File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20378ms, 88.34% of 23067ms total Dropped 722 nodes (cum <= 115.33ms) flat flat% sum% cum cum% 0 0% 0% 22920ms 99.36% __libc_start_call_main 0 0% 0% 22920ms 99.36% __libc_start_main_impl 0 0% 0% 22920ms 99.36% _start 0 0% 0% 22905ms 99.30% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 22905ms 99.30% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 22905ms 99.30% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 22905ms 99.30% main 0 0% 0% 22871ms 99.15% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 22871ms 99.15% CxxTest::TestRunner::runTest (inline) 0 0% 0% 22871ms 99.15% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0043% 0.0043% 22862ms 99.11% AbstractCellBasedSimulation::Solve 0 0% 0.0043% 13042ms 56.54% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0043% 8671ms 37.59% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0087% 0.013% 8251ms 35.77% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.035% 0.048% 8072ms 34.99% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.048% 7690ms 33.34% NodeBasedCellPopulation::Update 1147ms 4.97% 5.02% 7481ms 32.43% RepulsionForce::AddForceContribution (partial-inline) 6ms 0.026% 5.05% 5657ms 24.52% DistributedBoxCollection::CalculateInteriorNodePairs 2120ms 9.19% 14.24% 4895ms 21.22% std::_Rb_tree::_M_lower_bound (inline) 17ms 0.074% 14.31% 4529ms 19.63% NodeAttributes::RemoveDuplicateNeighbours 0 0% 14.31% 4520ms 19.60% OffLatticeSimulation::ApplyBoundaries 10ms 0.043% 14.35% 4325ms 18.75% std::__sort (inline) 0 0% 14.35% 4325ms 18.75% std::sort (inline) 185ms 0.8% 15.16% 3817ms 16.55% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 6ms 0.026% 15.18% 3426ms 14.85% AbstractCellPopulation::Iterator::operator++ (inline) 187ms 0.81% 15.99% 3390ms 14.70% AbstractCellPopulation::Iterator::IsRealCell (inline) 68ms 0.29% 16.29% 3347ms 14.51% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 211ms 0.91% 17.20% 3185ms 13.81% std::_Rb_tree::find (inline) 0 0% 17.20% 3185ms 13.81% std::map::find (inline) 37ms 0.16% 17.36% 2854ms 12.37% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2735ms 11.86% 29.22% 2735ms 11.86% std::_Rb_tree::_S_right (inline) 248ms 1.08% 30.29% 2427ms 10.52% std::map::operator[] (partial-inline) 185ms 0.8% 31.10% 2420ms 10.49% std::__introsort_loop 30ms 0.13% 31.23% 2367ms 10.26% PlaneBoundaryCondition::ImposeBoundaryCondition 154ms 0.67% 31.89% 2311ms 10.02% AbstractMesh::GetNode 54ms 0.23% 32.13% 2288ms 9.92% NodesOnlyMesh::GetNodeOrHaloNode 28ms 0.12% 32.25% 2246ms 9.74% AbstractCellPopulation::GetLocationIndexUsingCell 96ms 0.42% 32.67% 2163ms 9.38% NodesOnlyMesh::SolveNodeMapping 0 0% 32.67% 2157ms 9.35% std::__unguarded_partition_pivot (inline) 25ms 0.11% 32.77% 2152ms 9.33% PlaneBoundaryCondition::VerifyBoundaryCondition 1011ms 4.38% 37.16% 1961ms 8.50% std::__unguarded_partition (inline) 0 0% 37.16% 1947ms 8.44% std::_Rb_tree::lower_bound (inline) 0 0% 37.16% 1947ms 8.44% std::map::lower_bound (inline) 5ms 0.022% 37.18% 1893ms 8.21% std::__final_insertion_sort (inline) 148ms 0.64% 37.82% 1814ms 7.86% DistributedBoxCollection::AddPairsFromBox 104ms 0.45% 38.27% 1678ms 7.27% std::__unguarded_insertion_sort (inline) 598ms 2.59% 40.86% 1642ms 7.12% std::__unguarded_linear_insert (inline) 14ms 0.061% 40.92% 1535ms 6.65% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 30ms 0.13% 41.05% 1514ms 6.56% AbstractCellPopulation::GetCellUsingLocationIndex 1490ms 6.46% 47.51% 1490ms 6.46% __gnu_cxx::__normal_iterator::operator-- (inline) 40ms 0.17% 47.69% 1283ms 5.56% boost::numeric::ublas::c_vector::c_vector (partial-inline) 48ms 0.21% 47.90% 1165ms 5.05% boost::numeric::ublas::vector_assign (inline) 1ms 0.0043% 47.90% 1123ms 4.87% NodeBasedCellPopulation::UpdateCellProcessLocation 7ms 0.03% 47.93% 1079ms 4.68% DistributedBoxCollection::CalculateBoundaryNodePairs 252ms 1.09% 49.02% 1045ms 4.53% boost::numeric::ublas::indexing_vector_assign 201ms 0.87% 49.89% 850ms 3.68% __dynamic_cast 147ms 0.64% 50.53% 800ms 3.47% AbstractMesh::GetVectorFromAtoB 17ms 0.074% 50.60% 797ms 3.46% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 50.60% 781ms 3.39% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 50.60% 762ms 3.30% boost::numeric::ublas::norm_2 (inline) 606ms 2.63% 53.23% 762ms 3.30% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 53.23% 762ms 3.30% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 214ms 0.93% 54.16% 750ms 3.25% NodeAttributes::AddNeighbour 0 0% 54.16% 709ms 3.07% AbstractCellPopulation::WriteResultsToFiles 340ms 1.47% 55.63% 707ms 3.06% DistributedBoxCollection::CalculateContainingBox (partial-inline) 674ms 2.92% 58.56% 674ms 2.92% boost::numeric::ublas::c_vector::operator() 5ms 0.022% 58.58% 645ms 2.80% boost::numeric::ublas::c_vector::operator= (inline) 42ms 0.18% 58.76% 619ms 2.68% std::__copy_move::__copy_m (inline) 0 0% 58.76% 619ms 2.68% std::__copy_move_a (inline) 0 0% 58.76% 619ms 2.68% std::__copy_move_a1 (inline) 0 0% 58.76% 619ms 2.68% std::__copy_move_a2 (inline) 0 0% 58.76% 619ms 2.68% std::copy (inline) 534ms 2.31% 61.07% 609ms 2.64% std::vector::push_back (inline) 591ms 2.56% 63.64% 591ms 2.56% __memcpy_avx_unaligned_erms 234ms 1.01% 64.65% 547ms 2.37% __cxxabiv1::__si_class_type_info::__do_dyncast 6ms 0.026% 64.68% 537ms 2.33% CellPropertyCollection::GetPropertiesType (inline) 535ms 2.32% 67.00% 535ms 2.32% boost::numeric::ublas::same_impl_ex 33ms 0.14% 67.14% 533ms 2.31% boost::detail::shared_count::~shared_count (inline) 0 0% 67.14% 533ms 2.31% boost::shared_ptr::~shared_ptr (inline) 31ms 0.13% 67.27% 527ms 2.28% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.0087% 67.28% 525ms 2.28% AbstractCentreBasedCellPopulation::GetDampingConstant 1ms 0.0043% 67.29% 521ms 2.26% AbstractCellBasedSimulation::DoCellBirth 492ms 2.13% 69.42% 493ms 2.14% boost::detail::sp_counted_base::release 490ms 2.12% 71.54% 490ms 2.12% std::_Rb_tree_increment 60ms 0.26% 71.80% 481ms 2.09% std::__new_allocator::allocate (inline) 471ms 2.04% 73.85% 471ms 2.04% __strcmp_avx2 2ms 0.0087% 73.85% 462ms 2.00% NodeBasedCellPopulation::WriteVtkResultsToFile 0 0% 73.85% 459ms 1.99% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 73.85% 456ms 1.98% std::allocator_traits::allocate (inline) 5ms 0.022% 73.88% 446ms 1.93% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 19ms 0.082% 73.96% 445ms 1.93% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 73.96% 429ms 1.86% std::_Rb_tree::_M_create_node (inline) 49ms 0.21% 74.17% 414ms 1.79% std::_Rb_tree::_M_copy (inline) 22ms 0.095% 74.27% 413ms 1.79% operator new 119ms 0.52% 74.78% 411ms 1.78% std::_Rb_tree::_M_erase 127ms 0.55% 75.33% 389ms 1.69% Node::GetRadius 108ms 0.47% 75.80% 386ms 1.67% __GI___libc_malloc 1ms 0.0043% 75.81% 378ms 1.64% AbstractCellProperty::IsSubType (inline) 0 0% 75.81% 375ms 1.63% std::_Rb_tree::_M_get_node (inline) 4ms 0.017% 75.82% 364ms 1.58% Cell::GetMutationState 1ms 0.0043% 75.83% 364ms 1.58% std::set::set (inline) 124ms 0.54% 76.36% 363ms 1.57% std::_Rb_tree::_M_clone_node (inline) 0 0% 76.36% 350ms 1.52% boost::numeric::ublas::c_vector::assign (inline) 9ms 0.039% 76.40% 338ms 1.47% boost::numeric::ublas::vector_binary::size (inline) 9ms 0.039% 76.44% 313ms 1.36% NodeBasedCellPopulation::UpdateMapsAfterRemesh 36ms 0.16% 76.60% 306ms 1.33% std::_Rb_tree::~_Rb_tree (inline) 300ms 1.30% 77.90% 300ms 1.30% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 77.90% 297ms 1.29% boost::numeric::ublas::inner_prod (inline) 2ms 0.0087% 77.91% 297ms 1.29% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 19ms 0.082% 77.99% 295ms 1.28% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 77.99% 295ms 1.28% std::_Rb_tree::_Alloc_node::operator() (inline) 287ms 1.24% 79.23% 287ms 1.24% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 79.23% 285ms 1.24% NodesOnlyMesh::ReMesh 2ms 0.0087% 79.24% 276ms 1.20% NodesOnlyMesh::UpdateNodeIndices 272ms 1.18% 80.42% 272ms 1.18% Node::CheckForNodeAttributes 0 0% 80.42% 271ms 1.17% std::_Rb_tree::_M_drop_node (inline) 3ms 0.013% 80.44% 264ms 1.14% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 80.44% 263ms 1.14% NodesOnlyMesh::UpdateBoxCollection 5ms 0.022% 80.46% 248ms 1.08% DistributedBoxCollection::GetProcessOwningNode 95ms 0.41% 80.87% 240ms 1.04% boost::numeric::ublas::vector_inner_prod::apply (inline) 5ms 0.022% 80.89% 233ms 1.01% std::__new_allocator::deallocate (inline) 9ms 0.039% 80.93% 232ms 1.01% std::_Rb_tree::_M_emplace_hint_unique 132ms 0.57% 81.50% 222ms 0.96% _int_malloc 0 0% 81.50% 220ms 0.95% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 2ms 0.0087% 81.51% 219ms 0.95% NodesOnlyMesh::AddNodesToBoxes 0 0% 81.51% 219ms 0.95% VtkMeshWriter::WriteFiles 0 0% 81.51% 218ms 0.95% std::set::~set (inline) 103ms 0.45% 81.96% 217ms 0.94% boost::shared_ptr::shared_ptr (inline) 17ms 0.074% 82.03% 210ms 0.91% std::__insertion_sort (inline) 0 0% 82.03% 207ms 0.9% NodesOnlyMesh::ResizeBoxCollection 19ms 0.082% 82.11% 205ms 0.89% NodesOnlyMesh::IsANodeCloseToDomainBoundary 67ms 0.29% 82.40% 205ms 0.89% __GI___libc_free 0 0% 82.40% 204ms 0.88% std::allocator_traits::deallocate (inline) 0 0% 82.40% 201ms 0.87% std::_Rb_tree::_M_put_node (inline) 1ms 0.0043% 82.41% 199ms 0.86% vtkXMLWriterBase::Write 0 0% 82.41% 198ms 0.86% vtkStreamingDemandDrivenPipeline::Update 197ms 0.85% 83.26% 197ms 0.85% Node::GetIndex 0 0% 83.26% 197ms 0.85% vtkDemandDrivenPipeline::ProcessRequest 196ms 0.85% 84.11% 196ms 0.85% [libchaste_cell_based.so] 0 0% 84.11% 196ms 0.85% vtkExecutive::CallAlgorithm 1ms 0.0043% 84.12% 196ms 0.85% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 84.12% 195ms 0.85% vtkCompositeDataPipeline::ExecuteData 0 0% 84.12% 195ms 0.85% vtkDemandDrivenPipeline::ExecuteData 0 0% 84.12% 195ms 0.85% vtkStreamingDemandDrivenPipeline::ProcessRequest 94ms 0.41% 84.52% 190ms 0.82% std::__move_median_to_first (inline) 0 0% 84.52% 178ms 0.77% Cell::HasCellProperty (inline) 2ms 0.0087% 84.53% 178ms 0.77% CellPropertyCollection::HasProperty 0 0% 84.53% 165ms 0.72% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 84.53% 165ms 0.72% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 7ms 0.03% 84.56% 164ms 0.71% Cell::ReadyToDivide 163ms 0.71% 85.27% 163ms 0.71% std::__adjacent_find (inline) 0 0% 85.27% 163ms 0.71% std::__unique (inline) 0 0% 85.27% 163ms 0.71% std::unique (inline) 0 0% 85.27% 159ms 0.69% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 84ms 0.36% 85.63% 154ms 0.67% Node::AddNeighbour 0 0% 85.63% 152ms 0.66% std::_Rb_tree::clear (inline) 6ms 0.026% 85.66% 151ms 0.65% AbstractCellProperty::IsType (inline) 12ms 0.052% 85.71% 146ms 0.63% boost::numeric::ublas::vector_reference::operator() (inline) 145ms 0.63% 86.34% 145ms 0.63% [libchaste_mesh.so] 0 0% 86.34% 142ms 0.62% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 140ms 0.61% 86.95% 140ms 0.61% Node::IsDeleted 126ms 0.55% 87.49% 138ms 0.6% _int_free 0 0% 87.49% 138ms 0.6% vtkXMLWriter::WriteBinaryData 0 0% 87.49% 136ms 0.59% AbstractCellPopulation::SetCellUsingLocationIndex 6ms 0.026% 87.52% 136ms 0.59% DistributedBoxCollection::GetIsPeriodicAllDims 0 0% 87.52% 135ms 0.59% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.52% 134ms 0.58% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 87.52% 134ms 0.58% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.52% 134ms 0.58% vtkXMLWriter::WriteCompressionBlock 1ms 0.0043% 87.52% 130ms 0.56% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 87.52% 127ms 0.55% boost::numeric::ublas::vector_binary::operator() (inline) 2ms 0.0087% 87.53% 125ms 0.54% Cell::GetCellId 0 0% 87.53% 125ms 0.54% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 87.53% 122ms 0.53% vtkDataCompressor::Compress 1ms 0.0043% 87.54% 121ms 0.52% compress2 0 0% 87.54% 121ms 0.52% vtkZLibDataCompressor::CompressBuffer 120ms 0.52% 88.06% 120ms 0.52% boost::shared_ptr::operator-> (inline) 60ms 0.26% 88.32% 119ms 0.52% crc32 0 0% 88.32% 119ms 0.52% deflate 6ms 0.026% 88.34% 116ms 0.5% NodeBasedCellPopulation::SetNode 0 0% 88.34% 116ms 0.5% vtkXMLWriter::WritePointsAppendedData