File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 19981ms, 87.49% of 22838ms total Dropped 740 nodes (cum <= 114.19ms) flat flat% sum% cum cum% 0 0% 0% 22753ms 99.63% __libc_start_call_main 0 0% 0% 22753ms 99.63% __libc_start_main_impl 0 0% 0% 22753ms 99.63% _start 0 0% 0% 22740ms 99.57% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 22740ms 99.57% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 22740ms 99.57% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 22740ms 99.57% main 0 0% 0% 22706ms 99.42% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 22706ms 99.42% CxxTest::TestRunner::runTest (inline) 0 0% 0% 22706ms 99.42% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 22700ms 99.40% AbstractCellBasedSimulation::Solve 0 0% 0% 15434ms 67.58% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0044% 0.0044% 11649ms 51.01% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0044% 0.0088% 11520ms 50.44% AbstractNumericalMethod::ComputeForcesIncludingDamping 70ms 0.31% 0.32% 10922ms 47.82% AbstractTwoBodyInteractionForce::AddForceContribution 1075ms 4.71% 5.02% 9872ms 43.23% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 3638ms 15.93% 20.95% 6637ms 29.06% std::_Rb_tree::_M_lower_bound (inline) 0 0% 20.95% 6483ms 28.39% AbstractCellBasedSimulation::UpdateCellPopulation 28ms 0.12% 21.07% 6090ms 26.67% NodesOnlyMesh::GetNodeOrHaloNode 285ms 1.25% 22.32% 6070ms 26.58% AbstractMesh::GetNode 295ms 1.29% 23.61% 5972ms 26.15% std::_Rb_tree::find (inline) 0 0% 23.61% 5972ms 26.15% std::map::find (inline) 421ms 1.84% 25.46% 5789ms 25.35% NodesOnlyMesh::SolveNodeMapping 1ms 0.0044% 25.46% 5641ms 24.70% NodeBasedCellPopulation::Update 5ms 0.022% 25.48% 4339ms 19.00% DistributedBoxCollection::CalculateInteriorNodePairs 0 0% 25.48% 3535ms 15.48% OffLatticeSimulation::ApplyBoundaries 17ms 0.074% 25.56% 3335ms 14.60% NodeAttributes::RemoveDuplicateNeighbours 4ms 0.018% 25.58% 3212ms 14.06% std::__sort (inline) 0 0% 25.58% 3212ms 14.06% std::sort (inline) 134ms 0.59% 26.16% 3099ms 13.57% boost::numeric::ublas::c_vector::c_vector (partial-inline) 86ms 0.38% 26.54% 3034ms 13.28% boost::numeric::ublas::vector_assign (inline) 2964ms 12.98% 39.52% 2964ms 12.98% std::_Rb_tree::_S_right (inline) 127ms 0.56% 40.07% 2548ms 11.16% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 2ms 0.0088% 40.08% 2453ms 10.74% AbstractCellPopulation::Iterator::operator++ (inline) 94ms 0.41% 40.49% 2441ms 10.69% AbstractCellPopulation::Iterator::IsRealCell (inline) 11ms 0.048% 40.54% 2053ms 8.99% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 139ms 0.61% 41.15% 1865ms 8.17% std::__introsort_loop 64ms 0.28% 41.43% 1835ms 8.03% PlaneBoundaryCondition::ImposeBoundaryCondition 52ms 0.23% 41.66% 1700ms 7.44% PlaneBoundaryCondition::VerifyBoundaryCondition 0 0% 41.66% 1668ms 7.30% std::__unguarded_partition_pivot (inline) 38ms 0.17% 41.83% 1526ms 6.68% AbstractCellPopulation::GetLocationIndexUsingCell 453ms 1.98% 43.81% 1506ms 6.59% boost::numeric::ublas::indexing_vector_assign 736ms 3.22% 47.03% 1492ms 6.53% std::__unguarded_partition (inline) 119ms 0.52% 47.55% 1392ms 6.10% DistributedBoxCollection::AddPairsFromBox 174ms 0.76% 48.31% 1391ms 6.09% std::map::operator[] (partial-inline) 2ms 0.0088% 48.32% 1339ms 5.86% std::__final_insertion_sort (inline) 72ms 0.32% 48.64% 1170ms 5.12% std::__unguarded_insertion_sort (inline) 385ms 1.69% 50.32% 1130ms 4.95% std::__unguarded_linear_insert (inline) 1097ms 4.80% 55.13% 1097ms 4.80% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 55.13% 1012ms 4.43% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 55.13% 1005ms 4.40% std::_Rb_tree::lower_bound (inline) 0 0% 55.13% 1005ms 4.40% std::map::lower_bound (inline) 0 0% 55.13% 1004ms 4.40% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 968ms 4.24% 59.37% 968ms 4.24% boost::numeric::ublas::same_impl_ex 146ms 0.64% 60.01% 844ms 3.70% AbstractMesh::GetVectorFromAtoB 25ms 0.11% 60.11% 829ms 3.63% boost::numeric::ublas::detail::expression_type_check (inline) 39ms 0.17% 60.29% 799ms 3.50% boost::numeric::ublas::detail::equals 12ms 0.053% 60.34% 729ms 3.19% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 60.34% 725ms 3.17% boost::numeric::ublas::norm_inf (inline) 370ms 1.62% 61.96% 725ms 3.17% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 61.96% 704ms 3.08% DistributedBoxCollection::CalculateBoundaryNodePairs 0 0% 61.96% 688ms 3.01% NodeBasedCellPopulation::UpdateCellProcessLocation 27ms 0.12% 62.08% 636ms 2.78% boost::detail::shared_count::~shared_count (inline) 0 0% 62.08% 636ms 2.78% boost::shared_ptr::~shared_ptr (inline) 34ms 0.15% 62.23% 617ms 2.70% std::_Rb_tree_const_iterator::operator++ (inline) 598ms 2.62% 64.84% 605ms 2.65% boost::detail::sp_counted_base::release 570ms 2.50% 67.34% 570ms 2.50% std::_Rb_tree_increment 0 0% 67.34% 566ms 2.48% AbstractCentreBasedCellPopulation::GetDampingConstant 68ms 0.3% 67.64% 555ms 2.43% boost::numeric::ublas::vector_binary::size (inline) 66ms 0.29% 67.93% 525ms 2.30% std::__new_allocator::allocate (inline) 246ms 1.08% 69.00% 514ms 2.25% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 69.00% 512ms 2.24% AbstractCellPopulation::WriteResultsToFiles 3ms 0.013% 69.02% 505ms 2.21% AbstractCellBasedSimulation::DoCellBirth 70ms 0.31% 69.32% 458ms 2.01% operator new 450ms 1.97% 71.29% 450ms 1.97% boost::numeric::ublas::c_vector::operator() 103ms 0.45% 71.74% 408ms 1.79% NodeAttributes::AddAppliedForceContribution 182ms 0.8% 72.54% 402ms 1.76% NodeAttributes::AddNeighbour 8ms 0.035% 72.58% 398ms 1.74% CellPropertyCollection::GetPropertiesType (inline) 152ms 0.67% 73.24% 384ms 1.68% __GI___libc_malloc 255ms 1.12% 74.36% 363ms 1.59% __dynamic_cast 218ms 0.95% 75.31% 357ms 1.56% std::vector::push_back (inline) 3ms 0.013% 75.33% 356ms 1.56% Cell::GetMutationState 3ms 0.013% 75.34% 346ms 1.52% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 75.34% 337ms 1.48% AbstractCellBasedSimulation::DoCellRemoval (inline) 9ms 0.039% 75.38% 327ms 1.43% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 75.38% 314ms 1.37% std::allocator_traits::allocate (inline) 0 0% 75.38% 305ms 1.34% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 75.38% 305ms 1.34% boost::numeric::ublas::c_vector::plus_assign (inline) 84ms 0.37% 75.75% 297ms 1.30% __GI___libc_free 0 0% 75.75% 287ms 1.26% boost::numeric::ublas::norm_2 (inline) 245ms 1.07% 76.82% 287ms 1.26% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 76.82% 282ms 1.23% std::_Rb_tree::_M_create_node (inline) 0 0% 76.82% 265ms 1.16% std::_Rb_tree::_M_get_node (inline) 1ms 0.0044% 76.82% 248ms 1.09% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 3ms 0.013% 76.84% 246ms 1.08% AbstractCellPopulation::GetCellUsingLocationIndex 238ms 1.04% 77.88% 238ms 1.04% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 19ms 0.083% 77.96% 230ms 1.01% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 77.96% 230ms 1.01% boost::numeric::ublas::vector::vector (inline) 0 0% 77.96% 213ms 0.93% AbstractCellProperty::IsSubType (inline) 0 0% 77.96% 213ms 0.93% Cell::HasCellProperty (inline) 1ms 0.0044% 77.97% 213ms 0.93% CellPropertyCollection::HasProperty 44ms 0.19% 78.16% 212ms 0.93% Node::GetRadius 6ms 0.026% 78.19% 212ms 0.93% std::_Rb_tree::_M_emplace_hint_unique 211ms 0.92% 79.11% 211ms 0.92% __gnu_cxx::__normal_iterator::operator++ (inline) 187ms 0.82% 79.93% 211ms 0.92% _int_free 0 0% 79.93% 205ms 0.9% NodesOnlyMesh::ReMesh 204ms 0.89% 80.82% 204ms 0.89% NodeBasedCellPopulation::GetNode 48ms 0.21% 81.03% 202ms 0.88% std::_Rb_tree::_M_erase (partial-inline) 2ms 0.0088% 81.04% 196ms 0.86% NodesOnlyMesh::UpdateNodeIndices 7ms 0.031% 81.07% 195ms 0.85% Cell::ReadyToDivide 5ms 0.022% 81.09% 193ms 0.85% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 81.09% 192ms 0.84% boost::numeric::ublas::scalar_traits::norm_inf (inline) 0 0% 81.09% 192ms 0.84% boost::numeric::ublas::scalar_traits::type_abs (inline) 0 0% 81.09% 192ms 0.84% boost_numeric_ublas_abs (inline) 192ms 0.84% 81.93% 192ms 0.84% std::abs (inline) 181ms 0.79% 82.73% 181ms 0.79% Node::GetIndex 170ms 0.74% 83.47% 181ms 0.79% boost::shared_ptr::shared_ptr (inline) 3ms 0.013% 83.48% 176ms 0.77% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 83.48% 172ms 0.75% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 83.48% 171ms 0.75% VtkMeshWriter::WriteFiles 0 0% 83.48% 170ms 0.74% NodesOnlyMesh::UpdateBoxCollection 168ms 0.74% 84.22% 168ms 0.74% boost::shared_ptr::operator-> (inline) 4ms 0.018% 84.24% 168ms 0.74% std::_Rb_tree::_Rb_tree (partial-inline) 9ms 0.039% 84.28% 167ms 0.73% std::__insertion_sort (inline) 70ms 0.31% 84.58% 167ms 0.73% std::__move_median_to_first (inline) 7ms 0.031% 84.61% 163ms 0.71% DistributedBoxCollection::GetProcessOwningNode 17ms 0.074% 84.69% 162ms 0.71% std::_Rb_tree::_M_copy (inline) 0 0% 84.69% 159ms 0.7% boost::numeric::ublas::c_vector::assign (inline) 0 0% 84.69% 157ms 0.69% std::_Rb_tree::_Alloc_node::operator() (inline) 155ms 0.68% 85.37% 155ms 0.68% Node::CheckForNodeAttributes 0 0% 85.37% 155ms 0.68% vtkStreamingDemandDrivenPipeline::Update 0 0% 85.37% 155ms 0.68% vtkXMLWriterBase::Write 0 0% 85.37% 153ms 0.67% boost::numeric::ublas::inner_prod (inline) 94ms 0.41% 85.78% 152ms 0.67% _int_malloc 5ms 0.022% 85.80% 152ms 0.67% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 85.80% 152ms 0.67% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 85.80% 152ms 0.67% vtkDemandDrivenPipeline::ProcessRequest 0 0% 85.80% 152ms 0.67% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 85.80% 151ms 0.66% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 85.80% 151ms 0.66% vtkExecutive::CallAlgorithm 0 0% 85.80% 150ms 0.66% std::_Rb_tree::_M_drop_node (inline) 1ms 0.0044% 85.80% 150ms 0.66% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 85.80% 149ms 0.65% vtkDemandDrivenPipeline::ExecuteData 0 0% 85.80% 148ms 0.65% vtkCompositeDataPipeline::ExecuteData 147ms 0.64% 86.45% 147ms 0.64% [libchaste_cell_based.so] 19ms 0.083% 86.53% 143ms 0.63% std::_Rb_tree::_M_clone_node (inline) 0 0% 86.53% 138ms 0.6% NodesOnlyMesh::AddNodesToBoxes 88ms 0.39% 86.92% 137ms 0.6% std::vector::emplace_back (inline) 12ms 0.053% 86.97% 133ms 0.58% std::_Rb_tree::~_Rb_tree (inline) 0 0% 86.97% 125ms 0.55% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1ms 0.0044% 86.97% 124ms 0.54% std::__new_allocator::deallocate (inline) 0 0% 86.97% 120ms 0.53% AbstractCellProperty::IsType (inline) 88ms 0.39% 87.36% 120ms 0.53% Node::AddNeighbour 30ms 0.13% 87.49% 119ms 0.52% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 87.49% 118ms 0.52% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 87.49% 118ms 0.52% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 87.49% 117ms 0.51% std::allocator_traits::deallocate (inline) 0 0% 87.49% 116ms 0.51% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData