File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 23510ms, 89.93% of 26142ms total Dropped 851 nodes (cum <= 130.71ms) flat flat% sum% cum cum% 0 0% 0% 26007ms 99.48% __libc_start_call_main 0 0% 0% 26007ms 99.48% __libc_start_main_impl 0 0% 0% 26007ms 99.48% _start 0 0% 0% 25989ms 99.41% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 25989ms 99.41% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 25989ms 99.41% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 25989ms 99.41% main 0 0% 0% 25945ms 99.25% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 25945ms 99.25% CxxTest::TestRunner::runTest (inline) 0 0% 0% 25944ms 99.24% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 25934ms 99.20% AbstractCellBasedSimulation::Solve 3ms 0.011% 0.011% 14710ms 56.27% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.011% 9970ms 38.14% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.015% 0.027% 9713ms 37.15% ForwardEulerNumericalMethod::UpdateAllNodePositions 17ms 0.065% 0.092% 9515ms 36.40% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.092% 8794ms 33.64% NodeBasedCellPopulation::Update 1396ms 5.34% 5.43% 8516ms 32.58% RepulsionForce::AddForceContribution (partial-inline) 9ms 0.034% 5.47% 6624ms 25.34% DistributedBoxCollection::CalculateInteriorNodePairs 2153ms 8.24% 13.70% 5258ms 20.11% std::_Rb_tree::_M_lower_bound (inline) 16ms 0.061% 13.76% 4686ms 17.93% NodeAttributes::RemoveDuplicateNeighbours 0 0% 13.76% 4611ms 17.64% OffLatticeSimulation::ApplyBoundaries 4ms 0.015% 13.78% 4505ms 17.23% std::__sort (inline) 0 0% 13.78% 4505ms 17.23% std::sort (inline) 206ms 0.79% 14.57% 4373ms 16.73% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 248ms 0.95% 15.52% 3410ms 13.04% std::_Rb_tree::find (inline) 0 0% 15.52% 3409ms 13.04% std::map::find (inline) 77ms 0.29% 15.81% 3302ms 12.63% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 9ms 0.034% 15.84% 3208ms 12.27% AbstractCellPopulation::Iterator::operator++ (inline) 160ms 0.61% 16.46% 3167ms 12.11% AbstractCellPopulation::Iterator::IsRealCell 3095ms 11.84% 28.30% 3095ms 11.84% std::_Rb_tree::_S_right (inline) 28ms 0.11% 28.40% 2746ms 10.50% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 179ms 0.68% 29.09% 2684ms 10.27% std::__introsort_loop 179ms 0.68% 29.77% 2599ms 9.94% std::map::operator[] (partial-inline) 147ms 0.56% 30.33% 2536ms 9.70% DistributedBoxCollection::AddPairsFromBox 21ms 0.08% 30.41% 2485ms 9.51% PlaneBoundaryCondition::ImposeBoundaryCondition 153ms 0.59% 31.00% 2455ms 9.39% AbstractMesh::GetNode 61ms 0.23% 31.23% 2432ms 9.30% NodesOnlyMesh::GetNodeOrHaloNode 0 0% 31.23% 2426ms 9.28% std::__unguarded_partition_pivot (inline) 81ms 0.31% 31.54% 2310ms 8.84% NodesOnlyMesh::SolveNodeMapping 45ms 0.17% 31.72% 2260ms 8.65% AbstractCellPopulation::GetLocationIndexUsingCell 1042ms 3.99% 35.70% 2156ms 8.25% std::__unguarded_partition (inline) 0 0% 35.70% 2129ms 8.14% std::_Rb_tree::lower_bound (inline) 0 0% 35.70% 2129ms 8.14% std::map::lower_bound (inline) 10ms 0.038% 35.74% 2126ms 8.13% PlaneBoundaryCondition::VerifyBoundaryCondition 26ms 0.099% 35.84% 1881ms 7.20% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 36ms 0.14% 35.98% 1854ms 7.09% AbstractCellPopulation::GetCellUsingLocationIndex 3ms 0.011% 35.99% 1816ms 6.95% std::__final_insertion_sort (inline) 111ms 0.42% 36.41% 1609ms 6.15% std::__unguarded_insertion_sort (inline) 590ms 2.26% 38.67% 1528ms 5.85% std::__unguarded_linear_insert (inline) 1374ms 5.26% 43.93% 1374ms 5.26% __gnu_cxx::__normal_iterator::operator-- (inline) 34ms 0.13% 44.06% 1324ms 5.06% boost::numeric::ublas::c_vector::c_vector (partial-inline) 7ms 0.027% 44.08% 1184ms 4.53% boost::numeric::ublas::vector_assign (inline) 2ms 0.0077% 44.09% 1171ms 4.48% NodeBasedCellPopulation::UpdateCellProcessLocation 5ms 0.019% 44.11% 1120ms 4.28% DistributedBoxCollection::CalculateBoundaryNodePairs 246ms 0.94% 45.05% 1090ms 4.17% boost::numeric::ublas::indexing_vector_assign 343ms 1.31% 46.36% 1043ms 3.99% __dynamic_cast 40ms 0.15% 46.52% 1020ms 3.90% std::_Rb_tree_const_iterator::operator++ (inline) 350ms 1.34% 47.85% 979ms 3.74% NodeAttributes::AddNeighbour 960ms 3.67% 51.53% 960ms 3.67% std::_Rb_tree_increment 22ms 0.084% 51.61% 945ms 3.61% CellPropertyCollection::GetPropertiesType (inline) 17ms 0.065% 51.68% 921ms 3.52% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 6ms 0.023% 51.70% 882ms 3.37% AbstractCentreBasedCellPopulation::GetDampingConstant 371ms 1.42% 53.12% 857ms 3.28% DistributedBoxCollection::CalculateContainingBox (partial-inline) 191ms 0.73% 53.85% 848ms 3.24% AbstractMesh::GetVectorFromAtoB 0 0% 53.85% 845ms 3.23% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 53.85% 824ms 3.15% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 53.85% 823ms 3.15% boost::numeric::ublas::norm_2 (inline) 628ms 2.40% 56.25% 823ms 3.15% boost::numeric::ublas::vector_norm_2::apply (inline) 3ms 0.011% 56.26% 817ms 3.13% boost::numeric::ublas::c_vector::operator= (inline) 28ms 0.11% 56.37% 794ms 3.04% std::__copy_move::__copy_m (inline) 0 0% 56.37% 794ms 3.04% std::__copy_move_a (inline) 0 0% 56.37% 794ms 3.04% std::__copy_move_a1 (inline) 0 0% 56.37% 794ms 3.04% std::__copy_move_a2 (inline) 0 0% 56.37% 794ms 3.04% std::copy (inline) 793ms 3.03% 59.40% 793ms 3.03% __memcpy_avx_unaligned_erms 0 0% 59.40% 789ms 3.02% AbstractCellPopulation::WriteResultsToFiles 627ms 2.40% 61.80% 743ms 2.84% std::vector::push_back (inline) 719ms 2.75% 64.55% 719ms 2.75% boost::numeric::ublas::c_vector::operator() 6ms 0.023% 64.57% 705ms 2.70% AbstractCellBasedSimulation::DoCellBirth 2ms 0.0077% 64.58% 678ms 2.59% Cell::GetMutationState 27ms 0.1% 64.69% 650ms 2.49% std::_Rb_tree::_Rb_tree (partial-inline) 43ms 0.16% 64.85% 616ms 2.36% std::_Rb_tree::_M_copy (inline) 132ms 0.5% 65.35% 608ms 2.33% std::__new_allocator::allocate (inline) 0 0% 65.35% 585ms 2.24% std::allocator_traits::allocate (inline) 280ms 1.07% 66.43% 571ms 2.18% __cxxabiv1::__si_class_type_info::__do_dyncast 571ms 2.18% 68.61% 571ms 2.18% boost::numeric::ublas::same_impl_ex 0 0% 68.61% 566ms 2.17% std::_Rb_tree::_M_create_node (inline) 209ms 0.8% 69.41% 561ms 2.15% std::_Rb_tree::_M_clone_node (inline) 4ms 0.015% 69.42% 531ms 2.03% std::set::set (inline) 0 0% 69.42% 517ms 1.98% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 69.42% 505ms 1.93% std::_Rb_tree::_M_get_node (inline) 1ms 0.0038% 69.43% 503ms 1.92% AbstractCellProperty::IsSubType (inline) 156ms 0.6% 70.03% 483ms 1.85% std::_Rb_tree::_M_erase 32ms 0.12% 70.15% 475ms 1.82% boost::detail::shared_count::~shared_count (inline) 0 0% 70.15% 475ms 1.82% boost::shared_ptr::~shared_ptr (inline) 33ms 0.13% 70.27% 474ms 1.81% operator new 0 0% 70.27% 471ms 1.80% AbstractCellBasedSimulation::DoCellRemoval (inline) 459ms 1.76% 72.03% 459ms 1.76% __strcmp_avx2 4ms 0.015% 72.04% 455ms 1.74% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 118ms 0.45% 72.50% 430ms 1.64% __GI___libc_malloc 410ms 1.57% 74.06% 429ms 1.64% boost::detail::sp_counted_base::release 93ms 0.36% 74.42% 412ms 1.58% boost::numeric::ublas::vector_binary::size (inline) 0 0% 74.42% 402ms 1.54% std::_Rb_tree::_Alloc_node::operator() (inline) 397ms 1.52% 75.94% 397ms 1.52% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 75.94% 387ms 1.48% boost::numeric::ublas::c_vector::assign (inline) 0 0% 75.94% 377ms 1.44% boost::numeric::ublas::inner_prod (inline) 2ms 0.0077% 75.95% 377ms 1.44% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 15ms 0.057% 76.00% 375ms 1.43% boost::numeric::ublas::vector_scalar_binary::evaluate 333ms 1.27% 77.28% 363ms 1.39% Node::AddNeighbour 94ms 0.36% 77.64% 361ms 1.38% Node::GetRadius 0 0% 77.64% 342ms 1.31% NodesOnlyMesh::ReMesh 43ms 0.16% 77.80% 342ms 1.31% std::_Rb_tree::~_Rb_tree (inline) 7ms 0.027% 77.83% 333ms 1.27% NodesOnlyMesh::UpdateNodeIndices 0 0% 77.83% 328ms 1.25% NodesOnlyMesh::UpdateBoxCollection 327ms 1.25% 79.08% 327ms 1.25% __gnu_cxx::__normal_iterator::operator++ (inline) 5ms 0.019% 79.10% 319ms 1.22% CellPropertyCollection::HasProperty 0 0% 79.10% 317ms 1.21% Cell::HasCellProperty (inline) 9ms 0.034% 79.13% 311ms 1.19% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 6ms 0.023% 79.16% 310ms 1.19% NodeBasedCellPopulation::UpdateMapsAfterRemesh 132ms 0.5% 79.66% 310ms 1.19% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 79.66% 308ms 1.18% std::_Rb_tree::_M_drop_node (inline) 7ms 0.027% 79.69% 299ms 1.14% Cell::ReadyToDivide 5ms 0.019% 79.71% 291ms 1.11% std::_Rb_tree::_M_emplace_hint_unique 287ms 1.10% 80.80% 287ms 1.10% Node::CheckForNodeAttributes 4ms 0.015% 80.82% 286ms 1.09% DistributedBoxCollection::GetProcessOwningNode 116ms 0.44% 81.26% 269ms 1.03% std::__move_median_to_first (inline) 129ms 0.49% 81.76% 263ms 1.01% _int_malloc 7ms 0.027% 81.78% 257ms 0.98% std::__new_allocator::deallocate (inline) 0 0% 81.78% 255ms 0.98% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 81.78% 254ms 0.97% VtkMeshWriter::WriteFiles 83ms 0.32% 82.10% 242ms 0.93% __GI___libc_free 0 0% 82.10% 234ms 0.9% NodesOnlyMesh::AddNodesToBoxes 0 0% 82.10% 234ms 0.9% std::allocator_traits::deallocate (inline) 0 0% 82.10% 232ms 0.89% std::_Rb_tree::_M_put_node (inline) 0 0% 82.10% 228ms 0.87% std::set::~set (inline) 225ms 0.86% 82.96% 225ms 0.86% Node::GetIndex 0 0% 82.96% 222ms 0.85% vtkStreamingDemandDrivenPipeline::Update 0 0% 82.96% 222ms 0.85% vtkXMLWriterBase::Write 0 0% 82.96% 221ms 0.85% vtkDemandDrivenPipeline::ProcessRequest 0 0% 82.96% 220ms 0.84% vtkCompositeDataPipeline::ExecuteData 0 0% 82.96% 220ms 0.84% vtkDemandDrivenPipeline::ExecuteData 0 0% 82.96% 220ms 0.84% vtkExecutive::CallAlgorithm 0 0% 82.96% 220ms 0.84% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 82.96% 219ms 0.84% vtkXMLUnstructuredDataWriter::ProcessRequest 106ms 0.41% 83.37% 216ms 0.83% boost::shared_ptr::shared_ptr (inline) 20ms 0.077% 83.44% 213ms 0.81% boost::numeric::ublas::vector_reference::operator() (inline) 205ms 0.78% 84.23% 205ms 0.78% boost::shared_ptr::operator-> (inline) 204ms 0.78% 85.01% 204ms 0.78% [libchaste_cell_based.so] 29ms 0.11% 85.12% 204ms 0.78% std::__insertion_sort (inline) 2ms 0.0077% 85.13% 203ms 0.78% AbstractCellProperty::IsType (inline) 0 0% 85.13% 203ms 0.78% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 85.13% 203ms 0.78% std::_Rb_tree::clear (inline) 201ms 0.77% 85.90% 201ms 0.77% [libchaste_mesh.so] 2ms 0.0077% 85.90% 176ms 0.67% Cell::GetCellId 0 0% 85.90% 176ms 0.67% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.90% 176ms 0.67% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 85.90% 169ms 0.65% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 168ms 0.64% 86.55% 168ms 0.64% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 0 0% 86.55% 168ms 0.64% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 75ms 0.29% 86.83% 167ms 0.64% AbstractCellCycleModel::GetAge 0 0% 86.83% 164ms 0.63% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 86.83% 162ms 0.62% NodesOnlyMesh::ResizeBoxCollection 3ms 0.011% 86.84% 162ms 0.62% boost::numeric::ublas::c_vector::operator[] (inline) 11ms 0.042% 86.89% 160ms 0.61% NodesOnlyMesh::IsANodeCloseToDomainBoundary 150ms 0.57% 87.46% 159ms 0.61% _int_free 0 0% 87.46% 157ms 0.6% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 76ms 0.29% 87.75% 153ms 0.59% AbstractCellProperty::IsSame 0 0% 87.75% 146ms 0.56% vtkXMLWriter::WriteBinaryData 144ms 0.55% 88.30% 145ms 0.55% std::__adjacent_find (inline) 0 0% 88.30% 145ms 0.55% std::__unique (inline) 0 0% 88.30% 145ms 0.55% std::unique (inline) 143ms 0.55% 88.85% 143ms 0.55% __ieee754_log_fma 3ms 0.011% 88.86% 141ms 0.54% AbstractCellPopulation::SetCellUsingLocationIndex 4ms 0.015% 88.88% 141ms 0.54% AbstractNumericalMethod::SafeNodePositionUpdate 139ms 0.53% 89.41% 139ms 0.53% Node::rGetLocation 1ms 0.0038% 89.41% 138ms 0.53% vtkXMLWriter::WriteBinaryDataInternal 0 0% 89.41% 137ms 0.52% vtkXMLWriter::WriteBinaryDataBlock 0 0% 89.41% 137ms 0.52% vtkXMLWriter::WriteCompressionBlock 133ms 0.51% 89.92% 133ms 0.51% Node::IsDeleted 2ms 0.0077% 89.93% 132ms 0.5% NodeBasedCellPopulation::AcceptCellWriter 0 0% 89.93% 132ms 0.5% vtkXMLWriter::WritePointsAppendedData 1ms 0.0038% 89.93% 131ms 0.5% Cell::GetCellProliferativeType