File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 29289ms, 88.42% of 33124ms total Dropped 893 nodes (cum <= 165.62ms) flat flat% sum% cum cum% 0 0% 0% 32969ms 99.53% __libc_start_call_main 0 0% 0% 32969ms 99.53% __libc_start_main_impl 0 0% 0% 32969ms 99.53% _start 0 0% 0% 32952ms 99.48% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 32952ms 99.48% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 32952ms 99.48% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 32952ms 99.48% main 0 0% 0% 32915ms 99.37% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 32915ms 99.37% CxxTest::TestRunner::runTest (inline) 0 0% 0% 32915ms 99.37% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 32907ms 99.34% AbstractCellBasedSimulation::Solve 3ms 0.0091% 0.0091% 22744ms 68.66% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.003% 0.012% 17911ms 54.07% ForwardEulerNumericalMethod::UpdateAllNodePositions 9ms 0.027% 0.039% 17721ms 53.50% AbstractNumericalMethod::ComputeForcesIncludingDamping 235ms 0.71% 0.75% 17037ms 51.43% AbstractTwoBodyInteractionForce::AddForceContribution 1427ms 4.31% 5.06% 14234ms 42.97% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4320ms 13.04% 18.10% 9499ms 28.68% std::_Rb_tree::_M_lower_bound (inline) 0 0% 18.10% 8974ms 27.09% AbstractCellBasedSimulation::UpdateCellPopulation 347ms 1.05% 19.15% 8680ms 26.20% std::_Rb_tree::find (inline) 0 0% 19.15% 8679ms 26.20% std::map::find (inline) 124ms 0.37% 19.52% 8436ms 25.47% NodesOnlyMesh::GetNodeOrHaloNode 497ms 1.50% 21.02% 8314ms 25.10% AbstractMesh::GetNode 0 0% 21.02% 7913ms 23.89% NodeBasedCellPopulation::Update 329ms 0.99% 22.01% 7821ms 23.61% NodesOnlyMesh::SolveNodeMapping 5ms 0.015% 22.03% 5822ms 17.58% DistributedBoxCollection::CalculateInteriorNodePairs 223ms 0.67% 22.70% 5401ms 16.31% boost::numeric::ublas::vector_assign (inline) 180ms 0.54% 23.25% 5298ms 15.99% boost::numeric::ublas::c_vector::c_vector (partial-inline) 5139ms 15.51% 38.76% 5139ms 15.51% std::_Rb_tree::_S_right (inline) 2ms 0.006% 38.77% 4540ms 13.71% OffLatticeSimulation::ApplyBoundaries 22ms 0.066% 38.83% 4531ms 13.68% NodeAttributes::RemoveDuplicateNeighbours 10ms 0.03% 38.86% 4353ms 13.14% std::__sort (inline) 0 0% 38.86% 4353ms 13.14% std::sort (inline) 5ms 0.015% 38.88% 3437ms 10.38% AbstractCellPopulation::Iterator::operator++ (inline) 194ms 0.59% 39.46% 3409ms 10.29% AbstractCellPopulation::Iterator::IsRealCell 59ms 0.18% 39.64% 3393ms 10.24% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 1026ms 3.10% 42.74% 3138ms 9.47% boost::numeric::ublas::indexing_vector_assign 20ms 0.06% 42.80% 2865ms 8.65% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 202ms 0.61% 43.41% 2502ms 7.55% std::__introsort_loop 23ms 0.069% 43.48% 2338ms 7.06% PlaneBoundaryCondition::ImposeBoundaryCondition 25ms 0.075% 43.55% 2280ms 6.88% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 43.55% 2227ms 6.72% std::__unguarded_partition_pivot (inline) 16ms 0.048% 43.60% 2200ms 6.64% PlaneBoundaryCondition::VerifyBoundaryCondition 1040ms 3.14% 46.74% 2006ms 6.06% std::__unguarded_partition (inline) 132ms 0.4% 47.14% 1932ms 5.83% DistributedBoxCollection::AddPairsFromBox 2ms 0.006% 47.15% 1839ms 5.55% std::__final_insertion_sort (inline) 229ms 0.69% 47.84% 1758ms 5.31% std::map::operator[] (partial-inline) 88ms 0.27% 48.10% 1643ms 4.96% std::__unguarded_insertion_sort (inline) 586ms 1.77% 49.87% 1587ms 4.79% std::__unguarded_linear_insert (inline) 1465ms 4.42% 54.30% 1465ms 4.42% __gnu_cxx::__normal_iterator::operator-- (inline) 1399ms 4.22% 58.52% 1399ms 4.22% boost::numeric::ublas::same_impl_ex 121ms 0.37% 58.88% 1352ms 4.08% AbstractMesh::GetVectorFromAtoB 0 0% 58.88% 1254ms 3.79% std::_Rb_tree::lower_bound (inline) 0 0% 58.88% 1254ms 3.79% std::map::lower_bound (inline) 0 0% 58.88% 1233ms 3.72% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 58.88% 1219ms 3.68% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 58.88% 1147ms 3.46% NodeBasedCellPopulation::UpdateCellProcessLocation 1144ms 3.45% 62.34% 1144ms 3.45% boost::numeric::ublas::c_vector::operator() 4ms 0.012% 62.35% 1098ms 3.31% DistributedBoxCollection::CalculateBoundaryNodePairs 20ms 0.06% 62.41% 947ms 2.86% boost::numeric::ublas::detail::expression_type_check (inline) 149ms 0.45% 62.86% 900ms 2.72% boost::numeric::ublas::detail::equals 17ms 0.051% 62.91% 846ms 2.55% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 104ms 0.31% 63.23% 831ms 2.51% boost::numeric::ublas::vector_binary::size (inline) 226ms 0.68% 63.91% 818ms 2.47% NodeAttributes::AddAppliedForceContribution 407ms 1.23% 65.14% 805ms 2.43% DistributedBoxCollection::CalculateContainingBox (partial-inline) 1ms 0.003% 65.14% 749ms 2.26% AbstractCellPopulation::WriteResultsToFiles 198ms 0.6% 65.74% 732ms 2.21% NodeAttributes::AddNeighbour 82ms 0.25% 65.99% 713ms 2.15% std::__new_allocator::allocate (inline) 503ms 1.52% 67.50% 709ms 2.14% __dynamic_cast 0 0% 67.50% 708ms 2.14% boost::numeric::ublas::norm_inf (inline) 421ms 1.27% 68.77% 708ms 2.14% boost::numeric::ublas::vector_norm_inf::apply (inline) 43ms 0.13% 68.90% 643ms 1.94% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.006% 68.91% 632ms 1.91% AbstractCentreBasedCellPopulation::GetDampingConstant 533ms 1.61% 70.52% 629ms 1.90% std::vector::push_back (inline) 114ms 0.34% 70.86% 628ms 1.90% operator new 3ms 0.0091% 70.87% 597ms 1.80% AbstractCellBasedSimulation::DoCellBirth 593ms 1.79% 72.66% 593ms 1.79% std::_Rb_tree_increment 0 0% 72.66% 592ms 1.79% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 72.66% 592ms 1.79% boost::numeric::ublas::c_vector::plus_assign (inline) 221ms 0.67% 73.33% 569ms 1.72% __GI___libc_free 0 0% 73.33% 525ms 1.58% boost::numeric::ublas::norm_2 (inline) 410ms 1.24% 74.57% 525ms 1.58% boost::numeric::ublas::vector_norm_2::apply (inline) 8ms 0.024% 74.59% 513ms 1.55% CellPropertyCollection::GetPropertiesType (inline) 187ms 0.56% 75.16% 511ms 1.54% __GI___libc_malloc 2ms 0.006% 75.16% 488ms 1.47% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 75.16% 463ms 1.40% AbstractCellBasedSimulation::DoCellRemoval (inline) 8ms 0.024% 75.19% 444ms 1.34% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 37ms 0.11% 75.30% 439ms 1.33% boost::detail::shared_count::~shared_count (inline) 0 0% 75.30% 439ms 1.33% boost::shared_ptr::~shared_ptr (inline) 1ms 0.003% 75.30% 435ms 1.31% Cell::GetMutationState 392ms 1.18% 76.49% 395ms 1.19% boost::detail::sp_counted_base::release 0 0% 76.49% 394ms 1.19% std::allocator_traits::allocate (inline) 386ms 1.17% 77.65% 386ms 1.17% Node::GetIndex 0 0% 77.65% 363ms 1.10% std::_Rb_tree::_M_create_node (inline) 33ms 0.1% 77.75% 352ms 1.06% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 77.75% 352ms 1.06% boost::numeric::ublas::vector::vector (inline) 313ms 0.94% 78.70% 348ms 1.05% _int_free 9ms 0.027% 78.72% 341ms 1.03% boost::numeric::ublas::vector_reference::operator() (inline) 131ms 0.4% 79.12% 331ms 1% Node::GetRadius 325ms 0.98% 80.10% 325ms 0.98% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 80.10% 321ms 0.97% std::_Rb_tree::_M_get_node (inline) 8ms 0.024% 80.12% 320ms 0.97% NodeBasedCellPopulation::UpdateMapsAfterRemesh 315ms 0.95% 81.07% 315ms 0.95% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 81.07% 311ms 0.94% NodesOnlyMesh::ReMesh 1ms 0.003% 81.08% 300ms 0.91% NodesOnlyMesh::UpdateNodeIndices 2ms 0.006% 81.08% 298ms 0.9% AbstractCellProperty::IsSubType (inline) 0 0% 81.08% 297ms 0.9% boost::numeric::ublas::inner_prod (inline) 2ms 0.006% 81.09% 295ms 0.89% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 22ms 0.066% 81.16% 293ms 0.88% boost::numeric::ublas::vector_scalar_binary::evaluate 4ms 0.012% 81.17% 283ms 0.85% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 279ms 0.84% 82.01% 279ms 0.84% [libchaste_cell_based.so] 5ms 0.015% 82.03% 277ms 0.84% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 82.03% 276ms 0.83% NodesOnlyMesh::UpdateBoxCollection 8ms 0.024% 82.05% 275ms 0.83% std::_Rb_tree::_M_emplace_hint_unique 3ms 0.0091% 82.06% 274ms 0.83% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 82.06% 268ms 0.81% boost::numeric::ublas::vector_binary::operator() (inline) 104ms 0.31% 82.37% 267ms 0.81% std::_Rb_tree::_M_erase (partial-inline) 3ms 0.0091% 82.38% 260ms 0.78% DistributedBoxCollection::GetProcessOwningNode 0 0% 82.38% 249ms 0.75% boost::numeric::ublas::c_vector::assign (inline) 0 0% 82.38% 245ms 0.74% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 82.38% 243ms 0.73% VtkMeshWriter::WriteFiles 104ms 0.31% 82.70% 235ms 0.71% boost::numeric::ublas::vector_inner_prod::apply (inline) 87ms 0.26% 82.96% 229ms 0.69% Node::AddNeighbour 228ms 0.69% 83.65% 228ms 0.69% NodeBasedCellPopulation::GetNode 122ms 0.37% 84.01% 228ms 0.69% _int_malloc 224ms 0.68% 84.69% 225ms 0.68% Node::ConstructNodeAttributes (inline) 1ms 0.003% 84.69% 222ms 0.67% NodesOnlyMesh::AddNodesToBoxes 87ms 0.26% 84.96% 217ms 0.66% std::__move_median_to_first (inline) 5ms 0.015% 84.97% 216ms 0.65% CellPropertyCollection::HasProperty 0 0% 84.97% 215ms 0.65% Cell::HasCellProperty (inline) 212ms 0.64% 85.61% 212ms 0.64% Node::CheckForNodeAttributes 0 0% 85.61% 210ms 0.63% vtkStreamingDemandDrivenPipeline::Update 0 0% 85.61% 210ms 0.63% vtkXMLWriterBase::Write 0 0% 85.61% 208ms 0.63% vtkDemandDrivenPipeline::ProcessRequest 0 0% 85.61% 207ms 0.62% vtkCompositeDataPipeline::ExecuteData 0 0% 85.61% 207ms 0.62% vtkDemandDrivenPipeline::ExecuteData 0 0% 85.61% 207ms 0.62% vtkExecutive::CallAlgorithm 0 0% 85.61% 207ms 0.62% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 85.61% 207ms 0.62% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 85.61% 203ms 0.61% std::_Rb_tree::_Alloc_node::operator() (inline) 3ms 0.0091% 85.62% 197ms 0.59% std::_Rb_tree::_Rb_tree (partial-inline) 120ms 0.36% 85.98% 196ms 0.59% Node::AddAppliedForceContribution 16ms 0.048% 86.03% 194ms 0.59% std::__insertion_sort (inline) 91ms 0.27% 86.31% 192ms 0.58% boost::shared_ptr::shared_ptr (inline) 1ms 0.003% 86.31% 191ms 0.58% NodesOnlyMesh::ResizeBoxCollection 68ms 0.21% 86.51% 191ms 0.58% std::__find_if (inline) 0 0% 86.51% 191ms 0.58% std::find_if (inline) 0 0% 86.51% 191ms 0.58% std::none_of (inline) 24ms 0.072% 86.59% 190ms 0.57% std::_Rb_tree::_M_copy (inline) 19ms 0.057% 86.64% 189ms 0.57% NodesOnlyMesh::IsANodeCloseToDomainBoundary 186ms 0.56% 87.21% 186ms 0.56% __strcmp_avx2 184ms 0.56% 87.76% 184ms 0.56% Node::rGetLocation 2ms 0.006% 87.77% 181ms 0.55% Cell::ReadyToDivide 26ms 0.078% 87.85% 181ms 0.55% std::__new_allocator::deallocate (inline) 170ms 0.51% 88.36% 170ms 0.51% [libchaste_mesh.so] 21ms 0.063% 88.42% 166ms 0.5% std::_Rb_tree::_M_clone_node (inline) 0 0% 88.42% 166ms 0.5% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 88.42% 166ms 0.5% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData