File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 14063ms, 89.95% of 15634ms total Dropped 615 nodes (cum <= 78.17ms) flat flat% sum% cum cum% 0 0% 0% 15569ms 99.58% __libc_start_call_main 0 0% 0% 15569ms 99.58% __libc_start_main_impl 0 0% 0% 15569ms 99.58% _start 0 0% 0% 15556ms 99.50% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 15556ms 99.50% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 15556ms 99.50% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 15556ms 99.50% main 0 0% 0% 15526ms 99.31% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 15526ms 99.31% CxxTest::TestRunner::runTest (inline) 0 0% 0% 15526ms 99.31% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 15520ms 99.27% AbstractCellBasedSimulation::Solve 1ms 0.0064% 0.0064% 8918ms 57.04% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0064% 5911ms 37.81% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.019% 0.026% 5296ms 33.87% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 0.026% 5214ms 33.35% NodeBasedCellPopulation::Update 0 0% 0.026% 5178ms 33.12% AbstractNumericalMethod::ComputeForcesIncludingDamping 796ms 5.09% 5.12% 4838ms 30.95% RepulsionForce::AddForceContribution (partial-inline) 5ms 0.032% 5.15% 3897ms 24.93% DistributedBoxCollection::CalculateInteriorNodePairs 0 0% 5.15% 3427ms 21.92% OffLatticeSimulation::ApplyBoundaries 11ms 0.07% 5.22% 3281ms 20.99% NodeAttributes::RemoveDuplicateNeighbours 6ms 0.038% 5.26% 3158ms 20.20% std::__sort (inline) 0 0% 5.26% 3158ms 20.20% std::sort (inline) 1602ms 10.25% 15.50% 3152ms 20.16% std::_Rb_tree::_M_lower_bound (inline) 136ms 0.87% 16.37% 2504ms 16.02% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 100ms 0.64% 17.01% 2463ms 15.75% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 3ms 0.019% 17.03% 2411ms 15.42% AbstractCellPopulation::Iterator::operator++ (inline) 104ms 0.67% 17.70% 2401ms 15.36% AbstractCellPopulation::Iterator::IsRealCell (inline) 17ms 0.11% 17.81% 2013ms 12.88% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 165ms 1.06% 18.86% 1981ms 12.67% std::_Rb_tree::find (inline) 0 0% 18.86% 1981ms 12.67% std::map::find (inline) 138ms 0.88% 19.75% 1842ms 11.78% std::__introsort_loop 53ms 0.34% 20.08% 1774ms 11.35% PlaneBoundaryCondition::ImposeBoundaryCondition 231ms 1.48% 21.56% 1755ms 11.23% std::map::operator[] (partial-inline) 94ms 0.6% 22.16% 1686ms 10.78% AbstractMesh::GetNode 34ms 0.22% 22.38% 1653ms 10.57% PlaneBoundaryCondition::VerifyBoundaryCondition 4ms 0.026% 22.41% 1642ms 10.50% NodesOnlyMesh::GetNodeOrHaloNode 0 0% 22.41% 1628ms 10.41% std::__unguarded_partition_pivot (inline) 100ms 0.64% 23.05% 1595ms 10.20% NodesOnlyMesh::SolveNodeMapping 1527ms 9.77% 32.81% 1527ms 9.77% std::_Rb_tree::_S_right (inline) 48ms 0.31% 33.12% 1509ms 9.65% AbstractCellPopulation::GetLocationIndexUsingCell 767ms 4.91% 38.03% 1480ms 9.47% std::__unguarded_partition (inline) 0 0% 38.03% 1348ms 8.62% std::_Rb_tree::lower_bound (inline) 0 0% 38.03% 1348ms 8.62% std::map::lower_bound (inline) 0 0% 38.03% 1310ms 8.38% std::__final_insertion_sort (inline) 65ms 0.42% 38.44% 1154ms 7.38% std::__unguarded_insertion_sort (inline) 367ms 2.35% 40.79% 1133ms 7.25% std::__unguarded_linear_insert (inline) 1057ms 6.76% 47.55% 1057ms 6.76% __gnu_cxx::__normal_iterator::operator-- (inline) 96ms 0.61% 48.16% 1033ms 6.61% DistributedBoxCollection::AddPairsFromBox 13ms 0.083% 48.25% 1031ms 6.59% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 13ms 0.083% 48.33% 1014ms 6.49% AbstractCellPopulation::GetCellUsingLocationIndex 24ms 0.15% 48.48% 766ms 4.90% boost::numeric::ublas::c_vector::c_vector (partial-inline) 3ms 0.019% 48.50% 743ms 4.75% DistributedBoxCollection::CalculateBoundaryNodePairs 18ms 0.12% 48.62% 741ms 4.74% boost::detail::shared_count::~shared_count (inline) 0 0% 48.62% 741ms 4.74% boost::shared_ptr::~shared_ptr (inline) 17ms 0.11% 48.73% 729ms 4.66% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 707ms 4.52% 53.25% 714ms 4.57% boost::detail::sp_counted_base::release 23ms 0.15% 53.40% 681ms 4.36% boost::numeric::ublas::vector_assign (inline) 0 0% 53.40% 659ms 4.22% NodeBasedCellPopulation::UpdateCellProcessLocation 159ms 1.02% 54.41% 630ms 4.03% boost::numeric::ublas::indexing_vector_assign 0 0% 54.41% 587ms 3.75% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 54.41% 577ms 3.69% boost::numeric::ublas::norm_2 (inline) 393ms 2.51% 56.93% 577ms 3.69% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 56.93% 577ms 3.69% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 132ms 0.84% 57.77% 561ms 3.59% __dynamic_cast 238ms 1.52% 59.29% 535ms 3.42% DistributedBoxCollection::CalculateContainingBox (partial-inline) 83ms 0.53% 59.82% 487ms 3.12% AbstractMesh::GetVectorFromAtoB 0 0% 59.82% 433ms 2.77% AbstractCellPopulation::WriteResultsToFiles 417ms 2.67% 62.49% 417ms 2.67% boost::numeric::ublas::c_vector::operator() 2ms 0.013% 62.50% 393ms 2.51% boost::numeric::ublas::c_vector::operator= (inline) 32ms 0.2% 62.71% 387ms 2.48% std::__copy_move::__copy_m (inline) 0 0% 62.71% 387ms 2.48% std::__copy_move_a (inline) 0 0% 62.71% 387ms 2.48% std::__copy_move_a1 (inline) 0 0% 62.71% 387ms 2.48% std::__copy_move_a2 (inline) 0 0% 62.71% 387ms 2.48% std::copy (inline) 367ms 2.35% 65.06% 367ms 2.35% __memcpy_avx512_unaligned_erms 1ms 0.0064% 65.06% 366ms 2.34% AbstractCellBasedSimulation::DoCellBirth 173ms 1.11% 66.17% 355ms 2.27% __cxxabiv1::__si_class_type_info::__do_dyncast 101ms 0.65% 66.82% 355ms 2.27% std::_Rb_tree::~_Rb_tree (inline) 36ms 0.23% 67.05% 354ms 2.26% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 67.05% 331ms 2.12% AbstractCellBasedSimulation::DoCellRemoval (inline) 5ms 0.032% 67.08% 325ms 2.08% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 46ms 0.29% 67.37% 325ms 2.08% std::_Rb_tree::_M_erase 1ms 0.0064% 67.38% 319ms 2.04% CellPropertyCollection::GetPropertiesType (inline) 319ms 2.04% 69.42% 319ms 2.04% boost::numeric::ublas::same_impl_ex 19ms 0.12% 69.54% 317ms 2.03% std::_Rb_tree::_Rb_tree (partial-inline) 2ms 0.013% 69.55% 316ms 2.02% AbstractCentreBasedCellPopulation::GetDampingConstant 312ms 2.00% 71.55% 312ms 2.00% std::_Rb_tree_increment 27ms 0.17% 71.72% 309ms 1.98% std::__new_allocator::allocate (inline) 0 0% 71.72% 301ms 1.93% std::allocator_traits::allocate (inline) 294ms 1.88% 73.60% 294ms 1.88% __strcmp_evex 0 0% 73.60% 294ms 1.88% std::set::~set (inline) 1ms 0.0064% 73.61% 293ms 1.87% NodeBasedCellPopulation::WriteVtkResultsToFile 31ms 0.2% 73.81% 290ms 1.85% std::_Rb_tree::_M_copy (inline) 14ms 0.09% 73.90% 282ms 1.80% operator new 105ms 0.67% 74.57% 276ms 1.77% NodeAttributes::AddNeighbour 0 0% 74.57% 273ms 1.75% std::_Rb_tree::_M_create_node (inline) 0 0% 74.57% 268ms 1.71% std::_Rb_tree::_M_drop_node (inline) 108ms 0.69% 75.26% 260ms 1.66% __GI___libc_malloc 0 0% 75.26% 260ms 1.66% std::_Rb_tree::_M_get_node (inline) 0 0% 75.26% 260ms 1.66% std::set::set (inline) 104ms 0.67% 75.92% 257ms 1.64% std::_Rb_tree::_M_clone_node (inline) 3ms 0.019% 75.94% 239ms 1.53% AbstractCellProperty::IsSubType (inline) 25ms 0.16% 76.10% 225ms 1.44% Node::GetRadius 3ms 0.019% 76.12% 223ms 1.43% Cell::GetMutationState 6ms 0.038% 76.16% 220ms 1.41% boost::numeric::ublas::vector_binary::size (inline) 0 0% 76.16% 216ms 1.38% boost::numeric::ublas::c_vector::assign (inline) 170ms 1.09% 77.25% 211ms 1.35% std::vector::push_back (inline) 182ms 1.16% 78.41% 206ms 1.32% boost::shared_ptr::shared_ptr (inline) 202ms 1.29% 79.70% 202ms 1.29% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 79.70% 190ms 1.22% NodesOnlyMesh::ReMesh 1ms 0.0064% 79.71% 188ms 1.20% NodesOnlyMesh::UpdateNodeIndices 186ms 1.19% 80.90% 186ms 1.19% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 185ms 1.18% 82.08% 185ms 1.18% [libchaste_cell_based.so] 0 0% 82.08% 182ms 1.16% std::_Rb_tree::_Alloc_node::operator() (inline) 178ms 1.14% 83.22% 178ms 1.14% Node::CheckForNodeAttributes 3ms 0.019% 83.24% 177ms 1.13% NodeBasedCellPopulation::UpdateMapsAfterRemesh 10ms 0.064% 83.31% 176ms 1.13% std::_Rb_tree::_M_emplace_hint_unique 5ms 0.032% 83.34% 172ms 1.10% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 83.34% 170ms 1.09% NodesOnlyMesh::UpdateBoxCollection 1ms 0.0064% 83.34% 169ms 1.08% std::__new_allocator::deallocate (inline) 3ms 0.019% 83.36% 161ms 1.03% DistributedBoxCollection::GetProcessOwningNode 15ms 0.096% 83.46% 156ms 1% std::__insertion_sort (inline) 0 0% 83.46% 154ms 0.99% std::_Rb_tree::_M_put_node (inline) 0 0% 83.46% 154ms 0.99% std::allocator_traits::deallocate (inline) 0 0% 83.46% 149ms 0.95% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 83.46% 146ms 0.93% boost::numeric::ublas::inner_prod (inline) 1ms 0.0064% 83.47% 146ms 0.93% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 145ms 0.93% 84.39% 145ms 0.93% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 10ms 0.064% 84.46% 145ms 0.93% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 84.46% 143ms 0.91% NodesOnlyMesh::AddNodesToBoxes 31ms 0.2% 84.66% 141ms 0.9% __GI___libc_free 139ms 0.89% 85.54% 139ms 0.89% Node::GetIndex 68ms 0.43% 85.98% 138ms 0.88% std::__move_median_to_first (inline) 91ms 0.58% 86.56% 137ms 0.88% Node::AddNeighbour 0 0% 86.56% 136ms 0.87% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 86.56% 135ms 0.86% VtkMeshWriter::WriteFiles 37ms 0.24% 86.80% 121ms 0.77% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 86.80% 121ms 0.77% vtkStreamingDemandDrivenPipeline::Update 0 0% 86.80% 121ms 0.77% vtkXMLWriterBase::Write 0 0% 86.80% 120ms 0.77% vtkExecutive::CallAlgorithm 0 0% 86.80% 120ms 0.77% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 86.80% 119ms 0.76% vtkDemandDrivenPipeline::ProcessRequest 0 0% 86.80% 119ms 0.76% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 86.80% 118ms 0.75% vtkCompositeDataPipeline::ExecuteData 0 0% 86.80% 118ms 0.75% vtkDemandDrivenPipeline::ExecuteData 0 0% 86.80% 117ms 0.75% std::__new_allocator::destroy (inline) 0 0% 86.80% 117ms 0.75% std::allocator_traits::destroy (inline) 0 0% 86.80% 116ms 0.74% std::_Rb_tree::_M_destroy_node (inline) 67ms 0.43% 87.23% 115ms 0.74% _int_malloc 3ms 0.019% 87.25% 111ms 0.71% CellPropertyCollection::HasProperty 111ms 0.71% 87.96% 111ms 0.71% boost::shared_ptr::operator-> (inline) 0 0% 87.96% 109ms 0.7% Cell::HasCellProperty (inline) 109ms 0.7% 88.65% 109ms 0.7% [libchaste_mesh.so] 99ms 0.63% 89.29% 108ms 0.69% _int_free 0 0% 89.29% 102ms 0.65% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 89.29% 100ms 0.64% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 89.29% 100ms 0.64% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 4ms 0.026% 89.31% 99ms 0.63% Cell::ReadyToDivide 0 0% 89.31% 96ms 0.61% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 80ms 0.51% 89.82% 95ms 0.61% std::__adjacent_find (inline) 0 0% 89.82% 95ms 0.61% std::__unique (inline) 0 0% 89.82% 95ms 0.61% std::unique (inline) 3ms 0.019% 89.84% 93ms 0.59% AbstractCellProperty::IsType (inline) 2ms 0.013% 89.86% 93ms 0.59% std::_Rb_tree::_M_insert_unique 0 0% 89.86% 93ms 0.59% std::set::insert (inline) 0 0% 89.86% 91ms 0.58% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 89.86% 89ms 0.57% NodesOnlyMesh::ResizeBoxCollection 5ms 0.032% 89.89% 88ms 0.56% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 89.89% 86ms 0.55% vtkXMLWriter::WriteBinaryData 4ms 0.026% 89.91% 85ms 0.54% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 1ms 0.0064% 89.92% 85ms 0.54% Cell::GetCellId 3ms 0.019% 89.94% 85ms 0.54% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 89.94% 83ms 0.53% vtkXMLWriter::WriteBinaryDataBlock 0 0% 89.94% 83ms 0.53% vtkXMLWriter::WriteBinaryDataInternal 0 0% 89.94% 83ms 0.53% vtkXMLWriter::WriteCompressionBlock 0 0% 89.94% 83ms 0.53% vtkXMLWriter::WritePointsAppendedData 2ms 0.013% 89.95% 82ms 0.52% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 89.95% 81ms 0.52% AbstractCellPopulation::SetCellUsingLocationIndex 0 0% 89.95% 80ms 0.51% std::_Rb_tree::clear (inline)