File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20937ms, 88.60% of 23632ms total Dropped 785 nodes (cum <= 118.16ms) flat flat% sum% cum cum% 0 0% 0% 23501ms 99.45% __libc_start_call_main 0 0% 0% 23501ms 99.45% __libc_start_main_impl 0 0% 0% 23501ms 99.45% _start 0 0% 0% 23486ms 99.38% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 23486ms 99.38% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 23486ms 99.38% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 23486ms 99.38% main 0 0% 0% 23452ms 99.24% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 23451ms 99.23% CxxTest::TestRunner::runTest (inline) 0 0% 0% 23451ms 99.23% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 23444ms 99.20% AbstractCellBasedSimulation::Solve 6ms 0.025% 0.025% 13807ms 58.43% OffLatticeSimulation::UpdateCellLocationsAndTopology 3ms 0.013% 0.038% 8992ms 38.05% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.034% 0.072% 8817ms 37.31% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.072% 8470ms 35.84% AbstractCellBasedSimulation::UpdateCellPopulation 1218ms 5.15% 5.23% 8230ms 34.83% RepulsionForce::AddForceContribution (partial-inline) 0 0% 5.23% 7436ms 31.47% NodeBasedCellPopulation::Update 8ms 0.034% 5.26% 5444ms 23.04% DistributedBoxCollection::CalculateInteriorNodePairs 2043ms 8.65% 13.90% 4808ms 20.35% std::_Rb_tree::_M_lower_bound (inline) 0 0% 13.90% 4549ms 19.25% OffLatticeSimulation::ApplyBoundaries 22ms 0.093% 14.00% 4248ms 17.98% NodeAttributes::RemoveDuplicateNeighbours 5ms 0.021% 14.02% 4083ms 17.28% std::__sort (inline) 0 0% 14.02% 4083ms 17.28% std::sort (inline) 167ms 0.71% 14.73% 3730ms 15.78% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 3ms 0.013% 14.74% 3458ms 14.63% AbstractCellPopulation::Iterator::operator++ (inline) 254ms 1.07% 15.81% 3420ms 14.47% AbstractCellPopulation::Iterator::IsRealCell (inline) 67ms 0.28% 16.10% 3311ms 14.01% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 214ms 0.91% 17.00% 3111ms 13.16% std::_Rb_tree::find (inline) 0 0% 17.00% 3111ms 13.16% std::map::find (inline) 27ms 0.11% 17.12% 2843ms 12.03% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2730ms 11.55% 28.67% 2730ms 11.55% std::_Rb_tree::_S_right (inline) 241ms 1.02% 29.69% 2451ms 10.37% std::map::operator[] (partial-inline) 156ms 0.66% 30.35% 2381ms 10.08% std::__introsort_loop 31ms 0.13% 30.48% 2347ms 9.93% PlaneBoundaryCondition::ImposeBoundaryCondition 141ms 0.6% 31.08% 2270ms 9.61% AbstractMesh::GetNode 61ms 0.26% 31.33% 2249ms 9.52% NodesOnlyMesh::GetNodeOrHaloNode 37ms 0.16% 31.49% 2212ms 9.36% AbstractCellPopulation::GetLocationIndexUsingCell 29ms 0.12% 31.61% 2202ms 9.32% PlaneBoundaryCondition::VerifyBoundaryCondition 46ms 0.19% 31.81% 2190ms 9.27% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 31.81% 2143ms 9.07% std::__unguarded_partition_pivot (inline) 82ms 0.35% 32.16% 2133ms 9.03% NodesOnlyMesh::SolveNodeMapping 37ms 0.16% 32.31% 2012ms 8.51% boost::numeric::ublas::vector_assign (inline) 0 0% 32.31% 1932ms 8.18% std::_Rb_tree::lower_bound (inline) 0 0% 32.31% 1932ms 8.18% std::map::lower_bound (inline) 983ms 4.16% 36.47% 1931ms 8.17% std::__unguarded_partition (inline) 485ms 2.05% 38.52% 1919ms 8.12% boost::numeric::ublas::indexing_vector_assign 176ms 0.74% 39.27% 1799ms 7.61% AbstractMesh::GetVectorFromAtoB 150ms 0.63% 39.90% 1768ms 7.48% DistributedBoxCollection::AddPairsFromBox 1ms 0.0042% 39.91% 1695ms 7.17% std::__final_insertion_sort (inline) 87ms 0.37% 40.28% 1490ms 6.31% std::__unguarded_insertion_sort (inline) 11ms 0.047% 40.32% 1472ms 6.23% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 535ms 2.26% 42.59% 1461ms 6.18% std::__unguarded_linear_insert (inline) 27ms 0.11% 42.70% 1458ms 6.17% AbstractCellPopulation::GetCellUsingLocationIndex 1342ms 5.68% 48.38% 1342ms 5.68% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 48.38% 1140ms 4.82% NodeBasedCellPopulation::UpdateCellProcessLocation 1071ms 4.53% 52.91% 1071ms 4.53% boost::numeric::ublas::c_vector::operator() 4ms 0.017% 52.93% 1064ms 4.50% DistributedBoxCollection::CalculateBoundaryNodePairs 245ms 1.04% 53.96% 949ms 4.02% __dynamic_cast 840ms 3.55% 57.52% 840ms 3.55% boost::numeric::ublas::same_impl_ex 385ms 1.63% 59.15% 836ms 3.54% DistributedBoxCollection::CalculateContainingBox (partial-inline) 11ms 0.047% 59.20% 775ms 3.28% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 189ms 0.8% 59.99% 727ms 3.08% NodeAttributes::AddNeighbour 0 0% 59.99% 707ms 2.99% AbstractCellPopulation::WriteResultsToFiles 0 0% 59.99% 656ms 2.78% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 59.99% 645ms 2.73% boost::numeric::ublas::norm_2 (inline) 517ms 2.19% 62.18% 645ms 2.73% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 62.18% 645ms 2.73% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 40ms 0.17% 62.35% 616ms 2.61% boost::numeric::ublas::vector_binary::size (inline) 310ms 1.31% 63.66% 607ms 2.57% __cxxabiv1::__si_class_type_info::__do_dyncast 538ms 2.28% 65.94% 599ms 2.53% std::vector::push_back (inline) 2ms 0.0085% 65.95% 557ms 2.36% AbstractCellBasedSimulation::DoCellBirth 2ms 0.0085% 65.96% 547ms 2.31% CellPropertyCollection::GetPropertiesType (inline) 40ms 0.17% 66.13% 532ms 2.25% boost::detail::shared_count::~shared_count (inline) 0 0% 66.13% 532ms 2.25% boost::shared_ptr::~shared_ptr (inline) 4ms 0.017% 66.14% 518ms 2.19% AbstractCentreBasedCellPopulation::GetDampingConstant 74ms 0.31% 66.46% 512ms 2.17% std::__new_allocator::allocate (inline) 37ms 0.16% 66.61% 510ms 2.16% boost::numeric::ublas::c_vector::operator= (inline) 35ms 0.15% 66.76% 505ms 2.14% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 66.76% 490ms 2.07% std::allocator_traits::allocate (inline) 481ms 2.04% 68.80% 484ms 2.05% boost::detail::sp_counted_base::release 0 0% 68.80% 476ms 2.01% AbstractCellBasedSimulation::DoCellRemoval (inline) 467ms 1.98% 70.77% 467ms 1.98% std::_Rb_tree_increment 3ms 0.013% 70.79% 466ms 1.97% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 70.79% 466ms 1.97% std::_Rb_tree::_M_create_node (inline) 9ms 0.038% 70.82% 457ms 1.93% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 7ms 0.03% 70.85% 456ms 1.93% std::__copy_move::__copy_m (inline) 0 0% 70.85% 456ms 1.93% std::__copy_move_a (inline) 0 0% 70.85% 456ms 1.93% std::__copy_move_a1 (inline) 0 0% 70.85% 456ms 1.93% std::__copy_move_a2 (inline) 0 0% 70.85% 456ms 1.93% std::copy (inline) 15ms 0.063% 70.92% 451ms 1.91% boost::numeric::ublas::vector_reference::operator() (inline) 22ms 0.093% 71.01% 429ms 1.82% operator new 428ms 1.81% 72.82% 428ms 1.81% __strcmp_avx2 0 0% 72.82% 428ms 1.81% boost::numeric::ublas::vector_binary::operator() (inline) 33ms 0.14% 72.96% 423ms 1.79% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 72.96% 418ms 1.77% std::_Rb_tree::_M_get_node (inline) 3ms 0.013% 72.97% 416ms 1.76% AbstractCellProperty::IsSubType (inline) 413ms 1.75% 74.72% 413ms 1.75% __memcpy_avx_unaligned_erms 111ms 0.47% 75.19% 399ms 1.69% __GI___libc_malloc 141ms 0.6% 75.79% 398ms 1.68% Node::GetRadius 137ms 0.58% 76.37% 387ms 1.64% std::_Rb_tree::_M_erase 41ms 0.17% 76.54% 384ms 1.62% std::_Rb_tree::_M_copy (inline) 0 0% 76.54% 370ms 1.57% Cell::GetMutationState 350ms 1.48% 78.02% 350ms 1.48% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 3ms 0.013% 78.03% 347ms 1.47% std::set::set (inline) 111ms 0.47% 78.50% 343ms 1.45% std::_Rb_tree::_M_clone_node (inline) 0 0% 78.50% 335ms 1.42% boost::numeric::ublas::inner_prod (inline) 2ms 0.0085% 78.51% 335ms 1.42% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 15ms 0.063% 78.58% 333ms 1.41% boost::numeric::ublas::vector_scalar_binary::evaluate 7ms 0.03% 78.61% 327ms 1.38% NodeBasedCellPopulation::UpdateMapsAfterRemesh 35ms 0.15% 78.75% 307ms 1.30% std::_Rb_tree::~_Rb_tree (inline) 0 0% 78.75% 304ms 1.29% NodesOnlyMesh::ReMesh 0 0% 78.75% 302ms 1.28% std::_Rb_tree::_Alloc_node::operator() (inline) 3ms 0.013% 78.77% 297ms 1.26% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 3ms 0.013% 78.78% 290ms 1.23% NodesOnlyMesh::UpdateNodeIndices 0 0% 78.78% 290ms 1.23% boost::numeric::ublas::c_vector::assign (inline) 9ms 0.038% 78.82% 281ms 1.19% DistributedBoxCollection::GetProcessOwningNode 9ms 0.038% 78.85% 278ms 1.18% std::_Rb_tree::_M_emplace_hint_unique 116ms 0.49% 79.35% 276ms 1.17% boost::numeric::ublas::vector_inner_prod::apply (inline) 267ms 1.13% 80.48% 267ms 1.13% __gnu_cxx::__normal_iterator::operator++ (inline) 265ms 1.12% 81.60% 265ms 1.12% Node::CheckForNodeAttributes 0 0% 81.60% 243ms 1.03% NodesOnlyMesh::UpdateBoxCollection 0 0% 81.60% 238ms 1.01% std::_Rb_tree::_M_drop_node (inline) 0 0% 81.60% 236ms 1% std::set::~set (inline) 141ms 0.6% 82.19% 228ms 0.96% _int_malloc 0 0% 82.19% 224ms 0.95% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 82.19% 223ms 0.94% VtkMeshWriter::WriteFiles 223ms 0.94% 83.14% 223ms 0.94% [libchaste_cell_based.so] 0 0% 83.14% 215ms 0.91% NodesOnlyMesh::AddNodesToBoxes 100ms 0.42% 83.56% 210ms 0.89% std::__move_median_to_first (inline) 118ms 0.5% 84.06% 208ms 0.88% boost::shared_ptr::shared_ptr (inline) 14ms 0.059% 84.12% 204ms 0.86% std::__insertion_sort (inline) 0 0% 84.12% 202ms 0.85% vtkStreamingDemandDrivenPipeline::Update 0 0% 84.12% 202ms 0.85% vtkXMLWriterBase::Write 0 0% 84.12% 201ms 0.85% vtkDemandDrivenPipeline::ProcessRequest 0 0% 84.12% 201ms 0.85% vtkExecutive::CallAlgorithm 0 0% 84.12% 201ms 0.85% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 84.12% 200ms 0.85% vtkCompositeDataPipeline::ExecuteData 0 0% 84.12% 200ms 0.85% vtkDemandDrivenPipeline::ExecuteData 0 0% 84.12% 200ms 0.85% vtkXMLUnstructuredDataWriter::ProcessRequest 2ms 0.0085% 84.13% 189ms 0.8% std::__new_allocator::deallocate (inline) 176ms 0.74% 84.87% 176ms 0.74% Node::GetIndex 4ms 0.017% 84.89% 175ms 0.74% CellPropertyCollection::HasProperty 0 0% 84.89% 174ms 0.74% Cell::HasCellProperty (inline) 62ms 0.26% 85.15% 170ms 0.72% __GI___libc_free 0 0% 85.15% 169ms 0.72% std::allocator_traits::deallocate (inline) 0 0% 85.15% 167ms 0.71% std::_Rb_tree::_M_put_node (inline) 0 0% 85.15% 164ms 0.69% NodesOnlyMesh::ResizeBoxCollection 0 0% 85.15% 164ms 0.69% std::_Rb_tree::_Auto_node::_Auto_node (inline) 16ms 0.068% 85.22% 163ms 0.69% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 85.22% 162ms 0.69% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.22% 162ms 0.69% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 3ms 0.013% 85.23% 161ms 0.68% AbstractCellProperty::IsType (inline) 160ms 0.68% 85.91% 160ms 0.68% [libchaste_mesh.so] 5ms 0.021% 85.93% 159ms 0.67% Cell::ReadyToDivide 0 0% 85.93% 159ms 0.67% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 152ms 0.64% 86.57% 152ms 0.64% Node::IsDeleted 79ms 0.33% 86.91% 143ms 0.61% Node::AddNeighbour 3ms 0.013% 86.92% 138ms 0.58% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 86.92% 136ms 0.58% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 86.92% 135ms 0.57% vtkXMLWriter::WriteBinaryData 134ms 0.57% 87.49% 134ms 0.57% boost::shared_ptr::operator-> (inline) 0 0% 87.49% 130ms 0.55% std::_Rb_tree::clear (inline) 125ms 0.53% 88.02% 130ms 0.55% std::__adjacent_find (inline) 0 0% 88.02% 130ms 0.55% std::__unique (inline) 0 0% 88.02% 130ms 0.55% std::unique (inline) 0 0% 88.02% 129ms 0.55% AbstractCellPopulation::SetCellUsingLocationIndex 0 0% 88.02% 129ms 0.55% vtkXMLWriter::WriteBinaryDataInternal 128ms 0.54% 88.56% 128ms 0.54% Node::rGetLocation 0 0% 88.56% 128ms 0.54% vtkXMLWriter::WriteBinaryDataBlock 0 0% 88.56% 128ms 0.54% vtkXMLWriter::WriteCompressionBlock 4ms 0.017% 88.57% 126ms 0.53% boost::numeric::ublas::c_vector::operator[] (inline) 3ms 0.013% 88.59% 124ms 0.52% NodeBasedCellPopulation::SetNode 0 0% 88.59% 124ms 0.52% vtkXMLWriter::WritePointsAppendedData 1ms 0.0042% 88.59% 123ms 0.52% Cell::GetCellId 1ms 0.0042% 88.60% 121ms 0.51% std::_Rb_tree::_M_insert_unique 0 0% 88.60% 121ms 0.51% std::set::insert (inline)