File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 16368ms, 89.69% of 18249ms total Dropped 703 nodes (cum <= 91.25ms) flat flat% sum% cum cum% 0 0% 0% 18178ms 99.61% __libc_start_call_main 0 0% 0% 18178ms 99.61% __libc_start_main_impl 0 0% 0% 18178ms 99.61% _start 0 0% 0% 18165ms 99.54% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 18165ms 99.54% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 18165ms 99.54% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 18165ms 99.54% main 0 0% 0% 18126ms 99.33% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 18126ms 99.33% CxxTest::TestRunner::runTest (inline) 0 0% 0% 18126ms 99.33% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 18118ms 99.28% AbstractCellBasedSimulation::Solve 1ms 0.0055% 0.0055% 10259ms 56.22% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0055% 6922ms 37.93% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0055% 0.011% 6368ms 34.90% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.044% 0.055% 6222ms 34.10% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.055% 6188ms 33.91% NodeBasedCellPopulation::Update 1038ms 5.69% 5.74% 5713ms 31.31% RepulsionForce::AddForceContribution (partial-inline) 8ms 0.044% 5.79% 4576ms 25.08% DistributedBoxCollection::CalculateInteriorNodePairs 1805ms 9.89% 15.68% 3912ms 21.44% std::_Rb_tree::_M_lower_bound (inline) 0 0% 15.68% 3667ms 20.09% OffLatticeSimulation::ApplyBoundaries 4ms 0.022% 15.70% 3534ms 19.37% NodeAttributes::RemoveDuplicateNeighbours 3ms 0.016% 15.72% 3405ms 18.66% std::__sort (inline) 0 0% 15.72% 3405ms 18.66% std::sort (inline) 66ms 0.36% 16.08% 2661ms 14.58% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 193ms 1.06% 17.14% 2634ms 14.43% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 182ms 1% 18.13% 2590ms 14.19% std::_Rb_tree::find (inline) 0 0% 18.13% 2590ms 14.19% std::map::find (inline) 2ms 0.011% 18.14% 2442ms 13.38% AbstractCellPopulation::Iterator::operator++ (inline) 89ms 0.49% 18.63% 2427ms 13.30% AbstractCellPopulation::Iterator::IsRealCell (inline) 21ms 0.12% 18.75% 2159ms 11.83% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2062ms 11.30% 30.05% 2062ms 11.30% std::_Rb_tree::_S_right (inline) 32ms 0.18% 30.22% 1952ms 10.70% PlaneBoundaryCondition::ImposeBoundaryCondition 44ms 0.24% 30.46% 1906ms 10.44% AbstractCellPopulation::GetLocationIndexUsingCell 122ms 0.67% 31.13% 1901ms 10.42% std::__introsort_loop 153ms 0.84% 31.97% 1895ms 10.38% std::map::operator[] (partial-inline) 61ms 0.33% 32.30% 1843ms 10.10% NodesOnlyMesh::GetNodeOrHaloNode 131ms 0.72% 33.02% 1835ms 10.06% AbstractMesh::GetNode 0 0% 33.02% 1726ms 9.46% std::__unguarded_partition_pivot (inline) 6ms 0.033% 33.05% 1715ms 9.40% PlaneBoundaryCondition::VerifyBoundaryCondition 96ms 0.53% 33.58% 1708ms 9.36% NodesOnlyMesh::SolveNodeMapping 760ms 4.16% 37.74% 1549ms 8.49% std::__unguarded_partition (inline) 0 0% 37.74% 1537ms 8.42% std::_Rb_tree::lower_bound (inline) 0 0% 37.74% 1537ms 8.42% std::map::lower_bound (inline) 1ms 0.0055% 37.75% 1498ms 8.21% std::__final_insertion_sort (inline) 119ms 0.65% 38.40% 1493ms 8.18% DistributedBoxCollection::AddPairsFromBox 91ms 0.5% 38.90% 1320ms 7.23% std::__unguarded_insertion_sort (inline) 470ms 2.58% 41.48% 1258ms 6.89% std::__unguarded_linear_insert (inline) 14ms 0.077% 41.55% 1178ms 6.46% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 25ms 0.14% 41.69% 1161ms 6.36% AbstractCellPopulation::GetCellUsingLocationIndex 1106ms 6.06% 47.75% 1106ms 6.06% __gnu_cxx::__normal_iterator::operator-- (inline) 33ms 0.18% 47.93% 958ms 5.25% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 47.93% 897ms 4.92% NodeBasedCellPopulation::UpdateCellProcessLocation 3ms 0.016% 47.95% 850ms 4.66% boost::numeric::ublas::vector_assign (inline) 5ms 0.027% 47.98% 847ms 4.64% DistributedBoxCollection::CalculateBoundaryNodePairs 152ms 0.83% 48.81% 772ms 4.23% boost::numeric::ublas::indexing_vector_assign 11ms 0.06% 48.87% 755ms 4.14% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 294ms 1.61% 50.48% 690ms 3.78% DistributedBoxCollection::CalculateContainingBox (partial-inline) 135ms 0.74% 51.22% 632ms 3.46% AbstractMesh::GetVectorFromAtoB 0 0% 51.22% 630ms 3.45% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 51.22% 606ms 3.32% boost::numeric::ublas::norm_2 (inline) 491ms 2.69% 53.91% 606ms 3.32% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 53.91% 606ms 3.32% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 149ms 0.82% 54.73% 598ms 3.28% NodeAttributes::AddNeighbour 3ms 0.016% 54.74% 588ms 3.22% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 54.74% 575ms 3.15% AbstractCellPopulation::WriteResultsToFiles 23ms 0.13% 54.87% 573ms 3.14% std::__copy_move::__copy_m (inline) 0 0% 54.87% 573ms 3.14% std::__copy_move_a (inline) 0 0% 54.87% 573ms 3.14% std::__copy_move_a1 (inline) 0 0% 54.87% 573ms 3.14% std::__copy_move_a2 (inline) 0 0% 54.87% 573ms 3.14% std::copy (inline) 564ms 3.09% 57.96% 564ms 3.09% __memcpy_avx512_unaligned_erms 3ms 0.016% 57.98% 559ms 3.06% CellPropertyCollection::GetPropertiesType (inline) 542ms 2.97% 60.95% 542ms 2.97% boost::numeric::ublas::c_vector::operator() 447ms 2.45% 63.40% 497ms 2.72% std::vector::push_back (inline) 3ms 0.016% 63.41% 470ms 2.58% AbstractCentreBasedCellPopulation::GetDampingConstant 25ms 0.14% 63.55% 458ms 2.51% std::_Rb_tree_const_iterator::operator++ (inline) 456ms 2.50% 66.05% 456ms 2.50% boost::numeric::ublas::same_impl_ex 0 0% 66.05% 419ms 2.30% AbstractCellProperty::IsSubType (inline) 137ms 0.75% 66.80% 419ms 2.30% __dynamic_cast 418ms 2.29% 69.09% 418ms 2.29% std::_Rb_tree_increment 20ms 0.11% 69.20% 403ms 2.21% std::_Rb_tree::_Rb_tree (partial-inline) 83ms 0.45% 69.65% 401ms 2.20% std::__new_allocator::allocate (inline) 0 0% 69.65% 384ms 2.10% AbstractCellBasedSimulation::DoCellRemoval (inline) 1ms 0.0055% 69.66% 381ms 2.09% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 69.66% 380ms 2.08% std::allocator_traits::allocate (inline) 41ms 0.22% 69.88% 376ms 2.06% std::_Rb_tree::_M_copy (inline) 24ms 0.13% 70.01% 375ms 2.05% boost::detail::shared_count::~shared_count (inline) 0 0% 70.01% 375ms 2.05% boost::shared_ptr::~shared_ptr (inline) 1ms 0.0055% 70.02% 373ms 2.04% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 70.02% 370ms 2.03% std::_Rb_tree::_M_create_node (inline) 5ms 0.027% 70.05% 353ms 1.93% Cell::GetMutationState 2ms 0.011% 70.06% 349ms 1.91% AbstractCellBasedSimulation::DoCellBirth 4ms 0.022% 70.08% 342ms 1.87% std::set::set (inline) 335ms 1.84% 71.92% 341ms 1.87% boost::detail::sp_counted_base::release 94ms 0.52% 72.43% 327ms 1.79% std::_Rb_tree::_M_clone_node (inline) 0 0% 72.43% 327ms 1.79% std::_Rb_tree::_M_get_node (inline) 28ms 0.15% 72.58% 311ms 1.70% operator new 70ms 0.38% 72.97% 310ms 1.70% Node::GetRadius 79ms 0.43% 73.40% 306ms 1.68% std::_Rb_tree::_M_erase 0 0% 73.40% 303ms 1.66% boost::numeric::ublas::inner_prod (inline) 1ms 0.0055% 73.41% 303ms 1.66% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 21ms 0.12% 73.52% 302ms 1.65% boost::numeric::ublas::vector_scalar_binary::evaluate 71ms 0.39% 73.91% 294ms 1.61% boost::numeric::ublas::vector_binary::size (inline) 284ms 1.56% 75.47% 284ms 1.56% __gnu_cxx::__normal_iterator::operator++ (inline) 87ms 0.48% 75.94% 274ms 1.50% __GI___libc_malloc 0 0% 75.94% 271ms 1.49% std::_Rb_tree::_Alloc_node::operator() (inline) 106ms 0.58% 76.52% 255ms 1.40% boost::numeric::ublas::vector_inner_prod::apply (inline) 5ms 0.027% 76.55% 246ms 1.35% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 76.55% 245ms 1.34% boost::numeric::ublas::c_vector::assign (inline) 244ms 1.34% 77.89% 244ms 1.34% Node::CheckForNodeAttributes 244ms 1.34% 79.23% 244ms 1.34% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 79.23% 243ms 1.33% NodesOnlyMesh::ReMesh 2ms 0.011% 79.24% 237ms 1.30% NodesOnlyMesh::UpdateNodeIndices 4ms 0.022% 79.26% 236ms 1.29% NodeBasedCellPopulation::UpdateMapsAfterRemesh 8ms 0.044% 79.30% 228ms 1.25% DistributedBoxCollection::GetProcessOwningNode 0 0% 79.30% 225ms 1.23% NodesOnlyMesh::UpdateBoxCollection 22ms 0.12% 79.42% 221ms 1.21% std::_Rb_tree::~_Rb_tree (inline) 0 0% 79.42% 220ms 1.21% std::_Rb_tree::_M_drop_node (inline) 8ms 0.044% 79.47% 205ms 1.12% std::_Rb_tree::_M_emplace_hint_unique 108ms 0.59% 80.06% 198ms 1.08% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 80.06% 189ms 1.04% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 2ms 0.011% 80.07% 187ms 1.02% NodesOnlyMesh::AddNodesToBoxes 0 0% 80.07% 187ms 1.02% VtkMeshWriter::WriteFiles 2ms 0.011% 80.08% 183ms 1.00% std::__new_allocator::deallocate (inline) 18ms 0.099% 80.18% 177ms 0.97% std::__insertion_sort (inline) 77ms 0.42% 80.60% 176ms 0.96% std::__move_median_to_first (inline) 92ms 0.5% 81.11% 175ms 0.96% boost::shared_ptr::shared_ptr (inline) 173ms 0.95% 82.05% 173ms 0.95% [libchaste_mesh.so] 173ms 0.95% 83.00% 173ms 0.95% __strcmp_evex 0 0% 83.00% 170ms 0.93% std::_Rb_tree::_M_put_node (inline) 0 0% 83.00% 170ms 0.93% std::allocator_traits::deallocate (inline) 0 0% 83.00% 169ms 0.93% std::set::~set (inline) 168ms 0.92% 83.92% 168ms 0.92% Node::GetIndex 0 0% 83.92% 168ms 0.92% vtkStreamingDemandDrivenPipeline::Update 0 0% 83.92% 168ms 0.92% vtkXMLWriterBase::Write 0 0% 83.92% 166ms 0.91% vtkDemandDrivenPipeline::ProcessRequest 143ms 0.78% 84.71% 165ms 0.9% Node::AddNeighbour 8ms 0.044% 84.75% 164ms 0.9% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 84.75% 164ms 0.9% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 84.75% 161ms 0.88% vtkDemandDrivenPipeline::ExecuteData 44ms 0.24% 84.99% 160ms 0.88% __GI___libc_free 1ms 0.0055% 85.00% 160ms 0.88% vtkCompositeDataPipeline::ExecuteData 0 0% 85.00% 160ms 0.88% vtkExecutive::CallAlgorithm 0 0% 85.00% 159ms 0.87% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 85.00% 156ms 0.85% boost::numeric::ublas::vector_binary::operator() (inline) 79ms 0.43% 85.43% 147ms 0.81% _int_malloc 0 0% 85.43% 142ms 0.78% Cell::GetCellId 0 0% 85.43% 141ms 0.77% NodesOnlyMesh::ResizeBoxCollection 6ms 0.033% 85.46% 140ms 0.77% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 85.46% 136ms 0.75% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.46% 136ms 0.75% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 85.46% 134ms 0.73% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 85.46% 126ms 0.69% std::_Rb_tree::clear (inline) 119ms 0.65% 86.11% 119ms 0.65% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 1ms 0.0055% 86.12% 117ms 0.64% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 111ms 0.61% 86.73% 115ms 0.63% _int_free 3ms 0.016% 86.74% 113ms 0.62% boost::numeric::ublas::c_vector::operator[] (inline) 111ms 0.61% 87.35% 111ms 0.61% __ieee754_log_fma 0 0% 87.35% 111ms 0.61% vtkXMLWriter::WriteBinaryData 110ms 0.6% 87.96% 110ms 0.6% std::__adjacent_find (inline) 0 0% 87.96% 110ms 0.6% std::__unique (inline) 0 0% 87.96% 110ms 0.6% std::unique (inline) 0 0% 87.96% 110ms 0.6% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.96% 110ms 0.6% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.96% 110ms 0.6% vtkXMLWriter::WriteCompressionBlock 108ms 0.59% 88.55% 108ms 0.59% Node::IsDeleted 0 0% 88.55% 105ms 0.58% vtkXMLWriter::WritePointsAppendedData 6ms 0.033% 88.58% 104ms 0.57% DistributedBoxCollection::GetIsPeriodicAllDims 3ms 0.016% 88.60% 101ms 0.55% AbstractNumericalMethod::SafeNodePositionUpdate 101ms 0.55% 89.15% 101ms 0.55% [libchaste_cell_based.so] 1ms 0.0055% 89.16% 99ms 0.54% AbstractCellPopulation::SetCellUsingLocationIndex 0 0% 89.16% 99ms 0.54% std::_Rb_tree::_Auto_node::_Auto_node (inline) 3ms 0.016% 89.17% 98ms 0.54% Cell::GetCellProliferativeType 94ms 0.52% 89.69% 94ms 0.52% Node::rGetLocation 1ms 0.0055% 89.69% 93ms 0.51% NodeBasedCellPopulation::AcceptCellWriter