File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16474ms, 82.84% of 19886ms total Dropped 789 nodes (cum <= 99.43ms) flat flat% sum% cum cum% 0 0% 0% 19838ms 99.76% __libc_start_call_main 0 0% 0% 19838ms 99.76% __libc_start_main_impl 0 0% 0% 19838ms 99.76% _start 0 0% 0% 19818ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19818ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19818ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19818ms 99.66% main 0 0% 0% 19782ms 99.48% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19782ms 99.48% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19782ms 99.48% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 1ms 0.005% 0.005% 19755ms 99.34% AbstractCellBasedSimulation::Solve 0 0% 0.005% 15324ms 77.06% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.015% 0.02% 10128ms 50.93% AbstractCellBasedSimulation::DoCellBirth 3ms 0.015% 0.035% 10030ms 50.44% Cell::ReadyToDivide 4ms 0.02% 0.055% 9967ms 50.12% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.01% 0.065% 9819ms 49.38% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 9ms 0.045% 0.11% 9811ms 49.34% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.015% 0.13% 9796ms 49.26% CellCycleModelOdeHandler::SolveOdeToTime 65ms 0.33% 0.45% 9617ms 48.36% AbstractOneStepIvpOdeSolver::InternalSolve 888ms 4.47% 4.92% 8812ms 44.31% RungeKutta4IvpOdeSolver::CalculateNextYValue 3665ms 18.43% 23.35% 7717ms 38.81% WntCellCycleOdeSystem::EvaluateYDerivatives 2ms 0.01% 23.36% 5087ms 25.58% MeshBasedCellPopulation::Update 210ms 1.06% 24.41% 4106ms 20.65% AbstractCellProperty::IsType (inline) 7ms 0.035% 24.45% 3949ms 19.86% Cylindrical2dMesh::ReMesh 543ms 2.73% 27.18% 2836ms 14.26% AbstractCellProperty::IsSame 0 0% 27.18% 2448ms 12.31% OffLatticeSimulation::UpdateCellLocationsAndTopology 416ms 2.09% 29.27% 2293ms 11.53% std::type_info::operator== (inline) 1ms 0.005% 29.28% 2138ms 10.75% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 29.28% 2108ms 10.60% MutableMesh::ReMesh 8ms 0.04% 29.32% 2077ms 10.44% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 29.32% 1980ms 9.96% AbstractCellPopulation::WriteResultsToFiles 1865ms 9.38% 38.70% 1865ms 9.38% __strcmp_avx2 762ms 3.83% 42.53% 1796ms 9.03% std::_Rb_tree::_M_lower_bound (inline) 161ms 0.81% 43.34% 1609ms 8.09% TetrahedralMesh::EdgeIterator::operator++ 86ms 0.43% 43.77% 1336ms 6.72% std::_Rb_tree::find (inline) 0 0% 43.77% 1094ms 5.50% MeshBasedCellPopulation::UpdateNodePairs 6ms 0.03% 43.80% 1083ms 5.45% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 6ms 0.03% 43.83% 1075ms 5.41% TetrahedralMesh::ImportFromMesher 34ms 0.17% 44.00% 1039ms 5.22% operator new 212ms 1.07% 45.07% 988ms 4.97% __GI___libc_malloc 6ms 0.03% 45.10% 978ms 4.92% MeshBasedCellPopulation::SpringIterator::operator++ 12ms 0.06% 45.16% 964ms 4.85% std::set::insert (inline) 18ms 0.091% 45.25% 952ms 4.79% std::_Rb_tree::_M_insert_unique 53ms 0.27% 45.51% 936ms 4.71% std::__new_allocator::allocate (inline) 0 0% 45.51% 930ms 4.68% std::allocator_traits::allocate (inline) 0 0% 45.51% 779ms 3.92% std::set::count (inline) 1ms 0.005% 45.52% 778ms 3.91% triangulate 2ms 0.01% 45.53% 746ms 3.75% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 0 0% 45.53% 706ms 3.55% delaunay 2ms 0.01% 45.54% 705ms 3.55% divconqdelaunay 44ms 0.22% 45.76% 687ms 3.45% std::map::operator[] (partial-inline) 1ms 0.005% 45.77% 684ms 3.44% AbstractTwoBodyInteractionForce::AddForceContribution 404ms 2.03% 47.80% 684ms 3.44% _int_malloc 677ms 3.40% 51.20% 677ms 3.40% std::_Rb_tree::_S_right (inline) 7ms 0.035% 51.24% 672ms 3.38% CellPopulationElementWriter::Visit 208ms 1.05% 52.28% 671ms 3.37% __dynamic_cast 608ms 3.06% 55.34% 622ms 3.13% WntCellCycleOdeSystem::CalculateStoppingEvent 15ms 0.075% 55.42% 612ms 3.08% std::less::operator() (inline) 3ms 0.015% 55.43% 605ms 3.04% MeshBasedCellPopulation::AcceptCellWriter 597ms 3.00% 58.43% 597ms 3.00% std::operator< (inline) 22ms 0.11% 58.54% 593ms 2.98% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 2ms 0.01% 58.55% 590ms 2.97% CellPropertyCollection::GetPropertiesType (inline) 0 0% 58.55% 589ms 2.96% std::_Rb_tree::_M_create_node (inline) 0 0% 58.55% 564ms 2.84% std::_Rb_tree::_M_get_node (inline) 22ms 0.11% 58.66% 562ms 2.83% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 58.66% 557ms 2.80% std::_Rb_tree::lower_bound (inline) 0 0% 58.66% 557ms 2.80% std::map::lower_bound (inline) 0 0% 58.66% 552ms 2.78% std::map::find (inline) 32ms 0.16% 58.83% 549ms 2.76% std::_Rb_tree::_M_insert_ (inline) 6ms 0.03% 58.86% 540ms 2.72% Element::Element 13ms 0.065% 58.92% 532ms 2.68% MutableMesh::ReIndex 0 0% 58.92% 532ms 2.68% std::_Rb_tree::_Alloc_node::operator() (inline) 12ms 0.06% 58.98% 502ms 2.52% Cylindrical2dMesh::ReconstructCylindricalMesh 7ms 0.035% 59.02% 496ms 2.49% Cylindrical2dMesh::CorrectNonPeriodicMesh 3ms 0.015% 59.03% 488ms 2.45% AbstractCellProperty::IsSubType (inline) 1ms 0.005% 59.04% 475ms 2.39% std::ostream::operator<< (inline) 302ms 1.52% 60.56% 474ms 2.38% AbstractCellMutationState::AbstractCellMutationState 57ms 0.29% 60.84% 474ms 2.38% std::ostream::_M_insert 9ms 0.045% 60.89% 468ms 2.35% Element::RegisterWithNodes (inline) 10ms 0.05% 60.94% 456ms 2.29% Node::AddElement 138ms 0.69% 61.63% 451ms 2.27% __GI___libc_free 159ms 0.8% 62.43% 385ms 1.94% std::_Rb_tree::_M_get_insert_unique_pos 10ms 0.05% 62.48% 371ms 1.87% std::_Rb_tree::erase 19ms 0.096% 62.58% 368ms 1.85% Node::RemoveElement 2ms 0.01% 62.59% 368ms 1.85% std::_Vector_base::_M_allocate (inline) 0 0% 62.59% 368ms 1.85% std::set::erase (inline) 6ms 0.03% 62.62% 354ms 1.78% std::__new_allocator::deallocate (inline) 96ms 0.48% 63.10% 347ms 1.74% std::_Rb_tree::_M_erase 13ms 0.065% 63.17% 346ms 1.74% divconqrecurse 0 0% 63.17% 345ms 1.73% std::allocator_traits::deallocate (inline) 4ms 0.02% 63.19% 335ms 1.68% Cell::GetMutationState 10ms 0.05% 63.24% 331ms 1.66% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 139ms 0.7% 63.93% 327ms 1.64% __cxxabiv1::__si_class_type_info::__do_dyncast 2ms 0.01% 63.94% 325ms 1.63% LegacyCellProliferativeTypesWriter::VisitCell 97ms 0.49% 64.43% 323ms 1.62% mergehulls 20ms 0.1% 64.53% 321ms 1.61% Element::ResetIndex 9ms 0.045% 64.58% 317ms 1.59% AbstractCellPopulation::GetLocationIndexUsingCell 315ms 1.58% 66.16% 315ms 1.58% std::type_info::name (inline) 251ms 1.26% 67.42% 313ms 1.57% _int_free 0 0% 67.42% 310ms 1.56% std::_Rb_tree::_M_drop_node (inline) 2ms 0.01% 67.43% 307ms 1.54% NodeLocationWriter::Visit 17ms 0.085% 67.52% 307ms 1.54% std::_Rb_tree::~_Rb_tree (inline) 35ms 0.18% 67.70% 300ms 1.51% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 67.70% 296ms 1.49% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 67.70% 294ms 1.48% Cell::GetCellProliferativeType 9ms 0.045% 67.74% 284ms 1.43% std::vector::push_back (inline) 0 0% 67.74% 283ms 1.42% std::set::~set (inline) 0 0% 67.74% 277ms 1.39% std::_Rb_tree::_M_put_node (inline) 17ms 0.085% 67.83% 264ms 1.33% AbstractTetrahedralElement::CalculateJacobian 14ms 0.07% 67.90% 264ms 1.33% std::num_put::_M_insert_float 15ms 0.075% 67.97% 264ms 1.33% std::vector::_M_realloc_insert 254ms 1.28% 69.25% 255ms 1.28% std::vector::operator[] (inline) 250ms 1.26% 70.51% 250ms 1.26% [libchaste_cell_based.so] 9ms 0.045% 70.55% 248ms 1.25% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 3ms 0.015% 70.57% 243ms 1.22% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 4ms 0.02% 70.59% 241ms 1.21% alternateaxes 12ms 0.06% 70.65% 240ms 1.21% std::_Rb_tree::_Rb_tree (partial-inline) 227ms 1.14% 71.79% 235ms 1.18% vertexmedian 61ms 0.31% 72.10% 230ms 1.16% ApcOneHitCellMutationState::ApcOneHitCellMutationState 2ms 0.01% 72.11% 230ms 1.16% TetrahedralMesh::RefreshJacobianCachedData 46ms 0.23% 72.34% 225ms 1.13% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 2ms 0.01% 72.35% 224ms 1.13% AbstractCellPopulation::IsCellAttachedToLocationIndex 3ms 0.015% 72.36% 219ms 1.10% std::set::set (inline) 11ms 0.055% 72.42% 218ms 1.10% std::_Rb_tree::_M_erase_aux (inline) 2ms 0.01% 72.43% 211ms 1.06% MeshBasedCellPopulation::GetDampingConstant 2ms 0.01% 72.44% 209ms 1.05% AbstractCentreBasedCellPopulation::GetDampingConstant 23ms 0.12% 72.55% 209ms 1.05% std::_Rb_tree::_M_copy (inline) 4ms 0.02% 72.57% 208ms 1.05% std::__cxx11::collate::do_transform 153ms 0.77% 73.34% 205ms 1.03% AbstractElement::GetNodeGlobalIndex 18ms 0.091% 73.43% 205ms 1.03% Element::MarkAsDeleted 22ms 0.11% 73.54% 200ms 1.01% AbstractTetrahedralElement::RefreshJacobian 1ms 0.005% 73.55% 196ms 0.99% OffLatticeSimulation::ApplyBoundaries 2ms 0.01% 73.56% 194ms 0.98% ___vsnprintf 1ms 0.005% 73.56% 193ms 0.97% __vsnprintf_internal (inline) 4ms 0.02% 73.58% 191ms 0.96% AbstractTetrahedralElement::CalculateInverseJacobian 19ms 0.096% 73.68% 189ms 0.95% __printf_buffer 6ms 0.03% 73.71% 185ms 0.93% AbstractTetrahedralElement::AbstractTetrahedralElement 15ms 0.075% 73.79% 185ms 0.93% TetrahedralMesh::Clear 58ms 0.29% 74.08% 185ms 0.93% std::_Rb_tree::_M_clone_node (inline) 137ms 0.69% 74.77% 184ms 0.93% malloc_consolidate 60ms 0.3% 75.07% 182ms 0.92% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 4ms 0.02% 75.09% 164ms 0.82% CellPropertyCollection::HasProperty 163ms 0.82% 75.91% 163ms 0.82% Node::GetIndex 57ms 0.29% 76.19% 161ms 0.81% AbstractElement::GetNodeLocation 4ms 0.02% 76.21% 161ms 0.81% CellProliferativeTypesWriter::VisitCell 0 0% 76.21% 159ms 0.8% Cell::HasCellProperty (inline) 1ms 0.005% 76.22% 156ms 0.78% __printf_fp_spec (inline) 5ms 0.025% 76.24% 155ms 0.78% __printf_fp_l_buffer 101ms 0.51% 76.75% 154ms 0.77% std::_Rb_tree::equal_range (inline) 10ms 0.05% 76.80% 153ms 0.77% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 3ms 0.015% 76.82% 151ms 0.76% boost::numeric::ublas::vector_assign (inline) 7ms 0.035% 76.85% 146ms 0.73% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 54ms 0.27% 77.12% 144ms 0.72% __printf_fp_buffer_1 142ms 0.71% 77.84% 142ms 0.71% unlink_chunk 13ms 0.065% 77.90% 140ms 0.7% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 0 0% 77.90% 139ms 0.7% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 137ms 0.69% 78.59% 137ms 0.69% std::vector::size (inline) 3ms 0.015% 78.61% 128ms 0.64% MeshBasedCellPopulation::SpringsEnd (inline) 128ms 0.64% 79.25% 128ms 0.64% std::_Rb_tree_insert_and_rebalance 0 0% 79.25% 127ms 0.64% AbstractCellBasedWriter::OpenOutputFileForAppend 127ms 0.64% 79.89% 127ms 0.64% incircle 44ms 0.22% 80.11% 124ms 0.62% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 0 0% 80.11% 123ms 0.62% OutputFileHandler::OpenOutputFile 72ms 0.36% 80.47% 121ms 0.61% Cylindrical2dMesh::GetVectorFromAtoB 1ms 0.005% 80.48% 120ms 0.6% Cell::SetCellProliferativeType 46ms 0.23% 80.71% 116ms 0.58% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 6ms 0.03% 80.74% 116ms 0.58% boost::numeric::ublas::c_vector::c_vector (inline) 115ms 0.58% 81.32% 115ms 0.58% AbstractElement::IsDeleted 38ms 0.19% 81.51% 113ms 0.57% boost::numeric::ublas::indexing_vector_assign 26ms 0.13% 81.64% 112ms 0.56% std::num_put::_M_insert_int 18ms 0.091% 81.73% 111ms 0.56% boost::detail::shared_count::~shared_count (inline) 0 0% 81.73% 111ms 0.56% boost::shared_ptr::~shared_ptr (inline) 102ms 0.51% 82.24% 111ms 0.56% vertexsort 0 0% 82.24% 108ms 0.54% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 82.24% 108ms 0.54% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 14ms 0.07% 82.31% 106ms 0.53% MeshBasedCellPopulation::SpringIterator::SpringIterator 3ms 0.015% 82.33% 104ms 0.52% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 2ms 0.01% 82.34% 104ms 0.52% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 100ms 0.5% 82.84% 100ms 0.5% std::_Rb_tree_rebalance_for_erase