File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 19814ms, 88.57% of 22371ms total Dropped 771 nodes (cum <= 111.86ms) flat flat% sum% cum cum% 0 0% 0% 22215ms 99.30% __libc_start_call_main 0 0% 0% 22215ms 99.30% __libc_start_main_impl 0 0% 0% 22215ms 99.30% _start 0 0% 0% 22200ms 99.24% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 22200ms 99.24% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 22200ms 99.24% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 22200ms 99.24% main 0 0% 0% 22166ms 99.08% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 22166ms 99.08% CxxTest::TestRunner::runTest (inline) 0 0% 0% 22166ms 99.08% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 22157ms 99.04% AbstractCellBasedSimulation::Solve 4ms 0.018% 0.018% 12359ms 55.25% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.0089% 0.027% 8605ms 38.46% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.027% 7676ms 34.31% NodeBasedCellPopulation::Update 1ms 0.0045% 0.031% 7579ms 33.88% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.013% 0.045% 7382ms 33.00% AbstractNumericalMethod::ComputeForcesIncludingDamping 1221ms 5.46% 5.50% 6756ms 30.20% RepulsionForce::AddForceContribution (partial-inline) 10ms 0.045% 5.55% 5642ms 25.22% DistributedBoxCollection::CalculateInteriorNodePairs 2157ms 9.64% 15.19% 4844ms 21.65% std::_Rb_tree::_M_lower_bound (inline) 0 0% 15.19% 4527ms 20.24% OffLatticeSimulation::ApplyBoundaries 13ms 0.058% 15.25% 4467ms 19.97% NodeAttributes::RemoveDuplicateNeighbours 8ms 0.036% 15.28% 4276ms 19.11% std::__sort (inline) 0 0% 15.28% 4276ms 19.11% std::sort (inline) 2ms 0.0089% 15.29% 3435ms 15.35% AbstractCellPopulation::Iterator::operator++ (inline) 185ms 0.83% 16.12% 3406ms 15.23% AbstractCellPopulation::Iterator::IsRealCell 67ms 0.3% 16.42% 3398ms 15.19% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 226ms 1.01% 17.43% 3139ms 14.03% std::_Rb_tree::find (inline) 0 0% 17.43% 3138ms 14.03% std::map::find (inline) 242ms 1.08% 18.51% 3126ms 13.97% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 25ms 0.11% 18.62% 2893ms 12.93% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2663ms 11.90% 30.53% 2663ms 11.90% std::_Rb_tree::_S_right (inline) 249ms 1.11% 31.64% 2437ms 10.89% std::map::operator[] (partial-inline) 201ms 0.9% 32.54% 2402ms 10.74% std::__introsort_loop 29ms 0.13% 32.67% 2335ms 10.44% PlaneBoundaryCondition::ImposeBoundaryCondition 41ms 0.18% 32.85% 2290ms 10.24% AbstractCellPopulation::GetLocationIndexUsingCell 138ms 0.62% 33.47% 2280ms 10.19% AbstractMesh::GetNode 71ms 0.32% 33.78% 2265ms 10.12% NodesOnlyMesh::GetNodeOrHaloNode 10ms 0.045% 33.83% 2192ms 9.80% PlaneBoundaryCondition::VerifyBoundaryCondition 93ms 0.42% 34.25% 2150ms 9.61% NodesOnlyMesh::SolveNodeMapping 0 0% 34.25% 2119ms 9.47% std::__unguarded_partition_pivot (inline) 0 0% 34.25% 1950ms 8.72% std::_Rb_tree::lower_bound (inline) 0 0% 34.25% 1950ms 8.72% std::map::lower_bound (inline) 997ms 4.46% 38.70% 1913ms 8.55% std::__unguarded_partition (inline) 0 0% 38.70% 1862ms 8.32% std::__final_insertion_sort (inline) 156ms 0.7% 39.40% 1779ms 7.95% DistributedBoxCollection::AddPairsFromBox 88ms 0.39% 39.79% 1658ms 7.41% std::__unguarded_insertion_sort (inline) 582ms 2.60% 42.39% 1633ms 7.30% std::__unguarded_linear_insert (inline) 1458ms 6.52% 48.91% 1458ms 6.52% __gnu_cxx::__normal_iterator::operator-- (inline) 24ms 0.11% 49.02% 1447ms 6.47% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 23ms 0.1% 49.12% 1418ms 6.34% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 49.12% 1144ms 5.11% NodeBasedCellPopulation::UpdateCellProcessLocation 48ms 0.21% 49.34% 1139ms 5.09% boost::numeric::ublas::c_vector::c_vector (partial-inline) 7ms 0.031% 49.37% 1090ms 4.87% DistributedBoxCollection::CalculateBoundaryNodePairs 24ms 0.11% 49.47% 1022ms 4.57% boost::numeric::ublas::vector_assign (inline) 264ms 1.18% 50.65% 915ms 4.09% boost::numeric::ublas::indexing_vector_assign 17ms 0.076% 50.73% 813ms 3.63% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 152ms 0.68% 51.41% 750ms 3.35% AbstractMesh::GetVectorFromAtoB 0 0% 51.41% 750ms 3.35% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 347ms 1.55% 52.96% 742ms 3.32% DistributedBoxCollection::CalculateContainingBox (partial-inline) 199ms 0.89% 53.85% 740ms 3.31% NodeAttributes::AddNeighbour 0 0% 53.85% 735ms 3.29% boost::numeric::ublas::norm_2 (inline) 581ms 2.60% 56.45% 735ms 3.29% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 56.45% 735ms 3.29% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 56.45% 732ms 3.27% AbstractCellPopulation::WriteResultsToFiles 4ms 0.018% 56.47% 688ms 3.08% boost::numeric::ublas::c_vector::operator= (inline) 10ms 0.045% 56.51% 666ms 2.98% CellPropertyCollection::GetPropertiesType (inline) 22ms 0.098% 56.61% 660ms 2.95% std::__copy_move::__copy_m (inline) 0 0% 56.61% 660ms 2.95% std::__copy_move_a (inline) 0 0% 56.61% 660ms 2.95% std::__copy_move_a1 (inline) 0 0% 56.61% 660ms 2.95% std::__copy_move_a2 (inline) 0 0% 56.61% 660ms 2.95% std::copy (inline) 654ms 2.92% 59.53% 654ms 2.92% __memcpy_avx_unaligned_erms 541ms 2.42% 61.95% 611ms 2.73% std::vector::push_back (inline) 590ms 2.64% 64.59% 590ms 2.64% boost::numeric::ublas::c_vector::operator() 0 0% 64.59% 568ms 2.54% AbstractCentreBasedCellPopulation::GetDampingConstant 2ms 0.0089% 64.60% 509ms 2.28% AbstractCellProperty::IsSubType (inline) 124ms 0.55% 65.15% 508ms 2.27% __dynamic_cast 30ms 0.13% 65.29% 505ms 2.26% boost::detail::shared_count::~shared_count (inline) 0 0% 65.29% 505ms 2.26% boost::shared_ptr::~shared_ptr (inline) 72ms 0.32% 65.61% 499ms 2.23% std::__new_allocator::allocate (inline) 0 0% 65.61% 479ms 2.14% std::allocator_traits::allocate (inline) 38ms 0.17% 65.78% 474ms 2.12% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 65.78% 473ms 2.11% NodeBasedCellPopulation::WriteVtkResultsToFile 4ms 0.018% 65.80% 466ms 2.08% AbstractCellBasedSimulation::DoCellBirth 459ms 2.05% 67.85% 462ms 2.07% boost::detail::sp_counted_base::release 0 0% 67.85% 461ms 2.06% AbstractCellBasedSimulation::DoCellRemoval (inline) 6ms 0.027% 67.87% 451ms 2.02% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 4ms 0.018% 67.89% 447ms 2.00% Cell::GetMutationState 0 0% 67.89% 443ms 1.98% std::_Rb_tree::_M_create_node (inline) 18ms 0.08% 67.97% 439ms 1.96% std::_Rb_tree::_Rb_tree (partial-inline) 436ms 1.95% 69.92% 436ms 1.95% boost::numeric::ublas::same_impl_ex 433ms 1.94% 71.86% 433ms 1.94% std::_Rb_tree_increment 24ms 0.11% 71.96% 418ms 1.87% operator new 39ms 0.17% 72.14% 409ms 1.83% std::_Rb_tree::_M_copy (inline) 0 0% 72.14% 401ms 1.79% std::_Rb_tree::_M_get_node (inline) 147ms 0.66% 72.80% 379ms 1.69% Node::GetRadius 109ms 0.49% 73.28% 379ms 1.69% __GI___libc_malloc 124ms 0.55% 73.84% 371ms 1.66% std::_Rb_tree::_M_erase 113ms 0.51% 74.34% 367ms 1.64% std::_Rb_tree::_M_clone_node (inline) 4ms 0.018% 74.36% 362ms 1.62% std::set::set (inline) 5ms 0.022% 74.38% 318ms 1.42% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 74.38% 315ms 1.41% std::_Rb_tree::_Alloc_node::operator() (inline) 311ms 1.39% 75.77% 311ms 1.39% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 75.77% 308ms 1.38% NodesOnlyMesh::ReMesh 156ms 0.7% 76.47% 301ms 1.35% __cxxabiv1::__si_class_type_info::__do_dyncast 1ms 0.0045% 76.47% 297ms 1.33% NodesOnlyMesh::UpdateNodeIndices 39ms 0.17% 76.65% 295ms 1.32% std::_Rb_tree::~_Rb_tree (inline) 0 0% 76.65% 294ms 1.31% boost::numeric::ublas::inner_prod (inline) 13ms 0.058% 76.71% 294ms 1.31% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 76.71% 294ms 1.31% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 289ms 1.29% 78.00% 289ms 1.29% __gnu_cxx::__normal_iterator::operator++ (inline) 13ms 0.058% 78.06% 283ms 1.27% boost::numeric::ublas::vector_binary::size (inline) 0 0% 78.06% 254ms 1.14% NodesOnlyMesh::UpdateBoxCollection 0 0% 78.06% 252ms 1.13% boost::numeric::ublas::c_vector::assign (inline) 97ms 0.43% 78.49% 244ms 1.09% boost::numeric::ublas::vector_inner_prod::apply (inline) 2ms 0.0089% 78.50% 243ms 1.09% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 242ms 1.08% 79.58% 242ms 1.08% Node::CheckForNodeAttributes 0 0% 79.58% 241ms 1.08% std::_Rb_tree::_M_drop_node (inline) 12ms 0.054% 79.63% 238ms 1.06% std::_Rb_tree::_M_emplace_hint_unique 234ms 1.05% 80.68% 234ms 1.05% __strcmp_avx2 6ms 0.027% 80.71% 232ms 1.04% DistributedBoxCollection::GetProcessOwningNode 1ms 0.0045% 80.71% 228ms 1.02% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 80.71% 226ms 1.01% VtkMeshWriter::WriteFiles 0 0% 80.71% 225ms 1.01% std::set::~set (inline) 130ms 0.58% 81.29% 219ms 0.98% _int_malloc 3ms 0.013% 81.31% 217ms 0.97% NodesOnlyMesh::AddNodesToBoxes 0 0% 81.31% 216ms 0.97% NodesOnlyMesh::ResizeBoxCollection 22ms 0.098% 81.40% 215ms 0.96% NodesOnlyMesh::IsANodeCloseToDomainBoundary 5ms 0.022% 81.43% 206ms 0.92% std::__new_allocator::deallocate (inline) 204ms 0.91% 82.34% 204ms 0.91% Node::GetIndex 20ms 0.089% 82.43% 204ms 0.91% std::__insertion_sort (inline) 107ms 0.48% 82.91% 203ms 0.91% std::__move_median_to_first (inline) 1ms 0.0045% 82.91% 195ms 0.87% vtkStreamingDemandDrivenPipeline::Update 0 0% 82.91% 195ms 0.87% vtkXMLWriterBase::Write 0 0% 82.91% 193ms 0.86% vtkDemandDrivenPipeline::ProcessRequest 0 0% 82.91% 193ms 0.86% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 82.91% 192ms 0.86% vtkDemandDrivenPipeline::ExecuteData 0 0% 82.91% 191ms 0.85% vtkCompositeDataPipeline::ExecuteData 0 0% 82.91% 191ms 0.85% vtkExecutive::CallAlgorithm 0 0% 82.91% 191ms 0.85% vtkXMLUnstructuredDataWriter::ProcessRequest 82ms 0.37% 83.28% 187ms 0.84% boost::shared_ptr::shared_ptr (inline) 68ms 0.3% 83.58% 184ms 0.82% __GI___libc_free 0 0% 83.58% 184ms 0.82% std::allocator_traits::deallocate (inline) 0 0% 83.58% 183ms 0.82% std::_Rb_tree::_M_put_node (inline) 0 0% 83.58% 163ms 0.73% vtkXMLUnstructuredDataWriter::WriteAPiece 1ms 0.0045% 83.59% 163ms 0.73% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 156ms 0.7% 84.28% 162ms 0.72% std::__adjacent_find (inline) 0 0% 84.28% 162ms 0.72% std::__unique (inline) 0 0% 84.28% 162ms 0.72% std::unique (inline) 0 0% 84.28% 158ms 0.71% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 154ms 0.69% 84.97% 154ms 0.69% [libchaste_cell_based.so] 2ms 0.0089% 84.98% 153ms 0.68% Cell::GetCellId 152ms 0.68% 85.66% 152ms 0.68% Node::IsDeleted 151ms 0.67% 86.33% 151ms 0.67% [libchaste_mesh.so] 0 0% 86.33% 150ms 0.67% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 18ms 0.08% 86.42% 150ms 0.67% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 86.42% 148ms 0.66% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 2ms 0.0089% 86.42% 148ms 0.66% AbstractNumericalMethod::SafeNodePositionUpdate 69ms 0.31% 86.73% 145ms 0.65% Node::AddNeighbour 4ms 0.018% 86.75% 144ms 0.64% DistributedBoxCollection::GetIsPeriodicAllDims 0 0% 86.75% 138ms 0.62% boost::numeric::ublas::vector_binary::operator() (inline) 4ms 0.018% 86.77% 134ms 0.6% NodeBasedCellPopulation::SetNode 0 0% 86.77% 133ms 0.59% std::_Rb_tree::clear (inline) 131ms 0.59% 87.35% 131ms 0.59% boost::shared_ptr::operator-> (inline) 0 0% 87.35% 128ms 0.57% std::_Rb_tree::_Auto_node::_Auto_node (inline) 3ms 0.013% 87.37% 128ms 0.57% std::_Rb_tree::_M_insert_unique 0 0% 87.37% 128ms 0.57% std::set::insert (inline) 2ms 0.0089% 87.38% 128ms 0.57% tbb::detail::r1::parallel_pipeline 0 0% 87.38% 127ms 0.57% vtkXMLWriter::WriteBinaryData 3ms 0.013% 87.39% 125ms 0.56% NodesOnlyMesh::SetNode 0 0% 87.39% 122ms 0.55% clone3 0 0% 87.39% 122ms 0.55% start_thread 0 0% 87.39% 122ms 0.55% tbb::detail::r1::reset 1ms 0.0045% 87.39% 122ms 0.55% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.39% 121ms 0.54% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.39% 121ms 0.54% vtkXMLWriter::WriteCompressionBlock 44ms 0.2% 87.59% 120ms 0.54% tbb::detail::r1::wait_bounded_queue_monitor 119ms 0.53% 88.12% 119ms 0.53% __ieee754_log_fma 0 0% 88.12% 119ms 0.53% vtkXMLWriter::WritePointsAppendedData 0 0% 88.12% 117ms 0.52% AbstractCellPopulation::SetCellUsingLocationIndex 0 0% 88.12% 117ms 0.52% Cell::GetCellProliferativeType 100ms 0.45% 88.57% 116ms 0.52% _int_free 0 0% 88.57% 112ms 0.5% NodeBasedCellPopulation::AcceptCellWriter