File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 22249ms, 89.54% of 24847ms total Dropped 801 nodes (cum <= 124.23ms) flat flat% sum% cum cum% 0 0% 0% 24736ms 99.55% __libc_start_call_main 0 0% 0% 24736ms 99.55% __libc_start_main_impl 0 0% 0% 24736ms 99.55% _start 0 0% 0% 24718ms 99.48% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 24718ms 99.48% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 24718ms 99.48% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 24718ms 99.48% main 0 0% 0% 24681ms 99.33% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 24681ms 99.33% CxxTest::TestRunner::runTest (inline) 0 0% 0% 24681ms 99.33% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 24672ms 99.30% AbstractCellBasedSimulation::Solve 1ms 0.004% 0.004% 14083ms 56.68% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.004% 9383ms 37.76% AbstractCellBasedSimulation::UpdateCellPopulation 5ms 0.02% 0.024% 9137ms 36.77% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.032% 0.056% 8966ms 36.08% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.056% 8302ms 33.41% NodeBasedCellPopulation::Update 1321ms 5.32% 5.37% 8270ms 33.28% RepulsionForce::AddForceContribution (partial-inline) 12ms 0.048% 5.42% 6051ms 24.35% DistributedBoxCollection::CalculateInteriorNodePairs 2167ms 8.72% 14.14% 5209ms 20.96% std::_Rb_tree::_M_lower_bound (inline) 10ms 0.04% 14.18% 4745ms 19.10% NodeAttributes::RemoveDuplicateNeighbours 1ms 0.004% 14.19% 4635ms 18.65% OffLatticeSimulation::ApplyBoundaries 7ms 0.028% 14.21% 4400ms 17.71% std::__sort (inline) 0 0% 14.21% 4400ms 17.71% std::sort (inline) 174ms 0.7% 14.92% 4182ms 16.83% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 287ms 1.16% 16.07% 3553ms 14.30% std::_Rb_tree::find (inline) 0 0% 16.07% 3553ms 14.30% std::map::find (inline) 76ms 0.31% 16.38% 3436ms 13.83% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 1ms 0.004% 16.38% 3175ms 12.78% AbstractCellPopulation::Iterator::operator++ (inline) 164ms 0.66% 17.04% 3148ms 12.67% AbstractCellPopulation::Iterator::IsRealCell (inline) 3003ms 12.09% 29.13% 3003ms 12.09% std::_Rb_tree::_S_right (inline) 16ms 0.064% 29.19% 2766ms 11.13% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 180ms 0.72% 29.92% 2576ms 10.37% std::__introsort_loop 148ms 0.6% 30.51% 2504ms 10.08% AbstractMesh::GetNode 67ms 0.27% 30.78% 2500ms 10.06% NodesOnlyMesh::GetNodeOrHaloNode 192ms 0.77% 31.55% 2446ms 9.84% std::map::operator[] (partial-inline) 15ms 0.06% 31.61% 2442ms 9.83% PlaneBoundaryCondition::ImposeBoundaryCondition 40ms 0.16% 31.77% 2360ms 9.50% AbstractCellPopulation::GetLocationIndexUsingCell 102ms 0.41% 32.18% 2357ms 9.49% NodesOnlyMesh::SolveNodeMapping 0 0% 32.18% 2320ms 9.34% std::__unguarded_partition_pivot (inline) 12ms 0.048% 32.23% 2192ms 8.82% PlaneBoundaryCondition::VerifyBoundaryCondition 136ms 0.55% 32.78% 2092ms 8.42% DistributedBoxCollection::AddPairsFromBox 1101ms 4.43% 37.21% 2065ms 8.31% std::__unguarded_partition (inline) 0 0% 37.21% 1984ms 7.98% std::_Rb_tree::lower_bound (inline) 0 0% 37.21% 1984ms 7.98% std::map::lower_bound (inline) 1ms 0.004% 37.22% 1814ms 7.30% std::__final_insertion_sort (inline) 17ms 0.068% 37.28% 1723ms 6.93% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 32ms 0.13% 37.41% 1703ms 6.85% AbstractCellPopulation::GetCellUsingLocationIndex 130ms 0.52% 37.94% 1653ms 6.65% std::__unguarded_insertion_sort (inline) 526ms 2.12% 40.05% 1545ms 6.22% std::__unguarded_linear_insert (inline) 1442ms 5.80% 45.86% 1442ms 5.80% __gnu_cxx::__normal_iterator::operator-- (inline) 5ms 0.02% 45.88% 1260ms 5.07% DistributedBoxCollection::CalculateBoundaryNodePairs 50ms 0.2% 46.08% 1243ms 5.00% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 46.08% 1156ms 4.65% NodeBasedCellPopulation::UpdateCellProcessLocation 9ms 0.036% 46.11% 1109ms 4.46% boost::numeric::ublas::vector_assign (inline) 295ms 1.19% 47.30% 1068ms 4.30% __dynamic_cast 216ms 0.87% 48.17% 1017ms 4.09% boost::numeric::ublas::indexing_vector_assign 14ms 0.056% 48.23% 1008ms 4.06% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 231ms 0.93% 49.16% 833ms 3.35% NodeAttributes::AddNeighbour 388ms 1.56% 50.72% 827ms 3.33% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 50.72% 823ms 3.31% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 50.72% 815ms 3.28% boost::numeric::ublas::norm_2 (inline) 658ms 2.65% 53.37% 815ms 3.28% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 53.37% 815ms 3.28% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 191ms 0.77% 54.14% 808ms 3.25% AbstractMesh::GetVectorFromAtoB 6ms 0.024% 54.16% 789ms 3.18% boost::numeric::ublas::c_vector::operator= (inline) 32ms 0.13% 54.29% 771ms 3.10% std::__copy_move::__copy_m (inline) 0 0% 54.29% 771ms 3.10% std::__copy_move_a (inline) 0 0% 54.29% 771ms 3.10% std::__copy_move_a1 (inline) 0 0% 54.29% 771ms 3.10% std::__copy_move_a2 (inline) 0 0% 54.29% 771ms 3.10% std::copy (inline) 746ms 3.00% 57.29% 746ms 3.00% __memcpy_avx_unaligned_erms 0 0% 57.29% 740ms 2.98% AbstractCellPopulation::WriteResultsToFiles 701ms 2.82% 60.11% 701ms 2.82% boost::numeric::ublas::c_vector::operator() 39ms 0.16% 60.27% 678ms 2.73% std::_Rb_tree_const_iterator::operator++ (inline) 601ms 2.42% 62.69% 665ms 2.68% std::vector::push_back (inline) 294ms 1.18% 63.87% 645ms 2.60% __cxxabiv1::__si_class_type_info::__do_dyncast 632ms 2.54% 66.41% 632ms 2.54% std::_Rb_tree_increment 8ms 0.032% 66.45% 626ms 2.52% AbstractCentreBasedCellPopulation::GetDampingConstant 5ms 0.02% 66.47% 623ms 2.51% CellPropertyCollection::GetPropertiesType (inline) 3ms 0.012% 66.48% 595ms 2.39% AbstractCellBasedSimulation::DoCellBirth 85ms 0.34% 66.82% 575ms 2.31% std::__new_allocator::allocate (inline) 39ms 0.16% 66.98% 563ms 2.27% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 66.98% 554ms 2.23% std::allocator_traits::allocate (inline) 0 0% 66.98% 530ms 2.13% std::_Rb_tree::_M_create_node (inline) 528ms 2.13% 69.10% 528ms 2.13% __strcmp_avx2 520ms 2.09% 71.20% 520ms 2.09% boost::numeric::ublas::same_impl_ex 44ms 0.18% 71.37% 517ms 2.08% std::_Rb_tree::_M_copy (inline) 0 0% 71.37% 491ms 1.98% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 71.37% 486ms 1.96% AbstractCellBasedSimulation::DoCellRemoval (inline) 24ms 0.097% 71.47% 485ms 1.95% operator new 0 0% 71.47% 481ms 1.94% std::_Rb_tree::_M_get_node (inline) 44ms 0.18% 71.65% 479ms 1.93% boost::detail::shared_count::~shared_count (inline) 0 0% 71.65% 479ms 1.93% boost::shared_ptr::~shared_ptr (inline) 3ms 0.012% 71.66% 477ms 1.92% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 151ms 0.61% 72.27% 467ms 1.88% std::_Rb_tree::_M_clone_node (inline) 3ms 0.012% 72.28% 458ms 1.84% std::set::set (inline) 151ms 0.61% 72.89% 455ms 1.83% __GI___libc_malloc 114ms 0.46% 73.34% 443ms 1.78% std::_Rb_tree::_M_erase 7ms 0.028% 73.37% 439ms 1.77% Cell::GetMutationState 404ms 1.63% 75.00% 419ms 1.69% boost::detail::sp_counted_base::release 1ms 0.004% 75.00% 418ms 1.68% AbstractCellProperty::IsSubType (inline) 102ms 0.41% 75.41% 382ms 1.54% Node::GetRadius 0 0% 75.41% 372ms 1.50% std::_Rb_tree::_Alloc_node::operator() (inline) 73ms 0.29% 75.71% 365ms 1.47% std::_Rb_tree::~_Rb_tree (inline) 84ms 0.34% 76.05% 361ms 1.45% boost::numeric::ublas::vector_binary::size (inline) 0 0% 76.05% 359ms 1.44% boost::numeric::ublas::inner_prod (inline) 2ms 0.008% 76.05% 359ms 1.44% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 15ms 0.06% 76.11% 357ms 1.44% boost::numeric::ublas::vector_scalar_binary::evaluate 351ms 1.41% 77.53% 351ms 1.41% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 77.53% 350ms 1.41% boost::numeric::ublas::c_vector::assign (inline) 0 0% 77.53% 329ms 1.32% NodesOnlyMesh::ReMesh 0 0% 77.53% 320ms 1.29% std::_Rb_tree::_M_drop_node (inline) 4ms 0.016% 77.54% 318ms 1.28% NodesOnlyMesh::UpdateNodeIndices 310ms 1.25% 78.79% 311ms 1.25% std::__adjacent_find (inline) 0 0% 78.79% 311ms 1.25% std::__unique (inline) 0 0% 78.79% 311ms 1.25% std::unique (inline) 6ms 0.024% 78.81% 310ms 1.25% NodeBasedCellPopulation::UpdateMapsAfterRemesh 6ms 0.024% 78.84% 310ms 1.25% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 9ms 0.036% 78.87% 292ms 1.18% DistributedBoxCollection::GetProcessOwningNode 0 0% 78.87% 291ms 1.17% NodesOnlyMesh::UpdateBoxCollection 115ms 0.46% 79.34% 289ms 1.16% boost::numeric::ublas::vector_inner_prod::apply (inline) 3ms 0.012% 79.35% 288ms 1.16% std::__new_allocator::deallocate (inline) 284ms 1.14% 80.49% 284ms 1.14% Node::CheckForNodeAttributes 278ms 1.12% 81.61% 278ms 1.12% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 81.61% 277ms 1.11% std::set::~set (inline) 10ms 0.04% 81.65% 270ms 1.09% std::_Rb_tree::_M_emplace_hint_unique 0 0% 81.65% 264ms 1.06% std::allocator_traits::deallocate (inline) 84ms 0.34% 81.99% 260ms 1.05% __GI___libc_free 0 0% 81.99% 259ms 1.04% std::_Rb_tree::_M_put_node (inline) 202ms 0.81% 82.80% 257ms 1.03% Node::AddNeighbour 100ms 0.4% 83.21% 249ms 1.00% std::__move_median_to_first (inline) 146ms 0.59% 83.79% 244ms 0.98% _int_malloc 1ms 0.004% 83.80% 239ms 0.96% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 83.80% 238ms 0.96% VtkMeshWriter::WriteFiles 0 0% 83.80% 235ms 0.95% Cell::HasCellProperty (inline) 3ms 0.012% 83.81% 235ms 0.95% NodesOnlyMesh::AddNodesToBoxes 0 0% 83.81% 234ms 0.94% CellPropertyCollection::HasProperty 7ms 0.028% 83.84% 225ms 0.91% Cell::ReadyToDivide 14ms 0.056% 83.89% 224ms 0.9% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 83.89% 221ms 0.89% boost::numeric::ublas::vector_binary::operator() (inline) 220ms 0.89% 84.78% 220ms 0.89% [libchaste_mesh.so] 0 0% 84.78% 210ms 0.85% vtkStreamingDemandDrivenPipeline::Update 0 0% 84.78% 210ms 0.85% vtkXMLWriterBase::Write 0 0% 84.78% 208ms 0.84% vtkDemandDrivenPipeline::ProcessRequest 0 0% 84.78% 205ms 0.83% vtkExecutive::CallAlgorithm 0 0% 84.78% 205ms 0.83% vtkStreamingDemandDrivenPipeline::ProcessRequest 2ms 0.008% 84.79% 205ms 0.83% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 84.79% 204ms 0.82% vtkDemandDrivenPipeline::ExecuteData 203ms 0.82% 85.60% 203ms 0.82% Node::GetIndex 0 0% 85.60% 201ms 0.81% vtkCompositeDataPipeline::ExecuteData 95ms 0.38% 85.99% 198ms 0.8% boost::shared_ptr::shared_ptr (inline) 186ms 0.75% 86.73% 186ms 0.75% [libchaste_cell_based.so] 156ms 0.63% 87.36% 176ms 0.71% _int_free 0 0% 87.36% 171ms 0.69% AbstractCellProperty::IsType (inline) 0 0% 87.36% 169ms 0.68% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 87.36% 169ms 0.68% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 87.36% 168ms 0.68% std::_Rb_tree::clear (inline) 0 0% 87.36% 167ms 0.67% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 87.36% 160ms 0.64% NodesOnlyMesh::ResizeBoxCollection 8ms 0.032% 87.39% 160ms 0.64% std::__insertion_sort (inline) 10ms 0.04% 87.44% 159ms 0.64% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 87.44% 158ms 0.64% std::_Rb_tree::_Auto_node::_Auto_node (inline) 150ms 0.6% 88.04% 150ms 0.6% Node::rGetLocation 0 0% 88.04% 147ms 0.59% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 4ms 0.016% 88.05% 137ms 0.55% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 88.05% 137ms 0.55% vtkXMLWriter::WriteBinaryData 0 0% 88.05% 136ms 0.55% vtkXMLWriter::WriteBinaryDataBlock 0 0% 88.05% 136ms 0.55% vtkXMLWriter::WriteBinaryDataInternal 0 0% 88.05% 136ms 0.55% vtkXMLWriter::WriteCompressionBlock 55ms 0.22% 88.28% 134ms 0.54% AbstractCellProperty::IsSame 0 0% 88.28% 132ms 0.53% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 131ms 0.53% 88.80% 131ms 0.53% Node::IsDeleted 2ms 0.008% 88.81% 130ms 0.52% AbstractCellPopulation::SetCellUsingLocationIndex 130ms 0.52% 89.33% 130ms 0.52% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 49ms 0.2% 89.53% 129ms 0.52% AbstractCellCycleModel::GetAge 0 0% 89.53% 128ms 0.52% vtkXMLWriter::WritePointsAppendedData 3ms 0.012% 89.54% 127ms 0.51% AbstractNumericalMethod::SafeNodePositionUpdate