File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 23109ms, 89.33% of 25868ms total Dropped 775 nodes (cum <= 129.34ms) flat flat% sum% cum cum% 0 0% 0% 25793ms 99.71% __libc_start_call_main 0 0% 0% 25793ms 99.71% __libc_start_main_impl 0 0% 0% 25793ms 99.71% _start 0 0% 0% 25778ms 99.65% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 25778ms 99.65% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 25778ms 99.65% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 25778ms 99.65% main 0 0% 0% 25741ms 99.51% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 25741ms 99.51% CxxTest::TestRunner::runTest (inline) 0 0% 0% 25741ms 99.51% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0039% 0.0039% 25732ms 99.47% AbstractCellBasedSimulation::Solve 3ms 0.012% 0.015% 15005ms 58.01% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.015% 9538ms 36.87% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0077% 0.023% 9206ms 35.59% ForwardEulerNumericalMethod::UpdateAllNodePositions 7ms 0.027% 0.05% 9008ms 34.82% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.05% 8330ms 32.20% NodeBasedCellPopulation::Update 910ms 3.52% 3.57% 8183ms 31.63% RepulsionForce::AddForceContribution (partial-inline) 5ms 0.019% 3.59% 6270ms 24.24% DistributedBoxCollection::CalculateInteriorNodePairs 2ms 0.0077% 3.60% 5446ms 21.05% OffLatticeSimulation::ApplyBoundaries 2246ms 8.68% 12.28% 5038ms 19.48% std::_Rb_tree::_M_lower_bound (inline) 216ms 0.84% 13.11% 4591ms 17.75% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 17ms 0.066% 13.18% 4552ms 17.60% NodeAttributes::RemoveDuplicateNeighbours 8ms 0.031% 13.21% 4361ms 16.86% std::__sort (inline) 0 0% 13.21% 4361ms 16.86% std::sort (inline) 227ms 0.88% 14.09% 3984ms 15.40% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 0 0% 14.09% 3720ms 14.38% AbstractCellPopulation::Iterator::operator++ (inline) 213ms 0.82% 14.91% 3715ms 14.36% AbstractCellPopulation::Iterator::IsRealCell 361ms 1.40% 16.31% 3351ms 12.95% std::_Rb_tree::find (inline) 0 0% 16.31% 3351ms 12.95% std::map::find (inline) 31ms 0.12% 16.43% 3132ms 12.11% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 143ms 0.55% 16.98% 2763ms 10.68% AbstractMesh::GetNode 76ms 0.29% 17.27% 2762ms 10.68% NodesOnlyMesh::GetNodeOrHaloNode 61ms 0.24% 17.51% 2751ms 10.63% PlaneBoundaryCondition::ImposeBoundaryCondition 221ms 0.85% 18.36% 2695ms 10.42% std::__introsort_loop 62ms 0.24% 18.60% 2693ms 10.41% PlaneBoundaryCondition::VerifyBoundaryCondition 318ms 1.23% 19.83% 2692ms 10.41% std::map::operator[] (partial-inline) 180ms 0.7% 20.53% 2627ms 10.16% NodesOnlyMesh::SolveNodeMapping 2ms 0.0077% 20.54% 2380ms 9.20% std::__unguarded_partition_pivot (inline) 110ms 0.43% 20.96% 2276ms 8.80% AbstractCellPopulation::GetLocationIndexUsingCell 370ms 1.43% 22.39% 2259ms 8.73% DistributedBoxCollection::AddPairsFromBox 2212ms 8.55% 30.94% 2212ms 8.55% std::_Rb_tree::_S_right (inline) 773ms 2.99% 33.93% 2131ms 8.24% std::__unguarded_partition (inline) 0 0% 33.93% 2069ms 8.00% std::_Rb_tree::lower_bound (inline) 0 0% 33.93% 2069ms 8.00% std::map::lower_bound (inline) 19ms 0.073% 34.00% 1929ms 7.46% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 35ms 0.14% 34.14% 1860ms 7.19% AbstractCellPopulation::GetCellUsingLocationIndex 1ms 0.0039% 34.14% 1657ms 6.41% std::__final_insertion_sort (inline) 62ms 0.24% 34.38% 1509ms 5.83% boost::numeric::ublas::c_vector::c_vector (partial-inline) 148ms 0.57% 34.95% 1487ms 5.75% std::__unguarded_insertion_sort (inline) 13ms 0.05% 35.00% 1333ms 5.15% boost::numeric::ublas::vector_assign (inline) 698ms 2.70% 37.70% 1234ms 4.77% std::__unguarded_linear_insert (inline) 26ms 0.1% 37.80% 1216ms 4.70% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 37.80% 1183ms 4.57% NodeBasedCellPopulation::UpdateCellProcessLocation 286ms 1.11% 38.91% 1176ms 4.55% boost::numeric::ublas::indexing_vector_assign 403ms 1.56% 40.47% 1143ms 4.42% __dynamic_cast 9ms 0.035% 40.50% 977ms 3.78% DistributedBoxCollection::CalculateBoundaryNodePairs 123ms 0.48% 40.98% 953ms 3.68% AbstractMesh::GetVectorFromAtoB 31ms 0.12% 41.10% 854ms 3.30% boost::detail::shared_count::~shared_count (inline) 0 0% 41.10% 854ms 3.30% boost::shared_ptr::~shared_ptr (inline) 369ms 1.43% 42.52% 820ms 3.17% NodeAttributes::AddNeighbour 390ms 1.51% 44.03% 809ms 3.13% DistributedBoxCollection::CalculateContainingBox (partial-inline) 808ms 3.12% 47.15% 808ms 3.12% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 12ms 0.046% 47.20% 807ms 3.12% CellPropertyCollection::GetPropertiesType (inline) 784ms 3.03% 50.23% 801ms 3.10% boost::detail::sp_counted_base::release 34ms 0.13% 50.36% 794ms 3.07% std::_Rb_tree_const_iterator::operator++ (inline) 5ms 0.019% 50.38% 756ms 2.92% AbstractCentreBasedCellPopulation::GetDampingConstant 755ms 2.92% 53.30% 755ms 2.92% [libchaste_cell_based.so] 95ms 0.37% 53.67% 747ms 2.89% std::__new_allocator::allocate (inline) 741ms 2.86% 56.53% 741ms 2.86% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 56.53% 738ms 2.85% AbstractCellPopulation::WriteResultsToFiles 0 0% 56.53% 730ms 2.82% std::allocator_traits::allocate (inline) 22ms 0.085% 56.62% 725ms 2.80% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 56.62% 711ms 2.75% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 37ms 0.14% 56.76% 689ms 2.66% std::_Rb_tree::_M_copy (inline) 0 0% 56.76% 687ms 2.66% std::_Rb_tree::_M_create_node (inline) 687ms 2.66% 59.42% 687ms 2.66% std::_Rb_tree_increment 0 0% 59.42% 684ms 2.64% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 59.42% 683ms 2.64% boost::numeric::ublas::norm_2 (inline) 509ms 1.97% 61.38% 683ms 2.64% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 61.38% 648ms 2.51% std::_Rb_tree::_M_get_node (inline) 222ms 0.86% 62.24% 640ms 2.47% std::_Rb_tree::_M_clone_node (inline) 3ms 0.012% 62.25% 628ms 2.43% AbstractCellBasedSimulation::DoCellBirth 44ms 0.17% 62.42% 628ms 2.43% operator new 237ms 0.92% 63.34% 615ms 2.38% __cxxabiv1::__si_class_type_info::__do_dyncast 603ms 2.33% 65.67% 603ms 2.33% std::_Rb_tree::_S_left (inline) 601ms 2.32% 68.00% 601ms 2.32% boost::numeric::ublas::c_vector::operator() 0 0% 68.00% 599ms 2.32% std::set::set (inline) 21ms 0.081% 68.08% 597ms 2.31% boost::numeric::ublas::c_vector::operator= (inline) 2ms 0.0077% 68.08% 596ms 2.30% Cell::GetMutationState 0 0% 68.08% 579ms 2.24% AbstractCellBasedSimulation::DoCellRemoval (inline) 7ms 0.027% 68.11% 568ms 2.20% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 225ms 0.87% 68.98% 563ms 2.18% __GI___libc_malloc 41ms 0.16% 69.14% 561ms 2.17% std::__copy_move::__copy_m (inline) 0 0% 69.14% 561ms 2.17% std::__copy_move_a (inline) 0 0% 69.14% 561ms 2.17% std::__copy_move_a1 (inline) 0 0% 69.14% 561ms 2.17% std::__copy_move_a2 (inline) 0 0% 69.14% 561ms 2.17% std::copy (inline) 557ms 2.15% 71.29% 557ms 2.15% boost::numeric::ublas::same_impl_ex 383ms 1.48% 72.77% 528ms 2.04% std::vector::push_back (inline) 520ms 2.01% 74.78% 520ms 2.01% __gnu_cxx::__normal_iterator::operator++ (inline) 504ms 1.95% 76.73% 504ms 1.95% __strcmp_evex 503ms 1.94% 78.68% 503ms 1.94% [libchaste_mesh.so] 503ms 1.94% 80.62% 503ms 1.94% __memcpy_evex_unaligned_erms 4ms 0.015% 80.64% 500ms 1.93% AbstractCellProperty::IsSubType (inline) 97ms 0.37% 81.01% 499ms 1.93% std::_Rb_tree::_M_erase 0 0% 81.01% 488ms 1.89% std::_Rb_tree::_Alloc_node::operator() (inline) 4ms 0.015% 81.03% 467ms 1.81% NodeBasedCellPopulation::WriteVtkResultsToFile 131ms 0.51% 81.53% 455ms 1.76% boost::numeric::ublas::vector_binary::size (inline) 98ms 0.38% 81.91% 455ms 1.76% std::_Rb_tree::~_Rb_tree (inline) 0 0% 81.91% 392ms 1.52% std::_Rb_tree::_M_drop_node (inline) 0 0% 81.91% 371ms 1.43% std::set::~set (inline) 0 0% 81.91% 365ms 1.41% boost::numeric::ublas::c_vector::assign (inline) 35ms 0.14% 82.05% 363ms 1.40% Node::GetRadius 0 0% 82.05% 345ms 1.33% NodesOnlyMesh::ReMesh 3ms 0.012% 82.06% 337ms 1.30% NodesOnlyMesh::UpdateNodeIndices 0 0% 82.06% 334ms 1.29% NodesOnlyMesh::UpdateBoxCollection 6ms 0.023% 82.08% 312ms 1.21% NodeBasedCellPopulation::UpdateMapsAfterRemesh 6ms 0.023% 82.11% 305ms 1.18% std::_Rb_tree::_M_emplace_hint_unique 2ms 0.0077% 82.11% 301ms 1.16% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 11ms 0.043% 82.16% 295ms 1.14% std::__new_allocator::deallocate (inline) 2ms 0.0077% 82.16% 284ms 1.10% DistributedBoxCollection::GetProcessOwningNode 0 0% 82.16% 282ms 1.09% boost::numeric::ublas::inner_prod (inline) 3ms 0.012% 82.17% 281ms 1.09% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 249ms 0.96% 83.14% 279ms 1.08% boost::shared_ptr::shared_ptr (inline) 10ms 0.039% 83.18% 278ms 1.07% boost::numeric::ublas::vector_scalar_binary::evaluate 3ms 0.012% 83.19% 270ms 1.04% NodesOnlyMesh::AddNodesToBoxes 156ms 0.6% 83.79% 269ms 1.04% _int_malloc 0 0% 83.79% 264ms 1.02% std::allocator_traits::deallocate (inline) 260ms 1.01% 84.80% 260ms 1.01% Node::CheckForNodeAttributes 0 0% 84.80% 260ms 1.01% std::_Rb_tree::_M_put_node (inline) 59ms 0.23% 85.02% 259ms 1.00% __GI___libc_free 3ms 0.012% 85.04% 253ms 0.98% CellPropertyCollection::HasProperty 0 0% 85.04% 251ms 0.97% Cell::HasCellProperty (inline) 65ms 0.25% 85.29% 244ms 0.94% std::__move_median_to_first (inline) 64ms 0.25% 85.53% 234ms 0.9% boost::numeric::ublas::vector_inner_prod::apply (inline) 3ms 0.012% 85.55% 221ms 0.85% Cell::ReadyToDivide 0 0% 85.55% 204ms 0.79% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 85.55% 200ms 0.77% std::iter_swap (inline) 200ms 0.77% 86.32% 200ms 0.77% std::swap (inline) 0 0% 86.32% 199ms 0.77% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 86.32% 193ms 0.75% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 86.32% 192ms 0.74% VtkMeshWriter::WriteFiles 168ms 0.65% 86.97% 191ms 0.74% _int_free 188ms 0.73% 87.70% 188ms 0.73% boost::shared_ptr::operator-> (inline) 15ms 0.058% 87.75% 186ms 0.72% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 87.75% 183ms 0.71% NodesOnlyMesh::ResizeBoxCollection 7ms 0.027% 87.78% 181ms 0.7% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 87.78% 170ms 0.66% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 34ms 0.13% 87.91% 169ms 0.65% std::__insertion_sort (inline) 0 0% 87.91% 169ms 0.65% vtkStreamingDemandDrivenPipeline::Update 0 0% 87.91% 169ms 0.65% vtkXMLWriterBase::Write 8ms 0.031% 87.94% 168ms 0.65% AbstractCellProperty::IsType (inline) 1ms 0.0039% 87.95% 167ms 0.65% vtkDemandDrivenPipeline::ProcessRequest 0 0% 87.95% 166ms 0.64% std::_Rb_tree::clear (inline) 0 0% 87.95% 166ms 0.64% vtkExecutive::CallAlgorithm 0 0% 87.95% 166ms 0.64% vtkStreamingDemandDrivenPipeline::ProcessRequest 2ms 0.0077% 87.95% 166ms 0.64% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 87.95% 164ms 0.63% vtkCompositeDataPipeline::ExecuteData 0 0% 87.95% 164ms 0.63% vtkDemandDrivenPipeline::ExecuteData 94ms 0.36% 88.32% 161ms 0.62% AbstractCellCycleModel::GetAge 0 0% 88.32% 156ms 0.6% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 3ms 0.012% 88.33% 152ms 0.59% AbstractNumericalMethod::SafeNodePositionUpdate 2ms 0.0077% 88.34% 150ms 0.58% Cell::GetCellId 148ms 0.57% 88.91% 148ms 0.57% Node::GetIndex 0 0% 88.91% 144ms 0.56% std::__new_allocator::destroy (inline) 0 0% 88.91% 144ms 0.56% std::allocator_traits::destroy (inline) 103ms 0.4% 89.31% 143ms 0.55% std::__adjacent_find (inline) 0 0% 89.31% 143ms 0.55% std::__unique (inline) 0 0% 89.31% 143ms 0.55% std::unique (inline) 0 0% 89.31% 142ms 0.55% Cell::GetCellProliferativeType 0 0% 89.31% 142ms 0.55% std::map::map (inline) 1ms 0.0039% 89.31% 141ms 0.55% DistributedBoxCollection::GetIsPeriodicAllDims 2ms 0.0077% 89.32% 140ms 0.54% NodeBasedCellPopulation::SetNode 0 0% 89.32% 140ms 0.54% std::_Rb_tree::_M_destroy_node (inline) 0 0% 89.32% 138ms 0.53% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 89.32% 138ms 0.53% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 89.32% 137ms 0.53% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 3ms 0.012% 89.33% 133ms 0.51% NodeBasedCellPopulation::AcceptCellWriter 0 0% 89.33% 133ms 0.51% NodesOnlyMesh::SetNode 1ms 0.0039% 89.33% 132ms 0.51% std::_Rb_tree::_M_insert_unique 0 0% 89.33% 132ms 0.51% std::set::insert (inline) 0 0% 89.33% 131ms 0.51% AbstractCellPopulation::SetCellUsingLocationIndex