File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 11923ms, 87.87% of 13569ms total Dropped 712 nodes (cum <= 67.84ms) flat flat% sum% cum cum% 0 0% 0% 13535ms 99.75% __libc_start_call_main 0 0% 0% 13535ms 99.75% __libc_start_main_impl 0 0% 0% 13535ms 99.75% _start 0 0% 0% 13518ms 99.62% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 13518ms 99.62% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 13518ms 99.62% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 13518ms 99.62% main 0 0% 0% 13480ms 99.34% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 13480ms 99.34% CxxTest::TestRunner::runTest (inline) 0 0% 0% 13480ms 99.34% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 13462ms 99.21% AbstractCellBasedSimulation::Solve 1ms 0.0074% 0.0074% 10284ms 75.79% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.0074% 6337ms 46.70% AbstractCellBasedSimulation::DoCellBirth 5ms 0.037% 0.044% 6255ms 46.10% Cell::ReadyToDivide 1ms 0.0074% 0.052% 6214ms 45.80% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.052% 6124ms 45.13% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 7ms 0.052% 0.1% 6122ms 45.12% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 0.1% 6112ms 45.04% CellCycleModelOdeHandler::SolveOdeToTime 35ms 0.26% 0.36% 5998ms 44.20% AbstractOneStepIvpOdeSolver::InternalSolve 571ms 4.21% 4.57% 5345ms 39.39% RungeKutta4IvpOdeSolver::CalculateNextYValue 2377ms 17.52% 22.09% 4566ms 33.65% WntCellCycleOdeSystem::EvaluateYDerivatives 3ms 0.022% 22.11% 3862ms 28.46% MeshBasedCellPopulation::Update 1ms 0.0074% 22.12% 2939ms 21.66% Cylindrical2dMesh::ReMesh 186ms 1.37% 23.49% 2295ms 16.91% AbstractCellProperty::IsType (inline) 1ms 0.0074% 23.49% 1835ms 13.52% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 23.49% 1619ms 11.93% MutableMesh::ReMesh 0 0% 23.49% 1592ms 11.73% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.015% 23.51% 1551ms 11.43% AbstractNumericalMethod::ComputeForcesIncludingDamping 599ms 4.41% 27.92% 1351ms 9.96% std::_Rb_tree::_M_lower_bound (inline) 0 0% 27.92% 1339ms 9.87% AbstractCellPopulation::WriteResultsToFiles 131ms 0.97% 28.89% 1315ms 9.69% TetrahedralMesh::EdgeIterator::operator++ 32ms 0.24% 29.13% 1067ms 7.86% std::_Rb_tree::find (inline) 127ms 0.94% 30.06% 894ms 6.59% AbstractCellProperty::IsSame 0 0% 30.06% 892ms 6.57% MeshBasedCellPopulation::UpdateNodePairs 2ms 0.015% 30.08% 856ms 6.31% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 39ms 0.29% 30.36% 855ms 6.30% operator new 5ms 0.037% 30.40% 839ms 6.18% TetrahedralMesh::ImportFromMesher 261ms 1.92% 32.32% 808ms 5.95% __GI___libc_malloc 2ms 0.015% 32.34% 792ms 5.84% std::set::insert (inline) 10ms 0.074% 32.41% 790ms 5.82% std::_Rb_tree::_M_insert_unique 9ms 0.066% 32.48% 784ms 5.78% MeshBasedCellPopulation::SpringIterator::operator++ 15ms 0.11% 32.59% 767ms 5.65% std::type_info::operator== (inline) 747ms 5.51% 38.09% 747ms 5.51% __strcmp_evex 729ms 5.37% 43.47% 729ms 5.37% [libchaste_cell_based.so] 21ms 0.15% 43.62% 721ms 5.31% std::__new_allocator::allocate (inline) 0 0% 43.62% 717ms 5.28% std::allocator_traits::allocate (inline) 0 0% 43.62% 663ms 4.89% std::set::count (inline) 0 0% 43.62% 612ms 4.51% triangulate 0 0% 43.62% 558ms 4.11% delaunay 1ms 0.0074% 43.63% 557ms 4.10% divconqdelaunay 8ms 0.059% 43.69% 532ms 3.92% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 510ms 3.76% 47.45% 510ms 3.76% std::_Rb_tree::_S_right (inline) 28ms 0.21% 47.65% 499ms 3.68% std::_Rb_tree::_M_insert_ (inline) 489ms 3.60% 51.26% 489ms 3.60% WntCellCycleOdeSystem::CalculateStoppingEvent 3ms 0.022% 51.28% 482ms 3.55% CellPopulationElementWriter::Visit 52ms 0.38% 51.66% 481ms 3.54% std::map::operator[] (partial-inline) 0 0% 51.66% 480ms 3.54% AbstractTwoBodyInteractionForce::AddForceContribution 276ms 2.03% 53.70% 480ms 3.54% _int_malloc 0 0% 53.70% 466ms 3.43% std::_Rb_tree::_M_create_node (inline) 0 0% 53.70% 456ms 3.36% std::_Rb_tree::_M_get_node (inline) 4ms 0.029% 53.73% 448ms 3.30% Element::Element 8ms 0.059% 53.78% 440ms 3.24% AbstractCellPopulation::GetCellUsingLocationIndex 17ms 0.13% 53.91% 429ms 3.16% Cylindrical2dMesh::ReconstructCylindricalMesh 12ms 0.088% 54.00% 429ms 3.16% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 0 0% 54.00% 421ms 3.10% std::_Rb_tree::_Alloc_node::operator() (inline) 221ms 1.63% 55.63% 418ms 3.08% AbstractCellMutationState::AbstractCellMutationState 10ms 0.074% 55.70% 414ms 3.05% MeshBasedCellPopulation::AcceptCellWriter 7ms 0.052% 55.75% 410ms 3.02% Element::RegisterWithNodes (inline) 108ms 0.8% 56.55% 407ms 3.00% __dynamic_cast 0 0% 56.55% 403ms 2.97% std::map::find (inline) 18ms 0.13% 56.68% 399ms 2.94% Node::AddElement 6ms 0.044% 56.72% 387ms 2.85% CellPropertyCollection::GetPropertiesType (inline) 16ms 0.12% 56.84% 371ms 2.73% std::less::operator() (inline) 0 0% 56.84% 355ms 2.62% std::_Rb_tree::lower_bound (inline) 0 0% 56.84% 355ms 2.62% std::map::lower_bound (inline) 355ms 2.62% 59.46% 355ms 2.62% std::operator< (inline) 90ms 0.66% 60.12% 346ms 2.55% __GI___libc_free 0 0% 60.12% 337ms 2.48% std::_Rb_tree::_M_drop_node (inline) 65ms 0.48% 60.60% 335ms 2.47% std::_Rb_tree::_M_erase 6ms 0.044% 60.65% 334ms 2.46% MutableMesh::ReIndex 38ms 0.28% 60.93% 334ms 2.46% std::_Rb_tree::~_Rb_tree (inline) 0 0% 60.93% 318ms 2.34% std::ostream::operator<< (inline) 34ms 0.25% 61.18% 317ms 2.34% std::ostream::_M_insert 0 0% 61.18% 316ms 2.33% std::set::~set (inline) 12ms 0.088% 61.26% 308ms 2.27% std::_Rb_tree::erase 0 0% 61.26% 305ms 2.25% std::set::erase (inline) 4ms 0.029% 61.29% 303ms 2.23% AbstractCellProperty::IsSubType (inline) 5ms 0.037% 61.33% 290ms 2.14% Cylindrical2dMesh::CorrectNonPeriodicMesh 6ms 0.044% 61.38% 289ms 2.13% Node::RemoveElement 5ms 0.037% 61.41% 288ms 2.12% std::__new_allocator::deallocate (inline) 0 0% 61.41% 284ms 2.09% std::allocator_traits::deallocate (inline) 121ms 0.89% 62.30% 281ms 2.07% std::_Rb_tree::_M_get_insert_unique_pos 265ms 1.95% 64.26% 265ms 1.95% [libchaste_crypt.so] 0 0% 64.26% 261ms 1.92% std::_Vector_base::_M_allocate (inline) 14ms 0.1% 64.36% 253ms 1.86% divconqrecurse 220ms 1.62% 65.98% 252ms 1.86% _int_free 0 0% 65.98% 239ms 1.76% std::_Rb_tree::_M_put_node (inline) 3ms 0.022% 66.00% 234ms 1.72% boost::detail::shared_count::~shared_count (inline) 0 0% 66.00% 234ms 1.72% boost::shared_ptr::~shared_ptr (inline) 78ms 0.57% 66.58% 233ms 1.72% mergehulls 1ms 0.0074% 66.59% 230ms 1.70% Cell::GetMutationState 10ms 0.074% 66.66% 230ms 1.70% Element::ResetIndex 225ms 1.66% 68.32% 227ms 1.67% boost::detail::sp_counted_base::release 0 0% 68.32% 223ms 1.64% AbstractCellPopulation::Iterator::operator++ (inline) 1ms 0.0074% 68.32% 222ms 1.64% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 1ms 0.0074% 68.33% 222ms 1.64% LegacyCellProliferativeTypesWriter::VisitCell 2ms 0.015% 68.35% 220ms 1.62% ApcOneHitCellMutationState::ApcOneHitCellMutationState 19ms 0.14% 68.49% 219ms 1.61% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 68.49% 216ms 1.59% Cell::GetCellProliferativeType 95ms 0.7% 69.19% 211ms 1.56% __cxxabiv1::__si_class_type_info::__do_dyncast 1ms 0.0074% 69.19% 207ms 1.53% NodeLocationWriter::Visit 14ms 0.1% 69.30% 200ms 1.47% std::_Rb_tree::_M_erase_aux (inline) 2ms 0.015% 69.31% 199ms 1.47% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 3ms 0.022% 69.33% 199ms 1.47% alternateaxes 3ms 0.022% 69.36% 196ms 1.44% AbstractCellPopulation::IsCellAttachedToLocationIndex 194ms 1.43% 70.79% 196ms 1.44% std::vector::operator[] (inline) 177ms 1.30% 72.09% 196ms 1.44% vertexmedian 8ms 0.059% 72.15% 195ms 1.44% std::_Rb_tree::_Rb_tree 0 0% 72.15% 190ms 1.40% std::set::set (inline) 17ms 0.13% 72.28% 179ms 1.32% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 7ms 0.052% 72.33% 178ms 1.31% std::vector::push_back (inline) 12ms 0.088% 72.42% 177ms 1.30% std::num_put::_M_insert_float 2ms 0.015% 72.43% 176ms 1.30% AbstractCellPopulation::GetLocationIndexUsingCell 23ms 0.17% 72.60% 172ms 1.27% std::_Rb_tree::_M_copy (inline) 27ms 0.2% 72.80% 167ms 1.23% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 6ms 0.044% 72.84% 167ms 1.23% Element::MarkAsDeleted 4ms 0.029% 72.87% 165ms 1.22% AbstractTetrahedralElement::CalculateJacobian 7ms 0.052% 72.92% 162ms 1.19% std::vector::_M_realloc_insert 158ms 1.16% 74.09% 158ms 1.16% [libchaste_mesh.so] 1ms 0.0074% 74.10% 157ms 1.16% MeshBasedCellPopulation::GetDampingConstant 0 0% 74.10% 157ms 1.16% OffLatticeSimulation::ApplyBoundaries 2ms 0.015% 74.11% 156ms 1.15% std::__cxx11::collate::do_transform 0 0% 74.11% 155ms 1.14% AbstractCentreBasedCellPopulation::GetDampingConstant 3ms 0.022% 74.13% 155ms 1.14% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.0074% 74.14% 150ms 1.11% ___vsnprintf 0 0% 74.14% 149ms 1.10% __vsnprintf_internal (inline) 0 0% 74.14% 147ms 1.08% TetrahedralMesh::RefreshJacobianCachedData 15ms 0.11% 74.25% 147ms 1.08% __printf_buffer 72ms 0.53% 74.78% 145ms 1.07% std::_Rb_tree::_M_clone_node (inline) 25ms 0.18% 74.96% 137ms 1.01% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 104ms 0.77% 75.73% 136ms 1.00% malloc_consolidate 2ms 0.015% 75.75% 131ms 0.97% AbstractTetrahedralElement::CalculateInverseJacobian 130ms 0.96% 76.70% 130ms 0.96% std::_Rb_tree_insert_and_rebalance 1ms 0.0074% 76.71% 125ms 0.92% __printf_fp_spec (inline) 3ms 0.022% 76.73% 124ms 0.91% TetrahedralMesh::Clear 6ms 0.044% 76.78% 124ms 0.91% __printf_fp_l_buffer 5ms 0.037% 76.81% 122ms 0.9% AbstractTetrahedralElement::AbstractTetrahedralElement 32ms 0.24% 77.05% 122ms 0.9% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 20ms 0.15% 77.20% 120ms 0.88% AbstractTetrahedralElement::RefreshJacobian 119ms 0.88% 78.08% 119ms 0.88% std::vector::size (inline) 4ms 0.029% 78.10% 116ms 0.85% CellPropertyCollection::HasProperty 0 0% 78.10% 115ms 0.85% Cell::HasCellProperty (inline) 30ms 0.22% 78.33% 114ms 0.84% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 0 0% 78.33% 114ms 0.84% CellProliferativeTypesWriter::VisitCell 46ms 0.34% 78.66% 114ms 0.84% __printf_fp_buffer_1 108ms 0.8% 79.46% 108ms 0.8% std::type_info::name (inline) 44ms 0.32% 79.78% 107ms 0.79% AbstractElement::GetNodeGlobalIndex 101ms 0.74% 80.53% 101ms 0.74% AbstractCellProperty::AbstractCellProperty 2ms 0.015% 80.54% 100ms 0.74% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 80.54% 100ms 0.74% std::__new_allocator::destroy (inline) 0 0% 80.54% 100ms 0.74% std::allocator_traits::destroy (inline) 86ms 0.63% 81.18% 100ms 0.74% vertexsort 0 0% 81.18% 99ms 0.73% std::_Rb_tree::_M_destroy_node (inline) 57ms 0.42% 81.60% 99ms 0.73% std::_Rb_tree::equal_range (inline) 98ms 0.72% 82.32% 98ms 0.72% incircle 7ms 0.052% 82.37% 98ms 0.72% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 98ms 0.72% 83.09% 98ms 0.72% std::_Rb_tree::_S_left (inline) 6ms 0.044% 83.14% 91ms 0.67% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 39ms 0.29% 83.43% 90ms 0.66% AbstractElement::GetNodeLocation 1ms 0.0074% 83.43% 89ms 0.66% boost::numeric::ublas::vector_assign (inline) 1ms 0.0074% 83.44% 88ms 0.65% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 86ms 0.63% 84.07% 86ms 0.63% unlink_chunk 16ms 0.12% 84.19% 84ms 0.62% std::num_put::_M_insert_int 12ms 0.088% 84.28% 83ms 0.61% TetrahedralMesh::EdgesEnd (partial-inline) 82ms 0.6% 84.88% 82ms 0.6% Node::GetIndex 82ms 0.6% 85.49% 82ms 0.6% [libchaste_ode.so] 13ms 0.096% 85.58% 81ms 0.6% MeshBasedCellPopulation::SpringIterator::SpringIterator 2ms 0.015% 85.60% 81ms 0.6% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 85.60% 80ms 0.59% AbstractCellBasedSimulation::DoCellRemoval (inline) 3ms 0.022% 85.62% 80ms 0.59% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 4ms 0.029% 85.65% 78ms 0.57% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 85.65% 78ms 0.57% std::vector::_M_default_append 0 0% 85.65% 78ms 0.57% std::vector::resize (inline) 2ms 0.015% 85.67% 77ms 0.57% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 0 0% 85.67% 76ms 0.56% Cell::SetCellProliferativeType 6ms 0.044% 85.71% 76ms 0.56% Cylindrical2dMesh::CreateMirrorNodes 0 0% 85.71% 75ms 0.55% NodeMap::NodeMap 2ms 0.015% 85.72% 74ms 0.55% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 2ms 0.015% 85.74% 74ms 0.55% std::_Rb_tree::_M_emplace_hint_unique 48ms 0.35% 86.09% 73ms 0.54% Cylindrical2dMesh::GetVectorFromAtoB 73ms 0.54% 86.63% 73ms 0.54% std::_Rb_tree_increment 0 0% 86.63% 71ms 0.52% Node::~Node 71ms 0.52% 87.15% 71ms 0.52% std::_Rb_tree_rebalance_for_erase 40ms 0.29% 87.45% 69ms 0.51% TimeStepper::AdvanceOneTimeStep 57ms 0.42% 87.87% 68ms 0.5% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline)