File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20698ms, 89.55% of 23114ms total Dropped 731 nodes (cum <= 115.57ms) flat flat% sum% cum cum% 0 0% 0% 22956ms 99.32% __libc_start_call_main 0 0% 0% 22956ms 99.32% __libc_start_main_impl 0 0% 0% 22956ms 99.32% _start 0 0% 0% 22941ms 99.25% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 22941ms 99.25% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 22941ms 99.25% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 22941ms 99.25% main 0 0% 0% 22908ms 99.11% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 22908ms 99.11% CxxTest::TestRunner::runTest (inline) 0 0% 0% 22907ms 99.10% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 22899ms 99.07% AbstractCellBasedSimulation::Solve 0 0% 0% 13105ms 56.70% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0% 8628ms 37.33% AbstractCellBasedSimulation::UpdateCellPopulation 6ms 0.026% 0.026% 8261ms 35.74% ForwardEulerNumericalMethod::UpdateAllNodePositions 11ms 0.048% 0.074% 8087ms 34.99% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.074% 7622ms 32.98% NodeBasedCellPopulation::Update 1159ms 5.01% 5.09% 7510ms 32.49% RepulsionForce::AddForceContribution (partial-inline) 12ms 0.052% 5.14% 5631ms 24.36% DistributedBoxCollection::CalculateInteriorNodePairs 2078ms 8.99% 14.13% 4996ms 21.61% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.0043% 14.13% 4539ms 19.64% OffLatticeSimulation::ApplyBoundaries 17ms 0.074% 14.21% 4436ms 19.19% NodeAttributes::RemoveDuplicateNeighbours 6ms 0.026% 14.23% 4260ms 18.43% std::__sort (inline) 0 0% 14.23% 4260ms 18.43% std::sort (inline) 191ms 0.83% 15.06% 3790ms 16.40% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 6ms 0.026% 15.09% 3415ms 14.77% AbstractCellPopulation::Iterator::operator++ (inline) 177ms 0.77% 15.85% 3387ms 14.65% AbstractCellPopulation::Iterator::IsRealCell (inline) 57ms 0.25% 16.10% 3326ms 14.39% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 200ms 0.87% 16.96% 3201ms 13.85% std::_Rb_tree::find (inline) 0 0% 16.96% 3201ms 13.85% std::map::find (inline) 2868ms 12.41% 29.37% 2868ms 12.41% std::_Rb_tree::_S_right (inline) 23ms 0.1% 29.47% 2848ms 12.32% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 218ms 0.94% 30.41% 2507ms 10.85% std::map::operator[] (partial-inline) 199ms 0.86% 31.28% 2449ms 10.60% std::__introsort_loop 32ms 0.14% 31.41% 2386ms 10.32% PlaneBoundaryCondition::ImposeBoundaryCondition 43ms 0.19% 31.60% 2348ms 10.16% AbstractCellPopulation::GetLocationIndexUsingCell 140ms 0.61% 32.21% 2226ms 9.63% AbstractMesh::GetNode 44ms 0.19% 32.40% 2216ms 9.59% NodesOnlyMesh::GetNodeOrHaloNode 0 0% 32.40% 2164ms 9.36% std::__unguarded_partition_pivot (inline) 16ms 0.069% 32.47% 2152ms 9.31% PlaneBoundaryCondition::VerifyBoundaryCondition 71ms 0.31% 32.77% 2088ms 9.03% NodesOnlyMesh::SolveNodeMapping 0 0% 32.77% 2012ms 8.70% std::_Rb_tree::lower_bound (inline) 0 0% 32.77% 2012ms 8.70% std::map::lower_bound (inline) 1016ms 4.40% 37.17% 1980ms 8.57% std::__unguarded_partition (inline) 2ms 0.0087% 37.18% 1804ms 7.80% std::__final_insertion_sort (inline) 165ms 0.71% 37.89% 1774ms 7.68% DistributedBoxCollection::AddPairsFromBox 96ms 0.42% 38.31% 1611ms 6.97% std::__unguarded_insertion_sort (inline) 582ms 2.52% 40.82% 1541ms 6.67% std::__unguarded_linear_insert (inline) 17ms 0.074% 40.90% 1512ms 6.54% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 21ms 0.091% 40.99% 1493ms 6.46% AbstractCellPopulation::GetCellUsingLocationIndex 1417ms 6.13% 47.12% 1417ms 6.13% __gnu_cxx::__normal_iterator::operator-- (inline) 65ms 0.28% 47.40% 1345ms 5.82% boost::numeric::ublas::c_vector::c_vector (partial-inline) 42ms 0.18% 47.58% 1197ms 5.18% boost::numeric::ublas::vector_assign (inline) 2ms 0.0087% 47.59% 1137ms 4.92% NodeBasedCellPopulation::UpdateCellProcessLocation 255ms 1.10% 48.69% 1067ms 4.62% boost::numeric::ublas::indexing_vector_assign 4ms 0.017% 48.71% 1039ms 4.50% DistributedBoxCollection::CalculateBoundaryNodePairs 203ms 0.88% 49.59% 913ms 3.95% __dynamic_cast 145ms 0.63% 50.22% 810ms 3.50% AbstractMesh::GetVectorFromAtoB 19ms 0.082% 50.30% 785ms 3.40% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 369ms 1.60% 51.89% 780ms 3.37% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 51.89% 764ms 3.31% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 51.89% 743ms 3.21% boost::numeric::ublas::norm_2 (inline) 572ms 2.47% 54.37% 743ms 3.21% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 54.37% 743ms 3.21% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 189ms 0.82% 55.19% 720ms 3.11% NodeAttributes::AddNeighbour 0 0% 55.19% 714ms 3.09% AbstractCellPopulation::WriteResultsToFiles 7ms 0.03% 55.22% 714ms 3.09% boost::numeric::ublas::c_vector::operator= (inline) 39ms 0.17% 55.39% 692ms 2.99% std::__copy_move::__copy_m (inline) 0 0% 55.39% 692ms 2.99% std::__copy_move_a (inline) 0 0% 55.39% 692ms 2.99% std::__copy_move_a1 (inline) 0 0% 55.39% 692ms 2.99% std::__copy_move_a2 (inline) 0 0% 55.39% 692ms 2.99% std::copy (inline) 677ms 2.93% 58.32% 677ms 2.93% boost::numeric::ublas::c_vector::operator() 673ms 2.91% 61.23% 673ms 2.91% __memcpy_avx_unaligned_erms 277ms 1.20% 62.43% 602ms 2.60% __cxxabiv1::__si_class_type_info::__do_dyncast 531ms 2.30% 64.72% 597ms 2.58% std::vector::push_back (inline) 1ms 0.0043% 64.73% 549ms 2.38% AbstractCellBasedSimulation::DoCellBirth 535ms 2.31% 67.04% 535ms 2.31% boost::numeric::ublas::same_impl_ex 27ms 0.12% 67.16% 513ms 2.22% boost::detail::shared_count::~shared_count (inline) 0 0% 67.16% 513ms 2.22% boost::shared_ptr::~shared_ptr (inline) 5ms 0.022% 67.18% 500ms 2.16% CellPropertyCollection::GetPropertiesType (inline) 77ms 0.33% 67.51% 500ms 2.16% std::__new_allocator::allocate (inline) 0 0% 67.51% 495ms 2.14% AbstractCentreBasedCellPopulation::GetDampingConstant 41ms 0.18% 67.69% 495ms 2.14% std::_Rb_tree_const_iterator::operator++ (inline) 484ms 2.09% 69.78% 484ms 2.09% __strcmp_avx2 470ms 2.03% 71.82% 477ms 2.06% boost::detail::sp_counted_base::release 0 0% 71.82% 477ms 2.06% std::allocator_traits::allocate (inline) 2ms 0.0087% 71.83% 469ms 2.03% NodeBasedCellPopulation::WriteVtkResultsToFile 460ms 1.99% 73.82% 460ms 1.99% std::_Rb_tree_increment 0 0% 73.82% 457ms 1.98% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 73.82% 457ms 1.98% std::_Rb_tree::_M_create_node (inline) 26ms 0.11% 73.93% 456ms 1.97% std::_Rb_tree::_Rb_tree (partial-inline) 3ms 0.013% 73.94% 446ms 1.93% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 32ms 0.14% 74.08% 419ms 1.81% operator new 33ms 0.14% 74.22% 417ms 1.80% std::_Rb_tree::_M_copy (inline) 0 0% 74.22% 406ms 1.76% std::_Rb_tree::_M_get_node (inline) 124ms 0.54% 74.76% 388ms 1.68% Node::GetRadius 2ms 0.0087% 74.77% 387ms 1.67% AbstractCellProperty::IsSubType (inline) 129ms 0.56% 75.33% 383ms 1.66% std::_Rb_tree::_M_clone_node (inline) 23ms 0.1% 75.43% 379ms 1.64% boost::numeric::ublas::vector_binary::size (inline) 112ms 0.48% 75.91% 378ms 1.64% std::_Rb_tree::_M_erase 124ms 0.54% 76.45% 377ms 1.63% __GI___libc_malloc 6ms 0.026% 76.47% 375ms 1.62% std::set::set (inline) 0 0% 76.47% 336ms 1.45% boost::numeric::ublas::c_vector::assign (inline) 3ms 0.013% 76.49% 334ms 1.45% Cell::GetMutationState 0 0% 76.49% 334ms 1.45% boost::numeric::ublas::inner_prod (inline) 3ms 0.013% 76.50% 334ms 1.45% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 14ms 0.061% 76.56% 331ms 1.43% boost::numeric::ublas::vector_scalar_binary::evaluate 319ms 1.38% 77.94% 319ms 1.38% __gnu_cxx::__normal_iterator::operator++ (inline) 9ms 0.039% 77.98% 315ms 1.36% NodeBasedCellPopulation::UpdateMapsAfterRemesh 312ms 1.35% 79.33% 312ms 1.35% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 79.33% 303ms 1.31% std::_Rb_tree::_Alloc_node::operator() (inline) 41ms 0.18% 79.51% 296ms 1.28% std::_Rb_tree::~_Rb_tree (inline) 0 0% 79.51% 292ms 1.26% NodesOnlyMesh::ReMesh 2ms 0.0087% 79.51% 285ms 1.23% NodesOnlyMesh::UpdateNodeIndices 6ms 0.026% 79.54% 277ms 1.20% std::_Rb_tree::_M_emplace_hint_unique 6ms 0.026% 79.57% 265ms 1.15% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 264ms 1.14% 80.71% 264ms 1.14% Node::CheckForNodeAttributes 0 0% 80.71% 262ms 1.13% NodesOnlyMesh::UpdateBoxCollection 0 0% 80.71% 258ms 1.12% std::_Rb_tree::_M_drop_node (inline) 111ms 0.48% 81.19% 255ms 1.10% boost::numeric::ublas::vector_inner_prod::apply (inline) 6ms 0.026% 81.21% 247ms 1.07% DistributedBoxCollection::GetProcessOwningNode 0 0% 81.21% 230ms 1% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 3ms 0.013% 81.23% 230ms 1% std::__new_allocator::deallocate (inline) 0 0% 81.23% 226ms 0.98% VtkMeshWriter::WriteFiles 0 0% 81.23% 223ms 0.96% NodesOnlyMesh::AddNodesToBoxes 0 0% 81.23% 218ms 0.94% std::set::~set (inline) 1ms 0.0043% 81.23% 213ms 0.92% NodesOnlyMesh::ResizeBoxCollection 129ms 0.56% 81.79% 212ms 0.92% _int_malloc 14ms 0.061% 81.85% 210ms 0.91% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 81.85% 204ms 0.88% std::allocator_traits::deallocate (inline) 0 0% 81.85% 200ms 0.87% vtkStreamingDemandDrivenPipeline::Update 0 0% 81.85% 200ms 0.87% vtkXMLWriterBase::Write 73ms 0.32% 82.17% 199ms 0.86% __GI___libc_free 0 0% 82.17% 199ms 0.86% std::_Rb_tree::_M_put_node (inline) 0 0% 82.17% 199ms 0.86% vtkExecutive::CallAlgorithm 0 0% 82.17% 199ms 0.86% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 82.17% 198ms 0.86% vtkCompositeDataPipeline::ExecuteData 0 0% 82.17% 198ms 0.86% vtkDemandDrivenPipeline::ExecuteData 0 0% 82.17% 198ms 0.86% vtkDemandDrivenPipeline::ProcessRequest 0 0% 82.17% 198ms 0.86% vtkXMLUnstructuredDataWriter::ProcessRequest 18ms 0.078% 82.24% 191ms 0.83% std::__insertion_sort (inline) 100ms 0.43% 82.68% 183ms 0.79% boost::shared_ptr::shared_ptr (inline) 68ms 0.29% 82.97% 181ms 0.78% std::__move_median_to_first (inline) 180ms 0.78% 83.75% 180ms 0.78% [libchaste_cell_based.so] 3ms 0.013% 83.76% 175ms 0.76% CellPropertyCollection::HasProperty 0 0% 83.76% 173ms 0.75% Cell::HasCellProperty (inline) 172ms 0.74% 84.51% 172ms 0.74% Node::GetIndex 0 0% 84.51% 170ms 0.74% vtkXMLUnstructuredDataWriter::WriteAPiece 1ms 0.0043% 84.51% 170ms 0.74% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 1ms 0.0043% 84.52% 166ms 0.72% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 6ms 0.026% 84.54% 165ms 0.71% AbstractCellProperty::IsType (inline) 92ms 0.4% 84.94% 161ms 0.7% Node::AddNeighbour 5ms 0.022% 84.96% 157ms 0.68% Cell::ReadyToDivide 0 0% 84.96% 154ms 0.67% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 84.96% 151ms 0.65% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 10ms 0.043% 85.00% 150ms 0.65% DistributedBoxCollection::GetIsPeriodicAllDims 148ms 0.64% 85.65% 148ms 0.64% [libchaste_mesh.so] 12ms 0.052% 85.70% 146ms 0.63% boost::numeric::ublas::vector_reference::operator() (inline) 145ms 0.63% 86.32% 145ms 0.63% Node::IsDeleted 142ms 0.61% 86.94% 142ms 0.61% std::__adjacent_find (inline) 0 0% 86.94% 142ms 0.61% std::__unique (inline) 0 0% 86.94% 142ms 0.61% std::unique (inline) 139ms 0.6% 87.54% 139ms 0.6% boost::shared_ptr::operator-> (inline) 0 0% 87.54% 138ms 0.6% std::_Rb_tree::clear (inline) 0 0% 87.54% 137ms 0.59% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 87.54% 137ms 0.59% vtkXMLWriter::WriteBinaryData 1ms 0.0043% 87.54% 135ms 0.58% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.54% 134ms 0.58% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.54% 134ms 0.58% vtkXMLWriter::WriteCompressionBlock 0 0% 87.54% 133ms 0.58% vtkXMLWriter::WritePointsAppendedData 2ms 0.0087% 87.55% 129ms 0.56% AbstractCellPopulation::SetCellUsingLocationIndex 0 0% 87.55% 129ms 0.56% boost::numeric::ublas::vector_binary::operator() (inline) 1ms 0.0043% 87.56% 128ms 0.55% tbb::detail::r1::parallel_pipeline 38ms 0.16% 87.72% 127ms 0.55% AbstractCellProperty::IsSame 114ms 0.49% 88.21% 126ms 0.55% _int_free 124ms 0.54% 88.75% 124ms 0.54% Node::rGetLocation 124ms 0.54% 89.29% 124ms 0.54% __ieee754_log_fma 0 0% 89.29% 124ms 0.54% clone3 0 0% 89.29% 124ms 0.54% start_thread 1ms 0.0043% 89.29% 121ms 0.52% tbb::detail::r1::reset 9ms 0.039% 89.33% 119ms 0.51% boost::numeric::ublas::c_vector::operator[] (inline) 50ms 0.22% 89.55% 116ms 0.5% tbb::detail::r1::wait_bounded_queue_monitor