File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 21793ms, 88.71% of 24567ms total Dropped 819 nodes (cum <= 122.83ms) flat flat% sum% cum cum% 0 0% 0% 24406ms 99.34% __libc_start_call_main 0 0% 0% 24406ms 99.34% __libc_start_main_impl 0 0% 0% 24406ms 99.34% _start 0 0% 0% 24391ms 99.28% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 24391ms 99.28% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 24391ms 99.28% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 24391ms 99.28% main 0 0% 0% 24356ms 99.14% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 24356ms 99.14% CxxTest::TestRunner::runTest (inline) 0 0% 0% 24356ms 99.14% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 24347ms 99.10% AbstractCellBasedSimulation::Solve 2ms 0.0081% 0.0081% 13705ms 55.79% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0081% 9395ms 38.24% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0081% 0.016% 8769ms 35.69% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.041% 0.057% 8578ms 34.92% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.057% 8241ms 33.54% NodeBasedCellPopulation::Update 1198ms 4.88% 4.93% 7761ms 31.59% RepulsionForce::AddForceContribution (partial-inline) 10ms 0.041% 4.97% 6139ms 24.99% DistributedBoxCollection::CalculateInteriorNodePairs 2056ms 8.37% 13.34% 5003ms 20.36% std::_Rb_tree::_M_lower_bound (inline) 21ms 0.085% 13.43% 4592ms 18.69% NodeAttributes::RemoveDuplicateNeighbours 0 0% 13.43% 4576ms 18.63% OffLatticeSimulation::ApplyBoundaries 8ms 0.033% 13.46% 4416ms 17.98% std::__sort (inline) 0 0% 13.46% 4416ms 17.98% std::sort (inline) 173ms 0.7% 14.17% 4099ms 16.68% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 1ms 0.0041% 14.17% 3386ms 13.78% AbstractCellPopulation::Iterator::operator++ (inline) 173ms 0.7% 14.87% 3365ms 13.70% AbstractCellPopulation::Iterator::IsRealCell (inline) 74ms 0.3% 15.17% 3359ms 13.67% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 240ms 0.98% 16.15% 3316ms 13.50% std::_Rb_tree::find (inline) 0 0% 16.15% 3315ms 13.49% std::map::find (inline) 2921ms 11.89% 28.04% 2921ms 11.89% std::_Rb_tree::_S_right (inline) 27ms 0.11% 28.15% 2872ms 11.69% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 190ms 0.77% 28.92% 2560ms 10.42% std::__introsort_loop 230ms 0.94% 29.86% 2457ms 10.00% std::map::operator[] (partial-inline) 35ms 0.14% 30.00% 2409ms 9.81% PlaneBoundaryCondition::ImposeBoundaryCondition 134ms 0.55% 30.55% 2346ms 9.55% AbstractMesh::GetNode 54ms 0.22% 30.77% 2309ms 9.40% NodesOnlyMesh::GetNodeOrHaloNode 0 0% 30.77% 2295ms 9.34% std::__unguarded_partition_pivot (inline) 32ms 0.13% 30.90% 2256ms 9.18% AbstractCellPopulation::GetLocationIndexUsingCell 77ms 0.31% 31.21% 2215ms 9.02% NodesOnlyMesh::SolveNodeMapping 140ms 0.57% 31.78% 2189ms 8.91% DistributedBoxCollection::AddPairsFromBox 15ms 0.061% 31.84% 2166ms 8.82% PlaneBoundaryCondition::VerifyBoundaryCondition 997ms 4.06% 35.90% 2014ms 8.20% std::__unguarded_partition (inline) 0 0% 35.90% 1949ms 7.93% std::_Rb_tree::lower_bound (inline) 0 0% 35.90% 1949ms 7.93% std::map::lower_bound (inline) 2ms 0.0081% 35.91% 1845ms 7.51% std::__final_insertion_sort (inline) 24ms 0.098% 36.01% 1646ms 6.70% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 83ms 0.34% 36.35% 1626ms 6.62% std::__unguarded_insertion_sort (inline) 29ms 0.12% 36.46% 1618ms 6.59% AbstractCellPopulation::GetCellUsingLocationIndex 604ms 2.46% 38.92% 1605ms 6.53% std::__unguarded_linear_insert (inline) 1503ms 6.12% 45.04% 1503ms 6.12% __gnu_cxx::__normal_iterator::operator-- (inline) 59ms 0.24% 45.28% 1300ms 5.29% boost::numeric::ublas::c_vector::c_vector (partial-inline) 1ms 0.0041% 45.28% 1195ms 4.86% NodeBasedCellPopulation::UpdateCellProcessLocation 50ms 0.2% 45.49% 1143ms 4.65% boost::numeric::ublas::vector_assign (inline) 5ms 0.02% 45.51% 1099ms 4.47% DistributedBoxCollection::CalculateBoundaryNodePairs 283ms 1.15% 46.66% 1016ms 4.14% boost::numeric::ublas::indexing_vector_assign 295ms 1.20% 47.86% 968ms 3.94% __dynamic_cast 44ms 0.18% 48.04% 895ms 3.64% std::_Rb_tree_const_iterator::operator++ (inline) 186ms 0.76% 48.80% 847ms 3.45% AbstractMesh::GetVectorFromAtoB 845ms 3.44% 52.24% 845ms 3.44% std::_Rb_tree_increment 26ms 0.11% 52.34% 788ms 3.21% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 12ms 0.049% 52.39% 788ms 3.21% CellPropertyCollection::GetPropertiesType (inline) 360ms 1.47% 53.86% 761ms 3.10% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 53.86% 758ms 3.09% AbstractCellPopulation::WriteResultsToFiles 2ms 0.0081% 53.86% 754ms 3.07% AbstractCentreBasedCellPopulation::GetDampingConstant 189ms 0.77% 54.63% 714ms 2.91% NodeAttributes::AddNeighbour 0 0% 54.63% 712ms 2.90% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 1ms 0.0041% 54.64% 704ms 2.87% AbstractCellBasedSimulation::DoCellBirth 0 0% 54.64% 697ms 2.84% boost::numeric::ublas::norm_2 (inline) 535ms 2.18% 56.82% 697ms 2.84% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 56.82% 697ms 2.84% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 668ms 2.72% 59.54% 668ms 2.72% boost::numeric::ublas::c_vector::operator() 8ms 0.033% 59.57% 651ms 2.65% boost::numeric::ublas::c_vector::operator= (inline) 634ms 2.58% 62.15% 634ms 2.58% __memcpy_avx_unaligned_erms 22ms 0.09% 62.24% 633ms 2.58% std::__copy_move::__copy_m (inline) 0 0% 62.24% 633ms 2.58% std::__copy_move_a (inline) 0 0% 62.24% 633ms 2.58% std::__copy_move_a1 (inline) 0 0% 62.24% 633ms 2.58% std::__copy_move_a2 (inline) 0 0% 62.24% 631ms 2.57% std::copy (inline) 109ms 0.44% 62.68% 618ms 2.52% std::__new_allocator::allocate (inline) 519ms 2.11% 64.79% 607ms 2.47% std::vector::push_back (inline) 0 0% 64.79% 593ms 2.41% std::allocator_traits::allocate (inline) 31ms 0.13% 64.92% 586ms 2.39% std::_Rb_tree::_Rb_tree (partial-inline) 6ms 0.024% 64.94% 582ms 2.37% Cell::GetMutationState 276ms 1.12% 66.07% 572ms 2.33% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 66.07% 561ms 2.28% std::_Rb_tree::_M_create_node (inline) 57ms 0.23% 66.30% 544ms 2.21% std::_Rb_tree::_M_copy (inline) 28ms 0.11% 66.41% 514ms 2.09% boost::detail::shared_count::~shared_count (inline) 0 0% 66.41% 514ms 2.09% boost::shared_ptr::~shared_ptr (inline) 34ms 0.14% 66.55% 511ms 2.08% operator new 3ms 0.012% 66.56% 492ms 2.00% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 66.56% 490ms 1.99% std::_Rb_tree::_M_get_node (inline) 488ms 1.99% 68.55% 488ms 1.99% boost::numeric::ublas::same_impl_ex 183ms 0.74% 69.30% 486ms 1.98% std::_Rb_tree::_M_clone_node (inline) 473ms 1.93% 71.22% 480ms 1.95% boost::detail::sp_counted_base::release 4ms 0.016% 71.24% 475ms 1.93% std::set::set (inline) 115ms 0.47% 71.71% 472ms 1.92% __GI___libc_malloc 452ms 1.84% 73.55% 452ms 1.84% __strcmp_avx2 0 0% 73.55% 448ms 1.82% AbstractCellBasedSimulation::DoCellRemoval (inline) 120ms 0.49% 74.03% 446ms 1.82% Node::AddNeighbour 137ms 0.56% 74.59% 446ms 1.82% std::_Rb_tree::_M_erase 6ms 0.024% 74.62% 431ms 1.75% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 3ms 0.012% 74.63% 413ms 1.68% AbstractCellProperty::IsSubType (inline) 380ms 1.55% 76.18% 380ms 1.55% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 76.18% 375ms 1.53% std::_Rb_tree::_Alloc_node::operator() (inline) 115ms 0.47% 76.64% 373ms 1.52% Node::GetRadius 356ms 1.45% 78.09% 356ms 1.45% Node::ConstructNodeAttributes (inline) 0 0% 78.09% 344ms 1.40% boost::numeric::ublas::inner_prod (inline) 2ms 0.0081% 78.10% 344ms 1.40% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 78.10% 342ms 1.39% boost::numeric::ublas::c_vector::assign (inline) 27ms 0.11% 78.21% 342ms 1.39% boost::numeric::ublas::vector_scalar_binary::evaluate 2ms 0.0081% 78.22% 338ms 1.38% CellPropertyCollection::HasProperty 0 0% 78.22% 337ms 1.37% Cell::HasCellProperty (inline) 23ms 0.094% 78.31% 336ms 1.37% boost::numeric::ublas::vector_binary::size (inline) 0 0% 78.31% 327ms 1.33% NodesOnlyMesh::ReMesh 1ms 0.0041% 78.32% 319ms 1.30% NodeBasedCellPopulation::UpdateMapsAfterRemesh 316ms 1.29% 79.60% 316ms 1.29% __gnu_cxx::__normal_iterator::operator++ (inline) 4ms 0.016% 79.62% 313ms 1.27% Cell::ReadyToDivide 30ms 0.12% 79.74% 313ms 1.27% std::_Rb_tree::~_Rb_tree (inline) 3ms 0.012% 79.75% 309ms 1.26% NodesOnlyMesh::UpdateNodeIndices 171ms 0.7% 80.45% 303ms 1.23% _int_malloc 2ms 0.0081% 80.46% 292ms 1.19% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 80.46% 284ms 1.16% std::_Rb_tree::_M_drop_node (inline) 0 0% 80.46% 282ms 1.15% NodesOnlyMesh::UpdateBoxCollection 279ms 1.14% 81.59% 279ms 1.14% Node::CheckForNodeAttributes 6ms 0.024% 81.62% 278ms 1.13% std::_Rb_tree::_M_emplace_hint_unique 99ms 0.4% 82.02% 277ms 1.13% std::__move_median_to_first (inline) 11ms 0.045% 82.07% 275ms 1.12% DistributedBoxCollection::GetProcessOwningNode 97ms 0.39% 82.46% 265ms 1.08% boost::numeric::ublas::vector_inner_prod::apply (inline) 3ms 0.012% 82.47% 250ms 1.02% std::__new_allocator::deallocate (inline) 0 0% 82.47% 239ms 0.97% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 82.47% 238ms 0.97% VtkMeshWriter::WriteFiles 0 0% 82.47% 226ms 0.92% std::allocator_traits::deallocate (inline) 1ms 0.0041% 82.48% 225ms 0.92% NodesOnlyMesh::AddNodesToBoxes 0 0% 82.48% 225ms 0.92% std::_Rb_tree::_M_put_node (inline) 86ms 0.35% 82.83% 220ms 0.9% __GI___libc_free 22ms 0.09% 82.92% 217ms 0.88% std::__insertion_sort (inline) 10ms 0.041% 82.96% 209ms 0.85% AbstractCellProperty::IsType (inline) 88ms 0.36% 83.32% 204ms 0.83% boost::shared_ptr::shared_ptr (inline) 0 0% 83.32% 203ms 0.83% std::set::~set (inline) 0 0% 83.32% 202ms 0.82% vtkStreamingDemandDrivenPipeline::Update 0 0% 83.32% 202ms 0.82% vtkXMLWriterBase::Write 0 0% 83.32% 200ms 0.81% vtkDemandDrivenPipeline::ProcessRequest 198ms 0.81% 84.12% 198ms 0.81% boost::shared_ptr::operator-> (inline) 0 0% 84.12% 198ms 0.81% vtkExecutive::CallAlgorithm 0 0% 84.12% 197ms 0.8% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 84.12% 197ms 0.8% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 84.12% 196ms 0.8% vtkCompositeDataPipeline::ExecuteData 0 0% 84.12% 196ms 0.8% vtkDemandDrivenPipeline::ExecuteData 0 0% 84.12% 187ms 0.76% NodesOnlyMesh::ResizeBoxCollection 0 0% 84.12% 186ms 0.76% std::_Rb_tree::_Auto_node::_Auto_node (inline) 12ms 0.049% 84.17% 185ms 0.75% NodesOnlyMesh::IsANodeCloseToDomainBoundary 183ms 0.74% 84.91% 183ms 0.74% [libchaste_cell_based.so] 0 0% 84.91% 180ms 0.73% std::_Rb_tree::clear (inline) 171ms 0.7% 85.61% 171ms 0.7% Node::GetIndex 0 0% 85.61% 168ms 0.68% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.61% 168ms 0.68% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 73ms 0.3% 85.91% 164ms 0.67% AbstractCellProperty::IsSame 0 0% 85.91% 161ms 0.66% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 2ms 0.0081% 85.92% 155ms 0.63% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 85.92% 154ms 0.63% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 2ms 0.0081% 85.92% 153ms 0.62% Cell::GetCellId 71ms 0.29% 86.21% 144ms 0.59% AbstractCellCycleModel::GetAge 142ms 0.58% 86.79% 142ms 0.58% [libchaste_mesh.so] 138ms 0.56% 87.35% 140ms 0.57% std::__adjacent_find (inline) 0 0% 87.35% 140ms 0.57% std::__unique (inline) 0 0% 87.35% 140ms 0.57% std::unique (inline) 1ms 0.0041% 87.36% 139ms 0.57% AbstractNumericalMethod::SafeNodePositionUpdate 5ms 0.02% 87.38% 139ms 0.57% DistributedBoxCollection::GetIsPeriodicAllDims 138ms 0.56% 87.94% 138ms 0.56% Node::IsDeleted 4ms 0.016% 87.96% 138ms 0.56% std::_Rb_tree::_M_insert_unique 0 0% 87.96% 138ms 0.56% std::set::insert (inline) 125ms 0.51% 88.46% 134ms 0.55% _int_free 0 0% 88.46% 133ms 0.54% vtkXMLWriter::WriteBinaryData 0 0% 88.46% 132ms 0.54% boost::numeric::ublas::vector_binary::operator() (inline) 2ms 0.0081% 88.47% 128ms 0.52% AbstractCellPopulation::SetCellUsingLocationIndex 1ms 0.0041% 88.48% 128ms 0.52% vtkXMLWriter::WriteBinaryDataInternal 1ms 0.0041% 88.48% 127ms 0.52% NodeBasedCellPopulation::SetNode 0 0% 88.48% 127ms 0.52% clone3 0 0% 88.48% 127ms 0.52% start_thread 0 0% 88.48% 127ms 0.52% std::map::clear (inline) 0 0% 88.48% 127ms 0.52% tbb::detail::r1::parallel_pipeline 1ms 0.0041% 88.48% 127ms 0.52% vtkXMLWriter::WriteBinaryDataBlock 9ms 0.037% 88.52% 126ms 0.51% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 88.52% 126ms 0.51% vtkXMLWriter::WriteCompressionBlock 0 0% 88.52% 124ms 0.5% NodeBasedCellPopulation::AcceptCellWriter 0 0% 88.52% 124ms 0.5% tbb::detail::r1::reset 46ms 0.19% 88.71% 123ms 0.5% tbb::detail::r1::wait_bounded_queue_monitor