File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 22288ms, 89.69% of 24850ms total Dropped 824 nodes (cum <= 124.25ms) flat flat% sum% cum cum% 0 0% 0% 24721ms 99.48% __libc_start_call_main 0 0% 0% 24721ms 99.48% __libc_start_main_impl 0 0% 0% 24721ms 99.48% _start 0 0% 0% 24704ms 99.41% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 24704ms 99.41% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 24704ms 99.41% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 24704ms 99.41% main 0 0% 0% 24660ms 99.24% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 24660ms 99.24% CxxTest::TestRunner::runTest (inline) 0 0% 0% 24660ms 99.24% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 2ms 0.008% 0.008% 24650ms 99.20% AbstractCellBasedSimulation::Solve 5ms 0.02% 0.028% 14131ms 56.87% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.004% 0.032% 9282ms 37.35% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.008% 0.04% 9150ms 36.82% ForwardEulerNumericalMethod::UpdateAllNodePositions 9ms 0.036% 0.076% 8962ms 36.06% AbstractNumericalMethod::ComputeForcesIncludingDamping 1342ms 5.40% 5.48% 8238ms 33.15% RepulsionForce::AddForceContribution (partial-inline) 0 0% 5.48% 8194ms 32.97% NodeBasedCellPopulation::Update 7ms 0.028% 5.51% 6113ms 24.60% DistributedBoxCollection::CalculateInteriorNodePairs 2189ms 8.81% 14.31% 5268ms 21.20% std::_Rb_tree::_M_lower_bound (inline) 0 0% 14.31% 4650ms 18.71% OffLatticeSimulation::ApplyBoundaries 9ms 0.036% 14.35% 4604ms 18.53% NodeAttributes::RemoveDuplicateNeighbours 5ms 0.02% 14.37% 4439ms 17.86% std::__sort (inline) 0 0% 14.37% 4439ms 17.86% std::sort (inline) 205ms 0.82% 15.20% 4138ms 16.65% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 245ms 0.99% 16.18% 3468ms 13.96% std::_Rb_tree::find (inline) 0 0% 16.18% 3468ms 13.96% std::map::find (inline) 81ms 0.33% 16.51% 3386ms 13.63% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 6ms 0.024% 16.53% 3204ms 12.89% AbstractCellPopulation::Iterator::operator++ (inline) 156ms 0.63% 17.16% 3176ms 12.78% AbstractCellPopulation::Iterator::IsRealCell (inline) 3065ms 12.33% 29.49% 3065ms 12.33% std::_Rb_tree::_S_right (inline) 25ms 0.1% 29.59% 2799ms 11.26% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 222ms 0.89% 30.49% 2611ms 10.51% std::map::operator[] (partial-inline) 168ms 0.68% 31.16% 2581ms 10.39% std::__introsort_loop 155ms 0.62% 31.79% 2527ms 10.17% AbstractMesh::GetNode 55ms 0.22% 32.01% 2499ms 10.06% NodesOnlyMesh::GetNodeOrHaloNode 24ms 0.097% 32.10% 2489ms 10.02% PlaneBoundaryCondition::ImposeBoundaryCondition 129ms 0.52% 32.62% 2374ms 9.55% NodesOnlyMesh::SolveNodeMapping 0 0% 32.62% 2323ms 9.35% std::__unguarded_partition_pivot (inline) 30ms 0.12% 32.74% 2316ms 9.32% AbstractCellPopulation::GetLocationIndexUsingCell 11ms 0.044% 32.79% 2160ms 8.69% PlaneBoundaryCondition::VerifyBoundaryCondition 1027ms 4.13% 36.92% 2096ms 8.43% std::__unguarded_partition (inline) 152ms 0.61% 37.53% 2092ms 8.42% DistributedBoxCollection::AddPairsFromBox 0 0% 37.53% 2087ms 8.40% std::_Rb_tree::lower_bound (inline) 0 0% 37.53% 2087ms 8.40% std::map::lower_bound (inline) 2ms 0.008% 37.54% 1849ms 7.44% std::__final_insertion_sort (inline) 19ms 0.076% 37.62% 1723ms 6.93% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 31ms 0.12% 37.74% 1696ms 6.82% AbstractCellPopulation::GetCellUsingLocationIndex 110ms 0.44% 38.19% 1638ms 6.59% std::__unguarded_insertion_sort (inline) 631ms 2.54% 40.72% 1572ms 6.33% std::__unguarded_linear_insert (inline) 1386ms 5.58% 46.30% 1386ms 5.58% __gnu_cxx::__normal_iterator::operator-- (inline) 61ms 0.25% 46.55% 1347ms 5.42% boost::numeric::ublas::c_vector::c_vector (partial-inline) 3ms 0.012% 46.56% 1191ms 4.79% boost::numeric::ublas::vector_assign (inline) 0 0% 46.56% 1168ms 4.70% NodeBasedCellPopulation::UpdateCellProcessLocation 6ms 0.024% 46.58% 1098ms 4.42% DistributedBoxCollection::CalculateBoundaryNodePairs 227ms 0.91% 47.50% 1081ms 4.35% boost::numeric::ublas::indexing_vector_assign 22ms 0.089% 47.59% 950ms 3.82% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 288ms 1.16% 48.74% 934ms 3.76% __dynamic_cast 147ms 0.59% 49.34% 873ms 3.51% AbstractMesh::GetVectorFromAtoB 380ms 1.53% 50.87% 835ms 3.36% DistributedBoxCollection::CalculateContainingBox (partial-inline) 253ms 1.02% 51.88% 835ms 3.36% NodeAttributes::AddNeighbour 3ms 0.012% 51.90% 811ms 3.26% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 51.90% 809ms 3.26% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 51.90% 795ms 3.20% boost::numeric::ublas::norm_2 (inline) 631ms 2.54% 54.43% 795ms 3.20% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 54.43% 795ms 3.20% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 35ms 0.14% 54.58% 795ms 3.20% std::__copy_move::__copy_m (inline) 0 0% 54.58% 795ms 3.20% std::__copy_move_a (inline) 0 0% 54.58% 795ms 3.20% std::__copy_move_a1 (inline) 0 0% 54.58% 795ms 3.20% std::__copy_move_a2 (inline) 0 0% 54.58% 795ms 3.20% std::copy (inline) 779ms 3.13% 57.71% 779ms 3.13% __memcpy_avx_unaligned_erms 0 0% 57.71% 770ms 3.10% AbstractCellPopulation::WriteResultsToFiles 708ms 2.85% 60.56% 708ms 2.85% boost::numeric::ublas::c_vector::operator() 583ms 2.35% 62.91% 676ms 2.72% std::vector::push_back (inline) 10ms 0.04% 62.95% 662ms 2.66% CellPropertyCollection::GetPropertiesType (inline) 31ms 0.12% 63.07% 644ms 2.59% std::_Rb_tree_const_iterator::operator++ (inline) 4ms 0.016% 63.09% 641ms 2.58% AbstractCentreBasedCellPopulation::GetDampingConstant 4ms 0.016% 63.10% 625ms 2.52% AbstractCellBasedSimulation::DoCellBirth 596ms 2.40% 65.50% 596ms 2.40% std::_Rb_tree_increment 82ms 0.33% 65.83% 566ms 2.28% std::__new_allocator::allocate (inline) 548ms 2.21% 68.04% 548ms 2.21% boost::numeric::ublas::same_impl_ex 0 0% 68.04% 540ms 2.17% std::allocator_traits::allocate (inline) 35ms 0.14% 68.18% 538ms 2.16% boost::detail::shared_count::~shared_count (inline) 0 0% 68.18% 538ms 2.16% boost::shared_ptr::~shared_ptr (inline) 33ms 0.13% 68.31% 530ms 2.13% std::_Rb_tree::_Rb_tree (partial-inline) 247ms 0.99% 69.30% 528ms 2.12% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 69.30% 508ms 2.04% NodeBasedCellPopulation::WriteVtkResultsToFile 472ms 1.90% 71.20% 490ms 1.97% boost::detail::sp_counted_base::release 0 0% 71.20% 490ms 1.97% std::_Rb_tree::_M_create_node (inline) 483ms 1.94% 73.15% 483ms 1.94% __strcmp_avx2 21ms 0.085% 73.23% 483ms 1.94% operator new 36ms 0.14% 73.38% 476ms 1.92% std::_Rb_tree::_M_copy (inline) 0 0% 73.38% 461ms 1.86% AbstractCellBasedSimulation::DoCellRemoval (inline) 1ms 0.004% 73.38% 454ms 1.83% Cell::GetMutationState 136ms 0.55% 73.93% 454ms 1.83% __GI___libc_malloc 3ms 0.012% 73.94% 452ms 1.82% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 3ms 0.012% 73.95% 450ms 1.81% std::set::set (inline) 0 0% 73.95% 443ms 1.78% std::_Rb_tree::_M_get_node (inline) 1ms 0.004% 73.96% 437ms 1.76% AbstractCellProperty::IsSubType (inline) 153ms 0.62% 74.57% 431ms 1.73% std::_Rb_tree::_M_clone_node (inline) 117ms 0.47% 75.04% 427ms 1.72% std::_Rb_tree::_M_erase 103ms 0.41% 75.46% 423ms 1.70% boost::numeric::ublas::vector_binary::size (inline) 81ms 0.33% 75.78% 360ms 1.45% Node::GetRadius 0 0% 75.78% 350ms 1.41% boost::numeric::ublas::inner_prod (inline) 2ms 0.008% 75.79% 350ms 1.41% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 13ms 0.052% 75.84% 348ms 1.40% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 75.84% 345ms 1.39% NodesOnlyMesh::ReMesh 0 0% 75.84% 344ms 1.38% boost::numeric::ublas::c_vector::assign (inline) 2ms 0.008% 75.85% 333ms 1.34% NodesOnlyMesh::UpdateNodeIndices 332ms 1.34% 77.19% 332ms 1.34% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 330ms 1.33% 78.52% 330ms 1.33% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 78.52% 326ms 1.31% std::_Rb_tree::_Alloc_node::operator() (inline) 32ms 0.13% 78.64% 321ms 1.29% std::_Rb_tree::~_Rb_tree (inline) 4ms 0.016% 78.66% 314ms 1.26% NodeBasedCellPopulation::UpdateMapsAfterRemesh 12ms 0.048% 78.71% 302ms 1.22% std::_Rb_tree::_M_emplace_hint_unique 0 0% 78.71% 297ms 1.20% std::_Rb_tree::_M_drop_node (inline) 290ms 1.17% 79.88% 290ms 1.17% Node::CheckForNodeAttributes 123ms 0.49% 80.37% 283ms 1.14% boost::numeric::ublas::vector_inner_prod::apply (inline) 4ms 0.016% 80.39% 278ms 1.12% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 1ms 0.004% 80.39% 270ms 1.09% NodesOnlyMesh::UpdateBoxCollection 3ms 0.012% 80.40% 260ms 1.05% DistributedBoxCollection::GetProcessOwningNode 144ms 0.58% 80.98% 258ms 1.04% _int_malloc 0 0% 80.98% 254ms 1.02% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 3ms 0.012% 80.99% 254ms 1.02% CellPropertyCollection::HasProperty 0 0% 80.99% 253ms 1.02% Cell::HasCellProperty (inline) 0 0% 80.99% 253ms 1.02% VtkMeshWriter::WriteFiles 7ms 0.028% 81.02% 247ms 0.99% std::__new_allocator::deallocate (inline) 216ms 0.87% 81.89% 246ms 0.99% Node::AddNeighbour 0 0% 81.89% 232ms 0.93% std::allocator_traits::deallocate (inline) 7ms 0.028% 81.92% 231ms 0.93% Cell::ReadyToDivide 0 0% 81.92% 230ms 0.93% std::_Rb_tree::_M_put_node (inline) 110ms 0.44% 82.36% 225ms 0.91% std::__move_median_to_first (inline) 2ms 0.008% 82.37% 220ms 0.89% NodesOnlyMesh::AddNodesToBoxes 0 0% 82.37% 218ms 0.88% vtkStreamingDemandDrivenPipeline::Update 0 0% 82.37% 218ms 0.88% vtkXMLWriterBase::Write 78ms 0.31% 82.68% 217ms 0.87% __GI___libc_free 121ms 0.49% 83.17% 216ms 0.87% boost::shared_ptr::shared_ptr (inline) 0 0% 83.17% 215ms 0.87% vtkDemandDrivenPipeline::ProcessRequest 0 0% 83.17% 215ms 0.87% vtkExecutive::CallAlgorithm 0 0% 83.17% 215ms 0.87% vtkStreamingDemandDrivenPipeline::ProcessRequest 1ms 0.004% 83.18% 214ms 0.86% AbstractCellProperty::IsType (inline) 214ms 0.86% 84.04% 214ms 0.86% Node::GetIndex 0 0% 84.04% 213ms 0.86% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 84.04% 212ms 0.85% vtkCompositeDataPipeline::ExecuteData 0 0% 84.04% 212ms 0.85% vtkDemandDrivenPipeline::ExecuteData 0 0% 84.04% 210ms 0.85% std::set::~set (inline) 27ms 0.11% 84.14% 209ms 0.84% std::__insertion_sort (inline) 0 0% 84.14% 206ms 0.83% boost::numeric::ublas::vector_binary::operator() (inline) 205ms 0.82% 84.97% 205ms 0.82% [libchaste_mesh.so] 14ms 0.056% 85.03% 203ms 0.82% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 85.03% 183ms 0.74% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.03% 183ms 0.74% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 85.03% 176ms 0.71% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 174ms 0.7% 85.73% 174ms 0.7% [libchaste_cell_based.so] 0 0% 85.73% 171ms 0.69% NodesOnlyMesh::ResizeBoxCollection 18ms 0.072% 85.80% 169ms 0.68% NodesOnlyMesh::IsANodeCloseToDomainBoundary 58ms 0.23% 86.03% 167ms 0.67% AbstractCellProperty::IsSame 164ms 0.66% 86.69% 164ms 0.66% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 0 0% 86.69% 164ms 0.66% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 86.69% 155ms 0.62% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 86.69% 153ms 0.62% std::_Rb_tree::clear (inline) 0 0% 86.69% 149ms 0.6% vtkXMLWriter::WriteBinaryData 1ms 0.004% 86.70% 148ms 0.6% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 86.70% 146ms 0.59% vtkXMLWriter::WriteBinaryDataInternal 7ms 0.028% 86.72% 145ms 0.58% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 86.72% 145ms 0.58% vtkXMLWriter::WriteBinaryDataBlock 0 0% 86.72% 145ms 0.58% vtkXMLWriter::WriteCompressionBlock 143ms 0.58% 87.30% 143ms 0.58% Node::rGetLocation 143ms 0.58% 87.88% 143ms 0.58% __ieee754_log_fma 141ms 0.57% 88.44% 141ms 0.57% Node::IsDeleted 130ms 0.52% 88.97% 139ms 0.56% _int_free 0 0% 88.97% 137ms 0.55% vtkXMLWriter::WritePointsAppendedData 2ms 0.008% 88.97% 135ms 0.54% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 88.97% 134ms 0.54% Cell::GetCellId 132ms 0.53% 89.51% 133ms 0.54% std::__adjacent_find (inline) 0 0% 89.51% 133ms 0.54% std::__unique (inline) 0 0% 89.51% 133ms 0.54% std::unique (inline) 0 0% 89.51% 131ms 0.53% AbstractCellPopulation::SetCellUsingLocationIndex 45ms 0.18% 89.69% 128ms 0.52% AbstractCellCycleModel::GetAge 1ms 0.004% 89.69% 128ms 0.52% NodeBasedCellPopulation::AcceptCellWriter