File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16880ms, 83.44% of 20230ms total Dropped 810 nodes (cum <= 101.15ms) flat flat% sum% cum cum% 0 0% 0% 20187ms 99.79% __libc_start_call_main 0 0% 0% 20187ms 99.79% __libc_start_main_impl 0 0% 0% 20187ms 99.79% _start 0 0% 0% 20169ms 99.70% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 20169ms 99.70% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 20169ms 99.70% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 20169ms 99.70% main 0 0% 0% 20133ms 99.52% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 20133ms 99.52% CxxTest::TestRunner::runTest (inline) 0 0% 0% 20133ms 99.52% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 20106ms 99.39% AbstractCellBasedSimulation::Solve 0 0% 0% 15629ms 77.26% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0099% 0.0099% 10171ms 50.28% AbstractCellBasedSimulation::DoCellBirth 3ms 0.015% 0.025% 10076ms 49.81% Cell::ReadyToDivide 3ms 0.015% 0.04% 10009ms 49.48% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.0099% 0.049% 9848ms 48.68% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 16ms 0.079% 0.13% 9834ms 48.61% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.0099% 0.14% 9817ms 48.53% CellCycleModelOdeHandler::SolveOdeToTime 79ms 0.39% 0.53% 9616ms 47.53% AbstractOneStepIvpOdeSolver::InternalSolve 896ms 4.43% 4.96% 8767ms 43.34% RungeKutta4IvpOdeSolver::CalculateNextYValue 3591ms 17.75% 22.71% 7621ms 37.67% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 22.71% 5347ms 26.43% MeshBasedCellPopulation::Update 7ms 0.035% 22.74% 4139ms 20.46% Cylindrical2dMesh::ReMesh 194ms 0.96% 23.70% 4088ms 20.21% AbstractCellProperty::IsType (inline) 584ms 2.89% 26.59% 2845ms 14.06% AbstractCellProperty::IsSame 1ms 0.0049% 26.59% 2486ms 12.29% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 26.59% 2335ms 11.54% MutableMesh::ReMesh 403ms 1.99% 28.59% 2261ms 11.18% std::type_info::operator== (inline) 1ms 0.0049% 28.59% 2188ms 10.82% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.03% 28.62% 2140ms 10.58% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 28.62% 1984ms 9.81% AbstractCellPopulation::WriteResultsToFiles 1929ms 9.54% 38.16% 1929ms 9.54% __strcmp_avx2 763ms 3.77% 41.93% 1826ms 9.03% std::_Rb_tree::_M_lower_bound (inline) 164ms 0.81% 42.74% 1733ms 8.57% TetrahedralMesh::EdgeIterator::operator++ 55ms 0.27% 43.01% 1357ms 6.71% std::_Rb_tree::find (inline) 10ms 0.049% 43.06% 1240ms 6.13% TetrahedralMesh::ImportFromMesher 0 0% 43.06% 1173ms 5.80% MeshBasedCellPopulation::UpdateNodePairs 6ms 0.03% 43.09% 1135ms 5.61% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 83ms 0.41% 43.50% 1098ms 5.43% operator new 21ms 0.1% 43.60% 1042ms 5.15% MeshBasedCellPopulation::SpringIterator::operator++ 247ms 1.22% 44.82% 1002ms 4.95% __GI___libc_malloc 13ms 0.064% 44.89% 984ms 4.86% std::set::insert (inline) 26ms 0.13% 45.02% 971ms 4.80% std::_Rb_tree::_M_insert_unique 40ms 0.2% 45.22% 960ms 4.75% std::__new_allocator::allocate (inline) 0 0% 45.22% 957ms 4.73% std::allocator_traits::allocate (inline) 0 0% 45.22% 863ms 4.27% std::set::count (inline) 2ms 0.0099% 45.22% 819ms 4.05% triangulate 5ms 0.025% 45.25% 751ms 3.71% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 5ms 0.025% 45.27% 730ms 3.61% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 45.27% 728ms 3.60% delaunay 5ms 0.025% 45.30% 727ms 3.59% divconqdelaunay 65ms 0.32% 45.62% 693ms 3.43% std::map::operator[] (partial-inline) 29ms 0.14% 45.76% 688ms 3.40% std::less::operator() (inline) 395ms 1.95% 47.72% 687ms 3.40% _int_malloc 9ms 0.044% 47.76% 685ms 3.39% CellPopulationElementWriter::Visit 183ms 0.9% 48.67% 684ms 3.38% __dynamic_cast 659ms 3.26% 51.92% 659ms 3.26% std::operator< (inline) 641ms 3.17% 55.09% 641ms 3.17% std::_Rb_tree::_S_right (inline) 632ms 3.12% 58.22% 640ms 3.16% WntCellCycleOdeSystem::CalculateStoppingEvent 4ms 0.02% 58.24% 607ms 3.00% MeshBasedCellPopulation::AcceptCellWriter 0 0% 58.24% 598ms 2.96% std::_Rb_tree::_M_create_node (inline) 34ms 0.17% 58.40% 596ms 2.95% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 28ms 0.14% 58.54% 594ms 2.94% std::_Rb_tree::_M_insert_ (inline) 28ms 0.14% 58.68% 592ms 2.93% AbstractCellPopulation::GetCellUsingLocationIndex 4ms 0.02% 58.70% 585ms 2.89% CellPropertyCollection::GetPropertiesType (inline) 0 0% 58.70% 571ms 2.82% std::_Rb_tree::_M_get_node (inline) 0 0% 58.70% 561ms 2.77% std::_Rb_tree::lower_bound (inline) 0 0% 58.70% 561ms 2.77% std::map::lower_bound (inline) 0 0% 58.70% 549ms 2.71% std::_Rb_tree::_Alloc_node::operator() (inline) 9ms 0.044% 58.74% 538ms 2.66% Element::Element 10ms 0.049% 58.79% 531ms 2.62% MutableMesh::ReIndex 2ms 0.0099% 58.80% 517ms 2.56% AbstractCellProperty::IsSubType (inline) 3ms 0.015% 58.82% 492ms 2.43% std::ostream::operator<< (inline) 0 0% 58.82% 491ms 2.43% std::map::find (inline) 4ms 0.02% 58.84% 489ms 2.42% Element::RegisterWithNodes (inline) 194ms 0.96% 59.80% 489ms 2.42% __GI___libc_free 69ms 0.34% 60.14% 487ms 2.41% std::ostream::_M_insert 9ms 0.044% 60.18% 480ms 2.37% Node::AddElement 9ms 0.044% 60.23% 478ms 2.36% Cylindrical2dMesh::ReconstructCylindricalMesh 14ms 0.069% 60.30% 470ms 2.32% Cylindrical2dMesh::CorrectNonPeriodicMesh 311ms 1.54% 61.83% 453ms 2.24% AbstractCellMutationState::AbstractCellMutationState 22ms 0.11% 61.94% 392ms 1.94% std::__new_allocator::deallocate (inline) 4ms 0.02% 61.96% 390ms 1.93% std::_Vector_base::_M_allocate (inline) 0 0% 61.96% 387ms 1.91% std::allocator_traits::deallocate (inline) 145ms 0.72% 62.68% 378ms 1.87% __cxxabiv1::__si_class_type_info::__do_dyncast 13ms 0.064% 62.74% 372ms 1.84% divconqrecurse 111ms 0.55% 63.29% 367ms 1.81% std::_Rb_tree::_M_erase 7ms 0.035% 63.33% 363ms 1.79% std::vector::push_back (inline) 98ms 0.48% 63.81% 353ms 1.74% mergehulls 130ms 0.64% 64.45% 351ms 1.74% std::_Rb_tree::_M_get_insert_unique_pos 41ms 0.2% 64.66% 348ms 1.72% std::vector::_M_realloc_insert 31ms 0.15% 64.81% 345ms 1.71% std::_Rb_tree::~_Rb_tree (inline) 2ms 0.0099% 64.82% 338ms 1.67% Cell::GetMutationState 5ms 0.025% 64.84% 332ms 1.64% std::set::erase (inline) 9ms 0.044% 64.89% 331ms 1.64% Node::RemoveElement 7ms 0.035% 64.92% 329ms 1.63% std::_Rb_tree::erase 31ms 0.15% 65.08% 328ms 1.62% Element::ResetIndex 3ms 0.015% 65.09% 326ms 1.61% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 0 0% 65.09% 321ms 1.59% std::set::~set (inline) 4ms 0.02% 65.11% 314ms 1.55% LegacyCellProliferativeTypesWriter::VisitCell 5ms 0.025% 65.14% 310ms 1.53% Cell::GetCellProliferativeType 0 0% 65.14% 309ms 1.53% std::_Rb_tree::_M_drop_node (inline) 1ms 0.0049% 65.14% 306ms 1.51% NodeLocationWriter::Visit 1ms 0.0049% 65.15% 297ms 1.47% AbstractCellPopulation::GetLocationIndexUsingCell 251ms 1.24% 66.39% 295ms 1.46% _int_free 278ms 1.37% 67.76% 278ms 1.37% std::vector::operator[] (inline) 0 0% 67.76% 275ms 1.36% AbstractCellPopulation::Iterator::operator++ (inline) 24ms 0.12% 67.88% 273ms 1.35% AbstractCellPopulation::Iterator::IsRealCell (inline) 14ms 0.069% 67.95% 271ms 1.34% std::num_put::_M_insert_float 0 0% 67.95% 268ms 1.32% std::_Rb_tree::_M_put_node (inline) 266ms 1.31% 69.26% 266ms 1.31% std::type_info::name (inline) 8ms 0.04% 69.30% 251ms 1.24% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 10ms 0.049% 69.35% 251ms 1.24% AbstractTetrahedralElement::CalculateJacobian 0 0% 69.35% 251ms 1.24% TetrahedralMesh::RefreshJacobianCachedData 2ms 0.0099% 69.36% 241ms 1.19% alternateaxes 13ms 0.064% 69.43% 241ms 1.19% std::_Rb_tree::_Rb_tree (partial-inline) 226ms 1.12% 70.54% 239ms 1.18% vertexmedian 232ms 1.15% 71.69% 232ms 1.15% [libchaste_cell_based.so] 4ms 0.02% 71.71% 228ms 1.13% AbstractCellPopulation::IsCellAttachedToLocationIndex 61ms 0.3% 72.01% 228ms 1.13% ApcOneHitCellMutationState::ApcOneHitCellMutationState 16ms 0.079% 72.09% 226ms 1.12% TetrahedralMesh::Clear 7ms 0.035% 72.13% 226ms 1.12% std::__cxx11::collate::do_transform 1ms 0.0049% 72.13% 221ms 1.09% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 10ms 0.049% 72.18% 215ms 1.06% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.0049% 72.18% 215ms 1.06% std::set::set (inline) 1ms 0.0049% 72.19% 214ms 1.06% ___vsnprintf 0 0% 72.19% 213ms 1.05% __vsnprintf_internal (inline) 11ms 0.054% 72.24% 213ms 1.05% std::_Rb_tree::_M_erase_aux (inline) 22ms 0.11% 72.35% 211ms 1.04% __printf_buffer 50ms 0.25% 72.60% 210ms 1.04% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 20ms 0.099% 72.70% 203ms 1.00% std::_Rb_tree::_M_copy (inline) 71ms 0.35% 73.05% 198ms 0.98% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 198ms 0.98% 74.03% 198ms 0.98% Node::GetIndex 0 0% 74.03% 197ms 0.97% OffLatticeSimulation::ApplyBoundaries 151ms 0.75% 74.78% 192ms 0.95% AbstractElement::GetNodeGlobalIndex 20ms 0.099% 74.87% 192ms 0.95% AbstractTetrahedralElement::RefreshJacobian 18ms 0.089% 74.96% 187ms 0.92% Element::MarkAsDeleted 2ms 0.0099% 74.97% 183ms 0.9% __printf_fp_spec (inline) 0 0% 74.97% 182ms 0.9% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 74.97% 182ms 0.9% MeshBasedCellPopulation::GetDampingConstant 52ms 0.26% 75.23% 182ms 0.9% std::_Rb_tree::_M_clone_node (inline) 4ms 0.02% 75.25% 181ms 0.89% __printf_fp_l_buffer 127ms 0.63% 75.88% 180ms 0.89% malloc_consolidate 2ms 0.0099% 75.89% 178ms 0.88% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 88ms 0.43% 76.32% 172ms 0.85% __printf_fp_buffer_1 6ms 0.03% 76.35% 171ms 0.85% CellPropertyCollection::HasProperty 1ms 0.0049% 76.36% 170ms 0.84% Cell::HasCellProperty (inline) 4ms 0.02% 76.38% 163ms 0.81% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 76.38% 159ms 0.79% CellProliferativeTypesWriter::VisitCell 159ms 0.79% 77.16% 159ms 0.79% incircle 61ms 0.3% 77.46% 153ms 0.76% AbstractElement::GetNodeLocation 153ms 0.76% 78.22% 153ms 0.76% std::_Rb_tree_insert_and_rebalance 1ms 0.0049% 78.23% 149ms 0.74% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 147ms 0.73% 78.95% 147ms 0.73% unlink_chunk 39ms 0.19% 79.14% 142ms 0.7% TetrahedralMesh::EdgesEnd 1ms 0.0049% 79.15% 140ms 0.69% boost::numeric::ublas::vector_assign (inline) 136ms 0.67% 79.82% 136ms 0.67% std::vector::size (inline) 1ms 0.0049% 79.83% 133ms 0.66% Cell::SetCellProliferativeType 15ms 0.074% 79.90% 133ms 0.66% std::_Vector_base::_M_deallocate (inline) 5ms 0.025% 79.93% 132ms 0.65% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 54ms 0.27% 80.19% 131ms 0.65% std::__ostream_insert 40ms 0.2% 80.39% 128ms 0.63% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 2ms 0.0099% 80.40% 128ms 0.63% MeshBasedCellPopulation::SpringsEnd (inline) 7ms 0.035% 80.43% 122ms 0.6% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 26ms 0.13% 80.56% 121ms 0.6% boost::numeric::ublas::indexing_vector_assign 119ms 0.59% 81.15% 119ms 0.59% AbstractElement::IsDeleted 82ms 0.41% 81.56% 118ms 0.58% std::_Rb_tree::equal_range (inline) 14ms 0.069% 81.63% 117ms 0.58% boost::detail::shared_count::~shared_count (inline) 0 0% 81.63% 117ms 0.58% boost::shared_ptr::~shared_ptr (inline) 40ms 0.2% 81.82% 116ms 0.57% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 20ms 0.099% 81.92% 115ms 0.57% Node::~Node 0 0% 81.92% 114ms 0.56% AbstractCellBasedWriter::OpenOutputFileForAppend 1ms 0.0049% 81.93% 112ms 0.55% OutputFileHandler::OpenOutputFile 110ms 0.54% 82.47% 110ms 0.54% AbstractCellProperty::~AbstractCellProperty 0 0% 82.47% 109ms 0.54% AbstractCellBasedSimulation::DoCellRemoval (inline) 9ms 0.044% 82.52% 109ms 0.54% boost::numeric::ublas::c_vector::c_vector 100ms 0.49% 83.01% 105ms 0.52% vertexsort 60ms 0.3% 83.31% 104ms 0.51% Cylindrical2dMesh::GetVectorFromAtoB 25ms 0.12% 83.43% 104ms 0.51% std::num_put::_M_insert_int 0 0% 83.43% 103ms 0.51% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 2ms 0.0099% 83.44% 102ms 0.5% CryptSimulationBoundaryCondition::ImposeBoundaryCondition