File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 11746ms, 86.22% of 13623ms total Dropped 686 nodes (cum <= 68.11ms) flat flat% sum% cum cum% 0 0% 0% 13589ms 99.75% __libc_start_call_main 0 0% 0% 13589ms 99.75% __libc_start_main_impl 0 0% 0% 13589ms 99.75% _start 0 0% 0% 13571ms 99.62% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 13571ms 99.62% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 13571ms 99.62% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 13571ms 99.62% main 0 0% 0% 13537ms 99.37% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 13537ms 99.37% CxxTest::TestRunner::runTest (inline) 0 0% 0% 13537ms 99.37% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 13519ms 99.24% AbstractCellBasedSimulation::Solve 0 0% 0% 10305ms 75.64% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 6313ms 46.34% AbstractCellBasedSimulation::DoCellBirth 6ms 0.044% 0.044% 6224ms 45.69% Cell::ReadyToDivide 1ms 0.0073% 0.051% 6181ms 45.37% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0073% 0.059% 6057ms 44.46% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 4ms 0.029% 0.088% 6050ms 44.41% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.015% 0.1% 6040ms 44.34% CellCycleModelOdeHandler::SolveOdeToTime 36ms 0.26% 0.37% 5911ms 43.39% AbstractOneStepIvpOdeSolver::InternalSolve 502ms 3.68% 4.05% 5270ms 38.68% RungeKutta4IvpOdeSolver::CalculateNextYValue 2413ms 17.71% 21.76% 4525ms 33.22% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 21.76% 3905ms 28.66% MeshBasedCellPopulation::Update 2ms 0.015% 21.78% 2984ms 21.90% Cylindrical2dMesh::ReMesh 243ms 1.78% 23.56% 2225ms 16.33% AbstractCellProperty::IsType (inline) 1ms 0.0073% 23.57% 1825ms 13.40% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 23.57% 1651ms 12.12% MutableMesh::ReMesh 0 0% 23.57% 1580ms 11.60% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0073% 23.58% 1547ms 11.36% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 23.58% 1383ms 10.15% AbstractCellPopulation::WriteResultsToFiles 117ms 0.86% 24.44% 1344ms 9.87% TetrahedralMesh::EdgeIterator::operator++ 611ms 4.49% 28.92% 1332ms 9.78% std::_Rb_tree::_M_lower_bound (inline) 24ms 0.18% 29.10% 1027ms 7.54% std::_Rb_tree::find (inline) 44ms 0.32% 29.42% 904ms 6.64% operator new 1ms 0.0073% 29.43% 893ms 6.56% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.029% 29.46% 887ms 6.51% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 312ms 2.29% 31.75% 852ms 6.25% __GI___libc_malloc 10ms 0.073% 31.82% 843ms 6.19% TetrahedralMesh::ImportFromMesher 16ms 0.12% 31.94% 817ms 6.00% std::set::insert (inline) 5ms 0.037% 31.98% 808ms 5.93% MeshBasedCellPopulation::SpringIterator::operator++ 12ms 0.088% 32.06% 801ms 5.88% std::_Rb_tree::_M_insert_unique 113ms 0.83% 32.89% 784ms 5.75% AbstractCellProperty::IsSame 19ms 0.14% 33.03% 777ms 5.70% std::__new_allocator::allocate (inline) 0 0% 33.03% 773ms 5.67% std::allocator_traits::allocate (inline) 720ms 5.29% 38.32% 720ms 5.29% [libchaste_cell_based.so] 15ms 0.11% 38.43% 671ms 4.93% std::type_info::operator== (inline) 0 0% 38.43% 667ms 4.90% std::set::count (inline) 2ms 0.015% 38.44% 631ms 4.63% triangulate 622ms 4.57% 43.01% 622ms 4.57% __strcmp_evex 0 0% 43.01% 568ms 4.17% delaunay 2ms 0.015% 43.02% 568ms 4.17% divconqdelaunay 5ms 0.037% 43.06% 543ms 3.99% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 30ms 0.22% 43.28% 530ms 3.89% std::_Rb_tree::_M_insert_ (inline) 0 0% 43.28% 520ms 3.82% std::_Rb_tree::_M_create_node (inline) 0 0% 43.28% 512ms 3.76% std::_Rb_tree::_M_get_node (inline) 2ms 0.015% 43.29% 487ms 3.57% CellPopulationElementWriter::Visit 478ms 3.51% 46.80% 478ms 3.51% std::_Rb_tree::_S_right (inline) 47ms 0.35% 47.15% 477ms 3.50% std::map::operator[] (partial-inline) 0 0% 47.15% 476ms 3.49% std::_Rb_tree::_Alloc_node::operator() (inline) 464ms 3.41% 50.55% 464ms 3.41% WntCellCycleOdeSystem::CalculateStoppingEvent 287ms 2.11% 52.66% 464ms 3.41% _int_malloc 2ms 0.015% 52.68% 440ms 3.23% AbstractTwoBodyInteractionForce::AddForceContribution 26ms 0.19% 52.87% 435ms 3.19% Cylindrical2dMesh::ReconstructCylindricalMesh 4ms 0.029% 52.90% 430ms 3.16% Element::Element 3ms 0.022% 52.92% 430ms 3.16% MeshBasedCellPopulation::AcceptCellWriter 8ms 0.059% 52.98% 419ms 3.08% CellPropertyCollection::GetPropertiesType (inline) 9ms 0.066% 53.04% 417ms 3.06% AbstractCellPopulation::GetCellUsingLocationIndex 119ms 0.87% 53.92% 412ms 3.02% __dynamic_cast 213ms 1.56% 55.48% 402ms 2.95% AbstractCellMutationState::AbstractCellMutationState 3ms 0.022% 55.50% 401ms 2.94% Element::RegisterWithNodes (inline) 22ms 0.16% 55.66% 398ms 2.92% Node::AddElement 19ms 0.14% 55.80% 389ms 2.86% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 11ms 0.081% 55.88% 365ms 2.68% MutableMesh::ReIndex 11ms 0.081% 55.96% 365ms 2.68% std::less::operator() (inline) 67ms 0.49% 56.46% 364ms 2.67% __GI___libc_free 0 0% 56.46% 358ms 2.63% std::map::find (inline) 0 0% 56.46% 357ms 2.62% std::_Rb_tree::lower_bound (inline) 0 0% 56.46% 357ms 2.62% std::map::lower_bound (inline) 354ms 2.60% 59.05% 354ms 2.60% std::operator< (inline) 47ms 0.35% 59.40% 338ms 2.48% std::_Rb_tree::~_Rb_tree (inline) 66ms 0.48% 59.88% 328ms 2.41% std::_Rb_tree::_M_erase 1ms 0.0073% 59.89% 327ms 2.40% AbstractCellProperty::IsSubType (inline) 0 0% 59.89% 323ms 2.37% std::_Rb_tree::_M_drop_node (inline) 0 0% 59.89% 313ms 2.30% std::set::~set (inline) 8ms 0.059% 59.95% 305ms 2.24% std::_Rb_tree::erase 0 0% 59.95% 303ms 2.22% std::ostream::operator<< (inline) 0 0% 59.95% 302ms 2.22% std::set::erase (inline) 10ms 0.073% 60.02% 301ms 2.21% Cylindrical2dMesh::CorrectNonPeriodicMesh 46ms 0.34% 60.36% 298ms 2.19% std::ostream::_M_insert 12ms 0.088% 60.45% 297ms 2.18% Node::RemoveElement 258ms 1.89% 62.34% 297ms 2.18% _int_free 5ms 0.037% 62.38% 293ms 2.15% std::__new_allocator::deallocate (inline) 291ms 2.14% 64.52% 291ms 2.14% [libchaste_crypt.so] 0 0% 64.52% 290ms 2.13% std::allocator_traits::deallocate (inline) 7ms 0.051% 64.57% 264ms 1.94% divconqrecurse 0 0% 64.57% 261ms 1.92% std::_Vector_base::_M_allocate (inline) 114ms 0.84% 65.40% 259ms 1.90% std::_Rb_tree::_M_get_insert_unique_pos 76ms 0.56% 65.96% 252ms 1.85% mergehulls 8ms 0.059% 66.02% 251ms 1.84% boost::detail::shared_count::~shared_count (inline) 0 0% 66.02% 251ms 1.84% boost::shared_ptr::~shared_ptr (inline) 2ms 0.015% 66.04% 245ms 1.80% Cell::GetCellProliferativeType 1ms 0.0073% 66.04% 242ms 1.78% LegacyCellProliferativeTypesWriter::VisitCell 238ms 1.75% 67.79% 242ms 1.78% std::vector::operator[] (inline) 19ms 0.14% 67.93% 239ms 1.75% Element::ResetIndex 0 0% 67.93% 239ms 1.75% std::_Rb_tree::_M_put_node (inline) 235ms 1.73% 69.65% 237ms 1.74% boost::detail::sp_counted_base::release 1ms 0.0073% 69.66% 231ms 1.70% AbstractCellPopulation::Iterator::operator++ (inline) 26ms 0.19% 69.85% 230ms 1.69% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 69.85% 226ms 1.66% ApcOneHitCellMutationState::ApcOneHitCellMutationState 3ms 0.022% 69.87% 224ms 1.64% Cell::GetMutationState 120ms 0.88% 70.76% 223ms 1.64% __cxxabiv1::__si_class_type_info::__do_dyncast 5ms 0.037% 70.79% 212ms 1.56% std::_Rb_tree::_Rb_tree (partial-inline) 3ms 0.022% 70.81% 211ms 1.55% AbstractCellPopulation::IsCellAttachedToLocationIndex 0 0% 70.81% 205ms 1.50% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 10ms 0.073% 70.89% 204ms 1.50% std::vector::push_back (inline) 0 0% 70.89% 202ms 1.48% std::set::set (inline) 9ms 0.066% 70.95% 197ms 1.45% std::_Rb_tree::_M_erase_aux (inline) 23ms 0.17% 71.12% 195ms 1.43% std::_Rb_tree::_M_copy (inline) 2ms 0.015% 71.14% 194ms 1.42% alternateaxes 21ms 0.15% 71.29% 193ms 1.42% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 1ms 0.0073% 71.30% 192ms 1.41% NodeLocationWriter::Visit 180ms 1.32% 72.62% 191ms 1.40% vertexmedian 186ms 1.37% 73.99% 186ms 1.37% [libchaste_mesh.so] 0 0% 73.99% 185ms 1.36% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 10ms 0.073% 74.06% 182ms 1.34% std::vector::_M_realloc_insert 15ms 0.11% 74.17% 180ms 1.32% AbstractTetrahedralElement::CalculateJacobian 6ms 0.044% 74.21% 178ms 1.31% AbstractCellPopulation::GetLocationIndexUsingCell 14ms 0.1% 74.32% 172ms 1.26% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 69ms 0.51% 74.82% 169ms 1.24% std::_Rb_tree::_M_clone_node (inline) 2ms 0.015% 74.84% 167ms 1.23% Element::MarkAsDeleted 17ms 0.12% 74.96% 167ms 1.23% std::num_put::_M_insert_float 2ms 0.015% 74.98% 165ms 1.21% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 74.98% 158ms 1.16% TetrahedralMesh::RefreshJacobianCachedData 0 0% 74.98% 157ms 1.15% MeshBasedCellPopulation::GetDampingConstant 2ms 0.015% 74.99% 156ms 1.15% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 74.99% 148ms 1.09% OffLatticeSimulation::ApplyBoundaries 5ms 0.037% 75.03% 146ms 1.07% AbstractTetrahedralElement::CalculateInverseJacobian 7ms 0.051% 75.08% 140ms 1.03% std::__cxx11::collate::do_transform 136ms 1% 76.08% 136ms 1% std::_Rb_tree_insert_and_rebalance 31ms 0.23% 76.30% 132ms 0.97% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 96ms 0.7% 77.01% 130ms 0.95% malloc_consolidate 1ms 0.0073% 77.02% 128ms 0.94% ___vsnprintf 0 0% 77.02% 127ms 0.93% __vsnprintf_internal (inline) 11ms 0.081% 77.10% 125ms 0.92% __printf_buffer 1ms 0.0073% 77.10% 121ms 0.89% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 2ms 0.015% 77.12% 120ms 0.88% TetrahedralMesh::Clear 3ms 0.022% 77.14% 119ms 0.87% CellPropertyCollection::HasProperty 10ms 0.073% 77.22% 119ms 0.87% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 0 0% 77.22% 118ms 0.87% Cell::HasCellProperty (inline) 1ms 0.0073% 77.22% 118ms 0.87% CellProliferativeTypesWriter::VisitCell 13ms 0.095% 77.32% 116ms 0.85% AbstractTetrahedralElement::RefreshJacobian 24ms 0.18% 77.49% 114ms 0.84% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 3ms 0.022% 77.52% 112ms 0.82% AbstractTetrahedralElement::AbstractTetrahedralElement 45ms 0.33% 77.85% 110ms 0.81% AbstractElement::GetNodeGlobalIndex 26ms 0.19% 78.04% 109ms 0.8% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 106ms 0.78% 78.82% 106ms 0.78% incircle 96ms 0.7% 79.52% 105ms 0.77% vertexsort 104ms 0.76% 80.28% 104ms 0.76% AbstractCellProperty::AbstractCellProperty 4ms 0.029% 80.31% 103ms 0.76% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 3ms 0.022% 80.33% 102ms 0.75% __printf_fp_l_buffer 0 0% 80.33% 102ms 0.75% __printf_fp_spec (inline) 102ms 0.75% 81.08% 102ms 0.75% std::type_info::name (inline) 59ms 0.43% 81.52% 101ms 0.74% std::_Rb_tree::equal_range (inline) 4ms 0.029% 81.55% 100ms 0.73% Cell::SetCellProliferativeType 100ms 0.73% 82.28% 100ms 0.73% std::vector::size (inline) 37ms 0.27% 82.55% 96ms 0.7% __printf_fp_buffer_1 2ms 0.015% 82.57% 91ms 0.67% boost::numeric::ublas::vector_assign (inline) 90ms 0.66% 83.23% 90ms 0.66% std::_Rb_tree_rebalance_for_erase 0 0% 83.23% 87ms 0.64% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 83.23% 86ms 0.63% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 83.23% 85ms 0.62% std::__new_allocator::destroy (inline) 0 0% 83.23% 85ms 0.62% std::allocator_traits::destroy (inline) 0 0% 83.23% 84ms 0.62% std::_Rb_tree::_M_destroy_node (inline) 34ms 0.25% 83.48% 83ms 0.61% AbstractElement::GetNodeLocation 81ms 0.59% 84.07% 81ms 0.59% std::_Rb_tree::_S_left (inline) 43ms 0.32% 84.39% 78ms 0.57% Cylindrical2dMesh::GetVectorFromAtoB 78ms 0.57% 84.96% 78ms 0.57% Node::GetIndex 15ms 0.11% 85.07% 78ms 0.57% TetrahedralMesh::EdgesEnd 5ms 0.037% 85.11% 75ms 0.55% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 1ms 0.0073% 85.11% 74ms 0.54% MeshBasedCellPopulation::SpringsEnd (inline) 3ms 0.022% 85.14% 73ms 0.54% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 4ms 0.029% 85.16% 73ms 0.54% std::_Rb_tree::_M_emplace_hint_unique 3ms 0.022% 85.19% 72ms 0.53% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.0073% 85.19% 71ms 0.52% std::_Rb_tree_const_iterator::operator++ (inline) 70ms 0.51% 85.71% 70ms 0.51% [libchaste_ode.so] 70ms 0.51% 86.22% 70ms 0.51% unlink_chunk