File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 22463ms, 88.40% of 25410ms total Dropped 808 nodes (cum <= 127.05ms) flat flat% sum% cum cum% 0 0% 0% 25252ms 99.38% __libc_start_call_main 0 0% 0% 25252ms 99.38% __libc_start_main_impl 0 0% 0% 25252ms 99.38% _start 0 0% 0% 25237ms 99.32% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 25237ms 99.32% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 25237ms 99.32% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 25237ms 99.32% main 0 0% 0% 25196ms 99.16% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 25196ms 99.16% CxxTest::TestRunner::runTest (inline) 0 0% 0% 25196ms 99.16% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 25187ms 99.12% AbstractCellBasedSimulation::Solve 3ms 0.012% 0.012% 14152ms 55.69% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.012% 9763ms 38.42% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.016% 0.028% 9110ms 35.85% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.031% 0.059% 8938ms 35.18% AbstractNumericalMethod::ComputeForcesIncludingDamping 2ms 0.0079% 0.067% 8533ms 33.58% NodeBasedCellPopulation::Update 1246ms 4.90% 4.97% 7959ms 31.32% RepulsionForce::AddForceContribution (partial-inline) 7ms 0.028% 5.00% 6218ms 24.47% DistributedBoxCollection::CalculateInteriorNodePairs 2152ms 8.47% 13.47% 5094ms 20.05% std::_Rb_tree::_M_lower_bound (inline) 11ms 0.043% 13.51% 4703ms 18.51% NodeAttributes::RemoveDuplicateNeighbours 0 0% 13.51% 4655ms 18.32% OffLatticeSimulation::ApplyBoundaries 9ms 0.035% 13.55% 4385ms 17.26% std::__sort (inline) 0 0% 13.55% 4385ms 17.26% std::sort (inline) 191ms 0.75% 14.30% 4196ms 16.51% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 2ms 0.0079% 14.31% 3565ms 14.03% AbstractCellPopulation::Iterator::operator++ (inline) 207ms 0.81% 15.12% 3543ms 13.94% AbstractCellPopulation::Iterator::IsRealCell (inline) 72ms 0.28% 15.40% 3434ms 13.51% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 263ms 1.04% 16.44% 3287ms 12.94% std::_Rb_tree::find (inline) 0 0% 16.44% 3286ms 12.93% std::map::find (inline) 21ms 0.083% 16.52% 2988ms 11.76% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2899ms 11.41% 27.93% 2899ms 11.41% std::_Rb_tree::_S_right (inline) 235ms 0.92% 28.85% 2619ms 10.31% std::map::operator[] (partial-inline) 209ms 0.82% 29.68% 2527ms 9.94% std::__introsort_loop 31ms 0.12% 29.80% 2451ms 9.65% PlaneBoundaryCondition::ImposeBoundaryCondition 170ms 0.67% 30.47% 2354ms 9.26% AbstractMesh::GetNode 34ms 0.13% 30.60% 2336ms 9.19% AbstractCellPopulation::GetLocationIndexUsingCell 33ms 0.13% 30.73% 2326ms 9.15% NodesOnlyMesh::GetNodeOrHaloNode 280ms 1.10% 31.83% 2309ms 9.09% DistributedBoxCollection::AddPairsFromBox 0 0% 31.83% 2241ms 8.82% std::__unguarded_partition_pivot (inline) 22ms 0.087% 31.92% 2203ms 8.67% PlaneBoundaryCondition::VerifyBoundaryCondition 82ms 0.32% 32.24% 2187ms 8.61% NodesOnlyMesh::SolveNodeMapping 0 0% 32.24% 2089ms 8.22% std::_Rb_tree::lower_bound (inline) 0 0% 32.24% 2089ms 8.22% std::map::lower_bound (inline) 1000ms 3.94% 36.18% 1936ms 7.62% std::__unguarded_partition (inline) 0 0% 36.18% 1847ms 7.27% std::__final_insertion_sort (inline) 39ms 0.15% 36.33% 1795ms 7.06% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 27ms 0.11% 36.44% 1748ms 6.88% AbstractCellPopulation::GetCellUsingLocationIndex 93ms 0.37% 36.80% 1641ms 6.46% std::__unguarded_insertion_sort (inline) 537ms 2.11% 38.92% 1584ms 6.23% std::__unguarded_linear_insert (inline) 1506ms 5.93% 44.84% 1506ms 5.93% __gnu_cxx::__normal_iterator::operator-- (inline) 58ms 0.23% 45.07% 1311ms 5.16% boost::numeric::ublas::c_vector::c_vector (partial-inline) 7ms 0.028% 45.10% 1281ms 5.04% DistributedBoxCollection::CalculateBoundaryNodePairs 0 0% 45.10% 1241ms 4.88% NodeBasedCellPopulation::UpdateCellProcessLocation 41ms 0.16% 45.26% 1186ms 4.67% boost::numeric::ublas::vector_assign (inline) 290ms 1.14% 46.40% 1052ms 4.14% boost::numeric::ublas::indexing_vector_assign 306ms 1.20% 47.61% 1031ms 4.06% __dynamic_cast 39ms 0.15% 47.76% 1000ms 3.94% std::_Rb_tree_const_iterator::operator++ (inline) 953ms 3.75% 51.51% 953ms 3.75% std::_Rb_tree_increment 23ms 0.091% 51.60% 934ms 3.68% CellPropertyCollection::GetPropertiesType (inline) 401ms 1.58% 53.18% 915ms 3.60% NodeAttributes::AddNeighbour 4ms 0.016% 53.20% 885ms 3.48% AbstractCentreBasedCellPopulation::GetDampingConstant 161ms 0.63% 53.83% 800ms 3.15% AbstractMesh::GetVectorFromAtoB 0 0% 53.83% 772ms 3.04% AbstractCellPopulation::WriteResultsToFiles 22ms 0.087% 53.92% 772ms 3.04% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 335ms 1.32% 55.23% 762ms 3.00% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 55.23% 761ms 2.99% AbstractCellBasedSimulation::DoCellBirth 0 0% 55.23% 749ms 2.95% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 55.23% 727ms 2.86% boost::numeric::ublas::norm_2 (inline) 569ms 2.24% 57.47% 727ms 2.86% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 57.47% 727ms 2.86% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 707ms 2.78% 60.26% 707ms 2.78% boost::numeric::ublas::c_vector::operator() 8ms 0.031% 60.29% 699ms 2.75% boost::numeric::ublas::c_vector::operator= (inline) 46ms 0.18% 60.47% 691ms 2.72% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 60.47% 682ms 2.68% Cell::GetMutationState 45ms 0.18% 60.65% 673ms 2.65% std::__copy_move::__copy_m (inline) 0 0% 60.65% 673ms 2.65% std::__copy_move_a (inline) 0 0% 60.65% 673ms 2.65% std::__copy_move_a1 (inline) 0 0% 60.65% 673ms 2.65% std::__copy_move_a2 (inline) 0 0% 60.65% 673ms 2.65% std::copy (inline) 154ms 0.61% 61.25% 660ms 2.60% std::__new_allocator::allocate (inline) 514ms 2.02% 63.27% 647ms 2.55% std::vector::push_back (inline) 0 0% 63.27% 645ms 2.54% std::allocator_traits::allocate (inline) 643ms 2.53% 65.80% 643ms 2.53% __memcpy_avx_unaligned_erms 50ms 0.2% 66.00% 632ms 2.49% std::_Rb_tree::_M_copy (inline) 0 0% 66.00% 628ms 2.47% std::_Rb_tree::_M_create_node (inline) 257ms 1.01% 67.01% 602ms 2.37% __cxxabiv1::__si_class_type_info::__do_dyncast 202ms 0.79% 67.81% 582ms 2.29% std::_Rb_tree::_M_clone_node (inline) 2ms 0.0079% 67.82% 558ms 2.20% std::set::set (inline) 0 0% 67.82% 549ms 2.16% std::_Rb_tree::_M_get_node (inline) 42ms 0.17% 67.98% 515ms 2.03% boost::detail::shared_count::~shared_count (inline) 0 0% 67.98% 515ms 2.03% boost::shared_ptr::~shared_ptr (inline) 2ms 0.0079% 67.99% 502ms 1.98% NodeBasedCellPopulation::WriteVtkResultsToFile 493ms 1.94% 69.93% 493ms 1.94% __strcmp_avx2 198ms 0.78% 70.71% 492ms 1.94% std::_Rb_tree::_M_erase 32ms 0.13% 70.83% 491ms 1.93% operator new 461ms 1.81% 72.65% 468ms 1.84% boost::detail::sp_counted_base::release 0 0% 72.65% 467ms 1.84% AbstractCellBasedSimulation::DoCellRemoval (inline) 467ms 1.84% 74.49% 467ms 1.84% boost::numeric::ublas::same_impl_ex 106ms 0.42% 74.90% 452ms 1.78% __GI___libc_malloc 0 0% 74.90% 451ms 1.77% AbstractCellProperty::IsSubType (inline) 2ms 0.0079% 74.91% 448ms 1.76% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 74.91% 445ms 1.75% std::_Rb_tree::_Alloc_node::operator() (inline) 418ms 1.65% 76.56% 418ms 1.65% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 2ms 0.0079% 76.56% 382ms 1.50% CellPropertyCollection::HasProperty 130ms 0.51% 77.08% 382ms 1.50% Node::GetRadius 0 0% 77.08% 380ms 1.50% Cell::HasCellProperty (inline) 8ms 0.031% 77.11% 379ms 1.49% Cell::ReadyToDivide 41ms 0.16% 77.27% 366ms 1.44% std::_Rb_tree::~_Rb_tree (inline) 1ms 0.0039% 77.27% 363ms 1.43% NodesOnlyMesh::ReMesh 1ms 0.0039% 77.28% 346ms 1.36% NodesOnlyMesh::UpdateNodeIndices 0 0% 77.28% 338ms 1.33% boost::numeric::ublas::c_vector::assign (inline) 3ms 0.012% 77.29% 332ms 1.31% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 77.29% 330ms 1.30% boost::numeric::ublas::inner_prod (inline) 1ms 0.0039% 77.29% 330ms 1.30% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 15ms 0.059% 77.35% 329ms 1.29% boost::numeric::ublas::vector_scalar_binary::evaluate 24ms 0.094% 77.45% 314ms 1.24% boost::numeric::ublas::vector_binary::size (inline) 172ms 0.68% 78.12% 304ms 1.20% _int_malloc 98ms 0.39% 78.51% 300ms 1.18% std::__move_median_to_first (inline) 5ms 0.02% 78.53% 295ms 1.16% std::_Rb_tree::_M_emplace_hint_unique 0 0% 78.53% 292ms 1.15% std::_Rb_tree::_M_drop_node (inline) 287ms 1.13% 79.66% 287ms 1.13% std::__adjacent_find (inline) 0 0% 79.66% 287ms 1.13% std::__unique (inline) 0 0% 79.66% 287ms 1.13% std::unique (inline) 0 0% 79.66% 279ms 1.10% NodesOnlyMesh::UpdateBoxCollection 260ms 1.02% 80.68% 260ms 1.02% Node::CheckForNodeAttributes 106ms 0.42% 81.10% 260ms 1.02% boost::numeric::ublas::vector_inner_prod::apply (inline) 2ms 0.0079% 81.11% 258ms 1.02% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 258ms 1.02% 82.12% 258ms 1.02% __gnu_cxx::__normal_iterator::operator++ (inline) 7ms 0.028% 82.15% 245ms 0.96% DistributedBoxCollection::GetProcessOwningNode 0 0% 82.15% 241ms 0.95% std::set::~set (inline) 0 0% 82.15% 236ms 0.93% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 82.15% 235ms 0.92% VtkMeshWriter::WriteFiles 234ms 0.92% 83.07% 234ms 0.92% boost::shared_ptr::operator-> (inline) 3ms 0.012% 83.08% 226ms 0.89% std::__new_allocator::deallocate (inline) 0 0% 83.08% 225ms 0.89% NodesOnlyMesh::ResizeBoxCollection 11ms 0.043% 83.12% 224ms 0.88% NodesOnlyMesh::IsANodeCloseToDomainBoundary 2ms 0.0079% 83.13% 220ms 0.87% NodesOnlyMesh::AddNodesToBoxes 0 0% 83.13% 211ms 0.83% vtkStreamingDemandDrivenPipeline::Update 0 0% 83.13% 211ms 0.83% vtkXMLWriterBase::Write 0 0% 83.13% 209ms 0.82% std::allocator_traits::deallocate (inline) 0 0% 83.13% 209ms 0.82% vtkDemandDrivenPipeline::ProcessRequest 72ms 0.28% 83.42% 207ms 0.81% __GI___libc_free 0 0% 83.42% 207ms 0.81% std::_Rb_tree::_M_put_node (inline) 0 0% 83.42% 207ms 0.81% vtkStreamingDemandDrivenPipeline::ProcessRequest 15ms 0.059% 83.48% 206ms 0.81% std::__insertion_sort (inline) 1ms 0.0039% 83.48% 206ms 0.81% vtkCompositeDataPipeline::ExecuteData 0 0% 83.48% 205ms 0.81% vtkDemandDrivenPipeline::ExecuteData 0 0% 83.48% 205ms 0.81% vtkExecutive::CallAlgorithm 0 0% 83.48% 204ms 0.8% vtkXMLUnstructuredDataWriter::ProcessRequest 199ms 0.78% 84.26% 199ms 0.78% Node::GetIndex 0 0% 84.26% 193ms 0.76% std::_Rb_tree::clear (inline) 7ms 0.028% 84.29% 192ms 0.76% AbstractCellProperty::IsType (inline) 86ms 0.34% 84.63% 186ms 0.73% boost::shared_ptr::shared_ptr (inline) 0 0% 84.63% 183ms 0.72% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 84.63% 178ms 0.7% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 84.63% 178ms 0.7% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 84.63% 172ms 0.68% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 169ms 0.67% 85.29% 169ms 0.67% [libchaste_cell_based.so] 0 0% 85.29% 166ms 0.65% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 85.29% 165ms 0.65% Cell::GetCellId 165ms 0.65% 85.94% 165ms 0.65% Node::IsDeleted 7ms 0.028% 85.97% 157ms 0.62% DistributedBoxCollection::GetIsPeriodicAllDims 87ms 0.34% 86.31% 156ms 0.61% AbstractCellProperty::IsSame 153ms 0.6% 86.91% 153ms 0.6% [libchaste_mesh.so] 0 0% 86.91% 152ms 0.6% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 87ms 0.34% 87.26% 146ms 0.57% Node::AddNeighbour 68ms 0.27% 87.52% 142ms 0.56% AbstractCellCycleModel::GetAge 0 0% 87.52% 140ms 0.55% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 87.52% 140ms 0.55% std::map::clear (inline) 0 0% 87.52% 138ms 0.54% vtkXMLWriter::WriteBinaryData 0 0% 87.52% 137ms 0.54% Cell::GetCellProliferativeType 17ms 0.067% 87.59% 137ms 0.54% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 87.59% 137ms 0.54% std::map::map (inline) 0 0% 87.59% 137ms 0.54% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.59% 137ms 0.54% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.59% 136ms 0.54% vtkXMLWriter::WriteCompressionBlock 121ms 0.48% 88.07% 135ms 0.53% _int_free 82ms 0.32% 88.39% 133ms 0.52% std::vector::emplace_back (inline) 1ms 0.0039% 88.39% 132ms 0.52% std::_Rb_tree::_M_insert_unique 0 0% 88.39% 132ms 0.52% std::set::insert (inline) 2ms 0.0079% 88.40% 129ms 0.51% boost::numeric::ublas::c_vector::operator[] (inline)