File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20128ms, 87.70% of 22950ms total Dropped 764 nodes (cum <= 114.75ms) flat flat% sum% cum cum% 0 0% 0% 22813ms 99.40% __libc_start_call_main 0 0% 0% 22813ms 99.40% __libc_start_main_impl 0 0% 0% 22813ms 99.40% _start 0 0% 0% 22799ms 99.34% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 22799ms 99.34% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 22799ms 99.34% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 22799ms 99.34% main 0 0% 0% 22765ms 99.19% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 22765ms 99.19% CxxTest::TestRunner::runTest (inline) 0 0% 0% 22765ms 99.19% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0044% 0.0044% 22757ms 99.16% AbstractCellBasedSimulation::Solve 1ms 0.0044% 0.0087% 12987ms 56.59% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0087% 8607ms 37.50% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0087% 0.017% 8193ms 35.70% ForwardEulerNumericalMethod::UpdateAllNodePositions 12ms 0.052% 0.07% 8016ms 34.93% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.07% 7616ms 33.19% NodeBasedCellPopulation::Update 1222ms 5.32% 5.39% 7443ms 32.43% RepulsionForce::AddForceContribution (partial-inline) 10ms 0.044% 5.44% 5604ms 24.42% DistributedBoxCollection::CalculateInteriorNodePairs 2104ms 9.17% 14.61% 4866ms 21.20% std::_Rb_tree::_M_lower_bound (inline) 0 0% 14.61% 4506ms 19.63% OffLatticeSimulation::ApplyBoundaries 18ms 0.078% 14.68% 4465ms 19.46% NodeAttributes::RemoveDuplicateNeighbours 5ms 0.022% 14.71% 4301ms 18.74% std::__sort (inline) 0 0% 14.71% 4301ms 18.74% std::sort (inline) 165ms 0.72% 15.42% 3736ms 16.28% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 5ms 0.022% 15.45% 3366ms 14.67% AbstractCellPopulation::Iterator::operator++ (inline) 60ms 0.26% 15.71% 3358ms 14.63% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 176ms 0.77% 16.47% 3337ms 14.54% AbstractCellPopulation::Iterator::IsRealCell (inline) 237ms 1.03% 17.51% 3193ms 13.91% std::_Rb_tree::find (inline) 0 0% 17.51% 3193ms 13.91% std::map::find (inline) 28ms 0.12% 17.63% 2848ms 12.41% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2711ms 11.81% 29.44% 2711ms 11.81% std::_Rb_tree::_S_right (inline) 280ms 1.22% 30.66% 2469ms 10.76% std::map::operator[] (partial-inline) 166ms 0.72% 31.39% 2426ms 10.57% std::__introsort_loop 41ms 0.18% 31.56% 2380ms 10.37% AbstractCellPopulation::GetLocationIndexUsingCell 35ms 0.15% 31.72% 2359ms 10.28% PlaneBoundaryCondition::ImposeBoundaryCondition 144ms 0.63% 32.34% 2198ms 9.58% AbstractMesh::GetNode 43ms 0.19% 32.53% 2173ms 9.47% NodesOnlyMesh::GetNodeOrHaloNode 0 0% 32.53% 2165ms 9.43% std::__unguarded_partition_pivot (inline) 17ms 0.074% 32.61% 2147ms 9.36% PlaneBoundaryCondition::VerifyBoundaryCondition 61ms 0.27% 32.87% 2061ms 8.98% NodesOnlyMesh::SolveNodeMapping 1026ms 4.47% 37.34% 1940ms 8.45% std::__unguarded_partition (inline) 0 0% 37.34% 1937ms 8.44% std::_Rb_tree::lower_bound (inline) 0 0% 37.34% 1937ms 8.44% std::map::lower_bound (inline) 0 0% 37.34% 1868ms 8.14% std::__final_insertion_sort (inline) 164ms 0.71% 38.06% 1754ms 7.64% DistributedBoxCollection::AddPairsFromBox 74ms 0.32% 38.38% 1657ms 7.22% std::__unguarded_insertion_sort (inline) 605ms 2.64% 41.02% 1649ms 7.19% std::__unguarded_linear_insert (inline) 1488ms 6.48% 47.50% 1488ms 6.48% __gnu_cxx::__normal_iterator::operator-- (inline) 16ms 0.07% 47.57% 1426ms 6.21% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 25ms 0.11% 47.68% 1405ms 6.12% AbstractCellPopulation::GetCellUsingLocationIndex 37ms 0.16% 47.84% 1332ms 5.80% boost::numeric::ublas::c_vector::c_vector (partial-inline) 43ms 0.19% 48.03% 1215ms 5.29% boost::numeric::ublas::vector_assign (inline) 0 0% 48.03% 1172ms 5.11% NodeBasedCellPopulation::UpdateCellProcessLocation 287ms 1.25% 49.28% 1093ms 4.76% boost::numeric::ublas::indexing_vector_assign 2ms 0.0087% 49.29% 1067ms 4.65% DistributedBoxCollection::CalculateBoundaryNodePairs 253ms 1.10% 50.39% 958ms 4.17% __dynamic_cast 153ms 0.67% 51.05% 837ms 3.65% AbstractMesh::GetVectorFromAtoB 20ms 0.087% 51.14% 789ms 3.44% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 336ms 1.46% 52.61% 759ms 3.31% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 52.61% 753ms 3.28% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 52.61% 736ms 3.21% boost::numeric::ublas::norm_2 (inline) 584ms 2.54% 55.15% 736ms 3.21% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 55.15% 736ms 3.21% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 729ms 3.18% 58.33% 729ms 3.18% boost::numeric::ublas::c_vector::operator() 197ms 0.86% 59.19% 709ms 3.09% NodeAttributes::AddNeighbour 0 0% 59.19% 703ms 3.06% AbstractCellPopulation::WriteResultsToFiles 7ms 0.031% 59.22% 677ms 2.95% boost::numeric::ublas::c_vector::operator= (inline) 36ms 0.16% 59.37% 663ms 2.89% std::__copy_move::__copy_m (inline) 0 0% 59.37% 663ms 2.89% std::__copy_move_a (inline) 0 0% 59.37% 663ms 2.89% std::__copy_move_a1 (inline) 0 0% 59.37% 663ms 2.89% std::__copy_move_a2 (inline) 0 0% 59.37% 663ms 2.89% std::copy (inline) 647ms 2.82% 62.19% 647ms 2.82% __memcpy_avx_unaligned_erms 510ms 2.22% 64.41% 582ms 2.54% std::vector::push_back (inline) 280ms 1.22% 65.63% 580ms 2.53% __cxxabiv1::__si_class_type_info::__do_dyncast 3ms 0.013% 65.65% 544ms 2.37% AbstractCellBasedSimulation::DoCellBirth 5ms 0.022% 65.67% 531ms 2.31% CellPropertyCollection::GetPropertiesType (inline) 508ms 2.21% 67.88% 508ms 2.21% boost::numeric::ublas::same_impl_ex 5ms 0.022% 67.90% 504ms 2.20% AbstractCentreBasedCellPopulation::GetDampingConstant 67ms 0.29% 68.20% 502ms 2.19% std::__new_allocator::allocate (inline) 40ms 0.17% 68.37% 494ms 2.15% std::_Rb_tree_const_iterator::operator++ (inline) 44ms 0.19% 68.56% 491ms 2.14% boost::detail::shared_count::~shared_count (inline) 0 0% 68.56% 491ms 2.14% boost::shared_ptr::~shared_ptr (inline) 0 0% 68.56% 482ms 2.10% std::allocator_traits::allocate (inline) 1ms 0.0044% 68.57% 459ms 2.00% NodeBasedCellPopulation::WriteVtkResultsToFile 459ms 2.00% 70.57% 459ms 2.00% __strcmp_avx2 452ms 1.97% 72.54% 452ms 1.97% std::_Rb_tree_increment 0 0% 72.54% 445ms 1.94% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 72.54% 443ms 1.93% std::_Rb_tree::_M_create_node (inline) 429ms 1.87% 74.41% 439ms 1.91% boost::detail::sp_counted_base::release 5ms 0.022% 74.43% 437ms 1.90% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 26ms 0.11% 74.54% 433ms 1.89% operator new 11ms 0.048% 74.59% 428ms 1.86% std::_Rb_tree::_Rb_tree (partial-inline) 100ms 0.44% 75.02% 402ms 1.75% __GI___libc_malloc 50ms 0.22% 75.24% 402ms 1.75% std::_Rb_tree::_M_copy (inline) 2ms 0.0087% 75.25% 390ms 1.70% AbstractCellProperty::IsSubType (inline) 0 0% 75.25% 390ms 1.70% std::_Rb_tree::_M_get_node (inline) 127ms 0.55% 75.80% 383ms 1.67% std::_Rb_tree::_M_erase 119ms 0.52% 76.32% 362ms 1.58% Node::GetRadius 0 0% 76.32% 355ms 1.55% boost::numeric::ublas::c_vector::assign (inline) 5ms 0.022% 76.34% 353ms 1.54% Cell::GetMutationState 108ms 0.47% 76.81% 352ms 1.53% std::_Rb_tree::_M_clone_node (inline) 30ms 0.13% 76.95% 351ms 1.53% boost::numeric::ublas::vector_binary::size (inline) 2ms 0.0087% 76.95% 343ms 1.49% std::set::set (inline) 0 0% 76.95% 331ms 1.44% boost::numeric::ublas::inner_prod (inline) 2ms 0.0087% 76.96% 330ms 1.44% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 14ms 0.061% 77.02% 328ms 1.43% boost::numeric::ublas::vector_scalar_binary::evaluate 6ms 0.026% 77.05% 319ms 1.39% NodeBasedCellPopulation::UpdateMapsAfterRemesh 311ms 1.36% 78.41% 311ms 1.36% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 78.41% 307ms 1.34% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 78.41% 304ms 1.32% NodesOnlyMesh::ReMesh 39ms 0.17% 78.58% 302ms 1.32% std::_Rb_tree::~_Rb_tree (inline) 1ms 0.0044% 78.58% 295ms 1.29% NodesOnlyMesh::UpdateNodeIndices 280ms 1.22% 79.80% 280ms 1.22% __gnu_cxx::__normal_iterator::operator++ (inline) 2ms 0.0087% 79.81% 269ms 1.17% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 6ms 0.026% 79.83% 257ms 1.12% DistributedBoxCollection::GetProcessOwningNode 257ms 1.12% 80.95% 257ms 1.12% Node::CheckForNodeAttributes 148ms 0.64% 81.60% 255ms 1.11% _int_malloc 0 0% 81.60% 254ms 1.11% std::_Rb_tree::_M_drop_node (inline) 99ms 0.43% 82.03% 253ms 1.10% boost::numeric::ublas::vector_inner_prod::apply (inline) 10ms 0.044% 82.07% 252ms 1.10% std::_Rb_tree::_M_emplace_hint_unique 0 0% 82.07% 223ms 0.97% NodesOnlyMesh::UpdateBoxCollection 103ms 0.45% 82.52% 220ms 0.96% std::__move_median_to_first (inline) 0 0% 82.52% 219ms 0.95% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 82.52% 217ms 0.95% VtkMeshWriter::WriteFiles 6ms 0.026% 82.55% 215ms 0.94% std::__new_allocator::deallocate (inline) 0 0% 82.55% 213ms 0.93% std::set::~set (inline) 15ms 0.065% 82.61% 211ms 0.92% std::__insertion_sort (inline) 0 0% 82.61% 209ms 0.91% NodesOnlyMesh::ResizeBoxCollection 15ms 0.065% 82.68% 208ms 0.91% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 82.68% 197ms 0.86% NodesOnlyMesh::AddNodesToBoxes 0 0% 82.68% 194ms 0.85% vtkXMLWriterBase::Write 0 0% 82.68% 193ms 0.84% vtkStreamingDemandDrivenPipeline::Update 0 0% 82.68% 192ms 0.84% vtkDemandDrivenPipeline::ProcessRequest 0 0% 82.68% 191ms 0.83% vtkExecutive::CallAlgorithm 190ms 0.83% 83.51% 190ms 0.83% Node::GetIndex 93ms 0.41% 83.91% 190ms 0.83% boost::shared_ptr::shared_ptr (inline) 0 0% 83.91% 190ms 0.83% vtkCompositeDataPipeline::ExecuteData 0 0% 83.91% 190ms 0.83% vtkDemandDrivenPipeline::ExecuteData 0 0% 83.91% 190ms 0.83% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 83.91% 190ms 0.83% vtkXMLUnstructuredDataWriter::ProcessRequest 65ms 0.28% 84.20% 187ms 0.81% __GI___libc_free 185ms 0.81% 85.00% 185ms 0.81% [libchaste_cell_based.so] 0 0% 85.00% 184ms 0.8% std::allocator_traits::deallocate (inline) 0 0% 85.00% 180ms 0.78% std::_Rb_tree::_M_put_node (inline) 0 0% 85.00% 172ms 0.75% Cell::HasCellProperty (inline) 4ms 0.017% 85.02% 172ms 0.75% CellPropertyCollection::HasProperty 0 0% 85.02% 165ms 0.72% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.02% 165ms 0.72% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 85.02% 161ms 0.7% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 10ms 0.044% 85.06% 156ms 0.68% boost::numeric::ublas::vector_reference::operator() (inline) 2ms 0.0087% 85.07% 155ms 0.68% Cell::ReadyToDivide 11ms 0.048% 85.12% 151ms 0.66% DistributedBoxCollection::GetIsPeriodicAllDims 84ms 0.37% 85.49% 150ms 0.65% Node::AddNeighbour 2ms 0.0087% 85.49% 145ms 0.63% AbstractCellProperty::IsType (inline) 0 0% 85.49% 142ms 0.62% Cell::GetCellId 0 0% 85.49% 141ms 0.61% std::_Rb_tree::clear (inline) 0 0% 85.49% 136ms 0.59% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 85.49% 135ms 0.59% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 135ms 0.59% 86.08% 135ms 0.59% [libchaste_mesh.so] 0 0% 86.08% 134ms 0.58% vtkXMLWriter::WriteBinaryData 0 0% 86.08% 133ms 0.58% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 3ms 0.013% 86.10% 129ms 0.56% AbstractNumericalMethod::SafeNodePositionUpdate 127ms 0.55% 86.65% 129ms 0.56% std::__adjacent_find (inline) 0 0% 86.65% 129ms 0.56% std::__unique (inline) 0 0% 86.65% 129ms 0.56% std::unique (inline) 1ms 0.0044% 86.65% 129ms 0.56% vtkXMLWriter::WriteBinaryDataInternal 0 0% 86.65% 128ms 0.56% vtkXMLWriter::WriteBinaryDataBlock 0 0% 86.65% 128ms 0.56% vtkXMLWriter::WriteCompressionBlock 0 0% 86.65% 126ms 0.55% boost::numeric::ublas::vector_binary::operator() (inline) 122ms 0.53% 87.19% 122ms 0.53% boost::shared_ptr::operator-> (inline) 0 0% 87.19% 122ms 0.53% vtkXMLWriter::WritePointsAppendedData 104ms 0.45% 87.64% 121ms 0.53% _int_free 12ms 0.052% 87.69% 121ms 0.53% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 87.69% 121ms 0.53% std::map::clear (inline) 3ms 0.013% 87.70% 115ms 0.5% NodeBasedCellPopulation::SetNode