File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 30118ms, 88.57% of 34004ms total Dropped 812 nodes (cum <= 170.02ms) flat flat% sum% cum cum% 0 0% 0% 33851ms 99.55% __libc_start_call_main 0 0% 0% 33851ms 99.55% __libc_start_main_impl 0 0% 0% 33851ms 99.55% _start 0 0% 0% 33835ms 99.50% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 33835ms 99.50% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 33835ms 99.50% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 33835ms 99.50% main 0 0% 0% 33800ms 99.40% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 33800ms 99.40% CxxTest::TestRunner::runTest (inline) 0 0% 0% 33800ms 99.40% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 33792ms 99.38% AbstractCellBasedSimulation::Solve 1ms 0.0029% 0.0029% 23759ms 69.87% OffLatticeSimulation::UpdateCellLocationsAndTopology 6ms 0.018% 0.021% 18824ms 55.36% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.024% 0.044% 18627ms 54.78% AbstractNumericalMethod::ComputeForcesIncludingDamping 201ms 0.59% 0.64% 17949ms 52.78% AbstractTwoBodyInteractionForce::AddForceContribution 1406ms 4.13% 4.77% 15028ms 44.19% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4165ms 12.25% 17.02% 9257ms 27.22% std::_Rb_tree::_M_lower_bound (inline) 0 0% 17.02% 8843ms 26.01% AbstractCellBasedSimulation::UpdateCellPopulation 370ms 1.09% 18.11% 8479ms 24.94% std::_Rb_tree::find (inline) 0 0% 18.11% 8478ms 24.93% std::map::find (inline) 268ms 0.79% 18.89% 8292ms 24.39% NodesOnlyMesh::GetNodeOrHaloNode 477ms 1.40% 20.30% 8037ms 23.64% AbstractMesh::GetNode 0 0% 20.30% 7802ms 22.94% NodeBasedCellPopulation::Update 312ms 0.92% 21.22% 7564ms 22.24% NodesOnlyMesh::SolveNodeMapping 239ms 0.7% 21.92% 6372ms 18.74% boost::numeric::ublas::vector_assign (inline) 169ms 0.5% 22.42% 6267ms 18.43% boost::numeric::ublas::c_vector::c_vector (partial-inline) 8ms 0.024% 22.44% 5767ms 16.96% DistributedBoxCollection::CalculateInteriorNodePairs 5058ms 14.87% 37.31% 5058ms 14.87% std::_Rb_tree::_S_right (inline) 1ms 0.0029% 37.32% 4663ms 13.71% OffLatticeSimulation::ApplyBoundaries 17ms 0.05% 37.37% 4486ms 13.19% NodeAttributes::RemoveDuplicateNeighbours 6ms 0.018% 37.38% 4307ms 12.67% std::__sort (inline) 0 0% 37.38% 4307ms 12.67% std::sort (inline) 1164ms 3.42% 40.81% 3705ms 10.90% boost::numeric::ublas::indexing_vector_assign 1ms 0.0029% 40.81% 3511ms 10.33% AbstractCellPopulation::Iterator::operator++ (inline) 187ms 0.55% 41.36% 3491ms 10.27% AbstractCellPopulation::Iterator::IsRealCell (inline) 68ms 0.2% 41.56% 3461ms 10.18% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 24ms 0.071% 41.63% 2965ms 8.72% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 29ms 0.085% 41.72% 2462ms 7.24% PlaneBoundaryCondition::ImposeBoundaryCondition 188ms 0.55% 42.27% 2459ms 7.23% std::__introsort_loop 40ms 0.12% 42.39% 2333ms 6.86% AbstractCellPopulation::GetLocationIndexUsingCell 19ms 0.056% 42.44% 2200ms 6.47% PlaneBoundaryCondition::VerifyBoundaryCondition 2ms 0.0059% 42.45% 2195ms 6.46% std::__unguarded_partition_pivot (inline) 965ms 2.84% 45.29% 1952ms 5.74% std::__unguarded_partition (inline) 185ms 0.54% 45.83% 1891ms 5.56% DistributedBoxCollection::AddPairsFromBox 1ms 0.0029% 45.83% 1842ms 5.42% std::__final_insertion_sort (inline) 1757ms 5.17% 51.00% 1757ms 5.17% boost::numeric::ublas::same_impl_ex 235ms 0.69% 51.69% 1736ms 5.11% std::map::operator[] (partial-inline) 71ms 0.21% 51.90% 1635ms 4.81% std::__unguarded_insertion_sort (inline) 600ms 1.76% 53.66% 1602ms 4.71% std::__unguarded_linear_insert (inline) 144ms 0.42% 54.09% 1537ms 4.52% AbstractMesh::GetVectorFromAtoB 1497ms 4.40% 58.49% 1497ms 4.40% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 58.49% 1304ms 3.83% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 58.49% 1292ms 3.80% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 58.49% 1239ms 3.64% std::_Rb_tree::lower_bound (inline) 0 0% 58.49% 1239ms 3.64% std::map::lower_bound (inline) 1198ms 3.52% 62.01% 1198ms 3.52% boost::numeric::ublas::c_vector::operator() 0 0% 62.01% 1175ms 3.46% NodeBasedCellPopulation::UpdateCellProcessLocation 6ms 0.018% 62.03% 1071ms 3.15% DistributedBoxCollection::CalculateBoundaryNodePairs 20ms 0.059% 62.09% 1040ms 3.06% boost::numeric::ublas::detail::expression_type_check (inline) 177ms 0.52% 62.61% 996ms 2.93% boost::numeric::ublas::detail::equals 136ms 0.4% 63.01% 983ms 2.89% boost::numeric::ublas::vector_binary::size (inline) 277ms 0.81% 63.82% 931ms 2.74% NodeAttributes::AddAppliedForceContribution 18ms 0.053% 63.88% 818ms 2.41% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 358ms 1.05% 64.93% 783ms 2.30% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 64.93% 779ms 2.29% boost::numeric::ublas::norm_inf (inline) 439ms 1.29% 66.22% 779ms 2.29% boost::numeric::ublas::vector_norm_inf::apply (inline) 251ms 0.74% 66.96% 762ms 2.24% NodeAttributes::AddNeighbour 0 0% 66.96% 724ms 2.13% AbstractCellPopulation::WriteResultsToFiles 74ms 0.22% 67.18% 708ms 2.08% std::__new_allocator::allocate (inline) 284ms 0.84% 68.01% 684ms 2.01% __GI___libc_free 458ms 1.35% 69.36% 659ms 1.94% __dynamic_cast 0 0% 69.36% 654ms 1.92% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 69.36% 654ms 1.92% boost::numeric::ublas::c_vector::plus_assign (inline) 97ms 0.29% 69.64% 636ms 1.87% operator new 2ms 0.0059% 69.65% 603ms 1.77% AbstractCentreBasedCellPopulation::GetDampingConstant 1ms 0.0029% 69.65% 585ms 1.72% AbstractCellBasedSimulation::DoCellBirth 511ms 1.50% 71.16% 583ms 1.71% std::vector::push_back (inline) 30ms 0.088% 71.24% 565ms 1.66% std::_Rb_tree_const_iterator::operator++ (inline) 205ms 0.6% 71.85% 532ms 1.56% __GI___libc_malloc 0 0% 71.85% 525ms 1.54% boost::numeric::ublas::norm_2 (inline) 415ms 1.22% 73.07% 525ms 1.54% boost::numeric::ublas::vector_norm_2::apply (inline) 525ms 1.54% 74.61% 525ms 1.54% std::_Rb_tree_increment 6ms 0.018% 74.63% 474ms 1.39% CellPropertyCollection::GetPropertiesType (inline) 0 0% 74.63% 474ms 1.39% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 74.63% 456ms 1.34% AbstractCellBasedSimulation::DoCellRemoval (inline) 8ms 0.024% 74.65% 441ms 1.30% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 31ms 0.091% 74.74% 433ms 1.27% boost::detail::shared_count::~shared_count (inline) 0 0% 74.74% 433ms 1.27% boost::shared_ptr::~shared_ptr (inline) 428ms 1.26% 76.00% 428ms 1.26% NodeBasedCellPopulation::GetNode 0 0% 76.00% 421ms 1.24% Cell::GetMutationState 342ms 1.01% 77.01% 401ms 1.18% _int_free 394ms 1.16% 78.17% 397ms 1.17% boost::detail::sp_counted_base::release 0 0% 78.17% 380ms 1.12% std::allocator_traits::allocate (inline) 376ms 1.11% 79.27% 376ms 1.11% Node::GetIndex 39ms 0.11% 79.39% 367ms 1.08% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 79.39% 367ms 1.08% boost::numeric::ublas::vector::vector (inline) 147ms 0.43% 79.82% 350ms 1.03% Node::GetRadius 0 0% 79.82% 343ms 1.01% std::_Rb_tree::_M_create_node (inline) 325ms 0.96% 80.78% 325ms 0.96% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 80.78% 324ms 0.95% boost::numeric::ublas::inner_prod (inline) 18ms 0.053% 80.83% 323ms 0.95% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 80.83% 323ms 0.95% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 12ms 0.035% 80.86% 321ms 0.94% NodeBasedCellPopulation::UpdateMapsAfterRemesh 13ms 0.038% 80.90% 321ms 0.94% boost::numeric::ublas::vector_reference::operator() (inline) 2ms 0.0059% 80.91% 311ms 0.91% AbstractCellProperty::IsSubType (inline) 0 0% 80.91% 306ms 0.9% NodesOnlyMesh::ReMesh 0 0% 80.91% 304ms 0.89% std::_Rb_tree::_M_get_node (inline) 298ms 0.88% 81.78% 298ms 0.88% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 4ms 0.012% 81.80% 295ms 0.87% NodesOnlyMesh::UpdateNodeIndices 3ms 0.0088% 81.81% 290ms 0.85% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 81.81% 286ms 0.84% boost::numeric::ublas::c_vector::assign (inline) 3ms 0.0088% 81.81% 274ms 0.81% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 6ms 0.018% 81.83% 273ms 0.8% DistributedBoxCollection::GetProcessOwningNode 0 0% 81.83% 270ms 0.79% AbstractCellPopulation::GetCellUsingLocationIndex 266ms 0.78% 82.61% 266ms 0.78% [libchaste_cell_based.so] 109ms 0.32% 82.93% 263ms 0.77% boost::numeric::ublas::vector_inner_prod::apply (inline) 7ms 0.021% 82.95% 262ms 0.77% std::_Rb_tree::_M_emplace_hint_unique 0 0% 82.95% 248ms 0.73% NodesOnlyMesh::UpdateBoxCollection 113ms 0.33% 83.29% 244ms 0.72% std::_Rb_tree::_M_erase (partial-inline) 236ms 0.69% 83.98% 236ms 0.69% [libchaste_mesh.so] 121ms 0.36% 84.34% 235ms 0.69% std::__move_median_to_first (inline) 135ms 0.4% 84.73% 231ms 0.68% _int_malloc 176ms 0.52% 85.25% 227ms 0.67% Node::AddAppliedForceContribution 0 0% 85.25% 225ms 0.66% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 85.25% 223ms 0.66% VtkMeshWriter::WriteFiles 0 0% 85.25% 222ms 0.65% boost::numeric::ublas::vector_binary::operator() (inline) 216ms 0.64% 85.89% 216ms 0.64% Node::CheckForNodeAttributes 24ms 0.071% 85.96% 206ms 0.61% std::__insertion_sort (inline) 0 0% 85.96% 204ms 0.6% NodesOnlyMesh::ResizeBoxCollection 11ms 0.032% 85.99% 203ms 0.6% NodesOnlyMesh::IsANodeCloseToDomainBoundary 1ms 0.0029% 85.99% 203ms 0.6% vtkXMLWriterBase::Write 1ms 0.0029% 86.00% 202ms 0.59% NodesOnlyMesh::AddNodesToBoxes 0 0% 86.00% 202ms 0.59% vtkStreamingDemandDrivenPipeline::Update 0 0% 86.00% 198ms 0.58% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 86.00% 198ms 0.58% vtkDemandDrivenPipeline::ProcessRequest 0 0% 86.00% 198ms 0.58% vtkExecutive::CallAlgorithm 1ms 0.0029% 86.00% 197ms 0.58% vtkStreamingDemandDrivenPipeline::ProcessRequest 38ms 0.11% 86.11% 196ms 0.58% boost::numeric::ublas::c_vector::clear (inline) 0 0% 86.11% 195ms 0.57% vtkCompositeDataPipeline::ExecuteData 0 0% 86.11% 195ms 0.57% vtkDemandDrivenPipeline::ExecuteData 1ms 0.0029% 86.11% 195ms 0.57% vtkXMLUnstructuredDataWriter::ProcessRequest 4ms 0.012% 86.13% 189ms 0.56% std::_Rb_tree::_Rb_tree (partial-inline) 188ms 0.55% 86.68% 188ms 0.55% __strcmp_avx2 95ms 0.28% 86.96% 182ms 0.54% std::__find_if (inline) 0 0% 86.96% 182ms 0.54% std::find_if (inline) 0 0% 86.96% 182ms 0.54% std::none_of (inline) 181ms 0.53% 87.49% 181ms 0.53% boost::numeric::ublas::c_vector::size (inline) 17ms 0.05% 87.54% 181ms 0.53% std::_Rb_tree::_M_copy (inline) 0 0% 87.54% 177ms 0.52% boost::numeric::ublas::vector_reference::size (inline) 4ms 0.012% 87.55% 175ms 0.51% CellPropertyCollection::HasProperty 175ms 0.51% 88.07% 175ms 0.51% Node::IsDeleted 0 0% 88.07% 173ms 0.51% Cell::HasCellProperty (inline) 172ms 0.51% 88.57% 172ms 0.51% Node::rGetLocation