File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 22097ms, 89.62% of 24656ms total Dropped 810 nodes (cum <= 123.28ms) flat flat% sum% cum cum% 0 0% 0% 24513ms 99.42% __libc_start_call_main 0 0% 0% 24513ms 99.42% __libc_start_main_impl 0 0% 0% 24513ms 99.42% _start 0 0% 0% 24496ms 99.35% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 24496ms 99.35% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 24496ms 99.35% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 24496ms 99.35% main 0 0% 0% 24458ms 99.20% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 24458ms 99.20% CxxTest::TestRunner::runTest (inline) 0 0% 0% 24458ms 99.20% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 24449ms 99.16% AbstractCellBasedSimulation::Solve 2ms 0.0081% 0.0081% 13825ms 56.07% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0041% 0.012% 9393ms 38.10% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0081% 0.02% 9026ms 36.61% ForwardEulerNumericalMethod::UpdateAllNodePositions 7ms 0.028% 0.049% 8849ms 35.89% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.049% 8373ms 33.96% NodeBasedCellPopulation::Update 1365ms 5.54% 5.58% 8090ms 32.81% RepulsionForce::AddForceContribution (partial-inline) 10ms 0.041% 5.63% 6246ms 25.33% DistributedBoxCollection::CalculateInteriorNodePairs 2192ms 8.89% 14.52% 4734ms 19.20% std::_Rb_tree::_M_lower_bound (inline) 12ms 0.049% 14.56% 4638ms 18.81% NodeAttributes::RemoveDuplicateNeighbours 1ms 0.0041% 14.57% 4492ms 18.22% OffLatticeSimulation::ApplyBoundaries 4ms 0.016% 14.58% 4438ms 18.00% std::__sort (inline) 0 0% 14.58% 4438ms 18.00% std::sort (inline) 201ms 0.82% 15.40% 4061ms 16.47% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 80ms 0.32% 15.72% 3113ms 12.63% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 263ms 1.07% 16.79% 3083ms 12.50% std::_Rb_tree::find (inline) 0 0% 16.79% 3082ms 12.50% std::map::find (inline) 3ms 0.012% 16.80% 2925ms 11.86% AbstractCellPopulation::Iterator::operator++ (inline) 157ms 0.64% 17.44% 2891ms 11.73% AbstractCellPopulation::Iterator::IsRealCell (inline) 196ms 0.79% 18.23% 2554ms 10.36% std::__introsort_loop 2498ms 10.13% 28.37% 2498ms 10.13% std::_Rb_tree::_S_right (inline) 35ms 0.14% 28.51% 2479ms 10.05% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 177ms 0.72% 29.23% 2422ms 9.82% std::map::operator[] (partial-inline) 23ms 0.093% 29.32% 2389ms 9.69% PlaneBoundaryCondition::ImposeBoundaryCondition 173ms 0.7% 30.02% 2286ms 9.27% AbstractMesh::GetNode 57ms 0.23% 30.25% 2277ms 9.24% NodesOnlyMesh::GetNodeOrHaloNode 0 0% 30.25% 2277ms 9.24% std::__unguarded_partition_pivot (inline) 154ms 0.62% 30.88% 2235ms 9.06% DistributedBoxCollection::AddPairsFromBox 55ms 0.22% 31.10% 2161ms 8.76% AbstractCellPopulation::GetLocationIndexUsingCell 98ms 0.4% 31.50% 2117ms 8.59% NodesOnlyMesh::SolveNodeMapping 15ms 0.061% 31.56% 2102ms 8.53% PlaneBoundaryCondition::VerifyBoundaryCondition 949ms 3.85% 35.41% 2028ms 8.23% std::__unguarded_partition (inline) 0 0% 35.41% 1970ms 7.99% std::_Rb_tree::lower_bound (inline) 0 0% 35.41% 1970ms 7.99% std::map::lower_bound (inline) 2ms 0.0081% 35.42% 1877ms 7.61% std::__final_insertion_sort (inline) 32ms 0.13% 35.55% 1695ms 6.87% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 34ms 0.14% 35.68% 1660ms 6.73% AbstractCellPopulation::GetCellUsingLocationIndex 122ms 0.49% 36.18% 1654ms 6.71% std::__unguarded_insertion_sort (inline) 548ms 2.22% 38.40% 1577ms 6.40% std::__unguarded_linear_insert (inline) 1430ms 5.80% 44.20% 1430ms 5.80% __gnu_cxx::__normal_iterator::operator-- (inline) 59ms 0.24% 44.44% 1294ms 5.25% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 44.44% 1199ms 4.86% NodeBasedCellPopulation::UpdateCellProcessLocation 7ms 0.028% 44.47% 1131ms 4.59% DistributedBoxCollection::CalculateBoundaryNodePairs 6ms 0.024% 44.49% 1123ms 4.55% boost::numeric::ublas::vector_assign (inline) 223ms 0.9% 45.40% 1051ms 4.26% boost::numeric::ublas::indexing_vector_assign 273ms 1.11% 46.50% 1000ms 4.06% __dynamic_cast 25ms 0.1% 46.61% 929ms 3.77% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 405ms 1.64% 48.25% 900ms 3.65% DistributedBoxCollection::CalculateContainingBox (partial-inline) 306ms 1.24% 49.49% 888ms 3.60% NodeAttributes::AddNeighbour 175ms 0.71% 50.20% 860ms 3.49% AbstractMesh::GetVectorFromAtoB 36ms 0.15% 50.34% 802ms 3.25% std::_Rb_tree_const_iterator::operator++ (inline) 4ms 0.016% 50.36% 797ms 3.23% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 50.36% 773ms 3.14% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 55ms 0.22% 50.58% 773ms 3.14% std::__copy_move::__copy_m (inline) 0 0% 50.58% 773ms 3.14% std::__copy_move_a (inline) 0 0% 50.58% 773ms 3.14% std::__copy_move_a1 (inline) 0 0% 50.58% 773ms 3.14% std::__copy_move_a2 (inline) 0 0% 50.58% 773ms 3.14% std::copy (inline) 759ms 3.08% 53.66% 759ms 3.08% std::_Rb_tree_increment 0 0% 53.66% 758ms 3.07% boost::numeric::ublas::norm_2 (inline) 612ms 2.48% 56.14% 758ms 3.07% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 56.14% 758ms 3.07% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 744ms 3.02% 59.16% 744ms 3.02% boost::numeric::ublas::c_vector::operator() 0 0% 59.16% 740ms 3.00% AbstractCellPopulation::WriteResultsToFiles 737ms 2.99% 62.15% 737ms 2.99% __memcpy_avx_unaligned_erms 11ms 0.045% 62.20% 713ms 2.89% CellPropertyCollection::GetPropertiesType (inline) 3ms 0.012% 62.21% 675ms 2.74% AbstractCentreBasedCellPopulation::GetDampingConstant 581ms 2.36% 64.56% 646ms 2.62% std::vector::push_back (inline) 61ms 0.25% 64.81% 593ms 2.41% std::_Rb_tree::_Rb_tree (partial-inline) 276ms 1.12% 65.93% 578ms 2.34% __cxxabiv1::__si_class_type_info::__do_dyncast 573ms 2.32% 68.26% 573ms 2.32% boost::numeric::ublas::same_impl_ex 10ms 0.041% 68.30% 560ms 2.27% AbstractCellBasedSimulation::DoCellBirth 112ms 0.45% 68.75% 549ms 2.23% std::__new_allocator::allocate (inline) 0 0% 68.75% 533ms 2.16% std::allocator_traits::allocate (inline) 513ms 2.08% 70.83% 513ms 2.08% __strcmp_avx2 34ms 0.14% 70.97% 512ms 2.08% std::_Rb_tree::_M_copy (inline) 0 0% 70.97% 508ms 2.06% std::_Rb_tree::_M_create_node (inline) 0 0% 70.97% 490ms 1.99% NodeBasedCellPopulation::WriteVtkResultsToFile 5ms 0.02% 70.99% 487ms 1.98% std::set::set (inline) 3ms 0.012% 71.00% 482ms 1.95% Cell::GetMutationState 147ms 0.6% 71.60% 473ms 1.92% std::_Rb_tree::_M_clone_node (inline) 35ms 0.14% 71.74% 467ms 1.89% boost::detail::shared_count::~shared_count (inline) 0 0% 71.74% 467ms 1.89% boost::shared_ptr::~shared_ptr (inline) 0 0% 71.74% 459ms 1.86% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 71.74% 446ms 1.81% std::_Rb_tree::_M_get_node (inline) 3ms 0.012% 71.75% 444ms 1.80% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 22ms 0.089% 71.84% 437ms 1.77% operator new 0 0% 71.84% 429ms 1.74% AbstractCellProperty::IsSubType (inline) 409ms 1.66% 73.50% 423ms 1.72% boost::detail::sp_counted_base::release 0 0% 73.50% 416ms 1.69% boost::numeric::ublas::inner_prod (inline) 3ms 0.012% 73.51% 415ms 1.68% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 106ms 0.43% 73.94% 413ms 1.68% boost::numeric::ublas::vector_binary::size (inline) 22ms 0.089% 74.03% 412ms 1.67% boost::numeric::ublas::vector_scalar_binary::evaluate 115ms 0.47% 74.50% 404ms 1.64% __GI___libc_malloc 111ms 0.45% 74.95% 393ms 1.59% std::_Rb_tree::_M_erase 384ms 1.56% 76.50% 384ms 1.56% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 76.50% 363ms 1.47% std::_Rb_tree::_Alloc_node::operator() (inline) 84ms 0.34% 76.85% 360ms 1.46% Node::GetRadius 7ms 0.028% 76.87% 343ms 1.39% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 76.87% 343ms 1.39% boost::numeric::ublas::c_vector::assign (inline) 145ms 0.59% 77.46% 341ms 1.38% boost::numeric::ublas::vector_inner_prod::apply (inline) 3ms 0.012% 77.47% 323ms 1.31% DistributedBoxCollection::GetProcessOwningNode 323ms 1.31% 78.78% 323ms 1.31% __gnu_cxx::__normal_iterator::operator++ (inline) 1ms 0.0041% 78.79% 321ms 1.30% NodesOnlyMesh::ReMesh 2ms 0.0081% 78.80% 312ms 1.27% NodeBasedCellPopulation::UpdateMapsAfterRemesh 3ms 0.012% 78.81% 310ms 1.26% NodesOnlyMesh::UpdateNodeIndices 40ms 0.16% 78.97% 309ms 1.25% std::_Rb_tree::~_Rb_tree (inline) 296ms 1.20% 80.17% 296ms 1.20% Node::CheckForNodeAttributes 244ms 0.99% 81.16% 287ms 1.16% Node::AddNeighbour 0 0% 81.16% 277ms 1.12% std::_Rb_tree::_M_drop_node (inline) 0 0% 81.16% 275ms 1.12% NodesOnlyMesh::UpdateBoxCollection 14ms 0.057% 81.22% 275ms 1.12% std::_Rb_tree::_M_emplace_hint_unique 0 0% 81.22% 245ms 0.99% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 81.22% 245ms 0.99% CellPropertyCollection::HasProperty 119ms 0.48% 81.70% 245ms 0.99% boost::shared_ptr::shared_ptr (inline) 111ms 0.45% 82.15% 245ms 0.99% std::__move_median_to_first (inline) 0 0% 82.15% 244ms 0.99% Cell::HasCellProperty (inline) 0 0% 82.15% 244ms 0.99% VtkMeshWriter::WriteFiles 125ms 0.51% 82.66% 239ms 0.97% _int_malloc 0 0% 82.66% 239ms 0.97% std::set::~set (inline) 5ms 0.02% 82.68% 232ms 0.94% Cell::ReadyToDivide 2ms 0.0081% 82.69% 232ms 0.94% std::__new_allocator::deallocate (inline) 4ms 0.016% 82.70% 226ms 0.92% NodesOnlyMesh::AddNodesToBoxes 0 0% 82.70% 224ms 0.91% boost::numeric::ublas::vector_binary::operator() (inline) 17ms 0.069% 82.77% 221ms 0.9% boost::numeric::ublas::vector_reference::operator() (inline) 27ms 0.11% 82.88% 221ms 0.9% std::__insertion_sort (inline) 75ms 0.3% 83.18% 218ms 0.88% __GI___libc_free 0 0% 83.18% 218ms 0.88% std::allocator_traits::deallocate (inline) 0 0% 83.18% 218ms 0.88% vtkStreamingDemandDrivenPipeline::Update 0 0% 83.18% 218ms 0.88% vtkXMLWriterBase::Write 0 0% 83.18% 217ms 0.88% vtkDemandDrivenPipeline::ProcessRequest 0 0% 83.18% 216ms 0.88% std::_Rb_tree::_M_put_node (inline) 0 0% 83.18% 214ms 0.87% vtkExecutive::CallAlgorithm 0 0% 83.18% 212ms 0.86% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 83.18% 212ms 0.86% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 83.18% 211ms 0.86% vtkDemandDrivenPipeline::ExecuteData 0 0% 83.18% 210ms 0.85% vtkCompositeDataPipeline::ExecuteData 209ms 0.85% 84.03% 209ms 0.85% Node::GetIndex 197ms 0.8% 84.83% 197ms 0.8% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 3ms 0.012% 84.84% 193ms 0.78% AbstractCellProperty::IsType (inline) 188ms 0.76% 85.61% 188ms 0.76% [libchaste_mesh.so] 0 0% 85.61% 181ms 0.73% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.61% 181ms 0.73% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 85.61% 173ms 0.7% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 170ms 0.69% 86.30% 170ms 0.69% std::__adjacent_find (inline) 0 0% 86.30% 170ms 0.69% std::__unique (inline) 0 0% 86.30% 170ms 0.69% std::unique (inline) 0 0% 86.30% 166ms 0.67% NodesOnlyMesh::ResizeBoxCollection 166ms 0.67% 86.97% 166ms 0.67% [libchaste_cell_based.so] 14ms 0.057% 87.03% 164ms 0.67% NodesOnlyMesh::IsANodeCloseToDomainBoundary 1ms 0.0041% 87.03% 161ms 0.65% Cell::GetCellId 3ms 0.012% 87.04% 156ms 0.63% boost::numeric::ublas::c_vector::operator[] (inline) 57ms 0.23% 87.27% 151ms 0.61% AbstractCellProperty::IsSame 0 0% 87.27% 149ms 0.6% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 87.27% 148ms 0.6% vtkXMLWriter::WriteBinaryData 0 0% 87.27% 145ms 0.59% std::_Rb_tree::_Auto_node::_Auto_node (inline) 130ms 0.53% 87.80% 143ms 0.58% _int_free 73ms 0.3% 88.10% 141ms 0.57% AbstractCellCycleModel::GetAge 139ms 0.56% 88.66% 139ms 0.56% __ieee754_log_fma 138ms 0.56% 89.22% 138ms 0.56% boost::shared_ptr::operator-> (inline) 0 0% 89.22% 137ms 0.56% vtkXMLWriter::WriteBinaryDataBlock 0 0% 89.22% 137ms 0.56% vtkXMLWriter::WriteBinaryDataInternal 0 0% 89.22% 137ms 0.56% vtkXMLWriter::WriteCompressionBlock 0 0% 89.22% 134ms 0.54% std::_Rb_tree::clear (inline) 0 0% 89.22% 134ms 0.54% vtkXMLWriter::WritePointsAppendedData 2ms 0.0081% 89.23% 132ms 0.54% AbstractNumericalMethod::SafeNodePositionUpdate 96ms 0.39% 89.62% 126ms 0.51% boost::detail::shared_count::shared_count (inline) 1ms 0.0041% 89.62% 126ms 0.51% boost::numeric::ublas::scalar_traits::type_sqrt (inline)