File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 13989ms, 85.90% of 16285ms total Dropped 739 nodes (cum <= 81.42ms) flat flat% sum% cum cum% 0 0% 0% 16249ms 99.78% __libc_start_call_main 0 0% 0% 16249ms 99.78% __libc_start_main_impl 0 0% 0% 16249ms 99.78% _start 0 0% 0% 16230ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 16230ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 16230ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 16230ms 99.66% main 0 0% 0% 16195ms 99.45% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 16195ms 99.45% CxxTest::TestRunner::runTest (inline) 0 0% 0% 16195ms 99.45% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 16174ms 99.32% AbstractCellBasedSimulation::Solve 0 0% 0% 12400ms 76.14% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 7768ms 47.70% AbstractCellBasedSimulation::DoCellBirth 4ms 0.025% 0.025% 7686ms 47.20% Cell::ReadyToDivide 3ms 0.018% 0.043% 7640ms 46.91% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.043% 7501ms 46.06% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 9ms 0.055% 0.098% 7497ms 46.04% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.0061% 0.1% 7485ms 45.96% CellCycleModelOdeHandler::SolveOdeToTime 44ms 0.27% 0.37% 7332ms 45.02% AbstractOneStepIvpOdeSolver::InternalSolve 661ms 4.06% 4.43% 6595ms 40.50% RungeKutta4IvpOdeSolver::CalculateNextYValue 2952ms 18.13% 22.56% 5687ms 34.92% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 22.56% 4526ms 27.79% MeshBasedCellPopulation::Update 1ms 0.0061% 22.57% 3423ms 21.02% Cylindrical2dMesh::ReMesh 324ms 1.99% 24.56% 2854ms 17.53% AbstractCellProperty::IsType (inline) 1ms 0.0061% 24.56% 2186ms 13.42% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 24.56% 1895ms 11.64% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0061% 24.57% 1870ms 11.48% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 24.57% 1869ms 11.48% MutableMesh::ReMesh 744ms 4.57% 29.14% 1593ms 9.78% std::_Rb_tree::_M_lower_bound (inline) 0 0% 29.14% 1582ms 9.71% AbstractCellPopulation::WriteResultsToFiles 142ms 0.87% 30.01% 1524ms 9.36% TetrahedralMesh::EdgeIterator::operator++ 46ms 0.28% 30.29% 1274ms 7.82% std::_Rb_tree::find (inline) 141ms 0.87% 31.16% 1228ms 7.54% AbstractCellProperty::IsSame 39ms 0.24% 31.40% 1087ms 6.67% std::type_info::operator== (inline) 1075ms 6.60% 38.00% 1075ms 6.60% __strcmp_evex 0 0% 38.00% 1064ms 6.53% MeshBasedCellPopulation::UpdateNodePairs 52ms 0.32% 38.32% 1011ms 6.21% operator new 7ms 0.043% 38.36% 987ms 6.06% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 25ms 0.15% 38.51% 953ms 5.85% MeshBasedCellPopulation::SpringIterator::operator++ 5ms 0.031% 38.54% 942ms 5.78% TetrahedralMesh::ImportFromMesher 345ms 2.12% 40.66% 942ms 5.78% __GI___libc_malloc 13ms 0.08% 40.74% 930ms 5.71% std::set::insert (inline) 9ms 0.055% 40.80% 915ms 5.62% std::_Rb_tree::_M_insert_unique 19ms 0.12% 40.91% 854ms 5.24% std::__new_allocator::allocate (inline) 0 0% 40.91% 845ms 5.19% std::allocator_traits::allocate (inline) 784ms 4.81% 45.73% 784ms 4.81% [libchaste_cell_based.so] 0 0% 45.73% 775ms 4.76% std::set::count (inline) 0 0% 45.73% 724ms 4.45% triangulate 7ms 0.043% 45.77% 641ms 3.94% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 0 0% 45.77% 639ms 3.92% delaunay 4ms 0.025% 45.80% 638ms 3.92% divconqdelaunay 2ms 0.012% 45.81% 610ms 3.75% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 45.81% 599ms 3.68% std::_Rb_tree::_M_create_node (inline) 0 0% 45.81% 584ms 3.59% std::_Rb_tree::_M_get_node (inline) 46ms 0.28% 46.09% 581ms 3.57% std::_Rb_tree::_M_insert_ (inline) 22ms 0.14% 46.23% 551ms 3.38% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 7ms 0.043% 46.27% 547ms 3.36% CellPopulationElementWriter::Visit 545ms 3.35% 49.62% 545ms 3.35% std::_Rb_tree::_S_right (inline) 0 0% 49.62% 540ms 3.32% std::_Rb_tree::_Alloc_node::operator() (inline) 528ms 3.24% 52.86% 528ms 3.24% WntCellCycleOdeSystem::CalculateStoppingEvent 38ms 0.23% 53.09% 527ms 3.24% std::map::operator[] (partial-inline) 17ms 0.1% 53.20% 524ms 3.22% MeshBasedCellPopulation::AcceptCellWriter 149ms 0.91% 54.11% 522ms 3.21% __dynamic_cast 3ms 0.018% 54.13% 512ms 3.14% CellPropertyCollection::GetPropertiesType (inline) 315ms 1.93% 56.06% 507ms 3.11% _int_malloc 0 0% 56.06% 497ms 3.05% std::map::find (inline) 3ms 0.018% 56.08% 496ms 3.05% Element::Element 17ms 0.1% 56.19% 492ms 3.02% Cylindrical2dMesh::ReconstructCylindricalMesh 12ms 0.074% 56.26% 487ms 2.99% AbstractCellPopulation::GetCellUsingLocationIndex 254ms 1.56% 57.82% 479ms 2.94% AbstractCellMutationState::AbstractCellMutationState 8ms 0.049% 57.87% 476ms 2.92% Element::RegisterWithNodes (inline) 22ms 0.14% 58.00% 467ms 2.87% Node::AddElement 17ms 0.1% 58.11% 422ms 2.59% std::less::operator() (inline) 82ms 0.5% 58.61% 412ms 2.53% __GI___libc_free 405ms 2.49% 61.10% 405ms 2.49% std::operator< (inline) 12ms 0.074% 61.17% 402ms 2.47% Cylindrical2dMesh::CorrectNonPeriodicMesh 0 0% 61.17% 390ms 2.39% std::_Rb_tree::lower_bound (inline) 0 0% 61.17% 390ms 2.39% std::map::lower_bound (inline) 5ms 0.031% 61.20% 389ms 2.39% AbstractCellProperty::IsSubType (inline) 0 0% 61.20% 387ms 2.38% std::_Rb_tree::_M_drop_node (inline) 72ms 0.44% 61.65% 382ms 2.35% std::_Rb_tree::_M_erase 1ms 0.0061% 61.65% 381ms 2.34% std::ostream::operator<< (inline) 47ms 0.29% 61.94% 378ms 2.32% std::ostream::_M_insert 5ms 0.031% 61.97% 375ms 2.30% MutableMesh::ReIndex 34ms 0.21% 62.18% 371ms 2.28% std::_Rb_tree::~_Rb_tree (inline) 13ms 0.08% 62.26% 362ms 2.22% std::__new_allocator::deallocate (inline) 0 0% 62.26% 356ms 2.19% std::set::~set (inline) 0 0% 62.26% 348ms 2.14% std::allocator_traits::deallocate (inline) 344ms 2.11% 64.37% 344ms 2.11% [libchaste_crypt.so] 8ms 0.049% 64.42% 335ms 2.06% std::_Rb_tree::erase 0 0% 64.42% 334ms 2.05% std::set::erase (inline) 11ms 0.068% 64.49% 330ms 2.03% Node::RemoveElement 152ms 0.93% 65.42% 325ms 2.00% std::_Rb_tree::_M_get_insert_unique_pos 269ms 1.65% 67.07% 319ms 1.96% _int_free 13ms 0.08% 67.15% 310ms 1.90% divconqrecurse 0 0% 67.15% 300ms 1.84% Cell::GetMutationState 0 0% 67.15% 293ms 1.80% std::_Rb_tree::_M_put_node (inline) 78ms 0.48% 67.63% 290ms 1.78% mergehulls 10ms 0.061% 67.69% 276ms 1.69% boost::detail::shared_count::~shared_count (inline) 0 0% 67.69% 276ms 1.69% boost::shared_ptr::~shared_ptr (inline) 14ms 0.086% 67.78% 269ms 1.65% Element::ResetIndex 1ms 0.0061% 67.79% 267ms 1.64% Cell::GetCellProliferativeType 0 0% 67.79% 266ms 1.63% LegacyCellProliferativeTypesWriter::VisitCell 13ms 0.08% 67.87% 263ms 1.61% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 67.87% 261ms 1.60% std::_Vector_base::_M_allocate (inline) 115ms 0.71% 68.57% 258ms 1.58% __cxxabiv1::__si_class_type_info::__do_dyncast 252ms 1.55% 70.12% 254ms 1.56% boost::detail::sp_counted_base::release 0 0% 70.12% 253ms 1.55% NodeLocationWriter::Visit 2ms 0.012% 70.13% 253ms 1.55% std::set::set (inline) 0 0% 70.13% 249ms 1.53% AbstractCellPopulation::Iterator::operator++ (inline) 243ms 1.49% 71.62% 249ms 1.53% std::vector::operator[] (inline) 21ms 0.13% 71.75% 248ms 1.52% AbstractCellPopulation::Iterator::IsRealCell (inline) 21ms 0.13% 71.88% 244ms 1.50% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 6ms 0.037% 71.92% 242ms 1.49% ApcOneHitCellMutationState::ApcOneHitCellMutationState 24ms 0.15% 72.07% 240ms 1.47% std::_Rb_tree::_M_copy (inline) 1ms 0.0061% 72.07% 237ms 1.46% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 1ms 0.0061% 72.08% 228ms 1.40% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 14ms 0.086% 72.16% 220ms 1.35% AbstractCellPopulation::GetLocationIndexUsingCell 4ms 0.025% 72.19% 220ms 1.35% AbstractCellPopulation::IsCellAttachedToLocationIndex 16ms 0.098% 72.29% 218ms 1.34% std::num_put::_M_insert_float 25ms 0.15% 72.44% 212ms 1.30% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 3ms 0.018% 72.46% 212ms 1.30% alternateaxes 14ms 0.086% 72.55% 211ms 1.30% std::_Rb_tree::_M_erase_aux (inline) 13ms 0.08% 72.63% 210ms 1.29% std::vector::push_back (inline) 93ms 0.57% 73.20% 209ms 1.28% std::_Rb_tree::_M_clone_node (inline) 191ms 1.17% 74.37% 208ms 1.28% vertexmedian 201ms 1.23% 75.60% 201ms 1.23% [libchaste_mesh.so] 6ms 0.037% 75.64% 197ms 1.21% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.0061% 75.65% 192ms 1.18% MeshBasedCellPopulation::GetDampingConstant 0 0% 75.65% 190ms 1.17% AbstractCentreBasedCellPopulation::GetDampingConstant 8ms 0.049% 75.70% 190ms 1.17% Element::MarkAsDeleted 0 0% 75.70% 190ms 1.17% OffLatticeSimulation::ApplyBoundaries 6ms 0.037% 75.73% 185ms 1.14% std::vector::_M_realloc_insert 13ms 0.08% 75.81% 182ms 1.12% AbstractTetrahedralElement::CalculateJacobian 1ms 0.0061% 75.82% 179ms 1.10% TetrahedralMesh::RefreshJacobianCachedData 4ms 0.025% 75.84% 172ms 1.06% std::__cxx11::collate::do_transform 1ms 0.0061% 75.85% 166ms 1.02% ___vsnprintf 1ms 0.0061% 75.86% 165ms 1.01% __vsnprintf_internal (inline) 19ms 0.12% 75.97% 163ms 1.00% __printf_buffer 4ms 0.025% 76.00% 152ms 0.93% AbstractTetrahedralElement::CalculateInverseJacobian 52ms 0.32% 76.32% 146ms 0.9% AbstractElement::GetNodeGlobalIndex 140ms 0.86% 77.18% 140ms 0.86% std::vector::size (inline) 4ms 0.025% 77.20% 138ms 0.85% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 106ms 0.65% 77.85% 137ms 0.84% malloc_consolidate 1ms 0.0061% 77.86% 136ms 0.84% boost::numeric::ublas::vector_assign (inline) 1ms 0.0061% 77.86% 134ms 0.82% __printf_fp_spec (inline) 5ms 0.031% 77.89% 133ms 0.82% __printf_fp_l_buffer 26ms 0.16% 78.05% 132ms 0.81% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 0 0% 78.05% 132ms 0.81% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 0 0% 78.05% 131ms 0.8% CellProliferativeTypesWriter::VisitCell 0 0% 78.05% 130ms 0.8% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 129ms 0.79% 78.85% 129ms 0.79% incircle 1ms 0.0061% 78.85% 128ms 0.79% TetrahedralMesh::Clear 128ms 0.79% 79.64% 128ms 0.79% std::_Rb_tree_insert_and_rebalance 19ms 0.12% 79.75% 125ms 0.77% AbstractTetrahedralElement::RefreshJacobian 53ms 0.33% 80.08% 124ms 0.76% __printf_fp_buffer_1 5ms 0.031% 80.11% 123ms 0.76% CellPropertyCollection::HasProperty 121ms 0.74% 80.85% 121ms 0.74% AbstractCellProperty::AbstractCellProperty 1ms 0.0061% 80.86% 121ms 0.74% AbstractTetrahedralElement::AbstractTetrahedralElement 5ms 0.031% 80.89% 121ms 0.74% boost::numeric::ublas::c_vector::c_vector (inline) 73ms 0.45% 81.34% 121ms 0.74% std::_Rb_tree::equal_range (inline) 0 0% 81.34% 120ms 0.74% Cell::HasCellProperty (inline) 5ms 0.031% 81.37% 112ms 0.69% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 110ms 0.68% 82.04% 110ms 0.68% std::_Rb_tree::_S_left (inline) 108ms 0.66% 82.71% 108ms 0.66% std::type_info::name (inline) 4ms 0.025% 82.73% 107ms 0.66% Cell::SetCellProliferativeType 8ms 0.049% 82.78% 106ms 0.65% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 82.78% 105ms 0.64% AbstractCellBasedSimulation::DoCellRemoval (inline) 48ms 0.29% 83.08% 103ms 0.63% Cylindrical2dMesh::GetVectorFromAtoB 0 0% 83.08% 102ms 0.63% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 2ms 0.012% 83.09% 102ms 0.63% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 91ms 0.56% 83.65% 101ms 0.62% vertexsort 7ms 0.043% 83.69% 99ms 0.61% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 5ms 0.031% 83.72% 99ms 0.61% std::_Rb_tree::_M_emplace_hint_unique 1ms 0.0061% 83.73% 99ms 0.61% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.012% 83.74% 97ms 0.6% Cylindrical2dMesh::CreateMirrorNodes 1ms 0.0061% 83.75% 96ms 0.59% MeshBasedCellPopulation::SpringsEnd (inline) 26ms 0.16% 83.91% 96ms 0.59% boost::numeric::ublas::indexing_vector_assign 30ms 0.18% 84.09% 95ms 0.58% std::num_put::_M_insert_int 0 0% 84.09% 94ms 0.58% std::_Rb_tree::_M_destroy_node (inline) 0 0% 84.09% 94ms 0.58% std::__new_allocator::destroy (inline) 0 0% 84.09% 94ms 0.58% std::allocator_traits::destroy (inline) 93ms 0.57% 84.66% 93ms 0.57% std::_Rb_tree_increment 28ms 0.17% 84.83% 91ms 0.56% AbstractElement::GetNodeLocation 2ms 0.012% 84.84% 91ms 0.56% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 59ms 0.36% 85.21% 88ms 0.54% TimeStepper::AdvanceOneTimeStep 87ms 0.53% 85.74% 87ms 0.53% [libchaste_ode.so] 26ms 0.16% 85.90% 85ms 0.52% std::__ostream_insert