File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 17273ms, 86.03% of 20077ms total Dropped 789 nodes (cum <= 100.39ms) flat flat% sum% cum cum% 0 0% 0% 20029ms 99.76% __libc_start_call_main 0 0% 0% 20029ms 99.76% __libc_start_main_impl 0 0% 0% 20029ms 99.76% _start 0 0% 0% 20009ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 20009ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 20009ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 20009ms 99.66% main 0 0% 0% 19967ms 99.45% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19967ms 99.45% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19967ms 99.45% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19941ms 99.32% AbstractCellBasedSimulation::Solve 0 0% 0% 15395ms 76.68% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.015% 0.015% 10065ms 50.13% AbstractCellBasedSimulation::DoCellBirth 3ms 0.015% 0.03% 9960ms 49.61% Cell::ReadyToDivide 4ms 0.02% 0.05% 9872ms 49.17% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.01% 0.06% 9734ms 48.48% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 12ms 0.06% 0.12% 9730ms 48.46% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.01% 0.13% 9718ms 48.40% CellCycleModelOdeHandler::SolveOdeToTime 69ms 0.34% 0.47% 9513ms 47.38% AbstractOneStepIvpOdeSolver::InternalSolve 889ms 4.43% 4.90% 8668ms 43.17% RungeKutta4IvpOdeSolver::CalculateNextYValue 3579ms 17.83% 22.73% 7577ms 37.74% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.005% 22.73% 5206ms 25.93% MeshBasedCellPopulation::Update 114ms 0.57% 23.30% 4045ms 20.15% AbstractCellProperty::IsType (inline) 4ms 0.02% 23.32% 4015ms 20.00% Cylindrical2dMesh::ReMesh 651ms 3.24% 26.56% 2823ms 14.06% AbstractCellProperty::IsSame 1ms 0.005% 26.57% 2527ms 12.59% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.005% 26.57% 2223ms 11.07% MutableMesh::ReMesh 2ms 0.01% 26.58% 2213ms 11.02% ForwardEulerNumericalMethod::UpdateAllNodePositions 399ms 1.99% 28.57% 2172ms 10.82% std::type_info::operator== (inline) 7ms 0.035% 28.60% 2164ms 10.78% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.005% 28.61% 2015ms 10.04% AbstractCellPopulation::WriteResultsToFiles 839ms 4.18% 32.79% 1880ms 9.36% std::_Rb_tree::_M_lower_bound (inline) 1695ms 8.44% 41.23% 1695ms 8.44% __strcmp_avx2 181ms 0.9% 42.13% 1685ms 8.39% TetrahedralMesh::EdgeIterator::operator++ 66ms 0.33% 42.46% 1404ms 6.99% std::_Rb_tree::find (inline) 1ms 0.005% 42.47% 1155ms 5.75% MeshBasedCellPopulation::UpdateNodePairs 8ms 0.04% 42.51% 1136ms 5.66% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 12ms 0.06% 42.57% 1112ms 5.54% TetrahedralMesh::ImportFromMesher 65ms 0.32% 42.89% 1102ms 5.49% operator new 11ms 0.055% 42.94% 1031ms 5.14% MeshBasedCellPopulation::SpringIterator::operator++ 239ms 1.19% 44.14% 1025ms 5.11% __GI___libc_malloc 8ms 0.04% 44.17% 1016ms 5.06% std::set::insert (inline) 12ms 0.06% 44.23% 1008ms 5.02% std::_Rb_tree::_M_insert_unique 33ms 0.16% 44.40% 971ms 4.84% std::__new_allocator::allocate (inline) 0 0% 44.40% 966ms 4.81% std::allocator_traits::allocate (inline) 1ms 0.005% 44.40% 838ms 4.17% triangulate 0 0% 44.40% 831ms 4.14% std::set::count (inline) 0 0% 44.40% 770ms 3.84% delaunay 1ms 0.005% 44.41% 770ms 3.84% divconqdelaunay 3ms 0.015% 44.42% 745ms 3.71% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 59ms 0.29% 44.72% 731ms 3.64% std::map::operator[] (partial-inline) 1ms 0.005% 44.72% 727ms 3.62% AbstractTwoBodyInteractionForce::AddForceContribution 708ms 3.53% 48.25% 708ms 3.53% std::_Rb_tree::_S_right (inline) 9ms 0.045% 48.29% 705ms 3.51% CellPopulationElementWriter::Visit 390ms 1.94% 50.24% 695ms 3.46% _int_malloc 646ms 3.22% 53.45% 658ms 3.28% WntCellCycleOdeSystem::CalculateStoppingEvent 29ms 0.14% 53.60% 647ms 3.22% std::less::operator() (inline) 0 0% 53.60% 638ms 3.18% std::_Rb_tree::_M_create_node (inline) 186ms 0.93% 54.53% 626ms 3.12% __dynamic_cast 32ms 0.16% 54.68% 618ms 3.08% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 618ms 3.08% 57.76% 618ms 3.08% std::operator< (inline) 24ms 0.12% 57.88% 616ms 3.07% std::_Rb_tree::_M_insert_ (inline) 0 0% 57.88% 609ms 3.03% std::_Rb_tree::_M_get_node (inline) 3ms 0.015% 57.90% 594ms 2.96% MeshBasedCellPopulation::AcceptCellWriter 4ms 0.02% 57.92% 592ms 2.95% CellPropertyCollection::GetPropertiesType (inline) 23ms 0.11% 58.03% 591ms 2.94% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 58.03% 583ms 2.90% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 58.03% 580ms 2.89% std::_Rb_tree::lower_bound (inline) 0 0% 58.03% 580ms 2.89% std::map::lower_bound (inline) 6ms 0.03% 58.06% 569ms 2.83% Element::Element 0 0% 58.06% 563ms 2.80% std::map::find (inline) 10ms 0.05% 58.11% 544ms 2.71% Cylindrical2dMesh::ReconstructCylindricalMesh 14ms 0.07% 58.18% 501ms 2.50% Element::RegisterWithNodes (inline) 1ms 0.005% 58.19% 496ms 2.47% std::ostream::operator<< (inline) 79ms 0.39% 58.58% 495ms 2.47% std::ostream::_M_insert 345ms 1.72% 60.30% 490ms 2.44% AbstractCellMutationState::AbstractCellMutationState 8ms 0.04% 60.34% 488ms 2.43% MutableMesh::ReIndex 12ms 0.06% 60.40% 488ms 2.43% Node::AddElement 3ms 0.015% 60.41% 472ms 2.35% AbstractCellProperty::IsSubType (inline) 10ms 0.05% 60.46% 447ms 2.23% Cylindrical2dMesh::CorrectNonPeriodicMesh 22ms 0.11% 60.57% 425ms 2.12% divconqrecurse 129ms 0.64% 61.21% 397ms 1.98% __GI___libc_free 124ms 0.62% 61.83% 397ms 1.98% mergehulls 136ms 0.68% 62.51% 380ms 1.89% std::_Rb_tree::_M_get_insert_unique_pos 8ms 0.04% 62.55% 371ms 1.85% std::_Rb_tree::erase 1ms 0.005% 62.55% 371ms 1.85% std::set::erase (inline) 8ms 0.04% 62.59% 359ms 1.79% Node::RemoveElement 1ms 0.005% 62.60% 358ms 1.78% std::_Vector_base::_M_allocate (inline) 357ms 1.78% 64.38% 357ms 1.78% std::type_info::name (inline) 113ms 0.56% 64.94% 349ms 1.74% std::_Rb_tree::_M_erase 31ms 0.15% 65.09% 331ms 1.65% std::_Rb_tree::~_Rb_tree (inline) 161ms 0.8% 65.90% 328ms 1.63% __cxxabiv1::__si_class_type_info::__do_dyncast 23ms 0.11% 66.01% 324ms 1.61% Element::ResetIndex 1ms 0.005% 66.02% 323ms 1.61% NodeLocationWriter::Visit 0 0% 66.02% 319ms 1.59% Cell::GetMutationState 8ms 0.04% 66.06% 318ms 1.58% std::__new_allocator::deallocate (inline) 2ms 0.01% 66.07% 315ms 1.57% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 66.07% 315ms 1.57% std::allocator_traits::deallocate (inline) 3ms 0.015% 66.08% 314ms 1.56% AbstractCellPopulation::GetLocationIndexUsingCell 4ms 0.02% 66.10% 314ms 1.56% Cell::GetCellProliferativeType 0 0% 66.10% 312ms 1.55% std::set::~set (inline) 41ms 0.2% 66.30% 311ms 1.55% AbstractCellPopulation::Iterator::IsRealCell (inline) 5ms 0.025% 66.33% 293ms 1.46% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 24ms 0.12% 66.45% 293ms 1.46% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 66.45% 290ms 1.44% std::_Rb_tree::_M_drop_node (inline) 3ms 0.015% 66.46% 289ms 1.44% LegacyCellProliferativeTypesWriter::VisitCell 17ms 0.085% 66.55% 277ms 1.38% AbstractTetrahedralElement::CalculateJacobian 22ms 0.11% 66.66% 277ms 1.38% std::num_put::_M_insert_float 214ms 1.07% 67.72% 267ms 1.33% _int_free 0 0% 67.72% 261ms 1.30% std::set::set (inline) 254ms 1.27% 68.99% 256ms 1.28% std::vector::operator[] (inline) 3ms 0.015% 69.00% 253ms 1.26% AbstractCellPopulation::IsCellAttachedToLocationIndex 3ms 0.015% 69.02% 252ms 1.26% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 0 0% 69.02% 248ms 1.24% std::_Rb_tree::_M_put_node (inline) 8ms 0.04% 69.06% 244ms 1.22% std::vector::push_back (inline) 3ms 0.015% 69.07% 242ms 1.21% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.005% 69.08% 241ms 1.20% TetrahedralMesh::RefreshJacobianCachedData 74ms 0.37% 69.45% 238ms 1.19% ApcOneHitCellMutationState::ApcOneHitCellMutationState 24ms 0.12% 69.57% 233ms 1.16% std::_Rb_tree::_M_copy (inline) 16ms 0.08% 69.65% 229ms 1.14% std::vector::_M_realloc_insert 5ms 0.025% 69.67% 228ms 1.14% alternateaxes 48ms 0.24% 69.91% 225ms 1.12% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 7ms 0.035% 69.95% 224ms 1.12% std::_Rb_tree::_M_erase_aux (inline) 216ms 1.08% 71.02% 223ms 1.11% vertexmedian 219ms 1.09% 72.11% 219ms 1.09% [libchaste_cell_based.so] 28ms 0.14% 72.25% 211ms 1.05% AbstractTetrahedralElement::RefreshJacobian 62ms 0.31% 72.56% 209ms 1.04% std::_Rb_tree::_M_clone_node (inline) 46ms 0.23% 72.79% 208ms 1.04% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 12ms 0.06% 72.85% 206ms 1.03% Element::MarkAsDeleted 0 0% 72.85% 205ms 1.02% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 72.85% 205ms 1.02% MeshBasedCellPopulation::GetDampingConstant 2ms 0.01% 72.86% 205ms 1.02% std::__cxx11::collate::do_transform 17ms 0.085% 72.94% 202ms 1.01% TetrahedralMesh::Clear 8ms 0.04% 72.98% 199ms 0.99% AbstractTetrahedralElement::CalculateInverseJacobian 152ms 0.76% 73.74% 197ms 0.98% AbstractElement::GetNodeGlobalIndex 4ms 0.02% 73.76% 196ms 0.98% ___vsnprintf 1ms 0.005% 73.77% 193ms 0.96% OffLatticeSimulation::ApplyBoundaries 0 0% 73.77% 192ms 0.96% __vsnprintf_internal (inline) 145ms 0.72% 74.49% 187ms 0.93% malloc_consolidate 21ms 0.1% 74.59% 186ms 0.93% __printf_buffer 6ms 0.03% 74.62% 185ms 0.92% CellPropertyCollection::HasProperty 6ms 0.03% 74.65% 183ms 0.91% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 74.65% 181ms 0.9% Cell::HasCellProperty (inline) 3ms 0.015% 74.67% 179ms 0.89% CellProliferativeTypesWriter::VisitCell 179ms 0.89% 75.56% 179ms 0.89% std::_Rb_tree_insert_and_rebalance 173ms 0.86% 76.42% 173ms 0.86% incircle 171ms 0.85% 77.27% 171ms 0.85% Node::GetIndex 68ms 0.34% 77.61% 167ms 0.83% AbstractElement::GetNodeLocation 4ms 0.02% 77.63% 162ms 0.81% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 50ms 0.25% 77.88% 156ms 0.78% TetrahedralMesh::EdgesEnd 1ms 0.005% 77.89% 152ms 0.76% __printf_fp_spec (inline) 7ms 0.035% 77.92% 151ms 0.75% MeshBasedCellPopulation::SpringsEnd (inline) 3ms 0.015% 77.93% 151ms 0.75% __printf_fp_l_buffer 151ms 0.75% 78.69% 151ms 0.75% unlink_chunk 103ms 0.51% 79.20% 149ms 0.74% std::_Rb_tree::equal_range (inline) 147ms 0.73% 79.93% 147ms 0.73% std::vector::size (inline) 10ms 0.05% 79.98% 144ms 0.72% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 68ms 0.34% 80.32% 141ms 0.7% __printf_fp_buffer_1 51ms 0.25% 80.57% 130ms 0.65% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 1ms 0.005% 80.58% 130ms 0.65% boost::numeric::ublas::vector_assign (inline) 77ms 0.38% 80.96% 127ms 0.63% Cylindrical2dMesh::GetVectorFromAtoB 1ms 0.005% 80.97% 127ms 0.63% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 11ms 0.055% 81.02% 124ms 0.62% boost::detail::shared_count::~shared_count (inline) 0 0% 81.02% 124ms 0.62% boost::shared_ptr::~shared_ptr (inline) 0 0% 81.02% 123ms 0.61% AbstractCellBasedSimulation::DoCellRemoval (inline) 34ms 0.17% 81.19% 121ms 0.6% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 10ms 0.05% 81.24% 121ms 0.6% Node::~Node 2ms 0.01% 81.25% 117ms 0.58% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 47ms 0.23% 81.49% 117ms 0.58% std::__ostream_insert 0 0% 81.49% 114ms 0.57% AbstractCellBasedWriter::OpenOutputFileForAppend 13ms 0.065% 81.55% 114ms 0.57% boost::numeric::ublas::c_vector::c_vector (inline) 23ms 0.11% 81.67% 112ms 0.56% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 108ms 0.54% 82.20% 112ms 0.56% boost::detail::sp_counted_base::release 0 0% 82.20% 110ms 0.55% OutputFileHandler::OpenOutputFile 109ms 0.54% 82.75% 109ms 0.54% boost::shared_ptr::operator-> (inline) 100ms 0.5% 83.24% 108ms 0.54% vertexsort 1ms 0.005% 83.25% 107ms 0.53% Cell::SetCellProliferativeType 106ms 0.53% 83.78% 106ms 0.53% AbstractCellProperty::~AbstractCellProperty 36ms 0.18% 83.96% 104ms 0.52% boost::numeric::ublas::indexing_vector_assign 103ms 0.51% 84.47% 103ms 0.51% AbstractCellMutationState::~AbstractCellMutationState 2ms 0.01% 84.48% 103ms 0.51% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 103ms 0.51% 84.99% 103ms 0.51% [libchaste_mesh.so] 103ms 0.51% 85.51% 103ms 0.51% std::_Rb_tree_increment 4ms 0.02% 85.53% 103ms 0.51% std::operator<< (inline) 0 0% 85.53% 102ms 0.51% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 102ms 0.51% 86.03% 102ms 0.51% AbstractElement::IsDeleted