File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 30128ms, 89.46% of 33676ms total Dropped 811 nodes (cum <= 168.38ms) flat flat% sum% cum cum% 0 0% 0% 33523ms 99.55% __libc_start_call_main 0 0% 0% 33523ms 99.55% __libc_start_main_impl 0 0% 0% 33523ms 99.55% _start 0 0% 0% 33506ms 99.50% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 33506ms 99.50% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 33506ms 99.50% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 33506ms 99.50% main 0 0% 0% 33469ms 99.39% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 33469ms 99.39% CxxTest::TestRunner::runTest (inline) 0 0% 0% 33469ms 99.39% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.003% 0.003% 33462ms 99.36% AbstractCellBasedSimulation::Solve 3ms 0.0089% 0.012% 23616ms 70.13% OffLatticeSimulation::UpdateCellLocationsAndTopology 6ms 0.018% 0.03% 18886ms 56.08% ForwardEulerNumericalMethod::UpdateAllNodePositions 9ms 0.027% 0.056% 18688ms 55.49% AbstractNumericalMethod::ComputeForcesIncludingDamping 157ms 0.47% 0.52% 18097ms 53.74% AbstractTwoBodyInteractionForce::AddForceContribution 1447ms 4.30% 4.82% 15310ms 45.46% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4348ms 12.91% 17.73% 9608ms 28.53% std::_Rb_tree::_M_lower_bound (inline) 331ms 0.98% 18.71% 8705ms 25.85% std::_Rb_tree::find (inline) 0 0% 18.71% 8705ms 25.85% std::map::find (inline) 0 0% 18.71% 8634ms 25.64% AbstractCellBasedSimulation::UpdateCellPopulation 146ms 0.43% 19.15% 8429ms 25.03% NodesOnlyMesh::GetNodeOrHaloNode 499ms 1.48% 20.63% 8265ms 24.54% AbstractMesh::GetNode 274ms 0.81% 21.44% 7769ms 23.07% NodesOnlyMesh::SolveNodeMapping 0 0% 21.44% 7628ms 22.65% NodeBasedCellPopulation::Update 180ms 0.53% 21.98% 6391ms 18.98% boost::numeric::ublas::vector_assign (inline) 173ms 0.51% 22.49% 6215ms 18.46% boost::numeric::ublas::c_vector::c_vector (partial-inline) 8ms 0.024% 22.51% 5630ms 16.72% DistributedBoxCollection::CalculateInteriorNodePairs 5236ms 15.55% 38.06% 5236ms 15.55% std::_Rb_tree::_S_right (inline) 18ms 0.053% 38.12% 4467ms 13.26% NodeAttributes::RemoveDuplicateNeighbours 1ms 0.003% 38.12% 4463ms 13.25% OffLatticeSimulation::ApplyBoundaries 9ms 0.027% 38.15% 4306ms 12.79% std::__sort (inline) 0 0% 38.15% 4306ms 12.79% std::sort (inline) 1164ms 3.46% 41.60% 3659ms 10.87% boost::numeric::ublas::indexing_vector_assign 2ms 0.0059% 41.61% 3373ms 10.02% AbstractCellPopulation::Iterator::operator++ (inline) 74ms 0.22% 41.83% 3366ms 10.00% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 180ms 0.53% 42.36% 3364ms 9.99% AbstractCellPopulation::Iterator::IsRealCell (inline) 33ms 0.098% 42.46% 2887ms 8.57% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 195ms 0.58% 43.04% 2409ms 7.15% std::__introsort_loop 48ms 0.14% 43.18% 2335ms 6.93% AbstractCellPopulation::GetLocationIndexUsingCell 28ms 0.083% 43.27% 2333ms 6.93% PlaneBoundaryCondition::ImposeBoundaryCondition 1ms 0.003% 43.27% 2134ms 6.34% std::__unguarded_partition_pivot (inline) 20ms 0.059% 43.33% 2129ms 6.32% PlaneBoundaryCondition::VerifyBoundaryCondition 986ms 2.93% 46.26% 1941ms 5.76% std::__unguarded_partition (inline) 1ms 0.003% 46.26% 1886ms 5.60% std::__final_insertion_sort (inline) 154ms 0.46% 46.72% 1778ms 5.28% DistributedBoxCollection::AddPairsFromBox 212ms 0.63% 47.35% 1750ms 5.20% std::map::operator[] (partial-inline) 1673ms 4.97% 52.31% 1673ms 4.97% boost::numeric::ublas::same_impl_ex 89ms 0.26% 52.58% 1668ms 4.95% std::__unguarded_insertion_sort (inline) 616ms 1.83% 54.41% 1652ms 4.91% std::__unguarded_linear_insert (inline) 145ms 0.43% 54.84% 1620ms 4.81% AbstractMesh::GetVectorFromAtoB 1457ms 4.33% 59.16% 1457ms 4.33% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 59.16% 1318ms 3.91% std::_Rb_tree::lower_bound (inline) 0 0% 59.16% 1318ms 3.91% std::map::lower_bound (inline) 0 0% 59.16% 1203ms 3.57% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 59.16% 1186ms 3.52% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 59.16% 1169ms 3.47% NodeBasedCellPopulation::UpdateCellProcessLocation 1151ms 3.42% 62.58% 1151ms 3.42% boost::numeric::ublas::c_vector::operator() 21ms 0.062% 62.64% 1075ms 3.19% boost::numeric::ublas::detail::expression_type_check (inline) 157ms 0.47% 63.11% 1056ms 3.14% boost::numeric::ublas::vector_binary::size (inline) 9ms 0.027% 63.14% 1052ms 3.12% DistributedBoxCollection::CalculateBoundaryNodePairs 211ms 0.63% 63.76% 1031ms 3.06% boost::numeric::ublas::detail::equals 224ms 0.67% 64.43% 920ms 2.73% NodeAttributes::AddAppliedForceContribution 70ms 0.21% 64.64% 841ms 2.50% std::__new_allocator::allocate (inline) 264ms 0.78% 65.42% 817ms 2.43% __GI___libc_free 17ms 0.05% 65.47% 789ms 2.34% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 90ms 0.27% 65.74% 776ms 2.30% operator new 0 0% 65.74% 775ms 2.30% boost::numeric::ublas::norm_inf (inline) 445ms 1.32% 67.06% 775ms 2.30% boost::numeric::ublas::vector_norm_inf::apply (inline) 353ms 1.05% 68.11% 774ms 2.30% DistributedBoxCollection::CalculateContainingBox (partial-inline) 217ms 0.64% 68.75% 745ms 2.21% NodeAttributes::AddNeighbour 0 0% 68.75% 720ms 2.14% AbstractCellPopulation::WriteResultsToFiles 515ms 1.53% 70.28% 719ms 2.14% __dynamic_cast 0 0% 70.28% 696ms 2.07% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 70.28% 696ms 2.07% boost::numeric::ublas::c_vector::plus_assign (inline) 246ms 0.73% 71.01% 683ms 2.03% __GI___libc_malloc 2ms 0.0059% 71.02% 596ms 1.77% AbstractCellBasedSimulation::DoCellBirth 525ms 1.56% 72.58% 582ms 1.73% std::vector::push_back (inline) 512ms 1.52% 74.10% 546ms 1.62% _int_free 1ms 0.003% 74.10% 534ms 1.59% AbstractCentreBasedCellPopulation::GetDampingConstant 28ms 0.083% 74.18% 503ms 1.49% std::_Rb_tree_const_iterator::operator++ (inline) 10ms 0.03% 74.21% 485ms 1.44% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 74.21% 485ms 1.44% boost::numeric::ublas::vector::vector (inline) 475ms 1.41% 75.62% 475ms 1.41% std::_Rb_tree_increment 1ms 0.003% 75.63% 472ms 1.40% NodeBasedCellPopulation::WriteVtkResultsToFile 8ms 0.024% 75.65% 433ms 1.29% CellPropertyCollection::GetPropertiesType (inline) 0 0% 75.65% 428ms 1.27% boost::numeric::ublas::norm_2 (inline) 357ms 1.06% 76.71% 428ms 1.27% boost::numeric::ublas::vector_norm_2::apply (inline) 413ms 1.23% 77.94% 413ms 1.23% Node::GetIndex 0 0% 77.94% 409ms 1.21% AbstractCellBasedSimulation::DoCellRemoval (inline) 4ms 0.012% 77.95% 401ms 1.19% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 31ms 0.092% 78.04% 377ms 1.12% boost::detail::shared_count::~shared_count (inline) 0 0% 78.04% 377ms 1.12% boost::shared_ptr::~shared_ptr (inline) 0 0% 78.04% 366ms 1.09% std::allocator_traits::allocate (inline) 1ms 0.003% 78.04% 364ms 1.08% Cell::GetMutationState 338ms 1.00% 79.05% 341ms 1.01% boost::detail::sp_counted_base::release 112ms 0.33% 79.38% 340ms 1.01% Node::GetRadius 0 0% 79.38% 317ms 0.94% std::_Rb_tree::_M_create_node (inline) 2ms 0.0059% 79.39% 316ms 0.94% AbstractCellProperty::IsSubType (inline) 20ms 0.059% 79.45% 314ms 0.93% boost::numeric::ublas::vector_reference::operator() (inline) 310ms 0.92% 80.37% 310ms 0.92% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 80.37% 302ms 0.9% boost::numeric::ublas::inner_prod (inline) 4ms 0.012% 80.38% 301ms 0.89% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 80.38% 300ms 0.89% NodesOnlyMesh::ReMesh 11ms 0.033% 80.41% 300ms 0.89% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 80.41% 300ms 0.89% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 2ms 0.0059% 80.42% 292ms 0.87% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 7ms 0.021% 80.44% 289ms 0.86% NodesOnlyMesh::UpdateNodeIndices 0 0% 80.44% 283ms 0.84% std::_Rb_tree::_M_get_node (inline) 279ms 0.83% 81.27% 279ms 0.83% __gnu_cxx::__normal_iterator::operator++ (inline) 7ms 0.021% 81.29% 275ms 0.82% DistributedBoxCollection::GetProcessOwningNode 3ms 0.0089% 81.30% 270ms 0.8% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 5ms 0.015% 81.31% 265ms 0.79% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 81.31% 262ms 0.78% NodesOnlyMesh::UpdateBoxCollection 250ms 0.74% 82.05% 250ms 0.74% [libchaste_cell_based.so] 105ms 0.31% 82.36% 248ms 0.74% std::_Rb_tree::_M_erase (partial-inline) 242ms 0.72% 83.08% 242ms 0.72% Node::CheckForNodeAttributes 79ms 0.23% 83.32% 239ms 0.71% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 83.32% 236ms 0.7% boost::numeric::ublas::c_vector::assign (inline) 232ms 0.69% 84.01% 232ms 0.69% Node::rGetLocation 230ms 0.68% 84.69% 230ms 0.68% NodeBasedCellPopulation::GetNode 135ms 0.4% 85.09% 229ms 0.68% _int_malloc 0 0% 85.09% 228ms 0.68% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 85.09% 228ms 0.68% VtkMeshWriter::WriteFiles 1ms 0.003% 85.09% 226ms 0.67% NodesOnlyMesh::AddNodesToBoxes 226ms 0.67% 85.76% 226ms 0.67% boost::numeric::ublas::c_vector::size (inline) 224ms 0.67% 86.43% 224ms 0.67% boost::numeric::ublas::scalar_plus_assign::apply (inline) 114ms 0.34% 86.77% 221ms 0.66% std::__find_if (inline) 0 0% 86.77% 221ms 0.66% std::find_if (inline) 0 0% 86.77% 221ms 0.66% std::none_of (inline) 4ms 0.012% 86.78% 220ms 0.65% std::_Rb_tree::_M_emplace_hint_unique 0 0% 86.78% 218ms 0.65% boost::numeric::ublas::vector_binary::operator() (inline) 25ms 0.074% 86.85% 217ms 0.64% std::__insertion_sort (inline) 0 0% 86.85% 214ms 0.64% NodesOnlyMesh::ResizeBoxCollection 6ms 0.018% 86.87% 213ms 0.63% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 86.87% 213ms 0.63% boost::numeric::ublas::vector_reference::size (inline) 0 0% 86.87% 207ms 0.61% tcache_get (inline) 207ms 0.61% 87.49% 207ms 0.61% tcache_get_n (inline) 5ms 0.015% 87.50% 198ms 0.59% CellPropertyCollection::HasProperty 0 0% 87.50% 198ms 0.59% vtkDemandDrivenPipeline::ProcessRequest 0 0% 87.50% 198ms 0.59% vtkStreamingDemandDrivenPipeline::Update 0 0% 87.50% 198ms 0.59% vtkXMLWriterBase::Write 0 0% 87.50% 196ms 0.58% Cell::HasCellProperty (inline) 0 0% 87.50% 196ms 0.58% vtkDemandDrivenPipeline::ExecuteData 0 0% 87.50% 196ms 0.58% vtkExecutive::CallAlgorithm 0 0% 87.50% 196ms 0.58% vtkStreamingDemandDrivenPipeline::ProcessRequest 195ms 0.58% 88.08% 195ms 0.58% [libchaste_mesh.so] 195ms 0.58% 88.66% 195ms 0.58% __strcmp_avx2 0 0% 88.66% 195ms 0.58% vtkCompositeDataPipeline::ExecuteData 0 0% 88.66% 195ms 0.58% vtkXMLUnstructuredDataWriter::ProcessRequest 89ms 0.26% 88.92% 191ms 0.57% std::__move_median_to_first (inline) 5ms 0.015% 88.94% 185ms 0.55% Cell::ReadyToDivide 0 0% 88.94% 183ms 0.54% std::_Rb_tree::_Alloc_node::operator() (inline) 36ms 0.11% 89.05% 182ms 0.54% std::__new_allocator::deallocate (inline) 138ms 0.41% 89.46% 180ms 0.53% Node::AddAppliedForceContribution 3ms 0.0089% 89.46% 175ms 0.52% std::_Rb_tree::_Rb_tree (partial-inline)