File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 19953ms, 88.85% of 22457ms total Dropped 766 nodes (cum <= 112.28ms) flat flat% sum% cum cum% 0 0% 0% 22307ms 99.33% __libc_start_call_main 0 0% 0% 22307ms 99.33% __libc_start_main_impl 0 0% 0% 22307ms 99.33% _start 0 0% 0% 22291ms 99.26% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 22291ms 99.26% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 22291ms 99.26% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 22291ms 99.26% main 0 0% 0% 22252ms 99.09% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 22252ms 99.09% CxxTest::TestRunner::runTest (inline) 0 0% 0% 22252ms 99.09% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 22244ms 99.05% AbstractCellBasedSimulation::Solve 1ms 0.0045% 0.0045% 12418ms 55.30% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0045% 8596ms 38.28% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.0045% 7682ms 34.21% NodeBasedCellPopulation::Update 1ms 0.0045% 0.0089% 7624ms 33.95% ForwardEulerNumericalMethod::UpdateAllNodePositions 7ms 0.031% 0.04% 7433ms 33.10% AbstractNumericalMethod::ComputeForcesIncludingDamping 1201ms 5.35% 5.39% 6759ms 30.10% RepulsionForce::AddForceContribution (partial-inline) 7ms 0.031% 5.42% 5675ms 25.27% DistributedBoxCollection::CalculateInteriorNodePairs 2054ms 9.15% 14.57% 4671ms 20.80% std::_Rb_tree::_M_lower_bound (inline) 0 0% 14.57% 4467ms 19.89% OffLatticeSimulation::ApplyBoundaries 16ms 0.071% 14.64% 4456ms 19.84% NodeAttributes::RemoveDuplicateNeighbours 8ms 0.036% 14.67% 4283ms 19.07% std::__sort (inline) 0 0% 14.67% 4283ms 19.07% std::sort (inline) 2ms 0.0089% 14.68% 3310ms 14.74% AbstractCellPopulation::Iterator::operator++ (inline) 201ms 0.9% 15.58% 3295ms 14.67% AbstractCellPopulation::Iterator::IsRealCell 56ms 0.25% 15.83% 3285ms 14.63% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 210ms 0.94% 16.76% 3075ms 13.69% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 230ms 1.02% 17.79% 3041ms 13.54% std::_Rb_tree::find (inline) 0 0% 17.79% 3041ms 13.54% std::map::find (inline) 22ms 0.098% 17.88% 2788ms 12.41% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2577ms 11.48% 29.36% 2577ms 11.48% std::_Rb_tree::_S_right (inline) 175ms 0.78% 30.14% 2443ms 10.88% std::__introsort_loop 246ms 1.10% 31.23% 2392ms 10.65% std::map::operator[] (partial-inline) 27ms 0.12% 31.35% 2317ms 10.32% PlaneBoundaryCondition::ImposeBoundaryCondition 41ms 0.18% 31.54% 2263ms 10.08% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 31.54% 2186ms 9.73% std::__unguarded_partition_pivot (inline) 145ms 0.65% 32.18% 2173ms 9.68% AbstractMesh::GetNode 19ms 0.085% 32.27% 2150ms 9.57% PlaneBoundaryCondition::VerifyBoundaryCondition 49ms 0.22% 32.48% 2131ms 9.49% NodesOnlyMesh::GetNodeOrHaloNode 96ms 0.43% 32.91% 2034ms 9.06% NodesOnlyMesh::SolveNodeMapping 982ms 4.37% 37.28% 1953ms 8.70% std::__unguarded_partition (inline) 0 0% 37.28% 1877ms 8.36% std::_Rb_tree::lower_bound (inline) 0 0% 37.28% 1877ms 8.36% std::map::lower_bound (inline) 151ms 0.67% 37.96% 1848ms 8.23% DistributedBoxCollection::AddPairsFromBox 2ms 0.0089% 37.97% 1831ms 8.15% std::__final_insertion_sort (inline) 99ms 0.44% 38.41% 1636ms 7.29% std::__unguarded_insertion_sort (inline) 587ms 2.61% 41.02% 1585ms 7.06% std::__unguarded_linear_insert (inline) 1489ms 6.63% 47.65% 1489ms 6.63% __gnu_cxx::__normal_iterator::operator-- (inline) 23ms 0.1% 47.75% 1427ms 6.35% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 21ms 0.094% 47.85% 1393ms 6.20% AbstractCellPopulation::GetCellUsingLocationIndex 1ms 0.0045% 47.85% 1192ms 5.31% NodeBasedCellPopulation::UpdateCellProcessLocation 31ms 0.14% 47.99% 1168ms 5.20% boost::numeric::ublas::c_vector::c_vector (partial-inline) 5ms 0.022% 48.01% 1049ms 4.67% DistributedBoxCollection::CalculateBoundaryNodePairs 29ms 0.13% 48.14% 1044ms 4.65% boost::numeric::ublas::vector_assign (inline) 275ms 1.22% 49.37% 960ms 4.27% boost::numeric::ublas::indexing_vector_assign 17ms 0.076% 49.44% 823ms 3.66% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 153ms 0.68% 50.12% 810ms 3.61% AbstractMesh::GetVectorFromAtoB 388ms 1.73% 51.85% 750ms 3.34% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 51.85% 748ms 3.33% AbstractCellPopulation::WriteResultsToFiles 0 0% 51.85% 732ms 3.26% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 166ms 0.74% 52.59% 718ms 3.20% NodeAttributes::AddNeighbour 0 0% 52.59% 715ms 3.18% boost::numeric::ublas::norm_2 (inline) 548ms 2.44% 55.03% 715ms 3.18% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 55.03% 715ms 3.18% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 7ms 0.031% 55.06% 712ms 3.17% CellPropertyCollection::GetPropertiesType (inline) 4ms 0.018% 55.08% 696ms 3.10% boost::numeric::ublas::c_vector::operator= (inline) 36ms 0.16% 55.24% 679ms 3.02% std::__copy_move::__copy_m (inline) 0 0% 55.24% 679ms 3.02% std::__copy_move_a (inline) 0 0% 55.24% 679ms 3.02% std::__copy_move_a1 (inline) 0 0% 55.24% 679ms 3.02% std::__copy_move_a2 (inline) 0 0% 55.24% 679ms 3.02% std::copy (inline) 655ms 2.92% 58.16% 655ms 2.92% __memcpy_avx_unaligned_erms 552ms 2.46% 60.61% 624ms 2.78% std::vector::push_back (inline) 2ms 0.0089% 60.62% 599ms 2.67% AbstractCentreBasedCellPopulation::GetDampingConstant 586ms 2.61% 63.23% 586ms 2.61% boost::numeric::ublas::c_vector::operator() 41ms 0.18% 63.41% 565ms 2.52% std::_Rb_tree_const_iterator::operator++ (inline) 58ms 0.26% 63.67% 540ms 2.40% std::__new_allocator::allocate (inline) 2ms 0.0089% 63.68% 538ms 2.40% AbstractCellProperty::IsSubType (inline) 157ms 0.7% 64.38% 537ms 2.39% __dynamic_cast 0 0% 64.38% 526ms 2.34% std::allocator_traits::allocate (inline) 517ms 2.30% 66.68% 517ms 2.30% std::_Rb_tree_increment 32ms 0.14% 66.83% 504ms 2.24% boost::detail::shared_count::~shared_count (inline) 0 0% 66.83% 504ms 2.24% boost::shared_ptr::~shared_ptr (inline) 489ms 2.18% 69.00% 489ms 2.18% boost::numeric::ublas::same_impl_ex 2ms 0.0089% 69.01% 485ms 2.16% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 69.01% 481ms 2.14% std::_Rb_tree::_M_create_node (inline) 2ms 0.0089% 69.02% 478ms 2.13% AbstractCellBasedSimulation::DoCellBirth 19ms 0.085% 69.11% 478ms 2.13% operator new 1ms 0.0045% 69.11% 476ms 2.12% Cell::GetMutationState 11ms 0.049% 69.16% 469ms 2.09% std::_Rb_tree::_Rb_tree (partial-inline) 455ms 2.03% 71.18% 461ms 2.05% boost::detail::sp_counted_base::release 147ms 0.65% 71.84% 454ms 2.02% __GI___libc_malloc 55ms 0.24% 72.08% 441ms 1.96% std::_Rb_tree::_M_copy (inline) 181ms 0.81% 72.89% 439ms 1.95% Node::GetRadius 1ms 0.0045% 72.89% 434ms 1.93% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 72.89% 430ms 1.91% std::_Rb_tree::_M_get_node (inline) 4ms 0.018% 72.91% 417ms 1.86% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 137ms 0.61% 73.52% 403ms 1.79% std::_Rb_tree::_M_erase 124ms 0.55% 74.07% 385ms 1.71% std::_Rb_tree::_M_clone_node (inline) 7ms 0.031% 74.11% 381ms 1.70% std::set::set (inline) 24ms 0.11% 74.21% 339ms 1.51% boost::numeric::ublas::vector_binary::size (inline) 0 0% 74.21% 337ms 1.50% std::_Rb_tree::_Alloc_node::operator() (inline) 10ms 0.045% 74.26% 327ms 1.46% NodeBasedCellPopulation::UpdateMapsAfterRemesh 24ms 0.11% 74.36% 315ms 1.40% std::_Rb_tree::~_Rb_tree (inline) 0 0% 74.36% 313ms 1.39% boost::numeric::ublas::inner_prod (inline) 16ms 0.071% 74.44% 313ms 1.39% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 74.44% 313ms 1.39% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 74.44% 303ms 1.35% NodesOnlyMesh::ReMesh 299ms 1.33% 75.77% 299ms 1.33% __gnu_cxx::__normal_iterator::operator++ (inline) 142ms 0.63% 76.40% 293ms 1.30% __cxxabiv1::__si_class_type_info::__do_dyncast 293ms 1.30% 77.70% 293ms 1.30% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 1ms 0.0045% 77.71% 292ms 1.30% NodesOnlyMesh::UpdateNodeIndices 2ms 0.0089% 77.72% 282ms 1.26% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 10ms 0.045% 77.76% 269ms 1.20% std::_Rb_tree::_M_emplace_hint_unique 268ms 1.19% 78.96% 268ms 1.19% Node::CheckForNodeAttributes 0 0% 78.96% 267ms 1.19% std::_Rb_tree::_M_drop_node (inline) 3ms 0.013% 78.97% 263ms 1.17% DistributedBoxCollection::GetProcessOwningNode 149ms 0.66% 79.63% 257ms 1.14% _int_malloc 98ms 0.44% 80.07% 257ms 1.14% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 80.07% 254ms 1.13% boost::numeric::ublas::c_vector::assign (inline) 0 0% 80.07% 237ms 1.06% NodesOnlyMesh::UpdateBoxCollection 237ms 1.06% 81.12% 237ms 1.06% __strcmp_avx2 115ms 0.51% 81.64% 232ms 1.03% std::__move_median_to_first (inline) 0 0% 81.64% 231ms 1.03% std::set::~set (inline) 0 0% 81.64% 228ms 1.02% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 81.64% 227ms 1.01% VtkMeshWriter::WriteFiles 116ms 0.52% 82.15% 218ms 0.97% boost::shared_ptr::shared_ptr (inline) 3ms 0.013% 82.17% 212ms 0.94% std::__new_allocator::deallocate (inline) 0 0% 82.17% 208ms 0.93% vtkStreamingDemandDrivenPipeline::Update 0 0% 82.17% 208ms 0.93% vtkXMLWriterBase::Write 2ms 0.0089% 82.17% 207ms 0.92% NodesOnlyMesh::AddNodesToBoxes 0 0% 82.17% 207ms 0.92% NodesOnlyMesh::ResizeBoxCollection 16ms 0.071% 82.25% 205ms 0.91% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 82.25% 205ms 0.91% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 82.25% 204ms 0.91% vtkDemandDrivenPipeline::ProcessRequest 0 0% 82.25% 203ms 0.9% vtkCompositeDataPipeline::ExecuteData 0 0% 82.25% 203ms 0.9% vtkDemandDrivenPipeline::ExecuteData 0 0% 82.25% 203ms 0.9% vtkExecutive::CallAlgorithm 0 0% 82.25% 203ms 0.9% vtkXMLUnstructuredDataWriter::ProcessRequest 66ms 0.29% 82.54% 196ms 0.87% __GI___libc_free 0 0% 82.54% 194ms 0.86% std::allocator_traits::deallocate (inline) 91ms 0.41% 82.95% 193ms 0.86% Node::AddNeighbour 23ms 0.1% 83.05% 193ms 0.86% std::__insertion_sort (inline) 0 0% 83.05% 192ms 0.85% std::_Rb_tree::_M_put_node (inline) 188ms 0.84% 83.88% 188ms 0.84% Node::GetIndex 0 0% 83.88% 178ms 0.79% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 83.88% 178ms 0.79% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 83.88% 172ms 0.77% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 158ms 0.7% 84.59% 158ms 0.7% Node::IsDeleted 16ms 0.071% 84.66% 156ms 0.69% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 84.66% 155ms 0.69% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 1ms 0.0045% 84.66% 154ms 0.69% AbstractNumericalMethod::SafeNodePositionUpdate 152ms 0.68% 85.34% 152ms 0.68% boost::shared_ptr::operator-> (inline) 1ms 0.0045% 85.35% 149ms 0.66% Cell::GetCellId 0 0% 85.35% 148ms 0.66% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 85.35% 144ms 0.64% std::_Rb_tree::_Auto_node::_Auto_node (inline) 143ms 0.64% 85.98% 143ms 0.64% [libchaste_mesh.so] 5ms 0.022% 86.00% 140ms 0.62% DistributedBoxCollection::GetIsPeriodicAllDims 138ms 0.61% 86.62% 140ms 0.62% std::__adjacent_find (inline) 0 0% 86.62% 140ms 0.62% std::__unique (inline) 0 0% 86.62% 140ms 0.62% std::unique (inline) 1ms 0.0045% 86.62% 140ms 0.62% vtkXMLWriter::WriteBinaryData 0 0% 86.62% 139ms 0.62% Cell::GetCellProliferativeType 2ms 0.0089% 86.63% 139ms 0.62% NodeBasedCellPopulation::SetNode 135ms 0.6% 87.23% 135ms 0.6% [libchaste_cell_based.so] 0 0% 87.23% 135ms 0.6% std::_Rb_tree::clear (inline) 1ms 0.0045% 87.24% 134ms 0.6% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.24% 133ms 0.59% vtkXMLWriter::WriteBinaryDataBlock 1ms 0.0045% 87.24% 132ms 0.59% std::_Rb_tree::_M_insert_unique 0 0% 87.24% 132ms 0.59% std::set::insert (inline) 0 0% 87.24% 132ms 0.59% vtkXMLWriter::WriteCompressionBlock 12ms 0.053% 87.30% 131ms 0.58% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 87.30% 131ms 0.58% boost::numeric::ublas::vector_binary::operator() (inline) 5ms 0.022% 87.32% 130ms 0.58% NodesOnlyMesh::SetNode 116ms 0.52% 87.83% 130ms 0.58% _int_free 0 0% 87.83% 127ms 0.57% NodeBasedCellPopulation::AcceptCellWriter 2ms 0.0089% 87.84% 122ms 0.54% AbstractCellPopulation::SetCellUsingLocationIndex 0 0% 87.84% 122ms 0.54% vtkXMLWriter::WritePointsAppendedData 0 0% 87.84% 116ms 0.52% tbb::detail::r1::parallel_pipeline 0 0% 87.84% 115ms 0.51% clone3 0 0% 87.84% 115ms 0.51% start_thread 113ms 0.5% 88.35% 113ms 0.5% Node::ConstructNodeAttributes (inline) 113ms 0.5% 88.85% 113ms 0.5% __ieee754_log_fma