File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 23436ms, 89.25% of 26260ms total Dropped 847 nodes (cum <= 131.30ms) flat flat% sum% cum cum% 0 0% 0% 26109ms 99.42% __libc_start_call_main 0 0% 0% 26109ms 99.42% __libc_start_main_impl 0 0% 0% 26109ms 99.42% _start 0 0% 0% 26092ms 99.36% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 26092ms 99.36% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 26092ms 99.36% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 26092ms 99.36% main 0 0% 0% 26050ms 99.20% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 26050ms 99.20% CxxTest::TestRunner::runTest (inline) 0 0% 0% 26050ms 99.20% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0038% 0.0038% 26041ms 99.17% AbstractCellBasedSimulation::Solve 1ms 0.0038% 0.0076% 14666ms 55.85% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0076% 10101ms 38.47% AbstractCellBasedSimulation::UpdateCellPopulation 7ms 0.027% 0.034% 9477ms 36.09% ForwardEulerNumericalMethod::UpdateAllNodePositions 14ms 0.053% 0.088% 9265ms 35.28% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.088% 8875ms 33.80% NodeBasedCellPopulation::Update 1477ms 5.62% 5.71% 8322ms 31.69% RepulsionForce::AddForceContribution (partial-inline) 13ms 0.05% 5.76% 6647ms 25.31% DistributedBoxCollection::CalculateInteriorNodePairs 2304ms 8.77% 14.54% 4985ms 18.98% std::_Rb_tree::_M_lower_bound (inline) 20ms 0.076% 14.61% 4861ms 18.51% NodeAttributes::RemoveDuplicateNeighbours 0 0% 14.61% 4803ms 18.29% OffLatticeSimulation::ApplyBoundaries 6ms 0.023% 14.63% 4655ms 17.73% std::__sort (inline) 0 0% 14.63% 4655ms 17.73% std::sort (inline) 199ms 0.76% 15.39% 4036ms 15.37% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 73ms 0.28% 15.67% 3364ms 12.81% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 265ms 1.01% 16.68% 3300ms 12.57% std::_Rb_tree::find (inline) 0 0% 16.68% 3299ms 12.56% std::map::find (inline) 6ms 0.023% 16.70% 3164ms 12.05% AbstractCellPopulation::Iterator::operator++ (inline) 212ms 0.81% 17.51% 3135ms 11.94% AbstractCellPopulation::Iterator::IsRealCell (inline) 221ms 0.84% 18.35% 2820ms 10.74% std::__introsort_loop 27ms 0.1% 18.45% 2676ms 10.19% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 23ms 0.088% 18.54% 2631ms 10.02% PlaneBoundaryCondition::ImposeBoundaryCondition 2629ms 10.01% 28.55% 2629ms 10.01% std::_Rb_tree::_S_right (inline) 0 0% 28.55% 2510ms 9.56% std::__unguarded_partition_pivot (inline) 210ms 0.8% 29.35% 2502ms 9.53% std::map::operator[] (partial-inline) 167ms 0.64% 29.99% 2477ms 9.43% DistributedBoxCollection::AddPairsFromBox 179ms 0.68% 30.67% 2368ms 9.02% AbstractMesh::GetNode 54ms 0.21% 30.88% 2365ms 9.01% AbstractCellPopulation::GetLocationIndexUsingCell 48ms 0.18% 31.06% 2320ms 8.83% NodesOnlyMesh::GetNodeOrHaloNode 85ms 0.32% 31.38% 2193ms 8.35% NodesOnlyMesh::SolveNodeMapping 1048ms 3.99% 35.37% 2172ms 8.27% std::__unguarded_partition (inline) 10ms 0.038% 35.41% 2170ms 8.26% PlaneBoundaryCondition::VerifyBoundaryCondition 0 0% 35.41% 1984ms 7.56% std::_Rb_tree::lower_bound (inline) 0 0% 35.41% 1984ms 7.56% std::map::lower_bound (inline) 0 0% 35.41% 1829ms 6.96% std::__final_insertion_sort (inline) 21ms 0.08% 35.49% 1762ms 6.71% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 18ms 0.069% 35.56% 1734ms 6.60% AbstractCellPopulation::GetCellUsingLocationIndex 106ms 0.4% 35.96% 1639ms 6.24% std::__unguarded_insertion_sort (inline) 612ms 2.33% 38.29% 1570ms 5.98% std::__unguarded_linear_insert (inline) 1456ms 5.54% 43.84% 1456ms 5.54% __gnu_cxx::__normal_iterator::operator-- (inline) 67ms 0.26% 44.09% 1339ms 5.10% boost::numeric::ublas::c_vector::c_vector (partial-inline) 8ms 0.03% 44.12% 1209ms 4.60% DistributedBoxCollection::CalculateBoundaryNodePairs 0 0% 44.12% 1207ms 4.60% NodeBasedCellPopulation::UpdateCellProcessLocation 7ms 0.027% 44.15% 1139ms 4.34% boost::numeric::ublas::vector_assign (inline) 225ms 0.86% 45.01% 1041ms 3.96% boost::numeric::ublas::indexing_vector_assign 37ms 0.14% 45.15% 1037ms 3.95% std::_Rb_tree_const_iterator::operator++ (inline) 19ms 0.072% 45.22% 986ms 3.75% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 970ms 3.69% 48.91% 970ms 3.69% std::_Rb_tree_increment 303ms 1.15% 50.07% 934ms 3.56% __dynamic_cast 25ms 0.095% 50.16% 901ms 3.43% CellPropertyCollection::GetPropertiesType (inline) 187ms 0.71% 50.88% 885ms 3.37% AbstractMesh::GetVectorFromAtoB 414ms 1.58% 52.45% 883ms 3.36% DistributedBoxCollection::CalculateContainingBox (partial-inline) 3ms 0.011% 52.46% 833ms 3.17% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 52.46% 823ms 3.13% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 3ms 0.011% 52.48% 816ms 3.11% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 52.48% 808ms 3.08% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 52.48% 807ms 3.07% boost::numeric::ublas::norm_2 (inline) 632ms 2.41% 54.88% 807ms 3.07% boost::numeric::ublas::vector_norm_2::apply (inline) 30ms 0.11% 55.00% 795ms 3.03% std::__copy_move::__copy_m (inline) 0 0% 55.00% 795ms 3.03% std::__copy_move_a (inline) 0 0% 55.00% 795ms 3.03% std::__copy_move_a1 (inline) 0 0% 55.00% 795ms 3.03% std::__copy_move_a2 (inline) 0 0% 55.00% 794ms 3.02% std::copy (inline) 188ms 0.72% 55.71% 787ms 3.00% NodeAttributes::AddNeighbour 786ms 2.99% 58.71% 786ms 2.99% __memcpy_avx_unaligned_erms 0 0% 58.71% 781ms 2.97% AbstractCellPopulation::WriteResultsToFiles 747ms 2.84% 61.55% 747ms 2.84% boost::numeric::ublas::c_vector::operator() 5ms 0.019% 61.57% 743ms 2.83% AbstractCellBasedSimulation::DoCellBirth 85ms 0.32% 61.89% 711ms 2.71% std::_Rb_tree::_Rb_tree (partial-inline) 596ms 2.27% 64.16% 706ms 2.69% std::vector::push_back (inline) 5ms 0.019% 64.18% 650ms 2.48% Cell::GetMutationState 56ms 0.21% 64.39% 615ms 2.34% std::_Rb_tree::_M_copy (inline) 122ms 0.46% 64.86% 593ms 2.26% std::__new_allocator::allocate (inline) 5ms 0.019% 64.88% 593ms 2.26% std::set::set (inline) 0 0% 64.88% 576ms 2.19% std::allocator_traits::allocate (inline) 0 0% 64.88% 559ms 2.13% std::_Rb_tree::_M_create_node (inline) 210ms 0.8% 65.68% 557ms 2.12% std::_Rb_tree::_M_clone_node (inline) 248ms 0.94% 66.62% 530ms 2.02% __cxxabiv1::__si_class_type_info::__do_dyncast 1ms 0.0038% 66.63% 525ms 2.00% NodeBasedCellPopulation::WriteVtkResultsToFile 519ms 1.98% 68.60% 519ms 1.98% boost::numeric::ublas::same_impl_ex 0 0% 68.60% 486ms 1.85% std::_Rb_tree::_M_get_node (inline) 0 0% 68.60% 483ms 1.84% AbstractCellBasedSimulation::DoCellRemoval (inline) 4ms 0.015% 68.62% 473ms 1.80% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 30ms 0.11% 68.73% 470ms 1.79% operator new 143ms 0.54% 69.28% 460ms 1.75% std::_Rb_tree::_M_erase 48ms 0.18% 69.46% 448ms 1.71% boost::detail::shared_count::~shared_count (inline) 0 0% 69.46% 448ms 1.71% boost::shared_ptr::~shared_ptr (inline) 0 0% 69.46% 441ms 1.68% AbstractCellProperty::IsSubType (inline) 136ms 0.52% 69.98% 431ms 1.64% __GI___libc_malloc 431ms 1.64% 71.62% 431ms 1.64% __strcmp_avx2 419ms 1.60% 73.21% 419ms 1.60% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 102ms 0.39% 73.60% 406ms 1.55% Node::GetRadius 0 0% 73.60% 400ms 1.52% std::_Rb_tree::_Alloc_node::operator() (inline) 99ms 0.38% 73.98% 398ms 1.52% boost::numeric::ublas::vector_binary::size (inline) 387ms 1.47% 75.45% 387ms 1.47% [libchaste_mesh.so] 370ms 1.41% 76.86% 387ms 1.47% boost::detail::sp_counted_base::release 68ms 0.26% 77.12% 387ms 1.47% std::_Rb_tree::~_Rb_tree (inline) 1ms 0.0038% 77.12% 381ms 1.45% CellPropertyCollection::HasProperty 0 0% 77.12% 380ms 1.45% Cell::HasCellProperty (inline) 18ms 0.069% 77.19% 378ms 1.44% Cell::ReadyToDivide 0 0% 77.19% 370ms 1.41% boost::numeric::ublas::inner_prod (inline) 13ms 0.05% 77.24% 369ms 1.41% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 77.24% 369ms 1.41% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 77.24% 360ms 1.37% boost::numeric::ublas::c_vector::assign (inline) 182ms 0.69% 77.94% 349ms 1.33% Node::AddNeighbour 125ms 0.48% 78.41% 334ms 1.27% std::__move_median_to_first (inline) 5ms 0.019% 78.43% 324ms 1.23% NodeBasedCellPopulation::UpdateMapsAfterRemesh 2ms 0.0076% 78.44% 324ms 1.23% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 78.44% 318ms 1.21% NodesOnlyMesh::ReMesh 316ms 1.20% 79.64% 316ms 1.20% Node::CheckForNodeAttributes 159ms 0.61% 80.25% 314ms 1.20% boost::numeric::ublas::vector_inner_prod::apply (inline) 11ms 0.042% 80.29% 311ms 1.18% DistributedBoxCollection::GetProcessOwningNode 5ms 0.019% 80.31% 308ms 1.17% std::_Rb_tree::_M_emplace_hint_unique 7ms 0.027% 80.34% 306ms 1.17% NodesOnlyMesh::UpdateNodeIndices 0 0% 80.34% 305ms 1.16% std::_Rb_tree::_M_drop_node (inline) 298ms 1.13% 81.47% 298ms 1.13% __gnu_cxx::__normal_iterator::operator++ (inline) 1ms 0.0038% 81.47% 286ms 1.09% NodesOnlyMesh::UpdateBoxCollection 0 0% 81.47% 270ms 1.03% std::set::~set (inline) 0 0% 81.47% 262ms 1% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 7ms 0.027% 81.50% 260ms 0.99% std::__new_allocator::deallocate (inline) 0 0% 81.50% 259ms 0.99% VtkMeshWriter::WriteFiles 107ms 0.41% 81.91% 255ms 0.97% _int_malloc 104ms 0.4% 82.30% 253ms 0.96% boost::shared_ptr::shared_ptr (inline) 0 0% 82.30% 242ms 0.92% std::allocator_traits::deallocate (inline) 0 0% 82.30% 234ms 0.89% vtkStreamingDemandDrivenPipeline::Update 0 0% 82.30% 234ms 0.89% vtkXMLWriterBase::Write 0 0% 82.30% 233ms 0.89% std::_Rb_tree::_M_put_node (inline) 0 0% 82.30% 233ms 0.89% vtkDemandDrivenPipeline::ProcessRequest 0 0% 82.30% 231ms 0.88% vtkStreamingDemandDrivenPipeline::ProcessRequest 77ms 0.29% 82.60% 230ms 0.88% __GI___libc_free 1ms 0.0038% 82.60% 230ms 0.88% vtkCompositeDataPipeline::ExecuteData 0 0% 82.60% 230ms 0.88% vtkExecutive::CallAlgorithm 0 0% 82.60% 229ms 0.87% vtkDemandDrivenPipeline::ExecuteData 0 0% 82.60% 228ms 0.87% vtkXMLUnstructuredDataWriter::ProcessRequest 216ms 0.82% 83.42% 216ms 0.82% Node::GetIndex 3ms 0.011% 83.43% 209ms 0.8% NodesOnlyMesh::AddNodesToBoxes 205ms 0.78% 84.22% 205ms 0.78% boost::shared_ptr::operator-> (inline) 32ms 0.12% 84.34% 204ms 0.78% boost::numeric::ublas::vector_reference::operator() (inline) 193ms 0.73% 85.07% 193ms 0.73% [libchaste_cell_based.so] 0 0% 85.07% 191ms 0.73% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.07% 191ms 0.73% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 21ms 0.08% 85.15% 190ms 0.72% std::__insertion_sort (inline) 4ms 0.015% 85.17% 189ms 0.72% AbstractCellProperty::IsType (inline) 0 0% 85.17% 181ms 0.69% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 179ms 0.68% 85.85% 180ms 0.69% Node::ConstructNodeAttributes (inline) 0 0% 85.85% 177ms 0.67% Cell::GetCellId 0 0% 85.85% 174ms 0.66% NodesOnlyMesh::ResizeBoxCollection 16ms 0.061% 85.91% 172ms 0.65% NodesOnlyMesh::IsANodeCloseToDomainBoundary 6ms 0.023% 85.93% 166ms 0.63% boost::numeric::ublas::c_vector::operator[] (inline) 161ms 0.61% 86.55% 163ms 0.62% std::__adjacent_find (inline) 0 0% 86.55% 163ms 0.62% std::__unique (inline) 0 0% 86.55% 163ms 0.62% std::unique (inline) 1ms 0.0038% 86.55% 162ms 0.62% std::_Rb_tree::clear (inline) 161ms 0.61% 87.16% 161ms 0.61% __gnu_cxx::__ops::_Val_less_iter::operator() (inline) 1ms 0.0038% 87.17% 160ms 0.61% AbstractCellPopulation::SetCellUsingLocationIndex 0 0% 87.17% 159ms 0.61% std::_Rb_tree::_Auto_node::_Auto_node (inline) 77ms 0.29% 87.46% 155ms 0.59% AbstractCellCycleModel::GetAge 136ms 0.52% 87.98% 152ms 0.58% _int_free 0 0% 87.98% 152ms 0.58% vtkXMLWriter::WriteBinaryData 77ms 0.29% 88.27% 151ms 0.58% AbstractCellProperty::IsSame 0 0% 88.27% 151ms 0.58% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 3ms 0.011% 88.28% 150ms 0.57% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 88.28% 149ms 0.57% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 108ms 0.41% 88.69% 148ms 0.56% boost::detail::shared_count::shared_count (inline) 0 0% 88.69% 148ms 0.56% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 88.69% 145ms 0.55% vtkXMLWriter::WritePointsAppendedData 1ms 0.0038% 88.70% 144ms 0.55% vtkXMLWriter::WriteBinaryDataBlock 0 0% 88.70% 144ms 0.55% vtkXMLWriter::WriteBinaryDataInternal 0 0% 88.70% 142ms 0.54% vtkXMLWriter::WriteCompressionBlock 137ms 0.52% 89.22% 137ms 0.52% Node::rGetLocation 7ms 0.027% 89.25% 135ms 0.51% NodeBasedCellPopulation::SetNode