File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20540ms, 89.41% of 22973ms total Dropped 777 nodes (cum <= 114.86ms) flat flat% sum% cum cum% 0 0% 0% 22854ms 99.48% __libc_start_call_main 0 0% 0% 22854ms 99.48% __libc_start_main_impl 0 0% 0% 22854ms 99.48% _start 0 0% 0% 22839ms 99.42% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 22839ms 99.42% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 22839ms 99.42% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 22839ms 99.42% main 0 0% 0% 22805ms 99.27% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 22805ms 99.27% CxxTest::TestRunner::runTest (inline) 0 0% 0% 22805ms 99.27% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 22797ms 99.23% AbstractCellBasedSimulation::Solve 2ms 0.0087% 0.0087% 13030ms 56.72% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0087% 8610ms 37.48% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.017% 0.026% 8241ms 35.87% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.044% 0.07% 8079ms 35.17% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.0044% 0.074% 7602ms 33.09% NodeBasedCellPopulation::Update 1181ms 5.14% 5.21% 7454ms 32.45% RepulsionForce::AddForceContribution (partial-inline) 8ms 0.035% 5.25% 5592ms 24.34% DistributedBoxCollection::CalculateInteriorNodePairs 2063ms 8.98% 14.23% 4939ms 21.50% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.0044% 14.23% 4531ms 19.72% OffLatticeSimulation::ApplyBoundaries 15ms 0.065% 14.30% 4506ms 19.61% NodeAttributes::RemoveDuplicateNeighbours 6ms 0.026% 14.33% 4335ms 18.87% std::__sort (inline) 0 0% 14.33% 4335ms 18.87% std::sort (inline) 154ms 0.67% 15.00% 3722ms 16.20% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 6ms 0.026% 15.02% 3428ms 14.92% AbstractCellPopulation::Iterator::operator++ (inline) 206ms 0.9% 15.92% 3402ms 14.81% AbstractCellPopulation::Iterator::IsRealCell (inline) 59ms 0.26% 16.18% 3365ms 14.65% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 223ms 0.97% 17.15% 3253ms 14.16% std::_Rb_tree::find (inline) 0 0% 17.15% 3253ms 14.16% std::map::find (inline) 23ms 0.1% 17.25% 2879ms 12.53% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2841ms 12.37% 29.61% 2841ms 12.37% std::_Rb_tree::_S_right (inline) 146ms 0.64% 30.25% 2467ms 10.74% std::__introsort_loop 257ms 1.12% 31.37% 2445ms 10.64% std::map::operator[] (partial-inline) 32ms 0.14% 31.51% 2373ms 10.33% PlaneBoundaryCondition::ImposeBoundaryCondition 140ms 0.61% 32.12% 2351ms 10.23% AbstractMesh::GetNode 46ms 0.2% 32.32% 2341ms 10.19% NodesOnlyMesh::GetNodeOrHaloNode 0 0% 32.32% 2242ms 9.76% std::__unguarded_partition_pivot (inline) 26ms 0.11% 32.43% 2240ms 9.75% AbstractCellPopulation::GetLocationIndexUsingCell 77ms 0.34% 32.76% 2214ms 9.64% NodesOnlyMesh::SolveNodeMapping 19ms 0.083% 32.85% 2157ms 9.39% PlaneBoundaryCondition::VerifyBoundaryCondition 1004ms 4.37% 37.22% 2024ms 8.81% std::__unguarded_partition (inline) 0 0% 37.22% 1936ms 8.43% std::_Rb_tree::lower_bound (inline) 0 0% 37.22% 1936ms 8.43% std::map::lower_bound (inline) 0 0% 37.22% 1859ms 8.09% std::__final_insertion_sort (inline) 148ms 0.64% 37.86% 1732ms 7.54% DistributedBoxCollection::AddPairsFromBox 84ms 0.37% 38.23% 1646ms 7.16% std::__unguarded_insertion_sort (inline) 564ms 2.46% 40.68% 1614ms 7.03% std::__unguarded_linear_insert (inline) 1500ms 6.53% 47.21% 1500ms 6.53% __gnu_cxx::__normal_iterator::operator-- (inline) 21ms 0.091% 47.30% 1499ms 6.53% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 32ms 0.14% 47.44% 1473ms 6.41% AbstractCellPopulation::GetCellUsingLocationIndex 54ms 0.24% 47.68% 1262ms 5.49% boost::numeric::ublas::c_vector::c_vector (partial-inline) 1ms 0.0044% 47.68% 1149ms 5.00% NodeBasedCellPopulation::UpdateCellProcessLocation 48ms 0.21% 47.89% 1126ms 4.90% boost::numeric::ublas::vector_assign (inline) 6ms 0.026% 47.92% 1066ms 4.64% DistributedBoxCollection::CalculateBoundaryNodePairs 268ms 1.17% 49.08% 1009ms 4.39% boost::numeric::ublas::indexing_vector_assign 238ms 1.04% 50.12% 893ms 3.89% __dynamic_cast 167ms 0.73% 50.85% 795ms 3.46% AbstractMesh::GetVectorFromAtoB 16ms 0.07% 50.92% 781ms 3.40% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 50.92% 767ms 3.34% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 50.92% 751ms 3.27% boost::numeric::ublas::norm_2 (inline) 589ms 2.56% 53.48% 751ms 3.27% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 53.48% 751ms 3.27% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 336ms 1.46% 54.94% 749ms 3.26% DistributedBoxCollection::CalculateContainingBox (partial-inline) 205ms 0.89% 55.84% 739ms 3.22% NodeAttributes::AddNeighbour 7ms 0.03% 55.87% 714ms 3.11% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 55.87% 700ms 3.05% AbstractCellPopulation::WriteResultsToFiles 34ms 0.15% 56.01% 691ms 3.01% std::__copy_move::__copy_m (inline) 0 0% 56.01% 691ms 3.01% std::__copy_move_a (inline) 0 0% 56.01% 691ms 3.01% std::__copy_move_a1 (inline) 0 0% 56.01% 691ms 3.01% std::__copy_move_a2 (inline) 0 0% 56.01% 690ms 3.00% std::copy (inline) 674ms 2.93% 58.95% 674ms 2.93% __memcpy_avx_unaligned_erms 670ms 2.92% 61.86% 670ms 2.92% boost::numeric::ublas::c_vector::operator() 532ms 2.32% 64.18% 592ms 2.58% std::vector::push_back (inline) 2ms 0.0087% 64.19% 562ms 2.45% AbstractCellBasedSimulation::DoCellBirth 3ms 0.013% 64.20% 558ms 2.43% AbstractCentreBasedCellPopulation::GetDampingConstant 5ms 0.022% 64.22% 531ms 2.31% CellPropertyCollection::GetPropertiesType (inline) 225ms 0.98% 65.20% 524ms 2.28% __cxxabiv1::__si_class_type_info::__do_dyncast 46ms 0.2% 65.40% 506ms 2.20% std::_Rb_tree_const_iterator::operator++ (inline) 29ms 0.13% 65.53% 490ms 2.13% boost::detail::shared_count::~shared_count (inline) 0 0% 65.53% 490ms 2.13% boost::shared_ptr::~shared_ptr (inline) 484ms 2.11% 67.64% 484ms 2.11% boost::numeric::ublas::same_impl_ex 66ms 0.29% 67.92% 471ms 2.05% std::__new_allocator::allocate (inline) 464ms 2.02% 69.94% 464ms 2.02% __strcmp_avx2 456ms 1.98% 71.93% 456ms 1.98% std::_Rb_tree_increment 0 0% 71.93% 456ms 1.98% std::allocator_traits::allocate (inline) 1ms 0.0044% 71.93% 450ms 1.96% NodeBasedCellPopulation::WriteVtkResultsToFile 441ms 1.92% 73.85% 445ms 1.94% boost::detail::sp_counted_base::release 0 0% 73.85% 444ms 1.93% AbstractCellBasedSimulation::DoCellRemoval (inline) 30ms 0.13% 73.98% 442ms 1.92% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 73.98% 433ms 1.88% std::_Rb_tree::_M_create_node (inline) 5ms 0.022% 74.00% 429ms 1.87% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 24ms 0.1% 74.11% 400ms 1.74% operator new 37ms 0.16% 74.27% 395ms 1.72% std::_Rb_tree::_M_copy (inline) 2ms 0.0087% 74.28% 394ms 1.72% AbstractCellProperty::IsSubType (inline) 147ms 0.64% 74.92% 390ms 1.70% Node::GetRadius 0 0% 74.92% 388ms 1.69% std::_Rb_tree::_M_get_node (inline) 120ms 0.52% 75.44% 377ms 1.64% std::_Rb_tree::_M_erase 2ms 0.0087% 75.45% 367ms 1.60% Cell::GetMutationState 4ms 0.017% 75.47% 367ms 1.60% std::set::set (inline) 103ms 0.45% 75.92% 366ms 1.59% __GI___libc_malloc 360ms 1.57% 77.48% 360ms 1.57% __gnu_cxx::__normal_iterator::operator++ (inline) 124ms 0.54% 78.02% 358ms 1.56% std::_Rb_tree::_M_clone_node (inline) 0 0% 78.02% 343ms 1.49% boost::numeric::ublas::inner_prod (inline) 3ms 0.013% 78.04% 342ms 1.49% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 11ms 0.048% 78.08% 339ms 1.48% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 78.08% 329ms 1.43% boost::numeric::ublas::c_vector::assign (inline) 325ms 1.41% 79.50% 325ms 1.41% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 3ms 0.013% 79.51% 324ms 1.41% NodeBasedCellPopulation::UpdateMapsAfterRemesh 20ms 0.087% 79.60% 311ms 1.35% boost::numeric::ublas::vector_binary::size (inline) 0 0% 79.60% 296ms 1.29% NodesOnlyMesh::ReMesh 4ms 0.017% 79.62% 286ms 1.24% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 106ms 0.46% 80.08% 285ms 1.24% boost::numeric::ublas::vector_inner_prod::apply (inline) 2ms 0.0087% 80.09% 282ms 1.23% NodesOnlyMesh::UpdateNodeIndices 32ms 0.14% 80.22% 280ms 1.22% std::_Rb_tree::~_Rb_tree (inline) 0 0% 80.22% 279ms 1.21% std::_Rb_tree::_Alloc_node::operator() (inline) 6ms 0.026% 80.25% 270ms 1.18% DistributedBoxCollection::GetProcessOwningNode 253ms 1.10% 81.35% 253ms 1.10% Node::CheckForNodeAttributes 7ms 0.03% 81.38% 251ms 1.09% std::_Rb_tree::_M_emplace_hint_unique 0 0% 81.38% 249ms 1.08% std::_Rb_tree::_M_drop_node (inline) 0 0% 81.38% 244ms 1.06% NodesOnlyMesh::UpdateBoxCollection 5ms 0.022% 81.40% 225ms 0.98% std::__new_allocator::deallocate (inline) 147ms 0.64% 82.04% 223ms 0.97% _int_malloc 0 0% 82.04% 222ms 0.97% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 82.04% 222ms 0.97% VtkMeshWriter::WriteFiles 18ms 0.078% 82.12% 213ms 0.93% std::__insertion_sort (inline) 91ms 0.4% 82.52% 211ms 0.92% std::__move_median_to_first (inline) 0 0% 82.52% 204ms 0.89% std::set::~set (inline) 0 0% 82.52% 201ms 0.87% vtkStreamingDemandDrivenPipeline::Update 0 0% 82.52% 201ms 0.87% vtkXMLWriterBase::Write 0 0% 82.52% 200ms 0.87% NodesOnlyMesh::AddNodesToBoxes 66ms 0.29% 82.81% 198ms 0.86% __GI___libc_free 0 0% 82.81% 198ms 0.86% vtkDemandDrivenPipeline::ProcessRequest 0 0% 82.81% 198ms 0.86% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 82.81% 196ms 0.85% std::allocator_traits::deallocate (inline) 0 0% 82.81% 196ms 0.85% vtkDemandDrivenPipeline::ExecuteData 0 0% 82.81% 195ms 0.85% NodesOnlyMesh::ResizeBoxCollection 0 0% 82.81% 195ms 0.85% vtkExecutive::CallAlgorithm 7ms 0.03% 82.84% 194ms 0.84% CellPropertyCollection::HasProperty 14ms 0.061% 82.90% 194ms 0.84% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 82.90% 194ms 0.84% vtkCompositeDataPipeline::ExecuteData 0 0% 82.90% 194ms 0.84% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 82.90% 192ms 0.84% Cell::HasCellProperty (inline) 0 0% 82.90% 192ms 0.84% std::_Rb_tree::_M_put_node (inline) 178ms 0.77% 83.67% 178ms 0.77% [libchaste_cell_based.so] 81ms 0.35% 84.02% 176ms 0.77% boost::shared_ptr::shared_ptr (inline) 3ms 0.013% 84.04% 172ms 0.75% Cell::ReadyToDivide 14ms 0.061% 84.10% 166ms 0.72% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 84.10% 163ms 0.71% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 84.10% 163ms 0.71% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 5ms 0.022% 84.12% 162ms 0.71% AbstractCellProperty::IsType (inline) 161ms 0.7% 84.82% 161ms 0.7% Node::GetIndex 0 0% 84.82% 159ms 0.69% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 84.82% 154ms 0.67% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 84.82% 154ms 0.67% std::_Rb_tree::_Auto_node::_Auto_node (inline) 15ms 0.065% 84.89% 149ms 0.65% DistributedBoxCollection::GetIsPeriodicAllDims 147ms 0.64% 85.53% 147ms 0.64% [libchaste_mesh.so] 2ms 0.0087% 85.54% 142ms 0.62% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 140ms 0.61% 86.14% 141ms 0.61% std::__adjacent_find (inline) 0 0% 86.14% 141ms 0.61% std::__unique (inline) 0 0% 86.14% 141ms 0.61% std::unique (inline) 0 0% 86.14% 140ms 0.61% std::_Rb_tree::clear (inline) 71ms 0.31% 86.45% 139ms 0.61% Node::AddNeighbour 0 0% 86.45% 139ms 0.61% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 4ms 0.017% 86.47% 136ms 0.59% AbstractCellPopulation::SetCellUsingLocationIndex 0 0% 86.47% 134ms 0.58% vtkXMLWriter::WriteBinaryData 116ms 0.5% 86.98% 132ms 0.57% _int_free 0 0% 86.98% 128ms 0.56% vtkXMLWriter::WriteBinaryDataBlock 0 0% 86.98% 128ms 0.56% vtkXMLWriter::WriteBinaryDataInternal 0 0% 86.98% 128ms 0.56% vtkXMLWriter::WriteCompressionBlock 127ms 0.55% 87.53% 127ms 0.55% Node::IsDeleted 127ms 0.55% 88.08% 127ms 0.55% boost::shared_ptr::operator-> (inline) 54ms 0.24% 88.32% 126ms 0.55% AbstractCellProperty::IsSame 10ms 0.044% 88.36% 125ms 0.54% boost::numeric::ublas::c_vector::operator[] (inline) 123ms 0.54% 88.90% 123ms 0.54% __ieee754_log_fma 0 0% 88.90% 123ms 0.54% vtkXMLWriter::WritePointsAppendedData 118ms 0.51% 89.41% 118ms 0.51% Node::rGetLocation