File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 30540ms, 89.63% of 34073ms total Dropped 826 nodes (cum <= 170.37ms) flat flat% sum% cum cum% 0 0% 0% 33927ms 99.57% __libc_start_call_main 0 0% 0% 33927ms 99.57% __libc_start_main_impl 0 0% 0% 33927ms 99.57% _start 0 0% 0% 33911ms 99.52% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 33911ms 99.52% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 33911ms 99.52% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 33911ms 99.52% main 0 0% 0% 33876ms 99.42% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 33876ms 99.42% CxxTest::TestRunner::runTest (inline) 0 0% 0% 33876ms 99.42% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 33867ms 99.40% AbstractCellBasedSimulation::Solve 3ms 0.0088% 0.0088% 23691ms 69.53% OffLatticeSimulation::UpdateCellLocationsAndTopology 5ms 0.015% 0.023% 18924ms 55.54% ForwardEulerNumericalMethod::UpdateAllNodePositions 14ms 0.041% 0.065% 18745ms 55.01% AbstractNumericalMethod::ComputeForcesIncludingDamping 181ms 0.53% 0.6% 17974ms 52.75% AbstractTwoBodyInteractionForce::AddForceContribution 1539ms 4.52% 5.11% 15118ms 44.37% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4452ms 13.07% 18.18% 9173ms 26.92% std::_Rb_tree::_M_lower_bound (inline) 0 0% 18.18% 8976ms 26.34% AbstractCellBasedSimulation::UpdateCellPopulation 362ms 1.06% 19.24% 8305ms 24.37% std::_Rb_tree::find (inline) 0 0% 19.24% 8304ms 24.37% std::map::find (inline) 163ms 0.48% 19.72% 8089ms 23.74% NodesOnlyMesh::GetNodeOrHaloNode 0 0% 19.72% 7910ms 23.21% NodeBasedCellPopulation::Update 480ms 1.41% 21.13% 7903ms 23.19% AbstractMesh::GetNode 339ms 0.99% 22.12% 7429ms 21.80% NodesOnlyMesh::SolveNodeMapping 220ms 0.65% 22.77% 6504ms 19.09% boost::numeric::ublas::vector_assign (inline) 194ms 0.57% 23.34% 6311ms 18.52% boost::numeric::ublas::c_vector::c_vector (partial-inline) 5ms 0.015% 23.35% 5894ms 17.30% DistributedBoxCollection::CalculateInteriorNodePairs 4685ms 13.75% 37.10% 4685ms 13.75% std::_Rb_tree::_S_right (inline) 17ms 0.05% 37.15% 4500ms 13.21% NodeAttributes::RemoveDuplicateNeighbours 0 0% 37.15% 4461ms 13.09% OffLatticeSimulation::ApplyBoundaries 4ms 0.012% 37.16% 4321ms 12.68% std::__sort (inline) 0 0% 37.16% 4321ms 12.68% std::sort (inline) 1174ms 3.45% 40.61% 3653ms 10.72% boost::numeric::ublas::indexing_vector_assign 3ms 0.0088% 40.62% 3395ms 9.96% AbstractCellPopulation::Iterator::operator++ (inline) 69ms 0.2% 40.82% 3372ms 9.90% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 185ms 0.54% 41.36% 3366ms 9.88% AbstractCellPopulation::Iterator::IsRealCell (inline) 23ms 0.068% 41.43% 2855ms 8.38% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 186ms 0.55% 41.98% 2507ms 7.36% std::__introsort_loop 37ms 0.11% 42.09% 2338ms 6.86% PlaneBoundaryCondition::ImposeBoundaryCondition 40ms 0.12% 42.20% 2335ms 6.85% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 42.20% 2248ms 6.60% std::__unguarded_partition_pivot (inline) 19ms 0.056% 42.26% 2123ms 6.23% PlaneBoundaryCondition::VerifyBoundaryCondition 1047ms 3.07% 45.33% 2011ms 5.90% std::__unguarded_partition (inline) 173ms 0.51% 45.84% 2003ms 5.88% DistributedBoxCollection::AddPairsFromBox 0 0% 45.84% 1810ms 5.31% std::__final_insertion_sort (inline) 208ms 0.61% 46.45% 1762ms 5.17% std::map::operator[] (partial-inline) 1707ms 5.01% 51.46% 1707ms 5.01% boost::numeric::ublas::same_impl_ex 83ms 0.24% 51.70% 1623ms 4.76% std::__unguarded_insertion_sort (inline) 591ms 1.73% 53.44% 1586ms 4.65% std::__unguarded_linear_insert (inline) 115ms 0.34% 53.78% 1577ms 4.63% AbstractMesh::GetVectorFromAtoB 1458ms 4.28% 58.05% 1458ms 4.28% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 58.05% 1311ms 3.85% std::_Rb_tree::lower_bound (inline) 0 0% 58.05% 1311ms 3.85% std::map::lower_bound (inline) 0 0% 58.05% 1256ms 3.69% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 58.05% 1240ms 3.64% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1ms 0.0029% 58.06% 1132ms 3.32% NodeBasedCellPopulation::UpdateCellProcessLocation 24ms 0.07% 58.13% 1122ms 3.29% boost::numeric::ublas::detail::expression_type_check (inline) 1ms 0.0029% 58.13% 1092ms 3.20% DistributedBoxCollection::CalculateBoundaryNodePairs 1091ms 3.20% 61.33% 1091ms 3.20% boost::numeric::ublas::c_vector::operator() 224ms 0.66% 61.99% 1077ms 3.16% boost::numeric::ublas::detail::equals 166ms 0.49% 62.48% 1002ms 2.94% boost::numeric::ublas::vector_binary::size (inline) 199ms 0.58% 63.06% 928ms 2.72% NodeAttributes::AddAppliedForceContribution 413ms 1.21% 64.27% 843ms 2.47% DistributedBoxCollection::CalculateContainingBox (partial-inline) 388ms 1.14% 65.41% 843ms 2.47% __GI___libc_free 64ms 0.19% 65.60% 830ms 2.44% std::__new_allocator::allocate (inline) 0 0% 65.60% 807ms 2.37% boost::numeric::ublas::norm_inf (inline) 468ms 1.37% 66.97% 807ms 2.37% boost::numeric::ublas::vector_norm_inf::apply (inline) 17ms 0.05% 67.02% 780ms 2.29% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 555ms 1.63% 68.65% 774ms 2.27% __dynamic_cast 97ms 0.28% 68.94% 768ms 2.25% operator new 0 0% 68.94% 732ms 2.15% AbstractCellPopulation::WriteResultsToFiles 0 0% 68.94% 729ms 2.14% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 68.94% 729ms 2.14% boost::numeric::ublas::c_vector::plus_assign (inline) 3ms 0.0088% 68.95% 703ms 2.06% AbstractCentreBasedCellPopulation::GetDampingConstant 166ms 0.49% 69.43% 700ms 2.05% NodeAttributes::AddNeighbour 248ms 0.73% 70.16% 668ms 1.96% __GI___libc_malloc 37ms 0.11% 70.27% 662ms 1.94% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.0059% 70.28% 627ms 1.84% AbstractCellBasedSimulation::DoCellBirth 623ms 1.83% 72.10% 623ms 1.83% std::_Rb_tree_increment 532ms 1.56% 73.67% 606ms 1.78% std::vector::push_back (inline) 9ms 0.026% 73.69% 572ms 1.68% CellPropertyCollection::GetPropertiesType (inline) 19ms 0.056% 73.75% 496ms 1.46% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 73.75% 496ms 1.46% boost::numeric::ublas::vector::vector (inline) 2ms 0.0059% 73.75% 475ms 1.39% NodeBasedCellPopulation::WriteVtkResultsToFile 3ms 0.0088% 73.76% 470ms 1.38% Cell::GetMutationState 0 0% 73.76% 449ms 1.32% boost::numeric::ublas::norm_2 (inline) 351ms 1.03% 74.79% 449ms 1.32% boost::numeric::ublas::vector_norm_2::apply (inline) 401ms 1.18% 75.97% 447ms 1.31% _int_free 0 0% 75.97% 439ms 1.29% AbstractCellBasedSimulation::DoCellRemoval (inline) 7ms 0.021% 75.99% 428ms 1.26% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 2ms 0.0059% 76.00% 367ms 1.08% AbstractCellProperty::IsSubType (inline) 0 0% 76.00% 353ms 1.04% std::allocator_traits::allocate (inline) 352ms 1.03% 77.03% 352ms 1.03% Node::GetIndex 123ms 0.36% 77.39% 350ms 1.03% Node::GetRadius 36ms 0.11% 77.50% 349ms 1.02% boost::detail::shared_count::~shared_count (inline) 0 0% 77.50% 349ms 1.02% boost::shared_ptr::~shared_ptr (inline) 3ms 0.0088% 77.50% 323ms 0.95% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 321ms 0.94% 78.45% 321ms 0.94% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 5ms 0.015% 78.46% 320ms 0.94% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 78.46% 311ms 0.91% std::_Rb_tree::_M_create_node (inline) 308ms 0.9% 79.36% 308ms 0.9% __gnu_cxx::__normal_iterator::operator++ (inline) 1ms 0.0029% 79.37% 307ms 0.9% NodeBasedCellPopulation::UpdateMapsAfterRemesh 301ms 0.88% 80.25% 306ms 0.9% boost::detail::sp_counted_base::release 2ms 0.0059% 80.26% 301ms 0.88% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 91ms 0.27% 80.52% 300ms 0.88% Node::AddNeighbour 0 0% 80.52% 289ms 0.85% boost::numeric::ublas::inner_prod (inline) 2ms 0.0059% 80.53% 288ms 0.85% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 22ms 0.065% 80.59% 286ms 0.84% boost::numeric::ublas::vector_scalar_binary::evaluate 4ms 0.012% 80.61% 284ms 0.83% DistributedBoxCollection::GetProcessOwningNode 0 0% 80.61% 282ms 0.83% NodesOnlyMesh::ReMesh 123ms 0.36% 80.97% 278ms 0.82% std::_Rb_tree::_M_erase (partial-inline) 2ms 0.0059% 80.97% 270ms 0.79% NodesOnlyMesh::UpdateNodeIndices 0 0% 80.97% 270ms 0.79% std::_Rb_tree::_M_get_node (inline) 0 0% 80.97% 265ms 0.78% boost::numeric::ublas::c_vector::assign (inline) 256ms 0.75% 81.72% 256ms 0.75% [libchaste_cell_based.so] 1ms 0.0029% 81.73% 252ms 0.74% NodesOnlyMesh::UpdateBoxCollection 250ms 0.73% 82.46% 251ms 0.74% Node::ConstructNodeAttributes (inline) 8ms 0.023% 82.48% 249ms 0.73% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 82.48% 245ms 0.72% Cell::HasCellProperty (inline) 5ms 0.015% 82.50% 245ms 0.72% CellPropertyCollection::HasProperty 11ms 0.032% 82.53% 242ms 0.71% std::_Rb_tree::_M_emplace_hint_unique 239ms 0.7% 83.23% 239ms 0.7% Node::CheckForNodeAttributes 5ms 0.015% 83.25% 235ms 0.69% Cell::ReadyToDivide 98ms 0.29% 83.54% 235ms 0.69% std::__move_median_to_first (inline) 0 0% 83.54% 233ms 0.68% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 233ms 0.68% 84.22% 233ms 0.68% Node::rGetLocation 0 0% 84.22% 233ms 0.68% VtkMeshWriter::WriteFiles 228ms 0.67% 84.89% 228ms 0.67% NodeBasedCellPopulation::GetNode 90ms 0.26% 85.15% 223ms 0.65% std::__find_if (inline) 0 0% 85.15% 223ms 0.65% std::find_if (inline) 0 0% 85.15% 223ms 0.65% std::none_of (inline) 135ms 0.4% 85.55% 222ms 0.65% _int_malloc 111ms 0.33% 85.87% 218ms 0.64% boost::numeric::ublas::vector_inner_prod::apply (inline) 1ms 0.0029% 85.88% 209ms 0.61% NodesOnlyMesh::AddNodesToBoxes 209ms 0.61% 86.49% 209ms 0.61% [libchaste_mesh.so] 0 0% 86.49% 205ms 0.6% vtkDemandDrivenPipeline::ProcessRequest 0 0% 86.49% 205ms 0.6% vtkStreamingDemandDrivenPipeline::Update 0 0% 86.49% 205ms 0.6% vtkXMLWriterBase::Write 163ms 0.48% 86.97% 204ms 0.6% Node::AddAppliedForceContribution 204ms 0.6% 87.57% 204ms 0.6% __strcmp_avx2 203ms 0.6% 88.16% 203ms 0.6% boost::numeric::ublas::c_vector::size (inline) 0 0% 88.16% 203ms 0.6% vtkDemandDrivenPipeline::ExecuteData 0 0% 88.16% 203ms 0.6% vtkExecutive::CallAlgorithm 0 0% 88.16% 203ms 0.6% vtkStreamingDemandDrivenPipeline::ProcessRequest 1ms 0.0029% 88.17% 202ms 0.59% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 88.17% 202ms 0.59% vtkCompositeDataPipeline::ExecuteData 0 0% 88.17% 202ms 0.59% vtkXMLUnstructuredDataWriter::ProcessRequest 200ms 0.59% 88.75% 200ms 0.59% boost::numeric::ublas::scalar_plus_assign::apply (inline) 22ms 0.065% 88.82% 198ms 0.58% std::_Rb_tree::_M_copy (inline) 0 0% 88.82% 196ms 0.58% tcache_get (inline) 196ms 0.58% 89.39% 196ms 0.58% tcache_get_n (inline) 0 0% 89.39% 194ms 0.57% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 89.39% 188ms 0.55% boost::numeric::ublas::vector_reference::size (inline) 17ms 0.05% 89.44% 187ms 0.55% std::__insertion_sort (inline) 28ms 0.082% 89.53% 183ms 0.54% std::__new_allocator::deallocate (inline) 23ms 0.068% 89.59% 176ms 0.52% std::_Rb_tree::_M_clone_node (inline) 0 0% 89.59% 175ms 0.51% NodesOnlyMesh::ResizeBoxCollection 2ms 0.0059% 89.60% 174ms 0.51% AbstractCellProperty::IsType (inline) 11ms 0.032% 89.63% 174ms 0.51% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 89.63% 171ms 0.5% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 89.63% 171ms 0.5% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData