File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16682ms, 84.95% of 19637ms total Dropped 790 nodes (cum <= 98.19ms) flat flat% sum% cum cum% 0 0% 0% 19590ms 99.76% __libc_start_call_main 0 0% 0% 19590ms 99.76% __libc_start_main_impl 0 0% 0% 19590ms 99.76% _start 0 0% 0% 19567ms 99.64% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19567ms 99.64% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19567ms 99.64% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19567ms 99.64% main 0 0% 0% 19528ms 99.44% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19528ms 99.44% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19528ms 99.44% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19501ms 99.31% AbstractCellBasedSimulation::Solve 0 0% 0% 14916ms 75.96% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.015% 0.015% 9490ms 48.33% AbstractCellBasedSimulation::DoCellBirth 6ms 0.031% 0.046% 9393ms 47.83% Cell::ReadyToDivide 1ms 0.0051% 0.051% 9306ms 47.39% AbstractPhaseBasedCellCycleModel::ReadyToDivide 3ms 0.015% 0.066% 9173ms 46.71% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 16ms 0.081% 0.15% 9165ms 46.67% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 4ms 0.02% 0.17% 9145ms 46.57% CellCycleModelOdeHandler::SolveOdeToTime 55ms 0.28% 0.45% 9009ms 45.88% AbstractOneStepIvpOdeSolver::InternalSolve 1028ms 5.24% 5.68% 8064ms 41.07% RungeKutta4IvpOdeSolver::CalculateNextYValue 2800ms 14.26% 19.94% 6843ms 34.85% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.0051% 19.95% 5305ms 27.02% MeshBasedCellPopulation::Update 4ms 0.02% 19.97% 4080ms 20.78% Cylindrical2dMesh::ReMesh 89ms 0.45% 20.42% 4033ms 20.54% AbstractCellProperty::IsType (inline) 411ms 2.09% 22.51% 2603ms 13.26% AbstractCellProperty::IsSame 3ms 0.015% 22.53% 2536ms 12.91% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 22.53% 2261ms 11.51% MutableMesh::ReMesh 0 0% 22.53% 2208ms 11.24% ForwardEulerNumericalMethod::UpdateAllNodePositions 276ms 1.41% 23.93% 2192ms 11.16% std::type_info::operator== (inline) 9ms 0.046% 23.98% 2157ms 10.98% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 23.98% 2040ms 10.39% AbstractCellPopulation::WriteResultsToFiles 2026ms 10.32% 34.30% 2026ms 10.32% __strcmp_avx2 834ms 4.25% 38.54% 1938ms 9.87% std::_Rb_tree::_M_lower_bound (inline) 164ms 0.84% 39.38% 1723ms 8.77% TetrahedralMesh::EdgeIterator::operator++ 65ms 0.33% 39.71% 1439ms 7.33% std::_Rb_tree::find (inline) 1ms 0.0051% 39.72% 1187ms 6.04% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.025% 39.74% 1155ms 5.88% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 51ms 0.26% 40.00% 1116ms 5.68% operator new 16ms 0.081% 40.08% 1094ms 5.57% TetrahedralMesh::ImportFromMesher 19ms 0.097% 40.18% 1050ms 5.35% MeshBasedCellPopulation::SpringIterator::operator++ 263ms 1.34% 41.52% 1046ms 5.33% __GI___libc_malloc 16ms 0.081% 41.60% 1030ms 5.25% std::set::insert (inline) 9ms 0.046% 41.65% 1014ms 5.16% std::_Rb_tree::_M_insert_unique 36ms 0.18% 41.83% 982ms 5.00% std::__new_allocator::allocate (inline) 0 0% 41.83% 977ms 4.98% std::allocator_traits::allocate (inline) 0 0% 41.83% 905ms 4.61% triangulate 0 0% 41.83% 862ms 4.39% std::set::count (inline) 0 0% 41.83% 805ms 4.10% delaunay 4ms 0.02% 41.85% 805ms 4.10% divconqdelaunay 4ms 0.02% 41.87% 779ms 3.97% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 771ms 3.93% 45.80% 771ms 3.93% WntCellCycleOdeSystem::CalculateStoppingEvent 713ms 3.63% 49.43% 713ms 3.63% std::_Rb_tree::_S_right (inline) 44ms 0.22% 49.65% 709ms 3.61% std::map::operator[] (partial-inline) 381ms 1.94% 51.59% 702ms 3.57% _int_malloc 10ms 0.051% 51.64% 697ms 3.55% CellPopulationElementWriter::Visit 0 0% 51.64% 694ms 3.53% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 51.64% 677ms 3.45% std::_Rb_tree::_M_create_node (inline) 16ms 0.081% 51.72% 665ms 3.39% std::less::operator() (inline) 649ms 3.30% 55.03% 649ms 3.30% std::operator< (inline) 0 0% 55.03% 643ms 3.27% std::_Rb_tree::_M_get_node (inline) 40ms 0.2% 55.23% 641ms 3.26% std::_Rb_tree::_M_insert_ (inline) 24ms 0.12% 55.35% 633ms 3.22% AbstractCellPopulation::GetCellUsingLocationIndex 5ms 0.025% 55.38% 625ms 3.18% MeshBasedCellPopulation::AcceptCellWriter 182ms 0.93% 56.31% 619ms 3.15% __dynamic_cast 0 0% 56.31% 619ms 3.15% std::_Rb_tree::_Alloc_node::operator() (inline) 6ms 0.031% 56.34% 606ms 3.09% CellPropertyCollection::GetPropertiesType (inline) 24ms 0.12% 56.46% 604ms 3.08% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 13ms 0.066% 56.53% 590ms 3.00% Element::Element 0 0% 56.53% 581ms 2.96% std::_Rb_tree::lower_bound (inline) 0 0% 56.53% 581ms 2.96% std::map::lower_bound (inline) 0 0% 56.53% 571ms 2.91% std::map::find (inline) 10ms 0.051% 56.58% 527ms 2.68% Cylindrical2dMesh::ReconstructCylindricalMesh 16ms 0.081% 56.66% 525ms 2.67% Element::RegisterWithNodes (inline) 13ms 0.066% 56.72% 510ms 2.60% Node::AddElement 5ms 0.025% 56.75% 506ms 2.58% MutableMesh::ReIndex 78ms 0.4% 57.15% 492ms 2.51% std::ostream::_M_insert 0 0% 57.15% 492ms 2.51% std::ostream::operator<< (inline) 3ms 0.015% 57.16% 488ms 2.49% AbstractCellProperty::IsSubType (inline) 18ms 0.092% 57.25% 485ms 2.47% Cylindrical2dMesh::CorrectNonPeriodicMesh 321ms 1.63% 58.89% 475ms 2.42% AbstractCellMutationState::AbstractCellMutationState 17ms 0.087% 58.98% 404ms 2.06% divconqrecurse 118ms 0.6% 59.58% 380ms 1.94% mergehulls 9ms 0.046% 59.62% 377ms 1.92% std::_Rb_tree::erase 1ms 0.0051% 59.63% 376ms 1.91% std::set::erase (inline) 115ms 0.59% 60.21% 375ms 1.91% __GI___libc_free 142ms 0.72% 60.94% 365ms 1.86% std::_Rb_tree::_M_get_insert_unique_pos 8ms 0.041% 60.98% 362ms 1.84% Node::RemoveElement 28ms 0.14% 61.12% 340ms 1.73% Element::ResetIndex 1ms 0.0051% 61.12% 335ms 1.71% std::_Vector_base::_M_allocate (inline) 145ms 0.74% 61.86% 323ms 1.64% __cxxabiv1::__si_class_type_info::__do_dyncast 3ms 0.015% 61.88% 322ms 1.64% AbstractCellPopulation::GetLocationIndexUsingCell 3ms 0.015% 61.89% 322ms 1.64% Cell::GetCellProliferativeType 4ms 0.02% 61.91% 320ms 1.63% Cell::GetMutationState 320ms 1.63% 63.54% 320ms 1.63% [libchaste_cell_based.so] 14ms 0.071% 63.61% 315ms 1.60% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 101ms 0.51% 64.13% 310ms 1.58% std::_Rb_tree::_M_erase 29ms 0.15% 64.28% 309ms 1.57% std::_Rb_tree::~_Rb_tree (inline) 2ms 0.01% 64.29% 305ms 1.55% NodeLocationWriter::Visit 1ms 0.0051% 64.29% 304ms 1.55% AbstractCellPopulation::Iterator::operator++ (inline) 1ms 0.0051% 64.30% 304ms 1.55% LegacyCellProliferativeTypesWriter::VisitCell 29ms 0.15% 64.44% 302ms 1.54% AbstractCellPopulation::Iterator::IsRealCell (inline) 15ms 0.076% 64.52% 299ms 1.52% std::_Rb_tree::_Rb_tree (partial-inline) 9ms 0.046% 64.57% 289ms 1.47% std::__new_allocator::deallocate (inline) 0 0% 64.57% 288ms 1.47% std::set::~set (inline) 0 0% 64.57% 285ms 1.45% std::allocator_traits::deallocate (inline) 282ms 1.44% 66.00% 285ms 1.45% std::vector::operator[] (inline) 0 0% 66.00% 271ms 1.38% std::_Rb_tree::_M_drop_node (inline) 17ms 0.087% 66.09% 270ms 1.37% std::num_put::_M_insert_float 1ms 0.0051% 66.09% 269ms 1.37% std::set::set (inline) 3ms 0.015% 66.11% 266ms 1.35% alternateaxes 250ms 1.27% 67.38% 263ms 1.34% vertexmedian 108ms 0.55% 67.93% 262ms 1.33% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 17ms 0.087% 68.02% 257ms 1.31% AbstractTetrahedralElement::CalculateJacobian 97ms 0.49% 68.51% 257ms 1.31% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 202ms 1.03% 69.54% 257ms 1.31% _int_free 16ms 0.081% 69.62% 255ms 1.30% std::vector::push_back (inline) 23ms 0.12% 69.74% 254ms 1.29% std::_Rb_tree::_M_copy (inline) 58ms 0.3% 70.04% 246ms 1.25% ApcOneHitCellMutationState::ApcOneHitCellMutationState 5ms 0.025% 70.06% 239ms 1.22% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 6ms 0.031% 70.09% 235ms 1.20% AbstractCellPopulation::IsCellAttachedToLocationIndex 0 0% 70.09% 235ms 1.20% std::_Rb_tree::_M_put_node (inline) 3ms 0.015% 70.11% 233ms 1.19% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 70.11% 233ms 1.19% TetrahedralMesh::RefreshJacobianCachedData 72ms 0.37% 70.47% 229ms 1.17% std::_Rb_tree::_M_clone_node (inline) 12ms 0.061% 70.54% 223ms 1.14% std::vector::_M_realloc_insert 146ms 0.74% 71.28% 222ms 1.13% AbstractElement::GetNodeGlobalIndex 2ms 0.01% 71.29% 222ms 1.13% MeshBasedCellPopulation::GetDampingConstant 1ms 0.0051% 71.29% 220ms 1.12% AbstractCentreBasedCellPopulation::GetDampingConstant 7ms 0.036% 71.33% 217ms 1.11% std::__cxx11::collate::do_transform 0 0% 71.33% 213ms 1.08% OffLatticeSimulation::ApplyBoundaries 15ms 0.076% 71.41% 209ms 1.06% AbstractTetrahedralElement::CalculateInverseJacobian 20ms 0.1% 71.51% 209ms 1.06% std::_Rb_tree::_M_erase_aux (inline) 4ms 0.02% 71.53% 205ms 1.04% ___vsnprintf 0 0% 71.53% 201ms 1.02% __vsnprintf_internal (inline) 30ms 0.15% 71.68% 200ms 1.02% AbstractTetrahedralElement::RefreshJacobian 27ms 0.14% 71.82% 199ms 1.01% __printf_buffer 18ms 0.092% 71.91% 198ms 1.01% Element::MarkAsDeleted 5ms 0.025% 71.94% 192ms 0.98% CellProliferativeTypesWriter::VisitCell 133ms 0.68% 72.61% 192ms 0.98% malloc_consolidate 17ms 0.087% 72.70% 186ms 0.95% TetrahedralMesh::Clear 182ms 0.93% 73.63% 182ms 0.93% [libchaste_crypt.so] 179ms 0.91% 74.54% 179ms 0.91% std::vector::size (inline) 5ms 0.025% 74.56% 173ms 0.88% CellPropertyCollection::HasProperty 0 0% 74.56% 171ms 0.87% Cell::HasCellProperty (inline) 171ms 0.87% 75.43% 171ms 0.87% unlink_chunk 113ms 0.58% 76.01% 170ms 0.87% std::_Rb_tree::equal_range (inline) 7ms 0.036% 76.05% 166ms 0.85% AbstractTetrahedralElement::AbstractTetrahedralElement 166ms 0.85% 76.89% 166ms 0.85% incircle 38ms 0.19% 77.08% 165ms 0.84% TetrahedralMesh::EdgesEnd (partial-inline) 6ms 0.031% 77.11% 163ms 0.83% __printf_fp_l_buffer 0 0% 77.11% 163ms 0.83% __printf_fp_spec (inline) 4ms 0.02% 77.14% 162ms 0.82% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 159ms 0.81% 77.94% 159ms 0.81% std::type_info::name (inline) 56ms 0.29% 78.23% 153ms 0.78% __printf_fp_buffer_1 62ms 0.32% 78.55% 151ms 0.77% AbstractElement::GetNodeLocation 151ms 0.77% 79.31% 151ms 0.77% std::_Rb_tree_insert_and_rebalance 10ms 0.051% 79.37% 148ms 0.75% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 92ms 0.47% 79.83% 148ms 0.75% Cylindrical2dMesh::GetVectorFromAtoB 142ms 0.72% 80.56% 142ms 0.72% Node::GetIndex 3ms 0.015% 80.57% 135ms 0.69% MeshBasedCellPopulation::SpringsEnd (inline) 44ms 0.22% 80.80% 133ms 0.68% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 55ms 0.28% 81.08% 131ms 0.67% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 2ms 0.01% 81.09% 130ms 0.66% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 1ms 0.0051% 81.09% 129ms 0.66% AbstractCellBasedWriter::OpenOutputFileForAppend 2ms 0.01% 81.10% 128ms 0.65% boost::numeric::ublas::vector_assign (inline) 112ms 0.57% 81.67% 125ms 0.64% vertexsort 0 0% 81.67% 124ms 0.63% OutputFileHandler::OpenOutputFile 68ms 0.35% 82.02% 124ms 0.63% TetrahedralMesh::EdgeIterator::EdgeIterator 0 0% 82.02% 121ms 0.62% AbstractCellBasedSimulation::DoCellRemoval (inline) 14ms 0.071% 82.09% 121ms 0.62% boost::detail::shared_count::~shared_count (inline) 0 0% 82.09% 121ms 0.62% boost::shared_ptr::~shared_ptr (inline) 1ms 0.0051% 82.10% 118ms 0.6% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 0 0% 82.10% 114ms 0.58% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 4ms 0.02% 82.12% 114ms 0.58% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 16ms 0.081% 82.20% 114ms 0.58% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 82.20% 113ms 0.58% Cell::SetCellProliferativeType 5ms 0.025% 82.22% 111ms 0.57% boost::numeric::ublas::c_vector::c_vector (inline) 8ms 0.041% 82.26% 110ms 0.56% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 52ms 0.26% 82.53% 108ms 0.55% boost::shared_ptr::shared_ptr (inline) 30ms 0.15% 82.68% 108ms 0.55% std::num_put::_M_insert_int 6ms 0.031% 82.71% 106ms 0.54% Node::~Node 13ms 0.066% 82.78% 102ms 0.52% MeshBasedCellPopulation::SpringIterator::SpringIterator 29ms 0.15% 82.93% 102ms 0.52% boost::numeric::ublas::indexing_vector_assign 102ms 0.52% 83.44% 102ms 0.52% boost::shared_ptr::operator-> (inline) 96ms 0.49% 83.93% 101ms 0.51% boost::detail::sp_counted_base::release 100ms 0.51% 84.44% 100ms 0.51% AbstractCellMutationState::~AbstractCellMutationState 100ms 0.51% 84.95% 100ms 0.51% std::_Rb_tree_increment