File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 16930ms, 88.22% of 19190ms total Dropped 751 nodes (cum <= 95.95ms) flat flat% sum% cum cum% 0 0% 0% 19041ms 99.22% __libc_start_call_main 0 0% 0% 19041ms 99.22% __libc_start_main_impl 0 0% 0% 19041ms 99.22% _start 0 0% 0% 19026ms 99.15% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19026ms 99.15% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19026ms 99.15% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19026ms 99.15% main 0 0% 0% 18992ms 98.97% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 18992ms 98.97% CxxTest::TestRunner::runTest (inline) 0 0% 0% 18992ms 98.97% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 18985ms 98.93% AbstractCellBasedSimulation::Solve 6ms 0.031% 0.031% 10938ms 57.00% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.01% 0.042% 7239ms 37.72% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.01% 0.052% 7151ms 37.26% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.052% 7149ms 37.25% AbstractCellBasedSimulation::UpdateCellPopulation 1209ms 6.30% 6.35% 6523ms 33.99% RepulsionForce::AddForceContribution (partial-inline) 0 0% 6.35% 6372ms 33.20% NodeBasedCellPopulation::Update 4ms 0.021% 6.37% 5548ms 28.91% DistributedBoxCollection::CalculateInteriorNodePairs 1ms 0.0052% 6.38% 3510ms 18.29% OffLatticeSimulation::ApplyBoundaries 27ms 0.14% 6.52% 3470ms 18.08% NodeAttributes::RemoveDuplicateNeighbours 1ms 0.0052% 6.52% 3295ms 17.17% std::__sort (inline) 0 0% 6.52% 3295ms 17.17% std::sort (inline) 157ms 0.82% 7.34% 2901ms 15.12% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 1257ms 6.55% 13.89% 2805ms 14.62% std::_Rb_tree::_M_lower_bound (inline) 3ms 0.016% 13.91% 2368ms 12.34% AbstractCellPopulation::Iterator::operator++ (inline) 180ms 0.94% 14.85% 2348ms 12.24% AbstractCellPopulation::Iterator::IsRealCell 69ms 0.36% 15.21% 2324ms 12.11% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 41ms 0.21% 15.42% 2219ms 11.56% AbstractCellPopulation::GetLocationIndexUsingCell 228ms 1.19% 16.61% 2142ms 11.16% std::map::operator[] (partial-inline) 122ms 0.64% 17.24% 1942ms 10.12% std::__introsort_loop 28ms 0.15% 17.39% 1941ms 10.11% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 159ms 0.83% 18.22% 1842ms 9.60% DistributedBoxCollection::AddPairsFromBox 21ms 0.11% 18.33% 1832ms 9.55% PlaneBoundaryCondition::ImposeBoundaryCondition 0 0% 18.33% 1778ms 9.27% std::_Rb_tree::lower_bound (inline) 0 0% 18.33% 1778ms 9.27% std::map::lower_bound (inline) 0 0% 18.33% 1744ms 9.09% std::__unguarded_partition_pivot (inline) 10ms 0.052% 18.38% 1677ms 8.74% PlaneBoundaryCondition::VerifyBoundaryCondition 780ms 4.06% 22.44% 1597ms 8.32% std::__unguarded_partition (inline) 1507ms 7.85% 30.30% 1507ms 7.85% std::_Rb_tree::_S_right (inline) 18ms 0.094% 30.39% 1472ms 7.67% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 23ms 0.12% 30.51% 1451ms 7.56% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 30.51% 1351ms 7.04% std::__final_insertion_sort (inline) 559ms 2.91% 33.42% 1245ms 6.49% std::__unguarded_linear_insert (inline) 64ms 0.33% 33.76% 1209ms 6.30% std::__unguarded_insertion_sort (inline) 110ms 0.57% 34.33% 1144ms 5.96% std::_Rb_tree::find (inline) 0 0% 34.33% 1144ms 5.96% std::map::find (inline) 69ms 0.36% 34.69% 1132ms 5.90% boost::numeric::ublas::c_vector::c_vector (partial-inline) 1103ms 5.75% 40.44% 1103ms 5.75% __gnu_cxx::__normal_iterator::operator-- (inline) 47ms 0.24% 40.68% 987ms 5.14% boost::numeric::ublas::vector_assign (inline) 234ms 1.22% 41.90% 933ms 4.86% __dynamic_cast 280ms 1.46% 43.36% 886ms 4.62% boost::numeric::ublas::indexing_vector_assign 166ms 0.87% 44.23% 787ms 4.10% AbstractMesh::GetVectorFromAtoB 180ms 0.94% 45.16% 778ms 4.05% NodeAttributes::AddNeighbour 0 0% 45.16% 737ms 3.84% NodeBasedCellPopulation::UpdateCellProcessLocation 0 0% 45.16% 734ms 3.82% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 45.16% 717ms 3.74% boost::numeric::ublas::norm_2 (inline) 556ms 2.90% 48.06% 717ms 3.74% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 48.06% 717ms 3.74% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 48.06% 662ms 3.45% AbstractCellPopulation::WriteResultsToFiles 31ms 0.16% 48.22% 660ms 3.44% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 597ms 3.11% 51.33% 653ms 3.40% std::vector::push_back (inline) 303ms 1.58% 52.91% 610ms 3.18% DistributedBoxCollection::CalculateContainingBox (partial-inline) 284ms 1.48% 54.39% 603ms 3.14% __cxxabiv1::__si_class_type_info::__do_dyncast 4ms 0.021% 54.41% 594ms 3.10% boost::numeric::ublas::c_vector::operator= (inline) 38ms 0.2% 54.61% 578ms 3.01% std::__copy_move::__copy_m (inline) 0 0% 54.61% 578ms 3.01% std::__copy_move_a (inline) 0 0% 54.61% 578ms 3.01% std::__copy_move_a1 (inline) 0 0% 54.61% 578ms 3.01% std::__copy_move_a2 (inline) 0 0% 54.61% 578ms 3.01% std::copy (inline) 562ms 2.93% 57.54% 562ms 2.93% __memcpy_avx_unaligned_erms 7ms 0.036% 57.58% 559ms 2.91% AbstractCentreBasedCellPopulation::GetDampingConstant 4ms 0.021% 57.60% 527ms 2.75% CellPropertyCollection::GetPropertiesType (inline) 28ms 0.15% 57.74% 519ms 2.70% std::_Rb_tree_const_iterator::operator++ (inline) 507ms 2.64% 60.39% 507ms 2.64% boost::numeric::ublas::c_vector::operator() 472ms 2.46% 62.85% 472ms 2.46% std::_Rb_tree_increment 464ms 2.42% 65.26% 464ms 2.42% __strcmp_avx2 445ms 2.32% 67.58% 445ms 2.32% boost::numeric::ublas::same_impl_ex 4ms 0.021% 67.60% 433ms 2.26% AbstractCellBasedSimulation::DoCellBirth 2ms 0.01% 67.61% 421ms 2.19% NodeBasedCellPopulation::WriteVtkResultsToFile 147ms 0.77% 68.38% 410ms 2.14% Node::GetRadius 22ms 0.11% 68.49% 398ms 2.07% boost::detail::shared_count::~shared_count (inline) 0 0% 68.49% 398ms 2.07% boost::shared_ptr::~shared_ptr (inline) 32ms 0.17% 68.66% 394ms 2.05% std::_Rb_tree::_Rb_tree (partial-inline) 9ms 0.047% 68.71% 384ms 2.00% Cell::GetMutationState 4ms 0.021% 68.73% 383ms 2.00% std::set::set (inline) 2ms 0.01% 68.74% 382ms 1.99% AbstractCellProperty::IsSubType (inline) 45ms 0.23% 68.97% 375ms 1.95% NodesOnlyMesh::GetNodeOrHaloNode 67ms 0.35% 69.32% 367ms 1.91% std::__new_allocator::allocate (inline) 363ms 1.89% 71.21% 364ms 1.90% boost::detail::sp_counted_base::release 0 0% 71.21% 357ms 1.86% std::allocator_traits::allocate (inline) 32ms 0.17% 71.38% 354ms 1.84% std::_Rb_tree::_M_copy (inline) 0 0% 71.38% 343ms 1.79% std::_Rb_tree::_M_create_node (inline) 0 0% 71.38% 342ms 1.78% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 71.38% 335ms 1.75% boost::numeric::ublas::inner_prod (inline) 2ms 0.01% 71.39% 334ms 1.74% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 24ms 0.13% 71.52% 332ms 1.73% boost::numeric::ublas::vector_scalar_binary::evaluate 3ms 0.016% 71.53% 328ms 1.71% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 112ms 0.58% 72.12% 320ms 1.67% std::_Rb_tree::_M_clone_node (inline) 172ms 0.9% 73.01% 314ms 1.64% AbstractMesh::GetNode 0 0% 73.01% 307ms 1.60% std::_Rb_tree::_M_get_node (inline) 4ms 0.021% 73.03% 304ms 1.58% NodeBasedCellPopulation::UpdateMapsAfterRemesh 19ms 0.099% 73.13% 298ms 1.55% operator new 22ms 0.11% 73.25% 295ms 1.54% boost::numeric::ublas::vector_binary::size (inline) 80ms 0.42% 73.66% 277ms 1.44% std::_Rb_tree::_M_erase (partial-inline) 84ms 0.44% 74.10% 276ms 1.44% __GI___libc_malloc 268ms 1.40% 75.50% 268ms 1.40% Node::CheckForNodeAttributes 0 0% 75.50% 265ms 1.38% std::_Rb_tree::_Alloc_node::operator() (inline) 39ms 0.2% 75.70% 265ms 1.38% std::_Rb_tree::~_Rb_tree (inline) 0 0% 75.70% 260ms 1.35% boost::numeric::ublas::c_vector::assign (inline) 106ms 0.55% 76.25% 248ms 1.29% boost::numeric::ublas::vector_inner_prod::apply (inline) 94ms 0.49% 76.74% 234ms 1.22% boost::shared_ptr::shared_ptr (inline) 1ms 0.0052% 76.75% 224ms 1.17% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 76.75% 222ms 1.16% VtkMeshWriter::WriteFiles 0 0% 76.75% 216ms 1.13% std::set::~set (inline) 214ms 1.12% 77.86% 214ms 1.12% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 77.86% 202ms 1.05% NodesOnlyMesh::UpdateBoxCollection 0 0% 77.86% 202ms 1.05% vtkStreamingDemandDrivenPipeline::Update 0 0% 77.86% 202ms 1.05% vtkXMLWriterBase::Write 0 0% 77.86% 201ms 1.05% vtkDemandDrivenPipeline::ProcessRequest 1ms 0.0052% 77.87% 200ms 1.04% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 77.87% 200ms 1.04% vtkExecutive::CallAlgorithm 0 0% 77.87% 199ms 1.04% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 77.87% 199ms 1.04% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 77.87% 198ms 1.03% vtkCompositeDataPipeline::ExecuteData 0 0% 77.87% 198ms 1.03% vtkDemandDrivenPipeline::ExecuteData 195ms 1.02% 78.88% 195ms 1.02% [libchaste_mesh.so] 0 0% 78.88% 195ms 1.02% std::_Rb_tree::_M_drop_node (inline) 2ms 0.01% 78.90% 193ms 1.01% DistributedBoxCollection::GetProcessOwningNode 191ms 1% 79.89% 191ms 1% Node::GetIndex 189ms 0.98% 80.88% 189ms 0.98% [libchaste_cell_based.so] 2ms 0.01% 80.89% 180ms 0.94% CellPropertyCollection::HasProperty 0 0% 80.89% 179ms 0.93% Cell::HasCellProperty (inline) 0 0% 80.89% 171ms 0.89% NodesOnlyMesh::AddNodesToBoxes 0 0% 80.89% 166ms 0.87% NodesOnlyMesh::ResizeBoxCollection 0 0% 80.89% 166ms 0.87% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 80.89% 166ms 0.87% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 13ms 0.068% 80.95% 165ms 0.86% NodesOnlyMesh::IsANodeCloseToDomainBoundary 3ms 0.016% 80.97% 164ms 0.85% Cell::ReadyToDivide 0 0% 80.97% 163ms 0.85% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 155ms 0.81% 81.78% 155ms 0.81% __gnu_cxx::__normal_iterator::operator++ (inline) 5ms 0.026% 81.80% 150ms 0.78% AbstractCellProperty::IsType (inline) 3ms 0.016% 81.82% 149ms 0.78% std::__new_allocator::deallocate (inline) 81ms 0.42% 82.24% 147ms 0.77% std::__move_median_to_first (inline) 80ms 0.42% 82.66% 144ms 0.75% _int_malloc 130ms 0.68% 83.34% 143ms 0.75% NodesOnlyMesh::SolveNodeMapping 14ms 0.073% 83.41% 142ms 0.74% std::__insertion_sort (inline) 79ms 0.41% 83.82% 140ms 0.73% boost::detail::shared_count::shared_count (inline) 139ms 0.72% 84.54% 139ms 0.72% Node::IsDeleted 139ms 0.72% 85.27% 139ms 0.72% std::__adjacent_find (inline) 0 0% 85.27% 139ms 0.72% std::__unique (inline) 0 0% 85.27% 139ms 0.72% std::unique (inline) 0 0% 85.27% 138ms 0.72% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 85.27% 137ms 0.71% vtkXMLWriter::WriteBinaryData 4ms 0.021% 85.29% 136ms 0.71% std::_Rb_tree::_M_emplace_hint_unique 0 0% 85.29% 133ms 0.69% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 64ms 0.33% 85.62% 133ms 0.69% Node::AddNeighbour 20ms 0.1% 85.73% 132ms 0.69% boost::numeric::ublas::vector_reference::operator() (inline) 47ms 0.24% 85.97% 130ms 0.68% __GI___libc_free 0 0% 85.97% 130ms 0.68% vtkXMLWriter::WriteBinaryDataBlock 0 0% 85.97% 130ms 0.68% vtkXMLWriter::WriteBinaryDataInternal 0 0% 85.97% 130ms 0.68% vtkXMLWriter::WriteCompressionBlock 6ms 0.031% 86.00% 129ms 0.67% AbstractCellPopulation::SetCellUsingLocationIndex 0 0% 86.00% 128ms 0.67% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 86.00% 124ms 0.65% vtkXMLWriter::WritePointsAppendedData 38ms 0.2% 86.20% 120ms 0.63% AbstractCellProperty::IsSame 0 0% 86.20% 119ms 0.62% std::allocator_traits::deallocate (inline) 2ms 0.01% 86.21% 117ms 0.61% Cell::GetCellId 1ms 0.0052% 86.22% 116ms 0.6% NodeBasedCellPopulation::AcceptCellWriter 11ms 0.057% 86.27% 116ms 0.6% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 86.27% 116ms 0.6% tbb::detail::r1::parallel_pipeline 0 0% 86.27% 115ms 0.6% clone3 0 0% 86.27% 115ms 0.6% start_thread 4ms 0.021% 86.29% 114ms 0.59% DistributedBoxCollection::GetIsPeriodicAllDims 0 0% 86.29% 114ms 0.59% std::_Rb_tree::_M_put_node (inline) 0 0% 86.29% 114ms 0.59% tbb::detail::r1::reset 112ms 0.58% 86.88% 112ms 0.58% Node::rGetLocation 112ms 0.58% 87.46% 112ms 0.58% __ieee754_log_fma 39ms 0.2% 87.67% 111ms 0.58% AbstractCellCycleModel::GetAge 0 0% 87.67% 111ms 0.58% DistributedBoxCollection::CalculateBoundaryNodePairs 0 0% 87.67% 111ms 0.58% compress2 46ms 0.24% 87.91% 111ms 0.58% tbb::detail::r1::wait_bounded_queue_monitor 0 0% 87.91% 111ms 0.58% vtkDataCompressor::Compress 0 0% 87.91% 111ms 0.58% vtkZLibDataCompressor::CompressBuffer 3ms 0.016% 87.92% 110ms 0.57% std::_Rb_tree::_M_insert_unique 0 0% 87.92% 110ms 0.57% std::set::insert (inline) 55ms 0.29% 88.21% 107ms 0.56% crc32 0 0% 88.21% 107ms 0.56% deflate 3ms 0.016% 88.22% 100ms 0.52% Cell::GetCellProliferativeType