ReMesh 0 0% 79.23% 308ms 1.34% boost::numeric::ublas::inner_prod (inline) 0 0% 79.23% 306ms 1.33% std::_Rb_tree::_Alloc_node::operator() (inline) 17ms 0.074% 79.30% 305ms 1.32% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 79.30% 305ms 1.32% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 1ms 0.0043% 79.31% 303ms 1.32% NodesOnlyMesh::UpdateNodeIndices 0 0% 79.31% 298ms 1.29% boost::numeric::ublas::c_vector::assign (inline) 2ms 0.0087% 79.31% 277ms 1.20% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 79.31% 277ms 1.20% std::_Rb_tree::_M_drop_node (inline) 12ms 0.052% 79.37% 266ms 1.15% std::_Rb_tree::_M_emplace_hint_unique 265ms 1.15% 80.52% 265ms 1.15% Node::CheckForNodeAttributes 7ms 0.03% 80.55% 260ms 1.13% DistributedBoxCollection::GetProcessOwningNode 0 0% 80.55% 254ms 1.10% std::set::~set (inline) 0 0% 80.55% 253ms 1.10% NodesOnlyMesh::UpdateBoxCollection 99ms 0.43% 80.98% 243ms 1.05% boost::numeric::ublas::vector_inner_prod::apply (inline) 5ms 0.022% 81.00% 237ms 1.03% std::__new_allocator::deallocate (inline) 0 0% 81.00% 230ms 1% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 81.00% 230ms 1% VtkMeshWriter::WriteFiles 141ms 0.61% 81.61% 226ms 0.98% _int_malloc 19ms 0.082% 81.69% 222ms 0.96% std::__insertion_sort (inline) 0 0% 81.69% 217ms 0.94% std::allocator_traits::deallocate (inline) 0 0% 81.69% 216ms 0.94% std::_Rb_tree::_M_put_node (inline) 0 0% 81.69% 209ms 0.91% NodesOnlyMesh::AddNodesToBoxes 71ms 0.31% 82.00% 209ms 0.91% __GI___libc_free 208ms 0.9% 82.91% 208ms 0.9% Node::GetIndex 0 0% 82.91% 204ms 0.89% Cell::HasCellProperty (inline) 2ms 0.0087% 82.91% 204ms 0.89% CellPropertyCollection::HasProperty 0 0% 82.91% 202ms 0.88% vtkStreamingDemandDrivenPipeline::Update 0 0% 82.91% 202ms 0.88% vtkXMLWriterBase::Write 0 0% 82.91% 201ms 0.87% vtkDemandDrivenPipeline::ProcessRequest 0 0% 82.91% 200ms 0.87% vtkExecutive::CallAlgorithm 0 0% 82.91% 200ms 0.87% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 82.91% 199ms 0.86% vtkCompositeDataPipeline::ExecuteData 0 0% 82.91% 199ms 0.86% vtkDemandDrivenPipeline::ExecuteData 0 0% 82.91% 198ms 0.86% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 82.91% 192ms 0.83% NodesOnlyMesh::ResizeBoxCollection 89ms 0.39% 83.30% 192ms 0.83% std::__move_median_to_first (inline) 13ms 0.056% 83.36% 191ms 0.83% NodesOnlyMesh::IsANodeCloseToDomainBoundary 4ms 0.017% 83.37% 190ms 0.82% AbstractCellProperty::IsType (inline) 91ms 0.4% 83.77% 189ms 0.82% boost::shared_ptr::shared_ptr (inline) 4ms 0.017% 83.79% 180ms 0.78% Cell::ReadyToDivide 180ms 0.78% 84.57% 180ms 0.78% [libchaste_cell_based.so] 0 0% 84.57% 175ms 0.76% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 84.57% 175ms 0.76% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 84.57% 172ms 0.75% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 152ms 0.66% 85.23% 152ms 0.66% Node::IsDeleted 3ms 0.013% 85.24% 152ms 0.66% std::_Rb_tree::clear (inline) 0 0% 85.24% 151ms 0.66% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 147ms 0.64% 85.88% 148ms 0.64% std::__adjacent_find (inline) 0 0% 85.88% 148ms 0.64% std::__unique (inline) 0 0% 85.88% 148ms 0.64% std::unique (inline) 84ms 0.36% 86.24% 147ms 0.64% Node::AddNeighbour 147ms 0.64% 86.88% 147ms 0.64% [libchaste_mesh.so] 1ms 0.0043% 86.89% 144ms 0.63% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 143ms 0.62% 87.51% 143ms 0.62% boost::shared_ptr::operator-> (inline) 4ms 0.017% 87.52% 142ms 0.62% DistributedBoxCollection::GetIsPeriodicAllDims 0 0% 87.52% 142ms 0.62% std::_Rb_tree::_Auto_node::_Auto_node (inline) 50ms 0.22% 87.74% 141ms 0.61% AbstractCellProperty::IsSame 0 0% 87.74% 141ms 0.61% vtkXMLWriter::WriteBinaryData 13ms 0.056% 87.80% 140ms 0.61% boost::numeric::ublas::vector_reference::operator() (inline) 1ms 0.0043% 87.80% 138ms 0.6% Cell::GetCellId 120ms 0.52% 88.32% 138ms 0.6% _int_free 0 0% 88.32% 137ms 0.59% vtkXMLWriter::WriteBinaryDataBlock 0 0% 88.32% 137ms 0.59% vtkXMLWriter::WriteBinaryDataInternal 0 0% 88.32% 137ms 0.59% vtkXMLWriter::WriteCompressionBlock 0 0% 88.32% 129ms 0.56% vtkXMLWriter::WritePointsAppendedData 1ms 0.0043% 88.33% 125ms 0.54% AbstractCellPopulation::SetCellUsingLocationIndex 0 0% 88.33% 124ms 0.54% boost::numeric::ublas::vector_binary::operator() (inline) 1ms 0.0043% 88.33% 117ms 0.51% compress2 0 0% 88.33% 117ms 0.51% vtkDataCompressor::Compress 0 0% 88.33% 117ms 0.51% vtkZLibDataCompressor::CompressBuffer 116ms 0.5% 88.83% 116ms 0.5% __ieee754_log_fma 59ms 0.26% 89.09% 116ms 0.5% crc32 0 0% 89.09% 116ms 0.5% deflate