File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 21195ms, 88.79% of 23870ms total Dropped 762 nodes (cum <= 119.35ms) flat flat% sum% cum cum% 0 0% 0% 23712ms 99.34% __libc_start_call_main 0 0% 0% 23712ms 99.34% __libc_start_main_impl 0 0% 0% 23712ms 99.34% _start 0 0% 0% 23696ms 99.27% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 23696ms 99.27% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 23696ms 99.27% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 23696ms 99.27% main 0 0% 0% 23659ms 99.12% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 23659ms 99.12% CxxTest::TestRunner::runTest (inline) 0 0% 0% 23659ms 99.12% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 23651ms 99.08% AbstractCellBasedSimulation::Solve 0 0% 0% 13266ms 55.58% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0% 9154ms 38.35% AbstractCellBasedSimulation::UpdateCellPopulation 5ms 0.021% 0.021% 8464ms 35.46% ForwardEulerNumericalMethod::UpdateAllNodePositions 14ms 0.059% 0.08% 8258ms 34.60% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.08% 8064ms 33.78% NodeBasedCellPopulation::Update 1235ms 5.17% 5.25% 7553ms 31.64% RepulsionForce::AddForceContribution (partial-inline) 15ms 0.063% 5.32% 5885ms 24.65% DistributedBoxCollection::CalculateInteriorNodePairs 2138ms 8.96% 14.27% 4932ms 20.66% std::_Rb_tree::_M_lower_bound (inline) 19ms 0.08% 14.35% 4607ms 19.30% NodeAttributes::RemoveDuplicateNeighbours 2ms 0.0084% 14.36% 4523ms 18.95% OffLatticeSimulation::ApplyBoundaries 5ms 0.021% 14.38% 4287ms 17.96% std::__sort (inline) 0 0% 14.38% 4287ms 17.96% std::sort (inline) 179ms 0.75% 15.13% 3858ms 16.16% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 1ms 0.0042% 15.14% 3458ms 14.49% AbstractCellPopulation::Iterator::operator++ (inline) 173ms 0.72% 15.86% 3437ms 14.40% AbstractCellPopulation::Iterator::IsRealCell (inline) 73ms 0.31% 16.17% 3426ms 14.35% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 234ms 0.98% 17.15% 3181ms 13.33% std::_Rb_tree::find (inline) 0 0% 17.15% 3181ms 13.33% std::map::find (inline) 18ms 0.075% 17.22% 2918ms 12.22% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2749ms 11.52% 28.74% 2749ms 11.52% std::_Rb_tree::_S_right (inline) 259ms 1.09% 29.82% 2510ms 10.52% std::map::operator[] (partial-inline) 200ms 0.84% 30.66% 2456ms 10.29% std::__introsort_loop 25ms 0.1% 30.77% 2385ms 9.99% PlaneBoundaryCondition::ImposeBoundaryCondition 29ms 0.12% 30.89% 2345ms 9.82% AbstractCellPopulation::GetLocationIndexUsingCell 167ms 0.7% 31.59% 2261ms 9.47% AbstractMesh::GetNode 54ms 0.23% 31.81% 2228ms 9.33% NodesOnlyMesh::GetNodeOrHaloNode 0 0% 31.81% 2176ms 9.12% std::__unguarded_partition_pivot (inline) 17ms 0.071% 31.89% 2136ms 8.95% PlaneBoundaryCondition::VerifyBoundaryCondition 78ms 0.33% 32.21% 2098ms 8.79% NodesOnlyMesh::SolveNodeMapping 180ms 0.75% 32.97% 2087ms 8.74% DistributedBoxCollection::AddPairsFromBox 0 0% 32.97% 2005ms 8.40% std::_Rb_tree::lower_bound (inline) 0 0% 32.97% 2005ms 8.40% std::map::lower_bound (inline) 1016ms 4.26% 37.22% 1920ms 8.04% std::__unguarded_partition (inline) 0 0% 37.22% 1825ms 7.65% std::__final_insertion_sort (inline) 91ms 0.38% 37.60% 1622ms 6.80% std::__unguarded_insertion_sort (inline) 526ms 2.20% 39.81% 1580ms 6.62% std::__unguarded_linear_insert (inline) 21ms 0.088% 39.90% 1571ms 6.58% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 28ms 0.12% 40.01% 1541ms 6.46% AbstractCellPopulation::GetCellUsingLocationIndex 1489ms 6.24% 46.25% 1489ms 6.24% __gnu_cxx::__normal_iterator::operator-- (inline) 48ms 0.2% 46.45% 1267ms 5.31% boost::numeric::ublas::c_vector::c_vector (partial-inline) 6ms 0.025% 46.48% 1216ms 5.09% DistributedBoxCollection::CalculateBoundaryNodePairs 3ms 0.013% 46.49% 1197ms 5.01% NodeBasedCellPopulation::UpdateCellProcessLocation 35ms 0.15% 46.64% 1151ms 4.82% boost::numeric::ublas::vector_assign (inline) 268ms 1.12% 47.76% 1040ms 4.36% boost::numeric::ublas::indexing_vector_assign 275ms 1.15% 48.91% 935ms 3.92% __dynamic_cast 162ms 0.68% 49.59% 806ms 3.38% AbstractMesh::GetVectorFromAtoB 8ms 0.034% 49.62% 767ms 3.21% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 49.62% 736ms 3.08% AbstractCellPopulation::WriteResultsToFiles 0 0% 49.62% 729ms 3.05% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 47ms 0.2% 49.82% 724ms 3.03% std::_Rb_tree_const_iterator::operator++ (inline) 4ms 0.017% 49.84% 709ms 2.97% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 49.84% 707ms 2.96% boost::numeric::ublas::norm_2 (inline) 544ms 2.28% 52.12% 707ms 2.96% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 52.12% 707ms 2.96% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 309ms 1.29% 53.41% 701ms 2.94% DistributedBoxCollection::CalculateContainingBox (partial-inline) 37ms 0.16% 53.57% 686ms 2.87% std::__copy_move::__copy_m (inline) 0 0% 53.57% 686ms 2.87% std::__copy_move_a (inline) 0 0% 53.57% 686ms 2.87% std::__copy_move_a1 (inline) 0 0% 53.57% 686ms 2.87% std::__copy_move_a2 (inline) 0 0% 53.57% 686ms 2.87% std::copy (inline) 179ms 0.75% 54.32% 684ms 2.87% NodeAttributes::AddNeighbour 671ms 2.81% 57.13% 671ms 2.81% boost::numeric::ublas::c_vector::operator() 669ms 2.80% 59.93% 669ms 2.80% std::_Rb_tree_increment 668ms 2.80% 62.73% 668ms 2.80% __memcpy_avx_unaligned_erms 8ms 0.034% 62.76% 648ms 2.71% CellPropertyCollection::GetPropertiesType (inline) 3ms 0.013% 62.77% 635ms 2.66% AbstractCellBasedSimulation::DoCellBirth 3ms 0.013% 62.79% 629ms 2.64% AbstractCentreBasedCellPopulation::GetDampingConstant 502ms 2.10% 64.89% 600ms 2.51% std::vector::push_back (inline) 243ms 1.02% 65.91% 540ms 2.26% __cxxabiv1::__si_class_type_info::__do_dyncast 31ms 0.13% 66.04% 521ms 2.18% boost::detail::shared_count::~shared_count (inline) 0 0% 66.04% 521ms 2.18% boost::shared_ptr::~shared_ptr (inline) 508ms 2.13% 68.17% 508ms 2.13% boost::numeric::ublas::same_impl_ex 23ms 0.096% 68.26% 503ms 2.11% std::_Rb_tree::_Rb_tree (partial-inline) 88ms 0.37% 68.63% 488ms 2.04% std::__new_allocator::allocate (inline) 0 0% 68.63% 487ms 2.04% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 68.63% 479ms 2.01% std::allocator_traits::allocate (inline) 473ms 1.98% 70.61% 478ms 2.00% boost::detail::sp_counted_base::release 45ms 0.19% 70.80% 467ms 1.96% std::_Rb_tree::_M_copy (inline) 2ms 0.0084% 70.81% 464ms 1.94% Cell::GetMutationState 461ms 1.93% 72.74% 461ms 1.93% __strcmp_avx2 0 0% 72.74% 454ms 1.90% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 72.74% 448ms 1.88% std::_Rb_tree::_M_create_node (inline) 4ms 0.017% 72.76% 441ms 1.85% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 147ms 0.62% 73.37% 421ms 1.76% std::_Rb_tree::_M_clone_node (inline) 2ms 0.0084% 73.38% 418ms 1.75% AbstractCellProperty::IsSubType (inline) 3ms 0.013% 73.39% 414ms 1.73% std::set::set (inline) 114ms 0.48% 73.87% 411ms 1.72% std::_Rb_tree::_M_erase 30ms 0.13% 74.00% 398ms 1.67% operator new 0 0% 74.00% 387ms 1.62% std::_Rb_tree::_M_get_node (inline) 89ms 0.37% 74.37% 361ms 1.51% __GI___libc_malloc 123ms 0.52% 74.88% 350ms 1.47% Node::GetRadius 339ms 1.42% 76.30% 339ms 1.42% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 76.30% 336ms 1.41% boost::numeric::ublas::c_vector::assign (inline) 0 0% 76.30% 332ms 1.39% boost::numeric::ublas::inner_prod (inline) 5ms 0.021% 76.33% 332ms 1.39% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 3ms 0.013% 76.34% 329ms 1.38% NodeBasedCellPopulation::UpdateMapsAfterRemesh 16ms 0.067% 76.41% 327ms 1.37% boost::numeric::ublas::vector_scalar_binary::evaluate 26ms 0.11% 76.51% 324ms 1.36% boost::numeric::ublas::vector_binary::size (inline) 51ms 0.21% 76.73% 324ms 1.36% std::_Rb_tree::~_Rb_tree (inline) 0 0% 76.73% 320ms 1.34% NodesOnlyMesh::ReMesh 0 0% 76.73% 319ms 1.34% std::_Rb_tree::_Alloc_node::operator() (inline) 5ms 0.021% 76.75% 307ms 1.29% NodesOnlyMesh::UpdateNodeIndices 92ms 0.39% 77.13% 289ms 1.21% Node::AddNeighbour 287ms 1.20% 78.34% 287ms 1.20% std::__adjacent_find (inline) 0 0% 78.34% 287ms 1.20% std::__unique (inline) 0 0% 78.34% 287ms 1.20% std::unique (inline) 0 0% 78.34% 281ms 1.18% std::_Rb_tree::_M_drop_node (inline) 108ms 0.45% 78.79% 271ms 1.14% boost::numeric::ublas::vector_inner_prod::apply (inline) 5ms 0.021% 78.81% 267ms 1.12% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 261ms 1.09% 79.90% 261ms 1.09% __gnu_cxx::__normal_iterator::operator++ (inline) 107ms 0.45% 80.35% 252ms 1.06% std::__move_median_to_first (inline) 0 0% 80.35% 251ms 1.05% NodesOnlyMesh::UpdateBoxCollection 2ms 0.0084% 80.36% 247ms 1.03% DistributedBoxCollection::GetProcessOwningNode 11ms 0.046% 80.41% 246ms 1.03% std::_Rb_tree::_M_emplace_hint_unique 3ms 0.013% 80.42% 244ms 1.02% std::__new_allocator::deallocate (inline) 129ms 0.54% 80.96% 236ms 0.99% _int_malloc 0 0% 80.96% 236ms 0.99% std::set::~set (inline) 0 0% 80.96% 235ms 0.98% Cell::HasCellProperty (inline) 3ms 0.013% 80.97% 235ms 0.98% CellPropertyCollection::HasProperty 235ms 0.98% 81.96% 235ms 0.98% Node::CheckForNodeAttributes 0 0% 81.96% 232ms 0.97% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 81.96% 228ms 0.96% VtkMeshWriter::WriteFiles 222ms 0.93% 82.89% 224ms 0.94% Node::ConstructNodeAttributes (inline) 0 0% 82.89% 222ms 0.93% std::allocator_traits::deallocate (inline) 66ms 0.28% 83.16% 217ms 0.91% __GI___libc_free 0 0% 83.16% 216ms 0.9% NodesOnlyMesh::ResizeBoxCollection 0 0% 83.16% 216ms 0.9% std::_Rb_tree::_M_put_node (inline) 9ms 0.038% 83.20% 215ms 0.9% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 83.20% 209ms 0.88% vtkStreamingDemandDrivenPipeline::Update 0 0% 83.20% 209ms 0.88% vtkXMLWriterBase::Write 2ms 0.0084% 83.21% 207ms 0.87% Cell::ReadyToDivide 0 0% 83.21% 207ms 0.87% vtkDemandDrivenPipeline::ProcessRequest 204ms 0.85% 84.06% 204ms 0.85% Node::GetIndex 0 0% 84.06% 204ms 0.85% vtkCompositeDataPipeline::ExecuteData 0 0% 84.06% 204ms 0.85% vtkDemandDrivenPipeline::ExecuteData 0 0% 84.06% 204ms 0.85% vtkExecutive::CallAlgorithm 0 0% 84.06% 204ms 0.85% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 84.06% 204ms 0.85% vtkXMLUnstructuredDataWriter::ProcessRequest 14ms 0.059% 84.12% 203ms 0.85% std::__insertion_sort (inline) 3ms 0.013% 84.13% 200ms 0.84% NodesOnlyMesh::AddNodesToBoxes 197ms 0.83% 84.96% 197ms 0.83% [libchaste_cell_based.so] 0 0% 84.96% 177ms 0.74% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 84.96% 177ms 0.74% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 2ms 0.0084% 84.97% 176ms 0.74% AbstractCellProperty::IsType (inline) 78ms 0.33% 85.30% 171ms 0.72% boost::shared_ptr::shared_ptr (inline) 0 0% 85.30% 169ms 0.71% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 168ms 0.7% 86.00% 168ms 0.7% boost::shared_ptr::operator-> (inline) 13ms 0.054% 86.05% 162ms 0.68% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 86.05% 158ms 0.66% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 86.05% 156ms 0.65% std::_Rb_tree::clear (inline) 0 0% 86.05% 151ms 0.63% vtkXMLWriter::WriteBinaryData 136ms 0.57% 86.62% 150ms 0.63% _int_free 0 0% 86.62% 145ms 0.61% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 3ms 0.013% 86.64% 145ms 0.61% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 86.64% 142ms 0.59% AbstractCellPopulation::SetCellUsingLocationIndex 0 0% 86.64% 141ms 0.59% vtkXMLWriter::WriteBinaryDataBlock 0 0% 86.64% 141ms 0.59% vtkXMLWriter::WriteBinaryDataInternal 0 0% 86.64% 141ms 0.59% vtkXMLWriter::WriteCompressionBlock 5ms 0.021% 86.66% 140ms 0.59% DistributedBoxCollection::GetIsPeriodicAllDims 0 0% 86.66% 137ms 0.57% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 55ms 0.23% 86.89% 134ms 0.56% AbstractCellProperty::IsSame 133ms 0.56% 87.44% 133ms 0.56% Node::IsDeleted 131ms 0.55% 87.99% 131ms 0.55% Node::rGetLocation 131ms 0.55% 88.54% 131ms 0.55% [libchaste_mesh.so] 0 0% 88.54% 130ms 0.54% Cell::GetCellId 0 0% 88.54% 129ms 0.54% std::_Rb_tree::_Auto_node::_Auto_node (inline) 5ms 0.021% 88.56% 128ms 0.54% NodeBasedCellPopulation::SetNode 0 0% 88.56% 128ms 0.54% vtkXMLWriter::WritePointsAppendedData 0 0% 88.56% 125ms 0.52% tbb::detail::r1::parallel_pipeline 0 0% 88.56% 122ms 0.51% clone3 0 0% 88.56% 122ms 0.51% start_thread 0 0% 88.56% 122ms 0.51% tbb::detail::r1::reset 55ms 0.23% 88.79% 120ms 0.5% tbb::detail::r1::wait_bounded_queue_monitor