File: TestRepresentative3dNodeBasedSimulation Type: cpu Showing nodes accounting for 30222ms, 89.17% of 33892ms total Dropped 800 nodes (cum <= 169.46ms) flat flat% sum% cum cum% 0 0% 0% 33726ms 99.51% __libc_start_call_main 0 0% 0% 33726ms 99.51% __libc_start_main_impl 0 0% 0% 33726ms 99.51% _start 0 0% 0% 33709ms 99.46% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 33709ms 99.46% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 33709ms 99.46% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 33709ms 99.46% main 0 0% 0% 33671ms 99.35% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 33671ms 99.35% CxxTest::TestRunner::runTest (inline) 0 0% 0% 33671ms 99.35% Test3dTissueRepresentativeSimulation::Test3dNodeBasedInBoxWithSloughing 0 0% 0% 33662ms 99.32% AbstractCellBasedSimulation::Solve 1ms 0.003% 0.003% 23798ms 70.22% OffLatticeSimulation::UpdateCellLocationsAndTopology 3ms 0.0089% 0.012% 18991ms 56.03% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.018% 0.03% 18819ms 55.53% AbstractNumericalMethod::ComputeForcesIncludingDamping 187ms 0.55% 0.58% 18160ms 53.58% AbstractTwoBodyInteractionForce::AddForceContribution 1506ms 4.44% 5.02% 15356ms 45.31% SimpleLogarithmicRepulsionForce::CalculateForceBetweenNodes (partial-inline) 4341ms 12.81% 17.83% 9536ms 28.14% std::_Rb_tree::_M_lower_bound (inline) 369ms 1.09% 18.92% 8754ms 25.83% std::_Rb_tree::find (inline) 0 0% 18.92% 8754ms 25.83% std::map::find (inline) 0 0% 18.92% 8673ms 25.59% AbstractCellBasedSimulation::UpdateCellPopulation 148ms 0.44% 19.36% 8539ms 25.19% NodesOnlyMesh::GetNodeOrHaloNode 483ms 1.43% 20.78% 8377ms 24.72% AbstractMesh::GetNode 311ms 0.92% 21.70% 7901ms 23.31% NodesOnlyMesh::SolveNodeMapping 0 0% 21.70% 7660ms 22.60% NodeBasedCellPopulation::Update 241ms 0.71% 22.41% 6380ms 18.82% boost::numeric::ublas::vector_assign (inline) 180ms 0.53% 22.94% 6224ms 18.36% boost::numeric::ublas::c_vector::c_vector (partial-inline) 3ms 0.0089% 22.95% 5639ms 16.64% DistributedBoxCollection::CalculateInteriorNodePairs 5166ms 15.24% 38.19% 5166ms 15.24% std::_Rb_tree::_S_right (inline) 0 0% 38.19% 4515ms 13.32% OffLatticeSimulation::ApplyBoundaries 15ms 0.044% 38.24% 4462ms 13.17% NodeAttributes::RemoveDuplicateNeighbours 10ms 0.03% 38.27% 4275ms 12.61% std::__sort (inline) 0 0% 38.27% 4275ms 12.61% std::sort (inline) 1172ms 3.46% 41.73% 3596ms 10.61% boost::numeric::ublas::indexing_vector_assign 2ms 0.0059% 41.73% 3498ms 10.32% AbstractCellPopulation::Iterator::operator++ (inline) 192ms 0.57% 42.30% 3469ms 10.24% AbstractCellPopulation::Iterator::IsRealCell 87ms 0.26% 42.56% 3410ms 10.06% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 26ms 0.077% 42.63% 2925ms 8.63% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 190ms 0.56% 43.19% 2453ms 7.24% std::__introsort_loop 19ms 0.056% 43.25% 2349ms 6.93% PlaneBoundaryCondition::ImposeBoundaryCondition 31ms 0.091% 43.34% 2241ms 6.61% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 43.34% 2198ms 6.49% std::__unguarded_partition_pivot (inline) 16ms 0.047% 43.39% 2166ms 6.39% PlaneBoundaryCondition::VerifyBoundaryCondition 1070ms 3.16% 46.54% 1995ms 5.89% std::__unguarded_partition (inline) 0 0% 46.54% 1810ms 5.34% std::__final_insertion_sort (inline) 160ms 0.47% 47.02% 1787ms 5.27% DistributedBoxCollection::AddPairsFromBox 217ms 0.64% 47.66% 1744ms 5.15% std::map::operator[] (partial-inline) 1730ms 5.10% 52.76% 1730ms 5.10% boost::numeric::ublas::same_impl_ex 128ms 0.38% 53.14% 1631ms 4.81% AbstractMesh::GetVectorFromAtoB 86ms 0.25% 53.39% 1626ms 4.80% std::__unguarded_insertion_sort (inline) 559ms 1.65% 55.04% 1585ms 4.68% std::__unguarded_linear_insert (inline) 1489ms 4.39% 59.44% 1489ms 4.39% __gnu_cxx::__normal_iterator::operator-- (inline) 0 0% 59.44% 1267ms 3.74% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 59.44% 1249ms 3.69% std::_Rb_tree::lower_bound (inline) 0 0% 59.44% 1249ms 3.69% std::map::lower_bound (inline) 0 0% 59.44% 1247ms 3.68% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 59.44% 1151ms 3.40% NodeBasedCellPopulation::UpdateCellProcessLocation 1090ms 3.22% 62.65% 1090ms 3.22% boost::numeric::ublas::c_vector::operator() 159ms 0.47% 63.12% 1072ms 3.16% boost::numeric::ublas::vector_binary::size (inline) 23ms 0.068% 63.19% 1059ms 3.12% boost::numeric::ublas::detail::expression_type_check (inline) 4ms 0.012% 63.20% 1056ms 3.12% DistributedBoxCollection::CalculateBoundaryNodePairs 184ms 0.54% 63.74% 1008ms 2.97% boost::numeric::ublas::detail::equals 211ms 0.62% 64.37% 917ms 2.71% NodeAttributes::AddAppliedForceContribution 395ms 1.17% 65.53% 838ms 2.47% __GI___libc_free 55ms 0.16% 65.69% 823ms 2.43% std::__new_allocator::allocate (inline) 12ms 0.035% 65.73% 783ms 2.31% AbstractCentreBasedCellPopulation::GetLocationOfCellCentre 0 0% 65.73% 782ms 2.31% boost::numeric::ublas::norm_inf (inline) 422ms 1.25% 66.97% 782ms 2.31% boost::numeric::ublas::vector_norm_inf::apply (inline) 354ms 1.04% 68.02% 779ms 2.30% DistributedBoxCollection::CalculateContainingBox (partial-inline) 86ms 0.25% 68.27% 771ms 2.27% operator new 200ms 0.59% 68.86% 756ms 2.23% NodeAttributes::AddNeighbour 0 0% 68.86% 725ms 2.14% AbstractCellPopulation::WriteResultsToFiles 504ms 1.49% 70.35% 724ms 2.14% __dynamic_cast 0 0% 70.35% 706ms 2.08% boost::numeric::ublas::c_vector::operator+= (inline) 0 0% 70.35% 706ms 2.08% boost::numeric::ublas::c_vector::plus_assign (inline) 224ms 0.66% 71.01% 681ms 2.01% __GI___libc_malloc 553ms 1.63% 72.64% 612ms 1.81% std::vector::push_back (inline) 4ms 0.012% 72.65% 597ms 1.76% AbstractCentreBasedCellPopulation::GetDampingConstant 1ms 0.003% 72.66% 593ms 1.75% AbstractCellBasedSimulation::DoCellBirth 34ms 0.1% 72.76% 492ms 1.45% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 72.76% 485ms 1.43% boost::numeric::ublas::norm_2 (inline) 382ms 1.13% 73.88% 485ms 1.43% boost::numeric::ublas::vector_norm_2::apply (inline) 3ms 0.0089% 73.89% 484ms 1.43% NodeBasedCellPopulation::WriteVtkResultsToFile 9ms 0.027% 73.92% 481ms 1.42% CellPropertyCollection::GetPropertiesType (inline) 18ms 0.053% 73.97% 470ms 1.39% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 73.97% 470ms 1.39% boost::numeric::ublas::vector::vector (inline) 450ms 1.33% 75.30% 450ms 1.33% std::_Rb_tree_increment 393ms 1.16% 76.46% 437ms 1.29% _int_free 0 0% 76.46% 419ms 1.24% AbstractCellBasedSimulation::DoCellRemoval (inline) 415ms 1.22% 77.68% 415ms 1.22% Node::GetIndex 3ms 0.0089% 77.69% 414ms 1.22% Cell::GetMutationState 5ms 0.015% 77.71% 402ms 1.19% PlaneBasedCellKiller::CheckAndLabelCellsForApoptosisOrDeath 36ms 0.11% 77.81% 401ms 1.18% boost::detail::shared_count::~shared_count (inline) 0 0% 77.81% 401ms 1.18% boost::shared_ptr::~shared_ptr (inline) 0 0% 77.81% 371ms 1.09% std::allocator_traits::allocate (inline) 357ms 1.05% 78.87% 359ms 1.06% boost::detail::sp_counted_base::release 3ms 0.0089% 78.88% 348ms 1.03% AbstractCellProperty::IsSubType (inline) 0 0% 78.88% 339ms 1.00% std::_Rb_tree::_M_create_node (inline) 0 0% 78.88% 331ms 0.98% boost::numeric::ublas::inner_prod (inline) 1ms 0.003% 78.88% 329ms 0.97% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 18ms 0.053% 78.93% 328ms 0.97% boost::numeric::ublas::vector_scalar_binary::evaluate 128ms 0.38% 79.31% 325ms 0.96% Node::GetRadius 0 0% 79.31% 313ms 0.92% NodesOnlyMesh::ReMesh 5ms 0.015% 79.33% 307ms 0.91% NodeBasedCellPopulation::UpdateMapsAfterRemesh 3ms 0.0089% 79.33% 305ms 0.9% NodesOnlyMesh::UpdateNodeIndices 0 0% 79.33% 299ms 0.88% std::_Rb_tree::_M_get_node (inline) 298ms 0.88% 80.21% 298ms 0.88% __gnu_cxx::__ops::_Iter_less_iter::operator() (inline) 1ms 0.003% 80.22% 284ms 0.84% NodeBasedCellPopulation::GetCellUsingLocationIndex (partial-inline) 4ms 0.012% 80.23% 281ms 0.83% AbstractCellPopulation::GetCellUsingLocationIndex 3ms 0.0089% 80.24% 276ms 0.81% NodesOnlyMesh::CalculateNodesOutsideLocalDomain 3ms 0.0089% 80.25% 276ms 0.81% std::_Rb_tree::_M_emplace_hint_unique 0 0% 80.25% 274ms 0.81% NodesOnlyMesh::UpdateBoxCollection 274ms 0.81% 81.05% 274ms 0.81% [libchaste_cell_based.so] 13ms 0.038% 81.09% 273ms 0.81% boost::numeric::ublas::vector_reference::operator() (inline) 270ms 0.8% 81.89% 270ms 0.8% __gnu_cxx::__normal_iterator::operator++ (inline) 124ms 0.37% 82.26% 266ms 0.78% boost::numeric::ublas::vector_inner_prod::apply (inline) 110ms 0.32% 82.58% 261ms 0.77% std::_Rb_tree::_M_erase (partial-inline) 10ms 0.03% 82.61% 255ms 0.75% DistributedBoxCollection::GetProcessOwningNode 0 0% 82.61% 253ms 0.75% boost::numeric::ublas::c_vector::assign (inline) 157ms 0.46% 83.07% 246ms 0.73% _int_malloc 2ms 0.0059% 83.08% 233ms 0.69% NodesOnlyMesh::AddNodesToBoxes 0 0% 83.08% 228ms 0.67% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 83.08% 228ms 0.67% VtkMeshWriter::WriteFiles 221ms 0.65% 83.73% 222ms 0.66% NodeBasedCellPopulation::GetNode 214ms 0.63% 84.36% 214ms 0.63% boost::numeric::ublas::scalar_plus_assign::apply (inline) 211ms 0.62% 84.98% 211ms 0.62% boost::numeric::ublas::c_vector::size (inline) 0 0% 84.98% 208ms 0.61% tcache_get (inline) 208ms 0.61% 85.60% 208ms 0.61% tcache_get_n (inline) 155ms 0.46% 86.06% 206ms 0.61% Node::AddAppliedForceContribution 205ms 0.6% 86.66% 205ms 0.6% Node::CheckForNodeAttributes 0 0% 86.66% 204ms 0.6% NodesOnlyMesh::ResizeBoxCollection 203ms 0.6% 87.26% 203ms 0.6% [libchaste_mesh.so] 17ms 0.05% 87.31% 202ms 0.6% NodesOnlyMesh::IsANodeCloseToDomainBoundary 201ms 0.59% 87.90% 201ms 0.59% Node::rGetLocation 0 0% 87.90% 199ms 0.59% boost::numeric::ublas::vector_reference::size (inline) 0 0% 87.90% 198ms 0.58% vtkStreamingDemandDrivenPipeline::Update 0 0% 87.90% 198ms 0.58% vtkXMLWriterBase::Write 88ms 0.26% 88.16% 197ms 0.58% std::__move_median_to_first (inline) 0 0% 88.16% 197ms 0.58% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 88.16% 196ms 0.58% vtkDemandDrivenPipeline::ProcessRequest 0 0% 88.16% 195ms 0.58% vtkDemandDrivenPipeline::ExecuteData 1ms 0.003% 88.17% 194ms 0.57% vtkExecutive::CallAlgorithm 81ms 0.24% 88.40% 193ms 0.57% std::__find_if (inline) 0 0% 88.40% 193ms 0.57% std::find_if (inline) 0 0% 88.40% 193ms 0.57% std::none_of (inline) 0 0% 88.40% 193ms 0.57% vtkCompositeDataPipeline::ExecuteData 0 0% 88.40% 193ms 0.57% vtkXMLUnstructuredDataWriter::ProcessRequest 185ms 0.55% 88.95% 185ms 0.55% __strcmp_avx2 0 0% 88.95% 184ms 0.54% boost::numeric::ublas::vector_binary::operator() (inline) 16ms 0.047% 89.00% 184ms 0.54% std::__insertion_sort (inline) 3ms 0.0089% 89.01% 182ms 0.54% CellPropertyCollection::HasProperty 0 0% 89.01% 181ms 0.53% Cell::HasCellProperty (inline) 35ms 0.1% 89.11% 180ms 0.53% std::__new_allocator::deallocate (inline) 0 0% 89.11% 173ms 0.51% std::_Rb_tree::_Alloc_node::operator() (inline) 13ms 0.038% 89.15% 173ms 0.51% std::_Rb_tree::_Rb_tree (partial-inline) 8ms 0.024% 89.17% 172ms 0.51% Cell::ReadyToDivide 0 0% 89.17% 171ms 0.5% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 89.17% 171ms 0.5% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData