File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 21203ms, 88.50% of 23957ms total Dropped 756 nodes (cum <= 119.78ms) flat flat% sum% cum cum% 0 0% 0% 23797ms 99.33% __libc_start_call_main 0 0% 0% 23797ms 99.33% __libc_start_main_impl 0 0% 0% 23797ms 99.33% _start 0 0% 0% 23782ms 99.27% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 23782ms 99.27% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 23782ms 99.27% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 23782ms 99.27% main 0 0% 0% 23743ms 99.11% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 23743ms 99.11% CxxTest::TestRunner::runTest (inline) 0 0% 0% 23743ms 99.11% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 23734ms 99.07% AbstractCellBasedSimulation::Solve 0 0% 0% 13453ms 56.15% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0% 9072ms 37.87% AbstractCellBasedSimulation::UpdateCellPopulation 5ms 0.021% 0.021% 8585ms 35.84% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.042% 0.063% 8413ms 35.12% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.063% 7998ms 33.38% NodeBasedCellPopulation::Update 1232ms 5.14% 5.21% 7681ms 32.06% RepulsionForce::AddForceContribution (partial-inline) 9ms 0.038% 5.24% 5904ms 24.64% DistributedBoxCollection::CalculateInteriorNodePairs 2093ms 8.74% 13.98% 4902ms 20.46% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.0042% 13.98% 4574ms 19.09% OffLatticeSimulation::ApplyBoundaries 17ms 0.071% 14.05% 4524ms 18.88% NodeAttributes::RemoveDuplicateNeighbours 11ms 0.046% 14.10% 4359ms 18.20% std::__sort (inline) 0 0% 14.10% 4359ms 18.20% std::sort (inline) 175ms 0.73% 14.83% 3906ms 16.30% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 7ms 0.029% 14.86% 3472ms 14.49% AbstractCellPopulation::Iterator::operator++ (inline) 214ms 0.89% 15.75% 3448ms 14.39% AbstractCellPopulation::Iterator::IsRealCell (inline) 71ms 0.3% 16.05% 3375ms 14.09% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 271ms 1.13% 17.18% 3233ms 13.50% std::_Rb_tree::find (inline) 0 0% 17.18% 3233ms 13.50% std::map::find (inline) 15ms 0.063% 17.24% 2892ms 12.07% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2763ms 11.53% 28.78% 2763ms 11.53% std::_Rb_tree::_S_right (inline) 260ms 1.09% 29.86% 2513ms 10.49% std::map::operator[] (partial-inline) 179ms 0.75% 30.61% 2497ms 10.42% std::__introsort_loop 29ms 0.12% 30.73% 2373ms 9.91% PlaneBoundaryCondition::ImposeBoundaryCondition 20ms 0.083% 30.81% 2298ms 9.59% AbstractCellPopulation::GetLocationIndexUsingCell 60ms 0.25% 31.06% 2287ms 9.55% NodesOnlyMesh::GetNodeOrHaloNode 142ms 0.59% 31.66% 2276ms 9.50% AbstractMesh::GetNode 0 0% 31.66% 2222ms 9.27% std::__unguarded_partition_pivot (inline) 26ms 0.11% 31.77% 2200ms 9.18% PlaneBoundaryCondition::VerifyBoundaryCondition 85ms 0.35% 32.12% 2138ms 8.92% NodesOnlyMesh::SolveNodeMapping 163ms 0.68% 32.80% 2020ms 8.43% DistributedBoxCollection::AddPairsFromBox 997ms 4.16% 36.96% 2004ms 8.36% std::__unguarded_partition (inline) 0 0% 36.96% 1966ms 8.21% std::_Rb_tree::lower_bound (inline) 0 0% 36.96% 1966ms 8.21% std::map::lower_bound (inline) 4ms 0.017% 36.98% 1851ms 7.73% std::__final_insertion_sort (inline) 21ms 0.088% 37.07% 1671ms 6.97% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 26ms 0.11% 37.17% 1644ms 6.86% AbstractCellPopulation::GetCellUsingLocationIndex 583ms 2.43% 39.61% 1611ms 6.72% std::__unguarded_linear_insert (inline) 88ms 0.37% 39.98% 1609ms 6.72% std::__unguarded_insertion_sort (inline) 1478ms 6.17% 46.15% 1478ms 6.17% __gnu_cxx::__normal_iterator::operator-- (inline) 71ms 0.3% 46.44% 1334ms 5.57% boost::numeric::ublas::c_vector::c_vector (partial-inline) 46ms 0.19% 46.63% 1197ms 5.00% boost::numeric::ublas::vector_assign (inline) 1ms 0.0042% 46.64% 1175ms 4.90% NodeBasedCellPopulation::UpdateCellProcessLocation 9ms 0.038% 46.68% 1103ms 4.60% DistributedBoxCollection::CalculateBoundaryNodePairs 304ms 1.27% 47.94% 1061ms 4.43% boost::numeric::ublas::indexing_vector_assign 248ms 1.04% 48.98% 938ms 3.92% __dynamic_cast 154ms 0.64% 49.62% 823ms 3.44% AbstractMesh::GetVectorFromAtoB 364ms 1.52% 51.14% 796ms 3.32% DistributedBoxCollection::CalculateContainingBox (partial-inline) 14ms 0.058% 51.20% 792ms 3.31% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 51.20% 788ms 3.29% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 51.20% 767ms 3.20% boost::numeric::ublas::norm_2 (inline) 608ms 2.54% 53.74% 767ms 3.20% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 53.74% 767ms 3.20% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 53.74% 734ms 3.06% AbstractCellPopulation::WriteResultsToFiles 207ms 0.86% 54.60% 729ms 3.04% NodeAttributes::AddNeighbour 697ms 2.91% 57.51% 697ms 2.91% boost::numeric::ublas::c_vector::operator() 47ms 0.2% 57.71% 691ms 2.88% std::_Rb_tree_const_iterator::operator++ (inline) 10ms 0.042% 57.75% 679ms 2.83% CellPropertyCollection::GetPropertiesType (inline) 6ms 0.025% 57.77% 666ms 2.78% boost::numeric::ublas::c_vector::operator= (inline) 1ms 0.0042% 57.78% 651ms 2.72% AbstractCentreBasedCellPopulation::GetDampingConstant 39ms 0.16% 57.94% 644ms 2.69% std::__copy_move::__copy_m (inline) 0 0% 57.94% 644ms 2.69% std::__copy_move_a (inline) 0 0% 57.94% 644ms 2.69% std::__copy_move_a1 (inline) 0 0% 57.94% 644ms 2.69% std::__copy_move_a2 (inline) 0 0% 57.94% 644ms 2.69% std::copy (inline) 640ms 2.67% 60.61% 640ms 2.67% std::_Rb_tree_increment 619ms 2.58% 63.20% 619ms 2.58% __memcpy_avx_unaligned_erms 95ms 0.4% 63.59% 606ms 2.53% std::__new_allocator::allocate (inline) 4ms 0.017% 63.61% 605ms 2.53% AbstractCellBasedSimulation::DoCellBirth 520ms 2.17% 65.78% 585ms 2.44% std::vector::push_back (inline) 0 0% 65.78% 578ms 2.41% std::allocator_traits::allocate (inline) 227ms 0.95% 66.73% 546ms 2.28% __cxxabiv1::__si_class_type_info::__do_dyncast 40ms 0.17% 66.89% 538ms 2.25% boost::detail::shared_count::~shared_count (inline) 0 0% 66.89% 538ms 2.25% boost::shared_ptr::~shared_ptr (inline) 15ms 0.063% 66.96% 532ms 2.22% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 66.96% 529ms 2.21% std::_Rb_tree::_M_create_node (inline) 508ms 2.12% 69.08% 508ms 2.12% __strcmp_avx2 29ms 0.12% 69.20% 506ms 2.11% operator new 34ms 0.14% 69.34% 499ms 2.08% std::_Rb_tree::_M_copy (inline) 474ms 1.98% 71.32% 485ms 2.02% boost::detail::sp_counted_base::release 5ms 0.021% 71.34% 477ms 1.99% Cell::GetMutationState 0 0% 71.34% 475ms 1.98% std::_Rb_tree::_M_get_node (inline) 1ms 0.0042% 71.34% 473ms 1.97% NodeBasedCellPopulation::WriteVtkResultsToFile 472ms 1.97% 73.31% 472ms 1.97% boost::numeric::ublas::same_impl_ex 138ms 0.58% 73.89% 471ms 1.97% __GI___libc_malloc 0 0% 73.89% 469ms 1.96% AbstractCellBasedSimulation::DoCellRemoval (inline) 139ms 0.58% 74.47% 460ms 1.92% std::_Rb_tree::_M_clone_node (inline) 4ms 0.017% 74.49% 453ms 1.89% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 147ms 0.61% 75.10% 451ms 1.88% std::_Rb_tree::_M_erase 5ms 0.021% 75.12% 433ms 1.81% AbstractCellProperty::IsSubType (inline) 1ms 0.0042% 75.13% 431ms 1.80% std::set::set (inline) 156ms 0.65% 75.78% 378ms 1.58% Node::GetRadius 0 0% 75.78% 368ms 1.54% std::_Rb_tree::_Alloc_node::operator() (inline) 38ms 0.16% 75.94% 350ms 1.46% std::_Rb_tree::~_Rb_tree (inline) 0 0% 75.94% 333ms 1.39% boost::numeric::ublas::c_vector::assign (inline) 322ms 1.34% 77.28% 322ms 1.34% __gnu_cxx::__normal_iterator::operator++ (inline) 322ms 1.34% 78.62% 322ms 1.34% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 78.62% 313ms 1.31% NodesOnlyMesh::ReMesh 5ms 0.021% 78.65% 311ms 1.30% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 78.65% 311ms 1.30% boost::numeric::ublas::inner_prod (inline) 1ms 0.0042% 78.65% 311ms 1.30% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 22ms 0.092% 78.74% 310ms 1.29% boost::numeric::ublas::vector_scalar_binary::evaluate 35ms 0.15% 78.89% 306ms 1.28% boost::numeric::ublas::vector_binary::size (inline) 0 0% 78.89% 297ms 1.24% NodesOnlyMesh::UpdateNodeIndices 89ms 0.37% 79.26% 295ms 1.23% Node::AddNeighbour 0 0% 79.26% 294ms 1.23% std::_Rb_tree::_M_drop_node (inline) 12ms 0.05% 79.31% 287ms 1.20% std::_Rb_tree::_M_emplace_hint_unique 0 0% 79.31% 279ms 1.16% NodesOnlyMesh::UpdateBoxCollection 149ms 0.62% 79.93% 272ms 1.14% _int_malloc 2ms 0.0083% 79.94% 268ms 1.12% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 79.94% 264ms 1.10% std::set::~set (inline) 1ms 0.0042% 79.94% 252ms 1.05% DistributedBoxCollection::GetProcessOwningNode 102ms 0.43% 80.37% 250ms 1.04% boost::numeric::ublas::vector_inner_prod::apply (inline) 3ms 0.013% 80.38% 248ms 1.04% std::__new_allocator::deallocate (inline) 17ms 0.071% 80.45% 238ms 0.99% std::__insertion_sort (inline) 236ms 0.99% 81.44% 237ms 0.99% Node::ConstructNodeAttributes (inline) 1ms 0.0042% 81.44% 233ms 0.97% NodesOnlyMesh::AddNodesToBoxes 0 0% 81.44% 228ms 0.95% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 227ms 0.95% 82.39% 227ms 0.95% Node::CheckForNodeAttributes 0 0% 82.39% 226ms 0.94% VtkMeshWriter::WriteFiles 89ms 0.37% 82.76% 224ms 0.94% __GI___libc_free 0 0% 82.76% 220ms 0.92% std::allocator_traits::deallocate (inline) 0 0% 82.76% 218ms 0.91% std::_Rb_tree::_M_put_node (inline) 110ms 0.46% 83.22% 215ms 0.9% std::__move_median_to_first (inline) 0 0% 83.22% 203ms 0.85% vtkStreamingDemandDrivenPipeline::Update 0 0% 83.22% 203ms 0.85% vtkXMLWriterBase::Write 0 0% 83.22% 202ms 0.84% vtkDemandDrivenPipeline::ProcessRequest 0 0% 83.22% 201ms 0.84% NodesOnlyMesh::ResizeBoxCollection 0 0% 83.22% 201ms 0.84% vtkCompositeDataPipeline::ExecuteData 0 0% 83.22% 201ms 0.84% vtkDemandDrivenPipeline::ExecuteData 0 0% 83.22% 201ms 0.84% vtkExecutive::CallAlgorithm 0 0% 83.22% 201ms 0.84% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 83.22% 201ms 0.84% vtkXMLUnstructuredDataWriter::ProcessRequest 2ms 0.0083% 83.23% 200ms 0.83% CellPropertyCollection::HasProperty 12ms 0.05% 83.28% 200ms 0.83% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 83.28% 199ms 0.83% Cell::HasCellProperty (inline) 196ms 0.82% 84.10% 196ms 0.82% [libchaste_cell_based.so] 9ms 0.038% 84.13% 186ms 0.78% Cell::ReadyToDivide 184ms 0.77% 84.90% 184ms 0.77% Node::GetIndex 87ms 0.36% 85.27% 178ms 0.74% boost::shared_ptr::shared_ptr (inline) 0 0% 85.27% 177ms 0.74% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.27% 177ms 0.74% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 85.27% 170ms 0.71% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 165ms 0.69% 85.95% 165ms 0.69% boost::shared_ptr::operator-> (inline) 0 0% 85.95% 161ms 0.67% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 85.95% 160ms 0.67% std::_Rb_tree::clear (inline) 2ms 0.0083% 85.96% 155ms 0.65% AbstractCellProperty::IsType (inline) 17ms 0.071% 86.03% 154ms 0.64% boost::numeric::ublas::vector_reference::operator() (inline) 1ms 0.0042% 86.04% 153ms 0.64% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 3ms 0.013% 86.05% 149ms 0.62% DistributedBoxCollection::GetIsPeriodicAllDims 147ms 0.61% 86.66% 147ms 0.61% [libchaste_mesh.so] 141ms 0.59% 87.25% 141ms 0.59% Node::IsDeleted 0 0% 87.25% 138ms 0.58% vtkXMLWriter::WriteBinaryData 125ms 0.52% 87.77% 135ms 0.56% _int_free 131ms 0.55% 88.32% 134ms 0.56% std::__adjacent_find (inline) 0 0% 88.32% 134ms 0.56% std::__unique (inline) 0 0% 88.32% 134ms 0.56% std::unique (inline) 0 0% 88.32% 133ms 0.56% Cell::GetCellId 0 0% 88.32% 131ms 0.55% vtkXMLWriter::WriteBinaryDataBlock 0 0% 88.32% 131ms 0.55% vtkXMLWriter::WriteBinaryDataInternal 0 0% 88.32% 131ms 0.55% vtkXMLWriter::WriteCompressionBlock 0 0% 88.32% 130ms 0.54% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 88.32% 129ms 0.54% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 88.32% 126ms 0.53% tbb::detail::r1::parallel_pipeline 0 0% 88.32% 125ms 0.52% vtkXMLWriter::WritePointsAppendedData 0 0% 88.32% 124ms 0.52% AbstractCellPopulation::SetCellUsingLocationIndex 0 0% 88.32% 124ms 0.52% clone3 0 0% 88.32% 124ms 0.52% start_thread 0 0% 88.32% 124ms 0.52% tbb::detail::r1::reset 43ms 0.18% 88.50% 121ms 0.51% AbstractCellCycleModel::GetAge 1ms 0.0042% 88.50% 121ms 0.51% Cell::GetCellProliferativeType 0 0% 88.50% 120ms 0.5% NodeBasedCellPopulation::AcceptCellWriter