File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16637ms, 83.45% of 19936ms total Dropped 765 nodes (cum <= 99.68ms) flat flat% sum% cum cum% 0 0% 0% 19892ms 99.78% __libc_start_call_main 0 0% 0% 19892ms 99.78% __libc_start_main_impl 0 0% 0% 19892ms 99.78% _start 0 0% 0% 19873ms 99.68% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19873ms 99.68% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19873ms 99.68% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19873ms 99.68% main 0 0% 0% 19841ms 99.52% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19841ms 99.52% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19841ms 99.52% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19814ms 99.39% AbstractCellBasedSimulation::Solve 1ms 0.005% 0.005% 15362ms 77.06% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.01% 0.015% 10137ms 50.85% AbstractCellBasedSimulation::DoCellBirth 5ms 0.025% 0.04% 10033ms 50.33% Cell::ReadyToDivide 5ms 0.025% 0.065% 9966ms 49.99% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.005% 0.07% 9840ms 49.36% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 9ms 0.045% 0.12% 9828ms 49.30% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.01% 0.13% 9816ms 49.24% CellCycleModelOdeHandler::SolveOdeToTime 71ms 0.36% 0.48% 9656ms 48.43% AbstractOneStepIvpOdeSolver::InternalSolve 875ms 4.39% 4.87% 8839ms 44.34% RungeKutta4IvpOdeSolver::CalculateNextYValue 3601ms 18.06% 22.93% 7720ms 38.72% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 22.93% 5104ms 25.60% MeshBasedCellPopulation::Update 202ms 1.01% 23.95% 4163ms 20.88% AbstractCellProperty::IsType (inline) 8ms 0.04% 23.99% 3924ms 19.68% Cylindrical2dMesh::ReMesh 552ms 2.77% 26.76% 2884ms 14.47% AbstractCellProperty::IsSame 0 0% 26.76% 2484ms 12.46% OffLatticeSimulation::UpdateCellLocationsAndTopology 419ms 2.10% 28.86% 2332ms 11.70% std::type_info::operator== (inline) 0 0% 28.86% 2173ms 10.90% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.005% 28.86% 2160ms 10.83% MutableMesh::ReMesh 15ms 0.075% 28.94% 2119ms 10.63% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 28.94% 1963ms 9.85% AbstractCellPopulation::WriteResultsToFiles 1899ms 9.53% 38.46% 1899ms 9.53% __strcmp_avx2 790ms 3.96% 42.43% 1834ms 9.20% std::_Rb_tree::_M_lower_bound (inline) 179ms 0.9% 43.32% 1691ms 8.48% TetrahedralMesh::EdgeIterator::operator++ 68ms 0.34% 43.66% 1392ms 6.98% std::_Rb_tree::find (inline) 1ms 0.005% 43.67% 1155ms 5.79% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.02% 43.69% 1120ms 5.62% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 12ms 0.06% 43.75% 1064ms 5.34% TetrahedralMesh::ImportFromMesher 21ms 0.11% 43.86% 1029ms 5.16% MeshBasedCellPopulation::SpringIterator::operator++ 50ms 0.25% 44.11% 983ms 4.93% operator new 10ms 0.05% 44.16% 953ms 4.78% std::set::insert (inline) 15ms 0.075% 44.23% 943ms 4.73% std::_Rb_tree::_M_insert_unique 223ms 1.12% 45.35% 919ms 4.61% __GI___libc_malloc 48ms 0.24% 45.59% 886ms 4.44% std::__new_allocator::allocate (inline) 0 0% 45.59% 878ms 4.40% std::allocator_traits::allocate (inline) 0 0% 45.59% 863ms 4.33% std::set::count (inline) 0 0% 45.59% 842ms 4.22% triangulate 0 0% 45.59% 776ms 3.89% delaunay 1ms 0.005% 45.60% 776ms 3.89% divconqdelaunay 2ms 0.01% 45.61% 724ms 3.63% AbstractTwoBodyInteractionForce::AddForceContribution 4ms 0.02% 45.63% 710ms 3.56% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 59ms 0.3% 45.92% 710ms 3.56% std::map::operator[] (partial-inline) 6ms 0.03% 45.95% 707ms 3.55% CellPopulationElementWriter::Visit 669ms 3.36% 49.31% 669ms 3.36% std::_Rb_tree::_S_right (inline) 27ms 0.14% 49.44% 667ms 3.35% std::less::operator() (inline) 640ms 3.21% 52.65% 640ms 3.21% std::operator< (inline) 370ms 1.86% 54.51% 629ms 3.16% _int_malloc 164ms 0.82% 55.33% 624ms 3.13% __dynamic_cast 23ms 0.12% 55.45% 614ms 3.08% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 599ms 3.00% 58.45% 610ms 3.06% WntCellCycleOdeSystem::CalculateStoppingEvent 0 0% 58.45% 590ms 2.96% std::_Rb_tree::_M_create_node (inline) 20ms 0.1% 58.55% 575ms 2.88% AbstractCellPopulation::GetCellUsingLocationIndex 20ms 0.1% 58.65% 574ms 2.88% std::_Rb_tree::_M_insert_ (inline) 0 0% 58.65% 570ms 2.86% std::_Rb_tree::_M_get_node (inline) 2ms 0.01% 58.66% 565ms 2.83% MeshBasedCellPopulation::AcceptCellWriter 0 0% 58.66% 562ms 2.82% std::_Rb_tree::lower_bound (inline) 0 0% 58.66% 562ms 2.82% std::map::lower_bound (inline) 3ms 0.015% 58.68% 546ms 2.74% Element::Element 13ms 0.065% 58.74% 541ms 2.71% Cylindrical2dMesh::ReconstructCylindricalMesh 0 0% 58.74% 530ms 2.66% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 58.74% 525ms 2.63% std::map::find (inline) 4ms 0.02% 58.76% 515ms 2.58% CellPropertyCollection::GetPropertiesType (inline) 345ms 1.73% 60.49% 492ms 2.47% AbstractCellMutationState::AbstractCellMutationState 1ms 0.005% 60.50% 489ms 2.45% std::ostream::operator<< (inline) 78ms 0.39% 60.89% 488ms 2.45% std::ostream::_M_insert 10ms 0.05% 60.94% 483ms 2.42% MutableMesh::ReIndex 3ms 0.015% 60.96% 459ms 2.30% Element::RegisterWithNodes (inline) 2ms 0.01% 60.97% 455ms 2.28% Node::AddElement 3ms 0.015% 60.98% 445ms 2.23% AbstractCellProperty::IsSubType (inline) 20ms 0.1% 61.08% 443ms 2.22% Cylindrical2dMesh::CorrectNonPeriodicMesh 151ms 0.76% 61.84% 417ms 2.09% __GI___libc_free 17ms 0.085% 61.92% 402ms 2.02% divconqrecurse 4ms 0.02% 61.94% 395ms 1.98% std::set::erase (inline) 8ms 0.04% 61.98% 394ms 1.98% std::_Rb_tree::erase 13ms 0.065% 62.05% 393ms 1.97% Node::RemoveElement 113ms 0.57% 62.62% 374ms 1.88% mergehulls 114ms 0.57% 63.19% 361ms 1.81% std::_Rb_tree::_M_erase 14ms 0.07% 63.26% 356ms 1.79% std::__new_allocator::deallocate (inline) 131ms 0.66% 63.91% 354ms 1.78% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 63.91% 351ms 1.76% std::allocator_traits::deallocate (inline) 32ms 0.16% 64.08% 339ms 1.70% std::_Rb_tree::~_Rb_tree (inline) 150ms 0.75% 64.83% 322ms 1.62% __cxxabiv1::__si_class_type_info::__do_dyncast 21ms 0.11% 64.93% 320ms 1.61% Element::ResetIndex 0 0% 64.93% 315ms 1.58% std::_Rb_tree::_M_drop_node (inline) 3ms 0.015% 64.95% 311ms 1.56% std::_Vector_base::_M_allocate (inline) 0 0% 64.95% 303ms 1.52% std::set::~set (inline) 38ms 0.19% 65.14% 302ms 1.51% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 65.14% 301ms 1.51% AbstractCellPopulation::Iterator::operator++ (inline) 3ms 0.015% 65.15% 296ms 1.48% Cell::GetCellProliferativeType 5ms 0.025% 65.18% 293ms 1.47% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 65.18% 293ms 1.47% LegacyCellProliferativeTypesWriter::VisitCell 3ms 0.015% 65.19% 293ms 1.47% NodeLocationWriter::Visit 293ms 1.47% 66.66% 293ms 1.47% std::type_info::name (inline) 11ms 0.055% 66.72% 289ms 1.45% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 16ms 0.08% 66.80% 283ms 1.42% AbstractTetrahedralElement::CalculateJacobian 0 0% 66.80% 283ms 1.42% std::_Rb_tree::_M_put_node (inline) 282ms 1.41% 68.21% 283ms 1.42% std::vector::operator[] (inline) 223ms 1.12% 69.33% 265ms 1.33% _int_free 22ms 0.11% 69.44% 261ms 1.31% std::num_put::_M_insert_float 3ms 0.015% 69.46% 260ms 1.30% Cell::GetMutationState 2ms 0.01% 69.47% 258ms 1.29% alternateaxes 242ms 1.21% 70.68% 253ms 1.27% vertexmedian 18ms 0.09% 70.77% 252ms 1.26% std::_Rb_tree::_Rb_tree (partial-inline) 246ms 1.23% 72.01% 246ms 1.23% [libchaste_cell_based.so] 13ms 0.065% 72.07% 245ms 1.23% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 7ms 0.035% 72.11% 242ms 1.21% std::vector::push_back (inline) 14ms 0.07% 72.18% 238ms 1.19% std::_Rb_tree::_M_erase_aux (inline) 8ms 0.04% 72.22% 232ms 1.16% AbstractCellPopulation::IsCellAttachedToLocationIndex 36ms 0.18% 72.40% 231ms 1.16% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 0 0% 72.40% 231ms 1.16% TetrahedralMesh::RefreshJacobianCachedData 1ms 0.005% 72.40% 231ms 1.16% std::set::set (inline) 15ms 0.075% 72.48% 230ms 1.15% std::vector::_M_realloc_insert 4ms 0.02% 72.50% 228ms 1.14% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 29ms 0.15% 72.64% 226ms 1.13% AbstractTetrahedralElement::RefreshJacobian 76ms 0.38% 73.02% 220ms 1.10% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 63ms 0.32% 73.34% 217ms 1.09% ApcOneHitCellMutationState::ApcOneHitCellMutationState 19ms 0.095% 73.43% 214ms 1.07% Element::MarkAsDeleted 16ms 0.08% 73.52% 203ms 1.02% std::_Rb_tree::_M_copy (inline) 8ms 0.04% 73.56% 202ms 1.01% AbstractTetrahedralElement::CalculateInverseJacobian 3ms 0.015% 73.57% 200ms 1.00% std::__cxx11::collate::do_transform 1ms 0.005% 73.58% 192ms 0.96% ___vsnprintf 0 0% 73.58% 191ms 0.96% __vsnprintf_internal (inline) 6ms 0.03% 73.61% 188ms 0.94% AbstractTetrahedralElement::AbstractTetrahedralElement 20ms 0.1% 73.71% 188ms 0.94% __printf_buffer 142ms 0.71% 74.42% 185ms 0.93% AbstractElement::GetNodeGlobalIndex 0 0% 74.42% 182ms 0.91% OffLatticeSimulation::ApplyBoundaries 51ms 0.26% 74.67% 182ms 0.91% std::_Rb_tree::_M_clone_node (inline) 178ms 0.89% 75.57% 178ms 0.89% std::_Rb_tree_insert_and_rebalance 80ms 0.4% 75.97% 176ms 0.88% AbstractElement::GetNodeLocation 1ms 0.005% 75.97% 172ms 0.86% MeshBasedCellPopulation::GetDampingConstant 1ms 0.005% 75.98% 171ms 0.86% AbstractCentreBasedCellPopulation::GetDampingConstant 26ms 0.13% 76.11% 167ms 0.84% TetrahedralMesh::Clear 163ms 0.82% 76.93% 163ms 0.82% incircle 119ms 0.6% 77.52% 163ms 0.82% malloc_consolidate 162ms 0.81% 78.34% 162ms 0.81% Node::GetIndex 6ms 0.03% 78.37% 156ms 0.78% __printf_fp_l_buffer 0 0% 78.37% 156ms 0.78% __printf_fp_spec (inline) 5ms 0.025% 78.39% 155ms 0.78% CellProliferativeTypesWriter::VisitCell 102ms 0.51% 78.90% 152ms 0.76% std::_Rb_tree::equal_range (inline) 75ms 0.38% 79.28% 146ms 0.73% __printf_fp_buffer_1 3ms 0.015% 79.29% 141ms 0.71% CellPropertyCollection::HasProperty 2ms 0.01% 79.30% 141ms 0.71% boost::numeric::ublas::vector_assign (inline) 0 0% 79.30% 138ms 0.69% Cell::HasCellProperty (inline) 41ms 0.21% 79.51% 131ms 0.66% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 6ms 0.03% 79.54% 130ms 0.65% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 1ms 0.005% 79.54% 129ms 0.65% MeshBasedCellPopulation::SpringsEnd (inline) 36ms 0.18% 79.73% 128ms 0.64% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 3ms 0.015% 79.74% 126ms 0.63% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 126ms 0.63% 80.37% 126ms 0.63% unlink_chunk 38ms 0.19% 80.56% 125ms 0.63% TetrahedralMesh::EdgesEnd (partial-inline) 124ms 0.62% 81.18% 124ms 0.62% AbstractCellMutationState::~AbstractCellMutationState 0 0% 81.18% 120ms 0.6% AbstractCellBasedSimulation::DoCellRemoval (inline) 15ms 0.075% 81.26% 120ms 0.6% boost::detail::shared_count::~shared_count (inline) 0 0% 81.26% 120ms 0.6% boost::shared_ptr::~shared_ptr (inline) 119ms 0.6% 81.86% 119ms 0.6% std::vector::size (inline) 11ms 0.055% 81.91% 118ms 0.59% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 1ms 0.005% 81.92% 117ms 0.59% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 11ms 0.055% 81.97% 117ms 0.59% boost::numeric::ublas::c_vector::c_vector (inline) 2ms 0.01% 81.98% 116ms 0.58% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 106ms 0.53% 82.51% 110ms 0.55% vertexsort 31ms 0.16% 82.67% 108ms 0.54% boost::numeric::ublas::indexing_vector_assign 27ms 0.14% 82.80% 107ms 0.54% std::num_put::_M_insert_int 0 0% 82.80% 105ms 0.53% Cell::SetCellProliferativeType 3ms 0.015% 82.82% 104ms 0.52% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 104ms 0.52% 83.34% 104ms 0.52% std::_Rb_tree_rebalance_for_erase 22ms 0.11% 83.45% 103ms 0.52% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 83.45% 100ms 0.5% AbstractCellBasedWriter::OpenOutputFileForAppend