File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 15844ms, 85.80% of 18467ms total Dropped 771 nodes (cum <= 92.33ms) flat flat% sum% cum cum% 0 0% 0% 18425ms 99.77% __libc_start_call_main 0 0% 0% 18425ms 99.77% __libc_start_main_impl 0 0% 0% 18425ms 99.77% _start 0 0% 0% 18405ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 18405ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 18405ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 18405ms 99.66% main 0 0% 0% 18365ms 99.45% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 18365ms 99.45% CxxTest::TestRunner::runTest (inline) 0 0% 0% 18365ms 99.45% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 18341ms 99.32% AbstractCellBasedSimulation::Solve 0 0% 0% 14053ms 76.10% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0054% 0.0054% 8782ms 47.56% AbstractCellBasedSimulation::DoCellBirth 7ms 0.038% 0.043% 8685ms 47.03% Cell::ReadyToDivide 2ms 0.011% 0.054% 8645ms 46.81% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.054% 8497ms 46.01% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 12ms 0.065% 0.12% 8492ms 45.98% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.016% 0.14% 8474ms 45.89% CellCycleModelOdeHandler::SolveOdeToTime 57ms 0.31% 0.44% 8310ms 45.00% AbstractOneStepIvpOdeSolver::InternalSolve 818ms 4.43% 4.87% 7408ms 40.11% RungeKutta4IvpOdeSolver::CalculateNextYValue 3384ms 18.32% 23.20% 6309ms 34.16% WntCellCycleOdeSystem::EvaluateYDerivatives 3ms 0.016% 23.21% 5147ms 27.87% MeshBasedCellPopulation::Update 2ms 0.011% 23.23% 3901ms 21.12% Cylindrical2dMesh::ReMesh 374ms 2.03% 25.25% 3059ms 16.56% AbstractCellProperty::IsType (inline) 1ms 0.0054% 25.26% 2475ms 13.40% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0054% 25.26% 2190ms 11.86% MutableMesh::ReMesh 0 0% 25.26% 2147ms 11.63% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 25.26% 2095ms 11.34% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.0054% 25.27% 1803ms 9.76% AbstractCellPopulation::WriteResultsToFiles 158ms 0.86% 26.12% 1779ms 9.63% TetrahedralMesh::EdgeIterator::operator++ 874ms 4.73% 30.86% 1752ms 9.49% std::_Rb_tree::_M_lower_bound (inline) 38ms 0.21% 31.06% 1435ms 7.77% std::_Rb_tree::find (inline) 173ms 0.94% 32.00% 1226ms 6.64% AbstractCellProperty::IsSame 0 0% 32.00% 1205ms 6.53% MeshBasedCellPopulation::UpdateNodePairs 53ms 0.29% 32.28% 1189ms 6.44% operator new 6ms 0.032% 32.32% 1143ms 6.19% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 420ms 2.27% 34.59% 1121ms 6.07% __GI___libc_malloc 14ms 0.076% 34.67% 1089ms 5.90% std::set::insert (inline) 1087ms 5.89% 40.55% 1087ms 5.89% __strcmp_evex 8ms 0.043% 40.60% 1077ms 5.83% TetrahedralMesh::ImportFromMesher 12ms 0.065% 40.66% 1075ms 5.82% MeshBasedCellPopulation::SpringIterator::operator++ 6ms 0.032% 40.69% 1075ms 5.82% std::_Rb_tree::_M_insert_unique 22ms 0.12% 40.81% 1053ms 5.70% std::type_info::operator== (inline) 23ms 0.12% 40.94% 994ms 5.38% std::__new_allocator::allocate (inline) 0 0% 40.94% 991ms 5.37% std::allocator_traits::allocate (inline) 975ms 5.28% 46.22% 975ms 5.28% [libchaste_cell_based.so] 0 0% 46.22% 923ms 5.00% std::set::count (inline) 2ms 0.011% 46.23% 874ms 4.73% triangulate 0 0% 46.23% 802ms 4.34% delaunay 2ms 0.011% 46.24% 801ms 4.34% divconqdelaunay 9ms 0.049% 46.29% 752ms 4.07% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 45ms 0.24% 46.53% 693ms 3.75% std::_Rb_tree::_M_insert_ (inline) 2ms 0.011% 46.54% 690ms 3.74% AbstractTwoBodyInteractionForce::AddForceContribution 689ms 3.73% 50.27% 689ms 3.73% WntCellCycleOdeSystem::CalculateStoppingEvent 0 0% 50.27% 683ms 3.70% std::_Rb_tree::_M_create_node (inline) 0 0% 50.27% 672ms 3.64% std::_Rb_tree::_M_get_node (inline) 164ms 0.89% 51.16% 649ms 3.51% __dynamic_cast 0 0% 51.16% 621ms 3.36% std::_Rb_tree::_Alloc_node::operator() (inline) 10ms 0.054% 51.22% 619ms 3.35% CellPopulationElementWriter::Visit 24ms 0.13% 51.35% 609ms 3.30% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 367ms 1.99% 53.33% 595ms 3.22% _int_malloc 2ms 0.011% 53.34% 585ms 3.17% MeshBasedCellPopulation::AcceptCellWriter 4ms 0.022% 53.37% 576ms 3.12% CellPropertyCollection::GetPropertiesType (inline) 2ms 0.011% 53.38% 571ms 3.09% Element::Element 5ms 0.027% 53.40% 565ms 3.06% Element::RegisterWithNodes (inline) 66ms 0.36% 53.76% 563ms 3.05% std::map::operator[] (partial-inline) 29ms 0.16% 53.92% 547ms 2.96% Node::AddElement 535ms 2.90% 56.81% 535ms 2.90% std::_Rb_tree::_S_right (inline) 13ms 0.07% 56.89% 529ms 2.86% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 56.89% 509ms 2.76% std::map::find (inline) 34ms 0.18% 57.07% 503ms 2.72% Cylindrical2dMesh::ReconstructCylindricalMesh 235ms 1.27% 58.34% 500ms 2.71% AbstractCellMutationState::AbstractCellMutationState 7ms 0.038% 58.38% 485ms 2.63% Cylindrical2dMesh::CorrectNonPeriodicMesh 9ms 0.049% 58.43% 483ms 2.62% std::less::operator() (inline) 99ms 0.54% 58.96% 480ms 2.60% __GI___libc_free 474ms 2.57% 61.53% 474ms 2.57% std::operator< (inline) 3ms 0.016% 61.55% 473ms 2.56% AbstractCellProperty::IsSubType (inline) 4ms 0.022% 61.57% 441ms 2.39% MutableMesh::ReIndex 0 0% 61.57% 414ms 2.24% std::_Rb_tree::_M_drop_node (inline) 0 0% 61.57% 409ms 2.21% std::_Rb_tree::lower_bound (inline) 0 0% 61.57% 409ms 2.21% std::map::lower_bound (inline) 9ms 0.049% 61.62% 406ms 2.20% std::__new_allocator::deallocate (inline) 0 0% 61.62% 406ms 2.20% std::ostream::operator<< (inline) 54ms 0.29% 61.91% 403ms 2.18% std::ostream::_M_insert 0 0% 61.91% 402ms 2.18% std::allocator_traits::deallocate (inline) 70ms 0.38% 62.29% 388ms 2.10% std::_Rb_tree::~_Rb_tree (inline) 15ms 0.081% 62.37% 379ms 2.05% divconqrecurse 164ms 0.89% 63.26% 376ms 2.04% std::_Rb_tree::_M_get_insert_unique_pos 335ms 1.81% 65.07% 374ms 2.03% _int_free 372ms 2.01% 67.09% 372ms 2.01% [libchaste_crypt.so] 0 0% 67.09% 365ms 1.98% std::set::~set (inline) 49ms 0.27% 67.35% 357ms 1.93% std::_Rb_tree::_M_erase 102ms 0.55% 67.90% 355ms 1.92% mergehulls 150ms 0.81% 68.72% 350ms 1.90% __cxxabiv1::__si_class_type_info::__do_dyncast 11ms 0.06% 68.78% 344ms 1.86% std::_Rb_tree::erase 0 0% 68.78% 342ms 1.85% std::set::erase (inline) 1ms 0.0054% 68.78% 339ms 1.84% LegacyCellProliferativeTypesWriter::VisitCell 8ms 0.043% 68.83% 327ms 1.77% Node::RemoveElement 0 0% 68.83% 327ms 1.77% std::_Rb_tree::_M_put_node (inline) 4ms 0.022% 68.85% 322ms 1.74% Cell::GetMutationState 0 0% 68.85% 319ms 1.73% std::_Vector_base::_M_allocate (inline) 14ms 0.076% 68.92% 309ms 1.67% Element::ResetIndex 1ms 0.0054% 68.93% 301ms 1.63% Cell::GetCellProliferativeType 0 0% 68.93% 291ms 1.58% AbstractCellPopulation::Iterator::operator++ (inline) 37ms 0.2% 69.13% 287ms 1.55% AbstractCellPopulation::Iterator::IsRealCell (inline) 22ms 0.12% 69.25% 280ms 1.52% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 266ms 1.44% 70.69% 276ms 1.49% std::vector::operator[] (inline) 4ms 0.022% 70.71% 274ms 1.48% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 70.71% 273ms 1.48% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 7ms 0.038% 70.75% 268ms 1.45% boost::detail::shared_count::~shared_count (inline) 0 0% 70.75% 268ms 1.45% boost::shared_ptr::~shared_ptr (inline) 9ms 0.049% 70.80% 264ms 1.43% AbstractCellPopulation::GetLocationIndexUsingCell 3ms 0.016% 70.81% 262ms 1.42% std::set::set (inline) 2ms 0.011% 70.82% 258ms 1.40% alternateaxes 255ms 1.38% 72.20% 257ms 1.39% boost::detail::sp_counted_base::release 229ms 1.24% 73.44% 255ms 1.38% vertexmedian 39ms 0.21% 73.66% 253ms 1.37% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 253ms 1.37% 75.03% 253ms 1.37% [libchaste_mesh.so] 25ms 0.14% 75.16% 247ms 1.34% std::_Rb_tree::_M_copy (inline) 17ms 0.092% 75.25% 236ms 1.28% AbstractTetrahedralElement::CalculateJacobian 0 0% 75.25% 236ms 1.28% ApcOneHitCellMutationState::ApcOneHitCellMutationState 2ms 0.011% 75.26% 235ms 1.27% std::vector::push_back (inline) 1ms 0.0054% 75.27% 234ms 1.27% NodeLocationWriter::Visit 0 0% 75.27% 232ms 1.26% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 9ms 0.049% 75.32% 226ms 1.22% std::vector::_M_realloc_insert 10ms 0.054% 75.37% 222ms 1.20% std::_Rb_tree::_M_erase_aux (inline) 0 0% 75.37% 221ms 1.20% OffLatticeSimulation::ApplyBoundaries 2ms 0.011% 75.38% 217ms 1.18% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 75.38% 213ms 1.15% TetrahedralMesh::RefreshJacobianCachedData 84ms 0.45% 75.84% 211ms 1.14% std::_Rb_tree::_M_clone_node (inline) 13ms 0.07% 75.91% 211ms 1.14% std::num_put::_M_insert_float 9ms 0.049% 75.96% 209ms 1.13% AbstractCellPopulation::IsCellAttachedToLocationIndex 4ms 0.022% 75.98% 197ms 1.07% AbstractTetrahedralElement::CalculateInverseJacobian 14ms 0.076% 76.05% 189ms 1.02% Element::MarkAsDeleted 5ms 0.027% 76.08% 178ms 0.96% std::__cxx11::collate::do_transform 1ms 0.0054% 76.09% 172ms 0.93% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 76.09% 172ms 0.93% MeshBasedCellPopulation::GetDampingConstant 133ms 0.72% 76.81% 170ms 0.92% malloc_consolidate 37ms 0.2% 77.01% 169ms 0.92% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 0 0% 77.01% 169ms 0.92% ___vsnprintf 2ms 0.011% 77.02% 169ms 0.92% __vsnprintf_internal (inline) 12ms 0.065% 77.08% 162ms 0.88% __printf_buffer 159ms 0.86% 77.94% 159ms 0.86% std::_Rb_tree_insert_and_rebalance 19ms 0.1% 78.05% 157ms 0.85% AbstractTetrahedralElement::RefreshJacobian 134ms 0.73% 78.77% 152ms 0.82% vertexsort 151ms 0.82% 79.59% 151ms 0.82% incircle 0 0% 79.59% 150ms 0.81% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 0 0% 79.59% 146ms 0.79% CellProliferativeTypesWriter::VisitCell 146ms 0.79% 80.38% 146ms 0.79% std::vector::size (inline) 6ms 0.032% 80.41% 145ms 0.79% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 3ms 0.016% 80.43% 144ms 0.78% AbstractTetrahedralElement::AbstractTetrahedralElement 2ms 0.011% 80.44% 144ms 0.78% TetrahedralMesh::Clear 3ms 0.016% 80.46% 143ms 0.77% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 57ms 0.31% 80.77% 141ms 0.76% AbstractElement::GetNodeGlobalIndex 0 0% 80.77% 141ms 0.76% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 139ms 0.75% 81.52% 139ms 0.75% std::_Rb_tree::_S_left (inline) 2ms 0.011% 81.53% 137ms 0.74% boost::numeric::ublas::vector_assign (inline) 1ms 0.0054% 81.53% 136ms 0.74% Cell::HasCellProperty (inline) 1ms 0.0054% 81.54% 136ms 0.74% CellPropertyCollection::HasProperty 2ms 0.011% 81.55% 136ms 0.74% __printf_fp_l_buffer 0 0% 81.55% 136ms 0.74% __printf_fp_spec (inline) 134ms 0.73% 82.28% 134ms 0.73% std::type_info::name (inline) 54ms 0.29% 82.57% 131ms 0.71% __printf_fp_buffer_1 6ms 0.032% 82.60% 129ms 0.7% boost::numeric::ublas::c_vector::c_vector (inline) 7ms 0.038% 82.64% 127ms 0.69% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 52ms 0.28% 82.92% 124ms 0.67% AbstractElement::GetNodeLocation 0 0% 82.92% 122ms 0.66% AbstractCellBasedSimulation::DoCellRemoval (inline) 5ms 0.027% 82.95% 120ms 0.65% Cell::SetCellProliferativeType 5ms 0.027% 82.98% 120ms 0.65% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 8ms 0.043% 83.02% 119ms 0.64% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 118ms 0.64% 83.66% 118ms 0.64% AbstractCellProperty::AbstractCellProperty 3ms 0.016% 83.67% 114ms 0.62% MeshBasedCellPopulation::SpringsEnd (inline) 60ms 0.32% 84.00% 113ms 0.61% Cylindrical2dMesh::GetVectorFromAtoB 24ms 0.13% 84.13% 112ms 0.61% std::num_put::_M_insert_int 11ms 0.06% 84.19% 110ms 0.6% TetrahedralMesh::EdgesEnd (partial-inline) 53ms 0.29% 84.48% 110ms 0.6% std::_Rb_tree::equal_range (inline) 9ms 0.049% 84.52% 102ms 0.55% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 47ms 0.25% 84.78% 101ms 0.55% std::__ostream_insert 24ms 0.13% 84.91% 100ms 0.54% boost::numeric::ublas::indexing_vector_assign 94ms 0.51% 85.42% 94ms 0.51% Node::GetIndex 70ms 0.38% 85.80% 93ms 0.5% TetrahedralMesh::EdgeIterator::EdgeIterator