File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20478ms, 89.56% of 22866ms total Dropped 724 nodes (cum <= 114.33ms) flat flat% sum% cum cum% 0 0% 0% 22728ms 99.40% __libc_start_call_main 0 0% 0% 22728ms 99.40% __libc_start_main_impl 0 0% 0% 22728ms 99.40% _start 0 0% 0% 22713ms 99.33% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 22713ms 99.33% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 22713ms 99.33% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 22713ms 99.33% main 0 0% 0% 22679ms 99.18% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 22679ms 99.18% CxxTest::TestRunner::runTest (inline) 0 0% 0% 22679ms 99.18% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 22672ms 99.15% AbstractCellBasedSimulation::Solve 0 0% 0% 12865ms 56.26% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0% 8620ms 37.70% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 8145ms 35.62% ForwardEulerNumericalMethod::UpdateAllNodePositions 7ms 0.031% 0.031% 7989ms 34.94% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.031% 7613ms 33.29% NodeBasedCellPopulation::Update 1188ms 5.20% 5.23% 7384ms 32.29% RepulsionForce::AddForceContribution (partial-inline) 3ms 0.013% 5.24% 5590ms 24.45% DistributedBoxCollection::CalculateInteriorNodePairs 2134ms 9.33% 14.57% 4855ms 21.23% std::_Rb_tree::_M_lower_bound (inline) 23ms 0.1% 14.67% 4489ms 19.63% NodeAttributes::RemoveDuplicateNeighbours 0 0% 14.67% 4440ms 19.42% OffLatticeSimulation::ApplyBoundaries 5ms 0.022% 14.69% 4307ms 18.84% std::__sort (inline) 0 0% 14.69% 4307ms 18.84% std::sort (inline) 171ms 0.75% 15.44% 3683ms 16.11% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 2ms 0.0087% 15.45% 3425ms 14.98% AbstractCellPopulation::Iterator::operator++ (inline) 172ms 0.75% 16.20% 3400ms 14.87% AbstractCellPopulation::Iterator::IsRealCell 70ms 0.31% 16.51% 3374ms 14.76% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 243ms 1.06% 17.57% 3156ms 13.80% std::_Rb_tree::find (inline) 0 0% 17.57% 3155ms 13.80% std::map::find (inline) 23ms 0.1% 17.67% 2922ms 12.78% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2676ms 11.70% 29.38% 2676ms 11.70% std::_Rb_tree::_S_right (inline) 178ms 0.78% 30.15% 2472ms 10.81% std::__introsort_loop 231ms 1.01% 31.16% 2444ms 10.69% std::map::operator[] (partial-inline) 27ms 0.12% 31.28% 2321ms 10.15% PlaneBoundaryCondition::ImposeBoundaryCondition 27ms 0.12% 31.40% 2281ms 9.98% AbstractCellPopulation::GetLocationIndexUsingCell 149ms 0.65% 32.05% 2223ms 9.72% AbstractMesh::GetNode 43ms 0.19% 32.24% 2210ms 9.67% NodesOnlyMesh::GetNodeOrHaloNode 1ms 0.0044% 32.24% 2209ms 9.66% std::__unguarded_partition_pivot (inline) 15ms 0.066% 32.31% 2119ms 9.27% PlaneBoundaryCondition::VerifyBoundaryCondition 87ms 0.38% 32.69% 2079ms 9.09% NodesOnlyMesh::SolveNodeMapping 1027ms 4.49% 37.18% 2017ms 8.82% std::__unguarded_partition (inline) 0 0% 37.18% 1965ms 8.59% std::_Rb_tree::lower_bound (inline) 0 0% 37.18% 1965ms 8.59% std::map::lower_bound (inline) 0 0% 37.18% 1827ms 7.99% std::__final_insertion_sort (inline) 142ms 0.62% 37.80% 1747ms 7.64% DistributedBoxCollection::AddPairsFromBox 104ms 0.45% 38.26% 1634ms 7.15% std::__unguarded_insertion_sort (inline) 564ms 2.47% 40.72% 1545ms 6.76% std::__unguarded_linear_insert (inline) 14ms 0.061% 40.79% 1525ms 6.67% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 22ms 0.096% 40.88% 1508ms 6.59% AbstractCellPopulation::GetCellUsingLocationIndex 1457ms 6.37% 47.25% 1457ms 6.37% __gnu_cxx::__normal_iterator::operator-- (inline) 61ms 0.27% 47.52% 1288ms 5.63% boost::numeric::ublas::c_vector::c_vector (partial-inline) 44ms 0.19% 47.71% 1175ms 5.14% boost::numeric::ublas::vector_assign (inline) 0 0% 47.71% 1157ms 5.06% NodeBasedCellPopulation::UpdateCellProcessLocation 3ms 0.013% 47.73% 1065ms 4.66% DistributedBoxCollection::CalculateBoundaryNodePairs 294ms 1.29% 49.01% 1058ms 4.63% boost::numeric::ublas::indexing_vector_assign 211ms 0.92% 49.93% 884ms 3.87% __dynamic_cast 165ms 0.72% 50.66% 824ms 3.60% AbstractMesh::GetVectorFromAtoB 21ms 0.092% 50.75% 772ms 3.38% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 355ms 1.55% 52.30% 771ms 3.37% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 52.30% 749ms 3.28% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 52.30% 734ms 3.21% boost::numeric::ublas::norm_2 (inline) 562ms 2.46% 54.76% 734ms 3.21% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 54.76% 734ms 3.21% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 211ms 0.92% 55.68% 712ms 3.11% NodeAttributes::AddNeighbour 0 0% 55.68% 705ms 3.08% AbstractCellPopulation::WriteResultsToFiles 7ms 0.031% 55.71% 674ms 2.95% boost::numeric::ublas::c_vector::operator= (inline) 659ms 2.88% 58.59% 659ms 2.88% boost::numeric::ublas::c_vector::operator() 39ms 0.17% 58.76% 650ms 2.84% std::__copy_move::__copy_m (inline) 0 0% 58.76% 650ms 2.84% std::__copy_move_a (inline) 0 0% 58.76% 650ms 2.84% std::__copy_move_a1 (inline) 0 0% 58.76% 650ms 2.84% std::__copy_move_a2 (inline) 0 0% 58.76% 649ms 2.84% std::copy (inline) 628ms 2.75% 61.51% 628ms 2.75% __memcpy_avx_unaligned_erms 250ms 1.09% 62.60% 567ms 2.48% __cxxabiv1::__si_class_type_info::__do_dyncast 2ms 0.0087% 62.61% 566ms 2.48% AbstractCellBasedSimulation::DoCellBirth 499ms 2.18% 64.79% 558ms 2.44% std::vector::push_back (inline) 8ms 0.035% 64.83% 540ms 2.36% CellPropertyCollection::GetPropertiesType (inline) 5ms 0.022% 64.85% 524ms 2.29% AbstractCentreBasedCellPopulation::GetDampingConstant 42ms 0.18% 65.04% 495ms 2.16% boost::detail::shared_count::~shared_count (inline) 0 0% 65.04% 495ms 2.16% boost::shared_ptr::~shared_ptr (inline) 479ms 2.09% 67.13% 479ms 2.09% boost::numeric::ublas::same_impl_ex 76ms 0.33% 67.46% 478ms 2.09% std::__new_allocator::allocate (inline) 28ms 0.12% 67.59% 476ms 2.08% std::_Rb_tree_const_iterator::operator++ (inline) 469ms 2.05% 69.64% 469ms 2.05% __strcmp_avx2 1ms 0.0044% 69.64% 461ms 2.02% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 69.64% 457ms 2.00% std::allocator_traits::allocate (inline) 443ms 1.94% 71.58% 447ms 1.95% boost::detail::sp_counted_base::release 15ms 0.066% 71.64% 442ms 1.93% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 71.64% 440ms 1.92% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 71.64% 436ms 1.91% std::_Rb_tree::_M_create_node (inline) 8ms 0.035% 71.68% 435ms 1.90% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 435ms 1.90% 73.58% 435ms 1.90% std::_Rb_tree_increment 47ms 0.21% 73.79% 415ms 1.81% std::_Rb_tree::_M_copy (inline) 23ms 0.1% 73.89% 397ms 1.74% operator new 4ms 0.017% 73.90% 394ms 1.72% AbstractCellProperty::IsSubType (inline) 133ms 0.58% 74.49% 392ms 1.71% std::_Rb_tree::_M_erase 148ms 0.65% 75.13% 387ms 1.69% Node::GetRadius 0 0% 75.13% 386ms 1.69% std::_Rb_tree::_M_get_node (inline) 5ms 0.022% 75.16% 369ms 1.61% std::set::set (inline) 8ms 0.035% 75.19% 368ms 1.61% Cell::GetMutationState 115ms 0.5% 75.69% 368ms 1.61% std::_Rb_tree::_M_clone_node (inline) 106ms 0.46% 76.16% 364ms 1.59% __GI___libc_malloc 8ms 0.035% 76.19% 335ms 1.47% NodeBasedCellPopulation::UpdateMapsAfterRemesh 26ms 0.11% 76.31% 330ms 1.44% boost::numeric::ublas::vector_binary::size (inline) 325ms 1.42% 77.73% 325ms 1.42% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 77.73% 311ms 1.36% std::_Rb_tree::_Alloc_node::operator() (inline) 307ms 1.34% 79.07% 307ms 1.34% __gnu_cxx::__normal_iterator::operator++ (inline) 40ms 0.17% 79.24% 306ms 1.34% std::_Rb_tree::~_Rb_tree (inline) 0 0% 79.24% 299ms 1.31% boost::numeric::ublas::inner_prod (inline) 1ms 0.0044% 79.25% 299ms 1.31% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 79.25% 298ms 1.30% boost::numeric::ublas::c_vector::assign (inline) 11ms 0.048% 79.30% 298ms 1.30% boost::numeric::ublas::vector_scalar_binary::evaluate 4ms 0.017% 79.31% 283ms 1.24% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 1ms 0.0044% 79.32% 275ms 1.20% NodesOnlyMesh::UpdateBoxCollection 8ms 0.035% 79.35% 265ms 1.16% DistributedBoxCollection::GetProcessOwningNode 0 0% 79.35% 265ms 1.16% NodesOnlyMesh::ReMesh 2ms 0.0087% 79.36% 252ms 1.10% NodesOnlyMesh::UpdateNodeIndices 102ms 0.45% 79.81% 249ms 1.09% boost::numeric::ublas::vector_inner_prod::apply (inline) 14ms 0.061% 79.87% 248ms 1.08% std::_Rb_tree::_M_emplace_hint_unique 246ms 1.08% 80.95% 246ms 1.08% Node::CheckForNodeAttributes 0 0% 80.95% 242ms 1.06% std::_Rb_tree::_M_drop_node (inline) 3ms 0.013% 80.96% 229ms 1.00% NodesOnlyMesh::AddNodesToBoxes 0 0% 80.96% 226ms 0.99% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 80.96% 225ms 0.98% std::set::~set (inline) 0 0% 80.96% 224ms 0.98% VtkMeshWriter::WriteFiles 0 0% 80.96% 220ms 0.96% NodesOnlyMesh::ResizeBoxCollection 13ms 0.057% 81.02% 219ms 0.96% NodesOnlyMesh::IsANodeCloseToDomainBoundary 7ms 0.031% 81.05% 213ms 0.93% std::__new_allocator::deallocate (inline) 209ms 0.91% 81.96% 209ms 0.91% Node::GetIndex 121ms 0.53% 82.49% 203ms 0.89% _int_malloc 0 0% 82.49% 200ms 0.87% vtkStreamingDemandDrivenPipeline::Update 0 0% 82.49% 200ms 0.87% vtkXMLWriterBase::Write 0 0% 82.49% 199ms 0.87% vtkDemandDrivenPipeline::ProcessRequest 196ms 0.86% 83.35% 196ms 0.86% [libchaste_cell_based.so] 74ms 0.32% 83.67% 195ms 0.85% __GI___libc_free 0 0% 83.67% 195ms 0.85% vtkCompositeDataPipeline::ExecuteData 0 0% 83.67% 195ms 0.85% vtkDemandDrivenPipeline::ExecuteData 0 0% 83.67% 195ms 0.85% vtkStreamingDemandDrivenPipeline::ProcessRequest 17ms 0.074% 83.74% 193ms 0.84% std::__insertion_sort (inline) 0 0% 83.74% 193ms 0.84% vtkExecutive::CallAlgorithm 0 0% 83.74% 193ms 0.84% vtkXMLUnstructuredDataWriter::ProcessRequest 91ms 0.4% 84.14% 187ms 0.82% boost::shared_ptr::shared_ptr (inline) 81ms 0.35% 84.50% 187ms 0.82% std::__move_median_to_first (inline) 0 0% 84.50% 184ms 0.8% std::allocator_traits::deallocate (inline) 0 0% 84.50% 181ms 0.79% std::_Rb_tree::_M_put_node (inline) 0 0% 84.50% 177ms 0.77% Cell::HasCellProperty (inline) 1ms 0.0044% 84.50% 177ms 0.77% CellPropertyCollection::HasProperty 0 0% 84.50% 171ms 0.75% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 84.50% 171ms 0.75% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 4ms 0.017% 84.52% 165ms 0.72% Cell::ReadyToDivide 0 0% 84.52% 165ms 0.72% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 162ms 0.71% 85.23% 162ms 0.71% [libchaste_mesh.so] 2ms 0.0087% 85.24% 161ms 0.7% AbstractCellProperty::IsType (inline) 8ms 0.035% 85.27% 157ms 0.69% boost::numeric::ublas::vector_reference::operator() (inline) 8ms 0.035% 85.31% 152ms 0.66% DistributedBoxCollection::GetIsPeriodicAllDims 150ms 0.66% 85.96% 150ms 0.66% std::__adjacent_find (inline) 0 0% 85.96% 150ms 0.66% std::__unique (inline) 0 0% 85.96% 150ms 0.66% std::unique (inline) 0 0% 85.96% 147ms 0.64% std::_Rb_tree::clear (inline) 69ms 0.3% 86.26% 146ms 0.64% Node::AddNeighbour 145ms 0.63% 86.90% 145ms 0.63% Node::IsDeleted 0 0% 86.90% 145ms 0.63% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 86.90% 141ms 0.62% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 141ms 0.62% 87.51% 141ms 0.62% boost::shared_ptr::operator-> (inline) 0 0% 87.51% 140ms 0.61% boost::numeric::ublas::vector_binary::operator() (inline) 2ms 0.0087% 87.52% 136ms 0.59% Cell::GetCellId 0 0% 87.52% 133ms 0.58% vtkXMLWriter::WriteBinaryData 46ms 0.2% 87.72% 130ms 0.57% AbstractCellProperty::IsSame 1ms 0.0044% 87.73% 128ms 0.56% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.73% 128ms 0.56% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.73% 127ms 0.56% vtkXMLWriter::WriteCompressionBlock 0 0% 87.73% 125ms 0.55% AbstractCellPopulation::SetCellUsingLocationIndex 0 0% 87.73% 125ms 0.55% std::_Rb_tree::_Auto_node::_Auto_node (inline) 121ms 0.53% 88.26% 121ms 0.53% Node::rGetLocation 111ms 0.49% 88.74% 121ms 0.53% _int_free 8ms 0.035% 88.78% 121ms 0.53% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 88.78% 119ms 0.52% compress2 0 0% 88.78% 119ms 0.52% vtkDataCompressor::Compress 0 0% 88.78% 119ms 0.52% vtkXMLWriter::WritePointsAppendedData 0 0% 88.78% 119ms 0.52% vtkZLibDataCompressor::CompressBuffer 117ms 0.51% 89.29% 117ms 0.51% Node::ConstructNodeAttributes (inline) 60ms 0.26% 89.55% 117ms 0.51% crc32 0 0% 89.55% 117ms 0.51% deflate 1ms 0.0044% 89.56% 115ms 0.5% std::_Rb_tree::_M_insert_unique 0 0% 89.56% 115ms 0.5% std::set::insert (inline)