File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 31314ms, 86.87% of 36046ms total Dropped 808 nodes (cum <= 180.23ms) flat flat% sum% cum cum% 0 0% 0% 35915ms 99.64% __libc_start_call_main 0 0% 0% 35915ms 99.64% __libc_start_main_impl 0 0% 0% 35915ms 99.64% _start 0 0% 0% 35899ms 99.59% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 35899ms 99.59% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 35899ms 99.59% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 35899ms 99.59% main 0 0% 0% 35856ms 99.47% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 35856ms 99.47% CxxTest::TestRunner::runTest (inline) 0 0% 0% 35856ms 99.47% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 35848ms 99.45% AbstractCellBasedSimulation::Solve 1ms 0.0028% 0.0028% 24805ms 68.81% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.0055% 0.0083% 19831ms 55.02% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.022% 0.031% 19638ms 54.48% AbstractNumericalMethod::ComputeForcesIncludingDamping 415ms 1.15% 1.18% 18360ms 50.93% AbstractTwoBodyInteractionForce::AddForceContribution 1521ms 4.22% 5.40% 15336ms 42.55% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 1ms 0.0028% 5.40% 9761ms 27.08% AbstractCellBasedSimulation::UpdateCellPopulation 4397ms 12.20% 17.60% 9486ms 26.32% std::_Rb_tree::_M_lower_bound (inline) 0 0% 17.60% 8505ms 23.59% NodeBasedCellPopulation::Update 299ms 0.83% 18.43% 8447ms 23.43% std::_Rb_tree::find (inline) 0 0% 18.43% 8447ms 23.43% std::map::find (inline) 171ms 0.47% 18.91% 8151ms 22.61% NodesOnlyMesh::GetNodeOrHaloNode 435ms 1.21% 20.11% 7991ms 22.17% AbstractMesh::GetNode 270ms 0.75% 20.86% 7564ms 20.98% NodesOnlyMesh::SolveNodeMapping 233ms 0.65% 21.51% 6563ms 18.21% boost::numeric::ublas::vector_assign (inline) 251ms 0.7% 22.20% 6423ms 17.82% boost::numeric::ublas::c_vector::c_vector (partial-inline) 10ms 0.028% 22.23% 6368ms 17.67% DistributedBoxCollection::CalculateInteriorNodePairs 5050ms 14.01% 36.24% 5050ms 14.01% std::_Rb_tree::_S_right (inline) 18ms 0.05% 36.29% 4598ms 12.76% NodeAttributes::RemoveDuplicateNeighbours 2ms 0.0055% 36.30% 4540ms 12.60% OffLatticeSimulation::ApplyBoundaries 7ms 0.019% 36.32% 4408ms 12.23% std::__sort (inline) 0 0% 36.32% 4408ms 12.23% std::sort (inline) 1407ms 3.90% 40.22% 3719ms 10.32% boost::numeric::ublas::indexing_vector_assign 2ms 0.0055% 40.23% 3412ms 9.47% AbstractCellPopulation::Iterator::operator++ (inline) 203ms 0.56% 40.79% 3395ms 9.42% AbstractCellPopulation::Iterator::IsRealCell (inline) 74ms 0.21% 40.99% 3337ms 9.26% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 25ms 0.069% 41.06% 2853ms 7.91% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 228ms 0.63% 41.70% 2611ms 7.24% std::__introsort_loop 331ms 0.92% 42.61% 2427ms 6.73% DistributedBoxCollection::AddPairsFromBox 23ms 0.064% 42.68% 2399ms 6.66% PlaneBoundaryCondition::ImposeBoundaryCondition 1ms 0.0028% 42.68% 2303ms 6.39% std::__unguarded_partition_pivot (inline) 27ms 0.075% 42.76% 2300ms 6.38% AbstractCellPopulation::GetLocationIndexUsingCell 16ms 0.044% 42.80% 2139ms 5.93% PlaneBoundaryCondition::VerifyBoundaryCondition 1018ms 2.82% 45.63% 2039ms 5.66% std::__unguarded_partition (inline) 196ms 0.54% 46.17% 1912ms 5.30% std::map::operator[] (partial-inline) 0 0% 46.17% 1786ms 4.95% std::__final_insertion_sort (inline) 1770ms 4.91% 51.08% 1770ms 4.91% boost::numeric::ublas::same_impl_ex 134ms 0.37% 51.45% 1694ms 4.70% AbstractMesh::GetVectorFromAtoB 93ms 0.26% 51.71% 1589ms 4.41% std::__unguarded_insertion_sort (inline) 573ms 1.59% 53.30% 1540ms 4.27% std::__unguarded_linear_insert (inline) 1474ms 4.09% 57.39% 1474ms 4.09% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 57.39% 1429ms 3.96% std::_Rb_tree::lower_bound (inline) 0 0% 57.39% 1429ms 3.96% std::map::lower_bound (inline) 0 0% 57.39% 1268ms 3.52% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 57.39% 1246ms 3.46% NodeBasedCellPopulation::UpdateCellProcessLocation 0 0% 57.39% 1241ms 3.44% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 57.39% 1187ms 3.29% AbstractCentreBasedCellPopulation::GetDampingConstant 7ms 0.019% 57.41% 1104ms 3.06% DistributedBoxCollection::CalculateBoundaryNodePairs 13ms 0.036% 57.44% 1084ms 3.01% boost::numeric::ublas::detail::expression_type_check (inline) 217ms 0.6% 58.05% 1047ms 2.90% boost::numeric::ublas::detail::equals 178ms 0.49% 58.54% 1008ms 2.80% std::__new_allocator::allocate (inline) 41ms 0.11% 58.65% 1005ms 2.79% std::_Rb_tree_const_iterator::operator++ (inline) 141ms 0.39% 59.04% 996ms 2.76% boost::numeric::ublas::vector_binary::size (inline) 983ms 2.73% 61.77% 983ms 2.73% boost::numeric::ublas::c_vector::operator() 963ms 2.67% 64.44% 963ms 2.67% std::_Rb_tree_increment 428ms 1.19% 65.63% 962ms 2.67% NodeAttributes::AddNeighbour 199ms 0.55% 66.18% 943ms 2.62% NodeAttributes::AddAppliedForceContribution 469ms 1.30% 67.48% 916ms 2.54% __GI___libc_free 42ms 0.12% 67.60% 843ms 2.34% CellPropertyCollection::GetPropertiesType (inline) 89ms 0.25% 67.85% 830ms 2.30% operator new 612ms 1.70% 69.54% 809ms 2.24% __dynamic_cast 0 0% 69.54% 801ms 2.22% boost::numeric::ublas::norm_inf (inline) 468ms 1.30% 70.84% 801ms 2.22% boost::numeric::ublas::vector_norm_inf::apply (inline) 378ms 1.05% 71.89% 799ms 2.22% DistributedBoxCollection::CalculateContainingBox (partial-inline) 24ms 0.067% 71.96% 795ms 2.21% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 71.96% 783ms 2.17% AbstractCellBasedSimulation::DoCellBirth 0 0% 71.96% 756ms 2.10% AbstractCellPopulation::WriteResultsToFiles 2ms 0.0055% 71.96% 745ms 2.07% Cell::GetMutationState 0 0% 71.96% 744ms 2.06% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 71.96% 744ms 2.06% boost::numeric::ublas::c_vector::plus_assign (inline) 261ms 0.72% 72.69% 737ms 2.04% __GI___libc_malloc 532ms 1.48% 74.16% 652ms 1.81% std::vector::push_back (inline) 0 0% 74.16% 566ms 1.57% std::_Rb_tree::_M_create_node (inline) 0 0% 74.16% 557ms 1.55% std::allocator_traits::allocate (inline) 1ms 0.0028% 74.17% 546ms 1.51% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 2ms 0.0055% 74.17% 545ms 1.51% AbstractCellPopulation::GetCellUsingLocationIndex 2ms 0.0055% 74.18% 480ms 1.33% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 74.18% 470ms 1.30% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 74.18% 467ms 1.30% boost::numeric::ublas::norm_2 (inline) 370ms 1.03% 75.20% 467ms 1.30% boost::numeric::ublas::vector_norm_2::apply (inline) 15ms 0.042% 75.25% 466ms 1.29% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 75.25% 466ms 1.29% boost::numeric::ublas::vector::vector (inline) 0 0% 75.25% 463ms 1.28% std::_Rb_tree::_M_get_node (inline) 406ms 1.13% 76.37% 442ms 1.23% _int_free 6ms 0.017% 76.39% 441ms 1.22% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 3ms 0.0083% 76.40% 418ms 1.16% std::_Rb_tree::_Rb_tree (partial-inline) 21ms 0.058% 76.46% 411ms 1.14% std::_Rb_tree::_M_copy (inline) 30ms 0.083% 76.54% 407ms 1.13% boost::detail::shared_count::~shared_count (inline) 0 0% 76.54% 407ms 1.13% boost::shared_ptr::~shared_ptr (inline) 0 0% 76.54% 393ms 1.09% std::_Rb_tree::_Alloc_node::operator() (inline) 45ms 0.12% 76.66% 388ms 1.08% std::_Rb_tree::_M_clone_node (inline) 163ms 0.45% 77.12% 384ms 1.07% std::_Rb_tree::_M_erase 1ms 0.0028% 77.12% 380ms 1.05% AbstractCellProperty::IsSubType (inline) 0 0% 77.12% 374ms 1.04% Cell::HasCellProperty (inline) 3ms 0.0083% 77.13% 374ms 1.04% CellPropertyCollection::HasProperty 357ms 0.99% 78.12% 368ms 1.02% boost::detail::sp_counted_base::release 362ms 1.00% 79.12% 362ms 1.00% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 10ms 0.028% 79.15% 359ms 1% Cell::ReadyToDivide 8ms 0.022% 79.17% 341ms 0.95% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 79.17% 329ms 0.91% NodesOnlyMesh::ReMesh 1ms 0.0028% 79.17% 320ms 0.89% NodesOnlyMesh::UpdateNodeIndices 117ms 0.32% 79.50% 314ms 0.87% Node::GetRadius 309ms 0.86% 80.36% 309ms 0.86% Node::GetIndex 309ms 0.86% 81.21% 309ms 0.86% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 81.21% 304ms 0.84% boost::numeric::ublas::inner_prod (inline) 1ms 0.0028% 81.22% 304ms 0.84% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 17ms 0.047% 81.26% 303ms 0.84% boost::numeric::ublas::vector_scalar_binary::evaluate 5ms 0.014% 81.28% 296ms 0.82% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 81.28% 290ms 0.8% NodesOnlyMesh::UpdateBoxCollection 9ms 0.025% 81.30% 287ms 0.8% std::_Rb_tree::_M_emplace_hint_unique 137ms 0.38% 81.68% 286ms 0.79% _int_malloc 281ms 0.78% 82.46% 281ms 0.78% [libchaste_cell_based.so] 2ms 0.0055% 82.47% 280ms 0.78% DistributedBoxCollection::GetProcessOwningNode 14ms 0.039% 82.51% 265ms 0.74% boost::numeric::ublas::vector_reference::operator() (inline) 91ms 0.25% 82.76% 261ms 0.72% std::__move_median_to_first (inline) 248ms 0.69% 83.45% 248ms 0.69% NodeBasedCellPopulation::GetNode 245ms 0.68% 84.13% 245ms 0.68% boost::shared_ptr::operator-> (inline) 0 0% 84.13% 243ms 0.67% boost::numeric::ublas::c_vector::assign (inline) 1ms 0.0028% 84.13% 242ms 0.67% std::set::set (inline) 1ms 0.0028% 84.13% 240ms 0.67% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 84.13% 238ms 0.66% VtkMeshWriter::WriteFiles 33ms 0.092% 84.22% 237ms 0.66% std::__new_allocator::deallocate (inline) 105ms 0.29% 84.51% 236ms 0.65% boost::numeric::ublas::vector_inner_prod::apply (inline) 228ms 0.63% 85.15% 228ms 0.63% Node::rGetLocation 0 0% 85.15% 224ms 0.62% NodesOnlyMesh::AddNodesToBoxes 0 0% 85.15% 222ms 0.62% std::_Rb_tree::_M_drop_node (inline) 1ms 0.0028% 85.15% 217ms 0.6% NodesOnlyMesh::ResizeBoxCollection 11ms 0.031% 85.18% 215ms 0.6% NodesOnlyMesh::IsANodeCloseToDomainBoundary 213ms 0.59% 85.77% 213ms 0.59% Node::CheckForNodeAttributes 0 0% 85.77% 213ms 0.59% std::_Rb_tree::clear (inline) 11ms 0.031% 85.80% 212ms 0.59% std::_Rb_tree::~_Rb_tree (inline) 0 0% 85.80% 207ms 0.57% vtkDemandDrivenPipeline::ProcessRequest 0 0% 85.80% 207ms 0.57% vtkStreamingDemandDrivenPipeline::Update 0 0% 85.80% 207ms 0.57% vtkXMLWriterBase::Write 0 0% 85.80% 205ms 0.57% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 85.80% 204ms 0.57% vtkDemandDrivenPipeline::ExecuteData 1ms 0.0028% 85.80% 203ms 0.56% vtkCompositeDataPipeline::ExecuteData 0 0% 85.80% 201ms 0.56% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 85.80% 201ms 0.56% vtkExecutive::CallAlgorithm 0 0% 85.80% 201ms 0.56% vtkXMLUnstructuredDataWriter::ProcessRequest 4ms 0.011% 85.82% 197ms 0.55% AbstractCellProperty::IsType (inline) 14ms 0.039% 85.85% 197ms 0.55% std::__insertion_sort (inline) 0 0% 85.85% 185ms 0.51% tcache_get (inline) 185ms 0.51% 86.37% 185ms 0.51% tcache_get_n (inline) 182ms 0.5% 86.87% 182ms 0.5% [libchaste_mesh.so] 0 0% 86.87% 181ms 0.5% std::allocator_traits::deallocate (inline)