File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20669ms, 89.60% of 23069ms total Dropped 785 nodes (cum <= 115.34ms) flat flat% sum% cum cum% 0 0% 0% 22921ms 99.36% __libc_start_call_main 0 0% 0% 22921ms 99.36% __libc_start_main_impl 0 0% 0% 22921ms 99.36% _start 0 0% 0% 22904ms 99.28% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 22904ms 99.28% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 22904ms 99.28% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 22904ms 99.28% main 0 0% 0% 22861ms 99.10% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 22861ms 99.10% CxxTest::TestRunner::runTest (inline) 0 0% 0% 22861ms 99.10% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0043% 0.0043% 22853ms 99.06% AbstractCellBasedSimulation::Solve 1ms 0.0043% 0.0087% 13066ms 56.64% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0087% 8585ms 37.21% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0043% 0.013% 8185ms 35.48% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.043% 0.056% 8017ms 34.75% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.056% 7562ms 32.78% NodeBasedCellPopulation::Update 1245ms 5.40% 5.45% 7422ms 32.17% RepulsionForce::AddForceContribution (partial-inline) 10ms 0.043% 5.50% 5533ms 23.98% DistributedBoxCollection::CalculateInteriorNodePairs 2113ms 9.16% 14.66% 4975ms 21.57% std::_Rb_tree::_M_lower_bound (inline) 0 0% 14.66% 4584ms 19.87% OffLatticeSimulation::ApplyBoundaries 12ms 0.052% 14.71% 4306ms 18.67% NodeAttributes::RemoveDuplicateNeighbours 4ms 0.017% 14.73% 4140ms 17.95% std::__sort (inline) 0 0% 14.73% 4140ms 17.95% std::sort (inline) 177ms 0.77% 15.49% 3744ms 16.23% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 2ms 0.0087% 15.50% 3490ms 15.13% AbstractCellPopulation::Iterator::operator++ (inline) 209ms 0.91% 16.41% 3463ms 15.01% AbstractCellPopulation::Iterator::IsRealCell (inline) 69ms 0.3% 16.71% 3431ms 14.87% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 224ms 0.97% 17.68% 3183ms 13.80% std::_Rb_tree::find (inline) 0 0% 17.68% 3182ms 13.79% std::map::find (inline) 30ms 0.13% 17.81% 2954ms 12.81% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2826ms 12.25% 30.06% 2826ms 12.25% std::_Rb_tree::_S_right (inline) 246ms 1.07% 31.12% 2570ms 11.14% std::map::operator[] (partial-inline) 167ms 0.72% 31.85% 2382ms 10.33% std::__introsort_loop 43ms 0.19% 32.03% 2379ms 10.31% AbstractCellPopulation::GetLocationIndexUsingCell 19ms 0.082% 32.12% 2375ms 10.30% PlaneBoundaryCondition::ImposeBoundaryCondition 16ms 0.069% 32.19% 2208ms 9.57% PlaneBoundaryCondition::VerifyBoundaryCondition 119ms 0.52% 32.70% 2175ms 9.43% AbstractMesh::GetNode 43ms 0.19% 32.89% 2159ms 9.36% NodesOnlyMesh::GetNodeOrHaloNode 2ms 0.0087% 32.90% 2144ms 9.29% std::__unguarded_partition_pivot (inline) 85ms 0.37% 33.27% 2062ms 8.94% NodesOnlyMesh::SolveNodeMapping 0 0% 33.27% 2030ms 8.80% std::_Rb_tree::lower_bound (inline) 0 0% 33.27% 2030ms 8.80% std::map::lower_bound (inline) 994ms 4.31% 37.57% 1915ms 8.30% std::__unguarded_partition (inline) 133ms 0.58% 38.15% 1813ms 7.86% DistributedBoxCollection::AddPairsFromBox 0 0% 38.15% 1749ms 7.58% std::__final_insertion_sort (inline) 13ms 0.056% 38.21% 1551ms 6.72% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 96ms 0.42% 38.62% 1533ms 6.65% std::__unguarded_insertion_sort (inline) 29ms 0.13% 38.75% 1531ms 6.64% AbstractCellPopulation::GetCellUsingLocationIndex 515ms 2.23% 40.98% 1500ms 6.50% std::__unguarded_linear_insert (inline) 1416ms 6.14% 47.12% 1416ms 6.14% __gnu_cxx::__normal_iterator::operator-- (inline) 45ms 0.2% 47.31% 1221ms 5.29% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 47.31% 1143ms 4.95% NodeBasedCellPopulation::UpdateCellProcessLocation 30ms 0.13% 47.44% 1118ms 4.85% boost::numeric::ublas::vector_assign (inline) 5ms 0.022% 47.47% 1067ms 4.63% DistributedBoxCollection::CalculateBoundaryNodePairs 280ms 1.21% 48.68% 1019ms 4.42% boost::numeric::ublas::indexing_vector_assign 252ms 1.09% 49.77% 938ms 4.07% __dynamic_cast 392ms 1.70% 51.47% 821ms 3.56% DistributedBoxCollection::CalculateContainingBox (partial-inline) 13ms 0.056% 51.53% 809ms 3.51% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 147ms 0.64% 52.17% 783ms 3.39% AbstractMesh::GetVectorFromAtoB 0 0% 52.17% 743ms 3.22% AbstractCellPopulation::WriteResultsToFiles 0 0% 52.17% 735ms 3.19% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 52.17% 717ms 3.11% boost::numeric::ublas::norm_2 (inline) 553ms 2.40% 54.56% 717ms 3.11% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 54.56% 717ms 3.11% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 181ms 0.78% 55.35% 696ms 3.02% NodeAttributes::AddNeighbour 674ms 2.92% 58.27% 674ms 2.92% boost::numeric::ublas::c_vector::operator() 4ms 0.017% 58.29% 671ms 2.91% boost::numeric::ublas::c_vector::operator= (inline) 30ms 0.13% 58.42% 652ms 2.83% std::__copy_move::__copy_m (inline) 0 0% 58.42% 652ms 2.83% std::__copy_move_a (inline) 0 0% 58.42% 652ms 2.83% std::__copy_move_a1 (inline) 0 0% 58.42% 652ms 2.83% std::__copy_move_a2 (inline) 0 0% 58.42% 651ms 2.82% std::copy (inline) 643ms 2.79% 61.20% 643ms 2.79% __memcpy_avx_unaligned_erms 3ms 0.013% 61.22% 582ms 2.52% CellPropertyCollection::GetPropertiesType (inline) 26ms 0.11% 61.33% 581ms 2.52% std::_Rb_tree_const_iterator::operator++ (inline) 513ms 2.22% 63.55% 577ms 2.50% std::vector::push_back (inline) 285ms 1.24% 64.79% 572ms 2.48% __cxxabiv1::__si_class_type_info::__do_dyncast 1ms 0.0043% 64.79% 559ms 2.42% AbstractCellBasedSimulation::DoCellBirth 552ms 2.39% 67.19% 552ms 2.39% std::_Rb_tree_increment 39ms 0.17% 67.35% 548ms 2.38% boost::detail::shared_count::~shared_count (inline) 0 0% 67.35% 548ms 2.38% boost::shared_ptr::~shared_ptr (inline) 4ms 0.017% 67.37% 538ms 2.33% AbstractCentreBasedCellPopulation::GetDampingConstant 64ms 0.28% 67.65% 504ms 2.18% std::__new_allocator::allocate (inline) 2ms 0.0087% 67.66% 492ms 2.13% NodeBasedCellPopulation::WriteVtkResultsToFile 488ms 2.12% 69.77% 492ms 2.13% boost::detail::sp_counted_base::release 0 0% 69.77% 484ms 2.10% std::allocator_traits::allocate (inline) 0 0% 69.77% 461ms 2.00% AbstractCellBasedSimulation::DoCellRemoval (inline) 461ms 2.00% 71.77% 461ms 2.00% __strcmp_avx2 0 0% 71.77% 444ms 1.92% std::_Rb_tree::_M_create_node (inline) 443ms 1.92% 73.69% 443ms 1.92% boost::numeric::ublas::same_impl_ex 3ms 0.013% 73.70% 441ms 1.91% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 30ms 0.13% 73.84% 434ms 1.88% operator new 144ms 0.62% 74.46% 425ms 1.84% std::_Rb_tree::_M_erase 0 0% 74.46% 409ms 1.77% std::_Rb_tree::_M_get_node (inline) 1ms 0.0043% 74.46% 407ms 1.76% AbstractCellProperty::IsSubType (inline) 16ms 0.069% 74.53% 405ms 1.76% std::_Rb_tree::_Rb_tree (partial-inline) 111ms 0.48% 75.01% 393ms 1.70% __GI___libc_malloc 0 0% 75.01% 392ms 1.70% Cell::GetMutationState 149ms 0.65% 75.66% 387ms 1.68% Node::GetRadius 34ms 0.15% 75.81% 377ms 1.63% std::_Rb_tree::_M_copy (inline) 119ms 0.52% 76.32% 338ms 1.47% std::_Rb_tree::_M_clone_node (inline) 39ms 0.17% 76.49% 333ms 1.44% std::_Rb_tree::~_Rb_tree (inline) 0 0% 76.49% 328ms 1.42% NodesOnlyMesh::ReMesh 2ms 0.0087% 76.50% 328ms 1.42% std::set::set (inline) 0 0% 76.50% 319ms 1.38% boost::numeric::ublas::inner_prod (inline) 1ms 0.0043% 76.51% 319ms 1.38% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 16ms 0.069% 76.57% 318ms 1.38% boost::numeric::ublas::vector_scalar_binary::evaluate 4ms 0.017% 76.59% 317ms 1.37% NodesOnlyMesh::UpdateNodeIndices 10ms 0.043% 76.64% 313ms 1.36% NodeBasedCellPopulation::UpdateMapsAfterRemesh 302ms 1.31% 77.94% 302ms 1.31% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 19ms 0.082% 78.03% 297ms 1.29% boost::numeric::ublas::vector_binary::size (inline) 14ms 0.061% 78.09% 294ms 1.27% std::_Rb_tree::_M_emplace_hint_unique 0 0% 78.09% 288ms 1.25% boost::numeric::ublas::c_vector::assign (inline) 285ms 1.24% 79.32% 285ms 1.24% __gnu_cxx::__normal_iterator::operator++ (inline) 4ms 0.017% 79.34% 284ms 1.23% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 79.34% 281ms 1.22% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 79.34% 274ms 1.19% std::_Rb_tree::_M_drop_node (inline) 11ms 0.048% 79.39% 270ms 1.17% DistributedBoxCollection::GetProcessOwningNode 0 0% 79.39% 268ms 1.16% NodesOnlyMesh::UpdateBoxCollection 95ms 0.41% 79.80% 262ms 1.14% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 79.80% 244ms 1.06% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 79.80% 244ms 1.06% std::set::~set (inline) 0 0% 79.80% 243ms 1.05% VtkMeshWriter::WriteFiles 240ms 1.04% 80.84% 240ms 1.04% Node::CheckForNodeAttributes 137ms 0.59% 81.43% 239ms 1.04% _int_malloc 3ms 0.013% 81.45% 228ms 0.99% std::__new_allocator::deallocate (inline) 0 0% 81.45% 226ms 0.98% NodesOnlyMesh::AddNodesToBoxes 112ms 0.49% 81.93% 224ms 0.97% std::__move_median_to_first (inline) 15ms 0.065% 82.00% 216ms 0.94% std::__insertion_sort (inline) 55ms 0.24% 82.24% 208ms 0.9% __GI___libc_free 0 0% 82.24% 208ms 0.9% vtkStreamingDemandDrivenPipeline::Update 0 0% 82.24% 208ms 0.9% vtkXMLWriterBase::Write 0 0% 82.24% 207ms 0.9% std::allocator_traits::deallocate (inline) 0 0% 82.24% 207ms 0.9% vtkDemandDrivenPipeline::ProcessRequest 0 0% 82.24% 206ms 0.89% vtkDemandDrivenPipeline::ExecuteData 0 0% 82.24% 206ms 0.89% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 82.24% 205ms 0.89% vtkCompositeDataPipeline::ExecuteData 1ms 0.0043% 82.24% 205ms 0.89% vtkExecutive::CallAlgorithm 1ms 0.0043% 82.24% 204ms 0.88% vtkXMLUnstructuredDataWriter::ProcessRequest 5ms 0.022% 82.27% 203ms 0.88% CellPropertyCollection::HasProperty 0 0% 82.27% 202ms 0.88% Cell::HasCellProperty (inline) 0 0% 82.27% 202ms 0.88% std::_Rb_tree::_M_put_node (inline) 201ms 0.87% 83.14% 201ms 0.87% Node::GetIndex 104ms 0.45% 83.59% 189ms 0.82% boost::shared_ptr::shared_ptr (inline) 3ms 0.013% 83.60% 183ms 0.79% Cell::ReadyToDivide 85ms 0.37% 83.97% 181ms 0.78% Node::AddNeighbour 176ms 0.76% 84.73% 176ms 0.76% [libchaste_cell_based.so] 0 0% 84.73% 174ms 0.75% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 84.73% 174ms 0.75% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 84.73% 171ms 0.74% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 16ms 0.069% 84.80% 168ms 0.73% boost::numeric::ublas::vector_reference::operator() (inline) 3ms 0.013% 84.82% 166ms 0.72% AbstractCellProperty::IsType (inline) 0 0% 84.82% 166ms 0.72% NodesOnlyMesh::ResizeBoxCollection 8ms 0.035% 84.85% 165ms 0.72% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 84.85% 163ms 0.71% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 84.85% 159ms 0.69% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 84.85% 155ms 0.67% std::_Rb_tree::clear (inline) 132ms 0.57% 85.42% 153ms 0.66% _int_free 0 0% 85.42% 149ms 0.65% vtkXMLWriter::WriteBinaryData 146ms 0.63% 86.05% 146ms 0.63% [libchaste_mesh.so] 0 0% 86.05% 143ms 0.62% vtkXMLWriter::WriteBinaryDataBlock 0 0% 86.05% 143ms 0.62% vtkXMLWriter::WriteBinaryDataInternal 0 0% 86.05% 143ms 0.62% vtkXMLWriter::WriteCompressionBlock 55ms 0.24% 86.29% 142ms 0.62% AbstractCellCycleModel::GetAge 0 0% 86.29% 142ms 0.62% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 49ms 0.21% 86.51% 140ms 0.61% AbstractCellProperty::IsSame 0 0% 86.51% 140ms 0.61% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 136ms 0.59% 87.10% 138ms 0.6% std::__adjacent_find (inline) 0 0% 87.10% 138ms 0.6% std::__unique (inline) 0 0% 87.10% 138ms 0.6% std::unique (inline) 1ms 0.0043% 87.10% 136ms 0.59% Cell::GetCellId 0 0% 87.10% 134ms 0.58% vtkXMLWriter::WritePointsAppendedData 131ms 0.57% 87.67% 131ms 0.57% Node::IsDeleted 1ms 0.0043% 87.67% 130ms 0.56% DistributedBoxCollection::GetIsPeriodicAllDims 129ms 0.56% 88.23% 130ms 0.56% Node::ConstructNodeAttributes (inline) 126ms 0.55% 88.78% 126ms 0.55% boost::shared_ptr::operator-> (inline) 123ms 0.53% 89.31% 123ms 0.53% __ieee754_log_fma 2ms 0.0087% 89.32% 122ms 0.53% std::_Rb_tree::_M_insert_unique 0 0% 89.32% 122ms 0.53% std::set::insert (inline) 0 0% 89.32% 121ms 0.52% compress2 0 0% 89.32% 121ms 0.52% vtkDataCompressor::Compress 0 0% 89.32% 121ms 0.52% vtkZLibDataCompressor::CompressBuffer 3ms 0.013% 89.33% 120ms 0.52% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 89.33% 120ms 0.52% std::map::clear (inline) 2ms 0.0087% 89.34% 119ms 0.52% AbstractCellPopulation::SetCellUsingLocationIndex 58ms 0.25% 89.59% 119ms 0.52% crc32 0 0% 89.59% 119ms 0.52% deflate 1ms 0.0043% 89.60% 116ms 0.5% AbstractNumericalMethod::SafeNodePositionUpdate