File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 10487ms, 86.22% of 12163ms total Dropped 684 nodes (cum <= 60.81ms) flat flat% sum% cum cum% 0 0% 0% 12132ms 99.75% __libc_start_call_main 0 0% 0% 12132ms 99.75% __libc_start_main_impl 0 0% 0% 12132ms 99.75% _start 0 0% 0% 12119ms 99.64% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 12119ms 99.64% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 12119ms 99.64% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 12119ms 99.64% main 0 0% 0% 12083ms 99.34% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 12083ms 99.34% CxxTest::TestRunner::runTest (inline) 0 0% 0% 12083ms 99.34% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 12067ms 99.21% AbstractCellBasedSimulation::Solve 0 0% 0% 9316ms 76.59% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 5957ms 48.98% AbstractCellBasedSimulation::DoCellBirth 2ms 0.016% 0.016% 5901ms 48.52% Cell::ReadyToDivide 3ms 0.025% 0.041% 5879ms 48.34% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.041% 5790ms 47.60% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.0082% 0.049% 5785ms 47.56% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.0082% 0.058% 5781ms 47.53% CellCycleModelOdeHandler::SolveOdeToTime 51ms 0.42% 0.48% 5687ms 46.76% AbstractOneStepIvpOdeSolver::InternalSolve 621ms 5.11% 5.58% 5095ms 41.89% RungeKutta4IvpOdeSolver::CalculateNextYValue 2301ms 18.92% 24.50% 4306ms 35.40% WntCellCycleOdeSystem::EvaluateYDerivatives 2ms 0.016% 24.52% 3287ms 27.02% MeshBasedCellPopulation::Update 4ms 0.033% 24.55% 2485ms 20.43% Cylindrical2dMesh::ReMesh 64ms 0.53% 25.08% 1957ms 16.09% AbstractCellProperty::IsType (inline) 0 0% 25.08% 1590ms 13.07% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 25.08% 1363ms 11.21% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 25.08% 1355ms 11.14% MutableMesh::ReMesh 3ms 0.025% 25.10% 1336ms 10.98% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 25.10% 1157ms 9.51% AbstractCellPopulation::WriteResultsToFiles 602ms 4.95% 30.05% 1140ms 9.37% std::_Rb_tree::_M_lower_bound (inline) 122ms 1.00% 31.05% 1133ms 9.32% TetrahedralMesh::EdgeIterator::operator++ 216ms 1.78% 32.83% 1099ms 9.04% AbstractCellProperty::IsSame 148ms 1.22% 34.05% 883ms 7.26% std::type_info::operator== (inline) 43ms 0.35% 34.40% 876ms 7.20% std::_Rb_tree::find (inline) 822ms 6.76% 41.16% 822ms 6.76% __strcmp_evex 3ms 0.025% 41.18% 780ms 6.41% MeshBasedCellPopulation::UpdateNodePairs 3ms 0.025% 41.21% 732ms 6.02% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 7ms 0.058% 41.26% 696ms 5.72% MeshBasedCellPopulation::SpringIterator::operator++ 35ms 0.29% 41.55% 681ms 5.60% operator new 8ms 0.066% 41.62% 679ms 5.58% TetrahedralMesh::ImportFromMesher 260ms 2.14% 43.76% 638ms 5.25% __GI___libc_malloc 9ms 0.074% 43.83% 634ms 5.21% std::set::insert (inline) 12ms 0.099% 43.93% 624ms 5.13% std::_Rb_tree::_M_insert_unique 12ms 0.099% 44.03% 573ms 4.71% std::__new_allocator::allocate (inline) 0 0% 44.03% 572ms 4.70% std::allocator_traits::allocate (inline) 0 0% 44.03% 550ms 4.52% std::set::count (inline) 0 0% 44.03% 520ms 4.28% triangulate 7ms 0.058% 44.08% 470ms 3.86% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 0 0% 44.08% 469ms 3.86% delaunay 1ms 0.0082% 44.09% 469ms 3.86% divconqdelaunay 451ms 3.71% 47.80% 451ms 3.71% WntCellCycleOdeSystem::CalculateStoppingEvent 41ms 0.34% 48.14% 423ms 3.48% std::map::operator[] (partial-inline) 3ms 0.025% 48.16% 400ms 3.29% AbstractTwoBodyInteractionForce::AddForceContribution 4ms 0.033% 48.20% 394ms 3.24% CellPopulationElementWriter::Visit 14ms 0.12% 48.31% 383ms 3.15% std::less::operator() (inline) 0 0% 48.31% 372ms 3.06% std::_Rb_tree::_M_create_node (inline) 13ms 0.11% 48.42% 371ms 3.05% Cylindrical2dMesh::ReconstructCylindricalMesh 369ms 3.03% 51.45% 369ms 3.03% std::operator< (inline) 14ms 0.12% 51.57% 363ms 2.98% MeshBasedCellPopulation::AcceptCellWriter 12ms 0.099% 51.66% 362ms 2.98% AbstractCellPopulation::GetCellUsingLocationIndex 75ms 0.62% 52.28% 362ms 2.98% __dynamic_cast 0 0% 52.28% 362ms 2.98% std::_Rb_tree::_M_get_node (inline) 26ms 0.21% 52.50% 358ms 2.94% std::_Rb_tree::_M_insert_ (inline) 16ms 0.13% 52.63% 355ms 2.92% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 187ms 1.54% 54.16% 349ms 2.87% _int_malloc 6ms 0.049% 54.21% 341ms 2.80% Element::Element 331ms 2.72% 56.93% 331ms 2.72% std::_Rb_tree::_S_right (inline) 4ms 0.033% 56.97% 330ms 2.71% CellPropertyCollection::GetPropertiesType (inline) 43ms 0.35% 57.32% 330ms 2.71% std::_Rb_tree::~_Rb_tree (inline) 0 0% 57.32% 327ms 2.69% std::_Rb_tree::_M_drop_node (inline) 199ms 1.64% 58.96% 325ms 2.67% AbstractCellMutationState::AbstractCellMutationState 6ms 0.049% 59.01% 323ms 2.66% MutableMesh::ReIndex 0 0% 59.01% 323ms 2.66% std::map::find (inline) 0 0% 59.01% 322ms 2.65% std::_Rb_tree::_Alloc_node::operator() (inline) 65ms 0.53% 59.54% 315ms 2.59% __GI___libc_free 0 0% 59.54% 314ms 2.58% std::_Rb_tree::lower_bound (inline) 0 0% 59.54% 314ms 2.58% std::map::lower_bound (inline) 0 0% 59.54% 308ms 2.53% std::set::~set (inline) 43ms 0.35% 59.89% 304ms 2.50% std::_Rb_tree::_M_erase 15ms 0.12% 60.02% 290ms 2.38% Element::RegisterWithNodes (inline) 8ms 0.066% 60.08% 274ms 2.25% Node::AddElement 7ms 0.058% 60.14% 273ms 2.24% Cylindrical2dMesh::CorrectNonPeriodicMesh 2ms 0.016% 60.16% 269ms 2.21% std::_Rb_tree::erase 0 0% 60.16% 269ms 2.21% std::set::erase (inline) 7ms 0.058% 60.22% 268ms 2.20% std::__new_allocator::deallocate (inline) 0 0% 60.22% 266ms 2.19% AbstractCellProperty::IsSubType (inline) 0 0% 60.22% 266ms 2.19% std::allocator_traits::deallocate (inline) 7ms 0.058% 60.27% 265ms 2.18% Node::RemoveElement 25ms 0.21% 60.48% 259ms 2.13% std::ostream::_M_insert 0 0% 60.48% 259ms 2.13% std::ostream::operator<< (inline) 94ms 0.77% 61.25% 255ms 2.10% std::_Rb_tree::_M_get_insert_unique_pos 231ms 1.90% 63.15% 250ms 2.06% _int_free 0 0% 63.15% 243ms 2.00% std::_Rb_tree::_M_put_node (inline) 242ms 1.99% 65.14% 242ms 1.99% std::vector::operator[] (inline) 6ms 0.049% 65.19% 235ms 1.93% boost::detail::shared_count::~shared_count (inline) 0 0% 65.19% 235ms 1.93% boost::shared_ptr::~shared_ptr (inline) 6ms 0.049% 65.24% 225ms 1.85% divconqrecurse 219ms 1.80% 67.04% 223ms 1.83% boost::detail::sp_counted_base::release 67ms 0.55% 67.59% 213ms 1.75% mergehulls 0 0% 67.59% 210ms 1.73% std::_Vector_base::_M_allocate (inline) 11ms 0.09% 67.68% 208ms 1.71% Element::ResetIndex 114ms 0.94% 68.62% 204ms 1.68% __cxxabiv1::__si_class_type_info::__do_dyncast 1ms 0.0082% 68.63% 196ms 1.61% Cell::GetCellProliferativeType 3ms 0.025% 68.65% 187ms 1.54% Cell::GetMutationState 0 0% 68.65% 185ms 1.52% AbstractCellPopulation::Iterator::operator++ (inline) 10ms 0.082% 68.73% 183ms 1.50% AbstractCellPopulation::Iterator::IsRealCell (inline) 6ms 0.049% 68.78% 179ms 1.47% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.0082% 68.79% 177ms 1.46% NodeLocationWriter::Visit 9ms 0.074% 68.86% 177ms 1.46% std::_Rb_tree::_Rb_tree 0 0% 68.86% 175ms 1.44% LegacyCellProliferativeTypesWriter::VisitCell 8ms 0.066% 68.93% 174ms 1.43% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 7ms 0.058% 68.99% 171ms 1.41% std::_Rb_tree::_M_erase_aux (inline) 0 0% 68.99% 170ms 1.40% std::set::set (inline) 168ms 1.38% 70.37% 168ms 1.38% [libchaste_cell_based.so] 12ms 0.099% 70.47% 165ms 1.36% AbstractTetrahedralElement::CalculateJacobian 4ms 0.033% 70.50% 162ms 1.33% AbstractCellPopulation::IsCellAttachedToLocationIndex 28ms 0.23% 70.73% 159ms 1.31% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 2ms 0.016% 70.75% 159ms 1.31% alternateaxes 20ms 0.16% 70.91% 157ms 1.29% std::_Rb_tree::_M_copy (inline) 152ms 1.25% 72.16% 157ms 1.29% vertexmedian 17ms 0.14% 72.30% 155ms 1.27% std::num_put::_M_insert_float 52ms 0.43% 72.73% 153ms 1.26% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 9ms 0.074% 72.80% 152ms 1.25% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 7ms 0.058% 72.86% 149ms 1.23% std::vector::push_back (inline) 1ms 0.0082% 72.87% 141ms 1.16% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.0082% 72.88% 141ms 1.16% TetrahedralMesh::RefreshJacobianCachedData 5ms 0.041% 72.92% 140ms 1.15% Element::MarkAsDeleted 2ms 0.016% 72.93% 139ms 1.14% AbstractCentreBasedCellPopulation::GetDampingConstant 42ms 0.35% 73.28% 139ms 1.14% ApcOneHitCellMutationState::ApcOneHitCellMutationState 0 0% 73.28% 139ms 1.14% MeshBasedCellPopulation::GetDampingConstant 8ms 0.066% 73.35% 137ms 1.13% std::vector::_M_realloc_insert 70ms 0.58% 73.92% 136ms 1.12% std::_Rb_tree::_M_clone_node (inline) 0 0% 73.92% 135ms 1.11% OffLatticeSimulation::ApplyBoundaries 98ms 0.81% 74.73% 131ms 1.08% AbstractElement::GetNodeGlobalIndex 1ms 0.0082% 74.73% 125ms 1.03% TetrahedralMesh::Clear 3ms 0.025% 74.76% 122ms 1.00% AbstractTetrahedralElement::CalculateInverseJacobian 12ms 0.099% 74.86% 116ms 0.95% AbstractTetrahedralElement::RefreshJacobian 2ms 0.016% 74.87% 114ms 0.94% std::__cxx11::collate::do_transform 112ms 0.92% 75.80% 112ms 0.92% std::vector::size (inline) 4ms 0.033% 75.83% 111ms 0.91% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 75.83% 111ms 0.91% ___vsnprintf 0 0% 75.83% 111ms 0.91% __vsnprintf_internal (inline) 14ms 0.12% 75.94% 110ms 0.9% __printf_buffer 79ms 0.65% 76.59% 109ms 0.9% malloc_consolidate 36ms 0.3% 76.89% 107ms 0.88% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 104ms 0.86% 77.74% 104ms 0.86% incircle 0 0% 77.74% 102ms 0.84% CellProliferativeTypesWriter::VisitCell 58ms 0.48% 78.22% 100ms 0.82% std::_Rb_tree::equal_range (inline) 95ms 0.78% 79.00% 95ms 0.78% AbstractCellMutationState::~AbstractCellMutationState 59ms 0.49% 79.49% 95ms 0.78% AbstractElement::GetNodeLocation 6ms 0.049% 79.54% 95ms 0.78% __printf_fp_l_buffer 0 0% 79.54% 95ms 0.78% __printf_fp_spec (inline) 27ms 0.22% 79.76% 90ms 0.74% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 3ms 0.025% 79.78% 89ms 0.73% MeshBasedCellPopulation::SpringsEnd (inline) 39ms 0.32% 80.10% 89ms 0.73% __printf_fp_buffer_1 22ms 0.18% 80.28% 88ms 0.72% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 2ms 0.016% 80.30% 85ms 0.7% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 4ms 0.033% 80.33% 85ms 0.7% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 0 0% 80.33% 85ms 0.7% std::__new_allocator::destroy (inline) 0 0% 80.33% 85ms 0.7% std::allocator_traits::destroy (inline) 84ms 0.69% 81.02% 84ms 0.69% AbstractCellProperty::~AbstractCellProperty 0 0% 81.02% 84ms 0.69% std::_Rb_tree::_M_destroy_node (inline) 46ms 0.38% 81.40% 82ms 0.67% Cylindrical2dMesh::GetVectorFromAtoB 5ms 0.041% 81.44% 82ms 0.67% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 82ms 0.67% 82.12% 82ms 0.67% std::_Rb_tree_insert_and_rebalance 2ms 0.016% 82.13% 81ms 0.67% boost::numeric::ublas::vector_assign (inline) 4ms 0.033% 82.17% 80ms 0.66% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 1ms 0.0082% 82.18% 80ms 0.66% Node::~Node 77ms 0.63% 82.81% 79ms 0.65% vertexsort 5ms 0.041% 82.85% 76ms 0.62% TetrahedralMesh::EdgesEnd (partial-inline) 4ms 0.033% 82.88% 73ms 0.6% boost::numeric::ublas::c_vector::c_vector (inline) 73ms 0.6% 83.48% 73ms 0.6% unlink_chunk 0 0% 83.48% 72ms 0.59% AbstractCellBasedSimulation::DoCellRemoval (inline) 14ms 0.12% 83.60% 71ms 0.58% MeshBasedCellPopulation::SpringIterator::SpringIterator 70ms 0.58% 84.17% 70ms 0.58% std::_Rb_tree_rebalance_for_erase 3ms 0.025% 84.20% 69ms 0.57% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 21ms 0.17% 84.37% 69ms 0.57% std::num_put::_M_insert_int 0 0% 84.37% 68ms 0.56% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 2ms 0.016% 84.39% 68ms 0.56% std::_Rb_tree::_M_emplace_hint_unique 3ms 0.025% 84.41% 66ms 0.54% CellPropertyCollection::HasProperty 43ms 0.35% 84.77% 66ms 0.54% TimeStepper::AdvanceOneTimeStep 3ms 0.025% 84.79% 64ms 0.53% Cell::SetCellProliferativeType 49ms 0.4% 85.19% 64ms 0.53% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 64ms 0.53% 85.72% 64ms 0.53% [libchaste_mesh.so] 0 0% 85.72% 62ms 0.51% Cell::HasCellProperty (inline) 61ms 0.5% 86.22% 61ms 0.5% TetrahedralMesh::EdgeIterator::operator!=