File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 20436ms, 88.86% of 22998ms total Dropped 760 nodes (cum <= 114.99ms) flat flat% sum% cum cum% 0 0% 0% 22856ms 99.38% __libc_start_call_main 0 0% 0% 22856ms 99.38% __libc_start_main_impl 0 0% 0% 22856ms 99.38% _start 0 0% 0% 22841ms 99.32% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 22841ms 99.32% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 22841ms 99.32% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 22841ms 99.32% main 0 0% 0% 22807ms 99.17% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 22807ms 99.17% CxxTest::TestRunner::runTest (inline) 0 0% 0% 22807ms 99.17% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 1ms 0.0043% 0.0043% 22799ms 99.13% AbstractCellBasedSimulation::Solve 1ms 0.0043% 0.0087% 12976ms 56.42% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.0087% 8646ms 37.59% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.017% 0.026% 8233ms 35.80% ForwardEulerNumericalMethod::UpdateAllNodePositions 9ms 0.039% 0.065% 8072ms 35.10% AbstractNumericalMethod::ComputeForcesIncludingDamping 2ms 0.0087% 0.074% 7649ms 33.26% NodeBasedCellPopulation::Update 1211ms 5.27% 5.34% 7461ms 32.44% RepulsionForce::AddForceContribution (partial-inline) 5ms 0.022% 5.36% 5634ms 24.50% DistributedBoxCollection::CalculateInteriorNodePairs 2065ms 8.98% 14.34% 4848ms 21.08% std::_Rb_tree::_M_lower_bound (inline) 0 0% 14.34% 4465ms 19.41% OffLatticeSimulation::ApplyBoundaries 17ms 0.074% 14.41% 4455ms 19.37% NodeAttributes::RemoveDuplicateNeighbours 3ms 0.013% 14.43% 4282ms 18.62% std::__sort (inline) 0 0% 14.43% 4282ms 18.62% std::sort (inline) 203ms 0.88% 15.31% 3731ms 16.22% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 6ms 0.026% 15.34% 3375ms 14.68% AbstractCellPopulation::Iterator::operator++ (inline) 67ms 0.29% 15.63% 3371ms 14.66% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 154ms 0.67% 16.30% 3339ms 14.52% AbstractCellPopulation::Iterator::IsRealCell 252ms 1.10% 17.39% 3214ms 13.98% std::_Rb_tree::find (inline) 0 0% 17.39% 3214ms 13.98% std::map::find (inline) 24ms 0.1% 17.50% 2845ms 12.37% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2738ms 11.91% 29.40% 2738ms 11.91% std::_Rb_tree::_S_right (inline) 192ms 0.83% 30.24% 2434ms 10.58% std::__introsort_loop 34ms 0.15% 30.39% 2351ms 10.22% AbstractCellPopulation::GetLocationIndexUsingCell 209ms 0.91% 31.29% 2342ms 10.18% std::map::operator[] (partial-inline) 24ms 0.1% 31.40% 2303ms 10.01% PlaneBoundaryCondition::ImposeBoundaryCondition 150ms 0.65% 32.05% 2220ms 9.65% AbstractMesh::GetNode 32ms 0.14% 32.19% 2200ms 9.57% NodesOnlyMesh::GetNodeOrHaloNode 1ms 0.0043% 32.19% 2166ms 9.42% std::__unguarded_partition_pivot (inline) 19ms 0.083% 32.28% 2162ms 9.40% PlaneBoundaryCondition::VerifyBoundaryCondition 73ms 0.32% 32.59% 2072ms 9.01% NodesOnlyMesh::SolveNodeMapping 1007ms 4.38% 36.97% 1940ms 8.44% std::__unguarded_partition (inline) 0 0% 36.97% 1911ms 8.31% std::_Rb_tree::lower_bound (inline) 0 0% 36.97% 1911ms 8.31% std::map::lower_bound (inline) 0 0% 36.97% 1844ms 8.02% std::__final_insertion_sort (inline) 146ms 0.63% 37.61% 1775ms 7.72% DistributedBoxCollection::AddPairsFromBox 92ms 0.4% 38.01% 1633ms 7.10% std::__unguarded_insertion_sort (inline) 594ms 2.58% 40.59% 1615ms 7.02% std::__unguarded_linear_insert (inline) 19ms 0.083% 40.67% 1468ms 6.38% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 1467ms 6.38% 47.05% 1467ms 6.38% __gnu_cxx::__normal_iterator::operator-- (inline) 25ms 0.11% 47.16% 1445ms 6.28% AbstractCellPopulation::GetCellUsingLocationIndex 49ms 0.21% 47.37% 1189ms 5.17% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 47.37% 1138ms 4.95% NodeBasedCellPopulation::UpdateCellProcessLocation 36ms 0.16% 47.53% 1082ms 4.70% boost::numeric::ublas::vector_assign (inline) 7ms 0.03% 47.56% 1054ms 4.58% DistributedBoxCollection::CalculateBoundaryNodePairs 270ms 1.17% 48.73% 986ms 4.29% boost::numeric::ublas::indexing_vector_assign 271ms 1.18% 49.91% 933ms 4.06% __dynamic_cast 22ms 0.096% 50.01% 855ms 3.72% std::_Rb_tree_const_iterator::operator++ (inline) 16ms 0.07% 50.08% 817ms 3.55% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 803ms 3.49% 53.57% 803ms 3.49% std::_Rb_tree_increment 0 0% 53.57% 796ms 3.46% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 387ms 1.68% 55.25% 786ms 3.42% DistributedBoxCollection::CalculateContainingBox (partial-inline) 0 0% 55.25% 785ms 3.41% boost::numeric::ublas::norm_2 (inline) 614ms 2.67% 57.92% 785ms 3.41% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 57.92% 785ms 3.41% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 177ms 0.77% 58.69% 776ms 3.37% AbstractMesh::GetVectorFromAtoB 0 0% 58.69% 724ms 3.15% AbstractCellPopulation::WriteResultsToFiles 7ms 0.03% 58.72% 672ms 2.92% boost::numeric::ublas::c_vector::operator= (inline) 650ms 2.83% 61.55% 650ms 2.83% boost::numeric::ublas::c_vector::operator() 40ms 0.17% 61.72% 645ms 2.80% std::__copy_move::__copy_m (inline) 0 0% 61.72% 645ms 2.80% std::__copy_move_a (inline) 0 0% 61.72% 645ms 2.80% std::__copy_move_a1 (inline) 0 0% 61.72% 645ms 2.80% std::__copy_move_a2 (inline) 0 0% 61.72% 645ms 2.80% std::copy (inline) 620ms 2.70% 64.42% 620ms 2.70% __memcpy_avx_unaligned_erms 0 0% 64.42% 551ms 2.40% AbstractCellBasedSimulation::DoCellBirth 242ms 1.05% 65.47% 539ms 2.34% __cxxabiv1::__si_class_type_info::__do_dyncast 5ms 0.022% 65.49% 530ms 2.30% CellPropertyCollection::GetPropertiesType (inline) 87ms 0.38% 65.87% 527ms 2.29% std::__new_allocator::allocate (inline) 3ms 0.013% 65.88% 526ms 2.29% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 65.88% 501ms 2.18% std::allocator_traits::allocate (inline) 39ms 0.17% 66.05% 499ms 2.17% boost::detail::shared_count::~shared_count (inline) 0 0% 66.05% 499ms 2.17% boost::shared_ptr::~shared_ptr (inline) 196ms 0.85% 66.91% 495ms 2.15% NodeAttributes::AddNeighbour 20ms 0.087% 66.99% 480ms 2.09% std::_Rb_tree::_Rb_tree (partial-inline) 1ms 0.0043% 67.00% 470ms 2.04% NodeBasedCellPopulation::WriteVtkResultsToFile 467ms 2.03% 69.03% 467ms 2.03% boost::numeric::ublas::same_impl_ex 463ms 2.01% 71.04% 463ms 2.01% __strcmp_avx2 454ms 1.97% 73.02% 457ms 1.99% boost::detail::sp_counted_base::release 0 0% 73.02% 455ms 1.98% std::_Rb_tree::_M_create_node (inline) 44ms 0.19% 73.21% 453ms 1.97% std::_Rb_tree::_M_copy (inline) 0 0% 73.21% 443ms 1.93% AbstractCellBasedSimulation::DoCellRemoval (inline) 22ms 0.096% 73.30% 440ms 1.91% operator new 5ms 0.022% 73.32% 432ms 1.88% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 2ms 0.0087% 73.33% 418ms 1.82% AbstractCellProperty::IsSubType (inline) 162ms 0.7% 74.04% 413ms 1.80% Node::GetRadius 143ms 0.62% 74.66% 413ms 1.80% __GI___libc_malloc 124ms 0.54% 75.20% 408ms 1.77% std::_Rb_tree::_M_clone_node (inline) 0 0% 75.20% 404ms 1.76% std::_Rb_tree::_M_get_node (inline) 123ms 0.53% 75.73% 391ms 1.70% std::_Rb_tree::_M_erase 3ms 0.013% 75.75% 387ms 1.68% std::set::set (inline) 6ms 0.026% 75.77% 361ms 1.57% Cell::GetMutationState 296ms 1.29% 77.06% 351ms 1.53% std::vector::push_back (inline) 0 0% 77.06% 333ms 1.45% std::_Rb_tree::_Alloc_node::operator() (inline) 323ms 1.40% 78.46% 323ms 1.40% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 0 0% 78.46% 313ms 1.36% boost::numeric::ublas::c_vector::assign (inline) 5ms 0.022% 78.49% 309ms 1.34% NodeBasedCellPopulation::UpdateMapsAfterRemesh 40ms 0.17% 78.66% 304ms 1.32% std::_Rb_tree::~_Rb_tree (inline) 0 0% 78.66% 303ms 1.32% boost::numeric::ublas::inner_prod (inline) 15ms 0.065% 78.72% 302ms 1.31% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 78.72% 302ms 1.31% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 17ms 0.074% 78.80% 293ms 1.27% boost::numeric::ublas::vector_binary::size (inline) 0 0% 78.80% 287ms 1.25% NodesOnlyMesh::ReMesh 4ms 0.017% 78.82% 275ms 1.20% NodesOnlyMesh::UpdateNodeIndices 2ms 0.0087% 78.82% 266ms 1.16% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 0 0% 78.82% 264ms 1.15% NodesOnlyMesh::UpdateBoxCollection 264ms 1.15% 79.97% 264ms 1.15% __gnu_cxx::__normal_iterator::operator++ (inline) 0 0% 79.97% 260ms 1.13% std::_Rb_tree::_M_drop_node (inline) 259ms 1.13% 81.10% 259ms 1.13% Node::CheckForNodeAttributes 5ms 0.022% 81.12% 254ms 1.10% DistributedBoxCollection::GetProcessOwningNode 94ms 0.41% 81.53% 247ms 1.07% boost::numeric::ublas::vector_inner_prod::apply (inline) 1ms 0.0043% 81.53% 232ms 1.01% NodesOnlyMesh::AddNodesToBoxes 125ms 0.54% 82.08% 226ms 0.98% _int_malloc 0 0% 82.08% 226ms 0.98% std::set::~set (inline) 1ms 0.0043% 82.08% 225ms 0.98% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 82.08% 223ms 0.97% VtkMeshWriter::WriteFiles 2ms 0.0087% 82.09% 223ms 0.97% std::__new_allocator::deallocate (inline) 5ms 0.022% 82.11% 222ms 0.97% std::_Rb_tree::_M_emplace_hint_unique 97ms 0.42% 82.53% 221ms 0.96% std::__move_median_to_first (inline) 109ms 0.47% 83.01% 219ms 0.95% boost::shared_ptr::shared_ptr (inline) 25ms 0.11% 83.12% 211ms 0.92% std::__insertion_sort (inline) 0 0% 83.12% 209ms 0.91% NodesOnlyMesh::ResizeBoxCollection 0 0% 83.12% 209ms 0.91% std::allocator_traits::deallocate (inline) 16ms 0.07% 83.19% 208ms 0.9% NodesOnlyMesh::IsANodeCloseToDomainBoundary 0 0% 83.19% 203ms 0.88% std::_Rb_tree::_M_put_node (inline) 84ms 0.37% 83.55% 202ms 0.88% __GI___libc_free 0 0% 83.55% 198ms 0.86% vtkStreamingDemandDrivenPipeline::Update 0 0% 83.55% 198ms 0.86% vtkXMLWriterBase::Write 0 0% 83.55% 197ms 0.86% vtkDemandDrivenPipeline::ProcessRequest 0 0% 83.55% 194ms 0.84% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 83.55% 192ms 0.83% vtkExecutive::CallAlgorithm 0 0% 83.55% 191ms 0.83% vtkDemandDrivenPipeline::ExecuteData 0 0% 83.55% 190ms 0.83% vtkCompositeDataPipeline::ExecuteData 0 0% 83.55% 190ms 0.83% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 83.55% 188ms 0.82% Cell::HasCellProperty (inline) 1ms 0.0043% 83.56% 187ms 0.81% CellPropertyCollection::HasProperty 0 0% 83.56% 173ms 0.75% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 83.56% 173ms 0.75% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 83.56% 172ms 0.75% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 3ms 0.013% 83.57% 163ms 0.71% AbstractCellProperty::IsType (inline) 162ms 0.7% 84.27% 162ms 0.7% [libchaste_cell_based.so] 162ms 0.7% 84.98% 162ms 0.7% [libchaste_mesh.so] 5ms 0.022% 85.00% 161ms 0.7% Cell::ReadyToDivide 154ms 0.67% 85.67% 154ms 0.67% Node::IsDeleted 0 0% 85.67% 152ms 0.66% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 85.67% 147ms 0.64% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 145ms 0.63% 86.30% 145ms 0.63% __ieee754_log_fma 0 0% 86.30% 144ms 0.63% vtkXMLWriter::WriteBinaryData 0 0% 86.30% 143ms 0.62% std::_Rb_tree::clear (inline) 0 0% 86.30% 142ms 0.62% vtkXMLWriter::WriteBinaryDataInternal 0 0% 86.30% 141ms 0.61% vtkXMLWriter::WriteBinaryDataBlock 0 0% 86.30% 141ms 0.61% vtkXMLWriter::WriteCompressionBlock 134ms 0.58% 86.88% 137ms 0.6% std::__adjacent_find (inline) 0 0% 86.88% 137ms 0.6% std::__unique (inline) 0 0% 86.88% 137ms 0.6% std::unique (inline) 15ms 0.065% 86.95% 136ms 0.59% boost::numeric::ublas::vector_reference::operator() (inline) 10ms 0.043% 86.99% 134ms 0.58% DistributedBoxCollection::GetIsPeriodicAllDims 134ms 0.58% 87.57% 134ms 0.58% Node::GetIndex 10ms 0.043% 87.62% 132ms 0.57% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 87.62% 128ms 0.56% vtkXMLWriter::WritePointsAppendedData 0 0% 87.62% 125ms 0.54% Cell::GetCellId 0 0% 87.62% 125ms 0.54% boost::numeric::ublas::vector_binary::operator() (inline) 2ms 0.0087% 87.63% 122ms 0.53% AbstractCellPopulation::SetCellUsingLocationIndex 0 0% 87.63% 122ms 0.53% std::_Rb_tree::_Auto_node::_Auto_node (inline) 34ms 0.15% 87.77% 121ms 0.53% AbstractCellProperty::IsSame 0 0% 87.77% 121ms 0.53% compress2 0 0% 87.77% 121ms 0.53% vtkDataCompressor::Compress 0 0% 87.77% 121ms 0.53% vtkZLibDataCompressor::CompressBuffer 106ms 0.46% 88.23% 118ms 0.51% _int_free 63ms 0.27% 88.51% 118ms 0.51% crc32 0 0% 88.51% 118ms 0.51% deflate 81ms 0.35% 88.86% 117ms 0.51% Node::AddNeighbour