File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20607ms, 89.50% of 23024ms total Dropped 754 nodes (cum <= 115.12ms) flat flat% sum% cum cum% 0 0% 0% 22865ms 99.31% __libc_start_call_main 0 0% 0% 22865ms 99.31% __libc_start_main_impl 0 0% 0% 22865ms 99.31% _start 0 0% 0% 22850ms 99.24% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 22850ms 99.24% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 22850ms 99.24% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 22850ms 99.24% main 0 0% 0% 22813ms 99.08% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 22813ms 99.08% CxxTest::TestRunner::runTest (inline) 0 0% 0% 22813ms 99.08% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 22805ms 99.05% AbstractCellBasedSimulation::Solve 0 0% 0% 13065ms 56.75% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0% 8595ms 37.33% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.017% 0.017% 8254ms 35.85% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.043% 0.061% 8080ms 35.09% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.061% 7603ms 33.02% NodeBasedCellPopulation::Update 1230ms 5.34% 5.40% 7490ms 32.53% RepulsionForce::AddForceContribution (partial-inline) 4ms 0.017% 5.42% 5583ms 24.25% DistributedBoxCollection::CalculateInteriorNodePairs 2054ms 8.92% 14.34% 4869ms 21.15% std::_Rb_tree::_M_lower_bound (inline) 0 0% 14.34% 4537ms 19.71% OffLatticeSimulation::ApplyBoundaries 21ms 0.091% 14.43% 4471ms 19.42% NodeAttributes::RemoveDuplicateNeighbours 5ms 0.022% 14.45% 4283ms 18.60% std::__sort (inline) 0 0% 14.45% 4283ms 18.60% std::sort (inline) 202ms 0.88% 15.33% 3754ms 16.30% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 1ms 0.0043% 15.34% 3397ms 14.75% AbstractCellPopulation::Iterator::operator++ (inline) 167ms 0.73% 16.06% 3376ms 14.66% AbstractCellPopulation::Iterator::IsRealCell (inline) 63ms 0.27% 16.34% 3330ms 14.46% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 236ms 1.03% 17.36% 3219ms 13.98% std::_Rb_tree::find (inline) 0 0% 17.36% 3219ms 13.98% std::map::find (inline) 21ms 0.091% 17.45% 2869ms 12.46% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2766ms 12.01% 29.46% 2766ms 12.01% std::_Rb_tree::_S_right (inline) 175ms 0.76% 30.22% 2494ms 10.83% std::__introsort_loop 246ms 1.07% 31.29% 2419ms 10.51% std::map::operator[] (partial-inline) 40ms 0.17% 31.47% 2382ms 10.35% PlaneBoundaryCondition::ImposeBoundaryCondition 151ms 0.66% 32.12% 2299ms 9.99% AbstractMesh::GetNode 43ms 0.19% 32.31% 2283ms 9.92% NodesOnlyMesh::GetNodeOrHaloNode 48ms 0.21% 32.52% 2257ms 9.80% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.0043% 32.52% 2231ms 9.69% std::__unguarded_partition_pivot (inline) 24ms 0.1% 32.63% 2155ms 9.36% PlaneBoundaryCondition::VerifyBoundaryCondition 85ms 0.37% 33.00% 2154ms 9.36% NodesOnlyMesh::SolveNodeMapping 1011ms 4.39% 37.39% 2011ms 8.73% std::__unguarded_partition (inline) 0 0% 37.39% 1907ms 8.28% std::_Rb_tree::lower_bound (inline) 0 0% 37.39% 1907ms 8.28% std::map::lower_bound (inline) 2ms 0.0087% 37.40% 1784ms 7.75% std::__final_insertion_sort (inline) 159ms 0.69% 38.09% 1738ms 7.55% DistributedBoxCollection::AddPairsFromBox 82ms 0.36% 38.44% 1571ms 6.82% std::__unguarded_insertion_sort (inline) 606ms 2.63% 41.07% 1532ms 6.65% std::__unguarded_linear_insert (inline) 28ms 0.12% 41.20% 1491ms 6.48% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 21ms 0.091% 41.29% 1457ms 6.33% AbstractCellPopulation::GetCellUsingLocationIndex 1391ms 6.04% 47.33% 1391ms 6.04% __gnu_cxx::__normal_iterator::operator-- (inline) 65ms 0.28% 47.61% 1268ms 5.51% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 47.61% 1140ms 4.95% NodeBasedCellPopulation::UpdateCellProcessLocation 44ms 0.19% 47.80% 1124ms 4.88% boost::numeric::ublas::vector_assign (inline) 4ms 0.017% 47.82% 1062ms 4.61% DistributedBoxCollection::CalculateBoundaryNodePairs 255ms 1.11% 48.93% 996ms 4.33% boost::numeric::ublas::indexing_vector_assign 247ms 1.07% 50.00% 901ms 3.91% __dynamic_cast 0 0% 50.00% 816ms 3.54% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 50.00% 792ms 3.44% boost::numeric::ublas::norm_2 (inline) 595ms 2.58% 52.58% 792ms 3.44% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 52.58% 792ms 3.44% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 29ms 0.13% 52.71% 790ms 3.43% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 357ms 1.55% 54.26% 762ms 3.31% DistributedBoxCollection::CalculateContainingBox (partial-inline) 161ms 0.7% 54.96% 754ms 3.27% AbstractMesh::GetVectorFromAtoB 189ms 0.82% 55.78% 707ms 3.07% NodeAttributes::AddNeighbour 0 0% 55.78% 699ms 3.04% AbstractCellPopulation::WriteResultsToFiles 4ms 0.017% 55.80% 699ms 3.04% boost::numeric::ublas::c_vector::operator= (inline) 40ms 0.17% 55.97% 675ms 2.93% std::__copy_move::__copy_m (inline) 0 0% 55.97% 675ms 2.93% std::__copy_move_a (inline) 0 0% 55.97% 675ms 2.93% std::__copy_move_a1 (inline) 0 0% 55.97% 675ms 2.93% std::__copy_move_a2 (inline) 0 0% 55.97% 675ms 2.93% std::copy (inline) 673ms 2.92% 58.90% 673ms 2.92% boost::numeric::ublas::c_vector::operator() 652ms 2.83% 61.73% 652ms 2.83% __memcpy_avx_unaligned_erms 517ms 2.25% 63.97% 586ms 2.55% std::vector::push_back (inline) 0 0% 63.97% 543ms 2.36% AbstractCellBasedSimulation::DoCellBirth 257ms 1.12% 65.09% 543ms 2.36% __cxxabiv1::__si_class_type_info::__do_dyncast 9ms 0.039% 65.13% 524ms 2.28% AbstractCentreBasedCellPopulation::GetDampingConstant 3ms 0.013% 65.14% 504ms 2.19% CellPropertyCollection::GetPropertiesType (inline) 74ms 0.32% 65.46% 500ms 2.17% std::__new_allocator::allocate (inline) 487ms 2.12% 67.58% 487ms 2.12% boost::numeric::ublas::same_impl_ex 33ms 0.14% 67.72% 485ms 2.11% boost::detail::shared_count::~shared_count (inline) 0 0% 67.72% 485ms 2.11% boost::shared_ptr::~shared_ptr (inline) 0 0% 67.72% 480ms 2.08% std::allocator_traits::allocate (inline) 48ms 0.21% 67.93% 473ms 2.05% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.0043% 67.93% 461ms 2.00% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 67.93% 460ms 2.00% std::_Rb_tree::_M_create_node (inline) 29ms 0.13% 68.06% 460ms 2.00% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 68.06% 448ms 1.95% AbstractCellBasedSimulation::DoCellRemoval (inline) 438ms 1.90% 69.96% 444ms 1.93% boost::detail::sp_counted_base::release 442ms 1.92% 71.88% 442ms 1.92% __strcmp_avx2 4ms 0.017% 71.90% 437ms 1.90% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 57ms 0.25% 72.15% 424ms 1.84% std::_Rb_tree::_M_copy (inline) 25ms 0.11% 72.26% 419ms 1.82% operator new 416ms 1.81% 74.06% 416ms 1.81% std::_Rb_tree_increment 0 0% 74.06% 404ms 1.75% std::_Rb_tree::_M_get_node (inline) 4ms 0.017% 74.08% 388ms 1.69% std::set::set (inline) 131ms 0.57% 74.65% 387ms 1.68% Node::GetRadius 120ms 0.52% 75.17% 386ms 1.68% __GI___libc_malloc 0 0% 75.17% 371ms 1.61% AbstractCellProperty::IsSubType (inline) 112ms 0.49% 75.66% 366ms 1.59% std::_Rb_tree::_M_clone_node (inline) 0 0% 75.66% 360ms 1.56% boost::numeric::ublas::c_vector::assign (inline) 129ms 0.56% 76.22% 346ms 1.50% std::_Rb_tree::_M_erase 340ms 1.48% 77.69% 340ms 1.48% __gnu_cxx::__normal_iterator::operator++ (inline) 4ms 0.017% 77.71% 330ms 1.43% Cell::GetMutationState 9ms 0.039% 77.75% 323ms 1.40% NodeBasedCellPopulation::UpdateMapsAfterRemesh 319ms 1.39% 79.13% 319ms 1.39% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 79.13% 314ms 1.36% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 79.13% 310ms 1.35% boost::numeric::ublas::inner_prod (inline) 6ms 0.026% 79.16% 308ms 1.34% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 25ms 0.11% 79.27% 307ms 1.33% boost::numeric::ublas::vector_binary::size (inline) 15ms 0.065% 79.33% 302ms 1.31% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 79.33% 278ms 1.21% NodesOnlyMesh::ReMesh 35ms 0.15% 79.49% 272ms 1.18% std::_Rb_tree::~_Rb_tree (inline) 2ms 0.0087% 79.50% 270ms 1.17% NodesOnlyMesh::UpdateNodeIndices 3ms 0.013% 79.51% 266ms 1.16% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 10ms 0.043% 79.55% 266ms 1.16% std::_Rb_tree::_M_emplace_hint_unique 265ms 1.15% 80.70% 265ms 1.15% Node::CheckForNodeAttributes 0 0% 80.70% 258ms 1.12% NodesOnlyMesh::UpdateBoxCollection 4ms 0.017% 80.72% 250ms 1.09% DistributedBoxCollection::GetProcessOwningNode 101ms 0.44% 81.16% 241ms 1.05% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 81.16% 226ms 0.98% NodesOnlyMesh::ResizeBoxCollection 24ms 0.1% 81.26% 225ms 0.98% NodesOnlyMesh::IsANodeCloseToDomainBoundary 1ms 0.0043% 81.27% 223ms 0.97% NodesOnlyMesh::AddNodesToBoxes 0 0% 81.27% 221ms 0.96% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 81.27% 219ms 0.95% VtkMeshWriter::WriteFiles 118ms 0.51% 81.78% 219ms 0.95% _int_malloc 0 0% 81.78% 216ms 0.94% std::_Rb_tree::_M_drop_node (inline) 102ms 0.44% 82.22% 216ms 0.94% std::__move_median_to_first (inline) 21ms 0.091% 82.31% 211ms 0.92% std::__insertion_sort (inline) 203ms 0.88% 83.20% 203ms 0.88% Node::GetIndex 3ms 0.013% 83.21% 195ms 0.85% std::__new_allocator::deallocate (inline) 193ms 0.84% 84.05% 193ms 0.84% [libchaste_cell_based.so] 87ms 0.38% 84.42% 186ms 0.81% boost::shared_ptr::shared_ptr (inline) 0 0% 84.42% 186ms 0.81% std::set::~set (inline) 0 0% 84.42% 186ms 0.81% vtkStreamingDemandDrivenPipeline::Update 0 0% 84.42% 186ms 0.81% vtkXMLWriterBase::Write 0 0% 84.42% 185ms 0.8% vtkDemandDrivenPipeline::ProcessRequest 0 0% 84.42% 184ms 0.8% vtkDemandDrivenPipeline::ExecuteData 0 0% 84.42% 184ms 0.8% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 84.42% 183ms 0.79% vtkCompositeDataPipeline::ExecuteData 0 0% 84.42% 181ms 0.79% vtkExecutive::CallAlgorithm 0 0% 84.42% 181ms 0.79% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 84.42% 175ms 0.76% Cell::HasCellProperty (inline) 5ms 0.022% 84.45% 175ms 0.76% CellPropertyCollection::HasProperty 0 0% 84.45% 175ms 0.76% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 84.45% 174ms 0.76% std::allocator_traits::deallocate (inline) 0 0% 84.45% 171ms 0.74% std::_Rb_tree::_M_put_node (inline) 54ms 0.23% 84.68% 170ms 0.74% __GI___libc_free 0 0% 84.68% 165ms 0.72% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 84.68% 165ms 0.72% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 84.68% 163ms 0.71% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 6ms 0.026% 84.71% 159ms 0.69% Cell::ReadyToDivide 7ms 0.03% 84.74% 155ms 0.67% AbstractCellProperty::IsType (inline) 147ms 0.64% 85.38% 152ms 0.66% std::__adjacent_find (inline) 0 0% 85.38% 152ms 0.66% std::__unique (inline) 0 0% 85.38% 152ms 0.66% std::unique (inline) 6ms 0.026% 85.40% 149ms 0.65% DistributedBoxCollection::GetIsPeriodicAllDims 149ms 0.65% 86.05% 149ms 0.65% [libchaste_mesh.so] 148ms 0.64% 86.69% 148ms 0.64% boost::shared_ptr::operator-> (inline) 0 0% 86.69% 146ms 0.63% std::_Rb_tree::_Auto_node::_Auto_node (inline) 140ms 0.61% 87.30% 140ms 0.61% Node::IsDeleted 70ms 0.3% 87.60% 138ms 0.6% Node::AddNeighbour 0 0% 87.60% 136ms 0.59% vtkXMLWriter::WriteBinaryData 1ms 0.0043% 87.61% 133ms 0.58% AbstractCellPopulation::SetCellUsingLocationIndex 0 0% 87.61% 133ms 0.58% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.61% 133ms 0.58% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.61% 133ms 0.58% vtkXMLWriter::WriteCompressionBlock 20ms 0.087% 87.70% 132ms 0.57% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 87.70% 131ms 0.57% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 130ms 0.56% 88.26% 130ms 0.56% __ieee754_log_fma 0 0% 88.26% 126ms 0.55% clone3 0 0% 88.26% 126ms 0.55% start_thread 0 0% 88.26% 126ms 0.55% std::_Rb_tree::clear (inline) 0 0% 88.26% 126ms 0.55% tbb::detail::r1::parallel_pipeline 0 0% 88.26% 125ms 0.54% tbb::detail::r1::reset 53ms 0.23% 88.49% 124ms 0.54% tbb::detail::r1::wait_bounded_queue_monitor 0 0% 88.49% 124ms 0.54% vtkXMLWriter::WritePointsAppendedData 2ms 0.0087% 88.50% 122ms 0.53% AbstractNumericalMethod::SafeNodePositionUpdate 6ms 0.026% 88.53% 122ms 0.53% boost::numeric::ublas::c_vector::operator[] (inline) 121ms 0.53% 89.05% 121ms 0.53% Node::rGetLocation 104ms 0.45% 89.50% 116ms 0.5% _int_free