File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 30835ms, 89.50% of 34454ms total Dropped 803 nodes (cum <= 172.27ms) flat flat% sum% cum cum% 0 0% 0% 34313ms 99.59% __libc_start_call_main 0 0% 0% 34313ms 99.59% __libc_start_main_impl 0 0% 0% 34313ms 99.59% _start 0 0% 0% 34295ms 99.54% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 34295ms 99.54% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 34295ms 99.54% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 34295ms 99.54% main 0 0% 0% 34253ms 99.42% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 34253ms 99.42% CxxTest::TestRunner::runTest (inline) 0 0% 0% 34253ms 99.42% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 34245ms 99.39% AbstractCellBasedSimulation::Solve 3ms 0.0087% 0.0087% 24095ms 69.93% OffLatticeSimulation::UpdateCellLocationsAndTopology 4ms 0.012% 0.02% 19197ms 55.72% ForwardEulerNumericalMethod::UpdateAllNodePositions 9ms 0.026% 0.046% 19024ms 55.22% AbstractNumericalMethod::ComputeForcesIncludingDamping 195ms 0.57% 0.61% 18294ms 53.10% AbstractTwoBodyInteractionForce::AddForceContribution 1517ms 4.40% 5.02% 15410ms 44.73% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4385ms 12.73% 17.74% 9562ms 27.75% std::_Rb_tree::_M_lower_bound (inline) 0 0% 17.74% 8981ms 26.07% AbstractCellBasedSimulation::UpdateCellPopulation 312ms 0.91% 18.65% 8623ms 25.03% std::_Rb_tree::find (inline) 0 0% 18.65% 8623ms 25.03% std::map::find (inline) 148ms 0.43% 19.08% 8457ms 24.55% NodesOnlyMesh::GetNodeOrHaloNode 493ms 1.43% 20.51% 8250ms 23.94% AbstractMesh::GetNode 0 0% 20.51% 7940ms 23.05% NodeBasedCellPopulation::Update 298ms 0.86% 21.37% 7762ms 22.53% NodesOnlyMesh::SolveNodeMapping 205ms 0.59% 21.97% 6532ms 18.96% boost::numeric::ublas::vector_assign (inline) 223ms 0.65% 22.62% 6396ms 18.56% boost::numeric::ublas::c_vector::c_vector (partial-inline) 6ms 0.017% 22.63% 5897ms 17.12% DistributedBoxCollection::CalculateInteriorNodePairs 5145ms 14.93% 37.57% 5145ms 14.93% std::_Rb_tree::_S_right (inline) 3ms 0.0087% 37.57% 4598ms 13.35% OffLatticeSimulation::ApplyBoundaries 13ms 0.038% 37.61% 4486ms 13.02% NodeAttributes::RemoveDuplicateNeighbours 2ms 0.0058% 37.62% 4328ms 12.56% std::__sort (inline) 0 0% 37.62% 4328ms 12.56% std::sort (inline) 1207ms 3.50% 41.12% 3609ms 10.47% boost::numeric::ublas::indexing_vector_assign 6ms 0.017% 41.14% 3493ms 10.14% AbstractCellPopulation::Iterator::operator++ (inline) 202ms 0.59% 41.73% 3465ms 10.06% AbstractCellPopulation::Iterator::IsRealCell 73ms 0.21% 41.94% 3452ms 10.02% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 29ms 0.084% 42.02% 2937ms 8.52% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 197ms 0.57% 42.59% 2488ms 7.22% std::__introsort_loop 26ms 0.075% 42.67% 2405ms 6.98% PlaneBoundaryCondition::ImposeBoundaryCondition 50ms 0.15% 42.81% 2308ms 6.70% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 42.81% 2215ms 6.43% std::__unguarded_partition_pivot (inline) 20ms 0.058% 42.87% 2190ms 6.36% PlaneBoundaryCondition::VerifyBoundaryCondition 166ms 0.48% 43.35% 2014ms 5.85% DistributedBoxCollection::AddPairsFromBox 1011ms 2.93% 46.29% 1985ms 5.76% std::__unguarded_partition (inline) 240ms 0.7% 46.98% 1854ms 5.38% std::map::operator[] (partial-inline) 2ms 0.0058% 46.99% 1836ms 5.33% std::__final_insertion_sort (inline) 84ms 0.24% 47.23% 1645ms 4.77% std::__unguarded_insertion_sort (inline) 110ms 0.32% 47.55% 1616ms 4.69% AbstractMesh::GetVectorFromAtoB 585ms 1.70% 49.25% 1609ms 4.67% std::__unguarded_linear_insert (inline) 1600ms 4.64% 53.90% 1600ms 4.64% boost::numeric::ublas::same_impl_ex 1492ms 4.33% 58.23% 1492ms 4.33% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 58.23% 1344ms 3.90% std::_Rb_tree::lower_bound (inline) 0 0% 58.23% 1344ms 3.90% std::map::lower_bound (inline) 0 0% 58.23% 1231ms 3.57% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 58.23% 1215ms 3.53% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 58.23% 1134ms 3.29% NodeBasedCellPopulation::UpdateCellProcessLocation 1110ms 3.22% 61.45% 1110ms 3.22% boost::numeric::ublas::c_vector::operator() 26ms 0.075% 61.52% 1082ms 3.14% boost::numeric::ublas::detail::expression_type_check (inline) 8ms 0.023% 61.55% 1071ms 3.11% DistributedBoxCollection::CalculateBoundaryNodePairs 218ms 0.63% 62.18% 1033ms 3.00% boost::numeric::ublas::detail::equals 169ms 0.49% 62.67% 1018ms 2.95% boost::numeric::ublas::vector_binary::size (inline) 74ms 0.21% 62.88% 1008ms 2.93% std::__new_allocator::allocate (inline) 239ms 0.69% 63.58% 937ms 2.72% NodeAttributes::AddAppliedForceContribution 108ms 0.31% 63.89% 932ms 2.71% operator new 433ms 1.26% 65.15% 826ms 2.40% __GI___libc_free 356ms 1.03% 66.18% 818ms 2.37% __GI___libc_malloc 24ms 0.07% 66.25% 812ms 2.36% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 357ms 1.04% 67.29% 775ms 2.25% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 67.29% 772ms 2.24% boost::numeric::ublas::norm_inf (inline) 421ms 1.22% 68.51% 772ms 2.24% boost::numeric::ublas::vector_norm_inf::apply (inline) 224ms 0.65% 69.16% 757ms 2.20% NodeAttributes::AddNeighbour 0 0% 69.16% 733ms 2.13% AbstractCellPopulation::WriteResultsToFiles 483ms 1.40% 70.56% 701ms 2.03% __dynamic_cast 0 0% 70.56% 698ms 2.03% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 70.56% 698ms 2.03% boost::numeric::ublas::c_vector::plus_assign (inline) 1ms 0.0029% 70.56% 668ms 1.94% AbstractCentreBasedCellPopulation::GetDampingConstant 533ms 1.55% 72.11% 642ms 1.86% std::vector::push_back (inline) 18ms 0.052% 72.16% 632ms 1.83% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 72.16% 632ms 1.83% boost::numeric::ublas::vector::vector (inline) 31ms 0.09% 72.25% 571ms 1.66% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.0058% 72.26% 558ms 1.62% AbstractCellBasedSimulation::DoCellBirth 523ms 1.52% 73.78% 523ms 1.52% std::_Rb_tree_increment 9ms 0.026% 73.80% 515ms 1.49% CellPropertyCollection::GetPropertiesType (inline) 0 0% 73.80% 480ms 1.39% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 73.80% 476ms 1.38% NodeBasedCellPopulation::WriteVtkResultsToFile 8ms 0.023% 73.83% 468ms 1.36% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 462ms 1.34% 75.17% 462ms 1.34% Node::GetIndex 0 0% 75.17% 459ms 1.33% boost::numeric::ublas::norm_2 (inline) 374ms 1.09% 76.25% 459ms 1.33% boost::numeric::ublas::vector_norm_2::apply (inline) 3ms 0.0087% 76.26% 449ms 1.30% Cell::GetMutationState 23ms 0.067% 76.33% 413ms 1.20% boost::detail::shared_count::~shared_count (inline) 0 0% 76.33% 413ms 1.20% boost::shared_ptr::~shared_ptr (inline) 0 0% 76.33% 394ms 1.14% std::allocator_traits::allocate (inline) 353ms 1.02% 77.35% 393ms 1.14% _int_free 383ms 1.11% 78.46% 386ms 1.12% boost::detail::sp_counted_base::release 135ms 0.39% 78.86% 360ms 1.04% Node::GetRadius 0 0% 78.86% 359ms 1.04% std::_Rb_tree::_M_create_node (inline) 3ms 0.0087% 78.86% 346ms 1.00% AbstractCellProperty::IsSubType (inline) 14ms 0.041% 78.91% 327ms 0.95% boost::numeric::ublas::vector_reference::operator() (inline) 8ms 0.023% 78.93% 322ms 0.93% NodeBasedCellPopulation::UpdateMapsAfterRemesh 2ms 0.0058% 78.93% 316ms 0.92% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 316ms 0.92% 79.85% 316ms 0.92% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 4ms 0.012% 79.86% 313ms 0.91% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 79.86% 313ms 0.91% std::_Rb_tree::_M_get_node (inline) 0 0% 79.86% 307ms 0.89% boost::numeric::ublas::inner_prod (inline) 6ms 0.017% 79.88% 307ms 0.89% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 23ms 0.067% 79.95% 301ms 0.87% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 79.95% 300ms 0.87% NodesOnlyMesh::ReMesh 4ms 0.012% 79.96% 291ms 0.84% NodesOnlyMesh::UpdateNodeIndices 291ms 0.84% 80.80% 291ms 0.84% __gnu_cxx::__normal_iterator::operator++ (inline) 285ms 0.83% 81.63% 285ms 0.83% [libchaste_cell_based.so] 132ms 0.38% 82.01% 282ms 0.82% std::_Rb_tree::_M_erase (partial-inline) 0 0% 82.01% 275ms 0.8% boost::numeric::ublas::c_vector::assign (inline) 9ms 0.026% 82.04% 270ms 0.78% std::_Rb_tree::_M_emplace_hint_unique 0 0% 82.04% 263ms 0.76% NodesOnlyMesh::UpdateBoxCollection 254ms 0.74% 82.78% 254ms 0.74% [libchaste_mesh.so] 2ms 0.0058% 82.78% 248ms 0.72% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 244ms 0.71% 83.49% 244ms 0.71% Node::CheckForNodeAttributes 147ms 0.43% 83.92% 244ms 0.71% _int_malloc 110ms 0.32% 84.24% 241ms 0.7% boost::numeric::ublas::vector_inner_prod::apply (inline) 236ms 0.68% 84.92% 236ms 0.68% NodeBasedCellPopulation::GetNode 1ms 0.0029% 84.92% 234ms 0.68% DistributedBoxCollection::GetProcessOwningNode 0 0% 84.92% 232ms 0.67% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 84.92% 228ms 0.66% VtkMeshWriter::WriteFiles 109ms 0.32% 85.24% 226ms 0.66% std::__move_median_to_first (inline) 219ms 0.64% 85.88% 219ms 0.64% boost::numeric::ublas::c_vector::size (inline) 2ms 0.0058% 85.88% 215ms 0.62% NodesOnlyMesh::AddNodesToBoxes 0 0% 85.88% 215ms 0.62% tcache_get (inline) 215ms 0.62% 86.51% 215ms 0.62% tcache_get_n (inline) 0 0% 86.51% 210ms 0.61% std::_Rb_tree::_Alloc_node::operator() (inline) 209ms 0.61% 87.11% 209ms 0.61% Node::rGetLocation 0 0% 87.11% 207ms 0.6% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 87.11% 207ms 0.6% vtkStreamingDemandDrivenPipeline::Update 0 0% 87.11% 207ms 0.6% vtkXMLWriterBase::Write 7ms 0.02% 87.13% 206ms 0.6% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 87.13% 205ms 0.59% vtkDemandDrivenPipeline::ExecuteData 0 0% 87.13% 205ms 0.59% vtkDemandDrivenPipeline::ProcessRequest 0 0% 87.13% 205ms 0.59% vtkStreamingDemandDrivenPipeline::ProcessRequest 5ms 0.015% 87.15% 204ms 0.59% CellPropertyCollection::HasProperty 204ms 0.59% 87.74% 204ms 0.59% __strcmp_avx2 0 0% 87.74% 204ms 0.59% vtkExecutive::CallAlgorithm 1ms 0.0029% 87.74% 203ms 0.59% Cell::HasCellProperty (inline) 0 0% 87.74% 203ms 0.59% boost::numeric::ublas::vector_reference::size (inline) 0 0% 87.74% 203ms 0.59% vtkCompositeDataPipeline::ExecuteData 0 0% 87.74% 203ms 0.59% vtkXMLUnstructuredDataWriter::ProcessRequest 200ms 0.58% 88.32% 200ms 0.58% boost::numeric::ublas::scalar_plus_assign::apply (inline) 0 0% 88.32% 198ms 0.57% NodesOnlyMesh::ResizeBoxCollection 20ms 0.058% 88.38% 198ms 0.57% std::_Rb_tree::_M_copy (inline) 15ms 0.044% 88.43% 196ms 0.57% NodesOnlyMesh::IsANodeCloseToDomainBoundary 78ms 0.23% 88.65% 192ms 0.56% std::__find_if (inline) 0 0% 88.65% 192ms 0.56% std::find_if (inline) 0 0% 88.65% 192ms 0.56% std::none_of (inline) 16ms 0.046% 88.70% 189ms 0.55% std::__insertion_sort (inline) 1ms 0.0029% 88.70% 184ms 0.53% AbstractCellProperty::IsType (inline) 91ms 0.26% 88.96% 182ms 0.53% boost::shared_ptr::shared_ptr (inline) 28ms 0.081% 89.05% 182ms 0.53% std::__new_allocator::deallocate (inline) 131ms 0.38% 89.43% 179ms 0.52% Node::AddAppliedForceContribution 24ms 0.07% 89.50% 178ms 0.52% std::_Rb_tree::_M_clone_node (inline)