File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 21887ms, 88.67% of 24684ms total Dropped 806 nodes (cum <= 123.42ms) flat flat% sum% cum cum% 0 0% 0% 24546ms 99.44% __libc_start_call_main 0 0% 0% 24546ms 99.44% __libc_start_main_impl 0 0% 0% 24546ms 99.44% _start 0 0% 0% 24526ms 99.36% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 24526ms 99.36% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 24526ms 99.36% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 24526ms 99.36% main 0 0% 0% 24484ms 99.19% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 24484ms 99.19% CxxTest::TestRunner::runTest (inline) 0 0% 0% 24484ms 99.19% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 24475ms 99.15% AbstractCellBasedSimulation::Solve 1ms 0.0041% 0.0041% 14189ms 57.48% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0041% 0.0081% 9172ms 37.16% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 0.0081% 9059ms 36.70% AbstractCellBasedSimulation::UpdateCellPopulation 16ms 0.065% 0.073% 8974ms 36.36% AbstractNumericalMethod::ComputeForcesIncludingDamping 1356ms 5.49% 5.57% 8288ms 33.58% RepulsionForce::AddForceContribution (partial-inline) 0 0% 5.57% 7973ms 32.30% NodeBasedCellPopulation::Update 6ms 0.024% 5.59% 5879ms 23.82% DistributedBoxCollection::CalculateInteriorNodePairs 2220ms 8.99% 14.58% 5317ms 21.54% std::_Rb_tree::_M_lower_bound (inline) 0 0% 14.58% 4718ms 19.11% OffLatticeSimulation::ApplyBoundaries 14ms 0.057% 14.64% 4499ms 18.23% NodeAttributes::RemoveDuplicateNeighbours 2ms 0.0081% 14.65% 4324ms 17.52% std::__sort (inline) 0 0% 14.65% 4324ms 17.52% std::sort (inline) 182ms 0.74% 15.39% 4188ms 16.97% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 277ms 1.12% 16.51% 3490ms 14.14% std::_Rb_tree::find (inline) 0 0% 16.51% 3490ms 14.14% std::map::find (inline) 74ms 0.3% 16.81% 3489ms 14.13% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 4ms 0.016% 16.82% 3254ms 13.18% AbstractCellPopulation::Iterator::operator++ (inline) 150ms 0.61% 17.43% 3215ms 13.02% AbstractCellPopulation::Iterator::IsRealCell (inline) 3080ms 12.48% 29.91% 3080ms 12.48% std::_Rb_tree::_S_right (inline) 21ms 0.085% 30.00% 2822ms 11.43% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 209ms 0.85% 30.84% 2619ms 10.61% std::map::operator[] (partial-inline) 184ms 0.75% 31.59% 2615ms 10.59% AbstractMesh::GetNode 181ms 0.73% 32.32% 2592ms 10.50% std::__introsort_loop 57ms 0.23% 32.55% 2581ms 10.46% NodesOnlyMesh::GetNodeOrHaloNode 27ms 0.11% 32.66% 2482ms 10.06% PlaneBoundaryCondition::ImposeBoundaryCondition 105ms 0.43% 33.09% 2434ms 9.86% NodesOnlyMesh::SolveNodeMapping 0 0% 33.09% 2315ms 9.38% std::__unguarded_partition_pivot (inline) 26ms 0.11% 33.19% 2292ms 9.29% AbstractCellPopulation::GetLocationIndexUsingCell 8ms 0.032% 33.22% 2236ms 9.06% PlaneBoundaryCondition::VerifyBoundaryCondition 0 0% 33.22% 2127ms 8.62% std::_Rb_tree::lower_bound (inline) 0 0% 33.22% 2127ms 8.62% std::map::lower_bound (inline) 1007ms 4.08% 37.30% 2064ms 8.36% std::__unguarded_partition (inline) 139ms 0.56% 37.87% 2008ms 8.13% DistributedBoxCollection::AddPairsFromBox 16ms 0.065% 37.93% 1774ms 7.19% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 27ms 0.11% 38.04% 1752ms 7.10% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 38.04% 1727ms 7.00% std::__final_insertion_sort (inline) 95ms 0.38% 38.43% 1528ms 6.19% std::__unguarded_insertion_sort (inline) 509ms 2.06% 40.49% 1480ms 6.00% std::__unguarded_linear_insert (inline) 1399ms 5.67% 46.16% 1399ms 5.67% __gnu_cxx::__normal_iterator::operator-- (inline) 55ms 0.22% 46.38% 1227ms 4.97% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 46.38% 1176ms 4.76% NodeBasedCellPopulation::UpdateCellProcessLocation 5ms 0.02% 46.40% 1097ms 4.44% DistributedBoxCollection::CalculateBoundaryNodePairs 5ms 0.02% 46.42% 1081ms 4.38% boost::numeric::ublas::vector_assign (inline) 19ms 0.077% 46.50% 1007ms 4.08% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 187ms 0.76% 47.25% 993ms 4.02% boost::numeric::ublas::indexing_vector_assign 271ms 1.10% 48.35% 939ms 3.80% __dynamic_cast 188ms 0.76% 49.11% 821ms 3.33% AbstractMesh::GetVectorFromAtoB 395ms 1.60% 50.71% 821ms 3.33% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 50.71% 819ms 3.32% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 228ms 0.92% 51.64% 816ms 3.31% NodeAttributes::AddNeighbour 0 0% 51.64% 806ms 3.27% boost::numeric::ublas::norm_2 (inline) 637ms 2.58% 54.22% 806ms 3.27% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 54.22% 806ms 3.27% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 4ms 0.016% 54.23% 755ms 3.06% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 54.23% 743ms 3.01% AbstractCellPopulation::WriteResultsToFiles 39ms 0.16% 54.39% 734ms 2.97% std::__copy_move::__copy_m (inline) 0 0% 54.39% 734ms 2.97% std::__copy_move_a (inline) 0 0% 54.39% 734ms 2.97% std::__copy_move_a1 (inline) 0 0% 54.39% 734ms 2.97% std::__copy_move_a2 (inline) 0 0% 54.39% 734ms 2.97% std::copy (inline) 713ms 2.89% 57.28% 713ms 2.89% __memcpy_avx_unaligned_erms 681ms 2.76% 60.04% 681ms 2.76% boost::numeric::ublas::c_vector::operator() 587ms 2.38% 62.42% 657ms 2.66% std::vector::push_back (inline) 5ms 0.02% 62.44% 627ms 2.54% AbstractCellBasedSimulation::DoCellBirth 32ms 0.13% 62.57% 611ms 2.48% std::_Rb_tree_const_iterator::operator++ (inline) 5ms 0.02% 62.59% 596ms 2.41% AbstractCentreBasedCellPopulation::GetDampingConstant 5ms 0.02% 62.61% 595ms 2.41% CellPropertyCollection::GetPropertiesType (inline) 560ms 2.27% 64.88% 560ms 2.27% std::_Rb_tree_increment 96ms 0.39% 65.26% 547ms 2.22% std::__new_allocator::allocate (inline) 35ms 0.14% 65.41% 546ms 2.21% boost::detail::shared_count::~shared_count (inline) 0 0% 65.41% 546ms 2.21% boost::shared_ptr::~shared_ptr (inline) 38ms 0.15% 65.56% 544ms 2.20% std::_Rb_tree::_Rb_tree (partial-inline) 257ms 1.04% 66.60% 535ms 2.17% __cxxabiv1::__si_class_type_info::__do_dyncast 527ms 2.13% 68.74% 527ms 2.13% boost::numeric::ublas::same_impl_ex 0 0% 68.74% 521ms 2.11% std::allocator_traits::allocate (inline) 479ms 1.94% 70.68% 501ms 2.03% boost::detail::sp_counted_base::release 1ms 0.0041% 70.68% 492ms 1.99% NodeBasedCellPopulation::WriteVtkResultsToFile 35ms 0.14% 70.82% 490ms 1.99% std::_Rb_tree::_M_copy (inline) 0 0% 70.82% 490ms 1.99% std::_Rb_tree::_M_create_node (inline) 460ms 1.86% 72.69% 460ms 1.86% __strcmp_avx2 0 0% 72.69% 459ms 1.86% AbstractCellBasedSimulation::DoCellRemoval (inline) 3ms 0.012% 72.70% 459ms 1.86% std::set::set (inline) 104ms 0.42% 73.12% 458ms 1.86% std::_Rb_tree::_M_erase 0 0% 73.12% 448ms 1.81% std::_Rb_tree::_M_get_node (inline) 3ms 0.012% 73.13% 446ms 1.81% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 28ms 0.11% 73.25% 446ms 1.81% operator new 153ms 0.62% 73.87% 445ms 1.80% std::_Rb_tree::_M_clone_node (inline) 82ms 0.33% 74.20% 418ms 1.69% Node::GetRadius 1ms 0.0041% 74.20% 411ms 1.67% AbstractCellProperty::IsSubType (inline) 129ms 0.52% 74.72% 409ms 1.66% __GI___libc_malloc 1ms 0.0041% 74.73% 405ms 1.64% Cell::GetMutationState 89ms 0.36% 75.09% 382ms 1.55% boost::numeric::ublas::vector_binary::size (inline) 0 0% 75.09% 362ms 1.47% boost::numeric::ublas::inner_prod (inline) 19ms 0.077% 75.17% 360ms 1.46% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 75.17% 360ms 1.46% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 50ms 0.2% 75.37% 356ms 1.44% std::_Rb_tree::~_Rb_tree (inline) 355ms 1.44% 76.81% 355ms 1.44% __gnu_cxx::__normal_iterator::operator++ (inline) 347ms 1.41% 78.21% 347ms 1.41% Node::CheckForNodeAttributes 346ms 1.40% 79.61% 346ms 1.40% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 79.61% 344ms 1.39% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 79.61% 342ms 1.39% NodesOnlyMesh::ReMesh 0 0% 79.61% 340ms 1.38% std::_Rb_tree::_M_drop_node (inline) 3ms 0.012% 79.63% 332ms 1.35% NodesOnlyMesh::UpdateNodeIndices 3ms 0.012% 79.64% 314ms 1.27% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 8ms 0.032% 79.67% 311ms 1.26% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 79.67% 301ms 1.22% boost::numeric::ublas::c_vector::assign (inline) 12ms 0.049% 79.72% 297ms 1.20% DistributedBoxCollection::GetProcessOwningNode 118ms 0.48% 80.20% 294ms 1.19% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 80.20% 292ms 1.18% NodesOnlyMesh::UpdateBoxCollection 6ms 0.024% 80.22% 286ms 1.16% std::__new_allocator::deallocate (inline) 12ms 0.049% 80.27% 283ms 1.15% std::_Rb_tree::_M_emplace_hint_unique 0 0% 80.27% 267ms 1.08% std::allocator_traits::deallocate (inline) 0 0% 80.27% 266ms 1.08% std::_Rb_tree::_M_put_node (inline) 0 0% 80.27% 262ms 1.06% std::set::~set (inline) 89ms 0.36% 80.63% 252ms 1.02% __GI___libc_free 110ms 0.45% 81.08% 246ms 1% std::__move_median_to_first (inline) 195ms 0.79% 81.87% 245ms 0.99% Node::AddNeighbour 4ms 0.016% 81.88% 241ms 0.98% NodesOnlyMesh::AddNodesToBoxes 1ms 0.0041% 81.89% 240ms 0.97% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 81.89% 238ms 0.96% VtkMeshWriter::WriteFiles 232ms 0.94% 82.83% 232ms 0.94% [libchaste_mesh.so] 116ms 0.47% 83.30% 226ms 0.92% _int_malloc 0 0% 83.30% 218ms 0.88% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 83.30% 214ms 0.87% Cell::HasCellProperty (inline) 4ms 0.016% 83.31% 214ms 0.87% CellPropertyCollection::HasProperty 93ms 0.38% 83.69% 212ms 0.86% boost::shared_ptr::shared_ptr (inline) 17ms 0.069% 83.76% 211ms 0.85% Cell::ReadyToDivide 1ms 0.0041% 83.76% 210ms 0.85% vtkStreamingDemandDrivenPipeline::Update 0 0% 83.76% 210ms 0.85% vtkXMLWriterBase::Write 17ms 0.069% 83.83% 209ms 0.85% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 83.83% 205ms 0.83% vtkDemandDrivenPipeline::ProcessRequest 0 0% 83.83% 205ms 0.83% vtkStreamingDemandDrivenPipeline::ProcessRequest 204ms 0.83% 84.66% 204ms 0.83% Node::GetIndex 0 0% 84.66% 204ms 0.83% vtkExecutive::CallAlgorithm 0 0% 84.66% 203ms 0.82% vtkDemandDrivenPipeline::ExecuteData 0 0% 84.66% 203ms 0.82% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 84.66% 202ms 0.82% vtkCompositeDataPipeline::ExecuteData 16ms 0.065% 84.72% 199ms 0.81% std::__insertion_sort (inline) 194ms 0.79% 85.51% 194ms 0.79% [libchaste_cell_based.so] 1ms 0.0041% 85.51% 171ms 0.69% AbstractCellProperty::IsType (inline) 0 0% 85.51% 171ms 0.69% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.51% 171ms 0.69% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 85.51% 167ms 0.68% std::_Rb_tree::clear (inline) 165ms 0.67% 86.18% 165ms 0.67% __ieee754_log_fma 0 0% 86.18% 165ms 0.67% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 86.18% 164ms 0.66% NodesOnlyMesh::ResizeBoxCollection 7ms 0.028% 86.21% 163ms 0.66% NodesOnlyMesh::IsANodeCloseToDomainBoundary 145ms 0.59% 86.80% 162ms 0.66% _int_free 1ms 0.0041% 86.80% 152ms 0.62% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 86.80% 146ms 0.59% std::_Rb_tree::_Auto_node::_Auto_node (inline) 4ms 0.016% 86.82% 144ms 0.58% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 86.82% 143ms 0.58% AbstractNumericalMethod::SafeNodePositionUpdate 1ms 0.0041% 86.82% 143ms 0.58% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 141ms 0.57% 87.39% 142ms 0.58% std::__adjacent_find (inline) 0 0% 87.39% 142ms 0.58% std::__unique (inline) 0 0% 87.39% 142ms 0.58% std::unique (inline) 0 0% 87.39% 139ms 0.56% vtkXMLWriter::WriteBinaryData 1ms 0.0041% 87.40% 137ms 0.56% Cell::GetCellId 134ms 0.54% 87.94% 134ms 0.54% Node::rGetLocation 49ms 0.2% 88.14% 132ms 0.53% AbstractCellProperty::IsSame 2ms 0.0081% 88.15% 132ms 0.53% NodeBasedCellPopulation::SetNode 0 0% 88.15% 130ms 0.53% vtkXMLWriter::WriteBinaryDataBlock 0 0% 88.15% 130ms 0.53% vtkXMLWriter::WriteBinaryDataInternal 0 0% 88.15% 130ms 0.53% vtkXMLWriter::WriteCompressionBlock 129ms 0.52% 88.67% 129ms 0.52% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 0 0% 88.67% 129ms 0.52% vtkXMLWriter::WritePointsAppendedData