File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 22087ms, 89.93% of 24561ms total Dropped 774 nodes (cum <= 122.81ms) flat flat% sum% cum cum% 0 0% 0% 24432ms 99.47% __libc_start_call_main 0 0% 0% 24432ms 99.47% __libc_start_main_impl 0 0% 0% 24432ms 99.47% _start 0 0% 0% 24416ms 99.41% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 24416ms 99.41% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 24416ms 99.41% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 24416ms 99.41% main 0 0% 0% 24373ms 99.23% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 24373ms 99.23% CxxTest::TestRunner::runTest (inline) 0 0% 0% 24373ms 99.23% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 24364ms 99.20% AbstractCellBasedSimulation::Solve 1ms 0.0041% 0.0041% 13838ms 56.34% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0041% 9311ms 37.91% AbstractCellBasedSimulation::UpdateCellPopulation 6ms 0.024% 0.029% 8959ms 36.48% ForwardEulerNumericalMethod::UpdateAllNodePositions 13ms 0.053% 0.081% 8764ms 35.68% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.081% 8276ms 33.70% NodeBasedCellPopulation::Update 1385ms 5.64% 5.72% 8093ms 32.95% RepulsionForce::AddForceContribution (partial-inline) 8ms 0.033% 5.75% 6025ms 24.53% DistributedBoxCollection::CalculateInteriorNodePairs 2149ms 8.75% 14.50% 4859ms 19.78% std::_Rb_tree::_M_lower_bound (inline) 18ms 0.073% 14.58% 4743ms 19.31% NodeAttributes::RemoveDuplicateNeighbours 0 0% 14.58% 4582ms 18.66% OffLatticeSimulation::ApplyBoundaries 3ms 0.012% 14.59% 4416ms 17.98% std::__sort (inline) 0 0% 14.59% 4416ms 17.98% std::sort (inline) 191ms 0.78% 15.37% 3967ms 16.15% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 262ms 1.07% 16.43% 3262ms 13.28% std::_Rb_tree::find (inline) 0 0% 16.43% 3261ms 13.28% std::map::find (inline) 81ms 0.33% 16.76% 3225ms 13.13% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 0 0% 16.76% 3070ms 12.50% AbstractCellPopulation::Iterator::operator++ (inline) 154ms 0.63% 17.39% 3038ms 12.37% AbstractCellPopulation::Iterator::IsRealCell (inline) 2672ms 10.88% 28.27% 2672ms 10.88% std::_Rb_tree::_S_right (inline) 40ms 0.16% 28.43% 2629ms 10.70% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 171ms 0.7% 29.13% 2489ms 10.13% std::__introsort_loop 21ms 0.086% 29.21% 2437ms 9.92% PlaneBoundaryCondition::ImposeBoundaryCondition 166ms 0.68% 29.89% 2363ms 9.62% AbstractMesh::GetNode 193ms 0.79% 30.67% 2351ms 9.57% std::map::operator[] (partial-inline) 49ms 0.2% 30.87% 2330ms 9.49% NodesOnlyMesh::GetNodeOrHaloNode 50ms 0.2% 31.08% 2262ms 9.21% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 31.08% 2242ms 9.13% std::__unguarded_partition_pivot (inline) 98ms 0.4% 31.48% 2200ms 8.96% NodesOnlyMesh::SolveNodeMapping 15ms 0.061% 31.54% 2145ms 8.73% PlaneBoundaryCondition::VerifyBoundaryCondition 172ms 0.7% 32.24% 2058ms 8.38% DistributedBoxCollection::AddPairsFromBox 1050ms 4.28% 36.51% 2012ms 8.19% std::__unguarded_partition (inline) 0 0% 36.51% 1922ms 7.83% std::__final_insertion_sort (inline) 0 0% 36.51% 1891ms 7.70% std::_Rb_tree::lower_bound (inline) 0 0% 36.51% 1891ms 7.70% std::map::lower_bound (inline) 106ms 0.43% 36.94% 1719ms 7.00% std::__unguarded_insertion_sort (inline) 622ms 2.53% 39.48% 1667ms 6.79% std::__unguarded_linear_insert (inline) 65ms 0.26% 39.74% 1574ms 6.41% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 31ms 0.13% 39.87% 1508ms 6.14% AbstractCellPopulation::GetCellUsingLocationIndex 1491ms 6.07% 45.94% 1491ms 6.07% __gnu_cxx::__normal_iterator::operator-- (inline) 5ms 0.02% 45.96% 1274ms 5.19% DistributedBoxCollection::CalculateBoundaryNodePairs 44ms 0.18% 46.14% 1267ms 5.16% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 46.14% 1166ms 4.75% NodeBasedCellPopulation::UpdateCellProcessLocation 7ms 0.029% 46.17% 1119ms 4.56% boost::numeric::ublas::vector_assign (inline) 199ms 0.81% 46.98% 1033ms 4.21% boost::numeric::ublas::indexing_vector_assign 22ms 0.09% 47.07% 963ms 3.92% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 276ms 1.12% 48.19% 930ms 3.79% __dynamic_cast 191ms 0.78% 48.97% 862ms 3.51% AbstractMesh::GetVectorFromAtoB 398ms 1.62% 50.59% 858ms 3.49% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 50.59% 835ms 3.40% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 50.59% 826ms 3.36% boost::numeric::ublas::norm_2 (inline) 652ms 2.65% 53.24% 826ms 3.36% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 53.24% 826ms 3.36% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 251ms 1.02% 54.26% 814ms 3.31% NodeAttributes::AddNeighbour 3ms 0.012% 54.28% 805ms 3.28% boost::numeric::ublas::c_vector::operator= (inline) 38ms 0.15% 54.43% 783ms 3.19% std::__copy_move::__copy_m (inline) 0 0% 54.43% 783ms 3.19% std::__copy_move_a (inline) 0 0% 54.43% 783ms 3.19% std::__copy_move_a1 (inline) 0 0% 54.43% 783ms 3.19% std::__copy_move_a2 (inline) 0 0% 54.43% 783ms 3.19% std::copy (inline) 764ms 3.11% 57.54% 764ms 3.11% __memcpy_avx_unaligned_erms 0 0% 57.54% 739ms 3.01% AbstractCellPopulation::WriteResultsToFiles 669ms 2.72% 60.27% 669ms 2.72% boost::numeric::ublas::c_vector::operator() 29ms 0.12% 60.38% 642ms 2.61% std::_Rb_tree_const_iterator::operator++ (inline) 5ms 0.02% 60.40% 635ms 2.59% CellPropertyCollection::GetPropertiesType (inline) 560ms 2.28% 62.68% 635ms 2.59% std::vector::push_back (inline) 6ms 0.024% 62.71% 598ms 2.43% AbstractCentreBasedCellPopulation::GetDampingConstant 598ms 2.43% 65.14% 598ms 2.43% std::_Rb_tree_increment 589ms 2.40% 67.54% 589ms 2.40% boost::numeric::ublas::same_impl_ex 7ms 0.029% 67.57% 582ms 2.37% AbstractCellBasedSimulation::DoCellBirth 267ms 1.09% 68.66% 545ms 2.22% __cxxabiv1::__si_class_type_info::__do_dyncast 45ms 0.18% 68.84% 533ms 2.17% boost::detail::shared_count::~shared_count (inline) 0 0% 68.84% 533ms 2.17% boost::shared_ptr::~shared_ptr (inline) 75ms 0.31% 69.15% 524ms 2.13% std::__new_allocator::allocate (inline) 0 0% 69.15% 506ms 2.06% std::allocator_traits::allocate (inline) 29ms 0.12% 69.26% 497ms 2.02% std::_Rb_tree::_Rb_tree (partial-inline) 2ms 0.0081% 69.27% 492ms 2.00% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 69.27% 480ms 1.95% std::_Rb_tree::_M_create_node (inline) 460ms 1.87% 71.15% 474ms 1.93% boost::detail::sp_counted_base::release 2ms 0.0081% 71.15% 457ms 1.86% Cell::GetMutationState 0 0% 71.15% 452ms 1.84% AbstractCellBasedSimulation::DoCellRemoval (inline) 39ms 0.16% 71.31% 452ms 1.84% std::_Rb_tree::_M_copy (inline) 29ms 0.12% 71.43% 445ms 1.81% operator new 434ms 1.77% 73.20% 434ms 1.77% __strcmp_avx2 3ms 0.012% 73.21% 433ms 1.76% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 73.21% 432ms 1.76% std::_Rb_tree::_M_get_node (inline) 114ms 0.46% 73.67% 421ms 1.71% std::_Rb_tree::_M_erase 2ms 0.0081% 73.68% 418ms 1.70% AbstractCellProperty::IsSubType (inline) 11ms 0.045% 73.73% 415ms 1.69% std::set::set (inline) 115ms 0.47% 74.19% 412ms 1.68% __GI___libc_malloc 129ms 0.53% 74.72% 408ms 1.66% std::_Rb_tree::_M_clone_node (inline) 94ms 0.38% 75.10% 391ms 1.59% boost::numeric::ublas::vector_binary::size (inline) 0 0% 75.10% 377ms 1.53% boost::numeric::ublas::inner_prod (inline) 5ms 0.02% 75.12% 376ms 1.53% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 17ms 0.069% 75.19% 371ms 1.51% boost::numeric::ublas::vector_scalar_binary::evaluate 78ms 0.32% 75.51% 368ms 1.50% Node::GetRadius 0 0% 75.51% 334ms 1.36% NodesOnlyMesh::ReMesh 0 0% 75.51% 329ms 1.34% std::_Rb_tree::_Alloc_node::operator() (inline) 58ms 0.24% 75.75% 329ms 1.34% std::_Rb_tree::~_Rb_tree (inline) 3ms 0.012% 75.76% 325ms 1.32% NodesOnlyMesh::UpdateNodeIndices 322ms 1.31% 77.07% 322ms 1.31% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 77.07% 321ms 1.31% boost::numeric::ublas::c_vector::assign (inline) 3ms 0.012% 77.08% 315ms 1.28% NodeBasedCellPopulation::UpdateMapsAfterRemesh 129ms 0.53% 77.61% 306ms 1.25% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 77.61% 301ms 1.23% std::_Rb_tree::_M_drop_node (inline) 0 0% 77.61% 295ms 1.20% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 294ms 1.20% 78.80% 294ms 1.20% std::__adjacent_find (inline) 0 0% 78.80% 294ms 1.20% std::__unique (inline) 0 0% 78.80% 294ms 1.20% std::unique (inline) 293ms 1.19% 80.00% 293ms 1.19% Node::CheckForNodeAttributes 9ms 0.037% 80.03% 286ms 1.16% DistributedBoxCollection::GetProcessOwningNode 0 0% 80.03% 271ms 1.10% NodesOnlyMesh::UpdateBoxCollection 14ms 0.057% 80.09% 267ms 1.09% std::_Rb_tree::_M_emplace_hint_unique 264ms 1.07% 81.17% 264ms 1.07% __gnu_cxx::__normal_iterator::operator++ (inline) 8ms 0.033% 81.20% 261ms 1.06% std::__new_allocator::deallocate (inline) 209ms 0.85% 82.05% 250ms 1.02% Node::AddNeighbour 0 0% 82.05% 245ms 1% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 82.05% 244ms 0.99% VtkMeshWriter::WriteFiles 133ms 0.54% 82.59% 243ms 0.99% _int_malloc 97ms 0.39% 82.99% 240ms 0.98% boost::shared_ptr::shared_ptr (inline) 0 0% 82.99% 240ms 0.98% std::set::~set (inline) 0 0% 82.99% 233ms 0.95% std::allocator_traits::deallocate (inline) 0 0% 82.99% 232ms 0.94% std::_Rb_tree::_M_put_node (inline) 230ms 0.94% 83.92% 230ms 0.94% [libchaste_mesh.so] 81ms 0.33% 84.25% 230ms 0.94% __GI___libc_free 101ms 0.41% 84.66% 226ms 0.92% std::__move_median_to_first (inline) 6ms 0.024% 84.69% 222ms 0.9% NodesOnlyMesh::AddNodesToBoxes 1ms 0.0041% 84.69% 221ms 0.9% vtkStreamingDemandDrivenPipeline::Update 0 0% 84.69% 221ms 0.9% vtkXMLWriterBase::Write 0 0% 84.69% 218ms 0.89% vtkDemandDrivenPipeline::ProcessRequest 0 0% 84.69% 218ms 0.89% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 84.69% 216ms 0.88% vtkCompositeDataPipeline::ExecuteData 0 0% 84.69% 216ms 0.88% vtkDemandDrivenPipeline::ExecuteData 0 0% 84.69% 216ms 0.88% vtkExecutive::CallAlgorithm 1ms 0.0041% 84.70% 215ms 0.88% vtkXMLUnstructuredDataWriter::ProcessRequest 214ms 0.87% 85.57% 214ms 0.87% Node::GetIndex 0 0% 85.57% 210ms 0.86% Cell::HasCellProperty (inline) 1ms 0.0041% 85.57% 210ms 0.86% CellPropertyCollection::HasProperty 13ms 0.053% 85.62% 208ms 0.85% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 85.62% 204ms 0.83% boost::numeric::ublas::vector_binary::operator() (inline) 20ms 0.081% 85.70% 203ms 0.83% std::__insertion_sort (inline) 4ms 0.016% 85.72% 197ms 0.8% Cell::ReadyToDivide 0 0% 85.72% 176ms 0.72% NodesOnlyMesh::ResizeBoxCollection 3ms 0.012% 85.73% 175ms 0.71% AbstractCellProperty::IsType (inline) 20ms 0.081% 85.81% 175ms 0.71% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 85.81% 174ms 0.71% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.81% 174ms 0.71% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 172ms 0.7% 86.52% 172ms 0.7% [libchaste_cell_based.so] 0 0% 86.52% 164ms 0.67% std::_Rb_tree::clear (inline) 0 0% 86.52% 162ms 0.66% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 86.52% 151ms 0.61% std::_Rb_tree::_Auto_node::_Auto_node (inline) 149ms 0.61% 87.12% 149ms 0.61% Node::rGetLocation 142ms 0.58% 87.70% 148ms 0.6% _int_free 0 0% 87.70% 144ms 0.59% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 109ms 0.44% 88.14% 143ms 0.58% boost::detail::shared_count::shared_count (inline) 0 0% 88.14% 142ms 0.58% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 88.14% 142ms 0.58% vtkXMLWriter::WriteBinaryData 2ms 0.0081% 88.15% 138ms 0.56% AbstractNumericalMethod::SafeNodePositionUpdate 3ms 0.012% 88.16% 138ms 0.56% boost::numeric::ublas::c_vector::operator[] (inline) 1ms 0.0041% 88.17% 133ms 0.54% Cell::GetCellId 0 0% 88.17% 132ms 0.54% vtkXMLWriter::WriteBinaryDataInternal 48ms 0.2% 88.36% 131ms 0.53% AbstractCellProperty::IsSame 0 0% 88.36% 130ms 0.53% vtkXMLWriter::WriteBinaryDataBlock 0 0% 88.36% 130ms 0.53% vtkXMLWriter::WriteCompressionBlock 128ms 0.52% 88.88% 128ms 0.52% __ieee754_log_fma 0 0% 88.88% 128ms 0.52% vtkXMLWriter::WritePointsAppendedData 7ms 0.029% 88.91% 127ms 0.52% NodeBasedCellPopulation::SetNode 125ms 0.51% 89.42% 125ms 0.51% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 124ms 0.5% 89.93% 124ms 0.5% Node::IsDeleted