File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 21022ms, 89.11% of 23590ms total Dropped 752 nodes (cum <= 117.95ms) flat flat% sum% cum cum% 0 0% 0% 23449ms 99.40% __libc_start_call_main 0 0% 0% 23449ms 99.40% __libc_start_main_impl 0 0% 0% 23449ms 99.40% _start 0 0% 0% 23434ms 99.34% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 23434ms 99.34% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 23434ms 99.34% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 23434ms 99.34% main 0 0% 0% 23397ms 99.18% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 23397ms 99.18% CxxTest::TestRunner::runTest (inline) 0 0% 0% 23397ms 99.18% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 23389ms 99.15% AbstractCellBasedSimulation::Solve 2ms 0.0085% 0.0085% 13443ms 56.99% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0085% 8748ms 37.08% AbstractCellBasedSimulation::UpdateCellPopulation 6ms 0.025% 0.034% 8584ms 36.39% ForwardEulerNumericalMethod::UpdateAllNodePositions 12ms 0.051% 0.085% 8400ms 35.61% AbstractNumericalMethod::ComputeForcesIncludingDamping 1179ms 5.00% 5.08% 7815ms 33.13% RepulsionForce::AddForceContribution (partial-inline) 0 0% 5.08% 7737ms 32.80% NodeBasedCellPopulation::Update 8ms 0.034% 5.12% 5708ms 24.20% DistributedBoxCollection::CalculateInteriorNodePairs 2104ms 8.92% 14.04% 4996ms 21.18% std::_Rb_tree::_M_lower_bound (inline) 0 0% 14.04% 4589ms 19.45% OffLatticeSimulation::ApplyBoundaries 19ms 0.081% 14.12% 4500ms 19.08% NodeAttributes::RemoveDuplicateNeighbours 6ms 0.025% 14.14% 4324ms 18.33% std::__sort (inline) 0 0% 14.14% 4324ms 18.33% std::sort (inline) 158ms 0.67% 14.81% 3796ms 16.09% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 71ms 0.3% 15.11% 3490ms 14.79% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 4ms 0.017% 15.13% 3483ms 14.76% AbstractCellPopulation::Iterator::operator++ (inline) 170ms 0.72% 15.85% 3456ms 14.65% AbstractCellPopulation::Iterator::IsRealCell 252ms 1.07% 16.92% 3214ms 13.62% std::_Rb_tree::find (inline) 0 0% 16.92% 3214ms 13.62% std::map::find (inline) 24ms 0.1% 17.02% 2981ms 12.64% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2845ms 12.06% 29.08% 2845ms 12.06% std::_Rb_tree::_S_right (inline) 242ms 1.03% 30.11% 2566ms 10.88% std::map::operator[] (partial-inline) 206ms 0.87% 30.98% 2439ms 10.34% std::__introsort_loop 33ms 0.14% 31.12% 2392ms 10.14% PlaneBoundaryCondition::ImposeBoundaryCondition 34ms 0.14% 31.26% 2342ms 9.93% AbstractCellPopulation::GetLocationIndexUsingCell 158ms 0.67% 31.93% 2266ms 9.61% AbstractMesh::GetNode 51ms 0.22% 32.15% 2252ms 9.55% NodesOnlyMesh::GetNodeOrHaloNode 22ms 0.093% 32.24% 2197ms 9.31% PlaneBoundaryCondition::VerifyBoundaryCondition 0 0% 32.24% 2156ms 9.14% std::__unguarded_partition_pivot (inline) 71ms 0.3% 32.54% 2112ms 8.95% NodesOnlyMesh::SolveNodeMapping 0 0% 32.54% 2056ms 8.72% std::_Rb_tree::lower_bound (inline) 0 0% 32.54% 2056ms 8.72% std::map::lower_bound (inline) 1033ms 4.38% 36.92% 1954ms 8.28% std::__unguarded_partition (inline) 2ms 0.0085% 36.93% 1879ms 7.97% std::__final_insertion_sort (inline) 133ms 0.56% 37.49% 1826ms 7.74% DistributedBoxCollection::AddPairsFromBox 76ms 0.32% 37.82% 1753ms 7.43% boost::numeric::ublas::c_vector::c_vector (partial-inline) 100ms 0.42% 38.24% 1647ms 6.98% std::__unguarded_insertion_sort (inline) 589ms 2.50% 40.74% 1633ms 6.92% std::__unguarded_linear_insert (inline) 46ms 0.19% 40.93% 1573ms 6.67% boost::numeric::ublas::vector_assign (inline) 19ms 0.081% 41.01% 1551ms 6.57% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 26ms 0.11% 41.12% 1523ms 6.46% AbstractCellPopulation::GetCellUsingLocationIndex 366ms 1.55% 42.67% 1475ms 6.25% boost::numeric::ublas::indexing_vector_assign 1456ms 6.17% 48.85% 1456ms 6.17% __gnu_cxx::__normal_iterator::operator-- (inline) 168ms 0.71% 49.56% 1257ms 5.33% AbstractMesh::GetVectorFromAtoB 0 0% 49.56% 1161ms 4.92% NodeBasedCellPopulation::UpdateCellProcessLocation 8ms 0.034% 49.59% 1058ms 4.48% DistributedBoxCollection::CalculateBoundaryNodePairs 239ms 1.01% 50.61% 868ms 3.68% __dynamic_cast 27ms 0.11% 50.72% 826ms 3.50% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 375ms 1.59% 52.31% 777ms 3.29% DistributedBoxCollection::CalculateContainingBox (partial-inline) 178ms 0.75% 53.06% 745ms 3.16% NodeAttributes::AddNeighbour 0 0% 53.06% 731ms 3.10% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 1ms 0.0042% 53.07% 727ms 3.08% AbstractCellPopulation::WriteResultsToFiles 0 0% 53.07% 722ms 3.06% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 53.07% 721ms 3.06% boost::numeric::ublas::norm_2 (inline) 568ms 2.41% 55.48% 721ms 3.06% boost::numeric::ublas::vector_norm_2::apply (inline) 718ms 3.04% 58.52% 718ms 3.04% boost::numeric::ublas::same_impl_ex 677ms 2.87% 61.39% 677ms 2.87% boost::numeric::ublas::c_vector::operator() 45ms 0.19% 61.58% 661ms 2.80% boost::numeric::ublas::vector_binary::size (inline) 564ms 2.39% 63.97% 642ms 2.72% std::vector::push_back (inline) 37ms 0.16% 64.13% 575ms 2.44% std::_Rb_tree_const_iterator::operator++ (inline) 3ms 0.013% 64.14% 557ms 2.36% CellPropertyCollection::GetPropertiesType (inline) 4ms 0.017% 64.16% 543ms 2.30% AbstractCellBasedSimulation::DoCellBirth 239ms 1.01% 65.17% 535ms 2.27% __cxxabiv1::__si_class_type_info::__do_dyncast 534ms 2.26% 67.44% 534ms 2.26% std::_Rb_tree_increment 2ms 0.0085% 67.44% 515ms 2.18% AbstractCentreBasedCellPopulation::GetDampingConstant 70ms 0.3% 67.74% 509ms 2.16% std::__new_allocator::allocate (inline) 29ms 0.12% 67.86% 505ms 2.14% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 67.86% 490ms 2.08% std::allocator_traits::allocate (inline) 28ms 0.12% 67.98% 482ms 2.04% std::_Rb_tree::_Rb_tree (partial-inline) 35ms 0.15% 68.13% 474ms 2.01% boost::detail::shared_count::~shared_count (inline) 0 0% 68.13% 474ms 2.01% boost::shared_ptr::~shared_ptr (inline) 1ms 0.0042% 68.13% 470ms 1.99% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 68.13% 467ms 1.98% AbstractCellBasedSimulation::DoCellRemoval (inline) 6ms 0.025% 68.16% 457ms 1.94% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 13ms 0.055% 68.22% 452ms 1.92% std::__copy_move::__copy_m (inline) 0 0% 68.22% 452ms 1.92% std::__copy_move_a (inline) 0 0% 68.22% 452ms 1.92% std::__copy_move_a1 (inline) 0 0% 68.22% 452ms 1.92% std::__copy_move_a2 (inline) 0 0% 68.22% 452ms 1.92% std::copy (inline) 141ms 0.6% 68.81% 450ms 1.91% Node::GetRadius 445ms 1.89% 70.70% 445ms 1.89% __memcpy_avx_unaligned_erms 0 0% 70.70% 444ms 1.88% std::_Rb_tree::_M_create_node (inline) 47ms 0.2% 70.90% 442ms 1.87% std::_Rb_tree::_M_copy (inline) 28ms 0.12% 71.02% 437ms 1.85% operator new 424ms 1.80% 72.81% 429ms 1.82% boost::detail::sp_counted_base::release 423ms 1.79% 74.61% 423ms 1.79% __strcmp_avx2 0 0% 74.61% 407ms 1.73% std::_Rb_tree::_M_get_node (inline) 123ms 0.52% 75.13% 401ms 1.70% __GI___libc_malloc 6ms 0.025% 75.15% 397ms 1.68% std::set::set (inline) 146ms 0.62% 75.77% 395ms 1.67% std::_Rb_tree::_M_clone_node (inline) 6ms 0.025% 75.80% 384ms 1.63% AbstractCellProperty::IsSubType (inline) 3ms 0.013% 75.81% 368ms 1.56% Cell::GetMutationState 0 0% 75.81% 357ms 1.51% boost::numeric::ublas::c_vector::assign (inline) 103ms 0.44% 76.25% 355ms 1.50% std::_Rb_tree::_M_erase 321ms 1.36% 77.61% 321ms 1.36% Node::CheckForNodeAttributes 1ms 0.0042% 77.61% 316ms 1.34% NodesOnlyMesh::ReMesh 0 0% 77.61% 309ms 1.31% std::_Rb_tree::_Alloc_node::operator() (inline) 4ms 0.017% 77.63% 307ms 1.30% NodesOnlyMesh::UpdateNodeIndices 6ms 0.025% 77.66% 305ms 1.29% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 77.66% 303ms 1.28% boost::numeric::ublas::inner_prod (inline) 3ms 0.013% 77.67% 302ms 1.28% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 17ms 0.072% 77.74% 299ms 1.27% boost::numeric::ublas::vector_scalar_binary::evaluate 292ms 1.24% 78.98% 292ms 1.24% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 4ms 0.017% 79.00% 290ms 1.23% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 286ms 1.21% 80.21% 286ms 1.21% __gnu_cxx::__normal_iterator::operator++ (inline) 5ms 0.021% 80.23% 272ms 1.15% DistributedBoxCollection::GetProcessOwningNode 0 0% 80.23% 268ms 1.14% NodesOnlyMesh::UpdateBoxCollection 5ms 0.021% 80.25% 268ms 1.14% std::_Rb_tree::_M_emplace_hint_unique 34ms 0.14% 80.39% 265ms 1.12% std::_Rb_tree::~_Rb_tree (inline) 0 0% 80.39% 249ms 1.06% std::_Rb_tree::_M_drop_node (inline) 96ms 0.41% 80.80% 237ms 1.00% boost::numeric::ublas::vector_inner_prod::apply (inline) 135ms 0.57% 81.37% 234ms 0.99% _int_malloc 21ms 0.089% 81.46% 230ms 0.97% std::__insertion_sort (inline) 0 0% 81.46% 228ms 0.97% NodesOnlyMesh::AddNodesToBoxes 0 0% 81.46% 222ms 0.94% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 81.46% 221ms 0.94% VtkMeshWriter::WriteFiles 3ms 0.013% 81.48% 215ms 0.91% std::__new_allocator::deallocate (inline) 0 0% 81.48% 207ms 0.88% std::set::~set (inline) 104ms 0.44% 81.92% 205ms 0.87% boost::shared_ptr::shared_ptr (inline) 0 0% 81.92% 205ms 0.87% vtkDemandDrivenPipeline::ProcessRequest 0 0% 81.92% 205ms 0.87% vtkStreamingDemandDrivenPipeline::Update 0 0% 81.92% 205ms 0.87% vtkXMLWriterBase::Write 204ms 0.86% 82.78% 204ms 0.86% [libchaste_cell_based.so] 0 0% 82.78% 204ms 0.86% vtkDemandDrivenPipeline::ExecuteData 0 0% 82.78% 204ms 0.86% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 82.78% 202ms 0.86% vtkExecutive::CallAlgorithm 102ms 0.43% 83.21% 201ms 0.85% std::__move_median_to_first (inline) 0 0% 83.21% 201ms 0.85% vtkCompositeDataPipeline::ExecuteData 0 0% 83.21% 201ms 0.85% vtkXMLUnstructuredDataWriter::ProcessRequest 72ms 0.31% 83.52% 195ms 0.83% __GI___libc_free 187ms 0.79% 84.31% 187ms 0.79% Node::GetIndex 0 0% 84.31% 187ms 0.79% NodesOnlyMesh::ResizeBoxCollection 0 0% 84.31% 187ms 0.79% std::allocator_traits::deallocate (inline) 14ms 0.059% 84.37% 185ms 0.78% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 84.37% 182ms 0.77% std::_Rb_tree::_M_put_node (inline) 180ms 0.76% 85.13% 180ms 0.76% boost::numeric::ublas::c_vector::size (inline) 0 0% 85.13% 177ms 0.75% boost::numeric::ublas::vector_reference::size (inline) 2ms 0.0085% 85.14% 176ms 0.75% CellPropertyCollection::HasProperty 0 0% 85.14% 175ms 0.74% Cell::HasCellProperty (inline) 0 0% 85.14% 172ms 0.73% vtkXMLUnstructuredDataWriter::WriteAPiece 1ms 0.0042% 85.15% 172ms 0.73% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 85.15% 168ms 0.71% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 77ms 0.33% 85.47% 165ms 0.7% Node::AddNeighbour 6ms 0.025% 85.50% 163ms 0.69% Cell::ReadyToDivide 20ms 0.085% 85.58% 151ms 0.64% boost::numeric::ublas::vector_reference::operator() (inline) 149ms 0.63% 86.21% 149ms 0.63% Node::IsDeleted 146ms 0.62% 86.83% 147ms 0.62% std::__adjacent_find (inline) 0 0% 86.83% 147ms 0.62% std::__unique (inline) 0 0% 86.83% 147ms 0.62% std::unique (inline) 2ms 0.0085% 86.84% 146ms 0.62% AbstractCellProperty::IsType (inline) 0 0% 86.84% 144ms 0.61% std::_Rb_tree::clear (inline) 1ms 0.0042% 86.85% 143ms 0.61% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 137ms 0.58% 87.43% 137ms 0.58% boost::shared_ptr::operator-> (inline) 0 0% 87.43% 136ms 0.58% vtkXMLWriter::WriteBinaryData 0 0% 87.43% 135ms 0.57% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 87.43% 132ms 0.56% vtkXMLWriter::WriteBinaryDataInternal 38ms 0.16% 87.59% 131ms 0.56% AbstractCellCycleModel::GetAge 2ms 0.0085% 87.60% 131ms 0.56% Cell::GetCellId 0 0% 87.60% 131ms 0.56% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 87.60% 131ms 0.56% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.60% 131ms 0.56% vtkXMLWriter::WriteCompressionBlock 6ms 0.025% 87.62% 130ms 0.55% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 87.62% 128ms 0.54% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 4ms 0.017% 87.64% 127ms 0.54% DistributedBoxCollection::GetIsPeriodicAllDims 108ms 0.46% 88.10% 123ms 0.52% _int_free 122ms 0.52% 88.61% 122ms 0.52% [libchaste_mesh.so] 118ms 0.5% 89.11% 120ms 0.51% Node::ConstructNodeAttributes (inline) 0 0% 89.11% 119ms 0.5% vtkXMLWriter::WritePointsAppendedData