File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 23298ms, 88.09% of 26449ms total Dropped 806 nodes (cum <= 132.25ms) flat flat% sum% cum cum% 0 0% 0% 26350ms 99.63% __libc_start_call_main 0 0% 0% 26350ms 99.63% __libc_start_main_impl 0 0% 0% 26350ms 99.63% _start 0 0% 0% 26333ms 99.56% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 26333ms 99.56% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 26333ms 99.56% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 26333ms 99.56% main 0 0% 0% 26297ms 99.43% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 26297ms 99.43% CxxTest::TestRunner::runTest (inline) 0 0% 0% 26297ms 99.43% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 26290ms 99.40% AbstractCellBasedSimulation::Solve 1ms 0.0038% 0.0038% 18268ms 69.07% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.0076% 0.011% 14399ms 54.44% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.023% 0.034% 14255ms 53.90% AbstractNumericalMethod::ComputeForcesIncludingDamping 92ms 0.35% 0.38% 13580ms 51.34% AbstractTwoBodyInteractionForce::AddForceContribution 1107ms 4.19% 4.57% 11691ms 44.20% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 3354ms 12.68% 17.25% 7644ms 28.90% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.0038% 17.25% 7080ms 26.77% AbstractCellBasedSimulation::UpdateCellPopulation 289ms 1.09% 18.34% 7009ms 26.50% std::_Rb_tree::find (inline) 0 0% 18.34% 7009ms 26.50% std::map::find (inline) 162ms 0.61% 18.96% 6913ms 26.14% NodesOnlyMesh::GetNodeOrHaloNode 407ms 1.54% 20.50% 6747ms 25.51% AbstractMesh::GetNode 304ms 1.15% 21.65% 6345ms 23.99% NodesOnlyMesh::SolveNodeMapping 0 0% 21.65% 6230ms 23.55% NodeBasedCellPopulation::Update 7ms 0.026% 21.67% 4627ms 17.49% DistributedBoxCollection::CalculateInteriorNodePairs 133ms 0.5% 22.17% 4505ms 17.03% boost::numeric::ublas::vector_assign (inline) 141ms 0.53% 22.71% 4484ms 16.95% boost::numeric::ublas::c_vector::c_vector (partial-inline) 4278ms 16.17% 38.88% 4278ms 16.17% std::_Rb_tree::_S_right (inline) 0 0% 38.88% 3624ms 13.70% OffLatticeSimulation::ApplyBoundaries 8ms 0.03% 38.91% 3423ms 12.94% NodeAttributes::RemoveDuplicateNeighbours 2ms 0.0076% 38.92% 3279ms 12.40% std::__sort (inline) 0 0% 38.92% 3279ms 12.40% std::sort (inline) 52ms 0.2% 39.12% 2673ms 10.11% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 1ms 0.0038% 39.12% 2462ms 9.31% AbstractCellPopulation::Iterator::operator++ (inline) 768ms 2.90% 42.02% 2462ms 9.31% boost::numeric::ublas::indexing_vector_assign 113ms 0.43% 42.45% 2440ms 9.23% AbstractCellPopulation::Iterator::IsRealCell (inline) 16ms 0.06% 42.51% 2132ms 8.06% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 117ms 0.44% 42.95% 1956ms 7.40% std::__introsort_loop 15ms 0.057% 43.01% 1920ms 7.26% PlaneBoundaryCondition::ImposeBoundaryCondition 37ms 0.14% 43.15% 1790ms 6.77% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 43.15% 1781ms 6.73% std::__unguarded_partition_pivot (inline) 15ms 0.057% 43.21% 1704ms 6.44% PlaneBoundaryCondition::VerifyBoundaryCondition 95ms 0.36% 43.57% 1638ms 6.19% DistributedBoxCollection::AddPairsFromBox 768ms 2.90% 46.47% 1588ms 6.00% std::__unguarded_partition (inline) 0 0% 46.47% 1347ms 5.09% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 152ms 0.57% 47.05% 1337ms 5.06% std::map::operator[] (partial-inline) 0 0% 47.05% 1335ms 5.05% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1ms 0.0038% 47.05% 1321ms 4.99% std::__final_insertion_sort (inline) 72ms 0.27% 47.32% 1163ms 4.40% std::__unguarded_insertion_sort (inline) 1134ms 4.29% 51.61% 1134ms 4.29% boost::numeric::ublas::same_impl_ex 372ms 1.41% 53.02% 1111ms 4.20% std::__unguarded_linear_insert (inline) 20ms 0.076% 53.09% 1108ms 4.19% boost::numeric::ublas::detail::expression_type_check (inline) 99ms 0.37% 53.47% 1087ms 4.11% AbstractMesh::GetVectorFromAtoB 1080ms 4.08% 57.55% 1080ms 4.08% __gnu_cxx::__normal_iterator::operator-- (inline) 85ms 0.32% 57.87% 1070ms 4.05% boost::numeric::ublas::detail::equals 0 0% 57.87% 991ms 3.75% std::_Rb_tree::lower_bound (inline) 0 0% 57.87% 991ms 3.75% std::map::lower_bound (inline) 0 0% 57.87% 967ms 3.66% boost::numeric::ublas::norm_inf (inline) 438ms 1.66% 59.53% 967ms 3.66% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 59.53% 874ms 3.30% NodeBasedCellPopulation::UpdateCellProcessLocation 870ms 3.29% 62.82% 870ms 3.29% boost::numeric::ublas::c_vector::operator() 5ms 0.019% 62.83% 868ms 3.28% DistributedBoxCollection::CalculateBoundaryNodePairs 15ms 0.057% 62.89% 811ms 3.07% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 146ms 0.55% 63.44% 730ms 2.76% boost::numeric::ublas::vector_binary::size (inline) 324ms 1.22% 64.67% 695ms 2.63% DistributedBoxCollection::CalculateContainingBox (partial-inline) 3ms 0.011% 64.68% 629ms 2.38% AbstractCentreBasedCellPopulation::GetDampingConstant 436ms 1.65% 66.33% 599ms 2.26% __dynamic_cast 160ms 0.6% 66.93% 593ms 2.24% NodeAttributes::AddAppliedForceContribution 0 0% 66.93% 581ms 2.20% AbstractCellPopulation::WriteResultsToFiles 109ms 0.41% 67.34% 574ms 2.17% NodeAttributes::AddNeighbour 21ms 0.079% 67.42% 551ms 2.08% std::_Rb_tree_const_iterator::operator++ (inline) 72ms 0.27% 67.70% 549ms 2.08% std::__new_allocator::allocate (inline) 464ms 1.75% 69.45% 529ms 2.00% std::vector::push_back (inline) 517ms 1.95% 71.41% 517ms 1.95% std::_Rb_tree_increment 74ms 0.28% 71.69% 477ms 1.80% operator new 6ms 0.023% 71.71% 466ms 1.76% AbstractCellBasedSimulation::DoCellBirth 9ms 0.034% 71.74% 466ms 1.76% CellPropertyCollection::GetPropertiesType (inline) 0 0% 71.74% 433ms 1.64% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 71.74% 433ms 1.64% boost::numeric::ublas::c_vector::plus_assign (inline) 2ms 0.0076% 71.75% 412ms 1.56% Cell::GetMutationState 134ms 0.51% 72.26% 412ms 1.56% __GI___libc_free 133ms 0.5% 72.76% 399ms 1.51% __GI___libc_malloc 2ms 0.0076% 72.77% 387ms 1.46% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 72.77% 383ms 1.45% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 72.77% 380ms 1.44% boost::numeric::ublas::norm_2 (inline) 303ms 1.15% 73.91% 380ms 1.44% boost::numeric::ublas::vector_norm_2::apply (inline) 6ms 0.023% 73.93% 375ms 1.42% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 22ms 0.083% 74.02% 369ms 1.40% boost::detail::shared_count::~shared_count (inline) 0 0% 74.02% 369ms 1.40% boost::shared_ptr::~shared_ptr (inline) 0 0% 74.02% 358ms 1.35% boost::numeric::ublas::scalar_traits::norm_inf (inline) 0 0% 74.02% 358ms 1.35% boost::numeric::ublas::scalar_traits::type_abs (inline) 1ms 0.0038% 74.02% 357ms 1.35% boost_numeric_ublas_abs (inline) 356ms 1.35% 75.37% 356ms 1.35% std::abs (inline) 335ms 1.27% 76.63% 345ms 1.30% boost::detail::sp_counted_base::release 336ms 1.27% 77.90% 336ms 1.27% Node::GetIndex 0 0% 77.90% 317ms 1.20% std::allocator_traits::allocate (inline) 1ms 0.0038% 77.91% 298ms 1.13% AbstractCellProperty::IsSubType (inline) 289ms 1.09% 79.00% 289ms 1.09% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 79.00% 284ms 1.07% std::_Rb_tree::_M_create_node (inline) 240ms 0.91% 79.91% 278ms 1.05% _int_free 2ms 0.0076% 79.92% 276ms 1.04% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 0 0% 79.92% 275ms 1.04% boost::numeric::ublas::inner_prod (inline) 1ms 0.0038% 79.92% 274ms 1.04% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 16ms 0.06% 79.98% 273ms 1.03% boost::numeric::ublas::vector_scalar_binary::evaluate 4ms 0.015% 80.00% 271ms 1.02% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 80.00% 271ms 1.02% NodesOnlyMesh::ReMesh 1ms 0.0038% 80.00% 257ms 0.97% NodesOnlyMesh::UpdateNodeIndices 255ms 0.96% 80.96% 255ms 0.96% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 80.96% 254ms 0.96% std::_Rb_tree::_M_get_node (inline) 81ms 0.31% 81.27% 243ms 0.92% std::_Rb_tree::_M_erase (partial-inline) 3ms 0.011% 81.28% 235ms 0.89% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 81.28% 235ms 0.89% boost::numeric::ublas::vector::vector (inline) 7ms 0.026% 81.31% 234ms 0.88% boost::numeric::ublas::vector_reference::operator() (inline) 3ms 0.011% 81.32% 232ms 0.88% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 2ms 0.0076% 81.33% 230ms 0.87% NodeBasedCellPopulation::UpdateMapsAfterRemesh 96ms 0.36% 81.69% 225ms 0.85% boost::numeric::ublas::vector_inner_prod::apply (inline) 224ms 0.85% 82.54% 224ms 0.85% [libchaste_mesh.so] 10ms 0.038% 82.57% 220ms 0.83% DistributedBoxCollection::GetProcessOwningNode 58ms 0.22% 82.79% 220ms 0.83% Node::GetRadius 0 0% 82.79% 217ms 0.82% NodesOnlyMesh::UpdateBoxCollection 121ms 0.46% 83.25% 194ms 0.73% Node::AddNeighbour 3ms 0.011% 83.26% 194ms 0.73% std::_Rb_tree::_M_emplace_hint_unique 80ms 0.3% 83.56% 191ms 0.72% std::__move_median_to_first (inline) 0 0% 83.56% 190ms 0.72% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 106ms 0.4% 83.97% 190ms 0.72% _int_malloc 0 0% 83.97% 188ms 0.71% VtkMeshWriter::WriteFiles 0 0% 83.97% 187ms 0.71% boost::numeric::ublas::c_vector::assign (inline) 9ms 0.034% 84.00% 187ms 0.71% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 84.00% 183ms 0.69% Cell::HasCellProperty (inline) 1ms 0.0038% 84.00% 183ms 0.69% CellPropertyCollection::HasProperty 0 0% 84.00% 179ms 0.68% boost::numeric::ublas::vector_binary::operator() (inline) 16ms 0.06% 84.06% 175ms 0.66% std::_Rb_tree::_M_copy (inline) 28ms 0.11% 84.17% 175ms 0.66% std::__new_allocator::deallocate (inline) 174ms 0.66% 84.83% 174ms 0.66% [libchaste_cell_based.so] 0 0% 84.83% 173ms 0.65% NodesOnlyMesh::AddNodesToBoxes 0 0% 84.83% 173ms 0.65% std::_Rb_tree::_Alloc_node::operator() (inline) 170ms 0.64% 85.47% 170ms 0.64% __strcmp_evex 169ms 0.64% 86.11% 169ms 0.64% Node::CheckForNodeAttributes 3ms 0.011% 86.12% 167ms 0.63% Cell::ReadyToDivide 167ms 0.63% 86.75% 167ms 0.63% Node::rGetLocation 0 0% 86.75% 163ms 0.62% vtkStreamingDemandDrivenPipeline::Update 0 0% 86.75% 163ms 0.62% vtkXMLWriterBase::Write 0 0% 86.75% 162ms 0.61% vtkDemandDrivenPipeline::ProcessRequest 160ms 0.6% 87.36% 161ms 0.61% NodeBasedCellPopulation::GetNode 5ms 0.019% 87.38% 159ms 0.6% AbstractCellProperty::IsType (inline) 0 0% 87.38% 158ms 0.6% vtkExecutive::CallAlgorithm 23ms 0.087% 87.46% 157ms 0.59% std::_Rb_tree::_M_clone_node (inline) 0 0% 87.46% 157ms 0.59% std::_Rb_tree::_M_drop_node (inline) 18ms 0.068% 87.53% 157ms 0.59% std::__insertion_sort (inline) 0 0% 87.53% 156ms 0.59% vtkDemandDrivenPipeline::ExecuteData 0 0% 87.53% 156ms 0.59% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 87.53% 155ms 0.59% vtkCompositeDataPipeline::ExecuteData 0 0% 87.53% 155ms 0.59% vtkXMLUnstructuredDataWriter::ProcessRequest 147ms 0.56% 88.09% 147ms 0.56% boost::numeric::ublas::c_vector::size (inline) 0 0% 88.09% 146ms 0.55% std::_Rb_tree::clear (inline) 0 0% 88.09% 141ms 0.53% std::_Rb_tree::_M_put_node (inline) 0 0% 88.09% 141ms 0.53% std::allocator_traits::deallocate (inline)