File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 19694ms, 87.57% of 22490ms total Dropped 709 nodes (cum <= 112.45ms) flat flat% sum% cum cum% 0 0% 0% 22413ms 99.66% __libc_start_call_main 0 0% 0% 22413ms 99.66% __libc_start_main_impl 0 0% 0% 22413ms 99.66% _start 0 0% 0% 22400ms 99.60% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 22400ms 99.60% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 22400ms 99.60% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 22400ms 99.60% main 0 0% 0% 22369ms 99.46% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 22369ms 99.46% CxxTest::TestRunner::runTest (inline) 0 0% 0% 22369ms 99.46% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 22363ms 99.44% AbstractCellBasedSimulation::Solve 1ms 0.0044% 0.0044% 15454ms 68.71% OffLatticeSimulation::UpdateCellLocationsAndTopology 3ms 0.013% 0.018% 11731ms 52.16% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.0089% 0.027% 11597ms 51.57% AbstractNumericalMethod::ComputeForcesIncludingDamping 72ms 0.32% 0.35% 11207ms 49.83% AbstractTwoBodyInteractionForce::AddForceContribution 1147ms 5.10% 5.45% 10107ms 44.94% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 3642ms 16.19% 21.64% 6513ms 28.96% std::_Rb_tree::_M_lower_bound (inline) 0 0% 21.64% 6124ms 27.23% AbstractCellBasedSimulation::UpdateCellPopulation 28ms 0.12% 21.77% 6108ms 27.16% NodesOnlyMesh::GetNodeOrHaloNode 308ms 1.37% 23.13% 6075ms 27.01% AbstractMesh::GetNode 298ms 1.33% 24.46% 5920ms 26.32% std::_Rb_tree::find (inline) 0 0% 24.46% 5918ms 26.31% std::map::find (inline) 446ms 1.98% 26.44% 5773ms 25.67% NodesOnlyMesh::SolveNodeMapping 0 0% 26.44% 5424ms 24.12% NodeBasedCellPopulation::Update 5ms 0.022% 26.47% 4072ms 18.11% DistributedBoxCollection::CalculateInteriorNodePairs 0 0% 26.47% 3520ms 15.65% OffLatticeSimulation::ApplyBoundaries 19ms 0.084% 26.55% 3358ms 14.93% NodeAttributes::RemoveDuplicateNeighbours 4ms 0.018% 26.57% 3226ms 14.34% std::__sort (inline) 0 0% 26.57% 3226ms 14.34% std::sort (inline) 138ms 0.61% 27.18% 3177ms 14.13% boost::numeric::ublas::c_vector::c_vector (partial-inline) 83ms 0.37% 27.55% 3126ms 13.90% boost::numeric::ublas::vector_assign (inline) 2825ms 12.56% 40.11% 2825ms 12.56% std::_Rb_tree::_S_right (inline) 152ms 0.68% 40.79% 2452ms 10.90% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 1ms 0.0044% 40.79% 2411ms 10.72% AbstractCellPopulation::Iterator::operator++ (inline) 119ms 0.53% 41.32% 2395ms 10.65% AbstractCellPopulation::Iterator::IsRealCell (inline) 18ms 0.08% 41.40% 1972ms 8.77% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 134ms 0.6% 42.00% 1852ms 8.23% std::__introsort_loop 60ms 0.27% 42.26% 1825ms 8.11% PlaneBoundaryCondition::ImposeBoundaryCondition 44ms 0.2% 42.46% 1695ms 7.54% PlaneBoundaryCondition::VerifyBoundaryCondition 0 0% 42.46% 1637ms 7.28% std::__unguarded_partition_pivot (inline) 480ms 2.13% 44.59% 1499ms 6.67% boost::numeric::ublas::indexing_vector_assign 52ms 0.23% 44.82% 1485ms 6.60% AbstractCellPopulation::GetLocationIndexUsingCell 685ms 3.05% 47.87% 1478ms 6.57% std::__unguarded_partition (inline) 1ms 0.0044% 47.87% 1370ms 6.09% std::__final_insertion_sort (inline) 183ms 0.81% 48.69% 1345ms 5.98% std::map::operator[] (partial-inline) 75ms 0.33% 49.02% 1216ms 5.41% std::__unguarded_insertion_sort (inline) 1164ms 5.18% 54.20% 1164ms 5.18% __gnu_cxx::__normal_iterator::operator-- (inline) 367ms 1.63% 55.83% 1142ms 5.08% std::__unguarded_linear_insert (inline) 128ms 0.57% 56.40% 1118ms 4.97% DistributedBoxCollection::AddPairsFromBox 0 0% 56.40% 1035ms 4.60% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 56.40% 1027ms 4.57% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 56.40% 962ms 4.28% std::_Rb_tree::lower_bound (inline) 0 0% 56.40% 962ms 4.28% std::map::lower_bound (inline) 877ms 3.90% 60.30% 877ms 3.90% boost::numeric::ublas::same_impl_ex 24ms 0.11% 60.40% 836ms 3.72% boost::numeric::ublas::detail::expression_type_check (inline) 153ms 0.68% 61.08% 834ms 3.71% AbstractMesh::GetVectorFromAtoB 45ms 0.2% 61.29% 806ms 3.58% boost::numeric::ublas::detail::equals 15ms 0.067% 61.35% 743ms 3.30% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 4ms 0.018% 61.37% 743ms 3.30% DistributedBoxCollection::CalculateBoundaryNodePairs 0 0% 61.37% 732ms 3.25% NodeBasedCellPopulation::UpdateCellProcessLocation 0 0% 61.37% 729ms 3.24% boost::numeric::ublas::norm_inf (inline) 317ms 1.41% 62.78% 729ms 3.24% boost::numeric::ublas::vector_norm_inf::apply (inline) 28ms 0.12% 62.90% 594ms 2.64% boost::detail::shared_count::~shared_count (inline) 0 0% 62.90% 594ms 2.64% boost::shared_ptr::~shared_ptr (inline) 560ms 2.49% 65.39% 563ms 2.50% boost::detail::sp_counted_base::release 251ms 1.12% 66.51% 547ms 2.43% DistributedBoxCollection::CalculateContainingBox (partial-inline) 70ms 0.31% 66.82% 511ms 2.27% boost::numeric::ublas::vector_binary::size (inline) 486ms 2.16% 68.98% 486ms 2.16% boost::numeric::ublas::c_vector::operator() 42ms 0.19% 69.17% 486ms 2.16% std::__new_allocator::allocate (inline) 0 0% 69.17% 468ms 2.08% AbstractCellPopulation::WriteResultsToFiles 75ms 0.33% 69.50% 440ms 1.96% operator new 126ms 0.56% 70.06% 433ms 1.93% NodeAttributes::AddAppliedForceContribution 32ms 0.14% 70.20% 393ms 1.75% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 70.20% 374ms 1.66% AbstractCellBasedSimulation::DoCellBirth 1ms 0.0044% 70.21% 366ms 1.63% AbstractCentreBasedCellPopulation::GetDampingConstant 158ms 0.7% 70.91% 360ms 1.60% __GI___libc_malloc 355ms 1.58% 72.49% 355ms 1.58% std::_Rb_tree_increment 84ms 0.37% 72.86% 332ms 1.48% __GI___libc_free 212ms 0.94% 73.81% 328ms 1.46% __dynamic_cast 0 0% 73.81% 326ms 1.45% AbstractCellBasedSimulation::DoCellRemoval (inline) 1ms 0.0044% 73.81% 323ms 1.44% NodeBasedCellPopulation::WriteVtkResultsToFile 4ms 0.018% 73.83% 320ms 1.42% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 123ms 0.55% 74.38% 311ms 1.38% NodeAttributes::AddNeighbour 0 0% 74.38% 307ms 1.37% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 74.38% 307ms 1.37% boost::numeric::ublas::c_vector::plus_assign (inline) 0 0% 74.38% 306ms 1.36% boost::numeric::ublas::norm_2 (inline) 268ms 1.19% 75.57% 306ms 1.36% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 75.57% 271ms 1.20% std::allocator_traits::allocate (inline) 187ms 0.83% 76.40% 257ms 1.14% std::vector::push_back (inline) 0 0% 76.40% 251ms 1.12% boost::numeric::ublas::scalar_traits::norm_inf (inline) 0 0% 76.40% 251ms 1.12% boost::numeric::ublas::scalar_traits::type_abs (inline) 4ms 0.018% 76.42% 250ms 1.11% CellPropertyCollection::GetPropertiesType (inline) 0 0% 76.42% 250ms 1.11% boost_numeric_ublas_abs (inline) 250ms 1.11% 77.53% 250ms 1.11% std::abs (inline) 199ms 0.88% 78.41% 246ms 1.09% _int_free 0 0% 78.41% 245ms 1.09% NodesOnlyMesh::ReMesh 26ms 0.12% 78.53% 241ms 1.07% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 78.53% 241ms 1.07% boost::numeric::ublas::vector::vector (inline) 1ms 0.0044% 78.53% 236ms 1.05% NodesOnlyMesh::UpdateNodeIndices 49ms 0.22% 78.75% 232ms 1.03% Node::GetRadius 227ms 1.01% 79.76% 227ms 1.01% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 79.76% 226ms 1.00% std::_Rb_tree::_M_create_node (inline) 225ms 1.00% 80.76% 225ms 1.00% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 80.76% 220ms 0.98% std::_Rb_tree::_M_get_node (inline) 0 0% 80.76% 217ms 0.96% Cell::GetMutationState 9ms 0.04% 80.80% 196ms 0.87% std::_Rb_tree::_M_emplace_hint_unique 193ms 0.86% 81.66% 193ms 0.86% NodeBasedCellPopulation::GetNode 5ms 0.022% 81.68% 193ms 0.86% NodeBasedCellPopulation::UpdateMapsAfterRemesh 45ms 0.2% 81.88% 193ms 0.86% std::_Rb_tree::_M_erase (partial-inline) 0 0% 81.88% 192ms 0.85% NodesOnlyMesh::UpdateBoxCollection 4ms 0.018% 81.90% 191ms 0.85% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 81.90% 191ms 0.85% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 0 0% 81.90% 176ms 0.78% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 175ms 0.78% 82.68% 175ms 0.78% Node::GetIndex 0 0% 82.68% 173ms 0.77% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 82.68% 171ms 0.76% AbstractCellProperty::IsSubType (inline) 0 0% 82.68% 169ms 0.75% boost::numeric::ublas::inner_prod (inline) 8ms 0.036% 82.71% 168ms 0.75% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 82.71% 168ms 0.75% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 167ms 0.74% 83.45% 167ms 0.74% Node::CheckForNodeAttributes 2ms 0.0089% 83.46% 166ms 0.74% DistributedBoxCollection::GetProcessOwningNode 0 0% 83.46% 164ms 0.73% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 83.46% 164ms 0.73% VtkMeshWriter::WriteFiles 163ms 0.72% 84.19% 163ms 0.72% [libchaste_cell_based.so] 0 0% 84.19% 161ms 0.72% boost::numeric::ublas::c_vector::assign (inline) 144ms 0.64% 84.83% 160ms 0.71% boost::shared_ptr::shared_ptr (inline) 0 0% 84.83% 158ms 0.7% NodesOnlyMesh::AddNodesToBoxes 19ms 0.084% 84.91% 153ms 0.68% std::__insertion_sort (inline) 0 0% 84.91% 148ms 0.66% vtkStreamingDemandDrivenPipeline::Update 0 0% 84.91% 148ms 0.66% vtkXMLWriterBase::Write 0 0% 84.91% 147ms 0.65% vtkStreamingDemandDrivenPipeline::ProcessRequest 71ms 0.32% 85.23% 146ms 0.65% std::__move_median_to_first (inline) 0 0% 85.23% 146ms 0.65% vtkDemandDrivenPipeline::ProcessRequest 0 0% 85.23% 144ms 0.64% vtkCompositeDataPipeline::ExecuteData 0 0% 85.23% 144ms 0.64% vtkDemandDrivenPipeline::ExecuteData 0 0% 85.23% 144ms 0.64% vtkExecutive::CallAlgorithm 0 0% 85.23% 144ms 0.64% vtkXMLUnstructuredDataWriter::ProcessRequest 34ms 0.15% 85.38% 141ms 0.63% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 85.38% 138ms 0.61% std::_Rb_tree::_M_drop_node (inline) 0 0% 85.38% 136ms 0.6% boost::numeric::ublas::vector_reference::operator() (inline) 75ms 0.33% 85.71% 134ms 0.6% _int_malloc 0 0% 85.71% 130ms 0.58% boost::numeric::ublas::c_vector::operator/= (inline) 53ms 0.24% 85.95% 130ms 0.58% boost::numeric::ublas::vector_assign_scalar (inline) 2ms 0.0089% 85.96% 129ms 0.57% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 85.96% 126ms 0.56% std::_Rb_tree::_Alloc_node::operator() (inline) 8ms 0.036% 85.99% 126ms 0.56% std::_Rb_tree::_M_copy (inline) 123ms 0.55% 86.54% 123ms 0.55% [libchaste_mesh.so] 2ms 0.0089% 86.55% 120ms 0.53% std::__new_allocator::deallocate (inline) 27ms 0.12% 86.67% 118ms 0.52% std::_Rb_tree::_M_clone_node (inline) 11ms 0.049% 86.72% 116ms 0.52% std::_Rb_tree::~_Rb_tree (inline) 108ms 0.48% 87.20% 116ms 0.52% std::__find_if (inline) 0 0% 87.20% 116ms 0.52% std::find_if (inline) 0 0% 87.20% 116ms 0.52% std::none_of (inline) 83ms 0.37% 87.57% 115ms 0.51% Node::AddNeighbour