File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16860ms, 84.53% of 19946ms total Dropped 783 nodes (cum <= 99.73ms) flat flat% sum% cum cum% 0 0% 0% 19900ms 99.77% __libc_start_call_main 0 0% 0% 19900ms 99.77% __libc_start_main_impl 0 0% 0% 19900ms 99.77% _start 0 0% 0% 19881ms 99.67% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19881ms 99.67% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19881ms 99.67% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19881ms 99.67% main 0 0% 0% 19843ms 99.48% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19843ms 99.48% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19843ms 99.48% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19816ms 99.35% AbstractCellBasedSimulation::Solve 0 0% 0% 15360ms 77.01% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 10110ms 50.69% AbstractCellBasedSimulation::DoCellBirth 3ms 0.015% 0.015% 10034ms 50.31% Cell::ReadyToDivide 5ms 0.025% 0.04% 9974ms 50.01% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.04% 9818ms 49.22% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 16ms 0.08% 0.12% 9816ms 49.21% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.015% 0.14% 9799ms 49.13% CellCycleModelOdeHandler::SolveOdeToTime 67ms 0.34% 0.47% 9634ms 48.30% AbstractOneStepIvpOdeSolver::InternalSolve 893ms 4.48% 4.95% 8833ms 44.28% RungeKutta4IvpOdeSolver::CalculateNextYValue 3631ms 18.20% 23.15% 7714ms 38.67% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 23.15% 5147ms 25.80% MeshBasedCellPopulation::Update 166ms 0.83% 23.98% 4096ms 20.54% AbstractCellProperty::IsType (inline) 2ms 0.01% 23.99% 3978ms 19.94% Cylindrical2dMesh::ReMesh 588ms 2.95% 26.94% 2882ms 14.45% AbstractCellProperty::IsSame 1ms 0.005% 26.95% 2467ms 12.37% OffLatticeSimulation::UpdateCellLocationsAndTopology 417ms 2.09% 29.04% 2294ms 11.50% std::type_info::operator== (inline) 1ms 0.005% 29.04% 2160ms 10.83% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.005% 29.05% 2157ms 10.81% MutableMesh::ReMesh 8ms 0.04% 29.09% 2113ms 10.59% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 29.09% 1983ms 9.94% AbstractCellPopulation::WriteResultsToFiles 1850ms 9.28% 38.36% 1850ms 9.28% __strcmp_avx2 806ms 4.04% 42.40% 1848ms 9.27% std::_Rb_tree::_M_lower_bound (inline) 169ms 0.85% 43.25% 1722ms 8.63% TetrahedralMesh::EdgeIterator::operator++ 60ms 0.3% 43.55% 1375ms 6.89% std::_Rb_tree::find (inline) 4ms 0.02% 43.57% 1134ms 5.69% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1ms 0.005% 43.58% 1126ms 5.65% MeshBasedCellPopulation::UpdateNodePairs 18ms 0.09% 43.67% 1090ms 5.46% TetrahedralMesh::ImportFromMesher 50ms 0.25% 43.92% 1056ms 5.29% operator new 14ms 0.07% 43.99% 1024ms 5.13% MeshBasedCellPopulation::SpringIterator::operator++ 14ms 0.07% 44.06% 1005ms 5.04% std::set::insert (inline) 200ms 1.00% 45.06% 996ms 4.99% __GI___libc_malloc 21ms 0.11% 45.17% 990ms 4.96% std::_Rb_tree::_M_insert_unique 36ms 0.18% 45.35% 922ms 4.62% std::__new_allocator::allocate (inline) 0 0% 45.35% 917ms 4.60% std::allocator_traits::allocate (inline) 0 0% 45.35% 845ms 4.24% std::set::count (inline) 0 0% 45.35% 824ms 4.13% triangulate 1ms 0.005% 45.35% 750ms 3.76% delaunay 4ms 0.02% 45.37% 748ms 3.75% divconqdelaunay 5ms 0.025% 45.40% 738ms 3.70% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 55ms 0.28% 45.67% 707ms 3.54% std::map::operator[] (partial-inline) 3ms 0.015% 45.69% 705ms 3.53% AbstractTwoBodyInteractionForce::AddForceContribution 397ms 1.99% 47.68% 700ms 3.51% _int_malloc 6ms 0.03% 47.71% 683ms 3.42% CellPopulationElementWriter::Visit 666ms 3.34% 51.05% 666ms 3.34% std::_Rb_tree::_S_right (inline) 21ms 0.11% 51.15% 661ms 3.31% std::less::operator() (inline) 640ms 3.21% 54.36% 640ms 3.21% std::operator< (inline) 178ms 0.89% 55.25% 638ms 3.20% __dynamic_cast 601ms 3.01% 58.27% 612ms 3.07% WntCellCycleOdeSystem::CalculateStoppingEvent 19ms 0.095% 58.36% 593ms 2.97% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 35ms 0.18% 58.54% 591ms 2.96% std::_Rb_tree::_M_insert_ (inline) 0 0% 58.54% 584ms 2.93% std::_Rb_tree::_M_create_node (inline) 2ms 0.01% 58.55% 583ms 2.92% MeshBasedCellPopulation::AcceptCellWriter 3ms 0.015% 58.56% 577ms 2.89% CellPropertyCollection::GetPropertiesType (inline) 22ms 0.11% 58.67% 567ms 2.84% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 58.67% 564ms 2.83% std::_Rb_tree::lower_bound (inline) 0 0% 58.67% 564ms 2.83% std::map::lower_bound (inline) 0 0% 58.67% 553ms 2.77% std::_Rb_tree::_M_get_node (inline) 9ms 0.045% 58.72% 547ms 2.74% Element::Element 17ms 0.085% 58.80% 531ms 2.66% MutableMesh::ReIndex 0 0% 58.80% 526ms 2.64% std::map::find (inline) 0 0% 58.80% 525ms 2.63% std::_Rb_tree::_Alloc_node::operator() (inline) 11ms 0.055% 58.86% 501ms 2.51% Cylindrical2dMesh::CorrectNonPeriodicMesh 11ms 0.055% 58.91% 500ms 2.51% Cylindrical2dMesh::ReconstructCylindricalMesh 7ms 0.035% 58.95% 478ms 2.40% Element::RegisterWithNodes (inline) 9ms 0.045% 58.99% 474ms 2.38% Node::AddElement 3ms 0.015% 59.01% 473ms 2.37% AbstractCellProperty::IsSubType (inline) 2ms 0.01% 59.02% 468ms 2.35% std::ostream::operator<< (inline) 61ms 0.31% 59.33% 466ms 2.34% std::ostream::_M_insert 325ms 1.63% 60.95% 461ms 2.31% AbstractCellMutationState::AbstractCellMutationState 135ms 0.68% 61.63% 390ms 1.96% __GI___libc_free 146ms 0.73% 62.36% 378ms 1.90% std::_Rb_tree::_M_get_insert_unique_pos 20ms 0.1% 62.46% 366ms 1.83% Node::RemoveElement 2ms 0.01% 62.47% 366ms 1.83% std::_Vector_base::_M_allocate (inline) 22ms 0.11% 62.58% 365ms 1.83% divconqrecurse 2ms 0.01% 62.59% 359ms 1.80% std::set::erase (inline) 12ms 0.06% 62.65% 358ms 1.79% std::_Rb_tree::erase 169ms 0.85% 63.50% 346ms 1.73% __cxxabiv1::__si_class_type_info::__do_dyncast 31ms 0.16% 63.66% 344ms 1.72% Element::ResetIndex 107ms 0.54% 64.19% 336ms 1.68% mergehulls 8ms 0.04% 64.23% 333ms 1.67% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 21ms 0.11% 64.34% 332ms 1.66% std::__new_allocator::deallocate (inline) 0 0% 64.34% 324ms 1.62% std::allocator_traits::deallocate (inline) 6ms 0.03% 64.37% 316ms 1.58% Cell::GetCellProliferativeType 89ms 0.45% 64.82% 315ms 1.58% std::_Rb_tree::_M_erase 1ms 0.005% 64.82% 314ms 1.57% LegacyCellProliferativeTypesWriter::VisitCell 5ms 0.025% 64.85% 296ms 1.48% Cell::GetMutationState 3ms 0.015% 64.86% 290ms 1.45% NodeLocationWriter::Visit 9ms 0.045% 64.91% 289ms 1.45% AbstractCellPopulation::GetLocationIndexUsingCell 28ms 0.14% 65.05% 288ms 1.44% std::_Rb_tree::~_Rb_tree (inline) 287ms 1.44% 66.48% 287ms 1.44% std::type_info::name (inline) 13ms 0.065% 66.55% 284ms 1.42% std::vector::push_back (inline) 0 0% 66.55% 281ms 1.41% std::_Rb_tree::_M_drop_node (inline) 274ms 1.37% 67.92% 274ms 1.37% std::vector::operator[] (inline) 19ms 0.095% 68.02% 266ms 1.33% std::num_put::_M_insert_float 15ms 0.075% 68.09% 264ms 1.32% std::vector::_M_realloc_insert 1ms 0.005% 68.10% 261ms 1.31% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 68.10% 260ms 1.30% std::set::~set (inline) 26ms 0.13% 68.23% 259ms 1.30% AbstractCellPopulation::Iterator::IsRealCell (inline) 196ms 0.98% 69.21% 255ms 1.28% _int_free 20ms 0.1% 69.31% 252ms 1.26% AbstractTetrahedralElement::CalculateJacobian 6ms 0.03% 69.34% 250ms 1.25% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 69.34% 248ms 1.24% std::_Rb_tree::_M_put_node (inline) 2ms 0.01% 69.35% 244ms 1.22% AbstractCellPopulation::IsCellAttachedToLocationIndex 240ms 1.20% 70.56% 240ms 1.20% [libchaste_cell_based.so] 2ms 0.01% 70.57% 236ms 1.18% alternateaxes 221ms 1.11% 71.67% 234ms 1.17% vertexmedian 3ms 0.015% 71.69% 233ms 1.17% std::set::set (inline) 63ms 0.32% 72.00% 230ms 1.15% ApcOneHitCellMutationState::ApcOneHitCellMutationState 25ms 0.13% 72.13% 226ms 1.13% std::_Rb_tree::_M_copy (inline) 80ms 0.4% 72.53% 224ms 1.12% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 8ms 0.04% 72.57% 215ms 1.08% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 7ms 0.035% 72.61% 212ms 1.06% std::_Rb_tree::_M_erase_aux (inline) 1ms 0.005% 72.61% 211ms 1.06% TetrahedralMesh::RefreshJacobianCachedData 161ms 0.81% 73.42% 206ms 1.03% AbstractElement::GetNodeGlobalIndex 5ms 0.025% 73.44% 205ms 1.03% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2ms 0.01% 73.45% 205ms 1.03% std::__cxx11::collate::do_transform 52ms 0.26% 73.71% 202ms 1.01% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 1ms 0.005% 73.72% 198ms 0.99% ___vsnprintf 70ms 0.35% 74.07% 198ms 0.99% std::_Rb_tree::_M_clone_node (inline) 0 0% 74.07% 197ms 0.99% __vsnprintf_internal (inline) 0 0% 74.07% 191ms 0.96% OffLatticeSimulation::ApplyBoundaries 17ms 0.085% 74.16% 189ms 0.95% __printf_buffer 144ms 0.72% 74.88% 189ms 0.95% malloc_consolidate 8ms 0.04% 74.92% 188ms 0.94% Element::MarkAsDeleted 16ms 0.08% 75.00% 183ms 0.92% AbstractTetrahedralElement::RefreshJacobian 9ms 0.045% 75.04% 182ms 0.91% AbstractTetrahedralElement::CalculateInverseJacobian 179ms 0.9% 75.94% 179ms 0.9% std::_Rb_tree_insert_and_rebalance 5ms 0.025% 75.97% 174ms 0.87% AbstractTetrahedralElement::AbstractTetrahedralElement 5ms 0.025% 75.99% 172ms 0.86% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 75.99% 172ms 0.86% MeshBasedCellPopulation::GetDampingConstant 166ms 0.83% 76.82% 166ms 0.83% Node::GetIndex 3ms 0.015% 76.84% 165ms 0.83% __printf_fp_l_buffer 0 0% 76.84% 165ms 0.83% __printf_fp_spec (inline) 20ms 0.1% 76.94% 164ms 0.82% TetrahedralMesh::Clear 75ms 0.38% 77.31% 154ms 0.77% __printf_fp_buffer_1 3ms 0.015% 77.33% 150ms 0.75% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 68ms 0.34% 77.67% 148ms 0.74% AbstractElement::GetNodeLocation 148ms 0.74% 78.41% 148ms 0.74% unlink_chunk 5ms 0.025% 78.44% 147ms 0.74% CellProliferativeTypesWriter::VisitCell 3ms 0.015% 78.45% 146ms 0.73% boost::numeric::ublas::vector_assign (inline) 4ms 0.02% 78.47% 144ms 0.72% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 88ms 0.44% 78.91% 139ms 0.7% Cylindrical2dMesh::GetVectorFromAtoB 96ms 0.48% 79.39% 137ms 0.69% std::_Rb_tree::equal_range (inline) 4ms 0.02% 79.41% 136ms 0.68% CellPropertyCollection::HasProperty 6ms 0.03% 79.44% 134ms 0.67% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 0 0% 79.44% 133ms 0.67% Cell::HasCellProperty (inline) 34ms 0.17% 79.61% 132ms 0.66% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 132ms 0.66% 80.28% 132ms 0.66% incircle 125ms 0.63% 80.90% 132ms 0.66% vertexsort 130ms 0.65% 81.56% 130ms 0.65% std::vector::size (inline) 13ms 0.065% 81.62% 128ms 0.64% boost::numeric::ublas::c_vector::c_vector (inline) 127ms 0.64% 82.26% 127ms 0.64% AbstractElement::IsDeleted 4ms 0.02% 82.28% 127ms 0.64% Cell::SetCellProliferativeType 46ms 0.23% 82.51% 125ms 0.63% std::__ostream_insert 41ms 0.21% 82.71% 115ms 0.58% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 1ms 0.005% 82.72% 113ms 0.57% AbstractCellBasedWriter::OpenOutputFileForAppend 13ms 0.065% 82.78% 113ms 0.57% boost::detail::shared_count::~shared_count (inline) 0 0% 82.78% 113ms 0.57% boost::shared_ptr::~shared_ptr (inline) 26ms 0.13% 82.91% 112ms 0.56% boost::numeric::ublas::indexing_vector_assign 0 0% 82.91% 110ms 0.55% OutputFileHandler::OpenOutputFile 5ms 0.025% 82.94% 108ms 0.54% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 3ms 0.015% 82.95% 107ms 0.54% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 104ms 0.52% 83.48% 104ms 0.52% AbstractCellMutationState::~AbstractCellMutationState 0 0% 83.48% 103ms 0.52% AbstractCellBasedSimulation::DoCellRemoval (inline) 3ms 0.015% 83.49% 103ms 0.52% MeshBasedCellPopulation::SpringsEnd (inline) 102ms 0.51% 84.00% 102ms 0.51% boost::shared_ptr::operator-> (inline) 102ms 0.51% 84.51% 102ms 0.51% std::_Rb_tree_rebalance_for_erase 0 0% 84.51% 101ms 0.51% std::operator<< (inline) 3ms 0.015% 84.53% 100ms 0.5% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath