File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 23247ms, 89.63% of 25937ms total Dropped 847 nodes (cum <= 129.69ms) flat flat% sum% cum cum% 0 0% 0% 25803ms 99.48% __libc_start_call_main 0 0% 0% 25803ms 99.48% __libc_start_main_impl 0 0% 0% 25803ms 99.48% _start 0 0% 0% 25785ms 99.41% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 25785ms 99.41% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 25785ms 99.41% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 25785ms 99.41% main 0 0% 0% 25743ms 99.25% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 25743ms 99.25% CxxTest::TestRunner::runTest (inline) 0 0% 0% 25743ms 99.25% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0039% 0.0039% 25734ms 99.22% AbstractCellBasedSimulation::Solve 2ms 0.0077% 0.012% 14588ms 56.24% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0039% 0.015% 9909ms 38.20% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.015% 0.031% 9543ms 36.79% ForwardEulerNumericalMethod::UpdateAllNodePositions 25ms 0.096% 0.13% 9347ms 36.04% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.13% 8742ms 33.70% NodeBasedCellPopulation::Update 1344ms 5.18% 5.31% 8414ms 32.44% RepulsionForce::AddForceContribution (partial-inline) 17ms 0.066% 5.37% 6450ms 24.87% DistributedBoxCollection::CalculateInteriorNodePairs 2165ms 8.35% 13.72% 5253ms 20.25% std::_Rb_tree::_M_lower_bound (inline) 8ms 0.031% 13.75% 4770ms 18.39% NodeAttributes::RemoveDuplicateNeighbours 0 0% 13.75% 4666ms 17.99% OffLatticeSimulation::ApplyBoundaries 2ms 0.0077% 13.76% 4468ms 17.23% std::__sort (inline) 0 0% 13.76% 4468ms 17.23% std::sort (inline) 207ms 0.8% 14.56% 4329ms 16.69% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 270ms 1.04% 15.60% 3470ms 13.38% std::_Rb_tree::find (inline) 0 0% 15.60% 3469ms 13.37% std::map::find (inline) 86ms 0.33% 15.93% 3309ms 12.76% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 0 0% 15.93% 3126ms 12.05% AbstractCellPopulation::Iterator::operator++ (inline) 162ms 0.62% 16.56% 3105ms 11.97% AbstractCellPopulation::Iterator::IsRealCell (inline) 3056ms 11.78% 28.34% 3056ms 11.78% std::_Rb_tree::_S_right (inline) 31ms 0.12% 28.46% 2685ms 10.35% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 185ms 0.71% 29.17% 2632ms 10.15% std::__introsort_loop 205ms 0.79% 29.96% 2571ms 9.91% std::map::operator[] (partial-inline) 169ms 0.65% 30.61% 2479ms 9.56% AbstractMesh::GetNode 21ms 0.081% 30.69% 2479ms 9.56% PlaneBoundaryCondition::ImposeBoundaryCondition 43ms 0.17% 30.86% 2453ms 9.46% NodesOnlyMesh::GetNodeOrHaloNode 138ms 0.53% 31.39% 2420ms 9.33% DistributedBoxCollection::AddPairsFromBox 0 0% 31.39% 2366ms 9.12% std::__unguarded_partition_pivot (inline) 96ms 0.37% 31.76% 2316ms 8.93% NodesOnlyMesh::SolveNodeMapping 40ms 0.15% 31.92% 2305ms 8.89% AbstractCellPopulation::GetLocationIndexUsingCell 18ms 0.069% 31.99% 2187ms 8.43% PlaneBoundaryCondition::VerifyBoundaryCondition 1078ms 4.16% 36.14% 2096ms 8.08% std::__unguarded_partition (inline) 0 0% 36.14% 2080ms 8.02% std::_Rb_tree::lower_bound (inline) 0 0% 36.14% 2080ms 8.02% std::map::lower_bound (inline) 21ms 0.081% 36.22% 1861ms 7.18% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 20ms 0.077% 36.30% 1834ms 7.07% AbstractCellPopulation::GetCellUsingLocationIndex 2ms 0.0077% 36.31% 1832ms 7.06% std::__final_insertion_sort (inline) 113ms 0.44% 36.74% 1629ms 6.28% std::__unguarded_insertion_sort (inline) 561ms 2.16% 38.91% 1561ms 6.02% std::__unguarded_linear_insert (inline) 1490ms 5.74% 44.65% 1490ms 5.74% __gnu_cxx::__normal_iterator::operator-- (inline) 6ms 0.023% 44.67% 1261ms 4.86% DistributedBoxCollection::CalculateBoundaryNodePairs 29ms 0.11% 44.79% 1250ms 4.82% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 44.79% 1179ms 4.55% NodeBasedCellPopulation::UpdateCellProcessLocation 5ms 0.019% 44.80% 1135ms 4.38% boost::numeric::ublas::vector_assign (inline) 229ms 0.88% 45.69% 1058ms 4.08% boost::numeric::ublas::indexing_vector_assign 32ms 0.12% 45.81% 985ms 3.80% std::_Rb_tree_const_iterator::operator++ (inline) 276ms 1.06% 46.88% 962ms 3.71% __dynamic_cast 22ms 0.085% 46.96% 956ms 3.69% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 942ms 3.63% 50.59% 942ms 3.63% std::_Rb_tree_increment 327ms 1.26% 51.85% 912ms 3.52% NodeAttributes::AddNeighbour 393ms 1.52% 53.37% 861ms 3.32% DistributedBoxCollection::CalculateContainingBox (partial-inline) 192ms 0.74% 54.11% 823ms 3.17% AbstractMesh::GetVectorFromAtoB 12ms 0.046% 54.15% 818ms 3.15% CellPropertyCollection::GetPropertiesType (inline) 3ms 0.012% 54.17% 817ms 3.15% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 54.17% 817ms 3.15% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 54.17% 807ms 3.11% boost::numeric::ublas::norm_2 (inline) 628ms 2.42% 56.59% 807ms 3.11% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 56.59% 807ms 3.11% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 5ms 0.019% 56.61% 803ms 3.10% AbstractCentreBasedCellPopulation::GetDampingConstant 38ms 0.15% 56.75% 796ms 3.07% std::__copy_move::__copy_m (inline) 0 0% 56.75% 796ms 3.07% std::__copy_move_a (inline) 0 0% 56.75% 796ms 3.07% std::__copy_move_a1 (inline) 0 0% 56.75% 796ms 3.07% std::__copy_move_a2 (inline) 0 0% 56.75% 796ms 3.07% std::copy (inline) 780ms 3.01% 59.76% 780ms 3.01% __memcpy_avx_unaligned_erms 0 0% 59.76% 767ms 2.96% AbstractCellPopulation::WriteResultsToFiles 741ms 2.86% 62.62% 741ms 2.86% boost::numeric::ublas::c_vector::operator() 583ms 2.25% 64.86% 695ms 2.68% std::vector::push_back (inline) 5ms 0.019% 64.88% 685ms 2.64% AbstractCellBasedSimulation::DoCellBirth 31ms 0.12% 65.00% 619ms 2.39% std::_Rb_tree::_Rb_tree (partial-inline) 127ms 0.49% 65.49% 619ms 2.39% std::__new_allocator::allocate (inline) 3ms 0.012% 65.50% 608ms 2.34% Cell::GetMutationState 0 0% 65.50% 596ms 2.30% std::allocator_traits::allocate (inline) 44ms 0.17% 65.67% 575ms 2.22% std::_Rb_tree::_M_copy (inline) 258ms 0.99% 66.67% 565ms 2.18% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 66.67% 563ms 2.17% std::_Rb_tree::_M_create_node (inline) 531ms 2.05% 68.72% 531ms 2.05% boost::numeric::ublas::same_impl_ex 172ms 0.66% 69.38% 526ms 2.03% std::_Rb_tree::_M_clone_node (inline) 56ms 0.22% 69.60% 504ms 1.94% boost::detail::shared_count::~shared_count (inline) 0 0% 69.60% 504ms 1.94% boost::shared_ptr::~shared_ptr (inline) 0 0% 69.60% 503ms 1.94% NodeBasedCellPopulation::WriteVtkResultsToFile 146ms 0.56% 70.16% 502ms 1.94% std::_Rb_tree::_M_erase 6ms 0.023% 70.18% 499ms 1.92% std::set::set (inline) 0 0% 70.18% 497ms 1.92% std::_Rb_tree::_M_get_node (inline) 486ms 1.87% 72.06% 486ms 1.87% __strcmp_avx2 28ms 0.11% 72.16% 483ms 1.86% operator new 0 0% 72.16% 480ms 1.85% AbstractCellBasedSimulation::DoCellRemoval (inline) 4ms 0.015% 72.18% 463ms 1.79% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 131ms 0.51% 72.68% 447ms 1.72% __GI___libc_malloc 422ms 1.63% 74.31% 434ms 1.67% boost::detail::sp_counted_base::release 4ms 0.015% 74.33% 430ms 1.66% AbstractCellProperty::IsSubType (inline) 0 0% 74.33% 403ms 1.55% std::_Rb_tree::_Alloc_node::operator() (inline) 80ms 0.31% 74.63% 397ms 1.53% std::_Rb_tree::~_Rb_tree (inline) 0 0% 74.63% 382ms 1.47% boost::numeric::ublas::c_vector::assign (inline) 92ms 0.35% 74.99% 381ms 1.47% boost::numeric::ublas::vector_binary::size (inline) 89ms 0.34% 75.33% 378ms 1.46% Node::GetRadius 0 0% 75.33% 376ms 1.45% boost::numeric::ublas::inner_prod (inline) 1ms 0.0039% 75.34% 373ms 1.44% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 10ms 0.039% 75.37% 372ms 1.43% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 75.37% 368ms 1.42% NodesOnlyMesh::ReMesh 368ms 1.42% 76.79% 368ms 1.42% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 4ms 0.015% 76.81% 355ms 1.37% NodesOnlyMesh::UpdateNodeIndices 0 0% 76.81% 347ms 1.34% std::_Rb_tree::_M_drop_node (inline) 0 0% 76.81% 332ms 1.28% Cell::HasCellProperty (inline) 1ms 0.0039% 76.81% 332ms 1.28% CellPropertyCollection::HasProperty 12ms 0.046% 76.86% 330ms 1.27% Cell::ReadyToDivide 295ms 1.14% 78.00% 330ms 1.27% Node::AddNeighbour 6ms 0.023% 78.02% 312ms 1.20% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 78.02% 306ms 1.18% NodesOnlyMesh::UpdateBoxCollection 133ms 0.51% 78.53% 305ms 1.18% boost::numeric::ublas::vector_inner_prod::apply (inline) 3ms 0.012% 78.54% 303ms 1.17% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 298ms 1.15% 79.69% 298ms 1.15% Node::CheckForNodeAttributes 10ms 0.039% 79.73% 296ms 1.14% std::__new_allocator::deallocate (inline) 5ms 0.019% 79.75% 291ms 1.12% DistributedBoxCollection::GetProcessOwningNode 0 0% 79.75% 291ms 1.12% std::set::~set (inline) 13ms 0.05% 79.80% 286ms 1.10% std::_Rb_tree::_M_emplace_hint_unique 0 0% 79.80% 279ms 1.08% std::allocator_traits::deallocate (inline) 277ms 1.07% 80.87% 278ms 1.07% std::__adjacent_find (inline) 0 0% 80.87% 278ms 1.07% std::__unique (inline) 0 0% 80.87% 278ms 1.07% std::unique (inline) 0 0% 80.87% 273ms 1.05% std::_Rb_tree::_M_put_node (inline) 140ms 0.54% 81.41% 268ms 1.03% _int_malloc 101ms 0.39% 81.80% 262ms 1.01% std::__move_median_to_first (inline) 258ms 0.99% 82.79% 258ms 0.99% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 82.79% 249ms 0.96% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 74ms 0.29% 83.08% 249ms 0.96% __GI___libc_free 0 0% 83.08% 248ms 0.96% VtkMeshWriter::WriteFiles 125ms 0.48% 83.56% 246ms 0.95% boost::shared_ptr::shared_ptr (inline) 1ms 0.0039% 83.56% 236ms 0.91% NodesOnlyMesh::AddNodesToBoxes 230ms 0.89% 84.45% 230ms 0.89% [libchaste_mesh.so] 0 0% 84.45% 220ms 0.85% vtkStreamingDemandDrivenPipeline::Update 0 0% 84.45% 220ms 0.85% vtkXMLWriterBase::Write 0 0% 84.45% 218ms 0.84% vtkDemandDrivenPipeline::ProcessRequest 216ms 0.83% 85.28% 216ms 0.83% Node::GetIndex 0 0% 85.28% 216ms 0.83% vtkStreamingDemandDrivenPipeline::ProcessRequest 10ms 0.039% 85.32% 215ms 0.83% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 85.32% 214ms 0.83% vtkCompositeDataPipeline::ExecuteData 0 0% 85.32% 214ms 0.83% vtkDemandDrivenPipeline::ExecuteData 0 0% 85.32% 213ms 0.82% vtkExecutive::CallAlgorithm 1ms 0.0039% 85.33% 213ms 0.82% vtkXMLUnstructuredDataWriter::ProcessRequest 4ms 0.015% 85.34% 212ms 0.82% AbstractCellProperty::IsType (inline) 0 0% 85.34% 203ms 0.78% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 85.34% 203ms 0.78% std::_Rb_tree::clear (inline) 14ms 0.054% 85.40% 201ms 0.77% std::__insertion_sort (inline) 0 0% 85.40% 187ms 0.72% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.40% 187ms 0.72% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 85.40% 180ms 0.69% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 178ms 0.69% 86.08% 178ms 0.69% [libchaste_cell_based.so] 159ms 0.61% 86.69% 174ms 0.67% _int_free 2ms 0.0077% 86.70% 170ms 0.66% Cell::GetCellId 71ms 0.27% 86.98% 167ms 0.64% AbstractCellProperty::IsSame 163ms 0.63% 87.60% 163ms 0.63% boost::shared_ptr::operator-> (inline) 0 0% 87.60% 161ms 0.62% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 87.60% 160ms 0.62% std::_Rb_tree::_Auto_node::_Auto_node (inline) 158ms 0.61% 88.21% 158ms 0.61% __ieee754_log_fma 0 0% 88.21% 150ms 0.58% vtkXMLWriter::WriteBinaryData 148ms 0.57% 88.78% 148ms 0.57% Node::rGetLocation 0 0% 88.78% 147ms 0.57% vtkXMLWriter::WriteBinaryDataInternal 0 0% 88.78% 144ms 0.56% vtkXMLWriter::WriteBinaryDataBlock 0 0% 88.78% 144ms 0.56% vtkXMLWriter::WriteCompressionBlock 0 0% 88.78% 142ms 0.55% std::map::clear (inline) 0 0% 88.78% 141ms 0.54% NodesOnlyMesh::ResizeBoxCollection 0 0% 88.78% 141ms 0.54% vtkXMLWriter::WritePointsAppendedData 72ms 0.28% 89.06% 140ms 0.54% AbstractCellCycleModel::GetAge 9ms 0.035% 89.10% 140ms 0.54% NodesOnlyMesh::IsANodeCloseToDomainBoundary 3ms 0.012% 89.11% 137ms 0.53% boost::numeric::ublas::c_vector::operator[] (inline) 134ms 0.52% 89.62% 134ms 0.52% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 1ms 0.0039% 89.63% 133ms 0.51% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 89.63% 132ms 0.51% boost::numeric::ublas::scalar_traits::type_sqrt (inline)