File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 22180ms, 88.59% of 25036ms total Dropped 815 nodes (cum <= 125.18ms) flat flat% sum% cum cum% 0 0% 0% 24884ms 99.39% __libc_start_call_main 0 0% 0% 24884ms 99.39% __libc_start_main_impl 0 0% 0% 24884ms 99.39% _start 0 0% 0% 24869ms 99.33% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 24869ms 99.33% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 24869ms 99.33% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 24869ms 99.33% main 0 0% 0% 24829ms 99.17% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 24829ms 99.17% CxxTest::TestRunner::runTest (inline) 0 0% 0% 24829ms 99.17% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.004% 0.004% 24821ms 99.14% AbstractCellBasedSimulation::Solve 4ms 0.016% 0.02% 14018ms 55.99% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.02% 9553ms 38.16% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.012% 0.032% 9058ms 36.18% ForwardEulerNumericalMethod::UpdateAllNodePositions 9ms 0.036% 0.068% 8888ms 35.50% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.068% 8376ms 33.46% NodeBasedCellPopulation::Update 1132ms 4.52% 4.59% 8000ms 31.95% RepulsionForce::AddForceContribution (partial-inline) 9ms 0.036% 4.63% 6226ms 24.87% DistributedBoxCollection::CalculateInteriorNodePairs 2201ms 8.79% 13.42% 5170ms 20.65% std::_Rb_tree::_M_lower_bound (inline) 0 0% 13.42% 4638ms 18.53% OffLatticeSimulation::ApplyBoundaries 19ms 0.076% 13.49% 4598ms 18.37% NodeAttributes::RemoveDuplicateNeighbours 4ms 0.016% 13.51% 4415ms 17.63% std::__sort (inline) 0 0% 13.51% 4415ms 17.63% std::sort (inline) 180ms 0.72% 14.23% 4133ms 16.51% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 67ms 0.27% 14.50% 3594ms 14.36% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 3ms 0.012% 14.51% 3581ms 14.30% AbstractCellPopulation::Iterator::operator++ (inline) 201ms 0.8% 15.31% 3553ms 14.19% AbstractCellPopulation::Iterator::IsRealCell (inline) 234ms 0.93% 16.24% 3347ms 13.37% std::_Rb_tree::find (inline) 0 0% 16.24% 3347ms 13.37% std::map::find (inline) 27ms 0.11% 16.35% 3044ms 12.16% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2936ms 11.73% 28.08% 2936ms 11.73% std::_Rb_tree::_S_right (inline) 231ms 0.92% 29.00% 2596ms 10.37% std::map::operator[] (partial-inline) 227ms 0.91% 29.91% 2549ms 10.18% std::__introsort_loop 28ms 0.11% 30.02% 2399ms 9.58% PlaneBoundaryCondition::ImposeBoundaryCondition 161ms 0.64% 30.66% 2388ms 9.54% AbstractMesh::GetNode 50ms 0.2% 30.86% 2376ms 9.49% NodesOnlyMesh::GetNodeOrHaloNode 39ms 0.16% 31.02% 2374ms 9.48% AbstractCellPopulation::GetLocationIndexUsingCell 273ms 1.09% 32.11% 2280ms 9.11% DistributedBoxCollection::AddPairsFromBox 0 0% 32.11% 2244ms 8.96% std::__unguarded_partition_pivot (inline) 18ms 0.072% 32.18% 2239ms 8.94% PlaneBoundaryCondition::VerifyBoundaryCondition 94ms 0.38% 32.56% 2229ms 8.90% NodesOnlyMesh::SolveNodeMapping 0 0% 32.56% 2079ms 8.30% std::_Rb_tree::lower_bound (inline) 0 0% 32.56% 2079ms 8.30% std::map::lower_bound (inline) 1010ms 4.03% 36.59% 1986ms 7.93% std::__unguarded_partition (inline) 2ms 0.008% 36.60% 1858ms 7.42% std::__final_insertion_sort (inline) 19ms 0.076% 36.68% 1771ms 7.07% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 23ms 0.092% 36.77% 1748ms 6.98% AbstractCellPopulation::GetCellUsingLocationIndex 88ms 0.35% 37.12% 1662ms 6.64% std::__unguarded_insertion_sort (inline) 658ms 2.63% 39.75% 1632ms 6.52% std::__unguarded_linear_insert (inline) 1422ms 5.68% 45.43% 1422ms 5.68% __gnu_cxx::__normal_iterator::operator-- (inline) 46ms 0.18% 45.61% 1281ms 5.12% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 45.61% 1214ms 4.85% NodeBasedCellPopulation::UpdateCellProcessLocation 45ms 0.18% 45.79% 1176ms 4.70% boost::numeric::ublas::vector_assign (inline) 4ms 0.016% 45.81% 1140ms 4.55% DistributedBoxCollection::CalculateBoundaryNodePairs 296ms 1.18% 46.99% 1055ms 4.21% boost::numeric::ublas::indexing_vector_assign 299ms 1.19% 48.18% 983ms 3.93% __dynamic_cast 45ms 0.18% 48.36% 897ms 3.58% std::_Rb_tree_const_iterator::operator++ (inline) 376ms 1.50% 49.86% 864ms 3.45% NodeAttributes::AddNeighbour 16ms 0.064% 49.93% 859ms 3.43% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 850ms 3.40% 53.32% 850ms 3.40% std::_Rb_tree_increment 17ms 0.068% 53.39% 827ms 3.30% CellPropertyCollection::GetPropertiesType (inline) 380ms 1.52% 54.91% 822ms 3.28% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 54.91% 822ms 3.28% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 54.91% 809ms 3.23% boost::numeric::ublas::norm_2 (inline) 658ms 2.63% 57.54% 809ms 3.23% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 57.54% 809ms 3.23% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 5ms 0.02% 57.56% 793ms 3.17% AbstractCentreBasedCellPopulation::GetDampingConstant 152ms 0.61% 58.16% 789ms 3.15% AbstractMesh::GetVectorFromAtoB 0 0% 58.16% 757ms 3.02% AbstractCellPopulation::WriteResultsToFiles 726ms 2.90% 61.06% 726ms 2.90% boost::numeric::ublas::c_vector::operator() 2ms 0.008% 61.07% 724ms 2.89% AbstractCellBasedSimulation::DoCellBirth 8ms 0.032% 61.10% 662ms 2.64% boost::numeric::ublas::c_vector::operator= (inline) 31ms 0.12% 61.23% 642ms 2.56% std::__copy_move::__copy_m (inline) 0 0% 61.23% 642ms 2.56% std::__copy_move_a (inline) 0 0% 61.23% 642ms 2.56% std::__copy_move_a1 (inline) 0 0% 61.23% 642ms 2.56% std::__copy_move_a2 (inline) 0 0% 61.23% 642ms 2.56% std::copy (inline) 625ms 2.50% 63.72% 625ms 2.50% __memcpy_avx_unaligned_erms 1ms 0.004% 63.73% 615ms 2.46% Cell::GetMutationState 486ms 1.94% 65.67% 612ms 2.44% std::vector::push_back (inline) 115ms 0.46% 66.13% 589ms 2.35% std::__new_allocator::allocate (inline) 34ms 0.14% 66.26% 582ms 2.32% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 66.26% 572ms 2.28% std::allocator_traits::allocate (inline) 239ms 0.95% 67.22% 551ms 2.20% __cxxabiv1::__si_class_type_info::__do_dyncast 54ms 0.22% 67.43% 539ms 2.15% std::_Rb_tree::_M_copy (inline) 0 0% 67.43% 538ms 2.15% std::_Rb_tree::_M_create_node (inline) 182ms 0.73% 68.16% 498ms 1.99% std::_Rb_tree::_M_erase 493ms 1.97% 70.13% 493ms 1.97% __strcmp_avx2 2ms 0.008% 70.14% 492ms 1.97% NodeBasedCellPopulation::WriteVtkResultsToFile 167ms 0.67% 70.81% 483ms 1.93% std::_Rb_tree::_M_clone_node (inline) 3ms 0.012% 70.82% 480ms 1.92% std::set::set (inline) 30ms 0.12% 70.94% 473ms 1.89% operator new 36ms 0.14% 71.08% 471ms 1.88% boost::detail::shared_count::~shared_count (inline) 0 0% 71.08% 471ms 1.88% boost::shared_ptr::~shared_ptr (inline) 0 0% 71.08% 469ms 1.87% std::_Rb_tree::_M_get_node (inline) 0 0% 71.08% 452ms 1.81% AbstractCellBasedSimulation::DoCellRemoval (inline) 4ms 0.016% 71.10% 450ms 1.80% AbstractCellProperty::IsSubType (inline) 3ms 0.012% 71.11% 446ms 1.78% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 124ms 0.5% 71.60% 440ms 1.76% __GI___libc_malloc 436ms 1.74% 73.35% 436ms 1.74% boost::numeric::ublas::same_impl_ex 422ms 1.69% 75.03% 426ms 1.70% boost::detail::sp_counted_base::release 152ms 0.61% 75.64% 405ms 1.62% Node::GetRadius 49ms 0.2% 75.83% 376ms 1.50% std::_Rb_tree::~_Rb_tree (inline) 0 0% 75.83% 370ms 1.48% std::_Rb_tree::_Alloc_node::operator() (inline) 369ms 1.47% 77.31% 369ms 1.47% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 77.31% 337ms 1.35% NodesOnlyMesh::ReMesh 0 0% 77.31% 337ms 1.35% boost::numeric::ublas::c_vector::assign (inline) 0 0% 77.31% 324ms 1.29% NodesOnlyMesh::UpdateNodeIndices 0 0% 77.31% 318ms 1.27% Cell::HasCellProperty (inline) 0 0% 77.31% 318ms 1.27% CellPropertyCollection::HasProperty 9ms 0.036% 77.34% 316ms 1.26% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 77.34% 315ms 1.26% boost::numeric::ublas::inner_prod (inline) 17ms 0.068% 77.41% 314ms 1.25% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 77.41% 314ms 1.25% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 77.41% 309ms 1.23% std::_Rb_tree::_M_drop_node (inline) 298ms 1.19% 78.60% 298ms 1.19% __gnu_cxx::__normal_iterator::operator++ (inline) 6ms 0.024% 78.63% 297ms 1.19% Cell::ReadyToDivide 1ms 0.004% 78.63% 292ms 1.17% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 16ms 0.064% 78.69% 287ms 1.15% boost::numeric::ublas::vector_binary::size (inline) 8ms 0.032% 78.73% 286ms 1.14% std::_Rb_tree::_M_emplace_hint_unique 8ms 0.032% 78.76% 279ms 1.11% DistributedBoxCollection::GetProcessOwningNode 0 0% 78.76% 277ms 1.11% std::set::~set (inline) 143ms 0.57% 79.33% 275ms 1.10% _int_malloc 0 0% 79.33% 270ms 1.08% NodesOnlyMesh::UpdateBoxCollection 9ms 0.036% 79.37% 268ms 1.07% std::__new_allocator::deallocate (inline) 105ms 0.42% 79.79% 259ms 1.03% boost::numeric::ublas::vector_inner_prod::apply (inline) 258ms 1.03% 80.82% 258ms 1.03% Node::CheckForNodeAttributes 110ms 0.44% 81.25% 255ms 1.02% std::__move_median_to_first (inline) 103ms 0.41% 81.67% 244ms 0.97% __GI___libc_free 0 0% 81.67% 241ms 0.96% std::allocator_traits::deallocate (inline) 1ms 0.004% 81.67% 236ms 0.94% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 81.67% 236ms 0.94% std::_Rb_tree::_M_put_node (inline) 0 0% 81.67% 231ms 0.92% VtkMeshWriter::WriteFiles 0 0% 81.67% 215ms 0.86% NodesOnlyMesh::AddNodesToBoxes 210ms 0.84% 82.51% 210ms 0.84% boost::shared_ptr::operator-> (inline) 6ms 0.024% 82.53% 208ms 0.83% AbstractCellProperty::IsType (inline) 207ms 0.83% 83.36% 207ms 0.83% Node::GetIndex 0 0% 83.36% 203ms 0.81% vtkStreamingDemandDrivenPipeline::Update 0 0% 83.36% 203ms 0.81% vtkXMLWriterBase::Write 104ms 0.42% 83.78% 201ms 0.8% boost::shared_ptr::shared_ptr (inline) 0 0% 83.78% 201ms 0.8% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 83.78% 200ms 0.8% vtkDemandDrivenPipeline::ProcessRequest 0 0% 83.78% 200ms 0.8% vtkExecutive::CallAlgorithm 0 0% 83.78% 199ms 0.79% vtkCompositeDataPipeline::ExecuteData 0 0% 83.78% 199ms 0.79% vtkDemandDrivenPipeline::ExecuteData 0 0% 83.78% 199ms 0.79% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 83.78% 195ms 0.78% std::_Rb_tree::clear (inline) 12ms 0.048% 83.82% 194ms 0.77% std::__insertion_sort (inline) 0 0% 83.82% 192ms 0.77% NodesOnlyMesh::ResizeBoxCollection 14ms 0.056% 83.88% 191ms 0.76% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 83.88% 175ms 0.7% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 83.88% 175ms 0.7% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 83.88% 171ms 0.68% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 83.88% 168ms 0.67% std::_Rb_tree::_Auto_node::_Auto_node (inline) 10ms 0.04% 83.92% 164ms 0.66% boost::numeric::ublas::vector_reference::operator() (inline) 68ms 0.27% 84.19% 161ms 0.64% AbstractCellProperty::IsSame 2ms 0.008% 84.20% 160ms 0.64% Cell::GetCellId 158ms 0.63% 84.83% 158ms 0.63% [libchaste_cell_based.so] 1ms 0.004% 84.83% 154ms 0.62% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 145ms 0.58% 85.41% 149ms 0.6% std::__adjacent_find (inline) 0 0% 85.41% 149ms 0.6% std::__unique (inline) 0 0% 85.41% 149ms 0.6% std::unique (inline) 147ms 0.59% 86.00% 147ms 0.59% Node::rGetLocation 0 0% 86.00% 147ms 0.59% boost::numeric::ublas::vector_binary::operator() (inline) 146ms 0.58% 86.58% 146ms 0.58% [libchaste_mesh.so] 6ms 0.024% 86.61% 146ms 0.58% boost::numeric::ublas::c_vector::operator[] (inline) 81ms 0.32% 86.93% 145ms 0.58% Node::AddNeighbour 144ms 0.58% 87.51% 144ms 0.58% Node::IsDeleted 0 0% 87.51% 143ms 0.57% std::map::clear (inline) 122ms 0.49% 87.99% 141ms 0.56% _int_free 5ms 0.02% 88.01% 139ms 0.56% DistributedBoxCollection::GetIsPeriodicAllDims 0 0% 88.01% 139ms 0.56% vtkXMLWriter::WriteBinaryData 0 0% 88.01% 136ms 0.54% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 4ms 0.016% 88.03% 133ms 0.53% AbstractCellPopulation::SetCellUsingLocationIndex 0 0% 88.03% 132ms 0.53% vtkXMLWriter::WriteBinaryDataBlock 0 0% 88.03% 132ms 0.53% vtkXMLWriter::WriteBinaryDataInternal 0 0% 88.03% 132ms 0.53% vtkXMLWriter::WriteCompressionBlock 57ms 0.23% 88.26% 127ms 0.51% AbstractCellCycleModel::GetAge 84ms 0.34% 88.59% 126ms 0.5% std::vector::emplace_back (inline)