File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 23647ms, 88.05% of 26857ms total Dropped 786 nodes (cum <= 134.28ms) flat flat% sum% cum cum% 0 0% 0% 26762ms 99.65% __libc_start_call_main 0 0% 0% 26762ms 99.65% __libc_start_main_impl 0 0% 0% 26762ms 99.65% _start 0 0% 0% 26747ms 99.59% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 26747ms 99.59% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 26747ms 99.59% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 26747ms 99.59% main 0 0% 0% 26708ms 99.45% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 26708ms 99.45% CxxTest::TestRunner::runTest (inline) 0 0% 0% 26708ms 99.45% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0037% 0.0037% 26700ms 99.42% AbstractCellBasedSimulation::Solve 4ms 0.015% 0.019% 18539ms 69.03% OffLatticeSimulation::UpdateCellLocationsAndTopology 5ms 0.019% 0.037% 14674ms 54.64% ForwardEulerNumericalMethod::UpdateAllNodePositions 5ms 0.019% 0.056% 14508ms 54.02% AbstractNumericalMethod::ComputeForcesIncludingDamping 100ms 0.37% 0.43% 13845ms 51.55% AbstractTwoBodyInteractionForce::AddForceContribution 1158ms 4.31% 4.74% 11827ms 44.04% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 3486ms 12.98% 17.72% 7774ms 28.95% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.0037% 17.72% 7231ms 26.92% AbstractCellBasedSimulation::UpdateCellPopulation 283ms 1.05% 18.78% 7111ms 26.48% std::_Rb_tree::find (inline) 0 0% 18.78% 7110ms 26.47% std::map::find (inline) 142ms 0.53% 19.31% 7006ms 26.09% NodesOnlyMesh::GetNodeOrHaloNode 398ms 1.48% 20.79% 6870ms 25.58% AbstractMesh::GetNode 294ms 1.09% 21.88% 6474ms 24.11% NodesOnlyMesh::SolveNodeMapping 1ms 0.0037% 21.89% 6376ms 23.74% NodeBasedCellPopulation::Update 4ms 0.015% 21.90% 4749ms 17.68% DistributedBoxCollection::CalculateInteriorNodePairs 127ms 0.47% 22.37% 4545ms 16.92% boost::numeric::ublas::vector_assign (inline) 109ms 0.41% 22.78% 4518ms 16.82% boost::numeric::ublas::c_vector::c_vector (partial-inline) 4245ms 15.81% 38.59% 4245ms 15.81% std::_Rb_tree::_S_right (inline) 0 0% 38.59% 3587ms 13.36% OffLatticeSimulation::ApplyBoundaries 7ms 0.026% 38.61% 3558ms 13.25% NodeAttributes::RemoveDuplicateNeighbours 3ms 0.011% 38.62% 3394ms 12.64% std::__sort (inline) 0 0% 38.62% 3394ms 12.64% std::sort (inline) 60ms 0.22% 38.85% 2603ms 9.69% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 859ms 3.20% 42.04% 2566ms 9.55% boost::numeric::ublas::indexing_vector_assign 5ms 0.019% 42.06% 2446ms 9.11% AbstractCellPopulation::Iterator::operator++ (inline) 105ms 0.39% 42.45% 2419ms 9.01% AbstractCellPopulation::Iterator::IsRealCell (inline) 19ms 0.071% 42.53% 2157ms 8.03% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 120ms 0.45% 42.97% 1972ms 7.34% std::__introsort_loop 15ms 0.056% 43.03% 1879ms 7.00% PlaneBoundaryCondition::ImposeBoundaryCondition 49ms 0.18% 43.21% 1813ms 6.75% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 43.21% 1779ms 6.62% std::__unguarded_partition_pivot (inline) 7ms 0.026% 43.24% 1708ms 6.36% PlaneBoundaryCondition::VerifyBoundaryCondition 110ms 0.41% 43.65% 1670ms 6.22% DistributedBoxCollection::AddPairsFromBox 783ms 2.92% 46.56% 1603ms 5.97% std::__unguarded_partition (inline) 0 0% 46.56% 1433ms 5.34% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 46.56% 1416ms 5.27% std::__final_insertion_sort (inline) 0 0% 46.56% 1414ms 5.26% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 143ms 0.53% 47.09% 1363ms 5.08% std::map::operator[] (partial-inline) 84ms 0.31% 47.41% 1261ms 4.70% std::__unguarded_insertion_sort (inline) 1232ms 4.59% 51.99% 1232ms 4.59% boost::numeric::ublas::same_impl_ex 134ms 0.5% 52.49% 1204ms 4.48% AbstractMesh::GetVectorFromAtoB 438ms 1.63% 54.12% 1184ms 4.41% std::__unguarded_linear_insert (inline) 3ms 0.011% 54.13% 1116ms 4.16% boost::numeric::ublas::detail::expression_type_check (inline) 109ms 0.41% 54.54% 1081ms 4.03% boost::numeric::ublas::detail::equals 1062ms 3.95% 58.49% 1062ms 3.95% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 58.49% 1019ms 3.79% std::_Rb_tree::lower_bound (inline) 0 0% 58.49% 1019ms 3.79% std::map::lower_bound (inline) 0 0% 58.49% 963ms 3.59% boost::numeric::ublas::norm_inf (inline) 437ms 1.63% 60.12% 963ms 3.59% boost::numeric::ublas::vector_norm_inf::apply (inline) 899ms 3.35% 63.47% 899ms 3.35% boost::numeric::ublas::c_vector::operator() 2ms 0.0074% 63.48% 868ms 3.23% DistributedBoxCollection::CalculateBoundaryNodePairs 0 0% 63.48% 861ms 3.21% NodeBasedCellPopulation::UpdateCellProcessLocation 125ms 0.47% 63.94% 754ms 2.81% boost::numeric::ublas::vector_binary::size (inline) 11ms 0.041% 63.98% 732ms 2.73% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 302ms 1.12% 65.11% 628ms 2.34% DistributedBoxCollection::CalculateContainingBox (partial-inline) 4ms 0.015% 65.12% 615ms 2.29% AbstractCentreBasedCellPopulation::GetDampingConstant 158ms 0.59% 65.71% 615ms 2.29% NodeAttributes::AddAppliedForceContribution 113ms 0.42% 66.13% 602ms 2.24% NodeAttributes::AddNeighbour 0 0% 66.13% 582ms 2.17% AbstractCellPopulation::WriteResultsToFiles 410ms 1.53% 67.66% 577ms 2.15% __dynamic_cast 80ms 0.3% 67.96% 562ms 2.09% std::__new_allocator::allocate (inline) 488ms 1.82% 69.77% 549ms 2.04% std::vector::push_back (inline) 28ms 0.1% 69.88% 544ms 2.03% std::_Rb_tree_const_iterator::operator++ (inline) 508ms 1.89% 71.77% 508ms 1.89% std::_Rb_tree_increment 3ms 0.011% 71.78% 497ms 1.85% AbstractCellBasedSimulation::DoCellBirth 79ms 0.29% 72.07% 479ms 1.78% operator new 0 0% 72.07% 470ms 1.75% boost::numeric::ublas::norm_2 (inline) 354ms 1.32% 73.39% 470ms 1.75% boost::numeric::ublas::vector_norm_2::apply (inline) 17ms 0.063% 73.46% 468ms 1.74% CellPropertyCollection::GetPropertiesType (inline) 0 0% 73.46% 457ms 1.70% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 73.46% 457ms 1.70% boost::numeric::ublas::c_vector::plus_assign (inline) 155ms 0.58% 74.03% 400ms 1.49% __GI___libc_malloc 2ms 0.0074% 74.04% 397ms 1.48% Cell::GetMutationState 2ms 0.0074% 74.05% 386ms 1.44% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 74.05% 362ms 1.35% boost::numeric::ublas::scalar_traits::norm_inf (inline) 0 0% 74.05% 362ms 1.35% boost::numeric::ublas::scalar_traits::type_abs (inline) 0 0% 74.05% 361ms 1.34% boost_numeric_ublas_abs (inline) 361ms 1.34% 75.39% 361ms 1.34% std::abs (inline) 0 0% 75.39% 356ms 1.33% AbstractCellBasedSimulation::DoCellRemoval (inline) 1ms 0.0037% 75.40% 349ms 1.30% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 118ms 0.44% 75.83% 344ms 1.28% __GI___libc_free 334ms 1.24% 77.08% 334ms 1.24% Node::GetIndex 0 0% 77.08% 328ms 1.22% std::allocator_traits::allocate (inline) 0 0% 77.08% 311ms 1.16% std::_Rb_tree::_M_create_node (inline) 21ms 0.078% 77.16% 302ms 1.12% boost::detail::shared_count::~shared_count (inline) 0 0% 77.16% 302ms 1.12% boost::shared_ptr::~shared_ptr (inline) 2ms 0.0074% 77.16% 288ms 1.07% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 5ms 0.019% 77.18% 286ms 1.06% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 77.18% 286ms 1.06% boost::numeric::ublas::inner_prod (inline) 2ms 0.0074% 77.19% 286ms 1.06% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 14ms 0.052% 77.24% 284ms 1.06% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 77.24% 283ms 1.05% AbstractCellProperty::IsSubType (inline) 271ms 1.01% 78.25% 278ms 1.04% boost::detail::sp_counted_base::release 0 0% 78.25% 269ms 1.00% std::_Rb_tree::_M_get_node (inline) 266ms 0.99% 79.24% 266ms 0.99% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 262ms 0.98% 80.22% 262ms 0.98% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 80.22% 261ms 0.97% NodesOnlyMesh::ReMesh 26ms 0.097% 80.31% 260ms 0.97% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 80.31% 260ms 0.97% boost::numeric::ublas::vector::vector (inline) 1ms 0.0037% 80.32% 253ms 0.94% NodesOnlyMesh::UpdateNodeIndices 82ms 0.31% 80.62% 237ms 0.88% std::_Rb_tree::_M_erase (inline) 0 0% 80.62% 236ms 0.88% NodesOnlyMesh::UpdateBoxCollection 236ms 0.88% 81.50% 236ms 0.88% [libchaste_mesh.so] 6ms 0.022% 81.52% 227ms 0.85% NodeBasedCellPopulation::UpdateMapsAfterRemesh 197ms 0.73% 82.26% 225ms 0.84% _int_free 93ms 0.35% 82.60% 223ms 0.83% boost::numeric::ublas::vector_inner_prod::apply (inline) 3ms 0.011% 82.62% 223ms 0.83% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 82.62% 216ms 0.8% boost::numeric::ublas::c_vector::assign (inline) 15ms 0.056% 82.67% 216ms 0.8% std::_Rb_tree::_M_copy (inline) 13ms 0.048% 82.72% 213ms 0.79% boost::numeric::ublas::vector_reference::operator() (inline) 126ms 0.47% 83.19% 211ms 0.79% Node::AddNeighbour 0 0% 83.19% 209ms 0.78% std::_Rb_tree::_Alloc_node::operator() (inline) 57ms 0.21% 83.40% 203ms 0.76% Node::GetRadius 8ms 0.03% 83.43% 201ms 0.75% std::_Rb_tree::_M_emplace_hint_unique 1ms 0.0037% 83.43% 197ms 0.73% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 28ms 0.1% 83.54% 197ms 0.73% std::_Rb_tree::_M_clone_node (inline) 2ms 0.0074% 83.55% 194ms 0.72% NodesOnlyMesh::AddNodesToBoxes 194ms 0.72% 84.27% 194ms 0.72% [libchaste_cell_based.so] 0 0% 84.27% 193ms 0.72% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 84.27% 193ms 0.72% VtkMeshWriter::WriteFiles 1ms 0.0037% 84.27% 189ms 0.7% CellPropertyCollection::HasProperty 0 0% 84.27% 188ms 0.7% Cell::HasCellProperty (inline) 3ms 0.011% 84.28% 184ms 0.69% DistributedBoxCollection::GetProcessOwningNode 98ms 0.36% 84.65% 183ms 0.68% _int_malloc 7ms 0.026% 84.67% 175ms 0.65% Cell::ReadyToDivide 175ms 0.65% 85.33% 175ms 0.65% __strcmp_evex 82ms 0.31% 85.63% 174ms 0.65% std::__move_median_to_first (inline) 0 0% 85.63% 169ms 0.63% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 85.63% 165ms 0.61% vtkStreamingDemandDrivenPipeline::Update 0 0% 85.63% 165ms 0.61% vtkXMLWriterBase::Write 164ms 0.61% 86.24% 164ms 0.61% NodeBasedCellPopulation::GetNode 0 0% 86.24% 163ms 0.61% vtkDemandDrivenPipeline::ProcessRequest 0 0% 86.24% 163ms 0.61% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 86.24% 162ms 0.6% vtkDemandDrivenPipeline::ExecuteData 27ms 0.1% 86.34% 161ms 0.6% std::__new_allocator::deallocate (inline) 0 0% 86.34% 161ms 0.6% vtkCompositeDataPipeline::ExecuteData 0 0% 86.34% 161ms 0.6% vtkExecutive::CallAlgorithm 0 0% 86.34% 161ms 0.6% vtkXMLUnstructuredDataWriter::ProcessRequest 2ms 0.0074% 86.35% 155ms 0.58% AbstractCellProperty::IsType (inline) 155ms 0.58% 86.93% 155ms 0.58% Node::CheckForNodeAttributes 17ms 0.063% 86.99% 155ms 0.58% std::__insertion_sort (inline) 0 0% 86.99% 151ms 0.56% std::_Rb_tree::_M_drop_node (inline) 141ms 0.53% 87.52% 142ms 0.53% std::__adjacent_find (inline) 0 0% 87.52% 142ms 0.53% std::__unique (inline) 0 0% 87.52% 142ms 0.53% std::unique (inline) 0 0% 87.52% 141ms 0.53% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 87.52% 141ms 0.53% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 87.52% 140ms 0.52% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 87.52% 138ms 0.51% NodesOnlyMesh::ResizeBoxCollection 138ms 0.51% 88.03% 138ms 0.51% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 5ms 0.019% 88.05% 137ms 0.51% NodesOnlyMesh::IsANodeCloseToDomainBoundary