File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16899ms, 85.84% of 19686ms total Dropped 751 nodes (cum <= 98.43ms) flat flat% sum% cum cum% 0 0% 0% 19644ms 99.79% __libc_start_call_main 0 0% 0% 19644ms 99.79% __libc_start_main_impl 0 0% 0% 19644ms 99.79% _start 0 0% 0% 19625ms 99.69% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19625ms 99.69% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19625ms 99.69% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19625ms 99.69% main 0 0% 0% 19591ms 99.52% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19591ms 99.52% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19591ms 99.52% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19565ms 99.39% AbstractCellBasedSimulation::Solve 0 0% 0% 15154ms 76.98% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.01% 0.01% 9951ms 50.55% AbstractCellBasedSimulation::DoCellBirth 4ms 0.02% 0.03% 9836ms 49.96% Cell::ReadyToDivide 3ms 0.015% 0.046% 9752ms 49.54% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.046% 9628ms 48.91% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 12ms 0.061% 0.11% 9620ms 48.87% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.015% 0.12% 9604ms 48.79% CellCycleModelOdeHandler::SolveOdeToTime 70ms 0.36% 0.48% 9449ms 48.00% AbstractOneStepIvpOdeSolver::InternalSolve 846ms 4.30% 4.77% 8596ms 43.67% RungeKutta4IvpOdeSolver::CalculateNextYValue 2933ms 14.90% 19.67% 7539ms 38.30% WntCellCycleOdeSystem::EvaluateYDerivatives 3ms 0.015% 19.69% 5075ms 25.78% MeshBasedCellPopulation::Update 199ms 1.01% 20.70% 4654ms 23.64% AbstractCellProperty::IsType (inline) 4ms 0.02% 20.72% 3943ms 20.03% Cylindrical2dMesh::ReMesh 518ms 2.63% 23.35% 3373ms 17.13% AbstractCellProperty::IsSame 409ms 2.08% 25.43% 2855ms 14.50% std::type_info::operator== (inline) 0 0% 25.43% 2434ms 12.36% OffLatticeSimulation::UpdateCellLocationsAndTopology 2369ms 12.03% 37.46% 2369ms 12.03% __strcmp_avx2 0 0% 37.46% 2151ms 10.93% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 37.46% 2135ms 10.85% MutableMesh::ReMesh 17ms 0.086% 37.55% 2095ms 10.64% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 37.55% 1975ms 10.03% AbstractCellPopulation::WriteResultsToFiles 778ms 3.95% 41.50% 1784ms 9.06% std::_Rb_tree::_M_lower_bound (inline) 146ms 0.74% 42.24% 1614ms 8.20% TetrahedralMesh::EdgeIterator::operator++ 61ms 0.31% 42.55% 1311ms 6.66% std::_Rb_tree::find (inline) 0 0% 42.55% 1091ms 5.54% MeshBasedCellPopulation::UpdateNodePairs 47ms 0.24% 42.79% 1089ms 5.53% operator new 16ms 0.081% 42.87% 1081ms 5.49% TetrahedralMesh::ImportFromMesher 12ms 0.061% 42.93% 1069ms 5.43% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 211ms 1.07% 44.01% 1025ms 5.21% __GI___libc_malloc 12ms 0.061% 44.07% 982ms 4.99% MeshBasedCellPopulation::SpringIterator::operator++ 16ms 0.081% 44.15% 982ms 4.99% std::set::insert (inline) 8ms 0.041% 44.19% 966ms 4.91% std::_Rb_tree::_M_insert_unique 48ms 0.24% 44.43% 964ms 4.90% std::__new_allocator::allocate (inline) 0 0% 44.43% 958ms 4.87% std::allocator_traits::allocate (inline) 1ms 0.0051% 44.44% 802ms 4.07% triangulate 0 0% 44.44% 761ms 3.87% std::set::count (inline) 4ms 0.02% 44.46% 730ms 3.71% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 384ms 1.95% 46.41% 730ms 3.71% _int_malloc 0 0% 46.41% 727ms 3.69% delaunay 1ms 0.0051% 46.41% 727ms 3.69% divconqdelaunay 0 0% 46.41% 708ms 3.60% AbstractTwoBodyInteractionForce::AddForceContribution 67ms 0.34% 46.75% 708ms 3.60% std::map::operator[] (partial-inline) 8ms 0.041% 46.79% 703ms 3.57% CellPopulationElementWriter::Visit 666ms 3.38% 50.18% 666ms 3.38% std::_Rb_tree::_S_right (inline) 617ms 3.13% 53.31% 630ms 3.20% WntCellCycleOdeSystem::CalculateStoppingEvent 207ms 1.05% 54.36% 628ms 3.19% __dynamic_cast 0 0% 54.36% 604ms 3.07% std::_Rb_tree::_M_create_node (inline) 23ms 0.12% 54.48% 598ms 3.04% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 15ms 0.076% 54.56% 596ms 3.03% std::less::operator() (inline) 9ms 0.046% 54.60% 592ms 3.01% CellPropertyCollection::GetPropertiesType (inline) 21ms 0.11% 54.71% 592ms 3.01% std::_Rb_tree::_M_insert_ (inline) 4ms 0.02% 54.73% 588ms 2.99% MeshBasedCellPopulation::AcceptCellWriter 581ms 2.95% 57.68% 581ms 2.95% std::operator< (inline) 0 0% 57.68% 572ms 2.91% std::_Rb_tree::_M_get_node (inline) 15ms 0.076% 57.76% 563ms 2.86% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 57.76% 557ms 2.83% std::_Rb_tree::lower_bound (inline) 0 0% 57.76% 557ms 2.83% std::map::lower_bound (inline) 0 0% 57.76% 548ms 2.78% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 57.76% 545ms 2.77% std::map::find (inline) 8ms 0.041% 57.80% 540ms 2.74% Element::Element 5ms 0.025% 57.82% 527ms 2.68% MutableMesh::ReIndex 4ms 0.02% 57.84% 488ms 2.48% std::ostream::operator<< (inline) 12ms 0.061% 57.90% 487ms 2.47% Cylindrical2dMesh::ReconstructCylindricalMesh 349ms 1.77% 59.68% 485ms 2.46% AbstractCellMutationState::AbstractCellMutationState 77ms 0.39% 60.07% 484ms 2.46% std::ostream::_M_insert 3ms 0.015% 60.08% 480ms 2.44% AbstractCellProperty::IsSubType (inline) 11ms 0.056% 60.14% 474ms 2.41% Cylindrical2dMesh::CorrectNonPeriodicMesh 13ms 0.066% 60.21% 467ms 2.37% Element::RegisterWithNodes (inline) 11ms 0.056% 60.26% 448ms 2.28% Node::AddElement 151ms 0.77% 61.03% 401ms 2.04% __GI___libc_free 5ms 0.025% 61.05% 391ms 1.99% std::_Vector_base::_M_allocate (inline) 156ms 0.79% 61.85% 366ms 1.86% std::_Rb_tree::_M_get_insert_unique_pos 121ms 0.61% 62.46% 359ms 1.82% std::_Rb_tree::_M_erase 7ms 0.036% 62.50% 357ms 1.81% std::_Rb_tree::erase 2ms 0.01% 62.51% 357ms 1.81% std::set::erase (inline) 20ms 0.1% 62.61% 355ms 1.80% Node::RemoveElement 25ms 0.13% 62.73% 337ms 1.71% std::_Rb_tree::~_Rb_tree (inline) 13ms 0.066% 62.80% 333ms 1.69% divconqrecurse 21ms 0.11% 62.91% 327ms 1.66% Element::ResetIndex 172ms 0.87% 63.78% 324ms 1.65% __cxxabiv1::__si_class_type_info::__do_dyncast 10ms 0.051% 63.83% 321ms 1.63% std::__new_allocator::deallocate (inline) 2ms 0.01% 63.84% 320ms 1.63% LegacyCellProliferativeTypesWriter::VisitCell 317ms 1.61% 65.45% 317ms 1.61% std::type_info::name (inline) 5ms 0.025% 65.48% 316ms 1.61% Cell::GetCellProliferativeType 0 0% 65.48% 314ms 1.60% std::allocator_traits::deallocate (inline) 0 0% 65.48% 314ms 1.60% std::set::~set (inline) 85ms 0.43% 65.91% 313ms 1.59% mergehulls 39ms 0.2% 66.11% 312ms 1.58% AbstractCellPopulation::Iterator::IsRealCell (inline) 2ms 0.01% 66.12% 312ms 1.58% Cell::GetMutationState 14ms 0.071% 66.19% 312ms 1.58% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 1ms 0.0051% 66.19% 310ms 1.57% AbstractCellPopulation::Iterator::operator++ (inline) 3ms 0.015% 66.21% 300ms 1.52% AbstractCellPopulation::GetLocationIndexUsingCell 2ms 0.01% 66.22% 289ms 1.47% NodeLocationWriter::Visit 0 0% 66.22% 285ms 1.45% std::_Rb_tree::_M_drop_node (inline) 19ms 0.097% 66.32% 275ms 1.40% AbstractTetrahedralElement::CalculateJacobian 16ms 0.081% 66.40% 268ms 1.36% std::vector::push_back (inline) 13ms 0.066% 66.46% 263ms 1.34% std::_Rb_tree::_Rb_tree (partial-inline) 7ms 0.036% 66.50% 252ms 1.28% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 250ms 1.27% 67.77% 250ms 1.27% std::vector::operator[] (inline) 14ms 0.071% 67.84% 249ms 1.26% std::num_put::_M_insert_float 206ms 1.05% 68.89% 248ms 1.26% _int_free 0 0% 68.89% 248ms 1.26% std::_Rb_tree::_M_put_node (inline) 2ms 0.01% 68.90% 246ms 1.25% alternateaxes 8ms 0.041% 68.94% 245ms 1.24% AbstractCellPopulation::IsCellAttachedToLocationIndex 222ms 1.13% 70.07% 244ms 1.24% vertexmedian 0 0% 70.07% 243ms 1.23% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 10ms 0.051% 70.12% 242ms 1.23% std::_Rb_tree::_M_erase_aux (inline) 21ms 0.11% 70.22% 241ms 1.22% std::vector::_M_realloc_insert 1ms 0.0051% 70.23% 237ms 1.20% std::set::set (inline) 1ms 0.0051% 70.23% 234ms 1.19% TetrahedralMesh::RefreshJacobianCachedData 55ms 0.28% 70.51% 233ms 1.18% ApcOneHitCellMutationState::ApcOneHitCellMutationState 23ms 0.12% 70.63% 233ms 1.18% std::_Rb_tree::_M_copy (inline) 223ms 1.13% 71.76% 223ms 1.13% [libchaste_cell_based.so] 161ms 0.82% 72.58% 217ms 1.10% malloc_consolidate 25ms 0.13% 72.71% 212ms 1.08% AbstractTetrahedralElement::RefreshJacobian 31ms 0.16% 72.86% 211ms 1.07% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 56ms 0.28% 73.15% 209ms 1.06% std::_Rb_tree::_M_clone_node (inline) 78ms 0.4% 73.54% 203ms 1.03% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 2ms 0.01% 73.55% 198ms 1.01% MeshBasedCellPopulation::GetDampingConstant 2ms 0.01% 73.56% 197ms 1.00% std::__cxx11::collate::do_transform 10ms 0.051% 73.62% 196ms 1% AbstractTetrahedralElement::CalculateInverseJacobian 2ms 0.01% 73.63% 195ms 0.99% AbstractCentreBasedCellPopulation::GetDampingConstant 146ms 0.74% 74.37% 189ms 0.96% AbstractElement::GetNodeGlobalIndex 1ms 0.0051% 74.37% 188ms 0.95% ___vsnprintf 0 0% 74.37% 187ms 0.95% __vsnprintf_internal (inline) 16ms 0.081% 74.45% 185ms 0.94% __printf_buffer 13ms 0.066% 74.52% 184ms 0.93% Element::MarkAsDeleted 184ms 0.93% 75.45% 184ms 0.93% std::_Rb_tree_insert_and_rebalance 1ms 0.0051% 75.46% 179ms 0.91% AbstractTetrahedralElement::AbstractTetrahedralElement 13ms 0.066% 75.53% 179ms 0.91% TetrahedralMesh::Clear 174ms 0.88% 76.41% 174ms 0.88% Node::GetIndex 1ms 0.0051% 76.41% 173ms 0.88% OffLatticeSimulation::ApplyBoundaries 67ms 0.34% 76.76% 166ms 0.84% AbstractElement::GetNodeLocation 10ms 0.051% 76.81% 161ms 0.82% __printf_fp_l_buffer 0 0% 76.81% 161ms 0.82% __printf_fp_spec (inline) 0 0% 76.81% 158ms 0.8% Cell::HasCellProperty (inline) 3ms 0.015% 76.82% 158ms 0.8% CellPropertyCollection::HasProperty 154ms 0.78% 77.60% 154ms 0.78% unlink_chunk 1ms 0.0051% 77.61% 151ms 0.77% CellProliferativeTypesWriter::VisitCell 70ms 0.36% 77.96% 148ms 0.75% __printf_fp_buffer_1 47ms 0.24% 78.20% 146ms 0.74% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 7ms 0.036% 78.24% 142ms 0.72% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 1ms 0.0051% 78.24% 137ms 0.7% boost::numeric::ublas::vector_assign (inline) 88ms 0.45% 78.69% 136ms 0.69% Cylindrical2dMesh::GetVectorFromAtoB 128ms 0.65% 79.34% 136ms 0.69% vertexsort 133ms 0.68% 80.02% 133ms 0.68% incircle 0 0% 80.02% 126ms 0.64% AbstractCellBasedSimulation::DoCellRemoval (inline) 9ms 0.046% 80.06% 126ms 0.64% boost::numeric::ublas::c_vector::c_vector (inline) 6ms 0.03% 80.09% 126ms 0.64% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 125ms 0.63% 80.73% 125ms 0.63% std::vector::size (inline) 16ms 0.081% 80.81% 122ms 0.62% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 22ms 0.11% 80.92% 122ms 0.62% std::num_put::_M_insert_int 0 0% 80.92% 120ms 0.61% AbstractCellBasedWriter::OpenOutputFileForAppend 41ms 0.21% 81.13% 120ms 0.61% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 0 0% 81.13% 119ms 0.6% OutputFileHandler::OpenOutputFile 0 0% 81.13% 119ms 0.6% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 13ms 0.066% 81.19% 119ms 0.6% boost::detail::shared_count::~shared_count (inline) 0 0% 81.19% 119ms 0.6% boost::shared_ptr::~shared_ptr (inline) 81ms 0.41% 81.61% 115ms 0.58% std::_Rb_tree::equal_range (inline) 1ms 0.0051% 81.61% 114ms 0.58% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 113ms 0.57% 82.19% 113ms 0.57% std::_Rb_tree_rebalance_for_erase 24ms 0.12% 82.31% 109ms 0.55% TetrahedralMesh::EdgesEnd (partial-inline) 29ms 0.15% 82.45% 109ms 0.55% boost::numeric::ublas::indexing_vector_assign 78ms 0.4% 82.85% 108ms 0.55% TimeStepper::AdvanceOneTimeStep 108ms 0.55% 83.40% 108ms 0.55% std::_Rb_tree_increment 104ms 0.53% 83.93% 104ms 0.53% AbstractCellMutationState::~AbstractCellMutationState 5ms 0.025% 83.95% 104ms 0.53% MeshBasedCellPopulation::SpringsEnd (inline) 7ms 0.036% 83.99% 104ms 0.53% std::_Rb_tree_const_iterator::operator++ (inline) 15ms 0.076% 84.06% 102ms 0.52% Node::~Node 51ms 0.26% 84.32% 102ms 0.52% std::__ostream_insert 98ms 0.5% 84.82% 101ms 0.51% boost::detail::sp_counted_base::release 100ms 0.51% 85.33% 100ms 0.51% AbstractCellProperty::~AbstractCellProperty 100ms 0.51% 85.84% 100ms 0.51% AbstractElement::IsDeleted 0 0% 85.84% 99ms 0.5% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 1ms 0.0051% 85.84% 99ms 0.5% std::vector::resize (inline)