File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 21097ms, 88.94% of 23721ms total Dropped 763 nodes (cum <= 118.61ms) flat flat% sum% cum cum% 0 0% 0% 23583ms 99.42% __libc_start_call_main 0 0% 0% 23583ms 99.42% __libc_start_main_impl 0 0% 0% 23583ms 99.42% _start 0 0% 0% 23568ms 99.36% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 23568ms 99.36% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 23568ms 99.36% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 23568ms 99.36% main 0 0% 0% 23530ms 99.19% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 23530ms 99.19% CxxTest::TestRunner::runTest (inline) 0 0% 0% 23530ms 99.19% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 23522ms 99.16% AbstractCellBasedSimulation::Solve 4ms 0.017% 0.017% 13273ms 55.95% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.017% 9043ms 38.12% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.013% 0.03% 8432ms 35.55% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.042% 0.072% 8240ms 34.74% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.0042% 0.076% 7995ms 33.70% NodeBasedCellPopulation::Update 1192ms 5.03% 5.10% 7612ms 32.09% RepulsionForce::AddForceContribution (partial-inline) 12ms 0.051% 5.15% 5943ms 25.05% DistributedBoxCollection::CalculateInteriorNodePairs 2154ms 9.08% 14.23% 5001ms 21.08% std::_Rb_tree::_M_lower_bound (inline) 0 0% 14.23% 4552ms 19.19% OffLatticeSimulation::ApplyBoundaries 21ms 0.089% 14.32% 4472ms 18.85% NodeAttributes::RemoveDuplicateNeighbours 3ms 0.013% 14.33% 4277ms 18.03% std::__sort (inline) 0 0% 14.33% 4277ms 18.03% std::sort (inline) 194ms 0.82% 15.15% 3907ms 16.47% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 1ms 0.0042% 15.16% 3478ms 14.66% AbstractCellPopulation::Iterator::operator++ (inline) 225ms 0.95% 16.10% 3452ms 14.55% AbstractCellPopulation::Iterator::IsRealCell (inline) 52ms 0.22% 16.32% 3379ms 14.24% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 239ms 1.01% 17.33% 3221ms 13.58% std::_Rb_tree::find (inline) 0 0% 17.33% 3221ms 13.58% std::map::find (inline) 32ms 0.13% 17.47% 2920ms 12.31% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2801ms 11.81% 29.27% 2801ms 11.81% std::_Rb_tree::_S_right (inline) 221ms 0.93% 30.21% 2482ms 10.46% std::map::operator[] (partial-inline) 173ms 0.73% 30.93% 2475ms 10.43% std::__introsort_loop 28ms 0.12% 31.05% 2390ms 10.08% PlaneBoundaryCondition::ImposeBoundaryCondition 164ms 0.69% 31.74% 2340ms 9.86% AbstractMesh::GetNode 41ms 0.17% 31.92% 2329ms 9.82% NodesOnlyMesh::GetNodeOrHaloNode 29ms 0.12% 32.04% 2276ms 9.59% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.0042% 32.04% 2232ms 9.41% std::__unguarded_partition_pivot (inline) 95ms 0.4% 32.44% 2180ms 9.19% NodesOnlyMesh::SolveNodeMapping 25ms 0.11% 32.55% 2162ms 9.11% PlaneBoundaryCondition::VerifyBoundaryCondition 229ms 0.97% 33.51% 2051ms 8.65% DistributedBoxCollection::AddPairsFromBox 0 0% 33.51% 2031ms 8.56% std::_Rb_tree::lower_bound (inline) 0 0% 33.51% 2031ms 8.56% std::map::lower_bound (inline) 1059ms 4.46% 37.98% 2017ms 8.50% std::__unguarded_partition (inline) 2ms 0.0084% 37.99% 1797ms 7.58% std::__final_insertion_sort (inline) 87ms 0.37% 38.35% 1593ms 6.72% std::__unguarded_insertion_sort (inline) 561ms 2.36% 40.72% 1556ms 6.56% std::__unguarded_linear_insert (inline) 18ms 0.076% 40.80% 1554ms 6.55% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 34ms 0.14% 40.94% 1531ms 6.45% AbstractCellPopulation::GetCellUsingLocationIndex 1461ms 6.16% 47.10% 1461ms 6.16% __gnu_cxx::__normal_iterator::operator-- (inline) 48ms 0.2% 47.30% 1296ms 5.46% boost::numeric::ublas::c_vector::c_vector (partial-inline) 44ms 0.19% 47.49% 1181ms 4.98% boost::numeric::ublas::vector_assign (inline) 0 0% 47.49% 1157ms 4.88% NodeBasedCellPopulation::UpdateCellProcessLocation 4ms 0.017% 47.50% 1073ms 4.52% DistributedBoxCollection::CalculateBoundaryNodePairs 289ms 1.22% 48.72% 1068ms 4.50% boost::numeric::ublas::indexing_vector_assign 219ms 0.92% 49.64% 881ms 3.71% __dynamic_cast 174ms 0.73% 50.38% 826ms 3.48% AbstractMesh::GetVectorFromAtoB 378ms 1.59% 51.97% 818ms 3.45% DistributedBoxCollection::CalculateContainingBox (partial-inline) 269ms 1.13% 53.10% 771ms 3.25% NodeAttributes::AddNeighbour 18ms 0.076% 53.18% 767ms 3.23% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 53.18% 731ms 3.08% AbstractCellPopulation::WriteResultsToFiles 0 0% 53.18% 727ms 3.06% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 53.18% 711ms 3.00% boost::numeric::ublas::norm_2 (inline) 571ms 2.41% 55.59% 711ms 3.00% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 55.59% 711ms 3.00% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 709ms 2.99% 58.58% 709ms 2.99% boost::numeric::ublas::c_vector::operator() 3ms 0.013% 58.59% 682ms 2.88% boost::numeric::ublas::c_vector::operator= (inline) 27ms 0.11% 58.70% 678ms 2.86% std::_Rb_tree_const_iterator::operator++ (inline) 40ms 0.17% 58.87% 662ms 2.79% std::__copy_move::__copy_m (inline) 0 0% 58.87% 662ms 2.79% std::__copy_move_a (inline) 0 0% 58.87% 662ms 2.79% std::__copy_move_a1 (inline) 0 0% 58.87% 662ms 2.79% std::__copy_move_a2 (inline) 0 0% 58.87% 662ms 2.79% std::copy (inline) 648ms 2.73% 61.60% 648ms 2.73% std::_Rb_tree_increment 639ms 2.69% 64.30% 639ms 2.69% __memcpy_avx_unaligned_erms 502ms 2.12% 66.41% 595ms 2.51% std::vector::push_back (inline) 5ms 0.021% 66.43% 575ms 2.42% CellPropertyCollection::GetPropertiesType (inline) 2ms 0.0084% 66.44% 564ms 2.38% AbstractCellBasedSimulation::DoCellBirth 7ms 0.03% 66.47% 558ms 2.35% AbstractCentreBasedCellPopulation::GetDampingConstant 241ms 1.02% 67.49% 552ms 2.33% __cxxabiv1::__si_class_type_info::__do_dyncast 517ms 2.18% 69.67% 517ms 2.18% boost::numeric::ublas::same_impl_ex 0 0% 69.67% 483ms 2.04% AbstractCellBasedSimulation::DoCellRemoval (inline) 17ms 0.072% 69.74% 479ms 2.02% std::_Rb_tree::_Rb_tree (partial-inline) 92ms 0.39% 70.13% 479ms 2.02% std::__new_allocator::allocate (inline) 478ms 2.02% 72.14% 478ms 2.02% __strcmp_avx2 1ms 0.0042% 72.15% 475ms 2.00% NodeBasedCellPopulation::WriteVtkResultsToFile 5ms 0.021% 72.17% 469ms 1.98% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 29ms 0.12% 72.29% 469ms 1.98% boost::detail::shared_count::~shared_count (inline) 0 0% 72.29% 469ms 1.98% boost::shared_ptr::~shared_ptr (inline) 0 0% 72.29% 458ms 1.93% std::allocator_traits::allocate (inline) 44ms 0.19% 72.48% 457ms 1.93% std::_Rb_tree::_M_copy (inline) 0 0% 72.48% 435ms 1.83% std::_Rb_tree::_M_create_node (inline) 428ms 1.80% 74.28% 433ms 1.83% boost::detail::sp_counted_base::release 134ms 0.56% 74.85% 413ms 1.74% std::_Rb_tree::_M_clone_node (inline) 1ms 0.0042% 74.85% 402ms 1.69% Cell::GetMutationState 134ms 0.56% 75.41% 391ms 1.65% Node::GetRadius 137ms 0.58% 75.99% 391ms 1.65% std::_Rb_tree::_M_erase 0 0% 75.99% 387ms 1.63% std::_Rb_tree::_M_get_node (inline) 2ms 0.0084% 76.00% 382ms 1.61% std::set::set (inline) 23ms 0.097% 76.10% 377ms 1.59% operator new 1ms 0.0042% 76.10% 371ms 1.56% AbstractCellProperty::IsSubType (inline) 0 0% 76.10% 353ms 1.49% boost::numeric::ublas::c_vector::assign (inline) 100ms 0.42% 76.52% 346ms 1.46% __GI___libc_malloc 0 0% 76.52% 341ms 1.44% NodesOnlyMesh::ReMesh 0 0% 76.52% 334ms 1.41% boost::numeric::ublas::inner_prod (inline) 1ms 0.0042% 76.53% 334ms 1.41% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 23ms 0.097% 76.62% 333ms 1.40% boost::numeric::ublas::vector_scalar_binary::evaluate 1ms 0.0042% 76.63% 327ms 1.38% NodesOnlyMesh::UpdateNodeIndices 24ms 0.1% 76.73% 324ms 1.37% boost::numeric::ublas::vector_binary::size (inline) 0 0% 76.73% 324ms 1.37% std::_Rb_tree::_Alloc_node::operator() (inline) 315ms 1.33% 78.06% 315ms 1.33% __gnu_cxx::__normal_iterator::operator++ (inline) 309ms 1.30% 79.36% 309ms 1.30% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 8ms 0.034% 79.39% 291ms 1.23% NodeBasedCellPopulation::UpdateMapsAfterRemesh 5ms 0.021% 79.41% 285ms 1.20% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 44ms 0.19% 79.60% 282ms 1.19% std::_Rb_tree::~_Rb_tree (inline) 1ms 0.0042% 79.60% 281ms 1.18% NodesOnlyMesh::UpdateBoxCollection 268ms 1.13% 80.73% 268ms 1.13% Node::CheckForNodeAttributes 4ms 0.017% 80.75% 265ms 1.12% DistributedBoxCollection::GetProcessOwningNode 97ms 0.41% 81.16% 257ms 1.08% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 81.16% 248ms 1.05% std::_Rb_tree::_M_drop_node (inline) 0 0% 81.16% 235ms 0.99% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 1ms 0.0042% 81.16% 233ms 0.98% VtkMeshWriter::WriteFiles 10ms 0.042% 81.21% 230ms 0.97% std::_Rb_tree::_M_emplace_hint_unique 0 0% 81.21% 223ms 0.94% NodesOnlyMesh::AddNodesToBoxes 4ms 0.017% 81.22% 221ms 0.93% CellPropertyCollection::HasProperty 4ms 0.017% 81.24% 221ms 0.93% std::__new_allocator::deallocate (inline) 0 0% 81.24% 220ms 0.93% Cell::HasCellProperty (inline) 89ms 0.38% 81.62% 209ms 0.88% std::__move_median_to_first (inline) 0 0% 81.62% 208ms 0.88% std::set::~set (inline) 1ms 0.0042% 81.62% 206ms 0.87% vtkXMLWriterBase::Write 1ms 0.0042% 81.62% 205ms 0.86% vtkStreamingDemandDrivenPipeline::Update 0 0% 81.62% 204ms 0.86% vtkDemandDrivenPipeline::ProcessRequest 0 0% 81.62% 203ms 0.86% vtkDemandDrivenPipeline::ExecuteData 0 0% 81.62% 203ms 0.86% vtkStreamingDemandDrivenPipeline::ProcessRequest 21ms 0.089% 81.71% 202ms 0.85% std::__insertion_sort (inline) 110ms 0.46% 82.18% 201ms 0.85% _int_malloc 0 0% 82.18% 201ms 0.85% vtkCompositeDataPipeline::ExecuteData 0 0% 82.18% 201ms 0.85% vtkExecutive::CallAlgorithm 0 0% 82.18% 201ms 0.85% vtkXMLUnstructuredDataWriter::ProcessRequest 199ms 0.84% 83.02% 199ms 0.84% [libchaste_cell_based.so] 0 0% 83.02% 197ms 0.83% std::allocator_traits::deallocate (inline) 0 0% 83.02% 196ms 0.83% std::_Rb_tree::_M_put_node (inline) 74ms 0.31% 83.33% 193ms 0.81% __GI___libc_free 7ms 0.03% 83.36% 192ms 0.81% Cell::ReadyToDivide 190ms 0.8% 84.16% 190ms 0.8% Node::GetIndex 0 0% 84.16% 190ms 0.8% NodesOnlyMesh::ResizeBoxCollection 12ms 0.051% 84.21% 189ms 0.8% NodesOnlyMesh::IsANodeCloseToDomainBoundary 87ms 0.37% 84.57% 177ms 0.75% boost::shared_ptr::shared_ptr (inline) 0 0% 84.57% 174ms 0.73% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 84.57% 174ms 0.73% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 84.57% 168ms 0.71% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 84.57% 166ms 0.7% std::_Rb_tree::clear (inline) 1ms 0.0042% 84.58% 163ms 0.69% AbstractCellProperty::IsType (inline) 157ms 0.66% 85.24% 162ms 0.68% std::__adjacent_find (inline) 0 0% 85.24% 162ms 0.68% std::__unique (inline) 0 0% 85.24% 162ms 0.68% std::unique (inline) 157ms 0.66% 85.90% 157ms 0.66% boost::shared_ptr::operator-> (inline) 150ms 0.63% 86.54% 150ms 0.63% [libchaste_mesh.so] 147ms 0.62% 87.15% 147ms 0.62% Node::IsDeleted 0 0% 87.15% 144ms 0.61% vtkXMLWriter::WriteBinaryData 73ms 0.31% 87.46% 141ms 0.59% Node::AddNeighbour 12ms 0.051% 87.51% 141ms 0.59% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 87.51% 141ms 0.59% vtkXMLWriter::WriteBinaryDataInternal 1ms 0.0042% 87.52% 139ms 0.59% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 87.52% 139ms 0.59% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.52% 137ms 0.58% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 87.52% 136ms 0.57% vtkXMLWriter::WriteCompressionBlock 9ms 0.038% 87.56% 133ms 0.56% DistributedBoxCollection::GetIsPeriodicAllDims 129ms 0.54% 88.10% 129ms 0.54% __ieee754_log_fma 4ms 0.017% 88.12% 127ms 0.54% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 88.12% 125ms 0.53% vtkXMLWriter::WritePointsAppendedData 49ms 0.21% 88.32% 123ms 0.52% AbstractCellProperty::IsSame 0 0% 88.32% 121ms 0.51% std::map::clear (inline) 32ms 0.13% 88.46% 120ms 0.51% AbstractCellCycleModel::GetAge 112ms 0.47% 88.93% 120ms 0.51% _int_free 2ms 0.0084% 88.94% 120ms 0.51% boost::numeric::ublas::c_vector::operator[] (inline)