File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20694ms, 89.11% of 23222ms total Dropped 773 nodes (cum <= 116.11ms) flat flat% sum% cum cum% 0 0% 0% 23060ms 99.30% __libc_start_call_main 0 0% 0% 23060ms 99.30% __libc_start_main_impl 0 0% 0% 23060ms 99.30% _start 0 0% 0% 23044ms 99.23% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 23044ms 99.23% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 23044ms 99.23% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 23044ms 99.23% main 0 0% 0% 23004ms 99.06% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 23004ms 99.06% CxxTest::TestRunner::runTest (inline) 0 0% 0% 23003ms 99.06% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 22996ms 99.03% AbstractCellBasedSimulation::Solve 1ms 0.0043% 0.0043% 13076ms 56.31% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0043% 8713ms 37.52% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.017% 0.022% 8264ms 35.59% ForwardEulerNumericalMethod::UpdateAllNodePositions 13ms 0.056% 0.078% 8070ms 34.75% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.078% 7723ms 33.26% NodeBasedCellPopulation::Update 1192ms 5.13% 5.21% 7449ms 32.08% RepulsionForce::AddForceContribution (partial-inline) 9ms 0.039% 5.25% 5667ms 24.40% DistributedBoxCollection::CalculateInteriorNodePairs 2042ms 8.79% 14.04% 4857ms 20.92% std::_Rb_tree::_M_lower_bound (inline) 0 0% 14.04% 4510ms 19.42% OffLatticeSimulation::ApplyBoundaries 30ms 0.13% 14.17% 4495ms 19.36% NodeAttributes::RemoveDuplicateNeighbours 9ms 0.039% 14.21% 4317ms 18.59% std::__sort (inline) 0 0% 14.21% 4317ms 18.59% std::sort (inline) 193ms 0.83% 15.04% 3788ms 16.31% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 0 0% 15.04% 3381ms 14.56% AbstractCellPopulation::Iterator::operator++ (inline) 173ms 0.74% 15.79% 3357ms 14.46% AbstractCellPopulation::Iterator::IsRealCell 72ms 0.31% 16.10% 3317ms 14.28% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 238ms 1.02% 17.12% 3186ms 13.72% std::_Rb_tree::find (inline) 0 0% 17.12% 3186ms 13.72% std::map::find (inline) 24ms 0.1% 17.23% 2824ms 12.16% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2783ms 11.98% 29.21% 2783ms 11.98% std::_Rb_tree::_S_right (inline) 186ms 0.8% 30.01% 2492ms 10.73% std::__introsort_loop 239ms 1.03% 31.04% 2416ms 10.40% std::map::operator[] (partial-inline) 32ms 0.14% 31.18% 2358ms 10.15% PlaneBoundaryCondition::ImposeBoundaryCondition 163ms 0.7% 31.88% 2297ms 9.89% AbstractMesh::GetNode 43ms 0.19% 32.06% 2252ms 9.70% NodesOnlyMesh::GetNodeOrHaloNode 1ms 0.0043% 32.07% 2234ms 9.62% std::__unguarded_partition_pivot (inline) 38ms 0.16% 32.23% 2218ms 9.55% AbstractCellPopulation::GetLocationIndexUsingCell 21ms 0.09% 32.32% 2152ms 9.27% PlaneBoundaryCondition::VerifyBoundaryCondition 87ms 0.37% 32.70% 2139ms 9.21% NodesOnlyMesh::SolveNodeMapping 1065ms 4.59% 37.28% 2024ms 8.72% std::__unguarded_partition (inline) 0 0% 37.28% 1930ms 8.31% std::_Rb_tree::lower_bound (inline) 0 0% 37.28% 1930ms 8.31% std::map::lower_bound (inline) 156ms 0.67% 37.96% 1834ms 7.90% DistributedBoxCollection::AddPairsFromBox 1ms 0.0043% 37.96% 1815ms 7.82% std::__final_insertion_sort (inline) 100ms 0.43% 38.39% 1637ms 7.05% std::__unguarded_insertion_sort (inline) 575ms 2.48% 40.87% 1561ms 6.72% std::__unguarded_linear_insert (inline) 25ms 0.11% 40.97% 1514ms 6.52% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 18ms 0.078% 41.05% 1482ms 6.38% AbstractCellPopulation::GetCellUsingLocationIndex 1427ms 6.15% 47.20% 1427ms 6.15% __gnu_cxx::__normal_iterator::operator-- (inline) 41ms 0.18% 47.37% 1278ms 5.50% boost::numeric::ublas::c_vector::c_vector (partial-inline) 37ms 0.16% 47.53% 1180ms 5.08% boost::numeric::ublas::vector_assign (inline) 1ms 0.0043% 47.54% 1139ms 4.90% NodeBasedCellPopulation::UpdateCellProcessLocation 8ms 0.034% 47.57% 1093ms 4.71% DistributedBoxCollection::CalculateBoundaryNodePairs 289ms 1.24% 48.82% 1060ms 4.56% boost::numeric::ublas::indexing_vector_assign 254ms 1.09% 49.91% 901ms 3.88% __dynamic_cast 356ms 1.53% 51.44% 790ms 3.40% DistributedBoxCollection::CalculateContainingBox (partial-inline) 15ms 0.065% 51.51% 772ms 3.32% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 158ms 0.68% 52.19% 761ms 3.28% AbstractMesh::GetVectorFromAtoB 0 0% 52.19% 727ms 3.13% AbstractCellPopulation::WriteResultsToFiles 0 0% 52.19% 715ms 3.08% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 52.19% 702ms 3.02% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 174ms 0.75% 52.94% 701ms 3.02% NodeAttributes::AddNeighbour 0 0% 52.94% 701ms 3.02% boost::numeric::ublas::norm_2 (inline) 556ms 2.39% 55.33% 701ms 3.02% boost::numeric::ublas::vector_norm_2::apply (inline) 690ms 2.97% 58.30% 690ms 2.97% boost::numeric::ublas::c_vector::operator() 9ms 0.039% 58.34% 667ms 2.87% boost::numeric::ublas::c_vector::operator= (inline) 37ms 0.16% 58.50% 646ms 2.78% std::__copy_move::__copy_m (inline) 0 0% 58.50% 646ms 2.78% std::__copy_move_a (inline) 0 0% 58.50% 646ms 2.78% std::__copy_move_a1 (inline) 0 0% 58.50% 646ms 2.78% std::__copy_move_a2 (inline) 0 0% 58.50% 646ms 2.78% std::copy (inline) 619ms 2.67% 61.17% 619ms 2.67% __memcpy_avx_unaligned_erms 527ms 2.27% 63.44% 587ms 2.53% std::vector::push_back (inline) 0 0% 63.44% 581ms 2.50% AbstractCellBasedSimulation::DoCellBirth 34ms 0.15% 63.58% 569ms 2.45% std::_Rb_tree_const_iterator::operator++ (inline) 5ms 0.022% 63.60% 552ms 2.38% CellPropertyCollection::GetPropertiesType (inline) 4ms 0.017% 63.62% 541ms 2.33% AbstractCentreBasedCellPopulation::GetDampingConstant 255ms 1.10% 64.72% 534ms 2.30% __cxxabiv1::__si_class_type_info::__do_dyncast 531ms 2.29% 67.01% 531ms 2.29% std::_Rb_tree_increment 37ms 0.16% 67.16% 518ms 2.23% boost::detail::shared_count::~shared_count (inline) 0 0% 67.16% 518ms 2.23% boost::shared_ptr::~shared_ptr (inline) 67ms 0.29% 67.45% 486ms 2.09% std::__new_allocator::allocate (inline) 3ms 0.013% 67.47% 484ms 2.08% NodeBasedCellPopulation::WriteVtkResultsToFile 465ms 2.00% 69.47% 472ms 2.03% boost::detail::sp_counted_base::release 467ms 2.01% 71.48% 467ms 2.01% boost::numeric::ublas::same_impl_ex 0 0% 71.48% 462ms 1.99% std::allocator_traits::allocate (inline) 29ms 0.12% 71.60% 439ms 1.89% std::_Rb_tree::_Rb_tree (partial-inline) 437ms 1.88% 73.49% 437ms 1.88% __strcmp_avx2 0 0% 73.49% 434ms 1.87% std::_Rb_tree::_M_create_node (inline) 130ms 0.56% 74.05% 418ms 1.80% Node::GetRadius 29ms 0.12% 74.17% 418ms 1.80% operator new 0 0% 74.17% 409ms 1.76% AbstractCellBasedSimulation::DoCellRemoval (inline) 37ms 0.16% 74.33% 400ms 1.72% std::_Rb_tree::_M_copy (inline) 3ms 0.013% 74.34% 394ms 1.70% AbstractCellProperty::IsSubType (inline) 6ms 0.026% 74.37% 393ms 1.69% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 124ms 0.53% 74.90% 391ms 1.68% std::_Rb_tree::_M_erase 8ms 0.034% 74.94% 386ms 1.66% Cell::GetMutationState 99ms 0.43% 75.36% 386ms 1.66% __GI___libc_malloc 0 0% 75.36% 380ms 1.64% std::_Rb_tree::_M_get_node (inline) 100ms 0.43% 75.79% 363ms 1.56% std::_Rb_tree::_M_clone_node (inline) 0 0% 75.79% 348ms 1.50% boost::numeric::ublas::c_vector::assign (inline) 2ms 0.0086% 75.80% 342ms 1.47% std::set::set (inline) 45ms 0.19% 76.00% 321ms 1.38% std::_Rb_tree::~_Rb_tree (inline) 0 0% 76.00% 319ms 1.37% boost::numeric::ublas::inner_prod (inline) 3ms 0.013% 76.01% 318ms 1.37% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 15ms 0.065% 76.07% 315ms 1.36% boost::numeric::ublas::vector_scalar_binary::evaluate 313ms 1.35% 77.42% 313ms 1.35% __gnu_cxx::__normal_iterator::operator++ (inline) 22ms 0.095% 77.52% 313ms 1.35% boost::numeric::ublas::vector_binary::size (inline) 7ms 0.03% 77.55% 309ms 1.33% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 77.55% 307ms 1.32% std::_Rb_tree::_Alloc_node::operator() (inline) 301ms 1.30% 78.84% 301ms 1.30% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 4ms 0.017% 78.86% 300ms 1.29% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 78.86% 300ms 1.29% NodesOnlyMesh::UpdateBoxCollection 292ms 1.26% 80.12% 292ms 1.26% Node::CheckForNodeAttributes 4ms 0.017% 80.14% 281ms 1.21% DistributedBoxCollection::GetProcessOwningNode 0 0% 80.14% 270ms 1.16% NodesOnlyMesh::ReMesh 3ms 0.013% 80.15% 259ms 1.12% NodesOnlyMesh::UpdateNodeIndices 0 0% 80.15% 252ms 1.09% std::_Rb_tree::_M_drop_node (inline) 99ms 0.43% 80.57% 249ms 1.07% boost::numeric::ublas::vector_inner_prod::apply (inline) 10ms 0.043% 80.62% 247ms 1.06% std::_Rb_tree::_M_emplace_hint_unique 0 0% 80.62% 244ms 1.05% NodesOnlyMesh::AddNodesToBoxes 0 0% 80.62% 236ms 1.02% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 80.62% 235ms 1.01% VtkMeshWriter::WriteFiles 0 0% 80.62% 233ms 1.00% std::set::~set (inline) 140ms 0.6% 81.22% 232ms 1% _int_malloc 98ms 0.42% 81.64% 222ms 0.96% Node::AddNeighbour 0 0% 81.64% 212ms 0.91% vtkStreamingDemandDrivenPipeline::Update 0 0% 81.64% 212ms 0.91% vtkXMLWriterBase::Write 0 0% 81.64% 210ms 0.9% vtkDemandDrivenPipeline::ProcessRequest 0 0% 81.64% 209ms 0.9% vtkExecutive::CallAlgorithm 110ms 0.47% 82.12% 208ms 0.9% boost::shared_ptr::shared_ptr (inline) 0 0% 82.12% 207ms 0.89% NodesOnlyMesh::ResizeBoxCollection 1ms 0.0043% 82.12% 207ms 0.89% std::__new_allocator::deallocate (inline) 105ms 0.45% 82.57% 206ms 0.89% std::__move_median_to_first (inline) 0 0% 82.57% 206ms 0.89% vtkStreamingDemandDrivenPipeline::ProcessRequest 15ms 0.065% 82.64% 205ms 0.88% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 82.64% 205ms 0.88% vtkCompositeDataPipeline::ExecuteData 0 0% 82.64% 205ms 0.88% vtkDemandDrivenPipeline::ExecuteData 0 0% 82.64% 205ms 0.88% vtkXMLUnstructuredDataWriter::ProcessRequest 67ms 0.29% 82.93% 187ms 0.81% __GI___libc_free 5ms 0.022% 82.95% 185ms 0.8% CellPropertyCollection::HasProperty 0 0% 82.95% 183ms 0.79% Cell::HasCellProperty (inline) 182ms 0.78% 83.73% 182ms 0.78% [libchaste_cell_based.so] 0 0% 83.73% 181ms 0.78% std::_Rb_tree::_M_put_node (inline) 0 0% 83.73% 181ms 0.78% std::allocator_traits::deallocate (inline) 0 0% 83.73% 178ms 0.77% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 83.73% 178ms 0.77% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 9ms 0.039% 83.77% 177ms 0.76% std::__insertion_sort (inline) 7ms 0.03% 83.80% 174ms 0.75% Cell::ReadyToDivide 8ms 0.034% 83.83% 173ms 0.74% AbstractCellProperty::IsType (inline) 0 0% 83.83% 170ms 0.73% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 161ms 0.69% 84.53% 163ms 0.7% Node::ConstructNodeAttributes (inline) 154ms 0.66% 85.19% 154ms 0.66% Node::GetIndex 1ms 0.0043% 85.20% 151ms 0.65% AbstractNumericalMethod::SafeNodePositionUpdate 2ms 0.0086% 85.20% 144ms 0.62% DistributedBoxCollection::GetIsPeriodicAllDims 144ms 0.62% 85.82% 144ms 0.62% [libchaste_mesh.so] 0 0% 85.82% 141ms 0.61% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 85.82% 141ms 0.61% vtkXMLWriter::WriteBinaryData 134ms 0.58% 86.40% 138ms 0.59% std::__adjacent_find (inline) 0 0% 86.40% 138ms 0.59% std::__unique (inline) 0 0% 86.40% 138ms 0.59% std::unique (inline) 0 0% 86.40% 135ms 0.58% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 134ms 0.58% 86.98% 134ms 0.58% Node::IsDeleted 134ms 0.58% 87.55% 134ms 0.58% boost::shared_ptr::operator-> (inline) 1ms 0.0043% 87.56% 132ms 0.57% Cell::GetCellId 0 0% 87.56% 132ms 0.57% std::_Rb_tree::clear (inline) 0 0% 87.56% 131ms 0.56% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.56% 131ms 0.56% vtkXMLWriter::WriteBinaryDataInternal 1ms 0.0043% 87.56% 130ms 0.56% AbstractCellPopulation::SetCellUsingLocationIndex 6ms 0.026% 87.59% 130ms 0.56% NodeBasedCellPopulation::SetNode 0 0% 87.59% 130ms 0.56% tbb::detail::r1::parallel_pipeline 0 0% 87.59% 130ms 0.56% vtkXMLWriter::WriteCompressionBlock 0 0% 87.59% 129ms 0.56% boost::numeric::ublas::vector_binary::operator() (inline) 128ms 0.55% 88.14% 128ms 0.55% Node::rGetLocation 0 0% 88.14% 128ms 0.55% clone3 0 0% 88.14% 128ms 0.55% start_thread 0 0% 88.14% 127ms 0.55% std::_Rb_tree::_Auto_node::_Auto_node (inline) 2ms 0.0086% 88.15% 126ms 0.54% tbb::detail::r1::reset 14ms 0.06% 88.21% 125ms 0.54% boost::numeric::ublas::vector_reference::operator() (inline) 6ms 0.026% 88.24% 124ms 0.53% boost::numeric::ublas::c_vector::operator[] (inline) 49ms 0.21% 88.45% 120ms 0.52% AbstractCellProperty::IsSame 3ms 0.013% 88.46% 120ms 0.52% NodesOnlyMesh::SetNode 104ms 0.45% 88.91% 120ms 0.52% _int_free 0 0% 88.91% 119ms 0.51% vtkXMLWriter::WritePointsAppendedData 0 0% 88.91% 118ms 0.51% vtkDataCompressor::Compress 0 0% 88.91% 117ms 0.5% compress2 48ms 0.21% 89.11% 117ms 0.5% tbb::detail::r1::wait_bounded_queue_monitor 0 0% 89.11% 117ms 0.5% vtkZLibDataCompressor::CompressBuffer