File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 23252ms, 89.11% of 26095ms total Dropped 846 nodes (cum <= 130.47ms) flat flat% sum% cum cum% 0 0% 0% 25955ms 99.46% __libc_start_call_main 0 0% 0% 25955ms 99.46% __libc_start_main_impl 0 0% 0% 25955ms 99.46% _start 0 0% 0% 25936ms 99.39% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 25936ms 99.39% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 25936ms 99.39% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 25936ms 99.39% main 0 0% 0% 25892ms 99.22% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 25892ms 99.22% CxxTest::TestRunner::runTest (inline) 0 0% 0% 25892ms 99.22% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 25883ms 99.19% AbstractCellBasedSimulation::Solve 1ms 0.0038% 0.0038% 14535ms 55.70% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0038% 10010ms 38.36% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.011% 0.015% 9463ms 36.26% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.038% 0.054% 9266ms 35.51% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.054% 8730ms 33.45% NodeBasedCellPopulation::Update 1342ms 5.14% 5.20% 8286ms 31.75% RepulsionForce::AddForceContribution (partial-inline) 8ms 0.031% 5.23% 6489ms 24.87% DistributedBoxCollection::CalculateInteriorNodePairs 2235ms 8.56% 13.79% 4972ms 19.05% std::_Rb_tree::_M_lower_bound (inline) 18ms 0.069% 13.86% 4740ms 18.16% NodeAttributes::RemoveDuplicateNeighbours 0 0% 13.86% 4705ms 18.03% OffLatticeSimulation::ApplyBoundaries 8ms 0.031% 13.89% 4531ms 17.36% std::__sort (inline) 0 0% 13.89% 4531ms 17.36% std::sort (inline) 194ms 0.74% 14.63% 4160ms 15.94% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 253ms 0.97% 15.60% 3263ms 12.50% std::_Rb_tree::find (inline) 0 0% 15.60% 3263ms 12.50% std::map::find (inline) 67ms 0.26% 15.86% 3260ms 12.49% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 3ms 0.011% 15.87% 3206ms 12.29% AbstractCellPopulation::Iterator::operator++ (inline) 207ms 0.79% 16.67% 3178ms 12.18% AbstractCellPopulation::Iterator::IsRealCell (inline) 218ms 0.84% 17.50% 2817ms 10.80% std::__introsort_loop 2723ms 10.43% 27.94% 2723ms 10.43% std::_Rb_tree::_S_right (inline) 32ms 0.12% 28.06% 2690ms 10.31% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 28.06% 2523ms 9.67% std::__unguarded_partition_pivot (inline) 33ms 0.13% 28.19% 2497ms 9.57% PlaneBoundaryCondition::ImposeBoundaryCondition 213ms 0.82% 29.00% 2492ms 9.55% std::map::operator[] (partial-inline) 184ms 0.71% 29.71% 2451ms 9.39% DistributedBoxCollection::AddPairsFromBox 159ms 0.61% 30.32% 2392ms 9.17% AbstractMesh::GetNode 60ms 0.23% 30.55% 2362ms 9.05% NodesOnlyMesh::GetNodeOrHaloNode 113ms 0.43% 30.98% 2241ms 8.59% NodesOnlyMesh::SolveNodeMapping 21ms 0.08% 31.06% 2208ms 8.46% PlaneBoundaryCondition::VerifyBoundaryCondition 30ms 0.11% 31.17% 2195ms 8.41% AbstractCellPopulation::GetLocationIndexUsingCell 1034ms 3.96% 35.14% 2172ms 8.32% std::__unguarded_partition (inline) 0 0% 35.14% 2000ms 7.66% std::_Rb_tree::lower_bound (inline) 0 0% 35.14% 2000ms 7.66% std::map::lower_bound (inline) 14ms 0.054% 35.19% 1834ms 7.03% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 33ms 0.13% 35.32% 1815ms 6.96% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 35.32% 1705ms 6.53% std::__final_insertion_sort (inline) 109ms 0.42% 35.73% 1520ms 5.82% std::__unguarded_insertion_sort (inline) 497ms 1.90% 37.64% 1440ms 5.52% std::__unguarded_linear_insert (inline) 1399ms 5.36% 43.00% 1399ms 5.36% __gnu_cxx::__normal_iterator::operator-- (inline) 71ms 0.27% 43.27% 1352ms 5.18% boost::numeric::ublas::c_vector::c_vector (partial-inline) 2ms 0.0077% 43.28% 1220ms 4.68% NodeBasedCellPopulation::UpdateCellProcessLocation 8ms 0.031% 43.31% 1213ms 4.65% DistributedBoxCollection::CalculateBoundaryNodePairs 7ms 0.027% 43.34% 1201ms 4.60% boost::numeric::ublas::vector_assign (inline) 210ms 0.8% 44.14% 1085ms 4.16% boost::numeric::ublas::indexing_vector_assign 26ms 0.1% 44.24% 1068ms 4.09% std::_Rb_tree_const_iterator::operator++ (inline) 1032ms 3.95% 48.20% 1032ms 3.95% std::_Rb_tree_increment 310ms 1.19% 49.38% 995ms 3.81% __dynamic_cast 21ms 0.08% 49.47% 948ms 3.63% CellPropertyCollection::GetPropertiesType (inline) 328ms 1.26% 50.72% 934ms 3.58% NodeAttributes::AddNeighbour 16ms 0.061% 50.78% 911ms 3.49% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 394ms 1.51% 52.29% 880ms 3.37% DistributedBoxCollection::CalculateContainingBox (partial-inline) 3ms 0.011% 52.31% 870ms 3.33% AbstractCentreBasedCellPopulation::GetDampingConstant 177ms 0.68% 52.98% 869ms 3.33% AbstractMesh::GetVectorFromAtoB 0 0% 52.98% 831ms 3.18% AbstractCellPopulation::WriteResultsToFiles 0 0% 52.98% 804ms 3.08% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 6ms 0.023% 53.01% 798ms 3.06% AbstractCellBasedSimulation::DoCellBirth 0 0% 53.01% 788ms 3.02% boost::numeric::ublas::norm_2 (inline) 631ms 2.42% 55.42% 788ms 3.02% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 55.42% 788ms 3.02% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 6ms 0.023% 55.45% 779ms 2.99% boost::numeric::ublas::c_vector::operator= (inline) 758ms 2.90% 58.35% 758ms 2.90% boost::numeric::ublas::c_vector::operator() 26ms 0.1% 58.45% 758ms 2.90% std::__copy_move::__copy_m (inline) 0 0% 58.45% 758ms 2.90% std::__copy_move_a (inline) 0 0% 58.45% 758ms 2.90% std::__copy_move_a1 (inline) 0 0% 58.45% 758ms 2.90% std::__copy_move_a2 (inline) 0 0% 58.45% 758ms 2.90% std::copy (inline) 748ms 2.87% 61.32% 748ms 2.87% __memcpy_avx_unaligned_erms 603ms 2.31% 63.63% 706ms 2.71% std::vector::push_back (inline) 1ms 0.0038% 63.63% 685ms 2.63% Cell::GetMutationState 48ms 0.18% 63.82% 663ms 2.54% std::_Rb_tree::_Rb_tree (partial-inline) 127ms 0.49% 64.30% 602ms 2.31% std::__new_allocator::allocate (inline) 47ms 0.18% 64.48% 598ms 2.29% std::_Rb_tree::_M_copy (inline) 302ms 1.16% 65.64% 581ms 2.23% __cxxabiv1::__si_class_type_info::__do_dyncast 569ms 2.18% 67.82% 569ms 2.18% boost::numeric::ublas::same_impl_ex 0 0% 67.82% 569ms 2.18% std::allocator_traits::allocate (inline) 1ms 0.0038% 67.83% 558ms 2.14% NodeBasedCellPopulation::WriteVtkResultsToFile 25ms 0.096% 67.92% 553ms 2.12% boost::detail::shared_count::~shared_count (inline) 0 0% 67.92% 553ms 2.12% boost::shared_ptr::~shared_ptr (inline) 197ms 0.75% 68.68% 541ms 2.07% std::_Rb_tree::_M_clone_node (inline) 0 0% 68.68% 540ms 2.07% std::_Rb_tree::_M_create_node (inline) 3ms 0.011% 68.69% 536ms 2.05% std::set::set (inline) 495ms 1.90% 70.58% 514ms 1.97% boost::detail::sp_counted_base::release 153ms 0.59% 71.17% 483ms 1.85% std::_Rb_tree::_M_erase 0 0% 71.17% 482ms 1.85% AbstractCellBasedSimulation::DoCellRemoval (inline) 23ms 0.088% 71.26% 479ms 1.84% operator new 0 0% 71.26% 463ms 1.77% std::_Rb_tree::_M_get_node (inline) 8ms 0.031% 71.29% 462ms 1.77% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 71.29% 460ms 1.76% AbstractCellProperty::IsSubType (inline) 128ms 0.49% 71.78% 451ms 1.73% __GI___libc_malloc 446ms 1.71% 73.49% 446ms 1.71% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 432ms 1.66% 75.14% 432ms 1.66% __strcmp_avx2 0 0% 75.14% 427ms 1.64% Cell::HasCellProperty (inline) 2ms 0.0077% 75.15% 427ms 1.64% CellPropertyCollection::HasProperty 16ms 0.061% 75.21% 416ms 1.59% Cell::ReadyToDivide 0 0% 75.21% 414ms 1.59% boost::numeric::ublas::inner_prod (inline) 20ms 0.077% 75.29% 413ms 1.58% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 75.29% 413ms 1.58% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 89ms 0.34% 75.63% 387ms 1.48% boost::numeric::ublas::vector_binary::size (inline) 91ms 0.35% 75.98% 386ms 1.48% Node::GetRadius 0 0% 75.98% 386ms 1.48% std::_Rb_tree::_Alloc_node::operator() (inline) 55ms 0.21% 76.19% 369ms 1.41% std::_Rb_tree::~_Rb_tree (inline) 367ms 1.41% 77.60% 367ms 1.41% __gnu_cxx::__normal_iterator::operator++ (inline) 325ms 1.25% 78.84% 361ms 1.38% Node::AddNeighbour 150ms 0.57% 79.42% 351ms 1.35% boost::numeric::ublas::vector_inner_prod::apply (inline) 116ms 0.44% 79.86% 349ms 1.34% std::__move_median_to_first (inline) 0 0% 79.86% 347ms 1.33% NodesOnlyMesh::ReMesh 0 0% 79.86% 336ms 1.29% boost::numeric::ublas::c_vector::assign (inline) 2ms 0.0077% 79.87% 334ms 1.28% NodesOnlyMesh::UpdateNodeIndices 3ms 0.011% 79.88% 321ms 1.23% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 79.88% 320ms 1.23% std::_Rb_tree::_M_drop_node (inline) 9ms 0.034% 79.92% 308ms 1.18% DistributedBoxCollection::GetProcessOwningNode 307ms 1.18% 81.09% 307ms 1.18% Node::CheckForNodeAttributes 8ms 0.031% 81.12% 297ms 1.14% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 81.12% 297ms 1.14% NodesOnlyMesh::UpdateBoxCollection 7ms 0.027% 81.15% 279ms 1.07% std::_Rb_tree::_M_emplace_hint_unique 0 0% 81.15% 278ms 1.07% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 116ms 0.44% 81.59% 277ms 1.06% _int_malloc 0 0% 81.59% 274ms 1.05% VtkMeshWriter::WriteFiles 6ms 0.023% 81.62% 270ms 1.03% std::__new_allocator::deallocate (inline) 0 0% 81.62% 263ms 1.01% std::set::~set (inline) 0 0% 81.62% 245ms 0.94% std::allocator_traits::deallocate (inline) 75ms 0.29% 81.90% 240ms 0.92% __GI___libc_free 1ms 0.0038% 81.91% 240ms 0.92% vtkStreamingDemandDrivenPipeline::Update 0 0% 81.91% 240ms 0.92% vtkXMLWriterBase::Write 108ms 0.41% 82.32% 239ms 0.92% boost::shared_ptr::shared_ptr (inline) 0 0% 82.32% 239ms 0.92% std::_Rb_tree::_M_put_node (inline) 0 0% 82.32% 237ms 0.91% vtkDemandDrivenPipeline::ProcessRequest 0 0% 82.32% 233ms 0.89% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 82.32% 232ms 0.89% vtkDemandDrivenPipeline::ExecuteData 0 0% 82.32% 231ms 0.89% vtkCompositeDataPipeline::ExecuteData 0 0% 82.32% 230ms 0.88% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 82.32% 230ms 0.88% vtkExecutive::CallAlgorithm 0 0% 82.32% 230ms 0.88% vtkXMLUnstructuredDataWriter::ProcessRequest 1ms 0.0038% 82.33% 227ms 0.87% NodesOnlyMesh::AddNodesToBoxes 226ms 0.87% 83.19% 226ms 0.87% boost::shared_ptr::operator-> (inline) 15ms 0.057% 83.25% 224ms 0.86% boost::numeric::ublas::vector_reference::operator() (inline) 221ms 0.85% 84.10% 221ms 0.85% Node::GetIndex 215ms 0.82% 84.92% 215ms 0.82% [libchaste_mesh.so] 1ms 0.0038% 84.92% 211ms 0.81% AbstractCellProperty::IsType (inline) 0 0% 84.92% 195ms 0.75% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 84.92% 195ms 0.75% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 18ms 0.069% 84.99% 185ms 0.71% std::__insertion_sort (inline) 0 0% 84.99% 185ms 0.71% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 184ms 0.71% 85.70% 184ms 0.71% [libchaste_cell_based.so] 0 0% 85.70% 183ms 0.7% Cell::GetCellId 0 0% 85.70% 182ms 0.7% std::_Rb_tree::clear (inline) 0 0% 85.70% 177ms 0.68% NodesOnlyMesh::ResizeBoxCollection 6ms 0.023% 85.72% 176ms 0.67% NodesOnlyMesh::IsANodeCloseToDomainBoundary 1ms 0.0038% 85.73% 169ms 0.65% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 81ms 0.31% 86.04% 167ms 0.64% AbstractCellProperty::IsSame 154ms 0.59% 86.63% 164ms 0.63% _int_free 161ms 0.62% 87.24% 162ms 0.62% std::__adjacent_find (inline) 0 0% 87.24% 162ms 0.62% std::__unique (inline) 0 0% 87.24% 162ms 0.62% std::unique (inline) 159ms 0.61% 87.85% 159ms 0.61% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 3ms 0.011% 87.86% 154ms 0.59% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 87.86% 154ms 0.59% std::_Rb_tree::_Auto_node::_Auto_node (inline) 2ms 0.0077% 87.87% 150ms 0.57% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 87.87% 150ms 0.57% vtkXMLWriter::WriteBinaryData 0 0% 87.87% 148ms 0.57% vtkXMLWriter::WritePointsAppendedData 0 0% 87.87% 143ms 0.55% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.87% 143ms 0.55% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.87% 143ms 0.55% vtkXMLWriter::WriteCompressionBlock 0 0% 87.87% 139ms 0.53% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 87.87% 138ms 0.53% AbstractCentreBasedCellPopulation::CreateCellPair 136ms 0.52% 88.39% 136ms 0.52% __ieee754_log_fma 75ms 0.29% 88.68% 134ms 0.51% AbstractCellCycleModel::GetAge 0 0% 88.68% 134ms 0.51% std::map::map (inline) 3ms 0.011% 88.69% 133ms 0.51% DistributedBoxCollection::GetIsPeriodicAllDims 4ms 0.015% 88.71% 133ms 0.51% NodeBasedCellPopulation::SetNode 1ms 0.0038% 88.71% 131ms 0.5% NodeBasedCellPopulation::AcceptCellWriter 103ms 0.39% 89.11% 131ms 0.5% boost::detail::shared_count::shared_count (inline)