File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20416ms, 88.36% of 23106ms total Dropped 726 nodes (cum <= 115.53ms) flat flat% sum% cum cum% 0 0% 0% 22956ms 99.35% __libc_start_call_main 0 0% 0% 22956ms 99.35% __libc_start_main_impl 0 0% 0% 22956ms 99.35% _start 0 0% 0% 22941ms 99.29% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 22941ms 99.29% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 22941ms 99.29% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 22941ms 99.29% main 0 0% 0% 22899ms 99.10% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 22899ms 99.10% CxxTest::TestRunner::runTest (inline) 0 0% 0% 22898ms 99.10% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 22890ms 99.07% AbstractCellBasedSimulation::Solve 3ms 0.013% 0.013% 13064ms 56.54% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.013% 8637ms 37.38% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0043% 0.017% 8273ms 35.80% ForwardEulerNumericalMethod::UpdateAllNodePositions 9ms 0.039% 0.056% 8073ms 34.94% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.056% 7640ms 33.07% NodeBasedCellPopulation::Update 1194ms 5.17% 5.22% 7489ms 32.41% RepulsionForce::AddForceContribution (partial-inline) 6ms 0.026% 5.25% 5609ms 24.28% DistributedBoxCollection::CalculateInteriorNodePairs 2079ms 9.00% 14.25% 5016ms 21.71% std::_Rb_tree::_M_lower_bound (inline) 2ms 0.0087% 14.26% 4530ms 19.61% OffLatticeSimulation::ApplyBoundaries 9ms 0.039% 14.29% 4476ms 19.37% NodeAttributes::RemoveDuplicateNeighbours 6ms 0.026% 14.32% 4293ms 18.58% std::__sort (inline) 0 0% 14.32% 4293ms 18.58% std::sort (inline) 190ms 0.82% 15.14% 3771ms 16.32% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 7ms 0.03% 15.17% 3477ms 15.05% AbstractCellPopulation::Iterator::operator++ (inline) 188ms 0.81% 15.99% 3439ms 14.88% AbstractCellPopulation::Iterator::IsRealCell (inline) 76ms 0.33% 16.32% 3405ms 14.74% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 228ms 0.99% 17.30% 3297ms 14.27% std::_Rb_tree::find (inline) 0 0% 17.30% 3297ms 14.27% std::map::find (inline) 25ms 0.11% 17.41% 2912ms 12.60% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2906ms 12.58% 29.99% 2906ms 12.58% std::_Rb_tree::_S_right (inline) 174ms 0.75% 30.74% 2464ms 10.66% std::__introsort_loop 225ms 0.97% 31.71% 2445ms 10.58% std::map::operator[] (partial-inline) 24ms 0.1% 31.82% 2338ms 10.12% PlaneBoundaryCondition::ImposeBoundaryCondition 104ms 0.45% 32.27% 2311ms 10.00% AbstractMesh::GetNode 54ms 0.23% 32.50% 2303ms 9.97% NodesOnlyMesh::GetNodeOrHaloNode 27ms 0.12% 32.62% 2251ms 9.74% AbstractCellPopulation::GetLocationIndexUsingCell 80ms 0.35% 32.97% 2212ms 9.57% NodesOnlyMesh::SolveNodeMapping 1ms 0.0043% 32.97% 2204ms 9.54% std::__unguarded_partition_pivot (inline) 16ms 0.069% 33.04% 2190ms 9.48% PlaneBoundaryCondition::VerifyBoundaryCondition 1032ms 4.47% 37.51% 2000ms 8.66% std::__unguarded_partition (inline) 0 0% 37.51% 1974ms 8.54% std::_Rb_tree::lower_bound (inline) 0 0% 37.51% 1974ms 8.54% std::map::lower_bound (inline) 3ms 0.013% 37.52% 1822ms 7.89% std::__final_insertion_sort (inline) 164ms 0.71% 38.23% 1766ms 7.64% DistributedBoxCollection::AddPairsFromBox 92ms 0.4% 38.63% 1626ms 7.04% std::__unguarded_insertion_sort (inline) 18ms 0.078% 38.70% 1588ms 6.87% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 35ms 0.15% 38.86% 1566ms 6.78% AbstractCellPopulation::GetCellUsingLocationIndex 587ms 2.54% 41.40% 1558ms 6.74% std::__unguarded_linear_insert (inline) 1445ms 6.25% 47.65% 1445ms 6.25% __gnu_cxx::__normal_iterator::operator-- (inline) 58ms 0.25% 47.90% 1244ms 5.38% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 47.90% 1160ms 5.02% NodeBasedCellPopulation::UpdateCellProcessLocation 35ms 0.15% 48.05% 1108ms 4.80% boost::numeric::ublas::vector_assign (inline) 6ms 0.026% 48.08% 1074ms 4.65% DistributedBoxCollection::CalculateBoundaryNodePairs 271ms 1.17% 49.25% 985ms 4.26% boost::numeric::ublas::indexing_vector_assign 262ms 1.13% 50.39% 902ms 3.90% __dynamic_cast 0 0% 50.39% 825ms 3.57% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 50.39% 801ms 3.47% boost::numeric::ublas::norm_2 (inline) 649ms 2.81% 53.19% 801ms 3.47% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 53.19% 801ms 3.47% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 22ms 0.095% 53.29% 799ms 3.46% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 380ms 1.64% 54.93% 772ms 3.34% DistributedBoxCollection::CalculateContainingBox (partial-inline) 172ms 0.74% 55.68% 744ms 3.22% AbstractMesh::GetVectorFromAtoB 0 0% 55.68% 704ms 3.05% AbstractCellPopulation::WriteResultsToFiles 6ms 0.026% 55.70% 698ms 3.02% boost::numeric::ublas::c_vector::operator= (inline) 38ms 0.16% 55.87% 681ms 2.95% std::__copy_move::__copy_m (inline) 0 0% 55.87% 681ms 2.95% std::__copy_move_a (inline) 0 0% 55.87% 681ms 2.95% std::__copy_move_a1 (inline) 0 0% 55.87% 681ms 2.95% std::__copy_move_a2 (inline) 0 0% 55.87% 681ms 2.95% std::copy (inline) 668ms 2.89% 58.76% 668ms 2.89% __memcpy_avx_unaligned_erms 198ms 0.86% 59.62% 667ms 2.89% NodeAttributes::AddNeighbour 648ms 2.80% 62.42% 648ms 2.80% boost::numeric::ublas::c_vector::operator() 5ms 0.022% 62.44% 566ms 2.45% AbstractCellBasedSimulation::DoCellBirth 468ms 2.03% 64.47% 544ms 2.35% std::vector::push_back (inline) 3ms 0.013% 64.48% 530ms 2.29% CellPropertyCollection::GetPropertiesType (inline) 233ms 1.01% 65.49% 525ms 2.27% __cxxabiv1::__si_class_type_info::__do_dyncast 30ms 0.13% 65.62% 514ms 2.22% boost::detail::shared_count::~shared_count (inline) 0 0% 65.62% 514ms 2.22% boost::shared_ptr::~shared_ptr (inline) 1ms 0.0043% 65.62% 511ms 2.21% AbstractCentreBasedCellPopulation::GetDampingConstant 61ms 0.26% 65.89% 508ms 2.20% std::__new_allocator::allocate (inline) 0 0% 65.89% 495ms 2.14% std::allocator_traits::allocate (inline) 487ms 2.11% 68.00% 487ms 2.11% boost::numeric::ublas::same_impl_ex 27ms 0.12% 68.11% 485ms 2.10% std::_Rb_tree_const_iterator::operator++ (inline) 473ms 2.05% 70.16% 475ms 2.06% boost::detail::sp_counted_base::release 2ms 0.0087% 70.17% 453ms 1.96% NodeBasedCellPopulation::WriteVtkResultsToFile 24ms 0.1% 70.27% 446ms 1.93% std::_Rb_tree::_Rb_tree (partial-inline) 444ms 1.92% 72.19% 444ms 1.92% __strcmp_avx2 34ms 0.15% 72.34% 444ms 1.92% operator new 0 0% 72.34% 440ms 1.90% std::_Rb_tree::_M_create_node (inline) 436ms 1.89% 74.23% 436ms 1.89% std::_Rb_tree_increment 0 0% 74.23% 429ms 1.86% AbstractCellBasedSimulation::DoCellRemoval (inline) 6ms 0.026% 74.25% 417ms 1.80% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 43ms 0.19% 74.44% 414ms 1.79% std::_Rb_tree::_M_copy (inline) 2ms 0.0087% 74.45% 413ms 1.79% AbstractCellProperty::IsSubType (inline) 0 0% 74.45% 405ms 1.75% std::_Rb_tree::_M_get_node (inline) 131ms 0.57% 75.02% 404ms 1.75% Node::GetRadius 118ms 0.51% 75.53% 404ms 1.75% __GI___libc_malloc 119ms 0.52% 76.04% 375ms 1.62% std::_Rb_tree::_M_erase 132ms 0.57% 76.61% 369ms 1.60% std::_Rb_tree::_M_clone_node (inline) 5ms 0.022% 76.63% 363ms 1.57% std::set::set (inline) 2ms 0.0087% 76.64% 346ms 1.50% Cell::GetMutationState 0 0% 76.64% 338ms 1.46% boost::numeric::ublas::c_vector::assign (inline) 0 0% 76.64% 329ms 1.42% boost::numeric::ublas::inner_prod (inline) 4ms 0.017% 76.66% 329ms 1.42% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 17ms 0.074% 76.73% 325ms 1.41% boost::numeric::ublas::vector_scalar_binary::evaluate 317ms 1.37% 78.11% 317ms 1.37% __gnu_cxx::__normal_iterator::operator++ (inline) 9ms 0.039% 78.14% 314ms 1.36% NodeBasedCellPopulation::UpdateMapsAfterRemesh 308ms 1.33% 79.48% 308ms 1.33% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 49ms 0.21% 79.69% 307ms 1.33% std::_Rb_tree::~_Rb_tree (inline) 0 0% 79.69% 306ms 1.32% std::_Rb_tree::_Alloc_node::operator() (inline) 16ms 0.069% 79.76% 296ms 1.28% boost::numeric::ublas::vector_binary::size (inline) 280ms 1.21% 80.97% 280ms 1.21% Node::CheckForNodeAttributes 0 0% 80.97% 279ms 1.21% NodesOnlyMesh::ReMesh 0 0% 80.97% 276ms 1.19% NodesOnlyMesh::UpdateBoxCollection 1ms 0.0043% 80.97% 271ms 1.17% NodesOnlyMesh::UpdateNodeIndices 4ms 0.017% 80.99% 270ms 1.17% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 96ms 0.42% 81.41% 264ms 1.14% boost::numeric::ublas::vector_inner_prod::apply (inline) 2ms 0.0087% 81.42% 254ms 1.10% DistributedBoxCollection::GetProcessOwningNode 7ms 0.03% 81.45% 246ms 1.06% std::_Rb_tree::_M_emplace_hint_unique 0 0% 81.45% 242ms 1.05% std::_Rb_tree::_M_drop_node (inline) 140ms 0.61% 82.05% 238ms 1.03% _int_malloc 0 0% 82.05% 236ms 1.02% NodesOnlyMesh::AddNodesToBoxes 0 0% 82.05% 228ms 0.99% std::set::~set (inline) 0 0% 82.05% 223ms 0.97% NodesOnlyMesh::ResizeBoxCollection 15ms 0.065% 82.12% 222ms 0.96% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 82.12% 217ms 0.94% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 82.12% 216ms 0.93% VtkMeshWriter::WriteFiles 4ms 0.017% 82.13% 210ms 0.91% std::__new_allocator::deallocate (inline) 0 0% 82.13% 199ms 0.86% vtkDemandDrivenPipeline::ProcessRequest 0 0% 82.13% 199ms 0.86% vtkStreamingDemandDrivenPipeline::Update 0 0% 82.13% 199ms 0.86% vtkXMLWriterBase::Write 91ms 0.39% 82.53% 198ms 0.86% std::__move_median_to_first (inline) 0 0% 82.53% 197ms 0.85% vtkCompositeDataPipeline::ExecuteData 0 0% 82.53% 197ms 0.85% vtkDemandDrivenPipeline::ExecuteData 0 0% 82.53% 197ms 0.85% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 82.53% 196ms 0.85% vtkExecutive::CallAlgorithm 0 0% 82.53% 195ms 0.84% vtkXMLUnstructuredDataWriter::ProcessRequest 17ms 0.074% 82.60% 193ms 0.84% std::__insertion_sort (inline) 188ms 0.81% 83.42% 188ms 0.81% Node::GetIndex 122ms 0.53% 83.94% 181ms 0.78% Node::AddNeighbour 0 0% 83.94% 180ms 0.78% std::allocator_traits::deallocate (inline) 177ms 0.77% 84.71% 177ms 0.77% [libchaste_cell_based.so] 89ms 0.39% 85.09% 177ms 0.77% boost::shared_ptr::shared_ptr (inline) 57ms 0.25% 85.34% 176ms 0.76% __GI___libc_free 0 0% 85.34% 175ms 0.76% std::_Rb_tree::_M_put_node (inline) 0 0% 85.34% 170ms 0.74% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.34% 170ms 0.74% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 85.34% 168ms 0.73% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 85.34% 166ms 0.72% Cell::HasCellProperty (inline) 2ms 0.0087% 85.35% 166ms 0.72% CellPropertyCollection::HasProperty 4ms 0.017% 85.37% 154ms 0.67% DistributedBoxCollection::GetIsPeriodicAllDims 153ms 0.66% 86.03% 154ms 0.67% std::__adjacent_find (inline) 0 0% 86.03% 154ms 0.67% std::__unique (inline) 0 0% 86.03% 154ms 0.67% std::unique (inline) 6ms 0.026% 86.06% 151ms 0.65% Cell::ReadyToDivide 12ms 0.052% 86.11% 146ms 0.63% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 86.11% 145ms 0.63% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 86.11% 142ms 0.61% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 86.11% 140ms 0.61% vtkXMLWriter::WriteBinaryData 139ms 0.6% 86.71% 139ms 0.6% Node::IsDeleted 138ms 0.6% 87.31% 138ms 0.6% [libchaste_mesh.so] 0 0% 87.31% 137ms 0.59% vtkXMLWriter::WriteBinaryDataInternal 6ms 0.026% 87.33% 135ms 0.58% AbstractCellProperty::IsType (inline) 0 0% 87.33% 135ms 0.58% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.33% 135ms 0.58% vtkXMLWriter::WriteCompressionBlock 0 0% 87.33% 134ms 0.58% std::_Rb_tree::_Auto_node::_Auto_node (inline) 2ms 0.0087% 87.34% 133ms 0.58% std::_Rb_tree::_M_insert_unique 0 0% 87.34% 133ms 0.58% std::set::insert (inline) 4ms 0.017% 87.36% 131ms 0.57% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 87.36% 131ms 0.57% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 87.36% 127ms 0.55% std::_Rb_tree::clear (inline) 0 0% 87.36% 124ms 0.54% vtkXMLWriter::WritePointsAppendedData 1ms 0.0043% 87.36% 123ms 0.53% AbstractCellPopulation::SetCellUsingLocationIndex 1ms 0.0043% 87.37% 119ms 0.52% Cell::GetCellId 3ms 0.013% 87.38% 118ms 0.51% NodeBasedCellPopulation::SetNode 108ms 0.47% 87.85% 118ms 0.51% _int_free 118ms 0.51% 88.36% 118ms 0.51% boost::shared_ptr::operator-> (inline) 0 0% 88.36% 116ms 0.5% tbb::detail::r1::parallel_pipeline