File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20943ms, 89.09% of 23507ms total Dropped 778 nodes (cum <= 117.53ms) flat flat% sum% cum cum% 0 0% 0% 23343ms 99.30% __libc_start_call_main 0 0% 0% 23343ms 99.30% __libc_start_main_impl 0 0% 0% 23343ms 99.30% _start 0 0% 0% 23328ms 99.24% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 23328ms 99.24% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 23328ms 99.24% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 23328ms 99.24% main 0 0% 0% 23289ms 99.07% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 23289ms 99.07% CxxTest::TestRunner::runTest (inline) 0 0% 0% 23289ms 99.07% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 23281ms 99.04% AbstractCellBasedSimulation::Solve 0 0% 0% 13152ms 55.95% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0% 8933ms 38.00% AbstractCellBasedSimulation::UpdateCellPopulation 5ms 0.021% 0.021% 8367ms 35.59% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.043% 0.064% 8184ms 34.82% AbstractNumericalMethod::ComputeForcesIncludingDamping 2ms 0.0085% 0.072% 7922ms 33.70% NodeBasedCellPopulation::Update 1204ms 5.12% 5.19% 7522ms 32.00% RepulsionForce::AddForceContribution (partial-inline) 5ms 0.021% 5.22% 5874ms 24.99% DistributedBoxCollection::CalculateInteriorNodePairs 2068ms 8.80% 14.01% 4799ms 20.42% std::_Rb_tree::_M_lower_bound (inline) 16ms 0.068% 14.08% 4523ms 19.24% NodeAttributes::RemoveDuplicateNeighbours 0 0% 14.08% 4511ms 19.19% OffLatticeSimulation::ApplyBoundaries 5ms 0.021% 14.10% 4340ms 18.46% std::__sort (inline) 0 0% 14.10% 4340ms 18.46% std::sort (inline) 157ms 0.67% 14.77% 3845ms 16.36% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 2ms 0.0085% 14.78% 3414ms 14.52% AbstractCellPopulation::Iterator::operator++ (inline) 242ms 1.03% 15.81% 3389ms 14.42% AbstractCellPopulation::Iterator::IsRealCell (inline) 72ms 0.31% 16.11% 3284ms 13.97% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 236ms 1.00% 17.12% 3109ms 13.23% std::_Rb_tree::find (inline) 0 0% 17.12% 3108ms 13.22% std::map::find (inline) 33ms 0.14% 17.26% 2810ms 11.95% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2681ms 11.41% 28.66% 2681ms 11.41% std::_Rb_tree::_S_right (inline) 210ms 0.89% 29.56% 2513ms 10.69% std::__introsort_loop 211ms 0.9% 30.45% 2401ms 10.21% std::map::operator[] (partial-inline) 29ms 0.12% 30.58% 2380ms 10.12% PlaneBoundaryCondition::ImposeBoundaryCondition 2ms 0.0085% 30.59% 2240ms 9.53% std::__unguarded_partition_pivot (inline) 27ms 0.11% 30.70% 2234ms 9.50% AbstractCellPopulation::GetLocationIndexUsingCell 121ms 0.51% 31.22% 2208ms 9.39% AbstractMesh::GetNode 63ms 0.27% 31.48% 2208ms 9.39% NodesOnlyMesh::GetNodeOrHaloNode 15ms 0.064% 31.55% 2131ms 9.07% PlaneBoundaryCondition::VerifyBoundaryCondition 82ms 0.35% 31.90% 2093ms 8.90% NodesOnlyMesh::SolveNodeMapping 1042ms 4.43% 36.33% 2038ms 8.67% std::__unguarded_partition (inline) 175ms 0.74% 37.07% 1984ms 8.44% DistributedBoxCollection::AddPairsFromBox 0 0% 37.07% 1951ms 8.30% std::_Rb_tree::lower_bound (inline) 0 0% 37.07% 1951ms 8.30% std::map::lower_bound (inline) 0 0% 37.07% 1818ms 7.73% std::__final_insertion_sort (inline) 93ms 0.4% 37.47% 1612ms 6.86% std::__unguarded_insertion_sort (inline) 581ms 2.47% 39.94% 1550ms 6.59% std::__unguarded_linear_insert (inline) 19ms 0.081% 40.02% 1537ms 6.54% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 38ms 0.16% 40.18% 1511ms 6.43% AbstractCellPopulation::GetCellUsingLocationIndex 1437ms 6.11% 46.30% 1437ms 6.11% __gnu_cxx::__normal_iterator::operator-- (inline) 42ms 0.18% 46.48% 1308ms 5.56% boost::numeric::ublas::c_vector::c_vector (partial-inline) 36ms 0.15% 46.63% 1182ms 5.03% boost::numeric::ublas::vector_assign (inline) 1ms 0.0043% 46.63% 1120ms 4.76% NodeBasedCellPopulation::UpdateCellProcessLocation 4ms 0.017% 46.65% 1082ms 4.60% DistributedBoxCollection::CalculateBoundaryNodePairs 296ms 1.26% 47.91% 1062ms 4.52% boost::numeric::ublas::indexing_vector_assign 229ms 0.97% 48.88% 904ms 3.85% __dynamic_cast 375ms 1.60% 50.48% 818ms 3.48% DistributedBoxCollection::CalculateContainingBox (partial-inline) 188ms 0.8% 51.28% 814ms 3.46% AbstractMesh::GetVectorFromAtoB 15ms 0.064% 51.34% 795ms 3.38% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 51.34% 768ms 3.27% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 51.34% 753ms 3.20% boost::numeric::ublas::norm_2 (inline) 582ms 2.48% 53.82% 753ms 3.20% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 53.82% 753ms 3.20% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 202ms 0.86% 54.68% 727ms 3.09% NodeAttributes::AddNeighbour 0 0% 54.68% 723ms 3.08% AbstractCellPopulation::WriteResultsToFiles 699ms 2.97% 57.65% 699ms 2.97% boost::numeric::ublas::c_vector::operator() 7ms 0.03% 57.68% 673ms 2.86% boost::numeric::ublas::c_vector::operator= (inline) 40ms 0.17% 57.85% 643ms 2.74% std::__copy_move::__copy_m (inline) 0 0% 57.85% 643ms 2.74% std::__copy_move_a (inline) 0 0% 57.85% 643ms 2.74% std::__copy_move_a1 (inline) 0 0% 57.85% 643ms 2.74% std::__copy_move_a2 (inline) 0 0% 57.85% 642ms 2.73% std::copy (inline) 32ms 0.14% 57.99% 624ms 2.65% std::_Rb_tree_const_iterator::operator++ (inline) 618ms 2.63% 60.62% 618ms 2.63% __memcpy_avx_unaligned_erms 525ms 2.23% 62.85% 591ms 2.51% std::vector::push_back (inline) 587ms 2.50% 65.35% 587ms 2.50% std::_Rb_tree_increment 8ms 0.034% 65.38% 573ms 2.44% AbstractCentreBasedCellPopulation::GetDampingConstant 5ms 0.021% 65.40% 570ms 2.42% CellPropertyCollection::GetPropertiesType (inline) 1ms 0.0043% 65.41% 567ms 2.41% AbstractCellBasedSimulation::DoCellBirth 264ms 1.12% 66.53% 567ms 2.41% __cxxabiv1::__si_class_type_info::__do_dyncast 87ms 0.37% 66.90% 536ms 2.28% std::__new_allocator::allocate (inline) 0 0% 66.90% 522ms 2.22% std::allocator_traits::allocate (inline) 512ms 2.18% 69.08% 512ms 2.18% boost::numeric::ublas::same_impl_ex 32ms 0.14% 69.21% 505ms 2.15% boost::detail::shared_count::~shared_count (inline) 0 0% 69.21% 505ms 2.15% boost::shared_ptr::~shared_ptr (inline) 0 0% 69.21% 493ms 2.10% std::_Rb_tree::_M_create_node (inline) 1ms 0.0043% 69.22% 487ms 2.07% NodeBasedCellPopulation::WriteVtkResultsToFile 13ms 0.055% 69.27% 476ms 2.02% std::_Rb_tree::_Rb_tree (partial-inline) 459ms 1.95% 71.23% 467ms 1.99% boost::detail::sp_counted_base::release 47ms 0.2% 71.43% 457ms 1.94% std::_Rb_tree::_M_copy (inline) 30ms 0.13% 71.55% 449ms 1.91% operator new 0 0% 71.55% 444ms 1.89% AbstractCellBasedSimulation::DoCellRemoval (inline) 440ms 1.87% 73.42% 440ms 1.87% __strcmp_avx2 6ms 0.026% 73.45% 435ms 1.85% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 73.45% 433ms 1.84% std::_Rb_tree::_M_get_node (inline) 4ms 0.017% 73.47% 414ms 1.76% Cell::GetMutationState 129ms 0.55% 74.02% 409ms 1.74% __GI___libc_malloc 117ms 0.5% 74.51% 409ms 1.74% std::_Rb_tree::_M_clone_node (inline) 7ms 0.03% 74.54% 396ms 1.68% std::set::set (inline) 138ms 0.59% 75.13% 394ms 1.68% Node::GetRadius 114ms 0.48% 75.62% 381ms 1.62% std::_Rb_tree::_M_erase 0 0% 75.62% 357ms 1.52% boost::numeric::ublas::c_vector::assign (inline) 5ms 0.021% 75.64% 355ms 1.51% AbstractCellProperty::IsSubType (inline) 0 0% 75.64% 354ms 1.51% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 75.64% 342ms 1.45% boost::numeric::ublas::inner_prod (inline) 2ms 0.0085% 75.65% 342ms 1.45% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 16ms 0.068% 75.71% 340ms 1.45% boost::numeric::ublas::vector_scalar_binary::evaluate 329ms 1.40% 77.11% 329ms 1.40% __gnu_cxx::__normal_iterator::operator++ (inline) 29ms 0.12% 77.24% 329ms 1.40% boost::numeric::ublas::vector_binary::size (inline) 322ms 1.37% 78.61% 322ms 1.37% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 53ms 0.23% 78.83% 313ms 1.33% std::_Rb_tree::~_Rb_tree (inline) 0 0% 78.83% 307ms 1.31% NodesOnlyMesh::UpdateBoxCollection 10ms 0.043% 78.87% 286ms 1.22% NodeBasedCellPopulation::UpdateMapsAfterRemesh 1ms 0.0043% 78.88% 286ms 1.22% NodesOnlyMesh::ReMesh 4ms 0.017% 78.90% 273ms 1.16% NodesOnlyMesh::UpdateNodeIndices 94ms 0.4% 79.30% 272ms 1.16% boost::numeric::ublas::vector_inner_prod::apply (inline) 75ms 0.32% 79.61% 270ms 1.15% Node::AddNeighbour 4ms 0.017% 79.63% 270ms 1.15% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 262ms 1.11% 80.75% 262ms 1.11% Node::CheckForNodeAttributes 6ms 0.026% 80.77% 257ms 1.09% DistributedBoxCollection::GetProcessOwningNode 0 0% 80.77% 255ms 1.08% std::_Rb_tree::_M_drop_node (inline) 1ms 0.0043% 80.78% 254ms 1.08% NodesOnlyMesh::AddNodesToBoxes 0 0% 80.78% 242ms 1.03% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 80.78% 239ms 1.02% VtkMeshWriter::WriteFiles 5ms 0.021% 80.80% 239ms 1.02% std::_Rb_tree::_M_emplace_hint_unique 0 0% 80.80% 235ms 1% std::set::~set (inline) 121ms 0.51% 81.31% 226ms 0.96% _int_malloc 1ms 0.0043% 81.32% 224ms 0.95% std::__new_allocator::deallocate (inline) 215ms 0.91% 82.23% 216ms 0.92% Node::ConstructNodeAttributes (inline) 114ms 0.48% 82.72% 215ms 0.91% boost::shared_ptr::shared_ptr (inline) 0 0% 82.72% 208ms 0.88% NodesOnlyMesh::ResizeBoxCollection 9ms 0.038% 82.75% 207ms 0.88% NodesOnlyMesh::IsANodeCloseToDomainBoundary 16ms 0.068% 82.82% 206ms 0.88% std::__insertion_sort (inline) 85ms 0.36% 83.18% 205ms 0.87% __GI___libc_free 0 0% 83.18% 200ms 0.85% vtkDemandDrivenPipeline::ProcessRequest 0 0% 83.18% 200ms 0.85% vtkStreamingDemandDrivenPipeline::Update 0 0% 83.18% 200ms 0.85% vtkXMLWriterBase::Write 0 0% 83.18% 199ms 0.85% vtkExecutive::CallAlgorithm 0 0% 83.18% 198ms 0.84% vtkCompositeDataPipeline::ExecuteData 0 0% 83.18% 198ms 0.84% vtkDemandDrivenPipeline::ExecuteData 0 0% 83.18% 198ms 0.84% vtkStreamingDemandDrivenPipeline::ProcessRequest 1ms 0.0043% 83.19% 198ms 0.84% vtkXMLUnstructuredDataWriter::ProcessRequest 93ms 0.4% 83.58% 196ms 0.83% std::__move_median_to_first (inline) 0 0% 83.58% 192ms 0.82% std::allocator_traits::deallocate (inline) 0 0% 83.58% 188ms 0.8% std::_Rb_tree::_M_put_node (inline) 185ms 0.79% 84.37% 185ms 0.79% Node::GetIndex 179ms 0.76% 85.13% 179ms 0.76% [libchaste_cell_based.so] 0 0% 85.13% 175ms 0.74% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 85.13% 175ms 0.74% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 5ms 0.021% 85.15% 170ms 0.72% CellPropertyCollection::HasProperty 0 0% 85.15% 170ms 0.72% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 85.15% 169ms 0.72% Cell::HasCellProperty (inline) 9ms 0.038% 85.19% 164ms 0.7% Cell::ReadyToDivide 158ms 0.67% 85.86% 158ms 0.67% Node::IsDeleted 18ms 0.077% 85.94% 156ms 0.66% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 85.94% 155ms 0.66% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 153ms 0.65% 86.59% 153ms 0.65% [libchaste_mesh.so] 2ms 0.0085% 86.60% 152ms 0.65% DistributedBoxCollection::GetIsPeriodicAllDims 149ms 0.63% 87.23% 149ms 0.63% boost::shared_ptr::operator-> (inline) 0 0% 87.23% 147ms 0.63% boost::numeric::ublas::vector_binary::operator() (inline) 142ms 0.6% 87.84% 146ms 0.62% std::__adjacent_find (inline) 0 0% 87.84% 146ms 0.62% std::__unique (inline) 0 0% 87.84% 146ms 0.62% std::unique (inline) 0 0% 87.84% 146ms 0.62% vtkXMLWriter::WriteBinaryData 0 0% 87.84% 142ms 0.6% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.84% 142ms 0.6% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.84% 141ms 0.6% vtkXMLWriter::WriteCompressionBlock 0 0% 87.84% 139ms 0.59% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 87.84% 139ms 0.59% std::_Rb_tree::clear (inline) 1ms 0.0043% 87.84% 134ms 0.57% tbb::detail::r1::parallel_pipeline 0 0% 87.84% 129ms 0.55% clone3 0 0% 87.84% 129ms 0.55% start_thread 0 0% 87.84% 128ms 0.54% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 87.84% 128ms 0.54% tbb::detail::r1::reset 0 0% 87.84% 128ms 0.54% vtkXMLWriter::WritePointsAppendedData 4ms 0.017% 87.86% 126ms 0.54% AbstractCellProperty::IsType (inline) 5ms 0.021% 87.88% 125ms 0.53% AbstractNumericalMethod::SafeNodePositionUpdate 46ms 0.2% 88.08% 125ms 0.53% tbb::detail::r1::wait_bounded_queue_monitor 8ms 0.034% 88.11% 122ms 0.52% boost::numeric::ublas::c_vector::operator[] (inline) 113ms 0.48% 88.59% 120ms 0.51% _int_free 0 0% 88.59% 120ms 0.51% compress2 0 0% 88.59% 120ms 0.51% std::_Rb_tree::_M_insert_unique 0 0% 88.59% 120ms 0.51% std::set::insert (inline) 0 0% 88.59% 120ms 0.51% vtkDataCompressor::Compress 0 0% 88.59% 120ms 0.51% vtkZLibDataCompressor::CompressBuffer 118ms 0.5% 89.09% 118ms 0.5% __ieee754_log_fma