File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 21838ms, 88.16% of 24771ms total Dropped 832 nodes (cum <= 123.86ms) flat flat% sum% cum cum% 0 0% 0% 24626ms 99.41% __libc_start_call_main 0 0% 0% 24626ms 99.41% __libc_start_main_impl 0 0% 0% 24626ms 99.41% _start 0 0% 0% 24608ms 99.34% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 24608ms 99.34% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 24608ms 99.34% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 24608ms 99.34% main 0 0% 0% 24565ms 99.17% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 24565ms 99.17% CxxTest::TestRunner::runTest (inline) 0 0% 0% 24565ms 99.17% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.004% 0.004% 24556ms 99.13% AbstractCellBasedSimulation::Solve 1ms 0.004% 0.0081% 14069ms 56.80% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0081% 9271ms 37.43% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.016% 0.024% 9147ms 36.93% ForwardEulerNumericalMethod::UpdateAllNodePositions 19ms 0.077% 0.1% 8958ms 36.16% AbstractNumericalMethod::ComputeForcesIncludingDamping 1331ms 5.37% 5.47% 8233ms 33.24% RepulsionForce::AddForceContribution (partial-inline) 0 0% 5.47% 8195ms 33.08% NodeBasedCellPopulation::Update 11ms 0.044% 5.52% 6099ms 24.62% DistributedBoxCollection::CalculateInteriorNodePairs 2167ms 8.75% 14.27% 5047ms 20.37% std::_Rb_tree::_M_lower_bound (inline) 13ms 0.052% 14.32% 4643ms 18.74% NodeAttributes::RemoveDuplicateNeighbours 0 0% 14.32% 4602ms 18.58% OffLatticeSimulation::ApplyBoundaries 2ms 0.0081% 14.33% 4478ms 18.08% std::__sort (inline) 0 0% 14.33% 4478ms 18.08% std::sort (inline) 218ms 0.88% 15.21% 4076ms 16.45% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 254ms 1.03% 16.23% 3337ms 13.47% std::_Rb_tree::find (inline) 0 0% 16.23% 3334ms 13.46% std::map::find (inline) 55ms 0.22% 16.45% 3267ms 13.19% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 4ms 0.016% 16.47% 3172ms 12.81% AbstractCellPopulation::Iterator::operator++ (inline) 245ms 0.99% 17.46% 3138ms 12.67% AbstractCellPopulation::Iterator::IsRealCell (inline) 2852ms 11.51% 28.97% 2852ms 11.51% std::_Rb_tree::_S_right (inline) 30ms 0.12% 29.09% 2660ms 10.74% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 178ms 0.72% 29.81% 2621ms 10.58% std::__introsort_loop 202ms 0.82% 30.63% 2503ms 10.10% std::map::operator[] (partial-inline) 149ms 0.6% 31.23% 2471ms 9.98% AbstractMesh::GetNode 60ms 0.24% 31.47% 2455ms 9.91% NodesOnlyMesh::GetNodeOrHaloNode 28ms 0.11% 31.59% 2446ms 9.87% PlaneBoundaryCondition::ImposeBoundaryCondition 0 0% 31.59% 2344ms 9.46% std::__unguarded_partition_pivot (inline) 102ms 0.41% 32.00% 2325ms 9.39% NodesOnlyMesh::SolveNodeMapping 45ms 0.18% 32.18% 2231ms 9.01% AbstractCellPopulation::GetLocationIndexUsingCell 15ms 0.061% 32.24% 2156ms 8.70% PlaneBoundaryCondition::VerifyBoundaryCondition 998ms 4.03% 36.27% 2110ms 8.52% std::__unguarded_partition (inline) 137ms 0.55% 36.82% 2077ms 8.38% DistributedBoxCollection::AddPairsFromBox 0 0% 36.82% 2017ms 8.14% std::_Rb_tree::lower_bound (inline) 0 0% 36.82% 2017ms 8.14% std::map::lower_bound (inline) 2ms 0.0081% 36.83% 1855ms 7.49% std::__final_insertion_sort (inline) 108ms 0.44% 37.27% 1656ms 6.69% std::__unguarded_insertion_sort (inline) 17ms 0.069% 37.33% 1632ms 6.59% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 28ms 0.11% 37.45% 1606ms 6.48% AbstractCellPopulation::GetCellUsingLocationIndex 614ms 2.48% 39.93% 1570ms 6.34% std::__unguarded_linear_insert (inline) 1423ms 5.74% 45.67% 1423ms 5.74% __gnu_cxx::__normal_iterator::operator-- (inline) 60ms 0.24% 45.91% 1281ms 5.17% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 45.91% 1149ms 4.64% NodeBasedCellPopulation::UpdateCellProcessLocation 4ms 0.016% 45.93% 1131ms 4.57% boost::numeric::ublas::vector_assign (inline) 3ms 0.012% 45.94% 1118ms 4.51% DistributedBoxCollection::CalculateBoundaryNodePairs 202ms 0.82% 46.76% 1048ms 4.23% boost::numeric::ublas::indexing_vector_assign 269ms 1.09% 47.84% 958ms 3.87% __dynamic_cast 19ms 0.077% 47.92% 940ms 3.79% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 180ms 0.73% 48.65% 856ms 3.46% AbstractMesh::GetVectorFromAtoB 0 0% 48.65% 855ms 3.45% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 48.65% 851ms 3.44% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 48.65% 850ms 3.43% boost::numeric::ublas::norm_2 (inline) 676ms 2.73% 51.37% 850ms 3.43% boost::numeric::ublas::vector_norm_2::apply (inline) 368ms 1.49% 52.86% 832ms 3.36% DistributedBoxCollection::CalculateContainingBox (partial-inline) 3ms 0.012% 52.87% 816ms 3.29% boost::numeric::ublas::c_vector::operator= (inline) 38ms 0.15% 53.03% 801ms 3.23% std::__copy_move::__copy_m (inline) 0 0% 53.03% 801ms 3.23% std::__copy_move_a (inline) 0 0% 53.03% 801ms 3.23% std::__copy_move_a1 (inline) 0 0% 53.03% 801ms 3.23% std::__copy_move_a2 (inline) 0 0% 53.03% 801ms 3.23% std::copy (inline) 777ms 3.14% 56.16% 777ms 3.14% __memcpy_avx_unaligned_erms 0 0% 56.16% 761ms 3.07% AbstractCellPopulation::WriteResultsToFiles 717ms 2.89% 59.06% 717ms 2.89% boost::numeric::ublas::c_vector::operator() 174ms 0.7% 59.76% 715ms 2.89% NodeAttributes::AddNeighbour 40ms 0.16% 59.92% 711ms 2.87% std::_Rb_tree_const_iterator::operator++ (inline) 644ms 2.60% 62.52% 644ms 2.60% std::_Rb_tree_increment 540ms 2.18% 64.70% 623ms 2.52% std::vector::push_back (inline) 5ms 0.02% 64.72% 620ms 2.50% AbstractCentreBasedCellPopulation::GetDampingConstant 8ms 0.032% 64.75% 617ms 2.49% CellPropertyCollection::GetPropertiesType (inline) 11ms 0.044% 64.80% 603ms 2.43% AbstractCellBasedSimulation::DoCellBirth 583ms 2.35% 67.15% 583ms 2.35% boost::numeric::ublas::same_impl_ex 263ms 1.06% 68.21% 572ms 2.31% __cxxabiv1::__si_class_type_info::__do_dyncast 24ms 0.097% 68.31% 534ms 2.16% std::_Rb_tree::_Rb_tree (partial-inline) 80ms 0.32% 68.63% 528ms 2.13% std::__new_allocator::allocate (inline) 1ms 0.004% 68.64% 512ms 2.07% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 68.64% 509ms 2.05% std::allocator_traits::allocate (inline) 46ms 0.19% 68.82% 491ms 1.98% std::_Rb_tree::_M_copy (inline) 0 0% 68.82% 478ms 1.93% std::_Rb_tree::_M_create_node (inline) 473ms 1.91% 70.73% 473ms 1.91% __strcmp_avx2 0 0% 70.73% 471ms 1.90% AbstractCellBasedSimulation::DoCellRemoval (inline) 3ms 0.012% 70.74% 461ms 1.86% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 32ms 0.13% 70.87% 461ms 1.86% boost::detail::shared_count::~shared_count (inline) 0 0% 70.87% 461ms 1.86% boost::shared_ptr::~shared_ptr (inline) 2ms 0.0081% 70.88% 451ms 1.82% Cell::GetMutationState 16ms 0.065% 70.95% 448ms 1.81% operator new 125ms 0.5% 71.45% 442ms 1.78% std::_Rb_tree::_M_erase 4ms 0.016% 71.47% 440ms 1.78% std::set::set (inline) 148ms 0.6% 72.06% 439ms 1.77% std::_Rb_tree::_M_clone_node (inline) 0 0% 72.06% 422ms 1.70% std::_Rb_tree::_M_get_node (inline) 128ms 0.52% 72.58% 421ms 1.70% __GI___libc_malloc 411ms 1.66% 74.24% 421ms 1.70% boost::detail::sp_counted_base::release 2ms 0.0081% 74.25% 407ms 1.64% AbstractCellProperty::IsSubType (inline) 92ms 0.37% 74.62% 404ms 1.63% boost::numeric::ublas::vector_binary::size (inline) 83ms 0.34% 74.95% 398ms 1.61% Node::GetRadius 372ms 1.50% 76.46% 372ms 1.50% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 76.46% 364ms 1.47% boost::numeric::ublas::inner_prod (inline) 1ms 0.004% 76.46% 363ms 1.47% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 12ms 0.048% 76.51% 362ms 1.46% boost::numeric::ublas::vector_scalar_binary::evaluate 1ms 0.004% 76.51% 352ms 1.42% NodesOnlyMesh::ReMesh 3ms 0.012% 76.52% 340ms 1.37% NodesOnlyMesh::UpdateNodeIndices 339ms 1.37% 77.89% 339ms 1.37% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 45ms 0.18% 78.08% 333ms 1.34% std::_Rb_tree::~_Rb_tree (inline) 0 0% 78.08% 327ms 1.32% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 78.08% 323ms 1.30% boost::numeric::ublas::c_vector::assign (inline) 4ms 0.016% 78.09% 319ms 1.29% NodeBasedCellPopulation::UpdateMapsAfterRemesh 318ms 1.28% 79.38% 318ms 1.28% Node::CheckForNodeAttributes 0 0% 79.38% 305ms 1.23% std::_Rb_tree::_M_drop_node (inline) 115ms 0.46% 79.84% 294ms 1.19% boost::numeric::ublas::vector_inner_prod::apply (inline) 285ms 1.15% 80.99% 285ms 1.15% [libchaste_mesh.so] 8ms 0.032% 81.02% 282ms 1.14% std::_Rb_tree::_M_emplace_hint_unique 0 0% 81.02% 270ms 1.09% NodesOnlyMesh::UpdateBoxCollection 0 0% 81.02% 267ms 1.08% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 81.02% 266ms 1.07% VtkMeshWriter::WriteFiles 1ms 0.004% 81.03% 262ms 1.06% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 3ms 0.012% 81.04% 256ms 1.03% std::__new_allocator::deallocate (inline) 3ms 0.012% 81.05% 248ms 1.00% DistributedBoxCollection::GetProcessOwningNode 161ms 0.65% 81.70% 247ms 1% Node::AddNeighbour 0 0% 81.70% 245ms 0.99% std::set::~set (inline) 131ms 0.53% 82.23% 244ms 0.99% _int_malloc 76ms 0.31% 82.54% 236ms 0.95% __GI___libc_free 136ms 0.55% 83.09% 236ms 0.95% boost::shared_ptr::shared_ptr (inline) 232ms 0.94% 84.02% 232ms 0.94% Node::GetIndex 0 0% 84.02% 232ms 0.94% std::allocator_traits::deallocate (inline) 0 0% 84.02% 232ms 0.94% vtkStreamingDemandDrivenPipeline::Update 0 0% 84.02% 232ms 0.94% vtkXMLWriterBase::Write 103ms 0.42% 84.44% 230ms 0.93% std::__move_median_to_first (inline) 0 0% 84.44% 230ms 0.93% vtkDemandDrivenPipeline::ProcessRequest 0 0% 84.44% 229ms 0.92% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 84.44% 228ms 0.92% std::_Rb_tree::_M_put_node (inline) 0 0% 84.44% 227ms 0.92% vtkDemandDrivenPipeline::ExecuteData 0 0% 84.44% 226ms 0.91% vtkCompositeDataPipeline::ExecuteData 3ms 0.012% 84.45% 225ms 0.91% NodesOnlyMesh::AddNodesToBoxes 0 0% 84.45% 225ms 0.91% vtkExecutive::CallAlgorithm 0 0% 84.45% 225ms 0.91% vtkXMLUnstructuredDataWriter::ProcessRequest 3ms 0.012% 84.46% 224ms 0.9% CellPropertyCollection::HasProperty 0 0% 84.46% 221ms 0.89% Cell::HasCellProperty (inline) 0 0% 84.46% 216ms 0.87% boost::numeric::ublas::vector_binary::operator() (inline) 13ms 0.052% 84.51% 212ms 0.86% boost::numeric::ublas::vector_reference::operator() (inline) 5ms 0.02% 84.53% 205ms 0.83% Cell::ReadyToDivide 20ms 0.081% 84.62% 197ms 0.8% std::__insertion_sort (inline) 0 0% 84.62% 185ms 0.75% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 84.62% 185ms 0.75% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 84.62% 176ms 0.71% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 84.62% 175ms 0.71% std::_Rb_tree::clear (inline) 174ms 0.7% 85.32% 174ms 0.7% [libchaste_cell_based.so] 8ms 0.032% 85.35% 159ms 0.64% boost::numeric::ublas::c_vector::operator[] (inline) 141ms 0.57% 85.92% 158ms 0.64% _int_free 0 0% 85.92% 156ms 0.63% NodesOnlyMesh::ResizeBoxCollection 2ms 0.0081% 85.93% 155ms 0.63% AbstractCellProperty::IsType (inline) 9ms 0.036% 85.96% 154ms 0.62% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 85.96% 153ms 0.62% vtkXMLWriter::WriteBinaryData 0 0% 85.96% 151ms 0.61% std::_Rb_tree::_Auto_node::_Auto_node (inline) 148ms 0.6% 86.56% 148ms 0.6% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 0 0% 86.56% 144ms 0.58% vtkXMLWriter::WriteBinaryDataBlock 0 0% 86.56% 144ms 0.58% vtkXMLWriter::WriteBinaryDataInternal 0 0% 86.56% 144ms 0.58% vtkXMLWriter::WriteCompressionBlock 0 0% 86.56% 143ms 0.58% AbstractCellPopulation::SetCellUsingLocationIndex 1ms 0.004% 86.56% 142ms 0.57% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 86.56% 142ms 0.57% vtkXMLWriter::WritePointsAppendedData 0 0% 86.56% 140ms 0.57% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 138ms 0.56% 87.12% 138ms 0.56% std::__adjacent_find (inline) 0 0% 87.12% 138ms 0.56% std::__unique (inline) 0 0% 87.12% 138ms 0.56% std::unique (inline) 0 0% 87.12% 133ms 0.54% std::map::clear (inline) 3ms 0.012% 87.13% 130ms 0.52% AbstractNumericalMethod::SafeNodePositionUpdate 129ms 0.52% 87.65% 129ms 0.52% Node::rGetLocation 1ms 0.004% 87.66% 125ms 0.5% Cell::GetCellId 124ms 0.5% 88.16% 124ms 0.5% __ieee754_log_fma