File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 30624ms, 87.22% of 35111ms total Dropped 834 nodes (cum <= 175.56ms) flat flat% sum% cum cum% 0 0% 0% 34975ms 99.61% __libc_start_call_main 0 0% 0% 34975ms 99.61% __libc_start_main_impl 0 0% 0% 34975ms 99.61% _start 0 0% 0% 34955ms 99.56% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 34955ms 99.56% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 34955ms 99.56% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 34955ms 99.56% main 0 0% 0% 34913ms 99.44% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 34913ms 99.44% CxxTest::TestRunner::runTest (inline) 0 0% 0% 34913ms 99.44% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0028% 0.0028% 34904ms 99.41% AbstractCellBasedSimulation::Solve 3ms 0.0085% 0.011% 24009ms 68.38% OffLatticeSimulation::UpdateCellLocationsAndTopology 6ms 0.017% 0.028% 18999ms 54.11% ForwardEulerNumericalMethod::UpdateAllNodePositions 13ms 0.037% 0.066% 18823ms 53.61% AbstractNumericalMethod::ComputeForcesIncludingDamping 138ms 0.39% 0.46% 17787ms 50.66% AbstractTwoBodyInteractionForce::AddForceContribution 1506ms 4.29% 4.75% 15026ms 42.80% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4340ms 12.36% 17.11% 9811ms 27.94% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.0028% 17.11% 9660ms 27.51% AbstractCellBasedSimulation::UpdateCellPopulation 405ms 1.15% 18.26% 9048ms 25.77% std::_Rb_tree::find (inline) 0 0% 18.26% 9043ms 25.76% std::map::find (inline) 177ms 0.5% 18.77% 8896ms 25.34% NodesOnlyMesh::GetNodeOrHaloNode 511ms 1.46% 20.22% 8727ms 24.86% AbstractMesh::GetNode 0 0% 20.22% 8527ms 24.29% NodeBasedCellPopulation::Update 362ms 1.03% 21.26% 8218ms 23.41% NodesOnlyMesh::SolveNodeMapping 5ms 0.014% 21.27% 6396ms 18.22% DistributedBoxCollection::CalculateInteriorNodePairs 216ms 0.62% 21.88% 5770ms 16.43% boost::numeric::ublas::vector_assign (inline) 148ms 0.42% 22.31% 5589ms 15.92% boost::numeric::ublas::c_vector::c_vector (partial-inline) 5453ms 15.53% 37.84% 5453ms 15.53% std::_Rb_tree::_S_right (inline) 1ms 0.0028% 37.84% 4635ms 13.20% OffLatticeSimulation::ApplyBoundaries 9ms 0.026% 37.87% 4626ms 13.18% NodeAttributes::RemoveDuplicateNeighbours 5ms 0.014% 37.88% 4441ms 12.65% std::__sort (inline) 0 0% 37.88% 4441ms 12.65% std::sort (inline) 1162ms 3.31% 41.19% 3399ms 9.68% boost::numeric::ublas::indexing_vector_assign 91ms 0.26% 41.45% 3350ms 9.54% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 3ms 0.0085% 41.46% 3174ms 9.04% AbstractCellPopulation::Iterator::operator++ (inline) 157ms 0.45% 41.90% 3132ms 8.92% AbstractCellPopulation::Iterator::IsRealCell 28ms 0.08% 41.98% 2695ms 7.68% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 152ms 0.43% 42.42% 2573ms 7.33% std::__introsort_loop 25ms 0.071% 42.49% 2454ms 6.99% PlaneBoundaryCondition::ImposeBoundaryCondition 143ms 0.41% 42.90% 2376ms 6.77% DistributedBoxCollection::AddPairsFromBox 0 0% 42.90% 2336ms 6.65% std::__unguarded_partition_pivot (inline) 44ms 0.13% 43.02% 2257ms 6.43% AbstractCellPopulation::GetLocationIndexUsingCell 20ms 0.057% 43.08% 2180ms 6.21% PlaneBoundaryCondition::VerifyBoundaryCondition 1001ms 2.85% 45.93% 2077ms 5.92% std::__unguarded_partition (inline) 1ms 0.0028% 45.93% 1858ms 5.29% std::__final_insertion_sort (inline) 174ms 0.5% 46.43% 1755ms 5.00% std::map::operator[] (partial-inline) 126ms 0.36% 46.79% 1660ms 4.73% std::__unguarded_insertion_sort (inline) 620ms 1.77% 48.55% 1586ms 4.52% std::__unguarded_linear_insert (inline) 1508ms 4.29% 52.85% 1508ms 4.29% boost::numeric::ublas::same_impl_ex 127ms 0.36% 53.21% 1454ms 4.14% AbstractMesh::GetVectorFromAtoB 1412ms 4.02% 57.23% 1412ms 4.02% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 57.23% 1276ms 3.63% std::_Rb_tree::lower_bound (inline) 0 0% 57.23% 1276ms 3.63% std::map::lower_bound (inline) 0 0% 57.23% 1273ms 3.63% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 57.23% 1260ms 3.59% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 57.23% 1203ms 3.43% NodeBasedCellPopulation::UpdateCellProcessLocation 1159ms 3.30% 60.53% 1159ms 3.30% boost::numeric::ublas::c_vector::operator() 5ms 0.014% 60.55% 1120ms 3.19% DistributedBoxCollection::CalculateBoundaryNodePairs 2ms 0.0057% 60.55% 1080ms 3.08% boost::numeric::ublas::detail::expression_type_check (inline) 256ms 0.73% 61.28% 1036ms 2.95% boost::numeric::ublas::detail::equals 22ms 0.063% 61.34% 1011ms 2.88% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 10ms 0.028% 61.37% 934ms 2.66% AbstractCentreBasedCellPopulation::GetDampingConstant 29ms 0.083% 61.45% 914ms 2.60% std::_Rb_tree_const_iterator::operator++ (inline) 118ms 0.34% 61.79% 912ms 2.60% std::__new_allocator::allocate (inline) 207ms 0.59% 62.38% 894ms 2.55% NodeAttributes::AddAppliedForceContribution 181ms 0.52% 62.89% 889ms 2.53% boost::numeric::ublas::vector_binary::size (inline) 855ms 2.44% 65.33% 855ms 2.44% std::_Rb_tree_increment 407ms 1.16% 66.49% 854ms 2.43% DistributedBoxCollection::CalculateContainingBox (partial-inline) 78ms 0.22% 66.71% 802ms 2.28% operator new 555ms 1.58% 68.29% 787ms 2.24% __dynamic_cast 0 0% 68.29% 758ms 2.16% AbstractCellPopulation::WriteResultsToFiles 165ms 0.47% 68.76% 723ms 2.06% NodeAttributes::AddNeighbour 349ms 0.99% 69.76% 718ms 2.04% __GI___libc_malloc 0 0% 69.76% 715ms 2.04% boost::numeric::ublas::norm_inf (inline) 462ms 1.32% 71.07% 715ms 2.04% boost::numeric::ublas::vector_norm_inf::apply (inline) 14ms 0.04% 71.11% 689ms 1.96% CellPropertyCollection::GetPropertiesType (inline) 0 0% 71.11% 687ms 1.96% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 71.11% 687ms 1.96% boost::numeric::ublas::c_vector::plus_assign (inline) 556ms 1.58% 72.70% 663ms 1.89% std::vector::push_back (inline) 6ms 0.017% 72.71% 629ms 1.79% AbstractCellBasedSimulation::DoCellBirth 7ms 0.02% 72.73% 608ms 1.73% Cell::GetMutationState 0 0% 72.73% 558ms 1.59% boost::numeric::ublas::norm_2 (inline) 451ms 1.28% 74.02% 558ms 1.59% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 74.02% 502ms 1.43% AbstractCellBasedSimulation::DoCellRemoval (inline) 1ms 0.0028% 74.02% 498ms 1.42% NodeBasedCellPopulation::WriteVtkResultsToFile 4ms 0.011% 74.03% 491ms 1.40% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 14ms 0.04% 74.07% 475ms 1.35% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 74.07% 475ms 1.35% boost::numeric::ublas::vector::vector (inline) 153ms 0.44% 74.51% 466ms 1.33% __GI___libc_free 456ms 1.30% 75.81% 456ms 1.30% Node::GetIndex 0 0% 75.81% 451ms 1.28% std::allocator_traits::allocate (inline) 30ms 0.085% 75.89% 431ms 1.23% boost::detail::shared_count::~shared_count (inline) 0 0% 75.89% 431ms 1.23% boost::shared_ptr::~shared_ptr (inline) 0 0% 75.89% 422ms 1.20% std::_Rb_tree::_M_create_node (inline) 1ms 0.0028% 75.89% 414ms 1.18% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 9ms 0.026% 75.92% 412ms 1.17% AbstractCellPopulation::GetCellUsingLocationIndex 382ms 1.09% 77.01% 393ms 1.12% boost::detail::sp_counted_base::release 0 0% 77.01% 389ms 1.11% boost::numeric::ublas::inner_prod (inline) 2ms 0.0057% 77.01% 386ms 1.10% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 15ms 0.043% 77.06% 384ms 1.09% boost::numeric::ublas::vector_scalar_binary::evaluate 3ms 0.0085% 77.06% 379ms 1.08% AbstractCellProperty::IsSubType (inline) 0 0% 77.06% 362ms 1.03% NodesOnlyMesh::ReMesh 361ms 1.03% 78.09% 361ms 1.03% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 78.09% 360ms 1.03% std::_Rb_tree::_M_get_node (inline) 6ms 0.017% 78.11% 351ms 1% NodesOnlyMesh::UpdateNodeIndices 342ms 0.97% 79.08% 342ms 0.97% [libchaste_mesh.so] 112ms 0.32% 79.40% 339ms 0.97% std::_Rb_tree::_M_erase (partial-inline) 165ms 0.47% 79.87% 324ms 0.92% Node::AddNeighbour 7ms 0.02% 79.89% 319ms 0.91% NodeBasedCellPopulation::UpdateMapsAfterRemesh 319ms 0.91% 80.80% 319ms 0.91% __gnu_cxx::__normal_iterator::operator++ (inline) 124ms 0.35% 81.15% 313ms 0.89% boost::numeric::ublas::vector_inner_prod::apply (inline) 265ms 0.75% 81.91% 312ms 0.89% _int_free 86ms 0.24% 82.15% 307ms 0.87% Node::GetRadius 5ms 0.014% 82.17% 307ms 0.87% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 21ms 0.06% 82.23% 307ms 0.87% std::_Rb_tree::_Rb_tree (partial-inline) 18ms 0.051% 82.28% 305ms 0.87% std::_Rb_tree::_M_emplace_hint_unique 10ms 0.028% 82.31% 289ms 0.82% DistributedBoxCollection::GetProcessOwningNode 0 0% 82.31% 282ms 0.8% boost::numeric::ublas::c_vector::assign (inline) 15ms 0.043% 82.35% 282ms 0.8% boost::numeric::ublas::vector_reference::operator() (inline) 32ms 0.091% 82.44% 280ms 0.8% std::_Rb_tree::_M_copy (inline) 0 0% 82.44% 270ms 0.77% NodesOnlyMesh::UpdateBoxCollection 0 0% 82.44% 269ms 0.77% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 82.44% 267ms 0.76% std::_Rb_tree::_Alloc_node::operator() (inline) 151ms 0.43% 82.87% 263ms 0.75% _int_malloc 109ms 0.31% 83.18% 256ms 0.73% std::__move_median_to_first (inline) 254ms 0.72% 83.91% 254ms 0.72% [libchaste_cell_based.so] 0 0% 83.91% 249ms 0.71% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 83.91% 249ms 0.71% VtkMeshWriter::WriteFiles 22ms 0.063% 83.97% 247ms 0.7% std::_Rb_tree::_M_clone_node (inline) 4ms 0.011% 83.98% 243ms 0.69% CellPropertyCollection::HasProperty 0 0% 83.98% 238ms 0.68% Cell::HasCellProperty (inline) 14ms 0.04% 84.02% 234ms 0.67% Cell::ReadyToDivide 231ms 0.66% 84.68% 231ms 0.66% Node::CheckForNodeAttributes 0 0% 84.68% 220ms 0.63% vtkStreamingDemandDrivenPipeline::Update 0 0% 84.68% 220ms 0.63% vtkXMLWriterBase::Write 0 0% 84.68% 217ms 0.62% vtkDemandDrivenPipeline::ProcessRequest 0 0% 84.68% 216ms 0.62% vtkCompositeDataPipeline::ExecuteData 0 0% 84.68% 216ms 0.62% vtkDemandDrivenPipeline::ExecuteData 0 0% 84.68% 216ms 0.62% vtkExecutive::CallAlgorithm 0 0% 84.68% 216ms 0.62% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 84.68% 216ms 0.62% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 84.68% 210ms 0.6% std::_Rb_tree::_M_drop_node (inline) 2ms 0.0057% 84.68% 208ms 0.59% NodesOnlyMesh::AddNodesToBoxes 206ms 0.59% 85.27% 206ms 0.59% NodeBasedCellPopulation::GetNode 70ms 0.2% 85.47% 204ms 0.58% std::__find_if (inline) 10ms 0.028% 85.50% 204ms 0.58% std::__new_allocator::deallocate (inline) 0 0% 85.50% 204ms 0.58% std::find_if (inline) 0 0% 85.50% 204ms 0.58% std::none_of (inline) 198ms 0.56% 86.06% 198ms 0.56% Node::ConstructNodeAttributes (inline) 0 0% 86.06% 197ms 0.56% std::_Rb_tree::clear (inline) 25ms 0.071% 86.13% 197ms 0.56% std::__insertion_sort (inline) 195ms 0.56% 86.69% 195ms 0.56% __strcmp_avx2 187ms 0.53% 87.22% 187ms 0.53% Node::rGetLocation 0 0% 87.22% 183ms 0.52% std::allocator_traits::deallocate (inline) 0 0% 87.22% 180ms 0.51% std::_Rb_tree::_M_put_node (inline) 0 0% 87.22% 178ms 0.51% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 87.22% 178ms 0.51% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 87.22% 177ms 0.5% AbstractCellProperty::IsType (inline)