File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20350ms, 88.54% of 22985ms total Dropped 738 nodes (cum <= 114.92ms) flat flat% sum% cum cum% 0 0% 0% 22852ms 99.42% __libc_start_call_main 0 0% 0% 22852ms 99.42% __libc_start_main_impl 0 0% 0% 22852ms 99.42% _start 0 0% 0% 22837ms 99.36% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 22837ms 99.36% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 22837ms 99.36% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 22837ms 99.36% main 0 0% 0% 22802ms 99.20% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 22802ms 99.20% CxxTest::TestRunner::runTest (inline) 0 0% 0% 22802ms 99.20% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0044% 0.0044% 22794ms 99.17% AbstractCellBasedSimulation::Solve 3ms 0.013% 0.017% 13051ms 56.78% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0044% 0.022% 8600ms 37.42% AbstractCellBasedSimulation::UpdateCellPopulation 5ms 0.022% 0.044% 8221ms 35.77% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.044% 0.087% 8042ms 34.99% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.087% 7599ms 33.06% NodeBasedCellPopulation::Update 1174ms 5.11% 5.19% 7475ms 32.52% RepulsionForce::AddForceContribution (partial-inline) 8ms 0.035% 5.23% 5570ms 24.23% DistributedBoxCollection::CalculateInteriorNodePairs 2108ms 9.17% 14.40% 5017ms 21.83% std::_Rb_tree::_M_lower_bound (inline) 0 0% 14.40% 4542ms 19.76% OffLatticeSimulation::ApplyBoundaries 18ms 0.078% 14.48% 4482ms 19.50% NodeAttributes::RemoveDuplicateNeighbours 7ms 0.03% 14.51% 4299ms 18.70% std::__sort (inline) 0 0% 14.51% 4299ms 18.70% std::sort (inline) 170ms 0.74% 15.25% 3750ms 16.31% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 64ms 0.28% 15.53% 3458ms 15.04% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 2ms 0.0087% 15.54% 3450ms 15.01% AbstractCellPopulation::Iterator::operator++ (inline) 190ms 0.83% 16.36% 3421ms 14.88% AbstractCellPopulation::Iterator::IsRealCell 242ms 1.05% 17.42% 3273ms 14.24% std::_Rb_tree::find (inline) 0 0% 17.42% 3271ms 14.23% std::map::find (inline) 24ms 0.1% 17.52% 2918ms 12.70% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2857ms 12.43% 29.95% 2857ms 12.43% std::_Rb_tree::_S_right (inline) 222ms 0.97% 30.92% 2507ms 10.91% std::map::operator[] (partial-inline) 178ms 0.77% 31.69% 2415ms 10.51% std::__introsort_loop 31ms 0.13% 31.83% 2388ms 10.39% PlaneBoundaryCondition::ImposeBoundaryCondition 131ms 0.57% 32.40% 2327ms 10.12% AbstractMesh::GetNode 41ms 0.18% 32.57% 2314ms 10.07% NodesOnlyMesh::GetNodeOrHaloNode 37ms 0.16% 32.73% 2278ms 9.91% AbstractCellPopulation::GetLocationIndexUsingCell 67ms 0.29% 33.03% 2199ms 9.57% NodesOnlyMesh::SolveNodeMapping 0 0% 33.03% 2159ms 9.39% std::__unguarded_partition_pivot (inline) 18ms 0.078% 33.10% 2154ms 9.37% PlaneBoundaryCondition::VerifyBoundaryCondition 0 0% 33.10% 2006ms 8.73% std::_Rb_tree::lower_bound (inline) 0 0% 33.10% 2006ms 8.73% std::map::lower_bound (inline) 1000ms 4.35% 37.45% 1969ms 8.57% std::__unguarded_partition (inline) 3ms 0.013% 37.47% 1875ms 8.16% std::__final_insertion_sort (inline) 150ms 0.65% 38.12% 1691ms 7.36% DistributedBoxCollection::AddPairsFromBox 78ms 0.34% 38.46% 1670ms 7.27% std::__unguarded_insertion_sort (inline) 661ms 2.88% 41.34% 1652ms 7.19% std::__unguarded_linear_insert (inline) 17ms 0.074% 41.41% 1529ms 6.65% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 29ms 0.13% 41.54% 1509ms 6.57% AbstractCellPopulation::GetCellUsingLocationIndex 1483ms 6.45% 47.99% 1483ms 6.45% __gnu_cxx::__normal_iterator::operator-- (inline) 47ms 0.2% 48.19% 1310ms 5.70% boost::numeric::ublas::c_vector::c_vector (partial-inline) 32ms 0.14% 48.33% 1182ms 5.14% boost::numeric::ublas::vector_assign (inline) 1ms 0.0044% 48.34% 1153ms 5.02% NodeBasedCellPopulation::UpdateCellProcessLocation 313ms 1.36% 49.70% 1081ms 4.70% boost::numeric::ublas::indexing_vector_assign 5ms 0.022% 49.72% 1062ms 4.62% DistributedBoxCollection::CalculateBoundaryNodePairs 245ms 1.07% 50.79% 873ms 3.80% __dynamic_cast 25ms 0.11% 50.89% 840ms 3.65% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 192ms 0.84% 51.73% 801ms 3.48% AbstractMesh::GetVectorFromAtoB 0 0% 51.73% 794ms 3.45% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 51.73% 777ms 3.38% boost::numeric::ublas::norm_2 (inline) 626ms 2.72% 54.45% 777ms 3.38% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 54.45% 777ms 3.38% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 384ms 1.67% 56.12% 775ms 3.37% DistributedBoxCollection::CalculateContainingBox (partial-inline) 193ms 0.84% 56.96% 708ms 3.08% NodeAttributes::AddNeighbour 5ms 0.022% 56.98% 683ms 2.97% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 56.98% 681ms 2.96% AbstractCellPopulation::WriteResultsToFiles 33ms 0.14% 57.13% 662ms 2.88% std::__copy_move::__copy_m (inline) 0 0% 57.13% 662ms 2.88% std::__copy_move_a (inline) 0 0% 57.13% 662ms 2.88% std::__copy_move_a1 (inline) 0 0% 57.13% 662ms 2.88% std::__copy_move_a2 (inline) 0 0% 57.13% 662ms 2.88% std::copy (inline) 652ms 2.84% 59.97% 652ms 2.84% boost::numeric::ublas::c_vector::operator() 638ms 2.78% 62.74% 638ms 2.78% __memcpy_avx_unaligned_erms 511ms 2.22% 64.96% 575ms 2.50% std::vector::push_back (inline) 6ms 0.026% 64.99% 541ms 2.35% AbstractCellBasedSimulation::DoCellBirth 6ms 0.026% 65.02% 527ms 2.29% CellPropertyCollection::GetPropertiesType (inline) 230ms 1.00% 66.02% 521ms 2.27% __cxxabiv1::__si_class_type_info::__do_dyncast 66ms 0.29% 66.30% 512ms 2.23% std::__new_allocator::allocate (inline) 503ms 2.19% 68.49% 503ms 2.19% boost::numeric::ublas::same_impl_ex 0 0% 68.49% 502ms 2.18% std::allocator_traits::allocate (inline) 4ms 0.017% 68.51% 483ms 2.10% AbstractCentreBasedCellPopulation::GetDampingConstant 25ms 0.11% 68.62% 473ms 2.06% boost::detail::shared_count::~shared_count (inline) 0 0% 68.62% 473ms 2.06% boost::shared_ptr::~shared_ptr (inline) 0 0% 68.62% 472ms 2.05% std::_Rb_tree::_M_create_node (inline) 0 0% 68.62% 458ms 1.99% AbstractCellBasedSimulation::DoCellRemoval (inline) 5ms 0.022% 68.64% 449ms 1.95% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 23ms 0.1% 68.74% 449ms 1.95% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 68.74% 443ms 1.93% NodeBasedCellPopulation::WriteVtkResultsToFile 26ms 0.11% 68.85% 443ms 1.93% operator new 442ms 1.92% 70.78% 442ms 1.92% __strcmp_avx2 433ms 1.88% 72.66% 436ms 1.90% boost::detail::sp_counted_base::release 36ms 0.16% 72.82% 434ms 1.89% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 72.82% 419ms 1.82% std::_Rb_tree::_M_get_node (inline) 33ms 0.14% 72.96% 414ms 1.80% std::_Rb_tree::_M_copy (inline) 142ms 0.62% 73.58% 410ms 1.78% __GI___libc_malloc 0 0% 73.58% 407ms 1.77% boost::numeric::ublas::c_vector::assign (inline) 0 0% 73.58% 403ms 1.75% AbstractCellProperty::IsSubType (inline) 397ms 1.73% 75.31% 397ms 1.73% std::_Rb_tree_increment 120ms 0.52% 75.83% 379ms 1.65% std::_Rb_tree::_M_clone_node (inline) 137ms 0.6% 76.42% 376ms 1.64% Node::GetRadius 4ms 0.017% 76.44% 366ms 1.59% std::set::set (inline) 107ms 0.47% 76.91% 341ms 1.48% std::_Rb_tree::_M_erase 0 0% 76.91% 331ms 1.44% Cell::GetMutationState 20ms 0.087% 76.99% 331ms 1.44% boost::numeric::ublas::vector_binary::size (inline) 0 0% 76.99% 324ms 1.41% std::_Rb_tree::_Alloc_node::operator() (inline) 4ms 0.017% 77.01% 304ms 1.32% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 77.01% 303ms 1.32% boost::numeric::ublas::inner_prod (inline) 4ms 0.017% 77.03% 303ms 1.32% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 302ms 1.31% 78.34% 302ms 1.31% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 78.34% 299ms 1.30% NodesOnlyMesh::ReMesh 11ms 0.048% 78.39% 299ms 1.30% boost::numeric::ublas::vector_scalar_binary::evaluate 1ms 0.0044% 78.39% 288ms 1.25% NodesOnlyMesh::UpdateNodeIndices 5ms 0.022% 78.42% 280ms 1.22% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 4ms 0.017% 78.43% 279ms 1.21% std::_Rb_tree::_M_emplace_hint_unique 0 0% 78.43% 270ms 1.17% NodesOnlyMesh::UpdateBoxCollection 267ms 1.16% 79.60% 267ms 1.16% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 41ms 0.18% 79.77% 265ms 1.15% std::_Rb_tree::~_Rb_tree (inline) 10ms 0.044% 79.82% 257ms 1.12% DistributedBoxCollection::GetProcessOwningNode 249ms 1.08% 80.90% 249ms 1.08% Node::CheckForNodeAttributes 87ms 0.38% 81.28% 237ms 1.03% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 81.28% 231ms 1.01% std::_Rb_tree::_M_drop_node (inline) 139ms 0.6% 81.88% 229ms 1% _int_malloc 3ms 0.013% 81.90% 226ms 0.98% NodesOnlyMesh::AddNodesToBoxes 0 0% 81.90% 211ms 0.92% NodesOnlyMesh::ResizeBoxCollection 15ms 0.065% 81.96% 210ms 0.91% NodesOnlyMesh::IsANodeCloseToDomainBoundary 209ms 0.91% 82.87% 209ms 0.91% Node::GetIndex 0 0% 82.87% 203ms 0.88% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 82.87% 203ms 0.88% VtkMeshWriter::WriteFiles 20ms 0.087% 82.96% 202ms 0.88% std::__insertion_sort (inline) 3ms 0.013% 82.97% 201ms 0.87% std::__new_allocator::deallocate (inline) 0 0% 82.97% 200ms 0.87% std::set::~set (inline) 108ms 0.47% 83.44% 199ms 0.87% boost::shared_ptr::shared_ptr (inline) 188ms 0.82% 84.26% 188ms 0.82% [libchaste_cell_based.so] 0 0% 84.26% 186ms 0.81% vtkExecutive::CallAlgorithm 0 0% 84.26% 186ms 0.81% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 84.26% 186ms 0.81% vtkStreamingDemandDrivenPipeline::Update 0 0% 84.26% 186ms 0.81% vtkXMLWriterBase::Write 0 0% 84.26% 185ms 0.8% vtkCompositeDataPipeline::ExecuteData 0 0% 84.26% 185ms 0.8% vtkDemandDrivenPipeline::ExecuteData 0 0% 84.26% 185ms 0.8% vtkDemandDrivenPipeline::ProcessRequest 0 0% 84.26% 185ms 0.8% vtkXMLUnstructuredDataWriter::ProcessRequest 90ms 0.39% 84.65% 182ms 0.79% std::__move_median_to_first (inline) 80ms 0.35% 85.00% 179ms 0.78% __GI___libc_free 0 0% 85.00% 174ms 0.76% std::allocator_traits::deallocate (inline) 0 0% 85.00% 172ms 0.75% std::_Rb_tree::_M_put_node (inline) 2ms 0.0087% 85.01% 165ms 0.72% CellPropertyCollection::HasProperty 0 0% 85.01% 164ms 0.71% Cell::HasCellProperty (inline) 0 0% 85.01% 158ms 0.69% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.01% 158ms 0.69% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 16ms 0.07% 85.08% 157ms 0.68% boost::numeric::ublas::vector_reference::operator() (inline) 1ms 0.0044% 85.08% 156ms 0.68% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 153ms 0.67% 85.75% 153ms 0.67% [libchaste_mesh.so] 152ms 0.66% 86.41% 152ms 0.66% std::__adjacent_find (inline) 0 0% 86.41% 152ms 0.66% std::__unique (inline) 0 0% 86.41% 152ms 0.66% std::unique (inline) 3ms 0.013% 86.42% 149ms 0.65% Cell::ReadyToDivide 0 0% 86.42% 148ms 0.64% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1ms 0.0044% 86.43% 143ms 0.62% AbstractCellProperty::IsType (inline) 8ms 0.035% 86.46% 143ms 0.62% DistributedBoxCollection::GetIsPeriodicAllDims 77ms 0.34% 86.80% 143ms 0.62% Node::AddNeighbour 0 0% 86.80% 141ms 0.61% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 86.80% 138ms 0.6% Cell::GetCellId 1ms 0.0044% 86.80% 138ms 0.6% std::_Rb_tree::clear (inline) 2ms 0.0087% 86.81% 137ms 0.6% AbstractCellPopulation::SetCellUsingLocationIndex 0 0% 86.81% 135ms 0.59% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 135ms 0.59% 87.40% 135ms 0.59% Node::IsDeleted 0 0% 87.40% 133ms 0.58% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 87.40% 132ms 0.57% vtkXMLWriter::WriteBinaryData 131ms 0.57% 87.97% 131ms 0.57% boost::shared_ptr::operator-> (inline) 0 0% 87.97% 128ms 0.56% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.97% 128ms 0.56% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.97% 128ms 0.56% vtkXMLWriter::WriteCompressionBlock 2ms 0.0087% 87.97% 121ms 0.53% AbstractNumericalMethod::SafeNodePositionUpdate 119ms 0.52% 88.49% 119ms 0.52% __ieee754_log_fma 0 0% 88.49% 116ms 0.5% vtkXMLWriter::WritePointsAppendedData 10ms 0.044% 88.54% 115ms 0.5% boost::numeric::ublas::c_vector::operator[] (inline)