File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 21746ms, 88.55% of 24559ms total Dropped 811 nodes (cum <= 122.80ms) flat flat% sum% cum cum% 0 0% 0% 24434ms 99.49% __libc_start_call_main 0 0% 0% 24434ms 99.49% __libc_start_main_impl 0 0% 0% 24434ms 99.49% _start 0 0% 0% 24416ms 99.42% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 24416ms 99.42% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 24416ms 99.42% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 24416ms 99.42% main 0 0% 0% 24375ms 99.25% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 24375ms 99.25% CxxTest::TestRunner::runTest (inline) 0 0% 0% 24375ms 99.25% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0041% 0.0041% 24367ms 99.22% AbstractCellBasedSimulation::Solve 5ms 0.02% 0.024% 13918ms 56.67% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0041% 0.029% 9223ms 37.55% AbstractCellBasedSimulation::UpdateCellPopulation 5ms 0.02% 0.049% 9082ms 36.98% ForwardEulerNumericalMethod::UpdateAllNodePositions 12ms 0.049% 0.098% 8880ms 36.16% AbstractNumericalMethod::ComputeForcesIncludingDamping 1379ms 5.62% 5.71% 8238ms 33.54% RepulsionForce::AddForceContribution (partial-inline) 0 0% 5.71% 8184ms 33.32% NodeBasedCellPopulation::Update 6ms 0.024% 5.74% 6078ms 24.75% DistributedBoxCollection::CalculateInteriorNodePairs 2156ms 8.78% 14.52% 5076ms 20.67% std::_Rb_tree::_M_lower_bound (inline) 11ms 0.045% 14.56% 4617ms 18.80% NodeAttributes::RemoveDuplicateNeighbours 0 0% 14.56% 4545ms 18.51% OffLatticeSimulation::ApplyBoundaries 2ms 0.0081% 14.57% 4435ms 18.06% std::__sort (inline) 0 0% 14.57% 4435ms 18.06% std::sort (inline) 181ms 0.74% 15.31% 4040ms 16.45% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 282ms 1.15% 16.45% 3373ms 13.73% std::_Rb_tree::find (inline) 0 0% 16.45% 3373ms 13.73% std::map::find (inline) 66ms 0.27% 16.72% 3296ms 13.42% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 4ms 0.016% 16.74% 3075ms 12.52% AbstractCellPopulation::Iterator::operator++ (inline) 152ms 0.62% 17.36% 3038ms 12.37% AbstractCellPopulation::Iterator::IsRealCell (inline) 2882ms 11.74% 29.09% 2882ms 11.74% std::_Rb_tree::_S_right (inline) 27ms 0.11% 29.20% 2645ms 10.77% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 173ms 0.7% 29.91% 2604ms 10.60% std::__introsort_loop 184ms 0.75% 30.66% 2463ms 10.03% std::map::operator[] (partial-inline) 17ms 0.069% 30.73% 2442ms 9.94% PlaneBoundaryCondition::ImposeBoundaryCondition 165ms 0.67% 31.40% 2401ms 9.78% AbstractMesh::GetNode 43ms 0.18% 31.57% 2355ms 9.59% NodesOnlyMesh::GetNodeOrHaloNode 0 0% 31.57% 2355ms 9.59% std::__unguarded_partition_pivot (inline) 47ms 0.19% 31.76% 2288ms 9.32% AbstractCellPopulation::GetLocationIndexUsingCell 105ms 0.43% 32.19% 2240ms 9.12% NodesOnlyMesh::SolveNodeMapping 1011ms 4.12% 36.31% 2109ms 8.59% std::__unguarded_partition (inline) 13ms 0.053% 36.36% 2103ms 8.56% PlaneBoundaryCondition::VerifyBoundaryCondition 138ms 0.56% 36.92% 2100ms 8.55% DistributedBoxCollection::AddPairsFromBox 0 0% 36.92% 2022ms 8.23% std::_Rb_tree::lower_bound (inline) 0 0% 36.92% 2022ms 8.23% std::map::lower_bound (inline) 0 0% 36.92% 1827ms 7.44% std::__final_insertion_sort (inline) 20ms 0.081% 37.00% 1688ms 6.87% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 24ms 0.098% 37.10% 1658ms 6.75% AbstractCellPopulation::GetCellUsingLocationIndex 124ms 0.5% 37.61% 1628ms 6.63% std::__unguarded_insertion_sort (inline) 577ms 2.35% 39.96% 1543ms 6.28% std::__unguarded_linear_insert (inline) 1392ms 5.67% 45.62% 1392ms 5.67% __gnu_cxx::__normal_iterator::operator-- (inline) 46ms 0.19% 45.81% 1250ms 5.09% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 45.81% 1167ms 4.75% NodeBasedCellPopulation::UpdateCellProcessLocation 8ms 0.033% 45.84% 1132ms 4.61% DistributedBoxCollection::CalculateBoundaryNodePairs 10ms 0.041% 45.89% 1114ms 4.54% boost::numeric::ublas::vector_assign (inline) 204ms 0.83% 46.72% 1020ms 4.15% boost::numeric::ublas::indexing_vector_assign 247ms 1.01% 47.72% 968ms 3.94% __dynamic_cast 28ms 0.11% 47.84% 959ms 3.90% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 47.84% 857ms 3.49% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 187ms 0.76% 48.60% 853ms 3.47% AbstractMesh::GetVectorFromAtoB 362ms 1.47% 50.07% 848ms 3.45% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 50.07% 838ms 3.41% boost::numeric::ublas::norm_2 (inline) 666ms 2.71% 52.78% 838ms 3.41% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 52.78% 838ms 3.41% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 2ms 0.0081% 52.79% 826ms 3.36% boost::numeric::ublas::c_vector::operator= (inline) 810ms 3.30% 56.09% 810ms 3.30% __memcpy_avx_unaligned_erms 27ms 0.11% 56.20% 809ms 3.29% std::__copy_move::__copy_m (inline) 0 0% 56.20% 809ms 3.29% std::__copy_move_a (inline) 0 0% 56.20% 809ms 3.29% std::__copy_move_a1 (inline) 0 0% 56.20% 809ms 3.29% std::__copy_move_a2 (inline) 0 0% 56.20% 809ms 3.29% std::copy (inline) 148ms 0.6% 56.80% 784ms 3.19% NodeAttributes::AddNeighbour 0 0% 56.80% 746ms 3.04% AbstractCellPopulation::WriteResultsToFiles 708ms 2.88% 59.68% 708ms 2.88% boost::numeric::ublas::c_vector::operator() 635ms 2.59% 62.27% 708ms 2.88% std::vector::push_back (inline) 17ms 0.069% 62.34% 641ms 2.61% std::_Rb_tree_const_iterator::operator++ (inline) 602ms 2.45% 64.79% 602ms 2.45% std::_Rb_tree_increment 10ms 0.041% 64.83% 598ms 2.43% CellPropertyCollection::GetPropertiesType (inline) 298ms 1.21% 66.05% 593ms 2.41% __cxxabiv1::__si_class_type_info::__do_dyncast 4ms 0.016% 66.06% 572ms 2.33% AbstractCellBasedSimulation::DoCellBirth 2ms 0.0081% 66.07% 569ms 2.32% AbstractCentreBasedCellPopulation::GetDampingConstant 554ms 2.26% 68.33% 554ms 2.26% boost::numeric::ublas::same_impl_ex 33ms 0.13% 68.46% 541ms 2.20% std::_Rb_tree::_Rb_tree (partial-inline) 101ms 0.41% 68.87% 529ms 2.15% std::__new_allocator::allocate (inline) 31ms 0.13% 69.00% 509ms 2.07% boost::detail::shared_count::~shared_count (inline) 0 0% 69.00% 509ms 2.07% boost::shared_ptr::~shared_ptr (inline) 0 0% 69.00% 509ms 2.07% std::allocator_traits::allocate (inline) 33ms 0.13% 69.13% 497ms 2.02% std::_Rb_tree::_M_copy (inline) 4ms 0.016% 69.15% 492ms 2.00% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 69.15% 475ms 1.93% std::_Rb_tree::_M_create_node (inline) 455ms 1.85% 71.00% 468ms 1.91% boost::detail::sp_counted_base::release 467ms 1.90% 72.90% 467ms 1.90% __strcmp_avx2 0 0% 72.90% 465ms 1.89% AbstractCellBasedSimulation::DoCellRemoval (inline) 161ms 0.66% 73.56% 458ms 1.86% std::_Rb_tree::_M_clone_node (inline) 8ms 0.033% 73.59% 453ms 1.84% std::set::set (inline) 6ms 0.024% 73.61% 452ms 1.84% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 73.61% 430ms 1.75% std::_Rb_tree::_M_get_node (inline) 34ms 0.14% 73.75% 423ms 1.72% operator new 4ms 0.016% 73.77% 414ms 1.69% Cell::GetMutationState 1ms 0.0041% 73.77% 410ms 1.67% AbstractCellProperty::IsSubType (inline) 105ms 0.43% 74.20% 405ms 1.65% std::_Rb_tree::_M_erase 87ms 0.35% 74.56% 400ms 1.63% boost::numeric::ublas::vector_binary::size (inline) 81ms 0.33% 74.88% 388ms 1.58% Node::GetRadius 110ms 0.45% 75.33% 378ms 1.54% __GI___libc_malloc 0 0% 75.33% 378ms 1.54% boost::numeric::ublas::inner_prod (inline) 1ms 0.0041% 75.34% 377ms 1.54% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 15ms 0.061% 75.40% 376ms 1.53% boost::numeric::ublas::vector_scalar_binary::evaluate 343ms 1.40% 76.79% 343ms 1.40% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 340ms 1.38% 78.18% 340ms 1.38% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 78.18% 339ms 1.38% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 78.18% 331ms 1.35% NodesOnlyMesh::ReMesh 3ms 0.012% 78.19% 322ms 1.31% NodesOnlyMesh::UpdateNodeIndices 42ms 0.17% 78.36% 317ms 1.29% std::_Rb_tree::~_Rb_tree (inline) 314ms 1.28% 79.64% 314ms 1.28% Node::CheckForNodeAttributes 3ms 0.012% 79.65% 312ms 1.27% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 79.65% 306ms 1.25% boost::numeric::ublas::c_vector::assign (inline) 7ms 0.029% 79.68% 304ms 1.24% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 136ms 0.55% 80.24% 299ms 1.22% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 80.24% 294ms 1.20% std::_Rb_tree::_M_drop_node (inline) 6ms 0.024% 80.26% 281ms 1.14% DistributedBoxCollection::GetProcessOwningNode 0 0% 80.26% 271ms 1.10% NodesOnlyMesh::UpdateBoxCollection 262ms 1.07% 81.33% 262ms 1.07% Node::GetIndex 12ms 0.049% 81.38% 257ms 1.05% std::_Rb_tree::_M_emplace_hint_unique 6ms 0.024% 81.40% 252ms 1.03% std::__new_allocator::deallocate (inline) 0 0% 81.40% 248ms 1.01% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 246ms 1.00% 82.40% 246ms 1.00% [libchaste_mesh.so] 0 0% 82.40% 245ms 1% VtkMeshWriter::WriteFiles 165ms 0.67% 83.07% 244ms 0.99% Node::AddNeighbour 125ms 0.51% 83.58% 242ms 0.99% std::__move_median_to_first (inline) 0 0% 83.58% 232ms 0.94% std::allocator_traits::deallocate (inline) 0 0% 83.58% 231ms 0.94% std::_Rb_tree::_M_put_node (inline) 2ms 0.0081% 83.59% 227ms 0.92% NodesOnlyMesh::AddNodesToBoxes 80ms 0.33% 83.92% 226ms 0.92% __GI___libc_free 120ms 0.49% 84.40% 222ms 0.9% _int_malloc 0 0% 84.40% 221ms 0.9% std::set::~set (inline) 0 0% 84.40% 217ms 0.88% vtkDemandDrivenPipeline::ProcessRequest 0 0% 84.40% 217ms 0.88% vtkStreamingDemandDrivenPipeline::Update 0 0% 84.40% 217ms 0.88% vtkXMLWriterBase::Write 0 0% 84.40% 215ms 0.88% vtkDemandDrivenPipeline::ExecuteData 0 0% 84.40% 215ms 0.88% vtkExecutive::CallAlgorithm 0 0% 84.40% 215ms 0.88% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 84.40% 214ms 0.87% vtkCompositeDataPipeline::ExecuteData 0 0% 84.40% 214ms 0.87% vtkXMLUnstructuredDataWriter::ProcessRequest 96ms 0.39% 84.80% 208ms 0.85% boost::shared_ptr::shared_ptr (inline) 2ms 0.0081% 84.80% 205ms 0.83% CellPropertyCollection::HasProperty 0 0% 84.80% 204ms 0.83% Cell::HasCellProperty (inline) 17ms 0.069% 84.87% 199ms 0.81% std::__insertion_sort (inline) 6ms 0.024% 84.90% 193ms 0.79% Cell::ReadyToDivide 13ms 0.053% 84.95% 191ms 0.78% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 84.95% 190ms 0.77% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 84.95% 180ms 0.73% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 84.95% 180ms 0.73% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 177ms 0.72% 85.67% 177ms 0.72% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 0 0% 85.67% 175ms 0.71% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 2ms 0.0081% 85.68% 162ms 0.66% NodesOnlyMesh::ResizeBoxCollection 12ms 0.049% 85.73% 159ms 0.65% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 85.73% 157ms 0.64% AbstractCellProperty::IsType (inline) 1ms 0.0041% 85.73% 151ms 0.61% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 3ms 0.012% 85.74% 151ms 0.61% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 85.74% 150ms 0.61% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 150ms 0.61% 86.36% 150ms 0.61% std::__adjacent_find (inline) 0 0% 86.36% 150ms 0.61% std::__unique (inline) 0 0% 86.36% 150ms 0.61% std::unique (inline) 0 0% 86.36% 149ms 0.61% std::_Rb_tree::clear (inline) 0 0% 86.36% 146ms 0.59% vtkXMLWriter::WriteBinaryData 131ms 0.53% 86.89% 145ms 0.59% _int_free 2ms 0.0081% 86.90% 142ms 0.58% AbstractNumericalMethod::SafeNodePositionUpdate 141ms 0.57% 87.47% 141ms 0.57% [libchaste_cell_based.so] 1ms 0.0041% 87.48% 140ms 0.57% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.48% 139ms 0.57% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.48% 139ms 0.57% vtkXMLWriter::WriteCompressionBlock 0 0% 87.48% 136ms 0.55% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 87.48% 135ms 0.55% vtkXMLWriter::WritePointsAppendedData 130ms 0.53% 88.00% 130ms 0.53% Node::rGetLocation 128ms 0.52% 88.53% 128ms 0.52% __ieee754_log_fma 4ms 0.016% 88.54% 127ms 0.52% NodeBasedCellPopulation::SetNode 1ms 0.0041% 88.55% 124ms 0.5% AbstractCellPopulation::SetCellUsingLocationIndex