File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 15806ms, 83.36% of 18962ms total Dropped 836 nodes (cum <= 94.81ms) flat flat% sum% cum cum% 0 0% 0% 18915ms 99.75% __libc_start_call_main 0 0% 0% 18915ms 99.75% __libc_start_main_impl 0 0% 0% 18915ms 99.75% _start 0 0% 0% 18896ms 99.65% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 18896ms 99.65% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 18896ms 99.65% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 18896ms 99.65% main 0 0% 0% 18861ms 99.47% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 18861ms 99.47% CxxTest::TestRunner::runTest (inline) 0 0% 0% 18861ms 99.47% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 18835ms 99.33% AbstractCellBasedSimulation::Solve 0 0% 0% 15008ms 79.15% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 10106ms 53.30% AbstractCellBasedSimulation::DoCellBirth 13ms 0.069% 0.069% 10023ms 52.86% Cell::ReadyToDivide 5ms 0.026% 0.095% 9927ms 52.35% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.095% 9784ms 51.60% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 17ms 0.09% 0.18% 9774ms 51.55% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.011% 0.2% 9755ms 51.44% CellCycleModelOdeHandler::SolveOdeToTime 93ms 0.49% 0.69% 9553ms 50.38% AbstractOneStepIvpOdeSolver::InternalSolve 897ms 4.73% 5.42% 8721ms 45.99% RungeKutta4IvpOdeSolver::CalculateNextYValue 3629ms 19.14% 24.55% 7586ms 40.01% WntCellCycleOdeSystem::EvaluateYDerivatives 3ms 0.016% 24.57% 4801ms 25.32% MeshBasedCellPopulation::Update 4ms 0.021% 24.59% 4113ms 21.69% Cylindrical2dMesh::ReMesh 92ms 0.49% 25.08% 4015ms 21.17% AbstractCellProperty::IsType (inline) 556ms 2.93% 28.01% 2826ms 14.90% AbstractCellProperty::IsSame 432ms 2.28% 30.29% 2270ms 11.97% std::type_info::operator== (inline) 0 0% 30.29% 2267ms 11.96% MutableMesh::ReMesh 1ms 0.0053% 30.29% 2024ms 10.67% AbstractCellPopulation::WriteResultsToFiles 1846ms 9.74% 40.03% 1846ms 9.74% __strcmp_avx2 1ms 0.0053% 40.03% 1796ms 9.47% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 40.03% 1513ms 7.98% ForwardEulerNumericalMethod::UpdateAllNodePositions 14ms 0.074% 40.11% 1463ms 7.72% AbstractNumericalMethod::ComputeForcesIncludingDamping 17ms 0.09% 40.20% 1141ms 6.02% TetrahedralMesh::ImportFromMesher 475ms 2.51% 42.70% 1072ms 5.65% std::_Rb_tree::_M_lower_bound (inline) 52ms 0.27% 42.98% 972ms 5.13% operator new 187ms 0.99% 43.96% 904ms 4.77% __GI___libc_malloc 43ms 0.23% 44.19% 848ms 4.47% std::__new_allocator::allocate (inline) 0 0% 44.19% 843ms 4.45% std::allocator_traits::allocate (inline) 2ms 0.011% 44.20% 827ms 4.36% triangulate 0 0% 44.20% 743ms 3.92% delaunay 1ms 0.0053% 44.20% 743ms 3.92% divconqdelaunay 250ms 1.32% 45.52% 735ms 3.88% __dynamic_cast 52ms 0.27% 45.80% 726ms 3.83% std::map::operator[] (partial-inline) 3ms 0.016% 45.81% 725ms 3.82% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 0 0% 45.81% 720ms 3.80% AbstractTwoBodyInteractionForce::AddForceContribution 9ms 0.047% 45.86% 691ms 3.64% CellPopulationElementWriter::Visit 680ms 3.59% 49.45% 680ms 3.59% std::_Rb_tree::_S_right (inline) 29ms 0.15% 49.60% 657ms 3.46% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 13ms 0.069% 49.67% 655ms 3.45% CellPropertyCollection::GetPropertiesType (inline) 4ms 0.021% 49.69% 649ms 3.42% MeshBasedCellPopulation::UpdateNodePairs 397ms 2.09% 51.78% 649ms 3.42% _int_malloc 625ms 3.30% 55.08% 631ms 3.33% WntCellCycleOdeSystem::CalculateStoppingEvent 16ms 0.084% 55.16% 612ms 3.23% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 55.16% 593ms 3.13% MeshBasedCellPopulation::AcceptCellWriter 0 0% 55.16% 578ms 3.05% std::_Rb_tree::lower_bound (inline) 0 0% 55.16% 578ms 3.05% std::map::lower_bound (inline) 1ms 0.0053% 55.17% 545ms 2.87% Element::Element 53ms 0.28% 55.45% 539ms 2.84% TetrahedralMesh::EdgeIterator::operator++ 3ms 0.016% 55.46% 527ms 2.78% AbstractCellProperty::IsSubType (inline) 8ms 0.042% 55.51% 517ms 2.73% MutableMesh::ReIndex 35ms 0.18% 55.69% 517ms 2.73% std::_Rb_tree::find (inline) 4ms 0.021% 55.71% 512ms 2.70% std::_Rb_tree::_M_insert_unique 0 0% 55.71% 512ms 2.70% std::set::insert (inline) 0 0% 55.71% 510ms 2.69% std::map::find (inline) 7ms 0.037% 55.75% 492ms 2.59% Cylindrical2dMesh::ReconstructCylindricalMesh 9ms 0.047% 55.80% 483ms 2.55% Cylindrical2dMesh::CorrectNonPeriodicMesh 164ms 0.86% 56.66% 481ms 2.54% __GI___libc_free 9ms 0.047% 56.71% 475ms 2.51% Element::RegisterWithNodes (inline) 324ms 1.71% 58.42% 470ms 2.48% AbstractCellMutationState::AbstractCellMutationState 12ms 0.063% 58.48% 470ms 2.48% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 58.48% 468ms 2.47% std::ostream::operator<< (inline) 72ms 0.38% 58.86% 467ms 2.46% std::ostream::_M_insert 9ms 0.047% 58.91% 459ms 2.42% Node::AddElement 0 0% 58.91% 450ms 2.37% std::_Rb_tree::_M_create_node (inline) 0 0% 58.91% 428ms 2.26% std::_Rb_tree::_M_get_node (inline) 6ms 0.032% 58.94% 421ms 2.22% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 30ms 0.16% 59.10% 409ms 2.16% std::__new_allocator::deallocate (inline) 0 0% 59.10% 402ms 2.12% std::allocator_traits::deallocate (inline) 0 0% 59.10% 391ms 2.06% std::_Rb_tree::_Alloc_node::operator() (inline) 11ms 0.058% 59.16% 385ms 2.03% std::_Rb_tree::erase 0 0% 59.16% 385ms 2.03% std::set::erase (inline) 15ms 0.079% 59.23% 379ms 2.00% Node::RemoveElement 22ms 0.12% 59.35% 373ms 1.97% std::_Rb_tree::_M_insert_ (inline) 162ms 0.85% 60.20% 371ms 1.96% __cxxabiv1::__si_class_type_info::__do_dyncast 13ms 0.069% 60.27% 364ms 1.92% divconqrecurse 3ms 0.016% 60.29% 355ms 1.87% Cell::GetCellProliferativeType 1ms 0.0053% 60.29% 353ms 1.86% Cell::GetMutationState 106ms 0.56% 60.85% 346ms 1.82% mergehulls 96ms 0.51% 61.36% 325ms 1.71% std::_Rb_tree::_M_erase 31ms 0.16% 61.52% 322ms 1.70% Element::ResetIndex 3ms 0.016% 61.54% 318ms 1.68% NodeLocationWriter::Visit 222ms 1.17% 62.71% 316ms 1.67% _int_free 316ms 1.67% 64.38% 316ms 1.67% std::type_info::name (inline) 3ms 0.016% 64.39% 305ms 1.61% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 3ms 0.016% 64.41% 301ms 1.59% std::_Vector_base::_M_allocate (inline) 3ms 0.016% 64.42% 298ms 1.57% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 64.42% 298ms 1.57% std::_Rb_tree::_M_drop_node (inline) 4ms 0.021% 64.44% 286ms 1.51% LegacyCellProliferativeTypesWriter::VisitCell 23ms 0.12% 64.57% 279ms 1.47% AbstractTetrahedralElement::CalculateJacobian 13ms 0.069% 64.63% 275ms 1.45% std::_Rb_tree::~_Rb_tree (inline) 265ms 1.40% 66.03% 266ms 1.40% std::vector::operator[] (inline) 0 0% 66.03% 262ms 1.38% std::_Rb_tree::_M_put_node (inline) 7ms 0.037% 66.07% 262ms 1.38% std::vector::push_back (inline) 1ms 0.0053% 66.07% 261ms 1.38% TetrahedralMesh::RefreshJacobianCachedData 12ms 0.063% 66.14% 260ms 1.37% std::num_put::_M_insert_float 2ms 0.011% 66.15% 259ms 1.37% AbstractCellPopulation::Iterator::operator++ (inline) 28ms 0.15% 66.30% 256ms 1.35% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.0053% 66.30% 254ms 1.34% std::set::set (inline) 10ms 0.053% 66.35% 253ms 1.33% std::_Rb_tree::_Rb_tree 0 0% 66.35% 248ms 1.31% std::set::~set (inline) 6ms 0.032% 66.39% 247ms 1.30% AbstractCellPopulation::IsCellAttachedToLocationIndex 15ms 0.079% 66.46% 245ms 1.29% std::vector::_M_realloc_insert 1ms 0.0053% 66.47% 244ms 1.29% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 66.47% 244ms 1.29% MeshBasedCellPopulation::GetDampingConstant 2ms 0.011% 66.48% 242ms 1.28% alternateaxes 230ms 1.21% 67.69% 239ms 1.26% vertexmedian 10ms 0.053% 67.75% 233ms 1.23% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 30ms 0.16% 67.90% 232ms 1.22% TetrahedralMesh::Clear 69ms 0.36% 68.27% 229ms 1.21% ApcOneHitCellMutationState::ApcOneHitCellMutationState 9ms 0.047% 68.32% 229ms 1.21% std::_Rb_tree::_M_erase_aux (inline) 14ms 0.074% 68.39% 225ms 1.19% std::_Rb_tree::_M_copy (inline) 165ms 0.87% 69.26% 221ms 1.17% AbstractElement::GetNodeGlobalIndex 16ms 0.084% 69.34% 215ms 1.13% AbstractTetrahedralElement::CalculateInverseJacobian 28ms 0.15% 69.49% 212ms 1.12% AbstractTetrahedralElement::RefreshJacobian 37ms 0.2% 69.69% 208ms 1.10% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 13ms 0.069% 69.76% 208ms 1.10% Element::MarkAsDeleted 86ms 0.45% 70.21% 207ms 1.09% std::_Rb_tree::_M_clone_node (inline) 1ms 0.0053% 70.21% 207ms 1.09% std::__cxx11::collate::do_transform 3ms 0.016% 70.23% 203ms 1.07% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 41ms 0.22% 70.45% 201ms 1.06% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 6ms 0.032% 70.48% 200ms 1.05% ___vsnprintf 142ms 0.75% 71.23% 200ms 1.05% malloc_consolidate 1ms 0.0053% 71.23% 199ms 1.05% CellProliferativeTypesWriter::VisitCell 0 0% 71.23% 195ms 1.03% __vsnprintf_internal (inline) 23ms 0.12% 71.35% 192ms 1.01% __printf_buffer 187ms 0.99% 72.34% 187ms 0.99% [libchaste_cell_based.so] 4ms 0.021% 72.36% 182ms 0.96% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 72.36% 181ms 0.95% std::_Hashtable::count (inline) 2ms 0.011% 72.37% 181ms 0.95% std::_Hashtable::find (inline) 0 0% 72.37% 181ms 0.95% std::unordered_set::count (inline) 0 0% 72.37% 179ms 0.94% OffLatticeSimulation::ApplyBoundaries 63ms 0.33% 72.70% 165ms 0.87% AbstractElement::GetNodeLocation 3ms 0.016% 72.72% 157ms 0.83% CellPropertyCollection::HasProperty 156ms 0.82% 73.54% 156ms 0.82% std::vector::size (inline) 1ms 0.0053% 73.55% 155ms 0.82% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 0 0% 73.55% 154ms 0.81% Cell::HasCellProperty (inline) 1ms 0.0053% 73.55% 152ms 0.8% __printf_fp_spec (inline) 96ms 0.51% 74.06% 152ms 0.8% std::_Rb_tree::equal_range (inline) 151ms 0.8% 74.85% 151ms 0.8% Node::GetIndex 7ms 0.037% 74.89% 151ms 0.8% __printf_fp_l_buffer 146ms 0.77% 75.66% 146ms 0.77% incircle 146ms 0.77% 76.43% 146ms 0.77% unlink_chunk 65ms 0.34% 76.77% 138ms 0.73% __printf_fp_buffer_1 0 0% 76.77% 137ms 0.72% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 67ms 0.35% 77.13% 135ms 0.71% std::_Rb_tree::_M_get_insert_unique_pos (inline) 0 0% 77.13% 132ms 0.7% std::_Hashtable::_M_insert (inline) 7ms 0.037% 77.16% 132ms 0.7% std::_Hashtable::_M_insert_unique_aux (inline) 0 0% 77.16% 132ms 0.7% std::__detail::_Insert_base::insert (inline) 0 0% 77.16% 132ms 0.7% std::unordered_set::insert (inline) 54ms 0.28% 77.45% 130ms 0.69% std::_Hashtable::_M_find_before_node (inline) 0 0% 77.45% 130ms 0.69% std::_Hashtable::_M_find_node (inline) 122ms 0.64% 78.09% 129ms 0.68% vertexsort 43ms 0.23% 78.32% 126ms 0.66% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 8ms 0.042% 78.36% 125ms 0.66% std::_Hashtable::_M_insert_unique 0 0% 78.36% 121ms 0.64% AbstractCellBasedWriter::OpenOutputFileForAppend 12ms 0.063% 78.43% 121ms 0.64% Node::~Node 37ms 0.2% 78.62% 119ms 0.63% TetrahedralMesh::EdgeIterator::EdgeIterator 40ms 0.21% 78.83% 118ms 0.62% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 2ms 0.011% 78.84% 118ms 0.62% Cell::SetCellProliferativeType 0 0% 78.84% 118ms 0.62% OutputFileHandler::OpenOutputFile 115ms 0.61% 79.45% 115ms 0.61% AbstractCellMutationState::~AbstractCellMutationState 44ms 0.23% 79.68% 113ms 0.6% std::__ostream_insert 112ms 0.59% 80.27% 112ms 0.59% AbstractCellProperty::~AbstractCellProperty 35ms 0.18% 80.46% 110ms 0.58% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 1ms 0.0053% 80.46% 108ms 0.57% std::vector::resize (inline) 107ms 0.56% 81.03% 107ms 0.56% std::_Rb_tree_insert_and_rebalance 1ms 0.0053% 81.03% 107ms 0.56% std::vector::_M_default_append 7ms 0.037% 81.07% 106ms 0.56% MeshBasedCellPopulation::SpringsEnd 103ms 0.54% 81.61% 103ms 0.54% std::_Rb_tree_increment 103ms 0.54% 82.15% 103ms 0.54% std::_Rb_tree_rebalance_for_erase 101ms 0.53% 82.69% 101ms 0.53% TetrahedralMesh::EdgeIterator::operator!= 0 0% 82.69% 101ms 0.53% boost::numeric::ublas::vector_assign (inline) 10ms 0.053% 82.74% 100ms 0.53% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 82.74% 99ms 0.52% AbstractCellBasedSimulation::DoCellRemoval (inline) 1ms 0.0053% 82.74% 99ms 0.52% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 82.74% 99ms 0.52% NodeMap::NodeMap 0 0% 82.74% 99ms 0.52% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 14ms 0.074% 82.82% 99ms 0.52% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 82.82% 99ms 0.52% std::_Hashtable::~_Hashtable (inline) 0 0% 82.82% 99ms 0.52% std::unordered_set::~unordered_set (inline) 1ms 0.0053% 82.82% 98ms 0.52% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 97ms 0.51% 83.34% 97ms 0.51% [libchaste_mesh.so] 2ms 0.011% 83.35% 97ms 0.51% std::operator<< (inline) 2ms 0.011% 83.36% 96ms 0.51% std::_Rb_tree::_M_emplace_hint_unique