File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 30397ms, 87.98% of 34551ms total Dropped 862 nodes (cum <= 172.75ms) flat flat% sum% cum cum% 0 0% 0% 34379ms 99.50% __libc_start_call_main 0 0% 0% 34379ms 99.50% __libc_start_main_impl 0 0% 0% 34379ms 99.50% _start 0 0% 0% 34364ms 99.46% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 34364ms 99.46% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 34364ms 99.46% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 34364ms 99.46% main 0 0% 0% 34328ms 99.35% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 34328ms 99.35% CxxTest::TestRunner::runTest (inline) 0 0% 0% 34328ms 99.35% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 34319ms 99.33% AbstractCellBasedSimulation::Solve 3ms 0.0087% 0.0087% 23395ms 67.71% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.0058% 0.014% 18439ms 53.37% ForwardEulerNumericalMethod::UpdateAllNodePositions 12ms 0.035% 0.049% 18238ms 52.79% AbstractNumericalMethod::ComputeForcesIncludingDamping 240ms 0.69% 0.74% 17023ms 49.27% AbstractTwoBodyInteractionForce::AddForceContribution 1457ms 4.22% 4.96% 14227ms 41.18% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 0 0% 4.96% 9680ms 28.02% AbstractCellBasedSimulation::UpdateCellPopulation 4435ms 12.84% 17.80% 9579ms 27.72% std::_Rb_tree::_M_lower_bound (inline) 352ms 1.02% 18.82% 8647ms 25.03% std::_Rb_tree::find (inline) 0 0% 18.82% 8645ms 25.02% std::map::find (inline) 0 0% 18.82% 8506ms 24.62% NodeBasedCellPopulation::Update 150ms 0.43% 19.25% 8432ms 24.40% NodesOnlyMesh::GetNodeOrHaloNode 518ms 1.50% 20.75% 8271ms 23.94% AbstractMesh::GetNode 313ms 0.91% 21.65% 7755ms 22.45% NodesOnlyMesh::SolveNodeMapping 10ms 0.029% 21.68% 6358ms 18.40% DistributedBoxCollection::CalculateInteriorNodePairs 217ms 0.63% 22.31% 5436ms 15.73% boost::numeric::ublas::vector_assign (inline) 159ms 0.46% 22.77% 5335ms 15.44% boost::numeric::ublas::c_vector::c_vector (partial-inline) 5119ms 14.82% 37.59% 5119ms 14.82% std::_Rb_tree::_S_right (inline) 16ms 0.046% 37.63% 4627ms 13.39% NodeAttributes::RemoveDuplicateNeighbours 1ms 0.0029% 37.64% 4562ms 13.20% OffLatticeSimulation::ApplyBoundaries 8ms 0.023% 37.66% 4461ms 12.91% std::__sort (inline) 0 0% 37.66% 4461ms 12.91% std::sort (inline) 83ms 0.24% 37.90% 3405ms 9.85% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 5ms 0.014% 37.91% 3395ms 9.83% AbstractCellPopulation::Iterator::operator++ (inline) 191ms 0.55% 38.47% 3373ms 9.76% AbstractCellPopulation::Iterator::IsRealCell (inline) 997ms 2.89% 41.35% 3083ms 8.92% boost::numeric::ublas::indexing_vector_assign 27ms 0.078% 41.43% 2856ms 8.27% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 236ms 0.68% 42.11% 2582ms 7.47% std::__introsort_loop 34ms 0.098% 42.21% 2390ms 6.92% PlaneBoundaryCondition::ImposeBoundaryCondition 140ms 0.41% 42.62% 2373ms 6.87% DistributedBoxCollection::AddPairsFromBox 36ms 0.1% 42.72% 2300ms 6.66% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.0029% 42.73% 2267ms 6.56% std::__unguarded_partition_pivot (inline) 18ms 0.052% 42.78% 2170ms 6.28% PlaneBoundaryCondition::VerifyBoundaryCondition 1079ms 3.12% 45.90% 2028ms 5.87% std::__unguarded_partition (inline) 0 0% 45.90% 1869ms 5.41% std::__final_insertion_sort (inline) 205ms 0.59% 46.49% 1833ms 5.31% std::map::operator[] (partial-inline) 84ms 0.24% 46.74% 1671ms 4.84% std::__unguarded_insertion_sort (inline) 603ms 1.75% 48.48% 1635ms 4.73% std::__unguarded_linear_insert (inline) 1498ms 4.34% 52.82% 1498ms 4.34% __gnu_cxx::__normal_iterator::operator-- (inline) 1430ms 4.14% 56.96% 1430ms 4.14% boost::numeric::ublas::same_impl_ex 0 0% 56.96% 1370ms 3.97% std::_Rb_tree::lower_bound (inline) 0 0% 56.96% 1370ms 3.97% std::map::lower_bound (inline) 153ms 0.44% 57.40% 1340ms 3.88% AbstractMesh::GetVectorFromAtoB 0 0% 57.40% 1217ms 3.52% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 57.40% 1198ms 3.47% NodeBasedCellPopulation::UpdateCellProcessLocation 0 0% 57.40% 1198ms 3.47% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1171ms 3.39% 60.79% 1171ms 3.39% boost::numeric::ublas::c_vector::operator() 6ms 0.017% 60.81% 1129ms 3.27% AbstractCentreBasedCellPopulation::GetDampingConstant 5ms 0.014% 60.82% 1129ms 3.27% DistributedBoxCollection::CalculateBoundaryNodePairs 16ms 0.046% 60.87% 997ms 2.89% boost::numeric::ublas::detail::expression_type_check (inline) 44ms 0.13% 60.99% 991ms 2.87% std::_Rb_tree_const_iterator::operator++ (inline) 181ms 0.52% 61.52% 952ms 2.76% boost::numeric::ublas::detail::equals 943ms 2.73% 64.25% 943ms 2.73% std::_Rb_tree_increment 120ms 0.35% 64.59% 879ms 2.54% boost::numeric::ublas::vector_binary::size (inline) 17ms 0.049% 64.64% 847ms 2.45% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 634ms 1.83% 66.48% 824ms 2.38% __dynamic_cast 16ms 0.046% 66.52% 815ms 2.36% CellPropertyCollection::GetPropertiesType (inline) 218ms 0.63% 67.16% 814ms 2.36% NodeAttributes::AddAppliedForceContribution 162ms 0.47% 67.62% 799ms 2.31% std::__new_allocator::allocate (inline) 380ms 1.10% 68.72% 774ms 2.24% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 68.72% 771ms 2.23% AbstractCellPopulation::WriteResultsToFiles 1ms 0.0029% 68.73% 727ms 2.10% Cell::GetMutationState 0 0% 68.73% 727ms 2.10% boost::numeric::ublas::norm_inf (inline) 426ms 1.23% 69.96% 727ms 2.10% boost::numeric::ublas::vector_norm_inf::apply (inline) 2ms 0.0058% 69.97% 719ms 2.08% AbstractCellBasedSimulation::DoCellBirth 179ms 0.52% 70.48% 687ms 1.99% NodeAttributes::AddNeighbour 230ms 0.67% 71.15% 661ms 1.91% __GI___libc_free 109ms 0.32% 71.47% 636ms 1.84% operator new 508ms 1.47% 72.94% 617ms 1.79% std::vector::push_back (inline) 0 0% 72.94% 596ms 1.72% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 72.94% 596ms 1.72% boost::numeric::ublas::c_vector::plus_assign (inline) 122ms 0.35% 73.29% 542ms 1.57% Node::AddNeighbour 173ms 0.5% 73.79% 525ms 1.52% __GI___libc_malloc 4ms 0.012% 73.80% 509ms 1.47% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 4ms 0.012% 73.81% 502ms 1.45% AbstractCellPopulation::GetCellUsingLocationIndex 3ms 0.0087% 73.82% 500ms 1.45% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 73.82% 490ms 1.42% boost::numeric::ublas::norm_2 (inline) 391ms 1.13% 74.95% 490ms 1.42% boost::numeric::ublas::vector_norm_2::apply (inline) 488ms 1.41% 76.37% 488ms 1.41% Node::ConstructNodeAttributes (inline) 0 0% 76.37% 479ms 1.39% std::allocator_traits::allocate (inline) 0 0% 76.37% 474ms 1.37% std::_Rb_tree::_M_create_node (inline) 0 0% 76.37% 454ms 1.31% AbstractCellBasedSimulation::DoCellRemoval (inline) 7ms 0.02% 76.39% 441ms 1.28% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 387ms 1.12% 77.51% 430ms 1.24% _int_free 4ms 0.012% 77.52% 411ms 1.19% std::_Rb_tree::_Rb_tree (partial-inline) 35ms 0.1% 77.62% 410ms 1.19% boost::detail::shared_count::~shared_count (inline) 0 0% 77.62% 410ms 1.19% boost::shared_ptr::~shared_ptr (inline) 39ms 0.11% 77.73% 403ms 1.17% std::_Rb_tree::_M_copy (inline) 0 0% 77.73% 403ms 1.17% std::_Rb_tree::_M_get_node (inline) 2ms 0.0058% 77.74% 387ms 1.12% AbstractCellProperty::IsSubType (inline) 177ms 0.51% 78.25% 371ms 1.07% std::_Rb_tree::_M_erase 361ms 1.04% 79.29% 367ms 1.06% boost::detail::sp_counted_base::release 363ms 1.05% 80.34% 363ms 1.05% Node::GetIndex 68ms 0.2% 80.54% 363ms 1.05% std::_Rb_tree::_M_clone_node (inline) 38ms 0.11% 80.65% 358ms 1.04% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 80.65% 358ms 1.04% boost::numeric::ublas::vector::vector (inline) 5ms 0.014% 80.67% 346ms 1.00% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 80.67% 344ms 1% std::_Rb_tree::_Alloc_node::operator() (inline) 14ms 0.041% 80.71% 342ms 0.99% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 80.71% 340ms 0.98% boost::numeric::ublas::inner_prod (inline) 3ms 0.0087% 80.72% 336ms 0.97% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 17ms 0.049% 80.76% 333ms 0.96% boost::numeric::ublas::vector_scalar_binary::evaluate 1ms 0.0029% 80.77% 323ms 0.93% NodesOnlyMesh::ReMesh 316ms 0.91% 81.68% 316ms 0.91% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 4ms 0.012% 81.69% 313ms 0.91% NodesOnlyMesh::UpdateNodeIndices 4ms 0.012% 81.71% 304ms 0.88% CellPropertyCollection::HasProperty 303ms 0.88% 82.58% 303ms 0.88% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 82.58% 301ms 0.87% Cell::HasCellProperty (inline) 13ms 0.038% 82.62% 289ms 0.84% Cell::ReadyToDivide 104ms 0.3% 82.92% 289ms 0.84% Node::GetRadius 0 0% 82.92% 282ms 0.82% NodesOnlyMesh::UpdateBoxCollection 0 0% 82.92% 274ms 0.79% boost::numeric::ublas::c_vector::assign (inline) 97ms 0.28% 83.20% 261ms 0.76% boost::numeric::ublas::vector_inner_prod::apply (inline) 12ms 0.035% 83.24% 258ms 0.75% std::_Rb_tree::_M_emplace_hint_unique 2ms 0.0058% 83.24% 254ms 0.74% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 83.24% 249ms 0.72% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 2ms 0.0058% 83.25% 249ms 0.72% std::set::set (inline) 248ms 0.72% 83.97% 248ms 0.72% [libchaste_cell_based.so] 1ms 0.0029% 83.97% 247ms 0.71% VtkMeshWriter::WriteFiles 141ms 0.41% 84.38% 247ms 0.71% _int_malloc 0 0% 84.38% 245ms 0.71% boost::numeric::ublas::vector_binary::operator() (inline) 242ms 0.7% 85.08% 242ms 0.7% NodeBasedCellPopulation::GetNode 9ms 0.026% 85.10% 240ms 0.69% DistributedBoxCollection::GetProcessOwningNode 92ms 0.27% 85.37% 236ms 0.68% std::__move_median_to_first (inline) 1ms 0.0029% 85.37% 222ms 0.64% NodesOnlyMesh::ResizeBoxCollection 19ms 0.055% 85.43% 219ms 0.63% NodesOnlyMesh::IsANodeCloseToDomainBoundary 1ms 0.0029% 85.43% 217ms 0.63% NodesOnlyMesh::AddNodesToBoxes 216ms 0.63% 86.06% 216ms 0.63% boost::shared_ptr::operator-> (inline) 0 0% 86.06% 213ms 0.62% vtkDemandDrivenPipeline::ProcessRequest 0 0% 86.06% 213ms 0.62% vtkStreamingDemandDrivenPipeline::Update 0 0% 86.06% 213ms 0.62% vtkXMLWriterBase::Write 0 0% 86.06% 210ms 0.61% vtkDemandDrivenPipeline::ExecuteData 0 0% 86.06% 210ms 0.61% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 86.06% 208ms 0.6% vtkCompositeDataPipeline::ExecuteData 0 0% 86.06% 208ms 0.6% vtkExecutive::CallAlgorithm 0 0% 86.06% 208ms 0.6% vtkXMLUnstructuredDataWriter::ProcessRequest 207ms 0.6% 86.65% 207ms 0.6% Node::CheckForNodeAttributes 0 0% 86.65% 207ms 0.6% std::_Rb_tree::clear (inline) 89ms 0.26% 86.91% 204ms 0.59% std::__find_if (inline) 0 0% 86.91% 204ms 0.59% std::find_if (inline) 0 0% 86.91% 204ms 0.59% std::none_of (inline) 13ms 0.038% 86.95% 198ms 0.57% std::__insertion_sort (inline) 6ms 0.017% 86.97% 197ms 0.57% std::_Rb_tree::~_Rb_tree (inline) 27ms 0.078% 87.05% 197ms 0.57% std::__new_allocator::deallocate (inline) 132ms 0.38% 87.43% 195ms 0.56% Node::AddAppliedForceContribution 188ms 0.54% 87.97% 188ms 0.54% [libchaste_mesh.so] 0 0% 87.97% 180ms 0.52% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 87.97% 180ms 0.52% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 2ms 0.0058% 87.98% 178ms 0.52% AbstractCellProperty::IsType (inline) 0 0% 87.98% 177ms 0.51% std::_Rb_tree::_M_drop_node (inline) 0 0% 87.98% 173ms 0.5% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData