File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16714ms, 84.32% of 19821ms total Dropped 783 nodes (cum <= 99.11ms) flat flat% sum% cum cum% 0 0% 0% 19777ms 99.78% __libc_start_call_main 0 0% 0% 19777ms 99.78% __libc_start_main_impl 0 0% 0% 19777ms 99.78% _start 0 0% 0% 19758ms 99.68% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19758ms 99.68% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19758ms 99.68% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19758ms 99.68% main 0 0% 0% 19721ms 99.50% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19721ms 99.50% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19721ms 99.50% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 1ms 0.005% 0.005% 19695ms 99.36% AbstractCellBasedSimulation::Solve 0 0% 0.005% 15290ms 77.14% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.01% 0.015% 10115ms 51.03% AbstractCellBasedSimulation::DoCellBirth 0 0% 0.015% 10022ms 50.56% Cell::ReadyToDivide 10ms 0.05% 0.066% 9955ms 50.22% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.005% 0.071% 9798ms 49.43% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 11ms 0.055% 0.13% 9791ms 49.40% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.015% 0.14% 9777ms 49.33% CellCycleModelOdeHandler::SolveOdeToTime 66ms 0.33% 0.47% 9618ms 48.52% AbstractOneStepIvpOdeSolver::InternalSolve 907ms 4.58% 5.05% 8823ms 44.51% RungeKutta4IvpOdeSolver::CalculateNextYValue 3625ms 18.29% 23.34% 7717ms 38.93% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 23.34% 5077ms 25.61% MeshBasedCellPopulation::Update 177ms 0.89% 24.23% 4141ms 20.89% AbstractCellProperty::IsType (inline) 7ms 0.035% 24.27% 3906ms 19.71% Cylindrical2dMesh::ReMesh 547ms 2.76% 27.03% 2878ms 14.52% AbstractCellProperty::IsSame 0 0% 27.03% 2472ms 12.47% OffLatticeSimulation::UpdateCellLocationsAndTopology 406ms 2.05% 29.08% 2331ms 11.76% std::type_info::operator== (inline) 1ms 0.005% 29.08% 2173ms 10.96% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 29.08% 2144ms 10.82% MutableMesh::ReMesh 15ms 0.076% 29.16% 2112ms 10.66% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 29.16% 1925ms 9.71% AbstractCellPopulation::WriteResultsToFiles 1879ms 9.48% 38.64% 1879ms 9.48% __strcmp_avx2 753ms 3.80% 42.43% 1802ms 9.09% std::_Rb_tree::_M_lower_bound (inline) 168ms 0.85% 43.28% 1672ms 8.44% TetrahedralMesh::EdgeIterator::operator++ 57ms 0.29% 43.57% 1357ms 6.85% std::_Rb_tree::find (inline) 1ms 0.005% 43.57% 1137ms 5.74% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.02% 43.60% 1100ms 5.55% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 59ms 0.3% 43.89% 1071ms 5.40% operator new 13ms 0.066% 43.96% 1040ms 5.25% TetrahedralMesh::ImportFromMesher 8ms 0.04% 44.00% 1005ms 5.07% MeshBasedCellPopulation::SpringIterator::operator++ 240ms 1.21% 45.21% 1001ms 5.05% __GI___libc_malloc 9ms 0.045% 45.26% 983ms 4.96% std::set::insert (inline) 19ms 0.096% 45.35% 974ms 4.91% std::_Rb_tree::_M_insert_unique 34ms 0.17% 45.52% 938ms 4.73% std::__new_allocator::allocate (inline) 0 0% 45.52% 931ms 4.70% std::allocator_traits::allocate (inline) 0 0% 45.52% 837ms 4.22% std::set::count (inline) 1ms 0.005% 45.53% 831ms 4.19% triangulate 1ms 0.005% 45.53% 737ms 3.72% delaunay 4ms 0.02% 45.55% 736ms 3.71% divconqdelaunay 1ms 0.005% 45.56% 713ms 3.60% AbstractTwoBodyInteractionForce::AddForceContribution 2ms 0.01% 45.57% 704ms 3.55% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 390ms 1.97% 47.54% 700ms 3.53% _int_malloc 691ms 3.49% 51.02% 691ms 3.49% std::_Rb_tree::_S_right (inline) 8ms 0.04% 51.06% 678ms 3.42% CellPopulationElementWriter::Visit 59ms 0.3% 51.36% 662ms 3.34% std::map::operator[] (partial-inline) 621ms 3.13% 54.49% 631ms 3.18% WntCellCycleOdeSystem::CalculateStoppingEvent 16ms 0.081% 54.57% 627ms 3.16% std::less::operator() (inline) 25ms 0.13% 54.70% 615ms 3.10% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 34ms 0.17% 54.87% 614ms 3.10% std::_Rb_tree::_M_insert_ (inline) 611ms 3.08% 57.95% 611ms 3.08% std::operator< (inline) 172ms 0.87% 58.82% 610ms 3.08% __dynamic_cast 0 0% 58.82% 594ms 3.00% std::_Rb_tree::_M_create_node (inline) 0 0% 58.82% 573ms 2.89% std::_Rb_tree::_M_get_node (inline) 20ms 0.1% 58.92% 563ms 2.84% AbstractCellPopulation::GetCellUsingLocationIndex 9ms 0.045% 58.97% 559ms 2.82% MeshBasedCellPopulation::AcceptCellWriter 0 0% 58.97% 544ms 2.74% std::_Rb_tree::_Alloc_node::operator() (inline) 5ms 0.025% 58.99% 535ms 2.70% Element::Element 5ms 0.025% 59.02% 527ms 2.66% CellPropertyCollection::GetPropertiesType (inline) 0 0% 59.02% 524ms 2.64% std::_Rb_tree::lower_bound (inline) 0 0% 59.02% 524ms 2.64% std::map::lower_bound (inline) 10ms 0.05% 59.07% 517ms 2.61% Cylindrical2dMesh::ReconstructCylindricalMesh 0 0% 59.07% 514ms 2.59% std::map::find (inline) 5ms 0.025% 59.09% 497ms 2.51% Element::RegisterWithNodes (inline) 7ms 0.035% 59.13% 492ms 2.48% MutableMesh::ReIndex 320ms 1.61% 60.74% 486ms 2.45% AbstractCellMutationState::AbstractCellMutationState 10ms 0.05% 60.79% 486ms 2.45% Node::AddElement 3ms 0.015% 60.81% 475ms 2.40% std::ostream::operator<< (inline) 51ms 0.26% 61.07% 472ms 2.38% std::ostream::_M_insert 3ms 0.015% 61.08% 454ms 2.29% Cylindrical2dMesh::CorrectNonPeriodicMesh 0 0% 61.08% 444ms 2.24% AbstractCellProperty::IsSubType (inline) 179ms 0.9% 61.98% 444ms 2.24% __GI___libc_free 7ms 0.035% 62.02% 382ms 1.93% std::_Rb_tree::erase 12ms 0.061% 62.08% 381ms 1.92% divconqrecurse 1ms 0.005% 62.09% 380ms 1.92% std::set::erase (inline) 14ms 0.071% 62.16% 375ms 1.89% Node::RemoveElement 11ms 0.055% 62.21% 372ms 1.88% std::__new_allocator::deallocate (inline) 0 0% 62.21% 369ms 1.86% std::allocator_traits::deallocate (inline) 107ms 0.54% 62.75% 360ms 1.82% mergehulls 1ms 0.005% 62.76% 359ms 1.81% std::_Vector_base::_M_allocate (inline) 90ms 0.45% 63.21% 353ms 1.78% std::_Rb_tree::_M_erase 139ms 0.7% 63.91% 341ms 1.72% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 63.91% 328ms 1.65% std::_Rb_tree::_M_drop_node (inline) 11ms 0.055% 63.97% 322ms 1.62% Element::ResetIndex 22ms 0.11% 64.08% 318ms 1.60% std::_Rb_tree::~_Rb_tree (inline) 140ms 0.71% 64.78% 316ms 1.59% __cxxabiv1::__si_class_type_info::__do_dyncast 309ms 1.56% 66.34% 309ms 1.56% std::type_info::name (inline) 3ms 0.015% 66.36% 305ms 1.54% Cell::GetCellProliferativeType 5ms 0.025% 66.38% 301ms 1.52% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 3ms 0.015% 66.40% 301ms 1.52% NodeLocationWriter::Visit 0 0% 66.40% 297ms 1.50% std::_Rb_tree::_M_put_node (inline) 0 0% 66.40% 296ms 1.49% std::set::~set (inline) 4ms 0.02% 66.42% 280ms 1.41% LegacyCellProliferativeTypesWriter::VisitCell 41ms 0.21% 66.63% 278ms 1.40% AbstractCellPopulation::Iterator::IsRealCell 0 0% 66.63% 278ms 1.40% AbstractCellPopulation::Iterator::operator++ (inline) 7ms 0.035% 66.66% 269ms 1.36% AbstractCellPopulation::GetLocationIndexUsingCell 12ms 0.061% 66.72% 268ms 1.35% std::num_put::_M_insert_float 2ms 0.01% 66.73% 265ms 1.34% Cell::GetMutationState 220ms 1.11% 67.84% 265ms 1.34% _int_free 8ms 0.04% 67.88% 263ms 1.33% std::vector::push_back (inline) 16ms 0.081% 67.96% 261ms 1.32% AbstractTetrahedralElement::CalculateJacobian 56ms 0.28% 68.25% 259ms 1.31% ApcOneHitCellMutationState::ApcOneHitCellMutationState 17ms 0.086% 68.33% 259ms 1.31% std::_Rb_tree::_Rb_tree (partial-inline) 253ms 1.28% 69.61% 253ms 1.28% [libchaste_cell_based.so] 249ms 1.26% 70.86% 251ms 1.27% std::vector::operator[] (inline) 3ms 0.015% 70.88% 245ms 1.24% TetrahedralMesh::RefreshJacobianCachedData 17ms 0.086% 70.97% 242ms 1.22% std::vector::_M_realloc_insert 13ms 0.066% 71.03% 234ms 1.18% std::_Rb_tree::_M_erase_aux (inline) 3ms 0.015% 71.05% 233ms 1.18% alternateaxes 2ms 0.01% 71.06% 231ms 1.17% std::set::set (inline) 6ms 0.03% 71.09% 230ms 1.16% AbstractCellPopulation::IsCellAttachedToLocationIndex 216ms 1.09% 72.18% 230ms 1.16% vertexmedian 2ms 0.01% 72.19% 224ms 1.13% std::__cxx11::collate::do_transform 3ms 0.015% 72.20% 216ms 1.09% ___vsnprintf 0 0% 72.20% 214ms 1.08% __vsnprintf_internal (inline) 25ms 0.13% 72.33% 212ms 1.07% __printf_buffer 28ms 0.14% 72.47% 212ms 1.07% std::_Rb_tree::_M_copy (inline) 8ms 0.04% 72.51% 211ms 1.06% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 8ms 0.04% 72.55% 209ms 1.05% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 8ms 0.04% 72.59% 208ms 1.05% AbstractTetrahedralElement::CalculateInverseJacobian 10ms 0.05% 72.64% 204ms 1.03% Element::MarkAsDeleted 137ms 0.69% 73.33% 203ms 1.02% malloc_consolidate 80ms 0.4% 73.73% 201ms 1.01% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 39ms 0.2% 73.93% 200ms 1.01% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 27ms 0.14% 74.07% 192ms 0.97% AbstractTetrahedralElement::RefreshJacobian 142ms 0.72% 74.78% 191ms 0.96% AbstractElement::GetNodeGlobalIndex 187ms 0.94% 75.73% 187ms 0.94% Node::GetIndex 2ms 0.01% 75.74% 186ms 0.94% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 75.74% 186ms 0.94% MeshBasedCellPopulation::GetDampingConstant 0 0% 75.74% 180ms 0.91% OffLatticeSimulation::ApplyBoundaries 53ms 0.27% 76.01% 180ms 0.91% std::_Rb_tree::_M_clone_node (inline) 174ms 0.88% 76.88% 174ms 0.88% std::_Rb_tree_insert_and_rebalance 6ms 0.03% 76.91% 170ms 0.86% __printf_fp_l_buffer 0 0% 76.91% 170ms 0.86% __printf_fp_spec (inline) 2ms 0.01% 76.92% 164ms 0.83% AbstractTetrahedralElement::AbstractTetrahedralElement 161ms 0.81% 77.74% 161ms 0.81% unlink_chunk 1ms 0.005% 77.74% 160ms 0.81% CellProliferativeTypesWriter::VisitCell 74ms 0.37% 78.11% 156ms 0.79% __printf_fp_buffer_1 156ms 0.79% 78.90% 156ms 0.79% incircle 4ms 0.02% 78.92% 154ms 0.78% boost::numeric::ublas::vector_assign (inline) 78ms 0.39% 79.31% 152ms 0.77% AbstractElement::GetNodeLocation 11ms 0.055% 79.37% 151ms 0.76% TetrahedralMesh::Clear 4ms 0.02% 79.39% 147ms 0.74% CellPropertyCollection::HasProperty 95ms 0.48% 79.87% 146ms 0.74% std::_Rb_tree::equal_range (inline) 0 0% 79.87% 145ms 0.73% Cell::HasCellProperty (inline) 1ms 0.005% 79.87% 142ms 0.72% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 47ms 0.24% 80.11% 140ms 0.71% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 29ms 0.15% 80.26% 136ms 0.69% TetrahedralMesh::EdgesEnd 34ms 0.17% 80.43% 135ms 0.68% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 78ms 0.39% 80.82% 135ms 0.68% Cylindrical2dMesh::GetVectorFromAtoB 8ms 0.04% 80.86% 135ms 0.68% boost::numeric::ublas::c_vector::c_vector (inline) 10ms 0.05% 80.91% 133ms 0.67% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 133ms 0.67% 81.59% 133ms 0.67% std::vector::size (inline) 4ms 0.02% 81.61% 130ms 0.66% MeshBasedCellPopulation::SpringsEnd (inline) 6ms 0.03% 81.64% 127ms 0.64% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 31ms 0.16% 81.79% 123ms 0.62% boost::numeric::ublas::indexing_vector_assign 44ms 0.22% 82.01% 122ms 0.62% std::__ostream_insert 0 0% 82.01% 117ms 0.59% Cell::SetCellProliferativeType 114ms 0.58% 82.59% 114ms 0.58% AbstractElement::IsDeleted 111ms 0.56% 83.15% 111ms 0.56% AbstractCellProperty::~AbstractCellProperty 110ms 0.55% 83.70% 110ms 0.55% AbstractCellMutationState::~AbstractCellMutationState 12ms 0.061% 83.76% 110ms 0.55% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 0 0% 83.76% 109ms 0.55% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 83.76% 108ms 0.54% OutputFileHandler::OpenOutputFile 18ms 0.091% 83.86% 106ms 0.53% std::num_put::_M_insert_int 90ms 0.45% 84.31% 102ms 0.51% vertexsort 0 0% 84.31% 100ms 0.5% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 3ms 0.015% 84.32% 100ms 0.5% std::operator<< (inline)