File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 32104ms, 88.76% of 36170ms total Dropped 853 nodes (cum <= 180.85ms) flat flat% sum% cum cum% 0 0% 0% 36008ms 99.55% __libc_start_call_main 0 0% 0% 36008ms 99.55% __libc_start_main_impl 0 0% 0% 36008ms 99.55% _start 0 0% 0% 35991ms 99.51% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 35991ms 99.51% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 35991ms 99.51% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 35991ms 99.51% main 0 0% 0% 35952ms 99.40% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 35952ms 99.40% CxxTest::TestRunner::runTest (inline) 0 0% 0% 35952ms 99.40% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0028% 0.0028% 35944ms 99.38% AbstractCellBasedSimulation::Solve 1ms 0.0028% 0.0055% 24932ms 68.93% OffLatticeSimulation::UpdateCellLocationsAndTopology 4ms 0.011% 0.017% 19923ms 55.08% ForwardEulerNumericalMethod::UpdateAllNodePositions 11ms 0.03% 0.047% 19730ms 54.55% AbstractNumericalMethod::ComputeForcesIncludingDamping 164ms 0.45% 0.5% 18417ms 50.92% AbstractTwoBodyInteractionForce::AddForceContribution 1458ms 4.03% 4.53% 15505ms 42.87% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4379ms 12.11% 16.64% 9788ms 27.06% std::_Rb_tree::_M_lower_bound (inline) 0 0% 16.64% 9753ms 26.96% AbstractCellBasedSimulation::UpdateCellPopulation 321ms 0.89% 17.53% 8786ms 24.29% std::_Rb_tree::find (inline) 0 0% 17.53% 8786ms 24.29% std::map::find (inline) 0 0% 17.53% 8508ms 23.52% NodeBasedCellPopulation::Update 127ms 0.35% 17.88% 8485ms 23.46% NodesOnlyMesh::GetNodeOrHaloNode 479ms 1.32% 19.20% 8357ms 23.10% AbstractMesh::GetNode 321ms 0.89% 20.09% 7883ms 21.79% NodesOnlyMesh::SolveNodeMapping 218ms 0.6% 20.69% 6398ms 17.69% boost::numeric::ublas::vector_assign (inline) 10ms 0.028% 20.72% 6334ms 17.51% DistributedBoxCollection::CalculateInteriorNodePairs 244ms 0.67% 21.39% 6334ms 17.51% boost::numeric::ublas::c_vector::c_vector (partial-inline) 5380ms 14.87% 36.27% 5380ms 14.87% std::_Rb_tree::_S_right (inline) 13ms 0.036% 36.30% 4627ms 12.79% NodeAttributes::RemoveDuplicateNeighbours 2ms 0.0055% 36.31% 4595ms 12.70% OffLatticeSimulation::ApplyBoundaries 9ms 0.025% 36.33% 4440ms 12.28% std::__sort (inline) 0 0% 36.33% 4440ms 12.28% std::sort (inline) 4ms 0.011% 36.35% 3598ms 9.95% AbstractCellPopulation::Iterator::operator++ (inline) 181ms 0.5% 36.85% 3574ms 9.88% AbstractCellPopulation::Iterator::IsRealCell (inline) 1110ms 3.07% 39.91% 3527ms 9.75% boost::numeric::ublas::indexing_vector_assign 75ms 0.21% 40.12% 3494ms 9.66% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 21ms 0.058% 40.18% 3026ms 8.37% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 194ms 0.54% 40.72% 2560ms 7.08% std::__introsort_loop 22ms 0.061% 40.78% 2421ms 6.69% PlaneBoundaryCondition::ImposeBoundaryCondition 333ms 0.92% 41.70% 2367ms 6.54% DistributedBoxCollection::AddPairsFromBox 47ms 0.13% 41.83% 2361ms 6.53% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.0028% 41.83% 2278ms 6.30% std::__unguarded_partition_pivot (inline) 21ms 0.058% 41.89% 2172ms 6.00% PlaneBoundaryCondition::VerifyBoundaryCondition 1066ms 2.95% 44.84% 2018ms 5.58% std::__unguarded_partition (inline) 206ms 0.57% 45.41% 1880ms 5.20% std::map::operator[] (partial-inline) 2ms 0.0055% 45.41% 1867ms 5.16% std::__final_insertion_sort (inline) 105ms 0.29% 45.70% 1660ms 4.59% std::__unguarded_insertion_sort (inline) 1632ms 4.51% 50.21% 1632ms 4.51% boost::numeric::ublas::same_impl_ex 613ms 1.69% 51.91% 1605ms 4.44% std::__unguarded_linear_insert (inline) 131ms 0.36% 52.27% 1594ms 4.41% AbstractMesh::GetVectorFromAtoB 1453ms 4.02% 56.29% 1453ms 4.02% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 56.29% 1400ms 3.87% std::_Rb_tree::lower_bound (inline) 0 0% 56.29% 1400ms 3.87% std::map::lower_bound (inline) 0 0% 56.29% 1310ms 3.62% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 56.29% 1292ms 3.57% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 5ms 0.014% 56.30% 1239ms 3.43% AbstractCentreBasedCellPopulation::GetDampingConstant 1ms 0.0028% 56.30% 1216ms 3.36% NodeBasedCellPopulation::UpdateCellProcessLocation 1160ms 3.21% 59.51% 1160ms 3.21% boost::numeric::ublas::c_vector::operator() 1ms 0.0028% 59.51% 1117ms 3.09% DistributedBoxCollection::CalculateBoundaryNodePairs 19ms 0.053% 59.57% 1113ms 3.08% boost::numeric::ublas::detail::expression_type_check (inline) 188ms 0.52% 60.09% 1079ms 2.98% boost::numeric::ublas::detail::equals 177ms 0.49% 60.58% 1063ms 2.94% boost::numeric::ublas::vector_binary::size (inline) 38ms 0.11% 60.68% 995ms 2.75% std::_Rb_tree_const_iterator::operator++ (inline) 172ms 0.48% 61.16% 993ms 2.75% std::__new_allocator::allocate (inline) 961ms 2.66% 63.81% 961ms 2.66% std::_Rb_tree_increment 229ms 0.63% 64.45% 911ms 2.52% NodeAttributes::AddAppliedForceContribution 428ms 1.18% 65.63% 908ms 2.51% NodeAttributes::AddNeighbour 423ms 1.17% 66.80% 893ms 2.47% __GI___libc_free 19ms 0.053% 66.85% 880ms 2.43% CellPropertyCollection::GetPropertiesType (inline) 0 0% 66.85% 846ms 2.34% boost::numeric::ublas::norm_inf (inline) 479ms 1.32% 68.18% 846ms 2.34% boost::numeric::ublas::vector_norm_inf::apply (inline) 82ms 0.23% 68.40% 821ms 2.27% operator new 606ms 1.68% 70.08% 817ms 2.26% __dynamic_cast 2ms 0.0055% 70.08% 807ms 2.23% Cell::GetMutationState 360ms 1% 71.08% 795ms 2.20% DistributedBoxCollection::CalculateContainingBox (partial-inline) 15ms 0.041% 71.12% 778ms 2.15% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 71.12% 767ms 2.12% AbstractCellPopulation::WriteResultsToFiles 1ms 0.0028% 71.12% 765ms 2.12% AbstractCellBasedSimulation::DoCellBirth 250ms 0.69% 71.81% 740ms 2.05% __GI___libc_malloc 0 0% 71.81% 682ms 1.89% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 71.81% 682ms 1.89% boost::numeric::ublas::c_vector::plus_assign (inline) 477ms 1.32% 73.13% 612ms 1.69% std::vector::push_back (inline) 5ms 0.014% 73.15% 553ms 1.53% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 6ms 0.017% 73.16% 548ms 1.52% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 73.16% 539ms 1.49% std::allocator_traits::allocate (inline) 0 0% 73.16% 524ms 1.45% std::_Rb_tree::_M_create_node (inline) 1ms 0.0028% 73.17% 495ms 1.37% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 73.17% 478ms 1.32% AbstractCellBasedSimulation::DoCellRemoval (inline) 17ms 0.047% 73.21% 471ms 1.30% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 73.21% 471ms 1.30% boost::numeric::ublas::vector::vector (inline) 420ms 1.16% 74.37% 465ms 1.29% _int_free 0 0% 74.37% 464ms 1.28% boost::numeric::ublas::norm_2 (inline) 381ms 1.05% 75.43% 464ms 1.28% boost::numeric::ublas::vector_norm_2::apply (inline) 5ms 0.014% 75.44% 463ms 1.28% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 442ms 1.22% 76.66% 442ms 1.22% Node::GetIndex 18ms 0.05% 76.71% 429ms 1.19% boost::detail::shared_count::~shared_count (inline) 0 0% 76.71% 429ms 1.19% boost::shared_ptr::~shared_ptr (inline) 0 0% 76.71% 428ms 1.18% std::_Rb_tree::_M_get_node (inline) 31ms 0.086% 76.80% 426ms 1.18% std::_Rb_tree::_Rb_tree (partial-inline) 400ms 1.11% 77.90% 407ms 1.13% boost::detail::sp_counted_base::release 3ms 0.0083% 77.91% 400ms 1.11% AbstractCellProperty::IsSubType (inline) 30ms 0.083% 78.00% 391ms 1.08% std::_Rb_tree::_M_copy (inline) 180ms 0.5% 78.49% 371ms 1.03% std::_Rb_tree::_M_erase 62ms 0.17% 78.66% 361ms 1% std::_Rb_tree::_M_clone_node (inline) 0 0% 78.66% 360ms 1% std::_Rb_tree::_Alloc_node::operator() (inline) 3ms 0.0083% 78.67% 358ms 0.99% CellPropertyCollection::HasProperty 0 0% 78.67% 356ms 0.98% Cell::HasCellProperty (inline) 10ms 0.028% 78.70% 351ms 0.97% Cell::ReadyToDivide 335ms 0.93% 79.63% 335ms 0.93% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 5ms 0.014% 79.64% 333ms 0.92% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 79.64% 317ms 0.88% NodesOnlyMesh::ReMesh 112ms 0.31% 79.95% 311ms 0.86% Node::GetRadius 0 0% 79.95% 310ms 0.86% NodesOnlyMesh::UpdateBoxCollection 1ms 0.0028% 79.95% 305ms 0.84% NodesOnlyMesh::UpdateNodeIndices 141ms 0.39% 80.34% 305ms 0.84% _int_malloc 7ms 0.019% 80.36% 302ms 0.83% boost::numeric::ublas::vector_reference::operator() (inline) 291ms 0.8% 81.17% 291ms 0.8% [libchaste_cell_based.so] 4ms 0.011% 81.18% 288ms 0.8% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 286ms 0.79% 81.97% 286ms 0.79% __gnu_cxx::__normal_iterator::operator++ (inline) 11ms 0.03% 82.00% 274ms 0.76% std::_Rb_tree::_M_emplace_hint_unique 5ms 0.014% 82.01% 269ms 0.74% DistributedBoxCollection::GetProcessOwningNode 0 0% 82.01% 259ms 0.72% boost::numeric::ublas::inner_prod (inline) 13ms 0.036% 82.05% 258ms 0.71% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 82.05% 258ms 0.71% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 107ms 0.3% 82.34% 251ms 0.69% std::__move_median_to_first (inline) 113ms 0.31% 82.66% 250ms 0.69% std::__find_if (inline) 0 0% 82.66% 250ms 0.69% std::find_if (inline) 0 0% 82.66% 250ms 0.69% std::none_of (inline) 249ms 0.69% 83.35% 249ms 0.69% boost::shared_ptr::operator-> (inline) 0 0% 83.35% 242ms 0.67% std::set::set (inline) 0 0% 83.35% 239ms 0.66% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 83.35% 237ms 0.66% VtkMeshWriter::WriteFiles 0 0% 83.35% 235ms 0.65% boost::numeric::ublas::c_vector::assign (inline) 1ms 0.0028% 83.35% 234ms 0.65% NodesOnlyMesh::AddNodesToBoxes 230ms 0.64% 83.98% 230ms 0.64% NodeBasedCellPopulation::GetNode 45ms 0.12% 84.11% 221ms 0.61% std::__new_allocator::deallocate (inline) 215ms 0.59% 84.70% 215ms 0.59% Node::rGetLocation 2ms 0.0055% 84.71% 214ms 0.59% AbstractCellProperty::IsType (inline) 210ms 0.58% 85.29% 210ms 0.58% Node::CheckForNodeAttributes 87ms 0.24% 85.53% 208ms 0.58% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 85.53% 206ms 0.57% std::_Rb_tree::clear (inline) 19ms 0.053% 85.58% 205ms 0.57% std::__insertion_sort (inline) 162ms 0.45% 86.03% 203ms 0.56% Node::AddAppliedForceContribution 0 0% 86.03% 203ms 0.56% NodesOnlyMesh::ResizeBoxCollection 0 0% 86.03% 203ms 0.56% vtkStreamingDemandDrivenPipeline::Update 0 0% 86.03% 203ms 0.56% vtkXMLWriterBase::Write 202ms 0.56% 86.59% 202ms 0.56% boost::numeric::ublas::scalar_plus_assign::apply (inline) 0 0% 86.59% 202ms 0.56% vtkDemandDrivenPipeline::ProcessRequest 0 0% 86.59% 202ms 0.56% vtkStreamingDemandDrivenPipeline::ProcessRequest 10ms 0.028% 86.62% 201ms 0.56% NodesOnlyMesh::IsANodeCloseToDomainBoundary 201ms 0.56% 87.17% 201ms 0.56% __strcmp_avx2 0 0% 87.17% 201ms 0.56% vtkDemandDrivenPipeline::ExecuteData 0 0% 87.17% 200ms 0.55% vtkCompositeDataPipeline::ExecuteData 0 0% 87.17% 200ms 0.55% vtkExecutive::CallAlgorithm 0 0% 87.17% 200ms 0.55% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 87.17% 196ms 0.54% boost::numeric::ublas::vector_binary::operator() (inline) 11ms 0.03% 87.20% 193ms 0.53% std::_Rb_tree::~_Rb_tree (inline) 190ms 0.53% 87.73% 190ms 0.53% boost::numeric::ublas::c_vector::size (inline) 0 0% 87.73% 187ms 0.52% tcache_get (inline) 187ms 0.52% 88.24% 187ms 0.52% tcache_get_n (inline) 186ms 0.51% 88.76% 186ms 0.51% [libchaste_mesh.so] 0 0% 88.76% 184ms 0.51% std::map::map (inline) 0 0% 88.76% 181ms 0.5% boost::numeric::ublas::vector_reference::size (inline)