File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 32736ms, 89.52% of 36567ms total Dropped 845 nodes (cum <= 182.84ms) flat flat% sum% cum cum% 0 0% 0% 36432ms 99.63% __libc_start_call_main 0 0% 0% 36432ms 99.63% __libc_start_main_impl 0 0% 0% 36432ms 99.63% _start 0 0% 0% 36414ms 99.58% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 36414ms 99.58% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 36414ms 99.58% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 36414ms 99.58% main 0 0% 0% 36372ms 99.47% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 36372ms 99.47% CxxTest::TestRunner::runTest (inline) 0 0% 0% 36372ms 99.47% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0027% 0.0027% 36363ms 99.44% AbstractCellBasedSimulation::Solve 3ms 0.0082% 0.011% 25101ms 68.64% OffLatticeSimulation::UpdateCellLocationsAndTopology 3ms 0.0082% 0.019% 20003ms 54.70% ForwardEulerNumericalMethod::UpdateAllNodePositions 18ms 0.049% 0.068% 19820ms 54.20% AbstractNumericalMethod::ComputeForcesIncludingDamping 192ms 0.53% 0.59% 18469ms 50.51% AbstractTwoBodyInteractionForce::AddForceContribution 1542ms 4.22% 4.81% 15597ms 42.65% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 0 0% 4.81% 9960ms 27.24% AbstractCellBasedSimulation::UpdateCellPopulation 4370ms 11.95% 16.76% 9862ms 26.97% std::_Rb_tree::_M_lower_bound (inline) 347ms 0.95% 17.71% 8869ms 24.25% std::_Rb_tree::find (inline) 0 0% 17.71% 8869ms 24.25% std::map::find (inline) 1ms 0.0027% 17.71% 8678ms 23.73% NodeBasedCellPopulation::Update 156ms 0.43% 18.14% 8621ms 23.58% NodesOnlyMesh::GetNodeOrHaloNode 475ms 1.30% 19.44% 8472ms 23.17% AbstractMesh::GetNode 300ms 0.82% 20.26% 8001ms 21.88% NodesOnlyMesh::SolveNodeMapping 210ms 0.57% 20.83% 6515ms 17.82% boost::numeric::ublas::vector_assign (inline) 5ms 0.014% 20.85% 6498ms 17.77% DistributedBoxCollection::CalculateInteriorNodePairs 166ms 0.45% 21.30% 6311ms 17.26% boost::numeric::ublas::c_vector::c_vector (partial-inline) 5472ms 14.96% 36.26% 5472ms 14.96% std::_Rb_tree::_S_right (inline) 2ms 0.0055% 36.27% 4640ms 12.69% OffLatticeSimulation::ApplyBoundaries 24ms 0.066% 36.34% 4606ms 12.60% NodeAttributes::RemoveDuplicateNeighbours 7ms 0.019% 36.36% 4417ms 12.08% std::__sort (inline) 0 0% 36.36% 4417ms 12.08% std::sort (inline) 1189ms 3.25% 39.61% 3578ms 9.78% boost::numeric::ublas::indexing_vector_assign 1ms 0.0027% 39.61% 3476ms 9.51% AbstractCellPopulation::Iterator::operator++ (inline) 225ms 0.62% 40.22% 3454ms 9.45% AbstractCellPopulation::Iterator::IsRealCell 75ms 0.21% 40.43% 3435ms 9.39% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 32ms 0.088% 40.52% 2921ms 7.99% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 358ms 0.98% 41.50% 2521ms 6.89% DistributedBoxCollection::AddPairsFromBox 233ms 0.64% 42.13% 2518ms 6.89% std::__introsort_loop 20ms 0.055% 42.19% 2453ms 6.71% PlaneBoundaryCondition::ImposeBoundaryCondition 55ms 0.15% 42.34% 2321ms 6.35% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 42.34% 2210ms 6.04% std::__unguarded_partition_pivot (inline) 21ms 0.057% 42.40% 2184ms 5.97% PlaneBoundaryCondition::VerifyBoundaryCondition 960ms 2.63% 45.02% 1946ms 5.32% std::__unguarded_partition (inline) 198ms 0.54% 45.56% 1933ms 5.29% std::map::operator[] (partial-inline) 1ms 0.0027% 45.57% 1891ms 5.17% std::__final_insertion_sort (inline) 107ms 0.29% 45.86% 1697ms 4.64% std::__unguarded_insertion_sort (inline) 634ms 1.73% 47.59% 1639ms 4.48% std::__unguarded_linear_insert (inline) 148ms 0.4% 48.00% 1628ms 4.45% AbstractMesh::GetVectorFromAtoB 1564ms 4.28% 52.27% 1564ms 4.28% boost::numeric::ublas::same_impl_ex 1465ms 4.01% 56.28% 1465ms 4.01% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 56.28% 1419ms 3.88% std::_Rb_tree::lower_bound (inline) 0 0% 56.28% 1419ms 3.88% std::map::lower_bound (inline) 6ms 0.016% 56.30% 1268ms 3.47% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 56.30% 1251ms 3.42% NodeBasedCellPopulation::UpdateCellProcessLocation 0 0% 56.30% 1204ms 3.29% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 56.30% 1185ms 3.24% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 10ms 0.027% 56.32% 1127ms 3.08% DistributedBoxCollection::CalculateBoundaryNodePairs 1127ms 3.08% 59.41% 1127ms 3.08% boost::numeric::ublas::c_vector::operator() 175ms 0.48% 59.88% 1122ms 3.07% std::__new_allocator::allocate (inline) 48ms 0.13% 60.02% 1058ms 2.89% std::_Rb_tree_const_iterator::operator++ (inline) 22ms 0.06% 60.08% 1057ms 2.89% boost::numeric::ublas::detail::expression_type_check (inline) 186ms 0.51% 60.58% 1007ms 2.75% boost::numeric::ublas::detail::equals 1007ms 2.75% 63.34% 1007ms 2.75% std::_Rb_tree_increment 168ms 0.46% 63.80% 995ms 2.72% boost::numeric::ublas::vector_binary::size (inline) 459ms 1.26% 65.05% 963ms 2.63% NodeAttributes::AddNeighbour 147ms 0.4% 65.46% 952ms 2.60% operator new 60ms 0.16% 65.62% 934ms 2.55% CellPropertyCollection::GetPropertiesType (inline) 403ms 1.10% 66.72% 915ms 2.50% __GI___libc_free 182ms 0.5% 67.22% 868ms 2.37% NodeAttributes::AddAppliedForceContribution 615ms 1.68% 68.90% 816ms 2.23% __dynamic_cast 5ms 0.014% 68.91% 814ms 2.23% Cell::GetMutationState 14ms 0.038% 68.95% 801ms 2.19% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 253ms 0.69% 69.64% 798ms 2.18% __GI___libc_malloc 0 0% 69.64% 795ms 2.17% AbstractCellPopulation::WriteResultsToFiles 357ms 0.98% 70.62% 791ms 2.16% DistributedBoxCollection::CalculateContainingBox (partial-inline) 11ms 0.03% 70.65% 789ms 2.16% AbstractCellBasedSimulation::DoCellBirth 0 0% 70.65% 766ms 2.09% boost::numeric::ublas::norm_inf (inline) 431ms 1.18% 71.83% 766ms 2.09% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 71.83% 686ms 1.88% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 71.83% 686ms 1.88% boost::numeric::ublas::c_vector::plus_assign (inline) 127ms 0.35% 72.18% 663ms 1.81% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 72.18% 663ms 1.81% boost::numeric::ublas::vector::vector (inline) 501ms 1.37% 73.55% 640ms 1.75% std::vector::push_back (inline) 0 0% 73.55% 586ms 1.60% std::allocator_traits::allocate (inline) 0 0% 73.55% 557ms 1.52% std::_Rb_tree::_M_create_node (inline) 3ms 0.0082% 73.56% 530ms 1.45% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 5ms 0.014% 73.57% 526ms 1.44% AbstractCellPopulation::GetCellUsingLocationIndex 2ms 0.0055% 73.57% 511ms 1.40% NodeBasedCellPopulation::WriteVtkResultsToFile 463ms 1.27% 74.84% 509ms 1.39% _int_free 0 0% 74.84% 488ms 1.33% AbstractCellBasedSimulation::DoCellRemoval (inline) 4ms 0.011% 74.85% 465ms 1.27% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 74.85% 461ms 1.26% std::_Rb_tree::_M_get_node (inline) 444ms 1.21% 76.07% 444ms 1.21% Node::GetIndex 0 0% 76.07% 438ms 1.20% boost::numeric::ublas::norm_2 (inline) 347ms 0.95% 77.01% 438ms 1.20% boost::numeric::ublas::vector_norm_2::apply (inline) 7ms 0.019% 77.03% 433ms 1.18% std::_Rb_tree::_Rb_tree (partial-inline) 40ms 0.11% 77.14% 422ms 1.15% std::_Rb_tree::_M_copy (inline) 0 0% 77.14% 411ms 1.12% AbstractCellProperty::IsSubType (inline) 174ms 0.48% 77.62% 406ms 1.11% std::_Rb_tree::_M_erase 36ms 0.098% 77.72% 395ms 1.08% boost::detail::shared_count::~shared_count (inline) 0 0% 77.72% 395ms 1.08% boost::shared_ptr::~shared_ptr (inline) 62ms 0.17% 77.89% 381ms 1.04% std::_Rb_tree::_M_clone_node (inline) 0 0% 77.89% 371ms 1.01% std::_Rb_tree::_Alloc_node::operator() (inline) 368ms 1.01% 78.89% 368ms 1.01% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 78.89% 355ms 0.97% Cell::HasCellProperty (inline) 2ms 0.0055% 78.90% 355ms 0.97% CellPropertyCollection::HasProperty 346ms 0.95% 79.85% 355ms 0.97% boost::detail::sp_counted_base::release 14ms 0.038% 79.88% 353ms 0.97% Cell::ReadyToDivide 130ms 0.36% 80.24% 353ms 0.97% Node::GetRadius 1ms 0.0027% 80.24% 352ms 0.96% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 80.24% 346ms 0.95% boost::numeric::ublas::inner_prod (inline) 3ms 0.0082% 80.25% 344ms 0.94% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 20ms 0.055% 80.30% 341ms 0.93% boost::numeric::ublas::vector_scalar_binary::evaluate 160ms 0.44% 80.74% 339ms 0.93% _int_malloc 1ms 0.0027% 80.74% 333ms 0.91% NodesOnlyMesh::ReMesh 4ms 0.011% 80.76% 320ms 0.88% NodesOnlyMesh::UpdateNodeIndices 7ms 0.019% 80.78% 316ms 0.86% std::_Rb_tree::_M_emplace_hint_unique 307ms 0.84% 81.61% 307ms 0.84% __gnu_cxx::__normal_iterator::operator++ (inline) 303ms 0.83% 82.44% 303ms 0.83% [libchaste_cell_based.so] 0 0% 82.44% 293ms 0.8% NodesOnlyMesh::UpdateBoxCollection 13ms 0.036% 82.48% 285ms 0.78% boost::numeric::ublas::vector_reference::operator() (inline) 2ms 0.0055% 82.48% 280ms 0.77% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 128ms 0.35% 82.83% 271ms 0.74% boost::numeric::ublas::vector_inner_prod::apply (inline) 6ms 0.016% 82.85% 270ms 0.74% DistributedBoxCollection::GetProcessOwningNode 0 0% 82.85% 263ms 0.72% boost::numeric::ublas::c_vector::assign (inline) 43ms 0.12% 82.97% 262ms 0.72% std::__new_allocator::deallocate (inline) 89ms 0.24% 83.21% 259ms 0.71% std::__move_median_to_first (inline) 249ms 0.68% 83.89% 249ms 0.68% boost::shared_ptr::operator-> (inline) 0 0% 83.89% 248ms 0.68% std::set::set (inline) 0 0% 83.89% 246ms 0.67% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 83.89% 243ms 0.66% VtkMeshWriter::WriteFiles 0 0% 83.89% 237ms 0.65% std::_Rb_tree::clear (inline) 236ms 0.65% 84.54% 236ms 0.65% Node::CheckForNodeAttributes 0 0% 84.54% 226ms 0.62% std::_Rb_tree::_M_drop_node (inline) 105ms 0.29% 84.83% 218ms 0.6% std::__find_if (inline) 0 0% 84.83% 218ms 0.6% std::find_if (inline) 0 0% 84.83% 218ms 0.6% std::none_of (inline) 216ms 0.59% 85.42% 216ms 0.59% NodeBasedCellPopulation::GetNode 0 0% 85.42% 216ms 0.59% vtkXMLWriterBase::Write 0 0% 85.42% 215ms 0.59% vtkStreamingDemandDrivenPipeline::Update 0 0% 85.42% 214ms 0.59% vtkDemandDrivenPipeline::ProcessRequest 212ms 0.58% 86.00% 212ms 0.58% boost::numeric::ublas::c_vector::size (inline) 0 0% 86.00% 211ms 0.58% vtkDemandDrivenPipeline::ExecuteData 0 0% 86.00% 211ms 0.58% vtkStreamingDemandDrivenPipeline::ProcessRequest 210ms 0.57% 86.57% 210ms 0.57% Node::rGetLocation 210ms 0.57% 87.14% 210ms 0.57% boost::numeric::ublas::scalar_plus_assign::apply (inline) 10ms 0.027% 87.17% 210ms 0.57% std::_Rb_tree::~_Rb_tree (inline) 0 0% 87.17% 210ms 0.57% vtkCompositeDataPipeline::ExecuteData 0 0% 87.17% 210ms 0.57% vtkExecutive::CallAlgorithm 0 0% 87.17% 210ms 0.57% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 87.17% 205ms 0.56% NodesOnlyMesh::ResizeBoxCollection 0 0% 87.17% 205ms 0.56% boost::numeric::ublas::vector_binary::operator() (inline) 11ms 0.03% 87.20% 204ms 0.56% NodesOnlyMesh::IsANodeCloseToDomainBoundary 204ms 0.56% 87.76% 204ms 0.56% [libchaste_mesh.so] 4ms 0.011% 87.77% 203ms 0.56% AbstractCellProperty::IsType (inline) 0 0% 87.77% 201ms 0.55% boost::numeric::ublas::vector_reference::size (inline) 0 0% 87.77% 201ms 0.55% tcache_get (inline) 201ms 0.55% 88.32% 201ms 0.55% tcache_get_n (inline) 14ms 0.038% 88.36% 193ms 0.53% std::__insertion_sort (inline) 0 0% 88.36% 191ms 0.52% std::allocator_traits::deallocate (inline) 151ms 0.41% 88.77% 189ms 0.52% Node::AddAppliedForceContribution 2ms 0.0055% 88.78% 189ms 0.52% NodesOnlyMesh::AddNodesToBoxes 0 0% 88.78% 189ms 0.52% std::_Rb_tree::_M_put_node (inline) 187ms 0.51% 89.29% 187ms 0.51% __strcmp_avx2 0 0% 89.29% 186ms 0.51% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 89.29% 185ms 0.51% std::map::map (inline) 86ms 0.24% 89.52% 183ms 0.5% boost::shared_ptr::shared_ptr (inline) 0 0% 89.52% 183ms 0.5% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 89.52% 183ms 0.5% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData