File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20464ms, 88.47% of 23132ms total Dropped 768 nodes (cum <= 115.66ms) flat flat% sum% cum cum% 0 0% 0% 22987ms 99.37% __libc_start_call_main 0 0% 0% 22987ms 99.37% __libc_start_main_impl 0 0% 0% 22987ms 99.37% _start 0 0% 0% 22971ms 99.30% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 22971ms 99.30% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 22971ms 99.30% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 22971ms 99.30% main 0 0% 0% 22934ms 99.14% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 22933ms 99.14% CxxTest::TestRunner::runTest (inline) 0 0% 0% 22933ms 99.14% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 22925ms 99.11% AbstractCellBasedSimulation::Solve 2ms 0.0086% 0.0086% 13125ms 56.74% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0086% 8638ms 37.34% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.017% 0.026% 8344ms 36.07% ForwardEulerNumericalMethod::UpdateAllNodePositions 7ms 0.03% 0.056% 8175ms 35.34% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.056% 7647ms 33.06% NodeBasedCellPopulation::Update 1239ms 5.36% 5.41% 7564ms 32.70% RepulsionForce::AddForceContribution (partial-inline) 9ms 0.039% 5.45% 5637ms 24.37% DistributedBoxCollection::CalculateInteriorNodePairs 2107ms 9.11% 14.56% 4917ms 21.26% std::_Rb_tree::_M_lower_bound (inline) 0 0% 14.56% 4493ms 19.42% OffLatticeSimulation::ApplyBoundaries 19ms 0.082% 14.64% 4479ms 19.36% NodeAttributes::RemoveDuplicateNeighbours 7ms 0.03% 14.67% 4298ms 18.58% std::__sort (inline) 0 0% 14.67% 4298ms 18.58% std::sort (inline) 179ms 0.77% 15.45% 3747ms 16.20% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 1ms 0.0043% 15.45% 3353ms 14.50% AbstractCellPopulation::Iterator::operator++ (inline) 219ms 0.95% 16.40% 3333ms 14.41% AbstractCellPopulation::Iterator::IsRealCell (inline) 70ms 0.3% 16.70% 3331ms 14.40% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 228ms 0.99% 17.69% 3201ms 13.84% std::_Rb_tree::find (inline) 0 0% 17.69% 3201ms 13.84% std::map::find (inline) 17ms 0.073% 17.76% 2804ms 12.12% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2775ms 12.00% 29.76% 2775ms 12.00% std::_Rb_tree::_S_right (inline) 232ms 1.00% 30.76% 2465ms 10.66% std::map::operator[] (partial-inline) 194ms 0.84% 31.60% 2416ms 10.44% std::__introsort_loop 28ms 0.12% 31.72% 2330ms 10.07% PlaneBoundaryCondition::ImposeBoundaryCondition 147ms 0.64% 32.35% 2301ms 9.95% AbstractMesh::GetNode 63ms 0.27% 32.63% 2300ms 9.94% NodesOnlyMesh::GetNodeOrHaloNode 31ms 0.13% 32.76% 2280ms 9.86% AbstractCellPopulation::GetLocationIndexUsingCell 19ms 0.082% 32.84% 2163ms 9.35% PlaneBoundaryCondition::VerifyBoundaryCondition 86ms 0.37% 33.21% 2157ms 9.32% NodesOnlyMesh::SolveNodeMapping 0 0% 33.21% 2153ms 9.31% std::__unguarded_partition_pivot (inline) 0 0% 33.21% 1974ms 8.53% std::_Rb_tree::lower_bound (inline) 0 0% 33.21% 1974ms 8.53% std::map::lower_bound (inline) 1018ms 4.40% 37.61% 1950ms 8.43% std::__unguarded_partition (inline) 2ms 0.0086% 37.62% 1874ms 8.10% std::__final_insertion_sort (inline) 147ms 0.64% 38.26% 1763ms 7.62% DistributedBoxCollection::AddPairsFromBox 71ms 0.31% 38.57% 1682ms 7.27% std::__unguarded_insertion_sort (inline) 610ms 2.64% 41.20% 1658ms 7.17% std::__unguarded_linear_insert (inline) 22ms 0.095% 41.30% 1524ms 6.59% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 27ms 0.12% 41.41% 1496ms 6.47% AbstractCellPopulation::GetCellUsingLocationIndex 1474ms 6.37% 47.79% 1474ms 6.37% __gnu_cxx::__normal_iterator::operator-- (inline) 60ms 0.26% 48.05% 1253ms 5.42% boost::numeric::ublas::c_vector::c_vector (partial-inline) 1ms 0.0043% 48.05% 1121ms 4.85% NodeBasedCellPopulation::UpdateCellProcessLocation 33ms 0.14% 48.19% 1104ms 4.77% boost::numeric::ublas::vector_assign (inline) 2ms 0.0086% 48.20% 1065ms 4.60% DistributedBoxCollection::CalculateBoundaryNodePairs 281ms 1.21% 49.42% 986ms 4.26% boost::numeric::ublas::indexing_vector_assign 243ms 1.05% 50.47% 936ms 4.05% __dynamic_cast 160ms 0.69% 51.16% 808ms 3.49% AbstractMesh::GetVectorFromAtoB 12ms 0.052% 51.21% 807ms 3.49% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 373ms 1.61% 52.82% 786ms 3.40% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 52.82% 778ms 3.36% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 52.82% 757ms 3.27% boost::numeric::ublas::norm_2 (inline) 591ms 2.55% 55.38% 757ms 3.27% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 55.38% 757ms 3.27% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 55.38% 713ms 3.08% AbstractCellPopulation::WriteResultsToFiles 195ms 0.84% 56.22% 693ms 3.00% NodeAttributes::AddNeighbour 9ms 0.039% 56.26% 671ms 2.90% boost::numeric::ublas::c_vector::operator= (inline) 43ms 0.19% 56.45% 651ms 2.81% std::__copy_move::__copy_m (inline) 0 0% 56.45% 651ms 2.81% std::__copy_move_a (inline) 0 0% 56.45% 651ms 2.81% std::__copy_move_a1 (inline) 0 0% 56.45% 651ms 2.81% std::__copy_move_a2 (inline) 0 0% 56.45% 651ms 2.81% std::copy (inline) 621ms 2.68% 59.13% 621ms 2.68% boost::numeric::ublas::c_vector::operator() 618ms 2.67% 61.80% 618ms 2.67% __memcpy_avx_unaligned_erms 278ms 1.20% 63.00% 579ms 2.50% __cxxabiv1::__si_class_type_info::__do_dyncast 9ms 0.039% 63.04% 566ms 2.45% CellPropertyCollection::GetPropertiesType (inline) 493ms 2.13% 65.17% 564ms 2.44% std::vector::push_back (inline) 1ms 0.0043% 65.18% 546ms 2.36% AbstractCellBasedSimulation::DoCellBirth 5ms 0.022% 65.20% 544ms 2.35% AbstractCentreBasedCellPopulation::GetDampingConstant 508ms 2.20% 67.40% 508ms 2.20% boost::numeric::ublas::same_impl_ex 77ms 0.33% 67.73% 496ms 2.14% std::__new_allocator::allocate (inline) 37ms 0.16% 67.89% 492ms 2.13% std::_Rb_tree_const_iterator::operator++ (inline) 33ms 0.14% 68.03% 477ms 2.06% boost::detail::shared_count::~shared_count (inline) 0 0% 68.03% 477ms 2.06% boost::shared_ptr::~shared_ptr (inline) 0 0% 68.03% 473ms 2.04% std::allocator_traits::allocate (inline) 3ms 0.013% 68.04% 471ms 2.04% NodeBasedCellPopulation::WriteVtkResultsToFile 465ms 2.01% 70.05% 465ms 2.01% __strcmp_avx2 0 0% 70.05% 463ms 2.00% std::_Rb_tree::_M_create_node (inline) 20ms 0.086% 70.14% 458ms 1.98% std::_Rb_tree::_Rb_tree (partial-inline) 450ms 1.95% 72.09% 450ms 1.95% std::_Rb_tree_increment 0 0% 72.09% 445ms 1.92% AbstractCellBasedSimulation::DoCellRemoval (inline) 435ms 1.88% 73.97% 440ms 1.90% boost::detail::sp_counted_base::release 8ms 0.035% 74.00% 433ms 1.87% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 37ms 0.16% 74.16% 425ms 1.84% std::_Rb_tree::_M_copy (inline) 25ms 0.11% 74.27% 415ms 1.79% operator new 2ms 0.0086% 74.28% 413ms 1.79% AbstractCellProperty::IsSubType (inline) 121ms 0.52% 74.80% 412ms 1.78% std::_Rb_tree::_M_erase 140ms 0.61% 75.41% 394ms 1.70% Node::GetRadius 0 0% 75.41% 394ms 1.70% std::_Rb_tree::_M_get_node (inline) 124ms 0.54% 75.94% 386ms 1.67% std::_Rb_tree::_M_clone_node (inline) 2ms 0.0086% 75.95% 379ms 1.64% Cell::GetMutationState 110ms 0.48% 76.43% 376ms 1.63% __GI___libc_malloc 3ms 0.013% 76.44% 376ms 1.63% std::set::set (inline) 0 0% 76.44% 336ms 1.45% boost::numeric::ublas::inner_prod (inline) 3ms 0.013% 76.45% 336ms 1.45% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 18ms 0.078% 76.53% 333ms 1.44% boost::numeric::ublas::vector_scalar_binary::evaluate 20ms 0.086% 76.62% 327ms 1.41% boost::numeric::ublas::vector_binary::size (inline) 5ms 0.022% 76.64% 323ms 1.40% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 76.64% 323ms 1.40% std::_Rb_tree::_Alloc_node::operator() (inline) 31ms 0.13% 76.77% 304ms 1.31% std::_Rb_tree::~_Rb_tree (inline) 294ms 1.27% 78.04% 294ms 1.27% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 78.04% 283ms 1.22% NodesOnlyMesh::ReMesh 0 0% 78.04% 279ms 1.21% std::_Rb_tree::_M_drop_node (inline) 117ms 0.51% 78.55% 278ms 1.20% boost::numeric::ublas::vector_inner_prod::apply (inline) 277ms 1.20% 79.75% 277ms 1.20% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 4ms 0.017% 79.76% 275ms 1.19% NodesOnlyMesh::UpdateNodeIndices 0 0% 79.76% 274ms 1.18% boost::numeric::ublas::c_vector::assign (inline) 263ms 1.14% 80.90% 263ms 1.14% Node::CheckForNodeAttributes 5ms 0.022% 80.92% 260ms 1.12% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 80.92% 259ms 1.12% NodesOnlyMesh::UpdateBoxCollection 9ms 0.039% 80.96% 259ms 1.12% std::_Rb_tree::_M_emplace_hint_unique 5ms 0.022% 80.98% 250ms 1.08% std::__new_allocator::deallocate (inline) 2ms 0.0086% 80.99% 248ms 1.07% DistributedBoxCollection::GetProcessOwningNode 109ms 0.47% 81.46% 226ms 0.98% boost::shared_ptr::shared_ptr (inline) 0 0% 81.46% 225ms 0.97% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 77ms 0.33% 81.80% 225ms 0.97% __GI___libc_free 0 0% 81.80% 223ms 0.96% VtkMeshWriter::WriteFiles 128ms 0.55% 82.35% 223ms 0.96% _int_malloc 0 0% 82.35% 223ms 0.96% std::allocator_traits::deallocate (inline) 0 0% 82.35% 221ms 0.96% std::_Rb_tree::_M_put_node (inline) 0 0% 82.35% 220ms 0.95% NodesOnlyMesh::AddNodesToBoxes 0 0% 82.35% 212ms 0.92% std::set::~set (inline) 210ms 0.91% 83.26% 210ms 0.91% Node::GetIndex 0 0% 83.26% 208ms 0.9% NodesOnlyMesh::ResizeBoxCollection 16ms 0.069% 83.33% 206ms 0.89% NodesOnlyMesh::IsANodeCloseToDomainBoundary 102ms 0.44% 83.77% 201ms 0.87% std::__move_median_to_first (inline) 0 0% 83.77% 191ms 0.83% vtkStreamingDemandDrivenPipeline::Update 0 0% 83.77% 191ms 0.83% vtkXMLWriterBase::Write 25ms 0.11% 83.88% 190ms 0.82% std::__insertion_sort (inline) 0 0% 83.88% 190ms 0.82% vtkDemandDrivenPipeline::ProcessRequest 0 0% 83.88% 190ms 0.82% vtkExecutive::CallAlgorithm 0 0% 83.88% 189ms 0.82% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 83.88% 188ms 0.81% vtkCompositeDataPipeline::ExecuteData 0 0% 83.88% 188ms 0.81% vtkDemandDrivenPipeline::ExecuteData 0 0% 83.88% 188ms 0.81% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 83.88% 169ms 0.73% vtkXMLUnstructuredDataWriter::WriteAPiece 1ms 0.0043% 83.88% 169ms 0.73% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 83.88% 167ms 0.72% Cell::HasCellProperty (inline) 5ms 0.022% 83.90% 167ms 0.72% CellPropertyCollection::HasProperty 165ms 0.71% 84.61% 165ms 0.71% [libchaste_cell_based.so] 0 0% 84.61% 165ms 0.71% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 83ms 0.36% 84.97% 157ms 0.68% Node::AddNeighbour 4ms 0.017% 84.99% 155ms 0.67% Cell::ReadyToDivide 0 0% 84.99% 153ms 0.66% std::_Rb_tree::clear (inline) 148ms 0.64% 85.63% 150ms 0.65% std::__adjacent_find (inline) 0 0% 85.63% 150ms 0.65% std::__unique (inline) 0 0% 85.63% 150ms 0.65% std::unique (inline) 137ms 0.59% 86.22% 148ms 0.64% _int_free 2ms 0.0086% 86.23% 146ms 0.63% AbstractCellProperty::IsType (inline) 5ms 0.022% 86.25% 144ms 0.62% DistributedBoxCollection::GetIsPeriodicAllDims 144ms 0.62% 86.88% 144ms 0.62% [libchaste_mesh.so] 0 0% 86.88% 142ms 0.61% Cell::GetCellId 0 0% 86.88% 141ms 0.61% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 86.88% 140ms 0.61% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 86.88% 138ms 0.6% vtkXMLWriter::WriteBinaryData 16ms 0.069% 86.94% 136ms 0.59% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 86.94% 134ms 0.58% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 86.94% 134ms 0.58% vtkXMLWriter::WriteBinaryDataInternal 132ms 0.57% 87.52% 132ms 0.57% boost::shared_ptr::operator-> (inline) 0 0% 87.52% 132ms 0.57% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.52% 132ms 0.57% vtkXMLWriter::WriteCompressionBlock 0 0% 87.52% 130ms 0.56% AbstractCellPopulation::SetCellUsingLocationIndex 9ms 0.039% 87.55% 129ms 0.56% boost::numeric::ublas::c_vector::operator[] (inline) 120ms 0.52% 88.07% 120ms 0.52% Node::rGetLocation 0 0% 88.07% 119ms 0.51% std::map::clear (inline) 0 0% 88.07% 119ms 0.51% vtkXMLWriter::WritePointsAppendedData 91ms 0.39% 88.47% 117ms 0.51% boost::detail::shared_count::shared_count (inline)