File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20238ms, 87.49% of 23133ms total Dropped 783 nodes (cum <= 115.67ms) flat flat% sum% cum cum% 0 0% 0% 22989ms 99.38% __libc_start_call_main 0 0% 0% 22989ms 99.38% __libc_start_main_impl 0 0% 0% 22989ms 99.38% _start 0 0% 0% 22973ms 99.31% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 22973ms 99.31% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 22973ms 99.31% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 22973ms 99.31% main 0 0% 0% 22938ms 99.16% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 22938ms 99.16% CxxTest::TestRunner::runTest (inline) 0 0% 0% 22938ms 99.16% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 22931ms 99.13% AbstractCellBasedSimulation::Solve 1ms 0.0043% 0.0043% 13044ms 56.39% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0043% 8686ms 37.55% AbstractCellBasedSimulation::UpdateCellPopulation 6ms 0.026% 0.03% 8240ms 35.62% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.026% 0.056% 8095ms 34.99% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.056% 7683ms 33.21% NodeBasedCellPopulation::Update 1181ms 5.11% 5.16% 7481ms 32.34% RepulsionForce::AddForceContribution (partial-inline) 3ms 0.013% 5.17% 5645ms 24.40% DistributedBoxCollection::CalculateInteriorNodePairs 2084ms 9.01% 14.18% 4896ms 21.16% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.0043% 14.19% 4495ms 19.43% OffLatticeSimulation::ApplyBoundaries 19ms 0.082% 14.27% 4479ms 19.36% NodeAttributes::RemoveDuplicateNeighbours 7ms 0.03% 14.30% 4297ms 18.58% std::__sort (inline) 0 0% 14.30% 4297ms 18.58% std::sort (inline) 208ms 0.9% 15.20% 3877ms 16.76% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 1ms 0.0043% 15.20% 3428ms 14.82% AbstractCellPopulation::Iterator::operator++ (inline) 209ms 0.9% 16.11% 3405ms 14.72% AbstractCellPopulation::Iterator::IsRealCell (inline) 81ms 0.35% 16.46% 3404ms 14.71% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 232ms 1.00% 17.46% 3109ms 13.44% std::_Rb_tree::find (inline) 0 0% 17.46% 3109ms 13.44% std::map::find (inline) 19ms 0.082% 17.54% 2899ms 12.53% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2764ms 11.95% 29.49% 2764ms 11.95% std::_Rb_tree::_S_right (inline) 243ms 1.05% 30.54% 2554ms 11.04% std::map::operator[] (partial-inline) 184ms 0.8% 31.34% 2439ms 10.54% std::__introsort_loop 22ms 0.095% 31.43% 2313ms 10.00% PlaneBoundaryCondition::ImposeBoundaryCondition 57ms 0.25% 31.68% 2267ms 9.80% NodesOnlyMesh::GetNodeOrHaloNode 40ms 0.17% 31.85% 2263ms 9.78% AbstractCellPopulation::GetLocationIndexUsingCell 149ms 0.64% 32.49% 2249ms 9.72% AbstractMesh::GetNode 1ms 0.0043% 32.50% 2184ms 9.44% std::__unguarded_partition_pivot (inline) 14ms 0.061% 32.56% 2181ms 9.43% PlaneBoundaryCondition::VerifyBoundaryCondition 86ms 0.37% 32.93% 2105ms 9.10% NodesOnlyMesh::SolveNodeMapping 0 0% 32.93% 2040ms 8.82% std::_Rb_tree::lower_bound (inline) 0 0% 32.93% 2040ms 8.82% std::map::lower_bound (inline) 1041ms 4.50% 37.43% 1991ms 8.61% std::__unguarded_partition (inline) 1ms 0.0043% 37.44% 1848ms 7.99% std::__final_insertion_sort (inline) 145ms 0.63% 38.06% 1796ms 7.76% DistributedBoxCollection::AddPairsFromBox 104ms 0.45% 38.51% 1631ms 7.05% std::__unguarded_insertion_sort (inline) 21ms 0.091% 38.60% 1597ms 6.90% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 583ms 2.52% 41.12% 1591ms 6.88% std::__unguarded_linear_insert (inline) 30ms 0.13% 41.25% 1575ms 6.81% AbstractCellPopulation::GetCellUsingLocationIndex 1444ms 6.24% 47.49% 1444ms 6.24% __gnu_cxx::__normal_iterator::operator-- (inline) 47ms 0.2% 47.70% 1207ms 5.22% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 47.70% 1142ms 4.94% NodeBasedCellPopulation::UpdateCellProcessLocation 47ms 0.2% 47.90% 1095ms 4.73% boost::numeric::ublas::vector_assign (inline) 3ms 0.013% 47.91% 1070ms 4.63% DistributedBoxCollection::CalculateBoundaryNodePairs 258ms 1.12% 49.03% 975ms 4.21% __dynamic_cast 283ms 1.22% 50.25% 964ms 4.17% boost::numeric::ublas::indexing_vector_assign 13ms 0.056% 50.31% 816ms 3.53% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 148ms 0.64% 50.95% 788ms 3.41% AbstractMesh::GetVectorFromAtoB 343ms 1.48% 52.43% 784ms 3.39% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 52.43% 737ms 3.19% AbstractCellPopulation::WriteResultsToFiles 195ms 0.84% 53.27% 699ms 3.02% NodeAttributes::AddNeighbour 0 0% 53.27% 686ms 2.97% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 675ms 2.92% 56.19% 675ms 2.92% boost::numeric::ublas::c_vector::operator() 0 0% 56.19% 667ms 2.88% boost::numeric::ublas::norm_2 (inline) 531ms 2.30% 58.49% 667ms 2.88% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 58.49% 667ms 2.88% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 5ms 0.022% 58.51% 664ms 2.87% boost::numeric::ublas::c_vector::operator= (inline) 38ms 0.16% 58.67% 651ms 2.81% std::__copy_move::__copy_m (inline) 0 0% 58.67% 651ms 2.81% std::__copy_move_a (inline) 0 0% 58.67% 651ms 2.81% std::__copy_move_a1 (inline) 0 0% 58.67% 651ms 2.81% std::__copy_move_a2 (inline) 0 0% 58.67% 651ms 2.81% std::copy (inline) 630ms 2.72% 61.40% 630ms 2.72% __memcpy_avx_unaligned_erms 6ms 0.026% 61.42% 603ms 2.61% CellPropertyCollection::GetPropertiesType (inline) 274ms 1.18% 62.61% 574ms 2.48% __cxxabiv1::__si_class_type_info::__do_dyncast 503ms 2.17% 64.78% 560ms 2.42% std::vector::push_back (inline) 1ms 0.0043% 64.79% 557ms 2.41% AbstractCentreBasedCellPopulation::GetDampingConstant 1ms 0.0043% 64.79% 536ms 2.32% AbstractCellBasedSimulation::DoCellBirth 72ms 0.31% 65.10% 531ms 2.30% std::__new_allocator::allocate (inline) 0 0% 65.10% 514ms 2.22% std::allocator_traits::allocate (inline) 32ms 0.14% 65.24% 506ms 2.19% std::_Rb_tree::_Rb_tree (partial-inline) 38ms 0.16% 65.40% 502ms 2.17% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 65.40% 491ms 2.12% std::_Rb_tree::_M_create_node (inline) 42ms 0.18% 65.59% 484ms 2.09% boost::detail::shared_count::~shared_count (inline) 0 0% 65.59% 484ms 2.09% boost::shared_ptr::~shared_ptr (inline) 481ms 2.08% 67.67% 481ms 2.08% __strcmp_avx2 0 0% 67.67% 480ms 2.07% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 67.67% 467ms 2.02% AbstractCellBasedSimulation::DoCellRemoval (inline) 459ms 1.98% 69.65% 459ms 1.98% std::_Rb_tree_increment 5ms 0.022% 69.67% 457ms 1.98% AbstractCellProperty::IsSubType (inline) 2ms 0.0086% 69.68% 456ms 1.97% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 31ms 0.13% 69.81% 456ms 1.97% operator new 453ms 1.96% 71.77% 453ms 1.96% boost::numeric::ublas::same_impl_ex 46ms 0.2% 71.97% 452ms 1.95% std::_Rb_tree::_M_copy (inline) 0 0% 71.97% 437ms 1.89% std::_Rb_tree::_M_get_node (inline) 433ms 1.87% 73.84% 435ms 1.88% boost::detail::sp_counted_base::release 139ms 0.6% 74.44% 424ms 1.83% __GI___libc_malloc 4ms 0.017% 74.46% 411ms 1.78% Cell::GetMutationState 128ms 0.55% 75.01% 404ms 1.75% std::_Rb_tree::_M_clone_node (inline) 3ms 0.013% 75.03% 397ms 1.72% std::set::set (inline) 118ms 0.51% 75.54% 388ms 1.68% std::_Rb_tree::_M_erase 128ms 0.55% 76.09% 380ms 1.64% Node::GetRadius 0 0% 76.09% 348ms 1.50% boost::numeric::ublas::inner_prod (inline) 0 0% 76.09% 346ms 1.50% std::_Rb_tree::_Alloc_node::operator() (inline) 1ms 0.0043% 76.09% 345ms 1.49% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 17ms 0.073% 76.17% 344ms 1.49% boost::numeric::ublas::vector_scalar_binary::evaluate 33ms 0.14% 76.31% 323ms 1.40% boost::numeric::ublas::vector_binary::size (inline) 309ms 1.34% 77.65% 309ms 1.34% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 42ms 0.18% 77.83% 304ms 1.31% std::_Rb_tree::~_Rb_tree (inline) 2ms 0.0086% 77.84% 302ms 1.31% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 77.84% 301ms 1.30% NodesOnlyMesh::ReMesh 295ms 1.28% 79.11% 295ms 1.28% __gnu_cxx::__normal_iterator::operator++ (inline) 2ms 0.0086% 79.12% 290ms 1.25% NodesOnlyMesh::UpdateNodeIndices 0 0% 79.12% 287ms 1.24% boost::numeric::ublas::c_vector::assign (inline) 0 0% 79.12% 285ms 1.23% NodesOnlyMesh::UpdateBoxCollection 6ms 0.026% 79.15% 271ms 1.17% std::_Rb_tree::_M_emplace_hint_unique 93ms 0.4% 79.55% 269ms 1.16% boost::numeric::ublas::vector_inner_prod::apply (inline) 4ms 0.017% 79.57% 268ms 1.16% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 264ms 1.14% 80.71% 264ms 1.14% Node::CheckForNodeAttributes 0 0% 80.71% 258ms 1.12% std::_Rb_tree::_M_drop_node (inline) 2ms 0.0086% 80.72% 253ms 1.09% DistributedBoxCollection::GetProcessOwningNode 1ms 0.0043% 80.72% 246ms 1.06% NodesOnlyMesh::AddNodesToBoxes 0 0% 80.72% 244ms 1.05% std::set::~set (inline) 133ms 0.57% 81.30% 234ms 1.01% _int_malloc 0 0% 81.30% 229ms 0.99% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 81.30% 228ms 0.99% VtkMeshWriter::WriteFiles 18ms 0.078% 81.37% 216ms 0.93% std::__insertion_sort (inline) 1ms 0.0043% 81.38% 214ms 0.93% NodesOnlyMesh::ResizeBoxCollection 13ms 0.056% 81.43% 211ms 0.91% NodesOnlyMesh::IsANodeCloseToDomainBoundary 5ms 0.022% 81.46% 206ms 0.89% std::__new_allocator::deallocate (inline) 0 0% 81.46% 203ms 0.88% vtkStreamingDemandDrivenPipeline::Update 0 0% 81.46% 203ms 0.88% vtkXMLWriterBase::Write 0 0% 81.46% 200ms 0.86% vtkDemandDrivenPipeline::ProcessRequest 108ms 0.47% 81.92% 199ms 0.86% Node::AddNeighbour 1ms 0.0043% 81.93% 199ms 0.86% vtkExecutive::CallAlgorithm 0 0% 81.93% 199ms 0.86% vtkStreamingDemandDrivenPipeline::ProcessRequest 197ms 0.85% 82.78% 197ms 0.85% Node::GetIndex 109ms 0.47% 83.25% 197ms 0.85% boost::shared_ptr::shared_ptr (inline) 0 0% 83.25% 197ms 0.85% vtkCompositeDataPipeline::ExecuteData 0 0% 83.25% 197ms 0.85% vtkDemandDrivenPipeline::ExecuteData 0 0% 83.25% 197ms 0.85% vtkXMLUnstructuredDataWriter::ProcessRequest 91ms 0.39% 83.64% 189ms 0.82% std::__move_median_to_first (inline) 0 0% 83.64% 182ms 0.79% std::allocator_traits::deallocate (inline) 181ms 0.78% 84.42% 181ms 0.78% [libchaste_cell_based.so] 73ms 0.32% 84.74% 180ms 0.78% __GI___libc_free 0 0% 84.74% 177ms 0.77% std::_Rb_tree::_M_put_node (inline) 4ms 0.017% 84.76% 170ms 0.73% CellPropertyCollection::HasProperty 0 0% 84.76% 170ms 0.73% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 84.76% 170ms 0.73% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 169ms 0.73% 85.49% 169ms 0.73% [libchaste_mesh.so] 0 0% 85.49% 168ms 0.73% Cell::HasCellProperty (inline) 5ms 0.022% 85.51% 166ms 0.72% Cell::ReadyToDivide 14ms 0.061% 85.57% 165ms 0.71% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 85.57% 164ms 0.71% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 85.57% 158ms 0.68% boost::numeric::ublas::vector_binary::operator() (inline) 150ms 0.65% 86.22% 150ms 0.65% Node::IsDeleted 8ms 0.035% 86.25% 146ms 0.63% DistributedBoxCollection::GetIsPeriodicAllDims 0 0% 86.25% 145ms 0.63% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 86.25% 145ms 0.63% std::_Rb_tree::clear (inline) 143ms 0.62% 86.87% 145ms 0.63% std::__adjacent_find (inline) 0 0% 86.87% 145ms 0.63% std::__unique (inline) 0 0% 86.87% 145ms 0.63% std::unique (inline) 0 0% 86.87% 144ms 0.62% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 86.87% 144ms 0.62% Cell::GetCellId 7ms 0.03% 86.90% 142ms 0.61% AbstractCellProperty::IsType (inline) 0 0% 86.90% 141ms 0.61% vtkXMLWriter::WriteBinaryData 5ms 0.022% 86.92% 140ms 0.61% boost::numeric::ublas::c_vector::operator[] (inline) 1ms 0.0043% 86.93% 134ms 0.58% std::_Rb_tree::_M_insert_unique 0 0% 86.93% 134ms 0.58% std::set::insert (inline) 0 0% 86.93% 132ms 0.57% vtkXMLWriter::WriteBinaryDataBlock 0 0% 86.93% 132ms 0.57% vtkXMLWriter::WriteBinaryDataInternal 0 0% 86.93% 132ms 0.57% vtkXMLWriter::WriteCompressionBlock 123ms 0.53% 87.46% 123ms 0.53% __ieee754_log_fma 0 0% 87.46% 121ms 0.52% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 87.46% 121ms 0.52% vtkXMLWriter::WritePointsAppendedData 0 0% 87.46% 119ms 0.51% NodeBasedCellPopulation::AcceptCellWriter 3ms 0.013% 87.47% 116ms 0.5% AbstractCellPopulation::SetCellUsingLocationIndex 2ms 0.0086% 87.48% 116ms 0.5% Cell::GetCellProliferativeType 0 0% 87.48% 116ms 0.5% compress2 1ms 0.0043% 87.49% 116ms 0.5% deflate 0 0% 87.49% 116ms 0.5% vtkDataCompressor::Compress 0 0% 87.49% 116ms 0.5% vtkZLibDataCompressor::CompressBuffer