File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16813ms, 86.01% of 19548ms total Dropped 767 nodes (cum <= 97.74ms) flat flat% sum% cum cum% 0 0% 0% 19503ms 99.77% __libc_start_call_main 0 0% 0% 19503ms 99.77% __libc_start_main_impl 0 0% 0% 19503ms 99.77% _start 0 0% 0% 19481ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19481ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19481ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19481ms 99.66% main 0 0% 0% 19444ms 99.47% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19444ms 99.47% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19444ms 99.47% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19416ms 99.32% AbstractCellBasedSimulation::Solve 0 0% 0% 14821ms 75.82% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 9341ms 47.78% AbstractCellBasedSimulation::DoCellBirth 4ms 0.02% 0.02% 9225ms 47.19% Cell::ReadyToDivide 3ms 0.015% 0.036% 9157ms 46.84% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0051% 0.041% 9000ms 46.04% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 16ms 0.082% 0.12% 8993ms 46.00% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 8ms 0.041% 0.16% 8971ms 45.89% CellCycleModelOdeHandler::SolveOdeToTime 57ms 0.29% 0.46% 8800ms 45.02% AbstractOneStepIvpOdeSolver::InternalSolve 1073ms 5.49% 5.94% 7945ms 40.64% RungeKutta4IvpOdeSolver::CalculateNextYValue 2782ms 14.23% 20.18% 6699ms 34.27% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.0051% 20.18% 5357ms 27.40% MeshBasedCellPopulation::Update 5ms 0.026% 20.21% 4146ms 21.21% Cylindrical2dMesh::ReMesh 58ms 0.3% 20.50% 3929ms 20.10% AbstractCellProperty::IsType (inline) 0 0% 20.50% 2596ms 13.28% OffLatticeSimulation::UpdateCellLocationsAndTopology 347ms 1.78% 22.28% 2543ms 13.01% AbstractCellProperty::IsSame 0 0% 22.28% 2287ms 11.70% MutableMesh::ReMesh 0 0% 22.28% 2242ms 11.47% ForwardEulerNumericalMethod::UpdateAllNodePositions 219ms 1.12% 23.40% 2196ms 11.23% std::type_info::operator== (inline) 15ms 0.077% 23.48% 2187ms 11.19% AbstractNumericalMethod::ComputeForcesIncludingDamping 2110ms 10.79% 34.27% 2110ms 10.79% __strcmp_avx2 0 0% 34.27% 1993ms 10.20% AbstractCellPopulation::WriteResultsToFiles 799ms 4.09% 38.36% 1915ms 9.80% std::_Rb_tree::_M_lower_bound (inline) 166ms 0.85% 39.21% 1703ms 8.71% TetrahedralMesh::EdgeIterator::operator++ 76ms 0.39% 39.59% 1438ms 7.36% std::_Rb_tree::find (inline) 0 0% 39.59% 1175ms 6.01% MeshBasedCellPopulation::UpdateNodePairs 7ms 0.036% 39.63% 1151ms 5.89% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 15ms 0.077% 39.71% 1150ms 5.88% TetrahedralMesh::ImportFromMesher 50ms 0.26% 39.96% 1079ms 5.52% operator new 14ms 0.072% 40.03% 1035ms 5.29% MeshBasedCellPopulation::SpringIterator::operator++ 236ms 1.21% 41.24% 1003ms 5.13% __GI___libc_malloc 7ms 0.036% 41.28% 995ms 5.09% std::set::insert (inline) 12ms 0.061% 41.34% 987ms 5.05% std::_Rb_tree::_M_insert_unique 30ms 0.15% 41.49% 912ms 4.67% std::__new_allocator::allocate (inline) 0 0% 41.49% 907ms 4.64% std::allocator_traits::allocate (inline) 1ms 0.0051% 41.50% 890ms 4.55% triangulate 0 0% 41.50% 874ms 4.47% std::set::count (inline) 0 0% 41.50% 820ms 4.19% delaunay 4ms 0.02% 41.52% 820ms 4.19% divconqdelaunay 57ms 0.29% 41.81% 739ms 3.78% std::map::operator[] (partial-inline) 1ms 0.0051% 41.82% 731ms 3.74% AbstractTwoBodyInteractionForce::AddForceContribution 3ms 0.015% 41.83% 731ms 3.74% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 726ms 3.71% 45.54% 726ms 3.71% std::_Rb_tree::_S_right (inline) 400ms 2.05% 47.59% 696ms 3.56% _int_malloc 6ms 0.031% 47.62% 684ms 3.50% CellPopulationElementWriter::Visit 678ms 3.47% 51.09% 678ms 3.47% WntCellCycleOdeSystem::CalculateStoppingEvent 21ms 0.11% 51.20% 669ms 3.42% std::less::operator() (inline) 648ms 3.31% 54.51% 648ms 3.31% std::operator< (inline) 22ms 0.11% 54.62% 643ms 3.29% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 194ms 0.99% 55.62% 641ms 3.28% __dynamic_cast 22ms 0.11% 55.73% 621ms 3.18% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 55.73% 610ms 3.12% std::_Rb_tree::_M_create_node (inline) 35ms 0.18% 55.91% 598ms 3.06% std::_Rb_tree::_M_insert_ (inline) 6ms 0.031% 55.94% 590ms 3.02% CellPropertyCollection::GetPropertiesType (inline) 8ms 0.041% 55.98% 585ms 2.99% MeshBasedCellPopulation::AcceptCellWriter 0 0% 55.98% 580ms 2.97% std::_Rb_tree::lower_bound (inline) 0 0% 55.98% 580ms 2.97% std::map::lower_bound (inline) 0 0% 55.98% 578ms 2.96% std::_Rb_tree::_M_get_node (inline) 0 0% 55.98% 561ms 2.87% std::map::find (inline) 2ms 0.01% 55.99% 549ms 2.81% Element::Element 11ms 0.056% 56.05% 544ms 2.78% MutableMesh::ReIndex 0 0% 56.05% 542ms 2.77% std::_Rb_tree::_Alloc_node::operator() (inline) 1ms 0.0051% 56.05% 509ms 2.60% std::ostream::operator<< (inline) 78ms 0.4% 56.45% 507ms 2.59% std::ostream::_M_insert 13ms 0.067% 56.52% 504ms 2.58% Element::RegisterWithNodes (inline) 10ms 0.051% 56.57% 502ms 2.57% Cylindrical2dMesh::CorrectNonPeriodicMesh 12ms 0.061% 56.63% 487ms 2.49% Cylindrical2dMesh::ReconstructCylindricalMesh 13ms 0.067% 56.70% 485ms 2.48% Node::AddElement 4ms 0.02% 56.72% 471ms 2.41% AbstractCellProperty::IsSubType (inline) 152ms 0.78% 57.49% 466ms 2.38% __GI___libc_free 286ms 1.46% 58.96% 436ms 2.23% AbstractCellMutationState::AbstractCellMutationState 8ms 0.041% 59.00% 397ms 2.03% std::__new_allocator::deallocate (inline) 106ms 0.54% 59.54% 394ms 2.02% std::_Rb_tree::_M_erase 0 0% 59.54% 390ms 2.00% std::allocator_traits::deallocate (inline) 16ms 0.082% 59.62% 383ms 1.96% Node::RemoveElement 6ms 0.031% 59.65% 382ms 1.95% std::_Rb_tree::erase 0 0% 59.65% 382ms 1.95% std::set::erase (inline) 138ms 0.71% 60.36% 378ms 1.93% std::_Rb_tree::_M_get_insert_unique_pos 24ms 0.12% 60.48% 372ms 1.90% std::_Rb_tree::~_Rb_tree (inline) 15ms 0.077% 60.56% 366ms 1.87% divconqrecurse 31ms 0.16% 60.72% 363ms 1.86% Element::ResetIndex 0 0% 60.72% 362ms 1.85% std::_Rb_tree::_M_drop_node (inline) 359ms 1.84% 62.55% 359ms 1.84% [libchaste_cell_based.so] 121ms 0.62% 63.17% 342ms 1.75% mergehulls 0 0% 63.17% 338ms 1.73% std::set::~set (inline) 9ms 0.046% 63.22% 333ms 1.70% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 44ms 0.23% 63.44% 331ms 1.69% AbstractCellPopulation::Iterator::IsRealCell (inline) 2ms 0.01% 63.45% 331ms 1.69% std::_Vector_base::_M_allocate (inline) 0 0% 63.45% 329ms 1.68% AbstractCellPopulation::Iterator::operator++ (inline) 10ms 0.051% 63.51% 327ms 1.67% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 63.51% 324ms 1.66% std::_Rb_tree::_M_put_node (inline) 6ms 0.031% 63.54% 322ms 1.65% Cell::GetCellProliferativeType 152ms 0.78% 64.31% 321ms 1.64% __cxxabiv1::__si_class_type_info::__do_dyncast 258ms 1.32% 65.63% 314ms 1.61% _int_free 1ms 0.0051% 65.64% 310ms 1.59% NodeLocationWriter::Visit 8ms 0.041% 65.68% 305ms 1.56% Cell::GetMutationState 8ms 0.041% 65.72% 304ms 1.56% alternateaxes 279ms 1.43% 67.15% 294ms 1.50% vertexmedian 2ms 0.01% 67.16% 290ms 1.48% LegacyCellProliferativeTypesWriter::VisitCell 28ms 0.14% 67.30% 285ms 1.46% std::_Rb_tree::_Rb_tree (partial-inline) 22ms 0.11% 67.41% 277ms 1.42% std::num_put::_M_insert_float 14ms 0.072% 67.49% 274ms 1.40% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 10ms 0.051% 67.54% 263ms 1.35% std::vector::push_back (inline) 2ms 0.01% 67.55% 257ms 1.31% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 101ms 0.52% 68.06% 255ms 1.30% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 13ms 0.067% 68.13% 254ms 1.30% std::_Rb_tree::_M_erase_aux (inline) 25ms 0.13% 68.26% 251ms 1.28% AbstractTetrahedralElement::CalculateJacobian 1ms 0.0051% 68.26% 250ms 1.28% std::set::set (inline) 246ms 1.26% 69.52% 248ms 1.27% std::vector::operator[] (inline) 4ms 0.02% 69.54% 239ms 1.22% AbstractCellPopulation::IsCellAttachedToLocationIndex 9ms 0.046% 69.59% 238ms 1.22% std::vector::_M_realloc_insert 6ms 0.031% 69.62% 235ms 1.20% std::__cxx11::collate::do_transform 83ms 0.42% 70.04% 232ms 1.19% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 61ms 0.31% 70.36% 231ms 1.18% ApcOneHitCellMutationState::ApcOneHitCellMutationState 26ms 0.13% 70.49% 231ms 1.18% std::_Rb_tree::_M_copy (inline) 0 0% 70.49% 225ms 1.15% ___vsnprintf 1ms 0.0051% 70.49% 225ms 1.15% __vsnprintf_internal (inline) 21ms 0.11% 70.60% 223ms 1.14% __printf_buffer 17ms 0.087% 70.69% 221ms 1.13% TetrahedralMesh::Clear 1ms 0.0051% 70.69% 216ms 1.10% OffLatticeSimulation::ApplyBoundaries 0 0% 70.69% 213ms 1.09% TetrahedralMesh::RefreshJacobianCachedData 14ms 0.072% 70.76% 208ms 1.06% Element::MarkAsDeleted 1ms 0.0051% 70.77% 202ms 1.03% MeshBasedCellPopulation::GetDampingConstant 68ms 0.35% 71.12% 202ms 1.03% std::_Rb_tree::_M_clone_node (inline) 1ms 0.0051% 71.12% 201ms 1.03% AbstractCentreBasedCellPopulation::GetDampingConstant 15ms 0.077% 71.20% 195ms 1% __printf_fp_l_buffer 0 0% 71.20% 195ms 1% __printf_fp_spec (inline) 2ms 0.01% 71.21% 188ms 0.96% CellProliferativeTypesWriter::VisitCell 11ms 0.056% 71.27% 181ms 0.93% AbstractTetrahedralElement::CalculateInverseJacobian 2ms 0.01% 71.28% 180ms 0.92% AbstractTetrahedralElement::AbstractTetrahedralElement 23ms 0.12% 71.39% 179ms 0.92% AbstractTetrahedralElement::RefreshJacobian 84ms 0.43% 71.82% 176ms 0.9% __printf_fp_buffer_1 129ms 0.66% 72.48% 172ms 0.88% malloc_consolidate 170ms 0.87% 73.35% 170ms 0.87% std::_Rb_tree_insert_and_rebalance 119ms 0.61% 73.96% 169ms 0.86% AbstractElement::GetNodeGlobalIndex 46ms 0.24% 74.20% 163ms 0.83% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 163ms 0.83% 75.03% 163ms 0.83% Node::GetIndex 3ms 0.015% 75.05% 162ms 0.83% boost::numeric::ublas::vector_assign (inline) 4ms 0.02% 75.07% 156ms 0.8% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 3ms 0.015% 75.08% 150ms 0.77% CellPropertyCollection::HasProperty 1ms 0.0051% 75.09% 149ms 0.76% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 0 0% 75.09% 147ms 0.75% Cell::HasCellProperty (inline) 7ms 0.036% 75.12% 147ms 0.75% MeshBasedCellPopulation::SpringsEnd (inline) 147ms 0.75% 75.87% 147ms 0.75% std::vector::size (inline) 145ms 0.74% 76.62% 145ms 0.74% incircle 142ms 0.73% 77.34% 142ms 0.73% [libchaste_crypt.so] 52ms 0.27% 77.61% 141ms 0.72% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 33ms 0.17% 77.78% 140ms 0.72% TetrahedralMesh::EdgesEnd (partial-inline) 87ms 0.45% 78.22% 139ms 0.71% Cylindrical2dMesh::GetVectorFromAtoB 131ms 0.67% 78.89% 139ms 0.71% vertexsort 138ms 0.71% 79.60% 138ms 0.71% unlink_chunk 53ms 0.27% 79.87% 136ms 0.7% AbstractElement::GetNodeLocation 4ms 0.02% 79.89% 136ms 0.7% Cell::SetCellProliferativeType 136ms 0.7% 80.59% 136ms 0.7% std::type_info::name (inline) 7ms 0.036% 80.62% 135ms 0.69% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 48ms 0.25% 80.87% 134ms 0.69% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 7ms 0.036% 80.90% 134ms 0.69% boost::numeric::ublas::c_vector::c_vector (inline) 85ms 0.43% 81.34% 133ms 0.68% std::_Rb_tree::equal_range (inline) 132ms 0.68% 82.01% 132ms 0.68% AbstractCellMutationState::~AbstractCellMutationState 2ms 0.01% 82.02% 127ms 0.65% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 5ms 0.026% 82.05% 126ms 0.64% Node::~Node 35ms 0.18% 82.23% 125ms 0.64% boost::numeric::ublas::indexing_vector_assign 0 0% 82.23% 124ms 0.63% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 82.23% 123ms 0.63% OutputFileHandler::OpenOutputFile 0 0% 82.23% 121ms 0.62% AbstractCellBasedSimulation::DoCellRemoval (inline) 34ms 0.17% 82.40% 121ms 0.62% std::__ostream_insert 18ms 0.092% 82.49% 115ms 0.59% MeshBasedCellPopulation::SpringIterator::SpringIterator 1ms 0.0051% 82.50% 115ms 0.59% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 82.50% 113ms 0.58% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 113ms 0.58% 83.08% 113ms 0.58% std::_Rb_tree_increment 28ms 0.14% 83.22% 113ms 0.58% std::num_put::_M_insert_int 12ms 0.061% 83.28% 111ms 0.57% boost::detail::shared_count::~shared_count (inline) 0 0% 83.28% 111ms 0.57% boost::shared_ptr::~shared_ptr (inline) 111ms 0.57% 83.85% 111ms 0.57% std::_Rb_tree_rebalance_for_erase 71ms 0.36% 84.21% 110ms 0.56% TimeStepper::AdvanceOneTimeStep 107ms 0.55% 84.76% 107ms 0.55% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 6ms 0.031% 84.79% 107ms 0.55% std::_Rb_tree_const_iterator::operator++ (inline) 77ms 0.39% 85.19% 106ms 0.54% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 5ms 0.026% 85.21% 102ms 0.52% std::_Rb_tree::_M_emplace_hint_unique 6ms 0.031% 85.24% 99ms 0.51% Cylindrical2dMesh::CreateMirrorNodes 52ms 0.27% 85.51% 99ms 0.51% boost::shared_ptr::shared_ptr (inline) 98ms 0.5% 86.01% 98ms 0.5% [libchaste_mesh.so]