File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 17050ms, 84.06% of 20283ms total Dropped 836 nodes (cum <= 101.42ms) flat flat% sum% cum cum% 0 0% 0% 20222ms 99.70% __libc_start_call_main 0 0% 0% 20222ms 99.70% __libc_start_main_impl 0 0% 0% 20222ms 99.70% _start 0 0% 0% 20198ms 99.58% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 20198ms 99.58% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 20198ms 99.58% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 20198ms 99.58% main 0 0% 0% 20156ms 99.37% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 20156ms 99.37% CxxTest::TestRunner::runTest (inline) 0 0% 0% 20155ms 99.37% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 20129ms 99.24% AbstractCellBasedSimulation::Solve 0 0% 0% 15236ms 75.12% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0099% 0.0099% 9426ms 46.47% AbstractCellBasedSimulation::DoCellBirth 8ms 0.039% 0.049% 9311ms 45.91% Cell::ReadyToDivide 8ms 0.039% 0.089% 9177ms 45.24% AbstractPhaseBasedCellCycleModel::ReadyToDivide 3ms 0.015% 0.1% 9036ms 44.55% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 19ms 0.094% 0.2% 9026ms 44.50% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.015% 0.21% 9003ms 44.39% CellCycleModelOdeHandler::SolveOdeToTime 78ms 0.38% 0.6% 8791ms 43.34% AbstractOneStepIvpOdeSolver::InternalSolve 974ms 4.80% 5.40% 7854ms 38.72% RungeKutta4IvpOdeSolver::CalculateNextYValue 2829ms 13.95% 19.35% 6692ms 32.99% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.0049% 19.35% 5679ms 28.00% MeshBasedCellPopulation::Update 5ms 0.025% 19.38% 4471ms 22.04% Cylindrical2dMesh::ReMesh 75ms 0.37% 19.75% 3921ms 19.33% AbstractCellProperty::IsType (inline) 2ms 0.0099% 19.76% 2697ms 13.30% OffLatticeSimulation::UpdateCellLocationsAndTopology 357ms 1.76% 21.52% 2515ms 12.40% AbstractCellProperty::IsSame 0 0% 21.52% 2484ms 12.25% MutableMesh::ReMesh 1ms 0.0049% 21.52% 2367ms 11.67% ForwardEulerNumericalMethod::UpdateAllNodePositions 11ms 0.054% 21.57% 2315ms 11.41% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 21.57% 2185ms 10.77% AbstractCellPopulation::WriteResultsToFiles 206ms 1.02% 22.59% 2158ms 10.64% std::type_info::operator== (inline) 2058ms 10.15% 32.74% 2058ms 10.15% __strcmp_avx2 843ms 4.16% 36.89% 1906ms 9.40% std::_Rb_tree::_M_lower_bound (inline) 151ms 0.74% 37.64% 1721ms 8.48% TetrahedralMesh::EdgeIterator::operator++ 79ms 0.39% 38.03% 1385ms 6.83% std::_Rb_tree::find (inline) 14ms 0.069% 38.10% 1272ms 6.27% TetrahedralMesh::ImportFromMesher 39ms 0.19% 38.29% 1184ms 5.84% operator new 0 0% 38.29% 1157ms 5.70% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.025% 38.31% 1144ms 5.64% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 261ms 1.29% 39.60% 1128ms 5.56% __GI___libc_malloc 32ms 0.16% 39.76% 1043ms 5.14% std::__new_allocator::allocate (inline) 7ms 0.035% 39.79% 1036ms 5.11% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 39.79% 1036ms 5.11% std::allocator_traits::allocate (inline) 8ms 0.039% 39.83% 1030ms 5.08% std::set::insert (inline) 15ms 0.074% 39.91% 1022ms 5.04% std::_Rb_tree::_M_insert_unique 0 0% 39.91% 895ms 4.41% triangulate 0 0% 39.91% 860ms 4.24% std::set::count (inline) 0 0% 39.91% 825ms 4.07% delaunay 4ms 0.02% 39.93% 823ms 4.06% divconqdelaunay 5ms 0.025% 39.95% 818ms 4.03% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 53ms 0.26% 40.21% 801ms 3.95% std::map::operator[] (partial-inline) 0 0% 40.21% 777ms 3.83% AbstractTwoBodyInteractionForce::AddForceContribution 411ms 2.03% 42.24% 771ms 3.80% _int_malloc 752ms 3.71% 45.94% 752ms 3.71% WntCellCycleOdeSystem::CalculateStoppingEvent 4ms 0.02% 45.96% 734ms 3.62% CellPopulationElementWriter::Visit 10ms 0.049% 46.01% 733ms 3.61% CellPropertyCollection::GetPropertiesType (inline) 718ms 3.54% 49.55% 718ms 3.54% std::_Rb_tree::_S_right (inline) 258ms 1.27% 50.83% 708ms 3.49% __dynamic_cast 0 0% 50.83% 691ms 3.41% std::_Rb_tree::_M_create_node (inline) 14ms 0.069% 50.89% 674ms 3.32% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 5ms 0.025% 50.92% 657ms 3.24% MeshBasedCellPopulation::AcceptCellWriter 22ms 0.11% 51.03% 647ms 3.19% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 51.03% 646ms 3.18% std::_Rb_tree::_M_get_node (inline) 39ms 0.19% 51.22% 637ms 3.14% std::_Rb_tree::_M_insert_ (inline) 0 0% 51.22% 633ms 3.12% std::_Rb_tree::lower_bound (inline) 0 0% 51.22% 633ms 3.12% std::map::lower_bound (inline) 20ms 0.099% 51.32% 622ms 3.07% std::less::operator() (inline) 0 0% 51.32% 615ms 3.03% std::_Rb_tree::_Alloc_node::operator() (inline) 602ms 2.97% 54.29% 602ms 2.97% std::operator< (inline) 6ms 0.03% 54.32% 578ms 2.85% Element::Element 7ms 0.035% 54.35% 573ms 2.83% MutableMesh::ReIndex 0 0% 54.35% 530ms 2.61% AbstractCellProperty::IsSubType (inline) 16ms 0.079% 54.43% 525ms 2.59% Element::RegisterWithNodes (inline) 0 0% 54.43% 523ms 2.58% std::map::find (inline) 9ms 0.044% 54.47% 514ms 2.53% Cylindrical2dMesh::ReconstructCylindricalMesh 0 0% 54.47% 507ms 2.50% std::ostream::operator<< (inline) 67ms 0.33% 54.80% 506ms 2.49% std::ostream::_M_insert 13ms 0.064% 54.87% 504ms 2.48% Node::AddElement 12ms 0.059% 54.93% 502ms 2.47% Cylindrical2dMesh::CorrectNonPeriodicMesh 141ms 0.7% 55.62% 485ms 2.39% __GI___libc_free 153ms 0.75% 56.38% 443ms 2.18% std::_Rb_tree::_M_erase 10ms 0.049% 56.43% 439ms 2.16% std::_Rb_tree::erase 2ms 0.0099% 56.44% 439ms 2.16% std::set::erase (inline) 289ms 1.42% 57.86% 433ms 2.13% AbstractCellMutationState::AbstractCellMutationState 19ms 0.094% 57.95% 433ms 2.13% Node::RemoveElement 24ms 0.12% 58.07% 416ms 2.05% std::_Rb_tree::~_Rb_tree (inline) 4ms 0.02% 58.09% 394ms 1.94% Cell::GetMutationState 0 0% 58.09% 390ms 1.92% std::_Vector_base::_M_allocate (inline) 12ms 0.059% 58.15% 389ms 1.92% divconqrecurse 0 0% 58.15% 389ms 1.92% std::set::~set (inline) 29ms 0.14% 58.30% 377ms 1.86% Element::ResetIndex 2ms 0.0099% 58.30% 376ms 1.85% Cell::GetCellProliferativeType 104ms 0.51% 58.82% 372ms 1.83% mergehulls 153ms 0.75% 59.57% 370ms 1.82% std::_Rb_tree::_M_get_insert_unique_pos 12ms 0.059% 59.63% 361ms 1.78% std::__new_allocator::deallocate (inline) 0 0% 59.63% 356ms 1.76% std::allocator_traits::deallocate (inline) 271ms 1.34% 60.97% 343ms 1.69% _int_free 0 0% 60.97% 343ms 1.69% std::_Rb_tree::_M_drop_node (inline) 338ms 1.67% 62.63% 338ms 1.67% [libchaste_cell_based.so] 157ms 0.77% 63.41% 330ms 1.63% __cxxabiv1::__si_class_type_info::__do_dyncast 32ms 0.16% 63.57% 326ms 1.61% TetrahedralMesh::Clear 11ms 0.054% 63.62% 315ms 1.55% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 13ms 0.064% 63.68% 315ms 1.55% std::_Rb_tree::_Rb_tree (partial-inline) 1ms 0.0049% 63.69% 310ms 1.53% NodeLocationWriter::Visit 8ms 0.039% 63.73% 307ms 1.51% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.0049% 63.73% 307ms 1.51% AbstractCellPopulation::Iterator::operator++ (inline) 52ms 0.26% 63.99% 306ms 1.51% AbstractCellPopulation::Iterator::IsRealCell (inline) 3ms 0.015% 64.00% 303ms 1.49% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 64.00% 301ms 1.48% std::_Rb_tree::_M_put_node (inline) 4ms 0.02% 64.02% 296ms 1.46% MeshBasedCellPopulation::GetDampingConstant 4ms 0.02% 64.04% 292ms 1.44% AbstractCentreBasedCellPopulation::GetDampingConstant 2ms 0.0099% 64.05% 286ms 1.41% std::set::set (inline) 0 0% 64.05% 283ms 1.40% TetrahedralMesh::RefreshJacobianCachedData 3ms 0.015% 64.07% 282ms 1.39% alternateaxes 277ms 1.37% 65.43% 282ms 1.39% std::vector::operator[] (inline) 257ms 1.27% 66.70% 279ms 1.38% vertexmedian 9ms 0.044% 66.75% 277ms 1.37% std::vector::push_back (inline) 25ms 0.12% 66.87% 275ms 1.36% std::num_put::_M_insert_float 29ms 0.14% 67.01% 268ms 1.32% std::_Rb_tree::_M_copy (inline) 6ms 0.03% 67.04% 262ms 1.29% AbstractCellPopulation::IsCellAttachedToLocationIndex 20ms 0.099% 67.14% 261ms 1.29% AbstractTetrahedralElement::CalculateJacobian 20ms 0.099% 67.24% 259ms 1.28% std::vector::_M_realloc_insert 14ms 0.069% 67.31% 256ms 1.26% std::_Rb_tree::_M_erase_aux (inline) 11ms 0.054% 67.36% 248ms 1.22% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 6ms 0.03% 67.39% 234ms 1.15% AbstractTetrahedralElement::CalculateInverseJacobian 55ms 0.27% 67.66% 234ms 1.15% ApcOneHitCellMutationState::ApcOneHitCellMutationState 4ms 0.02% 67.68% 232ms 1.14% CellProliferativeTypesWriter::VisitCell 93ms 0.46% 68.14% 231ms 1.14% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 16ms 0.079% 68.22% 228ms 1.12% Element::MarkAsDeleted 81ms 0.4% 68.62% 228ms 1.12% std::_Rb_tree::_M_clone_node (inline) 4ms 0.02% 68.64% 224ms 1.10% std::__cxx11::collate::do_transform 80ms 0.39% 69.03% 223ms 1.10% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 1ms 0.0049% 69.04% 220ms 1.08% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 3ms 0.015% 69.05% 220ms 1.08% CellPropertyCollection::HasProperty 158ms 0.78% 69.83% 220ms 1.08% malloc_consolidate 0 0% 69.83% 218ms 1.07% Cell::HasCellProperty (inline) 2ms 0.0099% 69.84% 213ms 1.05% ___vsnprintf 0 0% 69.84% 211ms 1.04% __vsnprintf_internal (inline) 143ms 0.71% 70.55% 209ms 1.03% AbstractElement::GetNodeGlobalIndex 30ms 0.15% 70.69% 209ms 1.03% __printf_buffer 0 0% 70.69% 204ms 1.01% OffLatticeSimulation::ApplyBoundaries 24ms 0.12% 70.81% 199ms 0.98% AbstractTetrahedralElement::RefreshJacobian 11ms 0.054% 70.87% 199ms 0.98% Node::~Node 197ms 0.97% 71.84% 197ms 0.97% unlink_chunk 123ms 0.61% 72.44% 177ms 0.87% std::_Rb_tree::equal_range (inline) 3ms 0.015% 72.46% 172ms 0.85% AbstractTetrahedralElement::AbstractTetrahedralElement 172ms 0.85% 73.31% 172ms 0.85% std::_Rb_tree_increment 43ms 0.21% 73.52% 171ms 0.84% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 12ms 0.059% 73.58% 170ms 0.84% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 169ms 0.83% 74.41% 169ms 0.83% std::vector::size (inline) 168ms 0.83% 75.24% 168ms 0.83% incircle 7ms 0.035% 75.27% 167ms 0.82% __printf_fp_l_buffer 0 0% 75.27% 167ms 0.82% __printf_fp_spec (inline) 165ms 0.81% 76.09% 165ms 0.81% AbstractCellMutationState::~AbstractCellMutationState 57ms 0.28% 76.37% 165ms 0.81% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 5ms 0.025% 76.39% 165ms 0.81% std::_Rb_tree_const_iterator::operator++ (inline) 164ms 0.81% 77.20% 164ms 0.81% Node::GetIndex 160ms 0.79% 77.99% 160ms 0.79% std::type_info::name (inline) 6ms 0.03% 78.02% 158ms 0.78% boost::numeric::ublas::vector_assign (inline) 71ms 0.35% 78.37% 156ms 0.77% __printf_fp_buffer_1 70ms 0.35% 78.72% 155ms 0.76% AbstractElement::GetNodeLocation 154ms 0.76% 79.48% 154ms 0.76% std::_Rb_tree_insert_and_rebalance 3ms 0.015% 79.49% 148ms 0.73% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 142ms 0.7% 80.19% 142ms 0.7% [libchaste_crypt.so] 0 0% 80.19% 141ms 0.7% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 80.19% 140ms 0.69% OutputFileHandler::OpenOutputFile 6ms 0.03% 80.22% 140ms 0.69% boost::numeric::ublas::c_vector::c_vector (inline) 90ms 0.44% 80.66% 136ms 0.67% Cylindrical2dMesh::GetVectorFromAtoB 129ms 0.64% 81.30% 135ms 0.67% vertexsort 1ms 0.0049% 81.30% 130ms 0.64% AbstractCellBasedSimulation::DoCellRemoval (inline) 8ms 0.039% 81.34% 130ms 0.64% MeshBasedCellPopulation::SpringsEnd (inline) 129ms 0.64% 81.98% 129ms 0.64% std::_Rb_tree_rebalance_for_erase 34ms 0.17% 82.15% 126ms 0.62% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 125ms 0.62% 82.76% 125ms 0.62% AbstractElement::IsDeleted 15ms 0.074% 82.84% 125ms 0.62% boost::detail::shared_count::~shared_count (inline) 0 0% 82.84% 125ms 0.62% boost::shared_ptr::~shared_ptr (inline) 6ms 0.03% 82.87% 124ms 0.61% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1ms 0.0049% 82.87% 124ms 0.61% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 37ms 0.18% 83.05% 124ms 0.61% boost::numeric::ublas::indexing_vector_assign 20ms 0.099% 83.15% 122ms 0.6% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 83.15% 121ms 0.6% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 121ms 0.6% 83.75% 121ms 0.6% boost::shared_ptr::operator-> (inline) 2ms 0.0099% 83.76% 115ms 0.57% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 8ms 0.039% 83.80% 115ms 0.57% Cylindrical2dMesh::CreateMirrorNodes 2ms 0.0099% 83.81% 115ms 0.57% std::_Rb_tree::_M_emplace_hint_unique 37ms 0.18% 83.99% 108ms 0.53% std::__ostream_insert 0 0% 83.99% 107ms 0.53% std::vector::_M_default_append 0 0% 83.99% 107ms 0.53% std::vector::resize (inline) 14ms 0.069% 84.06% 105ms 0.52% std::num_put::_M_insert_int 0 0% 84.06% 104ms 0.51% Cell::SetCellProliferativeType