File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 21060ms, 88.95% of 23676ms total Dropped 776 nodes (cum <= 118.38ms) flat flat% sum% cum cum% 0 0% 0% 23515ms 99.32% __libc_start_call_main 0 0% 0% 23515ms 99.32% __libc_start_main_impl 0 0% 0% 23515ms 99.32% _start 0 0% 0% 23500ms 99.26% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 23500ms 99.26% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 23500ms 99.26% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 23500ms 99.26% main 0 0% 0% 23466ms 99.11% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 23466ms 99.11% CxxTest::TestRunner::runTest (inline) 0 0% 0% 23466ms 99.11% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 23458ms 99.08% AbstractCellBasedSimulation::Solve 1ms 0.0042% 0.0042% 13343ms 56.36% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0042% 8889ms 37.54% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.013% 0.017% 8447ms 35.68% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.013% 0.03% 8272ms 34.94% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.03% 7855ms 33.18% NodeBasedCellPopulation::Update 1161ms 4.90% 4.93% 7610ms 32.14% RepulsionForce::AddForceContribution (partial-inline) 9ms 0.038% 4.97% 5707ms 24.10% DistributedBoxCollection::CalculateInteriorNodePairs 2135ms 9.02% 13.99% 5010ms 21.16% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.0042% 13.99% 4603ms 19.44% OffLatticeSimulation::ApplyBoundaries 16ms 0.068% 14.06% 4562ms 19.27% NodeAttributes::RemoveDuplicateNeighbours 6ms 0.025% 14.09% 4269ms 18.03% std::__sort (inline) 0 0% 14.09% 4269ms 18.03% std::sort (inline) 170ms 0.72% 14.80% 3882ms 16.40% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 2ms 0.0084% 14.81% 3516ms 14.85% AbstractCellPopulation::Iterator::operator++ (inline) 169ms 0.71% 15.53% 3496ms 14.77% AbstractCellPopulation::Iterator::IsRealCell 70ms 0.3% 15.82% 3468ms 14.65% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 247ms 1.04% 16.87% 3247ms 13.71% std::_Rb_tree::find (inline) 0 0% 16.87% 3246ms 13.71% std::map::find (inline) 24ms 0.1% 16.97% 2992ms 12.64% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2841ms 12.00% 28.97% 2841ms 12.00% std::_Rb_tree::_S_right (inline) 264ms 1.12% 30.08% 2576ms 10.88% std::map::operator[] (partial-inline) 167ms 0.71% 30.79% 2431ms 10.27% std::__introsort_loop 23ms 0.097% 30.88% 2414ms 10.20% PlaneBoundaryCondition::ImposeBoundaryCondition 35ms 0.15% 31.03% 2372ms 10.02% AbstractCellPopulation::GetLocationIndexUsingCell 130ms 0.55% 31.58% 2265ms 9.57% AbstractMesh::GetNode 49ms 0.21% 31.79% 2250ms 9.50% NodesOnlyMesh::GetNodeOrHaloNode 12ms 0.051% 31.84% 2188ms 9.24% PlaneBoundaryCondition::VerifyBoundaryCondition 1ms 0.0042% 31.84% 2162ms 9.13% std::__unguarded_partition_pivot (inline) 61ms 0.26% 32.10% 2139ms 9.03% NodesOnlyMesh::SolveNodeMapping 0 0% 32.10% 2039ms 8.61% std::_Rb_tree::lower_bound (inline) 0 0% 32.10% 2039ms 8.61% std::map::lower_bound (inline) 1066ms 4.50% 36.60% 1922ms 8.12% std::__unguarded_partition (inline) 180ms 0.76% 37.36% 1892ms 7.99% DistributedBoxCollection::AddPairsFromBox 1ms 0.0042% 37.37% 1828ms 7.72% std::__final_insertion_sort (inline) 88ms 0.37% 37.74% 1602ms 6.77% std::__unguarded_insertion_sort (inline) 541ms 2.29% 40.02% 1584ms 6.69% std::__unguarded_linear_insert (inline) 33ms 0.14% 40.16% 1573ms 6.64% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 25ms 0.11% 40.27% 1535ms 6.48% AbstractCellPopulation::GetCellUsingLocationIndex 1421ms 6.00% 46.27% 1421ms 6.00% __gnu_cxx::__normal_iterator::operator-- (inline) 58ms 0.24% 46.52% 1279ms 5.40% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 46.52% 1207ms 5.10% NodeBasedCellPopulation::UpdateCellProcessLocation 2ms 0.0084% 46.52% 1172ms 4.95% DistributedBoxCollection::CalculateBoundaryNodePairs 46ms 0.19% 46.72% 1123ms 4.74% boost::numeric::ublas::vector_assign (inline) 277ms 1.17% 47.89% 1013ms 4.28% boost::numeric::ublas::indexing_vector_assign 261ms 1.10% 48.99% 928ms 3.92% __dynamic_cast 22ms 0.093% 49.08% 816ms 3.45% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 166ms 0.7% 49.78% 809ms 3.42% AbstractMesh::GetVectorFromAtoB 0 0% 49.78% 785ms 3.32% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 214ms 0.9% 50.69% 765ms 3.23% NodeAttributes::AddNeighbour 0 0% 50.69% 764ms 3.23% boost::numeric::ublas::norm_2 (inline) 618ms 2.61% 53.30% 764ms 3.23% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 53.30% 764ms 3.23% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 341ms 1.44% 54.74% 761ms 3.21% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 54.74% 741ms 3.13% AbstractCellPopulation::WriteResultsToFiles 4ms 0.017% 54.76% 686ms 2.90% boost::numeric::ublas::c_vector::operator= (inline) 674ms 2.85% 57.60% 674ms 2.85% boost::numeric::ublas::c_vector::operator() 36ms 0.15% 57.75% 666ms 2.81% std::__copy_move::__copy_m (inline) 0 0% 57.75% 666ms 2.81% std::__copy_move_a (inline) 0 0% 57.75% 666ms 2.81% std::__copy_move_a1 (inline) 0 0% 57.75% 666ms 2.81% std::__copy_move_a2 (inline) 0 0% 57.75% 666ms 2.81% std::copy (inline) 650ms 2.75% 60.50% 650ms 2.75% __memcpy_avx_unaligned_erms 25ms 0.11% 60.61% 614ms 2.59% std::_Rb_tree_const_iterator::operator++ (inline) 548ms 2.31% 62.92% 614ms 2.59% std::vector::push_back (inline) 4ms 0.017% 62.94% 603ms 2.55% CellPropertyCollection::GetPropertiesType (inline) 2ms 0.0084% 62.95% 593ms 2.50% AbstractCentreBasedCellPopulation::GetDampingConstant 1ms 0.0042% 62.95% 586ms 2.48% AbstractCellBasedSimulation::DoCellBirth 581ms 2.45% 65.40% 581ms 2.45% std::_Rb_tree_increment 49ms 0.21% 65.61% 549ms 2.32% boost::detail::shared_count::~shared_count (inline) 0 0% 65.61% 549ms 2.32% boost::shared_ptr::~shared_ptr (inline) 256ms 1.08% 66.69% 544ms 2.30% __cxxabiv1::__si_class_type_info::__do_dyncast 82ms 0.35% 67.04% 516ms 2.18% std::__new_allocator::allocate (inline) 512ms 2.16% 69.20% 512ms 2.16% boost::numeric::ublas::same_impl_ex 0 0% 69.20% 497ms 2.10% std::allocator_traits::allocate (inline) 491ms 2.07% 71.27% 492ms 2.08% boost::detail::sp_counted_base::release 0 0% 71.27% 490ms 2.07% NodeBasedCellPopulation::WriteVtkResultsToFile 24ms 0.1% 71.38% 474ms 2.00% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 71.38% 467ms 1.97% std::_Rb_tree::_M_create_node (inline) 0 0% 71.38% 447ms 1.89% AbstractCellBasedSimulation::DoCellRemoval (inline) 446ms 1.88% 73.26% 446ms 1.88% __strcmp_avx2 7ms 0.03% 73.29% 436ms 1.84% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 37ms 0.16% 73.45% 430ms 1.82% operator new 43ms 0.18% 73.63% 429ms 1.81% std::_Rb_tree::_M_copy (inline) 6ms 0.025% 73.65% 422ms 1.78% Cell::GetMutationState 5ms 0.021% 73.67% 414ms 1.75% AbstractCellProperty::IsSubType (inline) 0 0% 73.67% 411ms 1.74% std::_Rb_tree::_M_get_node (inline) 117ms 0.49% 74.17% 402ms 1.70% std::_Rb_tree::_M_erase 4ms 0.017% 74.18% 399ms 1.69% std::set::set (inline) 142ms 0.6% 74.78% 396ms 1.67% Node::GetRadius 122ms 0.52% 75.30% 389ms 1.64% __GI___libc_malloc 114ms 0.48% 75.78% 383ms 1.62% std::_Rb_tree::_M_clone_node (inline) 32ms 0.14% 75.92% 364ms 1.54% boost::numeric::ublas::vector_binary::size (inline) 0 0% 75.92% 343ms 1.45% boost::numeric::ublas::c_vector::assign (inline) 49ms 0.21% 76.12% 334ms 1.41% std::_Rb_tree::~_Rb_tree (inline) 7ms 0.03% 76.15% 333ms 1.41% NodeBasedCellPopulation::UpdateMapsAfterRemesh 0 0% 76.15% 323ms 1.36% NodesOnlyMesh::ReMesh 0 0% 76.15% 321ms 1.36% boost::numeric::ublas::inner_prod (inline) 2ms 0.0084% 76.16% 321ms 1.36% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 22ms 0.093% 76.25% 319ms 1.35% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 76.25% 319ms 1.35% std::_Rb_tree::_Alloc_node::operator() (inline) 7ms 0.03% 76.28% 308ms 1.30% NodesOnlyMesh::UpdateNodeIndices 304ms 1.28% 77.57% 304ms 1.28% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 2ms 0.0084% 77.58% 286ms 1.21% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 77.58% 274ms 1.16% std::_Rb_tree::_M_drop_node (inline) 9ms 0.038% 77.61% 273ms 1.15% std::_Rb_tree::_M_emplace_hint_unique 267ms 1.13% 78.74% 267ms 1.13% __gnu_cxx::__normal_iterator::operator++ (inline) 8ms 0.034% 78.78% 266ms 1.12% DistributedBoxCollection::GetProcessOwningNode 259ms 1.09% 79.87% 259ms 1.09% Node::CheckForNodeAttributes 256ms 1.08% 80.95% 257ms 1.09% std::__adjacent_find (inline) 0 0% 80.95% 257ms 1.09% std::__unique (inline) 0 0% 80.95% 257ms 1.09% std::unique (inline) 0 0% 80.95% 256ms 1.08% std::set::~set (inline) 92ms 0.39% 81.34% 248ms 1.05% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 81.34% 243ms 1.03% NodesOnlyMesh::UpdateBoxCollection 104ms 0.44% 81.78% 236ms 1% std::__move_median_to_first (inline) 7ms 0.03% 81.81% 233ms 0.98% std::__new_allocator::deallocate (inline) 1ms 0.0042% 81.81% 229ms 0.97% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 81.81% 227ms 0.96% VtkMeshWriter::WriteFiles 19ms 0.08% 81.89% 225ms 0.95% std::__insertion_sort (inline) 118ms 0.5% 82.39% 217ms 0.92% _int_malloc 0 0% 82.39% 213ms 0.9% std::allocator_traits::deallocate (inline) 0 0% 82.39% 211ms 0.89% std::_Rb_tree::_M_put_node (inline) 0 0% 82.39% 206ms 0.87% NodesOnlyMesh::ResizeBoxCollection 12ms 0.051% 82.44% 205ms 0.87% NodesOnlyMesh::IsANodeCloseToDomainBoundary 80ms 0.34% 82.78% 205ms 0.87% __GI___libc_free 0 0% 82.78% 205ms 0.87% vtkStreamingDemandDrivenPipeline::Update 0 0% 82.78% 205ms 0.87% vtkXMLWriterBase::Write 104ms 0.44% 83.22% 204ms 0.86% boost::shared_ptr::shared_ptr (inline) 0 0% 83.22% 203ms 0.86% vtkDemandDrivenPipeline::ProcessRequest 1ms 0.0042% 83.22% 203ms 0.86% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 83.22% 202ms 0.85% NodesOnlyMesh::AddNodesToBoxes 0 0% 83.22% 202ms 0.85% vtkDemandDrivenPipeline::ExecuteData 0 0% 83.22% 201ms 0.85% vtkCompositeDataPipeline::ExecuteData 0 0% 83.22% 201ms 0.85% vtkExecutive::CallAlgorithm 0 0% 83.22% 201ms 0.85% vtkXMLUnstructuredDataWriter::ProcessRequest 2ms 0.0084% 83.23% 200ms 0.84% CellPropertyCollection::HasProperty 0 0% 83.23% 199ms 0.84% Cell::HasCellProperty (inline) 8ms 0.034% 83.27% 191ms 0.81% Cell::ReadyToDivide 183ms 0.77% 84.04% 183ms 0.77% Node::GetIndex 183ms 0.77% 84.81% 183ms 0.77% [libchaste_cell_based.so] 0 0% 84.81% 175ms 0.74% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 84.81% 175ms 0.74% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 84.81% 173ms 0.73% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 6ms 0.025% 84.84% 161ms 0.68% AbstractCellProperty::IsType (inline) 159ms 0.67% 85.51% 159ms 0.67% Node::IsDeleted 0 0% 85.51% 149ms 0.63% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 149ms 0.63% 86.14% 149ms 0.63% boost::shared_ptr::operator-> (inline) 0 0% 86.14% 148ms 0.63% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 86.14% 147ms 0.62% Cell::GetCellId 79ms 0.33% 86.47% 147ms 0.62% Node::AddNeighbour 147ms 0.62% 87.09% 147ms 0.62% [libchaste_mesh.so] 0 0% 87.09% 141ms 0.6% vtkXMLWriter::WriteBinaryData 3ms 0.013% 87.11% 140ms 0.59% AbstractCellPopulation::SetCellUsingLocationIndex 1ms 0.0042% 87.11% 139ms 0.59% std::_Rb_tree::clear (inline) 0 0% 87.11% 137ms 0.58% vtkXMLWriter::WriteBinaryDataBlock 0 0% 87.11% 137ms 0.58% vtkXMLWriter::WriteBinaryDataInternal 0 0% 87.11% 137ms 0.58% vtkXMLWriter::WriteCompressionBlock 0 0% 87.11% 131ms 0.55% tbb::detail::r1::parallel_pipeline 130ms 0.55% 87.66% 130ms 0.55% __ieee754_log_fma 15ms 0.063% 87.72% 130ms 0.55% boost::numeric::ublas::vector_reference::operator() (inline) 7ms 0.03% 87.75% 128ms 0.54% DistributedBoxCollection::GetIsPeriodicAllDims 0 0% 87.75% 126ms 0.53% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 87.75% 126ms 0.53% clone3 0 0% 87.75% 126ms 0.53% start_thread 0 0% 87.75% 125ms 0.53% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 87.75% 125ms 0.53% tbb::detail::r1::reset 112ms 0.47% 88.22% 124ms 0.52% _int_free 0 0% 88.22% 123ms 0.52% vtkXMLWriter::WritePointsAppendedData 5ms 0.021% 88.25% 122ms 0.52% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 88.25% 121ms 0.51% vtkDataCompressor::Compress 120ms 0.51% 88.75% 120ms 0.51% Node::rGetLocation 0 0% 88.75% 120ms 0.51% compress2 0 0% 88.75% 120ms 0.51% vtkZLibDataCompressor::CompressBuffer 47ms 0.2% 88.95% 119ms 0.5% AbstractCellProperty::IsSame