File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 30303ms, 89.69% of 33785ms total Dropped 804 nodes (cum <= 168.93ms) flat flat% sum% cum cum% 0 0% 0% 33637ms 99.56% __libc_start_call_main 0 0% 0% 33637ms 99.56% __libc_start_main_impl 0 0% 0% 33637ms 99.56% _start 0 0% 0% 33620ms 99.51% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 33620ms 99.51% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 33620ms 99.51% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 33620ms 99.51% main 0 0% 0% 33582ms 99.40% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 33582ms 99.40% CxxTest::TestRunner::runTest (inline) 0 0% 0% 33582ms 99.40% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 33574ms 99.38% AbstractCellBasedSimulation::Solve 2ms 0.0059% 0.0059% 23678ms 70.08% OffLatticeSimulation::UpdateCellLocationsAndTopology 3ms 0.0089% 0.015% 18840ms 55.76% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.012% 0.027% 18681ms 55.29% AbstractNumericalMethod::ComputeForcesIncludingDamping 175ms 0.52% 0.54% 18043ms 53.41% AbstractTwoBodyInteractionForce::AddForceContribution 1408ms 4.17% 4.71% 15100ms 44.69% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4459ms 13.20% 17.91% 9724ms 28.78% std::_Rb_tree::_M_lower_bound (inline) 332ms 0.98% 18.89% 8872ms 26.26% std::_Rb_tree::find (inline) 0 0% 18.89% 8872ms 26.26% std::map::find (inline) 0 0% 18.89% 8752ms 25.90% AbstractCellBasedSimulation::UpdateCellPopulation 162ms 0.48% 19.37% 8648ms 25.60% NodesOnlyMesh::GetNodeOrHaloNode 484ms 1.43% 20.81% 8453ms 25.02% AbstractMesh::GetNode 340ms 1.01% 21.81% 7970ms 23.59% NodesOnlyMesh::SolveNodeMapping 0 0% 21.81% 7719ms 22.85% NodeBasedCellPopulation::Update 214ms 0.63% 22.44% 6152ms 18.21% boost::numeric::ublas::vector_assign (inline) 196ms 0.58% 23.03% 6050ms 17.91% boost::numeric::ublas::c_vector::c_vector (partial-inline) 8ms 0.024% 23.05% 5592ms 16.55% DistributedBoxCollection::CalculateInteriorNodePairs 5234ms 15.49% 38.54% 5234ms 15.49% std::_Rb_tree::_S_right (inline) 0 0% 38.54% 4560ms 13.50% OffLatticeSimulation::ApplyBoundaries 16ms 0.047% 38.59% 4524ms 13.39% NodeAttributes::RemoveDuplicateNeighbours 7ms 0.021% 38.61% 4212ms 12.47% std::__sort (inline) 0 0% 38.61% 4212ms 12.47% std::sort (inline) 4ms 0.012% 38.62% 3461ms 10.24% AbstractCellPopulation::Iterator::operator++ (inline) 63ms 0.19% 38.81% 3457ms 10.23% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 148ms 0.44% 39.25% 3430ms 10.15% AbstractCellPopulation::Iterator::IsRealCell (inline) 1091ms 3.23% 42.47% 3422ms 10.13% boost::numeric::ublas::indexing_vector_assign 28ms 0.083% 42.56% 2966ms 8.78% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 23ms 0.068% 42.63% 2368ms 7.01% PlaneBoundaryCondition::ImposeBoundaryCondition 35ms 0.1% 42.73% 2355ms 6.97% AbstractCellPopulation::GetLocationIndexUsingCell 180ms 0.53% 43.26% 2345ms 6.94% std::__introsort_loop 15ms 0.044% 43.31% 2192ms 6.49% PlaneBoundaryCondition::VerifyBoundaryCondition 0 0% 43.31% 2078ms 6.15% std::__unguarded_partition_pivot (inline) 1014ms 3.00% 46.31% 1862ms 5.51% std::__unguarded_partition (inline) 0 0% 46.31% 1855ms 5.49% std::__final_insertion_sort (inline) 143ms 0.42% 46.73% 1776ms 5.26% DistributedBoxCollection::AddPairsFromBox 223ms 0.66% 47.39% 1750ms 5.18% std::map::operator[] (partial-inline) 82ms 0.24% 47.63% 1677ms 4.96% std::__unguarded_insertion_sort (inline) 579ms 1.71% 49.35% 1634ms 4.84% std::__unguarded_linear_insert (inline) 1563ms 4.63% 53.97% 1563ms 4.63% boost::numeric::ublas::same_impl_ex 1474ms 4.36% 58.34% 1474ms 4.36% __gnu_cxx::__normal_iterator::operator-- (inline) 119ms 0.35% 58.69% 1471ms 4.35% AbstractMesh::GetVectorFromAtoB 0 0% 58.69% 1329ms 3.93% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 58.69% 1320ms 3.91% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1307ms 3.87% 62.56% 1307ms 3.87% boost::numeric::ublas::c_vector::operator() 0 0% 62.56% 1277ms 3.78% std::_Rb_tree::lower_bound (inline) 0 0% 62.56% 1277ms 3.78% std::map::lower_bound (inline) 5ms 0.015% 62.57% 1188ms 3.52% DistributedBoxCollection::CalculateBoundaryNodePairs 29ms 0.086% 62.66% 1099ms 3.25% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 62.66% 1079ms 3.19% NodeBasedCellPopulation::UpdateCellProcessLocation 182ms 0.54% 63.20% 1051ms 3.11% boost::numeric::ublas::detail::equals 272ms 0.81% 64.00% 956ms 2.83% NodeAttributes::AddAppliedForceContribution 129ms 0.38% 64.38% 926ms 2.74% boost::numeric::ublas::vector_binary::size (inline) 342ms 1.01% 65.40% 841ms 2.49% DistributedBoxCollection::CalculateContainingBox (partial-inline) 343ms 1.02% 66.41% 833ms 2.47% __GI___libc_free 0 0% 66.41% 815ms 2.41% boost::numeric::ublas::norm_inf (inline) 505ms 1.49% 67.91% 815ms 2.41% boost::numeric::ublas::vector_norm_inf::apply (inline) 20ms 0.059% 67.97% 810ms 2.40% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 79ms 0.23% 68.20% 758ms 2.24% std::__new_allocator::allocate (inline) 0 0% 68.20% 712ms 2.11% AbstractCellPopulation::WriteResultsToFiles 186ms 0.55% 68.75% 707ms 2.09% NodeAttributes::AddNeighbour 486ms 1.44% 70.19% 694ms 2.05% __dynamic_cast 0 0% 70.19% 684ms 2.02% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 70.19% 684ms 2.02% boost::numeric::ublas::c_vector::plus_assign (inline) 115ms 0.34% 70.53% 677ms 2.00% operator new 0 0% 70.53% 578ms 1.71% AbstractCentreBasedCellPopulation::GetDampingConstant 520ms 1.54% 72.07% 571ms 1.69% std::vector::push_back (inline) 188ms 0.56% 72.62% 561ms 1.66% __GI___libc_malloc 2ms 0.0059% 72.63% 536ms 1.59% AbstractCellBasedSimulation::DoCellBirth 0 0% 72.63% 514ms 1.52% boost::numeric::ublas::norm_2 (inline) 409ms 1.21% 73.84% 514ms 1.52% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 73.84% 496ms 1.47% AbstractCellBasedSimulation::DoCellRemoval (inline) 447ms 1.32% 75.16% 489ms 1.45% _int_free 27ms 0.08% 75.24% 484ms 1.43% std::_Rb_tree_const_iterator::operator++ (inline) 3ms 0.0089% 75.25% 475ms 1.41% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 9ms 0.027% 75.28% 471ms 1.39% CellPropertyCollection::GetPropertiesType (inline) 1ms 0.003% 75.28% 460ms 1.36% NodeBasedCellPopulation::WriteVtkResultsToFile 451ms 1.33% 76.62% 451ms 1.33% std::_Rb_tree_increment 24ms 0.071% 76.69% 420ms 1.24% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 76.69% 420ms 1.24% boost::numeric::ublas::vector::vector (inline) 33ms 0.098% 76.79% 416ms 1.23% boost::detail::shared_count::~shared_count (inline) 0 0% 76.79% 416ms 1.23% boost::shared_ptr::~shared_ptr (inline) 4ms 0.012% 76.80% 403ms 1.19% Cell::GetMutationState 364ms 1.08% 77.87% 373ms 1.10% boost::detail::sp_counted_base::release 0 0% 77.87% 362ms 1.07% std::allocator_traits::allocate (inline) 134ms 0.4% 78.27% 348ms 1.03% Node::GetRadius 345ms 1.02% 79.29% 345ms 1.02% Node::GetIndex 11ms 0.033% 79.33% 343ms 1.02% boost::numeric::ublas::vector_reference::operator() (inline) 2ms 0.0059% 79.33% 341ms 1.01% AbstractCellProperty::IsSubType (inline) 0 0% 79.33% 339ms 1.00% boost::numeric::ublas::inner_prod (inline) 1ms 0.003% 79.33% 337ms 1% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 19ms 0.056% 79.39% 336ms 0.99% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 79.39% 328ms 0.97% std::_Rb_tree::_M_create_node (inline) 324ms 0.96% 80.35% 324ms 0.96% [libchaste_cell_based.so] 0 0% 80.35% 310ms 0.92% NodesOnlyMesh::ReMesh 5ms 0.015% 80.36% 303ms 0.9% NodesOnlyMesh::UpdateNodeIndices 5ms 0.015% 80.38% 294ms 0.87% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 80.38% 292ms 0.86% std::_Rb_tree::_M_get_node (inline) 288ms 0.85% 81.23% 288ms 0.85% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 5ms 0.015% 81.25% 284ms 0.84% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 279ms 0.83% 82.07% 282ms 0.83% std::__adjacent_find (inline) 0 0% 82.07% 282ms 0.83% std::__unique (inline) 0 0% 82.07% 282ms 0.83% std::unique (inline) 0 0% 82.07% 280ms 0.83% NodesOnlyMesh::UpdateBoxCollection 115ms 0.34% 82.41% 269ms 0.8% boost::numeric::ublas::vector_inner_prod::apply (inline) 104ms 0.31% 82.72% 269ms 0.8% std::_Rb_tree::_M_erase (partial-inline) 10ms 0.03% 82.75% 268ms 0.79% DistributedBoxCollection::GetProcessOwningNode 113ms 0.33% 83.08% 267ms 0.79% std::__find_if (inline) 0 0% 83.08% 267ms 0.79% std::find_if (inline) 0 0% 83.08% 267ms 0.79% std::none_of (inline) 4ms 0.012% 83.10% 263ms 0.78% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 3ms 0.0089% 83.10% 259ms 0.77% AbstractCellPopulation::GetCellUsingLocationIndex 7ms 0.021% 83.13% 250ms 0.74% std::_Rb_tree::_M_emplace_hint_unique 0 0% 83.13% 247ms 0.73% NodesOnlyMesh::AddNodesToBoxes 0 0% 83.13% 247ms 0.73% boost::numeric::ublas::c_vector::assign (inline) 245ms 0.73% 83.85% 245ms 0.73% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 83.85% 229ms 0.68% boost::numeric::ublas::vector_binary::operator() (inline) 228ms 0.67% 84.53% 228ms 0.67% Node::CheckForNodeAttributes 0 0% 84.53% 221ms 0.65% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 84.53% 221ms 0.65% VtkMeshWriter::WriteFiles 127ms 0.38% 84.90% 221ms 0.65% _int_malloc 103ms 0.3% 85.21% 214ms 0.63% std::__move_median_to_first (inline) 204ms 0.6% 85.81% 204ms 0.6% NodeBasedCellPopulation::GetNode 204ms 0.6% 86.41% 204ms 0.6% boost::numeric::ublas::scalar_plus_assign::apply (inline) 93ms 0.28% 86.69% 201ms 0.59% Node::AddNeighbour 199ms 0.59% 87.28% 199ms 0.59% [libchaste_mesh.so] 0 0% 87.28% 197ms 0.58% vtkStreamingDemandDrivenPipeline::Update 0 0% 87.28% 197ms 0.58% vtkXMLWriterBase::Write 0 0% 87.28% 195ms 0.58% vtkDemandDrivenPipeline::ProcessRequest 0 0% 87.28% 194ms 0.57% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 87.28% 193ms 0.57% vtkDemandDrivenPipeline::ExecuteData 191ms 0.57% 87.84% 191ms 0.57% Node::rGetLocation 0 0% 87.84% 190ms 0.56% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 87.84% 190ms 0.56% vtkCompositeDataPipeline::ExecuteData 0 0% 87.84% 190ms 0.56% vtkExecutive::CallAlgorithm 0 0% 87.84% 190ms 0.56% vtkXMLUnstructuredDataWriter::ProcessRequest 33ms 0.098% 87.94% 189ms 0.56% std::__new_allocator::deallocate (inline) 186ms 0.55% 88.49% 186ms 0.55% __strcmp_avx2 123ms 0.36% 88.86% 178ms 0.53% Node::AddAppliedForceContribution 13ms 0.038% 88.89% 178ms 0.53% std::__insertion_sort (inline) 3ms 0.0089% 88.90% 177ms 0.52% std::_Rb_tree::_Rb_tree (partial-inline) 87ms 0.26% 89.16% 174ms 0.52% boost::shared_ptr::shared_ptr (inline) 0 0% 89.16% 172ms 0.51% Cell::HasCellProperty (inline) 1ms 0.003% 89.16% 171ms 0.51% CellPropertyCollection::HasProperty 11ms 0.033% 89.20% 170ms 0.5% std::_Rb_tree::_M_copy (inline) 168ms 0.5% 89.69% 169ms 0.5% Node::ConstructNodeAttributes (inline)