File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20607ms, 89.34% of 23065ms total Dropped 755 nodes (cum <= 115.33ms) flat flat% sum% cum cum% 0 0% 0% 22915ms 99.35% __libc_start_call_main 0 0% 0% 22915ms 99.35% __libc_start_main_impl 0 0% 0% 22915ms 99.35% _start 0 0% 0% 22900ms 99.28% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 22900ms 99.28% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 22900ms 99.28% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 22900ms 99.28% main 0 0% 0% 22867ms 99.14% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 22867ms 99.14% CxxTest::TestRunner::runTest (inline) 0 0% 0% 22867ms 99.14% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 22860ms 99.11% AbstractCellBasedSimulation::Solve 3ms 0.013% 0.013% 13022ms 56.46% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.013% 8646ms 37.49% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.017% 0.03% 8298ms 35.98% ForwardEulerNumericalMethod::UpdateAllNodePositions 9ms 0.039% 0.069% 8119ms 35.20% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.069% 7649ms 33.16% NodeBasedCellPopulation::Update 1229ms 5.33% 5.40% 7505ms 32.54% RepulsionForce::AddForceContribution (partial-inline) 5ms 0.022% 5.42% 5595ms 24.26% DistributedBoxCollection::CalculateInteriorNodePairs 2038ms 8.84% 14.26% 4828ms 20.93% std::_Rb_tree::_M_lower_bound (inline) 16ms 0.069% 14.32% 4479ms 19.42% NodeAttributes::RemoveDuplicateNeighbours 0 0% 14.32% 4474ms 19.40% OffLatticeSimulation::ApplyBoundaries 4ms 0.017% 14.34% 4303ms 18.66% std::__sort (inline) 0 0% 14.34% 4303ms 18.66% std::sort (inline) 186ms 0.81% 15.15% 3781ms 16.39% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 4ms 0.017% 15.17% 3412ms 14.79% AbstractCellPopulation::Iterator::operator++ (inline) 192ms 0.83% 16.00% 3387ms 14.68% AbstractCellPopulation::Iterator::IsRealCell 61ms 0.26% 16.26% 3307ms 14.34% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 240ms 1.04% 17.30% 3104ms 13.46% std::_Rb_tree::find (inline) 0 0% 17.30% 3104ms 13.46% std::map::find (inline) 26ms 0.11% 17.42% 2866ms 12.43% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2750ms 11.92% 29.34% 2750ms 11.92% std::_Rb_tree::_S_right (inline) 174ms 0.75% 30.09% 2461ms 10.67% std::__introsort_loop 216ms 0.94% 31.03% 2454ms 10.64% std::map::operator[] (partial-inline) 22ms 0.095% 31.13% 2326ms 10.08% PlaneBoundaryCondition::ImposeBoundaryCondition 35ms 0.15% 31.28% 2271ms 9.85% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 31.28% 2217ms 9.61% std::__unguarded_partition_pivot (inline) 141ms 0.61% 31.89% 2201ms 9.54% AbstractMesh::GetNode 40ms 0.17% 32.06% 2187ms 9.48% NodesOnlyMesh::GetNodeOrHaloNode 13ms 0.056% 32.12% 2148ms 9.31% PlaneBoundaryCondition::VerifyBoundaryCondition 99ms 0.43% 32.55% 2063ms 8.94% NodesOnlyMesh::SolveNodeMapping 1018ms 4.41% 36.96% 2013ms 8.73% std::__unguarded_partition (inline) 0 0% 36.96% 1988ms 8.62% std::_Rb_tree::lower_bound (inline) 0 0% 36.96% 1988ms 8.62% std::map::lower_bound (inline) 0 0% 36.96% 1835ms 7.96% std::__final_insertion_sort (inline) 137ms 0.59% 37.55% 1758ms 7.62% DistributedBoxCollection::AddPairsFromBox 98ms 0.42% 37.98% 1663ms 7.21% std::__unguarded_insertion_sort (inline) 22ms 0.095% 38.08% 1625ms 7.05% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 41ms 0.18% 38.25% 1598ms 6.93% AbstractCellPopulation::GetCellUsingLocationIndex 584ms 2.53% 40.78% 1587ms 6.88% std::__unguarded_linear_insert (inline) 1467ms 6.36% 47.15% 1467ms 6.36% __gnu_cxx::__normal_iterator::operator-- (inline) 62ms 0.27% 47.41% 1243ms 5.39% boost::numeric::ublas::c_vector::c_vector (partial-inline) 1ms 0.0043% 47.42% 1182ms 5.12% NodeBasedCellPopulation::UpdateCellProcessLocation 35ms 0.15% 47.57% 1100ms 4.77% boost::numeric::ublas::vector_assign (inline) 6ms 0.026% 47.60% 1094ms 4.74% DistributedBoxCollection::CalculateBoundaryNodePairs 269ms 1.17% 48.76% 989ms 4.29% boost::numeric::ublas::indexing_vector_assign 214ms 0.93% 49.69% 856ms 3.71% __dynamic_cast 175ms 0.76% 50.45% 815ms 3.53% AbstractMesh::GetVectorFromAtoB 361ms 1.57% 52.01% 800ms 3.47% DistributedBoxCollection::CalculateContainingBox (partial-inline) 24ms 0.1% 52.12% 781ms 3.39% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 212ms 0.92% 53.04% 751ms 3.26% NodeAttributes::AddNeighbour 0 0% 53.04% 711ms 3.08% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 53.04% 705ms 3.06% AbstractCellPopulation::WriteResultsToFiles 0 0% 53.04% 691ms 3.00% boost::numeric::ublas::norm_2 (inline) 549ms 2.38% 55.42% 691ms 3.00% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 55.42% 691ms 3.00% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 676ms 2.93% 58.35% 676ms 2.93% boost::numeric::ublas::c_vector::operator() 2ms 0.0087% 58.36% 669ms 2.90% boost::numeric::ublas::c_vector::operator= (inline) 38ms 0.16% 58.52% 648ms 2.81% std::__copy_move::__copy_m (inline) 0 0% 58.52% 648ms 2.81% std::__copy_move_a (inline) 0 0% 58.52% 648ms 2.81% std::__copy_move_a1 (inline) 0 0% 58.52% 648ms 2.81% std::__copy_move_a2 (inline) 0 0% 58.52% 648ms 2.81% std::copy (inline) 628ms 2.72% 61.24% 628ms 2.72% __memcpy_avx_unaligned_erms 539ms 2.34% 63.58% 607ms 2.63% std::vector::push_back (inline) 6ms 0.026% 63.61% 581ms 2.52% AbstractCellBasedSimulation::DoCellBirth 2ms 0.0087% 63.62% 538ms 2.33% AbstractCentreBasedCellPopulation::GetDampingConstant 11ms 0.048% 63.66% 538ms 2.33% CellPropertyCollection::GetPropertiesType (inline) 240ms 1.04% 64.70% 525ms 2.28% __cxxabiv1::__si_class_type_info::__do_dyncast 41ms 0.18% 64.88% 504ms 2.19% std::_Rb_tree_const_iterator::operator++ (inline) 41ms 0.18% 65.06% 486ms 2.11% boost::detail::shared_count::~shared_count (inline) 0 0% 65.06% 486ms 2.11% boost::shared_ptr::~shared_ptr (inline) 480ms 2.08% 67.14% 480ms 2.08% boost::numeric::ublas::same_impl_ex 70ms 0.3% 67.44% 475ms 2.06% std::__new_allocator::allocate (inline) 3ms 0.013% 67.46% 467ms 2.02% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 67.46% 465ms 2.02% std::allocator_traits::allocate (inline) 460ms 1.99% 69.45% 460ms 1.99% std::_Rb_tree_increment 456ms 1.98% 71.43% 456ms 1.98% __strcmp_avx2 17ms 0.074% 71.50% 445ms 1.93% std::_Rb_tree::_Rb_tree (partial-inline) 434ms 1.88% 73.38% 436ms 1.89% boost::detail::sp_counted_base::release 0 0% 73.38% 435ms 1.89% std::_Rb_tree::_M_create_node (inline) 0 0% 73.38% 416ms 1.80% AbstractCellBasedSimulation::DoCellRemoval (inline) 149ms 0.65% 74.03% 410ms 1.78% std::_Rb_tree::_M_erase 47ms 0.2% 74.23% 409ms 1.77% std::_Rb_tree::_M_copy (inline) 3ms 0.013% 74.25% 406ms 1.76% AbstractCellProperty::IsSubType (inline) 4ms 0.017% 74.26% 405ms 1.76% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 24ms 0.1% 74.37% 405ms 1.76% operator new 0 0% 74.37% 388ms 1.68% std::_Rb_tree::_M_get_node (inline) 110ms 0.48% 74.85% 377ms 1.63% __GI___libc_malloc 3ms 0.013% 74.86% 372ms 1.61% std::set::set (inline) 150ms 0.65% 75.51% 369ms 1.60% Node::GetRadius 6ms 0.026% 75.53% 362ms 1.57% Cell::GetMutationState 127ms 0.55% 76.08% 362ms 1.57% std::_Rb_tree::_M_clone_node (inline) 34ms 0.15% 76.23% 338ms 1.47% boost::numeric::ublas::vector_binary::size (inline) 43ms 0.19% 76.42% 334ms 1.45% std::_Rb_tree::~_Rb_tree (inline) 0 0% 76.42% 331ms 1.44% boost::numeric::ublas::inner_prod (inline) 24ms 0.1% 76.52% 331ms 1.44% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 76.52% 331ms 1.44% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 4ms 0.017% 76.54% 322ms 1.40% NodeBasedCellPopulation::UpdateMapsAfterRemesh 321ms 1.39% 77.93% 321ms 1.39% __gnu_cxx::__normal_iterator::operator++ (inline) 306ms 1.33% 79.26% 306ms 1.33% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 79.26% 303ms 1.31% NodesOnlyMesh::ReMesh 4ms 0.017% 79.28% 297ms 1.29% NodesOnlyMesh::UpdateNodeIndices 0 0% 79.28% 297ms 1.29% boost::numeric::ublas::c_vector::assign (inline) 1ms 0.0043% 79.28% 296ms 1.28% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 79.28% 284ms 1.23% std::_Rb_tree::_Alloc_node::operator() (inline) 7ms 0.03% 79.31% 280ms 1.21% DistributedBoxCollection::GetProcessOwningNode 0 0% 79.31% 259ms 1.12% std::set::~set (inline) 0 0% 79.31% 256ms 1.11% NodesOnlyMesh::UpdateBoxCollection 122ms 0.53% 79.84% 255ms 1.11% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 79.84% 251ms 1.09% std::_Rb_tree::_M_drop_node (inline) 8ms 0.035% 79.87% 250ms 1.08% std::_Rb_tree::_M_emplace_hint_unique 113ms 0.49% 80.36% 240ms 1.04% boost::shared_ptr::shared_ptr (inline) 234ms 1.01% 81.38% 234ms 1.01% Node::CheckForNodeAttributes 138ms 0.6% 81.98% 230ms 1% _int_malloc 1ms 0.0043% 81.98% 229ms 0.99% NodesOnlyMesh::AddNodesToBoxes 6ms 0.026% 82.01% 220ms 0.95% std::__new_allocator::deallocate (inline) 0 0% 82.01% 216ms 0.94% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 82.01% 213ms 0.92% VtkMeshWriter::WriteFiles 0 0% 82.01% 205ms 0.89% Cell::HasCellProperty (inline) 4ms 0.017% 82.02% 205ms 0.89% CellPropertyCollection::HasProperty 0 0% 82.02% 204ms 0.88% NodesOnlyMesh::ResizeBoxCollection 12ms 0.052% 82.08% 203ms 0.88% NodesOnlyMesh::IsANodeCloseToDomainBoundary 94ms 0.41% 82.48% 198ms 0.86% std::__move_median_to_first (inline) 0 0% 82.48% 194ms 0.84% vtkStreamingDemandDrivenPipeline::Update 0 0% 82.48% 194ms 0.84% vtkXMLWriterBase::Write 60ms 0.26% 82.74% 193ms 0.84% __GI___libc_free 0 0% 82.74% 193ms 0.84% vtkDemandDrivenPipeline::ProcessRequest 0 0% 82.74% 192ms 0.83% vtkCompositeDataPipeline::ExecuteData 0 0% 82.74% 192ms 0.83% vtkDemandDrivenPipeline::ExecuteData 0 0% 82.74% 192ms 0.83% vtkExecutive::CallAlgorithm 0 0% 82.74% 192ms 0.83% vtkStreamingDemandDrivenPipeline::ProcessRequest 191ms 0.83% 83.57% 191ms 0.83% [libchaste_cell_based.so] 0 0% 83.57% 191ms 0.83% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 83.57% 186ms 0.81% std::allocator_traits::deallocate (inline) 185ms 0.8% 84.37% 185ms 0.8% Node::GetIndex 0 0% 84.37% 184ms 0.8% std::_Rb_tree::_M_put_node (inline) 180ms 0.78% 85.15% 180ms 0.78% Node::IsDeleted 2ms 0.0087% 85.16% 173ms 0.75% AbstractCellProperty::IsType (inline) 18ms 0.078% 85.24% 172ms 0.75% std::__insertion_sort (inline) 0 0% 85.24% 171ms 0.74% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.24% 171ms 0.74% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 4ms 0.017% 85.26% 168ms 0.73% Cell::ReadyToDivide 0 0% 85.26% 166ms 0.72% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 85.26% 151ms 0.65% std::_Rb_tree::_Auto_node::_Auto_node (inline) 13ms 0.056% 85.32% 150ms 0.65% boost::numeric::ublas::c_vector::operator[] (inline) 83ms 0.36% 85.68% 141ms 0.61% Node::AddNeighbour 0 0% 85.68% 141ms 0.61% vtkXMLWriter::WriteBinaryData 136ms 0.59% 86.26% 140ms 0.61% std::__adjacent_find (inline) 0 0% 86.26% 140ms 0.61% std::__unique (inline) 0 0% 86.26% 140ms 0.61% std::unique (inline) 12ms 0.052% 86.32% 139ms 0.6% boost::numeric::ublas::vector_reference::operator() (inline) 1ms 0.0043% 86.32% 139ms 0.6% std::_Rb_tree::clear (inline) 1ms 0.0043% 86.33% 136ms 0.59% AbstractCellPopulation::SetCellUsingLocationIndex 0 0% 86.33% 136ms 0.59% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 4ms 0.017% 86.34% 135ms 0.59% DistributedBoxCollection::GetIsPeriodicAllDims 135ms 0.59% 86.93% 135ms 0.59% [libchaste_mesh.so] 134ms 0.58% 87.51% 134ms 0.58% __ieee754_log_fma 0 0% 87.51% 134ms 0.58% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.51% 134ms 0.58% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.51% 134ms 0.58% vtkXMLWriter::WriteCompressionBlock 116ms 0.5% 88.01% 133ms 0.58% _int_free 37ms 0.16% 88.17% 132ms 0.57% AbstractCellProperty::IsSame 0 0% 88.17% 132ms 0.57% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 88.17% 131ms 0.57% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 2ms 0.0087% 88.18% 127ms 0.55% Cell::GetCellId 91ms 0.39% 88.58% 127ms 0.55% boost::detail::shared_count::shared_count (inline) 125ms 0.54% 89.12% 125ms 0.54% boost::shared_ptr::operator-> (inline) 0 0% 89.12% 122ms 0.53% tbb::detail::r1::parallel_pipeline 0 0% 89.12% 121ms 0.52% vtkXMLWriter::WritePointsAppendedData 0 0% 89.12% 117ms 0.51% clone3 0 0% 89.12% 117ms 0.51% start_thread 0 0% 89.12% 117ms 0.51% tbb::detail::r1::reset 0 0% 89.12% 117ms 0.51% vtkDataCompressor::Compress 0 0% 89.12% 116ms 0.5% compress2 52ms 0.23% 89.34% 116ms 0.5% tbb::detail::r1::wait_bounded_queue_monitor 0 0% 89.34% 116ms 0.5% vtkZLibDataCompressor::CompressBuffer