File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 23507ms, 87.99% of 26715ms total Dropped 778 nodes (cum <= 133.57ms) flat flat% sum% cum cum% 0 0% 0% 26628ms 99.67% __libc_start_call_main 0 0% 0% 26628ms 99.67% __libc_start_main_impl 0 0% 0% 26628ms 99.67% _start 0 0% 0% 26613ms 99.62% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 26613ms 99.62% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 26613ms 99.62% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 26613ms 99.62% main 0 0% 0% 26578ms 99.49% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 26578ms 99.49% CxxTest::TestRunner::runTest (inline) 0 0% 0% 26578ms 99.49% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 26570ms 99.46% AbstractCellBasedSimulation::Solve 1ms 0.0037% 0.0037% 18491ms 69.22% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.0075% 0.011% 14594ms 54.63% ForwardEulerNumericalMethod::UpdateAllNodePositions 17ms 0.064% 0.075% 14430ms 54.01% AbstractNumericalMethod::ComputeForcesIncludingDamping 94ms 0.35% 0.43% 13803ms 51.67% AbstractTwoBodyInteractionForce::AddForceContribution 1156ms 4.33% 4.75% 11783ms 44.11% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 3466ms 12.97% 17.73% 7607ms 28.47% std::_Rb_tree::_M_lower_bound (inline) 0 0% 17.73% 7149ms 26.76% AbstractCellBasedSimulation::UpdateCellPopulation 301ms 1.13% 18.85% 6975ms 26.11% std::_Rb_tree::find (inline) 0 0% 18.85% 6975ms 26.11% std::map::find (inline) 175ms 0.66% 19.51% 6869ms 25.71% NodesOnlyMesh::GetNodeOrHaloNode 419ms 1.57% 21.08% 6711ms 25.12% AbstractMesh::GetNode 0 0% 21.08% 6312ms 23.63% NodeBasedCellPopulation::Update 282ms 1.06% 22.13% 6296ms 23.57% NodesOnlyMesh::SolveNodeMapping 7ms 0.026% 22.16% 4700ms 17.59% DistributedBoxCollection::CalculateInteriorNodePairs 127ms 0.48% 22.64% 4507ms 16.87% boost::numeric::ublas::vector_assign (inline) 121ms 0.45% 23.09% 4463ms 16.71% boost::numeric::ublas::c_vector::c_vector (partial-inline) 4089ms 15.31% 38.39% 4089ms 15.31% std::_Rb_tree::_S_right (inline) 1ms 0.0037% 38.40% 3622ms 13.56% OffLatticeSimulation::ApplyBoundaries 8ms 0.03% 38.43% 3551ms 13.29% NodeAttributes::RemoveDuplicateNeighbours 6ms 0.022% 38.45% 3409ms 12.76% std::__sort (inline) 0 0% 38.45% 3409ms 12.76% std::sort (inline) 56ms 0.21% 38.66% 2618ms 9.80% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 841ms 3.15% 41.81% 2564ms 9.60% boost::numeric::ublas::indexing_vector_assign 2ms 0.0075% 41.82% 2430ms 9.10% AbstractCellPopulation::Iterator::operator++ (inline) 119ms 0.45% 42.26% 2413ms 9.03% AbstractCellPopulation::Iterator::IsRealCell 19ms 0.071% 42.33% 2106ms 7.88% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 128ms 0.48% 42.81% 1953ms 7.31% std::__introsort_loop 15ms 0.056% 42.87% 1907ms 7.14% PlaneBoundaryCondition::ImposeBoundaryCondition 32ms 0.12% 42.99% 1837ms 6.88% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 42.99% 1763ms 6.60% std::__unguarded_partition_pivot (inline) 17ms 0.064% 43.05% 1714ms 6.42% PlaneBoundaryCondition::VerifyBoundaryCondition 109ms 0.41% 43.46% 1633ms 6.11% DistributedBoxCollection::AddPairsFromBox 758ms 2.84% 46.30% 1576ms 5.90% std::__unguarded_partition (inline) 0 0% 46.30% 1448ms 5.42% std::__final_insertion_sort (inline) 144ms 0.54% 46.84% 1391ms 5.21% std::map::operator[] (partial-inline) 0 0% 46.84% 1349ms 5.05% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 46.84% 1340ms 5.02% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 86ms 0.32% 47.16% 1279ms 4.79% std::__unguarded_insertion_sort (inline) 1233ms 4.62% 51.77% 1233ms 4.62% boost::numeric::ublas::same_impl_ex 465ms 1.74% 53.51% 1224ms 4.58% std::__unguarded_linear_insert (inline) 122ms 0.46% 53.97% 1192ms 4.46% AbstractMesh::GetVectorFromAtoB 1083ms 4.05% 58.02% 1083ms 4.05% __gnu_cxx::__normal_iterator::operator-- (inline) 8ms 0.03% 58.05% 1043ms 3.90% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 58.05% 1014ms 3.80% std::_Rb_tree::lower_bound (inline) 0 0% 58.05% 1014ms 3.80% std::map::lower_bound (inline) 87ms 0.33% 58.38% 1008ms 3.77% boost::numeric::ublas::detail::equals 917ms 3.43% 61.81% 917ms 3.43% boost::numeric::ublas::c_vector::operator() 0 0% 61.81% 914ms 3.42% boost::numeric::ublas::norm_inf (inline) 408ms 1.53% 63.34% 914ms 3.42% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 63.34% 888ms 3.32% NodeBasedCellPopulation::UpdateCellProcessLocation 5ms 0.019% 63.36% 857ms 3.21% DistributedBoxCollection::CalculateBoundaryNodePairs 12ms 0.045% 63.40% 762ms 2.85% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 134ms 0.5% 63.90% 725ms 2.71% boost::numeric::ublas::vector_binary::size (inline) 178ms 0.67% 64.57% 661ms 2.47% NodeAttributes::AddNeighbour 294ms 1.10% 65.67% 659ms 2.47% DistributedBoxCollection::CalculateContainingBox (partial-inline) 472ms 1.77% 67.44% 642ms 2.40% __dynamic_cast 178ms 0.67% 68.10% 635ms 2.38% NodeAttributes::AddAppliedForceContribution 4ms 0.015% 68.12% 585ms 2.19% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 68.12% 578ms 2.16% AbstractCellPopulation::WriteResultsToFiles 93ms 0.35% 68.47% 569ms 2.13% std::__new_allocator::allocate (inline) 481ms 1.80% 70.27% 538ms 2.01% std::vector::push_back (inline) 20ms 0.075% 70.34% 517ms 1.94% std::_Rb_tree_const_iterator::operator++ (inline) 487ms 1.82% 72.17% 487ms 1.82% std::_Rb_tree_increment 61ms 0.23% 72.39% 482ms 1.80% operator new 5ms 0.019% 72.41% 464ms 1.74% AbstractCellBasedSimulation::DoCellBirth 0 0% 72.41% 457ms 1.71% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 72.41% 457ms 1.71% boost::numeric::ublas::c_vector::plus_assign (inline) 0 0% 72.41% 435ms 1.63% boost::numeric::ublas::norm_2 (inline) 349ms 1.31% 73.72% 435ms 1.63% boost::numeric::ublas::vector_norm_2::apply (inline) 3ms 0.011% 73.73% 429ms 1.61% CellPropertyCollection::GetPropertiesType (inline) 147ms 0.55% 74.28% 421ms 1.58% __GI___libc_malloc 3ms 0.011% 74.29% 386ms 1.44% NodeBasedCellPopulation::WriteVtkResultsToFile 2ms 0.0075% 74.30% 385ms 1.44% Cell::GetMutationState 0 0% 74.30% 373ms 1.40% AbstractCellBasedSimulation::DoCellRemoval (inline) 4ms 0.015% 74.31% 366ms 1.37% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 74.31% 365ms 1.37% boost::numeric::ublas::scalar_traits::norm_inf (inline) 0 0% 74.31% 365ms 1.37% boost::numeric::ublas::scalar_traits::type_abs (inline) 2ms 0.0075% 74.32% 364ms 1.36% boost_numeric_ublas_abs (inline) 362ms 1.36% 75.68% 362ms 1.36% std::abs (inline) 111ms 0.42% 76.09% 345ms 1.29% __GI___libc_free 336ms 1.26% 77.35% 336ms 1.26% Node::GetIndex 0 0% 77.35% 325ms 1.22% std::allocator_traits::allocate (inline) 19ms 0.071% 77.42% 315ms 1.18% boost::detail::shared_count::~shared_count (inline) 0 0% 77.42% 315ms 1.18% boost::shared_ptr::~shared_ptr (inline) 0 0% 77.42% 301ms 1.13% std::_Rb_tree::_M_create_node (inline) 290ms 1.09% 78.51% 295ms 1.10% boost::detail::sp_counted_base::release 0 0% 78.51% 290ms 1.09% boost::numeric::ublas::inner_prod (inline) 10ms 0.037% 78.54% 288ms 1.08% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 78.54% 288ms 1.08% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 279ms 1.04% 79.59% 279ms 1.04% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 3ms 0.011% 79.60% 278ms 1.04% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 0 0% 79.60% 276ms 1.03% AbstractCellProperty::IsSubType (inline) 6ms 0.022% 79.62% 275ms 1.03% AbstractCellPopulation::GetCellUsingLocationIndex 20ms 0.075% 79.70% 264ms 0.99% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 79.70% 264ms 0.99% boost::numeric::ublas::vector::vector (inline) 0 0% 79.70% 262ms 0.98% std::_Rb_tree::_M_get_node (inline) 259ms 0.97% 80.67% 259ms 0.97% __gnu_cxx::__normal_iterator::operator++ (inline) 3ms 0.011% 80.68% 241ms 0.9% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 95ms 0.36% 81.03% 239ms 0.89% boost::numeric::ublas::vector_inner_prod::apply (inline) 208ms 0.78% 81.81% 233ms 0.87% _int_free 11ms 0.041% 81.85% 233ms 0.87% std::_Rb_tree::_M_emplace_hint_unique 0 0% 81.85% 230ms 0.86% NodesOnlyMesh::ReMesh 5ms 0.019% 81.87% 228ms 0.85% DistributedBoxCollection::GetProcessOwningNode 50ms 0.19% 82.06% 227ms 0.85% Node::GetRadius 5ms 0.019% 82.08% 227ms 0.85% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 82.08% 226ms 0.85% NodesOnlyMesh::UpdateNodeIndices 68ms 0.25% 82.33% 222ms 0.83% std::_Rb_tree::_M_erase (partial-inline) 0 0% 82.33% 216ms 0.81% boost::numeric::ublas::c_vector::assign (inline) 0 0% 82.33% 211ms 0.79% NodesOnlyMesh::UpdateBoxCollection 6ms 0.022% 82.35% 207ms 0.77% boost::numeric::ublas::vector_reference::operator() (inline) 205ms 0.77% 83.12% 205ms 0.77% [libchaste_cell_based.so] 5ms 0.019% 83.14% 200ms 0.75% std::_Rb_tree::_Rb_tree (partial-inline) 199ms 0.74% 83.89% 199ms 0.74% [libchaste_mesh.so] 113ms 0.42% 84.31% 196ms 0.73% _int_malloc 173ms 0.65% 84.96% 193ms 0.72% Node::AddNeighbour 22ms 0.082% 85.04% 192ms 0.72% std::_Rb_tree::_M_copy (inline) 1ms 0.0037% 85.04% 190ms 0.71% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 85.04% 186ms 0.7% VtkMeshWriter::WriteFiles 184ms 0.69% 85.73% 184ms 0.69% Node::CheckForNodeAttributes 82ms 0.31% 86.04% 182ms 0.68% std::__move_median_to_first (inline) 1ms 0.0037% 86.04% 176ms 0.66% NodesOnlyMesh::AddNodesToBoxes 0 0% 86.04% 175ms 0.66% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 86.04% 173ms 0.65% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 86.04% 172ms 0.64% vtkDemandDrivenPipeline::ProcessRequest 0 0% 86.04% 172ms 0.64% vtkStreamingDemandDrivenPipeline::Update 0 0% 86.04% 172ms 0.64% vtkXMLWriterBase::Write 21ms 0.079% 86.12% 169ms 0.63% std::_Rb_tree::_M_clone_node (inline) 17ms 0.064% 86.18% 169ms 0.63% std::__insertion_sort (inline) 0 0% 86.18% 168ms 0.63% vtkExecutive::CallAlgorithm 0 0% 86.18% 168ms 0.63% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 86.18% 167ms 0.63% vtkCompositeDataPipeline::ExecuteData 0 0% 86.18% 167ms 0.63% vtkDemandDrivenPipeline::ExecuteData 0 0% 86.18% 167ms 0.63% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 86.18% 166ms 0.62% Cell::HasCellProperty (inline) 2ms 0.0075% 86.19% 166ms 0.62% CellPropertyCollection::HasProperty 163ms 0.61% 86.80% 163ms 0.61% __strcmp_evex 26ms 0.097% 86.90% 163ms 0.61% std::__new_allocator::deallocate (inline) 156ms 0.58% 87.48% 156ms 0.58% NodeBasedCellPopulation::GetNode 10ms 0.037% 87.52% 155ms 0.58% Cell::ReadyToDivide 0 0% 87.52% 148ms 0.55% NodesOnlyMesh::ResizeBoxCollection 10ms 0.037% 87.56% 147ms 0.55% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 87.56% 143ms 0.54% std::_Rb_tree::_M_drop_node (inline) 70ms 0.26% 87.82% 141ms 0.53% boost::shared_ptr::shared_ptr (inline) 0 0% 87.82% 141ms 0.53% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 87.82% 141ms 0.53% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 9ms 0.034% 87.85% 140ms 0.52% std::_Rb_tree::~_Rb_tree (inline) 34ms 0.13% 87.98% 140ms 0.52% std::__find_if (inline) 0 0% 87.98% 140ms 0.52% std::find_if (inline) 0 0% 87.98% 140ms 0.52% std::none_of (inline) 0 0% 87.98% 137ms 0.51% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 3ms 0.011% 87.99% 134ms 0.5% AbstractCellProperty::IsType (inline)