File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 32603ms, 87.53% of 37249ms total Dropped 854 nodes (cum <= 186.25ms) flat flat% sum% cum cum% 0 0% 0% 37158ms 99.76% __libc_start_call_main 0 0% 0% 37158ms 99.76% __libc_start_main_impl 0 0% 0% 37158ms 99.76% _start 0 0% 0% 37139ms 99.70% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 37139ms 99.70% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 37139ms 99.70% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 37139ms 99.70% main 0 0% 0% 37105ms 99.61% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 37105ms 99.61% CxxTest::TestRunner::runTest (inline) 0 0% 0% 37105ms 99.61% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0027% 0.0027% 37097ms 99.59% AbstractCellBasedSimulation::Solve 1ms 0.0027% 0.0054% 25896ms 69.52% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0027% 0.0081% 19726ms 52.96% ForwardEulerNumericalMethod::UpdateAllNodePositions 5ms 0.013% 0.021% 19555ms 52.50% AbstractNumericalMethod::ComputeForcesIncludingDamping 269ms 0.72% 0.74% 18812ms 50.50% AbstractTwoBodyInteractionForce::AddForceContribution 1203ms 3.23% 3.97% 16793ms 45.08% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4955ms 13.30% 17.28% 11416ms 30.65% std::_Rb_tree::_M_lower_bound (inline) 216ms 0.58% 17.86% 11161ms 29.96% NodesOnlyMesh::GetNodeOrHaloNode 337ms 0.9% 18.76% 10947ms 29.39% AbstractMesh::GetNode 896ms 2.41% 21.17% 10616ms 28.50% NodesOnlyMesh::SolveNodeMapping 552ms 1.48% 22.65% 10599ms 28.45% std::_Rb_tree::find (inline) 0 0% 22.65% 10599ms 28.45% std::map::find (inline) 0 0% 22.65% 10003ms 26.85% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 22.65% 8825ms 23.69% NodeBasedCellPopulation::Update 2ms 0.0054% 22.65% 6679ms 17.93% DistributedBoxCollection::CalculateInteriorNodePairs 0 0% 22.65% 5852ms 15.71% OffLatticeSimulation::ApplyBoundaries 5550ms 14.90% 37.55% 5550ms 14.90% std::_Rb_tree::_S_right (inline) 177ms 0.48% 38.03% 5302ms 14.23% boost::numeric::ublas::vector_assign (inline) 15ms 0.04% 38.07% 5230ms 14.04% NodeAttributes::RemoveDuplicateNeighbours 81ms 0.22% 38.29% 5192ms 13.94% boost::numeric::ublas::c_vector::c_vector (partial-inline) 6ms 0.016% 38.30% 5023ms 13.48% std::__sort (inline) 0 0% 38.30% 5023ms 13.48% std::sort (inline) 324ms 0.87% 39.17% 4200ms 11.28% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 6ms 0.016% 39.19% 4024ms 10.80% AbstractCellPopulation::Iterator::operator++ (inline) 225ms 0.6% 39.79% 4010ms 10.77% AbstractCellPopulation::Iterator::IsRealCell 45ms 0.12% 39.91% 3329ms 8.94% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 243ms 0.65% 40.56% 3009ms 8.08% std::__introsort_loop 77ms 0.21% 40.77% 2967ms 7.97% PlaneBoundaryCondition::ImposeBoundaryCondition 63ms 0.17% 40.94% 2885ms 7.75% PlaneBoundaryCondition::VerifyBoundaryCondition 7ms 0.019% 40.96% 2678ms 7.19% std::__unguarded_partition_pivot (inline) 856ms 2.30% 43.26% 2420ms 6.50% std::__unguarded_partition (inline) 115ms 0.31% 43.57% 2369ms 6.36% AbstractCellPopulation::GetLocationIndexUsingCell 692ms 1.86% 45.42% 2286ms 6.14% boost::numeric::ublas::indexing_vector_assign 210ms 0.56% 45.99% 2077ms 5.58% std::map::operator[] (partial-inline) 123ms 0.33% 46.32% 2022ms 5.43% DistributedBoxCollection::AddPairsFromBox 0 0% 46.32% 2002ms 5.37% std::__final_insertion_sort (inline) 135ms 0.36% 46.68% 1792ms 4.81% std::__unguarded_insertion_sort (inline) 0 0% 46.68% 1784ms 4.79% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 46.68% 1763ms 4.73% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 32ms 0.086% 46.77% 1643ms 4.41% boost::numeric::ublas::detail::expression_type_check (inline) 854ms 2.29% 49.06% 1605ms 4.31% std::__unguarded_linear_insert (inline) 213ms 0.57% 49.63% 1556ms 4.18% boost::numeric::ublas::detail::equals 0 0% 49.63% 1485ms 3.99% std::_Rb_tree::lower_bound (inline) 0 0% 49.63% 1485ms 3.99% std::map::lower_bound (inline) 0 0% 49.63% 1292ms 3.47% boost::numeric::ublas::norm_inf (inline) 425ms 1.14% 50.77% 1292ms 3.47% boost::numeric::ublas::vector_norm_inf::apply (inline) 21ms 0.056% 50.83% 1260ms 3.38% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 50.83% 1205ms 3.23% NodeBasedCellPopulation::UpdateCellProcessLocation 1195ms 3.21% 54.04% 1195ms 3.21% boost::numeric::ublas::same_impl_ex 197ms 0.53% 54.57% 1192ms 3.20% AbstractMesh::GetVectorFromAtoB 1147ms 3.08% 57.64% 1147ms 3.08% __gnu_cxx::__normal_iterator::operator-- (inline) 9ms 0.024% 57.67% 1079ms 2.90% DistributedBoxCollection::CalculateBoundaryNodePairs 113ms 0.3% 57.97% 1029ms 2.76% std::__new_allocator::allocate (inline) 935ms 2.51% 60.48% 935ms 2.51% std::_Rb_tree::_S_left (inline) 73ms 0.2% 60.68% 885ms 2.38% operator new 358ms 0.96% 61.64% 865ms 2.32% DistributedBoxCollection::CalculateContainingBox (partial-inline) 854ms 2.29% 63.93% 854ms 2.29% [libchaste_cell_based.so] 15ms 0.04% 63.97% 838ms 2.25% boost::detail::shared_count::~shared_count (inline) 0 0% 63.97% 838ms 2.25% boost::shared_ptr::~shared_ptr (inline) 798ms 2.14% 66.11% 811ms 2.18% boost::detail::sp_counted_base::release 412ms 1.11% 67.22% 782ms 2.10% NodeAttributes::AddNeighbour 265ms 0.71% 67.93% 764ms 2.05% __GI___libc_malloc 558ms 1.50% 69.43% 731ms 1.96% __dynamic_cast 0 0% 69.43% 726ms 1.95% AbstractCellPopulation::WriteResultsToFiles 2ms 0.0054% 69.44% 695ms 1.87% AbstractCentreBasedCellPopulation::GetDampingConstant 694ms 1.86% 71.30% 694ms 1.86% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 32ms 0.086% 71.38% 693ms 1.86% std::_Rb_tree_const_iterator::operator++ (inline) 679ms 1.82% 73.21% 679ms 1.82% [libchaste_mesh.so] 0 0% 73.21% 673ms 1.81% boost::numeric::ublas::scalar_traits::type_abs (inline) 666ms 1.79% 75.00% 666ms 1.79% boost::numeric::ublas::c_vector::operator() 3ms 0.0081% 75.00% 643ms 1.73% boost_numeric_ublas_abs (inline) 256ms 0.69% 75.69% 642ms 1.72% NodeAttributes::AddAppliedForceContribution 0 0% 75.69% 642ms 1.72% boost::numeric::ublas::scalar_traits::norm_inf (inline) 640ms 1.72% 77.41% 640ms 1.72% std::abs (inline) 0 0% 77.41% 606ms 1.63% AbstractCellBasedSimulation::DoCellRemoval (inline) 601ms 1.61% 79.02% 601ms 1.61% __gnu_cxx::__normal_iterator::operator++ (inline) 5ms 0.013% 79.04% 599ms 1.61% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 60ms 0.16% 79.20% 599ms 1.61% boost::numeric::ublas::vector_binary::size (inline) 584ms 1.57% 80.76% 584ms 1.57% std::_Rb_tree_increment 4ms 0.011% 80.78% 571ms 1.53% AbstractCellBasedSimulation::DoCellBirth 0 0% 80.78% 540ms 1.45% std::allocator_traits::allocate (inline) 152ms 0.41% 81.18% 501ms 1.35% __GI___libc_free 4ms 0.011% 81.19% 493ms 1.32% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 81.19% 493ms 1.32% boost::numeric::ublas::vector::vector (inline) 0 0% 81.19% 492ms 1.32% boost::numeric::ublas::norm_2 (inline) 366ms 0.98% 82.18% 492ms 1.32% boost::numeric::ublas::vector_norm_2::apply (inline) 348ms 0.93% 83.11% 482ms 1.29% std::vector::push_back (inline) 0 0% 83.11% 479ms 1.29% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 83.11% 471ms 1.26% std::_Rb_tree::_M_create_node (inline) 8ms 0.021% 83.13% 469ms 1.26% CellPropertyCollection::GetPropertiesType (inline) 0 0% 83.13% 448ms 1.20% std::_Rb_tree::_M_get_node (inline) 2ms 0.0054% 83.14% 410ms 1.10% Cell::GetMutationState 0 0% 83.14% 386ms 1.04% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 83.14% 386ms 1.04% boost::numeric::ublas::c_vector::plus_assign (inline) 13ms 0.035% 83.17% 381ms 1.02% std::_Rb_tree::_M_emplace_hint_unique 0 0% 83.17% 369ms 0.99% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 83.17% 358ms 0.96% NodesOnlyMesh::ReMesh 0 0% 83.17% 354ms 0.95% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 1ms 0.0027% 83.18% 351ms 0.94% AbstractCellPopulation::GetCellUsingLocationIndex 5ms 0.013% 83.19% 346ms 0.93% NodesOnlyMesh::UpdateNodeIndices 259ms 0.7% 83.88% 346ms 0.93% _int_free 1ms 0.0027% 83.89% 322ms 0.86% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 83.89% 321ms 0.86% NodesOnlyMesh::UpdateBoxCollection 3ms 0.0081% 83.89% 312ms 0.84% NodeBasedCellPopulation::UpdateMapsAfterRemesh 1ms 0.0027% 83.90% 310ms 0.83% Node::GetRadius 2ms 0.0054% 83.90% 309ms 0.83% DistributedBoxCollection::GetProcessOwningNode 5ms 0.013% 83.92% 303ms 0.81% AbstractCellProperty::IsSubType (inline) 175ms 0.47% 84.39% 293ms 0.79% _int_malloc 0 0% 84.39% 276ms 0.74% NodesOnlyMesh::AddNodesToBoxes 17ms 0.046% 84.43% 271ms 0.73% std::_Rb_tree::_Rb_tree (partial-inline) 228ms 0.61% 85.04% 265ms 0.71% boost::shared_ptr::shared_ptr (inline) 21ms 0.056% 85.10% 252ms 0.68% std::_Rb_tree::_M_copy (inline) 83ms 0.22% 85.32% 245ms 0.66% std::__move_median_to_first (inline) 44ms 0.12% 85.44% 244ms 0.66% std::_Rb_tree::_M_erase (partial-inline) 243ms 0.65% 86.09% 243ms 0.65% Node::CheckForNodeAttributes 0 0% 86.09% 242ms 0.65% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 86.09% 229ms 0.61% std::_Rb_tree::_Auto_node::_Auto_node (inline) 49ms 0.13% 86.23% 229ms 0.61% std::_Rb_tree::_M_clone_node (inline) 0 0% 86.23% 228ms 0.61% std::iter_swap (inline) 228ms 0.61% 86.84% 228ms 0.61% std::swap (inline) 4ms 0.011% 86.85% 220ms 0.59% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 86.85% 215ms 0.58% boost::numeric::ublas::inner_prod (inline) 11ms 0.03% 86.88% 215ms 0.58% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 86.88% 215ms 0.58% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 86.88% 210ms 0.56% boost::numeric::ublas::c_vector::assign (inline) 28ms 0.075% 86.95% 210ms 0.56% std::__insertion_sort (inline) 0 0% 86.95% 205ms 0.55% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 14ms 0.038% 86.99% 205ms 0.55% std::__new_allocator::deallocate (inline) 0 0% 86.99% 202ms 0.54% VtkMeshWriter::WriteFiles 198ms 0.53% 87.52% 198ms 0.53% NodeBasedCellPopulation::GetNode 2ms 0.0054% 87.53% 196ms 0.53% CellPropertyCollection::HasProperty 0 0% 87.53% 194ms 0.52% Cell::HasCellProperty (inline) 0 0% 87.53% 194ms 0.52% std::_Rb_tree::_M_drop_node (inline)