File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 22009ms, 89.55% of 24578ms total Dropped 833 nodes (cum <= 122.89ms) flat flat% sum% cum cum% 0 0% 0% 24445ms 99.46% __libc_start_call_main 0 0% 0% 24445ms 99.46% __libc_start_main_impl 0 0% 0% 24445ms 99.46% _start 0 0% 0% 24427ms 99.39% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 24427ms 99.39% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 24427ms 99.39% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 24427ms 99.39% main 0 0% 0% 24386ms 99.22% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 24386ms 99.22% CxxTest::TestRunner::runTest (inline) 0 0% 0% 24386ms 99.22% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 24377ms 99.18% AbstractCellBasedSimulation::Solve 2ms 0.0081% 0.0081% 14001ms 56.97% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0081% 9185ms 37.37% AbstractCellBasedSimulation::UpdateCellPopulation 5ms 0.02% 0.028% 9102ms 37.03% ForwardEulerNumericalMethod::UpdateAllNodePositions 18ms 0.073% 0.1% 8922ms 36.30% AbstractNumericalMethod::ComputeForcesIncludingDamping 1342ms 5.46% 5.56% 8203ms 33.38% RepulsionForce::AddForceContribution (partial-inline) 0 0% 5.56% 8133ms 33.09% NodeBasedCellPopulation::Update 10ms 0.041% 5.60% 6000ms 24.41% DistributedBoxCollection::CalculateInteriorNodePairs 2093ms 8.52% 14.12% 5057ms 20.58% std::_Rb_tree::_M_lower_bound (inline) 10ms 0.041% 14.16% 4597ms 18.70% NodeAttributes::RemoveDuplicateNeighbours 0 0% 14.16% 4580ms 18.63% OffLatticeSimulation::ApplyBoundaries 2ms 0.0081% 14.17% 4419ms 17.98% std::__sort (inline) 0 0% 14.17% 4419ms 17.98% std::sort (inline) 185ms 0.75% 14.92% 4127ms 16.79% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 213ms 0.87% 15.79% 3267ms 13.29% std::_Rb_tree::find (inline) 0 0% 15.79% 3267ms 13.29% std::map::find (inline) 105ms 0.43% 16.21% 3240ms 13.18% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 3ms 0.012% 16.23% 3083ms 12.54% AbstractCellPopulation::Iterator::operator++ (inline) 150ms 0.61% 16.84% 3056ms 12.43% AbstractCellPopulation::Iterator::IsRealCell (inline) 2949ms 12.00% 28.83% 2949ms 12.00% std::_Rb_tree::_S_right (inline) 32ms 0.13% 28.96% 2625ms 10.68% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 158ms 0.64% 29.61% 2542ms 10.34% std::__introsort_loop 219ms 0.89% 30.50% 2530ms 10.29% std::map::operator[] (partial-inline) 29ms 0.12% 30.62% 2436ms 9.91% PlaneBoundaryCondition::ImposeBoundaryCondition 165ms 0.67% 31.29% 2404ms 9.78% AbstractMesh::GetNode 53ms 0.22% 31.50% 2392ms 9.73% NodesOnlyMesh::GetNodeOrHaloNode 0 0% 31.50% 2309ms 9.39% std::__unguarded_partition_pivot (inline) 98ms 0.4% 31.90% 2248ms 9.15% NodesOnlyMesh::SolveNodeMapping 47ms 0.19% 32.09% 2170ms 8.83% AbstractCellPopulation::GetLocationIndexUsingCell 12ms 0.049% 32.14% 2144ms 8.72% PlaneBoundaryCondition::VerifyBoundaryCondition 997ms 4.06% 36.20% 2058ms 8.37% std::__unguarded_partition (inline) 0 0% 36.20% 2019ms 8.21% std::_Rb_tree::lower_bound (inline) 0 0% 36.20% 2019ms 8.21% std::map::lower_bound (inline) 167ms 0.68% 36.88% 2002ms 8.15% DistributedBoxCollection::AddPairsFromBox 0 0% 36.88% 1875ms 7.63% std::__final_insertion_sort (inline) 18ms 0.073% 36.95% 1770ms 7.20% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 36ms 0.15% 37.10% 1745ms 7.10% AbstractCellPopulation::GetCellUsingLocationIndex 121ms 0.49% 37.59% 1659ms 6.75% std::__unguarded_insertion_sort (inline) 609ms 2.48% 40.07% 1578ms 6.42% std::__unguarded_linear_insert (inline) 1397ms 5.68% 45.75% 1397ms 5.68% __gnu_cxx::__normal_iterator::operator-- (inline) 55ms 0.22% 45.98% 1268ms 5.16% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 45.98% 1164ms 4.74% NodeBasedCellPopulation::UpdateCellProcessLocation 9ms 0.037% 46.01% 1129ms 4.59% DistributedBoxCollection::CalculateBoundaryNodePairs 1ms 0.0041% 46.02% 1108ms 4.51% boost::numeric::ublas::vector_assign (inline) 214ms 0.87% 46.89% 1024ms 4.17% boost::numeric::ublas::indexing_vector_assign 26ms 0.11% 46.99% 975ms 3.97% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 283ms 1.15% 48.14% 963ms 3.92% __dynamic_cast 440ms 1.79% 49.93% 893ms 3.63% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 49.93% 868ms 3.53% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 49.93% 854ms 3.47% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 49.93% 853ms 3.47% boost::numeric::ublas::norm_2 (inline) 658ms 2.68% 52.61% 853ms 3.47% boost::numeric::ublas::vector_norm_2::apply (inline) 5ms 0.02% 52.63% 809ms 3.29% boost::numeric::ublas::c_vector::operator= (inline) 155ms 0.63% 53.26% 805ms 3.28% AbstractMesh::GetVectorFromAtoB 212ms 0.86% 54.13% 792ms 3.22% NodeAttributes::AddNeighbour 31ms 0.13% 54.25% 790ms 3.21% std::__copy_move::__copy_m (inline) 0 0% 54.25% 790ms 3.21% std::__copy_move_a (inline) 0 0% 54.25% 790ms 3.21% std::__copy_move_a1 (inline) 0 0% 54.25% 790ms 3.21% std::__copy_move_a2 (inline) 0 0% 54.25% 789ms 3.21% std::copy (inline) 776ms 3.16% 57.41% 776ms 3.16% __memcpy_avx_unaligned_erms 744ms 3.03% 60.44% 744ms 3.03% boost::numeric::ublas::c_vector::operator() 0 0% 60.44% 736ms 2.99% AbstractCellPopulation::WriteResultsToFiles 578ms 2.35% 62.79% 655ms 2.66% std::vector::push_back (inline) 34ms 0.14% 62.93% 629ms 2.56% std::_Rb_tree_const_iterator::operator++ (inline) 8ms 0.033% 62.96% 624ms 2.54% AbstractCentreBasedCellPopulation::GetDampingConstant 9ms 0.037% 63.00% 616ms 2.51% CellPropertyCollection::GetPropertiesType (inline) 574ms 2.34% 65.33% 574ms 2.34% std::_Rb_tree_increment 4ms 0.016% 65.35% 569ms 2.32% AbstractCellBasedSimulation::DoCellBirth 262ms 1.07% 66.41% 555ms 2.26% __cxxabiv1::__si_class_type_info::__do_dyncast 42ms 0.17% 66.58% 550ms 2.24% std::_Rb_tree::_Rb_tree (partial-inline) 545ms 2.22% 68.80% 545ms 2.22% boost::numeric::ublas::same_impl_ex 94ms 0.38% 69.18% 545ms 2.22% std::__new_allocator::allocate (inline) 0 0% 69.18% 526ms 2.14% std::allocator_traits::allocate (inline) 43ms 0.17% 69.36% 515ms 2.10% boost::detail::shared_count::~shared_count (inline) 0 0% 69.36% 515ms 2.10% boost::shared_ptr::~shared_ptr (inline) 0 0% 69.36% 501ms 2.04% std::_Rb_tree::_M_create_node (inline) 0 0% 69.36% 498ms 2.03% NodeBasedCellPopulation::WriteVtkResultsToFile 38ms 0.15% 69.51% 493ms 2.01% std::_Rb_tree::_M_copy (inline) 0 0% 69.51% 480ms 1.95% AbstractCellBasedSimulation::DoCellRemoval (inline) 470ms 1.91% 71.43% 470ms 1.91% __strcmp_avx2 5ms 0.02% 71.45% 463ms 1.88% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 431ms 1.75% 73.20% 458ms 1.86% boost::detail::sp_counted_base::release 0 0% 73.20% 455ms 1.85% std::_Rb_tree::_M_get_node (inline) 161ms 0.66% 73.85% 452ms 1.84% std::_Rb_tree::_M_clone_node (inline) 4ms 0.016% 73.87% 452ms 1.84% std::set::set (inline) 26ms 0.11% 73.98% 451ms 1.83% operator new 107ms 0.44% 74.41% 449ms 1.83% std::_Rb_tree::_M_erase 3ms 0.012% 74.42% 424ms 1.73% Cell::GetMutationState 130ms 0.53% 74.95% 419ms 1.70% __GI___libc_malloc 0 0% 74.95% 418ms 1.70% boost::numeric::ublas::inner_prod (inline) 1ms 0.0041% 74.96% 416ms 1.69% AbstractCellProperty::IsSubType (inline) 3ms 0.012% 74.97% 416ms 1.69% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 102ms 0.42% 75.38% 413ms 1.68% boost::numeric::ublas::vector_binary::size (inline) 18ms 0.073% 75.46% 413ms 1.68% boost::numeric::ublas::vector_scalar_binary::evaluate 82ms 0.33% 75.79% 383ms 1.56% Node::GetRadius 0 0% 75.79% 365ms 1.49% boost::numeric::ublas::c_vector::assign (inline) 359ms 1.46% 77.25% 359ms 1.46% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 52ms 0.21% 77.46% 357ms 1.45% std::_Rb_tree::~_Rb_tree (inline) 0 0% 77.46% 355ms 1.44% NodesOnlyMesh::ReMesh 349ms 1.42% 78.88% 349ms 1.42% __gnu_cxx::__normal_iterator::operator++ (inline) 5ms 0.02% 78.90% 344ms 1.40% NodesOnlyMesh::UpdateNodeIndices 0 0% 78.90% 340ms 1.38% std::_Rb_tree::_Alloc_node::operator() (inline) 9ms 0.037% 78.94% 334ms 1.36% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 78.94% 334ms 1.36% std::_Rb_tree::_M_drop_node (inline) 144ms 0.59% 79.53% 333ms 1.35% boost::numeric::ublas::vector_inner_prod::apply (inline) 314ms 1.28% 80.80% 314ms 1.28% Node::CheckForNodeAttributes 5ms 0.02% 80.82% 300ms 1.22% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 9ms 0.037% 80.86% 292ms 1.19% std::_Rb_tree::_M_emplace_hint_unique 0 0% 80.86% 284ms 1.16% NodesOnlyMesh::UpdateBoxCollection 7ms 0.028% 80.89% 282ms 1.15% DistributedBoxCollection::GetProcessOwningNode 5ms 0.02% 80.91% 270ms 1.10% std::__new_allocator::deallocate (inline) 0 0% 80.91% 267ms 1.09% std::set::~set (inline) 0 0% 80.91% 254ms 1.03% std::allocator_traits::deallocate (inline) 0 0% 80.91% 253ms 1.03% std::_Rb_tree::_M_put_node (inline) 121ms 0.49% 81.40% 250ms 1.02% std::__move_median_to_first (inline) 109ms 0.44% 81.85% 245ms 1% boost::shared_ptr::shared_ptr (inline) 82ms 0.33% 82.18% 244ms 0.99% __GI___libc_free 238ms 0.97% 83.15% 238ms 0.97% Node::GetIndex 1ms 0.0041% 83.15% 236ms 0.96% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 1ms 0.0041% 83.16% 235ms 0.96% VtkMeshWriter::WriteFiles 134ms 0.55% 83.70% 234ms 0.95% _int_malloc 1ms 0.0041% 83.70% 229ms 0.93% NodesOnlyMesh::AddNodesToBoxes 18ms 0.073% 83.78% 227ms 0.92% boost::numeric::ublas::vector_reference::operator() (inline) 186ms 0.76% 84.53% 224ms 0.91% Node::AddNeighbour 21ms 0.085% 84.62% 216ms 0.88% std::__insertion_sort (inline) 0 0% 84.62% 212ms 0.86% vtkStreamingDemandDrivenPipeline::Update 0 0% 84.62% 212ms 0.86% vtkXMLWriterBase::Write 0 0% 84.62% 211ms 0.86% vtkDemandDrivenPipeline::ProcessRequest 209ms 0.85% 85.47% 209ms 0.85% [libchaste_mesh.so] 0 0% 85.47% 209ms 0.85% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 85.47% 209ms 0.85% vtkDemandDrivenPipeline::ExecuteData 0 0% 85.47% 209ms 0.85% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 85.47% 207ms 0.84% vtkExecutive::CallAlgorithm 0 0% 85.47% 206ms 0.84% vtkCompositeDataPipeline::ExecuteData 0 0% 85.47% 206ms 0.84% vtkXMLUnstructuredDataWriter::ProcessRequest 1ms 0.0041% 85.47% 199ms 0.81% CellPropertyCollection::HasProperty 0 0% 85.47% 198ms 0.81% Cell::HasCellProperty (inline) 7ms 0.028% 85.50% 181ms 0.74% Cell::ReadyToDivide 0 0% 85.50% 178ms 0.72% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.50% 178ms 0.72% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 85.50% 175ms 0.71% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 85.50% 166ms 0.68% AbstractCellProperty::IsType (inline) 149ms 0.61% 86.11% 161ms 0.66% _int_free 0 0% 86.11% 161ms 0.66% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 86.11% 161ms 0.66% std::_Rb_tree::clear (inline) 157ms 0.64% 86.75% 157ms 0.64% [libchaste_cell_based.so] 4ms 0.016% 86.76% 157ms 0.64% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 86.76% 157ms 0.64% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 1ms 0.0041% 86.77% 149ms 0.61% vtkXMLWriter::WriteBinaryData 144ms 0.59% 87.35% 145ms 0.59% __ieee754_log_fma 0 0% 87.35% 143ms 0.58% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.35% 143ms 0.58% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.35% 143ms 0.58% vtkXMLWriter::WriteCompressionBlock 3ms 0.012% 87.37% 142ms 0.58% AbstractCellPopulation::SetCellUsingLocationIndex 2ms 0.0081% 87.37% 141ms 0.57% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 140ms 0.57% 87.94% 140ms 0.57% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 139ms 0.57% 88.51% 139ms 0.57% std::__adjacent_find (inline) 0 0% 88.51% 139ms 0.57% std::__unique (inline) 0 0% 88.51% 139ms 0.57% std::unique (inline) 138ms 0.56% 89.07% 138ms 0.56% Node::rGetLocation 103ms 0.42% 89.49% 136ms 0.55% boost::detail::shared_count::shared_count (inline) 1ms 0.0041% 89.49% 133ms 0.54% Cell::GetCellId 0 0% 89.49% 133ms 0.54% NodesOnlyMesh::ResizeBoxCollection 13ms 0.053% 89.55% 132ms 0.54% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 89.55% 132ms 0.54% vtkXMLWriter::WritePointsAppendedData