File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 17037ms, 84.10% of 20257ms total Dropped 812 nodes (cum <= 101.28ms) flat flat% sum% cum cum% 0 0% 0% 20211ms 99.77% __libc_start_call_main 0 0% 0% 20211ms 99.77% __libc_start_main_impl 0 0% 0% 20211ms 99.77% _start 0 0% 0% 20190ms 99.67% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 20190ms 99.67% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 20190ms 99.67% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 20190ms 99.67% main 0 0% 0% 20153ms 99.49% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 20153ms 99.49% CxxTest::TestRunner::runTest (inline) 0 0% 0% 20153ms 99.49% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 2ms 0.0099% 0.0099% 20125ms 99.35% AbstractCellBasedSimulation::Solve 0 0% 0.0099% 15579ms 76.91% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0099% 0.02% 10238ms 50.54% AbstractCellBasedSimulation::DoCellBirth 4ms 0.02% 0.039% 10140ms 50.06% Cell::ReadyToDivide 4ms 0.02% 0.059% 10061ms 49.67% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0049% 0.064% 9920ms 48.97% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 15ms 0.074% 0.14% 9913ms 48.94% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.015% 0.15% 9895ms 48.85% CellCycleModelOdeHandler::SolveOdeToTime 75ms 0.37% 0.52% 9731ms 48.04% AbstractOneStepIvpOdeSolver::InternalSolve 898ms 4.43% 4.96% 8923ms 44.05% RungeKutta4IvpOdeSolver::CalculateNextYValue 3709ms 18.31% 23.27% 7795ms 38.48% WntCellCycleOdeSystem::EvaluateYDerivatives 2ms 0.0099% 23.28% 5240ms 25.87% MeshBasedCellPopulation::Update 168ms 0.83% 24.11% 4161ms 20.54% AbstractCellProperty::IsType (inline) 5ms 0.025% 24.13% 4038ms 19.93% Cylindrical2dMesh::ReMesh 572ms 2.82% 26.95% 2916ms 14.40% AbstractCellProperty::IsSame 0 0% 26.95% 2515ms 12.42% OffLatticeSimulation::UpdateCellLocationsAndTopology 407ms 2.01% 28.96% 2344ms 11.57% std::type_info::operator== (inline) 0 0% 28.96% 2223ms 10.97% MutableMesh::ReMesh 1ms 0.0049% 28.97% 2213ms 10.92% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.049% 29.02% 2160ms 10.66% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 29.02% 2019ms 9.97% AbstractCellPopulation::WriteResultsToFiles 1877ms 9.27% 38.28% 1877ms 9.27% __strcmp_avx2 812ms 4.01% 42.29% 1875ms 9.26% std::_Rb_tree::_M_lower_bound (inline) 166ms 0.82% 43.11% 1727ms 8.53% TetrahedralMesh::EdgeIterator::operator++ 67ms 0.33% 43.44% 1411ms 6.97% std::_Rb_tree::find (inline) 0 0% 43.44% 1160ms 5.73% MeshBasedCellPopulation::UpdateNodePairs 7ms 0.035% 43.48% 1141ms 5.63% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 18ms 0.089% 43.57% 1123ms 5.54% TetrahedralMesh::ImportFromMesher 52ms 0.26% 43.82% 1087ms 5.37% operator new 19ms 0.094% 43.92% 1042ms 5.14% MeshBasedCellPopulation::SpringIterator::operator++ 234ms 1.16% 45.07% 1026ms 5.06% __GI___libc_malloc 13ms 0.064% 45.14% 999ms 4.93% std::set::insert (inline) 23ms 0.11% 45.25% 986ms 4.87% std::_Rb_tree::_M_insert_unique 44ms 0.22% 45.47% 962ms 4.75% std::__new_allocator::allocate (inline) 0 0% 45.47% 958ms 4.73% std::allocator_traits::allocate (inline) 0 0% 45.47% 880ms 4.34% std::set::count (inline) 1ms 0.0049% 45.47% 837ms 4.13% triangulate 0 0% 45.47% 753ms 3.72% delaunay 1ms 0.0049% 45.48% 752ms 3.71% divconqdelaunay 5ms 0.025% 45.50% 738ms 3.64% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 2ms 0.0099% 45.51% 732ms 3.61% AbstractTwoBodyInteractionForce::AddForceContribution 409ms 2.02% 47.53% 721ms 3.56% _int_malloc 5ms 0.025% 47.55% 696ms 3.44% CellPopulationElementWriter::Visit 20ms 0.099% 47.65% 674ms 3.33% std::less::operator() (inline) 44ms 0.22% 47.87% 664ms 3.28% std::map::operator[] (partial-inline) 655ms 3.23% 51.10% 655ms 3.23% std::_Rb_tree::_S_right (inline) 654ms 3.23% 54.33% 654ms 3.23% std::operator< (inline) 635ms 3.13% 57.47% 641ms 3.16% WntCellCycleOdeSystem::CalculateStoppingEvent 206ms 1.02% 58.48% 631ms 3.11% __dynamic_cast 0 0% 58.48% 628ms 3.10% std::_Rb_tree::_M_create_node (inline) 24ms 0.12% 58.60% 618ms 3.05% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 15ms 0.074% 58.68% 606ms 2.99% std::_Rb_tree::_M_insert_ (inline) 0 0% 58.68% 597ms 2.95% std::_Rb_tree::_M_get_node (inline) 2ms 0.0099% 58.69% 589ms 2.91% MeshBasedCellPopulation::AcceptCellWriter 0 0% 58.69% 576ms 2.84% std::_Rb_tree::_Alloc_node::operator() (inline) 28ms 0.14% 58.82% 572ms 2.82% AbstractCellPopulation::GetCellUsingLocationIndex 5ms 0.025% 58.85% 565ms 2.79% CellPropertyCollection::GetPropertiesType (inline) 0 0% 58.85% 549ms 2.71% std::_Rb_tree::lower_bound (inline) 0 0% 58.85% 549ms 2.71% std::map::lower_bound (inline) 0 0% 58.85% 528ms 2.61% std::map::find (inline) 6ms 0.03% 58.88% 526ms 2.60% Cylindrical2dMesh::ReconstructCylindricalMesh 8ms 0.039% 58.92% 523ms 2.58% Element::Element 10ms 0.049% 58.97% 510ms 2.52% MutableMesh::ReIndex 0 0% 58.97% 508ms 2.51% std::ostream::operator<< (inline) 71ms 0.35% 59.32% 507ms 2.50% std::ostream::_M_insert 16ms 0.079% 59.40% 490ms 2.42% Element::RegisterWithNodes (inline) 335ms 1.65% 61.05% 478ms 2.36% AbstractCellMutationState::AbstractCellMutationState 10ms 0.049% 61.10% 477ms 2.35% Node::AddElement 4ms 0.02% 61.12% 470ms 2.32% AbstractCellProperty::IsSubType (inline) 12ms 0.059% 61.18% 458ms 2.26% Cylindrical2dMesh::CorrectNonPeriodicMesh 148ms 0.73% 61.91% 433ms 2.14% __GI___libc_free 19ms 0.094% 62.00% 401ms 1.98% divconqrecurse 5ms 0.025% 62.03% 395ms 1.95% std::set::erase (inline) 10ms 0.049% 62.08% 390ms 1.93% std::_Rb_tree::erase 9ms 0.044% 62.12% 389ms 1.92% Node::RemoveElement 91ms 0.45% 62.57% 376ms 1.86% mergehulls 122ms 0.6% 63.17% 370ms 1.83% std::_Rb_tree::_M_erase 4ms 0.02% 63.19% 365ms 1.80% std::_Vector_base::_M_allocate (inline) 141ms 0.7% 63.89% 357ms 1.76% std::_Rb_tree::_M_get_insert_unique_pos 10ms 0.049% 63.94% 351ms 1.73% std::__new_allocator::deallocate (inline) 0 0% 63.94% 344ms 1.70% std::allocator_traits::deallocate (inline) 27ms 0.13% 64.07% 338ms 1.67% std::_Rb_tree::~_Rb_tree (inline) 22ms 0.11% 64.18% 336ms 1.66% Element::ResetIndex 3ms 0.015% 64.20% 326ms 1.61% Cell::GetCellProliferativeType 2ms 0.0099% 64.20% 323ms 1.59% NodeLocationWriter::Visit 0 0% 64.20% 323ms 1.59% std::set::~set (inline) 3ms 0.015% 64.22% 319ms 1.57% LegacyCellProliferativeTypesWriter::VisitCell 166ms 0.82% 65.04% 314ms 1.55% __cxxabiv1::__si_class_type_info::__do_dyncast 305ms 1.51% 66.54% 305ms 1.51% std::type_info::name (inline) 15ms 0.074% 66.62% 300ms 1.48% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 5ms 0.025% 66.64% 299ms 1.48% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 66.64% 296ms 1.46% std::_Rb_tree::_M_drop_node (inline) 234ms 1.16% 67.80% 285ms 1.41% _int_free 23ms 0.11% 67.91% 279ms 1.38% std::_Rb_tree::_Rb_tree (partial-inline) 18ms 0.089% 68.00% 279ms 1.38% std::num_put::_M_insert_float 19ms 0.094% 68.09% 277ms 1.37% std::vector::push_back (inline) 2ms 0.0099% 68.10% 273ms 1.35% Cell::GetMutationState 37ms 0.18% 68.29% 271ms 1.34% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 68.29% 268ms 1.32% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 68.29% 268ms 1.32% std::_Rb_tree::_M_put_node (inline) 265ms 1.31% 69.60% 268ms 1.32% std::vector::operator[] (inline) 16ms 0.079% 69.67% 260ms 1.28% AbstractTetrahedralElement::CalculateJacobian 2ms 0.0099% 69.68% 250ms 1.23% std::set::set (inline) 1ms 0.0049% 69.69% 249ms 1.23% TetrahedralMesh::RefreshJacobianCachedData 248ms 1.22% 70.91% 248ms 1.22% [libchaste_cell_based.so] 9ms 0.044% 70.96% 246ms 1.21% std::vector::_M_realloc_insert 7ms 0.035% 70.99% 242ms 1.19% AbstractCellPopulation::IsCellAttachedToLocationIndex 15ms 0.074% 71.07% 241ms 1.19% std::_Rb_tree::_M_erase_aux (inline) 4ms 0.02% 71.09% 239ms 1.18% alternateaxes 17ms 0.084% 71.17% 236ms 1.17% std::_Rb_tree::_M_copy (inline) 62ms 0.31% 71.48% 234ms 1.16% ApcOneHitCellMutationState::ApcOneHitCellMutationState 221ms 1.09% 72.57% 234ms 1.16% vertexmedian 9ms 0.044% 72.61% 231ms 1.14% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 5ms 0.025% 72.64% 224ms 1.11% std::__cxx11::collate::do_transform 11ms 0.054% 72.69% 222ms 1.10% AbstractTetrahedralElement::CalculateInverseJacobian 27ms 0.13% 72.82% 216ms 1.07% TetrahedralMesh::Clear 71ms 0.35% 73.17% 216ms 1.07% std::_Rb_tree::_M_clone_node (inline) 11ms 0.054% 73.23% 212ms 1.05% Element::MarkAsDeleted 24ms 0.12% 73.35% 211ms 1.04% AbstractTetrahedralElement::RefreshJacobian 51ms 0.25% 73.60% 211ms 1.04% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 67ms 0.33% 73.93% 211ms 1.04% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 3ms 0.015% 73.94% 209ms 1.03% ___vsnprintf 0 0% 73.94% 206ms 1.02% __vsnprintf_internal (inline) 23ms 0.11% 74.06% 204ms 1.01% __printf_buffer 1ms 0.0049% 74.06% 201ms 0.99% OffLatticeSimulation::ApplyBoundaries 7ms 0.035% 74.10% 195ms 0.96% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2ms 0.0099% 74.11% 191ms 0.94% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 74.11% 191ms 0.94% MeshBasedCellPopulation::GetDampingConstant 144ms 0.71% 74.82% 188ms 0.93% AbstractElement::GetNodeGlobalIndex 140ms 0.69% 75.51% 185ms 0.91% malloc_consolidate 180ms 0.89% 76.40% 180ms 0.89% incircle 0 0% 76.40% 177ms 0.87% Cell::HasCellProperty (inline) 5ms 0.025% 76.42% 177ms 0.87% CellPropertyCollection::HasProperty 172ms 0.85% 77.27% 172ms 0.85% Node::GetIndex 1ms 0.0049% 77.28% 170ms 0.84% __printf_fp_spec (inline) 2ms 0.0099% 77.29% 169ms 0.83% __printf_fp_l_buffer 1ms 0.0049% 77.29% 168ms 0.83% boost::numeric::ublas::vector_assign (inline) 168ms 0.83% 78.12% 168ms 0.83% std::_Rb_tree_insert_and_rebalance 4ms 0.02% 78.14% 167ms 0.82% CellProliferativeTypesWriter::VisitCell 83ms 0.41% 78.55% 164ms 0.81% __printf_fp_buffer_1 75ms 0.37% 78.92% 163ms 0.8% AbstractElement::GetNodeLocation 8ms 0.039% 78.96% 148ms 0.73% boost::numeric::ublas::c_vector::c_vector (inline) 4ms 0.02% 78.98% 147ms 0.73% AbstractTetrahedralElement::AbstractTetrahedralElement 105ms 0.52% 79.50% 146ms 0.72% std::_Rb_tree::equal_range (inline) 141ms 0.7% 80.19% 141ms 0.7% unlink_chunk 139ms 0.69% 80.88% 139ms 0.69% std::vector::size (inline) 8ms 0.039% 80.92% 136ms 0.67% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 36ms 0.18% 81.10% 136ms 0.67% boost::numeric::ublas::indexing_vector_assign 43ms 0.21% 81.31% 135ms 0.67% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 3ms 0.015% 81.32% 135ms 0.67% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 33ms 0.16% 81.49% 130ms 0.64% TetrahedralMesh::EdgesEnd 9ms 0.044% 81.53% 125ms 0.62% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 49ms 0.24% 81.77% 124ms 0.61% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 3ms 0.015% 81.79% 123ms 0.61% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 0 0% 81.79% 122ms 0.6% AbstractCellBasedWriter::OpenOutputFileForAppend 61ms 0.3% 82.09% 122ms 0.6% Cylindrical2dMesh::GetVectorFromAtoB 0 0% 82.09% 119ms 0.59% OutputFileHandler::OpenOutputFile 4ms 0.02% 82.11% 118ms 0.58% MeshBasedCellPopulation::SpringsEnd (inline) 8ms 0.039% 82.15% 116ms 0.57% Node::~Node 115ms 0.57% 82.72% 115ms 0.57% std::_Rb_tree_rebalance_for_erase 4ms 0.02% 82.74% 114ms 0.56% Cell::SetCellProliferativeType 108ms 0.53% 83.27% 108ms 0.53% AbstractCellMutationState::~AbstractCellMutationState 0 0% 83.27% 107ms 0.53% std::vector::resize (inline) 22ms 0.11% 83.38% 106ms 0.52% std::num_put::_M_insert_int 0 0% 83.38% 106ms 0.52% std::vector::_M_default_append 1ms 0.0049% 83.38% 104ms 0.51% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 42ms 0.21% 83.59% 104ms 0.51% std::__ostream_insert 96ms 0.47% 84.06% 104ms 0.51% vertexsort 0 0% 84.06% 103ms 0.51% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 8ms 0.039% 84.10% 102ms 0.5% boost::detail::shared_count::~shared_count (inline) 0 0% 84.10% 102ms 0.5% boost::shared_ptr::~shared_ptr (inline)