File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 21079ms, 88.28% of 23877ms total Dropped 775 nodes (cum <= 119.39ms) flat flat% sum% cum cum% 0 0% 0% 23736ms 99.41% __libc_start_call_main 0 0% 0% 23736ms 99.41% __libc_start_main_impl 0 0% 0% 23736ms 99.41% _start 0 0% 0% 23720ms 99.34% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 23720ms 99.34% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 23720ms 99.34% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 23720ms 99.34% main 0 0% 0% 23684ms 99.19% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 23684ms 99.19% CxxTest::TestRunner::runTest (inline) 0 0% 0% 23684ms 99.19% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 23676ms 99.16% AbstractCellBasedSimulation::Solve 2ms 0.0084% 0.0084% 13495ms 56.52% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0084% 8940ms 37.44% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.017% 0.025% 8685ms 36.37% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.017% 0.042% 8491ms 35.56% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.042% 7875ms 32.98% NodeBasedCellPopulation::Update 1243ms 5.21% 5.25% 7776ms 32.57% RepulsionForce::AddForceContribution (partial-inline) 11ms 0.046% 5.29% 5838ms 24.45% DistributedBoxCollection::CalculateInteriorNodePairs 2107ms 8.82% 14.12% 4947ms 20.72% std::_Rb_tree::_M_lower_bound (inline) 18ms 0.075% 14.19% 4499ms 18.84% NodeAttributes::RemoveDuplicateNeighbours 0 0% 14.19% 4479ms 18.76% OffLatticeSimulation::ApplyBoundaries 6ms 0.025% 14.22% 4344ms 18.19% std::__sort (inline) 0 0% 14.22% 4344ms 18.19% std::sort (inline) 196ms 0.82% 15.04% 3874ms 16.22% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 4ms 0.017% 15.06% 3408ms 14.27% AbstractCellPopulation::Iterator::operator++ (inline) 191ms 0.8% 15.86% 3381ms 14.16% AbstractCellPopulation::Iterator::IsRealCell 73ms 0.31% 16.16% 3378ms 14.15% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 246ms 1.03% 17.19% 3226ms 13.51% std::_Rb_tree::find (inline) 0 0% 17.19% 3226ms 13.51% std::map::find (inline) 19ms 0.08% 17.27% 2883ms 12.07% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2805ms 11.75% 29.02% 2805ms 11.75% std::_Rb_tree::_S_right (inline) 225ms 0.94% 29.96% 2492ms 10.44% std::map::operator[] (partial-inline) 185ms 0.77% 30.74% 2489ms 10.42% std::__introsort_loop 32ms 0.13% 30.87% 2320ms 9.72% PlaneBoundaryCondition::ImposeBoundaryCondition 138ms 0.58% 31.45% 2316ms 9.70% AbstractMesh::GetNode 60ms 0.25% 31.70% 2292ms 9.60% NodesOnlyMesh::GetNodeOrHaloNode 0 0% 31.70% 2235ms 9.36% std::__unguarded_partition_pivot (inline) 32ms 0.13% 31.83% 2208ms 9.25% AbstractCellPopulation::GetLocationIndexUsingCell 107ms 0.45% 32.28% 2184ms 9.15% NodesOnlyMesh::SolveNodeMapping 27ms 0.11% 32.40% 2159ms 9.04% PlaneBoundaryCondition::VerifyBoundaryCondition 1040ms 4.36% 36.75% 1996ms 8.36% std::__unguarded_partition (inline) 0 0% 36.75% 1984ms 8.31% std::_Rb_tree::lower_bound (inline) 0 0% 36.75% 1984ms 8.31% std::map::lower_bound (inline) 172ms 0.72% 37.47% 1966ms 8.23% DistributedBoxCollection::AddPairsFromBox 2ms 0.0084% 37.48% 1847ms 7.74% std::__final_insertion_sort (inline) 92ms 0.39% 37.86% 1634ms 6.84% std::__unguarded_insertion_sort (inline) 18ms 0.075% 37.94% 1621ms 6.79% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 31ms 0.13% 38.07% 1593ms 6.67% AbstractCellPopulation::GetCellUsingLocationIndex 550ms 2.30% 40.37% 1593ms 6.67% std::__unguarded_linear_insert (inline) 1474ms 6.17% 46.55% 1474ms 6.17% __gnu_cxx::__normal_iterator::operator-- (inline) 55ms 0.23% 46.78% 1301ms 5.45% boost::numeric::ublas::c_vector::c_vector (partial-inline) 39ms 0.16% 46.94% 1188ms 4.98% boost::numeric::ublas::vector_assign (inline) 0 0% 46.94% 1169ms 4.90% NodeBasedCellPopulation::UpdateCellProcessLocation 281ms 1.18% 48.12% 1084ms 4.54% boost::numeric::ublas::indexing_vector_assign 6ms 0.025% 48.14% 1070ms 4.48% DistributedBoxCollection::CalculateBoundaryNodePairs 248ms 1.04% 49.18% 963ms 4.03% __dynamic_cast 159ms 0.67% 49.85% 832ms 3.48% AbstractMesh::GetVectorFromAtoB 22ms 0.092% 49.94% 791ms 3.31% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 345ms 1.44% 51.38% 767ms 3.21% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 51.38% 749ms 3.14% AbstractCellPopulation::WriteResultsToFiles 0 0% 51.38% 744ms 3.12% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 51.38% 727ms 3.04% boost::numeric::ublas::norm_2 (inline) 552ms 2.31% 53.70% 727ms 3.04% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 53.70% 727ms 3.04% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 203ms 0.85% 54.55% 702ms 2.94% NodeAttributes::AddNeighbour 664ms 2.78% 57.33% 664ms 2.78% boost::numeric::ublas::c_vector::operator() 40ms 0.17% 57.49% 663ms 2.78% std::_Rb_tree_const_iterator::operator++ (inline) 13ms 0.054% 57.55% 646ms 2.71% CellPropertyCollection::GetPropertiesType (inline) 2ms 0.0084% 57.56% 642ms 2.69% AbstractCentreBasedCellPopulation::GetDampingConstant 3ms 0.013% 57.57% 639ms 2.68% AbstractCellBasedSimulation::DoCellBirth 5ms 0.021% 57.59% 630ms 2.64% boost::numeric::ublas::c_vector::operator= (inline) 620ms 2.60% 60.19% 620ms 2.60% std::_Rb_tree_increment 42ms 0.18% 60.36% 607ms 2.54% std::__copy_move::__copy_m (inline) 0 0% 60.36% 607ms 2.54% std::__copy_move_a (inline) 0 0% 60.36% 607ms 2.54% std::__copy_move_a1 (inline) 0 0% 60.36% 607ms 2.54% std::__copy_move_a2 (inline) 0 0% 60.36% 607ms 2.54% std::copy (inline) 299ms 1.25% 61.62% 586ms 2.45% __cxxabiv1::__si_class_type_info::__do_dyncast 584ms 2.45% 64.06% 584ms 2.45% __memcpy_avx_unaligned_erms 496ms 2.08% 66.14% 564ms 2.36% std::vector::push_back (inline) 544ms 2.28% 68.42% 544ms 2.28% boost::numeric::ublas::same_impl_ex 73ms 0.31% 68.72% 542ms 2.27% std::__new_allocator::allocate (inline) 0 0% 68.72% 529ms 2.22% std::allocator_traits::allocate (inline) 36ms 0.15% 68.87% 512ms 2.14% boost::detail::shared_count::~shared_count (inline) 0 0% 68.87% 512ms 2.14% boost::shared_ptr::~shared_ptr (inline) 29ms 0.12% 69.00% 504ms 2.11% std::_Rb_tree::_Rb_tree (partial-inline) 2ms 0.0084% 69.00% 495ms 2.07% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 69.00% 491ms 2.06% std::_Rb_tree::_M_create_node (inline) 470ms 1.97% 70.97% 470ms 1.97% __strcmp_avx2 458ms 1.92% 72.89% 466ms 1.95% boost::detail::sp_counted_base::release 24ms 0.1% 72.99% 466ms 1.95% operator new 48ms 0.2% 73.19% 463ms 1.94% std::_Rb_tree::_M_copy (inline) 3ms 0.013% 73.20% 451ms 1.89% Cell::GetMutationState 4ms 0.017% 73.22% 437ms 1.83% AbstractCellProperty::IsSubType (inline) 117ms 0.49% 73.71% 434ms 1.82% __GI___libc_malloc 136ms 0.57% 74.28% 432ms 1.81% Node::GetRadius 0 0% 74.28% 426ms 1.78% std::_Rb_tree::_M_get_node (inline) 0 0% 74.28% 425ms 1.78% AbstractCellBasedSimulation::DoCellRemoval (inline) 3ms 0.013% 74.29% 415ms 1.74% std::set::set (inline) 130ms 0.54% 74.84% 413ms 1.73% std::_Rb_tree::_M_clone_node (inline) 11ms 0.046% 74.88% 407ms 1.70% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 133ms 0.56% 75.44% 383ms 1.60% std::_Rb_tree::_M_erase 34ms 0.14% 75.58% 351ms 1.47% boost::numeric::ublas::vector_binary::size (inline) 2ms 0.0084% 75.59% 342ms 1.43% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 75.59% 333ms 1.39% std::_Rb_tree::_Alloc_node::operator() (inline) 331ms 1.39% 76.98% 331ms 1.39% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 76.98% 314ms 1.32% boost::numeric::ublas::c_vector::assign (inline) 0 0% 76.98% 313ms 1.31% boost::numeric::ublas::inner_prod (inline) 14ms 0.059% 77.04% 312ms 1.31% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 77.04% 312ms 1.31% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 311ms 1.30% 78.34% 311ms 1.30% Node::CheckForNodeAttributes 307ms 1.29% 79.62% 307ms 1.29% __gnu_cxx::__normal_iterator::operator++ (inline) 41ms 0.17% 79.80% 294ms 1.23% std::_Rb_tree::~_Rb_tree (inline) 10ms 0.042% 79.84% 283ms 1.19% std::_Rb_tree::_M_emplace_hint_unique 3ms 0.013% 79.85% 277ms 1.16% CellPropertyCollection::HasProperty 4ms 0.017% 79.87% 277ms 1.16% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 79.87% 276ms 1.16% Cell::HasCellProperty (inline) 0 0% 79.87% 274ms 1.15% NodesOnlyMesh::ReMesh 0 0% 79.87% 270ms 1.13% NodesOnlyMesh::UpdateBoxCollection 146ms 0.61% 80.48% 268ms 1.12% _int_malloc 5ms 0.021% 80.50% 265ms 1.11% DistributedBoxCollection::GetProcessOwningNode 2ms 0.0084% 80.51% 264ms 1.11% NodesOnlyMesh::UpdateNodeIndices 80ms 0.34% 80.84% 262ms 1.10% Node::AddNeighbour 10ms 0.042% 80.89% 255ms 1.07% Cell::ReadyToDivide 114ms 0.48% 81.36% 255ms 1.07% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 81.36% 238ms 1% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 100ms 0.42% 81.78% 236ms 0.99% std::__move_median_to_first (inline) 0 0% 81.78% 235ms 0.98% std::_Rb_tree::_M_drop_node (inline) 0 0% 81.78% 234ms 0.98% VtkMeshWriter::WriteFiles 3ms 0.013% 81.79% 223ms 0.93% NodesOnlyMesh::AddNodesToBoxes 8ms 0.034% 81.83% 222ms 0.93% AbstractCellProperty::IsType (inline) 214ms 0.9% 82.72% 214ms 0.9% [libchaste_cell_based.so] 0 0% 82.72% 213ms 0.89% vtkStreamingDemandDrivenPipeline::Update 0 0% 82.72% 213ms 0.89% vtkXMLWriterBase::Write 1ms 0.0042% 82.73% 212ms 0.89% vtkDemandDrivenPipeline::ProcessRequest 21ms 0.088% 82.82% 211ms 0.88% std::__insertion_sort (inline) 210ms 0.88% 83.70% 210ms 0.88% Node::ConstructNodeAttributes (inline) 2ms 0.0084% 83.70% 210ms 0.88% std::__new_allocator::deallocate (inline) 0 0% 83.70% 209ms 0.88% vtkExecutive::CallAlgorithm 0 0% 83.70% 208ms 0.87% vtkDemandDrivenPipeline::ExecuteData 0 0% 83.70% 208ms 0.87% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 83.70% 207ms 0.87% vtkCompositeDataPipeline::ExecuteData 0 0% 83.70% 207ms 0.87% vtkXMLUnstructuredDataWriter::ProcessRequest 201ms 0.84% 84.55% 201ms 0.84% Node::GetIndex 0 0% 84.55% 201ms 0.84% NodesOnlyMesh::ResizeBoxCollection 15ms 0.063% 84.61% 200ms 0.84% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 84.61% 193ms 0.81% std::set::~set (inline) 73ms 0.31% 84.91% 191ms 0.8% __GI___libc_free 0 0% 84.91% 185ms 0.77% std::allocator_traits::deallocate (inline) 88ms 0.37% 85.28% 183ms 0.77% boost::shared_ptr::shared_ptr (inline) 0 0% 85.28% 183ms 0.77% std::_Rb_tree::_M_put_node (inline) 0 0% 85.28% 178ms 0.75% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.28% 178ms 0.75% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 85.28% 171ms 0.72% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 48ms 0.2% 85.48% 164ms 0.69% AbstractCellProperty::IsSame 0 0% 85.48% 158ms 0.66% std::_Rb_tree::_Auto_node::_Auto_node (inline) 3ms 0.013% 85.50% 155ms 0.65% AbstractCellPopulation::SetCellUsingLocationIndex 0 0% 85.50% 153ms 0.64% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 151ms 0.63% 86.13% 151ms 0.63% boost::shared_ptr::operator-> (inline) 149ms 0.62% 86.75% 149ms 0.62% [libchaste_mesh.so] 5ms 0.021% 86.77% 147ms 0.62% boost::numeric::ublas::c_vector::operator[] (inline) 146ms 0.61% 87.39% 146ms 0.61% Node::IsDeleted 0 0% 87.39% 145ms 0.61% std::_Rb_tree::clear (inline) 1ms 0.0042% 87.39% 142ms 0.59% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 71ms 0.3% 87.69% 140ms 0.59% NodeAttributes::AddAppliedForceContribution 4ms 0.017% 87.70% 137ms 0.57% AbstractNumericalMethod::SafeNodePositionUpdate 6ms 0.025% 87.73% 137ms 0.57% DistributedBoxCollection::GetIsPeriodicAllDims 9ms 0.038% 87.77% 137ms 0.57% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 87.77% 135ms 0.57% Cell::GetCellId 0 0% 87.77% 133ms 0.56% vtkXMLWriter::WriteBinaryData 0 0% 87.77% 128ms 0.54% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 87.77% 127ms 0.53% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.77% 127ms 0.53% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.77% 127ms 0.53% vtkXMLWriter::WriteCompressionBlock 121ms 0.51% 88.27% 125ms 0.52% std::__adjacent_find (inline) 0 0% 88.27% 125ms 0.52% std::__unique (inline) 0 0% 88.27% 125ms 0.52% std::unique (inline) 2ms 0.0084% 88.28% 123ms 0.52% NodeBasedCellPopulation::SetNode 0 0% 88.28% 120ms 0.5% vtkXMLWriter::WritePointsAppendedData