File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20584ms, 89.38% of 23030ms total Dropped 738 nodes (cum <= 115.15ms) flat flat% sum% cum cum% 0 0% 0% 22898ms 99.43% __libc_start_call_main 0 0% 0% 22898ms 99.43% __libc_start_main_impl 0 0% 0% 22898ms 99.43% _start 0 0% 0% 22882ms 99.36% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 22882ms 99.36% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 22882ms 99.36% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 22882ms 99.36% main 0 0% 0% 22844ms 99.19% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 22844ms 99.19% CxxTest::TestRunner::runTest (inline) 0 0% 0% 22844ms 99.19% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0043% 0.0043% 22836ms 99.16% AbstractCellBasedSimulation::Solve 3ms 0.013% 0.017% 13045ms 56.64% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.017% 8617ms 37.42% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0087% 0.026% 8281ms 35.96% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.026% 0.052% 8093ms 35.14% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.052% 7605ms 33.02% NodeBasedCellPopulation::Update 1184ms 5.14% 5.19% 7495ms 32.54% RepulsionForce::AddForceContribution (partial-inline) 9ms 0.039% 5.23% 5560ms 24.14% DistributedBoxCollection::CalculateInteriorNodePairs 2055ms 8.92% 14.16% 4912ms 21.33% std::_Rb_tree::_M_lower_bound (inline) 0 0% 14.16% 4476ms 19.44% OffLatticeSimulation::ApplyBoundaries 19ms 0.083% 14.24% 4449ms 19.32% NodeAttributes::RemoveDuplicateNeighbours 3ms 0.013% 14.25% 4270ms 18.54% std::__sort (inline) 0 0% 14.25% 4270ms 18.54% std::sort (inline) 165ms 0.72% 14.97% 3762ms 16.34% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 58ms 0.25% 15.22% 3438ms 14.93% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 5ms 0.022% 15.24% 3436ms 14.92% AbstractCellPopulation::Iterator::operator++ (inline) 155ms 0.67% 15.91% 3410ms 14.81% AbstractCellPopulation::Iterator::IsRealCell 238ms 1.03% 16.95% 3212ms 13.95% std::_Rb_tree::find (inline) 0 0% 16.95% 3212ms 13.95% std::map::find (inline) 18ms 0.078% 17.03% 2919ms 12.67% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2818ms 12.24% 29.26% 2818ms 12.24% std::_Rb_tree::_S_right (inline) 229ms 0.99% 30.26% 2479ms 10.76% std::map::operator[] (partial-inline) 195ms 0.85% 31.10% 2424ms 10.53% std::__introsort_loop 33ms 0.14% 31.25% 2294ms 9.96% PlaneBoundaryCondition::ImposeBoundaryCondition 31ms 0.13% 31.38% 2282ms 9.91% AbstractCellPopulation::GetLocationIndexUsingCell 150ms 0.65% 32.03% 2250ms 9.77% AbstractMesh::GetNode 34ms 0.15% 32.18% 2218ms 9.63% NodesOnlyMesh::GetNodeOrHaloNode 16ms 0.069% 32.25% 2181ms 9.47% PlaneBoundaryCondition::VerifyBoundaryCondition 0 0% 32.25% 2157ms 9.37% std::__unguarded_partition_pivot (inline) 82ms 0.36% 32.61% 2105ms 9.14% NodesOnlyMesh::SolveNodeMapping 0 0% 32.61% 1964ms 8.53% std::_Rb_tree::lower_bound (inline) 0 0% 32.61% 1964ms 8.53% std::map::lower_bound (inline) 994ms 4.32% 36.92% 1949ms 8.46% std::__unguarded_partition (inline) 1ms 0.0043% 36.93% 1842ms 8.00% std::__final_insertion_sort (inline) 153ms 0.66% 37.59% 1731ms 7.52% DistributedBoxCollection::AddPairsFromBox 103ms 0.45% 38.04% 1639ms 7.12% std::__unguarded_insertion_sort (inline) 582ms 2.53% 40.56% 1584ms 6.88% std::__unguarded_linear_insert (inline) 25ms 0.11% 40.67% 1583ms 6.87% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 23ms 0.1% 40.77% 1552ms 6.74% AbstractCellPopulation::GetCellUsingLocationIndex 1446ms 6.28% 47.05% 1446ms 6.28% __gnu_cxx::__normal_iterator::operator-- (inline) 56ms 0.24% 47.29% 1196ms 5.19% boost::numeric::ublas::c_vector::c_vector (partial-inline) 1ms 0.0043% 47.30% 1169ms 5.08% NodeBasedCellPopulation::UpdateCellProcessLocation 6ms 0.026% 47.33% 1079ms 4.69% DistributedBoxCollection::CalculateBoundaryNodePairs 42ms 0.18% 47.51% 1063ms 4.62% boost::numeric::ublas::vector_assign (inline) 260ms 1.13% 48.64% 973ms 4.22% __dynamic_cast 284ms 1.23% 49.87% 960ms 4.17% boost::numeric::ublas::indexing_vector_assign 20ms 0.087% 49.96% 827ms 3.59% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 372ms 1.62% 51.57% 795ms 3.45% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 51.57% 782ms 3.40% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 159ms 0.69% 52.26% 775ms 3.37% AbstractMesh::GetVectorFromAtoB 0 0% 52.26% 765ms 3.32% boost::numeric::ublas::norm_2 (inline) 608ms 2.64% 54.90% 765ms 3.32% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 54.90% 765ms 3.32% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 222ms 0.96% 55.87% 730ms 3.17% NodeAttributes::AddNeighbour 0 0% 55.87% 703ms 3.05% AbstractCellPopulation::WriteResultsToFiles 4ms 0.017% 55.88% 661ms 2.87% boost::numeric::ublas::c_vector::operator= (inline) 643ms 2.79% 58.68% 643ms 2.79% boost::numeric::ublas::c_vector::operator() 27ms 0.12% 58.79% 638ms 2.77% std::__copy_move::__copy_m (inline) 0 0% 58.79% 638ms 2.77% std::__copy_move_a (inline) 0 0% 58.79% 638ms 2.77% std::__copy_move_a1 (inline) 0 0% 58.79% 638ms 2.77% std::__copy_move_a2 (inline) 0 0% 58.79% 638ms 2.77% std::copy (inline) 630ms 2.74% 61.53% 630ms 2.74% __memcpy_avx_unaligned_erms 507ms 2.20% 63.73% 573ms 2.49% std::vector::push_back (inline) 0 0% 63.73% 561ms 2.44% AbstractCellBasedSimulation::DoCellBirth 269ms 1.17% 64.90% 561ms 2.44% __cxxabiv1::__si_class_type_info::__do_dyncast 5ms 0.022% 64.92% 549ms 2.38% CellPropertyCollection::GetPropertiesType (inline) 7ms 0.03% 64.95% 530ms 2.30% AbstractCentreBasedCellPopulation::GetDampingConstant 70ms 0.3% 65.25% 520ms 2.26% std::__new_allocator::allocate (inline) 512ms 2.22% 67.48% 512ms 2.22% __strcmp_avx2 27ms 0.12% 67.59% 500ms 2.17% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 67.59% 500ms 2.17% std::allocator_traits::allocate (inline) 0 0% 67.59% 488ms 2.12% std::_Rb_tree::_M_create_node (inline) 29ms 0.13% 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% 464ms 2.01% NodeBasedCellPopulation::WriteVtkResultsToFile 42ms 0.18% 67.90% 461ms 2.00% std::_Rb_tree::_M_copy (inline) 458ms 1.99% 69.89% 458ms 1.99% boost::numeric::ublas::same_impl_ex 0 0% 69.89% 451ms 1.96% AbstractCellBasedSimulation::DoCellRemoval (inline) 25ms 0.11% 70.00% 446ms 1.94% operator new 439ms 1.91% 71.91% 445ms 1.93% boost::detail::sp_counted_base::release 28ms 0.12% 72.03% 439ms 1.91% std::_Rb_tree_const_iterator::operator++ (inline) 4ms 0.017% 72.05% 433ms 1.88% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 72.05% 433ms 1.88% std::_Rb_tree::_M_get_node (inline) 6ms 0.026% 72.07% 422ms 1.83% AbstractCellProperty::IsSubType (inline) 146ms 0.63% 72.71% 417ms 1.81% std::_Rb_tree::_M_clone_node (inline) 140ms 0.61% 73.31% 416ms 1.81% __GI___libc_malloc 411ms 1.78% 75.10% 411ms 1.78% std::_Rb_tree_increment 3ms 0.013% 75.11% 401ms 1.74% std::set::set (inline) 146ms 0.63% 75.74% 396ms 1.72% Node::GetRadius 115ms 0.5% 76.24% 378ms 1.64% std::_Rb_tree::_M_erase 1ms 0.0043% 76.25% 369ms 1.60% Cell::GetMutationState 0 0% 76.25% 334ms 1.45% std::_Rb_tree::_Alloc_node::operator() (inline) 7ms 0.03% 76.28% 322ms 1.40% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 76.28% 317ms 1.38% NodesOnlyMesh::ReMesh 315ms 1.37% 77.65% 315ms 1.37% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 2ms 0.0087% 77.66% 307ms 1.33% NodesOnlyMesh::UpdateNodeIndices 44ms 0.19% 77.85% 303ms 1.32% std::_Rb_tree::~_Rb_tree (inline) 0 0% 77.85% 302ms 1.31% boost::numeric::ublas::inner_prod (inline) 19ms 0.083% 77.93% 302ms 1.31% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 77.93% 302ms 1.31% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 77.93% 299ms 1.30% boost::numeric::ublas::c_vector::assign (inline) 3ms 0.013% 77.94% 296ms 1.29% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 24ms 0.1% 78.05% 295ms 1.28% boost::numeric::ublas::vector_binary::size (inline) 288ms 1.25% 79.30% 288ms 1.25% __gnu_cxx::__normal_iterator::operator++ (inline) 10ms 0.043% 79.34% 286ms 1.24% std::_Rb_tree::_M_emplace_hint_unique 4ms 0.017% 79.36% 278ms 1.21% DistributedBoxCollection::GetProcessOwningNode 0 0% 79.36% 262ms 1.14% NodesOnlyMesh::UpdateBoxCollection 0 0% 79.36% 258ms 1.12% std::_Rb_tree::_M_drop_node (inline) 257ms 1.12% 80.47% 257ms 1.12% Node::CheckForNodeAttributes 107ms 0.46% 80.94% 245ms 1.06% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 80.94% 237ms 1.03% std::set::~set (inline) 4ms 0.017% 80.96% 235ms 1.02% std::__new_allocator::deallocate (inline) 1ms 0.0043% 80.96% 230ms 1% NodesOnlyMesh::AddNodesToBoxes 0 0% 80.96% 226ms 0.98% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 226ms 0.98% 81.94% 226ms 0.98% Node::GetIndex 0 0% 81.94% 224ms 0.97% VtkMeshWriter::WriteFiles 139ms 0.6% 82.54% 222ms 0.96% _int_malloc 82ms 0.36% 82.90% 219ms 0.95% __GI___libc_free 0 0% 82.90% 205ms 0.89% Cell::HasCellProperty (inline) 3ms 0.013% 82.91% 205ms 0.89% CellPropertyCollection::HasProperty 104ms 0.45% 83.37% 203ms 0.88% std::__move_median_to_first (inline) 115ms 0.5% 83.86% 202ms 0.88% boost::shared_ptr::shared_ptr (inline) 20ms 0.087% 83.95% 202ms 0.88% std::__insertion_sort (inline) 0 0% 83.95% 201ms 0.87% std::allocator_traits::deallocate (inline) 0 0% 83.95% 197ms 0.86% std::_Rb_tree::_M_put_node (inline) 0 0% 83.95% 196ms 0.85% vtkStreamingDemandDrivenPipeline::Update 0 0% 83.95% 196ms 0.85% vtkXMLWriterBase::Write 0 0% 83.95% 195ms 0.85% vtkDemandDrivenPipeline::ExecuteData 0 0% 83.95% 195ms 0.85% vtkDemandDrivenPipeline::ProcessRequest 0 0% 83.95% 195ms 0.85% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 83.95% 194ms 0.84% vtkCompositeDataPipeline::ExecuteData 0 0% 83.95% 194ms 0.84% vtkExecutive::CallAlgorithm 0 0% 83.95% 194ms 0.84% vtkXMLUnstructuredDataWriter::ProcessRequest 3ms 0.013% 83.96% 184ms 0.8% AbstractCellProperty::IsType (inline) 1ms 0.0043% 83.97% 184ms 0.8% NodesOnlyMesh::ResizeBoxCollection 10ms 0.043% 84.01% 181ms 0.79% NodesOnlyMesh::IsANodeCloseToDomainBoundary 178ms 0.77% 84.79% 178ms 0.77% [libchaste_cell_based.so] 0 0% 84.79% 168ms 0.73% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 84.79% 168ms 0.73% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 84.79% 166ms 0.72% Cell::ReadyToDivide 1ms 0.0043% 84.79% 162ms 0.7% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 9ms 0.039% 84.83% 161ms 0.7% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 84.83% 154ms 0.67% std::_Rb_tree::_Auto_node::_Auto_node (inline) 152ms 0.66% 85.49% 152ms 0.66% Node::IsDeleted 43ms 0.19% 85.68% 145ms 0.63% AbstractCellProperty::IsSame 64ms 0.28% 85.95% 145ms 0.63% Node::AddNeighbour 0 0% 85.95% 144ms 0.63% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 144ms 0.63% 86.58% 144ms 0.63% std::__adjacent_find (inline) 0 0% 86.58% 144ms 0.63% std::__unique (inline) 0 0% 86.58% 144ms 0.63% std::unique (inline) 12ms 0.052% 86.63% 143ms 0.62% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 86.63% 138ms 0.6% vtkXMLWriter::WriteBinaryData 116ms 0.5% 87.13% 137ms 0.59% _int_free 1ms 0.0043% 87.14% 135ms 0.59% AbstractCellPopulation::SetCellUsingLocationIndex 135ms 0.59% 87.72% 135ms 0.59% Node::rGetLocation 0 0% 87.72% 135ms 0.59% std::_Rb_tree::clear (inline) 3ms 0.013% 87.74% 133ms 0.58% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 87.74% 132ms 0.57% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.74% 132ms 0.57% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.74% 132ms 0.57% vtkXMLWriter::WriteCompressionBlock 0 0% 87.74% 131ms 0.57% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 2ms 0.0087% 87.75% 129ms 0.56% Cell::GetCellId 129ms 0.56% 88.31% 129ms 0.56% [libchaste_mesh.so] 6ms 0.026% 88.33% 126ms 0.55% DistributedBoxCollection::GetIsPeriodicAllDims 0 0% 88.33% 123ms 0.53% vtkXMLWriter::WritePointsAppendedData 2ms 0.0087% 88.34% 122ms 0.53% std::_Rb_tree::_M_insert_unique 0 0% 88.34% 122ms 0.53% std::set::insert (inline) 121ms 0.53% 88.87% 121ms 0.53% boost::shared_ptr::operator-> (inline) 118ms 0.51% 89.38% 118ms 0.51% __ieee754_log_fma 0 0% 89.38% 116ms 0.5% boost::numeric::ublas::vector_binary::operator() (inline)