File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16365ms, 84.67% of 19328ms total Dropped 780 nodes (cum <= 96.64ms) flat flat% sum% cum cum% 0 0% 0% 19284ms 99.77% __libc_start_call_main 0 0% 0% 19284ms 99.77% __libc_start_main_impl 0 0% 0% 19284ms 99.77% _start 0 0% 0% 19262ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19262ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19262ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19262ms 99.66% main 0 0% 0% 19221ms 99.45% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19221ms 99.45% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19221ms 99.45% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19194ms 99.31% AbstractCellBasedSimulation::Solve 0 0% 0% 14639ms 75.74% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 9266ms 47.94% AbstractCellBasedSimulation::DoCellBirth 5ms 0.026% 0.026% 9168ms 47.43% Cell::ReadyToDivide 4ms 0.021% 0.047% 9087ms 47.01% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.01% 0.057% 8966ms 46.39% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 10ms 0.052% 0.11% 8951ms 46.31% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.01% 0.12% 8941ms 46.26% CellCycleModelOdeHandler::SolveOdeToTime 74ms 0.38% 0.5% 8792ms 45.49% AbstractOneStepIvpOdeSolver::InternalSolve 1012ms 5.24% 5.74% 7877ms 40.75% RungeKutta4IvpOdeSolver::CalculateNextYValue 2782ms 14.39% 20.13% 6657ms 34.44% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 20.13% 5269ms 27.26% MeshBasedCellPopulation::Update 4ms 0.021% 20.15% 4051ms 20.96% Cylindrical2dMesh::ReMesh 62ms 0.32% 20.47% 3885ms 20.10% AbstractCellProperty::IsType (inline) 0 0% 20.47% 2551ms 13.20% OffLatticeSimulation::UpdateCellLocationsAndTopology 333ms 1.72% 22.20% 2498ms 12.92% AbstractCellProperty::IsSame 0 0% 22.20% 2233ms 11.55% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 22.20% 2229ms 11.53% MutableMesh::ReMesh 11ms 0.057% 22.25% 2189ms 11.33% AbstractNumericalMethod::ComputeForcesIncludingDamping 239ms 1.24% 23.49% 2165ms 11.20% std::type_info::operator== (inline) 2030ms 10.50% 33.99% 2030ms 10.50% __strcmp_avx2 0 0% 33.99% 2002ms 10.36% AbstractCellPopulation::WriteResultsToFiles 828ms 4.28% 38.28% 1922ms 9.94% std::_Rb_tree::_M_lower_bound (inline) 182ms 0.94% 39.22% 1686ms 8.72% TetrahedralMesh::EdgeIterator::operator++ 61ms 0.32% 39.53% 1401ms 7.25% std::_Rb_tree::find (inline) 0 0% 39.53% 1185ms 6.13% MeshBasedCellPopulation::UpdateNodePairs 6ms 0.031% 39.56% 1156ms 5.98% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 19ms 0.098% 39.66% 1101ms 5.70% TetrahedralMesh::ImportFromMesher 15ms 0.078% 39.74% 1045ms 5.41% MeshBasedCellPopulation::SpringIterator::operator++ 34ms 0.18% 39.92% 998ms 5.16% operator new 18ms 0.093% 40.01% 954ms 4.94% std::set::insert (inline) 250ms 1.29% 41.30% 951ms 4.92% __GI___libc_malloc 12ms 0.062% 41.36% 936ms 4.84% std::_Rb_tree::_M_insert_unique 46ms 0.24% 41.60% 892ms 4.62% std::__new_allocator::allocate (inline) 0 0% 41.60% 886ms 4.58% std::allocator_traits::allocate (inline) 2ms 0.01% 41.61% 879ms 4.55% triangulate 0 0% 41.61% 844ms 4.37% std::set::count (inline) 1ms 0.0052% 41.62% 796ms 4.12% delaunay 3ms 0.016% 41.63% 795ms 4.11% divconqdelaunay 69ms 0.36% 41.99% 742ms 3.84% std::map::operator[] (partial-inline) 1ms 0.0052% 42.00% 736ms 3.81% AbstractTwoBodyInteractionForce::AddForceContribution 736ms 3.81% 45.80% 736ms 3.81% std::_Rb_tree::_S_right (inline) 735ms 3.80% 49.61% 735ms 3.80% WntCellCycleOdeSystem::CalculateStoppingEvent 2ms 0.01% 49.62% 730ms 3.78% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 5ms 0.026% 49.64% 726ms 3.76% CellPopulationElementWriter::Visit 23ms 0.12% 49.76% 631ms 3.26% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 15ms 0.078% 49.84% 618ms 3.20% std::less::operator() (inline) 170ms 0.88% 50.72% 616ms 3.19% __dynamic_cast 362ms 1.87% 52.59% 609ms 3.15% _int_malloc 22ms 0.11% 52.71% 607ms 3.14% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 52.71% 605ms 3.13% std::_Rb_tree::lower_bound (inline) 0 0% 52.71% 605ms 3.13% std::map::lower_bound (inline) 603ms 3.12% 55.83% 603ms 3.12% std::operator< (inline) 7ms 0.036% 55.86% 577ms 2.99% MeshBasedCellPopulation::AcceptCellWriter 33ms 0.17% 56.03% 572ms 2.96% std::_Rb_tree::_M_insert_ (inline) 0 0% 56.03% 569ms 2.94% std::_Rb_tree::_M_create_node (inline) 0 0% 56.03% 556ms 2.88% std::map::find (inline) 3ms 0.016% 56.05% 553ms 2.86% CellPropertyCollection::GetPropertiesType (inline) 4ms 0.021% 56.07% 553ms 2.86% Element::Element 0 0% 56.07% 548ms 2.84% std::_Rb_tree::_M_get_node (inline) 0 0% 56.07% 522ms 2.70% std::_Rb_tree::_Alloc_node::operator() (inline) 13ms 0.067% 56.14% 517ms 2.67% Cylindrical2dMesh::ReconstructCylindricalMesh 9ms 0.047% 56.18% 507ms 2.62% MutableMesh::ReIndex 7ms 0.036% 56.22% 491ms 2.54% Cylindrical2dMesh::CorrectNonPeriodicMesh 10ms 0.052% 56.27% 485ms 2.51% Element::RegisterWithNodes (inline) 0 0% 56.27% 475ms 2.46% std::ostream::operator<< (inline) 70ms 0.36% 56.63% 474ms 2.45% std::ostream::_M_insert 12ms 0.062% 56.69% 470ms 2.43% Node::AddElement 3ms 0.016% 56.71% 457ms 2.36% AbstractCellProperty::IsSubType (inline) 128ms 0.66% 57.37% 432ms 2.24% __GI___libc_free 1ms 0.0052% 57.38% 426ms 2.20% std::set::erase (inline) 6ms 0.031% 57.41% 425ms 2.20% std::_Rb_tree::erase 275ms 1.42% 58.83% 424ms 2.19% AbstractCellMutationState::AbstractCellMutationState 13ms 0.067% 58.90% 422ms 2.18% Node::RemoveElement 13ms 0.067% 58.97% 395ms 2.04% divconqrecurse 12ms 0.062% 59.03% 385ms 1.99% std::__new_allocator::deallocate (inline) 0 0% 59.03% 379ms 1.96% std::allocator_traits::deallocate (inline) 110ms 0.57% 59.60% 376ms 1.95% mergehulls 112ms 0.58% 60.18% 370ms 1.91% std::_Rb_tree::_M_erase 146ms 0.76% 60.93% 352ms 1.82% std::_Rb_tree::_M_get_insert_unique_pos 20ms 0.1% 61.04% 349ms 1.81% Element::ResetIndex 4ms 0.021% 61.06% 342ms 1.77% std::_Vector_base::_M_allocate (inline) 0 0% 61.06% 341ms 1.76% std::_Rb_tree::_M_drop_node (inline) 23ms 0.12% 61.18% 340ms 1.76% std::_Rb_tree::~_Rb_tree (inline) 173ms 0.9% 62.07% 335ms 1.73% __cxxabiv1::__si_class_type_info::__do_dyncast 330ms 1.71% 63.78% 330ms 1.71% [libchaste_cell_based.so] 8ms 0.041% 63.82% 325ms 1.68% AbstractCellPopulation::GetLocationIndexUsingCell 10ms 0.052% 63.87% 321ms 1.66% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 0 0% 63.87% 321ms 1.66% std::set::~set (inline) 309ms 1.60% 65.47% 312ms 1.61% std::vector::operator[] (inline) 0 0% 65.47% 306ms 1.58% std::_Rb_tree::_M_put_node (inline) 4ms 0.021% 65.49% 304ms 1.57% LegacyCellProliferativeTypesWriter::VisitCell 254ms 1.31% 66.80% 302ms 1.56% _int_free 1ms 0.0052% 66.81% 294ms 1.52% Cell::GetMutationState 2ms 0.01% 66.82% 292ms 1.51% NodeLocationWriter::Visit 0 0% 66.82% 287ms 1.48% alternateaxes 0 0% 66.82% 286ms 1.48% AbstractCellPopulation::Iterator::operator++ (inline) 268ms 1.39% 68.21% 286ms 1.48% vertexmedian 33ms 0.17% 68.38% 284ms 1.47% AbstractCellPopulation::Iterator::IsRealCell (inline) 2ms 0.01% 68.39% 284ms 1.47% Cell::GetCellProliferativeType 9ms 0.047% 68.43% 280ms 1.45% std::vector::push_back (inline) 14ms 0.072% 68.51% 266ms 1.38% AbstractCellPopulation::IsCellAttachedToLocationIndex 20ms 0.1% 68.61% 263ms 1.36% std::num_put::_M_insert_float 20ms 0.1% 68.71% 261ms 1.35% std::vector::_M_realloc_insert 17ms 0.088% 68.80% 260ms 1.35% std::_Rb_tree::_Rb_tree (partial-inline) 11ms 0.057% 68.86% 244ms 1.26% std::_Rb_tree::_M_erase_aux (inline) 56ms 0.29% 69.15% 242ms 1.25% ApcOneHitCellMutationState::ApcOneHitCellMutationState 1ms 0.0052% 69.15% 241ms 1.25% std::set::set (inline) 96ms 0.5% 69.65% 239ms 1.24% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 10ms 0.052% 69.70% 232ms 1.20% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 17ms 0.088% 69.79% 230ms 1.19% AbstractTetrahedralElement::CalculateJacobian 96ms 0.5% 70.29% 228ms 1.18% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 0 0% 70.29% 224ms 1.16% OffLatticeSimulation::ApplyBoundaries 16ms 0.083% 70.37% 219ms 1.13% Element::MarkAsDeleted 0 0% 70.37% 218ms 1.13% TetrahedralMesh::RefreshJacobianCachedData 3ms 0.016% 70.38% 217ms 1.12% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 18ms 0.093% 70.48% 211ms 1.09% std::_Rb_tree::_M_copy (inline) 1ms 0.0052% 70.48% 202ms 1.05% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 70.48% 202ms 1.05% MeshBasedCellPopulation::GetDampingConstant 2ms 0.01% 70.49% 201ms 1.04% std::__cxx11::collate::do_transform 3ms 0.016% 70.51% 194ms 1.00% ___vsnprintf 0 0% 70.51% 191ms 0.99% __vsnprintf_internal (inline) 11ms 0.057% 70.57% 190ms 0.98% AbstractTetrahedralElement::CalculateInverseJacobian 31ms 0.16% 70.73% 190ms 0.98% __printf_buffer 60ms 0.31% 71.04% 190ms 0.98% std::_Rb_tree::_M_clone_node (inline) 131ms 0.68% 71.71% 181ms 0.94% AbstractElement::GetNodeGlobalIndex 9ms 0.047% 71.76% 178ms 0.92% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 109ms 0.56% 72.33% 178ms 0.92% std::_Rb_tree::equal_range (inline) 176ms 0.91% 73.24% 176ms 0.91% Node::GetIndex 12ms 0.062% 73.30% 173ms 0.9% TetrahedralMesh::Clear 168ms 0.87% 74.17% 168ms 0.87% incircle 20ms 0.1% 74.27% 167ms 0.86% AbstractTetrahedralElement::RefreshJacobian 5ms 0.026% 74.30% 166ms 0.86% AbstractTetrahedralElement::AbstractTetrahedralElement 2ms 0.01% 74.31% 165ms 0.85% CellPropertyCollection::HasProperty 0 0% 74.31% 164ms 0.85% Cell::HasCellProperty (inline) 162ms 0.84% 75.14% 162ms 0.84% AbstractCellMutationState::~AbstractCellMutationState 119ms 0.62% 75.76% 158ms 0.82% malloc_consolidate 51ms 0.26% 76.02% 155ms 0.8% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 152ms 0.79% 76.81% 152ms 0.79% [libchaste_crypt.so] 150ms 0.78% 77.59% 150ms 0.78% std::_Rb_tree_insert_and_rebalance 5ms 0.026% 77.61% 149ms 0.77% __printf_fp_l_buffer 0 0% 77.61% 149ms 0.77% __printf_fp_spec (inline) 4ms 0.021% 77.63% 148ms 0.77% CellProliferativeTypesWriter::VisitCell 85ms 0.44% 78.07% 147ms 0.76% Cylindrical2dMesh::GetVectorFromAtoB 46ms 0.24% 78.31% 145ms 0.75% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 142ms 0.73% 79.05% 142ms 0.73% std::vector::size (inline) 0 0% 79.05% 140ms 0.72% boost::numeric::ublas::vector_assign (inline) 42ms 0.22% 79.26% 139ms 0.72% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 67ms 0.35% 79.61% 139ms 0.72% __printf_fp_buffer_1 139ms 0.72% 80.33% 139ms 0.72% std::type_info::name (inline) 25ms 0.13% 80.46% 138ms 0.71% TetrahedralMesh::EdgesEnd (partial-inline) 9ms 0.047% 80.50% 131ms 0.68% MeshBasedCellPopulation::SpringsEnd (inline) 20ms 0.1% 80.61% 128ms 0.66% boost::detail::shared_count::~shared_count (inline) 0 0% 80.61% 128ms 0.66% boost::shared_ptr::~shared_ptr (inline) 9ms 0.047% 80.66% 126ms 0.65% boost::numeric::ublas::c_vector::c_vector (inline) 45ms 0.23% 80.89% 124ms 0.64% AbstractElement::GetNodeLocation 5ms 0.026% 80.91% 116ms 0.6% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 116ms 0.6% 81.51% 116ms 0.6% unlink_chunk 0 0% 81.51% 114ms 0.59% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 112ms 0.58% 82.09% 112ms 0.58% std::_Rb_tree_rebalance_for_erase 0 0% 82.09% 110ms 0.57% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 2ms 0.01% 82.10% 110ms 0.57% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 0 0% 82.10% 107ms 0.55% AbstractCellBasedWriter::OpenOutputFileForAppend 101ms 0.52% 82.63% 107ms 0.55% boost::detail::sp_counted_base::release 25ms 0.13% 82.76% 107ms 0.55% boost::numeric::ublas::indexing_vector_assign 0 0% 82.76% 106ms 0.55% OutputFileHandler::OpenOutputFile 3ms 0.016% 82.77% 104ms 0.54% Node::~Node 98ms 0.51% 83.28% 103ms 0.53% vertexsort 0 0% 83.28% 102ms 0.53% AbstractCellBasedSimulation::DoCellRemoval (inline) 102ms 0.53% 83.81% 102ms 0.53% TetrahedralMesh::EdgeIterator::operator!= 67ms 0.35% 84.15% 101ms 0.52% TetrahedralMesh::EdgeIterator::EdgeIterator 12ms 0.062% 84.21% 98ms 0.51% MeshBasedCellPopulation::SpringIterator::SpringIterator 26ms 0.13% 84.35% 98ms 0.51% std::__ostream_insert 62ms 0.32% 84.67% 97ms 0.5% TimeStepper::AdvanceOneTimeStep