File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 30837ms, 89.03% of 34636ms total Dropped 816 nodes (cum <= 173.18ms) flat flat% sum% cum cum% 0 0% 0% 34500ms 99.61% __libc_start_call_main 0 0% 0% 34500ms 99.61% __libc_start_main_impl 0 0% 0% 34500ms 99.61% _start 0 0% 0% 34484ms 99.56% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 34484ms 99.56% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 34484ms 99.56% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 34484ms 99.56% main 0 0% 0% 34445ms 99.45% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 34445ms 99.45% CxxTest::TestRunner::runTest (inline) 0 0% 0% 34445ms 99.45% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 34437ms 99.43% AbstractCellBasedSimulation::Solve 1ms 0.0029% 0.0029% 24127ms 69.66% OffLatticeSimulation::UpdateCellLocationsAndTopology 6ms 0.017% 0.02% 19283ms 55.67% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.017% 0.038% 19090ms 55.12% AbstractNumericalMethod::ComputeForcesIncludingDamping 211ms 0.61% 0.65% 18241ms 52.66% AbstractTwoBodyInteractionForce::AddForceContribution 1490ms 4.30% 4.95% 15406ms 44.48% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4339ms 12.53% 17.48% 9466ms 27.33% std::_Rb_tree::_M_lower_bound (inline) 0 0% 17.48% 9122ms 26.34% AbstractCellBasedSimulation::UpdateCellPopulation 374ms 1.08% 18.56% 8627ms 24.91% std::_Rb_tree::find (inline) 0 0% 18.56% 8627ms 24.91% std::map::find (inline) 154ms 0.44% 19.00% 8356ms 24.13% NodesOnlyMesh::GetNodeOrHaloNode 495ms 1.43% 20.43% 8190ms 23.65% AbstractMesh::GetNode 0 0% 20.43% 8014ms 23.14% NodeBasedCellPopulation::Update 314ms 0.91% 21.34% 7697ms 22.22% NodesOnlyMesh::SolveNodeMapping 218ms 0.63% 21.97% 6451ms 18.63% boost::numeric::ublas::vector_assign (inline) 210ms 0.61% 22.57% 6362ms 18.37% boost::numeric::ublas::c_vector::c_vector (partial-inline) 10ms 0.029% 22.60% 5986ms 17.28% DistributedBoxCollection::CalculateInteriorNodePairs 5085ms 14.68% 37.28% 5085ms 14.68% std::_Rb_tree::_S_right (inline) 0 0% 37.28% 4529ms 13.08% OffLatticeSimulation::ApplyBoundaries 18ms 0.052% 37.33% 4500ms 12.99% NodeAttributes::RemoveDuplicateNeighbours 7ms 0.02% 37.35% 4327ms 12.49% std::__sort (inline) 0 0% 37.35% 4327ms 12.49% std::sort (inline) 1166ms 3.37% 40.72% 3622ms 10.46% boost::numeric::ublas::indexing_vector_assign 2ms 0.0058% 40.73% 3478ms 10.04% AbstractCellPopulation::Iterator::operator++ (inline) 173ms 0.5% 41.23% 3451ms 9.96% AbstractCellPopulation::Iterator::IsRealCell (inline) 81ms 0.23% 41.46% 3442ms 9.94% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 25ms 0.072% 41.53% 2965ms 8.56% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 216ms 0.62% 42.16% 2499ms 7.22% std::__introsort_loop 25ms 0.072% 42.23% 2367ms 6.83% PlaneBoundaryCondition::ImposeBoundaryCondition 50ms 0.14% 42.37% 2358ms 6.81% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 42.37% 2204ms 6.36% std::__unguarded_partition_pivot (inline) 18ms 0.052% 42.42% 2161ms 6.24% PlaneBoundaryCondition::VerifyBoundaryCondition 157ms 0.45% 42.88% 2096ms 6.05% DistributedBoxCollection::AddPairsFromBox 1036ms 2.99% 45.87% 1971ms 5.69% std::__unguarded_partition (inline) 0 0% 45.87% 1817ms 5.25% std::__final_insertion_sort (inline) 201ms 0.58% 46.45% 1736ms 5.01% std::map::operator[] (partial-inline) 1669ms 4.82% 51.27% 1669ms 4.82% boost::numeric::ublas::same_impl_ex 118ms 0.34% 51.61% 1642ms 4.74% AbstractMesh::GetVectorFromAtoB 89ms 0.26% 51.87% 1594ms 4.60% std::__unguarded_insertion_sort (inline) 581ms 1.68% 53.54% 1594ms 4.60% std::__unguarded_linear_insert (inline) 1469ms 4.24% 57.78% 1469ms 4.24% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 57.78% 1296ms 3.74% std::_Rb_tree::lower_bound (inline) 0 0% 57.78% 1296ms 3.74% std::map::lower_bound (inline) 0 0% 57.78% 1216ms 3.51% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 57.78% 1192ms 3.44% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 57.78% 1143ms 3.30% NodeBasedCellPopulation::UpdateCellProcessLocation 1118ms 3.23% 61.01% 1118ms 3.23% boost::numeric::ublas::c_vector::operator() 4ms 0.012% 61.02% 1072ms 3.10% DistributedBoxCollection::CalculateBoundaryNodePairs 17ms 0.049% 61.07% 1058ms 3.05% boost::numeric::ublas::detail::expression_type_check (inline) 181ms 0.52% 61.59% 1043ms 3.01% boost::numeric::ublas::vector_binary::size (inline) 210ms 0.61% 62.20% 1020ms 2.94% boost::numeric::ublas::detail::equals 103ms 0.3% 62.50% 886ms 2.56% std::__new_allocator::allocate (inline) 193ms 0.56% 63.06% 862ms 2.49% NodeAttributes::AddAppliedForceContribution 407ms 1.18% 64.23% 852ms 2.46% __GI___libc_free 23ms 0.066% 64.30% 808ms 2.33% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 4ms 0.012% 64.31% 796ms 2.30% AbstractCentreBasedCellPopulation::GetDampingConstant 99ms 0.29% 64.59% 782ms 2.26% operator new 365ms 1.05% 65.65% 777ms 2.24% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 65.65% 767ms 2.21% boost::numeric::ublas::norm_inf (inline) 456ms 1.32% 66.97% 767ms 2.21% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 66.97% 742ms 2.14% AbstractCellPopulation::WriteResultsToFiles 198ms 0.57% 67.54% 740ms 2.14% NodeAttributes::AddNeighbour 508ms 1.47% 69.00% 737ms 2.13% __dynamic_cast 33ms 0.095% 69.10% 705ms 2.04% std::_Rb_tree_const_iterator::operator++ (inline) 261ms 0.75% 69.85% 679ms 1.96% __GI___libc_malloc 671ms 1.94% 71.79% 671ms 1.94% std::_Rb_tree_increment 0 0% 71.79% 669ms 1.93% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 71.79% 669ms 1.93% boost::numeric::ublas::c_vector::plus_assign (inline) 3ms 0.0087% 71.80% 641ms 1.85% AbstractCellBasedSimulation::DoCellBirth 540ms 1.56% 73.36% 628ms 1.81% std::vector::push_back (inline) 11ms 0.032% 73.39% 626ms 1.81% CellPropertyCollection::GetPropertiesType (inline) 1ms 0.0029% 73.39% 546ms 1.58% Cell::GetMutationState 15ms 0.043% 73.44% 501ms 1.45% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 73.44% 501ms 1.45% boost::numeric::ublas::vector::vector (inline) 1ms 0.0029% 73.44% 474ms 1.37% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 73.44% 467ms 1.35% AbstractCellBasedSimulation::DoCellRemoval (inline) 3ms 0.0087% 73.45% 450ms 1.30% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 73.45% 449ms 1.30% boost::numeric::ublas::norm_2 (inline) 369ms 1.07% 74.51% 449ms 1.30% boost::numeric::ublas::vector_norm_2::apply (inline) 409ms 1.18% 75.69% 441ms 1.27% _int_free 0 0% 75.69% 400ms 1.15% std::allocator_traits::allocate (inline) 28ms 0.081% 75.77% 399ms 1.15% boost::detail::shared_count::~shared_count (inline) 0 0% 75.77% 399ms 1.15% boost::shared_ptr::~shared_ptr (inline) 375ms 1.08% 76.86% 375ms 1.08% Node::GetIndex 358ms 1.03% 77.89% 363ms 1.05% boost::detail::sp_counted_base::release 0 0% 77.89% 363ms 1.05% std::_Rb_tree::_M_create_node (inline) 1ms 0.0029% 77.89% 356ms 1.03% AbstractCellProperty::IsSubType (inline) 111ms 0.32% 78.21% 353ms 1.02% Node::AddNeighbour 0 0% 78.21% 343ms 0.99% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 6ms 0.017% 78.23% 341ms 0.98% AbstractCellPopulation::GetCellUsingLocationIndex 120ms 0.35% 78.58% 337ms 0.97% Node::GetRadius 8ms 0.023% 78.60% 331ms 0.96% NodeBasedCellPopulation::UpdateMapsAfterRemesh 16ms 0.046% 78.65% 318ms 0.92% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 78.65% 315ms 0.91% std::_Rb_tree::_M_get_node (inline) 0 0% 78.65% 309ms 0.89% boost::numeric::ublas::inner_prod (inline) 1ms 0.0029% 78.65% 308ms 0.89% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 14ms 0.04% 78.69% 307ms 0.89% boost::numeric::ublas::vector_scalar_binary::evaluate 142ms 0.41% 79.10% 299ms 0.86% std::_Rb_tree::_M_erase (partial-inline) 296ms 0.85% 79.95% 296ms 0.85% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 284ms 0.82% 80.77% 284ms 0.82% [libchaste_cell_based.so] 0 0% 80.77% 280ms 0.81% NodesOnlyMesh::ReMesh 279ms 0.81% 81.58% 279ms 0.81% Node::ConstructNodeAttributes (inline) 275ms 0.79% 82.37% 275ms 0.79% __gnu_cxx::__normal_iterator::operator++ (inline) 4ms 0.012% 82.39% 274ms 0.79% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 3ms 0.0087% 82.39% 271ms 0.78% NodesOnlyMesh::UpdateNodeIndices 266ms 0.77% 83.16% 266ms 0.77% NodeBasedCellPopulation::GetNode 9ms 0.026% 83.19% 257ms 0.74% DistributedBoxCollection::GetProcessOwningNode 0 0% 83.19% 251ms 0.72% Cell::HasCellProperty (inline) 1ms 0.0029% 83.19% 251ms 0.72% CellPropertyCollection::HasProperty 0 0% 83.19% 251ms 0.72% boost::numeric::ublas::c_vector::assign (inline) 0 0% 83.19% 250ms 0.72% NodesOnlyMesh::UpdateBoxCollection 8ms 0.023% 83.21% 245ms 0.71% std::_Rb_tree::_Rb_tree (partial-inline) 93ms 0.27% 83.48% 242ms 0.7% boost::numeric::ublas::vector_inner_prod::apply (inline) 239ms 0.69% 84.17% 239ms 0.69% Node::rGetLocation 12ms 0.035% 84.21% 239ms 0.69% std::_Rb_tree::_M_emplace_hint_unique 236ms 0.68% 84.89% 236ms 0.68% boost::numeric::ublas::c_vector::size (inline) 0 0% 84.89% 236ms 0.68% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 84.89% 234ms 0.68% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 232ms 0.67% 85.56% 232ms 0.67% Node::CheckForNodeAttributes 0 0% 85.56% 231ms 0.67% VtkMeshWriter::WriteFiles 113ms 0.33% 85.88% 230ms 0.66% std::__find_if (inline) 0 0% 85.88% 230ms 0.66% std::find_if (inline) 0 0% 85.88% 230ms 0.66% std::none_of (inline) 17ms 0.049% 85.93% 229ms 0.66% std::_Rb_tree::_M_copy (inline) 10ms 0.029% 85.96% 228ms 0.66% Cell::ReadyToDivide 107ms 0.31% 86.27% 228ms 0.66% std::__move_median_to_first (inline) 123ms 0.36% 86.63% 225ms 0.65% _int_malloc 20ms 0.058% 86.68% 223ms 0.64% std::__insertion_sort (inline) 0 0% 86.68% 213ms 0.61% boost::numeric::ublas::vector_reference::size (inline) 212ms 0.61% 87.30% 212ms 0.61% __strcmp_avx2 34ms 0.098% 87.39% 212ms 0.61% std::_Rb_tree::_M_clone_node (inline) 0 0% 87.39% 211ms 0.61% NodesOnlyMesh::AddNodesToBoxes 0 0% 87.39% 208ms 0.6% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 87.39% 204ms 0.59% vtkStreamingDemandDrivenPipeline::Update 0 0% 87.39% 204ms 0.59% vtkXMLWriterBase::Write 0 0% 87.39% 203ms 0.59% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 87.39% 200ms 0.58% vtkDemandDrivenPipeline::ProcessRequest 1ms 0.0029% 87.40% 199ms 0.57% NodesOnlyMesh::ResizeBoxCollection 0 0% 87.40% 199ms 0.57% vtkDemandDrivenPipeline::ExecuteData 0 0% 87.40% 199ms 0.57% vtkExecutive::CallAlgorithm 1ms 0.0029% 87.40% 197ms 0.57% vtkXMLUnstructuredDataWriter::ProcessRequest 7ms 0.02% 87.42% 196ms 0.57% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 87.42% 196ms 0.57% vtkCompositeDataPipeline::ExecuteData 4ms 0.012% 87.43% 188ms 0.54% AbstractCellProperty::IsType (inline) 152ms 0.44% 87.87% 185ms 0.53% Node::AddAppliedForceContribution 39ms 0.11% 87.98% 184ms 0.53% std::__new_allocator::deallocate (inline) 0 0% 87.98% 184ms 0.53% tcache_get (inline) 184ms 0.53% 88.51% 184ms 0.53% tcache_get_n (inline) 179ms 0.52% 89.03% 179ms 0.52% [libchaste_mesh.so]