File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 13836ms, 87.18% of 15870ms total Dropped 723 nodes (cum <= 79.35ms) flat flat% sum% cum cum% 0 0% 0% 15834ms 99.77% __libc_start_call_main 0 0% 0% 15834ms 99.77% __libc_start_main_impl 0 0% 0% 15834ms 99.77% _start 0 0% 0% 15816ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 15816ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 15816ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 15816ms 99.66% main 0 0% 0% 15787ms 99.48% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 15787ms 99.48% CxxTest::TestRunner::runTest (inline) 0 0% 0% 15787ms 99.48% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 15766ms 99.34% AbstractCellBasedSimulation::Solve 0 0% 0% 12028ms 75.79% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 7448ms 46.93% AbstractCellBasedSimulation::DoCellBirth 2ms 0.013% 0.013% 7369ms 46.43% Cell::ReadyToDivide 4ms 0.025% 0.038% 7318ms 46.11% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.013% 0.05% 7199ms 45.36% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 9ms 0.057% 0.11% 7193ms 45.32% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.0063% 0.11% 7181ms 45.25% CellCycleModelOdeHandler::SolveOdeToTime 42ms 0.26% 0.38% 7042ms 44.37% AbstractOneStepIvpOdeSolver::InternalSolve 620ms 3.91% 4.28% 6296ms 39.67% RungeKutta4IvpOdeSolver::CalculateNextYValue 2912ms 18.35% 22.63% 5448ms 34.33% WntCellCycleOdeSystem::EvaluateYDerivatives 2ms 0.013% 22.65% 4475ms 28.20% MeshBasedCellPopulation::Update 1ms 0.0063% 22.65% 3378ms 21.29% Cylindrical2dMesh::ReMesh 349ms 2.20% 24.85% 2659ms 16.75% AbstractCellProperty::IsType (inline) 1ms 0.0063% 24.86% 2180ms 13.74% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0063% 24.86% 1907ms 12.02% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 24.86% 1877ms 11.83% MutableMesh::ReMesh 1ms 0.0063% 24.87% 1863ms 11.74% AbstractNumericalMethod::ComputeForcesIncludingDamping 752ms 4.74% 29.61% 1566ms 9.87% std::_Rb_tree::_M_lower_bound (inline) 0 0% 29.61% 1554ms 9.79% AbstractCellPopulation::WriteResultsToFiles 130ms 0.82% 30.43% 1533ms 9.66% TetrahedralMesh::EdgeIterator::operator++ 39ms 0.25% 30.67% 1227ms 7.73% std::_Rb_tree::find (inline) 0 0% 30.67% 1059ms 6.67% MeshBasedCellPopulation::UpdateNodePairs 149ms 0.94% 31.61% 1050ms 6.62% AbstractCellProperty::IsSame 6ms 0.038% 31.65% 1009ms 6.36% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 37ms 0.23% 31.88% 994ms 6.26% operator new 327ms 2.06% 33.94% 946ms 5.96% __GI___libc_malloc 11ms 0.069% 34.01% 941ms 5.93% MeshBasedCellPopulation::SpringIterator::operator++ 6ms 0.038% 34.05% 918ms 5.78% TetrahedralMesh::ImportFromMesher 10ms 0.063% 34.11% 916ms 5.77% std::set::insert (inline) 7ms 0.044% 34.16% 905ms 5.70% std::_Rb_tree::_M_insert_unique 17ms 0.11% 34.27% 901ms 5.68% std::type_info::operator== (inline) 881ms 5.55% 39.82% 881ms 5.55% __strcmp_evex 10ms 0.063% 39.88% 851ms 5.36% std::__new_allocator::allocate (inline) 0 0% 39.88% 847ms 5.34% std::allocator_traits::allocate (inline) 803ms 5.06% 44.94% 803ms 5.06% [libchaste_cell_based.so] 0 0% 44.94% 790ms 4.98% std::set::count (inline) 2ms 0.013% 44.95% 747ms 4.71% triangulate 0 0% 44.95% 662ms 4.17% delaunay 2ms 0.013% 44.97% 660ms 4.16% divconqdelaunay 1ms 0.0063% 44.97% 621ms 3.91% AbstractTwoBodyInteractionForce::AddForceContribution 11ms 0.069% 45.04% 621ms 3.91% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 24ms 0.15% 45.19% 571ms 3.60% std::_Rb_tree::_M_insert_ (inline) 560ms 3.53% 48.72% 560ms 3.53% WntCellCycleOdeSystem::CalculateStoppingEvent 0 0% 48.72% 552ms 3.48% std::_Rb_tree::_M_create_node (inline) 5ms 0.032% 48.75% 549ms 3.46% CellPopulationElementWriter::Visit 18ms 0.11% 48.87% 549ms 3.46% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 0 0% 48.87% 542ms 3.42% std::_Rb_tree::_M_get_node (inline) 315ms 1.98% 50.85% 531ms 3.35% _int_malloc 55ms 0.35% 51.20% 528ms 3.33% std::map::operator[] (partial-inline) 0 0% 51.20% 518ms 3.26% std::_Rb_tree::_Alloc_node::operator() (inline) 518ms 3.26% 54.46% 518ms 3.26% std::_Rb_tree::_S_right (inline) 133ms 0.84% 55.30% 511ms 3.22% __dynamic_cast 13ms 0.082% 55.38% 491ms 3.09% AbstractCellPopulation::GetCellUsingLocationIndex 9ms 0.057% 55.44% 484ms 3.05% MeshBasedCellPopulation::AcceptCellWriter 7ms 0.044% 55.48% 483ms 3.04% Element::Element 17ms 0.11% 55.59% 461ms 2.90% Cylindrical2dMesh::ReconstructCylindricalMesh 239ms 1.51% 57.10% 458ms 2.89% AbstractCellMutationState::AbstractCellMutationState 4ms 0.025% 57.12% 452ms 2.85% CellPropertyCollection::GetPropertiesType (inline) 20ms 0.13% 57.25% 442ms 2.79% Node::AddElement 4ms 0.025% 57.27% 441ms 2.78% Element::RegisterWithNodes (inline) 0 0% 57.27% 436ms 2.75% std::map::find (inline) 19ms 0.12% 57.39% 424ms 2.67% std::less::operator() (inline) 109ms 0.69% 58.08% 423ms 2.67% __GI___libc_free 0 0% 58.08% 419ms 2.64% std::_Rb_tree::lower_bound (inline) 0 0% 58.08% 419ms 2.64% std::map::lower_bound (inline) 11ms 0.069% 58.15% 416ms 2.62% Cylindrical2dMesh::CorrectNonPeriodicMesh 405ms 2.55% 60.70% 405ms 2.55% std::operator< (inline) 1ms 0.0063% 60.71% 392ms 2.47% std::ostream::operator<< (inline) 40ms 0.25% 60.96% 389ms 2.45% std::ostream::_M_insert 3ms 0.019% 60.98% 376ms 2.37% MutableMesh::ReIndex 53ms 0.33% 61.31% 366ms 2.31% std::_Rb_tree::~_Rb_tree (inline) 0 0% 61.31% 364ms 2.29% std::_Rb_tree::_M_drop_node (inline) 65ms 0.41% 61.72% 355ms 2.24% std::_Rb_tree::_M_erase 2ms 0.013% 61.73% 351ms 2.21% AbstractCellProperty::IsSubType (inline) 0 0% 61.73% 350ms 2.21% std::set::~set (inline) 12ms 0.076% 61.81% 347ms 2.19% std::__new_allocator::deallocate (inline) 343ms 2.16% 63.97% 343ms 2.16% [libchaste_crypt.so] 0 0% 63.97% 342ms 2.16% std::allocator_traits::deallocate (inline) 5ms 0.032% 64.00% 331ms 2.09% std::_Rb_tree::erase 0 0% 64.00% 331ms 2.09% std::set::erase (inline) 134ms 0.84% 64.85% 327ms 2.06% std::_Rb_tree::_M_get_insert_unique_pos 8ms 0.05% 64.90% 321ms 2.02% Node::RemoveElement 9ms 0.057% 64.95% 321ms 2.02% divconqrecurse 264ms 1.66% 66.62% 309ms 1.95% _int_free 91ms 0.57% 67.19% 307ms 1.93% mergehulls 0 0% 67.19% 305ms 1.92% std::_Vector_base::_M_allocate (inline) 0 0% 67.19% 282ms 1.78% std::_Rb_tree::_M_put_node (inline) 134ms 0.84% 68.03% 274ms 1.73% __cxxabiv1::__si_class_type_info::__do_dyncast 11ms 0.069% 68.10% 274ms 1.73% boost::detail::shared_count::~shared_count (inline) 0 0% 68.10% 274ms 1.73% boost::shared_ptr::~shared_ptr (inline) 1ms 0.0063% 68.11% 265ms 1.67% NodeLocationWriter::Visit 2ms 0.013% 68.12% 254ms 1.60% LegacyCellProliferativeTypesWriter::VisitCell 3ms 0.019% 68.14% 252ms 1.59% Cell::GetCellProliferativeType 0 0% 68.14% 252ms 1.59% Cell::GetMutationState 249ms 1.57% 69.71% 252ms 1.59% boost::detail::sp_counted_base::release 21ms 0.13% 69.84% 248ms 1.56% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 13ms 0.082% 69.92% 245ms 1.54% Element::ResetIndex 2ms 0.013% 69.94% 243ms 1.53% AbstractCellPopulation::Iterator::operator++ (inline) 17ms 0.11% 70.04% 241ms 1.52% std::num_put::_M_insert_float 19ms 0.12% 70.16% 237ms 1.49% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.0063% 70.17% 237ms 1.49% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 11ms 0.069% 70.24% 225ms 1.42% std::_Rb_tree::_Rb_tree (partial-inline) 214ms 1.35% 71.59% 223ms 1.41% std::vector::operator[] (inline) 5ms 0.032% 71.62% 221ms 1.39% alternateaxes 0 0% 71.62% 219ms 1.38% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 15ms 0.095% 71.71% 219ms 1.38% std::_Rb_tree::_M_erase_aux (inline) 11ms 0.069% 71.78% 218ms 1.37% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 71.78% 217ms 1.37% ApcOneHitCellMutationState::ApcOneHitCellMutationState 195ms 1.23% 73.01% 213ms 1.34% vertexmedian 32ms 0.2% 73.21% 212ms 1.34% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 4ms 0.025% 73.24% 211ms 1.33% std::set::set (inline) 9ms 0.057% 73.30% 211ms 1.33% std::vector::push_back (inline) 23ms 0.14% 73.44% 200ms 1.26% std::_Rb_tree::_M_copy (inline) 5ms 0.032% 73.47% 197ms 1.24% AbstractCellPopulation::IsCellAttachedToLocationIndex 7ms 0.044% 73.52% 193ms 1.22% AbstractTetrahedralElement::CalculateJacobian 4ms 0.025% 73.54% 193ms 1.22% std::__cxx11::collate::do_transform 4ms 0.025% 73.57% 193ms 1.22% std::vector::_M_realloc_insert 0 0% 73.57% 192ms 1.21% TetrahedralMesh::RefreshJacobianCachedData 192ms 1.21% 74.78% 192ms 1.21% [libchaste_mesh.so] 10ms 0.063% 74.84% 190ms 1.20% Element::MarkAsDeleted 1ms 0.0063% 74.85% 185ms 1.17% ___vsnprintf 0 0% 74.85% 184ms 1.16% __vsnprintf_internal (inline) 0 0% 74.85% 183ms 1.15% OffLatticeSimulation::ApplyBoundaries 14ms 0.088% 74.93% 181ms 1.14% __printf_buffer 0 0% 74.93% 178ms 1.12% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 66ms 0.42% 75.35% 169ms 1.06% std::_Rb_tree::_M_clone_node (inline) 3ms 0.019% 75.37% 167ms 1.05% MeshBasedCellPopulation::GetDampingConstant 5ms 0.032% 75.40% 165ms 1.04% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 75.40% 164ms 1.03% AbstractCentreBasedCellPopulation::GetDampingConstant 123ms 0.78% 76.18% 159ms 1.00% malloc_consolidate 68ms 0.43% 76.60% 151ms 0.95% AbstractElement::GetNodeGlobalIndex 151ms 0.95% 77.56% 151ms 0.95% incircle 4ms 0.025% 77.58% 150ms 0.95% __printf_fp_l_buffer 0 0% 77.58% 150ms 0.95% __printf_fp_spec (inline) 17ms 0.11% 77.69% 148ms 0.93% AbstractTetrahedralElement::RefreshJacobian 1ms 0.0063% 77.69% 139ms 0.88% boost::numeric::ublas::vector_assign (inline) 51ms 0.32% 78.02% 138ms 0.87% __printf_fp_buffer_1 138ms 0.87% 78.88% 138ms 0.87% std::_Rb_tree_insert_and_rebalance 1ms 0.0063% 78.89% 135ms 0.85% TetrahedralMesh::Clear 0 0% 78.89% 132ms 0.83% CellProliferativeTypesWriter::VisitCell 4ms 0.025% 78.92% 130ms 0.82% MeshBasedCellPopulation::SpringsEnd (inline) 23ms 0.14% 79.06% 128ms 0.81% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 127ms 0.8% 79.86% 127ms 0.8% std::_Rb_tree::_S_left (inline) 2ms 0.013% 79.87% 126ms 0.79% CellPropertyCollection::HasProperty 125ms 0.79% 80.66% 125ms 0.79% std::vector::size (inline) 4ms 0.025% 80.69% 124ms 0.78% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 80.69% 123ms 0.78% Cell::HasCellProperty (inline) 5ms 0.032% 80.72% 123ms 0.78% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 16ms 0.1% 80.82% 120ms 0.76% TetrahedralMesh::EdgesEnd (partial-inline) 4ms 0.025% 80.84% 119ms 0.75% boost::numeric::ublas::c_vector::c_vector (inline) 7ms 0.044% 80.89% 116ms 0.73% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 105ms 0.66% 81.55% 113ms 0.71% vertexsort 112ms 0.71% 82.26% 112ms 0.71% AbstractCellProperty::AbstractCellProperty 35ms 0.22% 82.48% 112ms 0.71% boost::numeric::ublas::indexing_vector_assign 52ms 0.33% 82.80% 111ms 0.7% AbstractElement::GetNodeLocation 1ms 0.0063% 82.81% 111ms 0.7% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 0 0% 82.81% 109ms 0.69% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 52ms 0.33% 83.14% 108ms 0.68% std::_Rb_tree::equal_range (inline) 107ms 0.67% 83.81% 107ms 0.67% std::type_info::name (inline) 0 0% 83.81% 104ms 0.66% AbstractCellBasedSimulation::DoCellRemoval (inline) 52ms 0.33% 84.14% 102ms 0.64% Cylindrical2dMesh::GetVectorFromAtoB 80ms 0.5% 84.64% 101ms 0.64% TetrahedralMesh::EdgeIterator::EdgeIterator 1ms 0.0063% 84.65% 101ms 0.64% std::_Rb_tree_const_iterator::operator++ (inline) 4ms 0.025% 84.68% 99ms 0.62% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 16ms 0.1% 84.78% 98ms 0.62% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 84.78% 97ms 0.61% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 4ms 0.025% 84.80% 96ms 0.6% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 4ms 0.025% 84.83% 89ms 0.56% Cell::SetCellProliferativeType 89ms 0.56% 85.39% 89ms 0.56% std::_Rb_tree_increment 88ms 0.55% 85.94% 88ms 0.55% Node::GetIndex 2ms 0.013% 85.95% 87ms 0.55% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 85ms 0.54% 86.49% 85ms 0.54% [libchaste_ode.so] 85ms 0.54% 87.03% 85ms 0.54% std::_Rb_tree_rebalance_for_erase 0 0% 87.03% 84ms 0.53% std::__new_allocator::destroy (inline) 0 0% 87.03% 84ms 0.53% std::allocator_traits::destroy (inline) 0 0% 87.03% 83ms 0.52% std::_Rb_tree::_M_destroy_node (inline) 25ms 0.16% 87.18% 80ms 0.5% std::num_put::_M_insert_int 0 0% 87.18% 80ms 0.5% std::vector::resize (inline)