File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 14314ms, 86.33% of 16581ms total Dropped 760 nodes (cum <= 82.91ms) flat flat% sum% cum cum% 0 0% 0% 16545ms 99.78% __libc_start_call_main 0 0% 0% 16545ms 99.78% __libc_start_main_impl 0 0% 0% 16545ms 99.78% _start 0 0% 0% 16527ms 99.67% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 16527ms 99.67% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 16527ms 99.67% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 16527ms 99.67% main 0 0% 0% 16492ms 99.46% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 16492ms 99.46% CxxTest::TestRunner::runTest (inline) 0 0% 0% 16492ms 99.46% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 1ms 0.006% 0.006% 16472ms 99.34% AbstractCellBasedSimulation::Solve 0 0% 0.006% 12634ms 76.20% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.006% 0.012% 7842ms 47.30% AbstractCellBasedSimulation::DoCellBirth 4ms 0.024% 0.036% 7741ms 46.69% Cell::ReadyToDivide 5ms 0.03% 0.066% 7696ms 46.41% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.066% 7557ms 45.58% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 6ms 0.036% 0.1% 7547ms 45.52% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.006% 0.11% 7539ms 45.47% CellCycleModelOdeHandler::SolveOdeToTime 41ms 0.25% 0.36% 7392ms 44.58% AbstractOneStepIvpOdeSolver::InternalSolve 657ms 3.96% 4.32% 6650ms 40.11% RungeKutta4IvpOdeSolver::CalculateNextYValue 3006ms 18.13% 22.45% 5741ms 34.62% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 22.45% 4682ms 28.24% MeshBasedCellPopulation::Update 4ms 0.024% 22.47% 3564ms 21.49% Cylindrical2dMesh::ReMesh 335ms 2.02% 24.49% 2843ms 17.15% AbstractCellProperty::IsType (inline) 0 0% 24.49% 2230ms 13.45% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 24.49% 1993ms 12.02% MutableMesh::ReMesh 1ms 0.006% 24.50% 1961ms 11.83% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.006% 24.50% 1924ms 11.60% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 24.50% 1603ms 9.67% AbstractCellPopulation::WriteResultsToFiles 744ms 4.49% 28.99% 1601ms 9.66% std::_Rb_tree::_M_lower_bound (inline) 137ms 0.83% 29.82% 1549ms 9.34% TetrahedralMesh::EdgeIterator::operator++ 38ms 0.23% 30.05% 1277ms 7.70% std::_Rb_tree::find (inline) 161ms 0.97% 31.02% 1192ms 7.19% AbstractCellProperty::IsSame 0 0% 31.02% 1078ms 6.50% MeshBasedCellPopulation::UpdateNodePairs 52ms 0.31% 31.33% 1076ms 6.49% operator new 9ms 0.054% 31.39% 1055ms 6.36% TetrahedralMesh::ImportFromMesher 1037ms 6.25% 37.64% 1037ms 6.25% __strcmp_evex 38ms 0.23% 37.87% 1031ms 6.22% std::type_info::operator== (inline) 10ms 0.06% 37.93% 1020ms 6.15% std::set::insert (inline) 352ms 2.12% 40.05% 1015ms 6.12% __GI___libc_malloc 6ms 0.036% 40.09% 1010ms 6.09% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 11ms 0.066% 40.15% 1010ms 6.09% std::_Rb_tree::_M_insert_unique 17ms 0.1% 40.26% 940ms 5.67% MeshBasedCellPopulation::SpringIterator::operator++ 22ms 0.13% 40.39% 925ms 5.58% std::__new_allocator::allocate (inline) 0 0% 40.39% 919ms 5.54% std::allocator_traits::allocate (inline) 869ms 5.24% 45.63% 869ms 5.24% [libchaste_cell_based.so] 0 0% 45.63% 790ms 4.76% std::set::count (inline) 1ms 0.006% 45.64% 749ms 4.52% triangulate 0 0% 45.64% 669ms 4.03% delaunay 5ms 0.03% 45.67% 666ms 4.02% divconqdelaunay 44ms 0.27% 45.93% 651ms 3.93% std::_Rb_tree::_M_insert_ (inline) 1ms 0.006% 45.94% 645ms 3.89% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 45.94% 634ms 3.82% std::_Rb_tree::_M_create_node (inline) 0 0% 45.94% 621ms 3.75% std::_Rb_tree::_M_get_node (inline) 9ms 0.054% 45.99% 620ms 3.74% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 30ms 0.18% 46.17% 578ms 3.49% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 0 0% 46.17% 576ms 3.47% std::_Rb_tree::_Alloc_node::operator() (inline) 358ms 2.16% 48.33% 571ms 3.44% _int_malloc 6ms 0.036% 48.37% 567ms 3.42% CellPopulationElementWriter::Visit 566ms 3.41% 51.78% 566ms 3.41% WntCellCycleOdeSystem::CalculateStoppingEvent 5ms 0.03% 51.81% 559ms 3.37% Element::Element 61ms 0.37% 52.18% 547ms 3.30% std::map::operator[] (partial-inline) 545ms 3.29% 55.47% 545ms 3.29% std::_Rb_tree::_S_right (inline) 132ms 0.8% 56.26% 544ms 3.28% __dynamic_cast 8ms 0.048% 56.31% 536ms 3.23% Element::RegisterWithNodes (inline) 20ms 0.12% 56.43% 529ms 3.19% Node::AddElement 24ms 0.14% 56.58% 501ms 3.02% Cylindrical2dMesh::ReconstructCylindricalMesh 12ms 0.072% 56.65% 496ms 2.99% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 56.65% 485ms 2.93% std::map::find (inline) 8ms 0.048% 56.70% 482ms 2.91% MeshBasedCellPopulation::AcceptCellWriter 6ms 0.036% 56.73% 479ms 2.89% CellPropertyCollection::GetPropertiesType (inline) 9ms 0.054% 56.79% 451ms 2.72% std::less::operator() (inline) 110ms 0.66% 57.45% 450ms 2.71% __GI___libc_free 442ms 2.67% 60.12% 442ms 2.67% std::operator< (inline) 220ms 1.33% 61.44% 430ms 2.59% AbstractCellMutationState::AbstractCellMutationState 11ms 0.066% 61.51% 421ms 2.54% Cylindrical2dMesh::CorrectNonPeriodicMesh 0 0% 61.51% 398ms 2.40% std::_Rb_tree::lower_bound (inline) 0 0% 61.51% 398ms 2.40% std::map::lower_bound (inline) 0 0% 61.51% 397ms 2.39% std::_Rb_tree::_M_drop_node (inline) 17ms 0.1% 61.61% 390ms 2.35% std::__new_allocator::deallocate (inline) 3ms 0.018% 61.63% 389ms 2.35% AbstractCellProperty::IsSubType (inline) 0 0% 61.63% 383ms 2.31% std::allocator_traits::deallocate (inline) 59ms 0.36% 61.99% 372ms 2.24% std::_Rb_tree::~_Rb_tree (inline) 2ms 0.012% 62.00% 369ms 2.23% MutableMesh::ReIndex 0 0% 62.00% 367ms 2.21% std::ostream::operator<< (inline) 50ms 0.3% 62.30% 366ms 2.21% std::ostream::_M_insert 0 0% 62.30% 353ms 2.13% std::set::~set (inline) 53ms 0.32% 62.62% 352ms 2.12% std::_Rb_tree::_M_erase 146ms 0.88% 63.50% 349ms 2.10% std::_Rb_tree::_M_get_insert_unique_pos 342ms 2.06% 65.56% 342ms 2.06% [libchaste_crypt.so] 279ms 1.68% 67.25% 336ms 2.03% _int_free 5ms 0.03% 67.28% 333ms 2.01% std::_Rb_tree::erase 0 0% 67.28% 332ms 2.00% std::set::erase (inline) 9ms 0.054% 67.33% 324ms 1.95% divconqrecurse 6ms 0.036% 67.37% 323ms 1.95% Node::RemoveElement 0 0% 67.37% 316ms 1.91% std::_Rb_tree::_M_put_node (inline) 92ms 0.55% 67.92% 308ms 1.86% mergehulls 0 0% 67.92% 298ms 1.80% std::_Vector_base::_M_allocate (inline) 134ms 0.81% 68.73% 294ms 1.77% __cxxabiv1::__si_class_type_info::__do_dyncast 8ms 0.048% 68.78% 285ms 1.72% boost::detail::shared_count::~shared_count (inline) 0 0% 68.78% 285ms 1.72% boost::shared_ptr::~shared_ptr (inline) 2ms 0.012% 68.79% 281ms 1.69% Cell::GetMutationState 268ms 1.62% 70.41% 271ms 1.63% boost::detail::sp_counted_base::release 6ms 0.036% 70.44% 268ms 1.62% Cell::GetCellProliferativeType 1ms 0.006% 70.45% 265ms 1.60% AbstractCellPopulation::Iterator::operator++ (inline) 17ms 0.1% 70.55% 262ms 1.58% AbstractCellPopulation::Iterator::IsRealCell 12ms 0.072% 70.62% 262ms 1.58% std::_Rb_tree::_Rb_tree 16ms 0.096% 70.72% 261ms 1.57% Element::ResetIndex 3ms 0.018% 70.74% 260ms 1.57% LegacyCellProliferativeTypesWriter::VisitCell 12ms 0.072% 70.81% 256ms 1.54% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 0 0% 70.81% 253ms 1.53% std::set::set (inline) 6ms 0.036% 70.85% 249ms 1.50% std::vector::push_back (inline) 2ms 0.012% 70.86% 248ms 1.50% NodeLocationWriter::Visit 235ms 1.42% 72.28% 245ms 1.48% std::vector::operator[] (inline) 14ms 0.084% 72.36% 242ms 1.46% AbstractCellPopulation::GetLocationIndexUsingCell 13ms 0.078% 72.44% 230ms 1.39% std::_Rb_tree::_M_copy (inline) 1ms 0.006% 72.44% 229ms 1.38% ApcOneHitCellMutationState::ApcOneHitCellMutationState 10ms 0.06% 72.50% 228ms 1.38% std::vector::_M_realloc_insert 7ms 0.042% 72.55% 225ms 1.36% std::_Rb_tree::_M_erase_aux (inline) 1ms 0.006% 72.55% 223ms 1.34% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 0 0% 72.55% 223ms 1.34% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 4ms 0.024% 72.58% 220ms 1.33% AbstractCellPopulation::IsCellAttachedToLocationIndex 19ms 0.11% 72.69% 218ms 1.31% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 10ms 0.06% 72.75% 214ms 1.29% std::num_put::_M_insert_float 213ms 1.28% 74.04% 213ms 1.28% [libchaste_mesh.so] 5ms 0.03% 74.07% 212ms 1.28% alternateaxes 101ms 0.61% 74.68% 210ms 1.27% std::_Rb_tree::_M_clone_node (inline) 187ms 1.13% 75.80% 207ms 1.25% vertexmedian 4ms 0.024% 75.83% 201ms 1.21% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 11ms 0.066% 75.89% 197ms 1.19% AbstractTetrahedralElement::CalculateJacobian 8ms 0.048% 75.94% 196ms 1.18% Element::MarkAsDeleted 5ms 0.03% 75.97% 186ms 1.12% std::__cxx11::collate::do_transform 0 0% 75.97% 184ms 1.11% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 75.97% 184ms 1.11% MeshBasedCellPopulation::GetDampingConstant 2ms 0.012% 75.98% 176ms 1.06% ___vsnprintf 1ms 0.006% 75.99% 174ms 1.05% OffLatticeSimulation::ApplyBoundaries 2ms 0.012% 76.00% 174ms 1.05% __vsnprintf_internal (inline) 0 0% 76.00% 173ms 1.04% TetrahedralMesh::RefreshJacobianCachedData 12ms 0.072% 76.08% 169ms 1.02% __printf_buffer 2ms 0.012% 76.09% 160ms 0.96% AbstractTetrahedralElement::CalculateInverseJacobian 150ms 0.9% 76.99% 150ms 0.9% std::_Rb_tree_insert_and_rebalance 59ms 0.36% 77.35% 145ms 0.87% AbstractElement::GetNodeGlobalIndex 24ms 0.14% 77.49% 145ms 0.87% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 3ms 0.018% 77.51% 141ms 0.85% __printf_fp_l_buffer 0 0% 77.51% 141ms 0.85% __printf_fp_spec (inline) 57ms 0.34% 77.85% 136ms 0.82% __printf_fp_buffer_1 135ms 0.81% 78.67% 135ms 0.81% incircle 0 0% 78.67% 133ms 0.8% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 104ms 0.63% 79.30% 133ms 0.8% malloc_consolidate 133ms 0.8% 80.10% 133ms 0.8% std::vector::size (inline) 1ms 0.006% 80.10% 131ms 0.79% TetrahedralMesh::Clear 20ms 0.12% 80.22% 131ms 0.79% TetrahedralMesh::EdgesEnd (partial-inline) 3ms 0.018% 80.24% 131ms 0.79% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 8ms 0.048% 80.29% 129ms 0.78% AbstractTetrahedralElement::RefreshJacobian 2ms 0.012% 80.30% 129ms 0.78% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 2ms 0.012% 80.31% 126ms 0.76% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 80.31% 125ms 0.75% CellProliferativeTypesWriter::VisitCell 1ms 0.006% 80.32% 125ms 0.75% boost::numeric::ublas::vector_assign (inline) 2ms 0.012% 80.33% 123ms 0.74% AbstractTetrahedralElement::AbstractTetrahedralElement 116ms 0.7% 81.03% 116ms 0.7% std::_Rb_tree::_S_left (inline) 109ms 0.66% 81.69% 114ms 0.69% vertexsort 0 0% 81.69% 112ms 0.68% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 4ms 0.024% 81.71% 110ms 0.66% CellPropertyCollection::HasProperty 0 0% 81.71% 108ms 0.65% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 81.71% 108ms 0.65% Cell::HasCellProperty (inline) 108ms 0.65% 82.37% 108ms 0.65% std::type_info::name (inline) 43ms 0.26% 82.62% 107ms 0.65% AbstractElement::GetNodeLocation 64ms 0.39% 83.01% 106ms 0.64% std::_Rb_tree::equal_range (inline) 3ms 0.018% 83.03% 102ms 0.62% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 5ms 0.03% 83.06% 101ms 0.61% Cell::SetCellProliferativeType 17ms 0.1% 83.16% 101ms 0.61% MeshBasedCellPopulation::SpringIterator::SpringIterator 100ms 0.6% 83.76% 100ms 0.6% AbstractCellProperty::AbstractCellProperty 5ms 0.03% 83.79% 98ms 0.59% boost::numeric::ublas::c_vector::c_vector (inline) 2ms 0.012% 83.81% 95ms 0.57% std::_Rb_tree_const_iterator::operator++ (inline) 79ms 0.48% 84.28% 94ms 0.57% TetrahedralMesh::EdgeIterator::EdgeIterator 4ms 0.024% 84.31% 92ms 0.55% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 4ms 0.024% 84.33% 89ms 0.54% Cylindrical2dMesh::CreateMirrorNodes 89ms 0.54% 84.87% 89ms 0.54% std::_Rb_tree_increment 4ms 0.024% 84.89% 88ms 0.53% std::_Rb_tree::_M_emplace_hint_unique 87ms 0.52% 85.42% 87ms 0.52% Node::GetIndex 47ms 0.28% 85.70% 85ms 0.51% Cylindrical2dMesh::GetVectorFromAtoB 16ms 0.096% 85.80% 84ms 0.51% std::num_put::_M_insert_int 84ms 0.51% 86.30% 84ms 0.51% unlink_chunk 4ms 0.024% 86.33% 83ms 0.5% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes