File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16675ms, 84.51% of 19732ms total Dropped 759 nodes (cum <= 98.66ms) flat flat% sum% cum cum% 0 0% 0% 19689ms 99.78% __libc_start_call_main 0 0% 0% 19689ms 99.78% __libc_start_main_impl 0 0% 0% 19689ms 99.78% _start 0 0% 0% 19671ms 99.69% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19671ms 99.69% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19671ms 99.69% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19671ms 99.69% main 0 0% 0% 19636ms 99.51% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19636ms 99.51% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19636ms 99.51% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19609ms 99.38% AbstractCellBasedSimulation::Solve 1ms 0.0051% 0.0051% 15243ms 77.25% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0051% 0.01% 10070ms 51.03% AbstractCellBasedSimulation::DoCellBirth 3ms 0.015% 0.025% 9993ms 50.64% Cell::ReadyToDivide 6ms 0.03% 0.056% 9919ms 50.27% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.01% 0.066% 9783ms 49.58% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 11ms 0.056% 0.12% 9771ms 49.52% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.0051% 0.13% 9758ms 49.45% CellCycleModelOdeHandler::SolveOdeToTime 67ms 0.34% 0.47% 9600ms 48.65% AbstractOneStepIvpOdeSolver::InternalSolve 852ms 4.32% 4.78% 8755ms 44.37% RungeKutta4IvpOdeSolver::CalculateNextYValue 3548ms 17.98% 22.77% 7678ms 38.91% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.0051% 22.77% 5041ms 25.55% MeshBasedCellPopulation::Update 188ms 0.95% 23.72% 4173ms 21.15% AbstractCellProperty::IsType (inline) 8ms 0.041% 23.76% 3917ms 19.85% Cylindrical2dMesh::ReMesh 558ms 2.83% 26.59% 2888ms 14.64% AbstractCellProperty::IsSame 1ms 0.0051% 26.60% 2448ms 12.41% OffLatticeSimulation::UpdateCellLocationsAndTopology 429ms 2.17% 28.77% 2330ms 11.81% std::type_info::operator== (inline) 1ms 0.0051% 28.78% 2144ms 10.87% ForwardEulerNumericalMethod::UpdateAllNodePositions 13ms 0.066% 28.84% 2104ms 10.66% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 28.84% 2094ms 10.61% MutableMesh::ReMesh 0 0% 28.84% 1915ms 9.71% AbstractCellPopulation::WriteResultsToFiles 1859ms 9.42% 38.26% 1859ms 9.42% __strcmp_avx2 812ms 4.12% 42.38% 1797ms 9.11% std::_Rb_tree::_M_lower_bound (inline) 160ms 0.81% 43.19% 1625ms 8.24% TetrahedralMesh::EdgeIterator::operator++ 79ms 0.4% 43.59% 1320ms 6.69% std::_Rb_tree::find (inline) 0 0% 43.59% 1097ms 5.56% MeshBasedCellPopulation::UpdateNodePairs 11ms 0.056% 43.64% 1097ms 5.56% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 15ms 0.076% 43.72% 1060ms 5.37% TetrahedralMesh::ImportFromMesher 50ms 0.25% 43.97% 1037ms 5.26% operator new 6ms 0.03% 44.00% 981ms 4.97% MeshBasedCellPopulation::SpringIterator::operator++ 214ms 1.08% 45.09% 976ms 4.95% __GI___libc_malloc 14ms 0.071% 45.16% 954ms 4.83% std::set::insert (inline) 10ms 0.051% 45.21% 940ms 4.76% std::_Rb_tree::_M_insert_unique 28ms 0.14% 45.35% 876ms 4.44% std::__new_allocator::allocate (inline) 0 0% 45.35% 869ms 4.40% std::allocator_traits::allocate (inline) 0 0% 45.35% 806ms 4.08% std::set::count (inline) 0 0% 45.35% 776ms 3.93% triangulate 3ms 0.015% 45.37% 726ms 3.68% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 63ms 0.32% 45.69% 722ms 3.66% std::map::operator[] (partial-inline) 1ms 0.0051% 45.69% 713ms 3.61% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 45.69% 702ms 3.56% delaunay 2ms 0.01% 45.70% 702ms 3.56% divconqdelaunay 8ms 0.041% 45.74% 696ms 3.53% CellPopulationElementWriter::Visit 397ms 2.01% 47.75% 692ms 3.51% _int_malloc 656ms 3.32% 51.08% 656ms 3.32% std::_Rb_tree::_S_right (inline) 640ms 3.24% 54.32% 655ms 3.32% WntCellCycleOdeSystem::CalculateStoppingEvent 178ms 0.9% 55.23% 623ms 3.16% __dynamic_cast 25ms 0.13% 55.35% 614ms 3.11% std::less::operator() (inline) 18ms 0.091% 55.44% 611ms 3.10% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 589ms 2.98% 58.43% 589ms 2.98% std::operator< (inline) 22ms 0.11% 58.54% 579ms 2.93% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 58.54% 576ms 2.92% std::_Rb_tree::lower_bound (inline) 0 0% 58.54% 576ms 2.92% std::map::lower_bound (inline) 0 0% 58.54% 571ms 2.89% std::_Rb_tree::_M_create_node (inline) 28ms 0.14% 58.68% 565ms 2.86% std::_Rb_tree::_M_insert_ (inline) 6ms 0.03% 58.71% 562ms 2.85% MeshBasedCellPopulation::AcceptCellWriter 4ms 0.02% 58.73% 559ms 2.83% CellPropertyCollection::GetPropertiesType (inline) 7ms 0.035% 58.77% 540ms 2.74% MutableMesh::ReIndex 0 0% 58.77% 537ms 2.72% std::_Rb_tree::_M_get_node (inline) 10ms 0.051% 58.82% 520ms 2.64% Element::Element 0 0% 58.82% 512ms 2.59% std::map::find (inline) 0 0% 58.82% 509ms 2.58% std::_Rb_tree::_Alloc_node::operator() (inline) 14ms 0.071% 58.89% 502ms 2.54% Cylindrical2dMesh::CorrectNonPeriodicMesh 342ms 1.73% 60.62% 487ms 2.47% AbstractCellMutationState::AbstractCellMutationState 1ms 0.0051% 60.63% 480ms 2.43% std::ostream::operator<< (inline) 65ms 0.33% 60.96% 478ms 2.42% std::ostream::_M_insert 13ms 0.066% 61.02% 472ms 2.39% Cylindrical2dMesh::ReconstructCylindricalMesh 9ms 0.046% 61.07% 444ms 2.25% Element::RegisterWithNodes (inline) 3ms 0.015% 61.08% 434ms 2.20% AbstractCellProperty::IsSubType (inline) 4ms 0.02% 61.10% 434ms 2.20% Node::AddElement 151ms 0.77% 61.87% 428ms 2.17% __GI___libc_free 13ms 0.066% 61.93% 377ms 1.91% Node::RemoveElement 9ms 0.046% 61.98% 375ms 1.90% std::_Rb_tree::erase 0 0% 61.98% 375ms 1.90% std::set::erase (inline) 148ms 0.75% 62.73% 365ms 1.85% std::_Rb_tree::_M_get_insert_unique_pos 28ms 0.14% 62.87% 362ms 1.83% Element::ResetIndex 10ms 0.051% 62.92% 351ms 1.78% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 110ms 0.56% 63.48% 344ms 1.74% std::_Rb_tree::_M_erase 15ms 0.076% 63.56% 342ms 1.73% std::__new_allocator::deallocate (inline) 0 0% 63.56% 340ms 1.72% std::allocator_traits::deallocate (inline) 4ms 0.02% 63.58% 336ms 1.70% std::_Vector_base::_M_allocate (inline) 135ms 0.68% 64.26% 326ms 1.65% __cxxabiv1::__si_class_type_info::__do_dyncast 320ms 1.62% 65.88% 320ms 1.62% std::type_info::name (inline) 13ms 0.066% 65.95% 317ms 1.61% divconqrecurse 14ms 0.071% 66.02% 316ms 1.60% std::_Rb_tree::~_Rb_tree (inline) 0 0% 66.02% 308ms 1.56% std::_Rb_tree::_M_drop_node (inline) 2ms 0.01% 66.03% 301ms 1.53% Cell::GetMutationState 5ms 0.025% 66.06% 299ms 1.52% LegacyCellProliferativeTypesWriter::VisitCell 94ms 0.48% 66.53% 299ms 1.52% mergehulls 8ms 0.041% 66.57% 295ms 1.50% NodeLocationWriter::Visit 0 0% 66.57% 293ms 1.48% std::set::~set (inline) 3ms 0.015% 66.59% 292ms 1.48% AbstractCellPopulation::Iterator::operator++ (inline) 29ms 0.15% 66.73% 289ms 1.46% AbstractCellPopulation::Iterator::IsRealCell (inline) 2ms 0.01% 66.74% 285ms 1.44% Cell::GetCellProliferativeType 278ms 1.41% 68.15% 278ms 1.41% std::vector::operator[] (inline) 227ms 1.15% 69.30% 277ms 1.40% _int_free 0 0% 69.30% 273ms 1.38% std::_Rb_tree::_M_put_node (inline) 15ms 0.076% 69.38% 262ms 1.33% AbstractTetrahedralElement::CalculateJacobian 8ms 0.041% 69.42% 252ms 1.28% std::vector::push_back (inline) 8ms 0.041% 69.46% 249ms 1.26% AbstractCellPopulation::GetLocationIndexUsingCell 8ms 0.041% 69.50% 249ms 1.26% AbstractCellPopulation::IsCellAttachedToLocationIndex 249ms 1.26% 70.76% 249ms 1.26% [libchaste_cell_based.so] 13ms 0.066% 70.83% 247ms 1.25% std::num_put::_M_insert_float 1ms 0.0051% 70.83% 240ms 1.22% alternateaxes 16ms 0.081% 70.92% 239ms 1.21% std::vector::_M_realloc_insert 217ms 1.10% 72.02% 237ms 1.20% vertexmedian 10ms 0.051% 72.07% 236ms 1.20% std::_Rb_tree::_Rb_tree (partial-inline) 73ms 0.37% 72.44% 231ms 1.17% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 3ms 0.015% 72.45% 230ms 1.17% TetrahedralMesh::RefreshJacobianCachedData 64ms 0.32% 72.78% 228ms 1.16% ApcOneHitCellMutationState::ApcOneHitCellMutationState 12ms 0.061% 72.84% 225ms 1.14% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 7ms 0.035% 72.87% 220ms 1.11% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 13ms 0.066% 72.94% 219ms 1.11% std::_Rb_tree::_M_erase_aux (inline) 50ms 0.25% 73.19% 214ms 1.08% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 3ms 0.015% 73.21% 209ms 1.06% std::set::set (inline) 28ms 0.14% 73.35% 204ms 1.03% AbstractTetrahedralElement::RefreshJacobian 4ms 0.02% 73.37% 201ms 1.02% std::__cxx11::collate::do_transform 26ms 0.13% 73.50% 199ms 1.01% std::_Rb_tree::_M_copy (inline) 1ms 0.0051% 73.50% 195ms 0.99% MeshBasedCellPopulation::GetDampingConstant 1ms 0.0051% 73.51% 194ms 0.98% AbstractCentreBasedCellPopulation::GetDampingConstant 9ms 0.046% 73.56% 194ms 0.98% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 73.56% 192ms 0.97% ___vsnprintf 0 0% 73.56% 192ms 0.97% __vsnprintf_internal (inline) 16ms 0.081% 73.64% 191ms 0.97% Element::MarkAsDeleted 23ms 0.12% 73.75% 188ms 0.95% __printf_buffer 131ms 0.66% 74.42% 186ms 0.94% AbstractElement::GetNodeGlobalIndex 4ms 0.02% 74.44% 184ms 0.93% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 74.44% 179ms 0.91% OffLatticeSimulation::ApplyBoundaries 119ms 0.6% 75.04% 179ms 0.91% malloc_consolidate 10ms 0.051% 75.09% 172ms 0.87% TetrahedralMesh::Clear 49ms 0.25% 75.34% 171ms 0.87% std::_Rb_tree::_M_clone_node (inline) 171ms 0.87% 76.21% 171ms 0.87% unlink_chunk 5ms 0.025% 76.23% 168ms 0.85% CellPropertyCollection::HasProperty 0 0% 76.23% 165ms 0.84% Cell::HasCellProperty (inline) 3ms 0.015% 76.25% 164ms 0.83% CellProliferativeTypesWriter::VisitCell 11ms 0.056% 76.30% 158ms 0.8% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 158ms 0.8% 77.10% 158ms 0.8% std::_Rb_tree_insert_and_rebalance 100ms 0.51% 77.61% 155ms 0.79% std::_Rb_tree::equal_range (inline) 58ms 0.29% 77.90% 154ms 0.78% AbstractElement::GetNodeLocation 5ms 0.025% 77.93% 150ms 0.76% __printf_fp_l_buffer 0 0% 77.93% 150ms 0.76% __printf_fp_spec (inline) 147ms 0.74% 78.67% 147ms 0.74% Node::GetIndex 41ms 0.21% 78.88% 146ms 0.74% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 70ms 0.35% 79.24% 141ms 0.71% __printf_fp_buffer_1 122ms 0.62% 79.86% 137ms 0.69% vertexsort 0 0% 79.86% 131ms 0.66% AbstractCellBasedSimulation::DoCellRemoval (inline) 131ms 0.66% 80.52% 131ms 0.66% std::vector::size (inline) 8ms 0.041% 80.56% 130ms 0.66% boost::detail::shared_count::~shared_count (inline) 0 0% 80.56% 130ms 0.66% boost::shared_ptr::~shared_ptr (inline) 6ms 0.03% 80.59% 129ms 0.65% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 2ms 0.01% 80.60% 128ms 0.65% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 80.60% 126ms 0.64% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 1ms 0.0051% 80.61% 126ms 0.64% boost::numeric::ublas::vector_assign (inline) 13ms 0.066% 80.67% 121ms 0.61% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 121ms 0.61% 81.28% 121ms 0.61% incircle 80ms 0.41% 81.69% 118ms 0.6% Cylindrical2dMesh::GetVectorFromAtoB 116ms 0.59% 82.28% 118ms 0.6% boost::detail::sp_counted_base::release 28ms 0.14% 82.42% 117ms 0.59% std::num_put::_M_insert_int 113ms 0.57% 82.99% 113ms 0.57% [libchaste_mesh.so] 42ms 0.21% 83.20% 113ms 0.57% std::__ostream_insert 109ms 0.55% 83.76% 109ms 0.55% AbstractCellMutationState::~AbstractCellMutationState 29ms 0.15% 83.90% 109ms 0.55% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 10ms 0.051% 83.95% 109ms 0.55% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.0051% 83.96% 104ms 0.53% Cell::SetCellProliferativeType 5ms 0.025% 83.99% 104ms 0.53% boost::numeric::ublas::c_vector::c_vector (inline) 103ms 0.52% 84.51% 103ms 0.52% std::_Rb_tree_increment