File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20876ms, 89.28% of 23383ms total Dropped 733 nodes (cum <= 116.92ms) flat flat% sum% cum cum% 0 0% 0% 23227ms 99.33% __libc_start_call_main 0 0% 0% 23227ms 99.33% __libc_start_main_impl 0 0% 0% 23227ms 99.33% _start 0 0% 0% 23211ms 99.26% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 23211ms 99.26% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 23211ms 99.26% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 23211ms 99.26% main 0 0% 0% 23174ms 99.11% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 23174ms 99.11% CxxTest::TestRunner::runTest (inline) 0 0% 0% 23174ms 99.11% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 23166ms 99.07% AbstractCellBasedSimulation::Solve 1ms 0.0043% 0.0043% 13110ms 56.07% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0043% 0.0086% 8856ms 37.87% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0086% 0.017% 8330ms 35.62% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.026% 0.043% 8151ms 34.86% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.043% 7813ms 33.41% NodeBasedCellPopulation::Update 1247ms 5.33% 5.38% 7492ms 32.04% RepulsionForce::AddForceContribution (partial-inline) 4ms 0.017% 5.39% 5706ms 24.40% DistributedBoxCollection::CalculateInteriorNodePairs 2023ms 8.65% 14.04% 4829ms 20.65% std::_Rb_tree::_M_lower_bound (inline) 13ms 0.056% 14.10% 4554ms 19.48% NodeAttributes::RemoveDuplicateNeighbours 0 0% 14.10% 4520ms 19.33% OffLatticeSimulation::ApplyBoundaries 6ms 0.026% 14.13% 4365ms 18.67% std::__sort (inline) 0 0% 14.13% 4365ms 18.67% std::sort (inline) 155ms 0.66% 14.79% 3765ms 16.10% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 1ms 0.0043% 14.79% 3434ms 14.69% AbstractCellPopulation::Iterator::operator++ (inline) 210ms 0.9% 15.69% 3418ms 14.62% AbstractCellPopulation::Iterator::IsRealCell (inline) 81ms 0.35% 16.04% 3375ms 14.43% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 261ms 1.12% 17.15% 3208ms 13.72% std::_Rb_tree::find (inline) 0 0% 17.15% 3208ms 13.72% std::map::find (inline) 24ms 0.1% 17.26% 2866ms 12.26% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2757ms 11.79% 29.05% 2757ms 11.79% std::_Rb_tree::_S_right (inline) 175ms 0.75% 29.80% 2518ms 10.77% std::__introsort_loop 32ms 0.14% 29.93% 2394ms 10.24% PlaneBoundaryCondition::ImposeBoundaryCondition 249ms 1.06% 31.00% 2390ms 10.22% std::map::operator[] (partial-inline) 32ms 0.14% 31.13% 2315ms 9.90% AbstractCellPopulation::GetLocationIndexUsingCell 151ms 0.65% 31.78% 2270ms 9.71% AbstractMesh::GetNode 0 0% 31.78% 2259ms 9.66% std::__unguarded_partition_pivot (inline) 45ms 0.19% 31.97% 2245ms 9.60% NodesOnlyMesh::GetNodeOrHaloNode 17ms 0.073% 32.04% 2126ms 9.09% PlaneBoundaryCondition::VerifyBoundaryCondition 67ms 0.29% 32.33% 2124ms 9.08% NodesOnlyMesh::SolveNodeMapping 1044ms 4.46% 36.80% 2042ms 8.73% std::__unguarded_partition (inline) 0 0% 36.80% 1906ms 8.15% std::_Rb_tree::lower_bound (inline) 0 0% 36.80% 1906ms 8.15% std::map::lower_bound (inline) 148ms 0.63% 37.43% 1854ms 7.93% DistributedBoxCollection::AddPairsFromBox 0 0% 37.43% 1841ms 7.87% std::__final_insertion_sort (inline) 86ms 0.37% 37.80% 1640ms 7.01% std::__unguarded_insertion_sort (inline) 588ms 2.51% 40.31% 1615ms 6.91% std::__unguarded_linear_insert (inline) 1507ms 6.44% 46.76% 1507ms 6.44% __gnu_cxx::__normal_iterator::operator-- (inline) 14ms 0.06% 46.82% 1462ms 6.25% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 32ms 0.14% 46.95% 1445ms 6.18% AbstractCellPopulation::GetCellUsingLocationIndex 33ms 0.14% 47.09% 1203ms 5.14% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 47.09% 1164ms 4.98% NodeBasedCellPopulation::UpdateCellProcessLocation 5ms 0.021% 47.12% 1119ms 4.79% DistributedBoxCollection::CalculateBoundaryNodePairs 44ms 0.19% 47.30% 1095ms 4.68% boost::numeric::ublas::vector_assign (inline) 280ms 1.20% 48.50% 976ms 4.17% boost::numeric::ublas::indexing_vector_assign 287ms 1.23% 49.73% 930ms 3.98% __dynamic_cast 13ms 0.056% 49.78% 802ms 3.43% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 49.78% 788ms 3.37% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 377ms 1.61% 51.40% 769ms 3.29% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 51.40% 769ms 3.29% boost::numeric::ublas::norm_2 (inline) 591ms 2.53% 53.92% 769ms 3.29% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 53.92% 769ms 3.29% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 178ms 0.76% 54.69% 758ms 3.24% AbstractMesh::GetVectorFromAtoB 0 0% 54.69% 725ms 3.10% AbstractCellPopulation::WriteResultsToFiles 1ms 0.0043% 54.69% 691ms 2.96% boost::numeric::ublas::c_vector::operator= (inline) 683ms 2.92% 57.61% 683ms 2.92% boost::numeric::ublas::c_vector::operator() 35ms 0.15% 57.76% 678ms 2.90% std::__copy_move::__copy_m (inline) 0 0% 57.76% 678ms 2.90% std::__copy_move_a (inline) 0 0% 57.76% 678ms 2.90% std::__copy_move_a1 (inline) 0 0% 57.76% 678ms 2.90% std::__copy_move_a2 (inline) 0 0% 57.76% 678ms 2.90% std::copy (inline) 670ms 2.87% 60.63% 670ms 2.87% __memcpy_avx_unaligned_erms 173ms 0.74% 61.37% 656ms 2.81% NodeAttributes::AddNeighbour 4ms 0.017% 61.38% 584ms 2.50% CellPropertyCollection::GetPropertiesType (inline) 33ms 0.14% 61.52% 583ms 2.49% std::_Rb_tree_const_iterator::operator++ (inline) 5ms 0.021% 61.54% 576ms 2.46% AbstractCentreBasedCellPopulation::GetDampingConstant 3ms 0.013% 61.56% 570ms 2.44% AbstractCellBasedSimulation::DoCellBirth 480ms 2.05% 63.61% 565ms 2.42% std::vector::push_back (inline) 548ms 2.34% 65.95% 548ms 2.34% std::_Rb_tree_increment 256ms 1.09% 67.05% 543ms 2.32% __cxxabiv1::__si_class_type_info::__do_dyncast 42ms 0.18% 67.23% 512ms 2.19% boost::detail::shared_count::~shared_count (inline) 0 0% 67.23% 512ms 2.19% boost::shared_ptr::~shared_ptr (inline) 63ms 0.27% 67.50% 503ms 2.15% std::__new_allocator::allocate (inline) 0 0% 67.50% 484ms 2.07% std::allocator_traits::allocate (inline) 1ms 0.0043% 67.50% 482ms 2.06% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 67.50% 472ms 2.02% AbstractCellBasedSimulation::DoCellRemoval (inline) 21ms 0.09% 67.59% 465ms 1.99% std::_Rb_tree::_Rb_tree (partial-inline) 464ms 1.98% 69.58% 464ms 1.98% boost::numeric::ublas::same_impl_ex 455ms 1.95% 71.52% 461ms 1.97% boost::detail::sp_counted_base::release 5ms 0.021% 71.54% 456ms 1.95% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 71.54% 447ms 1.91% std::_Rb_tree::_M_create_node (inline) 21ms 0.09% 71.63% 439ms 1.88% operator new 44ms 0.19% 71.82% 434ms 1.86% std::_Rb_tree::_M_copy (inline) 427ms 1.83% 73.65% 427ms 1.83% __strcmp_avx2 143ms 0.61% 74.26% 420ms 1.80% std::_Rb_tree::_M_erase 112ms 0.48% 74.74% 410ms 1.75% __GI___libc_malloc 5ms 0.021% 74.76% 409ms 1.75% Cell::GetMutationState 2ms 0.0086% 74.77% 408ms 1.74% AbstractCellProperty::IsSubType (inline) 130ms 0.56% 75.32% 402ms 1.72% Node::GetRadius 0 0% 75.32% 393ms 1.68% std::_Rb_tree::_M_get_node (inline) 122ms 0.52% 75.85% 389ms 1.66% std::_Rb_tree::_M_clone_node (inline) 3ms 0.013% 75.86% 367ms 1.57% std::set::set (inline) 0 0% 75.86% 346ms 1.48% boost::numeric::ublas::c_vector::assign (inline) 335ms 1.43% 77.29% 335ms 1.43% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 77.29% 333ms 1.42% boost::numeric::ublas::inner_prod (inline) 2ms 0.0086% 77.30% 333ms 1.42% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 17ms 0.073% 77.37% 331ms 1.42% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 77.37% 331ms 1.42% std::_Rb_tree::_Alloc_node::operator() (inline) 21ms 0.09% 77.46% 321ms 1.37% boost::numeric::ublas::vector_binary::size (inline) 10ms 0.043% 77.51% 315ms 1.35% NodeBasedCellPopulation::UpdateMapsAfterRemesh 30ms 0.13% 77.63% 311ms 1.33% std::_Rb_tree::~_Rb_tree (inline) 0 0% 77.63% 294ms 1.26% NodesOnlyMesh::ReMesh 0 0% 77.63% 293ms 1.25% NodesOnlyMesh::UpdateBoxCollection 288ms 1.23% 78.86% 288ms 1.23% __gnu_cxx::__normal_iterator::operator++ (inline) 6ms 0.026% 78.89% 285ms 1.22% NodesOnlyMesh::UpdateNodeIndices 280ms 1.20% 80.09% 280ms 1.20% Node::CheckForNodeAttributes 2ms 0.0086% 80.10% 277ms 1.18% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 80.10% 268ms 1.15% std::_Rb_tree::_M_drop_node (inline) 4ms 0.017% 80.11% 265ms 1.13% DistributedBoxCollection::GetProcessOwningNode 95ms 0.41% 80.52% 264ms 1.13% boost::numeric::ublas::vector_inner_prod::apply (inline) 114ms 0.49% 81.01% 254ms 1.09% Node::AddNeighbour 146ms 0.62% 81.63% 250ms 1.07% _int_malloc 5ms 0.021% 81.65% 241ms 1.03% NodesOnlyMesh::AddNodesToBoxes 4ms 0.017% 81.67% 236ms 1.01% std::__new_allocator::deallocate (inline) 1ms 0.0043% 81.67% 235ms 1.01% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 12ms 0.051% 81.73% 235ms 1.01% std::_Rb_tree::_M_emplace_hint_unique 0 0% 81.73% 231ms 0.99% VtkMeshWriter::WriteFiles 0 0% 81.73% 220ms 0.94% NodesOnlyMesh::ResizeBoxCollection 18ms 0.077% 81.80% 219ms 0.94% NodesOnlyMesh::IsANodeCloseToDomainBoundary 90ms 0.38% 82.19% 214ms 0.92% std::__move_median_to_first (inline) 0 0% 82.19% 213ms 0.91% std::set::~set (inline) 79ms 0.34% 82.53% 211ms 0.9% __GI___libc_free 0 0% 82.53% 206ms 0.88% vtkStreamingDemandDrivenPipeline::Update 0 0% 82.53% 206ms 0.88% vtkXMLWriterBase::Write 0 0% 82.53% 205ms 0.88% std::allocator_traits::deallocate (inline) 0 0% 82.53% 204ms 0.87% vtkDemandDrivenPipeline::ProcessRequest 0 0% 82.53% 203ms 0.87% vtkStreamingDemandDrivenPipeline::ProcessRequest 96ms 0.41% 82.94% 202ms 0.86% boost::shared_ptr::shared_ptr (inline) 0 0% 82.94% 202ms 0.86% std::_Rb_tree::_M_put_node (inline) 0 0% 82.94% 202ms 0.86% vtkDemandDrivenPipeline::ExecuteData 22ms 0.094% 83.03% 201ms 0.86% std::__insertion_sort (inline) 0 0% 83.03% 201ms 0.86% vtkCompositeDataPipeline::ExecuteData 0 0% 83.03% 201ms 0.86% vtkExecutive::CallAlgorithm 0 0% 83.03% 201ms 0.86% vtkXMLUnstructuredDataWriter::ProcessRequest 185ms 0.79% 83.82% 185ms 0.79% Node::GetIndex 183ms 0.78% 84.60% 183ms 0.78% [libchaste_cell_based.so] 0 0% 84.60% 175ms 0.75% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 84.60% 175ms 0.75% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 84.60% 171ms 0.73% Cell::HasCellProperty (inline) 1ms 0.0043% 84.61% 171ms 0.73% CellPropertyCollection::HasProperty 8ms 0.034% 84.64% 170ms 0.73% Cell::ReadyToDivide 168ms 0.72% 85.36% 169ms 0.72% Node::ConstructNodeAttributes (inline) 164ms 0.7% 86.06% 166ms 0.71% std::__adjacent_find (inline) 0 0% 86.06% 166ms 0.71% std::__unique (inline) 0 0% 86.06% 166ms 0.71% std::unique (inline) 0 0% 86.06% 166ms 0.71% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 86.06% 154ms 0.66% std::_Rb_tree::clear (inline) 0 0% 86.06% 152ms 0.65% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 10ms 0.043% 86.11% 151ms 0.65% boost::numeric::ublas::vector_reference::operator() (inline) 149ms 0.64% 86.74% 149ms 0.64% Node::IsDeleted 8ms 0.034% 86.78% 147ms 0.63% DistributedBoxCollection::GetIsPeriodicAllDims 2ms 0.0086% 86.79% 146ms 0.62% AbstractCellProperty::IsType (inline) 0 0% 86.79% 143ms 0.61% vtkXMLWriter::WriteBinaryData 137ms 0.59% 87.37% 137ms 0.59% boost::shared_ptr::operator-> (inline) 0 0% 87.37% 136ms 0.58% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 9ms 0.038% 87.41% 136ms 0.58% boost::numeric::ublas::c_vector::operator[] (inline) 135ms 0.58% 87.99% 135ms 0.58% [libchaste_mesh.so] 0 0% 87.99% 135ms 0.58% vtkXMLWriter::WriteBinaryDataInternal 134ms 0.57% 88.56% 134ms 0.57% __ieee754_log_fma 0 0% 88.56% 134ms 0.57% vtkXMLWriter::WriteBinaryDataBlock 0 0% 88.56% 134ms 0.57% vtkXMLWriter::WriteCompressionBlock 115ms 0.49% 89.05% 132ms 0.56% _int_free 2ms 0.0086% 89.06% 128ms 0.55% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 89.06% 127ms 0.54% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 89.06% 125ms 0.53% Cell::GetCellId 0 0% 89.06% 125ms 0.53% tbb::detail::r1::parallel_pipeline 3ms 0.013% 89.07% 123ms 0.53% std::_Rb_tree::_M_insert_unique 0 0% 89.07% 123ms 0.53% std::set::insert (inline) 0 0% 89.07% 122ms 0.52% clone3 0 0% 89.07% 122ms 0.52% start_thread 2ms 0.0086% 89.08% 121ms 0.52% AbstractCellPopulation::SetCellUsingLocationIndex 0 0% 89.08% 120ms 0.51% tbb::detail::r1::reset 46ms 0.2% 89.28% 118ms 0.5% tbb::detail::r1::wait_bounded_queue_monitor 0 0% 89.28% 118ms 0.5% vtkDataCompressor::Compress 0 0% 89.28% 118ms 0.5% vtkXMLWriter::WritePointsAppendedData 0 0% 89.28% 118ms 0.5% vtkZLibDataCompressor::CompressBuffer 0 0% 89.28% 117ms 0.5% compress2