File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 19882ms, 89.17% of 22296ms total Dropped 755 nodes (cum <= 111.48ms) flat flat% sum% cum cum% 0 0% 0% 22224ms 99.68% __libc_start_call_main 0 0% 0% 22224ms 99.68% __libc_start_main_impl 0 0% 0% 22224ms 99.68% _start 0 0% 0% 22209ms 99.61% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 22209ms 99.61% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 22209ms 99.61% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 22209ms 99.61% main 0 0% 0% 22174ms 99.45% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 22174ms 99.45% CxxTest::TestRunner::runTest (inline) 0 0% 0% 22174ms 99.45% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 22167ms 99.42% AbstractCellBasedSimulation::Solve 2ms 0.009% 0.009% 12540ms 56.24% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.009% 8563ms 38.41% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.009% 7482ms 33.56% NodeBasedCellPopulation::Update 3ms 0.013% 0.022% 7190ms 32.25% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.027% 0.049% 7031ms 31.53% AbstractNumericalMethod::ComputeForcesIncludingDamping 821ms 3.68% 3.73% 6469ms 29.01% RepulsionForce::AddForceContribution (partial-inline) 3ms 0.013% 3.75% 5690ms 25.52% DistributedBoxCollection::CalculateInteriorNodePairs 0 0% 3.75% 5068ms 22.73% OffLatticeSimulation::ApplyBoundaries 2050ms 9.19% 12.94% 4754ms 21.32% std::_Rb_tree::_M_lower_bound (inline) 15ms 0.067% 13.01% 4396ms 19.72% NodeAttributes::RemoveDuplicateNeighbours 1ms 0.0045% 13.01% 4214ms 18.90% std::__sort (inline) 0 0% 13.01% 4214ms 18.90% std::sort (inline) 286ms 1.28% 14.29% 3798ms 17.03% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 3ms 0.013% 14.31% 3601ms 16.15% AbstractCellPopulation::Iterator::operator++ (inline) 179ms 0.8% 15.11% 3588ms 16.09% AbstractCellPopulation::Iterator::IsRealCell (inline) 160ms 0.72% 15.83% 3506ms 15.72% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 236ms 1.06% 16.89% 3049ms 13.68% std::_Rb_tree::find (inline) 0 0% 16.89% 3049ms 13.68% std::map::find (inline) 30ms 0.13% 17.02% 3036ms 13.62% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 214ms 0.96% 17.98% 2567ms 11.51% std::__introsort_loop 84ms 0.38% 18.36% 2566ms 11.51% AbstractMesh::GetNode 63ms 0.28% 18.64% 2565ms 11.50% PlaneBoundaryCondition::ImposeBoundaryCondition 38ms 0.17% 18.81% 2528ms 11.34% NodesOnlyMesh::GetNodeOrHaloNode 38ms 0.17% 18.98% 2503ms 11.23% PlaneBoundaryCondition::VerifyBoundaryCondition 208ms 0.93% 19.91% 2496ms 11.19% std::map::operator[] (partial-inline) 235ms 1.05% 20.97% 2488ms 11.16% NodesOnlyMesh::SolveNodeMapping 2360ms 10.58% 31.55% 2360ms 10.58% std::_Rb_tree::_S_right (inline) 1ms 0.0045% 31.56% 2262ms 10.15% std::__unguarded_partition_pivot (inline) 85ms 0.38% 31.94% 2120ms 9.51% AbstractCellPopulation::GetLocationIndexUsingCell 670ms 3.01% 34.94% 2065ms 9.26% std::__unguarded_partition (inline) 0 0% 34.94% 1977ms 8.87% std::_Rb_tree::lower_bound (inline) 0 0% 34.94% 1977ms 8.87% std::map::lower_bound (inline) 125ms 0.56% 35.50% 1781ms 7.99% DistributedBoxCollection::AddPairsFromBox 0 0% 35.50% 1643ms 7.37% std::__final_insertion_sort (inline) 9ms 0.04% 35.54% 1502ms 6.74% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 19ms 0.085% 35.63% 1483ms 6.65% AbstractCellPopulation::GetCellUsingLocationIndex 132ms 0.59% 36.22% 1436ms 6.44% std::__unguarded_insertion_sort (inline) 662ms 2.97% 39.19% 1266ms 5.68% std::__unguarded_linear_insert (inline) 48ms 0.22% 39.41% 1140ms 5.11% boost::numeric::ublas::c_vector::c_vector (partial-inline) 26ms 0.12% 39.52% 1116ms 5.01% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 39.52% 1044ms 4.68% NodeBasedCellPopulation::UpdateCellProcessLocation 4ms 0.018% 39.54% 972ms 4.36% boost::numeric::ublas::vector_assign (inline) 951ms 4.27% 43.81% 951ms 4.27% __gnu_cxx::__normal_iterator::operator-- (inline) 36ms 0.16% 43.97% 931ms 4.18% boost::detail::shared_count::~shared_count (inline) 0 0% 43.97% 931ms 4.18% boost::shared_ptr::~shared_ptr (inline) 3ms 0.013% 43.98% 901ms 4.04% DistributedBoxCollection::CalculateBoundaryNodePairs 855ms 3.83% 47.82% 862ms 3.87% boost::detail::sp_counted_base::release 190ms 0.85% 48.67% 849ms 3.81% boost::numeric::ublas::indexing_vector_assign 231ms 1.04% 49.70% 827ms 3.71% __dynamic_cast 108ms 0.48% 50.19% 729ms 3.27% AbstractMesh::GetVectorFromAtoB 300ms 1.35% 51.53% 687ms 3.08% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 51.53% 637ms 2.86% AbstractCellPopulation::WriteResultsToFiles 25ms 0.11% 51.65% 636ms 2.85% std::_Rb_tree_const_iterator::operator++ (inline) 632ms 2.83% 54.48% 632ms 2.83% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 299ms 1.34% 55.82% 609ms 2.73% NodeAttributes::AddNeighbour 8ms 0.036% 55.86% 584ms 2.62% boost::numeric::ublas::c_vector::operator= (inline) 28ms 0.13% 55.98% 567ms 2.54% std::__copy_move::__copy_m (inline) 0 0% 55.98% 567ms 2.54% std::__copy_move_a (inline) 0 0% 55.98% 567ms 2.54% std::__copy_move_a1 (inline) 0 0% 55.98% 567ms 2.54% std::__copy_move_a2 (inline) 0 0% 55.98% 567ms 2.54% std::copy (inline) 561ms 2.52% 58.50% 561ms 2.52% [libchaste_cell_based.so] 47ms 0.21% 58.71% 546ms 2.45% std::__new_allocator::allocate (inline) 1ms 0.0045% 58.71% 543ms 2.44% AbstractCellBasedSimulation::DoCellBirth 0 0% 58.71% 538ms 2.41% AbstractCellBasedSimulation::DoCellRemoval (inline) 4ms 0.018% 58.73% 534ms 2.40% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 534ms 2.40% 61.13% 534ms 2.40% __memcpy_avx512_unaligned_erms 534ms 2.40% 63.52% 534ms 2.40% std::_Rb_tree_increment 0 0% 63.52% 522ms 2.34% std::allocator_traits::allocate (inline) 10ms 0.045% 63.57% 520ms 2.33% CellPropertyCollection::GetPropertiesType (inline) 6ms 0.027% 63.59% 515ms 2.31% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 63.59% 512ms 2.30% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 509ms 2.28% 65.88% 509ms 2.28% __gnu_cxx::__normal_iterator::operator++ (inline) 22ms 0.099% 65.98% 501ms 2.25% operator new 0 0% 65.98% 495ms 2.22% boost::numeric::ublas::norm_2 (inline) 392ms 1.76% 67.73% 495ms 2.22% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 67.73% 495ms 2.22% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 493ms 2.21% 69.95% 493ms 2.21% boost::numeric::ublas::same_impl_ex 0 0% 69.95% 490ms 2.20% std::_Rb_tree::_M_create_node (inline) 32ms 0.14% 70.09% 480ms 2.15% std::_Rb_tree::_Rb_tree (partial-inline) 472ms 2.12% 72.21% 472ms 2.12% boost::numeric::ublas::c_vector::operator() 203ms 0.91% 73.12% 470ms 2.11% __cxxabiv1::__si_class_type_info::__do_dyncast 171ms 0.77% 73.88% 469ms 2.10% __GI___libc_malloc 468ms 2.10% 75.98% 468ms 2.10% [libchaste_mesh.so] 0 0% 75.98% 467ms 2.09% std::_Rb_tree::_M_get_node (inline) 33ms 0.15% 76.13% 438ms 1.96% std::_Rb_tree::_M_copy (inline) 3ms 0.013% 76.14% 420ms 1.88% NodeBasedCellPopulation::WriteVtkResultsToFile 3ms 0.013% 76.16% 415ms 1.86% std::set::set (inline) 286ms 1.28% 77.44% 409ms 1.83% std::vector::push_back (inline) 65ms 0.29% 77.73% 403ms 1.81% std::_Rb_tree::_M_erase 180ms 0.81% 78.54% 401ms 1.80% std::_Rb_tree::_M_clone_node (inline) 105ms 0.47% 79.01% 397ms 1.78% std::_Rb_tree::~_Rb_tree (inline) 386ms 1.73% 80.74% 386ms 1.73% __strcmp_evex 2ms 0.009% 80.75% 371ms 1.66% Cell::GetMutationState 5ms 0.022% 80.77% 361ms 1.62% AbstractCellProperty::IsSubType (inline) 18ms 0.081% 80.85% 360ms 1.61% boost::numeric::ublas::vector_binary::size (inline) 342ms 1.53% 82.39% 342ms 1.53% std::_Rb_tree::_S_left (inline) 0 0% 82.39% 341ms 1.53% std::set::~set (inline) 0 0% 82.39% 333ms 1.49% std::_Rb_tree::_M_drop_node (inline) 3ms 0.013% 82.40% 311ms 1.39% std::_Rb_tree::_M_emplace_hint_unique 8ms 0.036% 82.44% 300ms 1.35% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 82.44% 294ms 1.32% NodesOnlyMesh::ReMesh 0 0% 82.44% 284ms 1.27% std::_Rb_tree::_Alloc_node::operator() (inline) 1ms 0.0045% 82.44% 281ms 1.26% NodesOnlyMesh::UpdateNodeIndices 5ms 0.022% 82.46% 267ms 1.20% Node::GetRadius 0 0% 82.46% 262ms 1.18% NodesOnlyMesh::UpdateBoxCollection 216ms 0.97% 83.43% 258ms 1.16% boost::shared_ptr::shared_ptr (inline) 3ms 0.013% 83.45% 254ms 1.14% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 83.45% 245ms 1.10% boost::numeric::ublas::c_vector::assign (inline) 7ms 0.031% 83.48% 245ms 1.10% std::__new_allocator::deallocate (inline) 158ms 0.71% 84.19% 241ms 1.08% _int_malloc 2ms 0.009% 84.19% 235ms 1.05% DistributedBoxCollection::GetProcessOwningNode 0 0% 84.19% 221ms 0.99% std::allocator_traits::deallocate (inline) 0 0% 84.19% 218ms 0.98% std::_Rb_tree::_M_put_node (inline) 0 0% 84.19% 218ms 0.98% std::iter_swap (inline) 218ms 0.98% 85.17% 218ms 0.98% std::swap (inline) 52ms 0.23% 85.41% 216ms 0.97% __GI___libc_free 209ms 0.94% 86.34% 209ms 0.94% Node::CheckForNodeAttributes 1ms 0.0045% 86.35% 207ms 0.93% NodesOnlyMesh::AddNodesToBoxes 32ms 0.14% 86.49% 207ms 0.93% std::__insertion_sort (inline) 0 0% 86.49% 206ms 0.92% std::_Rb_tree::_Auto_node::_Auto_node (inline) 3ms 0.013% 86.50% 199ms 0.89% CellPropertyCollection::HasProperty 0 0% 86.50% 196ms 0.88% Cell::HasCellProperty (inline) 53ms 0.24% 86.74% 188ms 0.84% std::__move_median_to_first (inline) 6ms 0.027% 86.77% 187ms 0.84% Cell::ReadyToDivide 1ms 0.0045% 86.77% 184ms 0.83% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 86.77% 180ms 0.81% boost::numeric::ublas::inner_prod (inline) 2ms 0.009% 86.78% 180ms 0.81% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 86.78% 178ms 0.8% VtkMeshWriter::WriteFiles 5ms 0.022% 86.80% 178ms 0.8% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 86.80% 166ms 0.74% NodesOnlyMesh::ResizeBoxCollection 13ms 0.058% 86.86% 164ms 0.74% NodesOnlyMesh::IsANodeCloseToDomainBoundary 129ms 0.58% 87.44% 162ms 0.73% _int_free 0 0% 87.44% 158ms 0.71% vtkStreamingDemandDrivenPipeline::Update 0 0% 87.44% 158ms 0.71% vtkXMLWriterBase::Write 0 0% 87.44% 155ms 0.7% vtkDemandDrivenPipeline::ProcessRequest 0 0% 87.44% 155ms 0.7% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 87.44% 152ms 0.68% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 87.44% 152ms 0.68% vtkExecutive::CallAlgorithm 0 0% 87.44% 151ms 0.68% vtkCompositeDataPipeline::ExecuteData 0 0% 87.44% 151ms 0.68% vtkDemandDrivenPipeline::ExecuteData 0 0% 87.44% 151ms 0.68% vtkXMLUnstructuredDataWriter::ProcessRequest 14ms 0.063% 87.50% 150ms 0.67% AbstractCellProperty::IsType (inline) 33ms 0.15% 87.65% 148ms 0.66% boost::numeric::ublas::vector_inner_prod::apply (inline) 66ms 0.3% 87.95% 143ms 0.64% std::__adjacent_find (inline) 0 0% 87.95% 143ms 0.64% std::__unique (inline) 0 0% 87.95% 143ms 0.64% std::unique (inline) 141ms 0.63% 88.58% 141ms 0.63% boost::shared_ptr::operator-> (inline) 2ms 0.009% 88.59% 140ms 0.63% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 88.59% 133ms 0.6% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 88.59% 133ms 0.6% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 3ms 0.013% 88.60% 131ms 0.59% AbstractCellPopulation::SetCellUsingLocationIndex 0 0% 88.60% 131ms 0.59% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 88.60% 128ms 0.57% std::_Rb_tree::clear (inline) 3ms 0.013% 88.62% 126ms 0.57% DistributedBoxCollection::GetIsPeriodicAllDims 1ms 0.0045% 88.62% 125ms 0.56% AbstractNumericalMethod::SafeNodePositionUpdate 3ms 0.013% 88.63% 124ms 0.56% std::_Rb_tree::_M_insert_unique 0 0% 88.63% 124ms 0.56% std::set::insert (inline) 0 0% 88.63% 123ms 0.55% std::_Rb_tree::_M_destroy_node (inline) 0 0% 88.63% 123ms 0.55% std::__new_allocator::destroy (inline) 0 0% 88.63% 123ms 0.55% std::allocator_traits::destroy (inline) 0 0% 88.63% 122ms 0.55% Cell::GetCellId 118ms 0.53% 89.16% 118ms 0.53% Node::GetIndex 2ms 0.009% 89.17% 112ms 0.5% NodeBasedCellPopulation::SetNode