File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 28276ms, 87.78% of 32213ms total Dropped 783 nodes (cum <= 161.06ms) flat flat% sum% cum cum% 0 0% 0% 32112ms 99.69% __libc_start_call_main 0 0% 0% 32112ms 99.69% __libc_start_main_impl 0 0% 0% 32112ms 99.69% _start 0 0% 0% 32095ms 99.63% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 32095ms 99.63% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 32095ms 99.63% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 32095ms 99.63% main 0 0% 0% 32061ms 99.53% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 32061ms 99.53% CxxTest::TestRunner::runTest (inline) 0 0% 0% 32061ms 99.53% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 32053ms 99.50% AbstractCellBasedSimulation::Solve 0 0% 0% 22276ms 69.15% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.0062% 0.0062% 16705ms 51.86% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.0093% 0.016% 16530ms 51.31% AbstractNumericalMethod::ComputeForcesIncludingDamping 224ms 0.7% 0.71% 15917ms 49.41% AbstractTwoBodyInteractionForce::AddForceContribution 1069ms 3.32% 4.03% 14396ms 44.69% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4447ms 13.80% 17.83% 10350ms 32.13% std::_Rb_tree::_M_lower_bound (inline) 226ms 0.7% 18.54% 9727ms 30.20% NodesOnlyMesh::GetNodeOrHaloNode 220ms 0.68% 19.22% 9507ms 29.51% AbstractMesh::GetNode 410ms 1.27% 20.49% 9364ms 29.07% std::_Rb_tree::find (inline) 0 0% 20.49% 9364ms 29.07% std::map::find (inline) 751ms 2.33% 22.82% 9294ms 28.85% NodesOnlyMesh::SolveNodeMapping 0 0% 22.82% 8719ms 27.07% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0031% 22.83% 7641ms 23.72% NodeBasedCellPopulation::Update 6ms 0.019% 22.84% 5767ms 17.90% DistributedBoxCollection::CalculateInteriorNodePairs 0 0% 22.84% 5258ms 16.32% OffLatticeSimulation::ApplyBoundaries 5106ms 15.85% 38.70% 5106ms 15.85% std::_Rb_tree::_S_right (inline) 7ms 0.022% 38.72% 4591ms 14.25% NodeAttributes::RemoveDuplicateNeighbours 6ms 0.019% 38.74% 4415ms 13.71% std::__sort (inline) 0 0% 38.74% 4415ms 13.71% std::sort (inline) 145ms 0.45% 39.19% 4392ms 13.63% boost::numeric::ublas::vector_assign (inline) 57ms 0.18% 39.36% 4338ms 13.47% boost::numeric::ublas::c_vector::c_vector (partial-inline) 268ms 0.83% 40.19% 3936ms 12.22% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 5ms 0.016% 40.21% 3685ms 11.44% AbstractCellPopulation::Iterator::operator++ (inline) 174ms 0.54% 40.75% 3667ms 11.38% AbstractCellPopulation::Iterator::IsRealCell (inline) 21ms 0.065% 40.82% 3099ms 9.62% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 59ms 0.18% 41.00% 2674ms 8.30% PlaneBoundaryCondition::ImposeBoundaryCondition 229ms 0.71% 41.71% 2642ms 8.20% std::__introsort_loop 50ms 0.16% 41.87% 2584ms 8.02% PlaneBoundaryCondition::VerifyBoundaryCondition 8ms 0.025% 41.89% 2305ms 7.16% std::__unguarded_partition_pivot (inline) 110ms 0.34% 42.23% 2255ms 7.00% AbstractCellPopulation::GetLocationIndexUsingCell 726ms 2.25% 44.49% 2096ms 6.51% std::__unguarded_partition (inline) 166ms 0.52% 45.00% 1979ms 6.14% std::map::operator[] (partial-inline) 476ms 1.48% 46.48% 1847ms 5.73% boost::numeric::ublas::indexing_vector_assign 1ms 0.0031% 46.48% 1762ms 5.47% std::__final_insertion_sort (inline) 132ms 0.41% 46.89% 1716ms 5.33% DistributedBoxCollection::AddPairsFromBox 110ms 0.34% 47.23% 1574ms 4.89% std::__unguarded_insertion_sort (inline) 0 0% 47.23% 1540ms 4.78% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 47.23% 1517ms 4.71% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 47.23% 1472ms 4.57% std::_Rb_tree::lower_bound (inline) 0 0% 47.23% 1472ms 4.57% std::map::lower_bound (inline) 36ms 0.11% 47.34% 1437ms 4.46% boost::numeric::ublas::detail::expression_type_check (inline) 733ms 2.28% 49.62% 1407ms 4.37% std::__unguarded_linear_insert (inline) 189ms 0.59% 50.21% 1361ms 4.23% boost::numeric::ublas::detail::equals 0 0% 50.21% 1159ms 3.60% boost::numeric::ublas::norm_inf (inline) 439ms 1.36% 51.57% 1159ms 3.60% boost::numeric::ublas::vector_norm_inf::apply (inline) 16ms 0.05% 51.62% 1150ms 3.57% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 51.62% 1085ms 3.37% NodeBasedCellPopulation::UpdateCellProcessLocation 189ms 0.59% 52.21% 1051ms 3.26% AbstractMesh::GetVectorFromAtoB 1028ms 3.19% 55.40% 1028ms 3.19% boost::numeric::ublas::same_impl_ex 1019ms 3.16% 58.56% 1019ms 3.16% __gnu_cxx::__normal_iterator::operator-- (inline) 5ms 0.016% 58.58% 943ms 2.93% DistributedBoxCollection::CalculateBoundaryNodePairs 68ms 0.21% 58.79% 814ms 2.53% std::__new_allocator::allocate (inline) 812ms 2.52% 61.31% 812ms 2.52% std::_Rb_tree::_S_left (inline) 744ms 2.31% 63.62% 744ms 2.31% [libchaste_cell_based.so] 73ms 0.23% 63.84% 721ms 2.24% operator new 17ms 0.053% 63.90% 708ms 2.20% boost::detail::shared_count::~shared_count (inline) 0 0% 63.90% 708ms 2.20% boost::shared_ptr::~shared_ptr (inline) 292ms 0.91% 64.80% 707ms 2.19% DistributedBoxCollection::CalculateContainingBox (partial-inline) 666ms 2.07% 66.87% 675ms 2.10% boost::detail::sp_counted_base::release 0 0% 66.87% 645ms 2.00% AbstractCellPopulation::WriteResultsToFiles 631ms 1.96% 68.83% 631ms 1.96% boost::numeric::ublas::c_vector::operator() 624ms 1.94% 70.77% 624ms 1.94% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 448ms 1.39% 72.16% 620ms 1.92% __dynamic_cast 218ms 0.68% 72.83% 618ms 1.92% __GI___libc_malloc 291ms 0.9% 73.74% 600ms 1.86% NodeAttributes::AddNeighbour 7ms 0.022% 73.76% 587ms 1.82% AbstractCentreBasedCellPopulation::GetDampingConstant 575ms 1.78% 75.54% 575ms 1.78% [libchaste_mesh.so] 34ms 0.11% 75.65% 571ms 1.77% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 75.65% 547ms 1.70% boost::numeric::ublas::scalar_traits::type_abs (inline) 0 0% 75.65% 543ms 1.69% AbstractCellBasedSimulation::DoCellRemoval (inline) 42ms 0.13% 75.78% 540ms 1.68% boost::numeric::ublas::vector_binary::size (inline) 0 0% 75.78% 537ms 1.67% boost::numeric::ublas::scalar_traits::norm_inf (inline) 2ms 0.0062% 75.79% 535ms 1.66% boost_numeric_ublas_abs (inline) 0 0% 75.79% 533ms 1.65% AbstractCellBasedSimulation::DoCellBirth 533ms 1.65% 77.44% 533ms 1.65% std::abs (inline) 13ms 0.04% 77.48% 529ms 1.64% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 515ms 1.60% 79.08% 515ms 1.60% __gnu_cxx::__normal_iterator::operator++ (inline) 173ms 0.54% 79.62% 478ms 1.48% NodeAttributes::AddAppliedForceContribution 0 0% 79.62% 478ms 1.48% std::allocator_traits::allocate (inline) 469ms 1.46% 81.07% 469ms 1.46% std::_Rb_tree_increment 0 0% 81.07% 444ms 1.38% std::_Rb_tree::_M_create_node (inline) 137ms 0.43% 81.50% 443ms 1.38% __GI___libc_free 4ms 0.012% 81.51% 440ms 1.37% CellPropertyCollection::GetPropertiesType (inline) 4ms 0.012% 81.52% 426ms 1.32% NodeBasedCellPopulation::WriteVtkResultsToFile 288ms 0.89% 82.42% 417ms 1.29% std::vector::push_back (inline) 0 0% 82.42% 413ms 1.28% std::_Rb_tree::_M_get_node (inline) 0 0% 82.42% 390ms 1.21% Cell::GetMutationState 0 0% 82.42% 381ms 1.18% boost::numeric::ublas::norm_2 (inline) 275ms 0.85% 83.27% 381ms 1.18% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 83.27% 342ms 1.06% NodesOnlyMesh::ReMesh 16ms 0.05% 83.32% 341ms 1.06% std::_Rb_tree::_M_emplace_hint_unique 0 0% 83.32% 336ms 1.04% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 83.32% 336ms 1.04% boost::numeric::ublas::vector::vector (inline) 2ms 0.0062% 83.33% 334ms 1.04% NodesOnlyMesh::UpdateNodeIndices 0 0% 83.33% 319ms 0.99% boost::numeric::ublas::vector_binary::operator() (inline) 5ms 0.016% 83.34% 311ms 0.97% NodeBasedCellPopulation::UpdateMapsAfterRemesh 236ms 0.73% 84.07% 305ms 0.95% _int_free 0 0% 84.07% 305ms 0.95% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 84.07% 305ms 0.95% boost::numeric::ublas::c_vector::plus_assign (inline) 0 0% 84.07% 284ms 0.88% AbstractCellProperty::IsSubType (inline) 3ms 0.0093% 84.08% 282ms 0.88% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 4ms 0.012% 84.10% 276ms 0.86% AbstractCellPopulation::GetCellUsingLocationIndex 40ms 0.12% 84.22% 270ms 0.84% std::_Rb_tree::_M_erase (partial-inline) 0 0% 84.22% 268ms 0.83% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 174ms 0.54% 84.76% 259ms 0.8% _int_malloc 1ms 0.0031% 84.76% 252ms 0.78% Node::GetRadius 0 0% 84.76% 248ms 0.77% NodesOnlyMesh::UpdateBoxCollection 2ms 0.0062% 84.77% 246ms 0.76% DistributedBoxCollection::GetProcessOwningNode 4ms 0.012% 84.78% 239ms 0.74% std::_Rb_tree::_Rb_tree (partial-inline) 210ms 0.65% 85.43% 238ms 0.74% boost::shared_ptr::shared_ptr (inline) 13ms 0.04% 85.47% 230ms 0.71% std::_Rb_tree::_M_copy (inline) 7ms 0.022% 85.50% 226ms 0.7% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 85.50% 226ms 0.7% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 85.50% 226ms 0.7% std::_Rb_tree::_M_drop_node (inline) 0 0% 85.50% 218ms 0.68% std::_Rb_tree::_Auto_node::_Auto_node (inline) 49ms 0.15% 85.65% 216ms 0.67% std::_Rb_tree::_M_clone_node (inline) 214ms 0.66% 86.31% 214ms 0.66% Node::CheckForNodeAttributes 17ms 0.053% 86.37% 213ms 0.66% std::__new_allocator::deallocate (inline) 1ms 0.0031% 86.37% 201ms 0.62% NodesOnlyMesh::AddNodesToBoxes 0 0% 86.37% 195ms 0.61% std::iter_swap (inline) 195ms 0.61% 86.97% 195ms 0.61% std::swap (inline) 56ms 0.17% 87.15% 189ms 0.59% std::__move_median_to_first (inline) 0 0% 87.15% 188ms 0.58% std::allocator_traits::deallocate (inline) 0 0% 87.15% 187ms 0.58% Cell::HasCellProperty (inline) 0 0% 87.15% 187ms 0.58% CellPropertyCollection::HasProperty 19ms 0.059% 87.21% 187ms 0.58% std::__insertion_sort (inline) 0 0% 87.21% 186ms 0.58% boost::numeric::ublas::c_vector::assign (inline) 0 0% 87.21% 186ms 0.58% std::_Rb_tree::_M_put_node (inline) 0 0% 87.21% 179ms 0.56% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 3ms 0.0093% 87.22% 179ms 0.56% Cell::ReadyToDivide 0 0% 87.22% 179ms 0.56% VtkMeshWriter::WriteFiles 0 0% 87.22% 176ms 0.55% boost::numeric::ublas::inner_prod (inline) 6ms 0.019% 87.23% 175ms 0.54% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 87.23% 175ms 0.54% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 175ms 0.54% 87.78% 175ms 0.54% boost::shared_ptr::operator-> (inline)