File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 13850ms, 86.71% of 15973ms total Dropped 679 nodes (cum <= 79.86ms) flat flat% sum% cum cum% 0 0% 0% 15939ms 99.79% __libc_start_call_main 0 0% 0% 15939ms 99.79% __libc_start_main_impl 0 0% 0% 15939ms 99.79% _start 0 0% 0% 15921ms 99.67% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 15921ms 99.67% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 15921ms 99.67% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 15921ms 99.67% main 0 0% 0% 15892ms 99.49% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 15892ms 99.49% CxxTest::TestRunner::runTest (inline) 0 0% 0% 15892ms 99.49% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 15873ms 99.37% AbstractCellBasedSimulation::Solve 0 0% 0% 12138ms 75.99% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 7521ms 47.09% AbstractCellBasedSimulation::DoCellBirth 3ms 0.019% 0.019% 7426ms 46.49% Cell::ReadyToDivide 4ms 0.025% 0.044% 7393ms 46.28% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0063% 0.05% 7265ms 45.48% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 15ms 0.094% 0.14% 7259ms 45.45% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.013% 0.16% 7241ms 45.33% CellCycleModelOdeHandler::SolveOdeToTime 66ms 0.41% 0.57% 7106ms 44.49% AbstractOneStepIvpOdeSolver::InternalSolve 657ms 4.11% 4.68% 6296ms 39.42% RungeKutta4IvpOdeSolver::CalculateNextYValue 2893ms 18.11% 22.79% 5391ms 33.75% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 22.79% 4521ms 28.30% MeshBasedCellPopulation::Update 3ms 0.019% 22.81% 3412ms 21.36% Cylindrical2dMesh::ReMesh 310ms 1.94% 24.75% 2606ms 16.32% AbstractCellProperty::IsType (inline) 0 0% 24.75% 2170ms 13.59% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 24.75% 1910ms 11.96% MutableMesh::ReMesh 1ms 0.0063% 24.76% 1890ms 11.83% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0063% 24.77% 1854ms 11.61% AbstractNumericalMethod::ComputeForcesIncludingDamping 726ms 4.55% 29.31% 1620ms 10.14% std::_Rb_tree::_M_lower_bound (inline) 0 0% 29.31% 1562ms 9.78% AbstractCellPopulation::WriteResultsToFiles 144ms 0.9% 30.21% 1540ms 9.64% TetrahedralMesh::EdgeIterator::operator++ 38ms 0.24% 30.45% 1268ms 7.94% std::_Rb_tree::find (inline) 0 0% 30.45% 1082ms 6.77% MeshBasedCellPopulation::UpdateNodePairs 128ms 0.8% 31.25% 1060ms 6.64% AbstractCellProperty::IsSame 45ms 0.28% 31.53% 1002ms 6.27% operator new 2ms 0.013% 31.55% 990ms 6.20% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 16ms 0.1% 31.65% 984ms 6.16% MeshBasedCellPopulation::SpringIterator::operator++ 351ms 2.20% 33.84% 951ms 5.95% __GI___libc_malloc 8ms 0.05% 33.89% 937ms 5.87% TetrahedralMesh::ImportFromMesher 23ms 0.14% 34.04% 932ms 5.83% std::type_info::operator== (inline) 16ms 0.1% 34.14% 895ms 5.60% std::set::insert (inline) 894ms 5.60% 39.74% 894ms 5.60% __strcmp_evex 24ms 0.15% 39.89% 879ms 5.50% std::_Rb_tree::_M_insert_unique 20ms 0.13% 40.01% 852ms 5.33% std::__new_allocator::allocate (inline) 0 0% 40.01% 848ms 5.31% std::allocator_traits::allocate (inline) 0 0% 40.01% 767ms 4.80% std::set::count (inline) 1ms 0.0063% 40.02% 752ms 4.71% triangulate 748ms 4.68% 44.70% 748ms 4.68% [libchaste_cell_based.so] 0 0% 44.70% 686ms 4.29% delaunay 3ms 0.019% 44.72% 685ms 4.29% divconqdelaunay 6ms 0.038% 44.76% 641ms 4.01% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 3ms 0.019% 44.78% 605ms 3.79% AbstractTwoBodyInteractionForce::AddForceContribution 589ms 3.69% 48.46% 589ms 3.69% WntCellCycleOdeSystem::CalculateStoppingEvent 580ms 3.63% 52.09% 580ms 3.63% std::_Rb_tree::_S_right (inline) 55ms 0.34% 52.44% 555ms 3.47% std::map::operator[] (partial-inline) 10ms 0.063% 52.50% 551ms 3.45% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 28ms 0.18% 52.68% 546ms 3.42% std::_Rb_tree::_M_insert_ (inline) 0 0% 52.68% 545ms 3.41% std::_Rb_tree::_M_create_node (inline) 0 0% 52.68% 538ms 3.37% std::_Rb_tree::_M_get_node (inline) 11ms 0.069% 52.75% 532ms 3.33% AbstractCellPopulation::GetCellUsingLocationIndex 8ms 0.05% 52.80% 529ms 3.31% CellPopulationElementWriter::Visit 160ms 1.00% 53.80% 523ms 3.27% __dynamic_cast 284ms 1.78% 55.58% 505ms 3.16% _int_malloc 0 0% 55.58% 504ms 3.16% std::_Rb_tree::_Alloc_node::operator() (inline) 7ms 0.044% 55.62% 501ms 3.14% MeshBasedCellPopulation::AcceptCellWriter 0 0% 55.62% 499ms 3.12% std::map::find (inline) 20ms 0.13% 55.74% 498ms 3.12% Cylindrical2dMesh::ReconstructCylindricalMesh 8ms 0.05% 55.79% 497ms 3.11% CellPropertyCollection::GetPropertiesType (inline) 4ms 0.025% 55.82% 463ms 2.90% Element::Element 6ms 0.038% 55.86% 442ms 2.77% Element::RegisterWithNodes (inline) 102ms 0.64% 56.50% 441ms 2.76% __GI___libc_free 11ms 0.069% 56.56% 440ms 2.75% std::less::operator() (inline) 28ms 0.18% 56.74% 431ms 2.70% Node::AddElement 0 0% 56.74% 430ms 2.69% std::_Rb_tree::lower_bound (inline) 0 0% 56.74% 430ms 2.69% std::map::lower_bound (inline) 429ms 2.69% 59.43% 429ms 2.69% std::operator< (inline) 215ms 1.35% 60.77% 426ms 2.67% AbstractCellMutationState::AbstractCellMutationState 64ms 0.4% 61.17% 398ms 2.49% std::_Rb_tree::~_Rb_tree (inline) 7ms 0.044% 61.22% 393ms 2.46% AbstractCellProperty::IsSubType (inline) 4ms 0.025% 61.24% 389ms 2.44% MutableMesh::ReIndex 0 0% 61.24% 387ms 2.42% std::_Rb_tree::_M_drop_node (inline) 75ms 0.47% 61.71% 371ms 2.32% std::_Rb_tree::_M_erase 10ms 0.063% 61.77% 370ms 2.32% std::__new_allocator::deallocate (inline) 369ms 2.31% 64.08% 369ms 2.31% [libchaste_crypt.so] 0 0% 64.08% 369ms 2.31% std::set::~set (inline) 0 0% 64.08% 368ms 2.30% std::allocator_traits::deallocate (inline) 11ms 0.069% 64.15% 362ms 2.27% Cylindrical2dMesh::CorrectNonPeriodicMesh 0 0% 64.15% 349ms 2.18% std::ostream::operator<< (inline) 51ms 0.32% 64.47% 346ms 2.17% std::ostream::_M_insert 287ms 1.80% 66.27% 336ms 2.10% _int_free 5ms 0.031% 66.30% 333ms 2.08% std::_Rb_tree::erase 12ms 0.075% 66.37% 330ms 2.07% divconqrecurse 0 0% 66.37% 329ms 2.06% std::set::erase (inline) 10ms 0.063% 66.44% 318ms 1.99% Node::RemoveElement 1ms 0.0063% 66.44% 311ms 1.95% std::_Vector_base::_M_allocate (inline) 101ms 0.63% 67.08% 310ms 1.94% mergehulls 123ms 0.77% 67.85% 309ms 1.93% std::_Rb_tree::_M_get_insert_unique_pos (inline) 0 0% 67.85% 308ms 1.93% std::_Rb_tree::_M_put_node (inline) 2ms 0.013% 67.86% 301ms 1.88% Cell::GetMutationState 3ms 0.019% 67.88% 293ms 1.83% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 67.88% 270ms 1.69% AbstractCellPopulation::Iterator::operator++ (inline) 24ms 0.15% 68.03% 266ms 1.67% AbstractCellPopulation::Iterator::IsRealCell 123ms 0.77% 68.80% 265ms 1.66% __cxxabiv1::__si_class_type_info::__do_dyncast 22ms 0.14% 68.94% 264ms 1.65% Element::ResetIndex 15ms 0.094% 69.03% 262ms 1.64% boost::detail::shared_count::~shared_count (inline) 0 0% 69.03% 262ms 1.64% boost::shared_ptr::~shared_ptr (inline) 0 0% 69.03% 253ms 1.58% Cell::GetCellProliferativeType 1ms 0.0063% 69.04% 250ms 1.57% NodeLocationWriter::Visit 241ms 1.51% 70.54% 244ms 1.53% boost::detail::sp_counted_base::release 9ms 0.056% 70.60% 244ms 1.53% std::_Rb_tree::_Rb_tree (partial-inline) 8ms 0.05% 70.65% 243ms 1.52% std::vector::push_back (inline) 227ms 1.42% 72.07% 238ms 1.49% std::vector::operator[] (inline) 15ms 0.094% 72.17% 232ms 1.45% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 7ms 0.044% 72.21% 230ms 1.44% AbstractCellPopulation::IsCellAttachedToLocationIndex 1ms 0.0063% 72.22% 230ms 1.44% std::set::set (inline) 15ms 0.094% 72.31% 228ms 1.43% AbstractCellPopulation::GetLocationIndexUsingCell 7ms 0.044% 72.35% 224ms 1.40% std::vector::_M_realloc_insert 24ms 0.15% 72.50% 222ms 1.39% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 0 0% 72.50% 220ms 1.38% ApcOneHitCellMutationState::ApcOneHitCellMutationState 4ms 0.025% 72.53% 219ms 1.37% alternateaxes 22ms 0.14% 72.67% 215ms 1.35% std::_Rb_tree::_M_copy (inline) 195ms 1.22% 73.89% 215ms 1.35% vertexmedian 5ms 0.031% 73.92% 211ms 1.32% std::_Rb_tree::_M_erase_aux (inline) 19ms 0.12% 74.04% 210ms 1.31% AbstractTetrahedralElement::CalculateJacobian 1ms 0.0063% 74.04% 209ms 1.31% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.0063% 74.05% 208ms 1.30% TetrahedralMesh::RefreshJacobianCachedData 207ms 1.30% 75.35% 207ms 1.30% [libchaste_mesh.so] 14ms 0.088% 75.43% 207ms 1.30% std::num_put::_M_insert_float 0 0% 75.43% 205ms 1.28% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 0 0% 75.43% 195ms 1.22% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 7ms 0.044% 75.48% 191ms 1.20% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.0063% 75.48% 188ms 1.18% MeshBasedCellPopulation::GetDampingConstant 1ms 0.0063% 75.49% 187ms 1.17% AbstractCentreBasedCellPopulation::GetDampingConstant 79ms 0.49% 75.98% 187ms 1.17% std::_Rb_tree::_M_clone_node (inline) 4ms 0.025% 76.01% 185ms 1.16% Element::MarkAsDeleted 1ms 0.0063% 76.02% 184ms 1.15% OffLatticeSimulation::ApplyBoundaries 7ms 0.044% 76.06% 167ms 1.05% std::__cxx11::collate::do_transform 1ms 0.0063% 76.07% 158ms 0.99% ___vsnprintf 0 0% 76.07% 157ms 0.98% __vsnprintf_internal (inline) 1ms 0.0063% 76.07% 156ms 0.98% TetrahedralMesh::Clear 119ms 0.75% 76.82% 156ms 0.98% malloc_consolidate 10ms 0.063% 76.88% 153ms 0.96% __printf_buffer 138ms 0.86% 77.74% 138ms 0.86% incircle 18ms 0.11% 77.86% 131ms 0.82% AbstractTetrahedralElement::RefreshJacobian 130ms 0.81% 78.67% 130ms 0.81% std::_Rb_tree_insert_and_rebalance 116ms 0.73% 79.40% 127ms 0.8% vertexsort 1ms 0.0063% 79.40% 124ms 0.78% __printf_fp_l_buffer 0 0% 79.40% 124ms 0.78% __printf_fp_spec (inline) 63ms 0.39% 79.80% 124ms 0.78% std::_Rb_tree::equal_range (inline) 123ms 0.77% 80.57% 123ms 0.77% std::vector::size (inline) 48ms 0.3% 80.87% 122ms 0.76% AbstractElement::GetNodeGlobalIndex 1ms 0.0063% 80.87% 122ms 0.76% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 2ms 0.013% 80.89% 122ms 0.76% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 122ms 0.76% 81.65% 122ms 0.76% std::_Rb_tree::_S_left (inline) 46ms 0.29% 81.94% 119ms 0.75% __printf_fp_buffer_1 11ms 0.069% 82.01% 118ms 0.74% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 2ms 0.013% 82.02% 117ms 0.73% AbstractTetrahedralElement::AbstractTetrahedralElement 8ms 0.05% 82.07% 117ms 0.73% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 116ms 0.73% 82.80% 116ms 0.73% std::type_info::name (inline) 0 0% 82.80% 113ms 0.71% Cell::HasCellProperty (inline) 3ms 0.019% 82.81% 113ms 0.71% CellPropertyCollection::HasProperty 112ms 0.7% 83.52% 112ms 0.7% AbstractCellProperty::AbstractCellProperty 4ms 0.025% 83.54% 110ms 0.69% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 83.54% 109ms 0.68% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 1ms 0.0063% 83.55% 109ms 0.68% boost::numeric::ublas::vector_assign (inline) 4ms 0.025% 83.57% 105ms 0.66% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 13ms 0.081% 83.65% 104ms 0.65% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 83.65% 102ms 0.64% CellProliferativeTypesWriter::VisitCell 0 0% 83.65% 98ms 0.61% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 34ms 0.21% 83.87% 97ms 0.61% AbstractElement::GetNodeLocation 17ms 0.11% 83.97% 97ms 0.61% MeshBasedCellPopulation::SpringIterator::SpringIterator 2ms 0.013% 83.99% 96ms 0.6% Cell::SetCellProliferativeType 0 0% 83.99% 95ms 0.59% AbstractCellBasedSimulation::DoCellRemoval (inline) 60ms 0.38% 84.36% 93ms 0.58% Cylindrical2dMesh::GetVectorFromAtoB 93ms 0.58% 84.94% 93ms 0.58% [libchaste_ode.so] 5ms 0.031% 84.97% 91ms 0.57% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 22ms 0.14% 85.11% 89ms 0.56% boost::numeric::ublas::indexing_vector_assign 0 0% 85.11% 88ms 0.55% Node::~Node 86ms 0.54% 85.65% 86ms 0.54% Node::GetIndex 1ms 0.0063% 85.66% 85ms 0.53% boost::numeric::ublas::c_vector::c_vector (inline) 85ms 0.53% 86.19% 85ms 0.53% std::_Rb_tree_rebalance_for_erase 30ms 0.19% 86.38% 84ms 0.53% Determinant (inline) 53ms 0.33% 86.71% 81ms 0.51% TimeStepper::AdvanceOneTimeStep