File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 9901ms, 85.77% of 11544ms total Dropped 664 nodes (cum <= 57.72ms) flat flat% sum% cum cum% 0 0% 0% 11515ms 99.75% __libc_start_call_main 0 0% 0% 11515ms 99.75% __libc_start_main_impl 0 0% 0% 11515ms 99.75% _start 0 0% 0% 11500ms 99.62% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 11500ms 99.62% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 11500ms 99.62% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 11500ms 99.62% main 0 0% 0% 11469ms 99.35% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 11469ms 99.35% CxxTest::TestRunner::runTest (inline) 0 0% 0% 11469ms 99.35% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 11453ms 99.21% AbstractCellBasedSimulation::Solve 0 0% 0% 8848ms 76.65% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.017% 0.017% 5696ms 49.34% AbstractCellBasedSimulation::DoCellBirth 1ms 0.0087% 0.026% 5632ms 48.79% Cell::ReadyToDivide 4ms 0.035% 0.061% 5597ms 48.48% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0087% 0.069% 5502ms 47.66% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 5ms 0.043% 0.11% 5499ms 47.64% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.026% 0.14% 5492ms 47.57% CellCycleModelOdeHandler::SolveOdeToTime 57ms 0.49% 0.63% 5403ms 46.80% AbstractOneStepIvpOdeSolver::InternalSolve 542ms 4.70% 5.33% 4849ms 42.00% RungeKutta4IvpOdeSolver::CalculateNextYValue 2036ms 17.64% 22.96% 4144ms 35.90% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 22.96% 3065ms 26.55% MeshBasedCellPopulation::Update 2ms 0.017% 22.98% 2299ms 19.92% Cylindrical2dMesh::ReMesh 43ms 0.37% 23.35% 2059ms 17.84% AbstractCellProperty::IsType (inline) 0 0% 23.35% 1453ms 12.59% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 23.35% 1279ms 11.08% MutableMesh::ReMesh 205ms 1.78% 25.13% 1236ms 10.71% AbstractCellProperty::IsSame 0 0% 25.13% 1227ms 10.63% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.017% 25.15% 1206ms 10.45% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 25.15% 1151ms 9.97% AbstractCellPopulation::WriteResultsToFiles 543ms 4.70% 29.85% 1093ms 9.47% std::_Rb_tree::_M_lower_bound (inline) 110ms 0.95% 30.80% 1078ms 9.34% TetrahedralMesh::EdgeIterator::operator++ 225ms 1.95% 32.75% 1031ms 8.93% std::type_info::operator== (inline) 875ms 7.58% 40.33% 875ms 7.58% __strcmp_evex 42ms 0.36% 40.70% 842ms 7.29% std::_Rb_tree::find (inline) 1ms 0.0087% 40.71% 749ms 6.49% MeshBasedCellPopulation::UpdateNodePairs 9ms 0.078% 40.78% 676ms 5.86% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 8ms 0.069% 40.85% 675ms 5.85% MeshBasedCellPopulation::SpringIterator::operator++ 9ms 0.078% 40.93% 605ms 5.24% std::set::insert (inline) 8ms 0.069% 41.00% 596ms 5.16% std::_Rb_tree::_M_insert_unique 3ms 0.026% 41.03% 592ms 5.13% TetrahedralMesh::ImportFromMesher 27ms 0.23% 41.26% 588ms 5.09% operator new 206ms 1.78% 43.04% 551ms 4.77% __GI___libc_malloc 0 0% 43.04% 545ms 4.72% std::set::count (inline) 0 0% 43.04% 535ms 4.63% triangulate 14ms 0.12% 43.17% 517ms 4.48% std::__new_allocator::allocate (inline) 0 0% 43.17% 515ms 4.46% std::allocator_traits::allocate (inline) 0 0% 43.17% 481ms 4.17% delaunay 0 0% 43.17% 480ms 4.16% divconqdelaunay 8ms 0.069% 43.23% 415ms 3.59% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 4ms 0.035% 43.27% 410ms 3.55% CellPopulationElementWriter::Visit 400ms 3.47% 46.73% 400ms 3.47% WntCellCycleOdeSystem::CalculateStoppingEvent 46ms 0.4% 47.13% 387ms 3.35% std::map::operator[] (partial-inline) 0 0% 47.13% 377ms 3.27% AbstractTwoBodyInteractionForce::AddForceContribution 10ms 0.087% 47.22% 373ms 3.23% std::less::operator() (inline) 363ms 3.14% 50.36% 364ms 3.15% std::operator< (inline) 349ms 3.02% 53.39% 349ms 3.02% std::_Rb_tree::_S_right (inline) 11ms 0.095% 53.48% 342ms 2.96% AbstractCellPopulation::GetCellUsingLocationIndex 17ms 0.15% 53.63% 339ms 2.94% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 20ms 0.17% 53.80% 329ms 2.85% std::_Rb_tree::_M_insert_ (inline) 13ms 0.11% 53.92% 321ms 2.78% MeshBasedCellPopulation::AcceptCellWriter 0 0% 53.92% 319ms 2.76% std::_Rb_tree::_M_create_node (inline) 0 0% 53.92% 313ms 2.71% std::_Rb_tree::_M_get_node (inline) 37ms 0.32% 54.24% 304ms 2.63% __GI___libc_free 182ms 1.58% 55.81% 301ms 2.61% _int_malloc 0 0% 55.81% 299ms 2.59% std::_Rb_tree::lower_bound (inline) 0 0% 55.81% 299ms 2.59% std::map::lower_bound (inline) 14ms 0.12% 55.93% 297ms 2.57% Cylindrical2dMesh::ReconstructCylindricalMesh 6ms 0.052% 55.99% 297ms 2.57% Element::Element 64ms 0.55% 56.54% 295ms 2.56% __dynamic_cast 0 0% 56.54% 294ms 2.55% std::map::find (inline) 0 0% 56.54% 293ms 2.54% std::_Rb_tree::_Alloc_node::operator() (inline) 5ms 0.043% 56.58% 292ms 2.53% MutableMesh::ReIndex 49ms 0.42% 57.01% 288ms 2.49% std::_Rb_tree::~_Rb_tree (inline) 0 0% 57.01% 282ms 2.44% std::_Rb_tree::_M_drop_node (inline) 2ms 0.017% 57.03% 280ms 2.43% CellPropertyCollection::GetPropertiesType (inline) 8ms 0.069% 57.09% 279ms 2.42% Element::RegisterWithNodes (inline) 1ms 0.0087% 57.10% 277ms 2.40% Cylindrical2dMesh::CorrectNonPeriodicMesh 174ms 1.51% 58.61% 271ms 2.35% AbstractCellMutationState::AbstractCellMutationState 11ms 0.095% 58.71% 268ms 2.32% Node::AddElement 243ms 2.10% 60.81% 265ms 2.30% _int_free 0 0% 60.81% 263ms 2.28% std::set::~set (inline) 39ms 0.34% 61.15% 259ms 2.24% std::_Rb_tree::_M_erase 98ms 0.85% 62.00% 259ms 2.24% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 62.00% 248ms 2.15% std::ostream::operator<< (inline) 11ms 0.095% 62.09% 245ms 2.12% boost::detail::shared_count::~shared_count (inline) 0 0% 62.09% 245ms 2.12% boost::shared_ptr::~shared_ptr (inline) 23ms 0.2% 62.29% 245ms 2.12% std::ostream::_M_insert 9ms 0.078% 62.37% 235ms 2.04% std::__new_allocator::deallocate (inline) 1ms 0.0087% 62.38% 234ms 2.03% AbstractCellProperty::IsSubType (inline) 227ms 1.97% 64.35% 231ms 2.00% boost::detail::sp_counted_base::release 0 0% 64.35% 229ms 1.98% std::allocator_traits::deallocate (inline) 5ms 0.043% 64.39% 218ms 1.89% std::_Rb_tree::erase 1ms 0.0087% 64.40% 217ms 1.88% std::set::erase (inline) 7ms 0.061% 64.46% 214ms 1.85% divconqrecurse 7ms 0.061% 64.52% 213ms 1.85% Node::RemoveElement 207ms 1.79% 66.31% 208ms 1.80% std::vector::operator[] (inline) 56ms 0.49% 66.80% 203ms 1.76% mergehulls 0 0% 66.80% 202ms 1.75% std::_Vector_base::_M_allocate (inline) 0 0% 66.80% 191ms 1.65% std::_Rb_tree::_M_put_node (inline) 15ms 0.13% 66.93% 187ms 1.62% Element::ResetIndex 0 0% 66.93% 183ms 1.59% AbstractCellPopulation::Iterator::operator++ (inline) 13ms 0.11% 67.04% 182ms 1.58% AbstractCellPopulation::Iterator::IsRealCell (inline) 2ms 0.017% 67.06% 179ms 1.55% alternateaxes 7ms 0.061% 67.12% 176ms 1.52% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 162ms 1.40% 68.52% 175ms 1.52% vertexmedian 11ms 0.095% 68.62% 172ms 1.49% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 68.62% 172ms 1.49% LegacyCellProliferativeTypesWriter::VisitCell 3ms 0.026% 68.64% 171ms 1.48% AbstractCellPopulation::IsCellAttachedToLocationIndex 2ms 0.017% 68.66% 170ms 1.47% Cell::GetCellProliferativeType 96ms 0.83% 69.49% 170ms 1.47% __cxxabiv1::__si_class_type_info::__do_dyncast 15ms 0.13% 69.62% 164ms 1.42% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 1ms 0.0087% 69.63% 164ms 1.42% NodeLocationWriter::Visit 7ms 0.061% 69.69% 157ms 1.36% std::vector::push_back (inline) 48ms 0.42% 70.11% 154ms 1.33% ApcOneHitCellMutationState::ApcOneHitCellMutationState 63ms 0.55% 70.65% 151ms 1.31% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 1ms 0.0087% 70.66% 148ms 1.28% Cell::GetMutationState 9ms 0.078% 70.74% 147ms 1.27% std::_Rb_tree::_Rb_tree (partial-inline) 16ms 0.14% 70.88% 147ms 1.27% std::num_put::_M_insert_float 63ms 0.55% 71.42% 146ms 1.26% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 0 0% 71.42% 145ms 1.26% OffLatticeSimulation::ApplyBoundaries 145ms 1.26% 72.68% 145ms 1.26% [libchaste_cell_based.so] 7ms 0.061% 72.74% 145ms 1.26% std::vector::_M_realloc_insert 1ms 0.0087% 72.75% 141ms 1.22% TetrahedralMesh::RefreshJacobianCachedData 1ms 0.0087% 72.76% 138ms 1.20% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 7ms 0.061% 72.82% 136ms 1.18% std::_Rb_tree::_M_erase_aux (inline) 0 0% 72.82% 135ms 1.17% std::set::set (inline) 7ms 0.061% 72.88% 133ms 1.15% AbstractTetrahedralElement::CalculateJacobian 5ms 0.043% 72.92% 125ms 1.08% Element::MarkAsDeleted 5ms 0.043% 72.96% 124ms 1.07% AbstractTetrahedralElement::CalculateInverseJacobian 16ms 0.14% 73.10% 124ms 1.07% std::_Rb_tree::_M_copy (inline) 3ms 0.026% 73.13% 117ms 1.01% std::__cxx11::collate::do_transform 85ms 0.74% 73.87% 116ms 1.00% AbstractElement::GetNodeGlobalIndex 116ms 1.00% 74.87% 116ms 1.00% std::vector::size (inline) 2ms 0.017% 74.89% 111ms 0.96% ___vsnprintf 17ms 0.15% 75.03% 109ms 0.94% __printf_buffer 0 0% 75.03% 109ms 0.94% __vsnprintf_internal (inline) 47ms 0.41% 75.44% 108ms 0.94% std::_Rb_tree::_M_clone_node (inline) 98ms 0.85% 76.29% 98ms 0.85% [libchaste_crypt.so] 1ms 0.0087% 76.30% 97ms 0.84% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 76.30% 97ms 0.84% MeshBasedCellPopulation::GetDampingConstant 11ms 0.095% 76.39% 95ms 0.82% AbstractTetrahedralElement::RefreshJacobian 4ms 0.035% 76.43% 94ms 0.81% CellPropertyCollection::HasProperty 0 0% 76.43% 93ms 0.81% Cell::HasCellProperty (inline) 92ms 0.8% 77.23% 92ms 0.8% incircle 0 0% 77.23% 92ms 0.8% std::_Rb_tree::_M_destroy_node (inline) 0 0% 77.23% 92ms 0.8% std::__new_allocator::destroy (inline) 0 0% 77.23% 92ms 0.8% std::allocator_traits::destroy (inline) 1ms 0.0087% 77.23% 91ms 0.79% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 8ms 0.069% 77.30% 90ms 0.78% TetrahedralMesh::EdgesEnd (partial-inline) 15ms 0.13% 77.43% 89ms 0.77% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 4ms 0.035% 77.47% 89ms 0.77% MeshBasedCellPopulation::SpringsEnd (inline) 2ms 0.017% 77.49% 88ms 0.76% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 0 0% 77.49% 87ms 0.75% AbstractCellBasedSimulation::DoCellRemoval (inline) 1ms 0.0087% 77.49% 87ms 0.75% TetrahedralMesh::Clear 2ms 0.017% 77.51% 85ms 0.74% AbstractTetrahedralElement::AbstractTetrahedralElement 3ms 0.026% 77.54% 85ms 0.74% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 2ms 0.017% 77.56% 84ms 0.73% __printf_fp_spec (inline) 5ms 0.043% 77.60% 83ms 0.72% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 48ms 0.42% 78.01% 83ms 0.72% std::_Rb_tree::equal_range (inline) 23ms 0.2% 78.21% 82ms 0.71% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 3ms 0.026% 78.24% 82ms 0.71% __printf_fp_l_buffer 82ms 0.71% 78.95% 82ms 0.71% boost::shared_ptr::operator-> (inline) 57ms 0.49% 79.44% 82ms 0.71% malloc_consolidate 3ms 0.026% 79.47% 82ms 0.71% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 82ms 0.71% 80.18% 82ms 0.71% std::_Rb_tree_insert_and_rebalance 1ms 0.0087% 80.19% 81ms 0.7% CellProliferativeTypesWriter::VisitCell 55ms 0.48% 80.67% 81ms 0.7% Cylindrical2dMesh::GetVectorFromAtoB 74ms 0.64% 81.31% 81ms 0.7% vertexsort 79ms 0.68% 81.99% 79ms 0.68% AbstractCellMutationState::~AbstractCellMutationState 28ms 0.24% 82.23% 78ms 0.68% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 34ms 0.29% 82.53% 78ms 0.68% TetrahedralMesh::EdgeIterator::EdgeIterator 25ms 0.22% 82.74% 78ms 0.68% __printf_fp_buffer_1 1ms 0.0087% 82.75% 77ms 0.67% boost::numeric::ublas::vector_assign (inline) 2ms 0.017% 82.77% 75ms 0.65% Cell::SetCellProliferativeType 75ms 0.65% 83.42% 75ms 0.65% [libchaste_mesh.so] 0 0% 83.42% 73ms 0.63% AbstractCellBasedWriter::OpenOutputFileForAppend 48ms 0.42% 83.84% 73ms 0.63% AbstractElement::GetNodeLocation 0 0% 83.84% 73ms 0.63% OutputFileHandler::OpenOutputFile 0 0% 83.84% 71ms 0.62% boost::numeric::ublas::c_vector::c_vector (inline) 7ms 0.061% 83.90% 66ms 0.57% MeshBasedCellPopulation::SpringIterator::SpringIterator 17ms 0.15% 84.04% 66ms 0.57% std::num_put::_M_insert_int 65ms 0.56% 84.61% 65ms 0.56% AbstractCellProperty::~AbstractCellProperty 37ms 0.32% 84.93% 64ms 0.55% TimeStepper::AdvanceOneTimeStep 4ms 0.035% 84.96% 62ms 0.54% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 11ms 0.095% 85.06% 62ms 0.54% std::_Rb_tree_const_iterator::operator++ (inline) 62ms 0.54% 85.59% 62ms 0.54% std::_Rb_tree_increment 20ms 0.17% 85.77% 60ms 0.52% boost::numeric::ublas::indexing_vector_assign 0 0% 85.77% 59ms 0.51% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend