File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 16726ms, 89.50% of 18688ms total Dropped 679 nodes (cum <= 93.44ms) flat flat% sum% cum cum% 0 0% 0% 18634ms 99.71% __libc_start_call_main 0 0% 0% 18634ms 99.71% __libc_start_main_impl 0 0% 0% 18634ms 99.71% _start 0 0% 0% 18620ms 99.64% main 0 0% 0% 18619ms 99.63% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 18619ms 99.63% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 18619ms 99.63% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 18582ms 99.43% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 18582ms 99.43% CxxTest::TestRunner::runTest (inline) 0 0% 0% 18582ms 99.43% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0054% 0.0054% 18576ms 99.40% AbstractCellBasedSimulation::Solve 2ms 0.011% 0.016% 10411ms 55.71% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.016% 7301ms 39.07% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0054% 0.021% 6417ms 34.34% NodeBasedCellPopulation::Update 1ms 0.0054% 0.027% 5989ms 32.05% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0054% 0.032% 5841ms 31.26% AbstractNumericalMethod::ComputeForcesIncludingDamping 786ms 4.21% 4.24% 5425ms 29.03% RepulsionForce::AddForceContribution (partial-inline) 11ms 0.059% 4.30% 4776ms 25.56% DistributedBoxCollection::CalculateInteriorNodePairs 0 0% 4.30% 4170ms 22.31% OffLatticeSimulation::ApplyBoundaries 21ms 0.11% 4.41% 3887ms 20.80% NodeAttributes::RemoveDuplicateNeighbours 1467ms 7.85% 12.26% 3856ms 20.63% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.0054% 12.26% 3737ms 20.00% std::__sort (inline) 0 0% 12.26% 3737ms 20.00% std::sort (inline) 254ms 1.36% 13.62% 3019ms 16.15% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 3ms 0.016% 13.64% 3009ms 16.10% AbstractCellPopulation::Iterator::operator++ (inline) 163ms 0.87% 14.51% 3003ms 16.07% AbstractCellPopulation::Iterator::IsRealCell 109ms 0.58% 15.10% 2898ms 15.51% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 8ms 0.043% 15.14% 2495ms 13.35% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 201ms 1.08% 16.21% 2440ms 13.06% std::_Rb_tree::find (inline) 0 0% 16.21% 2440ms 13.06% std::map::find (inline) 188ms 1.01% 17.22% 2272ms 12.16% std::__introsort_loop 62ms 0.33% 17.55% 2129ms 11.39% PlaneBoundaryCondition::ImposeBoundaryCondition 2128ms 11.39% 28.94% 2128ms 11.39% std::_Rb_tree::_S_right (inline) 180ms 0.96% 29.90% 2091ms 11.19% std::map::operator[] (partial-inline) 86ms 0.46% 30.36% 2088ms 11.17% AbstractMesh::GetNode 35ms 0.19% 30.55% 2052ms 10.98% NodesOnlyMesh::GetNodeOrHaloNode 40ms 0.21% 30.76% 2041ms 10.92% PlaneBoundaryCondition::VerifyBoundaryCondition 20ms 0.11% 30.87% 2009ms 10.75% std::__unguarded_partition_pivot (inline) 188ms 1.01% 31.88% 2004ms 10.72% NodesOnlyMesh::SolveNodeMapping 707ms 3.78% 35.66% 1798ms 9.62% std::__unguarded_partition (inline) 74ms 0.4% 36.06% 1665ms 8.91% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 36.06% 1646ms 8.81% std::_Rb_tree::lower_bound (inline) 0 0% 36.06% 1646ms 8.81% std::map::lower_bound (inline) 0 0% 36.06% 1463ms 7.83% std::__final_insertion_sort (inline) 107ms 0.57% 36.63% 1435ms 7.68% DistributedBoxCollection::AddPairsFromBox 12ms 0.064% 36.69% 1357ms 7.26% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 13ms 0.07% 36.76% 1336ms 7.15% AbstractCellPopulation::GetCellUsingLocationIndex 99ms 0.53% 37.29% 1320ms 7.06% std::__unguarded_insertion_sort (inline) 603ms 3.23% 40.52% 1173ms 6.28% std::__unguarded_linear_insert (inline) 64ms 0.34% 40.86% 924ms 4.94% boost::numeric::ublas::c_vector::c_vector (partial-inline) 6ms 0.032% 40.89% 877ms 4.69% DistributedBoxCollection::CalculateBoundaryNodePairs 1ms 0.0054% 40.90% 870ms 4.66% NodeBasedCellPopulation::UpdateCellProcessLocation 869ms 4.65% 45.55% 869ms 4.65% __gnu_cxx::__normal_iterator::operator-- (inline) 9ms 0.048% 45.60% 780ms 4.17% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 6ms 0.032% 45.63% 770ms 4.12% boost::detail::shared_count::~shared_count (inline) 0 0% 45.63% 770ms 4.12% boost::shared_ptr::~shared_ptr (inline) 8ms 0.043% 45.67% 750ms 4.01% boost::numeric::ublas::vector_assign (inline) 740ms 3.96% 49.63% 749ms 4.01% boost::detail::sp_counted_base::release 169ms 0.9% 50.54% 669ms 3.58% boost::numeric::ublas::indexing_vector_assign 71ms 0.38% 50.92% 579ms 3.10% AbstractMesh::GetVectorFromAtoB 172ms 0.92% 51.84% 546ms 2.92% __dynamic_cast 0 0% 51.84% 538ms 2.88% AbstractCellPopulation::WriteResultsToFiles 235ms 1.26% 53.09% 533ms 2.85% DistributedBoxCollection::CalculateContainingBox (partial-inline) 65ms 0.35% 53.44% 515ms 2.76% std::__new_allocator::allocate (inline) 0 0% 53.44% 506ms 2.71% std::allocator_traits::allocate (inline) 27ms 0.14% 53.59% 495ms 2.65% std::_Rb_tree_const_iterator::operator++ (inline) 216ms 1.16% 54.74% 492ms 2.63% NodeAttributes::AddNeighbour 3ms 0.016% 54.76% 485ms 2.60% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 54.76% 483ms 2.58% std::_Rb_tree::_M_create_node (inline) 476ms 2.55% 57.30% 476ms 2.55% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 31ms 0.17% 57.47% 471ms 2.52% std::__copy_move::__copy_m (inline) 0 0% 57.47% 471ms 2.52% std::__copy_move_a (inline) 0 0% 57.47% 471ms 2.52% std::__copy_move_a1 (inline) 0 0% 57.47% 471ms 2.52% std::__copy_move_a2 (inline) 0 0% 57.47% 471ms 2.52% std::copy (inline) 3ms 0.016% 57.49% 464ms 2.48% AbstractCellBasedSimulation::DoCellBirth 11ms 0.059% 57.54% 455ms 2.43% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 57.54% 453ms 2.42% std::_Rb_tree::_M_get_node (inline) 26ms 0.14% 57.68% 443ms 2.37% operator new 27ms 0.14% 57.83% 438ms 2.34% std::_Rb_tree::_M_copy (inline) 0 0% 57.83% 436ms 2.33% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 432ms 2.31% 60.14% 432ms 2.31% __memcpy_avx512_unaligned_erms 424ms 2.27% 62.41% 424ms 2.27% [libchaste_cell_based.so] 0 0% 62.41% 420ms 2.25% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 62.41% 419ms 2.24% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 62.41% 419ms 2.24% boost::numeric::ublas::norm_2 (inline) 342ms 1.83% 64.24% 419ms 2.24% boost::numeric::ublas::vector_norm_2::apply (inline) 413ms 2.21% 66.45% 413ms 2.21% __gnu_cxx::__normal_iterator::operator++ (inline) 413ms 2.21% 68.66% 413ms 2.21% boost::numeric::ublas::same_impl_ex 406ms 2.17% 70.83% 406ms 2.17% [libchaste_mesh.so] 405ms 2.17% 73.00% 405ms 2.17% std::_Rb_tree_increment 8ms 0.043% 73.04% 404ms 2.16% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 133ms 0.71% 73.75% 402ms 2.15% __GI___libc_malloc 151ms 0.81% 74.56% 400ms 2.14% std::_Rb_tree::_M_clone_node (inline) 1ms 0.0054% 74.57% 389ms 2.08% std::set::set (inline) 386ms 2.07% 76.63% 386ms 2.07% boost::numeric::ublas::c_vector::operator() 5ms 0.027% 76.66% 380ms 2.03% AbstractCentreBasedCellPopulation::GetDampingConstant 8ms 0.043% 76.70% 366ms 1.96% CellPropertyCollection::GetPropertiesType (inline) 41ms 0.22% 76.92% 365ms 1.95% std::_Rb_tree::_M_erase 2ms 0.011% 76.93% 355ms 1.90% NodeBasedCellPopulation::WriteVtkResultsToFile 83ms 0.44% 77.38% 348ms 1.86% std::_Rb_tree::~_Rb_tree (inline) 257ms 1.38% 78.75% 339ms 1.81% std::vector::push_back (inline) 0 0% 78.75% 324ms 1.73% std::_Rb_tree::_M_drop_node (inline) 0 0% 78.75% 302ms 1.62% std::_Rb_tree::_Alloc_node::operator() (inline) 159ms 0.85% 79.60% 293ms 1.57% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 79.60% 290ms 1.55% std::set::~set (inline) 3ms 0.016% 79.62% 285ms 1.53% boost::numeric::ublas::vector_binary::size (inline) 267ms 1.43% 81.05% 267ms 1.43% std::_Rb_tree::_S_left (inline) 0 0% 81.05% 266ms 1.42% NodesOnlyMesh::ReMesh 4ms 0.021% 81.07% 265ms 1.42% std::_Rb_tree::_M_emplace_hint_unique 6ms 0.032% 81.10% 261ms 1.40% NodeBasedCellPopulation::UpdateMapsAfterRemesh 1ms 0.0054% 81.11% 261ms 1.40% NodesOnlyMesh::UpdateNodeIndices 1ms 0.0054% 81.11% 242ms 1.29% AbstractCellProperty::IsSubType (inline) 3ms 0.016% 81.13% 236ms 1.26% Cell::GetMutationState 206ms 1.10% 82.23% 236ms 1.26% boost::shared_ptr::shared_ptr (inline) 2ms 0.011% 82.24% 231ms 1.24% Node::GetRadius 155ms 0.83% 83.07% 222ms 1.19% _int_malloc 219ms 1.17% 84.24% 219ms 1.17% __strcmp_evex 6ms 0.032% 84.27% 212ms 1.13% std::__new_allocator::deallocate (inline) 0 0% 84.27% 210ms 1.12% NodesOnlyMesh::UpdateBoxCollection 0 0% 84.27% 203ms 1.09% boost::numeric::ublas::c_vector::assign (inline) 54ms 0.29% 84.56% 194ms 1.04% __GI___libc_free 0 0% 84.56% 194ms 1.04% std::allocator_traits::deallocate (inline) 0 0% 84.56% 192ms 1.03% std::_Rb_tree::_M_put_node (inline) 0 0% 84.56% 187ms 1.00% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 3ms 0.016% 84.58% 183ms 0.98% DistributedBoxCollection::GetProcessOwningNode 0 0% 84.58% 181ms 0.97% std::_Rb_tree::_Auto_node::_Auto_node (inline) 54ms 0.29% 84.87% 179ms 0.96% std::__move_median_to_first (inline) 0 0% 84.87% 177ms 0.95% boost::numeric::ublas::inner_prod (inline) 3ms 0.016% 84.88% 177ms 0.95% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 84.88% 174ms 0.93% NodesOnlyMesh::AddNodesToBoxes 2ms 0.011% 84.89% 174ms 0.93% boost::numeric::ublas::vector_scalar_binary::evaluate 171ms 0.92% 85.81% 171ms 0.92% Node::CheckForNodeAttributes 2ms 0.011% 85.82% 169ms 0.9% CellPropertyCollection::HasProperty 0 0% 85.82% 167ms 0.89% Cell::HasCellProperty (inline) 0 0% 85.82% 156ms 0.83% std::iter_swap (inline) 156ms 0.83% 86.65% 156ms 0.83% std::swap (inline) 155ms 0.83% 87.48% 155ms 0.83% boost::shared_ptr::operator-> (inline) 46ms 0.25% 87.73% 152ms 0.81% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 87.73% 148ms 0.79% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 87.73% 148ms 0.79% VtkMeshWriter::WriteFiles 0 0% 87.73% 143ms 0.77% Cell::ReadyToDivide 18ms 0.096% 87.83% 143ms 0.77% std::__insertion_sort (inline) 0 0% 87.83% 140ms 0.75% std::_Rb_tree::_M_destroy_node (inline) 0 0% 87.83% 140ms 0.75% std::__new_allocator::destroy (inline) 0 0% 87.83% 140ms 0.75% std::allocator_traits::destroy (inline) 127ms 0.68% 88.51% 139ms 0.74% _int_free 0 0% 88.51% 131ms 0.7% vtkCompositeDataPipeline::ExecuteData 0 0% 88.51% 131ms 0.7% vtkDemandDrivenPipeline::ExecuteData 0 0% 88.51% 131ms 0.7% vtkDemandDrivenPipeline::ProcessRequest 0 0% 88.51% 131ms 0.7% vtkExecutive::CallAlgorithm 0 0% 88.51% 131ms 0.7% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 88.51% 131ms 0.7% vtkStreamingDemandDrivenPipeline::Update 0 0% 88.51% 131ms 0.7% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 88.51% 131ms 0.7% vtkXMLWriterBase::Write 0 0% 88.51% 123ms 0.66% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 88.51% 120ms 0.64% std::_Rb_tree::clear (inline) 0 0% 88.51% 118ms 0.63% NodesOnlyMesh::ResizeBoxCollection 5ms 0.027% 88.53% 117ms 0.63% AbstractCellProperty::IsType (inline) 10ms 0.054% 88.59% 117ms 0.63% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 88.59% 115ms 0.62% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 88.59% 115ms 0.62% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 2ms 0.011% 88.60% 110ms 0.59% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 88.60% 110ms 0.59% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 88.60% 108ms 0.58% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 2ms 0.011% 88.61% 107ms 0.57% AbstractCellPopulation::SetCellUsingLocationIndex 49ms 0.26% 88.87% 107ms 0.57% std::__adjacent_find (inline) 0 0% 88.87% 107ms 0.57% std::__unique (inline) 0 0% 88.87% 107ms 0.57% std::unique (inline) 1ms 0.0054% 88.88% 106ms 0.57% std::set::insert (inline) 0 0% 88.88% 105ms 0.56% std::_Rb_tree::_M_insert_unique 99ms 0.53% 89.40% 102ms 0.55% Node::ConstructNodeAttributes (inline) 15ms 0.08% 89.49% 101ms 0.54% Node::AddNeighbour 1ms 0.0054% 89.49% 101ms 0.54% NodeBasedCellPopulation::SetNode 2ms 0.011% 89.50% 96ms 0.51% NodesOnlyMesh::SetNode 0 0% 89.50% 94ms 0.5% Cell::GetCellProliferativeType 0 0% 89.50% 94ms 0.5% vtkXMLWriter::WriteBinaryData