File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16885ms, 84.08% of 20082ms total Dropped 780 nodes (cum <= 100.41ms) flat flat% sum% cum cum% 0 0% 0% 20038ms 99.78% __libc_start_call_main 0 0% 0% 20038ms 99.78% __libc_start_main_impl 0 0% 0% 20038ms 99.78% _start 0 0% 0% 20019ms 99.69% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 20019ms 99.69% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 20019ms 99.69% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 20019ms 99.69% main 0 0% 0% 19978ms 99.48% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19978ms 99.48% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19978ms 99.48% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19952ms 99.35% AbstractCellBasedSimulation::Solve 0 0% 0% 15451ms 76.94% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.005% 0.005% 10155ms 50.57% AbstractCellBasedSimulation::DoCellBirth 3ms 0.015% 0.02% 10071ms 50.15% Cell::ReadyToDivide 2ms 0.01% 0.03% 10012ms 49.86% AbstractPhaseBasedCellCycleModel::ReadyToDivide 16ms 0.08% 0.11% 9868ms 49.14% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 0.11% 9868ms 49.14% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.005% 0.11% 9850ms 49.05% CellCycleModelOdeHandler::SolveOdeToTime 63ms 0.31% 0.43% 9674ms 48.17% AbstractOneStepIvpOdeSolver::InternalSolve 845ms 4.21% 4.64% 8860ms 44.12% RungeKutta4IvpOdeSolver::CalculateNextYValue 3720ms 18.52% 23.16% 7817ms 38.93% WntCellCycleOdeSystem::EvaluateYDerivatives 3ms 0.015% 23.17% 5176ms 25.77% MeshBasedCellPopulation::Update 191ms 0.95% 24.13% 4129ms 20.56% AbstractCellProperty::IsType (inline) 7ms 0.035% 24.16% 3963ms 19.73% Cylindrical2dMesh::ReMesh 565ms 2.81% 26.97% 2865ms 14.27% AbstractCellProperty::IsSame 0 0% 26.97% 2516ms 12.53% OffLatticeSimulation::UpdateCellLocationsAndTopology 422ms 2.10% 29.08% 2300ms 11.45% std::type_info::operator== (inline) 1ms 0.005% 29.08% 2197ms 10.94% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 29.08% 2175ms 10.83% MutableMesh::ReMesh 11ms 0.055% 29.14% 2158ms 10.75% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 29.14% 1979ms 9.85% AbstractCellPopulation::WriteResultsToFiles 795ms 3.96% 33.09% 1845ms 9.19% std::_Rb_tree::_M_lower_bound (inline) 1824ms 9.08% 42.18% 1824ms 9.08% __strcmp_avx2 166ms 0.83% 43.00% 1710ms 8.52% TetrahedralMesh::EdgeIterator::operator++ 65ms 0.32% 43.33% 1411ms 7.03% std::_Rb_tree::find (inline) 0 0% 43.33% 1163ms 5.79% MeshBasedCellPopulation::UpdateNodePairs 11ms 0.055% 43.38% 1126ms 5.61% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 19ms 0.095% 43.48% 1097ms 5.46% TetrahedralMesh::ImportFromMesher 39ms 0.19% 43.67% 1082ms 5.39% operator new 10ms 0.05% 43.72% 1052ms 5.24% MeshBasedCellPopulation::SpringIterator::operator++ 223ms 1.11% 44.83% 1018ms 5.07% __GI___libc_malloc 7ms 0.035% 44.87% 989ms 4.92% std::set::insert (inline) 10ms 0.05% 44.92% 982ms 4.89% std::_Rb_tree::_M_insert_unique 50ms 0.25% 45.16% 937ms 4.67% std::__new_allocator::allocate (inline) 0 0% 45.16% 926ms 4.61% std::allocator_traits::allocate (inline) 0 0% 45.16% 864ms 4.30% std::set::count (inline) 1ms 0.005% 45.17% 830ms 4.13% triangulate 0 0% 45.17% 763ms 3.80% delaunay 3ms 0.015% 45.18% 763ms 3.80% divconqdelaunay 409ms 2.04% 47.22% 724ms 3.61% _int_malloc 2ms 0.01% 47.23% 718ms 3.58% AbstractTwoBodyInteractionForce::AddForceContribution 6ms 0.03% 47.26% 713ms 3.55% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 11ms 0.055% 47.32% 686ms 3.42% CellPopulationElementWriter::Visit 48ms 0.24% 47.56% 683ms 3.40% std::map::operator[] (partial-inline) 669ms 3.33% 50.89% 669ms 3.33% std::_Rb_tree::_S_right (inline) 28ms 0.14% 51.03% 666ms 3.32% std::less::operator() (inline) 196ms 0.98% 52.00% 652ms 3.25% __dynamic_cast 638ms 3.18% 55.18% 638ms 3.18% std::operator< (inline) 617ms 3.07% 58.25% 629ms 3.13% WntCellCycleOdeSystem::CalculateStoppingEvent 0 0% 58.25% 610ms 3.04% std::_Rb_tree::_M_create_node (inline) 9ms 0.045% 58.30% 604ms 3.01% CellPropertyCollection::GetPropertiesType (inline) 24ms 0.12% 58.42% 598ms 2.98% std::_Rb_tree::_M_insert_ (inline) 22ms 0.11% 58.53% 582ms 2.90% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 0 0% 58.53% 571ms 2.84% std::_Rb_tree::_M_get_node (inline) 2ms 0.01% 58.54% 568ms 2.83% MeshBasedCellPopulation::AcceptCellWriter 0 0% 58.54% 557ms 2.77% std::_Rb_tree::_Alloc_node::operator() (inline) 15ms 0.075% 58.61% 546ms 2.72% AbstractCellPopulation::GetCellUsingLocationIndex 6ms 0.03% 58.64% 546ms 2.72% Element::Element 0 0% 58.64% 543ms 2.70% std::map::find (inline) 0 0% 58.64% 538ms 2.68% std::_Rb_tree::lower_bound (inline) 0 0% 58.64% 538ms 2.68% std::map::lower_bound (inline) 8ms 0.04% 58.68% 523ms 2.60% Cylindrical2dMesh::ReconstructCylindricalMesh 12ms 0.06% 58.74% 512ms 2.55% MutableMesh::ReIndex 1ms 0.005% 58.74% 481ms 2.40% AbstractCellProperty::IsSubType (inline) 7ms 0.035% 58.78% 471ms 2.35% Element::RegisterWithNodes (inline) 17ms 0.085% 58.86% 469ms 2.34% Cylindrical2dMesh::CorrectNonPeriodicMesh 7ms 0.035% 58.90% 467ms 2.33% Node::AddElement 53ms 0.26% 59.16% 460ms 2.29% std::ostream::_M_insert 0 0% 59.16% 460ms 2.29% std::ostream::operator<< (inline) 303ms 1.51% 60.67% 454ms 2.26% AbstractCellMutationState::AbstractCellMutationState 141ms 0.7% 61.37% 421ms 2.10% __GI___libc_free 16ms 0.08% 61.45% 402ms 2.00% divconqrecurse 119ms 0.59% 62.05% 377ms 1.88% mergehulls 139ms 0.69% 62.74% 374ms 1.86% std::_Rb_tree::_M_get_insert_unique_pos 18ms 0.09% 62.83% 359ms 1.79% Node::RemoveElement 4ms 0.02% 62.85% 359ms 1.79% std::_Vector_base::_M_allocate (inline) 10ms 0.05% 62.90% 357ms 1.78% std::_Rb_tree::erase 1ms 0.005% 62.90% 357ms 1.78% std::set::erase (inline) 115ms 0.57% 63.47% 339ms 1.69% std::_Rb_tree::_M_erase 167ms 0.83% 64.31% 335ms 1.67% __cxxabiv1::__si_class_type_info::__do_dyncast 22ms 0.11% 64.42% 329ms 1.64% std::_Rb_tree::~_Rb_tree (inline) 7ms 0.035% 64.45% 326ms 1.62% Cell::GetMutationState 10ms 0.05% 64.50% 324ms 1.61% std::__new_allocator::deallocate (inline) 21ms 0.1% 64.61% 322ms 1.60% Element::ResetIndex 0 0% 64.61% 318ms 1.58% std::allocator_traits::deallocate (inline) 4ms 0.02% 64.63% 315ms 1.57% Cell::GetCellProliferativeType 11ms 0.055% 64.68% 314ms 1.56% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 7ms 0.035% 64.71% 309ms 1.54% AbstractCellPopulation::GetLocationIndexUsingCell 2ms 0.01% 64.72% 306ms 1.52% NodeLocationWriter::Visit 0 0% 64.72% 306ms 1.52% std::set::~set (inline) 0 0% 64.72% 301ms 1.50% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 64.72% 300ms 1.49% std::_Rb_tree::_M_drop_node (inline) 299ms 1.49% 66.21% 299ms 1.49% std::type_info::name (inline) 35ms 0.17% 66.39% 297ms 1.48% AbstractCellPopulation::Iterator::IsRealCell (inline) 4ms 0.02% 66.41% 289ms 1.44% LegacyCellProliferativeTypesWriter::VisitCell 228ms 1.14% 67.54% 280ms 1.39% _int_free 19ms 0.095% 67.64% 266ms 1.32% std::num_put::_M_insert_float 7ms 0.035% 67.67% 263ms 1.31% std::vector::push_back (inline) 12ms 0.06% 67.73% 260ms 1.29% std::_Rb_tree::_Rb_tree (partial-inline) 21ms 0.1% 67.84% 256ms 1.27% AbstractTetrahedralElement::CalculateJacobian 0 0% 67.84% 254ms 1.26% std::_Rb_tree::_M_put_node (inline) 8ms 0.04% 67.88% 252ms 1.25% AbstractCellPopulation::IsCellAttachedToLocationIndex 247ms 1.23% 69.11% 247ms 1.23% [libchaste_cell_based.so] 13ms 0.065% 69.17% 247ms 1.23% std::vector::_M_realloc_insert 8ms 0.04% 69.21% 243ms 1.21% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 0 0% 69.21% 242ms 1.21% alternateaxes 229ms 1.14% 70.35% 242ms 1.21% vertexmedian 4ms 0.02% 70.37% 234ms 1.17% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 60ms 0.3% 70.67% 233ms 1.16% ApcOneHitCellMutationState::ApcOneHitCellMutationState 232ms 1.16% 71.83% 233ms 1.16% std::vector::operator[] (inline) 3ms 0.015% 71.84% 230ms 1.15% std::set::set (inline) 25ms 0.12% 71.96% 228ms 1.14% std::_Rb_tree::_M_copy (inline) 2ms 0.01% 71.97% 224ms 1.12% TetrahedralMesh::RefreshJacobianCachedData 13ms 0.065% 72.04% 222ms 1.11% std::_Rb_tree::_M_erase_aux (inline) 6ms 0.03% 72.07% 215ms 1.07% std::__cxx11::collate::do_transform 156ms 0.78% 72.85% 213ms 1.06% malloc_consolidate 0 0% 72.85% 210ms 1.05% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 72.85% 210ms 1.05% MeshBasedCellPopulation::GetDampingConstant 21ms 0.1% 72.95% 208ms 1.04% Element::MarkAsDeleted 1ms 0.005% 72.96% 208ms 1.04% ___vsnprintf 0 0% 72.96% 207ms 1.03% __vsnprintf_internal (inline) 20ms 0.1% 73.06% 206ms 1.03% __printf_buffer 0 0% 73.06% 201ms 1.00% OffLatticeSimulation::ApplyBoundaries 58ms 0.29% 73.34% 201ms 1.00% std::_Rb_tree::_M_clone_node (inline) 24ms 0.12% 73.46% 197ms 0.98% AbstractTetrahedralElement::RefreshJacobian 162ms 0.81% 74.27% 196ms 0.98% AbstractElement::GetNodeGlobalIndex 195ms 0.97% 75.24% 195ms 0.97% Node::GetIndex 66ms 0.33% 75.57% 194ms 0.97% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 6ms 0.03% 75.60% 191ms 0.95% AbstractTetrahedralElement::AbstractTetrahedralElement 34ms 0.17% 75.77% 191ms 0.95% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 189ms 0.94% 76.71% 189ms 0.94% std::_Rb_tree_insert_and_rebalance 11ms 0.055% 76.77% 185ms 0.92% AbstractTetrahedralElement::CalculateInverseJacobian 15ms 0.075% 76.84% 179ms 0.89% TetrahedralMesh::Clear 7ms 0.035% 76.87% 170ms 0.85% __printf_fp_l_buffer 0 0% 76.87% 170ms 0.85% __printf_fp_spec (inline) 3ms 0.015% 76.89% 169ms 0.84% CellProliferativeTypesWriter::VisitCell 1ms 0.005% 76.89% 160ms 0.8% boost::numeric::ublas::vector_assign (inline) 65ms 0.32% 77.22% 158ms 0.79% AbstractElement::GetNodeLocation 75ms 0.37% 77.59% 155ms 0.77% __printf_fp_buffer_1 154ms 0.77% 78.36% 154ms 0.77% incircle 7ms 0.035% 78.39% 148ms 0.74% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 43ms 0.21% 78.61% 147ms 0.73% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 34ms 0.17% 78.78% 147ms 0.73% TetrahedralMesh::EdgesEnd 7ms 0.035% 78.81% 142ms 0.71% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 0 0% 78.81% 140ms 0.7% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 140ms 0.7% 79.51% 140ms 0.7% unlink_chunk 4ms 0.02% 79.53% 137ms 0.68% CellPropertyCollection::HasProperty 6ms 0.03% 79.56% 134ms 0.67% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 79.56% 133ms 0.66% Cell::HasCellProperty (inline) 83ms 0.41% 79.97% 132ms 0.66% Cylindrical2dMesh::GetVectorFromAtoB 86ms 0.43% 80.40% 132ms 0.66% std::_Rb_tree::equal_range (inline) 0 0% 80.40% 129ms 0.64% AbstractCellBasedWriter::OpenOutputFileForAppend 15ms 0.075% 80.48% 129ms 0.64% boost::detail::shared_count::~shared_count (inline) 0 0% 80.48% 129ms 0.64% boost::shared_ptr::~shared_ptr (inline) 129ms 0.64% 81.12% 129ms 0.64% std::vector::size (inline) 44ms 0.22% 81.34% 127ms 0.63% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 0 0% 81.34% 126ms 0.63% OutputFileHandler::OpenOutputFile 124ms 0.62% 81.95% 124ms 0.62% AbstractCellMutationState::~AbstractCellMutationState 12ms 0.06% 82.01% 123ms 0.61% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 35ms 0.17% 82.19% 123ms 0.61% boost::numeric::ublas::indexing_vector_assign 2ms 0.01% 82.20% 122ms 0.61% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 82.20% 120ms 0.6% AbstractCellBasedSimulation::DoCellRemoval (inline) 1ms 0.005% 82.20% 119ms 0.59% Cell::SetCellProliferativeType 0 0% 82.20% 112ms 0.56% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 110ms 0.55% 82.75% 112ms 0.56% boost::detail::sp_counted_base::release 4ms 0.02% 82.77% 109ms 0.54% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 105ms 0.52% 83.29% 105ms 0.52% std::_Rb_tree_rebalance_for_erase 43ms 0.21% 83.51% 104ms 0.52% std::__ostream_insert 0 0% 83.51% 103ms 0.51% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 25ms 0.12% 83.63% 103ms 0.51% std::num_put::_M_insert_int 90ms 0.45% 84.08% 103ms 0.51% vertexsort