File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16716ms, 84.41% of 19803ms total Dropped 780 nodes (cum <= 99.02ms) flat flat% sum% cum cum% 0 0% 0% 19757ms 99.77% __libc_start_call_main 0 0% 0% 19757ms 99.77% __libc_start_main_impl 0 0% 0% 19757ms 99.77% _start 0 0% 0% 19736ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19736ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19736ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19736ms 99.66% main 0 0% 0% 19693ms 99.44% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19693ms 99.44% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19693ms 99.44% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19666ms 99.31% AbstractCellBasedSimulation::Solve 0 0% 0% 15082ms 76.16% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.005% 0.005% 9603ms 48.49% AbstractCellBasedSimulation::DoCellBirth 4ms 0.02% 0.025% 9495ms 47.95% Cell::ReadyToDivide 5ms 0.025% 0.05% 9416ms 47.55% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.01% 0.061% 9258ms 46.75% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 8ms 0.04% 0.1% 9249ms 46.71% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.015% 0.12% 9235ms 46.63% CellCycleModelOdeHandler::SolveOdeToTime 61ms 0.31% 0.42% 9055ms 45.73% AbstractOneStepIvpOdeSolver::InternalSolve 1035ms 5.23% 5.65% 8154ms 41.18% RungeKutta4IvpOdeSolver::CalculateNextYValue 2918ms 14.74% 20.39% 6881ms 34.75% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 20.39% 5367ms 27.10% MeshBasedCellPopulation::Update 2ms 0.01% 20.40% 4159ms 21.00% Cylindrical2dMesh::ReMesh 75ms 0.38% 20.77% 3954ms 19.97% AbstractCellProperty::IsType (inline) 342ms 1.73% 22.50% 2589ms 13.07% AbstractCellProperty::IsSame 1ms 0.005% 22.51% 2553ms 12.89% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 22.51% 2248ms 11.35% MutableMesh::ReMesh 269ms 1.36% 23.87% 2247ms 11.35% std::type_info::operator== (inline) 1ms 0.005% 23.87% 2246ms 11.34% ForwardEulerNumericalMethod::UpdateAllNodePositions 12ms 0.061% 23.93% 2196ms 11.09% AbstractNumericalMethod::ComputeForcesIncludingDamping 2089ms 10.55% 34.48% 2089ms 10.55% __strcmp_avx2 1ms 0.005% 34.48% 2023ms 10.22% AbstractCellPopulation::WriteResultsToFiles 779ms 3.93% 38.42% 1858ms 9.38% std::_Rb_tree::_M_lower_bound (inline) 187ms 0.94% 39.36% 1681ms 8.49% TetrahedralMesh::EdgeIterator::operator++ 81ms 0.41% 39.77% 1361ms 6.87% std::_Rb_tree::find (inline) 1ms 0.005% 39.78% 1174ms 5.93% MeshBasedCellPopulation::UpdateNodePairs 7ms 0.035% 39.81% 1145ms 5.78% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 11ms 0.056% 39.87% 1141ms 5.76% TetrahedralMesh::ImportFromMesher 44ms 0.22% 40.09% 1091ms 5.51% operator new 15ms 0.076% 40.17% 1037ms 5.24% MeshBasedCellPopulation::SpringIterator::operator++ 241ms 1.22% 41.38% 1032ms 5.21% __GI___libc_malloc 15ms 0.076% 41.46% 988ms 4.99% std::set::insert (inline) 17ms 0.086% 41.54% 973ms 4.91% std::_Rb_tree::_M_insert_unique 29ms 0.15% 41.69% 947ms 4.78% std::__new_allocator::allocate (inline) 0 0% 41.69% 944ms 4.77% std::allocator_traits::allocate (inline) 0 0% 41.69% 850ms 4.29% triangulate 0 0% 41.69% 824ms 4.16% std::set::count (inline) 0 0% 41.69% 783ms 3.95% delaunay 5ms 0.025% 41.72% 782ms 3.95% divconqdelaunay 73ms 0.37% 42.08% 771ms 3.89% std::map::operator[] (partial-inline) 6ms 0.03% 42.11% 770ms 3.89% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 3ms 0.015% 42.13% 758ms 3.83% AbstractTwoBodyInteractionForce::AddForceContribution 744ms 3.76% 45.89% 744ms 3.76% WntCellCycleOdeSystem::CalculateStoppingEvent 729ms 3.68% 49.57% 729ms 3.68% std::_Rb_tree::_S_right (inline) 7ms 0.035% 49.60% 713ms 3.60% CellPopulationElementWriter::Visit 394ms 1.99% 51.59% 689ms 3.48% _int_malloc 203ms 1.03% 52.62% 660ms 3.33% __dynamic_cast 34ms 0.17% 52.79% 659ms 3.33% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 21ms 0.11% 52.90% 643ms 3.25% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 52.90% 619ms 3.13% std::_Rb_tree::_M_create_node (inline) 17ms 0.086% 52.98% 618ms 3.12% std::less::operator() (inline) 601ms 3.03% 56.02% 601ms 3.03% std::operator< (inline) 0 0% 56.02% 597ms 3.01% std::_Rb_tree::lower_bound (inline) 0 0% 56.02% 597ms 3.01% std::map::lower_bound (inline) 7ms 0.035% 56.05% 592ms 2.99% MeshBasedCellPopulation::AcceptCellWriter 35ms 0.18% 56.23% 587ms 2.96% std::_Rb_tree::_M_insert_ (inline) 0 0% 56.23% 585ms 2.95% std::_Rb_tree::_M_get_node (inline) 1ms 0.005% 56.23% 574ms 2.90% CellPropertyCollection::GetPropertiesType (inline) 10ms 0.05% 56.28% 561ms 2.83% MutableMesh::ReIndex 0 0% 56.28% 554ms 2.80% std::_Rb_tree::_Alloc_node::operator() (inline) 5ms 0.025% 56.31% 537ms 2.71% Element::Element 0 0% 56.31% 535ms 2.70% std::map::find (inline) 7ms 0.035% 56.34% 516ms 2.61% Cylindrical2dMesh::CorrectNonPeriodicMesh 1ms 0.005% 56.35% 491ms 2.48% std::ostream::operator<< (inline) 15ms 0.076% 56.43% 489ms 2.47% Element::RegisterWithNodes (inline) 74ms 0.37% 56.80% 489ms 2.47% std::ostream::_M_insert 1ms 0.005% 56.80% 480ms 2.42% AbstractCellProperty::IsSubType (inline) 12ms 0.061% 56.87% 471ms 2.38% Node::AddElement 143ms 0.72% 57.59% 470ms 2.37% __GI___libc_free 10ms 0.05% 57.64% 460ms 2.32% Cylindrical2dMesh::ReconstructCylindricalMesh 291ms 1.47% 59.11% 432ms 2.18% AbstractCellMutationState::AbstractCellMutationState 115ms 0.58% 59.69% 406ms 2.05% std::_Rb_tree::_M_erase 13ms 0.066% 59.75% 391ms 1.97% std::__new_allocator::deallocate (inline) 0 0% 59.75% 388ms 1.96% std::allocator_traits::deallocate (inline) 1ms 0.005% 59.76% 387ms 1.95% std::set::erase (inline) 16ms 0.081% 59.84% 386ms 1.95% std::_Rb_tree::erase 11ms 0.056% 59.89% 376ms 1.90% Node::RemoveElement 27ms 0.14% 60.03% 374ms 1.89% std::_Rb_tree::~_Rb_tree (inline) 137ms 0.69% 60.72% 369ms 1.86% std::_Rb_tree::_M_get_insert_unique_pos 2ms 0.01% 60.73% 361ms 1.82% std::_Vector_base::_M_allocate (inline) 0 0% 60.73% 358ms 1.81% std::_Rb_tree::_M_drop_node (inline) 0 0% 60.73% 352ms 1.78% std::set::~set (inline) 26ms 0.13% 60.86% 349ms 1.76% Element::ResetIndex 9ms 0.045% 60.91% 345ms 1.74% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 335ms 1.69% 62.60% 337ms 1.70% std::vector::operator[] (inline) 166ms 0.84% 63.44% 335ms 1.69% __cxxabiv1::__si_class_type_info::__do_dyncast 15ms 0.076% 63.52% 334ms 1.69% divconqrecurse 270ms 1.36% 64.88% 326ms 1.65% _int_free 0 0% 64.88% 326ms 1.65% std::_Rb_tree::_M_put_node (inline) 324ms 1.64% 66.52% 324ms 1.64% [libchaste_cell_based.so] 101ms 0.51% 67.03% 312ms 1.58% mergehulls 0 0% 67.03% 307ms 1.55% Cell::GetMutationState 1ms 0.005% 67.03% 304ms 1.54% Cell::GetCellProliferativeType 4ms 0.02% 67.05% 303ms 1.53% LegacyCellProliferativeTypesWriter::VisitCell 8ms 0.04% 67.09% 297ms 1.50% AbstractCellPopulation::GetLocationIndexUsingCell 3ms 0.015% 67.11% 287ms 1.45% alternateaxes 14ms 0.071% 67.18% 285ms 1.44% std::vector::push_back (inline) 269ms 1.36% 68.54% 282ms 1.42% vertexmedian 2ms 0.01% 68.55% 281ms 1.42% NodeLocationWriter::Visit 0 0% 68.55% 279ms 1.41% AbstractCellPopulation::Iterator::operator++ (inline) 52ms 0.26% 68.81% 276ms 1.39% AbstractCellPopulation::Iterator::IsRealCell (inline) 11ms 0.056% 68.86% 269ms 1.36% std::_Rb_tree::_Rb_tree (partial-inline) 8ms 0.04% 68.90% 264ms 1.33% AbstractCellPopulation::IsCellAttachedToLocationIndex 16ms 0.081% 68.98% 264ms 1.33% std::vector::_M_realloc_insert 21ms 0.11% 69.09% 247ms 1.25% AbstractTetrahedralElement::CalculateJacobian 15ms 0.076% 69.17% 245ms 1.24% std::num_put::_M_insert_float 55ms 0.28% 69.44% 242ms 1.22% ApcOneHitCellMutationState::ApcOneHitCellMutationState 2ms 0.01% 69.45% 242ms 1.22% std::set::set (inline) 89ms 0.45% 69.90% 238ms 1.20% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 21ms 0.11% 70.01% 235ms 1.19% TetrahedralMesh::Clear 25ms 0.13% 70.14% 232ms 1.17% std::_Rb_tree::_M_copy (inline) 10ms 0.05% 70.19% 230ms 1.16% std::_Rb_tree::_M_erase_aux (inline) 1ms 0.005% 70.19% 228ms 1.15% TetrahedralMesh::RefreshJacobianCachedData 99ms 0.5% 70.69% 226ms 1.14% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 7ms 0.035% 70.73% 219ms 1.11% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 5ms 0.025% 70.75% 211ms 1.07% std::__cxx11::collate::do_transform 134ms 0.68% 71.43% 207ms 1.05% AbstractElement::GetNodeGlobalIndex 16ms 0.081% 71.51% 206ms 1.04% Element::MarkAsDeleted 5ms 0.025% 71.53% 204ms 1.03% AbstractTetrahedralElement::CalculateInverseJacobian 3ms 0.015% 71.55% 203ms 1.03% MeshBasedCellPopulation::GetDampingConstant 59ms 0.3% 71.85% 201ms 1.01% std::_Rb_tree::_M_clone_node (inline) 3ms 0.015% 71.86% 200ms 1.01% AbstractCentreBasedCellPopulation::GetDampingConstant 2ms 0.01% 71.87% 199ms 1.00% ___vsnprintf 0 0% 71.87% 197ms 0.99% __vsnprintf_internal (inline) 21ms 0.11% 71.98% 195ms 0.98% __printf_buffer 1ms 0.005% 71.98% 194ms 0.98% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 71.98% 191ms 0.96% OffLatticeSimulation::ApplyBoundaries 129ms 0.65% 72.64% 185ms 0.93% malloc_consolidate 26ms 0.13% 72.77% 181ms 0.91% AbstractTetrahedralElement::RefreshJacobian 6ms 0.03% 72.80% 177ms 0.89% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 6ms 0.03% 72.83% 167ms 0.84% AbstractTetrahedralElement::AbstractTetrahedralElement 167ms 0.84% 73.67% 167ms 0.84% std::vector::size (inline) 164ms 0.83% 74.50% 164ms 0.83% unlink_chunk 1ms 0.005% 74.50% 163ms 0.82% CellPropertyCollection::HasProperty 0 0% 74.50% 162ms 0.82% Cell::HasCellProperty (inline) 12ms 0.061% 74.56% 161ms 0.81% __printf_fp_l_buffer 0 0% 74.56% 161ms 0.81% __printf_fp_spec (inline) 8ms 0.04% 74.60% 159ms 0.8% CellProliferativeTypesWriter::VisitCell 3ms 0.015% 74.62% 159ms 0.8% boost::numeric::ublas::vector_assign (inline) 158ms 0.8% 75.42% 158ms 0.8% std::_Rb_tree_insert_and_rebalance 154ms 0.78% 76.20% 154ms 0.78% std::type_info::name (inline) 32ms 0.16% 76.36% 153ms 0.77% TetrahedralMesh::EdgesEnd (partial-inline) 151ms 0.76% 77.12% 151ms 0.76% Node::GetIndex 81ms 0.41% 77.53% 150ms 0.76% Cylindrical2dMesh::GetVectorFromAtoB 62ms 0.31% 77.84% 149ms 0.75% __printf_fp_buffer_1 2ms 0.01% 77.85% 148ms 0.75% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 60ms 0.3% 78.15% 147ms 0.74% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 138ms 0.7% 78.85% 147ms 0.74% vertexsort 98ms 0.49% 79.35% 144ms 0.73% std::_Rb_tree::equal_range (inline) 8ms 0.04% 79.39% 143ms 0.72% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 8ms 0.04% 79.43% 142ms 0.72% Node::~Node 142ms 0.72% 80.14% 142ms 0.72% [libchaste_crypt.so] 141ms 0.71% 80.86% 141ms 0.71% incircle 43ms 0.22% 81.07% 137ms 0.69% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 6ms 0.03% 81.10% 135ms 0.68% boost::numeric::ublas::c_vector::c_vector (inline) 133ms 0.67% 81.78% 133ms 0.67% AbstractCellMutationState::~AbstractCellMutationState 56ms 0.28% 82.06% 130ms 0.66% AbstractElement::GetNodeLocation 37ms 0.19% 82.25% 130ms 0.66% boost::numeric::ublas::indexing_vector_assign 5ms 0.025% 82.27% 127ms 0.64% MeshBasedCellPopulation::SpringsEnd (inline) 49ms 0.25% 82.52% 126ms 0.64% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 2ms 0.01% 82.53% 126ms 0.64% Cell::SetCellProliferativeType 26ms 0.13% 82.66% 120ms 0.61% std::num_put::_M_insert_int 0 0% 82.66% 117ms 0.59% AbstractCellBasedWriter::OpenOutputFileForAppend 81ms 0.41% 83.07% 115ms 0.58% TetrahedralMesh::EdgeIterator::EdgeIterator 0 0% 83.07% 114ms 0.58% OutputFileHandler::OpenOutputFile 12ms 0.061% 83.13% 113ms 0.57% Cylindrical2dMesh::CreateMirrorNodes 50ms 0.25% 83.38% 111ms 0.56% boost::shared_ptr::shared_ptr (inline) 31ms 0.16% 83.54% 110ms 0.56% std::__ostream_insert 1ms 0.005% 83.54% 108ms 0.55% AbstractCellBasedSimulation::DoCellRemoval (inline) 1ms 0.005% 83.55% 105ms 0.53% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 13ms 0.066% 83.61% 105ms 0.53% boost::detail::shared_count::~shared_count (inline) 0 0% 83.61% 105ms 0.53% boost::shared_ptr::~shared_ptr (inline) 48ms 0.24% 83.86% 105ms 0.53% std::basic_filebuf::xsputn 104ms 0.53% 84.38% 104ms 0.53% std::_Rb_tree_rebalance_for_erase 1ms 0.005% 84.39% 101ms 0.51% std::_Rb_tree::_M_emplace_hint_unique 3ms 0.015% 84.40% 100ms 0.5% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 2ms 0.01% 84.41% 100ms 0.5% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath