File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16551ms, 85.24% of 19417ms total Dropped 799 nodes (cum <= 97.08ms) flat flat% sum% cum cum% 0 0% 0% 19375ms 99.78% __libc_start_call_main 0 0% 0% 19375ms 99.78% __libc_start_main_impl 0 0% 0% 19375ms 99.78% _start 0 0% 0% 19355ms 99.68% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19355ms 99.68% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19355ms 99.68% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19355ms 99.68% main 0 0% 0% 19315ms 99.47% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19315ms 99.47% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19315ms 99.47% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19291ms 99.35% AbstractCellBasedSimulation::Solve 0 0% 0% 14837ms 76.41% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0052% 0.0052% 9270ms 47.74% AbstractCellBasedSimulation::DoCellBirth 8ms 0.041% 0.046% 9160ms 47.18% Cell::ReadyToDivide 6ms 0.031% 0.077% 9107ms 46.90% AbstractPhaseBasedCellCycleModel::ReadyToDivide 3ms 0.015% 0.093% 8939ms 46.04% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 11ms 0.057% 0.15% 8927ms 45.98% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.015% 0.16% 8908ms 45.88% CellCycleModelOdeHandler::SolveOdeToTime 51ms 0.26% 0.43% 8728ms 44.95% AbstractOneStepIvpOdeSolver::InternalSolve 865ms 4.45% 4.88% 7833ms 40.34% RungeKutta4IvpOdeSolver::CalculateNextYValue 3356ms 17.28% 22.17% 6699ms 34.50% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 22.17% 5436ms 28.00% MeshBasedCellPopulation::Update 2ms 0.01% 22.18% 4163ms 21.44% Cylindrical2dMesh::ReMesh 315ms 1.62% 23.80% 3482ms 17.93% AbstractCellProperty::IsType (inline) 0 0% 23.80% 2560ms 13.18% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0052% 23.80% 2281ms 11.75% MutableMesh::ReMesh 0 0% 23.80% 2177ms 11.21% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.015% 23.82% 2127ms 10.95% AbstractNumericalMethod::ComputeForcesIncludingDamping 903ms 4.65% 28.47% 1920ms 9.89% std::_Rb_tree::_M_lower_bound (inline) 0 0% 28.47% 1883ms 9.70% AbstractCellPopulation::WriteResultsToFiles 168ms 0.87% 29.34% 1844ms 9.50% TetrahedralMesh::EdgeIterator::operator++ 177ms 0.91% 30.25% 1611ms 8.30% AbstractCellProperty::IsSame 52ms 0.27% 30.51% 1526ms 7.86% std::_Rb_tree::find (inline) 69ms 0.36% 30.87% 1434ms 7.39% std::type_info::operator== (inline) 1407ms 7.25% 38.12% 1407ms 7.25% __strcmp_evex 1ms 0.0052% 38.12% 1238ms 6.38% MeshBasedCellPopulation::UpdateNodePairs 44ms 0.23% 38.35% 1224ms 6.30% operator new 7ms 0.036% 38.38% 1199ms 6.18% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 6ms 0.031% 38.41% 1162ms 5.98% TetrahedralMesh::ImportFromMesher 430ms 2.21% 40.63% 1160ms 5.97% __GI___libc_malloc 19ms 0.098% 40.73% 1134ms 5.84% std::set::insert (inline) 21ms 0.11% 40.84% 1113ms 5.73% std::_Rb_tree::_M_insert_unique 13ms 0.067% 40.90% 1106ms 5.70% MeshBasedCellPopulation::SpringIterator::operator++ 1012ms 5.21% 46.11% 1012ms 5.21% [libchaste_cell_based.so] 17ms 0.088% 46.20% 989ms 5.09% std::__new_allocator::allocate (inline) 0 0% 46.20% 983ms 5.06% std::allocator_traits::allocate (inline) 0 0% 46.20% 951ms 4.90% std::set::count (inline) 3ms 0.015% 46.22% 871ms 4.49% triangulate 0 0% 46.22% 788ms 4.06% delaunay 2ms 0.01% 46.23% 787ms 4.05% divconqdelaunay 6ms 0.031% 46.26% 757ms 3.90% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 46ms 0.24% 46.50% 705ms 3.63% std::_Rb_tree::_M_insert_ (inline) 3ms 0.015% 46.51% 677ms 3.49% AbstractTwoBodyInteractionForce::AddForceContribution 675ms 3.48% 49.99% 675ms 3.48% WntCellCycleOdeSystem::CalculateStoppingEvent 13ms 0.067% 50.05% 665ms 3.42% CellPopulationElementWriter::Visit 191ms 0.98% 51.04% 665ms 3.42% __dynamic_cast 0 0% 51.04% 665ms 3.42% std::_Rb_tree::_M_create_node (inline) 661ms 3.40% 54.44% 661ms 3.40% std::_Rb_tree::_S_right (inline) 58ms 0.3% 54.74% 661ms 3.40% std::map::operator[] (partial-inline) 0 0% 54.74% 651ms 3.35% std::_Rb_tree::_M_get_node (inline) 388ms 2.00% 56.74% 628ms 3.23% _int_malloc 11ms 0.057% 56.80% 615ms 3.17% MeshBasedCellPopulation::AcceptCellWriter 18ms 0.093% 56.89% 601ms 3.10% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 0 0% 56.89% 588ms 3.03% std::_Rb_tree::_Alloc_node::operator() (inline) 291ms 1.50% 58.39% 584ms 3.01% AbstractCellMutationState::AbstractCellMutationState 3ms 0.015% 58.40% 582ms 3.00% Element::Element 0 0% 58.40% 573ms 2.95% std::map::find (inline) 2ms 0.01% 58.41% 566ms 2.91% CellPropertyCollection::GetPropertiesType (inline) 5ms 0.026% 58.44% 561ms 2.89% Element::RegisterWithNodes (inline) 20ms 0.1% 58.54% 549ms 2.83% Node::AddElement 118ms 0.61% 59.15% 533ms 2.75% __GI___libc_free 16ms 0.082% 59.23% 526ms 2.71% Cylindrical2dMesh::ReconstructCylindricalMesh 8ms 0.041% 59.27% 525ms 2.70% AbstractCellPopulation::GetCellUsingLocationIndex 19ms 0.098% 59.37% 521ms 2.68% std::less::operator() (inline) 8ms 0.041% 59.41% 515ms 2.65% MutableMesh::ReIndex 502ms 2.59% 62.00% 502ms 2.59% std::operator< (inline) 0 0% 62.00% 485ms 2.50% std::_Rb_tree::lower_bound (inline) 0 0% 62.00% 485ms 2.50% std::map::lower_bound (inline) 4ms 0.021% 62.02% 478ms 2.46% AbstractCellProperty::IsSubType (inline) 11ms 0.057% 62.07% 474ms 2.44% Cylindrical2dMesh::CorrectNonPeriodicMesh 0 0% 62.07% 474ms 2.44% std::_Rb_tree::_M_drop_node (inline) 71ms 0.37% 62.44% 466ms 2.40% std::_Rb_tree::_M_erase 39ms 0.2% 62.64% 457ms 2.35% std::_Rb_tree::~_Rb_tree (inline) 3ms 0.015% 62.66% 442ms 2.28% std::ostream::operator<< (inline) 68ms 0.35% 63.01% 435ms 2.24% std::ostream::_M_insert 0 0% 63.01% 428ms 2.20% std::set::~set (inline) 4ms 0.021% 63.03% 421ms 2.17% std::__new_allocator::deallocate (inline) 0 0% 63.03% 412ms 2.12% std::allocator_traits::deallocate (inline) 351ms 1.81% 64.83% 411ms 2.12% _int_free 12ms 0.062% 64.90% 398ms 2.05% std::_Rb_tree::erase 0 0% 64.90% 397ms 2.04% std::set::erase (inline) 10ms 0.052% 64.95% 389ms 2.00% Node::RemoveElement 11ms 0.057% 65.00% 389ms 2.00% divconqrecurse 166ms 0.85% 65.86% 387ms 1.99% std::_Rb_tree::_M_get_insert_unique_pos 104ms 0.54% 66.40% 371ms 1.91% mergehulls 1ms 0.0052% 66.40% 357ms 1.84% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 66.40% 356ms 1.83% AbstractCellPopulation::Iterator::operator++ (inline) 34ms 0.18% 66.58% 354ms 1.82% AbstractCellPopulation::Iterator::IsRealCell (inline) 11ms 0.057% 66.63% 354ms 1.82% boost::detail::shared_count::~shared_count (inline) 0 0% 66.63% 354ms 1.82% boost::shared_ptr::~shared_ptr (inline) 0 0% 66.63% 352ms 1.81% std::_Rb_tree::_M_put_node (inline) 346ms 1.78% 68.41% 346ms 1.78% [libchaste_crypt.so] 159ms 0.82% 69.23% 338ms 1.74% __cxxabiv1::__si_class_type_info::__do_dyncast 336ms 1.73% 70.96% 337ms 1.74% boost::detail::sp_counted_base::release 1ms 0.0052% 70.97% 336ms 1.73% Cell::GetCellProliferativeType 0 0% 70.97% 332ms 1.71% std::_Vector_base::_M_allocate (inline) 21ms 0.11% 71.08% 329ms 1.69% Element::ResetIndex 22ms 0.11% 71.19% 318ms 1.64% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 0 0% 71.19% 303ms 1.56% ApcOneHitCellMutationState::ApcOneHitCellMutationState 1ms 0.0052% 71.20% 301ms 1.55% Cell::GetMutationState 19ms 0.098% 71.29% 291ms 1.50% AbstractCellPopulation::GetLocationIndexUsingCell 27ms 0.14% 71.43% 288ms 1.48% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 0 0% 71.43% 284ms 1.46% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 1ms 0.0052% 71.44% 282ms 1.45% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 9ms 0.046% 71.48% 267ms 1.38% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.0052% 71.49% 267ms 1.38% NodeLocationWriter::Visit 8ms 0.041% 71.53% 262ms 1.35% std::vector::push_back (inline) 0 0% 71.53% 260ms 1.34% OffLatticeSimulation::ApplyBoundaries 3ms 0.015% 71.55% 256ms 1.32% alternateaxes 3ms 0.015% 71.56% 255ms 1.31% AbstractCellPopulation::IsCellAttachedToLocationIndex 248ms 1.28% 72.84% 254ms 1.31% std::vector::operator[] (inline) 228ms 1.17% 74.01% 252ms 1.30% vertexmedian 8ms 0.041% 74.05% 245ms 1.26% std::vector::_M_realloc_insert 12ms 0.062% 74.12% 240ms 1.24% std::_Rb_tree::_M_erase_aux (inline) 18ms 0.093% 74.21% 240ms 1.24% std::num_put::_M_insert_float 12ms 0.062% 74.27% 239ms 1.23% std::_Rb_tree::_Rb_tree 0 0% 74.27% 231ms 1.19% std::set::set (inline) 13ms 0.067% 74.34% 224ms 1.15% AbstractTetrahedralElement::CalculateJacobian 0 0% 74.34% 224ms 1.15% TetrahedralMesh::RefreshJacobianCachedData 23ms 0.12% 74.46% 212ms 1.09% std::_Rb_tree::_M_copy (inline) 210ms 1.08% 75.54% 210ms 1.08% [libchaste_mesh.so] 1ms 0.0052% 75.54% 207ms 1.07% Element::MarkAsDeleted 3ms 0.015% 75.56% 206ms 1.06% std::__cxx11::collate::do_transform 2ms 0.01% 75.57% 201ms 1.04% ___vsnprintf 0 0% 75.57% 199ms 1.02% __vsnprintf_internal (inline) 17ms 0.088% 75.66% 196ms 1.01% __printf_buffer 1ms 0.0052% 75.66% 191ms 0.98% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.0052% 75.67% 180ms 0.93% TetrahedralMesh::Clear 177ms 0.91% 76.58% 177ms 0.91% std::_Rb_tree_insert_and_rebalance 85ms 0.44% 77.01% 176ms 0.91% std::_Rb_tree::_M_clone_node (inline) 2ms 0.01% 77.03% 165ms 0.85% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 77.03% 165ms 0.85% MeshBasedCellPopulation::GetDampingConstant 163ms 0.84% 77.86% 163ms 0.84% incircle 122ms 0.63% 78.49% 163ms 0.84% malloc_consolidate 30ms 0.15% 78.65% 162ms 0.83% AbstractTetrahedralElement::RefreshJacobian 3ms 0.015% 78.66% 160ms 0.82% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 159ms 0.82% 79.48% 159ms 0.82% AbstractCellProperty::AbstractCellProperty 2ms 0.01% 79.49% 159ms 0.82% __printf_fp_l_buffer 0 0% 79.49% 159ms 0.82% __printf_fp_spec (inline) 33ms 0.17% 79.66% 157ms 0.81% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 3ms 0.015% 79.68% 157ms 0.81% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 71ms 0.37% 80.04% 155ms 0.8% __printf_fp_buffer_1 1ms 0.0052% 80.05% 150ms 0.77% CellPropertyCollection::HasProperty 0 0% 80.05% 149ms 0.77% Cell::HasCellProperty (inline) 85ms 0.44% 80.49% 149ms 0.77% std::_Rb_tree::equal_range (inline) 1ms 0.0052% 80.49% 146ms 0.75% CellProliferativeTypesWriter::VisitCell 146ms 0.75% 81.24% 146ms 0.75% std::vector::size (inline) 7ms 0.036% 81.28% 145ms 0.75% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 6ms 0.031% 81.31% 142ms 0.73% AbstractTetrahedralElement::AbstractTetrahedralElement 65ms 0.33% 81.64% 141ms 0.73% AbstractElement::GetNodeGlobalIndex 141ms 0.73% 82.37% 141ms 0.73% std::_Rb_tree::_S_left (inline) 11ms 0.057% 82.43% 139ms 0.72% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 20ms 0.1% 82.53% 137ms 0.71% TetrahedralMesh::EdgesEnd (partial-inline) 128ms 0.66% 83.19% 137ms 0.71% vertexsort 1ms 0.0052% 83.20% 132ms 0.68% boost::numeric::ublas::vector_assign (inline) 3ms 0.015% 83.21% 131ms 0.67% Cell::SetCellProliferativeType 0 0% 83.21% 130ms 0.67% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 83.21% 127ms 0.65% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 4ms 0.021% 83.23% 126ms 0.65% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 83.23% 125ms 0.64% std::__new_allocator::destroy (inline) 0 0% 83.23% 125ms 0.64% std::allocator_traits::destroy (inline) 0 0% 83.23% 124ms 0.64% std::_Rb_tree::_M_destroy_node (inline) 1ms 0.0052% 83.24% 123ms 0.63% MeshBasedCellPopulation::SpringsEnd (inline) 8ms 0.041% 83.28% 121ms 0.62% boost::numeric::ublas::c_vector::c_vector (inline) 6ms 0.031% 83.31% 120ms 0.62% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 120ms 0.62% 83.93% 120ms 0.62% std::type_info::name (inline) 49ms 0.25% 84.18% 118ms 0.61% AbstractElement::GetNodeLocation 5ms 0.026% 84.20% 117ms 0.6% Cylindrical2dMesh::CreateMirrorNodes 6ms 0.031% 84.24% 117ms 0.6% std::_Rb_tree::_M_emplace_hint_unique 2ms 0.01% 84.25% 114ms 0.59% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 4ms 0.021% 84.27% 104ms 0.54% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.01% 84.28% 103ms 0.53% Node::~Node 57ms 0.29% 84.57% 101ms 0.52% Cylindrical2dMesh::GetVectorFromAtoB 19ms 0.098% 84.67% 100ms 0.52% MeshBasedCellPopulation::SpringIterator::SpringIterator 80ms 0.41% 85.08% 100ms 0.52% TetrahedralMesh::EdgeIterator::EdgeIterator 31ms 0.16% 85.24% 99ms 0.51% std::num_put::_M_insert_int