File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 24567ms, 88.09% of 27890ms total Dropped 798 nodes (cum <= 139.45ms) flat flat% sum% cum cum% 0 0% 0% 27806ms 99.70% __libc_start_call_main 0 0% 0% 27806ms 99.70% __libc_start_main_impl 0 0% 0% 27806ms 99.70% _start 0 0% 0% 27791ms 99.65% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 27791ms 99.65% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 27791ms 99.65% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 27791ms 99.65% main 0 0% 0% 27752ms 99.51% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 27752ms 99.51% CxxTest::TestRunner::runTest (inline) 0 0% 0% 27752ms 99.51% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0036% 0.0036% 27745ms 99.48% AbstractCellBasedSimulation::Solve 1ms 0.0036% 0.0072% 18823ms 67.49% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.0072% 0.014% 14861ms 53.28% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.022% 0.036% 14712ms 52.75% AbstractNumericalMethod::ComputeForcesIncludingDamping 95ms 0.34% 0.38% 13764ms 49.35% AbstractTwoBodyInteractionForce::AddForceContribution 1182ms 4.24% 4.61% 11742ms 42.10% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 0 0% 4.61% 7911ms 28.37% AbstractCellBasedSimulation::UpdateCellPopulation 3473ms 12.45% 17.07% 7709ms 27.64% std::_Rb_tree::_M_lower_bound (inline) 278ms 1% 18.06% 6971ms 24.99% std::_Rb_tree::find (inline) 0 0% 18.06% 6971ms 24.99% std::map::find (inline) 0 0% 18.06% 6946ms 24.90% NodeBasedCellPopulation::Update 151ms 0.54% 18.61% 6853ms 24.57% NodesOnlyMesh::GetNodeOrHaloNode 395ms 1.42% 20.02% 6692ms 23.99% AbstractMesh::GetNode 289ms 1.04% 21.06% 6305ms 22.61% NodesOnlyMesh::SolveNodeMapping 6ms 0.022% 21.08% 5250ms 18.82% DistributedBoxCollection::CalculateInteriorNodePairs 155ms 0.56% 21.63% 4502ms 16.14% boost::numeric::ublas::vector_assign (inline) 121ms 0.43% 22.07% 4486ms 16.08% boost::numeric::ublas::c_vector::c_vector (partial-inline) 4196ms 15.04% 37.11% 4196ms 15.04% std::_Rb_tree::_S_right (inline) 11ms 0.039% 37.15% 3691ms 13.23% NodeAttributes::RemoveDuplicateNeighbours 0 0% 37.15% 3647ms 13.08% OffLatticeSimulation::ApplyBoundaries 2ms 0.0072% 37.16% 3554ms 12.74% std::__sort (inline) 0 0% 37.16% 3554ms 12.74% std::sort (inline) 53ms 0.19% 37.35% 2643ms 9.48% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 829ms 2.97% 40.32% 2551ms 9.15% boost::numeric::ublas::indexing_vector_assign 2ms 0.0072% 40.33% 2525ms 9.05% AbstractCellPopulation::Iterator::operator++ (inline) 115ms 0.41% 40.74% 2514ms 9.01% AbstractCellPopulation::Iterator::IsRealCell (inline) 24ms 0.086% 40.83% 2199ms 7.88% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 174ms 0.62% 41.45% 2136ms 7.66% std::__introsort_loop 129ms 0.46% 41.91% 2083ms 7.47% DistributedBoxCollection::AddPairsFromBox 19ms 0.068% 41.98% 1945ms 6.97% PlaneBoundaryCondition::ImposeBoundaryCondition 0 0% 41.98% 1887ms 6.77% std::__unguarded_partition_pivot (inline) 42ms 0.15% 42.13% 1854ms 6.65% AbstractCellPopulation::GetLocationIndexUsingCell 9ms 0.032% 42.17% 1702ms 6.10% PlaneBoundaryCondition::VerifyBoundaryCondition 783ms 2.81% 44.97% 1616ms 5.79% std::__unguarded_partition (inline) 163ms 0.58% 45.56% 1467ms 5.26% std::map::operator[] (partial-inline) 1ms 0.0036% 45.56% 1414ms 5.07% std::__final_insertion_sort (inline) 0 0% 45.56% 1337ms 4.79% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 45.56% 1321ms 4.74% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1271ms 4.56% 50.12% 1271ms 4.56% boost::numeric::ublas::same_impl_ex 81ms 0.29% 50.41% 1248ms 4.47% std::__unguarded_insertion_sort (inline) 147ms 0.53% 50.94% 1196ms 4.29% AbstractMesh::GetVectorFromAtoB 460ms 1.65% 52.59% 1194ms 4.28% std::__unguarded_linear_insert (inline) 1098ms 3.94% 56.52% 1098ms 3.94% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 56.52% 1083ms 3.88% std::_Rb_tree::lower_bound (inline) 0 0% 56.52% 1083ms 3.88% std::map::lower_bound (inline) 10ms 0.036% 56.56% 1040ms 3.73% boost::numeric::ublas::detail::expression_type_check (inline) 97ms 0.35% 56.91% 1003ms 3.60% boost::numeric::ublas::detail::equals 0 0% 56.91% 947ms 3.40% NodeBasedCellPopulation::UpdateCellProcessLocation 8ms 0.029% 56.93% 910ms 3.26% AbstractCentreBasedCellPopulation::GetDampingConstant 6ms 0.022% 56.96% 905ms 3.24% DistributedBoxCollection::CalculateBoundaryNodePairs 0 0% 56.96% 898ms 3.22% boost::numeric::ublas::norm_inf (inline) 389ms 1.39% 58.35% 898ms 3.22% boost::numeric::ublas::vector_norm_inf::apply (inline) 27ms 0.097% 58.45% 873ms 3.13% std::_Rb_tree_const_iterator::operator++ (inline) 864ms 3.10% 61.55% 864ms 3.10% boost::numeric::ublas::c_vector::operator() 827ms 2.97% 64.51% 827ms 2.97% std::_Rb_tree_increment 291ms 1.04% 65.55% 779ms 2.79% NodeAttributes::AddNeighbour 132ms 0.47% 66.03% 754ms 2.70% boost::numeric::ublas::vector_binary::size (inline) 12ms 0.043% 66.07% 715ms 2.56% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 18ms 0.065% 66.13% 687ms 2.46% CellPropertyCollection::GetPropertiesType (inline) 299ms 1.07% 67.21% 655ms 2.35% DistributedBoxCollection::CalculateContainingBox (partial-inline) 445ms 1.60% 68.80% 629ms 2.26% __dynamic_cast 0 0% 68.80% 622ms 2.23% AbstractCellPopulation::WriteResultsToFiles 109ms 0.39% 69.19% 612ms 2.19% std::__new_allocator::allocate (inline) 147ms 0.53% 69.72% 608ms 2.18% NodeAttributes::AddAppliedForceContribution 3ms 0.011% 69.73% 603ms 2.16% AbstractCellBasedSimulation::DoCellBirth 6ms 0.022% 69.75% 603ms 2.16% Cell::GetMutationState 485ms 1.74% 71.49% 580ms 2.08% std::vector::push_back (inline) 54ms 0.19% 71.69% 502ms 1.80% operator new 0 0% 71.69% 461ms 1.65% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 71.69% 461ms 1.65% boost::numeric::ublas::c_vector::plus_assign (inline) 153ms 0.55% 72.23% 443ms 1.59% __GI___libc_malloc 0 0% 72.23% 439ms 1.57% boost::numeric::ublas::norm_2 (inline) 344ms 1.23% 73.47% 439ms 1.57% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 73.47% 414ms 1.48% NodeBasedCellPopulation::WriteVtkResultsToFile 136ms 0.49% 73.95% 388ms 1.39% __GI___libc_free 3ms 0.011% 73.97% 380ms 1.36% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 6ms 0.022% 73.99% 376ms 1.35% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 73.99% 373ms 1.34% std::allocator_traits::allocate (inline) 0 0% 73.99% 361ms 1.29% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 73.99% 358ms 1.28% std::_Rb_tree::_M_create_node (inline) 0 0% 73.99% 347ms 1.24% boost::numeric::ublas::scalar_traits::norm_inf (inline) 0 0% 73.99% 347ms 1.24% boost::numeric::ublas::scalar_traits::type_abs (inline) 0 0% 73.99% 346ms 1.24% boost_numeric_ublas_abs (inline) 346ms 1.24% 75.23% 346ms 1.24% std::abs (inline) 5ms 0.018% 75.25% 345ms 1.24% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 339ms 1.22% 76.46% 339ms 1.22% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 329ms 1.18% 77.64% 329ms 1.18% Node::GetIndex 1ms 0.0036% 77.64% 313ms 1.12% AbstractCellProperty::IsSubType (inline) 0 0% 77.64% 309ms 1.11% std::_Rb_tree::_M_get_node (inline) 34ms 0.12% 77.77% 308ms 1.10% boost::detail::shared_count::~shared_count (inline) 0 0% 77.77% 308ms 1.10% boost::shared_ptr::~shared_ptr (inline) 271ms 0.97% 78.74% 300ms 1.08% Node::AddNeighbour 0 0% 78.74% 293ms 1.05% Cell::HasCellProperty (inline) 1ms 0.0036% 78.74% 293ms 1.05% CellPropertyCollection::HasProperty 8ms 0.029% 78.77% 285ms 1.02% Cell::ReadyToDivide 0 0% 78.77% 283ms 1.01% boost::numeric::ublas::inner_prod (inline) 13ms 0.047% 78.82% 279ms 1.00% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 78.82% 279ms 1.00% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 86ms 0.31% 79.13% 278ms 1% std::_Rb_tree::_M_erase 262ms 0.94% 80.06% 272ms 0.98% boost::detail::sp_counted_base::release 85ms 0.3% 80.37% 266ms 0.95% std::__move_median_to_first (inline) 1ms 0.0036% 80.37% 261ms 0.94% NodeBasedCellPopulation::UpdateMapsAfterRemesh 21ms 0.075% 80.45% 260ms 0.93% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 80.45% 260ms 0.93% boost::numeric::ublas::vector::vector (inline) 17ms 0.061% 80.51% 257ms 0.92% std::_Rb_tree::_Rb_tree (partial-inline) 1ms 0.0036% 80.51% 253ms 0.91% NodesOnlyMesh::ReMesh 222ms 0.8% 81.31% 252ms 0.9% _int_free 3ms 0.011% 81.32% 246ms 0.88% NodesOnlyMesh::UpdateNodeIndices 4ms 0.014% 81.33% 241ms 0.86% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 241ms 0.86% 82.20% 241ms 0.86% __gnu_cxx::__normal_iterator::operator++ (inline) 21ms 0.075% 82.27% 235ms 0.84% std::_Rb_tree::_M_copy (inline) 111ms 0.4% 82.67% 230ms 0.82% boost::numeric::ublas::vector_inner_prod::apply (inline) 6ms 0.022% 82.69% 229ms 0.82% DistributedBoxCollection::GetProcessOwningNode 0 0% 82.69% 222ms 0.8% std::_Rb_tree::_Alloc_node::operator() (inline) 7ms 0.025% 82.72% 221ms 0.79% std::_Rb_tree::_M_emplace_hint_unique 60ms 0.22% 82.93% 220ms 0.79% Node::GetRadius 0 0% 82.93% 220ms 0.79% boost::numeric::ublas::c_vector::assign (inline) 0 0% 82.93% 217ms 0.78% NodesOnlyMesh::UpdateBoxCollection 115ms 0.41% 83.35% 217ms 0.78% _int_malloc 214ms 0.77% 84.11% 214ms 0.77% [libchaste_mesh.so] 31ms 0.11% 84.22% 214ms 0.77% std::_Rb_tree::_M_clone_node (inline) 8ms 0.029% 84.25% 213ms 0.76% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 84.25% 206ms 0.74% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 84.25% 206ms 0.74% VtkMeshWriter::WriteFiles 205ms 0.74% 84.99% 205ms 0.74% [libchaste_cell_based.so] 21ms 0.075% 85.06% 191ms 0.68% std::__new_allocator::deallocate (inline) 0 0% 85.06% 183ms 0.66% vtkStreamingDemandDrivenPipeline::Update 0 0% 85.06% 183ms 0.66% vtkXMLWriterBase::Write 0 0% 85.06% 181ms 0.65% vtkDemandDrivenPipeline::ProcessRequest 0 0% 85.06% 180ms 0.65% std::_Rb_tree::_M_drop_node (inline) 1ms 0.0036% 85.07% 178ms 0.64% vtkDemandDrivenPipeline::ExecuteData 0 0% 85.07% 178ms 0.64% vtkExecutive::CallAlgorithm 0 0% 85.07% 178ms 0.64% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 85.07% 176ms 0.63% vtkCompositeDataPipeline::ExecuteData 175ms 0.63% 85.69% 175ms 0.63% __strcmp_evex 0 0% 85.69% 175ms 0.63% vtkXMLUnstructuredDataWriter::ProcessRequest 168ms 0.6% 86.30% 168ms 0.6% Node::CheckForNodeAttributes 1ms 0.0036% 86.30% 166ms 0.6% AbstractCellProperty::IsType (inline) 22ms 0.079% 86.38% 165ms 0.59% std::__insertion_sort (inline) 0 0% 86.38% 163ms 0.58% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 86.38% 162ms 0.58% NodesOnlyMesh::AddNodesToBoxes 160ms 0.57% 86.95% 160ms 0.57% boost::shared_ptr::operator-> (inline) 0 0% 86.95% 159ms 0.57% std::allocator_traits::deallocate (inline) 158ms 0.57% 87.52% 158ms 0.57% NodeBasedCellPopulation::GetNode 0 0% 87.52% 156ms 0.56% std::_Rb_tree::_M_put_node (inline) 0 0% 87.52% 156ms 0.56% std::_Rb_tree::clear (inline) 1ms 0.0036% 87.52% 150ms 0.54% std::set::set (inline) 0 0% 87.52% 146ms 0.52% NodesOnlyMesh::ResizeBoxCollection 13ms 0.047% 87.57% 145ms 0.52% NodesOnlyMesh::IsANodeCloseToDomainBoundary 140ms 0.5% 88.07% 140ms 0.5% Node::rGetLocation 4ms 0.014% 88.09% 140ms 0.5% std::_Rb_tree::~_Rb_tree (inline)