File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 15725ms, 83.63% of 18803ms total Dropped 811 nodes (cum <= 94.02ms) flat flat% sum% cum cum% 0 0% 0% 18758ms 99.76% __libc_start_call_main 0 0% 0% 18758ms 99.76% __libc_start_main_impl 0 0% 0% 18758ms 99.76% _start 0 0% 0% 18739ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 18739ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 18739ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 18739ms 99.66% main 0 0% 0% 18703ms 99.47% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 18703ms 99.47% CxxTest::TestRunner::runTest (inline) 0 0% 0% 18703ms 99.47% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 18677ms 99.33% AbstractCellBasedSimulation::Solve 1ms 0.0053% 0.0053% 14912ms 79.31% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.011% 0.016% 10032ms 53.35% AbstractCellBasedSimulation::DoCellBirth 12ms 0.064% 0.08% 9951ms 52.92% Cell::ReadyToDivide 3ms 0.016% 0.096% 9870ms 52.49% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0053% 0.1% 9724ms 51.72% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 19ms 0.1% 0.2% 9711ms 51.65% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.016% 0.22% 9690ms 51.53% CellCycleModelOdeHandler::SolveOdeToTime 84ms 0.45% 0.66% 9505ms 50.55% AbstractOneStepIvpOdeSolver::InternalSolve 877ms 4.66% 5.33% 8705ms 46.30% RungeKutta4IvpOdeSolver::CalculateNextYValue 3655ms 19.44% 24.77% 7605ms 40.45% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.0053% 24.77% 4765ms 25.34% MeshBasedCellPopulation::Update 3ms 0.016% 24.79% 4092ms 21.76% Cylindrical2dMesh::ReMesh 109ms 0.58% 25.37% 3992ms 21.23% AbstractCellProperty::IsType (inline) 588ms 3.13% 28.50% 2778ms 14.77% AbstractCellProperty::IsSame 0 0% 28.50% 2265ms 12.05% MutableMesh::ReMesh 388ms 2.06% 30.56% 2190ms 11.65% std::type_info::operator== (inline) 0 0% 30.56% 1998ms 10.63% AbstractCellPopulation::WriteResultsToFiles 1ms 0.0053% 30.56% 1764ms 9.38% OffLatticeSimulation::UpdateCellLocationsAndTopology 1756ms 9.34% 39.90% 1756ms 9.34% __strcmp_avx2 0 0% 39.90% 1493ms 7.94% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.053% 39.96% 1443ms 7.67% AbstractNumericalMethod::ComputeForcesIncludingDamping 14ms 0.074% 40.03% 1153ms 6.13% TetrahedralMesh::ImportFromMesher 499ms 2.65% 42.68% 1045ms 5.56% std::_Rb_tree::_M_lower_bound (inline) 47ms 0.25% 42.93% 1016ms 5.40% operator new 207ms 1.10% 44.04% 959ms 5.10% __GI___libc_malloc 46ms 0.24% 44.28% 895ms 4.76% std::__new_allocator::allocate (inline) 0 0% 44.28% 890ms 4.73% std::allocator_traits::allocate (inline) 2ms 0.011% 44.29% 831ms 4.42% triangulate 0 0% 44.29% 740ms 3.94% delaunay 1ms 0.0053% 44.30% 739ms 3.93% divconqdelaunay 1ms 0.0053% 44.30% 736ms 3.91% AbstractTwoBodyInteractionForce::AddForceContribution 3ms 0.016% 44.32% 735ms 3.91% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 57ms 0.3% 44.62% 732ms 3.89% std::map::operator[] (partial-inline) 412ms 2.19% 46.81% 677ms 3.60% _int_malloc 7ms 0.037% 46.85% 673ms 3.58% CellPopulationElementWriter::Visit 209ms 1.11% 47.96% 649ms 3.45% __dynamic_cast 31ms 0.16% 48.13% 648ms 3.45% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 628ms 3.34% 51.47% 628ms 3.34% std::_Rb_tree::_S_right (inline) 610ms 3.24% 54.71% 621ms 3.30% WntCellCycleOdeSystem::CalculateStoppingEvent 3ms 0.016% 54.73% 620ms 3.30% MeshBasedCellPopulation::UpdateNodePairs 8ms 0.043% 54.77% 607ms 3.23% CellPropertyCollection::GetPropertiesType (inline) 13ms 0.069% 54.84% 597ms 3.18% AbstractCellPopulation::GetCellUsingLocationIndex 6ms 0.032% 54.87% 578ms 3.07% MeshBasedCellPopulation::AcceptCellWriter 0 0% 54.87% 575ms 3.06% std::_Rb_tree::lower_bound (inline) 0 0% 54.87% 575ms 3.06% std::map::lower_bound (inline) 9ms 0.048% 54.92% 553ms 2.94% Element::Element 2ms 0.011% 54.93% 543ms 2.89% std::_Rb_tree::_M_insert_unique 0 0% 54.93% 543ms 2.89% std::set::insert (inline) 49ms 0.26% 55.19% 519ms 2.76% TetrahedralMesh::EdgeIterator::operator++ 2ms 0.011% 55.20% 513ms 2.73% std::ostream::operator<< (inline) 13ms 0.069% 55.27% 512ms 2.72% MutableMesh::ReIndex 9ms 0.048% 55.32% 511ms 2.72% Cylindrical2dMesh::ReconstructCylindricalMesh 77ms 0.41% 55.73% 511ms 2.72% std::ostream::_M_insert 1ms 0.0053% 55.73% 492ms 2.62% AbstractCellProperty::IsSubType (inline) 28ms 0.15% 55.88% 490ms 2.61% std::_Rb_tree::find (inline) 0 0% 55.88% 482ms 2.56% std::map::find (inline) 8ms 0.043% 55.92% 481ms 2.56% Cylindrical2dMesh::CorrectNonPeriodicMesh 8ms 0.043% 55.96% 480ms 2.55% Element::RegisterWithNodes (inline) 0 0% 55.96% 480ms 2.55% std::_Rb_tree::_M_create_node (inline) 9ms 0.048% 56.01% 472ms 2.51% Node::AddElement 317ms 1.69% 57.70% 464ms 2.47% AbstractCellMutationState::AbstractCellMutationState 0 0% 57.70% 457ms 2.43% std::_Rb_tree::_M_get_node (inline) 169ms 0.9% 58.60% 456ms 2.43% __GI___libc_free 6ms 0.032% 58.63% 437ms 2.32% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 58.63% 420ms 2.23% std::_Rb_tree::_Alloc_node::operator() (inline) 27ms 0.14% 58.77% 412ms 2.19% std::_Rb_tree::_M_insert_ (inline) 6ms 0.032% 58.80% 401ms 2.13% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 2ms 0.011% 58.82% 399ms 2.12% std::set::erase (inline) 8ms 0.043% 58.86% 397ms 2.11% std::_Rb_tree::erase 14ms 0.074% 58.93% 386ms 2.05% Node::RemoveElement 21ms 0.11% 59.04% 352ms 1.87% std::__new_allocator::deallocate (inline) 1ms 0.0053% 59.05% 346ms 1.84% Cell::GetMutationState 0 0% 59.05% 343ms 1.82% std::allocator_traits::deallocate (inline) 19ms 0.1% 59.15% 335ms 1.78% divconqrecurse 329ms 1.75% 60.90% 329ms 1.75% std::type_info::name (inline) 1ms 0.0053% 60.91% 325ms 1.73% NodeLocationWriter::Visit 24ms 0.13% 61.03% 323ms 1.72% Element::ResetIndex 151ms 0.8% 61.84% 315ms 1.68% __cxxabiv1::__si_class_type_info::__do_dyncast 87ms 0.46% 62.30% 313ms 1.66% mergehulls 6ms 0.032% 62.33% 307ms 1.63% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 3ms 0.016% 62.35% 305ms 1.62% std::_Vector_base::_M_allocate (inline) 6ms 0.032% 62.38% 293ms 1.56% Cell::GetCellProliferativeType 13ms 0.069% 62.45% 293ms 1.56% std::num_put::_M_insert_float 1ms 0.0053% 62.45% 291ms 1.55% LegacyCellProliferativeTypesWriter::VisitCell 209ms 1.11% 63.56% 287ms 1.53% _int_free 97ms 0.52% 64.08% 285ms 1.52% std::_Rb_tree::_M_erase 9ms 0.048% 64.13% 281ms 1.49% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 64.13% 278ms 1.48% AbstractCellPopulation::Iterator::operator++ (inline) 32ms 0.17% 64.30% 275ms 1.46% AbstractCellPopulation::Iterator::IsRealCell (inline) 18ms 0.096% 64.39% 274ms 1.46% std::vector::push_back (inline) 3ms 0.016% 64.41% 271ms 1.44% alternateaxes 268ms 1.43% 65.84% 269ms 1.43% std::vector::operator[] (inline) 257ms 1.37% 67.20% 268ms 1.43% vertexmedian 0 0% 67.20% 266ms 1.41% std::_Rb_tree::_M_drop_node (inline) 10ms 0.053% 67.26% 249ms 1.32% AbstractTetrahedralElement::CalculateJacobian 11ms 0.059% 67.31% 249ms 1.32% std::_Rb_tree::_M_erase_aux (inline) 0 0% 67.31% 246ms 1.31% TetrahedralMesh::RefreshJacobianCachedData 10ms 0.053% 67.37% 245ms 1.30% std::vector::_M_realloc_insert 9ms 0.048% 67.41% 243ms 1.29% AbstractCellPopulation::IsCellAttachedToLocationIndex 30ms 0.16% 67.57% 242ms 1.29% TetrahedralMesh::Clear 4ms 0.021% 67.60% 239ms 1.27% std::set::set (inline) 13ms 0.069% 67.66% 237ms 1.26% std::_Rb_tree::~_Rb_tree (inline) 14ms 0.074% 67.74% 235ms 1.25% std::_Rb_tree::_Rb_tree 4ms 0.021% 67.76% 233ms 1.24% std::__cxx11::collate::do_transform 3ms 0.016% 67.78% 229ms 1.22% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 67.78% 229ms 1.22% MeshBasedCellPopulation::GetDampingConstant 0 0% 67.78% 229ms 1.22% std::_Rb_tree::_M_put_node (inline) 13ms 0.069% 67.85% 227ms 1.21% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 20ms 0.11% 67.95% 221ms 1.18% Element::MarkAsDeleted 13ms 0.069% 68.02% 220ms 1.17% AbstractTetrahedralElement::CalculateInverseJacobian 5ms 0.027% 68.05% 220ms 1.17% ___vsnprintf 43ms 0.23% 68.28% 219ms 1.16% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 0 0% 68.28% 219ms 1.16% std::set::~set (inline) 0 0% 68.28% 215ms 1.14% __vsnprintf_internal (inline) 2ms 0.011% 68.29% 213ms 1.13% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 18ms 0.096% 68.38% 212ms 1.13% __printf_buffer 25ms 0.13% 68.52% 208ms 1.11% std::_Rb_tree::_M_copy (inline) 27ms 0.14% 68.66% 204ms 1.08% AbstractTetrahedralElement::RefreshJacobian 51ms 0.27% 68.93% 204ms 1.08% ApcOneHitCellMutationState::ApcOneHitCellMutationState 38ms 0.2% 69.13% 200ms 1.06% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 194ms 1.03% 70.16% 194ms 1.03% [libchaste_cell_based.so] 136ms 0.72% 70.89% 187ms 0.99% AbstractElement::GetNodeGlobalIndex 131ms 0.7% 71.58% 186ms 0.99% malloc_consolidate 0 0% 71.58% 184ms 0.98% OffLatticeSimulation::ApplyBoundaries 1ms 0.0053% 71.59% 184ms 0.98% __printf_fp_spec (inline) 7ms 0.037% 71.63% 183ms 0.97% __printf_fp_l_buffer 69ms 0.37% 71.99% 181ms 0.96% std::_Rb_tree::_M_clone_node (inline) 3ms 0.016% 72.01% 170ms 0.9% AbstractTetrahedralElement::AbstractTetrahedralElement 2ms 0.011% 72.02% 169ms 0.9% CellProliferativeTypesWriter::VisitCell 0 0% 72.02% 169ms 0.9% std::_Hashtable::count (inline) 1ms 0.0053% 72.03% 169ms 0.9% std::_Hashtable::find (inline) 0 0% 72.03% 169ms 0.9% std::unordered_set::count (inline) 71ms 0.38% 72.40% 168ms 0.89% __printf_fp_buffer_1 75ms 0.4% 72.80% 162ms 0.86% AbstractElement::GetNodeLocation 156ms 0.83% 73.63% 156ms 0.83% Node::GetIndex 106ms 0.56% 74.20% 153ms 0.81% std::_Rb_tree::equal_range (inline) 147ms 0.78% 74.98% 147ms 0.78% unlink_chunk 4ms 0.021% 75.00% 146ms 0.78% CellPropertyCollection::HasProperty 0 0% 75.00% 142ms 0.76% Cell::HasCellProperty (inline) 142ms 0.76% 75.75% 142ms 0.76% incircle 142ms 0.76% 76.51% 142ms 0.76% std::vector::size (inline) 0 0% 76.51% 137ms 0.73% std::_Hashtable::_M_insert (inline) 7ms 0.037% 76.55% 137ms 0.73% std::_Hashtable::_M_insert_unique_aux (inline) 0 0% 76.55% 137ms 0.73% std::__detail::_Insert_base::insert (inline) 0 0% 76.55% 137ms 0.73% std::unordered_set::insert (inline) 47ms 0.25% 76.80% 134ms 0.71% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 54ms 0.29% 77.08% 134ms 0.71% std::_Hashtable::_M_find_before_node (inline) 0 0% 77.08% 134ms 0.71% std::_Hashtable::_M_find_node (inline) 8ms 0.043% 77.13% 132ms 0.7% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 1ms 0.0053% 77.13% 131ms 0.7% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 38ms 0.2% 77.33% 130ms 0.69% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 8ms 0.043% 77.38% 130ms 0.69% std::_Hashtable::_M_insert_unique 72ms 0.38% 77.76% 129ms 0.69% std::_Rb_tree::_M_get_insert_unique_pos (inline) 128ms 0.68% 78.44% 128ms 0.68% AbstractCellMutationState::~AbstractCellMutationState 6ms 0.032% 78.47% 128ms 0.68% Node::~Node 118ms 0.63% 79.10% 128ms 0.68% vertexsort 9ms 0.048% 79.15% 125ms 0.66% MeshBasedCellPopulation::SpringsEnd 0 0% 79.15% 123ms 0.65% AbstractCellBasedWriter::OpenOutputFileForAppend 46ms 0.24% 79.39% 122ms 0.65% TetrahedralMesh::EdgeIterator::EdgeIterator 1ms 0.0053% 79.40% 119ms 0.63% OutputFileHandler::OpenOutputFile 1ms 0.0053% 79.40% 119ms 0.63% boost::numeric::ublas::vector_assign (inline) 15ms 0.08% 79.48% 117ms 0.62% boost::detail::shared_count::~shared_count (inline) 0 0% 79.48% 117ms 0.62% boost::shared_ptr::~shared_ptr (inline) 0 0% 79.48% 114ms 0.61% AbstractCellBasedSimulation::DoCellRemoval (inline) 10ms 0.053% 79.54% 113ms 0.6% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.0053% 79.54% 112ms 0.6% Cell::SetCellProliferativeType 112ms 0.6% 80.14% 112ms 0.6% std::_Rb_tree_increment 46ms 0.24% 80.38% 110ms 0.59% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 108ms 0.57% 80.96% 108ms 0.57% AbstractCellProperty::~AbstractCellProperty 0 0% 80.96% 106ms 0.56% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 22ms 0.12% 81.07% 106ms 0.56% TetrahedralMesh::EdgesEnd (partial-inline) 1ms 0.0053% 81.08% 105ms 0.56% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 102ms 0.54% 81.62% 102ms 0.54% std::_Rb_tree_insert_and_rebalance 23ms 0.12% 81.74% 102ms 0.54% std::num_put::_M_insert_int 42ms 0.22% 81.97% 101ms 0.54% std::__ostream_insert 97ms 0.52% 82.48% 100ms 0.53% boost::detail::sp_counted_base::release 6ms 0.032% 82.51% 100ms 0.53% boost::numeric::ublas::c_vector::c_vector (inline) 4ms 0.021% 82.53% 100ms 0.53% std::_Rb_tree::_M_emplace_hint_unique 100ms 0.53% 83.07% 100ms 0.53% std::_Rb_tree_rebalance_for_erase 2ms 0.011% 83.08% 98ms 0.52% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 9ms 0.048% 83.13% 95ms 0.51% Cylindrical2dMesh::CreateMirrorNodes 95ms 0.51% 83.63% 95ms 0.51% boost::shared_ptr::operator-> (inline)