File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20819ms, 88.47% of 23532ms total Dropped 769 nodes (cum <= 117.66ms) flat flat% sum% cum cum% 0 0% 0% 23376ms 99.34% __libc_start_call_main 0 0% 0% 23376ms 99.34% __libc_start_main_impl 0 0% 0% 23376ms 99.34% _start 0 0% 0% 23360ms 99.27% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 23360ms 99.27% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 23360ms 99.27% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 23360ms 99.27% main 0 0% 0% 23323ms 99.11% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 23323ms 99.11% CxxTest::TestRunner::runTest (inline) 0 0% 0% 23323ms 99.11% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 23315ms 99.08% AbstractCellBasedSimulation::Solve 2ms 0.0085% 0.0085% 13174ms 55.98% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0085% 8954ms 38.05% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0085% 0.017% 8365ms 35.55% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.042% 0.059% 8171ms 34.72% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.059% 7893ms 33.54% NodeBasedCellPopulation::Update 1221ms 5.19% 5.25% 7507ms 31.90% RepulsionForce::AddForceContribution (partial-inline) 9ms 0.038% 5.29% 5843ms 24.83% DistributedBoxCollection::CalculateInteriorNodePairs 2043ms 8.68% 13.97% 4828ms 20.52% std::_Rb_tree::_M_lower_bound (inline) 0 0% 13.97% 4536ms 19.28% OffLatticeSimulation::ApplyBoundaries 22ms 0.093% 14.06% 4533ms 19.26% NodeAttributes::RemoveDuplicateNeighbours 6ms 0.025% 14.09% 4363ms 18.54% std::__sort (inline) 0 0% 14.09% 4363ms 18.54% std::sort (inline) 167ms 0.71% 14.80% 3789ms 16.10% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 1ms 0.0042% 14.80% 3482ms 14.80% AbstractCellPopulation::Iterator::operator++ (inline) 212ms 0.9% 15.70% 3456ms 14.69% AbstractCellPopulation::Iterator::IsRealCell 75ms 0.32% 16.02% 3339ms 14.19% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 218ms 0.93% 16.95% 3150ms 13.39% std::_Rb_tree::find (inline) 0 0% 16.95% 3150ms 13.39% std::map::find (inline) 18ms 0.076% 17.02% 2890ms 12.28% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2737ms 11.63% 28.65% 2737ms 11.63% std::_Rb_tree::_S_right (inline) 200ms 0.85% 29.50% 2536ms 10.78% std::__introsort_loop 241ms 1.02% 30.53% 2402ms 10.21% std::map::operator[] (partial-inline) 26ms 0.11% 30.64% 2377ms 10.10% PlaneBoundaryCondition::ImposeBoundaryCondition 28ms 0.12% 30.76% 2274ms 9.66% AbstractCellPopulation::GetLocationIndexUsingCell 175ms 0.74% 31.50% 2254ms 9.58% AbstractMesh::GetNode 0 0% 31.50% 2251ms 9.57% std::__unguarded_partition_pivot (inline) 46ms 0.2% 31.70% 2217ms 9.42% NodesOnlyMesh::GetNodeOrHaloNode 15ms 0.064% 31.76% 2159ms 9.17% PlaneBoundaryCondition::VerifyBoundaryCondition 76ms 0.32% 32.08% 2084ms 8.86% NodesOnlyMesh::SolveNodeMapping 1040ms 4.42% 36.50% 2033ms 8.64% std::__unguarded_partition (inline) 175ms 0.74% 37.25% 1951ms 8.29% DistributedBoxCollection::AddPairsFromBox 0 0% 37.25% 1923ms 8.17% std::_Rb_tree::lower_bound (inline) 0 0% 37.25% 1923ms 8.17% std::map::lower_bound (inline) 1ms 0.0042% 37.25% 1819ms 7.73% std::__final_insertion_sort (inline) 100ms 0.42% 37.68% 1619ms 6.88% std::__unguarded_insertion_sort (inline) 575ms 2.44% 40.12% 1574ms 6.69% std::__unguarded_linear_insert (inline) 22ms 0.093% 40.21% 1511ms 6.42% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 29ms 0.12% 40.34% 1481ms 6.29% AbstractCellPopulation::GetCellUsingLocationIndex 1476ms 6.27% 46.61% 1476ms 6.27% __gnu_cxx::__normal_iterator::operator-- (inline) 51ms 0.22% 46.83% 1324ms 5.63% boost::numeric::ublas::c_vector::c_vector (partial-inline) 31ms 0.13% 46.96% 1190ms 5.06% boost::numeric::ublas::vector_assign (inline) 1ms 0.0042% 46.96% 1134ms 4.82% NodeBasedCellPopulation::UpdateCellProcessLocation 6ms 0.025% 46.99% 1102ms 4.68% DistributedBoxCollection::CalculateBoundaryNodePairs 314ms 1.33% 48.32% 1091ms 4.64% boost::numeric::ublas::indexing_vector_assign 256ms 1.09% 49.41% 947ms 4.02% __dynamic_cast 161ms 0.68% 50.09% 813ms 3.45% AbstractMesh::GetVectorFromAtoB 344ms 1.46% 51.56% 758ms 3.22% DistributedBoxCollection::CalculateContainingBox (partial-inline) 18ms 0.076% 51.63% 757ms 3.22% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 51.63% 727ms 3.09% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 51.63% 726ms 3.09% AbstractCellPopulation::WriteResultsToFiles 0 0% 51.63% 708ms 3.01% boost::numeric::ublas::norm_2 (inline) 526ms 2.24% 53.87% 708ms 3.01% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 53.87% 708ms 3.01% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 5ms 0.021% 53.89% 699ms 2.97% boost::numeric::ublas::c_vector::operator= (inline) 35ms 0.15% 54.04% 685ms 2.91% std::__copy_move::__copy_m (inline) 0 0% 54.04% 685ms 2.91% std::__copy_move_a (inline) 0 0% 54.04% 685ms 2.91% std::__copy_move_a1 (inline) 0 0% 54.04% 685ms 2.91% std::__copy_move_a2 (inline) 0 0% 54.04% 685ms 2.91% std::copy (inline) 677ms 2.88% 56.91% 677ms 2.88% boost::numeric::ublas::c_vector::operator() 162ms 0.69% 57.60% 676ms 2.87% NodeAttributes::AddNeighbour 665ms 2.83% 60.43% 665ms 2.83% __memcpy_avx_unaligned_erms 43ms 0.18% 60.61% 645ms 2.74% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.0085% 60.62% 618ms 2.63% AbstractCellBasedSimulation::DoCellBirth 4ms 0.017% 60.64% 599ms 2.55% CellPropertyCollection::GetPropertiesType (inline) 591ms 2.51% 63.15% 591ms 2.51% std::_Rb_tree_increment 8ms 0.034% 63.18% 589ms 2.50% AbstractCentreBasedCellPopulation::GetDampingConstant 514ms 2.18% 65.37% 586ms 2.49% std::vector::push_back (inline) 254ms 1.08% 66.45% 569ms 2.42% __cxxabiv1::__si_class_type_info::__do_dyncast 36ms 0.15% 66.60% 504ms 2.14% boost::detail::shared_count::~shared_count (inline) 0 0% 66.60% 504ms 2.14% boost::shared_ptr::~shared_ptr (inline) 86ms 0.37% 66.96% 502ms 2.13% std::__new_allocator::allocate (inline) 487ms 2.07% 69.03% 487ms 2.07% boost::numeric::ublas::same_impl_ex 483ms 2.05% 71.09% 483ms 2.05% __strcmp_avx2 3ms 0.013% 71.10% 477ms 2.03% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 71.10% 475ms 2.02% std::allocator_traits::allocate (inline) 12ms 0.051% 71.15% 472ms 2.01% std::_Rb_tree::_Rb_tree (partial-inline) 448ms 1.90% 73.05% 458ms 1.95% boost::detail::sp_counted_base::release 0 0% 73.05% 452ms 1.92% std::_Rb_tree::_M_create_node (inline) 39ms 0.17% 73.22% 449ms 1.91% std::_Rb_tree::_M_copy (inline) 0 0% 73.22% 441ms 1.87% AbstractCellBasedSimulation::DoCellRemoval (inline) 6ms 0.025% 73.24% 424ms 1.80% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1ms 0.0042% 73.25% 420ms 1.78% Cell::GetMutationState 22ms 0.093% 73.34% 416ms 1.77% operator new 126ms 0.54% 73.88% 412ms 1.75% std::_Rb_tree::_M_erase 132ms 0.56% 74.44% 410ms 1.74% std::_Rb_tree::_M_clone_node (inline) 5ms 0.021% 74.46% 408ms 1.73% AbstractCellProperty::IsSubType (inline) 0 0% 74.46% 387ms 1.64% std::_Rb_tree::_M_get_node (inline) 5ms 0.021% 74.48% 387ms 1.64% std::set::set (inline) 103ms 0.44% 74.92% 385ms 1.64% __GI___libc_malloc 132ms 0.56% 75.48% 361ms 1.53% Node::GetRadius 0 0% 75.48% 357ms 1.52% boost::numeric::ublas::c_vector::assign (inline) 16ms 0.068% 75.55% 339ms 1.44% boost::numeric::ublas::vector_binary::size (inline) 333ms 1.42% 76.96% 333ms 1.42% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 76.96% 327ms 1.39% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 76.96% 322ms 1.37% boost::numeric::ublas::inner_prod (inline) 4ms 0.017% 76.98% 322ms 1.37% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 3ms 0.013% 76.99% 319ms 1.36% NodeBasedCellPopulation::UpdateMapsAfterRemesh 26ms 0.11% 77.10% 318ms 1.35% boost::numeric::ublas::vector_scalar_binary::evaluate 36ms 0.15% 77.26% 307ms 1.30% std::_Rb_tree::~_Rb_tree (inline) 0 0% 77.26% 295ms 1.25% NodesOnlyMesh::ReMesh 292ms 1.24% 78.50% 292ms 1.24% __gnu_cxx::__normal_iterator::operator++ (inline) 4ms 0.017% 78.51% 290ms 1.23% NodesOnlyMesh::UpdateNodeIndices 0 0% 78.51% 269ms 1.14% std::_Rb_tree::_M_drop_node (inline) 0 0% 78.51% 268ms 1.14% NodesOnlyMesh::UpdateBoxCollection 2ms 0.0085% 78.52% 248ms 1.05% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 111ms 0.47% 78.99% 244ms 1.04% boost::numeric::ublas::vector_inner_prod::apply (inline) 240ms 1.02% 80.01% 240ms 1.02% Node::CheckForNodeAttributes 4ms 0.017% 80.03% 238ms 1.01% std::_Rb_tree::_M_emplace_hint_unique 3ms 0.013% 80.04% 235ms 1% DistributedBoxCollection::GetProcessOwningNode 81ms 0.34% 80.39% 234ms 0.99% Node::AddNeighbour 5ms 0.021% 80.41% 234ms 0.99% std::__new_allocator::deallocate (inline) 131ms 0.56% 80.97% 231ms 0.98% _int_malloc 0 0% 80.97% 228ms 0.97% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 80.97% 226ms 0.96% VtkMeshWriter::WriteFiles 122ms 0.52% 81.48% 222ms 0.94% boost::shared_ptr::shared_ptr (inline) 1ms 0.0042% 81.49% 221ms 0.94% NodesOnlyMesh::AddNodesToBoxes 0 0% 81.49% 220ms 0.93% std::set::~set (inline) 78ms 0.33% 81.82% 215ms 0.91% std::__move_median_to_first (inline) 0 0% 81.82% 214ms 0.91% std::allocator_traits::deallocate (inline) 0 0% 81.82% 213ms 0.91% std::_Rb_tree::_M_put_node (inline) 0 0% 81.82% 210ms 0.89% Cell::HasCellProperty (inline) 3ms 0.013% 81.83% 210ms 0.89% CellPropertyCollection::HasProperty 204ms 0.87% 82.70% 204ms 0.87% [libchaste_cell_based.so] 0 0% 82.70% 204ms 0.87% vtkStreamingDemandDrivenPipeline::Update 0 0% 82.70% 204ms 0.87% vtkXMLWriterBase::Write 66ms 0.28% 82.98% 203ms 0.86% __GI___libc_free 0 0% 82.98% 202ms 0.86% vtkDemandDrivenPipeline::ProcessRequest 0 0% 82.98% 200ms 0.85% vtkExecutive::CallAlgorithm 0 0% 82.98% 200ms 0.85% vtkStreamingDemandDrivenPipeline::ProcessRequest 199ms 0.85% 83.83% 199ms 0.85% Node::GetIndex 0 0% 83.83% 199ms 0.85% NodesOnlyMesh::ResizeBoxCollection 18ms 0.076% 83.90% 199ms 0.85% std::__insertion_sort (inline) 0 0% 83.90% 199ms 0.85% vtkDemandDrivenPipeline::ExecuteData 0 0% 83.90% 198ms 0.84% vtkCompositeDataPipeline::ExecuteData 0 0% 83.90% 198ms 0.84% vtkXMLUnstructuredDataWriter::ProcessRequest 10ms 0.042% 83.95% 197ms 0.84% NodesOnlyMesh::IsANodeCloseToDomainBoundary 6ms 0.025% 83.97% 196ms 0.83% Cell::ReadyToDivide 181ms 0.77% 84.74% 181ms 0.77% Node::ConstructNodeAttributes (inline) 176ms 0.75% 85.49% 176ms 0.75% boost::shared_ptr::operator-> (inline) 0 0% 85.49% 168ms 0.71% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.49% 168ms 0.71% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 5ms 0.021% 85.51% 165ms 0.7% AbstractCellProperty::IsType (inline) 0 0% 85.51% 164ms 0.7% std::_Rb_tree::clear (inline) 0 0% 85.51% 163ms 0.69% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 85.51% 154ms 0.65% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 152ms 0.65% 86.16% 152ms 0.65% [libchaste_mesh.so] 144ms 0.61% 86.77% 144ms 0.61% Node::IsDeleted 0 0% 86.77% 143ms 0.61% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 10ms 0.042% 86.81% 140ms 0.59% DistributedBoxCollection::GetIsPeriodicAllDims 14ms 0.059% 86.87% 138ms 0.59% boost::numeric::ublas::vector_reference::operator() (inline) 128ms 0.54% 87.41% 137ms 0.58% _int_free 135ms 0.57% 87.99% 137ms 0.58% std::__adjacent_find (inline) 0 0% 87.99% 137ms 0.58% std::__unique (inline) 0 0% 87.99% 137ms 0.58% std::unique (inline) 1ms 0.0042% 87.99% 137ms 0.58% vtkXMLWriter::WriteBinaryData 4ms 0.017% 88.01% 134ms 0.57% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 88.01% 132ms 0.56% vtkXMLWriter::WriteBinaryDataInternal 0 0% 88.01% 131ms 0.56% vtkXMLWriter::WriteBinaryDataBlock 0 0% 88.01% 131ms 0.56% vtkXMLWriter::WriteCompressionBlock 0 0% 88.01% 125ms 0.53% std::_Rb_tree::_Auto_node::_Auto_node (inline) 50ms 0.21% 88.22% 124ms 0.53% AbstractCellProperty::IsSame 0 0% 88.22% 123ms 0.52% vtkXMLWriter::WritePointsAppendedData 4ms 0.017% 88.24% 122ms 0.52% Cell::GetCellId 2ms 0.0085% 88.25% 122ms 0.52% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 88.25% 122ms 0.52% tbb::detail::r1::parallel_pipeline 0 0% 88.25% 121ms 0.51% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 88.25% 121ms 0.51% clone3 0 0% 88.25% 121ms 0.51% start_thread 1ms 0.0042% 88.25% 121ms 0.51% std::_Rb_tree::_M_insert_unique 0 0% 88.25% 121ms 0.51% std::set::insert (inline) 0 0% 88.25% 120ms 0.51% tbb::detail::r1::reset 46ms 0.2% 88.45% 120ms 0.51% tbb::detail::r1::wait_bounded_queue_monitor 0 0% 88.45% 119ms 0.51% std::map::clear (inline) 6ms 0.025% 88.47% 118ms 0.5% NodeBasedCellPopulation::SetNode