File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 14999ms, 86.19% of 17403ms total Dropped 754 nodes (cum <= 87.02ms) flat flat% sum% cum cum% 0 0% 0% 17362ms 99.76% __libc_start_call_main 0 0% 0% 17362ms 99.76% __libc_start_main_impl 0 0% 0% 17362ms 99.76% _start 0 0% 0% 17343ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 17343ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 17343ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 17343ms 99.66% main 0 0% 0% 17310ms 99.47% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 17310ms 99.47% CxxTest::TestRunner::runTest (inline) 0 0% 0% 17310ms 99.47% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 17289ms 99.34% AbstractCellBasedSimulation::Solve 0 0% 0% 13287ms 76.35% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.011% 0.011% 8311ms 47.76% AbstractCellBasedSimulation::DoCellBirth 11ms 0.063% 0.075% 8218ms 47.22% Cell::ReadyToDivide 3ms 0.017% 0.092% 8160ms 46.89% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0057% 0.098% 8039ms 46.19% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 13ms 0.075% 0.17% 8031ms 46.15% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.0057% 0.18% 8015ms 46.06% CellCycleModelOdeHandler::SolveOdeToTime 39ms 0.22% 0.4% 7849ms 45.10% AbstractOneStepIvpOdeSolver::InternalSolve 748ms 4.30% 4.70% 7037ms 40.44% RungeKutta4IvpOdeSolver::CalculateNextYValue 3219ms 18.50% 23.20% 6024ms 34.61% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 23.20% 4844ms 27.83% MeshBasedCellPopulation::Update 2ms 0.011% 23.21% 3644ms 20.94% Cylindrical2dMesh::ReMesh 366ms 2.10% 25.31% 2909ms 16.72% AbstractCellProperty::IsType (inline) 1ms 0.0057% 25.32% 2343ms 13.46% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.011% 25.33% 2041ms 11.73% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 25.33% 2040ms 11.72% MutableMesh::ReMesh 0 0% 25.33% 1992ms 11.45% AbstractNumericalMethod::ComputeForcesIncludingDamping 168ms 0.97% 26.29% 1685ms 9.68% TetrahedralMesh::EdgeIterator::operator++ 824ms 4.73% 31.03% 1665ms 9.57% std::_Rb_tree::_M_lower_bound (inline) 0 0% 31.03% 1656ms 9.52% AbstractCellPopulation::WriteResultsToFiles 36ms 0.21% 31.24% 1360ms 7.81% std::_Rb_tree::find (inline) 148ms 0.85% 32.09% 1166ms 6.70% AbstractCellProperty::IsSame 0 0% 32.09% 1153ms 6.63% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.023% 32.11% 1081ms 6.21% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 47ms 0.27% 32.38% 1076ms 6.18% operator new 16ms 0.092% 32.47% 1024ms 5.88% MeshBasedCellPopulation::SpringIterator::operator++ 396ms 2.28% 34.75% 1019ms 5.86% __GI___libc_malloc 9ms 0.052% 34.80% 1018ms 5.85% std::set::insert (inline) 20ms 0.11% 34.91% 1018ms 5.85% std::type_info::operator== (inline) 7ms 0.04% 34.95% 1012ms 5.82% TetrahedralMesh::ImportFromMesher 12ms 0.069% 35.02% 1009ms 5.80% std::_Rb_tree::_M_insert_unique 981ms 5.64% 40.66% 981ms 5.64% __strcmp_evex 17ms 0.098% 40.76% 914ms 5.25% std::__new_allocator::allocate (inline) 0 0% 40.76% 910ms 5.23% std::allocator_traits::allocate (inline) 906ms 5.21% 45.96% 906ms 5.21% [libchaste_cell_based.so] 0 0% 45.96% 850ms 4.88% std::set::count (inline) 0 0% 45.96% 817ms 4.69% triangulate 0 0% 45.96% 750ms 4.31% delaunay 0 0% 45.96% 748ms 4.30% divconqdelaunay 3ms 0.017% 45.98% 650ms 3.73% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 1ms 0.0057% 45.99% 649ms 3.73% AbstractTwoBodyInteractionForce::AddForceContribution 43ms 0.25% 46.23% 637ms 3.66% std::_Rb_tree::_M_insert_ (inline) 628ms 3.61% 49.84% 629ms 3.61% WntCellCycleOdeSystem::CalculateStoppingEvent 0 0% 49.84% 619ms 3.56% std::_Rb_tree::_M_create_node (inline) 0 0% 49.84% 612ms 3.52% std::_Rb_tree::_M_get_node (inline) 17ms 0.098% 49.94% 587ms 3.37% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 8ms 0.046% 49.99% 575ms 3.30% CellPopulationElementWriter::Visit 0 0% 49.99% 570ms 3.28% std::_Rb_tree::_Alloc_node::operator() (inline) 9ms 0.052% 50.04% 545ms 3.13% AbstractCellPopulation::GetCellUsingLocationIndex 150ms 0.86% 50.90% 539ms 3.10% __dynamic_cast 313ms 1.80% 52.70% 535ms 3.07% _int_malloc 56ms 0.32% 53.02% 535ms 3.07% std::map::operator[] (partial-inline) 4ms 0.023% 53.04% 534ms 3.07% Element::Element 529ms 3.04% 56.08% 529ms 3.04% std::_Rb_tree::_S_right (inline) 6ms 0.034% 56.12% 513ms 2.95% Element::RegisterWithNodes (inline) 8ms 0.046% 56.16% 513ms 2.95% MeshBasedCellPopulation::AcceptCellWriter 0 0% 56.16% 508ms 2.92% std::map::find (inline) 18ms 0.1% 56.27% 502ms 2.88% Node::AddElement 27ms 0.16% 56.42% 494ms 2.84% Cylindrical2dMesh::ReconstructCylindricalMesh 6ms 0.034% 56.46% 482ms 2.77% CellPropertyCollection::GetPropertiesType (inline) 237ms 1.36% 57.82% 479ms 2.75% AbstractCellMutationState::AbstractCellMutationState 11ms 0.063% 57.88% 463ms 2.66% std::less::operator() (inline) 93ms 0.53% 58.42% 457ms 2.63% __GI___libc_free 452ms 2.60% 61.01% 452ms 2.60% std::operator< (inline) 10ms 0.057% 61.07% 443ms 2.55% Cylindrical2dMesh::CorrectNonPeriodicMesh 1ms 0.0057% 61.08% 437ms 2.51% std::ostream::operator<< (inline) 57ms 0.33% 61.40% 434ms 2.49% std::ostream::_M_insert 6ms 0.034% 61.44% 418ms 2.40% MutableMesh::ReIndex 0 0% 61.44% 412ms 2.37% std::_Rb_tree::_M_drop_node (inline) 0 0% 61.44% 396ms 2.28% std::_Rb_tree::lower_bound (inline) 57ms 0.33% 61.77% 396ms 2.28% std::_Rb_tree::~_Rb_tree (inline) 0 0% 61.77% 396ms 2.28% std::map::lower_bound (inline) 16ms 0.092% 61.86% 380ms 2.18% divconqrecurse 2ms 0.011% 61.87% 375ms 2.15% AbstractCellProperty::IsSubType (inline) 58ms 0.33% 62.20% 375ms 2.15% std::_Rb_tree::_M_erase 0 0% 62.20% 375ms 2.15% std::set::~set (inline) 9ms 0.052% 62.25% 374ms 2.15% std::__new_allocator::deallocate (inline) 373ms 2.14% 64.40% 373ms 2.14% [libchaste_crypt.so] 0 0% 64.40% 368ms 2.11% std::allocator_traits::deallocate (inline) 145ms 0.83% 65.23% 360ms 2.07% std::_Rb_tree::_M_get_insert_unique_pos 308ms 1.77% 67.00% 358ms 2.06% _int_free 106ms 0.61% 67.61% 355ms 2.04% mergehulls 9ms 0.052% 67.66% 337ms 1.94% std::_Rb_tree::erase 0 0% 67.66% 336ms 1.93% std::set::erase (inline) 10ms 0.057% 67.72% 331ms 1.90% Node::RemoveElement 0 0% 67.72% 316ms 1.82% std::_Rb_tree::_M_put_node (inline) 8ms 0.046% 67.76% 298ms 1.71% boost::detail::shared_count::~shared_count (inline) 0 0% 67.76% 298ms 1.71% boost::shared_ptr::~shared_ptr (inline) 0 0% 67.76% 298ms 1.71% std::_Vector_base::_M_allocate (inline) 25ms 0.14% 67.91% 294ms 1.69% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 67.91% 293ms 1.68% Cell::GetMutationState 1ms 0.0057% 67.91% 292ms 1.68% AbstractCellPopulation::Iterator::operator++ (inline) 5ms 0.029% 67.94% 284ms 1.63% LegacyCellProliferativeTypesWriter::VisitCell 20ms 0.11% 68.06% 281ms 1.61% Element::ResetIndex 0 0% 68.06% 281ms 1.61% NodeLocationWriter::Visit 281ms 1.61% 69.67% 281ms 1.61% boost::detail::sp_counted_base::release 129ms 0.74% 70.41% 280ms 1.61% __cxxabiv1::__si_class_type_info::__do_dyncast 11ms 0.063% 70.48% 279ms 1.60% std::_Rb_tree::_Rb_tree (partial-inline) 22ms 0.13% 70.60% 277ms 1.59% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 2ms 0.011% 70.61% 267ms 1.53% std::set::set (inline) 256ms 1.47% 72.09% 260ms 1.49% std::vector::operator[] (inline) 5ms 0.029% 72.11% 258ms 1.48% Cell::GetCellProliferativeType 15ms 0.086% 72.20% 254ms 1.46% std::num_put::_M_insert_float 11ms 0.063% 72.26% 252ms 1.45% AbstractCellPopulation::GetLocationIndexUsingCell 29ms 0.17% 72.43% 251ms 1.44% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 27ms 0.16% 72.59% 249ms 1.43% std::_Rb_tree::_M_copy (inline) 0 0% 72.59% 246ms 1.41% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 5ms 0.029% 72.61% 243ms 1.40% alternateaxes 227ms 1.30% 73.92% 238ms 1.37% vertexmedian 1ms 0.0057% 73.92% 236ms 1.36% ApcOneHitCellMutationState::ApcOneHitCellMutationState 0 0% 73.92% 233ms 1.34% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 5ms 0.029% 73.95% 230ms 1.32% std::vector::push_back (inline) 4ms 0.023% 73.98% 223ms 1.28% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 18ms 0.1% 74.08% 223ms 1.28% std::_Rb_tree::_M_erase_aux (inline) 215ms 1.24% 75.31% 215ms 1.24% [libchaste_mesh.so] 5ms 0.029% 75.34% 215ms 1.24% std::__cxx11::collate::do_transform 13ms 0.075% 75.42% 211ms 1.21% AbstractTetrahedralElement::CalculateJacobian 93ms 0.53% 75.95% 211ms 1.21% std::_Rb_tree::_M_clone_node (inline) 5ms 0.029% 75.98% 211ms 1.21% std::vector::_M_realloc_insert 4ms 0.023% 76.00% 209ms 1.20% AbstractCellPopulation::IsCellAttachedToLocationIndex 1ms 0.0057% 76.01% 204ms 1.17% ___vsnprintf 1ms 0.0057% 76.02% 203ms 1.17% __vsnprintf_internal (inline) 0 0% 76.02% 201ms 1.15% OffLatticeSimulation::ApplyBoundaries 0 0% 76.02% 201ms 1.15% TetrahedralMesh::RefreshJacobianCachedData 17ms 0.098% 76.11% 195ms 1.12% __printf_buffer 4ms 0.023% 76.14% 186ms 1.07% AbstractTetrahedralElement::CalculateInverseJacobian 7ms 0.04% 76.18% 186ms 1.07% Element::MarkAsDeleted 1ms 0.0057% 76.18% 186ms 1.07% MeshBasedCellPopulation::GetDampingConstant 5ms 0.029% 76.21% 185ms 1.06% AbstractCentreBasedCellPopulation::GetDampingConstant 2ms 0.011% 76.22% 172ms 0.99% __printf_fp_l_buffer 0 0% 76.22% 172ms 0.99% __printf_fp_spec (inline) 70ms 0.4% 76.62% 163ms 0.94% __printf_fp_buffer_1 27ms 0.16% 76.78% 154ms 0.88% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 152ms 0.87% 77.65% 152ms 0.87% std::_Rb_tree_insert_and_rebalance 21ms 0.12% 77.77% 150ms 0.86% AbstractTetrahedralElement::RefreshJacobian 112ms 0.64% 78.42% 143ms 0.82% malloc_consolidate 0 0% 78.42% 141ms 0.81% TetrahedralMesh::Clear 141ms 0.81% 79.23% 141ms 0.81% std::_Rb_tree::_S_left (inline) 140ms 0.8% 80.03% 140ms 0.8% incircle 139ms 0.8% 80.83% 139ms 0.8% std::vector::size (inline) 10ms 0.057% 80.89% 137ms 0.79% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 0 0% 80.89% 134ms 0.77% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 0 0% 80.89% 132ms 0.76% CellProliferativeTypesWriter::VisitCell 0 0% 80.89% 129ms 0.74% AbstractCellBasedSimulation::DoCellRemoval (inline) 1ms 0.0057% 80.89% 127ms 0.73% AbstractTetrahedralElement::AbstractTetrahedralElement 3ms 0.017% 80.91% 125ms 0.72% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 4ms 0.023% 80.93% 122ms 0.7% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 41ms 0.24% 81.17% 121ms 0.7% AbstractElement::GetNodeGlobalIndex 103ms 0.59% 81.76% 120ms 0.69% vertexsort 3ms 0.017% 81.78% 118ms 0.68% boost::numeric::ublas::vector_assign (inline) 118ms 0.68% 82.46% 118ms 0.68% std::type_info::name (inline) 0 0% 82.46% 117ms 0.67% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 4ms 0.023% 82.48% 116ms 0.67% CellPropertyCollection::HasProperty 49ms 0.28% 82.76% 115ms 0.66% AbstractElement::GetNodeLocation 0 0% 82.76% 115ms 0.66% Cell::HasCellProperty (inline) 16ms 0.092% 82.85% 114ms 0.66% TetrahedralMesh::EdgesEnd 4ms 0.023% 82.88% 114ms 0.66% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 66ms 0.38% 83.26% 113ms 0.65% Cylindrical2dMesh::GetVectorFromAtoB 62ms 0.36% 83.61% 111ms 0.64% std::_Rb_tree::equal_range (inline) 107ms 0.61% 84.23% 107ms 0.61% AbstractCellProperty::AbstractCellProperty 5ms 0.029% 84.26% 103ms 0.59% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 7ms 0.04% 84.30% 103ms 0.59% boost::numeric::ublas::c_vector::c_vector (inline) 100ms 0.57% 84.87% 100ms 0.57% std::_Rb_tree_increment 7ms 0.04% 84.91% 98ms 0.56% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 98ms 0.56% 85.47% 98ms 0.56% counterclockwise 0 0% 85.47% 97ms 0.56% std::_Rb_tree::_M_destroy_node (inline) 2ms 0.011% 85.49% 97ms 0.56% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 85.49% 97ms 0.56% std::__new_allocator::destroy (inline) 0 0% 85.49% 97ms 0.56% std::allocator_traits::destroy (inline) 95ms 0.55% 86.03% 95ms 0.55% Node::GetIndex 24ms 0.14% 86.17% 95ms 0.55% std::num_put::_M_insert_int 2ms 0.011% 86.18% 94ms 0.54% MeshBasedCellPopulation::SpringsEnd (inline) 1ms 0.0057% 86.19% 92ms 0.53% Cell::SetCellProliferativeType