File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20751ms, 88.90% of 23341ms total Dropped 746 nodes (cum <= 116.70ms) flat flat% sum% cum cum% 0 0% 0% 23190ms 99.35% __libc_start_call_main 0 0% 0% 23190ms 99.35% __libc_start_main_impl 0 0% 0% 23190ms 99.35% _start 0 0% 0% 23175ms 99.29% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 23175ms 99.29% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 23175ms 99.29% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 23175ms 99.29% main 0 0% 0% 23140ms 99.14% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 23140ms 99.14% CxxTest::TestRunner::runTest (inline) 0 0% 0% 23140ms 99.14% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0043% 0.0043% 23132ms 99.10% AbstractCellBasedSimulation::Solve 2ms 0.0086% 0.013% 13153ms 56.35% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.013% 8774ms 37.59% AbstractCellBasedSimulation::UpdateCellPopulation 8ms 0.034% 0.047% 8301ms 35.56% ForwardEulerNumericalMethod::UpdateAllNodePositions 12ms 0.051% 0.099% 8106ms 34.73% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.0043% 0.1% 7757ms 33.23% NodeBasedCellPopulation::Update 1226ms 5.25% 5.36% 7506ms 32.16% RepulsionForce::AddForceContribution (partial-inline) 9ms 0.039% 5.39% 5722ms 24.51% DistributedBoxCollection::CalculateInteriorNodePairs 2122ms 9.09% 14.49% 5009ms 21.46% std::_Rb_tree::_M_lower_bound (inline) 0 0% 14.49% 4557ms 19.52% OffLatticeSimulation::ApplyBoundaries 17ms 0.073% 14.56% 4481ms 19.20% NodeAttributes::RemoveDuplicateNeighbours 2ms 0.0086% 14.57% 4294ms 18.40% std::__sort (inline) 0 0% 14.57% 4294ms 18.40% std::sort (inline) 184ms 0.79% 15.35% 3819ms 16.36% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 3ms 0.013% 15.37% 3451ms 14.79% AbstractCellPopulation::Iterator::operator++ (inline) 189ms 0.81% 16.18% 3427ms 14.68% AbstractCellPopulation::Iterator::IsRealCell 55ms 0.24% 16.41% 3360ms 14.40% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 217ms 0.93% 17.34% 3256ms 13.95% std::_Rb_tree::find (inline) 0 0% 17.34% 3254ms 13.94% std::map::find (inline) 21ms 0.09% 17.43% 2882ms 12.35% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2847ms 12.20% 29.63% 2847ms 12.20% std::_Rb_tree::_S_right (inline) 246ms 1.05% 30.68% 2521ms 10.80% std::map::operator[] (partial-inline) 183ms 0.78% 31.47% 2507ms 10.74% std::__introsort_loop 31ms 0.13% 31.60% 2367ms 10.14% PlaneBoundaryCondition::ImposeBoundaryCondition 38ms 0.16% 31.76% 2326ms 9.97% AbstractCellPopulation::GetLocationIndexUsingCell 165ms 0.71% 32.47% 2314ms 9.91% AbstractMesh::GetNode 49ms 0.21% 32.68% 2288ms 9.80% NodesOnlyMesh::GetNodeOrHaloNode 0 0% 32.68% 2237ms 9.58% std::__unguarded_partition_pivot (inline) 21ms 0.09% 32.77% 2189ms 9.38% PlaneBoundaryCondition::VerifyBoundaryCondition 75ms 0.32% 33.09% 2153ms 9.22% NodesOnlyMesh::SolveNodeMapping 1022ms 4.38% 37.47% 2005ms 8.59% std::__unguarded_partition (inline) 0 0% 37.47% 1983ms 8.50% std::_Rb_tree::lower_bound (inline) 0 0% 37.47% 1983ms 8.50% std::map::lower_bound (inline) 181ms 0.78% 38.25% 1856ms 7.95% DistributedBoxCollection::AddPairsFromBox 1ms 0.0043% 38.25% 1782ms 7.63% std::__final_insertion_sort (inline) 89ms 0.38% 38.63% 1589ms 6.81% std::__unguarded_insertion_sort (inline) 553ms 2.37% 41.00% 1547ms 6.63% std::__unguarded_linear_insert (inline) 14ms 0.06% 41.06% 1501ms 6.43% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 20ms 0.086% 41.15% 1485ms 6.36% AbstractCellPopulation::GetCellUsingLocationIndex 1449ms 6.21% 47.35% 1449ms 6.21% __gnu_cxx::__normal_iterator::operator-- (inline) 52ms 0.22% 47.58% 1250ms 5.36% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 47.58% 1190ms 5.10% NodeBasedCellPopulation::UpdateCellProcessLocation 33ms 0.14% 47.72% 1129ms 4.84% boost::numeric::ublas::vector_assign (inline) 5ms 0.021% 47.74% 1064ms 4.56% DistributedBoxCollection::CalculateBoundaryNodePairs 271ms 1.16% 48.90% 1044ms 4.47% boost::numeric::ublas::indexing_vector_assign 258ms 1.11% 50.01% 902ms 3.86% __dynamic_cast 379ms 1.62% 51.63% 811ms 3.47% DistributedBoxCollection::CalculateContainingBox (partial-inline) 17ms 0.073% 51.70% 788ms 3.38% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 209ms 0.9% 52.60% 774ms 3.32% NodeAttributes::AddNeighbour 152ms 0.65% 53.25% 760ms 3.26% AbstractMesh::GetVectorFromAtoB 0 0% 53.25% 728ms 3.12% AbstractCellPopulation::WriteResultsToFiles 0 0% 53.25% 726ms 3.11% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 53.25% 708ms 3.03% boost::numeric::ublas::norm_2 (inline) 562ms 2.41% 55.66% 708ms 3.03% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 55.66% 708ms 3.03% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 688ms 2.95% 58.61% 688ms 2.95% boost::numeric::ublas::c_vector::operator() 5ms 0.021% 58.63% 659ms 2.82% boost::numeric::ublas::c_vector::operator= (inline) 39ms 0.17% 58.79% 638ms 2.73% std::__copy_move::__copy_m (inline) 0 0% 58.79% 638ms 2.73% std::__copy_move_a (inline) 0 0% 58.79% 638ms 2.73% std::__copy_move_a1 (inline) 0 0% 58.79% 638ms 2.73% std::__copy_move_a2 (inline) 0 0% 58.79% 638ms 2.73% std::copy (inline) 564ms 2.42% 61.21% 638ms 2.73% std::vector::push_back (inline) 616ms 2.64% 63.85% 616ms 2.64% __memcpy_avx_unaligned_erms 4ms 0.017% 63.87% 553ms 2.37% AbstractCellBasedSimulation::DoCellBirth 43ms 0.18% 64.05% 535ms 2.29% std::_Rb_tree_const_iterator::operator++ (inline) 5ms 0.021% 64.07% 530ms 2.27% CellPropertyCollection::GetPropertiesType (inline) 4ms 0.017% 64.09% 525ms 2.25% AbstractCentreBasedCellPopulation::GetDampingConstant 232ms 0.99% 65.08% 518ms 2.22% __cxxabiv1::__si_class_type_info::__do_dyncast 52ms 0.22% 65.31% 511ms 2.19% std::__new_allocator::allocate (inline) 26ms 0.11% 65.42% 510ms 2.18% boost::detail::shared_count::~shared_count (inline) 0 0% 65.42% 510ms 2.18% boost::shared_ptr::~shared_ptr (inline) 508ms 2.18% 67.59% 508ms 2.18% boost::numeric::ublas::same_impl_ex 0 0% 67.59% 492ms 2.11% std::allocator_traits::allocate (inline) 489ms 2.10% 69.69% 489ms 2.10% std::_Rb_tree_increment 2ms 0.0086% 69.70% 477ms 2.04% NodeBasedCellPopulation::WriteVtkResultsToFile 466ms 2.00% 71.69% 472ms 2.02% boost::detail::sp_counted_base::release 461ms 1.98% 73.67% 461ms 1.98% __strcmp_avx2 32ms 0.14% 73.81% 461ms 1.98% operator new 0 0% 73.81% 460ms 1.97% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 73.81% 448ms 1.92% std::_Rb_tree::_M_create_node (inline) 5ms 0.021% 73.83% 447ms 1.92% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 18ms 0.077% 73.90% 436ms 1.87% std::_Rb_tree::_Rb_tree (partial-inline) 134ms 0.57% 74.48% 425ms 1.82% __GI___libc_malloc 41ms 0.18% 74.65% 403ms 1.73% std::_Rb_tree::_M_copy (inline) 0 0% 74.65% 403ms 1.73% std::_Rb_tree::_M_get_node (inline) 126ms 0.54% 75.19% 393ms 1.68% std::_Rb_tree::_M_erase 155ms 0.66% 75.86% 387ms 1.66% Node::GetRadius 2ms 0.0086% 75.87% 376ms 1.61% AbstractCellProperty::IsSubType (inline) 4ms 0.017% 75.88% 360ms 1.54% Cell::GetMutationState 116ms 0.5% 76.38% 356ms 1.53% std::_Rb_tree::_M_clone_node (inline) 0 0% 76.38% 346ms 1.48% std::set::set (inline) 0 0% 76.38% 342ms 1.47% boost::numeric::ublas::inner_prod (inline) 2ms 0.0086% 76.39% 342ms 1.47% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 27ms 0.12% 76.50% 340ms 1.46% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 76.50% 331ms 1.42% boost::numeric::ublas::c_vector::assign (inline) 0 0% 76.50% 325ms 1.39% NodesOnlyMesh::ReMesh 3ms 0.013% 76.52% 321ms 1.38% NodesOnlyMesh::UpdateNodeIndices 21ms 0.09% 76.61% 319ms 1.37% boost::numeric::ublas::vector_binary::size (inline) 313ms 1.34% 77.95% 313ms 1.34% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 311ms 1.33% 79.28% 311ms 1.33% __gnu_cxx::__normal_iterator::operator++ (inline) 6ms 0.026% 79.31% 309ms 1.32% NodeBasedCellPopulation::UpdateMapsAfterRemesh 30ms 0.13% 79.44% 305ms 1.31% std::_Rb_tree::~_Rb_tree (inline) 5ms 0.021% 79.46% 299ms 1.28% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 8ms 0.034% 79.49% 292ms 1.25% std::_Rb_tree::_M_emplace_hint_unique 0 0% 79.49% 287ms 1.23% std::_Rb_tree::_Alloc_node::operator() (inline) 3ms 0.013% 79.50% 281ms 1.20% DistributedBoxCollection::GetProcessOwningNode 0 0% 79.50% 268ms 1.15% std::_Rb_tree::_M_drop_node (inline) 106ms 0.45% 79.96% 267ms 1.14% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 79.96% 245ms 1.05% NodesOnlyMesh::UpdateBoxCollection 241ms 1.03% 80.99% 241ms 1.03% Node::CheckForNodeAttributes 146ms 0.63% 81.62% 239ms 1.02% _int_malloc 0 0% 81.62% 236ms 1.01% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 81.62% 234ms 1.00% VtkMeshWriter::WriteFiles 111ms 0.48% 82.09% 231ms 0.99% std::__move_median_to_first (inline) 0 0% 82.09% 223ms 0.96% std::set::~set (inline) 5ms 0.021% 82.11% 216ms 0.93% std::__new_allocator::deallocate (inline) 0 0% 82.11% 209ms 0.9% NodesOnlyMesh::AddNodesToBoxes 204ms 0.87% 82.99% 204ms 0.87% [libchaste_cell_based.so] 0 0% 82.99% 203ms 0.87% vtkStreamingDemandDrivenPipeline::Update 0 0% 82.99% 203ms 0.87% vtkXMLWriterBase::Write 0 0% 82.99% 202ms 0.87% vtkDemandDrivenPipeline::ProcessRequest 0 0% 82.99% 202ms 0.87% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 82.99% 201ms 0.86% vtkCompositeDataPipeline::ExecuteData 0 0% 82.99% 201ms 0.86% vtkDemandDrivenPipeline::ExecuteData 0 0% 82.99% 201ms 0.86% vtkExecutive::CallAlgorithm 0 0% 82.99% 201ms 0.86% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 82.99% 198ms 0.85% std::allocator_traits::deallocate (inline) 3ms 0.013% 83.00% 196ms 0.84% CellPropertyCollection::HasProperty 0 0% 83.00% 195ms 0.84% Cell::HasCellProperty (inline) 0 0% 83.00% 195ms 0.84% NodesOnlyMesh::ResizeBoxCollection 0 0% 83.00% 195ms 0.84% std::_Rb_tree::_M_put_node (inline) 18ms 0.077% 83.08% 193ms 0.83% NodesOnlyMesh::IsANodeCloseToDomainBoundary 66ms 0.28% 83.36% 193ms 0.83% __GI___libc_free 15ms 0.064% 83.42% 192ms 0.82% std::__insertion_sort (inline) 99ms 0.42% 83.85% 190ms 0.81% boost::shared_ptr::shared_ptr (inline) 12ms 0.051% 83.90% 180ms 0.77% Cell::ReadyToDivide 179ms 0.77% 84.67% 179ms 0.77% Node::GetIndex 0 0% 84.67% 171ms 0.73% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 84.67% 171ms 0.73% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 1ms 0.0043% 84.67% 165ms 0.71% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 5ms 0.021% 84.69% 162ms 0.69% AbstractCellProperty::IsType (inline) 0 0% 84.69% 161ms 0.69% std::_Rb_tree::_Auto_node::_Auto_node (inline) 155ms 0.66% 85.36% 158ms 0.68% std::__adjacent_find (inline) 0 0% 85.36% 158ms 0.68% std::__unique (inline) 0 0% 85.36% 158ms 0.68% std::unique (inline) 89ms 0.38% 85.74% 157ms 0.67% Node::AddNeighbour 15ms 0.064% 85.80% 149ms 0.64% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 85.80% 142ms 0.61% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 141ms 0.6% 86.41% 141ms 0.6% boost::shared_ptr::operator-> (inline) 140ms 0.6% 87.01% 140ms 0.6% [libchaste_mesh.so] 0 0% 87.01% 138ms 0.59% std::_Rb_tree::clear (inline) 2ms 0.0086% 87.01% 137ms 0.59% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 87.01% 135ms 0.58% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 12ms 0.051% 87.07% 134ms 0.57% DistributedBoxCollection::GetIsPeriodicAllDims 0 0% 87.07% 134ms 0.57% vtkXMLWriter::WriteBinaryData 133ms 0.57% 87.64% 133ms 0.57% Node::IsDeleted 0 0% 87.64% 130ms 0.56% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.64% 129ms 0.55% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.64% 129ms 0.55% vtkXMLWriter::WriteCompressionBlock 37ms 0.16% 87.79% 128ms 0.55% AbstractCellProperty::IsSame 120ms 0.51% 88.31% 127ms 0.54% _int_free 0 0% 88.31% 127ms 0.54% boost::numeric::ublas::vector_binary::operator() (inline) 126ms 0.54% 88.85% 126ms 0.54% __ieee754_log_fma 3ms 0.013% 88.86% 125ms 0.54% AbstractCellPopulation::SetCellUsingLocationIndex 0 0% 88.86% 123ms 0.53% vtkXMLWriter::WritePointsAppendedData 2ms 0.0086% 88.87% 121ms 0.52% Cell::GetCellId 4ms 0.017% 88.89% 121ms 0.52% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 88.89% 121ms 0.52% tbb::detail::r1::parallel_pipeline 4ms 0.017% 88.90% 118ms 0.51% NodeBasedCellPopulation::SetNode