File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 31268ms, 87.66% of 35669ms total Dropped 814 nodes (cum <= 178.34ms) flat flat% sum% cum cum% 0 0% 0% 35532ms 99.62% __libc_start_call_main 0 0% 0% 35532ms 99.62% __libc_start_main_impl 0 0% 0% 35532ms 99.62% _start 0 0% 0% 35513ms 99.56% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 35513ms 99.56% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 35513ms 99.56% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 35513ms 99.56% main 0 0% 0% 35470ms 99.44% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 35470ms 99.44% CxxTest::TestRunner::runTest (inline) 0 0% 0% 35470ms 99.44% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 35461ms 99.42% AbstractCellBasedSimulation::Solve 3ms 0.0084% 0.0084% 24972ms 70.01% OffLatticeSimulation::UpdateCellLocationsAndTopology 4ms 0.011% 0.02% 20068ms 56.26% ForwardEulerNumericalMethod::UpdateAllNodePositions 15ms 0.042% 0.062% 19878ms 55.73% AbstractNumericalMethod::ComputeForcesIncludingDamping 265ms 0.74% 0.8% 19063ms 53.44% AbstractTwoBodyInteractionForce::AddForceContribution 1596ms 4.47% 5.28% 15672ms 43.94% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4370ms 12.25% 17.53% 9741ms 27.31% std::_Rb_tree::_M_lower_bound (inline) 0 0% 17.53% 9258ms 25.96% AbstractCellBasedSimulation::UpdateCellPopulation 411ms 1.15% 18.68% 9047ms 25.36% std::_Rb_tree::find (inline) 0 0% 18.68% 9047ms 25.36% std::map::find (inline) 189ms 0.53% 19.21% 8805ms 24.69% NodesOnlyMesh::GetNodeOrHaloNode 463ms 1.30% 20.51% 8636ms 24.21% AbstractMesh::GetNode 0 0% 20.51% 8177ms 22.92% NodeBasedCellPopulation::Update 386ms 1.08% 21.59% 8177ms 22.92% NodesOnlyMesh::SolveNodeMapping 155ms 0.43% 22.03% 6497ms 18.21% boost::numeric::ublas::vector_assign (inline) 146ms 0.41% 22.44% 6186ms 17.34% boost::numeric::ublas::c_vector::c_vector (partial-inline) 13ms 0.036% 22.47% 6110ms 17.13% DistributedBoxCollection::CalculateInteriorNodePairs 5340ms 14.97% 37.44% 5340ms 14.97% std::_Rb_tree::_S_right (inline) 11ms 0.031% 37.48% 4634ms 12.99% NodeAttributes::RemoveDuplicateNeighbours 0 0% 37.48% 4576ms 12.83% OffLatticeSimulation::ApplyBoundaries 7ms 0.02% 37.49% 4452ms 12.48% std::__sort (inline) 0 0% 37.49% 4452ms 12.48% std::sort (inline) 1030ms 2.89% 40.38% 3572ms 10.01% boost::numeric::ublas::indexing_vector_assign 95ms 0.27% 40.65% 3313ms 9.29% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 2ms 0.0056% 40.65% 3108ms 8.71% AbstractCellPopulation::Iterator::operator++ (inline) 164ms 0.46% 41.11% 3066ms 8.60% AbstractCellPopulation::Iterator::IsRealCell 31ms 0.087% 41.20% 2675ms 7.50% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 183ms 0.51% 41.71% 2599ms 7.29% std::__introsort_loop 22ms 0.062% 41.78% 2446ms 6.86% PlaneBoundaryCondition::ImposeBoundaryCondition 0 0% 41.78% 2329ms 6.53% std::__unguarded_partition_pivot (inline) 60ms 0.17% 41.94% 2286ms 6.41% AbstractCellPopulation::GetLocationIndexUsingCell 17ms 0.048% 41.99% 2129ms 5.97% PlaneBoundaryCondition::VerifyBoundaryCondition 144ms 0.4% 42.40% 2106ms 5.90% DistributedBoxCollection::AddPairsFromBox 2086ms 5.85% 48.24% 2086ms 5.85% boost::numeric::ublas::same_impl_ex 1012ms 2.84% 51.08% 2064ms 5.79% std::__unguarded_partition (inline) 2ms 0.0056% 51.09% 1842ms 5.16% std::__final_insertion_sort (inline) 0 0% 51.09% 1794ms 5.03% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 51.09% 1784ms 5.00% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 153ms 0.43% 51.52% 1624ms 4.55% std::map::operator[] (partial-inline) 1ms 0.0028% 51.52% 1616ms 4.53% boost::numeric::ublas::detail::expression_type_check (inline) 130ms 0.36% 51.88% 1610ms 4.51% std::__unguarded_insertion_sort (inline) 269ms 0.75% 52.64% 1551ms 4.35% boost::numeric::ublas::detail::equals 180ms 0.5% 53.14% 1528ms 4.28% AbstractMesh::GetVectorFromAtoB 587ms 1.65% 54.79% 1522ms 4.27% std::__unguarded_linear_insert (inline) 1352ms 3.79% 58.58% 1352ms 3.79% __gnu_cxx::__normal_iterator::operator-- (inline) 218ms 0.61% 59.19% 1284ms 3.60% boost::numeric::ublas::vector_binary::size (inline) 1253ms 3.51% 62.70% 1253ms 3.51% boost::numeric::ublas::c_vector::operator() 0 0% 62.70% 1231ms 3.45% boost::numeric::ublas::norm_inf (inline) 563ms 1.58% 64.28% 1231ms 3.45% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 64.28% 1204ms 3.38% std::_Rb_tree::lower_bound (inline) 0 0% 64.28% 1204ms 3.38% std::map::lower_bound (inline) 0 0% 64.28% 1168ms 3.27% NodeBasedCellPopulation::UpdateCellProcessLocation 4ms 0.011% 64.29% 1110ms 3.11% DistributedBoxCollection::CalculateBoundaryNodePairs 220ms 0.62% 64.91% 1062ms 2.98% NodeAttributes::AddAppliedForceContribution 18ms 0.05% 64.96% 977ms 2.74% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 64.96% 842ms 2.36% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 64.96% 842ms 2.36% boost::numeric::ublas::c_vector::plus_assign (inline) 369ms 1.03% 65.99% 818ms 2.29% DistributedBoxCollection::CalculateContainingBox (partial-inline) 94ms 0.26% 66.26% 810ms 2.27% std::__new_allocator::allocate (inline) 185ms 0.52% 66.78% 780ms 2.19% NodeAttributes::AddNeighbour 0 0% 66.78% 746ms 2.09% AbstractCellPopulation::WriteResultsToFiles 11ms 0.031% 66.81% 743ms 2.08% AbstractCentreBasedCellPopulation::GetDampingConstant 504ms 1.41% 68.22% 730ms 2.05% __dynamic_cast 81ms 0.23% 68.45% 713ms 2.00% operator new 589ms 1.65% 70.10% 661ms 1.85% std::vector::push_back (inline) 27ms 0.076% 70.17% 655ms 1.84% std::_Rb_tree_const_iterator::operator++ (inline) 202ms 0.57% 70.74% 632ms 1.77% __GI___libc_malloc 619ms 1.74% 72.47% 619ms 1.74% std::_Rb_tree_increment 3ms 0.0084% 72.48% 592ms 1.66% AbstractCellBasedSimulation::DoCellBirth 178ms 0.5% 72.98% 592ms 1.66% __GI___libc_free 14ms 0.039% 73.02% 577ms 1.62% CellPropertyCollection::GetPropertiesType (inline) 0 0% 73.02% 563ms 1.58% boost::numeric::ublas::norm_2 (inline) 452ms 1.27% 74.29% 563ms 1.58% boost::numeric::ublas::vector_norm_2::apply (inline) 7ms 0.02% 74.31% 505ms 1.42% Cell::GetMutationState 0 0% 74.31% 488ms 1.37% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 74.31% 488ms 1.37% NodeBasedCellPopulation::WriteVtkResultsToFile 6ms 0.017% 74.33% 475ms 1.33% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 474ms 1.33% 75.65% 474ms 1.33% Node::GetIndex 44ms 0.12% 75.78% 432ms 1.21% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 75.78% 432ms 1.21% boost::numeric::ublas::vector::vector (inline) 0 0% 75.78% 422ms 1.18% std::allocator_traits::allocate (inline) 392ms 1.10% 76.88% 413ms 1.16% _int_free 21ms 0.059% 76.94% 405ms 1.14% boost::detail::shared_count::~shared_count (inline) 0 0% 76.94% 405ms 1.14% boost::shared_ptr::~shared_ptr (inline) 0 0% 76.94% 392ms 1.10% std::_Rb_tree::_M_create_node (inline) 386ms 1.08% 78.02% 386ms 1.08% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 302ms 0.85% 78.86% 385ms 1.08% Node::AddAppliedForceContribution 369ms 1.03% 79.90% 375ms 1.05% boost::detail::sp_counted_base::release 0 0% 79.90% 373ms 1.05% boost::numeric::ublas::inner_prod (inline) 18ms 0.05% 79.95% 371ms 1.04% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 79.95% 371ms 1.04% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 4ms 0.011% 79.96% 365ms 1.02% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 6ms 0.017% 79.98% 361ms 1.01% AbstractCellPopulation::GetCellUsingLocationIndex 2ms 0.0056% 79.98% 356ms 1% AbstractCellProperty::IsSubType (inline) 345ms 0.97% 80.95% 345ms 0.97% [libchaste_mesh.so] 0 0% 80.95% 343ms 0.96% std::_Rb_tree::_M_get_node (inline) 338ms 0.95% 81.90% 338ms 0.95% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 81.90% 337ms 0.94% NodesOnlyMesh::ReMesh 106ms 0.3% 82.19% 326ms 0.91% std::_Rb_tree::_M_erase (partial-inline) 2ms 0.0056% 82.20% 325ms 0.91% NodesOnlyMesh::UpdateNodeIndices 5ms 0.014% 82.21% 316ms 0.89% NodeBasedCellPopulation::UpdateMapsAfterRemesh 6ms 0.017% 82.23% 316ms 0.89% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 133ms 0.37% 82.60% 305ms 0.86% boost::numeric::ublas::vector_inner_prod::apply (inline) 8ms 0.022% 82.63% 294ms 0.82% DistributedBoxCollection::GetProcessOwningNode 76ms 0.21% 82.84% 278ms 0.78% Node::GetRadius 14ms 0.039% 82.88% 271ms 0.76% std::_Rb_tree::_Rb_tree (partial-inline) 9ms 0.025% 82.90% 267ms 0.75% std::_Rb_tree::_M_emplace_hint_unique 264ms 0.74% 83.64% 264ms 0.74% [libchaste_cell_based.so] 0 0% 83.64% 262ms 0.73% NodesOnlyMesh::UpdateBoxCollection 105ms 0.29% 83.94% 260ms 0.73% std::__move_median_to_first (inline) 153ms 0.43% 84.37% 259ms 0.73% Node::AddNeighbour 0 0% 84.37% 259ms 0.73% boost::numeric::ublas::c_vector::assign (inline) 19ms 0.053% 84.42% 253ms 0.71% std::_Rb_tree::_M_copy (inline) 0 0% 84.42% 249ms 0.7% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 1ms 0.0028% 84.42% 246ms 0.69% VtkMeshWriter::WriteFiles 0 0% 84.42% 246ms 0.69% std::_Rb_tree::_Alloc_node::operator() (inline) 130ms 0.36% 84.79% 239ms 0.67% _int_malloc 33ms 0.093% 84.88% 233ms 0.65% std::_Rb_tree::_M_clone_node (inline) 6ms 0.017% 84.90% 230ms 0.64% boost::numeric::ublas::vector_reference::operator() (inline) 28ms 0.078% 84.98% 230ms 0.64% std::__insertion_sort (inline) 0 0% 84.98% 229ms 0.64% Cell::HasCellProperty (inline) 3ms 0.0084% 84.98% 229ms 0.64% CellPropertyCollection::HasProperty 225ms 0.63% 85.61% 225ms 0.63% Node::CheckForNodeAttributes 223ms 0.63% 86.24% 223ms 0.63% __strcmp_avx2 7ms 0.02% 86.26% 220ms 0.62% Cell::ReadyToDivide 217ms 0.61% 86.87% 217ms 0.61% NodeBasedCellPopulation::GetNode 1ms 0.0028% 86.87% 216ms 0.61% vtkStreamingDemandDrivenPipeline::Update 0 0% 86.87% 216ms 0.61% vtkXMLWriterBase::Write 0 0% 86.87% 215ms 0.6% vtkDemandDrivenPipeline::ProcessRequest 0 0% 86.87% 212ms 0.59% vtkDemandDrivenPipeline::ExecuteData 0 0% 86.87% 212ms 0.59% vtkExecutive::CallAlgorithm 0 0% 86.87% 212ms 0.59% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 86.87% 211ms 0.59% std::_Rb_tree::_M_drop_node (inline) 0 0% 86.87% 211ms 0.59% vtkCompositeDataPipeline::ExecuteData 1ms 0.0028% 86.87% 211ms 0.59% vtkXMLUnstructuredDataWriter::ProcessRequest 7ms 0.02% 86.89% 206ms 0.58% std::__new_allocator::deallocate (inline) 79ms 0.22% 87.11% 204ms 0.57% std::__find_if (inline) 0 0% 87.11% 204ms 0.57% std::find_if (inline) 0 0% 87.11% 204ms 0.57% std::none_of (inline) 1ms 0.0028% 87.12% 201ms 0.56% NodesOnlyMesh::AddNodesToBoxes 0 0% 87.12% 198ms 0.56% std::_Rb_tree::clear (inline) 3ms 0.0084% 87.13% 193ms 0.54% AbstractCellProperty::IsType (inline) 191ms 0.54% 87.66% 191ms 0.54% Node::ConstructNodeAttributes (inline) 0 0% 87.66% 185ms 0.52% std::allocator_traits::deallocate (inline) 0 0% 87.66% 184ms 0.52% std::_Rb_tree::_M_put_node (inline) 0 0% 87.66% 183ms 0.51% boost::numeric::ublas::vector_binary::operator() (inline)