File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16801ms, 85.56% of 19637ms total Dropped 768 nodes (cum <= 98.19ms) flat flat% sum% cum cum% 0 0% 0% 19592ms 99.77% __libc_start_call_main 0 0% 0% 19592ms 99.77% __libc_start_main_impl 0 0% 0% 19592ms 99.77% _start 0 0% 0% 19571ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19571ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19571ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19571ms 99.66% main 0 0% 0% 19525ms 99.43% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19525ms 99.43% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19525ms 99.43% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 1ms 0.0051% 0.0051% 19499ms 99.30% AbstractCellBasedSimulation::Solve 0 0% 0.0051% 14917ms 75.96% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0051% 0.01% 9393ms 47.83% AbstractCellBasedSimulation::DoCellBirth 5ms 0.025% 0.036% 9296ms 47.34% Cell::ReadyToDivide 4ms 0.02% 0.056% 9217ms 46.94% AbstractPhaseBasedCellCycleModel::ReadyToDivide 4ms 0.02% 0.076% 9067ms 46.17% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 10ms 0.051% 0.13% 9054ms 46.11% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 6ms 0.031% 0.16% 9041ms 46.04% CellCycleModelOdeHandler::SolveOdeToTime 50ms 0.25% 0.41% 8874ms 45.19% AbstractOneStepIvpOdeSolver::InternalSolve 1004ms 5.11% 5.53% 7951ms 40.49% RungeKutta4IvpOdeSolver::CalculateNextYValue 2764ms 14.08% 19.60% 6761ms 34.43% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.0051% 19.61% 5414ms 27.57% MeshBasedCellPopulation::Update 3ms 0.015% 19.62% 4201ms 21.39% Cylindrical2dMesh::ReMesh 76ms 0.39% 20.01% 3990ms 20.32% AbstractCellProperty::IsType (inline) 1ms 0.0051% 20.01% 2599ms 13.24% OffLatticeSimulation::UpdateCellLocationsAndTopology 354ms 1.80% 21.82% 2587ms 13.17% AbstractCellProperty::IsSame 0 0% 21.82% 2281ms 11.62% MutableMesh::ReMesh 1ms 0.0051% 21.82% 2255ms 11.48% ForwardEulerNumericalMethod::UpdateAllNodePositions 255ms 1.30% 23.12% 2233ms 11.37% std::type_info::operator== (inline) 9ms 0.046% 23.17% 2211ms 11.26% AbstractNumericalMethod::ComputeForcesIncludingDamping 2066ms 10.52% 33.69% 2066ms 10.52% __strcmp_avx2 0 0% 33.69% 1976ms 10.06% AbstractCellPopulation::WriteResultsToFiles 823ms 4.19% 37.88% 1874ms 9.54% std::_Rb_tree::_M_lower_bound (inline) 175ms 0.89% 38.77% 1668ms 8.49% TetrahedralMesh::EdgeIterator::operator++ 55ms 0.28% 39.05% 1387ms 7.06% std::_Rb_tree::find (inline) 0 0% 39.05% 1176ms 5.99% MeshBasedCellPopulation::UpdateNodePairs 12ms 0.061% 39.11% 1149ms 5.85% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 16ms 0.081% 39.19% 1144ms 5.83% TetrahedralMesh::ImportFromMesher 53ms 0.27% 39.46% 1045ms 5.32% operator new 14ms 0.071% 39.53% 1038ms 5.29% MeshBasedCellPopulation::SpringIterator::operator++ 10ms 0.051% 39.58% 1009ms 5.14% std::set::insert (inline) 16ms 0.081% 39.66% 1000ms 5.09% std::_Rb_tree::_M_insert_unique 247ms 1.26% 40.92% 982ms 5.00% __GI___libc_malloc 32ms 0.16% 41.09% 913ms 4.65% std::__new_allocator::allocate (inline) 0 0% 41.09% 909ms 4.63% std::allocator_traits::allocate (inline) 3ms 0.015% 41.10% 858ms 4.37% triangulate 0 0% 41.10% 823ms 4.19% std::set::count (inline) 0 0% 41.10% 777ms 3.96% delaunay 1ms 0.0051% 41.11% 776ms 3.95% divconqdelaunay 741ms 3.77% 44.88% 741ms 3.77% WntCellCycleOdeSystem::CalculateStoppingEvent 727ms 3.70% 48.58% 727ms 3.70% std::_Rb_tree::_S_right (inline) 2ms 0.01% 48.59% 726ms 3.70% AbstractTwoBodyInteractionForce::AddForceContribution 5ms 0.025% 48.62% 724ms 3.69% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 54ms 0.27% 48.89% 712ms 3.63% std::map::operator[] (partial-inline) 6ms 0.031% 48.92% 689ms 3.51% CellPopulationElementWriter::Visit 252ms 1.28% 50.21% 686ms 3.49% __dynamic_cast 388ms 1.98% 52.18% 662ms 3.37% _int_malloc 10ms 0.051% 52.23% 640ms 3.26% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 7ms 0.036% 52.27% 637ms 3.24% CellPropertyCollection::GetPropertiesType (inline) 20ms 0.1% 52.37% 618ms 3.15% std::less::operator() (inline) 0 0% 52.37% 609ms 3.10% std::_Rb_tree::_M_create_node (inline) 37ms 0.19% 52.56% 601ms 3.06% std::_Rb_tree::_M_insert_ (inline) 18ms 0.092% 52.65% 600ms 3.06% AbstractCellPopulation::GetCellUsingLocationIndex 598ms 3.05% 55.70% 598ms 3.05% std::operator< (inline) 0 0% 55.70% 579ms 2.95% std::_Rb_tree::_M_get_node (inline) 6ms 0.031% 55.73% 567ms 2.89% MutableMesh::ReIndex 4ms 0.02% 55.75% 565ms 2.88% MeshBasedCellPopulation::AcceptCellWriter 0 0% 55.75% 558ms 2.84% std::_Rb_tree::lower_bound (inline) 0 0% 55.75% 558ms 2.84% std::map::find (inline) 0 0% 55.75% 558ms 2.84% std::map::lower_bound (inline) 0 0% 55.75% 547ms 2.79% std::_Rb_tree::_Alloc_node::operator() (inline) 4ms 0.02% 55.77% 542ms 2.76% Element::Element 7ms 0.036% 55.80% 507ms 2.58% Cylindrical2dMesh::CorrectNonPeriodicMesh 3ms 0.015% 55.82% 507ms 2.58% std::ostream::operator<< (inline) 3ms 0.015% 55.83% 504ms 2.57% AbstractCellProperty::IsSubType (inline) 61ms 0.31% 56.14% 504ms 2.57% std::ostream::_M_insert 11ms 0.056% 56.20% 501ms 2.55% Cylindrical2dMesh::ReconstructCylindricalMesh 13ms 0.066% 56.27% 499ms 2.54% Element::RegisterWithNodes (inline) 147ms 0.75% 57.01% 488ms 2.49% __GI___libc_free 11ms 0.056% 57.07% 484ms 2.46% Node::AddElement 294ms 1.50% 58.57% 448ms 2.28% AbstractCellMutationState::AbstractCellMutationState 19ms 0.097% 58.66% 426ms 2.17% Node::RemoveElement 6ms 0.031% 58.70% 420ms 2.14% std::_Rb_tree::erase 1ms 0.0051% 58.70% 419ms 2.13% std::set::erase (inline) 115ms 0.59% 59.29% 397ms 2.02% std::_Rb_tree::_M_erase 10ms 0.051% 59.34% 390ms 1.99% std::__new_allocator::deallocate (inline) 0 0% 59.34% 388ms 1.98% std::allocator_traits::deallocate (inline) 140ms 0.71% 60.05% 385ms 1.96% std::_Rb_tree::_M_get_insert_unique_pos 26ms 0.13% 60.18% 377ms 1.92% Element::ResetIndex 29ms 0.15% 60.33% 373ms 1.90% std::_Rb_tree::~_Rb_tree (inline) 16ms 0.081% 60.41% 368ms 1.87% divconqrecurse 2ms 0.01% 60.42% 354ms 1.80% Cell::GetMutationState 0 0% 60.42% 354ms 1.80% std::_Rb_tree::_M_drop_node (inline) 112ms 0.57% 60.99% 346ms 1.76% mergehulls 0 0% 60.99% 343ms 1.75% std::set::~set (inline) 7ms 0.036% 61.03% 340ms 1.73% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 267ms 1.36% 62.39% 340ms 1.73% _int_free 338ms 1.72% 64.11% 338ms 1.72% [libchaste_cell_based.so] 164ms 0.84% 64.94% 336ms 1.71% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 64.94% 330ms 1.68% std::_Vector_base::_M_allocate (inline) 2ms 0.01% 64.95% 326ms 1.66% Cell::GetCellProliferativeType 0 0% 64.95% 318ms 1.62% std::_Rb_tree::_M_put_node (inline) 3ms 0.015% 64.97% 317ms 1.61% NodeLocationWriter::Visit 7ms 0.036% 65.00% 302ms 1.54% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 65.00% 301ms 1.53% AbstractCellPopulation::Iterator::operator++ (inline) 38ms 0.19% 65.20% 298ms 1.52% AbstractCellPopulation::Iterator::IsRealCell (inline) 16ms 0.081% 65.28% 290ms 1.48% std::num_put::_M_insert_float 16ms 0.081% 65.36% 275ms 1.40% std::vector::push_back (inline) 6ms 0.031% 65.39% 265ms 1.35% alternateaxes 10ms 0.051% 65.44% 262ms 1.33% std::_Rb_tree::_Rb_tree (partial-inline) 2ms 0.01% 65.45% 259ms 1.32% LegacyCellProliferativeTypesWriter::VisitCell 240ms 1.22% 66.68% 259ms 1.32% vertexmedian 103ms 0.52% 67.20% 257ms 1.31% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 12ms 0.061% 67.26% 257ms 1.31% std::_Rb_tree::_M_erase_aux (inline) 1ms 0.0051% 67.27% 255ms 1.30% MeshBasedCellPopulation::GetDampingConstant 255ms 1.30% 68.56% 255ms 1.30% std::vector::operator[] (inline) 2ms 0.01% 68.57% 254ms 1.29% AbstractCentreBasedCellPopulation::GetDampingConstant 64ms 0.33% 68.90% 252ms 1.28% ApcOneHitCellMutationState::ApcOneHitCellMutationState 24ms 0.12% 69.02% 251ms 1.28% TetrahedralMesh::Clear 0 0% 69.02% 250ms 1.27% TetrahedralMesh::RefreshJacobianCachedData 6ms 0.031% 69.05% 250ms 1.27% std::__cxx11::collate::do_transform 14ms 0.071% 69.12% 246ms 1.25% AbstractTetrahedralElement::CalculateJacobian 99ms 0.5% 69.63% 246ms 1.25% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 17ms 0.087% 69.72% 245ms 1.25% std::vector::_M_realloc_insert 1ms 0.0051% 69.72% 237ms 1.21% ___vsnprintf 2ms 0.01% 69.73% 237ms 1.21% std::set::set (inline) 7ms 0.036% 69.77% 236ms 1.20% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 2ms 0.01% 69.78% 236ms 1.20% __vsnprintf_internal (inline) 4ms 0.02% 69.80% 234ms 1.19% AbstractCellPopulation::IsCellAttachedToLocationIndex 20ms 0.1% 69.90% 232ms 1.18% __printf_buffer 3ms 0.015% 69.91% 224ms 1.14% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.0051% 69.92% 224ms 1.14% OffLatticeSimulation::ApplyBoundaries 23ms 0.12% 70.04% 223ms 1.14% std::_Rb_tree::_M_copy (inline) 10ms 0.051% 70.09% 218ms 1.11% AbstractTetrahedralElement::CalculateInverseJacobian 14ms 0.071% 70.16% 216ms 1.10% Element::MarkAsDeleted 136ms 0.69% 70.85% 204ms 1.04% AbstractElement::GetNodeGlobalIndex 64ms 0.33% 71.18% 197ms 1.00% std::_Rb_tree::_M_clone_node (inline) 2ms 0.01% 71.19% 195ms 0.99% __printf_fp_l_buffer 0 0% 71.19% 195ms 0.99% __printf_fp_spec (inline) 80ms 0.41% 71.59% 191ms 0.97% __printf_fp_buffer_1 26ms 0.13% 71.73% 187ms 0.95% AbstractTetrahedralElement::RefreshJacobian 4ms 0.02% 71.75% 184ms 0.94% CellProliferativeTypesWriter::VisitCell 124ms 0.63% 72.38% 179ms 0.91% malloc_consolidate 176ms 0.9% 73.27% 176ms 0.9% std::vector::size (inline) 106ms 0.54% 73.81% 164ms 0.84% std::_Rb_tree::equal_range (inline) 160ms 0.81% 74.63% 160ms 0.81% std::_Rb_tree_insert_and_rebalance 8ms 0.041% 74.67% 158ms 0.8% AbstractTetrahedralElement::AbstractTetrahedralElement 11ms 0.056% 74.73% 155ms 0.79% MeshBasedCellPopulation::SpringsEnd (inline) 40ms 0.2% 74.93% 155ms 0.79% TetrahedralMesh::EdgesEnd (partial-inline) 155ms 0.79% 75.72% 155ms 0.79% std::type_info::name (inline) 150ms 0.76% 76.48% 150ms 0.76% Node::GetIndex 149ms 0.76% 77.24% 149ms 0.76% incircle 6ms 0.031% 77.27% 148ms 0.75% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 47ms 0.24% 77.51% 147ms 0.75% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 145ms 0.74% 78.25% 145ms 0.74% AbstractCellMutationState::~AbstractCellMutationState 6ms 0.031% 78.28% 144ms 0.73% boost::numeric::ublas::vector_assign (inline) 144ms 0.73% 79.01% 144ms 0.73% unlink_chunk 58ms 0.3% 79.31% 143ms 0.73% AbstractElement::GetNodeLocation 2ms 0.01% 79.32% 143ms 0.73% CellPropertyCollection::HasProperty 0 0% 79.32% 141ms 0.72% Cell::HasCellProperty (inline) 11ms 0.056% 79.38% 141ms 0.72% Node::~Node 8ms 0.041% 79.42% 141ms 0.72% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 88ms 0.45% 79.86% 140ms 0.71% Cylindrical2dMesh::GetVectorFromAtoB 2ms 0.01% 79.87% 138ms 0.7% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 138ms 0.7% 80.58% 138ms 0.7% std::_Rb_tree_increment 44ms 0.22% 80.80% 137ms 0.7% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 127ms 0.65% 81.45% 135ms 0.69% vertexsort 44ms 0.22% 81.67% 134ms 0.68% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 126ms 0.64% 82.31% 126ms 0.64% [libchaste_crypt.so] 3ms 0.015% 82.33% 126ms 0.64% std::_Rb_tree_const_iterator::operator++ (inline) 9ms 0.046% 82.38% 123ms 0.63% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.0051% 82.38% 119ms 0.61% Cell::SetCellProliferativeType 34ms 0.17% 82.55% 119ms 0.61% std::__ostream_insert 15ms 0.076% 82.63% 118ms 0.6% MeshBasedCellPopulation::SpringIterator::SpringIterator 9ms 0.046% 82.68% 116ms 0.59% boost::detail::shared_count::~shared_count (inline) 0 0% 82.68% 116ms 0.59% boost::shared_ptr::~shared_ptr (inline) 3ms 0.015% 82.69% 115ms 0.59% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 113ms 0.58% 83.27% 113ms 0.58% TetrahedralMesh::EdgeIterator::operator!= 26ms 0.13% 83.40% 113ms 0.58% boost::numeric::ublas::indexing_vector_assign 24ms 0.12% 83.52% 112ms 0.57% std::num_put::_M_insert_int 0 0% 83.52% 108ms 0.55% AbstractCellBasedSimulation::DoCellRemoval (inline) 1ms 0.0051% 83.53% 108ms 0.55% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 71ms 0.36% 83.89% 108ms 0.55% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 2ms 0.01% 83.90% 107ms 0.54% std::operator<< (inline) 106ms 0.54% 84.44% 106ms 0.54% [libchaste_mesh.so] 103ms 0.52% 84.96% 103ms 0.52% std::_Rb_tree_rebalance_for_erase 1ms 0.0051% 84.97% 101ms 0.51% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 10ms 0.051% 85.02% 100ms 0.51% Cylindrical2dMesh::CreateMirrorNodes 7ms 0.036% 85.05% 100ms 0.51% std::_Rb_tree::_M_emplace_hint_unique 99ms 0.5% 85.56% 99ms 0.5% boost::shared_ptr::operator-> (inline)