File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 22071ms, 89.62% of 24626ms total Dropped 801 nodes (cum <= 123.13ms) flat flat% sum% cum cum% 0 0% 0% 24490ms 99.45% __libc_start_call_main 0 0% 0% 24490ms 99.45% __libc_start_main_impl 0 0% 0% 24490ms 99.45% _start 0 0% 0% 24472ms 99.37% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 24472ms 99.37% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 24472ms 99.37% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 24472ms 99.37% main 0 0% 0% 24433ms 99.22% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 24433ms 99.22% CxxTest::TestRunner::runTest (inline) 0 0% 0% 24433ms 99.22% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0041% 0.0041% 24424ms 99.18% AbstractCellBasedSimulation::Solve 2ms 0.0081% 0.012% 14050ms 57.05% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.012% 9175ms 37.26% AbstractCellBasedSimulation::UpdateCellPopulation 7ms 0.028% 0.041% 9138ms 37.11% ForwardEulerNumericalMethod::UpdateAllNodePositions 7ms 0.028% 0.069% 8946ms 36.33% AbstractNumericalMethod::ComputeForcesIncludingDamping 1340ms 5.44% 5.51% 8256ms 33.53% RepulsionForce::AddForceContribution (partial-inline) 0 0% 5.51% 8127ms 33.00% NodeBasedCellPopulation::Update 10ms 0.041% 5.55% 6002ms 24.37% DistributedBoxCollection::CalculateInteriorNodePairs 2229ms 9.05% 14.60% 5205ms 21.14% std::_Rb_tree::_M_lower_bound (inline) 16ms 0.065% 14.67% 4626ms 18.79% NodeAttributes::RemoveDuplicateNeighbours 1ms 0.0041% 14.67% 4594ms 18.66% OffLatticeSimulation::ApplyBoundaries 4ms 0.016% 14.69% 4431ms 17.99% std::__sort (inline) 0 0% 14.69% 4431ms 17.99% std::sort (inline) 207ms 0.84% 15.53% 4142ms 16.82% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 239ms 0.97% 16.50% 3447ms 14.00% std::_Rb_tree::find (inline) 0 0% 16.50% 3446ms 13.99% std::map::find (inline) 74ms 0.3% 16.80% 3321ms 13.49% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 3ms 0.012% 16.81% 3147ms 12.78% AbstractCellPopulation::Iterator::operator++ (inline) 143ms 0.58% 17.39% 3109ms 12.62% AbstractCellPopulation::Iterator::IsRealCell 2940ms 11.94% 29.33% 2940ms 11.94% std::_Rb_tree::_S_right (inline) 31ms 0.13% 29.46% 2723ms 11.06% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 172ms 0.7% 30.16% 2607ms 10.59% std::__introsort_loop 194ms 0.79% 30.94% 2515ms 10.21% std::map::operator[] (partial-inline) 157ms 0.64% 31.58% 2508ms 10.18% AbstractMesh::GetNode 46ms 0.19% 31.77% 2480ms 10.07% NodesOnlyMesh::GetNodeOrHaloNode 22ms 0.089% 31.86% 2450ms 9.95% PlaneBoundaryCondition::ImposeBoundaryCondition 0 0% 31.86% 2359ms 9.58% std::__unguarded_partition_pivot (inline) 103ms 0.42% 32.27% 2356ms 9.57% NodesOnlyMesh::SolveNodeMapping 57ms 0.23% 32.51% 2283ms 9.27% AbstractCellPopulation::GetLocationIndexUsingCell 22ms 0.089% 32.60% 2143ms 8.70% PlaneBoundaryCondition::VerifyBoundaryCondition 1048ms 4.26% 36.85% 2120ms 8.61% std::__unguarded_partition (inline) 0 0% 36.85% 2050ms 8.32% std::_Rb_tree::lower_bound (inline) 0 0% 36.85% 2050ms 8.32% std::map::lower_bound (inline) 141ms 0.57% 37.42% 2011ms 8.17% DistributedBoxCollection::AddPairsFromBox 0 0% 37.42% 1819ms 7.39% std::__final_insertion_sort (inline) 23ms 0.093% 37.52% 1699ms 6.90% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 34ms 0.14% 37.66% 1669ms 6.78% AbstractCellPopulation::GetCellUsingLocationIndex 108ms 0.44% 38.09% 1608ms 6.53% std::__unguarded_insertion_sort (inline) 580ms 2.36% 40.45% 1565ms 6.36% std::__unguarded_linear_insert (inline) 1456ms 5.91% 46.36% 1456ms 5.91% __gnu_cxx::__normal_iterator::operator-- (inline) 41ms 0.17% 46.53% 1254ms 5.09% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 46.53% 1147ms 4.66% NodeBasedCellPopulation::UpdateCellProcessLocation 3ms 0.012% 46.54% 1118ms 4.54% DistributedBoxCollection::CalculateBoundaryNodePairs 2ms 0.0081% 46.55% 1114ms 4.52% boost::numeric::ublas::vector_assign (inline) 228ms 0.93% 47.47% 1029ms 4.18% boost::numeric::ublas::indexing_vector_assign 288ms 1.17% 48.64% 975ms 3.96% __dynamic_cast 22ms 0.089% 48.73% 928ms 3.77% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 203ms 0.82% 49.56% 894ms 3.63% AbstractMesh::GetVectorFromAtoB 393ms 1.60% 51.15% 849ms 3.45% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 51.15% 819ms 3.33% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 4ms 0.016% 51.17% 809ms 3.29% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 51.17% 802ms 3.26% boost::numeric::ublas::norm_2 (inline) 628ms 2.55% 53.72% 802ms 3.26% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 53.72% 802ms 3.26% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 44ms 0.18% 53.90% 792ms 3.22% std::__copy_move::__copy_m (inline) 0 0% 53.90% 792ms 3.22% std::__copy_move_a (inline) 0 0% 53.90% 792ms 3.22% std::__copy_move_a1 (inline) 0 0% 53.90% 792ms 3.22% std::__copy_move_a2 (inline) 0 0% 53.90% 792ms 3.22% std::copy (inline) 770ms 3.13% 57.03% 770ms 3.13% __memcpy_avx_unaligned_erms 0 0% 57.03% 754ms 3.06% AbstractCellPopulation::WriteResultsToFiles 157ms 0.64% 57.66% 730ms 2.96% NodeAttributes::AddNeighbour 698ms 2.83% 60.50% 698ms 2.83% boost::numeric::ublas::c_vector::operator() 44ms 0.18% 60.68% 673ms 2.73% std::_Rb_tree_const_iterator::operator++ (inline) 572ms 2.32% 63.00% 650ms 2.64% std::vector::push_back (inline) 9ms 0.037% 63.04% 641ms 2.60% CellPropertyCollection::GetPropertiesType (inline) 6ms 0.024% 63.06% 611ms 2.48% AbstractCentreBasedCellPopulation::GetDampingConstant 600ms 2.44% 65.50% 600ms 2.44% std::_Rb_tree_increment 2ms 0.0081% 65.50% 583ms 2.37% AbstractCellBasedSimulation::DoCellBirth 571ms 2.32% 67.82% 571ms 2.32% boost::numeric::ublas::same_impl_ex 266ms 1.08% 68.90% 559ms 2.27% __cxxabiv1::__si_class_type_info::__do_dyncast 84ms 0.34% 69.24% 517ms 2.10% std::__new_allocator::allocate (inline) 23ms 0.093% 69.34% 504ms 2.05% std::_Rb_tree::_Rb_tree (partial-inline) 1ms 0.0041% 69.34% 501ms 2.03% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 69.34% 500ms 2.03% std::allocator_traits::allocate (inline) 33ms 0.13% 69.48% 490ms 1.99% boost::detail::shared_count::~shared_count (inline) 0 0% 69.48% 490ms 1.99% boost::shared_ptr::~shared_ptr (inline) 475ms 1.93% 71.40% 475ms 1.93% __strcmp_avx2 43ms 0.17% 71.58% 474ms 1.92% std::_Rb_tree::_M_copy (inline) 0 0% 71.58% 470ms 1.91% std::_Rb_tree::_M_create_node (inline) 0 0% 71.58% 462ms 1.88% AbstractCellBasedSimulation::DoCellRemoval (inline) 6ms 0.024% 71.60% 454ms 1.84% Cell::GetMutationState 6ms 0.024% 71.63% 447ms 1.82% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 133ms 0.54% 72.17% 447ms 1.82% std::_Rb_tree::_M_erase 437ms 1.77% 73.94% 445ms 1.81% boost::detail::sp_counted_base::release 2ms 0.0081% 73.95% 434ms 1.76% AbstractCellProperty::IsSubType (inline) 31ms 0.13% 74.08% 432ms 1.75% operator new 157ms 0.64% 74.71% 430ms 1.75% std::_Rb_tree::_M_clone_node (inline) 0 0% 74.71% 428ms 1.74% std::_Rb_tree::_M_get_node (inline) 7ms 0.028% 74.74% 416ms 1.69% std::set::set (inline) 87ms 0.35% 75.10% 403ms 1.64% boost::numeric::ublas::vector_binary::size (inline) 107ms 0.43% 75.53% 391ms 1.59% __GI___libc_malloc 0 0% 75.53% 382ms 1.55% boost::numeric::ublas::inner_prod (inline) 3ms 0.012% 75.54% 380ms 1.54% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 21ms 0.085% 75.63% 377ms 1.53% boost::numeric::ublas::vector_scalar_binary::evaluate 79ms 0.32% 75.95% 354ms 1.44% Node::GetRadius 42ms 0.17% 76.12% 349ms 1.42% std::_Rb_tree::~_Rb_tree (inline) 346ms 1.41% 77.52% 346ms 1.41% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 77.52% 328ms 1.33% std::_Rb_tree::_Alloc_node::operator() (inline) 5ms 0.02% 77.54% 323ms 1.31% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 77.54% 317ms 1.29% NodesOnlyMesh::ReMesh 0 0% 77.54% 307ms 1.25% boost::numeric::ublas::c_vector::assign (inline) 0 0% 77.54% 302ms 1.23% std::_Rb_tree::_M_drop_node (inline) 3ms 0.012% 77.56% 300ms 1.22% NodesOnlyMesh::UpdateNodeIndices 299ms 1.21% 78.77% 299ms 1.21% __gnu_cxx::__normal_iterator::operator++ (inline) 125ms 0.51% 79.28% 297ms 1.21% boost::numeric::ublas::vector_inner_prod::apply (inline) 4ms 0.016% 79.29% 296ms 1.20% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 289ms 1.17% 80.47% 289ms 1.17% Node::CheckForNodeAttributes 0 0% 80.47% 289ms 1.17% NodesOnlyMesh::UpdateBoxCollection 7ms 0.028% 80.50% 278ms 1.13% DistributedBoxCollection::GetProcessOwningNode 8ms 0.032% 80.53% 271ms 1.10% std::_Rb_tree::_M_emplace_hint_unique 268ms 1.09% 81.62% 268ms 1.09% [libchaste_mesh.so] 3ms 0.012% 81.63% 259ms 1.05% std::__new_allocator::deallocate (inline) 0 0% 81.63% 252ms 1.02% std::set::~set (inline) 0 0% 81.63% 251ms 1.02% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 81.63% 248ms 1.01% VtkMeshWriter::WriteFiles 0 0% 81.63% 244ms 0.99% NodesOnlyMesh::AddNodesToBoxes 0 0% 81.63% 240ms 0.97% std::allocator_traits::deallocate (inline) 73ms 0.3% 81.93% 237ms 0.96% __GI___libc_free 0 0% 81.93% 236ms 0.96% std::_Rb_tree::_M_put_node (inline) 130ms 0.53% 82.45% 235ms 0.95% _int_malloc 103ms 0.42% 82.87% 234ms 0.95% std::__move_median_to_first (inline) 19ms 0.077% 82.95% 233ms 0.95% boost::numeric::ublas::vector_reference::operator() (inline) 117ms 0.48% 83.42% 226ms 0.92% boost::shared_ptr::shared_ptr (inline) 0 0% 83.42% 225ms 0.91% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 83.42% 219ms 0.89% vtkStreamingDemandDrivenPipeline::Update 0 0% 83.42% 219ms 0.89% vtkXMLWriterBase::Write 0 0% 83.42% 218ms 0.89% vtkExecutive::CallAlgorithm 0 0% 83.42% 218ms 0.89% vtkStreamingDemandDrivenPipeline::ProcessRequest 1ms 0.0041% 83.43% 218ms 0.89% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 83.43% 217ms 0.88% vtkDemandDrivenPipeline::ProcessRequest 0 0% 83.43% 216ms 0.88% vtkCompositeDataPipeline::ExecuteData 0 0% 83.43% 216ms 0.88% vtkDemandDrivenPipeline::ExecuteData 215ms 0.87% 84.30% 215ms 0.87% Node::GetIndex 130ms 0.53% 84.83% 214ms 0.87% Node::AddNeighbour 17ms 0.069% 84.90% 211ms 0.86% std::__insertion_sort (inline) 0 0% 84.90% 207ms 0.84% CellPropertyCollection::HasProperty 0 0% 84.90% 206ms 0.84% Cell::HasCellProperty (inline) 6ms 0.024% 84.92% 194ms 0.79% Cell::ReadyToDivide 0 0% 84.92% 179ms 0.73% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 84.92% 179ms 0.73% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 84.92% 177ms 0.72% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 4ms 0.016% 84.94% 166ms 0.67% AbstractCellProperty::IsType (inline) 149ms 0.61% 85.54% 164ms 0.67% _int_free 160ms 0.65% 86.19% 161ms 0.65% std::__adjacent_find (inline) 0 0% 86.19% 161ms 0.65% std::__unique (inline) 0 0% 86.19% 161ms 0.65% std::unique (inline) 0 0% 86.19% 159ms 0.65% NodesOnlyMesh::ResizeBoxCollection 159ms 0.65% 86.84% 159ms 0.65% [libchaste_cell_based.so] 0 0% 86.84% 159ms 0.65% std::_Rb_tree::clear (inline) 9ms 0.037% 86.88% 158ms 0.64% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 86.88% 151ms 0.61% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 86.88% 149ms 0.61% vtkXMLWriter::WriteBinaryData 148ms 0.6% 87.48% 148ms 0.6% __ieee754_log_fma 0 0% 87.48% 146ms 0.59% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.48% 146ms 0.59% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.48% 146ms 0.59% vtkXMLWriter::WriteCompressionBlock 145ms 0.59% 88.07% 145ms 0.59% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 143ms 0.58% 88.65% 143ms 0.58% Node::IsDeleted 0 0% 88.65% 142ms 0.58% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 88.65% 142ms 0.58% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 88.65% 142ms 0.58% vtkXMLWriter::WritePointsAppendedData 62ms 0.25% 88.90% 135ms 0.55% AbstractCellCycleModel::GetAge 2ms 0.0081% 88.91% 131ms 0.53% boost::numeric::ublas::c_vector::operator[] (inline) 1ms 0.0041% 88.91% 130ms 0.53% AbstractNumericalMethod::SafeNodePositionUpdate 1ms 0.0041% 88.91% 128ms 0.52% AbstractCellPopulation::SetCellUsingLocationIndex 46ms 0.19% 89.10% 127ms 0.52% AbstractCellProperty::IsSame 2ms 0.0081% 89.11% 127ms 0.52% Cell::GetCellId 127ms 0.52% 89.62% 127ms 0.52% Node::rGetLocation