File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 17082ms, 83.74% of 20399ms total Dropped 832 nodes (cum <= 102ms) flat flat% sum% cum cum% 0 0% 0% 20350ms 99.76% __libc_start_call_main 0 0% 0% 20350ms 99.76% __libc_start_main_impl 0 0% 0% 20350ms 99.76% _start 0 0% 0% 20330ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 20330ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 20330ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 20330ms 99.66% main 0 0% 0% 20289ms 99.46% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 20289ms 99.46% CxxTest::TestRunner::runTest (inline) 0 0% 0% 20289ms 99.46% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 20262ms 99.33% AbstractCellBasedSimulation::Solve 0 0% 0% 15619ms 76.57% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.015% 0.015% 10114ms 49.58% AbstractCellBasedSimulation::DoCellBirth 17ms 0.083% 0.098% 10017ms 49.11% Cell::ReadyToDivide 10ms 0.049% 0.15% 9900ms 48.53% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0049% 0.15% 9747ms 47.78% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 24ms 0.12% 0.27% 9736ms 47.73% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 9ms 0.044% 0.31% 9709ms 47.60% CellCycleModelOdeHandler::SolveOdeToTime 72ms 0.35% 0.67% 9513ms 46.63% AbstractOneStepIvpOdeSolver::InternalSolve 858ms 4.21% 4.87% 8650ms 42.40% RungeKutta4IvpOdeSolver::CalculateNextYValue 3603ms 17.66% 22.54% 7592ms 37.22% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 22.54% 5393ms 26.44% MeshBasedCellPopulation::Update 7ms 0.034% 22.57% 4223ms 20.70% Cylindrical2dMesh::ReMesh 105ms 0.51% 23.08% 4064ms 19.92% AbstractCellProperty::IsType (inline) 573ms 2.81% 25.89% 2843ms 13.94% AbstractCellProperty::IsSame 0 0% 25.89% 2532ms 12.41% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 25.89% 2374ms 11.64% MutableMesh::ReMesh 397ms 1.95% 27.84% 2270ms 11.13% std::type_info::operator== (inline) 1ms 0.0049% 27.84% 2219ms 10.88% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.049% 27.89% 2175ms 10.66% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 27.89% 2104ms 10.31% AbstractCellPopulation::WriteResultsToFiles 812ms 3.98% 31.87% 1877ms 9.20% std::_Rb_tree::_M_lower_bound (inline) 1808ms 8.86% 40.74% 1808ms 8.86% __strcmp_avx2 175ms 0.86% 41.60% 1708ms 8.37% TetrahedralMesh::EdgeIterator::operator++ 67ms 0.33% 41.92% 1410ms 6.91% std::_Rb_tree::find (inline) 16ms 0.078% 42.00% 1234ms 6.05% TetrahedralMesh::ImportFromMesher 0 0% 42.00% 1135ms 5.56% MeshBasedCellPopulation::UpdateNodePairs 59ms 0.29% 42.29% 1133ms 5.55% operator new 8ms 0.039% 42.33% 1131ms 5.54% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 232ms 1.14% 43.47% 1064ms 5.22% __GI___libc_malloc 4ms 0.02% 43.49% 1017ms 4.99% MeshBasedCellPopulation::SpringIterator::operator++ 28ms 0.14% 43.62% 994ms 4.87% std::__new_allocator::allocate (inline) 0 0% 43.62% 985ms 4.83% std::allocator_traits::allocate (inline) 11ms 0.054% 43.68% 956ms 4.69% std::set::insert (inline) 21ms 0.1% 43.78% 945ms 4.63% std::_Rb_tree::_M_insert_unique 0 0% 43.78% 904ms 4.43% std::set::count (inline) 0 0% 43.78% 814ms 3.99% triangulate 5ms 0.025% 43.81% 758ms 3.72% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 64ms 0.31% 44.12% 736ms 3.61% std::map::operator[] (partial-inline) 411ms 2.01% 46.13% 734ms 3.60% _int_malloc 0 0% 46.13% 721ms 3.53% delaunay 1ms 0.0049% 46.14% 720ms 3.53% divconqdelaunay 0 0% 46.14% 703ms 3.45% AbstractTwoBodyInteractionForce::AddForceContribution 11ms 0.054% 46.19% 683ms 3.35% CellPropertyCollection::GetPropertiesType (inline) 670ms 3.28% 49.48% 679ms 3.33% WntCellCycleOdeSystem::CalculateStoppingEvent 5ms 0.025% 49.50% 676ms 3.31% CellPopulationElementWriter::Visit 673ms 3.30% 52.80% 673ms 3.30% std::_Rb_tree::_S_right (inline) 9ms 0.044% 52.85% 658ms 3.23% std::less::operator() (inline) 649ms 3.18% 56.03% 649ms 3.18% std::operator< (inline) 223ms 1.09% 57.12% 635ms 3.11% __dynamic_cast 0 0% 57.12% 627ms 3.07% std::_Rb_tree::_M_create_node (inline) 3ms 0.015% 57.14% 623ms 3.05% MeshBasedCellPopulation::AcceptCellWriter 29ms 0.14% 57.28% 613ms 3.01% std::_Rb_tree::_M_insert_ (inline) 0 0% 57.28% 600ms 2.94% std::_Rb_tree::_M_get_node (inline) 36ms 0.18% 57.45% 593ms 2.91% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 20ms 0.098% 57.55% 588ms 2.88% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 57.55% 571ms 2.80% std::_Rb_tree::lower_bound (inline) 0 0% 57.55% 571ms 2.80% std::map::lower_bound (inline) 5ms 0.025% 57.58% 567ms 2.78% Element::Element 0 0% 57.58% 557ms 2.73% std::_Rb_tree::_Alloc_node::operator() (inline) 1ms 0.0049% 57.58% 530ms 2.60% std::ostream::operator<< (inline) 66ms 0.32% 57.90% 527ms 2.58% std::ostream::_M_insert 14ms 0.069% 57.97% 521ms 2.55% MutableMesh::ReIndex 1ms 0.0049% 57.98% 512ms 2.51% AbstractCellProperty::IsSubType (inline) 13ms 0.064% 58.04% 504ms 2.47% Cylindrical2dMesh::ReconstructCylindricalMesh 0 0% 58.04% 501ms 2.46% std::map::find (inline) 336ms 1.65% 59.69% 496ms 2.43% AbstractCellMutationState::AbstractCellMutationState 10ms 0.049% 59.74% 485ms 2.38% Element::RegisterWithNodes (inline) 7ms 0.034% 59.77% 474ms 2.32% Node::AddElement 14ms 0.069% 59.84% 467ms 2.29% Cylindrical2dMesh::CorrectNonPeriodicMesh 151ms 0.74% 60.58% 405ms 1.99% __GI___libc_free 1ms 0.0049% 60.59% 386ms 1.89% std::_Vector_base::_M_allocate (inline) 1ms 0.0049% 60.59% 384ms 1.88% std::set::erase (inline) 5ms 0.025% 60.62% 383ms 1.88% std::_Rb_tree::erase 7ms 0.034% 60.65% 377ms 1.85% Node::RemoveElement 7ms 0.034% 60.68% 363ms 1.78% Cell::GetMutationState 124ms 0.61% 61.29% 363ms 1.78% std::_Rb_tree::_M_erase 4ms 0.02% 61.31% 355ms 1.74% Cell::GetCellProliferativeType 27ms 0.13% 61.44% 347ms 1.70% std::_Rb_tree::~_Rb_tree (inline) 18ms 0.088% 61.53% 338ms 1.66% divconqrecurse 1ms 0.0049% 61.54% 337ms 1.65% NodeLocationWriter::Visit 26ms 0.13% 61.66% 328ms 1.61% Element::ResetIndex 324ms 1.59% 63.25% 324ms 1.59% std::type_info::name (inline) 16ms 0.078% 63.33% 323ms 1.58% std::__new_allocator::deallocate (inline) 13ms 0.064% 63.40% 320ms 1.57% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 159ms 0.78% 64.17% 319ms 1.56% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 64.17% 319ms 1.56% std::allocator_traits::deallocate (inline) 0 0% 64.17% 316ms 1.55% std::set::~set (inline) 117ms 0.57% 64.75% 311ms 1.52% std::_Rb_tree::_M_get_insert_unique_pos 81ms 0.4% 65.15% 309ms 1.51% mergehulls 0 0% 65.15% 299ms 1.47% std::_Rb_tree::_M_drop_node (inline) 27ms 0.13% 65.28% 298ms 1.46% std::num_put::_M_insert_float 2ms 0.0098% 65.29% 295ms 1.45% TetrahedralMesh::RefreshJacobianCachedData 19ms 0.093% 65.38% 294ms 1.44% AbstractTetrahedralElement::CalculateJacobian 36ms 0.18% 65.56% 293ms 1.44% TetrahedralMesh::Clear 9ms 0.044% 65.60% 285ms 1.40% AbstractCellPopulation::GetLocationIndexUsingCell 6ms 0.029% 65.63% 285ms 1.40% LegacyCellProliferativeTypesWriter::VisitCell 1ms 0.0049% 65.64% 281ms 1.38% AbstractCellPopulation::Iterator::operator++ (inline) 37ms 0.18% 65.82% 278ms 1.36% AbstractCellPopulation::Iterator::IsRealCell (inline) 8ms 0.039% 65.86% 262ms 1.28% std::vector::push_back (inline) 0 0% 65.86% 259ms 1.27% std::_Rb_tree::_M_put_node (inline) 15ms 0.074% 65.93% 258ms 1.26% std::_Rb_tree::_Rb_tree (partial-inline) 222ms 1.09% 67.02% 252ms 1.24% _int_free 10ms 0.049% 67.07% 250ms 1.23% AbstractCellPopulation::IsCellAttachedToLocationIndex 0 0% 67.07% 248ms 1.22% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 67.07% 248ms 1.22% MeshBasedCellPopulation::GetDampingConstant 246ms 1.21% 68.27% 247ms 1.21% std::vector::operator[] (inline) 24ms 0.12% 68.39% 245ms 1.20% std::vector::_M_realloc_insert 11ms 0.054% 68.44% 240ms 1.18% AbstractTetrahedralElement::CalculateInverseJacobian 20ms 0.098% 68.54% 238ms 1.17% std::_Rb_tree::_M_erase_aux (inline) 1ms 0.0049% 68.55% 236ms 1.16% std::set::set (inline) 3ms 0.015% 68.56% 232ms 1.14% alternateaxes 35ms 0.17% 68.73% 230ms 1.13% AbstractTetrahedralElement::RefreshJacobian 53ms 0.26% 68.99% 230ms 1.13% ApcOneHitCellMutationState::ApcOneHitCellMutationState 9ms 0.044% 69.04% 229ms 1.12% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 3ms 0.015% 69.05% 229ms 1.12% std::__cxx11::collate::do_transform 214ms 1.05% 70.10% 229ms 1.12% vertexmedian 2ms 0.0098% 70.11% 222ms 1.09% CellProliferativeTypesWriter::VisitCell 1ms 0.0049% 70.12% 221ms 1.08% ___vsnprintf 0 0% 70.12% 220ms 1.08% __vsnprintf_internal (inline) 19ms 0.093% 70.21% 217ms 1.06% __printf_buffer 40ms 0.2% 70.41% 215ms 1.05% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 24ms 0.12% 70.52% 214ms 1.05% std::_Rb_tree::_M_copy (inline) 5ms 0.025% 70.55% 213ms 1.04% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 39ms 0.19% 70.74% 213ms 1.04% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 146ms 0.72% 71.45% 207ms 1.01% malloc_consolidate 12ms 0.059% 71.51% 203ms 1% Element::MarkAsDeleted 201ms 0.99% 72.50% 201ms 0.99% [libchaste_cell_based.so] 1ms 0.0049% 72.50% 199ms 0.98% OffLatticeSimulation::ApplyBoundaries 1ms 0.0049% 72.51% 189ms 0.93% __printf_fp_spec (inline) 11ms 0.054% 72.56% 188ms 0.92% __printf_fp_l_buffer 9ms 0.044% 72.61% 187ms 0.92% CellPropertyCollection::HasProperty 64ms 0.31% 72.92% 187ms 0.92% std::_Rb_tree::_M_clone_node (inline) 9ms 0.044% 72.96% 185ms 0.91% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 72.96% 181ms 0.89% Cell::HasCellProperty (inline) 126ms 0.62% 73.58% 176ms 0.86% AbstractElement::GetNodeGlobalIndex 171ms 0.84% 74.42% 171ms 0.84% std::_Rb_tree_insert_and_rebalance 81ms 0.4% 74.82% 170ms 0.83% AbstractElement::GetNodeLocation 167ms 0.82% 75.64% 167ms 0.82% unlink_chunk 88ms 0.43% 76.07% 166ms 0.81% __printf_fp_buffer_1 164ms 0.8% 76.87% 164ms 0.8% Node::GetIndex 11ms 0.054% 76.93% 162ms 0.79% Node::~Node 16ms 0.078% 77.00% 152ms 0.75% std::_Rb_tree_const_iterator::operator++ (inline) 11ms 0.054% 77.06% 146ms 0.72% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 1ms 0.0049% 77.06% 146ms 0.72% boost::numeric::ublas::vector_assign (inline) 97ms 0.48% 77.54% 146ms 0.72% std::_Rb_tree::equal_range (inline) 144ms 0.71% 78.24% 144ms 0.71% std::_Rb_tree_increment 11ms 0.054% 78.30% 142ms 0.7% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 137ms 0.67% 78.97% 137ms 0.67% std::vector::size (inline) 0 0% 78.97% 135ms 0.66% AbstractCellBasedWriter::OpenOutputFileForAppend 135ms 0.66% 79.63% 135ms 0.66% incircle 123ms 0.6% 80.23% 135ms 0.66% vertexsort 1ms 0.0049% 80.24% 133ms 0.65% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 0 0% 80.24% 132ms 0.65% OutputFileHandler::OpenOutputFile 0 0% 80.24% 129ms 0.63% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 33ms 0.16% 80.40% 128ms 0.63% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 77ms 0.38% 80.78% 127ms 0.62% Cylindrical2dMesh::GetVectorFromAtoB 124ms 0.61% 81.39% 124ms 0.61% AbstractElement::IsDeleted 123ms 0.6% 81.99% 123ms 0.6% AbstractCellMutationState::~AbstractCellMutationState 5ms 0.025% 82.01% 123ms 0.6% MeshBasedCellPopulation::SpringsEnd (inline) 122ms 0.6% 82.61% 122ms 0.6% AbstractCellProperty::~AbstractCellProperty 31ms 0.15% 82.76% 122ms 0.6% TetrahedralMesh::EdgesEnd (partial-inline) 21ms 0.1% 82.87% 121ms 0.59% std::num_put::_M_insert_int 2ms 0.0098% 82.88% 116ms 0.57% std::vector::_M_default_append 0 0% 82.88% 116ms 0.57% std::vector::resize (inline) 11ms 0.054% 82.93% 114ms 0.56% boost::detail::shared_count::~shared_count (inline) 5ms 0.025% 82.96% 114ms 0.56% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 82.96% 114ms 0.56% boost::shared_ptr::~shared_ptr (inline) 36ms 0.18% 83.13% 113ms 0.55% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 1ms 0.0049% 83.14% 113ms 0.55% Cell::SetCellProliferativeType 0 0% 83.14% 109ms 0.53% AbstractCellBasedSimulation::DoCellRemoval (inline) 28ms 0.14% 83.27% 108ms 0.53% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 3ms 0.015% 83.29% 107ms 0.52% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 0 0% 83.29% 107ms 0.52% NodeMap::NodeMap 55ms 0.27% 83.56% 106ms 0.52% AbstractTetrahedralMesh::GetElement 33ms 0.16% 83.72% 106ms 0.52% boost::numeric::ublas::indexing_vector_assign 2ms 0.0098% 83.73% 104ms 0.51% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 2ms 0.0098% 83.74% 103ms 0.5% AbstractTetrahedralMesh::ElementIterator::operator++ (inline)