File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 15040ms, 86.57% of 17374ms total Dropped 764 nodes (cum <= 86.87ms) flat flat% sum% cum cum% 0 0% 0% 17333ms 99.76% __libc_start_call_main 0 0% 0% 17333ms 99.76% __libc_start_main_impl 0 0% 0% 17333ms 99.76% _start 0 0% 0% 17312ms 99.64% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 17312ms 99.64% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 17312ms 99.64% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 17312ms 99.64% main 0 0% 0% 17278ms 99.45% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 17278ms 99.45% CxxTest::TestRunner::runTest (inline) 0 0% 0% 17278ms 99.45% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 1ms 0.0058% 0.0058% 17255ms 99.32% AbstractCellBasedSimulation::Solve 0 0% 0.0058% 13201ms 75.98% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0058% 0.012% 8187ms 47.12% AbstractCellBasedSimulation::DoCellBirth 7ms 0.04% 0.052% 8088ms 46.55% Cell::ReadyToDivide 1ms 0.0058% 0.058% 8024ms 46.18% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.058% 7862ms 45.25% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 12ms 0.069% 0.13% 7859ms 45.23% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.012% 0.14% 7845ms 45.15% CellCycleModelOdeHandler::SolveOdeToTime 44ms 0.25% 0.39% 7698ms 44.31% AbstractOneStepIvpOdeSolver::InternalSolve 766ms 4.41% 4.80% 6882ms 39.61% RungeKutta4IvpOdeSolver::CalculateNextYValue 3243ms 18.67% 23.47% 5858ms 33.72% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 23.47% 4892ms 28.16% MeshBasedCellPopulation::Update 1ms 0.0058% 23.47% 3698ms 21.28% Cylindrical2dMesh::ReMesh 293ms 1.69% 25.16% 2769ms 15.94% AbstractCellProperty::IsType (inline) 0 0% 25.16% 2313ms 13.31% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 25.16% 2084ms 11.99% MutableMesh::ReMesh 0 0% 25.16% 2010ms 11.57% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.017% 25.18% 1957ms 11.26% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.0058% 25.18% 1737ms 10.00% AbstractCellPopulation::WriteResultsToFiles 174ms 1.00% 26.18% 1694ms 9.75% TetrahedralMesh::EdgeIterator::operator++ 851ms 4.90% 31.08% 1692ms 9.74% std::_Rb_tree::_M_lower_bound (inline) 52ms 0.3% 31.38% 1348ms 7.76% std::_Rb_tree::find (inline) 0 0% 31.38% 1156ms 6.65% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.0058% 31.39% 1091ms 6.28% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 60ms 0.35% 31.73% 1086ms 6.25% operator new 10ms 0.058% 31.79% 1051ms 6.05% std::set::insert (inline) 14ms 0.081% 31.87% 1041ms 5.99% std::_Rb_tree::_M_insert_unique 15ms 0.086% 31.96% 1030ms 5.93% MeshBasedCellPopulation::SpringIterator::operator++ 361ms 2.08% 34.03% 1010ms 5.81% __GI___libc_malloc 11ms 0.063% 34.10% 1007ms 5.80% TetrahedralMesh::ImportFromMesher 146ms 0.84% 34.94% 985ms 5.67% AbstractCellProperty::IsSame 17ms 0.098% 35.04% 949ms 5.46% std::__new_allocator::allocate (inline) 0 0% 35.04% 941ms 5.42% std::allocator_traits::allocate (inline) 877ms 5.05% 40.08% 877ms 5.05% [libchaste_cell_based.so] 0 0% 40.08% 863ms 4.97% std::set::count (inline) 839ms 4.83% 44.91% 839ms 4.83% __strcmp_evex 14ms 0.081% 44.99% 839ms 4.83% std::type_info::operator== (inline) 0 0% 44.99% 829ms 4.77% triangulate 0 0% 44.99% 747ms 4.30% delaunay 0 0% 44.99% 747ms 4.30% divconqdelaunay 12ms 0.069% 45.06% 709ms 4.08% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 49ms 0.28% 45.34% 661ms 3.80% std::_Rb_tree::_M_insert_ (inline) 0 0% 45.34% 637ms 3.67% std::_Rb_tree::_M_create_node (inline) 0 0% 45.34% 629ms 3.62% std::_Rb_tree::_M_get_node (inline) 611ms 3.52% 48.86% 611ms 3.52% WntCellCycleOdeSystem::CalculateStoppingEvent 1ms 0.0058% 48.87% 594ms 3.42% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 48.87% 593ms 3.41% std::_Rb_tree::_Alloc_node::operator() (inline) 11ms 0.063% 48.93% 585ms 3.37% CellPopulationElementWriter::Visit 13ms 0.075% 49.00% 570ms 3.28% MeshBasedCellPopulation::AcceptCellWriter 161ms 0.93% 49.93% 569ms 3.28% __dynamic_cast 58ms 0.33% 50.26% 565ms 3.25% std::map::operator[] (partial-inline) 2ms 0.012% 50.28% 553ms 3.18% CellPropertyCollection::GetPropertiesType (inline) 326ms 1.88% 52.15% 550ms 3.17% _int_malloc 31ms 0.18% 52.33% 547ms 3.15% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 7ms 0.04% 52.37% 545ms 3.14% Element::Element 7ms 0.04% 52.41% 525ms 3.02% Element::RegisterWithNodes (inline) 517ms 2.98% 55.39% 517ms 2.98% std::_Rb_tree::_S_right (inline) 263ms 1.51% 56.90% 516ms 2.97% AbstractCellMutationState::AbstractCellMutationState 22ms 0.13% 57.03% 511ms 2.94% Node::AddElement 9ms 0.052% 57.08% 506ms 2.91% AbstractCellPopulation::GetCellUsingLocationIndex 31ms 0.18% 57.26% 496ms 2.85% Cylindrical2dMesh::ReconstructCylindricalMesh 0 0% 57.26% 481ms 2.77% std::map::find (inline) 18ms 0.1% 57.36% 471ms 2.71% std::less::operator() (inline) 105ms 0.6% 57.97% 469ms 2.70% __GI___libc_free 453ms 2.61% 60.57% 453ms 2.61% std::operator< (inline) 3ms 0.017% 60.59% 446ms 2.57% AbstractCellProperty::IsSubType (inline) 0 0% 60.59% 437ms 2.52% std::_Rb_tree::lower_bound (inline) 0 0% 60.59% 437ms 2.52% std::map::lower_bound (inline) 11ms 0.063% 60.65% 426ms 2.45% Cylindrical2dMesh::CorrectNonPeriodicMesh 0 0% 60.65% 425ms 2.45% std::_Rb_tree::_M_drop_node (inline) 7ms 0.04% 60.69% 423ms 2.43% MutableMesh::ReIndex 10ms 0.058% 60.75% 400ms 2.30% std::__new_allocator::deallocate (inline) 47ms 0.27% 61.02% 397ms 2.29% std::ostream::_M_insert 0 0% 61.02% 397ms 2.29% std::ostream::operator<< (inline) 0 0% 61.02% 394ms 2.27% std::allocator_traits::deallocate (inline) 42ms 0.24% 61.26% 387ms 2.23% std::_Rb_tree::~_Rb_tree (inline) 54ms 0.31% 61.57% 386ms 2.22% std::_Rb_tree::_M_erase 377ms 2.17% 63.74% 377ms 2.17% [libchaste_crypt.so] 158ms 0.91% 64.65% 366ms 2.11% std::_Rb_tree::_M_get_insert_unique_pos 7ms 0.04% 64.69% 363ms 2.09% divconqrecurse 0 0% 64.69% 363ms 2.09% std::set::~set (inline) 304ms 1.75% 66.44% 358ms 2.06% _int_free 89ms 0.51% 66.96% 351ms 2.02% mergehulls 1ms 0.0058% 66.96% 337ms 1.94% LegacyCellProliferativeTypesWriter::VisitCell 8ms 0.046% 67.01% 331ms 1.91% std::_Rb_tree::erase 0 0% 67.01% 331ms 1.91% std::set::erase (inline) 9ms 0.052% 67.06% 330ms 1.90% Node::RemoveElement 0 0% 67.06% 330ms 1.90% std::_Rb_tree::_M_put_node (inline) 0 0% 67.06% 312ms 1.80% std::_Vector_base::_M_allocate (inline) 1ms 0.0058% 67.07% 311ms 1.79% Cell::GetMutationState 5ms 0.029% 67.09% 302ms 1.74% Cell::GetCellProliferativeType 8ms 0.046% 67.14% 302ms 1.74% boost::detail::shared_count::~shared_count (inline) 0 0% 67.14% 302ms 1.74% boost::shared_ptr::~shared_ptr (inline) 131ms 0.75% 67.89% 299ms 1.72% __cxxabiv1::__si_class_type_info::__do_dyncast 283ms 1.63% 69.52% 287ms 1.65% boost::detail::sp_counted_base::release 1ms 0.0058% 69.53% 283ms 1.63% AbstractCellPopulation::Iterator::operator++ (inline) 17ms 0.098% 69.63% 280ms 1.61% Element::ResetIndex 27ms 0.16% 69.78% 279ms 1.61% AbstractCellPopulation::Iterator::IsRealCell (inline) 15ms 0.086% 69.87% 265ms 1.53% std::_Rb_tree::_Rb_tree (partial-inline) 19ms 0.11% 69.98% 264ms 1.52% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 1ms 0.0058% 69.98% 263ms 1.51% NodeLocationWriter::Visit 0 0% 69.98% 257ms 1.48% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 250ms 1.44% 71.42% 256ms 1.47% std::vector::operator[] (inline) 0 0% 71.42% 251ms 1.44% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 5ms 0.029% 71.45% 250ms 1.44% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.0058% 71.46% 250ms 1.44% std::set::set (inline) 0 0% 71.46% 249ms 1.43% ApcOneHitCellMutationState::ApcOneHitCellMutationState 9ms 0.052% 71.51% 248ms 1.43% std::vector::push_back (inline) 3ms 0.017% 71.53% 247ms 1.42% alternateaxes 31ms 0.18% 71.70% 245ms 1.41% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 220ms 1.27% 72.97% 244ms 1.40% vertexmedian 19ms 0.11% 73.08% 234ms 1.35% AbstractTetrahedralElement::CalculateJacobian 14ms 0.081% 73.16% 231ms 1.33% std::_Rb_tree::_M_copy (inline) 5ms 0.029% 73.19% 231ms 1.33% std::_Rb_tree::_M_erase_aux (inline) 230ms 1.32% 74.51% 230ms 1.32% [libchaste_mesh.so] 1ms 0.0058% 74.52% 227ms 1.31% TetrahedralMesh::RefreshJacobianCachedData 6ms 0.035% 74.55% 226ms 1.30% AbstractCellPopulation::IsCellAttachedToLocationIndex 20ms 0.12% 74.67% 226ms 1.30% std::num_put::_M_insert_float 6ms 0.035% 74.70% 225ms 1.30% std::vector::_M_realloc_insert 10ms 0.058% 74.76% 211ms 1.21% AbstractTetrahedralElement::CalculateInverseJacobian 5ms 0.029% 74.79% 210ms 1.21% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 85ms 0.49% 75.28% 208ms 1.20% std::_Rb_tree::_M_clone_node (inline) 0 0% 75.28% 197ms 1.13% OffLatticeSimulation::ApplyBoundaries 3ms 0.017% 75.30% 192ms 1.11% Element::MarkAsDeleted 1ms 0.0058% 75.30% 187ms 1.08% MeshBasedCellPopulation::GetDampingConstant 1ms 0.0058% 75.31% 186ms 1.07% AbstractCentreBasedCellPopulation::GetDampingConstant 4ms 0.023% 75.33% 180ms 1.04% std::__cxx11::collate::do_transform 40ms 0.23% 75.56% 172ms 0.99% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 0 0% 75.56% 170ms 0.98% ___vsnprintf 0 0% 75.56% 170ms 0.98% __vsnprintf_internal (inline) 18ms 0.1% 75.66% 166ms 0.96% __printf_buffer 16ms 0.092% 75.76% 163ms 0.94% AbstractTetrahedralElement::RefreshJacobian 6ms 0.035% 75.79% 160ms 0.92% CellPropertyCollection::HasProperty 41ms 0.24% 76.03% 159ms 0.92% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 1ms 0.0058% 76.03% 159ms 0.92% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 0 0% 76.03% 156ms 0.9% Cell::HasCellProperty (inline) 129ms 0.74% 76.78% 155ms 0.89% malloc_consolidate 151ms 0.87% 77.64% 151ms 0.87% std::_Rb_tree_insert_and_rebalance 19ms 0.11% 77.75% 143ms 0.82% TetrahedralMesh::EdgesEnd (partial-inline) 2ms 0.012% 77.77% 142ms 0.82% TetrahedralMesh::Clear 1ms 0.0058% 77.77% 142ms 0.82% __printf_fp_spec (inline) 142ms 0.82% 78.59% 142ms 0.82% incircle 6ms 0.035% 78.62% 141ms 0.81% __printf_fp_l_buffer 2ms 0.012% 78.63% 137ms 0.79% AbstractTetrahedralElement::AbstractTetrahedralElement 136ms 0.78% 79.42% 136ms 0.78% AbstractCellProperty::AbstractCellProperty 50ms 0.29% 79.71% 133ms 0.77% __printf_fp_buffer_1 7ms 0.04% 79.75% 132ms 0.76% Cell::SetCellProliferativeType 3ms 0.017% 79.76% 132ms 0.76% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 47ms 0.27% 80.03% 129ms 0.74% AbstractElement::GetNodeLocation 0 0% 80.03% 128ms 0.74% CellProliferativeTypesWriter::VisitCell 128ms 0.74% 80.77% 128ms 0.74% std::type_info::name (inline) 127ms 0.73% 81.50% 127ms 0.73% std::vector::size (inline) 4ms 0.023% 81.52% 125ms 0.72% MeshBasedCellPopulation::SpringsEnd (inline) 110ms 0.63% 82.16% 124ms 0.71% vertexsort 123ms 0.71% 82.87% 123ms 0.71% std::_Rb_tree::_S_left (inline) 0 0% 82.87% 122ms 0.7% AbstractCellBasedSimulation::DoCellRemoval (inline) 1ms 0.0058% 82.87% 122ms 0.7% boost::numeric::ublas::vector_assign (inline) 2ms 0.012% 82.88% 120ms 0.69% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 44ms 0.25% 83.14% 118ms 0.68% AbstractElement::GetNodeGlobalIndex 8ms 0.046% 83.18% 114ms 0.66% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 7ms 0.04% 83.22% 114ms 0.66% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 86ms 0.49% 83.72% 104ms 0.6% TetrahedralMesh::EdgeIterator::EdgeIterator 1ms 0.0058% 83.72% 104ms 0.6% boost::numeric::ublas::c_vector::c_vector (inline) 103ms 0.59% 84.32% 103ms 0.59% counterclockwise 6ms 0.035% 84.35% 103ms 0.59% std::_Rb_tree_const_iterator::operator++ (inline) 43ms 0.25% 84.60% 103ms 0.59% std::num_put::_M_insert_int 100ms 0.58% 85.17% 100ms 0.58% std::_Rb_tree_increment 2ms 0.012% 85.18% 99ms 0.57% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 5ms 0.029% 85.21% 98ms 0.56% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 52ms 0.3% 85.51% 96ms 0.55% std::_Rb_tree::equal_range (inline) 0 0% 85.51% 96ms 0.55% std::__new_allocator::destroy (inline) 0 0% 85.51% 96ms 0.55% std::allocator_traits::destroy (inline) 95ms 0.55% 86.06% 95ms 0.55% [libchaste_ode.so] 0 0% 86.06% 95ms 0.55% std::_Rb_tree::_M_destroy_node (inline) 53ms 0.31% 86.36% 90ms 0.52% Cylindrical2dMesh::GetVectorFromAtoB 35ms 0.2% 86.57% 90ms 0.52% std::__ostream_insert