File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20420ms, 88.71% of 23018ms total Dropped 734 nodes (cum <= 115.09ms) flat flat% sum% cum cum% 0 0% 0% 22875ms 99.38% __libc_start_call_main 0 0% 0% 22875ms 99.38% __libc_start_main_impl 0 0% 0% 22875ms 99.38% _start 0 0% 0% 22860ms 99.31% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 22860ms 99.31% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 22860ms 99.31% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 22860ms 99.31% main 0 0% 0% 22820ms 99.14% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 22820ms 99.14% CxxTest::TestRunner::runTest (inline) 0 0% 0% 22820ms 99.14% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 22812ms 99.11% AbstractCellBasedSimulation::Solve 1ms 0.0043% 0.0043% 12988ms 56.43% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0043% 8638ms 37.53% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.017% 0.022% 8260ms 35.88% ForwardEulerNumericalMethod::UpdateAllNodePositions 9ms 0.039% 0.061% 8062ms 35.02% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.061% 7638ms 33.18% NodeBasedCellPopulation::Update 1206ms 5.24% 5.30% 7457ms 32.40% RepulsionForce::AddForceContribution (partial-inline) 10ms 0.043% 5.34% 5580ms 24.24% DistributedBoxCollection::CalculateInteriorNodePairs 2134ms 9.27% 14.61% 4871ms 21.16% std::_Rb_tree::_M_lower_bound (inline) 28ms 0.12% 14.74% 4456ms 19.36% NodeAttributes::RemoveDuplicateNeighbours 0 0% 14.74% 4447ms 19.32% OffLatticeSimulation::ApplyBoundaries 8ms 0.035% 14.77% 4278ms 18.59% std::__sort (inline) 0 0% 14.77% 4278ms 18.59% std::sort (inline) 189ms 0.82% 15.59% 3782ms 16.43% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 68ms 0.3% 15.89% 3332ms 14.48% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 5ms 0.022% 15.91% 3323ms 14.44% AbstractCellPopulation::Iterator::operator++ (inline) 170ms 0.74% 16.65% 3289ms 14.29% AbstractCellPopulation::Iterator::IsRealCell (inline) 231ms 1.00% 17.65% 3109ms 13.51% std::_Rb_tree::find (inline) 0 0% 17.65% 3108ms 13.50% std::map::find (inline) 18ms 0.078% 17.73% 2812ms 12.22% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2703ms 11.74% 29.47% 2703ms 11.74% std::_Rb_tree::_S_right (inline) 222ms 0.96% 30.44% 2514ms 10.92% std::map::operator[] (partial-inline) 195ms 0.85% 31.28% 2489ms 10.81% std::__introsort_loop 28ms 0.12% 31.41% 2304ms 10.01% PlaneBoundaryCondition::ImposeBoundaryCondition 45ms 0.2% 31.60% 2303ms 10.01% AbstractCellPopulation::GetLocationIndexUsingCell 159ms 0.69% 32.29% 2243ms 9.74% AbstractMesh::GetNode 0 0% 32.29% 2222ms 9.65% std::__unguarded_partition_pivot (inline) 49ms 0.21% 32.50% 2218ms 9.64% NodesOnlyMesh::GetNodeOrHaloNode 15ms 0.065% 32.57% 2142ms 9.31% PlaneBoundaryCondition::VerifyBoundaryCondition 97ms 0.42% 32.99% 2086ms 9.06% NodesOnlyMesh::SolveNodeMapping 1032ms 4.48% 37.48% 2015ms 8.75% std::__unguarded_partition (inline) 0 0% 37.48% 2014ms 8.75% std::_Rb_tree::lower_bound (inline) 0 0% 37.48% 2014ms 8.75% std::map::lower_bound (inline) 2ms 0.0087% 37.48% 1778ms 7.72% std::__final_insertion_sort (inline) 173ms 0.75% 38.24% 1738ms 7.55% DistributedBoxCollection::AddPairsFromBox 100ms 0.43% 38.67% 1582ms 6.87% std::__unguarded_insertion_sort (inline) 27ms 0.12% 38.79% 1521ms 6.61% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 572ms 2.49% 41.27% 1513ms 6.57% std::__unguarded_linear_insert (inline) 22ms 0.096% 41.37% 1489ms 6.47% AbstractCellPopulation::GetCellUsingLocationIndex 1389ms 6.03% 47.40% 1389ms 6.03% __gnu_cxx::__normal_iterator::operator-- (inline) 68ms 0.3% 47.70% 1317ms 5.72% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 47.70% 1193ms 5.18% NodeBasedCellPopulation::UpdateCellProcessLocation 44ms 0.19% 47.89% 1150ms 5.00% boost::numeric::ublas::vector_assign (inline) 6ms 0.026% 47.91% 1091ms 4.74% DistributedBoxCollection::CalculateBoundaryNodePairs 283ms 1.23% 49.14% 1024ms 4.45% boost::numeric::ublas::indexing_vector_assign 257ms 1.12% 50.26% 930ms 4.04% __dynamic_cast 23ms 0.1% 50.36% 815ms 3.54% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 164ms 0.71% 51.07% 809ms 3.51% AbstractMesh::GetVectorFromAtoB 366ms 1.59% 52.66% 794ms 3.45% DistributedBoxCollection::CalculateContainingBox (partial-inline) 215ms 0.93% 53.60% 747ms 3.25% NodeAttributes::AddNeighbour 0 0% 53.60% 717ms 3.11% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 53.60% 711ms 3.09% AbstractCellPopulation::WriteResultsToFiles 0 0% 53.60% 693ms 3.01% boost::numeric::ublas::norm_2 (inline) 554ms 2.41% 56.00% 693ms 3.01% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 56.00% 693ms 3.01% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 8ms 0.035% 56.04% 675ms 2.93% boost::numeric::ublas::c_vector::operator= (inline) 35ms 0.15% 56.19% 649ms 2.82% std::__copy_move::__copy_m (inline) 0 0% 56.19% 649ms 2.82% std::__copy_move_a (inline) 0 0% 56.19% 649ms 2.82% std::__copy_move_a1 (inline) 0 0% 56.19% 649ms 2.82% std::__copy_move_a2 (inline) 0 0% 56.19% 649ms 2.82% std::copy (inline) 641ms 2.78% 58.98% 641ms 2.78% boost::numeric::ublas::c_vector::operator() 632ms 2.75% 61.72% 632ms 2.75% __memcpy_avx_unaligned_erms 529ms 2.30% 64.02% 593ms 2.58% std::vector::push_back (inline) 1ms 0.0043% 64.02% 565ms 2.45% AbstractCellBasedSimulation::DoCellBirth 234ms 1.02% 65.04% 552ms 2.40% __cxxabiv1::__si_class_type_info::__do_dyncast 2ms 0.0087% 65.05% 545ms 2.37% AbstractCentreBasedCellPopulation::GetDampingConstant 5ms 0.022% 65.07% 526ms 2.29% CellPropertyCollection::GetPropertiesType (inline) 499ms 2.17% 67.24% 499ms 2.17% boost::numeric::ublas::same_impl_ex 58ms 0.25% 67.49% 490ms 2.13% std::__new_allocator::allocate (inline) 35ms 0.15% 67.64% 484ms 2.10% boost::detail::shared_count::~shared_count (inline) 0 0% 67.64% 484ms 2.10% boost::shared_ptr::~shared_ptr (inline) 481ms 2.09% 69.73% 481ms 2.09% __strcmp_avx2 41ms 0.18% 69.91% 472ms 2.05% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 69.91% 471ms 2.05% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 69.91% 470ms 2.04% std::allocator_traits::allocate (inline) 0 0% 69.91% 458ms 1.99% std::_Rb_tree::_M_create_node (inline) 14ms 0.061% 69.97% 445ms 1.93% std::_Rb_tree::_Rb_tree (partial-inline) 433ms 1.88% 71.85% 439ms 1.91% boost::detail::sp_counted_base::release 438ms 1.90% 73.76% 438ms 1.90% std::_Rb_tree_increment 0 0% 73.76% 435ms 1.89% AbstractCellBasedSimulation::DoCellRemoval (inline) 29ms 0.13% 73.88% 426ms 1.85% operator new 5ms 0.022% 73.90% 425ms 1.85% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 46ms 0.2% 74.10% 417ms 1.81% std::_Rb_tree::_M_copy (inline) 0 0% 74.10% 397ms 1.72% std::_Rb_tree::_M_get_node (inline) 124ms 0.54% 74.64% 396ms 1.72% __GI___libc_malloc 121ms 0.53% 75.17% 396ms 1.72% std::_Rb_tree::_M_erase 5ms 0.022% 75.19% 384ms 1.67% AbstractCellProperty::IsSubType (inline) 131ms 0.57% 75.76% 380ms 1.65% Node::GetRadius 2ms 0.0087% 75.77% 375ms 1.63% Cell::GetMutationState 126ms 0.55% 76.31% 371ms 1.61% std::_Rb_tree::_M_clone_node (inline) 6ms 0.026% 76.34% 365ms 1.59% std::set::set (inline) 0 0% 76.34% 333ms 1.45% NodesOnlyMesh::ReMesh 0 0% 76.34% 328ms 1.42% boost::numeric::ublas::c_vector::assign (inline) 6ms 0.026% 76.37% 327ms 1.42% NodeBasedCellPopulation::UpdateMapsAfterRemesh 3ms 0.013% 76.38% 327ms 1.42% NodesOnlyMesh::UpdateNodeIndices 0 0% 76.38% 325ms 1.41% boost::numeric::ublas::inner_prod (inline) 26ms 0.11% 76.49% 324ms 1.41% boost::numeric::ublas::vector_binary::size (inline) 1ms 0.0043% 76.50% 323ms 1.40% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 25ms 0.11% 76.61% 322ms 1.40% boost::numeric::ublas::vector_scalar_binary::evaluate 320ms 1.39% 78.00% 320ms 1.39% __gnu_cxx::__normal_iterator::operator++ (inline) 44ms 0.19% 78.19% 316ms 1.37% std::_Rb_tree::~_Rb_tree (inline) 309ms 1.34% 79.53% 309ms 1.34% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 79.53% 297ms 1.29% std::_Rb_tree::_Alloc_node::operator() (inline) 5ms 0.022% 79.55% 278ms 1.21% std::_Rb_tree::_M_emplace_hint_unique 4ms 0.017% 79.57% 268ms 1.16% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 79.57% 268ms 1.16% std::_Rb_tree::_M_drop_node (inline) 7ms 0.03% 79.60% 252ms 1.09% DistributedBoxCollection::GetProcessOwningNode 107ms 0.46% 80.06% 249ms 1.08% boost::numeric::ublas::vector_inner_prod::apply (inline) 248ms 1.08% 81.14% 248ms 1.08% Node::CheckForNodeAttributes 0 0% 81.14% 244ms 1.06% NodesOnlyMesh::UpdateBoxCollection 0 0% 81.14% 232ms 1.01% std::set::~set (inline) 135ms 0.59% 81.73% 226ms 0.98% _int_malloc 5ms 0.022% 81.75% 224ms 0.97% std::__new_allocator::deallocate (inline) 0 0% 81.75% 223ms 0.97% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 81.75% 223ms 0.97% VtkMeshWriter::WriteFiles 0 0% 81.75% 219ms 0.95% NodesOnlyMesh::ResizeBoxCollection 11ms 0.048% 81.80% 217ms 0.94% NodesOnlyMesh::IsANodeCloseToDomainBoundary 1ms 0.0043% 81.80% 209ms 0.91% NodesOnlyMesh::AddNodesToBoxes 103ms 0.45% 82.25% 205ms 0.89% std::__move_median_to_first (inline) 65ms 0.28% 82.53% 204ms 0.89% __GI___libc_free 0 0% 82.53% 199ms 0.86% std::allocator_traits::deallocate (inline) 0 0% 82.53% 199ms 0.86% vtkCompositeDataPipeline::ExecuteData 0 0% 82.53% 199ms 0.86% vtkDemandDrivenPipeline::ExecuteData 0 0% 82.53% 199ms 0.86% vtkDemandDrivenPipeline::ProcessRequest 0 0% 82.53% 199ms 0.86% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 82.53% 199ms 0.86% vtkStreamingDemandDrivenPipeline::Update 0 0% 82.53% 199ms 0.86% vtkXMLWriterBase::Write 0 0% 82.53% 198ms 0.86% vtkExecutive::CallAlgorithm 1ms 0.0043% 82.54% 198ms 0.86% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 82.54% 195ms 0.85% std::_Rb_tree::_M_put_node (inline) 18ms 0.078% 82.61% 194ms 0.84% std::__insertion_sort (inline) 0 0% 82.61% 190ms 0.83% Cell::HasCellProperty (inline) 2ms 0.0087% 82.62% 190ms 0.83% CellPropertyCollection::HasProperty 93ms 0.4% 83.03% 176ms 0.76% boost::shared_ptr::shared_ptr (inline) 7ms 0.03% 83.06% 173ms 0.75% Cell::ReadyToDivide 172ms 0.75% 83.80% 172ms 0.75% [libchaste_cell_based.so] 170ms 0.74% 84.54% 170ms 0.74% Node::GetIndex 4ms 0.017% 84.56% 163ms 0.71% AbstractCellProperty::IsType (inline) 0 0% 84.56% 162ms 0.7% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 84.56% 162ms 0.7% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 84.56% 161ms 0.7% std::_Rb_tree::_Auto_node::_Auto_node (inline) 5ms 0.022% 84.58% 159ms 0.69% DistributedBoxCollection::GetIsPeriodicAllDims 0 0% 84.58% 159ms 0.69% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 147ms 0.64% 85.22% 147ms 0.64% [libchaste_mesh.so] 15ms 0.065% 85.29% 145ms 0.63% boost::numeric::ublas::vector_reference::operator() (inline) 141ms 0.61% 85.90% 141ms 0.61% boost::shared_ptr::operator-> (inline) 0 0% 85.90% 140ms 0.61% boost::numeric::ublas::vector_binary::operator() (inline) 122ms 0.53% 86.43% 139ms 0.6% _int_free 2ms 0.0087% 86.44% 138ms 0.6% AbstractCellPopulation::SetCellUsingLocationIndex 1ms 0.0043% 86.44% 138ms 0.6% std::_Rb_tree::clear (inline) 0 0% 86.44% 137ms 0.6% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 3ms 0.013% 86.45% 136ms 0.59% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 86.45% 136ms 0.59% vtkXMLWriter::WriteBinaryData 134ms 0.58% 87.04% 135ms 0.59% std::__adjacent_find (inline) 0 0% 87.04% 135ms 0.59% std::__unique (inline) 0 0% 87.04% 135ms 0.59% std::unique (inline) 134ms 0.58% 87.62% 134ms 0.58% Node::IsDeleted 1ms 0.0043% 87.62% 133ms 0.58% vtkXMLWriter::WriteBinaryDataInternal 77ms 0.33% 87.96% 131ms 0.57% Node::AddNeighbour 1ms 0.0043% 87.96% 131ms 0.57% vtkXMLWriter::WriteBinaryDataBlock 1ms 0.0043% 87.97% 130ms 0.56% vtkXMLWriter::WriteCompressionBlock 44ms 0.19% 88.16% 126ms 0.55% AbstractCellProperty::IsSame 123ms 0.53% 88.69% 123ms 0.53% Node::rGetLocation 2ms 0.0087% 88.70% 121ms 0.53% Cell::GetCellId 3ms 0.013% 88.71% 120ms 0.52% NodeBasedCellPopulation::SetNode 0 0% 88.71% 119ms 0.52% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 88.71% 118ms 0.51% vtkXMLWriter::WritePointsAppendedData