File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20542ms, 88.52% of 23206ms total Dropped 768 nodes (cum <= 116.03ms) flat flat% sum% cum cum% 0 0% 0% 23040ms 99.28% __libc_start_call_main 0 0% 0% 23040ms 99.28% __libc_start_main_impl 0 0% 0% 23040ms 99.28% _start 0 0% 0% 23025ms 99.22% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 23025ms 99.22% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 23025ms 99.22% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 23025ms 99.22% main 0 0% 0% 22989ms 99.06% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 22989ms 99.06% CxxTest::TestRunner::runTest (inline) 0 0% 0% 22989ms 99.06% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0043% 0.0043% 22981ms 99.03% AbstractCellBasedSimulation::Solve 0 0% 0.0043% 13095ms 56.43% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0043% 8701ms 37.49% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0086% 0.013% 8286ms 35.71% ForwardEulerNumericalMethod::UpdateAllNodePositions 5ms 0.022% 0.034% 8105ms 34.93% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.034% 7688ms 33.13% NodeBasedCellPopulation::Update 1232ms 5.31% 5.34% 7510ms 32.36% RepulsionForce::AddForceContribution (partial-inline) 6ms 0.026% 5.37% 5676ms 24.46% DistributedBoxCollection::CalculateInteriorNodePairs 2028ms 8.74% 14.11% 4840ms 20.86% std::_Rb_tree::_M_lower_bound (inline) 0 0% 14.11% 4504ms 19.41% OffLatticeSimulation::ApplyBoundaries 18ms 0.078% 14.19% 4458ms 19.21% NodeAttributes::RemoveDuplicateNeighbours 7ms 0.03% 14.22% 4269ms 18.40% std::__sort (inline) 0 0% 14.22% 4269ms 18.40% std::sort (inline) 182ms 0.78% 15.00% 3793ms 16.34% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 5ms 0.022% 15.02% 3388ms 14.60% AbstractCellPopulation::Iterator::operator++ (inline) 208ms 0.9% 15.92% 3356ms 14.46% AbstractCellPopulation::Iterator::IsRealCell (inline) 67ms 0.29% 16.21% 3312ms 14.27% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 250ms 1.08% 17.28% 3145ms 13.55% std::_Rb_tree::find (inline) 0 0% 17.28% 3143ms 13.54% std::map::find (inline) 22ms 0.095% 17.38% 2833ms 12.21% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2768ms 11.93% 29.31% 2768ms 11.93% std::_Rb_tree::_S_right (inline) 178ms 0.77% 30.07% 2460ms 10.60% std::__introsort_loop 255ms 1.10% 31.17% 2446ms 10.54% std::map::operator[] (partial-inline) 39ms 0.17% 31.34% 2353ms 10.14% PlaneBoundaryCondition::ImposeBoundaryCondition 138ms 0.59% 31.94% 2275ms 9.80% AbstractMesh::GetNode 51ms 0.22% 32.16% 2265ms 9.76% AbstractCellPopulation::GetLocationIndexUsingCell 46ms 0.2% 32.35% 2253ms 9.71% NodesOnlyMesh::GetNodeOrHaloNode 0 0% 32.35% 2196ms 9.46% std::__unguarded_partition_pivot (inline) 16ms 0.069% 32.42% 2150ms 9.26% PlaneBoundaryCondition::VerifyBoundaryCondition 89ms 0.38% 32.81% 2141ms 9.23% NodesOnlyMesh::SolveNodeMapping 1004ms 4.33% 37.13% 2018ms 8.70% std::__unguarded_partition (inline) 0 0% 37.13% 1953ms 8.42% std::_Rb_tree::lower_bound (inline) 0 0% 37.13% 1953ms 8.42% std::map::lower_bound (inline) 172ms 0.74% 37.87% 1811ms 7.80% DistributedBoxCollection::AddPairsFromBox 3ms 0.013% 37.89% 1798ms 7.75% std::__final_insertion_sort (inline) 105ms 0.45% 38.34% 1594ms 6.87% std::__unguarded_insertion_sort (inline) 597ms 2.57% 40.91% 1552ms 6.69% std::__unguarded_linear_insert (inline) 32ms 0.14% 41.05% 1529ms 6.59% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 23ms 0.099% 41.15% 1490ms 6.42% AbstractCellPopulation::GetCellUsingLocationIndex 1421ms 6.12% 47.27% 1421ms 6.12% __gnu_cxx::__normal_iterator::operator-- (inline) 41ms 0.18% 47.45% 1300ms 5.60% boost::numeric::ublas::c_vector::c_vector (partial-inline) 44ms 0.19% 47.64% 1188ms 5.12% boost::numeric::ublas::vector_assign (inline) 0 0% 47.64% 1128ms 4.86% NodeBasedCellPopulation::UpdateCellProcessLocation 263ms 1.13% 48.77% 1078ms 4.65% boost::numeric::ublas::indexing_vector_assign 2ms 0.0086% 48.78% 1066ms 4.59% DistributedBoxCollection::CalculateBoundaryNodePairs 258ms 1.11% 49.89% 876ms 3.77% __dynamic_cast 164ms 0.71% 50.60% 806ms 3.47% AbstractMesh::GetVectorFromAtoB 19ms 0.082% 50.68% 787ms 3.39% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 372ms 1.60% 52.28% 787ms 3.39% DistributedBoxCollection::CalculateContainingBox (partial-inline) 212ms 0.91% 53.20% 777ms 3.35% NodeAttributes::AddNeighbour 0 0% 53.20% 739ms 3.18% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 53.20% 728ms 3.14% AbstractCellPopulation::WriteResultsToFiles 0 0% 53.20% 719ms 3.10% boost::numeric::ublas::norm_2 (inline) 561ms 2.42% 55.61% 719ms 3.10% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 55.61% 719ms 3.10% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 712ms 3.07% 58.68% 712ms 3.07% boost::numeric::ublas::c_vector::operator() 5ms 0.022% 58.70% 695ms 2.99% boost::numeric::ublas::c_vector::operator= (inline) 49ms 0.21% 58.92% 666ms 2.87% std::__copy_move::__copy_m (inline) 0 0% 58.92% 666ms 2.87% std::__copy_move_a (inline) 0 0% 58.92% 666ms 2.87% std::__copy_move_a1 (inline) 0 0% 58.92% 666ms 2.87% std::__copy_move_a2 (inline) 0 0% 58.92% 666ms 2.87% std::copy (inline) 565ms 2.43% 61.35% 637ms 2.74% std::vector::push_back (inline) 632ms 2.72% 64.07% 632ms 2.72% __memcpy_avx_unaligned_erms 1ms 0.0043% 64.08% 573ms 2.47% AbstractCellBasedSimulation::DoCellBirth 8ms 0.034% 64.11% 537ms 2.31% CellPropertyCollection::GetPropertiesType (inline) 533ms 2.30% 66.41% 533ms 2.30% boost::numeric::ublas::same_impl_ex 3ms 0.013% 66.42% 516ms 2.22% AbstractCentreBasedCellPopulation::GetDampingConstant 264ms 1.14% 67.56% 516ms 2.22% __cxxabiv1::__si_class_type_info::__do_dyncast 70ms 0.3% 67.86% 505ms 2.18% std::__new_allocator::allocate (inline) 32ms 0.14% 68.00% 502ms 2.16% std::_Rb_tree_const_iterator::operator++ (inline) 24ms 0.1% 68.10% 484ms 2.09% boost::detail::shared_count::~shared_count (inline) 0 0% 68.10% 484ms 2.09% boost::shared_ptr::~shared_ptr (inline) 0 0% 68.10% 483ms 2.08% std::allocator_traits::allocate (inline) 0 0% 68.10% 479ms 2.06% NodeBasedCellPopulation::WriteVtkResultsToFile 462ms 1.99% 70.09% 462ms 1.99% std::_Rb_tree_increment 34ms 0.15% 70.24% 461ms 1.99% std::_Rb_tree::_Rb_tree (partial-inline) 447ms 1.93% 72.17% 450ms 1.94% boost::detail::sp_counted_base::release 0 0% 72.17% 444ms 1.91% std::_Rb_tree::_M_create_node (inline) 0 0% 72.17% 440ms 1.90% AbstractCellBasedSimulation::DoCellRemoval (inline) 30ms 0.13% 72.30% 431ms 1.86% operator new 3ms 0.013% 72.31% 430ms 1.85% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 145ms 0.62% 72.93% 423ms 1.82% std::_Rb_tree::_M_erase 36ms 0.16% 73.09% 410ms 1.77% std::_Rb_tree::_M_copy (inline) 409ms 1.76% 74.85% 409ms 1.76% __strcmp_avx2 111ms 0.48% 75.33% 391ms 1.68% __GI___libc_malloc 0 0% 75.33% 378ms 1.63% std::_Rb_tree::_M_get_node (inline) 1ms 0.0043% 75.33% 377ms 1.62% AbstractCellProperty::IsSubType (inline) 111ms 0.48% 75.81% 374ms 1.61% std::_Rb_tree::_M_clone_node (inline) 145ms 0.62% 76.44% 373ms 1.61% Node::GetRadius 0 0% 76.44% 369ms 1.59% boost::numeric::ublas::c_vector::assign (inline) 4ms 0.017% 76.45% 364ms 1.57% std::set::set (inline) 3ms 0.013% 76.47% 358ms 1.54% Cell::GetMutationState 28ms 0.12% 76.59% 357ms 1.54% boost::numeric::ublas::vector_binary::size (inline) 0 0% 76.59% 355ms 1.53% boost::numeric::ublas::inner_prod (inline) 1ms 0.0043% 76.59% 354ms 1.53% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 17ms 0.073% 76.67% 353ms 1.52% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 76.67% 320ms 1.38% std::_Rb_tree::_Alloc_node::operator() (inline) 37ms 0.16% 76.82% 317ms 1.37% std::_Rb_tree::~_Rb_tree (inline) 10ms 0.043% 76.87% 308ms 1.33% NodeBasedCellPopulation::UpdateMapsAfterRemesh 307ms 1.32% 78.19% 307ms 1.32% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 293ms 1.26% 79.45% 293ms 1.26% __gnu_cxx::__normal_iterator::operator++ (inline) 112ms 0.48% 79.94% 279ms 1.20% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 79.94% 275ms 1.19% NodesOnlyMesh::ReMesh 3ms 0.013% 79.95% 273ms 1.18% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 79.95% 273ms 1.18% std::_Rb_tree::_M_drop_node (inline) 2ms 0.0086% 79.96% 269ms 1.16% NodesOnlyMesh::UpdateNodeIndices 0 0% 79.96% 265ms 1.14% NodesOnlyMesh::UpdateBoxCollection 10ms 0.043% 80.00% 260ms 1.12% DistributedBoxCollection::GetProcessOwningNode 139ms 0.6% 80.60% 243ms 1.05% _int_malloc 242ms 1.04% 81.64% 242ms 1.04% Node::CheckForNodeAttributes 4ms 0.017% 81.66% 238ms 1.03% std::_Rb_tree::_M_emplace_hint_unique 0 0% 81.66% 235ms 1.01% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 81.66% 234ms 1.01% std::set::~set (inline) 0 0% 81.66% 231ms 1% VtkMeshWriter::WriteFiles 116ms 0.5% 82.16% 222ms 0.96% boost::shared_ptr::shared_ptr (inline) 7ms 0.03% 82.19% 214ms 0.92% std::__new_allocator::deallocate (inline) 0 0% 82.19% 207ms 0.89% NodesOnlyMesh::AddNodesToBoxes 0 0% 82.19% 204ms 0.88% vtkStreamingDemandDrivenPipeline::Update 0 0% 82.19% 204ms 0.88% vtkXMLWriterBase::Write 0 0% 82.19% 203ms 0.87% vtkDemandDrivenPipeline::ProcessRequest 0 0% 82.19% 202ms 0.87% vtkCompositeDataPipeline::ExecuteData 0 0% 82.19% 202ms 0.87% vtkDemandDrivenPipeline::ExecuteData 0 0% 82.19% 202ms 0.87% vtkStreamingDemandDrivenPipeline::ProcessRequest 23ms 0.099% 82.29% 201ms 0.87% std::__insertion_sort (inline) 0 0% 82.29% 201ms 0.87% vtkExecutive::CallAlgorithm 0 0% 82.29% 201ms 0.87% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 82.29% 193ms 0.83% NodesOnlyMesh::ResizeBoxCollection 15ms 0.065% 82.35% 192ms 0.83% NodesOnlyMesh::IsANodeCloseToDomainBoundary 78ms 0.34% 82.69% 190ms 0.82% __GI___libc_free 0 0% 82.69% 190ms 0.82% std::allocator_traits::deallocate (inline) 0 0% 82.69% 189ms 0.81% std::_Rb_tree::_M_put_node (inline) 3ms 0.013% 82.70% 177ms 0.76% CellPropertyCollection::HasProperty 177ms 0.76% 83.47% 177ms 0.76% Node::GetIndex 0 0% 83.47% 174ms 0.75% Cell::HasCellProperty (inline) 0 0% 83.47% 174ms 0.75% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 83.47% 174ms 0.75% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 81ms 0.35% 83.81% 173ms 0.75% std::__move_median_to_first (inline) 172ms 0.74% 84.56% 172ms 0.74% [libchaste_cell_based.so] 6ms 0.026% 84.58% 168ms 0.72% Cell::ReadyToDivide 0 0% 84.58% 165ms 0.71% std::_Rb_tree::clear (inline) 0 0% 84.58% 162ms 0.7% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 5ms 0.022% 84.60% 161ms 0.69% AbstractCellProperty::IsType (inline) 154ms 0.66% 85.27% 154ms 0.66% Node::IsDeleted 153ms 0.66% 85.93% 154ms 0.66% std::__adjacent_find (inline) 0 0% 85.93% 154ms 0.66% std::__unique (inline) 0 0% 85.93% 154ms 0.66% std::unique (inline) 153ms 0.66% 86.59% 153ms 0.66% boost::shared_ptr::operator-> (inline) 15ms 0.065% 86.65% 146ms 0.63% boost::numeric::ublas::vector_reference::operator() (inline) 145ms 0.62% 87.27% 145ms 0.62% [libchaste_mesh.so] 0 0% 87.27% 144ms 0.62% vtkXMLWriter::WriteBinaryData 0 0% 87.27% 143ms 0.62% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 11ms 0.047% 87.32% 141ms 0.61% DistributedBoxCollection::GetIsPeriodicAllDims 0 0% 87.32% 137ms 0.59% vtkXMLWriter::WriteBinaryDataInternal 1ms 0.0043% 87.33% 136ms 0.59% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.33% 135ms 0.58% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 66ms 0.28% 87.61% 134ms 0.58% Node::AddNeighbour 0 0% 87.61% 134ms 0.58% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 87.61% 134ms 0.58% vtkXMLWriter::WriteCompressionBlock 1ms 0.0043% 87.62% 132ms 0.57% Cell::GetCellId 0 0% 87.62% 132ms 0.57% clone3 0 0% 87.62% 132ms 0.57% start_thread 0 0% 87.62% 132ms 0.57% tbb::detail::r1::parallel_pipeline 3ms 0.013% 87.63% 131ms 0.56% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 87.63% 129ms 0.56% tbb::detail::r1::reset 0 0% 87.63% 127ms 0.55% vtkXMLWriter::WritePointsAppendedData 46ms 0.2% 87.83% 126ms 0.54% tbb::detail::r1::wait_bounded_queue_monitor 0 0% 87.83% 124ms 0.53% AbstractCellPopulation::SetCellUsingLocationIndex 41ms 0.18% 88.00% 124ms 0.53% AbstractCellProperty::IsSame 0 0% 88.00% 124ms 0.53% std::_Rb_tree::_Auto_node::_Auto_node (inline) 120ms 0.52% 88.52% 120ms 0.52% __ieee754_log_fma