File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 16504ms, 87.77% of 18804ms total Dropped 724 nodes (cum <= 94.02ms) flat flat% sum% cum cum% 0 0% 0% 18694ms 99.42% __libc_start_call_main 0 0% 0% 18694ms 99.42% __libc_start_main_impl 0 0% 0% 18694ms 99.42% _start 0 0% 0% 18681ms 99.35% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 18681ms 99.35% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 18681ms 99.35% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 18681ms 99.35% main 0 0% 0% 18641ms 99.13% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 18641ms 99.13% CxxTest::TestRunner::runTest (inline) 0 0% 0% 18641ms 99.13% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 18634ms 99.10% AbstractCellBasedSimulation::Solve 4ms 0.021% 0.021% 10681ms 56.80% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.021% 7014ms 37.30% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.021% 0.043% 6915ms 36.77% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.016% 0.058% 6781ms 36.06% AbstractNumericalMethod::ComputeForcesIncludingDamping 1025ms 5.45% 5.51% 6285ms 33.42% RepulsionForce::AddForceContribution (partial-inline) 0 0% 5.51% 6224ms 33.10% NodeBasedCellPopulation::Update 8ms 0.043% 5.55% 4627ms 24.61% DistributedBoxCollection::CalculateInteriorNodePairs 1720ms 9.15% 14.70% 4017ms 21.36% std::_Rb_tree::_M_lower_bound (inline) 11ms 0.058% 14.76% 3575ms 19.01% NodeAttributes::RemoveDuplicateNeighbours 1ms 0.0053% 14.76% 3507ms 18.65% OffLatticeSimulation::ApplyBoundaries 1ms 0.0053% 14.77% 3413ms 18.15% std::__sort (inline) 0 0% 14.77% 3413ms 18.15% std::sort (inline) 150ms 0.8% 15.57% 3171ms 16.86% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 189ms 1.01% 16.57% 2622ms 13.94% std::_Rb_tree::find (inline) 0 0% 16.57% 2621ms 13.94% std::map::find (inline) 54ms 0.29% 16.86% 2538ms 13.50% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 1ms 0.0053% 16.86% 2397ms 12.75% AbstractCellPopulation::Iterator::operator++ (inline) 117ms 0.62% 17.49% 2372ms 12.61% AbstractCellPopulation::Iterator::IsRealCell (inline) 2271ms 12.08% 29.56% 2271ms 12.08% std::_Rb_tree::_S_right (inline) 18ms 0.096% 29.66% 2071ms 11.01% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 147ms 0.78% 30.44% 1963ms 10.44% std::map::operator[] (partial-inline) 134ms 0.71% 31.15% 1960ms 10.42% std::__introsort_loop 127ms 0.68% 31.83% 1919ms 10.21% AbstractMesh::GetNode 43ms 0.23% 32.06% 1901ms 10.11% NodesOnlyMesh::GetNodeOrHaloNode 25ms 0.13% 32.19% 1871ms 9.95% PlaneBoundaryCondition::ImposeBoundaryCondition 73ms 0.39% 32.58% 1794ms 9.54% NodesOnlyMesh::SolveNodeMapping 0 0% 32.58% 1769ms 9.41% std::__unguarded_partition_pivot (inline) 32ms 0.17% 32.75% 1737ms 9.24% AbstractCellPopulation::GetLocationIndexUsingCell 6ms 0.032% 32.78% 1635ms 8.69% PlaneBoundaryCondition::VerifyBoundaryCondition 0 0% 32.78% 1611ms 8.57% std::_Rb_tree::lower_bound (inline) 0 0% 32.78% 1611ms 8.57% std::map::lower_bound (inline) 802ms 4.27% 37.05% 1586ms 8.43% std::__unguarded_partition (inline) 125ms 0.66% 37.71% 1548ms 8.23% DistributedBoxCollection::AddPairsFromBox 0 0% 37.71% 1449ms 7.71% std::__final_insertion_sort (inline) 22ms 0.12% 37.83% 1339ms 7.12% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 90ms 0.48% 38.31% 1314ms 6.99% std::__unguarded_insertion_sort (inline) 26ms 0.14% 38.44% 1309ms 6.96% AbstractCellPopulation::GetCellUsingLocationIndex 487ms 2.59% 41.03% 1228ms 6.53% std::__unguarded_linear_insert (inline) 1097ms 5.83% 46.87% 1097ms 5.83% __gnu_cxx::__normal_iterator::operator-- (inline) 39ms 0.21% 47.08% 1006ms 5.35% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 47.08% 921ms 4.90% NodeBasedCellPopulation::UpdateCellProcessLocation 3ms 0.016% 47.09% 896ms 4.76% boost::numeric::ublas::vector_assign (inline) 2ms 0.011% 47.10% 849ms 4.51% DistributedBoxCollection::CalculateBoundaryNodePairs 173ms 0.92% 48.02% 831ms 4.42% boost::numeric::ublas::indexing_vector_assign 210ms 1.12% 49.14% 724ms 3.85% __dynamic_cast 11ms 0.058% 49.20% 710ms 3.78% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 129ms 0.69% 49.88% 645ms 3.43% AbstractMesh::GetVectorFromAtoB 0 0% 49.88% 639ms 3.40% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 276ms 1.47% 51.35% 626ms 3.33% DistributedBoxCollection::CalculateContainingBox (partial-inline) 2ms 0.011% 51.36% 622ms 3.31% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 51.36% 620ms 3.30% boost::numeric::ublas::norm_2 (inline) 487ms 2.59% 53.95% 620ms 3.30% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 53.95% 620ms 3.30% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 26ms 0.14% 54.09% 600ms 3.19% std::__copy_move::__copy_m (inline) 0 0% 54.09% 600ms 3.19% std::__copy_move_a (inline) 0 0% 54.09% 600ms 3.19% std::__copy_move_a1 (inline) 0 0% 54.09% 600ms 3.19% std::__copy_move_a2 (inline) 0 0% 54.09% 600ms 3.19% std::copy (inline) 579ms 3.08% 57.17% 579ms 3.08% __memcpy_avx512_unaligned_erms 125ms 0.66% 57.83% 577ms 3.07% NodeAttributes::AddNeighbour 0 0% 57.83% 573ms 3.05% AbstractCellPopulation::WriteResultsToFiles 569ms 3.03% 60.86% 569ms 3.03% boost::numeric::ublas::c_vector::operator() 450ms 2.39% 63.25% 526ms 2.80% std::vector::push_back (inline) 25ms 0.13% 63.39% 471ms 2.50% std::_Rb_tree_const_iterator::operator++ (inline) 3ms 0.016% 63.40% 445ms 2.37% AbstractCentreBasedCellPopulation::GetDampingConstant 7ms 0.037% 63.44% 445ms 2.37% CellPropertyCollection::GetPropertiesType (inline) 1ms 0.0053% 63.44% 444ms 2.36% AbstractCellBasedSimulation::DoCellBirth 431ms 2.29% 65.74% 431ms 2.29% std::_Rb_tree_increment 428ms 2.28% 68.01% 428ms 2.28% boost::numeric::ublas::same_impl_ex 203ms 1.08% 69.09% 423ms 2.25% __cxxabiv1::__si_class_type_info::__do_dyncast 79ms 0.42% 69.51% 422ms 2.24% std::__new_allocator::allocate (inline) 0 0% 69.51% 403ms 2.14% std::allocator_traits::allocate (inline) 34ms 0.18% 69.69% 401ms 2.13% std::_Rb_tree::_Rb_tree (partial-inline) 37ms 0.2% 69.89% 392ms 2.08% boost::detail::shared_count::~shared_count (inline) 0 0% 69.89% 392ms 2.08% boost::shared_ptr::~shared_ptr (inline) 1ms 0.0053% 69.89% 384ms 2.04% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 69.89% 372ms 1.98% std::_Rb_tree::_M_create_node (inline) 29ms 0.15% 70.05% 356ms 1.89% std::_Rb_tree::_M_copy (inline) 99ms 0.53% 70.58% 348ms 1.85% std::_Rb_tree::_M_erase 0 0% 70.58% 346ms 1.84% AbstractCellBasedSimulation::DoCellRemoval (inline) 333ms 1.77% 72.35% 345ms 1.83% boost::detail::sp_counted_base::release 343ms 1.82% 74.17% 343ms 1.82% __strcmp_evex 3ms 0.016% 74.19% 342ms 1.82% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 19ms 0.1% 74.29% 340ms 1.81% operator new 0 0% 74.29% 339ms 1.80% std::_Rb_tree::_M_get_node (inline) 4ms 0.021% 74.31% 332ms 1.77% std::set::set (inline) 104ms 0.55% 74.86% 324ms 1.72% std::_Rb_tree::_M_clone_node (inline) 86ms 0.46% 75.32% 319ms 1.70% __GI___libc_malloc 3ms 0.016% 75.34% 311ms 1.65% AbstractCellProperty::IsSubType (inline) 2ms 0.011% 75.35% 309ms 1.64% Cell::GetMutationState 80ms 0.43% 75.77% 304ms 1.62% boost::numeric::ublas::vector_binary::size (inline) 0 0% 75.77% 299ms 1.59% boost::numeric::ublas::inner_prod (inline) 1ms 0.0053% 75.78% 299ms 1.59% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 14ms 0.074% 75.85% 298ms 1.58% boost::numeric::ublas::vector_scalar_binary::evaluate 58ms 0.31% 76.16% 269ms 1.43% Node::GetRadius 32ms 0.17% 76.33% 266ms 1.41% std::_Rb_tree::~_Rb_tree (inline) 0 0% 76.33% 259ms 1.38% boost::numeric::ublas::c_vector::assign (inline) 0 0% 76.33% 252ms 1.34% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 76.33% 252ms 1.34% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 76.33% 247ms 1.31% NodesOnlyMesh::ReMesh 242ms 1.29% 77.62% 242ms 1.29% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 77.62% 242ms 1.29% std::_Rb_tree::_M_drop_node (inline) 0 0% 77.62% 240ms 1.28% NodesOnlyMesh::UpdateNodeIndices 98ms 0.52% 78.14% 240ms 1.28% boost::numeric::ublas::vector_inner_prod::apply (inline) 238ms 1.27% 79.40% 238ms 1.27% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 2ms 0.011% 79.41% 233ms 1.24% DistributedBoxCollection::GetProcessOwningNode 3ms 0.016% 79.43% 232ms 1.23% NodeBasedCellPopulation::UpdateMapsAfterRemesh 215ms 1.14% 80.57% 215ms 1.14% Node::CheckForNodeAttributes 5ms 0.027% 80.60% 205ms 1.09% std::_Rb_tree::_M_emplace_hint_unique 1ms 0.0053% 80.61% 198ms 1.05% std::__new_allocator::deallocate (inline) 0 0% 80.61% 195ms 1.04% std::set::~set (inline) 0 0% 80.61% 191ms 1.02% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 80.61% 189ms 1.01% VtkMeshWriter::WriteFiles 0 0% 80.61% 185ms 0.98% NodesOnlyMesh::UpdateBoxCollection 0 0% 80.61% 185ms 0.98% std::allocator_traits::deallocate (inline) 0 0% 80.61% 184ms 0.98% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 80.61% 184ms 0.98% std::_Rb_tree::_M_put_node (inline) 60ms 0.32% 80.92% 182ms 0.97% __GI___libc_free 99ms 0.53% 81.45% 182ms 0.97% _int_malloc 83ms 0.44% 81.89% 182ms 0.97% std::__move_median_to_first (inline) 13ms 0.069% 81.96% 180ms 0.96% boost::numeric::ublas::vector_reference::operator() (inline) 179ms 0.95% 82.91% 179ms 0.95% [libchaste_mesh.so] 0 0% 82.91% 174ms 0.93% vtkDemandDrivenPipeline::ProcessRequest 0 0% 82.91% 174ms 0.93% vtkStreamingDemandDrivenPipeline::Update 0 0% 82.91% 174ms 0.93% vtkXMLWriterBase::Write 0 0% 82.91% 171ms 0.91% vtkExecutive::CallAlgorithm 0 0% 82.91% 170ms 0.9% vtkDemandDrivenPipeline::ExecuteData 0 0% 82.91% 170ms 0.9% vtkStreamingDemandDrivenPipeline::ProcessRequest 116ms 0.62% 83.53% 169ms 0.9% Node::AddNeighbour 0 0% 83.53% 169ms 0.9% vtkCompositeDataPipeline::ExecuteData 0 0% 83.53% 169ms 0.9% vtkXMLUnstructuredDataWriter::ProcessRequest 168ms 0.89% 84.42% 168ms 0.89% Node::GetIndex 85ms 0.45% 84.88% 167ms 0.89% boost::shared_ptr::shared_ptr (inline) 1ms 0.0053% 84.88% 156ms 0.83% NodesOnlyMesh::AddNodesToBoxes 1ms 0.0053% 84.89% 155ms 0.82% CellPropertyCollection::HasProperty 0 0% 84.89% 154ms 0.82% Cell::HasCellProperty (inline) 0 0% 84.89% 147ms 0.78% NodesOnlyMesh::ResizeBoxCollection 10ms 0.053% 84.94% 146ms 0.78% NodesOnlyMesh::IsANodeCloseToDomainBoundary 145ms 0.77% 85.71% 145ms 0.77% [libchaste_cell_based.so] 0 0% 85.71% 144ms 0.77% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.71% 144ms 0.77% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 85.71% 136ms 0.72% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 18ms 0.096% 85.81% 135ms 0.72% std::__insertion_sort (inline) 3ms 0.016% 85.82% 134ms 0.71% Cell::ReadyToDivide 134ms 0.71% 86.53% 134ms 0.71% std::__adjacent_find (inline) 0 0% 86.53% 134ms 0.71% std::__unique (inline) 0 0% 86.53% 134ms 0.71% std::unique (inline) 0 0% 86.53% 121ms 0.64% std::_Rb_tree::clear (inline) 105ms 0.56% 87.09% 120ms 0.64% _int_free 0 0% 87.09% 120ms 0.64% std::_Rb_tree::_Auto_node::_Auto_node (inline) 2ms 0.011% 87.10% 118ms 0.63% AbstractCellProperty::IsType (inline) 117ms 0.62% 87.73% 117ms 0.62% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 0 0% 87.73% 114ms 0.61% vtkXMLWriter::WriteBinaryData 2ms 0.011% 87.74% 112ms 0.6% boost::numeric::ublas::c_vector::operator[] (inline) 1ms 0.0053% 87.74% 110ms 0.58% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 87.74% 108ms 0.57% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.74% 108ms 0.57% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.74% 108ms 0.57% vtkXMLWriter::WriteCompressionBlock 1ms 0.0053% 87.75% 107ms 0.57% DistributedBoxCollection::GetIsPeriodicAllDims 0 0% 87.75% 107ms 0.57% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 4ms 0.021% 87.77% 103ms 0.55% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 87.77% 101ms 0.54% Cell::GetCellId 0 0% 87.77% 99ms 0.53% vtkXMLWriter::WritePointsAppendedData