File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 21189ms, 89.84% of 23586ms total Dropped 759 nodes (cum <= 117.93ms) flat flat% sum% cum cum% 0 0% 0% 23419ms 99.29% __libc_start_call_main 0 0% 0% 23419ms 99.29% __libc_start_main_impl 0 0% 0% 23419ms 99.29% _start 0 0% 0% 23404ms 99.23% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 23404ms 99.23% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 23404ms 99.23% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 23404ms 99.23% main 0 0% 0% 23364ms 99.06% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 23364ms 99.06% CxxTest::TestRunner::runTest (inline) 1ms 0.0042% 0.0042% 23364ms 99.06% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0.0042% 23355ms 99.02% AbstractCellBasedSimulation::Solve 1ms 0.0042% 0.0085% 13276ms 56.29% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0085% 8902ms 37.74% AbstractCellBasedSimulation::UpdateCellPopulation 5ms 0.021% 0.03% 8388ms 35.56% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.034% 0.064% 8194ms 34.74% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.064% 7850ms 33.28% NodeBasedCellPopulation::Update 1193ms 5.06% 5.12% 7521ms 31.89% RepulsionForce::AddForceContribution (partial-inline) 4ms 0.017% 5.14% 5807ms 24.62% DistributedBoxCollection::CalculateInteriorNodePairs 2063ms 8.75% 13.89% 4940ms 20.94% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.0042% 13.89% 4566ms 19.36% OffLatticeSimulation::ApplyBoundaries 13ms 0.055% 13.94% 4470ms 18.95% NodeAttributes::RemoveDuplicateNeighbours 7ms 0.03% 13.97% 4292ms 18.20% std::__sort (inline) 0 0% 13.97% 4292ms 18.20% std::sort (inline) 175ms 0.74% 14.72% 3817ms 16.18% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 0 0% 14.72% 3471ms 14.72% AbstractCellPopulation::Iterator::operator++ (inline) 68ms 0.29% 15.00% 3465ms 14.69% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 203ms 0.86% 15.87% 3451ms 14.63% AbstractCellPopulation::Iterator::IsRealCell (inline) 260ms 1.10% 16.97% 3259ms 13.82% std::_Rb_tree::find (inline) 0 0% 16.97% 3259ms 13.82% std::map::find (inline) 25ms 0.11% 17.07% 2956ms 12.53% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2839ms 12.04% 29.11% 2839ms 12.04% std::_Rb_tree::_S_right (inline) 197ms 0.84% 29.95% 2491ms 10.56% std::__introsort_loop 232ms 0.98% 30.93% 2451ms 10.39% std::map::operator[] (partial-inline) 31ms 0.13% 31.06% 2388ms 10.12% PlaneBoundaryCondition::ImposeBoundaryCondition 42ms 0.18% 31.24% 2310ms 9.79% AbstractCellPopulation::GetLocationIndexUsingCell 144ms 0.61% 31.85% 2300ms 9.75% AbstractMesh::GetNode 40ms 0.17% 32.02% 2254ms 9.56% NodesOnlyMesh::GetNodeOrHaloNode 0 0% 32.02% 2222ms 9.42% std::__unguarded_partition_pivot (inline) 13ms 0.055% 32.07% 2177ms 9.23% PlaneBoundaryCondition::VerifyBoundaryCondition 89ms 0.38% 32.45% 2164ms 9.17% NodesOnlyMesh::SolveNodeMapping 1040ms 4.41% 36.86% 2008ms 8.51% std::__unguarded_partition (inline) 0 0% 36.86% 1958ms 8.30% std::_Rb_tree::lower_bound (inline) 0 0% 36.86% 1958ms 8.30% std::map::lower_bound (inline) 157ms 0.67% 37.53% 1920ms 8.14% DistributedBoxCollection::AddPairsFromBox 1ms 0.0042% 37.53% 1793ms 7.60% std::__final_insertion_sort (inline) 84ms 0.36% 37.89% 1600ms 6.78% std::__unguarded_insertion_sort (inline) 580ms 2.46% 40.35% 1561ms 6.62% std::__unguarded_linear_insert (inline) 21ms 0.089% 40.44% 1523ms 6.46% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 23ms 0.098% 40.53% 1494ms 6.33% AbstractCellPopulation::GetCellUsingLocationIndex 1432ms 6.07% 46.60% 1432ms 6.07% __gnu_cxx::__normal_iterator::operator-- (inline) 62ms 0.26% 46.87% 1368ms 5.80% boost::numeric::ublas::c_vector::c_vector (partial-inline) 50ms 0.21% 47.08% 1222ms 5.18% boost::numeric::ublas::vector_assign (inline) 0 0% 47.08% 1156ms 4.90% NodeBasedCellPopulation::UpdateCellProcessLocation 287ms 1.22% 48.30% 1083ms 4.59% boost::numeric::ublas::indexing_vector_assign 12ms 0.051% 48.35% 1063ms 4.51% DistributedBoxCollection::CalculateBoundaryNodePairs 245ms 1.04% 49.39% 976ms 4.14% __dynamic_cast 153ms 0.65% 50.03% 836ms 3.54% AbstractMesh::GetVectorFromAtoB 18ms 0.076% 50.11% 825ms 3.50% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 372ms 1.58% 51.69% 762ms 3.23% DistributedBoxCollection::CalculateContainingBox (partial-inline) 163ms 0.69% 52.38% 745ms 3.16% NodeAttributes::AddNeighbour 0 0% 52.38% 731ms 3.10% AbstractCellPopulation::WriteResultsToFiles 0 0% 52.38% 712ms 3.02% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 52.38% 694ms 2.94% boost::numeric::ublas::norm_2 (inline) 547ms 2.32% 54.70% 694ms 2.94% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 54.70% 694ms 2.94% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 687ms 2.91% 57.61% 687ms 2.91% boost::numeric::ublas::c_vector::operator() 5ms 0.021% 57.63% 685ms 2.90% boost::numeric::ublas::c_vector::operator= (inline) 41ms 0.17% 57.81% 662ms 2.81% std::__copy_move::__copy_m (inline) 0 0% 57.81% 662ms 2.81% std::__copy_move_a (inline) 0 0% 57.81% 662ms 2.81% std::__copy_move_a1 (inline) 0 0% 57.81% 662ms 2.81% std::__copy_move_a2 (inline) 0 0% 57.81% 662ms 2.81% std::copy (inline) 579ms 2.45% 60.26% 656ms 2.78% std::vector::push_back (inline) 6ms 0.025% 60.29% 638ms 2.70% CellPropertyCollection::GetPropertiesType (inline) 635ms 2.69% 62.98% 635ms 2.69% __memcpy_avx_unaligned_erms 289ms 1.23% 64.20% 612ms 2.59% __cxxabiv1::__si_class_type_info::__do_dyncast 35ms 0.15% 64.35% 610ms 2.59% std::_Rb_tree_const_iterator::operator++ (inline) 3ms 0.013% 64.36% 596ms 2.53% AbstractCentreBasedCellPopulation::GetDampingConstant 572ms 2.43% 66.79% 572ms 2.43% std::_Rb_tree_increment 2ms 0.0085% 66.80% 569ms 2.41% AbstractCellBasedSimulation::DoCellBirth 77ms 0.33% 67.12% 534ms 2.26% std::__new_allocator::allocate (inline) 515ms 2.18% 69.31% 515ms 2.18% boost::numeric::ublas::same_impl_ex 0 0% 69.31% 507ms 2.15% std::allocator_traits::allocate (inline) 493ms 2.09% 71.40% 493ms 2.09% __strcmp_avx2 26ms 0.11% 71.51% 485ms 2.06% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 71.51% 483ms 2.05% AbstractCellBasedSimulation::DoCellRemoval (inline) 1ms 0.0042% 71.51% 480ms 2.04% NodeBasedCellPopulation::WriteVtkResultsToFile 9ms 0.038% 71.55% 469ms 1.99% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 71.55% 467ms 1.98% std::_Rb_tree::_M_create_node (inline) 20ms 0.085% 71.64% 451ms 1.91% operator new 31ms 0.13% 71.77% 445ms 1.89% boost::detail::shared_count::~shared_count (inline) 0 0% 71.77% 445ms 1.89% boost::shared_ptr::~shared_ptr (inline) 46ms 0.2% 71.96% 442ms 1.87% std::_Rb_tree::_M_copy (inline) 144ms 0.61% 72.57% 432ms 1.83% __GI___libc_malloc 1ms 0.0042% 72.58% 428ms 1.81% Cell::GetMutationState 0 0% 72.58% 414ms 1.76% std::_Rb_tree::_M_get_node (inline) 400ms 1.70% 74.27% 409ms 1.73% boost::detail::sp_counted_base::release 4ms 0.017% 74.29% 408ms 1.73% AbstractCellProperty::IsSubType (inline) 137ms 0.58% 74.87% 395ms 1.67% std::_Rb_tree::_M_erase 131ms 0.56% 75.43% 394ms 1.67% std::_Rb_tree::_M_clone_node (inline) 138ms 0.59% 76.01% 392ms 1.66% Node::GetRadius 0 0% 76.01% 389ms 1.65% std::set::set (inline) 16ms 0.068% 76.08% 353ms 1.50% boost::numeric::ublas::vector_binary::size (inline) 0 0% 76.08% 335ms 1.42% boost::numeric::ublas::c_vector::assign (inline) 0 0% 76.08% 322ms 1.37% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 76.08% 319ms 1.35% boost::numeric::ublas::inner_prod (inline) 2ms 0.0085% 76.09% 319ms 1.35% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 19ms 0.081% 76.17% 317ms 1.34% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 76.17% 314ms 1.33% NodesOnlyMesh::ReMesh 6ms 0.025% 76.19% 310ms 1.31% NodeBasedCellPopulation::UpdateMapsAfterRemesh 308ms 1.31% 77.50% 308ms 1.31% __gnu_cxx::__normal_iterator::operator++ (inline) 2ms 0.0085% 77.51% 300ms 1.27% NodesOnlyMesh::UpdateNodeIndices 299ms 1.27% 78.78% 299ms 1.27% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 35ms 0.15% 78.92% 292ms 1.24% std::_Rb_tree::~_Rb_tree (inline) 263ms 1.12% 80.04% 263ms 1.12% Node::CheckForNodeAttributes 13ms 0.055% 80.09% 261ms 1.11% std::_Rb_tree::_M_emplace_hint_unique 0 0% 80.09% 259ms 1.10% NodesOnlyMesh::UpdateBoxCollection 88ms 0.37% 80.47% 255ms 1.08% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 80.47% 249ms 1.06% std::_Rb_tree::_M_drop_node (inline) 1ms 0.0042% 80.47% 242ms 1.03% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 85ms 0.36% 80.83% 240ms 1.02% Node::AddNeighbour 129ms 0.55% 81.38% 240ms 1.02% _int_malloc 0 0% 81.38% 235ms 1% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 81.38% 234ms 0.99% VtkMeshWriter::WriteFiles 2ms 0.0085% 81.39% 233ms 0.99% DistributedBoxCollection::GetProcessOwningNode 3ms 0.013% 81.40% 223ms 0.95% std::__new_allocator::deallocate (inline) 0 0% 81.40% 221ms 0.94% NodesOnlyMesh::ResizeBoxCollection 12ms 0.051% 81.45% 220ms 0.93% NodesOnlyMesh::IsANodeCloseToDomainBoundary 114ms 0.48% 81.93% 219ms 0.93% boost::shared_ptr::shared_ptr (inline) 2ms 0.0085% 81.94% 213ms 0.9% NodesOnlyMesh::AddNodesToBoxes 102ms 0.43% 82.38% 210ms 0.89% std::__move_median_to_first (inline) 0 0% 82.38% 206ms 0.87% vtkStreamingDemandDrivenPipeline::Update 0 0% 82.38% 206ms 0.87% vtkXMLWriterBase::Write 0 0% 82.38% 205ms 0.87% std::set::~set (inline) 1ms 0.0042% 82.38% 205ms 0.87% vtkDemandDrivenPipeline::ProcessRequest 0 0% 82.38% 203ms 0.86% vtkStreamingDemandDrivenPipeline::ProcessRequest 69ms 0.29% 82.67% 201ms 0.85% __GI___libc_free 0 0% 82.67% 201ms 0.85% vtkDemandDrivenPipeline::ExecuteData 0 0% 82.67% 201ms 0.85% vtkExecutive::CallAlgorithm 2ms 0.0085% 82.68% 200ms 0.85% CellPropertyCollection::HasProperty 0 0% 82.68% 199ms 0.84% Cell::HasCellProperty (inline) 0 0% 82.68% 199ms 0.84% vtkCompositeDataPipeline::ExecuteData 0 0% 82.68% 199ms 0.84% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 82.68% 196ms 0.83% std::allocator_traits::deallocate (inline) 0 0% 82.68% 193ms 0.82% std::_Rb_tree::_M_put_node (inline) 18ms 0.076% 82.76% 192ms 0.81% std::__insertion_sort (inline) 187ms 0.79% 83.55% 187ms 0.79% Node::GetIndex 186ms 0.79% 84.34% 186ms 0.79% Node::ConstructNodeAttributes (inline) 0 0% 84.34% 179ms 0.76% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 84.34% 179ms 0.76% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 84.34% 176ms 0.75% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 8ms 0.034% 84.37% 175ms 0.74% Cell::ReadyToDivide 3ms 0.013% 84.38% 171ms 0.73% AbstractCellProperty::IsType (inline) 169ms 0.72% 85.10% 169ms 0.72% [libchaste_cell_based.so] 162ms 0.69% 85.79% 162ms 0.69% Node::IsDeleted 0 0% 85.79% 162ms 0.69% std::_Rb_tree::clear (inline) 4ms 0.017% 85.81% 160ms 0.68% DistributedBoxCollection::GetIsPeriodicAllDims 147ms 0.62% 86.43% 147ms 0.62% [libchaste_mesh.so] 18ms 0.076% 86.50% 147ms 0.62% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 86.50% 145ms 0.61% std::_Rb_tree::_Auto_node::_Auto_node (inline) 145ms 0.61% 87.12% 145ms 0.61% std::__adjacent_find (inline) 0 0% 87.12% 145ms 0.61% std::__unique (inline) 0 0% 87.12% 145ms 0.61% std::unique (inline) 144ms 0.61% 87.73% 144ms 0.61% boost::shared_ptr::operator-> (inline) 0 0% 87.73% 143ms 0.61% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 87.73% 141ms 0.6% vtkXMLWriter::WriteBinaryData 1ms 0.0042% 87.73% 140ms 0.59% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 1ms 0.0042% 87.74% 140ms 0.59% Cell::GetCellId 5ms 0.021% 87.76% 139ms 0.59% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 87.76% 139ms 0.59% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.76% 138ms 0.59% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.76% 137ms 0.58% vtkXMLWriter::WriteCompressionBlock 135ms 0.57% 88.33% 135ms 0.57% __ieee754_log_fma 0 0% 88.33% 135ms 0.57% tbb::detail::r1::parallel_pipeline 124ms 0.53% 88.86% 131ms 0.56% _int_free 0 0% 88.86% 131ms 0.56% clone3 0 0% 88.86% 131ms 0.56% start_thread 0 0% 88.86% 130ms 0.55% boost::numeric::ublas::vector_binary::operator() (inline) 1ms 0.0042% 88.86% 130ms 0.55% tbb::detail::r1::reset 56ms 0.24% 89.10% 127ms 0.54% tbb::detail::r1::wait_bounded_queue_monitor 5ms 0.021% 89.12% 125ms 0.53% NodeBasedCellPopulation::SetNode 123ms 0.52% 89.64% 123ms 0.52% Node::rGetLocation 0 0% 89.64% 123ms 0.52% vtkXMLWriter::WritePointsAppendedData 46ms 0.2% 89.84% 121ms 0.51% AbstractCellProperty::IsSame 0 0% 89.84% 120ms 0.51% std::map::clear (inline) 0 0% 89.84% 120ms 0.51% vtkDataCompressor::Compress 0 0% 89.84% 119ms 0.5% AbstractCellPopulation::SetCellUsingLocationIndex 0 0% 89.84% 118ms 0.5% compress2 0 0% 89.84% 118ms 0.5% vtkZLibDataCompressor::CompressBuffer