File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20863ms, 89.43% of 23328ms total Dropped 743 nodes (cum <= 116.64ms) flat flat% sum% cum cum% 0 0% 0% 23189ms 99.40% __libc_start_call_main 0 0% 0% 23189ms 99.40% __libc_start_main_impl 0 0% 0% 23189ms 99.40% _start 0 0% 0% 23174ms 99.34% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 23174ms 99.34% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 23174ms 99.34% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 23174ms 99.34% main 0 0% 0% 23137ms 99.18% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 23137ms 99.18% CxxTest::TestRunner::runTest (inline) 0 0% 0% 23137ms 99.18% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 23128ms 99.14% AbstractCellBasedSimulation::Solve 0 0% 0% 13154ms 56.39% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0% 8779ms 37.63% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.013% 0.013% 8306ms 35.61% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.034% 0.047% 8136ms 34.88% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.047% 7738ms 33.17% NodeBasedCellPopulation::Update 1219ms 5.23% 5.27% 7473ms 32.03% RepulsionForce::AddForceContribution (partial-inline) 5ms 0.021% 5.29% 5713ms 24.49% DistributedBoxCollection::CalculateInteriorNodePairs 2052ms 8.80% 14.09% 4921ms 21.09% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.0043% 14.09% 4561ms 19.55% OffLatticeSimulation::ApplyBoundaries 21ms 0.09% 14.18% 4468ms 19.15% NodeAttributes::RemoveDuplicateNeighbours 6ms 0.026% 14.21% 4288ms 18.38% std::__sort (inline) 0 0% 14.21% 4288ms 18.38% std::sort (inline) 178ms 0.76% 14.97% 3849ms 16.50% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 3ms 0.013% 14.99% 3418ms 14.65% AbstractCellPopulation::Iterator::operator++ (inline) 198ms 0.85% 15.84% 3391ms 14.54% AbstractCellPopulation::Iterator::IsRealCell (inline) 73ms 0.31% 16.15% 3371ms 14.45% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 280ms 1.20% 17.35% 3303ms 14.16% std::_Rb_tree::find (inline) 0 0% 17.35% 3302ms 14.15% std::map::find (inline) 18ms 0.077% 17.43% 2851ms 12.22% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2826ms 12.11% 29.54% 2826ms 12.11% std::_Rb_tree::_S_right (inline) 163ms 0.7% 30.24% 2451ms 10.51% std::__introsort_loop 228ms 0.98% 31.22% 2394ms 10.26% std::map::operator[] (partial-inline) 31ms 0.13% 31.35% 2387ms 10.23% PlaneBoundaryCondition::ImposeBoundaryCondition 150ms 0.64% 31.99% 2369ms 10.16% AbstractMesh::GetNode 47ms 0.2% 32.19% 2367ms 10.15% NodesOnlyMesh::GetNodeOrHaloNode 38ms 0.16% 32.36% 2252ms 9.65% AbstractCellPopulation::GetLocationIndexUsingCell 85ms 0.36% 32.72% 2223ms 9.53% NodesOnlyMesh::SolveNodeMapping 0 0% 32.72% 2214ms 9.49% std::__unguarded_partition_pivot (inline) 12ms 0.051% 32.77% 2173ms 9.31% PlaneBoundaryCondition::VerifyBoundaryCondition 1051ms 4.51% 37.28% 2006ms 8.60% std::__unguarded_partition (inline) 0 0% 37.28% 1919ms 8.23% std::_Rb_tree::lower_bound (inline) 0 0% 37.28% 1919ms 8.23% std::map::lower_bound (inline) 119ms 0.51% 37.79% 1846ms 7.91% DistributedBoxCollection::AddPairsFromBox 1ms 0.0043% 37.79% 1831ms 7.85% std::__final_insertion_sort (inline) 101ms 0.43% 38.22% 1604ms 6.88% std::__unguarded_insertion_sort (inline) 621ms 2.66% 40.89% 1597ms 6.85% std::__unguarded_linear_insert (inline) 16ms 0.069% 40.96% 1562ms 6.70% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 27ms 0.12% 41.07% 1538ms 6.59% AbstractCellPopulation::GetCellUsingLocationIndex 1418ms 6.08% 47.15% 1418ms 6.08% __gnu_cxx::__normal_iterator::operator-- (inline) 54ms 0.23% 47.38% 1246ms 5.34% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 47.38% 1141ms 4.89% NodeBasedCellPopulation::UpdateCellProcessLocation 41ms 0.18% 47.56% 1122ms 4.81% boost::numeric::ublas::vector_assign (inline) 4ms 0.017% 47.57% 1094ms 4.69% DistributedBoxCollection::CalculateBoundaryNodePairs 268ms 1.15% 48.72% 1029ms 4.41% boost::numeric::ublas::indexing_vector_assign 251ms 1.08% 49.80% 949ms 4.07% __dynamic_cast 19ms 0.081% 49.88% 829ms 3.55% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 390ms 1.67% 51.55% 807ms 3.46% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 51.55% 774ms 3.32% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 51.55% 758ms 3.25% boost::numeric::ublas::norm_2 (inline) 592ms 2.54% 54.09% 758ms 3.25% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 54.09% 758ms 3.25% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 160ms 0.69% 54.78% 751ms 3.22% AbstractMesh::GetVectorFromAtoB 1ms 0.0043% 54.78% 735ms 3.15% AbstractCellPopulation::WriteResultsToFiles 165ms 0.71% 55.49% 722ms 3.09% NodeAttributes::AddNeighbour 712ms 3.05% 58.54% 712ms 3.05% boost::numeric::ublas::c_vector::operator() 556ms 2.38% 60.92% 630ms 2.70% std::vector::push_back (inline) 4ms 0.017% 60.94% 622ms 2.67% boost::numeric::ublas::c_vector::operator= (inline) 2ms 0.0086% 60.95% 619ms 2.65% AbstractCellBasedSimulation::DoCellBirth 38ms 0.16% 61.11% 614ms 2.63% std::__copy_move::__copy_m (inline) 0 0% 61.11% 614ms 2.63% std::__copy_move_a (inline) 0 0% 61.11% 614ms 2.63% std::__copy_move_a1 (inline) 0 0% 61.11% 614ms 2.63% std::__copy_move_a2 (inline) 0 0% 61.11% 614ms 2.63% std::copy (inline) 5ms 0.021% 61.13% 601ms 2.58% CellPropertyCollection::GetPropertiesType (inline) 593ms 2.54% 63.67% 593ms 2.54% __memcpy_avx_unaligned_erms 275ms 1.18% 64.85% 590ms 2.53% __cxxabiv1::__si_class_type_info::__do_dyncast 30ms 0.13% 64.98% 589ms 2.52% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.0043% 64.99% 587ms 2.52% AbstractCentreBasedCellPopulation::GetDampingConstant 559ms 2.40% 67.38% 559ms 2.40% std::_Rb_tree_increment 82ms 0.35% 67.73% 526ms 2.25% std::__new_allocator::allocate (inline) 34ms 0.15% 67.88% 513ms 2.20% boost::detail::shared_count::~shared_count (inline) 0 0% 67.88% 513ms 2.20% boost::shared_ptr::~shared_ptr (inline) 0 0% 67.88% 510ms 2.19% std::allocator_traits::allocate (inline) 3ms 0.013% 67.89% 483ms 2.07% NodeBasedCellPopulation::WriteVtkResultsToFile 12ms 0.051% 67.94% 483ms 2.07% std::_Rb_tree::_Rb_tree (partial-inline) 474ms 2.03% 69.98% 474ms 2.03% __strcmp_avx2 468ms 2.01% 71.98% 472ms 2.02% boost::detail::sp_counted_base::release 472ms 2.02% 74.01% 472ms 2.02% boost::numeric::ublas::same_impl_ex 0 0% 74.01% 468ms 2.01% std::_Rb_tree::_M_create_node (inline) 38ms 0.16% 74.17% 457ms 1.96% std::_Rb_tree::_M_copy (inline) 32ms 0.14% 74.31% 442ms 1.89% operator new 1ms 0.0043% 74.31% 432ms 1.85% AbstractCellProperty::IsSubType (inline) 0 0% 74.31% 421ms 1.80% AbstractCellBasedSimulation::DoCellRemoval (inline) 147ms 0.63% 74.94% 417ms 1.79% std::_Rb_tree::_M_clone_node (inline) 0 0% 74.94% 414ms 1.77% std::_Rb_tree::_M_get_node (inline) 3ms 0.013% 74.95% 412ms 1.77% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 5ms 0.021% 74.97% 404ms 1.73% Cell::GetMutationState 116ms 0.5% 75.47% 402ms 1.72% __GI___libc_malloc 120ms 0.51% 75.99% 398ms 1.71% std::_Rb_tree::_M_erase 5ms 0.021% 76.01% 392ms 1.68% std::set::set (inline) 137ms 0.59% 76.59% 376ms 1.61% Node::GetRadius 0 0% 76.59% 351ms 1.50% boost::numeric::ublas::c_vector::assign (inline) 345ms 1.48% 78.07% 345ms 1.48% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 78.07% 336ms 1.44% boost::numeric::ublas::inner_prod (inline) 5ms 0.021% 78.09% 336ms 1.44% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 21ms 0.09% 78.19% 331ms 1.42% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 78.19% 327ms 1.40% std::_Rb_tree::_Alloc_node::operator() (inline) 6ms 0.026% 78.21% 325ms 1.39% NodeBasedCellPopulation::UpdateMapsAfterRemesh 21ms 0.09% 78.30% 312ms 1.34% boost::numeric::ublas::vector_binary::size (inline) 30ms 0.13% 78.43% 304ms 1.30% std::_Rb_tree::~_Rb_tree (inline) 2ms 0.0086% 78.44% 276ms 1.18% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 78.44% 272ms 1.17% std::_Rb_tree::_M_drop_node (inline) 0 0% 78.44% 270ms 1.16% NodesOnlyMesh::ReMesh 6ms 0.026% 78.46% 268ms 1.15% DistributedBoxCollection::GetProcessOwningNode 104ms 0.45% 78.91% 268ms 1.15% boost::numeric::ublas::vector_inner_prod::apply (inline) 265ms 1.14% 80.05% 265ms 1.14% __gnu_cxx::__normal_iterator::operator++ (inline) 5ms 0.021% 80.07% 257ms 1.10% NodesOnlyMesh::UpdateNodeIndices 252ms 1.08% 81.15% 252ms 1.08% Node::CheckForNodeAttributes 5ms 0.021% 81.17% 247ms 1.06% std::_Rb_tree::_M_emplace_hint_unique 1ms 0.0043% 81.17% 241ms 1.03% NodesOnlyMesh::UpdateBoxCollection 127ms 0.54% 81.72% 236ms 1.01% _int_malloc 6ms 0.026% 81.74% 228ms 0.98% std::__new_allocator::deallocate (inline) 0 0% 81.74% 226ms 0.97% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 21ms 0.09% 81.83% 226ms 0.97% std::__insertion_sort (inline) 0 0% 81.83% 224ms 0.96% VtkMeshWriter::WriteFiles 0 0% 81.83% 221ms 0.95% std::set::~set (inline) 1ms 0.0043% 81.84% 219ms 0.94% CellPropertyCollection::HasProperty 0 0% 81.84% 218ms 0.93% Cell::HasCellProperty (inline) 0 0% 81.84% 207ms 0.89% vtkStreamingDemandDrivenPipeline::Update 0 0% 81.84% 207ms 0.89% vtkXMLWriterBase::Write 4ms 0.017% 81.85% 206ms 0.88% Cell::ReadyToDivide 0 0% 81.85% 206ms 0.88% vtkDemandDrivenPipeline::ProcessRequest 0 0% 81.85% 204ms 0.87% vtkExecutive::CallAlgorithm 0 0% 81.85% 204ms 0.87% vtkStreamingDemandDrivenPipeline::ProcessRequest 78ms 0.33% 82.19% 203ms 0.87% std::__move_median_to_first (inline) 0 0% 82.19% 203ms 0.87% std::allocator_traits::deallocate (inline) 0 0% 82.19% 203ms 0.87% vtkCompositeDataPipeline::ExecuteData 0 0% 82.19% 203ms 0.87% vtkDemandDrivenPipeline::ExecuteData 0 0% 82.19% 203ms 0.87% vtkXMLUnstructuredDataWriter::ProcessRequest 86ms 0.37% 82.56% 202ms 0.87% Node::AddNeighbour 0 0% 82.56% 201ms 0.86% std::_Rb_tree::_M_put_node (inline) 85ms 0.36% 82.92% 200ms 0.86% __GI___libc_free 0 0% 82.92% 198ms 0.85% NodesOnlyMesh::AddNodesToBoxes 0 0% 82.92% 196ms 0.84% NodesOnlyMesh::ResizeBoxCollection 12ms 0.051% 82.97% 194ms 0.83% NodesOnlyMesh::IsANodeCloseToDomainBoundary 94ms 0.4% 83.38% 184ms 0.79% boost::shared_ptr::shared_ptr (inline) 183ms 0.78% 84.16% 183ms 0.78% Node::GetIndex 182ms 0.78% 84.94% 182ms 0.78% [libchaste_cell_based.so] 0 0% 84.94% 171ms 0.73% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 84.94% 171ms 0.73% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 84.94% 170ms 0.73% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 4ms 0.017% 84.96% 168ms 0.72% AbstractCellProperty::IsType (inline) 160ms 0.69% 85.64% 160ms 0.69% Node::IsDeleted 158ms 0.68% 86.32% 158ms 0.68% boost::shared_ptr::operator-> (inline) 0 0% 86.32% 148ms 0.63% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 12ms 0.051% 86.37% 148ms 0.63% boost::numeric::ublas::vector_reference::operator() (inline) 141ms 0.6% 86.98% 144ms 0.62% std::__adjacent_find (inline) 0 0% 86.98% 144ms 0.62% std::__unique (inline) 0 0% 86.98% 144ms 0.62% std::unique (inline) 142ms 0.61% 87.59% 142ms 0.61% Node::ConstructNodeAttributes (inline) 0 0% 87.59% 141ms 0.6% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 87.59% 138ms 0.59% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 87.59% 137ms 0.59% vtkXMLWriter::WriteBinaryData 0 0% 87.59% 135ms 0.58% std::_Rb_tree::clear (inline) 0 0% 87.59% 133ms 0.57% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.59% 133ms 0.57% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.59% 133ms 0.57% vtkXMLWriter::WriteCompressionBlock 0 0% 87.59% 132ms 0.57% Cell::GetCellId 1ms 0.0043% 87.59% 131ms 0.56% AbstractCellPopulation::SetCellUsingLocationIndex 12ms 0.051% 87.64% 131ms 0.56% DistributedBoxCollection::GetIsPeriodicAllDims 45ms 0.19% 87.83% 129ms 0.55% AbstractCellProperty::IsSame 129ms 0.55% 88.39% 129ms 0.55% Node::rGetLocation 0 0% 88.39% 123ms 0.53% vtkXMLWriter::WritePointsAppendedData 121ms 0.52% 88.91% 121ms 0.52% [libchaste_mesh.so] 5ms 0.021% 88.93% 119ms 0.51% AbstractNumericalMethod::SafeNodePositionUpdate 118ms 0.51% 89.43% 118ms 0.51% __ieee754_log_fma 0 0% 89.43% 117ms 0.5% boost::numeric::ublas::vector_binary::operator() (inline)