File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20448ms, 89.05% of 22963ms total Dropped 750 nodes (cum <= 114.81ms) flat flat% sum% cum cum% 0 0% 0% 22810ms 99.33% __libc_start_call_main 0 0% 0% 22810ms 99.33% __libc_start_main_impl 0 0% 0% 22810ms 99.33% _start 0 0% 0% 22795ms 99.27% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 22795ms 99.27% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 22795ms 99.27% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 22795ms 99.27% main 0 0% 0% 22761ms 99.12% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 22761ms 99.12% CxxTest::TestRunner::runTest (inline) 0 0% 0% 22761ms 99.12% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 22753ms 99.09% AbstractCellBasedSimulation::Solve 2ms 0.0087% 0.0087% 12980ms 56.53% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0087% 8627ms 37.57% AbstractCellBasedSimulation::UpdateCellPopulation 7ms 0.03% 0.039% 8226ms 35.82% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.013% 0.052% 8042ms 35.02% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.052% 7625ms 33.21% NodeBasedCellPopulation::Update 1189ms 5.18% 5.23% 7459ms 32.48% RepulsionForce::AddForceContribution (partial-inline) 8ms 0.035% 5.26% 5608ms 24.42% DistributedBoxCollection::CalculateInteriorNodePairs 2059ms 8.97% 14.23% 4866ms 21.19% std::_Rb_tree::_M_lower_bound (inline) 0 0% 14.23% 4487ms 19.54% OffLatticeSimulation::ApplyBoundaries 21ms 0.091% 14.32% 4484ms 19.53% NodeAttributes::RemoveDuplicateNeighbours 8ms 0.035% 14.36% 4296ms 18.71% std::__sort (inline) 0 0% 14.36% 4296ms 18.71% std::sort (inline) 175ms 0.76% 15.12% 3780ms 16.46% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 1ms 0.0044% 15.12% 3435ms 14.96% AbstractCellPopulation::Iterator::operator++ (inline) 199ms 0.87% 15.99% 3416ms 14.88% AbstractCellPopulation::Iterator::IsRealCell (inline) 59ms 0.26% 16.25% 3381ms 14.72% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 236ms 1.03% 17.28% 3113ms 13.56% std::_Rb_tree::find (inline) 0 0% 17.28% 3113ms 13.56% std::map::find (inline) 20ms 0.087% 17.36% 2906ms 12.66% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2767ms 12.05% 29.41% 2767ms 12.05% std::_Rb_tree::_S_right (inline) 184ms 0.8% 30.21% 2463ms 10.73% std::__introsort_loop 196ms 0.85% 31.07% 2453ms 10.68% std::map::operator[] (partial-inline) 26ms 0.11% 31.18% 2315ms 10.08% PlaneBoundaryCondition::ImposeBoundaryCondition 47ms 0.2% 31.39% 2247ms 9.79% AbstractCellPopulation::GetLocationIndexUsingCell 57ms 0.25% 31.63% 2231ms 9.72% NodesOnlyMesh::GetNodeOrHaloNode 145ms 0.63% 32.26% 2228ms 9.70% AbstractMesh::GetNode 2ms 0.0087% 32.27% 2197ms 9.57% std::__unguarded_partition_pivot (inline) 28ms 0.12% 32.40% 2172ms 9.46% PlaneBoundaryCondition::VerifyBoundaryCondition 92ms 0.4% 32.80% 2089ms 9.10% NodesOnlyMesh::SolveNodeMapping 0 0% 32.80% 2008ms 8.74% std::_Rb_tree::lower_bound (inline) 0 0% 32.80% 2008ms 8.74% std::map::lower_bound (inline) 1043ms 4.54% 37.34% 1980ms 8.62% std::__unguarded_partition (inline) 0 0% 37.34% 1823ms 7.94% std::__final_insertion_sort (inline) 154ms 0.67% 38.01% 1759ms 7.66% DistributedBoxCollection::AddPairsFromBox 86ms 0.37% 38.38% 1630ms 7.10% std::__unguarded_insertion_sort (inline) 580ms 2.53% 40.91% 1621ms 7.06% std::__unguarded_linear_insert (inline) 21ms 0.091% 41.00% 1553ms 6.76% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 24ms 0.1% 41.11% 1525ms 6.64% AbstractCellPopulation::GetCellUsingLocationIndex 1494ms 6.51% 47.61% 1494ms 6.51% __gnu_cxx::__normal_iterator::operator-- (inline) 42ms 0.18% 47.79% 1265ms 5.51% boost::numeric::ublas::c_vector::c_vector (partial-inline) 33ms 0.14% 47.94% 1166ms 5.08% boost::numeric::ublas::vector_assign (inline) 0 0% 47.94% 1110ms 4.83% NodeBasedCellPopulation::UpdateCellProcessLocation 5ms 0.022% 47.96% 1082ms 4.71% DistributedBoxCollection::CalculateBoundaryNodePairs 312ms 1.36% 49.32% 1070ms 4.66% boost::numeric::ublas::indexing_vector_assign 258ms 1.12% 50.44% 928ms 4.04% __dynamic_cast 174ms 0.76% 51.20% 830ms 3.61% AbstractMesh::GetVectorFromAtoB 30ms 0.13% 51.33% 816ms 3.55% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 347ms 1.51% 52.84% 745ms 3.24% DistributedBoxCollection::CalculateContainingBox (partial-inline) 186ms 0.81% 53.65% 715ms 3.11% NodeAttributes::AddNeighbour 0 0% 53.65% 708ms 3.08% AbstractCellPopulation::WriteResultsToFiles 0 0% 53.65% 707ms 3.08% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 689ms 3.00% 56.65% 689ms 3.00% boost::numeric::ublas::c_vector::operator() 0 0% 56.65% 686ms 2.99% boost::numeric::ublas::norm_2 (inline) 530ms 2.31% 58.96% 686ms 2.99% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 58.96% 686ms 2.99% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 10ms 0.044% 59.00% 652ms 2.84% boost::numeric::ublas::c_vector::operator= (inline) 28ms 0.12% 59.13% 627ms 2.73% std::__copy_move::__copy_m (inline) 0 0% 59.13% 627ms 2.73% std::__copy_move_a (inline) 0 0% 59.13% 627ms 2.73% std::__copy_move_a1 (inline) 0 0% 59.13% 627ms 2.73% std::__copy_move_a2 (inline) 0 0% 59.13% 627ms 2.73% std::copy (inline) 607ms 2.64% 61.77% 607ms 2.64% __memcpy_avx_unaligned_erms 528ms 2.30% 64.07% 589ms 2.56% std::vector::push_back (inline) 46ms 0.2% 64.27% 562ms 2.45% boost::detail::shared_count::~shared_count (inline) 0 0% 64.27% 562ms 2.45% boost::shared_ptr::~shared_ptr (inline) 252ms 1.10% 65.37% 561ms 2.44% __cxxabiv1::__si_class_type_info::__do_dyncast 3ms 0.013% 65.38% 553ms 2.41% AbstractCellBasedSimulation::DoCellBirth 9ms 0.039% 65.42% 525ms 2.29% CellPropertyCollection::GetPropertiesType (inline) 3ms 0.013% 65.43% 513ms 2.23% AbstractCentreBasedCellPopulation::GetDampingConstant 502ms 2.19% 67.62% 507ms 2.21% boost::detail::sp_counted_base::release 70ms 0.3% 67.92% 495ms 2.16% std::__new_allocator::allocate (inline) 478ms 2.08% 70.00% 478ms 2.08% boost::numeric::ublas::same_impl_ex 0 0% 70.00% 477ms 2.08% std::allocator_traits::allocate (inline) 476ms 2.07% 72.08% 476ms 2.07% __strcmp_avx2 24ms 0.1% 72.18% 471ms 2.05% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.0087% 72.19% 470ms 2.05% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 72.19% 461ms 2.01% std::_Rb_tree::_M_create_node (inline) 22ms 0.096% 72.29% 458ms 1.99% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 72.29% 448ms 1.95% AbstractCellBasedSimulation::DoCellRemoval (inline) 3ms 0.013% 72.30% 440ms 1.92% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 434ms 1.89% 74.19% 434ms 1.89% std::_Rb_tree_increment 37ms 0.16% 74.35% 418ms 1.82% std::_Rb_tree::_M_copy (inline) 29ms 0.13% 74.48% 409ms 1.78% operator new 0 0% 74.48% 401ms 1.75% std::_Rb_tree::_M_get_node (inline) 2ms 0.0087% 74.49% 391ms 1.70% AbstractCellProperty::IsSubType (inline) 5ms 0.022% 74.51% 391ms 1.70% std::set::set (inline) 145ms 0.63% 75.14% 390ms 1.70% Node::GetRadius 118ms 0.51% 75.65% 380ms 1.65% std::_Rb_tree::_M_clone_node (inline) 117ms 0.51% 76.16% 377ms 1.64% __GI___libc_malloc 121ms 0.53% 76.69% 357ms 1.55% std::_Rb_tree::_M_erase 0 0% 76.69% 341ms 1.48% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 76.69% 335ms 1.46% Cell::GetMutationState 0 0% 76.69% 329ms 1.43% boost::numeric::ublas::c_vector::assign (inline) 4ms 0.017% 76.71% 317ms 1.38% NodeBasedCellPopulation::UpdateMapsAfterRemesh 24ms 0.1% 76.81% 316ms 1.38% boost::numeric::ublas::vector_binary::size (inline) 0 0% 76.81% 305ms 1.33% boost::numeric::ublas::inner_prod (inline) 16ms 0.07% 76.88% 303ms 1.32% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 76.88% 303ms 1.32% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 294ms 1.28% 78.16% 294ms 1.28% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 78.16% 293ms 1.28% NodesOnlyMesh::ReMesh 0 0% 78.16% 284ms 1.24% NodesOnlyMesh::UpdateNodeIndices 48ms 0.21% 78.37% 274ms 1.19% std::_Rb_tree::~_Rb_tree (inline) 266ms 1.16% 79.53% 266ms 1.16% __gnu_cxx::__normal_iterator::operator++ (inline) 255ms 1.11% 80.64% 255ms 1.11% Node::CheckForNodeAttributes 0 0% 80.64% 251ms 1.09% NodesOnlyMesh::UpdateBoxCollection 8ms 0.035% 80.67% 249ms 1.08% std::_Rb_tree::_M_emplace_hint_unique 2ms 0.0087% 80.68% 247ms 1.08% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 103ms 0.45% 81.13% 246ms 1.07% boost::numeric::ublas::vector_inner_prod::apply (inline) 4ms 0.017% 81.15% 232ms 1.01% DistributedBoxCollection::GetProcessOwningNode 0 0% 81.15% 231ms 1.01% std::_Rb_tree::_M_drop_node (inline) 229ms 1% 82.15% 229ms 1% Node::GetIndex 1ms 0.0044% 82.15% 224ms 0.98% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 82.15% 223ms 0.97% VtkMeshWriter::WriteFiles 133ms 0.58% 82.73% 217ms 0.94% _int_malloc 1ms 0.0044% 82.73% 214ms 0.93% NodesOnlyMesh::AddNodesToBoxes 214ms 0.93% 83.67% 214ms 0.93% [libchaste_cell_based.so] 6ms 0.026% 83.69% 209ms 0.91% std::__new_allocator::deallocate (inline) 98ms 0.43% 84.12% 206ms 0.9% std::__move_median_to_first (inline) 0 0% 84.12% 205ms 0.89% std::set::~set (inline) 0 0% 84.12% 203ms 0.88% NodesOnlyMesh::ResizeBoxCollection 20ms 0.087% 84.21% 202ms 0.88% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 84.21% 201ms 0.88% vtkStreamingDemandDrivenPipeline::Update 0 0% 84.21% 201ms 0.88% vtkXMLWriterBase::Write 0 0% 84.21% 199ms 0.87% vtkDemandDrivenPipeline::ProcessRequest 0 0% 84.21% 198ms 0.86% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 84.21% 197ms 0.86% vtkCompositeDataPipeline::ExecuteData 0 0% 84.21% 197ms 0.86% vtkDemandDrivenPipeline::ExecuteData 0 0% 84.21% 196ms 0.85% vtkExecutive::CallAlgorithm 2ms 0.0087% 84.21% 196ms 0.85% vtkXMLUnstructuredDataWriter::ProcessRequest 12ms 0.052% 84.27% 193ms 0.84% std::__insertion_sort (inline) 67ms 0.29% 84.56% 189ms 0.82% __GI___libc_free 78ms 0.34% 84.90% 187ms 0.81% boost::shared_ptr::shared_ptr (inline) 3ms 0.013% 84.91% 185ms 0.81% CellPropertyCollection::HasProperty 0 0% 84.91% 184ms 0.8% Cell::HasCellProperty (inline) 0 0% 84.91% 179ms 0.78% std::allocator_traits::deallocate (inline) 0 0% 84.91% 176ms 0.77% std::_Rb_tree::_M_put_node (inline) 0 0% 84.91% 170ms 0.74% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 84.91% 170ms 0.74% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 4ms 0.017% 84.93% 167ms 0.73% Cell::ReadyToDivide 15ms 0.065% 84.99% 166ms 0.72% boost::numeric::ublas::vector_reference::operator() (inline) 4ms 0.017% 85.01% 161ms 0.7% AbstractCellProperty::IsType (inline) 0 0% 85.01% 160ms 0.7% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 83ms 0.36% 85.37% 155ms 0.67% Node::AddNeighbour 153ms 0.67% 86.04% 155ms 0.67% std::__adjacent_find (inline) 0 0% 86.04% 155ms 0.67% std::__unique (inline) 0 0% 86.04% 155ms 0.67% std::unique (inline) 0 0% 86.04% 143ms 0.62% boost::numeric::ublas::vector_binary::operator() (inline) 142ms 0.62% 86.66% 142ms 0.62% [libchaste_mesh.so] 0 0% 86.66% 142ms 0.62% vtkXMLWriter::WriteBinaryData 0 0% 86.66% 138ms 0.6% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 1ms 0.0044% 86.66% 138ms 0.6% DistributedBoxCollection::GetIsPeriodicAllDims 0 0% 86.66% 138ms 0.6% std::_Rb_tree::clear (inline) 134ms 0.58% 87.24% 134ms 0.58% boost::shared_ptr::operator-> (inline) 1ms 0.0044% 87.25% 134ms 0.58% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.25% 134ms 0.58% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.25% 132ms 0.57% vtkXMLWriter::WriteCompressionBlock 0 0% 87.25% 130ms 0.57% Cell::GetCellId 128ms 0.56% 87.81% 128ms 0.56% Node::IsDeleted 0 0% 87.81% 127ms 0.55% AbstractCellPopulation::SetCellUsingLocationIndex 1ms 0.0044% 87.81% 127ms 0.55% std::set::insert (inline) 37ms 0.16% 87.97% 126ms 0.55% AbstractCellProperty::IsSame 0 0% 87.97% 126ms 0.55% std::_Rb_tree::_M_insert_unique 0 0% 87.97% 124ms 0.54% tbb::detail::r1::parallel_pipeline 122ms 0.53% 88.50% 122ms 0.53% __ieee754_log_fma 114ms 0.5% 89.00% 122ms 0.53% _int_free 8ms 0.035% 89.03% 122ms 0.53% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 89.03% 121ms 0.53% clone3 0 0% 89.03% 121ms 0.53% start_thread 1ms 0.0044% 89.04% 121ms 0.53% tbb::detail::r1::reset 0 0% 89.04% 120ms 0.52% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 89.04% 120ms 0.52% vtkXMLWriter::WritePointsAppendedData 0 0% 89.04% 117ms 0.51% vtkDataCompressor::Compress 0 0% 89.04% 116ms 0.51% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 89.04% 116ms 0.51% compress2 0 0% 89.04% 116ms 0.51% vtkZLibDataCompressor::CompressBuffer 2ms 0.0087% 89.05% 115ms 0.5% AbstractNumericalMethod::SafeNodePositionUpdate