File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 28511ms, 87.69% of 32512ms total Dropped 770 nodes (cum <= 162.56ms) flat flat% sum% cum cum% 0 0% 0% 32359ms 99.53% __libc_start_call_main 0 0% 0% 32359ms 99.53% __libc_start_main_impl 0 0% 0% 32359ms 99.53% _start 0 0% 0% 32343ms 99.48% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 32343ms 99.48% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 32343ms 99.48% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 32343ms 99.48% main 0 0% 0% 32307ms 99.37% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 32307ms 99.37% CxxTest::TestRunner::runTest (inline) 0 0% 0% 32307ms 99.37% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 32300ms 99.35% AbstractCellBasedSimulation::Solve 1ms 0.0031% 0.0031% 22532ms 69.30% OffLatticeSimulation::UpdateCellLocationsAndTopology 3ms 0.0092% 0.012% 17771ms 54.66% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.031% 0.043% 17573ms 54.05% AbstractNumericalMethod::ComputeForcesIncludingDamping 256ms 0.79% 0.83% 17004ms 52.30% AbstractTwoBodyInteractionForce::AddForceContribution 1436ms 4.42% 5.25% 14228ms 43.76% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4352ms 13.39% 18.63% 9584ms 29.48% std::_Rb_tree::_M_lower_bound (inline) 336ms 1.03% 19.67% 8723ms 26.83% std::_Rb_tree::find (inline) 0 0% 19.67% 8722ms 26.83% std::map::find (inline) 0 0% 19.67% 8614ms 26.49% AbstractCellBasedSimulation::UpdateCellPopulation 172ms 0.53% 20.20% 8566ms 26.35% NodesOnlyMesh::GetNodeOrHaloNode 507ms 1.56% 21.76% 8396ms 25.82% AbstractMesh::GetNode 319ms 0.98% 22.74% 7892ms 24.27% NodesOnlyMesh::SolveNodeMapping 0 0% 22.74% 7595ms 23.36% NodeBasedCellPopulation::Update 10ms 0.031% 22.77% 5564ms 17.11% DistributedBoxCollection::CalculateInteriorNodePairs 232ms 0.71% 23.48% 5381ms 16.55% boost::numeric::ublas::vector_assign (inline) 147ms 0.45% 23.93% 5234ms 16.10% boost::numeric::ublas::c_vector::c_vector (partial-inline) 5197ms 15.98% 39.92% 5197ms 15.98% std::_Rb_tree::_S_right (inline) 0 0% 39.92% 4491ms 13.81% OffLatticeSimulation::ApplyBoundaries 14ms 0.043% 39.96% 4487ms 13.80% NodeAttributes::RemoveDuplicateNeighbours 8ms 0.025% 39.99% 4302ms 13.23% std::__sort (inline) 0 0% 39.99% 4302ms 13.23% std::sort (inline) 88ms 0.27% 40.26% 3471ms 10.68% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 3ms 0.0092% 40.27% 3464ms 10.65% AbstractCellPopulation::Iterator::operator++ (inline) 157ms 0.48% 40.75% 3437ms 10.57% AbstractCellPopulation::Iterator::IsRealCell (inline) 992ms 3.05% 43.80% 3137ms 9.65% boost::numeric::ublas::indexing_vector_assign 27ms 0.083% 43.88% 2952ms 9.08% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 181ms 0.56% 44.44% 2498ms 7.68% std::__introsort_loop 24ms 0.074% 44.51% 2325ms 7.15% PlaneBoundaryCondition::ImposeBoundaryCondition 43ms 0.13% 44.65% 2248ms 6.91% AbstractCellPopulation::GetLocationIndexUsingCell 3ms 0.0092% 44.65% 2244ms 6.90% std::__unguarded_partition_pivot (inline) 11ms 0.034% 44.69% 2166ms 6.66% PlaneBoundaryCondition::VerifyBoundaryCondition 1014ms 3.12% 47.81% 2015ms 6.20% std::__unguarded_partition (inline) 0 0% 47.81% 1795ms 5.52% std::__final_insertion_sort (inline) 169ms 0.52% 48.33% 1718ms 5.28% DistributedBoxCollection::AddPairsFromBox 193ms 0.59% 48.92% 1706ms 5.25% std::map::operator[] (partial-inline) 100ms 0.31% 49.23% 1613ms 4.96% std::__unguarded_insertion_sort (inline) 566ms 1.74% 50.97% 1552ms 4.77% std::__unguarded_linear_insert (inline) 1470ms 4.52% 55.49% 1470ms 4.52% __gnu_cxx::__normal_iterator::operator-- (inline) 1429ms 4.40% 59.89% 1429ms 4.40% boost::numeric::ublas::same_impl_ex 117ms 0.36% 60.25% 1333ms 4.10% AbstractMesh::GetVectorFromAtoB 0 0% 60.25% 1265ms 3.89% std::_Rb_tree::lower_bound (inline) 0 0% 60.25% 1265ms 3.89% std::map::lower_bound (inline) 0 0% 60.25% 1214ms 3.73% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 60.25% 1198ms 3.68% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1165ms 3.58% 63.83% 1165ms 3.58% boost::numeric::ublas::c_vector::operator() 0 0% 63.83% 1135ms 3.49% NodeBasedCellPopulation::UpdateCellProcessLocation 5ms 0.015% 63.84% 1093ms 3.36% DistributedBoxCollection::CalculateBoundaryNodePairs 14ms 0.043% 63.89% 968ms 2.98% boost::numeric::ublas::detail::expression_type_check (inline) 173ms 0.53% 64.42% 922ms 2.84% boost::numeric::ublas::detail::equals 248ms 0.76% 65.18% 852ms 2.62% NodeAttributes::AddAppliedForceContribution 89ms 0.27% 65.46% 841ms 2.59% boost::numeric::ublas::vector_binary::size (inline) 24ms 0.074% 65.53% 829ms 2.55% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 350ms 1.08% 66.61% 760ms 2.34% DistributedBoxCollection::CalculateContainingBox (partial-inline) 509ms 1.57% 68.17% 703ms 2.16% __dynamic_cast 0 0% 68.17% 702ms 2.16% boost::numeric::ublas::norm_inf (inline) 424ms 1.30% 69.48% 702ms 2.16% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 69.48% 689ms 2.12% AbstractCellPopulation::WriteResultsToFiles 169ms 0.52% 70.00% 684ms 2.10% NodeAttributes::AddNeighbour 68ms 0.21% 70.20% 671ms 2.06% std::__new_allocator::allocate (inline) 0 0% 70.20% 604ms 1.86% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 70.20% 604ms 1.86% boost::numeric::ublas::c_vector::plus_assign (inline) 110ms 0.34% 70.54% 603ms 1.85% operator new 3ms 0.0092% 70.55% 582ms 1.79% AbstractCellBasedSimulation::DoCellBirth 515ms 1.58% 72.14% 577ms 1.77% std::vector::push_back (inline) 168ms 0.52% 72.65% 543ms 1.67% __GI___libc_free 5ms 0.015% 72.67% 512ms 1.57% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 72.67% 512ms 1.57% boost::numeric::ublas::norm_2 (inline) 399ms 1.23% 73.90% 512ms 1.57% boost::numeric::ublas::vector_norm_2::apply (inline) 161ms 0.5% 74.39% 488ms 1.50% __GI___libc_malloc 27ms 0.083% 74.47% 468ms 1.44% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 74.47% 452ms 1.39% NodeBasedCellPopulation::WriteVtkResultsToFile 442ms 1.36% 75.83% 442ms 1.36% std::_Rb_tree_increment 0 0% 75.83% 437ms 1.34% AbstractCellBasedSimulation::DoCellRemoval (inline) 1ms 0.0031% 75.84% 425ms 1.31% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 400ms 1.23% 77.07% 400ms 1.23% Node::GetIndex 3ms 0.0092% 77.08% 397ms 1.22% CellPropertyCollection::GetPropertiesType (inline) 37ms 0.11% 77.19% 395ms 1.21% boost::detail::shared_count::~shared_count (inline) 0 0% 77.19% 395ms 1.21% boost::shared_ptr::~shared_ptr (inline) 332ms 1.02% 78.21% 375ms 1.15% _int_free 35ms 0.11% 78.32% 359ms 1.10% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 78.32% 359ms 1.10% boost::numeric::ublas::vector::vector (inline) 12ms 0.037% 78.36% 355ms 1.09% boost::numeric::ublas::vector_reference::operator() (inline) 350ms 1.08% 79.43% 352ms 1.08% boost::detail::sp_counted_base::release 7ms 0.022% 79.45% 347ms 1.07% Cell::GetMutationState 0 0% 79.45% 347ms 1.07% std::allocator_traits::allocate (inline) 339ms 1.04% 80.50% 339ms 1.04% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 128ms 0.39% 80.89% 319ms 0.98% Node::GetRadius 0 0% 80.89% 312ms 0.96% std::_Rb_tree::_M_create_node (inline) 134ms 0.41% 81.30% 311ms 0.96% std::_Rb_tree::_M_erase (partial-inline) 0 0% 81.30% 307ms 0.94% boost::numeric::ublas::inner_prod (inline) 0 0% 81.30% 306ms 0.94% NodesOnlyMesh::ReMesh 1ms 0.0031% 81.31% 303ms 0.93% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 18ms 0.055% 81.36% 302ms 0.93% boost::numeric::ublas::vector_scalar_binary::evaluate 300ms 0.92% 82.28% 300ms 0.92% __gnu_cxx::__normal_iterator::operator++ (inline) 5ms 0.015% 82.30% 299ms 0.92% NodesOnlyMesh::UpdateNodeIndices 1ms 0.0031% 82.30% 298ms 0.92% NodeBasedCellPopulation::UpdateMapsAfterRemesh 2ms 0.0062% 82.31% 289ms 0.89% AbstractCellProperty::IsSubType (inline) 0 0% 82.31% 288ms 0.89% boost::numeric::ublas::vector_binary::operator() (inline) 5ms 0.015% 82.32% 271ms 0.83% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 82.32% 271ms 0.83% std::_Rb_tree::_M_get_node (inline) 3ms 0.0092% 82.33% 270ms 0.83% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 4ms 0.012% 82.34% 265ms 0.82% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 82.34% 260ms 0.8% NodesOnlyMesh::UpdateBoxCollection 0 0% 82.34% 254ms 0.78% boost::numeric::ublas::c_vector::assign (inline) 3ms 0.0092% 82.35% 252ms 0.78% DistributedBoxCollection::GetProcessOwningNode 3ms 0.0092% 82.36% 248ms 0.76% std::_Rb_tree::_M_emplace_hint_unique 246ms 0.76% 83.12% 246ms 0.76% [libchaste_cell_based.so] 91ms 0.28% 83.40% 233ms 0.72% boost::numeric::ublas::vector_inner_prod::apply (inline) 227ms 0.7% 84.10% 229ms 0.7% NodeBasedCellPopulation::GetNode 0 0% 84.10% 218ms 0.67% NodesOnlyMesh::AddNodesToBoxes 97ms 0.3% 84.40% 218ms 0.67% std::__move_median_to_first (inline) 0 0% 84.40% 213ms 0.66% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 132ms 0.41% 84.80% 213ms 0.66% _int_malloc 0 0% 84.80% 212ms 0.65% VtkMeshWriter::WriteFiles 205ms 0.63% 85.43% 205ms 0.63% Node::CheckForNodeAttributes 65ms 0.2% 85.63% 203ms 0.62% std::__find_if (inline) 0 0% 85.63% 203ms 0.62% std::find_if (inline) 0 0% 85.63% 203ms 0.62% std::none_of (inline) 0 0% 85.63% 202ms 0.62% NodesOnlyMesh::ResizeBoxCollection 22ms 0.068% 85.70% 201ms 0.62% NodesOnlyMesh::IsANodeCloseToDomainBoundary 201ms 0.62% 86.32% 201ms 0.62% [libchaste_mesh.so] 41ms 0.13% 86.45% 200ms 0.62% std::__new_allocator::deallocate (inline) 0 0% 86.45% 194ms 0.6% vtkDemandDrivenPipeline::ProcessRequest 0 0% 86.45% 194ms 0.6% vtkStreamingDemandDrivenPipeline::Update 0 0% 86.45% 194ms 0.6% vtkXMLWriterBase::Write 0 0% 86.45% 191ms 0.59% vtkCompositeDataPipeline::ExecuteData 0 0% 86.45% 191ms 0.59% vtkDemandDrivenPipeline::ExecuteData 0 0% 86.45% 191ms 0.59% vtkExecutive::CallAlgorithm 0 0% 86.45% 191ms 0.59% vtkStreamingDemandDrivenPipeline::ProcessRequest 2ms 0.0062% 86.45% 190ms 0.58% vtkXMLUnstructuredDataWriter::ProcessRequest 16ms 0.049% 86.50% 182ms 0.56% std::__insertion_sort (inline) 5ms 0.015% 86.52% 177ms 0.54% CellPropertyCollection::HasProperty 0 0% 86.52% 176ms 0.54% Cell::HasCellProperty (inline) 0 0% 86.52% 174ms 0.54% std::_Rb_tree::clear (inline) 111ms 0.34% 86.86% 173ms 0.53% Node::AddAppliedForceContribution 0 0% 86.86% 173ms 0.53% std::_Rb_tree::_Alloc_node::operator() (inline) 89ms 0.27% 87.13% 170ms 0.52% boost::shared_ptr::shared_ptr (inline) 169ms 0.52% 87.65% 169ms 0.52% __strcmp_avx2 7ms 0.022% 87.67% 169ms 0.52% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 87.67% 166ms 0.51% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 87.67% 166ms 0.51% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 87.67% 165ms 0.51% std::_Rb_tree::_M_drop_node (inline) 7ms 0.022% 87.69% 164ms 0.5% Cell::ReadyToDivide