File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20493ms, 88.77% of 23085ms total Dropped 728 nodes (cum <= 115.42ms) flat flat% sum% cum cum% 0 0% 0% 22942ms 99.38% __libc_start_call_main 0 0% 0% 22942ms 99.38% __libc_start_main_impl 0 0% 0% 22942ms 99.38% _start 0 0% 0% 22927ms 99.32% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 22927ms 99.32% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 22927ms 99.32% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 22927ms 99.32% main 0 0% 0% 22891ms 99.16% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 22891ms 99.16% CxxTest::TestRunner::runTest (inline) 0 0% 0% 22891ms 99.16% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 2ms 0.0087% 0.0087% 22883ms 99.12% AbstractCellBasedSimulation::Solve 0 0% 0.0087% 13032ms 56.45% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0087% 8653ms 37.48% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.0087% 8208ms 35.56% ForwardEulerNumericalMethod::UpdateAllNodePositions 7ms 0.03% 0.039% 8003ms 34.67% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.039% 7658ms 33.17% NodeBasedCellPopulation::Update 1197ms 5.19% 5.22% 7417ms 32.13% RepulsionForce::AddForceContribution (partial-inline) 10ms 0.043% 5.27% 5519ms 23.91% DistributedBoxCollection::CalculateInteriorNodePairs 2076ms 8.99% 14.26% 4889ms 21.18% std::_Rb_tree::_M_lower_bound (inline) 2ms 0.0087% 14.27% 4558ms 19.74% OffLatticeSimulation::ApplyBoundaries 21ms 0.091% 14.36% 4529ms 19.62% NodeAttributes::RemoveDuplicateNeighbours 5ms 0.022% 14.38% 4264ms 18.47% std::__sort (inline) 0 0% 14.38% 4264ms 18.47% std::sort (inline) 197ms 0.85% 15.24% 3733ms 16.17% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 1ms 0.0043% 15.24% 3483ms 15.09% AbstractCellPopulation::Iterator::operator++ (inline) 215ms 0.93% 16.17% 3448ms 14.94% AbstractCellPopulation::Iterator::IsRealCell 67ms 0.29% 16.46% 3398ms 14.72% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 250ms 1.08% 17.54% 3163ms 13.70% std::_Rb_tree::find (inline) 0 0% 17.54% 3163ms 13.70% std::map::find (inline) 25ms 0.11% 17.65% 2917ms 12.64% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2775ms 12.02% 29.67% 2775ms 12.02% std::_Rb_tree::_S_right (inline) 240ms 1.04% 30.71% 2520ms 10.92% std::map::operator[] (partial-inline) 26ms 0.11% 30.83% 2382ms 10.32% PlaneBoundaryCondition::ImposeBoundaryCondition 170ms 0.74% 31.56% 2377ms 10.30% std::__introsort_loop 25ms 0.11% 31.67% 2282ms 9.89% AbstractCellPopulation::GetLocationIndexUsingCell 169ms 0.73% 32.40% 2278ms 9.87% AbstractMesh::GetNode 40ms 0.17% 32.58% 2244ms 9.72% NodesOnlyMesh::GetNodeOrHaloNode 25ms 0.11% 32.68% 2173ms 9.41% PlaneBoundaryCondition::VerifyBoundaryCondition 67ms 0.29% 32.97% 2114ms 9.16% NodesOnlyMesh::SolveNodeMapping 1ms 0.0043% 32.98% 2099ms 9.09% std::__unguarded_partition_pivot (inline) 0 0% 32.98% 2001ms 8.67% std::_Rb_tree::lower_bound (inline) 0 0% 32.98% 2001ms 8.67% std::map::lower_bound (inline) 971ms 4.21% 37.18% 1884ms 8.16% std::__unguarded_partition (inline) 4ms 0.017% 37.20% 1880ms 8.14% std::__final_insertion_sort (inline) 164ms 0.71% 37.91% 1745ms 7.56% DistributedBoxCollection::AddPairsFromBox 103ms 0.45% 38.36% 1682ms 7.29% std::__unguarded_insertion_sort (inline) 586ms 2.54% 40.90% 1619ms 7.01% std::__unguarded_linear_insert (inline) 27ms 0.12% 41.01% 1513ms 6.55% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 30ms 0.13% 41.14% 1480ms 6.41% AbstractCellPopulation::GetCellUsingLocationIndex 1456ms 6.31% 47.45% 1456ms 6.31% __gnu_cxx::__normal_iterator::operator-- (inline) 62ms 0.27% 47.72% 1236ms 5.35% boost::numeric::ublas::c_vector::c_vector (partial-inline) 1ms 0.0043% 47.72% 1185ms 5.13% NodeBasedCellPopulation::UpdateCellProcessLocation 3ms 0.013% 47.74% 1175ms 5.09% DistributedBoxCollection::CalculateBoundaryNodePairs 40ms 0.17% 47.91% 1117ms 4.84% boost::numeric::ublas::vector_assign (inline) 271ms 1.17% 49.08% 1007ms 4.36% boost::numeric::ublas::indexing_vector_assign 227ms 0.98% 50.07% 893ms 3.87% __dynamic_cast 27ms 0.12% 50.18% 791ms 3.43% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 50.18% 766ms 3.32% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 149ms 0.65% 50.83% 759ms 3.29% AbstractMesh::GetVectorFromAtoB 342ms 1.48% 52.31% 753ms 3.26% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 52.31% 739ms 3.20% boost::numeric::ublas::norm_2 (inline) 594ms 2.57% 54.88% 739ms 3.20% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 54.88% 739ms 3.20% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 197ms 0.85% 55.74% 724ms 3.14% NodeAttributes::AddNeighbour 5ms 0.022% 55.76% 708ms 3.07% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 55.76% 704ms 3.05% AbstractCellPopulation::WriteResultsToFiles 686ms 2.97% 58.73% 686ms 2.97% boost::numeric::ublas::c_vector::operator() 35ms 0.15% 58.88% 680ms 2.95% std::__copy_move::__copy_m (inline) 0 0% 58.88% 680ms 2.95% std::__copy_move_a (inline) 0 0% 58.88% 680ms 2.95% std::__copy_move_a1 (inline) 0 0% 58.88% 680ms 2.95% std::__copy_move_a2 (inline) 0 0% 58.88% 680ms 2.95% std::copy (inline) 679ms 2.94% 61.82% 679ms 2.94% __memcpy_avx_unaligned_erms 525ms 2.27% 64.10% 584ms 2.53% std::vector::push_back (inline) 243ms 1.05% 65.15% 567ms 2.46% __cxxabiv1::__si_class_type_info::__do_dyncast 4ms 0.017% 65.17% 536ms 2.32% AbstractCellBasedSimulation::DoCellBirth 8ms 0.035% 65.20% 532ms 2.30% CellPropertyCollection::GetPropertiesType (inline) 0 0% 65.20% 515ms 2.23% AbstractCentreBasedCellPopulation::GetDampingConstant 490ms 2.12% 67.33% 490ms 2.12% boost::numeric::ublas::same_impl_ex 38ms 0.16% 67.49% 488ms 2.11% std::_Rb_tree_const_iterator::operator++ (inline) 52ms 0.23% 67.71% 474ms 2.05% std::__new_allocator::allocate (inline) 22ms 0.095% 67.81% 472ms 2.04% boost::detail::shared_count::~shared_count (inline) 0 0% 67.81% 472ms 2.04% boost::shared_ptr::~shared_ptr (inline) 464ms 2.01% 69.82% 464ms 2.01% __strcmp_avx2 0 0% 69.82% 463ms 2.01% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 69.82% 461ms 2.00% std::allocator_traits::allocate (inline) 0 0% 69.82% 459ms 1.99% AbstractCellBasedSimulation::DoCellRemoval (inline) 442ms 1.91% 71.73% 446ms 1.93% boost::detail::sp_counted_base::release 2ms 0.0087% 71.74% 444ms 1.92% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 444ms 1.92% 73.67% 444ms 1.92% std::_Rb_tree_increment 0 0% 73.67% 438ms 1.90% std::_Rb_tree::_M_create_node (inline) 36ms 0.16% 73.82% 420ms 1.82% operator new 11ms 0.048% 73.87% 419ms 1.82% std::_Rb_tree::_Rb_tree (partial-inline) 37ms 0.16% 74.03% 397ms 1.72% std::_Rb_tree::_M_copy (inline) 5ms 0.022% 74.05% 395ms 1.71% AbstractCellProperty::IsSubType (inline) 140ms 0.61% 74.66% 395ms 1.71% Node::GetRadius 0 0% 74.66% 389ms 1.69% std::_Rb_tree::_M_get_node (inline) 4ms 0.017% 74.68% 388ms 1.68% Cell::GetMutationState 115ms 0.5% 75.17% 385ms 1.67% std::_Rb_tree::_M_erase 114ms 0.49% 75.67% 376ms 1.63% __GI___libc_malloc 117ms 0.51% 76.18% 356ms 1.54% std::_Rb_tree::_M_clone_node (inline) 5ms 0.022% 76.20% 355ms 1.54% std::set::set (inline) 42ms 0.18% 76.38% 342ms 1.48% boost::numeric::ublas::vector_binary::size (inline) 0 0% 76.38% 321ms 1.39% boost::numeric::ublas::c_vector::assign (inline) 0 0% 76.38% 317ms 1.37% boost::numeric::ublas::inner_prod (inline) 15ms 0.065% 76.44% 317ms 1.37% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 76.44% 317ms 1.37% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 1ms 0.0043% 76.45% 315ms 1.36% NodeBasedCellPopulation::UpdateMapsAfterRemesh 2ms 0.0087% 76.46% 302ms 1.31% NodesOnlyMesh::ReMesh 299ms 1.30% 77.75% 299ms 1.30% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 2ms 0.0087% 77.76% 294ms 1.27% NodesOnlyMesh::UpdateNodeIndices 33ms 0.14% 77.90% 294ms 1.27% std::_Rb_tree::~_Rb_tree (inline) 0 0% 77.90% 291ms 1.26% std::_Rb_tree::_Alloc_node::operator() (inline) 2ms 0.0087% 77.91% 279ms 1.21% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 10ms 0.043% 77.96% 279ms 1.21% std::_Rb_tree::_M_emplace_hint_unique 272ms 1.18% 79.13% 272ms 1.18% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 79.13% 264ms 1.14% std::_Rb_tree::_M_drop_node (inline) 5ms 0.022% 79.16% 260ms 1.13% DistributedBoxCollection::GetProcessOwningNode 0 0% 79.16% 260ms 1.13% NodesOnlyMesh::UpdateBoxCollection 256ms 1.11% 80.26% 256ms 1.11% Node::CheckForNodeAttributes 100ms 0.43% 80.70% 249ms 1.08% boost::numeric::ublas::vector_inner_prod::apply (inline) 238ms 1.03% 81.73% 238ms 1.03% std::__adjacent_find (inline) 0 0% 81.73% 238ms 1.03% std::__unique (inline) 0 0% 81.73% 238ms 1.03% std::unique (inline) 0 0% 81.73% 235ms 1.02% NodesOnlyMesh::ResizeBoxCollection 7ms 0.03% 81.76% 234ms 1.01% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 81.76% 227ms 0.98% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 81.76% 227ms 0.98% VtkMeshWriter::WriteFiles 4ms 0.017% 81.78% 224ms 0.97% std::__new_allocator::deallocate (inline) 0 0% 81.78% 223ms 0.97% std::set::~set (inline) 1ms 0.0043% 81.78% 218ms 0.94% NodesOnlyMesh::AddNodesToBoxes 102ms 0.44% 82.22% 210ms 0.91% std::__move_median_to_first (inline) 117ms 0.51% 82.73% 205ms 0.89% _int_malloc 0 0% 82.73% 203ms 0.88% std::allocator_traits::deallocate (inline) 0 0% 82.73% 202ms 0.88% vtkStreamingDemandDrivenPipeline::Update 0 0% 82.73% 202ms 0.88% vtkXMLWriterBase::Write 1ms 0.0043% 82.73% 200ms 0.87% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 82.73% 199ms 0.86% std::_Rb_tree::_M_put_node (inline) 0 0% 82.73% 199ms 0.86% vtkCompositeDataPipeline::ExecuteData 0 0% 82.73% 199ms 0.86% vtkDemandDrivenPipeline::ExecuteData 0 0% 82.73% 199ms 0.86% vtkDemandDrivenPipeline::ProcessRequest 77ms 0.33% 83.07% 197ms 0.85% __GI___libc_free 0 0% 83.07% 197ms 0.85% vtkExecutive::CallAlgorithm 0 0% 83.07% 197ms 0.85% vtkXMLUnstructuredDataWriter::ProcessRequest 12ms 0.052% 83.12% 194ms 0.84% std::__insertion_sort (inline) 101ms 0.44% 83.56% 191ms 0.83% boost::shared_ptr::shared_ptr (inline) 188ms 0.81% 84.37% 188ms 0.81% Node::GetIndex 181ms 0.78% 85.15% 181ms 0.78% Node::IsDeleted 4ms 0.017% 85.17% 170ms 0.74% CellPropertyCollection::HasProperty 0 0% 85.17% 168ms 0.73% Cell::HasCellProperty (inline) 0 0% 85.17% 167ms 0.72% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.17% 167ms 0.72% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 1ms 0.0043% 85.18% 165ms 0.71% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 156ms 0.68% 85.85% 156ms 0.68% [libchaste_cell_based.so] 5ms 0.022% 85.87% 151ms 0.65% Cell::ReadyToDivide 5ms 0.022% 85.90% 149ms 0.65% DistributedBoxCollection::GetIsPeriodicAllDims 2ms 0.0087% 85.90% 148ms 0.64% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 85.90% 147ms 0.64% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 85.90% 146ms 0.63% std::_Rb_tree::clear (inline) 4ms 0.017% 85.92% 143ms 0.62% AbstractCellProperty::IsType (inline) 14ms 0.061% 85.98% 143ms 0.62% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 85.98% 140ms 0.61% vtkXMLWriter::WriteBinaryData 8ms 0.035% 86.02% 139ms 0.6% AbstractNumericalMethod::SafeNodePositionUpdate 139ms 0.6% 86.62% 139ms 0.6% [libchaste_mesh.so] 0 0% 86.62% 139ms 0.6% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 86.62% 139ms 0.6% vtkXMLWriter::WriteBinaryDataBlock 0 0% 86.62% 139ms 0.6% vtkXMLWriter::WriteBinaryDataInternal 0 0% 86.62% 139ms 0.6% vtkXMLWriter::WriteCompressionBlock 74ms 0.32% 86.94% 138ms 0.6% Node::AddNeighbour 0 0% 86.94% 135ms 0.58% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 86.94% 132ms 0.57% boost::numeric::ublas::vector_binary::operator() (inline) 1ms 0.0043% 86.94% 128ms 0.55% AbstractCellPopulation::SetCellUsingLocationIndex 127ms 0.55% 87.49% 127ms 0.55% boost::shared_ptr::operator-> (inline) 125ms 0.54% 88.04% 125ms 0.54% __ieee754_log_fma 0 0% 88.04% 121ms 0.52% compress2 0 0% 88.04% 121ms 0.52% vtkDataCompressor::Compress 0 0% 88.04% 121ms 0.52% vtkZLibDataCompressor::CompressBuffer 111ms 0.48% 88.52% 120ms 0.52% _int_free 53ms 0.23% 88.75% 120ms 0.52% crc32 0 0% 88.75% 120ms 0.52% deflate 6ms 0.026% 88.77% 119ms 0.52% NodeBasedCellPopulation::SetNode 0 0% 88.77% 118ms 0.51% vtkXMLWriter::WritePointsAppendedData