File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 19382ms, 89.68% of 21613ms total Dropped 716 nodes (cum <= 108.06ms) flat flat% sum% cum cum% 0 0% 0% 21548ms 99.70% __libc_start_call_main 0 0% 0% 21548ms 99.70% __libc_start_main_impl 0 0% 0% 21548ms 99.70% _start 0 0% 0% 21533ms 99.63% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 21533ms 99.63% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 21533ms 99.63% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 21533ms 99.63% main 0 0% 0% 21504ms 99.50% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 21504ms 99.50% CxxTest::TestRunner::runTest (inline) 0 0% 0% 21504ms 99.50% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 21497ms 99.46% AbstractCellBasedSimulation::Solve 3ms 0.014% 0.014% 12152ms 56.23% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.014% 8313ms 38.46% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.014% 7296ms 33.76% NodeBasedCellPopulation::Update 5ms 0.023% 0.037% 6948ms 32.15% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.019% 0.056% 6792ms 31.43% AbstractNumericalMethod::ComputeForcesIncludingDamping 809ms 3.74% 3.80% 6216ms 28.76% RepulsionForce::AddForceContribution (partial-inline) 5ms 0.023% 3.82% 5535ms 25.61% DistributedBoxCollection::CalculateInteriorNodePairs 0 0% 3.82% 4936ms 22.84% OffLatticeSimulation::ApplyBoundaries 1970ms 9.11% 12.94% 4547ms 21.04% std::_Rb_tree::_M_lower_bound (inline) 21ms 0.097% 13.03% 4394ms 20.33% NodeAttributes::RemoveDuplicateNeighbours 2ms 0.0093% 13.04% 4214ms 19.50% std::__sort (inline) 0 0% 13.04% 4214ms 19.50% std::sort (inline) 245ms 1.13% 14.18% 3692ms 17.08% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 2ms 0.0093% 14.19% 3522ms 16.30% AbstractCellPopulation::Iterator::operator++ (inline) 195ms 0.9% 15.09% 3521ms 16.29% AbstractCellPopulation::Iterator::IsRealCell (inline) 137ms 0.63% 15.72% 3325ms 15.38% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 242ms 1.12% 16.84% 3028ms 14.01% std::_Rb_tree::find (inline) 0 0% 16.84% 3028ms 14.01% std::map::find (inline) 28ms 0.13% 16.97% 2947ms 13.64% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 92ms 0.43% 17.40% 2568ms 11.88% AbstractMesh::GetNode 41ms 0.19% 17.59% 2550ms 11.80% NodesOnlyMesh::GetNodeOrHaloNode 61ms 0.28% 17.87% 2500ms 11.57% PlaneBoundaryCondition::ImposeBoundaryCondition 203ms 0.94% 18.81% 2495ms 11.54% std::__introsort_loop 222ms 1.03% 19.84% 2481ms 11.48% NodesOnlyMesh::SolveNodeMapping 42ms 0.19% 20.03% 2436ms 11.27% PlaneBoundaryCondition::VerifyBoundaryCondition 189ms 0.87% 20.90% 2307ms 10.67% std::map::operator[] (partial-inline) 2272ms 10.51% 31.42% 2272ms 10.51% std::_Rb_tree::_S_right (inline) 2ms 0.0093% 31.43% 2199ms 10.17% std::__unguarded_partition_pivot (inline) 681ms 3.15% 34.58% 1999ms 9.25% std::__unguarded_partition (inline) 97ms 0.45% 35.03% 1980ms 9.16% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 35.03% 1808ms 8.37% std::_Rb_tree::lower_bound (inline) 0 0% 35.03% 1808ms 8.37% std::map::lower_bound (inline) 0 0% 35.03% 1709ms 7.91% std::__final_insertion_sort (inline) 114ms 0.53% 35.55% 1591ms 7.36% DistributedBoxCollection::AddPairsFromBox 113ms 0.52% 36.08% 1542ms 7.13% std::__unguarded_insertion_sort (inline) 10ms 0.046% 36.12% 1445ms 6.69% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 19ms 0.088% 36.21% 1425ms 6.59% AbstractCellPopulation::GetCellUsingLocationIndex 691ms 3.20% 39.41% 1363ms 6.31% std::__unguarded_linear_insert (inline) 64ms 0.3% 39.70% 1081ms 5.00% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 39.70% 1054ms 4.88% NodeBasedCellPopulation::UpdateCellProcessLocation 15ms 0.069% 39.77% 1051ms 4.86% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 1030ms 4.77% 44.54% 1030ms 4.77% __gnu_cxx::__normal_iterator::operator-- (inline) 2ms 0.0093% 44.55% 892ms 4.13% boost::numeric::ublas::vector_assign (inline) 23ms 0.11% 44.65% 891ms 4.12% boost::detail::shared_count::~shared_count (inline) 0 0% 44.65% 891ms 4.12% boost::shared_ptr::~shared_ptr (inline) 4ms 0.019% 44.67% 880ms 4.07% DistributedBoxCollection::CalculateBoundaryNodePairs 831ms 3.84% 48.52% 843ms 3.90% boost::detail::sp_counted_base::release 203ms 0.94% 49.46% 778ms 3.60% boost::numeric::ublas::indexing_vector_assign 269ms 1.24% 50.70% 755ms 3.49% __dynamic_cast 314ms 1.45% 52.15% 740ms 3.42% DistributedBoxCollection::CalculateContainingBox (partial-inline) 101ms 0.47% 52.62% 669ms 3.10% AbstractMesh::GetVectorFromAtoB 0 0% 52.62% 602ms 2.79% AbstractCellPopulation::WriteResultsToFiles 15ms 0.069% 52.69% 587ms 2.72% std::_Rb_tree_const_iterator::operator++ (inline) 577ms 2.67% 55.36% 577ms 2.67% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 57ms 0.26% 55.62% 567ms 2.62% std::__new_allocator::allocate (inline) 4ms 0.019% 55.64% 555ms 2.57% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 55.64% 553ms 2.56% std::allocator_traits::allocate (inline) 27ms 0.12% 55.77% 541ms 2.50% std::__copy_move::__copy_m (inline) 0 0% 55.77% 541ms 2.50% std::__copy_move_a (inline) 0 0% 55.77% 541ms 2.50% std::__copy_move_a1 (inline) 0 0% 55.77% 541ms 2.50% std::__copy_move_a2 (inline) 0 0% 55.77% 540ms 2.50% std::copy (inline) 256ms 1.18% 56.95% 539ms 2.49% NodeAttributes::AddNeighbour 539ms 2.49% 59.45% 539ms 2.49% [libchaste_cell_based.so] 0 0% 59.45% 524ms 2.42% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 3ms 0.014% 59.46% 523ms 2.42% AbstractCentreBasedCellPopulation::GetDampingConstant 10ms 0.046% 59.51% 522ms 2.42% CellPropertyCollection::GetPropertiesType (inline) 1ms 0.0046% 59.51% 516ms 2.39% AbstractCellBasedSimulation::DoCellBirth 0 0% 59.51% 514ms 2.38% std::_Rb_tree::_M_create_node (inline) 511ms 2.36% 61.87% 511ms 2.36% __gnu_cxx::__normal_iterator::operator++ (inline) 19ms 0.088% 61.96% 507ms 2.35% operator new 0 0% 61.96% 506ms 2.34% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 61.96% 505ms 2.34% boost::numeric::ublas::norm_2 (inline) 426ms 1.97% 63.93% 505ms 2.34% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 63.93% 499ms 2.31% AbstractCellBasedSimulation::DoCellRemoval (inline) 499ms 2.31% 66.24% 499ms 2.31% std::_Rb_tree_increment 498ms 2.30% 68.55% 498ms 2.30% [libchaste_mesh.so] 497ms 2.30% 70.85% 497ms 2.30% __memcpy_avx512_unaligned_erms 9ms 0.042% 70.89% 490ms 2.27% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 70.89% 486ms 2.25% std::_Rb_tree::_M_get_node (inline) 484ms 2.24% 73.13% 484ms 2.24% boost::numeric::ublas::c_vector::operator() 165ms 0.76% 73.89% 478ms 2.21% __GI___libc_malloc 19ms 0.088% 73.98% 473ms 2.19% std::_Rb_tree::_Rb_tree (partial-inline) 33ms 0.15% 74.13% 445ms 2.06% std::_Rb_tree::_M_copy (inline) 438ms 2.03% 76.16% 438ms 2.03% boost::numeric::ublas::same_impl_ex 97ms 0.45% 76.61% 426ms 1.97% std::_Rb_tree::~_Rb_tree (inline) 49ms 0.23% 76.83% 423ms 1.96% std::_Rb_tree::_M_erase 0 0% 76.83% 407ms 1.88% std::set::set (inline) 150ms 0.69% 77.53% 404ms 1.87% std::_Rb_tree::_M_clone_node (inline) 2ms 0.0093% 77.54% 399ms 1.85% NodeBasedCellPopulation::WriteVtkResultsToFile 195ms 0.9% 78.44% 395ms 1.83% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 78.44% 374ms 1.73% std::_Rb_tree::_M_drop_node (inline) 3ms 0.014% 78.45% 371ms 1.72% Cell::GetMutationState 0 0% 78.45% 367ms 1.70% std::set::~set (inline) 265ms 1.23% 79.68% 365ms 1.69% std::vector::push_back (inline) 4ms 0.019% 79.70% 341ms 1.58% AbstractCellProperty::IsSubType (inline) 8ms 0.037% 79.73% 328ms 1.52% boost::numeric::ublas::vector_binary::size (inline) 317ms 1.47% 81.20% 317ms 1.47% std::_Rb_tree::_S_left (inline) 0 0% 81.20% 312ms 1.44% NodesOnlyMesh::ReMesh 0 0% 81.20% 312ms 1.44% std::_Rb_tree::_Alloc_node::operator() (inline) 5ms 0.023% 81.22% 310ms 1.43% std::_Rb_tree::_M_emplace_hint_unique 309ms 1.43% 82.65% 309ms 1.43% __strcmp_evex 2ms 0.0093% 82.66% 303ms 1.40% NodesOnlyMesh::UpdateNodeIndices 3ms 0.014% 82.68% 275ms 1.27% Node::GetRadius 4ms 0.019% 82.70% 275ms 1.27% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 8ms 0.037% 82.73% 272ms 1.26% std::__new_allocator::deallocate (inline) 3ms 0.014% 82.75% 267ms 1.24% NodeBasedCellPopulation::UpdateMapsAfterRemesh 2ms 0.0093% 82.76% 263ms 1.22% DistributedBoxCollection::GetProcessOwningNode 165ms 0.76% 83.52% 259ms 1.20% _int_malloc 0 0% 83.52% 249ms 1.15% NodesOnlyMesh::UpdateBoxCollection 0 0% 83.52% 243ms 1.12% boost::numeric::ublas::c_vector::assign (inline) 0 0% 83.52% 238ms 1.10% std::allocator_traits::deallocate (inline) 204ms 0.94% 84.46% 234ms 1.08% boost::shared_ptr::shared_ptr (inline) 0 0% 84.46% 233ms 1.08% std::_Rb_tree::_M_put_node (inline) 63ms 0.29% 84.75% 232ms 1.07% __GI___libc_free 0 0% 84.75% 211ms 0.98% NodesOnlyMesh::AddNodesToBoxes 210ms 0.97% 85.73% 210ms 0.97% Node::CheckForNodeAttributes 0 0% 85.73% 202ms 0.93% std::_Rb_tree::_Auto_node::_Auto_node (inline) 63ms 0.29% 86.02% 191ms 0.88% std::__move_median_to_first (inline) 0 0% 86.02% 185ms 0.86% std::iter_swap (inline) 185ms 0.86% 86.87% 185ms 0.86% std::swap (inline) 0 0% 86.87% 183ms 0.85% Cell::HasCellProperty (inline) 3ms 0.014% 86.89% 183ms 0.85% CellPropertyCollection::HasProperty 0 0% 86.89% 174ms 0.81% boost::numeric::ublas::inner_prod (inline) 9ms 0.042% 86.93% 174ms 0.81% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 86.93% 174ms 0.81% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 171ms 0.79% 87.72% 171ms 0.79% boost::shared_ptr::operator-> (inline) 18ms 0.083% 87.80% 167ms 0.77% std::__insertion_sort (inline) 0 0% 87.80% 165ms 0.76% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 87.80% 165ms 0.76% VtkMeshWriter::WriteFiles 137ms 0.63% 88.44% 164ms 0.76% _int_free 8ms 0.037% 88.47% 160ms 0.74% Cell::ReadyToDivide 0 0% 88.47% 153ms 0.71% NodesOnlyMesh::ResizeBoxCollection 7ms 0.032% 88.51% 152ms 0.7% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 88.51% 151ms 0.7% std::__new_allocator::destroy (inline) 0 0% 88.51% 151ms 0.7% std::allocator_traits::destroy (inline) 0 0% 88.51% 148ms 0.68% vtkStreamingDemandDrivenPipeline::Update 0 0% 88.51% 148ms 0.68% vtkXMLWriterBase::Write 0 0% 88.51% 147ms 0.68% std::_Rb_tree::_M_destroy_node (inline) 0 0% 88.51% 147ms 0.68% vtkCompositeDataPipeline::ExecuteData 0 0% 88.51% 147ms 0.68% vtkDemandDrivenPipeline::ExecuteData 0 0% 88.51% 147ms 0.68% vtkDemandDrivenPipeline::ProcessRequest 0 0% 88.51% 147ms 0.68% vtkExecutive::CallAlgorithm 0 0% 88.51% 147ms 0.68% vtkStreamingDemandDrivenPipeline::ProcessRequest 1ms 0.0046% 88.51% 147ms 0.68% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 88.51% 146ms 0.68% boost::numeric::ublas::vector_binary::operator() (inline) 2ms 0.0093% 88.52% 141ms 0.65% Cell::GetCellId 28ms 0.13% 88.65% 137ms 0.63% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 88.65% 135ms 0.62% std::_Rb_tree::_M_insert_unique 0 0% 88.65% 135ms 0.62% std::set::insert (inline) 55ms 0.25% 88.90% 131ms 0.61% std::__adjacent_find (inline) 0 0% 88.90% 131ms 0.61% std::__unique (inline) 0 0% 88.90% 131ms 0.61% std::unique (inline) 6ms 0.028% 88.93% 129ms 0.6% AbstractCellProperty::IsType (inline) 2ms 0.0093% 88.94% 127ms 0.59% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 2ms 0.0093% 88.95% 126ms 0.58% AbstractCellPopulation::SetCellUsingLocationIndex 0 0% 88.95% 125ms 0.58% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 88.95% 125ms 0.58% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 88.95% 125ms 0.58% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 5ms 0.023% 88.97% 118ms 0.55% boost::numeric::ublas::c_vector::operator[] (inline) 117ms 0.54% 89.52% 117ms 0.54% Node::GetIndex 1ms 0.0046% 89.52% 115ms 0.53% DistributedBoxCollection::GetIsPeriodicAllDims 1ms 0.0046% 89.52% 113ms 0.52% AbstractNumericalMethod::SafeNodePositionUpdate 33ms 0.15% 89.68% 110ms 0.51% std::_Rb_tree::_M_insert_ (inline) 0 0% 89.68% 110ms 0.51% std::_Rb_tree::clear (inline)