File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 10129ms, 84.58% of 11976ms total Dropped 632 nodes (cum <= 59.88ms) flat flat% sum% cum cum% 0 0% 0% 11944ms 99.73% __libc_start_call_main 0 0% 0% 11944ms 99.73% __libc_start_main_impl 0 0% 0% 11944ms 99.73% _start 0 0% 0% 11929ms 99.61% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 11929ms 99.61% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 11929ms 99.61% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 11929ms 99.61% main 0 0% 0% 11897ms 99.34% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 11897ms 99.34% CxxTest::TestRunner::runTest (inline) 0 0% 0% 11897ms 99.34% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 1ms 0.0084% 0.0084% 11881ms 99.21% AbstractCellBasedSimulation::Solve 0 0% 0.0084% 9113ms 76.09% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0084% 0.017% 5823ms 48.62% AbstractCellBasedSimulation::DoCellBirth 1ms 0.0084% 0.025% 5756ms 48.06% Cell::ReadyToDivide 1ms 0.0084% 0.033% 5732ms 47.86% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.033% 5662ms 47.28% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 8ms 0.067% 0.1% 5657ms 47.24% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 0.1% 5649ms 47.17% CellCycleModelOdeHandler::SolveOdeToTime 49ms 0.41% 0.51% 5564ms 46.46% AbstractOneStepIvpOdeSolver::InternalSolve 585ms 4.88% 5.39% 5016ms 41.88% RungeKutta4IvpOdeSolver::CalculateNextYValue 2236ms 18.67% 24.06% 4268ms 35.64% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 24.06% 3196ms 26.69% MeshBasedCellPopulation::Update 2ms 0.017% 24.08% 2424ms 20.24% Cylindrical2dMesh::ReMesh 63ms 0.53% 24.61% 1997ms 16.68% AbstractCellProperty::IsType (inline) 0 0% 24.61% 1565ms 13.07% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 24.61% 1347ms 11.25% MutableMesh::ReMesh 0 0% 24.61% 1314ms 10.97% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0084% 24.62% 1284ms 10.72% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 24.62% 1197ms 9.99% AbstractCellPopulation::WriteResultsToFiles 209ms 1.75% 26.36% 1127ms 9.41% AbstractCellProperty::IsSame 573ms 4.78% 31.15% 1124ms 9.39% std::_Rb_tree::_M_lower_bound (inline) 132ms 1.10% 32.25% 1096ms 9.15% TetrahedralMesh::EdgeIterator::operator++ 166ms 1.39% 33.63% 918ms 7.67% std::type_info::operator== (inline) 41ms 0.34% 33.98% 865ms 7.22% std::_Rb_tree::find (inline) 844ms 7.05% 41.02% 844ms 7.05% __strcmp_evex 2ms 0.017% 41.04% 758ms 6.33% MeshBasedCellPopulation::UpdateNodePairs 2ms 0.017% 41.06% 685ms 5.72% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 6ms 0.05% 41.11% 669ms 5.59% MeshBasedCellPopulation::SpringIterator::operator++ 8ms 0.067% 41.17% 642ms 5.36% std::set::insert (inline) 32ms 0.27% 41.44% 634ms 5.29% operator new 13ms 0.11% 41.55% 634ms 5.29% std::_Rb_tree::_M_insert_unique 12ms 0.1% 41.65% 614ms 5.13% TetrahedralMesh::ImportFromMesher 217ms 1.81% 43.46% 594ms 4.96% __GI___libc_malloc 11ms 0.092% 43.55% 565ms 4.72% std::__new_allocator::allocate (inline) 0 0% 43.55% 564ms 4.71% triangulate 0 0% 43.55% 563ms 4.70% std::allocator_traits::allocate (inline) 0 0% 43.55% 559ms 4.67% std::set::count (inline) 0 0% 43.55% 518ms 4.33% delaunay 4ms 0.033% 43.59% 518ms 4.33% divconqdelaunay 2ms 0.017% 43.60% 452ms 3.77% AbstractTwoBodyInteractionForce::AddForceContribution 3ms 0.025% 43.63% 441ms 3.68% CellPopulationElementWriter::Visit 10ms 0.084% 43.71% 436ms 3.64% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 51ms 0.43% 44.14% 427ms 3.57% std::map::operator[] (partial-inline) 11ms 0.092% 44.23% 411ms 3.43% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 405ms 3.38% 47.61% 406ms 3.39% WntCellCycleOdeSystem::CalculateStoppingEvent 15ms 0.13% 47.74% 396ms 3.31% std::less::operator() (inline) 12ms 0.1% 47.84% 395ms 3.30% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 47.84% 390ms 3.26% std::_Rb_tree::_M_create_node (inline) 0 0% 47.84% 381ms 3.18% std::_Rb_tree::_M_get_node (inline) 381ms 3.18% 51.02% 381ms 3.18% std::operator< (inline) 29ms 0.24% 51.26% 368ms 3.07% std::_Rb_tree::_M_insert_ (inline) 0 0% 51.26% 357ms 2.98% std::_Rb_tree::_Alloc_node::operator() (inline) 187ms 1.56% 52.82% 348ms 2.91% AbstractCellMutationState::AbstractCellMutationState 1ms 0.0084% 52.83% 338ms 2.82% Element::Element 78ms 0.65% 53.48% 336ms 2.81% __dynamic_cast 14ms 0.12% 53.60% 335ms 2.80% MeshBasedCellPopulation::AcceptCellWriter 330ms 2.76% 56.35% 330ms 2.76% std::_Rb_tree::_S_right (inline) 13ms 0.11% 56.46% 326ms 2.72% Element::RegisterWithNodes (inline) 187ms 1.56% 58.02% 326ms 2.72% _int_malloc 0 0% 58.02% 317ms 2.65% std::_Rb_tree::lower_bound (inline) 0 0% 58.02% 317ms 2.65% std::map::lower_bound (inline) 8ms 0.067% 58.09% 314ms 2.62% Node::AddElement 5ms 0.042% 58.13% 308ms 2.57% MutableMesh::ReIndex 0 0% 58.13% 306ms 2.56% std::map::find (inline) 8ms 0.067% 58.20% 301ms 2.51% Cylindrical2dMesh::ReconstructCylindricalMesh 2ms 0.017% 58.22% 287ms 2.40% CellPropertyCollection::GetPropertiesType (inline) 63ms 0.53% 58.74% 287ms 2.40% __GI___libc_free 59ms 0.49% 59.24% 274ms 2.29% std::_Rb_tree::~_Rb_tree (inline) 0 0% 59.24% 271ms 2.26% std::_Rb_tree::_M_drop_node (inline) 5ms 0.042% 59.28% 266ms 2.22% Cylindrical2dMesh::CorrectNonPeriodicMesh 0 0% 59.28% 257ms 2.15% std::ostream::operator<< (inline) 30ms 0.25% 59.53% 256ms 2.14% std::ostream::_M_insert 0 0% 59.53% 255ms 2.13% std::set::~set (inline) 38ms 0.32% 59.84% 254ms 2.12% std::_Rb_tree::_M_erase 97ms 0.81% 60.65% 253ms 2.11% std::_Rb_tree::_M_get_insert_unique_pos 5ms 0.042% 60.70% 245ms 2.05% std::_Rb_tree::erase 0 0% 60.70% 244ms 2.04% std::set::erase (inline) 5ms 0.042% 60.74% 237ms 1.98% Node::RemoveElement 6ms 0.05% 60.79% 230ms 1.92% boost::detail::shared_count::~shared_count (inline) 0 0% 60.79% 230ms 1.92% boost::shared_ptr::~shared_ptr (inline) 6ms 0.05% 60.84% 228ms 1.90% divconqrecurse 1ms 0.0084% 60.85% 227ms 1.90% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 60.85% 227ms 1.90% AbstractCellProperty::IsSubType (inline) 6ms 0.05% 60.90% 227ms 1.90% std::__new_allocator::deallocate (inline) 205ms 1.71% 62.61% 224ms 1.87% _int_free 22ms 0.18% 62.79% 223ms 1.86% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 62.79% 223ms 1.86% std::allocator_traits::deallocate (inline) 222ms 1.85% 64.65% 222ms 1.85% boost::detail::sp_counted_base::release 218ms 1.82% 66.47% 219ms 1.83% std::vector::operator[] (inline) 57ms 0.48% 66.94% 214ms 1.79% mergehulls 8ms 0.067% 67.01% 213ms 1.78% Element::ResetIndex 5ms 0.042% 67.05% 205ms 1.71% AbstractCellPopulation::GetLocationIndexUsingCell 13ms 0.11% 67.16% 196ms 1.64% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 67.16% 192ms 1.60% std::_Rb_tree::_M_put_node (inline) 102ms 0.85% 68.01% 190ms 1.59% __cxxabiv1::__si_class_type_info::__do_dyncast 2ms 0.017% 68.03% 184ms 1.54% alternateaxes 14ms 0.12% 68.14% 183ms 1.53% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 0 0% 68.14% 183ms 1.53% std::set::set (inline) 182ms 1.52% 69.66% 182ms 1.52% [libchaste_cell_based.so] 0 0% 69.66% 182ms 1.52% std::_Vector_base::_M_allocate (inline) 168ms 1.40% 71.07% 181ms 1.51% vertexmedian 3ms 0.025% 71.09% 176ms 1.47% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 68ms 0.57% 71.66% 173ms 1.44% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 0 0% 71.66% 173ms 1.44% OffLatticeSimulation::ApplyBoundaries 0 0% 71.66% 172ms 1.44% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 71.66% 168ms 1.40% LegacyCellProliferativeTypesWriter::VisitCell 1ms 0.0084% 71.67% 167ms 1.39% Cell::GetCellProliferativeType 20ms 0.17% 71.84% 164ms 1.37% std::_Rb_tree::_M_copy (inline) 47ms 0.39% 72.23% 162ms 1.35% ApcOneHitCellMutationState::ApcOneHitCellMutationState 27ms 0.23% 72.45% 161ms 1.34% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 10ms 0.084% 72.54% 160ms 1.34% AbstractTetrahedralElement::CalculateJacobian 0 0% 72.54% 160ms 1.34% NodeLocationWriter::Visit 0 0% 72.54% 159ms 1.33% TetrahedralMesh::RefreshJacobianCachedData 0 0% 72.54% 157ms 1.31% Cell::GetMutationState 12ms 0.1% 72.64% 152ms 1.27% std::_Rb_tree::_M_erase_aux (inline) 13ms 0.11% 72.75% 151ms 1.26% std::num_put::_M_insert_float 6ms 0.05% 72.80% 149ms 1.24% AbstractCellPopulation::IsCellAttachedToLocationIndex 51ms 0.43% 73.22% 144ms 1.20% std::_Rb_tree::_M_clone_node (inline) 5ms 0.042% 73.26% 143ms 1.19% AbstractTetrahedralElement::CalculateInverseJacobian 8ms 0.067% 73.33% 134ms 1.12% Element::MarkAsDeleted 11ms 0.092% 73.42% 134ms 1.12% std::vector::push_back (inline) 21ms 0.18% 73.60% 129ms 1.08% AbstractTetrahedralElement::RefreshJacobian 0 0% 73.60% 125ms 1.04% std::__cxx11::collate::do_transform 2ms 0.017% 73.61% 122ms 1.02% ___vsnprintf 12ms 0.1% 73.71% 121ms 1.01% __printf_buffer 0 0% 73.71% 120ms 1.00% __vsnprintf_internal (inline) 6ms 0.05% 73.76% 120ms 1.00% std::vector::_M_realloc_insert 2ms 0.017% 73.78% 106ms 0.89% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 73.78% 106ms 0.89% MeshBasedCellPopulation::GetDampingConstant 104ms 0.87% 74.65% 104ms 0.87% incircle 41ms 0.34% 74.99% 100ms 0.84% __printf_fp_buffer_1 0 0% 74.99% 100ms 0.84% __printf_fp_l_buffer 0 0% 74.99% 100ms 0.84% __printf_fp_spec (inline) 2ms 0.017% 75.01% 97ms 0.81% AbstractTetrahedralElement::AbstractTetrahedralElement 90ms 0.75% 75.76% 96ms 0.8% vertexsort 56ms 0.47% 76.23% 95ms 0.79% std::_Rb_tree::equal_range (inline) 60ms 0.5% 76.73% 94ms 0.78% AbstractElement::GetNodeLocation 0 0% 76.73% 92ms 0.77% AbstractCellBasedSimulation::DoCellRemoval (inline) 2ms 0.017% 76.75% 92ms 0.77% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 67ms 0.56% 77.30% 92ms 0.77% malloc_consolidate 92ms 0.77% 78.07% 92ms 0.77% std::_Rb_tree_insert_and_rebalance 19ms 0.16% 78.23% 90ms 0.75% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 89ms 0.74% 78.97% 89ms 0.74% AbstractCellMutationState::~AbstractCellMutationState 3ms 0.025% 79.00% 88ms 0.73% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 0 0% 79.00% 88ms 0.73% boost::numeric::ublas::vector_assign (inline) 26ms 0.22% 79.22% 86ms 0.72% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 5ms 0.042% 79.26% 86ms 0.72% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 0 0% 79.26% 85ms 0.71% CellProliferativeTypesWriter::VisitCell 3ms 0.025% 79.28% 85ms 0.71% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 52ms 0.43% 79.72% 85ms 0.71% Cylindrical2dMesh::GetVectorFromAtoB 1ms 0.0084% 79.73% 84ms 0.7% TetrahedralMesh::Clear 31ms 0.26% 79.98% 83ms 0.69% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 62ms 0.52% 80.50% 82ms 0.68% AbstractElement::GetNodeGlobalIndex 82ms 0.68% 81.19% 82ms 0.68% std::vector::size (inline) 15ms 0.13% 81.31% 81ms 0.68% TetrahedralMesh::EdgesEnd (partial-inline) 4ms 0.033% 81.35% 80ms 0.67% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 81.35% 80ms 0.67% std::_Rb_tree::_M_destroy_node (inline) 0 0% 81.35% 80ms 0.67% std::__new_allocator::destroy (inline) 0 0% 81.35% 80ms 0.67% std::allocator_traits::destroy (inline) 3ms 0.025% 81.37% 79ms 0.66% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 77ms 0.64% 82.01% 77ms 0.64% AbstractCellProperty::~AbstractCellProperty 1ms 0.0084% 82.02% 74ms 0.62% boost::numeric::ublas::c_vector::c_vector (inline) 20ms 0.17% 82.19% 74ms 0.62% std::__ostream_insert 37ms 0.31% 82.50% 72ms 0.6% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 70ms 0.58% 83.08% 70ms 0.58% Node::GetIndex 0 0% 83.08% 68ms 0.57% AbstractCellBasedWriter::OpenOutputFileForAppend 1ms 0.0084% 83.09% 68ms 0.57% OutputFileHandler::OpenOutputFile 20ms 0.17% 83.26% 68ms 0.57% boost::numeric::ublas::indexing_vector_assign 0 0% 83.26% 67ms 0.56% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 0 0% 83.26% 66ms 0.55% Cell::HasCellProperty (inline) 3ms 0.025% 83.28% 66ms 0.55% CellPropertyCollection::HasProperty 4ms 0.033% 83.32% 65ms 0.54% Cylindrical2dMesh::CreateMirrorNodes 31ms 0.26% 83.58% 63ms 0.53% TimeStepper::AdvanceOneTimeStep 0 0% 83.58% 63ms 0.53% std::operator<< (inline) 8ms 0.067% 83.64% 62ms 0.52% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 83.64% 61ms 0.51% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 16ms 0.13% 83.78% 61ms 0.51% std::num_put::_M_insert_int 60ms 0.5% 84.28% 60ms 0.5% [libchaste_mesh.so] 36ms 0.3% 84.58% 60ms 0.5% boost::numeric::ublas::c_matrix::operator()