File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 22837ms, 89.19% of 25605ms total Dropped 797 nodes (cum <= 128.03ms) flat flat% sum% cum cum% 0 0% 0% 25510ms 99.63% __libc_start_call_main 0 0% 0% 25510ms 99.63% __libc_start_main_impl 0 0% 0% 25510ms 99.63% _start 0 0% 0% 25492ms 99.56% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 25492ms 99.56% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 25492ms 99.56% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 25492ms 99.56% main 0 0% 0% 25453ms 99.41% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 25453ms 99.41% CxxTest::TestRunner::runTest (inline) 0 0% 0% 25453ms 99.41% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 25445ms 99.38% AbstractCellBasedSimulation::Solve 2ms 0.0078% 0.0078% 14307ms 55.88% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0078% 9915ms 38.72% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0039% 0.012% 8704ms 33.99% NodeBasedCellPopulation::Update 3ms 0.012% 0.023% 8132ms 31.76% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.012% 0.035% 7925ms 30.95% AbstractNumericalMethod::ComputeForcesIncludingDamping 979ms 3.82% 3.86% 7272ms 28.40% RepulsionForce::AddForceContribution (partial-inline) 4ms 0.016% 3.87% 6578ms 25.69% DistributedBoxCollection::CalculateInteriorNodePairs 1ms 0.0039% 3.88% 5895ms 23.02% OffLatticeSimulation::ApplyBoundaries 2293ms 8.96% 12.83% 5434ms 21.22% std::_Rb_tree::_M_lower_bound (inline) 15ms 0.059% 12.89% 5261ms 20.55% NodeAttributes::RemoveDuplicateNeighbours 3ms 0.012% 12.90% 5059ms 19.76% std::__sort (inline) 0 0% 12.90% 5059ms 19.76% std::sort (inline) 339ms 1.32% 14.23% 4396ms 17.17% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 5ms 0.02% 14.25% 4183ms 16.34% AbstractCellPopulation::Iterator::operator++ (inline) 215ms 0.84% 15.09% 4172ms 16.29% AbstractCellPopulation::Iterator::IsRealCell 157ms 0.61% 15.70% 3962ms 15.47% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 302ms 1.18% 16.88% 3637ms 14.20% std::_Rb_tree::find (inline) 0 0% 16.88% 3637ms 14.20% std::map::find (inline) 47ms 0.18% 17.06% 3533ms 13.80% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 98ms 0.38% 17.45% 3065ms 11.97% AbstractMesh::GetNode 63ms 0.25% 17.69% 3042ms 11.88% NodesOnlyMesh::GetNodeOrHaloNode 237ms 0.93% 18.62% 3010ms 11.76% std::__introsort_loop 56ms 0.22% 18.84% 3005ms 11.74% PlaneBoundaryCondition::ImposeBoundaryCondition 279ms 1.09% 19.93% 2978ms 11.63% NodesOnlyMesh::SolveNodeMapping 57ms 0.22% 20.15% 2889ms 11.28% PlaneBoundaryCondition::VerifyBoundaryCondition 2751ms 10.74% 30.89% 2751ms 10.74% std::_Rb_tree::_S_right (inline) 227ms 0.89% 31.78% 2725ms 10.64% std::map::operator[] (partial-inline) 4ms 0.016% 31.79% 2693ms 10.52% std::__unguarded_partition_pivot (inline) 824ms 3.22% 35.01% 2451ms 9.57% std::__unguarded_partition (inline) 125ms 0.49% 35.50% 2419ms 9.45% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 35.50% 2146ms 8.38% std::_Rb_tree::lower_bound (inline) 0 0% 35.50% 2146ms 8.38% std::map::lower_bound (inline) 0 0% 35.50% 2043ms 7.98% std::__final_insertion_sort (inline) 125ms 0.49% 35.99% 1885ms 7.36% DistributedBoxCollection::AddPairsFromBox 126ms 0.49% 36.48% 1829ms 7.14% std::__unguarded_insertion_sort (inline) 12ms 0.047% 36.53% 1732ms 6.76% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 28ms 0.11% 36.64% 1705ms 6.66% AbstractCellPopulation::GetCellUsingLocationIndex 854ms 3.34% 39.97% 1605ms 6.27% std::__unguarded_linear_insert (inline) 17ms 0.066% 40.04% 1269ms 4.96% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 1ms 0.0039% 40.04% 1222ms 4.77% NodeBasedCellPopulation::UpdateCellProcessLocation 71ms 0.28% 40.32% 1219ms 4.76% boost::numeric::ublas::c_vector::c_vector (partial-inline) 1202ms 4.69% 45.01% 1202ms 4.69% __gnu_cxx::__normal_iterator::operator-- (inline) 15ms 0.059% 45.07% 1088ms 4.25% DistributedBoxCollection::CalculateBoundaryNodePairs 27ms 0.11% 45.18% 1085ms 4.24% boost::detail::shared_count::~shared_count (inline) 0 0% 45.18% 1085ms 4.24% boost::shared_ptr::~shared_ptr (inline) 1025ms 4.00% 49.18% 1036ms 4.05% boost::detail::sp_counted_base::release 5ms 0.02% 49.20% 1031ms 4.03% boost::numeric::ublas::vector_assign (inline) 239ms 0.93% 50.13% 923ms 3.60% boost::numeric::ublas::indexing_vector_assign 278ms 1.09% 51.22% 885ms 3.46% __dynamic_cast 355ms 1.39% 52.61% 875ms 3.42% DistributedBoxCollection::CalculateContainingBox (partial-inline) 100ms 0.39% 53.00% 756ms 2.95% AbstractMesh::GetVectorFromAtoB 0 0% 53.00% 743ms 2.90% AbstractCellPopulation::WriteResultsToFiles 703ms 2.75% 55.74% 703ms 2.75% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 32ms 0.12% 55.87% 667ms 2.60% std::_Rb_tree_const_iterator::operator++ (inline) 657ms 2.57% 58.43% 657ms 2.57% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 58.43% 648ms 2.53% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 646ms 2.52% 60.96% 646ms 2.52% [libchaste_cell_based.so] 2ms 0.0078% 60.96% 642ms 2.51% boost::numeric::ublas::c_vector::operator= (inline) 297ms 1.16% 62.12% 640ms 2.50% NodeAttributes::AddNeighbour 0 0% 62.12% 632ms 2.47% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 62.12% 631ms 2.46% boost::numeric::ublas::norm_2 (inline) 514ms 2.01% 64.13% 631ms 2.46% boost::numeric::ublas::vector_norm_2::apply (inline) 33ms 0.13% 64.26% 627ms 2.45% std::__copy_move::__copy_m (inline) 0 0% 64.26% 627ms 2.45% std::__copy_move_a (inline) 0 0% 64.26% 627ms 2.45% std::__copy_move_a1 (inline) 0 0% 64.26% 627ms 2.45% std::__copy_move_a2 (inline) 0 0% 64.26% 627ms 2.45% std::copy (inline) 0 0% 64.26% 610ms 2.38% AbstractCellBasedSimulation::DoCellRemoval (inline) 2ms 0.0078% 64.27% 600ms 2.34% AbstractCellBasedSimulation::DoCellBirth 56ms 0.22% 64.49% 597ms 2.33% std::__new_allocator::allocate (inline) 2ms 0.0078% 64.50% 595ms 2.32% AbstractCentreBasedCellPopulation::GetDampingConstant 8ms 0.031% 64.53% 595ms 2.32% CellPropertyCollection::GetPropertiesType (inline) 10ms 0.039% 64.57% 594ms 2.32% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 64.57% 577ms 2.25% std::allocator_traits::allocate (inline) 571ms 2.23% 66.80% 571ms 2.23% [libchaste_mesh.so] 571ms 2.23% 69.03% 571ms 2.23% __memcpy_avx512_unaligned_erms 21ms 0.082% 69.11% 554ms 2.16% std::_Rb_tree::_Rb_tree (partial-inline) 30ms 0.12% 69.22% 540ms 2.11% operator new 539ms 2.11% 71.33% 539ms 2.11% boost::numeric::ublas::c_vector::operator() 0 0% 71.33% 535ms 2.09% std::_Rb_tree::_M_create_node (inline) 535ms 2.09% 73.42% 535ms 2.09% std::_Rb_tree_increment 532ms 2.08% 75.50% 532ms 2.08% boost::numeric::ublas::same_impl_ex 39ms 0.15% 75.65% 527ms 2.06% std::_Rb_tree::_M_copy (inline) 181ms 0.71% 76.36% 504ms 1.97% __GI___libc_malloc 0 0% 76.36% 504ms 1.97% std::_Rb_tree::_M_get_node (inline) 122ms 0.48% 76.83% 498ms 1.94% std::_Rb_tree::~_Rb_tree (inline) 2ms 0.0078% 76.84% 495ms 1.93% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 76.84% 488ms 1.91% std::set::set (inline) 68ms 0.27% 77.11% 482ms 1.88% std::_Rb_tree::_M_erase (partial-inline) 236ms 0.92% 78.03% 478ms 1.87% __cxxabiv1::__si_class_type_info::__do_dyncast 219ms 0.86% 78.88% 475ms 1.86% std::_Rb_tree::_M_clone_node (inline) 314ms 1.23% 80.11% 456ms 1.78% std::vector::push_back (inline) 0 0% 80.11% 433ms 1.69% std::set::~set (inline) 0 0% 80.11% 416ms 1.62% std::_Rb_tree::_M_drop_node (inline) 5ms 0.02% 80.13% 414ms 1.62% AbstractCellProperty::IsSubType (inline) 3ms 0.012% 80.14% 414ms 1.62% Cell::GetMutationState 397ms 1.55% 81.69% 397ms 1.55% std::_Rb_tree::_S_left (inline) 385ms 1.50% 83.19% 385ms 1.50% __strcmp_evex 9ms 0.035% 83.23% 383ms 1.50% boost::numeric::ublas::vector_binary::size (inline) 10ms 0.039% 83.27% 352ms 1.37% std::_Rb_tree::_M_emplace_hint_unique 0 0% 83.27% 344ms 1.34% NodesOnlyMesh::ReMesh 3ms 0.012% 83.28% 335ms 1.31% NodesOnlyMesh::UpdateNodeIndices 8ms 0.031% 83.31% 325ms 1.27% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 83.31% 320ms 1.25% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 83.31% 304ms 1.19% std::_Rb_tree::_Alloc_node::operator() (inline) 3ms 0.012% 83.32% 301ms 1.18% DistributedBoxCollection::GetProcessOwningNode 11ms 0.043% 83.37% 288ms 1.12% std::__new_allocator::deallocate (inline) 0 0% 83.37% 284ms 1.11% NodesOnlyMesh::UpdateBoxCollection 1ms 0.0039% 83.37% 265ms 1.03% Node::GetRadius 225ms 0.88% 84.25% 263ms 1.03% boost::shared_ptr::shared_ptr (inline) 0 0% 84.25% 255ms 1% std::allocator_traits::deallocate (inline) 162ms 0.63% 84.88% 254ms 0.99% _int_malloc 0 0% 84.88% 253ms 0.99% std::_Rb_tree::_M_put_node (inline) 0 0% 84.88% 246ms 0.96% boost::numeric::ublas::c_vector::assign (inline) 71ms 0.28% 85.16% 245ms 0.96% __GI___libc_free 4ms 0.016% 85.17% 243ms 0.95% NodesOnlyMesh::AddNodesToBoxes 0 0% 85.17% 231ms 0.9% std::_Rb_tree::_Auto_node::_Auto_node (inline) 76ms 0.3% 85.47% 230ms 0.9% std::__move_median_to_first (inline) 0 0% 85.47% 226ms 0.88% std::iter_swap (inline) 226ms 0.88% 86.35% 226ms 0.88% std::swap (inline) 1ms 0.0039% 86.36% 214ms 0.84% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 26ms 0.1% 86.46% 214ms 0.84% std::__insertion_sort (inline) 0 0% 86.46% 212ms 0.83% VtkMeshWriter::WriteFiles 0 0% 86.46% 210ms 0.82% boost::numeric::ublas::inner_prod (inline) 209ms 0.82% 87.28% 209ms 0.82% Node::CheckForNodeAttributes 12ms 0.047% 87.32% 209ms 0.82% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 87.32% 209ms 0.82% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 5ms 0.02% 87.34% 197ms 0.77% CellPropertyCollection::HasProperty 0 0% 87.34% 194ms 0.76% Cell::HasCellProperty (inline) 0 0% 87.34% 187ms 0.73% vtkDemandDrivenPipeline::ProcessRequest 0 0% 87.34% 187ms 0.73% vtkStreamingDemandDrivenPipeline::Update 0 0% 87.34% 187ms 0.73% vtkXMLWriterBase::Write 0 0% 87.34% 186ms 0.73% vtkDemandDrivenPipeline::ExecuteData 1ms 0.0039% 87.35% 186ms 0.73% vtkExecutive::CallAlgorithm 0 0% 87.35% 186ms 0.73% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 87.35% 185ms 0.72% NodesOnlyMesh::ResizeBoxCollection 0 0% 87.35% 185ms 0.72% vtkCompositeDataPipeline::ExecuteData 0 0% 87.35% 185ms 0.72% vtkXMLUnstructuredDataWriter::ProcessRequest 10ms 0.039% 87.39% 183ms 0.71% NodesOnlyMesh::IsANodeCloseToDomainBoundary 41ms 0.16% 87.55% 175ms 0.68% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 87.55% 174ms 0.68% std::__new_allocator::destroy (inline) 0 0% 87.55% 174ms 0.68% std::allocator_traits::destroy (inline) 0 0% 87.55% 173ms 0.68% std::_Rb_tree::_M_destroy_node (inline) 8ms 0.031% 87.58% 171ms 0.67% Cell::ReadyToDivide 142ms 0.55% 88.13% 169ms 0.66% _int_free 0 0% 88.13% 163ms 0.64% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 88.13% 163ms 0.64% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 162ms 0.63% 88.76% 162ms 0.63% boost::shared_ptr::operator-> (inline) 75ms 0.29% 89.06% 161ms 0.63% std::__adjacent_find (inline) 0 0% 89.06% 161ms 0.63% std::__unique (inline) 0 0% 89.06% 161ms 0.63% std::unique (inline) 0 0% 89.06% 160ms 0.62% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 89.06% 156ms 0.61% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 4ms 0.016% 89.07% 153ms 0.6% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 3ms 0.012% 89.08% 151ms 0.59% AbstractNumericalMethod::SafeNodePositionUpdate 9ms 0.035% 89.12% 148ms 0.58% AbstractCellProperty::IsType (inline) 7ms 0.027% 89.15% 142ms 0.55% boost::numeric::ublas::c_vector::operator[] (inline) 1ms 0.0039% 89.15% 141ms 0.55% Cell::GetCellId 0 0% 89.15% 139ms 0.54% vtkXMLWriter::WriteBinaryData 0 0% 89.15% 136ms 0.53% vtkXMLWriter::WriteBinaryDataBlock 0 0% 89.15% 136ms 0.53% vtkXMLWriter::WriteBinaryDataInternal 0 0% 89.15% 136ms 0.53% vtkXMLWriter::WriteCompressionBlock 6ms 0.023% 89.17% 135ms 0.53% AbstractCellPopulation::SetCellUsingLocationIndex 4ms 0.016% 89.19% 134ms 0.52% NodeBasedCellPopulation::SetNode 0 0% 89.19% 130ms 0.51% vtkXMLWriter::WritePointsAppendedData