File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20779ms, 89.37% of 23251ms total Dropped 736 nodes (cum <= 116.25ms) flat flat% sum% cum cum% 0 0% 0% 23076ms 99.25% __libc_start_call_main 0 0% 0% 23076ms 99.25% __libc_start_main_impl 0 0% 0% 23076ms 99.25% _start 0 0% 0% 23061ms 99.18% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 23061ms 99.18% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 23061ms 99.18% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 23061ms 99.18% main 0 0% 0% 23024ms 99.02% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 23024ms 99.02% CxxTest::TestRunner::runTest (inline) 0 0% 0% 23024ms 99.02% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 23016ms 98.99% AbstractCellBasedSimulation::Solve 4ms 0.017% 0.017% 13085ms 56.28% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.017% 8769ms 37.71% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.017% 0.034% 8312ms 35.75% ForwardEulerNumericalMethod::UpdateAllNodePositions 9ms 0.039% 0.073% 8132ms 34.97% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.073% 7730ms 33.25% NodeBasedCellPopulation::Update 1197ms 5.15% 5.22% 7474ms 32.14% RepulsionForce::AddForceContribution (partial-inline) 13ms 0.056% 5.28% 5738ms 24.68% DistributedBoxCollection::CalculateInteriorNodePairs 2114ms 9.09% 14.37% 4918ms 21.15% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.0043% 14.37% 4492ms 19.32% OffLatticeSimulation::ApplyBoundaries 11ms 0.047% 14.42% 4453ms 19.15% NodeAttributes::RemoveDuplicateNeighbours 9ms 0.039% 14.46% 4274ms 18.38% std::__sort (inline) 0 0% 14.46% 4274ms 18.38% std::sort (inline) 195ms 0.84% 15.30% 3831ms 16.48% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 4ms 0.017% 15.32% 3431ms 14.76% AbstractCellPopulation::Iterator::operator++ (inline) 198ms 0.85% 16.17% 3402ms 14.63% AbstractCellPopulation::Iterator::IsRealCell (inline) 63ms 0.27% 16.44% 3340ms 14.36% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 221ms 0.95% 17.39% 3190ms 13.72% std::_Rb_tree::find (inline) 0 0% 17.39% 3189ms 13.72% std::map::find (inline) 33ms 0.14% 17.53% 2866ms 12.33% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2771ms 11.92% 29.45% 2771ms 11.92% std::_Rb_tree::_S_right (inline) 155ms 0.67% 30.11% 2549ms 10.96% std::__introsort_loop 246ms 1.06% 31.17% 2469ms 10.62% std::map::operator[] (partial-inline) 24ms 0.1% 31.28% 2323ms 9.99% PlaneBoundaryCondition::ImposeBoundaryCondition 1ms 0.0043% 31.28% 2304ms 9.91% std::__unguarded_partition_pivot (inline) 142ms 0.61% 31.89% 2287ms 9.84% AbstractMesh::GetNode 34ms 0.15% 32.04% 2277ms 9.79% AbstractCellPopulation::GetLocationIndexUsingCell 38ms 0.16% 32.20% 2260ms 9.72% NodesOnlyMesh::GetNodeOrHaloNode 16ms 0.069% 32.27% 2168ms 9.32% PlaneBoundaryCondition::VerifyBoundaryCondition 92ms 0.4% 32.67% 2148ms 9.24% NodesOnlyMesh::SolveNodeMapping 1068ms 4.59% 37.26% 2092ms 9.00% std::__unguarded_partition (inline) 0 0% 37.26% 1980ms 8.52% std::_Rb_tree::lower_bound (inline) 0 0% 37.26% 1980ms 8.52% std::map::lower_bound (inline) 143ms 0.62% 37.87% 1894ms 8.15% DistributedBoxCollection::AddPairsFromBox 2ms 0.0086% 37.88% 1714ms 7.37% std::__final_insertion_sort (inline) 29ms 0.12% 38.01% 1553ms 6.68% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 72ms 0.31% 38.32% 1532ms 6.59% std::__unguarded_insertion_sort (inline) 29ms 0.12% 38.44% 1512ms 6.50% AbstractCellPopulation::GetCellUsingLocationIndex 566ms 2.43% 40.88% 1495ms 6.43% std::__unguarded_linear_insert (inline) 1417ms 6.09% 46.97% 1417ms 6.09% __gnu_cxx::__normal_iterator::operator-- (inline) 73ms 0.31% 47.28% 1246ms 5.36% boost::numeric::ublas::c_vector::c_vector (partial-inline) 1ms 0.0043% 47.29% 1128ms 4.85% NodeBasedCellPopulation::UpdateCellProcessLocation 44ms 0.19% 47.48% 1101ms 4.74% boost::numeric::ublas::vector_assign (inline) 14ms 0.06% 47.54% 1058ms 4.55% DistributedBoxCollection::CalculateBoundaryNodePairs 283ms 1.22% 48.75% 1011ms 4.35% boost::numeric::ublas::indexing_vector_assign 251ms 1.08% 49.83% 950ms 4.09% __dynamic_cast 24ms 0.1% 49.94% 809ms 3.48% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 147ms 0.63% 50.57% 791ms 3.40% AbstractMesh::GetVectorFromAtoB 342ms 1.47% 52.04% 758ms 3.26% DistributedBoxCollection::CalculateContainingBox (partial-inline) 187ms 0.8% 52.85% 740ms 3.18% NodeAttributes::AddNeighbour 0 0% 52.85% 725ms 3.12% AbstractCellPopulation::WriteResultsToFiles 0 0% 52.85% 706ms 3.04% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 52.85% 692ms 2.98% boost::numeric::ublas::norm_2 (inline) 536ms 2.31% 55.15% 692ms 2.98% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 55.15% 692ms 2.98% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 654ms 2.81% 57.96% 654ms 2.81% boost::numeric::ublas::c_vector::operator() 6ms 0.026% 57.99% 653ms 2.81% boost::numeric::ublas::c_vector::operator= (inline) 551ms 2.37% 60.36% 647ms 2.78% std::vector::push_back (inline) 40ms 0.17% 60.53% 627ms 2.70% std::__copy_move::__copy_m (inline) 0 0% 60.53% 627ms 2.70% std::__copy_move_a (inline) 0 0% 60.53% 627ms 2.70% std::__copy_move_a1 (inline) 0 0% 60.53% 627ms 2.70% std::__copy_move_a2 (inline) 0 0% 60.53% 627ms 2.70% std::copy (inline) 11ms 0.047% 60.58% 615ms 2.65% CellPropertyCollection::GetPropertiesType (inline) 609ms 2.62% 63.20% 609ms 2.62% __memcpy_avx_unaligned_erms 3ms 0.013% 63.21% 595ms 2.56% AbstractCellBasedSimulation::DoCellBirth 5ms 0.022% 63.23% 591ms 2.54% AbstractCentreBasedCellPopulation::GetDampingConstant 259ms 1.11% 64.35% 580ms 2.49% __cxxabiv1::__si_class_type_info::__do_dyncast 28ms 0.12% 64.47% 569ms 2.45% std::_Rb_tree_const_iterator::operator++ (inline) 544ms 2.34% 66.81% 544ms 2.34% std::_Rb_tree_increment 37ms 0.16% 66.96% 490ms 2.11% boost::detail::shared_count::~shared_count (inline) 0 0% 66.96% 490ms 2.11% boost::shared_ptr::~shared_ptr (inline) 489ms 2.10% 69.07% 489ms 2.10% boost::numeric::ublas::same_impl_ex 4ms 0.017% 69.09% 483ms 2.08% NodeBasedCellPopulation::WriteVtkResultsToFile 477ms 2.05% 71.14% 477ms 2.05% __strcmp_avx2 80ms 0.34% 71.48% 473ms 2.03% std::__new_allocator::allocate (inline) 34ms 0.15% 71.63% 466ms 2.00% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 71.63% 451ms 1.94% std::allocator_traits::allocate (inline) 0 0% 71.63% 444ms 1.91% AbstractCellBasedSimulation::DoCellRemoval (inline) 433ms 1.86% 73.49% 441ms 1.90% boost::detail::sp_counted_base::release 6ms 0.026% 73.52% 434ms 1.87% Cell::GetMutationState 3ms 0.013% 73.53% 432ms 1.86% AbstractCellProperty::IsSubType (inline) 3ms 0.013% 73.54% 429ms 1.85% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 73.54% 423ms 1.82% std::_Rb_tree::_M_create_node (inline) 41ms 0.18% 73.72% 419ms 1.80% std::_Rb_tree::_M_copy (inline) 144ms 0.62% 74.34% 402ms 1.73% Node::GetRadius 3ms 0.013% 74.35% 397ms 1.71% std::set::set (inline) 29ms 0.12% 74.47% 395ms 1.70% operator new 116ms 0.5% 74.97% 386ms 1.66% std::_Rb_tree::_M_erase 133ms 0.57% 75.55% 378ms 1.63% std::_Rb_tree::_M_clone_node (inline) 0 0% 75.55% 374ms 1.61% std::_Rb_tree::_M_get_node (inline) 108ms 0.46% 76.01% 364ms 1.57% __GI___libc_malloc 3ms 0.013% 76.02% 339ms 1.46% NodeBasedCellPopulation::UpdateMapsAfterRemesh 18ms 0.077% 76.10% 327ms 1.41% boost::numeric::ublas::vector_binary::size (inline) 325ms 1.40% 77.50% 325ms 1.40% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 77.50% 325ms 1.40% boost::numeric::ublas::inner_prod (inline) 19ms 0.082% 77.58% 323ms 1.39% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 77.58% 323ms 1.39% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 77.58% 308ms 1.32% boost::numeric::ublas::c_vector::assign (inline) 303ms 1.30% 78.88% 303ms 1.30% __gnu_cxx::__normal_iterator::operator++ (inline) 42ms 0.18% 79.06% 295ms 1.27% std::_Rb_tree::~_Rb_tree (inline) 0 0% 79.06% 293ms 1.26% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 79.06% 288ms 1.24% NodesOnlyMesh::ReMesh 2ms 0.0086% 79.07% 275ms 1.18% NodesOnlyMesh::UpdateNodeIndices 265ms 1.14% 80.21% 265ms 1.14% Node::CheckForNodeAttributes 2ms 0.0086% 80.22% 261ms 1.12% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 80.22% 259ms 1.11% std::_Rb_tree::_M_drop_node (inline) 7ms 0.03% 80.25% 249ms 1.07% DistributedBoxCollection::GetProcessOwningNode 100ms 0.43% 80.68% 249ms 1.07% boost::numeric::ublas::vector_inner_prod::apply (inline) 5ms 0.022% 80.70% 243ms 1.05% std::_Rb_tree::_M_emplace_hint_unique 0 0% 80.70% 237ms 1.02% NodesOnlyMesh::UpdateBoxCollection 0 0% 80.70% 227ms 0.98% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 80.70% 226ms 0.97% VtkMeshWriter::WriteFiles 2ms 0.0086% 80.71% 222ms 0.95% std::__new_allocator::deallocate (inline) 0 0% 80.71% 215ms 0.92% std::set::~set (inline) 119ms 0.51% 81.22% 207ms 0.89% _int_malloc 88ms 0.38% 81.60% 207ms 0.89% std::__move_median_to_first (inline) 0 0% 81.60% 200ms 0.86% NodesOnlyMesh::AddNodesToBoxes 0 0% 81.60% 200ms 0.86% std::allocator_traits::deallocate (inline) 80ms 0.34% 81.94% 199ms 0.86% Node::AddNeighbour 79ms 0.34% 82.28% 197ms 0.85% __GI___libc_free 0 0% 82.28% 197ms 0.85% std::_Rb_tree::_M_put_node (inline) 97ms 0.42% 82.70% 196ms 0.84% boost::shared_ptr::shared_ptr (inline) 1ms 0.0043% 82.71% 195ms 0.84% vtkStreamingDemandDrivenPipeline::Update 0 0% 82.71% 195ms 0.84% vtkXMLWriterBase::Write 2ms 0.0086% 82.71% 194ms 0.83% CellPropertyCollection::HasProperty 0 0% 82.71% 194ms 0.83% vtkExecutive::CallAlgorithm 0 0% 82.71% 194ms 0.83% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 82.71% 193ms 0.83% Cell::HasCellProperty (inline) 193ms 0.83% 83.54% 193ms 0.83% Node::GetIndex 0 0% 83.54% 193ms 0.83% vtkCompositeDataPipeline::ExecuteData 0 0% 83.54% 193ms 0.83% vtkDemandDrivenPipeline::ExecuteData 0 0% 83.54% 193ms 0.83% vtkDemandDrivenPipeline::ProcessRequest 0 0% 83.54% 193ms 0.83% vtkXMLUnstructuredDataWriter::ProcessRequest 191ms 0.82% 84.37% 191ms 0.82% [libchaste_cell_based.so] 0 0% 84.37% 188ms 0.81% NodesOnlyMesh::ResizeBoxCollection 21ms 0.09% 84.46% 186ms 0.8% NodesOnlyMesh::IsANodeCloseToDomainBoundary 20ms 0.086% 84.54% 180ms 0.77% std::__insertion_sort (inline) 5ms 0.022% 84.56% 176ms 0.76% Cell::ReadyToDivide 0 0% 84.56% 171ms 0.74% vtkXMLUnstructuredDataWriter::WriteAPiece 1ms 0.0043% 84.57% 171ms 0.74% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 84.57% 166ms 0.71% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 4ms 0.017% 84.59% 160ms 0.69% AbstractCellProperty::IsType (inline) 159ms 0.68% 85.27% 159ms 0.68% boost::shared_ptr::operator-> (inline) 0 0% 85.27% 154ms 0.66% std::_Rb_tree::clear (inline) 150ms 0.65% 85.91% 152ms 0.65% std::__adjacent_find (inline) 0 0% 85.91% 152ms 0.65% std::__unique (inline) 0 0% 85.91% 152ms 0.65% std::unique (inline) 150ms 0.65% 86.56% 150ms 0.65% Node::IsDeleted 7ms 0.03% 86.59% 150ms 0.65% boost::numeric::ublas::c_vector::operator[] (inline) 149ms 0.64% 87.23% 149ms 0.64% Node::ConstructNodeAttributes (inline) 13ms 0.056% 87.29% 141ms 0.61% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 87.29% 141ms 0.61% tbb::detail::r1::parallel_pipeline 0 0% 87.29% 140ms 0.6% clone3 0 0% 87.29% 140ms 0.6% start_thread 0 0% 87.29% 139ms 0.6% AbstractCellPopulation::SetCellUsingLocationIndex 1ms 0.0043% 87.29% 139ms 0.6% tbb::detail::r1::reset 53ms 0.23% 87.52% 137ms 0.59% tbb::detail::r1::wait_bounded_queue_monitor 136ms 0.58% 88.10% 136ms 0.58% [libchaste_mesh.so] 0 0% 88.10% 135ms 0.58% vtkXMLWriter::WriteBinaryData 0 0% 88.10% 133ms 0.57% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 88.10% 132ms 0.57% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 88.10% 130ms 0.56% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 88.10% 129ms 0.55% vtkXMLWriter::WriteBinaryDataBlock 0 0% 88.10% 129ms 0.55% vtkXMLWriter::WriteBinaryDataInternal 128ms 0.55% 88.65% 128ms 0.55% __ieee754_log_fma 0 0% 88.65% 128ms 0.55% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 88.65% 128ms 0.55% vtkXMLWriter::WriteCompressionBlock 42ms 0.18% 88.83% 123ms 0.53% AbstractCellProperty::IsSame 4ms 0.017% 88.85% 123ms 0.53% AbstractNumericalMethod::SafeNodePositionUpdate 9ms 0.039% 88.89% 121ms 0.52% DistributedBoxCollection::GetIsPeriodicAllDims 0 0% 88.89% 121ms 0.52% std::map::clear (inline) 111ms 0.48% 89.37% 118ms 0.51% _int_free