File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 30588ms, 88.06% of 34736ms total Dropped 842 nodes (cum <= 173.68ms) flat flat% sum% cum cum% 0 0% 0% 34599ms 99.61% __libc_start_call_main 0 0% 0% 34599ms 99.61% __libc_start_main_impl 0 0% 0% 34599ms 99.61% _start 0 0% 0% 34579ms 99.55% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 34579ms 99.55% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 34579ms 99.55% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 34579ms 99.55% main 0 0% 0% 34537ms 99.43% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 34537ms 99.43% CxxTest::TestRunner::runTest (inline) 0 0% 0% 34537ms 99.43% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0029% 0.0029% 34528ms 99.40% AbstractCellBasedSimulation::Solve 0 0% 0.0029% 23875ms 68.73% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.0058% 0.0086% 18854ms 54.28% ForwardEulerNumericalMethod::UpdateAllNodePositions 5ms 0.014% 0.023% 18653ms 53.70% AbstractNumericalMethod::ComputeForcesIncludingDamping 166ms 0.48% 0.5% 17750ms 51.10% AbstractTwoBodyInteractionForce::AddForceContribution 1528ms 4.40% 4.90% 15050ms 43.33% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4494ms 12.94% 17.84% 9845ms 28.34% std::_Rb_tree::_M_lower_bound (inline) 0 0% 17.84% 9419ms 27.12% AbstractCellBasedSimulation::UpdateCellPopulation 391ms 1.13% 18.96% 9033ms 26.00% std::_Rb_tree::find (inline) 0 0% 18.96% 9030ms 26.00% std::map::find (inline) 198ms 0.57% 19.53% 8874ms 25.55% NodesOnlyMesh::GetNodeOrHaloNode 522ms 1.50% 21.04% 8677ms 24.98% AbstractMesh::GetNode 0 0% 21.04% 8341ms 24.01% NodeBasedCellPopulation::Update 337ms 0.97% 22.01% 8159ms 23.49% NodesOnlyMesh::SolveNodeMapping 8ms 0.023% 22.03% 6171ms 17.77% DistributedBoxCollection::CalculateInteriorNodePairs 180ms 0.52% 22.55% 5768ms 16.61% boost::numeric::ublas::vector_assign (inline) 165ms 0.48% 23.02% 5684ms 16.36% boost::numeric::ublas::c_vector::c_vector (partial-inline) 5292ms 15.23% 38.26% 5292ms 15.23% std::_Rb_tree::_S_right (inline) 1ms 0.0029% 38.26% 4718ms 13.58% OffLatticeSimulation::ApplyBoundaries 6ms 0.017% 38.28% 4609ms 13.27% NodeAttributes::RemoveDuplicateNeighbours 2ms 0.0058% 38.28% 4429ms 12.75% std::__sort (inline) 0 0% 38.28% 4429ms 12.75% std::sort (inline) 1131ms 3.26% 41.54% 3498ms 10.07% boost::numeric::ublas::indexing_vector_assign 84ms 0.24% 41.78% 3358ms 9.67% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 2ms 0.0058% 41.79% 3247ms 9.35% AbstractCellPopulation::Iterator::operator++ (inline) 169ms 0.49% 42.27% 3218ms 9.26% AbstractCellPopulation::Iterator::IsRealCell 30ms 0.086% 42.36% 2789ms 8.03% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 196ms 0.56% 42.92% 2550ms 7.34% std::__introsort_loop 24ms 0.069% 42.99% 2506ms 7.21% PlaneBoundaryCondition::ImposeBoundaryCondition 0 0% 42.99% 2282ms 6.57% std::__unguarded_partition_pivot (inline) 45ms 0.13% 43.12% 2275ms 6.55% AbstractCellPopulation::GetLocationIndexUsingCell 16ms 0.046% 43.17% 2211ms 6.37% PlaneBoundaryCondition::VerifyBoundaryCondition 148ms 0.43% 43.59% 2195ms 6.32% DistributedBoxCollection::AddPairsFromBox 969ms 2.79% 46.38% 2050ms 5.90% std::__unguarded_partition (inline) 0 0% 46.38% 1877ms 5.40% std::__final_insertion_sort (inline) 166ms 0.48% 46.86% 1724ms 4.96% std::map::operator[] (partial-inline) 1703ms 4.90% 51.76% 1703ms 4.90% boost::numeric::ublas::same_impl_ex 112ms 0.32% 52.09% 1686ms 4.85% std::__unguarded_insertion_sort (inline) 625ms 1.80% 53.89% 1611ms 4.64% std::__unguarded_linear_insert (inline) 154ms 0.44% 54.33% 1592ms 4.58% AbstractMesh::GetVectorFromAtoB 1419ms 4.09% 58.41% 1419ms 4.09% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 58.41% 1388ms 4.00% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 58.41% 1375ms 3.96% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 58.41% 1304ms 3.75% std::_Rb_tree::lower_bound (inline) 0 0% 58.41% 1304ms 3.75% std::map::lower_bound (inline) 1195ms 3.44% 61.86% 1195ms 3.44% boost::numeric::ublas::c_vector::operator() 0 0% 61.86% 1192ms 3.43% NodeBasedCellPopulation::UpdateCellProcessLocation 1ms 0.0029% 61.86% 1148ms 3.30% boost::numeric::ublas::detail::expression_type_check (inline) 8ms 0.023% 61.88% 1136ms 3.27% DistributedBoxCollection::CalculateBoundaryNodePairs 259ms 0.75% 62.63% 1100ms 3.17% boost::numeric::ublas::detail::equals 162ms 0.47% 63.09% 984ms 2.83% boost::numeric::ublas::vector_binary::size (inline) 21ms 0.06% 63.15% 924ms 2.66% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 443ms 1.28% 64.43% 911ms 2.62% DistributedBoxCollection::CalculateContainingBox (partial-inline) 218ms 0.63% 65.06% 858ms 2.47% NodeAttributes::AddAppliedForceContribution 286ms 0.82% 65.88% 852ms 2.45% NodeAttributes::AddNeighbour 4ms 0.012% 65.89% 844ms 2.43% AbstractCentreBasedCellPopulation::GetDampingConstant 583ms 1.68% 67.57% 793ms 2.28% __dynamic_cast 0 0% 67.57% 791ms 2.28% boost::numeric::ublas::norm_inf (inline) 490ms 1.41% 68.98% 791ms 2.28% boost::numeric::ublas::vector_norm_inf::apply (inline) 33ms 0.095% 69.08% 772ms 2.22% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 69.08% 758ms 2.18% AbstractCellPopulation::WriteResultsToFiles 729ms 2.10% 71.17% 729ms 2.10% std::_Rb_tree_increment 101ms 0.29% 71.46% 714ms 2.06% std::__new_allocator::allocate (inline) 565ms 1.63% 73.09% 654ms 1.88% std::vector::push_back (inline) 0 0% 73.09% 640ms 1.84% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 73.09% 640ms 1.84% boost::numeric::ublas::c_vector::plus_assign (inline) 13ms 0.037% 73.13% 637ms 1.83% CellPropertyCollection::GetPropertiesType (inline) 88ms 0.25% 73.38% 614ms 1.77% operator new 4ms 0.012% 73.39% 598ms 1.72% AbstractCellBasedSimulation::DoCellBirth 0 0% 73.39% 597ms 1.72% boost::numeric::ublas::norm_2 (inline) 469ms 1.35% 74.74% 597ms 1.72% boost::numeric::ublas::vector_norm_2::apply (inline) 5ms 0.014% 74.76% 561ms 1.62% Cell::GetMutationState 176ms 0.51% 75.26% 523ms 1.51% __GI___libc_malloc 0 0% 75.26% 506ms 1.46% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 75.26% 480ms 1.38% AbstractCellBasedSimulation::DoCellRemoval (inline) 4ms 0.012% 75.28% 470ms 1.35% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 32ms 0.092% 75.37% 418ms 1.20% boost::detail::shared_count::~shared_count (inline) 0 0% 75.37% 418ms 1.20% boost::shared_ptr::~shared_ptr (inline) 139ms 0.4% 75.77% 413ms 1.19% __GI___libc_free 0 0% 75.77% 407ms 1.17% std::allocator_traits::allocate (inline) 403ms 1.16% 76.93% 403ms 1.16% Node::GetIndex 0 0% 76.93% 395ms 1.14% boost::numeric::ublas::inner_prod (inline) 1ms 0.0029% 76.93% 390ms 1.12% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 18ms 0.052% 76.98% 389ms 1.12% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 76.98% 387ms 1.11% std::_Rb_tree::_M_create_node (inline) 372ms 1.07% 78.05% 383ms 1.10% boost::detail::sp_counted_base::release 3ms 0.0086% 78.06% 365ms 1.05% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 7ms 0.02% 78.08% 362ms 1.04% AbstractCellPopulation::GetCellUsingLocationIndex 2ms 0.0058% 78.09% 358ms 1.03% AbstractCellProperty::IsSubType (inline) 7ms 0.02% 78.11% 353ms 1.02% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 35ms 0.1% 78.21% 342ms 0.98% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 78.21% 342ms 0.98% boost::numeric::ublas::vector::vector (inline) 332ms 0.96% 79.17% 332ms 0.96% __gnu_cxx::__normal_iterator::operator++ (inline) 1ms 0.0029% 79.17% 330ms 0.95% NodesOnlyMesh::ReMesh 0 0% 79.17% 330ms 0.95% std::_Rb_tree::_M_get_node (inline) 4ms 0.012% 79.18% 328ms 0.94% DistributedBoxCollection::GetProcessOwningNode 155ms 0.45% 79.63% 323ms 0.93% boost::numeric::ublas::vector_inner_prod::apply (inline) 3ms 0.0086% 79.63% 317ms 0.91% NodesOnlyMesh::UpdateNodeIndices 311ms 0.9% 80.53% 311ms 0.9% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 4ms 0.012% 80.54% 308ms 0.89% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 80.54% 301ms 0.87% NodesOnlyMesh::UpdateBoxCollection 0 0% 80.54% 301ms 0.87% boost::numeric::ublas::c_vector::assign (inline) 10ms 0.029% 80.57% 300ms 0.86% boost::numeric::ublas::vector_reference::operator() (inline) 66ms 0.19% 80.76% 284ms 0.82% Node::GetRadius 238ms 0.69% 81.45% 274ms 0.79% _int_free 268ms 0.77% 82.22% 268ms 0.77% [libchaste_cell_based.so] 111ms 0.32% 82.54% 266ms 0.77% std::_Rb_tree::_M_erase (partial-inline) 12ms 0.035% 82.57% 263ms 0.76% std::_Rb_tree::_Rb_tree (partial-inline) 226ms 0.65% 83.22% 254ms 0.73% Node::AddNeighbour 9ms 0.026% 83.25% 254ms 0.73% std::_Rb_tree::_M_emplace_hint_unique 3ms 0.0086% 83.26% 253ms 0.73% NodesOnlyMesh::AddNodesToBoxes 1ms 0.0029% 83.26% 250ms 0.72% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 83.26% 249ms 0.72% VtkMeshWriter::WriteFiles 15ms 0.043% 83.30% 245ms 0.71% std::_Rb_tree::_M_copy (inline) 0 0% 83.30% 244ms 0.7% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 83.30% 240ms 0.69% boost::numeric::ublas::vector_binary::operator() (inline) 144ms 0.41% 83.72% 238ms 0.69% _int_malloc 229ms 0.66% 84.38% 229ms 0.66% Node::CheckForNodeAttributes 33ms 0.095% 84.47% 229ms 0.66% std::_Rb_tree::_M_clone_node (inline) 0 0% 84.47% 228ms 0.66% CellPropertyCollection::HasProperty 124ms 0.36% 84.83% 228ms 0.66% std::__move_median_to_first (inline) 0 0% 84.83% 226ms 0.65% Cell::HasCellProperty (inline) 223ms 0.64% 85.47% 223ms 0.64% [libchaste_mesh.so] 0 0% 85.47% 223ms 0.64% vtkStreamingDemandDrivenPipeline::Update 0 0% 85.47% 223ms 0.64% vtkXMLWriterBase::Write 10ms 0.029% 85.50% 221ms 0.64% Cell::ReadyToDivide 0 0% 85.50% 220ms 0.63% vtkDemandDrivenPipeline::ProcessRequest 0 0% 85.50% 218ms 0.63% vtkExecutive::CallAlgorithm 0 0% 85.50% 217ms 0.62% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 85.50% 217ms 0.62% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 85.50% 216ms 0.62% vtkCompositeDataPipeline::ExecuteData 0 0% 85.50% 216ms 0.62% vtkDemandDrivenPipeline::ExecuteData 214ms 0.62% 86.12% 214ms 0.62% NodeBasedCellPopulation::GetNode 204ms 0.59% 86.70% 204ms 0.59% __strcmp_avx2 19ms 0.055% 86.76% 191ms 0.55% std::__insertion_sort (inline) 100ms 0.29% 87.05% 190ms 0.55% boost::shared_ptr::shared_ptr (inline) 0 0% 87.05% 180ms 0.52% AbstractCellProperty::IsType (inline) 0 0% 87.05% 180ms 0.52% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 87.05% 180ms 0.52% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 177ms 0.51% 87.55% 177ms 0.51% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 175ms 0.5% 88.06% 175ms 0.5% Node::rGetLocation 0 0% 88.06% 175ms 0.5% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData