File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 21083ms, 89.84% of 23467ms total Dropped 759 nodes (cum <= 117.33ms) flat flat% sum% cum cum% 0 0% 0% 23344ms 99.48% __libc_start_call_main 0 0% 0% 23344ms 99.48% __libc_start_main_impl 0 0% 0% 23344ms 99.48% _start 0 0% 0% 23329ms 99.41% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 23329ms 99.41% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 23329ms 99.41% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 23329ms 99.41% main 0 0% 0% 23295ms 99.27% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 23295ms 99.27% CxxTest::TestRunner::runTest (inline) 0 0% 0% 23295ms 99.27% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 23287ms 99.23% AbstractCellBasedSimulation::Solve 0 0% 0% 13331ms 56.81% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0% 8945ms 38.12% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.017% 0.017% 8506ms 36.25% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.043% 0.06% 8336ms 35.52% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.06% 7896ms 33.65% NodeBasedCellPopulation::Update 1191ms 5.08% 5.13% 7624ms 32.49% RepulsionForce::AddForceContribution (partial-inline) 7ms 0.03% 5.16% 5820ms 24.80% DistributedBoxCollection::CalculateInteriorNodePairs 2144ms 9.14% 14.30% 5014ms 21.37% std::_Rb_tree::_M_lower_bound (inline) 0 0% 14.30% 4546ms 19.37% OffLatticeSimulation::ApplyBoundaries 20ms 0.085% 14.39% 4449ms 18.96% NodeAttributes::RemoveDuplicateNeighbours 11ms 0.047% 14.43% 4269ms 18.19% std::__sort (inline) 0 0% 14.43% 4269ms 18.19% std::sort (inline) 190ms 0.81% 15.24% 3876ms 16.52% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 2ms 0.0085% 15.25% 3444ms 14.68% AbstractCellPopulation::Iterator::operator++ (inline) 62ms 0.26% 15.52% 3411ms 14.54% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 181ms 0.77% 16.29% 3410ms 14.53% AbstractCellPopulation::Iterator::IsRealCell (inline) 231ms 0.98% 17.27% 3230ms 13.76% std::_Rb_tree::find (inline) 0 0% 17.27% 3230ms 13.76% std::map::find (inline) 27ms 0.12% 17.39% 2903ms 12.37% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2826ms 12.04% 29.43% 2826ms 12.04% std::_Rb_tree::_S_right (inline) 253ms 1.08% 30.51% 2546ms 10.85% std::map::operator[] (partial-inline) 175ms 0.75% 31.25% 2409ms 10.27% std::__introsort_loop 24ms 0.1% 31.35% 2341ms 9.98% PlaneBoundaryCondition::ImposeBoundaryCondition 33ms 0.14% 31.50% 2338ms 9.96% AbstractCellPopulation::GetLocationIndexUsingCell 146ms 0.62% 32.12% 2286ms 9.74% AbstractMesh::GetNode 46ms 0.2% 32.31% 2272ms 9.68% NodesOnlyMesh::GetNodeOrHaloNode 15ms 0.064% 32.38% 2205ms 9.40% PlaneBoundaryCondition::VerifyBoundaryCondition 0 0% 32.38% 2159ms 9.20% std::__unguarded_partition_pivot (inline) 84ms 0.36% 32.74% 2145ms 9.14% NodesOnlyMesh::SolveNodeMapping 0 0% 32.74% 2042ms 8.70% std::_Rb_tree::lower_bound (inline) 0 0% 32.74% 2042ms 8.70% std::map::lower_bound (inline) 198ms 0.84% 33.58% 1974ms 8.41% DistributedBoxCollection::AddPairsFromBox 995ms 4.24% 37.82% 1956ms 8.34% std::__unguarded_partition (inline) 0 0% 37.82% 1848ms 7.87% std::__final_insertion_sort (inline) 67ms 0.29% 38.10% 1653ms 7.04% std::__unguarded_insertion_sort (inline) 629ms 2.68% 40.78% 1640ms 6.99% std::__unguarded_linear_insert (inline) 24ms 0.1% 40.89% 1587ms 6.76% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 20ms 0.085% 40.97% 1556ms 6.63% AbstractCellPopulation::GetCellUsingLocationIndex 1439ms 6.13% 47.10% 1439ms 6.13% __gnu_cxx::__normal_iterator::operator-- (inline) 54ms 0.23% 47.33% 1357ms 5.78% boost::numeric::ublas::c_vector::c_vector (partial-inline) 41ms 0.17% 47.51% 1231ms 5.25% boost::numeric::ublas::vector_assign (inline) 1ms 0.0043% 47.51% 1175ms 5.01% NodeBasedCellPopulation::UpdateCellProcessLocation 310ms 1.32% 48.83% 1113ms 4.74% boost::numeric::ublas::indexing_vector_assign 7ms 0.03% 48.86% 1066ms 4.54% DistributedBoxCollection::CalculateBoundaryNodePairs 281ms 1.20% 50.06% 934ms 3.98% __dynamic_cast 180ms 0.77% 50.83% 921ms 3.92% AbstractMesh::GetVectorFromAtoB 389ms 1.66% 52.49% 816ms 3.48% DistributedBoxCollection::CalculateContainingBox (partial-inline) 13ms 0.055% 52.54% 810ms 3.45% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 274ms 1.17% 53.71% 788ms 3.36% NodeAttributes::AddNeighbour 0 0% 53.71% 725ms 3.09% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 710ms 3.03% 56.73% 710ms 3.03% boost::numeric::ublas::c_vector::operator() 0 0% 56.73% 706ms 3.01% boost::numeric::ublas::norm_2 (inline) 545ms 2.32% 59.06% 706ms 3.01% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 59.06% 706ms 3.01% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 15ms 0.064% 59.12% 663ms 2.83% CellPropertyCollection::GetPropertiesType (inline) 38ms 0.16% 59.28% 635ms 2.71% std::_Rb_tree_const_iterator::operator++ (inline) 14ms 0.06% 59.34% 623ms 2.65% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 59.34% 618ms 2.63% AbstractCentreBasedCellPopulation::GetDampingConstant 513ms 2.19% 61.53% 608ms 2.59% std::vector::push_back (inline) 28ms 0.12% 61.65% 592ms 2.52% std::__copy_move::__copy_m (inline) 0 0% 61.65% 592ms 2.52% std::__copy_move_a (inline) 0 0% 61.65% 592ms 2.52% std::__copy_move_a1 (inline) 0 0% 61.65% 592ms 2.52% std::__copy_move_a2 (inline) 0 0% 61.65% 592ms 2.52% std::copy (inline) 589ms 2.51% 64.16% 589ms 2.51% std::_Rb_tree_increment 567ms 2.42% 66.57% 567ms 2.42% __memcpy_avx_unaligned_erms 3ms 0.013% 66.59% 560ms 2.39% AbstractCellBasedSimulation::DoCellBirth 288ms 1.23% 67.81% 549ms 2.34% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 67.81% 542ms 2.31% AbstractCellPopulation::WriteResultsToFiles 536ms 2.28% 70.10% 536ms 2.28% boost::numeric::ublas::same_impl_ex 79ms 0.34% 70.44% 523ms 2.23% std::__new_allocator::allocate (inline) 41ms 0.17% 70.61% 513ms 2.19% boost::detail::shared_count::~shared_count (inline) 0 0% 70.61% 513ms 2.19% boost::shared_ptr::~shared_ptr (inline) 0 0% 70.61% 508ms 2.16% std::allocator_traits::allocate (inline) 0 0% 70.61% 489ms 2.08% AbstractCellBasedSimulation::DoCellRemoval (inline) 18ms 0.077% 70.69% 478ms 2.04% std::_Rb_tree::_Rb_tree (partial-inline) 8ms 0.034% 70.72% 464ms 1.98% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 452ms 1.93% 72.65% 462ms 1.97% boost::detail::sp_counted_base::release 0 0% 72.65% 459ms 1.96% Cell::GetMutationState 0 0% 72.65% 455ms 1.94% std::_Rb_tree::_M_create_node (inline) 34ms 0.14% 72.79% 447ms 1.90% std::_Rb_tree::_M_copy (inline) 6ms 0.026% 72.82% 439ms 1.87% AbstractCellProperty::IsSubType (inline) 28ms 0.12% 72.94% 439ms 1.87% operator new 0 0% 72.94% 414ms 1.76% std::_Rb_tree::_M_get_node (inline) 145ms 0.62% 73.55% 408ms 1.74% std::_Rb_tree::_M_clone_node (inline) 139ms 0.59% 74.15% 406ms 1.73% __GI___libc_malloc 139ms 0.59% 74.74% 405ms 1.73% std::_Rb_tree::_M_erase 3ms 0.013% 74.75% 403ms 1.72% std::set::set (inline) 395ms 1.68% 76.43% 395ms 1.68% __strcmp_avx2 163ms 0.69% 77.13% 386ms 1.64% Node::GetRadius 26ms 0.11% 77.24% 343ms 1.46% boost::numeric::ublas::vector_binary::size (inline) 2ms 0.0085% 77.25% 340ms 1.45% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 77.25% 324ms 1.38% boost::numeric::ublas::inner_prod (inline) 5ms 0.021% 77.27% 323ms 1.38% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 3ms 0.013% 77.28% 321ms 1.37% NodeBasedCellPopulation::UpdateMapsAfterRemesh 19ms 0.081% 77.36% 318ms 1.36% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 77.36% 318ms 1.36% std::_Rb_tree::_Alloc_node::operator() (inline) 1ms 0.0043% 77.37% 316ms 1.35% NodesOnlyMesh::ReMesh 6ms 0.026% 77.39% 308ms 1.31% NodesOnlyMesh::UpdateNodeIndices 36ms 0.15% 77.55% 308ms 1.31% std::_Rb_tree::~_Rb_tree (inline) 304ms 1.30% 78.84% 304ms 1.30% __gnu_cxx::__normal_iterator::operator++ (inline) 302ms 1.29% 80.13% 302ms 1.29% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 80.13% 290ms 1.24% boost::numeric::ublas::c_vector::assign (inline) 0 0% 80.13% 289ms 1.23% NodesOnlyMesh::UpdateBoxCollection 3ms 0.013% 80.14% 283ms 1.21% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 7ms 0.03% 80.17% 267ms 1.14% DistributedBoxCollection::GetProcessOwningNode 0 0% 80.17% 260ms 1.11% std::_Rb_tree::_M_drop_node (inline) 9ms 0.038% 80.21% 251ms 1.07% std::_Rb_tree::_M_emplace_hint_unique 103ms 0.44% 80.65% 247ms 1.05% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 80.65% 244ms 1.04% NodesOnlyMesh::AddNodesToBoxes 130ms 0.55% 81.20% 233ms 0.99% _int_malloc 0 0% 81.20% 228ms 0.97% std::set::~set (inline) 225ms 0.96% 82.16% 225ms 0.96% Node::CheckForNodeAttributes 2ms 0.0085% 82.17% 216ms 0.92% std::__new_allocator::deallocate (inline) 212ms 0.9% 83.07% 212ms 0.9% [libchaste_cell_based.so] 0 0% 83.07% 200ms 0.85% NodesOnlyMesh::ResizeBoxCollection 16ms 0.068% 83.14% 199ms 0.85% NodesOnlyMesh::IsANodeCloseToDomainBoundary 100ms 0.43% 83.57% 197ms 0.84% std::__move_median_to_first (inline) 96ms 0.41% 83.98% 196ms 0.84% boost::shared_ptr::shared_ptr (inline) 10ms 0.043% 84.02% 195ms 0.83% std::__insertion_sort (inline) 194ms 0.83% 84.85% 194ms 0.83% Node::GetIndex 73ms 0.31% 85.16% 191ms 0.81% __GI___libc_free 15ms 0.064% 85.22% 186ms 0.79% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 85.22% 185ms 0.79% std::allocator_traits::deallocate (inline) 12ms 0.051% 85.27% 183ms 0.78% Cell::ReadyToDivide 3ms 0.013% 85.29% 182ms 0.78% CellPropertyCollection::HasProperty 0 0% 85.29% 182ms 0.78% std::_Rb_tree::_M_put_node (inline) 0 0% 85.29% 180ms 0.77% Cell::HasCellProperty (inline) 154ms 0.66% 85.94% 154ms 0.66% boost::shared_ptr::operator-> (inline) 0 0% 85.94% 153ms 0.65% std::_Rb_tree::clear (inline) 147ms 0.63% 86.57% 150ms 0.64% std::__adjacent_find (inline) 0 0% 86.57% 150ms 0.64% std::__unique (inline) 0 0% 86.57% 150ms 0.64% std::unique (inline) 0 0% 86.57% 148ms 0.63% boost::numeric::ublas::vector_binary::operator() (inline) 13ms 0.055% 86.62% 147ms 0.63% boost::numeric::ublas::c_vector::operator[] (inline) 2ms 0.0085% 86.63% 145ms 0.62% Cell::GetCellId 6ms 0.026% 86.66% 145ms 0.62% DistributedBoxCollection::GetIsPeriodicAllDims 4ms 0.017% 86.67% 144ms 0.61% AbstractCellProperty::IsType (inline) 83ms 0.35% 87.03% 144ms 0.61% Node::AddNeighbour 51ms 0.22% 87.25% 140ms 0.6% AbstractCellCycleModel::GetAge 0 0% 87.25% 138ms 0.59% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 87.25% 137ms 0.58% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1ms 0.0043% 87.25% 133ms 0.57% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 2ms 0.0085% 87.26% 131ms 0.56% AbstractCellPopulation::SetCellUsingLocationIndex 130ms 0.55% 87.81% 130ms 0.55% Node::IsDeleted 126ms 0.54% 88.35% 126ms 0.54% __ieee754_log_fma 125ms 0.53% 88.88% 125ms 0.53% [libchaste_mesh.so] 3ms 0.013% 88.90% 124ms 0.53% std::_Rb_tree::_M_insert_unique 0 0% 88.90% 124ms 0.53% std::set::insert (inline) 118ms 0.5% 89.40% 118ms 0.5% Node::rGetLocation 104ms 0.44% 89.84% 118ms 0.5% _int_free