File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 29985ms, 87.91% of 34108ms total Dropped 779 nodes (cum <= 170.54ms) flat flat% sum% cum cum% 0 0% 0% 33958ms 99.56% __libc_start_call_main 0 0% 0% 33958ms 99.56% __libc_start_main_impl 0 0% 0% 33958ms 99.56% _start 0 0% 0% 33941ms 99.51% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 33941ms 99.51% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 33941ms 99.51% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 33941ms 99.51% main 0 0% 0% 33907ms 99.41% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 33907ms 99.41% CxxTest::TestRunner::runTest (inline) 0 0% 0% 33907ms 99.41% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 33899ms 99.39% AbstractCellBasedSimulation::Solve 4ms 0.012% 0.012% 23715ms 69.53% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.012% 18760ms 55.00% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.018% 0.029% 18585ms 54.49% AbstractNumericalMethod::ComputeForcesIncludingDamping 184ms 0.54% 0.57% 17854ms 52.35% AbstractTwoBodyInteractionForce::AddForceContribution 1427ms 4.18% 4.75% 14948ms 43.83% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4316ms 12.65% 17.41% 9572ms 28.06% std::_Rb_tree::_M_lower_bound (inline) 0 0% 17.41% 8983ms 26.34% AbstractCellBasedSimulation::UpdateCellPopulation 360ms 1.06% 18.46% 8695ms 25.49% std::_Rb_tree::find (inline) 0 0% 18.46% 8695ms 25.49% std::map::find (inline) 154ms 0.45% 18.91% 8460ms 24.80% NodesOnlyMesh::GetNodeOrHaloNode 527ms 1.55% 20.46% 8258ms 24.21% AbstractMesh::GetNode 0 0% 20.46% 7905ms 23.18% NodeBasedCellPopulation::Update 304ms 0.89% 21.35% 7734ms 22.68% NodesOnlyMesh::SolveNodeMapping 213ms 0.62% 21.97% 6088ms 17.85% boost::numeric::ublas::vector_assign (inline) 188ms 0.55% 22.53% 5976ms 17.52% boost::numeric::ublas::c_vector::c_vector (partial-inline) 16ms 0.047% 22.57% 5841ms 17.13% DistributedBoxCollection::CalculateInteriorNodePairs 5221ms 15.31% 37.88% 5221ms 15.31% std::_Rb_tree::_S_right (inline) 1ms 0.0029% 37.88% 4635ms 13.59% OffLatticeSimulation::ApplyBoundaries 11ms 0.032% 37.91% 4499ms 13.19% NodeAttributes::RemoveDuplicateNeighbours 2ms 0.0059% 37.92% 4315ms 12.65% std::__sort (inline) 0 0% 37.92% 4315ms 12.65% std::sort (inline) 1184ms 3.47% 41.39% 3518ms 10.31% boost::numeric::ublas::indexing_vector_assign 4ms 0.012% 41.40% 3498ms 10.26% AbstractCellPopulation::Iterator::operator++ (inline) 80ms 0.23% 41.64% 3477ms 10.19% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 180ms 0.53% 42.17% 3472ms 10.18% AbstractCellPopulation::Iterator::IsRealCell 32ms 0.094% 42.26% 2982ms 8.74% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 190ms 0.56% 42.82% 2481ms 7.27% std::__introsort_loop 32ms 0.094% 42.91% 2442ms 7.16% PlaneBoundaryCondition::ImposeBoundaryCondition 37ms 0.11% 43.02% 2414ms 7.08% AbstractCellPopulation::GetLocationIndexUsingCell 2ms 0.0059% 43.03% 2213ms 6.49% std::__unguarded_partition_pivot (inline) 10ms 0.029% 43.05% 2192ms 6.43% PlaneBoundaryCondition::VerifyBoundaryCondition 1041ms 3.05% 46.11% 1993ms 5.84% std::__unguarded_partition (inline) 191ms 0.56% 46.67% 1949ms 5.71% DistributedBoxCollection::AddPairsFromBox 266ms 0.78% 47.45% 1846ms 5.41% std::map::operator[] (partial-inline) 0 0% 47.45% 1831ms 5.37% std::__final_insertion_sort (inline) 1715ms 5.03% 52.47% 1715ms 5.03% boost::numeric::ublas::same_impl_ex 87ms 0.26% 52.73% 1621ms 4.75% std::__unguarded_insertion_sort (inline) 596ms 1.75% 54.48% 1583ms 4.64% std::__unguarded_linear_insert (inline) 141ms 0.41% 54.89% 1459ms 4.28% AbstractMesh::GetVectorFromAtoB 1439ms 4.22% 59.11% 1439ms 4.22% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 59.11% 1335ms 3.91% std::_Rb_tree::lower_bound (inline) 0 0% 59.11% 1335ms 3.91% std::map::lower_bound (inline) 0 0% 59.11% 1291ms 3.79% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 59.11% 1283ms 3.76% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 59.11% 1150ms 3.37% NodeBasedCellPopulation::UpdateCellProcessLocation 1148ms 3.37% 62.48% 1148ms 3.37% boost::numeric::ublas::c_vector::operator() 9ms 0.026% 62.50% 1102ms 3.23% DistributedBoxCollection::CalculateBoundaryNodePairs 25ms 0.073% 62.57% 1036ms 3.04% boost::numeric::ublas::detail::expression_type_check (inline) 163ms 0.48% 63.05% 989ms 2.90% boost::numeric::ublas::detail::equals 139ms 0.41% 63.46% 988ms 2.90% boost::numeric::ublas::vector_binary::size (inline) 207ms 0.61% 64.07% 897ms 2.63% NodeAttributes::AddAppliedForceContribution 24ms 0.07% 64.14% 822ms 2.41% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 385ms 1.13% 65.27% 816ms 2.39% DistributedBoxCollection::CalculateContainingBox (partial-inline) 331ms 0.97% 66.24% 800ms 2.35% __GI___libc_free 0 0% 66.24% 786ms 2.30% boost::numeric::ublas::norm_inf (inline) 442ms 1.30% 67.53% 786ms 2.30% boost::numeric::ublas::vector_norm_inf::apply (inline) 235ms 0.69% 68.22% 780ms 2.29% NodeAttributes::AddNeighbour 0 0% 68.22% 731ms 2.14% AbstractCellPopulation::WriteResultsToFiles 87ms 0.26% 68.48% 694ms 2.03% std::__new_allocator::allocate (inline) 478ms 1.40% 69.88% 690ms 2.02% __dynamic_cast 0 0% 69.88% 690ms 2.02% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 69.88% 690ms 2.02% boost::numeric::ublas::c_vector::plus_assign (inline) 5ms 0.015% 69.89% 678ms 1.99% AbstractCentreBasedCellPopulation::GetDampingConstant 32ms 0.094% 69.99% 653ms 1.91% std::_Rb_tree_const_iterator::operator++ (inline) 543ms 1.59% 71.58% 626ms 1.84% std::vector::push_back (inline) 4ms 0.012% 71.59% 620ms 1.82% AbstractCellBasedSimulation::DoCellBirth 617ms 1.81% 73.40% 617ms 1.81% std::_Rb_tree_increment 102ms 0.3% 73.70% 607ms 1.78% operator new 8ms 0.023% 73.72% 531ms 1.56% CellPropertyCollection::GetPropertiesType (inline) 0 0% 73.72% 505ms 1.48% boost::numeric::ublas::norm_2 (inline) 415ms 1.22% 74.94% 505ms 1.48% boost::numeric::ublas::vector_norm_2::apply (inline) 191ms 0.56% 75.50% 496ms 1.45% __GI___libc_malloc 3ms 0.0088% 75.51% 487ms 1.43% NodeBasedCellPopulation::WriteVtkResultsToFile 414ms 1.21% 76.72% 469ms 1.38% _int_free 0 0% 76.72% 458ms 1.34% AbstractCellBasedSimulation::DoCellRemoval (inline) 2ms 0.0059% 76.73% 458ms 1.34% Cell::GetMutationState 4ms 0.012% 76.74% 444ms 1.30% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 418ms 1.23% 77.96% 418ms 1.23% Node::GetIndex 37ms 0.11% 78.07% 418ms 1.23% boost::detail::shared_count::~shared_count (inline) 0 0% 78.07% 418ms 1.23% boost::shared_ptr::~shared_ptr (inline) 0 0% 78.07% 377ms 1.11% std::allocator_traits::allocate (inline) 370ms 1.08% 79.16% 374ms 1.10% boost::detail::sp_counted_base::release 35ms 0.1% 79.26% 352ms 1.03% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 79.26% 352ms 1.03% boost::numeric::ublas::vector::vector (inline) 0 0% 79.26% 350ms 1.03% std::_Rb_tree::_M_create_node (inline) 4ms 0.012% 79.27% 336ms 0.99% AbstractCellProperty::IsSubType (inline) 0 0% 79.27% 326ms 0.96% boost::numeric::ublas::inner_prod (inline) 11ms 0.032% 79.30% 325ms 0.95% boost::numeric::ublas::vector_reference::operator() (inline) 15ms 0.044% 79.35% 325ms 0.95% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 79.35% 325ms 0.95% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 8ms 0.023% 79.37% 322ms 0.94% NodeBasedCellPopulation::UpdateMapsAfterRemesh 319ms 0.94% 80.31% 319ms 0.94% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 318ms 0.93% 81.24% 318ms 0.93% __gnu_cxx::__normal_iterator::operator++ (inline) 5ms 0.015% 81.25% 312ms 0.91% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 4ms 0.012% 81.27% 307ms 0.9% AbstractCellPopulation::GetCellUsingLocationIndex 121ms 0.35% 81.62% 306ms 0.9% Node::GetRadius 0 0% 81.62% 301ms 0.88% std::_Rb_tree::_M_get_node (inline) 0 0% 81.62% 296ms 0.87% NodesOnlyMesh::ReMesh 1ms 0.0029% 81.62% 289ms 0.85% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 4ms 0.012% 81.63% 281ms 0.82% NodesOnlyMesh::UpdateNodeIndices 0 0% 81.63% 275ms 0.81% NodesOnlyMesh::UpdateBoxCollection 105ms 0.31% 81.94% 274ms 0.8% boost::numeric::ublas::vector_inner_prod::apply (inline) 92ms 0.27% 82.21% 272ms 0.8% std::_Rb_tree::_M_erase (partial-inline) 271ms 0.79% 83.01% 271ms 0.79% [libchaste_cell_based.so] 10ms 0.029% 83.04% 269ms 0.79% DistributedBoxCollection::GetProcessOwningNode 0 0% 83.04% 266ms 0.78% boost::numeric::ublas::c_vector::assign (inline) 246ms 0.72% 83.76% 246ms 0.72% NodeBasedCellPopulation::GetNode 6ms 0.018% 83.78% 245ms 0.72% std::_Rb_tree::_M_emplace_hint_unique 177ms 0.52% 84.29% 237ms 0.69% Node::AddAppliedForceContribution 3ms 0.0088% 84.30% 237ms 0.69% NodesOnlyMesh::AddNodesToBoxes 0 0% 84.30% 229ms 0.67% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 84.30% 229ms 0.67% VtkMeshWriter::WriteFiles 110ms 0.32% 84.63% 225ms 0.66% std::__find_if (inline) 0 0% 84.63% 225ms 0.66% std::find_if (inline) 0 0% 84.63% 225ms 0.66% std::none_of (inline) 126ms 0.37% 84.99% 218ms 0.64% _int_malloc 0 0% 84.99% 216ms 0.63% std::_Rb_tree::_Alloc_node::operator() (inline) 9ms 0.026% 85.02% 215ms 0.63% std::_Rb_tree::_Rb_tree (partial-inline) 79ms 0.23% 85.25% 215ms 0.63% std::__move_median_to_first (inline) 0 0% 85.25% 214ms 0.63% Cell::HasCellProperty (inline) 8ms 0.023% 85.28% 214ms 0.63% CellPropertyCollection::HasProperty 18ms 0.053% 85.33% 210ms 0.62% std::__insertion_sort (inline) 0 0% 85.33% 204ms 0.6% vtkDemandDrivenPipeline::ProcessRequest 0 0% 85.33% 204ms 0.6% vtkStreamingDemandDrivenPipeline::Update 0 0% 85.33% 204ms 0.6% vtkXMLWriterBase::Write 0 0% 85.33% 203ms 0.6% vtkExecutive::CallAlgorithm 5ms 0.015% 85.34% 202ms 0.59% Cell::ReadyToDivide 18ms 0.053% 85.40% 202ms 0.59% std::_Rb_tree::_M_copy (inline) 0 0% 85.40% 202ms 0.59% vtkDemandDrivenPipeline::ExecuteData 0 0% 85.40% 202ms 0.59% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 85.40% 201ms 0.59% vtkCompositeDataPipeline::ExecuteData 0 0% 85.40% 201ms 0.59% vtkXMLUnstructuredDataWriter::ProcessRequest 200ms 0.59% 85.98% 200ms 0.59% Node::CheckForNodeAttributes 0 0% 85.98% 199ms 0.58% boost::numeric::ublas::vector_binary::operator() (inline) 28ms 0.082% 86.06% 199ms 0.58% std::__new_allocator::deallocate (inline) 1ms 0.0029% 86.07% 192ms 0.56% NodesOnlyMesh::ResizeBoxCollection 190ms 0.56% 86.62% 190ms 0.56% Node::rGetLocation 190ms 0.56% 87.18% 190ms 0.56% [libchaste_mesh.so] 189ms 0.55% 87.74% 189ms 0.55% __strcmp_avx2 20ms 0.059% 87.79% 188ms 0.55% NodesOnlyMesh::IsANodeCloseToDomainBoundary 27ms 0.079% 87.87% 184ms 0.54% std::_Rb_tree::_M_clone_node (inline) 0 0% 87.87% 178ms 0.52% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 87.87% 178ms 0.52% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 87.87% 175ms 0.51% std::_Rb_tree::_M_drop_node (inline) 1ms 0.0029% 87.88% 173ms 0.51% boost::numeric::ublas::vector_binary_scalar1::operator() (inline) 12ms 0.035% 87.91% 172ms 0.5% std::_Rb_tree::~_Rb_tree (inline) 0 0% 87.91% 171ms 0.5% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData