File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 11560ms, 86.70% of 13333ms total Dropped 678 nodes (cum <= 66.67ms) flat flat% sum% cum cum% 0 0% 0% 13302ms 99.77% __libc_start_call_main 0 0% 0% 13302ms 99.77% __libc_start_main_impl 0 0% 0% 13302ms 99.77% _start 0 0% 0% 13285ms 99.64% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 13285ms 99.64% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 13285ms 99.64% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 13285ms 99.64% main 0 0% 0% 13250ms 99.38% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 13250ms 99.38% CxxTest::TestRunner::runTest (inline) 0 0% 0% 13250ms 99.38% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 13232ms 99.24% AbstractCellBasedSimulation::Solve 0 0% 0% 10129ms 75.97% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 6225ms 46.69% AbstractCellBasedSimulation::DoCellBirth 8ms 0.06% 0.06% 6131ms 45.98% Cell::ReadyToDivide 1ms 0.0075% 0.068% 6098ms 45.74% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.068% 5985ms 44.89% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 7ms 0.053% 0.12% 5980ms 44.85% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 0.12% 5969ms 44.77% CellCycleModelOdeHandler::SolveOdeToTime 35ms 0.26% 0.38% 5859ms 43.94% AbstractOneStepIvpOdeSolver::InternalSolve 522ms 3.92% 4.30% 5240ms 39.30% RungeKutta4IvpOdeSolver::CalculateNextYValue 2269ms 17.02% 21.32% 4510ms 33.83% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 21.32% 3813ms 28.60% MeshBasedCellPopulation::Update 2ms 0.015% 21.33% 2881ms 21.61% Cylindrical2dMesh::ReMesh 188ms 1.41% 22.74% 2322ms 17.42% AbstractCellProperty::IsType (inline) 2ms 0.015% 22.76% 1794ms 13.46% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 22.76% 1574ms 11.81% MutableMesh::ReMesh 1ms 0.0075% 22.76% 1525ms 11.44% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 22.76% 1488ms 11.16% AbstractNumericalMethod::ComputeForcesIncludingDamping 574ms 4.31% 27.07% 1333ms 10.00% std::_Rb_tree::_M_lower_bound (inline) 116ms 0.87% 27.94% 1321ms 9.91% TetrahedralMesh::EdgeIterator::operator++ 0 0% 27.94% 1306ms 9.80% AbstractCellPopulation::WriteResultsToFiles 32ms 0.24% 28.18% 1042ms 7.82% std::_Rb_tree::find (inline) 107ms 0.8% 28.98% 922ms 6.92% AbstractCellProperty::IsSame 3ms 0.023% 29.00% 908ms 6.81% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.0075% 29.01% 871ms 6.53% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 45ms 0.34% 29.35% 865ms 6.49% operator new 8ms 0.06% 29.41% 830ms 6.23% std::set::insert (inline) 20ms 0.15% 29.56% 822ms 6.17% std::_Rb_tree::_M_insert_unique 11ms 0.083% 29.64% 815ms 6.11% std::type_info::operator== (inline) 12ms 0.09% 29.73% 814ms 6.11% MeshBasedCellPopulation::SpringIterator::operator++ 6ms 0.045% 29.78% 811ms 6.08% TetrahedralMesh::ImportFromMesher 248ms 1.86% 31.64% 809ms 6.07% __GI___libc_malloc 791ms 5.93% 37.57% 791ms 5.93% __strcmp_evex 14ms 0.11% 37.67% 737ms 5.53% std::__new_allocator::allocate (inline) 0 0% 37.67% 735ms 5.51% std::allocator_traits::allocate (inline) 715ms 5.36% 43.04% 715ms 5.36% [libchaste_cell_based.so] 0 0% 43.04% 648ms 4.86% std::set::count (inline) 0 0% 43.04% 596ms 4.47% triangulate 0 0% 43.04% 536ms 4.02% delaunay 2ms 0.015% 43.05% 536ms 4.02% divconqdelaunay 32ms 0.24% 43.29% 532ms 3.99% std::_Rb_tree::_M_insert_ (inline) 0 0% 43.29% 505ms 3.79% std::_Rb_tree::_M_create_node (inline) 4ms 0.03% 43.32% 501ms 3.76% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 0 0% 43.32% 498ms 3.74% std::_Rb_tree::_M_get_node (inline) 494ms 3.71% 47.03% 494ms 3.71% std::_Rb_tree::_S_right (inline) 1ms 0.0075% 47.03% 493ms 3.70% CellPopulationElementWriter::Visit 297ms 2.23% 49.26% 492ms 3.69% _int_malloc 42ms 0.32% 49.58% 473ms 3.55% std::map::operator[] (partial-inline) 468ms 3.51% 53.09% 468ms 3.51% WntCellCycleOdeSystem::CalculateStoppingEvent 0 0% 53.09% 453ms 3.40% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 53.09% 446ms 3.35% AbstractTwoBodyInteractionForce::AddForceContribution 27ms 0.2% 53.29% 436ms 3.27% Cylindrical2dMesh::ReconstructCylindricalMesh 107ms 0.8% 54.09% 421ms 3.16% __dynamic_cast 0 0% 54.09% 418ms 3.14% Element::Element 5ms 0.038% 54.13% 409ms 3.07% Element::RegisterWithNodes (inline) 23ms 0.17% 54.30% 406ms 3.05% Node::AddElement 209ms 1.57% 55.87% 401ms 3.01% AbstractCellMutationState::AbstractCellMutationState 11ms 0.083% 55.95% 398ms 2.99% MeshBasedCellPopulation::AcceptCellWriter 6ms 0.045% 56.00% 395ms 2.96% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 56.00% 391ms 2.93% std::map::find (inline) 18ms 0.14% 56.13% 381ms 2.86% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 2ms 0.015% 56.15% 380ms 2.85% CellPropertyCollection::GetPropertiesType (inline) 73ms 0.55% 56.69% 375ms 2.81% __GI___libc_free 7ms 0.053% 56.75% 366ms 2.75% std::less::operator() (inline) 359ms 2.69% 59.44% 359ms 2.69% std::operator< (inline) 0 0% 59.44% 354ms 2.66% std::_Rb_tree::lower_bound (inline) 0 0% 59.44% 354ms 2.66% std::map::lower_bound (inline) 7ms 0.053% 59.49% 327ms 2.45% MutableMesh::ReIndex 0 0% 59.49% 327ms 2.45% std::_Rb_tree::_M_drop_node (inline) 8ms 0.06% 59.55% 315ms 2.36% std::__new_allocator::deallocate (inline) 5ms 0.038% 59.59% 314ms 2.36% AbstractCellProperty::IsSubType (inline) 0 0% 59.59% 308ms 2.31% std::allocator_traits::deallocate (inline) 8ms 0.06% 59.65% 307ms 2.30% Cylindrical2dMesh::CorrectNonPeriodicMesh 33ms 0.25% 59.90% 304ms 2.28% std::_Rb_tree::~_Rb_tree (inline) 267ms 2.00% 61.90% 302ms 2.27% _int_free 51ms 0.38% 62.28% 301ms 2.26% std::_Rb_tree::_M_erase 290ms 2.18% 64.46% 290ms 2.18% [libchaste_crypt.so] 1ms 0.0075% 64.46% 288ms 2.16% std::ostream::operator<< (inline) 33ms 0.25% 64.71% 284ms 2.13% std::ostream::_M_insert 0 0% 64.71% 278ms 2.09% std::set::~set (inline) 8ms 0.06% 64.77% 274ms 2.06% std::_Rb_tree::erase 5ms 0.038% 64.81% 273ms 2.05% Node::RemoveElement 0 0% 64.81% 273ms 2.05% std::set::erase (inline) 115ms 0.86% 65.67% 271ms 2.03% std::_Rb_tree::_M_get_insert_unique_pos 10ms 0.075% 65.75% 267ms 2.00% divconqrecurse 19ms 0.14% 65.89% 251ms 1.88% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.0075% 65.90% 250ms 1.88% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 65.90% 248ms 1.86% std::_Rb_tree::_M_put_node (inline) 11ms 0.083% 65.98% 247ms 1.85% boost::detail::shared_count::~shared_count (inline) 0 0% 65.98% 247ms 1.85% boost::shared_ptr::~shared_ptr (inline) 69ms 0.52% 66.50% 247ms 1.85% mergehulls 0 0% 66.50% 237ms 1.78% std::_Vector_base::_M_allocate (inline) 231ms 1.73% 68.23% 232ms 1.74% boost::detail::sp_counted_base::release 2ms 0.015% 68.24% 230ms 1.73% LegacyCellProliferativeTypesWriter::VisitCell 1ms 0.0075% 68.25% 223ms 1.67% Cell::GetCellProliferativeType 0 0% 68.25% 222ms 1.67% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 118ms 0.89% 69.14% 222ms 1.67% __cxxabiv1::__si_class_type_info::__do_dyncast 10ms 0.075% 69.21% 214ms 1.61% Element::ResetIndex 11ms 0.083% 69.29% 202ms 1.52% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 69.29% 197ms 1.48% Cell::GetMutationState 2ms 0.015% 69.31% 196ms 1.47% ApcOneHitCellMutationState::ApcOneHitCellMutationState 196ms 1.47% 70.78% 196ms 1.47% std::vector::operator[] (inline) 10ms 0.075% 70.85% 194ms 1.46% AbstractCellPopulation::GetLocationIndexUsingCell 21ms 0.16% 71.01% 194ms 1.46% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 3ms 0.023% 71.03% 192ms 1.44% AbstractCellPopulation::IsCellAttachedToLocationIndex 2ms 0.015% 71.05% 190ms 1.43% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 16ms 0.12% 71.17% 188ms 1.41% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 0 0% 71.17% 187ms 1.40% NodeLocationWriter::Visit 1ms 0.0075% 71.18% 186ms 1.40% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 5ms 0.038% 71.21% 186ms 1.40% std::vector::push_back (inline) 0 0% 71.21% 183ms 1.37% std::set::set (inline) 18ms 0.14% 71.35% 181ms 1.36% std::_Rb_tree::_M_copy (inline) 1ms 0.0075% 71.36% 179ms 1.34% alternateaxes 165ms 1.24% 72.59% 178ms 1.34% vertexmedian 11ms 0.083% 72.68% 176ms 1.32% std::_Rb_tree::_M_erase_aux (inline) 2ms 0.015% 72.69% 175ms 1.31% AbstractTetrahedralElement::CalculateJacobian 1ms 0.0075% 72.70% 174ms 1.31% OffLatticeSimulation::ApplyBoundaries 6ms 0.045% 72.74% 172ms 1.29% std::vector::_M_realloc_insert 6ms 0.045% 72.79% 170ms 1.28% Element::MarkAsDeleted 11ms 0.083% 72.87% 161ms 1.21% std::num_put::_M_insert_float 67ms 0.5% 73.37% 159ms 1.19% std::_Rb_tree::_M_clone_node (inline) 157ms 1.18% 74.55% 157ms 1.18% [libchaste_mesh.so] 0 0% 74.55% 152ms 1.14% TetrahedralMesh::RefreshJacobianCachedData 29ms 0.22% 74.77% 149ms 1.12% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 146ms 1.10% 75.86% 146ms 1.10% std::_Rb_tree_insert_and_rebalance 1ms 0.0075% 75.87% 141ms 1.06% AbstractTetrahedralElement::CalculateInverseJacobian 4ms 0.03% 75.90% 131ms 0.98% std::__cxx11::collate::do_transform 0 0% 75.90% 127ms 0.95% ___vsnprintf 0 0% 75.90% 127ms 0.95% __vsnprintf_internal (inline) 33ms 0.25% 76.15% 126ms 0.95% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 12ms 0.09% 76.24% 125ms 0.94% __printf_buffer 52ms 0.39% 76.63% 124ms 0.93% AbstractElement::GetNodeGlobalIndex 90ms 0.68% 77.30% 124ms 0.93% malloc_consolidate 123ms 0.92% 78.23% 123ms 0.92% std::vector::size (inline) 122ms 0.92% 79.14% 122ms 0.92% AbstractCellProperty::AbstractCellProperty 14ms 0.11% 79.25% 120ms 0.9% AbstractTetrahedralElement::RefreshJacobian 36ms 0.27% 79.52% 119ms 0.89% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 3ms 0.023% 79.54% 119ms 0.89% TetrahedralMesh::Clear 3ms 0.023% 79.56% 116ms 0.87% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 79.56% 116ms 0.87% MeshBasedCellPopulation::GetDampingConstant 4ms 0.03% 79.59% 109ms 0.82% __printf_fp_l_buffer 0 0% 79.59% 109ms 0.82% __printf_fp_spec (inline) 1ms 0.0075% 79.60% 107ms 0.8% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 107ms 0.8% 80.40% 107ms 0.8% incircle 105ms 0.79% 81.19% 105ms 0.79% std::_Rb_tree::_S_left (inline) 3ms 0.023% 81.21% 104ms 0.78% AbstractTetrahedralElement::AbstractTetrahedralElement 38ms 0.29% 81.50% 103ms 0.77% __printf_fp_buffer_1 3ms 0.023% 81.52% 98ms 0.74% boost::numeric::ublas::vector_assign (inline) 4ms 0.03% 81.55% 97ms 0.73% MeshBasedCellPopulation::SpringsEnd (inline) 8ms 0.06% 81.61% 97ms 0.73% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 37ms 0.28% 81.89% 95ms 0.71% AbstractElement::GetNodeLocation 55ms 0.41% 82.30% 92ms 0.69% std::_Rb_tree::equal_range (inline) 0 0% 82.30% 90ms 0.68% AbstractCellBasedSimulation::DoCellRemoval (inline) 7ms 0.053% 82.35% 90ms 0.68% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 90ms 0.68% 83.03% 90ms 0.68% unlink_chunk 1ms 0.0075% 83.03% 89ms 0.67% Cell::SetCellProliferativeType 4ms 0.03% 83.06% 89ms 0.67% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 13ms 0.098% 83.16% 89ms 0.67% TetrahedralMesh::EdgesEnd 1ms 0.0075% 83.17% 88ms 0.66% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 83.17% 87ms 0.65% CellProliferativeTypesWriter::VisitCell 3ms 0.023% 83.19% 85ms 0.64% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 77ms 0.58% 83.77% 85ms 0.64% vertexsort 81ms 0.61% 84.38% 81ms 0.61% TetrahedralMesh::EdgeIterator::operator!= 1ms 0.0075% 84.38% 80ms 0.6% CellPropertyCollection::HasProperty 0 0% 84.38% 79ms 0.59% std::_Rb_tree::_M_destroy_node (inline) 0 0% 84.38% 79ms 0.59% std::__new_allocator::destroy (inline) 0 0% 84.38% 79ms 0.59% std::allocator_traits::destroy (inline) 0 0% 84.38% 78ms 0.59% Cell::HasCellProperty (inline) 12ms 0.09% 84.47% 78ms 0.59% MeshBasedCellPopulation::SpringIterator::SpringIterator 7ms 0.053% 84.53% 77ms 0.58% Cylindrical2dMesh::CreateMirrorNodes 1ms 0.0075% 84.53% 77ms 0.58% std::_Rb_tree::_M_emplace_hint_unique 77ms 0.58% 85.11% 77ms 0.58% std::type_info::name (inline) 0 0% 85.11% 74ms 0.56% Node::~Node 4ms 0.03% 85.14% 71ms 0.53% boost::numeric::ublas::c_vector::c_vector (inline) 31ms 0.23% 85.37% 68ms 0.51% Determinant (inline) 53ms 0.4% 85.77% 68ms 0.51% TetrahedralMesh::EdgeIterator::EdgeIterator 5ms 0.038% 85.81% 68ms 0.51% std::_Rb_tree_const_iterator::operator++ (inline) 15ms 0.11% 85.92% 68ms 0.51% std::num_put::_M_insert_int 37ms 0.28% 86.20% 67ms 0.5% Cylindrical2dMesh::GetVectorFromAtoB 67ms 0.5% 86.70% 67ms 0.5% Node::GetIndex