File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 22879ms, 90.45% of 25295ms total Dropped 809 nodes (cum <= 126.47ms) flat flat% sum% cum cum% 0 0% 0% 25225ms 99.72% __libc_start_call_main 0 0% 0% 25225ms 99.72% __libc_start_main_impl 0 0% 0% 25225ms 99.72% _start 0 0% 0% 25207ms 99.65% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 25207ms 99.65% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 25207ms 99.65% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 25207ms 99.65% main 0 0% 0% 25173ms 99.52% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 25173ms 99.52% CxxTest::TestRunner::runTest (inline) 0 0% 0% 25173ms 99.52% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.004% 0.004% 25164ms 99.48% AbstractCellBasedSimulation::Solve 0 0% 0.004% 14324ms 56.63% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.004% 9650ms 38.15% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.004% 8450ms 33.41% NodeBasedCellPopulation::Update 5ms 0.02% 0.024% 8153ms 32.23% ForwardEulerNumericalMethod::UpdateAllNodePositions 5ms 0.02% 0.043% 7984ms 31.56% AbstractNumericalMethod::ComputeForcesIncludingDamping 1007ms 3.98% 4.02% 7402ms 29.26% RepulsionForce::AddForceContribution (partial-inline) 6ms 0.024% 4.05% 6409ms 25.34% DistributedBoxCollection::CalculateInteriorNodePairs 0 0% 4.05% 5856ms 23.15% OffLatticeSimulation::ApplyBoundaries 2510ms 9.92% 13.97% 5581ms 22.06% std::_Rb_tree::_M_lower_bound (inline) 12ms 0.047% 14.02% 5123ms 20.25% NodeAttributes::RemoveDuplicateNeighbours 1ms 0.004% 14.02% 4922ms 19.46% std::__sort (inline) 0 0% 14.02% 4922ms 19.46% std::sort (inline) 278ms 1.10% 15.12% 4338ms 17.15% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 1ms 0.004% 15.13% 4109ms 16.24% AbstractCellPopulation::Iterator::operator++ (inline) 203ms 0.8% 15.93% 4101ms 16.21% AbstractCellPopulation::Iterator::IsRealCell 160ms 0.63% 16.56% 4058ms 16.04% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 298ms 1.18% 17.74% 3652ms 14.44% std::_Rb_tree::find (inline) 0 0% 17.74% 3652ms 14.44% std::map::find (inline) 38ms 0.15% 17.89% 3444ms 13.62% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 93ms 0.37% 18.26% 3063ms 12.11% AbstractMesh::GetNode 61ms 0.24% 18.50% 3055ms 12.08% NodesOnlyMesh::GetNodeOrHaloNode 73ms 0.29% 18.79% 2979ms 11.78% PlaneBoundaryCondition::ImposeBoundaryCondition 263ms 1.04% 19.83% 2975ms 11.76% NodesOnlyMesh::SolveNodeMapping 254ms 1.00% 20.83% 2971ms 11.75% std::__introsort_loop 242ms 0.96% 21.79% 2882ms 11.39% std::map::operator[] (partial-inline) 67ms 0.26% 22.05% 2877ms 11.37% PlaneBoundaryCondition::VerifyBoundaryCondition 2691ms 10.64% 32.69% 2691ms 10.64% std::_Rb_tree::_S_right (inline) 6ms 0.024% 32.71% 2630ms 10.40% std::__unguarded_partition_pivot (inline) 86ms 0.34% 33.05% 2454ms 9.70% AbstractCellPopulation::GetLocationIndexUsingCell 788ms 3.12% 36.17% 2394ms 9.46% std::__unguarded_partition (inline) 0 0% 36.17% 2275ms 8.99% std::_Rb_tree::lower_bound (inline) 0 0% 36.17% 2275ms 8.99% std::map::lower_bound (inline) 0 0% 36.17% 1946ms 7.69% std::__final_insertion_sort (inline) 113ms 0.45% 36.62% 1852ms 7.32% DistributedBoxCollection::AddPairsFromBox 143ms 0.57% 37.18% 1759ms 6.95% std::__unguarded_insertion_sort (inline) 12ms 0.047% 37.23% 1688ms 6.67% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 21ms 0.083% 37.31% 1656ms 6.55% AbstractCellPopulation::GetCellUsingLocationIndex 827ms 3.27% 40.58% 1545ms 6.11% std::__unguarded_linear_insert (inline) 36ms 0.14% 40.72% 1281ms 5.06% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 43ms 0.17% 40.89% 1190ms 4.70% boost::numeric::ublas::c_vector::c_vector (partial-inline) 1ms 0.004% 40.90% 1182ms 4.67% NodeBasedCellPopulation::UpdateCellProcessLocation 28ms 0.11% 41.01% 1131ms 4.47% boost::detail::shared_count::~shared_count (inline) 0 0% 41.01% 1131ms 4.47% boost::shared_ptr::~shared_ptr (inline) 1100ms 4.35% 45.36% 1100ms 4.35% __gnu_cxx::__normal_iterator::operator-- (inline) 1065ms 4.21% 49.57% 1072ms 4.24% boost::detail::sp_counted_base::release 11ms 0.043% 49.61% 1023ms 4.04% DistributedBoxCollection::CalculateBoundaryNodePairs 3ms 0.012% 49.62% 1011ms 4.00% boost::numeric::ublas::vector_assign (inline) 196ms 0.77% 50.40% 875ms 3.46% boost::numeric::ublas::indexing_vector_assign 221ms 0.87% 51.27% 860ms 3.40% __dynamic_cast 321ms 1.27% 52.54% 792ms 3.13% DistributedBoxCollection::CalculateContainingBox (partial-inline) 121ms 0.48% 53.02% 787ms 3.11% AbstractMesh::GetVectorFromAtoB 0 0% 53.02% 717ms 2.83% AbstractCellPopulation::WriteResultsToFiles 681ms 2.69% 55.71% 681ms 2.69% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 7ms 0.028% 55.74% 645ms 2.55% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 55.74% 632ms 2.50% AbstractCellBasedSimulation::DoCellRemoval (inline) 26ms 0.1% 55.84% 630ms 2.49% std::_Rb_tree_const_iterator::operator++ (inline) 53ms 0.21% 56.05% 630ms 2.49% std::__new_allocator::allocate (inline) 27ms 0.11% 56.16% 626ms 2.47% std::__copy_move::__copy_m (inline) 0 0% 56.16% 626ms 2.47% std::__copy_move_a (inline) 0 0% 56.16% 626ms 2.47% std::__copy_move_a1 (inline) 0 0% 56.16% 626ms 2.47% std::__copy_move_a2 (inline) 0 0% 56.16% 626ms 2.47% std::copy (inline) 268ms 1.06% 57.22% 621ms 2.46% NodeAttributes::AddNeighbour 6ms 0.024% 57.24% 620ms 2.45% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 604ms 2.39% 59.63% 604ms 2.39% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 59.63% 604ms 2.39% std::allocator_traits::allocate (inline) 596ms 2.36% 61.98% 596ms 2.36% [libchaste_cell_based.so] 0 0% 61.98% 590ms 2.33% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 589ms 2.33% 64.31% 589ms 2.33% __memcpy_avx512_unaligned_erms 0 0% 64.31% 577ms 2.28% boost::numeric::ublas::norm_2 (inline) 460ms 1.82% 66.13% 577ms 2.28% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 66.13% 577ms 2.28% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 24ms 0.095% 66.23% 577ms 2.28% operator new 569ms 2.25% 68.48% 569ms 2.25% [libchaste_mesh.so] 4ms 0.016% 68.49% 567ms 2.24% AbstractCellBasedSimulation::DoCellBirth 556ms 2.20% 70.69% 556ms 2.20% boost::numeric::ublas::c_vector::operator() 0 0% 70.69% 552ms 2.18% std::_Rb_tree::_M_create_node (inline) 177ms 0.7% 71.39% 541ms 2.14% __GI___libc_malloc 2ms 0.0079% 71.40% 538ms 2.13% AbstractCentreBasedCellPopulation::GetDampingConstant 538ms 2.13% 73.52% 538ms 2.13% std::_Rb_tree_increment 5ms 0.02% 73.54% 536ms 2.12% CellPropertyCollection::GetPropertiesType (inline) 0 0% 73.54% 528ms 2.09% std::_Rb_tree::_M_get_node (inline) 26ms 0.1% 73.65% 503ms 1.99% std::_Rb_tree::_Rb_tree (partial-inline) 205ms 0.81% 74.46% 502ms 1.98% __cxxabiv1::__si_class_type_info::__do_dyncast 494ms 1.95% 76.41% 494ms 1.95% boost::numeric::ublas::same_impl_ex 69ms 0.27% 76.68% 488ms 1.93% std::_Rb_tree::_M_erase 110ms 0.43% 77.12% 479ms 1.89% std::_Rb_tree::~_Rb_tree (inline) 38ms 0.15% 77.27% 471ms 1.86% std::_Rb_tree::_M_copy (inline) 4ms 0.016% 77.28% 467ms 1.85% NodeBasedCellPopulation::WriteVtkResultsToFile 321ms 1.27% 78.55% 457ms 1.81% std::vector::push_back (inline) 433ms 1.71% 80.26% 433ms 1.71% __strcmp_evex 0 0% 80.26% 426ms 1.68% std::set::set (inline) 0 0% 80.26% 420ms 1.66% std::_Rb_tree::_M_drop_node (inline) 172ms 0.68% 80.94% 417ms 1.65% std::_Rb_tree::_M_clone_node (inline) 0 0% 80.94% 413ms 1.63% std::set::~set (inline) 1ms 0.004% 80.95% 394ms 1.56% Cell::GetMutationState 393ms 1.55% 82.50% 393ms 1.55% std::_Rb_tree::_S_left (inline) 4ms 0.016% 82.52% 379ms 1.50% AbstractCellProperty::IsSubType (inline) 17ms 0.067% 82.59% 365ms 1.44% boost::numeric::ublas::vector_binary::size (inline) 5ms 0.02% 82.61% 365ms 1.44% std::_Rb_tree::_M_emplace_hint_unique 0 0% 82.61% 344ms 1.36% NodesOnlyMesh::ReMesh 4ms 0.016% 82.62% 341ms 1.35% Node::GetRadius 0 0% 82.62% 336ms 1.33% NodesOnlyMesh::UpdateNodeIndices 3ms 0.012% 82.63% 322ms 1.27% NodeBasedCellPopulation::UpdateMapsAfterRemesh 1ms 0.004% 82.64% 305ms 1.21% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 8ms 0.032% 82.67% 305ms 1.21% std::__new_allocator::deallocate (inline) 208ms 0.82% 83.49% 299ms 1.18% _int_malloc 0 0% 83.49% 294ms 1.16% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 83.49% 290ms 1.15% NodesOnlyMesh::UpdateBoxCollection 3ms 0.012% 83.50% 280ms 1.11% DistributedBoxCollection::GetProcessOwningNode 0 0% 83.50% 271ms 1.07% std::allocator_traits::deallocate (inline) 71ms 0.28% 83.78% 270ms 1.07% __GI___libc_free 0 0% 83.78% 264ms 1.04% std::_Rb_tree::_M_put_node (inline) 0 0% 83.78% 258ms 1.02% std::_Rb_tree::_Auto_node::_Auto_node (inline) 256ms 1.01% 84.80% 256ms 1.01% Node::CheckForNodeAttributes 213ms 0.84% 85.64% 256ms 1.01% boost::shared_ptr::shared_ptr (inline) 0 0% 85.64% 253ms 1.00% boost::numeric::ublas::c_vector::assign (inline) 1ms 0.004% 85.64% 246ms 0.97% NodesOnlyMesh::AddNodesToBoxes 0 0% 85.64% 230ms 0.91% boost::numeric::ublas::inner_prod (inline) 1ms 0.004% 85.65% 230ms 0.91% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 11ms 0.043% 85.69% 229ms 0.91% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 85.69% 228ms 0.9% std::iter_swap (inline) 228ms 0.9% 86.59% 228ms 0.9% std::swap (inline) 91ms 0.36% 86.95% 225ms 0.89% std::__move_median_to_first (inline) 0 0% 86.95% 205ms 0.81% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 86.95% 204ms 0.81% VtkMeshWriter::WriteFiles 163ms 0.64% 87.59% 193ms 0.76% _int_free 26ms 0.1% 87.70% 187ms 0.74% std::__insertion_sort (inline) 0 0% 87.70% 184ms 0.73% Cell::HasCellProperty (inline) 1ms 0.004% 87.70% 184ms 0.73% CellPropertyCollection::HasProperty 0 0% 87.70% 184ms 0.73% boost::numeric::ublas::vector_binary::operator() (inline) 35ms 0.14% 87.84% 184ms 0.73% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 87.84% 171ms 0.68% vtkStreamingDemandDrivenPipeline::Update 0 0% 87.84% 171ms 0.68% vtkXMLWriterBase::Write 0 0% 87.84% 167ms 0.66% vtkDemandDrivenPipeline::ProcessRequest 0 0% 87.84% 167ms 0.66% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 87.84% 166ms 0.66% vtkDemandDrivenPipeline::ExecuteData 0 0% 87.84% 165ms 0.65% std::__new_allocator::destroy (inline) 0 0% 87.84% 165ms 0.65% std::allocator_traits::destroy (inline) 0 0% 87.84% 164ms 0.65% vtkCompositeDataPipeline::ExecuteData 0 0% 87.84% 164ms 0.65% vtkExecutive::CallAlgorithm 0 0% 87.84% 163ms 0.64% std::_Rb_tree::_M_destroy_node (inline) 86ms 0.34% 88.18% 161ms 0.64% std::__adjacent_find (inline) 0 0% 88.18% 161ms 0.64% std::__unique (inline) 0 0% 88.18% 161ms 0.64% std::unique (inline) 0 0% 88.18% 161ms 0.64% vtkXMLUnstructuredDataWriter::ProcessRequest 4ms 0.016% 88.20% 158ms 0.62% Cell::ReadyToDivide 3ms 0.012% 88.21% 155ms 0.61% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 88.21% 155ms 0.61% NodesOnlyMesh::ResizeBoxCollection 2ms 0.0079% 88.22% 154ms 0.61% AbstractCellPopulation::SetCellUsingLocationIndex 9ms 0.036% 88.25% 153ms 0.6% NodesOnlyMesh::IsANodeCloseToDomainBoundary 145ms 0.57% 88.82% 145ms 0.57% boost::shared_ptr::operator-> (inline) 1ms 0.004% 88.83% 139ms 0.55% AbstractCellProperty::IsType (inline) 0 0% 88.83% 137ms 0.54% std::_Rb_tree::clear (inline) 0 0% 88.83% 137ms 0.54% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 88.83% 137ms 0.54% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 88.83% 135ms 0.53% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 134ms 0.53% 89.36% 134ms 0.53% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 131ms 0.52% 89.88% 133ms 0.53% __ieee754_log_fma 131ms 0.52% 90.39% 131ms 0.52% Node::GetIndex 14ms 0.055% 90.45% 127ms 0.5% boost::numeric::ublas::vector_reference::operator() (inline)