File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 21878ms, 89.04% of 24572ms total Dropped 816 nodes (cum <= 122.86ms) flat flat% sum% cum cum% 0 0% 0% 24442ms 99.47% __libc_start_call_main 0 0% 0% 24442ms 99.47% __libc_start_main_impl 0 0% 0% 24442ms 99.47% _start 0 0% 0% 24424ms 99.40% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 24424ms 99.40% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 24424ms 99.40% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 24424ms 99.40% main 0 0% 0% 24384ms 99.23% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 24384ms 99.23% CxxTest::TestRunner::runTest (inline) 0 0% 0% 24384ms 99.23% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 24375ms 99.20% AbstractCellBasedSimulation::Solve 3ms 0.012% 0.012% 14040ms 57.14% OffLatticeSimulation::UpdateCellLocationsAndTopology 6ms 0.024% 0.037% 9137ms 37.18% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 0.037% 9116ms 37.10% AbstractCellBasedSimulation::UpdateCellPopulation 9ms 0.037% 0.073% 8946ms 36.41% AbstractNumericalMethod::ComputeForcesIncludingDamping 1354ms 5.51% 5.58% 8264ms 33.63% RepulsionForce::AddForceContribution (partial-inline) 1ms 0.0041% 5.59% 8077ms 32.87% NodeBasedCellPopulation::Update 6ms 0.024% 5.61% 5974ms 24.31% DistributedBoxCollection::CalculateInteriorNodePairs 2104ms 8.56% 14.17% 5042ms 20.52% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.0041% 14.18% 4566ms 18.58% OffLatticeSimulation::ApplyBoundaries 8ms 0.033% 14.21% 4564ms 18.57% NodeAttributes::RemoveDuplicateNeighbours 4ms 0.016% 14.23% 4367ms 17.77% std::__sort (inline) 0 0% 14.23% 4367ms 17.77% std::sort (inline) 197ms 0.8% 15.03% 4113ms 16.74% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 74ms 0.3% 15.33% 3347ms 13.62% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 258ms 1.05% 16.38% 3309ms 13.47% std::_Rb_tree::find (inline) 0 0% 16.38% 3306ms 13.45% std::map::find (inline) 1ms 0.0041% 16.38% 3201ms 13.03% AbstractCellPopulation::Iterator::operator++ (inline) 157ms 0.64% 17.02% 3172ms 12.91% AbstractCellPopulation::Iterator::IsRealCell (inline) 2913ms 11.85% 28.88% 2913ms 11.85% std::_Rb_tree::_S_right (inline) 28ms 0.11% 28.99% 2761ms 11.24% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 255ms 1.04% 30.03% 2590ms 10.54% std::map::operator[] (partial-inline) 184ms 0.75% 30.78% 2546ms 10.36% std::__introsort_loop 173ms 0.7% 31.48% 2476ms 10.08% AbstractMesh::GetNode 19ms 0.077% 31.56% 2476ms 10.08% PlaneBoundaryCondition::ImposeBoundaryCondition 50ms 0.2% 31.76% 2460ms 10.01% NodesOnlyMesh::GetNodeOrHaloNode 104ms 0.42% 32.19% 2308ms 9.39% NodesOnlyMesh::SolveNodeMapping 0 0% 32.19% 2282ms 9.29% std::__unguarded_partition_pivot (inline) 60ms 0.24% 32.43% 2258ms 9.19% AbstractCellPopulation::GetLocationIndexUsingCell 13ms 0.053% 32.48% 2089ms 8.50% PlaneBoundaryCondition::VerifyBoundaryCondition 992ms 4.04% 36.52% 2054ms 8.36% std::__unguarded_partition (inline) 0 0% 36.52% 2026ms 8.25% std::_Rb_tree::lower_bound (inline) 0 0% 36.52% 2026ms 8.25% std::map::lower_bound (inline) 150ms 0.61% 37.13% 2019ms 8.22% DistributedBoxCollection::AddPairsFromBox 0 0% 37.13% 1817ms 7.39% std::__final_insertion_sort (inline) 23ms 0.094% 37.23% 1744ms 7.10% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 26ms 0.11% 37.33% 1709ms 6.96% AbstractCellPopulation::GetCellUsingLocationIndex 109ms 0.44% 37.77% 1644ms 6.69% std::__unguarded_insertion_sort (inline) 594ms 2.42% 40.19% 1559ms 6.34% std::__unguarded_linear_insert (inline) 52ms 0.21% 40.40% 1410ms 5.74% boost::numeric::ublas::c_vector::c_vector (partial-inline) 1381ms 5.62% 46.02% 1381ms 5.62% __gnu_cxx::__normal_iterator::operator-- (inline) 2ms 0.0081% 46.03% 1262ms 5.14% boost::numeric::ublas::vector_assign (inline) 307ms 1.25% 47.28% 1166ms 4.75% boost::numeric::ublas::indexing_vector_assign 0 0% 47.28% 1165ms 4.74% NodeBasedCellPopulation::UpdateCellProcessLocation 7ms 0.028% 47.31% 1115ms 4.54% DistributedBoxCollection::CalculateBoundaryNodePairs 207ms 0.84% 48.15% 966ms 3.93% AbstractMesh::GetVectorFromAtoB 272ms 1.11% 49.26% 920ms 3.74% __dynamic_cast 20ms 0.081% 49.34% 909ms 3.70% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 426ms 1.73% 51.07% 848ms 3.45% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 51.07% 819ms 3.33% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 51.07% 802ms 3.26% boost::numeric::ublas::norm_2 (inline) 628ms 2.56% 53.63% 802ms 3.26% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 53.63% 802ms 3.26% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 53.63% 742ms 3.02% AbstractCellPopulation::WriteResultsToFiles 149ms 0.61% 54.24% 726ms 2.95% NodeAttributes::AddNeighbour 10ms 0.041% 54.28% 708ms 2.88% boost::numeric::ublas::c_vector::operator= (inline) 686ms 2.79% 57.07% 686ms 2.79% boost::numeric::ublas::c_vector::operator() 17ms 0.069% 57.14% 677ms 2.76% std::__copy_move::__copy_m (inline) 0 0% 57.14% 677ms 2.76% std::__copy_move_a (inline) 0 0% 57.14% 677ms 2.76% std::__copy_move_a1 (inline) 0 0% 57.14% 677ms 2.76% std::__copy_move_a2 (inline) 0 0% 57.14% 677ms 2.76% std::copy (inline) 574ms 2.34% 59.47% 671ms 2.73% std::vector::push_back (inline) 655ms 2.67% 62.14% 655ms 2.67% __memcpy_avx_unaligned_erms 30ms 0.12% 62.26% 644ms 2.62% std::_Rb_tree_const_iterator::operator++ (inline) 4ms 0.016% 62.28% 617ms 2.51% AbstractCellBasedSimulation::DoCellBirth 13ms 0.053% 62.33% 610ms 2.48% CellPropertyCollection::GetPropertiesType (inline) 6ms 0.024% 62.36% 592ms 2.41% AbstractCentreBasedCellPopulation::GetDampingConstant 107ms 0.44% 62.79% 591ms 2.41% std::__new_allocator::allocate (inline) 584ms 2.38% 65.17% 584ms 2.38% std::_Rb_tree_increment 576ms 2.34% 67.51% 576ms 2.34% boost::numeric::ublas::same_impl_ex 0 0% 67.51% 564ms 2.30% std::allocator_traits::allocate (inline) 32ms 0.13% 67.64% 546ms 2.22% std::_Rb_tree::_Rb_tree (partial-inline) 276ms 1.12% 68.77% 538ms 2.19% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 68.77% 530ms 2.16% std::_Rb_tree::_M_create_node (inline) 46ms 0.19% 68.95% 519ms 2.11% boost::detail::shared_count::~shared_count (inline) 0 0% 68.95% 519ms 2.11% boost::shared_ptr::~shared_ptr (inline) 27ms 0.11% 69.06% 503ms 2.05% std::_Rb_tree::_M_copy (inline) 1ms 0.0041% 69.07% 494ms 2.01% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 69.07% 485ms 1.97% std::_Rb_tree::_M_get_node (inline) 28ms 0.11% 69.18% 482ms 1.96% operator new 158ms 0.64% 69.82% 471ms 1.92% std::_Rb_tree::_M_clone_node (inline) 146ms 0.59% 70.42% 460ms 1.87% std::_Rb_tree::_M_erase 442ms 1.80% 72.22% 455ms 1.85% boost::detail::sp_counted_base::release 134ms 0.55% 72.76% 450ms 1.83% __GI___libc_malloc 5ms 0.02% 72.78% 449ms 1.83% std::set::set (inline) 429ms 1.75% 74.53% 429ms 1.75% __strcmp_avx2 0 0% 74.53% 422ms 1.72% AbstractCellBasedSimulation::DoCellRemoval (inline) 4ms 0.016% 74.54% 416ms 1.69% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 3ms 0.012% 74.56% 412ms 1.68% Cell::GetMutationState 2ms 0.0081% 74.56% 409ms 1.66% AbstractCellProperty::IsSubType (inline) 89ms 0.36% 74.93% 400ms 1.63% boost::numeric::ublas::vector_binary::size (inline) 120ms 0.49% 75.42% 389ms 1.58% Node::GetRadius 362ms 1.47% 76.89% 362ms 1.47% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 76.89% 362ms 1.47% boost::numeric::ublas::c_vector::assign (inline) 0 0% 76.89% 361ms 1.47% boost::numeric::ublas::inner_prod (inline) 3ms 0.012% 76.90% 361ms 1.47% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 49ms 0.2% 77.10% 360ms 1.47% std::_Rb_tree::~_Rb_tree (inline) 19ms 0.077% 77.18% 358ms 1.46% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 77.18% 354ms 1.44% NodesOnlyMesh::ReMesh 6ms 0.024% 77.20% 346ms 1.41% NodesOnlyMesh::UpdateNodeIndices 0 0% 77.20% 344ms 1.40% std::_Rb_tree::_Alloc_node::operator() (inline) 314ms 1.28% 78.48% 314ms 1.28% __gnu_cxx::__normal_iterator::operator++ (inline) 12ms 0.049% 78.53% 309ms 1.26% std::_Rb_tree::_M_emplace_hint_unique 0 0% 78.53% 305ms 1.24% std::_Rb_tree::_M_drop_node (inline) 7ms 0.028% 78.56% 303ms 1.23% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 78.56% 289ms 1.18% NodesOnlyMesh::UpdateBoxCollection 136ms 0.55% 79.11% 289ms 1.18% boost::numeric::ublas::vector_inner_prod::apply (inline) 2ms 0.0081% 79.12% 284ms 1.16% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 6ms 0.024% 79.14% 273ms 1.11% DistributedBoxCollection::GetProcessOwningNode 272ms 1.11% 80.25% 272ms 1.11% Node::CheckForNodeAttributes 0 0% 80.25% 264ms 1.07% std::set::~set (inline) 263ms 1.07% 81.32% 263ms 1.07% [libchaste_mesh.so] 143ms 0.58% 81.90% 258ms 1.05% _int_malloc 6ms 0.024% 81.93% 250ms 1.02% CellPropertyCollection::HasProperty 0 0% 81.93% 247ms 1.01% Cell::HasCellProperty (inline) 173ms 0.7% 82.63% 247ms 1.01% Node::AddNeighbour 0 0% 82.63% 243ms 0.99% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 82.63% 239ms 0.97% VtkMeshWriter::WriteFiles 3ms 0.012% 82.64% 238ms 0.97% std::__new_allocator::deallocate (inline) 232ms 0.94% 83.59% 232ms 0.94% Node::GetIndex 2ms 0.0081% 83.60% 229ms 0.93% NodesOnlyMesh::AddNodesToBoxes 9ms 0.037% 83.63% 228ms 0.93% Cell::ReadyToDivide 102ms 0.42% 84.05% 227ms 0.92% std::__move_median_to_first (inline) 223ms 0.91% 84.95% 223ms 0.91% [libchaste_cell_based.so] 0 0% 84.95% 220ms 0.9% std::allocator_traits::deallocate (inline) 0 0% 84.95% 217ms 0.88% std::_Rb_tree::_M_put_node (inline) 0 0% 84.95% 212ms 0.86% vtkXMLWriterBase::Write 0 0% 84.95% 211ms 0.86% vtkStreamingDemandDrivenPipeline::Update 0 0% 84.95% 210ms 0.85% vtkDemandDrivenPipeline::ProcessRequest 0 0% 84.95% 210ms 0.85% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 84.95% 209ms 0.85% vtkDemandDrivenPipeline::ExecuteData 0 0% 84.95% 208ms 0.85% vtkCompositeDataPipeline::ExecuteData 0 0% 84.95% 207ms 0.84% vtkExecutive::CallAlgorithm 0 0% 84.95% 207ms 0.84% vtkXMLUnstructuredDataWriter::ProcessRequest 58ms 0.24% 85.19% 204ms 0.83% __GI___libc_free 100ms 0.41% 85.60% 202ms 0.82% boost::shared_ptr::shared_ptr (inline) 0 0% 85.60% 190ms 0.77% AbstractCellProperty::IsType (inline) 17ms 0.069% 85.67% 190ms 0.77% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 85.67% 186ms 0.76% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 85.67% 181ms 0.74% boost::numeric::ublas::vector_binary::operator() (inline) 1ms 0.0041% 85.67% 181ms 0.74% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.67% 180ms 0.73% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 85.67% 175ms 0.71% NodesOnlyMesh::ResizeBoxCollection 18ms 0.073% 85.74% 174ms 0.71% NodesOnlyMesh::IsANodeCloseToDomainBoundary 172ms 0.7% 86.44% 173ms 0.7% std::__adjacent_find (inline) 17ms 0.069% 86.51% 173ms 0.7% std::__insertion_sort (inline) 0 0% 86.51% 173ms 0.7% std::__unique (inline) 0 0% 86.51% 173ms 0.7% std::unique (inline) 172ms 0.7% 87.21% 172ms 0.7% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 0 0% 87.21% 171ms 0.7% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 1ms 0.0041% 87.22% 168ms 0.68% std::_Rb_tree::clear (inline) 58ms 0.24% 87.45% 151ms 0.61% AbstractCellProperty::IsSame 1ms 0.0041% 87.46% 147ms 0.6% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 2ms 0.0081% 87.47% 144ms 0.59% Cell::GetCellId 128ms 0.52% 87.99% 144ms 0.59% _int_free 3ms 0.012% 88.00% 144ms 0.59% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 88.00% 144ms 0.59% vtkXMLWriter::WriteBinaryData 0 0% 88.00% 138ms 0.56% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 88.00% 136ms 0.55% vtkXMLWriter::WriteBinaryDataBlock 0 0% 88.00% 136ms 0.55% vtkXMLWriter::WriteBinaryDataInternal 0 0% 88.00% 136ms 0.55% vtkXMLWriter::WriteCompressionBlock 0 0% 88.00% 134ms 0.55% AbstractNumericalMethod::SafeNodePositionUpdate 131ms 0.53% 88.53% 131ms 0.53% __ieee754_log_fma 0 0% 88.53% 131ms 0.53% vtkXMLWriter::WritePointsAppendedData 0 0% 88.53% 130ms 0.53% AbstractCellPopulation::SetCellUsingLocationIndex 124ms 0.5% 89.04% 124ms 0.5% Node::rGetLocation