File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 22020ms, 89.37% of 24638ms total Dropped 806 nodes (cum <= 123.19ms) flat flat% sum% cum cum% 0 0% 0% 24513ms 99.49% __libc_start_call_main 0 0% 0% 24513ms 99.49% __libc_start_main_impl 0 0% 0% 24513ms 99.49% _start 0 0% 0% 24495ms 99.42% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 24495ms 99.42% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 24495ms 99.42% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 24495ms 99.42% main 0 0% 0% 24454ms 99.25% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 24454ms 99.25% CxxTest::TestRunner::runTest (inline) 0 0% 0% 24454ms 99.25% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 24445ms 99.22% AbstractCellBasedSimulation::Solve 0 0% 0% 14069ms 57.10% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0% 9159ms 37.17% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.012% 0.012% 9099ms 36.93% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.032% 0.045% 8932ms 36.25% AbstractNumericalMethod::ComputeForcesIncludingDamping 1359ms 5.52% 5.56% 8244ms 33.46% RepulsionForce::AddForceContribution (partial-inline) 0 0% 5.56% 8092ms 32.84% NodeBasedCellPopulation::Update 3ms 0.012% 5.57% 6011ms 24.40% DistributedBoxCollection::CalculateInteriorNodePairs 2193ms 8.90% 14.47% 5134ms 20.84% std::_Rb_tree::_M_lower_bound (inline) 0 0% 14.47% 4644ms 18.85% OffLatticeSimulation::ApplyBoundaries 13ms 0.053% 14.53% 4622ms 18.76% NodeAttributes::RemoveDuplicateNeighbours 1ms 0.0041% 14.53% 4432ms 17.99% std::__sort (inline) 0 0% 14.53% 4432ms 17.99% std::sort (inline) 184ms 0.75% 15.28% 4090ms 16.60% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 244ms 0.99% 16.27% 3464ms 14.06% std::_Rb_tree::find (inline) 0 0% 16.27% 3464ms 14.06% std::map::find (inline) 86ms 0.35% 16.62% 3365ms 13.66% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 1ms 0.0041% 16.62% 3169ms 12.86% AbstractCellPopulation::Iterator::operator++ (inline) 155ms 0.63% 17.25% 3140ms 12.74% AbstractCellPopulation::Iterator::IsRealCell 2914ms 11.83% 29.08% 2914ms 11.83% std::_Rb_tree::_S_right (inline) 17ms 0.069% 29.15% 2729ms 11.08% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 172ms 0.7% 29.84% 2559ms 10.39% std::__introsort_loop 173ms 0.7% 30.55% 2519ms 10.22% AbstractMesh::GetNode 48ms 0.19% 30.74% 2499ms 10.14% NodesOnlyMesh::GetNodeOrHaloNode 19ms 0.077% 30.82% 2468ms 10.02% PlaneBoundaryCondition::ImposeBoundaryCondition 209ms 0.85% 31.67% 2443ms 9.92% std::map::operator[] (partial-inline) 99ms 0.4% 32.07% 2352ms 9.55% NodesOnlyMesh::SolveNodeMapping 0 0% 32.07% 2309ms 9.37% std::__unguarded_partition_pivot (inline) 50ms 0.2% 32.27% 2212ms 8.98% AbstractCellPopulation::GetLocationIndexUsingCell 20ms 0.081% 32.35% 2176ms 8.83% PlaneBoundaryCondition::VerifyBoundaryCondition 997ms 4.05% 36.40% 2070ms 8.40% std::__unguarded_partition (inline) 142ms 0.58% 36.98% 2008ms 8.15% DistributedBoxCollection::AddPairsFromBox 0 0% 36.98% 1945ms 7.89% std::_Rb_tree::lower_bound (inline) 0 0% 36.98% 1945ms 7.89% std::map::lower_bound (inline) 0 0% 36.98% 1870ms 7.59% std::__final_insertion_sort (inline) 28ms 0.11% 37.09% 1744ms 7.08% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 40ms 0.16% 37.25% 1705ms 6.92% AbstractCellPopulation::GetCellUsingLocationIndex 107ms 0.43% 37.69% 1691ms 6.86% std::__unguarded_insertion_sort (inline) 609ms 2.47% 40.16% 1597ms 6.48% std::__unguarded_linear_insert (inline) 1449ms 5.88% 46.04% 1449ms 5.88% __gnu_cxx::__normal_iterator::operator-- (inline) 67ms 0.27% 46.31% 1288ms 5.23% boost::numeric::ublas::c_vector::c_vector (partial-inline) 1ms 0.0041% 46.31% 1168ms 4.74% NodeBasedCellPopulation::UpdateCellProcessLocation 8ms 0.032% 46.35% 1130ms 4.59% boost::numeric::ublas::vector_assign (inline) 5ms 0.02% 46.37% 1100ms 4.46% DistributedBoxCollection::CalculateBoundaryNodePairs 224ms 0.91% 47.28% 1046ms 4.25% boost::numeric::ublas::indexing_vector_assign 21ms 0.085% 47.36% 983ms 3.99% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 283ms 1.15% 48.51% 936ms 3.80% __dynamic_cast 0 0% 48.51% 864ms 3.51% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 230ms 0.93% 49.44% 849ms 3.45% NodeAttributes::AddNeighbour 0 0% 49.44% 849ms 3.45% boost::numeric::ublas::norm_2 (inline) 694ms 2.82% 52.26% 849ms 3.45% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 52.26% 849ms 3.45% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 409ms 1.66% 53.92% 848ms 3.44% DistributedBoxCollection::CalculateContainingBox (partial-inline) 181ms 0.73% 54.66% 837ms 3.40% AbstractMesh::GetVectorFromAtoB 4ms 0.016% 54.67% 764ms 3.10% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 54.67% 741ms 3.01% AbstractCellPopulation::WriteResultsToFiles 38ms 0.15% 54.83% 740ms 3.00% std::__copy_move::__copy_m (inline) 0 0% 54.83% 740ms 3.00% std::__copy_move_a (inline) 0 0% 54.83% 740ms 3.00% std::__copy_move_a1 (inline) 0 0% 54.83% 740ms 3.00% std::__copy_move_a2 (inline) 0 0% 54.83% 740ms 3.00% std::copy (inline) 720ms 2.92% 57.75% 720ms 2.92% __memcpy_avx_unaligned_erms 615ms 2.50% 60.24% 689ms 2.80% std::vector::push_back (inline) 674ms 2.74% 62.98% 674ms 2.74% boost::numeric::ublas::c_vector::operator() 10ms 0.041% 63.02% 635ms 2.58% CellPropertyCollection::GetPropertiesType (inline) 3ms 0.012% 63.03% 603ms 2.45% AbstractCentreBasedCellPopulation::GetDampingConstant 21ms 0.085% 63.12% 588ms 2.39% std::_Rb_tree_const_iterator::operator++ (inline) 5ms 0.02% 63.14% 580ms 2.35% AbstractCellBasedSimulation::DoCellBirth 568ms 2.31% 65.44% 568ms 2.31% boost::numeric::ublas::same_impl_ex 42ms 0.17% 65.61% 548ms 2.22% boost::detail::shared_count::~shared_count (inline) 0 0% 65.61% 548ms 2.22% boost::shared_ptr::~shared_ptr (inline) 547ms 2.22% 67.83% 547ms 2.22% std::_Rb_tree_increment 107ms 0.43% 68.27% 541ms 2.20% std::__new_allocator::allocate (inline) 276ms 1.12% 69.39% 539ms 2.19% __cxxabiv1::__si_class_type_info::__do_dyncast 37ms 0.15% 69.54% 533ms 2.16% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 69.54% 526ms 2.13% std::allocator_traits::allocate (inline) 0 0% 69.54% 497ms 2.02% std::_Rb_tree::_M_create_node (inline) 1ms 0.0041% 69.54% 487ms 1.98% NodeBasedCellPopulation::WriteVtkResultsToFile 474ms 1.92% 71.47% 487ms 1.98% boost::detail::sp_counted_base::release 0 0% 71.47% 486ms 1.97% AbstractCellBasedSimulation::DoCellRemoval (inline) 44ms 0.18% 71.65% 481ms 1.95% std::_Rb_tree::_M_copy (inline) 3ms 0.012% 71.66% 472ms 1.92% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1ms 0.0041% 71.66% 445ms 1.81% AbstractCellProperty::IsSubType (inline) 0 0% 71.66% 440ms 1.79% std::_Rb_tree::_M_get_node (inline) 18ms 0.073% 71.73% 432ms 1.75% operator new 142ms 0.58% 72.31% 431ms 1.75% std::_Rb_tree::_M_clone_node (inline) 5ms 0.02% 72.33% 426ms 1.73% std::set::set (inline) 4ms 0.016% 72.35% 423ms 1.72% Cell::GetMutationState 419ms 1.70% 74.05% 419ms 1.70% __strcmp_avx2 123ms 0.5% 74.55% 416ms 1.69% std::_Rb_tree::_M_erase 103ms 0.42% 74.97% 406ms 1.65% __GI___libc_malloc 92ms 0.37% 75.34% 395ms 1.60% boost::numeric::ublas::vector_binary::size (inline) 0 0% 75.34% 379ms 1.54% boost::numeric::ublas::inner_prod (inline) 13ms 0.053% 75.39% 377ms 1.53% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 75.39% 377ms 1.53% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 88ms 0.36% 75.75% 367ms 1.49% Node::GetRadius 349ms 1.42% 77.17% 349ms 1.42% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 338ms 1.37% 78.54% 338ms 1.37% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 78.54% 336ms 1.36% std::_Rb_tree::_Alloc_node::operator() (inline) 57ms 0.23% 78.77% 334ms 1.36% std::_Rb_tree::~_Rb_tree (inline) 7ms 0.028% 78.80% 325ms 1.32% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 78.80% 323ms 1.31% NodesOnlyMesh::ReMesh 0 0% 78.80% 323ms 1.31% boost::numeric::ublas::c_vector::assign (inline) 2ms 0.0081% 78.81% 317ms 1.29% NodesOnlyMesh::UpdateNodeIndices 3ms 0.012% 78.82% 311ms 1.26% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 129ms 0.52% 79.34% 310ms 1.26% boost::numeric::ublas::vector_inner_prod::apply (inline) 7ms 0.028% 79.37% 291ms 1.18% DistributedBoxCollection::GetProcessOwningNode 0 0% 79.37% 289ms 1.17% std::_Rb_tree::_M_drop_node (inline) 13ms 0.053% 79.42% 289ms 1.17% std::_Rb_tree::_M_emplace_hint_unique 280ms 1.14% 80.56% 280ms 1.14% Node::CheckForNodeAttributes 1ms 0.0041% 80.56% 271ms 1.10% NodesOnlyMesh::UpdateBoxCollection 148ms 0.6% 81.16% 264ms 1.07% _int_malloc 0 0% 81.16% 254ms 1.03% std::set::~set (inline) 195ms 0.79% 81.95% 247ms 1.00% Node::AddNeighbour 0 0% 81.95% 244ms 0.99% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 81.95% 244ms 0.99% VtkMeshWriter::WriteFiles 4ms 0.016% 81.97% 242ms 0.98% std::__new_allocator::deallocate (inline) 100ms 0.41% 82.38% 237ms 0.96% std::__move_median_to_first (inline) 234ms 0.95% 83.33% 234ms 0.95% [libchaste_mesh.so] 105ms 0.43% 83.75% 229ms 0.93% boost::shared_ptr::shared_ptr (inline) 0 0% 83.75% 224ms 0.91% std::allocator_traits::deallocate (inline) 1ms 0.0041% 83.76% 223ms 0.91% NodesOnlyMesh::AddNodesToBoxes 0 0% 83.76% 221ms 0.9% Cell::HasCellProperty (inline) 2ms 0.0081% 83.76% 221ms 0.9% CellPropertyCollection::HasProperty 0 0% 83.76% 220ms 0.89% std::_Rb_tree::_M_put_node (inline) 219ms 0.89% 84.65% 219ms 0.89% Node::GetIndex 73ms 0.3% 84.95% 216ms 0.88% __GI___libc_free 0 0% 84.95% 214ms 0.87% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 84.95% 209ms 0.85% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 84.95% 209ms 0.85% vtkStreamingDemandDrivenPipeline::Update 0 0% 84.95% 209ms 0.85% vtkXMLWriterBase::Write 8ms 0.032% 84.98% 208ms 0.84% Cell::ReadyToDivide 0 0% 84.98% 207ms 0.84% vtkDemandDrivenPipeline::ExecuteData 0 0% 84.98% 207ms 0.84% vtkDemandDrivenPipeline::ProcessRequest 0 0% 84.98% 207ms 0.84% vtkExecutive::CallAlgorithm 0 0% 84.98% 205ms 0.83% vtkCompositeDataPipeline::ExecuteData 0 0% 84.98% 205ms 0.83% vtkXMLUnstructuredDataWriter::ProcessRequest 11ms 0.045% 85.03% 201ms 0.82% boost::numeric::ublas::vector_reference::operator() (inline) 14ms 0.057% 85.08% 179ms 0.73% std::__insertion_sort (inline) 0 0% 85.08% 179ms 0.73% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.08% 179ms 0.73% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 85.08% 174ms 0.71% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 1ms 0.0041% 85.09% 169ms 0.69% AbstractCellProperty::IsType (inline) 166ms 0.67% 85.76% 166ms 0.67% std::__adjacent_find (inline) 0 0% 85.76% 166ms 0.67% std::__unique (inline) 0 0% 85.76% 166ms 0.67% std::unique (inline) 164ms 0.67% 86.43% 164ms 0.67% [libchaste_cell_based.so] 0 0% 86.43% 161ms 0.65% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 86.43% 157ms 0.64% std::_Rb_tree::clear (inline) 153ms 0.62% 87.05% 153ms 0.62% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 0 0% 87.05% 153ms 0.62% vtkXMLWriter::WriteBinaryData 3ms 0.012% 87.06% 150ms 0.61% Cell::GetCellId 0 0% 87.06% 149ms 0.6% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 87.06% 149ms 0.6% NodesOnlyMesh::ResizeBoxCollection 12ms 0.049% 87.11% 148ms 0.6% NodesOnlyMesh::IsANodeCloseToDomainBoundary 4ms 0.016% 87.13% 148ms 0.6% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 87.13% 146ms 0.59% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.13% 145ms 0.59% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.13% 144ms 0.58% vtkXMLWriter::WriteCompressionBlock 128ms 0.52% 87.65% 142ms 0.58% _int_free 140ms 0.57% 88.21% 140ms 0.57% __ieee754_log_fma 136ms 0.55% 88.77% 136ms 0.55% Node::rGetLocation 0 0% 88.77% 136ms 0.55% vtkXMLWriter::WritePointsAppendedData 1ms 0.0041% 88.77% 135ms 0.55% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 47ms 0.19% 88.96% 132ms 0.54% AbstractCellProperty::IsSame 2ms 0.0081% 88.97% 126ms 0.51% AbstractCellPopulation::SetCellUsingLocationIndex 1ms 0.0041% 88.97% 125ms 0.51% AbstractNumericalMethod::SafeNodePositionUpdate 99ms 0.4% 89.37% 124ms 0.5% boost::detail::shared_count::shared_count (inline)