File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16784ms, 84.49% of 19864ms total Dropped 767 nodes (cum <= 99.32ms) flat flat% sum% cum cum% 0 0% 0% 19820ms 99.78% __libc_start_call_main 0 0% 0% 19820ms 99.78% __libc_start_main_impl 0 0% 0% 19820ms 99.78% _start 0 0% 0% 19801ms 99.68% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19801ms 99.68% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19801ms 99.68% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19801ms 99.68% main 0 0% 0% 19762ms 99.49% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19762ms 99.49% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19762ms 99.49% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19734ms 99.35% AbstractCellBasedSimulation::Solve 0 0% 0% 15335ms 77.20% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.01% 0.01% 10086ms 50.78% AbstractCellBasedSimulation::DoCellBirth 5ms 0.025% 0.035% 9995ms 50.32% Cell::ReadyToDivide 2ms 0.01% 0.045% 9923ms 49.95% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.005% 0.05% 9811ms 49.39% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 11ms 0.055% 0.11% 9804ms 49.36% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.015% 0.12% 9789ms 49.28% CellCycleModelOdeHandler::SolveOdeToTime 76ms 0.38% 0.5% 9621ms 48.43% AbstractOneStepIvpOdeSolver::InternalSolve 869ms 4.37% 4.88% 8785ms 44.23% RungeKutta4IvpOdeSolver::CalculateNextYValue 3666ms 18.46% 23.33% 7720ms 38.86% WntCellCycleOdeSystem::EvaluateYDerivatives 2ms 0.01% 23.34% 5130ms 25.83% MeshBasedCellPopulation::Update 192ms 0.97% 24.31% 4086ms 20.57% AbstractCellProperty::IsType (inline) 2ms 0.01% 24.32% 3952ms 19.90% Cylindrical2dMesh::ReMesh 548ms 2.76% 27.08% 2887ms 14.53% AbstractCellProperty::IsSame 1ms 0.005% 27.08% 2484ms 12.51% OffLatticeSimulation::UpdateCellLocationsAndTopology 426ms 2.14% 29.23% 2339ms 11.78% std::type_info::operator== (inline) 0 0% 29.23% 2150ms 10.82% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 29.23% 2120ms 10.67% MutableMesh::ReMesh 7ms 0.035% 29.26% 2108ms 10.61% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.005% 29.27% 1910ms 9.62% AbstractCellPopulation::WriteResultsToFiles 1848ms 9.30% 38.57% 1848ms 9.30% __strcmp_avx2 776ms 3.91% 42.48% 1816ms 9.14% std::_Rb_tree::_M_lower_bound (inline) 155ms 0.78% 43.26% 1697ms 8.54% TetrahedralMesh::EdgeIterator::operator++ 54ms 0.27% 43.53% 1382ms 6.96% std::_Rb_tree::find (inline) 0 0% 43.53% 1152ms 5.80% MeshBasedCellPopulation::UpdateNodePairs 7ms 0.035% 43.57% 1132ms 5.70% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 24ms 0.12% 43.69% 1063ms 5.35% TetrahedralMesh::ImportFromMesher 53ms 0.27% 43.95% 1057ms 5.32% operator new 11ms 0.055% 44.01% 1038ms 5.23% MeshBasedCellPopulation::SpringIterator::operator++ 11ms 0.055% 44.06% 1011ms 5.09% std::set::insert (inline) 17ms 0.086% 44.15% 1000ms 5.03% std::_Rb_tree::_M_insert_unique 232ms 1.17% 45.32% 993ms 5.00% __GI___libc_malloc 45ms 0.23% 45.54% 930ms 4.68% std::__new_allocator::allocate (inline) 0 0% 45.54% 924ms 4.65% std::allocator_traits::allocate (inline) 0 0% 45.54% 840ms 4.23% std::set::count (inline) 2ms 0.01% 45.55% 810ms 4.08% triangulate 0 0% 45.55% 729ms 3.67% delaunay 3ms 0.015% 45.57% 729ms 3.67% divconqdelaunay 4ms 0.02% 45.59% 699ms 3.52% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 2ms 0.01% 45.60% 686ms 3.45% AbstractTwoBodyInteractionForce::AddForceContribution 387ms 1.95% 47.55% 684ms 3.44% _int_malloc 59ms 0.3% 47.85% 663ms 3.34% std::map::operator[] (partial-inline) 661ms 3.33% 51.17% 661ms 3.33% std::_Rb_tree::_S_right (inline) 20ms 0.1% 51.27% 650ms 3.27% std::less::operator() (inline) 641ms 3.23% 54.50% 648ms 3.26% WntCellCycleOdeSystem::CalculateStoppingEvent 5ms 0.025% 54.53% 637ms 3.21% CellPopulationElementWriter::Visit 630ms 3.17% 57.70% 630ms 3.17% std::operator< (inline) 0 0% 57.70% 620ms 3.12% std::_Rb_tree::_M_create_node (inline) 19ms 0.096% 57.79% 604ms 3.04% std::_Rb_tree::_M_insert_ (inline) 0 0% 57.79% 589ms 2.97% std::_Rb_tree::_M_get_node (inline) 18ms 0.091% 57.88% 572ms 2.88% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 0 0% 57.88% 561ms 2.82% std::_Rb_tree::_Alloc_node::operator() (inline) 159ms 0.8% 58.68% 555ms 2.79% __dynamic_cast 25ms 0.13% 58.81% 546ms 2.75% AbstractCellPopulation::GetCellUsingLocationIndex 2ms 0.01% 58.82% 543ms 2.73% MeshBasedCellPopulation::AcceptCellWriter 0 0% 58.82% 541ms 2.72% std::map::find (inline) 6ms 0.03% 58.85% 537ms 2.70% Element::Element 10ms 0.05% 58.90% 529ms 2.66% MutableMesh::ReIndex 20ms 0.1% 59.00% 516ms 2.60% Cylindrical2dMesh::CorrectNonPeriodicMesh 0 0% 59.00% 515ms 2.59% std::_Rb_tree::lower_bound (inline) 0 0% 59.00% 515ms 2.59% std::map::lower_bound (inline) 5ms 0.025% 59.03% 511ms 2.57% CellPropertyCollection::GetPropertiesType (inline) 9ms 0.045% 59.07% 500ms 2.52% Element::RegisterWithNodes (inline) 2ms 0.01% 59.08% 494ms 2.49% std::ostream::operator<< (inline) 58ms 0.29% 59.37% 491ms 2.47% std::ostream::_M_insert 12ms 0.06% 59.43% 485ms 2.44% Node::AddElement 7ms 0.035% 59.47% 480ms 2.42% Cylindrical2dMesh::ReconstructCylindricalMesh 325ms 1.64% 61.11% 469ms 2.36% AbstractCellMutationState::AbstractCellMutationState 4ms 0.02% 61.13% 388ms 1.95% AbstractCellProperty::IsSubType (inline) 157ms 0.79% 61.92% 384ms 1.93% __GI___libc_free 158ms 0.8% 62.71% 379ms 1.91% std::_Rb_tree::_M_get_insert_unique_pos 7ms 0.035% 62.75% 379ms 1.91% std::_Rb_tree::erase 1ms 0.005% 62.75% 379ms 1.91% std::set::erase (inline) 124ms 0.62% 63.38% 374ms 1.88% std::_Rb_tree::_M_erase 12ms 0.06% 63.44% 372ms 1.87% Node::RemoveElement 32ms 0.16% 63.60% 366ms 1.84% Element::ResetIndex 14ms 0.07% 63.67% 359ms 1.81% divconqrecurse 19ms 0.096% 63.76% 343ms 1.73% std::__new_allocator::deallocate (inline) 7ms 0.035% 63.80% 342ms 1.72% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 109ms 0.55% 64.35% 339ms 1.71% mergehulls 19ms 0.096% 64.44% 339ms 1.71% std::_Rb_tree::~_Rb_tree (inline) 4ms 0.02% 64.46% 339ms 1.71% std::_Vector_base::_M_allocate (inline) 0 0% 64.46% 337ms 1.70% std::allocator_traits::deallocate (inline) 1ms 0.005% 64.47% 332ms 1.67% NodeLocationWriter::Visit 0 0% 64.47% 316ms 1.59% std::_Rb_tree::_M_drop_node (inline) 0 0% 64.47% 309ms 1.56% std::set::~set (inline) 5ms 0.025% 64.49% 305ms 1.54% AbstractCellPopulation::GetLocationIndexUsingCell 141ms 0.71% 65.20% 303ms 1.53% __cxxabiv1::__si_class_type_info::__do_dyncast 6ms 0.03% 65.23% 297ms 1.50% Cell::GetMutationState 297ms 1.50% 66.73% 297ms 1.50% std::type_info::name (inline) 17ms 0.086% 66.81% 291ms 1.46% std::num_put::_M_insert_float 1ms 0.005% 66.82% 290ms 1.46% AbstractCellPopulation::Iterator::operator++ (inline) 37ms 0.19% 67.01% 288ms 1.45% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 67.01% 281ms 1.41% std::_Rb_tree::_M_put_node (inline) 4ms 0.02% 67.03% 277ms 1.39% LegacyCellProliferativeTypesWriter::VisitCell 2ms 0.01% 67.04% 259ms 1.30% Cell::GetCellProliferativeType 10ms 0.05% 67.09% 258ms 1.30% std::vector::push_back (inline) 9ms 0.045% 67.13% 252ms 1.27% std::_Rb_tree::_Rb_tree (partial-inline) 5ms 0.025% 67.16% 242ms 1.22% std::__cxx11::collate::do_transform 241ms 1.21% 68.37% 241ms 1.21% [libchaste_cell_based.so] 11ms 0.055% 68.43% 240ms 1.21% std::vector::_M_realloc_insert 239ms 1.20% 69.63% 240ms 1.21% std::vector::operator[] (inline) 13ms 0.065% 69.69% 232ms 1.17% std::_Rb_tree::_M_erase_aux (inline) 2ms 0.01% 69.70% 231ms 1.16% AbstractCellPopulation::IsCellAttachedToLocationIndex 14ms 0.07% 69.77% 231ms 1.16% AbstractTetrahedralElement::CalculateJacobian 5ms 0.025% 69.80% 230ms 1.16% alternateaxes 1ms 0.005% 69.80% 229ms 1.15% ___vsnprintf 3ms 0.015% 69.82% 228ms 1.15% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 0 0% 69.82% 228ms 1.15% __vsnprintf_internal (inline) 3ms 0.015% 69.83% 227ms 1.14% std::set::set (inline) 185ms 0.93% 70.77% 225ms 1.13% _int_free 4ms 0.02% 70.79% 224ms 1.13% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 213ms 1.07% 71.86% 224ms 1.13% vertexmedian 29ms 0.15% 72.00% 223ms 1.12% __printf_buffer 23ms 0.12% 72.12% 219ms 1.10% std::_Rb_tree::_M_copy (inline) 1ms 0.005% 72.13% 218ms 1.10% TetrahedralMesh::RefreshJacobianCachedData 52ms 0.26% 72.39% 217ms 1.09% ApcOneHitCellMutationState::ApcOneHitCellMutationState 62ms 0.31% 72.70% 209ms 1.05% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 153ms 0.77% 73.47% 208ms 1.05% AbstractElement::GetNodeGlobalIndex 0 0% 73.47% 206ms 1.04% OffLatticeSimulation::ApplyBoundaries 19ms 0.096% 73.57% 197ms 0.99% Element::MarkAsDeleted 39ms 0.2% 73.76% 196ms 0.99% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 1ms 0.005% 73.77% 195ms 0.98% MeshBasedCellPopulation::GetDampingConstant 3ms 0.015% 73.78% 194ms 0.98% AbstractCentreBasedCellPopulation::GetDampingConstant 51ms 0.26% 74.04% 191ms 0.96% std::_Rb_tree::_M_clone_node (inline) 6ms 0.03% 74.07% 186ms 0.94% AbstractTetrahedralElement::CalculateInverseJacobian 13ms 0.065% 74.13% 180ms 0.91% AbstractTetrahedralElement::RefreshJacobian 1ms 0.005% 74.14% 177ms 0.89% __printf_fp_spec (inline) 6ms 0.03% 74.17% 176ms 0.89% __printf_fp_l_buffer 175ms 0.88% 75.05% 175ms 0.88% std::_Rb_tree_insert_and_rebalance 112ms 0.56% 75.61% 167ms 0.84% malloc_consolidate 77ms 0.39% 76.00% 165ms 0.83% __printf_fp_buffer_1 6ms 0.03% 76.03% 164ms 0.83% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 6ms 0.03% 76.06% 158ms 0.8% AbstractTetrahedralElement::AbstractTetrahedralElement 158ms 0.8% 76.86% 158ms 0.8% Node::GetIndex 68ms 0.34% 77.20% 155ms 0.78% AbstractElement::GetNodeLocation 155ms 0.78% 77.98% 155ms 0.78% unlink_chunk 153ms 0.77% 78.75% 153ms 0.77% std::vector::size (inline) 15ms 0.076% 78.83% 151ms 0.76% TetrahedralMesh::Clear 146ms 0.73% 79.56% 146ms 0.73% incircle 100ms 0.5% 80.06% 146ms 0.73% std::_Rb_tree::equal_range (inline) 3ms 0.015% 80.08% 145ms 0.73% boost::numeric::ublas::vector_assign (inline) 6ms 0.03% 80.11% 144ms 0.72% CellPropertyCollection::HasProperty 0 0% 80.11% 140ms 0.7% Cell::HasCellProperty (inline) 6ms 0.03% 80.14% 139ms 0.7% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 1ms 0.005% 80.14% 137ms 0.69% CellProliferativeTypesWriter::VisitCell 120ms 0.6% 80.75% 132ms 0.66% vertexsort 10ms 0.05% 80.80% 131ms 0.66% boost::numeric::ublas::c_vector::c_vector (inline) 75ms 0.38% 81.18% 129ms 0.65% Cylindrical2dMesh::GetVectorFromAtoB 15ms 0.076% 81.25% 128ms 0.64% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 28ms 0.14% 81.39% 127ms 0.64% TetrahedralMesh::EdgesEnd 26ms 0.13% 81.52% 120ms 0.6% boost::numeric::ublas::indexing_vector_assign 37ms 0.19% 81.71% 118ms 0.59% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 0 0% 81.71% 117ms 0.59% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 81.71% 117ms 0.59% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 81.71% 115ms 0.58% OutputFileHandler::OpenOutputFile 44ms 0.22% 81.93% 115ms 0.58% std::__ostream_insert 114ms 0.57% 82.51% 114ms 0.57% AbstractElement::IsDeleted 113ms 0.57% 83.07% 113ms 0.57% std::_Rb_tree_rebalance_for_erase 3ms 0.015% 83.09% 111ms 0.56% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 5ms 0.025% 83.12% 110ms 0.55% boost::detail::shared_count::~shared_count (inline) 0 0% 83.12% 110ms 0.55% boost::shared_ptr::~shared_ptr (inline) 32ms 0.16% 83.28% 109ms 0.55% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 2ms 0.01% 83.29% 105ms 0.53% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 25ms 0.13% 83.41% 105ms 0.53% std::num_put::_M_insert_int 102ms 0.51% 83.93% 103ms 0.52% boost::detail::sp_counted_base::release 13ms 0.065% 83.99% 101ms 0.51% std::_Rb_tree_const_iterator::operator++ (inline) 100ms 0.5% 84.49% 100ms 0.5% std::_Rb_tree_increment