File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16483ms, 83.07% of 19842ms total Dropped 814 nodes (cum <= 99.21ms) flat flat% sum% cum cum% 0 0% 0% 19796ms 99.77% __libc_start_call_main 0 0% 0% 19796ms 99.77% __libc_start_main_impl 0 0% 0% 19796ms 99.77% _start 0 0% 0% 19775ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19775ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19775ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19775ms 99.66% main 0 0% 0% 19734ms 99.46% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19734ms 99.46% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19734ms 99.46% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19707ms 99.32% AbstractCellBasedSimulation::Solve 0 0% 0% 14976ms 75.48% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.005% 0.005% 9369ms 47.22% AbstractCellBasedSimulation::DoCellBirth 18ms 0.091% 0.096% 9274ms 46.74% Cell::ReadyToDivide 9ms 0.045% 0.14% 9150ms 46.11% AbstractPhaseBasedCellCycleModel::ReadyToDivide 3ms 0.015% 0.16% 9013ms 45.42% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 17ms 0.086% 0.24% 9001ms 45.36% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.01% 0.25% 8981ms 45.26% CellCycleModelOdeHandler::SolveOdeToTime 72ms 0.36% 0.61% 8770ms 44.20% AbstractOneStepIvpOdeSolver::InternalSolve 1022ms 5.15% 5.77% 7841ms 39.52% RungeKutta4IvpOdeSolver::CalculateNextYValue 2691ms 13.56% 19.33% 6610ms 33.31% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 19.33% 5489ms 27.66% MeshBasedCellPopulation::Update 4ms 0.02% 19.35% 4251ms 21.42% Cylindrical2dMesh::ReMesh 61ms 0.31% 19.66% 3954ms 19.93% AbstractCellProperty::IsType (inline) 1ms 0.005% 19.66% 2627ms 13.24% OffLatticeSimulation::UpdateCellLocationsAndTopology 352ms 1.77% 21.43% 2564ms 12.92% AbstractCellProperty::IsSame 0 0% 21.43% 2339ms 11.79% MutableMesh::ReMesh 0 0% 21.43% 2323ms 11.71% ForwardEulerNumericalMethod::UpdateAllNodePositions 9ms 0.045% 21.48% 2269ms 11.44% AbstractNumericalMethod::ComputeForcesIncludingDamping 208ms 1.05% 22.53% 2212ms 11.15% std::type_info::operator== (inline) 2136ms 10.77% 33.29% 2136ms 10.77% __strcmp_avx2 0 0% 33.29% 2098ms 10.57% AbstractCellPopulation::WriteResultsToFiles 749ms 3.77% 37.07% 1869ms 9.42% std::_Rb_tree::_M_lower_bound (inline) 174ms 0.88% 37.94% 1761ms 8.88% TetrahedralMesh::EdgeIterator::operator++ 87ms 0.44% 38.38% 1406ms 7.09% std::_Rb_tree::find (inline) 1ms 0.005% 38.39% 1199ms 6.04% MeshBasedCellPopulation::UpdateNodePairs 16ms 0.081% 38.47% 1173ms 5.91% TetrahedralMesh::ImportFromMesher 6ms 0.03% 38.50% 1153ms 5.81% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 43ms 0.22% 38.72% 1080ms 5.44% operator new 9ms 0.045% 38.76% 1079ms 5.44% MeshBasedCellPopulation::SpringIterator::operator++ 243ms 1.22% 39.99% 1028ms 5.18% __GI___libc_malloc 20ms 0.1% 40.09% 985ms 4.96% std::set::insert (inline) 17ms 0.086% 40.17% 965ms 4.86% std::_Rb_tree::_M_insert_unique 38ms 0.19% 40.36% 953ms 4.80% std::__new_allocator::allocate (inline) 0 0% 40.36% 949ms 4.78% std::allocator_traits::allocate (inline) 0 0% 40.36% 864ms 4.35% std::set::count (inline) 0 0% 40.36% 862ms 4.34% triangulate 1ms 0.005% 40.37% 784ms 3.95% AbstractTwoBodyInteractionForce::AddForceContribution 2ms 0.01% 40.38% 773ms 3.90% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 1ms 0.005% 40.38% 771ms 3.89% delaunay 6ms 0.03% 40.41% 769ms 3.88% divconqdelaunay 62ms 0.31% 40.73% 764ms 3.85% std::map::operator[] (partial-inline) 746ms 3.76% 44.49% 746ms 3.76% std::_Rb_tree::_S_right (inline) 737ms 3.71% 48.20% 737ms 3.71% WntCellCycleOdeSystem::CalculateStoppingEvent 9ms 0.045% 48.25% 729ms 3.67% CellPopulationElementWriter::Visit 377ms 1.90% 50.15% 720ms 3.63% _int_malloc 19ms 0.096% 50.24% 689ms 3.47% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 208ms 1.05% 51.29% 682ms 3.44% __dynamic_cast 16ms 0.081% 51.37% 650ms 3.28% std::less::operator() (inline) 19ms 0.096% 51.47% 648ms 3.27% AbstractCellPopulation::GetCellUsingLocationIndex 634ms 3.20% 54.66% 634ms 3.20% std::operator< (inline) 3ms 0.015% 54.68% 621ms 3.13% CellPropertyCollection::GetPropertiesType (inline) 0 0% 54.68% 616ms 3.10% std::_Rb_tree::_M_create_node (inline) 5ms 0.025% 54.70% 608ms 3.06% MeshBasedCellPopulation::AcceptCellWriter 0 0% 54.70% 593ms 2.99% std::_Rb_tree::_M_get_node (inline) 0 0% 54.70% 583ms 2.94% std::_Rb_tree::lower_bound (inline) 0 0% 54.70% 583ms 2.94% std::map::lower_bound (inline) 42ms 0.21% 54.91% 567ms 2.86% std::_Rb_tree::_M_insert_ (inline) 9ms 0.045% 54.96% 559ms 2.82% MutableMesh::ReIndex 6ms 0.03% 54.99% 550ms 2.77% Element::Element 0 0% 54.99% 542ms 2.73% std::map::find (inline) 0 0% 54.99% 536ms 2.70% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 54.99% 517ms 2.61% AbstractCellProperty::IsSubType (inline) 158ms 0.8% 55.79% 517ms 2.61% __GI___libc_free 0 0% 55.79% 492ms 2.48% std::ostream::operator<< (inline) 68ms 0.34% 56.13% 490ms 2.47% std::ostream::_M_insert 11ms 0.055% 56.18% 483ms 2.43% Cylindrical2dMesh::ReconstructCylindricalMesh 11ms 0.055% 56.24% 480ms 2.42% Cylindrical2dMesh::CorrectNonPeriodicMesh 12ms 0.06% 56.30% 477ms 2.40% Element::RegisterWithNodes (inline) 10ms 0.05% 56.35% 459ms 2.31% Node::AddElement 264ms 1.33% 57.68% 413ms 2.08% AbstractCellMutationState::AbstractCellMutationState 113ms 0.57% 58.25% 413ms 2.08% std::_Rb_tree::_M_erase 13ms 0.066% 58.32% 400ms 2.02% std::__new_allocator::deallocate (inline) 6ms 0.03% 58.35% 395ms 1.99% std::_Rb_tree::erase 1ms 0.005% 58.35% 394ms 1.99% std::set::erase (inline) 0 0% 58.35% 390ms 1.97% std::allocator_traits::deallocate (inline) 17ms 0.086% 58.44% 389ms 1.96% Node::RemoveElement 164ms 0.83% 59.26% 382ms 1.93% std::_Rb_tree::_M_get_insert_unique_pos 381ms 1.92% 61.18% 381ms 1.92% [libchaste_cell_based.so] 24ms 0.12% 61.30% 377ms 1.90% std::_Rb_tree::~_Rb_tree (inline) 17ms 0.086% 61.39% 373ms 1.88% divconqrecurse 0 0% 61.39% 367ms 1.85% std::_Rb_tree::_M_drop_node (inline) 267ms 1.35% 62.74% 356ms 1.79% _int_free 0 0% 62.74% 356ms 1.79% std::_Vector_base::_M_allocate (inline) 154ms 0.78% 63.51% 355ms 1.79% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 63.51% 351ms 1.77% std::set::~set (inline) 107ms 0.54% 64.05% 350ms 1.76% mergehulls 25ms 0.13% 64.18% 343ms 1.73% Element::ResetIndex 2ms 0.01% 64.19% 342ms 1.72% Cell::GetMutationState 0 0% 64.19% 325ms 1.64% std::_Rb_tree::_M_put_node (inline) 314ms 1.58% 65.77% 318ms 1.60% std::vector::operator[] (inline) 2ms 0.01% 65.78% 316ms 1.59% Cell::GetCellProliferativeType 6ms 0.03% 65.81% 315ms 1.59% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 3ms 0.015% 65.83% 315ms 1.59% LegacyCellProliferativeTypesWriter::VisitCell 1ms 0.005% 65.83% 293ms 1.48% NodeLocationWriter::Visit 28ms 0.14% 65.97% 292ms 1.47% std::_Rb_tree::_Rb_tree (partial-inline) 9ms 0.045% 66.02% 282ms 1.42% AbstractCellPopulation::GetLocationIndexUsingCell 25ms 0.13% 66.14% 274ms 1.38% TetrahedralMesh::Clear 2ms 0.01% 66.15% 273ms 1.38% AbstractCellPopulation::Iterator::operator++ (inline) 40ms 0.2% 66.35% 270ms 1.36% AbstractCellPopulation::Iterator::IsRealCell (inline) 4ms 0.02% 66.37% 267ms 1.35% std::set::set (inline) 16ms 0.081% 66.45% 264ms 1.33% std::vector::push_back (inline) 6ms 0.03% 66.49% 259ms 1.31% AbstractCellPopulation::IsCellAttachedToLocationIndex 12ms 0.06% 66.55% 257ms 1.30% std::num_put::_M_insert_float 3ms 0.015% 66.56% 256ms 1.29% alternateaxes 242ms 1.22% 67.78% 253ms 1.28% vertexmedian 0 0% 67.78% 252ms 1.27% TetrahedralMesh::RefreshJacobianCachedData 15ms 0.076% 67.86% 244ms 1.23% AbstractTetrahedralElement::CalculateJacobian 0 0% 67.86% 242ms 1.22% MeshBasedCellPopulation::GetDampingConstant 63ms 0.32% 68.17% 240ms 1.21% ApcOneHitCellMutationState::ApcOneHitCellMutationState 16ms 0.081% 68.25% 240ms 1.21% std::_Rb_tree::_M_erase_aux (inline) 13ms 0.066% 68.32% 240ms 1.21% std::vector::_M_realloc_insert 1ms 0.005% 68.32% 239ms 1.20% AbstractCentreBasedCellPopulation::GetDampingConstant 102ms 0.51% 68.84% 238ms 1.20% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 22ms 0.11% 68.95% 237ms 1.19% std::_Rb_tree::_M_copy (inline) 96ms 0.48% 69.43% 226ms 1.14% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 6ms 0.03% 69.46% 225ms 1.13% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 12ms 0.06% 69.52% 221ms 1.11% AbstractTetrahedralElement::CalculateInverseJacobian 168ms 0.85% 70.37% 221ms 1.11% malloc_consolidate 63ms 0.32% 70.69% 213ms 1.07% std::_Rb_tree::_M_clone_node (inline) 2ms 0.01% 70.70% 211ms 1.06% std::__cxx11::collate::do_transform 0 0% 70.70% 208ms 1.05% Cell::HasCellProperty (inline) 7ms 0.035% 70.73% 208ms 1.05% CellPropertyCollection::HasProperty 1ms 0.005% 70.74% 201ms 1.01% ___vsnprintf 0 0% 70.74% 200ms 1.01% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 70.74% 200ms 1.01% __vsnprintf_internal (inline) 146ms 0.74% 71.47% 199ms 1.00% AbstractElement::GetNodeGlobalIndex 23ms 0.12% 71.59% 199ms 1.00% __printf_buffer 11ms 0.055% 71.65% 197ms 0.99% Element::MarkAsDeleted 27ms 0.14% 71.78% 189ms 0.95% AbstractTetrahedralElement::RefreshJacobian 0 0% 71.78% 183ms 0.92% OffLatticeSimulation::ApplyBoundaries 4ms 0.02% 71.80% 182ms 0.92% CellProliferativeTypesWriter::VisitCell 173ms 0.87% 72.67% 173ms 0.87% unlink_chunk 4ms 0.02% 72.69% 172ms 0.87% AbstractTetrahedralElement::AbstractTetrahedralElement 9ms 0.045% 72.74% 171ms 0.86% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 170ms 0.86% 73.60% 170ms 0.86% Node::GetIndex 48ms 0.24% 73.84% 168ms 0.85% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 12ms 0.06% 73.90% 166ms 0.84% __printf_fp_l_buffer 0 0% 73.90% 166ms 0.84% __printf_fp_spec (inline) 7ms 0.035% 73.93% 163ms 0.82% Node::~Node 63ms 0.32% 74.25% 159ms 0.8% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 28ms 0.14% 74.39% 158ms 0.8% TetrahedralMesh::EdgesEnd (partial-inline) 156ms 0.79% 75.18% 156ms 0.79% std::_Rb_tree_insert_and_rebalance 97ms 0.49% 75.67% 153ms 0.77% std::_Rb_tree::equal_range (inline) 63ms 0.32% 75.99% 152ms 0.77% __printf_fp_buffer_1 151ms 0.76% 76.75% 151ms 0.76% incircle 148ms 0.75% 77.49% 148ms 0.75% AbstractCellMutationState::~AbstractCellMutationState 147ms 0.74% 78.23% 147ms 0.74% std::vector::size (inline) 80ms 0.4% 78.64% 141ms 0.71% Cylindrical2dMesh::GetVectorFromAtoB 60ms 0.3% 78.94% 140ms 0.71% AbstractElement::GetNodeLocation 6ms 0.03% 78.97% 137ms 0.69% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 9ms 0.045% 79.01% 136ms 0.69% MeshBasedCellPopulation::SpringsEnd (inline) 2ms 0.01% 79.02% 135ms 0.68% boost::numeric::ublas::vector_assign (inline) 135ms 0.68% 79.70% 135ms 0.68% std::type_info::name (inline) 1ms 0.005% 79.71% 132ms 0.67% AbstractCellBasedWriter::OpenOutputFileForAppend 40ms 0.2% 79.91% 130ms 0.66% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 130ms 0.66% 80.57% 130ms 0.66% [libchaste_crypt.so] 0 0% 80.57% 128ms 0.65% OutputFileHandler::OpenOutputFile 89ms 0.45% 81.02% 125ms 0.63% TetrahedralMesh::EdgeIterator::EdgeIterator 2ms 0.01% 81.03% 125ms 0.63% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 8ms 0.04% 81.07% 125ms 0.63% std::_Rb_tree_const_iterator::operator++ (inline) 125ms 0.63% 81.70% 125ms 0.63% std::_Rb_tree_increment 14ms 0.071% 81.77% 124ms 0.62% boost::detail::shared_count::~shared_count (inline) 0 0% 81.77% 124ms 0.62% boost::shared_ptr::~shared_ptr (inline) 112ms 0.56% 82.33% 123ms 0.62% vertexsort 7ms 0.035% 82.37% 120ms 0.6% std::_Rb_tree::_M_emplace_hint_unique 0 0% 82.37% 117ms 0.59% AbstractCellBasedSimulation::DoCellRemoval (inline) 45ms 0.23% 82.59% 116ms 0.58% std::__ostream_insert 29ms 0.15% 82.74% 116ms 0.58% std::num_put::_M_insert_int 0 0% 82.74% 115ms 0.58% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 1ms 0.005% 82.74% 112ms 0.56% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 10ms 0.05% 82.79% 109ms 0.55% Cylindrical2dMesh::CreateMirrorNodes 7ms 0.035% 82.83% 108ms 0.54% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.005% 82.83% 104ms 0.52% Cell::SetCellProliferativeType 10ms 0.05% 82.88% 100ms 0.5% MeshBasedCellPopulation::SpringIterator::SpringIterator 37ms 0.19% 83.07% 100ms 0.5% std::basic_filebuf::xsputn